[med-svn] [stacks] 01/03: Imported Upstream version 1.42

Sat Aug 13 09:04:16 UTC 2016

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tille pushed a commit to branch master
in repository stacks.

commit df2c72a14c851c4a3d4d47691218acf25cecde46
Author: Andreas Tille <tille at debian.org>
Date:   Sat Aug 13 10:48:52 2016 +0200

    Imported Upstream version 1.42
---
 ChangeLog                                          |   23 +
 Makefile.am                                        |   28 +-
 Makefile.in                                        |  548 +-
 README                                             |   33 +-
 configure                                          |   54 +-
 configure.ac                                       |   25 +-
 htslib/._INSTALL                                   |  Bin 0 -> 181 bytes
 htslib/._LICENSE                                   |  Bin 0 -> 181 bytes
 htslib/._Makefile                                  |  Bin 0 -> 181 bytes
 htslib/._NEWS                                      |  Bin 0 -> 181 bytes
 htslib/._README                                    |  Bin 0 -> 181 bytes
 htslib/._bgzf.c                                    |  Bin 0 -> 181 bytes
 htslib/._bgzip.c                                   |  Bin 0 -> 181 bytes
 htslib/._cram                                      |  Bin 0 -> 181 bytes
 htslib/._faidx.c                                   |  Bin 0 -> 181 bytes
 htslib/._hfile.c                                   |  Bin 0 -> 181 bytes
 htslib/._hfile_internal.h                          |  Bin 0 -> 181 bytes
 htslib/._hfile_irods.c                             |  Bin 0 -> 181 bytes
 htslib/._hfile_libcurl.c                           |  Bin 0 -> 181 bytes
 htslib/._hfile_net.c                               |  Bin 0 -> 181 bytes
 htslib/._hts.c                                     |  Bin 0 -> 181 bytes
 htslib/._hts_internal.h                            |  Bin 0 -> 181 bytes
 htslib/._htsfile.c                                 |  Bin 0 -> 181 bytes
 htslib/._htslib                                    |  Bin 0 -> 181 bytes
 htslib/._htslib.pc.in                              |  Bin 0 -> 181 bytes
 htslib/._htslib_vars.mk                            |  Bin 0 -> 181 bytes
 htslib/._kfunc.c                                   |  Bin 0 -> 181 bytes
 htslib/._knetfile.c                                |  Bin 0 -> 181 bytes
 htslib/._kstring.c                                 |  Bin 0 -> 181 bytes
 htslib/._md5.c                                     |  Bin 0 -> 181 bytes
 htslib/._plugin.c                                  |  Bin 0 -> 181 bytes
 htslib/._regidx.c                                  |  Bin 0 -> 181 bytes
 htslib/._sam.c                                     |  Bin 0 -> 181 bytes
 htslib/._synced_bcf_reader.c                       |  Bin 0 -> 181 bytes
 htslib/._tabix.c                                   |  Bin 0 -> 181 bytes
 htslib/._tbx.c                                     |  Bin 0 -> 181 bytes
 htslib/._vcf.c                                     |  Bin 0 -> 181 bytes
 htslib/._vcf_sweep.c                               |  Bin 0 -> 181 bytes
 htslib/._vcfutils.c                                |  Bin 0 -> 181 bytes
 htslib/INSTALL                                     |  102 +
 htslib/LICENSE                                     |   69 +
 htslib/Makefile                                    |  426 ++
 htslib/NEWS                                        |  109 +
 htslib/README                                      |    5 +
 htslib/bgzf.c                                      | 1330 +++++
 htslib/bgzip.c                                     |  311 ++
 htslib/cram/._cram.h                               |  Bin 0 -> 181 bytes
 htslib/cram/._cram_codecs.c                        |  Bin 0 -> 181 bytes
 htslib/cram/._cram_codecs.h                        |  Bin 0 -> 181 bytes
 htslib/cram/._cram_decode.c                        |  Bin 0 -> 181 bytes
 htslib/cram/._cram_decode.h                        |  Bin 0 -> 181 bytes
 htslib/cram/._cram_encode.c                        |  Bin 0 -> 181 bytes
 htslib/cram/._cram_encode.h                        |  Bin 0 -> 181 bytes
 htslib/cram/._cram_external.c                      |  Bin 0 -> 181 bytes
 htslib/cram/._cram_index.c                         |  Bin 0 -> 181 bytes
 htslib/cram/._cram_index.h                         |  Bin 0 -> 181 bytes
 htslib/cram/._cram_io.c                            |  Bin 0 -> 181 bytes
 htslib/cram/._cram_io.h                            |  Bin 0 -> 181 bytes
 htslib/cram/._cram_samtools.c                      |  Bin 0 -> 181 bytes
 htslib/cram/._cram_samtools.h                      |  Bin 0 -> 181 bytes
 htslib/cram/._cram_stats.c                         |  Bin 0 -> 181 bytes
 htslib/cram/._cram_stats.h                         |  Bin 0 -> 181 bytes
 htslib/cram/._cram_structs.h                       |  Bin 0 -> 181 bytes
 htslib/cram/._files.c                              |  Bin 0 -> 181 bytes
 htslib/cram/._mFILE.c                              |  Bin 0 -> 181 bytes
 htslib/cram/._mFILE.h                              |  Bin 0 -> 181 bytes
 htslib/cram/._misc.h                               |  Bin 0 -> 181 bytes
 htslib/cram/._open_trace_file.c                    |  Bin 0 -> 181 bytes
 htslib/cram/._open_trace_file.h                    |  Bin 0 -> 181 bytes
 htslib/cram/._os.h                                 |  Bin 0 -> 181 bytes
 htslib/cram/._pooled_alloc.c                       |  Bin 0 -> 181 bytes
 htslib/cram/._pooled_alloc.h                       |  Bin 0 -> 181 bytes
 htslib/cram/._rANS_byte.h                          |  Bin 0 -> 181 bytes
 htslib/cram/._rANS_static.c                        |  Bin 0 -> 181 bytes
 htslib/cram/._rANS_static.h                        |  Bin 0 -> 181 bytes
 htslib/cram/._sam_header.c                         |  Bin 0 -> 181 bytes
 htslib/cram/._sam_header.h                         |  Bin 0 -> 181 bytes
 htslib/cram/._string_alloc.c                       |  Bin 0 -> 181 bytes
 htslib/cram/._string_alloc.h                       |  Bin 0 -> 181 bytes
 htslib/cram/._thread_pool.c                        |  Bin 0 -> 181 bytes
 htslib/cram/._thread_pool.h                        |  Bin 0 -> 181 bytes
 htslib/cram/._vlen.c                               |  Bin 0 -> 181 bytes
 htslib/cram/._vlen.h                               |  Bin 0 -> 181 bytes
 htslib/cram/._zfio.c                               |  Bin 0 -> 181 bytes
 htslib/cram/._zfio.h                               |  Bin 0 -> 181 bytes
 htslib/cram/cram.h                                 |   61 +
 htslib/cram/cram_codecs.c                          | 1950 +++++++
 htslib/cram/cram_codecs.h                          |  194 +
 htslib/cram/cram_decode.c                          | 3159 +++++++++++
 htslib/cram/cram_decode.h                          |  112 +
 htslib/cram/cram_encode.c                          | 3105 +++++++++++
 htslib/cram/cram_encode.h                          |  105 +
 htslib/cram/cram_external.c                        |  377 ++
 htslib/cram/cram_index.c                           |  582 +++
 htslib/cram/cram_index.h                           |   99 +
 htslib/cram/cram_io.c                              | 4604 ++++++++++++++++
 htslib/cram/cram_io.h                              |  669 +++
 htslib/cram/cram_samtools.c                        |  149 +
 htslib/cram/cram_samtools.h                        |  105 +
 htslib/cram/cram_stats.c                           |  448 ++
 htslib/cram/cram_stats.h                           |   59 +
 htslib/cram/cram_structs.h                         |  821 +++
 htslib/cram/files.c                                |   74 +
 htslib/cram/mFILE.c                                |  694 +++
 htslib/cram/mFILE.h                                |   89 +
 htslib/cram/misc.h                                 |  110 +
 htslib/cram/open_trace_file.c                      |  414 ++
 htslib/cram/open_trace_file.h                      |  125 +
 htslib/cram/os.h                                   |  308 ++
 htslib/cram/pooled_alloc.c                         |  188 +
 htslib/cram/pooled_alloc.h                         |   64 +
 htslib/cram/rANS_byte.h                            |  336 ++
 htslib/cram/rANS_static.c                          |  868 ++++
 htslib/cram/rANS_static.h                          |   51 +
 htslib/cram/sam_header.c                           | 1268 +++++
 htslib/cram/sam_header.h                           |  459 ++
 htslib/cram/string_alloc.c                         |  155 +
 htslib/cram/string_alloc.h                         |   68 +
 htslib/cram/thread_pool.c                          |  757 +++
 htslib/cram/thread_pool.h                          |  218 +
 htslib/cram/vlen.c                                 |  430 ++
 htslib/cram/vlen.h                                 |   48 +
 htslib/cram/zfio.c                                 |  183 +
 htslib/cram/zfio.h                                 |   62 +
 htslib/faidx.c                                     |  525 ++
 htslib/hfile.c                                     |  751 +++
 htslib/hfile_internal.h                            |  139 +
 htslib/hfile_irods.c                               |  259 +
 htslib/hfile_libcurl.c                             |  917 ++++
 htslib/hfile_net.c                                 |  112 +
 htslib/hts.c                                       | 2066 ++++++++
 htslib/hts_internal.h                              |   90 +
 htslib/htsfile.c                                   |  234 +
 htslib/htslib.pc.in                                |   10 +
 htslib/htslib/._bgzf.h                             |  Bin 0 -> 181 bytes
 htslib/htslib/._cram.h                             |  Bin 0 -> 181 bytes
 htslib/htslib/._faidx.h                            |  Bin 0 -> 181 bytes
 htslib/htslib/._hfile.h                            |  Bin 0 -> 181 bytes
 htslib/htslib/._hts.h                              |  Bin 0 -> 181 bytes
 htslib/htslib/._hts_defs.h                         |  Bin 0 -> 181 bytes
 htslib/htslib/._kbitset.h                          |  Bin 0 -> 181 bytes
 htslib/htslib/._kfunc.h                            |  Bin 0 -> 181 bytes
 htslib/htslib/._khash.h                            |  Bin 0 -> 181 bytes
 htslib/htslib/._khash_str2int.h                    |  Bin 0 -> 181 bytes
 htslib/htslib/._klist.h                            |  Bin 0 -> 181 bytes
 htslib/htslib/._knetfile.h                         |  Bin 0 -> 181 bytes
 htslib/htslib/._kseq.h                             |  Bin 0 -> 181 bytes
 htslib/htslib/._ksort.h                            |  Bin 0 -> 181 bytes
 htslib/htslib/._kstring.h                          |  Bin 0 -> 181 bytes
 htslib/htslib/._regidx.h                           |  Bin 0 -> 181 bytes
 htslib/htslib/._sam.h                              |  Bin 0 -> 181 bytes
 htslib/htslib/._synced_bcf_reader.h                |  Bin 0 -> 181 bytes
 htslib/htslib/._tbx.h                              |  Bin 0 -> 181 bytes
 htslib/htslib/._vcf.h                              |  Bin 0 -> 181 bytes
 htslib/htslib/._vcf_sweep.h                        |  Bin 0 -> 181 bytes
 htslib/htslib/._vcfutils.h                         |  Bin 0 -> 181 bytes
 htslib/htslib/bgzf.h                               |  335 ++
 htslib/htslib/cram.h                               |  492 ++
 htslib/htslib/faidx.h                              |  137 +
 htslib/htslib/hfile.h                              |  215 +
 htslib/htslib/hts.h                                |  639 +++
 htslib/htslib/hts_defs.h                           |   72 +
 htslib/htslib/kbitset.h                            |  160 +
 htslib/htslib/kfunc.h                              |   83 +
 htslib/htslib/khash.h                              |  627 +++
 htslib/htslib/khash_str2int.h                      |  133 +
 htslib/htslib/klist.h                              |  135 +
 htslib/htslib/knetfile.h                           |  101 +
 htslib/htslib/kseq.h                               |  253 +
 htslib/htslib/ksort.h                              |  285 +
 htslib/htslib/kstring.h                            |  277 +
 htslib/htslib/regidx.h                             |  154 +
 htslib/htslib/sam.h                                |  454 ++
 htslib/htslib/synced_bcf_reader.h                  |  302 ++
 htslib/htslib/tbx.h                                |   79 +
 htslib/htslib/vcf.h                                |  914 ++++
 htslib/htslib/vcf_sweep.h                          |   47 +
 htslib/htslib/vcfutils.h                           |  134 +
 htslib/htslib_vars.mk                              |   49 +
 htslib/kfunc.c                                     |  282 +
 htslib/knetfile.c                                  |  634 +++
 htslib/kstring.c                                   |  276 +
 htslib/md5.c                                       |  386 ++
 htslib/plugin.c                                    |  171 +
 htslib/regidx.c                                    |  340 ++
 htslib/sam.c                                       | 2073 ++++++++
 htslib/synced_bcf_reader.c                         | 1284 +++++
 htslib/tabix.c                                     |  544 ++
 htslib/tbx.c                                       |  333 ++
 htslib/vcf.c                                       | 3483 +++++++++++++
 htslib/vcf_sweep.c                                 |  183 +
 htslib/vcfutils.c                                  |  691 +++
 scripts/ref_map.pl                                 |    2 +-
 src/BamI.h                                         |   41 +-
 src/BamUnalignedI.h                                |   35 +-
 src/BowtieI.h                                      |    4 +-
 src/GappedAln.h                                    |    6 +-
 src/MetaPopInfo.cc                                 |  347 ++
 src/MetaPopInfo.h                                  |  111 +
 src/PopMap.h                                       |  247 +-
 src/PopSum.h                                       |  146 +-
 src/SamI.h                                         |    4 +-
 src/Tsv.h                                          |    2 +-
 src/Vcf.cc                                         |  506 ++
 src/Vcf.h                                          |  467 ++
 src/aln_utils.cc                                   |    7 +-
 src/catalog_utils.cc                               |   58 +-
 src/catalog_utils.h                                |   44 +
 src/clone_filter.cc                                | 1336 ++---
 src/cstacks.cc                                     |   38 +-
 src/export_formats.cc                              | 3333 ++++++++++++
 src/export_formats.h                               |   70 +
 src/file_io.cc                                     |    3 +-
 ...ype_dictionaries.h => genotype_dictionaries.cc} |  224 +-
 src/genotype_dictionaries.h                        |  558 +-
 src/genotypes.cc                                   |  110 +-
 src/input.cc                                       |    4 +-
 src/kmers.cc                                       |    2 +-
 src/locus.cc                                       |    2 +-
 src/mstack.cc                                      |    4 +-
 src/ordered.h                                      |   26 +-
 src/populations.cc                                 | 5484 ++++----------------
 src/populations.h                                  |  131 +-
 src/pstacks.cc                                     |  904 ++--
 src/{renz.h => renz.cc}                            |  119 +-
 src/renz.h                                         |  219 +-
 src/rxstacks.cc                                    |  136 +-
 src/smoothing.h                                    |   13 +-
 src/smoothing_utils.h                              |    4 +-
 src/sql_utilities.cc                               |  299 ++
 src/sql_utilities.h                                |  305 +-
 src/sstacks.cc                                     |   16 +-
 src/stacks.h                                       |    6 +-
 src/ustacks.cc                                     |    8 +-
 234 files changed, 56367 insertions(+), 7505 deletions(-)

diff --git a/ChangeLog b/ChangeLog
index 6642845..0ae3d94 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,26 @@
+Stacks 1.42 - Aug 05, 2016
+--------------------------
+	Feature: populations program is now able to calculate populations statistics using arbitrary VCF files
+	as input.
+	Feature: Upgraded to the latest release of HTSLib (1.3.1) for reading BAM files. Embedded the library
+	in the Stacks distribution to remove previous libbam dependency.
+	Feature: Added an output directory option to 'populations' (--out_path).
+	Feature: Added restriction enzymes BsaHI, HpaII, NcoI; corrected NdeI.
+	Bugfix: Made the VCF output by 'populations' more standard-compliant.
+	Bugfix: Some output files included 0-based genomic coordinates, changed them to 1-based.
+	Bugfix: Replaced populations IDs with populations names in 'populations' output.
+	Bugfix: Corrected a bug affecting clone_filter when input was non-gzipped paired-end data.
+
+Stacks 1.41 - June 22, 2016
+---------------------------
+	Bugfix: the kernel-smoothing procedure in populations (used for Fst, Pi, heterozygosity etc. smoothing) 
+	was not functioning at sizes larger than the default size. A bug was creating incorrect weights for the
+	smoothing operation when the sliding window size was set to a large value causing the smoothing
+	window to have a maximum size after which increasing the size did not change the smoothing. 
+	Bugfix: cstacks was reporting gapped alignments even when --gapped was not enabled. This affected
+	a small number of (mostly) confounded catalog loci.
+	Feature: Added the Csp6I restriction enzyme.
+
 Stacks 1.40 - May 04, 2016
 --------------------------
 	Feature: Changed process_radtags and process_shortreads to print FASTQ/FASTA headers using
diff --git a/Makefile.am b/Makefile.am
index 96e3b88..4ad1fbe 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -27,21 +27,21 @@ cstacks_SOURCES = src/cstacks.h src/cstacks.cc src/constants.h \
 	src/kmers.h src/kmers.cc src/utils.h src/utils.cc \
 	src/GappedAln.h src/aln_utils.h src/aln_utils.cc \
 	src/DNASeq.h src/DNASeq.cc src/DNANSeq.h src/DNANSeq.cc \
-	src/input.h src/input.cc src/sql_utilities.h
+	src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc
 
 hstacks_SOURCES = src/hstacks.h src/hstacks.cc src/constants.h \
 	src/stacks.h src/stacks.cc src/locus.h src/locus.cc \
 	src/kmers.h src/kmers.cc \
 	src/DNASeq.h src/DNASeq.cc src/DNANSeq.h src/DNANSeq.cc \
 	src/utils.h src/utils.cc \
-	src/input.h src/input.cc src/sql_utilities.h
+	src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc
 
 sstacks_SOURCES = src/sstacks.h src/sstacks.cc src/constants.h \
 	src/stacks.h src/stacks.cc src/locus.h src/locus.cc \
 	src/kmers.h src/kmers.cc \
 	src/GappedAln.h src/aln_utils.h src/aln_utils.cc \
 	src/DNASeq.h src/DNASeq.cc src/DNANSeq.h src/DNANSeq.cc src/utils.h src/utils.cc \
-	src/input.h src/input.cc src/sql_utilities.h
+	src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc
 
 rxstacks_SOURCES = src/rxstacks.h src/rxstacks.cc src/constants.h \
 	src/stacks.h src/stacks.cc src/locus.h src/locus.cc \
@@ -49,7 +49,8 @@ rxstacks_SOURCES = src/rxstacks.h src/rxstacks.cc src/constants.h \
 	src/mst.h src/mst.cc \
 	src/models.h src/models.cc \
 	src/aln_utils.h src/aln_utils.cc src/utils.h src/utils.cc \
-	src/input.h src/input.cc src/sql_utilities.h
+	src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc \
+	src/MetaPopInfo.h src/MetaPopInfo.cc
 
 process_radtags_SOURCES = src/process_radtags.h src/process_radtags.cc src/constants.h \
 	src/utils.h src/utils.cc src/log_utils.h src/log_utils.cc \
@@ -57,7 +58,7 @@ process_radtags_SOURCES = src/process_radtags.h src/process_radtags.cc src/const
 	src/clean.h src/clean.cc \
 	src/file_io.h src/file_io.cc \
 	src/input.h src/input.cc src/BustardI.h src/BamUnalignedI.h src/FastqI.h src/gzFastq.h \
-	src/renz.h
+	src/renz.h src/renz.cc
 
 process_shortreads_SOURCES = src/process_shortreads.h src/process_shortreads.cc src/constants.h \
 	src/clean.h src/clean.cc \
@@ -88,21 +89,24 @@ genotypes_SOURCES = src/genotypes.h src/genotypes.cc src/constants.h \
 	src/stacks.h src/stacks.cc src/locus.h src/locus.cc \
 	src/DNASeq.h src/DNASeq.cc src/DNANSeq.h src/DNANSeq.cc \
 	src/aln_utils.h src/aln_utils.cc \
-	src/PopMap.h src/genotype_dictionaries.h \
-	src/input.h src/input.cc src/sql_utilities.h src/renz.h
+	src/PopMap.h src/genotype_dictionaries.h src/genotype_dictionaries.cc\
+	src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc src/renz.h src/renz.cc \
+	src/MetaPopInfo.h src/MetaPopInfo.cc
 
 populations_SOURCES = src/populations.h src/populations.cc src/constants.h \
 	src/utils.h src/utils.cc src/catalog_utils.h src/catalog_utils.cc \
 	src/log_utils.h src/log_utils.cc \
 	src/stacks.h src/stacks.cc src/locus.h src/locus.cc \
 	src/DNASeq.h src/DNASeq.cc src/DNANSeq.h src/DNANSeq.cc \
-	src/PopMap.h src/PopSum.h src/aln_utils.h src/aln_utils.cc src/genotype_dictionaries.h \
-	src/input.h src/input.cc src/sql_utilities.h src/renz.h \
-	src/bootstrap.h src/ordered.h src/smoothing.h src/smoothing_utils.h
+	src/PopMap.h src/PopSum.h src/aln_utils.h src/aln_utils.cc src/genotype_dictionaries.h src/genotype_dictionaries.cc \
+	src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc src/renz.h src/renz.cc \
+	src/bootstrap.h src/ordered.h src/smoothing.h src/smoothing_utils.h \
+	src/export_formats.h src/export_formats.cc \
+	src/MetaPopInfo.h src/MetaPopInfo.cc src/Vcf.h src/Vcf.cc
 
 phasedstacks_SOURCES = src/phasedstacks.h src/phasedstacks.cc src/constants.h \
 	src/locus.h src/locus.cc \
-	src/input.h src/input.cc src/sql_utilities.h \
+	src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc \
 	src/log_utils.h src/log_utils.cc \
 	src/utils.h src/utils.cc src/catalog_utils.h src/catalog_utils.cc 
 
@@ -163,6 +167,8 @@ TESTS = tests/process_radtags.t tests/kmer_filter.t tests/ustacks.t tests/pstack
 
 EXTRA_DIST = $(nobase_pkgdata_DATA) LICENSE INSTALL README ChangeLog $(TESTS)
 
+SUBDIRS = htslib .
+
 pkglocalstatedir = $(localstatedir)/$(PACKAGE)
 
 debug:
diff --git a/Makefile.in b/Makefile.in
index c7e396b..7a479ef 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -129,7 +129,8 @@ am_cstacks_OBJECTS = src/cstacks-cstacks.$(OBJEXT) \
 	src/cstacks-stacks.$(OBJEXT) src/cstacks-locus.$(OBJEXT) \
 	src/cstacks-kmers.$(OBJEXT) src/cstacks-utils.$(OBJEXT) \
 	src/cstacks-aln_utils.$(OBJEXT) src/cstacks-DNASeq.$(OBJEXT) \
-	src/cstacks-DNANSeq.$(OBJEXT) src/cstacks-input.$(OBJEXT)
+	src/cstacks-DNANSeq.$(OBJEXT) src/cstacks-input.$(OBJEXT) \
+	src/cstacks-sql_utilities.$(OBJEXT)
 cstacks_OBJECTS = $(am_cstacks_OBJECTS)
 cstacks_LDADD = $(LDADD)
 cstacks_LINK = $(CXXLD) $(cstacks_CXXFLAGS) $(CXXFLAGS) \
@@ -150,7 +151,11 @@ am_genotypes_OBJECTS = src/genotypes-genotypes.$(OBJEXT) \
 	src/genotypes-stacks.$(OBJEXT) src/genotypes-locus.$(OBJEXT) \
 	src/genotypes-DNASeq.$(OBJEXT) src/genotypes-DNANSeq.$(OBJEXT) \
 	src/genotypes-aln_utils.$(OBJEXT) \
-	src/genotypes-input.$(OBJEXT)
+	src/genotypes-genotype_dictionaries.$(OBJEXT) \
+	src/genotypes-input.$(OBJEXT) \
+	src/genotypes-sql_utilities.$(OBJEXT) \
+	src/genotypes-renz.$(OBJEXT) \
+	src/genotypes-MetaPopInfo.$(OBJEXT)
 genotypes_OBJECTS = $(am_genotypes_OBJECTS)
 genotypes_LDADD = $(LDADD)
 genotypes_LINK = $(CXXLD) $(genotypes_CXXFLAGS) $(CXXFLAGS) \
@@ -159,7 +164,8 @@ am_hstacks_OBJECTS = src/hstacks-hstacks.$(OBJEXT) \
 	src/hstacks-stacks.$(OBJEXT) src/hstacks-locus.$(OBJEXT) \
 	src/hstacks-kmers.$(OBJEXT) src/hstacks-DNASeq.$(OBJEXT) \
 	src/hstacks-DNANSeq.$(OBJEXT) src/hstacks-utils.$(OBJEXT) \
-	src/hstacks-input.$(OBJEXT)
+	src/hstacks-input.$(OBJEXT) \
+	src/hstacks-sql_utilities.$(OBJEXT)
 hstacks_OBJECTS = $(am_hstacks_OBJECTS)
 hstacks_LDADD = $(LDADD)
 hstacks_LINK = $(CXXLD) $(hstacks_CXXFLAGS) $(CXXFLAGS) \
@@ -176,6 +182,7 @@ kmer_filter_LINK = $(CXXLD) $(kmer_filter_CXXFLAGS) $(CXXFLAGS) \
 am_phasedstacks_OBJECTS = src/phasedstacks-phasedstacks.$(OBJEXT) \
 	src/phasedstacks-locus.$(OBJEXT) \
 	src/phasedstacks-input.$(OBJEXT) \
+	src/phasedstacks-sql_utilities.$(OBJEXT) \
 	src/phasedstacks-log_utils.$(OBJEXT) \
 	src/phasedstacks-utils.$(OBJEXT) \
 	src/phasedstacks-catalog_utils.$(OBJEXT)
@@ -192,7 +199,13 @@ am_populations_OBJECTS = src/populations-populations.$(OBJEXT) \
 	src/populations-DNASeq.$(OBJEXT) \
 	src/populations-DNANSeq.$(OBJEXT) \
 	src/populations-aln_utils.$(OBJEXT) \
-	src/populations-input.$(OBJEXT)
+	src/populations-genotype_dictionaries.$(OBJEXT) \
+	src/populations-input.$(OBJEXT) \
+	src/populations-sql_utilities.$(OBJEXT) \
+	src/populations-renz.$(OBJEXT) \
+	src/populations-export_formats.$(OBJEXT) \
+	src/populations-MetaPopInfo.$(OBJEXT) \
+	src/populations-Vcf.$(OBJEXT)
 populations_OBJECTS = $(am_populations_OBJECTS)
 populations_LDADD = $(LDADD)
 populations_LINK = $(CXXLD) $(populations_CXXFLAGS) $(CXXFLAGS) \
@@ -204,7 +217,8 @@ am_process_radtags_OBJECTS =  \
 	src/process_radtags-write.$(OBJEXT) \
 	src/process_radtags-clean.$(OBJEXT) \
 	src/process_radtags-file_io.$(OBJEXT) \
-	src/process_radtags-input.$(OBJEXT)
+	src/process_radtags-input.$(OBJEXT) \
+	src/process_radtags-renz.$(OBJEXT)
 process_radtags_OBJECTS = $(am_process_radtags_OBJECTS)
 process_radtags_DEPENDENCIES = $(am__DEPENDENCIES_1)
 process_radtags_LINK = $(CXXLD) $(process_radtags_CXXFLAGS) \
@@ -236,7 +250,9 @@ am_rxstacks_OBJECTS = src/rxstacks-rxstacks.$(OBJEXT) \
 	src/rxstacks-DNANSeq.$(OBJEXT) src/rxstacks-DNASeq.$(OBJEXT) \
 	src/rxstacks-mst.$(OBJEXT) src/rxstacks-models.$(OBJEXT) \
 	src/rxstacks-aln_utils.$(OBJEXT) src/rxstacks-utils.$(OBJEXT) \
-	src/rxstacks-input.$(OBJEXT)
+	src/rxstacks-input.$(OBJEXT) \
+	src/rxstacks-sql_utilities.$(OBJEXT) \
+	src/rxstacks-MetaPopInfo.$(OBJEXT)
 rxstacks_OBJECTS = $(am_rxstacks_OBJECTS)
 rxstacks_LDADD = $(LDADD)
 rxstacks_LINK = $(CXXLD) $(rxstacks_CXXFLAGS) $(CXXFLAGS) \
@@ -245,7 +261,8 @@ am_sstacks_OBJECTS = src/sstacks-sstacks.$(OBJEXT) \
 	src/sstacks-stacks.$(OBJEXT) src/sstacks-locus.$(OBJEXT) \
 	src/sstacks-kmers.$(OBJEXT) src/sstacks-aln_utils.$(OBJEXT) \
 	src/sstacks-DNASeq.$(OBJEXT) src/sstacks-DNANSeq.$(OBJEXT) \
-	src/sstacks-utils.$(OBJEXT) src/sstacks-input.$(OBJEXT)
+	src/sstacks-utils.$(OBJEXT) src/sstacks-input.$(OBJEXT) \
+	src/sstacks-sql_utilities.$(OBJEXT)
 sstacks_OBJECTS = $(am_sstacks_OBJECTS)
 sstacks_LDADD = $(LDADD)
 sstacks_LINK = $(CXXLD) $(sstacks_CXXFLAGS) $(CXXFLAGS) \
@@ -346,12 +363,28 @@ DIST_SOURCES = $(clone_filter_SOURCES) $(cstacks_SOURCES) \
 	$(populations_SOURCES) $(process_radtags_SOURCES) \
 	$(process_shortreads_SOURCES) $(pstacks_SOURCES) \
 	$(rxstacks_SOURCES) $(sstacks_SOURCES) $(ustacks_SOURCES)
+RECURSIVE_TARGETS = all-recursive check-recursive cscopelist-recursive \
+	ctags-recursive dvi-recursive html-recursive info-recursive \
+	install-data-recursive install-dvi-recursive \
+	install-exec-recursive install-html-recursive \
+	install-info-recursive install-pdf-recursive \
+	install-ps-recursive install-recursive installcheck-recursive \
+	installdirs-recursive pdf-recursive ps-recursive \
+	tags-recursive uninstall-recursive
 am__can_run_installinfo = \
   case $$AM_UPDATE_INFO_DIR in \
     n|no|NO) false;; \
     *) (install-info --version) >/dev/null 2>&1;; \
   esac
 DATA = $(nobase_pkgdata_DATA)
+RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive	\
+  distclean-recursive maintainer-clean-recursive
+am__recursive_targets = \
+  $(RECURSIVE_TARGETS) \
+  $(RECURSIVE_CLEAN_TARGETS) \
+  $(am__extra_recursive_targets)
+AM_RECURSIVE_TARGETS = $(am__recursive_targets:-recursive=) TAGS CTAGS \
+	cscope check recheck distdir dist dist-all distcheck
 am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) \
 	$(LISP)config.h.in
 # Read a list of newline-separated strings from the standard input,
@@ -373,7 +406,6 @@ am__define_uniq_tagged_files = \
 ETAGS = etags
 CTAGS = ctags
 CSCOPE = cscope
-AM_RECURSIVE_TARGETS = cscope check recheck
 am__tty_colors_dummy = \
   mgn= red= grn= lgn= blu= brg= std=; \
   am__color_tests=no
@@ -549,6 +581,7 @@ TEST_LOGS = $(am__test_logs2:.test.log=.log)
 TEST_LOG_DRIVER = $(SHELL) $(top_srcdir)/config/test-driver
 TEST_LOG_COMPILE = $(TEST_LOG_COMPILER) $(AM_TEST_LOG_FLAGS) \
 	$(TEST_LOG_FLAGS)
+DIST_SUBDIRS = $(SUBDIRS)
 am__DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/config.h.in \
 	$(top_srcdir)/config/compile $(top_srcdir)/config/depcomp \
 	$(top_srcdir)/config/install-sh $(top_srcdir)/config/missing \
@@ -564,6 +597,31 @@ am__remove_distdir = \
       || { sleep 5 && rm -rf "$(distdir)"; }; \
   else :; fi
 am__post_remove_distdir = $(am__remove_distdir)
+am__relativize = \
+  dir0=`pwd`; \
+  sed_first='s,^\([^/]*\)/.*$$,\1,'; \
+  sed_rest='s,^[^/]*/*,,'; \
+  sed_last='s,^.*/\([^/]*\)$$,\1,'; \
+  sed_butlast='s,/*[^/]*$$,,'; \
+  while test -n "$$dir1"; do \
+    first=`echo "$$dir1" | sed -e "$$sed_first"`; \
+    if test "$$first" != "."; then \
+      if test "$$first" = ".."; then \
+        dir2=`echo "$$dir0" | sed -e "$$sed_last"`/"$$dir2"; \
+        dir0=`echo "$$dir0" | sed -e "$$sed_butlast"`; \
+      else \
+        first2=`echo "$$dir2" | sed -e "$$sed_first"`; \
+        if test "$$first2" = "$$first"; then \
+          dir2=`echo "$$dir2" | sed -e "$$sed_rest"`; \
+        else \
+          dir2="../$$dir2"; \
+        fi; \
+        dir0="$$dir0"/"$$first"; \
+      fi; \
+    fi; \
+    dir1=`echo "$$dir1" | sed -e "$$sed_rest"`; \
+  done; \
+  reldir="$$dir2"
 DIST_ARCHIVES = $(distdir).tar.gz
 GZIP_ENV = --best
 DIST_TARGETS = dist-gzip
@@ -693,21 +751,21 @@ cstacks_SOURCES = src/cstacks.h src/cstacks.cc src/constants.h \
 	src/kmers.h src/kmers.cc src/utils.h src/utils.cc \
 	src/GappedAln.h src/aln_utils.h src/aln_utils.cc \
 	src/DNASeq.h src/DNASeq.cc src/DNANSeq.h src/DNANSeq.cc \
-	src/input.h src/input.cc src/sql_utilities.h
+	src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc
 
 hstacks_SOURCES = src/hstacks.h src/hstacks.cc src/constants.h \
 	src/stacks.h src/stacks.cc src/locus.h src/locus.cc \
 	src/kmers.h src/kmers.cc \
 	src/DNASeq.h src/DNASeq.cc src/DNANSeq.h src/DNANSeq.cc \
 	src/utils.h src/utils.cc \
-	src/input.h src/input.cc src/sql_utilities.h
+	src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc
 
 sstacks_SOURCES = src/sstacks.h src/sstacks.cc src/constants.h \
 	src/stacks.h src/stacks.cc src/locus.h src/locus.cc \
 	src/kmers.h src/kmers.cc \
 	src/GappedAln.h src/aln_utils.h src/aln_utils.cc \
 	src/DNASeq.h src/DNASeq.cc src/DNANSeq.h src/DNANSeq.cc src/utils.h src/utils.cc \
-	src/input.h src/input.cc src/sql_utilities.h
+	src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc
 
 rxstacks_SOURCES = src/rxstacks.h src/rxstacks.cc src/constants.h \
 	src/stacks.h src/stacks.cc src/locus.h src/locus.cc \
@@ -715,7 +773,8 @@ rxstacks_SOURCES = src/rxstacks.h src/rxstacks.cc src/constants.h \
 	src/mst.h src/mst.cc \
 	src/models.h src/models.cc \
 	src/aln_utils.h src/aln_utils.cc src/utils.h src/utils.cc \
-	src/input.h src/input.cc src/sql_utilities.h
+	src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc \
+	src/MetaPopInfo.h src/MetaPopInfo.cc
 
 process_radtags_SOURCES = src/process_radtags.h src/process_radtags.cc src/constants.h \
 	src/utils.h src/utils.cc src/log_utils.h src/log_utils.cc \
@@ -723,7 +782,7 @@ process_radtags_SOURCES = src/process_radtags.h src/process_radtags.cc src/const
 	src/clean.h src/clean.cc \
 	src/file_io.h src/file_io.cc \
 	src/input.h src/input.cc src/BustardI.h src/BamUnalignedI.h src/FastqI.h src/gzFastq.h \
-	src/renz.h
+	src/renz.h src/renz.cc
 
 process_shortreads_SOURCES = src/process_shortreads.h src/process_shortreads.cc src/constants.h \
 	src/clean.h src/clean.cc \
@@ -754,21 +813,24 @@ genotypes_SOURCES = src/genotypes.h src/genotypes.cc src/constants.h \
 	src/stacks.h src/stacks.cc src/locus.h src/locus.cc \
 	src/DNASeq.h src/DNASeq.cc src/DNANSeq.h src/DNANSeq.cc \
 	src/aln_utils.h src/aln_utils.cc \
-	src/PopMap.h src/genotype_dictionaries.h \
-	src/input.h src/input.cc src/sql_utilities.h src/renz.h
+	src/PopMap.h src/genotype_dictionaries.h src/genotype_dictionaries.cc\
+	src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc src/renz.h src/renz.cc \
+	src/MetaPopInfo.h src/MetaPopInfo.cc
 
 populations_SOURCES = src/populations.h src/populations.cc src/constants.h \
 	src/utils.h src/utils.cc src/catalog_utils.h src/catalog_utils.cc \
 	src/log_utils.h src/log_utils.cc \
 	src/stacks.h src/stacks.cc src/locus.h src/locus.cc \
 	src/DNASeq.h src/DNASeq.cc src/DNANSeq.h src/DNANSeq.cc \
-	src/PopMap.h src/PopSum.h src/aln_utils.h src/aln_utils.cc src/genotype_dictionaries.h \
-	src/input.h src/input.cc src/sql_utilities.h src/renz.h \
-	src/bootstrap.h src/ordered.h src/smoothing.h src/smoothing_utils.h
+	src/PopMap.h src/PopSum.h src/aln_utils.h src/aln_utils.cc src/genotype_dictionaries.h src/genotype_dictionaries.cc \
+	src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc src/renz.h src/renz.cc \
+	src/bootstrap.h src/ordered.h src/smoothing.h src/smoothing_utils.h \
+	src/export_formats.h src/export_formats.cc \
+	src/MetaPopInfo.h src/MetaPopInfo.cc src/Vcf.h src/Vcf.cc
 
 phasedstacks_SOURCES = src/phasedstacks.h src/phasedstacks.cc src/constants.h \
 	src/locus.h src/locus.cc \
-	src/input.h src/input.cc src/sql_utilities.h \
+	src/input.h src/input.cc src/sql_utilities.h src/sql_utilities.cc \
 	src/log_utils.h src/log_utils.cc \
 	src/utils.h src/utils.cc src/catalog_utils.h src/catalog_utils.cc 
 
@@ -824,9 +886,10 @@ nobase_pkgdata_DATA = sql/mysql.cnf.dist sql/catalog_index.sql sql/stacks.sql sq
 LOG_DRIVER = env AM_TAP_AWK='$(AWK)' $(SHELL) $(abs_top_srcdir)/tests/tap-driver.sh
 TESTS = tests/process_radtags.t tests/kmer_filter.t tests/ustacks.t tests/pstacks.t
 EXTRA_DIST = $(nobase_pkgdata_DATA) LICENSE INSTALL README ChangeLog $(TESTS)
+SUBDIRS = htslib .
 pkglocalstatedir = $(localstatedir)/$(PACKAGE)
 all: config.h
-	$(MAKE) $(AM_MAKEFLAGS) all-am
+	$(MAKE) $(AM_MAKEFLAGS) all-recursive
 
 .SUFFIXES:
 .SUFFIXES: .cc .log .o .obj .test .test$(EXEEXT) .trs
@@ -962,6 +1025,8 @@ src/cstacks-DNANSeq.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
 src/cstacks-input.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
+src/cstacks-sql_utilities.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
 
 cstacks$(EXEEXT): $(cstacks_OBJECTS) $(cstacks_DEPENDENCIES) $(EXTRA_cstacks_DEPENDENCIES) 
 	@rm -f cstacks$(EXEEXT)
@@ -1004,8 +1069,16 @@ src/genotypes-DNANSeq.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
 src/genotypes-aln_utils.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
+src/genotypes-genotype_dictionaries.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
 src/genotypes-input.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
+src/genotypes-sql_utilities.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/genotypes-renz.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/genotypes-MetaPopInfo.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
 
 genotypes$(EXEEXT): $(genotypes_OBJECTS) $(genotypes_DEPENDENCIES) $(EXTRA_genotypes_DEPENDENCIES) 
 	@rm -f genotypes$(EXEEXT)
@@ -1026,6 +1099,8 @@ src/hstacks-utils.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
 src/hstacks-input.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
+src/hstacks-sql_utilities.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
 
 hstacks$(EXEEXT): $(hstacks_OBJECTS) $(hstacks_DEPENDENCIES) $(EXTRA_hstacks_DEPENDENCIES) 
 	@rm -f hstacks$(EXEEXT)
@@ -1050,6 +1125,8 @@ src/phasedstacks-locus.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
 src/phasedstacks-input.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
+src/phasedstacks-sql_utilities.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
 src/phasedstacks-log_utils.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
 src/phasedstacks-utils.$(OBJEXT): src/$(am__dirstamp) \
@@ -1078,8 +1155,20 @@ src/populations-DNANSeq.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
 src/populations-aln_utils.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
+src/populations-genotype_dictionaries.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
 src/populations-input.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
+src/populations-sql_utilities.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/populations-renz.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/populations-export_formats.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/populations-MetaPopInfo.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/populations-Vcf.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
 
 populations$(EXEEXT): $(populations_OBJECTS) $(populations_DEPENDENCIES) $(EXTRA_populations_DEPENDENCIES) 
 	@rm -f populations$(EXEEXT)
@@ -1098,6 +1187,8 @@ src/process_radtags-file_io.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
 src/process_radtags-input.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
+src/process_radtags-renz.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
 
 process_radtags$(EXEEXT): $(process_radtags_OBJECTS) $(process_radtags_DEPENDENCIES) $(EXTRA_process_radtags_DEPENDENCIES) 
 	@rm -f process_radtags$(EXEEXT)
@@ -1162,6 +1253,10 @@ src/rxstacks-utils.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
 src/rxstacks-input.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
+src/rxstacks-sql_utilities.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
+src/rxstacks-MetaPopInfo.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
 
 rxstacks$(EXEEXT): $(rxstacks_OBJECTS) $(rxstacks_DEPENDENCIES) $(EXTRA_rxstacks_DEPENDENCIES) 
 	@rm -f rxstacks$(EXEEXT)
@@ -1184,6 +1279,8 @@ src/sstacks-utils.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
 src/sstacks-input.$(OBJEXT): src/$(am__dirstamp) \
 	src/$(DEPDIR)/$(am__dirstamp)
+src/sstacks-sql_utilities.$(OBJEXT): src/$(am__dirstamp) \
+	src/$(DEPDIR)/$(am__dirstamp)
 
 sstacks$(EXEEXT): $(sstacks_OBJECTS) $(sstacks_DEPENDENCIES) $(EXTRA_sstacks_DEPENDENCIES) 
 	@rm -f sstacks$(EXEEXT)
@@ -1273,6 +1370,7 @@ distclean-compile:
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/cstacks-input.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/cstacks-kmers.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/cstacks-locus.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/cstacks-sql_utilities.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/cstacks-stacks.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/cstacks-utils.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/estacks-DNANSeq.Po at am__quote@
@@ -1285,12 +1383,16 @@ distclean-compile:
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/estacks-utils.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/genotypes-DNANSeq.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/genotypes-DNASeq.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/genotypes-MetaPopInfo.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/genotypes-aln_utils.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/genotypes-catalog_utils.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/genotypes-genotype_dictionaries.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/genotypes-genotypes.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/genotypes-input.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/genotypes-locus.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/genotypes-log_utils.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/genotypes-renz.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/genotypes-sql_utilities.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/genotypes-stacks.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/genotypes-utils.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/hstacks-DNANSeq.Po at am__quote@
@@ -1299,6 +1401,7 @@ distclean-compile:
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/hstacks-input.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/hstacks-kmers.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/hstacks-locus.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/hstacks-sql_utilities.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/hstacks-stacks.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/hstacks-utils.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/kmer_filter-input.Po at am__quote@
@@ -1311,15 +1414,22 @@ distclean-compile:
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/phasedstacks-locus.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/phasedstacks-log_utils.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/phasedstacks-phasedstacks.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/phasedstacks-sql_utilities.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/phasedstacks-utils.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/populations-DNANSeq.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/populations-DNASeq.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/populations-MetaPopInfo.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/populations-Vcf.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/populations-aln_utils.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/populations-catalog_utils.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/populations-export_formats.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/populations-genotype_dictionaries.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/populations-input.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/populations-locus.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/populations-log_utils.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/populations-populations.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/populations-renz.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/populations-sql_utilities.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/populations-stacks.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/populations-utils.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/process_radtags-clean.Po at am__quote@
@@ -1327,6 +1437,7 @@ distclean-compile:
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/process_radtags-input.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/process_radtags-log_utils.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/process_radtags-process_radtags.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/process_radtags-renz.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/process_radtags-utils.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/process_radtags-write.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/process_shortreads-clean.Po at am__quote@
@@ -1347,12 +1458,14 @@ distclean-compile:
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/pstacks-utils.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/rxstacks-DNANSeq.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/rxstacks-DNASeq.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/rxstacks-MetaPopInfo.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/rxstacks-aln_utils.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/rxstacks-input.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/rxstacks-locus.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/rxstacks-models.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/rxstacks-mst.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/rxstacks-rxstacks.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/rxstacks-sql_utilities.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/rxstacks-stacks.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/rxstacks-utils.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/sstacks-DNANSeq.Po at am__quote@
@@ -1361,6 +1474,7 @@ distclean-compile:
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/sstacks-input.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/sstacks-kmers.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/sstacks-locus.Po at am__quote@
+ at AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/sstacks-sql_utilities.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/sstacks-sstacks.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/sstacks-stacks.Po at am__quote@
 @AMDEP_TRUE@@am__include@ @am__quote at src/$(DEPDIR)/sstacks-utils.Po at am__quote@
@@ -1617,6 +1731,20 @@ src/cstacks-input.obj: src/input.cc
 @AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
 @am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cstacks_CXXFLAGS) $(CXXFLAGS) -c -o src/cstacks-input.obj `if test -f 'src/input.cc'; then $(CYGPATH_W) 'src/input.cc'; else $(CYGPATH_W) '$(srcdir)/src/input.cc'; fi`
 
+src/cstacks-sql_utilities.o: src/sql_utilities.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cstacks_CXXFLAGS) $(CXXFLAGS) -MT src/cstacks-sql_utilities.o -MD -MP -MF src/$(DEPDIR)/cstacks-sql_utilities.Tpo -c -o src/cstacks-sql_utilities.o `test -f 'src/sql_utilities.cc' || echo '$(srcdir)/'`src/sql_utilities.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/cstacks-sql_utilities.Tpo src/$(DEPDIR)/cstacks-sql_utilities.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	$(AM_V_CXX)source='src/sql_utilities.cc' object='src/cstacks-sql_utilities.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cstacks_CXXFLAGS) $(CXXFLAGS) -c -o src/cstacks-sql_utilities.o `test -f 'src/sql_utilities.cc' || echo '$(srcdir)/'`src/sql_utilities.cc
+
+src/cstacks-sql_utilities.obj: src/sql_utilities.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cstacks_CXXFLAGS) $(CXXFLAGS) -MT src/cstacks-sql_utilities.obj -MD -MP -MF src/$(DEPDIR)/cstacks-sql_utilities.Tpo -c -o src/cstacks-sql_utilities.obj `if test -f 'src/sql_utilities.cc'; then $(CYGPATH_W) 'src/sql_utilities.cc'; else $(CYGPATH_W) '$(srcdir)/src/sql_utilities.cc'; fi`
+ at am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/cstacks-sql_utilities.Tpo src/$(DEPDIR)/cstacks-sql_utilities.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	$(AM_V_CXX)source='src/sql_utilities.cc' object='src/cstacks-sql_utilities.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(cstacks_CXXFLAGS) $(CXXFLAGS) -c -o src/cstacks-sql_utilities.obj `if test -f 'src/sql_utilities.cc'; then $(CYGPATH_W) 'src/sql_utilities.cc'; else $(CYGPATH_W) '$(srcdir)/src/sql_utilities.cc'; fi`
+
 src/estacks-estacks.o: src/estacks.cc
 @am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(estacks_CXXFLAGS) $(CXXFLAGS) -MT src/estacks-estacks.o -MD -MP -MF src/$(DEPDIR)/estacks-estacks.Tpo -c -o src/estacks-estacks.o `test -f 'src/estacks.cc' || echo '$(srcdir)/'`src/estacks.cc
 @am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/estacks-estacks.Tpo src/$(DEPDIR)/estacks-estacks.Po
@@ -1855,6 +1983,20 @@ src/genotypes-aln_utils.obj: src/aln_utils.cc
 @AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
 @am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(genotypes_CXXFLAGS) $(CXXFLAGS) -c -o src/genotypes-aln_utils.obj `if test -f 'src/aln_utils.cc'; then $(CYGPATH_W) 'src/aln_utils.cc'; else $(CYGPATH_W) '$(srcdir)/src/aln_utils.cc'; fi`
 
+src/genotypes-genotype_dictionaries.o: src/genotype_dictionaries.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(genotypes_CXXFLAGS) $(CXXFLAGS) -MT src/genotypes-genotype_dictionaries.o -MD -MP -MF src/$(DEPDIR)/genotypes-genotype_dictionaries.Tpo -c -o src/genotypes-genotype_dictionaries.o `test -f 'src/genotype_dictionaries.cc' || echo '$(srcdir)/'`src/genotype_dictionaries.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/genotypes-genotype_dictionaries.Tpo src/$(DEPDIR)/genotypes-genotype_dictionaries.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	$(AM_V_CXX)source='src/genotype_dictionaries.cc' object='src/genotypes-genotype_dictionaries.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(genotypes_CXXFLAGS) $(CXXFLAGS) -c -o src/genotypes-genotype_dictionaries.o `test -f 'src/genotype_dictionaries.cc' || echo '$(srcdir)/'`src/genotype_dictionaries.cc
+
+src/genotypes-genotype_dictionaries.obj: src/genotype_dictionaries.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(genotypes_CXXFLAGS) $(CXXFLAGS) -MT src/genotypes-genotype_dictionaries.obj -MD -MP -MF src/$(DEPDIR)/genotypes-genotype_dictionaries.Tpo -c -o src/genotypes-genotype_dictionaries.obj `if test -f 'src/genotype_dictionaries.cc'; then $(CYGPATH_W) 'src/genotype_dictionaries.cc'; else $(CYGPATH_W) '$(srcdir)/src/genotype_dictionaries.cc'; fi`
+ at am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/genotypes-genotype_dictionaries.Tpo src/$(DEPDIR)/genotypes-genotype_dictionaries.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	$(AM_V_CXX)source='src/genotype_dictionaries.cc' object='src/genotypes-genotype_dictionaries.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(genotypes_CXXFLAGS) $(CXXFLAGS) -c -o src/genotypes-genotype_dictionaries.obj `if test -f 'src/genotype_dictionaries.cc'; then $(CYGPATH_W) 'src/genotype_dictionaries.cc'; else $(CYGPATH_W) '$(srcdir)/src/genotype_dictionaries.cc'; fi`
+
 src/genotypes-input.o: src/input.cc
 @am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(genotypes_CXXFLAGS) $(CXXFLAGS) -MT src/genotypes-input.o -MD -MP -MF src/$(DEPDIR)/genotypes-input.Tpo -c -o src/genotypes-input.o `test -f 'src/input.cc' || echo '$(srcdir)/'`src/input.cc
 @am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/genotypes-input.Tpo src/$(DEPDIR)/genotypes-input.Po
@@ -1869,6 +2011,48 @@ src/genotypes-input.obj: src/input.cc
 @AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
 @am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(genotypes_CXXFLAGS) $(CXXFLAGS) -c -o src/genotypes-input.obj `if test -f 'src/input.cc'; then $(CYGPATH_W) 'src/input.cc'; else $(CYGPATH_W) '$(srcdir)/src/input.cc'; fi`
 
+src/genotypes-sql_utilities.o: src/sql_utilities.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(genotypes_CXXFLAGS) $(CXXFLAGS) -MT src/genotypes-sql_utilities.o -MD -MP -MF src/$(DEPDIR)/genotypes-sql_utilities.Tpo -c -o src/genotypes-sql_utilities.o `test -f 'src/sql_utilities.cc' || echo '$(srcdir)/'`src/sql_utilities.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/genotypes-sql_utilities.Tpo src/$(DEPDIR)/genotypes-sql_utilities.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	$(AM_V_CXX)source='src/sql_utilities.cc' object='src/genotypes-sql_utilities.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(genotypes_CXXFLAGS) $(CXXFLAGS) -c -o src/genotypes-sql_utilities.o `test -f 'src/sql_utilities.cc' || echo '$(srcdir)/'`src/sql_utilities.cc
+
+src/genotypes-sql_utilities.obj: src/sql_utilities.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(genotypes_CXXFLAGS) $(CXXFLAGS) -MT src/genotypes-sql_utilities.obj -MD -MP -MF src/$(DEPDIR)/genotypes-sql_utilities.Tpo -c -o src/genotypes-sql_utilities.obj `if test -f 'src/sql_utilities.cc'; then $(CYGPATH_W) 'src/sql_utilities.cc'; else $(CYGPATH_W) '$(srcdir)/src/sql_utilities.cc'; fi`
+ at am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/genotypes-sql_utilities.Tpo src/$(DEPDIR)/genotypes-sql_utilities.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	$(AM_V_CXX)source='src/sql_utilities.cc' object='src/genotypes-sql_utilities.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(genotypes_CXXFLAGS) $(CXXFLAGS) -c -o src/genotypes-sql_utilities.obj `if test -f 'src/sql_utilities.cc'; then $(CYGPATH_W) 'src/sql_utilities.cc'; else $(CYGPATH_W) '$(srcdir)/src/sql_utilities.cc'; fi`
+
+src/genotypes-renz.o: src/renz.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(genotypes_CXXFLAGS) $(CXXFLAGS) -MT src/genotypes-renz.o -MD -MP -MF src/$(DEPDIR)/genotypes-renz.Tpo -c -o src/genotypes-renz.o `test -f 'src/renz.cc' || echo '$(srcdir)/'`src/renz.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/genotypes-renz.Tpo src/$(DEPDIR)/genotypes-renz.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	$(AM_V_CXX)source='src/renz.cc' object='src/genotypes-renz.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(genotypes_CXXFLAGS) $(CXXFLAGS) -c -o src/genotypes-renz.o `test -f 'src/renz.cc' || echo '$(srcdir)/'`src/renz.cc
+
+src/genotypes-renz.obj: src/renz.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(genotypes_CXXFLAGS) $(CXXFLAGS) -MT src/genotypes-renz.obj -MD -MP -MF src/$(DEPDIR)/genotypes-renz.Tpo -c -o src/genotypes-renz.obj `if test -f 'src/renz.cc'; then $(CYGPATH_W) 'src/renz.cc'; else $(CYGPATH_W) '$(srcdir)/src/renz.cc'; fi`
+ at am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/genotypes-renz.Tpo src/$(DEPDIR)/genotypes-renz.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	$(AM_V_CXX)source='src/renz.cc' object='src/genotypes-renz.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(genotypes_CXXFLAGS) $(CXXFLAGS) -c -o src/genotypes-renz.obj `if test -f 'src/renz.cc'; then $(CYGPATH_W) 'src/renz.cc'; else $(CYGPATH_W) '$(srcdir)/src/renz.cc'; fi`
+
+src/genotypes-MetaPopInfo.o: src/MetaPopInfo.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(genotypes_CXXFLAGS) $(CXXFLAGS) -MT src/genotypes-MetaPopInfo.o -MD -MP -MF src/$(DEPDIR)/genotypes-MetaPopInfo.Tpo -c -o src/genotypes-MetaPopInfo.o `test -f 'src/MetaPopInfo.cc' || echo '$(srcdir)/'`src/MetaPopInfo.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/genotypes-MetaPopInfo.Tpo src/$(DEPDIR)/genotypes-MetaPopInfo.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	$(AM_V_CXX)source='src/MetaPopInfo.cc' object='src/genotypes-MetaPopInfo.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(genotypes_CXXFLAGS) $(CXXFLAGS) -c -o src/genotypes-MetaPopInfo.o `test -f 'src/MetaPopInfo.cc' || echo '$(srcdir)/'`src/MetaPopInfo.cc
+
+src/genotypes-MetaPopInfo.obj: src/MetaPopInfo.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(genotypes_CXXFLAGS) $(CXXFLAGS) -MT src/genotypes-MetaPopInfo.obj -MD -MP -MF src/$(DEPDIR)/genotypes-MetaPopInfo.Tpo -c -o src/genotypes-MetaPopInfo.obj `if test -f 'src/MetaPopInfo.cc'; then $(CYGPATH_W) 'src/MetaPopInfo.cc'; else $(CYGPATH_W) '$(srcdir)/src/MetaPopInfo.cc'; fi`
+ at am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/genotypes-MetaPopInfo.Tpo src/$(DEPDIR)/genotypes-MetaPopInfo.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	$(AM_V_CXX)source='src/MetaPopInfo.cc' object='src/genotypes-MetaPopInfo.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(genotypes_CXXFLAGS) $(CXXFLAGS) -c -o src/genotypes-MetaPopInfo.obj `if test -f 'src/MetaPopInfo.cc'; then $(CYGPATH_W) 'src/MetaPopInfo.cc'; else $(CYGPATH_W) '$(srcdir)/src/MetaPopInfo.cc'; fi`
+
 src/hstacks-hstacks.o: src/hstacks.cc
 @am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(hstacks_CXXFLAGS) $(CXXFLAGS) -MT src/hstacks-hstacks.o -MD -MP -MF src/$(DEPDIR)/hstacks-hstacks.Tpo -c -o src/hstacks-hstacks.o `test -f 'src/hstacks.cc' || echo '$(srcdir)/'`src/hstacks.cc
 @am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/hstacks-hstacks.Tpo src/$(DEPDIR)/hstacks-hstacks.Po
@@ -1981,6 +2165,20 @@ src/hstacks-input.obj: src/input.cc
 @AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
 @am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(hstacks_CXXFLAGS) $(CXXFLAGS) -c -o src/hstacks-input.obj `if test -f 'src/input.cc'; then $(CYGPATH_W) 'src/input.cc'; else $(CYGPATH_W) '$(srcdir)/src/input.cc'; fi`
 
+src/hstacks-sql_utilities.o: src/sql_utilities.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(hstacks_CXXFLAGS) $(CXXFLAGS) -MT src/hstacks-sql_utilities.o -MD -MP -MF src/$(DEPDIR)/hstacks-sql_utilities.Tpo -c -o src/hstacks-sql_utilities.o `test -f 'src/sql_utilities.cc' || echo '$(srcdir)/'`src/sql_utilities.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/hstacks-sql_utilities.Tpo src/$(DEPDIR)/hstacks-sql_utilities.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	$(AM_V_CXX)source='src/sql_utilities.cc' object='src/hstacks-sql_utilities.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(hstacks_CXXFLAGS) $(CXXFLAGS) -c -o src/hstacks-sql_utilities.o `test -f 'src/sql_utilities.cc' || echo '$(srcdir)/'`src/sql_utilities.cc
+
+src/hstacks-sql_utilities.obj: src/sql_utilities.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(hstacks_CXXFLAGS) $(CXXFLAGS) -MT src/hstacks-sql_utilities.obj -MD -MP -MF src/$(DEPDIR)/hstacks-sql_utilities.Tpo -c -o src/hstacks-sql_utilities.obj `if test -f 'src/sql_utilities.cc'; then $(CYGPATH_W) 'src/sql_utilities.cc'; else $(CYGPATH_W) '$(srcdir)/src/sql_utilities.cc'; fi`
+ at am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/hstacks-sql_utilities.Tpo src/$(DEPDIR)/hstacks-sql_utilities.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	$(AM_V_CXX)source='src/sql_utilities.cc' object='src/hstacks-sql_utilities.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(hstacks_CXXFLAGS) $(CXXFLAGS) -c -o src/hstacks-sql_utilities.obj `if test -f 'src/sql_utilities.cc'; then $(CYGPATH_W) 'src/sql_utilities.cc'; else $(CYGPATH_W) '$(srcdir)/src/sql_utilities.cc'; fi`
+
 src/kmer_filter-kmer_filter.o: src/kmer_filter.cc
 @am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(kmer_filter_CXXFLAGS) $(CXXFLAGS) -MT src/kmer_filter-kmer_filter.o -MD -MP -MF src/$(DEPDIR)/kmer_filter-kmer_filter.Tpo -c -o src/kmer_filter-kmer_filter.o `test -f 'src/kmer_filter.cc' || echo '$(srcdir)/'`src/kmer_filter.cc
 @am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/kmer_filter-kmer_filter.Tpo src/$(DEPDIR)/kmer_filter-kmer_filter.Po
@@ -2093,6 +2291,20 @@ src/phasedstacks-input.obj: src/input.cc
 @AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
 @am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(phasedstacks_CXXFLAGS) $(CXXFLAGS) -c -o src/phasedstacks-input.obj `if test -f 'src/input.cc'; then $(CYGPATH_W) 'src/input.cc'; else $(CYGPATH_W) '$(srcdir)/src/input.cc'; fi`
 
+src/phasedstacks-sql_utilities.o: src/sql_utilities.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(phasedstacks_CXXFLAGS) $(CXXFLAGS) -MT src/phasedstacks-sql_utilities.o -MD -MP -MF src/$(DEPDIR)/phasedstacks-sql_utilities.Tpo -c -o src/phasedstacks-sql_utilities.o `test -f 'src/sql_utilities.cc' || echo '$(srcdir)/'`src/sql_utilities.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/phasedstacks-sql_utilities.Tpo src/$(DEPDIR)/phasedstacks-sql_utilities.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	$(AM_V_CXX)source='src/sql_utilities.cc' object='src/phasedstacks-sql_utilities.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(phasedstacks_CXXFLAGS) $(CXXFLAGS) -c -o src/phasedstacks-sql_utilities.o `test -f 'src/sql_utilities.cc' || echo '$(srcdir)/'`src/sql_utilities.cc
+
+src/phasedstacks-sql_utilities.obj: src/sql_utilities.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(phasedstacks_CXXFLAGS) $(CXXFLAGS) -MT src/phasedstacks-sql_utilities.obj -MD -MP -MF src/$(DEPDIR)/phasedstacks-sql_utilities.Tpo -c -o src/phasedstacks-sql_utilities.obj `if test -f 'src/sql_utilities.cc'; then $(CYGPATH_W) 'src/sql_utilities.cc'; else $(CYGPATH_W) '$(srcdir)/src/sql_utilities.cc'; fi`
+ at am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/phasedstacks-sql_utilities.Tpo src/$(DEPDIR)/phasedstacks-sql_utilities.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	$(AM_V_CXX)source='src/sql_utilities.cc' object='src/phasedstacks-sql_utilities.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(phasedstacks_CXXFLAGS) $(CXXFLAGS) -c -o src/phasedstacks-sql_utilities.obj `if test -f 'src/sql_utilities.cc'; then $(CYGPATH_W) 'src/sql_utilities.cc'; else $(CYGPATH_W) '$(srcdir)/src/sql_utilities.cc'; fi`
+
 src/phasedstacks-log_utils.o: src/log_utils.cc
 @am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(phasedstacks_CXXFLAGS) $(CXXFLAGS) -MT src/phasedstacks-log_utils.o -MD -MP -MF src/$(DEPDIR)/phasedstacks-log_utils.Tpo -c -o src/phasedstacks-log_utils.o `test -f 'src/log_utils.cc' || echo '$(srcdir)/'`src/log_utils.cc
 @am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/phasedstacks-log_utils.Tpo src/$(DEPDIR)/phasedstacks-log_utils.Po
@@ -2261,6 +2473,20 @@ src/populations-aln_utils.obj: src/aln_utils.cc
 @AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
 @am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(populations_CXXFLAGS) $(CXXFLAGS) -c -o src/populations-aln_utils.obj `if test -f 'src/aln_utils.cc'; then $(CYGPATH_W) 'src/aln_utils.cc'; else $(CYGPATH_W) '$(srcdir)/src/aln_utils.cc'; fi`
 
+src/populations-genotype_dictionaries.o: src/genotype_dictionaries.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(populations_CXXFLAGS) $(CXXFLAGS) -MT src/populations-genotype_dictionaries.o -MD -MP -MF src/$(DEPDIR)/populations-genotype_dictionaries.Tpo -c -o src/populations-genotype_dictionaries.o `test -f 'src/genotype_dictionaries.cc' || echo '$(srcdir)/'`src/genotype_dictionaries.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/populations-genotype_dictionaries.Tpo src/$(DEPDIR)/populations-genotype_dictionaries.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	$(AM_V_CXX)source='src/genotype_dictionaries.cc' object='src/populations-genotype_dictionaries.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(populations_CXXFLAGS) $(CXXFLAGS) -c -o src/populations-genotype_dictionaries.o `test -f 'src/genotype_dictionaries.cc' || echo '$(srcdir)/'`src/genotype_dictionaries.cc
+
+src/populations-genotype_dictionaries.obj: src/genotype_dictionaries.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(populations_CXXFLAGS) $(CXXFLAGS) -MT src/populations-genotype_dictionaries.obj -MD -MP -MF src/$(DEPDIR)/populations-genotype_dictionaries.Tpo -c -o src/populations-genotype_dictionaries.obj `if test -f 'src/genotype_dictionaries.cc'; then $(CYGPATH_W) 'src/genotype_dictionaries.cc'; else $(CYGPATH_W) '$(srcdir)/src/genotype_dictionaries.cc'; fi`
+ at am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/populations-genotype_dictionaries.Tpo src/$(DEPDIR)/populations-genotype_dictionaries.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	$(AM_V_CXX)source='src/genotype_dictionaries.cc' object='src/populations-genotype_dictionaries.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(populations_CXXFLAGS) $(CXXFLAGS) -c -o src/populations-genotype_dictionaries.obj `if test -f 'src/genotype_dictionaries.cc'; then $(CYGPATH_W) 'src/genotype_dictionaries.cc'; else $(CYGPATH_W) '$(srcdir)/src/genotype_dictionaries.cc'; fi`
+
 src/populations-input.o: src/input.cc
 @am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(populations_CXXFLAGS) $(CXXFLAGS) -MT src/populations-input.o -MD -MP -MF src/$(DEPDIR)/populations-input.Tpo -c -o src/populations-input.o `test -f 'src/input.cc' || echo '$(srcdir)/'`src/input.cc
 @am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/populations-input.Tpo src/$(DEPDIR)/populations-input.Po
@@ -2275,6 +2501,76 @@ src/populations-input.obj: src/input.cc
 @AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
 @am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(populations_CXXFLAGS) $(CXXFLAGS) -c -o src/populations-input.obj `if test -f 'src/input.cc'; then $(CYGPATH_W) 'src/input.cc'; else $(CYGPATH_W) '$(srcdir)/src/input.cc'; fi`
 
+src/populations-sql_utilities.o: src/sql_utilities.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(populations_CXXFLAGS) $(CXXFLAGS) -MT src/populations-sql_utilities.o -MD -MP -MF src/$(DEPDIR)/populations-sql_utilities.Tpo -c -o src/populations-sql_utilities.o `test -f 'src/sql_utilities.cc' || echo '$(srcdir)/'`src/sql_utilities.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/populations-sql_utilities.Tpo src/$(DEPDIR)/populations-sql_utilities.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	$(AM_V_CXX)source='src/sql_utilities.cc' object='src/populations-sql_utilities.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(populations_CXXFLAGS) $(CXXFLAGS) -c -o src/populations-sql_utilities.o `test -f 'src/sql_utilities.cc' || echo '$(srcdir)/'`src/sql_utilities.cc
+
+src/populations-sql_utilities.obj: src/sql_utilities.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(populations_CXXFLAGS) $(CXXFLAGS) -MT src/populations-sql_utilities.obj -MD -MP -MF src/$(DEPDIR)/populations-sql_utilities.Tpo -c -o src/populations-sql_utilities.obj `if test -f 'src/sql_utilities.cc'; then $(CYGPATH_W) 'src/sql_utilities.cc'; else $(CYGPATH_W) '$(srcdir)/src/sql_utilities.cc'; fi`
+ at am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/populations-sql_utilities.Tpo src/$(DEPDIR)/populations-sql_utilities.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	$(AM_V_CXX)source='src/sql_utilities.cc' object='src/populations-sql_utilities.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(populations_CXXFLAGS) $(CXXFLAGS) -c -o src/populations-sql_utilities.obj `if test -f 'src/sql_utilities.cc'; then $(CYGPATH_W) 'src/sql_utilities.cc'; else $(CYGPATH_W) '$(srcdir)/src/sql_utilities.cc'; fi`
+
+src/populations-renz.o: src/renz.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(populations_CXXFLAGS) $(CXXFLAGS) -MT src/populations-renz.o -MD -MP -MF src/$(DEPDIR)/populations-renz.Tpo -c -o src/populations-renz.o `test -f 'src/renz.cc' || echo '$(srcdir)/'`src/renz.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/populations-renz.Tpo src/$(DEPDIR)/populations-renz.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	$(AM_V_CXX)source='src/renz.cc' object='src/populations-renz.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(populations_CXXFLAGS) $(CXXFLAGS) -c -o src/populations-renz.o `test -f 'src/renz.cc' || echo '$(srcdir)/'`src/renz.cc
+
+src/populations-renz.obj: src/renz.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(populations_CXXFLAGS) $(CXXFLAGS) -MT src/populations-renz.obj -MD -MP -MF src/$(DEPDIR)/populations-renz.Tpo -c -o src/populations-renz.obj `if test -f 'src/renz.cc'; then $(CYGPATH_W) 'src/renz.cc'; else $(CYGPATH_W) '$(srcdir)/src/renz.cc'; fi`
+ at am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/populations-renz.Tpo src/$(DEPDIR)/populations-renz.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	$(AM_V_CXX)source='src/renz.cc' object='src/populations-renz.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(populations_CXXFLAGS) $(CXXFLAGS) -c -o src/populations-renz.obj `if test -f 'src/renz.cc'; then $(CYGPATH_W) 'src/renz.cc'; else $(CYGPATH_W) '$(srcdir)/src/renz.cc'; fi`
+
+src/populations-export_formats.o: src/export_formats.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(populations_CXXFLAGS) $(CXXFLAGS) -MT src/populations-export_formats.o -MD -MP -MF src/$(DEPDIR)/populations-export_formats.Tpo -c -o src/populations-export_formats.o `test -f 'src/export_formats.cc' || echo '$(srcdir)/'`src/export_formats.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/populations-export_formats.Tpo src/$(DEPDIR)/populations-export_formats.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	$(AM_V_CXX)source='src/export_formats.cc' object='src/populations-export_formats.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(populations_CXXFLAGS) $(CXXFLAGS) -c -o src/populations-export_formats.o `test -f 'src/export_formats.cc' || echo '$(srcdir)/'`src/export_formats.cc
+
+src/populations-export_formats.obj: src/export_formats.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(populations_CXXFLAGS) $(CXXFLAGS) -MT src/populations-export_formats.obj -MD -MP -MF src/$(DEPDIR)/populations-export_formats.Tpo -c -o src/populations-export_formats.obj `if test -f 'src/export_formats.cc'; then $(CYGPATH_W) 'src/export_formats.cc'; else $(CYGPATH_W) '$(srcdir)/src/export_formats.cc'; fi`
+ at am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/populations-export_formats.Tpo src/$(DEPDIR)/populations-export_formats.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	$(AM_V_CXX)source='src/export_formats.cc' object='src/populations-export_formats.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(populations_CXXFLAGS) $(CXXFLAGS) -c -o src/populations-export_formats.obj `if test -f 'src/export_formats.cc'; then $(CYGPATH_W) 'src/export_formats.cc'; else $(CYGPATH_W) '$(srcdir)/src/export_formats.cc'; fi`
+
+src/populations-MetaPopInfo.o: src/MetaPopInfo.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(populations_CXXFLAGS) $(CXXFLAGS) -MT src/populations-MetaPopInfo.o -MD -MP -MF src/$(DEPDIR)/populations-MetaPopInfo.Tpo -c -o src/populations-MetaPopInfo.o `test -f 'src/MetaPopInfo.cc' || echo '$(srcdir)/'`src/MetaPopInfo.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/populations-MetaPopInfo.Tpo src/$(DEPDIR)/populations-MetaPopInfo.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	$(AM_V_CXX)source='src/MetaPopInfo.cc' object='src/populations-MetaPopInfo.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(populations_CXXFLAGS) $(CXXFLAGS) -c -o src/populations-MetaPopInfo.o `test -f 'src/MetaPopInfo.cc' || echo '$(srcdir)/'`src/MetaPopInfo.cc
+
+src/populations-MetaPopInfo.obj: src/MetaPopInfo.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(populations_CXXFLAGS) $(CXXFLAGS) -MT src/populations-MetaPopInfo.obj -MD -MP -MF src/$(DEPDIR)/populations-MetaPopInfo.Tpo -c -o src/populations-MetaPopInfo.obj `if test -f 'src/MetaPopInfo.cc'; then $(CYGPATH_W) 'src/MetaPopInfo.cc'; else $(CYGPATH_W) '$(srcdir)/src/MetaPopInfo.cc'; fi`
+ at am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/populations-MetaPopInfo.Tpo src/$(DEPDIR)/populations-MetaPopInfo.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	$(AM_V_CXX)source='src/MetaPopInfo.cc' object='src/populations-MetaPopInfo.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(populations_CXXFLAGS) $(CXXFLAGS) -c -o src/populations-MetaPopInfo.obj `if test -f 'src/MetaPopInfo.cc'; then $(CYGPATH_W) 'src/MetaPopInfo.cc'; else $(CYGPATH_W) '$(srcdir)/src/MetaPopInfo.cc'; fi`
+
+src/populations-Vcf.o: src/Vcf.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(populations_CXXFLAGS) $(CXXFLAGS) -MT src/populations-Vcf.o -MD -MP -MF src/$(DEPDIR)/populations-Vcf.Tpo -c -o src/populations-Vcf.o `test -f 'src/Vcf.cc' || echo '$(srcdir)/'`src/Vcf.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/populations-Vcf.Tpo src/$(DEPDIR)/populations-Vcf.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	$(AM_V_CXX)source='src/Vcf.cc' object='src/populations-Vcf.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(populations_CXXFLAGS) $(CXXFLAGS) -c -o src/populations-Vcf.o `test -f 'src/Vcf.cc' || echo '$(srcdir)/'`src/Vcf.cc
+
+src/populations-Vcf.obj: src/Vcf.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(populations_CXXFLAGS) $(CXXFLAGS) -MT src/populations-Vcf.obj -MD -MP -MF src/$(DEPDIR)/populations-Vcf.Tpo -c -o src/populations-Vcf.obj `if test -f 'src/Vcf.cc'; then $(CYGPATH_W) 'src/Vcf.cc'; else $(CYGPATH_W) '$(srcdir)/src/Vcf.cc'; fi`
+ at am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/populations-Vcf.Tpo src/$(DEPDIR)/populations-Vcf.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	$(AM_V_CXX)source='src/Vcf.cc' object='src/populations-Vcf.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(populations_CXXFLAGS) $(CXXFLAGS) -c -o src/populations-Vcf.obj `if test -f 'src/Vcf.cc'; then $(CYGPATH_W) 'src/Vcf.cc'; else $(CYGPATH_W) '$(srcdir)/src/Vcf.cc'; fi`
+
 src/process_radtags-process_radtags.o: src/process_radtags.cc
 @am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(process_radtags_CXXFLAGS) $(CXXFLAGS) -MT src/process_radtags-process_radtags.o -MD -MP -MF src/$(DEPDIR)/process_radtags-process_radtags.Tpo -c -o src/process_radtags-process_radtags.o `test -f 'src/process_radtags.cc' || echo '$(srcdir)/'`src/process_radtags.cc
 @am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/process_radtags-process_radtags.Tpo src/$(DEPDIR)/process_radtags-process_radtags.Po
@@ -2373,6 +2669,20 @@ src/process_radtags-input.obj: src/input.cc
 @AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
 @am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(process_radtags_CXXFLAGS) $(CXXFLAGS) -c -o src/process_radtags-input.obj `if test -f 'src/input.cc'; then $(CYGPATH_W) 'src/input.cc'; else $(CYGPATH_W) '$(srcdir)/src/input.cc'; fi`
 
+src/process_radtags-renz.o: src/renz.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(process_radtags_CXXFLAGS) $(CXXFLAGS) -MT src/process_radtags-renz.o -MD -MP -MF src/$(DEPDIR)/process_radtags-renz.Tpo -c -o src/process_radtags-renz.o `test -f 'src/renz.cc' || echo '$(srcdir)/'`src/renz.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/process_radtags-renz.Tpo src/$(DEPDIR)/process_radtags-renz.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	$(AM_V_CXX)source='src/renz.cc' object='src/process_radtags-renz.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(process_radtags_CXXFLAGS) $(CXXFLAGS) -c -o src/process_radtags-renz.o `test -f 'src/renz.cc' || echo '$(srcdir)/'`src/renz.cc
+
+src/process_radtags-renz.obj: src/renz.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(process_radtags_CXXFLAGS) $(CXXFLAGS) -MT src/process_radtags-renz.obj -MD -MP -MF src/$(DEPDIR)/process_radtags-renz.Tpo -c -o src/process_radtags-renz.obj `if test -f 'src/renz.cc'; then $(CYGPATH_W) 'src/renz.cc'; else $(CYGPATH_W) '$(srcdir)/src/renz.cc'; fi`
+ at am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/process_radtags-renz.Tpo src/$(DEPDIR)/process_radtags-renz.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	$(AM_V_CXX)source='src/renz.cc' object='src/process_radtags-renz.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(process_radtags_CXXFLAGS) $(CXXFLAGS) -c -o src/process_radtags-renz.obj `if test -f 'src/renz.cc'; then $(CYGPATH_W) 'src/renz.cc'; else $(CYGPATH_W) '$(srcdir)/src/renz.cc'; fi`
+
 src/process_shortreads-process_shortreads.o: src/process_shortreads.cc
 @am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(process_shortreads_CXXFLAGS) $(CXXFLAGS) -MT src/process_shortreads-process_shortreads.o -MD -MP -MF src/$(DEPDIR)/process_shortreads-process_shortreads.Tpo -c -o src/process_shortreads-process_shortreads.o `test -f 'src/process_shortreads.cc' || echo '$(srcdir)/'`src/process_shortreads.cc
 @am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/process_shortreads-process_shortreads.Tpo src/$(DEPDIR)/process_shortreads-process_shortreads.Po
@@ -2737,6 +3047,34 @@ src/rxstacks-input.obj: src/input.cc
 @AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
 @am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(rxstacks_CXXFLAGS) $(CXXFLAGS) -c -o src/rxstacks-input.obj `if test -f 'src/input.cc'; then $(CYGPATH_W) 'src/input.cc'; else $(CYGPATH_W) '$(srcdir)/src/input.cc'; fi`
 
+src/rxstacks-sql_utilities.o: src/sql_utilities.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(rxstacks_CXXFLAGS) $(CXXFLAGS) -MT src/rxstacks-sql_utilities.o -MD -MP -MF src/$(DEPDIR)/rxstacks-sql_utilities.Tpo -c -o src/rxstacks-sql_utilities.o `test -f 'src/sql_utilities.cc' || echo '$(srcdir)/'`src/sql_utilities.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/rxstacks-sql_utilities.Tpo src/$(DEPDIR)/rxstacks-sql_utilities.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	$(AM_V_CXX)source='src/sql_utilities.cc' object='src/rxstacks-sql_utilities.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(rxstacks_CXXFLAGS) $(CXXFLAGS) -c -o src/rxstacks-sql_utilities.o `test -f 'src/sql_utilities.cc' || echo '$(srcdir)/'`src/sql_utilities.cc
+
+src/rxstacks-sql_utilities.obj: src/sql_utilities.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(rxstacks_CXXFLAGS) $(CXXFLAGS) -MT src/rxstacks-sql_utilities.obj -MD -MP -MF src/$(DEPDIR)/rxstacks-sql_utilities.Tpo -c -o src/rxstacks-sql_utilities.obj `if test -f 'src/sql_utilities.cc'; then $(CYGPATH_W) 'src/sql_utilities.cc'; else $(CYGPATH_W) '$(srcdir)/src/sql_utilities.cc'; fi`
+ at am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/rxstacks-sql_utilities.Tpo src/$(DEPDIR)/rxstacks-sql_utilities.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	$(AM_V_CXX)source='src/sql_utilities.cc' object='src/rxstacks-sql_utilities.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(rxstacks_CXXFLAGS) $(CXXFLAGS) -c -o src/rxstacks-sql_utilities.obj `if test -f 'src/sql_utilities.cc'; then $(CYGPATH_W) 'src/sql_utilities.cc'; else $(CYGPATH_W) '$(srcdir)/src/sql_utilities.cc'; fi`
+
+src/rxstacks-MetaPopInfo.o: src/MetaPopInfo.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(rxstacks_CXXFLAGS) $(CXXFLAGS) -MT src/rxstacks-MetaPopInfo.o -MD -MP -MF src/$(DEPDIR)/rxstacks-MetaPopInfo.Tpo -c -o src/rxstacks-MetaPopInfo.o `test -f 'src/MetaPopInfo.cc' || echo '$(srcdir)/'`src/MetaPopInfo.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/rxstacks-MetaPopInfo.Tpo src/$(DEPDIR)/rxstacks-MetaPopInfo.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	$(AM_V_CXX)source='src/MetaPopInfo.cc' object='src/rxstacks-MetaPopInfo.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(rxstacks_CXXFLAGS) $(CXXFLAGS) -c -o src/rxstacks-MetaPopInfo.o `test -f 'src/MetaPopInfo.cc' || echo '$(srcdir)/'`src/MetaPopInfo.cc
+
+src/rxstacks-MetaPopInfo.obj: src/MetaPopInfo.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(rxstacks_CXXFLAGS) $(CXXFLAGS) -MT src/rxstacks-MetaPopInfo.obj -MD -MP -MF src/$(DEPDIR)/rxstacks-MetaPopInfo.Tpo -c -o src/rxstacks-MetaPopInfo.obj `if test -f 'src/MetaPopInfo.cc'; then $(CYGPATH_W) 'src/MetaPopInfo.cc'; else $(CYGPATH_W) '$(srcdir)/src/MetaPopInfo.cc'; fi`
+ at am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/rxstacks-MetaPopInfo.Tpo src/$(DEPDIR)/rxstacks-MetaPopInfo.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	$(AM_V_CXX)source='src/MetaPopInfo.cc' object='src/rxstacks-MetaPopInfo.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(rxstacks_CXXFLAGS) $(CXXFLAGS) -c -o src/rxstacks-MetaPopInfo.obj `if test -f 'src/MetaPopInfo.cc'; then $(CYGPATH_W) 'src/MetaPopInfo.cc'; else $(CYGPATH_W) '$(srcdir)/src/MetaPopInfo.cc'; fi`
+
 src/sstacks-sstacks.o: src/sstacks.cc
 @am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sstacks_CXXFLAGS) $(CXXFLAGS) -MT src/sstacks-sstacks.o -MD -MP -MF src/$(DEPDIR)/sstacks-sstacks.Tpo -c -o src/sstacks-sstacks.o `test -f 'src/sstacks.cc' || echo '$(srcdir)/'`src/sstacks.cc
 @am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/sstacks-sstacks.Tpo src/$(DEPDIR)/sstacks-sstacks.Po
@@ -2863,6 +3201,20 @@ src/sstacks-input.obj: src/input.cc
 @AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
 @am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sstacks_CXXFLAGS) $(CXXFLAGS) -c -o src/sstacks-input.obj `if test -f 'src/input.cc'; then $(CYGPATH_W) 'src/input.cc'; else $(CYGPATH_W) '$(srcdir)/src/input.cc'; fi`
 
+src/sstacks-sql_utilities.o: src/sql_utilities.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sstacks_CXXFLAGS) $(CXXFLAGS) -MT src/sstacks-sql_utilities.o -MD -MP -MF src/$(DEPDIR)/sstacks-sql_utilities.Tpo -c -o src/sstacks-sql_utilities.o `test -f 'src/sql_utilities.cc' || echo '$(srcdir)/'`src/sql_utilities.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/sstacks-sql_utilities.Tpo src/$(DEPDIR)/sstacks-sql_utilities.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	$(AM_V_CXX)source='src/sql_utilities.cc' object='src/sstacks-sql_utilities.o' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sstacks_CXXFLAGS) $(CXXFLAGS) -c -o src/sstacks-sql_utilities.o `test -f 'src/sql_utilities.cc' || echo '$(srcdir)/'`src/sql_utilities.cc
+
+src/sstacks-sql_utilities.obj: src/sql_utilities.cc
+ at am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sstacks_CXXFLAGS) $(CXXFLAGS) -MT src/sstacks-sql_utilities.obj -MD -MP -MF src/$(DEPDIR)/sstacks-sql_utilities.Tpo -c -o src/sstacks-sql_utilities.obj `if test -f 'src/sql_utilities.cc'; then $(CYGPATH_W) 'src/sql_utilities.cc'; else $(CYGPATH_W) '$(srcdir)/src/sql_utilities.cc'; fi`
+ at am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/sstacks-sql_utilities.Tpo src/$(DEPDIR)/sstacks-sql_utilities.Po
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	$(AM_V_CXX)source='src/sql_utilities.cc' object='src/sstacks-sql_utilities.obj' libtool=no @AMDEPBACKSLASH@
+ at AMDEP_TRUE@@am__fastdepCXX_FALSE@	DEPDIR=$(DEPDIR) $(CXXDEPMODE) $(depcomp) @AMDEPBACKSLASH@
+ at am__fastdepCXX_FALSE@	$(AM_V_CXX at am__nodep@)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(sstacks_CXXFLAGS) $(CXXFLAGS) -c -o src/sstacks-sql_utilities.obj `if test -f 'src/sql_utilities.cc'; then $(CYGPATH_W) 'src/sql_utilities.cc'; else $(CYGPATH_W) '$(srcdir)/src/sql_utilities.cc'; fi`
+
 src/ustacks-ustacks.o: src/ustacks.cc
 @am__fastdepCXX_TRUE@	$(AM_V_CXX)$(CXX) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(ustacks_CXXFLAGS) $(CXXFLAGS) -MT src/ustacks-ustacks.o -MD -MP -MF src/$(DEPDIR)/ustacks-ustacks.Tpo -c -o src/ustacks-ustacks.o `test -f 'src/ustacks.cc' || echo '$(srcdir)/'`src/ustacks.cc
 @am__fastdepCXX_TRUE@	$(AM_V_at)$(am__mv) src/$(DEPDIR)/ustacks-ustacks.Tpo src/$(DEPDIR)/ustacks-ustacks.Po
@@ -3055,14 +3407,61 @@ uninstall-nobase_pkgdataDATA:
 	$(am__nobase_strip_setup); files=`$(am__nobase_strip)`; \
 	dir='$(DESTDIR)$(pkgdatadir)'; $(am__uninstall_files_from_dir)
 
+# This directory's subdirectories are mostly independent; you can cd
+# into them and run 'make' without going through this Makefile.
+# To change the values of 'make' variables: instead of editing Makefiles,
+# (1) if the variable is set in 'config.status', edit 'config.status'
+#     (which will cause the Makefiles to be regenerated when you run 'make');
+# (2) otherwise, pass the desired values on the 'make' command line.
+$(am__recursive_targets):
+	@fail=; \
+	if $(am__make_keepgoing); then \
+	  failcom='fail=yes'; \
+	else \
+	  failcom='exit 1'; \
+	fi; \
+	dot_seen=no; \
+	target=`echo $@ | sed s/-recursive//`; \
+	case "$@" in \
+	  distclean-* | maintainer-clean-*) list='$(DIST_SUBDIRS)' ;; \
+	  *) list='$(SUBDIRS)' ;; \
+	esac; \
+	for subdir in $$list; do \
+	  echo "Making $$target in $$subdir"; \
+	  if test "$$subdir" = "."; then \
+	    dot_seen=yes; \
+	    local_target="$$target-am"; \
+	  else \
+	    local_target="$$target"; \
+	  fi; \
+	  ($(am__cd) $$subdir && $(MAKE) $(AM_MAKEFLAGS) $$local_target) \
+	  || eval $$failcom; \
+	done; \
+	if test "$$dot_seen" = "no"; then \
+	  $(MAKE) $(AM_MAKEFLAGS) "$$target-am" || exit 1; \
+	fi; test -z "$$fail"
+
 ID: $(am__tagged_files)
 	$(am__define_uniq_tagged_files); mkid -fID $$unique
-tags: tags-am
+tags: tags-recursive
 TAGS: tags
 
 tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
 	set x; \
 	here=`pwd`; \
+	if ($(ETAGS) --etags-include --version) >/dev/null 2>&1; then \
+	  include_option=--etags-include; \
+	  empty_fix=.; \
+	else \
+	  include_option=--include; \
+	  empty_fix=; \
+	fi; \
+	list='$(SUBDIRS)'; for subdir in $$list; do \
+	  if test "$$subdir" = .; then :; else \
+	    test ! -f $$subdir/TAGS || \
+	      set "$$@" "$$include_option=$$here/$$subdir/TAGS"; \
+	  fi; \
+	done; \
 	$(am__define_uniq_tagged_files); \
 	shift; \
 	if test -z "$(ETAGS_ARGS)$$*$$unique"; then :; else \
@@ -3075,7 +3474,7 @@ tags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
 	      $$unique; \
 	  fi; \
 	fi
-ctags: ctags-am
+ctags: ctags-recursive
 
 CTAGS: ctags
 ctags-am: $(TAGS_DEPENDENCIES) $(am__tagged_files)
@@ -3094,7 +3493,7 @@ cscope: cscope.files
 clean-cscope:
 	-rm -f cscope.files
 cscope.files: clean-cscope cscopelist
-cscopelist: cscopelist-am
+cscopelist: cscopelist-recursive
 
 cscopelist-am: $(am__tagged_files)
 	list='$(am__tagged_files)'; \
@@ -3330,6 +3729,31 @@ distdir: $(DISTFILES)
 	    || exit 1; \
 	  fi; \
 	done
+	@list='$(DIST_SUBDIRS)'; for subdir in $$list; do \
+	  if test "$$subdir" = .; then :; else \
+	    $(am__make_dryrun) \
+	      || test -d "$(distdir)/$$subdir" \
+	      || $(MKDIR_P) "$(distdir)/$$subdir" \
+	      || exit 1; \
+	    dir1=$$subdir; dir2="$(distdir)/$$subdir"; \
+	    $(am__relativize); \
+	    new_distdir=$$reldir; \
+	    dir1=$$subdir; dir2="$(top_distdir)"; \
+	    $(am__relativize); \
+	    new_top_distdir=$$reldir; \
+	    echo " (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) top_distdir="$$new_top_distdir" distdir="$$new_distdir" \\"; \
+	    echo "     am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)"; \
+	    ($(am__cd) $$subdir && \
+	      $(MAKE) $(AM_MAKEFLAGS) \
+	        top_distdir="$$new_top_distdir" \
+	        distdir="$$new_distdir" \
+		am__remove_distdir=: \
+		am__skip_length_check=: \
+		am__skip_mode_fix=: \
+	        distdir) \
+	      || exit 1; \
+	  fi; \
+	done
 	-test -n "$(am__skip_mode_fix)" \
 	|| find "$(distdir)" -type d ! -perm -755 \
 		-exec chmod u+rwx,go+rx {} \; -o \
@@ -3463,21 +3887,22 @@ distcleancheck: distclean
 	       exit 1; } >&2
 check-am: all-am
 	$(MAKE) $(AM_MAKEFLAGS) check-TESTS
-check: check-am
+check: check-recursive
 all-am: Makefile $(PROGRAMS) $(SCRIPTS) $(DATA) config.h
-installdirs:
+installdirs: installdirs-recursive
+installdirs-am:
 	for dir in "$(DESTDIR)$(bindir)" "$(DESTDIR)$(bindir)" "$(DESTDIR)$(pkgdatadir)"; do \
 	  test -z "$$dir" || $(MKDIR_P) "$$dir"; \
 	done
-install: install-am
-install-exec: install-exec-am
-install-data: install-data-am
-uninstall: uninstall-am
+install: install-recursive
+install-exec: install-exec-recursive
+install-data: install-data-recursive
+uninstall: uninstall-recursive
 
 install-am: all-am
 	@$(MAKE) $(AM_MAKEFLAGS) install-exec-am install-data-am
 
-installcheck: installcheck-am
+installcheck: installcheck-recursive
 install-strip:
 	if test -z '$(STRIP)'; then \
 	  $(MAKE) $(AM_MAKEFLAGS) INSTALL_PROGRAM="$(INSTALL_STRIP_PROGRAM)" \
@@ -3504,74 +3929,74 @@ distclean-generic:
 maintainer-clean-generic:
 	@echo "This command is intended for maintainers to use"
 	@echo "it deletes files that may require special tools to rebuild."
-clean: clean-am
+clean: clean-recursive
 
 clean-am: clean-binPROGRAMS clean-generic mostlyclean-am
 
-distclean: distclean-am
+distclean: distclean-recursive
 	-rm -f $(am__CONFIG_DISTCLEAN_FILES)
 	-rm -rf src/$(DEPDIR)
 	-rm -f Makefile
 distclean-am: clean-am distclean-compile distclean-generic \
 	distclean-hdr distclean-tags
 
-dvi: dvi-am
+dvi: dvi-recursive
 
 dvi-am:
 
-html: html-am
+html: html-recursive
 
 html-am:
 
-info: info-am
+info: info-recursive
 
 info-am:
 
 install-data-am: install-nobase_pkgdataDATA
 	@$(NORMAL_INSTALL)
 	$(MAKE) $(AM_MAKEFLAGS) install-data-hook
-install-dvi: install-dvi-am
+install-dvi: install-dvi-recursive
 
 install-dvi-am:
 
 install-exec-am: install-binPROGRAMS install-dist_binSCRIPTS
 
-install-html: install-html-am
+install-html: install-html-recursive
 
 install-html-am:
 
-install-info: install-info-am
+install-info: install-info-recursive
 
 install-info-am:
 
 install-man:
 
-install-pdf: install-pdf-am
+install-pdf: install-pdf-recursive
 
 install-pdf-am:
 
-install-ps: install-ps-am
+install-ps: install-ps-recursive
 
 install-ps-am:
 
 installcheck-am:
 
-maintainer-clean: maintainer-clean-am
+maintainer-clean: maintainer-clean-recursive
 	-rm -f $(am__CONFIG_DISTCLEAN_FILES)
 	-rm -rf $(top_srcdir)/autom4te.cache
 	-rm -rf src/$(DEPDIR)
 	-rm -f Makefile
 maintainer-clean-am: distclean-am maintainer-clean-generic
 
-mostlyclean: mostlyclean-am
+mostlyclean: mostlyclean-recursive
 
 mostlyclean-am: mostlyclean-compile mostlyclean-generic
 
-pdf: pdf-am
+pdf: pdf-recursive
 
 pdf-am:
 
-ps: ps-am
+ps: ps-recursive
 
 ps-am:
 
@@ -3579,23 +4004,24 @@ uninstall-am: uninstall-binPROGRAMS uninstall-dist_binSCRIPTS \
 	uninstall-nobase_pkgdataDATA
 	@$(NORMAL_INSTALL)
 	$(MAKE) $(AM_MAKEFLAGS) uninstall-hook
-.MAKE: all check-am install-am install-data-am install-strip \
-	uninstall-am
-
-.PHONY: CTAGS GTAGS TAGS all all-am am--refresh check check-TESTS \
-	check-am clean clean-binPROGRAMS clean-cscope clean-generic \
-	cscope cscopelist-am ctags ctags-am dist dist-all dist-bzip2 \
-	dist-gzip dist-lzip dist-shar dist-tarZ dist-xz dist-zip \
-	distcheck distclean distclean-compile distclean-generic \
-	distclean-hdr distclean-tags distcleancheck distdir \
-	distuninstallcheck dvi dvi-am html html-am info info-am \
-	install install-am install-binPROGRAMS install-data \
-	install-data-am install-data-hook install-dist_binSCRIPTS \
-	install-dvi install-dvi-am install-exec install-exec-am \
-	install-html install-html-am install-info install-info-am \
-	install-man install-nobase_pkgdataDATA install-pdf \
-	install-pdf-am install-ps install-ps-am install-strip \
-	installcheck installcheck-am installdirs maintainer-clean \
+.MAKE: $(am__recursive_targets) all check-am install-am \
+	install-data-am install-strip uninstall-am
+
+.PHONY: $(am__recursive_targets) CTAGS GTAGS TAGS all all-am \
+	am--refresh check check-TESTS check-am clean clean-binPROGRAMS \
+	clean-cscope clean-generic cscope cscopelist-am ctags ctags-am \
+	dist dist-all dist-bzip2 dist-gzip dist-lzip dist-shar \
+	dist-tarZ dist-xz dist-zip distcheck distclean \
+	distclean-compile distclean-generic distclean-hdr \
+	distclean-tags distcleancheck distdir distuninstallcheck dvi \
+	dvi-am html html-am info info-am install install-am \
+	install-binPROGRAMS install-data install-data-am \
+	install-data-hook install-dist_binSCRIPTS install-dvi \
+	install-dvi-am install-exec install-exec-am install-html \
+	install-html-am install-info install-info-am install-man \
+	install-nobase_pkgdataDATA install-pdf install-pdf-am \
+	install-ps install-ps-am install-strip installcheck \
+	installcheck-am installdirs installdirs-am maintainer-clean \
 	maintainer-clean-generic mostlyclean mostlyclean-compile \
 	mostlyclean-generic pdf pdf-am ps ps-am recheck tags tags-am \
 	uninstall uninstall-am uninstall-binPROGRAMS \
diff --git a/README b/README
index 6ac640c..82774f4 100644
--- a/README
+++ b/README
@@ -25,16 +25,7 @@ cpan tool.
 
 1. Install optional components:
 
-The performance of Stacks can be improved by installing two, optional external libraries.
-First, to enable reading of BAM files, install Samtools: 
-
-    http://samtools.sourceforge.net/.
-
-    Note: Stacks is not yet compatible with newer Samtools versions that use HTSlib. For
-    now, you must use Samtools version 0.1.19, which was the last non-HTSlib version:
-       http://sourceforge.net/projects/samtools/files/samtools/0.1.19/
-
-Second, to lower memory usage install Google's SparseHash class.
+If you would like to lower memory usage install Google's SparseHash class.
 
     http://code.google.com/p/sparsehash/
 
@@ -43,16 +34,14 @@ package manager. If you are using Ubuntu, you can install the following packages
 
 % sudo apt-get install libdbd-mysql-perl
 % sudo apt-get install libsparsehash-dev
-% sudo apt-get install samtools
-% sudo apt-get install libbam-dev
 
 A similar set of commands can be executed on Debian using apt-get, or on a RedHat derived Linux
 system using yum, or another package manager on other Linux distributions.
 
 2. Build the software. Stacks uses the standard autotools install:
 
-% tar xfvz stacks_x.xx.tar.gz
-% cd stacks_x.xx
+% tar xfvz stacks-x.xx.tar.gz
+% cd stacks-x.xx
 % ./configure
 
 You can change the root of the install location (/usr/local/ on most
@@ -61,21 +50,9 @@ the configure script.
 
 % ./configure --prefix=/home/smith/local
 
-You can enable Sparsehash and BAM by adding the following options:
-
-% ./configure --enable-sparsehash --enable-bam
-
-You probably need to specify the BAM library location:
-
-% ./configure --enable-bam \
-              --with-bam-include-path=/usr/local/include/bam \
-              --with-bam-lib-path=/usr/local/lib
-
-Or, if you installed with Ubuntu packages:
+You can enable Sparsehash by adding the following options:
 
-% ./configure --enable-bam \
-              --with-bam-include-path=/usr/include/samtools \
-              --with-bam-lib-path=/usr/lib
+% ./configure --enable-sparsehash
 
 % make
 
diff --git a/configure b/configure
index 02e451f..25d6f19 100755
--- a/configure
+++ b/configure
@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for Stacks 1.40.
+# Generated by GNU Autoconf 2.69 for Stacks 1.42.
 #
 #
 # Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc.
@@ -577,8 +577,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='Stacks'
 PACKAGE_TARNAME='stacks'
-PACKAGE_VERSION='1.40'
-PACKAGE_STRING='Stacks 1.40'
+PACKAGE_VERSION='1.42'
+PACKAGE_STRING='Stacks 1.42'
 PACKAGE_BUGREPORT=''
 PACKAGE_URL=''
 
@@ -724,8 +724,6 @@ ac_user_opts='
 enable_option_checking
 enable_silent_rules
 enable_bam
-with_bam_include_path
-with_bam_lib_path
 enable_sparsehash
 with_sparsehash_include_path
 enable_dependency_tracking
@@ -1283,7 +1281,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures Stacks 1.40 to adapt to many kinds of systems.
+\`configure' configures Stacks 1.42 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1349,7 +1347,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of Stacks 1.40:";;
+     short | recursive ) echo "Configuration of Stacks 1.42:";;
    esac
   cat <<\_ACEOF
 
@@ -1359,8 +1357,7 @@ Optional Features:
   --enable-FEATURE[=ARG]  include FEATURE [ARG=yes]
   --enable-silent-rules   less verbose build output (undo: "make V=1")
   --disable-silent-rules  verbose build output (undo: "make V=0")
-  --enable-bam            Enable Samtools' use of BAM files (requires BAM
-                          library to be installed).
+  --disable-bam           Disable use of BAM files through HTSLib.
   --enable-sparsehash     Enable the use of Google Sparsehash (must be
                           installed).
   --enable-dependency-tracking
@@ -1372,9 +1369,6 @@ Optional Features:
 Optional Packages:
   --with-PACKAGE[=ARG]    use PACKAGE [ARG=yes]
   --without-PACKAGE       do not use PACKAGE (same as --with-PACKAGE=no)
-  --with-bam-include-path location of Samtools BAM headers, defaults to
-                          /usr/include/bam
-  --with-bam-lib-path     location of Samtools BAM library
   --with-sparsehash-include-path
                           location of Google Sparsehash headers
 
@@ -1456,7 +1450,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-Stacks configure 1.40
+Stacks configure 1.42
 generated by GNU Autoconf 2.69
 
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -1913,7 +1907,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by Stacks $as_me 1.40, which was
+It was created by Stacks $as_me 1.42, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   $ $0 $@
@@ -2776,7 +2770,7 @@ fi
 
 # Define the identity of the package.
  PACKAGE='stacks'
- VERSION='1.40'
+ VERSION='1.42'
 
 
 cat >>confdefs.h <<_ACEOF
@@ -2874,42 +2868,32 @@ ac_config_headers="$ac_config_headers config.h"
 
 
 
-# Get BAM library and include locations if requested
+#
+# Get BAM, aka HTSLib library and include locations if requested
+#
 # Check whether --enable-bam was given.
 if test "${enable_bam+set}" = set; then :
   enableval=$enable_bam;
 fi
 
 
-if test "x$enable_bam" = "xyes"; then :
+if test "x$enable_bam" != "xno"; then :
 
 
 $as_echo "#define HAVE_BAM 1" >>confdefs.h
 
 
-# Check whether --with-bam-include-path was given.
-if test "${with_bam_include_path+set}" = set; then :
-  withval=$with_bam_include_path; BAM_CFLAGS="-I$withval"
-else
-  BAM_CFLAGS='-I/usr/include/bam'
-fi
-
-
-
-
-# Check whether --with-bam-lib-path was given.
-if test "${with_bam_lib_path+set}" = set; then :
-  withval=$with_bam_lib_path; BAM_LIBS="$withval/libbam.a"
-else
-  BAM_LIBS='/usr/lib/libbam.a'
-fi
+BAM_CFLAGS='-I./htslib/htslib'
 
+BAM_LIBS='./htslib/libhts.a'
 
 
 
 fi
 
+#
 # Enable use of Google Sparsehash and get include location if requested.
+#
 # Check whether --enable-sparsehash was given.
 if test "${enable_sparsehash+set}" = set; then :
   enableval=$enable_sparsehash;
@@ -6225,7 +6209,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by Stacks $as_me 1.40, which was
+This file was extended by Stacks $as_me 1.42, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -6291,7 +6275,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-Stacks config.status 1.40
+Stacks config.status 1.42
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"
 
diff --git a/configure.ac b/configure.ac
index dac7cdd..fb4e057 100644
--- a/configure.ac
+++ b/configure.ac
@@ -2,35 +2,32 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ(2.59)
-AC_INIT([Stacks], [1.40])
+AC_INIT([Stacks], [1.42])
 AC_CONFIG_AUX_DIR([config])
 AM_INIT_AUTOMAKE([-Wall -Werror foreign parallel-tests subdir-objects])
 AC_CONFIG_SRCDIR([src/ustacks.cc])
 AC_CONFIG_HEADERS([config.h])
 m4_pattern_allow([AC_OPENMP])
 
-# Get BAM library and include locations if requested
+#
+# Get BAM, aka HTSLib library and include locations if requested
+#
 AC_ARG_ENABLE([bam],
-    AS_HELP_STRING([--enable-bam], [Enable Samtools' use of BAM files (requires BAM library to be installed).]))
+    AS_HELP_STRING([--disable-bam], [Disable use of BAM files through HTSLib.]))
 
-AS_IF([test "x$enable_bam" = "xyes"], [
+AS_IF([test "x$enable_bam" != "xno"], [
 AC_DEFINE([HAVE_BAM], [1], [Enable compilation with Samtools BAM library])
-AC_ARG_WITH([bam-include-path],
-  [AS_HELP_STRING([--with-bam-include-path],
-    [location of Samtools BAM headers, defaults to /usr/include/bam])],
-  [BAM_CFLAGS="-I$withval"],
-  [BAM_CFLAGS='-I/usr/include/bam'])
-AC_SUBST([BAM_CFLAGS])
 
-AC_ARG_WITH([bam-lib-path],
-  [AS_HELP_STRING([--with-bam-lib-path], [location of Samtools BAM library])],
-  [BAM_LIBS="$withval/libbam.a"],
-  [BAM_LIBS='/usr/lib/libbam.a'])
+BAM_CFLAGS='-I./htslib/htslib'
+AC_SUBST([BAM_CFLAGS])
+BAM_LIBS='./htslib/libhts.a'
 AC_SUBST([BAM_LIBS])
 
 ])
 
+#
 # Enable use of Google Sparsehash and get include location if requested.
+#
 AC_ARG_ENABLE([sparsehash],
     AS_HELP_STRING([--enable-sparsehash], [Enable the use of Google Sparsehash (must be installed).]))
 
diff --git a/htslib/._INSTALL b/htslib/._INSTALL
new file mode 100644
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diff --git a/htslib/._hts.c b/htslib/._hts.c
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diff --git a/htslib/._htsfile.c b/htslib/._htsfile.c
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diff --git a/htslib/._knetfile.c b/htslib/._knetfile.c
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diff --git a/htslib/._sam.c b/htslib/._sam.c
new file mode 100644
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diff --git a/htslib/._synced_bcf_reader.c b/htslib/._synced_bcf_reader.c
new file mode 100644
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diff --git a/htslib/._tabix.c b/htslib/._tabix.c
new file mode 100644
index 0000000..8252204
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diff --git a/htslib/._tbx.c b/htslib/._tbx.c
new file mode 100644
index 0000000..8252204
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diff --git a/htslib/._vcf.c b/htslib/._vcf.c
new file mode 100644
index 0000000..8252204
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diff --git a/htslib/._vcf_sweep.c b/htslib/._vcf_sweep.c
new file mode 100644
index 0000000..8252204
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diff --git a/htslib/._vcfutils.c b/htslib/._vcfutils.c
new file mode 100644
index 0000000..8252204
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diff --git a/htslib/INSTALL b/htslib/INSTALL
new file mode 100644
index 0000000..48602e4
--- /dev/null
+++ b/htslib/INSTALL
@@ -0,0 +1,102 @@
+Basic Installation
+==================
+
+To build and install HTSlib, 'cd' to the htslib-1.x directory containing
+the package's source and type the following commands:
+
+    ./configure
+    make
+    make install
+
+The './configure' command checks your build environment and allows various
+optional functionality to be enabled (see Configuration below).  If you
+don't want to select any optional functionality, you may wish to omit
+configure and just type 'make; make install' as for previous versions
+of HTSlib.  However if the build fails you should run './configure' as
+it can diagnose the common reasons for build failures.
+
+The 'make' command builds the HTSlib library and and various useful
+utilities: bgzip, htsfile, and tabix.  If compilation fails you should
+run './configure' as it can diagnose problems with your build environment
+that cause build failures.
+
+The 'make install' command installs the libraries, library header files,
+utilities, several manual pages, and a pkgconfig file to /usr/local.
+The installation location can be changed by configuring with --prefix=DIR
+or via 'make prefix=DIR install' (see Installation Locations below).
+
+
+Configuration
+=============
+
+By default, './configure' examines your build environment, checking for
+requirements such as the zlib development files, and arranges for a plain
+HTSlib build.  The following configure options can be used to enable
+various features and specify further optional external requirements:
+
+--enable-plugins
+    Use plugins to implement exotic file access protocols and other
+    specialised facilities.  This enables such facilities to be developed
+    and packaged outwith HTSlib, and somewhat isolates HTSlib-using programs
+    from their library dependencies.  By default, any enabled pluggable
+    facilities (such as iRODS and libcurl file access) are built directly
+    within HTSlib.
+
+--with-plugin-dir=DIR
+    Specifies the directory into which plugins built while building HTSlib
+    should be installed; by default, LIBEXECDIR/htslib.
+
+--with-plugin-path=DIR:DIR:DIR...
+    Specifies the list of directories that HTSlib will search for plugins.
+    By default, only the directory specified via --with-plugin-dir will be
+    searched; you can use --with-plugin-path='DIR:$(plugindir):DIR' and so
+    on to cause additional directories to be searched.
+
+--with-irods[=DIR]
+    Specifies the location of the iRODS client library to use to enable
+    access to data objects stored in iRODS (<http://irods.org/>) via file
+    paths like 'irods:DATAOBJ'.  DIR is the base of an iRODS source tree
+    such that the library is present as DIR/lib/core/obj/libRodsAPI.* and
+    headers are present under DIR/lib/api/include and so on.  If '=DIR' is
+    omitted, $IRODS_HOME will be used as a base directory.
+
+--enable-libcurl
+    Use libcurl (<http://curl.haxx.se/>) to implement network access to
+    remote files via FTP, HTTP, HTTPS, S3, etc.  By default, HTSlib uses
+    its own simple networking code to provide access via FTP and HTTP only.
+
+The configure script also accepts the usual options and environment variables
+for tuning installation locations and compilers: type './configure --help'
+for details.  For example,
+
+    ./configure CC=icc --prefix=/opt/icc-compiled
+
+would specify that HTSlib is to be built with icc and installed into bin,
+lib, etc subdirectories under /opt/icc-compiled.
+
+
+Installation Locations
+======================
+
+By default, 'make install' installs HTSlib libraries under /usr/local/lib,
+HTSlib header files under /usr/local/include, utility programs under
+/usr/local/bin, etc.  (To be precise, the header files are installed within
+a fixed 'htslib' subdirectory under the specified .../include location.)
+
+You can specify a different location to install HTSlib by configuring
+with --prefix=DIR or specify locations for particular parts of HTSlib by
+configuring with --libdir=DIR and so on.  Type './configure --help' for
+the full list of such install directory options.
+
+Alternatively you can specify different locations at install time by
+typing 'make prefix=DIR install' or 'make libdir=DIR install' and so on.
+Consult the list of prefix/exec_prefix/etc variables near the top of the
+Makefile for the full list of such variables that can be overridden.
+
+You can also specify a staging area by typing 'make DESTDIR=DIR install',
+possibly in conjunction with other --prefix or prefix=DIR settings.
+For example,
+
+    make DESTDIR=/tmp/staging prefix=/opt
+
+would install into bin, lib, etc subdirectories under /tmp/staging/opt.
diff --git a/htslib/LICENSE b/htslib/LICENSE
new file mode 100644
index 0000000..03db010
--- /dev/null
+++ b/htslib/LICENSE
@@ -0,0 +1,69 @@
+[Files in this distribution outwith the cram/ subdirectory are distributed
+according to the terms of the following MIT/Expat license.]
+
+The MIT/Expat License
+
+Copyright (C) 2012-2014 Genome Research Ltd.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.
+
+
+[Files within the cram/ subdirectory in this distribution are distributed
+according to the terms of the following Modified 3-Clause BSD license.]
+
+The Modified-BSD License
+
+Copyright (C) 2012-2014 Genome Research Ltd.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice,
+   this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the names Genome Research Ltd and Wellcome Trust Sanger Institute
+   nor the names of its contributors may be used to endorse or promote products
+   derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR ITS CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+
+[The use of a range of years within a copyright notice in this distribution
+should be interpreted as being equivalent to a list of years including the
+first and last year specified and all consecutive years between them.
+
+For example, a copyright notice that reads "Copyright (C) 2005, 2007-2009,
+2011-2012" should be interpreted as being identical to a notice that reads
+"Copyright (C) 2005, 2007, 2008, 2009, 2011, 2012" and a copyright notice
+that reads "Copyright (C) 2005-2012" should be interpreted as being identical
+to a notice that reads "Copyright (C) 2005, 2006, 2007, 2008, 2009, 2010,
+2011, 2012".]
diff --git a/htslib/Makefile b/htslib/Makefile
new file mode 100644
index 0000000..06fd7bd
--- /dev/null
+++ b/htslib/Makefile
@@ -0,0 +1,426 @@
+# Makefile for htslib, a C library for high-throughput sequencing data formats.
+#
+#    Copyright (C) 2013-2015 Genome Research Ltd.
+#
+#    Author: John Marshall <jm18 at sanger.ac.uk>
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+# DEALINGS IN THE SOFTWARE.
+
+CC     = gcc
+AR     = ar
+RANLIB = ranlib
+
+CPPFLAGS =
+# TODO: probably update cram code to make it compile cleanly with -Wc++-compat
+CFLAGS   = -g -Wall -O2
+EXTRA_CFLAGS_PIC = -fpic
+LDFLAGS  =
+LIBS     =
+
+# For now these don't work too well as samtools also needs to know to
+# add -lbz2 and -llzma if linking against the static libhts.a library.
+# TODO This needs configury and adding to htslib.pc.in.
+#
+# # Bzip2 support; optionally used by CRAM.
+# HAVE_LIBBZ2 := $(shell echo -e "\#include <bzlib.h>\012int main(void){return 0;}" > .test.c && $(CC) $(CFLAGS) $(CPPFLAGS) -o .test .test.c -lbz2 2>/dev/null && echo yes)
+# ifeq "$(HAVE_LIBBZ2)" "yes"
+# CPPFLAGS += -DHAVE_LIBBZ2
+# LIBS     += -lbz2
+# endif
+#
+# # Lzma support; optionally used by CRAM.
+# HAVE_LIBLZMA := $(shell echo -e "\#include <lzma.h>\012int main(void){return 0;}" > .test.c && $(CC) $(CFLAGS) $(CPPFLAGS) -o .test .test.c -llzma 2>/dev/null && echo yes)
+# ifeq "$(HAVE_LIBLZMA)" "yes"
+# CPPFLAGS += -DHAVE_LIBLZMA
+# LIBS     += -llzma
+# endif
+
+prefix      = /usr/local
+exec_prefix = $(prefix)
+bindir      = $(exec_prefix)/bin
+includedir  = $(prefix)/include
+libdir      = $(exec_prefix)/lib
+libexecdir  = $(exec_prefix)/libexec
+datarootdir = $(prefix)/share
+mandir      = $(datarootdir)/man
+man1dir     = $(mandir)/man1
+man5dir     = $(mandir)/man5
+pkgconfigdir= $(libdir)/pkgconfig
+
+MKDIR_P = mkdir -p
+INSTALL = install -p
+INSTALL_PROGRAM = $(INSTALL)
+INSTALL_DATA    = $(INSTALL) -m 644
+INSTALL_DIR     = $(MKDIR_P) -m 755
+
+# Set by config.mk if plugins are enabled
+plugindir =
+
+BUILT_PROGRAMS = \
+	bgzip \
+	htsfile \
+	tabix
+
+BUILT_TEST_PROGRAMS = \
+	test/fieldarith \
+	test/hfile \
+	test/sam \
+	test/test-regidx \
+	test/test_view \
+	test/test-vcf-api \
+	test/test-vcf-sweep
+
+# all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS)
+all: lib-static
+
+HTSPREFIX =
+include htslib_vars.mk
+
+
+PACKAGE_VERSION  = 1.3.1
+LIBHTS_SOVERSION = 1
+
+
+# $(NUMERIC_VERSION) is for items that must have a numeric X.Y.Z string
+# even if this is a dirty or untagged Git working tree.
+NUMERIC_VERSION = $(PACKAGE_VERSION)
+
+# If building from a Git repository, replace $(PACKAGE_VERSION) with the Git
+# description of the working tree: either a release tag with the same value
+# as $(PACKAGE_VERSION) above, or an exact description likely based on a tag.
+# Much of this is also GNU Make-specific.  If you don't have GNU Make and/or
+# are not building from a Git repository, comment out this conditional.
+ifneq "$(wildcard .git)" ""
+original_version := $(PACKAGE_VERSION)
+PACKAGE_VERSION := $(shell git describe --always --dirty)
+
+# Unless the Git description matches /\d*\.\d*(\.\d*)?/, i.e., is exactly a tag
+# with a numeric name, revert $(NUMERIC_VERSION) to the original version number
+# written above, but with the patchlevel field bumped to 255.
+ifneq "$(subst ..,.,$(subst 0,,$(subst 1,,$(subst 2,,$(subst 3,,$(subst 4,,$(subst 5,,$(subst 6,,$(subst 7,,$(subst 8,,$(subst 9,,$(PACKAGE_VERSION))))))))))))" "."
+empty :=
+NUMERIC_VERSION := $(subst $(empty) ,.,$(wordlist 1,2,$(subst ., ,$(original_version))) 255)
+endif
+
+# Force version.h to be remade if $(PACKAGE_VERSION) has changed.
+version.h: $(if $(wildcard version.h),$(if $(findstring "$(PACKAGE_VERSION)",$(shell cat version.h)),,force))
+endif
+
+version.h:
+	echo '#define HTS_VERSION "$(PACKAGE_VERSION)"' > $@
+
+print-version:
+	@echo $(PACKAGE_VERSION)
+
+
+.SUFFIXES: .bundle .c .o .pico .so
+
+.c.o:
+	$(CC) $(CFLAGS) -I. $(CPPFLAGS) -c -o $@ $<
+
+.c.pico:
+	$(CC) $(CFLAGS) -I. $(CPPFLAGS) $(EXTRA_CFLAGS_PIC) -c -o $@ $<
+
+
+LIBHTS_OBJS = \
+	kfunc.o \
+	knetfile.o \
+	kstring.o \
+	bgzf.o \
+	faidx.o \
+	hfile.o \
+	hfile_net.o \
+	hts.o \
+	md5.o \
+	regidx.o \
+	sam.o \
+	synced_bcf_reader.o \
+	vcf_sweep.o \
+	tbx.o \
+	vcf.o \
+	vcfutils.o \
+	cram/cram_codecs.o \
+	cram/cram_decode.o \
+	cram/cram_encode.o \
+	cram/cram_external.o \
+	cram/cram_index.o \
+	cram/cram_io.o \
+	cram/cram_samtools.o \
+	cram/cram_stats.o \
+	cram/files.o \
+	cram/mFILE.o \
+	cram/open_trace_file.o \
+	cram/pooled_alloc.o \
+	cram/rANS_static.o \
+	cram/sam_header.o \
+	cram/string_alloc.o \
+	cram/thread_pool.o \
+	cram/vlen.o \
+	cram/zfio.o
+
+PLUGIN_OBJS =
+
+cram_h = cram/cram.h $(cram_samtools_h) $(cram_sam_header_h) $(cram_structs_h) $(cram_io_h) cram/cram_encode.h cram/cram_decode.h cram/cram_stats.h cram/cram_codecs.h cram/cram_index.h $(htslib_cram_h)
+cram_io_h = cram/cram_io.h $(cram_misc_h)
+cram_misc_h = cram/misc.h cram/os.h
+cram_sam_header_h = cram/sam_header.h cram/string_alloc.h cram/pooled_alloc.h $(htslib_khash_h) $(htslib_kstring_h)
+cram_samtools_h = cram/cram_samtools.h $(htslib_sam_h) $(cram_sam_header_h)
+cram_structs_h = cram/cram_structs.h cram/thread_pool.h cram/string_alloc.h $(htslib_khash_h)
+cram_open_trace_file_h = cram/open_trace_file.h cram/mFILE.h
+hfile_internal_h = hfile_internal.h $(htslib_hfile_h)
+hts_internal_h = hts_internal.h $(htslib_hts_h)
+
+
+# To be effective, config.mk needs to appear after most Makefile variables are
+# set but before most rules appear, so that it can both use previously-set
+# variables in its own rules' prerequisites and also update variables for use
+# in later rules' prerequisites.
+
+# If your make doesn't accept -include, change this to 'include' if you are
+# using the configure script or just comment the line out if you are not.
+-include config.mk
+
+# Usually config.h is generated by running configure or config.status,
+# but if those aren't used create a default config.h here.
+config.h:
+	echo '/* Empty config.h generated by Makefile */' > $@
+
+
+lib-static: libhts.a
+
+# $(shell), :=, and ifeq/.../endif are GNU Make-specific.  If you don't have
+# GNU Make, comment out the parts of this conditional that don't apply.
+PLATFORM := $(shell uname -s)
+ifeq "$(PLATFORM)" "Darwin"
+SHLIB_FLAVOUR = dylib
+lib-shared: libhts.dylib
+BUILT_PLUGINS = $(PLUGIN_OBJS:.o=.bundle)
+else
+SHLIB_FLAVOUR = so
+lib-shared: libhts.so
+BUILT_PLUGINS = $(PLUGIN_OBJS:.o=.so)
+endif
+
+plugins: $(BUILT_PLUGINS)
+
+
+libhts.a: $(LIBHTS_OBJS)
+	@-rm -f $@
+	$(AR) -rc $@ $(LIBHTS_OBJS)
+	-$(RANLIB) $@
+
+
+# The target here is libhts.so, as that is the built file that other rules
+# depend upon and that is used when -lhts appears in other program's recipes.
+# As a byproduct invisible to make, libhts.so.NN is also created, as it is the
+# file used at runtime (when $LD_LIBRARY_PATH includes the build directory).
+
+libhts.so: $(LIBHTS_OBJS:.o=.pico)
+	$(CC) -shared -Wl,-soname,libhts.so.$(LIBHTS_SOVERSION) -pthread $(LDFLAGS) -o $@ $(LIBHTS_OBJS:.o=.pico) -lz -lm $(LIBS)
+	ln -sf $@ libhts.so.$(LIBHTS_SOVERSION)
+
+# Similarly this also creates libhts.NN.dylib as a byproduct, so that programs
+# when run can find this uninstalled shared library (when $DYLD_LIBRARY_PATH
+# includes this project's build directory).
+
+libhts.dylib: $(LIBHTS_OBJS)
+	$(CC) -dynamiclib -install_name $(libdir)/libhts.$(LIBHTS_SOVERSION).dylib -current_version $(NUMERIC_VERSION) -compatibility_version $(LIBHTS_SOVERSION) $(LDFLAGS) -o $@ $(LIBHTS_OBJS) -lz $(LIBS)
+	ln -sf $@ libhts.$(LIBHTS_SOVERSION).dylib
+
+
+.pico.so:
+	$(CC) -shared -Wl,-E -pthread $(LDFLAGS) -o $@ $< $(LIBS)
+
+.o.bundle:
+	$(CC) -bundle -Wl,-undefined,dynamic_lookup $(LDFLAGS) -o $@ $< $(LIBS)
+
+
+bgzf.o bgzf.pico: bgzf.c config.h $(htslib_hts_h) $(htslib_bgzf_h) $(htslib_hfile_h) $(htslib_khash_h)
+kstring.o kstring.pico: kstring.c config.h $(htslib_kstring_h)
+knetfile.o knetfile.pico: knetfile.c config.h $(htslib_knetfile_h)
+hfile.o hfile.pico: hfile.c config.h $(htslib_hfile_h) $(hfile_internal_h) $(hts_internal_h) $(htslib_khash_h)
+hfile_irods.o hfile_irods.pico: hfile_irods.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h)
+hfile_libcurl.o hfile_libcurl.pico: hfile_libcurl.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h)
+hfile_net.o hfile_net.pico: hfile_net.c config.h $(hfile_internal_h) $(htslib_knetfile_h)
+hts.o hts.pico: hts.c config.h version.h $(htslib_hts_h) $(htslib_bgzf_h) $(cram_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_ksort_h) $(hts_internal_h)
+vcf.o vcf.pico: vcf.c config.h $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_tbx_h) $(htslib_hfile_h) $(hts_internal_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_kstring_h) $(htslib_khash_str2int_h)
+sam.o sam.pico: sam.c config.h $(htslib_sam_h) $(htslib_bgzf_h) $(cram_h) $(hts_internal_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_kstring_h)
+tbx.o tbx.pico: tbx.c config.h $(htslib_tbx_h) $(htslib_bgzf_h) $(htslib_khash_h)
+faidx.o faidx.pico: faidx.c config.h $(htslib_bgzf_h) $(htslib_faidx_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kstring_h)
+synced_bcf_reader.o synced_bcf_reader.pico: synced_bcf_reader.c config.h $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(htslib_bgzf_h)
+vcf_sweep.o vcf_sweep.pico: vcf_sweep.c config.h $(htslib_vcf_sweep_h) $(htslib_bgzf_h)
+vcfutils.o vcfutils.pico: vcfutils.c config.h $(htslib_vcfutils_h) $(htslib_kbitset_h)
+kfunc.o kfunc.pico: kfunc.c config.h $(htslib_kfunc_h)
+regidx.o regidx.pico: regidx.c config.h $(htslib_hts_h) $(htslib_kstring_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(htslib_regidx_h)
+md5.o md5.pico: md5.c config.h $(htslib_hts_h)
+plugin.o plugin.pico: plugin.c config.h $(hts_internal_h) $(htslib_kstring_h)
+
+cram/cram_codecs.o cram/cram_codecs.pico: cram/cram_codecs.c config.h $(cram_h)
+cram/cram_decode.o cram/cram_decode.pico: cram/cram_decode.c config.h $(cram_h) cram/os.h $(htslib_hts_h)
+cram/cram_encode.o cram/cram_encode.pico: cram/cram_encode.c config.h $(cram_h) cram/os.h $(htslib_hts_h)
+cram/cram_external.o cram/cram_external.pico: cram/cram_external.c config.h $(htslib_hfile_h) $(cram_h)
+cram/cram_index.o cram/cram_index.pico: cram/cram_index.c config.h $(htslib_hfile_h) $(cram_h) cram/os.h cram/zfio.h $(hts_internal_h)
+cram/cram_io.o cram/cram_io.pico: cram/cram_io.c config.h $(cram_h) cram/os.h $(htslib_hts_h) $(cram_open_trace_file_h) cram/rANS_static.h $(htslib_hfile_h) $(htslib_bgzf_h) $(htslib_faidx_h)
+cram/cram_samtools.o cram/cram_samtools.pico: cram/cram_samtools.c config.h $(cram_h) $(htslib_sam_h)
+cram/cram_stats.o cram/cram_stats.pico: cram/cram_stats.c config.h $(cram_h) cram/os.h
+cram/files.o cram/files.pico: cram/files.c config.h $(cram_misc_h)
+cram/mFILE.o cram/mFILE.pico: cram/mFILE.c config.h cram/os.h cram/mFILE.h cram/vlen.h
+cram/open_trace_file.o cram/open_trace_file.pico: cram/open_trace_file.c config.h cram/os.h $(cram_open_trace_file_h) $(cram_misc_h) $(htslib_hfile_h)
+cram/pooled_alloc.o cram/pooled_alloc.pico: cram/pooled_alloc.c config.h cram/pooled_alloc.h
+cram/rANS_static.o cram/rANS_static.pico: cram/rANS_static.c config.h cram/rANS_static.h cram/rANS_byte.h
+cram/sam_header.o cram/sam_header.pico: cram/sam_header.c config.h $(cram_sam_header_h) cram/string_alloc.h
+cram/string_alloc.o cram/string_alloc.pico: cram/string_alloc.c config.h cram/string_alloc.h
+cram/thread_pool.o cram/thread_pool.pico: cram/thread_pool.c config.h cram/thread_pool.h
+cram/vlen.o cram/vlen.pico: cram/vlen.c config.h cram/vlen.h cram/os.h
+cram/zfio.o cram/zfio.pico: cram/zfio.c config.h cram/os.h cram/zfio.h
+
+
+bgzip: bgzip.o libhts.a
+	$(CC) -pthread $(LDFLAGS) -o $@ bgzip.o libhts.a -lz $(LIBS)
+
+htsfile: htsfile.o libhts.a
+	$(CC) -pthread $(LDFLAGS) -o $@ htsfile.o libhts.a -lz $(LIBS)
+
+tabix: tabix.o libhts.a
+	$(CC) -pthread $(LDFLAGS) -o $@ tabix.o libhts.a -lz $(LIBS)
+
+bgzip.o: bgzip.c config.h $(htslib_bgzf_h) $(htslib_hts_h)
+htsfile.o: htsfile.c config.h $(htslib_hfile_h) $(htslib_hts_h) $(htslib_sam_h) $(htslib_vcf_h)
+tabix.o: tabix.c config.h $(htslib_tbx_h) $(htslib_sam_h) $(htslib_vcf_h) $(htslib_kseq_h) $(htslib_bgzf_h) $(htslib_hts_h) $(htslib_regidx_h)
+
+
+# For tests that might use it, set $REF_PATH explicitly to use only reference
+# areas within the test suite (or set it to ':' to use no reference areas).
+check test: htsfile $(BUILT_TEST_PROGRAMS)
+	test/fieldarith test/fieldarith.sam
+	test/hfile
+	test/sam test/ce.fa test/faidx.fa
+	test/test-regidx
+	cd test && REF_PATH=: ./test.pl
+
+test/fieldarith: test/fieldarith.o libhts.a
+	$(CC) -pthread $(LDFLAGS) -o $@ test/fieldarith.o libhts.a -lz $(LIBS)
+
+test/hfile: test/hfile.o libhts.a
+	$(CC) -pthread $(LDFLAGS) -o $@ test/hfile.o libhts.a -lz $(LIBS)
+
+test/sam: test/sam.o libhts.a
+	$(CC) -pthread $(LDFLAGS) -o $@ test/sam.o libhts.a -lz $(LIBS)
+
+test/test-regidx: test/test-regidx.o libhts.a
+	$(CC) -pthread $(LDFLAGS) -o $@ test/test-regidx.o libhts.a -lz $(LIBS)
+
+test/test_view: test/test_view.o libhts.a
+	$(CC) -pthread $(LDFLAGS) -o $@ test/test_view.o libhts.a -lz $(LIBS)
+
+test/test-vcf-api: test/test-vcf-api.o libhts.a
+	$(CC) -pthread $(LDFLAGS) -o $@ test/test-vcf-api.o libhts.a -lz $(LIBS)
+
+test/test-vcf-sweep: test/test-vcf-sweep.o libhts.a
+	$(CC) -pthread $(LDFLAGS) -o $@ test/test-vcf-sweep.o libhts.a -lz $(LIBS)
+
+test/fieldarith.o: test/fieldarith.c config.h $(htslib_sam_h)
+test/hfile.o: test/hfile.c config.h $(htslib_hfile_h) $(htslib_hts_defs_h)
+test/sam.o: test/sam.c config.h $(htslib_hts_defs_h) $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h)
+test/test-regidx.o: test/test-regidx.c config.h $(htslib_regidx_h)
+test/test_view.o: test/test_view.c config.h $(cram_h) $(htslib_sam_h)
+test/test-vcf-api.o: test/test-vcf-api.c config.h $(htslib_hts_h) $(htslib_vcf_h) $(htslib_kstring_h) $(htslib_kseq_h)
+test/test-vcf-sweep.o: test/test-vcf-sweep.c config.h $(htslib_vcf_sweep_h)
+
+
+# install: libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) installdirs install-$(SHLIB_FLAVOUR) install-pkgconfig
+# 	$(INSTALL_PROGRAM) $(BUILT_PROGRAMS) $(DESTDIR)$(bindir)
+# 	if test -n "$(BUILT_PLUGINS)"; then $(INSTALL_PROGRAM) $(BUILT_PLUGINS) $(DESTDIR)$(plugindir); fi
+# 	$(INSTALL_DATA) htslib/*.h $(DESTDIR)$(includedir)/htslib
+# 	$(INSTALL_DATA) libhts.a $(DESTDIR)$(libdir)/libhts.a
+# 	$(INSTALL_DATA) htsfile.1 tabix.1 $(DESTDIR)$(man1dir)
+# 	$(INSTALL_DATA) faidx.5 sam.5 vcf.5 $(DESTDIR)$(man5dir)
+
+installdirs:
+	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(includedir) $(DESTDIR)$(includedir)/htslib $(DESTDIR)$(libdir) $(DESTDIR)$(man1dir) $(DESTDIR)$(man5dir) $(DESTDIR)$(pkgconfigdir)
+	if test -n "$(plugindir)"; then $(INSTALL_DIR) $(DESTDIR)$(plugindir); fi
+
+# After installation, the real file in $(libdir) will be libhts.so.X.Y.Z,
+# with symlinks libhts.so (used via -lhts during linking of client programs)
+# and libhts.so.NN (used by client executables at runtime).
+
+install-so: libhts.so installdirs
+	$(INSTALL_DATA) libhts.so $(DESTDIR)$(libdir)/libhts.so.$(PACKAGE_VERSION)
+	ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so
+	ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so.$(LIBHTS_SOVERSION)
+
+install-dylib: libhts.dylib installdirs
+	$(INSTALL_PROGRAM) libhts.dylib $(DESTDIR)$(libdir)/libhts.$(PACKAGE_VERSION).dylib
+	ln -sf libhts.$(PACKAGE_VERSION).dylib $(DESTDIR)$(libdir)/libhts.dylib
+	ln -sf libhts.$(PACKAGE_VERSION).dylib $(DESTDIR)$(libdir)/libhts.$(LIBHTS_SOVERSION).dylib
+
+# Substitute these pseudo-autoconf variables only at install time
+# so that "make install prefix=/prefix/path" etc continue to work.
+install-pkgconfig: installdirs
+	sed -e 's#@includedir@#$(includedir)#g;s#@libdir@#$(libdir)#g;s#@PACKAGE_VERSION@#$(PACKAGE_VERSION)#g' htslib.pc.in > $(DESTDIR)$(pkgconfigdir)/htslib.pc
+	chmod 644 $(DESTDIR)$(pkgconfigdir)/htslib.pc
+
+# A pkg-config file (suitable for copying to $PKG_CONFIG_PATH) that provides
+# flags for building against the uninstalled library in this build directory.
+htslib-uninstalled.pc: htslib.pc.in
+	sed -e 's#@includedir@#'`pwd`'#g;s#@libdir@#'`pwd`'#g' htslib.pc.in > $@
+
+
+testclean:
+	-rm -f test/*.tmp test/*.tmp.*
+
+mostlyclean: testclean
+	-rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM version.h
+
+clean: mostlyclean clean-$(SHLIB_FLAVOUR)
+	-rm -f libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) $(BUILT_TEST_PROGRAMS)
+
+distclean maintainer-clean: clean
+	-rm -f config.cache config.h config.log config.mk config.status
+	-rm -f TAGS *-uninstalled.pc
+
+clean-so:
+	-rm -f libhts.so libhts.so.*
+
+clean-dylib:
+	-rm -f libhts.dylib libhts.*.dylib
+
+
+tags TAGS:
+	ctags -f TAGS *.[ch] cram/*.[ch] htslib/*.h
+
+# We recommend libhts-using programs be built against a separate htslib
+# installation.  However if you feel that you must bundle htslib source
+# code with your program, this hook enables Automake-style "make dist"
+# for this subdirectory.  If you do bundle an htslib snapshot, please
+# add identifying information to $(PACKAGE_VERSION) as appropriate.
+# (The wildcards attempt to omit non-exported files (.git*, README.md,
+# etc) and other detritus that might be in the top-level directory.)
+distdir:
+	tar -c *.[ch15] [ILMNRcht]*[ELSbcekmnt] | (cd $(distdir) && tar -x)
+	+cd $(distdir) && $(MAKE) distclean
+
+force:
+
+
+.PHONY: all check clean distclean distdir force
+.PHONY: install install-pkgconfig installdirs lib-shared lib-static
+.PHONY: maintainer-clean mostlyclean plugins print-version tags test testclean
+.PHONY: clean-so install-so
+.PHONY: clean-dylib install-dylib
diff --git a/htslib/NEWS b/htslib/NEWS
new file mode 100644
index 0000000..b7bc4d4
--- /dev/null
+++ b/htslib/NEWS
@@ -0,0 +1,109 @@
+Noteworthy changes in release 1.3.1 (22 April 2016)
+
+* Improved error checking and reporting, especially of I/O errors when
+  writing output files (#17, #315, PR #271, PR #317).
+
+* Build fixes for 32-bit systems; be sure to run configure to enable
+  large file support and access to 2GiB+ files.
+
+* Numerous VCF parsing fixes (#321, #322, #323, #324, #325; PR #370).
+  Particular thanks to Kostya Kortchinsky of the Google Security Team
+  for testing and numerous input parsing bug reports.
+
+* HTSlib now prints an informational message when initially creating a
+  CRAM reference cache in the default location under your $HOME directory.
+  (No message is printed if you are using $REF_CACHE to specify a location.)
+
+* Avoided rare race condition when caching downloaded CRAM reference sequence
+  files, by using distinctive names for temporary files (in addition to O_EXCL,
+  which has always been used).  Occasional corruption would previously occur
+  when multiple tools were simultaneously caching the same reference sequences
+  on an NFS filesystem that did not support O_EXCL (PR #320).
+
+* Prevented race condition in file access plugin loading (PR #341).
+
+* Fixed mpileup memory leak, so no more "[bam_plp_destroy] memory leak [...]
+  Continue anyway" warning messages (#299).
+
+* Various minor CRAM fixes.
+
+* Fixed documentation problems #348 and #358.
+
+
+Noteworthy changes in release 1.3  (15 December 2015)
+
+* Files can now be accessed via HTTPS and Amazon S3 in addition to HTTP
+  and FTP, when HTSlib is configured to use libcurl for network file access
+  rather than the included basic knetfile networking.
+
+* HTSlib can be built to use remote access hFILE backends (such as iRODS
+  and libcurl) via a plugin mechanism.  This allows other backends to be
+  easily added and facilitates building tools that use HTSlib, as they
+  don't need to be linked with the backends' various required libraries.
+
+* When writing CRAM output, sam_open() etc now default to writing CRAM v3.0
+  rather than v2.1.
+
+* fai_build() and samtools faidx now accept initial whitespace in ">"
+  headers (e.g., "> chr1 description" is taken to refer to "chr1").
+
+* tabix --only-header works again (was broken in 1.2.x; #249).
+
+* HTSlib's configure script and Makefile now fully support the standard
+  convention of allowing CC/CPPFLAGS/CFLAGS/LDFLAGS/LIBS to be overridden
+  as needed.  Previously the Makefile listened to $(LDLIBS) instead; if you
+  were overriding that, you should now override LIBS rather than LDLIBS.
+
+* Fixed bugs #168, #172, #176, #197, #206, #225, #245, #265, #295, and #296.
+
+
+Noteworthy changes in release 1.2.1  (3 February 2015)
+
+* Reinstated hts_file_type() and FT_* macros, which were available until 1.1
+  but briefly removed in 1.2.  This function is deprecated and will be removed
+  in a future release -- you should use hts_detect_format() etc instead
+
+
+Noteworthy changes in release 1.2  (2 February 2015)
+
+* HTSlib now has a configure script which checks your build environment
+  and allows for selection of optional extras.  See INSTALL for details
+
+* By default, reference sequences are fetched from the EBI CRAM Reference
+  Registry and cached in your $HOME cache directory.  This behaviour can
+  be controlled by setting REF_PATH and REF_CACHE enviroment variables
+  (see the samtools(1) man page for details)
+
+* Numerous CRAM improvements:
+  - Support for CRAM v3.0, an upcoming revision to CRAM supporting
+    better compression and per-container checksums
+  - EOF checking for v2.1 and v3.0 (similar to checking BAM EOF blocks)
+  - Non-standard values for PNEXT and TLEN fields are now preserved
+  - hts_set_fai_filename() now provides a reference file when encoding
+  - Generated read names are now numbered from 1, rather than being
+    labelled 'slice:record-in-slice'
+  - Multi-threading and speed improvements
+
+* New htsfile command for identifying file formats, and corresponding
+  file format detection APIs
+
+* New tabix --regions FILE, --targets FILE options for filtering via BED files
+
+* Optional iRODS file access, disabled by default.  Configure with --with-irods
+  to enable accessing iRODS data objects directly via 'irods:DATAOBJ'
+
+* All occurences of 2^29 in the source have been eliminated, so indexing
+  and querying against reference sequences larger than 512Mbp works (when
+  using CSI indices)
+
+* Support for plain GZIP compression in various places
+
+* VCF header editing speed improvements
+
+* Added seq_nt16_int[] (equivalent to the samtools API's bam_nt16_nt4_table)
+
+* Reinstated faidx_fetch_nseq(), which was accidentally removed from 1.1.
+  Now faidx_fetch_nseq() and faidx_nseq() are equivalent; eventually
+  faidx_fetch_nseq() will be deprecated and removed [#156]
+
+* Fixed bugs #141, #152, #155, #158, #159, and various memory leaks
diff --git a/htslib/README b/htslib/README
new file mode 100644
index 0000000..4225bec
--- /dev/null
+++ b/htslib/README
@@ -0,0 +1,5 @@
+HTSlib is an implementation of a unified C library for accessing common file
+formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing
+data.  It is the core library used by samtools and bcftools.
+
+See INSTALL for building and installation instructions.
diff --git a/htslib/bgzf.c b/htslib/bgzf.c
new file mode 100644
index 0000000..a6c8897
--- /dev/null
+++ b/htslib/bgzf.c
@@ -0,0 +1,1330 @@
+/* The MIT License
+
+   Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology
+                 2011, 2012 Attractive Chaos <attractor at live.co.uk>
+   Copyright (C) 2009, 2013-2016 Genome Research Ltd
+
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+*/
+
+#include <config.h>
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <errno.h>
+#include <unistd.h>
+#include <assert.h>
+#include <pthread.h>
+#include <sys/types.h>
+#include <inttypes.h>
+
+#include "htslib/hts.h"
+#include "htslib/bgzf.h"
+#include "htslib/hfile.h"
+
+#define BGZF_CACHE
+#define BGZF_MT
+
+#define BLOCK_HEADER_LENGTH 18
+#define BLOCK_FOOTER_LENGTH 8
+
+
+/* BGZF/GZIP header (speciallized from RFC 1952; little endian):
+ +---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+
+ | 31|139|  8|  4|              0|  0|255|      6| 66| 67|      2|BLK_LEN|
+ +---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+---+
+  BGZF extension:
+                ^                              ^   ^   ^
+                |                              |   |   |
+               FLG.EXTRA                     XLEN  B   C
+
+  BGZF format is compatible with GZIP. It limits the size of each compressed
+  block to 2^16 bytes and adds and an extra "BC" field in the gzip header which
+  records the size.
+
+*/
+static const uint8_t g_magic[19] = "\037\213\010\4\0\0\0\0\0\377\6\0\102\103\2\0\0\0";
+
+#ifdef BGZF_CACHE
+typedef struct {
+    int size;
+    uint8_t *block;
+    int64_t end_offset;
+} cache_t;
+#include "htslib/khash.h"
+KHASH_MAP_INIT_INT64(cache, cache_t)
+#endif
+
+typedef struct
+{
+    uint64_t uaddr;  // offset w.r.t. uncompressed data
+    uint64_t caddr;  // offset w.r.t. compressed data
+}
+bgzidx1_t;
+
+struct __bgzidx_t
+{
+    int noffs, moffs;       // the size of the index, n:used, m:allocated
+    bgzidx1_t *offs;        // offsets
+    uint64_t ublock_addr;   // offset of the current block (uncompressed data)
+};
+
+void bgzf_index_destroy(BGZF *fp);
+int bgzf_index_add_block(BGZF *fp);
+
+static inline void packInt16(uint8_t *buffer, uint16_t value)
+{
+    buffer[0] = value;
+    buffer[1] = value >> 8;
+}
+
+static inline int unpackInt16(const uint8_t *buffer)
+{
+    return buffer[0] | buffer[1] << 8;
+}
+
+static inline void packInt32(uint8_t *buffer, uint32_t value)
+{
+    buffer[0] = value;
+    buffer[1] = value >> 8;
+    buffer[2] = value >> 16;
+    buffer[3] = value >> 24;
+}
+
+static const char *bgzf_zerr(int errnum, z_stream *zs)
+{
+    static char buffer[32];
+
+    /* Return zs->msg if available.
+       zlib doesn't set this very reliably.  Looking at the source suggests
+       that it may get set to a useful message for deflateInit2, inflateInit2
+       and inflate when it returns Z_DATA_ERROR. For inflate with other
+       return codes, deflate, deflateEnd and inflateEnd it doesn't appear
+       to be useful.  For the likely non-useful cases, the caller should
+       pass NULL into zs. */
+
+    if (zs && zs->msg) return zs->msg;
+
+    // gzerror OF((gzFile file, int *errnum)
+    switch (errnum) {
+    case Z_ERRNO:
+        return strerror(errno);
+    case Z_STREAM_ERROR:
+        return "invalid parameter/compression level, or inconsistent stream state";
+    case Z_DATA_ERROR:
+        return "invalid or incomplete IO";
+    case Z_MEM_ERROR:
+        return "out of memory";
+    case Z_BUF_ERROR:
+        return "progress temporarily not possible, or in() / out() returned an error";
+    case Z_VERSION_ERROR:
+        return "zlib version mismatch";
+    case Z_OK: // 0: maybe gzgets error Z_NULL
+    default:
+        snprintf(buffer, sizeof(buffer), "[%d] unknown", errnum);
+        return buffer;  // FIXME: Not thread-safe.
+    }
+}
+
+static BGZF *bgzf_read_init(hFILE *hfpr)
+{
+    BGZF *fp;
+    uint8_t magic[18];
+    ssize_t n = hpeek(hfpr, magic, 18);
+    if (n < 0) return NULL;
+
+    fp = (BGZF*)calloc(1, sizeof(BGZF));
+    if (fp == NULL) return NULL;
+
+    fp->is_write = 0;
+    fp->is_compressed = (n==2 && magic[0]==0x1f && magic[1]==0x8b);
+    fp->uncompressed_block = malloc(BGZF_MAX_BLOCK_SIZE);
+    fp->compressed_block = malloc(BGZF_MAX_BLOCK_SIZE);
+    fp->is_compressed = (n==18 && magic[0]==0x1f && magic[1]==0x8b) ? 1 : 0;
+    fp->is_gzip = ( !fp->is_compressed || ((magic[3]&4) && memcmp(&magic[12], "BC\2\0",4)==0) ) ? 0 : 1;
+#ifdef BGZF_CACHE
+    fp->cache = kh_init(cache);
+#endif
+    return fp;
+}
+
+// get the compress level from the mode string: compress_level==-1 for the default level, -2 plain uncompressed
+static int mode2level(const char *__restrict mode)
+{
+    int i, compress_level = -1;
+    for (i = 0; mode[i]; ++i)
+        if (mode[i] >= '0' && mode[i] <= '9') break;
+    if (mode[i]) compress_level = (int)mode[i] - '0';
+    if (strchr(mode, 'u')) compress_level = -2;
+    return compress_level;
+}
+static BGZF *bgzf_write_init(const char *mode)
+{
+    BGZF *fp;
+    fp = (BGZF*)calloc(1, sizeof(BGZF));
+    if (fp == NULL) goto mem_fail;
+    fp->is_write = 1;
+    int compress_level = mode2level(mode);
+    if ( compress_level==-2 )
+    {
+        fp->is_compressed = 0;
+        return fp;
+    }
+    fp->is_compressed = 1;
+
+    fp->uncompressed_block = malloc(BGZF_MAX_BLOCK_SIZE);
+    if (fp->uncompressed_block == NULL) goto mem_fail;
+    fp->compressed_block = malloc(BGZF_MAX_BLOCK_SIZE);
+    if (fp->compressed_block == NULL) goto mem_fail;
+
+    fp->compress_level = compress_level < 0? Z_DEFAULT_COMPRESSION : compress_level; // Z_DEFAULT_COMPRESSION==-1
+    if (fp->compress_level > 9) fp->compress_level = Z_DEFAULT_COMPRESSION;
+    if ( strchr(mode,'g') )
+    {
+        // gzip output
+        fp->is_gzip = 1;
+        fp->gz_stream = (z_stream*)calloc(1,sizeof(z_stream));
+        if (fp->gz_stream == NULL) goto mem_fail;
+        fp->gz_stream->zalloc = NULL;
+        fp->gz_stream->zfree  = NULL;
+        fp->gz_stream->msg    = NULL;
+
+        int ret = deflateInit2(fp->gz_stream, fp->compress_level, Z_DEFLATED, 15|16, 8, Z_DEFAULT_STRATEGY);
+        if (ret!=Z_OK) {
+            if (hts_verbose >= 1) {
+                fprintf(stderr, "[E::%s] deflateInit2 failed: %s\n",
+                        __func__, bgzf_zerr(ret, fp->gz_stream));
+            }
+            goto fail;
+        }
+    }
+    return fp;
+
+ mem_fail:
+    if (hts_verbose >= 1) {
+        fprintf(stderr, "[E::%s] %s\n", __func__, strerror(errno));
+    }
+ fail:
+    if (fp != NULL) {
+        free(fp->uncompressed_block);
+        free(fp->compressed_block);
+        free(fp->gz_stream);
+        free(fp);
+    }
+    return NULL;
+}
+
+BGZF *bgzf_open(const char *path, const char *mode)
+{
+    BGZF *fp = 0;
+    assert(compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE);
+    if (strchr(mode, 'r')) {
+        hFILE *fpr;
+        if ((fpr = hopen(path, mode)) == 0) return 0;
+        fp = bgzf_read_init(fpr);
+        if (fp == 0) { hclose_abruptly(fpr); return NULL; }
+        fp->fp = fpr;
+    } else if (strchr(mode, 'w') || strchr(mode, 'a')) {
+        hFILE *fpw;
+        if ((fpw = hopen(path, mode)) == 0) return 0;
+        fp = bgzf_write_init(mode);
+        if (fp == NULL) return NULL;
+        fp->fp = fpw;
+    }
+    else { errno = EINVAL; return 0; }
+
+    fp->is_be = ed_is_big();
+    return fp;
+}
+
+BGZF *bgzf_dopen(int fd, const char *mode)
+{
+    BGZF *fp = 0;
+    assert(compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE);
+    if (strchr(mode, 'r')) {
+        hFILE *fpr;
+        if ((fpr = hdopen(fd, mode)) == 0) return 0;
+        fp = bgzf_read_init(fpr);
+        if (fp == 0) { hclose_abruptly(fpr); return NULL; } // FIXME this closes fd
+        fp->fp = fpr;
+    } else if (strchr(mode, 'w') || strchr(mode, 'a')) {
+        hFILE *fpw;
+        if ((fpw = hdopen(fd, mode)) == 0) return 0;
+        fp = bgzf_write_init(mode);
+        if (fp == NULL) return NULL;
+        fp->fp = fpw;
+    }
+    else { errno = EINVAL; return 0; }
+
+    fp->is_be = ed_is_big();
+    return fp;
+}
+
+BGZF *bgzf_hopen(hFILE *hfp, const char *mode)
+{
+    BGZF *fp = NULL;
+    assert(compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE);
+    if (strchr(mode, 'r')) {
+        fp = bgzf_read_init(hfp);
+        if (fp == NULL) return NULL;
+    } else if (strchr(mode, 'w') || strchr(mode, 'a')) {
+        fp = bgzf_write_init(mode);
+        if (fp == NULL) return NULL;
+    }
+    else { errno = EINVAL; return 0; }
+
+    fp->fp = hfp;
+    fp->is_be = ed_is_big();
+    return fp;
+}
+
+int bgzf_compress(void *_dst, size_t *dlen, const void *src, size_t slen, int level)
+{
+    uint32_t crc;
+    z_stream zs;
+    uint8_t *dst = (uint8_t*)_dst;
+
+    // compress the body
+    zs.zalloc = NULL; zs.zfree = NULL;
+    zs.msg = NULL;
+    zs.next_in  = (Bytef*)src;
+    zs.avail_in = slen;
+    zs.next_out = dst + BLOCK_HEADER_LENGTH;
+    zs.avail_out = *dlen - BLOCK_HEADER_LENGTH - BLOCK_FOOTER_LENGTH;
+    int ret = deflateInit2(&zs, level, Z_DEFLATED, -15, 8, Z_DEFAULT_STRATEGY); // -15 to disable zlib header/footer
+    if (ret!=Z_OK) {
+        if (hts_verbose >= 1) {
+            fprintf(stderr, "[E::%s] deflateInit2 failed: %s\n",
+                    __func__, bgzf_zerr(ret, &zs));
+        }
+        return -1;
+    }
+    if ((ret = deflate(&zs, Z_FINISH)) != Z_STREAM_END) {
+        if (hts_verbose >= 1) {
+            fprintf(stderr, "[E::%s] deflate failed: %s\n",
+                    __func__, bgzf_zerr(ret, ret == Z_DATA_ERROR ? &zs : NULL));
+        }
+        return -1;
+    }
+    if ((ret = deflateEnd(&zs)) != Z_OK) {
+        if (hts_verbose >= 1) {
+            fprintf(stderr, "[E::%s] deflateEnd failed: %s\n",
+                    __func__, bgzf_zerr(ret, NULL));
+        }
+        return -1;
+    }
+    *dlen = zs.total_out + BLOCK_HEADER_LENGTH + BLOCK_FOOTER_LENGTH;
+    // write the header
+    memcpy(dst, g_magic, BLOCK_HEADER_LENGTH); // the last two bytes are a place holder for the length of the block
+    packInt16(&dst[16], *dlen - 1); // write the compressed length; -1 to fit 2 bytes
+    // write the footer
+    crc = crc32(crc32(0L, NULL, 0L), (Bytef*)src, slen);
+    packInt32((uint8_t*)&dst[*dlen - 8], crc);
+    packInt32((uint8_t*)&dst[*dlen - 4], slen);
+    return 0;
+}
+
+static int bgzf_gzip_compress(BGZF *fp, void *_dst, size_t *dlen, const void *src, size_t slen, int level)
+{
+    uint8_t *dst = (uint8_t*)_dst;
+    z_stream *zs = fp->gz_stream;
+    int flush = slen ? Z_NO_FLUSH : Z_FINISH;
+    zs->next_in   = (Bytef*)src;
+    zs->avail_in  = slen;
+    zs->next_out  = dst;
+    zs->avail_out = *dlen;
+    int ret = deflate(zs, flush);
+    if (ret == Z_STREAM_ERROR) {
+        if (hts_verbose >= 1) {
+            fprintf(stderr, "[E::%s] deflate failed: %s\n",
+                    __func__, bgzf_zerr(ret, NULL));
+        }
+        return -1;
+    }
+    *dlen = *dlen - zs->avail_out;
+    return 0;
+}
+
+// Deflate the block in fp->uncompressed_block into fp->compressed_block. Also adds an extra field that stores the compressed block length.
+static int deflate_block(BGZF *fp, int block_length)
+{
+    size_t comp_size = BGZF_MAX_BLOCK_SIZE;
+    int ret;
+    if ( !fp->is_gzip )
+        ret = bgzf_compress(fp->compressed_block, &comp_size, fp->uncompressed_block, block_length, fp->compress_level);
+    else
+        ret = bgzf_gzip_compress(fp, fp->compressed_block, &comp_size, fp->uncompressed_block, block_length, fp->compress_level);
+
+    if ( ret != 0 )
+    {
+        if (hts_verbose >= 3) {
+            fprintf(stderr, "[E::%s] compression error %d\n", __func__, ret);
+        }
+        fp->errcode |= BGZF_ERR_ZLIB;
+        return -1;
+    }
+    fp->block_offset = 0;
+    return comp_size;
+}
+
+// Inflate the block in fp->compressed_block into fp->uncompressed_block
+static int inflate_block(BGZF* fp, int block_length)
+{
+    z_stream zs;
+    zs.zalloc = NULL;
+    zs.zfree = NULL;
+    zs.msg = NULL;
+    zs.next_in = (Bytef*)fp->compressed_block + 18;
+    zs.avail_in = block_length - 16;
+    zs.next_out = (Bytef*)fp->uncompressed_block;
+    zs.avail_out = BGZF_MAX_BLOCK_SIZE;
+
+    int ret = inflateInit2(&zs, -15);
+    if (ret != Z_OK) {
+        if (hts_verbose >= 1) {
+            fprintf(stderr, "[E::%s] inflateInit2 failed: %s\n",
+                    __func__, bgzf_zerr(ret, &zs));
+        }
+        fp->errcode |= BGZF_ERR_ZLIB;
+        return -1;
+    }
+    if ((ret = inflate(&zs, Z_FINISH)) != Z_STREAM_END) {
+        if (hts_verbose >= 1) {
+            fprintf(stderr, "[E::%s] inflate failed: %s\n",
+                    __func__, bgzf_zerr(ret, ret == Z_DATA_ERROR ? &zs : NULL));
+        }
+        if ((ret = inflateEnd(&zs)) != Z_OK) {
+            if (hts_verbose >= 2) {
+                fprintf(stderr, "[E::%s] inflateEnd failed: %s\n",
+                        __func__, bgzf_zerr(ret, NULL));
+            }
+        }
+        fp->errcode |= BGZF_ERR_ZLIB;
+        return -1;
+    }
+    if ((ret = inflateEnd(&zs)) != Z_OK) {
+        if (hts_verbose >= 1) {
+            fprintf(stderr, "[E::%s] inflateEnd failed: %s\n",
+                    __func__, bgzf_zerr(ret, NULL));
+        }
+        fp->errcode |= BGZF_ERR_ZLIB;
+        return -1;
+    }
+    return zs.total_out;
+}
+
+static int inflate_gzip_block(BGZF *fp, int cached)
+{
+    int ret = Z_OK;
+    do
+    {
+        if ( !cached && fp->gz_stream->avail_out!=0 )
+        {
+            fp->gz_stream->avail_in = hread(fp->fp, fp->compressed_block, BGZF_BLOCK_SIZE);
+            if ( fp->gz_stream->avail_in<=0 ) return fp->gz_stream->avail_in;
+            if ( fp->gz_stream->avail_in==0 ) break;
+            fp->gz_stream->next_in = fp->compressed_block;
+        }
+        else cached = 0;
+        do
+        {
+            fp->gz_stream->next_out = (Bytef*)fp->uncompressed_block + fp->block_offset;
+            fp->gz_stream->avail_out = BGZF_MAX_BLOCK_SIZE - fp->block_offset;
+            fp->gz_stream->msg = NULL;
+            ret = inflate(fp->gz_stream, Z_NO_FLUSH);
+            if ( ret==Z_BUF_ERROR ) continue;   // non-critical error
+            if ( ret<0 ) {
+                if (hts_verbose >= 1) {
+                    fprintf(stderr, "[E::%s] inflate failed: %s\n",
+                            __func__,
+                            bgzf_zerr(ret, ret == Z_DATA_ERROR ? fp->gz_stream : NULL));
+                }
+                fp->errcode |= BGZF_ERR_ZLIB;
+                return -1;
+            }
+            unsigned int have = BGZF_MAX_BLOCK_SIZE - fp->gz_stream->avail_out;
+            if ( have ) return have;
+        }
+        while ( fp->gz_stream->avail_out == 0 );
+    }
+    while (ret != Z_STREAM_END);
+    return BGZF_MAX_BLOCK_SIZE - fp->gz_stream->avail_out;
+}
+
+// Returns: 0 on success (BGZF header); -1 on non-BGZF GZIP header; -2 on error
+static int check_header(const uint8_t *header)
+{
+    if ( header[0] != 31 || header[1] != 139 || header[2] != 8 ) return -2;
+    return ((header[3] & 4) != 0
+            && unpackInt16((uint8_t*)&header[10]) == 6
+            && header[12] == 'B' && header[13] == 'C'
+            && unpackInt16((uint8_t*)&header[14]) == 2) ? 0 : -1;
+}
+
+#ifdef BGZF_CACHE
+static void free_cache(BGZF *fp)
+{
+    khint_t k;
+    khash_t(cache) *h = (khash_t(cache)*)fp->cache;
+    if (fp->is_write) return;
+    for (k = kh_begin(h); k < kh_end(h); ++k)
+        if (kh_exist(h, k)) free(kh_val(h, k).block);
+    kh_destroy(cache, h);
+}
+
+static int load_block_from_cache(BGZF *fp, int64_t block_address)
+{
+    khint_t k;
+    cache_t *p;
+    khash_t(cache) *h = (khash_t(cache)*)fp->cache;
+    k = kh_get(cache, h, block_address);
+    if (k == kh_end(h)) return 0;
+    p = &kh_val(h, k);
+    if (fp->block_length != 0) fp->block_offset = 0;
+    fp->block_address = block_address;
+    fp->block_length = p->size;
+    memcpy(fp->uncompressed_block, p->block, BGZF_MAX_BLOCK_SIZE);
+    if ( hseek(fp->fp, p->end_offset, SEEK_SET) < 0 )
+    {
+        // todo: move the error up
+        fprintf(stderr,"Could not hseek to %"PRId64"\n", p->end_offset);
+        exit(1);
+    }
+    return p->size;
+}
+
+static void cache_block(BGZF *fp, int size)
+{
+    int ret;
+    khint_t k;
+    cache_t *p;
+    khash_t(cache) *h = (khash_t(cache)*)fp->cache;
+    if (BGZF_MAX_BLOCK_SIZE >= fp->cache_size) return;
+    if ((kh_size(h) + 1) * BGZF_MAX_BLOCK_SIZE > (uint32_t)fp->cache_size) {
+        /* A better way would be to remove the oldest block in the
+         * cache, but here we remove a random one for simplicity. This
+         * should not have a big impact on performance. */
+        for (k = kh_begin(h); k < kh_end(h); ++k)
+            if (kh_exist(h, k)) break;
+        if (k < kh_end(h)) {
+            free(kh_val(h, k).block);
+            kh_del(cache, h, k);
+        }
+    }
+    k = kh_put(cache, h, fp->block_address, &ret);
+    if (ret == 0) return; // if this happens, a bug!
+    p = &kh_val(h, k);
+    p->size = fp->block_length;
+    p->end_offset = fp->block_address + size;
+    p->block = (uint8_t*)malloc(BGZF_MAX_BLOCK_SIZE);
+    memcpy(kh_val(h, k).block, fp->uncompressed_block, BGZF_MAX_BLOCK_SIZE);
+}
+#else
+static void free_cache(BGZF *fp) {}
+static int load_block_from_cache(BGZF *fp, int64_t block_address) {return 0;}
+static void cache_block(BGZF *fp, int size) {}
+#endif
+
+int bgzf_read_block(BGZF *fp)
+{
+    uint8_t header[BLOCK_HEADER_LENGTH], *compressed_block;
+    int count, size = 0, block_length, remaining;
+
+    // Reading an uncompressed file
+    if ( !fp->is_compressed )
+    {
+        count = hread(fp->fp, fp->uncompressed_block, BGZF_MAX_BLOCK_SIZE);
+        if (count < 0)  // Error
+        {
+            fp->errcode |= BGZF_ERR_IO;
+            return -1;
+        }
+        else if (count == 0)  // EOF
+        {
+            fp->block_length = 0;
+            return 0;
+        }
+        if (fp->block_length != 0) fp->block_offset = 0;
+        fp->block_address += count;
+        fp->block_length = count;
+        return 0;
+    }
+
+    // Reading compressed file
+    int64_t block_address;
+    block_address = htell(fp->fp);
+    if ( fp->is_gzip && fp->gz_stream ) // is this is a initialized gzip stream?
+    {
+        count = inflate_gzip_block(fp, 0);
+        if ( count<0 )
+        {
+            fp->errcode |= BGZF_ERR_ZLIB;
+            return -1;
+        }
+        fp->block_length = count;
+        fp->block_address = block_address;
+        return 0;
+    }
+    if (fp->cache_size && load_block_from_cache(fp, block_address)) return 0;
+    count = hread(fp->fp, header, sizeof(header));
+    if (count == 0) { // no data read
+        fp->block_length = 0;
+        return 0;
+    }
+    int ret;
+    if ( count != sizeof(header) || (ret=check_header(header))==-2 )
+    {
+        fp->errcode |= BGZF_ERR_HEADER;
+        return -1;
+    }
+    if ( ret==-1 )
+    {
+        // GZIP, not BGZF
+        uint8_t *cblock = (uint8_t*)fp->compressed_block;
+        memcpy(cblock, header, sizeof(header));
+        count = hread(fp->fp, cblock+sizeof(header), BGZF_BLOCK_SIZE - sizeof(header)) + sizeof(header);
+        int nskip = 10;
+
+        // Check optional fields to skip: FLG.FNAME,FLG.FCOMMENT,FLG.FHCRC,FLG.FEXTRA
+        // Note: Some of these fields are untested, I did not have appropriate data available
+        if ( header[3] & 0x4 ) // FLG.FEXTRA
+        {
+            nskip += unpackInt16(&cblock[nskip]) + 2;
+        }
+        if ( header[3] & 0x8 ) // FLG.FNAME
+        {
+            while ( nskip<count && cblock[nskip] ) nskip++;
+            nskip++;
+        }
+        if ( header[3] & 0x10 ) // FLG.FCOMMENT
+        {
+            while ( nskip<count && cblock[nskip] ) nskip++;
+            nskip++;
+        }
+        if ( header[3] & 0x2 ) nskip += 2;  //  FLG.FHCRC
+
+        /* FIXME: Should handle this better.  There's no reason why
+           someone shouldn't include a massively long comment in their
+           gzip stream. */
+        if ( nskip >= count )
+        {
+            fp->errcode |= BGZF_ERR_HEADER;
+            return -1;
+        }
+
+        fp->is_gzip = 1;
+        fp->gz_stream = (z_stream*) calloc(1,sizeof(z_stream));
+        int ret = inflateInit2(fp->gz_stream, -15);
+        if (ret != Z_OK)
+        {
+            if (hts_verbose >= 1) {
+                fprintf(stderr, "[E::%s] inflateInit2 failed: %s",
+                        __func__, bgzf_zerr(ret, fp->gz_stream));
+            }
+            fp->errcode |= BGZF_ERR_ZLIB;
+            return -1;
+        }
+        fp->gz_stream->avail_in = count - nskip;
+        fp->gz_stream->next_in  = cblock + nskip;
+        count = inflate_gzip_block(fp, 1);
+        if ( count<0 )
+        {
+            fp->errcode |= BGZF_ERR_ZLIB;
+            return -1;
+        }
+        fp->block_length = count;
+        fp->block_address = block_address;
+        if ( fp->idx_build_otf ) return -1; // cannot build index for gzip
+        return 0;
+    }
+    size = count;
+    block_length = unpackInt16((uint8_t*)&header[16]) + 1; // +1 because when writing this number, we used "-1"
+    compressed_block = (uint8_t*)fp->compressed_block;
+    memcpy(compressed_block, header, BLOCK_HEADER_LENGTH);
+    remaining = block_length - BLOCK_HEADER_LENGTH;
+    count = hread(fp->fp, &compressed_block[BLOCK_HEADER_LENGTH], remaining);
+    if (count != remaining) {
+        fp->errcode |= BGZF_ERR_IO;
+        return -1;
+    }
+    size += count;
+    if ((count = inflate_block(fp, block_length)) < 0) {
+        if (hts_verbose >= 2) fprintf(stderr, "[E::%s] inflate_block error %d\n", __func__, count);
+        fp->errcode |= BGZF_ERR_ZLIB;
+        return -1;
+    }
+    if (fp->block_length != 0) fp->block_offset = 0; // Do not reset offset if this read follows a seek.
+    fp->block_address = block_address;
+    fp->block_length = count;
+    if ( fp->idx_build_otf )
+    {
+        bgzf_index_add_block(fp);
+        fp->idx->ublock_addr += count;
+    }
+    cache_block(fp, size);
+    return 0;
+}
+
+ssize_t bgzf_read(BGZF *fp, void *data, size_t length)
+{
+    ssize_t bytes_read = 0;
+    uint8_t *output = (uint8_t*)data;
+    if (length <= 0) return 0;
+    assert(fp->is_write == 0);
+    while (bytes_read < length) {
+        int copy_length, available = fp->block_length - fp->block_offset;
+        uint8_t *buffer;
+        if (available <= 0) {
+            int ret = bgzf_read_block(fp);
+            if (ret != 0) {
+                if (hts_verbose >= 2) {
+                    fprintf(stderr, "[E::%s] bgzf_read_block error %d after %zd of %zu bytes\n", __func__, ret, bytes_read, length);
+                }
+                fp->errcode |= BGZF_ERR_ZLIB;
+                return -1;
+            }
+            available = fp->block_length - fp->block_offset;
+            if (available <= 0) break;
+        }
+        copy_length = length - bytes_read < available? length - bytes_read : available;
+        buffer = (uint8_t*)fp->uncompressed_block;
+        memcpy(output, buffer + fp->block_offset, copy_length);
+        fp->block_offset += copy_length;
+        output += copy_length;
+        bytes_read += copy_length;
+    }
+    if (fp->block_offset == fp->block_length) {
+        fp->block_address = htell(fp->fp);
+        fp->block_offset = fp->block_length = 0;
+    }
+    fp->uncompressed_address += bytes_read;
+    return bytes_read;
+}
+
+ssize_t bgzf_raw_read(BGZF *fp, void *data, size_t length)
+{
+    return hread(fp->fp, data, length);
+}
+
+#ifdef BGZF_MT
+
+typedef struct {
+    struct bgzf_mtaux_t *mt;
+    void *buf;
+    int i, errcode, toproc, compress_level;
+} worker_t;
+
+typedef struct bgzf_mtaux_t {
+    int n_threads, n_blks, curr, done;
+    volatile int proc_cnt;
+    void **blk;
+    int *len;
+    worker_t *w;
+    pthread_t *tid;
+    pthread_mutex_t lock;
+    pthread_cond_t cv;
+} mtaux_t;
+
+static int worker_aux(worker_t *w)
+{
+    int i, stop = 0;
+    // wait for condition: to process or all done
+    pthread_mutex_lock(&w->mt->lock);
+    while (!w->toproc && !w->mt->done)
+        pthread_cond_wait(&w->mt->cv, &w->mt->lock);
+    if (w->mt->done) stop = 1;
+    w->toproc = 0;
+    pthread_mutex_unlock(&w->mt->lock);
+    if (stop) return 1; // to quit the thread
+    w->errcode = 0;
+    for (i = w->i; i < w->mt->curr; i += w->mt->n_threads) {
+        size_t clen = BGZF_MAX_BLOCK_SIZE;
+        int ret = bgzf_compress(w->buf, &clen, w->mt->blk[i], w->mt->len[i], w->compress_level);
+        if (ret != 0) {
+            if (hts_verbose >= 2) fprintf(stderr, "[E::%s] bgzf_compress error %d\n", __func__, ret);
+            w->errcode |= BGZF_ERR_ZLIB; // Report error
+            // We're not going to do any more, so set remaining lengths to 0
+            for (; i < w->mt->curr; i += w->mt->n_threads) w->mt->len[i] = 0;
+            break; // Give up
+        } else {
+            memcpy(w->mt->blk[i], w->buf, clen);
+            w->mt->len[i] = clen;
+        }
+    }
+    __sync_fetch_and_add(&w->mt->proc_cnt, 1);
+    return 0;
+}
+
+static void *mt_worker(void *data)
+{
+    while (worker_aux((worker_t*)data) == 0);
+    return 0;
+}
+
+int bgzf_mt(BGZF *fp, int n_threads, int n_sub_blks)
+{
+    int i;
+    mtaux_t *mt;
+    pthread_attr_t attr;
+    if (!fp->is_write || fp->mt || n_threads <= 1) return -1;
+    mt = (mtaux_t*)calloc(1, sizeof(mtaux_t));
+    mt->n_threads = n_threads;
+    mt->n_blks = n_threads * n_sub_blks;
+    mt->len = (int*)calloc(mt->n_blks, sizeof(int));
+    mt->blk = (void**)calloc(mt->n_blks, sizeof(void*));
+    for (i = 0; i < mt->n_blks; ++i)
+        mt->blk[i] = malloc(BGZF_MAX_BLOCK_SIZE);
+    mt->tid = (pthread_t*)calloc(mt->n_threads, sizeof(pthread_t)); // tid[0] is not used, as the worker 0 is launched by the master
+    mt->w = (worker_t*)calloc(mt->n_threads, sizeof(worker_t));
+    for (i = 0; i < mt->n_threads; ++i) {
+        mt->w[i].i = i;
+        mt->w[i].mt = mt;
+        mt->w[i].compress_level = fp->compress_level;
+        mt->w[i].buf = malloc(BGZF_MAX_BLOCK_SIZE);
+    }
+    pthread_attr_init(&attr);
+    pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
+    pthread_mutex_init(&mt->lock, 0);
+    pthread_cond_init(&mt->cv, 0);
+    for (i = 1; i < mt->n_threads; ++i) // worker 0 is effectively launched by the master thread
+        pthread_create(&mt->tid[i], &attr, mt_worker, &mt->w[i]);
+    fp->mt = mt;
+    return 0;
+}
+
+static void mt_destroy(mtaux_t *mt)
+{
+    int i;
+    // signal all workers to quit
+    pthread_mutex_lock(&mt->lock);
+    mt->done = 1; mt->proc_cnt = 0;
+    pthread_cond_broadcast(&mt->cv);
+    pthread_mutex_unlock(&mt->lock);
+    for (i = 1; i < mt->n_threads; ++i) pthread_join(mt->tid[i], 0); // worker 0 is effectively launched by the master thread
+    // free other data allocated on heap
+    for (i = 0; i < mt->n_blks; ++i) free(mt->blk[i]);
+    for (i = 0; i < mt->n_threads; ++i) free(mt->w[i].buf);
+    free(mt->blk); free(mt->len); free(mt->w); free(mt->tid);
+    pthread_cond_destroy(&mt->cv);
+    pthread_mutex_destroy(&mt->lock);
+    free(mt);
+}
+
+static void mt_queue(BGZF *fp)
+{
+    mtaux_t *mt = fp->mt;
+    assert(mt->curr < mt->n_blks); // guaranteed by the caller
+    memcpy(mt->blk[mt->curr], fp->uncompressed_block, fp->block_offset);
+    mt->len[mt->curr] = fp->block_offset;
+    fp->block_offset = 0;
+    ++mt->curr;
+}
+
+static int mt_flush_queue(BGZF *fp)
+{
+    int i;
+    mtaux_t *mt = fp->mt;
+    // signal all the workers to compress
+    pthread_mutex_lock(&mt->lock);
+    for (i = 0; i < mt->n_threads; ++i) mt->w[i].toproc = 1;
+    mt->proc_cnt = 0;
+    pthread_cond_broadcast(&mt->cv);
+    pthread_mutex_unlock(&mt->lock);
+    // worker 0 is doing things here
+    worker_aux(&mt->w[0]);
+    // wait for all the threads to complete
+    while (mt->proc_cnt < mt->n_threads);
+    // dump data to disk
+    for (i = 0; i < mt->n_threads; ++i) fp->errcode |= mt->w[i].errcode;
+    if (fp->errcode == 0) {
+        /* Only try to write if all the threads worked, as otherwise we
+           could get a file with holes in it */
+        for (i = 0; i < mt->curr; ++i) {
+            if (hwrite(fp->fp, mt->blk[i], mt->len[i]) != mt->len[i]) {
+                fp->errcode |= BGZF_ERR_IO;
+                break;
+            }
+        }
+    }
+    mt->curr = 0;
+    return (fp->errcode == 0)? 0 : -1;
+}
+
+static int lazy_flush(BGZF *fp)
+{
+    if (fp->mt) {
+        if (fp->block_offset) mt_queue(fp);
+        return (fp->mt->curr < fp->mt->n_blks)? 0 : mt_flush_queue(fp);
+    }
+    else return bgzf_flush(fp);
+}
+
+#else  // ~ #ifdef BGZF_MT
+
+int bgzf_mt(BGZF *fp, int n_threads, int n_sub_blks)
+{
+    return 0;
+}
+
+static inline int lazy_flush(BGZF *fp)
+{
+    return bgzf_flush(fp);
+}
+
+#endif // ~ #ifdef BGZF_MT
+
+int bgzf_flush(BGZF *fp)
+{
+    if (!fp->is_write) return 0;
+#ifdef BGZF_MT
+    if (fp->mt) {
+        if (fp->block_offset) mt_queue(fp); // guaranteed that assertion does not fail
+        return mt_flush_queue(fp);
+    }
+#endif
+    while (fp->block_offset > 0) {
+        int block_length;
+        if ( fp->idx_build_otf )
+        {
+            bgzf_index_add_block(fp);
+            fp->idx->ublock_addr += fp->block_offset;
+        }
+        block_length = deflate_block(fp, fp->block_offset);
+        if (block_length < 0) {
+            if (hts_verbose >= 3) fprintf(stderr, "[E::%s] deflate_block error %d\n", __func__, block_length);
+            return -1;
+        }
+        if (hwrite(fp->fp, fp->compressed_block, block_length) != block_length) {
+            if (hts_verbose >= 1) fprintf(stderr, "[E::%s] hwrite error (wrong size)\n", __func__);
+            fp->errcode |= BGZF_ERR_IO; // possibly truncated file
+            return -1;
+        }
+        fp->block_address += block_length;
+    }
+    return 0;
+}
+
+int bgzf_flush_try(BGZF *fp, ssize_t size)
+{
+    if (fp->block_offset + size > BGZF_BLOCK_SIZE) return lazy_flush(fp);
+    return 0;
+}
+
+ssize_t bgzf_write(BGZF *fp, const void *data, size_t length)
+{
+    if ( !fp->is_compressed )
+        return hwrite(fp->fp, data, length);
+
+    const uint8_t *input = (const uint8_t*)data;
+    ssize_t remaining = length;
+    assert(fp->is_write);
+    while (remaining > 0) {
+        uint8_t* buffer = (uint8_t*)fp->uncompressed_block;
+        int copy_length = BGZF_BLOCK_SIZE - fp->block_offset;
+        if (copy_length > remaining) copy_length = remaining;
+        memcpy(buffer + fp->block_offset, input, copy_length);
+        fp->block_offset += copy_length;
+        input += copy_length;
+        remaining -= copy_length;
+        if (fp->block_offset == BGZF_BLOCK_SIZE) {
+            if (lazy_flush(fp) != 0) return -1;
+        }
+    }
+    return length - remaining;
+}
+
+ssize_t bgzf_raw_write(BGZF *fp, const void *data, size_t length)
+{
+    return hwrite(fp->fp, data, length);
+}
+
+int bgzf_close(BGZF* fp)
+{
+    int ret, block_length;
+    if (fp == 0) return -1;
+    if (fp->is_write && fp->is_compressed) {
+        if (bgzf_flush(fp) != 0) return -1;
+        fp->compress_level = -1;
+        block_length = deflate_block(fp, 0); // write an empty block
+        if (block_length < 0) {
+            if (hts_verbose >= 3) fprintf(stderr, "[E::%s] deflate_block error %d\n", __func__, block_length);
+            return -1;
+        }
+        if (hwrite(fp->fp, fp->compressed_block, block_length) < 0
+            || hflush(fp->fp) != 0) {
+            if (hts_verbose >= 1) fprintf(stderr, "[E::%s] file write error\n", __func__);
+            fp->errcode |= BGZF_ERR_IO;
+            return -1;
+        }
+#ifdef BGZF_MT
+        if (fp->mt) mt_destroy(fp->mt);
+#endif
+    }
+    if ( fp->is_gzip )
+    {
+        if (!fp->is_write) ret = inflateEnd(fp->gz_stream);
+        else ret = deflateEnd(fp->gz_stream);
+        if (ret != Z_OK && hts_verbose >= 1)
+            fprintf(stderr, "[E::%s] inflateEnd/deflateEnd failed: %s\n",
+                    __func__, bgzf_zerr(ret, NULL));
+        free(fp->gz_stream);
+    }
+    ret = hclose(fp->fp);
+    if (ret != 0) return -1;
+    bgzf_index_destroy(fp);
+    free(fp->uncompressed_block);
+    free(fp->compressed_block);
+    free_cache(fp);
+    free(fp);
+    return 0;
+}
+
+void bgzf_set_cache_size(BGZF *fp, int cache_size)
+{
+    if (fp) fp->cache_size = cache_size;
+}
+
+int bgzf_check_EOF(BGZF *fp)
+{
+    uint8_t buf[28];
+    off_t offset = htell(fp->fp);
+    if (hseek(fp->fp, -28, SEEK_END) < 0) {
+        if (errno == ESPIPE) { hclearerr(fp->fp); return 2; }
+        else return -1;
+    }
+    if ( hread(fp->fp, buf, 28) != 28 ) return -1;
+    if ( hseek(fp->fp, offset, SEEK_SET) < 0 ) return -1;
+    return (memcmp("\037\213\010\4\0\0\0\0\0\377\6\0\102\103\2\0\033\0\3\0\0\0\0\0\0\0\0\0", buf, 28) == 0)? 1 : 0;
+}
+
+int64_t bgzf_seek(BGZF* fp, int64_t pos, int where)
+{
+    int block_offset;
+    int64_t block_address;
+
+    if (fp->is_write || where != SEEK_SET) {
+        fp->errcode |= BGZF_ERR_MISUSE;
+        return -1;
+    }
+    block_offset = pos & 0xFFFF;
+    block_address = pos >> 16;
+    if (hseek(fp->fp, block_address, SEEK_SET) < 0) {
+        fp->errcode |= BGZF_ERR_IO;
+        return -1;
+    }
+    fp->block_length = 0;  // indicates current block has not been loaded
+    fp->block_address = block_address;
+    fp->block_offset = block_offset;
+    return 0;
+}
+
+int bgzf_is_bgzf(const char *fn)
+{
+    uint8_t buf[16];
+    int n;
+    hFILE *fp;
+    if ((fp = hopen(fn, "r")) == 0) return 0;
+    n = hread(fp, buf, 16);
+    if ( hclose(fp) < 0 ) return -1;
+    if (n != 16) return 0;
+    return memcmp(g_magic, buf, 16) == 0? 1 : 0;
+}
+
+int bgzf_getc(BGZF *fp)
+{
+    int c;
+    if (fp->block_offset >= fp->block_length) {
+        if (bgzf_read_block(fp) != 0) return -2; /* error */
+        if (fp->block_length == 0) return -1; /* end-of-file */
+    }
+    c = ((unsigned char*)fp->uncompressed_block)[fp->block_offset++];
+    if (fp->block_offset == fp->block_length) {
+        fp->block_address = htell(fp->fp);
+        fp->block_offset = 0;
+        fp->block_length = 0;
+    }
+    fp->uncompressed_address++;
+    return c;
+}
+
+#ifndef kroundup32
+#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
+#endif
+
+int bgzf_getline(BGZF *fp, int delim, kstring_t *str)
+{
+    int l, state = 0;
+    unsigned char *buf = (unsigned char*)fp->uncompressed_block;
+    str->l = 0;
+    do {
+        if (fp->block_offset >= fp->block_length) {
+            if (bgzf_read_block(fp) != 0) { state = -2; break; }
+            if (fp->block_length == 0) { state = -1; break; }
+        }
+        for (l = fp->block_offset; l < fp->block_length && buf[l] != delim; ++l);
+        if (l < fp->block_length) state = 1;
+        l -= fp->block_offset;
+        if (str->l + l + 1 >= str->m) {
+            str->m = str->l + l + 2;
+            kroundup32(str->m);
+            str->s = (char*)realloc(str->s, str->m);
+        }
+        memcpy(str->s + str->l, buf + fp->block_offset, l);
+        str->l += l;
+        fp->block_offset += l + 1;
+        if (fp->block_offset >= fp->block_length) {
+            fp->block_address = htell(fp->fp);
+            fp->block_offset = 0;
+            fp->block_length = 0;
+        }
+    } while (state == 0);
+    if (str->l == 0 && state < 0) return state;
+    fp->uncompressed_address += str->l;
+    if ( delim=='\n' && str->l>0 && str->s[str->l-1]=='\r' ) str->l--;
+    str->s[str->l] = 0;
+    return str->l;
+}
+
+void bgzf_index_destroy(BGZF *fp)
+{
+    if ( !fp->idx ) return;
+    free(fp->idx->offs);
+    free(fp->idx);
+    fp->idx = NULL;
+    fp->idx_build_otf = 0;
+}
+
+int bgzf_index_build_init(BGZF *fp)
+{
+    bgzf_index_destroy(fp);
+    fp->idx = (bgzidx_t*) calloc(1,sizeof(bgzidx_t));
+    if ( !fp->idx ) return -1;
+    fp->idx_build_otf = 1;  // build index on the fly
+    return 0;
+}
+
+int bgzf_index_add_block(BGZF *fp)
+{
+    fp->idx->noffs++;
+    if ( fp->idx->noffs > fp->idx->moffs )
+    {
+        fp->idx->moffs = fp->idx->noffs;
+        kroundup32(fp->idx->moffs);
+        fp->idx->offs = (bgzidx1_t*) realloc(fp->idx->offs, fp->idx->moffs*sizeof(bgzidx1_t));
+        if ( !fp->idx->offs ) return -1;
+    }
+    fp->idx->offs[ fp->idx->noffs-1 ].uaddr = fp->idx->ublock_addr;
+    fp->idx->offs[ fp->idx->noffs-1 ].caddr = fp->block_address;
+    return 0;
+}
+
+static inline int fwrite_uint64(uint64_t x, FILE *f)
+{
+    if (ed_is_big()) x = ed_swap_8(x);
+    if (fwrite(&x, sizeof x, 1, f) != 1) return -1;
+    return 0;
+}
+
+int bgzf_index_dump(BGZF *fp, const char *bname, const char *suffix)
+{
+    if (bgzf_flush(fp) != 0) return -1;
+
+    assert(fp->idx);
+    char *tmp = NULL;
+    if ( suffix )
+    {
+        int blen = strlen(bname);
+        int slen = strlen(suffix);
+        tmp = (char*) malloc(blen + slen + 1);
+        if ( !tmp ) return -1;
+        memcpy(tmp,bname,blen);
+        memcpy(tmp+blen,suffix,slen+1);
+    }
+
+    FILE *idx = fopen(tmp?tmp:bname,"wb");
+    if ( tmp ) free(tmp);
+    if ( !idx ) {
+        if (hts_verbose > 1)
+        {
+            fprintf(stderr, "[E::%s] Error opening %s%s : %s\n",
+                    __func__, bname, suffix ? suffix : "", strerror(errno));
+        }
+        return -1;
+    }
+
+    // Note that the index contains one extra record when indexing files opened
+    // for reading. The terminating record is not present when opened for writing.
+    // This is not a bug.
+
+    int i;
+    if (fwrite_uint64(fp->idx->noffs - 1, idx) < 0) goto fail;
+    for (i=1; i<fp->idx->noffs; i++)
+    {
+        if (fwrite_uint64(fp->idx->offs[i].caddr, idx) < 0) goto fail;
+        if (fwrite_uint64(fp->idx->offs[i].uaddr, idx) < 0) goto fail;
+    }
+
+    if (fclose(idx) < 0)
+    {
+        if (hts_verbose > 1)
+        {
+            fprintf(stderr, "[E::%s] Error on closing %s%s : %s\n",
+                    __func__, bname, suffix ? suffix : "", strerror(errno));
+        }
+        return -1;
+    }
+    return 0;
+
+ fail:
+    if (hts_verbose > 1)
+    {
+        fprintf(stderr, "[E::%s] Error writing to %s%s : %s\n",
+                __func__, bname, suffix ? suffix : "", strerror(errno));
+    }
+    fclose(idx);
+    return -1;
+}
+
+static inline int fread_uint64(uint64_t *xptr, FILE *f)
+{
+    if (fread(xptr, sizeof *xptr, 1, f) != 1) return -1;
+    if (ed_is_big()) ed_swap_8p(xptr);
+    return 0;
+}
+
+int bgzf_index_load(BGZF *fp, const char *bname, const char *suffix)
+{
+    char *tmp = NULL;
+    if ( suffix )
+    {
+        int blen = strlen(bname);
+        int slen = strlen(suffix);
+        tmp = (char*) malloc(blen + slen + 1);
+        if ( !tmp ) return -1;
+        memcpy(tmp,bname,blen);
+        memcpy(tmp+blen,suffix,slen+1);
+    }
+
+    FILE *idx = fopen(tmp?tmp:bname,"rb");
+    if ( tmp ) free(tmp);
+    if ( !idx ) {
+        if (hts_verbose > 1) {
+            fprintf(stderr, "[E::%s] Error opening %s%s : %s\n",
+                    __func__, bname, suffix ? suffix : "", strerror(errno));
+        }
+        return -1;
+    }
+
+    fp->idx = (bgzidx_t*) calloc(1,sizeof(bgzidx_t));
+    if (fp->idx == NULL) goto fail;
+    uint64_t x;
+    if (fread_uint64(&x, idx) < 0) goto fail;
+
+    fp->idx->noffs = fp->idx->moffs = x + 1;
+    fp->idx->offs  = (bgzidx1_t*) malloc(fp->idx->moffs*sizeof(bgzidx1_t));
+    if (fp->idx->offs == NULL) goto fail;
+    fp->idx->offs[0].caddr = fp->idx->offs[0].uaddr = 0;
+
+    int i;
+    for (i=1; i<fp->idx->noffs; i++)
+    {
+        if (fread_uint64(&fp->idx->offs[i].caddr, idx) < 0) goto fail;
+        if (fread_uint64(&fp->idx->offs[i].uaddr, idx) < 0) goto fail;
+    }
+
+    if (fclose(idx) != 0) goto fail;
+    return 0;
+
+ fail:
+    if (hts_verbose > 1)
+    {
+        fprintf(stderr, "[E::%s] Error reading %s%s : %s\n",
+                __func__, bname, suffix ? suffix : "", strerror(errno));
+    }
+    fclose(idx);
+    if (fp->idx) {
+        free(fp->idx->offs);
+        free(fp->idx);
+        fp->idx = NULL;
+    }
+    return -1;
+}
+
+int bgzf_useek(BGZF *fp, long uoffset, int where)
+{
+    if ( !fp->is_compressed )
+    {
+        if (hseek(fp->fp, uoffset, SEEK_SET) < 0)
+        {
+            fp->errcode |= BGZF_ERR_IO;
+            return -1;
+        }
+        fp->block_length = 0;  // indicates current block has not been loaded
+        fp->block_address = uoffset;
+        fp->block_offset = 0;
+        if (bgzf_read_block(fp) < 0) {
+            fp->errcode |= BGZF_ERR_IO;
+            return -1;
+        }
+        fp->uncompressed_address = uoffset;
+        return 0;
+    }
+
+    if ( !fp->idx )
+    {
+        fp->errcode |= BGZF_ERR_IO;
+        return -1;
+    }
+
+    // binary search
+    int ilo = 0, ihi = fp->idx->noffs - 1;
+    while ( ilo<=ihi )
+    {
+        int i = (ilo+ihi)*0.5;
+        if ( uoffset < fp->idx->offs[i].uaddr ) ihi = i - 1;
+        else if ( uoffset >= fp->idx->offs[i].uaddr ) ilo = i + 1;
+        else break;
+    }
+    int i = ilo-1;
+    if (hseek(fp->fp, fp->idx->offs[i].caddr, SEEK_SET) < 0)
+    {
+        fp->errcode |= BGZF_ERR_IO;
+        return -1;
+    }
+    fp->block_length = 0;  // indicates current block has not been loaded
+    fp->block_address = fp->idx->offs[i].caddr;
+    fp->block_offset = 0;
+    if ( bgzf_read_block(fp) < 0 ) {
+        fp->errcode |= BGZF_ERR_IO;
+        return -1;
+    }
+    if ( uoffset - fp->idx->offs[i].uaddr > 0 )
+    {
+        fp->block_offset = uoffset - fp->idx->offs[i].uaddr;
+        assert( fp->block_offset <= fp->block_length );     // todo: skipped, unindexed, blocks
+    }
+    fp->uncompressed_address = uoffset;
+    return 0;
+}
+
+long bgzf_utell(BGZF *fp)
+{
+    return fp->uncompressed_address;    // currently maintained only when reading
+}
diff --git a/htslib/bgzip.c b/htslib/bgzip.c
new file mode 100644
index 0000000..fa005b9
--- /dev/null
+++ b/htslib/bgzip.c
@@ -0,0 +1,311 @@
+/* bgzip.c -- Block compression/decompression utility.
+
+   Copyright (C) 2008, 2009 Broad Institute / Massachusetts Institute of Technology
+   Copyright (C) 2010, 2013-2016 Genome Research Ltd.
+
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+
+   The above copyright notices and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+*/
+
+#include <config.h>
+
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+#include <fcntl.h>
+#include <unistd.h>
+#include <errno.h>
+#include <stdarg.h>
+#include <getopt.h>
+#include <sys/stat.h>
+#include "htslib/bgzf.h"
+#include "htslib/hts.h"
+
+static const int WINDOW_SIZE = 64 * 1024;
+
+static void error(const char *format, ...)
+{
+    va_list ap;
+    va_start(ap, format);
+    vfprintf(stderr, format, ap);
+    va_end(ap);
+    exit(EXIT_FAILURE);
+}
+
+static int confirm_overwrite(const char *fn)
+{
+    int save_errno = errno;
+    int ret = 0;
+
+    if (isatty(STDIN_FILENO)) {
+        char c;
+        fprintf(stderr, "[bgzip] %s already exists; do you wish to overwrite (y or n)? ", fn);
+        if (scanf("%c", &c) == 1 && (c == 'Y' || c == 'y')) ret = 1;
+    }
+
+    errno = save_errno;
+    return ret;
+}
+
+static int bgzip_main_usage(void)
+{
+    fprintf(stderr, "\n");
+    fprintf(stderr, "Version: %s\n", hts_version());
+    fprintf(stderr, "Usage:   bgzip [OPTIONS] [FILE] ...\n");
+    fprintf(stderr, "Options:\n");
+    fprintf(stderr, "   -b, --offset INT        decompress at virtual file pointer (0-based uncompressed offset)\n");
+    fprintf(stderr, "   -c, --stdout            write on standard output, keep original files unchanged\n");
+    fprintf(stderr, "   -d, --decompress        decompress\n");
+    fprintf(stderr, "   -f, --force             overwrite files without asking\n");
+    fprintf(stderr, "   -h, --help              give this help\n");
+    fprintf(stderr, "   -i, --index             compress and create BGZF index\n");
+    fprintf(stderr, "   -I, --index-name FILE   name of BGZF index file [file.gz.gzi]\n");
+    fprintf(stderr, "   -r, --reindex           (re)index compressed file\n");
+    fprintf(stderr, "   -s, --size INT          decompress INT bytes (uncompressed size)\n");
+    fprintf(stderr, "   -@, --threads INT       number of compression threads to use [1]\n");
+    fprintf(stderr, "\n");
+    return 1;
+}
+
+int main(int argc, char **argv)
+{
+    int c, compress, pstdout, is_forced, index = 0, reindex = 0;
+    BGZF *fp;
+    void *buffer;
+    long start, end, size;
+    char *index_fname = NULL;
+    int threads = 1;
+
+    static const struct option loptions[] =
+    {
+        {"help", no_argument, NULL, 'h'},
+        {"offset", required_argument, NULL, 'b'},
+        {"stdout", no_argument, NULL, 'c'},
+        {"decompress", no_argument, NULL, 'd'},
+        {"force", no_argument, NULL, 'f'},
+        {"index", no_argument, NULL, 'i'},
+        {"index-name", required_argument, NULL, 'I'},
+        {"reindex", no_argument, NULL, 'r'},
+        {"size", required_argument, NULL, 's'},
+        {"threads", required_argument, NULL, '@'},
+        {"version", no_argument, NULL, 1},
+        {NULL, 0, NULL, 0}
+    };
+
+    compress = 1; pstdout = 0; start = 0; size = -1; end = -1; is_forced = 0;
+    while((c  = getopt_long(argc, argv, "cdh?fb:@:s:iI:r",loptions,NULL)) >= 0){
+        switch(c){
+        case 'd': compress = 0; break;
+        case 'c': pstdout = 1; break;
+        case 'b': start = atol(optarg); compress = 0; pstdout = 1; break;
+        case 's': size = atol(optarg); pstdout = 1; break;
+        case 'f': is_forced = 1; break;
+        case 'i': index = 1; break;
+        case 'I': index_fname = optarg; break;
+        case 'r': reindex = 1; compress = 0; break;
+        case '@': threads = atoi(optarg); break;
+        case 1:
+            printf(
+"bgzip (htslib) %s\n"
+"Copyright (C) 2016 Genome Research Ltd.\n", hts_version());
+            return EXIT_SUCCESS;
+        case 'h':
+        case '?': return bgzip_main_usage();
+        }
+    }
+    if (size >= 0) end = start + size;
+    if (end >= 0 && end < start) {
+        fprintf(stderr, "[bgzip] Illegal region: [%ld, %ld]\n", start, end);
+        return 1;
+    }
+    if (compress == 1) {
+        struct stat sbuf;
+        int f_src = fileno(stdin);
+
+        if ( argc>optind )
+        {
+            if ( stat(argv[optind],&sbuf)<0 )
+            {
+                fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]);
+                return 1;
+            }
+
+            if ((f_src = open(argv[optind], O_RDONLY)) < 0) {
+                fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]);
+                return 1;
+            }
+
+            if (pstdout)
+                fp = bgzf_open("-", "w");
+            else
+            {
+                char *name = malloc(strlen(argv[optind]) + 5);
+                strcpy(name, argv[optind]);
+                strcat(name, ".gz");
+                fp = bgzf_open(name, is_forced? "w" : "wx");
+                if (fp == NULL && errno == EEXIST && confirm_overwrite(name))
+                    fp = bgzf_open(name, "w");
+                if (fp == NULL) {
+                    fprintf(stderr, "[bgzip] can't create %s: %s\n", name, strerror(errno));
+                    free(name);
+                    return 1;
+                }
+                free(name);
+            }
+        }
+        else if (!pstdout && isatty(fileno((FILE *)stdout)) )
+            return bgzip_main_usage();
+        else if ( index && !index_fname )
+        {
+            fprintf(stderr, "[bgzip] Index file name expected when writing to stdout\n");
+            return 1;
+        }
+        else
+            fp = bgzf_open("-", "w");
+
+        if (threads > 1)
+            bgzf_mt(fp, threads, 256);
+
+        if ( index ) bgzf_index_build_init(fp);
+        buffer = malloc(WINDOW_SIZE);
+        while ((c = read(f_src, buffer, WINDOW_SIZE)) > 0)
+            if (bgzf_write(fp, buffer, c) < 0) error("Could not write %d bytes: Error %d\n", c, fp->errcode);
+        if ( index )
+        {
+            if (index_fname) {
+                if (bgzf_index_dump(fp, index_fname, NULL) < 0)
+                    error("Could not write index to '%s'\n", index_fname);
+            } else {
+                if (bgzf_index_dump(fp, argv[optind], ".gz.gzi") < 0)
+                    error("Could not write index to '%s.gz.gzi'", argv[optind]);
+            }
+        }
+        if (bgzf_close(fp) < 0) error("Close failed: Error %d", fp->errcode);
+        if (argc > optind && !pstdout) unlink(argv[optind]);
+        free(buffer);
+        close(f_src);
+        return 0;
+    }
+    else if ( reindex )
+    {
+        if ( argc>optind )
+        {
+            fp = bgzf_open(argv[optind], "r");
+            if ( !fp ) error("[bgzip] Could not open file: %s\n", argv[optind]);
+        }
+        else
+        {
+            if ( !index_fname ) error("[bgzip] Index file name expected when reading from stdin\n");
+            fp = bgzf_open("-", "r");
+            if ( !fp ) error("[bgzip] Could not read from stdin: %s\n", strerror(errno));
+        }
+
+        buffer = malloc(BGZF_BLOCK_SIZE);
+        bgzf_index_build_init(fp);
+        int ret;
+        while ( (ret=bgzf_read(fp, buffer, BGZF_BLOCK_SIZE))>0 ) ;
+        free(buffer);
+        if ( ret<0 ) error("Is the file gzipped or bgzipped? The latter is required for indexing.\n");
+
+        if ( index_fname ) {
+            if (bgzf_index_dump(fp, index_fname, NULL) < 0)
+                error("Could not write index to '%s'\n", index_fname);
+        } else {
+            if (bgzf_index_dump(fp, argv[optind], ".gzi") < 0)
+                error("Could not write index to '%s.gzi'\n", argv[optind]);
+        }
+
+        if ( bgzf_close(fp)<0 ) error("Close failed: Error %d\n",fp->errcode);
+        return 0;
+    }
+    else
+    {
+        struct stat sbuf;
+        int f_dst;
+
+        if ( argc>optind )
+        {
+            if ( stat(argv[optind],&sbuf)<0 )
+            {
+                fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]);
+                return 1;
+            }
+            char *name;
+            int len = strlen(argv[optind]);
+            if ( strcmp(argv[optind]+len-3,".gz") )
+            {
+                fprintf(stderr, "[bgzip] %s: unknown suffix -- ignored\n", argv[optind]);
+                return 1;
+            }
+            fp = bgzf_open(argv[optind], "r");
+            if (fp == NULL) {
+                fprintf(stderr, "[bgzip] Could not open file: %s\n", argv[optind]);
+                return 1;
+            }
+
+            if (pstdout) {
+                f_dst = fileno(stdout);
+            }
+            else {
+                const int wrflags = O_WRONLY | O_CREAT | O_TRUNC;
+                name = strdup(argv[optind]);
+                name[strlen(name) - 3] = '\0';
+                f_dst = open(name, is_forced? wrflags : wrflags|O_EXCL, 0666);
+                if (f_dst < 0 && errno == EEXIST && confirm_overwrite(name))
+                    f_dst = open(name, wrflags, 0666);
+                if (f_dst < 0) {
+                    fprintf(stderr, "[bgzip] can't create %s: %s\n", name, strerror(errno));
+                    free(name);
+                    return 1;
+                }
+                free(name);
+            }
+        }
+        else if (!pstdout && isatty(fileno((FILE *)stdin)) )
+            return bgzip_main_usage();
+        else
+        {
+            f_dst = fileno(stdout);
+            fp = bgzf_open("-", "r");
+            if (fp == NULL) {
+                fprintf(stderr, "[bgzip] Could not read from stdin: %s\n", strerror(errno));
+                return 1;
+            }
+        }
+        buffer = malloc(WINDOW_SIZE);
+        if ( start>0 )
+        {
+            if ( bgzf_index_load(fp, argv[optind], ".gzi") < 0 ) error("Could not load index: %s.gzi\n", argv[optind]);
+            if ( bgzf_useek(fp, start, SEEK_SET) < 0 ) error("Could not seek to %d-th (uncompressd) byte\n", start);
+        }
+        while (1) {
+            if (end < 0) c = bgzf_read(fp, buffer, WINDOW_SIZE);
+            else c = bgzf_read(fp, buffer, (end - start > WINDOW_SIZE)? WINDOW_SIZE:(end - start));
+            if (c == 0) break;
+            if (c < 0) error("Could not read %d bytes: Error %d\n", (end - start > WINDOW_SIZE)? WINDOW_SIZE:(end - start), fp->errcode);
+            start += c;
+            if ( write(f_dst, buffer, c) != c ) error("Could not write %d bytes\n", c);
+            if (end >= 0 && start >= end) break;
+        }
+        free(buffer);
+        if (bgzf_close(fp) < 0) error("Close failed: Error %d\n",fp->errcode);
+        if (!pstdout) unlink(argv[optind]);
+        return 0;
+    }
+    return 0;
+}
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diff --git a/htslib/cram/._zfio.c b/htslib/cram/._zfio.c
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diff --git a/htslib/cram/cram.h b/htslib/cram/cram.h
new file mode 100644
index 0000000..c4e8809
--- /dev/null
+++ b/htslib/cram/cram.h
@@ -0,0 +1,61 @@
+/*
+Copyright (c) 2012-2013 Genome Research Ltd.
+Author: James Bonfield <jkb at sanger.ac.uk>
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+Institute nor the names of its contributors may be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+/*! \file
+ * CRAM interface.
+ *
+ * Consider using the higher level hts_*() API for programs that wish to
+ * be file format agnostic (see htslib/hts.h).
+ *
+ * This API should be used for CRAM specific code. The specifics of the
+ * public API are implemented in cram_io.h, cram_encode.h and cram_decode.h
+ * although these should not be included directly (use this file instead).
+ */
+
+#ifndef _CRAM_H_
+#define _CRAM_H_
+
+#include "cram/cram_samtools.h"
+#include "cram/sam_header.h"
+#include "cram_structs.h"
+#include "cram_io.h"
+#include "cram_encode.h"
+#include "cram_decode.h"
+#include "cram_stats.h"
+#include "cram_codecs.h"
+#include "cram_index.h"
+
+// Validate against the external cram.h,
+//
+// This contains duplicated portions from cram_io.h and cram_structs.h,
+// so we want to ensure that the prototypes match.
+#include "htslib/cram.h"
+
+#endif
diff --git a/htslib/cram/cram_codecs.c b/htslib/cram/cram_codecs.c
new file mode 100644
index 0000000..0e073c6
--- /dev/null
+++ b/htslib/cram/cram_codecs.c
@@ -0,0 +1,1950 @@
+/*
+Copyright (c) 2012-2013 Genome Research Ltd.
+Author: James Bonfield <jkb at sanger.ac.uk>
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+Institute nor the names of its contributors may be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+/*
+ * FIXME: add checking of cram_external_type to return NULL on unsupported
+ * {codec,type} tuples.
+ */
+
+#include <config.h>
+
+#include <stdlib.h>
+#include <string.h>
+#include <assert.h>
+#include <limits.h>
+
+#include "cram/cram.h"
+
+/*
+ * ---------------------------------------------------------------------------
+ * Block bit-level I/O functions.
+ * All defined static here to promote easy inlining by the compiler.
+ */
+
+#if 0
+/* Get a single bit, MSB first */
+static signed int get_bit_MSB(cram_block *block) {
+    unsigned int val;
+
+    if (block->byte > block->alloc)
+	return -1;
+
+    val = block->data[block->byte] >> block->bit;
+    if (--block->bit == -1) {
+	block->bit = 7;
+	block->byte++;
+	//printf("(%02X)", block->data[block->byte]);
+    }
+
+    //printf("-B%d-", val&1);
+
+    return val & 1;
+}
+#endif
+
+/*
+ * Count number of successive 0 and 1 bits
+ */
+static int get_one_bits_MSB(cram_block *block) {
+    int n = 0, b;
+    if (block->byte >= block->uncomp_size)
+        return -1;
+    do {
+	b = block->data[block->byte] >> block->bit;
+	if (--block->bit == -1) {
+	    block->bit = 7;
+	    block->byte++;
+	    if (block->byte == block->uncomp_size && (b&1))
+	        return -1;
+	}
+	n++;
+    } while (b&1);
+
+    return n-1;
+}
+
+static int get_zero_bits_MSB(cram_block *block) {
+    int n = 0, b;
+    if (block->byte >= block->uncomp_size)
+        return -1;
+    do {
+	b = block->data[block->byte] >> block->bit;
+	if (--block->bit == -1) {
+	    block->bit = 7;
+	    block->byte++;
+	    if (block->byte == block->uncomp_size && !(b&1))
+	        return -1;
+	}
+	n++;
+    } while (!(b&1));
+
+    return n-1;
+}
+
+#if 0
+/* Stores a single bit */
+static void store_bit_MSB(cram_block *block, unsigned int bit) {
+    if (block->byte >= block->alloc) {
+	block->alloc = block->alloc ? block->alloc*2 : 1024;
+	block->data = realloc(block->data, block->alloc);
+    }
+
+    if (bit)
+	block->data[block->byte] |= (1 << block->bit);
+
+    if (--block->bit == -1) {
+	block->bit = 7;
+	block->byte++;
+	block->data[block->byte] = 0;
+    }
+}
+#endif
+
+#if 0
+/* Rounds to the next whole byte boundary first */
+static void store_bytes_MSB(cram_block *block, char *bytes, int len) {
+    if (block->bit != 7) {
+	block->bit = 7;
+	block->byte++;
+    }
+
+    while (block->byte + len >= block->alloc) {
+	block->alloc = block->alloc ? block->alloc*2 : 1024;
+	block->data = realloc(block->data, block->alloc);
+    }
+
+    memcpy(&block->data[block->byte], bytes, len);
+    block->byte += len;
+}
+#endif
+
+/* Local optimised copy for inlining */
+static inline unsigned int get_bits_MSB(cram_block *block, int nbits) {
+    unsigned int val = 0;
+    int i;
+
+#if 0
+    // Fits within the current byte */
+    if (nbits <= block->bit+1) {
+	val = (block->data[block->byte]>>(block->bit-(nbits-1))) & ((1<<nbits)-1);
+	if ((block->bit -= nbits) == -1) {
+	    block->bit = 7;
+	    block->byte++;
+	}
+	return val;
+    }
+
+    // partial first byte
+    val = block->data[block->byte] & ((1<<(block->bit+1))-1);
+    nbits -= block->bit+1;
+    block->bit = 7;
+    block->byte++;
+
+    // whole middle bytes
+    while (nbits >= 8) {
+	val = (val << 8) | block->data[block->byte++];
+	nbits -= 8;
+    }
+
+    val <<= nbits;
+    val |= (block->data[block->byte]>>(block->bit-(nbits-1))) & ((1<<nbits)-1);
+    block->bit -= nbits;
+    return val;
+#endif
+
+#if 0
+    /* Inefficient implementation! */
+    //printf("{");
+    for (i = 0; i < nbits; i++)
+	//val = (val << 1) | get_bit_MSB(block);
+	GET_BIT_MSB(block, val);
+#endif
+
+#if 1
+    /* Combination of 1st two methods */
+    if (nbits <= block->bit+1) {
+	val = (block->data[block->byte]>>(block->bit-(nbits-1))) & ((1<<nbits)-1);
+	if ((block->bit -= nbits) == -1) {
+	    block->bit = 7;
+	    block->byte++;
+	}
+	return val;
+    }
+
+    switch(nbits) {
+//    case 15: GET_BIT_MSB(block, val);
+//    case 14: GET_BIT_MSB(block, val);
+//    case 13: GET_BIT_MSB(block, val);
+//    case 12: GET_BIT_MSB(block, val);
+//    case 11: GET_BIT_MSB(block, val);
+//    case 10: GET_BIT_MSB(block, val);
+//    case  9: GET_BIT_MSB(block, val);
+    case  8: GET_BIT_MSB(block, val);
+    case  7: GET_BIT_MSB(block, val);
+    case  6: GET_BIT_MSB(block, val);
+    case  5: GET_BIT_MSB(block, val);
+    case  4: GET_BIT_MSB(block, val);
+    case  3: GET_BIT_MSB(block, val);
+    case  2: GET_BIT_MSB(block, val);
+    case  1: GET_BIT_MSB(block, val);
+	break;
+
+    default:
+	for (i = 0; i < nbits; i++)
+	    //val = (val << 1) | get_bit_MSB(block);
+	    GET_BIT_MSB(block, val);
+    }
+#endif
+
+    //printf("=0x%x}", val);
+
+    return val;
+}
+
+/*
+ * Can store up to 24-bits worth of data encoded in an integer value
+ * Possibly we'd want to have a less optimal store_bits function when dealing
+ * with nbits > 24, but for now we assume the codes generated are never
+ * that big. (Given this is only possible with 121392 or more
+ * characters with exactly the correct frequency distribution we check
+ * for it elsewhere.)
+ */
+static int store_bits_MSB(cram_block *block, unsigned int val, int nbits) {
+    /* fprintf(stderr, " store_bits: %02x %d\n", val, nbits); */
+
+    /*
+     * Use slow mode until we tweak the huffman generator to never generate
+     * codes longer than 24-bits.
+     */
+    unsigned int mask;
+
+    if (block->byte+4 >= block->alloc) {
+	if (block->byte) {
+	    block->alloc *= 2;
+	    block->data = realloc(block->data, block->alloc + 4);
+	    if (!block->data)
+		return -1;
+	} else {
+	    block->alloc = 1024;
+	    block->data = realloc(block->data, block->alloc + 4);
+	    if (!block->data)
+		return -1;
+	    block->data[0] = 0; // initialise first byte of buffer
+	}
+    }
+
+    /* fits in current bit-field */
+    if (nbits <= block->bit+1) {
+	block->data[block->byte] |= (val << (block->bit+1-nbits));
+	if ((block->bit-=nbits) == -1) {
+	    block->bit = 7;
+	    block->byte++;
+	    block->data[block->byte] = 0;
+	}
+	return 0;
+    }
+
+    block->data[block->byte] |= (val >> (nbits -= block->bit+1));
+    block->bit = 7;
+    block->byte++;
+    block->data[block->byte] = 0;
+				 
+    mask = 1<<(nbits-1);
+    do {
+	if (val & mask)
+	    block->data[block->byte] |= (1 << block->bit);
+	if (--block->bit == -1) {
+	    block->bit = 7;
+	    block->byte++;
+	    block->data[block->byte] = 0;
+	}
+	mask >>= 1;
+    } while(--nbits);
+
+    return 0;
+}
+
+/*
+ * Returns the next 'size' bytes from a block, or NULL if insufficient
+ * data left.This is just a pointer into the block data and not an
+ * allocated object, so do not free the result.
+ */
+static char *cram_extract_block(cram_block *b, int size) {
+    char *cp = (char *)b->data + b->idx;
+    b->idx += size;
+    if (b->idx > b->uncomp_size)
+	return NULL;
+
+    return cp;
+}
+
+/*
+ * ---------------------------------------------------------------------------
+ * EXTERNAL
+ */
+int cram_external_decode_int(cram_slice *slice, cram_codec *c,
+			     cram_block *in, char *out, int *out_size) {
+    int l;
+    char *cp;
+    cram_block *b;
+
+    /* Find the external block */
+    b = cram_get_block_by_id(slice, c->external.content_id);
+    if (!b)
+        return *out_size?-1:0;
+
+    cp = (char *)b->data + b->idx;
+    // E_INT and E_LONG are guaranteed single item queries
+    l = safe_itf8_get(cp, (char *)b->data + b->uncomp_size, (int32_t *)out);
+    b->idx += l;
+    *out_size = 1;
+
+    return l > 0 ? 0 : -1;
+}
+
+int cram_external_decode_char(cram_slice *slice, cram_codec *c,
+			      cram_block *in, char *out,
+			      int *out_size) {
+    char *cp;
+    cram_block *b;
+
+    /* Find the external block */
+    b = cram_get_block_by_id(slice, c->external.content_id);
+    if (!b)
+        return *out_size?-1:0;
+
+    cp = cram_extract_block(b, *out_size);
+    if (!cp)
+	return -1;
+
+    if (out)
+	memcpy(out, cp, *out_size);
+    return 0;
+}
+
+static int cram_external_decode_block(cram_slice *slice, cram_codec *c,
+				      cram_block *in, char *out_,
+				      int *out_size) {
+    char *cp;
+    cram_block *b = NULL;
+    cram_block *out = (cram_block *)out_;
+
+    /* Find the external block */
+    b = cram_get_block_by_id(slice, c->external.content_id);
+    if (!b)
+        return *out_size?-1:0;
+
+    cp = cram_extract_block(b, *out_size);
+    if (!cp)
+	return -1;
+
+    BLOCK_APPEND(out, cp, *out_size);
+    return 0;
+}
+
+void cram_external_decode_free(cram_codec *c) {
+    if (c)
+	free(c);
+}
+
+cram_codec *cram_external_decode_init(char *data, int size,
+				      enum cram_external_type option,
+				      int version) {
+    cram_codec *c;
+    char *cp = data;
+
+    if (!(c = malloc(sizeof(*c))))
+	return NULL;
+
+    c->codec  = E_EXTERNAL;
+    if (option == E_INT || option == E_LONG)
+	c->decode = cram_external_decode_int;
+    else if (option == E_BYTE_ARRAY || option == E_BYTE)
+	c->decode = cram_external_decode_char;
+    else
+	c->decode = cram_external_decode_block;
+    c->free   = cram_external_decode_free;
+    
+    cp += itf8_get(cp, &c->external.content_id);
+
+    if (cp - data != size) {
+	fprintf(stderr, "Malformed external header stream\n");
+	free(c);
+	return NULL;
+    }
+
+    c->external.type = option;
+
+    return c;
+}
+
+int cram_external_encode_int(cram_slice *slice, cram_codec *c,
+			     char *in, int in_size) {
+    uint32_t *i32 = (uint32_t *)in;
+
+    itf8_put_blk(c->out, *i32);
+    return 0;
+}
+
+int cram_external_encode_char(cram_slice *slice, cram_codec *c,
+			      char *in, int in_size) {
+    BLOCK_APPEND(c->out, in, in_size);
+    return 0;
+}
+
+void cram_external_encode_free(cram_codec *c) {
+    if (!c)
+	return;
+    free(c);
+}
+
+int cram_external_encode_store(cram_codec *c, cram_block *b, char *prefix,
+			       int version) {
+    char tmp[99], *tp = tmp;
+    int len = 0;
+
+    if (prefix) {
+	size_t l = strlen(prefix);
+	BLOCK_APPEND(b, prefix, l);
+	len += l;
+    }
+
+    tp += itf8_put(tp, c->e_external.content_id);
+    len += itf8_put_blk(b, c->codec);
+    len += itf8_put_blk(b, tp-tmp);
+    BLOCK_APPEND(b, tmp, tp-tmp);
+    len += tp-tmp;
+
+    return len;
+}
+
+cram_codec *cram_external_encode_init(cram_stats *st,
+				      enum cram_external_type option,
+				      void *dat,
+				      int version) {
+    cram_codec *c;
+
+    c = malloc(sizeof(*c));
+    if (!c)
+	return NULL;
+    c->codec = E_EXTERNAL;
+    c->free = cram_external_encode_free;
+    if (option == E_INT || option == E_LONG)
+	c->encode = cram_external_encode_int;
+    else if (option == E_BYTE_ARRAY || option == E_BYTE)
+	c->encode = cram_external_encode_char;
+    else
+	abort();
+    c->store = cram_external_encode_store;
+
+    c->e_external.content_id = (size_t)dat;
+
+    return c;
+}
+
+/*
+ * ---------------------------------------------------------------------------
+ * BETA
+ */
+int cram_beta_decode_int(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) {
+    int32_t *out_i = (int32_t *)out;
+    int i, n;
+
+    if (c->beta.nbits) {
+        if (cram_not_enough_bits(in, c->beta.nbits))
+            return -1;
+
+	for (i = 0, n = *out_size; i < n; i++)
+	    out_i[i] = get_bits_MSB(in, c->beta.nbits) - c->beta.offset;
+    } else {
+	for (i = 0, n = *out_size; i < n; i++)
+	    out_i[i] = -c->beta.offset;
+    }
+
+    return 0;
+}
+
+int cram_beta_decode_char(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) {
+    int i, n;
+
+
+    if (c->beta.nbits) {
+        if (cram_not_enough_bits(in, c->beta.nbits))
+            return -1;
+
+	if (out)
+	    for (i = 0, n = *out_size; i < n; i++)
+		out[i] = get_bits_MSB(in, c->beta.nbits) - c->beta.offset;
+	else
+	    for (i = 0, n = *out_size; i < n; i++)
+		get_bits_MSB(in, c->beta.nbits);
+    } else {
+	if (out)
+	    for (i = 0, n = *out_size; i < n; i++)
+		out[i] = -c->beta.offset;
+    }
+
+    return 0;
+}
+
+void cram_beta_decode_free(cram_codec *c) {
+    if (c)
+	free(c);
+}
+
+cram_codec *cram_beta_decode_init(char *data, int size,
+				  enum cram_external_type option,
+				  int version) {
+    cram_codec *c;
+    char *cp = data;
+
+    if (!(c = malloc(sizeof(*c))))
+	return NULL;
+
+    c->codec  = E_BETA;
+    if (option == E_INT || option == E_LONG)
+	c->decode = cram_beta_decode_int;
+    else if (option == E_BYTE_ARRAY || option == E_BYTE)
+	c->decode = cram_beta_decode_char;
+    else
+	abort();
+    c->free   = cram_beta_decode_free;
+    
+    cp += itf8_get(cp, &c->beta.offset);
+    cp += itf8_get(cp, &c->beta.nbits);
+
+    if (cp - data != size
+        || c->beta.nbits < 0 || c->beta.nbits > 8 * sizeof(int)) {
+	fprintf(stderr, "Malformed beta header stream\n");
+	free(c);
+	return NULL;
+    }
+
+    return c;
+}
+
+int cram_beta_encode_store(cram_codec *c, cram_block *b,
+			   char *prefix, int version) {
+    int len = 0;
+
+    if (prefix) {
+	size_t l = strlen(prefix);
+	BLOCK_APPEND(b, prefix, l);
+	len += l;
+    }
+
+    len += itf8_put_blk(b, c->codec);
+    len += itf8_put_blk(b, itf8_size(c->e_beta.offset)
+			+ itf8_size(c->e_beta.nbits)); // codec length
+    len += itf8_put_blk(b, c->e_beta.offset);
+    len += itf8_put_blk(b, c->e_beta.nbits);
+
+    return len;
+}
+
+int cram_beta_encode_int(cram_slice *slice, cram_codec *c,
+			 char *in, int in_size) {
+    int *syms = (int *)in;
+    int i, r = 0;
+
+    for (i = 0; i < in_size; i++)
+	r |= store_bits_MSB(c->out, syms[i] + c->e_beta.offset,
+			    c->e_beta.nbits);
+
+    return r;
+}
+
+int cram_beta_encode_char(cram_slice *slice, cram_codec *c,
+			  char *in, int in_size) {
+    unsigned char *syms = (unsigned char *)in;
+    int i, r = 0;
+
+    for (i = 0; i < in_size; i++)
+	r |= store_bits_MSB(c->out, syms[i] + c->e_beta.offset,
+			    c->e_beta.nbits);
+
+    return r;
+}
+
+void cram_beta_encode_free(cram_codec *c) {
+    if (c) free(c);
+}
+
+cram_codec *cram_beta_encode_init(cram_stats *st,
+				  enum cram_external_type option,
+				  void *dat,
+				  int version) {
+    cram_codec *c;
+    int min_val, max_val, len = 0;
+
+    c = malloc(sizeof(*c));
+    if (!c)
+	return NULL;
+    c->codec  = E_BETA;
+    c->free   = cram_beta_encode_free;
+    if (option == E_INT)
+	c->encode = cram_beta_encode_int;
+    else
+	c->encode = cram_beta_encode_char;
+    c->store  = cram_beta_encode_store;
+
+    if (dat) {
+	min_val = ((int *)dat)[0];
+	max_val = ((int *)dat)[1];
+    } else {
+	min_val = INT_MAX;
+	max_val = INT_MIN;
+	int i;
+	for (i = 0; i < MAX_STAT_VAL; i++) {
+	    if (!st->freqs[i])
+		continue;
+	    if (min_val > i)
+		min_val = i;
+	    max_val = i;
+	}
+	if (st->h) {
+	    khint_t k;
+
+	    for (k = kh_begin(st->h); k != kh_end(st->h); k++) {
+		if (!kh_exist(st->h, k))
+		    continue;
+	    
+		i = kh_key(st->h, k);
+		if (min_val > i)
+		    min_val = i;
+		if (max_val < i)
+		    max_val = i;
+	    }
+	}
+    }
+
+    assert(max_val >= min_val);
+    c->e_beta.offset = -min_val;
+    max_val -= min_val;
+    while (max_val) {
+	len++;
+	max_val >>= 1;
+    }
+    c->e_beta.nbits = len;
+
+    return c;
+}
+
+/*
+ * ---------------------------------------------------------------------------
+ * SUBEXP
+ */
+int cram_subexp_decode(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) {
+    int32_t *out_i = (int32_t *)out;
+    int n, count;
+    int k = c->subexp.k;
+
+    for (count = 0, n = *out_size; count < n; count++) {
+	int i = 0, tail;
+	int val;
+
+	/* Get number of 1s */
+	//while (get_bit_MSB(in) == 1) i++;
+	i = get_one_bits_MSB(in);
+        if (i < 0 || cram_not_enough_bits(in, i > 0 ? i + k - 1 : k))
+            return -1;
+	/*
+	 * Val is
+	 * i > 0:  2^(k+i-1) + k+i-1 bits
+	 * i = 0:  k bits
+	 */
+	if (i) {
+	    tail = i + k-1;
+	    val = 0;
+	    while (tail) {
+		//val = val<<1; val |= get_bit_MSB(in);
+		GET_BIT_MSB(in, val);
+		tail--;
+	    }
+	    val += 1 << (i + k-1);
+	} else {
+	    tail = k;
+	    val = 0;
+	    while (tail) {
+		//val = val<<1; val |= get_bit_MSB(in);
+		GET_BIT_MSB(in, val);
+		tail--;
+	    }
+	}
+
+	out_i[count] = val - c->subexp.offset;
+    }
+
+    return 0;
+}
+
+void cram_subexp_decode_free(cram_codec *c) {
+    if (c)
+	free(c);
+}
+
+cram_codec *cram_subexp_decode_init(char *data, int size,
+				    enum cram_external_type option,
+				    int version) {
+    cram_codec *c;
+    char *cp = data;
+
+    if (!(c = malloc(sizeof(*c))))
+	return NULL;
+
+    c->codec  = E_SUBEXP;
+    c->decode = cram_subexp_decode;
+    c->free   = cram_subexp_decode_free;
+    c->subexp.k = -1;
+
+    cp += safe_itf8_get(cp, data + size, &c->subexp.offset);
+    cp += safe_itf8_get(cp, data + size, &c->subexp.k);
+
+    if (cp - data != size || c->subexp.k < 0) {
+	fprintf(stderr, "Malformed subexp header stream\n");
+	free(c);
+	return NULL;
+    }
+
+    return c;
+}
+
+/*
+ * ---------------------------------------------------------------------------
+ * GAMMA
+ */
+int cram_gamma_decode(cram_slice *slice, cram_codec *c, cram_block *in, char *out, int *out_size) {
+    int32_t *out_i = (int32_t *)out;
+    int i, n;
+
+    for (i = 0, n = *out_size; i < n; i++) {
+	int nz = 0;
+	int val;
+	//while (get_bit_MSB(in) == 0) nz++;
+	nz = get_zero_bits_MSB(in);
+        if (cram_not_enough_bits(in, nz))
+            return -1;
+	val = 1;
+	while (nz > 0) {
+	    //val <<= 1; val |= get_bit_MSB(in);
+	    GET_BIT_MSB(in, val);
+	    nz--;
+	}
+
+	out_i[i] = val - c->gamma.offset;
+    }
+
+    return 0;
+}
+
+void cram_gamma_decode_free(cram_codec *c) {
+    if (c)
+	free(c);
+}
+
+cram_codec *cram_gamma_decode_init(char *data, int size,
+				   enum cram_external_type option,
+				   int version) {
+    cram_codec *c;
+    char *cp = data;
+
+    if (!(c = malloc(sizeof(*c))))
+	return NULL;
+
+    c->codec  = E_GAMMA;
+    c->decode = cram_gamma_decode;
+    c->free   = cram_gamma_decode_free;
+    
+    cp += itf8_get(cp, &c->gamma.offset);
+
+    if (cp - data != size) {
+	fprintf(stderr, "Malformed gamma header stream\n");
+	free(c);
+	return NULL;
+    }
+
+    return c;
+}
+
+/*
+ * ---------------------------------------------------------------------------
+ * HUFFMAN
+ */
+
+static int code_sort(const void *vp1, const void *vp2) {
+    const cram_huffman_code *c1 = (const cram_huffman_code *)vp1;
+    const cram_huffman_code *c2 = (const cram_huffman_code *)vp2;
+
+    if (c1->len != c2->len)
+	return c1->len - c2->len;
+    else
+	return c1->symbol - c2->symbol;
+}
+
+void cram_huffman_decode_free(cram_codec *c) {
+    if (!c)
+	return;
+
+    if (c->huffman.codes)
+	free(c->huffman.codes);
+    free(c);
+}
+
+int cram_huffman_decode_null(cram_slice *slice, cram_codec *c,
+			     cram_block *in, char *out, int *out_size) {
+    return -1;
+}
+
+int cram_huffman_decode_char0(cram_slice *slice, cram_codec *c,
+			      cram_block *in, char *out, int *out_size) {
+    int i, n;
+
+    if (!out)
+	return 0;
+
+    /* Special case of 0 length codes */
+    for (i = 0, n = *out_size; i < n; i++) {
+	out[i] = c->huffman.codes[0].symbol;
+    }
+    return 0;
+}
+
+int cram_huffman_decode_char(cram_slice *slice, cram_codec *c,
+			     cram_block *in, char *out, int *out_size) {
+    int i, n, ncodes = c->huffman.ncodes;
+    const cram_huffman_code * const codes = c->huffman.codes;
+
+    for (i = 0, n = *out_size; i < n; i++) {
+	int idx = 0;
+	int val = 0, len = 0, last_len = 0;
+
+	for (;;) {
+	    int dlen = codes[idx].len - last_len;
+	    if (cram_not_enough_bits(in, dlen))
+		return -1;
+
+	    //val <<= dlen;
+	    //val  |= get_bits_MSB(in, dlen);
+	    //last_len = (len += dlen);
+
+	    last_len = (len += dlen);
+	    for (; dlen; dlen--) GET_BIT_MSB(in, val);
+
+	    idx = val - codes[idx].p;
+	    if (idx >= ncodes || idx < 0)
+		return -1;
+
+	    if (codes[idx].code == val && codes[idx].len == len) {
+		out[i] = codes[idx].symbol;
+		break;
+	    }
+	}
+    }
+
+    return 0;
+}
+
+int cram_huffman_decode_int0(cram_slice *slice, cram_codec *c,
+			     cram_block *in, char *out, int *out_size) {
+    int32_t *out_i = (int32_t *)out;
+    int i, n;
+    const cram_huffman_code * const codes = c->huffman.codes;
+
+    /* Special case of 0 length codes */
+    for (i = 0, n = *out_size; i < n; i++) {
+	out_i[i] = codes[0].symbol;
+    }
+    return 0;
+}
+
+int cram_huffman_decode_int(cram_slice *slice, cram_codec *c,
+			    cram_block *in, char *out, int *out_size) {
+    int32_t *out_i = (int32_t *)out;
+    int i, n, ncodes = c->huffman.ncodes;
+    const cram_huffman_code * const codes = c->huffman.codes;
+
+    for (i = 0, n = *out_size; i < n; i++) {
+	int idx = 0;
+	int val = 0, len = 0, last_len = 0;
+
+	// Now one bit at a time for remaining checks
+	for (;;) {
+	    int dlen = codes[idx].len - last_len;
+	    if (cram_not_enough_bits(in, dlen))
+		return -1;
+	    
+	    //val <<= dlen;
+	    //val  |= get_bits_MSB(in, dlen);
+	    //last_len = (len += dlen);
+
+	    last_len = (len += dlen);
+	    for (; dlen; dlen--) GET_BIT_MSB(in, val);
+
+	    idx = val - codes[idx].p;
+	    if (idx >= ncodes || idx < 0)
+		return -1;
+
+	    if (codes[idx].code == val && codes[idx].len == len) {
+		out_i[i] = codes[idx].symbol;
+		break;
+	    }
+	}
+    }
+
+    return 0;
+}
+
+/*
+ * Initialises a huffman decoder from an encoding data stream.
+ */
+cram_codec *cram_huffman_decode_init(char *data, int size,
+				     enum cram_external_type option,
+				     int version) {
+    int32_t ncodes = 0, i, j;
+    char *cp = data, *data_end = &data[size];
+    cram_codec *h;
+    cram_huffman_code *codes;
+    int32_t val, last_len, max_len = 0;
+    int l;
+
+    cp += safe_itf8_get(cp, data_end, &ncodes);
+    h = calloc(1, sizeof(*h));
+    if (!h)
+	return NULL;
+
+    h->codec  = E_HUFFMAN;
+    h->free   = cram_huffman_decode_free;
+
+    h->huffman.ncodes = ncodes;
+    codes = h->huffman.codes = malloc(ncodes * sizeof(*codes));
+    if (!codes) {
+	free(h);
+	return NULL;
+    }
+
+    /* Read symbols and bit-lengths */
+    for (i = 0, l = 1; i < ncodes && l > 0; i++, cp += l) {
+	l = safe_itf8_get(cp, data_end, &codes[i].symbol);
+    }
+
+    if (l < 1) {
+	fprintf(stderr, "Malformed huffman header stream\n");
+	free(h);
+	return NULL;
+    }
+    cp += safe_itf8_get(cp, data_end, &i);
+    if (i != ncodes) {
+	fprintf(stderr, "Malformed huffman header stream\n");
+	free(h);
+	return NULL;
+    }
+
+    if (ncodes == 0) {
+	/* NULL huffman stream.  Ensure it returns an error if
+           anything tries to use it. */
+        h->decode = cram_huffman_decode_null;
+        return h;
+    }
+
+    for (i = 0, l = 1; i < ncodes; i++, cp += l) {
+        l = safe_itf8_get(cp, data_end, &codes[i].len);
+        if (l < 1)
+            break;
+	if (max_len < codes[i].len)
+	    max_len = codes[i].len;
+    }
+    if (l < 1 || cp - data != size || max_len >= ncodes) {
+	fprintf(stderr, "Malformed huffman header stream\n");
+	free(h);
+	return NULL;
+    }
+
+    /* Sort by bit length and then by symbol value */
+    qsort(codes, ncodes, sizeof(*codes), code_sort);
+
+    /* Assign canonical codes */
+    val = -1, last_len = 0;
+    for (i = 0; i < ncodes; i++) {
+	val++;
+	if (codes[i].len > last_len) {
+	    while (codes[i].len > last_len) {
+		val <<= 1;
+		last_len++;
+	    }
+	}
+	codes[i].code = val;
+    }
+
+    /*
+     * Compute the next starting point, offset by the i'th value.
+     * For example if codes 10, 11, 12, 13 are 30, 31, 32, 33 then
+     * codes[10..13].p = 30 - 10.
+     */
+    last_len = 0;
+    for (i = j = 0; i < ncodes; i++) {
+	if (codes[i].len > last_len) {
+	    j = codes[i].code - i;
+	    last_len = codes[i].len;
+	}
+	codes[i].p = j;
+    }
+
+//    puts("==HUFF LEN==");
+//    for (i = 0; i <= last_len+1; i++) {
+//	printf("len %d=%d prefix %d\n", i, h->huffman.lengths[i], h->huffman.prefix[i]); 
+//    }
+//    puts("===HUFFMAN CODES===");
+//    for (i = 0; i < ncodes; i++) {
+//	int j;
+//	printf("%d: %d %d %d ", i, codes[i].symbol, codes[i].len, codes[i].code);
+//	j = codes[i].len;
+//	while (j) {
+//	    putchar(codes[i].code & (1 << --j) ? '1' : '0');
+//	}
+//	printf(" %d\n", codes[i].code);
+//    }
+
+    if (option == E_BYTE || option == E_BYTE_ARRAY) {
+	if (h->huffman.codes[0].len == 0)
+	    h->decode = cram_huffman_decode_char0;
+	else
+	    h->decode = cram_huffman_decode_char;
+    } else if (option == E_BYTE_ARRAY_BLOCK) {
+	abort();
+    } else {
+	if (h->huffman.codes[0].len == 0)
+	    h->decode = cram_huffman_decode_int0;
+	else
+	    h->decode = cram_huffman_decode_int;
+    }
+
+    return (cram_codec *)h;
+}
+
+int cram_huffman_encode_char0(cram_slice *slice, cram_codec *c,
+			      char *in, int in_size) {
+    return 0;
+}
+
+int cram_huffman_encode_char(cram_slice *slice, cram_codec *c,
+			     char *in, int in_size) {
+    int i, code, len, r = 0;
+    unsigned char *syms = (unsigned char *)in;
+
+    while (in_size--) {
+	int sym = *syms++;
+	if (sym >= -1 && sym < MAX_HUFF) {
+	    i = c->e_huffman.val2code[sym+1];
+	    assert(c->e_huffman.codes[i].symbol == sym);
+	    code = c->e_huffman.codes[i].code;
+	    len  = c->e_huffman.codes[i].len;
+	} else {
+	    /* Slow - use a lookup table for when sym < MAX_HUFF? */
+	    for (i = 0; i < c->e_huffman.nvals; i++) {
+		if (c->e_huffman.codes[i].symbol == sym)
+		    break;
+	    }
+	    if (i == c->e_huffman.nvals)
+		return -1;
+    
+	    code = c->e_huffman.codes[i].code;
+	    len  = c->e_huffman.codes[i].len;
+	}
+
+	r |= store_bits_MSB(c->out, code, len);
+    }
+
+    return r;
+}
+
+int cram_huffman_encode_int0(cram_slice *slice, cram_codec *c,
+			     char *in, int in_size) {
+    return 0;
+}
+
+int cram_huffman_encode_int(cram_slice *slice, cram_codec *c,
+			    char *in, int in_size) {
+    int i, code, len, r = 0;
+    int *syms = (int *)in;
+
+    while (in_size--) {
+	int sym = *syms++;
+
+	if (sym >= -1 && sym < MAX_HUFF) {
+	    i = c->e_huffman.val2code[sym+1];
+	    assert(c->e_huffman.codes[i].symbol == sym);
+	    code = c->e_huffman.codes[i].code;
+	    len  = c->e_huffman.codes[i].len;
+	} else {
+	    /* Slow - use a lookup table for when sym < MAX_HUFFMAN_SYM? */
+	    for (i = 0; i < c->e_huffman.nvals; i++) {
+		if (c->e_huffman.codes[i].symbol == sym)
+		    break;
+	    }
+	    if (i == c->e_huffman.nvals)
+		return -1;
+    
+	    code = c->e_huffman.codes[i].code;
+	    len  = c->e_huffman.codes[i].len;
+	}
+
+	r |= store_bits_MSB(c->out, code, len);
+    }
+
+    return r;
+}
+
+void cram_huffman_encode_free(cram_codec *c) {
+    if (!c)
+	return;
+
+    if (c->e_huffman.codes)
+	free(c->e_huffman.codes);
+    free(c);
+}
+
+/*
+ * Encodes a huffman tree.
+ * Returns number of bytes written.
+ */
+int cram_huffman_encode_store(cram_codec *c, cram_block *b, char *prefix,
+			      int version) {
+    int i, len = 0;
+    cram_huffman_code *codes = c->e_huffman.codes;
+    /*
+     * Up to code length 127 means 2.5e+26 bytes of data required (worst
+     * case huffman tree needs symbols with freqs matching the Fibonacci
+     * series). So guaranteed 1 byte per code.
+     *
+     * Symbols themselves could be 5 bytes (eg -1 is 5 bytes in itf8).
+     *
+     * Therefore 6*ncodes + 5 + 5 + 1 + 5 is max memory
+     */
+    char *tmp = malloc(6*c->e_huffman.nvals+16);
+    char *tp = tmp;
+
+    if (!tmp)
+	return -1;
+
+    if (prefix) {
+	size_t l = strlen(prefix);
+	BLOCK_APPEND(b, prefix, l);
+	len += l;
+    }
+
+    tp += itf8_put(tp, c->e_huffman.nvals);
+    for (i = 0; i < c->e_huffman.nvals; i++) {
+	tp += itf8_put(tp, codes[i].symbol);
+    }
+
+    tp += itf8_put(tp, c->e_huffman.nvals);
+    for (i = 0; i < c->e_huffman.nvals; i++) {
+	tp += itf8_put(tp, codes[i].len);
+    }
+
+    len += itf8_put_blk(b, c->codec);
+    len += itf8_put_blk(b, tp-tmp);
+    BLOCK_APPEND(b, tmp, tp-tmp);
+    len += tp-tmp;
+
+    free(tmp);
+
+    return len;
+}
+
+cram_codec *cram_huffman_encode_init(cram_stats *st,
+				     enum cram_external_type option,
+				     void *dat,
+				     int version) {
+    int *vals = NULL, *freqs = NULL, vals_alloc = 0, *lens, code, len;
+    int nvals, i, ntot = 0, max_val = 0, min_val = INT_MAX, k;
+    cram_codec *c;
+    cram_huffman_code *codes;
+
+    c = malloc(sizeof(*c));
+    if (!c)
+	return NULL;
+    c->codec = E_HUFFMAN;
+
+    /* Count number of unique symbols */
+    for (nvals = i = 0; i < MAX_STAT_VAL; i++) {
+	if (!st->freqs[i])
+	    continue;
+	if (nvals >= vals_alloc) {
+	    vals_alloc = vals_alloc ? vals_alloc*2 : 1024;
+	    vals  = realloc(vals,  vals_alloc * sizeof(int));
+	    freqs = realloc(freqs, vals_alloc * sizeof(int));
+	    if (!vals || !freqs) {
+		if (vals)  free(vals);
+		if (freqs) free(freqs);
+		free(c);
+		return NULL;
+	    }
+	}
+	vals[nvals] = i;
+	freqs[nvals] = st->freqs[i];
+	assert(st->freqs[i] > 0);
+	ntot += freqs[nvals];
+	if (max_val < i) max_val = i;
+	if (min_val > i) min_val = i;
+	nvals++;
+    }
+    if (st->h) {
+	khint_t k;
+
+	for (k = kh_begin(st->h); k != kh_end(st->h); k++) {
+	    if (!kh_exist(st->h, k))
+		continue;
+	    if (nvals >= vals_alloc) {
+		vals_alloc = vals_alloc ? vals_alloc*2 : 1024;
+		vals  = realloc(vals,  vals_alloc * sizeof(int));
+		freqs = realloc(freqs, vals_alloc * sizeof(int));
+		if (!vals || !freqs)
+		    return NULL;
+	    }
+	    vals[nvals]= kh_key(st->h, k);
+	    freqs[nvals] = kh_val(st->h, k);
+	    assert(freqs[nvals] > 0);
+	    ntot += freqs[nvals];
+	    if (max_val < i) max_val = i;
+	    if (min_val > i) min_val = i;
+	    nvals++;
+	}
+    }
+
+    assert(nvals > 0);
+
+    freqs = realloc(freqs, 2*nvals*sizeof(*freqs));
+    lens = calloc(2*nvals, sizeof(*lens));
+    if (!lens || !freqs)
+	return NULL;
+
+    /* Inefficient, use pointers to form chain so we can insert and maintain
+     * a sorted list? This is currently O(nvals^2) complexity.
+     */
+    for (;;) {
+	int low1 = INT_MAX, low2 = INT_MAX;
+	int ind1 = 0, ind2 = 0;
+	for (i = 0; i < nvals; i++) {
+	    if (freqs[i] < 0)
+		continue;
+	    if (low1 > freqs[i]) 
+		low2 = low1, ind2 = ind1, low1 = freqs[i], ind1 = i;
+	    else if (low2 > freqs[i])
+		low2 = freqs[i], ind2 = i;
+	}
+	if (low2 == INT_MAX)
+	    break;
+
+	freqs[nvals] = low1 + low2;
+	lens[ind1] = nvals;
+	lens[ind2] = nvals;
+	freqs[ind1] *= -1;
+	freqs[ind2] *= -1;
+	nvals++;
+    }
+    nvals = nvals/2+1;
+
+    /* Assign lengths */
+    for (i = 0; i < nvals; i++) {
+	int code_len = 0;
+	for (k = lens[i]; k; k = lens[k])
+	    code_len++;
+	lens[i] = code_len;
+	freqs[i] *= -1;
+	//fprintf(stderr, "%d / %d => %d\n", vals[i], freqs[i], lens[i]);
+    }
+
+
+    /* Sort, need in a struct */
+    if (!(codes = malloc(nvals * sizeof(*codes))))
+	return NULL;
+    for (i = 0; i < nvals; i++) {
+	codes[i].symbol = vals[i];
+	codes[i].len = lens[i];
+    }
+    qsort(codes, nvals, sizeof(*codes), code_sort);
+
+    /*
+     * Generate canonical codes from lengths.
+     * Sort by length.
+     * Start with 0.
+     * Every new code of same length is +1.
+     * Every new code of new length is +1 then <<1 per extra length.
+     *
+     * /\
+     * a/\
+     * /\/\
+     * bcd/\
+     *    ef
+     * 
+     * a 1  0
+     * b 3  4 (0+1)<<2
+     * c 3  5
+     * d 3  6
+     * e 4  14  (6+1)<<1
+     * f 5  15     
+     */
+    code = 0; len = codes[0].len;
+    for (i = 0; i < nvals; i++) {
+	while (len != codes[i].len) {
+	    code<<=1;
+	    len++;
+	}
+	codes[i].code = code++;
+
+	if (codes[i].symbol >= -1 && codes[i].symbol < MAX_HUFF)
+	    c->e_huffman.val2code[codes[i].symbol+1] = i;
+
+	//fprintf(stderr, "sym %d, code %d, len %d\n",
+	//	codes[i].symbol, codes[i].code, codes[i].len);
+    }
+
+    free(lens);
+    free(vals);
+    free(freqs);
+
+    c->e_huffman.codes = codes;
+    c->e_huffman.nvals = nvals;
+
+    c->free = cram_huffman_encode_free;
+    if (option == E_BYTE || option == E_BYTE_ARRAY) {
+	if (c->e_huffman.codes[0].len == 0)
+	    c->encode = cram_huffman_encode_char0;
+	else
+	    c->encode = cram_huffman_encode_char;
+    } else {
+	if (c->e_huffman.codes[0].len == 0)
+	    c->encode = cram_huffman_encode_int0;
+	else
+	    c->encode = cram_huffman_encode_int;
+    }
+    c->store = cram_huffman_encode_store;
+
+    return c;
+}
+
+/*
+ * ---------------------------------------------------------------------------
+ * BYTE_ARRAY_LEN
+ */
+int cram_byte_array_len_decode(cram_slice *slice, cram_codec *c,
+			       cram_block *in, char *out,
+			       int *out_size) {
+    /* Fetch length */
+    int32_t len = 0, one = 1;
+    int r;
+
+    r = c->byte_array_len.len_codec->decode(slice, c->byte_array_len.len_codec,
+                                            in, (char *)&len, &one);
+    //printf("ByteArray Len=%d\n", len);
+
+    if (!r && c->byte_array_len.val_codec && len >= 0) {
+	r = c->byte_array_len.val_codec->decode(slice,
+						c->byte_array_len.val_codec,
+						in, out, &len);
+    } else {
+	return -1;
+    }
+
+    *out_size = len;
+
+    return r;
+}
+
+void cram_byte_array_len_decode_free(cram_codec *c) {
+    if (!c) return;
+
+    if (c->byte_array_len.len_codec)
+	c->byte_array_len.len_codec->free(c->byte_array_len.len_codec);
+
+    if (c->byte_array_len.val_codec)
+	c->byte_array_len.val_codec->free(c->byte_array_len.val_codec);
+
+    free(c);
+}
+
+cram_codec *cram_byte_array_len_decode_init(char *data, int size,
+					    enum cram_external_type option,
+					    int version) {
+    cram_codec *c;
+    char *cp   = data;
+    char *endp = data + size;
+    int32_t encoding = 0;
+    int32_t sub_size = -1;
+
+    if (!(c = malloc(sizeof(*c))))
+	return NULL;
+
+    c->codec  = E_BYTE_ARRAY_LEN;
+    c->decode = cram_byte_array_len_decode;
+    c->free   = cram_byte_array_len_decode_free;
+    
+    cp += safe_itf8_get(cp, endp, &encoding);
+    cp += safe_itf8_get(cp, endp, &sub_size);
+    if (sub_size < 0 || endp - cp < sub_size)
+        goto malformed;
+    c->byte_array_len.len_codec = cram_decoder_init(encoding, cp, sub_size,
+						    E_INT, version);
+    if (c->byte_array_len.len_codec == NULL)
+        goto no_codec;
+    cp += sub_size;
+
+    sub_size = -1;
+    cp += safe_itf8_get(cp, endp, &encoding);
+    cp += safe_itf8_get(cp, endp, &sub_size);
+    if (sub_size < 0 || endp - cp < sub_size)
+        goto malformed;
+    c->byte_array_len.val_codec = cram_decoder_init(encoding, cp, sub_size,
+						    option, version);
+    if (c->byte_array_len.val_codec == NULL)
+        goto no_codec;
+    cp += sub_size;
+
+    if (cp - data != size)
+        goto malformed;
+
+    return c;
+
+ malformed:
+    fprintf(stderr, "Malformed byte_array_len header stream\n");
+ no_codec:
+    free(c);
+    return NULL;
+}
+
+int cram_byte_array_len_encode(cram_slice *slice, cram_codec *c,
+			       char *in, int in_size) {
+    int32_t i32 = in_size;
+    int r = 0;
+
+    r |= c->e_byte_array_len.len_codec->encode(slice,
+					       c->e_byte_array_len.len_codec,
+					       (char *)&i32, 1);
+    r |= c->e_byte_array_len.val_codec->encode(slice,
+					       c->e_byte_array_len.val_codec,
+					       in, in_size);
+    return r;
+}
+
+void cram_byte_array_len_encode_free(cram_codec *c) {
+    if (!c)
+	return;
+
+    if (c->e_byte_array_len.len_codec)
+	c->e_byte_array_len.len_codec->free(c->e_byte_array_len.len_codec);
+
+    if (c->e_byte_array_len.val_codec)
+	c->e_byte_array_len.val_codec->free(c->e_byte_array_len.val_codec);
+
+    free(c);
+}
+
+int cram_byte_array_len_encode_store(cram_codec *c, cram_block *b,
+				     char *prefix, int version) {
+    int len = 0, len2, len3;
+    cram_codec *tc;
+    cram_block *b_len, *b_val;
+
+    if (prefix) {
+	size_t l = strlen(prefix);
+	BLOCK_APPEND(b, prefix, l);
+	len += l;
+    }
+
+    tc = c->e_byte_array_len.len_codec; 
+    b_len = cram_new_block(0, 0);
+    len2 = tc->store(tc, b_len, NULL, version);
+
+    tc = c->e_byte_array_len.val_codec;
+    b_val = cram_new_block(0, 0);
+    len3 = tc->store(tc, b_val, NULL, version);
+
+    len += itf8_put_blk(b, c->codec);
+    len += itf8_put_blk(b, len2+len3);
+    BLOCK_APPEND(b, BLOCK_DATA(b_len), BLOCK_SIZE(b_len));
+    BLOCK_APPEND(b, BLOCK_DATA(b_val), BLOCK_SIZE(b_val));
+
+    cram_free_block(b_len);
+    cram_free_block(b_val);
+
+    return len + len2 + len3;
+}
+
+cram_codec *cram_byte_array_len_encode_init(cram_stats *st,
+					    enum cram_external_type option,
+					    void *dat,
+					    int version) {
+    cram_codec *c;
+    cram_byte_array_len_encoder *e = (cram_byte_array_len_encoder *)dat;
+
+    c = malloc(sizeof(*c));
+    if (!c)
+	return NULL;
+    c->codec = E_BYTE_ARRAY_LEN;
+    c->free = cram_byte_array_len_encode_free;
+    c->encode = cram_byte_array_len_encode;
+    c->store = cram_byte_array_len_encode_store;
+
+    c->e_byte_array_len.len_codec = cram_encoder_init(e->len_encoding,
+						      NULL, E_INT, 
+						      e->len_dat,
+						      version);
+    c->e_byte_array_len.val_codec = cram_encoder_init(e->val_encoding,
+						      NULL, E_BYTE_ARRAY, 
+						      e->val_dat,
+						      version);
+
+    return c;
+}
+
+/*
+ * ---------------------------------------------------------------------------
+ * BYTE_ARRAY_STOP
+ */
+static int cram_byte_array_stop_decode_char(cram_slice *slice, cram_codec *c,
+					    cram_block *in, char *out,
+					    int *out_size) {
+    cram_block *b = NULL;
+    char *cp, ch;
+
+    b = cram_get_block_by_id(slice, c->byte_array_stop.content_id);
+    if (!b)
+        return *out_size?-1:0;
+
+    if (b->idx >= b->uncomp_size)
+	return -1;
+
+    cp = (char *)b->data + b->idx;
+    if (out) {
+	while ((ch = *cp) != (char)c->byte_array_stop.stop) {
+	    if (cp - (char *)b->data >= b->uncomp_size)
+		return -1;
+	    *out++ = ch;
+	    cp++;
+	}
+    } else {
+	// Consume input, but produce no output
+	while ((ch = *cp) != (char)c->byte_array_stop.stop) {
+	    if (cp - (char *)b->data >= b->uncomp_size)
+		return -1;
+	    cp++;
+	}
+    }
+
+    *out_size = cp - (char *)(b->data + b->idx);
+    b->idx = cp - (char *)b->data + 1;
+
+    return 0;
+}
+
+int cram_byte_array_stop_decode_block(cram_slice *slice, cram_codec *c,
+				      cram_block *in, char *out_,
+				      int *out_size) {
+    cram_block *b;
+    cram_block *out = (cram_block *)out_;
+    char *cp, *out_cp, *cp_end;
+    char stop;
+
+    b = cram_get_block_by_id(slice, c->byte_array_stop.content_id);
+    if (!b)
+        return *out_size?-1:0;
+
+    if (b->idx >= b->uncomp_size)
+	return -1;
+    cp = (char *)b->data + b->idx;
+    cp_end = (char *)b->data + b->uncomp_size;
+    out_cp = (char *)BLOCK_END(out);
+
+    stop = c->byte_array_stop.stop;
+    if (cp_end - cp < out->alloc - out->byte) {
+	while (cp != cp_end && *cp != stop)
+	    *out_cp++ = *cp++;
+	BLOCK_SIZE(out) = out_cp - (char *)BLOCK_DATA(out);
+    } else {
+	char *cp_start;
+	for (cp_start = cp; cp != cp_end && *cp != stop; cp++)
+	    ;
+	BLOCK_APPEND(out, cp_start, cp - cp_start);
+	BLOCK_GROW(out, cp - cp_start);
+    }
+
+    *out_size = cp - (char *)(b->data + b->idx);
+    b->idx = cp - (char *)b->data + 1;
+
+    return 0;
+}
+
+void cram_byte_array_stop_decode_free(cram_codec *c) {
+    if (!c) return;
+
+    free(c);
+}
+
+cram_codec *cram_byte_array_stop_decode_init(char *data, int size,
+					     enum cram_external_type option,
+					     int version) {
+    cram_codec *c;
+    unsigned char *cp = (unsigned char *)data;
+
+    if (!(c = malloc(sizeof(*c))))
+	return NULL;
+
+    c->codec  = E_BYTE_ARRAY_STOP;
+    switch (option) {
+    case E_BYTE_ARRAY_BLOCK:
+        c->decode = cram_byte_array_stop_decode_block;
+	break;
+    case E_BYTE_ARRAY:
+        c->decode = cram_byte_array_stop_decode_char;
+	break;
+    default:
+        fprintf(stderr, "byte_array_stop codec only supports BYTE_ARRAYs.\n");
+        free(c);
+        return NULL;
+    }
+    c->free   = cram_byte_array_stop_decode_free;
+    
+    c->byte_array_stop.stop = *cp++;
+    if (CRAM_MAJOR_VERS(version) == 1) {
+	c->byte_array_stop.content_id = cp[0] + (cp[1]<<8) + (cp[2]<<16)
+	    + (cp[3]<<24);
+	cp += 4;
+    } else {
+	cp += itf8_get(cp, &c->byte_array_stop.content_id);
+    }
+
+    if ((char *)cp - data != size) {
+	fprintf(stderr, "Malformed byte_array_stop header stream\n");
+	free(c);
+	return NULL;
+    }
+
+    return c;
+}
+
+int cram_byte_array_stop_encode(cram_slice *slice, cram_codec *c,
+				char *in, int in_size) {
+    BLOCK_APPEND(c->out, in, in_size);
+    BLOCK_APPEND_CHAR(c->out, c->e_byte_array_stop.stop);
+    return 0;
+}
+
+void cram_byte_array_stop_encode_free(cram_codec *c) {
+    if (!c)
+	return;
+    free(c);
+}
+
+int cram_byte_array_stop_encode_store(cram_codec *c, cram_block *b,
+				      char *prefix, int version) {
+    int len = 0;
+    char buf[20], *cp = buf;
+
+    if (prefix) {
+	size_t l = strlen(prefix);
+	BLOCK_APPEND(b, prefix, l);
+	len += l;
+    }
+
+    cp += itf8_put(cp, c->codec);
+
+    if (CRAM_MAJOR_VERS(version) == 1) {
+	cp += itf8_put(cp, 5);
+	*cp++ = c->e_byte_array_stop.stop;
+	*cp++ = (c->e_byte_array_stop.content_id >>  0) & 0xff;
+	*cp++ = (c->e_byte_array_stop.content_id >>  8) & 0xff;
+	*cp++ = (c->e_byte_array_stop.content_id >> 16) & 0xff;
+	*cp++ = (c->e_byte_array_stop.content_id >> 24) & 0xff;
+    } else {
+	cp += itf8_put(cp, 1 + itf8_size(c->e_byte_array_stop.content_id));
+	*cp++ = c->e_byte_array_stop.stop;
+	cp += itf8_put(cp, c->e_byte_array_stop.content_id);
+    }
+
+    BLOCK_APPEND(b, buf, cp-buf);
+    len += cp-buf;
+
+    return len;
+}
+
+cram_codec *cram_byte_array_stop_encode_init(cram_stats *st,
+					     enum cram_external_type option,
+					     void *dat,
+					     int version) {
+    cram_codec *c;
+
+    c = malloc(sizeof(*c));
+    if (!c)
+	return NULL;
+    c->codec = E_BYTE_ARRAY_STOP;
+    c->free = cram_byte_array_stop_encode_free;
+    c->encode = cram_byte_array_stop_encode;
+    c->store = cram_byte_array_stop_encode_store;
+
+    c->e_byte_array_stop.stop = ((int *)dat)[0];
+    c->e_byte_array_stop.content_id = ((int *)dat)[1];
+
+    return c;
+}
+
+/*
+ * ---------------------------------------------------------------------------
+ */
+
+const char *cram_encoding2str(enum cram_encoding t) {
+    switch (t) {
+    case E_NULL:            return "NULL";
+    case E_EXTERNAL:        return "EXTERNAL";
+    case E_GOLOMB:          return "GOLOMB";
+    case E_HUFFMAN:         return "HUFFMAN";
+    case E_BYTE_ARRAY_LEN:  return "BYTE_ARRAY_LEN";
+    case E_BYTE_ARRAY_STOP: return "BYTE_ARRAY_STOP";
+    case E_BETA:            return "BETA";
+    case E_SUBEXP:          return "SUBEXP";
+    case E_GOLOMB_RICE:     return "GOLOMB_RICE";
+    case E_GAMMA:           return "GAMMA";
+    case E_NUM_CODECS:
+    default:                return "?";
+    }
+}
+
+static cram_codec *(*decode_init[])(char *data,
+				    int size,
+				    enum cram_external_type option,
+				    int version) = {
+    NULL,
+    cram_external_decode_init,
+    NULL,
+    cram_huffman_decode_init,
+    cram_byte_array_len_decode_init,
+    cram_byte_array_stop_decode_init,
+    cram_beta_decode_init,
+    cram_subexp_decode_init,
+    NULL,
+    cram_gamma_decode_init,
+};
+
+cram_codec *cram_decoder_init(enum cram_encoding codec,
+			      char *data, int size,
+			      enum cram_external_type option,
+			      int version) {
+    if (codec >= E_NULL && codec < E_NUM_CODECS && decode_init[codec]) {
+	return decode_init[codec](data, size, option, version);
+    } else {
+	fprintf(stderr, "Unimplemented codec of type %s\n", cram_encoding2str(codec));
+	return NULL;
+    }
+}
+
+static cram_codec *(*encode_init[])(cram_stats *stx,
+				    enum cram_external_type option,
+				    void *opt,
+				    int version) = {
+    NULL,
+    cram_external_encode_init,
+    NULL,
+    cram_huffman_encode_init,
+    cram_byte_array_len_encode_init,
+    cram_byte_array_stop_encode_init,
+    cram_beta_encode_init,
+    NULL, //cram_subexp_encode_init,
+    NULL,
+    NULL, //cram_gamma_encode_init,
+};
+
+cram_codec *cram_encoder_init(enum cram_encoding codec,
+			      cram_stats *st,
+			      enum cram_external_type option,
+			      void *dat,
+			      int version) {
+    if (st && !st->nvals)
+	return NULL;
+
+    if (encode_init[codec]) {
+	cram_codec *r;
+	if ((r = encode_init[codec](st, option, dat, version)))
+	    r->out = NULL;
+	return r;
+    } else {
+	fprintf(stderr, "Unimplemented codec of type %s\n", cram_encoding2str(codec));
+	abort();
+    }
+}
+
+/*
+ * Returns the content_id used by this codec, also in id2 if byte_array_len.
+ * Returns -1 for the CORE block and -2 for unneeded.
+ * id2 is only filled out for BYTE_ARRAY_LEN which uses 2 codecs.
+ */
+int cram_codec_to_id(cram_codec *c, int *id2) {
+    int bnum1, bnum2 = -2;
+
+    switch (c->codec) {
+    case E_HUFFMAN:
+	bnum1 = c->huffman.ncodes == 1 ? -2 : -1;
+	break;
+    case E_GOLOMB:
+    case E_BETA:
+    case E_SUBEXP:
+    case E_GOLOMB_RICE:
+    case E_GAMMA:
+	bnum1 = -1;
+	break;
+    case E_EXTERNAL:
+	bnum1 = c->external.content_id;
+	break;
+    case E_BYTE_ARRAY_LEN:
+	bnum1 = cram_codec_to_id(c->byte_array_len.len_codec, NULL);
+	bnum2 = cram_codec_to_id(c->byte_array_len.val_codec, NULL);
+	break;
+    case E_BYTE_ARRAY_STOP:
+	bnum1 = c->byte_array_stop.content_id;
+	break;
+    case E_NULL:
+	bnum1 = -2;
+	break;
+    default:
+	fprintf(stderr, "Unknown codec type %d\n", c->codec);
+	bnum1 = -1;
+    }
+
+    if (id2)
+	*id2 = bnum2;
+    return bnum1;
+}
+
+
+/*
+ * cram_codec structures are specialised for decoding or encoding.
+ * Unfortunately this makes turning a decoder into an encoder (such as
+ * when transcoding files) problematic.
+ *
+ * This function converts a cram decoder codec into an encoder version
+ * in-place (ie it modifiers the codec itself).
+ *
+ * Returns 0 on success;
+ *        -1 on failure.
+ */
+int cram_codec_decoder2encoder(cram_fd *fd, cram_codec *c) {
+    int j;
+
+    switch (c->codec) {
+    case E_EXTERNAL:
+	// shares struct with decode
+	c->free = cram_external_encode_free;
+	c->store = cram_external_encode_store;
+	if (c->decode == cram_external_decode_int)
+	    c->encode = cram_external_encode_int;
+	else if (c->decode == cram_external_decode_char)
+	    c->encode = cram_external_encode_char;
+	else
+	    return -1;
+	break;
+
+    case E_HUFFMAN: {
+	// New structure, so switch.
+	// FIXME: we huffman and e_huffman structs amended, we could
+	// unify this.
+	cram_codec *t = malloc(sizeof(*t));
+	t->codec = E_HUFFMAN;
+	t->free = cram_huffman_encode_free;
+	t->store = cram_huffman_encode_store;
+	t->e_huffman.codes = c->huffman.codes;
+	t->e_huffman.nvals = c->huffman.ncodes;
+	for (j = 0; j < t->e_huffman.nvals; j++) {
+	    int32_t sym = t->e_huffman.codes[j].symbol;
+	    if (sym >= -1 && sym < MAX_HUFF)
+		t->e_huffman.val2code[sym+1] = j;
+	}
+
+	if (c->decode == cram_huffman_decode_char0)
+	    t->encode = cram_huffman_encode_char0;
+	else if (c->decode == cram_huffman_decode_char)
+	    t->encode = cram_huffman_encode_char;
+	else if (c->decode == cram_huffman_decode_int0)
+	    t->encode = cram_huffman_encode_int0;
+	else if (c->decode == cram_huffman_decode_int)
+	    t->encode = cram_huffman_encode_int;
+	else {
+	    free(t);
+	    return -1;
+	}
+	*c = *t;
+	free(t);
+	break;
+    }
+
+    case E_BETA:
+	// shares struct with decode
+	c->free = cram_beta_encode_free;
+	c->store = cram_beta_encode_store;
+	if (c->decode == cram_beta_decode_int)
+	    c->encode = cram_beta_encode_int;
+	else if (c->decode == cram_beta_decode_char)
+	    c->encode = cram_beta_encode_char;
+	else
+	    return -1;
+	break;
+
+    case E_BYTE_ARRAY_LEN: {
+	cram_codec *t = malloc(sizeof(*t));
+	t->codec = E_BYTE_ARRAY_LEN;
+	t->free   = cram_byte_array_len_encode_free;
+	t->store  = cram_byte_array_len_encode_store;
+	t->encode = cram_byte_array_len_encode;
+	t->e_byte_array_len.len_codec = c->byte_array_len.len_codec;
+	t->e_byte_array_len.val_codec = c->byte_array_len.val_codec;
+	if (cram_codec_decoder2encoder(fd, t->e_byte_array_len.len_codec) == -1 ||
+	    cram_codec_decoder2encoder(fd, t->e_byte_array_len.val_codec) == -1) {
+	    t->free(t);
+	    return -1;
+	}
+
+	// {len,val}_{encoding,dat} are undefined, but unused.
+	// Leaving them unset here means we can test that assertion.
+	*c = *t;
+	free(t);
+	break;
+    }
+
+    case E_BYTE_ARRAY_STOP:
+	// shares struct with decode
+	c->free   = cram_byte_array_stop_encode_free;
+	c->store  = cram_byte_array_stop_encode_store;
+	c->encode = cram_byte_array_stop_encode;
+	break;
+
+    default:
+	return -1;
+    }
+
+    return 0;
+}
diff --git a/htslib/cram/cram_codecs.h b/htslib/cram/cram_codecs.h
new file mode 100644
index 0000000..2c13c7e
--- /dev/null
+++ b/htslib/cram/cram_codecs.h
@@ -0,0 +1,194 @@
+/*
+Copyright (c) 2012-2013 Genome Research Ltd.
+Author: James Bonfield <jkb at sanger.ac.uk>
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+Institute nor the names of its contributors may be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+#ifndef _CRAM_ENCODINGS_H_
+#define _CRAM_ENCODINGS_H_
+
+#include <inttypes.h>
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+struct cram_codec;
+
+/*
+ * Slow but simple huffman decoder to start with.
+ * Read a bit at a time, keeping track of {length, value}
+ * eg. 1 1 0 1 => {1,1},  {2,3}, {3,6}, {4,13}
+ *
+ * Keep track of this through the huffman code table.
+ * For fast scanning we have an index of where the first code of length X
+ * appears.
+ */
+typedef struct {
+    int32_t symbol;
+    int32_t p; // next code start value, minus index to codes[]
+    int32_t code;
+    int32_t len;
+} cram_huffman_code;
+
+typedef struct {
+    int ncodes;
+    cram_huffman_code *codes;
+} cram_huffman_decoder;
+
+#define MAX_HUFF 128
+typedef struct {
+    cram_huffman_code *codes;
+    int nvals;
+    int val2code[MAX_HUFF+1]; // value to code lookup for small values
+} cram_huffman_encoder;
+
+typedef struct {
+    int32_t offset;
+    int32_t nbits;
+} cram_beta_decoder;
+
+typedef struct {
+    int32_t offset;
+} cram_gamma_decoder;
+
+typedef struct {
+    int32_t offset;
+    int32_t k;
+} cram_subexp_decoder;
+
+typedef struct {
+    int32_t content_id;
+    enum cram_external_type type;
+} cram_external_decoder;
+
+typedef struct {
+    struct cram_codec *len_codec;
+    struct cram_codec *val_codec;
+} cram_byte_array_len_decoder;
+
+typedef struct {
+    unsigned char stop;
+    int32_t content_id;
+} cram_byte_array_stop_decoder;
+
+typedef struct {
+    enum cram_encoding len_encoding;
+    enum cram_encoding val_encoding;
+    void *len_dat;
+    void *val_dat;
+    struct cram_codec *len_codec;
+    struct cram_codec *val_codec;
+} cram_byte_array_len_encoder;
+
+/*
+ * A generic codec structure.
+ */
+typedef struct cram_codec {
+    enum cram_encoding codec;
+    cram_block *out;
+    void (*free)(struct cram_codec *codec);
+    int (*decode)(cram_slice *slice, struct cram_codec *codec,
+		  cram_block *in, char *out, int *out_size);
+    int (*encode)(cram_slice *slice, struct cram_codec *codec,
+		  char *in, int in_size);
+    int (*store)(struct cram_codec *codec, cram_block *b, char *prefix,
+		 int version);
+    union {
+	cram_huffman_decoder         huffman;
+	cram_external_decoder        external;
+	cram_beta_decoder            beta;
+	cram_gamma_decoder           gamma;
+	cram_subexp_decoder          subexp;
+	cram_byte_array_len_decoder  byte_array_len;
+	cram_byte_array_stop_decoder byte_array_stop;
+
+	cram_huffman_encoder         e_huffman;
+	cram_external_decoder        e_external;
+	cram_byte_array_stop_decoder e_byte_array_stop;
+	cram_byte_array_len_encoder  e_byte_array_len;
+	cram_beta_decoder            e_beta;
+    };
+} cram_codec;
+
+const char *cram_encoding2str(enum cram_encoding t);
+
+cram_codec *cram_decoder_init(enum cram_encoding codec, char *data, int size,
+			      enum cram_external_type option,
+			      int version);
+cram_codec *cram_encoder_init(enum cram_encoding codec, cram_stats *st,
+			      enum cram_external_type option, void *dat,
+			      int version);
+
+//int cram_decode(void *codes, char *in, int in_size, char *out, int *out_size);
+//void cram_decoder_free(void *codes);
+
+//#define GET_BIT_MSB(b,v) (void)(v<<=1, v|=(b->data[b->byte] >> b->bit)&1, (--b->bit == -1) && (b->bit = 7, b->byte++))
+
+#define GET_BIT_MSB(b,v) (void)(v<<=1, v|=(b->data[b->byte] >> b->bit)&1, b->byte += (--b->bit<0), b->bit&=7)
+
+/*
+ * Check that enough bits are left in a block to satisy a bit-based decoder.
+ * Return  0 if there are enough
+ *         1 if not.
+ */
+
+static inline int cram_not_enough_bits(cram_block *blk, int nbits) {
+    if (nbits < 0 ||
+	(blk->byte >= blk->uncomp_size && nbits > 0) ||
+	(blk->uncomp_size - blk->byte <= INT32_MAX / 8 + 1 &&
+	 (blk->uncomp_size - blk->byte) * 8 + blk->bit - 7 < nbits)) {
+        return 1;
+    }
+    return 0;
+}
+
+/*
+ * Returns the content_id used by this codec, also in id2 if byte_array_len.
+ * Returns -1 for the CORE block and -2 for unneeded.
+ * id2 is only filled out for BYTE_ARRAY_LEN which uses 2 codecs.
+ */
+int cram_codec_to_id(cram_codec *c, int *id2);
+
+/*
+ * cram_codec structures are specialised for decoding or encoding.
+ * Unfortunately this makes turning a decoder into an encoder (such as
+ * when transcoding files) problematic.
+ *
+ * This function converts a cram decoder codec into an encoder version
+ * in-place (ie it modifiers the codec itself).
+ *
+ * Returns 0 on success;
+ *        -1 on failure.
+ */
+int cram_codec_decoder2encoder(cram_fd *fd, cram_codec *c);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _CRAM_ENCODINGS_H_ */
diff --git a/htslib/cram/cram_decode.c b/htslib/cram/cram_decode.c
new file mode 100644
index 0000000..7a3b5fc
--- /dev/null
+++ b/htslib/cram/cram_decode.c
@@ -0,0 +1,3159 @@
+/*
+Copyright (c) 2012-2014 Genome Research Ltd.
+Author: James Bonfield <jkb at sanger.ac.uk>
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+Institute nor the names of its contributors may be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+/*
+ * - In-memory decoding of CRAM data structures.
+ * - Iterator for reading CRAM record by record.
+ */
+
+#include <config.h>
+
+#include <stdio.h>
+#include <errno.h>
+#include <assert.h>
+#include <stdlib.h>
+#include <string.h>
+#include <zlib.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <math.h>
+#include <ctype.h>
+
+#include "cram/cram.h"
+#include "cram/os.h"
+#include "htslib/hts.h"
+
+//Whether CIGAR has just M or uses = and X to indicate match and mismatch
+//#define USE_X
+
+/* ----------------------------------------------------------------------
+ * CRAM compression headers
+ */
+
+/*
+ * Decodes the Tag Dictionary record in the preservation map
+ * Updates the cram compression header.
+ * 
+ * Returns number of bytes decoded on success
+ *        -1 on failure
+ */
+int cram_decode_TD(char *cp, const char *endp, cram_block_compression_hdr *h) {
+    char *op = cp;
+    unsigned char *dat;
+    cram_block *b;
+    int32_t blk_size = 0;
+    int nTL, i, sz;
+
+    if (!(b = cram_new_block(0, 0)))
+	return -1;
+
+    /* Decode */
+    cp += safe_itf8_get(cp, endp, &blk_size);
+    if (!blk_size) {
+	h->nTL = 0;
+	h->TL = NULL;
+	cram_free_block(b);
+	return cp - op;
+    }
+
+    if (blk_size < 0 || endp - cp < blk_size) {
+        cram_free_block(b);
+	return -1;
+    }
+
+    BLOCK_APPEND(b, cp, blk_size);
+    cp += blk_size;
+    sz = cp - op;
+    // Force nul termination if missing
+    if (BLOCK_DATA(b)[BLOCK_SIZE(b)-1])
+	BLOCK_APPEND_CHAR(b, '\0');
+
+    /* Set up TL lookup table */
+    dat = BLOCK_DATA(b);
+
+    // Count
+    for (nTL = i = 0; i < BLOCK_SIZE(b); i++) {
+	nTL++;
+	while (dat[i])
+	    i++;
+    }
+
+    // Copy
+    h->nTL = nTL;
+    if (!(h->TL = calloc(h->nTL, sizeof(unsigned char *)))) {
+        cram_free_block(b);
+        return -1;
+    }
+    for (nTL = i = 0; i < BLOCK_SIZE(b); i++) {
+	h->TL[nTL++] = &dat[i];
+	while (dat[i])
+	    i++;
+    }
+    h->TD_blk = b;
+    
+    return sz;
+}
+
+/*
+ * Decodes a CRAM block compression header.
+ * Returns header ptr on success
+ *         NULL on failure
+ */
+cram_block_compression_hdr *cram_decode_compression_header(cram_fd *fd,
+							   cram_block *b) {
+    char *cp, *endp, *cp_copy;
+    cram_block_compression_hdr *hdr = calloc(1, sizeof(*hdr));
+    int i;
+    int32_t map_size = 0, map_count = 0;
+
+    if (!hdr)
+	return NULL;
+
+    if (b->method != RAW) {
+	if (cram_uncompress_block(b)) {
+	    free(hdr);
+	    return NULL;
+	}
+    }
+
+    cp = (char *)b->data;
+    endp = cp + b->uncomp_size;
+
+    if (CRAM_MAJOR_VERS(fd->version) == 1) {
+	cp += safe_itf8_get(cp, endp, &hdr->ref_seq_id);
+	cp += safe_itf8_get(cp, endp, &hdr->ref_seq_start);
+	cp += safe_itf8_get(cp, endp, &hdr->ref_seq_span);
+	cp += safe_itf8_get(cp, endp, &hdr->num_records);
+	cp += safe_itf8_get(cp, endp, &hdr->num_landmarks);
+	if (!(hdr->landmark = malloc(hdr->num_landmarks * sizeof(int32_t)))) {
+	    free(hdr);
+	    return NULL;
+	}
+	for (i = 0; i < hdr->num_landmarks; i++) {
+	    cp += safe_itf8_get(cp, endp, &hdr->landmark[i]);
+	}
+    }
+
+    hdr->preservation_map = kh_init(map);
+
+    memset(hdr->rec_encoding_map, 0,
+	   CRAM_MAP_HASH * sizeof(hdr->rec_encoding_map[0]));
+    memset(hdr->tag_encoding_map, 0,
+	   CRAM_MAP_HASH * sizeof(hdr->tag_encoding_map[0]));
+
+    if (!hdr->preservation_map) {
+	cram_free_compression_header(hdr);
+	return NULL;
+    }
+
+    /* Initialise defaults for preservation map */
+    hdr->mapped_qs_included = 0;
+    hdr->unmapped_qs_included = 0;
+    hdr->unmapped_placed = 0;
+    hdr->qs_included = 0;
+    hdr->read_names_included = 0;
+    hdr->AP_delta = 1;
+    memcpy(hdr->substitution_matrix, "CGTNAGTNACTNACGNACGT", 20);
+
+    /* Preservation map */
+    cp += safe_itf8_get(cp, endp, &map_size); cp_copy = cp;
+    cp += safe_itf8_get(cp, endp, &map_count);
+    for (i = 0; i < map_count; i++) {
+	pmap_t hd;
+	khint_t k;
+	int r;
+
+	if (endp - cp < 2) {
+	    cram_free_compression_header(hdr);
+	    return NULL;
+	}
+	cp += 2;
+	switch(CRAM_KEY(cp[-2],cp[-1])) {
+	case CRAM_KEY('M','I'):
+	    hd.i = *cp++;
+	    k = kh_put(map, hdr->preservation_map, "MI", &r);
+	    if (-1 == r) {
+		cram_free_compression_header(hdr);
+                return NULL;
+            }
+
+	    kh_val(hdr->preservation_map, k) = hd;
+	    hdr->mapped_qs_included = hd.i;
+	    break;
+
+	case CRAM_KEY('U','I'):
+	    hd.i = *cp++;
+	    k = kh_put(map, hdr->preservation_map, "UI", &r);
+	    if (-1 == r) {
+		cram_free_compression_header(hdr);
+                return NULL;
+            }
+
+	    kh_val(hdr->preservation_map, k) = hd;
+	    hdr->unmapped_qs_included = hd.i;
+	    break;
+
+	case CRAM_KEY('P','I'):
+	    hd.i = *cp++;
+	    k = kh_put(map, hdr->preservation_map, "PI", &r);
+	    if (-1 == r) {
+		cram_free_compression_header(hdr);
+                return NULL;
+            }
+
+	    kh_val(hdr->preservation_map, k) = hd;
+	    hdr->unmapped_placed = hd.i;
+	    break;
+
+	case CRAM_KEY('R','N'):
+	    hd.i = *cp++;
+	    k = kh_put(map, hdr->preservation_map, "RN", &r);
+	    if (-1 == r) {
+		cram_free_compression_header(hdr);
+                return NULL;
+            }
+
+	    kh_val(hdr->preservation_map, k) = hd;
+	    hdr->read_names_included = hd.i;
+	    break;
+
+	case CRAM_KEY('A','P'):
+	    hd.i = *cp++;
+	    k = kh_put(map, hdr->preservation_map, "AP", &r);
+	    if (-1 == r) {
+		cram_free_compression_header(hdr);
+                return NULL;
+            }
+
+	    kh_val(hdr->preservation_map, k) = hd;
+	    hdr->AP_delta = hd.i;
+	    break;
+
+	case CRAM_KEY('R','R'):
+	    hd.i = *cp++;
+	    k = kh_put(map, hdr->preservation_map, "RR", &r);
+	    if (-1 == r) {
+		cram_free_compression_header(hdr);
+                return NULL;
+            }
+
+	    kh_val(hdr->preservation_map, k) = hd;
+	    fd->no_ref = !hd.i;
+	    break;
+
+	case CRAM_KEY('S','M'):
+	    if (endp - cp < 5) {
+	        cram_free_compression_header(hdr);
+		return NULL;
+	    }
+	    hdr->substitution_matrix[0][(cp[0]>>6)&3] = 'C';
+	    hdr->substitution_matrix[0][(cp[0]>>4)&3] = 'G';
+	    hdr->substitution_matrix[0][(cp[0]>>2)&3] = 'T';
+	    hdr->substitution_matrix[0][(cp[0]>>0)&3] = 'N';
+
+	    hdr->substitution_matrix[1][(cp[1]>>6)&3] = 'A';
+	    hdr->substitution_matrix[1][(cp[1]>>4)&3] = 'G';
+	    hdr->substitution_matrix[1][(cp[1]>>2)&3] = 'T';
+	    hdr->substitution_matrix[1][(cp[1]>>0)&3] = 'N';
+
+	    hdr->substitution_matrix[2][(cp[2]>>6)&3] = 'A';
+	    hdr->substitution_matrix[2][(cp[2]>>4)&3] = 'C';
+	    hdr->substitution_matrix[2][(cp[2]>>2)&3] = 'T';
+	    hdr->substitution_matrix[2][(cp[2]>>0)&3] = 'N';
+
+	    hdr->substitution_matrix[3][(cp[3]>>6)&3] = 'A';
+	    hdr->substitution_matrix[3][(cp[3]>>4)&3] = 'C';
+	    hdr->substitution_matrix[3][(cp[3]>>2)&3] = 'G';
+	    hdr->substitution_matrix[3][(cp[3]>>0)&3] = 'N';
+
+	    hdr->substitution_matrix[4][(cp[4]>>6)&3] = 'A';
+	    hdr->substitution_matrix[4][(cp[4]>>4)&3] = 'C';
+	    hdr->substitution_matrix[4][(cp[4]>>2)&3] = 'G';
+	    hdr->substitution_matrix[4][(cp[4]>>0)&3] = 'T';
+
+	    hd.p = cp;
+	    cp += 5;
+
+	    k = kh_put(map, hdr->preservation_map, "SM", &r);
+	    if (-1 == r) {
+		cram_free_compression_header(hdr);
+		return NULL;
+	    }
+	    kh_val(hdr->preservation_map, k) = hd;
+	    break;
+
+	case CRAM_KEY('T','D'): {
+	    int sz = cram_decode_TD(cp, endp, hdr); // tag dictionary
+	    if (sz < 0) {
+		cram_free_compression_header(hdr);
+		return NULL;
+	    }
+
+	    hd.p = cp;
+	    cp += sz;
+
+	    k = kh_put(map, hdr->preservation_map, "TD", &r);
+	    if (-1 == r) {
+		cram_free_compression_header(hdr);
+		return NULL;
+	    }
+	    kh_val(hdr->preservation_map, k) = hd;
+	    break;
+	}
+
+	default:
+	    fprintf(stderr, "Unrecognised preservation map key %c%c\n",
+		    cp[-2], cp[-1]);
+	    // guess byte;
+	    cp++;
+	    break;
+	}
+    }
+    if (cp - cp_copy != map_size) {
+	cram_free_compression_header(hdr);
+	return NULL;
+    }
+
+    /* Record encoding map */
+    cp += safe_itf8_get(cp, endp, &map_size); cp_copy = cp;
+    cp += safe_itf8_get(cp, endp, &map_count);
+    for (i = 0; i < map_count; i++) {
+	char *key = cp;
+	int32_t encoding = E_NULL;
+	int32_t size = 0;
+	cram_map *m = malloc(sizeof(*m)); // FIXME: use pooled_alloc
+
+	if (!m || endp - cp < 4) {
+	    free(m);
+	    cram_free_compression_header(hdr);
+	    return NULL;
+	}
+
+	cp += 2;
+	cp += safe_itf8_get(cp, endp, &encoding);
+	cp += safe_itf8_get(cp, endp, &size);
+
+	// Fill out cram_map purely for cram_dump to dump out.
+	m->key = (key[0]<<8)|key[1];
+	m->encoding = encoding;
+	m->size     = size;
+	m->offset   = cp - (char *)b->data;
+	m->codec = NULL;
+
+	if (m->encoding == E_NULL)
+	    continue;
+
+	if (size < 0 || endp - cp < size) {
+	    free(m);
+	    cram_free_compression_header(hdr);
+	    return NULL;
+	}
+
+	//printf("%s codes for %.2s\n", cram_encoding2str(encoding), key);
+
+	/*
+	 * For CRAM1.0 CF and BF are Byte and not Int.
+	 * Practically speaking it makes no difference unless we have a
+	 * 1.0 format file that stores these in EXTERNAL as only then
+	 * does Byte vs Int matter.
+	 *
+	 * Neither this C code nor Java reference implementations did this,
+	 * so we gloss over it and treat them as int.
+	 */
+
+	if (key[0] == 'B' && key[1] == 'F') {
+	    if (!(hdr->codecs[DS_BF] = cram_decoder_init(encoding, cp, size,
+							 E_INT,
+							 fd->version))) {
+		cram_free_compression_header(hdr);
+		return NULL;
+	    }
+	} else if (key[0] == 'C' && key[1] == 'F') {
+	    if (!(hdr->codecs[DS_CF] = cram_decoder_init(encoding, cp, size,
+							 E_INT,
+							 fd->version))) {
+		cram_free_compression_header(hdr);
+		return NULL;
+	    }
+	} else if (key[0] == 'R' && key[1] == 'I') {
+	    if (!(hdr->codecs[DS_RI] = cram_decoder_init(encoding, cp, size,
+							 E_INT,
+							 fd->version))) {
+		cram_free_compression_header(hdr);
+		return NULL;
+	    }
+	} else if (key[0] == 'R' && key[1] == 'L') {
+	    if (!(hdr->codecs[DS_RL] = cram_decoder_init(encoding, cp, size,
+							 E_INT,
+							 fd->version))) {
+		cram_free_compression_header(hdr);
+		return NULL;
+	    }
+	} else if (key[0] == 'A' && key[1] == 'P') {
+	    if (!(hdr->codecs[DS_AP] = cram_decoder_init(encoding, cp, size,
+							 E_INT,
+							 fd->version))) {
+		cram_free_compression_header(hdr);
+		return NULL;
+	    }
+	} else if (key[0] == 'R' && key[1] == 'G') {
+	    if (!(hdr->codecs[DS_RG] = cram_decoder_init(encoding, cp, size,
+							 E_INT,
+							 fd->version))) {
+		cram_free_compression_header(hdr);
+		return NULL;
+	    }
+	} else if (key[0] == 'M' && key[1] == 'F') {
+	    if (!(hdr->codecs[DS_MF] = cram_decoder_init(encoding, cp, size,
+							 E_INT,
+							 fd->version))) {
+		cram_free_compression_header(hdr);
+		return NULL;
+	    }
+	} else if (key[0] == 'N' && key[1] == 'S') {
+	    if (!(hdr->codecs[DS_NS] = cram_decoder_init(encoding, cp, size,
+							 E_INT,
+							 fd->version))) {
+		cram_free_compression_header(hdr);
+		return NULL;
+	    }
+	} else if (key[0] == 'N' && key[1] == 'P') {
+	    if (!(hdr->codecs[DS_NP] = cram_decoder_init(encoding, cp, size,
+							 E_INT,
+							 fd->version))) {
+		cram_free_compression_header(hdr);
+		return NULL;
+	    }
+	} else if (key[0] == 'T' && key[1] == 'S') {
+	    if (!(hdr->codecs[DS_TS] = cram_decoder_init(encoding, cp, size,
+							 E_INT,
+							 fd->version))) {
+		cram_free_compression_header(hdr);
+		return NULL;
+	    }
+	} else if (key[0] == 'N' && key[1] == 'F') {
+	    if (!(hdr->codecs[DS_NF] = cram_decoder_init(encoding, cp, size,
+							 E_INT,
+							 fd->version))) {
+		cram_free_compression_header(hdr);
+		return NULL;
+	    }
+	} else if (key[0] == 'T' && key[1] == 'C') {
+	    if (!(hdr->codecs[DS_TC] = cram_decoder_init(encoding, cp, size,
+							 E_BYTE,
+							 fd->version))) {
+		cram_free_compression_header(hdr);
+		return NULL;
+	    }
+	} else if (key[0] == 'T' && key[1] == 'N') {
+	    if (!(hdr->codecs[DS_TN] = cram_decoder_init(encoding, cp, size,
+							 E_INT,
+							 fd->version))) {
+		cram_free_compression_header(hdr);
+		return NULL;
+	    }
+	} else if (key[0] == 'F' && key[1] == 'N') {
+	    if (!(hdr->codecs[DS_FN] = cram_decoder_init(encoding, cp, size,
+							 E_INT,
+							 fd->version))) {
+		cram_free_compression_header(hdr);
+		return NULL;
+	    }
+	} else if (key[0] == 'F' && key[1] == 'C') {
+	    if (!(hdr->codecs[DS_FC] = cram_decoder_init(encoding, cp, size,
+							 E_BYTE,
+							 fd->version))) {
+		cram_free_compression_header(hdr);
+		return NULL;
+	    }
+	} else if (key[0] == 'F' && key[1] == 'P') {
+	    if (!(hdr->codecs[DS_FP] = cram_decoder_init(encoding, cp, size,
+							 E_INT,
+							 fd->version))) {
+		cram_free_compression_header(hdr);
+		return NULL;
+	    }
+	} else if (key[0] == 'B' && key[1] == 'S') {
+	    if (!(hdr->codecs[DS_BS] = cram_decoder_init(encoding, cp, size,
+							 E_BYTE,
+							 fd->version))) {
+		cram_free_compression_header(hdr);
+		return NULL;
+	    }
+	} else if (key[0] == 'I' && key[1] == 'N') {
+	    if (!(hdr->codecs[DS_IN] = cram_decoder_init(encoding, cp, size,
+							 E_BYTE_ARRAY,
+							 fd->version))) {
+		cram_free_compression_header(hdr);
+		return NULL;
+	    }
+	} else if (key[0] == 'S' && key[1] == 'C') {
+	    if (!(hdr->codecs[DS_SC] = cram_decoder_init(encoding, cp, size,
+							 E_BYTE_ARRAY,
+							 fd->version))) {
+		cram_free_compression_header(hdr);
+		return NULL;
+	    }
+	} else if (key[0] == 'D' && key[1] == 'L') {
+	    if (!(hdr->codecs[DS_DL] = cram_decoder_init(encoding, cp, size,
+							 E_INT,
+							 fd->version))) {
+		cram_free_compression_header(hdr);
+		return NULL;
+	    }
+	} else if (key[0] == 'B' && key[1] == 'A') {
+	    if (!(hdr->codecs[DS_BA] = cram_decoder_init(encoding, cp, size,
+							 E_BYTE,
+							 fd->version))) {
+		cram_free_compression_header(hdr);
+		return NULL;
+	    }
+	} else if (key[0] == 'B' && key[1] == 'B') {
+	    if (!(hdr->codecs[DS_BB] = cram_decoder_init(encoding, cp, size,
+							 E_BYTE_ARRAY,
+							 fd->version))) {
+		cram_free_compression_header(hdr);
+		return NULL;
+	    }
+	} else if (key[0] == 'R' && key[1] == 'S') {
+	    if (!(hdr->codecs[DS_RS] = cram_decoder_init(encoding, cp, size,
+							 E_INT,
+							 fd->version))) {
+		cram_free_compression_header(hdr);
+		return NULL;
+	    }
+	} else if (key[0] == 'P' && key[1] == 'D') {
+	    if (!(hdr->codecs[DS_PD] = cram_decoder_init(encoding, cp, size,
+							 E_INT,
+							 fd->version))) {
+		cram_free_compression_header(hdr);
+		return NULL;
+	    }
+	} else if (key[0] == 'H' && key[1] == 'C') {
+	    if (!(hdr->codecs[DS_HC] = cram_decoder_init(encoding, cp, size,
+							 E_INT,
+							 fd->version))) {
+		cram_free_compression_header(hdr);
+		return NULL;
+	    }
+	} else if (key[0] == 'M' && key[1] == 'Q') {
+	    if (!(hdr->codecs[DS_MQ] = cram_decoder_init(encoding, cp, size,
+							 E_INT,
+							 fd->version))) {
+		cram_free_compression_header(hdr);
+		return NULL;
+	    }
+	} else if (key[0] == 'R' && key[1] == 'N') {
+	    if (!(hdr->codecs[DS_RN] = cram_decoder_init(encoding, cp, size,
+							 E_BYTE_ARRAY_BLOCK,
+							 fd->version))) {
+		cram_free_compression_header(hdr);
+		return NULL;
+	    }
+	} else if (key[0] == 'Q' && key[1] == 'S') {
+	    if (!(hdr->codecs[DS_QS] = cram_decoder_init(encoding, cp, size,
+							 E_BYTE,
+							 fd->version))) {
+		cram_free_compression_header(hdr);
+		return NULL;
+	    }
+	} else if (key[0] == 'Q' && key[1] == 'Q') {
+	    if (!(hdr->codecs[DS_QQ] = cram_decoder_init(encoding, cp, size,
+							 E_BYTE_ARRAY,
+							 fd->version))) {
+		cram_free_compression_header(hdr);
+		return NULL;
+	    }
+	} else if (key[0] == 'T' && key[1] == 'L') {
+	    if (!(hdr->codecs[DS_TL] = cram_decoder_init(encoding, cp, size,
+							 E_INT,
+							 fd->version))) {
+		cram_free_compression_header(hdr);
+		return NULL;
+	    }
+	} else if (key[0] == 'T' && key[1] == 'M') {
+	} else if (key[0] == 'T' && key[1] == 'V') {
+	} else
+	    fprintf(stderr, "Unrecognised key: %.2s\n", key);
+
+	cp += size;
+
+	m->next = hdr->rec_encoding_map[CRAM_MAP(key[0], key[1])];
+	hdr->rec_encoding_map[CRAM_MAP(key[0], key[1])] = m;
+    }
+    if (cp - cp_copy != map_size) {
+	cram_free_compression_header(hdr);
+	return NULL;
+    }
+
+    /* Tag encoding map */
+    cp += safe_itf8_get(cp, endp, &map_size); cp_copy = cp;
+    cp += safe_itf8_get(cp, endp, &map_count);
+    for (i = 0; i < map_count; i++) {
+	int32_t encoding = E_NULL;
+	int32_t size = 0;
+	cram_map *m = malloc(sizeof(*m)); // FIXME: use pooled_alloc
+	char *key;
+
+	if (!m || endp - cp < 6) {
+	    free(m);
+	    cram_free_compression_header(hdr);
+	    return NULL;
+	}
+
+	key = cp + 1;
+	m->key = (key[0]<<16)|(key[1]<<8)|key[2];
+
+	cp += 4; // Strictly ITF8, but this suffices
+	cp += safe_itf8_get(cp, endp, &encoding);
+	cp += safe_itf8_get(cp, endp, &size);
+
+	m->encoding = encoding;
+	m->size     = size;
+	m->offset   = cp - (char *)b->data;
+	if (size < 0 || endp - cp < size ||
+	    !(m->codec = cram_decoder_init(encoding, cp, size,
+					   E_BYTE_ARRAY_BLOCK, fd->version))) {
+	    cram_free_compression_header(hdr);
+	    free(m);
+	    return NULL;
+	}
+	
+	cp += size;
+
+	m->next = hdr->tag_encoding_map[CRAM_MAP(key[0],key[1])];
+	hdr->tag_encoding_map[CRAM_MAP(key[0],key[1])] = m;
+    }
+    if (cp - cp_copy != map_size) {
+	cram_free_compression_header(hdr);
+	return NULL;
+    }
+
+    return hdr;
+}
+
+/*
+ * Note we also need to scan through the record encoding map to
+ * see which data series share the same block, either external or
+ * CORE. For example if we need the BF data series but MQ and CF
+ * are also encoded in the same block then we need to add those in
+ * as a dependency in order to correctly decode BF.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int cram_dependent_data_series(cram_fd *fd,
+			       cram_block_compression_hdr *hdr,
+			       cram_slice *s) {
+    int *block_used;
+    int core_used = 0;
+    int i;
+    static int i_to_id[] = {
+	DS_BF, DS_AP, DS_FP, DS_RL, DS_DL, DS_NF, DS_BA, DS_QS,
+	DS_FC, DS_FN, DS_BS, DS_IN, DS_RG, DS_MQ, DS_TL, DS_RN,
+	DS_NS, DS_NP, DS_TS, DS_MF, DS_CF, DS_RI, DS_RS, DS_PD,
+	DS_HC, DS_SC, DS_BB, DS_QQ,
+    };
+    uint32_t orig_ds;
+
+    /*
+     * Set the data_series bit field based on fd->required_fields
+     * contents.
+     */
+    if (fd->required_fields && fd->required_fields != INT_MAX) {
+	hdr->data_series = 0;
+
+	if (fd->required_fields & SAM_QNAME)
+	    hdr->data_series |= CRAM_RN;
+
+	if (fd->required_fields & SAM_FLAG)
+	    hdr->data_series |= CRAM_BF;
+
+	if (fd->required_fields & SAM_RNAME)
+	    hdr->data_series |= CRAM_RI | CRAM_BF;
+
+	if (fd->required_fields & SAM_POS)
+	    hdr->data_series |= CRAM_AP | CRAM_BF;
+
+	if (fd->required_fields & SAM_MAPQ)
+	    hdr->data_series |= CRAM_MQ;
+
+	if (fd->required_fields & SAM_CIGAR)
+	    hdr->data_series |= CRAM_CIGAR;
+
+	if (fd->required_fields & SAM_RNEXT)
+	    hdr->data_series |= CRAM_CF | CRAM_NF | CRAM_RI | CRAM_NS |CRAM_BF;
+
+	if (fd->required_fields & SAM_PNEXT)
+	    hdr->data_series |= CRAM_CF | CRAM_NF | CRAM_AP | CRAM_NP | CRAM_BF;
+
+	if (fd->required_fields & SAM_TLEN)
+	    hdr->data_series |= CRAM_CF | CRAM_NF | CRAM_AP | CRAM_TS |
+		CRAM_BF | CRAM_MF | CRAM_RI | CRAM_CIGAR;
+
+	if (fd->required_fields & SAM_SEQ)
+	    hdr->data_series |= CRAM_SEQ;
+
+	if (!(fd->required_fields & SAM_AUX))
+	    // No easy way to get MD/NM without other tags at present
+	    fd->decode_md = 0;
+
+	if (fd->required_fields & SAM_QUAL)
+	    hdr->data_series |= CRAM_QUAL;
+
+	if (fd->required_fields & SAM_AUX)
+	    hdr->data_series |= CRAM_RG | CRAM_TL | CRAM_aux;
+
+	if (fd->required_fields & SAM_RGAUX)
+	    hdr->data_series |= CRAM_RG | CRAM_BF;
+
+	// Always uncompress CORE block
+	if (cram_uncompress_block(s->block[0]))
+	    return -1;
+    } else {
+	hdr->data_series = CRAM_ALL;
+
+	for (i = 0; i < s->hdr->num_blocks; i++) {
+	    if (cram_uncompress_block(s->block[i]))
+		return -1;
+	}
+
+	return 0;
+    }
+
+    block_used = calloc(s->hdr->num_blocks+1, sizeof(int));
+    if (!block_used)
+	return -1;
+
+    do {
+	/*
+	 * Also set data_series based on code prerequisites. Eg if we need
+	 * CRAM_QS then we also need to know CRAM_RL so we know how long it
+	 * is, or if we need FC/FP then we also need FN (number of features).
+	 *
+	 * It's not reciprocal though. We may be needing to decode FN
+	 * but have no need to decode FC, FP and cigar ops.
+	 */
+	if (hdr->data_series & CRAM_RS)    hdr->data_series |= CRAM_FC|CRAM_FP;
+	if (hdr->data_series & CRAM_PD)    hdr->data_series |= CRAM_FC|CRAM_FP;
+	if (hdr->data_series & CRAM_HC)    hdr->data_series |= CRAM_FC|CRAM_FP;
+	if (hdr->data_series & CRAM_QS)    hdr->data_series |= CRAM_FC|CRAM_FP;
+	if (hdr->data_series & CRAM_IN)    hdr->data_series |= CRAM_FC|CRAM_FP;
+	if (hdr->data_series & CRAM_SC)    hdr->data_series |= CRAM_FC|CRAM_FP;
+	if (hdr->data_series & CRAM_BS)    hdr->data_series |= CRAM_FC|CRAM_FP;
+	if (hdr->data_series & CRAM_DL)    hdr->data_series |= CRAM_FC|CRAM_FP;
+	if (hdr->data_series & CRAM_BA)    hdr->data_series |= CRAM_FC|CRAM_FP;
+	if (hdr->data_series & CRAM_BB)    hdr->data_series |= CRAM_FC|CRAM_FP;
+	if (hdr->data_series & CRAM_QQ)    hdr->data_series |= CRAM_FC|CRAM_FP;
+
+	// cram_decode_seq() needs seq[] array
+	if (hdr->data_series & (CRAM_SEQ|CRAM_CIGAR)) hdr->data_series |= CRAM_RL;
+
+	if (hdr->data_series & CRAM_FP)    hdr->data_series |= CRAM_FC;
+	if (hdr->data_series & CRAM_FC)    hdr->data_series |= CRAM_FN;
+	if (hdr->data_series & CRAM_aux)   hdr->data_series |= CRAM_TL;
+	if (hdr->data_series & CRAM_MF)    hdr->data_series |= CRAM_CF;
+	if (hdr->data_series & CRAM_MQ)    hdr->data_series |= CRAM_BF;
+	if (hdr->data_series & CRAM_BS)    hdr->data_series |= CRAM_RI;
+	if (hdr->data_series & (CRAM_MF |CRAM_NS |CRAM_NP |CRAM_TS |CRAM_NF))
+	    hdr->data_series |= CRAM_CF;
+	if (!hdr->read_names_included && hdr->data_series & CRAM_RN)
+	    hdr->data_series |= CRAM_CF | CRAM_NF;
+	if (hdr->data_series & (CRAM_BA | CRAM_QS | CRAM_BB | CRAM_QQ))
+	    hdr->data_series |= CRAM_BF | CRAM_CF | CRAM_RL;
+
+	orig_ds = hdr->data_series;
+
+	// Find which blocks are in use.
+	for (i = 0; i < sizeof(i_to_id)/sizeof(*i_to_id); i++) {
+	    int bnum1, bnum2, j;
+	    cram_codec *c = hdr->codecs[i_to_id[i]];
+
+	    if (!(hdr->data_series & (1<<i)))
+		continue;
+
+	    if (!c)
+		continue;
+
+	    bnum1 = cram_codec_to_id(c, &bnum2);
+
+	    for (;;) {
+		switch (bnum1) {
+		case -2:
+		    break;
+
+		case -1:
+		    core_used = 1;
+		    break;
+
+		default:
+		    for (j = 0; j < s->hdr->num_blocks; j++) {
+			if (s->block[j]->content_type == EXTERNAL &&
+			    s->block[j]->content_id == bnum1) {
+			    block_used[j] = 1;
+			    if (cram_uncompress_block(s->block[j])) {
+				free(block_used);
+				return -1;
+			    }
+			}
+		    }
+		    break;
+		}
+
+		if (bnum2 == -2 || bnum1 == bnum2)
+		    break;
+
+		bnum1 = bnum2; // 2nd pass
+	    }
+	}
+
+	// Tags too
+	if ((fd->required_fields & SAM_AUX) ||
+	    (hdr->data_series & CRAM_aux)) {
+	    for (i = 0; i < CRAM_MAP_HASH; i++) {
+		int bnum1, bnum2, j;
+		cram_map *m = hdr->tag_encoding_map[i];
+
+		while (m) {
+		    cram_codec *c = m->codec;
+		    if (!c)
+			continue;
+
+		    bnum1 = cram_codec_to_id(c, &bnum2);
+
+		    for (;;) {
+			switch (bnum1) {
+			case -2:
+			    break;
+
+			case -1:
+			    core_used = 1;
+			    break;
+
+			default:
+			    for (j = 0; j < s->hdr->num_blocks; j++) {
+				if (s->block[j]->content_type == EXTERNAL &&
+				    s->block[j]->content_id == bnum1) {
+				    block_used[j] = 1;
+				    if (cram_uncompress_block(s->block[j])) {
+					free(block_used);
+					return -1;
+				    }
+				}
+			    }
+			    break;
+			}
+
+			if (bnum2 == -2 || bnum1 == bnum2)
+			    break;
+
+			bnum1 = bnum2; // 2nd pass
+		    }
+
+		    m = m->next;
+		}
+	    }
+	}
+
+	// We now know which blocks are in used, so repeat and find
+	// which other data series need to be added.
+	for (i = 0; i < sizeof(i_to_id)/sizeof(*i_to_id); i++) {
+	    int bnum1, bnum2, j;
+	    cram_codec *c = hdr->codecs[i_to_id[i]];
+
+	    if (!c)
+		continue;
+
+	    bnum1 = cram_codec_to_id(c, &bnum2);
+
+	    for (;;) {
+		switch (bnum1) {
+		case -2:
+		    break;
+
+		case -1:
+		    if (core_used) {
+			//printf(" + data series %08x:\n", 1<<i);
+			hdr->data_series |= 1<<i;
+		    }
+		    break;
+
+		default:
+		    for (j = 0; j < s->hdr->num_blocks; j++) {
+			if (s->block[j]->content_type == EXTERNAL &&
+			    s->block[j]->content_id == bnum1) {
+			    if (block_used[j]) {
+				//printf(" + data series %08x:\n", 1<<i);
+				hdr->data_series |= 1<<i;
+			    }
+			}
+		    }
+		    break;
+		}
+
+		if (bnum2 == -2 || bnum1 == bnum2)
+		    break;
+
+		bnum1 = bnum2; // 2nd pass
+	    }
+	}
+
+	// Tags too
+	for (i = 0; i < CRAM_MAP_HASH; i++) {
+	    int bnum1, bnum2, j;
+	    cram_map *m = hdr->tag_encoding_map[i];
+
+	    while (m) {
+		cram_codec *c = m->codec;
+		if (!c)
+		    continue;
+
+		bnum1 = cram_codec_to_id(c, &bnum2);
+		
+		for (;;) {
+		    switch (bnum1) {
+		    case -2:
+			break;
+
+		    case -1:
+			//printf(" + data series %08x:\n", CRAM_aux);
+			hdr->data_series |= CRAM_aux;
+			break;
+
+		    default:
+			for (j = 0; j < s->hdr->num_blocks; j++) {
+			    if (s->block[j]->content_type &&
+				s->block[j]->content_id == bnum1) {
+				if (block_used[j]) {
+				    //printf(" + data series %08x:\n",
+				    //       CRAM_aux);
+				    hdr->data_series |= CRAM_aux;
+				}
+			    }
+			}
+			break;
+		    }
+
+		    if (bnum2 == -2 || bnum1 == bnum2)
+			break;
+
+		    bnum1 = bnum2; // 2nd pass
+		}
+
+		m = m->next;
+	    }
+	}
+    } while (orig_ds != hdr->data_series);
+
+    free(block_used);
+    return 0;
+}
+
+/*
+ * Checks whether an external block is used solely by a single data series.
+ * Returns the codec type if so (EXTERNAL, BYTE_ARRAY_LEN, BYTE_ARRAY_STOP)
+ *         or 0 if not (E_NULL).
+ */
+static int cram_ds_unique(cram_block_compression_hdr *hdr, cram_codec *c,
+			  int id) {
+    int i, n_id = 0;
+    enum cram_encoding e_type = 0;
+
+    for (i = 0; i < DS_END; i++) {
+	cram_codec *c;
+	int bnum1, bnum2, old_n_id;
+
+	if (!(c = hdr->codecs[i]))
+	    continue;
+
+	bnum1 = cram_codec_to_id(c, &bnum2);
+
+	old_n_id = n_id;
+	if (bnum1 == id) {
+	    n_id++;
+	    e_type = c->codec;
+	}
+	if (bnum2 == id) {
+	    n_id++;
+	    e_type = c->codec;
+	}
+
+	if (n_id == old_n_id+2)
+	    n_id--; // len/val in same place counts once only.
+    }
+
+    return n_id == 1 ? e_type : 0;
+}
+
+/*
+ * Attempts to estimate the size of some blocks so we can preallocate them
+ * before decoding.  Although decoding will automatically grow the blocks,
+ * it is typically more efficient to preallocate.
+ */
+void cram_decode_estimate_sizes(cram_block_compression_hdr *hdr, cram_slice *s,
+				int *qual_size, int *name_size,
+				int *q_id) {
+    int bnum1, bnum2;
+    cram_codec *cd;
+
+    *qual_size = 0;
+    *name_size = 0;
+
+    /* Qual */
+    cd = hdr->codecs[DS_QS];
+    bnum1 = cram_codec_to_id(cd, &bnum2);
+    if (bnum1 < 0 && bnum2 >= 0) bnum1 = bnum2;
+    if (cram_ds_unique(hdr, cd, bnum1)) {
+	cram_block *b = cram_get_block_by_id(s, bnum1);
+	if (b) *qual_size = b->uncomp_size;
+	if (q_id && cd->codec == E_EXTERNAL)
+	    *q_id = bnum1;
+    }
+
+    /* Name */
+    cd = hdr->codecs[DS_RN];
+    bnum1 = cram_codec_to_id(cd, &bnum2);
+    if (bnum1 < 0 && bnum2 >= 0) bnum1 = bnum2;
+    if (cram_ds_unique(hdr, cd, bnum1)) {
+	cram_block *b = cram_get_block_by_id(s, bnum1);
+	if (b) *name_size = b->uncomp_size;
+    }
+}
+
+
+/* ----------------------------------------------------------------------
+ * CRAM slices
+ */
+
+/*
+ * Decodes a CRAM (un)mapped slice header block.
+ * Returns slice header ptr on success
+ *         NULL on failure
+ */
+cram_block_slice_hdr *cram_decode_slice_header(cram_fd *fd, cram_block *b) {
+    cram_block_slice_hdr *hdr;
+    char *cp;
+    char *cp_end;
+    int i;
+
+    if (b->method != RAW) {
+        /* Spec. says slice header should be RAW, but we can future-proof
+	   by trying to decode it if it isn't. */
+        if (cram_uncompress_block(b) < 0)
+            return NULL;
+    }
+    cp =  (char *)b->data;
+    cp_end = cp + b->uncomp_size;
+
+    if (b->content_type != MAPPED_SLICE &&
+	b->content_type != UNMAPPED_SLICE)
+	return NULL;
+
+    if (!(hdr  = calloc(1, sizeof(*hdr))))
+	return NULL;
+
+    hdr->content_type = b->content_type;
+
+    if (b->content_type == MAPPED_SLICE) {
+        cp += safe_itf8_get(cp,  cp_end, &hdr->ref_seq_id);
+        cp += safe_itf8_get(cp,  cp_end, &hdr->ref_seq_start);
+        cp += safe_itf8_get(cp,  cp_end, &hdr->ref_seq_span);
+    }
+    cp += safe_itf8_get(cp,  cp_end, &hdr->num_records);
+    hdr->record_counter = 0;
+    if (CRAM_MAJOR_VERS(fd->version) == 2) {
+	int32_t i32 = 0;
+	cp += safe_itf8_get(cp, cp_end, &i32);
+	hdr->record_counter = i32;
+    } else if (CRAM_MAJOR_VERS(fd->version) >= 3) {
+	cp += ltf8_get(cp, &hdr->record_counter);
+    }
+
+    cp += safe_itf8_get(cp, cp_end, &hdr->num_blocks);
+
+    cp += safe_itf8_get(cp, cp_end, &hdr->num_content_ids);
+    if (hdr->num_content_ids < 1 ||
+	hdr->num_content_ids >= SIZE_MAX / sizeof(int32_t)) {
+        /* Slice must have at least one data block,
+	   and malloc'd size shouldn't wrap. */
+        free(hdr);
+        return NULL;
+    }
+    hdr->block_content_ids = malloc(hdr->num_content_ids * sizeof(int32_t));
+    if (!hdr->block_content_ids) {
+	free(hdr);
+	return NULL;
+    }
+
+    for (i = 0; i < hdr->num_content_ids; i++) {
+	int l = safe_itf8_get(cp, cp_end,
+			      &hdr->block_content_ids[i]);
+	if (l <= 0) {
+	    free(hdr->block_content_ids);
+	    free(hdr);
+	    return NULL;
+	}
+	cp += l;
+    }
+
+    if (b->content_type == MAPPED_SLICE) {
+        cp += safe_itf8_get(cp,  cp_end, &hdr->ref_base_id);
+    }
+
+    if (CRAM_MAJOR_VERS(fd->version) != 1) {
+        if (cp_end - cp < 16) {
+            free(hdr->block_content_ids);
+            free(hdr);
+            return NULL;
+        }
+	memcpy(hdr->md5, cp, 16);
+    } else {
+	memset(hdr->md5, 0, 16);
+    }
+
+    return hdr;
+}
+
+
+#if 0
+/* Returns the number of bits set in val; it the highest bit used */
+static int nbits(int v) {
+    static const int MultiplyDeBruijnBitPosition[32] = {
+	1, 10, 2, 11, 14, 22, 3, 30, 12, 15, 17, 19, 23, 26, 4, 31,
+	9, 13, 21, 29, 16, 18, 25, 8, 20, 28, 24, 7, 27, 6, 5, 32
+    };
+
+    v |= v >> 1; // first up to set all bits 1 after the first 1 */
+    v |= v >> 2;
+    v |= v >> 4;
+    v |= v >> 8;
+    v |= v >> 16;
+
+    // DeBruijn magic to find top bit
+    return MultiplyDeBruijnBitPosition[(uint32_t)(v * 0x07C4ACDDU) >> 27];
+}
+#endif
+
+#if 0
+static int sort_freqs(const void *vp1, const void *vp2) {
+    const int i1 = *(const int *)vp1;
+    const int i2 = *(const int *)vp2;
+    return i1-i2;
+}
+#endif
+
+/* ----------------------------------------------------------------------
+ * Primary CRAM sequence decoder
+ */
+
+/*
+ * Internal part of cram_decode_slice().
+ * Generates the sequence, quality and cigar components.
+ */
+static int cram_decode_seq(cram_fd *fd, cram_container *c, cram_slice *s,
+			   cram_block *blk, cram_record *cr, SAM_hdr *bfd,
+			   int cf, char *seq, char *qual,
+			   int has_MD, int has_NM) {
+    int prev_pos = 0, f, r = 0, out_sz = 1;
+    int seq_pos = 1;
+    int cig_len = 0, ref_pos = cr->apos;
+    int32_t fn, i32;
+    enum cigar_op cig_op = BAM_CMATCH;
+    uint32_t *cigar = s->cigar;
+    uint32_t ncigar = s->ncigar;
+    uint32_t cigar_alloc = s->cigar_alloc;
+    uint32_t nm = 0;
+    int32_t md_dist = 0;
+    int orig_aux = 0;
+    int decode_md = fd->decode_md && s->ref && !has_MD;
+    int decode_nm = fd->decode_md && s->ref && !has_NM;
+    uint32_t ds = c->comp_hdr->data_series;
+
+    if ((ds & CRAM_QS) && !(cf & CRAM_FLAG_PRESERVE_QUAL_SCORES)) {
+	memset(qual, 255, cr->len);
+    }
+
+    if (cr->cram_flags & CRAM_FLAG_NO_SEQ)
+	decode_md = decode_nm = 0;
+
+    if (decode_md) {
+	orig_aux = BLOCK_SIZE(s->aux_blk);
+	BLOCK_APPEND(s->aux_blk, "MDZ", 3);
+    }
+    
+    if (ds & CRAM_FN) {
+	if (!c->comp_hdr->codecs[DS_FN]) return -1;
+	r |= c->comp_hdr->codecs[DS_FN]->decode(s,c->comp_hdr->codecs[DS_FN],
+						blk, (char *)&fn, &out_sz);
+        if (r) return r;
+    } else {
+	fn = 0;
+    }
+
+    ref_pos--; // count from 0
+    cr->cigar = ncigar;
+
+    if (!(ds & (CRAM_FC | CRAM_FP)))
+	goto skip_cigar;
+
+    for (f = 0; f < fn; f++) {
+	int32_t pos = 0;
+	char op;
+
+	if (ncigar+2 >= cigar_alloc) {
+	    cigar_alloc = cigar_alloc ? cigar_alloc*2 : 1024;
+	    s->cigar = cigar;
+	    if (!(cigar = realloc(cigar, cigar_alloc * sizeof(*cigar))))
+		return -1;
+	}
+
+	if (ds & CRAM_FC) {
+	    if (!c->comp_hdr->codecs[DS_FC]) return -1;
+	    r |= c->comp_hdr->codecs[DS_FC]->decode(s,
+						    c->comp_hdr->codecs[DS_FC],
+						    blk,
+						    &op,  &out_sz);
+	    if (r) return r;
+	}
+
+	if (!(ds & CRAM_FP))
+	    continue;
+
+	if (!c->comp_hdr->codecs[DS_FP]) return -1;
+	r |= c->comp_hdr->codecs[DS_FP]->decode(s,
+						c->comp_hdr->codecs[DS_FP],
+						blk,
+						(char *)&pos, &out_sz);
+	if (r) return r;
+	pos += prev_pos;
+
+	if (pos <= 0) {
+	    fprintf(stderr, "Error: feature position %d before start of read.\n",
+		    pos);
+	    return -1;
+	}
+
+	if (pos > seq_pos) {
+	    if (pos > cr->len+1)
+		return -1;
+
+	    if (s->ref && cr->ref_id >= 0) {
+		if (ref_pos + pos - seq_pos > bfd->ref[cr->ref_id].len) {
+		    static int whinged = 0;
+		    int rlen;
+		    if (!whinged)
+			fprintf(stderr, "Ref pos outside of ref "
+				"sequence boundary\n");
+		    whinged = 1;
+		    rlen = bfd->ref[cr->ref_id].len - ref_pos;
+		    if (rlen > 0) {
+			memcpy(&seq[seq_pos-1],
+			       &s->ref[ref_pos - s->ref_start +1], rlen);
+			if ((pos - seq_pos) - rlen > 0)
+			    memset(&seq[seq_pos-1+rlen], 'N',
+				   (pos - seq_pos) - rlen);
+		    } else {
+		        memset(&seq[seq_pos-1], 'N', cr->len - seq_pos + 1);
+		    }
+		} else {
+		    memcpy(&seq[seq_pos-1], &s->ref[ref_pos - s->ref_start +1],
+			   pos - seq_pos);
+		}
+	    }
+#ifdef USE_X
+	    if (cig_len && cig_op != BAM_CBASE_MATCH) {
+		cigar[ncigar++] = (cig_len<<4) + cig_op;
+		cig_len = 0;
+	    }
+	    cig_op = BAM_CBASE_MATCH;
+#else
+	    if (cig_len && cig_op != BAM_CMATCH) {
+		cigar[ncigar++] = (cig_len<<4) + cig_op;
+		cig_len = 0;
+	    }
+	    cig_op = BAM_CMATCH;
+#endif
+	    cig_len += pos - seq_pos;
+	    ref_pos += pos - seq_pos;
+	    if (md_dist >= 0)
+		md_dist += pos - seq_pos;
+	    seq_pos = pos;
+	}
+
+	prev_pos = pos;
+
+	if (!(ds & CRAM_FC))
+	    goto skip_cigar;
+
+	if (!(ds & CRAM_FC))
+	    continue;
+
+	switch(op) {
+	case 'S': { // soft clip: IN
+	    int32_t out_sz2 = 1;
+	    int have_sc = 0;
+
+	    if (cig_len) {
+		cigar[ncigar++] = (cig_len<<4) + cig_op;
+		cig_len = 0;
+	    }
+	    switch (CRAM_MAJOR_VERS(fd->version)) {
+	    case 1:
+	        if (ds & CRAM_IN) {
+		    r |= c->comp_hdr->codecs[DS_IN]
+			? c->comp_hdr->codecs[DS_IN]
+			             ->decode(s, c->comp_hdr->codecs[DS_IN],
+					      blk,
+					      cr->len ? &seq[pos-1] : NULL,
+					      &out_sz2)
+			: (seq[pos-1] = 'N', out_sz2 = 1, 0);
+		    have_sc = 1;
+		}
+		break;
+	    case 2:
+	    default:
+	        if (ds & CRAM_SC) {
+		    r |= c->comp_hdr->codecs[DS_SC]
+			? c->comp_hdr->codecs[DS_SC]
+			             ->decode(s, c->comp_hdr->codecs[DS_SC],
+					      blk,
+					      cr->len ? &seq[pos-1] : NULL,
+					      &out_sz2)
+			: (seq[pos-1] = 'N', out_sz2 = 1, 0);
+		    have_sc = 1;
+		}
+		break;
+
+//		default:
+//		    r |= c->comp_hdr->codecs[DS_BB]
+//			? c->comp_hdr->codecs[DS_BB]
+//			             ->decode(s, c->comp_hdr->codecs[DS_BB],
+//					      blk, &seq[pos-1], &out_sz2)
+//			: (seq[pos-1] = 'N', out_sz2 = 1, 0);
+	    }
+	    if (have_sc) {
+		if (r) return r;
+		cigar[ncigar++] = (out_sz2<<4) + BAM_CSOFT_CLIP;
+		cig_op = BAM_CSOFT_CLIP;
+		seq_pos += out_sz2;
+	    }
+	    break;
+	}
+
+	case 'X': { // Substitution; BS
+	    unsigned char base;
+#ifdef USE_X
+	    if (cig_len && cig_op != BAM_CBASE_MISMATCH) {
+		cigar[ncigar++] = (cig_len<<4) + cig_op;
+		cig_len = 0;
+	    }
+	    if (ds & CRAM_BS) {
+		if (!c->comp_hdr->codecs[DS_BS]) return -1;
+		r |= c->comp_hdr->codecs[DS_BS]
+		                ->decode(s, c->comp_hdr->codecs[DS_BS], blk,
+					 (char *)&base, &out_sz);
+		if (pos-1 < cr->len)
+		    seq[pos-1] = 'N'; // FIXME look up BS=base value
+	    }
+	    cig_op = BAM_CBASE_MISMATCH;
+#else
+	    int ref_base;
+	    if (cig_len && cig_op != BAM_CMATCH) {
+		cigar[ncigar++] = (cig_len<<4) + cig_op;
+		cig_len = 0;
+	    }
+	    if (ds & CRAM_BS) {
+		if (!c->comp_hdr->codecs[DS_BS]) return -1;
+		r |= c->comp_hdr->codecs[DS_BS]
+		                ->decode(s, c->comp_hdr->codecs[DS_BS], blk,
+					 (char *)&base, &out_sz);
+		if (r) return -1;
+		if (ref_pos >= bfd->ref[cr->ref_id].len || !s->ref) {
+		    if (pos-1 < cr->len)
+			seq[pos-1] = c->comp_hdr->
+			    substitution_matrix[fd->L1['N']][base];
+		    if (decode_md || decode_nm) {
+			if (md_dist >= 0 && decode_md)
+			    BLOCK_APPEND_UINT(s->aux_blk, md_dist);
+			md_dist = -1;
+			nm--;
+		    }
+		} else {
+		    unsigned char ref_call = ref_pos <= s->ref_end 
+			? (uc)s->ref[ref_pos - s->ref_start +1]
+			: 'N';
+		    ref_base = fd->L1[ref_call];
+		    if (pos-1 < cr->len)
+			seq[pos-1] = c->comp_hdr->
+			    substitution_matrix[ref_base][base];
+		    if (decode_md) {
+			BLOCK_APPEND_UINT(s->aux_blk, md_dist);
+			BLOCK_APPEND_CHAR(s->aux_blk, ref_call);
+			md_dist = 0;
+		    }
+		}
+	    }
+	    cig_op = BAM_CMATCH;
+#endif
+	    nm++;
+	    cig_len++;
+	    seq_pos++;
+	    ref_pos++;
+	    break;
+	}
+
+	case 'D': { // Deletion; DL
+	    if (cig_len && cig_op != BAM_CDEL) {
+		cigar[ncigar++] = (cig_len<<4) + cig_op;
+		cig_len = 0;
+	    }
+	    if (ds & CRAM_DL) {
+		if (!c->comp_hdr->codecs[DS_DL]) return -1;
+		r |= c->comp_hdr->codecs[DS_DL]
+		                ->decode(s, c->comp_hdr->codecs[DS_DL], blk,
+					 (char *)&i32, &out_sz);
+		if (r) return r;
+		if (decode_md || decode_nm) {
+		    if (md_dist >= 0 && decode_md)
+			BLOCK_APPEND_UINT(s->aux_blk, md_dist);
+		    if (ref_pos + i32 <= bfd->ref[cr->ref_id].len) {
+			if (decode_md) {
+			    BLOCK_APPEND_CHAR(s->aux_blk, '^');
+			    BLOCK_APPEND(s->aux_blk,
+					 &s->ref[ref_pos - s->ref_start +1],
+					 i32);
+			    md_dist = 0;
+			}
+			nm += i32;
+		    } else {
+			uint32_t dlen;
+			if (bfd->ref[cr->ref_id].len >= ref_pos) {
+			    if (decode_md) {
+				BLOCK_APPEND_CHAR(s->aux_blk, '^');
+				BLOCK_APPEND(s->aux_blk,
+					     &s->ref[ref_pos - s->ref_start+1],
+					     bfd->ref[cr->ref_id].len-ref_pos);
+				BLOCK_APPEND_UINT(s->aux_blk, 0);
+			    }
+			    dlen = i32 - (bfd->ref[cr->ref_id].len - ref_pos);
+			    nm += i32 - dlen;
+			} else {
+			    dlen = i32;
+			}
+
+			md_dist = -1;
+		    }
+		}
+		cig_op = BAM_CDEL;
+		cig_len += i32;
+		ref_pos += i32;
+		//printf("  %d: DL = %d (ret %d)\n", f, i32, r);
+	    }
+	    break;
+	}
+
+	case 'I': { // Insertion (several bases); IN
+	    int32_t out_sz2 = 1;
+
+	    if (cig_len && cig_op != BAM_CINS) {
+		cigar[ncigar++] = (cig_len<<4) + cig_op;
+		cig_len = 0;
+	    }
+
+	    if (ds & CRAM_IN) {
+		if (!c->comp_hdr->codecs[DS_IN]) return -1;
+		r |= c->comp_hdr->codecs[DS_IN]
+		                ->decode(s, c->comp_hdr->codecs[DS_IN], blk,
+					 cr->len ? &seq[pos-1] : NULL,
+					 &out_sz2);
+		if (r) return r;
+		cig_op = BAM_CINS;
+		cig_len += out_sz2;
+		seq_pos += out_sz2;
+		nm      += out_sz2;
+		//printf("  %d: IN(I) = %.*s (ret %d, out_sz %d)\n", f, out_sz2, dat, r, out_sz2);
+	    }
+	    break;
+	}
+
+	case 'i': { // Insertion (single base); BA
+	    if (cig_len && cig_op != BAM_CINS) {
+		cigar[ncigar++] = (cig_len<<4) + cig_op;
+		cig_len = 0;
+	    }
+	    if (ds & CRAM_BA) {
+		if (!c->comp_hdr->codecs[DS_BA]) return -1;
+		r |= c->comp_hdr->codecs[DS_BA]
+		                ->decode(s, c->comp_hdr->codecs[DS_BA], blk,
+					 cr->len ? &seq[pos-1] : NULL,
+					 &out_sz);
+		if (r) return r;
+	    }
+	    cig_op = BAM_CINS;
+	    cig_len++;
+	    seq_pos++;
+	    nm++;
+	    break;
+	}
+
+	case 'b': { // Several bases
+	    int32_t len = 1;
+
+	    if (cig_len && cig_op != BAM_CMATCH) {
+		cigar[ncigar++] = (cig_len<<4) + cig_op;
+		cig_len = 0;
+	    }
+
+	    if (ds & CRAM_BB) {
+		if (!c->comp_hdr->codecs[DS_BB]) return -1;
+		r |= c->comp_hdr->codecs[DS_BB]
+		    ->decode(s, c->comp_hdr->codecs[DS_BB], blk,
+			     cr->len ? &seq[pos-1] : NULL,
+			     &len);
+		if (r) return r;
+
+		if (decode_md || decode_nm) {
+		    int x;
+		    if (md_dist >= 0 && decode_md)
+			BLOCK_APPEND_UINT(s->aux_blk, md_dist);
+
+		    for (x = 0; x < len; x++) {
+			if (x && decode_md)
+			    BLOCK_APPEND_UINT(s->aux_blk, 0);
+			if (ref_pos+x >= bfd->ref[cr->ref_id].len || !s->ref) {
+			    md_dist = -1;
+			    break;
+			} else {
+			    if (decode_md) {
+				char r = s->ref[ref_pos+x-s->ref_start +1];
+				BLOCK_APPEND_CHAR(s->aux_blk, r);
+			    }
+			}
+		    }
+
+		    nm += x;
+		}
+	    }
+
+	    cig_op = BAM_CMATCH;
+
+	    cig_len+=len;
+	    seq_pos+=len;
+	    ref_pos+=len;
+	    //prev_pos+=len;
+	    break;
+	}
+
+	case 'q': { // Several quality values
+	    int32_t len = 1;
+
+	    if (cig_len && cig_op != BAM_CMATCH) {
+		cigar[ncigar++] = (cig_len<<4) + cig_op;
+		cig_len = 0;
+	    }
+
+	    if (ds & CRAM_QQ) {
+		if (!c->comp_hdr->codecs[DS_QQ]) return -1;
+		r |= c->comp_hdr->codecs[DS_QQ]
+		    ->decode(s, c->comp_hdr->codecs[DS_QQ], blk,
+			     (char *)&qual[pos-1], &len);
+		if (r) return r;
+	    }
+
+	    cig_op = BAM_CMATCH;
+
+	    cig_len+=len;
+	    seq_pos+=len;
+	    ref_pos+=len;
+	    //prev_pos+=len;
+	    break;
+	}
+
+	case 'B': { // Read base; BA, QS
+#ifdef USE_X
+	    if (cig_len && cig_op != BAM_CBASE_MISMATCH) {
+		cigar[ncigar++] = (cig_len<<4) + cig_op;
+		cig_len = 0;
+	    }
+#else
+	    if (cig_len && cig_op != BAM_CMATCH) {
+		cigar[ncigar++] = (cig_len<<4) + cig_op;
+		cig_len = 0;
+	    }
+#endif
+	    if (ds & CRAM_BA) {
+		if (!c->comp_hdr->codecs[DS_BA]) return -1;
+		r |= c->comp_hdr->codecs[DS_BA]
+		                ->decode(s, c->comp_hdr->codecs[DS_BA], blk,
+					 cr->len ? &seq[pos-1] : NULL,
+					 &out_sz);
+
+		if (decode_md || decode_nm) {
+		    if (md_dist >= 0 && decode_md)
+			BLOCK_APPEND_UINT(s->aux_blk, md_dist);
+		    if (ref_pos >= bfd->ref[cr->ref_id].len || !s->ref) {
+			md_dist = -1;
+		    } else {
+			if (decode_md)
+			    BLOCK_APPEND_CHAR(s->aux_blk,
+					      s->ref[ref_pos-s->ref_start +1]);
+			nm++;
+			md_dist = 0;
+		    }
+		}
+	    }
+	    if (ds & CRAM_QS) {
+		if (!c->comp_hdr->codecs[DS_QS]) return -1;
+		r |= c->comp_hdr->codecs[DS_QS]
+		                ->decode(s, c->comp_hdr->codecs[DS_QS], blk,
+					 (char *)&qual[pos-1], &out_sz);
+	    }
+#ifdef USE_X
+	    cig_op = BAM_CBASE_MISMATCH;
+#else
+	    cig_op = BAM_CMATCH;
+#endif
+	    cig_len++;
+	    seq_pos++;
+	    ref_pos++;
+	    //printf("  %d: BA/QS(B) = %c/%d (ret %d)\n", f, i32, qc, r);
+	    break;
+	}
+
+	case 'Q': { // Quality score; QS
+	    if (ds & CRAM_QS) {
+		if (!c->comp_hdr->codecs[DS_QS]) return -1;
+		r |= c->comp_hdr->codecs[DS_QS]
+		                ->decode(s, c->comp_hdr->codecs[DS_QS], blk,
+					 (char *)&qual[pos-1], &out_sz);
+		//printf("  %d: QS = %d (ret %d)\n", f, qc, r);
+	    }
+	    break;
+	}
+
+	case 'H': { // hard clip; HC
+	    if (cig_len && cig_op != BAM_CHARD_CLIP) {
+		cigar[ncigar++] = (cig_len<<4) + cig_op;
+		cig_len = 0;
+	    }
+	    if (ds & CRAM_HC) {
+		if (!c->comp_hdr->codecs[DS_HC]) return -1;
+		r |= c->comp_hdr->codecs[DS_HC]
+		                ->decode(s, c->comp_hdr->codecs[DS_HC], blk,
+					 (char *)&i32, &out_sz);
+		if (r) return r;
+		cig_op = BAM_CHARD_CLIP;
+		cig_len += i32;
+	    }
+	    break;
+	}
+
+	case 'P': { // padding; PD
+	    if (cig_len && cig_op != BAM_CPAD) {
+		cigar[ncigar++] = (cig_len<<4) + cig_op;
+		cig_len = 0;
+	    }
+	    if (ds & CRAM_PD) {
+		if (!c->comp_hdr->codecs[DS_PD]) return -1;
+		r |= c->comp_hdr->codecs[DS_PD]
+		                ->decode(s, c->comp_hdr->codecs[DS_PD], blk,
+					 (char *)&i32, &out_sz);
+		if (r) return r;
+		cig_op = BAM_CPAD;
+		cig_len += i32;
+		nm      += i32;
+	    }
+	    break;
+	}
+
+	case 'N': { // Ref skip; RS
+	    if (cig_len && cig_op != BAM_CREF_SKIP) {
+		cigar[ncigar++] = (cig_len<<4) + cig_op;
+		cig_len = 0;
+	    }
+	    if (ds & CRAM_RS) {
+		if (!c->comp_hdr->codecs[DS_RS]) return -1;
+		r |= c->comp_hdr->codecs[DS_RS]
+		                ->decode(s, c->comp_hdr->codecs[DS_RS], blk,
+					 (char *)&i32, &out_sz);
+		if (r) return r;
+		cig_op = BAM_CREF_SKIP;
+		cig_len += i32;
+		ref_pos += i32;
+		nm      += i32;
+	    }
+	    break;
+	}
+
+	default:
+            fprintf(stderr, "Error: Unknown feature code '%c'\n", op);
+	    return -1;
+	}
+    }
+
+    if (!(ds & CRAM_FC))
+	goto skip_cigar;
+
+    /* An implicit match op for any unaccounted for bases */
+    if ((ds & CRAM_FN) && cr->len >= seq_pos) {
+	if (s->ref) {
+	    if (ref_pos + cr->len - seq_pos + 1 > bfd->ref[cr->ref_id].len) {
+		static int whinged = 0;
+		int rlen;
+		if (!whinged)
+		    fprintf(stderr, "Ref pos outside of ref sequence boundary\n");
+		whinged = 1;
+		rlen = bfd->ref[cr->ref_id].len - ref_pos;
+		if (rlen > 0) {
+		    if (seq_pos-1 + rlen < cr->len)
+			memcpy(&seq[seq_pos-1],
+			       &s->ref[ref_pos - s->ref_start +1], rlen);
+		    if ((cr->len - seq_pos + 1) - rlen > 0)
+		        memset(&seq[seq_pos-1+rlen], 'N',
+                               (cr->len - seq_pos + 1) - rlen);
+		} else {
+		    if (cr->len - seq_pos + 1 > 0)
+			memset(&seq[seq_pos-1], 'N', cr->len - seq_pos + 1);
+		}
+	    } else {
+		if (cr->len - seq_pos + 1 > 0)
+		    memcpy(&seq[seq_pos-1], &s->ref[ref_pos - s->ref_start +1],
+			   cr->len - seq_pos + 1);
+		ref_pos += cr->len - seq_pos + 1;
+		if (md_dist >= 0)
+		    md_dist += cr->len - seq_pos + 1;
+	    }
+	}
+
+	if (ncigar+1 >= cigar_alloc) {
+	    cigar_alloc = cigar_alloc ? cigar_alloc*2 : 1024;
+	    s->cigar = cigar;
+	    if (!(cigar = realloc(cigar, cigar_alloc * sizeof(*cigar))))
+		return -1;
+	}
+#ifdef USE_X
+	if (cig_len && cig_op != BAM_CBASE_MATCH) {
+	    cigar[ncigar++] = (cig_len<<4) + cig_op;
+	    cig_len = 0;
+	}
+	cig_op = BAM_CBASE_MATCH;
+#else
+	if (cig_len && cig_op != BAM_CMATCH) {
+	    cigar[ncigar++] = (cig_len<<4) + cig_op;
+	    cig_len = 0;
+	}
+	cig_op = BAM_CMATCH;
+#endif
+	cig_len += cr->len - seq_pos+1;
+    }
+
+ skip_cigar:
+
+    if ((ds & CRAM_FN) && decode_md) {
+	if (md_dist >= 0)
+	    BLOCK_APPEND_UINT(s->aux_blk, md_dist);
+    }
+
+    if (cig_len) {
+	if (ncigar >= cigar_alloc) {
+	    cigar_alloc = cigar_alloc ? cigar_alloc*2 : 1024;
+	    s->cigar = cigar;
+	    if (!(cigar = realloc(cigar, cigar_alloc * sizeof(*cigar))))
+		return -1;
+	}
+
+	cigar[ncigar++] = (cig_len<<4) + cig_op;
+    }
+
+    cr->ncigar = ncigar - cr->cigar;
+    cr->aend = ref_pos;
+
+    //printf("2: %.*s %d .. %d\n", cr->name_len, DSTRING_STR(name_ds) + cr->name, cr->apos, ref_pos);
+
+    if (ds & CRAM_MQ) {
+	if (!c->comp_hdr->codecs[DS_MQ]) return -1;
+	r |= c->comp_hdr->codecs[DS_MQ]
+	                ->decode(s, c->comp_hdr->codecs[DS_MQ], blk,
+				 (char *)&cr->mqual, &out_sz);
+    } else {
+	cr->mqual = 40;
+    }
+
+    if ((ds & CRAM_QS) && (cf & CRAM_FLAG_PRESERVE_QUAL_SCORES)) {
+	int32_t out_sz2 = cr->len;
+
+	if (ds & CRAM_QS) {
+	    if (!c->comp_hdr->codecs[DS_QS]) return -1;
+	    r |= c->comp_hdr->codecs[DS_QS]
+		            ->decode(s, c->comp_hdr->codecs[DS_QS], blk,
+				     qual, &out_sz2);
+	}
+    }
+
+    s->cigar = cigar;
+    s->cigar_alloc = cigar_alloc;
+    s->ncigar = ncigar;
+
+    if (cr->cram_flags & CRAM_FLAG_NO_SEQ)
+	cr->len = 0;
+
+    if (decode_md) {
+	BLOCK_APPEND_CHAR(s->aux_blk, '\0'); // null terminate MD:Z:
+	cr->aux_size += BLOCK_SIZE(s->aux_blk) - orig_aux;
+    }
+
+    if (decode_nm) {
+	char buf[7];
+	buf[0] = 'N'; buf[1] = 'M'; buf[2] = 'I';
+	buf[3] = (nm>> 0) & 0xff;
+	buf[4] = (nm>> 8) & 0xff;
+	buf[5] = (nm>>16) & 0xff;
+	buf[6] = (nm>>24) & 0xff;
+	BLOCK_APPEND(s->aux_blk, buf, 7);
+	cr->aux_size += 7;
+    }
+
+    return r;
+}
+
+/*
+ * Quick and simple hash lookup for cram_map arrays
+ */
+static cram_map *map_find(cram_map **map, unsigned char *key, int id) {
+    cram_map *m;
+
+    m = map[CRAM_MAP(key[0],key[1])];
+    while (m && m->key != id)
+	m= m->next;
+
+    return m;
+}
+
+//#define map_find(M,K,I) M[CRAM_MAP(K[0],K[1])];while (m && m->key != I);m= m->next
+
+
+static int cram_decode_aux_1_0(cram_container *c, cram_slice *s,
+			       cram_block *blk, cram_record *cr) {
+    int i, r = 0, out_sz = 1;
+    unsigned char ntags;
+	    
+    if (!c->comp_hdr->codecs[DS_TC]) return -1;
+    r |= c->comp_hdr->codecs[DS_TC]->decode(s, c->comp_hdr->codecs[DS_TC], blk,
+					    (char *)&ntags, &out_sz);
+    cr->ntags = ntags;
+
+    //printf("TC=%d\n", cr->ntags);
+    cr->aux_size = 0;
+    cr->aux = BLOCK_SIZE(s->aux_blk);
+
+    for (i = 0; i < cr->ntags; i++) {
+	int32_t id, out_sz = 1;
+	unsigned char tag_data[3];
+	cram_map *m;
+
+	//printf("Tag %d/%d\n", i+1, cr->ntags);
+	if (!c->comp_hdr->codecs[DS_TN]) return -1;
+	r |= c->comp_hdr->codecs[DS_TN]->decode(s, c->comp_hdr->codecs[DS_TN],
+						blk, (char *)&id, &out_sz);
+	if (out_sz == 3) {
+	    tag_data[0] = ((char *)&id)[0];
+	    tag_data[1] = ((char *)&id)[1];
+	    tag_data[2] = ((char *)&id)[2];
+	} else {
+	    tag_data[0] = (id>>16) & 0xff;
+	    tag_data[1] = (id>>8)  & 0xff;
+	    tag_data[2] = id       & 0xff;
+	} 
+
+	m = map_find(c->comp_hdr->tag_encoding_map, tag_data, id);
+	if (!m)
+	    return -1;
+	BLOCK_APPEND(s->aux_blk, (char *)tag_data, 3);
+
+	if (!m->codec) return -1;
+	r |= m->codec->decode(s, m->codec, blk, (char *)s->aux_blk, &out_sz);
+
+	cr->aux_size += out_sz + 3;
+    }
+    
+    return r;
+}
+
+static int cram_decode_aux(cram_container *c, cram_slice *s,
+			   cram_block *blk, cram_record *cr,
+			   int *has_MD, int *has_NM) {
+    int i, r = 0, out_sz = 1;
+    int32_t TL = 0;
+    unsigned char *TN;
+    uint32_t ds = c->comp_hdr->data_series;
+	    
+    if (!(ds & (CRAM_TL|CRAM_aux))) {
+	cr->aux = 0;
+	cr->aux_size = 0;
+	return 0;
+    }
+
+    if (!c->comp_hdr->codecs[DS_TL]) return -1;
+    r |= c->comp_hdr->codecs[DS_TL]->decode(s, c->comp_hdr->codecs[DS_TL], blk,
+					    (char *)&TL, &out_sz);
+    if (r || TL < 0 || TL >= c->comp_hdr->nTL)
+	return -1;
+
+    TN = c->comp_hdr->TL[TL];
+    cr->ntags = strlen((char *)TN)/3; // optimise to remove strlen
+
+    //printf("TC=%d\n", cr->ntags);
+    cr->aux_size = 0;
+    cr->aux = BLOCK_SIZE(s->aux_blk);
+
+    if (!(ds & CRAM_aux))
+	return 0;
+
+    for (i = 0; i < cr->ntags; i++) {
+	int32_t id, out_sz = 1;
+	unsigned char tag_data[3];
+	cram_map *m;
+
+	if (TN[0] == 'M' && TN[1] == 'D' && has_MD)
+	    *has_MD = 1;
+	if (TN[0] == 'N' && TN[1] == 'M' && has_NM)
+	    *has_NM = 1;
+
+	//printf("Tag %d/%d\n", i+1, cr->ntags);
+	tag_data[0] = *TN++;
+	tag_data[1] = *TN++;
+	tag_data[2] = *TN++;
+	id = (tag_data[0]<<16) | (tag_data[1]<<8) | tag_data[2];
+
+	m = map_find(c->comp_hdr->tag_encoding_map, tag_data, id);
+	if (!m)
+	    return -1;
+	BLOCK_APPEND(s->aux_blk, (char *)tag_data, 3);
+
+	if (!m->codec) return -1;
+	r |= m->codec->decode(s, m->codec, blk, (char *)s->aux_blk, &out_sz);
+	if (r) break;
+	cr->aux_size += out_sz + 3;
+    }
+    
+    return r;
+}
+
+/* Resolve mate pair cross-references between recs within this slice */
+static int cram_decode_slice_xref(cram_slice *s, int required_fields) {
+    int rec;
+
+    if (!(required_fields & (SAM_RNEXT | SAM_PNEXT | SAM_TLEN))) {
+	for (rec = 0; rec < s->hdr->num_records; rec++) {
+	    cram_record *cr = &s->crecs[rec];
+
+	    cr->tlen = 0;
+	    cr->mate_pos = 0;
+	    cr->mate_ref_id = -1;
+	}
+
+	return 0;
+    }
+
+    for (rec = 0; rec < s->hdr->num_records; rec++) {
+	cram_record *cr = &s->crecs[rec];
+
+	if (cr->mate_line >= 0) {
+	    if (cr->mate_line < s->hdr->num_records) {
+		/*
+		 * On the first read, loop through computing lengths.
+		 * It's not perfect as we have one slice per reference so we
+		 * cannot detect when TLEN should be zero due to seqs that
+		 * map to multiple references.
+		 *
+		 * We also cannot set tlen correct when it spans a slice for
+		 * other reasons. This may make tlen too small. Should we
+		 * fix this by forcing TLEN to be stored verbatim in such cases?
+		 *
+		 * Or do we just admit defeat and output 0 for tlen? It's the
+		 * safe option...
+		 */
+		if (cr->tlen == INT_MIN) {
+		    int id1 = rec, id2 = rec;
+		    int aleft = cr->apos, aright = cr->aend;
+		    int tlen;
+		    int ref = cr->ref_id;
+
+		    // number of segments starting at the same point.
+		    int left_cnt = 0;
+
+		    do {
+			if (aleft > s->crecs[id2].apos)
+			    aleft = s->crecs[id2].apos, left_cnt = 1;
+			else if (aleft == s->crecs[id2].apos)
+			    left_cnt++;
+			if (aright < s->crecs[id2].aend)
+			    aright = s->crecs[id2].aend;
+			if (s->crecs[id2].mate_line == -1) {
+			    s->crecs[id2].mate_line = rec;
+			    break;
+			}
+			if (s->crecs[id2].mate_line <= id2 ||
+                            s->crecs[id2].mate_line >= s->hdr->num_records)
+			    return -1;
+			id2 = s->crecs[id2].mate_line;
+
+			if (s->crecs[id2].ref_id != ref)
+			    ref = -1;
+		    } while (id2 != id1);
+
+		    if (ref != -1) {
+			tlen = aright - aleft + 1;
+			id1 = id2 = rec;
+
+			/*
+			 * When we have two seqs with identical start and
+			 * end coordinates, set +/- tlen based on 1st/last
+			 * bit flags instead, as a tie breaker.
+			 */
+			if (s->crecs[id2].apos == aleft) {
+			    if (left_cnt == 1 || 
+				(s->crecs[id2].flags & BAM_FREAD1))
+				s->crecs[id2].tlen = tlen;
+			    else
+				s->crecs[id2].tlen = -tlen;
+			} else {
+			    s->crecs[id2].tlen = -tlen;
+			}
+
+			id2 = s->crecs[id2].mate_line;
+			while (id2 != id1) {
+			    if (s->crecs[id2].apos == aleft) {
+				if (left_cnt == 1 || 
+				    (s->crecs[id2].flags & BAM_FREAD1))
+				    s->crecs[id2].tlen = tlen;
+				else
+				    s->crecs[id2].tlen = -tlen;
+			    } else {
+				s->crecs[id2].tlen = -tlen;
+			    }
+			    id2 = s->crecs[id2].mate_line;
+			}
+		    } else {
+			id1 = id2 = rec;
+
+			s->crecs[id2].tlen = 0;
+			id2 = s->crecs[id2].mate_line;
+			while (id2 != id1) {
+			    s->crecs[id2].tlen = 0;
+			    id2 = s->crecs[id2].mate_line;
+			}
+		    }
+		}
+
+		cr->mate_pos = s->crecs[cr->mate_line].apos;
+		cr->mate_ref_id = s->crecs[cr->mate_line].ref_id;
+
+		// paired
+		cr->flags |= BAM_FPAIRED;
+
+		// set mate unmapped if needed
+		if (s->crecs[cr->mate_line].flags & BAM_FUNMAP) {
+		    cr->flags |= BAM_FMUNMAP;
+		    cr->tlen = 0;
+		}
+		if (cr->flags & BAM_FUNMAP) {
+		    cr->tlen = 0;
+		}
+
+		// set mate reversed if needed
+		if (s->crecs[cr->mate_line].flags & BAM_FREVERSE)
+		    cr->flags |= BAM_FMREVERSE;
+	    } else {
+		fprintf(stderr, "Mate line out of bounds: %d vs [0, %d]\n",
+			cr->mate_line, s->hdr->num_records-1);
+	    }
+
+	    /* FIXME: construct read names here too if needed */
+	} else {
+	    if (cr->mate_flags & CRAM_M_REVERSE) {
+		cr->flags |= BAM_FPAIRED | BAM_FMREVERSE;
+	    }
+	    if (cr->mate_flags & CRAM_M_UNMAP) {
+		cr->flags |= BAM_FMUNMAP;
+		//cr->mate_ref_id = -1;
+	    }
+	    if (!(cr->flags & BAM_FPAIRED))
+		cr->mate_ref_id = -1;
+	}
+
+	if (cr->tlen == INT_MIN)
+	    cr->tlen = 0; // Just incase
+    }
+    return 0;
+}
+
+static char *md5_print(unsigned char *md5, char *out) {
+    int i;
+    for (i = 0; i < 16; i++) {
+	out[i*2+0] = "0123456789abcdef"[md5[i]>>4];
+	out[i*2+1] = "0123456789abcdef"[md5[i]&15];
+    }
+    out[32] = 0;
+
+    return out;
+}
+
+/*
+ * Decode an entire slice from container blocks. Fills out s->crecs[] array.
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int cram_decode_slice(cram_fd *fd, cram_container *c, cram_slice *s,
+		      SAM_hdr *bfd) {
+    cram_block *blk = s->block[0];
+    int32_t bf, ref_id;
+    unsigned char cf;
+    int out_sz, r = 0;
+    int rec;
+    char *seq = NULL, *qual = NULL;
+    int unknown_rg = -1;
+    int embed_ref;
+    char **refs = NULL;
+    uint32_t ds;
+
+    if (cram_dependent_data_series(fd, c->comp_hdr, s) != 0)
+	return -1;
+
+    ds = c->comp_hdr->data_series;
+
+    blk->bit = 7; // MSB first
+
+    // Study the blocks and estimate approx sizes to preallocate.
+    // This looks to speed up decoding by around 8-9%.
+    // We can always shrink back down at the end if we overestimated.
+    // However it's likely that this also saves memory as own growth
+    // factor (*=1.5) is never applied.
+    {
+	int qsize, nsize, q_id;
+	cram_decode_estimate_sizes(c->comp_hdr, s, &qsize, &nsize, &q_id);
+	//fprintf(stderr, "qsize=%d nsize=%d\n", qsize, nsize);
+	
+	if (qsize && (ds & CRAM_RL)) BLOCK_RESIZE_EXACT(s->seqs_blk, qsize+1);
+	if (qsize && (ds & CRAM_RL)) BLOCK_RESIZE_EXACT(s->qual_blk, qsize+1);
+	if (nsize && (ds & CRAM_NS)) BLOCK_RESIZE_EXACT(s->name_blk, nsize+1);
+
+	// To do - consider using q_id here to usurp the quality block and
+	// avoid a memcpy during decode.
+	// Specifically when quality is an external block uniquely used by
+	// DS_QS only, then we can set s->qual_blk directly to this
+	// block and save the codec->decode() calls. (Approx 3% cpu saving)
+    }
+
+    /* Look for unknown RG, added as last by Java CRAM? */
+    if (bfd->nrg > 0 &&
+	bfd->rg[bfd->nrg-1].name != NULL &&
+	!strcmp(bfd->rg[bfd->nrg-1].name, "UNKNOWN"))
+	unknown_rg = bfd->nrg-1;
+
+    if (blk->content_type != CORE)
+	return -1;
+
+    if (s->crecs)
+	free(s->crecs);
+    if (!(s->crecs = malloc(s->hdr->num_records * sizeof(*s->crecs))))
+	return -1;
+
+    ref_id = s->hdr->ref_seq_id;
+    embed_ref = s->hdr->ref_base_id >= 0 ? 1 : 0;
+
+    if (ref_id >= 0) {
+	if (embed_ref) {
+	    cram_block *b;
+	    if (s->hdr->ref_base_id < 0) {
+		fprintf(stderr, "No reference specified and "
+			"no embedded reference is available.\n");
+		return -1;
+	    }
+	    b = cram_get_block_by_id(s, s->hdr->ref_base_id);
+	    if (!b)
+		return -1;
+	    if (cram_uncompress_block(b) != 0)
+		return -1;
+	    s->ref = (char *)BLOCK_DATA(b);
+	    s->ref_start = s->hdr->ref_seq_start;
+	    s->ref_end   = s->hdr->ref_seq_start + s->hdr->ref_seq_span-1;
+	} else if (!fd->no_ref) {
+	    //// Avoid Java cramtools bug by loading entire reference seq 
+	    //s->ref = cram_get_ref(fd, s->hdr->ref_seq_id, 1, 0);
+	    //s->ref_start = 1;
+
+	    if (fd->required_fields & SAM_SEQ)
+		s->ref =
+		cram_get_ref(fd, s->hdr->ref_seq_id,
+			     s->hdr->ref_seq_start,
+			     s->hdr->ref_seq_start + s->hdr->ref_seq_span -1);
+	    s->ref_start = s->hdr->ref_seq_start;
+	    s->ref_end   = s->hdr->ref_seq_start + s->hdr->ref_seq_span-1;
+
+	    /* Sanity check */
+	    if (s->ref_start < 0) {
+		fprintf(stderr, "Slice starts before base 1.\n");
+		s->ref_start = 0;
+	    }
+	    pthread_mutex_lock(&fd->ref_lock);
+	    pthread_mutex_lock(&fd->refs->lock);
+	    if ((fd->required_fields & SAM_SEQ) &&
+		s->ref_end > fd->refs->ref_id[ref_id]->length) {
+		s->ref_end = fd->refs->ref_id[ref_id]->length;
+	    }
+	    pthread_mutex_unlock(&fd->refs->lock);
+	    pthread_mutex_unlock(&fd->ref_lock);
+	}
+    }
+
+    if ((fd->required_fields & SAM_SEQ) &&
+	s->ref == NULL && s->hdr->ref_seq_id >= 0 && !fd->no_ref) {
+	fprintf(stderr, "Unable to fetch reference #%d %d..%d\n",
+		s->hdr->ref_seq_id, s->hdr->ref_seq_start,
+		s->hdr->ref_seq_start + s->hdr->ref_seq_span-1);
+	return -1;
+    }
+
+    if (CRAM_MAJOR_VERS(fd->version) != 1
+	&& (fd->required_fields & SAM_SEQ)
+	&& s->hdr->ref_seq_id >= 0
+	&& !fd->ignore_md5
+	&& memcmp(s->hdr->md5, "\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0", 16)) {
+	hts_md5_context *md5;
+	unsigned char digest[16];
+
+	if (s->ref && s->hdr->ref_seq_id >= 0) {
+	    int start, len;
+
+	    if (s->hdr->ref_seq_start >= s->ref_start) {
+		start = s->hdr->ref_seq_start - s->ref_start;
+	    } else {
+		fprintf(stderr, "Slice starts before base 1.\n");
+		start = 0;
+	    }
+
+	    if (s->hdr->ref_seq_span <= s->ref_end - s->ref_start + 1) {
+		len = s->hdr->ref_seq_span;
+	    } else {
+		fprintf(stderr, "Slice ends beyond reference end.\n");
+		len = s->ref_end - s->ref_start + 1;
+	    }
+
+	    if (!(md5 = hts_md5_init()))
+		return -1;
+	    if (start + len > s->ref_end - s->ref_start + 1)
+		len = s->ref_end - s->ref_start + 1 - start;
+	    if (len >= 0)
+		hts_md5_update(md5, s->ref + start, len);
+	    hts_md5_final(digest, md5);
+	    hts_md5_destroy(md5);
+	} else if (!s->ref && s->hdr->ref_base_id >= 0) {
+	    cram_block *b = cram_get_block_by_id(s, s->hdr->ref_base_id);
+	    if (b) {
+		if (!(md5 = hts_md5_init()))
+		    return -1;
+		hts_md5_update(md5, b->data, b->uncomp_size);
+		hts_md5_final(digest, md5);
+		hts_md5_destroy(md5);
+	    }
+	}
+
+	if ((!s->ref && s->hdr->ref_base_id < 0)
+	    || memcmp(digest, s->hdr->md5, 16) != 0) {
+	    char M[33];
+	    fprintf(stderr, "ERROR: md5sum reference mismatch for ref "
+		    "%d pos %d..%d\n", ref_id, s->ref_start, s->ref_end);
+	    fprintf(stderr, "CRAM: %s\n", md5_print(s->hdr->md5, M));
+	    fprintf(stderr, "Ref : %s\n", md5_print(digest, M));
+	    return -1;
+	}
+    }
+
+    if (ref_id == -2) {
+	pthread_mutex_lock(&fd->ref_lock);
+	pthread_mutex_lock(&fd->refs->lock);
+	refs = calloc(fd->refs->nref, sizeof(char *));
+	pthread_mutex_unlock(&fd->refs->lock);
+	pthread_mutex_unlock(&fd->ref_lock);
+	if (!refs)
+	    return -1;
+    }
+
+    int last_ref_id = -9; // Arbitrary -ve marker for not-yet-set
+    for (rec = 0; rec < s->hdr->num_records; rec++) {
+	cram_record *cr = &s->crecs[rec];
+	int has_MD, has_NM;
+
+	//fprintf(stderr, "Decode seq %d, %d/%d\n", rec, blk->byte, blk->bit);
+
+	cr->s = s;
+
+	out_sz = 1; /* decode 1 item */
+	if (ds & CRAM_BF) {
+	    if (!c->comp_hdr->codecs[DS_BF]) return -1;
+	    r |= c->comp_hdr->codecs[DS_BF]
+		            ->decode(s, c->comp_hdr->codecs[DS_BF], blk,
+				     (char *)&bf, &out_sz);
+	    if (r || bf < 0 ||
+		bf >= sizeof(fd->bam_flag_swap)/sizeof(*fd->bam_flag_swap))
+		return -1;
+	    bf = fd->bam_flag_swap[bf];
+	    cr->flags = bf;
+	} else {
+	    cr->flags = bf = 0x4; // unmapped
+	}
+
+	if (ds & CRAM_CF) {
+	    if (CRAM_MAJOR_VERS(fd->version) == 1) {
+		/* CF is byte in 1.0, int32 in 2.0 */
+		if (!c->comp_hdr->codecs[DS_CF]) return -1;
+		r |= c->comp_hdr->codecs[DS_CF]
+		                ->decode(s, c->comp_hdr->codecs[DS_CF], blk,
+				 	 (char *)&cf, &out_sz);
+		if (r) return -1;
+		cr->cram_flags = cf;
+	    } else {
+		if (!c->comp_hdr->codecs[DS_CF]) return -1;
+		r |= c->comp_hdr->codecs[DS_CF]
+		                ->decode(s, c->comp_hdr->codecs[DS_CF], blk,
+					 (char *)&cr->cram_flags, &out_sz);
+		if (r) return -1;
+		cf = cr->cram_flags;
+	    }
+	} else {
+	    cf = cr->cram_flags = 0;
+	}
+
+	if (CRAM_MAJOR_VERS(fd->version) != 1 && ref_id == -2) {
+	    if (ds & CRAM_RI) {
+		if (!c->comp_hdr->codecs[DS_RI]) return -1;
+		r |= c->comp_hdr->codecs[DS_RI]
+		                ->decode(s, c->comp_hdr->codecs[DS_RI], blk,
+					 (char *)&cr->ref_id, &out_sz);
+		if (r) return -1;
+		if ((fd->required_fields & (SAM_SEQ|SAM_TLEN))
+		    && cr->ref_id >= 0
+		    && cr->ref_id != last_ref_id) {
+		    if (!fd->no_ref) {
+			if (!refs[cr->ref_id])
+			    refs[cr->ref_id] = cram_get_ref(fd, cr->ref_id,
+							    1, 0);
+			s->ref = refs[cr->ref_id];
+
+			if (!fd->unsorted && last_ref_id >= 0 && refs[last_ref_id]) {
+			    cram_ref_decr(fd->refs, last_ref_id);
+			    refs[last_ref_id] = NULL;
+			}
+		    }
+		    s->ref_start = 1;
+		    pthread_mutex_lock(&fd->ref_lock);
+		    pthread_mutex_lock(&fd->refs->lock);
+		    s->ref_end = fd->refs->ref_id[cr->ref_id]->length;
+		    pthread_mutex_unlock(&fd->refs->lock);
+		    pthread_mutex_unlock(&fd->ref_lock);
+
+		    last_ref_id = cr->ref_id;
+		}
+	    } else {
+		cr->ref_id = -1;
+	    }
+	} else {
+	    cr->ref_id = ref_id; // Forced constant in CRAM 1.0
+	}
+	if (cr->ref_id >= bfd->nref) {
+	    fprintf(stderr, "Requested unknown reference ID %d\n", cr->ref_id);
+            return -1;
+	}
+
+	if (ds & CRAM_RL) {
+	    if (!c->comp_hdr->codecs[DS_RL]) return -1;
+	    r |= c->comp_hdr->codecs[DS_RL]
+		            ->decode(s, c->comp_hdr->codecs[DS_RL], blk,
+				     (char *)&cr->len, &out_sz);
+	    if (r) return r;
+	    if (cr->len < 0) {
+	        fprintf(stderr, "Read has negative length\n");
+		return -1;
+	    }
+	}
+
+	if (ds & CRAM_AP) {
+	    if (!c->comp_hdr->codecs[DS_AP]) return -1;
+	    r |= c->comp_hdr->codecs[DS_AP]
+		            ->decode(s, c->comp_hdr->codecs[DS_AP], blk,
+				     (char *)&cr->apos, &out_sz);
+	    if (r) return r;
+	    if (c->comp_hdr->AP_delta)
+		cr->apos += s->last_apos;
+	    s->last_apos=  cr->apos;
+	} else {
+	    cr->apos = c->ref_seq_start;
+	}
+		    
+	if (ds & CRAM_RG) {
+	    if (!c->comp_hdr->codecs[DS_RG]) return -1;
+	    r |= c->comp_hdr->codecs[DS_RG]
+		           ->decode(s, c->comp_hdr->codecs[DS_RG], blk,
+				    (char *)&cr->rg, &out_sz);
+	    if (r) return r;
+	    if (cr->rg == unknown_rg)
+		cr->rg = -1;
+	} else {
+	    cr->rg = -1;
+	}
+
+	cr->name_len = 0;
+
+	if (c->comp_hdr->read_names_included) {
+	    int32_t out_sz2 = 1;
+
+	    // Read directly into name cram_block
+	    cr->name = BLOCK_SIZE(s->name_blk);
+	    if (ds & CRAM_RN) {
+		if (!c->comp_hdr->codecs[DS_RN]) return -1;
+		r |= c->comp_hdr->codecs[DS_RN]
+		                ->decode(s, c->comp_hdr->codecs[DS_RN], blk,
+					 (char *)s->name_blk, &out_sz2);
+		if (r) return r;
+		cr->name_len = out_sz2;
+	    }
+	}
+
+	cr->mate_pos = 0;
+	cr->mate_line = -1;
+	cr->mate_ref_id = -1;
+	if ((ds & CRAM_CF) && (cf & CRAM_FLAG_DETACHED)) {
+	    if (ds & CRAM_MF) {
+		if (CRAM_MAJOR_VERS(fd->version) == 1) {
+		    /* MF is byte in 1.0, int32 in 2.0 */
+		    unsigned char mf;
+		    if (!c->comp_hdr->codecs[DS_MF]) return -1;
+		    r |= c->comp_hdr->codecs[DS_MF]
+			            ->decode(s, c->comp_hdr->codecs[DS_MF],
+					     blk, (char *)&mf, &out_sz);
+		    if (r) return r;
+		    cr->mate_flags = mf;
+		} else {
+		    if (!c->comp_hdr->codecs[DS_MF]) return -1;
+		    r |= c->comp_hdr->codecs[DS_MF]
+			            ->decode(s, c->comp_hdr->codecs[DS_MF],
+					     blk,
+					     (char *)&cr->mate_flags,
+					     &out_sz);
+		    if (r) return r;
+		}
+	    } else {
+		cr->mate_flags = 0;
+	    }
+
+	    if (!c->comp_hdr->read_names_included) {
+		int32_t out_sz2 = 1;
+	    
+		// Read directly into name cram_block
+		cr->name = BLOCK_SIZE(s->name_blk);
+		if (ds & CRAM_RN) {
+		    if (!c->comp_hdr->codecs[DS_RN]) return -1;
+		    r |= c->comp_hdr->codecs[DS_RN]
+			            ->decode(s, c->comp_hdr->codecs[DS_RN],
+					     blk, (char *)s->name_blk,
+					     &out_sz2);
+		    if (r) return r;
+		    cr->name_len = out_sz2;
+		}
+	    }
+		    
+	    if (ds & CRAM_NS) {
+		if (!c->comp_hdr->codecs[DS_NS]) return -1;
+		r |= c->comp_hdr->codecs[DS_NS]
+		                ->decode(s, c->comp_hdr->codecs[DS_NS], blk,
+					 (char *)&cr->mate_ref_id, &out_sz);
+		if (r) return r;
+	    }
+
+// Skip as mate_ref of "*" is legit. It doesn't mean unmapped, just unknown.
+//	    if (cr->mate_ref_id == -1 && cr->flags & 0x01) {
+//		/* Paired, but unmapped */
+//		cr->flags |= BAM_FMUNMAP;
+//	    }
+
+	    if (ds & CRAM_NP) {
+		if (!c->comp_hdr->codecs[DS_NP]) return -1;
+		r |= c->comp_hdr->codecs[DS_NP]
+		                ->decode(s, c->comp_hdr->codecs[DS_NP], blk,
+					 (char *)&cr->mate_pos, &out_sz);
+		if (r) return r;
+	    }
+
+	    if (ds & CRAM_TS) {
+		if (!c->comp_hdr->codecs[DS_TS]) return -1;
+		r |= c->comp_hdr->codecs[DS_TS]
+		                ->decode(s, c->comp_hdr->codecs[DS_TS], blk,
+					 (char *)&cr->tlen, &out_sz);
+		if (r) return r;
+	    } else {
+		cr->tlen = INT_MIN;
+	    }
+	} else if ((ds & CRAM_CF) && (cf & CRAM_FLAG_MATE_DOWNSTREAM)) {
+	    if (ds & CRAM_NF) {
+		if (!c->comp_hdr->codecs[DS_NF]) return -1;
+		r |= c->comp_hdr->codecs[DS_NF]
+		                ->decode(s, c->comp_hdr->codecs[DS_NF], blk,
+					 (char *)&cr->mate_line, &out_sz);
+		if (r) return r;
+		cr->mate_line += rec + 1;
+
+		//cr->name_len = sprintf(name, "%d", name_id++);
+		//cr->name = DSTRING_LEN(name_ds);
+		//dstring_nappend(name_ds, name, cr->name_len);
+
+		cr->mate_ref_id = -1;
+		cr->tlen = INT_MIN;
+		cr->mate_pos = 0;
+	    } else  {
+		cr->mate_flags = 0;
+		cr->tlen = INT_MIN;
+	    }
+	} else {
+	    cr->mate_flags = 0;
+	    cr->tlen = INT_MIN;
+	}
+	/*
+	else if (!name[0]) {
+	    //name[0] = '?'; name[1] = 0;
+	    //cr->name_len = 1;
+	    //cr->name=  DSTRING_LEN(s->name_ds);
+	    //dstring_nappend(s->name_ds, "?", 1);
+
+	    cr->mate_ref_id = -1;
+	    cr->tlen = 0;
+	    cr->mate_pos = 0;
+	}
+	*/
+
+	/* Auxiliary tags */
+	has_MD = has_NM = 0;
+	if (CRAM_MAJOR_VERS(fd->version) == 1)
+	    r |= cram_decode_aux_1_0(c, s, blk, cr);
+	else
+	    r |= cram_decode_aux(c, s, blk, cr, &has_MD, &has_NM);
+	if (r) return r;
+
+	/* Fake up dynamic string growth and appending */
+	if (ds & CRAM_RL) {
+	    cr->seq = BLOCK_SIZE(s->seqs_blk);
+	    BLOCK_GROW(s->seqs_blk, cr->len);
+	    seq = (char *)BLOCK_END(s->seqs_blk);
+	    BLOCK_SIZE(s->seqs_blk) += cr->len;
+
+	    if (!seq)
+		return -1;
+	
+	    cr->qual = BLOCK_SIZE(s->qual_blk);
+	    BLOCK_GROW(s->qual_blk, cr->len);
+	    qual = (char *)BLOCK_END(s->qual_blk);
+	    BLOCK_SIZE(s->qual_blk) += cr->len;
+
+	    if (!s->ref)
+		memset(seq, '=', cr->len);
+	}
+
+	if (!(bf & BAM_FUNMAP)) {
+            if ((ds & CRAM_AP) && cr->apos <= 0) {
+                fprintf(stderr,
+			"Read has alignment position %d but no unmapped flag\n",
+			cr->apos);
+		return -1;
+	    }
+	    /* Decode sequence and generate CIGAR */
+	    if (ds & (CRAM_SEQ | CRAM_MQ)) {
+		r |= cram_decode_seq(fd, c, s, blk, cr, bfd, cf, seq, qual,
+				     has_MD, has_NM);
+		if (r) return r;
+	    } else {
+		cr->cigar = 0;
+		cr->ncigar = 0;
+		cr->aend = cr->apos;
+		cr->mqual = 0;
+	    }
+	} else {
+	    int out_sz2 = cr->len;
+
+	    //puts("Unmapped");
+	    cr->cigar = 0;
+	    cr->ncigar = 0;
+	    cr->aend = cr->apos;
+	    cr->mqual = 0;
+
+	    if (ds & CRAM_BA && cr->len) {
+		if (!c->comp_hdr->codecs[DS_BA]) return -1;
+		r |= c->comp_hdr->codecs[DS_BA]
+		                ->decode(s, c->comp_hdr->codecs[DS_BA], blk,
+					 (char *)seq, &out_sz2);
+		if (r) return r;
+	    }
+
+	    if ((ds & CRAM_CF) && (cf & CRAM_FLAG_PRESERVE_QUAL_SCORES)) {
+		out_sz2 = cr->len;
+		if (ds & CRAM_QS && cr->len >= 0) {
+		    if (!c->comp_hdr->codecs[DS_QS]) return -1;
+		    r |= c->comp_hdr->codecs[DS_QS]
+			            ->decode(s, c->comp_hdr->codecs[DS_QS],
+					     blk, qual, &out_sz2);
+		    if (r) return r;
+		}
+	    } else {
+		if (ds & CRAM_RL)
+		    memset(qual, 255, cr->len);
+	    }
+	}
+    }
+
+    pthread_mutex_lock(&fd->ref_lock);
+    if (refs) {
+	int i;
+	for (i = 0; i < fd->refs->nref; i++) {
+	    if (refs[i])
+		cram_ref_decr(fd->refs, i);
+	}
+	free(refs);
+    } else if (ref_id >= 0 && s->ref != fd->ref_free && !embed_ref) {
+	cram_ref_decr(fd->refs, ref_id);
+    }
+    pthread_mutex_unlock(&fd->ref_lock);
+
+    /* Resolve mate pair cross-references between recs within this slice */
+    r |= cram_decode_slice_xref(s, fd->required_fields);
+
+    // Free the original blocks as we no longer need these.
+    {
+	int i;
+	for (i = 0; i < s->hdr->num_blocks; i++) {
+	    cram_block *b = s->block[i];
+	    cram_free_block(b);
+	    s->block[i] = NULL;
+	}
+    }
+
+    // Also see initial BLOCK_RESIZE_EXACT at top of function.
+    // As we grow blocks we overallocate by up to 50%. So shrink
+    // back to their final sizes here.
+    //
+//    fprintf(stderr, "%d %d // %d %d // %d %d // %d %d\n",
+//    	    (int)s->seqs_blk->byte, (int)s->seqs_blk->alloc, 
+//    	    (int)s->qual_blk->byte, (int)s->qual_blk->alloc, 
+//    	    (int)s->name_blk->byte, (int)s->name_blk->alloc, 
+//    	    (int)s->aux_blk->byte,  (int)s->aux_blk->alloc);
+    BLOCK_RESIZE_EXACT(s->seqs_blk, BLOCK_SIZE(s->seqs_blk)+1);
+    BLOCK_RESIZE_EXACT(s->qual_blk, BLOCK_SIZE(s->qual_blk)+1);
+    BLOCK_RESIZE_EXACT(s->name_blk, BLOCK_SIZE(s->name_blk)+1);
+    BLOCK_RESIZE_EXACT(s->aux_blk,  BLOCK_SIZE(s->aux_blk)+1);
+
+    return r;
+}
+
+typedef struct {
+    cram_fd *fd;
+    cram_container *c;
+    cram_slice *s;
+    SAM_hdr *h;
+    int exit_code;
+} cram_decode_job;
+
+void *cram_decode_slice_thread(void *arg) {
+    cram_decode_job *j = (cram_decode_job *)arg;
+
+    j->exit_code = cram_decode_slice(j->fd, j->c, j->s, j->h);
+
+    return j;
+}
+
+/*
+ * Spawn a multi-threaded version of cram_decode_slice().
+ */
+int cram_decode_slice_mt(cram_fd *fd, cram_container *c, cram_slice *s,
+			 SAM_hdr *bfd) {
+    cram_decode_job *j;
+    int nonblock;
+
+    if (!fd->pool)
+	return cram_decode_slice(fd, c, s, bfd);
+
+    if (!(j = malloc(sizeof(*j))))
+	return -1;
+
+    j->fd = fd;
+    j->c  = c;
+    j->s  = s;
+    j->h  = bfd;
+    
+    nonblock = t_pool_results_queue_sz(fd->rqueue) ? 1 : 0;
+
+    if (-1 == t_pool_dispatch2(fd->pool, fd->rqueue, cram_decode_slice_thread,
+			       j, nonblock)) {
+	/* Would block */
+	fd->job_pending = j;
+    } else {
+	fd->job_pending = NULL;
+    }
+
+    // flush too
+    return 0;
+}
+
+
+/* ----------------------------------------------------------------------
+ * CRAM sequence iterators.
+ */
+
+/*
+ * Converts a cram in-memory record into a bam in-memory record. We
+ * pass a pointer to a bam_seq_t pointer along with the a pointer to
+ * the allocated size. These can initially be pointers to NULL and zero.
+ *
+ * This function will reallocate the bam buffer as required and update
+ * (*bam)->alloc accordingly, allowing it to be used within a loop
+ * efficiently without needing to allocate new bam objects over and
+ * over again.
+ *
+ * Returns the used size of the bam record on success
+ *         -1 on failure.
+ */
+static int cram_to_bam(SAM_hdr *bfd, cram_fd *fd, cram_slice *s,
+		       cram_record *cr, int rec, bam_seq_t **bam) {
+    int bam_idx, rg_len;
+    char name_a[1024], *name;
+    int name_len;
+    char *aux, *aux_orig;
+    char *seq, *qual;
+
+    /* Assign names if not explicitly set */
+    if (fd->required_fields & SAM_QNAME) {
+	if (cr->name_len) {
+	    name = (char *)BLOCK_DATA(s->name_blk) + cr->name;
+	    name_len = cr->name_len;
+	} else {
+	    name = name_a;
+	    name_len = strlen(fd->prefix);
+	    memcpy(name, fd->prefix, name_len);
+	    name += name_len;
+	    *name++ = ':';
+	    if (cr->mate_line >= 0 && cr->mate_line < rec)
+		name = (char *)append_uint64((unsigned char *)name,
+					     s->hdr->record_counter +
+					     cr->mate_line + 1);
+	    else
+		name = (char *)append_uint64((unsigned char *)name,
+					     s->hdr->record_counter +
+					     rec + 1);
+	    name_len = name - name_a;
+	    name = name_a;
+	}
+    } else {
+	name = "?";
+	name_len = 1;
+    }
+
+    /* Generate BAM record */
+    if (cr->rg < -1 || cr->rg >= bfd->nrg)
+	return -1;
+    rg_len = (cr->rg != -1) ? bfd->rg[cr->rg].name_len + 4 : 0;
+
+    if (fd->required_fields & (SAM_SEQ | SAM_QUAL)) {
+	if (!BLOCK_DATA(s->seqs_blk))
+	    return -1;
+	seq = (char *)BLOCK_DATA(s->seqs_blk) + cr->seq;
+    } else {
+	seq = "*";
+	cr->len = 0;
+    }
+
+
+    if (fd->required_fields & SAM_QUAL) {
+	if (!BLOCK_DATA(s->qual_blk))
+	    return -1;
+	qual = (char *)BLOCK_DATA(s->qual_blk) + cr->qual;
+    } else {
+	qual = NULL;
+    }
+
+    bam_idx = bam_construct_seq(bam, cr->aux_size + rg_len,
+				name, name_len,
+				cr->flags,
+				cr->ref_id,
+				cr->apos,
+				cr->aend,
+				cr->mqual,
+				cr->ncigar, &s->cigar[cr->cigar],
+				cr->mate_ref_id,
+				cr->mate_pos,
+				cr->tlen,
+				cr->len,
+				seq,
+				qual);
+    if (bam_idx == -1)
+	return -1;
+
+    aux = aux_orig = (char *)bam_aux(*bam);
+
+    /* Auxiliary strings */
+    if (cr->aux_size != 0) {
+	memcpy(aux, BLOCK_DATA(s->aux_blk) + cr->aux, cr->aux_size);
+	aux += cr->aux_size;
+    }
+
+    /* RG:Z: */
+    if (cr->rg != -1) {
+	int len = bfd->rg[cr->rg].name_len;
+	*aux++ = 'R'; *aux++ = 'G'; *aux++ = 'Z';
+	memcpy(aux, bfd->rg[cr->rg].name, len);
+	aux += len;
+	*aux++ = 0;
+    }
+    
+    return bam_idx + (aux - aux_orig);
+}
+
+/*
+ * Here be dragons! The multi-threading code in this is crufty beyond belief.
+ */
+static cram_slice *cram_next_slice(cram_fd *fd, cram_container **cp) {
+    cram_container *c;
+    cram_slice *s = NULL;
+
+    if (!(c = fd->ctr)) {
+	// Load first container.
+	do {
+	    if (!(c = fd->ctr = cram_read_container(fd)))
+		return NULL;
+	} while (c->length == 0);
+
+	/*
+	 * The first container may be a result of a sub-range query.
+	 * In which case it may still not be the optimal starting point
+	 * due to skipped containers/slices in the index. 
+	 */
+	if (fd->range.refid != -2) {
+	    while (c->ref_seq_id != -2 &&
+		   (c->ref_seq_id < fd->range.refid ||
+		    c->ref_seq_start + c->ref_seq_span-1 < fd->range.start)) {
+		if (0 != cram_seek(fd, c->length, SEEK_CUR))
+		    return NULL;
+		cram_free_container(fd->ctr);
+		do {
+		    if (!(c = fd->ctr = cram_read_container(fd)))
+			return NULL;
+		} while (c->length == 0);
+	    }
+
+	    if (c->ref_seq_id != -2 && c->ref_seq_id != fd->range.refid)
+		return NULL;
+	}
+
+	if (!(c->comp_hdr_block = cram_read_block(fd)))
+	    return NULL;
+	if (c->comp_hdr_block->content_type != COMPRESSION_HEADER)
+	    return NULL;
+
+	c->comp_hdr = cram_decode_compression_header(fd, c->comp_hdr_block);
+	if (!c->comp_hdr)
+	    return NULL;
+	if (!c->comp_hdr->AP_delta &&
+	    sam_hdr_sort_order(fd->header) != ORDER_COORD) {
+	    pthread_mutex_lock(&fd->ref_lock);
+	    fd->unsorted = 1;
+	    pthread_mutex_unlock(&fd->ref_lock);
+	}
+    }
+
+    if ((s = c->slice)) {
+	c->slice = NULL;
+	cram_free_slice(s);
+	s = NULL;
+    }
+
+    if (c->curr_slice == c->max_slice) {
+	cram_free_container(c);
+	c = NULL;
+    }
+
+    /* Sorry this is so contorted! */
+    for (;;) {
+	if (fd->job_pending) {
+	    cram_decode_job *j = (cram_decode_job *)fd->job_pending;
+	    c = j->c;
+	    s = j->s;
+	    free(fd->job_pending);
+	    fd->job_pending = NULL;
+	} else if (!fd->ooc) {
+	empty_container:
+	    if (!c || c->curr_slice == c->max_slice) {
+		// new container
+		do {
+		    if (!(c = fd->ctr = cram_read_container(fd))) {
+			if (fd->pool) {
+			    fd->ooc = 1;
+			    break;
+			}
+
+			return NULL;
+		    }
+		} while (c->length == 0);
+		if (fd->ooc)
+		    break;
+
+		/* Skip containers not yet spanning our range */
+		if (fd->range.refid != -2 && c->ref_seq_id != -2) {
+		    fd->required_fields |= SAM_POS;
+
+		    if (c->ref_seq_id != fd->range.refid) {
+			cram_free_container(c);
+			fd->ctr = NULL;
+			fd->ooc = 1;
+			fd->eof = 1;
+			break;
+		    }
+
+		    if (c->ref_seq_start > fd->range.end) {
+			cram_free_container(c);
+			fd->ctr = NULL;
+			fd->ooc = 1;
+			fd->eof = 1;
+			break;
+		    }
+
+		    if (c->ref_seq_start + c->ref_seq_span-1 <
+			fd->range.start) {
+			c->curr_rec = c->max_rec;
+			c->curr_slice = c->max_slice;
+			cram_seek(fd, c->length, SEEK_CUR);
+			cram_free_container(c);
+			c = NULL;
+			continue;
+		    }
+		}
+
+		if (!(c->comp_hdr_block = cram_read_block(fd)))
+		    return NULL;
+		if (c->comp_hdr_block->content_type != COMPRESSION_HEADER)
+		    return NULL;
+
+		c->comp_hdr =
+		    cram_decode_compression_header(fd, c->comp_hdr_block);
+		if (!c->comp_hdr)
+		    return NULL;
+
+		if (!c->comp_hdr->AP_delta &&
+		    sam_hdr_sort_order(fd->header) != ORDER_COORD) {
+		    pthread_mutex_lock(&fd->ref_lock);
+		    fd->unsorted = 1;
+		    pthread_mutex_unlock(&fd->ref_lock);
+		}
+	    }
+
+	    if (c->num_records == 0) {
+		cram_free_container(c); c = NULL;
+		goto empty_container;
+	    }
+
+
+	    if (!(s = c->slice = cram_read_slice(fd)))
+		return NULL;
+	    c->curr_slice++;
+	    c->curr_rec = 0;
+	    c->max_rec = s->hdr->num_records;
+
+	    s->last_apos = s->hdr->ref_seq_start;
+	    
+	    /* Skip slices not yet spanning our range */
+	    if (fd->range.refid != -2 && s->hdr->ref_seq_id != -2) {
+		if (s->hdr->ref_seq_id != fd->range.refid) {
+		    fd->eof = 1;
+		    cram_free_slice(s);
+		    c->slice = NULL;
+		    return NULL;
+		}
+
+		if (s->hdr->ref_seq_start > fd->range.end) {
+		    fd->eof = 1;
+		    cram_free_slice(s);
+		    c->slice = NULL;
+		    return NULL;
+		}
+
+		if (s->hdr->ref_seq_start + s->hdr->ref_seq_span-1 <
+		    fd->range.start) {
+		    cram_free_slice(s);
+		    c->slice = NULL;
+		    cram_free_container(c);
+		    c = NULL;
+		    continue;
+		}
+	    }
+	}
+
+	/* Test decoding of 1st seq */
+	if (!c || !s)
+	    break;
+
+	if (cram_decode_slice_mt(fd, c, s, fd->header) != 0) {
+	    //	if (cram_decode_slice(fd, c, s, fd->header) != 0) {
+	    fprintf(stderr, "Failure to decode slice\n");
+	    cram_free_slice(s);
+	    c->slice = NULL;
+	    return NULL;
+	}
+
+	if (!fd->pool || fd->job_pending)
+	    break;
+
+	// Push it a bit far, to qsize in queue rather than pending arrival,
+	// as cram tends to be a bit bursty in decode timings.
+	if (t_pool_results_queue_len(fd->rqueue) > fd->pool->qsize)
+	    break;
+    }
+
+    if (fd->pool) {
+	t_pool_result *res;
+	cram_decode_job *j;
+	
+//	fprintf(stderr, "Thread pool len = %d, %d\n",
+//		t_pool_results_queue_len(fd->rqueue),
+//		t_pool_results_queue_sz(fd->rqueue));
+
+	if (fd->ooc && t_pool_results_queue_empty(fd->rqueue))
+	    return NULL;
+
+	res = t_pool_next_result_wait(fd->rqueue);
+
+	if (!res || !res->data) {
+	    fprintf(stderr, "t_pool_next_result failure\n");
+	    return NULL;
+	}
+
+	j = (cram_decode_job *)res->data;
+	c = j->c;
+	s = j->s;
+
+	fd->ctr = c;
+
+	t_pool_delete_result(res, 1);
+    }
+
+    *cp = c;
+    return s;
+}
+
+/*
+ * Read the next cram record and return it.
+ * Note that to decode cram_record the caller will need to look up some data
+ * in the current slice, pointed to by fd->ctr->slice. This is valid until
+ * the next call to cram_get_seq (which may invalidate it).
+ *
+ * Returns record pointer on success (do not free)
+ *        NULL on failure
+ */
+cram_record *cram_get_seq(cram_fd *fd) {
+    cram_container *c;
+    cram_slice *s;
+
+    for (;;) {
+	c = fd->ctr;
+	if (c && c->slice && c->curr_rec < c->max_rec) {
+	    s = c->slice;
+	} else {
+	    if (!(s = cram_next_slice(fd, &c)))
+		return NULL;
+	    continue; /* In case slice contains no records */
+	}
+
+	if (fd->range.refid != -2) {
+	    if (fd->range.refid == -1 && s->crecs[c->curr_rec].ref_id != -1) {
+		// Special case when looking for unmapped blocks at end.
+		// If these are mixed in with mapped data (c->ref_id == -2)
+		// then we need skip until we find the unmapped data, if at all
+		c->curr_rec++;
+		continue;
+	    }
+	    if (s->crecs[c->curr_rec].ref_id < fd->range.refid &&
+		s->crecs[c->curr_rec].ref_id != -1) {
+		// Looking for a mapped read, but not there yet.  Special case
+		// as -1 (unmapped) shouldn't be considered < refid.
+		c->curr_rec++;
+		continue;
+	    }
+
+	    if (s->crecs[c->curr_rec].ref_id != fd->range.refid) {
+		fd->eof = 1;
+		cram_free_slice(s);
+		c->slice = NULL;
+		return NULL;
+	    }
+
+	    if (fd->range.refid != -1 && s->crecs[c->curr_rec].apos > fd->range.end) {
+		fd->eof = 1;
+		cram_free_slice(s);
+		c->slice = NULL;
+		return NULL;
+	    }
+
+	    if (fd->range.refid != -1 && s->crecs[c->curr_rec].aend < fd->range.start) {
+		c->curr_rec++;
+		continue;
+	    }
+	}
+
+	break;
+    }
+
+    fd->ctr = c;
+    c->slice = s;
+    return &s->crecs[c->curr_rec++];
+}
+
+/*
+ * Read the next cram record and convert it to a bam_seq_t struct.
+ *
+ * Returns 0 on success
+ *        -1 on EOF or failure (check fd->err)
+ */
+int cram_get_bam_seq(cram_fd *fd, bam_seq_t **bam) {
+    cram_record *cr;
+    cram_container *c;
+    cram_slice *s;
+
+    if (!(cr = cram_get_seq(fd)))
+	return -1;
+
+    c = fd->ctr;
+    s = c->slice;
+
+    return cram_to_bam(fd->header, fd, s, cr, c->curr_rec-1, bam);
+}
diff --git a/htslib/cram/cram_decode.h b/htslib/cram/cram_decode.h
new file mode 100644
index 0000000..64b188e
--- /dev/null
+++ b/htslib/cram/cram_decode.h
@@ -0,0 +1,112 @@
+/*
+Copyright (c) 2012-2013 Genome Research Ltd.
+Author: James Bonfield <jkb at sanger.ac.uk>
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+Institute nor the names of its contributors may be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+/*! \file
+ * Include cram.h instead.
+ *
+ * This is an internal part of the CRAM system and is automatically included
+ * when you #include cram.h.
+ *
+ * Implements the decoding portion of CRAM I/O. Also see
+ * cram_codecs.[ch] for the actual encoding functions themselves.
+ */
+
+#ifndef _CRAM_READ_H_
+#define _CRAM_READ_H_
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/* ----------------------------------------------------------------------
+ * CRAM sequence iterators.
+ */
+
+/*! Read the next cram record and return it as a cram_record.
+ *
+ * Note that to decode cram_record the caller will need to look up some data
+ * in the current slice, pointed to by fd->ctr->slice. This is valid until
+ * the next call to cram_get_seq (which may invalidate it).
+ *
+ * @return
+ * Returns record pointer on success (do not free);
+ *        NULL on failure
+ */
+cram_record *cram_get_seq(cram_fd *fd);
+
+/*! Read the next cram record and convert it to a bam_seq_t struct.
+ *
+ * @return
+ * Returns 0 on success;
+ *        -1 on EOF or failure (check fd->err)
+ */
+int cram_get_bam_seq(cram_fd *fd, bam_seq_t **bam);
+
+
+/* ----------------------------------------------------------------------
+ * Internal functions
+ */
+
+/*! INTERNAL:
+ * Decodes a CRAM block compression header.
+ *
+ * @return
+ * Returns header ptr on success;
+ *         NULL on failure
+ */
+cram_block_compression_hdr *cram_decode_compression_header(cram_fd *fd,
+							   cram_block *b);
+
+/*! INTERNAL:
+ * Decodes a CRAM (un)mapped slice header block.
+ *
+ * @return
+ * Returns slice header ptr on success;
+ *         NULL on failure
+ */
+cram_block_slice_hdr *cram_decode_slice_header(cram_fd *fd, cram_block *b);
+
+
+/*! INTERNAL:
+ * Decode an entire slice from container blocks. Fills out s->crecs[] array.
+ *
+ * @return
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+int cram_decode_slice(cram_fd *fd, cram_container *c, cram_slice *s,
+		      SAM_hdr *hdr);
+
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/htslib/cram/cram_encode.c b/htslib/cram/cram_encode.c
new file mode 100644
index 0000000..5a9d64b
--- /dev/null
+++ b/htslib/cram/cram_encode.c
@@ -0,0 +1,3105 @@
+/*
+Copyright (c) 2012-2013 Genome Research Ltd.
+Author: James Bonfield <jkb at sanger.ac.uk>
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+Institute nor the names of its contributors may be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+#include <config.h>
+
+#include <stdio.h>
+#include <errno.h>
+#include <assert.h>
+#include <stdlib.h>
+#include <string.h>
+#include <zlib.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <math.h>
+#include <ctype.h>
+
+#include "cram/cram.h"
+#include "cram/os.h"
+#include "htslib/hts.h"
+
+#define Z_CRAM_STRAT Z_FILTERED
+//#define Z_CRAM_STRAT Z_RLE
+//#define Z_CRAM_STRAT Z_HUFFMAN_ONLY
+//#define Z_CRAM_STRAT Z_DEFAULT_STRATEGY
+
+static int process_one_read(cram_fd *fd, cram_container *c,
+			    cram_slice *s, cram_record *cr,
+			    bam_seq_t *b, int rnum);
+
+/*
+ * Returns index of val into key.
+ * Basically strchr(key, val)-key;
+ */
+static int sub_idx(char *key, char val) {
+    int i;
+
+    for (i = 0; *key && *key++ != val; i++);
+    return i;
+}
+
+/*
+ * Encodes a compression header block into a generic cram_block structure.
+ *
+ * Returns cram_block ptr on success
+ *         NULL on failure
+ */
+cram_block *cram_encode_compression_header(cram_fd *fd, cram_container *c,
+					   cram_block_compression_hdr *h) {
+    cram_block *cb  = cram_new_block(COMPRESSION_HEADER, 0);
+    cram_block *map = cram_new_block(COMPRESSION_HEADER, 0);
+    int i, mc;
+
+    if (!cb || !map)
+	return NULL;
+
+    /*
+     * This is a concatenation of several blocks of data:
+     * header + landmarks, preservation map, read encoding map, and the tag
+     * encoding map.
+     * All 4 are variable sized and we need to know how large these are
+     * before creating the compression header itself as this starts with
+     * the total size (stored as a variable length string).
+     */
+
+    // Duplicated from container itself, and removed in 1.1
+    if (CRAM_MAJOR_VERS(fd->version) == 1) {
+	itf8_put_blk(cb, h->ref_seq_id);
+	itf8_put_blk(cb, h->ref_seq_start);
+	itf8_put_blk(cb, h->ref_seq_span);
+	itf8_put_blk(cb, h->num_records);
+	itf8_put_blk(cb, h->num_landmarks);
+	for (i = 0; i < h->num_landmarks; i++) {
+	    itf8_put_blk(cb, h->landmark[i]);
+	}
+    }
+
+    if (h->preservation_map)
+	kh_destroy(map, h->preservation_map);
+
+    /* Create in-memory preservation map */
+    /* FIXME: should create this when we create the container */
+    {
+	khint_t k;
+	int r;
+
+	if (!(h->preservation_map = kh_init(map)))
+	    return NULL;
+
+	k = kh_put(map, h->preservation_map, "RN", &r);
+	if (-1 == r) return NULL;
+	kh_val(h->preservation_map, k).i = 1;
+
+	if (CRAM_MAJOR_VERS(fd->version) == 1) {
+	    k = kh_put(map, h->preservation_map, "PI", &r);
+	    if (-1 == r) return NULL;
+	    kh_val(h->preservation_map, k).i = 0;
+
+	    k = kh_put(map, h->preservation_map, "UI", &r);
+	    if (-1 == r) return NULL;
+	    kh_val(h->preservation_map, k).i = 1;
+
+	    k = kh_put(map, h->preservation_map, "MI", &r);
+	    if (-1 == r) return NULL;
+	    kh_val(h->preservation_map, k).i = 1;
+
+	} else {
+	    // Technically SM was in 1.0, but wasn't in Java impl.
+	    k = kh_put(map, h->preservation_map, "SM", &r);
+	    if (-1 == r) return NULL;
+	    kh_val(h->preservation_map, k).i = 0;
+
+	    k = kh_put(map, h->preservation_map, "TD", &r);
+	    if (-1 == r) return NULL;
+	    kh_val(h->preservation_map, k).i = 0;
+
+	    k = kh_put(map, h->preservation_map, "AP", &r);
+	    if (-1 == r) return NULL;
+	    kh_val(h->preservation_map, k).i = h->AP_delta;
+
+	    if (fd->no_ref || fd->embed_ref) {
+		// Reference Required == No
+		k = kh_put(map, h->preservation_map, "RR", &r);
+		if (-1 == r) return NULL;
+		kh_val(h->preservation_map, k).i = 0;
+	    }
+	}
+    }
+
+    /* Encode preservation map; could collapse this and above into one */
+    mc = 0;
+    BLOCK_SIZE(map) = 0;
+    if (h->preservation_map) {
+	khint_t k;
+
+	for (k = kh_begin(h->preservation_map);
+	     k != kh_end(h->preservation_map);
+	     k++) {
+	    const char *key;
+	    khash_t(map) *pmap = h->preservation_map;
+
+
+	    if (!kh_exist(pmap, k))
+		continue;
+
+	    key = kh_key(pmap, k);
+	    BLOCK_APPEND(map, key, 2);
+
+	    switch(CRAM_KEY(key[0], key[1])) {
+	    case CRAM_KEY('M','I'):
+		BLOCK_APPEND_CHAR(map, kh_val(pmap, k).i);
+		break;
+
+	    case CRAM_KEY('U','I'):
+		BLOCK_APPEND_CHAR(map, kh_val(pmap, k).i);
+		break;
+
+	    case CRAM_KEY('P','I'):
+		BLOCK_APPEND_CHAR(map, kh_val(pmap, k).i);
+		break;
+
+	    case CRAM_KEY('A','P'):
+		BLOCK_APPEND_CHAR(map, kh_val(pmap, k).i);
+		break;
+
+	    case CRAM_KEY('R','N'):
+		BLOCK_APPEND_CHAR(map, kh_val(pmap, k).i);
+		break;
+
+	    case CRAM_KEY('R','R'):
+		BLOCK_APPEND_CHAR(map, kh_val(pmap, k).i);
+		break;
+
+	    case CRAM_KEY('S','M'): {
+		char smat[5], *mp = smat;
+		*mp++ =
+		    (sub_idx("CGTN", h->substitution_matrix[0][0]) << 6) |
+		    (sub_idx("CGTN", h->substitution_matrix[0][1]) << 4) |
+		    (sub_idx("CGTN", h->substitution_matrix[0][2]) << 2) |
+		    (sub_idx("CGTN", h->substitution_matrix[0][3]) << 0);
+		*mp++ =
+		    (sub_idx("AGTN", h->substitution_matrix[1][0]) << 6) |
+		    (sub_idx("AGTN", h->substitution_matrix[1][1]) << 4) |
+		    (sub_idx("AGTN", h->substitution_matrix[1][2]) << 2) |
+		    (sub_idx("AGTN", h->substitution_matrix[1][3]) << 0);
+		*mp++ =
+		    (sub_idx("ACTN", h->substitution_matrix[2][0]) << 6) |
+		    (sub_idx("ACTN", h->substitution_matrix[2][1]) << 4) |
+		    (sub_idx("ACTN", h->substitution_matrix[2][2]) << 2) |
+		    (sub_idx("ACTN", h->substitution_matrix[2][3]) << 0);
+		*mp++ =
+		    (sub_idx("ACGN", h->substitution_matrix[3][0]) << 6) |
+		    (sub_idx("ACGN", h->substitution_matrix[3][1]) << 4) |
+		    (sub_idx("ACGN", h->substitution_matrix[3][2]) << 2) |
+		    (sub_idx("ACGN", h->substitution_matrix[3][3]) << 0);
+		*mp++ =
+		    (sub_idx("ACGT", h->substitution_matrix[4][0]) << 6) |
+		    (sub_idx("ACGT", h->substitution_matrix[4][1]) << 4) |
+		    (sub_idx("ACGT", h->substitution_matrix[4][2]) << 2) |
+		    (sub_idx("ACGT", h->substitution_matrix[4][3]) << 0);
+		BLOCK_APPEND(map, smat, 5);
+		break;
+	    }
+
+	    case CRAM_KEY('T','D'): {
+		itf8_put_blk(map, BLOCK_SIZE(h->TD_blk));
+		BLOCK_APPEND(map,
+			     BLOCK_DATA(h->TD_blk),
+			     BLOCK_SIZE(h->TD_blk));
+		break;
+	    }
+
+	    default:
+		fprintf(stderr, "Unknown preservation key '%.2s'\n", key);
+		break;
+	    }
+
+	    mc++;
+        }
+    }
+    itf8_put_blk(cb, BLOCK_SIZE(map) + itf8_size(mc));
+    itf8_put_blk(cb, mc);    
+    BLOCK_APPEND(cb, BLOCK_DATA(map), BLOCK_SIZE(map));
+    
+    /* rec encoding map */
+    mc = 0;
+    BLOCK_SIZE(map) = 0;
+    if (h->codecs[DS_BF]) {
+	if (-1 == h->codecs[DS_BF]->store(h->codecs[DS_BF], map, "BF",
+					  fd->version))
+	    return NULL;
+	mc++;
+    }
+    if (h->codecs[DS_CF]) {
+	if (-1 == h->codecs[DS_CF]->store(h->codecs[DS_CF], map, "CF",
+					  fd->version))
+	    return NULL;
+	mc++;
+    }
+    if (h->codecs[DS_RL]) {
+	if (-1 == h->codecs[DS_RL]->store(h->codecs[DS_RL], map, "RL",
+					  fd->version))
+	    return NULL;
+	mc++;
+    }
+    if (h->codecs[DS_AP]) {
+	if (-1 == h->codecs[DS_AP]->store(h->codecs[DS_AP], map, "AP",
+					  fd->version))
+	    return NULL;
+	mc++;
+    }
+    if (h->codecs[DS_RG]) {
+	if (-1 == h->codecs[DS_RG]->store(h->codecs[DS_RG], map, "RG",
+					  fd->version))
+	    return NULL;
+	mc++;
+    }
+    if (h->codecs[DS_MF]) {
+	if (-1 == h->codecs[DS_MF]->store(h->codecs[DS_MF], map, "MF",
+					  fd->version))
+	    return NULL;
+	mc++;
+    }
+    if (h->codecs[DS_NS]) {
+	if (-1 == h->codecs[DS_NS]->store(h->codecs[DS_NS], map, "NS",
+					  fd->version))
+	    return NULL;
+	mc++;
+    }
+    if (h->codecs[DS_NP]) {
+	if (-1 == h->codecs[DS_NP]->store(h->codecs[DS_NP], map, "NP",
+					  fd->version))
+	    return NULL;
+	mc++;
+    }
+    if (h->codecs[DS_TS]) {
+	if (-1 == h->codecs[DS_TS]->store(h->codecs[DS_TS], map, "TS",
+					  fd->version))
+	    return NULL;
+	mc++;
+    }
+    if (h->codecs[DS_NF]) {
+	if (-1 == h->codecs[DS_NF]->store(h->codecs[DS_NF], map, "NF",
+					  fd->version))
+	    return NULL;
+	mc++;
+    }
+    if (h->codecs[DS_TC]) {
+	if (-1 == h->codecs[DS_TC]->store(h->codecs[DS_TC], map, "TC",
+					  fd->version))
+	    return NULL;
+	mc++;
+    }
+    if (h->codecs[DS_TN]) {
+	if (-1 == h->codecs[DS_TN]->store(h->codecs[DS_TN], map, "TN",
+					  fd->version))
+	    return NULL;
+	mc++;
+    }
+    if (h->codecs[DS_TL]) {
+	if (-1 == h->codecs[DS_TL]->store(h->codecs[DS_TL], map, "TL",
+					  fd->version))
+	    return NULL;
+	mc++;
+    }
+    if (h->codecs[DS_FN]) {
+	if (-1 == h->codecs[DS_FN]->store(h->codecs[DS_FN], map, "FN",
+					  fd->version))
+	    return NULL;
+	mc++;
+    }
+    if (h->codecs[DS_FC]) {
+	if (-1 == h->codecs[DS_FC]->store(h->codecs[DS_FC], map, "FC",
+					  fd->version))
+	    return NULL;
+	mc++;
+    }
+    if (h->codecs[DS_FP]) {
+	if (-1 == h->codecs[DS_FP]->store(h->codecs[DS_FP], map, "FP",
+					  fd->version))
+	    return NULL;
+	mc++;
+    }
+    if (h->codecs[DS_BS]) {
+	if (-1 == h->codecs[DS_BS]->store(h->codecs[DS_BS], map, "BS",
+					  fd->version))
+	    return NULL;
+	mc++;
+    }
+    if (h->codecs[DS_IN]) {
+	if (-1 == h->codecs[DS_IN]->store(h->codecs[DS_IN], map, "IN",
+					  fd->version))
+	    return NULL;
+	mc++;
+    }
+    if (h->codecs[DS_DL]) {
+	if (-1 == h->codecs[DS_DL]->store(h->codecs[DS_DL], map, "DL",
+					  fd->version))
+	    return NULL;
+	mc++;
+    }
+    if (h->codecs[DS_BA]) {
+	if (-1 == h->codecs[DS_BA]->store(h->codecs[DS_BA], map, "BA",
+					  fd->version))
+	    return NULL;
+	mc++;
+    }
+    if (h->codecs[DS_BB]) {
+	if (-1 == h->codecs[DS_BB]->store(h->codecs[DS_BB], map, "BB",
+					  fd->version))
+	    return NULL;
+	mc++;
+    }
+    if (h->codecs[DS_MQ]) {
+	if (-1 == h->codecs[DS_MQ]->store(h->codecs[DS_MQ], map, "MQ",
+					  fd->version))
+	    return NULL;
+	mc++;
+    }
+    if (h->codecs[DS_RN]) {
+	if (-1 == h->codecs[DS_RN]->store(h->codecs[DS_RN], map, "RN",
+					  fd->version))
+	    return NULL;
+	mc++;
+    }
+    if (h->codecs[DS_QS]) {
+	if (-1 == h->codecs[DS_QS]->store(h->codecs[DS_QS], map, "QS",
+					  fd->version))
+	    return NULL;
+	mc++;
+    }
+    if (h->codecs[DS_QQ]) {
+	if (-1 == h->codecs[DS_QQ]->store(h->codecs[DS_QQ], map, "QQ",
+					  fd->version))
+	    return NULL;
+	mc++;
+    }
+    if (h->codecs[DS_RI]) {
+	if (-1 == h->codecs[DS_RI]->store(h->codecs[DS_RI], map, "RI",
+					  fd->version))
+	    return NULL;
+	mc++;
+    }
+    if (CRAM_MAJOR_VERS(fd->version) != 1) {
+	if (h->codecs[DS_SC]) {
+	    if (-1 == h->codecs[DS_SC]->store(h->codecs[DS_SC], map, "SC",
+					      fd->version))
+		return NULL;
+	    mc++;
+	}
+	if (h->codecs[DS_RS]) {
+	    if (-1 == h->codecs[DS_RS]->store(h->codecs[DS_RS], map, "RS",
+					      fd->version))
+		return NULL;
+	    mc++;
+	}
+	if (h->codecs[DS_PD]) {
+	    if (-1 == h->codecs[DS_PD]->store(h->codecs[DS_PD], map, "PD",
+					      fd->version))
+		return NULL;
+	    mc++;
+	}
+	if (h->codecs[DS_HC]) {
+	    if (-1 == h->codecs[DS_HC]->store(h->codecs[DS_HC], map, "HC",
+					      fd->version))
+		return NULL;
+	    mc++;
+	}
+    }
+    if (h->codecs[DS_TM]) {
+	if (-1 == h->codecs[DS_TM]->store(h->codecs[DS_TM], map, "TM",
+					  fd->version))
+	    return NULL;
+	mc++;
+    }
+    if (h->codecs[DS_TV]) {
+	if (-1 == h->codecs[DS_TV]->store(h->codecs[DS_TV], map, "TV",
+					  fd->version))
+	    return NULL;
+	mc++;
+    }
+    itf8_put_blk(cb, BLOCK_SIZE(map) + itf8_size(mc));
+    itf8_put_blk(cb, mc);    
+    BLOCK_APPEND(cb, BLOCK_DATA(map), BLOCK_SIZE(map));
+
+    /* tag encoding map */
+#if 0
+    mp = map; mc = 0;
+    if (h->tag_encoding_map) {
+        HashItem *hi;
+        HashIter *iter = HashTableIterCreate();
+	if (!iter)
+	    return NULL;
+
+        while ((hi = HashTableIterNext(h->tag_encoding_map, iter))) {
+            cram_map *m = hi->data.p;
+	    int sz;
+
+	    mp += itf8_put(mp, (hi->key[0]<<16)|(hi->key[1]<<8)|hi->key[2]);
+	    if (-1 == (sz = m->codec->store(m->codec, mp, NULL, fd->version)))
+		return NULL;
+	    mp += sz;
+	    mc++;
+        }
+
+        HashTableIterDestroy(iter);
+    }
+#else
+    mc = 0;
+    BLOCK_SIZE(map) = 0;
+    if (c->tags_used) {
+	khint_t k;
+
+#define TAG_ID(a) ((#a[0]<<8)+#a[1])
+
+	for (k = kh_begin(c->tags_used); k != kh_end(c->tags_used); k++) {
+	    int key;
+	    if (!kh_exist(c->tags_used, k))
+		continue;
+
+	    mc++;
+	    itf8_put_blk(map, kh_key(c->tags_used, k));
+
+	    // use block content id 4
+	    switch((key = kh_key(c->tags_used, k)) & 0xff) {
+	    case 'Z': case 'H':
+		// string as byte_array_stop
+		if (CRAM_MAJOR_VERS(fd->version) == 1) {
+		    BLOCK_APPEND(map,
+				 "\005" // BYTE_ARRAY_STOP
+				 "\005" // len
+				 "\t"   // stop-byte is also SAM separator
+				 DS_aux_S "\000\000\000",
+				 7);
+		} else {
+		    if (key>>8 == TAG_ID(OQ))
+			BLOCK_APPEND(map,
+				     "\005" // BYTE_ARRAY_STOP
+				     "\002" // len
+				     "\t"   // stop-byte is also SAM separator
+				     DS_aux_OQ_S,
+				     4);
+		    else if (key>>8 == TAG_ID(BQ))
+			BLOCK_APPEND(map,
+				     "\005" // BYTE_ARRAY_STOP
+				     "\002" // len
+				     "\t"   // stop-byte is also SAM separator
+				     DS_aux_BQ_S,
+				     4);
+		    else if (key>>8 == TAG_ID(BD))
+			BLOCK_APPEND(map,
+				     "\005" // BYTE_ARRAY_STOP
+				     "\002" // len
+				     "\t"   // stop-byte is also SAM separator
+				     DS_aux_BD_S,
+				     4);
+		    else if (key>>8 == TAG_ID(BI))
+			BLOCK_APPEND(map,
+				     "\005" // BYTE_ARRAY_STOP
+				     "\002" // len
+				     "\t"   // stop-byte is also SAM separator
+				     DS_aux_BI_S,
+				     4);
+		    else if ((key>>8 == TAG_ID(Q2)) ||
+			     (key>>8 == TAG_ID(U2)) ||
+			     (key>>8 == TAG_ID(QT)) ||
+			     (key>>8 == TAG_ID(CQ)))
+			BLOCK_APPEND(map,
+				     "\005" // BYTE_ARRAY_STOP
+				     "\002" // len
+				     "\t"   // stop-byte is also SAM separator
+				     DS_aux_oq_S,
+				     4);
+		    else if ((key>>8 == TAG_ID(R2)) ||
+			     (key>>8 == TAG_ID(E2)) ||
+			     (key>>8 == TAG_ID(CS)) ||
+			     (key>>8 == TAG_ID(BC)) ||
+			     (key>>8 == TAG_ID(RT)))
+			BLOCK_APPEND(map,
+				     "\005" // BYTE_ARRAY_STOP
+				     "\002" // len
+				     "\t"   // stop-byte is also SAM separator
+				     DS_aux_os_S,
+				     4);
+		    else
+			BLOCK_APPEND(map,
+				     "\005" // BYTE_ARRAY_STOP
+				     "\002" // len
+				     "\t"   // stop-byte is also SAM separator
+				     DS_aux_oz_S,
+				     4);
+		}
+		break;
+
+	    case 'A': case 'c': case 'C':
+		// byte array len, 1 byte
+		BLOCK_APPEND(map,
+			     "\004" // BYTE_ARRAY_LEN
+			     "\011" // length
+			     "\003" // HUFFMAN (len)
+			     "\004" // huffman-len
+			     "\001" // 1 symbol
+			     "\001" // symbol=1 byte value
+			     "\001" // 1 length
+			     "\000" // length=0
+			     "\001" // EXTERNAL (val)
+			     "\001" // external-len
+			     DS_aux_S,// content-id
+			     11);
+		break;
+
+	    case 's': case 'S':
+		// byte array len, 2 byte
+		BLOCK_APPEND(map,
+			     "\004" // BYTE_ARRAY_LEN
+			     "\011" // length
+			     "\003" // HUFFMAN (len)
+			     "\004" // huffman-len
+			     "\001" // 1 symbol
+			     "\002" // symbol=2 byte value
+			     "\001" // 1 length
+			     "\000" // length=0
+			     "\001" // EXTERNAL (val)
+			     "\001" // external-len
+			     DS_aux_S,// content-id
+			     11);
+		break;
+
+	    case 'i': case 'I': case 'f':
+		// byte array len, 4 byte
+		BLOCK_APPEND(map,
+			     "\004" // BYTE_ARRAY_LEN
+			     "\011" // length
+			     "\003" // HUFFMAN (len)
+			     "\004" // huffman-len
+			     "\001" // 1 symbol
+			     "\004" // symbol=4 byte value
+			     "\001" // 1 length
+			     "\000" // length=0
+			     "\001" // EXTERNAL (val)
+			     "\001" // external-len
+			     DS_aux_S,// content-id
+			     11);
+		break;
+
+	    case 'B':
+		// Byte array of variable size, but we generate our tag
+		// byte stream at the wrong stage (during reading and not
+		// after slice header construction). So we use
+		// BYTE_ARRAY_LEN with the length codec being external
+		// too.
+		if ((key>>8 == TAG_ID(FZ)) || (key>>8 == TAG_ID(ZM)))
+		    BLOCK_APPEND(map,
+				 "\004" // BYTE_ARRAY_LEN
+				 "\006" // length
+				 "\001" // EXTERNAL (len)
+				 "\001" // external-len
+				 DS_aux_FZ_S // content-id
+				 "\001" // EXTERNAL (val)
+				 "\001" // external-len
+				 DS_aux_FZ_S,// content-id
+				 8);
+		else
+		    BLOCK_APPEND(map,
+				 "\004" // BYTE_ARRAY_LEN
+				 "\006" // length
+				 "\001" // EXTERNAL (len)
+				 "\001" // external-len
+				 DS_aux_S // content-id
+				 "\001" // EXTERNAL (val)
+				 "\001" // external-len
+				 DS_aux_S,// content-id
+				 8);
+		break;
+
+	    default:
+		fprintf(stderr, "Unsupported SAM aux type '%c'\n",
+			kh_key(c->tags_used, k) & 0xff);
+	    }
+	    //mp += m->codec->store(m->codec, mp, NULL, fd->version);
+	}
+    }
+#endif
+    itf8_put_blk(cb, BLOCK_SIZE(map) + itf8_size(mc));
+    itf8_put_blk(cb, mc);    
+    BLOCK_APPEND(cb, BLOCK_DATA(map), BLOCK_SIZE(map));
+
+    if (fd->verbose)
+	fprintf(stderr, "Wrote compression block header in %d bytes\n",
+		(int)BLOCK_SIZE(cb));
+
+    BLOCK_UPLEN(cb);
+
+    cram_free_block(map);
+
+    return cb;
+}
+
+
+/*
+ * Encodes a slice compression header. 
+ *
+ * Returns cram_block on success
+ *         NULL on failure
+ */
+cram_block *cram_encode_slice_header(cram_fd *fd, cram_slice *s) {
+    char *buf;
+    char *cp;
+    cram_block *b = cram_new_block(MAPPED_SLICE, 0);
+    int j;
+
+    if (!b)
+	return NULL;
+
+    if (NULL == (cp = buf = malloc(16+5*(8+s->hdr->num_blocks)))) {
+	cram_free_block(b);
+	return NULL;
+    }
+
+    cp += itf8_put(cp, s->hdr->ref_seq_id);
+    cp += itf8_put(cp, s->hdr->ref_seq_start);
+    cp += itf8_put(cp, s->hdr->ref_seq_span);
+    cp += itf8_put(cp, s->hdr->num_records);
+    if (CRAM_MAJOR_VERS(fd->version) == 2)
+	cp += itf8_put(cp, s->hdr->record_counter);
+    else if (CRAM_MAJOR_VERS(fd->version) >= 3)
+	cp += ltf8_put(cp, s->hdr->record_counter);
+    cp += itf8_put(cp, s->hdr->num_blocks);
+    cp += itf8_put(cp, s->hdr->num_content_ids);
+    for (j = 0; j < s->hdr->num_content_ids; j++) {
+	cp += itf8_put(cp, s->hdr->block_content_ids[j]);
+    }
+    if (s->hdr->content_type == MAPPED_SLICE)
+	cp += itf8_put(cp, s->hdr->ref_base_id);
+
+    if (CRAM_MAJOR_VERS(fd->version) != 1) {
+	memcpy(cp, s->hdr->md5, 16); cp += 16;
+    }
+    
+    assert(cp-buf <= 16+5*(8+s->hdr->num_blocks));
+
+    b->data = (unsigned char *)buf;
+    b->comp_size = b->uncomp_size = cp-buf;
+
+    return b;
+}
+
+
+/*
+ * Encodes a single read.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+static int cram_encode_slice_read(cram_fd *fd,
+				  cram_container *c,
+				  cram_block_compression_hdr *h,
+				  cram_slice *s,
+				  cram_record *cr,
+				  int *last_pos) {
+    int r = 0;
+    int32_t i32;
+    unsigned char uc;
+
+    //fprintf(stderr, "Encode seq %d, %d/%d FN=%d, %s\n", rec, core->byte, core->bit, cr->nfeature, s->name_ds->str + cr->name);
+
+    //printf("BF=0x%x\n", cr->flags);
+    //	    bf = cram_flag_swap[cr->flags];
+    i32 = fd->cram_flag_swap[cr->flags & 0xfff];
+    r |= h->codecs[DS_BF]->encode(s, h->codecs[DS_BF], (char *)&i32, 1);
+
+    i32 = cr->cram_flags & CRAM_FLAG_MASK;
+    r |= h->codecs[DS_CF]->encode(s, h->codecs[DS_CF], (char *)&i32, 1);
+
+    if (CRAM_MAJOR_VERS(fd->version) != 1 && s->hdr->ref_seq_id == -2)
+	r |= h->codecs[DS_RI]->encode(s, h->codecs[DS_RI], (char *)&cr->ref_id, 1);
+
+    r |= h->codecs[DS_RL]->encode(s, h->codecs[DS_RL], (char *)&cr->len, 1);
+
+    if (c->pos_sorted) {
+	i32 = cr->apos - *last_pos;
+	r |= h->codecs[DS_AP]->encode(s, h->codecs[DS_AP], (char *)&i32, 1);
+	*last_pos = cr->apos;
+    } else {
+	i32 = cr->apos;
+	r |= h->codecs[DS_AP]->encode(s, h->codecs[DS_AP], (char *)&i32, 1);
+    }
+
+    r |= h->codecs[DS_RG]->encode(s, h->codecs[DS_RG], (char *)&cr->rg, 1);
+
+    if (c->comp_hdr->read_names_included) {
+	// RN codec: Already stored in block[3].
+    }
+
+    if (cr->cram_flags & CRAM_FLAG_DETACHED) {
+	i32 = cr->mate_flags;
+	r |= h->codecs[DS_MF]->encode(s, h->codecs[DS_MF], (char *)&i32, 1);
+
+	if (!c->comp_hdr->read_names_included) {
+	    // RN codec: Already stored in block[3].
+	}
+
+	r |= h->codecs[DS_NS]->encode(s, h->codecs[DS_NS],
+				      (char *)&cr->mate_ref_id, 1);
+
+	r |= h->codecs[DS_NP]->encode(s, h->codecs[DS_NP],
+				      (char *)&cr->mate_pos, 1);
+
+	r |= h->codecs[DS_TS]->encode(s, h->codecs[DS_TS],
+				      (char *)&cr->tlen, 1);
+    } else if (cr->cram_flags & CRAM_FLAG_MATE_DOWNSTREAM) {
+	r |= h->codecs[DS_NF]->encode(s, h->codecs[DS_NF],
+				      (char *)&cr->mate_line, 1);
+    }
+
+    /* Aux tags */
+    if (CRAM_MAJOR_VERS(fd->version) == 1) {
+	int j;
+	uc = cr->ntags;
+	r |= h->codecs[DS_TC]->encode(s, h->codecs[DS_TC], (char *)&uc, 1);
+
+	for (j = 0; j < cr->ntags; j++) {
+	    uint32_t i32 = s->TN[cr->TN_idx + j]; // id
+	    r |= h->codecs[DS_TN]->encode(s, h->codecs[DS_TN], (char *)&i32, 1);
+	}
+    } else {
+	r |= h->codecs[DS_TL]->encode(s, h->codecs[DS_TL], (char *)&cr->TL, 1);
+    }
+
+    // qual
+    // QS codec : Already stored in block[2].
+
+    // features (diffs)
+    if (!(cr->flags & BAM_FUNMAP)) {
+	int prev_pos = 0, j;
+
+	r |= h->codecs[DS_FN]->encode(s, h->codecs[DS_FN],
+				      (char *)&cr->nfeature, 1);
+	for (j = 0; j < cr->nfeature; j++) {
+	    cram_feature *f = &s->features[cr->feature + j];
+
+	    uc = f->X.code;
+	    r |= h->codecs[DS_FC]->encode(s, h->codecs[DS_FC], (char *)&uc, 1);
+	    i32 = f->X.pos - prev_pos;
+	    r |= h->codecs[DS_FP]->encode(s, h->codecs[DS_FP], (char *)&i32, 1);
+	    prev_pos = f->X.pos;
+
+	    switch(f->X.code) {
+		//char *seq;
+
+	    case 'X':
+		//fprintf(stderr, "    FC=%c FP=%d base=%d\n", f->X.code, i32, f->X.base);
+		
+		uc = f->X.base;
+		r |= h->codecs[DS_BS]->encode(s, h->codecs[DS_BS],
+					      (char *)&uc, 1);
+		break;
+	    case 'S':
+		// Already done
+//		r |= h->codecs[DS_SC]->encode(s, h->codecs[DS_SC],
+//					      BLOCK_DATA(s->soft_blk) + f->S.seq_idx,
+//					      f->S.len);
+
+//		if (IS_CRAM_3_VERS(fd)) {
+//		    r |= h->codecs[DS_BB]->encode(s, h->codecs[DS_BB], 
+//						  BLOCK_DATA(s->seqs_blk) + f->S.seq_idx,
+//						  f->S.len);
+//		}
+		break;
+	    case 'I':
+		//seq = DSTRING_STR(s->seqs_ds) + f->S.seq_idx;
+		//r |= h->codecs[DS_IN]->encode(s, h->codecs[DS_IN],
+		//			     seq, f->S.len);
+//		if (IS_CRAM_3_VERS(fd)) {
+//		    r |= h->codecs[DS_BB]->encode(s, h->codecs[DS_BB], 
+//						  BLOCK_DATA(s->seqs_blk) + f->I.seq_idx,
+//						  f->I.len);
+//		}
+		break;
+	    case 'i':
+		uc = f->i.base;
+		r |= h->codecs[DS_BA]->encode(s, h->codecs[DS_BA],
+					      (char *)&uc, 1);
+		//seq = DSTRING_STR(s->seqs_ds) + f->S.seq_idx;
+		//r |= h->codecs[DS_IN]->encode(s, h->codecs[DS_IN], 
+		//			     seq, 1);
+		break;
+	    case 'D':
+		i32 = f->D.len;
+		r |= h->codecs[DS_DL]->encode(s, h->codecs[DS_DL],
+					      (char *)&i32, 1);
+		break;
+
+	    case 'B':
+		//		    // Used when we try to store a non ACGTN base or an N
+		//		    // that aligns against a non ACGTN reference
+
+		uc  = f->B.base;
+		r |= h->codecs[DS_BA]->encode(s, h->codecs[DS_BA],
+					      (char *)&uc, 1);
+
+		//                  Already added
+		//		    uc  = f->B.qual;
+		//		    r |= h->codecs[DS_QS]->encode(s, h->codecs[DS_QS], 
+		//					     (char *)&uc, 1);
+		break;
+
+	    case 'b':
+		// string of bases
+		r |= h->codecs[DS_BB]->encode(s, h->codecs[DS_BB], 
+					      (char *)BLOCK_DATA(s->seqs_blk)
+					              + f->b.seq_idx,
+					      f->b.len);
+		break;
+
+	    case 'Q':
+		//                  Already added
+		//		    uc  = f->B.qual;
+		//		    r |= h->codecs[DS_QS]->encode(s, h->codecs[DS_QS], 
+		//					     (char *)&uc, 1);
+		break;
+
+	    case 'N':
+		i32 = f->N.len;
+		r |= h->codecs[DS_RS]->encode(s, h->codecs[DS_RS],
+					      (char *)&i32, 1);
+		break;
+		    
+	    case 'P':
+		i32 = f->P.len;
+		r |= h->codecs[DS_PD]->encode(s, h->codecs[DS_PD],
+					      (char *)&i32, 1);
+		break;
+		    
+	    case 'H':
+		i32 = f->H.len;
+		r |= h->codecs[DS_HC]->encode(s, h->codecs[DS_HC],
+					      (char *)&i32, 1);
+		break;
+		    
+
+	    default:
+		fprintf(stderr, "unhandled feature code %c\n",
+			f->X.code);
+		return -1;
+	    }
+	}
+
+	r |= h->codecs[DS_MQ]->encode(s, h->codecs[DS_MQ],
+				      (char *)&cr->mqual, 1);
+    } else {
+	char *seq = (char *)BLOCK_DATA(s->seqs_blk) + cr->seq;
+	if (cr->len)
+	    r |= h->codecs[DS_BA]->encode(s, h->codecs[DS_BA], seq, cr->len);
+    }
+
+    return r ? -1 : 0;
+}
+
+
+/*
+ * Applies various compression methods to specific blocks, depending on
+ * known observations of how data series compress.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+static int cram_compress_slice(cram_fd *fd, cram_slice *s) {
+    int level = fd->level, i;
+    int method = 1<<GZIP | 1<<GZIP_RLE, methodF = method;
+
+    /* Compress the CORE Block too, with minimal zlib level */
+    if (level > 5 && s->block[0]->uncomp_size > 500)
+	cram_compress_block(fd, s->block[0], NULL, GZIP, 1);
+ 
+    if (fd->use_bz2)
+	method |= 1<<BZIP2;
+
+    if (fd->use_rans)
+	method |= (1<<RANS0) | (1<<RANS1);
+
+    if (fd->use_lzma)
+	method |= (1<<LZMA);
+
+    /* Faster method for data series we only need entropy encoding on */
+    methodF = method & ~(1<<GZIP | 1<<BZIP2 | 1<<LZMA);
+    if (level >= 6)
+	methodF = method;
+    
+
+    /* Specific compression methods for certain block types */
+    if (cram_compress_block(fd, s->block[DS_IN], fd->m[DS_IN], //IN (seq)
+			    method, level))
+	return -1;
+
+    if (fd->level == 0) {
+	/* Do nothing */
+    } else if (fd->level == 1) {
+	if (cram_compress_block(fd, s->block[DS_QS], fd->m[DS_QS],
+				methodF, 1))
+	    return -1;
+	for (i = DS_aux; i <= DS_aux_oz; i++) {
+	    if (s->block[i])
+		if (cram_compress_block(fd, s->block[i], fd->m[i],
+					method, 1))
+		    return -1;
+	}
+    } else if (fd->level < 3) {
+	if (cram_compress_block(fd, s->block[DS_QS], fd->m[DS_QS],
+				method, 1))
+	    return -1;
+	if (cram_compress_block(fd, s->block[DS_BA], fd->m[DS_BA],
+				method, 1))
+	    return -1;
+	if (s->block[DS_BB])
+	    if (cram_compress_block(fd, s->block[DS_BB], fd->m[DS_BB],
+				    method, 1))
+	    return -1;
+	for (i = DS_aux; i <= DS_aux_oz; i++) {
+	    if (s->block[i])
+		if (cram_compress_block(fd, s->block[i], fd->m[i],
+					method, level))
+		    return -1;
+	}
+    } else {
+	if (cram_compress_block(fd, s->block[DS_QS], fd->m[DS_QS],
+				method, level))
+	    return -1;
+	if (cram_compress_block(fd, s->block[DS_BA], fd->m[DS_BA],
+				method, level))
+	    return -1;
+	if (s->block[DS_BB])
+	    if (cram_compress_block(fd, s->block[DS_BB], fd->m[DS_BB],
+				    method, level))
+	    return -1;
+	for (i = DS_aux; i <= DS_aux_oz; i++) {
+	    if (s->block[i])
+		if (cram_compress_block(fd, s->block[i], fd->m[i],
+					method, level))
+		    return -1;
+	}
+    }
+
+    // NAME: best is generally xz, bzip2, zlib then rans1
+    // It benefits well from a little bit extra compression level.
+    if (cram_compress_block(fd, s->block[DS_RN], fd->m[DS_RN],
+			    method & ~(1<<RANS0 | 1<<GZIP_RLE),
+			    MIN(9,level)))
+	return -1;
+
+    // NS shows strong local correlation as rearrangements are localised
+    if (s->block[DS_NS] != s->block[0])
+	if (cram_compress_block(fd, s->block[DS_NS], fd->m[DS_NS],
+				method, level))
+	    return -1;
+
+
+    /*
+     * Minimal compression of any block still uncompressed, bar CORE
+     */
+    {
+	int i;
+	for (i = 1; i < DS_END; i++) {
+	    if (!s->block[i] || s->block[i] == s->block[0])
+		continue;
+
+	    // fast methods only
+	    if (s->block[i]->method == RAW) {
+		cram_compress_block(fd, s->block[i], fd->m[i],
+				    methodF, level);
+	    }
+	}
+    }
+
+    return 0;
+}
+
+/*
+ * Encodes a single slice from a container
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+static int cram_encode_slice(cram_fd *fd, cram_container *c,
+			     cram_block_compression_hdr *h, cram_slice *s) {
+    int rec, r = 0, last_pos;
+    int embed_ref;
+    enum cram_DS_ID id;
+
+    embed_ref = fd->embed_ref && s->hdr->ref_seq_id != -1 ? 1 : 0;
+
+    /*
+     * Slice external blocks:
+     * ID 0 => base calls (insertions, soft-clip)
+     * ID 1 => qualities
+     * ID 2 => names
+     * ID 3 => TS (insert size), NP (next frag)
+     * ID 4 => tag values
+     * ID 6 => tag IDs (TN), if CRAM_V1.0
+     * ID 7 => TD tag dictionary, if !CRAM_V1.0
+     */
+
+    /* Create cram slice header */
+    s->hdr->ref_base_id = embed_ref ? DS_ref : -1;
+    s->hdr->record_counter = c->num_records + c->record_counter;
+    c->num_records += s->hdr->num_records;
+
+    s->block = calloc(DS_END, sizeof(s->block[0]));
+    s->hdr->block_content_ids = malloc(DS_END * sizeof(int32_t));
+    if (!s->block || !s->hdr->block_content_ids)
+	return -1;
+
+    // Create first fixed blocks, always external.
+    // CORE
+    if (!(s->block[0] = cram_new_block(CORE, 0)))
+	return -1;
+
+    // TN block for CRAM v1
+    if (CRAM_MAJOR_VERS(fd->version) == 1) {
+	if (h->codecs[DS_TN]->codec == E_EXTERNAL) {
+	    if (!(s->block[DS_TN] = cram_new_block(EXTERNAL,DS_TN))) return -1;
+	    h->codecs[DS_TN]->external.content_id = DS_TN;
+	} else {
+	    s->block[DS_TN] = s->block[0];
+	}
+	s->block[DS_TN] = s->block[DS_TN];
+    }
+
+    // Embedded reference
+    if (embed_ref) {
+	if (!(s->block[DS_ref] = cram_new_block(EXTERNAL, DS_ref)))
+	    return -1;
+	s->ref_id = DS_ref; // needed?
+	BLOCK_APPEND(s->block[DS_ref],
+		     c->ref + c->first_base - c->ref_start,
+		     c->last_base - c->first_base + 1);
+    }
+
+    /*
+     * All the data-series blocks if appropriate. 
+     */
+    for (id = DS_BF; id < DS_TN; id++) {
+	if (h->codecs[id] && (h->codecs[id]->codec == E_EXTERNAL ||
+			      h->codecs[id]->codec == E_BYTE_ARRAY_STOP ||
+			      h->codecs[id]->codec == E_BYTE_ARRAY_LEN)) {
+	    switch (h->codecs[id]->codec) {
+	    case E_EXTERNAL:
+		if (!(s->block[id] = cram_new_block(EXTERNAL, id)))
+		    return -1;
+		h->codecs[id]->external.content_id = id;
+		break;
+
+	    case E_BYTE_ARRAY_STOP:
+		if (!(s->block[id] = cram_new_block(EXTERNAL, id)))
+		    return -1;
+		h->codecs[id]->byte_array_stop.content_id = id;
+		break;
+
+	    case E_BYTE_ARRAY_LEN: {
+		cram_codec *cc;
+
+		cc = h->codecs[id]->e_byte_array_len.len_codec;
+		if (cc->codec == E_EXTERNAL) {
+		    int eid = cc->external.content_id;
+		    if (!(s->block[eid] = cram_new_block(EXTERNAL, eid)))
+			return -1;
+		    cc->external.content_id = eid;
+		    cc->out = s->block[eid];
+		}
+
+		cc = h->codecs[id]->e_byte_array_len.val_codec;
+		if (cc->codec == E_EXTERNAL) {
+		    int eid = cc->external.content_id;
+		    if (!s->block[eid])
+			if (!(s->block[eid] = cram_new_block(EXTERNAL, eid)))
+			    return -1;
+		    cc->external.content_id = eid;
+		    cc->out = s->block[eid];
+		}
+		break;
+	    }
+	    default:
+		break;
+	    }
+	} else {
+	    if (!(id == DS_BB && !h->codecs[DS_BB]))
+		s->block[id] = s->block[0];
+	}
+	if (h->codecs[id])
+	    h->codecs[id]->out = s->block[id];
+    }
+
+    /* Encode reads */
+    last_pos = s->hdr->ref_seq_start;
+    for (rec = 0; rec < s->hdr->num_records; rec++) {
+	cram_record *cr = &s->crecs[rec];
+	if (cram_encode_slice_read(fd, c, h, s, cr, &last_pos) == -1)
+	    return -1;
+    }
+
+    s->block[0]->uncomp_size = s->block[0]->byte + (s->block[0]->bit < 7);
+    s->block[0]->comp_size = s->block[0]->uncomp_size;
+
+    // Make sure the fixed blocks point to the correct sources
+    s->block[DS_IN] = s->base_blk; s->base_blk = NULL;
+    s->block[DS_QS] = s->qual_blk; s->qual_blk = NULL;
+    s->block[DS_RN] = s->name_blk; s->name_blk = NULL;
+    s->block[DS_SC] = s->soft_blk; s->soft_blk = NULL;
+    s->block[DS_aux]= s->aux_blk;  s->aux_blk  = NULL;
+    s->block[DS_aux_OQ]= s->aux_OQ_blk;  s->aux_OQ_blk  = NULL;
+    s->block[DS_aux_BQ]= s->aux_BQ_blk;  s->aux_BQ_blk  = NULL;
+    s->block[DS_aux_BD]= s->aux_BD_blk;  s->aux_BD_blk  = NULL;
+    s->block[DS_aux_BI]= s->aux_BI_blk;  s->aux_BI_blk  = NULL;
+    s->block[DS_aux_FZ]= s->aux_FZ_blk;  s->aux_FZ_blk  = NULL;
+    s->block[DS_aux_oq]= s->aux_oq_blk;  s->aux_oq_blk  = NULL;
+    s->block[DS_aux_os]= s->aux_os_blk;  s->aux_os_blk  = NULL;
+    s->block[DS_aux_oz]= s->aux_oz_blk;  s->aux_oz_blk  = NULL;
+
+    // Ensure block sizes are up to date.
+    for (id = 1; id < DS_END; id++) {
+	if (!s->block[id] || s->block[id] == s->block[0])
+	    continue;
+
+	if (s->block[id]->uncomp_size == 0)
+	    BLOCK_UPLEN(s->block[id]);
+    }
+
+    // Compress it all
+    if (cram_compress_slice(fd, s) == -1)
+	return -1;
+
+    // Collapse empty blocks and create hdr_block
+    {
+	int i, j;
+	for (i = j = 1; i < DS_END; i++) {
+	    if (!s->block[i] || s->block[i] == s->block[0])
+		continue;
+	    if (s->block[i]->uncomp_size == 0) {
+		cram_free_block(s->block[i]);
+		s->block[i] = NULL;
+		continue;
+	    }
+	    s->block[j] = s->block[i];
+	    s->hdr->block_content_ids[j-1] = s->block[i]->content_id;
+	    j++;
+	}
+	s->hdr->num_content_ids = j-1;
+	s->hdr->num_blocks = j;
+
+	if (!(s->hdr_block = cram_encode_slice_header(fd, s)))
+	    return -1;
+    }
+
+    return r ? -1 : 0;
+}
+
+/*
+ * Encodes all slices in a container into blocks.
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int cram_encode_container(cram_fd *fd, cram_container *c) {
+    int i, j, slice_offset;
+    cram_block_compression_hdr *h = c->comp_hdr;
+    cram_block *c_hdr;
+    int multi_ref = 0;
+    int r1, r2, sn, nref;
+    spare_bams *spares;
+
+    /* Cache references up-front if we have unsorted access patterns */
+    pthread_mutex_lock(&fd->ref_lock);
+    nref = fd->refs->nref;
+    pthread_mutex_unlock(&fd->ref_lock);
+
+    if (!fd->no_ref && c->refs_used) {
+	for (i = 0; i < nref; i++) {
+	    if (c->refs_used[i])
+		cram_get_ref(fd, i, 1, 0);
+	}
+    }
+
+    /* To create M5 strings */
+    /* Fetch reference sequence */
+    if (!fd->no_ref) {
+	bam_seq_t *b = c->bams[0];
+	char *ref;
+
+	ref = cram_get_ref(fd, bam_ref(b), 1, 0);
+	if (!ref && bam_ref(b) >= 0) {
+	    fprintf(stderr, "Failed to load reference #%d\n", bam_ref(b));
+	    return -1;
+	}
+	if ((c->ref_id = bam_ref(b)) >= 0) {
+	    c->ref_seq_id = c->ref_id;
+	    c->ref       = fd->refs->ref_id[c->ref_seq_id]->seq;
+	    c->ref_start = 1;
+	    c->ref_end   = fd->refs->ref_id[c->ref_seq_id]->length;
+	} else {
+	    c->ref_seq_id = c->ref_id; // FIXME remove one var!
+	}
+    } else {
+	c->ref_id = bam_ref(c->bams[0]);
+	cram_ref_incr(fd->refs, c->ref_id);
+	c->ref_seq_id = c->ref_id;
+    }
+
+    /* Turn bams into cram_records and gather basic stats */
+    for (r1 = sn = 0; r1 < c->curr_c_rec; sn++) {
+	cram_slice *s = c->slices[sn];
+	int first_base = INT_MAX, last_base = INT_MIN;
+
+	assert(sn < c->curr_slice);
+
+	/* FIXME: we could create our slice objects here too instead of
+	 * in cram_put_bam_seq. It's more natural here and also this is
+	 * bit is threaded so it's less work in the main thread.
+	 */
+
+	for (r2 = 0; r1 < c->curr_c_rec && r2 < c->max_rec; r1++, r2++) {
+	    cram_record *cr = &s->crecs[r2];
+	    bam_seq_t *b = c->bams[r1];
+
+	    /* If multi-ref we need to cope with changing reference per seq */
+	    if (c->multi_seq && !fd->no_ref) {
+		if (bam_ref(b) != c->ref_seq_id && bam_ref(b) >= 0) {
+		    if (c->ref_seq_id >= 0)
+			cram_ref_decr(fd->refs, c->ref_seq_id);
+
+		    if (!cram_get_ref(fd, bam_ref(b), 1, 0)) {
+			fprintf(stderr, "Failed to load reference #%d\n",
+				bam_ref(b));
+			return -1;
+		    }
+
+		    c->ref_seq_id = bam_ref(b); // overwritten later by -2
+		    assert(fd->refs->ref_id[c->ref_seq_id]->seq);
+		    c->ref       = fd->refs->ref_id[c->ref_seq_id]->seq;
+		    c->ref_start = 1;
+		    c->ref_end   = fd->refs->ref_id[c->ref_seq_id]->length;
+		}
+	    }
+
+	    if (process_one_read(fd, c, s, cr, b, r2) != 0)
+		return -1;
+
+	    if (first_base > cr->apos)
+		first_base = cr->apos;
+
+	    if (last_base < cr->aend)
+		last_base = cr->aend;
+	}
+
+	if (c->multi_seq) {
+	    s->hdr->ref_seq_id    = -2;
+	    s->hdr->ref_seq_start = 0;
+	    s->hdr->ref_seq_span  = 0;
+	} else {
+	    s->hdr->ref_seq_id    = c->ref_id;
+	    s->hdr->ref_seq_start = first_base;
+	    s->hdr->ref_seq_span  = last_base - first_base + 1;
+	}
+	s->hdr->num_records = r2;
+    }
+
+    if (c->multi_seq && !fd->no_ref) {
+	if (c->ref_seq_id >= 0)
+	    cram_ref_decr(fd->refs, c->ref_seq_id);
+    }
+
+    /* Link our bams[] array onto the spare bam list for reuse */
+    spares = malloc(sizeof(*spares));
+    pthread_mutex_lock(&fd->bam_list_lock);
+    spares->bams = c->bams;
+    spares->next = fd->bl;
+    fd->bl = spares;
+    pthread_mutex_unlock(&fd->bam_list_lock);
+    c->bams = NULL;
+
+    /* Detect if a multi-seq container */
+    cram_stats_encoding(fd, c->stats[DS_RI]);
+    multi_ref = c->stats[DS_RI]->nvals > 1;
+
+    if (multi_ref) {
+	if (fd->verbose)
+	    fprintf(stderr, "Multi-ref container\n");
+	c->ref_seq_id = -2;
+	c->ref_seq_start = 0;
+	c->ref_seq_span = 0;
+    }
+
+
+    /* Compute MD5s */
+    for (i = 0; i < c->curr_slice; i++) {
+	cram_slice *s = c->slices[i];
+	
+	if (CRAM_MAJOR_VERS(fd->version) != 1) {
+	    if (s->hdr->ref_seq_id >= 0 && c->multi_seq == 0 && !fd->no_ref) {
+		hts_md5_context *md5 = hts_md5_init();
+		if (!md5)
+		    return -1;
+		hts_md5_update(md5,
+			   c->ref + s->hdr->ref_seq_start - c->ref_start,
+			   s->hdr->ref_seq_span);
+		hts_md5_final(s->hdr->md5, md5);
+		hts_md5_destroy(md5);
+	    } else {
+		memset(s->hdr->md5, 0, 16);
+	    }
+	}
+    }
+
+    c->num_records = 0;
+    c->num_blocks = 1; // cram_block_compression_hdr
+    c->length = 0;
+
+    //fprintf(stderr, "=== BF ===\n");
+    h->codecs[DS_BF] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_BF]),
+					 c->stats[DS_BF], E_INT, NULL,
+					 fd->version);
+
+    //fprintf(stderr, "=== CF ===\n");
+    h->codecs[DS_CF] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_CF]),
+					 c->stats[DS_CF], E_INT, NULL,
+					 fd->version);
+//    fprintf(stderr, "=== RN ===\n");
+//    h->codecs[DS_RN] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_RN]),
+//				    c->stats[DS_RN], E_BYTE_ARRAY, NULL,
+//				    fd->version);
+
+    //fprintf(stderr, "=== AP ===\n");
+    if (c->pos_sorted) {
+	h->codecs[DS_AP] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_AP]),
+					     c->stats[DS_AP], E_INT, NULL,
+					     fd->version);
+    } else {
+	int p[2] = {0, c->max_apos};
+	h->codecs[DS_AP] = cram_encoder_init(E_BETA, NULL, E_INT, p,
+					     fd->version);
+    }
+
+    //fprintf(stderr, "=== RG ===\n");
+    h->codecs[DS_RG] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_RG]),
+					 c->stats[DS_RG], E_INT, NULL,
+					 fd->version);
+
+    //fprintf(stderr, "=== MQ ===\n");
+    h->codecs[DS_MQ] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_MQ]),
+					 c->stats[DS_MQ], E_INT, NULL,
+					 fd->version);
+
+    //fprintf(stderr, "=== NS ===\n");
+    h->codecs[DS_NS] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_NS]),
+					 c->stats[DS_NS], E_INT, NULL,
+					 fd->version);
+
+    //fprintf(stderr, "=== MF ===\n");
+    h->codecs[DS_MF] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_MF]),
+					 c->stats[DS_MF], E_INT, NULL,
+					 fd->version);
+
+    //fprintf(stderr, "=== TS ===\n");
+    h->codecs[DS_TS] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_TS]),
+					 c->stats[DS_TS], E_INT, NULL,
+					 fd->version);
+    //fprintf(stderr, "=== NP ===\n");
+    h->codecs[DS_NP] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_NP]),
+					 c->stats[DS_NP], E_INT, NULL,
+					 fd->version);
+    //fprintf(stderr, "=== NF ===\n");
+    h->codecs[DS_NF] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_NF]),
+					 c->stats[DS_NF], E_INT, NULL,
+					 fd->version);
+
+    //fprintf(stderr, "=== RL ===\n");
+    h->codecs[DS_RL] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_RL]),
+					 c->stats[DS_RL], E_INT, NULL,
+					 fd->version);
+
+    //fprintf(stderr, "=== FN ===\n");
+    h->codecs[DS_FN] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_FN]),
+					 c->stats[DS_FN], E_INT, NULL,
+					 fd->version);
+
+    //fprintf(stderr, "=== FC ===\n");
+    h->codecs[DS_FC] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_FC]),
+					 c->stats[DS_FC], E_BYTE, NULL,
+					 fd->version);
+
+    //fprintf(stderr, "=== FP ===\n");
+    h->codecs[DS_FP] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_FP]),
+					 c->stats[DS_FP], E_INT, NULL,
+					 fd->version);
+
+    //fprintf(stderr, "=== DL ===\n");
+    h->codecs[DS_DL] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_DL]),
+					 c->stats[DS_DL], E_INT, NULL,
+					 fd->version);
+
+    //fprintf(stderr, "=== BA ===\n");
+    h->codecs[DS_BA] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_BA]),
+					 c->stats[DS_BA], E_BYTE, NULL,
+					 fd->version);
+
+    if (CRAM_MAJOR_VERS(fd->version) >= 3) {
+	cram_byte_array_len_encoder e;
+
+	e.len_encoding = E_EXTERNAL;
+	e.len_dat = (void *)DS_BB_len;
+	//e.len_dat = (void *)DS_BB;
+
+	e.val_encoding = E_EXTERNAL;
+	e.val_dat = (void *)DS_BB;
+
+	h->codecs[DS_BB] = cram_encoder_init(E_BYTE_ARRAY_LEN, NULL,
+					     E_BYTE_ARRAY, (void *)&e,
+					     fd->version);
+    } else {
+	h->codecs[DS_BB] = NULL;
+    }
+
+    //fprintf(stderr, "=== BS ===\n");
+    h->codecs[DS_BS] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_BS]),
+					 c->stats[DS_BS], E_BYTE, NULL,
+					 fd->version);
+
+    if (CRAM_MAJOR_VERS(fd->version) == 1) {
+	h->codecs[DS_TL] = NULL;
+	h->codecs[DS_RI] = NULL;
+	h->codecs[DS_RS] = NULL;
+	h->codecs[DS_PD] = NULL;
+	h->codecs[DS_HC] = NULL;
+	h->codecs[DS_SC] = NULL;
+
+	//fprintf(stderr, "=== TC ===\n");
+	h->codecs[DS_TC] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_TC]),
+					     c->stats[DS_TC], E_BYTE, NULL,
+					     fd->version);
+
+    //fprintf(stderr, "=== TN ===\n");
+	h->codecs[DS_TN] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_TN]),
+					     c->stats[DS_TN], E_INT, NULL,
+					     fd->version);
+    } else {
+	h->codecs[DS_TC] = NULL;
+	h->codecs[DS_TN] = NULL;
+
+	//fprintf(stderr, "=== TL ===\n");
+	h->codecs[DS_TL] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_TL]),
+					     c->stats[DS_TL], E_INT, NULL,
+					     fd->version);
+
+
+	//fprintf(stderr, "=== RI ===\n");
+	h->codecs[DS_RI] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_RI]),
+					     c->stats[DS_RI], E_INT, NULL,
+					     fd->version);
+
+	//fprintf(stderr, "=== RS ===\n");
+	h->codecs[DS_RS] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_RS]),
+					     c->stats[DS_RS], E_INT, NULL,
+					     fd->version);
+
+	//fprintf(stderr, "=== PD ===\n");
+	h->codecs[DS_PD] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_PD]),
+					     c->stats[DS_PD], E_INT, NULL,
+					     fd->version);
+
+	//fprintf(stderr, "=== HC ===\n");
+	h->codecs[DS_HC] = cram_encoder_init(cram_stats_encoding(fd, c->stats[DS_HC]),
+					     c->stats[DS_HC], E_INT, NULL,
+					     fd->version);
+
+	//fprintf(stderr, "=== SC ===\n");
+	if (1) {
+	    int i2[2] = {0, DS_SC};
+
+	    h->codecs[DS_SC] = cram_encoder_init(E_BYTE_ARRAY_STOP, NULL,
+						 E_BYTE_ARRAY, (void *)i2,
+						 fd->version);
+	} else {
+	    // Appears to be no practical benefit to using this method,
+	    // but it may work better if we start mixing SC, IN and BB
+	    // elements into the same external block.
+	    cram_byte_array_len_encoder e;
+
+	    e.len_encoding = E_EXTERNAL;
+	    e.len_dat = (void *)DS_SC_len;
+
+	    e.val_encoding = E_EXTERNAL;
+	    e.val_dat = (void *)DS_SC;
+
+	    h->codecs[DS_SC] = cram_encoder_init(E_BYTE_ARRAY_LEN, NULL,
+						 E_BYTE_ARRAY, (void *)&e,
+						 fd->version);
+	}
+    }
+    
+    //fprintf(stderr, "=== IN ===\n");
+    {
+	int i2[2] = {0, DS_IN};
+	h->codecs[DS_IN] = cram_encoder_init(E_BYTE_ARRAY_STOP, NULL,
+					     E_BYTE_ARRAY, (void *)i2,
+					     fd->version);
+    }
+
+    h->codecs[DS_QS] = cram_encoder_init(E_EXTERNAL, NULL, E_BYTE,
+					 (void *)DS_QS,
+					 fd->version);
+    {
+	int i2[2] = {0, DS_RN};
+	h->codecs[DS_RN] = cram_encoder_init(E_BYTE_ARRAY_STOP, NULL,
+					     E_BYTE_ARRAY, (void *)i2,
+					     fd->version);
+    }
+
+
+    /* Encode slices */
+    for (i = 0; i < c->curr_slice; i++) {
+	if (fd->verbose)
+	    fprintf(stderr, "Encode slice %d\n", i);
+	if (cram_encode_slice(fd, c, h, c->slices[i]) != 0)
+	    return -1;
+    }
+
+    /* Create compression header */
+    {
+	h->ref_seq_id    = c->ref_seq_id;
+	h->ref_seq_start = c->ref_seq_start;
+	h->ref_seq_span  = c->ref_seq_span;
+	h->num_records   = c->num_records;
+	
+	h->mapped_qs_included = 0;   // fixme
+	h->unmapped_qs_included = 0; // fixme
+	h->AP_delta = c->pos_sorted;
+	// h->...  fixme
+	memcpy(h->substitution_matrix, CRAM_SUBST_MATRIX, 20);
+
+	if (!(c_hdr = cram_encode_compression_header(fd, c, h)))
+	    return -1;
+    }
+
+    /* Compute landmarks */
+    /* Fill out slice landmarks */
+    c->num_landmarks = c->curr_slice;
+    c->landmark = malloc(c->num_landmarks * sizeof(*c->landmark));
+    if (!c->landmark)
+	return -1;
+
+    /*
+     * Slice offset starts after the first block, so we need to simulate
+     * writing it to work out the correct offset
+     */
+    {
+	slice_offset = c_hdr->method == RAW
+	    ? c_hdr->uncomp_size
+	    : c_hdr->comp_size;
+	slice_offset += 2 + 4*(CRAM_MAJOR_VERS(fd->version) >= 3) +
+	    itf8_size(c_hdr->content_id) +
+	    itf8_size(c_hdr->comp_size) +
+	    itf8_size(c_hdr->uncomp_size);
+    }
+
+    c->ref_seq_id    = c->slices[0]->hdr->ref_seq_id;
+    c->ref_seq_start = c->slices[0]->hdr->ref_seq_start;
+    c->ref_seq_span  = c->slices[0]->hdr->ref_seq_span;
+    for (i = 0; i < c->curr_slice; i++) {
+	cram_slice *s = c->slices[i];
+	
+        c->num_blocks += s->hdr->num_blocks + 1; // slice header
+	c->landmark[i] = slice_offset;
+
+	if (s->hdr->ref_seq_start + s->hdr->ref_seq_span >
+	    c->ref_seq_start + c->ref_seq_span) {
+	    c->ref_seq_span = s->hdr->ref_seq_start + s->hdr->ref_seq_span
+		- c->ref_seq_start;
+	}
+	
+	slice_offset += s->hdr_block->method == RAW
+	    ? s->hdr_block->uncomp_size
+	    : s->hdr_block->comp_size;
+
+	slice_offset += 2 + 4*(CRAM_MAJOR_VERS(fd->version) >= 3) +
+	    itf8_size(s->hdr_block->content_id) +
+	    itf8_size(s->hdr_block->comp_size) +
+	    itf8_size(s->hdr_block->uncomp_size);
+
+	for (j = 0; j < s->hdr->num_blocks; j++) {
+	    slice_offset += 2 + 4*(CRAM_MAJOR_VERS(fd->version) >= 3) +
+		itf8_size(s->block[j]->content_id) +
+		itf8_size(s->block[j]->comp_size) +
+		itf8_size(s->block[j]->uncomp_size);
+
+	    slice_offset += s->block[j]->method == RAW
+		? s->block[j]->uncomp_size
+		: s->block[j]->comp_size;
+	}
+    }
+    c->length += slice_offset; // just past the final slice
+
+    c->comp_hdr_block = c_hdr;
+
+    if (c->ref_seq_id >= 0) {
+	cram_ref_decr(fd->refs, c->ref_seq_id);
+    }
+
+    /* Cache references up-front if we have unsorted access patterns */
+    if (!fd->no_ref && c->refs_used) {
+	for (i = 0; i < fd->refs->nref; i++) {
+	    if (c->refs_used[i])
+		cram_ref_decr(fd->refs, i);
+	}
+    }
+
+    return 0;
+}
+
+
+/*
+ * Adds a feature code to a read within a slice. For purposes of minimising
+ * memory allocations and fragmentation we have one array of features for all
+ * reads within the slice. We return the index into this array for this new
+ * feature.
+ *
+ * Returns feature index on success
+ *         -1 on failure.
+ */
+static int cram_add_feature(cram_container *c, cram_slice *s,
+			    cram_record *r, cram_feature *f) {
+    if (s->nfeatures >= s->afeatures) {
+	s->afeatures = s->afeatures ? s->afeatures*2 : 1024;
+	s->features = realloc(s->features, s->afeatures*sizeof(*s->features));
+	if (!s->features)
+	    return -1;
+    }
+
+    if (!r->nfeature++) {
+	r->feature = s->nfeatures;
+	cram_stats_add(c->stats[DS_FP], f->X.pos);
+    } else {
+	cram_stats_add(c->stats[DS_FP],
+		       f->X.pos - s->features[r->feature + r->nfeature-2].X.pos);
+    }
+    cram_stats_add(c->stats[DS_FC], f->X.code);
+
+    s->features[s->nfeatures++] = *f;
+
+    return 0;
+}
+
+static int cram_add_substitution(cram_fd *fd, cram_container *c,
+				 cram_slice *s, cram_record *r,
+				 int pos, char base, char qual, char ref) {
+    cram_feature f;
+
+    // seq=ACGTN vs ref=ACGT or seq=ACGT vs ref=ACGTN
+    if (fd->L2[(uc)base]<4 || (fd->L2[(uc)base]<5 && fd->L2[(uc)ref]<4)) {
+	f.X.pos = pos+1;
+	f.X.code = 'X';
+	f.X.base = fd->cram_sub_matrix[ref&0x1f][base&0x1f];
+	cram_stats_add(c->stats[DS_BS], f.X.base);
+    } else {
+	f.B.pos = pos+1;
+	f.B.code = 'B';
+	f.B.base = base;
+	f.B.qual = qual;
+	cram_stats_add(c->stats[DS_BA], f.B.base);
+	cram_stats_add(c->stats[DS_QS], f.B.qual);
+	BLOCK_APPEND_CHAR(s->qual_blk, qual);
+    }
+    return cram_add_feature(c, s, r, &f);
+}
+
+static int cram_add_bases(cram_fd *fd, cram_container *c,
+			  cram_slice *s, cram_record *r,
+			  int pos, int len, char *base) {
+    cram_feature f;
+
+    f.b.pos = pos+1;
+    f.b.code = 'b';
+    f.b.seq_idx = base - (char *)BLOCK_DATA(s->seqs_blk);
+    f.b.len = len;
+
+    return cram_add_feature(c, s, r, &f);
+}
+
+static int cram_add_base(cram_fd *fd, cram_container *c,
+			 cram_slice *s, cram_record *r,
+			 int pos, char base, char qual) {
+    cram_feature f;
+    f.B.pos = pos+1;
+    f.B.code = 'B';
+    f.B.base = base;
+    f.B.qual = qual;
+    cram_stats_add(c->stats[DS_BA], base);
+    cram_stats_add(c->stats[DS_QS], qual);
+    BLOCK_APPEND_CHAR(s->qual_blk, qual);
+    return cram_add_feature(c, s, r, &f);
+}
+
+static int cram_add_quality(cram_fd *fd, cram_container *c,
+			    cram_slice *s, cram_record *r,
+			    int pos, char qual) {
+    cram_feature f;
+    f.Q.pos = pos+1;
+    f.Q.code = 'Q';
+    f.Q.qual = qual;
+    cram_stats_add(c->stats[DS_QS], qual);
+    BLOCK_APPEND_CHAR(s->qual_blk, qual);
+    return cram_add_feature(c, s, r, &f);
+}
+
+static int cram_add_deletion(cram_container *c, cram_slice *s, cram_record *r,
+			     int pos, int len, char *base) {
+    cram_feature f;
+    f.D.pos = pos+1;
+    f.D.code = 'D';
+    f.D.len = len;
+    cram_stats_add(c->stats[DS_DL], len);
+    return cram_add_feature(c, s, r, &f);
+}
+
+static int cram_add_softclip(cram_container *c, cram_slice *s, cram_record *r,
+			     int pos, int len, char *base, int version) {
+    cram_feature f;
+    f.S.pos = pos+1;
+    f.S.code = 'S';
+    f.S.len = len;
+    switch (CRAM_MAJOR_VERS(version)) {
+    case 1:
+	f.S.seq_idx = BLOCK_SIZE(s->base_blk);
+	BLOCK_APPEND(s->base_blk, base, len);
+	BLOCK_APPEND_CHAR(s->base_blk, '\0');
+	break;
+
+    case 2:
+    default:
+	f.S.seq_idx = BLOCK_SIZE(s->soft_blk);
+	if (base) {
+	    BLOCK_APPEND(s->soft_blk, base, len);
+	} else {
+	    int i;
+	    for (i = 0; i < len; i++)
+		BLOCK_APPEND_CHAR(s->soft_blk, 'N');
+	}
+	BLOCK_APPEND_CHAR(s->soft_blk, '\0');
+	break;
+
+//    default:
+//	// v3.0 onwards uses BB data-series
+//	f.S.seq_idx = BLOCK_SIZE(s->soft_blk);
+    }
+    return cram_add_feature(c, s, r, &f);
+}
+
+static int cram_add_hardclip(cram_container *c, cram_slice *s, cram_record *r,
+			     int pos, int len, char *base) {
+    cram_feature f;
+    f.S.pos = pos+1;
+    f.S.code = 'H';
+    f.S.len = len;
+    cram_stats_add(c->stats[DS_HC], len);
+    return cram_add_feature(c, s, r, &f);
+}
+
+static int cram_add_skip(cram_container *c, cram_slice *s, cram_record *r,
+			     int pos, int len, char *base) {
+    cram_feature f;
+    f.S.pos = pos+1;
+    f.S.code = 'N';
+    f.S.len = len;
+    cram_stats_add(c->stats[DS_RS], len);
+    return cram_add_feature(c, s, r, &f);
+}
+
+static int cram_add_pad(cram_container *c, cram_slice *s, cram_record *r,
+			     int pos, int len, char *base) {
+    cram_feature f;
+    f.S.pos = pos+1;
+    f.S.code = 'P';
+    f.S.len = len;
+    cram_stats_add(c->stats[DS_PD], len);
+    return cram_add_feature(c, s, r, &f);
+}
+
+static int cram_add_insertion(cram_container *c, cram_slice *s, cram_record *r,
+			      int pos, int len, char *base) {
+    cram_feature f;
+    f.I.pos = pos+1;
+    if (len == 1) {
+	char b = base ? *base : 'N';
+	f.i.code = 'i';
+	f.i.base = b;
+	cram_stats_add(c->stats[DS_BA], b);
+    } else {
+	f.I.code = 'I';
+	f.I.len = len;
+	f.S.seq_idx = BLOCK_SIZE(s->base_blk);
+	if (base) {
+	    BLOCK_APPEND(s->base_blk, base, len);
+	} else {
+	    int i;
+	    for (i = 0; i < len; i++)
+		BLOCK_APPEND_CHAR(s->base_blk, 'N');
+	}
+	BLOCK_APPEND_CHAR(s->base_blk, '\0');
+    }
+    return cram_add_feature(c, s, r, &f);
+}
+
+/*
+ * Encodes auxiliary data.
+ * Returns the read-group parsed out of the BAM aux fields on success
+ *         NULL on failure or no rg present (FIXME)
+ */
+static char *cram_encode_aux_1_0(cram_fd *fd, bam_seq_t *b, cram_container *c,
+				 cram_slice *s, cram_record *cr) {
+    char *aux, *tmp, *rg = NULL;
+    int aux_size = bam_blk_size(b) -
+	((char *)bam_aux(b) - (char *)&bam_ref(b));
+	
+    /* Worst case is 1 nul char on every ??:Z: string, so +33% */
+    BLOCK_GROW(s->aux_blk, aux_size*1.34+1);
+    tmp = (char *)BLOCK_END(s->aux_blk);
+
+    aux = (char *)bam_aux(b);
+    cr->TN_idx = s->nTN;
+
+    while (aux[0] != 0) {
+	int32_t i32;
+	int r;
+
+	if (aux[0] == 'R' && aux[1] == 'G' && aux[2] == 'Z') {
+	    rg = &aux[3];
+	    while (*aux++);
+	    continue;
+	}
+	if (aux[0] == 'M' && aux[1] == 'D' && aux[2] == 'Z') {
+	    while (*aux++);
+	    continue;
+	}
+	if (aux[0] == 'N' && aux[1] == 'M') {
+	    switch(aux[2]) {
+	    case 'A': case 'C': case 'c': aux+=4; break;
+	    case 'I': case 'i': case 'f': aux+=7; break;
+	    default:
+		fprintf(stderr, "Unhandled type code for NM tag\n");
+		return NULL;
+	    }
+	    continue;
+	}
+
+	cr->ntags++;
+
+	i32 = (aux[0]<<16) | (aux[1]<<8) | aux[2];
+	kh_put(s_i2i, c->tags_used, i32, &r);
+	if (-1 == r)
+	    return NULL;
+
+	if (s->nTN >= s->aTN) {
+	    s->aTN = s->aTN ? s->aTN*2 : 1024;
+	    if (!(s->TN = realloc(s->TN, s->aTN * sizeof(*s->TN))))
+		return NULL;
+	}
+	s->TN[s->nTN++] = i32;
+	cram_stats_add(c->stats[DS_TN], i32);
+
+	switch(aux[2]) {
+	case 'A': case 'C': case 'c':
+	    aux+=3; //*tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++;
+	    *tmp++=*aux++;
+	    break;
+
+	case 'S': case 's':
+	    aux+=3; //*tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++;
+	    *tmp++=*aux++; *tmp++=*aux++;
+	    break;
+
+	case 'I': case 'i': case 'f':
+	    aux+=3; //*tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++;
+	    *tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++;
+	    break;
+
+	case 'd':
+	    aux+=3; //*tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++;
+	    *tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++;
+	    *tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++;
+	    break;
+
+	case 'Z': case 'H':
+	    aux+=3; //*tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++;
+	    while ((*tmp++=*aux++));
+	    *tmp++ = '\t'; // stop byte
+	    break;
+
+	case 'B': {
+	    int type = aux[3], blen;
+	    uint32_t count = (uint32_t)((((unsigned char *)aux)[4]<< 0) +
+					(((unsigned char *)aux)[5]<< 8) +
+					(((unsigned char *)aux)[6]<<16) +
+					(((unsigned char *)aux)[7]<<24));
+	    // skip TN field
+	    aux+=3; //*tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++;
+
+	    // We use BYTE_ARRAY_LEN with external length, so store that first
+	    switch (type) {
+	    case 'c': case 'C':
+		blen = count;
+		break;
+	    case 's': case 'S':
+		blen = 2*count;
+		break;
+	    case 'i': case 'I': case 'f':
+		blen = 4*count;
+		break;
+	    default:
+		fprintf(stderr, "Unknown sub-type '%c' for aux type 'B'\n",
+			type);
+		return NULL;
+		    
+	    }
+
+	    tmp += itf8_put(tmp, blen+5);
+
+	    *tmp++=*aux++; // sub-type & length
+	    *tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++;
+
+	    // The tag data itself
+	    memcpy(tmp, aux, blen); tmp += blen; aux += blen;
+
+	    //cram_stats_add(c->aux_B_stats, blen);
+	    break;
+	}
+	default:
+	    fprintf(stderr, "Unknown aux type '%c'\n", aux[2]);
+	    return NULL;
+	}
+    }
+    cram_stats_add(c->stats[DS_TC], cr->ntags);
+
+    cr->aux = BLOCK_SIZE(s->aux_blk);
+    cr->aux_size = (uc *)tmp - (BLOCK_DATA(s->aux_blk) + cr->aux);
+    BLOCK_SIZE(s->aux_blk) = (uc *)tmp - BLOCK_DATA(s->aux_blk);
+    assert(s->aux_blk->byte <= s->aux_blk->alloc);
+
+    return rg;
+}
+
+/*
+ * Encodes auxiliary data. Largely duplicated from above, but done so to
+ * keep it simple and avoid a myriad of version ifs.
+ *
+ * Returns the read-group parsed out of the BAM aux fields on success
+ *         NULL on failure or no rg present (FIXME)
+ */
+static char *cram_encode_aux(cram_fd *fd, bam_seq_t *b, cram_container *c,
+			     cram_slice *s, cram_record *cr) {
+    char *aux, *orig, *tmp, *rg = NULL;
+    int aux_size = bam_get_l_aux(b);
+    cram_block *td_b = c->comp_hdr->TD_blk;
+    int TD_blk_size = BLOCK_SIZE(td_b), new;
+    char *key;
+    khint_t k;
+
+
+    /* Worst case is 1 nul char on every ??:Z: string, so +33% */
+    BLOCK_GROW(s->aux_blk, aux_size*1.34+1);
+    tmp = (char *)BLOCK_END(s->aux_blk);
+
+
+    orig = aux = (char *)bam_aux(b);
+
+    // Copy aux keys to td_b and aux values to s->aux_blk
+    while (aux - orig < aux_size && aux[0] != 0) {
+	uint32_t i32;
+	int r;
+
+	// RG:Z
+	if (aux[0] == 'R' && aux[1] == 'G' && aux[2] == 'Z') {
+	    rg = &aux[3];
+	    while (*aux++);
+	    continue;
+	}
+
+	// MD:Z
+	if (aux[0] == 'M' && aux[1] == 'D' && aux[2] == 'Z') {
+	    if (cr->len && !fd->no_ref && !(cr->flags & BAM_FUNMAP)) {
+		while (*aux++);
+		continue;
+	    }
+	}
+
+	// NM:i
+	if (aux[0] == 'N' && aux[1] == 'M') {
+	    if (cr->len && !fd->no_ref && !(cr->flags & BAM_FUNMAP)) {
+		switch(aux[2]) {
+		case 'A': case 'C': case 'c': aux+=4; break;
+		case 'S': case 's':           aux+=5; break;
+		case 'I': case 'i': case 'f': aux+=7; break;
+		default:
+		    fprintf(stderr, "Unhandled type code for NM tag\n");
+		    return NULL;
+		}
+		continue;
+	    }
+	}
+
+	BLOCK_APPEND(td_b, aux, 3);
+
+	i32 = (aux[0]<<16) | (aux[1]<<8) | aux[2];
+	kh_put(s_i2i, c->tags_used, i32, &r);
+	if (-1 == r)
+	    return NULL;
+
+	// BQ:Z
+	if (aux[0] == 'B' && aux[1] == 'Q' && aux[2] == 'Z') {
+	    char *tmp;
+	    if (!s->aux_BQ_blk)
+		if (!(s->aux_BQ_blk = cram_new_block(EXTERNAL, DS_aux_BQ)))
+		    return NULL;
+	    BLOCK_GROW(s->aux_BQ_blk, aux_size*1.34+1);
+	    tmp = (char *)BLOCK_END(s->aux_BQ_blk);
+	    aux += 3;
+	    while ((*tmp++=*aux++));
+	    *tmp++ = '\t';
+	    BLOCK_SIZE(s->aux_BQ_blk) = (uc *)tmp - BLOCK_DATA(s->aux_BQ_blk);
+	    continue;
+	}
+
+	// BD:Z
+	if (aux[0] == 'B' && aux[1]=='D' && aux[2] == 'Z') {
+	    char *tmp;
+	    if (!s->aux_BD_blk)
+		if (!(s->aux_BD_blk = cram_new_block(EXTERNAL, DS_aux_BD)))
+		    return NULL;
+	    BLOCK_GROW(s->aux_BD_blk, aux_size*1.34+1);
+	    tmp = (char *)BLOCK_END(s->aux_BD_blk);
+	    aux += 3;
+	    while ((*tmp++=*aux++));
+	    *tmp++ = '\t';
+	    BLOCK_SIZE(s->aux_BD_blk) = (uc *)tmp - BLOCK_DATA(s->aux_BD_blk);
+	    continue;
+	}
+
+	// BI:Z
+	if (aux[0] == 'B' && aux[1]=='I' && aux[2] == 'Z') {
+	    char *tmp;
+	    if (!s->aux_BI_blk)
+		if (!(s->aux_BI_blk = cram_new_block(EXTERNAL, DS_aux_BI)))
+		    return NULL;
+	    BLOCK_GROW(s->aux_BI_blk, aux_size*1.34+1);
+	    tmp = (char *)BLOCK_END(s->aux_BI_blk);
+	    aux += 3;
+	    while ((*tmp++=*aux++));
+	    *tmp++ = '\t';
+	    BLOCK_SIZE(s->aux_BI_blk) = (uc *)tmp - BLOCK_DATA(s->aux_BI_blk);
+	    continue;
+	}
+
+	// OQ:Z:
+	if (aux[0] == 'O' && aux[1] == 'Q' && aux[2] == 'Z') {
+	    char *tmp;
+	    if (!s->aux_OQ_blk)
+		if (!(s->aux_OQ_blk = cram_new_block(EXTERNAL, DS_aux_OQ)))
+		    return NULL;
+	    BLOCK_GROW(s->aux_OQ_blk, aux_size*1.34+1);
+	    tmp = (char *)BLOCK_END(s->aux_OQ_blk);
+	    aux += 3;
+	    while ((*tmp++=*aux++));
+	    *tmp++ = '\t';
+	    BLOCK_SIZE(s->aux_OQ_blk) = (uc *)tmp - BLOCK_DATA(s->aux_OQ_blk);
+	    continue;
+	}
+
+	// FZ:B or ZM:B
+	if ((aux[0] == 'F' && aux[1] == 'Z' && aux[2] == 'B') ||
+	    (aux[0] == 'Z' && aux[1] == 'M' && aux[2] == 'B')) {
+	    int type = aux[3], blen;
+	    uint32_t count = (uint32_t)((((unsigned char *)aux)[4]<< 0) +
+					(((unsigned char *)aux)[5]<< 8) +
+					(((unsigned char *)aux)[6]<<16) +
+					(((unsigned char *)aux)[7]<<24));
+	    char *tmp;
+	    if (!s->aux_FZ_blk)
+		if (!(s->aux_FZ_blk = cram_new_block(EXTERNAL, DS_aux_FZ)))
+		    return NULL;
+	    BLOCK_GROW(s->aux_FZ_blk, aux_size*1.34+1);
+	    tmp = (char *)BLOCK_END(s->aux_FZ_blk);
+
+	    // skip TN field
+	    aux+=3;
+
+	    // We use BYTE_ARRAY_LEN with external length, so store that first
+	    switch (type) {
+	    case 'c': case 'C':
+		blen = count;
+		break;
+	    case 's': case 'S':
+		blen = 2*count;
+		break;
+	    case 'i': case 'I': case 'f':
+		blen = 4*count;
+		break;
+	    default:
+		fprintf(stderr, "Unknown sub-type '%c' for aux type 'B'\n",
+			type);
+		return NULL;
+		    
+	    }
+
+	    blen += 5; // sub-type & length
+	    tmp += itf8_put(tmp, blen);
+
+	    // The tag data itself
+	    memcpy(tmp, aux, blen); tmp += blen; aux += blen;
+
+	    BLOCK_SIZE(s->aux_FZ_blk) = (uc *)tmp - BLOCK_DATA(s->aux_FZ_blk);
+	    continue;
+	}
+
+	// Other quality data - {Q2,E2,U2,CQ}:Z and similar
+	if (((aux[0] == 'Q' && aux[1] == '2') ||
+	     (aux[0] == 'U' && aux[1] == '2') ||
+	     (aux[0] == 'Q' && aux[1] == 'T') ||
+	     (aux[0] == 'C' && aux[1] == 'Q')) && aux[2] == 'Z') {
+	    char *tmp;
+	    if (!s->aux_oq_blk)
+		if (!(s->aux_oq_blk = cram_new_block(EXTERNAL, DS_aux_oq)))
+		    return NULL;
+	    BLOCK_GROW(s->aux_oq_blk, aux_size*1.34+1);
+	    tmp = (char *)BLOCK_END(s->aux_oq_blk);
+	    aux += 3;
+	    while ((*tmp++=*aux++));
+	    *tmp++ = '\t';
+	    BLOCK_SIZE(s->aux_oq_blk) = (uc *)tmp - BLOCK_DATA(s->aux_oq_blk);
+	    continue;
+	}
+
+	// Other sequence data - {R2,E2,CS,BC,RT}:Z and similar
+	if (((aux[0] == 'R' && aux[1] == '2') ||
+	     (aux[0] == 'E' && aux[1] == '2') ||
+	     (aux[0] == 'C' && aux[1] == 'S') ||
+	     (aux[0] == 'B' && aux[1] == 'C') ||
+	     (aux[0] == 'R' && aux[1] == 'T')) && aux[2] == 'Z') {
+	    char *tmp;
+	    if (!s->aux_os_blk)
+		if (!(s->aux_os_blk = cram_new_block(EXTERNAL, DS_aux_os)))
+		    return NULL;
+	    BLOCK_GROW(s->aux_os_blk, aux_size*1.34+1);
+	    tmp = (char *)BLOCK_END(s->aux_os_blk);
+	    aux += 3;
+	    while ((*tmp++=*aux++));
+	    *tmp++ = '\t';
+	    BLOCK_SIZE(s->aux_os_blk) = (uc *)tmp - BLOCK_DATA(s->aux_os_blk);
+	    continue;
+	}
+
+
+	switch(aux[2]) {
+	case 'A': case 'C': case 'c':
+	    aux+=3;
+	    *tmp++=*aux++;
+	    break;
+
+	case 'S': case 's':
+	    aux+=3;
+	    *tmp++=*aux++; *tmp++=*aux++;
+	    break;
+
+	case 'I': case 'i': case 'f':
+	    aux+=3;
+	    *tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++;
+	    break;
+
+	case 'd':
+	    aux+=3; //*tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++;
+	    *tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++;
+	    *tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++; *tmp++=*aux++;
+	    break;
+
+	case 'Z': case 'H':
+	    {
+		char *tmp;
+		if (!s->aux_oz_blk)
+		    if (!(s->aux_oz_blk = cram_new_block(EXTERNAL, DS_aux_oz)))
+			return NULL;
+		BLOCK_GROW(s->aux_oz_blk, aux_size*1.34+1);
+		tmp = (char *)BLOCK_END(s->aux_oz_blk);
+		aux += 3;
+		while ((*tmp++=*aux++));
+		*tmp++ = '\t';
+		BLOCK_SIZE(s->aux_oz_blk) = (uc *)tmp -
+		    BLOCK_DATA(s->aux_oz_blk);
+	    }
+	    break;
+
+	case 'B': {
+	    int type = aux[3], blen;
+	    uint32_t count = (uint32_t)((((unsigned char *)aux)[4]<< 0) +
+					(((unsigned char *)aux)[5]<< 8) +
+					(((unsigned char *)aux)[6]<<16) +
+					(((unsigned char *)aux)[7]<<24));
+	    // skip TN field
+	    aux+=3;
+
+	    // We use BYTE_ARRAY_LEN with external length, so store that first
+	    switch (type) {
+	    case 'c': case 'C':
+		blen = count;
+		break;
+	    case 's': case 'S':
+		blen = 2*count;
+		break;
+	    case 'i': case 'I': case 'f':
+		blen = 4*count;
+		break;
+	    default:
+		fprintf(stderr, "Unknown sub-type '%c' for aux type 'B'\n",
+			type);
+		return NULL;
+		    
+	    }
+
+	    blen += 5; // sub-type & length
+	    tmp += itf8_put(tmp, blen);
+
+	    // The tag data itself
+	    memcpy(tmp, aux, blen); tmp += blen; aux += blen;
+
+	    //cram_stats_add(c->aux_B_stats, blen);
+	    break;
+	}
+	default:
+	    fprintf(stderr, "Unknown aux type '%c'\n", aux[2]);
+	    return NULL;
+	}
+    }
+
+    // FIXME: sort BLOCK_DATA(td_b) by char[3] triples
+    
+    // And and increment TD hash entry
+    BLOCK_APPEND_CHAR(td_b, 0);
+
+    // Duplicate key as BLOCK_DATA() can be realloced to a new pointer.
+    key = string_ndup(c->comp_hdr->TD_keys, 
+		      (char *)BLOCK_DATA(td_b) + TD_blk_size,
+		      BLOCK_SIZE(td_b) - TD_blk_size);
+    k = kh_put(m_s2i, c->comp_hdr->TD_hash, key, &new);
+    if (new < 0) {
+	return NULL;
+    } else if (new == 0) {
+	BLOCK_SIZE(td_b) = TD_blk_size;
+    } else {
+	kh_val(c->comp_hdr->TD_hash, k) = c->comp_hdr->nTL;
+	c->comp_hdr->nTL++;
+    }
+
+    cr->TL = kh_val(c->comp_hdr->TD_hash, k);
+    cram_stats_add(c->stats[DS_TL], cr->TL);
+
+    cr->aux = BLOCK_SIZE(s->aux_blk);
+    cr->aux_size = (uc *)tmp - (BLOCK_DATA(s->aux_blk) + cr->aux);
+    BLOCK_SIZE(s->aux_blk) = (uc *)tmp - BLOCK_DATA(s->aux_blk);
+    assert(s->aux_blk->byte <= s->aux_blk->alloc);
+
+    return rg;
+}
+
+
+/*
+ * Handles creation of a new container or new slice, flushing any
+ * existing containers when appropriate. 
+ *
+ * Really this is next slice, which may or may not lead to a new container.
+ *
+ * Returns cram_container pointer on success
+ *         NULL on failure.
+ */
+static cram_container *cram_next_container(cram_fd *fd, bam_seq_t *b) {
+    cram_container *c = fd->ctr;
+    cram_slice *s;
+    int i;
+
+    /* First occurence */
+    if (c->curr_ref == -2)
+	c->curr_ref = bam_ref(b);
+
+    if (c->slice) {
+	s = c->slice;
+	if (c->multi_seq) {
+	    s->hdr->ref_seq_id    = -2;
+	    s->hdr->ref_seq_start = 0;
+	    s->hdr->ref_seq_span  = 0;
+	} else {
+	    s->hdr->ref_seq_id    = c->curr_ref;
+	    s->hdr->ref_seq_start = c->first_base;
+	    s->hdr->ref_seq_span  = c->last_base - c->first_base + 1;
+	}
+	s->hdr->num_records   = c->curr_rec;
+
+	if (c->curr_slice == 0) {
+	    if (c->ref_seq_id != s->hdr->ref_seq_id)
+		c->ref_seq_id  = s->hdr->ref_seq_id;
+	    c->ref_seq_start = c->first_base;
+	}
+
+	c->curr_slice++;
+    }
+
+    /* Flush container */
+    if (c->curr_slice == c->max_slice ||
+	(bam_ref(b) != c->curr_ref && !c->multi_seq)) {
+	c->ref_seq_span = fd->last_base - c->ref_seq_start + 1;
+	if (fd->verbose)
+	    fprintf(stderr, "Flush container %d/%d..%d\n",
+		    c->ref_seq_id, c->ref_seq_start,
+		    c->ref_seq_start + c->ref_seq_span -1);
+
+	/* Encode slices */
+	if (fd->pool) {
+	    if (-1 == cram_flush_container_mt(fd, c))
+		return NULL;
+	} else {
+	    if (-1 == cram_flush_container(fd, c))
+		return NULL;
+
+	    // Move to sep func, as we need cram_flush_container for
+	    // the closing phase to flush the partial container.
+	    for (i = 0; i < c->max_slice; i++) {
+		cram_free_slice(c->slices[i]);
+		c->slices[i] = NULL;
+	    }
+
+	    c->slice = NULL;
+	    c->curr_slice = 0;
+
+	    /* Easy approach for purposes of freeing stats */
+	    cram_free_container(c);
+	}
+
+	c = fd->ctr = cram_new_container(fd->seqs_per_slice,
+					 fd->slices_per_container);
+	if (!c)
+	    return NULL;
+	c->record_counter = fd->record_counter;
+	c->curr_ref = bam_ref(b);
+    }
+
+    c->last_pos = c->first_base = c->last_base = bam_pos(b)+1;
+
+    /* New slice */
+    c->slice = c->slices[c->curr_slice] =
+	cram_new_slice(MAPPED_SLICE, c->max_rec);
+    if (!c->slice)
+	return NULL;
+
+    if (c->multi_seq) {
+	c->slice->hdr->ref_seq_id = -2;
+	c->slice->hdr->ref_seq_start = 0;
+	c->slice->last_apos = 1;
+    } else {
+	c->slice->hdr->ref_seq_id = bam_ref(b);
+	// wrong for unsorted data, will fix during encoding.
+	c->slice->hdr->ref_seq_start = bam_pos(b)+1;
+	c->slice->last_apos = bam_pos(b)+1;
+    }
+
+    c->curr_rec = 0;
+
+    return c;
+}
+
+/*
+ * Converts a single bam record into a cram record.
+ * Possibly used within a thread.
+ *
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+static int process_one_read(cram_fd *fd, cram_container *c,
+			    cram_slice *s, cram_record *cr,
+			    bam_seq_t *b, int rnum) {
+    int i, fake_qual = -1;
+    char *cp, *rg;
+    char *ref, *seq, *qual;
+
+    // FIXME: multi-ref containers
+
+    ref = c->ref;
+    cr->flags       = bam_flag(b);
+    cr->len         = bam_seq_len(b);
+
+    //fprintf(stderr, "%s => %d\n", rg ? rg : "\"\"", cr->rg);
+
+    // Fields to resolve later
+    //cr->mate_line;    // index to another cram_record
+    //cr->mate_flags;   // MF
+    //cr->ntags;        // TC
+    cr->ntags      = 0; //cram_stats_add(c->stats[DS_TC], cr->ntags);
+    if (CRAM_MAJOR_VERS(fd->version) == 1)
+	rg = cram_encode_aux_1_0(fd, b, c, s, cr);
+    else
+	rg = cram_encode_aux(fd, b, c, s, cr);
+
+    //cr->aux_size = b->blk_size - ((char *)bam_aux(b) - (char *)&bam_ref(b));
+    //cr->aux = DSTRING_LEN(s->aux_ds);
+    //dstring_nappend(s->aux_ds, bam_aux(b), cr->aux_size);
+
+    /* Read group, identified earlier */
+    if (rg) {
+	SAM_RG *brg = sam_hdr_find_rg(fd->header, rg);
+	cr->rg = brg ? brg->id : -1;
+    } else if (CRAM_MAJOR_VERS(fd->version) == 1) {
+	SAM_RG *brg = sam_hdr_find_rg(fd->header, "UNKNOWN");
+	assert(brg);
+    } else {
+	cr->rg = -1;
+    }
+    cram_stats_add(c->stats[DS_RG], cr->rg);
+
+    
+    cr->ref_id      = bam_ref(b);  cram_stats_add(c->stats[DS_RI], cr->ref_id);
+    cram_stats_add(c->stats[DS_BF], fd->cram_flag_swap[cr->flags & 0xfff]);
+
+    // Non reference based encoding means storing the bases verbatim as features, which in
+    // turn means every base also has a quality already stored.
+    if (!fd->no_ref || CRAM_MAJOR_VERS(fd->version) >= 3)
+	cr->cram_flags = CRAM_FLAG_PRESERVE_QUAL_SCORES;
+    else
+	cr->cram_flags = 0;
+
+    if (cr->len <= 0 && CRAM_MAJOR_VERS(fd->version) >= 3)
+	cr->cram_flags |= CRAM_FLAG_NO_SEQ;
+    //cram_stats_add(c->stats[DS_CF], cr->cram_flags & CRAM_FLAG_MASK);
+
+    c->num_bases   += cr->len;
+    cr->apos        = bam_pos(b)+1;
+    if (c->pos_sorted) {
+	if (cr->apos < s->last_apos) {
+	    c->pos_sorted = 0;
+	} else {
+	    cram_stats_add(c->stats[DS_AP], cr->apos - s->last_apos);
+	    s->last_apos = cr->apos;
+	}
+    } else {
+	//cram_stats_add(c->stats[DS_AP], cr->apos);
+    }
+    c->max_apos += (cr->apos > c->max_apos) * (cr->apos - c->max_apos);
+
+    cr->name        = BLOCK_SIZE(s->name_blk);
+    cr->name_len    = bam_name_len(b);
+    cram_stats_add(c->stats[DS_RN], cr->name_len);
+
+    BLOCK_APPEND(s->name_blk, bam_name(b), bam_name_len(b));
+
+
+    /*
+     * This seqs_ds is largely pointless and it could reuse the same memory
+     * over and over.
+     * s->base_blk is what we need for encoding.
+     */
+    cr->seq         = BLOCK_SIZE(s->seqs_blk);
+    cr->qual        = BLOCK_SIZE(s->qual_blk);
+    BLOCK_GROW(s->seqs_blk, cr->len+1);
+    BLOCK_GROW(s->qual_blk, cr->len);
+    seq = cp = (char *)BLOCK_END(s->seqs_blk);
+
+    *seq = 0;
+#ifdef ALLOW_UAC
+    {
+	// Convert seq 2 bases at a time for speed.
+	static const uint16_t code2base[256] = {
+	    15677, 16701, 17213, 19773, 18237, 21053, 21309, 22077,
+	    21565, 22333, 22845, 18493, 19261, 17469, 16957, 20029,
+	    15681, 16705, 17217, 19777, 18241, 21057, 21313, 22081,
+	    21569, 22337, 22849, 18497, 19265, 17473, 16961, 20033,
+	    15683, 16707, 17219, 19779, 18243, 21059, 21315, 22083,
+	    21571, 22339, 22851, 18499, 19267, 17475, 16963, 20035,
+	    15693, 16717, 17229, 19789, 18253, 21069, 21325, 22093,
+	    21581, 22349, 22861, 18509, 19277, 17485, 16973, 20045,
+	    15687, 16711, 17223, 19783, 18247, 21063, 21319, 22087,
+	    21575, 22343, 22855, 18503, 19271, 17479, 16967, 20039,
+	    15698, 16722, 17234, 19794, 18258, 21074, 21330, 22098,
+	    21586, 22354, 22866, 18514, 19282, 17490, 16978, 20050,
+	    15699, 16723, 17235, 19795, 18259, 21075, 21331, 22099,
+	    21587, 22355, 22867, 18515, 19283, 17491, 16979, 20051,
+	    15702, 16726, 17238, 19798, 18262, 21078, 21334, 22102,
+	    21590, 22358, 22870, 18518, 19286, 17494, 16982, 20054,
+	    15700, 16724, 17236, 19796, 18260, 21076, 21332, 22100,
+	    21588, 22356, 22868, 18516, 19284, 17492, 16980, 20052,
+	    15703, 16727, 17239, 19799, 18263, 21079, 21335, 22103,
+	    21591, 22359, 22871, 18519, 19287, 17495, 16983, 20055,
+	    15705, 16729, 17241, 19801, 18265, 21081, 21337, 22105,
+	    21593, 22361, 22873, 18521, 19289, 17497, 16985, 20057,
+	    15688, 16712, 17224, 19784, 18248, 21064, 21320, 22088,
+	    21576, 22344, 22856, 18504, 19272, 17480, 16968, 20040,
+	    15691, 16715, 17227, 19787, 18251, 21067, 21323, 22091,
+	    21579, 22347, 22859, 18507, 19275, 17483, 16971, 20043,
+	    15684, 16708, 17220, 19780, 18244, 21060, 21316, 22084,
+	    21572, 22340, 22852, 18500, 19268, 17476, 16964, 20036,
+	    15682, 16706, 17218, 19778, 18242, 21058, 21314, 22082,
+	    21570, 22338, 22850, 18498, 19266, 17474, 16962, 20034,
+	    15694, 16718, 17230, 19790, 18254, 21070, 21326, 22094,
+	    21582, 22350, 22862, 18510, 19278, 17486, 16974, 20046
+	};
+
+	int l2 = cr->len / 2;
+	unsigned char *from = (unsigned char *)bam_seq(b);
+	uint16_t *cpi = (uint16_t *)cp;
+	cp[0] = 0;
+	for (i = 0; i < l2; i++)
+	    cpi[i] = le_int2(code2base[from[i]]);
+	if ((i *= 2) < cr->len)
+	    cp[i] = seq_nt16_str[bam_seqi(bam_seq(b), i)];
+    }
+#else
+    for (i = 0; i < cr->len; i++)
+	cp[i] = seq_nt16_str[bam_seqi(bam_seq(b), i)];
+#endif
+    BLOCK_SIZE(s->seqs_blk) += cr->len;
+
+    qual = cp = (char *)bam_qual(b);
+
+    /* Copy and parse */
+    if (!(cr->flags & BAM_FUNMAP)) {
+	uint32_t *cig_to, *cig_from;
+	int apos = cr->apos-1, spos = 0;
+
+	cr->cigar       = s->ncigar;
+	cr->ncigar      = bam_cigar_len(b);
+	while (cr->cigar + cr->ncigar >= s->cigar_alloc) {
+	    s->cigar_alloc = s->cigar_alloc ? s->cigar_alloc*2 : 1024;
+	    s->cigar = realloc(s->cigar, s->cigar_alloc * sizeof(*s->cigar));
+	    if (!s->cigar)
+		return -1;
+	}
+
+	cig_to = (uint32_t *)s->cigar;
+	cig_from = (uint32_t *)bam_cigar(b);
+
+	cr->feature = 0;
+	cr->nfeature = 0;
+	for (i = 0; i < cr->ncigar; i++) {
+	    enum cigar_op cig_op = cig_from[i] & BAM_CIGAR_MASK;
+	    uint32_t cig_len = cig_from[i] >> BAM_CIGAR_SHIFT;
+	    cig_to[i] = cig_from[i];
+
+	    /* Can also generate events from here for CRAM diffs */
+
+	    switch (cig_op) {
+		int l;
+
+		// Don't trust = and X ops to be correct.
+	    case BAM_CMATCH:
+	    case BAM_CBASE_MATCH:
+	    case BAM_CBASE_MISMATCH:
+		//fprintf(stderr, "\nBAM_CMATCH\nR: %.*s\nS: %.*s\n",
+		//	cig_len, &ref[apos], cig_len, &seq[spos]);
+		l = 0;
+		if (!fd->no_ref && cr->len) {
+		    int end = cig_len+apos < c->ref_end
+			? cig_len : c->ref_end - apos;
+		    char *sp = &seq[spos];
+		    char *rp = &ref[apos];
+		    char *qp = &qual[spos];
+		    if (end > cr->len) {
+			fprintf(stderr, "CIGAR and query sequence are of "
+				"different length\n");
+			return -1;
+		    }
+		    for (l = 0; l < end; l++) {
+			if (rp[l] != sp[l]) {
+			    if (!sp[l])
+				break;
+			    if (0 && CRAM_MAJOR_VERS(fd->version) >= 3) {
+				// Disabled for the time being as it doesn't
+				// seem to gain us much.
+				int ol=l;
+				while (l<end && rp[l] != sp[l])
+				    l++;
+				if (l-ol > 1) {
+				    if (cram_add_bases(fd, c, s, cr, spos+ol,
+						       l-ol, &seq[spos+ol]))
+					return -1;
+				    l--;
+				} else {
+				    l = ol;
+				    if (cram_add_substitution(fd, c, s, cr,
+							      spos+l, sp[l],
+							      qp[l], rp[l]))
+					return -1;
+				}
+			    } else {
+				if (cram_add_substitution(fd, c, s, cr, spos+l,
+							  sp[l], qp[l], rp[l]))
+				    return -1;
+			    }
+			}
+		    }
+		    spos += l;
+		    apos += l;
+		}
+
+		if (l < cig_len && cr->len) {
+		    if (fd->no_ref) {
+			if (CRAM_MAJOR_VERS(fd->version) == 3) {
+			    if (cram_add_bases(fd, c, s, cr, spos,
+					       cig_len-l, &seq[spos]))
+				return -1;
+			    spos += cig_len-l;
+			} else {
+			    for (; l < cig_len && seq[spos]; l++, spos++) {
+				if (cram_add_base(fd, c, s, cr, spos,
+						  seq[spos], qual[spos]))
+				    return -1;
+			    }
+			}
+		    } else {
+			/* off end of sequence or non-ref based output */
+			for (; l < cig_len && seq[spos]; l++, spos++) {
+			    if (cram_add_base(fd, c, s, cr, spos,
+					      seq[spos], qual[spos]))
+				return -1;
+			}
+		    }
+		    apos += cig_len;
+		} else if (!cr->len) {
+		    /* Seq "*" */
+		    apos += cig_len;
+		    spos += cig_len;
+		}
+		break;
+		
+	    case BAM_CDEL:
+		if (cram_add_deletion(c, s, cr, spos, cig_len, &seq[spos]))
+		    return -1;
+		apos += cig_len;
+		break;
+
+	    case BAM_CREF_SKIP:
+		if (cram_add_skip(c, s, cr, spos, cig_len, &seq[spos]))
+		    return -1;
+		apos += cig_len;
+		break;
+
+	    case BAM_CINS:
+		if (cram_add_insertion(c, s, cr, spos, cig_len,
+				       cr->len ? &seq[spos] : NULL))
+		    return -1;
+		if (fd->no_ref && cr->len) {
+		    for (l = 0; l < cig_len; l++, spos++) {
+			cram_add_quality(fd, c, s, cr, spos, qual[spos]);
+		    }
+		} else {
+		    spos += cig_len;
+		}
+		break;
+
+	    case BAM_CSOFT_CLIP:
+		if (cram_add_softclip(c, s, cr, spos, cig_len,
+				      cr->len ? &seq[spos] : NULL,
+				      fd->version))
+		    return -1;
+		if (fd->no_ref &&
+		    !(cr->cram_flags & CRAM_FLAG_PRESERVE_QUAL_SCORES)) {
+		    if (cr->len) {
+			for (l = 0; l < cig_len; l++, spos++) {
+			    cram_add_quality(fd, c, s, cr, spos, qual[spos]);
+			}
+		    } else {
+			for (l = 0; l < cig_len; l++, spos++) {
+			    cram_add_quality(fd, c, s, cr, spos, -1);
+			}
+		    }
+		} else {
+		    spos += cig_len;
+		}
+		break;
+
+	    case BAM_CHARD_CLIP:
+		if (cram_add_hardclip(c, s, cr, spos, cig_len, &seq[spos]))
+		    return -1;
+		break;
+	
+	    case BAM_CPAD:
+		if (cram_add_pad(c, s, cr, spos, cig_len, &seq[spos]))
+		    return -1;
+		break;
+	    }
+	}
+	if (cr->len && spos != cr->len) {
+	    fprintf(stderr, "CIGAR and query sequence are of different "
+		    "length\n");
+	    return -1;
+	}
+	fake_qual = spos;
+	cr->aend = fd->no_ref ? apos : MIN(apos, c->ref_end);
+	cram_stats_add(c->stats[DS_FN], cr->nfeature);
+    } else {
+	// Unmapped
+	cr->cram_flags |= CRAM_FLAG_PRESERVE_QUAL_SCORES;
+	cr->cigar  = 0;
+	cr->ncigar = 0;
+	cr->nfeature = 0;
+	cr->aend = cr->apos;
+	for (i = 0; i < cr->len; i++)
+	    cram_stats_add(c->stats[DS_BA], seq[i]);
+	fake_qual = 0;
+    }
+
+    /*
+     * Append to the qual block now. We do this here as
+     * cram_add_substitution() can generate BA/QS events which need to 
+     * be in the qual block before we append the rest of the data.
+     */
+    if (cr->cram_flags & CRAM_FLAG_PRESERVE_QUAL_SCORES) {
+	/* Special case of seq "*" */
+	if (cr->len == 0) {
+	    cr->len = fake_qual;
+	    BLOCK_GROW(s->qual_blk, cr->len);
+	    cp = (char *)BLOCK_END(s->qual_blk);
+	    memset(cp, 255, cr->len);
+	} else {
+	    BLOCK_GROW(s->qual_blk, cr->len);
+	    cp = (char *)BLOCK_END(s->qual_blk);
+	    char *from = (char *)&bam_qual(b)[0];
+	    char *to = &cp[0];
+	    memcpy(to, from, cr->len);
+	    //for (i = 0; i < cr->len; i++) cp[i] = from[i];
+	}
+	BLOCK_SIZE(s->qual_blk) += cr->len;
+    } else {
+	if (cr->len == 0)
+	    cr->len = fake_qual >= 0 ? fake_qual : cr->aend - cr->apos + 1;
+    }
+
+    cram_stats_add(c->stats[DS_RL], cr->len);
+
+    /* Now we know apos and aend both, update mate-pair information */
+    {
+	int new;
+	khint_t k;
+	int sec = (cr->flags & BAM_FSECONDARY) ? 1 : 0;
+
+	//fprintf(stderr, "Checking %"PRId64"/%.*s\t", rnum,
+	//	cr->name_len, DSTRING_STR(s->name_ds)+cr->name);
+	if (cr->flags & BAM_FPAIRED) {
+	    char *key = string_ndup(s->pair_keys,
+				    (char *)BLOCK_DATA(s->name_blk)+cr->name,
+				    cr->name_len);
+	    if (!key)
+		return -1;
+
+	    k = kh_put(m_s2i, s->pair[sec], key, &new);
+	    if (-1 == new)
+		return -1;
+	    else if (new > 0)
+		kh_val(s->pair[sec], k) = rnum;
+	} else {
+	    new = 1;
+	}
+
+	if (new == 0) {
+	    cram_record *p = &s->crecs[kh_val(s->pair[sec], k)];
+	    int aleft, aright, sign;
+
+	    aleft = MIN(cr->apos, p->apos);
+	    aright = MAX(cr->aend, p->aend);
+	    if (cr->apos < p->apos) {
+		sign = 1;
+	    } else if (cr->apos > p->apos) {
+		sign = -1;
+	    } else if (cr->flags & BAM_FREAD1) {
+		sign = 1;
+	    } else {
+		sign = -1;
+	    }
+	    
+	    //fprintf(stderr, "paired %"PRId64"\n", kh_val(s->pair[sec], k));
+
+	    // This vs p: tlen, matepos, flags
+	    if (bam_ins_size(b) != sign*(aright-aleft+1))
+		goto detached;
+
+	    if (MAX(bam_mate_pos(b)+1, 0) != p->apos)
+		goto detached;
+
+	    if (((bam_flag(b) & BAM_FMUNMAP) != 0) !=
+		((p->flags & BAM_FUNMAP) != 0))
+		goto detached;
+
+	    if (((bam_flag(b) & BAM_FMREVERSE) != 0) !=
+		((p->flags & BAM_FREVERSE) != 0))
+		goto detached;
+
+
+	    // p vs this: tlen, matepos, flags
+	    if (p->ref_id != cr->ref_id)
+		goto detached;
+
+	    if (p->tlen != -sign*(aright-aleft+1))
+		goto detached;
+
+	    if (p->mate_pos != cr->apos)
+		goto detached;
+
+	    if (((p->flags & BAM_FMUNMAP) != 0) !=
+		((p->mate_flags & CRAM_M_UNMAP) != 0))
+		goto detached;
+
+	    if (((p->flags & BAM_FMREVERSE) != 0) !=
+		((p->mate_flags & CRAM_M_REVERSE) != 0))
+		goto detached;
+
+	    // Supplementary reads are just too ill defined
+	    if ((cr->flags & BAM_FSUPPLEMENTARY) ||
+		(p->flags & BAM_FSUPPLEMENTARY))
+		goto detached;
+
+	    /*
+	     * The fields below are unused when encoding this read as it is
+	     * no longer detached.  In theory they may get referred to when
+	     * processing a 3rd or 4th read in this template?, so we set them
+	     * here just to be sure.
+	     *
+	     * They do not need cram_stats_add() calls those as they are
+	     * not emitted.
+	     */
+	    cr->mate_pos = p->apos;
+	    cr->tlen = sign*(aright-aleft+1);
+	    cr->mate_flags =
+	    	((p->flags & BAM_FMUNMAP)   == BAM_FMUNMAP)   * CRAM_M_UNMAP +
+	    	((p->flags & BAM_FMREVERSE) == BAM_FMREVERSE) * CRAM_M_REVERSE;
+
+	    // Decrement statistics aggregated earlier
+	    if (p->cram_flags & CRAM_FLAG_STATS_ADDED) {
+		cram_stats_del(c->stats[DS_NP], p->mate_pos);
+		cram_stats_del(c->stats[DS_MF], p->mate_flags);
+		cram_stats_del(c->stats[DS_TS], p->tlen);
+		cram_stats_del(c->stats[DS_NS], p->mate_ref_id);
+	    }
+
+	    /* Similarly we could correct the p-> values too, but these will no
+	     * longer have any code that refers back to them as the new 'p'
+	     * for this template is our current 'cr'.
+	     */
+	    //p->mate_pos = cr->apos;
+	    //p->mate_flags =
+	    //	((cr->flags & BAM_FMUNMAP)   == BAM_FMUNMAP)  * CRAM_M_UNMAP +
+	    //	((cr->flags & BAM_FMREVERSE) == BAM_FMREVERSE)* CRAM_M_REVERSE;
+	    //p->tlen = p->apos - cr->aend;
+
+	    // Clear detached from cr flags
+	    cr->cram_flags &= ~CRAM_FLAG_DETACHED;
+	    cram_stats_add(c->stats[DS_CF], cr->cram_flags & CRAM_FLAG_MASK);
+
+	    // Clear detached from p flags and set downstream
+	    if (p->cram_flags & CRAM_FLAG_STATS_ADDED) {
+		cram_stats_del(c->stats[DS_CF], p->cram_flags & CRAM_FLAG_MASK);
+		p->cram_flags &= ~CRAM_FLAG_STATS_ADDED;
+	    }
+
+	    p->cram_flags  &= ~CRAM_FLAG_DETACHED;
+	    p->cram_flags  |=  CRAM_FLAG_MATE_DOWNSTREAM;
+	    cram_stats_add(c->stats[DS_CF], p->cram_flags & CRAM_FLAG_MASK);
+
+	    p->mate_line = rnum - (kh_val(s->pair[sec], k) + 1);
+	    cram_stats_add(c->stats[DS_NF], p->mate_line);
+
+	    kh_val(s->pair[sec], k) = rnum;
+	} else {
+	detached:
+	    //fprintf(stderr, "unpaired\n");
+
+	    /* Derive mate flags from this flag */
+	    cr->mate_flags = 0;
+	    if (bam_flag(b) & BAM_FMUNMAP)
+		cr->mate_flags |= CRAM_M_UNMAP;
+	    if (bam_flag(b) & BAM_FMREVERSE)
+		cr->mate_flags |= CRAM_M_REVERSE;
+
+	    cram_stats_add(c->stats[DS_MF], cr->mate_flags);
+
+	    cr->mate_pos    = MAX(bam_mate_pos(b)+1, 0);
+	    cram_stats_add(c->stats[DS_NP], cr->mate_pos);
+
+	    cr->tlen        = bam_ins_size(b);
+	    cram_stats_add(c->stats[DS_TS], cr->tlen);
+
+	    cr->cram_flags |= CRAM_FLAG_DETACHED;
+	    cram_stats_add(c->stats[DS_CF], cr->cram_flags & CRAM_FLAG_MASK);
+	    cram_stats_add(c->stats[DS_NS], bam_mate_ref(b));
+
+	    cr->cram_flags |= CRAM_FLAG_STATS_ADDED;
+	}
+    }
+
+    cr->mqual       = bam_map_qual(b);
+    cram_stats_add(c->stats[DS_MQ], cr->mqual);
+
+    cr->mate_ref_id = bam_mate_ref(b);
+
+    if (!(bam_flag(b) & BAM_FUNMAP)) {
+	if (c->first_base > cr->apos)
+	    c->first_base = cr->apos;
+
+	if (c->last_base < cr->aend)
+	    c->last_base = cr->aend;
+    }
+
+    return 0;
+}
+
+/*
+ * Write iterator: put BAM format sequences into a CRAM file.
+ * We buffer up a containers worth of data at a time.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int cram_put_bam_seq(cram_fd *fd, bam_seq_t *b) {
+    cram_container *c;
+
+    if (!fd->ctr) {
+	fd->ctr = cram_new_container(fd->seqs_per_slice,
+				     fd->slices_per_container);
+	if (!fd->ctr)
+	    return -1;
+	fd->ctr->record_counter = fd->record_counter;
+    }
+    c = fd->ctr;
+
+    if (!c->slice || c->curr_rec == c->max_rec ||
+	(bam_ref(b) != c->curr_ref && c->curr_ref >= -1)) {
+	int slice_rec, curr_rec, multi_seq = fd->multi_seq == 1;
+	int curr_ref = c->slice ? c->curr_ref : bam_ref(b);
+
+
+	/*
+	 * Start packing slices when we routinely have under 1/4tr full.
+	 *
+	 * This option isn't available if we choose to embed references
+	 * since we can only have one per slice.
+	 */
+	if (fd->multi_seq == -1 && c->curr_rec < c->max_rec/4+10 &&
+	    fd->last_slice && fd->last_slice < c->max_rec/4+10 &&
+	    !fd->embed_ref) {
+	    if (fd->verbose && !c->multi_seq)
+		fprintf(stderr, "Multi-ref enabled for this container\n");
+	    multi_seq = 1;
+	}
+
+	slice_rec = c->slice_rec;
+	curr_rec  = c->curr_rec;
+
+	if (CRAM_MAJOR_VERS(fd->version) == 1 ||
+	    c->curr_rec == c->max_rec || fd->multi_seq != 1 || !c->slice) {
+	    if (NULL == (c = cram_next_container(fd, b))) {
+		if (fd->ctr) {
+		    // prevent cram_close attempting to flush
+		    cram_free_container(fd->ctr);
+		    fd->ctr = NULL;
+		}
+		return -1;
+	    }
+	}
+
+	/*
+	 * Due to our processing order, some things we've already done we
+	 * cannot easily undo. So when we first notice we should be packing
+	 * multiple sequences per container we emit the small partial
+	 * container as-is and then start a fresh one in a different mode.
+	 */
+	if (multi_seq) {
+	    fd->multi_seq = 1;
+	    c->multi_seq = 1;
+	    c->pos_sorted = 0; // required atm for multi_seq slices
+
+	    if (!c->refs_used) {
+		pthread_mutex_lock(&fd->ref_lock);
+		c->refs_used = calloc(fd->refs->nref, sizeof(int));
+		pthread_mutex_unlock(&fd->ref_lock);
+		if (!c->refs_used)
+		    return -1;
+	    }
+	}
+
+	fd->last_slice = curr_rec - slice_rec;
+	c->slice_rec = c->curr_rec;
+
+	// Have we seen this reference before?
+	if (bam_ref(b) >= 0 && bam_ref(b) != curr_ref && !fd->embed_ref &&
+	    !fd->unsorted && multi_seq) {
+	    
+	    if (!c->refs_used) {
+		pthread_mutex_lock(&fd->ref_lock);
+		c->refs_used = calloc(fd->refs->nref, sizeof(int));
+		pthread_mutex_unlock(&fd->ref_lock);
+		if (!c->refs_used)
+		    return -1;
+	    } else if (c->refs_used && c->refs_used[bam_ref(b)]) {
+		pthread_mutex_lock(&fd->ref_lock);
+		fd->unsorted = 1;
+		pthread_mutex_unlock(&fd->ref_lock);
+		fd->multi_seq = 1;
+	    }
+	}
+
+	c->curr_ref = bam_ref(b);
+	if (c->refs_used && c->curr_ref >= 0) c->refs_used[c->curr_ref]++;
+    }
+
+    if (!c->bams) {
+	/* First time through, allocate a set of bam pointers */
+	pthread_mutex_lock(&fd->bam_list_lock);
+	if (fd->bl) {
+	    spare_bams *spare = fd->bl;
+	    c->bams = spare->bams;
+	    fd->bl = spare->next;
+	    free(spare);
+	} else {
+	    c->bams = calloc(c->max_c_rec, sizeof(bam_seq_t *));
+	    if (!c->bams)
+		return -1;
+	}
+	pthread_mutex_unlock(&fd->bam_list_lock);
+    }
+
+    /* Copy or alloc+copy the bam record, for later encoding */
+    if (c->bams[c->curr_c_rec])
+	bam_copy1(c->bams[c->curr_c_rec], b);
+    else
+	c->bams[c->curr_c_rec] = bam_dup(b);
+
+    c->curr_rec++;
+    c->curr_c_rec++;
+    fd->record_counter++;
+
+    return 0;
+}
diff --git a/htslib/cram/cram_encode.h b/htslib/cram/cram_encode.h
new file mode 100644
index 0000000..9131d6e
--- /dev/null
+++ b/htslib/cram/cram_encode.h
@@ -0,0 +1,105 @@
+/*
+Copyright (c) 2012-2013 Genome Research Ltd.
+Author: James Bonfield <jkb at sanger.ac.uk>
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+Institute nor the names of its contributors may be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+/*! \file
+ * Include cram.h instead.
+ *
+ * This is an internal part of the CRAM system and is automatically included
+ * when you #include cram.h.
+ *
+ * Implements the encoding portion of CRAM I/O. Also see
+ * cram_codecs.[ch] for the actual encoding functions themselves.
+ */
+
+#ifndef _CRAM_WRITE_H_
+#define _CRAM_WRITE_H_
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/* ----------------------------------------------------------------------
+ * CRAM sequence iterators.
+ */
+
+/*! Write iterator: put BAM format sequences into a CRAM file.
+ *
+ * We buffer up a containers worth of data at a time.
+ *
+ * FIXME: break this into smaller pieces.
+ *
+ * @return
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+int cram_put_bam_seq(cram_fd *fd, bam_seq_t *b);
+
+
+/* ----------------------------------------------------------------------
+ * Internal functions
+ */
+
+/*! INTERNAL:
+ * Encodes a compression header block into a generic cram_block structure.
+ *
+ * @return
+ * Returns cram_block ptr on success;
+ *         NULL on failure
+ */
+cram_block *cram_encode_compression_header(cram_fd *fd, cram_container *c,
+					   cram_block_compression_hdr *h);
+
+/*! INTERNAL:
+ * Encodes a slice compression header. 
+ *
+ * @return
+ * Returns cram_block on success;
+ *         NULL on failure
+ */
+cram_block *cram_encode_slice_header(cram_fd *fd, cram_slice *s);
+
+/*! INTERNAL:
+ * Encodes all slices in a container into blocks.
+ *
+ * @return
+ * Returns 0 on success;
+ *        -1 on failure
+ *
+ * FIXME: separate into encode_container and write_container. Ideally
+ * we should be able to do read_container / write_container or
+ * decode_container / encode_container.
+ */
+int cram_encode_container(cram_fd *fd, cram_container *c);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/htslib/cram/cram_external.c b/htslib/cram/cram_external.c
new file mode 100644
index 0000000..f5accf2
--- /dev/null
+++ b/htslib/cram/cram_external.c
@@ -0,0 +1,377 @@
+/*
+Copyright (c) 2015 Genome Research Ltd.
+Author: James Bonfield <jkb at sanger.ac.uk>
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice,
+this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice,
+this list of conditions and the following disclaimer in the documentation
+and/or other materials provided with the distribution.
+
+   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+Institute nor the names of its contributors may be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+/*! \file
+ * External CRAM interface.
+ *
+ * Internally we're happy to use macros and to grub around in the cram
+ * structures.  This isn't very sustainable for an externally usable
+ * ABI though, so we have anonymous structs and accessor functions too
+ * to permit software such as samtools reheader to manipulate cram
+ * containers and blocks in a robust manner.
+ */
+
+#include <config.h>
+
+#include "htslib/hfile.h"
+#include "cram/cram.h"
+
+/*
+ *-----------------------------------------------------------------------------
+ * cram_fd
+ */
+SAM_hdr *cram_fd_get_header(cram_fd *fd) { return fd->header; }
+void cram_fd_set_header(cram_fd *fd, SAM_hdr *hdr) { fd->header = hdr; }
+
+int cram_fd_get_version(cram_fd *fd) { return fd->version; }
+void cram_fd_set_version(cram_fd *fd, int vers) { fd->version = vers; }
+
+int cram_major_vers(cram_fd *fd) { return CRAM_MAJOR_VERS(fd->version); }
+int cram_minor_vers(cram_fd *fd) { return CRAM_MINOR_VERS(fd->version); }
+
+hFILE *cram_fd_get_fp(cram_fd *fd) { return fd->fp; }
+void cram_fd_set_fp(cram_fd *fd, hFILE *fp) { fd->fp = fp; }
+
+
+/*
+ *-----------------------------------------------------------------------------
+ * cram_container
+ */
+int32_t cram_container_get_length(cram_container *c) {
+    return c->length;
+}
+
+void cram_container_set_length(cram_container *c, int32_t length) {
+    c->length = length;
+}
+
+
+int32_t cram_container_get_num_blocks(cram_container *c) {
+    return c->num_blocks;
+}
+
+void cram_container_set_num_blocks(cram_container *c, int32_t num_blocks) {
+    c->num_blocks = num_blocks;
+}
+
+
+/* Returns the landmarks[] array and the number of elements
+ * in num_landmarks.
+ */
+int32_t *cram_container_get_landmarks(cram_container *c, int32_t *num_landmarks) {
+    *num_landmarks = c->num_landmarks;
+    return c->landmark;
+}
+
+/* Sets the landmarks[] array (pointer copy, not a memory dup) and
+ * num_landmarks value.
+ */
+void cram_container_set_landmarks(cram_container *c, int32_t num_landmarks,
+				  int32_t *landmarks) {
+    c->num_landmarks = num_landmarks;
+    c->landmark = landmarks;
+}
+
+
+/* Returns true if the container is empty (EOF marker) */
+int cram_container_is_empty(cram_fd *fd) {
+    return fd->empty_container;
+}
+
+
+/*
+ *-----------------------------------------------------------------------------
+ * cram_block_compression_hdr
+ */
+
+/*
+ * Utility function to edit an RG id.
+ * This is only possible if there is one single RG value used and it
+ * is in the container compression header using HUFFMAN or BETA
+ * codec.  In this case it is essentially hard coded and needs no
+ * editing of external (or worse, CORE) blocks.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+// Or arbitrary set compression header constant?
+
+static int cram_block_compression_hdr_set_DS(cram_block_compression_hdr *ch,
+					     int ds, int new_rg) {
+    if (!ch || !ch->codecs[ds])
+	return -1;
+
+    switch (ch->codecs[ds]->codec) {
+    case E_HUFFMAN:
+	if (ch->codecs[ds]->huffman.ncodes != 1)
+	    return -1;
+	ch->codecs[ds]->huffman.codes[0].symbol = new_rg;
+	return 0;
+
+    case E_BETA:
+	if (ch->codecs[ds]->beta.nbits != 0)
+	    return -1;
+	ch->codecs[ds]->beta.offset = -new_rg;
+	return 0;
+
+    default:
+	return -1;
+    }
+
+    return 0;
+}
+
+int cram_block_compression_hdr_set_rg(cram_block_compression_hdr *ch, int new_rg) {
+    return cram_block_compression_hdr_set_DS(ch, DS_RG, new_rg);
+}
+
+/*
+ * Converts a cram_block_compression_hdr struct used for decoding to
+ * one used for encoding.  Maybe this should be a transparent
+ * operation applied on-demand.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int cram_block_compression_hdr_decoder2encoder(cram_fd *fd,
+					       cram_block_compression_hdr *ch) {
+    int i;
+
+    if (!ch)
+	return -1;
+
+    for (i = 0; i < DS_END; i++) {
+	cram_codec *co = ch->codecs[i];
+	if (!co)
+	    continue;
+
+	if (-1 == cram_codec_decoder2encoder(fd, co))
+	    return -1;
+    }
+
+    return 0;
+}
+
+/*
+ *-----------------------------------------------------------------------------
+ * cram_slice
+ */
+int32_t cram_slice_hdr_get_num_blocks(cram_block_slice_hdr *hdr) {
+    return hdr->num_blocks;
+}
+
+
+/*
+ *-----------------------------------------------------------------------------
+ * cram_block
+ */
+int32_t cram_block_get_content_id(cram_block *b)  { return b->content_id; }
+int32_t cram_block_get_comp_size(cram_block *b)   { return b->comp_size; }
+int32_t cram_block_get_uncomp_size(cram_block *b) { return b->uncomp_size; }
+int32_t cram_block_get_crc32(cram_block *b)       { return b->crc32; }
+void *  cram_block_get_data(cram_block *b)        { return BLOCK_DATA(b); }
+int32_t cram_block_get_size(cram_block *b)        { return BLOCK_SIZE(b); }
+enum cram_content_type cram_block_get_content_type(cram_block *b) {
+    return b->content_type;
+}
+
+void cram_block_set_content_id(cram_block *b, int32_t id) { b->content_id = id; }
+void cram_block_set_comp_size(cram_block *b, int32_t size) { b->comp_size = size; }
+void cram_block_set_uncomp_size(cram_block *b, int32_t size) { b->uncomp_size = size; }
+void cram_block_set_crc32(cram_block *b, int32_t crc) { b->crc32 = crc; }
+void cram_block_set_data(cram_block *b, void *data) { BLOCK_DATA(b) = data; }
+void cram_block_set_size(cram_block *b, int32_t size) { BLOCK_SIZE(b) = size; }
+
+int cram_block_append(cram_block *b, void *data, int size) {
+    BLOCK_APPEND(b, data, size);
+    return BLOCK_DATA(b) ? 0 : -1; // It'll do for now...
+}
+void cram_block_update_size(cram_block *b) { BLOCK_UPLEN(b); }
+
+// Offset is known as "size" internally, but it can be confusing.
+size_t cram_block_get_offset(cram_block *b) { return BLOCK_SIZE(b); }
+void cram_block_set_offset(cram_block *b, size_t offset) { BLOCK_SIZE(b) = offset; }
+
+
+/*
+ * Copies the blocks representing the next num_slice slices from a
+ * container from 'in' to 'out'.  It is expected that the file pointer
+ * is just after the read of the cram_container and cram compression
+ * header.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int cram_copy_slice(cram_fd *in, cram_fd *out, int32_t num_slice) {
+    int32_t i, j;
+
+    for (i = 0; i < num_slice; i++) {
+	cram_block *blk;
+	cram_block_slice_hdr *hdr;
+
+	if (!(blk = cram_read_block(in)))
+	    return -1;
+	if (!(hdr = cram_decode_slice_header(in, blk))) {
+	    cram_free_block(blk);
+	    return -1;
+	}
+	if (cram_write_block(out, blk) != 0) {
+	    cram_free_block(blk);
+	    return -1;
+	}
+	cram_free_block(blk);
+
+	int num_blocks = cram_slice_hdr_get_num_blocks(hdr);
+	for (j = 0; j < num_blocks; j++) {
+	    blk = cram_read_block(in);
+	    if (!blk || cram_write_block(out, blk) != 0) {
+		if (blk) cram_free_block(blk);
+		return -1;
+	    }
+	    cram_free_block(blk);
+	}
+	cram_free_slice_header(hdr);
+    }
+
+    return 0;
+}
+
+/*
+ * Renumbers RG numbers in a cram compression header.
+ *
+ * CRAM stores RG as the Nth number in the header, rather than a
+ * string holding the ID: tag.  This is smaller in space, but means
+ * "samtools cat" to join files together that contain single but
+ * different RG lines needs a way of renumbering them.
+ *
+ * The file descriptor is expected to be immediately after the
+ * cram_container structure (ie before the cram compression header).
+ * Due to the nature of the CRAM format, this needs to read and write
+ * the blocks itself.  Note that there may be multiple slices within
+ * the container, meaning multiple compression headers to manipulate.
+ * Changing RG may change the size of the compression header and
+ * therefore the length field in the container.  Hence we rewrite all
+ * blocks just incase and also emit the adjusted container.
+ *
+ * The current implementation can only cope with renumbering a single
+ * RG (and only then if it is using HUFFMAN or BETA codecs).  In
+ * theory it *may* be possible to renumber multiple RGs if they use
+ * HUFFMAN to the CORE block or use an external block unshared by any
+ * other data series.  So we have an API that can be upgraded to
+ * support this, but do not implement it for now.  An example
+ * implementation of RG as an EXTERNAL block would be to find that
+ * block and rewrite it, returning the number of blocks consumed.
+ *
+ * Returns 0 on success;
+ *        -1 if unable to edit;
+ *        -2 on other errors (eg I/O).
+ */
+int cram_transcode_rg(cram_fd *in, cram_fd *out,
+		      cram_container *c,
+		      int nrg, int *in_rg, int *out_rg) {
+    int new_rg = *out_rg, old_size, new_size;
+    cram_block *o_blk, *n_blk;
+    cram_block_compression_hdr *ch;
+
+    if (nrg != 1) {
+	fprintf(stderr, "[%s] ERROR: not implemented for nrg != 1\n",
+		__func__);
+	return -2;
+    }
+
+    // Produce a new block holding the updated compression header,
+    // with RG transcoded to a new value. (Single only supported.)
+    o_blk = cram_read_block(in);
+    old_size = cram_block_size(o_blk);
+    ch = cram_decode_compression_header(in, o_blk);
+    if (cram_block_compression_hdr_set_rg(ch, new_rg) != 0)
+	return -1;
+    cram_block_compression_hdr_decoder2encoder(in, ch);
+    n_blk = cram_encode_compression_header(in, c, ch);
+    cram_free_compression_header(ch);
+
+    /*
+     * Warning: this has internal knowledge of the cram compression
+     * header format.
+     *
+     * The decoder doesn't set c->tags_used, so the encoder puts a two
+     * byte blank segment.  This means n_blk is too short.  We skip
+     * through the decoded old block (o_blk) and copy from there.
+     */
+    char *cp = cram_block_get_data(o_blk);
+    char *op = cp;
+    char *endp = cp + cram_block_get_uncomp_size(o_blk);
+    //fprintf(stderr, "sz = %d\n", (int)(endp-cp));
+    int32_t i32;
+
+    cp += safe_itf8_get(cp, endp, &i32);
+    cp += i32;
+    cp += safe_itf8_get(cp, endp, &i32);
+    cp += i32;
+    op = cp;
+    cp += safe_itf8_get(cp, endp, &i32);
+    i32 += (cp-op);
+
+    //fprintf(stderr, "remaining %d bytes\n", i32);
+    cram_block_set_size(n_blk, cram_block_get_size(n_blk)-2);
+    cram_block_append(n_blk, op, i32);
+    cram_block_update_size(n_blk);
+
+    new_size = cram_block_size(n_blk);
+
+    //fprintf(stderr, "size %d -> %d\n", old_size, new_size);
+
+    // Now we've constructedthe updated compression header,
+    // amend the container too (it may have changed size).
+    int32_t *landmarks, num_landmarks;
+    landmarks = cram_container_get_landmarks(c, &num_landmarks);
+
+    if (old_size != new_size) {
+	int diff = new_size - old_size, j;
+
+	for (j = 0; j < num_landmarks; j++)
+	    landmarks[j] += diff;
+	//cram_container_set_landmarks(c, num_landmarks, landmarks);
+	cram_container_set_length(c, cram_container_get_length(c) + diff);
+    }
+
+    // Finally write it all out; container, compression header,
+    // and then all the remaining slice blocks.
+    if (cram_write_container(out, c) != 0)
+	return -2;
+
+    cram_write_block(out, n_blk);
+    cram_free_block(o_blk);
+    cram_free_block(n_blk);
+
+    // Container num_blocks can be invalid, due to a bug.
+    // Instead we iterate in slice context instead.
+    return cram_copy_slice(in, out, num_landmarks);
+}
diff --git a/htslib/cram/cram_index.c b/htslib/cram/cram_index.c
new file mode 100644
index 0000000..9818991
--- /dev/null
+++ b/htslib/cram/cram_index.c
@@ -0,0 +1,582 @@
+/*
+Copyright (c) 2013-2014 Genome Research Ltd.
+Author: James Bonfield <jkb at sanger.ac.uk>
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+Institute nor the names of its contributors may be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+/*
+ * The index is a gzipped tab-delimited text file with one line per slice.
+ * The columns are:
+ * 1: reference number (0 to N-1, as per BAM ref_id)
+ * 2: reference position of 1st read in slice (1..?)
+ * 3: number of reads in slice
+ * 4: offset of container start (relative to end of SAM header, so 1st
+ *    container is offset 0).
+ * 5: slice number within container (ie which landmark).
+ *
+ * In memory, we hold this in a nested containment list. Each list element is
+ * a cram_index struct. Each element in turn can contain its own list of
+ * cram_index structs.
+ *
+ * Any start..end range which is entirely contained within another (and
+ * earlier as it is sorted) range will be held within it. This ensures that
+ * the outer list will never have containments and we can safely do a
+ * binary search to find the first range which overlaps any given coordinate.
+ */
+
+#include <config.h>
+
+#include <stdio.h>
+#include <errno.h>
+#include <assert.h>
+#include <stdlib.h>
+#include <string.h>
+#include <zlib.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <math.h>
+#include <ctype.h>
+
+#include "htslib/hfile.h"
+#include "hts_internal.h"
+#include "cram/cram.h"
+#include "cram/os.h"
+#include "cram/zfio.h"
+
+#if 0
+static void dump_index_(cram_index *e, int level) {
+    int i, n;
+    n = printf("%*s%d / %d .. %d, ", level*4, "", e->refid, e->start, e->end);
+    printf("%*soffset %"PRId64"\n", MAX(0,50-n), "", e->offset);
+    for (i = 0; i < e->nslice; i++) {
+	dump_index_(&e->e[i], level+1);
+    }
+}
+
+static void dump_index(cram_fd *fd) {
+    int i;
+    for (i = 0; i < fd->index_sz; i++) {
+	dump_index_(&fd->index[i], 0);
+    }
+}
+#endif
+
+static int kget_int32(kstring_t *k, size_t *pos, int32_t *val_p) {
+    int sign = 1;
+    int32_t val = 0;
+    size_t p = *pos;
+
+    while (p < k->l && (k->s[p] == ' ' || k->s[p] == '\t'))
+	   p++;
+
+    if (p < k->l && k->s[p] == '-')
+	sign = -1, p++;
+
+    if (p >= k->l || !(k->s[p] >= '0' && k->s[p] <= '9'))
+	return -1;
+
+    while (p < k->l && k->s[p] >= '0' && k->s[p] <= '9')
+	val = val*10 + k->s[p++]-'0';
+    
+    *pos = p;
+    *val_p = sign*val;
+
+    return 0;
+}
+
+static int kget_int64(kstring_t *k, size_t *pos, int64_t *val_p) {
+    int sign = 1;
+    int64_t val = 0;
+    size_t p = *pos;
+
+    while (p < k->l && (k->s[p] == ' ' || k->s[p] == '\t'))
+	   p++;
+
+    if (p < k->l && k->s[p] == '-')
+	sign = -1, p++;
+
+    if (p >= k->l || !(k->s[p] >= '0' && k->s[p] <= '9'))
+	return -1;
+
+    while (p < k->l && k->s[p] >= '0' && k->s[p] <= '9')
+	val = val*10 + k->s[p++]-'0';
+    
+    *pos = p;
+    *val_p = sign*val;
+
+    return 0;
+}
+
+/*
+ * Loads a CRAM .crai index into memory.
+ *
+ * Returns 0 for success
+ *        -1 for failure
+ */
+int cram_index_load(cram_fd *fd, const char *fn, const char *fn_idx) {
+    char *fn2 = NULL;
+    char buf[65536];
+    ssize_t len;
+    kstring_t kstr = {0};
+    FILE *fp;
+    cram_index *idx;
+    cram_index **idx_stack = NULL, *ep, e;
+    int idx_stack_alloc = 0, idx_stack_ptr = 0;
+    size_t pos = 0;
+
+    /* Check if already loaded */
+    if (fd->index)
+	return 0;
+
+    fd->index = calloc((fd->index_sz = 1), sizeof(*fd->index));
+    if (!fd->index)
+	return -1;
+
+    idx = &fd->index[0];
+    idx->refid = -1;
+    idx->start = INT_MIN;
+    idx->end   = INT_MAX;
+
+    idx_stack = calloc(++idx_stack_alloc, sizeof(*idx_stack));
+    idx_stack[idx_stack_ptr] = idx;
+
+    if (!fn_idx) {
+	fn2 = hts_idx_getfn(fn, ".crai");
+	if (!fn2) {
+	    free(idx_stack);
+	    return -1;
+	}
+	fn_idx = fn2;
+    }
+
+    if (!(fp = fopen(fn_idx, "r"))) {
+	perror(fn_idx);
+	free(idx_stack);
+	free(fn2);
+	return -1;
+    }
+
+    // Load the file into memory
+    while ((len = fread(buf, 1, 65536, fp)) > 0)
+	kputsn(buf, len, &kstr);
+    if (len < 0 || kstr.l < 2) {
+	if (kstr.s)
+	    free(kstr.s);
+	free(idx_stack);
+	free(fn2);
+	return -1;
+    }
+
+    if (fclose(fp)) {
+	if (kstr.s)
+	    free(kstr.s);
+	free(idx_stack);
+	free(fn2);
+	return -1;
+    }
+	
+
+    // Uncompress if required
+    if (kstr.s[0] == 31 && (uc)kstr.s[1] == 139) {
+	size_t l;
+	char *s = zlib_mem_inflate(kstr.s, kstr.l, &l);
+	free(kstr.s);
+	if (!s) {
+	    free(idx_stack);
+	    free(fn2);
+	    return -1;
+	}
+	kstr.s = s;
+	kstr.l = l;
+	kstr.m = l; // conservative estimate of the size allocated
+	kputsn("", 0, &kstr); // ensure kstr.s is NUL-terminated
+    }
+
+
+    // Parse it line at a time
+    do {
+	/* 1.1 layout */
+	if (kget_int32(&kstr, &pos, &e.refid) == -1) {
+	    free(kstr.s); free(idx_stack); free(fn2); return -1;
+	}
+	if (kget_int32(&kstr, &pos, &e.start) == -1) {
+	    free(kstr.s); free(idx_stack); free(fn2); return -1;
+	}
+	if (kget_int32(&kstr, &pos, &e.end) == -1) {
+	    free(kstr.s); free(idx_stack); free(fn2); return -1;
+	}
+	if (kget_int64(&kstr, &pos, &e.offset) == -1) {
+	    free(kstr.s); free(idx_stack); free(fn2); return -1;
+	}
+	if (kget_int32(&kstr, &pos, &e.slice) == -1) {
+	    free(kstr.s); free(idx_stack); free(fn2); return -1;
+	}
+	if (kget_int32(&kstr, &pos, &e.len) == -1) {
+	    free(kstr.s); free(idx_stack); free(fn2); return -1;
+	}
+
+	e.end += e.start-1;
+	//printf("%d/%d..%d\n", e.refid, e.start, e.end);
+
+	if (e.refid < -1) {
+	    free(kstr.s);
+	    free(idx_stack);
+	    free(fn2);
+	    fprintf(stderr, "Malformed index file, refid %d\n", e.refid);
+	    return -1;
+	}
+
+	if (e.refid != idx->refid) {
+	    if (fd->index_sz < e.refid+2) {
+		size_t index_end = fd->index_sz * sizeof(*fd->index);
+		fd->index_sz = e.refid+2;
+		fd->index = realloc(fd->index,
+				    fd->index_sz * sizeof(*fd->index));
+		memset(((char *)fd->index) + index_end, 0,
+		       fd->index_sz * sizeof(*fd->index) - index_end);
+	    }
+	    idx = &fd->index[e.refid+1];
+	    idx->refid = e.refid;
+	    idx->start = INT_MIN;
+	    idx->end   = INT_MAX;
+	    idx->nslice = idx->nalloc = 0;
+	    idx->e = NULL;
+	    idx_stack[(idx_stack_ptr = 0)] = idx;
+	}
+
+	while (!(e.start >= idx->start && e.end <= idx->end) || idx->end == 0) {
+	    idx = idx_stack[--idx_stack_ptr];
+	}
+
+	// Now contains, so append
+	if (idx->nslice+1 >= idx->nalloc) {
+	    idx->nalloc = idx->nalloc ? idx->nalloc*2 : 16;
+	    idx->e = realloc(idx->e, idx->nalloc * sizeof(*idx->e));
+	}
+
+	e.nalloc = e.nslice = 0; e.e = NULL;
+	*(ep = &idx->e[idx->nslice++]) = e;
+	idx = ep;
+
+	if (++idx_stack_ptr >= idx_stack_alloc) {
+	    idx_stack_alloc *= 2;
+	    idx_stack = realloc(idx_stack, idx_stack_alloc*sizeof(*idx_stack));
+	}
+	idx_stack[idx_stack_ptr] = idx;
+
+	while (pos < kstr.l && kstr.s[pos] != '\n')
+	    pos++;
+	pos++;
+    } while (pos < kstr.l);
+
+    free(idx_stack);
+    free(kstr.s);
+    free(fn2);
+
+    // dump_index(fd);
+
+    return 0;
+}
+
+static void cram_index_free_recurse(cram_index *e) {
+    if (e->e) {
+	int i;
+	for (i = 0; i < e->nslice; i++) {
+	    cram_index_free_recurse(&e->e[i]);
+	}
+	free(e->e);
+    }
+}
+
+void cram_index_free(cram_fd *fd) {
+    int i;
+
+    if (!fd->index)
+	return;
+    
+    for (i = 0; i < fd->index_sz; i++) {
+	cram_index_free_recurse(&fd->index[i]);
+    }
+    free(fd->index);
+
+    fd->index = NULL;
+}
+
+/*
+ * Searches the index for the first slice overlapping a reference ID
+ * and position, or one immediately preceding it if none is found in
+ * the index to overlap this position. (Our index may have missing
+ * entries, but we require at least one per reference.)
+ *
+ * If the index finds multiple slices overlapping this position we
+ * return the first one only. Subsequent calls should specifying
+ * "from" as the last slice we checked to find the next one. Otherwise
+ * set "from" to be NULL to find the first one.
+ *
+ * Returns the cram_index pointer on sucess
+ *         NULL on failure
+ */
+cram_index *cram_index_query(cram_fd *fd, int refid, int pos, 
+			     cram_index *from) {
+    int i, j, k;
+    cram_index *e;
+
+    if (refid+1 < 0 || refid+1 >= fd->index_sz)
+	return NULL;
+
+    if (!from)
+	from = &fd->index[refid+1];
+
+    // Ref with nothing aligned against it.
+    if (!from->e)
+	return NULL;
+
+    // This sequence is covered by the index, so binary search to find
+    // the optimal starting block.
+    i = 0, j = fd->index[refid+1].nslice-1;
+    for (k = j/2; k != i; k = (j-i)/2 + i) {
+	if (from->e[k].refid > refid) {
+	    j = k;
+	    continue;
+	}
+
+	if (from->e[k].refid < refid) {
+	    i = k;
+	    continue;
+	}
+
+	if (from->e[k].start >= pos) {
+	    j = k;
+	    continue;
+	}
+
+	if (from->e[k].start < pos) {
+	    i = k;
+	    continue;
+	}
+    }
+    // i==j or i==j-1. Check if j is better.
+    if (j >= 0 && from->e[j].start < pos && from->e[j].refid == refid)
+	i = j;
+
+    /* The above found *a* bin overlapping, but not necessarily the first */
+    while (i > 0 && from->e[i-1].end >= pos)
+	i--;
+
+    /* We may be one bin before the optimum, so check */
+    while (i+1 < from->nslice &&
+	   (from->e[i].refid < refid ||
+	    from->e[i].end < pos))
+	i++;
+
+    e = &from->e[i];
+
+    return e;
+}
+
+
+/*
+ * Skips to a container overlapping the start coordinate listed in
+ * cram_range.
+ *
+ * In theory we call cram_index_query multiple times, once per slice
+ * overlapping the range. However slices may be absent from the index
+ * which makes this problematic. Instead we find the left-most slice
+ * and then read from then on, skipping decoding of slices and/or
+ * whole containers when they don't overlap the specified cram_range.
+ *
+ * Returns 0 on success
+ *        -1 on general failure
+ *        -2 on no-data (empty chromosome)
+ */
+int cram_seek_to_refpos(cram_fd *fd, cram_range *r) {
+    cram_index *e;
+
+    // Ideally use an index, so see if we have one.
+    if ((e = cram_index_query(fd, r->refid, r->start, NULL))) {
+	if (0 != cram_seek(fd, e->offset, SEEK_SET))
+	    if (0 != cram_seek(fd, e->offset - fd->first_container, SEEK_CUR))
+		return -1;
+    } else {
+	// Absent from index, but this most likely means it simply has no data.
+	return -2;
+    }
+
+    if (fd->ctr) {
+	cram_free_container(fd->ctr);
+	fd->ctr = NULL;
+	fd->ooc = 0;
+    }
+
+    return 0;
+}
+
+
+/*
+ * A specialised form of cram_index_build (below) that deals with slices
+ * having multiple references in this (ref_id -2). In this scenario we
+ * decode the slice to look at the RI data series instead.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+static int cram_index_build_multiref(cram_fd *fd,
+				     cram_container *c,
+				     cram_slice *s,
+				     zfp *fp,
+				     off_t cpos,
+				     int32_t landmark,
+				     int sz) {
+    int i, ref = -2, ref_start = 0, ref_end;
+    char buf[1024];
+
+    if (0 != cram_decode_slice(fd, c, s, fd->header))
+	return -1;
+
+    ref_end = INT_MIN;
+    for (i = 0; i < s->hdr->num_records; i++) {
+	if (s->crecs[i].ref_id == ref) {
+	    if (ref_end < s->crecs[i].aend)
+		ref_end = s->crecs[i].aend;
+	    continue;
+	}
+
+	if (ref != -2) {
+	    sprintf(buf, "%d\t%d\t%d\t%"PRId64"\t%d\t%d\n",
+		    ref, ref_start, ref_end - ref_start + 1,
+		    (int64_t)cpos, landmark, sz);
+	    zfputs(buf, fp);
+	}
+
+	ref = s->crecs[i].ref_id;
+	ref_start = s->crecs[i].apos;
+	ref_end = INT_MIN;
+    }
+
+    if (ref != -2) {
+	sprintf(buf, "%d\t%d\t%d\t%"PRId64"\t%d\t%d\n",
+		ref, ref_start, ref_end - ref_start + 1,
+		(int64_t)cpos, landmark, sz);
+	zfputs(buf, fp);
+    }
+
+    return 0;
+}
+
+/*
+ * Builds an index file.
+ *
+ * fd is a newly opened cram file that we wish to index.
+ * fn_base is the filename of the associated CRAM file.
+ * fn_idx is the filename of the index file to be written;
+ * if NULL, we add ".crai" to fn_base to get the index filename.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int cram_index_build(cram_fd *fd, const char *fn_base, const char *fn_idx) {
+    cram_container *c;
+    off_t cpos, spos, hpos;
+    zfp *fp;
+    kstring_t fn_idx_str = {0};
+
+    if (! fn_idx) {
+        kputs(fn_base, &fn_idx_str);
+        kputs(".crai", &fn_idx_str);
+        fn_idx = fn_idx_str.s;
+    }
+
+    if (!(fp = zfopen(fn_idx, "wz"))) {
+        perror(fn_idx);
+        free(fn_idx_str.s);
+        return -1;
+    }
+
+    free(fn_idx_str.s);
+
+    cpos = htell(fd->fp);
+    while ((c = cram_read_container(fd))) {
+        int j;
+
+        if (fd->err) {
+            perror("Cram container read");
+            return -1;
+        }
+
+        hpos = htell(fd->fp);
+
+        if (!(c->comp_hdr_block = cram_read_block(fd)))
+            return -1;
+        assert(c->comp_hdr_block->content_type == COMPRESSION_HEADER);
+
+        c->comp_hdr = cram_decode_compression_header(fd, c->comp_hdr_block);
+        if (!c->comp_hdr)
+            return -1;
+
+        // 2.0 format
+        for (j = 0; j < c->num_landmarks; j++) {
+            char buf[1024];
+            cram_slice *s;
+            int sz;
+
+            spos = htell(fd->fp);
+            assert(spos - cpos - c->offset == c->landmark[j]);
+
+            if (!(s = cram_read_slice(fd))) {
+		zfclose(fp);
+		return -1;
+	    }
+
+            sz = (int)(htell(fd->fp) - spos);
+
+	    if (s->hdr->ref_seq_id == -2) {
+		cram_index_build_multiref(fd, c, s, fp,
+					  cpos, c->landmark[j], sz);
+	    } else {
+		sprintf(buf, "%d\t%d\t%d\t%"PRId64"\t%d\t%d\n",
+			s->hdr->ref_seq_id, s->hdr->ref_seq_start,
+			s->hdr->ref_seq_span, (int64_t)cpos,
+			c->landmark[j], sz);
+		zfputs(buf, fp);
+	    }
+
+            cram_free_slice(s);
+        }
+
+        cpos = htell(fd->fp);
+        assert(cpos == hpos + c->length);
+
+        cram_free_container(c);
+    }
+    if (fd->err) {
+	zfclose(fp);
+	return -1;
+    }
+	
+
+    return (zfclose(fp) >= 0)? 0 : -1;
+}
diff --git a/htslib/cram/cram_index.h b/htslib/cram/cram_index.h
new file mode 100644
index 0000000..c0429e0
--- /dev/null
+++ b/htslib/cram/cram_index.h
@@ -0,0 +1,99 @@
+/*
+Copyright (c) 2013 Genome Research Ltd.
+Author: James Bonfield <jkb at sanger.ac.uk>
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+Institute nor the names of its contributors may be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+#ifndef _CRAM_INDEX_H_
+#define _CRAM_INDEX_H_
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*
+ * Loads a CRAM .crai index into memory.
+ * Returns 0 for success
+ *        -1 for failure
+ */
+int cram_index_load(cram_fd *fd, const char *fn, const char *fn_idx);
+
+void cram_index_free(cram_fd *fd);
+
+/*
+ * Searches the index for the first slice overlapping a reference ID
+ * and position.
+ *
+ * Returns the cram_index pointer on sucess
+ *         NULL on failure
+ */
+cram_index *cram_index_query(cram_fd *fd, int refid, int pos, cram_index *frm);
+
+/*
+ * Skips to a container overlapping the start coordinate listed in
+ * cram_range.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int cram_seek_to_refpos(cram_fd *fd, cram_range *r);
+
+void cram_index_free(cram_fd *fd);
+
+/*
+ * Skips to a container overlapping the start coordinate listed in
+ * cram_range.
+ *
+ * In theory we call cram_index_query multiple times, once per slice
+ * overlapping the range. However slices may be absent from the index
+ * which makes this problematic. Instead we find the left-most slice
+ * and then read from then on, skipping decoding of slices and/or
+ * whole containers when they don't overlap the specified cram_range.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int cram_seek_to_refpos(cram_fd *fd, cram_range *r);
+
+/*
+ * Builds an index file.
+ *
+ * fd is a newly opened cram file that we wish to index.
+ * fn_base is the filename of the associated CRAM file.
+ * fn_idx is the filename of the index file to be written;
+ * if NULL, we add ".crai" to fn_base to get the index filename.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int cram_index_build(cram_fd *fd, const char *fn_base, const char *fn_idx);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/htslib/cram/cram_io.c b/htslib/cram/cram_io.c
new file mode 100644
index 0000000..a1f51a0
--- /dev/null
+++ b/htslib/cram/cram_io.c
@@ -0,0 +1,4604 @@
+/*
+Copyright (c) 2012-2014 Genome Research Ltd.
+Author: James Bonfield <jkb at sanger.ac.uk>
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+Institute nor the names of its contributors may be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+/*
+ * CRAM I/O primitives.
+ *
+ * - ITF8 encoding and decoding.
+ * - Block based I/O
+ * - Zlib inflating and deflating (memory)
+ * - CRAM basic data structure reading and writing
+ * - File opening / closing
+ * - Reference sequence handling
+ */
+
+/*
+ * TODO: BLOCK_GROW, BLOCK_RESIZE, BLOCK_APPEND and itf8_put_blk all need
+ * a way to return errors for when malloc fails.
+ */
+
+#include <config.h>
+
+#include <stdio.h>
+#include <errno.h>
+#include <assert.h>
+#include <stdlib.h>
+#include <string.h>
+#include <unistd.h>
+#include <zlib.h>
+#ifdef HAVE_LIBBZ2
+#include <bzlib.h>
+#endif
+#ifdef HAVE_LIBLZMA
+#include <lzma.h>
+#endif
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <math.h>
+#include <ctype.h>
+#include <time.h>
+
+#include "cram/cram.h"
+#include "cram/os.h"
+#include "htslib/hts.h"
+#include "cram/open_trace_file.h"
+#include "cram/rANS_static.h"
+
+//#define REF_DEBUG
+
+#ifdef REF_DEBUG
+#include <sys/syscall.h>
+#define gettid() (int)syscall(SYS_gettid)
+
+#define RP(...) fprintf (stderr, __VA_ARGS__)
+#else
+#define RP(...) 
+#endif
+
+#include "htslib/hfile.h"
+#include "htslib/bgzf.h"
+#include "htslib/faidx.h"
+
+#define TRIAL_SPAN 50
+#define NTRIALS 3
+
+
+/* ----------------------------------------------------------------------
+ * ITF8 encoding and decoding.
+ *
+* Also see the itf8_get and itf8_put macros in cram_io.h
+ */
+
+/*
+ * LEGACY: consider using itf8_decode_crc.
+ *
+ * Reads an integer in ITF-8 encoding from 'cp' and stores it in
+ * *val.
+ *
+ * Returns the number of bytes read on success
+ *        -1 on failure
+ */
+int itf8_decode(cram_fd *fd, int32_t *val_p) {
+    static int nbytes[16] = {
+	0,0,0,0, 0,0,0,0,                               // 0000xxxx - 0111xxxx
+	1,1,1,1,                                        // 1000xxxx - 1011xxxx
+	2,2,                                            // 1100xxxx - 1101xxxx
+	3,                                              // 1110xxxx
+	4,                                              // 1111xxxx
+    };
+
+    static int nbits[16] = {
+	0x7f, 0x7f, 0x7f, 0x7f, 0x7f, 0x7f, 0x7f, 0x7f, // 0000xxxx - 0111xxxx
+	0x3f, 0x3f, 0x3f, 0x3f,                         // 1000xxxx - 1011xxxx
+	0x1f, 0x1f,                                     // 1100xxxx - 1101xxxx
+	0x0f,                                           // 1110xxxx
+	0x0f,                                           // 1111xxxx
+    };
+
+    int32_t val = hgetc(fd->fp);
+    if (val == -1)
+	return -1;
+
+    int i = nbytes[val>>4];
+    val &= nbits[val>>4];
+
+    switch(i) {
+    case 0:
+	*val_p = val;
+	return 1;
+
+    case 1:
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	*val_p = val;
+	return 2;
+
+    case 2:
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	*val_p = val;
+	return 3;
+
+    case 3:
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	*val_p = val;
+	return 4;
+
+    case 4: // really 3.5 more, why make it different?
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	val = (val<<4) | (((unsigned char)hgetc(fd->fp)) & 0x0f);
+	*val_p = val;
+    }
+
+    return 5;
+}
+
+int itf8_decode_crc(cram_fd *fd, int32_t *val_p, uint32_t *crc) {
+    static int nbytes[16] = {
+	0,0,0,0, 0,0,0,0,                               // 0000xxxx - 0111xxxx
+	1,1,1,1,                                        // 1000xxxx - 1011xxxx
+	2,2,                                            // 1100xxxx - 1101xxxx
+	3,                                              // 1110xxxx
+	4,                                              // 1111xxxx
+    };
+
+    static int nbits[16] = {
+	0x7f, 0x7f, 0x7f, 0x7f, 0x7f, 0x7f, 0x7f, 0x7f, // 0000xxxx - 0111xxxx
+	0x3f, 0x3f, 0x3f, 0x3f,                         // 1000xxxx - 1011xxxx
+	0x1f, 0x1f,                                     // 1100xxxx - 1101xxxx
+	0x0f,                                           // 1110xxxx
+	0x0f,                                           // 1111xxxx
+    };
+    unsigned char c[5];
+
+    int32_t val = hgetc(fd->fp);
+    if (val == -1)
+	return -1;
+
+    c[0]=val;
+
+    int i = nbytes[val>>4];
+    val &= nbits[val>>4];
+
+    switch(i) {
+    case 0:
+	*val_p = val;
+	*crc = crc32(*crc, c, 1);
+	return 1;
+
+    case 1:
+	val = (val<<8) | (c[1]=hgetc(fd->fp));
+	*val_p = val;
+	*crc = crc32(*crc, c, 2);
+	return 2;
+
+    case 2:
+	val = (val<<8) | (c[1]=hgetc(fd->fp));
+	val = (val<<8) | (c[2]=hgetc(fd->fp));
+	*val_p = val;
+	*crc = crc32(*crc, c, 3);
+	return 3;
+
+    case 3:
+	val = (val<<8) | (c[1]=hgetc(fd->fp));
+	val = (val<<8) | (c[2]=hgetc(fd->fp));
+	val = (val<<8) | (c[3]=hgetc(fd->fp));
+	*val_p = val;
+	*crc = crc32(*crc, c, 4);
+	return 4;
+
+    case 4: // really 3.5 more, why make it different?
+	val = (val<<8) |   (c[1]=hgetc(fd->fp));
+	val = (val<<8) |   (c[2]=hgetc(fd->fp));
+	val = (val<<8) |   (c[3]=hgetc(fd->fp));
+	val = (val<<4) | (((c[4]=hgetc(fd->fp))) & 0x0f);
+	*val_p = val;
+	*crc = crc32(*crc, c, 5);
+    }
+
+    return 5;
+}
+
+/*
+ * Encodes and writes a single integer in ITF-8 format.
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int itf8_encode(cram_fd *fd, int32_t val) {
+    char buf[5];
+    int len = itf8_put(buf, val);
+    return hwrite(fd->fp, buf, len) == len ? 0 : -1;
+}
+ 
+const int itf8_bytes[16] = {
+    1, 1, 1, 1, 1, 1, 1, 1,
+    2, 2, 2, 2, 3, 3, 4, 5
+};
+
+#ifndef ITF8_MACROS
+/*
+ * As above, but decoding from memory
+ */
+int itf8_get(char *cp, int32_t *val_p) {
+    unsigned char *up = (unsigned char *)cp;
+    
+    if (up[0] < 0x80) {
+	*val_p =   up[0];
+	return 1;
+    } else if (up[0] < 0xc0) {
+	*val_p = ((up[0] <<8) |  up[1])                           & 0x3fff;
+	return 2;
+    } else if (up[0] < 0xe0) {
+	*val_p = ((up[0]<<16) | (up[1]<< 8) |  up[2])             & 0x1fffff;
+	return 3;
+    } else if (up[0] < 0xf0) {
+	*val_p = ((up[0]<<24) | (up[1]<<16) | (up[2]<<8) | up[3]) & 0x0fffffff;
+	return 4;
+    } else {
+	*val_p = ((up[0] & 0x0f)<<28) | (up[1]<<20) | (up[2]<<12) | (up[3]<<4) | (up[4] & 0x0f);
+	return 5;
+    }
+}
+
+/*
+ * Stores a value to memory in ITF-8 format.
+ *
+ * Returns the number of bytes required to store the number.
+ * This is a maximum of 5 bytes.
+ */
+int itf8_put(char *cp, int32_t val) {
+    if        (!(val & ~0x00000007f)) { // 1 byte
+	*cp = val;
+	return 1;
+    } else if (!(val & ~0x00003fff)) { // 2 byte
+	*cp++ = (val >> 8 ) | 0x80;
+	*cp   = val & 0xff;
+	return 2;
+    } else if (!(val & ~0x01fffff)) { // 3 byte
+	*cp++ = (val >> 16) | 0xc0;
+	*cp++ = (val >> 8 ) & 0xff;
+	*cp   = val & 0xff;
+	return 3;
+    } else if (!(val & ~0x0fffffff)) { // 4 byte
+	*cp++ = (val >> 24) | 0xe0;
+	*cp++ = (val >> 16) & 0xff;
+	*cp++ = (val >> 8 ) & 0xff;
+	*cp   = val & 0xff;
+	return 4;
+    } else {                           // 5 byte
+	*cp++ = 0xf0 | ((val>>28) & 0xff);
+	*cp++ = (val >> 20) & 0xff;
+	*cp++ = (val >> 12) & 0xff;
+	*cp++ = (val >> 4 ) & 0xff;
+	*cp = val & 0x0f;
+	return 5;
+    }
+}
+#endif
+
+/* 64-bit itf8 variant */
+int ltf8_put(char *cp, int64_t val) {
+    if        (!(val & ~((1LL<<7)-1))) {
+	*cp = val;
+	return 1;
+    } else if (!(val & ~((1LL<<(6+8))-1))) {
+	*cp++ = (val >> 8 ) | 0x80;
+	*cp   = val & 0xff;
+	return 2;
+    } else if (!(val & ~((1LL<<(5+2*8))-1))) {
+	*cp++ = (val >> 16) | 0xc0;
+	*cp++ = (val >> 8 ) & 0xff;
+	*cp   = val & 0xff;
+	return 3;
+    } else if (!(val & ~((1LL<<(4+3*8))-1))) {
+	*cp++ = (val >> 24) | 0xe0;
+	*cp++ = (val >> 16) & 0xff;
+	*cp++ = (val >> 8 ) & 0xff;
+	*cp   = val & 0xff;
+	return 4;
+    } else if (!(val & ~((1LL<<(3+4*8))-1))) {
+	*cp++ = (val >> 32) | 0xf0;
+	*cp++ = (val >> 24) & 0xff;
+	*cp++ = (val >> 16) & 0xff;
+	*cp++ = (val >> 8 ) & 0xff;
+	*cp   = val & 0xff;
+	return 5;
+    } else if (!(val & ~((1LL<<(2+5*8))-1))) {
+	*cp++ = (val >> 40) | 0xf8;
+	*cp++ = (val >> 32) & 0xff;
+	*cp++ = (val >> 24) & 0xff;
+	*cp++ = (val >> 16) & 0xff;
+	*cp++ = (val >> 8 ) & 0xff;
+	*cp   = val & 0xff;
+	return 6;
+    } else if (!(val & ~((1LL<<(1+6*8))-1))) {
+	*cp++ = (val >> 48) | 0xfc;
+	*cp++ = (val >> 40) & 0xff;
+	*cp++ = (val >> 32) & 0xff;
+	*cp++ = (val >> 24) & 0xff;
+	*cp++ = (val >> 16) & 0xff;
+	*cp++ = (val >> 8 ) & 0xff;
+	*cp   = val & 0xff;
+	return 7;
+    } else if (!(val & ~((1LL<<(7*8))-1))) {
+	*cp++ = (val >> 56) | 0xfe;
+	*cp++ = (val >> 48) & 0xff;
+	*cp++ = (val >> 40) & 0xff;
+	*cp++ = (val >> 32) & 0xff;
+	*cp++ = (val >> 24) & 0xff;
+	*cp++ = (val >> 16) & 0xff;
+	*cp++ = (val >> 8 ) & 0xff;
+	*cp   = val & 0xff;
+	return 8;
+    } else {
+	*cp++ = 0xff;
+	*cp++ = (val >> 56) & 0xff;
+	*cp++ = (val >> 48) & 0xff;
+	*cp++ = (val >> 40) & 0xff;
+	*cp++ = (val >> 32) & 0xff;
+	*cp++ = (val >> 24) & 0xff;
+	*cp++ = (val >> 16) & 0xff;
+	*cp++ = (val >> 8 ) & 0xff;
+	*cp   = val & 0xff;
+	return 9;
+    }
+}
+
+int ltf8_get(char *cp, int64_t *val_p) {
+    unsigned char *up = (unsigned char *)cp;
+    
+    if (up[0] < 0x80) {
+	*val_p =   up[0];
+	return 1;
+    } else if (up[0] < 0xc0) {
+	*val_p = (((uint64_t)up[0]<< 8) |
+		   (uint64_t)up[1]) & (((1LL<<(6+8)))-1);
+	return 2;
+    } else if (up[0] < 0xe0) {
+	*val_p = (((uint64_t)up[0]<<16) |
+		  ((uint64_t)up[1]<< 8) |
+		   (uint64_t)up[2]) & ((1LL<<(5+2*8))-1);
+	return 3;
+    } else if (up[0] < 0xf0) {
+	*val_p = (((uint64_t)up[0]<<24) |
+		  ((uint64_t)up[1]<<16) |
+		  ((uint64_t)up[2]<< 8) |
+		   (uint64_t)up[3]) & ((1LL<<(4+3*8))-1);
+	return 4;
+    } else if (up[0] < 0xf8) {
+	*val_p = (((uint64_t)up[0]<<32) |
+		  ((uint64_t)up[1]<<24) |
+		  ((uint64_t)up[2]<<16) |
+		  ((uint64_t)up[3]<< 8) |
+		   (uint64_t)up[4]) & ((1LL<<(3+4*8))-1);
+	return 5;
+    } else if (up[0] < 0xfc) {
+	*val_p = (((uint64_t)up[0]<<40) |
+		  ((uint64_t)up[1]<<32) |
+		  ((uint64_t)up[2]<<24) |
+		  ((uint64_t)up[3]<<16) |
+		  ((uint64_t)up[4]<< 8) |
+		   (uint64_t)up[5]) & ((1LL<<(2+5*8))-1);
+	return 6;
+    } else if (up[0] < 0xfe) {
+	*val_p = (((uint64_t)up[0]<<48) |
+		  ((uint64_t)up[1]<<40) |
+		  ((uint64_t)up[2]<<32) |
+		  ((uint64_t)up[3]<<24) |
+		  ((uint64_t)up[4]<<16) |
+		  ((uint64_t)up[5]<< 8) |
+		   (uint64_t)up[6]) & ((1LL<<(1+6*8))-1);
+	return 7;
+    } else if (up[0] < 0xff) {
+	*val_p = (((uint64_t)up[1]<<48) |
+		  ((uint64_t)up[2]<<40) |
+		  ((uint64_t)up[3]<<32) |
+		  ((uint64_t)up[4]<<24) |
+		  ((uint64_t)up[5]<<16) |
+		  ((uint64_t)up[6]<< 8) |
+		   (uint64_t)up[7]) & ((1LL<<(7*8))-1);
+	return 8;
+    } else {
+	*val_p = (((uint64_t)up[1]<<56) |
+		  ((uint64_t)up[2]<<48) |
+		  ((uint64_t)up[3]<<40) |
+		  ((uint64_t)up[4]<<32) |
+		  ((uint64_t)up[5]<<24) |
+		  ((uint64_t)up[6]<<16) |
+		  ((uint64_t)up[7]<< 8) |
+		   (uint64_t)up[8]);
+	return 9;
+    }
+}
+
+/*
+ * LEGACY: consider using ltf8_decode_crc.
+ */
+int ltf8_decode(cram_fd *fd, int64_t *val_p) {
+    int c = hgetc(fd->fp);
+    int64_t val = (unsigned char)c;
+    if (c == -1)
+	return -1;
+
+    if (val < 0x80) {
+	*val_p =   val;
+	return 1;
+
+    } else if (val < 0xc0) {
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	*val_p = val & (((1LL<<(6+8)))-1);
+	return 2;
+
+    } else if (val < 0xe0) {
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	*val_p = val & ((1LL<<(5+2*8))-1);
+	return 3;
+
+    } else if (val < 0xf0) {
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	*val_p = val & ((1LL<<(4+3*8))-1);
+	return 4;
+
+    } else if (val < 0xf8) {
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	*val_p = val & ((1LL<<(3+4*8))-1);
+	return 5;
+
+    } else if (val < 0xfc) {
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	*val_p = val & ((1LL<<(2+5*8))-1);
+	return 6;
+
+    } else if (val < 0xfe) {
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	*val_p = val & ((1LL<<(1+6*8))-1);
+	return 7;
+
+    } else if (val < 0xff) {
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	*val_p = val & ((1LL<<(7*8))-1);
+	return 8;
+
+    } else {
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	val = (val<<8) | (unsigned char)hgetc(fd->fp);
+	*val_p = val;
+    }
+
+    return 9;
+}
+
+int ltf8_decode_crc(cram_fd *fd, int64_t *val_p, uint32_t *crc) {
+    unsigned char c[9];
+    int64_t val = (unsigned char)hgetc(fd->fp);
+    if (val == -1)
+	return -1;
+
+    c[0] = val;
+
+    if (val < 0x80) {
+	*val_p =   val;
+	*crc = crc32(*crc, c, 1);
+	return 1;
+
+    } else if (val < 0xc0) {
+	val = (val<<8) | (c[1]=hgetc(fd->fp));;
+	*val_p = val & (((1LL<<(6+8)))-1);
+	*crc = crc32(*crc, c, 2);
+	return 2;
+
+    } else if (val < 0xe0) {
+	val = (val<<8) | (c[1]=hgetc(fd->fp));;
+	val = (val<<8) | (c[2]=hgetc(fd->fp));;
+	*val_p = val & ((1LL<<(5+2*8))-1);
+	*crc = crc32(*crc, c, 3);
+	return 3;
+
+    } else if (val < 0xf0) {
+	val = (val<<8) | (c[1]=hgetc(fd->fp));;
+	val = (val<<8) | (c[2]=hgetc(fd->fp));;
+	val = (val<<8) | (c[3]=hgetc(fd->fp));;
+	*val_p = val & ((1LL<<(4+3*8))-1);
+	*crc = crc32(*crc, c, 4);
+	return 4;
+
+    } else if (val < 0xf8) {
+	val = (val<<8) | (c[1]=hgetc(fd->fp));;
+	val = (val<<8) | (c[2]=hgetc(fd->fp));;
+	val = (val<<8) | (c[3]=hgetc(fd->fp));;
+	val = (val<<8) | (c[4]=hgetc(fd->fp));;
+	*val_p = val & ((1LL<<(3+4*8))-1);
+	*crc = crc32(*crc, c, 5);
+	return 5;
+
+    } else if (val < 0xfc) {
+	val = (val<<8) | (c[1]=hgetc(fd->fp));;
+	val = (val<<8) | (c[2]=hgetc(fd->fp));;
+	val = (val<<8) | (c[3]=hgetc(fd->fp));;
+	val = (val<<8) | (c[4]=hgetc(fd->fp));;
+	val = (val<<8) | (c[5]=hgetc(fd->fp));;
+	*val_p = val & ((1LL<<(2+5*8))-1);
+	*crc = crc32(*crc, c, 6);
+	return 6;
+
+    } else if (val < 0xfe) {
+	val = (val<<8) | (c[1]=hgetc(fd->fp));;
+	val = (val<<8) | (c[2]=hgetc(fd->fp));;
+	val = (val<<8) | (c[3]=hgetc(fd->fp));;
+	val = (val<<8) | (c[4]=hgetc(fd->fp));;
+	val = (val<<8) | (c[5]=hgetc(fd->fp));;
+	val = (val<<8) | (c[6]=hgetc(fd->fp));;
+	*val_p = val & ((1LL<<(1+6*8))-1);
+	*crc = crc32(*crc, c, 7);
+	return 7;
+
+    } else if (val < 0xff) {
+	val = (val<<8) | (c[1]=hgetc(fd->fp));;
+	val = (val<<8) | (c[2]=hgetc(fd->fp));;
+	val = (val<<8) | (c[3]=hgetc(fd->fp));;
+	val = (val<<8) | (c[4]=hgetc(fd->fp));;
+	val = (val<<8) | (c[5]=hgetc(fd->fp));;
+	val = (val<<8) | (c[6]=hgetc(fd->fp));;
+	val = (val<<8) | (c[7]=hgetc(fd->fp));;
+	*val_p = val & ((1LL<<(7*8))-1);
+	*crc = crc32(*crc, c, 8);
+	return 8;
+
+    } else {
+	val = (val<<8) | (c[1]=hgetc(fd->fp));;
+	val = (val<<8) | (c[2]=hgetc(fd->fp));;
+	val = (val<<8) | (c[3]=hgetc(fd->fp));;
+	val = (val<<8) | (c[4]=hgetc(fd->fp));;
+	val = (val<<8) | (c[5]=hgetc(fd->fp));;
+	val = (val<<8) | (c[6]=hgetc(fd->fp));;
+	val = (val<<8) | (c[7]=hgetc(fd->fp));;
+	val = (val<<8) | (c[8]=hgetc(fd->fp));;
+	*crc = crc32(*crc, c, 9);
+	*val_p = val;
+    }
+
+    return 9;
+}
+
+/*
+ * Pushes a value in ITF8 format onto the end of a block.
+ * This shouldn't be used for high-volume data as it is not the fastest
+ * method.
+ *
+ * Returns the number of bytes written
+ */
+int itf8_put_blk(cram_block *blk, int val) {
+    char buf[5];
+    int sz;
+
+    sz = itf8_put(buf, val);
+    BLOCK_APPEND(blk, buf, sz);
+    return sz;
+}
+
+/*
+ * Decodes a 32-bit little endian value from fd and stores in val.
+ *
+ * Returns the number of bytes read on success
+ *         -1 on failure
+ */
+int int32_decode(cram_fd *fd, int32_t *val) {
+    int32_t i;
+    if (4 != hread(fd->fp, &i, 4))
+	return -1;
+
+    *val = le_int4(i);
+    return 4;
+}
+
+/*
+ * Encodes a 32-bit little endian value 'val' and writes to fd.
+ *
+ * Returns the number of bytes written on success
+ *         -1 on failure
+ */
+int int32_encode(cram_fd *fd, int32_t val) {
+    val = le_int4(val);
+    if (4 != hwrite(fd->fp, &val, 4))
+	return -1;
+
+    return 4;
+}
+
+/* As int32_decoded/encode, but from/to blocks instead of cram_fd */
+int int32_get_blk(cram_block *b, int32_t *val) {
+    if (b->uncomp_size - BLOCK_SIZE(b) < 4)
+	return -1;
+
+    *val =
+	 b->data[b->byte  ]        |
+	(b->data[b->byte+1] <<  8) |
+	(b->data[b->byte+2] << 16) |
+	(b->data[b->byte+3] << 24);
+    BLOCK_SIZE(b) += 4;
+    return 4;
+}
+
+/* As int32_decoded/encode, but from/to blocks instead of cram_fd */
+int int32_put_blk(cram_block *b, int32_t val) {
+    unsigned char cp[4];
+    cp[0] = ( val      & 0xff);
+    cp[1] = ((val>>8)  & 0xff);
+    cp[2] = ((val>>16) & 0xff);
+    cp[3] = ((val>>24) & 0xff);
+
+    BLOCK_APPEND(b, cp, 4);
+    return b->data ? 0 : -1;
+}
+
+/* ----------------------------------------------------------------------
+ * zlib compression code - from Gap5's tg_iface_g.c
+ * They're static here as they're only used within the cram_compress_block
+ * and cram_uncompress_block functions, which are the external interface.
+ */
+char *zlib_mem_inflate(char *cdata, size_t csize, size_t *size) {
+    z_stream s;
+    unsigned char *data = NULL; /* Uncompressed output */
+    int data_alloc = 0;
+    int err;
+
+    /* Starting point at uncompressed size, and scale after that */
+    data = malloc(data_alloc = csize*1.2+100);
+    if (!data)
+	return NULL;
+
+    /* Initialise zlib stream */
+    s.zalloc = Z_NULL; /* use default allocation functions */
+    s.zfree  = Z_NULL;
+    s.opaque = Z_NULL;
+    s.next_in  = (unsigned char *)cdata;
+    s.avail_in = csize;
+    s.total_in = 0;
+    s.next_out  = data;
+    s.avail_out = data_alloc;
+    s.total_out = 0;
+
+    //err = inflateInit(&s);
+    err = inflateInit2(&s, 15 + 32);
+    if (err != Z_OK) {
+	fprintf(stderr, "zlib inflateInit error: %s\n", s.msg);
+	free(data);
+	return NULL;
+    }
+
+    /* Decode to 'data' array */
+    for (;s.avail_in;) {
+	unsigned char *data_tmp;
+	int alloc_inc;
+
+	s.next_out = &data[s.total_out];
+	err = inflate(&s, Z_NO_FLUSH);
+	if (err == Z_STREAM_END)
+	    break;
+
+	if (err != Z_OK) {
+	    fprintf(stderr, "zlib inflate error: %s\n", s.msg);
+	    if (data)
+		free(data);
+	    return NULL;
+	}
+
+	/* More to come, so realloc based on growth so far */
+	alloc_inc = (double)s.avail_in/s.total_in * s.total_out + 100;
+	data = realloc((data_tmp = data), data_alloc += alloc_inc);
+	if (!data) {
+	    free(data_tmp);
+	    return NULL;
+	}
+	s.avail_out += alloc_inc;
+    }
+    inflateEnd(&s);
+
+    *size = s.total_out;
+    return (char *)data;
+}
+
+static char *zlib_mem_deflate(char *data, size_t size, size_t *cdata_size,
+			      int level, int strat) {
+    z_stream s;
+    unsigned char *cdata = NULL; /* Compressed output */
+    int cdata_alloc = 0;
+    int cdata_pos = 0;
+    int err;
+
+    cdata = malloc(cdata_alloc = size*1.05+100);
+    if (!cdata)
+	return NULL;
+    cdata_pos = 0;
+
+    /* Initialise zlib stream */
+    s.zalloc = Z_NULL; /* use default allocation functions */
+    s.zfree  = Z_NULL;
+    s.opaque = Z_NULL;
+    s.next_in  = (unsigned char *)data;
+    s.avail_in = size;
+    s.total_in = 0;
+    s.next_out  = cdata;
+    s.avail_out = cdata_alloc;
+    s.total_out = 0;
+    s.data_type = Z_BINARY;
+
+    err = deflateInit2(&s, level, Z_DEFLATED, 15|16, 9, strat);
+    if (err != Z_OK) {
+	fprintf(stderr, "zlib deflateInit2 error: %s\n", s.msg);
+	return NULL;
+    }
+
+    /* Encode to 'cdata' array */
+    for (;s.avail_in;) {
+	s.next_out = &cdata[cdata_pos];
+	s.avail_out = cdata_alloc - cdata_pos;
+	if (cdata_alloc - cdata_pos <= 0) {
+	    fprintf(stderr, "Deflate produced larger output than expected. Abort\n"); 
+	    return NULL;
+	}
+	err = deflate(&s, Z_NO_FLUSH);
+	cdata_pos = cdata_alloc - s.avail_out;
+	if (err != Z_OK) {
+	    fprintf(stderr, "zlib deflate error: %s\n", s.msg);
+	    break;
+	}
+    }
+    if (deflate(&s, Z_FINISH) != Z_STREAM_END) {
+	fprintf(stderr, "zlib deflate error: %s\n", s.msg);
+    }
+    *cdata_size = s.total_out;
+
+    if (deflateEnd(&s) != Z_OK) {
+	fprintf(stderr, "zlib deflate error: %s\n", s.msg);
+    }
+    return (char *)cdata;
+}
+
+#ifdef HAVE_LIBLZMA
+/* ------------------------------------------------------------------------ */
+/*
+ * Data compression routines using liblzma (xz)
+ *
+ * On a test set this shrunk the main db from 136157104 bytes to 114796168, but
+ * caused tg_index to grow from 2m43.707s to 15m3.961s. Exporting as bfastq
+ * went from 18.3s to 36.3s. So decompression suffers too, but not as bad
+ * as compression times.
+ *
+ * For now we disable this functionality. If it's to be reenabled make sure you
+ * improve the mem_inflate implementation as it's just a test hack at the
+ * moment.
+ */
+
+static char *lzma_mem_deflate(char *data, size_t size, size_t *cdata_size,
+			      int level) {
+    char *out;
+    size_t out_size = lzma_stream_buffer_bound(size);
+    *cdata_size = 0;
+
+    out = malloc(out_size);
+
+    /* Single call compression */
+    if (LZMA_OK != lzma_easy_buffer_encode(level, LZMA_CHECK_CRC32, NULL,
+					   (uint8_t *)data, size,
+					   (uint8_t *)out, cdata_size,
+					   out_size))
+    	return NULL;
+
+    return out;
+}
+
+static char *lzma_mem_inflate(char *cdata, size_t csize, size_t *size) {
+    lzma_stream strm = LZMA_STREAM_INIT;
+    size_t out_size = 0, out_pos = 0;
+    char *out = NULL;
+    int r;
+
+    /* Initiate the decoder */
+    if (LZMA_OK != lzma_stream_decoder(&strm, 50000000, 0))
+	return NULL;
+
+    /* Decode loop */
+    strm.avail_in = csize;
+    strm.next_in = (uint8_t *)cdata;
+
+    for (;strm.avail_in;) {
+	if (strm.avail_in > out_size - out_pos) {
+	    out_size += strm.avail_in * 4 + 32768;
+	    out = realloc(out, out_size);
+	}
+	strm.avail_out = out_size - out_pos;
+	strm.next_out = (uint8_t *)&out[out_pos];
+
+	r = lzma_code(&strm, LZMA_RUN);
+	if (LZMA_OK != r && LZMA_STREAM_END != r) {
+	    fprintf(stderr, "r=%d\n", r);
+	    fprintf(stderr, "mem=%"PRId64"d\n", (int64_t)lzma_memusage(&strm));
+	    return NULL;
+	}
+
+	out_pos = strm.total_out;
+
+	if (r == LZMA_STREAM_END)
+	    break;
+    }
+
+    /* finish up any unflushed data; necessary? */
+    r = lzma_code(&strm, LZMA_FINISH);
+    if (r != LZMA_OK && r != LZMA_STREAM_END) {
+	fprintf(stderr, "r=%d\n", r);
+	return NULL;
+    }
+
+    out = realloc(out, strm.total_out);
+    *size = strm.total_out;
+
+    lzma_end(&strm);
+
+    return out;
+}
+#endif
+
+/* ----------------------------------------------------------------------
+ * CRAM blocks - the dynamically growable data block. We have code to
+ * create, update, (un)compress and read/write.
+ *
+ * These are derived from the deflate_interlaced.c blocks, but with the
+ * CRAM extension of content types and IDs.
+ */
+
+/*
+ * Allocates a new cram_block structure with a specified content_type and
+ * id.
+ *
+ * Returns block pointer on success
+ *         NULL on failure
+ */
+cram_block *cram_new_block(enum cram_content_type content_type,
+			   int content_id) {
+    cram_block *b = malloc(sizeof(*b));
+    if (!b)
+	return NULL;
+    b->method = b->orig_method = RAW;
+    b->content_type = content_type;
+    b->content_id = content_id;
+    b->comp_size = 0;
+    b->uncomp_size = 0;
+    b->data = NULL;
+    b->alloc = 0;
+    b->byte = 0;
+    b->bit = 7; // MSB
+
+    return b;
+}
+
+/*
+ * Reads a block from a cram file.
+ * Returns cram_block pointer on success.
+ *         NULL on failure
+ */
+cram_block *cram_read_block(cram_fd *fd) {
+    cram_block *b = malloc(sizeof(*b));
+    unsigned char c;
+    uint32_t crc = 0;
+    if (!b)
+	return NULL;
+
+    //fprintf(stderr, "Block at %d\n", (int)ftell(fd->fp));
+
+    if (-1 == (b->method      = hgetc(fd->fp))) { free(b); return NULL; }
+    c = b->method; crc = crc32(crc, &c, 1);
+    if (-1 == (b->content_type= hgetc(fd->fp))) { free(b); return NULL; }
+    c = b->content_type; crc = crc32(crc, &c, 1);
+    if (-1 == itf8_decode_crc(fd, &b->content_id, &crc))  { free(b); return NULL; }
+    if (-1 == itf8_decode_crc(fd, &b->comp_size, &crc))   { free(b); return NULL; }
+    if (-1 == itf8_decode_crc(fd, &b->uncomp_size, &crc)) { free(b); return NULL; }
+
+    //    fprintf(stderr, "  method %d, ctype %d, cid %d, csize %d, ucsize %d\n",
+    //	    b->method, b->content_type, b->content_id, b->comp_size, b->uncomp_size);
+
+    if (b->method == RAW) {
+	b->alloc = b->uncomp_size;
+	if (!(b->data = malloc(b->uncomp_size))){ free(b); return NULL; }
+	if (b->uncomp_size != hread(fd->fp, b->data, b->uncomp_size)) {
+	    free(b->data);
+	    free(b);
+	    return NULL;
+	}
+    } else {
+	b->alloc = b->comp_size;
+	if (!(b->data = malloc(b->comp_size)))  { free(b); return NULL; }
+	if (b->comp_size != hread(fd->fp, b->data, b->comp_size)) {
+	    free(b->data);
+	    free(b);
+	    return NULL;
+	}
+    }
+
+    if (CRAM_MAJOR_VERS(fd->version) >= 3) {
+	if (-1 == int32_decode(fd, (int32_t *)&b->crc32)) {
+	    free(b);
+	    return NULL;
+	}
+
+	crc = crc32(crc, b->data ? b->data : (uc *)"", b->alloc);
+	if (crc != b->crc32) {
+	    fprintf(stderr, "Block CRC32 failure\n");
+	    free(b->data);
+	    free(b);
+	    return NULL;
+	}
+    }
+
+    b->orig_method = b->method;
+    b->idx = 0;
+    b->byte = 0;
+    b->bit = 7; // MSB
+
+    return b;
+}
+
+
+/*
+ * Computes the size of a cram block, including the block
+ * header itself.
+ */
+uint32_t cram_block_size(cram_block *b) {
+    unsigned char dat[100], *cp = dat;;
+    uint32_t sz;
+
+    *cp++ = b->method;
+    *cp++ = b->content_type;
+    cp += itf8_put(cp, b->content_id);
+    cp += itf8_put(cp, b->comp_size);
+    cp += itf8_put(cp, b->uncomp_size);
+
+    sz = cp-dat + 4;
+    sz += b->method == RAW ? b->uncomp_size : b->comp_size;
+
+    return sz;
+}
+
+/*
+ * Writes a CRAM block.
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int cram_write_block(cram_fd *fd, cram_block *b) {
+    assert(b->method != RAW || (b->comp_size == b->uncomp_size));
+
+    if (hputc(b->method,       fd->fp)  == EOF) return -1;
+    if (hputc(b->content_type, fd->fp)  == EOF) return -1;
+    if (itf8_encode(fd, b->content_id)  ==  -1) return -1;
+    if (itf8_encode(fd, b->comp_size)   ==  -1) return -1;
+    if (itf8_encode(fd, b->uncomp_size) ==  -1) return -1;
+
+    if (b->method == RAW) {
+	if (b->uncomp_size != hwrite(fd->fp, b->data, b->uncomp_size))
+	    return -1;
+    } else {
+	if (b->comp_size != hwrite(fd->fp, b->data, b->comp_size))
+	    return -1;
+    }
+
+    if (CRAM_MAJOR_VERS(fd->version) >= 3) {
+	unsigned char dat[100], *cp = dat;;
+	uint32_t crc;
+
+	*cp++ = b->method;
+	*cp++ = b->content_type;
+	cp += itf8_put(cp, b->content_id);
+	cp += itf8_put(cp, b->comp_size);
+	cp += itf8_put(cp, b->uncomp_size);
+	crc = crc32(0L, dat, cp-dat);
+
+	if (b->method == RAW) {
+	    b->crc32 = crc32(crc, b->data ? b->data : (uc*)"", b->uncomp_size);
+	} else {
+	    b->crc32 = crc32(crc, b->data ? b->data : (uc*)"", b->comp_size);
+	}
+
+	if (-1 == int32_encode(fd, b->crc32))
+	    return -1;
+    }
+
+    return 0;
+}
+
+/*
+ * Frees a CRAM block, deallocating internal data too.
+ */
+void cram_free_block(cram_block *b) {
+    if (!b)
+	return;
+    if (b->data)
+	free(b->data);
+    free(b);
+}
+
+/*
+ * Uncompresses a CRAM block, if compressed.
+ */
+int cram_uncompress_block(cram_block *b) {
+    char *uncomp;
+    size_t uncomp_size = 0;
+
+    if (b->uncomp_size == 0) {
+	// blank block
+	b->method = RAW;
+	return 0;
+    }
+
+    switch (b->method) {
+    case RAW:
+	return 0;
+
+    case GZIP:
+	uncomp = zlib_mem_inflate((char *)b->data, b->comp_size, &uncomp_size);
+	if (!uncomp)
+	    return -1;
+	if ((int)uncomp_size != b->uncomp_size) {
+	    free(uncomp);
+	    return -1;
+	}
+	free(b->data);
+	b->data = (unsigned char *)uncomp;
+	b->alloc = uncomp_size;
+	b->method = RAW;
+	break;
+
+#ifdef HAVE_LIBBZ2
+    case BZIP2: {
+	unsigned int usize = b->uncomp_size;
+	if (!(uncomp = malloc(usize)))
+	    return -1;
+	if (BZ_OK != BZ2_bzBuffToBuffDecompress(uncomp, &usize,
+						(char *)b->data, b->comp_size,
+						0, 0)) {
+	    free(uncomp);
+	    return -1;
+	}
+	free(b->data);
+	b->data = (unsigned char *)uncomp;
+	b->alloc = usize;
+	b->method = RAW;
+	b->uncomp_size = usize; // Just incase it differs
+	break;
+    }
+#else
+    case BZIP2:
+	fprintf(stderr, "Bzip2 compression is not compiled into this "
+		"version.\nPlease rebuild and try again.\n");
+	return -1;
+#endif
+
+#ifdef HAVE_LIBLZMA
+    case LZMA:
+	uncomp = lzma_mem_inflate((char *)b->data, b->comp_size, &uncomp_size);
+	if (!uncomp)
+	    return -1;
+	if ((int)uncomp_size != b->uncomp_size)
+	    return -1;
+	free(b->data);
+	b->data = (unsigned char *)uncomp;
+	b->alloc = uncomp_size;
+	b->method = RAW;
+	break;
+#else
+    case LZMA:
+	fprintf(stderr, "Lzma compression is not compiled into this "
+		"version.\nPlease rebuild and try again.\n");
+	return -1;
+	break;
+#endif
+
+    case RANS: {
+	unsigned int usize = b->uncomp_size, usize2;
+	uncomp = (char *)rans_uncompress(b->data, b->comp_size, &usize2);
+	if (!uncomp || usize != usize2)
+ 	    return -1;
+	free(b->data);
+	b->data = (unsigned char *)uncomp;
+	b->alloc = usize2;
+	b->method = RAW;
+	b->uncomp_size = usize2; // Just incase it differs
+	//fprintf(stderr, "Expanded %d to %d\n", b->comp_size, b->uncomp_size);
+	break;
+    }
+
+    default:
+	return -1;
+    }
+
+    return 0;
+}
+
+static char *cram_compress_by_method(char *in, size_t in_size,
+				     size_t *out_size,
+				     enum cram_block_method method,
+				     int level, int strat) {
+    switch (method) {
+    case GZIP:
+	return zlib_mem_deflate(in, in_size, out_size, level, strat);
+
+    case BZIP2: {
+#ifdef HAVE_LIBBZ2
+	unsigned int comp_size = in_size*1.01 + 600;
+	char *comp = malloc(comp_size);
+	if (!comp)
+	    return NULL;
+
+	if (BZ_OK != BZ2_bzBuffToBuffCompress(comp, &comp_size,
+					      in, in_size,
+					      level, 0, 30)) {
+	    free(comp);
+	    return NULL;
+	}
+	*out_size = comp_size;
+	return comp;
+#else
+	return NULL;
+#endif
+    }
+
+    case LZMA:
+#ifdef HAVE_LIBLZMA
+	return lzma_mem_deflate(in, in_size, out_size, level);
+#else
+	return NULL;
+#endif
+
+    case RANS0: {
+	unsigned int out_size_i;
+	unsigned char *cp;
+	cp = rans_compress((unsigned char *)in, in_size, &out_size_i, 0);
+	*out_size = out_size_i;
+	return (char *)cp;
+    }
+
+    case RANS1: {
+	unsigned int out_size_i;
+	unsigned char *cp;
+	
+	cp = rans_compress((unsigned char *)in, in_size, &out_size_i, 1);
+	*out_size = out_size_i;
+	return (char *)cp;
+    }
+
+    case RAW:
+	break;
+
+    default:
+	return NULL;
+    }
+
+    return NULL;
+}
+
+
+/*
+ * Compresses a block using one of two different zlib strategies. If we only
+ * want one choice set strat2 to be -1.
+ *
+ * The logic here is that sometimes Z_RLE does a better job than Z_FILTERED
+ * or Z_DEFAULT_STRATEGY on quality data. If so, we'd rather use it as it is
+ * significantly faster.
+ *
+ * Method and level -1 implies defaults, as specified in cram_fd.
+ */
+int cram_compress_block(cram_fd *fd, cram_block *b, cram_metrics *metrics,
+			int method, int level) {
+
+    char *comp = NULL;
+    size_t comp_size = 0;
+    int strat;
+
+    if (b->method != RAW) {
+        // Maybe already compressed if s->block[0] was compressed and
+        // we have e.g. s->block[DS_BA] set to s->block[0] due to only
+        // one base type present and hence using E_HUFFMAN on block 0.
+        // A second explicit attempt to compress the same block then
+        // occurs.
+        return 0;
+    }
+
+    if (method == -1) {
+	method = 1<<GZIP;
+	if (fd->use_bz2)
+	    method |= 1<<BZIP2;
+	if (fd->use_lzma)
+	    method |= 1<<LZMA;
+    }
+
+    if (level == -1)
+	level = fd->level;
+
+    //fprintf(stderr, "IN: block %d, sz %d\n", b->content_id, b->uncomp_size);
+
+    if (method == RAW || level == 0 || b->uncomp_size == 0) {
+	b->method = RAW;
+	b->comp_size = b->uncomp_size;
+	//fprintf(stderr, "Skip block id %d\n", b->content_id);
+	return 0;
+    }
+
+    if (metrics) {
+	pthread_mutex_lock(&fd->metrics_lock);
+	if (metrics->trial > 0 || --metrics->next_trial <= 0) {
+	    size_t sz_best = INT_MAX;
+	    size_t sz_gz_rle = 0;
+	    size_t sz_gz_def = 0;
+	    size_t sz_rans0 = 0;
+	    size_t sz_rans1 = 0;
+	    size_t sz_bzip2 = 0;
+	    size_t sz_lzma = 0;
+	    int method_best = 0;
+	    char *c_best = NULL, *c = NULL;
+
+	    if (metrics->revised_method)
+		method = metrics->revised_method;
+	    else
+		metrics->revised_method = method;
+
+	    if (metrics->next_trial == 0) {
+		metrics->next_trial = TRIAL_SPAN;
+		metrics->trial = NTRIALS;
+		metrics->sz_gz_rle /= 2;
+		metrics->sz_gz_def /= 2;
+		metrics->sz_rans0  /= 2;
+		metrics->sz_rans1  /= 2;
+		metrics->sz_bzip2  /= 2;
+		metrics->sz_lzma   /= 2;
+	    }
+
+	    pthread_mutex_unlock(&fd->metrics_lock);
+	    
+	    if (method & (1<<GZIP_RLE)) {
+		c = cram_compress_by_method((char *)b->data, b->uncomp_size,
+					    &sz_gz_rle, GZIP, 1, Z_RLE);
+		if (c && sz_best > sz_gz_rle) {
+		    sz_best = sz_gz_rle;
+		    method_best = GZIP_RLE;
+		    if (c_best)
+			free(c_best);
+		    c_best = c;
+		} else if (c) {
+		    free(c);
+		} else {
+		    sz_gz_rle = b->uncomp_size*2+1000;
+		}
+
+		//fprintf(stderr, "Block %d; %d->%d\n", b->content_id, b->uncomp_size, sz_gz_rle);
+	    }
+
+	    if (method & (1<<GZIP)) {
+		c = cram_compress_by_method((char *)b->data, b->uncomp_size,
+					    &sz_gz_def, GZIP, level,
+					    Z_FILTERED);
+		if (c && sz_best > sz_gz_def) {
+		    sz_best = sz_gz_def;
+		    method_best = GZIP;
+		    if (c_best)
+			free(c_best);
+		    c_best = c;
+		} else if (c) {
+		    free(c);
+		} else {
+		    sz_gz_def = b->uncomp_size*2+1000;
+		}
+
+		//fprintf(stderr, "Block %d; %d->%d\n", b->content_id, b->uncomp_size, sz_gz_def);
+	    }
+
+	    if (method & (1<<RANS0)) {
+		c = cram_compress_by_method((char *)b->data, b->uncomp_size,
+					    &sz_rans0, RANS0, 0, 0);
+		if (c && sz_best > sz_rans0) {
+		    sz_best = sz_rans0;
+		    method_best = RANS0;
+		    if (c_best)
+			free(c_best);
+		    c_best = c;
+		} else if (c) {
+		    free(c);
+		} else {
+		    sz_rans0 = b->uncomp_size*2+1000;
+		}
+	    }
+
+	    if (method & (1<<RANS1)) {
+		c = cram_compress_by_method((char *)b->data, b->uncomp_size,
+					    &sz_rans1, RANS1, 0, 0);
+		if (c && sz_best > sz_rans1) {
+		    sz_best = sz_rans1;
+		    method_best = RANS1;
+		    if (c_best)
+			free(c_best);
+		    c_best = c;
+		} else if (c) {
+		    free(c);
+		} else {
+		    sz_rans1 = b->uncomp_size*2+1000;
+		}
+	    }
+
+	    if (method & (1<<BZIP2)) {
+		c = cram_compress_by_method((char *)b->data, b->uncomp_size,
+					    &sz_bzip2, BZIP2, level, 0);
+		if (c && sz_best > sz_bzip2) {
+		    sz_best = sz_bzip2;
+		    method_best = BZIP2;
+		    if (c_best)
+			free(c_best);
+		    c_best = c;
+		} else if (c) {
+		    free(c);
+		} else {
+		    sz_bzip2 = b->uncomp_size*2+1000;
+		}
+	    }
+
+	    if (method & (1<<LZMA)) {
+		c = cram_compress_by_method((char *)b->data, b->uncomp_size,
+					    &sz_lzma, LZMA, level, 0);
+		if (c && sz_best > sz_lzma) {
+		    sz_best = sz_lzma;
+		    method_best = LZMA;
+		    if (c_best)
+			free(c_best);
+		    c_best = c;
+		} else if (c) {
+		    free(c);
+		} else {
+		    sz_lzma = b->uncomp_size*2+1000;
+		}
+	    }
+
+	    //fprintf(stderr, "sz_best = %d\n", sz_best);
+
+	    free(b->data);
+	    b->data = (unsigned char *)c_best;
+	    //printf("method_best = %s\n", cram_block_method2str(method_best));
+	    b->method = method_best == GZIP_RLE ? GZIP : method_best;
+	    b->comp_size = sz_best;
+
+	    pthread_mutex_lock(&fd->metrics_lock);
+	    metrics->sz_gz_rle += sz_gz_rle;
+	    metrics->sz_gz_def += sz_gz_def;
+	    metrics->sz_rans0  += sz_rans0;
+	    metrics->sz_rans1  += sz_rans1;
+	    metrics->sz_bzip2  += sz_bzip2;
+	    metrics->sz_lzma   += sz_lzma;
+	    if (--metrics->trial == 0) {
+		int best_method = RAW;
+		int best_sz = INT_MAX;
+
+		// Scale methods by cost
+		if (fd->level <= 3) {
+		    metrics->sz_rans1  *= 1.02;
+		    metrics->sz_gz_def *= 1.04;
+		    metrics->sz_bzip2  *= 1.08;
+		    metrics->sz_lzma   *= 1.10;
+		} else if (fd->level <= 6) {
+		    metrics->sz_rans1  *= 1.01;
+		    metrics->sz_gz_def *= 1.02;
+		    metrics->sz_bzip2  *= 1.03;
+		    metrics->sz_lzma   *= 1.05;
+		}
+
+		if (method & (1<<GZIP_RLE) && best_sz > metrics->sz_gz_rle)
+		    best_sz = metrics->sz_gz_rle, best_method = GZIP_RLE;
+
+		if (method & (1<<GZIP) && best_sz > metrics->sz_gz_def)
+		    best_sz = metrics->sz_gz_def, best_method = GZIP;
+
+		if (method & (1<<RANS0) && best_sz > metrics->sz_rans0)
+		    best_sz = metrics->sz_rans0, best_method = RANS0;
+
+		if (method & (1<<RANS1) && best_sz > metrics->sz_rans1)
+		    best_sz = metrics->sz_rans1, best_method = RANS1;
+
+		if (method & (1<<BZIP2) && best_sz > metrics->sz_bzip2)
+		    best_sz = metrics->sz_bzip2, best_method = BZIP2;
+
+		if (method & (1<<LZMA) && best_sz > metrics->sz_lzma)
+		    best_sz = metrics->sz_lzma, best_method = LZMA;
+
+		if (best_method == GZIP_RLE) {
+		    metrics->method = GZIP;
+		    metrics->strat  = Z_RLE;
+		} else {
+		    metrics->method = best_method;
+		    metrics->strat  = Z_FILTERED;
+		}
+
+		// If we see at least MAXFAIL trials in a row for a specific
+		// compression method with more than MAXDELTA aggregate
+		// size then we drop this from the list of methods used
+		// for this block type.
+#define MAXDELTA 0.20
+#define MAXFAILS 4
+		if (best_method == GZIP_RLE) {
+		    metrics->gz_rle_cnt = 0;
+		    metrics->gz_rle_extra = 0;
+		} else if (best_sz < metrics->sz_gz_rle) {
+		    double r = (double)metrics->sz_gz_rle / best_sz - 1;
+		    if (++metrics->gz_rle_cnt >= MAXFAILS && 
+			(metrics->gz_rle_extra += r) >= MAXDELTA)
+			method &= ~(1<<GZIP_RLE);
+		}
+
+		if (best_method == GZIP) {
+		    metrics->gz_def_cnt = 0;
+		    metrics->gz_def_extra = 0;
+		} else if (best_sz < metrics->sz_gz_def) {
+		    double r = (double)metrics->sz_gz_def / best_sz - 1;
+		    if (++metrics->gz_def_cnt >= MAXFAILS &&
+			(metrics->gz_def_extra += r) >= MAXDELTA)
+			method &= ~(1<<GZIP);
+		}
+
+		if (best_method == RANS0) {
+		    metrics->rans0_cnt = 0;
+		    metrics->rans0_extra = 0;
+		} else if (best_sz < metrics->sz_rans0) {
+		    double r = (double)metrics->sz_rans0 / best_sz - 1;
+		    if (++metrics->rans0_cnt >= MAXFAILS &&
+			(metrics->rans0_extra += r) >= MAXDELTA)
+			method &= ~(1<<RANS0);
+		}
+
+		if (best_method == RANS1) {
+		    metrics->rans1_cnt = 0;
+		    metrics->rans1_extra = 0;
+		} else if (best_sz < metrics->sz_rans1) {
+		    double r = (double)metrics->sz_rans1 / best_sz - 1;
+		    if (++metrics->rans1_cnt >= MAXFAILS &&
+			(metrics->rans1_extra += r) >= MAXDELTA)
+			method &= ~(1<<RANS1);
+		}
+
+		if (best_method == BZIP2) {
+		    metrics->bzip2_cnt = 0;
+		    metrics->bzip2_extra = 0;
+		} else if (best_sz < metrics->sz_bzip2) {
+		    double r = (double)metrics->sz_bzip2 / best_sz - 1;
+		    if (++metrics->bzip2_cnt >= MAXFAILS &&
+			(metrics->bzip2_extra += r) >= MAXDELTA)
+			method &= ~(1<<BZIP2);
+		}
+
+		if (best_method == LZMA) {
+		    metrics->lzma_cnt = 0;
+		    metrics->lzma_extra = 0;
+		} else if (best_sz < metrics->sz_lzma) {
+		    double r = (double)metrics->sz_lzma / best_sz - 1;
+		    if (++metrics->lzma_cnt >= MAXFAILS &&
+			(metrics->lzma_extra += r) >= MAXDELTA)
+			method &= ~(1<<LZMA);
+		}
+
+		//if (method != metrics->revised_method)
+		//    fprintf(stderr, "%d: method from %x to %x\n",
+		//	    b->content_id, metrics->revised_method, method);
+		metrics->revised_method = method;
+	    }
+	    pthread_mutex_unlock(&fd->metrics_lock);
+	} else {
+	    strat = metrics->strat;
+	    method = metrics->method;
+
+	    pthread_mutex_unlock(&fd->metrics_lock);
+	    comp = cram_compress_by_method((char *)b->data, b->uncomp_size,
+					   &comp_size, method,
+					   level, strat);
+	    if (!comp)
+		return -1;
+	    free(b->data);
+	    b->data = (unsigned char *)comp;
+	    b->comp_size = comp_size;
+	    b->method = method;
+	}
+
+    } else {
+	// no cached metrics, so just do zlib?
+	comp = cram_compress_by_method((char *)b->data, b->uncomp_size,
+				       &comp_size, GZIP, level, Z_FILTERED);
+	if (!comp) {
+	    fprintf(stderr, "Compression failed!\n");
+	    return -1;
+	}
+	free(b->data);
+	b->data = (unsigned char *)comp;
+	b->comp_size = comp_size;
+	b->method = GZIP;
+    }
+
+    if (fd->verbose)
+	fprintf(stderr, "Compressed block ID %d from %d to %d by method %s\n",
+		b->content_id, b->uncomp_size, b->comp_size,
+		cram_block_method2str(b->method));
+
+    if (b->method == RANS1)
+	b->method = RANS0; // Spec just has RANS (not 0/1) with auto-sensing
+
+    return 0;
+}
+
+cram_metrics *cram_new_metrics(void) {
+    cram_metrics *m = calloc(1, sizeof(*m));
+    if (!m)
+	return NULL;
+    m->trial = NTRIALS-1;
+    m->next_trial = TRIAL_SPAN;
+    m->method = RAW;
+    m->strat = 0;
+    m->revised_method = 0;
+
+    return m;
+}
+
+char *cram_block_method2str(enum cram_block_method m) {
+    switch(m) {
+    case RAW:	   return "RAW";
+    case GZIP:	   return "GZIP";
+    case BZIP2:	   return "BZIP2";
+    case LZMA:     return "LZMA";
+    case RANS0:    return "RANS0";
+    case RANS1:    return "RANS1";
+    case GZIP_RLE: return "GZIP_RLE";
+    case ERROR:    break;
+    }
+    return "?";
+}
+
+char *cram_content_type2str(enum cram_content_type t) {
+    switch (t) {
+    case FILE_HEADER:         return "FILE_HEADER";
+    case COMPRESSION_HEADER:  return "COMPRESSION_HEADER";
+    case MAPPED_SLICE:        return "MAPPED_SLICE";
+    case UNMAPPED_SLICE:      return "UNMAPPED_SLICE";
+    case EXTERNAL:            return "EXTERNAL";
+    case CORE:                return "CORE";
+    case CT_ERROR:            break;
+    }
+    return "?";
+}
+
+/*
+ * Extra error checking on fclose to really ensure data is written.
+ * Care needs to be taken to handle pipes vs real files.
+ *
+ * Returns 0 on success
+ *        -1 on failure.
+ */
+int paranoid_fclose(FILE *fp) {
+    if (-1 == fflush(fp) && errno != EBADF) {
+	fclose(fp);
+	return -1;
+    }
+
+    errno = 0;
+    if (-1 == fsync(fileno(fp))) {
+	if (errno != EINVAL) { // eg pipe
+	    fclose(fp);
+	    return -1;
+	}
+    }
+    return fclose(fp);
+}
+
+/* ----------------------------------------------------------------------
+ * Reference sequence handling
+ *
+ * These revolve around the refs_t structure, which may potentially be
+ * shared between multiple cram_fd.
+ *
+ * We start with refs_create() to allocate an empty refs_t and then
+ * populate it with @SQ line data using refs_from_header(). This is done on
+ * cram_open().  Also at start up we can call cram_load_reference() which
+ * is used with "scramble -r foo.fa". This replaces the fd->refs with the
+ * new one specified. In either case refs2id() is then called which
+ * maps ref_entry names to @SQ ids (refs_t->ref_id[]).
+ *
+ * Later, possibly within a thread, we will want to know the actual ref
+ * seq itself, obtained by calling cram_get_ref().  This may use the
+ * UR: or M5: fields or the filename specified in the original
+ * cram_load_reference() call.
+ *
+ * Given the potential for multi-threaded reference usage, we have
+ * reference counting (sorry for the confusing double use of "ref") to
+ * track the number of callers interested in any specific reference.
+ */
+
+/*
+ * Frees/unmaps a reference sequence and associated file handles.
+ */
+static void ref_entry_free_seq(ref_entry *e) {
+    if (e->mf)
+	mfclose(e->mf);
+    if (e->seq && !e->mf)
+	free(e->seq);
+
+    e->seq = NULL;
+    e->mf = NULL;
+}
+
+void refs_free(refs_t *r) {
+    RP("refs_free()\n");
+
+    if (--r->count > 0)
+	return;
+
+    if (!r)
+	return;
+
+    if (r->pool)
+	string_pool_destroy(r->pool);
+
+    if (r->h_meta) {
+	khint_t k;
+
+	for (k = kh_begin(r->h_meta); k != kh_end(r->h_meta); k++) {
+	    ref_entry *e;
+
+	    if (!kh_exist(r->h_meta, k))
+		continue;
+	    if (!(e = kh_val(r->h_meta, k)))
+		continue;
+	    ref_entry_free_seq(e);
+	    free(e);
+	}
+
+	kh_destroy(refs, r->h_meta);
+    }
+    
+    if (r->ref_id)
+	free(r->ref_id);
+
+    if (r->fp)
+	bgzf_close(r->fp);
+
+    pthread_mutex_destroy(&r->lock);
+
+    free(r);
+}
+
+static refs_t *refs_create(void) {
+    refs_t *r = calloc(1, sizeof(*r));
+
+    RP("refs_create()\n");
+
+    if (!r)
+	return NULL;
+
+    if (!(r->pool = string_pool_create(8192)))
+	goto err;
+
+    r->ref_id = NULL; // see refs2id() to populate.
+    r->count = 1;
+    r->last = NULL;
+    r->last_id = -1;
+
+    if (!(r->h_meta = kh_init(refs)))
+	goto err;
+
+    pthread_mutex_init(&r->lock, NULL);
+
+    return r;
+
+ err:
+    refs_free(r);
+    return NULL;
+}
+
+/*
+ * Opens a reference fasta file as a BGZF stream, allowing for
+ * compressed files.  It automatically builds a .fai file if
+ * required and if compressed a .gzi bgzf index too.
+ *
+ * Returns a BGZF handle on success;
+ *         NULL on failure.
+ */
+static BGZF *bgzf_open_ref(char *fn, char *mode, int is_md5) {
+    BGZF *fp;
+
+    if (!is_md5) {
+	char fai_file[PATH_MAX];
+
+	snprintf(fai_file, PATH_MAX, "%s.fai", fn);
+	if (access(fai_file, R_OK) != 0)
+	    if (fai_build(fn) != 0)
+		return NULL;
+    }
+
+    if (!(fp = bgzf_open(fn, mode))) {
+	perror(fn);
+	return NULL;
+    }
+
+    if (fp->is_compressed == 1 && bgzf_index_load(fp, fn, ".gzi") < 0) {
+	fprintf(stderr, "Unable to load .gzi index '%s.gzi'\n", fn);
+	bgzf_close(fp);
+	return NULL;
+    }
+
+    return fp;
+}
+
+/*
+ * Loads a FAI file for a reference.fasta.
+ * "is_err" indicates whether failure to load is worthy of emitting an
+ * error message. In some cases (eg with embedded references) we
+ * speculatively load, just incase, and silently ignore errors.
+ *
+ * Returns the refs_t struct on success (maybe newly allocated);
+ *         NULL on failure
+ */
+static refs_t *refs_load_fai(refs_t *r_orig, char *fn, int is_err) {
+    struct stat sb;
+    FILE *fp = NULL;
+    char fai_fn[PATH_MAX];
+    char line[8192];
+    refs_t *r = r_orig;
+    size_t fn_l = strlen(fn);
+    int id = 0, id_alloc = 0;
+
+    RP("refs_load_fai %s\n", fn);
+
+    if (!r)
+	if (!(r = refs_create()))
+	    goto err;
+
+    /* Open reference, for later use */
+    if (stat(fn, &sb) != 0) {
+	if (is_err)
+	    perror(fn);
+	goto err;
+    }
+
+    if (r->fp)
+	if (bgzf_close(r->fp) != 0)
+	    goto err;
+    r->fp = NULL;
+
+    if (!(r->fn = string_dup(r->pool, fn)))
+	goto err;
+	
+    if (fn_l > 4 && strcmp(&fn[fn_l-4], ".fai") == 0)
+	r->fn[fn_l-4] = 0;
+
+    if (!(r->fp = bgzf_open_ref(r->fn, "r", 0)))
+	goto err;
+
+    /* Parse .fai file and load meta-data */
+    sprintf(fai_fn, "%.*s.fai", PATH_MAX-5, r->fn);
+
+    if (stat(fai_fn, &sb) != 0) {
+	if (is_err)
+	    perror(fai_fn);
+	goto err;
+    }
+    if (!(fp = fopen(fai_fn, "r"))) {
+	if (is_err)
+	    perror(fai_fn);
+	goto err;
+    }
+    while (fgets(line, 8192, fp) != NULL) {
+	ref_entry *e = malloc(sizeof(*e));
+	char *cp;
+	int n;
+	khint_t k;
+
+	if (!e)
+	    return NULL;
+
+	// id
+	for (cp = line; *cp && !isspace(*cp); cp++)
+	    ;
+	*cp++ = 0;
+	e->name = string_dup(r->pool, line);
+	
+	// length
+	while (*cp && isspace(*cp))
+	    cp++;
+	e->length = strtoll(cp, &cp, 10);
+
+	// offset
+	while (*cp && isspace(*cp))
+	    cp++;
+	e->offset = strtoll(cp, &cp, 10);
+
+	// bases per line
+	while (*cp && isspace(*cp))
+	    cp++;
+	e->bases_per_line = strtol(cp, &cp, 10);
+
+	// line length
+	while (*cp && isspace(*cp))
+	    cp++;
+	e->line_length = strtol(cp, &cp, 10);
+
+	// filename
+	e->fn = r->fn;
+
+	e->count = 0;
+	e->seq = NULL;
+	e->mf = NULL;
+	e->is_md5 = 0;
+
+	k = kh_put(refs, r->h_meta, e->name, &n);
+	if (-1 == n)  {
+	    free(e);
+	    return NULL;
+	}
+
+	if (n) {
+	    kh_val(r->h_meta, k) = e;
+	} else {
+	    ref_entry *re = kh_val(r->h_meta, k);
+	    if (re && (re->count != 0 || re->length != 0)) {
+		/* Keep old */
+		free(e);
+	    } else {
+		/* Replace old */
+		if (re)
+		    free(re);
+		kh_val(r->h_meta, k) = e;
+	    }
+	}
+
+	if (id >= id_alloc) {
+	    int x;
+
+	    id_alloc = id_alloc ?id_alloc*2 : 16;
+	    r->ref_id = realloc(r->ref_id, id_alloc * sizeof(*r->ref_id));
+
+	    for (x = id; x < id_alloc; x++)
+		r->ref_id[x] = NULL;
+	}
+	r->ref_id[id] = e;
+	r->nref = ++id;
+    }
+
+    return r;
+
+ err:
+    if (fp)
+	fclose(fp);
+
+    if (!r_orig)
+	refs_free(r);
+    
+    return NULL;
+}
+
+/*
+ * Verifies that the CRAM @SQ lines and .fai files match.
+ */
+static void sanitise_SQ_lines(cram_fd *fd) {
+    int i;
+
+    if (!fd->header)
+	return;
+
+    if (!fd->refs || !fd->refs->h_meta)
+	return;
+
+    for (i = 0; i < fd->header->nref; i++) {
+	char *name = fd->header->ref[i].name;
+	khint_t k = kh_get(refs, fd->refs->h_meta, name);
+	ref_entry *r;
+
+	// We may have @SQ lines which have no known .fai, but do not
+	// in themselves pose a problem because they are unused in the file.
+	if (k == kh_end(fd->refs->h_meta))
+	    continue;
+
+	if (!(r = (ref_entry *)kh_val(fd->refs->h_meta, k)))
+	    continue;
+
+	if (r->length && r->length != fd->header->ref[i].len) {
+	    assert(strcmp(r->name, fd->header->ref[i].name) == 0);
+
+	    // Should we also check MD5sums here to ensure the correct
+	    // reference was given?
+	    fprintf(stderr, "WARNING: Header @SQ length mismatch for "
+		    "ref %s, %d vs %d\n",
+		    r->name, fd->header->ref[i].len, (int)r->length);
+
+	    // Fixing the parsed @SQ header will make MD:Z: strings work
+	    // and also stop it producing N for the sequence.
+	    fd->header->ref[i].len = r->length;
+	}
+    }
+}
+
+/*
+ * Indexes references by the order they appear in a BAM file. This may not
+ * necessarily be the same order they appear in the fasta reference file.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int refs2id(refs_t *r, SAM_hdr *h) {
+    int i;
+
+    if (r->ref_id)
+	free(r->ref_id);
+    if (r->last)
+	r->last = NULL;
+
+    r->ref_id = calloc(h->nref, sizeof(*r->ref_id));
+    if (!r->ref_id)
+	return -1;
+
+    r->nref = h->nref;
+    for (i = 0; i < h->nref; i++) {
+	khint_t k = kh_get(refs, r->h_meta, h->ref[i].name);
+	if (k != kh_end(r->h_meta)) {
+	    r->ref_id[i] = kh_val(r->h_meta, k);
+	} else {
+	    fprintf(stderr, "Unable to find ref name '%s'\n",
+		    h->ref[i].name);
+	}
+    }
+
+    return 0;
+}
+
+/*
+ * Generates refs_t entries based on @SQ lines in the header.
+ * Returns 0 on success
+ *         -1 on failure
+ */
+static int refs_from_header(refs_t *r, cram_fd *fd, SAM_hdr *h) {
+    int i, j;
+
+    if (!r)
+	return -1;
+
+    if (!h || h->nref == 0)
+	return 0;
+
+    //fprintf(stderr, "refs_from_header for %p mode %c\n", fd, fd->mode);
+
+    /* Existing refs are fine, as long as they're compatible with the hdr. */
+    if (!(r->ref_id = realloc(r->ref_id, (r->nref + h->nref) * sizeof(*r->ref_id))))
+	return -1;
+
+    /* Copy info from h->ref[i] over to r */
+    for (i = 0, j = r->nref; i < h->nref; i++) {
+	SAM_hdr_type *ty;
+	SAM_hdr_tag *tag;
+	khint_t k;
+	int n;
+
+	k = kh_get(refs, r->h_meta, h->ref[i].name);
+	if (k != kh_end(r->h_meta))
+	    // Ref already known about
+	    continue;
+
+	if (!(r->ref_id[j] = calloc(1, sizeof(ref_entry))))
+	    return -1;
+
+	if (!h->ref[i].name)
+	    return -1;
+
+	r->ref_id[j]->name = string_dup(r->pool, h->ref[i].name);
+	r->ref_id[j]->length = 0; // marker for not yet loaded
+
+	/* Initialise likely filename if known */
+	if ((ty = sam_hdr_find(h, "SQ", "SN", h->ref[i].name))) {
+	    if ((tag = sam_hdr_find_key(h, ty, "M5", NULL))) {
+		r->ref_id[j]->fn = string_dup(r->pool, tag->str+3);
+		//fprintf(stderr, "Tagging @SQ %s / %s\n", r->ref_id[h]->name, r->ref_id[h]->fn);
+	    }
+	}
+
+	k = kh_put(refs, r->h_meta, r->ref_id[j]->name, &n);
+	if (n <= 0) // already exists or error
+	    return -1;
+	kh_val(r->h_meta, k) = r->ref_id[j];
+
+	j++;
+    }
+    r->nref = j;
+
+    return 0;
+}
+
+/*
+ * Attaches a header to a cram_fd.
+ *
+ * This should be used when creating a new cram_fd for writing where
+ * we have an SAM_hdr already constructed (eg from a file we've read
+ * in).
+ */
+int cram_set_header(cram_fd *fd, SAM_hdr *hdr) {
+    if (fd->header)
+	sam_hdr_free(fd->header);
+    fd->header = hdr;
+    return refs_from_header(fd->refs, fd, hdr);
+}
+
+/*
+ * Converts a directory and a filename into an expanded path, replacing %s
+ * in directory with the filename and %[0-9]+s with portions of the filename
+ * Any remaining parts of filename are added to the end with /%s.
+ */
+void expand_cache_path(char *path, char *dir, char *fn) {
+    char *cp;
+
+    while ((cp = strchr(dir, '%'))) {
+	strncpy(path, dir, cp-dir);
+	path += cp-dir;
+
+	if (*++cp == 's') {
+	    strcpy(path, fn);
+	    path += strlen(fn);
+	    fn += strlen(fn);
+	    cp++;
+	} else if (*cp >= '0' && *cp <= '9') {
+	    char *endp;
+	    long l;
+
+	    l = strtol(cp, &endp, 10);
+	    l = MIN(l, strlen(fn));
+	    if (*endp == 's') {
+		strncpy(path, fn, l);
+		path += l;
+		fn += l;
+		*path = 0;
+		cp = endp+1;
+	    } else {
+		*path++ = '%';
+		*path++ = *cp++;
+	    }
+	} else {
+	    *path++ = '%';
+	    *path++ = *cp++;
+	}
+	dir = cp;
+    }
+    strcpy(path, dir);
+    path += strlen(dir);
+    if (*fn && path[-1] != '/')
+	*path++ = '/';
+    strcpy(path, fn);
+}
+
+/*
+ * Make the directory containing path and any prefix directories.
+ */
+void mkdir_prefix(char *path, int mode) {
+    char *cp = strrchr(path, '/');
+    if (!cp)
+	return;
+
+    *cp = 0;
+    if (is_directory(path)) {
+	*cp = '/';
+	return;
+    }
+
+    if (mkdir(path, mode) == 0) {
+	chmod(path, mode);
+	*cp = '/';
+	return;
+    }
+
+    mkdir_prefix(path, mode);
+    mkdir(path, mode);
+    chmod(path, mode);
+    *cp = '/';
+}
+
+/*
+ * Return the cache directory to use, based on the first of these
+ * environment variables to be set to a non-empty value.
+ */
+static const char *get_cache_basedir(const char **extra) {
+    char *base;
+
+    *extra = "";
+
+    base = getenv("XDG_CACHE_HOME");
+    if (base && *base) return base;
+
+    base = getenv("HOME");
+    if (base && *base) { *extra = "/.cache"; return base; }
+
+    base = getenv("TMPDIR");
+    if (base && *base) return base;
+
+    base = getenv("TEMP");
+    if (base && *base) return base;
+
+    return "/tmp";
+}
+
+/*
+ * Return an integer representation of pthread_self().
+ */
+static unsigned get_int_threadid() {
+    pthread_t pt = pthread_self();
+    unsigned char *s = (unsigned char *) &pt;
+    size_t i;
+    unsigned h = 0;
+    for (i = 0; i < sizeof(pthread_t); i++)
+	h = (h << 5) - h + s[i];
+    return h;
+}
+
+/*
+ * Queries the M5 string from the header and attempts to populate the
+ * reference from this using the REF_PATH environment.
+ *
+ * Returns 0 on sucess
+ *        -1 on failure
+ */
+static int cram_populate_ref(cram_fd *fd, int id, ref_entry *r) {
+    char *ref_path = getenv("REF_PATH");
+    SAM_hdr_type *ty;
+    SAM_hdr_tag *tag;
+    char path[PATH_MAX], path_tmp[PATH_MAX];
+    char cache[PATH_MAX], cache_root[PATH_MAX];
+    char *local_cache = getenv("REF_CACHE");
+    mFILE *mf;
+    int local_path = 0;
+
+    if (fd->verbose)
+	fprintf(stderr, "cram_populate_ref on fd %p, id %d\n", fd, id);
+
+    cache_root[0] = '\0';
+
+    if (!ref_path || *ref_path == '\0') {
+	/*
+	 * If we have no ref path, we use the EBI server.
+	 * However to avoid spamming it we require a local ref cache too.
+	 */
+	ref_path = "http://www.ebi.ac.uk:80/ena/cram/md5/%s";
+	if (!local_cache || *local_cache == '\0') {
+	    const char *extra;
+	    const char *base = get_cache_basedir(&extra);
+	    snprintf(cache_root, PATH_MAX, "%s%s/hts-ref", base, extra);
+	    snprintf(cache,PATH_MAX, "%s%s/hts-ref/%%2s/%%2s/%%s", base, extra);
+	    local_cache = cache;
+	    if (fd->verbose)
+		fprintf(stderr, "Populating local cache: %s\n", local_cache);
+	}
+    }
+
+    if (!r->name)
+	return -1;
+
+    if (!(ty = sam_hdr_find(fd->header, "SQ", "SN", r->name)))
+	return -1;
+
+    if (!(tag = sam_hdr_find_key(fd->header, ty, "M5", NULL)))
+	goto no_M5;
+
+    if (fd->verbose)
+	fprintf(stderr, "Querying ref %s\n", tag->str+3);
+
+    /* Use cache if available */
+    if (local_cache && *local_cache) {
+	expand_cache_path(path, local_cache, tag->str+3);
+	local_path = 1;
+    }
+
+#ifndef HAVE_MMAP
+    char *path2;
+    /* Search local files in REF_PATH; we can open them and return as above */
+    if (!local_path && (path2 = find_path(tag->str+3, ref_path))) {
+	strncpy(path, path2, PATH_MAX);
+	free(path2);
+	if (is_file(path)) // incase it's too long
+	    local_path = 1;
+    }
+#endif
+
+    /* Found via REF_CACHE or local REF_PATH file */
+    if (local_path) {
+	struct stat sb;
+	BGZF *fp;
+
+	if (0 == stat(path, &sb) && (fp = bgzf_open(path, "r"))) {
+	    r->length = sb.st_size;
+	    r->offset = r->line_length = r->bases_per_line = 0;
+
+	    r->fn = string_dup(fd->refs->pool, path);
+
+	    if (fd->refs->fp)
+		if (bgzf_close(fd->refs->fp) != 0)
+		    return -1;
+	    fd->refs->fp = fp;
+	    fd->refs->fn = r->fn;
+	    r->is_md5 = 1;
+
+	    // Fall back to cram_get_ref() where it'll do the actual
+	    // reading of the file.
+	    return 0;
+	}
+    }
+
+
+    /* Otherwise search full REF_PATH; slower as loads entire file */
+    if ((mf = open_path_mfile(tag->str+3, ref_path, NULL))) {
+	size_t sz;
+	r->seq = mfsteal(mf, &sz);
+	if (r->seq) {
+	    r->mf = NULL;
+	} else {
+	    // keep mf around as we couldn't detach
+	    r->seq = mf->data;
+	    r->mf = mf;
+	}
+	r->length = sz;
+	r->is_md5 = 1;
+    } else {
+	refs_t *refs;
+	char *fn;
+
+    no_M5:
+	/* Failed to find in search path or M5 cache, see if @SQ UR: tag? */
+	if (!(tag = sam_hdr_find_key(fd->header, ty, "UR", NULL)))
+	    return -1;
+
+	fn = (strncmp(tag->str+3, "file:", 5) == 0)
+	    ? tag->str+8
+	    : tag->str+3;
+
+	if (fd->refs->fp) {
+	    if (bgzf_close(fd->refs->fp) != 0)
+		return -1;
+	    fd->refs->fp = NULL;
+	}
+	if (!(refs = refs_load_fai(fd->refs, fn, 0)))
+	    return -1;
+	sanitise_SQ_lines(fd);
+
+	fd->refs = refs;
+	if (fd->refs->fp) {
+	    if (bgzf_close(fd->refs->fp) != 0)
+		return -1;
+	    fd->refs->fp = NULL;
+	}
+
+	if (!fd->refs->fn)
+	    return -1;
+
+	if (-1 == refs2id(fd->refs, fd->header))
+	    return -1;
+	if (!fd->refs->ref_id || !fd->refs->ref_id[id])
+	    return -1;
+
+	// Local copy already, so fall back to cram_get_ref().
+	return 0;
+    }
+
+    /* Populate the local disk cache if required */
+    if (local_cache && *local_cache) {
+	int pid = (int) getpid();
+	unsigned thrid = get_int_threadid();
+	FILE *fp;
+
+	if (*cache_root && !is_directory(cache_root) && hts_verbose >= 1)
+	    fprintf(stderr,
+"Creating reference cache directory %s\n"
+"This may become large; see the samtools(1) manual page REF_CACHE discussion\n",
+		    cache_root);
+
+	expand_cache_path(path, local_cache, tag->str+3);
+	if (fd->verbose)
+	    fprintf(stderr, "Writing cache file '%s'\n", path);
+	mkdir_prefix(path, 01777);
+
+	do {
+	    // Attempt to further uniquify the temporary filename
+	    unsigned t = ((unsigned) time(NULL)) ^ ((unsigned) clock());
+	    thrid++; // Ensure filename changes even if time/clock haven't
+
+	    sprintf(path_tmp, "%s.tmp_%d_%u_%u", path, pid, thrid, t);
+	    fp = fopen(path_tmp, "wx");
+	} while (fp == NULL && errno == EEXIST);
+	if (!fp) {
+	    perror(path_tmp);
+
+	    // Not fatal - we have the data already so keep going.
+	    return 0;
+	}
+
+	// Check md5sum
+	hts_md5_context *md5;
+	char unsigned md5_buf1[16];
+	char md5_buf2[33];
+
+	if (!(md5 = hts_md5_init())) {
+	    unlink(path_tmp);
+	    fclose(fp);
+	    return -1;
+	}
+	hts_md5_update(md5, r->seq, r->length);
+	hts_md5_final(md5_buf1, md5);
+	hts_md5_destroy(md5);
+	hts_md5_hex(md5_buf2, md5_buf1);
+
+	if (strncmp(tag->str+3, md5_buf2, 32) != 0) {
+	    fprintf(stderr, "[E::%s] mismatching md5sum for downloaded reference.\n", __func__);
+	    unlink(path_tmp);
+	    fclose(fp);
+	    return -1;
+	}
+
+	if (r->length != fwrite(r->seq, 1, r->length, fp)) {
+	    perror(path);
+	}
+	if (-1 == paranoid_fclose(fp)) {
+	    unlink(path_tmp);
+	} else {
+	    if (0 == chmod(path_tmp, 0444))
+		rename(path_tmp, path);
+	    else
+		unlink(path_tmp);
+	}
+    }
+
+    return 0;
+}
+
+static void cram_ref_incr_locked(refs_t *r, int id) {
+    RP("%d INC REF %d, %d %p\n", gettid(), id, (int)(id>=0?r->ref_id[id]->count+1:-999), id>=0?r->ref_id[id]->seq:(char *)1);
+
+    if (id < 0 || !r->ref_id[id]->seq)
+	return;
+
+    if (r->last_id == id)
+	r->last_id = -1;
+
+    ++r->ref_id[id]->count;
+}
+
+void cram_ref_incr(refs_t *r, int id) {
+    pthread_mutex_lock(&r->lock);
+    cram_ref_incr_locked(r, id);
+    pthread_mutex_unlock(&r->lock);
+}
+
+static void cram_ref_decr_locked(refs_t *r, int id) {
+    RP("%d DEC REF %d, %d %p\n", gettid(), id, (int)(id>=0?r->ref_id[id]->count-1:-999), id>=0?r->ref_id[id]->seq:(char *)1);
+
+    if (id < 0 || !r->ref_id[id]->seq) {
+	assert(r->ref_id[id]->count >= 0);
+	return;
+    }
+
+    if (--r->ref_id[id]->count <= 0) {
+	assert(r->ref_id[id]->count == 0);
+	if (r->last_id >= 0) {
+	    if (r->ref_id[r->last_id]->count <= 0 &&
+		r->ref_id[r->last_id]->seq) {
+		RP("%d FREE REF %d (%p)\n", gettid(),
+		   r->last_id, r->ref_id[r->last_id]->seq);
+		ref_entry_free_seq(r->ref_id[r->last_id]);
+		r->ref_id[r->last_id]->length = 0;
+	    }
+	}
+	r->last_id = id;
+    }
+}
+
+void cram_ref_decr(refs_t *r, int id) {
+    pthread_mutex_lock(&r->lock);
+    cram_ref_decr_locked(r, id);
+    pthread_mutex_unlock(&r->lock);
+}
+
+/*
+ * Used by cram_ref_load and cram_ref_get. The file handle will have
+ * already been opened, so we can catch it. The ref_entry *e informs us
+ * of whether this is a multi-line fasta file or a raw MD5 style file.
+ * Either way we create a single contiguous sequence.
+ *
+ * Returns all or part of a reference sequence on success (malloced);
+ *         NULL on failure.
+ */
+static char *load_ref_portion(BGZF *fp, ref_entry *e, int start, int end) {
+    off_t offset, len;
+    char *seq;
+
+    if (end < start)
+	end = start;
+
+    /*
+     * Compute locations in file. This is trivial for the MD5 files, but
+     * is still necessary for the fasta variants.
+     */
+    offset = e->line_length
+	? e->offset + (start-1)/e->bases_per_line * e->line_length +
+	  (start-1) % e->bases_per_line
+	: start-1;
+
+    len = (e->line_length
+	   ? e->offset + (end-1)/e->bases_per_line * e->line_length + 
+	     (end-1) % e->bases_per_line
+	   : end-1) - offset + 1;
+
+    if (bgzf_useek(fp, offset, SEEK_SET) < 0) {
+	perror("bgzf_useek() on reference file");
+	return NULL;
+    }
+
+    if (len == 0 || !(seq = malloc(len))) {
+	return NULL;
+    }
+
+    if (len != bgzf_read(fp, seq, len)) {
+	perror("bgzf_read() on reference file");
+	free(seq);
+	return NULL;
+    }
+
+    /* Strip white-space if required. */
+    if (len != end-start+1) {
+	int i, j;
+	char *cp = seq;
+	char *cp_to;
+
+	for (i = j = 0; i < len; i++) {
+	    if (cp[i] >= '!' && cp[i] <= '~')
+		cp[j++] = toupper(cp[i]);
+	}
+	cp_to = cp+j;
+
+	if (cp_to - seq != end-start+1) {
+	    fprintf(stderr, "Malformed reference file?\n");
+	    free(seq);
+	    return NULL;
+	}
+    } else {
+	int i;
+	for (i = 0; i < len; i++) {
+	    seq[i] = toupper(seq[i]);
+	}
+    }
+
+    return seq;
+}
+
+/*
+ * Load the entire reference 'id'.
+ * This also increments the reference count by 1.
+ *
+ * Returns ref_entry on success;
+ *         NULL on failure
+ */
+ref_entry *cram_ref_load(refs_t *r, int id, int is_md5) {
+    ref_entry *e = r->ref_id[id];
+    int start = 1, end = e->length;
+    char *seq;
+
+    if (e->seq) {
+	return e;
+    }
+
+    assert(e->count == 0);
+
+    if (r->last) {
+#ifdef REF_DEBUG
+	int idx = 0;
+	for (idx = 0; idx < r->nref; idx++)
+	    if (r->last == r->ref_id[idx])
+		break;
+	RP("%d cram_ref_load DECR %d\n", gettid(), idx);
+#endif
+	assert(r->last->count > 0);
+	if (--r->last->count <= 0) {
+	    RP("%d FREE REF %d (%p)\n", gettid(), id, r->ref_id[id]->seq);
+	    if (r->last->seq)
+		ref_entry_free_seq(r->last);
+	}
+    }
+
+    /* Open file if it's not already the current open reference */
+    if (strcmp(r->fn, e->fn) || r->fp == NULL) {
+	if (r->fp)
+	    if (bgzf_close(r->fp) != 0)
+		return NULL;
+	r->fn = e->fn;
+	if (!(r->fp = bgzf_open_ref(r->fn, "r", is_md5)))
+	    return NULL;
+    }
+
+    RP("%d Loading ref %d (%d..%d)\n", gettid(), id, start, end);
+
+    if (!(seq = load_ref_portion(r->fp, e, start, end))) {
+	return NULL;
+    }
+
+    RP("%d Loaded ref %d (%d..%d) = %p\n", gettid(), id, start, end, seq);
+
+    RP("%d INC REF %d, %d\n", gettid(), id, (int)(e->count+1));
+    e->seq = seq;
+    e->mf = NULL;
+    e->count++;
+
+    /*
+     * Also keep track of last used ref so incr/decr loops on the same
+     * sequence don't cause load/free loops.
+     */
+    RP("%d cram_ref_load INCR %d => %d\n", gettid(), id, e->count+1);
+    r->last = e;
+    e->count++; 
+
+    return e;
+}
+
+/*
+ * Returns a portion of a reference sequence from start to end inclusive.
+ * The returned pointer is owned by either the cram_file fd or by the
+ * internal refs_t structure and should not be freed  by the caller.
+ *
+ * The difference is whether or not this refs_t is in use by just the one
+ * cram_fd or by multiples, or whether we have multiple threads accessing
+ * references. In either case fd->shared will be true and we start using
+ * reference counting to track the number of users of a specific reference
+ * sequence.
+ *
+ * Otherwise the ref seq returned is allocated as part of cram_fd itself
+ * and will be freed up on the next call to cram_get_ref or cram_close.
+ *
+ * To return the entire reference sequence, specify start as 1 and end
+ * as 0.
+ *
+ * To cease using a reference, call cram_ref_decr().
+ *
+ * Returns reference on success,
+ *         NULL on failure
+ */
+char *cram_get_ref(cram_fd *fd, int id, int start, int end) {
+    ref_entry *r;
+    char *seq;
+    int ostart = start;
+
+    if (id == -1)
+	return NULL;
+
+    /* FIXME: axiomatic query of r->seq being true?
+     * Or shortcut for unsorted data where we load once and never free?
+     */
+
+    //fd->shared_ref = 1; // hard code for now to simplify things
+
+    pthread_mutex_lock(&fd->ref_lock);
+
+    RP("%d cram_get_ref on fd %p, id %d, range %d..%d\n", gettid(), fd, id, start, end);
+
+    /*
+     * Unsorted data implies we want to fetch an entire reference at a time.
+     * We just deal with this at the moment by claiming we're sharing
+     * references instead, which has the same requirement.
+     */
+    if (fd->unsorted)
+	fd->shared_ref = 1;
+
+
+    /* Sanity checking: does this ID exist? */
+    if (id >= fd->refs->nref) {
+	fprintf(stderr, "No reference found for id %d\n", id);
+	pthread_mutex_unlock(&fd->ref_lock);
+	return NULL;
+    }
+
+    if (!fd->refs || !fd->refs->ref_id[id]) {
+	fprintf(stderr, "No reference found for id %d\n", id);
+	pthread_mutex_unlock(&fd->ref_lock);
+	return NULL;
+    }
+
+    if (!(r = fd->refs->ref_id[id])) {
+	fprintf(stderr, "No reference found for id %d\n", id);
+	pthread_mutex_unlock(&fd->ref_lock);
+	return NULL;
+    }
+
+
+    /*
+     * It has an entry, but may not have been populated yet.
+     * Any manually loaded .fai files have their lengths known.
+     * A ref entry computed from @SQ lines (M5 or UR field) will have
+     * r->length == 0 unless it's been loaded once and verified that we have
+     * an on-disk filename for it.
+     *
+     * 19 Sep 2013: Moved the lock here as the cram_populate_ref code calls
+     * open_path_mfile and libcurl, which isn't multi-thread safe unless I
+     * rewrite my code to have one curl handle per thread.
+     */
+    pthread_mutex_lock(&fd->refs->lock);
+    if (r->length == 0) {
+	if (cram_populate_ref(fd, id, r) == -1) {
+	    fprintf(stderr, "Failed to populate reference for id %d\n", id);
+	    pthread_mutex_unlock(&fd->refs->lock);
+	    pthread_mutex_unlock(&fd->ref_lock);
+	    return NULL;
+	}
+	r = fd->refs->ref_id[id];
+	if (fd->unsorted)
+	    cram_ref_incr_locked(fd->refs, id);
+    }
+
+
+    /*
+     * We now know that we the filename containing the reference, so check
+     * for limits. If it's over half the reference we'll load all of it in
+     * memory as this will speed up subsequent calls.
+     */
+    if (end < 1)
+	end = r->length;
+    if (end >= r->length)
+	end  = r->length; 
+    assert(start >= 1);
+
+    if (end - start >= 0.5*r->length || fd->shared_ref) {
+	start = 1;
+	end = r->length;
+    }
+    
+    /*
+     * Maybe we have it cached already? If so use it.
+     *
+     * Alternatively if we don't have the sequence but we're sharing
+     * references and/or are asking for the entire length of it, then
+     * load the full reference into the refs structure and return
+     * a pointer to that one instead.
+     */
+    if (fd->shared_ref || r->seq || (start == 1 && end == r->length)) {
+	char *cp;
+
+	if (id >= 0) {
+	    if (r->seq) {
+		cram_ref_incr_locked(fd->refs, id);
+	    } else {
+		ref_entry *e;
+		if (!(e = cram_ref_load(fd->refs, id, r->is_md5))) {
+		    pthread_mutex_unlock(&fd->refs->lock);
+		    pthread_mutex_unlock(&fd->ref_lock);
+		    return NULL;
+		}
+
+		/* unsorted data implies cache ref indefinitely, to avoid
+		 * continually loading and unloading.
+		 */
+		if (fd->unsorted)
+		    cram_ref_incr_locked(fd->refs, id);
+	    }	    
+
+	    fd->ref = NULL; /* We never access it directly */
+	    fd->ref_start = 1;
+	    fd->ref_end   = r->length;
+	    fd->ref_id    = id;
+
+	    cp = fd->refs->ref_id[id]->seq + ostart-1;
+	} else {
+	    fd->ref = NULL;
+	    cp = NULL;
+	}
+
+	RP("%d cram_get_ref returning for id %d, count %d\n", gettid(), id, (int)r->count);
+
+	pthread_mutex_unlock(&fd->refs->lock);
+	pthread_mutex_unlock(&fd->ref_lock);
+	return cp;
+    }
+
+    /*
+     * Otherwise we're not sharing, we don't have a copy of it already and
+     * we're only asking for a small portion of it.
+     *
+     * In this case load up just that segment ourselves, freeing any old
+     * small segments in the process.
+     */
+
+    /* Unmapped ref ID */
+    if (id < 0) {
+	if (fd->ref_free) {
+	    free(fd->ref_free);
+	    fd->ref_free = NULL;
+	}
+	fd->ref = NULL;
+	fd->ref_id = id;
+	pthread_mutex_unlock(&fd->refs->lock);
+	pthread_mutex_unlock(&fd->ref_lock);
+	return NULL;
+    }
+
+    /* Open file if it's not already the current open reference */
+    if (strcmp(fd->refs->fn, r->fn) || fd->refs->fp == NULL) {
+	if (fd->refs->fp)
+	    if (bgzf_close(fd->refs->fp) != 0)
+		return NULL;
+	fd->refs->fn = r->fn;
+	if (!(fd->refs->fp = bgzf_open_ref(fd->refs->fn, "r", r->is_md5))) {
+	    pthread_mutex_unlock(&fd->refs->lock);
+	    pthread_mutex_unlock(&fd->ref_lock);
+	    return NULL;
+	}
+    }
+
+    if (!(fd->ref = load_ref_portion(fd->refs->fp, r, start, end))) {
+	pthread_mutex_unlock(&fd->refs->lock);
+	pthread_mutex_unlock(&fd->ref_lock);
+	return NULL;
+    }
+
+    if (fd->ref_free)
+	free(fd->ref_free);
+
+    fd->ref_id    = id;
+    fd->ref_start = start;
+    fd->ref_end   = end;
+    fd->ref_free = fd->ref;
+    seq = fd->ref;
+
+    pthread_mutex_unlock(&fd->refs->lock);
+    pthread_mutex_unlock(&fd->ref_lock);
+
+    return seq + ostart - start;
+}
+
+/*
+ * If fd has been opened for reading, it may be permitted to specify 'fn'
+ * as NULL and let the code auto-detect the reference by parsing the
+ * SAM header @SQ lines.
+ */
+int cram_load_reference(cram_fd *fd, char *fn) {
+    int ret = 0;
+
+    if (fn) {
+	fd->refs = refs_load_fai(fd->refs, fn,
+				 !(fd->embed_ref && fd->mode == 'r'));
+	fn = fd->refs ? fd->refs->fn : NULL;
+	if (!fn)
+	    ret = -1;
+	sanitise_SQ_lines(fd);
+    }
+    fd->ref_fn = fn;
+
+    if ((!fd->refs || (fd->refs->nref == 0 && !fn)) && fd->header) {
+	if (fd->refs)
+	    refs_free(fd->refs);
+	if (!(fd->refs = refs_create()))
+	    return -1;
+	if (-1 == refs_from_header(fd->refs, fd, fd->header))
+	    return -1;
+    }
+
+    if (fd->header)
+	if (-1 == refs2id(fd->refs, fd->header))
+	    return -1;
+
+    return ret;
+}
+
+/* ----------------------------------------------------------------------
+ * Containers
+ */
+
+/*
+ * Creates a new container, specifying the maximum number of slices
+ * and records permitted.
+ *
+ * Returns cram_container ptr on success
+ *         NULL on failure
+ */
+cram_container *cram_new_container(int nrec, int nslice) {
+    cram_container *c = calloc(1, sizeof(*c));
+    enum cram_DS_ID id;
+
+    if (!c)
+	return NULL;
+
+    c->curr_ref = -2;
+
+    c->max_c_rec = nrec * nslice;
+    c->curr_c_rec = 0;
+
+    c->max_rec = nrec;
+    c->record_counter = 0;
+    c->num_bases = 0;
+
+    c->max_slice = nslice;
+    c->curr_slice = 0;
+
+    c->pos_sorted = 1;
+    c->max_apos   = 0;
+    c->multi_seq  = 0;
+
+    c->bams = NULL;
+
+    if (!(c->slices = (cram_slice **)calloc(nslice, sizeof(cram_slice *))))
+	goto err;
+    c->slice = NULL;
+
+    if (!(c->comp_hdr = cram_new_compression_header()))
+	goto err;
+    c->comp_hdr_block = NULL;
+
+    for (id = DS_RN; id < DS_TN; id++)
+	if (!(c->stats[id] = cram_stats_create())) goto err;
+    
+    //c->aux_B_stats = cram_stats_create();
+
+    if (!(c->tags_used = kh_init(s_i2i)))
+	goto err;
+    c->refs_used = 0;
+
+    return c;
+
+ err:
+    if (c) {
+	if (c->slices)
+	    free(c->slices);
+	free(c);
+    }
+    return NULL;
+}
+
+void cram_free_container(cram_container *c) {
+    enum cram_DS_ID id;
+    int i;
+
+    if (!c)
+	return;
+
+    if (c->refs_used)
+	free(c->refs_used);
+
+    if (c->landmark)
+	free(c->landmark);
+
+    if (c->comp_hdr)
+	cram_free_compression_header(c->comp_hdr);
+
+    if (c->comp_hdr_block)
+	cram_free_block(c->comp_hdr_block);
+
+    if (c->slices) {
+	for (i = 0; i < c->max_slice; i++)
+	    if (c->slices[i])
+		cram_free_slice(c->slices[i]);
+	free(c->slices);
+    }
+
+    for (id = DS_RN; id < DS_TN; id++)
+	if (c->stats[id]) cram_stats_free(c->stats[id]);
+
+    //if (c->aux_B_stats) cram_stats_free(c->aux_B_stats);
+    
+    if (c->tags_used) kh_destroy(s_i2i, c->tags_used);
+
+    free(c);
+}
+
+/*
+ * Reads a container header.
+ *
+ * Returns cram_container on success
+ *         NULL on failure or no container left (fd->err == 0).
+ */
+cram_container *cram_read_container(cram_fd *fd) {
+    cram_container c2, *c;
+    int i, s;
+    size_t rd = 0;
+    uint32_t crc = 0;
+    
+    fd->err = 0;
+    fd->eof = 0;
+
+    memset(&c2, 0, sizeof(c2));
+    if (CRAM_MAJOR_VERS(fd->version) == 1) {
+	if ((s = itf8_decode_crc(fd, &c2.length, &crc)) == -1) {
+	    fd->eof = fd->empty_container ? 1 : 2;
+	    return NULL;
+	} else {
+	    rd+=s;
+	}
+    } else {
+	uint32_t len;
+	if ((s = int32_decode(fd, &c2.length)) == -1) {
+	    if (CRAM_MAJOR_VERS(fd->version) == 2 &&
+		CRAM_MINOR_VERS(fd->version) == 0)
+		fd->eof = 1; // EOF blocks arrived in v2.1
+	    else
+		fd->eof = fd->empty_container ? 1 : 2;
+	    return NULL;
+	} else {
+	    rd+=s;
+	}
+	len = le_int4(c2.length);
+	crc = crc32(0L, (unsigned char *)&len, 4);
+    }
+    if ((s = itf8_decode_crc(fd, &c2.ref_seq_id, &crc))   == -1) return NULL; else rd+=s;
+    if ((s = itf8_decode_crc(fd, &c2.ref_seq_start, &crc))== -1) return NULL; else rd+=s;
+    if ((s = itf8_decode_crc(fd, &c2.ref_seq_span, &crc)) == -1) return NULL; else rd+=s;
+    if ((s = itf8_decode_crc(fd, &c2.num_records, &crc))  == -1) return NULL; else rd+=s;
+
+    if (CRAM_MAJOR_VERS(fd->version) == 1) {
+	c2.record_counter = 0;
+	c2.num_bases = 0;
+    } else {
+	if (CRAM_MAJOR_VERS(fd->version) >= 3) {
+	    if ((s = ltf8_decode_crc(fd, &c2.record_counter, &crc)) == -1)
+		return NULL;
+	    else
+		rd += s;
+	} else {
+	    int32_t i32;
+	    if ((s = itf8_decode_crc(fd, &i32, &crc)) == -1)
+		return NULL;
+	    else
+		rd += s;
+	    c2.record_counter = i32;
+	}
+
+	if ((s = ltf8_decode_crc(fd, &c2.num_bases, &crc))== -1)
+	    return NULL;
+	else
+	    rd += s;
+    }
+    if ((s = itf8_decode_crc(fd, &c2.num_blocks, &crc))   == -1) return NULL; else rd+=s;
+    if ((s = itf8_decode_crc(fd, &c2.num_landmarks, &crc))== -1) return NULL; else rd+=s;
+
+    if (!(c = calloc(1, sizeof(*c))))
+	return NULL;
+
+    *c = c2;
+
+    if (!(c->landmark = malloc(c->num_landmarks * sizeof(int32_t))) &&
+	c->num_landmarks) {
+	fd->err = errno;
+	cram_free_container(c);
+	return NULL;
+    }  
+    for (i = 0; i < c->num_landmarks; i++) {
+	if ((s = itf8_decode_crc(fd, &c->landmark[i], &crc)) == -1) {
+	    cram_free_container(c);
+	    return NULL;
+	} else {
+	    rd += s;
+	}
+    }
+
+    if (CRAM_MAJOR_VERS(fd->version) >= 3) {
+	if (-1 == int32_decode(fd, (int32_t *)&c->crc32))
+	    return NULL;
+	else
+	    rd+=4;
+
+	if (crc != c->crc32) {
+	    fprintf(stderr, "Container header CRC32 failure\n");
+	    cram_free_container(c);
+	    return NULL;
+	}
+    }
+
+    c->offset = rd;
+    c->slices = NULL;
+    c->curr_slice = 0;
+    c->max_slice = c->num_landmarks;
+    c->slice_rec = 0;
+    c->curr_rec = 0;
+    c->max_rec = 0;
+
+    if (c->ref_seq_id == -2) {
+	c->multi_seq = 1;
+	fd->multi_seq = 1;
+    }
+
+    fd->empty_container =
+	(c->num_records == 0 &&
+	 c->ref_seq_id == -1 &&
+	 c->ref_seq_start == 0x454f46 /* EOF */) ? 1 : 0;
+
+    return c;
+}
+
+
+/* MAXIMUM storage size needed for the container. */
+int cram_container_size(cram_container *c) {
+    return 55 + 5*c->num_landmarks;
+}
+
+
+/*
+ * Stores the container structure in dat and returns *size as the
+ * number of bytes written to dat[].  The input size of dat is also
+ * held in *size and should be initialised to cram_container_size(c).
+ *
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+int cram_store_container(cram_fd *fd, cram_container *c, char *dat, int *size)
+{
+    char *cp = dat;
+    int i;
+
+    // Check the input buffer is large enough according to our stated
+    // requirements. (NOTE: it may actually take less.)
+    if (cram_container_size(c) > *size)
+        return -1;
+
+    if (CRAM_MAJOR_VERS(fd->version) == 1) {
+	cp += itf8_put(cp, c->length);
+    } else {
+	*(int32_t *)cp = le_int4(c->length);
+	cp += 4;
+    }
+    if (c->multi_seq) {
+	cp += itf8_put(cp, -2);
+	cp += itf8_put(cp, 0);
+	cp += itf8_put(cp, 0);
+    } else {
+	cp += itf8_put(cp, c->ref_seq_id);
+	cp += itf8_put(cp, c->ref_seq_start);
+	cp += itf8_put(cp, c->ref_seq_span);
+    }
+    cp += itf8_put(cp, c->num_records);
+    if (CRAM_MAJOR_VERS(fd->version) == 2) {
+	cp += itf8_put(cp, c->record_counter);
+	cp += ltf8_put(cp, c->num_bases);
+    } else if (CRAM_MAJOR_VERS(fd->version) >= 3) {
+	cp += ltf8_put(cp, c->record_counter);
+	cp += ltf8_put(cp, c->num_bases);
+    }
+
+    cp += itf8_put(cp, c->num_blocks);
+    cp += itf8_put(cp, c->num_landmarks);
+    for (i = 0; i < c->num_landmarks; i++)
+	cp += itf8_put(cp, c->landmark[i]);
+
+    if (CRAM_MAJOR_VERS(fd->version) >= 3) {
+	c->crc32 = crc32(0L, (uc *)dat, cp-dat);
+	cp[0] =  c->crc32        & 0xff;
+	cp[1] = (c->crc32 >>  8) & 0xff;
+	cp[2] = (c->crc32 >> 16) & 0xff;
+	cp[3] = (c->crc32 >> 24) & 0xff;
+	cp += 4;
+    }
+
+    *size = cp-dat; // actual used size
+
+    return 0;
+}
+
+
+/*
+ * Writes a container structure.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int cram_write_container(cram_fd *fd, cram_container *c) {
+    char buf_a[1024], *buf = buf_a, *cp;
+    int i;
+
+    if (55 + c->num_landmarks * 5 >= 1024)
+	buf = malloc(55 + c->num_landmarks * 5);
+    cp = buf;
+
+    if (CRAM_MAJOR_VERS(fd->version) == 1) {
+	cp += itf8_put(cp, c->length);
+    } else {
+	*(int32_t *)cp = le_int4(c->length);
+	cp += 4;
+    }
+    if (c->multi_seq) {
+	cp += itf8_put(cp, -2);
+	cp += itf8_put(cp, 0);
+	cp += itf8_put(cp, 0);
+    } else {
+	cp += itf8_put(cp, c->ref_seq_id);
+	cp += itf8_put(cp, c->ref_seq_start);
+	cp += itf8_put(cp, c->ref_seq_span);
+    }
+    cp += itf8_put(cp, c->num_records);
+    if (CRAM_MAJOR_VERS(fd->version) == 2) {
+	cp += itf8_put(cp, c->record_counter);
+	cp += ltf8_put(cp, c->num_bases);
+    } else if (CRAM_MAJOR_VERS(fd->version) >= 3) {
+	cp += ltf8_put(cp, c->record_counter);
+	cp += ltf8_put(cp, c->num_bases);
+    }
+
+    cp += itf8_put(cp, c->num_blocks);
+    cp += itf8_put(cp, c->num_landmarks);
+    for (i = 0; i < c->num_landmarks; i++)
+	cp += itf8_put(cp, c->landmark[i]);
+
+    if (CRAM_MAJOR_VERS(fd->version) >= 3) {
+	c->crc32 = crc32(0L, (uc *)buf, cp-buf);
+	cp[0] =  c->crc32        & 0xff;
+	cp[1] = (c->crc32 >>  8) & 0xff;
+	cp[2] = (c->crc32 >> 16) & 0xff;
+	cp[3] = (c->crc32 >> 24) & 0xff;
+	cp += 4;
+    }
+
+    if (cp-buf != hwrite(fd->fp, buf, cp-buf)) {
+	if (buf != buf_a)
+	    free(buf);
+	return -1;
+    }
+
+    if (buf != buf_a)
+	free(buf);
+
+    return 0;
+}
+
+// common component shared by cram_flush_container{,_mt}
+static int cram_flush_container2(cram_fd *fd, cram_container *c) {
+    int i, j;
+
+    if (c->curr_slice > 0 && !c->slices)
+	return -1;
+
+    //fprintf(stderr, "Writing container %d, sum %u\n", c->record_counter, sum);
+
+    /* Write the container struct itself */
+    if (0 != cram_write_container(fd, c))
+	return -1;
+
+    /* And the compression header */
+    if (0 != cram_write_block(fd, c->comp_hdr_block))
+	return -1;
+
+    /* Followed by the slice blocks */
+    for (i = 0; i < c->curr_slice; i++) {
+	cram_slice *s = c->slices[i];
+
+	if (0 != cram_write_block(fd, s->hdr_block))
+	    return -1;
+
+	for (j = 0; j < s->hdr->num_blocks; j++) {
+	    if (0 != cram_write_block(fd, s->block[j]))
+		return -1;
+	}
+    }
+
+    return hflush(fd->fp) == 0 ? 0 : -1;
+}
+
+/*
+ * Flushes a completely or partially full container to disk, writing
+ * container structure, header and blocks. This also calls the encoder
+ * functions.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int cram_flush_container(cram_fd *fd, cram_container *c) {
+    /* Encode the container blocks and generate compression header */
+    if (0 != cram_encode_container(fd, c))
+	return -1;
+
+    return cram_flush_container2(fd, c);
+}
+
+typedef struct {
+    cram_fd *fd;
+    cram_container *c;
+} cram_job;
+
+void *cram_flush_thread(void *arg) {
+    cram_job *j = (cram_job *)arg;
+
+    /* Encode the container blocks and generate compression header */
+    if (0 != cram_encode_container(j->fd, j->c)) {
+	fprintf(stderr, "cram_encode_container failed\n");
+	return NULL;
+    }
+
+    return arg;
+}
+
+static int cram_flush_result(cram_fd *fd) {
+    int i, ret = 0;
+    t_pool_result *r;
+
+    while ((r = t_pool_next_result(fd->rqueue))) {
+	cram_job *j = (cram_job *)r->data;
+	cram_container *c;
+
+	if (!j) {
+	    t_pool_delete_result(r, 0);
+	    return -1;
+	}
+
+	fd = j->fd;
+	c = j->c;
+
+	if (0 != cram_flush_container2(fd, c))
+	    return -1;
+
+	/* Free the container */
+	for (i = 0; i < c->max_slice; i++) {
+	    cram_free_slice(c->slices[i]);
+	    c->slices[i] = NULL;
+	}
+
+	c->slice = NULL;
+	c->curr_slice = 0;
+
+	cram_free_container(c);
+
+	ret |= hflush(fd->fp) == 0 ? 0 : -1;
+
+	t_pool_delete_result(r, 1);
+    }
+
+    return ret;
+}
+
+int cram_flush_container_mt(cram_fd *fd, cram_container *c) {
+    cram_job *j;
+
+    if (!fd->pool)
+	return cram_flush_container(fd, c);
+
+    if (!(j = malloc(sizeof(*j))))
+	return -1;
+    j->fd = fd;
+    j->c = c;
+    
+    t_pool_dispatch(fd->pool, fd->rqueue, cram_flush_thread, j);
+
+    return cram_flush_result(fd);
+}
+
+/* ----------------------------------------------------------------------
+ * Compression headers; the first part of the container
+ */
+
+/*
+ * Creates a new blank container compression header
+ *
+ * Returns header ptr on success
+ *         NULL on failure
+ */
+cram_block_compression_hdr *cram_new_compression_header(void) {
+    cram_block_compression_hdr *hdr = calloc(1, sizeof(*hdr));
+    if (!hdr)
+	return NULL;
+
+    if (!(hdr->TD_blk = cram_new_block(CORE, 0))) {
+	free(hdr);
+	return NULL;
+    }
+
+    if (!(hdr->TD_hash = kh_init(m_s2i))) {
+	cram_free_block(hdr->TD_blk);
+	free(hdr);
+	return NULL;
+    }
+
+    if (!(hdr->TD_keys = string_pool_create(8192))) {
+	kh_destroy(m_s2i, hdr->TD_hash);
+	cram_free_block(hdr->TD_blk);
+	free(hdr);
+	return NULL;
+    }
+
+    return hdr;
+}
+
+void cram_free_compression_header(cram_block_compression_hdr *hdr) {
+    int i;
+
+    if (hdr->landmark)
+	free(hdr->landmark);
+
+    if (hdr->preservation_map)
+	kh_destroy(map, hdr->preservation_map);
+
+    for (i = 0; i < CRAM_MAP_HASH; i++) {
+	cram_map *m, *m2;
+	for (m = hdr->rec_encoding_map[i]; m; m = m2) {
+	    m2 = m->next;
+	    if (m->codec)
+		m->codec->free(m->codec);
+	    free(m);
+	}
+    }
+
+    for (i = 0; i < CRAM_MAP_HASH; i++) {
+	cram_map *m, *m2;
+	for (m = hdr->tag_encoding_map[i]; m; m = m2) {
+	    m2 = m->next;
+	    if (m->codec)
+		m->codec->free(m->codec);
+	    free(m);
+	}
+    }
+
+    for (i = 0; i < DS_END; i++) {
+	if (hdr->codecs[i])
+	    hdr->codecs[i]->free(hdr->codecs[i]);
+    }
+
+    if (hdr->TL)
+	free(hdr->TL);
+    if (hdr->TD_blk)
+	cram_free_block(hdr->TD_blk);
+    if (hdr->TD_hash)
+	kh_destroy(m_s2i, hdr->TD_hash);
+    if (hdr->TD_keys)
+	string_pool_destroy(hdr->TD_keys);
+
+    free(hdr);
+}
+
+
+/* ----------------------------------------------------------------------
+ * Slices and slice headers
+ */
+
+void cram_free_slice_header(cram_block_slice_hdr *hdr) {
+    if (!hdr)
+	return;
+
+    if (hdr->block_content_ids)
+	free(hdr->block_content_ids);
+
+    free(hdr);
+
+    return;
+}
+
+void cram_free_slice(cram_slice *s) {
+    if (!s)
+	return;
+
+    if (s->hdr_block)
+	cram_free_block(s->hdr_block);
+
+    if (s->block) {
+	int i;
+
+	if (s->hdr) {
+	    for (i = 0; i < s->hdr->num_blocks; i++) {
+		cram_free_block(s->block[i]);
+	    }
+	}
+	free(s->block);
+    }
+
+    if (s->block_by_id)
+	free(s->block_by_id);
+
+    if (s->hdr)
+	cram_free_slice_header(s->hdr);
+
+    if (s->seqs_blk)
+	cram_free_block(s->seqs_blk);
+
+    if (s->qual_blk)
+	cram_free_block(s->qual_blk);
+
+    if (s->name_blk)
+	cram_free_block(s->name_blk);
+
+    if (s->aux_blk)
+	cram_free_block(s->aux_blk);
+
+    if (s->aux_OQ_blk)
+	cram_free_block(s->aux_OQ_blk);
+
+    if (s->aux_BQ_blk)
+	cram_free_block(s->aux_BQ_blk);
+
+    if (s->aux_FZ_blk)
+	cram_free_block(s->aux_FZ_blk);
+
+    if (s->aux_oq_blk)
+	cram_free_block(s->aux_oq_blk);
+
+    if (s->aux_os_blk)
+	cram_free_block(s->aux_os_blk);
+
+    if (s->aux_oz_blk)
+	cram_free_block(s->aux_oz_blk);
+
+    if (s->base_blk)
+	cram_free_block(s->base_blk);
+
+    if (s->soft_blk)
+	cram_free_block(s->soft_blk);
+
+    if (s->cigar)
+	free(s->cigar);
+
+    if (s->crecs)
+	free(s->crecs);
+
+    if (s->features)
+	free(s->features);
+
+    if (s->TN)
+	free(s->TN);
+
+    if (s->pair_keys)
+	string_pool_destroy(s->pair_keys);
+
+    if (s->pair[0])
+	kh_destroy(m_s2i, s->pair[0]);
+    if (s->pair[1])
+	kh_destroy(m_s2i, s->pair[1]);
+
+    free(s);
+}
+
+/*
+ * Creates a new empty slice in memory, for subsequent writing to
+ * disk.
+ *
+ * Returns cram_slice ptr on success
+ *         NULL on failure
+ */
+cram_slice *cram_new_slice(enum cram_content_type type, int nrecs) {
+    cram_slice *s = calloc(1, sizeof(*s));
+    if (!s)
+	return NULL;
+
+    if (!(s->hdr = (cram_block_slice_hdr *)calloc(1, sizeof(*s->hdr))))
+	goto err;
+    s->hdr->content_type = type;
+
+    s->hdr_block = NULL;
+    s->block = NULL;
+    s->block_by_id = NULL;
+    s->last_apos = 0;
+    if (!(s->crecs = malloc(nrecs * sizeof(cram_record))))  goto err;
+    s->cigar = NULL;
+    s->cigar_alloc = 0;
+    s->ncigar = 0;
+
+    if (!(s->seqs_blk = cram_new_block(EXTERNAL, 0)))       goto err;
+    if (!(s->qual_blk = cram_new_block(EXTERNAL, DS_QS)))   goto err;
+    if (!(s->name_blk = cram_new_block(EXTERNAL, DS_RN)))   goto err;
+    if (!(s->aux_blk  = cram_new_block(EXTERNAL, DS_aux)))  goto err;
+    if (!(s->base_blk = cram_new_block(EXTERNAL, DS_IN)))   goto err;
+    if (!(s->soft_blk = cram_new_block(EXTERNAL, DS_SC)))   goto err;
+
+    s->features = NULL;
+    s->nfeatures = s->afeatures = 0;
+
+#ifndef TN_external
+    s->TN = NULL;
+    s->nTN = s->aTN = 0;
+#endif
+
+    // Volatile keys as we do realloc in dstring
+    if (!(s->pair_keys = string_pool_create(8192))) goto err;
+    if (!(s->pair[0] = kh_init(m_s2i)))             goto err;
+    if (!(s->pair[1] = kh_init(m_s2i)))             goto err;
+    
+#ifdef BA_external
+    s->BA_len = 0;
+#endif
+
+    return s;
+
+ err:
+    if (s)
+	cram_free_slice(s);
+
+    return NULL;
+}
+
+/*
+ * Loads an entire slice.
+ * FIXME: In 1.0 the native unit of slices within CRAM is broken
+ * as slices contain references to objects in other slices.
+ * To work around this while keeping the slice oriented outer loop
+ * we read all slices and stitch them together into a fake large
+ * slice instead.
+ *
+ * Returns cram_slice ptr on success
+ *         NULL on failure
+ */
+cram_slice *cram_read_slice(cram_fd *fd) {
+    cram_block *b = cram_read_block(fd);
+    cram_slice *s = calloc(1, sizeof(*s));
+    int i, n, max_id, min_id;
+
+    if (!b || !s)
+	goto err;
+
+    s->hdr_block = b;
+    switch (b->content_type) {
+    case MAPPED_SLICE:
+    case UNMAPPED_SLICE:
+	if (!(s->hdr = cram_decode_slice_header(fd, b)))
+	    goto err;
+	break;
+
+    default:
+	fprintf(stderr, "Unexpected block of type %s\n",
+		cram_content_type2str(b->content_type));
+	goto err;
+    }
+
+    if (s->hdr->num_blocks < 1) {
+        fprintf(stderr, "Slice does not include any data blocks.\n");
+	goto err;
+    }
+
+    s->block = calloc(n = s->hdr->num_blocks, sizeof(*s->block));
+    if (!s->block)
+	goto err;
+
+    for (max_id = i = 0, min_id = INT_MAX; i < n; i++) {
+	if (!(s->block[i] = cram_read_block(fd)))
+	    goto err;
+
+	if (s->block[i]->content_type == EXTERNAL) {
+	    if (max_id < s->block[i]->content_id)
+		max_id = s->block[i]->content_id;
+	    if (min_id > s->block[i]->content_id)
+		min_id = s->block[i]->content_id;
+	}
+    }
+    if (min_id >= 0 && max_id < 1024) {
+	if (!(s->block_by_id = calloc(1024, sizeof(s->block[0]))))
+	    goto err;
+
+	for (i = 0; i < n; i++) {
+	    if (s->block[i]->content_type != EXTERNAL)
+		continue;
+	    s->block_by_id[s->block[i]->content_id] = s->block[i];
+	}
+    }
+
+    /* Initialise encoding/decoding tables */
+    s->cigar = NULL;
+    s->cigar_alloc = 0;
+    s->ncigar = 0;
+
+    if (!(s->seqs_blk = cram_new_block(EXTERNAL, 0)))      goto err;
+    if (!(s->qual_blk = cram_new_block(EXTERNAL, DS_QS)))  goto err;
+    if (!(s->name_blk = cram_new_block(EXTERNAL, DS_RN)))  goto err;
+    if (!(s->aux_blk  = cram_new_block(EXTERNAL, DS_aux))) goto err;
+    if (!(s->base_blk = cram_new_block(EXTERNAL, DS_IN)))  goto err;
+    if (!(s->soft_blk = cram_new_block(EXTERNAL, DS_SC)))  goto err;
+
+    s->crecs = NULL;
+
+    s->last_apos = s->hdr->ref_seq_start;
+    
+    return s;
+
+ err:
+    if (b)
+	cram_free_block(b);
+    if (s) {
+	s->hdr_block = NULL;
+	cram_free_slice(s);
+    }
+    return NULL;
+}
+
+
+/* ----------------------------------------------------------------------
+ * CRAM file definition (header)
+ */
+
+/*
+ * Reads a CRAM file definition structure.
+ * Returns file_def ptr on success
+ *         NULL on failure
+ */
+cram_file_def *cram_read_file_def(cram_fd *fd) {
+    cram_file_def *def = malloc(sizeof(*def));
+    if (!def)
+	return NULL;
+
+    if (26 != hread(fd->fp, &def->magic[0], 26)) {
+	free(def);
+	return NULL;
+    }
+
+    if (memcmp(def->magic, "CRAM", 4) != 0) {
+	free(def);
+	return NULL;
+    }
+
+    if (def->major_version > 3) {
+	fprintf(stderr, "CRAM version number mismatch\n"
+		"Expected 1.x, 2.x or 3.x, got %d.%d\n",
+		def->major_version, def->minor_version);
+	free(def);
+	return NULL;
+    }
+
+    fd->first_container += 26;
+    fd->last_slice = 0;
+
+    return def;
+}
+
+/*
+ * Writes a cram_file_def structure to cram_fd.
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int cram_write_file_def(cram_fd *fd, cram_file_def *def) {
+    return (hwrite(fd->fp, &def->magic[0], 26) == 26) ? 0 : -1;
+}
+
+void cram_free_file_def(cram_file_def *def) {
+    if (def) free(def);
+}
+
+/* ----------------------------------------------------------------------
+ * SAM header I/O
+ */
+
+
+/*
+ * Reads the SAM header from the first CRAM data block.
+ * Also performs minimal parsing to extract read-group
+ * and sample information.
+
+ * Returns SAM hdr ptr on success
+ *         NULL on failure
+ */
+SAM_hdr *cram_read_SAM_hdr(cram_fd *fd) {
+    int32_t header_len;
+    char *header;
+    SAM_hdr *hdr;
+
+    /* 1.1 onwards stores the header in the first block of a container */
+    if (CRAM_MAJOR_VERS(fd->version) == 1) {
+	/* Length */
+	if (-1 == int32_decode(fd, &header_len))
+	    return NULL;
+
+	/* Alloc and read */
+	if (header_len < 0 || NULL == (header = malloc((size_t) header_len+1)))
+	    return NULL;
+
+	if (header_len != hread(fd->fp, header, header_len))
+	    return NULL;
+	header[header_len] = '\0';
+
+	fd->first_container += 4 + header_len;
+    } else {
+	cram_container *c = cram_read_container(fd);
+	cram_block *b;
+	int i, len;
+
+	if (!c)
+	    return NULL;
+
+	if (c->num_blocks < 1) {
+	    cram_free_container(c);
+	    return NULL;
+	}
+
+	if (!(b = cram_read_block(fd))) {
+	    cram_free_container(c);
+	    return NULL;
+	}
+	if (cram_uncompress_block(b) != 0) {
+	    cram_free_container(c);
+	    return NULL;
+	}
+
+	len = b->comp_size + 2 + 4*(CRAM_MAJOR_VERS(fd->version) >= 3) +
+	    itf8_size(b->content_id) + 
+	    itf8_size(b->uncomp_size) + 
+	    itf8_size(b->comp_size);
+
+	/* Extract header from 1st block */
+	if (-1 == int32_get_blk(b, &header_len) ||
+            header_len < 0 || /* Spec. says signed...  why? */
+	    b->uncomp_size - 4 < header_len) {
+	    cram_free_container(c);
+	    cram_free_block(b);
+	    return NULL;
+	}
+	if (NULL == (header = malloc((size_t) header_len+1))) {
+	    cram_free_container(c);
+	    cram_free_block(b);
+	    return NULL;
+	}
+	memcpy(header, BLOCK_END(b), header_len);
+	header[header_len]='\0';
+	cram_free_block(b);
+
+	/* Consume any remaining blocks */
+	for (i = 1; i < c->num_blocks; i++) {
+	    if (!(b = cram_read_block(fd))) {
+		cram_free_container(c);
+		return NULL;
+	    }
+	    len += b->comp_size + 2 + 4*(CRAM_MAJOR_VERS(fd->version) >= 3) +
+		itf8_size(b->content_id) + 
+		itf8_size(b->uncomp_size) + 
+		itf8_size(b->comp_size);
+	    cram_free_block(b);
+	}
+
+	if (c->length > 0 && len > 0 && c->length > len) {
+	    // Consume padding
+	    char *pads = malloc(c->length - len);
+	    if (!pads) {
+		cram_free_container(c);
+		return NULL;
+	    }
+
+	    if (c->length - len != hread(fd->fp, pads, c->length - len)) {
+		cram_free_container(c);
+		return NULL;
+	    }
+	    free(pads);
+	}
+
+	cram_free_container(c);
+    }
+
+    /* Parse */
+    hdr = sam_hdr_parse_(header, header_len);
+    free(header);
+
+    return hdr;
+}
+
+/*
+ * Converts 'in' to a full pathname to store in out.
+ * Out must be at least PATH_MAX bytes long.
+ */
+static void full_path(char *out, char *in) {
+    if (*in == '/') {
+	strncpy(out, in, PATH_MAX);
+	out[PATH_MAX-1] = 0;
+    } else {
+	int len;
+
+	// unable to get dir or out+in is too long
+	if (!getcwd(out, PATH_MAX) ||
+	    (len = strlen(out))+1+strlen(in) >= PATH_MAX) {
+	    strncpy(out, in, PATH_MAX);
+	    out[PATH_MAX-1] = 0;
+	    return;
+	}
+
+	sprintf(out+len, "/%.*s", PATH_MAX - len, in);
+
+	// FIXME: cope with `pwd`/../../../foo.fa ?
+    }
+}
+
+/*
+ * Writes a CRAM SAM header.
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int cram_write_SAM_hdr(cram_fd *fd, SAM_hdr *hdr) {
+    int header_len;
+    int blank_block = (CRAM_MAJOR_VERS(fd->version) >= 3);
+
+    /* Write CRAM MAGIC if not yet written. */
+    if (fd->file_def->major_version == 0) {
+	fd->file_def->major_version = CRAM_MAJOR_VERS(fd->version);
+	fd->file_def->minor_version = CRAM_MINOR_VERS(fd->version);
+	if (0 != cram_write_file_def(fd, fd->file_def))
+	    return -1;
+    }
+
+    /* 1.0 requires an UNKNOWN read-group */
+    if (CRAM_MAJOR_VERS(fd->version) == 1) {
+	if (!sam_hdr_find_rg(hdr, "UNKNOWN"))
+	    if (sam_hdr_add(hdr, "RG",
+			    "ID", "UNKNOWN", "SM", "UNKNOWN", NULL))
+		return -1;
+    }
+
+    /* Fix M5 strings */
+    if (fd->refs && !fd->no_ref) {
+	int i;
+	for (i = 0; i < hdr->nref; i++) {
+	    SAM_hdr_type *ty;
+	    char *ref;
+
+	    if (!(ty = sam_hdr_find(hdr, "SQ", "SN", hdr->ref[i].name)))
+		return -1;
+
+	    if (!sam_hdr_find_key(hdr, ty, "M5", NULL)) {
+		char unsigned buf[16];
+		char buf2[33];
+		int rlen;
+		hts_md5_context *md5;
+
+		if (!fd->refs ||
+		    !fd->refs->ref_id ||
+		    !fd->refs->ref_id[i]) {
+		    return -1;
+		}
+		rlen = fd->refs->ref_id[i]->length;
+		if (!(md5 = hts_md5_init()))
+		    return -1;
+		ref = cram_get_ref(fd, i, 1, rlen);
+		if (NULL == ref) return -1;
+		rlen = fd->refs->ref_id[i]->length; /* In case it just loaded */
+		hts_md5_update(md5, ref, rlen);
+		hts_md5_final(buf, md5);
+		hts_md5_destroy(md5);
+		cram_ref_decr(fd->refs, i);
+
+		hts_md5_hex(buf2, buf);
+		if (sam_hdr_update(hdr, ty, "M5", buf2, NULL))
+		    return -1;
+	    }
+
+	    if (fd->ref_fn) {
+		char ref_fn[PATH_MAX];
+		full_path(ref_fn, fd->ref_fn);
+		if (sam_hdr_update(hdr, ty, "UR", ref_fn, NULL))
+		    return -1;
+	    }
+	}
+    }
+
+    if (sam_hdr_rebuild(hdr))
+	return -1;
+
+    /* Length */
+    header_len = sam_hdr_length(hdr);
+    if (CRAM_MAJOR_VERS(fd->version) == 1) {
+	if (-1 == int32_encode(fd, header_len))
+	    return -1;
+
+	/* Text data */
+	if (header_len != hwrite(fd->fp, sam_hdr_str(hdr), header_len))
+	    return -1;
+    } else {
+	/* Create block(s) inside a container */
+	cram_block *b = cram_new_block(FILE_HEADER, 0);
+	cram_container *c = cram_new_container(0, 0);
+	int padded_length;
+	char *pads;
+	int is_cram_3 = (CRAM_MAJOR_VERS(fd->version) >= 3);
+
+	if (!b || !c) {
+	    if (b) cram_free_block(b);
+	    if (c) cram_free_container(c);
+	    return -1;
+	}
+
+	int32_put_blk(b, header_len);
+	BLOCK_APPEND(b, sam_hdr_str(hdr), header_len);
+	BLOCK_UPLEN(b);
+
+	// Compress header block if V3.0 and above
+	if (CRAM_MAJOR_VERS(fd->version) >= 3)
+	    cram_compress_block(fd, b, NULL, -1, -1);
+
+	if (blank_block) {
+	    c->length = b->comp_size + 2 + 4*is_cram_3 +
+		itf8_size(b->content_id)   + 
+		itf8_size(b->uncomp_size)  +
+		itf8_size(b->comp_size);
+
+	    c->num_blocks = 2;
+	    c->num_landmarks = 2;
+	    if (!(c->landmark = malloc(2*sizeof(*c->landmark)))) {
+		cram_free_block(b);
+		cram_free_container(c);
+		return -1;
+	    }
+	    c->landmark[0] = 0;
+	    c->landmark[1] = c->length;
+
+	    // Plus extra storage for uncompressed secondary blank block
+	    padded_length = MIN(c->length*.5, 10000);
+	    c->length += padded_length + 2 + 4*is_cram_3 +
+		itf8_size(b->content_id) + 
+		itf8_size(padded_length)*2;
+	} else {
+	    // Pad the block instead.
+	    c->num_blocks = 1;
+	    c->num_landmarks = 1;
+	    if (!(c->landmark = malloc(sizeof(*c->landmark))))
+		return -1;
+	    c->landmark[0] = 0;
+
+	    padded_length = MAX(c->length*1.5, 10000) - c->length;
+
+	    c->length = b->comp_size + padded_length +
+		2 + 4*is_cram_3 +
+		itf8_size(b->content_id)   + 
+		itf8_size(b->uncomp_size)  +
+		itf8_size(b->comp_size);
+
+	    if (NULL == (pads = calloc(1, padded_length))) {
+		cram_free_block(b);
+		cram_free_container(c);
+		return -1;
+	    }
+	    BLOCK_APPEND(b, pads, padded_length);
+	    BLOCK_UPLEN(b);
+	    free(pads);
+	}
+
+	if (-1 == cram_write_container(fd, c)) {
+	    cram_free_block(b);
+	    cram_free_container(c);
+	    return -1;
+	}
+
+	if (-1 == cram_write_block(fd, b)) {
+	    cram_free_block(b);
+	    cram_free_container(c);
+	    return -1;
+	}
+
+	if (blank_block) {
+	    BLOCK_RESIZE(b, padded_length);
+	    memset(BLOCK_DATA(b), 0, padded_length);
+	    BLOCK_SIZE(b) = padded_length;
+	    BLOCK_UPLEN(b);
+	    b->method = RAW;
+	    if (-1 == cram_write_block(fd, b)) {
+		cram_free_block(b);
+		cram_free_container(c);
+		return -1;
+	    }
+	}
+
+	cram_free_block(b);
+	cram_free_container(c);
+    }
+
+    if (-1 == refs_from_header(fd->refs, fd, fd->header))
+	return -1;
+    if (-1 == refs2id(fd->refs, fd->header))
+	return -1;
+
+    if (0 != hflush(fd->fp))
+	return -1;
+
+    RP("=== Finishing saving header ===\n");
+
+    return 0;
+}
+
+/* ----------------------------------------------------------------------
+ * The top-level cram opening, closing and option handling
+ */
+
+/*
+ * Initialises the lookup tables. These could be global statics, but they're
+ * clumsy to setup in a multi-threaded environment unless we generate
+ * verbatim code and include that.
+ */
+static void cram_init_tables(cram_fd *fd) {
+    int i;
+
+    memset(fd->L1, 4, 256);
+    fd->L1['A'] = 0; fd->L1['a'] = 0;
+    fd->L1['C'] = 1; fd->L1['c'] = 1;
+    fd->L1['G'] = 2; fd->L1['g'] = 2;
+    fd->L1['T'] = 3; fd->L1['t'] = 3;
+
+    memset(fd->L2, 5, 256);
+    fd->L2['A'] = 0; fd->L2['a'] = 0;
+    fd->L2['C'] = 1; fd->L2['c'] = 1;
+    fd->L2['G'] = 2; fd->L2['g'] = 2;
+    fd->L2['T'] = 3; fd->L2['t'] = 3;
+    fd->L2['N'] = 4; fd->L2['n'] = 4;
+
+    if (CRAM_MAJOR_VERS(fd->version) == 1) {
+	for (i = 0; i < 0x200; i++) {
+	    int f = 0;
+
+	    if (i & CRAM_FPAIRED)      f |= BAM_FPAIRED;
+	    if (i & CRAM_FPROPER_PAIR) f |= BAM_FPROPER_PAIR;
+	    if (i & CRAM_FUNMAP)       f |= BAM_FUNMAP;
+	    if (i & CRAM_FREVERSE)     f |= BAM_FREVERSE;
+	    if (i & CRAM_FREAD1)       f |= BAM_FREAD1;
+	    if (i & CRAM_FREAD2)       f |= BAM_FREAD2;
+	    if (i & CRAM_FSECONDARY)   f |= BAM_FSECONDARY;
+	    if (i & CRAM_FQCFAIL)      f |= BAM_FQCFAIL;
+	    if (i & CRAM_FDUP)         f |= BAM_FDUP;
+
+	    fd->bam_flag_swap[i]  = f;
+	}
+    
+	for (i = 0; i < 0x1000; i++) {
+	    int g = 0;
+
+	    if (i & BAM_FPAIRED)	   g |= CRAM_FPAIRED;
+	    if (i & BAM_FPROPER_PAIR)  g |= CRAM_FPROPER_PAIR;
+	    if (i & BAM_FUNMAP)        g |= CRAM_FUNMAP;
+	    if (i & BAM_FREVERSE)      g |= CRAM_FREVERSE;
+	    if (i & BAM_FREAD1)        g |= CRAM_FREAD1;
+	    if (i & BAM_FREAD2)        g |= CRAM_FREAD2;
+	    if (i & BAM_FSECONDARY)    g |= CRAM_FSECONDARY;
+	    if (i & BAM_FQCFAIL)       g |= CRAM_FQCFAIL;
+	    if (i & BAM_FDUP)          g |= CRAM_FDUP;
+
+	    fd->cram_flag_swap[i] = g;
+	}
+    } else {
+	/* NOP */
+	for (i = 0; i < 0x1000; i++)
+	    fd->bam_flag_swap[i] = i;
+	for (i = 0; i < 0x1000; i++)
+	    fd->cram_flag_swap[i] = i;
+    }
+
+    memset(fd->cram_sub_matrix, 4, 32*32);
+    for (i = 0; i < 32; i++) {
+	fd->cram_sub_matrix[i]['A'&0x1f]=0;
+	fd->cram_sub_matrix[i]['C'&0x1f]=1;
+	fd->cram_sub_matrix[i]['G'&0x1f]=2;
+	fd->cram_sub_matrix[i]['T'&0x1f]=3;
+	fd->cram_sub_matrix[i]['N'&0x1f]=4;
+    }
+    for (i = 0; i < 20; i+=4) {
+	int j;
+	for (j = 0; j < 20; j++) {
+	    fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j]=3;
+	    fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j]=3;
+	    fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j]=3;
+	    fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j]=3;
+	}
+	fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][CRAM_SUBST_MATRIX[i+0]&0x1f]=0;
+	fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][CRAM_SUBST_MATRIX[i+1]&0x1f]=1;
+	fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][CRAM_SUBST_MATRIX[i+2]&0x1f]=2;
+	fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][CRAM_SUBST_MATRIX[i+3]&0x1f]=3;
+    }
+}
+
+// Default version numbers for CRAM
+static int major_version = 3;
+static int minor_version = 0;
+
+/*
+ * Opens a CRAM file for read (mode "rb") or write ("wb").
+ * The filename may be "-" to indicate stdin or stdout.
+ *
+ * Returns file handle on success
+ *         NULL on failure.
+ */
+cram_fd *cram_open(const char *filename, const char *mode) {
+    hFILE *fp;
+    cram_fd *fd;
+    char fmode[3]= { mode[0], '\0', '\0' };
+
+    if (strlen(mode) > 1 && (mode[1] == 'b' || mode[1] == 'c')) {
+	fmode[1] = 'b';
+    }
+
+    fp = hopen(filename, fmode);
+    if (!fp)
+	return NULL;
+
+    fd = cram_dopen(fp, filename, mode);
+    if (!fd)
+	hclose_abruptly(fp);
+
+    return fd;
+}
+
+/* Opens an existing stream for reading or writing.
+ *
+ * Returns file handle on success;
+ *         NULL on failure.
+ */
+cram_fd *cram_dopen(hFILE *fp, const char *filename, const char *mode) {
+    int i;
+    char *cp;
+    cram_fd *fd = calloc(1, sizeof(*fd));
+    if (!fd)
+	return NULL;
+
+    fd->level = 5;
+    for (i = 0; mode[i]; i++) {
+	if (mode[i] >= '0' && mode[i] <= '9') {
+	    fd->level = mode[i] - '0';
+	    break;
+	}
+    }
+
+    fd->fp = fp;
+    fd->mode = *mode;
+    fd->first_container = 0;
+
+    if (fd->mode == 'r') {
+	/* Reader */
+
+	if (!(fd->file_def = cram_read_file_def(fd)))
+	    goto err;
+
+	fd->version = fd->file_def->major_version * 256 +
+	    fd->file_def->minor_version;
+
+	if (!(fd->header = cram_read_SAM_hdr(fd)))
+	    goto err;
+
+    } else {
+	/* Writer */
+	cram_file_def *def = calloc(1, sizeof(*def));
+	if (!def)
+	    return NULL;
+
+	fd->file_def = def;
+
+	def->magic[0] = 'C';
+	def->magic[1] = 'R';
+	def->magic[2] = 'A';
+	def->magic[3] = 'M';
+	def->major_version = 0; // Indicator to write file def later.
+	def->minor_version = 0;
+	memset(def->file_id, 0, 20);
+	strncpy(def->file_id, filename, 20);
+
+	fd->version = major_version * 256 + minor_version;
+
+	/* SAM header written later along with this file_def */
+    }
+
+    cram_init_tables(fd);
+
+    fd->prefix = strdup((cp = strrchr(filename, '/')) ? cp+1 : filename);
+    if (!fd->prefix)
+	goto err;
+    fd->first_base = fd->last_base = -1;
+    fd->record_counter = 0;
+
+    fd->ctr = NULL;
+    fd->refs  = refs_create();
+    if (!fd->refs)
+	goto err;
+    fd->ref_id = -2;
+    fd->ref = NULL;
+
+    fd->decode_md = 0;
+    fd->verbose = 0;
+    fd->seqs_per_slice = SEQS_PER_SLICE;
+    fd->slices_per_container = SLICE_PER_CNT;
+    fd->embed_ref = 0;
+    fd->no_ref = 0;
+    fd->ignore_md5 = 0;
+    fd->use_bz2 = 0;
+    fd->use_rans = (CRAM_MAJOR_VERS(fd->version) >= 3);
+    fd->use_lzma = 0;
+    fd->multi_seq = -1;
+    fd->unsorted   = 0;
+    fd->shared_ref = 0;
+
+    fd->index       = NULL;
+    fd->own_pool    = 0;
+    fd->pool        = NULL;
+    fd->rqueue      = NULL;
+    fd->job_pending = NULL;
+    fd->ooc         = 0;
+    fd->required_fields = INT_MAX;
+
+    for (i = 0; i < DS_END; i++)
+	fd->m[i] = cram_new_metrics();
+
+    fd->range.refid = -2; // no ref.
+    fd->eof = 1;          // See samtools issue #150
+    fd->ref_fn = NULL;
+
+    fd->bl = NULL;
+
+    /* Initialise dummy refs from the @SQ headers */
+    if (-1 == refs_from_header(fd->refs, fd, fd->header))
+	goto err;
+
+    return fd;
+
+ err:
+    if (fd)
+	free(fd);
+
+    return NULL;
+}
+
+/*
+ * Seek within a CRAM file.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int cram_seek(cram_fd *fd, off_t offset, int whence) {
+    char buf[65536];
+
+    fd->ooc = 0;
+
+    if (hseek(fd->fp, offset, whence) >= 0)
+	return 0;
+
+    if (!(whence == SEEK_CUR && offset >= 0))
+	return -1;
+
+    /* Couldn't fseek, but we're in SEEK_CUR mode so read instead */
+    while (offset > 0) {
+	int len = MIN(65536, offset);
+	if (len != hread(fd->fp, buf, len))
+	    return -1;
+	offset -= len;
+    }
+
+    return 0;
+}
+
+/*
+ * Flushes a CRAM file.
+ * Useful for when writing to stdout without wishing to close the stream.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int cram_flush(cram_fd *fd) {
+    if (!fd)
+	return -1;
+
+    if (fd->mode == 'w' && fd->ctr) {
+	if(fd->ctr->slice)
+	    fd->ctr->curr_slice++;
+	if (-1 == cram_flush_container_mt(fd, fd->ctr))
+	    return -1;
+    }
+
+    return 0;
+}
+
+/*
+ * Closes a CRAM file.
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int cram_close(cram_fd *fd) {
+    spare_bams *bl, *next;
+    int i;
+	
+    if (!fd)
+	return -1;
+
+    if (fd->mode == 'w' && fd->ctr) {
+	if(fd->ctr->slice)
+	    fd->ctr->curr_slice++;
+	if (-1 == cram_flush_container_mt(fd, fd->ctr))
+	    return -1;
+    }
+
+    if (fd->pool && fd->eof >= 0) {
+	t_pool_flush(fd->pool);
+
+	if (0 != cram_flush_result(fd))
+	    return -1;
+
+	pthread_mutex_destroy(&fd->metrics_lock);
+	pthread_mutex_destroy(&fd->ref_lock);
+	pthread_mutex_destroy(&fd->bam_list_lock);
+
+	fd->ctr = NULL; // prevent double freeing
+
+	//fprintf(stderr, "CRAM: destroy queue %p\n", fd->rqueue);
+
+	t_results_queue_destroy(fd->rqueue);
+    }
+
+    if (fd->mode == 'w') {
+	/* Write EOF block */
+	if (CRAM_MAJOR_VERS(fd->version) == 3) {
+	    if (38 != hwrite(fd->fp,
+			     "\x0f\x00\x00\x00\xff\xff\xff\xff" // Cont HDR
+			     "\x0f\xe0\x45\x4f\x46\x00\x00\x00" // Cont HDR
+			     "\x00\x01\x00"                     // Cont HDR
+			     "\x05\xbd\xd9\x4f"                 // CRC32
+			     "\x00\x01\x00\x06\x06"             // Comp.HDR blk
+			     "\x01\x00\x01\x00\x01\x00"         // Comp.HDR blk
+			     "\xee\x63\x01\x4b",                // CRC32
+			     38))
+		return -1;
+	} else {
+	    if (30 != hwrite(fd->fp,
+			     "\x0b\x00\x00\x00\xff\xff\xff\xff"
+			     "\x0f\xe0\x45\x4f\x46\x00\x00\x00"
+			     "\x00\x01\x00\x00\x01\x00\x06\x06"
+			     "\x01\x00\x01\x00\x01\x00", 30))
+		return -1;
+	}
+    }
+
+    for (bl = fd->bl; bl; bl = next) {
+	int i, max_rec = fd->seqs_per_slice * fd->slices_per_container;
+
+	next = bl->next;
+	for (i = 0; i < max_rec; i++) {
+	    if (bl->bams[i])
+		bam_free(bl->bams[i]);
+	}
+	free(bl->bams);
+	free(bl);
+    }
+
+    if (hclose(fd->fp) != 0)
+	return -1;
+
+    if (fd->file_def)
+	cram_free_file_def(fd->file_def);
+
+    if (fd->header)
+	sam_hdr_free(fd->header);
+
+    free(fd->prefix);
+
+    if (fd->ctr)
+	cram_free_container(fd->ctr);
+
+    if (fd->refs)
+	refs_free(fd->refs);
+    if (fd->ref_free)
+        free(fd->ref_free);
+
+    for (i = 0; i < DS_END; i++)
+	if (fd->m[i])
+	    free(fd->m[i]);
+
+    if (fd->index)
+	cram_index_free(fd);
+
+    if (fd->own_pool && fd->pool)
+	t_pool_destroy(fd->pool, 0);
+
+    free(fd);
+    return 0;
+}
+
+/*
+ * Returns 1 if we hit an EOF while reading.
+ */
+int cram_eof(cram_fd *fd) {
+    return fd->eof;
+}
+
+
+/* 
+ * Sets options on the cram_fd. See CRAM_OPT_* definitions in cram_structs.h.
+ * Use this immediately after opening.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int cram_set_option(cram_fd *fd, enum hts_fmt_option opt, ...) {
+    int r;
+    va_list args;
+
+    va_start(args, opt);
+    r = cram_set_voption(fd, opt, args);
+    va_end(args);
+
+    return r;
+}
+
+/*
+ * Sets options on the cram_fd. See CRAM_OPT_* definitions in cram_structs.h.
+ * Use this immediately after opening.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int cram_set_voption(cram_fd *fd, enum hts_fmt_option opt, va_list args) {
+    refs_t *refs;
+
+    if (!fd) {
+	errno = EBADF;
+	return -1;
+    }
+
+    switch (opt) {
+    case CRAM_OPT_DECODE_MD:
+	fd->decode_md = va_arg(args, int);
+	break;
+
+    case CRAM_OPT_PREFIX:
+	if (fd->prefix)
+	    free(fd->prefix);
+	if (!(fd->prefix = strdup(va_arg(args, char *))))
+	    return -1;
+	break;
+
+    case CRAM_OPT_VERBOSITY:
+	fd->verbose = va_arg(args, int);
+	break;
+
+    case CRAM_OPT_SEQS_PER_SLICE:
+	fd->seqs_per_slice = va_arg(args, int);
+	break;
+
+    case CRAM_OPT_SLICES_PER_CONTAINER:
+	fd->slices_per_container = va_arg(args, int);
+	break;
+
+    case CRAM_OPT_EMBED_REF:
+	fd->embed_ref = va_arg(args, int);
+	break;
+
+    case CRAM_OPT_NO_REF:
+	fd->no_ref = va_arg(args, int);
+	break;
+
+    case CRAM_OPT_IGNORE_MD5:
+	fd->ignore_md5 = va_arg(args, int);
+	break;
+
+    case CRAM_OPT_USE_BZIP2:
+	fd->use_bz2 = va_arg(args, int);
+	break;
+
+    case CRAM_OPT_USE_RANS:
+	fd->use_rans = va_arg(args, int);
+	break;
+
+    case CRAM_OPT_USE_LZMA:
+	fd->use_lzma = va_arg(args, int);
+	break;
+
+    case CRAM_OPT_SHARED_REF:
+	fd->shared_ref = 1;
+	refs = va_arg(args, refs_t *);
+	if (refs != fd->refs) {
+	    if (fd->refs)
+		refs_free(fd->refs);
+	    fd->refs = refs;
+	    fd->refs->count++;
+	}
+	break;
+
+    case CRAM_OPT_RANGE:
+	fd->range = *va_arg(args, cram_range *);
+	return cram_seek_to_refpos(fd, &fd->range);
+
+    case CRAM_OPT_REFERENCE:
+	return cram_load_reference(fd, va_arg(args, char *));
+
+    case CRAM_OPT_VERSION: {
+	int major, minor;
+	char *s = va_arg(args, char *);
+	if (2 != sscanf(s, "%d.%d", &major, &minor)) {
+	    fprintf(stderr, "Malformed version string %s\n", s);
+	    return -1;
+	}
+	if (!((major == 1 &&  minor == 0) ||
+	      (major == 2 && (minor == 0 || minor == 1)) ||
+	      (major == 3 &&  minor == 0))) {
+	    fprintf(stderr, "Unknown version string; "
+		    "use 1.0, 2.0, 2.1 or 3.0\n");
+	    errno = EINVAL;
+	    return -1;
+	}
+	fd->version = major*256 + minor;
+
+	if (CRAM_MAJOR_VERS(fd->version) >= 3)
+	    fd->use_rans = 1;
+	break;
+    }
+
+    case CRAM_OPT_MULTI_SEQ_PER_SLICE:
+	fd->multi_seq = va_arg(args, int);
+	break;
+
+    case CRAM_OPT_NTHREADS: {
+	int nthreads =  va_arg(args, int);
+        if (nthreads > 1) {
+            if (!(fd->pool = t_pool_init(nthreads*2, nthreads)))
+                return -1;
+
+	    fd->rqueue = t_results_queue_init();
+	    pthread_mutex_init(&fd->metrics_lock, NULL);
+	    pthread_mutex_init(&fd->ref_lock, NULL);
+	    pthread_mutex_init(&fd->bam_list_lock, NULL);
+	    fd->shared_ref = 1;
+	    fd->own_pool = 1;
+        }
+	break;
+    }
+
+    case CRAM_OPT_THREAD_POOL:
+	fd->pool = va_arg(args, t_pool *);
+	if (fd->pool) {
+	    fd->rqueue = t_results_queue_init();
+	    pthread_mutex_init(&fd->metrics_lock, NULL);
+	    pthread_mutex_init(&fd->ref_lock, NULL);
+	    pthread_mutex_init(&fd->bam_list_lock, NULL);
+	}
+	fd->shared_ref = 1; // Needed to avoid clobbering ref between threads
+	fd->own_pool = 0;
+
+	//fd->qsize = 1;
+	//fd->decoded = calloc(fd->qsize, sizeof(cram_container *));
+	//t_pool_dispatch(fd->pool, cram_decoder_thread, fd);
+	break;
+
+    case CRAM_OPT_REQUIRED_FIELDS:
+	fd->required_fields = va_arg(args, int);
+	break;
+
+    case HTS_OPT_COMPRESSION_LEVEL:
+	fd->level = va_arg(args, int);
+	break;
+
+    default:
+	fprintf(stderr, "Unknown CRAM option code %d\n", opt);
+	errno = EINVAL;
+	return -1;
+    }
+
+    return 0;
+}
diff --git a/htslib/cram/cram_io.h b/htslib/cram/cram_io.h
new file mode 100644
index 0000000..d3fe90e
--- /dev/null
+++ b/htslib/cram/cram_io.h
@@ -0,0 +1,669 @@
+/*
+Copyright (c) 2012-2014 Genome Research Ltd.
+Author: James Bonfield <jkb at sanger.ac.uk>
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+Institute nor the names of its contributors may be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+/*! \file
+ * Include cram.h instead.
+ *
+ * This is an internal part of the CRAM system and is automatically included
+ * when you #include cram.h.
+ *
+ * Implements the low level CRAM I/O primitives.
+ * This includes basic data types such as byte, int, ITF-8,
+ * maps, bitwise I/O, etc.
+ */
+
+#ifndef _CRAM_IO_H_
+#define _CRAM_IO_H_
+
+#define ITF8_MACROS
+
+#include <stdint.h>
+#include <cram/misc.h>
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/**@{ ----------------------------------------------------------------------
+ * ITF8 encoding and decoding.
+ *
+ * Also see the itf8_get and itf8_put macros.
+ */
+
+/*! INTERNAL: Converts two characters into an integer for use in switch{} */
+#define CRAM_KEY(a,b) (((a)<<8)|((b)))
+
+/*! Reads an integer in ITF-8 encoding from 'fd' and stores it in
+ * *val.
+ *
+ * @return
+ * Returns the number of bytes read on success;
+ *        -1 on failure
+ */
+int itf8_decode(cram_fd *fd, int32_t *val);
+
+#ifndef ITF8_MACROS
+/*! Reads an integer in ITF-8 encoding from 'cp' and stores it in
+ * *val.
+ *
+ * @return
+ * Returns the number of bytes read on success;
+ *        -1 on failure
+ */
+int itf8_get(char *cp, int32_t *val_p);
+
+/*! Stores a value to memory in ITF-8 format.
+ *
+ * @return
+ * Returns the number of bytes required to store the number.
+ * This is a maximum of 5 bytes.
+ */
+int itf8_put(char *cp, int32_t val);
+
+#else
+
+/*
+ * Macro implementations of the above
+ */
+#define itf8_get(c,v) (((uc)(c)[0]<0x80)?(*(v)=(uc)(c)[0],1):(((uc)(c)[0]<0xc0)?(*(v)=(((uc)(c)[0]<<8)|(uc)(c)[1])&0x3fff,2):(((uc)(c)[0]<0xe0)?(*(v)=(((uc)(c)[0]<<16)|((uc)(c)[1]<<8)|(uc)(c)[2])&0x1fffff,3):(((uc)(c)[0]<0xf0)?(*(v)=(((uc)(c)[0]<<24)|((uc)(c)[1]<<16)|((uc)(c)[2]<<8)|(uc)(c)[3])&0x0fffffff,4):(*(v)=(((uc)(c)[0]&0x0f)<<28)|((uc)(c)[1]<<20)|((uc)(c)[2]<<12)|((uc)(c)[3]<<4)|((uc)(c)[4]&0x0f),5)))))
+
+#define itf8_put(c,v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5))
+
+#define itf8_size(v) ((!((v)&~0x7f))?1:(!((v)&~0x3fff))?2:(!((v)&~0x1fffff))?3:(!((v)&~0xfffffff))?4:5)
+
+#endif
+
+int ltf8_get(char *cp, int64_t *val_p);
+int ltf8_put(char *cp, int64_t val);
+
+  /* Version of itf8_get that checks it hasn't run out of input */
+
+extern const int itf8_bytes[16];
+
+static inline int safe_itf8_get(const char *cp, const char *endp,
+                                int32_t *val_p) {
+    const unsigned char *up = (unsigned char *)cp;
+
+    if (endp - cp < 5 &&
+        (cp >= endp || endp - cp < itf8_bytes[up[0]>>4])) {
+        *val_p = 0;
+        return 0;
+    }
+
+    if (up[0] < 0x80) {
+        *val_p =   up[0];
+        return 1;
+    } else if (up[0] < 0xc0) {
+        *val_p = ((up[0] <<8) |  up[1])                           & 0x3fff;
+        return 2;
+    } else if (up[0] < 0xe0) {
+        *val_p = ((up[0]<<16) | (up[1]<< 8) |  up[2])             & 0x1fffff;
+        return 3;
+    } else if (up[0] < 0xf0) {
+        *val_p = ((up[0]<<24) | (up[1]<<16) | (up[2]<<8) | up[3]) & 0x0fffffff;
+        return 4;
+    } else {
+        *val_p = ((up[0] & 0x0f)<<28) | (up[1]<<20) | (up[2]<<12) | (up[3]<<4) | (up[4] & 0x0f);
+        return 5;
+    }
+}
+
+/*! Pushes a value in ITF8 format onto the end of a block.
+ *
+ * This shouldn't be used for high-volume data as it is not the fastest
+ * method.
+ *
+ * @return
+ * Returns the number of bytes written
+ */
+int itf8_put_blk(cram_block *blk, int val);
+
+/*! Pulls a literal 32-bit value from a block.
+ *
+ * @returns the number of bytes decoded;
+ *         -1 on failure.
+ */
+int int32_get_blk(cram_block *b, int32_t *val);
+
+/*! Pushes a literal 32-bit value onto the end of a block.
+ *
+ * @return
+ * Returns 0 on success;
+ *        -1 on failure.
+ */
+int int32_put_blk(cram_block *blk, int32_t val);
+
+
+/**@}*/
+/**@{ ----------------------------------------------------------------------
+ * CRAM blocks - the dynamically growable data block. We have code to
+ * create, update, (un)compress and read/write.
+ *
+ * These are derived from the deflate_interlaced.c blocks, but with the
+ * CRAM extension of content types and IDs.
+ */
+
+/*! Allocates a new cram_block structure with a specified content_type and
+ * id.
+ *
+ * @return
+ * Returns block pointer on success;
+ *         NULL on failure
+ */
+cram_block *cram_new_block(enum cram_content_type content_type,
+			   int content_id);
+
+/*! Reads a block from a cram file.
+ *
+ * @return
+ * Returns cram_block pointer on success;
+ *         NULL on failure
+ */
+cram_block *cram_read_block(cram_fd *fd);
+
+/*! Writes a CRAM block.
+ *
+ * @return
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+int cram_write_block(cram_fd *fd, cram_block *b);
+
+/*! Frees a CRAM block, deallocating internal data too.
+ */
+void cram_free_block(cram_block *b);
+
+/*! Uncompress a memory block using Zlib.
+ *
+ * @return
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+char *zlib_mem_inflate(char *cdata, size_t csize, size_t *size);
+
+/*! Uncompresses a CRAM block, if compressed.
+ *
+ * @return
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+int cram_uncompress_block(cram_block *b);
+
+/*! Compresses a block.
+ *
+ * Compresses a block using one of two different zlib strategies. If we only
+ * want one choice set strat2 to be -1.
+ *
+ * The logic here is that sometimes Z_RLE does a better job than Z_FILTERED
+ * or Z_DEFAULT_STRATEGY on quality data. If so, we'd rather use it as it is
+ * significantly faster.
+ *
+ * @return
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+int cram_compress_block(cram_fd *fd, cram_block *b, cram_metrics *metrics,
+			int method, int level);
+
+cram_metrics *cram_new_metrics(void);
+char *cram_block_method2str(enum cram_block_method m);
+char *cram_content_type2str(enum cram_content_type t);
+
+/*
+ * Find an external block by its content_id
+ */
+
+static inline cram_block *cram_get_block_by_id(cram_slice *slice, int id) {
+    if (slice->block_by_id && id >= 0 && id < 1024) {
+        return slice->block_by_id[id];
+    } else {
+        int i;
+        for (i = 0; i < slice->hdr->num_blocks; i++) {
+	    cram_block *b = slice->block[i];
+	    if (b && b->content_type == EXTERNAL && b->content_id == id)
+	        return b;
+	}
+    }
+    return NULL;
+}
+
+/* --- Accessor macros for manipulating blocks on a byte by byte basis --- */
+
+/* Block size and data pointer. */
+#define BLOCK_SIZE(b) ((b)->byte)
+#define BLOCK_DATA(b) ((b)->data)
+
+/* Returns the address one past the end of the block */
+#define BLOCK_END(b) (&(b)->data[(b)->byte])
+
+/* Request block to be at least 'l' bytes long */
+#define BLOCK_RESIZE(b,l)					\
+    do {							\
+	while((b)->alloc <= (l)) {				\
+	    (b)->alloc = (b)->alloc ? (b)->alloc*1.5 : 1024;	\
+	    (b)->data = realloc((b)->data, (b)->alloc);		\
+	}							\
+     } while(0)
+
+/* Make block exactly 'l' bytes long */
+#define BLOCK_RESIZE_EXACT(b,l)					\
+    do {							\
+        (b)->alloc = (l);                                       \
+        (b)->data = realloc((b)->data, (b)->alloc);		\
+     } while(0)
+
+/* Ensure the block can hold at least another 'l' bytes */
+#define BLOCK_GROW(b,l) BLOCK_RESIZE((b), BLOCK_SIZE((b)) + (l))
+
+/* Append string 's' of length 'l' */
+#define BLOCK_APPEND(b,s,l)		  \
+    do {				  \
+        BLOCK_GROW((b),(l));		  \
+        memcpy(BLOCK_END((b)), (s), (l)); \
+	BLOCK_SIZE((b)) += (l);		  \
+    } while (0)
+
+/* Append as single character 'c' */
+#define BLOCK_APPEND_CHAR(b,c)		  \
+    do {				  \
+        BLOCK_GROW((b),1);		  \
+	(b)->data[(b)->byte++] = (c);	  \
+    } while (0)
+
+/* Append a single unsigned integer */
+#define BLOCK_APPEND_UINT(b,i)		             \
+    do {					     \
+        unsigned char *cp;			     \
+        BLOCK_GROW((b),11);			     \
+	cp = &(b)->data[(b)->byte];		     \
+        (b)->byte += append_uint32(cp, (i)) - cp;	\
+    } while (0)
+
+static inline unsigned char *append_uint32(unsigned char *cp, uint32_t i) {
+    uint32_t j;
+
+    if (i == 0) {
+	*cp++ = '0';
+	return cp;
+    }
+
+    if (i < 100)        goto b1;
+    if (i < 10000)      goto b3;
+    if (i < 1000000)    goto b5;
+    if (i < 100000000)  goto b7;
+
+    if ((j = i / 1000000000)) {*cp++ = j + '0'; i -= j*1000000000; goto x8;}
+    if ((j = i / 100000000))  {*cp++ = j + '0'; i -= j*100000000;  goto x7;}
+ b7:if ((j = i / 10000000))   {*cp++ = j + '0'; i -= j*10000000;   goto x6;}
+    if ((j = i / 1000000))    {*cp++ = j + '0', i -= j*1000000;    goto x5;}
+ b5:if ((j = i / 100000))     {*cp++ = j + '0', i -= j*100000;     goto x4;}
+    if ((j = i / 10000))      {*cp++ = j + '0', i -= j*10000;      goto x3;}
+ b3:if ((j = i / 1000))       {*cp++ = j + '0', i -= j*1000;       goto x2;}
+    if ((j = i / 100))        {*cp++ = j + '0', i -= j*100;        goto x1;}
+ b1:if ((j = i / 10))         {*cp++ = j + '0', i -= j*10;         goto x0;}
+    if (i)                     *cp++ = i + '0';
+    return cp;
+
+ x8: *cp++ = i / 100000000 + '0', i %= 100000000;
+ x7: *cp++ = i / 10000000  + '0', i %= 10000000;
+ x6: *cp++ = i / 1000000   + '0', i %= 1000000;
+ x5: *cp++ = i / 100000    + '0', i %= 100000;
+ x4: *cp++ = i / 10000     + '0', i %= 10000;
+ x3: *cp++ = i / 1000      + '0', i %= 1000;
+ x2: *cp++ = i / 100       + '0', i %= 100;
+ x1: *cp++ = i / 10        + '0', i %= 10;
+ x0: *cp++ = i             + '0';
+
+    return cp;
+}
+
+static inline unsigned char *append_sub32(unsigned char *cp, uint32_t i) {
+    *cp++ = i / 100000000 + '0', i %= 100000000;
+    *cp++ = i / 10000000  + '0', i %= 10000000;
+    *cp++ = i / 1000000   + '0', i %= 1000000;
+    *cp++ = i / 100000    + '0', i %= 100000;
+    *cp++ = i / 10000     + '0', i %= 10000;
+    *cp++ = i / 1000      + '0', i %= 1000;
+    *cp++ = i / 100       + '0', i %= 100;
+    *cp++ = i / 10        + '0', i %= 10;
+    *cp++ = i             + '0';
+
+    return cp;
+}
+
+static inline unsigned char *append_uint64(unsigned char *cp, uint64_t i) {
+    uint64_t j;
+
+    if (i <= 0xffffffff)
+	return append_uint32(cp, i);
+
+    if ((j = i/1000000000) > 1000000000) {
+	cp = append_uint32(cp, j/1000000000);
+	j %= 1000000000;
+	cp = append_sub32(cp, j);
+    } else {
+	cp = append_uint32(cp, i / 1000000000);
+    }
+    cp = append_sub32(cp, i % 1000000000);
+
+    return cp;
+}
+
+#define BLOCK_UPLEN(b) \
+    (b)->comp_size = (b)->uncomp_size = BLOCK_SIZE((b))
+
+/**@}*/
+/**@{ ----------------------------------------------------------------------
+ * Reference sequence handling
+ */
+
+/*! Loads a reference set from fn and stores in the cram_fd.
+ *
+ * @return
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+int cram_load_reference(cram_fd *fd, char *fn);
+
+/*! Generates a lookup table in refs based on the SQ headers in SAM_hdr.
+ *
+ * Indexes references by the order they appear in a BAM file. This may not
+ * necessarily be the same order they appear in the fasta reference file.
+ *
+ * @return
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+int refs2id(refs_t *r, SAM_hdr *bfd);
+
+void refs_free(refs_t *r);
+
+/*! Returns a portion of a reference sequence from start to end inclusive.
+ *
+ * The returned pointer is owned by the cram_file fd and should not be freed
+ * by the caller. It is valid only until the next cram_get_ref is called
+ * with the same fd parameter (so is thread-safe if given multiple files).
+ *
+ * To return the entire reference sequence, specify start as 1 and end
+ * as 0.
+ *
+ * @return
+ * Returns reference on success;
+ *         NULL on failure
+ */
+char *cram_get_ref(cram_fd *fd, int id, int start, int end);
+void cram_ref_incr(refs_t *r, int id);
+void cram_ref_decr(refs_t *r, int id);
+/**@}*/
+/**@{ ----------------------------------------------------------------------
+ * Containers
+ */
+
+/*! Creates a new container, specifying the maximum number of slices
+ * and records permitted.
+ *
+ * @return
+ * Returns cram_container ptr on success;
+ *         NULL on failure
+ */
+cram_container *cram_new_container(int nrec, int nslice);
+void cram_free_container(cram_container *c);
+
+/*! Reads a container header.
+ *
+ * @return
+ * Returns cram_container on success;
+ *         NULL on failure or no container left (fd->err == 0).
+ */
+cram_container *cram_read_container(cram_fd *fd);
+
+/*! Writes a container structure.
+ *
+ * @return
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+int cram_write_container(cram_fd *fd, cram_container *h);
+
+/*! Flushes a container to disk.
+ *
+ * Flushes a completely or partially full container to disk, writing
+ * container structure, header and blocks. This also calls the encoder
+ * functions.
+ *
+ * @return
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+int cram_flush_container(cram_fd *fd, cram_container *c);
+int cram_flush_container_mt(cram_fd *fd, cram_container *c);
+
+
+/**@}*/
+/**@{ ----------------------------------------------------------------------
+ * Compression headers; the first part of the container
+ */
+
+/*! Creates a new blank container compression header
+ *
+ * @return
+ * Returns header ptr on success;
+ *         NULL on failure
+ */
+cram_block_compression_hdr *cram_new_compression_header(void);
+
+/*! Frees a cram_block_compression_hdr */
+void cram_free_compression_header(cram_block_compression_hdr *hdr);
+
+
+/**@}*/
+/**@{ ----------------------------------------------------------------------
+ * Slices and slice headers
+ */
+
+/*! Frees a slice header */
+void cram_free_slice_header(cram_block_slice_hdr *hdr);
+
+/*! Frees a slice */
+void cram_free_slice(cram_slice *s);
+
+/*! Creates a new empty slice in memory, for subsequent writing to
+ * disk.
+ *
+ * @return
+ * Returns cram_slice ptr on success;
+ *         NULL on failure
+ */
+cram_slice *cram_new_slice(enum cram_content_type type, int nrecs);
+
+/*! Loads an entire slice.
+ *
+ * FIXME: In 1.0 the native unit of slices within CRAM is broken
+ * as slices contain references to objects in other slices.
+ * To work around this while keeping the slice oriented outer loop
+ * we read all slices and stitch them together into a fake large
+ * slice instead.
+ *
+ * @return
+ * Returns cram_slice ptr on success;
+ *         NULL on failure
+ */
+cram_slice *cram_read_slice(cram_fd *fd);
+
+
+
+/**@}*/
+/**@{ ----------------------------------------------------------------------
+ * CRAM file definition (header)
+ */
+
+/*! Reads a CRAM file definition structure.
+ *
+ * @return
+ * Returns file_def ptr on success;
+ *         NULL on failure
+ */
+cram_file_def *cram_read_file_def(cram_fd *fd);
+
+/*! Writes a cram_file_def structure to cram_fd.
+ *
+ * @return
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+int cram_write_file_def(cram_fd *fd, cram_file_def *def);
+
+/*! Frees a cram_file_def structure. */
+void cram_free_file_def(cram_file_def *def);
+
+
+/**@}*/
+/**@{ ----------------------------------------------------------------------
+ * SAM header I/O
+ */
+
+/*! Reads the SAM header from the first CRAM data block.
+ *
+ * Also performs minimal parsing to extract read-group
+ * and sample information.
+ *
+ * @return
+ * Returns SAM hdr ptr on success;
+ *         NULL on failure
+ */
+SAM_hdr *cram_read_SAM_hdr(cram_fd *fd);
+
+/*! Writes a CRAM SAM header.
+ *
+ * @return
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+int cram_write_SAM_hdr(cram_fd *fd, SAM_hdr *hdr);
+
+
+/**@}*/
+/**@{ ----------------------------------------------------------------------
+ * The top-level cram opening, closing and option handling
+ */
+
+/*! Opens a CRAM file for read (mode "rb") or write ("wb").
+ *
+ * The filename may be "-" to indicate stdin or stdout.
+ *
+ * @return
+ * Returns file handle on success;
+ *         NULL on failure.
+ */
+cram_fd *cram_open(const char *filename, const char *mode);
+
+/*! Opens an existing stream for reading or writing.
+ *
+ * @return
+ * Returns file handle on success;
+ *         NULL on failure.
+ */
+cram_fd *cram_dopen(struct hFILE *fp, const char *filename, const char *mode);
+
+/*! Closes a CRAM file.
+ *
+ * @return
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+int cram_close(cram_fd *fd);
+
+/*
+ * Seek within a CRAM file.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int cram_seek(cram_fd *fd, off_t offset, int whence);
+
+/*
+ * Flushes a CRAM file.
+ * Useful for when writing to stdout without wishing to close the stream.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int cram_flush(cram_fd *fd);
+
+/*! Checks for end of file on a cram_fd stream.
+ *
+ * @return
+ * Returns 0 if not at end of file
+ *         1 if we hit an expected EOF (end of range or EOF block)
+ *         2 for other EOF (end of stream without EOF block)
+ */
+int cram_eof(cram_fd *fd);
+
+/*! Sets options on the cram_fd.
+ *
+ * See CRAM_OPT_* definitions in cram_structs.h.
+ * Use this immediately after opening.
+ *
+ * @return
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+int cram_set_option(cram_fd *fd, enum hts_fmt_option opt, ...);
+
+/*! Sets options on the cram_fd.
+ *
+ * See CRAM_OPT_* definitions in cram_structs.h.
+ * Use this immediately after opening.
+ *
+ * @return
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+int cram_set_voption(cram_fd *fd, enum hts_fmt_option opt, va_list args);
+
+/*!
+ * Attaches a header to a cram_fd.
+ *
+ * This should be used when creating a new cram_fd for writing where
+ * we have an SAM_hdr already constructed (eg from a file we've read
+ * in).
+ *
+ * @return
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+int cram_set_header(cram_fd *fd, SAM_hdr *hdr);
+
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _CRAM_IO_H_ */
diff --git a/htslib/cram/cram_samtools.c b/htslib/cram/cram_samtools.c
new file mode 100644
index 0000000..9e95c7b
--- /dev/null
+++ b/htslib/cram/cram_samtools.c
@@ -0,0 +1,149 @@
+/*
+Copyright (c) 2010-2013 Genome Research Ltd.
+Author: James Bonfield <jkb at sanger.ac.uk>
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+Institute nor the names of its contributors may be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+#include <config.h>
+
+#include <assert.h>
+#include <string.h>
+#include <stdlib.h>
+
+#include "cram/cram.h"
+#include "htslib/sam.h"
+
+/*---------------------------------------------------------------------------
+ * Samtools compatibility portion
+ */
+int bam_construct_seq(bam_seq_t **bp, size_t extra_len,
+		      const char *qname, size_t qname_len,
+		      int flag,
+		      int rname,      // Ref ID
+		      int pos,
+		      int end,        // aligned start/end coords
+		      int mapq,
+		      uint32_t ncigar, const uint32_t *cigar,
+		      int mrnm,       // Mate Ref ID
+		      int mpos,
+		      int isize,
+		      int len,
+		      const char *seq,
+		      const char *qual) {
+    static const char L[256] = {
+	15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
+	15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
+	15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
+	15,15,15,15,15,15,15,15,15,15,15,15,15, 0,15,15,
+	15, 1,14, 2,13,15,15, 4,11,15,15,12,15, 3,15,15,
+	15,15, 5, 6, 8,15, 7, 9,15,10,15,15,15,15,15,15,
+	15, 1,14, 2,13,15,15, 4,11,15,15,12,15, 3,15,15,
+	15,15, 5, 6, 8,15, 7, 9,15,10,15,15,15,15,15,15,
+	15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
+	15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
+	15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
+	15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
+	15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
+	15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
+	15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
+	15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15
+    };
+    bam1_t *b = (bam1_t *)*bp;
+    uint8_t *cp;
+    int i, bam_len;
+
+    //b->l_aux = extra_len; // we fill this out later
+
+    bam_len = qname_len + 1 + ncigar*4 + (len+1)/2 + len + extra_len;
+    if (b->m_data < bam_len) {
+	b->m_data = bam_len;
+	kroundup32(b->m_data);
+	b->data = (uint8_t*)realloc(b->data, b->m_data);
+	if (!b->data)
+	    return -1;
+    }
+    b->l_data = bam_len;
+
+    b->core.tid     = rname;
+    b->core.pos     = pos-1;
+    b->core.bin     = bam_reg2bin(pos, end);
+    b->core.qual    = mapq;
+    b->core.l_qname = qname_len+1;
+    b->core.flag    = flag;
+    b->core.n_cigar = ncigar;
+    b->core.l_qseq  = len;
+    b->core.mtid    = mrnm;
+    b->core.mpos    = mpos-1;
+    b->core.isize   = isize;
+
+    cp = b->data;
+
+    strncpy((char *)cp, qname, qname_len);
+    cp[qname_len] = 0;
+    cp += qname_len+1;
+    memcpy(cp, cigar, ncigar*4);
+    cp += ncigar*4;
+
+    for (i = 0; i+1 < len; i+=2) {
+	*cp++ = (L[(uc)seq[i]]<<4) + L[(uc)seq[i+1]];
+    }
+    if (i < len)
+	*cp++ = L[(uc)seq[i]]<<4;
+
+    if (qual)
+	memcpy(cp, qual, len);
+    else
+	memset(cp, '\xff', len);
+
+    return 0;
+}
+
+bam_hdr_t *cram_header_to_bam(SAM_hdr *h) {
+    int i;
+    bam_hdr_t *header = bam_hdr_init();
+
+    header->l_text = ks_len(&h->text);
+    header->text = malloc(header->l_text+1);
+    memcpy(header->text, ks_str(&h->text), header->l_text);
+    header->text[header->l_text] = 0;
+
+    header->n_targets = h->nref;
+    header->target_name = (char **)calloc(header->n_targets,
+					  sizeof(char *));
+    header->target_len = (uint32_t *)calloc(header->n_targets, 4);
+
+    for (i = 0; i < h->nref; i++) {
+	header->target_name[i] = strdup(h->ref[i].name);
+	header->target_len[i] = h->ref[i].len;
+    }
+
+    return header;
+}
+
+SAM_hdr *bam_header_to_cram(bam_hdr_t *h) {
+    return sam_hdr_parse_(h->text, h->l_text);
+}
diff --git a/htslib/cram/cram_samtools.h b/htslib/cram/cram_samtools.h
new file mode 100644
index 0000000..635e2e0
--- /dev/null
+++ b/htslib/cram/cram_samtools.h
@@ -0,0 +1,105 @@
+/*
+Copyright (c) 2010-2013 Genome Research Ltd.
+Author: James Bonfield <jkb at sanger.ac.uk>
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+Institute nor the names of its contributors may be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+#ifndef _CRAM_SAMTOOLS_H_
+#define _CRAM_SAMTOOLS_H_
+
+/* Samtools compatible API */
+#define bam_blk_size(b)  ((b)->l_data)
+#define bam_set_blk_size(b,v) ((b)->data_len = (v))
+
+#define bam_ref(b)       (b)->core.tid
+#define bam_pos(b)       (b)->core.pos
+#define bam_mate_pos(b)  (b)->core.mpos
+#define bam_mate_ref(b)  (b)->core.mtid
+#define bam_ins_size(b)  (b)->core.isize
+#define bam_seq_len(b)   (b)->core.l_qseq
+#define bam_cigar_len(b) (b)->core.n_cigar
+#define bam_flag(b)      (b)->core.flag
+#define bam_bin(b)       (b)->core.bin
+#define bam_map_qual(b)  (b)->core.qual
+#define bam_name_len(b)  (b)->core.l_qname
+#define bam_name(b)      bam_get_qname((b))
+#define bam_qual(b)      bam_get_qual((b))
+#define bam_seq(b)       bam_get_seq((b))
+#define bam_cigar(b)     bam_get_cigar((b))
+#define bam_aux(b)       bam_get_aux((b))
+
+#define bam_dup(b)       bam_copy1(bam_init1(), (b))
+
+#define bam_free(b)      bam_destroy1((b))
+
+#define bam_reg2bin(beg,end) hts_reg2bin((beg),(end),14,5)
+
+#include "htslib/sam.h"
+
+enum cigar_op {
+    BAM_CMATCH_=BAM_CMATCH,
+    BAM_CINS_=BAM_CINS,
+    BAM_CDEL_=BAM_CDEL,
+    BAM_CREF_SKIP_=BAM_CREF_SKIP,
+    BAM_CSOFT_CLIP_=BAM_CSOFT_CLIP,
+    BAM_CHARD_CLIP_=BAM_CHARD_CLIP,
+    BAM_CPAD_=BAM_CPAD,
+    BAM_CBASE_MATCH=BAM_CEQUAL,
+    BAM_CBASE_MISMATCH=BAM_CDIFF
+};
+
+typedef bam1_t bam_seq_t;
+
+#include "cram/sam_header.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+bam_hdr_t *cram_header_to_bam(SAM_hdr *h);
+SAM_hdr *bam_header_to_cram(bam_hdr_t *h);
+
+int bam_construct_seq(bam_seq_t **bp, size_t extra_len,
+		      const char *qname, size_t qname_len,
+		      int flag,
+		      int rname,      // Ref ID
+		      int pos,
+		      int end,        // aligned start/end coords
+		      int mapq,
+		      uint32_t ncigar, const uint32_t *cigar,
+		      int mrnm,       // Mate Ref ID
+		      int mpos,
+		      int isize,
+		      int len,
+		      const char *seq,
+		      const char *qual);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _CRAM_SAMTOOLS_H_ */
diff --git a/htslib/cram/cram_stats.c b/htslib/cram/cram_stats.c
new file mode 100644
index 0000000..c627d3e
--- /dev/null
+++ b/htslib/cram/cram_stats.c
@@ -0,0 +1,448 @@
+/*
+Copyright (c) 2012-2013 Genome Research Ltd.
+Author: James Bonfield <jkb at sanger.ac.uk>
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+Institute nor the names of its contributors may be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+#include <config.h>
+
+#include <stdio.h>
+#include <errno.h>
+#include <assert.h>
+#include <stdlib.h>
+#include <string.h>
+#include <zlib.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <math.h>
+#include <ctype.h>
+
+#include "cram/cram.h"
+#include "cram/os.h"
+
+cram_stats *cram_stats_create(void) {
+    return calloc(1, sizeof(cram_stats));
+}
+
+void cram_stats_add(cram_stats *st, int32_t val) {
+    st->nsamp++;
+
+    //assert(val >= 0);
+
+    if (val < MAX_STAT_VAL && val >= 0) {
+	st->freqs[val]++;
+    } else {
+	khint_t k;
+	int r;
+
+	if (!st->h) {
+	    st->h = kh_init(m_i2i);
+	}
+
+	k = kh_put(m_i2i, st->h, val, &r);
+	if (r == 0)
+	    kh_val(st->h, k)++;
+	else if (r != -1)
+	    kh_val(st->h, k) = 1;
+	else
+	    ; // FIXME: handle error
+    }
+}
+
+void cram_stats_del(cram_stats *st, int32_t val) {
+    st->nsamp--;
+
+    //assert(val >= 0);
+
+    if (val < MAX_STAT_VAL && val >= 0) {
+	st->freqs[val]--;
+	assert(st->freqs[val] >= 0);
+    } else if (st->h) {
+	khint_t k = kh_get(m_i2i, st->h, val);
+
+	if (k != kh_end(st->h)) {
+	    if (--kh_val(st->h, k) == 0)
+		kh_del(m_i2i, st->h, k);
+	} else {
+	    fprintf(stderr, "Failed to remove val %d from cram_stats\n", val);
+	    st->nsamp++;
+	}
+    } else {
+	fprintf(stderr, "Failed to remove val %d from cram_stats\n", val);
+	st->nsamp++;
+    }
+}
+
+void cram_stats_dump(cram_stats *st) {
+    int i;
+    fprintf(stderr, "cram_stats:\n");
+    for (i = 0; i < MAX_STAT_VAL; i++) {
+	if (!st->freqs[i])
+	    continue;
+	fprintf(stderr, "\t%d\t%d\n", i, st->freqs[i]);
+    }
+    if (st->h) {
+	khint_t k;
+	for (k = kh_begin(st->h); k != kh_end(st->h); k++) {
+	    if (!kh_exist(st->h, k))
+		continue;
+
+	    fprintf(stderr, "\t%d\t%d\n", kh_key(st->h, k), kh_val(st->h, k));
+	}
+    }
+}
+
+#if 1
+/* Returns the number of bits set in val; it the highest bit used */
+static int nbits(int v) {
+    static const int MultiplyDeBruijnBitPosition[32] = {
+	1, 10, 2, 11, 14, 22, 3, 30, 12, 15, 17, 19, 23, 26, 4, 31,
+	9, 13, 21, 29, 16, 18, 25, 8, 20, 28, 24, 7, 27, 6, 5, 32
+    };
+
+    v |= v >> 1; // first up to set all bits 1 after the first 1 */
+    v |= v >> 2;
+    v |= v >> 4;
+    v |= v >> 8;
+    v |= v >> 16;
+
+    // DeBruijn magic to find top bit
+    return MultiplyDeBruijnBitPosition[(uint32_t)(v * 0x07C4ACDDU) >> 27];
+}
+#endif
+
+/*
+ * Computes entropy from integer frequencies for various encoding methods and
+ * picks the best encoding.
+ *
+ * FIXME: we could reuse some of the code here for the actual encoding
+ * parameters too. Eg the best 'k' for SUBEXP or the code lengths for huffman.
+ *
+ * Returns the best codec to use.
+ */
+enum cram_encoding cram_stats_encoding(cram_fd *fd, cram_stats *st) {
+    enum cram_encoding best_encoding = E_NULL;
+    int best_size = INT_MAX, bits;
+    int nvals, i, ntot = 0, max_val = 0, min_val = INT_MAX, k;
+    int *vals = NULL, *freqs = NULL, vals_alloc = 0, *codes;
+
+    //cram_stats_dump(st);
+
+    /* Count number of unique symbols */
+    for (nvals = i = 0; i < MAX_STAT_VAL; i++) {
+	if (!st->freqs[i])
+	    continue;
+	if (nvals >= vals_alloc) {
+	    vals_alloc = vals_alloc ? vals_alloc*2 : 1024;
+	    vals  = realloc(vals,  vals_alloc * sizeof(int));
+	    freqs = realloc(freqs, vals_alloc * sizeof(int));
+	    if (!vals || !freqs) {
+		if (vals)  free(vals);
+		if (freqs) free(freqs);
+		return E_HUFFMAN; // Cannot do much else atm
+	    }
+	}
+	vals[nvals] = i;
+	freqs[nvals] = st->freqs[i];
+	ntot += freqs[nvals];
+	if (max_val < i) max_val = i;
+	if (min_val > i) min_val = i;
+	nvals++;
+    }
+    if (st->h) {
+	khint_t k;
+	int i;
+
+	for (k = kh_begin(st->h); k != kh_end(st->h); k++) {
+	    if (!kh_exist(st->h, k))
+		continue;
+
+	    if (nvals >= vals_alloc) {
+		vals_alloc = vals_alloc ? vals_alloc*2 : 1024;
+		vals  = realloc(vals,  vals_alloc * sizeof(int));
+		freqs = realloc(freqs, vals_alloc * sizeof(int));
+		if (!vals || !freqs)
+		    return E_HUFFMAN; // Cannot do much else atm
+	    }
+	    i = kh_key(st->h, k);
+	    vals[nvals]=i;
+	    freqs[nvals] = kh_val(st->h, k);
+	    ntot += freqs[nvals];
+	    if (max_val < i) max_val = i;
+	    if (min_val > i) min_val = i;
+	    nvals++;
+	}
+    }
+
+    st->nvals = nvals;
+    assert(ntot == st->nsamp);
+
+    if (nvals <= 1) {
+	free(vals);
+	free(freqs);
+	return E_HUFFMAN;
+    }
+
+    if (fd->verbose > 1)
+	fprintf(stderr, "Range = %d..%d, nvals=%d, ntot=%d\n",
+		min_val, max_val, nvals, ntot);
+
+    /* Theoretical entropy */
+//    if (fd->verbose > 1) {
+//	double dbits = 0;
+//	for (i = 0; i < nvals; i++) {
+//	    dbits += freqs[i] * log((double)freqs[i]/ntot);
+//	}
+//	dbits /= -log(2);
+//	if (fd->verbose > 1)
+//	    fprintf(stderr, "Entropy = %f\n", dbits);
+//    }
+
+    if (nvals > 1 && ntot > 256) {
+#if 0
+	/*
+	 * CRUDE huffman estimator. Round to closest and round up from 0
+	 * to 1 bit.
+	 *
+	 * With and without ITF8 incase we have a few discrete values but with
+	 * large magnitude.
+	 *
+	 * Note rans0/arith0 and Z_HUFFMAN_ONLY vs internal huffman can be
+	 * compared in this way, but order-1 (eg rans1) or maybe LZ77 modes
+	 * may detect the correlation of high bytes to low bytes in multi-
+	 * byte values. So this predictor breaks down.
+	 */
+	double dbits = 0;  // entropy + ~huffman
+	double dbitsH = 0;
+	double dbitsE = 0; // external entropy + ~huffman
+	double dbitsEH = 0;
+	int F[256] = {0}, n = 0;
+	double e = 0; // accumulated error bits
+	for (i = 0; i < nvals; i++) {
+	    double x; int X;
+	    unsigned int v = vals[i];
+
+	    //Better encoding would cope with sign.
+	    //v = ABS(vals[i])*2+(vals[i]<0);
+
+	    if (!(v & ~0x7f)) {
+		F[v]             += freqs[i], n+=freqs[i];
+	    } else if (!(v & ~0x3fff)) {
+		F[(v>>8) |0x80] += freqs[i];
+		F[ v     &0xff] += freqs[i], n+=2*freqs[i];
+	    } else if (!(v & ~0x1fffff)) {
+		F[(v>>16)|0xc0] += freqs[i];
+		F[(v>>8 )&0xff] += freqs[i];
+		F[ v     &0xff] += freqs[i], n+=3*freqs[i];
+	    } else if (!(v & ~0x0fffffff)) {
+		F[(v>>24)|0xe0] += freqs[i];
+		F[(v>>16)&0xff] += freqs[i];
+		F[(v>>8 )&0xff] += freqs[i];
+		F[ v     &0xff] += freqs[i], n+=4*freqs[i];
+	    } else {
+		F[(v>>28)|0xf0] += freqs[i];
+		F[(v>>20)&0xff] += freqs[i];
+		F[(v>>12)&0xff] += freqs[i];
+		F[(v>>4 )&0xff] += freqs[i];
+		F[ v     &0x0f] += freqs[i], n+=5*freqs[i];
+	    }
+
+	    x = -log((double)freqs[i]/ntot)/.69314718055994530941;
+	    X = x+0.5;
+	    if ((int)(x+((double)e/freqs[i])+.5)>X) {
+		X++;
+	    } else if ((int)(x+((double)e/freqs[i])+.5)<X) {
+		X--;
+	    }
+	    e-=freqs[i]*(X-x);
+	    X += (X==0);
+
+	    //fprintf(stderr, "Val %d = %d x %d (ent %f, %d) e %f\n", i, v, freqs[i], x, X, e);
+
+	    dbits  += freqs[i] * x;
+	    dbitsH += freqs[i] * X;
+	}
+
+	for (i = 0; i < 256; i++) {
+	    if (F[i]) {
+		double x = -log((double)F[i]/n)/.69314718055994530941;
+		int X = x+0.5;
+		X += (X==0);
+		dbitsE  += F[i] * x;
+		dbitsEH += F[i] * X;
+
+		//fprintf(stderr, "Val %d = %d x %d (e %f, %d)\n", i, i, F[i], x, X);
+	    }
+	}
+
+	//fprintf(stderr, "CORE Entropy = %f, %f\n", dbits/8, dbitsH/8);
+	//fprintf(stderr, "Ext. Entropy = %f, %f\n", dbitsE/8, dbitsEH/8);
+
+	if (dbitsE < 1000 || dbitsE / dbits > 1.1) {
+	    //fprintf(stderr, "=> %d < 200 ? E_HUFFMAN : E_BETA\n", nvals);
+	    free(vals); free(freqs);
+	    return nvals < 200 ? E_HUFFMAN : E_BETA;
+	}
+#endif
+	free(vals); free(freqs);
+	return E_EXTERNAL;
+    }
+
+    /*
+     * Avoid complex stats for now, just do heuristic of HUFFMAN for small
+     * alphabets and BETA for anything large.
+     */
+    free(vals); free(freqs);
+    return nvals < 200 ? E_HUFFMAN : E_BETA;
+    //return E_HUFFMAN;
+    //return E_EXTERNAL;
+
+
+    /* We only support huffman now anyway... */
+    //free(vals); free(freqs); return E_HUFFMAN;
+
+    /* Beta */
+    bits = nbits(max_val - min_val) * ntot;
+    if (fd->verbose > 1)
+	fprintf(stderr, "BETA    = %d\n", bits);
+    if (best_size > bits)
+	best_size = bits, best_encoding = E_BETA;
+
+#if 0
+    /* Unary */
+    if (min_val >= 0) {
+	for (bits = i = 0; i < nvals; i++)
+	    bits += freqs[i]*(vals[i]+1);
+	if (fd->verbose > 1)
+	    fprintf(stderr, "UNARY   = %d\n", bits);
+	if (best_size > bits)
+	    best_size = bits, best_encoding = E_NULL; //E_UNARY;
+    }
+
+    /* Gamma */
+    for (bits = i = 0; i < nvals; i++)
+	bits += ((nbits(vals[i]-min_val+1)-1) + nbits(vals[i]-min_val+1)) * freqs[i];
+    if (fd->verbose > 1)
+	fprintf(stderr, "GAMMA   = %d\n", bits);
+    if (best_size > bits)
+	best_size = bits, best_encoding = E_GAMMA;
+
+    /* Subexponential */
+    for (k = 0; k < 10; k++) {
+	for (bits = i = 0; i < nvals; i++) {
+	    if (vals[i]-min_val < (1<<k))
+		bits += (1 + k)*freqs[i];
+	    else
+		bits += (nbits(vals[i]-min_val)*2-k)*freqs[i];
+	}
+
+	if (fd->verbose > 1)
+	    fprintf(stderr, "SUBEXP%d = %d\n", k, bits);
+	if (best_size > bits)
+	    best_size = bits, best_encoding = E_SUBEXP;
+    }
+#endif
+
+    /* byte array len */
+
+    /* byte array stop */
+
+    /* External? Guesswork! */
+
+    /* Huffman */
+//    qsort(freqs, nvals, sizeof(freqs[0]), sort_freqs);
+//    for (i = 0; i < nvals; i++) {
+//	fprintf(stderr, "%d = %d\n", i, freqs[i]);
+//	vals[i] = 0;
+//    }
+
+    /* Grow freqs to 2*freqs, to store sums */
+    /* Vals holds link data */
+    freqs = realloc(freqs, 2*nvals*sizeof(*freqs));
+    codes = calloc(2*nvals, sizeof(*codes));
+    if (!freqs || !codes)
+	return E_HUFFMAN; // Cannot do much else atm
+
+    /* Inefficient, use pointers to form chain so we can insert and maintain
+     * a sorted list? This is currently O(nvals^2) complexity.
+     */
+    for (;;) {
+	int low1 = INT_MAX, low2 = INT_MAX;
+	int ind1 = 0, ind2 = 0;
+	for (i = 0; i < nvals; i++) {
+	    if (freqs[i] < 0)
+		continue;
+	    if (low1 > freqs[i]) 
+		low2 = low1, ind2 = ind1, low1 = freqs[i], ind1 = i;
+	    else if (low2 > freqs[i])
+		low2 = freqs[i], ind2 = i;
+	}
+	if (low2 == INT_MAX)
+	    break;
+
+	//fprintf(stderr, "Merge ind %d (%d), %d (%d) = %d+%d, => %d=%d\n",
+	//	ind1, vals[ind1], ind2, vals[ind2], low1, low2,
+	//	nvals, low1+low2);
+
+	freqs[nvals] = low1 + low2;
+	codes[ind1] = nvals;
+	codes[ind2] = nvals;
+	freqs[ind1] *= -1;
+	freqs[ind2] *= -1;
+	nvals++;
+    }
+    nvals = nvals/2+1;
+
+    for (i = 0; i < nvals; i++) {
+	int code_len = 0;
+	for (k = codes[i]; k; k = codes[k])
+	    code_len++;
+	codes[i] = code_len;
+	freqs[i] *= -1;
+	//fprintf(stderr, "%d / %d => %d\n", vals[i], freqs[i], codes[i]);
+    }
+
+    for (bits = i = 0; i < nvals; i++) {
+	bits += freqs[i] * codes[i];
+    }
+    if (fd->verbose > 1)
+	fprintf(stderr, "HUFFMAN = %d\n", bits);
+    if (best_size >= bits)
+	best_size = bits, best_encoding = E_HUFFMAN;
+    free(codes);
+
+    free(vals);
+    free(freqs);
+
+    return best_encoding;
+}
+
+void cram_stats_free(cram_stats *st) {
+    if (st->h)
+	kh_destroy(m_i2i, st->h);
+    free(st);
+}
diff --git a/htslib/cram/cram_stats.h b/htslib/cram/cram_stats.h
new file mode 100644
index 0000000..b471e68
--- /dev/null
+++ b/htslib/cram/cram_stats.h
@@ -0,0 +1,59 @@
+/*
+Copyright (c) 2012-2013 Genome Research Ltd.
+Author: James Bonfield <jkb at sanger.ac.uk>
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+Institute nor the names of its contributors may be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+#ifndef _CRAM_STATS_H_
+#define _CRAM_STATS_H_
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+cram_stats *cram_stats_create(void);
+void cram_stats_add(cram_stats *st, int32_t val);
+void cram_stats_del(cram_stats *st, int32_t val);
+void cram_stats_dump(cram_stats *st);
+void cram_stats_free(cram_stats *st);
+
+/*
+ * Computes entropy from integer frequencies for various encoding methods and
+ * picks the best encoding.
+ *
+ * FIXME: we could reuse some of the code here for the actual encoding
+ * parameters too. Eg the best 'k' for SUBEXP or the code lengths for huffman.
+ *
+ * Returns the best codec to use.
+ */
+enum cram_encoding cram_stats_encoding(cram_fd *fd, cram_stats *st);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/htslib/cram/cram_structs.h b/htslib/cram/cram_structs.h
new file mode 100644
index 0000000..d427a62
--- /dev/null
+++ b/htslib/cram/cram_structs.h
@@ -0,0 +1,821 @@
+/*
+Copyright (c) 2012-2013 Genome Research Ltd.
+Author: James Bonfield <jkb at sanger.ac.uk>
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+Institute nor the names of its contributors may be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+#ifndef _CRAM_STRUCTS_H_
+#define _CRAM_STRUCTS_H_
+
+/*
+ * Defines in-memory structs for the basic file-format objects in the
+ * CRAM format.
+ *
+ * The basic file format is:
+ *     File-def SAM-hdr Container Container ...
+ *
+ * Container:
+ *     Service-block data-block data-block ...
+ *
+ * Multiple blocks in a container are grouped together as slices,
+ * also sometimes referred to as landmarks in the spec.
+ */
+
+
+#include <stdint.h>
+
+#include "cram/thread_pool.h"
+#include "cram/string_alloc.h"
+#include "cram/mFILE.h"
+#include "htslib/khash.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+// Generic hash-map integer -> integer
+KHASH_MAP_INIT_INT(m_i2i, int)
+
+// Generic hash-set integer -> (existance)
+KHASH_SET_INIT_INT(s_i2i)
+
+// For brevity
+typedef unsigned char uc;
+
+/*
+ * A union for the preservation map. Required for khash.
+ */
+typedef union {
+    int i;
+    char *p;
+} pmap_t;
+
+// Generates static functions here which isn't ideal, but we have no way
+// currently to declare the kh_map_t structure here without also declaring a
+// duplicate in the .c files due to the nature of the KHASH macros.
+KHASH_MAP_INIT_STR(map, pmap_t)
+
+struct hFILE;
+
+#define SEQS_PER_SLICE 10000
+#define SLICE_PER_CNT  1
+
+#define CRAM_SUBST_MATRIX "CGTNAGTNACTNACGNACGT"
+
+#define MAX_STAT_VAL 1024
+//#define MAX_STAT_VAL 16
+typedef struct cram_stats {
+    int freqs[MAX_STAT_VAL];
+    khash_t(m_i2i) *h;
+    int nsamp; // total number of values added
+    int nvals; // total number of unique values added
+} cram_stats;
+
+/* NB: matches java impl, not the spec */
+enum cram_encoding {
+    E_NULL               = 0,
+    E_EXTERNAL           = 1,
+    E_GOLOMB             = 2,
+    E_HUFFMAN            = 3,
+    E_BYTE_ARRAY_LEN     = 4,
+    E_BYTE_ARRAY_STOP    = 5,
+    E_BETA               = 6,
+    E_SUBEXP             = 7,
+    E_GOLOMB_RICE        = 8,
+    E_GAMMA              = 9,
+    E_NUM_CODECS         = 10, /* Number of codecs, not a real one. */
+};
+
+enum cram_external_type {
+    E_INT                = 1,
+    E_LONG               = 2,
+    E_BYTE               = 3,
+    E_BYTE_ARRAY         = 4,
+    E_BYTE_ARRAY_BLOCK   = 5,
+};
+
+/* External IDs used by this implementation (only assumed during writing) */
+enum cram_DS_ID {
+    DS_CORE   = 0,
+    DS_aux    = 1, // aux_blk
+    DS_aux_OQ = 2,
+    DS_aux_BQ = 3,
+    DS_aux_BD = 4,
+    DS_aux_BI = 5,
+    DS_aux_FZ = 6, // also ZM:B
+    DS_aux_oq = 7, // other qualities
+    DS_aux_os = 8, // other sequences
+    DS_aux_oz = 9, // other strings
+    DS_ref,
+    DS_RN, // name_blk
+    DS_QS, // qual_blk
+    DS_IN, // base_blk
+    DS_SC, // soft_blk
+
+    DS_BF, // start loop
+    DS_CF,
+    DS_AP,
+    DS_RG,
+    DS_MQ,
+    DS_NS,
+    DS_MF,
+    DS_TS,
+    DS_NP,
+    DS_NF,
+    DS_RL,
+    DS_FN,
+    DS_FC,
+    DS_FP,
+    DS_DL,
+    DS_BA,
+    DS_BS,
+    DS_TL,
+    DS_RI,
+    DS_RS,
+    DS_PD,
+    DS_HC,
+    DS_BB,
+    DS_QQ,
+
+    DS_TN, // end loop
+
+    DS_RN_len,
+    DS_SC_len,
+    DS_BB_len,
+    DS_QQ_len,
+
+    DS_TC, // CRAM v1.0 tags
+    DS_TM, // test
+    DS_TV, // test
+    
+    DS_END,
+};
+
+/* "File Definition Structure" */
+typedef struct cram_file_def {
+    char    magic[4];
+    uint8_t major_version;
+    uint8_t minor_version;
+    char    file_id[20];      // Filename or SHA1 checksum
+} cram_file_def;
+
+#define CRAM_MAJOR_VERS(v) ((v) >> 8)
+#define CRAM_MINOR_VERS(v) ((v) & 0xff)
+
+struct cram_slice;
+
+enum cram_block_method {
+    ERROR    = -1,
+    RAW      = 0,
+    GZIP     = 1,
+    BZIP2    = 2,
+    LZMA     = 3,
+    RANS     = 4,  // Generic; either order
+    RANS0    = 4,
+    RANS1    = 10, // Not externalised; stored as RANS (generic)
+    GZIP_RLE = 11, // NB: not externalised in CRAM
+};
+
+enum cram_content_type {
+    CT_ERROR           = -1,
+    FILE_HEADER        = 0,
+    COMPRESSION_HEADER = 1,
+    MAPPED_SLICE       = 2,
+    UNMAPPED_SLICE     = 3, // CRAM V1.0 only
+    EXTERNAL           = 4,
+    CORE               = 5,
+};
+
+/* Compression metrics */
+typedef struct {
+    // number of trials and time to next trial
+    int trial;
+    int next_trial;
+
+    // aggregate sizes during trials
+    int sz_gz_rle;
+    int sz_gz_def;
+    int sz_rans0;
+    int sz_rans1;
+    int sz_bzip2;
+    int sz_lzma;
+
+    // resultant method from trials
+    int method;
+    int strat;
+
+    // Revisions of method, to allow culling of continually failing ones.
+    int gz_rle_cnt;
+    int gz_def_cnt;
+    int rans0_cnt;
+    int rans1_cnt;
+    int bzip2_cnt;
+    int lzma_cnt;
+    int revised_method;
+
+    double gz_rle_extra;
+    double gz_def_extra;
+    double rans0_extra;
+    double rans1_extra;
+    double bzip2_extra;
+    double lzma_extra;
+} cram_metrics;
+
+/* Block */
+typedef struct cram_block {
+    enum cram_block_method  method, orig_method;
+    enum cram_content_type  content_type;
+    int32_t  content_id;
+    int32_t  comp_size;
+    int32_t  uncomp_size;
+    uint32_t crc32;
+    int32_t  idx; /* offset into data */
+    unsigned char    *data;
+
+    // For bit I/O
+    size_t alloc;
+    size_t byte;
+    int bit;
+} cram_block;
+
+struct cram_codec; /* defined in cram_codecs.h */
+struct cram_map;
+
+#define CRAM_MAP_HASH 32
+#define CRAM_MAP(a,b) (((a)*3+(b))&(CRAM_MAP_HASH-1))
+
+/* Compression header block */
+typedef struct cram_block_compression_hdr {
+    int32_t ref_seq_id;
+    int32_t ref_seq_start;
+    int32_t ref_seq_span;
+    int32_t num_records;
+    int32_t num_landmarks;
+    int32_t *landmark;
+
+    /* Flags from preservation map */
+    int mapped_qs_included;
+    int unmapped_qs_included;
+    int unmapped_placed;
+    int qs_included;
+    int read_names_included;
+    int AP_delta;
+    // indexed by ref-base and subst. code
+    char substitution_matrix[5][4];
+
+    // TD Dictionary as a concatenated block
+    cram_block *TD_blk;          // Tag Dictionary
+    int nTL;		         // number of TL entries in TD
+    unsigned char **TL;          // array of size nTL, pointer into TD_blk.
+    khash_t(m_s2i) *TD_hash;     // Keyed on TD strings, map to TL[] indices
+    string_alloc_t *TD_keys;     // Pooled keys for TD hash.
+    
+    khash_t(map) *preservation_map;
+    struct cram_map *rec_encoding_map[CRAM_MAP_HASH];
+    struct cram_map *tag_encoding_map[CRAM_MAP_HASH];
+
+    struct cram_codec *codecs[DS_END];
+
+    char *uncomp; // A single block of uncompressed data
+    size_t uncomp_size, uncomp_alloc;
+
+    unsigned int data_series; // See cram_fields enum below
+} cram_block_compression_hdr;
+
+typedef struct cram_map {
+    int key;    /* 0xe0 + 3 bytes */
+    enum cram_encoding encoding;
+    int offset; /* Offset into a single block of memory */
+    int size;   /* Size */
+    struct cram_codec *codec;
+    struct cram_map *next; // for noddy internal hash
+} cram_map;
+
+/* Mapped or unmapped slice header block */
+typedef struct cram_block_slice_hdr {
+    enum cram_content_type content_type;
+    int32_t ref_seq_id;     /* if content_type == MAPPED_SLICE */
+    int32_t ref_seq_start;  /* if content_type == MAPPED_SLICE */
+    int32_t ref_seq_span;   /* if content_type == MAPPED_SLICE */
+    int32_t num_records;
+    int64_t record_counter;
+    int32_t num_blocks;
+    int32_t num_content_ids;
+    int32_t *block_content_ids;
+    int32_t ref_base_id;    /* if content_type == MAPPED_SLICE */
+    unsigned char md5[16];
+} cram_block_slice_hdr;
+
+struct ref_entry;
+
+/*
+ * Container.
+ *
+ * Conceptually a container is split into slices, and slices into blocks.
+ * However on disk it's just a list of blocks and we need to query the
+ * block types to identify the start/end points of the slices.
+ *
+ * OR... are landmarks the start/end points of slices?
+ */
+typedef struct cram_container {
+    int32_t  length;
+    int32_t  ref_seq_id;
+    int32_t  ref_seq_start;
+    int32_t  ref_seq_span;
+    int64_t  record_counter;
+    int64_t  num_bases;
+    int32_t  num_records;
+    int32_t  num_blocks;
+    int32_t  num_landmarks;
+    int32_t *landmark;
+
+    /* Size of container header above */
+    size_t   offset;
+    
+    /* Compression header is always the first block? */
+    cram_block_compression_hdr *comp_hdr;
+    cram_block *comp_hdr_block;
+
+    /* For construction purposes */
+    int max_slice, curr_slice;   // maximum number of slices
+    int max_rec, curr_rec;       // current and max recs per slice
+    int max_c_rec, curr_c_rec;   // current and max recs per container
+    int slice_rec;               // rec no. for start of this slice
+    int curr_ref;                // current ref ID. -2 for no previous
+    int last_pos;                // last record position
+    struct cram_slice **slices, *slice;
+    int pos_sorted;              // boolean, 1=>position sorted data
+    int max_apos;                // maximum position, used if pos_sorted==0
+    int last_slice;              // number of reads in last slice (0 for 1st)
+    int multi_seq;               // true if packing multi seqs per cont/slice
+    int unsorted;		 // true is AP_delta is 0.
+
+    /* Copied from fd before encoding, to allow multi-threading */
+    int ref_start, first_base, last_base, ref_id, ref_end;
+    char *ref;
+    //struct ref_entry *ref;
+
+    /* For multi-threading */
+    bam_seq_t **bams;
+
+    /* Statistics for encoding */
+    cram_stats *stats[DS_END];
+
+    khash_t(s_i2i) *tags_used; // set of tag types in use, for tag encoding map
+    int *refs_used;       // array of frequency of ref seq IDs
+
+    uint32_t crc32;       // CRC32
+} cram_container;
+
+/*
+ * A single cram record
+ */
+typedef struct cram_record {
+    struct cram_slice *s; // Filled out by cram_decode only
+
+    int32_t ref_id;       // fixed for all recs in slice?
+    int32_t flags;        // BF
+    int32_t cram_flags;   // CF
+    int32_t len;          // RL
+    int32_t apos;         // AP
+    int32_t rg;           // RG
+    int32_t name;         // RN; idx to s->names_blk
+    int32_t name_len;
+    int32_t mate_line;    // index to another cram_record
+    int32_t mate_ref_id;
+    int32_t mate_pos;     // NP
+    int32_t tlen;         // TS
+
+    // Auxiliary data
+    int32_t ntags;        // TC
+    int32_t aux;          // idx to s->aux_blk
+    int32_t aux_size;     // total size of packed ntags in aux_blk
+#ifndef TN_external
+    int32_t TN_idx;       // TN; idx to s->TN;
+#else
+    int32_t tn;           // idx to s->tn_blk
+#endif
+    int     TL;
+
+    int32_t seq;          // idx to s->seqs_blk
+    int32_t qual;         // idx to s->qual_blk
+    int32_t cigar;        // idx to s->cigar
+    int32_t ncigar;
+    int32_t aend;         // alignment end
+    int32_t mqual;        // MQ
+
+    int32_t feature;      // idx to s->feature
+    int32_t nfeature;     // number of features
+    int32_t mate_flags;   // MF
+} cram_record;
+
+// Accessor macros as an analogue of the bam ones
+#define cram_qname(c)    (&(c)->s->name_blk->data[(c)->name])
+#define cram_seq(c)      (&(c)->s->seqs_blk->data[(c)->seq])
+#define cram_qual(c)     (&(c)->s->qual_blk->data[(c)->qual])
+#define cram_aux(c)      (&(c)->s->aux_blk->data[(c)->aux])
+#define cram_seqi(c,i)   (cram_seq((c))[(i)])
+#define cram_name_len(c) ((c)->name_len)
+#define cram_strand(c)   (((c)->flags & BAM_FREVERSE) != 0)
+#define cram_mstrand(c)  (((c)->flags & BAM_FMREVERSE) != 0)
+#define cram_cigar(c)    (&((cr)->s->cigar)[(c)->cigar])
+
+/*
+ * A feature is a base difference, used for the sequence reference encoding.
+ * (We generate these internally when writing CRAM.)
+ */
+typedef struct cram_feature {
+    union {
+	struct {
+	    int pos;
+	    int code;
+	    int base;    // substitution code
+	} X;
+	struct {
+	    int pos;
+	    int code;
+	    int base;    // actual base & qual
+	    int qual;
+	} B;
+	struct {
+	    int pos;
+	    int code;
+	    int seq_idx; // index to s->seqs_blk
+	    int len;
+	} b;
+	struct {
+	    int pos;
+	    int code;
+	    int qual;
+	} Q;
+	struct {
+	    int pos;
+	    int code;
+	    int len;
+	    int seq_idx; // soft-clip multiple bases
+	} S;
+	struct {
+	    int pos;
+	    int code;
+	    int len;
+	    int seq_idx; // insertion multiple bases
+	} I;
+	struct {
+	    int pos;
+	    int code;
+	    int base; // insertion single base
+	} i;
+	struct {
+	    int pos;
+	    int code;
+	    int len;
+	} D;
+	struct {
+	    int pos;
+	    int code;
+	    int len;
+	} N;
+	struct {
+	    int pos;
+	    int code;
+	    int len;
+	} P;
+	struct {
+	    int pos;
+	    int code;
+	    int len;
+	} H;
+    };
+} cram_feature;
+
+/*
+ * A slice is really just a set of blocks, but it
+ * is the logical unit for decoding a number of
+ * sequences.
+ */
+typedef struct cram_slice {
+    cram_block_slice_hdr *hdr;
+    cram_block *hdr_block;
+    cram_block **block;
+    cram_block **block_by_id;
+
+    /* State used during encoding/decoding */
+    int last_apos, max_apos;
+
+    /* Array of decoded cram records */
+    cram_record *crecs;
+
+    /* An dynamically growing buffers for data pointed
+     * to by crecs[] array.
+     */
+    uint32_t  *cigar;
+    uint32_t   cigar_alloc;
+    uint32_t   ncigar;
+
+    cram_feature *features;
+    int           nfeatures;
+    int           afeatures; // allocated size of features
+
+#ifndef TN_external
+    // TN field (Tag Name)
+    uint32_t      *TN;
+    int           nTN, aTN;  // used and allocated size for TN[]
+#else
+    cram_block *tn_blk;
+    int tn_id;
+#endif
+
+    // For variable sized elements which are always external blocks.
+    cram_block *name_blk;
+    cram_block *seqs_blk;
+    cram_block *qual_blk;
+    cram_block *base_blk;
+    cram_block *soft_blk;
+    cram_block *aux_blk;
+    cram_block *aux_OQ_blk;
+    cram_block *aux_BQ_blk;
+    cram_block *aux_BD_blk;
+    cram_block *aux_BI_blk;
+    cram_block *aux_FZ_blk;
+    cram_block *aux_oq_blk;
+    cram_block *aux_os_blk;
+    cram_block *aux_oz_blk;
+
+    string_alloc_t *pair_keys; // Pooled keys for pair hash.
+    khash_t(m_s2i) *pair[2];   // for identifying read-pairs in this slice.
+
+    char *ref;               // slice of current reference
+    int ref_start;           // start position of current reference;
+    int ref_end;             // end position of current reference;
+    int ref_id;
+} cram_slice;
+
+/*-----------------------------------------------------------------------------
+ * Consider moving reference handling to cram_refs.[ch]
+ */
+// from fa.fai / samtools faidx files
+typedef struct ref_entry {
+    char *name;
+    char *fn;
+    int64_t length;
+    int64_t offset;
+    int bases_per_line;
+    int line_length;
+    int64_t count;	   // for shared references so we know to dealloc seq
+    char *seq;
+    mFILE *mf;
+    int is_md5;            // Reference comes from a raw seq found by MD5
+} ref_entry;
+
+KHASH_MAP_INIT_STR(refs, ref_entry*)
+
+// References structure.
+typedef struct {
+    string_alloc_t *pool;  // String pool for holding filenames and SN vals
+
+    khash_t(refs) *h_meta; // ref_entry*, index by name
+    ref_entry **ref_id;    // ref_entry*, index by ID
+    int nref;              // number of ref_entry
+
+    char *fn;              // current file opened
+    BGZF *fp;              // and the hFILE* to go with it.
+
+    int count;             // how many cram_fd sharing this refs struct
+
+    pthread_mutex_t lock;  // Mutex for multi-threaded updating
+    ref_entry *last;       // Last queried sequence
+    int last_id;           // Used in cram_ref_decr_locked to delay free
+} refs_t;
+
+/*-----------------------------------------------------------------------------
+ * CRAM index
+ *
+ * Detect format by number of entries per line.
+ * 5 => 1.0 (refid, start, nseq, C offset, slice)
+ * 6 => 1.1 (refid, start, span, C offset, S offset, S size)
+ *
+ * Indices are stored in a nested containment list, which is trivial to set
+ * up as the indices are on sorted data so we're appending to the nclist
+ * in sorted order. Basically if a slice entirely fits within a previous
+ * slice then we append to that slices list. This is done recursively.
+ *
+ * Lists are sorted on two dimensions: ref id + slice coords.
+ */
+typedef struct cram_index {
+    int nslice, nalloc;   // total number of slices
+    struct cram_index *e; // array of size nslice
+
+    int     refid;  // 1.0                 1.1
+    int     start;  // 1.0                 1.1
+    int     end;    //                     1.1
+    int     nseq;   // 1.0 - undocumented
+    int     slice;  // 1.0 landmark index, 1.1 landmark value
+    int     len;    //                     1.1 - size of slice in bytes
+    int64_t offset; // 1.0                 1.1
+} cram_index;
+
+typedef struct {
+    int refid;
+    int start;
+    int end;
+} cram_range;
+
+/*-----------------------------------------------------------------------------
+ */
+/* CRAM File handle */
+
+typedef struct spare_bams {
+    bam_seq_t **bams;
+    struct spare_bams *next;
+} spare_bams;
+
+typedef struct cram_fd {
+    struct hFILE  *fp;
+    int            mode;     // 'r' or 'w'
+    int            version;
+    cram_file_def *file_def;
+    SAM_hdr       *header;
+
+    char          *prefix;
+    int64_t        record_counter;
+    int            err;
+
+    // Most recent compression header decoded
+    //cram_block_compression_hdr *comp_hdr;
+    //cram_block_slice_hdr       *slice_hdr;
+
+    // Current container being processed.
+    cram_container *ctr;
+
+    // positions for encoding or decoding
+    int first_base, last_base;
+
+    // cached reference portion
+    refs_t *refs;              // ref meta-data structure
+    char *ref, *ref_free;      // current portion held in memory
+    int   ref_id;
+    int   ref_start;
+    int   ref_end;
+    char *ref_fn;   // reference fasta filename
+
+    // compression level and metrics
+    int level;
+    cram_metrics *m[DS_END];
+
+    // options
+    int decode_md; // Whether to export MD and NM tags
+    int verbose;
+    int seqs_per_slice;
+    int slices_per_container;
+    int embed_ref;
+    int no_ref;
+    int ignore_md5;
+    int use_bz2;
+    int use_rans;
+    int use_lzma;
+    int shared_ref;
+    unsigned int required_fields;
+    cram_range range;
+
+    // lookup tables, stored here so we can be trivially multi-threaded
+    unsigned int bam_flag_swap[0x1000]; // cram -> bam flags
+    unsigned int cram_flag_swap[0x1000];// bam -> cram flags
+    unsigned char L1[256];              // ACGT{*} ->0123{4}
+    unsigned char L2[256];              // ACGTN{*}->01234{5}
+    char cram_sub_matrix[32][32];	// base substituion codes
+
+    int         index_sz;
+    cram_index *index;                  // array, sizeof index_sz
+    off_t first_container;
+    int eof;
+    int last_slice;                     // number of recs encoded in last slice
+    int multi_seq;
+    int unsorted;
+    int empty_container; 		// Marker for EOF block
+    
+    // thread pool
+    int own_pool;
+    t_pool *pool;
+    t_results_queue *rqueue;
+    pthread_mutex_t metrics_lock;
+    pthread_mutex_t ref_lock;
+    spare_bams *bl;
+    pthread_mutex_t bam_list_lock;
+    void *job_pending;
+    int ooc;                            // out of containers.
+} cram_fd;
+
+// Translation of required fields to cram data series
+enum cram_fields {
+    CRAM_BF = 0x00000001,
+    CRAM_AP = 0x00000002,
+    CRAM_FP = 0x00000004,
+    CRAM_RL = 0x00000008,
+    CRAM_DL = 0x00000010,
+    CRAM_NF = 0x00000020,
+    CRAM_BA = 0x00000040,
+    CRAM_QS = 0x00000080,
+    CRAM_FC = 0x00000100,
+    CRAM_FN = 0x00000200,
+    CRAM_BS = 0x00000400,
+    CRAM_IN = 0x00000800,
+    CRAM_RG = 0x00001000,
+    CRAM_MQ = 0x00002000,
+    CRAM_TL = 0x00004000,
+    CRAM_RN = 0x00008000,
+    CRAM_NS = 0x00010000,
+    CRAM_NP = 0x00020000,
+    CRAM_TS = 0x00040000,
+    CRAM_MF = 0x00080000,
+    CRAM_CF = 0x00100000,
+    CRAM_RI = 0x00200000,
+    CRAM_RS = 0x00400000,
+    CRAM_PD = 0x00800000,
+    CRAM_HC = 0x01000000,
+    CRAM_SC = 0x02000000,
+    CRAM_BB = 0x04000000,
+    CRAM_BB_len = 0x08000000,
+    CRAM_QQ = 0x10000000,
+    CRAM_QQ_len = 0x20000000,
+    CRAM_aux= 0x40000000,
+    CRAM_ALL= 0x7fffffff,
+};
+
+// A CIGAR opcode, but not necessarily the implications of it. Eg FC/FP may
+// encode a base difference, but we don't need to know what it is for CIGAR.
+// If we have a soft-clip or insertion, we do need SC/IN though to know how
+// long that array is.
+#define CRAM_CIGAR (CRAM_FN | CRAM_FP | CRAM_FC | CRAM_DL | CRAM_IN | \
+		    CRAM_SC | CRAM_HC | CRAM_PD | CRAM_RS | CRAM_RL | CRAM_BF)
+
+#define CRAM_SEQ (CRAM_CIGAR | CRAM_BA | CRAM_BS | \
+		  CRAM_RL    | CRAM_AP | CRAM_BB)
+
+#define CRAM_QUAL (CRAM_CIGAR | CRAM_RL | CRAM_AP | CRAM_QS | CRAM_QQ)
+
+/* BF bitfields */
+/* Corrected in 1.1. Use bam_flag_swap[bf] and BAM_* macros for 1.0 & 1.1 */
+#define CRAM_FPAIRED      256
+#define CRAM_FPROPER_PAIR 128
+#define CRAM_FUNMAP        64
+#define CRAM_FREVERSE      32
+#define CRAM_FREAD1        16
+#define CRAM_FREAD2         8
+#define CRAM_FSECONDARY     4
+#define CRAM_FQCFAIL        2
+#define CRAM_FDUP           1
+
+#define DS_aux_S "\001"
+#define DS_aux_OQ_S "\002"
+#define DS_aux_BQ_S "\003"
+#define DS_aux_BD_S "\004"
+#define DS_aux_BI_S "\005"
+#define DS_aux_FZ_S "\006"
+#define DS_aux_oq_S "\007"
+#define DS_aux_os_S "\010"
+#define DS_aux_oz_S "\011"
+
+#define CRAM_M_REVERSE  1
+#define CRAM_M_UNMAP    2
+
+
+/* CF bitfields */
+#define CRAM_FLAG_PRESERVE_QUAL_SCORES (1<<0)
+#define CRAM_FLAG_DETACHED             (1<<1)
+#define CRAM_FLAG_MATE_DOWNSTREAM      (1<<2)
+#define CRAM_FLAG_NO_SEQ               (1<<3)
+#define CRAM_FLAG_MASK                 ((1<<4)-1)
+
+/* Internal only */
+#define CRAM_FLAG_STATS_ADDED          (1<<30)
+
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _CRAM_STRUCTS_H_ */
diff --git a/htslib/cram/files.c b/htslib/cram/files.c
new file mode 100644
index 0000000..bed5406
--- /dev/null
+++ b/htslib/cram/files.c
@@ -0,0 +1,74 @@
+/*
+Copyright (c) 1994, 1996-1997, 2000, 2003 MEDICAL RESEARCH COUNCIL
+All rights reserved
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1 Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2 Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3 Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF 
+MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or 
+promote products derived from this software without specific prior written 
+permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON 
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+#include <config.h>
+
+#include "cram/misc.h"
+
+#include <sys/types.h>
+#include <sys/stat.h>
+/* Alliant's Concentrix <sys/stat.h> is hugely deficient */
+/* Define things we require in this program              */
+/* Methinks S_IFMT and S_IFDIR aren't defined in POSIX   */
+#ifndef S_ISDIR
+#define S_ISDIR(m)      (((m)&S_IFMT) == S_IFDIR)
+#endif /*!S_ISDIR*/
+#ifndef S_ISREG
+#define S_ISREG(m)      (((m)&S_IFMT) == S_IFREG)
+#endif /*!S_ISREG*/
+
+int is_directory(char * fn)
+{
+    struct stat buf;
+    if ( stat(fn,&buf) ) return 0;
+    return S_ISDIR(buf.st_mode);
+}
+
+int is_file(char * fn)
+{
+    struct stat buf;
+    if ( stat(fn,&buf) ) return 0;
+    return S_ISREG(buf.st_mode);
+}
+
+int file_exists(char * fn)
+{
+    struct stat buf;
+    return ( stat(fn,&buf) == 0);
+}
+
+int file_size(char * fn)
+{
+    struct stat buf;
+    if ( stat(fn,&buf) != 0) return 0;
+    return buf.st_size;
+}
+
diff --git a/htslib/cram/mFILE.c b/htslib/cram/mFILE.c
new file mode 100644
index 0000000..0d4bd72
--- /dev/null
+++ b/htslib/cram/mFILE.c
@@ -0,0 +1,694 @@
+/*
+Copyright (c) 2005-2006, 2008-2009, 2013 Genome Research Ltd.
+Author: James Bonfield <jkb at sanger.ac.uk>
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+Institute nor the names of its contributors may be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+#include <config.h>
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <errno.h>
+#include <string.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <fcntl.h>
+#include <unistd.h>
+#include <stdarg.h>
+
+#include "cram/os.h"
+#include "cram/mFILE.h"
+#include "cram/vlen.h"
+
+#ifdef HAVE_MMAP
+#include <sys/mman.h>
+#endif
+
+/*
+ * This file contains memory-based versions of the most commonly used
+ * (by io_lib) stdio functions.
+ *
+ * Actual file IO takes place either on opening or closing an mFILE.
+ *
+ * Coupled to this are a bunch of rather scary macros which can be obtained
+ * by including stdio_hack.h. It is recommended though that you use mFILE.h
+ * instead and replace fopen with mfopen (etc). This is more or less
+ * mandatory if you wish to use both FILE and mFILE structs in a single file.
+ */
+
+static mFILE *m_channel[3];  /* stdin, stdout and stderr fakes */
+
+/*
+ * Reads the entirety of fp into memory. If 'fn' exists it is the filename
+ * associated with fp. This will be used for more optimal reading (via a
+ * stat to identify the size and a single read). Otherwise we use successive
+ * reads until EOF.
+ *
+ * Returns a malloced buffer on success of length *size
+ *         NULL on failure
+ */
+static char *mfload(FILE *fp, const char *fn, size_t *size, int binary) {
+    struct stat sb;
+    char *data = NULL;
+    size_t allocated = 0, used = 0;
+    int bufsize = 8192;
+
+#ifdef _WIN32
+    if (binary)
+	_setmode(_fileno(fp), _O_BINARY);
+    else 
+	_setmode(_fileno(fp), _O_TEXT);
+#endif
+
+    if (fn && -1 != stat(fn, &sb)) {
+	data = malloc(allocated = sb.st_size);
+	bufsize = sb.st_size;
+    } else {
+	fn = NULL;
+    }
+
+    do {
+	size_t len;
+	if (used + bufsize > allocated) {
+	    allocated += bufsize;
+	    data = realloc(data, allocated);
+	}
+	len = fread(data + used, 1, allocated - used, fp);
+	if (len > 0)
+	    used += len;
+    } while (!feof(fp) && (fn == NULL || used < sb.st_size));
+
+    *size = used;
+
+    return data;
+}
+
+
+#ifdef HAVE_MMAP
+/*
+ * mmaps in the file, but only for reading currently.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int mfmmap(mFILE *mf, FILE *fp, const char *fn) {
+    struct stat sb;
+
+    if (stat(fn, &sb) != 0)
+	return -1;
+
+    mf->size = sb.st_size;
+    mf->data = mmap(NULL, mf->size, PROT_READ, MAP_SHARED,
+		    fileno(fp), 0);
+
+    if (!mf->data)
+	return -1;
+
+    mf->alloced = 0;
+    return 0;
+}
+#endif
+
+
+/*
+ * Creates and returns m_channel[0].
+ * We initialise this on the first attempted read, which then slurps in
+ * all of stdin until EOF is met.
+ */
+mFILE *mstdin(void) {
+    if (m_channel[0])
+	return m_channel[0];
+
+    m_channel[0] = mfcreate(NULL, 0);
+    if (NULL == m_channel[0]) return NULL;
+    m_channel[0]->fp = stdin;
+    return m_channel[0];
+}
+
+static void init_mstdin(void) {
+    static int done_stdin = 0;
+    if (done_stdin)
+	return;
+
+    m_channel[0]->data = mfload(stdin, NULL, &m_channel[0]->size, 1);
+    m_channel[0]->mode = MF_READ;
+    done_stdin = 1;
+}
+
+/*
+ * Creates and returns m_channel[1]. This is the fake for stdout. It starts as
+ * an empty buffer which is physically written out only when mfflush or
+ * mfclose are called.
+ */
+mFILE *mstdout(void) {
+    if (m_channel[1])
+	return m_channel[1];
+
+    m_channel[1] = mfcreate(NULL, 0);
+    if (NULL == m_channel[1]) return NULL;
+    m_channel[1]->fp = stdout;
+    m_channel[1]->mode = MF_WRITE;
+    return m_channel[1];
+}
+
+/*
+ * Stderr as an mFILE.
+ * The code handles stderr by returning m_channel[2], but also checking
+ * for stderr in fprintf (the common usage of it) to auto-flush.
+ */
+mFILE *mstderr(void) {
+    if (m_channel[2])
+	return m_channel[2];
+
+    m_channel[2] = mfcreate(NULL, 0);
+    if (NULL == m_channel[2]) return NULL;
+    m_channel[2]->fp = stderr;
+    m_channel[2]->mode = MF_WRITE;
+    return m_channel[2];
+}
+
+
+/*
+ * For creating existing mFILE pointers directly from memory buffers.
+ */
+mFILE *mfcreate(char *data, int size) {
+    mFILE *mf = (mFILE *)malloc(sizeof(*mf));
+    if (NULL == mf) return NULL;
+    mf->fp = NULL;
+    mf->data = data;
+    mf->alloced = size;
+    mf->size = size;
+    mf->eof = 0;
+    mf->offset = 0;
+    mf->flush_pos = 0;
+    mf->mode = MF_READ | MF_WRITE;
+    return mf;
+}
+
+/*
+ * Recreate an existing mFILE to house new data/size.
+ * It also rewinds the file.
+ */
+void mfrecreate(mFILE *mf, char *data, int size) {
+    if (mf->data)
+	free(mf->data);
+    mf->data = data;
+    mf->size = size;
+    mf->alloced = size;
+    mf->eof = 0;
+    mf->offset = 0;
+    mf->flush_pos = 0;
+}
+
+
+/*
+ * Creates a new mFILE to contain the contents of the FILE pointer.
+ * This mFILE is purely for in-memory operations and has no links to the
+ * original FILE* it came from. It also doesn't close the FILE pointer.
+ * Consider using mfreopen() is you need different behaviour.
+ *
+ * Returns mFILE * on success
+ *         NULL on failure.
+ */ 
+mFILE *mfcreate_from(const char *path, const char *mode_str, FILE *fp) {
+   mFILE *mf; 
+
+    /* Open using mfreopen() */
+    if (NULL == (mf = mfreopen(path, mode_str, fp)))
+	return NULL;
+    
+    /* Disassociate from the input stream */
+    mf->fp = NULL;
+
+    return mf;
+}
+
+/*
+ * Converts a FILE * to an mFILE *.
+ * Use this for wrapper functions to turn external prototypes requring
+ * FILE * as an argument into internal code using mFILE *.
+ */
+mFILE *mfreopen(const char *path, const char *mode_str, FILE *fp) {
+    mFILE *mf;
+    int r = 0, w = 0, a = 0, b = 0, x = 0, mode = 0;
+
+    /* Parse mode:
+     * r = read file contents (if truncated => don't read)
+     * w = write on close
+     * a = position at end of buffer
+     * x = position at same location as the original fp, don't seek on flush
+     * + = for update (read and write)
+     * m = mmap (read only)
+     */
+    if (strchr(mode_str, 'r'))
+	r = 1, mode |= MF_READ;
+    if (strchr(mode_str, 'w'))
+	w = 1, mode |= MF_WRITE | MF_TRUNC;
+    if (strchr(mode_str, 'a'))
+	w = a = 1, mode |= MF_WRITE | MF_APPEND;
+    if (strchr(mode_str, 'b'))
+	b = 1, mode |= MF_BINARY;
+    if (strchr(mode_str, 'x'))
+	x = 1;
+    if (strchr(mode_str, '+')) {
+        w = 1, mode |= MF_READ | MF_WRITE;
+	if (a)
+	    r = 1;
+    }
+#ifdef HAVE_MMAP
+    if (strchr(mode_str, 'm'))
+	if (!w) mode |= MF_MMAP;
+#endif
+
+    if (r) {
+	mf = mfcreate(NULL, 0);
+	if (NULL == mf) return NULL;
+	if (!(mode & MF_TRUNC)) {
+#ifdef HAVE_MMAP
+	    if (mode & MF_MMAP) {
+		if (mfmmap(mf, fp, path) == -1) {
+		    mf->data = NULL;
+		    mode &= ~MF_MMAP;
+		}
+	    }
+#endif
+	    if (!mf->data) {
+		mf->data = mfload(fp, path, &mf->size, b);
+		mf->alloced = mf->size;
+		if (!a)
+		    fseek(fp, 0, SEEK_SET);
+	    }
+	}
+    } else if (w) {
+	/* Write - initialise the data structures */
+	mf = mfcreate(NULL, 0);
+	if (NULL == mf) return NULL;
+    } else {
+        fprintf(stderr, "Must specify either r, w or a for mode\n");
+        return NULL;
+    }
+    mf->fp = fp;
+    mf->mode = mode;
+
+    if (x) {
+	mf->mode |= MF_MODEX;
+    }
+    
+    if (a) {
+	mf->flush_pos = mf->size;
+	fseek(fp, 0, SEEK_END);
+    }
+
+    return mf;
+}
+
+/*
+ * Opens a file. If we have read access (r or a+) then it loads the entire
+ * file into memory. If We have write access then the pathname is stored.
+ * We do not actually write until an mfclose, which then checks this pathname.
+ */
+mFILE *mfopen(const char *path, const char *mode) {
+    FILE *fp;
+
+    if (NULL == (fp = fopen(path, mode)))
+	return NULL;
+    return mfreopen(path, mode, fp);
+}
+
+/*
+ * Closes an mFILE. If the filename is known (implying write access) then this
+ * also writes the data to disk.
+ *
+ * Stdout is handled by calling mfflush which writes to stdout if appropriate.
+ */
+int mfclose(mFILE *mf) {
+    if (!mf)
+	return -1;
+
+    mfflush(mf);
+
+#ifdef HAVE_MMAP
+    if ((mf->mode & MF_MMAP) && mf->data) {
+	/* Mmaped */
+	munmap(mf->data, mf->size);
+	mf->data = NULL;
+    }
+#endif
+
+    if (mf->fp)
+	fclose(mf->fp);
+
+    mfdestroy(mf);
+
+    return 0;
+}
+
+/*
+ * Closes the file pointer contained within the mFILE without destroying
+ * the in-memory data.
+ *
+ * Attempting to do this on an mmaped buffer is an error.
+ */
+int mfdetach(mFILE *mf) {
+    if (!mf)
+	return -1;
+
+    mfflush(mf);
+    if (mf->mode & MF_MMAP)
+	return -1;
+
+    if (mf->fp) {
+	fclose(mf->fp);
+	mf->fp = NULL;
+    }
+
+    return 0;
+}
+
+/*
+ * Destroys an mFILE structure but does not flush or close it
+ */
+int mfdestroy(mFILE *mf) {
+    if (!mf)
+	return -1;
+
+    if (mf->data)
+	free(mf->data);
+    free(mf);
+
+    return 0;
+}
+
+/*
+ * Steals that data out of an mFILE.  The mFILE itself will be closed.
+ * It is up to the caller to free the stolen buffer.  If size_out is
+ * not NULL, mf->size will be stored in it.
+ * This is more-or-less the opposite of mfcreate().
+ *
+ * Note, we cannot steal the allocated buffer from an mmaped mFILE.
+ */
+
+void *mfsteal(mFILE *mf, size_t *size_out) {
+    void *data;
+
+    if (!mf) return NULL;
+
+    data = mf->data;
+    
+    if (NULL != size_out) *size_out = mf->size;
+
+    if (mfdetach(mf) != 0)
+	return NULL;
+
+    mf->data = NULL;
+    mfdestroy(mf);
+
+    return data;
+}
+
+/*
+ * Seek/tell functions. Nothing more than updating and reporting an
+ * in-memory index. NB we can seek on stdin or stdout even provided we
+ * haven't been flushing.
+ */
+int mfseek(mFILE *mf, long offset, int whence) {
+    switch (whence) {
+    case SEEK_SET:
+	mf->offset = offset;
+	break;
+    case SEEK_CUR:
+	mf->offset += offset;
+	break;
+    case SEEK_END:
+	mf->offset = mf->size + offset;
+	break;
+    default:
+	errno = EINVAL;
+	return -1;
+    }
+
+    mf->eof = 0;
+    return 0;
+}
+
+long mftell(mFILE *mf) {
+    return mf->offset;
+}
+
+void mrewind(mFILE *mf) {
+    mf->offset = 0;
+    mf->eof = 0;
+}
+
+/*
+ * mftruncate is not directly a translation of ftruncate as the latter
+ * takes a file descriptor instead of a FILE *. It performs the analogous
+ * role though.
+ *
+ * If offset is -1 then the file is truncated to be the current file
+ * offset.
+ */
+void mftruncate(mFILE *mf, long offset) {
+    mf->size = offset != -1 ? offset : mf->offset;
+    if (mf->offset > mf->size)
+	mf->offset = mf->size;
+}
+
+int mfeof(mFILE *mf) {
+    return mf->eof;
+}
+
+/*
+ * mFILE read/write functions. Basically these turn fread/fwrite syntax
+ * into memcpy statements, with appropriate memory handling for writing.
+ */
+size_t mfread(void *ptr, size_t size, size_t nmemb, mFILE *mf) {
+    size_t len;
+    char *cptr = (char *)ptr;
+    
+    if (mf == m_channel[0]) init_mstdin();
+
+    if (mf->size <= mf->offset)
+	return 0;
+
+    len = size * nmemb <= mf->size - mf->offset
+	? size * nmemb
+	: mf->size - mf->offset;
+    if (!size)
+	return 0;
+
+    memcpy(cptr, &mf->data[mf->offset], len);
+    mf->offset += len;
+    
+    if (len != size * nmemb) {
+	mf->eof = 1;
+    }
+
+    return len / size;
+}
+
+size_t mfwrite(void *ptr, size_t size, size_t nmemb, mFILE *mf) {
+    if (!(mf->mode & MF_WRITE))
+	return 0;
+
+    /* Append mode => forced all writes to end of file */
+    if (mf->mode & MF_APPEND)
+	mf->offset = mf->size;
+
+    /* Make sure we have enough room */
+    while (size * nmemb + mf->offset > mf->alloced) {
+	size_t new_alloced = mf->alloced ? mf->alloced * 2 : 1024;
+	void * new_data = realloc(mf->data, new_alloced);
+	if (NULL == new_data) return 0;
+	mf->alloced = new_alloced;
+	mf->data    = new_data;
+    }
+
+    /* Record where we need to reflush from */
+    if (mf->offset < mf->flush_pos)
+	mf->flush_pos = mf->offset;
+
+    /* Copy the data over */
+    memcpy(&mf->data[mf->offset], ptr, size * nmemb);
+    mf->offset += size * nmemb;
+    if (mf->size < mf->offset)
+	mf->size = mf->offset;
+
+    return nmemb;
+}
+
+int mfgetc(mFILE *mf) {
+    if (mf == m_channel[0]) init_mstdin();
+    if (mf->offset < mf->size) {
+	return (unsigned char)mf->data[mf->offset++];
+    }
+
+    mf->eof = 1;
+    return -1;
+}
+
+int mungetc(int c, mFILE *mf) {
+    if (mf->offset > 0) {
+	mf->data[--mf->offset] = c;
+	return c;
+    }
+    
+    mf->eof = 1;
+    return -1;
+}
+
+char *mfgets(char *s, int size, mFILE *mf) {
+    int i;
+
+    if (mf == m_channel[0]) init_mstdin();
+    *s = 0;
+    for (i = 0; i < size-1;) {
+	if (mf->offset < mf->size) {
+	    s[i] = mf->data[mf->offset++];
+	    if (s[i++] == '\n')
+		break;
+	} else {
+	    mf->eof = 1;
+	    break;
+	}
+    }
+
+    s[i] = 0;
+    return i ? s : NULL;
+}
+
+/*
+ * Flushes an mFILE. If this is a real open of a file in write mode then
+ * mFILE->fp will be set. We then write out any new data in mFILE since the
+ * last flush. We cannot tell what may have been modified as we don't keep
+ * track of that, so we typically rewrite out the entire file contents between
+ * the last flush_pos and the end of file.
+ *
+ * For stderr/stdout we also reset the offsets so we cannot modify things
+ * we've already output.
+ */
+int mfflush(mFILE *mf) {
+    if (!mf->fp)
+	return 0;
+
+    /* FIXME: only do this when opened in write mode */
+    if (mf == m_channel[1] || mf == m_channel[2]) {
+	if (mf->flush_pos < mf->size) {
+	    size_t bytes = mf->size - mf->flush_pos;
+	    if (fwrite(mf->data + mf->flush_pos, 1, bytes, mf->fp) < bytes)
+		return -1;
+	    if (0 != fflush(mf->fp))
+		return -1;
+	}
+
+	/* Stdout & stderr are non-seekable streams so throw away the data */
+	mf->offset = mf->size = mf->flush_pos = 0;
+    }
+
+    /* only flush when opened in write mode */
+    if (mf->mode & MF_WRITE) {
+	if (mf->flush_pos < mf->size) {
+	    size_t bytes = mf->size - mf->flush_pos;
+	    if (!(mf->mode & MF_MODEX)) {
+		fseek(mf->fp, mf->flush_pos, SEEK_SET);
+	    }
+	    if (fwrite(mf->data + mf->flush_pos, 1, bytes, mf->fp) < bytes)
+		return -1;
+	    if (0 != fflush(mf->fp))
+		return -1;
+	}
+	if (ftell(mf->fp) != -1 &&
+	    ftruncate(fileno(mf->fp), ftell(mf->fp)) == -1)
+		return -1;
+	mf->flush_pos = mf->size;
+    }
+
+    return 0;
+}
+
+/*
+ * A wrapper around vsprintf() to write to an mFILE. This also uses vflen() to
+ * estimate how many additional bytes of storage will be required for the
+ * vsprintf to work.
+ */
+int mfprintf(mFILE *mf, char *fmt, ...) {
+    int ret;
+    size_t est_length;
+    va_list args;
+
+    va_start(args, fmt);
+    est_length = vflen(fmt, args);
+    va_end(args);
+    while (est_length + mf->offset > mf->alloced) {
+	size_t new_alloced = mf->alloced ? mf->alloced * 2 : 1024;
+	void * new_data    = realloc(mf->data, new_alloced);
+	if (NULL == new_data) return -1;
+	mf->alloced = new_alloced;
+	mf->data    = new_data;
+    }
+
+    va_start(args, fmt);
+    ret = vsprintf(&mf->data[mf->offset], fmt, args);
+    va_end(args);
+
+    if (ret > 0) {
+	mf->offset += ret;
+	if (mf->size < mf->offset)
+	    mf->size = mf->offset;
+    }
+
+    if (mf->fp == stderr) {
+	/* Auto-flush for stderr */
+	if (0 != mfflush(mf)) return -1;
+    }
+
+    return ret;
+}
+
+/*
+ * Converts an mFILE from binary to ascii mode by replacing all
+ * cr-nl with nl.
+ *
+ * Primarily used on windows when we've uncompressed a binary file which
+ * happens to be a text file (eg Experiment File). Previously we would have
+ * seeked back to the start and used _setmode(fileno(fp), _O_TEXT).
+ *
+ * Side effect: resets offset and flush_pos back to the start.
+ */
+void mfascii(mFILE *mf) {
+    size_t p1, p2;
+
+    for (p1 = p2 = 1; p1 < mf->size; p1++, p2++) {
+	if (mf->data[p1] == '\n' && mf->data[p1-1] == '\r') {
+	    p2--; /* delete the \r */
+	}
+	mf->data[p2] = mf->data[p1];
+    }
+    mf->size = p2;
+
+    mf->offset = mf->flush_pos = 0;
+}
diff --git a/htslib/cram/mFILE.h b/htslib/cram/mFILE.h
new file mode 100644
index 0000000..05a3a88
--- /dev/null
+++ b/htslib/cram/mFILE.h
@@ -0,0 +1,89 @@
+/*
+Copyright (c) 2005-2006, 2008-2009 Genome Research Ltd.
+Author: James Bonfield <jkb at sanger.ac.uk>
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+Institute nor the names of its contributors may be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+#ifndef _MFILE_H_
+#define _MFILE_H_
+
+#include <stdio.h>
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+typedef struct {
+    FILE *fp;
+    char *data;
+    size_t alloced;
+    int eof;
+    int mode; /* open mode in MF_?? define bit pattern */
+    size_t size;
+    size_t offset;
+    size_t flush_pos;
+} mFILE;
+
+#define MF_READ    1
+#define MF_WRITE   2
+#define MF_APPEND  4
+#define MF_BINARY  8
+#define MF_TRUNC  16
+#define MF_MODEX  32
+#define MF_MMAP   64
+
+mFILE *mfreopen(const char *path, const char *mode, FILE *fp);
+mFILE *mfopen(const char *path, const char *mode);
+int mfdetach(mFILE *mf);
+int mfclose(mFILE *mf);
+int mfdestroy(mFILE *mf);
+int mfseek(mFILE *mf, long offset, int whence);
+long mftell(mFILE *mf);
+void mrewind(mFILE *mf);
+void mftruncate(mFILE *mf, long offset);
+int mfeof(mFILE *mf);
+size_t mfread(void *ptr, size_t size, size_t nmemb, mFILE *mf);
+size_t mfwrite(void *ptr, size_t size, size_t nmemb, mFILE *mf);
+int mfgetc(mFILE *mf);
+int mungetc(int c, mFILE *mf);
+mFILE *mfcreate(char *data, int size);
+mFILE *mfcreate_from(const char *path, const char *mode_str, FILE *fp);
+void mfrecreate(mFILE *mf, char *data, int size);
+void *mfsteal(mFILE *mf, size_t *size_out);
+char *mfgets(char *s, int size, mFILE *mf);
+int mfflush(mFILE *mf);
+int mfprintf(mFILE *mf, char *fmt, ...);
+mFILE *mstdin(void);
+mFILE *mstdout(void);
+mFILE *mstderr(void);
+void mfascii(mFILE *mf);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _MFILE_H_ */
diff --git a/htslib/cram/misc.h b/htslib/cram/misc.h
new file mode 100644
index 0000000..681b28c
--- /dev/null
+++ b/htslib/cram/misc.h
@@ -0,0 +1,110 @@
+/*
+Copyright (c) 1994-1997, 2001-2002 MEDICAL RESEARCH COUNCIL
+All rights reserved
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1 Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2 Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3 Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF 
+MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or 
+promote products derived from this software without specific prior written 
+permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON 
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+/*
+Copyright (c) 2003-2013 Genome Research Ltd.
+
+Author: James Bonfield <jkb at sanger.ac.uk>
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+Institute nor the names of its contributors may be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+#ifndef _misc_h
+#define _misc_h
+
+#include "cram/os.h"
+
+#include <stdio.h>
+#include <stdarg.h>  /* varargs needed for v*printf() prototypes */
+#include <sys/types.h>
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*
+ * This informs gcc that crash() doesn't return, so it doesn't need to
+ * concern itself that code paths going via crash could mean some variables
+ * being undefined and then issuing uninitialised variable warnings.
+ * This particularly affected convert.
+ */
+#ifdef __GNUC__
+#    define __NORETURN__ __attribute__ ((__noreturn__))
+#else
+#    define __NORETURN__
+#endif
+
+/*
+ * Used for printf style argument checking. We can request a function such
+ * as vTcl_SetResult does argument checking, avoiding bugs with using
+ * %d and passing in a 64-bit record.
+ */
+#ifdef __GNUC__
+#    define __PRINTF_FORMAT__(a,b) __attribute__ ((format (printf, a, b)))
+#else
+#    define __PRINTF_FORMAT__(a,b)
+#endif
+
+extern int is_directory(char * fn);
+extern int is_file(char * fn);
+extern int file_size(char * fn);
+
+#define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) )
+#define MAX(A,B) ( ( (A) > (B) ) ? (A) : (B) )
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /*_misc_h*/
diff --git a/htslib/cram/open_trace_file.c b/htslib/cram/open_trace_file.c
new file mode 100644
index 0000000..62f4087
--- /dev/null
+++ b/htslib/cram/open_trace_file.c
@@ -0,0 +1,414 @@
+/*
+Author: James Bonfield
+
+Copyright (c) 2000-2001 MEDICAL RESEARCH COUNCIL
+All rights reserved
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3. Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF 
+MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or 
+promote products derived from this software without specific prior written 
+permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON 
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+/*
+Copyright (c) 2008, 2009, 2013, 2014 Genome Research Ltd.
+Author: James Bonfield <jkb at sanger.ac.uk>
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+Institute nor the names of its contributors may be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+#include <config.h>
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <unistd.h>
+#include <ctype.h>
+#include <limits.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include "cram/os.h"
+#ifndef PATH_MAX
+#  define PATH_MAX 1024
+#endif
+
+#include "cram/open_trace_file.h"
+#include "cram/misc.h"
+#include "htslib/hfile.h"
+
+/*
+ * Tokenises the search path splitting on colons (unix) or semicolons
+ * (windows).
+ * We also  explicitly add a "./" to the end of the search path
+ *
+ * Returns: A new search path with items separated by nul chars. Two nul
+ *          chars in a row represent the end of the tokenised path.
+ * Returns NULL for a failure.
+ *
+ * The returned data has been malloced. It is up to the caller to free this
+ * memory.
+ */
+char *tokenise_search_path(char *searchpath) {
+    char *newsearch;
+    unsigned int i, j;
+    size_t len;
+#ifdef _WIN32
+    char path_sep = ';';
+#else
+    char path_sep = ':';
+#endif
+
+    if (!searchpath)
+	searchpath="";
+
+    newsearch = (char *)malloc((len = strlen(searchpath))+5);
+    if (!newsearch)
+	return NULL;
+
+    for (i = 0, j = 0; i < len; i++) {
+	/* "::" => ":". Used for escaping colons in http://foo */
+	if (i < len-1 && searchpath[i] == ':' && searchpath[i+1] == ':') {
+	    newsearch[j++] = ':';
+	    i++;
+	    continue;
+	}
+
+	/* Handle http:// and ftp:// too without :: */
+	if (path_sep == ':') {
+	    if ((i == 0 || (i > 0 && searchpath[i-1] == ':')) &&
+		(!strncmp(&searchpath[i], "http:",     5) ||
+		 !strncmp(&searchpath[i], "ftp:",      4) ||
+		 !strncmp(&searchpath[i], "|http:",    6) ||
+		 !strncmp(&searchpath[i], "|ftp:",     5) ||
+		 !strncmp(&searchpath[i], "URL=http:", 9) ||
+		 !strncmp(&searchpath[i], "URL=ftp:",  8))) {
+		do {
+		    newsearch[j++] = searchpath[i];
+		} while (i<len && searchpath[i++] != ':');
+		if (searchpath[i] == ':')
+		    i++;
+		if (searchpath[i]=='/')
+		    newsearch[j++] = searchpath[i++];
+		if (searchpath[i]=='/')
+		    newsearch[j++] = searchpath[i++];
+		// Look for host:port
+		do {
+		    newsearch[j++] = searchpath[i++];
+		} while (i<len && searchpath[i] != ':' && searchpath[i] != '/');
+		newsearch[j++] = searchpath[i++];
+		if (searchpath[i] == ':')
+		    i++;
+	    }
+	}
+
+	if (searchpath[i] == path_sep) {
+	    /* Skip blank path components */
+	    if (j && newsearch[j-1] != 0)
+		newsearch[j++] = 0;
+	} else {
+	    newsearch[j++] = searchpath[i];
+	}
+    }
+
+    if (j)
+	newsearch[j++] = 0;
+    newsearch[j++] = '.';
+    newsearch[j++] = '/';
+    newsearch[j++] = 0;
+    newsearch[j++] = 0;
+    
+    return newsearch;
+}
+
+mFILE *find_file_url(char *file, char *url) {
+    char buf[8192], *cp;
+    mFILE *mf = NULL;
+    int maxlen = 8190 - strlen(file), len;
+    hFILE *hf;
+
+    /* Expand %s for the trace name */
+    for (cp = buf; *url && cp - buf < maxlen; url++) {
+	if (*url == '%' && *(url+1) == 's') {
+	    url++;
+	    cp += strlen(strcpy(cp, file));
+	} else {
+	    *cp++ = *url;
+	}
+    }
+    *cp++ = 0;
+
+    if (!(hf = hopen(buf, "r")))
+	return NULL;
+
+    if (NULL == (mf = mfcreate(NULL, 0)))
+	return NULL;
+    while ((len = hread(hf, buf, 8192)) > 0) {
+	if (mfwrite(buf, len, 1, mf) <= 0) {
+	    hclose_abruptly(hf);
+	    mfdestroy(mf);
+	    return NULL;
+	}
+    }
+    if (hclose(hf) < 0 || len < 0) {
+	mfdestroy(mf);
+	return NULL;
+    }
+
+    mrewind(mf);
+    return mf;
+}
+
+/*
+ * Takes a dirname possibly including % rules and appends the filename
+ * to it.
+ *
+ * Returns expanded pathname or NULL for malloc failure.
+ */
+static char *expand_path(char *file, char *dirname) {
+    size_t len = strlen(dirname);
+    size_t lenf = strlen(file);
+    char *cp, *path;
+
+    path = malloc(len+lenf+2); // worst expansion DIR/FILE
+    if (!path)
+	return NULL;
+
+    if (dirname[len-1] == '/')
+	len--;
+
+    /* Special case for "./" or absolute filenames */
+    if (*file == '/' || (len==1 && *dirname == '.')) {
+	sprintf(path, "%s", file);
+    } else {
+	/* Handle %[0-9]*s expansions, if required */
+	char *path_end = path;
+	*path = 0;
+	while ((cp = strchr(dirname, '%'))) {
+	    char *endp;
+	    long l = strtol(cp+1, &endp, 10);
+	    if (*endp != 's') {
+		strncpy(path_end, dirname, (endp+1)-dirname);
+		path_end += (endp+1)-dirname;
+		dirname = endp+1;
+		continue;
+	    }
+	    
+	    strncpy(path_end, dirname, cp-dirname);
+	    path_end += cp-dirname;
+	    if (l) {
+		strncpy(path_end, file, l);
+		path_end += MIN(strlen(file), l);
+		file     += MIN(strlen(file), l);
+	    } else {
+		strcpy(path_end, file);
+		path_end += strlen(file);
+		file     += strlen(file);
+	    }
+	    len -= (endp+1) - dirname;
+	    dirname = endp+1;
+	}
+	strncpy(path_end, dirname, len);
+	path_end += MIN(strlen(dirname), len);
+	*path_end = 0;
+	if (*file) {
+	    *path_end++ = '/';
+	    strcpy(path_end, file);
+	}
+    }
+
+    //fprintf(stderr, "*PATH=\"%s\"\n", path);
+    return path;
+}
+
+/*
+ * Searches for file in the directory 'dirname'. If it finds it, it opens
+ * it. This also searches for compressed versions of the file in dirname
+ * too.
+ *
+ * Returns mFILE pointer if found
+ *         NULL if not
+ */
+static mFILE *find_file_dir(char *file, char *dirname) {
+    char *path;
+    mFILE *mf = NULL;
+
+    path = expand_path(file, dirname);
+
+    if (is_file(path))
+	mf = mfopen(path, "rbm");
+
+    free(path);
+    return mf;
+}
+
+/*
+ * ------------------------------------------------------------------------
+ * Public functions below.
+ */
+
+/*
+ * Opens a trace file named 'file'. This is initially looked for as a
+ * pathname relative to a file named "relative_to". This may (for
+ * example) be the name of an experiment file referencing the trace
+ * file. In this case by passing relative_to as the experiment file
+ * filename the trace file will be picked up in the same directory as
+ * the experiment file. Relative_to may be supplied as NULL.
+ *
+ * 'file' is looked for at relative_to, then the current directory, and then
+ * all of the locations listed in 'path' (which is a colon separated list).
+ * If 'path' is NULL it uses the RAWDATA environment variable instead.
+ *
+ * Returns a mFILE pointer when found.
+ *           NULL otherwise.
+ */
+mFILE *open_path_mfile(char *file, char *path, char *relative_to) {
+    char *newsearch;
+    char *ele;
+    mFILE *fp;
+
+    /* Use path first */
+    if (!path)
+	path = getenv("RAWDATA");
+    if (NULL == (newsearch = tokenise_search_path(path)))
+	return NULL;
+    
+    /*
+     * Step through the search path testing out each component.
+     * We now look through each path element treating some prefixes as
+     * special, otherwise we treat the element as a directory.
+     */
+    for (ele = newsearch; *ele; ele += strlen(ele)+1) {
+	char *ele2;
+
+	/*
+	 * '|' prefixing a path component indicates that we do not
+	 * wish to perform the compression extension searching in that
+	 * location.
+	 *
+	 * NB: this has been removed from the htslib implementation.
+	 */
+	if (*ele == '|') {
+	    ele2 = ele+1;
+	} else {
+	    ele2 = ele;
+	}
+
+	if (0 == strncmp(ele2, "URL=", 4)) {
+	    if ((fp = find_file_url(file, ele2+4))) {
+		free(newsearch);
+		return fp;
+	    }
+	} else if (!strncmp(ele2, "http:", 5) ||
+		   !strncmp(ele2, "ftp:", 4)) {
+	    if ((fp = find_file_url(file, ele2))) {
+		free(newsearch);
+		return fp;
+	    }
+	} else if ((fp = find_file_dir(file, ele2))) {
+	    free(newsearch);
+	    return fp;
+	} 
+    }
+
+    free(newsearch);
+
+    /* Look in the same location as the incoming 'relative_to' filename */
+    if (relative_to) {
+	char *cp;
+	char relative_path[PATH_MAX+1];
+	strcpy(relative_path, relative_to);
+	if ((cp = strrchr(relative_path, '/')))
+	    *cp = 0;
+	if ((fp = find_file_dir(file, relative_path)))
+	    return fp;
+    }
+
+    return NULL;
+}
+
+
+/*
+ * As per open_path_mfile, but searching only for local filenames.
+ * This is useful as we may avoid doing a full mfopen and loading
+ * the entire file into memory.
+ *
+ * Returns the expanded pathname if found.
+ *         NULL if not
+ */
+char *find_path(char *file, char *path) {
+    char *newsearch;
+    char *ele;
+    char *outpath = NULL;
+
+    /* Use path first */
+    if (!path)
+	path = getenv("RAWDATA");
+    if (NULL == (newsearch = tokenise_search_path(path)))
+	return NULL;
+    
+    for (ele = newsearch; *ele; ele += strlen(ele)+1) {
+	char *ele2 = (*ele == '|') ? ele+1 : ele;
+
+	if (!strncmp(ele2, "URL=", 4) ||
+	    !strncmp(ele2, "http:", 5) ||
+	    !strncmp(ele2, "ftp:", 4)) {
+	    continue;
+	} else {
+	    outpath = expand_path(file, ele2);
+	    if (is_file(outpath)) {
+		free(newsearch);
+		return outpath;
+	    } else {
+		free(outpath);
+	    }
+	} 
+    }
+
+    free(newsearch);
+
+    return NULL;
+}
diff --git a/htslib/cram/open_trace_file.h b/htslib/cram/open_trace_file.h
new file mode 100644
index 0000000..a067dc6
--- /dev/null
+++ b/htslib/cram/open_trace_file.h
@@ -0,0 +1,125 @@
+/*
+Author: James Bonfield
+
+Copyright (c) 2000-2001 MEDICAL RESEARCH COUNCIL
+All rights reserved
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   . Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   . Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   . Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF 
+MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or 
+promote products derived from this software without specific prior written 
+permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON 
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+/*
+Copyright (c) 2008, 2009, 2013 Genome Research Ltd.
+Author: James Bonfield <jkb at sanger.ac.uk>
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+Institute nor the names of its contributors may be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+#ifndef _OPEN_TRACE_FILE_H_
+#define _OPEN_TRACE_FILE_H_
+
+#include "cram/mFILE.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*
+ * Tokenises the search path splitting on colons (unix) or semicolons
+ * (windows).
+ * We also  explicitly add a "./" to the end of the search path
+ *
+ * Returns: A new search path with items separated by nul chars. Two nul
+ *          chars in a row represent the end of the tokenised path.
+ * Returns NULL for a failure.
+ *
+ * The returned data has been malloced. It is up to the caller to free this
+ * memory.
+ */
+char *tokenise_search_path(char *searchpath);
+
+/*
+ * Opens a trace file named 'file'. This is initially looked for as a
+ * pathname relative to a file named "relative_to". This may (for
+ * example) be the name of an experiment file referencing the trace
+ * file. In this case by passing relative_to as the experiment file
+ * filename the trace file will be picked up in the same directory as
+ * the experiment file. Relative_to may be supplied as NULL.
+ *
+ * 'file' is looked for at relative_to, then the current directory, and then
+ * all of the locations listed in 'path' (which is a colon separated list).
+ * If 'path' is NULL it uses the RAWDATA environment variable instead.
+ *
+ * Returns a mFILE pointer when found.
+ *           NULL otherwise.
+ */
+mFILE *open_path_mfile(char *file, char *path, char *relative_to);
+
+/*
+ * Returns a mFILE containing the entire contents of the url;
+ *         NULL on failure.
+ */
+mFILE *find_file_url(char *file, char *url);
+
+
+/*
+ * As per open_path_mfile, but searching only for local filenames.
+ * This is useful as we may avoid doing a full mfopen and loading
+ * the entire file into memory.
+ *
+ * Returns the expanded pathname if found.
+ *         NULL if not
+ */
+char *find_path(char *file, char *path);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _OPEN_TRACE_FILE_H_ */
diff --git a/htslib/cram/os.h b/htslib/cram/os.h
new file mode 100644
index 0000000..22d8096
--- /dev/null
+++ b/htslib/cram/os.h
@@ -0,0 +1,308 @@
+/*
+Copyright (c) 1993, 1995-2002 MEDICAL RESEARCH COUNCIL
+All rights reserved
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1 Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2 Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3 Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF 
+MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or 
+promote products derived from this software without specific prior written 
+permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON 
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+/*
+Copyright (c) 2004, 2006, 2009-2011, 2013 Genome Research Ltd.
+Author: James Bonfield <jkb at sanger.ac.uk>
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+Institute nor the names of its contributors may be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+/*
+ * File: os.h
+ *
+ * Author: 
+ *         MRC Laboratory of Molecular Biology
+ *	   Hills Road
+ *	   Cambridge CB2 2QH
+ *	   United Kingdom
+ *
+ * Description: operating system specific type definitions
+ *
+ */
+
+#ifndef _OS_H_
+#define _OS_H_
+
+#include <limits.h>
+#include <inttypes.h>
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*-----------------------------------------------------------------------------
+ * Detection of endianness. The main part of this is done in autoconf, but
+ * for the case of MacOS FAT binaries we fall back on auto-sensing based on
+ * processor type too.
+ */
+
+/* Set by autoconf */
+#define SP_LITTLE_ENDIAN
+
+/* Mac FAT binaries or unknown. Auto detect based on CPU type */
+#if !defined(SP_BIG_ENDIAN) && !defined(SP_LITTLE_ENDIAN)
+
+/*
+ * x86 equivalents
+ */
+#if defined(__i386__) || defined(__i386) || defined(__amd64__) || defined(__amd64) || defined(__x86_64__) || defined(__x86_64) || defined(__i686__) || defined(__i686)
+#  if defined(SP_BIG_ENDIAN)
+#    undef SP_BIG_ENDIAN
+#  endif
+#  define SP_LITTLE_ENDIAN
+#endif
+
+/*
+ * DEC Alpha
+ */
+#if defined(__alpha__) || defined(__alpha)
+#  if defined(SP_LITTLE_ENDIAN)
+#    undef SP_LITTLE_ENDIAN
+#  endif
+#  define SP_BIG_ENDIAN
+#endif
+
+/*
+ * SUN Sparc
+ */
+#if defined(__sparc__) || defined(__sparc)
+#  if defined(SP_LITTLE_ENDIAN)
+#    undef SP_LITTLE_ENDIAN
+#  endif
+#  define SP_BIG_ENDIAN
+#endif
+
+/*
+ * PowerPC
+ */
+#if defined(__ppc__) || defined(__ppc)
+#  if defined(SP_LITTLE_ENDIAN)
+#    undef SP_LITTLE_ENDIAN
+#  endif
+#  define SP_BIG_ENDIAN
+#endif
+
+/* Some catch-alls */
+#if defined(__LITTLE_ENDIAN__) || defined(__LITTLEENDIAN__)
+#    define SP_LITTLE_ENDIAN
+#endif
+
+#if defined(__BIG_ENDIAN__) || defined(__BIGENDIAN__)
+#    define SP_BIG_ENDIAN
+#endif
+
+#if defined(SP_BIG_ENDIAN) && defined(SP_LITTLE_ENDIAN)
+#    error Both BIG and LITTLE endian defined. Fix os.h and/or Makefile
+#endif
+
+#if !defined(SP_BIG_ENDIAN) && !defined(SP_LITTLE_ENDIAN)
+#    error Neither BIG nor LITTLE endian defined. Fix os.h and/or Makefile
+#endif
+
+#endif
+
+/*-----------------------------------------------------------------------------
+ * Allow for unaligned memory access. This is used in BAM code as the packed
+ * structure has 4-byte cigar ints after the variable length name.
+ *
+ * Consider using AX_CHECK_ALIGNED_ACCESS_REQUIRED in autoconf.
+ */
+#if defined(__i386__) || defined(__i386) || defined(__amd64__) || defined(__amd64) || defined(__x86_64__) || defined(__x86_64) || defined(__i686__) || defined(__i686)
+#  define ALLOW_UAC
+#endif
+
+/*-----------------------------------------------------------------------------
+ * Byte swapping macros
+ */
+
+/*
+ * Our new swap runs at the same speed on Ultrix, but substantially faster
+ * (300% for swap_int4, ~50% for swap_int2) on an Alpha (due to the lack of
+ * decent 'char' support).
+ *
+ * They also have the ability to swap in situ (src == dst). Newer code now
+ * relies on this so don't change back!
+ */
+#define iswap_int8(x) \
+    (((x & 0x00000000000000ffLL) << 56) + \
+     ((x & 0x000000000000ff00LL) << 40) + \
+     ((x & 0x0000000000ff0000LL) << 24) + \
+     ((x & 0x00000000ff000000LL) <<  8) + \
+     ((x & 0x000000ff00000000LL) >>  8) + \
+     ((x & 0x0000ff0000000000LL) >> 24) + \
+     ((x & 0x00ff000000000000LL) >> 40) + \
+     ((x & 0xff00000000000000LL) >> 56))
+
+#define iswap_int4(x) \
+    (((x & 0x000000ff) << 24) + \
+     ((x & 0x0000ff00) <<  8) + \
+     ((x & 0x00ff0000) >>  8) + \
+     ((x & 0xff000000) >> 24))
+
+#define iswap_int2(x) \
+    (((x & 0x00ff) << 8) + \
+     ((x & 0xff00) >> 8))
+
+/*
+ * Linux systems may use byteswap.h to get assembly versions of byte-swap
+ * on intel systems. This can be as trivial as the bswap opcode, which works
+ * out at over 2-times faster than iswap_int4 above.
+ */
+#if 0
+#if defined(__linux__)
+#    include <byteswap.h>
+#    undef iswap_int8
+#    undef iswap_int4
+#    undef iswap_int2
+#    define iswap_int8 bswap_64
+#    define iswap_int4 bswap_32
+#    define iswap_int2 bswap_16
+#endif
+#endif
+
+
+/*
+ * Macros to specify that data read in is of a particular endianness.
+ * The macros here swap to the appropriate order for the particular machine
+ * running the macro and return the new answer. These may also be used when
+ * writing to a file to specify that we wish to write in (eg) big endian
+ * format.
+ *
+ * This leads to efficient code as most of the time these macros are
+ * trivial.
+ */
+#ifdef SP_BIG_ENDIAN
+#define le_int4(x) iswap_int4((x))
+#define le_int2(x) iswap_int2((x))
+#endif
+
+#ifdef SP_LITTLE_ENDIAN
+#define le_int4(x) (x)
+#define le_int2(x) (x)
+#endif
+
+/*-----------------------------------------------------------------------------
+ * <inttypes.h> definitions, incase they're not present
+ */
+
+#ifndef PRId64
+#define __PRI64__ "l"
+#define PRId64 __PRI64__ "d"
+#define PRId32 "d"
+#define PRId16 "d"
+#define PRId8  "d"
+#define PRIu64 __PRI64__ "u"
+#define PRIu32 "u"
+#define PRIu16 "u"
+#define PRIu8  "u"
+#endif
+
+/*-----------------------------------------------------------------------------
+ * Operating system specifics.
+ * These ought to be done by autoconf, but are legacy code.
+ */
+/*
+ * SunOS 4.x
+ * Even though we use the ANSI gcc, we make use the the standard SunOS 4.x
+ * libraries and include files, which are non-ansi
+ */
+#if defined(__sun__) && !defined(__svr4__)
+#define SEEK_SET 0
+#define SEEK_CUR 1
+#define SEEK_END 2
+#endif
+
+/*
+ * Microsoft Visual C++
+ * Windows
+ */
+#if defined(_MSC_VER)
+#define popen _popen
+#define pclose _pclose
+#define ftruncate(fd,len) _chsize(fd,len)
+#endif
+
+
+/*
+ * Microsoft Windows running MinGW
+ */
+#if defined(__MINGW32__)
+/* #define mkdir(filename,mode) mkdir((filename)) */
+#define sysconf(x) 512
+#define ftruncate(fd,len) _chsize(fd,len)
+#endif
+
+/* Generic WIN32 API issues */
+#ifdef _WIN32
+#  ifndef HAVE_FSEEKO
+#    if __MSVCRT_VERSION__ >= 0x800
+       /* if you have MSVCR80 installed then you can use these definitions: */
+#      define off_t __int64
+#      define fseeko _fseeki64
+#      define ftello _ftelli64
+#    else
+       /* otherwise we're stuck with 32-bit file support */
+#      define off_t long
+#      define fseeko fseek
+#      define ftello ftell
+#    endif
+#  endif /* !HAVE_FSEEKO */
+#endif /* _WIN32 */
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /*_OS_H_*/
diff --git a/htslib/cram/pooled_alloc.c b/htslib/cram/pooled_alloc.c
new file mode 100644
index 0000000..b15f88e
--- /dev/null
+++ b/htslib/cram/pooled_alloc.c
@@ -0,0 +1,188 @@
+/*
+Copyright (c) 2009 Genome Research Ltd.
+Author: Rob Davies <rmd at sanger.ac.uk>
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+Institute nor the names of its contributors may be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+#include <config.h>
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdint.h>
+
+#include "cram/pooled_alloc.h"
+#include "cram/misc.h"
+
+//#define TEST_MAIN
+
+#define PSIZE 1024*1024
+
+// credit to http://graphics.stanford.edu/~seander/bithacks.html
+static int next_power_2(unsigned int v) {
+    v--;
+    v |= v >> 1;
+    v |= v >> 2;
+    v |= v >> 4;
+    v |= v >> 8;
+    v |= v >> 16;
+    v++;
+
+    return v;
+}
+
+/*
+ * Creates a pool.
+ * Pool allocations are approx minimum of 1024*dsize or PSIZE.
+ * (Assumes we're not trying to use pools for >= 2Gb or more)
+ */
+pool_alloc_t *pool_create(size_t dsize) {
+    pool_alloc_t *p;
+
+    if (NULL == (p = (pool_alloc_t *)malloc(sizeof(*p))))
+	return NULL;
+
+    /* Minimum size is a pointer, for free list */
+    dsize = (dsize + sizeof(void *) - 1) & ~(sizeof(void *)-1);
+    if (dsize < sizeof(void *))
+	dsize = sizeof(void *);
+    p->dsize = dsize;
+    p->psize = MIN(PSIZE, next_power_2(p->dsize*1024));
+
+    p->npools = 0;
+    p->pools = NULL;
+    p->free  = NULL;
+
+    return p;
+}
+
+static pool_t *new_pool(pool_alloc_t *p) {
+    size_t n = p->psize / p->dsize;
+    pool_t *pool;
+    
+    pool = realloc(p->pools, (p->npools + 1) * sizeof(*p->pools));
+    if (NULL == pool) return NULL;
+    p->pools = pool;
+    pool = &p->pools[p->npools];
+
+    pool->pool = malloc(n * p->dsize);
+    if (NULL == pool->pool) return NULL;
+
+    pool->used = 0;
+
+    p->npools++;
+
+    return pool;
+}
+
+void pool_destroy(pool_alloc_t *p) {
+    size_t i;
+
+    for (i = 0; i < p->npools; i++) {
+        free(p->pools[i].pool);
+    }
+    free(p->pools);
+    free(p);
+}
+
+void *pool_alloc(pool_alloc_t *p) {
+    pool_t *pool;
+    void *ret;
+
+    /* Look on free list */
+    if (NULL != p->free) {
+        ret = p->free;
+	p->free = *((void **)p->free);
+	return ret;
+    }
+
+    /* Look for space in the last pool */
+    if (p->npools) {
+        pool = &p->pools[p->npools - 1];
+        if (pool->used + p->dsize < p->psize) {
+	    ret = ((char *) pool->pool) + pool->used;
+	    pool->used += p->dsize;
+	    return ret;
+	}
+    }
+
+    /* Need a new pool */
+    pool = new_pool(p);
+    if (NULL == pool) return NULL;
+
+    pool->used = p->dsize;
+    return pool->pool;
+}
+
+void pool_free(pool_alloc_t *p, void *ptr) {
+    *(void **)ptr = p->free;
+    p->free = ptr;
+}
+
+#ifdef TEST_MAIN
+typedef struct {
+    int x, y, z;
+} xyz;
+
+#define NP 10000
+int main(void) {
+    int i;
+    xyz *item;
+    xyz **items;
+    pool_alloc_t *p = pool_create(sizeof(xyz));
+
+    items = (xyz **)malloc(NP * sizeof(*items));
+
+    for (i = 0; i < NP; i++) {
+	item = pool_alloc(p);
+	item->x = i;
+	item->y = i+1;
+	item->z = i+2;
+	items[i] = item;
+    }
+
+    for (i = 0; i < NP; i++) {
+	item = items[i];
+	if (i % 3)
+	    pool_free(p, item);
+    }
+
+    for (i = 0; i < NP; i++) {
+	item = pool_alloc(p);
+	item->x = 1000000+i;
+	item->y = 1000000+i+1;
+	item->z = 1000000+i+2;
+    }
+
+    for (i = 0; i < NP; i++) {
+	item = items[i];
+	printf("%d\t%d\t%d\t%d\n", i, item->x, item->y, item->z);
+	pool_free(p, item);
+    }
+
+    return 0;
+}
+#endif
diff --git a/htslib/cram/pooled_alloc.h b/htslib/cram/pooled_alloc.h
new file mode 100644
index 0000000..e19e320
--- /dev/null
+++ b/htslib/cram/pooled_alloc.h
@@ -0,0 +1,64 @@
+/*
+Copyright (c) 2009 Genome Research Ltd.
+Author: Rob Davies <rmd at sanger.ac.uk>
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+Institute nor the names of its contributors may be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+#ifndef _POOLED_ALLOC_H_
+#define _POOLED_ALLOC_H_
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*
+ * Implements a pooled block allocator where all items are the same size,
+ * but we need many of them.
+ */
+typedef struct {
+    void   *pool;
+    size_t  used;
+} pool_t;
+
+typedef struct {
+    size_t dsize;
+    size_t psize;
+    size_t npools;
+    pool_t *pools;
+    void *free;
+} pool_alloc_t;
+
+pool_alloc_t *pool_create(size_t dsize);
+void pool_destroy(pool_alloc_t *p);
+void *pool_alloc(pool_alloc_t *p);
+void pool_free(pool_alloc_t *p, void *ptr);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /*_POOLED_ALLOC_H_*/
diff --git a/htslib/cram/rANS_byte.h b/htslib/cram/rANS_byte.h
new file mode 100644
index 0000000..c61ed9d
--- /dev/null
+++ b/htslib/cram/rANS_byte.h
@@ -0,0 +1,336 @@
+/* rans_byte.h originally from https://github.com/rygorous/ryg_rans
+ *
+ * This is a public-domain implementation of several rANS variants. rANS is an
+ * entropy coder from the ANS family, as described in Jarek Duda's paper
+ * "Asymmetric numeral systems" (http://arxiv.org/abs/1311.2540).
+ */
+
+/*-------------------------------------------------------------------------- */
+
+// Simple byte-aligned rANS encoder/decoder - public domain - Fabian 'ryg' Giesen 2014
+//
+// Not intended to be "industrial strength"; just meant to illustrate the general
+// idea.
+
+#ifndef RANS_BYTE_HEADER
+#define RANS_BYTE_HEADER
+
+#include <stdint.h>
+
+#ifdef assert
+#define RansAssert assert
+#else
+#define RansAssert(x)
+#endif
+
+// READ ME FIRST:
+//
+// This is designed like a typical arithmetic coder API, but there's three
+// twists you absolutely should be aware of before you start hacking:
+//
+// 1. You need to encode data in *reverse* - last symbol first. rANS works
+//    like a stack: last in, first out.
+// 2. Likewise, the encoder outputs bytes *in reverse* - that is, you give
+//    it a pointer to the *end* of your buffer (exclusive), and it will
+//    slowly move towards the beginning as more bytes are emitted.
+// 3. Unlike basically any other entropy coder implementation you might
+//    have used, you can interleave data from multiple independent rANS
+//    encoders into the same bytestream without any extra signaling;
+//    you can also just write some bytes by yourself in the middle if
+//    you want to. This is in addition to the usual arithmetic encoder
+//    property of being able to switch models on the fly. Writing raw
+//    bytes can be useful when you have some data that you know is
+//    incompressible, and is cheaper than going through the rANS encode
+//    function. Using multiple rANS coders on the same byte stream wastes
+//    a few bytes compared to using just one, but execution of two
+//    independent encoders can happen in parallel on superscalar and
+//    Out-of-Order CPUs, so this can be *much* faster in tight decoding
+//    loops.
+//
+//    This is why all the rANS functions take the write pointer as an
+//    argument instead of just storing it in some context struct.
+
+// --------------------------------------------------------------------------
+
+// L ('l' in the paper) is the lower bound of our normalization interval.
+// Between this and our byte-aligned emission, we use 31 (not 32!) bits.
+// This is done intentionally because exact reciprocals for 31-bit uints
+// fit in 32-bit uints: this permits some optimizations during encoding.
+#define RANS_BYTE_L (1u << 23)  // lower bound of our normalization interval
+
+// State for a rANS encoder. Yep, that's all there is to it.
+typedef uint32_t RansState;
+
+// Initialize a rANS encoder.
+static inline void RansEncInit(RansState* r)
+{
+    *r = RANS_BYTE_L;
+}
+
+// Renormalize the encoder. Internal function.
+static inline RansState RansEncRenorm(RansState x, uint8_t** pptr, uint32_t freq, uint32_t scale_bits)
+{
+    uint32_t x_max = ((RANS_BYTE_L >> scale_bits) << 8) * freq; // this turns into a shift.
+    if (x >= x_max) {
+        uint8_t* ptr = *pptr;
+        do {
+            *--ptr = (uint8_t) (x & 0xff);
+            x >>= 8;
+        } while (x >= x_max);
+        *pptr = ptr;
+    }
+    return x;
+}
+
+// Encodes a single symbol with range start "start" and frequency "freq".
+// All frequencies are assumed to sum to "1 << scale_bits", and the
+// resulting bytes get written to ptr (which is updated).
+//
+// NOTE: With rANS, you need to encode symbols in *reverse order*, i.e. from
+// beginning to end! Likewise, the output bytestream is written *backwards*:
+// ptr starts pointing at the end of the output buffer and keeps decrementing.
+static inline void RansEncPut(RansState* r, uint8_t** pptr, uint32_t start, uint32_t freq, uint32_t scale_bits)
+{
+    // renormalize
+    RansState x = RansEncRenorm(*r, pptr, freq, scale_bits);
+
+    // x = C(s,x)
+    *r = ((x / freq) << scale_bits) + (x % freq) + start;
+}
+
+// Flushes the rANS encoder.
+static inline void RansEncFlush(RansState* r, uint8_t** pptr)
+{
+    uint32_t x = *r;
+    uint8_t* ptr = *pptr;
+
+    ptr -= 4;
+    ptr[0] = (uint8_t) (x >> 0);
+    ptr[1] = (uint8_t) (x >> 8);
+    ptr[2] = (uint8_t) (x >> 16);
+    ptr[3] = (uint8_t) (x >> 24);
+
+    *pptr = ptr;
+}
+
+// Initializes a rANS decoder.
+// Unlike the encoder, the decoder works forwards as you'd expect.
+static inline void RansDecInit(RansState* r, uint8_t** pptr)
+{
+    uint32_t x;
+    uint8_t* ptr = *pptr;
+
+    x  = ptr[0] << 0;
+    x |= ptr[1] << 8;
+    x |= ptr[2] << 16;
+    x |= ptr[3] << 24;
+    ptr += 4;
+
+    *pptr = ptr;
+    *r = x;
+}
+
+// Returns the current cumulative frequency (map it to a symbol yourself!)
+static inline uint32_t RansDecGet(RansState* r, uint32_t scale_bits)
+{
+    return *r & ((1u << scale_bits) - 1);
+}
+
+// Advances in the bit stream by "popping" a single symbol with range start
+// "start" and frequency "freq". All frequencies are assumed to sum to "1 << scale_bits",
+// and the resulting bytes get written to ptr (which is updated).
+static inline void RansDecAdvance(RansState* r, uint8_t** pptr, uint32_t start, uint32_t freq, uint32_t scale_bits)
+{
+    uint32_t mask = (1u << scale_bits) - 1;
+
+    // s, x = D(x)
+    uint32_t x = *r;
+    x = freq * (x >> scale_bits) + (x & mask) - start;
+
+    // renormalize
+    if (x < RANS_BYTE_L) {
+        uint8_t* ptr = *pptr;
+        do x = (x << 8) | *ptr++; while (x < RANS_BYTE_L);
+        *pptr = ptr;
+    }
+
+    *r = x;
+}
+
+// --------------------------------------------------------------------------
+
+// That's all you need for a full encoder; below here are some utility
+// functions with extra convenience or optimizations.
+
+// Encoder symbol description
+// This (admittedly odd) selection of parameters was chosen to make
+// RansEncPutSymbol as cheap as possible.
+typedef struct {
+    uint32_t x_max;     // (Exclusive) upper bound of pre-normalization interval
+    uint32_t rcp_freq;  // Fixed-point reciprocal frequency
+    uint32_t bias;      // Bias
+    uint16_t cmpl_freq; // Complement of frequency: (1 << scale_bits) - freq
+    uint16_t rcp_shift; // Reciprocal shift
+} RansEncSymbol;
+
+// Decoder symbols are straightforward.
+typedef struct {
+    uint16_t start;     // Start of range.
+    uint16_t freq;      // Symbol frequency.
+} RansDecSymbol;
+
+// Initializes an encoder symbol to start "start" and frequency "freq"
+static inline void RansEncSymbolInit(RansEncSymbol* s, uint32_t start, uint32_t freq, uint32_t scale_bits)
+{
+    RansAssert(scale_bits <= 16);
+    RansAssert(start <= (1u << scale_bits));
+    RansAssert(freq <= (1u << scale_bits) - start);
+
+    // Say M := 1 << scale_bits.
+    //
+    // The original encoder does:
+    //   x_new = (x/freq)*M + start + (x%freq)
+    //
+    // The fast encoder does (schematically):
+    //   q     = mul_hi(x, rcp_freq) >> rcp_shift   (division)
+    //   r     = x - q*freq                         (remainder)
+    //   x_new = q*M + bias + r                     (new x)
+    // plugging in r into x_new yields:
+    //   x_new = bias + x + q*(M - freq)
+    //        =: bias + x + q*cmpl_freq             (*)
+    //
+    // and we can just precompute cmpl_freq. Now we just need to
+    // set up our parameters such that the original encoder and
+    // the fast encoder agree.
+
+    s->x_max = ((RANS_BYTE_L >> scale_bits) << 8) * freq;
+    s->cmpl_freq = (uint16_t) ((1 << scale_bits) - freq);
+    if (freq < 2) {
+        // freq=0 symbols are never valid to encode, so it doesn't matter what
+        // we set our values to.
+        //
+        // freq=1 is tricky, since the reciprocal of 1 is 1; unfortunately,
+        // our fixed-point reciprocal approximation can only multiply by values
+        // smaller than 1.
+        //
+        // So we use the "next best thing": rcp_freq=0xffffffff, rcp_shift=0.
+        // This gives:
+        //   q = mul_hi(x, rcp_freq) >> rcp_shift
+        //     = mul_hi(x, (1<<32) - 1)) >> 0
+        //     = floor(x - x/(2^32))
+        //     = x - 1 if 1 <= x < 2^32
+        // and we know that x>0 (x=0 is never in a valid normalization interval).
+        //
+        // So we now need to choose the other parameters such that
+        //   x_new = x*M + start
+        // plug it in:
+        //     x*M + start                   (desired result)
+        //   = bias + x + q*cmpl_freq        (*)
+        //   = bias + x + (x - 1)*(M - 1)    (plug in q=x-1, cmpl_freq)
+        //   = bias + 1 + (x - 1)*M
+        //   = x*M + (bias + 1 - M)
+        //
+        // so we have start = bias + 1 - M, or equivalently
+        //   bias = start + M - 1.
+        s->rcp_freq = ~0u;
+        s->rcp_shift = 0;
+        s->bias = start + (1 << scale_bits) - 1;
+    } else {
+        // Alverson, "Integer Division using reciprocals"
+        // shift=ceil(log2(freq))
+        uint32_t shift = 0;
+        while (freq > (1u << shift))
+            shift++;
+
+        s->rcp_freq = (uint32_t) (((1ull << (shift + 31)) + freq-1) / freq);
+        s->rcp_shift = shift - 1;
+
+        // With these values, 'q' is the correct quotient, so we
+        // have bias=start.
+        s->bias = start;
+    }
+
+    s->rcp_shift += 32; // Avoid the extra >>32 in RansEncPutSymbol
+}
+
+// Initialize a decoder symbol to start "start" and frequency "freq"
+static inline void RansDecSymbolInit(RansDecSymbol* s, uint32_t start, uint32_t freq)
+{
+    RansAssert(start <= (1 << 16));
+    RansAssert(freq <= (1 << 16) - start);
+    s->start = (uint16_t) start;
+    s->freq = (uint16_t) freq;
+}
+
+// Encodes a given symbol. This is faster than straight RansEnc since we can do
+// multiplications instead of a divide.
+//
+// See RansEncSymbolInit for a description of how this works.
+static inline void RansEncPutSymbol(RansState* r, uint8_t** pptr, RansEncSymbol const* sym)
+{
+    RansAssert(sym->x_max != 0); // can't encode symbol with freq=0
+
+    // renormalize
+    uint32_t x = *r;
+    uint32_t x_max = sym->x_max;
+
+    if (x >= x_max) {
+	uint8_t* ptr = *pptr;
+	do {
+	    *--ptr = (uint8_t) (x & 0xff);
+	    x >>= 8;
+	} while (x >= x_max);
+	*pptr = ptr;
+    }
+
+    // x = C(s,x)
+    // NOTE: written this way so we get a 32-bit "multiply high" when
+    // available. If you're on a 64-bit platform with cheap multiplies
+    // (e.g. x64), just bake the +32 into rcp_shift.
+    //uint32_t q = (uint32_t) (((uint64_t)x * sym->rcp_freq) >> 32) >> sym->rcp_shift;
+
+    // The extra >>32 has already been added to RansEncSymbolInit
+    uint32_t q = (uint32_t) (((uint64_t)x * sym->rcp_freq) >> sym->rcp_shift);
+    *r = x + sym->bias + q * sym->cmpl_freq;
+}
+
+// Equivalent to RansDecAdvance that takes a symbol.
+static inline void RansDecAdvanceSymbol(RansState* r, uint8_t** pptr, RansDecSymbol const* sym, uint32_t scale_bits)
+{
+    RansDecAdvance(r, pptr, sym->start, sym->freq, scale_bits);
+}
+
+// Advances in the bit stream by "popping" a single symbol with range start
+// "start" and frequency "freq". All frequencies are assumed to sum to "1 << scale_bits".
+// No renormalization or output happens.
+static inline void RansDecAdvanceStep(RansState* r, uint32_t start, uint32_t freq, uint32_t scale_bits)
+{
+    uint32_t mask = (1u << scale_bits) - 1;
+
+    // s, x = D(x)
+    uint32_t x = *r;
+    *r = freq * (x >> scale_bits) + (x & mask) - start;
+}
+
+// Equivalent to RansDecAdvanceStep that takes a symbol.
+static inline void RansDecAdvanceSymbolStep(RansState* r, RansDecSymbol const* sym, uint32_t scale_bits)
+{
+    RansDecAdvanceStep(r, sym->start, sym->freq, scale_bits);
+}
+
+// Renormalize.
+static inline void RansDecRenorm(RansState* r, uint8_t** pptr)
+{
+    // renormalize
+    uint32_t x = *r;
+
+    if (x < RANS_BYTE_L) {
+        uint8_t* ptr = *pptr;
+        do x = (x << 8) | *ptr++; while (x < RANS_BYTE_L);
+        *pptr = ptr;
+    }
+
+    *r = x;
+}
+
+#endif // RANS_BYTE_HEADER
diff --git a/htslib/cram/rANS_static.c b/htslib/cram/rANS_static.c
new file mode 100644
index 0000000..00eda5a
--- /dev/null
+++ b/htslib/cram/rANS_static.c
@@ -0,0 +1,868 @@
+/*
+ * Copyright (c) 2014 Genome Research Ltd.
+ * Author(s): James Bonfield
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ *    1. Redistributions of source code must retain the above copyright notice,
+ *       this list of conditions and the following disclaimer.
+ *
+ *    2. Redistributions in binary form must reproduce the above
+ *       copyright notice, this list of conditions and the following
+ *       disclaimer in the documentation and/or other materials provided
+ *       with the distribution.
+ *
+ *    3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+ *       Institute nor the names of its contributors may be used to endorse
+ *       or promote products derived from this software without specific
+ *       prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS
+ * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+ * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+ * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH
+ * LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+/*
+ * Author: James Bonfield, Wellcome Trust Sanger Institute. 2014
+ */
+
+#include <config.h>
+
+#include <stdint.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <unistd.h>
+#include <assert.h>
+#include <string.h>
+#include <sys/time.h>
+
+#include "cram/rANS_static.h"
+#include "cram/rANS_byte.h"
+
+#define TF_SHIFT 12
+#define TOTFREQ (1<<TF_SHIFT)
+
+#define ABS(a) ((a)>0?(a):-(a))
+#ifndef BLK_SIZE
+#  define BLK_SIZE 1024*1024
+#endif
+
+// Room to allow for expanded BLK_SIZE on worst case compression.
+#define BLK_SIZE2 ((int)(1.05*BLK_SIZE))
+
+/*-----------------------------------------------------------------------------
+ * Memory to memory compression functions.
+ *
+ * These are original versions without any manual loop unrolling. They
+ * are easier to understand, but can be up to 2x slower.
+ */
+
+unsigned char *rans_compress_O0(unsigned char *in, unsigned int in_size,
+				unsigned int *out_size) {
+    unsigned char *out_buf = malloc(1.05*in_size + 257*257*3 + 9);
+    unsigned char *cp, *out_end;
+    RansEncSymbol syms[256];
+    RansState rans0, rans1, rans2, rans3;
+    uint8_t* ptr;
+    int F[256] = {0}, i, j, tab_size, rle, x, fsum = 0;
+    int m = 0, M = 0;
+    uint64_t tr;
+
+    if (!out_buf)
+	return NULL;
+
+    ptr = out_end = out_buf + (int)(1.05*in_size) + 257*257*3 + 9;
+
+    // Compute statistics
+    for (i = 0; i < in_size; i++) {
+	F[in[i]]++;
+    }
+    tr = ((uint64_t)TOTFREQ<<31)/in_size + (1<<30)/in_size;
+
+    // Normalise so T[i] == TOTFREQ
+    for (m = M = j = 0; j < 256; j++) {
+	if (!F[j])
+	    continue;
+
+	if (m < F[j])
+	    m = F[j], M = j;
+
+	if ((F[j] = (F[j]*tr)>>31) == 0)
+	    F[j] = 1;
+	fsum += F[j];
+    }
+
+    fsum++;
+    if (fsum < TOTFREQ)
+	F[M] += TOTFREQ-fsum;
+    else
+	F[M] -= fsum-TOTFREQ;
+
+    //printf("F[%d]=%d\n", M, F[M]);
+    assert(F[M]>0);
+
+    // Encode statistics.
+    cp = out_buf+9;
+
+    for (x = rle = j = 0; j < 256; j++) {
+	if (F[j]) {
+	    // j
+	    if (rle) {
+		rle--;
+	    } else {
+		*cp++ = j;
+		if (!rle && j && F[j-1])  {
+		    for(rle=j+1; rle<256 && F[rle]; rle++)
+			;
+		    rle -= j+1;
+		    *cp++ = rle;
+		}
+		//fprintf(stderr, "%d: %d %d\n", j, rle, N[j]);
+	    }
+
+	    // F[j]
+	    if (F[j]<128) {
+		*cp++ = F[j];
+	    } else {
+		*cp++ = 128 | (F[j]>>8);
+		*cp++ = F[j]&0xff;
+	    }
+	    RansEncSymbolInit(&syms[j], x, F[j], TF_SHIFT);
+	    x += F[j];
+	}
+    }
+    *cp++ = 0;
+
+    //write(1, out_buf+4, cp-(out_buf+4));
+    tab_size = cp-out_buf;
+
+    RansEncInit(&rans0);
+    RansEncInit(&rans1);
+    RansEncInit(&rans2);
+    RansEncInit(&rans3);
+
+    switch (i=(in_size&3)) {
+    case 3: RansEncPutSymbol(&rans2, &ptr, &syms[in[in_size-(i-2)]]);
+    case 2: RansEncPutSymbol(&rans1, &ptr, &syms[in[in_size-(i-1)]]);
+    case 1: RansEncPutSymbol(&rans0, &ptr, &syms[in[in_size-(i-0)]]);
+    case 0:
+	break;
+    }
+    for (i=(in_size &~3); i>0; i-=4) {
+	RansEncSymbol *s3 = &syms[in[i-1]];
+	RansEncSymbol *s2 = &syms[in[i-2]];
+	RansEncSymbol *s1 = &syms[in[i-3]];
+	RansEncSymbol *s0 = &syms[in[i-4]];
+
+	RansEncPutSymbol(&rans3, &ptr, s3);
+	RansEncPutSymbol(&rans2, &ptr, s2);
+	RansEncPutSymbol(&rans1, &ptr, s1);
+	RansEncPutSymbol(&rans0, &ptr, s0);
+    }
+
+    RansEncFlush(&rans3, &ptr);
+    RansEncFlush(&rans2, &ptr);
+    RansEncFlush(&rans1, &ptr);
+    RansEncFlush(&rans0, &ptr);
+
+    // Finalise block size and return it
+    *out_size = (out_end - ptr) + tab_size;
+
+    cp = out_buf;
+
+    *cp++ = 0; // order
+    *cp++ = ((*out_size-9)>> 0) & 0xff;
+    *cp++ = ((*out_size-9)>> 8) & 0xff;
+    *cp++ = ((*out_size-9)>>16) & 0xff;
+    *cp++ = ((*out_size-9)>>24) & 0xff;
+
+    *cp++ = (in_size>> 0) & 0xff;
+    *cp++ = (in_size>> 8) & 0xff;
+    *cp++ = (in_size>>16) & 0xff;
+    *cp++ = (in_size>>24) & 0xff;
+
+    memmove(out_buf + tab_size, ptr, out_end-ptr);
+
+    return out_buf;
+}
+
+typedef struct {
+    struct {
+	int F;
+	int C;
+    } fc[256];
+    unsigned char *R;
+} ari_decoder;
+
+unsigned char *rans_uncompress_O0(unsigned char *in, unsigned int in_size,
+				  unsigned int *out_size) {
+    /* Load in the static tables */
+    unsigned char *cp = in + 9;
+    int i, j, x, out_sz, in_sz, rle;
+    char *out_buf;
+    ari_decoder D;
+    RansDecSymbol syms[256];
+
+    memset(&D, 0, sizeof(D));
+
+    if (*in++ != 0) // Order-0 check
+	return NULL;
+    
+    in_sz  = ((in[0])<<0) | ((in[1])<<8) | ((in[2])<<16) | ((in[3])<<24);
+    out_sz = ((in[4])<<0) | ((in[5])<<8) | ((in[6])<<16) | ((in[7])<<24);
+    if (in_sz != in_size-9)
+	return NULL;
+
+    out_buf = malloc(out_sz);
+    if (!out_buf)
+	return NULL;
+
+    //fprintf(stderr, "out_sz=%d\n", out_sz);
+
+    // Precompute reverse lookup of frequency.
+    rle = x = 0;
+    j = *cp++;
+    do {
+	if ((D.fc[j].F = *cp++) >= 128) {
+	    D.fc[j].F &= ~128;
+	    D.fc[j].F = ((D.fc[j].F & 127) << 8) | *cp++;
+	}
+	D.fc[j].C = x;
+
+	RansDecSymbolInit(&syms[j], D.fc[j].C, D.fc[j].F);
+
+	/* Build reverse lookup table */
+	if (!D.R) D.R = (unsigned char *)malloc(TOTFREQ);
+	memset(&D.R[x], j, D.fc[j].F);
+
+	x += D.fc[j].F;
+
+	if (!rle && j+1 == *cp) {
+	    j = *cp++;
+	    rle = *cp++;
+	} else if (rle) {
+	    rle--;
+	    j++;
+	} else {
+	    j = *cp++;
+	}
+    } while(j);
+
+    assert(x < TOTFREQ);
+
+    RansState rans0, rans1, rans2, rans3;
+    uint8_t *ptr = cp;
+    RansDecInit(&rans0, &ptr);
+    RansDecInit(&rans1, &ptr);
+    RansDecInit(&rans2, &ptr);
+    RansDecInit(&rans3, &ptr);
+
+    int out_end = (out_sz&~3);
+
+    RansState R[4];
+    R[0] = rans0;
+    R[1] = rans1;
+    R[2] = rans2;
+    R[3] = rans3;
+    uint32_t mask = (1u << TF_SHIFT)-1;
+
+    for (i=0; i < out_end; i+=4) {
+	uint32_t m[4] = {R[0] & mask,
+			 R[1] & mask,
+			 R[2] & mask,
+			 R[3] & mask};
+	uint8_t c[4] = {D.R[m[0]],
+			D.R[m[1]],
+			D.R[m[2]],
+			D.R[m[3]]};
+	out_buf[i+0] = c[0];
+	out_buf[i+1] = c[1];
+	out_buf[i+2] = c[2];
+	out_buf[i+3] = c[3];
+
+	// RansDecAdvanceSymbolStep(&R[0], &syms[c[0]], TF_SHIFT);
+	// RansDecAdvanceSymbolStep(&R[1], &syms[c[1]], TF_SHIFT);
+	// RansDecAdvanceSymbolStep(&R[2], &syms[c[2]], TF_SHIFT);
+	// RansDecAdvanceSymbolStep(&R[3], &syms[c[3]], TF_SHIFT);
+	R[0] = syms[c[0]].freq * (R[0]>>TF_SHIFT);
+	R[1] = syms[c[1]].freq * (R[1]>>TF_SHIFT);
+	R[2] = syms[c[2]].freq * (R[2]>>TF_SHIFT);
+	R[3] = syms[c[3]].freq * (R[3]>>TF_SHIFT);
+
+	R[0] += m[0] - syms[c[0]].start;
+	R[1] += m[1] - syms[c[1]].start;
+	R[2] += m[2] - syms[c[2]].start;
+	R[3] += m[3] - syms[c[3]].start;
+
+	RansDecRenorm(&R[0], &ptr);
+	RansDecRenorm(&R[1], &ptr);
+	RansDecRenorm(&R[2], &ptr);
+	RansDecRenorm(&R[3], &ptr);
+    }
+
+    rans0 = R[0];
+    rans1 = R[1];
+    rans2 = R[2];
+    rans3 = R[3];
+
+    switch(out_sz&3) {
+	unsigned char c;
+    case 0:
+	break;
+    case 1:
+	c = D.R[RansDecGet(&rans0, TF_SHIFT)];
+	RansDecAdvanceSymbol(&rans0, &ptr, &syms[c], TF_SHIFT);
+	out_buf[out_end] = c;
+	break;
+
+    case 2:
+	c = D.R[RansDecGet(&rans0, TF_SHIFT)];
+	RansDecAdvanceSymbol(&rans0, &ptr, &syms[c], TF_SHIFT);
+	out_buf[out_end] = c;
+
+	c = D.R[RansDecGet(&rans1, TF_SHIFT)];
+	RansDecAdvanceSymbol(&rans1, &ptr, &syms[c], TF_SHIFT);
+	out_buf[out_end+1] = c;
+	break;
+
+    case 3:
+	c = D.R[RansDecGet(&rans0, TF_SHIFT)];
+	RansDecAdvanceSymbol(&rans0, &ptr, &syms[c], TF_SHIFT);
+	out_buf[out_end] = c;
+
+	c = D.R[RansDecGet(&rans1, TF_SHIFT)];
+	RansDecAdvanceSymbol(&rans1, &ptr, &syms[c], TF_SHIFT);
+	out_buf[out_end+1] = c;
+
+	c = D.R[RansDecGet(&rans2, TF_SHIFT)];
+	RansDecAdvanceSymbol(&rans2, &ptr, &syms[c], TF_SHIFT);
+	out_buf[out_end+2] = c;
+	break;
+    }
+
+    *out_size = out_sz;
+
+    if (D.R) free(D.R);
+
+    return (unsigned char *)out_buf;
+}
+
+unsigned char *rans_compress_O1(unsigned char *in, unsigned int in_size,
+				unsigned int *out_size) {
+    unsigned char *out_buf = NULL, *out_end, *cp;
+    unsigned int last_i, tab_size, rle_i, rle_j;
+    RansEncSymbol (*syms)[256] = NULL;  /* syms[256][256] */
+    int (*F)[256] = NULL;               /* F[256][256]    */
+    int *T = NULL;                      /* T[256]         */
+    int i, j;
+    unsigned char c;
+
+    if (in_size < 4)
+	return rans_compress_O0(in, in_size, out_size);
+
+    syms = malloc(256 * sizeof(*syms));
+    if (!syms) goto cleanup;
+    F = calloc(256, sizeof(*F));
+    if (!F) goto cleanup;
+    T = calloc(256, sizeof(*T));
+    if (!T) goto cleanup;
+    out_buf = malloc(1.05*in_size + 257*257*3 + 9);
+    if (!out_buf) goto cleanup;
+
+    out_end = out_buf + (int)(1.05*in_size) + 257*257*3 + 9;
+    cp = out_buf+9;
+
+    //for (last = 0, i=in_size-1; i>=0; i--) {
+    //	F[last][c = in[i]]++;
+    //	T[last]++;
+    //	last = c;
+    //}
+
+    for (last_i=i=0; i<in_size; i++) {
+	F[last_i][c = in[i]]++;
+	T[last_i]++;
+	last_i = c;
+    }
+    F[0][in[1*(in_size>>2)]]++;
+    F[0][in[2*(in_size>>2)]]++;
+    F[0][in[3*(in_size>>2)]]++;
+    T[0]+=3;
+
+    // Normalise so T[i] == TOTFREQ
+    for (rle_i = i = 0; i < 256; i++) {
+	int t2, m, M;
+	unsigned int x;
+
+	if (T[i] == 0)
+	    continue;
+
+	//uint64_t p = (TOTFREQ * TOTFREQ) / t;
+	double p = ((double)TOTFREQ)/T[i];
+	for (t2 = m = M = j = 0; j < 256; j++) {
+	    if (!F[i][j])
+		continue;
+
+	    if (m < F[i][j])
+		m = F[i][j], M = j;
+
+	    //if ((F[i][j] = (F[i][j] * p) / TOTFREQ) == 0)
+	    if ((F[i][j] *= p) == 0)
+		F[i][j] = 1;
+	    t2 += F[i][j];
+	}
+
+	t2++;
+	if (t2 < TOTFREQ)
+	    F[i][M] += TOTFREQ-t2;
+	else
+	    F[i][M] -= t2-TOTFREQ;
+
+	// Store frequency table
+	// i
+	if (rle_i) {
+	    rle_i--;
+	} else {
+	    *cp++ = i;
+	    // FIXME: could use order-0 statistics to observe which alphabet
+	    // symbols are present and base RLE on that ordering instead.
+	    if (i && T[i-1]) {
+		for(rle_i=i+1; rle_i<256 && T[rle_i]; rle_i++)
+		    ;
+		rle_i -= i+1;
+		*cp++ = rle_i;
+	    }
+	}
+
+	int *F_i_ = F[i];
+	x = 0;
+	rle_j = 0;
+	for (j = 0; j < 256; j++) {
+	    if (F_i_[j]) {
+		//fprintf(stderr, "F[%d][%d]=%d, x=%d\n", i, j, F_i_[j], x);
+
+		// j
+		if (rle_j) {
+		    rle_j--;
+		} else {
+		    *cp++ = j;
+		    if (!rle_j && j && F_i_[j-1]) {
+			for(rle_j=j+1; rle_j<256 && F_i_[rle_j]; rle_j++)
+			    ;
+			rle_j -= j+1;
+			*cp++ = rle_j;
+		    }
+		}
+
+		// F_i_[j]
+		if (F_i_[j]<128) {
+		    *cp++ = F_i_[j];
+		} else {
+		    *cp++ = 128 | (F_i_[j]>>8);
+		    *cp++ = F_i_[j]&0xff;
+		}
+
+		RansEncSymbolInit(&syms[i][j], x, F_i_[j], TF_SHIFT);
+		x += F_i_[j];
+	    }
+	}
+	*cp++ = 0;
+    }
+    *cp++ = 0;
+
+    //write(1, out_buf+4, cp-(out_buf+4));
+    tab_size = cp - out_buf;
+    assert(tab_size < 257*257*3);
+
+    RansState rans0, rans1, rans2, rans3;
+    RansEncInit(&rans0);
+    RansEncInit(&rans1);
+    RansEncInit(&rans2);
+    RansEncInit(&rans3);
+
+    uint8_t* ptr = out_end;
+
+    int isz4 = in_size>>2;
+    int i0 = 1*isz4-2;
+    int i1 = 2*isz4-2;
+    int i2 = 3*isz4-2;
+    int i3 = 4*isz4-2;
+
+    unsigned char l0 = in[i0+1];
+    unsigned char l1 = in[i1+1];
+    unsigned char l2 = in[i2+1];
+    unsigned char l3 = in[i3+1];
+
+    // Deal with the remainder
+    l3 = in[in_size-1];
+    for (i3 = in_size-2; i3 > 4*isz4-2; i3--) {
+	unsigned char c3 = in[i3];
+	RansEncPutSymbol(&rans3, &ptr, &syms[c3][l3]);
+	l3 = c3;
+    }
+
+    for (; i0 >= 0; i0--, i1--, i2--, i3--) {
+	unsigned char c0, c1, c2, c3;
+	RansEncSymbol *s3 = &syms[c3 = in[i3]][l3];
+	RansEncSymbol *s2 = &syms[c2 = in[i2]][l2];
+	RansEncSymbol *s1 = &syms[c1 = in[i1]][l1];
+	RansEncSymbol *s0 = &syms[c0 = in[i0]][l0];
+
+	RansEncPutSymbol(&rans3, &ptr, s3);
+	RansEncPutSymbol(&rans2, &ptr, s2);
+	RansEncPutSymbol(&rans1, &ptr, s1);
+	RansEncPutSymbol(&rans0, &ptr, s0);
+
+	l0 = c0;
+	l1 = c1;
+	l2 = c2;
+	l3 = c3;
+    }
+
+    RansEncPutSymbol(&rans3, &ptr, &syms[0][l3]);
+    RansEncPutSymbol(&rans2, &ptr, &syms[0][l2]);
+    RansEncPutSymbol(&rans1, &ptr, &syms[0][l1]);
+    RansEncPutSymbol(&rans0, &ptr, &syms[0][l0]);
+
+    RansEncFlush(&rans3, &ptr);
+    RansEncFlush(&rans2, &ptr);
+    RansEncFlush(&rans1, &ptr);
+    RansEncFlush(&rans0, &ptr);
+
+    *out_size = (out_end - ptr) + tab_size;
+
+    cp = out_buf;
+    *cp++ = 1; // order
+
+    *cp++ = ((*out_size-9)>> 0) & 0xff;
+    *cp++ = ((*out_size-9)>> 8) & 0xff;
+    *cp++ = ((*out_size-9)>>16) & 0xff;
+    *cp++ = ((*out_size-9)>>24) & 0xff;
+
+    *cp++ = (in_size>> 0) & 0xff;
+    *cp++ = (in_size>> 8) & 0xff;
+    *cp++ = (in_size>>16) & 0xff;
+    *cp++ = (in_size>>24) & 0xff;
+
+    memmove(out_buf + tab_size, ptr, out_end-ptr);
+
+ cleanup:
+    free(syms);
+    free(F);
+    free(T);
+
+    return out_buf;
+}
+
+unsigned char *rans_uncompress_O1(unsigned char *in, unsigned int in_size,
+				  unsigned int *out_size) {
+    /* Load in the static tables */
+    unsigned char *cp = in + 9;
+    int i, j = -999, x, out_sz, in_sz, rle_i, rle_j;
+    char *out_buf = NULL;
+    ari_decoder *D = NULL;              /* D[256] */
+    RansDecSymbol (*syms)[256] = NULL;  /* syms[256][256] */
+
+    if (*in++ != 1) // Order-1 check
+	return NULL;
+
+    in_sz  = ((in[0])<<0) | ((in[1])<<8) | ((in[2])<<16) | ((in[3])<<24);
+    out_sz = ((in[4])<<0) | ((in[5])<<8) | ((in[6])<<16) | ((in[7])<<24);
+    if (in_sz != in_size-9)
+	return NULL;
+
+    D = calloc(256, sizeof(*D));
+    if (!D) goto cleanup;
+    syms = malloc(256 * sizeof(*syms));
+    if (!syms) goto cleanup;
+
+    //fprintf(stderr, "out_sz=%d\n", out_sz);
+
+    //i = *cp++;
+    rle_i = 0;
+    i = *cp++;
+    do {
+	rle_j = x = 0;
+	j = *cp++;
+	do {
+	    if ((D[i].fc[j].F = *cp++) >= 128) {
+		D[i].fc[j].F &= ~128;
+		D[i].fc[j].F = ((D[i].fc[j].F & 127) << 8) | *cp++;
+	    }
+	    D[i].fc[j].C = x;
+
+	    //fprintf(stderr, "i=%d j=%d F=%d C=%d\n", i, j, D[i].fc[j].F, D[i].fc[j].C);
+
+	    if (!D[i].fc[j].F)
+		D[i].fc[j].F = TOTFREQ;
+
+	    RansDecSymbolInit(&syms[i][j], D[i].fc[j].C, D[i].fc[j].F);
+
+	    /* Build reverse lookup table */
+	    if (!D[i].R) {
+                D[i].R = (unsigned char *)malloc(TOTFREQ);
+                if (!D[i].R)
+                    goto cleanup;
+            }
+	    memset(&D[i].R[x], j, D[i].fc[j].F);
+
+	    x += D[i].fc[j].F;
+	    assert(x <= TOTFREQ);
+
+	    if (!rle_j && j+1 == *cp) {
+		j = *cp++;
+		rle_j = *cp++;
+	    } else if (rle_j) {
+		rle_j--;
+		j++;
+	    } else {
+		j = *cp++;
+	    }
+	} while(j);
+
+	if (!rle_i && i+1 == *cp) {
+	    i = *cp++;
+	    rle_i = *cp++;
+	} else if (rle_i) {
+	    rle_i--;
+	    i++;
+	} else {
+	    i = *cp++;
+	}
+    } while (i);
+
+    // Precompute reverse lookup of frequency.
+
+    RansState rans0, rans1, rans2, rans3;
+    uint8_t *ptr = cp;
+    RansDecInit(&rans0, &ptr);
+    RansDecInit(&rans1, &ptr);
+    RansDecInit(&rans2, &ptr);
+    RansDecInit(&rans3, &ptr);
+
+    int isz4 = out_sz>>2;
+    int l0 = 0;
+    int l1 = 0;
+    int l2 = 0;
+    int l3 = 0;
+    int i4[] = {0*isz4, 1*isz4, 2*isz4, 3*isz4};
+
+    RansState R[4];
+    R[0] = rans0;
+    R[1] = rans1;
+    R[2] = rans2;
+    R[3] = rans3;
+
+    /* Allocate output buffer */
+    out_buf = malloc(out_sz);
+    if (!out_buf) goto cleanup;
+
+    for (; i4[0] < isz4; i4[0]++, i4[1]++, i4[2]++, i4[3]++) {
+	uint32_t m[4] = {R[0] & ((1u << TF_SHIFT)-1),
+			 R[1] & ((1u << TF_SHIFT)-1),
+			 R[2] & ((1u << TF_SHIFT)-1),
+			 R[3] & ((1u << TF_SHIFT)-1)};
+
+	uint8_t c[4] = {D[l0].R[m[0]],
+			D[l1].R[m[1]],
+			D[l2].R[m[2]],
+			D[l3].R[m[3]]};
+
+	out_buf[i4[0]] = c[0];
+	out_buf[i4[1]] = c[1];
+	out_buf[i4[2]] = c[2];
+	out_buf[i4[3]] = c[3];
+
+	//RansDecAdvanceSymbolStep(&R[0], &syms[l0][c[0]], TF_SHIFT);
+	//RansDecAdvanceSymbolStep(&R[1], &syms[l1][c[1]], TF_SHIFT);
+	//RansDecAdvanceSymbolStep(&R[2], &syms[l2][c[2]], TF_SHIFT);
+	//RansDecAdvanceSymbolStep(&R[3], &syms[l3][c[3]], TF_SHIFT);
+
+	R[0] = syms[l0][c[0]].freq * (R[0]>>TF_SHIFT);
+	R[1] = syms[l1][c[1]].freq * (R[1]>>TF_SHIFT);
+	R[2] = syms[l2][c[2]].freq * (R[2]>>TF_SHIFT);
+	R[3] = syms[l3][c[3]].freq * (R[3]>>TF_SHIFT);
+
+	R[0] += m[0] - syms[l0][c[0]].start;
+	R[1] += m[1] - syms[l1][c[1]].start;
+	R[2] += m[2] - syms[l2][c[2]].start;
+	R[3] += m[3] - syms[l3][c[3]].start;
+
+	RansDecRenorm(&R[0], &ptr);
+	RansDecRenorm(&R[1], &ptr);
+	RansDecRenorm(&R[2], &ptr);
+	RansDecRenorm(&R[3], &ptr);
+
+	l0 = c[0];
+	l1 = c[1];
+	l2 = c[2];
+	l3 = c[3];
+    }
+
+    rans0 = R[0];
+    rans1 = R[1];
+    rans2 = R[2];
+    rans3 = R[3];
+
+    // Remainder
+    for (; i4[3] < out_sz; i4[3]++) {
+	unsigned char c3 = D[l3].R[RansDecGet(&rans3, TF_SHIFT)];
+	out_buf[i4[3]] = c3;
+	RansDecAdvanceSymbol(&rans3, &ptr, &syms[l3][c3], TF_SHIFT);
+	l3 = c3;
+    }
+
+    *out_size = out_sz;
+
+ cleanup:
+    if (D) {
+        for (i = 0; i < 256; i++)
+            if (D[i].R) free(D[i].R);
+        free(D);
+    }
+    free(syms);
+
+    return (unsigned char *)out_buf;
+}
+
+/*-----------------------------------------------------------------------------
+ * Simple interface to the order-0 vs order-1 encoders and decoders.
+ */
+unsigned char *rans_compress(unsigned char *in, unsigned int in_size,
+			     unsigned int *out_size, int order) {
+    return order
+	? rans_compress_O1(in, in_size, out_size)
+	: rans_compress_O0(in, in_size, out_size);
+}
+
+unsigned char *rans_uncompress(unsigned char *in, unsigned int in_size,
+			       unsigned int *out_size) {
+    /* Both rans_uncompress functions need to be able to read at least 9
+       bytes. */
+    if (in_size < 9)
+        return NULL;
+    return in[0]
+	? rans_uncompress_O1(in, in_size, out_size)
+	: rans_uncompress_O0(in, in_size, out_size);
+}
+
+
+#ifdef TEST_MAIN
+/*-----------------------------------------------------------------------------
+ * Main.
+ *
+ * This is a simple command line tool for testing order-0 and order-1
+ * compression using the rANS codec. Simply compile with
+ *
+ * gcc -DTEST_MAIN -O3 -I. cram/rANS_static.c -o cram/rANS_static
+ *
+ * Usage: cram/rANS_static -o0 < file    > file.o0
+ *        cram/rANS_static -d  < file.o0 > file2
+ *
+ *        cram/rANS_static -o1 < file    > file.o1
+ *        cram/rANS_static -d  < file.o1 > file2
+ */
+int main(int argc, char **argv) {
+    int opt, order = 0;
+    unsigned char in_buf[BLK_SIZE2+257*257*3];
+    int decode = 0;
+    FILE *infp = stdin, *outfp = stdout;
+    struct timeval tv1, tv2;
+    size_t bytes = 0;
+
+    extern char *optarg;
+    extern int optind;
+
+    while ((opt = getopt(argc, argv, "o:d")) != -1) {
+	switch (opt) {
+	case 'o':
+	    order = atoi(optarg);
+	    break;
+
+	case 'd':
+	    decode = 1;
+	    break;
+	}
+    }
+
+    order = order ? 1 : 0; // Only support O(0) and O(1)
+
+    if (optind < argc) {
+	if (!(infp = fopen(argv[optind], "rb"))) {
+	    perror(argv[optind]);
+	    return 1;
+	}
+	optind++;
+    }
+
+    if (optind < argc) {
+	if (!(outfp = fopen(argv[optind], "wb"))) {
+	    perror(argv[optind]);
+	    return 1;
+	}
+	optind++;
+    }
+
+    gettimeofday(&tv1, NULL);
+
+    if (decode) {
+	// Only used in some test implementations of RC_GetFreq()
+	//RC_init();
+	//RC_init2();
+
+	for (;;) {
+	    uint32_t in_size, out_size;
+	    unsigned char *out;
+
+	    if (9 != fread(in_buf, 1, 9, infp))
+		break;
+	    in_size = *(int *)&in_buf[1];
+	    if (in_size != fread(in_buf+9, 1, in_size, infp)) {
+		fprintf(stderr, "Truncated input\n");
+		exit(1);
+	    }
+	    out = rans_uncompress(in_buf, in_size+9, &out_size);
+	    if (!out)
+		abort();
+
+	    fwrite(out, 1, out_size, outfp);
+	    free(out);
+
+	    bytes += out_size;
+	}
+    } else {
+	for (;;) {
+	    uint32_t in_size, out_size;
+	    unsigned char *out;
+
+	    in_size = fread(in_buf, 1, BLK_SIZE, infp);
+	    if (in_size <= 0)
+		break;
+
+	    out = rans_compress(in_buf, in_size, &out_size, order);
+
+	    fwrite(out, 1, out_size, outfp);
+	    free(out);
+
+	    bytes += in_size;
+	}
+    }
+
+    gettimeofday(&tv2, NULL);
+
+    fprintf(stderr, "Took %ld microseconds, %5.1f MB/s\n",
+	    (long)(tv2.tv_sec - tv1.tv_sec)*1000000 +
+	    tv2.tv_usec - tv1.tv_usec,
+	    (double)bytes / ((long)(tv2.tv_sec - tv1.tv_sec)*1000000 +
+			     tv2.tv_usec - tv1.tv_usec));
+    return 0;
+}
+#endif
diff --git a/htslib/cram/rANS_static.h b/htslib/cram/rANS_static.h
new file mode 100644
index 0000000..11f20b8
--- /dev/null
+++ b/htslib/cram/rANS_static.h
@@ -0,0 +1,51 @@
+/*
+ * Copyright (c) 2014 Genome Research Ltd.
+ * Author(s): James Bonfield
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ *    1. Redistributions of source code must retain the above copyright notice,
+ *       this list of conditions and the following disclaimer.
+ *
+ *    2. Redistributions in binary form must reproduce the above
+ *       copyright notice, this list of conditions and the following
+ *       disclaimer in the documentation and/or other materials provided
+ *       with the distribution.
+ *
+ *    3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+ *       Institute nor the names of its contributors may be used to endorse
+ *       or promote products derived from this software without specific
+ *       prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS
+ * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+ * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+ * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH
+ * LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+
+#ifndef RANS_STATIC_H
+#define RANS_STATIC_H
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+unsigned char *rans_compress(unsigned char *in, unsigned int in_size,
+			     unsigned int *out_size, int order);
+unsigned char *rans_uncompress(unsigned char *in, unsigned int in_size,
+			       unsigned int *out_size);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* RANS_STATIC_H */
diff --git a/htslib/cram/sam_header.c b/htslib/cram/sam_header.c
new file mode 100644
index 0000000..cc13d46
--- /dev/null
+++ b/htslib/cram/sam_header.c
@@ -0,0 +1,1268 @@
+/*
+Copyright (c) 2013 Genome Research Ltd.
+Author: James Bonfield <jkb at sanger.ac.uk>
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+Institute nor the names of its contributors may be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+#include <config.h>
+
+#include <string.h>
+#include <assert.h>
+
+#include "cram/sam_header.h"
+#include "cram/string_alloc.h"
+
+static void sam_hdr_error(char *msg, char *line, int len, int lno) {
+    int j;
+    
+    for (j = 0; j < len && line[j] != '\n'; j++)
+	;
+    fprintf(stderr, "%s at line %d: \"%.*s\"\n", msg, lno, j, line);
+}
+
+void sam_hdr_dump(SAM_hdr *hdr) {
+    khint_t k;
+    int i;
+
+    printf("===DUMP===\n");
+    for (k = kh_begin(hdr->h); k != kh_end(hdr->h); k++) {
+	SAM_hdr_type *t1, *t2;
+	char c[2];
+
+	if (!kh_exist(hdr->h, k))
+	    continue;
+
+	t1 = t2 = kh_val(hdr->h, k);
+	c[0] = kh_key(hdr->h, k)>>8;
+	c[1] = kh_key(hdr->h, k)&0xff;
+	printf("Type %.2s, count %d\n", c, t1->prev->order+1);
+
+	do {
+	    SAM_hdr_tag *tag;
+	    printf(">>>%d ", t1->order);
+	    for (tag = t1->tag; tag; tag=tag->next) {
+		printf("\"%.2s\":\"%.*s\"\t",
+		       tag->str, tag->len-3, tag->str+3);
+	    }
+	    putchar('\n');
+	    t1 = t1->next;
+	} while (t1 != t2);
+    }
+
+    /* Dump out PG chains */
+    printf("\n at PG chains:\n");
+    for (i = 0; i < hdr->npg_end; i++) {
+	int j;
+	printf("  %d:", i);
+	for (j = hdr->pg_end[i]; j != -1; j = hdr->pg[j].prev_id) {
+	    printf("%s%d(%.*s)", 
+		   j == hdr->pg_end[i] ? " " : "->",
+		   j, hdr->pg[j].name_len, hdr->pg[j].name);
+	}
+	printf("\n");
+    }
+
+    puts("===END DUMP===");
+}
+
+/* Updates the hash tables in the SAM_hdr structure.
+ *
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+static int sam_hdr_update_hashes(SAM_hdr *sh,
+				 int type,
+				 SAM_hdr_type *h_type) {
+    /* Add to reference hash? */
+    if ((type>>8) == 'S' && (type&0xff) == 'Q') {
+	SAM_hdr_tag *tag;
+	SAM_SQ *new_ref;
+	int nref = sh->nref;
+
+	new_ref = realloc(sh->ref, (sh->nref+1)*sizeof(*sh->ref));
+	if (!new_ref)
+	    return -1;
+	sh->ref = new_ref;
+
+	tag = h_type->tag;
+	sh->ref[nref].name = NULL;
+	sh->ref[nref].len  = 0;
+	sh->ref[nref].ty = h_type;
+	sh->ref[nref].tag  = tag;
+
+	while (tag) {
+	    if (tag->str[0] == 'S' && tag->str[1] == 'N') {
+		if (!(sh->ref[nref].name = malloc(tag->len)))
+		    return -1;
+		strncpy(sh->ref[nref].name, tag->str+3, tag->len-3);
+		sh->ref[nref].name[tag->len-3] = 0;
+	    } else if (tag->str[0] == 'L' && tag->str[1] == 'N') {
+		sh->ref[nref].len = atoi(tag->str+3);
+	    }
+	    tag = tag->next;
+	}
+
+	if (sh->ref[nref].name) {
+	    khint_t k;
+	    int r;
+	    k = kh_put(m_s2i, sh->ref_hash, sh->ref[nref].name, &r);
+	    if (-1 == r) return -1;
+	    kh_val(sh->ref_hash, k) = nref;
+	} else {
+	    return -1; // SN should be present, according to spec.
+	}
+
+	sh->nref++;
+    }
+
+    /* Add to read-group hash? */
+    if ((type>>8) == 'R' && (type&0xff) == 'G') {
+	SAM_hdr_tag *tag;
+	SAM_RG *new_rg;
+	int nrg = sh->nrg;
+
+	new_rg = realloc(sh->rg, (sh->nrg+1)*sizeof(*sh->rg));
+	if (!new_rg)
+	    return -1;
+	sh->rg = new_rg;
+
+	tag = h_type->tag;
+	sh->rg[nrg].name = NULL;
+	sh->rg[nrg].name_len = 0;
+	sh->rg[nrg].ty   = h_type;
+	sh->rg[nrg].tag  = tag;
+	sh->rg[nrg].id   = nrg;
+
+	while (tag) {
+	    if (tag->str[0] == 'I' && tag->str[1] == 'D') {
+		if (!(sh->rg[nrg].name = malloc(tag->len)))
+		    return -1;
+		strncpy(sh->rg[nrg].name, tag->str+3, tag->len-3);
+		sh->rg[nrg].name[tag->len-3] = 0;
+		sh->rg[nrg].name_len = strlen(sh->rg[nrg].name);
+	    }
+	    tag = tag->next;
+	}
+
+	if (sh->rg[nrg].name) {
+	    khint_t k;
+	    int r;
+	    k = kh_put(m_s2i, sh->rg_hash, sh->rg[nrg].name, &r);
+	    if (-1 == r) return -1;
+	    kh_val(sh->rg_hash, k) = nrg;
+	} else {
+	    return -1; // ID should be present, according to spec.
+	}
+
+	sh->nrg++;
+    }
+
+    /* Add to program hash? */
+    if ((type>>8) == 'P' && (type&0xff) == 'G') {
+	SAM_hdr_tag *tag;
+	SAM_PG *new_pg;
+	int npg = sh->npg;
+
+	new_pg = realloc(sh->pg, (sh->npg+1)*sizeof(*sh->pg));
+	if (!new_pg)
+	    return -1;
+	sh->pg = new_pg;
+
+	tag = h_type->tag;
+	sh->pg[npg].name = NULL;
+	sh->pg[npg].name_len = 0;
+	sh->pg[npg].ty  = h_type;
+	sh->pg[npg].tag  = tag;
+	sh->pg[npg].id   = npg;
+	sh->pg[npg].prev_id = -1;
+
+	while (tag) {
+	    if (tag->str[0] == 'I' && tag->str[1] == 'D') {
+		if (!(sh->pg[npg].name = malloc(tag->len)))
+		    return -1;
+		strncpy(sh->pg[npg].name, tag->str+3, tag->len-3);
+		sh->pg[npg].name[tag->len-3] = 0;
+		sh->pg[npg].name_len = strlen(sh->pg[npg].name);
+	    } else if (tag->str[0] == 'P' && tag->str[1] == 'P') {
+		// Resolve later if needed
+		khint_t k;
+		char tmp = tag->str[tag->len]; tag->str[tag->len] = 0;
+		k = kh_get(m_s2i, sh->pg_hash, tag->str+3);
+		tag->str[tag->len] = tmp;
+
+		if (k != kh_end(sh->pg_hash)) {
+		    int p_id = kh_val(sh->pg_hash, k);
+		    sh->pg[npg].prev_id = sh->pg[p_id].id;
+
+		    /* Unmark previous entry as a PG termination */
+		    if (sh->npg_end > 0 &&
+			sh->pg_end[sh->npg_end-1] == p_id) {
+			sh->npg_end--;
+		    } else {
+			int i;
+			for (i = 0; i < sh->npg_end; i++) {
+			    if (sh->pg_end[i] == p_id) {
+				memmove(&sh->pg_end[i], &sh->pg_end[i+1],
+					(sh->npg_end-i-1)*sizeof(*sh->pg_end));
+				sh->npg_end--;
+			    }
+			}
+		    }
+		} else {
+		    sh->pg[npg].prev_id = -1;
+		}
+	    }
+	    tag = tag->next;
+	}
+
+	if (sh->pg[npg].name) {
+	    khint_t k;
+	    int r;
+	    k = kh_put(m_s2i, sh->pg_hash, sh->pg[npg].name, &r);
+	    if (-1 == r) return -1;
+	    kh_val(sh->pg_hash, k) = npg;
+	} else {
+	    return -1; // ID should be present, according to spec.
+	}
+
+	/* Add to npg_end[] array. Remove later if we find a PP line */
+	if (sh->npg_end >= sh->npg_end_alloc) {
+	    int *new_pg_end;
+	    int  new_alloc = sh->npg_end_alloc ? sh->npg_end_alloc*2 : 4;
+
+	    new_pg_end = realloc(sh->pg_end, new_alloc * sizeof(int));
+	    if (!new_pg_end)
+		return -1;
+	    sh->npg_end_alloc = new_alloc;
+	    sh->pg_end = new_pg_end;
+	}
+	sh->pg_end[sh->npg_end++] = npg;
+
+	sh->npg++;
+    }
+
+    return 0;
+}
+
+/*
+ * Appends a formatted line to an existing SAM header.
+ * Line is a full SAM header record, eg "@SQ\tSN:foo\tLN:100", with
+ * optional new-line. If it contains more than 1 line then multiple lines
+ * will be added in order.
+ *
+ * Input text is of maximum length len or as terminated earlier by a NUL.
+ * Len may be 0 if unknown, in which case lines must be NUL-terminated.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int sam_hdr_add_lines(SAM_hdr *sh, const char *lines, int len) {
+    int i, lno, text_offset;
+    char *hdr;
+
+    if (!len)
+	len = strlen(lines);
+
+    text_offset = ks_len(&sh->text);
+    if (EOF == kputsn(lines, len, &sh->text))
+	return -1;
+    hdr = ks_str(&sh->text) + text_offset;
+
+    for (i = 0, lno = 1; i < len && hdr[i] != '\0'; i++, lno++) {
+	khint32_t type;
+	khint_t k;
+
+	int l_start = i, new;
+	SAM_hdr_type *h_type;
+	SAM_hdr_tag *h_tag, *last;
+
+	if (hdr[i] != '@') {
+	    int j;
+	    for (j = i; j < len && hdr[j] != '\0' && hdr[j] != '\n'; j++)
+		;
+	    sam_hdr_error("Header line does not start with '@'",
+			  &hdr[l_start], len - l_start, lno);
+	    return -1;
+	}
+
+	type = (hdr[i+1]<<8) | hdr[i+2];
+	if (hdr[i+1] < 'A' || hdr[i+1] > 'z' ||
+	    hdr[i+2] < 'A' || hdr[i+2] > 'z') {
+	    sam_hdr_error("Header line does not have a two character key",
+			  &hdr[l_start], len - l_start, lno);
+	    return -1;
+	}
+
+	i += 3;
+	if (hdr[i] == '\n')
+	    continue;
+
+	// Add the header line type
+	if (!(h_type = pool_alloc(sh->type_pool)))
+	    return -1;
+	if (-1 == (k = kh_put(sam_hdr, sh->h, type, &new)))
+	    return -1;
+
+	// Form the ring, either with self or other lines of this type
+	if (!new) {
+	    SAM_hdr_type *t = kh_val(sh->h, k), *p;
+	    p = t->prev;
+	    
+	    assert(p->next == t);
+	    p->next = h_type;
+	    h_type->prev = p;
+
+	    t->prev = h_type;
+	    h_type->next = t;
+	    h_type->order = p->order+1;
+	} else {
+	    kh_val(sh->h, k) = h_type;
+	    h_type->prev = h_type->next = h_type;
+	    h_type->order = 0;
+	}
+
+	// Parse the tags on this line
+	last = NULL;
+	if ((type>>8) == 'C' && (type&0xff) == 'O') {
+	    int j;
+	    if (hdr[i] != '\t') {
+		sam_hdr_error("Missing tab",
+			      &hdr[l_start], len - l_start, lno);
+		return -1;
+	    }
+
+	    for (j = ++i; j < len && hdr[j] != '\0' && hdr[j] != '\n'; j++)
+		;
+
+	    if (!(h_type->tag = h_tag = pool_alloc(sh->tag_pool)))
+		return -1;
+	    h_tag->str = string_ndup(sh->str_pool, &hdr[i], j-i);
+	    h_tag->len = j-i;
+	    h_tag->next = NULL;
+	    if (!h_tag->str)
+		return -1;
+
+	    i = j;
+
+	} else {
+	    do {
+		int j;
+		if (hdr[i] != '\t') {
+		    sam_hdr_error("Missing tab",
+				  &hdr[l_start], len - l_start, lno);
+		    return -1;
+		}
+
+		for (j = ++i; j < len && hdr[j] != '\0' && hdr[j] != '\n' && hdr[j] != '\t'; j++)
+		    ;
+	    
+		if (!(h_tag = pool_alloc(sh->tag_pool)))
+		    return -1;
+		h_tag->str = string_ndup(sh->str_pool, &hdr[i], j-i);
+		h_tag->len = j-i;
+		h_tag->next = NULL;
+		if (!h_tag->str)
+		    return -1;
+
+		if (h_tag->len < 3 || h_tag->str[2] != ':') {
+		    sam_hdr_error("Malformed key:value pair",
+				  &hdr[l_start], len - l_start, lno);
+		    return -1;
+		}
+	    
+		if (last)
+		    last->next = h_tag;
+		else
+		    h_type->tag = h_tag;
+
+		last = h_tag;
+		i = j;
+	    } while (i < len && hdr[i] != '\0' && hdr[i] != '\n');
+	}
+
+	/* Update RG/SQ hashes */
+	if (-1 == sam_hdr_update_hashes(sh, type, h_type))
+	    return -1;
+    }
+
+    return 0;
+}
+
+/*
+ * Adds a single line to a SAM header.
+ * Specify type and one or more key,value pairs, ending with the NULL key.
+ * Eg. sam_hdr_add(h, "SQ", "ID", "foo", "LN", "100", NULL).
+ *
+ * Returns index for specific entry on success (eg 2nd SQ, 4th RG)
+ *        -1 on failure
+ */
+int sam_hdr_add(SAM_hdr *sh, const char *type, ...) {
+    va_list args;
+    va_start(args, type);
+    return sam_hdr_vadd(sh, type, args, NULL);
+}
+
+/* 
+ * sam_hdr_add with a va_list interface.
+ *
+ * Note: this function invokes va_arg at least once, making the value
+ * of ap indeterminate after the return.  The caller should call
+ * va_start/va_end before/after calling this function or use va_copy.
+ */
+int sam_hdr_vadd(SAM_hdr *sh, const char *type, va_list ap, ...) {
+    va_list args;
+    SAM_hdr_type *h_type;
+    SAM_hdr_tag *h_tag, *last;
+    int new;
+    khint32_t type_i = (type[0]<<8) | type[1], k;
+
+    if (EOF == kputc_('@', &sh->text))
+	return -1;
+    if (EOF == kputsn(type, 2, &sh->text))
+	return -1;
+
+    if (!(h_type = pool_alloc(sh->type_pool)))
+	return -1;
+    if (-1 == (k = kh_put(sam_hdr, sh->h, type_i, &new)))
+	return -1;
+
+    // Form the ring, either with self or other lines of this type
+    if (!new) {
+	SAM_hdr_type *t = kh_val(sh->h, k), *p;
+	p = t->prev;
+	    
+	assert(p->next == t);
+	p->next = h_type;
+	h_type->prev = p;
+
+	t->prev = h_type;
+	h_type->next = t;
+	h_type->order = p->order + 1;
+    } else {
+	kh_val(sh->h, k) = h_type;
+	h_type->prev = h_type->next = h_type;
+	h_type->order = 0;
+    }
+
+    last = NULL;
+
+    // Any ... varargs
+    va_start(args, ap);
+    for (;;) {
+	char *k, *v;
+	int idx;
+	
+	if (!(k = (char *)va_arg(args, char *)))
+	    break;
+	v = va_arg(args, char *);
+
+	if (EOF == kputc_('\t', &sh->text))
+	    return -1;
+
+	if (!(h_tag = pool_alloc(sh->tag_pool)))
+	    return -1;
+	idx = ks_len(&sh->text);
+	
+	if (EOF == kputs(k, &sh->text))
+	    return -1;
+	if (EOF == kputc_(':', &sh->text))
+	    return -1;
+	if (EOF == kputs(v, &sh->text))
+	    return -1;
+
+	h_tag->len = ks_len(&sh->text) - idx;
+	h_tag->str = string_ndup(sh->str_pool,
+				 ks_str(&sh->text) + idx,
+				 h_tag->len);
+	h_tag->next = NULL;
+	if (!h_tag->str)
+	    return -1;
+
+	if (last)
+	    last->next = h_tag;
+	else
+	    h_type->tag = h_tag;
+	
+	last = h_tag;
+    }
+    va_end(args);
+
+    // Plus the specified va_list params
+    for (;;) {
+	char *k, *v;
+	int idx;
+	
+	if (!(k = (char *)va_arg(ap, char *)))
+	    break;
+	v = va_arg(ap, char *);
+
+	if (EOF == kputc_('\t', &sh->text))
+	    return -1;
+
+	if (!(h_tag = pool_alloc(sh->tag_pool)))
+	    return -1;
+	idx = ks_len(&sh->text);
+	
+	if (EOF == kputs(k, &sh->text))
+	    return -1;
+	if (EOF == kputc_(':', &sh->text))
+	    return -1;
+	if (EOF == kputs(v, &sh->text))
+	    return -1;
+
+	h_tag->len = ks_len(&sh->text) - idx;
+	h_tag->str = string_ndup(sh->str_pool,
+				 ks_str(&sh->text) + idx,
+				 h_tag->len);
+	h_tag->next = NULL;
+	if (!h_tag->str)
+	    return -1;
+
+	if (last)
+	    last->next = h_tag;
+	else
+	    h_type->tag = h_tag;
+	
+	last = h_tag;
+    }
+    va_end(ap);
+
+    if (EOF == kputc('\n', &sh->text))
+	return -1;
+
+    int itype = (type[0]<<8) | type[1];
+    if (-1 == sam_hdr_update_hashes(sh, itype, h_type))
+	return -1;
+
+    return h_type->order;
+}
+
+/*
+ * Returns the first header item matching 'type'. If ID is non-NULL it checks
+ * for the tag ID: and compares against the specified ID.
+ *
+ * Returns NULL if no type/ID is found
+ */
+SAM_hdr_type *sam_hdr_find(SAM_hdr *hdr, char *type,
+			   char *ID_key, char *ID_value) {
+    SAM_hdr_type *t1, *t2;
+    int itype = (type[0]<<8)|(type[1]);
+    khint_t k;
+
+    /* Special case for types we have prebuilt hashes on */
+    if (ID_key) {
+	if (type[0]   == 'S' && type[1]   == 'Q' &&
+	    ID_key[0] == 'S' && ID_key[1] == 'N') {
+	    k = kh_get(m_s2i, hdr->ref_hash, ID_value);
+	    return k != kh_end(hdr->ref_hash)
+		? hdr->ref[kh_val(hdr->ref_hash, k)].ty
+		: NULL;
+	}
+
+	if (type[0]   == 'R' && type[1]   == 'G' &&
+	    ID_key[0] == 'I' && ID_key[1] == 'D') {
+	    k = kh_get(m_s2i, hdr->rg_hash, ID_value);
+	    return k != kh_end(hdr->rg_hash)
+		? hdr->rg[kh_val(hdr->rg_hash, k)].ty
+		: NULL;
+	}
+
+	if (type[0]   == 'P' && type[1]   == 'G' &&
+	    ID_key[0] == 'I' && ID_key[1] == 'D') {
+	    k = kh_get(m_s2i, hdr->pg_hash, ID_value);
+	    return k != kh_end(hdr->pg_hash)
+		? hdr->pg[kh_val(hdr->pg_hash, k)].ty
+		: NULL;
+	}
+    }
+
+    k = kh_get(sam_hdr, hdr->h, itype);
+    if (k == kh_end(hdr->h))
+	return NULL;
+    
+    if (!ID_key)
+	return kh_val(hdr->h, k);
+
+    t1 = t2 = kh_val(hdr->h, k);
+    do {
+	SAM_hdr_tag *tag;
+	for (tag = t1->tag; tag; tag = tag->next) {
+	    if (tag->str[0] == ID_key[0] && tag->str[1] == ID_key[1]) {
+		char *cp1 = tag->str+3;
+		char *cp2 = ID_value;
+		while (*cp1 && *cp1 == *cp2)
+		    cp1++, cp2++;
+		if (*cp2 || *cp1)
+		    continue;
+		return t1;
+	    }
+	}
+	t1 = t1->next;
+    } while (t1 != t2);
+
+    return NULL;
+}
+
+/*
+ * As per SAM_hdr_type, but returns a complete line of formatted text
+ * for a specific head type/ID combination. If ID is NULL then it returns
+ * the first line of the specified type.
+ *
+ * The returned string is malloced and should be freed by the calling
+ * function with free().
+ *
+ * Returns NULL if no type/ID is found.
+ */
+char *sam_hdr_find_line(SAM_hdr *hdr, char *type,
+			char *ID_key, char *ID_value) {
+    SAM_hdr_type *ty = sam_hdr_find(hdr, type, ID_key, ID_value);
+    kstring_t ks = KS_INITIALIZER;
+    SAM_hdr_tag *tag;
+    int r = 0;
+
+    if (!ty)
+	return NULL;
+
+    // Paste together the line from the hashed copy
+    r |= (kputc_('@', &ks) == EOF);
+    r |= (kputs(type, &ks) == EOF);
+    for (tag = ty->tag; tag; tag = tag->next) {
+	r |= (kputc_('\t', &ks) == EOF);
+	r |= (kputsn(tag->str, tag->len, &ks) == EOF);
+    }
+
+    if (r) {
+	KS_FREE(&ks);
+	return NULL;
+    }
+
+    return ks_str(&ks);
+}
+
+
+/*
+ * Looks for a specific key in a single sam header line.
+ * If prev is non-NULL it also fills this out with the previous tag, to
+ * permit use in key removal. *prev is set to NULL when the tag is the first
+ * key in the list. When a tag isn't found, prev (if non NULL) will be the last
+ * tag in the existing list.
+ *
+ * Returns the tag pointer on success
+ *         NULL on failure
+ */
+SAM_hdr_tag *sam_hdr_find_key(SAM_hdr *sh,
+			      SAM_hdr_type *type,
+			      char *key,
+			      SAM_hdr_tag **prev) {
+    SAM_hdr_tag *tag, *p = NULL;
+
+    for (tag = type->tag; tag; p = tag, tag = tag->next) {
+	if (tag->str[0] == key[0] && tag->str[1] == key[1]) {
+	    if (prev)
+		*prev = p;
+	    return tag;
+	}
+    }
+
+    if (prev)
+	*prev = p;
+
+    return NULL;
+}
+
+
+/*
+ * Adds or updates tag key,value pairs in a header line.
+ * Eg for adding M5 tags to @SQ lines or updating sort order for the
+ * @HD line (although use the sam_hdr_sort_order() function for
+ * HD manipulation, which is a wrapper around this funuction).
+ *
+ * Specify multiple key,value pairs ending in NULL.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int sam_hdr_update(SAM_hdr *hdr, SAM_hdr_type *type, ...) {
+    va_list ap;
+
+    va_start(ap, type);
+    
+    for (;;) {
+	char *k, *v;
+	int idx;
+	SAM_hdr_tag *tag, *prev;
+
+	if (!(k = (char *)va_arg(ap, char *)))
+	    break;
+	v = va_arg(ap, char *);
+
+	tag = sam_hdr_find_key(hdr, type, k, &prev);
+	if (!tag) {
+	    if (!(tag = pool_alloc(hdr->tag_pool)))
+		return -1;
+	    if (prev)
+		prev->next = tag;
+	    else
+		type->tag = tag;
+
+	    tag->next = NULL;
+	}
+
+	idx = ks_len(&hdr->text);
+	if (ksprintf(&hdr->text, "%2.2s:%s", k, v) < 0)
+	    return -1;
+	tag->len = ks_len(&hdr->text) - idx;
+	tag->str = string_ndup(hdr->str_pool,
+			       ks_str(&hdr->text) + idx,
+			       tag->len);
+	if (!tag->str)
+	    return -1;
+    }
+
+    va_end(ap);
+
+    return 0;
+}
+
+#define K(a) (((a)[0]<<8)|((a)[1]))
+
+/*
+ * Returns the sort order:
+ */
+enum sam_sort_order sam_hdr_sort_order(SAM_hdr *hdr) {
+    return hdr->sort_order;
+}
+
+static enum sam_sort_order sam_hdr_parse_sort_order(SAM_hdr *hdr) {
+    khint_t k;
+    enum sam_sort_order so;
+
+    so = ORDER_UNKNOWN;
+    k = kh_get(sam_hdr, hdr->h, K("HD"));
+    if (k != kh_end(hdr->h)) {
+	SAM_hdr_type *ty = kh_val(hdr->h, k);
+	SAM_hdr_tag *tag;
+        for (tag = ty->tag; tag; tag = tag->next) {
+	    if (tag->str[0] == 'S' && tag->str[1] == 'O') {
+		if (strcmp(tag->str+3, "unsorted") == 0)
+		    so = ORDER_UNSORTED;
+		else if (strcmp(tag->str+3, "queryname") == 0)
+		    so = ORDER_NAME;
+		else if (strcmp(tag->str+3, "coordinate") == 0)
+		    so = ORDER_COORD;
+		else if (strcmp(tag->str+3, "unknown") != 0)
+		    fprintf(stderr, "Unknown sort order field: %s\n",
+			    tag->str+3);
+	    }
+	}
+    }
+
+    return so;
+}
+
+
+/*
+ * Reconstructs the kstring from the header hash table.
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int sam_hdr_rebuild(SAM_hdr *hdr) {
+    /* Order: HD then others */
+    kstring_t ks = KS_INITIALIZER;
+    khint_t k;
+
+
+    k = kh_get(sam_hdr, hdr->h, K("HD"));
+    if (k != kh_end(hdr->h)) {
+	SAM_hdr_type *ty = kh_val(hdr->h, k);
+	SAM_hdr_tag *tag;
+	if (EOF == kputs("@HD", &ks))
+	    return -1;
+	for (tag = ty->tag; tag; tag = tag->next) {
+	    if (EOF == kputc_('\t', &ks))
+		return -1;
+	    if (EOF == kputsn_(tag->str, tag->len, &ks))
+		return -1;
+	}
+	if (EOF == kputc('\n', &ks))
+	    return -1;
+    }
+
+    for (k = kh_begin(hdr->h); k != kh_end(hdr->h); k++) {
+	SAM_hdr_type *t1, *t2;
+
+	if (!kh_exist(hdr->h, k))
+	    continue;
+
+	if (kh_key(hdr->h, k) == K("HD"))
+	    continue;
+
+	t1 = t2 = kh_val(hdr->h, k);
+	do {
+	    SAM_hdr_tag *tag;
+	    char c[2];
+
+	    if (EOF == kputc_('@', &ks))
+		return -1;
+	    c[0] = kh_key(hdr->h, k)>>8;
+	    c[1] = kh_key(hdr->h, k)&0xff;
+	    if (EOF == kputsn_(c, 2, &ks))
+		return -1;
+	    for (tag = t1->tag; tag; tag=tag->next) {
+		if (EOF == kputc_('\t', &ks))
+		    return -1;
+		if (EOF == kputsn_(tag->str, tag->len, &ks))
+		    return -1;
+	    }
+	    if (EOF == kputc('\n', &ks))
+		return -1;
+	    t1 = t1->next;
+	} while (t1 != t2);
+    }
+
+    if (ks_str(&hdr->text))
+	KS_FREE(&hdr->text);
+
+    hdr->text = ks;
+
+    return 0;
+}
+
+
+/*
+ * Creates an empty SAM header, ready to be populated.
+ * 
+ * Returns a SAM_hdr struct on success (free with sam_hdr_free())
+ *         NULL on failure
+ */
+SAM_hdr *sam_hdr_new() {
+    SAM_hdr *sh = calloc(1, sizeof(*sh));
+
+    if (!sh)
+	return NULL;
+    
+    sh->h = kh_init(sam_hdr);
+    if (!sh->h)
+	goto err;
+
+    sh->ID_cnt = 1;
+    sh->ref_count = 1;
+
+    sh->nref = 0;
+    sh->ref  = NULL;
+    if (!(sh->ref_hash = kh_init(m_s2i)))
+	goto err;
+
+    sh->nrg = 0;
+    sh->rg  = NULL;
+    if (!(sh->rg_hash = kh_init(m_s2i)))
+	goto err;
+
+    sh->npg = 0;
+    sh->pg  = NULL;
+    sh->npg_end = sh->npg_end_alloc = 0;
+    sh->pg_end = NULL;
+    if (!(sh->pg_hash = kh_init(m_s2i)))
+	goto err;
+
+    KS_INIT(&sh->text);
+
+    if (!(sh->tag_pool = pool_create(sizeof(SAM_hdr_tag))))
+	goto err;
+
+    if (!(sh->type_pool = pool_create(sizeof(SAM_hdr_type))))
+	goto err;
+
+    if (!(sh->str_pool = string_pool_create(8192)))
+	goto err;
+
+    return sh;
+
+ err:
+    if (sh->h)
+	kh_destroy(sam_hdr, sh->h);
+
+    if (sh->tag_pool)
+	pool_destroy(sh->tag_pool);
+
+    if (sh->type_pool)
+	pool_destroy(sh->type_pool);
+
+    if (sh->str_pool)
+	string_pool_destroy(sh->str_pool);
+
+    free(sh);
+
+    return NULL;
+}
+
+
+/*
+ * Tokenises a SAM header into a hash table.
+ * Also extracts a few bits on specific data types, such as @RG lines.
+ *
+ * Returns a SAM_hdr struct on success (free with sam_hdr_free())
+ *         NULL on failure
+ */
+SAM_hdr *sam_hdr_parse_(const char *hdr, int len) {
+    /* Make an empty SAM_hdr */
+    SAM_hdr *sh;
+    
+    sh = sam_hdr_new();
+    if (NULL == sh) return NULL;
+
+    if (NULL == hdr) return sh; // empty header is permitted
+
+    /* Parse the header, line by line */
+    if (-1 == sam_hdr_add_lines(sh, hdr, len)) {
+	sam_hdr_free(sh);
+	return NULL;
+    }
+
+    /* Obtain sort order */
+    sh->sort_order = sam_hdr_parse_sort_order(sh);
+
+    //sam_hdr_dump(sh);
+    //sam_hdr_add(sh, "RG", "ID", "foo", "SM", "bar", NULL);
+    //sam_hdr_rebuild(sh);
+    //printf(">>%s<<", ks_str(sh->text));
+
+    //parse_references(sh);
+    //parse_read_groups(sh);
+
+    sam_hdr_link_pg(sh);
+    //sam_hdr_dump(sh);
+
+    return sh;
+}
+
+/*
+ * Produces a duplicate copy of hdr and returns it.
+ * Returns NULL on failure
+ */
+SAM_hdr *sam_hdr_dup(SAM_hdr *hdr) {
+    if (-1 == sam_hdr_rebuild(hdr))
+	return NULL;
+
+    return sam_hdr_parse_(sam_hdr_str(hdr), sam_hdr_length(hdr));
+}
+
+/*! Increments a reference count on hdr.
+ *
+ * This permits multiple files to share the same header, all calling
+ * sam_hdr_free when done, without causing errors for other open  files.
+ */
+void sam_hdr_incr_ref(SAM_hdr *hdr) {
+    hdr->ref_count++;
+}
+
+/*! Increments a reference count on hdr.
+ *
+ * This permits multiple files to share the same header, all calling
+ * sam_hdr_free when done, without causing errors for other open  files.
+ *
+ * If the reference count hits zero then the header is automatically
+ * freed. This makes it a synonym for sam_hdr_free().
+ */
+void sam_hdr_decr_ref(SAM_hdr *hdr) {
+    sam_hdr_free(hdr);
+}
+
+/*! Deallocates all storage used by a SAM_hdr struct.
+ *
+ * This also decrements the header reference count. If after decrementing 
+ * it is still non-zero then the header is assumed to be in use by another
+ * caller and the free is not done.
+ *
+ * This is a synonym for sam_hdr_dec_ref().
+ */
+void sam_hdr_free(SAM_hdr *hdr) {
+    if (!hdr)
+	return;
+
+    if (--hdr->ref_count > 0)
+	return;
+
+    if (ks_str(&hdr->text))
+	KS_FREE(&hdr->text);
+
+    if (hdr->h)
+	kh_destroy(sam_hdr, hdr->h);
+
+    if (hdr->ref_hash)
+	kh_destroy(m_s2i, hdr->ref_hash);
+
+    if (hdr->ref) {
+	int i;
+	for (i = 0; i < hdr->nref; i++)
+	    if (hdr->ref[i].name)
+		free(hdr->ref[i].name);
+	free(hdr->ref);
+    }
+
+    if (hdr->rg_hash)
+	kh_destroy(m_s2i, hdr->rg_hash);
+
+    if (hdr->rg) {
+	int i;
+	for (i = 0; i < hdr->nrg; i++)
+	    if (hdr->rg[i].name)
+		free(hdr->rg[i].name);
+	free(hdr->rg);
+    }
+
+    if (hdr->pg_hash)
+	kh_destroy(m_s2i, hdr->pg_hash);
+
+    if (hdr->pg) {
+	int i;
+	for (i = 0; i < hdr->npg; i++)
+	    if (hdr->pg[i].name)
+		free(hdr->pg[i].name);
+	free(hdr->pg);
+    }
+
+    if (hdr->pg_end)
+	free(hdr->pg_end);
+
+    if (hdr->type_pool)
+	pool_destroy(hdr->type_pool);
+
+    if (hdr->tag_pool)
+	pool_destroy(hdr->tag_pool);
+
+    if (hdr->str_pool)
+	string_pool_destroy(hdr->str_pool);
+
+    free(hdr);
+}
+
+int sam_hdr_length(SAM_hdr *hdr) {
+    return ks_len(&hdr->text);
+}
+
+char *sam_hdr_str(SAM_hdr *hdr) {
+    return ks_str(&hdr->text);
+}
+
+/*
+ * Looks up a reference sequence by name and returns the numerical ID.
+ * Returns -1 if unknown reference.
+ */
+int sam_hdr_name2ref(SAM_hdr *hdr, const char *ref) {
+    khint_t k = kh_get(m_s2i, hdr->ref_hash, ref);
+    return k == kh_end(hdr->ref_hash) ? -1 : kh_val(hdr->ref_hash, k);
+}
+
+/*
+ * Looks up a read-group by name and returns a pointer to the start of the
+ * associated tag list.
+ *
+ * Returns NULL on failure
+ */
+SAM_RG *sam_hdr_find_rg(SAM_hdr *hdr, const char *rg) {
+    khint_t k = kh_get(m_s2i, hdr->rg_hash, rg);
+    return k == kh_end(hdr->rg_hash)
+	? NULL
+	: &hdr->rg[kh_val(hdr->rg_hash, k)];
+}
+
+
+/*
+ * Fixes any PP links in @PG headers.
+ * If the entries are in order then this doesn't need doing, but incase
+ * our header is out of order this goes through the sh->pg[] array
+ * setting the prev_id field.
+ *
+ * Note we can have multiple complete chains. This code should identify the
+ * tails of these chains as these are the entries we have to link to in
+ * subsequent PP records.
+ *
+ * Returns 0 on sucess
+ *        -1 on failure (indicating broken PG/PP records)
+ */
+int sam_hdr_link_pg(SAM_hdr *hdr) {
+    int i, j, ret = 0;
+
+    hdr->npg_end_alloc = hdr->npg;
+    hdr->pg_end = realloc(hdr->pg_end, hdr->npg * sizeof(*hdr->pg_end));
+    if (!hdr->pg_end)
+	return -1;
+
+    for (i = 0; i < hdr->npg; i++)
+	hdr->pg_end[i] = i;
+
+    for (i = 0; i < hdr->npg; i++) {
+	khint_t k;
+	SAM_hdr_tag *tag;
+	char tmp;
+
+	for (tag = hdr->pg[i].tag; tag; tag = tag->next) {
+	    if (tag->str[0] == 'P' && tag->str[1] == 'P')
+		break;
+	}
+	if (!tag) {
+	    /* Chain start points */
+	    continue;
+	}
+
+	tmp = tag->str[tag->len]; tag->str[tag->len] = 0;
+	k = kh_get(m_s2i, hdr->pg_hash, tag->str+3);
+	tag->str[tag->len] = tmp;
+
+	if (k == kh_end(hdr->pg_hash)) {
+	    ret = -1;
+	    continue;
+	}
+
+	hdr->pg[i].prev_id = hdr->pg[kh_val(hdr->pg_hash, k)].id;
+	hdr->pg_end[kh_val(hdr->pg_hash, k)] = -1;
+    }
+
+    for (i = j = 0; i < hdr->npg; i++) {
+	if (hdr->pg_end[i] != -1)
+	    hdr->pg_end[j++] = hdr->pg_end[i];
+    }
+    hdr->npg_end = j;
+
+    return ret;
+}
+
+/*
+ * Returns a unique ID from a base name.
+ *
+ * The value returned is valid until the next call to
+ * this function.
+ */
+const char *sam_hdr_PG_ID(SAM_hdr *sh, const char *name) {
+    khint_t k = kh_get(m_s2i, sh->pg_hash, name);
+    if (k == kh_end(sh->pg_hash))
+	return name;
+
+    do {
+	sprintf(sh->ID_buf, "%.1000s.%d", name, sh->ID_cnt++);
+	k = kh_get(m_s2i, sh->pg_hash, sh->ID_buf);
+    } while (k != kh_end(sh->pg_hash));
+
+    return sh->ID_buf;
+}
+
+/*
+ * Add an @PG line.
+ *
+ * If we wish complete control over this use sam_hdr_add() directly. This
+ * function uses that, but attempts to do a lot of tedious house work for
+ * you too.
+ *
+ * - It will generate a suitable ID if the supplied one clashes.
+ * - It will generate multiple @PG records if we have multiple PG chains.
+ *
+ * Call it as per sam_hdr_add() with a series of key,value pairs ending
+ * in NULL.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int sam_hdr_add_PG(SAM_hdr *sh, const char *name, ...) {
+    va_list args;
+
+    if (sh->npg_end) {
+	/* Copy ends array to avoid us looping while modifying it */
+	int *end = malloc(sh->npg_end * sizeof(int));
+	int i, nends = sh->npg_end;
+
+	if (!end)
+	    return -1;
+
+	memcpy(end, sh->pg_end, nends * sizeof(*end));
+
+	for (i = 0; i < nends; i++) {
+	    va_start(args, name);
+	    if (-1 == sam_hdr_vadd(sh, "PG", args,
+				   "ID", sam_hdr_PG_ID(sh, name),
+				   "PN", name,
+				   "PP", sh->pg[end[i]].name,
+				   NULL)) {
+		free(end);
+		return  -1;
+	    }
+	    va_end(args);
+	}
+
+	free(end);
+    } else {
+	va_start(args, name);
+	if (-1 == sam_hdr_vadd(sh, "PG", args,
+			       "ID", sam_hdr_PG_ID(sh, name),
+			       "PN", name,
+			       NULL))
+	    return -1;
+	va_end(args);
+    }
+
+    //sam_hdr_dump(sh);
+
+    return 0;
+}
+
+/*
+ * A function to help with construction of CL tags in @PG records.
+ * Takes an argc, argv pair and returns a single space-separated string.
+ * This string should be deallocated by the calling function.
+ * 
+ * Returns malloced char * on success
+ *         NULL on failure
+ */
+char *stringify_argv(int argc, char *argv[]) {
+    char *str, *cp;
+    size_t nbytes = 1;
+    int i, j;
+
+    /* Allocate */
+    for (i = 0; i < argc; i++) {
+	nbytes += strlen(argv[i]) + 1;
+    }
+    if (!(str = malloc(nbytes)))
+	return NULL;
+
+    /* Copy */
+    cp = str;
+    for (i = 0; i < argc; i++) {
+	j = 0;
+	while (argv[i][j]) {
+	    if (argv[i][j] == '\t')
+		*cp++ = ' ';
+	    else
+		*cp++ = argv[i][j];
+	    j++;
+	}
+	*cp++ = ' ';
+    }
+    *cp++ = 0;
+
+    return str;
+}
diff --git a/htslib/cram/sam_header.h b/htslib/cram/sam_header.h
new file mode 100644
index 0000000..e312df4
--- /dev/null
+++ b/htslib/cram/sam_header.h
@@ -0,0 +1,459 @@
+/*
+Copyright (c) 2013-2014 Genome Research Ltd.
+Author: James Bonfield <jkb at sanger.ac.uk>
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+Institute nor the names of its contributors may be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+/*! \file
+ * SAM header parsing.
+ *
+ * These functions can be shared between SAM, BAM and CRAM file
+ * formats as all three internally use the same string encoding for
+ * header fields.
+ */ 
+
+/*
+ * TODO.
+ *
+ * - Sort order (parse to struct, enum type, updating funcs)
+ * - Removal of lines.
+ * - Updating of lines
+ */
+
+#ifndef _SAM_HDR_H_
+#define _SAM_HDR_H_
+
+#include <stdarg.h>
+
+#include "cram/string_alloc.h"
+#include "cram/pooled_alloc.h"
+
+#include "htslib/khash.h"
+#include "htslib/kstring.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+// For structure assignment. Eg kstring_t s = KS_INITIALIZER;
+#define KS_INITIALIZER {0,0,0}
+
+// For initialisation elsewhere. Eg KS_INIT(x->str);
+#define KS_INIT(ks) ((ks)->l = 0, (ks)->m = 0, (ks)->s = NULL)
+
+// Frees the string subfield only. Assumes 's' itself is static.
+#define KS_FREE(ks) do { if ((ks)->s) free((ks)->s); } while(0)
+
+/*
+ * Proposed new SAM header parsing
+
+1 @SQ ID:foo LN:100
+2 @SQ ID:bar LN:200
+3 @SQ ID:ram LN:300 UR:xyz
+4 @RG ID:r ...
+5 @RG ID:s ...
+
+Hash table for 2-char @keys without dup entries.
+If dup lines, we form a circular linked list. Ie hash keys = {RG, SQ}.
+
+HASH("SQ")--\
+            |
+    (3) <-> 1 <-> 2 <-> 3 <-> (1)
+
+HASH("RG")--\
+            |
+    (5) <-> 4 <-> 5 <-> (4)
+
+Items stored in the hash values also form their own linked lists:
+Ie SQ->ID(foo)->LN(100)
+   SQ->ID(bar)->LN(200)
+   SQ->ID(ram)->LN(300)->UR(xyz)
+   RG->ID(r)
+ */
+
+/*! A single key:value pair on a header line
+ *
+ * These form a linked list and hold strings. The strings are
+ * allocated from a string_alloc_t pool referenced in the master
+ * SAM_hdr structure. Do not attempt to free, malloc or manipulate
+ * these strings directly.
+ */
+typedef struct SAM_hdr_tag_s {
+    struct SAM_hdr_tag_s *next;
+    char *str;
+    int   len;
+} SAM_hdr_tag;
+
+/*! The parsed version of the SAM header string.
+ * 
+ * Each header type (SQ, RG, HD, etc) points to its own SAM_hdr_type
+ * struct via the main hash table h in the SAM_hdr struct.
+ *
+ * These in turn consist of circular bi-directional linked lists (ie
+ * rings) to hold the multiple instances of the same header type
+ * code. For example if we have 5 \@SQ lines the primary hash table
+ * will key on \@SQ pointing to the first SAM_hdr_type and that in turn
+ * will be part of a ring of 5 elements.
+ *
+ * For each SAM_hdr_type structure we also point to a SAM_hdr_tag
+ * structure which holds the tokenised attributes; the tab separated
+ * key:value pairs per line.
+ */
+typedef struct SAM_hdr_item_s {
+    struct SAM_hdr_item_s *next; // cirular
+    struct SAM_hdr_item_s *prev;
+    SAM_hdr_tag *tag;            // first tag
+    int order;                   // 0 upwards
+} SAM_hdr_type;
+
+/*! Parsed \@SQ lines */
+typedef struct {
+    char *name;
+    uint32_t len;
+    SAM_hdr_type *ty;
+    SAM_hdr_tag  *tag;
+} SAM_SQ;
+
+/*! Parsed \@RG lines */
+typedef struct {
+    char *name;
+    SAM_hdr_type *ty;
+    SAM_hdr_tag  *tag;
+    int name_len;
+    int id;           // numerical ID
+} SAM_RG;
+
+/*! Parsed \@PG lines */
+typedef struct {
+    char *name;
+    SAM_hdr_type *ty;
+    SAM_hdr_tag  *tag;
+    int name_len;
+    int id;           // numerical ID
+    int prev_id;      // -1 if none
+} SAM_PG;
+
+/*! Sort order parsed from @HD line */
+enum sam_sort_order {
+    ORDER_UNKNOWN  =-1,
+    ORDER_UNSORTED = 0,
+    ORDER_NAME     = 1,
+    ORDER_COORD    = 2,
+  //ORDER_COLLATE  = 3 // maybe one day!
+};
+
+KHASH_MAP_INIT_INT(sam_hdr, SAM_hdr_type*)
+KHASH_MAP_INIT_STR(m_s2i, int)
+
+/*! Primary structure for header manipulation
+ *
+ * The initial header text is held in the text kstring_t, but is also
+ * parsed out into SQ, RG and PG arrays. These have a hash table
+ * associated with each to allow lookup by ID or SN fields instead of
+ * their numeric array indices. Additionally PG has an array to hold
+ * the linked list start points (the last in a PP chain).
+ *
+ * Use the appropriate sam_hdr_* functions to edit the header, and 
+ * call sam_hdr_rebuild() any time the textual form needs to be
+ * updated again.
+ */
+typedef struct {
+    kstring_t text;           //!< concatenated text, indexed by SAM_hdr_tag
+    khash_t(sam_hdr) *h;
+    string_alloc_t *str_pool; //!< Pool of SAM_hdr_tag->str strings
+    pool_alloc_t   *type_pool;//!< Pool of SAM_hdr_type structs
+    pool_alloc_t   *tag_pool; //!< Pool of SAM_hdr_tag structs
+
+    // @SQ lines / references
+    int nref;                 //!< Number of \@SQ lines
+    SAM_SQ *ref;              //!< Array of parsed \@SQ lines
+    khash_t(m_s2i) *ref_hash; //!< Maps SQ SN field to sq[] index
+
+    // @RG lines / read-groups
+    int nrg;                  //!< Number of \@RG lines
+    SAM_RG *rg;               //!< Array of parsed \@RG lines
+    khash_t(m_s2i) *rg_hash;  //!< Maps RG ID field to rg[] index
+
+    // @PG lines / programs
+    int npg;                  //!< Number of \@PG lines
+    int npg_end;              //!< Number of terminating \@PG lines
+    int npg_end_alloc;        //!< Size of pg_end field
+    SAM_PG *pg;		      //!< Array of parsed \@PG lines
+    khash_t(m_s2i) *pg_hash;  //!< Maps PG ID field to pg[] index
+    int *pg_end;              //!< \@PG chain termination IDs
+
+    // @HD data
+    enum sam_sort_order sort_order; //!< @HD SO: field
+
+    // @cond internal
+    char ID_buf[1024];  // temporary buffer
+    int ID_cnt;
+    int ref_count;      // number of uses of this SAM_hdr
+    // @endcond
+} SAM_hdr;
+
+/*! Creates an empty SAM header, ready to be populated.
+ * 
+ * @return
+ * Returns a SAM_hdr struct on success (free with sam_hdr_free())
+ *         NULL on failure
+ */
+SAM_hdr *sam_hdr_new(void);
+
+/*! Tokenises a SAM header into a hash table.
+ *
+ * Also extracts a few bits on specific data types, such as @RG lines.
+ *
+ * @return
+ * Returns a SAM_hdr struct on success (free with sam_hdr_free());
+ *         NULL on failure
+ */
+SAM_hdr *sam_hdr_parse_(const char *hdr, int len);
+
+
+/*! Produces a duplicate copy of hdr and returns it.
+ * @return
+ * Returns NULL on failure
+ */
+SAM_hdr *sam_hdr_dup(SAM_hdr *hdr);
+
+
+/*! Increments a reference count on hdr.
+ *
+ * This permits multiple files to share the same header, all calling
+ * sam_hdr_free when done, without causing errors for other open  files.
+ */
+void sam_hdr_incr_ref(SAM_hdr *hdr);
+
+
+/*! Increments a reference count on hdr.
+ *
+ * This permits multiple files to share the same header, all calling
+ * sam_hdr_free when done, without causing errors for other open  files.
+ *
+ * If the reference count hits zero then the header is automatically
+ * freed. This makes it a synonym for sam_hdr_free().
+ */
+void sam_hdr_decr_ref(SAM_hdr *hdr);
+
+
+/*! Deallocates all storage used by a SAM_hdr struct.
+ *
+ * This also decrements the header reference count. If after decrementing 
+ * it is still non-zero then the header is assumed to be in use by another
+ * caller and the free is not done.
+ *
+ * This is a synonym for sam_hdr_dec_ref().
+ */
+void sam_hdr_free(SAM_hdr *hdr);
+
+/*! Returns the current length of the SAM_hdr in text form.
+ *
+ * Call sam_hdr_rebuild() first if editing has taken place.
+ */
+int sam_hdr_length(SAM_hdr *hdr);
+
+/*! Returns the string form of the SAM_hdr.
+ *
+ * Call sam_hdr_rebuild() first if editing has taken place.
+ */
+char *sam_hdr_str(SAM_hdr *hdr);
+
+/*! Appends a formatted line to an existing SAM header.
+ *
+ * Line is a full SAM header record, eg "@SQ\tSN:foo\tLN:100", with
+ * optional new-line. If it contains more than 1 line then multiple lines
+ * will be added in order.
+ *
+ * Input text is of maximum length len or as terminated earlier by a NUL.
+ * Len may be 0 if unknown, in which case lines must be NUL-terminated.
+ *
+ * @return
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+int sam_hdr_add_lines(SAM_hdr *sh, const char *lines, int len);
+
+/*! Adds a single line to a SAM header.
+ *
+ * Specify type and one or more key,value pairs, ending with the NULL key.
+ * Eg. sam_hdr_add(h, "SQ", "ID", "foo", "LN", "100", NULL).
+ *
+ * @return
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+int sam_hdr_add(SAM_hdr *sh, const char *type, ...);
+
+/*! Adds a single line to a SAM header.
+ *
+ * This is much like sam_hdr_add() but with the additional va_list
+ * argument. This is followed by specifying type and one or more
+ * key,value pairs, ending with the NULL key.
+ *
+ * Eg. sam_hdr_vadd(h, "SQ", args, "ID", "foo", "LN", "100", NULL).
+ *
+ * The purpose of the additional va_list parameter is to permit other
+ * varargs functions to call this while including their own additional
+ * parameters; an example is in sam_hdr_add_PG().
+ *
+ * Note: this function invokes va_arg at least once, making the value
+ * of ap indeterminate after the return.  The caller should call
+ * va_start/va_end before/after calling this function or use va_copy.
+ *
+ * @return
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+int sam_hdr_vadd(SAM_hdr *sh, const char *type, va_list ap, ...);
+
+/*!
+ * @return
+ * Returns the first header item matching 'type'. If ID is non-NULL it checks
+ * for the tag ID: and compares against the specified ID.
+ *
+ * Returns NULL if no type/ID is found
+ */
+SAM_hdr_type *sam_hdr_find(SAM_hdr *hdr, char *type,
+			   char *ID_key, char *ID_value);
+
+/*!
+ *
+ * As per SAM_hdr_type, but returns a complete line of formatted text
+ * for a specific head type/ID combination. If ID is NULL then it returns
+ * the first line of the specified type.
+ *
+ * The returned string is malloced and should be freed by the calling
+ * function with free().
+ *
+ * @return
+ * Returns NULL if no type/ID is found.
+ */
+char *sam_hdr_find_line(SAM_hdr *hdr, char *type,
+			char *ID_key, char *ID_value);
+
+/*! Looks for a specific key in a single sam header line.
+ *
+ * If prev is non-NULL it also fills this out with the previous tag, to
+ * permit use in key removal. *prev is set to NULL when the tag is the first
+ * key in the list. When a tag isn't found, prev (if non NULL) will be the last
+ * tag in the existing list.
+ *
+ * @return
+ * Returns the tag pointer on success;
+ *         NULL on failure
+ */
+SAM_hdr_tag *sam_hdr_find_key(SAM_hdr *sh,
+			      SAM_hdr_type *type,
+			      char *key,
+			      SAM_hdr_tag **prev);
+
+/*! Adds or updates tag key,value pairs in a header line.
+ *
+ * Eg for adding M5 tags to @SQ lines or updating sort order for the
+ * @HD line (although use the sam_hdr_sort_order() function for
+ * HD manipulation, which is a wrapper around this funuction).
+ *
+ * Specify multiple key,value pairs ending in NULL.
+ *
+ * @return
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+int sam_hdr_update(SAM_hdr *hdr, SAM_hdr_type *type, ...);
+
+/*! Returns the sort order from the @HD SO: field */
+enum sam_sort_order sam_hdr_sort_order(SAM_hdr *hdr);
+
+/*! Reconstructs the kstring from the header hash table.
+ * @return
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+int sam_hdr_rebuild(SAM_hdr *hdr);
+
+/*! Looks up a reference sequence by name and returns the numerical ID.
+ * @return
+ * Returns -1 if unknown reference.
+ */
+int sam_hdr_name2ref(SAM_hdr *hdr, const char *ref);
+
+/*! Looks up a read-group by name and returns a pointer to the start of the
+ * associated tag list.
+ *
+ * @return
+ * Returns NULL on failure
+ */
+SAM_RG *sam_hdr_find_rg(SAM_hdr *hdr, const char *rg);
+
+/*! Fixes any PP links in @PG headers.
+ *
+ * If the entries are in order then this doesn't need doing, but incase
+ * our header is out of order this goes through the sh->pg[] array
+ * setting the prev_id field.
+ *
+ * @return
+ * Returns 0 on sucess;
+ *        -1 on failure (indicating broken PG/PP records)
+ */
+int sam_hdr_link_pg(SAM_hdr *hdr);
+
+
+/*! Add an @PG line.
+ *
+ * If we wish complete control over this use sam_hdr_add() directly. This
+ * function uses that, but attempts to do a lot of tedious house work for
+ * you too.
+ *
+ * - It will generate a suitable ID if the supplied one clashes.
+ * - It will generate multiple @PG records if we have multiple PG chains.
+ *
+ * Call it as per sam_hdr_add() with a series of key,value pairs ending
+ * in NULL.
+ *
+ * @return
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+int sam_hdr_add_PG(SAM_hdr *sh, const char *name, ...);
+
+/*!
+ * A function to help with construction of CL tags in @PG records.
+ * Takes an argc, argv pair and returns a single space-separated string.
+ * This string should be deallocated by the calling function.
+ * 
+ * @return
+ * Returns malloced char * on success;
+ *         NULL on failure
+ */
+char *stringify_argv(int argc, char *argv[]);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _SAM_HDR_H_ */
diff --git a/htslib/cram/string_alloc.c b/htslib/cram/string_alloc.c
new file mode 100644
index 0000000..3e0e4e2
--- /dev/null
+++ b/htslib/cram/string_alloc.c
@@ -0,0 +1,155 @@
+/*
+Copyright (c) 2010 Genome Research Ltd.
+Author: Andrew Whitwham <aw7 at sanger.ac.uk>
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+Institute nor the names of its contributors may be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+
+/* 
+   A pooled string allocator intended to cut down on the
+   memory overhead of many small string allocations.
+   
+   Andrew Whitwham, September 2010.
+*/
+
+#include <config.h>
+
+#include <string.h>
+#include <stdlib.h>
+#include <stdio.h>
+
+#include "string_alloc.h"
+
+#define MIN_STR_SIZE 1024
+
+
+/* creates the string pool. max_length is the initial size
+   a single string can be.  Tha max_length can grow as
+   needed */
+
+string_alloc_t *string_pool_create(size_t max_length) {
+    string_alloc_t *a_str;
+    
+    if (NULL == (a_str = (string_alloc_t *)malloc(sizeof(*a_str)))) {
+    	return NULL;
+    }
+    
+    if (max_length < MIN_STR_SIZE) max_length = MIN_STR_SIZE;
+    
+    a_str->nstrings    = 0;
+    a_str->max_length  = max_length;
+    a_str->strings     = NULL;
+    
+    return a_str;
+}
+
+
+/* internal function to do the actual memory allocation */
+
+static string_t *new_string_pool(string_alloc_t *a_str) {
+    string_t *str;
+    
+    str = realloc(a_str->strings, (a_str->nstrings + 1) * sizeof(*a_str->strings));
+    
+    if (NULL == str) return NULL;
+    
+    a_str->strings = str;
+    str = &a_str->strings[a_str->nstrings];
+    
+    str->str = malloc(a_str->max_length);;
+    
+    if (NULL == str->str) return NULL;
+    
+    str->used = 0;
+    a_str->nstrings++;
+    
+    return str;
+}
+
+
+/* free allocated memory */
+
+void string_pool_destroy(string_alloc_t *a_str) {
+    size_t i;
+    
+    for (i = 0; i < a_str->nstrings; i++) {
+    	free(a_str->strings[i].str);
+    }
+    
+    free(a_str->strings);
+    free(a_str);
+}
+
+
+/* allocate space for a string */
+
+char *string_alloc(string_alloc_t *a_str, size_t length) {
+    string_t *str;
+    char *ret;
+    
+    if (length <= 0) return NULL;
+    
+    // add to last string pool if we have space
+    if (a_str->nstrings) {
+    	str = &a_str->strings[a_str->nstrings - 1];
+	
+	if (str->used + length < a_str->max_length) {
+	    ret = str->str + str->used;
+	    str->used += length;
+	    return ret;
+	}
+    }
+    
+    // increase the max length if needs be
+    if (length > a_str->max_length) a_str->max_length = length;
+	
+    // need a new string pool 
+    str = new_string_pool(a_str);
+    
+    if (NULL == str) return NULL;
+    
+    str->used = length;
+    return str->str;
+}
+
+
+/* equivalent to strdup */
+
+char *string_dup(string_alloc_t *a_str, char *instr) {
+    return string_ndup(a_str, instr, strlen(instr));
+}
+
+char *string_ndup(string_alloc_t *a_str, char *instr, size_t len) {
+    char *str = string_alloc(a_str, len + 1);
+    
+    if (NULL == str) return NULL;
+    
+    strncpy(str, instr, len);
+    str[len] = 0;
+    
+    return str;
+}
diff --git a/htslib/cram/string_alloc.h b/htslib/cram/string_alloc.h
new file mode 100644
index 0000000..e044673
--- /dev/null
+++ b/htslib/cram/string_alloc.h
@@ -0,0 +1,68 @@
+/*
+Copyright (c) 2010 Genome Research Ltd.
+Author: Andrew Whitwham <aw7 at sanger.ac.uk>
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+Institute nor the names of its contributors may be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+#ifndef _STRING_ALLOC_H_
+#define _STRING_ALLOC_H_
+
+#include <stdlib.h>
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/* 
+ * A pooled string allocator intended to cut down on the
+ * memory overhead of many small string allocations.
+ *
+ * Andrew Whitwham, September 2010.
+ */
+
+typedef struct {
+    char *str;
+    size_t used;
+} string_t;
+
+typedef struct {
+    size_t max_length;
+    size_t nstrings;
+    string_t *strings;
+} string_alloc_t;
+
+string_alloc_t *string_pool_create(size_t max_length);
+void string_pool_destroy(string_alloc_t *a_str);
+char *string_alloc(string_alloc_t *a_str, size_t length);
+char *string_dup(string_alloc_t *a_str, char *instr);
+char *string_ndup(string_alloc_t *a_str, char *instr, size_t len);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/htslib/cram/thread_pool.c b/htslib/cram/thread_pool.c
new file mode 100644
index 0000000..cf80edb
--- /dev/null
+++ b/htslib/cram/thread_pool.c
@@ -0,0 +1,757 @@
+/*
+Copyright (c) 2013 Genome Research Ltd.
+Author: James Bonfield <jkb at sanger.ac.uk>
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+Institute nor the names of its contributors may be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+#include <config.h>
+
+#include <stdlib.h>
+
+#include <signal.h>
+#include <errno.h>
+#include <stdio.h>
+#include <string.h>
+#include <sys/time.h>
+#include <assert.h>
+
+#include "cram/thread_pool.h"
+
+//#define DEBUG
+//#define DEBUG_TIME
+
+#define IN_ORDER
+
+#ifdef DEBUG
+static int worker_id(t_pool *p) {
+    int i;
+    pthread_t s = pthread_self();
+    for (i = 0; i < p->tsize; i++) {
+	if (pthread_equal(s, p->t[i].tid))
+	    return i;
+    }
+    return -1;
+}
+#endif
+
+/* ----------------------------------------------------------------------------
+ * A queue to hold results from the thread pool.
+ *
+ * Each thread pool may have jobs of multiple types being queued up and
+ * interleaved, so we allow several results queue per pool.
+ *
+ * The jobs themselves are expected to push their results onto their
+ * appropriate results queue.
+ */
+
+/*
+ * Adds a result to the end of the result queue.
+ *
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+static int t_pool_add_result(t_pool_job *j, void *data) {
+    t_results_queue *q = j->q;
+    t_pool_result *r;
+
+#ifdef DEBUG
+    fprintf(stderr, "%d: Adding resulting to queue %p, serial %d\n",
+	    worker_id(j->p), q, j->serial);
+#endif
+
+    /* No results queue is fine if we don't want any results back */
+    if (!q)
+	return 0;
+
+    if (!(r = malloc(sizeof(*r))))
+	return -1;
+
+    r->next = NULL;
+    r->data = data;
+    r->serial = j->serial;
+
+    pthread_mutex_lock(&q->result_m);
+    if (q->result_tail) {
+	q->result_tail->next = r;
+	q->result_tail = r;
+    } else {
+	q->result_head = q->result_tail = r;
+    }
+    q->queue_len++;
+    q->pending--;
+
+#ifdef DEBUG
+    fprintf(stderr, "%d: Broadcasting result_avail (id %d)\n",
+	    worker_id(j->p), r->serial);
+#endif
+    pthread_cond_signal(&q->result_avail_c);
+#ifdef DEBUG
+    fprintf(stderr, "%d: Broadcast complete\n", worker_id(j->p));
+#endif
+
+    pthread_mutex_unlock(&q->result_m);
+
+    return 0;
+}
+
+/* Core of t_pool_next_result() */
+static t_pool_result *t_pool_next_result_locked(t_results_queue *q) {
+    t_pool_result *r, *last;
+
+    for (last = NULL, r = q->result_head; r; last = r, r = r->next) {
+	if (r->serial == q->next_serial)
+	    break;
+    }
+
+    if (r) {
+	if (q->result_head == r)
+	    q->result_head = r->next;
+	else
+	    last->next = r->next;
+
+	if (q->result_tail == r)
+	    q->result_tail = last;
+
+	if (!q->result_head)
+	    q->result_tail = NULL;
+
+	q->next_serial++;
+	q->queue_len--;
+    }
+
+    return r;
+}
+
+/*
+ * Pulls a result off the head of the result queue. Caller should
+ * free it (and any internals as appropriate) after use. This doesn't
+ * wait for a result to be present.
+ *
+ * Results will be returned in strict order.
+ * 
+ * Returns t_pool_result pointer if a result is ready.
+ *         NULL if not.
+ */
+t_pool_result *t_pool_next_result(t_results_queue *q) {
+    t_pool_result *r;
+
+#ifdef DEBUG
+    fprintf(stderr, "Requesting next result on queue %p\n", q);
+#endif
+
+    pthread_mutex_lock(&q->result_m);
+    r = t_pool_next_result_locked(q);
+    pthread_mutex_unlock(&q->result_m);
+
+#ifdef DEBUG
+    fprintf(stderr, "(q=%p) Found %p\n", q, r);
+#endif
+
+    return r;
+}
+
+t_pool_result *t_pool_next_result_wait(t_results_queue *q) {
+    t_pool_result *r;
+
+#ifdef DEBUG
+    fprintf(stderr, "Waiting for result %d...\n", q->next_serial);
+#endif
+
+    pthread_mutex_lock(&q->result_m);
+    while (!(r = t_pool_next_result_locked(q))) {
+	/* Possible race here now avoided via _locked() call, but incase... */
+	struct timeval now;
+	struct timespec timeout;
+
+	gettimeofday(&now, NULL);
+	timeout.tv_sec = now.tv_sec + 10;
+	timeout.tv_nsec = now.tv_usec * 1000;
+
+	pthread_cond_timedwait(&q->result_avail_c, &q->result_m, &timeout);
+    }
+    pthread_mutex_unlock(&q->result_m);
+
+    return r;
+}
+
+/*
+ * Returns true if there are no items on the finished results queue and
+ * also none still pending.
+ */
+int t_pool_results_queue_empty(t_results_queue *q) {
+    int empty;
+
+    pthread_mutex_lock(&q->result_m);
+    empty = q->queue_len == 0 && q->pending == 0;
+    pthread_mutex_unlock(&q->result_m);
+
+    return empty;
+}
+
+
+/*
+ * Returns the number of completed jobs on the results queue.
+ */
+int t_pool_results_queue_len(t_results_queue *q) {
+    int len;
+
+    pthread_mutex_lock(&q->result_m);
+    len = q->queue_len;
+    pthread_mutex_unlock(&q->result_m);
+
+    return len;
+}
+
+int t_pool_results_queue_sz(t_results_queue *q) {
+    int len;
+
+    pthread_mutex_lock(&q->result_m);
+    len = q->queue_len + q->pending;
+    pthread_mutex_unlock(&q->result_m);
+
+    return len;
+}
+
+/*
+ * Frees a result 'r' and if free_data is true also frees
+ * the internal r->data result too.
+ */
+void t_pool_delete_result(t_pool_result *r, int free_data) {
+    if (!r)
+	return;
+
+    if (free_data && r->data)
+	free(r->data);
+
+    free(r);
+}
+
+/*
+ * Initialises a results queue.
+ *
+ * Results queue pointer on success;
+ *         NULL on failure
+ */
+t_results_queue *t_results_queue_init(void) {
+    t_results_queue *q = malloc(sizeof(*q));
+
+    pthread_mutex_init(&q->result_m, NULL);
+    pthread_cond_init(&q->result_avail_c, NULL);
+
+    q->result_head = NULL;
+    q->result_tail = NULL;
+    q->next_serial = 0;
+    q->curr_serial = 0;
+    q->queue_len   = 0;
+    q->pending     = 0;
+
+    return q;
+}
+
+/* Deallocates memory for a results queue */
+void t_results_queue_destroy(t_results_queue *q) {
+#ifdef DEBUG
+    fprintf(stderr, "Destroying results queue %p\n", q);
+#endif
+
+    if (!q)
+	return;
+
+    pthread_mutex_destroy(&q->result_m);
+    pthread_cond_destroy(&q->result_avail_c);
+
+    memset(q, 0xbb, sizeof(*q));
+    free(q);
+
+#ifdef DEBUG
+    fprintf(stderr, "Destroyed results queue %p\n", q);
+#endif
+}
+
+/* ----------------------------------------------------------------------------
+ * The thread pool.
+ */
+
+#define TDIFF(t2,t1) ((t2.tv_sec-t1.tv_sec)*1000000 + t2.tv_usec-t1.tv_usec)
+
+/*
+ * A worker thread.
+ *
+ * Each thread waits for the pool to be non-empty.
+ * As soon as this applies, one of them succeeds in getting the lock
+ * and then executes the job.
+ */
+static void *t_pool_worker(void *arg) {
+    t_pool_worker_t *w = (t_pool_worker_t *)arg;
+    t_pool *p = w->p;
+    t_pool_job *j;
+#ifdef DEBUG_TIME
+    struct timeval t1, t2, t3;
+#endif
+
+    for (;;) {
+	// Pop an item off the pool queue
+#ifdef DEBUG_TIME
+	gettimeofday(&t1, NULL);
+#endif
+
+	pthread_mutex_lock(&p->pool_m);
+
+#ifdef DEBUG_TIME
+	gettimeofday(&t2, NULL);
+	p->wait_time += TDIFF(t2,t1);
+	w->wait_time += TDIFF(t2,t1);
+#endif
+
+	// If there is something on the job list and a higher priority
+	// thread waiting, let it handle this instead.
+//	while (p->head && p->t_stack_top != -1 && p->t_stack_top < w->idx) {
+//	    pthread_mutex_unlock(&p->pool_m);
+//	    pthread_cond_signal(&p->t[p->t_stack_top].pending_c);
+//	    pthread_mutex_lock(&p->pool_m);
+//	}
+
+	while (!p->head && !p->shutdown) {
+	    p->nwaiting++;
+
+	    if (p->njobs == 0)
+		pthread_cond_signal(&p->empty_c);
+#ifdef DEBUG_TIME
+	    gettimeofday(&t2, NULL);
+#endif
+
+#ifdef IN_ORDER
+	    // Push this thread to the top of the waiting stack
+	    if (p->t_stack_top == -1 || p->t_stack_top > w->idx)
+		p->t_stack_top = w->idx;
+
+	    p->t_stack[w->idx] = 1;
+	    pthread_cond_wait(&w->pending_c, &p->pool_m);
+	    p->t_stack[w->idx] = 0;
+
+	    /* Find new t_stack_top */
+	    {
+		int i;
+		p->t_stack_top = -1;
+		for (i = 0; i < p->tsize; i++) {
+		    if (p->t_stack[i]) {
+			p->t_stack_top = i;
+			break;
+		    }
+		}
+	    }
+#else
+	    pthread_cond_wait(&p->pending_c, &p->pool_m);
+#endif
+
+#ifdef DEBUG_TIME
+	    gettimeofday(&t3, NULL);
+	    p->wait_time += TDIFF(t3,t2);
+	    w->wait_time += TDIFF(t3,t2);
+#endif
+	    p->nwaiting--;
+	}
+
+	if (p->shutdown) {
+#ifdef DEBUG_TIME
+	    p->total_time += TDIFF(t3,t1);
+#endif
+#ifdef DEBUG
+	    fprintf(stderr, "%d: Shutting down\n", worker_id(p));
+#endif
+	    pthread_mutex_unlock(&p->pool_m);
+	    pthread_exit(NULL);
+	}
+
+	j = p->head;
+	if (!(p->head = j->next))
+	    p->tail = NULL;
+
+	if (p->njobs-- >= p->qsize)
+	    pthread_cond_signal(&p->full_c);
+
+	if (p->njobs == 0)
+	    pthread_cond_signal(&p->empty_c);
+
+	pthread_mutex_unlock(&p->pool_m);
+	    
+	// We have job 'j' - now execute it.
+	t_pool_add_result(j, j->func(j->arg));	
+#ifdef DEBUG_TIME
+	pthread_mutex_lock(&p->pool_m);
+	gettimeofday(&t3, NULL);
+	p->total_time += TDIFF(t3,t1);
+	pthread_mutex_unlock(&p->pool_m);
+#endif
+	memset(j, 0xbb, sizeof(*j));
+	free(j);
+    }
+
+    return NULL;
+}
+
+/*
+ * Creates a worker pool of length qsize with tsize worker threads.
+ *
+ * Returns pool pointer on success;
+ *         NULL on failure
+ */
+t_pool *t_pool_init(int qsize, int tsize) {
+    int i;
+    t_pool *p = malloc(sizeof(*p));
+    p->qsize = qsize;
+    p->tsize = tsize;
+    p->njobs = 0;
+    p->nwaiting = 0;
+    p->shutdown = 0;
+    p->head = p->tail = NULL;
+    p->t_stack = NULL;
+#ifdef DEBUG_TIME
+    p->total_time = p->wait_time = 0;
+#endif
+
+    p->t = malloc(tsize * sizeof(p->t[0]));
+
+    pthread_mutex_init(&p->pool_m, NULL);
+    pthread_cond_init(&p->empty_c, NULL);
+    pthread_cond_init(&p->full_c, NULL);
+
+    pthread_mutex_lock(&p->pool_m);
+
+#ifdef IN_ORDER
+    if (!(p->t_stack = malloc(tsize * sizeof(*p->t_stack))))
+	return NULL;
+    p->t_stack_top = -1;
+
+    for (i = 0; i < tsize; i++) {
+	t_pool_worker_t *w = &p->t[i];
+	p->t_stack[i] = 0;
+	w->p = p;
+	w->idx = i;
+	w->wait_time = 0;
+	pthread_cond_init(&w->pending_c, NULL);
+	if (0 != pthread_create(&w->tid, NULL, t_pool_worker, w))
+	    return NULL;
+    }
+#else
+    pthread_cond_init(&p->pending_c, NULL);
+
+    for (i = 0; i < tsize; i++) {
+	t_pool_worker_t *w = &p->t[i];
+	w->p = p;
+	w->idx = i;
+	pthread_cond_init(&w->pending_c, NULL);
+	if (0 != pthread_create(&w->tid, NULL, t_pool_worker, w))
+	    return NULL;
+    }
+#endif
+
+    pthread_mutex_unlock(&p->pool_m);
+
+    return p;
+}
+
+/*
+ * Adds an item to the work pool.
+ *
+ * FIXME: Maybe return 1,0,-1 and distinguish between job dispathed vs
+ * result returned. Ie rather than blocking on full queue we're permitted
+ * to return early on "result available" event too.
+ * Caller would then have a while loop around t_pool_dispatch.
+ * Or, return -1 and set errno to EAGAIN to indicate job not yet submitted.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int t_pool_dispatch(t_pool *p, t_results_queue *q,
+		    void *(*func)(void *arg), void *arg) {
+    return t_pool_dispatch2(p, q, func, arg, 0);
+}
+
+/*
+ * As above but optional non-block flag.
+ *
+ * nonblock  0 => block if input queue is full
+ * nonblock +1 => don't block if input queue is full, but do not add task
+ * nonblock -1 => add task regardless of whether queue is full (over-size)
+ */
+int t_pool_dispatch2(t_pool *p, t_results_queue *q,
+		     void *(*func)(void *arg), void *arg, int nonblock) {
+    t_pool_job *j;
+
+#ifdef DEBUG
+    fprintf(stderr, "Dispatching job for queue %p, serial %d\n", q, q->curr_serial);
+#endif
+
+    pthread_mutex_lock(&p->pool_m);
+
+    if (p->njobs >= p->qsize && nonblock == 1) {
+	pthread_mutex_unlock(&p->pool_m);
+	errno = EAGAIN;
+	return -1;
+    }
+
+    if (!(j = malloc(sizeof(*j))))
+	return -1;
+    j->func = func;
+    j->arg = arg;
+    j->next = NULL;
+    j->p = p;
+    j->q = q;
+    if (q) {
+	pthread_mutex_lock(&q->result_m);
+	j->serial = q->curr_serial++;
+	q->pending++;
+	pthread_mutex_unlock(&q->result_m);
+    } else {
+	j->serial = 0;
+    }
+
+    // Check if queue is full
+    if (nonblock == 0)
+	while (p->njobs >= p->qsize)
+	    pthread_cond_wait(&p->full_c, &p->pool_m);
+
+    p->njobs++;
+    
+//    if (q->curr_serial % 100 == 0)
+//	fprintf(stderr, "p->njobs = %d    p->qsize = %d\n", p->njobs, p->qsize);
+
+    if (p->tail) {
+	p->tail->next = j;
+	p->tail = j;
+    } else {
+	p->head = p->tail = j;
+    }
+
+#ifdef DEBUG
+    fprintf(stderr, "Dispatched (serial %d)\n", j->serial);
+#endif
+
+    // Let a worker know we have data.
+#ifdef IN_ORDER
+    // Keep incoming queue at 1 per running thread, so there is always
+    // something waiting when they end their current task.  If we go above
+    // this signal to start more threads (if available). This has the effect
+    // of concentrating jobs to fewer cores when we are I/O bound, which in
+    // turn benefits systems with auto CPU frequency scaling.
+    if (p->t_stack_top >= 0 && p->njobs > p->tsize - p->nwaiting)
+	pthread_cond_signal(&p->t[p->t_stack_top].pending_c);
+#else
+    pthread_cond_signal(&p->pending_c);
+#endif
+
+    pthread_mutex_unlock(&p->pool_m);
+
+    return 0;
+}
+
+/*
+ * Flushes the pool, but doesn't exit. This simply drains the queue and
+ * ensures all worker threads have finished their current task.
+ *
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+int t_pool_flush(t_pool *p) {
+    int i;
+
+#ifdef DEBUG
+    fprintf(stderr, "Flushing pool %p\n", p);
+#endif
+
+    // Drains the queue
+    pthread_mutex_lock(&p->pool_m);
+
+    // Wake up everything for the final sprint!
+    for (i = 0; i < p->tsize; i++)
+	if (p->t_stack[i])
+	    pthread_cond_signal(&p->t[i].pending_c);
+
+    while (p->njobs || p->nwaiting != p->tsize)
+	pthread_cond_wait(&p->empty_c, &p->pool_m);
+
+    pthread_mutex_unlock(&p->pool_m);
+
+#ifdef DEBUG
+    fprintf(stderr, "Flushed complete for pool %p, njobs=%d, nwaiting=%d\n",
+	    p, p->njobs, p->nwaiting);
+#endif
+
+    return 0;
+}
+
+/*
+ * Destroys a thread pool. If 'kill' is true the threads are terminated now,
+ * otherwise they are joined into the main thread so they will finish their
+ * current work load.
+ *
+ * Use t_pool_destroy(p,0) after a t_pool_flush(p) on a normal shutdown or
+ * t_pool_destroy(p,1) to quickly exit after a fatal error.
+ */
+void t_pool_destroy(t_pool *p, int kill) {
+    int i;
+    
+#ifdef DEBUG
+    fprintf(stderr, "Destroying pool %p, kill=%d\n", p, kill);
+#endif
+
+    /* Send shutdown message to worker threads */
+    if (!kill) {
+	pthread_mutex_lock(&p->pool_m);
+	p->shutdown = 1;
+
+#ifdef DEBUG
+	fprintf(stderr, "Sending shutdown request\n");
+#endif
+
+#ifdef IN_ORDER
+	for (i = 0; i < p->tsize; i++)
+	    pthread_cond_signal(&p->t[i].pending_c);
+#else
+	pthread_cond_broadcast(&p->pending_c);
+#endif
+	pthread_mutex_unlock(&p->pool_m);
+
+#ifdef DEBUG
+	fprintf(stderr, "Shutdown complete\n");
+#endif
+	for (i = 0; i < p->tsize; i++)
+	    pthread_join(p->t[i].tid, NULL);
+    } else {
+	for (i = 0; i < p->tsize; i++)
+	    pthread_kill(p->t[i].tid, SIGINT);
+    }
+
+    pthread_mutex_destroy(&p->pool_m);
+    pthread_cond_destroy(&p->empty_c);
+    pthread_cond_destroy(&p->full_c);
+#ifdef IN_ORDER
+    for (i = 0; i < p->tsize; i++)
+	pthread_cond_destroy(&p->t[i].pending_c);
+#else
+    pthread_cond_destroy(&p->pending_c);
+#endif
+
+#ifdef DEBUG_TIME
+    fprintf(stderr, "Total time=%f\n", p->total_time / 1000000.0);
+    fprintf(stderr, "Wait  time=%f\n", p->wait_time  / 1000000.0);
+    fprintf(stderr, "%d%% utilisation\n",
+	    (int)(100 - ((100.0 * p->wait_time) / p->total_time + 0.5)));
+    for (i = 0; i < p->tsize; i++)
+	fprintf(stderr, "%d: Wait time=%f\n", i,
+		p->t[i].wait_time / 1000000.0);
+#endif
+
+    if (p->t_stack)
+	free(p->t_stack);
+
+    free(p->t);
+    free(p);
+
+#ifdef DEBUG
+    fprintf(stderr, "Destroyed pool %p\n", p);
+#endif
+}
+
+
+/*-----------------------------------------------------------------------------
+ * Test app.
+ */
+
+#ifdef TEST_MAIN
+
+#include <stdio.h>
+#include <math.h>
+
+void *doit(void *arg) {
+    int i, k, x = 0;
+    int job = *(int *)arg;
+    int *res;
+
+    printf("Worker: execute job %d\n", job);
+
+    usleep(random() % 1000000); // to coerce job completion out of order
+    if (0) {
+	for (k = 0; k < 100; k++) {
+	    for (i = 0; i < 100000; i++) {
+		x++;
+		x += x * sin(i);
+		x += x * cos(x);
+	    }
+	}
+	x *= 100;
+	x += job;
+    } else {
+	x = job*job;
+    }
+
+    printf("Worker: job %d terminating, x=%d\n", job, x);
+
+    free(arg);
+
+    res = malloc(sizeof(*res));
+    *res = x;
+
+    return res;
+}
+
+#define NTHREADS 8
+
+int main(int argc, char **argv) {
+    t_pool *p = t_pool_init(NTHREADS*2, NTHREADS);
+    t_results_queue *q = t_results_queue_init();
+    int i;
+    t_pool_result *r;
+
+    // Dispatch jobs
+    for (i = 0; i < 20; i++) {
+	int *ip = malloc(sizeof(*ip));
+	*ip = i;
+	printf("Submitting %d\n", i);
+	t_pool_dispatch(p, q, doit, ip);
+	
+	// Check for results
+	if ((r = t_pool_next_result(q))) {
+	    printf("RESULT: %d\n", *(int *)r->data);
+	    t_pool_delete_result(r, 1);
+	}
+    }
+
+    t_pool_flush(p);
+
+    while ((r = t_pool_next_result(q))) {
+	printf("RESULT: %d\n", *(int *)r->data);
+	t_pool_delete_result(r, 1);
+    }
+
+    t_pool_destroy(p, 0);
+    t_results_queue_destroy(q);
+
+    return 0;
+}
+#endif
diff --git a/htslib/cram/thread_pool.h b/htslib/cram/thread_pool.h
new file mode 100644
index 0000000..8158c85
--- /dev/null
+++ b/htslib/cram/thread_pool.h
@@ -0,0 +1,218 @@
+/*
+Copyright (c) 2013 Genome Research Ltd.
+Author: James Bonfield <jkb at sanger.ac.uk>
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+Institute nor the names of its contributors may be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+/*
+ * This file implements a thread pool for multi-threading applications.
+ * It consists of two distinct interfaces: thread pools an results queues.
+ *
+ * The pool of threads is given a function pointer and void* data to pass in.
+ * This means the pool can run jobs of multiple types, albeit first come
+ * first served with no job scheduling.
+ *
+ * Upon completion, the return value from the function pointer is added to
+ * a results queue. We may have multiple queues in use for the one pool.
+ *
+ * An example: reading from BAM and writing to CRAM with 10 threads. We'll
+ * have a pool of 10 threads and two results queues holding decoded BAM blocks
+ * and encoded CRAM blocks respectively.
+ */
+
+#ifndef _THREAD_POOL_H_
+#define _THREAD_POOL_H_
+
+#include <pthread.h>
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+struct t_pool;
+struct t_results_queue;
+
+typedef struct t_pool_job {
+    void *(*func)(void *arg);
+    void *arg;
+    struct t_pool_job *next;
+
+    struct t_pool *p;
+    struct t_results_queue *q;
+    int serial;
+} t_pool_job;
+
+typedef struct t_res {
+    struct t_res *next;
+    int serial; // sequential number for ordering
+    void *data; // result itself
+} t_pool_result;
+
+struct t_pool;
+
+typedef struct {
+    struct t_pool *p;
+    int idx;
+    pthread_t tid;
+    pthread_cond_t  pending_c;
+    long long wait_time;
+} t_pool_worker_t;
+
+typedef struct t_pool {
+    int qsize;    // size of queue
+    int njobs;    // pending job count
+    int nwaiting; // how many workers waiting for new jobs
+    int shutdown; // true if pool is being destroyed
+
+    // queue of pending jobs
+    t_pool_job *head, *tail;
+
+    // threads
+    int tsize;    // maximum number of jobs
+    t_pool_worker_t *t;
+
+    // Mutexes
+    pthread_mutex_t pool_m; // used when updating head/tail
+
+    pthread_cond_t  empty_c;
+    pthread_cond_t  pending_c; // not empty
+    pthread_cond_t  full_c;
+
+    // array of worker IDs free
+    int *t_stack, t_stack_top;
+
+    // Debugging to check wait time
+    long long total_time, wait_time;
+} t_pool;
+
+typedef struct t_results_queue {
+    t_pool_result *result_head;
+    t_pool_result *result_tail;
+    int next_serial;
+    int curr_serial;
+    int queue_len;  // number of items in queue
+    int pending;    // number of pending items (in progress or in pool list)
+    pthread_mutex_t result_m;
+    pthread_cond_t result_avail_c;
+} t_results_queue;
+
+
+/*
+ * Creates a worker pool of length qsize with tsize worker threads.
+ *
+ * Returns pool pointer on success;
+ *         NULL on failure
+ */
+t_pool *t_pool_init(int qsize, int tsize);
+
+/*
+ * Adds an item to the work pool.
+ *
+ * FIXME: Maybe return 1,0,-1 and distinguish between job dispathed vs
+ * result returned. Ie rather than blocking on full queue we're permitted
+ * to return early on "result available" event too.
+ * Caller would then have a while loop around t_pool_dispatch.
+ * Or, return -1 and set errno to E_AGAIN to indicate job not yet submitted.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int t_pool_dispatch(t_pool *p, t_results_queue *q,
+		    void *(*func)(void *arg), void *arg);
+int t_pool_dispatch2(t_pool *p, t_results_queue *q,
+		     void *(*func)(void *arg), void *arg, int nonblock);
+
+/*
+ * Flushes the pool, but doesn't exit. This simply drains the queue and
+ * ensures all worker threads have finished their current task.
+ *
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+int t_pool_flush(t_pool *p);
+
+/*
+ * Destroys a thread pool. If 'kill' is true the threads are terminated now,
+ * otherwise they are joined into the main thread so they will finish their
+ * current work load.
+ *
+ * Use t_pool_destroy(p,0) after a t_pool_flush(p) on a normal shutdown or
+ * t_pool_destroy(p,1) to quickly exit after a fatal error.
+ */
+void t_pool_destroy(t_pool *p, int kill);
+
+/*
+ * Pulls a result off the head of the result queue. Caller should
+ * free it (and any internals as appropriate) after use. This doesn't
+ * wait for a result to be present.
+ *
+ * Results will be returned in strict order.
+ * 
+ * Returns t_pool_result pointer if a result is ready.
+ *         NULL if not.
+ */
+t_pool_result *t_pool_next_result(t_results_queue *q);
+t_pool_result *t_pool_next_result_wait(t_results_queue *q);
+
+/*
+ * Frees a result 'r' and if free_data is true also frees
+ * the internal r->data result too.
+ */
+void t_pool_delete_result(t_pool_result *r, int free_data);
+
+/*
+ * Initialises a results queue.
+ *
+ * Results queue pointer on success;
+ *         NULL on failure
+ */
+t_results_queue *t_results_queue_init(void);
+
+/* Deallocates memory for a results queue */
+void t_results_queue_destroy(t_results_queue *q);
+
+/*
+ * Returns true if there are no items on the finished results queue and
+ * also none still pending.
+ */
+int t_pool_results_queue_empty(t_results_queue *q);
+
+/*
+ * Returns the number of completed jobs on the results queue.
+ */
+int t_pool_results_queue_len(t_results_queue *q);
+
+/*
+ * Returns the number of completed jobs plus the number queued up to run.
+ */
+int t_pool_results_queue_sz(t_results_queue *q);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _THREAD_POOL_H_ */
diff --git a/htslib/cram/vlen.c b/htslib/cram/vlen.c
new file mode 100644
index 0000000..0831741
--- /dev/null
+++ b/htslib/cram/vlen.c
@@ -0,0 +1,430 @@
+/*
+Author: James Bonfield (jkb at sanger.ac.uk)
+
+Copyright (c) 1995-1996 MEDICAL RESEARCH COUNCIL
+All rights reserved
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1 Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2 Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3 Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF 
+MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or 
+promote products derived from this software without specific prior written 
+permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON 
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+/*
+Copyright (c) 2004, 2009, 2011-2012 Genome Research Ltd.
+
+Author: James Bonfield <jkb at sanger.ac.uk>
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+Institute nor the names of its contributors may be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+#include <config.h>
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <stdarg.h>
+#include <sys/types.h>
+#include <string.h>
+
+#include "cram/vlen.h"
+#include "cram/os.h"
+
+#ifndef MAX
+#define MAX(a,b) ((a)>(b)?(a):(b))
+#endif
+
+#ifndef ABS
+#define ABS(a) ((a)>0?(a):-(a))
+#endif
+
+/* #define DEBUG_printf(a,n) printf(a,n) */
+#define DEBUG_printf(a,n)
+
+/*
+ * vlen: 27/10/95 written by James Bonfield, jkb at mrc-lmb.cam.ac.uk
+ *
+ * Given sprintf style of arguments this routine returns the maximum
+ * size of buffer needed to allocate to use with sprintf. It errs on
+ * the side of caution by being simplistic in its approach: we assume
+ * all numbers are of maximum length.
+ *
+ * Handles the usual type conversions (%[%diuaxXcfeEgGpns]), but not
+ * the 'wide' character conversions (%C and %S).
+ * Precision is handled in the correct formats, including %*.*
+ * notations.
+ * Additionally, some of the more dubious (but probably illegal) cases
+ * are supported (eg "%10%" will expand to "         %" on many
+ * systems).
+ *
+ * We also assume that the largest integer and larger pointer are 64
+ * bits, which at least covers the machines we'll need it for.
+ */
+int flen(char *fmt, ...)
+{
+    va_list args;
+
+    va_start(args, fmt);
+    return vflen(fmt, args);
+}
+
+int vflen(char *fmt, va_list ap)
+{
+    int len = 0;
+    char *cp, c;
+    long long l;
+    int i;
+    double d; 
+
+    /*
+     * This code modifies 'ap', but we do not know if va_list is a structure
+     * or a pointer to an array so we do not know if it is a local variable
+     * or not.
+     * C99 gets around this by defining va_copy() to make copies of ap, but
+     * this does not exist on all systems.
+     * For now, I just assume that when va_list is a pointer the system also
+     * provides a va_copy macro to work around this problem. The only system
+     * I have seen needing this so far was Linux on AMD64.
+     */
+#if defined(HAVE_VA_COPY)
+    va_list ap_local;
+    va_copy(ap_local, ap);
+#    define ap ap_local
+#endif
+
+    for(cp = fmt; *cp; cp++) {
+	switch(*cp) {
+
+	/* A format specifier */
+	case '%': {
+	    char *endp;
+	    long conv_len1=0, conv_len2=0, conv_len=0;
+	    signed int arg_size;
+
+	    /* Firstly, strip the modifier flags (+-#0 and [space]) */
+	    for(; (c=*++cp);) {
+		if ('#' == c)
+		    len+=2; /* Worst case of "0x" */
+		else if ('-' == c || '+' == c || ' ' == c)
+		    len++;
+		else
+		    break;
+	    }
+
+	    /* Width specifier */
+	    l = strtol(cp, &endp, 10);
+	    if (endp != cp) {
+		cp = endp;
+		conv_len = conv_len1 = l;
+	    } else if (*cp == '*') {
+		conv_len = conv_len1 = (int)va_arg(ap, int);
+		cp++;
+	    }
+
+	    /* Precision specifier */
+	    if ('.' == *cp) {
+		cp++;
+		conv_len2 = strtol(cp, &endp, 10);
+		if (endp != cp) {
+		    cp = endp;
+		} else if (*cp == '*') {
+		    conv_len2 = (int)va_arg(ap, int);
+		    cp++;
+		}
+		conv_len = MAX(conv_len1, conv_len2);
+	    }
+
+	    /* Short/long identifier */
+	    if ('h' == *cp) {
+		arg_size = -1; /* short */
+		cp++;
+	    } else if ('l' == *cp) {
+		arg_size = 1; /* long */
+		cp++;
+		if ('l' == *cp) {
+		    arg_size = 2; /* long long */
+		    cp++;
+		}
+	    } else {
+		arg_size = 0; /* int */
+	    }
+
+	    /* The actual type */
+	    switch (*cp) {
+	    case '%':
+		/*
+		 * Not real ANSI I suspect, but we'll allow for the
+		 * completely daft "%10%" example.
+		 */
+		len += MAX(conv_len1, 1);
+		break;
+
+	    case 'd':
+	    case 'i':
+	    case 'u':
+	    case 'a':
+	    case 'x':
+	    case 'X':
+		/* Remember: char and short are sent as int on the stack */
+		if (arg_size == -1)
+		    l = (long)va_arg(ap, int);
+		else if (arg_size == 1)
+		    l = va_arg(ap, long); 
+		else if (arg_size == 2)
+		    l = va_arg(ap, long long); 
+		else 
+		    l = (long)va_arg(ap, int);
+
+		DEBUG_printf("%d", l);
+
+		/*
+		 * No number can be more than 24 characters so we'll take
+		 * the max of conv_len and 24 (23 is len(2^64) in octal).
+		 * All that work above and we then go and estimate ;-),
+		 * but it's needed incase someone does %500d.
+		 */
+		len += MAX(conv_len, 23);
+		break;
+
+	    case 'c':
+		i = va_arg(ap, int);
+		DEBUG_printf("%c", i);
+		/*
+		 * Note that %10c and %.10c act differently.
+		 * Besides, I think precision is not really allowed for %c.
+		 */
+		len += MAX(conv_len1, i>=0x80 ?MB_CUR_MAX :1);
+		break;
+
+	    case 'f':
+		d = va_arg(ap, double);
+		DEBUG_printf("%f", d);
+		/*
+		 * Maybe "Inf" or "NaN", but we'll not worry about that.
+		 * Again, err on side of caution and take max of conv_len
+		 * and max length of a double. The worst case I can
+		 * think of is 317 characters (-1[308 zeros].000000)
+		 * without using precision codes. That's horrid. I
+		 * cheat and either use 317 or 15 depending on how
+		 * large the number is as I reckon 99% of floats
+		 * aren't that long.
+		 */
+		l = (ABS(d) > 1000000) ? 317 : 15;
+		l = MAX(l, conv_len1 + 2);
+		if (conv_len2) l += conv_len2 - 6;
+		len += l;
+		break;
+
+	    case 'e':
+	    case 'E':
+	    case 'g':
+	    case 'G':
+		d = va_arg(ap, double);
+		DEBUG_printf("%g", d);
+		/*
+		 * Maybe "Inf" or "NaN", but we'll not worry about that
+		 * Again, err on side of caution and take max of conv_len
+		 * and max length of a double (which defaults to only
+		 * '-' + 6 + '.' + 'E[+-]xxx' == 13.
+		 */
+		len += MAX(conv_len, 13);
+		break;
+
+	    case 'p':
+		l = (long)va_arg(ap, void *);
+		/*
+		 * Max pointer is 64bits == 16 chars (on alpha),
+		 * == 20 with + "0x".
+		 */
+		DEBUG_printf("%p", (void *)l);
+		len += MAX(conv_len, 20);
+		break;
+
+	    case 'n':
+		/* produces no output */
+		break;
+
+	    case 's': {
+		char *s = (char *)va_arg(ap, char *);
+		DEBUG_printf("%s", s);
+
+		if (!conv_len2) {
+		    len += MAX(conv_len, (int)strlen(s));
+		} else {
+		    len += conv_len;
+		}
+		break;
+	    }
+
+	    default:
+		/* wchar_t types of 'C' and 'S' aren't supported */
+		DEBUG_printf("Arg is %c\n", *cp);
+	    }
+	    
+	}
+
+	case '\0':
+	    break;
+
+	default:
+	    DEBUG_printf("%c", *cp);
+	    len++;
+	}
+    }
+
+    va_end(ap);
+
+    return len+1; /* one for the null character */
+}
+
+#if 0
+int main() {
+    int l;
+    char buf[10000];
+
+    sprintf(buf, "d: %d\n", 500);
+    l = flen("d: %d\n", 500);
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "");
+    l = flen("");
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%s\n","test");
+    l = flen("%s\n", "test");
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%c\n", 'a');
+    l = flen("%c\n", 'a');
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%31.30f\n", -9999.99);
+    l = flen("%31.30f\n", -9999.99);
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%f\n", -1e308);
+    l = flen("%f\n", -1e308);
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%.9f\n", -1e308);
+    l = flen("%.9f\n", -1e308);
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%10.20f\n", -1.999222333);
+    l = flen("%10.20f\n", -1.999222333);
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%#g\n", -3.14159265358e-222);
+    l = flen("%#g\n", -3.1415927e-222);
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%e\n", -123456789123456789.1);
+    l = flen("%e\n", -123456789123456789.1);
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%c %f %d %s %c %g %ld %s\n", 'a', 3.1, 9, "one", 'b', 4.2, 9, "two");
+    l = flen("%c %f %d %s %c %g %ld %s\n", 'a', 3.1, 9, "one", 'b', 4.2, 9, "two");
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%*.*e %*c\n", 10, 5, 9.0, 20, 'x');
+    l = flen("%*.*e %*c\n", 10, 5, 9.0, 20, 'x');
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%10c\n", 'z');
+    l = flen("%10c\n", 'z');
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%.10c\n", 'z');
+    l = flen("%.10c\n", 'z');
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%10d\n", 'z');
+    l = flen("%10d\n", 'z');
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%.10d\n", 'z');
+    l = flen("%.10d\n", 'z');
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%10%\n");
+    l = flen("%10%\n");
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%.10%\n");
+    l = flen("%.10%\n");
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%s\n", "0123456789");
+    l = flen("%s\n", "0123456789");
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%5s\n", "0123456789");
+    l = flen("%5s\n", "0123456789");
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%50s\n", "0123456789");
+    l = flen("%50s\n", "0123456789");
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%.5s\n", "0123456789");
+    l = flen("%.5s\n", "0123456789");
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%.50s\n", "0123456789");
+    l = flen("%.50s\n", "0123456789");
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%5.50s\n", "0123456789");
+    l = flen("%5.50s\n", "0123456789");
+    printf("%d %d\n\n", strlen(buf), l);
+
+    sprintf(buf, "%50.5s\n", "0123456789");
+    l = flen("%50.5s\n", "0123456789");
+    printf("%d %d\n\n", strlen(buf), l);
+
+    return 0;
+}
+#endif
diff --git a/htslib/cram/vlen.h b/htslib/cram/vlen.h
new file mode 100644
index 0000000..6b9b07c
--- /dev/null
+++ b/htslib/cram/vlen.h
@@ -0,0 +1,48 @@
+/*
+Author: James Bonfield (jkb at sanger.ac.uk)
+
+Copyright (c) 1995-1996 MEDICAL RESEARCH COUNCIL
+All rights reserved
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1 Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2 Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3 Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF 
+MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or 
+promote products derived from this software without specific prior written 
+permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR 
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON 
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+#ifndef _VLEN_H_
+#define _VLEN_H_
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+extern int vflen(char *fmt, va_list ap);
+extern int flen(char *fmt, ...);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _VLEN_H_ */
diff --git a/htslib/cram/zfio.c b/htslib/cram/zfio.c
new file mode 100644
index 0000000..46727c5
--- /dev/null
+++ b/htslib/cram/zfio.c
@@ -0,0 +1,183 @@
+/*
+Copyright (c) 2009-2013 Genome Research Ltd.
+Author: James Bonfield <jkb at sanger.ac.uk>
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+Institute nor the names of its contributors may be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+#include <config.h>
+
+#include <stdlib.h>
+#include <unistd.h>
+
+#include "cram/os.h"
+#include "cram/zfio.h"
+
+/* ------------------------------------------------------------------------ */
+/* Some wrappers around FILE * vs gzFile *, allowing for either */
+
+/*
+ * gzopen() works on both compressed and uncompressed data, but it has
+ * a significant performance hit even for uncompressed data (tested as
+ * 25s using FILE* to 46s via gzOpen and 66s via gzOpen when gzipped).
+ *
+ * Hence we use our own wrapper 'zfp' which is a FILE* when uncompressed
+ * and gzFile* when compressed. This also means we could hide bzopen in
+ * there too if desired.
+ */
+
+off_t zftello(zfp *zf) {
+    return zf->fp ? ftello(zf->fp) : -1;
+}
+
+int zfseeko(zfp *zf, off_t offset, int whence) {
+    return zf->fp ? fseeko(zf->fp, offset, whence) : -1;
+}
+
+
+/*
+ * A wrapper for either fgets or gzgets depending on what has been
+ * opened.
+ */
+char *zfgets(char *line, int size, zfp *zf) {
+    if (zf->fp)
+	return fgets(line, size, zf->fp);
+    else
+	return gzgets(zf->gz, line, size);
+}
+
+/*
+ * A wrapper for either fputs or gzputs depending on what has been
+ * opened.
+ */
+int zfputs(char *line, zfp *zf) {
+    if (zf->fp)
+	return fputs(line, zf->fp);
+    else
+	return gzputs(zf->gz, line) ? 0 : EOF;
+}
+
+/*
+ * Peeks at and returns the next character without consuming it from the
+ * input. (Ie a combination of getc and ungetc).
+ */
+int zfpeek(zfp *zf) {
+    int c;
+
+    if (zf->fp) {
+	c = getc(zf->fp);
+	if (c != EOF)
+	    ungetc(c, zf->fp);
+    } else {
+	c = gzgetc(zf->gz);
+	if (c != EOF)
+	    gzungetc(c, zf->gz);
+    }
+
+    return c;
+}
+
+/* A replacement for either feof of gzeof */
+int zfeof(zfp *zf) {
+    return zf->fp ? feof(zf->fp) : gzeof(zf->gz);
+}
+
+/* A replacement for either fopen or gzopen */
+zfp *zfopen(const char *path, const char *mode) {
+    char path2[1024];
+    zfp *zf;
+
+    if (!(zf = (zfp *)malloc(sizeof(*zf))))
+	return NULL;
+    zf->fp = NULL;
+    zf->gz = NULL;
+
+    /* Try normal fopen */
+    if (mode[0] != 'z' && mode[1] != 'z' &&
+	NULL != (zf->fp = fopen(path, mode))) {
+	unsigned char magic[2];
+	if (2 != fread(magic, 1, 2, zf->fp)) {
+	    free(zf);
+	    return NULL;
+	}
+	if (!(magic[0] == 0x1f &&
+	      magic[1] == 0x8b)) {
+	    fseeko(zf->fp, 0, SEEK_SET);
+	    return zf;
+	}
+
+	fclose(zf->fp);
+	zf->fp = NULL;
+    }
+
+#ifdef HAVE_POPEN
+    /*
+     * I've no idea why, by gzgets is VERY slow, maybe because it handles
+     * arbitrary seeks.
+     * popen to gzip -cd is 3 times faster though.
+     */
+    if (*mode == 'w') {
+    } else {
+	if (access(path, R_OK) == 0) {
+	    sprintf(path2, "gzip -cd < %.*s", 1000, path);
+	    if (NULL != (zf->fp = popen(path2, "r")))
+		return zf;
+	}
+	
+	sprintf(path2, "gzip -cd < %.*s.gz", 1000, path);
+	if (NULL != (zf->fp = popen(path2, "r")))
+	    return zf;
+
+	printf("Failed on %s\n", path);
+    } else {
+	sprintf(path2, "gzip > %.*s", 1000, path);
+	if (NULL != (zf->fp = popen(path2, "w")))
+	    return zf;
+	}
+	
+	printf("Failed on %s\n", path);
+    }
+#else
+    /* Gzopen instead */
+    if ((zf->gz = gzopen(path, mode)))
+	return zf;
+
+    sprintf(path2, "%.*s.gz", 1020, path);
+    if ((zf->gz = gzopen(path2, mode)))
+	return zf;
+#endif
+
+    perror(path);
+
+    free(zf);
+    return NULL;
+}
+
+int zfclose(zfp *zf) {
+    int r = (zf->fp) ? fclose(zf->fp) : gzclose(zf->gz);
+    free(zf);
+    return r;
+}
diff --git a/htslib/cram/zfio.h b/htslib/cram/zfio.h
new file mode 100644
index 0000000..ab9c9c9
--- /dev/null
+++ b/htslib/cram/zfio.h
@@ -0,0 +1,62 @@
+/*
+Copyright (c) 2009-2013 Genome Research Ltd.
+Author: James Bonfield <jkb at sanger.ac.uk>
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met:
+
+   1. Redistributions of source code must retain the above copyright notice, 
+this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright notice, 
+this list of conditions and the following disclaimer in the documentation 
+and/or other materials provided with the distribution.
+
+   3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+Institute nor the names of its contributors may be used to endorse or promote
+products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND 
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED 
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+#ifndef _ZFIO_H_
+#define _ZFIO_H_
+
+#include <stdio.h>
+#include <zlib.h>
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*
+ * Either a gzFile or a FILE.
+ */
+typedef struct {
+    FILE   *fp;
+    gzFile  gz;
+} zfp;
+
+off_t zftello(zfp *zf);
+int zfseeko(zfp *zf, off_t offset, int whence);
+char *zfgets(char *line, int size, zfp *zf);
+int zfputs(char *line, zfp *zf);
+zfp *zfopen(const char *path, const char *mode);
+int zfclose(zfp *zf);
+int zfpeek(zfp *zf);
+int zfeof(zfp *zf);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _ZFIO_H_ */
diff --git a/htslib/faidx.c b/htslib/faidx.c
new file mode 100644
index 0000000..7e3b2c6
--- /dev/null
+++ b/htslib/faidx.c
@@ -0,0 +1,525 @@
+/*  faidx.c -- FASTA random access.
+
+    Copyright (C) 2008, 2009, 2013-2016 Genome Research Ltd.
+    Portions copyright (C) 2011 Broad Institute.
+
+    Author: Heng Li <lh3 at sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <ctype.h>
+#include <string.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <inttypes.h>
+#include <errno.h>
+
+#include "htslib/bgzf.h"
+#include "htslib/faidx.h"
+#include "htslib/hfile.h"
+#include "htslib/khash.h"
+#include "htslib/kstring.h"
+
+typedef struct {
+    int32_t line_len, line_blen;
+    int64_t len;
+    uint64_t offset;
+} faidx1_t;
+KHASH_MAP_INIT_STR(s, faidx1_t)
+
+struct __faidx_t {
+    BGZF *bgzf;
+    int n, m;
+    char **name;
+    khash_t(s) *hash;
+};
+
+#ifndef kroundup32
+#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
+#endif
+
+static inline int fai_insert_index(faidx_t *idx, const char *name, int len, int line_len, int line_blen, uint64_t offset)
+{
+    if (!name) {
+        fprintf(stderr, "[fai_build_core] malformed line\n");
+        return -1;
+    }
+
+    char *name_key = strdup(name);
+    int absent;
+    khint_t k = kh_put(s, idx->hash, name_key, &absent);
+    faidx1_t *v = &kh_value(idx->hash, k);
+
+    if (! absent) {
+        fprintf(stderr, "[fai_build_core] ignoring duplicate sequence \"%s\" at byte offset %"PRIu64"\n", name, offset);
+        free(name_key);
+        return 0;
+    }
+
+    if (idx->n == idx->m) {
+        char **tmp;
+        idx->m = idx->m? idx->m<<1 : 16;
+        if (!(tmp = (char**)realloc(idx->name, sizeof(char*) * idx->m))) {
+            fprintf(stderr, "[fai_build_core] out of memory\n");
+            return -1;
+        }
+        idx->name = tmp;
+    }
+    idx->name[idx->n++] = name_key;
+    v->len = len;
+    v->line_len = line_len;
+    v->line_blen = line_blen;
+    v->offset = offset;
+
+    return 0;
+}
+
+faidx_t *fai_build_core(BGZF *bgzf)
+{
+    kstring_t name = { 0, 0, NULL };
+    int c;
+    int line_len, line_blen, state;
+    int l1, l2;
+    faidx_t *idx;
+    uint64_t offset;
+    int64_t len;
+
+    idx = (faidx_t*)calloc(1, sizeof(faidx_t));
+    idx->hash = kh_init(s);
+    len = line_len = line_blen = -1; state = 0; l1 = l2 = -1; offset = 0;
+    while ( (c=bgzf_getc(bgzf))>=0 ) {
+        if (c == '\n') { // an empty line
+            if (state == 1) {
+                offset = bgzf_utell(bgzf);
+                continue;
+            } else if ((state == 0 && len < 0) || state == 2) continue;
+            else if (state == 0) { state = 2; continue; }
+        }
+        if (c == '>') { // fasta header
+            if (len >= 0) {
+                if (fai_insert_index(idx, name.s, len, line_len, line_blen, offset) != 0)
+                    goto fail;
+            }
+
+            name.l = 0;
+            while ((c = bgzf_getc(bgzf)) >= 0)
+                if (! isspace(c)) kputc_(c, &name);
+                else if (name.l > 0 || c == '\n') break;
+            kputsn("", 0, &name);
+
+            if ( c<0 ) {
+                fprintf(stderr, "[fai_build_core] the last entry has no sequence\n");
+                goto fail;
+            }
+            if (c != '\n') while ( (c=bgzf_getc(bgzf))>=0 && c != '\n');
+            state = 1; len = 0;
+            offset = bgzf_utell(bgzf);
+        } else {
+            if (state == 3) {
+                fprintf(stderr, "[fai_build_core] inlined empty line is not allowed in sequence '%s'.\n", name.s);
+                goto fail;
+            }
+            if (state == 2) state = 3;
+            l1 = l2 = 0;
+            do {
+                ++l1;
+                if (isgraph(c)) ++l2;
+            } while ( (c=bgzf_getc(bgzf))>=0 && c != '\n');
+            if (state == 3 && l2) {
+                fprintf(stderr, "[fai_build_core] different line length in sequence '%s'.\n", name.s);
+                goto fail;
+            }
+            ++l1; len += l2;
+            if (state == 1) line_len = l1, line_blen = l2, state = 0;
+            else if (state == 0) {
+                if (l1 != line_len || l2 != line_blen) state = 2;
+            }
+        }
+    }
+
+    if (len >= 0) {
+        if (fai_insert_index(idx, name.s, len, line_len, line_blen, offset) != 0)
+            goto fail;
+    } else {
+        goto fail;
+    }
+
+    free(name.s);
+    return idx;
+
+fail:
+    free(name.s);
+    fai_destroy(idx);
+    return NULL;
+}
+
+void fai_save(const faidx_t *fai, FILE *fp)
+{
+    khint_t k;
+    int i;
+    for (i = 0; i < fai->n; ++i) {
+        faidx1_t x;
+        k = kh_get(s, fai->hash, fai->name[i]);
+        x = kh_value(fai->hash, k);
+#ifdef _WIN32
+        fprintf(fp, "%s\t%d\t%ld\t%d\t%d\n", fai->name[i], (int)x.len, (long)x.offset, (int)x.line_blen, (int)x.line_len);
+#else
+        fprintf(fp, "%s\t%d\t%lld\t%d\t%d\n", fai->name[i], (int)x.len, (long long)x.offset, (int)x.line_blen, (int)x.line_len);
+#endif
+    }
+}
+
+static faidx_t *fai_read(FILE *fp, const char *fname)
+{
+    faidx_t *fai;
+    char *buf, *p;
+    int len, line_len, line_blen;
+#ifdef _WIN32
+    long offset;
+#else
+    long long offset;
+#endif
+    fai = (faidx_t*)calloc(1, sizeof(faidx_t));
+    fai->hash = kh_init(s);
+    buf = (char*)calloc(0x10000, 1);
+    while (fgets(buf, 0x10000, fp)) {
+        for (p = buf; *p && isgraph(*p); ++p);
+        *p = 0; ++p;
+#ifdef _WIN32
+        sscanf(p, "%d%ld%d%d", &len, &offset, &line_blen, &line_len);
+#else
+        sscanf(p, "%d%lld%d%d", &len, &offset, &line_blen, &line_len);
+#endif
+        if (fai_insert_index(fai, buf, len, line_len, line_blen, offset) != 0) {
+            free(buf);
+            return NULL;
+        }
+    }
+    free(buf);
+    if (ferror(fp)) {
+        fprintf(stderr, "[fai_load] error while reading \"%s\": %s\n", fname, strerror(errno));
+        fai_destroy(fai);
+        return NULL;
+    }
+    return fai;
+}
+
+void fai_destroy(faidx_t *fai)
+{
+    int i;
+    for (i = 0; i < fai->n; ++i) free(fai->name[i]);
+    free(fai->name);
+    kh_destroy(s, fai->hash);
+    if (fai->bgzf) bgzf_close(fai->bgzf);
+    free(fai);
+}
+
+int fai_build(const char *fn)
+{
+    char *str;
+    BGZF *bgzf;
+    FILE *fp;
+    faidx_t *fai;
+    str = (char*)calloc(strlen(fn) + 5, 1);
+    sprintf(str, "%s.fai", fn);
+    bgzf = bgzf_open(fn, "r");
+    if ( !bgzf ) {
+        fprintf(stderr, "[fai_build] fail to open the FASTA file %s\n",fn);
+        free(str);
+        return -1;
+    }
+    if ( bgzf->is_compressed ) bgzf_index_build_init(bgzf);
+    fai = fai_build_core(bgzf);
+    if ( !fai )
+    {
+        if ( bgzf->is_compressed && bgzf->is_gzip ) fprintf(stderr,"Cannot index files compressed with gzip, please use bgzip\n");
+        bgzf_close(bgzf);
+        free(str);
+        return -1;
+    }
+    if ( bgzf->is_compressed ) {
+        if (bgzf_index_dump(bgzf, fn, ".gzi") < 0) {
+            fprintf(stderr, "[fai_build] fail to make bgzf index %s.gzi\n", fn);
+            fai_destroy(fai); free(str);
+            return -1;
+        }
+    }
+    if (bgzf_close(bgzf) < 0) {
+        fprintf(stderr, "[fai_build] Error on closing %s\n", fn);
+        fai_destroy(fai); free(str);
+        return -1;
+    }
+    fp = fopen(str, "wb");
+    if ( !fp ) {
+        fprintf(stderr, "[fai_build] fail to write FASTA index %s\n",str);
+        fai_destroy(fai); free(str);
+        return -1;
+    }
+    fai_save(fai, fp);
+    fclose(fp);
+    free(str);
+    fai_destroy(fai);
+    return 0;
+}
+
+static FILE *download_and_open(const char *fn)
+{
+    const int buf_size = 1 * 1024 * 1024;
+    uint8_t *buf;
+    FILE *fp;
+    hFILE *fp_remote;
+    const char *url = fn;
+    const char *p;
+    int l = strlen(fn);
+    for (p = fn + l - 1; p >= fn; --p)
+        if (*p == '/') break;
+    fn = p + 1;
+
+    // First try to open a local copy
+    fp = fopen(fn, "r");
+    if (fp)
+        return fp;
+
+    // If failed, download from remote and open
+    fp_remote = hopen(url, "rb");
+    if (fp_remote == 0) {
+        fprintf(stderr, "[download_from_remote] fail to open remote file %s\n",url);
+        return NULL;
+    }
+    if ((fp = fopen(fn, "wb")) == 0) {
+        fprintf(stderr, "[download_from_remote] fail to create file in the working directory %s\n",fn);
+        hclose_abruptly(fp_remote);
+        return NULL;
+    }
+    buf = (uint8_t*)calloc(buf_size, 1);
+    while ((l = hread(fp_remote, buf, buf_size)) > 0)
+        fwrite(buf, 1, l, fp);
+    free(buf);
+    fclose(fp);
+    if (hclose(fp_remote) != 0)
+        fprintf(stderr, "[download_from_remote] fail to close remote file %s\n", url);
+
+    return fopen(fn, "r");
+}
+
+faidx_t *fai_load(const char *fn)
+{
+    char *str;
+    FILE *fp;
+    faidx_t *fai;
+    str = (char*)calloc(strlen(fn) + 5, 1);
+    sprintf(str, "%s.fai", fn);
+
+    if (hisremote(str))
+    {
+        fp = download_and_open(str);
+        if ( !fp )
+        {
+            fprintf(stderr, "[fai_load] failed to open remote FASTA index %s\n", str);
+            free(str);
+            return 0;
+        }
+    }
+    else
+        fp = fopen(str, "rb");
+
+    if (fp == 0) {
+        fprintf(stderr, "[fai_load] build FASTA index.\n");
+        if (fai_build(fn) < 0) {
+            free(str);
+            return 0;
+        }
+        fp = fopen(str, "rb");
+        if (fp == 0) {
+            fprintf(stderr, "[fai_load] failed to open FASTA index: %s\n", strerror(errno));
+            free(str);
+            return 0;
+        }
+    }
+
+    fai = fai_read(fp, str);
+    fclose(fp);
+    free(str);
+    if (fai == NULL) {
+        return NULL;
+    }
+
+    fai->bgzf = bgzf_open(fn, "rb");
+    if (fai->bgzf == 0) {
+        fprintf(stderr, "[fai_load] fail to open FASTA file.\n");
+        return 0;
+    }
+    if ( fai->bgzf->is_compressed==1 )
+    {
+        if ( bgzf_index_load(fai->bgzf, fn, ".gzi") < 0 )
+        {
+            fprintf(stderr, "[fai_load] failed to load .gzi index: %s[.gzi]\n", fn);
+            fai_destroy(fai);
+            return NULL;
+        }
+    }
+    return fai;
+}
+
+char *fai_fetch(const faidx_t *fai, const char *str, int *len)
+{
+    char *s;
+    int c, i, l, k, name_end;
+    khiter_t iter;
+    faidx1_t val;
+    khash_t(s) *h;
+    int beg, end;
+
+    beg = end = -1;
+    h = fai->hash;
+    name_end = l = strlen(str);
+    s = (char*)malloc(l+1);
+    // remove space
+    for (i = k = 0; i < l; ++i)
+        if (!isspace(str[i])) s[k++] = str[i];
+    s[k] = 0; l = k;
+    // determine the sequence name
+    for (i = l - 1; i >= 0; --i) if (s[i] == ':') break; // look for colon from the end
+    if (i >= 0) name_end = i;
+    if (name_end < l) { // check if this is really the end
+        int n_hyphen = 0;
+        for (i = name_end + 1; i < l; ++i) {
+            if (s[i] == '-') ++n_hyphen;
+            else if (!isdigit(s[i]) && s[i] != ',') break;
+        }
+        if (i < l || n_hyphen > 1) name_end = l; // malformated region string; then take str as the name
+        s[name_end] = 0;
+        iter = kh_get(s, h, s);
+        if (iter == kh_end(h)) { // cannot find the sequence name
+            iter = kh_get(s, h, str); // try str as the name
+            if (iter == kh_end(h)) {
+                *len = 0;
+            free(s); return 0;
+            } else s[name_end] = ':', name_end = l;
+        }
+    } else iter = kh_get(s, h, str);
+    if(iter == kh_end(h)) {
+        fprintf(stderr, "[fai_fetch] Warning - Reference %s not found in FASTA file, returning empty sequence\n", str);
+        free(s);
+        *len = -2;
+        return 0;
+    };
+    val = kh_value(h, iter);
+    // parse the interval
+    if (name_end < l) {
+        for (i = k = name_end + 1; i < l; ++i)
+            if (s[i] != ',') s[k++] = s[i];
+        s[k] = 0;
+        beg = atoi(s + name_end + 1);
+        for (i = name_end + 1; i != k; ++i) if (s[i] == '-') break;
+        end = i < k? atoi(s + i + 1) : val.len;
+        if (beg > 0) --beg;
+    } else beg = 0, end = val.len;
+    if (beg >= val.len) beg = val.len;
+    if (end >= val.len) end = val.len;
+    if (beg > end) beg = end;
+    free(s);
+
+    // now retrieve the sequence
+    int ret = bgzf_useek(fai->bgzf, val.offset + beg / val.line_blen * val.line_len + beg % val.line_blen, SEEK_SET);
+    if ( ret<0 )
+    {
+        *len = -1;
+        fprintf(stderr, "[fai_fetch] Error: fai_fetch failed. (Seeking in a compressed, .gzi unindexed, file?)\n");
+        return NULL;
+    }
+    l = 0;
+    s = (char*)malloc(end - beg + 2);
+    while ( (c=bgzf_getc(fai->bgzf))>=0 && l < end - beg )
+        if (isgraph(c)) s[l++] = c;
+    s[l] = '\0';
+    *len = l;
+    return s;
+}
+
+int faidx_fetch_nseq(const faidx_t *fai)
+{
+    return fai->n;
+}
+
+int faidx_nseq(const faidx_t *fai)
+{
+    return fai->n;
+}
+
+const char *faidx_iseq(const faidx_t *fai, int i)
+{
+    return fai->name[i];
+}
+
+int faidx_seq_len(const faidx_t *fai, const char *seq)
+{
+    khint_t k = kh_get(s, fai->hash, seq);
+    if ( k == kh_end(fai->hash) ) return -1;
+    return kh_val(fai->hash, k).len;
+}
+
+char *faidx_fetch_seq(const faidx_t *fai, const char *c_name, int p_beg_i, int p_end_i, int *len)
+{
+    int l, c;
+    khiter_t iter;
+    faidx1_t val;
+    char *seq=NULL;
+
+    // Adjust position
+    iter = kh_get(s, fai->hash, c_name);
+    if (iter == kh_end(fai->hash))
+    {
+        *len = -2;
+        fprintf(stderr, "[fai_fetch_seq] The sequence \"%s\" not found\n", c_name);
+        return NULL;
+    }
+    val = kh_value(fai->hash, iter);
+    if(p_end_i < p_beg_i) p_beg_i = p_end_i;
+    if(p_beg_i < 0) p_beg_i = 0;
+    else if(val.len <= p_beg_i) p_beg_i = val.len - 1;
+    if(p_end_i < 0) p_end_i = 0;
+    else if(val.len <= p_end_i) p_end_i = val.len - 1;
+
+    // Now retrieve the sequence
+    int ret = bgzf_useek(fai->bgzf, val.offset + p_beg_i / val.line_blen * val.line_len + p_beg_i % val.line_blen, SEEK_SET);
+    if ( ret<0 )
+    {
+        *len = -1;
+        fprintf(stderr, "[fai_fetch_seq] Error: fai_fetch failed. (Seeking in a compressed, .gzi unindexed, file?)\n");
+        return NULL;
+    }
+    l = 0;
+    seq = (char*)malloc(p_end_i - p_beg_i + 2);
+    while ( (c=bgzf_getc(fai->bgzf))>=0 && l < p_end_i - p_beg_i + 1)
+        if (isgraph(c)) seq[l++] = c;
+    seq[l] = '\0';
+    *len = l;
+    return seq;
+}
+
+int faidx_has_seq(const faidx_t *fai, const char *seq)
+{
+    khiter_t iter = kh_get(s, fai->hash, seq);
+    if (iter == kh_end(fai->hash)) return 0;
+    return 1;
+}
+
diff --git a/htslib/hfile.c b/htslib/hfile.c
new file mode 100644
index 0000000..e8b05fc
--- /dev/null
+++ b/htslib/hfile.c
@@ -0,0 +1,751 @@
+/*  hfile.c -- buffered low-level input/output streams.
+
+    Copyright (C) 2013-2016 Genome Research Ltd.
+
+    Author: John Marshall <jm18 at sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <errno.h>
+
+#include <pthread.h>
+
+#include "htslib/hfile.h"
+#include "hfile_internal.h"
+
+#ifndef ENOTSUP
+#define ENOTSUP EINVAL
+#endif
+#ifndef EOVERFLOW
+#define EOVERFLOW ERANGE
+#endif
+#ifndef EPROTONOSUPPORT
+#define EPROTONOSUPPORT ENOSYS
+#endif
+
+/* hFILE fields are used as follows:
+
+   char *buffer;     // Pointer to the start of the I/O buffer
+   char *begin;      // First not-yet-read character / unused position
+   char *end;        // First unfilled/unfillable position
+   char *limit;      // Pointer to the first position past the buffer
+
+   const hFILE_backend *backend;  // Methods to refill/flush I/O buffer
+
+   off_t offset;     // Offset within the stream of buffer position 0
+   unsigned at_eof:1;// For reading, whether EOF has been seen
+   int has_errno;    // Error number from the last failure on this stream
+
+For reading, begin is the first unread character in the buffer and end is the
+first unfilled position:
+
+   -----------ABCDEFGHIJKLMNO---------------
+   ^buffer    ^begin         ^end           ^limit
+
+For writing, begin is the first unused position and end is unused so remains
+equal to buffer:
+
+   ABCDEFGHIJKLMNOPQRSTUVWXYZ---------------
+   ^buffer                   ^begin         ^limit
+   ^end
+
+Thus if begin > end then there is a non-empty write buffer, if begin < end
+then there is a non-empty read buffer, and if begin == end then both buffers
+are empty.  In all cases, the stream's file position indicator corresponds
+to the position pointed to by begin.  */
+
+hFILE *hfile_init(size_t struct_size, const char *mode, size_t capacity)
+{
+    hFILE *fp = (hFILE *) malloc(struct_size);
+    if (fp == NULL) goto error;
+
+    if (capacity == 0) capacity = 32768;
+    // FIXME For now, clamp input buffer sizes so mpileup doesn't eat memory
+    if (strchr(mode, 'r') && capacity > 32768) capacity = 32768;
+
+    fp->buffer = (char *) malloc(capacity);
+    if (fp->buffer == NULL) goto error;
+
+    fp->begin = fp->end = fp->buffer;
+    fp->limit = &fp->buffer[capacity];
+
+    fp->offset = 0;
+    fp->at_eof = 0;
+    fp->has_errno = 0;
+    return fp;
+
+error:
+    hfile_destroy(fp);
+    return NULL;
+}
+
+void hfile_destroy(hFILE *fp)
+{
+    int save = errno;
+    if (fp) free(fp->buffer);
+    free(fp);
+    errno = save;
+}
+
+static inline int writebuffer_is_nonempty(hFILE *fp)
+{
+    return fp->begin > fp->end;
+}
+
+/* Refills the read buffer from the backend (once, so may only partially
+   fill the buffer), returning the number of additional characters read
+   (which might be 0), or negative when an error occurred.  */
+static ssize_t refill_buffer(hFILE *fp)
+{
+    ssize_t n;
+
+    // Move any unread characters to the start of the buffer
+    if (fp->begin > fp->buffer) {
+        fp->offset += fp->begin - fp->buffer;
+        memmove(fp->buffer, fp->begin, fp->end - fp->begin);
+        fp->end = &fp->buffer[fp->end - fp->begin];
+        fp->begin = fp->buffer;
+    }
+
+    // Read into the available buffer space at fp->[end,limit)
+    if (fp->at_eof || fp->end == fp->limit) n = 0;
+    else {
+        n = fp->backend->read(fp, fp->end, fp->limit - fp->end);
+        if (n < 0) { fp->has_errno = errno; return n; }
+        else if (n == 0) fp->at_eof = 1;
+    }
+
+    fp->end += n;
+    return n;
+}
+
+/* Called only from hgetc(), when our buffer is empty.  */
+int hgetc2(hFILE *fp)
+{
+    return (refill_buffer(fp) > 0)? (unsigned char) *(fp->begin++) : EOF;
+}
+
+ssize_t hpeek(hFILE *fp, void *buffer, size_t nbytes)
+{
+    size_t n = fp->end - fp->begin;
+    while (n < nbytes) {
+        ssize_t ret = refill_buffer(fp);
+        if (ret < 0) return ret;
+        else if (ret == 0) break;
+        else n += ret;
+    }
+
+    if (n > nbytes) n = nbytes;
+    memcpy(buffer, fp->begin, n);
+    return n;
+}
+
+/* Called only from hread(); when called, our buffer is empty and nread bytes
+   have already been placed in the destination buffer.  */
+ssize_t hread2(hFILE *fp, void *destv, size_t nbytes, size_t nread)
+{
+    const size_t capacity = fp->limit - fp->buffer;
+    char *dest = (char *) destv;
+    dest += nread, nbytes -= nread;
+
+    // Read large requests directly into the destination buffer
+    while (nbytes * 2 >= capacity && !fp->at_eof) {
+        ssize_t n = fp->backend->read(fp, dest, nbytes);
+        if (n < 0) { fp->has_errno = errno; return n; }
+        else if (n == 0) fp->at_eof = 1;
+        fp->offset += n;
+        dest += n, nbytes -= n;
+        nread += n;
+    }
+
+    while (nbytes > 0 && !fp->at_eof) {
+        size_t n;
+        ssize_t ret = refill_buffer(fp);
+        if (ret < 0) return ret;
+
+        n = fp->end - fp->begin;
+        if (n > nbytes) n = nbytes;
+        memcpy(dest, fp->begin, n);
+        fp->begin += n;
+        dest += n, nbytes -= n;
+        nread += n;
+    }
+
+    return nread;
+}
+
+/* Flushes the write buffer, fp->[buffer,begin), out through the backend
+   returning 0 on success or negative if an error occurred.  */
+static ssize_t flush_buffer(hFILE *fp)
+{
+    const char *buffer = fp->buffer;
+    while (buffer < fp->begin) {
+        ssize_t n = fp->backend->write(fp, buffer, fp->begin - buffer);
+        if (n < 0) { fp->has_errno = errno; return n; }
+        buffer += n;
+        fp->offset += n;
+    }
+
+    fp->begin = fp->buffer;  // Leave the buffer empty
+    return 0;
+}
+
+int hflush(hFILE *fp)
+{
+    if (flush_buffer(fp) < 0) return EOF;
+    if (fp->backend->flush) {
+        if (fp->backend->flush(fp) < 0) { fp->has_errno = errno; return EOF; }
+    }
+    return 0;
+}
+
+/* Called only from hputc(), when our buffer is already full.  */
+int hputc2(int c, hFILE *fp)
+{
+    if (flush_buffer(fp) < 0) return EOF;
+    *(fp->begin++) = c;
+    return c;
+}
+
+/* Called only from hwrite() and hputs2(); when called, our buffer is full and
+   ncopied bytes from the source have already been copied to our buffer.  */
+ssize_t hwrite2(hFILE *fp, const void *srcv, size_t totalbytes, size_t ncopied)
+{
+    const char *src = (const char *) srcv;
+    ssize_t ret;
+    const size_t capacity = fp->limit - fp->buffer;
+    size_t remaining = totalbytes - ncopied;
+    src += ncopied;
+
+    ret = flush_buffer(fp);
+    if (ret < 0) return ret;
+
+    // Write large blocks out directly from the source buffer
+    while (remaining * 2 >= capacity) {
+        ssize_t n = fp->backend->write(fp, src, remaining);
+        if (n < 0) { fp->has_errno = errno; return n; }
+        fp->offset += n;
+        src += n, remaining -= n;
+    }
+
+    // Just buffer any remaining characters
+    memcpy(fp->begin, src, remaining);
+    fp->begin += remaining;
+
+    return totalbytes;
+}
+
+/* Called only from hputs(), when our buffer is already full.  */
+int hputs2(const char *text, size_t totalbytes, size_t ncopied, hFILE *fp)
+{
+    return (hwrite2(fp, text, totalbytes, ncopied) >= 0)? 0 : EOF;
+}
+
+off_t hseek(hFILE *fp, off_t offset, int whence)
+{
+    off_t curpos, pos;
+
+    if (writebuffer_is_nonempty(fp)) {
+        int ret = flush_buffer(fp);
+        if (ret < 0) return ret;
+    }
+
+    curpos = htell(fp);
+
+    // Relative offsets are given relative to the hFILE's stream position,
+    // which may differ from the backend's physical position due to buffering
+    // read-ahead.  Correct for this by converting to an absolute position.
+    if (whence == SEEK_CUR) {
+        if (curpos + offset < 0) {
+            // Either a negative offset resulted in a position before the
+            // start of the file, or we overflowed when given a positive offset
+            fp->has_errno = errno = (offset < 0)? EINVAL : EOVERFLOW;
+            return -1;
+        }
+
+        whence = SEEK_SET;
+        offset = curpos + offset;
+    }
+
+    // TODO Avoid seeking if the desired position is within our read buffer
+
+    pos = fp->backend->seek(fp, offset, whence);
+    if (pos < 0) { fp->has_errno = errno; return pos; }
+
+    // Seeking succeeded, so discard any non-empty read buffer
+    fp->begin = fp->end = fp->buffer;
+    fp->at_eof = 0;
+
+    fp->offset = pos;
+    return pos;
+}
+
+int hclose(hFILE *fp)
+{
+    int err = fp->has_errno;
+
+    if (writebuffer_is_nonempty(fp) && hflush(fp) < 0) err = fp->has_errno;
+    if (fp->backend->close(fp) < 0) err = errno;
+    hfile_destroy(fp);
+
+    if (err) {
+        errno = err;
+        return EOF;
+    }
+    else return 0;
+}
+
+void hclose_abruptly(hFILE *fp)
+{
+    int save = errno;
+    if (fp->backend->close(fp) < 0) { /* Ignore subsequent errors */ }
+    hfile_destroy(fp);
+    errno = save;
+}
+
+
+/***************************
+ * File descriptor backend *
+ ***************************/
+
+#ifndef _WIN32
+#include <sys/socket.h>
+#include <sys/stat.h>
+#define HAVE_STRUCT_STAT_ST_BLKSIZE
+#else
+#include <winsock2.h>
+#define HAVE_CLOSESOCKET
+#define HAVE_SETMODE
+#endif
+#include <fcntl.h>
+#include <unistd.h>
+
+/* For Unix, it doesn't matter whether a file descriptor is a socket.
+   However Windows insists on send()/recv() and its own closesocket()
+   being used when fd happens to be a socket.  */
+
+typedef struct {
+    hFILE base;
+    int fd;
+    unsigned is_socket:1;
+} hFILE_fd;
+
+static ssize_t fd_read(hFILE *fpv, void *buffer, size_t nbytes)
+{
+    hFILE_fd *fp = (hFILE_fd *) fpv;
+    ssize_t n;
+    do {
+        n = fp->is_socket? recv(fp->fd, buffer, nbytes, 0)
+                         : read(fp->fd, buffer, nbytes);
+    } while (n < 0 && errno == EINTR);
+    return n;
+}
+
+static ssize_t fd_write(hFILE *fpv, const void *buffer, size_t nbytes)
+{
+    hFILE_fd *fp = (hFILE_fd *) fpv;
+    ssize_t n;
+    do {
+        n = fp->is_socket?  send(fp->fd, buffer, nbytes, 0)
+                         : write(fp->fd, buffer, nbytes);
+    } while (n < 0 && errno == EINTR);
+    return n;
+}
+
+static off_t fd_seek(hFILE *fpv, off_t offset, int whence)
+{
+    hFILE_fd *fp = (hFILE_fd *) fpv;
+    return lseek(fp->fd, offset, whence);
+}
+
+static int fd_flush(hFILE *fpv)
+{
+    hFILE_fd *fp = (hFILE_fd *) fpv;
+    int ret;
+    do {
+#ifdef HAVE_FDATASYNC
+        ret = fdatasync(fp->fd);
+#else
+        ret = fsync(fp->fd);
+#endif
+        // Ignore invalid-for-fsync(2) errors due to being, e.g., a pipe,
+        // and operation-not-supported errors (Mac OS X)
+        if (ret < 0 && (errno == EINVAL || errno == ENOTSUP)) ret = 0;
+    } while (ret < 0 && errno == EINTR);
+    return ret;
+}
+
+static int fd_close(hFILE *fpv)
+{
+    hFILE_fd *fp = (hFILE_fd *) fpv;
+    int ret;
+    do {
+#ifdef HAVE_CLOSESOCKET
+        ret = fp->is_socket? closesocket(fp->fd) : close(fp->fd);
+#else
+        ret = close(fp->fd);
+#endif
+    } while (ret < 0 && errno == EINTR);
+    return ret;
+}
+
+static const struct hFILE_backend fd_backend =
+{
+    fd_read, fd_write, fd_seek, fd_flush, fd_close
+};
+
+static size_t blksize(int fd)
+{
+#ifdef HAVE_STRUCT_STAT_ST_BLKSIZE
+    struct stat sbuf;
+    if (fstat(fd, &sbuf) != 0) return 0;
+    return sbuf.st_blksize;
+#else
+    return 0;
+#endif
+}
+
+static hFILE *hopen_fd(const char *filename, const char *mode)
+{
+    hFILE_fd *fp = NULL;
+    int fd = open(filename, hfile_oflags(mode), 0666);
+    if (fd < 0) goto error;
+
+    fp = (hFILE_fd *) hfile_init(sizeof (hFILE_fd), mode, blksize(fd));
+    if (fp == NULL) goto error;
+
+    fp->fd = fd;
+    fp->is_socket = 0;
+    fp->base.backend = &fd_backend;
+    return &fp->base;
+
+error:
+    if (fd >= 0) { int save = errno; (void) close(fd); errno = save; }
+    hfile_destroy((hFILE *) fp);
+    return NULL;
+}
+
+hFILE *hdopen(int fd, const char *mode)
+{
+    hFILE_fd *fp = (hFILE_fd*) hfile_init(sizeof (hFILE_fd), mode, blksize(fd));
+    if (fp == NULL) return NULL;
+
+    fp->fd = fd;
+    fp->is_socket = (strchr(mode, 's') != NULL);
+    fp->base.backend = &fd_backend;
+    return &fp->base;
+}
+
+static hFILE *hopen_fd_fileuri(const char *url, const char *mode)
+{
+    if (strncmp(url, "file://localhost/", 17) == 0) url += 16;
+    else if (strncmp(url, "file:///", 8) == 0) url += 7;
+    else { errno = EPROTONOSUPPORT; return NULL; }
+
+    return hopen_fd(url, mode);
+}
+
+static hFILE *hopen_fd_stdinout(const char *mode)
+{
+    int fd = (strchr(mode, 'r') != NULL)? STDIN_FILENO : STDOUT_FILENO;
+#if defined HAVE_SETMODE && defined O_BINARY
+    if (setmode(fd, O_BINARY) < 0) return NULL;
+#endif
+    return hdopen(fd, mode);
+}
+
+int hfile_oflags(const char *mode)
+{
+    int rdwr = 0, flags = 0;
+    const char *s;
+    for (s = mode; *s; s++)
+        switch (*s) {
+        case 'r': rdwr = O_RDONLY;  break;
+        case 'w': rdwr = O_WRONLY; flags |= O_CREAT | O_TRUNC;  break;
+        case 'a': rdwr = O_WRONLY; flags |= O_CREAT | O_APPEND;  break;
+        case '+': rdwr = O_RDWR;  break;
+#ifdef O_CLOEXEC
+        case 'e': flags |= O_CLOEXEC;  break;
+#endif
+#ifdef O_EXCL
+        case 'x': flags |= O_EXCL;  break;
+#endif
+        default:  break;
+        }
+
+#ifdef O_BINARY
+    flags |= O_BINARY;
+#endif
+
+    return rdwr | flags;
+}
+
+
+/*********************
+ * In-memory backend *
+ *********************/
+
+typedef struct {
+    hFILE base;
+    const char *buffer;
+    size_t length, pos;
+} hFILE_mem;
+
+static ssize_t mem_read(hFILE *fpv, void *buffer, size_t nbytes)
+{
+    hFILE_mem *fp = (hFILE_mem *) fpv;
+    size_t avail = fp->length - fp->pos;
+    if (nbytes > avail) nbytes = avail;
+    memcpy(buffer, fp->buffer + fp->pos, nbytes);
+    fp->pos += nbytes;
+    return nbytes;
+}
+
+static off_t mem_seek(hFILE *fpv, off_t offset, int whence)
+{
+    hFILE_mem *fp = (hFILE_mem *) fpv;
+    size_t absoffset = (offset >= 0)? offset : -offset;
+    size_t origin;
+
+    switch (whence) {
+    case SEEK_SET: origin = 0; break;
+    case SEEK_CUR: origin = fp->pos; break;
+    case SEEK_END: origin = fp->length; break;
+    default: errno = EINVAL; return -1;
+    }
+
+    if ((offset  < 0 && absoffset > origin) ||
+        (offset >= 0 && absoffset > fp->length - origin)) {
+        errno = EINVAL;
+        return -1;
+    }
+
+    fp->pos = origin + offset;
+    return fp->pos;
+}
+
+static int mem_close(hFILE *fpv)
+{
+    return 0;
+}
+
+static const struct hFILE_backend mem_backend =
+{
+    mem_read, NULL, mem_seek, NULL, mem_close
+};
+
+static hFILE *hopen_mem(const char *data, const char *mode)
+{
+    if (strncmp(data, "data:", 5) == 0) data += 5;
+
+    // TODO Implement write modes, which will require memory allocation
+    if (strchr(mode, 'r') == NULL) { errno = EINVAL; return NULL; }
+
+    hFILE_mem *fp = (hFILE_mem *) hfile_init(sizeof (hFILE_mem), mode, 0);
+    if (fp == NULL) return NULL;
+
+    fp->buffer = data;
+    fp->length = strlen(data);
+    fp->pos = 0;
+    fp->base.backend = &mem_backend;
+    return &fp->base;
+}
+
+
+/*****************************************
+ * Plugin and hopen() backend dispatcher *
+ *****************************************/
+
+#include <ctype.h>
+
+#include "hts_internal.h"
+#include "htslib/khash.h"
+
+KHASH_MAP_INIT_STR(scheme_string, const struct hFILE_scheme_handler *);
+static khash_t(scheme_string) *schemes = NULL;
+
+struct hFILE_plugin_list {
+    struct hFILE_plugin plugin;
+    struct hFILE_plugin_list *next;
+};
+
+static struct hFILE_plugin_list *plugins = NULL;
+static pthread_mutex_t plugins_lock = PTHREAD_MUTEX_INITIALIZER;
+
+static void hfile_exit()
+{
+    pthread_mutex_lock(&plugins_lock);
+
+    kh_destroy(scheme_string, schemes);
+
+    while (plugins != NULL) {
+        struct hFILE_plugin_list *p = plugins;
+        if (p->plugin.destroy) p->plugin.destroy();
+#ifdef ENABLE_PLUGINS
+        if (p->plugin.obj) close_plugin(p->plugin.obj);
+#endif
+        plugins = p->next;
+        free(p);
+    }
+
+    pthread_mutex_unlock(&plugins_lock);
+    pthread_mutex_destroy(&plugins_lock);
+}
+
+void hfile_add_scheme_handler(const char *scheme,
+                              const struct hFILE_scheme_handler *handler)
+{
+    int absent;
+    khint_t k = kh_put(scheme_string, schemes, scheme, &absent);
+    if (absent || handler->priority > kh_value(schemes, k)->priority) {
+        kh_value(schemes, k) = handler;
+    }
+}
+
+static int init_add_plugin(void *obj, int (*init)(struct hFILE_plugin *),
+                           const char *pluginname)
+{
+    struct hFILE_plugin_list *p = malloc (sizeof (struct hFILE_plugin_list));
+    if (p == NULL) abort();
+
+    p->plugin.api_version = 1;
+    p->plugin.obj = obj;
+    p->plugin.name = NULL;
+    p->plugin.destroy = NULL;
+
+    int ret = (*init)(&p->plugin);
+
+    if (ret != 0) {
+        if (hts_verbose >= 4)
+            fprintf(stderr, "[W::load_hfile_plugins] "
+                    "initialisation failed for plugin \"%s\": %d\n",
+                    pluginname, ret);
+        free(p);
+        return ret;
+    }
+
+    if (hts_verbose >= 5)
+        fprintf(stderr, "[M::load_hfile_plugins] loaded \"%s\"\n", pluginname);
+
+    p->next = plugins, plugins = p;
+    return 0;
+}
+
+static void load_hfile_plugins()
+{
+    static const struct hFILE_scheme_handler
+        data = { hopen_mem, hfile_always_local, "built-in", 80 },
+        file = { hopen_fd_fileuri, hfile_always_local, "built-in", 80 };
+
+    schemes = kh_init(scheme_string);
+    if (schemes == NULL) abort();
+
+    hfile_add_scheme_handler("data", &data);
+    hfile_add_scheme_handler("file", &file);
+    init_add_plugin(NULL, hfile_plugin_init_net, "knetfile");
+
+#ifdef ENABLE_PLUGINS
+    struct hts_path_itr path;
+    const char *pluginname;
+    hts_path_itr_setup(&path, NULL, NULL, "hfile_", 6, NULL, 0);
+    while ((pluginname = hts_path_itr_next(&path)) != NULL) {
+        void *obj;
+        int (*init)(struct hFILE_plugin *) = (int (*)(struct hFILE_plugin *))
+            load_plugin(&obj, pluginname, "hfile_plugin_init");
+
+        if (init) {
+            if (init_add_plugin(obj, init, pluginname) != 0)
+                close_plugin(obj);
+        }
+    }
+#else
+
+#ifdef HAVE_IRODS
+    init_add_plugin(NULL, hfile_plugin_init_irods, "iRODS");
+#endif
+#ifdef HAVE_LIBCURL
+    init_add_plugin(NULL, hfile_plugin_init_libcurl, "libcurl");
+#endif
+
+#endif
+
+    // In the unlikely event atexit() fails, it's better to succeed here and
+    // carry on; then eventually when the program exits, we'll merely close
+    // down the plugins uncleanly, as if we had aborted.
+    (void) atexit(hfile_exit);
+}
+
+/* A filename like "foo:bar" in which we don't recognise the scheme is
+   either an ordinary file or an indication of a missing or broken plugin.
+   Try to open it as an ordinary file; but if there's no such file, set
+   errno distinctively to make the plugin issue apparent.  */
+static hFILE *hopen_unknown_scheme(const char *fname, const char *mode)
+{
+    hFILE *fp = hopen_fd(fname, mode);
+    if (fp == NULL && errno == ENOENT) errno = EPROTONOSUPPORT;
+    return fp;
+}
+
+/* Returns the appropriate handler, or NULL if the string isn't an URL.  */
+static const struct hFILE_scheme_handler *find_scheme_handler(const char *s)
+{
+    static const struct hFILE_scheme_handler unknown_scheme =
+        { hopen_unknown_scheme, hfile_always_local, "built-in", 0 };
+
+    char scheme[12];
+    int i;
+
+    for (i = 0; i < sizeof scheme; i++)
+        if (isalnum(s[i]) || s[i] == '+' || s[i] == '-' || s[i] == '.')
+            scheme[i] = tolower(s[i]);
+        else if (s[i] == ':') break;
+        else return NULL;
+
+    if (i == 0 || i >= sizeof scheme) return NULL;
+    scheme[i] = '\0';
+
+    pthread_mutex_lock(&plugins_lock);
+    if (! schemes) load_hfile_plugins();
+    pthread_mutex_unlock(&plugins_lock);
+
+    khint_t k = kh_get(scheme_string, schemes, scheme);
+    return (k != kh_end(schemes))? kh_value(schemes, k) : &unknown_scheme;
+}
+
+hFILE *hopen(const char *fname, const char *mode)
+{
+    const struct hFILE_scheme_handler *handler = find_scheme_handler(fname);
+    if (handler) return handler->open(fname, mode);
+    else if (strcmp(fname, "-") == 0) return hopen_fd_stdinout(mode);
+    else return hopen_fd(fname, mode);
+}
+
+int hfile_always_local (const char *fname) { return 0; }
+int hfile_always_remote(const char *fname) { return 1; }
+
+int hisremote(const char *fname)
+{
+    const struct hFILE_scheme_handler *handler = find_scheme_handler(fname);
+    return handler? handler->isremote(fname) : 0;
+}
diff --git a/htslib/hfile_internal.h b/htslib/hfile_internal.h
new file mode 100644
index 0000000..47b340a
--- /dev/null
+++ b/htslib/hfile_internal.h
@@ -0,0 +1,139 @@
+/*  hfile_internal.h -- internal parts of low-level input/output streams.
+
+    Copyright (C) 2013-2015 Genome Research Ltd.
+
+    Author: John Marshall <jm18 at sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#ifndef HFILE_INTERNAL_H
+#define HFILE_INTERNAL_H
+
+#include "htslib/hfile.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+struct hFILE_backend {
+    /* As per read(2), returning the number of bytes read (possibly 0) or
+       negative (and setting errno) on errors.  Front-end code will call this
+       repeatedly if necessary to attempt to get the desired byte count.  */
+    ssize_t (*read)(hFILE *fp, void *buffer, size_t nbytes) HTS_RESULT_USED;
+
+    /* As per write(2), returning the number of bytes written or negative (and
+       setting errno) on errors.  Front-end code will call this repeatedly if
+       necessary until the desired block is written or an error occurs.  */
+    ssize_t (*write)(hFILE *fp, const void *buffer, size_t nbytes)
+        HTS_RESULT_USED;
+
+    /* As per lseek(2), returning the resulting offset within the stream or
+       negative (and setting errno) on errors.  */
+    off_t (*seek)(hFILE *fp, off_t offset, int whence) HTS_RESULT_USED;
+
+    /* Performs low-level flushing, if any, e.g., fsync(2); for writing streams
+       only.  Returns 0 for success or negative (and sets errno) on errors. */
+    int (*flush)(hFILE *fp) HTS_RESULT_USED;
+
+    /* Closes the underlying stream (for output streams, the buffer will
+       already have been flushed), returning 0 for success or negative (and
+       setting errno) on errors, as per close(2).  */
+    int (*close)(hFILE *fp) HTS_RESULT_USED;
+};
+
+/* May be called by hopen_*() functions to decode a fopen()-style mode into
+   open(2)-style flags.  */
+int hfile_oflags(const char *mode);
+
+/* Must be called by hopen_*() functions to allocate the hFILE struct and set
+   up its base.  Capacity is a suggested buffer size (e.g., via fstat(2))
+   or 0 for a default-sized buffer.  */
+hFILE *hfile_init(size_t struct_size, const char *mode, size_t capacity);
+
+/* May be called by hopen_*() functions to undo the effects of hfile_init()
+   in the event opening the stream subsequently fails.  (This is safe to use
+   even if fp is NULL.  This takes care to preserve errno.)  */
+void hfile_destroy(hFILE *fp);
+
+
+struct hFILE_scheme_handler {
+    /* Opens a stream when dispatched by hopen(); should call hfile_init()
+       to malloc a struct "derived" from hFILE and initialise it appropriately,
+       including setting base.backend to its own backend vector.  */
+    hFILE *(*open)(const char *filename, const char *mode) HTS_RESULT_USED;
+
+    /* Returns whether the URL denotes remote storage when dispatched by
+       hisremote().  For simple cases, use one of hfile_always_*() below.  */
+    int (*isremote)(const char *filename) HTS_RESULT_USED;
+
+    /* The name of the plugin or other code providing this handler.  */
+    const char *provider;
+
+    /* If multiple handlers are registered for the same scheme, the one with
+       the highest priority is used; range is 0 (lowest) to 100 (highest).  */
+    int priority;
+};
+
+/* May be used as an isremote() function in simple cases.  */
+extern int hfile_always_local (const char *fname);
+extern int hfile_always_remote(const char *fname);
+
+/* Should be called by plugins for each URL scheme they wish to handle.  */
+void hfile_add_scheme_handler(const char *scheme,
+                              const struct hFILE_scheme_handler *handler);
+
+struct hFILE_plugin {
+    /* On entry, HTSlib's plugin API version (currently 1).  */
+    int api_version;
+
+    /* On entry, the plugin's handle as returned by dlopen() etc.  */
+    void *obj;
+
+    /* The plugin should fill this in with its (human-readable) name.  */
+    const char *name;
+
+    /* The plugin may wish to fill in a function to be called on closing.  */
+    void (*destroy)(void);
+};
+
+#ifdef ENABLE_PLUGINS
+#define PLUGIN_GLOBAL(identifier,suffix) identifier
+
+/* Plugins must define an entry point with this signature.  */
+extern int hfile_plugin_init(struct hFILE_plugin *self);
+
+#else
+#define PLUGIN_GLOBAL(identifier,suffix) identifier##suffix
+
+/* Only plugins distributed within the HTSlib source that might be built
+   even with --disable-plugins need to use PLUGIN_GLOBAL and be listed here;
+   others can simply define hfile_plugin_init().  */
+
+extern int hfile_plugin_init_irods(struct hFILE_plugin *self);
+extern int hfile_plugin_init_libcurl(struct hFILE_plugin *self);
+#endif
+
+/* This one is never built as a separate plugin.  */
+extern int hfile_plugin_init_net(struct hFILE_plugin *self);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/htslib/hfile_irods.c b/htslib/hfile_irods.c
new file mode 100644
index 0000000..84f622d
--- /dev/null
+++ b/htslib/hfile_irods.c
@@ -0,0 +1,259 @@
+/*  hfile_irods.c -- iRODS backend for low-level file streams.
+
+    Copyright (C) 2013, 2015 Genome Research Ltd.
+
+    Author: John Marshall <jm18 at sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <signal.h>
+#include <stdlib.h>
+#include <string.h>
+#include <errno.h>
+
+#include "hfile_internal.h"
+#include "htslib/hts.h"  // for hts_version() and hts_verbose
+#include "htslib/kstring.h"
+
+#include <rcConnect.h>
+#include <rcMisc.h>
+#include <dataObjOpen.h>
+#include <dataObjRead.h>
+#include <dataObjWrite.h>
+#include <dataObjLseek.h>
+#include <dataObjClose.h>
+
+typedef struct {
+    hFILE base;
+    int descriptor;
+} hFILE_irods;
+
+static int status_errno(int status)
+{
+    switch (status) {
+    case SYS_NO_API_PRIV: return EACCES;
+    case SYS_MALLOC_ERR: return ENOMEM;
+    case SYS_OUT_OF_FILE_DESC: return ENFILE;
+    case SYS_BAD_FILE_DESCRIPTOR: return EBADF;
+    case CAT_NO_ACCESS_PERMISSION: return EACCES;
+    case CAT_INVALID_AUTHENTICATION: return EACCES;
+    case CAT_NO_ROWS_FOUND: return ENOENT;
+    case CATALOG_ALREADY_HAS_ITEM_BY_THAT_NAME: return EEXIST;
+    default: return EIO;
+    }
+}
+
+static void set_errno(int status)
+{
+    int err = abs(status) % 1000;
+    errno = err? err : status_errno(status);
+}
+
+static struct {
+    rcComm_t *conn;
+    rodsEnv env;
+} irods = { NULL };
+
+static void irods_exit()
+{
+    if (irods.conn) { (void) rcDisconnect(irods.conn); }
+    irods.conn = NULL;
+}
+
+static int irods_init()
+{
+    kstring_t useragent = { 0, 0, NULL };
+    struct sigaction pipehandler;
+    rErrMsg_t err;
+    int ret, pipehandler_ret;
+
+    if (hts_verbose >= 5) rodsLogLevel(hts_verbose);
+
+    ret = getRodsEnv(&irods.env);
+    if (ret < 0) goto error;
+
+    // Set iRODS User-Agent, if our caller hasn't already done so.
+    kputs("htslib/", &useragent);
+    kputs(hts_version(), &useragent);
+    (void) setenv(SP_OPTION, useragent.s, 0);
+    free(useragent.s);
+
+    // Prior to iRODS 4.1, rcConnect() (even if it fails) installs its own
+    // SIGPIPE handler, which just prints a message and otherwise ignores the
+    // signal.  Most actual SIGPIPEs encountered will pertain to e.g. stdout
+    // rather than iRODS's connection, so we save and restore the existing
+    // state (by default, termination; or as already set by our caller).
+    pipehandler_ret = sigaction(SIGPIPE, NULL, &pipehandler);
+
+    irods.conn = rcConnect(irods.env.rodsHost, irods.env.rodsPort,
+                           irods.env.rodsUserName, irods.env.rodsZone,
+                           NO_RECONN, &err);
+    if (pipehandler_ret == 0) sigaction(SIGPIPE, &pipehandler, NULL);
+    if (irods.conn == NULL) { ret = err.status; goto error; }
+
+    if (strcmp(irods.env.rodsUserName, PUBLIC_USER_NAME) != 0) {
+#if defined IRODS_VERSION_INTEGER && IRODS_VERSION_INTEGER >= 4000000
+        ret = clientLogin(irods.conn, NULL, NULL);
+#else
+        ret = clientLogin(irods.conn);
+#endif
+        if (ret != 0) goto error;
+    }
+
+    return 0;
+
+error:
+    if (irods.conn) { (void) rcDisconnect(irods.conn); }
+    irods.conn = NULL;
+    set_errno(ret);
+    return -1;
+}
+
+static ssize_t irods_read(hFILE *fpv, void *buffer, size_t nbytes)
+{
+    hFILE_irods *fp = (hFILE_irods *) fpv;
+    openedDataObjInp_t args;
+    bytesBuf_t buf;
+    int ret;
+
+    memset(&args, 0, sizeof args);
+    args.l1descInx = fp->descriptor;
+    args.len = nbytes;
+
+    buf.buf = buffer;
+    buf.len = nbytes;
+
+    ret = rcDataObjRead(irods.conn, &args, &buf);
+    if (ret < 0) set_errno(ret);
+    return ret;
+}
+
+static ssize_t irods_write(hFILE *fpv, const void *buffer, size_t nbytes)
+{
+    hFILE_irods *fp = (hFILE_irods *) fpv;
+    openedDataObjInp_t args;
+    bytesBuf_t buf;
+    int ret;
+
+    memset(&args, 0, sizeof args);
+    args.l1descInx = fp->descriptor;
+    args.len = nbytes;
+
+    buf.buf = (void *) buffer; // ...the iRODS API is not const-correct here
+    buf.len = nbytes;
+
+    ret = rcDataObjWrite(irods.conn, &args, &buf);
+    if (ret < 0) set_errno(ret);
+    return ret;
+}
+
+static off_t irods_seek(hFILE *fpv, off_t offset, int whence)
+{
+    hFILE_irods *fp = (hFILE_irods *) fpv;
+    openedDataObjInp_t args;
+    fileLseekOut_t *out = NULL;
+    int ret;
+
+    memset(&args, 0, sizeof args);
+    args.l1descInx = fp->descriptor;
+    args.offset = offset;
+    args.whence = whence;
+
+    ret = rcDataObjLseek(irods.conn, &args, &out);
+
+    if (out) { offset = out->offset; free(out); }
+    else offset = -1;
+    if (ret < 0) { set_errno(ret); return -1; }
+    return offset;
+}
+
+static int irods_close(hFILE *fpv)
+{
+    hFILE_irods *fp = (hFILE_irods *) fpv;
+    openedDataObjInp_t args;
+    int ret;
+
+    memset(&args, 0, sizeof args);
+    args.l1descInx = fp->descriptor;
+
+    ret = rcDataObjClose(irods.conn, &args);
+    if (ret < 0) set_errno(ret);
+    return ret;
+}
+
+static const struct hFILE_backend irods_backend =
+{
+    irods_read, irods_write, irods_seek, NULL, irods_close
+};
+
+hFILE *hopen_irods(const char *filename, const char *mode)
+{
+    hFILE_irods *fp;
+    rodsPath_t path;
+    dataObjInp_t args;
+    int ret;
+
+    // Initialise the iRODS connection if this is the first use.
+    if (irods.conn == NULL) { if (irods_init() < 0) return NULL; }
+
+    if (strncmp(filename, "irods:", 6) == 0) filename += 6;
+    else { errno = EINVAL; return NULL; }
+
+    fp = (hFILE_irods *) hfile_init(sizeof (hFILE_irods), mode, 0);
+    if (fp == NULL) return NULL;
+
+    strncpy(path.inPath, filename, MAX_NAME_LEN-1);
+    path.inPath[MAX_NAME_LEN-1] = '\0';
+
+    ret = parseRodsPath(&path, &irods.env);
+    if (ret < 0) goto error;
+
+    memset(&args, 0, sizeof args);
+    strcpy(args.objPath, path.outPath);
+    args.openFlags = hfile_oflags(mode);
+    if (args.openFlags & O_CREAT) {
+        args.createMode = 0666;
+        addKeyVal(&args.condInput, DEST_RESC_NAME_KW,irods.env.rodsDefResource);
+    }
+
+    ret = rcDataObjOpen(irods.conn, &args);
+    if (ret < 0) goto error;
+    fp->descriptor = ret;
+
+    fp->base.backend = &irods_backend;
+    return &fp->base;
+
+error:
+    hfile_destroy((hFILE *) fp);
+    set_errno(ret);
+    return NULL;
+}
+
+int PLUGIN_GLOBAL(hfile_plugin_init,_irods)(struct hFILE_plugin *self)
+{
+    static const struct hFILE_scheme_handler handler =
+        { hopen_irods, hfile_always_remote, "iRODS", 50 };
+
+    self->name = "iRODS";
+    hfile_add_scheme_handler("irods", &handler);
+    self->destroy = irods_exit;
+    return 0;
+}
diff --git a/htslib/hfile_libcurl.c b/htslib/hfile_libcurl.c
new file mode 100644
index 0000000..457c8ce
--- /dev/null
+++ b/htslib/hfile_libcurl.c
@@ -0,0 +1,917 @@
+/*  hfile_libcurl.c -- libcurl backend for low-level file streams.
+
+    Copyright (C) 2015 Genome Research Ltd.
+
+    Author: John Marshall <jm18 at sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <ctype.h>
+#include <stdarg.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <time.h>
+#include <errno.h>
+#include <sys/select.h>
+
+#include "hfile_internal.h"
+#include "htslib/hts.h"  // for hts_version() and hts_verbose
+#include "htslib/kstring.h"
+
+#include <curl/curl.h>
+
+typedef struct {
+    hFILE base;
+    CURL *easy;
+    struct curl_slist *headers;
+    off_t file_size;
+    struct {
+        union { char *rd; const char *wr; } ptr;
+        size_t len;
+    } buffer;
+    CURLcode final_result;  // easy result code for finished transfers
+    // Flags for communicating with libcurl callbacks:
+    unsigned paused : 1;    // callback tells us that it has paused transfer
+    unsigned closing : 1;   // informs callback that hclose() has been invoked
+    unsigned finished : 1;  // wait_perform() tells us transfer is complete
+} hFILE_libcurl;
+
+static int http_status_errno(int status)
+{
+    if (status >= 500)
+        switch (status) {
+        case 501: return ENOSYS;
+        case 503: return EBUSY;
+        case 504: return ETIMEDOUT;
+        default:  return EIO;
+        }
+    else if (status >= 400)
+        switch (status) {
+        case 401: return EPERM;
+        case 403: return EACCES;
+        case 404: return ENOENT;
+        case 405: return EROFS;
+        case 407: return EPERM;
+        case 408: return ETIMEDOUT;
+        case 410: return ENOENT;
+        default:  return EINVAL;
+        }
+    else return 0;
+}
+
+static int easy_errno(CURL *easy, CURLcode err)
+{
+    long lval;
+
+    switch (err) {
+    case CURLE_OK:
+        return 0;
+
+    case CURLE_UNSUPPORTED_PROTOCOL:
+    case CURLE_URL_MALFORMAT:
+        return EINVAL;
+
+#if LIBCURL_VERSION_NUM >= 0x071505
+    case CURLE_NOT_BUILT_IN:
+        return ENOSYS;
+#endif
+
+    case CURLE_COULDNT_RESOLVE_PROXY:
+    case CURLE_COULDNT_RESOLVE_HOST:
+    case CURLE_FTP_CANT_GET_HOST:
+        return EDESTADDRREQ; // Lookup failure
+
+    case CURLE_COULDNT_CONNECT:
+    case CURLE_SEND_ERROR:
+    case CURLE_RECV_ERROR:
+        if (curl_easy_getinfo(easy, CURLINFO_OS_ERRNO, &lval) == CURLE_OK)
+            return lval;
+        else
+            return ECONNABORTED;
+
+    case CURLE_REMOTE_ACCESS_DENIED:
+    case CURLE_LOGIN_DENIED:
+    case CURLE_TFTP_PERM:
+        return EACCES;
+
+    case CURLE_PARTIAL_FILE:
+        return EPIPE;
+
+    case CURLE_HTTP_RETURNED_ERROR:
+        if (curl_easy_getinfo(easy, CURLINFO_RESPONSE_CODE, &lval) == CURLE_OK)
+            return http_status_errno(lval);
+        else
+            return EIO;
+
+    case CURLE_OUT_OF_MEMORY:
+        return ENOMEM;
+
+    case CURLE_OPERATION_TIMEDOUT:
+        return ETIMEDOUT;
+
+    case CURLE_RANGE_ERROR:
+        return ESPIPE;
+
+    case CURLE_SSL_CONNECT_ERROR:
+        // TODO return SSL error buffer messages
+        return ECONNABORTED;
+
+    case CURLE_FILE_COULDNT_READ_FILE:
+    case CURLE_TFTP_NOTFOUND:
+        return ENOENT;
+
+    case CURLE_TOO_MANY_REDIRECTS:
+        return ELOOP;
+
+    case CURLE_FILESIZE_EXCEEDED:
+        return EFBIG;
+
+    case CURLE_REMOTE_DISK_FULL:
+        return ENOSPC;
+
+    case CURLE_REMOTE_FILE_EXISTS:
+        return EEXIST;
+
+    default:
+        return EIO;
+    }
+}
+
+static int multi_errno(CURLMcode errm)
+{
+    switch (errm) {
+    case CURLM_CALL_MULTI_PERFORM:
+    case CURLM_OK:
+        return 0;
+
+    case CURLM_BAD_HANDLE:
+    case CURLM_BAD_EASY_HANDLE:
+    case CURLM_BAD_SOCKET:
+        return EBADF;
+
+    case CURLM_OUT_OF_MEMORY:
+        return ENOMEM;
+
+    default:
+        return EIO;
+    }
+}
+
+
+static struct {
+    CURLM *multi;
+    kstring_t useragent;
+    int nrunning;
+    unsigned perform_again : 1;
+} curl = { NULL, { 0, 0, NULL }, 0, 0 };
+
+static void libcurl_exit()
+{
+    (void) curl_multi_cleanup(curl.multi);
+    curl.multi = NULL;
+
+    free(curl.useragent.s);
+    curl.useragent.l = curl.useragent.m = 0; curl.useragent.s = NULL;
+
+    curl_global_cleanup();
+}
+
+
+static void process_messages()
+{
+    CURLMsg *msg;
+    int remaining;
+
+    while ((msg = curl_multi_info_read(curl.multi, &remaining)) != NULL) {
+        hFILE_libcurl *fp = NULL;
+        curl_easy_getinfo(msg->easy_handle, CURLINFO_PRIVATE, (char **) &fp);
+        switch (msg->msg) {
+        case CURLMSG_DONE:
+            fp->finished = 1;
+            fp->final_result = msg->data.result;
+            break;
+
+        default:
+            break;
+        }
+    }
+}
+
+static int wait_perform()
+{
+    fd_set rd, wr, ex;
+    int maxfd, nrunning;
+    long timeout;
+    CURLMcode errm;
+
+    FD_ZERO(&rd);
+    FD_ZERO(&wr);
+    FD_ZERO(&ex);
+    if (curl_multi_fdset(curl.multi, &rd, &wr, &ex, &maxfd) != CURLM_OK)
+        maxfd = -1, timeout = 1000;
+    else if (maxfd < 0)
+        timeout = 100;  // as recommended by curl_multi_fdset(3)
+    else {
+        if (curl_multi_timeout(curl.multi, &timeout) != CURLM_OK)
+            timeout = 1000;
+        else if (timeout < 0)
+            timeout = 10000;  // as recommended by curl_multi_timeout(3)
+    }
+
+    if (timeout > 0 && ! curl.perform_again) {
+        struct timeval tval;
+        tval.tv_sec  = (timeout / 1000);
+        tval.tv_usec = (timeout % 1000) * 1000;
+
+        if (select(maxfd + 1, &rd, &wr, &ex, &tval) < 0) return -1;
+    }
+
+    errm = curl_multi_perform(curl.multi, &nrunning);
+    curl.perform_again = 0;
+    if (errm == CURLM_CALL_MULTI_PERFORM) curl.perform_again = 1;
+    else if (errm != CURLM_OK) { errno = multi_errno(errm); return -1; }
+
+    if (nrunning < curl.nrunning) process_messages();
+    return 0;
+}
+
+
+static size_t recv_callback(char *ptr, size_t size, size_t nmemb, void *fpv)
+{
+    hFILE_libcurl *fp = (hFILE_libcurl *) fpv;
+    size_t n = size * nmemb;
+
+    if (n > fp->buffer.len) { fp->paused = 1; return CURL_WRITEFUNC_PAUSE; }
+    else if (n == 0) return 0;
+
+    memcpy(fp->buffer.ptr.rd, ptr, n);
+    fp->buffer.ptr.rd += n;
+    fp->buffer.len -= n;
+    return n;
+}
+
+static ssize_t libcurl_read(hFILE *fpv, void *bufferv, size_t nbytes)
+{
+    hFILE_libcurl *fp = (hFILE_libcurl *) fpv;
+    char *buffer = (char *) bufferv;
+    CURLcode err;
+
+    fp->buffer.ptr.rd = buffer;
+    fp->buffer.len = nbytes;
+    fp->paused = 0;
+    err = curl_easy_pause(fp->easy, CURLPAUSE_CONT);
+    if (err != CURLE_OK) { errno = easy_errno(fp->easy, err); return -1; }
+
+    while (! fp->paused && ! fp->finished)
+        if (wait_perform() < 0) return -1;
+
+    nbytes = fp->buffer.ptr.rd - buffer;
+    fp->buffer.ptr.rd = NULL;
+    fp->buffer.len = 0;
+
+    if (fp->finished && fp->final_result != CURLE_OK) {
+        errno = easy_errno(fp->easy, fp->final_result);
+        return -1;
+    }
+
+    return nbytes;
+}
+
+static size_t send_callback(char *ptr, size_t size, size_t nmemb, void *fpv)
+{
+    hFILE_libcurl *fp = (hFILE_libcurl *) fpv;
+    size_t n = size * nmemb;
+
+    if (fp->buffer.len == 0) {
+        // Send buffer is empty; normally pause, or signal EOF if we're closing
+        if (fp->closing) return 0;
+        else { fp->paused = 1; return CURL_READFUNC_PAUSE; }
+    }
+
+    if (n > fp->buffer.len) n = fp->buffer.len;
+    memcpy(ptr, fp->buffer.ptr.wr, n);
+    fp->buffer.ptr.wr += n;
+    fp->buffer.len -= n;
+    return n;
+}
+
+static ssize_t libcurl_write(hFILE *fpv, const void *bufferv, size_t nbytes)
+{
+    hFILE_libcurl *fp = (hFILE_libcurl *) fpv;
+    const char *buffer = (const char *) bufferv;
+    CURLcode err;
+
+    fp->buffer.ptr.wr = buffer;
+    fp->buffer.len = nbytes;
+    fp->paused = 0;
+    err = curl_easy_pause(fp->easy, CURLPAUSE_CONT);
+    if (err != CURLE_OK) { errno = easy_errno(fp->easy, err); return -1; }
+
+    while (! fp->paused && ! fp->finished)
+        if (wait_perform() < 0) return -1;
+
+    nbytes = fp->buffer.ptr.wr - buffer;
+    fp->buffer.ptr.wr = NULL;
+    fp->buffer.len = 0;
+
+    if (fp->finished && fp->final_result != CURLE_OK) {
+        errno = easy_errno(fp->easy, fp->final_result);
+        return -1;
+    }
+
+    return nbytes;
+}
+
+static off_t libcurl_seek(hFILE *fpv, off_t offset, int whence)
+{
+    hFILE_libcurl *fp = (hFILE_libcurl *) fpv;
+
+    CURLcode err;
+    CURLMcode errm;
+    off_t origin, pos;
+
+    switch (whence) {
+    case SEEK_SET:
+        origin = 0;
+        break;
+    case SEEK_CUR:
+        errno = ENOSYS;
+        return -1;
+    case SEEK_END:
+        if (fp->file_size < 0) { errno = ESPIPE; return -1; }
+        origin = fp->file_size;
+        break;
+    default:
+        errno = EINVAL;
+        return -1;
+    }
+
+    // Check 0 <= origin+offset < fp->file_size carefully, avoiding overflow
+    if ((offset < 0)? origin + offset < 0
+                : (fp->file_size >= 0 && offset > fp->file_size - origin)) {
+        errno = EINVAL;
+        return -1;
+    }
+
+    pos = origin + offset;
+
+    errm = curl_multi_remove_handle(curl.multi, fp->easy);
+    if (errm != CURLM_OK) { errno = multi_errno(errm); return -1; }
+    curl.nrunning--;
+
+    // TODO If we seem to be doing random access, use CURLOPT_RANGE to do
+    // limited reads (e.g. about a BAM block!) so seeking can reuse the
+    // existing connection more often.
+
+    if (pos <= 2147483647) err = curl_easy_setopt(fp->easy, CURLOPT_RESUME_FROM, (long) pos);
+    else err = curl_easy_setopt(fp->easy, CURLOPT_RESUME_FROM_LARGE, (curl_off_t) pos);
+    if (err != CURLE_OK) { errno = easy_errno(fp->easy, err); return -1; }
+
+    fp->buffer.len = 0;
+    fp->paused = fp->finished = 0;
+
+    errm = curl_multi_add_handle(curl.multi, fp->easy);
+    if (errm != CURLM_OK) { errno = multi_errno(errm); return -1; }
+    curl.nrunning++;
+
+    err = curl_easy_pause(fp->easy, CURLPAUSE_CONT);
+    if (err != CURLE_OK) { errno = easy_errno(fp->easy, err); return -1; }
+
+    while (! fp->paused && ! fp->finished)
+        if (wait_perform() < 0) return -1;
+
+    if (fp->finished && fp->final_result != CURLE_OK) {
+        errno = easy_errno(fp->easy, fp->final_result);
+        return -1;
+    }
+
+    return pos;
+}
+
+static int libcurl_close(hFILE *fpv)
+{
+    hFILE_libcurl *fp = (hFILE_libcurl *) fpv;
+    CURLcode err;
+    CURLMcode errm;
+    int save_errno = 0;
+
+    // Before closing the file, unpause it and perform on it so that uploads
+    // have the opportunity to signal EOF to the server -- see send_callback().
+
+    fp->buffer.len = 0;
+    fp->closing = 1;
+    fp->paused = 0;
+    err = curl_easy_pause(fp->easy, CURLPAUSE_CONT);
+    if (err != CURLE_OK) save_errno = easy_errno(fp->easy, err);
+
+    while (save_errno == 0 && ! fp->paused && ! fp->finished)
+        if (wait_perform() < 0) save_errno = errno;
+
+    if (fp->finished && fp->final_result != CURLE_OK)
+        save_errno = easy_errno(fp->easy, fp->final_result);
+
+    errm = curl_multi_remove_handle(curl.multi, fp->easy);
+    if (errm != CURLM_OK && save_errno == 0) save_errno = multi_errno(errm);
+    curl.nrunning--;
+
+    curl_easy_cleanup(fp->easy);
+
+    if (save_errno) { errno = save_errno; return -1; }
+    else return 0;
+}
+
+static const struct hFILE_backend libcurl_backend =
+{
+    libcurl_read, libcurl_write, libcurl_seek, NULL, libcurl_close
+};
+
+static int add_header(hFILE_libcurl *fp, const char *header)
+{
+    struct curl_slist *list = curl_slist_append(fp->headers, header);
+    if (list == NULL) { errno = ENOMEM; return -1; }
+    fp->headers = list;
+    return 0;
+}
+
+static int
+add_s3_settings(hFILE_libcurl *fp, const char *url, kstring_t *message);
+
+hFILE *hopen_libcurl(const char *url, const char *modes)
+{
+    hFILE_libcurl *fp;
+    char mode;
+    const char *s;
+    CURLcode err;
+    CURLMcode errm;
+    int save;
+
+    if ((s = strpbrk(modes, "rwa+")) != NULL) {
+        mode = *s;
+        if (strpbrk(&s[1], "rwa+")) mode = 'e';
+    }
+    else mode = '\0';
+
+    if (mode != 'r' && mode != 'w') { errno = EINVAL; return NULL; }
+
+    fp = (hFILE_libcurl *) hfile_init(sizeof (hFILE_libcurl), modes, 0);
+    if (fp == NULL) return NULL;
+
+    fp->easy = curl_easy_init();
+    if (fp->easy == NULL) { errno = ENOMEM; goto error; }
+
+    fp->headers = NULL;
+    fp->file_size = -1;
+    fp->buffer.ptr.rd = NULL;
+    fp->buffer.len = 0;
+    fp->final_result = (CURLcode) -1;
+    fp->paused = fp->closing = fp->finished = 0;
+
+    // Make a route to the hFILE_libcurl* given just a CURL* easy handle
+    err = curl_easy_setopt(fp->easy, CURLOPT_PRIVATE, fp);
+
+    if (mode == 'r') {
+        err |= curl_easy_setopt(fp->easy, CURLOPT_WRITEFUNCTION, recv_callback);
+        err |= curl_easy_setopt(fp->easy, CURLOPT_WRITEDATA, fp);
+    }
+    else {
+        err |= curl_easy_setopt(fp->easy, CURLOPT_READFUNCTION, send_callback);
+        err |= curl_easy_setopt(fp->easy, CURLOPT_READDATA, fp);
+        err |= curl_easy_setopt(fp->easy, CURLOPT_UPLOAD, 1L);
+        if (add_header(fp, "Transfer-Encoding: chunked") < 0) goto error;
+    }
+
+    if (tolower(url[0]) == 's' && url[1] == '3') {
+        // Construct the HTTP-Method/Content-MD5/Content-Type part of the
+        // message to be signed.  This will be destroyed by add_s3_settings().
+        kstring_t message = { 0, 0, NULL };
+        kputs((mode == 'r')? "GET\n" : "PUT\n", &message);
+        kputc('\n', &message);
+        kputc('\n', &message);
+        if (add_s3_settings(fp, url, &message) < 0) goto error;
+    }
+    else
+        err |= curl_easy_setopt(fp->easy, CURLOPT_URL, url);
+
+    err |= curl_easy_setopt(fp->easy, CURLOPT_USERAGENT, curl.useragent.s);
+    if (fp->headers)
+        err |= curl_easy_setopt(fp->easy, CURLOPT_HTTPHEADER, fp->headers);
+    err |= curl_easy_setopt(fp->easy, CURLOPT_FOLLOWLOCATION, 1L);
+    err |= curl_easy_setopt(fp->easy, CURLOPT_FAILONERROR, 1L);
+    if (hts_verbose >= 8)
+        err |= curl_easy_setopt(fp->easy, CURLOPT_VERBOSE, 1L);
+
+    if (err != 0) { errno = ENOSYS; goto error; }
+
+    errm = curl_multi_add_handle(curl.multi, fp->easy);
+    if (errm != CURLM_OK) { errno = multi_errno(errm); goto error; }
+    curl.nrunning++;
+
+    while (! fp->paused && ! fp->finished)
+        if (wait_perform() < 0) goto error_remove;
+
+    if (fp->finished && fp->final_result != CURLE_OK) {
+        errno = easy_errno(fp->easy, fp->final_result);
+        goto error_remove;
+    }
+
+    if (mode == 'r') {
+        double dval;
+        if (curl_easy_getinfo(fp->easy, CURLINFO_CONTENT_LENGTH_DOWNLOAD,
+                              &dval) == CURLE_OK && dval >= 0.0)
+            fp->file_size = (off_t) (dval + 0.1);
+    }
+
+    fp->base.backend = &libcurl_backend;
+    return &fp->base;
+
+error_remove:
+    save = errno;
+    (void) curl_multi_remove_handle(curl.multi, fp->easy);
+    curl.nrunning--;
+    errno = save;
+
+error:
+    save = errno;
+    curl_easy_cleanup(fp->easy);
+    if (fp->headers) curl_slist_free_all(fp->headers);
+    hfile_destroy((hFILE *) fp);
+    errno = save;
+    return NULL;
+}
+
+int PLUGIN_GLOBAL(hfile_plugin_init,_libcurl)(struct hFILE_plugin *self)
+{
+    static const struct hFILE_scheme_handler handler =
+        { hopen_libcurl, hfile_always_remote, "libcurl", 50 };
+
+    const curl_version_info_data *info;
+    const char * const *protocol;
+    CURLcode err;
+
+    err = curl_global_init(CURL_GLOBAL_ALL);
+    if (err != CURLE_OK) { errno = easy_errno(NULL, err); return -1; }
+
+    curl.multi = curl_multi_init();
+    if (curl.multi == NULL) { curl_global_cleanup(); errno = EIO; return -1; }
+
+    info = curl_version_info(CURLVERSION_NOW);
+    ksprintf(&curl.useragent, "htslib/%s libcurl/%s",
+             hts_version(), info->version);
+
+    curl.nrunning = 0;
+    curl.perform_again = 0;
+    self->name = "libcurl";
+    self->destroy = libcurl_exit;
+
+    for (protocol = info->protocols; *protocol; protocol++)
+        hfile_add_scheme_handler(*protocol, &handler);
+
+    hfile_add_scheme_handler("s3", &handler);
+    hfile_add_scheme_handler("s3+http", &handler);
+    if (info->features & CURL_VERSION_SSL)
+        hfile_add_scheme_handler("s3+https", &handler);
+
+    return 0;
+}
+
+
+/*******************
+ * Rewrite S3 URLs *
+ *******************/
+
+#if defined HAVE_COMMONCRYPTO
+
+#include <CommonCrypto/CommonHMAC.h>
+
+#define DIGEST_BUFSIZ CC_SHA1_DIGEST_LENGTH
+
+static size_t
+s3_sign(unsigned char *digest, kstring_t *key, kstring_t *message)
+{
+    CCHmac(kCCHmacAlgSHA1, key->s, key->l, message->s, message->l, digest);
+    return CC_SHA1_DIGEST_LENGTH;
+}
+
+#elif defined HAVE_HMAC
+
+#include <openssl/hmac.h>
+
+#define DIGEST_BUFSIZ EVP_MAX_MD_SIZE
+
+static size_t
+s3_sign(unsigned char *digest, kstring_t *key, kstring_t *message)
+{
+    unsigned int len;
+    HMAC(EVP_sha1(), key->s, key->l,
+         (unsigned char *) message->s, message->l, digest, &len);
+    return len;
+}
+
+#else
+#error No HMAC() routine found by configure
+#endif
+
+static void
+urldecode_kput(const char *s, int len, hFILE_libcurl *fp, kstring_t *str)
+{
+    if (memchr(s, '%', len) != NULL) {
+        int len2;
+        char *s2 = curl_easy_unescape(fp->easy, s, len, &len2);
+        if (s2 == NULL) abort();
+        kputsn(s2, len2, str);
+        curl_free(s2);
+    }
+    else kputsn(s, len, str);
+}
+
+static void base64_kput(const unsigned char *data, size_t len, kstring_t *str)
+{
+    static const char base64[] =
+        "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/";
+
+    size_t i = 0;
+    unsigned x = 0;
+    int bits = 0, pad = 0;
+
+    while (bits || i < len) {
+        if (bits < 6) {
+            x <<= 8, bits += 8;
+            if (i < len) x |= data[i++];
+            else pad++;
+        }
+
+        bits -= 6;
+        kputc(base64[(x >> bits) & 63], str);
+    }
+
+    str->l -= pad;
+    kputsn("==", pad, str);
+}
+
+static int is_dns_compliant(const char *s0, const char *slim)
+{
+    int has_nondigit = 0, len = 0;
+    const char *s;
+
+    for (s = s0; s < slim; len++, s++)
+        if (islower(*s))
+            has_nondigit = 1;
+        else if (*s == '-') {
+            has_nondigit = 1;
+            if (s == s0 || s+1 == slim) return 0;
+        }
+        else if (isdigit(*s))
+            ;
+        else if (*s == '.') {
+            if (s == s0 || ! isalnum(s[-1])) return 0;
+            if (s+1 == slim || ! isalnum(s[1])) return 0;
+        }
+        else return 0;
+
+    return has_nondigit && len >= 3 && len <= 63;
+}
+
+static FILE *expand_tilde_open(const char *fname, const char *mode)
+{
+    FILE *fp;
+
+    if (strncmp(fname, "~/", 2) == 0) {
+        kstring_t full_fname = { 0, 0, NULL };
+        const char *home = getenv("HOME");
+        if (! home) return NULL;
+
+        kputs(home, &full_fname);
+        kputs(&fname[1], &full_fname);
+
+        fp = fopen(full_fname.s, mode);
+        free(full_fname.s);
+    }
+    else
+        fp = fopen(fname, mode);
+
+    return fp;
+}
+
+static void parse_ini(const char *fname, const char *section, ...)
+{
+    kstring_t line = { 0, 0, NULL };
+    int active = 1;  // Start active, so global properties are accepted
+    char *s;
+
+    FILE *fp = expand_tilde_open(fname, "r");
+    if (fp == NULL) return;
+
+    while (line.l = 0, kgetline(&line, (kgets_func *) fgets, fp) >= 0)
+        if (line.s[0] == '[' && (s = strchr(line.s, ']')) != NULL) {
+            *s = '\0';
+            active = (strcmp(&line.s[1], section) == 0);
+        }
+        else if (active && (s = strpbrk(line.s, ":=")) != NULL) {
+            const char *key = line.s, *value = &s[1], *akey;
+            va_list args;
+
+            while (isspace(*key)) key++;
+            while (s > key && isspace(s[-1])) s--;
+            *s = '\0';
+
+            while (isspace(*value)) value++;
+            while (line.l > 0 && isspace(line.s[line.l-1]))
+                line.s[--line.l] = '\0';
+
+            va_start(args, section);
+            while ((akey = va_arg(args, const char *)) != NULL) {
+                kstring_t *avar = va_arg(args, kstring_t *);
+                if (strcmp(key, akey) == 0) { kputs(value, avar); break; }
+            }
+            va_end(args);
+        }
+
+    fclose(fp);
+    free(line.s);
+}
+
+static void parse_simple(const char *fname, kstring_t *id, kstring_t *secret)
+{
+    kstring_t text = { 0, 0, NULL };
+    char *s;
+    size_t len;
+
+    FILE *fp = expand_tilde_open(fname, "r");
+    if (fp == NULL) return;
+
+    while (kgetline(&text, (kgets_func *) fgets, fp) >= 0)
+        kputc(' ', &text);
+    fclose(fp);
+
+    s = text.s;
+    while (isspace(*s)) s++;
+    kputsn(s, len = strcspn(s, " \t"), id);
+
+    s += len;
+    while (isspace(*s)) s++;
+    kputsn(s, strcspn(s, " \t"), secret);
+
+    free(text.s);
+}
+
+static int
+add_s3_settings(hFILE_libcurl *fp, const char *s3url, kstring_t *message)
+{
+    int ret, save;
+    const char *bucket, *path;
+    char date_hdr[40];
+    CURLcode err;
+
+    kstring_t url = { 0, 0, NULL };
+    kstring_t profile = { 0, 0, NULL };
+    kstring_t id = { 0, 0, NULL };
+    kstring_t secret = { 0, 0, NULL };
+    kstring_t token = { 0, 0, NULL };
+    kstring_t token_hdr = { 0, 0, NULL };
+    kstring_t auth_hdr = { 0, 0, NULL };
+
+    time_t now = time(NULL);
+#ifdef HAVE_GMTIME_R
+    struct tm tm_buffer;
+    struct tm *tm = gmtime_r(&now, &tm_buffer);
+#else
+    struct tm *tm = gmtime(&now);
+#endif
+
+    strftime(date_hdr, sizeof date_hdr, "Date: %a, %d %b %Y %H:%M:%S GMT", tm);
+    if (add_header(fp, date_hdr) < 0) goto error;
+    kputs(&date_hdr[6], message);
+    kputc('\n', message);
+
+    // Our S3 URL format is s3[+SCHEME]://[ID[:SECRET[:TOKEN]]@]BUCKET/PATH
+
+    if (s3url[2] == '+') {
+        bucket = strchr(s3url, ':') + 1;
+        kputsn(&s3url[3], bucket - &s3url[3], &url);
+    }
+    else {
+        kputs("https:", &url);
+        bucket = &s3url[3];
+    }
+    while (*bucket == '/') kputc(*bucket++, &url);
+
+    path = bucket + strcspn(bucket, "/?#@");
+    if (*path == '@') {
+        const char *colon = strpbrk(bucket, ":@");
+        if (*colon != ':') {
+            urldecode_kput(bucket, colon - bucket, fp, &profile);
+        }
+        else {
+            const char *colon2 = strpbrk(&colon[1], ":@");
+            urldecode_kput(bucket, colon - bucket, fp, &id);
+            urldecode_kput(&colon[1], colon2 - &colon[1], fp, &secret);
+            if (*colon2 == ':')
+                urldecode_kput(&colon2[1], path - &colon2[1], fp, &token);
+        }
+
+        bucket = &path[1];
+        path = bucket + strcspn(bucket, "/?#");
+    }
+    else {
+        // If the URL has no ID[:SECRET]@, consider environment variables.
+        const char *v;
+        if ((v = getenv("AWS_ACCESS_KEY_ID")) != NULL) kputs(v, &id);
+        if ((v = getenv("AWS_SECRET_ACCESS_KEY")) != NULL) kputs(v, &secret);
+        if ((v = getenv("AWS_SESSION_TOKEN")) != NULL) kputs(v, &token);
+
+        if ((v = getenv("AWS_DEFAULT_PROFILE")) != NULL) kputs(v, &profile);
+        else if ((v = getenv("AWS_PROFILE")) != NULL) kputs(v, &profile);
+        else kputs("default", &profile);
+    }
+
+    // Use virtual hosted-style access if possible, otherwise path-style.
+    if (is_dns_compliant(bucket, path)) {
+        kputsn(bucket, path - bucket, &url);
+        kputs(".s3.amazonaws.com", &url);
+    }
+    else {
+        kputs("s3.amazonaws.com/", &url);
+        kputsn(bucket, path - bucket, &url);
+    }
+    kputs(path, &url);
+
+    if (id.l == 0) {
+        const char *v = getenv("AWS_SHARED_CREDENTIALS_FILE");
+        parse_ini(v? v : "~/.aws/credentials", profile.s,
+                  "aws_access_key_id", &id, "aws_secret_access_key", &secret,
+                  "aws_session_token", &token, NULL);
+    }
+    if (id.l == 0)
+        parse_ini("~/.s3cfg", profile.s, "access_key", &id,
+                  "secret_key", &secret, "access_token", &token, NULL);
+    if (id.l == 0)
+        parse_simple("~/.awssecret", &id, &secret);
+
+    if (token.l > 0) {
+        kputs("x-amz-security-token:", message);
+        kputs(token.s, message);
+        kputc('\n', message);
+
+        kputs("X-Amz-Security-Token: ", &token_hdr);
+        kputs(token.s, &token_hdr);
+        if (add_header(fp, token_hdr.s) < 0) goto error;
+    }
+
+    kputc('/', message);
+    kputs(bucket, message); // CanonicalizedResource is '/' + bucket + path
+
+    err = curl_easy_setopt(fp->easy, CURLOPT_URL, url.s);
+    if (err != CURLE_OK) { errno = easy_errno(fp->easy, err); goto error; }
+
+    // If we have no id/secret, we can't sign the request but will
+    // still be able to access public data sets.
+    if (id.l > 0 && secret.l > 0) {
+        unsigned char digest[DIGEST_BUFSIZ];
+        size_t digest_len = s3_sign(digest, &secret, message);
+
+        kputs("Authorization: AWS ", &auth_hdr);
+        kputs(id.s, &auth_hdr);
+        kputc(':', &auth_hdr);
+        base64_kput(digest, digest_len, &auth_hdr);
+
+        if (add_header(fp, auth_hdr.s) < 0) goto error;
+    }
+
+    ret = 0;
+    goto free_and_return;
+
+error:
+    ret = -1;
+
+free_and_return:
+    save = errno;
+    free(url.s);
+    free(profile.s);
+    free(id.s);
+    free(secret.s);
+    free(token.s);
+    free(token_hdr.s);
+    free(auth_hdr.s);
+    free(message->s);
+    errno = save;
+    return ret;
+}
diff --git a/htslib/hfile_net.c b/htslib/hfile_net.c
new file mode 100644
index 0000000..5443b22
--- /dev/null
+++ b/htslib/hfile_net.c
@@ -0,0 +1,112 @@
+/*  hfile_net.c -- network backend for low-level input/output streams.
+
+    Copyright (C) 2013-2015 Genome Research Ltd.
+
+    Author: John Marshall <jm18 at sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdlib.h>
+#include <errno.h>
+
+#include "hfile_internal.h"
+
+#include "htslib/knetfile.h"
+
+typedef struct {
+    hFILE base;
+    knetFile *netfp;
+} hFILE_net;
+
+static int net_inited = 0;
+
+#ifdef _WIN32
+static void net_exit(void)
+{
+    knet_win32_destroy();
+}
+#endif
+
+static int net_init(void)
+{
+#ifdef _WIN32
+    if (knet_win32_init() != 0) return -1;
+
+    // In the unlikely event atexit() fails, it's better to succeed here and
+    // carry on and do the I/O; then eventually when the program exits, we'll
+    // merely have failed to clean up properly, as if we had aborted.
+    (void) atexit(net_exit);
+#endif
+
+    net_inited = 1;
+    return 0;
+}
+
+static ssize_t net_read(hFILE *fpv, void *buffer, size_t nbytes)
+{
+    hFILE_net *fp = (hFILE_net *) fpv;
+    return knet_read(fp->netfp, buffer, nbytes);
+}
+
+static off_t net_seek(hFILE *fpv, off_t offset, int whence)
+{
+    hFILE_net *fp = (hFILE_net *) fpv;
+    return knet_seek(fp->netfp, offset, whence);
+}
+
+static int net_close(hFILE *fpv)
+{
+    hFILE_net *fp = (hFILE_net *) fpv;
+    return knet_close(fp->netfp);
+}
+
+static const struct hFILE_backend net_backend =
+{
+    net_read, NULL, net_seek, NULL, net_close
+};
+
+hFILE *hopen_net(const char *filename, const char *mode)
+{
+    hFILE_net *fp;
+
+    // Do any networking initialisation if this is the first use.
+    if (! net_inited) { if (net_init() < 0) return NULL; }
+
+    fp = (hFILE_net *) hfile_init(sizeof (hFILE_net), mode, 0);
+    if (fp == NULL) return NULL;
+
+    fp->netfp = knet_open(filename, mode);
+    if (fp->netfp == NULL) { hfile_destroy((hFILE *) fp); return NULL; }
+
+    fp->base.backend = &net_backend;
+    return &fp->base;
+}
+
+int hfile_plugin_init_net(struct hFILE_plugin *self)
+{
+    static const struct hFILE_scheme_handler handler =
+        { hopen_net, hfile_always_remote, "knetfile", 0 };
+
+    self->name = "knetfile";
+    hfile_add_scheme_handler("http", &handler);
+    hfile_add_scheme_handler("ftp",  &handler);
+    return 0;
+}
diff --git a/htslib/hts.c b/htslib/hts.c
new file mode 100644
index 0000000..aaf92e2
--- /dev/null
+++ b/htslib/hts.c
@@ -0,0 +1,2066 @@
+/*  hts.c -- format-neutral I/O, indexing, and iterator API functions.
+
+    Copyright (C) 2008, 2009, 2012-2016 Genome Research Ltd.
+    Copyright (C) 2012, 2013 Broad Institute.
+
+    Author: Heng Li <lh3 at sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <zlib.h>
+#include <ctype.h>
+#include <stdio.h>
+#include <string.h>
+#include <stdlib.h>
+#include <limits.h>
+#include <fcntl.h>
+#include <errno.h>
+#include <sys/stat.h>
+#include "htslib/bgzf.h"
+#include "htslib/hts.h"
+#include "cram/cram.h"
+#include "htslib/hfile.h"
+#include "version.h"
+#include "hts_internal.h"
+
+#include "htslib/kseq.h"
+#define KS_BGZF 1
+#if KS_BGZF
+    // bgzf now supports gzip-compressed files, the gzFile branch can be removed
+    KSTREAM_INIT2(, BGZF*, bgzf_read, 65536)
+#else
+    KSTREAM_INIT2(, gzFile, gzread, 16384)
+#endif
+
+#include "htslib/khash.h"
+KHASH_INIT2(s2i,, kh_cstr_t, int64_t, 1, kh_str_hash_func, kh_str_hash_equal)
+
+int hts_verbose = 3;
+
+const char *hts_version()
+{
+    return HTS_VERSION;
+}
+
+const unsigned char seq_nt16_table[256] = {
+    15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+    15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+    15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+     1, 2, 4, 8, 15,15,15,15, 15,15,15,15, 15, 0 /*=*/,15,15,
+    15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
+    15,15, 5, 6,  8,15, 7, 9, 15,10,15,15, 15,15,15,15,
+    15, 1,14, 2, 13,15,15, 4, 11,15,15,12, 15, 3,15,15,
+    15,15, 5, 6,  8,15, 7, 9, 15,10,15,15, 15,15,15,15,
+
+    15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+    15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+    15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+    15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+    15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+    15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+    15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15,
+    15,15,15,15, 15,15,15,15, 15,15,15,15, 15,15,15,15
+};
+
+const char seq_nt16_str[] = "=ACMGRSVTWYHKDBN";
+
+const int seq_nt16_int[] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 };
+
+/**********************
+ *** Basic file I/O ***
+ **********************/
+
+static enum htsFormatCategory format_category(enum htsExactFormat fmt)
+{
+    switch (fmt) {
+    case bam:
+    case sam:
+    case cram:
+        return sequence_data;
+
+    case vcf:
+    case bcf:
+        return variant_data;
+
+    case bai:
+    case crai:
+    case csi:
+    case gzi:
+    case tbi:
+        return index_file;
+
+    case bed:
+        return region_list;
+
+    case unknown_format:
+    case binary_format:
+    case text_format:
+    case format_maximum:
+        break;
+    }
+
+    return unknown_category;
+}
+
+// Decompress up to ten or so bytes by peeking at the file, which must be
+// positioned at the start of a GZIP block.
+static size_t decompress_peek(hFILE *fp, unsigned char *dest, size_t destsize)
+{
+    // Typically at most a couple of hundred bytes of input are required
+    // to get a few bytes of output from inflate(), so hopefully this buffer
+    // size suffices in general.
+    unsigned char buffer[512];
+    z_stream zs;
+    ssize_t npeek = hpeek(fp, buffer, sizeof buffer);
+
+    if (npeek < 0) return 0;
+
+    zs.zalloc = NULL;
+    zs.zfree = NULL;
+    zs.next_in = buffer;
+    zs.avail_in = npeek;
+    zs.next_out = dest;
+    zs.avail_out = destsize;
+    if (inflateInit2(&zs, 31) != Z_OK) return 0;
+
+    while (zs.total_out < destsize)
+        if (inflate(&zs, Z_SYNC_FLUSH) != Z_OK) break;
+
+    destsize = zs.total_out;
+    inflateEnd(&zs);
+
+    return destsize;
+}
+
+// Parse "x.y" text, taking care because the string is not NUL-terminated
+// and filling in major/minor only when the digits are followed by a delimiter,
+// so we don't misread "1.10" as "1.1" due to reaching the end of the buffer.
+static void
+parse_version(htsFormat *fmt, const unsigned char *u, const unsigned char *ulim)
+{
+    const char *s    = (const char *) u;
+    const char *slim = (const char *) ulim;
+    short v;
+
+    fmt->version.major = fmt->version.minor = -1;
+
+    for (v = 0; s < slim && isdigit_c(*s); s++)
+        v = 10 * v + *s - '0';
+
+    if (s < slim) {
+        fmt->version.major = v;
+        if (*s == '.') {
+            s++;
+            for (v = 0; s < slim && isdigit_c(*s); s++)
+                v = 10 * v + *s - '0';
+            if (s < slim)
+                fmt->version.minor = v;
+        }
+        else
+            fmt->version.minor = 0;
+    }
+}
+
+int hts_detect_format(hFILE *hfile, htsFormat *fmt)
+{
+    unsigned char s[21];
+    ssize_t len = hpeek(hfile, s, 18);
+    if (len < 0) return -1;
+
+    if (len >= 2 && s[0] == 0x1f && s[1] == 0x8b) {
+        // The stream is either gzip-compressed or BGZF-compressed.
+        // Determine which, and decompress the first few bytes.
+        fmt->compression = (len >= 18 && (s[3] & 4) &&
+                            memcmp(&s[12], "BC\2\0", 4) == 0)? bgzf : gzip;
+        len = decompress_peek(hfile, s, sizeof s);
+    }
+    else {
+        fmt->compression = no_compression;
+        len = hpeek(hfile, s, sizeof s);
+    }
+    if (len < 0) return -1;
+
+    fmt->compression_level = -1;
+    fmt->specific = NULL;
+
+    if (len >= 6 && memcmp(s,"CRAM",4) == 0 && s[4]>=1 && s[4]<=3 && s[5]<=1) {
+        fmt->category = sequence_data;
+        fmt->format = cram;
+        fmt->version.major = s[4], fmt->version.minor = s[5];
+        fmt->compression = custom;
+        return 0;
+    }
+    else if (len >= 4 && s[3] <= '\4') {
+        if (memcmp(s, "BAM\1", 4) == 0) {
+            fmt->category = sequence_data;
+            fmt->format = bam;
+            // TODO Decompress enough to pick version from @HD-VN header
+            fmt->version.major = 1, fmt->version.minor = -1;
+            return 0;
+        }
+        else if (memcmp(s, "BAI\1", 4) == 0) {
+            fmt->category = index_file;
+            fmt->format = bai;
+            fmt->version.major = -1, fmt->version.minor = -1;
+            return 0;
+        }
+        else if (memcmp(s, "BCF\4", 4) == 0) {
+            fmt->category = variant_data;
+            fmt->format = bcf;
+            fmt->version.major = 1, fmt->version.minor = -1;
+            return 0;
+        }
+        else if (memcmp(s, "BCF\2", 4) == 0) {
+            fmt->category = variant_data;
+            fmt->format = bcf;
+            fmt->version.major = s[3];
+            fmt->version.minor = (len >= 5 && s[4] <= 2)? s[4] : 0;
+            return 0;
+        }
+        else if (memcmp(s, "CSI\1", 4) == 0) {
+            fmt->category = index_file;
+            fmt->format = csi;
+            fmt->version.major = 1, fmt->version.minor = -1;
+            return 0;
+        }
+        else if (memcmp(s, "TBI\1", 4) == 0) {
+            fmt->category = index_file;
+            fmt->format = tbi;
+            fmt->version.major = -1, fmt->version.minor = -1;
+            return 0;
+        }
+    }
+    else if (len >= 16 && memcmp(s, "##fileformat=VCF", 16) == 0) {
+        fmt->category = variant_data;
+        fmt->format = vcf;
+        if (len >= 21 && s[16] == 'v')
+            parse_version(fmt, &s[17], &s[len]);
+        else
+            fmt->version.major = fmt->version.minor = -1;
+        return 0;
+    }
+    else if (len >= 4 && s[0] == '@' &&
+             (memcmp(s, "@HD\t", 4) == 0 || memcmp(s, "@SQ\t", 4) == 0 ||
+              memcmp(s, "@RG\t", 4) == 0 || memcmp(s, "@PG\t", 4) == 0)) {
+        fmt->category = sequence_data;
+        fmt->format = sam;
+        // @HD-VN is not guaranteed to be the first tag, but then @HD is
+        // not guaranteed to be present at all...
+        if (len >= 9 && memcmp(s, "@HD\tVN:", 7) == 0)
+            parse_version(fmt, &s[7], &s[len]);
+        else
+            fmt->version.major = 1, fmt->version.minor = -1;
+        return 0;
+    }
+    else {
+        // Various possibilities for tab-delimited text:
+        // .crai   (gzipped tab-delimited six columns: seqid 5*number)
+        // .bed    ([3..12] tab-delimited columns)
+        // .bedpe  (>= 10 tab-delimited columns)
+        // .sam    (tab-delimited >= 11 columns: seqid number seqid...)
+        // FIXME For now, assume it's SAM
+        fmt->category = sequence_data;
+        fmt->format = sam;
+        fmt->version.major = 1, fmt->version.minor = -1;
+        return 0;
+    }
+
+    fmt->category = unknown_category;
+    fmt->format = unknown_format;
+    fmt->version.major = fmt->version.minor = -1;
+    fmt->compression = no_compression;
+    return 0;
+}
+
+char *hts_format_description(const htsFormat *format)
+{
+    kstring_t str = { 0, 0, NULL };
+
+    switch (format->format) {
+    case sam:   kputs("SAM", &str); break;
+    case bam:   kputs("BAM", &str); break;
+    case cram:  kputs("CRAM", &str); break;
+    case vcf:   kputs("VCF", &str); break;
+    case bcf:
+        if (format->version.major == 1) kputs("Legacy BCF", &str);
+        else kputs("BCF", &str);
+        break;
+    case bai:   kputs("BAI", &str); break;
+    case crai:  kputs("CRAI", &str); break;
+    case csi:   kputs("CSI", &str); break;
+    case tbi:   kputs("Tabix", &str); break;
+    default:    kputs("unknown", &str); break;
+    }
+
+    if (format->version.major >= 0) {
+        kputs(" version ", &str);
+        kputw(format->version.major, &str);
+        if (format->version.minor >= 0) {
+            kputc('.', &str);
+            kputw(format->version.minor, &str);
+        }
+    }
+
+    switch (format->compression) {
+    case custom: kputs(" compressed", &str); break;
+    case gzip:   kputs(" gzip-compressed", &str); break;
+    case bgzf:
+        switch (format->format) {
+        case bam:
+        case bcf:
+        case csi:
+        case tbi:
+            // These are by definition BGZF, so just use the generic term
+            kputs(" compressed", &str);
+            break;
+        default:
+            kputs(" BGZF-compressed", &str);
+            break;
+        }
+        break;
+    default: break;
+    }
+
+    switch (format->category) {
+    case sequence_data: kputs(" sequence", &str); break;
+    case variant_data:  kputs(" variant calling", &str); break;
+    case index_file:    kputs(" index", &str); break;
+    case region_list:   kputs(" genomic region", &str); break;
+    default: break;
+    }
+
+    if (format->compression == no_compression)
+        switch (format->format) {
+        case sam:
+        case crai:
+        case vcf:
+        case bed:
+            kputs(" text", &str);
+            break;
+
+        default:
+            kputs(" data", &str);
+            break;
+        }
+    else
+        kputs(" data", &str);
+
+    return ks_release(&str);
+}
+
+htsFile *hts_open_format(const char *fn, const char *mode, const htsFormat *fmt)
+{
+    char smode[102], *cp, *cp2, *mode_c;
+    htsFile *fp = NULL;
+    hFILE *hfile;
+    char fmt_code = '\0';
+
+    strncpy(smode, mode, 100);
+    smode[100]=0;
+    if ((cp = strchr(smode, ',')))
+        *cp = '\0';
+
+    // Migrate format code (b or c) to the end of the smode buffer.
+    for (cp2 = cp = smode; *cp; cp++) {
+        if (*cp == 'b')
+            fmt_code = 'b';
+        else if (*cp == 'c')
+            fmt_code = 'c';
+        else
+            *cp2++ = *cp;
+    }
+    mode_c = cp2;
+    *cp2++ = fmt_code;
+    *cp2++ = 0;
+    *cp2++ = 0;
+
+    // Set or reset the format code if opts->format is used
+    if (fmt && fmt->format != unknown_format)
+        *mode_c = "\0g\0\0b\0c\0\0b\0g\0\0"[fmt->format];
+
+    hfile = hopen(fn, smode);
+    if (hfile == NULL) goto error;
+
+    fp = hts_hopen(hfile, fn, smode);
+    if (fp == NULL) goto error;
+
+    if (fmt && fmt->specific)
+        if (hts_opt_apply(fp, fmt->specific) != 0)
+            goto error;
+
+    return fp;
+
+error:
+    if (hts_verbose >= 2)
+        fprintf(stderr, "[E::%s] fail to open file '%s'\n", __func__, fn);
+
+    if (hfile)
+        hclose_abruptly(hfile);
+
+    return NULL;
+}
+
+htsFile *hts_open(const char *fn, const char *mode) {
+    return hts_open_format(fn, mode, NULL);
+}
+
+/*
+ * Splits str into a prefix, delimiter ('\0' or delim), and suffix, writing
+ * the prefix in lowercase into buf and returning a pointer to the suffix.
+ * On return, buf is always NUL-terminated; thus assumes that the "keyword"
+ * prefix should be one of several known values of maximum length buflen-2.
+ * (If delim is not found, returns a pointer to the '\0'.)
+ */
+static const char *
+scan_keyword(const char *str, char delim, char *buf, size_t buflen)
+{
+    size_t i = 0;
+    while (*str && *str != delim) {
+        if (i < buflen-1) buf[i++] = tolower_c(*str);
+        str++;
+    }
+
+    buf[i] = '\0';
+    return *str? str+1 : str;
+}
+
+/*
+ * Parses arg and appends it to the option list.
+ *
+ * Returns 0 on success;
+ *        -1 on failure.
+ */
+int hts_opt_add(hts_opt **opts, const char *c_arg) {
+    hts_opt *o, *t;
+    char *val;
+
+    if (!c_arg)
+        return -1;
+
+    if (!(o =  malloc(sizeof(*o))))
+        return -1;
+
+    if (!(o->arg = strdup(c_arg))) {
+        free(o);
+        return -1;
+    }
+
+    if (!(val = strchr(o->arg, '=')))
+        val = "1"; // assume boolean
+    else
+        *val++ = '\0';
+
+    if (strcmp(o->arg, "decode_md") == 0 ||
+        strcmp(o->arg, "DECODE_MD") == 0)
+        o->opt = CRAM_OPT_DECODE_MD, o->val.i = atoi(val);
+
+    else if (strcmp(o->arg, "verbosity") == 0 ||
+             strcmp(o->arg, "VERBOSITY") == 0)
+        o->opt = CRAM_OPT_VERBOSITY, o->val.i = atoi(val);
+
+    else if (strcmp(o->arg, "seqs_per_slice") == 0 ||
+             strcmp(o->arg, "SEQS_PER_SLICE") == 0)
+        o->opt = CRAM_OPT_SEQS_PER_SLICE, o->val.i = atoi(val);
+
+    else if (strcmp(o->arg, "slices_per_container") == 0 ||
+             strcmp(o->arg, "SLICES_PER_CONTAINER") == 0)
+        o->opt = CRAM_OPT_SLICES_PER_CONTAINER, o->val.i = atoi(val);
+
+    else if (strcmp(o->arg, "embed_ref") == 0 ||
+             strcmp(o->arg, "EMBED_REF") == 0)
+        o->opt = CRAM_OPT_EMBED_REF, o->val.i = atoi(val);
+
+    else if (strcmp(o->arg, "no_ref") == 0 ||
+             strcmp(o->arg, "NO_REF") == 0)
+        o->opt = CRAM_OPT_NO_REF, o->val.i = atoi(val);
+
+    else if (strcmp(o->arg, "ignore_md5") == 0 ||
+             strcmp(o->arg, "IGNORE_MD5") == 0)
+        o->opt = CRAM_OPT_IGNORE_MD5, o->val.i = atoi(val);
+
+    else if (strcmp(o->arg, "use_bzip2") == 0 ||
+             strcmp(o->arg, "USE_BZIP2") == 0)
+        o->opt = CRAM_OPT_USE_BZIP2, o->val.i = atoi(val);
+
+    else if (strcmp(o->arg, "use_rans") == 0 ||
+             strcmp(o->arg, "USE_RANS") == 0)
+        o->opt = CRAM_OPT_USE_RANS, o->val.i = atoi(val);
+
+    else if (strcmp(o->arg, "use_lzma") == 0 ||
+             strcmp(o->arg, "USE_LZMA") == 0)
+        o->opt = CRAM_OPT_USE_LZMA, o->val.i = atoi(val);
+
+    else if (strcmp(o->arg, "reference") == 0 ||
+             strcmp(o->arg, "REFERENCE") == 0)
+        o->opt = CRAM_OPT_REFERENCE, o->val.s = val;
+
+    else if (strcmp(o->arg, "version") == 0 ||
+             strcmp(o->arg, "VERSION") == 0)
+        o->opt = CRAM_OPT_VERSION, o->val.s =val;
+
+    else if (strcmp(o->arg, "multi_seq_per_slice") == 0 ||
+             strcmp(o->arg, "MULTI_SEQ_PER_SLICE") == 0)
+        o->opt = CRAM_OPT_MULTI_SEQ_PER_SLICE, o->val.i = atoi(val);
+
+    else if (strcmp(o->arg, "nthreads") == 0 ||
+             strcmp(o->arg, "NTHREADS") == 0)
+        o->opt = HTS_OPT_NTHREADS, o->val.i = atoi(val);
+
+    else if (strcmp(o->arg, "required_fields") == 0 ||
+             strcmp(o->arg, "REQUIRED_FIELDS") == 0)
+        o->opt = CRAM_OPT_REQUIRED_FIELDS, o->val.i = strtol(val, NULL, 0);
+
+    else {
+        fprintf(stderr, "Unknown option '%s'\n", o->arg);
+        free(o->arg);
+        free(o);
+        return -1;
+    }
+
+    o->next = NULL;
+
+    // Append; assumes small list.
+    if (*opts) {
+        t = *opts;
+        while (t->next)
+            t = t->next;
+        t->next = o;
+    } else {
+        *opts = o;
+    }
+
+    return 0;
+}
+
+/*
+ * Applies an hts_opt option list to a given htsFile.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int hts_opt_apply(htsFile *fp, hts_opt *opts) {
+    hts_opt *last = NULL;
+
+    for (; opts;  opts = (last=opts)->next)
+        if (hts_set_opt(fp,  opts->opt,  opts->val) != 0)
+            return -1;
+
+    return 0;
+}
+
+/*
+ * Frees an hts_opt list.
+ */
+void hts_opt_free(hts_opt *opts) {
+    hts_opt *last = NULL;
+    while (opts) {
+        opts = (last=opts)->next;
+        free(last->arg);
+        free(last);
+    }
+}
+
+
+/*
+ * Tokenise options as (key(=value)?,)*(key(=value)?)?
+ * NB: No provision for ',' appearing in the value!
+ * Add backslashing rules?
+ *
+ * This could be used as part of a general command line option parser or
+ * as a string concatenated onto the file open mode.
+ *
+ * Returns 0 on success
+ *        -1 on failure.
+ */
+int hts_parse_opt_list(htsFormat *fmt, const char *str) {
+    while (str && *str) {
+        const char *str_start;
+        int len;
+        char arg[8001];
+
+        while (*str && *str == ',')
+            str++;
+
+        for (str_start = str; *str && *str != ','; str++);
+        len = str - str_start;
+
+        // Produce a nul terminated copy of the option
+        strncpy(arg, str_start, len < 8000 ? len : 8000);
+        arg[len < 8000 ? len : 8000] = '\0';
+
+        if (hts_opt_add((hts_opt **)&fmt->specific, arg) != 0)
+            return -1;
+
+        if (*str)
+            str++;
+    }
+
+    return 0;
+}
+
+/*
+ * Accepts a string file format (sam, bam, cram, vcf, bam) optionally
+ * followed by a comma separated list of key=value options and splits
+ * these up into the fields of htsFormat struct.
+ *
+ * format is assumed to be already initialised, either to blank
+ * "unknown" values or via previous hts_opt_add calls.
+ *
+ * Returns 0 on success
+ *        -1 on failure.
+ */
+int hts_parse_format(htsFormat *format, const char *str) {
+    char fmt[8];
+    const char *cp = scan_keyword(str, ',', fmt, sizeof fmt);
+
+    format->version.minor = 0; // unknown
+    format->version.major = 0; // unknown
+
+    if (strcmp(fmt, "sam") == 0) {
+        format->category          = sequence_data;
+        format->format            = sam;
+        format->compression       = no_compression;;
+        format->compression_level = 0;
+    } else if (strcmp(fmt, "bam") == 0) {
+        format->category          = sequence_data;
+        format->format            = bam;
+        format->compression       = bgzf;
+        format->compression_level = -1;
+    } else if (strcmp(fmt, "cram") == 0) {
+        format->category          = sequence_data;
+        format->format            = cram;
+        format->compression       = custom;
+        format->compression_level = -1;
+    } else if (strcmp(fmt, "vcf") == 0) {
+        format->category          = variant_data;
+        format->format            = vcf;
+        format->compression       = no_compression;;
+        format->compression_level = 0;
+    } else if (strcmp(fmt, "bcf") == 0) {
+        format->category          = variant_data;
+        format->format            = bcf;
+        format->compression       = bgzf;
+        format->compression_level = -1;
+    } else {
+        return -1;
+    }
+
+    return hts_parse_opt_list(format, cp);
+}
+
+
+/*
+ * Tokenise options as (key(=value)?,)*(key(=value)?)?
+ * NB: No provision for ',' appearing in the value!
+ * Add backslashing rules?
+ *
+ * This could be used as part of a general command line option parser or
+ * as a string concatenated onto the file open mode.
+ *
+ * Returns 0 on success
+ *        -1 on failure.
+ */
+static int hts_process_opts(htsFile *fp, const char *opts) {
+    htsFormat fmt;
+
+    fmt.specific = NULL;
+    if (hts_parse_opt_list(&fmt, opts) != 0)
+        return -1;
+
+    if (hts_opt_apply(fp, fmt.specific) != 0) {
+        hts_opt_free(fmt.specific);
+        return -1;
+    }
+
+    hts_opt_free(fmt.specific);
+
+    return 0;
+}
+
+
+htsFile *hts_hopen(struct hFILE *hfile, const char *fn, const char *mode)
+{
+    htsFile *fp = (htsFile*)calloc(1, sizeof(htsFile));
+    char simple_mode[101], *cp, *opts;
+    simple_mode[100] = '\0';
+
+    if (fp == NULL) goto error;
+
+    fp->fn = strdup(fn);
+    fp->is_be = ed_is_big();
+
+    // Split mode into simple_mode,opts strings
+    if ((cp = strchr(mode, ','))) {
+        strncpy(simple_mode, mode, cp-mode <= 100 ? cp-mode : 100);
+        simple_mode[cp-mode] = '\0';
+        opts = cp+1;
+    } else {
+        strncpy(simple_mode, mode, 100);
+        opts = NULL;
+    }
+
+    if (strchr(simple_mode, 'r')) {
+        if (hts_detect_format(hfile, &fp->format) < 0) goto error;
+    }
+    else if (strchr(simple_mode, 'w') || strchr(simple_mode, 'a')) {
+        htsFormat *fmt = &fp->format;
+        fp->is_write = 1;
+
+        if (strchr(simple_mode, 'b')) fmt->format = binary_format;
+        else if (strchr(simple_mode, 'c')) fmt->format = cram;
+        else fmt->format = text_format;
+
+        if (strchr(simple_mode, 'z')) fmt->compression = bgzf;
+        else if (strchr(simple_mode, 'g')) fmt->compression = gzip;
+        else if (strchr(simple_mode, 'u')) fmt->compression = no_compression;
+        else {
+            // No compression mode specified, set to the default for the format
+            switch (fmt->format) {
+            case binary_format: fmt->compression = bgzf; break;
+            case cram: fmt->compression = custom; break;
+            case text_format: fmt->compression = no_compression; break;
+            default: abort();
+            }
+        }
+
+        // Fill in category (if determinable; e.g. 'b' could be BAM or BCF)
+        fmt->category = format_category(fmt->format);
+
+        fmt->version.major = fmt->version.minor = -1;
+        fmt->compression_level = -1;
+        fmt->specific = NULL;
+    }
+    else goto error;
+
+    switch (fp->format.format) {
+    case binary_format:
+    case bam:
+    case bcf:
+        fp->fp.bgzf = bgzf_hopen(hfile, simple_mode);
+        if (fp->fp.bgzf == NULL) goto error;
+        fp->is_bin = 1;
+        break;
+
+    case cram:
+        fp->fp.cram = cram_dopen(hfile, fn, simple_mode);
+        if (fp->fp.cram == NULL) goto error;
+        if (!fp->is_write)
+            cram_set_option(fp->fp.cram, CRAM_OPT_DECODE_MD, 1);
+        fp->is_cram = 1;
+        break;
+
+    case text_format:
+    case sam:
+    case vcf:
+        if (!fp->is_write) {
+        #if KS_BGZF
+            BGZF *gzfp = bgzf_hopen(hfile, simple_mode);
+        #else
+            // TODO Implement gzip hFILE adaptor
+            hclose(hfile); // This won't work, especially for stdin
+            gzFile gzfp = strcmp(fn, "-")? gzopen(fn, "rb") : gzdopen(fileno(stdin), "rb");
+        #endif
+            if (gzfp) fp->fp.voidp = ks_init(gzfp);
+            else goto error;
+        }
+        else if (fp->format.compression != no_compression) {
+            fp->fp.bgzf = bgzf_hopen(hfile, simple_mode);
+            if (fp->fp.bgzf == NULL) goto error;
+        }
+        else
+            fp->fp.hfile = hfile;
+        break;
+
+    default:
+        goto error;
+    }
+
+    if (opts)
+        hts_process_opts(fp, opts);
+
+    return fp;
+
+error:
+    if (hts_verbose >= 2)
+        fprintf(stderr, "[E::%s] fail to open file '%s'\n", __func__, fn);
+
+    if (fp) {
+        free(fp->fn);
+        free(fp->fn_aux);
+        free(fp);
+    }
+    return NULL;
+}
+
+int hts_close(htsFile *fp)
+{
+    int ret, save;
+
+    switch (fp->format.format) {
+    case binary_format:
+    case bam:
+    case bcf:
+        ret = bgzf_close(fp->fp.bgzf);
+        break;
+
+    case cram:
+        if (!fp->is_write) {
+            switch (cram_eof(fp->fp.cram)) {
+            case 2:
+                fprintf(stderr, "[W::%s] EOF marker is absent. The input is probably truncated.\n", __func__);
+                break;
+            case 0:  /* not at EOF, but may not have wanted all seqs */
+            default: /* case 1, expected EOF */
+                break;
+            }
+        }
+        ret = cram_close(fp->fp.cram);
+        break;
+
+    case text_format:
+    case sam:
+    case vcf:
+        if (!fp->is_write) {
+        #if KS_BGZF
+            BGZF *gzfp = ((kstream_t*)fp->fp.voidp)->f;
+            ret = bgzf_close(gzfp);
+        #else
+            gzFile gzfp = ((kstream_t*)fp->fp.voidp)->f;
+            ret = gzclose(gzfp);
+        #endif
+            ks_destroy((kstream_t*)fp->fp.voidp);
+        }
+        else if (fp->format.compression != no_compression)
+            ret = bgzf_close(fp->fp.bgzf);
+        else
+            ret = hclose(fp->fp.hfile);
+        break;
+
+    default:
+        ret = -1;
+        break;
+    }
+
+    save = errno;
+    free(fp->fn);
+    free(fp->fn_aux);
+    free(fp->line.s);
+    free(fp);
+    errno = save;
+    return ret;
+}
+
+const htsFormat *hts_get_format(htsFile *fp)
+{
+    return fp? &fp->format : NULL;
+}
+
+const char *hts_format_file_extension(const htsFormat *format) {
+    if (!format)
+        return "?";
+
+    switch (format->format) {
+    case sam:  return "sam";
+    case bam:  return "bam";
+    case bai:  return "bai";
+    case cram: return "cram";
+    case crai: return "crai";
+    case vcf:  return "vcf";
+    case bcf:  return "bcf";
+    case csi:  return "csi";
+    case gzi:  return "gzi";
+    case tbi:  return "tbi";
+    case bed:  return "bed";
+    default:   return "?";
+    }
+}
+
+int hts_set_opt(htsFile *fp, enum hts_fmt_option opt, ...) {
+    int r;
+    va_list args;
+
+    if (opt == HTS_OPT_NTHREADS) {
+        va_start(args, opt);
+        int nthreads = va_arg(args, int);
+        va_end(args);
+        return hts_set_threads(fp, nthreads);
+    }
+
+    if (fp->format.format != cram)
+        return 0;
+
+    va_start(args, opt);
+    r = cram_set_voption(fp->fp.cram, opt, args);
+    va_end(args);
+
+    return r;
+}
+
+int hts_set_threads(htsFile *fp, int n)
+{
+    if (fp->format.compression == bgzf) {
+        return bgzf_mt(fp->fp.bgzf, n, 256);
+    } else if (fp->format.format == cram) {
+        return hts_set_opt(fp, CRAM_OPT_NTHREADS, n);
+    }
+    else return 0;
+}
+
+int hts_set_fai_filename(htsFile *fp, const char *fn_aux)
+{
+    free(fp->fn_aux);
+    if (fn_aux) {
+        fp->fn_aux = strdup(fn_aux);
+        if (fp->fn_aux == NULL) return -1;
+    }
+    else fp->fn_aux = NULL;
+
+    if (fp->format.format == cram)
+        if (cram_set_option(fp->fp.cram, CRAM_OPT_REFERENCE, fp->fn_aux))
+            return -1;
+
+    return 0;
+}
+
+// For VCF/BCF backward sweeper. Not exposing these functions because their
+// future is uncertain. Things will probably have to change with hFILE...
+BGZF *hts_get_bgzfp(htsFile *fp)
+{
+    if ( fp->is_bin )
+        return fp->fp.bgzf;
+    else
+        return ((kstream_t*)fp->fp.voidp)->f;
+}
+int hts_useek(htsFile *fp, long uoffset, int where)
+{
+    if ( fp->is_bin )
+        return bgzf_useek(fp->fp.bgzf, uoffset, where);
+    else
+    {
+        ks_rewind((kstream_t*)fp->fp.voidp);
+        ((kstream_t*)fp->fp.voidp)->seek_pos = uoffset;
+        return bgzf_useek(((kstream_t*)fp->fp.voidp)->f, uoffset, where);
+    }
+}
+long hts_utell(htsFile *fp)
+{
+    if ( fp->is_bin )
+        return bgzf_utell(fp->fp.bgzf);
+    else
+        return ((kstream_t*)fp->fp.voidp)->seek_pos;
+}
+
+int hts_getline(htsFile *fp, int delimiter, kstring_t *str)
+{
+    int ret, dret;
+    ret = ks_getuntil((kstream_t*)fp->fp.voidp, delimiter, str, &dret);
+    ++fp->lineno;
+    return ret;
+}
+
+char **hts_readlist(const char *string, int is_file, int *_n)
+{
+    int m = 0, n = 0, dret;
+    char **s = 0;
+    if ( is_file )
+    {
+#if KS_BGZF
+        BGZF *fp = bgzf_open(string, "r");
+#else
+        gzFile fp = gzopen(string, "r");
+#endif
+        if ( !fp ) return NULL;
+
+        kstream_t *ks;
+        kstring_t str;
+        str.s = 0; str.l = str.m = 0;
+        ks = ks_init(fp);
+        while (ks_getuntil(ks, KS_SEP_LINE, &str, &dret) >= 0)
+        {
+            if (str.l == 0) continue;
+            n++;
+            hts_expand(char*,n,m,s);
+            s[n-1] = strdup(str.s);
+        }
+        ks_destroy(ks);
+#if KS_BGZF
+        bgzf_close(fp);
+#else
+        gzclose(fp);
+#endif
+        free(str.s);
+    }
+    else
+    {
+        const char *q = string, *p = string;
+        while ( 1 )
+        {
+            if (*p == ',' || *p == 0)
+            {
+                n++;
+                hts_expand(char*,n,m,s);
+                s[n-1] = (char*)calloc(p - q + 1, 1);
+                strncpy(s[n-1], q, p - q);
+                q = p + 1;
+            }
+            if ( !*p ) break;
+            p++;
+        }
+    }
+    s = (char**)realloc(s, n * sizeof(char*));
+    *_n = n;
+    return s;
+}
+
+char **hts_readlines(const char *fn, int *_n)
+{
+    int m = 0, n = 0, dret;
+    char **s = 0;
+#if KS_BGZF
+    BGZF *fp = bgzf_open(fn, "r");
+#else
+    gzFile fp = gzopen(fn, "r");
+#endif
+    if ( fp ) { // read from file
+        kstream_t *ks;
+        kstring_t str;
+        str.s = 0; str.l = str.m = 0;
+        ks = ks_init(fp);
+        while (ks_getuntil(ks, KS_SEP_LINE, &str, &dret) >= 0) {
+            if (str.l == 0) continue;
+            if (m == n) {
+                m = m? m<<1 : 16;
+                s = (char**)realloc(s, m * sizeof(char*));
+            }
+            s[n++] = strdup(str.s);
+        }
+        ks_destroy(ks);
+        #if KS_BGZF
+            bgzf_close(fp);
+        #else
+            gzclose(fp);
+        #endif
+        s = (char**)realloc(s, n * sizeof(char*));
+        free(str.s);
+    } else if (*fn == ':') { // read from string
+        const char *q, *p;
+        for (q = p = fn + 1;; ++p)
+            if (*p == ',' || *p == 0) {
+                if (m == n) {
+                    m = m? m<<1 : 16;
+                    s = (char**)realloc(s, m * sizeof(char*));
+                }
+                s[n] = (char*)calloc(p - q + 1, 1);
+                strncpy(s[n++], q, p - q);
+                q = p + 1;
+                if (*p == 0) break;
+            }
+    } else return 0;
+    s = (char**)realloc(s, n * sizeof(char*));
+    *_n = n;
+    return s;
+}
+
+// DEPRECATED: To be removed in a future HTSlib release
+int hts_file_type(const char *fname)
+{
+    int len = strlen(fname);
+    if ( !strcasecmp(".vcf.gz",fname+len-7) ) return FT_VCF_GZ;
+    if ( !strcasecmp(".vcf",fname+len-4) ) return FT_VCF;
+    if ( !strcasecmp(".bcf",fname+len-4) ) return FT_BCF_GZ;
+    if ( !strcmp("-",fname) ) return FT_STDIN;
+
+    hFILE *f = hopen(fname, "r");
+    if (f == NULL) return 0;
+
+    htsFormat fmt;
+    if (hts_detect_format(f, &fmt) < 0) { hclose_abruptly(f); return 0; }
+    if (hclose(f) < 0) return 0;
+
+    switch (fmt.format) {
+    case vcf: return (fmt.compression == no_compression)? FT_VCF : FT_VCF_GZ;
+    case bcf: return (fmt.compression == no_compression)? FT_BCF : FT_BCF_GZ;
+    default:  return 0;
+    }
+}
+
+/****************
+ *** Indexing ***
+ ****************/
+
+#define HTS_MIN_MARKER_DIST 0x10000
+
+// Finds the special meta bin
+//  ((1<<(3 * n_lvls + 3)) - 1) / 7 + 1
+#define META_BIN(idx) ((idx)->n_bins + 1)
+
+#define pair64_lt(a,b) ((a).u < (b).u)
+
+#include "htslib/ksort.h"
+KSORT_INIT(_off, hts_pair64_t, pair64_lt)
+
+typedef struct {
+    int32_t m, n;
+    uint64_t loff;
+    hts_pair64_t *list;
+} bins_t;
+
+#include "htslib/khash.h"
+KHASH_MAP_INIT_INT(bin, bins_t)
+typedef khash_t(bin) bidx_t;
+
+typedef struct {
+    int32_t n, m;
+    uint64_t *offset;
+} lidx_t;
+
+struct __hts_idx_t {
+    int fmt, min_shift, n_lvls, n_bins;
+    uint32_t l_meta;
+    int32_t n, m;
+    uint64_t n_no_coor;
+    bidx_t **bidx;
+    lidx_t *lidx;
+    uint8_t *meta;
+    struct {
+        uint32_t last_bin, save_bin;
+        int last_coor, last_tid, save_tid, finished;
+        uint64_t last_off, save_off;
+        uint64_t off_beg, off_end;
+        uint64_t n_mapped, n_unmapped;
+    } z; // keep internal states
+};
+
+static inline void insert_to_b(bidx_t *b, int bin, uint64_t beg, uint64_t end)
+{
+    khint_t k;
+    bins_t *l;
+    int absent;
+    k = kh_put(bin, b, bin, &absent);
+    l = &kh_value(b, k);
+    if (absent) {
+        l->m = 1; l->n = 0;
+        l->list = (hts_pair64_t*)calloc(l->m, sizeof(hts_pair64_t));
+    }
+    if (l->n == l->m) {
+        l->m <<= 1;
+        l->list = (hts_pair64_t*)realloc(l->list, l->m * sizeof(hts_pair64_t));
+    }
+    l->list[l->n].u = beg;
+    l->list[l->n++].v = end;
+}
+
+static inline void insert_to_l(lidx_t *l, int64_t _beg, int64_t _end, uint64_t offset, int min_shift)
+{
+    int i, beg, end;
+    beg = _beg >> min_shift;
+    end = (_end - 1) >> min_shift;
+    if (l->m < end + 1) {
+        int old_m = l->m;
+        l->m = end + 1;
+        kroundup32(l->m);
+        l->offset = (uint64_t*)realloc(l->offset, l->m * sizeof(uint64_t));
+        memset(l->offset + old_m, 0xff, 8 * (l->m - old_m)); // fill l->offset with (uint64_t)-1
+    }
+    if (beg == end) { // to save a loop in this case
+        if (l->offset[beg] == (uint64_t)-1) l->offset[beg] = offset;
+    } else {
+        for (i = beg; i <= end; ++i)
+            if (l->offset[i] == (uint64_t)-1) l->offset[i] = offset;
+    }
+    if (l->n < end + 1) l->n = end + 1;
+}
+
+hts_idx_t *hts_idx_init(int n, int fmt, uint64_t offset0, int min_shift, int n_lvls)
+{
+    hts_idx_t *idx;
+    idx = (hts_idx_t*)calloc(1, sizeof(hts_idx_t));
+    if (idx == NULL) return NULL;
+    idx->fmt = fmt;
+    idx->min_shift = min_shift;
+    idx->n_lvls = n_lvls;
+    idx->n_bins = ((1<<(3 * n_lvls + 3)) - 1) / 7;
+    idx->z.save_bin = idx->z.save_tid = idx->z.last_tid = idx->z.last_bin = 0xffffffffu;
+    idx->z.save_off = idx->z.last_off = idx->z.off_beg = idx->z.off_end = offset0;
+    idx->z.last_coor = 0xffffffffu;
+    if (n) {
+        idx->n = idx->m = n;
+        idx->bidx = (bidx_t**)calloc(n, sizeof(bidx_t*));
+        if (idx->bidx == NULL) { free(idx); return NULL; }
+        idx->lidx = (lidx_t*) calloc(n, sizeof(lidx_t));
+        if (idx->lidx == NULL) { free(idx->bidx); free(idx); return NULL; }
+    }
+    return idx;
+}
+
+static void update_loff(hts_idx_t *idx, int i, int free_lidx)
+{
+    bidx_t *bidx = idx->bidx[i];
+    lidx_t *lidx = &idx->lidx[i];
+    khint_t k;
+    int l;
+    uint64_t offset0 = 0;
+    if (bidx) {
+        k = kh_get(bin, bidx, META_BIN(idx));
+        if (k != kh_end(bidx))
+            offset0 = kh_val(bidx, k).list[0].u;
+        for (l = 0; l < lidx->n && lidx->offset[l] == (uint64_t)-1; ++l)
+            lidx->offset[l] = offset0;
+    } else l = 1;
+    for (; l < lidx->n; ++l) // fill missing values
+        if (lidx->offset[l] == (uint64_t)-1)
+            lidx->offset[l] = lidx->offset[l-1];
+    if (bidx == 0) return;
+    for (k = kh_begin(bidx); k != kh_end(bidx); ++k) // set loff
+        if (kh_exist(bidx, k))
+        {
+            if ( kh_key(bidx, k) < idx->n_bins )
+            {
+                int bot_bin = hts_bin_bot(kh_key(bidx, k), idx->n_lvls);
+                // disable linear index if bot_bin out of bounds
+                kh_val(bidx, k).loff = bot_bin < lidx->n ? lidx->offset[bot_bin] : 0;
+            }
+            else
+                kh_val(bidx, k).loff = 0;
+        }
+    if (free_lidx) {
+        free(lidx->offset);
+        lidx->m = lidx->n = 0;
+        lidx->offset = 0;
+    }
+}
+
+static void compress_binning(hts_idx_t *idx, int i)
+{
+    bidx_t *bidx = idx->bidx[i];
+    khint_t k;
+    int l, m;
+    if (bidx == 0) return;
+    // merge a bin to its parent if the bin is too small
+    for (l = idx->n_lvls; l > 0; --l) {
+        unsigned start = hts_bin_first(l);
+        for (k = kh_begin(bidx); k != kh_end(bidx); ++k) {
+            bins_t *p, *q;
+            if (!kh_exist(bidx, k) || kh_key(bidx, k) >= idx->n_bins || kh_key(bidx, k) < start) continue;
+            p = &kh_value(bidx, k);
+            if (l < idx->n_lvls && p->n > 1) ks_introsort(_off, p->n, p->list);
+            if ((p->list[p->n - 1].v>>16) - (p->list[0].u>>16) < HTS_MIN_MARKER_DIST) {
+                khint_t kp;
+                kp = kh_get(bin, bidx, hts_bin_parent(kh_key(bidx, k)));
+                if (kp == kh_end(bidx)) continue;
+                q = &kh_val(bidx, kp);
+                if (q->n + p->n > q->m) {
+                    q->m = q->n + p->n;
+                    kroundup32(q->m);
+                    q->list = (hts_pair64_t*)realloc(q->list, q->m * sizeof(hts_pair64_t));
+                }
+                memcpy(q->list + q->n, p->list, p->n * sizeof(hts_pair64_t));
+                q->n += p->n;
+                free(p->list);
+                kh_del(bin, bidx, k);
+            }
+        }
+    }
+    k = kh_get(bin, bidx, 0);
+    if (k != kh_end(bidx)) ks_introsort(_off, kh_val(bidx, k).n, kh_val(bidx, k).list);
+    // merge adjacent chunks that start from the same BGZF block
+    for (k = kh_begin(bidx); k != kh_end(bidx); ++k) {
+        bins_t *p;
+        if (!kh_exist(bidx, k) || kh_key(bidx, k) >= idx->n_bins) continue;
+        p = &kh_value(bidx, k);
+        for (l = 1, m = 0; l < p->n; ++l) {
+            if (p->list[m].v>>16 >= p->list[l].u>>16) {
+                if (p->list[m].v < p->list[l].v) p->list[m].v = p->list[l].v;
+            } else p->list[++m] = p->list[l];
+        }
+        p->n = m + 1;
+    }
+}
+
+void hts_idx_finish(hts_idx_t *idx, uint64_t final_offset)
+{
+    int i;
+    if (idx == NULL || idx->z.finished) return; // do not run this function on an empty index or multiple times
+    if (idx->z.save_tid >= 0) {
+        insert_to_b(idx->bidx[idx->z.save_tid], idx->z.save_bin, idx->z.save_off, final_offset);
+        insert_to_b(idx->bidx[idx->z.save_tid], META_BIN(idx), idx->z.off_beg, final_offset);
+        insert_to_b(idx->bidx[idx->z.save_tid], META_BIN(idx), idx->z.n_mapped, idx->z.n_unmapped);
+    }
+    for (i = 0; i < idx->n; ++i) {
+        update_loff(idx, i, (idx->fmt == HTS_FMT_CSI));
+        compress_binning(idx, i);
+    }
+    idx->z.finished = 1;
+}
+
+int hts_idx_push(hts_idx_t *idx, int tid, int beg, int end, uint64_t offset, int is_mapped)
+{
+    int bin;
+    if (tid<0) beg = -1, end = 0;
+    if (tid >= idx->m) { // enlarge the index
+        int32_t oldm = idx->m;
+        idx->m = idx->m? idx->m<<1 : 2;
+        idx->bidx = (bidx_t**)realloc(idx->bidx, idx->m * sizeof(bidx_t*));
+        idx->lidx = (lidx_t*) realloc(idx->lidx, idx->m * sizeof(lidx_t));
+        memset(&idx->bidx[oldm], 0, (idx->m - oldm) * sizeof(bidx_t*));
+        memset(&idx->lidx[oldm], 0, (idx->m - oldm) * sizeof(lidx_t));
+    }
+    if (idx->n < tid + 1) idx->n = tid + 1;
+    if (idx->z.finished) return 0;
+    if (idx->z.last_tid != tid || (idx->z.last_tid >= 0 && tid < 0)) { // change of chromosome
+        if ( tid>=0 && idx->n_no_coor )
+        {
+            if (hts_verbose >= 1) fprintf(stderr,"[E::%s] NO_COOR reads not in a single block at the end %d %d\n", __func__, tid,idx->z.last_tid);
+            return -1;
+        }
+        if (tid>=0 && idx->bidx[tid] != 0)
+        {
+            if (hts_verbose >= 1) fprintf(stderr, "[E::%s] chromosome blocks not continuous\n", __func__);
+            return -1;
+        }
+        idx->z.last_tid = tid;
+        idx->z.last_bin = 0xffffffffu;
+    } else if (tid >= 0 && idx->z.last_coor > beg) { // test if positions are out of order
+        if (hts_verbose >= 1) fprintf(stderr, "[E::%s] unsorted positions\n", __func__);
+        return -1;
+    }
+    if ( tid>=0 )
+    {
+        if (idx->bidx[tid] == 0) idx->bidx[tid] = kh_init(bin);
+        if ( is_mapped)
+            insert_to_l(&idx->lidx[tid], beg, end, idx->z.last_off, idx->min_shift); // last_off points to the start of the current record
+    }
+    else idx->n_no_coor++;
+    bin = hts_reg2bin(beg, end, idx->min_shift, idx->n_lvls);
+    if ((int)idx->z.last_bin != bin) { // then possibly write the binning index
+        if (idx->z.save_bin != 0xffffffffu) // save_bin==0xffffffffu only happens to the first record
+            insert_to_b(idx->bidx[idx->z.save_tid], idx->z.save_bin, idx->z.save_off, idx->z.last_off);
+        if (idx->z.last_bin == 0xffffffffu && idx->z.save_bin != 0xffffffffu) { // change of chr; keep meta information
+            idx->z.off_end = idx->z.last_off;
+            insert_to_b(idx->bidx[idx->z.save_tid], META_BIN(idx), idx->z.off_beg, idx->z.off_end);
+            insert_to_b(idx->bidx[idx->z.save_tid], META_BIN(idx), idx->z.n_mapped, idx->z.n_unmapped);
+            idx->z.n_mapped = idx->z.n_unmapped = 0;
+            idx->z.off_beg = idx->z.off_end;
+        }
+        idx->z.save_off = idx->z.last_off;
+        idx->z.save_bin = idx->z.last_bin = bin;
+        idx->z.save_tid = tid;
+    }
+    if (is_mapped) ++idx->z.n_mapped;
+    else ++idx->z.n_unmapped;
+    idx->z.last_off = offset;
+    idx->z.last_coor = beg;
+    return 0;
+}
+
+void hts_idx_destroy(hts_idx_t *idx)
+{
+    khint_t k;
+    int i;
+    if (idx == 0) return;
+
+    // For HTS_FMT_CRAI, idx actually points to a different type -- see sam.c
+    if (idx->fmt == HTS_FMT_CRAI) {
+        hts_cram_idx_t *cidx = (hts_cram_idx_t *) idx;
+        cram_index_free(cidx->cram);
+        free(cidx);
+        return;
+    }
+
+    for (i = 0; i < idx->m; ++i) {
+        bidx_t *bidx = idx->bidx[i];
+        free(idx->lidx[i].offset);
+        if (bidx == 0) continue;
+        for (k = kh_begin(bidx); k != kh_end(bidx); ++k)
+            if (kh_exist(bidx, k))
+                free(kh_value(bidx, k).list);
+        kh_destroy(bin, bidx);
+    }
+    free(idx->bidx); free(idx->lidx); free(idx->meta);
+    free(idx);
+}
+
+// The optimizer eliminates these ed_is_big() calls; still it would be good to
+// TODO Determine endianness at configure- or compile-time
+
+static inline ssize_t HTS_RESULT_USED idx_write_int32(BGZF *fp, int32_t x)
+{
+    if (ed_is_big()) x = ed_swap_4(x);
+    return bgzf_write(fp, &x, sizeof x);
+}
+
+static inline ssize_t HTS_RESULT_USED idx_write_uint32(BGZF *fp, uint32_t x)
+{
+    if (ed_is_big()) x = ed_swap_4(x);
+    return bgzf_write(fp, &x, sizeof x);
+}
+
+static inline ssize_t HTS_RESULT_USED idx_write_uint64(BGZF *fp, uint64_t x)
+{
+    if (ed_is_big()) x = ed_swap_8(x);
+    return bgzf_write(fp, &x, sizeof x);
+}
+
+static inline void swap_bins(bins_t *p)
+{
+    int i;
+    for (i = 0; i < p->n; ++i) {
+        ed_swap_8p(&p->list[i].u);
+        ed_swap_8p(&p->list[i].v);
+    }
+}
+
+static int hts_idx_save_core(const hts_idx_t *idx, BGZF *fp, int fmt)
+{
+    int32_t i, j;
+
+    #define check(ret) if ((ret) < 0) return -1
+
+    check(idx_write_int32(fp, idx->n));
+    if (fmt == HTS_FMT_TBI && idx->l_meta)
+        check(bgzf_write(fp, idx->meta, idx->l_meta));
+
+    for (i = 0; i < idx->n; ++i) {
+        khint_t k;
+        bidx_t *bidx = idx->bidx[i];
+        lidx_t *lidx = &idx->lidx[i];
+        // write binning index
+        check(idx_write_int32(fp, bidx? kh_size(bidx) : 0));
+        if (bidx)
+            for (k = kh_begin(bidx); k != kh_end(bidx); ++k)
+                if (kh_exist(bidx, k)) {
+                    bins_t *p = &kh_value(bidx, k);
+                    check(idx_write_uint32(fp, kh_key(bidx, k)));
+                    if (fmt == HTS_FMT_CSI) check(idx_write_uint64(fp, p->loff));
+                    //int j;for(j=0;j<p->n;++j)fprintf(stderr,"%d,%llx,%d,%llx:%llx\n",kh_key(bidx,k),kh_val(bidx, k).loff,j,p->list[j].u,p->list[j].v);
+                    check(idx_write_int32(fp, p->n));
+                    for (j = 0; j < p->n; ++j) {
+                        check(idx_write_uint64(fp, p->list[j].u));
+                        check(idx_write_uint64(fp, p->list[j].v));
+                    }
+                }
+
+        // write linear index
+        if (fmt != HTS_FMT_CSI) {
+            check(idx_write_int32(fp, lidx->n));
+            for (j = 0; j < lidx->n; ++j)
+                check(idx_write_uint64(fp, lidx->offset[j]));
+        }
+    }
+
+    check(idx_write_uint64(fp, idx->n_no_coor));
+    return 0;
+    #undef check
+}
+
+int hts_idx_save(const hts_idx_t *idx, const char *fn, int fmt)
+{
+    int ret, save;
+    char *fnidx = (char*)calloc(1, strlen(fn) + 5);
+    if (fnidx == NULL) return -1;
+
+    strcpy(fnidx, fn);
+    switch (fmt) {
+    case HTS_FMT_BAI: strcat(fnidx, ".bai"); break;
+    case HTS_FMT_CSI: strcat(fnidx, ".csi"); break;
+    case HTS_FMT_TBI: strcat(fnidx, ".tbi"); break;
+    default: abort();
+    }
+
+    ret = hts_idx_save_as(idx, fn, fnidx, fmt);
+    save = errno;
+    free(fnidx);
+    errno = save;
+    return ret;
+}
+
+int hts_idx_save_as(const hts_idx_t *idx, const char *fn, const char *fnidx, int fmt)
+{
+    BGZF *fp;
+
+    #define check(ret) if ((ret) < 0) goto fail
+
+    if (fnidx == NULL) return hts_idx_save(idx, fn, fmt);
+
+    fp = bgzf_open(fnidx, (fmt == HTS_FMT_BAI)? "wu" : "w");
+    if (fp == NULL) return -1;
+
+    if (fmt == HTS_FMT_CSI) {
+        check(bgzf_write(fp, "CSI\1", 4));
+        check(idx_write_int32(fp, idx->min_shift));
+        check(idx_write_int32(fp, idx->n_lvls));
+        check(idx_write_uint32(fp, idx->l_meta));
+        if (idx->l_meta) check(bgzf_write(fp, idx->meta, idx->l_meta));
+    } else if (fmt == HTS_FMT_TBI) {
+        check(bgzf_write(fp, "TBI\1", 4));
+    } else if (fmt == HTS_FMT_BAI) {
+        check(bgzf_write(fp, "BAI\1", 4));
+    } else abort();
+
+    check(hts_idx_save_core(idx, fp, fmt));
+
+    return bgzf_close(fp);
+    #undef check
+
+fail:
+    bgzf_close(fp);
+    return -1;
+}
+
+static int hts_idx_load_core(hts_idx_t *idx, BGZF *fp, int fmt)
+{
+    int32_t i, n, is_be;
+    is_be = ed_is_big();
+    if (idx == NULL) return -4;
+    for (i = 0; i < idx->n; ++i) {
+        bidx_t *h;
+        lidx_t *l = &idx->lidx[i];
+        uint32_t key;
+        int j, absent;
+        bins_t *p;
+        h = idx->bidx[i] = kh_init(bin);
+        if (bgzf_read(fp, &n, 4) != 4) return -1;
+        if (is_be) ed_swap_4p(&n);
+        for (j = 0; j < n; ++j) {
+            khint_t k;
+            if (bgzf_read(fp, &key, 4) != 4) return -1;
+            if (is_be) ed_swap_4p(&key);
+            k = kh_put(bin, h, key, &absent);
+            if (absent <= 0) return -3; // Duplicate bin number
+            p = &kh_val(h, k);
+            if (fmt == HTS_FMT_CSI) {
+                if (bgzf_read(fp, &p->loff, 8) != 8) return -1;
+                if (is_be) ed_swap_8p(&p->loff);
+            } else p->loff = 0;
+            if (bgzf_read(fp, &p->n, 4) != 4) return -1;
+            if (is_be) ed_swap_4p(&p->n);
+            p->m = p->n;
+            p->list = (hts_pair64_t*)malloc(p->m * sizeof(hts_pair64_t));
+            if (p->list == NULL) return -2;
+            if (bgzf_read(fp, p->list, p->n<<4) != p->n<<4) return -1;
+            if (is_be) swap_bins(p);
+        }
+        if (fmt != HTS_FMT_CSI) { // load linear index
+            int j;
+            if (bgzf_read(fp, &l->n, 4) != 4) return -1;
+            if (is_be) ed_swap_4p(&l->n);
+            l->m = l->n;
+            l->offset = (uint64_t*)malloc(l->n * sizeof(uint64_t));
+            if (l->offset == NULL) return -2;
+            if (bgzf_read(fp, l->offset, l->n << 3) != l->n << 3) return -1;
+            if (is_be) for (j = 0; j < l->n; ++j) ed_swap_8p(&l->offset[j]);
+            for (j = 1; j < l->n; ++j) // fill missing values; may happen given older samtools and tabix
+                if (l->offset[j] == 0) l->offset[j] = l->offset[j-1];
+            update_loff(idx, i, 1);
+        }
+    }
+    if (bgzf_read(fp, &idx->n_no_coor, 8) != 8) idx->n_no_coor = 0;
+    if (is_be) ed_swap_8p(&idx->n_no_coor);
+    return 0;
+}
+
+static hts_idx_t *hts_idx_load_local(const char *fn)
+{
+    uint8_t magic[4];
+    int i, is_be;
+    hts_idx_t *idx = NULL;
+    uint8_t *meta = NULL;
+    BGZF *fp = bgzf_open(fn, "r");
+    if (fp == NULL) return NULL;
+    is_be = ed_is_big();
+    if (bgzf_read(fp, magic, 4) != 4) goto fail;
+
+    if (memcmp(magic, "CSI\1", 4) == 0) {
+        uint32_t x[3], n;
+        if (bgzf_read(fp, x, 12) != 12) goto fail;
+        if (is_be) for (i = 0; i < 3; ++i) ed_swap_4p(&x[i]);
+        if (x[2]) {
+            if ((meta = (uint8_t*)malloc(x[2])) == NULL) goto fail;
+            if (bgzf_read(fp, meta, x[2]) != x[2]) goto fail;
+        }
+        if (bgzf_read(fp, &n, 4) != 4) goto fail;
+        if (is_be) ed_swap_4p(&n);
+        if ((idx = hts_idx_init(n, HTS_FMT_CSI, 0, x[0], x[1])) == NULL) goto fail;
+        idx->l_meta = x[2];
+        idx->meta = meta;
+        meta = NULL;
+        if (hts_idx_load_core(idx, fp, HTS_FMT_CSI) < 0) goto fail;
+    }
+    else if (memcmp(magic, "TBI\1", 4) == 0) {
+        uint32_t x[8];
+        if (bgzf_read(fp, x, 32) != 32) goto fail;
+        if (is_be) for (i = 0; i < 8; ++i) ed_swap_4p(&x[i]);
+        if ((idx = hts_idx_init(x[0], HTS_FMT_TBI, 0, 14, 5)) == NULL) goto fail;
+        idx->l_meta = 28 + x[7];
+        if ((idx->meta = (uint8_t*)malloc(idx->l_meta)) == NULL) goto fail;
+        memcpy(idx->meta, &x[1], 28);
+        if (bgzf_read(fp, idx->meta + 28, x[7]) != x[7]) goto fail;
+        if (hts_idx_load_core(idx, fp, HTS_FMT_TBI) < 0) goto fail;
+    }
+    else if (memcmp(magic, "BAI\1", 4) == 0) {
+        uint32_t n;
+        if (bgzf_read(fp, &n, 4) != 4) goto fail;
+        if (is_be) ed_swap_4p(&n);
+        idx = hts_idx_init(n, HTS_FMT_BAI, 0, 14, 5);
+        if (hts_idx_load_core(idx, fp, HTS_FMT_BAI) < 0) goto fail;
+    }
+    else { errno = EINVAL; goto fail; }
+
+    bgzf_close(fp);
+    return idx;
+
+fail:
+    bgzf_close(fp);
+    hts_idx_destroy(idx);
+    free(meta);
+    return NULL;
+}
+
+void hts_idx_set_meta(hts_idx_t *idx, int l_meta, uint8_t *meta, int is_copy)
+{
+    if (idx->meta) free(idx->meta);
+    idx->l_meta = l_meta;
+    if (is_copy) {
+        idx->meta = (uint8_t*)malloc(l_meta);
+        memcpy(idx->meta, meta, l_meta);
+    } else idx->meta = meta;
+}
+
+uint8_t *hts_idx_get_meta(hts_idx_t *idx, int *l_meta)
+{
+    *l_meta = idx->l_meta;
+    return idx->meta;
+}
+
+const char **hts_idx_seqnames(const hts_idx_t *idx, int *n, hts_id2name_f getid, void *hdr)
+{
+    if ( !idx->n )
+    {
+        *n = 0;
+        return NULL;
+    }
+
+    int tid = 0, i;
+    const char **names = (const char**) calloc(idx->n,sizeof(const char*));
+    for (i=0; i<idx->n; i++)
+    {
+        bidx_t *bidx = idx->bidx[i];
+        if ( !bidx ) continue;
+        names[tid++] = getid(hdr,i);
+    }
+    *n = tid;
+    return names;
+}
+
+int hts_idx_get_stat(const hts_idx_t* idx, int tid, uint64_t* mapped, uint64_t* unmapped)
+{
+    if ( idx->fmt == HTS_FMT_CRAI ) {
+        *mapped = 0; *unmapped = 0;
+        return -1;
+    }
+
+    bidx_t *h = idx->bidx[tid];
+    khint_t k = kh_get(bin, h, META_BIN(idx));
+    if (k != kh_end(h)) {
+        *mapped = kh_val(h, k).list[1].u;
+        *unmapped = kh_val(h, k).list[1].v;
+        return 0;
+    } else {
+        *mapped = 0; *unmapped = 0;
+        return -1;
+    }
+}
+
+uint64_t hts_idx_get_n_no_coor(const hts_idx_t* idx)
+{
+    return idx->n_no_coor;
+}
+
+/****************
+ *** Iterator ***
+ ****************/
+
+static inline int reg2bins(int64_t beg, int64_t end, hts_itr_t *itr, int min_shift, int n_lvls)
+{
+    int l, t, s = min_shift + (n_lvls<<1) + n_lvls;
+    if (beg >= end) return 0;
+    if (end >= 1LL<<s) end = 1LL<<s;
+    for (--end, l = 0, t = 0; l <= n_lvls; s -= 3, t += 1<<((l<<1)+l), ++l) {
+        int b, e, n, i;
+        b = t + (beg>>s); e = t + (end>>s); n = e - b + 1;
+        if (itr->bins.n + n > itr->bins.m) {
+            itr->bins.m = itr->bins.n + n;
+            kroundup32(itr->bins.m);
+            itr->bins.a = (int*)realloc(itr->bins.a, sizeof(int) * itr->bins.m);
+        }
+        for (i = b; i <= e; ++i) itr->bins.a[itr->bins.n++] = i;
+    }
+    return itr->bins.n;
+}
+
+hts_itr_t *hts_itr_query(const hts_idx_t *idx, int tid, int beg, int end, hts_readrec_func *readrec)
+{
+    int i, n_off, l, bin;
+    hts_pair64_t *off;
+    khint_t k;
+    bidx_t *bidx;
+    uint64_t min_off;
+    hts_itr_t *iter = 0;
+    if (tid < 0) {
+        int finished0 = 0;
+        uint64_t off0 = (uint64_t)-1;
+        khint_t k;
+        switch (tid) {
+        case HTS_IDX_START:
+            // Find the smallest offset, note that sequence ids may not be ordered sequentially
+            for (i=0; i<idx->n; i++)
+            {
+                bidx = idx->bidx[i];
+                k = kh_get(bin, bidx, META_BIN(idx));
+                if (k == kh_end(bidx)) continue;
+                if ( off0 > kh_val(bidx, k).list[0].u ) off0 = kh_val(bidx, k).list[0].u;
+            }
+            if ( off0==(uint64_t)-1 && idx->n_no_coor ) off0 = 0; // only no-coor reads in this bam
+            break;
+
+        case HTS_IDX_NOCOOR:
+            if ( idx->n>0 )
+            {
+                bidx = idx->bidx[idx->n - 1];
+                k = kh_get(bin, bidx, META_BIN(idx));
+                if (k != kh_end(bidx)) off0 = kh_val(bidx, k).list[0].v;
+            }
+            if ( off0==(uint64_t)-1 && idx->n_no_coor ) off0 = 0; // only no-coor reads in this bam
+            break;
+
+        case HTS_IDX_REST:
+            off0 = 0;
+            break;
+
+        case HTS_IDX_NONE:
+            finished0 = 1;
+            off0 = 0;
+            break;
+
+        default:
+            return 0;
+        }
+        if (off0 != (uint64_t)-1) {
+            iter = (hts_itr_t*)calloc(1, sizeof(hts_itr_t));
+            iter->read_rest = 1;
+            iter->finished = finished0;
+            iter->curr_off = off0;
+            iter->readrec = readrec;
+            return iter;
+        } else return 0;
+    }
+
+    if (beg < 0) beg = 0;
+    if (end < beg) return 0;
+    if (tid >= idx->n || (bidx = idx->bidx[tid]) == NULL) return 0;
+
+    iter = (hts_itr_t*)calloc(1, sizeof(hts_itr_t));
+    iter->tid = tid, iter->beg = beg, iter->end = end; iter->i = -1;
+    iter->readrec = readrec;
+
+    // compute min_off
+    bin = hts_bin_first(idx->n_lvls) + (beg>>idx->min_shift);
+    do {
+        int first;
+        k = kh_get(bin, bidx, bin);
+        if (k != kh_end(bidx)) break;
+        first = (hts_bin_parent(bin)<<3) + 1;
+        if (bin > first) --bin;
+        else bin = hts_bin_parent(bin);
+    } while (bin);
+    if (bin == 0) k = kh_get(bin, bidx, bin);
+    min_off = k != kh_end(bidx)? kh_val(bidx, k).loff : 0;
+    // retrieve bins
+    reg2bins(beg, end, iter, idx->min_shift, idx->n_lvls);
+    for (i = n_off = 0; i < iter->bins.n; ++i)
+        if ((k = kh_get(bin, bidx, iter->bins.a[i])) != kh_end(bidx))
+            n_off += kh_value(bidx, k).n;
+    if (n_off == 0) return iter;
+    off = (hts_pair64_t*)calloc(n_off, sizeof(hts_pair64_t));
+    for (i = n_off = 0; i < iter->bins.n; ++i) {
+        if ((k = kh_get(bin, bidx, iter->bins.a[i])) != kh_end(bidx)) {
+            int j;
+            bins_t *p = &kh_value(bidx, k);
+            for (j = 0; j < p->n; ++j)
+                if (p->list[j].v > min_off) off[n_off++] = p->list[j];
+        }
+    }
+    if (n_off == 0) {
+        free(off); return iter;
+    }
+    ks_introsort(_off, n_off, off);
+    // resolve completely contained adjacent blocks
+    for (i = 1, l = 0; i < n_off; ++i)
+        if (off[l].v < off[i].v) off[++l] = off[i];
+    n_off = l + 1;
+    // resolve overlaps between adjacent blocks; this may happen due to the merge in indexing
+    for (i = 1; i < n_off; ++i)
+        if (off[i-1].v >= off[i].u) off[i-1].v = off[i].u;
+    // merge adjacent blocks
+    for (i = 1, l = 0; i < n_off; ++i) {
+        if (off[l].v>>16 == off[i].u>>16) off[l].v = off[i].v;
+        else off[++l] = off[i];
+    }
+    n_off = l + 1;
+    iter->n_off = n_off; iter->off = off;
+    return iter;
+}
+
+void hts_itr_destroy(hts_itr_t *iter)
+{
+    if (iter) { free(iter->off); free(iter->bins.a); free(iter); }
+}
+
+static inline long long push_digit(long long i, char c)
+{
+    // ensure subtraction occurs first, avoiding overflow for >= MAX-48 or so
+    int digit = c - '0';
+    return 10 * i + digit;
+}
+
+long long hts_parse_decimal(const char *str, char **strend, int flags)
+{
+    long long n = 0;
+    int decimals = 0, e = 0, lost = 0;
+    char sign = '+', esign = '+';
+    const char *s;
+
+    while (isspace(*str)) str++;
+    s = str;
+
+    if (*s == '+' || *s == '-') sign = *s++;
+    while (*s)
+        if (isdigit(*s)) n = push_digit(n, *s++);
+        else if (*s == ',' && (flags & HTS_PARSE_THOUSANDS_SEP)) s++;
+        else break;
+
+    if (*s == '.') {
+        s++;
+        while (isdigit(*s)) decimals++, n = push_digit(n, *s++);
+    }
+
+    if (*s == 'E' || *s == 'e') {
+        s++;
+        if (*s == '+' || *s == '-') esign = *s++;
+        while (isdigit(*s)) e = push_digit(e, *s++);
+        if (esign == '-') e = -e;
+    }
+
+    e -= decimals;
+    while (e > 0) n *= 10, e--;
+    while (e < 0) lost += n % 10, n /= 10, e++;
+
+    if (lost > 0 && hts_verbose >= 3)
+        fprintf(stderr, "[W::%s] discarding fractional part of %.*s\n",
+                __func__, (int)(s - str), str);
+
+    if (strend) *strend = (char *) s;
+    else if (*s && hts_verbose >= 2)
+        fprintf(stderr, "[W::%s] ignoring unknown characters after %.*s[%s]\n",
+                __func__, (int)(s - str), str, s);
+
+    return (sign == '+')? n : -n;
+}
+
+const char *hts_parse_reg(const char *s, int *beg, int *end)
+{
+    char *hyphen;
+    const char *colon = strrchr(s, ':');
+    if (colon == NULL) {
+        *beg = 0; *end = INT_MAX;
+        return s + strlen(s);
+    }
+
+    *beg = hts_parse_decimal(colon+1, &hyphen, HTS_PARSE_THOUSANDS_SEP) - 1;
+    if (*beg < 0) *beg = 0;
+
+    if (*hyphen == '\0') *end = INT_MAX;
+    else if (*hyphen == '-') *end = hts_parse_decimal(hyphen+1, NULL, HTS_PARSE_THOUSANDS_SEP);
+    else return NULL;
+
+    if (*beg >= *end) return NULL;
+    return colon;
+}
+
+hts_itr_t *hts_itr_querys(const hts_idx_t *idx, const char *reg, hts_name2id_f getid, void *hdr, hts_itr_query_func *itr_query, hts_readrec_func *readrec)
+{
+    int tid, beg, end;
+    const char *q;
+
+    if (strcmp(reg, ".") == 0)
+        return itr_query(idx, HTS_IDX_START, 0, 0, readrec);
+    else if (strcmp(reg, "*") == 0)
+        return itr_query(idx, HTS_IDX_NOCOOR, 0, 0, readrec);
+
+    q = hts_parse_reg(reg, &beg, &end);
+    if (q) {
+        char *tmp = (char*)alloca(q - reg + 1);
+        strncpy(tmp, reg, q - reg);
+        tmp[q - reg] = 0;
+        tid = getid(hdr, tmp);
+    }
+    else {
+        // not parsable as a region, but possibly a sequence named "foo:a"
+        tid = getid(hdr, reg);
+        beg = 0; end = INT_MAX;
+    }
+
+    if (tid < 0) return NULL;
+    return itr_query(idx, tid, beg, end, readrec);
+}
+
+int hts_itr_next(BGZF *fp, hts_itr_t *iter, void *r, void *data)
+{
+    int ret, tid, beg, end;
+    if (iter == NULL || iter->finished) return -1;
+    if (iter->read_rest) {
+        if (iter->curr_off) { // seek to the start
+            if (bgzf_seek(fp, iter->curr_off, SEEK_SET) < 0) return -1;
+            iter->curr_off = 0; // only seek once
+        }
+        ret = iter->readrec(fp, data, r, &tid, &beg, &end);
+        if (ret < 0) iter->finished = 1;
+        iter->curr_tid = tid;
+        iter->curr_beg = beg;
+        iter->curr_end = end;
+        return ret;
+    }
+    if (iter->off == 0) return -1;
+    for (;;) {
+        if (iter->curr_off == 0 || iter->curr_off >= iter->off[iter->i].v) { // then jump to the next chunk
+            if (iter->i == iter->n_off - 1) { ret = -1; break; } // no more chunks
+            if (iter->i < 0 || iter->off[iter->i].v != iter->off[iter->i+1].u) { // not adjacent chunks; then seek
+                if (bgzf_seek(fp, iter->off[iter->i+1].u, SEEK_SET) < 0) return -1;
+                iter->curr_off = bgzf_tell(fp);
+            }
+            ++iter->i;
+        }
+        if ((ret = iter->readrec(fp, data, r, &tid, &beg, &end)) >= 0) {
+            iter->curr_off = bgzf_tell(fp);
+            if (tid != iter->tid || beg >= iter->end) { // no need to proceed
+                ret = -1; break;
+            } else if (end > iter->beg && iter->end > beg) {
+                iter->curr_tid = tid;
+                iter->curr_beg = beg;
+                iter->curr_end = end;
+                return ret;
+            }
+        } else break; // end of file or error
+    }
+    iter->finished = 1;
+    return ret;
+}
+
+/**********************
+ *** Retrieve index ***
+ **********************/
+
+static char *test_and_fetch(const char *fn)
+{
+    FILE *fp;
+    if (hisremote(fn)) {
+        const int buf_size = 1 * 1024 * 1024;
+        hFILE *fp_remote;
+        uint8_t *buf;
+        int l;
+        const char *p;
+        for (p = fn + strlen(fn) - 1; p >= fn; --p)
+            if (*p == '/') break;
+        ++p; // p now points to the local file name
+        // Attempt to open local file first
+        if ((fp = fopen((char*)p, "rb")) != 0)
+        {
+            fclose(fp);
+            return (char*)p;
+        }
+        // Attempt to open remote file. Stay quiet on failure, it is OK to fail when trying first .csi then .tbi index.
+        if ((fp_remote = hopen(fn, "r")) == 0) return 0;
+        if ((fp = fopen(p, "w")) == 0) {
+            if (hts_verbose >= 1) fprintf(stderr, "[E::%s] fail to create file '%s' in the working directory\n", __func__, p);
+            hclose_abruptly(fp_remote);
+            return 0;
+        }
+        if (hts_verbose >= 3) fprintf(stderr, "[M::%s] downloading file '%s' to local directory\n", __func__, fn);
+        buf = (uint8_t*)calloc(buf_size, 1);
+        while ((l = hread(fp_remote, buf, buf_size)) > 0) fwrite(buf, 1, l, fp);
+        free(buf);
+        fclose(fp);
+        if (hclose(fp_remote) != 0) fprintf(stderr, "[E::%s] fail to close remote file '%s'\n", __func__, fn);
+        return (char*)p;
+    } else {
+        if ((fp = fopen(fn, "rb")) == 0) return 0;
+        fclose(fp);
+        return (char*)fn;
+    }
+}
+
+char *hts_idx_getfn(const char *fn, const char *ext)
+{
+    int i, l_fn, l_ext;
+    char *fnidx, *ret;
+    l_fn = strlen(fn); l_ext = strlen(ext);
+    fnidx = (char*)calloc(l_fn + l_ext + 1, 1);
+    strcpy(fnidx, fn); strcpy(fnidx + l_fn, ext);
+    if ((ret = test_and_fetch(fnidx)) == 0) {
+        for (i = l_fn - 1; i > 0; --i)
+            if (fnidx[i] == '.') break;
+        strcpy(fnidx + i, ext);
+        ret = test_and_fetch(fnidx);
+    }
+    if (ret == 0) {
+        free(fnidx);
+        return 0;
+    }
+    l_fn = strlen(ret);
+    memmove(fnidx, ret, l_fn + 1);
+    return fnidx;
+}
+
+hts_idx_t *hts_idx_load(const char *fn, int fmt)
+{
+    char *fnidx;
+    hts_idx_t *idx;
+    fnidx = hts_idx_getfn(fn, ".csi");
+    if (! fnidx) fnidx = hts_idx_getfn(fn, fmt == HTS_FMT_BAI? ".bai" : ".tbi");
+    if (fnidx == 0) return 0;
+
+    idx = hts_idx_load2(fn, fnidx);
+    free(fnidx);
+    return idx;
+}
+
+hts_idx_t *hts_idx_load2(const char *fn, const char *fnidx)
+{
+    // Check that the index file is up to date, the main file might have changed
+    struct stat stat_idx,stat_main;
+    if ( !stat(fn, &stat_main) && !stat(fnidx, &stat_idx) )
+    {
+        if ( stat_idx.st_mtime < stat_main.st_mtime )
+            fprintf(stderr, "Warning: The index file is older than the data file: %s\n", fnidx);
+    }
+
+    return hts_idx_load_local(fnidx);
+}
diff --git a/htslib/hts_internal.h b/htslib/hts_internal.h
new file mode 100644
index 0000000..07d6a11
--- /dev/null
+++ b/htslib/hts_internal.h
@@ -0,0 +1,90 @@
+/*  hts_internal.h -- internal functions; not part of the public API.
+
+    Copyright (C) 2015-2016 Genome Research Ltd.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#ifndef HTSLIB_HTS_INTERNAL_H
+#define HTSLIB_HTS_INTERNAL_H
+
+#include <stddef.h>
+#include <ctype.h>
+
+#include "htslib/hts.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+// The <ctype.h> functions operate on ints such as are returned by fgetc(),
+// i.e., characters represented as unsigned-char-valued ints, or EOF.
+// To operate on plain chars (and to avoid warnings on some platforms),
+// technically one must cast to unsigned char everywhere (see CERT STR37-C)
+// or less painfully use these *_c() functions that operate on plain chars
+// (but not EOF, which must be considered separately where it is applicable).
+// TODO We may eventually wish to implement these functions directly without
+// using their <ctype.h> equivalents, and thus make them immune to locales.
+static inline int isalnum_c(char c) { return isalnum((unsigned char) c); }
+static inline int isalpha_c(char c) { return isalpha((unsigned char) c); }
+static inline int isdigit_c(char c) { return isdigit((unsigned char) c); }
+static inline int isgraph_c(char c) { return isgraph((unsigned char) c); }
+static inline int islower_c(char c) { return islower((unsigned char) c); }
+static inline int isprint_c(char c) { return isprint((unsigned char) c); }
+static inline int isspace_c(char c) { return isspace((unsigned char) c); }
+static inline int isupper_c(char c) { return isupper((unsigned char) c); }
+static inline char tolower_c(char c) { return tolower((unsigned char) c); }
+static inline char toupper_c(char c) { return toupper((unsigned char) c); }
+
+
+struct cram_fd;
+
+char *hts_idx_getfn(const char *fn, const char *ext);
+
+// The CRAM implementation stores the loaded index within the cram_fd rather
+// than separately as is done elsewhere in htslib.  So if p is a pointer to
+// an hts_idx_t with p->fmt == HTS_FMT_CRAI, then it actually points to an
+// hts_cram_idx_t and should be cast accordingly.
+typedef struct hts_cram_idx_t {
+    int fmt;
+    struct cram_fd *cram;
+} hts_cram_idx_t;
+
+
+struct hts_path_itr {
+    kstring_t path, entry;
+    void *dirv;  // DIR * privately
+    const char *pathdir, *prefix, *suffix;
+    size_t prefix_len, suffix_len, entry_dir_l;
+};
+
+void hts_path_itr_setup(struct hts_path_itr *itr, const char *path,
+    const char *builtin_path, const char *prefix, size_t prefix_len,
+    const char *suffix, size_t suffix_len);
+
+const char *hts_path_itr_next(struct hts_path_itr *itr);
+
+void *load_plugin(void **pluginp, const char *filename, const char *symbol);
+void *plugin_sym(void *plugin, const char *name, const char **errmsg);
+void close_plugin(void *plugin);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/htslib/htsfile.c b/htslib/htsfile.c
new file mode 100644
index 0000000..3fa0678
--- /dev/null
+++ b/htslib/htsfile.c
@@ -0,0 +1,234 @@
+/*  htsfile.c -- file identifier and minimal viewer.
+
+    Copyright (C) 2014-2016 Genome Research Ltd.
+
+    Author: John Marshall <jm18 at sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <errno.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <getopt.h>
+#include <unistd.h>
+
+#include "htslib/hfile.h"
+#include "htslib/hts.h"
+#include "htslib/sam.h"
+#include "htslib/vcf.h"
+
+enum { identify, view_headers, view_all } mode = identify;
+int show_headers = 1;
+int status = EXIT_SUCCESS;  /* Exit status from main */
+
+static htsFile *dup_stdout(const char *mode)
+{
+    int fd = dup(STDOUT_FILENO);
+    if (fd < 0) {
+        perror("htsfile: Couldn't duplicate stdout");
+        return NULL;
+    }
+    hFILE *hfp = hdopen(fd, mode);
+    return hfp? hts_hopen(hfp, "-", mode) : NULL;
+}
+
+static int view_sam(hFILE *hfp, const char *filename)
+{
+    samFile *in = hts_hopen(hfp, filename, "r");
+    bam_hdr_t *hdr = NULL;
+    samFile *out = NULL;
+    if (in == NULL) {
+        status = EXIT_FAILURE;
+        return 0;
+    }
+    hdr = sam_hdr_read(in);
+    if (hdr == NULL) {
+        status = EXIT_FAILURE;
+        goto clean;
+    }
+    out = dup_stdout("w");
+    if (out == NULL) {
+        status = EXIT_FAILURE;
+        goto clean;
+    }
+
+    if (show_headers) {
+        if (sam_hdr_write(out, hdr) != 0) {
+            status = EXIT_FAILURE;
+            goto clean;
+        }
+    }
+    if (mode == view_all) {
+        bam1_t *b = bam_init1();
+        int ret;
+        while ((ret = sam_read1(in, hdr, b)) >= 0) {
+            if (sam_write1(out, hdr, b) < 0) {
+                status = EXIT_FAILURE;
+                goto clean;
+            }
+        }
+        bam_destroy1(b);
+        if (ret != -1) // eof
+            status = EXIT_FAILURE;
+    }
+
+ clean:
+    if (hdr != NULL) bam_hdr_destroy(hdr);
+    if (out != NULL && hts_close(out) != 0)
+        status = EXIT_FAILURE;
+    if (hts_close(in) != 0)
+        status = EXIT_FAILURE;
+    return 1;
+}
+
+static int view_vcf(hFILE *hfp, const char *filename)
+{
+    vcfFile *in = hts_hopen(hfp, filename, "r");
+    bcf_hdr_t *hdr = NULL;
+    vcfFile *out = NULL;
+    if (in == NULL) {
+        status = EXIT_FAILURE;
+        return 0;
+    }
+    hdr = bcf_hdr_read(in);
+    if (hdr == NULL) {
+        status = EXIT_FAILURE;
+        goto clean;
+    }
+    out = dup_stdout("w");
+    if (out == NULL) {
+        status = EXIT_FAILURE;
+        goto clean;
+    }
+
+    if (show_headers) {
+        if (bcf_hdr_write(out, hdr) != 0) {
+            status = EXIT_FAILURE;
+            goto clean;
+        }
+    }
+    if (mode == view_all) {
+        bcf1_t *rec = bcf_init();
+        while (bcf_read(in, hdr, rec) >= 0) {
+            if (bcf_write(out, hdr, rec) < 0) {
+                status = EXIT_FAILURE;
+                goto clean;
+            }
+        }
+        bcf_destroy(rec);
+    }
+
+ clean:
+    if (hdr != NULL) bcf_hdr_destroy(hdr);
+    if (out != NULL) hts_close(out);
+    hts_close(in);
+    return 1;
+}
+
+static void usage(FILE *fp, int status)
+{
+    fprintf(fp,
+"Usage: htsfile [-chHv] FILE...\n"
+"Options:\n"
+"  -c, --view         Write textual form of FILEs to standard output\n"
+"  -h, --header-only  Display only headers in view mode, not records\n"
+"  -H, --no-header    Suppress header display in view mode\n"
+"  -v, --verbose      Increase verbosity of warnings and diagnostics\n");
+    exit(status);
+}
+
+int main(int argc, char **argv)
+{
+    static const struct option options[] = {
+        { "header-only", no_argument, NULL, 'h' },
+        { "no-header", no_argument, NULL, 'H' },
+        { "view", no_argument, NULL, 'c' },
+        { "verbose", no_argument, NULL, 'v' },
+        { "help", no_argument, NULL, '?' },
+        { "version", no_argument, NULL, 1 },
+        { NULL, 0, NULL, 0 }
+    };
+
+    int c, i;
+
+    status = EXIT_SUCCESS;
+    while ((c = getopt_long(argc, argv, "chHv?", options, NULL)) >= 0)
+        switch (c) {
+        case 'c': mode = view_all; break;
+        case 'h': mode = view_headers; show_headers = 1; break;
+        case 'H': show_headers = 0; break;
+        case 'v': hts_verbose++; break;
+        case 1:
+            printf(
+"htsfile (htslib) %s\n"
+"Copyright (C) 2016 Genome Research Ltd.\n",
+                   hts_version());
+            exit(EXIT_SUCCESS);
+            break;
+        case '?': usage(stdout, EXIT_SUCCESS); break;
+        default:  usage(stderr, EXIT_FAILURE); break;
+        }
+
+    if (optind == argc) usage(stderr, EXIT_FAILURE);
+
+    for (i = optind; i < argc; i++) {
+        htsFormat fmt;
+        hFILE *fp = hopen(argv[i], "r");
+        if (fp == NULL) {
+            fprintf(stderr, "htsfile: can't open \"%s\": %s\n", argv[i], strerror(errno));
+            status = EXIT_FAILURE;
+            continue;
+        }
+
+        if (hts_detect_format(fp, &fmt) < 0) {
+            fprintf(stderr, "htsfile: detecting \"%s\" format failed: %s\n", argv[i], strerror(errno));
+            hclose_abruptly(fp);
+            status = EXIT_FAILURE;
+            continue;
+        }
+
+        if (mode == identify) {
+            char *description = hts_format_description(&fmt);
+            printf("%s:\t%s\n", argv[i], description);
+            free(description);
+        }
+        else
+            switch (fmt.category) {
+            case sequence_data:
+                if (view_sam(fp, argv[i])) fp = NULL;
+                break;
+            case variant_data:
+                if (view_vcf(fp, argv[i])) fp = NULL;
+                break;
+            default:
+                fprintf(stderr, "htsfile: can't view %s: unknown format\n", argv[i]);
+                status = EXIT_FAILURE;
+                break;
+            }
+
+        if (fp && hclose(fp) < 0) {
+            fprintf(stderr, "htsfile: closing %s failed\n", argv[i]);
+            status = EXIT_FAILURE;
+        }
+    }
+
+    return status;
+}
diff --git a/htslib/htslib.pc.in b/htslib/htslib.pc.in
new file mode 100644
index 0000000..465de17
--- /dev/null
+++ b/htslib/htslib.pc.in
@@ -0,0 +1,10 @@
+includedir=@includedir@
+libdir=@libdir@
+
+Name: htslib
+Description: C library for high-throughput sequencing data formats
+Version: @PACKAGE_VERSION@
+Cflags: -I${includedir}
+Libs: -L${libdir} -lhts
+Libs.private: -L${libdir} -lhts -lm -lpthread
+Requires.private: zlib
diff --git a/htslib/htslib/._bgzf.h b/htslib/htslib/._bgzf.h
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diff --git a/htslib/htslib/._knetfile.h b/htslib/htslib/._knetfile.h
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diff --git a/htslib/htslib/._kseq.h b/htslib/htslib/._kseq.h
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diff --git a/htslib/htslib/._ksort.h b/htslib/htslib/._ksort.h
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diff --git a/htslib/htslib/._vcfutils.h b/htslib/htslib/._vcfutils.h
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diff --git a/htslib/htslib/bgzf.h b/htslib/htslib/bgzf.h
new file mode 100644
index 0000000..63e1c91
--- /dev/null
+++ b/htslib/htslib/bgzf.h
@@ -0,0 +1,335 @@
+/* The MIT License
+
+   Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology
+                 2011, 2012 Attractive Chaos <attractor at live.co.uk>
+   Copyright (C) 2009, 2013, 2014 Genome Research Ltd
+
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+*/
+
+/* The BGZF library was originally written by Bob Handsaker from the Broad
+ * Institute. It was later improved by the SAMtools developers. */
+
+#ifndef HTSLIB_BGZF_H
+#define HTSLIB_BGZF_H
+
+#include <stdint.h>
+#include <stdio.h>
+#include <zlib.h>
+#include <sys/types.h>
+
+#include "hts_defs.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+#define BGZF_BLOCK_SIZE     0xff00 // make sure compressBound(BGZF_BLOCK_SIZE) < BGZF_MAX_BLOCK_SIZE
+#define BGZF_MAX_BLOCK_SIZE 0x10000
+
+#define BGZF_ERR_ZLIB   1
+#define BGZF_ERR_HEADER 2
+#define BGZF_ERR_IO     4
+#define BGZF_ERR_MISUSE 8
+
+struct hFILE;
+struct bgzf_mtaux_t;
+typedef struct __bgzidx_t bgzidx_t;
+
+struct BGZF {
+    unsigned errcode:16, is_write:2, is_be:2;
+    signed compress_level:9;
+    unsigned is_compressed:2, is_gzip:1;
+    int cache_size;
+    int block_length, block_offset;
+    int64_t block_address, uncompressed_address;
+    void *uncompressed_block, *compressed_block;
+    void *cache; // a pointer to a hash table
+    struct hFILE *fp; // actual file handle
+    struct bgzf_mtaux_t *mt; // only used for multi-threading
+    bgzidx_t *idx;      // BGZF index
+    int idx_build_otf;  // build index on the fly, set by bgzf_index_build_init()
+    z_stream *gz_stream;// for gzip-compressed files
+};
+#ifndef HTS_BGZF_TYPEDEF
+typedef struct BGZF BGZF;
+#define HTS_BGZF_TYPEDEF
+#endif
+
+#ifndef KSTRING_T
+#define KSTRING_T kstring_t
+typedef struct __kstring_t {
+    size_t l, m;
+    char *s;
+} kstring_t;
+#endif
+
+    /******************
+     * Basic routines *
+     ******************/
+
+    /**
+     * Open an existing file descriptor for reading or writing.
+     *
+     * @param fd    file descriptor
+     * @param mode  mode matching /[rwag][u0-9]+/: 'r' for reading, 'w' for
+     *              writing, 'a' for appending, 'g' for gzip rather than BGZF
+     *              compression (with 'w' only), and digit specifies the zlib
+     *              compression level.
+     *              Note that there is a distinction between 'u' and '0': the
+     *              first yields plain uncompressed output whereas the latter
+     *              outputs uncompressed data wrapped in the zlib format.
+     * @return      BGZF file handler; 0 on error
+     */
+    BGZF* bgzf_dopen(int fd, const char *mode);
+
+    #define bgzf_fdopen(fd, mode) bgzf_dopen((fd), (mode)) // for backward compatibility
+
+    /**
+     * Open the specified file for reading or writing.
+     */
+    BGZF* bgzf_open(const char* path, const char *mode);
+
+    /**
+     * Open an existing hFILE stream for reading or writing.
+     */
+    BGZF* bgzf_hopen(struct hFILE *fp, const char *mode);
+
+    /**
+     * Close the BGZF and free all associated resources.
+     *
+     * @param fp    BGZF file handler
+     * @return      0 on success and -1 on error
+     */
+    int bgzf_close(BGZF *fp);
+
+    /**
+     * Read up to _length_ bytes from the file storing into _data_.
+     *
+     * @param fp     BGZF file handler
+     * @param data   data array to read into
+     * @param length size of data to read
+     * @return       number of bytes actually read; 0 on end-of-file and -1 on error
+     */
+    ssize_t bgzf_read(BGZF *fp, void *data, size_t length) HTS_RESULT_USED;
+
+    /**
+     * Write _length_ bytes from _data_ to the file.  If no I/O errors occur,
+     * the complete _length_ bytes will be written (or queued for writing).
+     *
+     * @param fp     BGZF file handler
+     * @param data   data array to write
+     * @param length size of data to write
+     * @return       number of bytes written (i.e., _length_); negative on error
+     */
+    ssize_t bgzf_write(BGZF *fp, const void *data, size_t length) HTS_RESULT_USED;
+
+    /**
+     * Read up to _length_ bytes directly from the underlying stream without
+     * decompressing.  Bypasses BGZF blocking, so must be used with care in
+     * specialised circumstances only.
+     *
+     * @param fp     BGZF file handler
+     * @param data   data array to read into
+     * @param length number of raw bytes to read
+     * @return       number of bytes actually read; 0 on end-of-file and -1 on error
+     */
+    ssize_t bgzf_raw_read(BGZF *fp, void *data, size_t length) HTS_RESULT_USED;
+
+    /**
+     * Write _length_ bytes directly to the underlying stream without
+     * compressing.  Bypasses BGZF blocking, so must be used with care
+     * in specialised circumstances only.
+     *
+     * @param fp     BGZF file handler
+     * @param data   data array to write
+     * @param length number of raw bytes to write
+     * @return       number of bytes actually written; -1 on error
+     */
+    ssize_t bgzf_raw_write(BGZF *fp, const void *data, size_t length) HTS_RESULT_USED;
+
+    /**
+     * Write the data in the buffer to the file.
+     *
+     * @param fp     BGZF file handle
+     * @return       0 on success and -1 on error
+     */
+    int bgzf_flush(BGZF *fp) HTS_RESULT_USED;
+
+    /**
+     * Return a virtual file pointer to the current location in the file.
+     * No interpetation of the value should be made, other than a subsequent
+     * call to bgzf_seek can be used to position the file at the same point.
+     * Return value is non-negative on success.
+     */
+    #define bgzf_tell(fp) (((fp)->block_address << 16) | ((fp)->block_offset & 0xFFFF))
+
+    /**
+     * Set the file to read from the location specified by _pos_.
+     *
+     * @param fp     BGZF file handler
+     * @param pos    virtual file offset returned by bgzf_tell()
+     * @param whence must be SEEK_SET
+     * @return       0 on success and -1 on error
+     */
+    int64_t bgzf_seek(BGZF *fp, int64_t pos, int whence) HTS_RESULT_USED;
+
+    /**
+     * Check if the BGZF end-of-file (EOF) marker is present
+     *
+     * @param fp    BGZF file handler opened for reading
+     * @return      1 if the EOF marker is present and correct;
+     *              2 if it can't be checked, e.g., because fp isn't seekable;
+     *              0 if the EOF marker is absent;
+     *              -1 (with errno set) on error
+     */
+    int bgzf_check_EOF(BGZF *fp);
+
+    /**
+     * Check if a file is in the BGZF format
+     *
+     * @param fn    file name
+     * @return      1 if _fn_ is BGZF; 0 if not or on I/O error
+     */
+     int bgzf_is_bgzf(const char *fn);
+
+    /*********************
+     * Advanced routines *
+     *********************/
+
+    /**
+     * Set the cache size. Only effective when compiled with -DBGZF_CACHE.
+     *
+     * @param fp    BGZF file handler
+     * @param size  size of cache in bytes; 0 to disable caching (default)
+     */
+    void bgzf_set_cache_size(BGZF *fp, int size);
+
+    /**
+     * Flush the file if the remaining buffer size is smaller than _size_
+     * @return      0 if flushing succeeded or was not needed; negative on error
+     */
+    int bgzf_flush_try(BGZF *fp, ssize_t size) HTS_RESULT_USED;
+
+    /**
+     * Read one byte from a BGZF file. It is faster than bgzf_read()
+     * @param fp     BGZF file handler
+     * @return       byte read; -1 on end-of-file or error
+     */
+    int bgzf_getc(BGZF *fp);
+
+    /**
+     * Read one line from a BGZF file. It is faster than bgzf_getc()
+     *
+     * @param fp     BGZF file handler
+     * @param delim  delimitor
+     * @param str    string to write to; must be initialized
+     * @return       length of the string; 0 on end-of-file; negative on error
+     */
+    int bgzf_getline(BGZF *fp, int delim, kstring_t *str);
+
+    /**
+     * Read the next BGZF block.
+     */
+    int bgzf_read_block(BGZF *fp) HTS_RESULT_USED;
+
+    /**
+     * Enable multi-threading (only effective on writing and when the
+     * library was compiled with -DBGZF_MT)
+     *
+     * @param fp          BGZF file handler; must be opened for writing
+     * @param n_threads   #threads used for writing
+     * @param n_sub_blks  #blocks processed by each thread; a value 64-256 is recommended
+     */
+    int bgzf_mt(BGZF *fp, int n_threads, int n_sub_blks);
+
+    /**
+     * Compress a single BGZF block.
+     *
+     * @param dst    output buffer (must have size >= BGZF_MAX_BLOCK_SIZE)
+     * @param dlen   size of output buffer; updated on return to the number
+     *               of bytes actually written to dst
+     * @param src    buffer to be compressed
+     * @param slen   size of data to compress (must be <= BGZF_BLOCK_SIZE)
+     * @param level  compression level
+     * @return       0 on success and negative on error
+     */
+    int bgzf_compress(void *dst, size_t *dlen, const void *src, size_t slen, int level);
+
+    /*******************
+     * bgzidx routines *
+     *******************/
+
+    /**
+     *  Position BGZF at the uncompressed offset
+     *
+     *  @param fp           BGZF file handler; must be opened for reading
+     *  @param uoffset      file offset in the uncompressed data
+     *  @param where        SEEK_SET supported atm
+     *
+     *  Returns 0 on success and -1 on error.
+     */
+    int bgzf_useek(BGZF *fp, long uoffset, int where) HTS_RESULT_USED;
+
+    /**
+     *  Position in uncompressed BGZF
+     *
+     *  @param fp           BGZF file handler; must be opened for reading
+     *
+     *  Returns the current offset on success and -1 on error.
+     */
+    long bgzf_utell(BGZF *fp);
+
+    /**
+     * Tell BGZF to build index while compressing.
+     *
+     * @param fp          BGZF file handler; can be opened for reading or writing.
+     *
+     * Returns 0 on success and -1 on error.
+     */
+    int bgzf_index_build_init(BGZF *fp);
+
+    /**
+     * Load BGZF index
+     *
+     * @param fp          BGZF file handler
+     * @param bname       base name
+     * @param suffix      suffix to add to bname (can be NULL)
+     *
+     * Returns 0 on success and -1 on error.
+     */
+    int bgzf_index_load(BGZF *fp, const char *bname, const char *suffix);
+
+    /**
+     * Save BGZF index
+     *
+     * @param fp          BGZF file handler
+     * @param bname       base name
+     * @param suffix      suffix to add to bname (can be NULL)
+     *
+     * Returns 0 on success and -1 on error.
+     */
+    int bgzf_index_dump(BGZF *fp,
+                        const char *bname, const char *suffix) HTS_RESULT_USED;
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/htslib/htslib/cram.h b/htslib/htslib/cram.h
new file mode 100644
index 0000000..bd54f39
--- /dev/null
+++ b/htslib/htslib/cram.h
@@ -0,0 +1,492 @@
+/*  cram.h -- public CRAM-specific API functions.
+
+    Copyright (C) 2015 Genome Research Ltd.
+
+    Author: James Bonfield <jkb at sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+/*! \file
+ * CRAM interface.
+ *
+ * Consider using the higher level hts_*() API for programs that wish to
+ * be file format agnostic (see htslib/hts.h).
+ *
+ * This API should be used for CRAM specific code. The specifics of the
+ * public API are implemented in cram_io.h, cram_encode.h and cram_decode.h
+ * although these should not be included directly (use this file instead).
+ */
+
+#ifndef HTSLIB_CRAM_H
+#define HTSLIB_CRAM_H
+
+#include <stdarg.h>
+#include <stdint.h>
+#include <sys/types.h>
+
+#include "hts.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+#ifndef _CRAM_STRUCTS_H_
+enum cram_block_method {
+    ERROR    = -1,
+    RAW      = 0,
+    GZIP     = 1,
+    BZIP2    = 2,
+    LZMA     = 3,
+    RANS     = 4,  // Generic; either order
+    RANS0    = 4,
+    RANS1    = 10, // Not externalised; stored as RANS (generic)
+    GZIP_RLE = 11, // NB: not externalised in CRAM
+};
+
+enum cram_content_type {
+    CT_ERROR           = -1,
+    FILE_HEADER        = 0,
+    COMPRESSION_HEADER = 1,
+    MAPPED_SLICE       = 2,
+    UNMAPPED_SLICE     = 3, // CRAM V1.0 only
+    EXTERNAL           = 4,
+    CORE               = 5,
+};
+
+// Opaque data types, see cram_structs for the fully fledged versions.
+typedef struct SAM_hdr SAM_hdr;
+typedef struct cram_file_def cram_file_def;
+typedef struct cram_fd cram_fd;
+typedef struct cram_container cram_container;
+typedef struct cram_block cram_block;
+typedef struct cram_slice cram_slice;
+typedef struct cram_metrics cram_metrics;
+typedef struct cram_block_slice_hdr cram_block_slice_hdr;
+typedef struct cram_block_compression_hdr cram_block_compression_hdr;
+typedef struct refs_t refs_t; // need this?
+
+struct hFILE;
+#endif
+
+// Accessor functions
+
+/*
+ *-----------------------------------------------------------------------------
+ * cram_fd
+ */
+SAM_hdr *cram_fd_get_header(cram_fd *fd);
+void cram_fd_set_header(cram_fd *fd, SAM_hdr *hdr);
+
+int cram_fd_get_version(cram_fd *fd);
+void cram_fd_set_version(cram_fd *fd, int vers);
+
+int cram_major_vers(cram_fd *fd);
+int cram_minor_vers(cram_fd *fd);
+
+struct hFILE *cram_fd_get_fp(cram_fd *fd);
+void cram_fd_set_fp(cram_fd *fd, struct hFILE *fp);
+
+
+/*
+ *-----------------------------------------------------------------------------
+ * cram_container
+ */
+int32_t cram_container_get_length(cram_container *c);
+void cram_container_set_length(cram_container *c, int32_t length);
+int32_t cram_container_get_num_blocks(cram_container *c);
+void cram_container_set_num_blocks(cram_container *c, int32_t num_blocks);
+int32_t *cram_container_get_landmarks(cram_container *c, int32_t *num_landmarks);
+void cram_container_set_landmarks(cram_container *c, int32_t num_landmarks,
+                                  int32_t *landmarks);
+
+/* Returns true if the container is empty (EOF marker) */
+int cram_container_is_empty(cram_fd *fd);
+
+
+/*
+ *-----------------------------------------------------------------------------
+ * cram_block
+ */
+int32_t cram_block_get_content_id(cram_block *b);
+int32_t cram_block_get_comp_size(cram_block *b);
+int32_t cram_block_get_uncomp_size(cram_block *b);
+int32_t cram_block_get_crc32(cram_block *b);
+void *  cram_block_get_data(cram_block *b);
+
+enum cram_content_type cram_block_get_content_type(cram_block *b);
+
+void cram_block_set_content_id(cram_block *b, int32_t id);
+void cram_block_set_comp_size(cram_block *b, int32_t size);
+void cram_block_set_uncomp_size(cram_block *b, int32_t size);
+void cram_block_set_crc32(cram_block *b, int32_t crc);
+void cram_block_set_data(cram_block *b, void *data);
+
+int cram_block_append(cram_block *b, void *data, int size);
+void cram_block_update_size(cram_block *b);
+
+// Offset is known as "size" internally, but it can be confusing.
+size_t cram_block_get_offset(cram_block *b);
+void cram_block_set_offset(cram_block *b, size_t offset);
+
+/*
+ * Computes the size of a cram block, including the block
+ * header itself.
+ */
+uint32_t cram_block_size(cram_block *b);
+
+/*
+ * Renumbers RG numbers in a cram compression header.
+ *
+ * CRAM stores RG as the Nth number in the header, rather than a
+ * string holding the ID: tag.  This is smaller in space, but means
+ * "samtools cat" to join files together that contain single but
+ * different RG lines needs a way of renumbering them.
+ *
+ * The file descriptor is expected to be immediately after the
+ * cram_container structure (ie before the cram compression header).
+ * Due to the nature of the CRAM format, this needs to read and write
+ * the blocks itself.  Note that there may be multiple slices within
+ * the container, meaning multiple compression headers to manipulate.
+ * Changing RG may change the size of the compression header and
+ * therefore the length field in the container.  Hence we rewrite all
+ * blocks just incase and also emit the adjusted container.
+ *
+ * The current implementation can only cope with renumbering a single
+ * RG (and only then if it is using HUFFMAN or BETA codecs).  In
+ * theory it *may* be possible to renumber multiple RGs if they use
+ * HUFFMAN to the CORE block or use an external block unshared by any
+ * other data series.  So we have an API that can be upgraded to
+ * support this, but do not implement it for now.  An example
+ * implementation of RG as an EXTERNAL block would be to find that
+ * block and rewrite it, returning the number of blocks consumed.
+ *
+ * Returns 0 on success;
+ *        -1 if unable to edit;
+ *        -2 on other errors (eg I/O).
+ */
+int cram_transcode_rg(cram_fd *in, cram_fd *out,
+                      cram_container *c,
+                      int nrg, int *in_rg, int *out_rg);
+
+/*
+ * Copies the blocks representing the next num_slice slices from a
+ * container from 'in' to 'out'.  It is expected that the file pointer
+ * is just after the read of the cram_container and cram compression
+ * header.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int cram_copy_slice(cram_fd *in, cram_fd *out, int32_t num_slice);
+
+/*
+ *-----------------------------------------------------------------------------
+ * SAM_hdr
+ */
+
+/*! Tokenises a SAM header into a hash table.
+ *
+ * Also extracts a few bits on specific data types, such as @RG lines.
+ *
+ * @return
+ * Returns a SAM_hdr struct on success (free with sam_hdr_free());
+ *         NULL on failure
+ */
+SAM_hdr *sam_hdr_parse_(const char *hdr, int len);
+
+
+/*
+ *-----------------------------------------------------------------------------
+ * cram_io basics
+ */
+
+/**@{ ----------------------------------------------------------------------
+ * CRAM blocks - the dynamically growable data block. We have code to
+ * create, update, (un)compress and read/write.
+ *
+ * These are derived from the deflate_interlaced.c blocks, but with the
+ * CRAM extension of content types and IDs.
+ */
+
+/*! Allocates a new cram_block structure with a specified content_type and
+ * id.
+ *
+ * @return
+ * Returns block pointer on success;
+ *         NULL on failure
+ */
+cram_block *cram_new_block(enum cram_content_type content_type,
+                           int content_id);
+
+/*! Reads a block from a cram file.
+ *
+ * @return
+ * Returns cram_block pointer on success;
+ *         NULL on failure
+ */
+cram_block *cram_read_block(cram_fd *fd);
+
+/*! Writes a CRAM block.
+ *
+ * @return
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+int cram_write_block(cram_fd *fd, cram_block *b);
+
+/*! Frees a CRAM block, deallocating internal data too.
+ */
+void cram_free_block(cram_block *b);
+
+/*! Uncompresses a CRAM block, if compressed.
+ *
+ * @return
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+int cram_uncompress_block(cram_block *b);
+
+/*! Compresses a block.
+ *
+ * Compresses a block using one of two different zlib strategies. If we only
+ * want one choice set strat2 to be -1.
+ *
+ * The logic here is that sometimes Z_RLE does a better job than Z_FILTERED
+ * or Z_DEFAULT_STRATEGY on quality data. If so, we'd rather use it as it is
+ * significantly faster.
+ *
+ * @return
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+int cram_compress_block(cram_fd *fd, cram_block *b, cram_metrics *metrics,
+                        int method, int level);
+
+/**@}*/
+/**@{ ----------------------------------------------------------------------
+ * Containers
+ */
+
+/*! Creates a new container, specifying the maximum number of slices
+ * and records permitted.
+ *
+ * @return
+ * Returns cram_container ptr on success;
+ *         NULL on failure
+ */
+cram_container *cram_new_container(int nrec, int nslice);
+void cram_free_container(cram_container *c);
+
+/*! Reads a container header.
+ *
+ * @return
+ * Returns cram_container on success;
+ *         NULL on failure or no container left (fd->err == 0).
+ */
+cram_container *cram_read_container(cram_fd *fd);
+
+/*! Writes a container structure.
+ *
+ * @return
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+int cram_write_container(cram_fd *fd, cram_container *h);
+
+/*
+ * Stores the container structure in dat and returns *size as the
+ * number of bytes written to dat[].  The input size of dat is also
+ * held in *size and should be initialised to cram_container_size(c).
+ *
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+int cram_store_container(cram_fd *fd, cram_container *c, char *dat, int *size);
+
+int cram_container_size(cram_container *c);
+
+/**@}*/
+/**@{ ----------------------------------------------------------------------
+ * The top-level cram opening, closing and option handling
+ */
+
+/*! Opens a CRAM file for read (mode "rb") or write ("wb").
+ *
+ * The filename may be "-" to indicate stdin or stdout.
+ *
+ * @return
+ * Returns file handle on success;
+ *         NULL on failure.
+ */
+cram_fd *cram_open(const char *filename, const char *mode);
+
+/*! Opens an existing stream for reading or writing.
+ *
+ * @return
+ * Returns file handle on success;
+ *         NULL on failure.
+ */
+cram_fd *cram_dopen(struct hFILE *fp, const char *filename, const char *mode);
+
+/*! Closes a CRAM file.
+ *
+ * @return
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+int cram_close(cram_fd *fd);
+
+/*
+ * Seek within a CRAM file.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int cram_seek(cram_fd *fd, off_t offset, int whence);
+
+/*
+ * Flushes a CRAM file.
+ * Useful for when writing to stdout without wishing to close the stream.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int cram_flush(cram_fd *fd);
+
+/*! Checks for end of file on a cram_fd stream.
+ *
+ * @return
+ * Returns 0 if not at end of file
+ *         1 if we hit an expected EOF (end of range or EOF block)
+ *         2 for other EOF (end of stream without EOF block)
+ */
+int cram_eof(cram_fd *fd);
+
+/*! Sets options on the cram_fd.
+ *
+ * See CRAM_OPT_* definitions in hts.h.
+ * Use this immediately after opening.
+ *
+ * @return
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+int cram_set_option(cram_fd *fd, enum hts_fmt_option opt, ...);
+
+/*! Sets options on the cram_fd.
+ *
+ * See CRAM_OPT_* definitions in hts.h.
+ * Use this immediately after opening.
+ *
+ * @return
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+int cram_set_voption(cram_fd *fd, enum hts_fmt_option opt, va_list args);
+
+/*!
+ * Attaches a header to a cram_fd.
+ *
+ * This should be used when creating a new cram_fd for writing where
+ * we have an SAM_hdr already constructed (eg from a file we've read
+ * in).
+ *
+ * @return
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+int cram_set_header(cram_fd *fd, SAM_hdr *hdr);
+
+
+/* As int32_decoded/encode, but from/to blocks instead of cram_fd */
+int int32_put_blk(cram_block *b, int32_t val);
+
+/**@}*/
+/**@{ -------------------------------------------------------------------*/
+/*! Deallocates all storage used by a SAM_hdr struct.
+ *
+ * This also decrements the header reference count. If after decrementing
+ * it is still non-zero then the header is assumed to be in use by another
+ * caller and the free is not done.
+ *
+ * This is a synonym for sam_hdr_dec_ref().
+ */
+void sam_hdr_free(SAM_hdr *hdr);
+
+/*! Returns the current length of the SAM_hdr in text form.
+ *
+ * Call sam_hdr_rebuild() first if editing has taken place.
+ */
+int sam_hdr_length(SAM_hdr *hdr);
+
+/*! Returns the string form of the SAM_hdr.
+ *
+ * Call sam_hdr_rebuild() first if editing has taken place.
+ */
+char *sam_hdr_str(SAM_hdr *hdr);
+
+/*! Appends a formatted line to an existing SAM header.
+ *
+ * Line is a full SAM header record, eg "@SQ\tSN:foo\tLN:100", with
+ * optional new-line. If it contains more than 1 line then multiple lines
+ * will be added in order.
+ *
+ * Len is the length of the text data, or 0 if unknown (in which case
+ * it should be null terminated).
+ *
+ * @return
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+
+/*! Add an @PG line.
+ *
+ * If we wish complete control over this use sam_hdr_add() directly. This
+ * function uses that, but attempts to do a lot of tedious house work for
+ * you too.
+ *
+ * - It will generate a suitable ID if the supplied one clashes.
+ * - It will generate multiple @PG records if we have multiple PG chains.
+ *
+ * Call it as per sam_hdr_add() with a series of key,value pairs ending
+ * in NULL.
+ *
+ * @return
+ * Returns 0 on success;
+ *        -1 on failure
+ */
+int sam_hdr_add_PG(SAM_hdr *sh, const char *name, ...);
+
+/*!
+ * A function to help with construction of CL tags in @PG records.
+ * Takes an argc, argv pair and returns a single space-separated string.
+ * This string should be deallocated by the calling function.
+ *
+ * @return
+ * Returns malloced char * on success;
+ *         NULL on failure
+ */
+char *stringify_argv(int argc, char *argv[]);
+/**@}*/
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/htslib/htslib/faidx.h b/htslib/htslib/faidx.h
new file mode 100644
index 0000000..62478ef
--- /dev/null
+++ b/htslib/htslib/faidx.h
@@ -0,0 +1,137 @@
+/* faidx.h -- FASTA random access.
+
+   Copyright (C) 2008, 2009, 2013, 2014 Genome Research Ltd.
+
+   Author: Heng Li <lh3 at sanger.ac.uk>
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+
+#ifndef HTSLIB_FAIDX_H
+#define HTSLIB_FAIDX_H
+
+#include "hts_defs.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*!
+  @header
+
+  Index FASTA files and extract subsequence.
+
+  The fai file index columns are:
+    - chromosome name
+    - chromosome length: number of bases
+    - offset: number of bytes to skip to get to the first base
+        from the beginning of the file, including the length
+        of the sequence description string (">chr ..\n")
+    - line length: number of bases per line (excluding \n)
+    - binary line length: number of bytes, including \n
+
+  @copyright The Wellcome Trust Sanger Institute.
+ */
+
+struct __faidx_t;
+typedef struct __faidx_t faidx_t;
+
+    /*!
+      @abstract   Build index for a FASTA or bgzip-compressed FASTA file.
+      @param  fn  FASTA file name
+      @return     0 on success; or -1 on failure
+      @discussion File "fn.fai" will be generated.
+     */
+    int fai_build(const char *fn) HTS_RESULT_USED;
+
+    /*!
+      @abstract    Destroy a faidx_t struct.
+      @param  fai  Pointer to the struct to be destroyed
+     */
+    void fai_destroy(faidx_t *fai);
+
+    /*!
+      @abstract   Load index from "fn.fai".
+      @param  fn  File name of the FASTA file
+     */
+    faidx_t *fai_load(const char *fn);
+
+    /*!
+      @abstract    Fetch the sequence in a region.
+      @param  fai  Pointer to the faidx_t struct
+      @param  reg  Region in the format "chr2:20,000-30,000"
+      @param  len  Length of the region; -2 if seq not present, -1 general error
+      @return      Pointer to the sequence; null on failure
+
+      @discussion The returned sequence is allocated by malloc family
+      and should be destroyed by end users by calling free() on it.
+     */
+    char *fai_fetch(const faidx_t *fai, const char *reg, int *len);
+
+    /*!
+      @abstract    Fetch the number of sequences.
+      @param  fai  Pointer to the faidx_t struct
+      @return      The number of sequences
+     */
+    int faidx_fetch_nseq(const faidx_t *fai) HTS_DEPRECATED("Please use faidx_nseq instead");
+
+    /*!
+      @abstract    Fetch the sequence in a region.
+      @param  fai  Pointer to the faidx_t struct
+      @param  c_name Region name
+      @param  p_beg_i  Beginning position number (zero-based)
+      @param  p_end_i  End position number (zero-based)
+      @param  len  Length of the region; -2 if c_name not present, -1 general error
+      @return      Pointer to the sequence; null on failure
+
+      @discussion The returned sequence is allocated by malloc family
+      and should be destroyed by end users by calling free() on it.
+     */
+    char *faidx_fetch_seq(const faidx_t *fai, const char *c_name, int p_beg_i, int p_end_i, int *len);
+
+    /*!
+      @abstract    Query if sequence is present
+      @param  fai  Pointer to the faidx_t struct
+      @param  seq  Sequence name
+      @return      1 if present or 0 if absent
+     */
+    int faidx_has_seq(const faidx_t *fai, const char *seq);
+
+    /*!
+      @abstract    Return number of sequences in fai index
+     */
+    int faidx_nseq(const faidx_t *fai);
+
+    /*!
+      @abstract    Return name of i-th sequence
+     */
+    const char *faidx_iseq(const faidx_t *fai, int i);
+
+    /*!
+      @abstract    Return sequence length, -1 if not present
+     */
+    int faidx_seq_len(const faidx_t *fai, const char *seq);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/htslib/htslib/hfile.h b/htslib/htslib/hfile.h
new file mode 100644
index 0000000..cd772dd
--- /dev/null
+++ b/htslib/htslib/hfile.h
@@ -0,0 +1,215 @@
+/*  hfile.h -- buffered low-level input/output streams.
+
+    Copyright (C) 2013-2015 Genome Research Ltd.
+
+    Author: John Marshall <jm18 at sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#ifndef HTSLIB_HFILE_H
+#define HTSLIB_HFILE_H
+
+#include <string.h>
+
+#include <sys/types.h>
+
+#include "hts_defs.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/* These fields are declared here solely for the benefit of the inline functions
+   below.  They may change in future releases.  User code should not use them
+   directly; you should imagine that hFILE is an opaque incomplete type.  */
+struct hFILE_backend;
+typedef struct hFILE {
+    char *buffer, *begin, *end, *limit;
+    const struct hFILE_backend *backend;
+    off_t offset;
+    unsigned at_eof:1;
+    int has_errno;
+} hFILE;
+
+/*!
+  @abstract  Open the named file or URL as a stream
+  @return    An hFILE pointer, or NULL (with errno set) if an error occurred.
+  @notes     The usual @c fopen(3) @a mode letters are supported: one of
+    @e r (read), @e w (write), @e a (append), optionally followed by any of
+    @e + (update), @e e (close on @c exec(2)), @e x (create exclusively).
+*/
+hFILE *hopen(const char *filename, const char *mode) HTS_RESULT_USED;
+
+/*!
+  @abstract  Associate a stream with an existing open file descriptor
+  @return    An hFILE pointer, or NULL (with errno set) if an error occurred.
+  @notes     For socket descriptors (on Windows), mode should contain 's'.
+*/
+hFILE *hdopen(int fd, const char *mode) HTS_RESULT_USED;
+
+/*!
+  @abstract  Report whether the file name or URL denotes remote storage
+  @return    0 if local, 1 if remote.
+  @notes     "Remote" means involving e.g. explicit network access, with the
+    implication that callers may wish to cache such files' contents locally.
+*/
+int hisremote(const char *filename) HTS_RESULT_USED;
+
+/*!
+  @abstract  Flush (for output streams) and close the stream
+  @return    0 if successful, or EOF (with errno set) if an error occurred.
+*/
+int hclose(hFILE *fp) HTS_RESULT_USED;
+
+/*!
+  @abstract  Close the stream, without flushing or propagating errors
+  @notes     For use while cleaning up after an error only.  Preserves errno.
+*/
+void hclose_abruptly(hFILE *fp);
+
+/*!
+  @abstract  Return the stream's error indicator
+  @return    Non-zero (in fact, an errno value) if an error has occurred.
+  @notes     This would be called herror() and return true/false to parallel
+    ferror(3), but a networking-related herror(3) function already exists.  */
+static inline int herrno(hFILE *fp)
+{
+    return fp->has_errno;
+}
+
+/*!
+  @abstract  Clear the stream's error indicator
+*/
+static inline void hclearerr(hFILE *fp)
+{
+    fp->has_errno = 0;
+}
+
+/*!
+  @abstract  Reposition the read/write stream offset
+  @return    The resulting offset within the stream (as per lseek(2)),
+    or negative if an error occurred.
+*/
+off_t hseek(hFILE *fp, off_t offset, int whence) HTS_RESULT_USED;
+
+/*!
+  @abstract  Report the current stream offset
+  @return    The offset within the stream, starting from zero.
+*/
+static inline off_t htell(hFILE *fp)
+{
+    return fp->offset + (fp->begin - fp->buffer);
+}
+
+/*!
+  @abstract  Read one character from the stream
+  @return    The character read, or EOF on end-of-file or error
+*/
+static inline int hgetc(hFILE *fp)
+{
+    extern int hgetc2(hFILE *);
+    return (fp->end > fp->begin)? (unsigned char) *(fp->begin++) : hgetc2(fp);
+}
+
+/*!
+  @abstract  Peek at characters to be read without removing them from buffers
+  @param fp      The file stream
+  @param buffer  The buffer to which the peeked bytes will be written
+  @param nbytes  The number of bytes to peek at; limited by the size of the
+    internal buffer, which could be as small as 4K.
+  @return    The number of bytes peeked, which may be less than nbytes if EOF
+    is encountered; or negative, if there was an I/O error.
+  @notes  The characters peeked at remain in the stream's internal buffer,
+    and will be returned by later hread() etc calls.
+*/
+ssize_t hpeek(hFILE *fp, void *buffer, size_t nbytes) HTS_RESULT_USED;
+
+/*!
+  @abstract  Read a block of characters from the file
+  @return    The number of bytes read, or negative if an error occurred.
+  @notes     The full nbytes requested will be returned, except as limited
+    by EOF or I/O errors.
+*/
+static inline ssize_t HTS_RESULT_USED
+hread(hFILE *fp, void *buffer, size_t nbytes)
+{
+    extern ssize_t hread2(hFILE *, void *, size_t, size_t);
+
+    size_t n = fp->end - fp->begin;
+    if (n > nbytes) n = nbytes;
+    memcpy(buffer, fp->begin, n);
+    fp->begin += n;
+    return (n == nbytes)? (ssize_t) n : hread2(fp, buffer, nbytes, n);
+}
+
+/*!
+  @abstract  Write a character to the stream
+  @return    The character written, or EOF if an error occurred.
+*/
+static inline int hputc(int c, hFILE *fp)
+{
+    extern int hputc2(int, hFILE *);
+    if (fp->begin < fp->limit) *(fp->begin++) = c;
+    else c = hputc2(c, fp);
+    return c;
+}
+
+/*!
+  @abstract  Write a string to the stream
+  @return    0 if successful, or EOF if an error occurred.
+*/
+static inline int hputs(const char *text, hFILE *fp)
+{
+    extern int hputs2(const char *, size_t, size_t, hFILE *);
+
+    size_t nbytes = strlen(text), n = fp->limit - fp->begin;
+    if (n > nbytes) n = nbytes;
+    memcpy(fp->begin, text, n);
+    fp->begin += n;
+    return (n == nbytes)? 0 : hputs2(text, nbytes, n, fp);
+}
+
+/*!
+  @abstract  Write a block of characters to the file
+  @return    Either nbytes, or negative if an error occurred.
+  @notes     In the absence of I/O errors, the full nbytes will be written.
+*/
+static inline ssize_t HTS_RESULT_USED
+hwrite(hFILE *fp, const void *buffer, size_t nbytes)
+{
+    extern ssize_t hwrite2(hFILE *, const void *, size_t, size_t);
+
+    size_t n = fp->limit - fp->begin;
+    if (n > nbytes) n = nbytes;
+    memcpy(fp->begin, buffer, n);
+    fp->begin += n;
+    return (n==nbytes)? (ssize_t) n : hwrite2(fp, buffer, nbytes, n);
+}
+
+/*!
+  @abstract  For writing streams, flush buffered output to the underlying stream
+  @return    0 if successful, or EOF if an error occurred.
+*/
+int hflush(hFILE *fp) HTS_RESULT_USED;
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/htslib/htslib/hts.h b/htslib/htslib/hts.h
new file mode 100644
index 0000000..1bac3a6
--- /dev/null
+++ b/htslib/htslib/hts.h
@@ -0,0 +1,639 @@
+/*  hts.h -- format-neutral I/O, indexing, and iterator API functions.
+
+    Copyright (C) 2012-2015 Genome Research Ltd.
+    Copyright (C) 2012 Broad Institute.
+
+    Author: Heng Li <lh3 at sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#ifndef HTSLIB_HTS_H
+#define HTSLIB_HTS_H
+
+#include <stddef.h>
+#include <stdint.h>
+
+#include "hts_defs.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+#ifndef HTS_BGZF_TYPEDEF
+typedef struct BGZF BGZF;
+#define HTS_BGZF_TYPEDEF
+#endif
+struct cram_fd;
+struct hFILE;
+
+#ifndef KSTRING_T
+#define KSTRING_T kstring_t
+typedef struct __kstring_t {
+    size_t l, m;
+    char *s;
+} kstring_t;
+#endif
+
+#ifndef kroundup32
+#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
+#endif
+
+/**
+ * hts_expand()  - expands memory block pointed to by $ptr;
+ * hts_expand0()   the latter sets the newly allocated part to 0.
+ *
+ * @param n     requested number of elements of type type_t
+ * @param m     size of memory allocated
+ */
+#define hts_expand(type_t, n, m, ptr) if ((n) > (m)) { \
+        (m) = (n); kroundup32(m); \
+        (ptr) = (type_t*)realloc((ptr), (m) * sizeof(type_t)); \
+    }
+#define hts_expand0(type_t, n, m, ptr) if ((n) > (m)) { \
+        int t = (m); (m) = (n); kroundup32(m); \
+        (ptr) = (type_t*)realloc((ptr), (m) * sizeof(type_t)); \
+        memset(((type_t*)ptr)+t,0,sizeof(type_t)*((m)-t)); \
+    }
+
+/************
+ * File I/O *
+ ************/
+
+// Add new entries only at the end (but before the *_maximum entry)
+// of these enums, as their numbering is part of the htslib ABI.
+
+enum htsFormatCategory {
+    unknown_category,
+    sequence_data,    // Sequence data -- SAM, BAM, CRAM, etc
+    variant_data,     // Variant calling data -- VCF, BCF, etc
+    index_file,       // Index file associated with some data file
+    region_list,      // Coordinate intervals or regions -- BED, etc
+    category_maximum = 32767
+};
+
+enum htsExactFormat {
+    unknown_format,
+    binary_format, text_format,
+    sam, bam, bai, cram, crai, vcf, bcf, csi, gzi, tbi, bed,
+    format_maximum = 32767
+};
+
+enum htsCompression {
+    no_compression, gzip, bgzf, custom,
+    compression_maximum = 32767
+};
+
+typedef struct htsFormat {
+    enum htsFormatCategory category;
+    enum htsExactFormat format;
+    struct { short major, minor; } version;
+    enum htsCompression compression;
+    short compression_level;  // currently unused
+    void *specific;  // format specific options; see struct hts_opt.
+} htsFormat;
+
+// Maintainers note htsFile cannot be an opaque structure because some of its
+// fields are part of libhts.so's ABI (hence these fields must not be moved):
+//  - fp is used in the public sam_itr_next()/etc macros
+//  - is_bin is used directly in samtools <= 1.1 and bcftools <= 1.1
+//  - is_write and is_cram are used directly in samtools <= 1.1
+//  - fp is used directly in samtools (up to and including current develop)
+//  - line is used directly in bcftools (up to and including current develop)
+typedef struct {
+    uint32_t is_bin:1, is_write:1, is_be:1, is_cram:1, dummy:28;
+    int64_t lineno;
+    kstring_t line;
+    char *fn, *fn_aux;
+    union {
+        BGZF *bgzf;
+        struct cram_fd *cram;
+        struct hFILE *hfile;
+        void *voidp;
+    } fp;
+    htsFormat format;
+} htsFile;
+
+// REQUIRED_FIELDS
+enum sam_fields {
+    SAM_QNAME = 0x00000001,
+    SAM_FLAG  = 0x00000002,
+    SAM_RNAME = 0x00000004,
+    SAM_POS   = 0x00000008,
+    SAM_MAPQ  = 0x00000010,
+    SAM_CIGAR = 0x00000020,
+    SAM_RNEXT = 0x00000040,
+    SAM_PNEXT = 0x00000080,
+    SAM_TLEN  = 0x00000100,
+    SAM_SEQ   = 0x00000200,
+    SAM_QUAL  = 0x00000400,
+    SAM_AUX   = 0x00000800,
+    SAM_RGAUX = 0x00001000,
+};
+
+// Mostly CRAM only, but this could also include other format options
+enum hts_fmt_option {
+    // CRAM specific
+    CRAM_OPT_DECODE_MD,
+    CRAM_OPT_PREFIX,
+    CRAM_OPT_VERBOSITY,  // make general
+    CRAM_OPT_SEQS_PER_SLICE,
+    CRAM_OPT_SLICES_PER_CONTAINER,
+    CRAM_OPT_RANGE,
+    CRAM_OPT_VERSION,    // rename to cram_version?
+    CRAM_OPT_EMBED_REF,
+    CRAM_OPT_IGNORE_MD5,
+    CRAM_OPT_REFERENCE,  // make general
+    CRAM_OPT_MULTI_SEQ_PER_SLICE,
+    CRAM_OPT_NO_REF,
+    CRAM_OPT_USE_BZIP2,
+    CRAM_OPT_SHARED_REF,
+    CRAM_OPT_NTHREADS,   // deprecated, use HTS_OPT_NTHREADS
+    CRAM_OPT_THREAD_POOL,// make general
+    CRAM_OPT_USE_LZMA,
+    CRAM_OPT_USE_RANS,
+    CRAM_OPT_REQUIRED_FIELDS,
+
+    // General purpose
+    HTS_OPT_COMPRESSION_LEVEL = 100,
+    HTS_OPT_NTHREADS,
+};
+
+// For backwards compatibility
+#define cram_option hts_fmt_option
+
+typedef struct hts_opt {
+    char *arg;                // string form, strdup()ed
+    enum hts_fmt_option opt;  // tokenised key
+    union {                   // ... and value
+        int i;
+        char *s;
+    } val;
+    struct hts_opt *next;
+} hts_opt;
+
+#define HTS_FILE_OPTS_INIT {{0},0}
+
+/**********************
+ * Exported functions *
+ **********************/
+
+/*
+ * Parses arg and appends it to the option list.
+ *
+ * Returns 0 on success;
+ *        -1 on failure.
+ */
+int hts_opt_add(hts_opt **opts, const char *c_arg);
+
+/*
+ * Applies an hts_opt option list to a given htsFile.
+ *
+ * Returns 0 on success
+ *        -1 on failure
+ */
+int hts_opt_apply(htsFile *fp, hts_opt *opts);
+
+/*
+ * Frees an hts_opt list.
+ */
+void hts_opt_free(hts_opt *opts);
+
+/*
+ * Accepts a string file format (sam, bam, cram, vcf, bam) optionally
+ * followed by a comma separated list of key=value options and splits
+ * these up into the fields of htsFormat struct.
+ *
+ * Returns 0 on success
+ *        -1 on failure.
+ */
+int hts_parse_format(htsFormat *opt, const char *str);
+
+/*
+ * Tokenise options as (key(=value)?,)*(key(=value)?)?
+ * NB: No provision for ',' appearing in the value!
+ * Add backslashing rules?
+ *
+ * This could be used as part of a general command line option parser or
+ * as a string concatenated onto the file open mode.
+ *
+ * Returns 0 on success
+ *        -1 on failure.
+ */
+int hts_parse_opt_list(htsFormat *opt, const char *str);
+
+extern int hts_verbose;
+
+/*! @abstract Table for converting a nucleotide character to 4-bit encoding.
+The input character may be either an IUPAC ambiguity code, '=' for 0, or
+'0'/'1'/'2'/'3' for a result of 1/2/4/8.  The result is encoded as 1/2/4/8
+for A/C/G/T or combinations of these bits for ambiguous bases.
+*/
+extern const unsigned char seq_nt16_table[256];
+
+/*! @abstract Table for converting a 4-bit encoded nucleotide to an IUPAC
+ambiguity code letter (or '=' when given 0).
+*/
+extern const char seq_nt16_str[];
+
+/*! @abstract Table for converting a 4-bit encoded nucleotide to about 2 bits.
+Returns 0/1/2/3 for 1/2/4/8 (i.e., A/C/G/T), or 4 otherwise (0 or ambiguous).
+*/
+extern const int seq_nt16_int[];
+
+/*!
+  @abstract  Get the htslib version number
+  @return    For released versions, a string like "N.N[.N]"; or git describe
+  output if using a library built within a Git repository.
+*/
+const char *hts_version(void);
+
+/*!
+  @abstract    Determine format by peeking at the start of a file
+  @param fp    File opened for reading, positioned at the beginning
+  @param fmt   Format structure that will be filled out on return
+  @return      0 for success, or negative if an error occurred.
+*/
+int hts_detect_format(struct hFILE *fp, htsFormat *fmt);
+
+/*!
+  @abstract    Get a human-readable description of the file format
+  @param fmt   Format structure holding type, version, compression, etc.
+  @return      Description string, to be freed by the caller after use.
+*/
+char *hts_format_description(const htsFormat *format);
+
+/*!
+  @abstract       Open a SAM/BAM/CRAM/VCF/BCF/etc file
+  @param fn       The file name or "-" for stdin/stdout
+  @param mode     Mode matching / [rwa][bceguxz0-9]* /
+  @discussion
+      With 'r' opens for reading; any further format mode letters are ignored
+      as the format is detected by checking the first few bytes or BGZF blocks
+      of the file.  With 'w' or 'a' opens for writing or appending, with format
+      specifier letters:
+        b  binary format (BAM, BCF, etc) rather than text (SAM, VCF, etc)
+        c  CRAM format
+        g  gzip compressed
+        u  uncompressed
+        z  bgzf compressed
+        [0-9]  zlib compression level
+      and with non-format option letters (for any of 'r'/'w'/'a'):
+        e  close the file on exec(2) (opens with O_CLOEXEC, where supported)
+        x  create the file exclusively (opens with O_EXCL, where supported)
+      Note that there is a distinction between 'u' and '0': the first yields
+      plain uncompressed output whereas the latter outputs uncompressed data
+      wrapped in the zlib format.
+  @example
+      [rw]b  .. compressed BCF, BAM, FAI
+      [rw]bu .. uncompressed BCF
+      [rw]z  .. compressed VCF
+      [rw]   .. uncompressed VCF
+*/
+htsFile *hts_open(const char *fn, const char *mode);
+
+/*!
+  @abstract       Open a SAM/BAM/CRAM/VCF/BCF/etc file
+  @param fn       The file name or "-" for stdin/stdout
+  @param mode     Open mode, as per hts_open()
+  @param fmt      Optional format specific parameters
+  @discussion
+      See hts_open() for description of fn and mode.
+      // TODO Update documentation for s/opts/fmt/
+      Opts contains a format string (sam, bam, cram, vcf, bcf) which will,
+      if defined, override mode.  Opts also contains a linked list of hts_opt
+      structures to apply to the open file handle.  These can contain things
+      like pointers to the reference or information on compression levels,
+      block sizes, etc.
+*/
+htsFile *hts_open_format(const char *fn, const char *mode, const htsFormat *fmt);
+
+/*!
+  @abstract       Open an existing stream as a SAM/BAM/CRAM/VCF/BCF/etc file
+  @param fn       The already-open file handle
+  @param mode     Open mode, as per hts_open()
+*/
+htsFile *hts_hopen(struct hFILE *fp, const char *fn, const char *mode);
+
+/*!
+  @abstract  Close a file handle, flushing buffered data for output streams
+  @param fp  The file handle to be closed
+  @return    0 for success, or negative if an error occurred.
+*/
+int hts_close(htsFile *fp);
+
+/*!
+  @abstract  Returns the file's format information
+  @param fp  The file handle
+  @return    Read-only pointer to the file's htsFormat.
+*/
+const htsFormat *hts_get_format(htsFile *fp);
+
+/*!
+  @ abstract      Returns a string containing the file format extension.
+  @ param format  Format structure containing the file type.
+  @ return        A string ("sam", "bam", etc) or "?" for unknown formats.
+ */
+const char *hts_format_file_extension(const htsFormat *format);
+
+/*!
+  @abstract  Sets a specified CRAM option on the open file handle.
+  @param fp  The file handle open the open file.
+  @param opt The CRAM_OPT_* option.
+  @param ... Optional arguments, dependent on the option used.
+  @return    0 for success, or negative if an error occurred.
+*/
+int hts_set_opt(htsFile *fp, enum hts_fmt_option opt, ...);
+
+int hts_getline(htsFile *fp, int delimiter, kstring_t *str);
+char **hts_readlines(const char *fn, int *_n);
+/*!
+    @abstract       Parse comma-separated list or read list from a file
+    @param list     File name or comma-separated list
+    @param is_file
+    @param _n       Size of the output array (number of items read)
+    @return         NULL on failure or pointer to newly allocated array of
+                    strings
+*/
+char **hts_readlist(const char *fn, int is_file, int *_n);
+
+/*!
+  @abstract  Create extra threads to aid compress/decompression for this file
+  @param fp  The file handle
+  @param n   The number of worker threads to create
+  @return    0 for success, or negative if an error occurred.
+  @notes     THIS THREADING API IS LIKELY TO CHANGE IN FUTURE.
+*/
+int hts_set_threads(htsFile *fp, int n);
+
+/*!
+  @abstract  Set .fai filename for a file opened for reading
+  @return    0 for success, negative on failure
+  @discussion
+      Called before *_hdr_read(), this provides the name of a .fai file
+      used to provide a reference list if the htsFile contains no @SQ headers.
+*/
+int hts_set_fai_filename(htsFile *fp, const char *fn_aux);
+
+/************
+ * Indexing *
+ ************/
+
+/*!
+These HTS_IDX_* macros are used as special tid values for hts_itr_query()/etc,
+producing iterators operating as follows:
+ - HTS_IDX_NOCOOR iterates over unmapped reads sorted at the end of the file
+ - HTS_IDX_START  iterates over the entire file
+ - HTS_IDX_REST   iterates from the current position to the end of the file
+ - HTS_IDX_NONE   always returns "no more alignment records"
+When one of these special tid values is used, beg and end are ignored.
+When REST or NONE is used, idx is also ignored and may be NULL.
+*/
+#define HTS_IDX_NOCOOR (-2)
+#define HTS_IDX_START  (-3)
+#define HTS_IDX_REST   (-4)
+#define HTS_IDX_NONE   (-5)
+
+#define HTS_FMT_CSI 0
+#define HTS_FMT_BAI 1
+#define HTS_FMT_TBI 2
+#define HTS_FMT_CRAI 3
+
+struct __hts_idx_t;
+typedef struct __hts_idx_t hts_idx_t;
+
+typedef struct {
+    uint64_t u, v;
+} hts_pair64_t;
+
+typedef int hts_readrec_func(BGZF *fp, void *data, void *r, int *tid, int *beg, int *end);
+
+typedef struct {
+    uint32_t read_rest:1, finished:1, dummy:29;
+    int tid, beg, end, n_off, i;
+    int curr_tid, curr_beg, curr_end;
+    uint64_t curr_off;
+    hts_pair64_t *off;
+    hts_readrec_func *readrec;
+    struct {
+        int n, m;
+        int *a;
+    } bins;
+} hts_itr_t;
+
+    #define hts_bin_first(l) (((1<<(((l)<<1) + (l))) - 1) / 7)
+    #define hts_bin_parent(l) (((l) - 1) >> 3)
+
+    hts_idx_t *hts_idx_init(int n, int fmt, uint64_t offset0, int min_shift, int n_lvls);
+    void hts_idx_destroy(hts_idx_t *idx);
+    int hts_idx_push(hts_idx_t *idx, int tid, int beg, int end, uint64_t offset, int is_mapped);
+    void hts_idx_finish(hts_idx_t *idx, uint64_t final_offset);
+
+/// Save an index to a file
+/** @param idx  Index to be written
+    @param fn   Input BAM/BCF/etc filename, to which .bai/.csi/etc will be added
+    @param fmt  One of the HTS_FMT_* index formats
+    @return  0 if successful, or negative if an error occurred.
+*/
+int hts_idx_save(const hts_idx_t *idx, const char *fn, int fmt) HTS_RESULT_USED;
+
+/// Save an index to a specific file
+/** @param idx    Index to be written
+    @param fn     Input BAM/BCF/etc filename
+    @param fnidx  Output filename, or NULL to add .bai/.csi/etc to @a fn
+    @param fmt    One of the HTS_FMT_* index formats
+    @return  0 if successful, or negative if an error occurred.
+*/
+int hts_idx_save_as(const hts_idx_t *idx, const char *fn, const char *fnidx, int fmt) HTS_RESULT_USED;
+
+/// Load an index file
+/** @param fn   BAM/BCF/etc filename, to which .bai/.csi/etc will be added or
+                the extension substituted, to search for an existing index file
+    @param fmt  One of the HTS_FMT_* index formats
+    @return  The index, or NULL if an error occurred.
+*/
+hts_idx_t *hts_idx_load(const char *fn, int fmt);
+
+/// Load a specific index file
+/** @param fn     Input BAM/BCF/etc filename
+    @param fnidx  The input index filename
+    @return  The index, or NULL if an error occurred.
+*/
+hts_idx_t *hts_idx_load2(const char *fn, const char *fnidx);
+
+    uint8_t *hts_idx_get_meta(hts_idx_t *idx, int *l_meta);
+    void hts_idx_set_meta(hts_idx_t *idx, int l_meta, uint8_t *meta, int is_copy);
+
+    int hts_idx_get_stat(const hts_idx_t* idx, int tid, uint64_t* mapped, uint64_t* unmapped);
+    uint64_t hts_idx_get_n_no_coor(const hts_idx_t* idx);
+
+
+#define HTS_PARSE_THOUSANDS_SEP 1  ///< Ignore ',' separators within numbers
+
+/// Parse a numeric string
+/** The number may be expressed in scientific notation, and optionally may
+    contain commas in the integer part (before any decimal point or E notation).
+    @param str     String to be parsed
+    @param strend  If non-NULL, set on return to point to the first character
+                   in @a str after those forming the parsed number
+    @param flags   Or'ed-together combination of HTS_PARSE_* flags
+    @return  Converted value of the parsed number.
+
+    When @a strend is NULL, a warning will be printed (if hts_verbose is 2
+    or more) if there are any trailing characters after the number.
+*/
+long long hts_parse_decimal(const char *str, char **strend, int flags);
+
+/// Parse a "CHR:START-END"-style region string
+/** @param str  String to be parsed
+    @param beg  Set on return to the 0-based start of the region
+    @param end  Set on return to the 1-based end of the region
+    @return  Pointer to the colon or '\0' after the reference sequence name,
+             or NULL if @a str could not be parsed.
+*/
+const char *hts_parse_reg(const char *str, int *beg, int *end);
+
+    hts_itr_t *hts_itr_query(const hts_idx_t *idx, int tid, int beg, int end, hts_readrec_func *readrec);
+    void hts_itr_destroy(hts_itr_t *iter);
+
+    typedef int (*hts_name2id_f)(void*, const char*);
+    typedef const char *(*hts_id2name_f)(void*, int);
+    typedef hts_itr_t *hts_itr_query_func(const hts_idx_t *idx, int tid, int beg, int end, hts_readrec_func *readrec);
+
+    hts_itr_t *hts_itr_querys(const hts_idx_t *idx, const char *reg, hts_name2id_f getid, void *hdr, hts_itr_query_func *itr_query, hts_readrec_func *readrec);
+    int hts_itr_next(BGZF *fp, hts_itr_t *iter, void *r, void *data) HTS_RESULT_USED;
+    const char **hts_idx_seqnames(const hts_idx_t *idx, int *n, hts_id2name_f getid, void *hdr); // free only the array, not the values
+
+    /**
+     * hts_file_type() - Convenience function to determine file type
+     * DEPRECATED:  This function has been replaced by hts_detect_format().
+     * It and these FT_* macros will be removed in a future HTSlib release.
+     */
+    #define FT_UNKN   0
+    #define FT_GZ     1
+    #define FT_VCF    2
+    #define FT_VCF_GZ (FT_GZ|FT_VCF)
+    #define FT_BCF    (1<<2)
+    #define FT_BCF_GZ (FT_GZ|FT_BCF)
+    #define FT_STDIN  (1<<3)
+    int hts_file_type(const char *fname);
+
+
+    /**********************
+     * MD5 implementation *
+     **********************/
+
+    struct hts_md5_context;
+    typedef struct hts_md5_context hts_md5_context;
+
+    /*! @abstract   Intialises an MD5 context.
+     *  @discussion
+     *    The expected use is to allocate an hts_md5_context using
+     *    hts_md5_init().  This pointer is then passed into one or more calls
+     *    of hts_md5_update() to compute successive internal portions of the
+     *    MD5 sum, which can then be externalised as a full 16-byte MD5sum
+     *    calculation by calling hts_md5_final().  This can then be turned
+     *    into ASCII via hts_md5_hex().
+     *
+     *    To dealloate any resources created by hts_md5_init() call the
+     *    hts_md5_destroy() function.
+     *
+     *  @return     hts_md5_context pointer on success, NULL otherwise.
+     */
+    hts_md5_context *hts_md5_init(void);
+
+    /*! @abstract Updates the context with the MD5 of the data. */
+    void hts_md5_update(hts_md5_context *ctx, const void *data, unsigned long size);
+
+    /*! @abstract Computes the final 128-bit MD5 hash from the given context */
+    void hts_md5_final(unsigned char *digest, hts_md5_context *ctx);
+
+    /*! @abstract Resets an md5_context to the initial state, as returned
+     *            by hts_md5_init().
+     */
+    void hts_md5_reset(hts_md5_context *ctx);
+
+    /*! @abstract Converts a 128-bit MD5 hash into a 33-byte nul-termninated
+     *            hex string.
+     */
+    void hts_md5_hex(char *hex, const unsigned char *digest);
+
+    /*! @abstract Deallocates any memory allocated by hts_md5_init. */
+    void hts_md5_destroy(hts_md5_context *ctx);
+
+
+static inline int hts_reg2bin(int64_t beg, int64_t end, int min_shift, int n_lvls)
+{
+    int l, s = min_shift, t = ((1<<((n_lvls<<1) + n_lvls)) - 1) / 7;
+    for (--end, l = n_lvls; l > 0; --l, s += 3, t -= 1<<((l<<1)+l))
+        if (beg>>s == end>>s) return t + (beg>>s);
+    return 0;
+}
+
+static inline int hts_bin_bot(int bin, int n_lvls)
+{
+    int l, b;
+    for (l = 0, b = bin; b; ++l, b = hts_bin_parent(b)); // compute the level of bin
+    return (bin - hts_bin_first(l)) << (n_lvls - l) * 3;
+}
+
+/**************
+ * Endianness *
+ **************/
+
+static inline int ed_is_big(void)
+{
+    long one= 1;
+    return !(*((char *)(&one)));
+}
+static inline uint16_t ed_swap_2(uint16_t v)
+{
+    return (uint16_t)(((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8));
+}
+static inline void *ed_swap_2p(void *x)
+{
+    *(uint16_t*)x = ed_swap_2(*(uint16_t*)x);
+    return x;
+}
+static inline uint32_t ed_swap_4(uint32_t v)
+{
+    v = ((v & 0x0000FFFFU) << 16) | (v >> 16);
+    return ((v & 0x00FF00FFU) << 8) | ((v & 0xFF00FF00U) >> 8);
+}
+static inline void *ed_swap_4p(void *x)
+{
+    *(uint32_t*)x = ed_swap_4(*(uint32_t*)x);
+    return x;
+}
+static inline uint64_t ed_swap_8(uint64_t v)
+{
+    v = ((v & 0x00000000FFFFFFFFLLU) << 32) | (v >> 32);
+    v = ((v & 0x0000FFFF0000FFFFLLU) << 16) | ((v & 0xFFFF0000FFFF0000LLU) >> 16);
+    return ((v & 0x00FF00FF00FF00FFLLU) << 8) | ((v & 0xFF00FF00FF00FF00LLU) >> 8);
+}
+static inline void *ed_swap_8p(void *x)
+{
+    *(uint64_t*)x = ed_swap_8(*(uint64_t*)x);
+    return x;
+}
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/htslib/htslib/hts_defs.h b/htslib/htslib/hts_defs.h
new file mode 100644
index 0000000..0a672c6
--- /dev/null
+++ b/htslib/htslib/hts_defs.h
@@ -0,0 +1,72 @@
+/*  hts_defs.h -- Miscellaneous definitions.
+
+    Copyright (C) 2013-2015 Genome Research Ltd.
+
+    Author: John Marshall <jm18 at sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#ifndef HTSLIB_HTS_DEFS_H
+#define HTSLIB_HTS_DEFS_H
+
+#ifdef __clang__
+#ifdef __has_attribute
+#define HTS_COMPILER_HAS(attribute) __has_attribute(attribute)
+#endif
+
+#elif defined __GNUC__
+#define HTS_GCC_AT_LEAST(major, minor) \
+    (__GNUC__ > (major) || (__GNUC__ == (major) && __GNUC_MINOR__ >= (minor)))
+#endif
+
+#ifndef HTS_COMPILER_HAS
+#define HTS_COMPILER_HAS(attribute) 0
+#endif
+#ifndef HTS_GCC_AT_LEAST
+#define HTS_GCC_AT_LEAST(major, minor) 0
+#endif
+
+#if HTS_COMPILER_HAS(__noreturn__) || HTS_GCC_AT_LEAST(3,0)
+#define HTS_NORETURN __attribute__ ((__noreturn__))
+#else
+#define HTS_NORETURN
+#endif
+
+// GCC introduced warn_unused_result in 3.4 but added -Wno-unused-result later
+#if HTS_COMPILER_HAS(__warn_unused_result__) || HTS_GCC_AT_LEAST(4,5)
+#define HTS_RESULT_USED __attribute__ ((__warn_unused_result__))
+#else
+#define HTS_RESULT_USED
+#endif
+
+#if HTS_COMPILER_HAS(__unused__) || HTS_GCC_AT_LEAST(3,0)
+#define HTS_UNUSED __attribute__ ((__unused__))
+#else
+#define HTS_UNUSED
+#endif
+
+#if HTS_COMPILER_HAS(__deprecated__) || HTS_GCC_AT_LEAST(4,5)
+#define HTS_DEPRECATED(message) __attribute__ ((__deprecated__ (message)))
+#elif HTS_GCC_AT_LEAST(3,1)
+#define HTS_DEPRECATED(message) __attribute__ ((__deprecated__))
+#else
+#define HTS_DEPRECATED(message)
+#endif
+
+#endif
diff --git a/htslib/htslib/kbitset.h b/htslib/htslib/kbitset.h
new file mode 100644
index 0000000..22fb34d
--- /dev/null
+++ b/htslib/htslib/kbitset.h
@@ -0,0 +1,160 @@
+/* The MIT License
+
+   Copyright (C) 2015 Genome Research Ltd.
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+
+#ifndef KBITSET_H
+#define KBITSET_H
+
+/* Example of using kbitset_t, which represents a subset of {0,..., N-1},
+   where N is the size specified in kbs_init().
+
+	kbitset_t *bset = kbs_init(100);
+	kbs_insert(bset, 5);
+	kbs_insert(bset, 68);
+	kbs_delete(bset, 37);
+	// ...
+
+	if (kbs_exists(bset, 68)) printf("68 present\n");
+
+	kbitset_iter itr;
+	int i;
+	kbs_start(&itr);
+	while ((i = kbs_next(bset, &itr)) >= 0)
+		printf("%d present\n", i);
+
+	kbs_destroy(bset);
+
+   Example of declaring a kbitset_t-using function in a header file, so that
+   only source files that actually use process() need to include <kbitset.h>:
+
+	struct kbitset_t;
+	void process(struct kbitset_t *bset);
+*/
+
+#include <limits.h>
+#include <stdlib.h>
+#include <string.h>
+
+#define KBS_ELTBITS (CHAR_BIT * sizeof (unsigned long))
+#define KBS_ELT(i)  ((i) / KBS_ELTBITS)
+#define KBS_MASK(i) (1UL << ((i) % KBS_ELTBITS))
+
+typedef struct kbitset_t {
+	size_t n;
+	unsigned long b[1];
+} kbitset_t;
+
+// Initialise a bit set capable of holding ni integers, 0 <= i < ni.
+// The set returned is empty if fill == 0, or all of [0,ni) otherwise.
+static inline kbitset_t *kbs_init2(size_t ni, int fill)
+{
+	size_t n = (ni + KBS_ELTBITS-1) / KBS_ELTBITS;
+	kbitset_t *bs =
+		(kbitset_t *) malloc(sizeof(kbitset_t) + n * sizeof(unsigned long));
+	if (bs == NULL) return NULL;
+	bs->n = n;
+	memset(bs->b, fill? ~0 : 0, n * sizeof (unsigned long));
+	bs->b[n] = ~0UL;
+	return bs;
+}
+
+// Initialise an empty bit set capable of holding ni integers, 0 <= i < ni.
+static inline kbitset_t *kbs_init(size_t ni)
+{
+	return kbs_init2(ni, 0);
+}
+
+// Destroy a bit set.
+static inline void kbs_destroy(kbitset_t *bs)
+{
+	free(bs);
+}
+
+// Reset the bit set to empty.
+static inline void kbs_clear(kbitset_t *bs)
+{
+	memset(bs->b, 0, bs->n * sizeof (unsigned long));
+}
+
+// Reset the bit set to all of [0,ni).
+static inline void kbs_insert_all(kbitset_t *bs)
+{
+	memset(bs->b, ~0, bs->n * sizeof (unsigned long));
+}
+
+// Insert an element into the bit set.
+static inline void kbs_insert(kbitset_t *bs, int i)
+{
+	bs->b[KBS_ELT(i)] |= KBS_MASK(i);
+}
+
+// Remove an element from the bit set.
+static inline void kbs_delete(kbitset_t *bs, int i)
+{
+	bs->b[KBS_ELT(i)] &= ~KBS_MASK(i);
+}
+
+// Test whether the bit set contains the element.
+static inline int kbs_exists(const kbitset_t *bs, int i)
+{
+	return (bs->b[KBS_ELT(i)] & KBS_MASK(i)) != 0;
+}
+
+typedef struct kbitset_iter_t {
+	unsigned long mask;
+	size_t elt;
+	int i;
+} kbitset_iter_t;
+
+// Initialise or reset a bit set iterator.
+static inline void kbs_start(kbitset_iter_t *itr)
+{
+	itr->mask = 1;
+	itr->elt = 0;
+	itr->i = 0;
+}
+
+// Return the next element contained in the bit set, or -1 if there are no more.
+static inline int kbs_next(const kbitset_t *bs, kbitset_iter_t *itr)
+{
+	unsigned long b = bs->b[itr->elt];
+
+	for (;;) {
+		if (itr->mask == 0) {
+			while ((b = bs->b[++itr->elt]) == 0) itr->i += KBS_ELTBITS;
+			if (itr->elt == bs->n) return -1;
+			itr->mask = 1;
+		}
+
+		if (b & itr->mask) break;
+
+		itr->i++;
+		itr->mask <<= 1;
+	}
+
+	itr->mask <<= 1;
+	return itr->i++;
+}
+
+#endif
diff --git a/htslib/htslib/kfunc.h b/htslib/htslib/kfunc.h
new file mode 100644
index 0000000..162c90d
--- /dev/null
+++ b/htslib/htslib/kfunc.h
@@ -0,0 +1,83 @@
+/* The MIT License
+
+   Copyright (C) 2010, 2013 Genome Research Ltd.
+   Copyright (C) 2011 Attractive Chaos <attractor at live.co.uk>
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+
+#ifndef HTSLIB_KFUNC_H
+#define HTSLIB_KFUNC_H
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/* Log gamma function
+ * \log{\Gamma(z)}
+ * AS245, 2nd algorithm, http://lib.stat.cmu.edu/apstat/245
+ */
+double kf_lgamma(double z);
+
+/* complementary error function
+ * \frac{2}{\sqrt{\pi}} \int_x^{\infty} e^{-t^2} dt
+ * AS66, 2nd algorithm, http://lib.stat.cmu.edu/apstat/66
+ */
+double kf_erfc(double x);
+
+/* The following computes regularized incomplete gamma functions.
+ * Formulas are taken from Wiki, with additional input from Numerical
+ * Recipes in C (for modified Lentz's algorithm) and AS245
+ * (http://lib.stat.cmu.edu/apstat/245).
+ *
+ * A good online calculator is available at:
+ *
+ *   http://www.danielsoper.com/statcalc/calc23.aspx
+ *
+ * It calculates upper incomplete gamma function, which equals
+ * kf_gammaq(s,z)*tgamma(s).
+ */
+
+double kf_gammap(double s, double z);
+double kf_gammaq(double s, double z);
+
+/* Regularized incomplete beta function. The method is taken from
+ * Numerical Recipe in C, 2nd edition, section 6.4. The following web
+ * page calculates the incomplete beta function, which equals
+ * kf_betai(a,b,x) * gamma(a) * gamma(b) / gamma(a+b):
+ *
+ *   http://www.danielsoper.com/statcalc/calc36.aspx
+ */
+double kf_betai(double a, double b, double x);
+
+/*
+ *    n11  n12  | n1_
+ *    n21  n22  | n2_
+ *   -----------+----
+ *    n_1  n_2  | n
+ */
+double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/htslib/htslib/khash.h b/htslib/htslib/khash.h
new file mode 100644
index 0000000..06fc7a3
--- /dev/null
+++ b/htslib/htslib/khash.h
@@ -0,0 +1,627 @@
+/* The MIT License
+
+   Copyright (c) 2008, 2009, 2011 by Attractive Chaos <attractor at live.co.uk>
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+
+/*
+  An example:
+
+#include "khash.h"
+KHASH_MAP_INIT_INT(32, char)
+int main() {
+	int ret, is_missing;
+	khiter_t k;
+	khash_t(32) *h = kh_init(32);
+	k = kh_put(32, h, 5, &ret);
+	kh_value(h, k) = 10;
+	k = kh_get(32, h, 10);
+	is_missing = (k == kh_end(h));
+	k = kh_get(32, h, 5);
+	kh_del(32, h, k);
+	for (k = kh_begin(h); k != kh_end(h); ++k)
+		if (kh_exist(h, k)) kh_value(h, k) = 1;
+	kh_destroy(32, h);
+	return 0;
+}
+*/
+
+/*
+  2013-05-02 (0.2.8):
+
+	* Use quadratic probing. When the capacity is power of 2, stepping function
+	  i*(i+1)/2 guarantees to traverse each bucket. It is better than double
+	  hashing on cache performance and is more robust than linear probing.
+
+	  In theory, double hashing should be more robust than quadratic probing.
+	  However, my implementation is probably not for large hash tables, because
+	  the second hash function is closely tied to the first hash function,
+	  which reduce the effectiveness of double hashing.
+
+	Reference: http://research.cs.vt.edu/AVresearch/hashing/quadratic.php
+
+  2011-12-29 (0.2.7):
+
+    * Minor code clean up; no actual effect.
+
+  2011-09-16 (0.2.6):
+
+	* The capacity is a power of 2. This seems to dramatically improve the
+	  speed for simple keys. Thank Zilong Tan for the suggestion. Reference:
+
+	   - http://code.google.com/p/ulib/
+	   - http://nothings.org/computer/judy/
+
+	* Allow to optionally use linear probing which usually has better
+	  performance for random input. Double hashing is still the default as it
+	  is more robust to certain non-random input.
+
+	* Added Wang's integer hash function (not used by default). This hash
+	  function is more robust to certain non-random input.
+
+  2011-02-14 (0.2.5):
+
+    * Allow to declare global functions.
+
+  2009-09-26 (0.2.4):
+
+    * Improve portability
+
+  2008-09-19 (0.2.3):
+
+	* Corrected the example
+	* Improved interfaces
+
+  2008-09-11 (0.2.2):
+
+	* Improved speed a little in kh_put()
+
+  2008-09-10 (0.2.1):
+
+	* Added kh_clear()
+	* Fixed a compiling error
+
+  2008-09-02 (0.2.0):
+
+	* Changed to token concatenation which increases flexibility.
+
+  2008-08-31 (0.1.2):
+
+	* Fixed a bug in kh_get(), which has not been tested previously.
+
+  2008-08-31 (0.1.1):
+
+	* Added destructor
+*/
+
+
+#ifndef __AC_KHASH_H
+#define __AC_KHASH_H
+
+/*!
+  @header
+
+  Generic hash table library.
+ */
+
+#define AC_VERSION_KHASH_H "0.2.8"
+
+#include <stdlib.h>
+#include <string.h>
+#include <limits.h>
+
+/* compiler specific configuration */
+
+#if UINT_MAX == 0xffffffffu
+typedef unsigned int khint32_t;
+#elif ULONG_MAX == 0xffffffffu
+typedef unsigned long khint32_t;
+#endif
+
+#if ULONG_MAX == ULLONG_MAX
+typedef unsigned long khint64_t;
+#else
+typedef unsigned long long khint64_t;
+#endif
+
+#ifndef kh_inline
+#ifdef _MSC_VER
+#define kh_inline __inline
+#else
+#define kh_inline inline
+#endif
+#endif /* kh_inline */
+
+#ifndef klib_unused
+#if (defined __clang__ && __clang_major__ >= 3) || (defined __GNUC__ && __GNUC__ >= 3)
+#define klib_unused __attribute__ ((__unused__))
+#else
+#define klib_unused
+#endif
+#endif /* klib_unused */
+
+typedef khint32_t khint_t;
+typedef khint_t khiter_t;
+
+#define __ac_isempty(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&2)
+#define __ac_isdel(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&1)
+#define __ac_iseither(flag, i) ((flag[i>>4]>>((i&0xfU)<<1))&3)
+#define __ac_set_isdel_false(flag, i) (flag[i>>4]&=~(1ul<<((i&0xfU)<<1)))
+#define __ac_set_isempty_false(flag, i) (flag[i>>4]&=~(2ul<<((i&0xfU)<<1)))
+#define __ac_set_isboth_false(flag, i) (flag[i>>4]&=~(3ul<<((i&0xfU)<<1)))
+#define __ac_set_isdel_true(flag, i) (flag[i>>4]|=1ul<<((i&0xfU)<<1))
+
+#define __ac_fsize(m) ((m) < 16? 1 : (m)>>4)
+
+#ifndef kroundup32
+#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
+#endif
+
+#ifndef kcalloc
+#define kcalloc(N,Z) calloc(N,Z)
+#endif
+#ifndef kmalloc
+#define kmalloc(Z) malloc(Z)
+#endif
+#ifndef krealloc
+#define krealloc(P,Z) realloc(P,Z)
+#endif
+#ifndef kfree
+#define kfree(P) free(P)
+#endif
+
+static const double __ac_HASH_UPPER = 0.77;
+
+#define __KHASH_TYPE(name, khkey_t, khval_t) \
+	typedef struct kh_##name##_s { \
+		khint_t n_buckets, size, n_occupied, upper_bound; \
+		khint32_t *flags; \
+		khkey_t *keys; \
+		khval_t *vals; \
+	} kh_##name##_t;
+
+#define __KHASH_PROTOTYPES(name, khkey_t, khval_t)	 					\
+	extern kh_##name##_t *kh_init_##name(void);							\
+	extern void kh_destroy_##name(kh_##name##_t *h);					\
+	extern void kh_clear_##name(kh_##name##_t *h);						\
+	extern khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key); 	\
+	extern int kh_resize_##name(kh_##name##_t *h, khint_t new_n_buckets); \
+	extern khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret); \
+	extern void kh_del_##name(kh_##name##_t *h, khint_t x);
+
+#define __KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) \
+	SCOPE kh_##name##_t *kh_init_##name(void) {							\
+		return (kh_##name##_t*)kcalloc(1, sizeof(kh_##name##_t));		\
+	}																	\
+	SCOPE void kh_destroy_##name(kh_##name##_t *h)						\
+	{																	\
+		if (h) {														\
+			kfree((void *)h->keys); kfree(h->flags);					\
+			kfree((void *)h->vals);										\
+			kfree(h);													\
+		}																\
+	}																	\
+	SCOPE void kh_clear_##name(kh_##name##_t *h)						\
+	{																	\
+		if (h && h->flags) {											\
+			memset(h->flags, 0xaa, __ac_fsize(h->n_buckets) * sizeof(khint32_t)); \
+			h->size = h->n_occupied = 0;								\
+		}																\
+	}																	\
+	SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) 	\
+	{																	\
+		if (h->n_buckets) {												\
+			khint_t k, i, last, mask, step = 0; \
+			mask = h->n_buckets - 1;									\
+			k = __hash_func(key); i = k & mask;							\
+			last = i; \
+			while (!__ac_isempty(h->flags, i) && (__ac_isdel(h->flags, i) || !__hash_equal(h->keys[i], key))) { \
+				i = (i + (++step)) & mask; \
+				if (i == last) return h->n_buckets;						\
+			}															\
+			return __ac_iseither(h->flags, i)? h->n_buckets : i;		\
+		} else return 0;												\
+	}																	\
+	SCOPE int kh_resize_##name(kh_##name##_t *h, khint_t new_n_buckets) \
+	{ /* This function uses 0.25*n_buckets bytes of working space instead of [sizeof(key_t+val_t)+.25]*n_buckets. */ \
+		khint32_t *new_flags = 0;										\
+		khint_t j = 1;													\
+		{																\
+			kroundup32(new_n_buckets); 									\
+			if (new_n_buckets < 4) new_n_buckets = 4;					\
+			if (h->size >= (khint_t)(new_n_buckets * __ac_HASH_UPPER + 0.5)) j = 0;	/* requested size is too small */ \
+			else { /* hash table size to be changed (shrink or expand); rehash */ \
+				new_flags = (khint32_t*)kmalloc(__ac_fsize(new_n_buckets) * sizeof(khint32_t));	\
+				if (!new_flags) return -1;								\
+				memset(new_flags, 0xaa, __ac_fsize(new_n_buckets) * sizeof(khint32_t)); \
+				if (h->n_buckets < new_n_buckets) {	/* expand */		\
+					khkey_t *new_keys = (khkey_t*)krealloc((void *)h->keys, new_n_buckets * sizeof(khkey_t)); \
+					if (!new_keys) { kfree(new_flags); return -1; }		\
+					h->keys = new_keys;									\
+					if (kh_is_map) {									\
+						khval_t *new_vals = (khval_t*)krealloc((void *)h->vals, new_n_buckets * sizeof(khval_t)); \
+						if (!new_vals) { kfree(new_flags); return -1; }	\
+						h->vals = new_vals;								\
+					}													\
+				} /* otherwise shrink */								\
+			}															\
+		}																\
+		if (j) { /* rehashing is needed */								\
+			for (j = 0; j != h->n_buckets; ++j) {						\
+				if (__ac_iseither(h->flags, j) == 0) {					\
+					khkey_t key = h->keys[j];							\
+					khval_t val;										\
+					khint_t new_mask;									\
+					new_mask = new_n_buckets - 1; 						\
+					if (kh_is_map) val = h->vals[j];					\
+					__ac_set_isdel_true(h->flags, j);					\
+					while (1) { /* kick-out process; sort of like in Cuckoo hashing */ \
+						khint_t k, i, step = 0; \
+						k = __hash_func(key);							\
+						i = k & new_mask;								\
+						while (!__ac_isempty(new_flags, i)) i = (i + (++step)) & new_mask; \
+						__ac_set_isempty_false(new_flags, i);			\
+						if (i < h->n_buckets && __ac_iseither(h->flags, i) == 0) { /* kick out the existing element */ \
+							{ khkey_t tmp = h->keys[i]; h->keys[i] = key; key = tmp; } \
+							if (kh_is_map) { khval_t tmp = h->vals[i]; h->vals[i] = val; val = tmp; } \
+							__ac_set_isdel_true(h->flags, i); /* mark it as deleted in the old hash table */ \
+						} else { /* write the element and jump out of the loop */ \
+							h->keys[i] = key;							\
+							if (kh_is_map) h->vals[i] = val;			\
+							break;										\
+						}												\
+					}													\
+				}														\
+			}															\
+			if (h->n_buckets > new_n_buckets) { /* shrink the hash table */ \
+				h->keys = (khkey_t*)krealloc((void *)h->keys, new_n_buckets * sizeof(khkey_t)); \
+				if (kh_is_map) h->vals = (khval_t*)krealloc((void *)h->vals, new_n_buckets * sizeof(khval_t)); \
+			}															\
+			kfree(h->flags); /* free the working space */				\
+			h->flags = new_flags;										\
+			h->n_buckets = new_n_buckets;								\
+			h->n_occupied = h->size;									\
+			h->upper_bound = (khint_t)(h->n_buckets * __ac_HASH_UPPER + 0.5); \
+		}																\
+		return 0;														\
+	}																	\
+	SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \
+	{																	\
+		khint_t x;														\
+		if (h->n_occupied >= h->upper_bound) { /* update the hash table */ \
+			if (h->n_buckets > (h->size<<1)) {							\
+				if (kh_resize_##name(h, h->n_buckets - 1) < 0) { /* clear "deleted" elements */ \
+					*ret = -1; return h->n_buckets;						\
+				}														\
+			} else if (kh_resize_##name(h, h->n_buckets + 1) < 0) { /* expand the hash table */ \
+				*ret = -1; return h->n_buckets;							\
+			}															\
+		} /* TODO: to implement automatically shrinking; resize() already support shrinking */ \
+		{																\
+			khint_t k, i, site, last, mask = h->n_buckets - 1, step = 0; \
+			x = site = h->n_buckets; k = __hash_func(key); i = k & mask; \
+			if (__ac_isempty(h->flags, i)) x = i; /* for speed up */	\
+			else {														\
+				last = i; \
+				while (!__ac_isempty(h->flags, i) && (__ac_isdel(h->flags, i) || !__hash_equal(h->keys[i], key))) { \
+					if (__ac_isdel(h->flags, i)) site = i;				\
+					i = (i + (++step)) & mask; \
+					if (i == last) { x = site; break; }					\
+				}														\
+				if (x == h->n_buckets) {								\
+					if (__ac_isempty(h->flags, i) && site != h->n_buckets) x = site; \
+					else x = i;											\
+				}														\
+			}															\
+		}																\
+		if (__ac_isempty(h->flags, x)) { /* not present at all */		\
+			h->keys[x] = key;											\
+			__ac_set_isboth_false(h->flags, x);							\
+			++h->size; ++h->n_occupied;									\
+			*ret = 1;													\
+		} else if (__ac_isdel(h->flags, x)) { /* deleted */				\
+			h->keys[x] = key;											\
+			__ac_set_isboth_false(h->flags, x);							\
+			++h->size;													\
+			*ret = 2;													\
+		} else *ret = 0; /* Don't touch h->keys[x] if present and not deleted */ \
+		return x;														\
+	}																	\
+	SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x)				\
+	{																	\
+		if (x != h->n_buckets && !__ac_iseither(h->flags, x)) {			\
+			__ac_set_isdel_true(h->flags, x);							\
+			--h->size;													\
+		}																\
+	}
+
+#define KHASH_DECLARE(name, khkey_t, khval_t)		 					\
+	__KHASH_TYPE(name, khkey_t, khval_t) 								\
+	__KHASH_PROTOTYPES(name, khkey_t, khval_t)
+
+#define KHASH_INIT2(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) \
+	__KHASH_TYPE(name, khkey_t, khval_t) 								\
+	__KHASH_IMPL(name, SCOPE, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
+
+#define KHASH_INIT(name, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) \
+	KHASH_INIT2(name, static kh_inline klib_unused, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal)
+
+/* --- BEGIN OF HASH FUNCTIONS --- */
+
+/*! @function
+  @abstract     Integer hash function
+  @param  key   The integer [khint32_t]
+  @return       The hash value [khint_t]
+ */
+#define kh_int_hash_func(key) (khint32_t)(key)
+/*! @function
+  @abstract     Integer comparison function
+ */
+#define kh_int_hash_equal(a, b) ((a) == (b))
+/*! @function
+  @abstract     64-bit integer hash function
+  @param  key   The integer [khint64_t]
+  @return       The hash value [khint_t]
+ */
+#define kh_int64_hash_func(key) (khint32_t)((key)>>33^(key)^(key)<<11)
+/*! @function
+  @abstract     64-bit integer comparison function
+ */
+#define kh_int64_hash_equal(a, b) ((a) == (b))
+/*! @function
+  @abstract     const char* hash function
+  @param  s     Pointer to a null terminated string
+  @return       The hash value
+ */
+static kh_inline khint_t __ac_X31_hash_string(const char *s)
+{
+	khint_t h = (khint_t)*s;
+	if (h) for (++s ; *s; ++s) h = (h << 5) - h + (khint_t)*s;
+	return h;
+}
+/*! @function
+  @abstract     Another interface to const char* hash function
+  @param  key   Pointer to a null terminated string [const char*]
+  @return       The hash value [khint_t]
+ */
+#define kh_str_hash_func(key) __ac_X31_hash_string(key)
+/*! @function
+  @abstract     Const char* comparison function
+ */
+#define kh_str_hash_equal(a, b) (strcmp(a, b) == 0)
+
+static kh_inline khint_t __ac_Wang_hash(khint_t key)
+{
+    key += ~(key << 15);
+    key ^=  (key >> 10);
+    key +=  (key << 3);
+    key ^=  (key >> 6);
+    key += ~(key << 11);
+    key ^=  (key >> 16);
+    return key;
+}
+#define kh_int_hash_func2(k) __ac_Wang_hash((khint_t)key)
+
+/* --- END OF HASH FUNCTIONS --- */
+
+/* Other convenient macros... */
+
+/*!
+  @abstract Type of the hash table.
+  @param  name  Name of the hash table [symbol]
+ */
+#define khash_t(name) kh_##name##_t
+
+/*! @function
+  @abstract     Initiate a hash table.
+  @param  name  Name of the hash table [symbol]
+  @return       Pointer to the hash table [khash_t(name)*]
+ */
+#define kh_init(name) kh_init_##name()
+
+/*! @function
+  @abstract     Destroy a hash table.
+  @param  name  Name of the hash table [symbol]
+  @param  h     Pointer to the hash table [khash_t(name)*]
+ */
+#define kh_destroy(name, h) kh_destroy_##name(h)
+
+/*! @function
+  @abstract     Reset a hash table without deallocating memory.
+  @param  name  Name of the hash table [symbol]
+  @param  h     Pointer to the hash table [khash_t(name)*]
+ */
+#define kh_clear(name, h) kh_clear_##name(h)
+
+/*! @function
+  @abstract     Resize a hash table.
+  @param  name  Name of the hash table [symbol]
+  @param  h     Pointer to the hash table [khash_t(name)*]
+  @param  s     New size [khint_t]
+ */
+#define kh_resize(name, h, s) kh_resize_##name(h, s)
+
+/*! @function
+  @abstract     Insert a key to the hash table.
+  @param  name  Name of the hash table [symbol]
+  @param  h     Pointer to the hash table [khash_t(name)*]
+  @param  k     Key [type of keys]
+  @param  r     Extra return code: -1 if the operation failed;
+                0 if the key is present in the hash table;
+                1 if the bucket is empty (never used); 2 if the element in
+				the bucket has been deleted [int*]
+  @return       Iterator to the inserted element [khint_t]
+ */
+#define kh_put(name, h, k, r) kh_put_##name(h, k, r)
+
+/*! @function
+  @abstract     Retrieve a key from the hash table.
+  @param  name  Name of the hash table [symbol]
+  @param  h     Pointer to the hash table [khash_t(name)*]
+  @param  k     Key [type of keys]
+  @return       Iterator to the found element, or kh_end(h) if the element is absent [khint_t]
+ */
+#define kh_get(name, h, k) kh_get_##name(h, k)
+
+/*! @function
+  @abstract     Remove a key from the hash table.
+  @param  name  Name of the hash table [symbol]
+  @param  h     Pointer to the hash table [khash_t(name)*]
+  @param  k     Iterator to the element to be deleted [khint_t]
+ */
+#define kh_del(name, h, k) kh_del_##name(h, k)
+
+/*! @function
+  @abstract     Test whether a bucket contains data.
+  @param  h     Pointer to the hash table [khash_t(name)*]
+  @param  x     Iterator to the bucket [khint_t]
+  @return       1 if containing data; 0 otherwise [int]
+ */
+#define kh_exist(h, x) (!__ac_iseither((h)->flags, (x)))
+
+/*! @function
+  @abstract     Get key given an iterator
+  @param  h     Pointer to the hash table [khash_t(name)*]
+  @param  x     Iterator to the bucket [khint_t]
+  @return       Key [type of keys]
+ */
+#define kh_key(h, x) ((h)->keys[x])
+
+/*! @function
+  @abstract     Get value given an iterator
+  @param  h     Pointer to the hash table [khash_t(name)*]
+  @param  x     Iterator to the bucket [khint_t]
+  @return       Value [type of values]
+  @discussion   For hash sets, calling this results in segfault.
+ */
+#define kh_val(h, x) ((h)->vals[x])
+
+/*! @function
+  @abstract     Alias of kh_val()
+ */
+#define kh_value(h, x) ((h)->vals[x])
+
+/*! @function
+  @abstract     Get the start iterator
+  @param  h     Pointer to the hash table [khash_t(name)*]
+  @return       The start iterator [khint_t]
+ */
+#define kh_begin(h) (khint_t)(0)
+
+/*! @function
+  @abstract     Get the end iterator
+  @param  h     Pointer to the hash table [khash_t(name)*]
+  @return       The end iterator [khint_t]
+ */
+#define kh_end(h) ((h)->n_buckets)
+
+/*! @function
+  @abstract     Get the number of elements in the hash table
+  @param  h     Pointer to the hash table [khash_t(name)*]
+  @return       Number of elements in the hash table [khint_t]
+ */
+#define kh_size(h) ((h)->size)
+
+/*! @function
+  @abstract     Get the number of buckets in the hash table
+  @param  h     Pointer to the hash table [khash_t(name)*]
+  @return       Number of buckets in the hash table [khint_t]
+ */
+#define kh_n_buckets(h) ((h)->n_buckets)
+
+/*! @function
+  @abstract     Iterate over the entries in the hash table
+  @param  h     Pointer to the hash table [khash_t(name)*]
+  @param  kvar  Variable to which key will be assigned
+  @param  vvar  Variable to which value will be assigned
+  @param  code  Block of code to execute
+ */
+#define kh_foreach(h, kvar, vvar, code) { khint_t __i;		\
+	for (__i = kh_begin(h); __i != kh_end(h); ++__i) {		\
+		if (!kh_exist(h,__i)) continue;						\
+		(kvar) = kh_key(h,__i);								\
+		(vvar) = kh_val(h,__i);								\
+		code;												\
+	} }
+
+/*! @function
+  @abstract     Iterate over the values in the hash table
+  @param  h     Pointer to the hash table [khash_t(name)*]
+  @param  vvar  Variable to which value will be assigned
+  @param  code  Block of code to execute
+ */
+#define kh_foreach_value(h, vvar, code) { khint_t __i;		\
+	for (__i = kh_begin(h); __i != kh_end(h); ++__i) {		\
+		if (!kh_exist(h,__i)) continue;						\
+		(vvar) = kh_val(h,__i);								\
+		code;												\
+	} }
+
+/* More conenient interfaces */
+
+/*! @function
+  @abstract     Instantiate a hash set containing integer keys
+  @param  name  Name of the hash table [symbol]
+ */
+#define KHASH_SET_INIT_INT(name)										\
+	KHASH_INIT(name, khint32_t, char, 0, kh_int_hash_func, kh_int_hash_equal)
+
+/*! @function
+  @abstract     Instantiate a hash map containing integer keys
+  @param  name  Name of the hash table [symbol]
+  @param  khval_t  Type of values [type]
+ */
+#define KHASH_MAP_INIT_INT(name, khval_t)								\
+	KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal)
+
+/*! @function
+  @abstract     Instantiate a hash map containing 64-bit integer keys
+  @param  name  Name of the hash table [symbol]
+ */
+#define KHASH_SET_INIT_INT64(name)										\
+	KHASH_INIT(name, khint64_t, char, 0, kh_int64_hash_func, kh_int64_hash_equal)
+
+/*! @function
+  @abstract     Instantiate a hash map containing 64-bit integer keys
+  @param  name  Name of the hash table [symbol]
+  @param  khval_t  Type of values [type]
+ */
+#define KHASH_MAP_INIT_INT64(name, khval_t)								\
+	KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal)
+
+typedef const char *kh_cstr_t;
+/*! @function
+  @abstract     Instantiate a hash map containing const char* keys
+  @param  name  Name of the hash table [symbol]
+ */
+#define KHASH_SET_INIT_STR(name)										\
+	KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal)
+
+/*! @function
+  @abstract     Instantiate a hash map containing const char* keys
+  @param  name  Name of the hash table [symbol]
+  @param  khval_t  Type of values [type]
+ */
+#define KHASH_MAP_INIT_STR(name, khval_t)								\
+	KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal)
+
+#endif /* __AC_KHASH_H */
diff --git a/htslib/htslib/khash_str2int.h b/htslib/htslib/khash_str2int.h
new file mode 100644
index 0000000..4bbc100
--- /dev/null
+++ b/htslib/htslib/khash_str2int.h
@@ -0,0 +1,133 @@
+/*  khash_str2int.h -- C-string to integer hash table.
+
+    Copyright (C) 2013 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3 at sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#ifndef HTSLIB_KHASH_STR2INT_H
+#define HTSLIB_KHASH_STR2INT_H
+
+#include <htslib/khash.h>
+
+KHASH_MAP_INIT_STR(str2int, int)
+
+/*
+ *  Wrappers for khash dictionaries used by mpileup.
+ */
+
+static inline void *khash_str2int_init(void)
+{
+    return kh_init(str2int);
+}
+
+/*
+ *  Destroy the hash structure, but not the keys
+ */
+static inline void khash_str2int_destroy(void *_hash)
+{
+    khash_t(str2int) *hash = (khash_t(str2int)*)_hash;
+    if (hash) kh_destroy(str2int, hash); // Note that strings are not freed.
+}
+
+/*
+ *  Destroys both the hash structure and the keys
+ */
+static inline void khash_str2int_destroy_free(void *_hash)
+{
+    khash_t(str2int) *hash = (khash_t(str2int)*)_hash;
+    khint_t k;
+    if (hash == 0) return;
+    for (k = 0; k < kh_end(hash); ++k)
+        if (kh_exist(hash, k)) free((char*)kh_key(hash, k));
+    kh_destroy(str2int, hash);
+}
+
+/*
+ *  Returns 1 if key exists or 0 if not
+ */
+static inline int khash_str2int_has_key(void *_hash, const char *str)
+{
+    khash_t(str2int) *hash = (khash_t(str2int)*)_hash;
+    khint_t k = kh_get(str2int, hash, str);
+    if ( k == kh_end(hash) ) return 0;
+    return 1;
+}
+
+/*
+ *  Returns 0 on success and -1 when the key is not present. On success,
+ *  *value is set, unless NULL is passed.
+ */
+static inline int khash_str2int_get(void *_hash, const char *str, int *value)
+{
+    khash_t(str2int) *hash = (khash_t(str2int)*)_hash;
+    khint_t k;
+    if ( !hash ) return -1;
+    k = kh_get(str2int, hash, str);
+    if ( k == kh_end(hash) ) return -1;
+    if ( !value ) return 0;
+    *value = kh_val(hash, k);
+    return 0;
+}
+
+/*
+ *  Add a new string to the dictionary, auto-incrementing the value.
+ *  On success returns the newly inserted integer id, on error -1
+ *  is returned. Note that the key must continue to exist throughout
+ *  the whole life of _hash.
+ */
+static inline int khash_str2int_inc(void *_hash, const char *str)
+{
+    khint_t k;
+    int ret;
+    khash_t(str2int) *hash = (khash_t(str2int)*)_hash;
+    if ( !hash ) return -1;
+    k = kh_put(str2int, hash, str, &ret);
+    if (ret == 0) return kh_val(hash, k);
+    kh_val(hash, k) = kh_size(hash) - 1;
+    return kh_val(hash, k);
+}
+
+/*
+ *  Set a new key,value pair. On success returns the bin index, on
+ *  error -1 is returned. Note that the key must contnue to exist
+ *  throughout the whole life of _hash.
+ */
+static inline int khash_str2int_set(void *_hash, const char *str, int value)
+{
+    khint_t k;
+    int ret;
+    khash_t(str2int) *hash = (khash_t(str2int)*)_hash;
+    if ( !hash ) return -1;
+    k = kh_put(str2int, hash, str, &ret);
+    kh_val(hash,k) = value;
+    return k;
+}
+
+/*
+ *  Return the number of keys in the hash table.
+ */
+static inline int khash_str2int_size(void *_hash)
+{
+    khash_t(str2int) *hash = (khash_t(str2int)*)_hash;
+    return kh_size(hash);
+}
+
+#endif
diff --git a/htslib/htslib/klist.h b/htslib/htslib/klist.h
new file mode 100644
index 0000000..adc3db1
--- /dev/null
+++ b/htslib/htslib/klist.h
@@ -0,0 +1,135 @@
+/* The MIT License
+
+   Copyright (c) 2008-2009, by Attractive Chaos <attractor at live.co.uk>
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+
+#ifndef _AC_KLIST_H
+#define _AC_KLIST_H
+
+#include <stdlib.h>
+
+#ifndef klib_unused
+#if (defined __clang__ && __clang_major__ >= 3) || (defined __GNUC__ && __GNUC__ >= 3)
+#define klib_unused __attribute__ ((__unused__))
+#else
+#define klib_unused
+#endif
+#endif /* klib_unused */
+
+#define KMEMPOOL_INIT2(SCOPE, name, kmptype_t, kmpfree_f)				\
+	typedef struct {													\
+		size_t cnt, n, max;												\
+		kmptype_t **buf;												\
+	} kmp_##name##_t;													\
+	SCOPE kmp_##name##_t *kmp_init_##name(void) {						\
+		return calloc(1, sizeof(kmp_##name##_t));						\
+	}																	\
+	SCOPE void kmp_destroy_##name(kmp_##name##_t *mp) {					\
+		size_t k;														\
+		for (k = 0; k < mp->n; ++k) {									\
+			kmpfree_f(mp->buf[k]); free(mp->buf[k]);					\
+		}																\
+		free(mp->buf); free(mp);										\
+	}																	\
+	SCOPE kmptype_t *kmp_alloc_##name(kmp_##name##_t *mp) {				\
+		++mp->cnt;														\
+		if (mp->n == 0) return calloc(1, sizeof(kmptype_t));			\
+		return mp->buf[--mp->n];										\
+	}																	\
+	SCOPE void kmp_free_##name(kmp_##name##_t *mp, kmptype_t *p) {		\
+		--mp->cnt;														\
+		if (mp->n == mp->max) {											\
+			mp->max = mp->max? mp->max<<1 : 16;							\
+			mp->buf = realloc(mp->buf, sizeof(kmptype_t *) * mp->max);	\
+		}																\
+		mp->buf[mp->n++] = p;											\
+	}
+
+#define KMEMPOOL_INIT(name, kmptype_t, kmpfree_f)						\
+	KMEMPOOL_INIT2(static inline klib_unused, name, kmptype_t, kmpfree_f)
+
+#define kmempool_t(name) kmp_##name##_t
+#define kmp_init(name) kmp_init_##name()
+#define kmp_destroy(name, mp) kmp_destroy_##name(mp)
+#define kmp_alloc(name, mp) kmp_alloc_##name(mp)
+#define kmp_free(name, mp, p) kmp_free_##name(mp, p)
+
+#define KLIST_INIT2(SCOPE, name, kltype_t, kmpfree_t)					\
+	struct __kl1_##name {												\
+		kltype_t data;													\
+		struct __kl1_##name *next;										\
+	};																	\
+	typedef struct __kl1_##name kl1_##name;								\
+	KMEMPOOL_INIT2(SCOPE, name, kl1_##name, kmpfree_t)					\
+	typedef struct {													\
+		kl1_##name *head, *tail;										\
+		kmp_##name##_t *mp;												\
+		size_t size;													\
+	} kl_##name##_t;													\
+	SCOPE kl_##name##_t *kl_init_##name(void) {							\
+		kl_##name##_t *kl = calloc(1, sizeof(kl_##name##_t));			\
+		kl->mp = kmp_init(name);										\
+		kl->head = kl->tail = kmp_alloc(name, kl->mp);					\
+		kl->head->next = 0;												\
+		return kl;														\
+	}																	\
+	SCOPE void kl_destroy_##name(kl_##name##_t *kl) {					\
+		kl1_##name *p;													\
+		for (p = kl->head; p != kl->tail; p = p->next)					\
+			kmp_free(name, kl->mp, p);									\
+		kmp_free(name, kl->mp, p);										\
+		kmp_destroy(name, kl->mp);										\
+		free(kl);														\
+	}																	\
+	SCOPE kltype_t *kl_pushp_##name(kl_##name##_t *kl) {				\
+		kl1_##name *q, *p = kmp_alloc(name, kl->mp);					\
+		q = kl->tail; p->next = 0; kl->tail->next = p; kl->tail = p;	\
+		++kl->size;														\
+		return &q->data;												\
+	}																	\
+	SCOPE int kl_shift_##name(kl_##name##_t *kl, kltype_t *d) {			\
+		kl1_##name *p;													\
+		if (kl->head->next == 0) return -1;								\
+		--kl->size;														\
+		p = kl->head; kl->head = kl->head->next;						\
+		if (d) *d = p->data;											\
+		kmp_free(name, kl->mp, p);										\
+		return 0;														\
+	}
+
+#define KLIST_INIT(name, kltype_t, kmpfree_t)							\
+	KLIST_INIT2(static inline klib_unused, name, kltype_t, kmpfree_t)
+
+#define kliter_t(name) kl1_##name
+#define klist_t(name) kl_##name##_t
+#define kl_val(iter) ((iter)->data)
+#define kl_next(iter) ((iter)->next)
+#define kl_begin(kl) ((kl)->head)
+#define kl_end(kl) ((kl)->tail)
+
+#define kl_init(name) kl_init_##name()
+#define kl_destroy(name, kl) kl_destroy_##name(kl)
+#define kl_pushp(name, kl) kl_pushp_##name(kl)
+#define kl_shift(name, kl, d) kl_shift_##name(kl, d)
+
+#endif
diff --git a/htslib/htslib/knetfile.h b/htslib/htslib/knetfile.h
new file mode 100644
index 0000000..b200a51
--- /dev/null
+++ b/htslib/htslib/knetfile.h
@@ -0,0 +1,101 @@
+/* The MIT License
+
+   Copyright (c) 2008 by Genome Research Ltd (GRL).
+                 2010 by Attractive Chaos <attractor at live.co.uk>
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+
+#ifndef KNETFILE_H
+#define KNETFILE_H
+
+#include <stdint.h>
+#include <fcntl.h>
+
+#ifndef _WIN32
+#define netread(fd, ptr, len) read(fd, ptr, len)
+#define netwrite(fd, ptr, len) write(fd, ptr, len)
+#define netclose(fd) close(fd)
+#else
+#include <winsock2.h>
+#define netread(fd, ptr, len) recv(fd, ptr, len, 0)
+#define netwrite(fd, ptr, len) send(fd, ptr, len, 0)
+#define netclose(fd) closesocket(fd)
+#endif
+
+// FIXME: currently I/O is unbuffered
+
+#define KNF_TYPE_LOCAL 1
+#define KNF_TYPE_FTP   2
+#define KNF_TYPE_HTTP  3
+
+typedef struct knetFile_s {
+	int type, fd;
+	int64_t offset;
+	char *host, *port;
+
+	// the following are for FTP only
+	int ctrl_fd, pasv_ip[4], pasv_port, max_response, no_reconnect, is_ready;
+	char *response, *retr, *size_cmd;
+	int64_t seek_offset; // for lazy seek
+    int64_t file_size;
+
+	// the following are for HTTP only
+	char *path, *http_host;
+} knetFile;
+
+#define knet_tell(fp) ((fp)->offset)
+#define knet_fileno(fp) ((fp)->fd)
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+#ifdef _WIN32
+	int knet_win32_init();
+	void knet_win32_destroy();
+#endif
+
+	knetFile *knet_open(const char *fn, const char *mode);
+
+	/* 
+	   This only works with local files.
+	 */
+	knetFile *knet_dopen(int fd, const char *mode);
+
+	/*
+	  If ->is_ready==0, this routine updates ->fd; otherwise, it simply
+	  reads from ->fd.
+	 */
+	ssize_t knet_read(knetFile *fp, void *buf, size_t len);
+
+	/*
+	  This routine only sets ->offset and ->is_ready=0. It does not
+	  communicate with the FTP server.
+	 */
+	off_t knet_seek(knetFile *fp, off_t off, int whence);
+	int knet_close(knetFile *fp);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/htslib/htslib/kseq.h b/htslib/htslib/kseq.h
new file mode 100644
index 0000000..e1a3eaa
--- /dev/null
+++ b/htslib/htslib/kseq.h
@@ -0,0 +1,253 @@
+/* The MIT License
+
+   Copyright (c) 2008, 2009, 2011 Attractive Chaos <attractor at live.co.uk>
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+
+/* Last Modified: 05MAR2012 */
+
+#ifndef AC_KSEQ_H
+#define AC_KSEQ_H
+
+#include <ctype.h>
+#include <string.h>
+#include <stdlib.h>
+
+#define KS_SEP_SPACE 0 // isspace(): \t, \n, \v, \f, \r
+#define KS_SEP_TAB   1 // isspace() && !' '
+#define KS_SEP_LINE  2 // line separator: "\n" (Unix) or "\r\n" (Windows)
+#define KS_SEP_MAX   2
+
+#define __KS_TYPE(type_t) \
+	typedef struct __kstream_t { \
+		int begin, end; \
+		int is_eof:2, bufsize:30; \
+        uint64_t seek_pos; \
+		type_t f; \
+		unsigned char *buf; \
+	} kstream_t;
+
+#define ks_eof(ks) ((ks)->is_eof && (ks)->begin >= (ks)->end)
+#define ks_rewind(ks) ((ks)->is_eof = (ks)->begin = (ks)->end = 0)
+
+#define __KS_BASIC(SCOPE, type_t, __bufsize) \
+	SCOPE kstream_t *ks_init(type_t f) \
+	{ \
+		kstream_t *ks = (kstream_t*)calloc(1, sizeof(kstream_t)); \
+		ks->f = f; ks->bufsize = __bufsize; \
+		ks->buf = (unsigned char*)malloc(__bufsize); \
+		return ks; \
+	} \
+	SCOPE void ks_destroy(kstream_t *ks) \
+	{ \
+		if (!ks) return; \
+		free(ks->buf); \
+		free(ks); \
+	}
+
+#define __KS_INLINED(__read) \
+	static inline int ks_getc(kstream_t *ks) \
+	{ \
+		if (ks->is_eof && ks->begin >= ks->end) return -1; \
+		if (ks->begin >= ks->end) { \
+			ks->begin = 0; \
+			ks->end = __read(ks->f, ks->buf, ks->bufsize); \
+			if (ks->end == 0) { ks->is_eof = 1; return -1; } \
+		} \
+        ks->seek_pos++; \
+		return (int)ks->buf[ks->begin++]; \
+	} \
+	static inline int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \
+	{ return ks_getuntil2(ks, delimiter, str, dret, 0); }
+
+#ifndef KSTRING_T
+#define KSTRING_T kstring_t
+typedef struct __kstring_t {
+	size_t l, m;
+	char *s;
+} kstring_t;
+#endif
+
+#ifndef kroundup32
+#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
+#endif
+
+#define __KS_GETUNTIL(SCOPE, __read) \
+	SCOPE int ks_getuntil2(kstream_t *ks, int delimiter, kstring_t *str, int *dret, int append)  \
+	{ \
+		int gotany = 0; \
+		if (dret) *dret = 0; \
+		str->l = append? str->l : 0; \
+        uint64_t seek_pos = str->l; \
+		for (;;) { \
+			int i; \
+			if (ks->begin >= ks->end) { \
+				if (!ks->is_eof) { \
+					ks->begin = 0; \
+					ks->end = __read(ks->f, ks->buf, ks->bufsize); \
+					if (ks->end == 0) { ks->is_eof = 1; break; } \
+				} else break; \
+			} \
+			if (delimiter == KS_SEP_LINE) {  \
+				for (i = ks->begin; i < ks->end; ++i)  \
+					if (ks->buf[i] == '\n') break; \
+			} else if (delimiter > KS_SEP_MAX) { \
+				for (i = ks->begin; i < ks->end; ++i) \
+					if (ks->buf[i] == delimiter) break; \
+			} else if (delimiter == KS_SEP_SPACE) { \
+				for (i = ks->begin; i < ks->end; ++i) \
+					if (isspace(ks->buf[i])) break; \
+			} else if (delimiter == KS_SEP_TAB) { \
+				for (i = ks->begin; i < ks->end; ++i) \
+					if (isspace(ks->buf[i]) && ks->buf[i] != ' ') break;  \
+			} else i = 0; /* never come to here! */ \
+			if (str->m - str->l < (size_t)(i - ks->begin + 1)) { \
+				str->m = str->l + (i - ks->begin) + 1; \
+				kroundup32(str->m); \
+				str->s = (char*)realloc(str->s, str->m); \
+			} \
+            seek_pos += i - ks->begin; if ( i < ks->end ) seek_pos++; \
+			gotany = 1; \
+			memcpy(str->s + str->l, ks->buf + ks->begin, i - ks->begin);  \
+			str->l = str->l + (i - ks->begin); \
+			ks->begin = i + 1; \
+			if (i < ks->end) { \
+				if (dret) *dret = ks->buf[i]; \
+				break; \
+			} \
+		} \
+		if (!gotany && ks_eof(ks)) return -1; \
+        ks->seek_pos += seek_pos; \
+		if (str->s == 0) { \
+			str->m = 1; \
+			str->s = (char*)calloc(1, 1); \
+		} else if (delimiter == KS_SEP_LINE && str->l > 1 && str->s[str->l-1] == '\r') --str->l; \
+		str->s[str->l] = '\0';											\
+		return str->l; \
+	}
+
+#define KSTREAM_INIT2(SCOPE, type_t, __read, __bufsize) \
+	__KS_TYPE(type_t) \
+	__KS_BASIC(SCOPE, type_t, __bufsize) \
+	__KS_GETUNTIL(SCOPE, __read) \
+	__KS_INLINED(__read)
+
+#define KSTREAM_INIT(type_t, __read, __bufsize) KSTREAM_INIT2(static, type_t, __read, __bufsize)
+
+#define KSTREAM_DECLARE(type_t, __read) \
+	__KS_TYPE(type_t) \
+	extern int ks_getuntil2(kstream_t *ks, int delimiter, kstring_t *str, int *dret, int append); \
+	extern kstream_t *ks_init(type_t f); \
+	extern void ks_destroy(kstream_t *ks); \
+	__KS_INLINED(__read)
+
+/******************
+ * FASTA/Q parser *
+ ******************/
+
+#define kseq_rewind(ks) ((ks)->last_char = (ks)->f->is_eof = (ks)->f->begin = (ks)->f->end = 0)
+
+#define __KSEQ_BASIC(SCOPE, type_t)										\
+	SCOPE kseq_t *kseq_init(type_t fd)									\
+	{																	\
+		kseq_t *s = (kseq_t*)calloc(1, sizeof(kseq_t));					\
+		s->f = ks_init(fd);												\
+		return s;														\
+	}																	\
+	SCOPE void kseq_destroy(kseq_t *ks)									\
+	{																	\
+		if (!ks) return;												\
+		free(ks->name.s); free(ks->comment.s); free(ks->seq.s);	free(ks->qual.s); \
+		ks_destroy(ks->f);												\
+		free(ks);														\
+	}
+
+/* Return value:
+   >=0  length of the sequence (normal)
+   -1   end-of-file
+   -2   truncated quality string
+ */
+#define __KSEQ_READ(SCOPE) \
+	SCOPE int kseq_read(kseq_t *seq) \
+	{ \
+		int c; \
+		kstream_t *ks = seq->f; \
+		if (seq->last_char == 0) { /* then jump to the next header line */ \
+			while ((c = ks_getc(ks)) != -1 && c != '>' && c != '@'); \
+			if (c == -1) return -1; /* end of file */ \
+			seq->last_char = c; \
+		} /* else: the first header char has been read in the previous call */ \
+		seq->comment.l = seq->seq.l = seq->qual.l = 0; /* reset all members */ \
+		if (ks_getuntil(ks, 0, &seq->name, &c) < 0) return -1; /* normal exit: EOF */ \
+		if (c != '\n') ks_getuntil(ks, KS_SEP_LINE, &seq->comment, 0); /* read FASTA/Q comment */ \
+		if (seq->seq.s == 0) { /* we can do this in the loop below, but that is slower */ \
+			seq->seq.m = 256; \
+			seq->seq.s = (char*)malloc(seq->seq.m); \
+		} \
+		while ((c = ks_getc(ks)) != -1 && c != '>' && c != '+' && c != '@') { \
+			if (c == '\n') continue; /* skip empty lines */ \
+			seq->seq.s[seq->seq.l++] = c; /* this is safe: we always have enough space for 1 char */ \
+			ks_getuntil2(ks, KS_SEP_LINE, &seq->seq, 0, 1); /* read the rest of the line */ \
+		} \
+		if (c == '>' || c == '@') seq->last_char = c; /* the first header char has been read */	\
+		if (seq->seq.l + 1 >= seq->seq.m) { /* seq->seq.s[seq->seq.l] below may be out of boundary */ \
+			seq->seq.m = seq->seq.l + 2; \
+			kroundup32(seq->seq.m); /* rounded to the next closest 2^k */ \
+			seq->seq.s = (char*)realloc(seq->seq.s, seq->seq.m); \
+		} \
+		seq->seq.s[seq->seq.l] = 0;	/* null terminated string */ \
+		if (c != '+') return seq->seq.l; /* FASTA */ \
+		if (seq->qual.m < seq->seq.m) {	/* allocate memory for qual in case insufficient */ \
+			seq->qual.m = seq->seq.m; \
+			seq->qual.s = (char*)realloc(seq->qual.s, seq->qual.m); \
+		} \
+		while ((c = ks_getc(ks)) != -1 && c != '\n'); /* skip the rest of '+' line */ \
+		if (c == -1) return -2; /* error: no quality string */ \
+		while (ks_getuntil2(ks, KS_SEP_LINE, &seq->qual, 0, 1) >= 0 && seq->qual.l < seq->seq.l); \
+		seq->last_char = 0;	/* we have not come to the next header line */ \
+		if (seq->seq.l != seq->qual.l) return -2; /* error: qual string is of a different length */ \
+		return seq->seq.l; \
+	}
+
+#define __KSEQ_TYPE(type_t)						\
+	typedef struct {							\
+		kstring_t name, comment, seq, qual;		\
+		int last_char;							\
+		kstream_t *f;							\
+	} kseq_t;
+
+#define KSEQ_INIT2(SCOPE, type_t, __read)		\
+	KSTREAM_INIT(type_t, __read, 16384)			\
+	__KSEQ_TYPE(type_t)							\
+	__KSEQ_BASIC(SCOPE, type_t)					\
+	__KSEQ_READ(SCOPE)
+
+#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
+
+#define KSEQ_DECLARE(type_t) \
+	__KS_TYPE(type_t) \
+	__KSEQ_TYPE(type_t) \
+	extern kseq_t *kseq_init(type_t fd); \
+	void kseq_destroy(kseq_t *ks); \
+	int kseq_read(kseq_t *seq);
+
+#endif
diff --git a/htslib/htslib/ksort.h b/htslib/htslib/ksort.h
new file mode 100644
index 0000000..aa0bb93
--- /dev/null
+++ b/htslib/htslib/ksort.h
@@ -0,0 +1,285 @@
+/* The MIT License
+
+   Copyright (c) 2008 Genome Research Ltd (GRL).
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+
+/* Contact: Heng Li <lh3 at sanger.ac.uk> */
+
+/*
+  2012-12-11 (0.1.4):
+
+    * Defined __ks_insertsort_##name as static to compile with C99.
+
+  2008-11-16 (0.1.4):
+
+    * Fixed a bug in introsort() that happens in rare cases.
+
+  2008-11-05 (0.1.3):
+
+    * Fixed a bug in introsort() for complex comparisons.
+
+	* Fixed a bug in mergesort(). The previous version is not stable.
+
+  2008-09-15 (0.1.2):
+
+	* Accelerated introsort. On my Mac (not on another Linux machine),
+	  my implementation is as fast as std::sort on random input.
+
+	* Added combsort and in introsort, switch to combsort if the
+	  recursion is too deep.
+
+  2008-09-13 (0.1.1):
+
+	* Added k-small algorithm
+
+  2008-09-05 (0.1.0):
+
+	* Initial version
+
+*/
+
+#ifndef AC_KSORT_H
+#define AC_KSORT_H
+
+#include <stdlib.h>
+#include <string.h>
+
+typedef struct {
+	void *left, *right;
+	int depth;
+} ks_isort_stack_t;
+
+#define KSORT_SWAP(type_t, a, b) { register type_t t=(a); (a)=(b); (b)=t; }
+
+#define KSORT_INIT(name, type_t, __sort_lt)								\
+	void ks_mergesort_##name(size_t n, type_t array[], type_t temp[])	\
+	{																	\
+		type_t *a2[2], *a, *b;											\
+		int curr, shift;												\
+																		\
+		a2[0] = array;													\
+		a2[1] = temp? temp : (type_t*)malloc(sizeof(type_t) * n);		\
+		for (curr = 0, shift = 0; (1ul<<shift) < n; ++shift) {			\
+			a = a2[curr]; b = a2[1-curr];								\
+			if (shift == 0) {											\
+				type_t *p = b, *i, *eb = a + n;							\
+				for (i = a; i < eb; i += 2) {							\
+					if (i == eb - 1) *p++ = *i;							\
+					else {												\
+						if (__sort_lt(*(i+1), *i)) {					\
+							*p++ = *(i+1); *p++ = *i;					\
+						} else {										\
+							*p++ = *i; *p++ = *(i+1);					\
+						}												\
+					}													\
+				}														\
+			} else {													\
+				size_t i, step = 1ul<<shift;							\
+				for (i = 0; i < n; i += step<<1) {						\
+					type_t *p, *j, *k, *ea, *eb;						\
+					if (n < i + step) {									\
+						ea = a + n; eb = a;								\
+					} else {											\
+						ea = a + i + step;								\
+						eb = a + (n < i + (step<<1)? n : i + (step<<1)); \
+					}													\
+					j = a + i; k = a + i + step; p = b + i;				\
+					while (j < ea && k < eb) {							\
+						if (__sort_lt(*k, *j)) *p++ = *k++;				\
+						else *p++ = *j++;								\
+					}													\
+					while (j < ea) *p++ = *j++;							\
+					while (k < eb) *p++ = *k++;							\
+				}														\
+			}															\
+			curr = 1 - curr;											\
+		}																\
+		if (curr == 1) {												\
+			type_t *p = a2[0], *i = a2[1], *eb = array + n;				\
+			for (; p < eb; ++i) *p++ = *i;								\
+		}																\
+		if (temp == 0) free(a2[1]);										\
+	}																	\
+	void ks_heapadjust_##name(size_t i, size_t n, type_t l[])			\
+	{																	\
+		size_t k = i;													\
+		type_t tmp = l[i];												\
+		while ((k = (k << 1) + 1) < n) {								\
+			if (k != n - 1 && __sort_lt(l[k], l[k+1])) ++k;				\
+			if (__sort_lt(l[k], tmp)) break;							\
+			l[i] = l[k]; i = k;											\
+		}																\
+		l[i] = tmp;														\
+	}																	\
+	void ks_heapmake_##name(size_t lsize, type_t l[])					\
+	{																	\
+		size_t i;														\
+		for (i = (lsize >> 1) - 1; i != (size_t)(-1); --i)				\
+			ks_heapadjust_##name(i, lsize, l);							\
+	}																	\
+	void ks_heapsort_##name(size_t lsize, type_t l[])					\
+	{																	\
+		size_t i;														\
+		for (i = lsize - 1; i > 0; --i) {								\
+			type_t tmp;													\
+			tmp = *l; *l = l[i]; l[i] = tmp; ks_heapadjust_##name(0, i, l); \
+		}																\
+	}																	\
+	static inline void __ks_insertsort_##name(type_t *s, type_t *t)		\
+	{																	\
+		type_t *i, *j, swap_tmp;										\
+		for (i = s + 1; i < t; ++i)										\
+			for (j = i; j > s && __sort_lt(*j, *(j-1)); --j) {			\
+				swap_tmp = *j; *j = *(j-1); *(j-1) = swap_tmp;			\
+			}															\
+	}																	\
+	void ks_combsort_##name(size_t n, type_t a[])						\
+	{																	\
+		const double shrink_factor = 1.2473309501039786540366528676643; \
+		int do_swap;													\
+		size_t gap = n;													\
+		type_t tmp, *i, *j;												\
+		do {															\
+			if (gap > 2) {												\
+				gap = (size_t)(gap / shrink_factor);					\
+				if (gap == 9 || gap == 10) gap = 11;					\
+			}															\
+			do_swap = 0;												\
+			for (i = a; i < a + n - gap; ++i) {							\
+				j = i + gap;											\
+				if (__sort_lt(*j, *i)) {								\
+					tmp = *i; *i = *j; *j = tmp;						\
+					do_swap = 1;										\
+				}														\
+			}															\
+		} while (do_swap || gap > 2);									\
+		if (gap != 1) __ks_insertsort_##name(a, a + n);					\
+	}																	\
+	void ks_introsort_##name(size_t n, type_t a[])						\
+	{																	\
+		int d;															\
+		ks_isort_stack_t *top, *stack;									\
+		type_t rp, swap_tmp;											\
+		type_t *s, *t, *i, *j, *k;										\
+																		\
+		if (n < 1) return;												\
+		else if (n == 2) {												\
+			if (__sort_lt(a[1], a[0])) { swap_tmp = a[0]; a[0] = a[1]; a[1] = swap_tmp; } \
+			return;														\
+		}																\
+		for (d = 2; 1ul<<d < n; ++d);									\
+		stack = (ks_isort_stack_t*)malloc(sizeof(ks_isort_stack_t) * ((sizeof(size_t)*d)+2)); \
+		top = stack; s = a; t = a + (n-1); d <<= 1;						\
+		while (1) {														\
+			if (s < t) {												\
+				if (--d == 0) {											\
+					ks_combsort_##name(t - s + 1, s);					\
+					t = s;												\
+					continue;											\
+				}														\
+				i = s; j = t; k = i + ((j-i)>>1) + 1;					\
+				if (__sort_lt(*k, *i)) {								\
+					if (__sort_lt(*k, *j)) k = j;						\
+				} else k = __sort_lt(*j, *i)? i : j;					\
+				rp = *k;												\
+				if (k != t) { swap_tmp = *k; *k = *t; *t = swap_tmp; }	\
+				for (;;) {												\
+					do ++i; while (__sort_lt(*i, rp));					\
+					do --j; while (i <= j && __sort_lt(rp, *j));		\
+					if (j <= i) break;									\
+					swap_tmp = *i; *i = *j; *j = swap_tmp;				\
+				}														\
+				swap_tmp = *i; *i = *t; *t = swap_tmp;					\
+				if (i-s > t-i) {										\
+					if (i-s > 16) { top->left = s; top->right = i-1; top->depth = d; ++top; } \
+					s = t-i > 16? i+1 : t;								\
+				} else {												\
+					if (t-i > 16) { top->left = i+1; top->right = t; top->depth = d; ++top; } \
+					t = i-s > 16? i-1 : s;								\
+				}														\
+			} else {													\
+				if (top == stack) {										\
+					free(stack);										\
+					__ks_insertsort_##name(a, a+n);						\
+					return;												\
+				} else { --top; s = (type_t*)top->left; t = (type_t*)top->right; d = top->depth; } \
+			}															\
+		}																\
+	}																	\
+	/* This function is adapted from: http://ndevilla.free.fr/median/ */ \
+	/* 0 <= kk < n */													\
+	type_t ks_ksmall_##name(size_t n, type_t arr[], size_t kk)			\
+	{																	\
+		type_t *low, *high, *k, *ll, *hh, *mid;							\
+		low = arr; high = arr + n - 1; k = arr + kk;					\
+		for (;;) {														\
+			if (high <= low) return *k;									\
+			if (high == low + 1) {										\
+				if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \
+				return *k;												\
+			}															\
+			mid = low + (high - low) / 2;								\
+			if (__sort_lt(*high, *mid)) KSORT_SWAP(type_t, *mid, *high); \
+			if (__sort_lt(*high, *low)) KSORT_SWAP(type_t, *low, *high); \
+			if (__sort_lt(*low, *mid)) KSORT_SWAP(type_t, *mid, *low);	\
+			KSORT_SWAP(type_t, *mid, *(low+1));							\
+			ll = low + 1; hh = high;									\
+			for (;;) {													\
+				do ++ll; while (__sort_lt(*ll, *low));					\
+				do --hh; while (__sort_lt(*low, *hh));					\
+				if (hh < ll) break;										\
+				KSORT_SWAP(type_t, *ll, *hh);							\
+			}															\
+			KSORT_SWAP(type_t, *low, *hh);								\
+			if (hh <= k) low = ll;										\
+			if (hh >= k) high = hh - 1;									\
+		}																\
+	}																	\
+	void ks_shuffle_##name(size_t n, type_t a[])						\
+	{																	\
+		int i, j;														\
+		for (i = n; i > 1; --i) {										\
+			type_t tmp;													\
+			j = (int)(drand48() * i);									\
+			tmp = a[j]; a[j] = a[i-1]; a[i-1] = tmp;					\
+		}																\
+	}
+
+#define ks_mergesort(name, n, a, t) ks_mergesort_##name(n, a, t)
+#define ks_introsort(name, n, a) ks_introsort_##name(n, a)
+#define ks_combsort(name, n, a) ks_combsort_##name(n, a)
+#define ks_heapsort(name, n, a) ks_heapsort_##name(n, a)
+#define ks_heapmake(name, n, a) ks_heapmake_##name(n, a)
+#define ks_heapadjust(name, i, n, a) ks_heapadjust_##name(i, n, a)
+#define ks_ksmall(name, n, a, k) ks_ksmall_##name(n, a, k)
+#define ks_shuffle(name, n, a) ks_shuffle_##name(n, a)
+
+#define ks_lt_generic(a, b) ((a) < (b))
+#define ks_lt_str(a, b) (strcmp((a), (b)) < 0)
+
+typedef const char *ksstr_t;
+
+#define KSORT_INIT_GENERIC(type_t) KSORT_INIT(type_t, type_t, ks_lt_generic)
+#define KSORT_INIT_STR KSORT_INIT(str, ksstr_t, ks_lt_str)
+
+#endif
diff --git a/htslib/htslib/kstring.h b/htslib/htslib/kstring.h
new file mode 100644
index 0000000..fd91bbe
--- /dev/null
+++ b/htslib/htslib/kstring.h
@@ -0,0 +1,277 @@
+/* The MIT License
+
+   Copyright (C) 2011 by Attractive Chaos <attractor at live.co.uk>
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+
+#ifndef KSTRING_H
+#define KSTRING_H
+
+#include <stdlib.h>
+#include <string.h>
+#include <stdarg.h>
+#include <stdint.h>
+#include <stdio.h>
+
+#ifndef kroundup32
+#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
+#endif
+
+#if defined __GNUC__ && (__GNUC__ > 2 || (__GNUC__ == 2 && __GNUC_MINOR__ > 4))
+#define KS_ATTR_PRINTF(fmt, arg) __attribute__((__format__ (__printf__, fmt, arg)))
+#else
+#define KS_ATTR_PRINTF(fmt, arg)
+#endif
+
+
+/* kstring_t is a simple non-opaque type whose fields are likely to be
+ * used directly by user code (but see also ks_str() and ks_len() below).
+ * A kstring_t object is initialised by either of
+ *       kstring_t str = { 0, 0, NULL };
+ *       kstring_t str; ...; str.l = str.m = 0; str.s = NULL;
+ * and either ownership of the underlying buffer should be given away before
+ * the object disappears (see ks_release() below) or the kstring_t should be
+ * destroyed with  free(str.s);  */
+#ifndef KSTRING_T
+#define KSTRING_T kstring_t
+typedef struct __kstring_t {
+	size_t l, m;
+	char *s;
+} kstring_t;
+#endif
+
+typedef struct {
+	uint64_t tab[4];
+	int sep, finished;
+	const char *p; // end of the current token
+} ks_tokaux_t;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+	int kvsprintf(kstring_t *s, const char *fmt, va_list ap) KS_ATTR_PRINTF(2,0);
+	int ksprintf(kstring_t *s, const char *fmt, ...) KS_ATTR_PRINTF(2,3);
+	int ksplit_core(char *s, int delimiter, int *_max, int **_offsets);
+	char *kstrstr(const char *str, const char *pat, int **_prep);
+	char *kstrnstr(const char *str, const char *pat, int n, int **_prep);
+	void *kmemmem(const void *_str, int n, const void *_pat, int m, int **_prep);
+
+	/* kstrtok() is similar to strtok_r() except that str is not
+	 * modified and both str and sep can be NULL. For efficiency, it is
+	 * actually recommended to set both to NULL in the subsequent calls
+	 * if sep is not changed. */
+	char *kstrtok(const char *str, const char *sep, ks_tokaux_t *aux);
+
+	/* kgetline() uses the supplied fgets()-like function to read a "\n"-
+	 * or "\r\n"-terminated line from fp.  The line read is appended to the
+	 * kstring without its terminator and 0 is returned; EOF is returned at
+	 * EOF or on error (determined by querying fp, as per fgets()). */
+	typedef char *kgets_func(char *, int, void *);
+	int kgetline(kstring_t *s, kgets_func *fgets, void *fp);
+
+#ifdef __cplusplus
+}
+#endif
+
+static inline int ks_resize(kstring_t *s, size_t size)
+{
+	if (s->m < size) {
+		char *tmp;
+		s->m = size;
+		kroundup32(s->m);
+		if ((tmp = (char*)realloc(s->s, s->m)))
+			s->s = tmp;
+		else
+			return -1;
+	}
+	return 0;
+}
+
+static inline char *ks_str(kstring_t *s)
+{
+	return s->s;
+}
+
+static inline size_t ks_len(kstring_t *s)
+{
+	return s->l;
+}
+
+// Give ownership of the underlying buffer away to something else (making
+// that something else responsible for freeing it), leaving the kstring_t
+// empty and ready to be used again, or ready to go out of scope without
+// needing  free(str.s)  to prevent a memory leak.
+static inline char *ks_release(kstring_t *s)
+{
+	char *ss = s->s;
+	s->l = s->m = 0;
+	s->s = NULL;
+	return ss;
+}
+
+static inline int kputsn(const char *p, int l, kstring_t *s)
+{
+	if (s->l + l + 1 >= s->m) {
+		char *tmp;
+		s->m = s->l + l + 2;
+		kroundup32(s->m);
+		if ((tmp = (char*)realloc(s->s, s->m)))
+			s->s = tmp;
+		else
+			return EOF;
+	}
+	memcpy(s->s + s->l, p, l);
+	s->l += l;
+	s->s[s->l] = 0;
+	return l;
+}
+
+static inline int kputs(const char *p, kstring_t *s)
+{
+	return kputsn(p, strlen(p), s);
+}
+
+static inline int kputc(int c, kstring_t *s)
+{
+	if (s->l + 1 >= s->m) {
+		char *tmp;
+		s->m = s->l + 2;
+		kroundup32(s->m);
+		if ((tmp = (char*)realloc(s->s, s->m)))
+			s->s = tmp;
+		else
+			return EOF;
+	}
+	s->s[s->l++] = c;
+	s->s[s->l] = 0;
+	return c;
+}
+
+static inline int kputc_(int c, kstring_t *s)
+{
+	if (s->l + 1 > s->m) {
+		char *tmp;
+		s->m = s->l + 1;
+		kroundup32(s->m);
+		if ((tmp = (char*)realloc(s->s, s->m)))
+			s->s = tmp;
+		else
+			return EOF;
+	}
+	s->s[s->l++] = c;
+	return 1;
+}
+
+static inline int kputsn_(const void *p, int l, kstring_t *s)
+{
+	if (s->l + l > s->m) {
+		char *tmp;
+		s->m = s->l + l;
+		kroundup32(s->m);
+		if ((tmp = (char*)realloc(s->s, s->m)))
+			s->s = tmp;
+		else
+			return EOF;
+	}
+	memcpy(s->s + s->l, p, l);
+	s->l += l;
+	return l;
+}
+
+static inline int kputw(int c, kstring_t *s)
+{
+	char buf[16];
+	int i, l = 0;
+	unsigned int x = c;
+	if (c < 0) x = -x;
+	do { buf[l++] = x%10 + '0'; x /= 10; } while (x > 0);
+	if (c < 0) buf[l++] = '-';
+	if (s->l + l + 1 >= s->m) {
+		char *tmp;
+		s->m = s->l + l + 2;
+		kroundup32(s->m);
+		if ((tmp = (char*)realloc(s->s, s->m)))
+			s->s = tmp;
+		else
+			return EOF;
+	}
+	for (i = l - 1; i >= 0; --i) s->s[s->l++] = buf[i];
+	s->s[s->l] = 0;
+	return 0;
+}
+
+static inline int kputuw(unsigned c, kstring_t *s)
+{
+	char buf[16];
+	int l, i;
+	unsigned x;
+	if (c == 0) return kputc('0', s);
+	for (l = 0, x = c; x > 0; x /= 10) buf[l++] = x%10 + '0';
+	if (s->l + l + 1 >= s->m) {
+		char *tmp;
+		s->m = s->l + l + 2;
+		kroundup32(s->m);
+		if ((tmp = (char*)realloc(s->s, s->m)))
+			s->s = tmp;
+		else
+			return EOF;
+	}
+	for (i = l - 1; i >= 0; --i) s->s[s->l++] = buf[i];
+	s->s[s->l] = 0;
+	return 0;
+}
+
+static inline int kputl(long c, kstring_t *s)
+{
+	char buf[32];
+	int i, l = 0;
+	unsigned long x = c;
+	if (c < 0) x = -x;
+	do { buf[l++] = x%10 + '0'; x /= 10; } while (x > 0);
+	if (c < 0) buf[l++] = '-';
+	if (s->l + l + 1 >= s->m) {
+		char *tmp;
+		s->m = s->l + l + 2;
+		kroundup32(s->m);
+		if ((tmp = (char*)realloc(s->s, s->m)))
+			s->s = tmp;
+		else
+			return EOF;
+	}
+	for (i = l - 1; i >= 0; --i) s->s[s->l++] = buf[i];
+	s->s[s->l] = 0;
+	return 0;
+}
+
+/*
+ * Returns 's' split by delimiter, with *n being the number of components;
+ *         NULL on failue.
+ */
+static inline int *ksplit(kstring_t *s, int delimiter, int *n)
+{
+	int max = 0, *offsets = 0;
+	*n = ksplit_core(s->s, delimiter, &max, &offsets);
+	return offsets;
+}
+
+#endif
diff --git a/htslib/htslib/regidx.h b/htslib/htslib/regidx.h
new file mode 100644
index 0000000..79e82b7
--- /dev/null
+++ b/htslib/htslib/regidx.h
@@ -0,0 +1,154 @@
+/* 
+    Copyright (C) 2014 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3 at sanger.ac.uk>
+
+    Permission is hereby granted, free of charge, to any person obtaining a copy
+    of this software and associated documentation files (the "Software"), to deal
+    in the Software without restriction, including without limitation the rights
+    to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+    copies of the Software, and to permit persons to whom the Software is
+    furnished to do so, subject to the following conditions:
+    
+    The above copyright notice and this permission notice shall be included in
+    all copies or substantial portions of the Software.
+    
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+    AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+    LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+    OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+    THE SOFTWARE.
+*/
+
+/*
+    Regions indexing with an optional payload. Inspired by samtools/bedidx.c.
+    This code is intended as future replacement of bcf_sr_regions_t.
+
+    Example of usage:
+
+        // Init the parser and print regions. In this example the payload is a
+        // pointer to a string. For the description of parse_custom and
+        // free_custom functions, see regidx_parse_f and regidx_free_f below,
+        // and for working example see test/test-regidx.c.
+        regidx_t *idx = regidx_init(in_fname,parse_custom,free_custom,sizeof(char*),NULL);
+
+        // Query overlap with chr:from-to
+        regitr_t itr;
+        if ( regidx_overlap(idx, chr,from,to, &itr) ) printf("There is an overlap!\n");
+
+        while ( REGITR_OVERLAP(itr,from,to) )
+        {
+            printf("[%d,%d] overlaps with [%d,%d], payload=%s\n", from,to, 
+                REGITR_START(itr), REGITR_END(itr), REGITR_PAYLOAD(itr,char*));
+            itr.i++;
+        }
+
+        regidx_destroy(regs);
+*/
+
+#ifndef HTSLIB_REGIDX_H
+#define HTSLIB_REGIDX_H
+
+#include <stdio.h>
+#include <inttypes.h>
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+typedef struct _regidx_t regidx_t;
+typedef struct
+{
+    uint32_t start, end;
+}
+reg_t;
+typedef struct
+{
+    int i, n;
+    reg_t *reg;
+    void *payload;
+}
+regitr_t;
+
+#define REGITR_START(itr) (itr).reg[(itr).i].start
+#define REGITR_END(itr)   (itr).reg[(itr).i].end
+#define REGITR_PAYLOAD(itr,type_t) ((type_t*)(itr).payload)[(itr).i]
+#define REGITR_OVERLAP(itr,from,to) (itr.i < itr.n && REGITR_START(itr)<=to && REGITR_END(itr)>=from )
+
+/*
+ *  regidx_parse_f - Function to parse one input line, such as regidx_parse_bed
+ *  or regidx_parse_tab below. The function is expected to set `chr_from` and
+ *  `chr_to` to point to first and last character of chromosome name and set
+ *  coordinates `reg->start` and `reg->end` (0-based, inclusive). If
+ *  regidx_init() was called with non-zero payload_size, the `payload` points
+ *  to a memory location of the payload_size and `usr` is data passed to
+ *  regidx_init(). Any memory allocated by the function will be freed by
+ *  regidx_free_f on regidx_destroy().
+ *
+ *  Return value: 0 on success, -1 to skip a record, -2 on fatal error.
+ */
+typedef int  (*regidx_parse_f)(const char *line, char **chr_beg, char **chr_end, reg_t *reg, void *payload, void *usr);
+typedef void (*regidx_free_f)(void *payload);
+
+int regidx_parse_bed(const char*,char**,char**,reg_t*,void*,void*);   // CHROM,FROM,TO (0-based,right-open)
+int regidx_parse_tab(const char*,char**,char**,reg_t*,void*,void*);   // CHROM,POS (1-based, inclusive)
+
+/*
+ *  regidx_init() - creates new index
+ *  @param fname:  input file name or NULL if regions will be added one-by-one via regidx_insert()
+ *  @param parsef: regidx_parse_bed, regidx_parse_tab or see description of regidx_parse_f. If NULL,
+ *                 the format will be autodected, currently either regidx_parse_tab (the default) or
+ *                 regidx_parse_bed (file must be named 'bed' or 'bed.gz') will be used. Note that
+ *                 the exact autodetection algorithm will change.
+ *  @param freef:  NULL or see description of regidx_parse_f
+ *  @param payload_size: 0 with regidx_parse_bed, regidx_parse_tab or see regidx_parse_f
+ *  @param usr:    optional user data passed to regidx_parse_f
+ *
+ *  Returns index on success or NULL on error.
+ */
+regidx_t *regidx_init(const char *fname, regidx_parse_f parsef, regidx_free_f freef, size_t payload_size, void *usr);
+
+/*
+ *  regidx_destroy() - free memory allocated by regidx_init
+ */
+void regidx_destroy(regidx_t *idx);
+
+/*
+ *  regidx_overlap() - check overlap of the location chr:from-to with regions
+ *  @param start,end:   0-based start, end coordinate (inclusive)
+ *  @param itr:         pointer to iterator, can be NULL if not needed
+ *
+ *  Returns 0 if there is no overlap or 1 if overlap is found. The overlapping
+ *  regions can be iterated as shown in the example above.
+ */
+int regidx_overlap(regidx_t *idx, const char *chr, uint32_t start, uint32_t end, regitr_t *itr);
+
+/*
+ *  regidx_insert() - add a new region. 
+ *
+ *  After last region has been added, call regidx_insert(idx,NULL) to
+ *  build the index.
+ *
+ *  Returns 0 on success or -1 on error.
+ */
+int regidx_insert(regidx_t *idx, char *line);
+
+/*
+ *  regidx_seq_names() - return list of all sequence names
+ */
+char **regidx_seq_names(regidx_t *idx, int *n);
+
+/*
+ *  regidx_seq_nregs() - number of regions
+ *  regidx_nregs()  - total number of regions
+ */
+int regidx_seq_nregs(regidx_t *idx, const char *seq);
+int regidx_nregs(regidx_t *idx);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/htslib/htslib/sam.h b/htslib/htslib/sam.h
new file mode 100644
index 0000000..7de8cd3
--- /dev/null
+++ b/htslib/htslib/sam.h
@@ -0,0 +1,454 @@
+/*  sam.h -- SAM and BAM file I/O and manipulation.
+
+    Copyright (C) 2008, 2009, 2013-2014 Genome Research Ltd.
+    Copyright (C) 2010, 2012, 2013 Broad Institute.
+
+    Author: Heng Li <lh3 at sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#ifndef HTSLIB_SAM_H
+#define HTSLIB_SAM_H
+
+#include <stdint.h>
+#include "hts.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/**********************
+ *** SAM/BAM header ***
+ **********************/
+
+/*! @typedef
+ @abstract Structure for the alignment header.
+ @field n_targets   number of reference sequences
+ @field l_text      length of the plain text in the header
+ @field target_len  lengths of the reference sequences
+ @field target_name names of the reference sequences
+ @field text        plain text
+ @field sdict       header dictionary
+ */
+
+typedef struct {
+    int32_t n_targets, ignore_sam_err;
+    uint32_t l_text;
+    uint32_t *target_len;
+    int8_t *cigar_tab;
+    char **target_name;
+    char *text;
+    void *sdict;
+} bam_hdr_t;
+
+/****************************
+ *** CIGAR related macros ***
+ ****************************/
+
+#define BAM_CMATCH      0
+#define BAM_CINS        1
+#define BAM_CDEL        2
+#define BAM_CREF_SKIP   3
+#define BAM_CSOFT_CLIP  4
+#define BAM_CHARD_CLIP  5
+#define BAM_CPAD        6
+#define BAM_CEQUAL      7
+#define BAM_CDIFF       8
+#define BAM_CBACK       9
+
+#define BAM_CIGAR_STR   "MIDNSHP=XB"
+#define BAM_CIGAR_SHIFT 4
+#define BAM_CIGAR_MASK  0xf
+#define BAM_CIGAR_TYPE  0x3C1A7
+
+#define bam_cigar_op(c) ((c)&BAM_CIGAR_MASK)
+#define bam_cigar_oplen(c) ((c)>>BAM_CIGAR_SHIFT)
+#define bam_cigar_opchr(c) (BAM_CIGAR_STR[bam_cigar_op(c)])
+#define bam_cigar_gen(l, o) ((l)<<BAM_CIGAR_SHIFT|(o))
+
+/* bam_cigar_type returns a bit flag with:
+ *   bit 1 set if the cigar operation consumes the query
+ *   bit 2 set if the cigar operation consumes the reference
+ *
+ * For reference, the unobfuscated truth table for this function is:
+ * BAM_CIGAR_TYPE  QUERY  REFERENCE
+ * --------------------------------
+ * BAM_CMATCH      1      1
+ * BAM_CINS        1      0
+ * BAM_CDEL        0      1
+ * BAM_CREF_SKIP   0      1
+ * BAM_CSOFT_CLIP  1      0
+ * BAM_CHARD_CLIP  0      0
+ * BAM_CPAD        0      0
+ * BAM_CEQUAL      1      1
+ * BAM_CDIFF       1      1
+ * BAM_CBACK       0      0
+ * --------------------------------
+ */
+#define bam_cigar_type(o) (BAM_CIGAR_TYPE>>((o)<<1)&3) // bit 1: consume query; bit 2: consume reference
+
+/*! @abstract the read is paired in sequencing, no matter whether it is mapped in a pair */
+#define BAM_FPAIRED        1
+/*! @abstract the read is mapped in a proper pair */
+#define BAM_FPROPER_PAIR   2
+/*! @abstract the read itself is unmapped; conflictive with BAM_FPROPER_PAIR */
+#define BAM_FUNMAP         4
+/*! @abstract the mate is unmapped */
+#define BAM_FMUNMAP        8
+/*! @abstract the read is mapped to the reverse strand */
+#define BAM_FREVERSE      16
+/*! @abstract the mate is mapped to the reverse strand */
+#define BAM_FMREVERSE     32
+/*! @abstract this is read1 */
+#define BAM_FREAD1        64
+/*! @abstract this is read2 */
+#define BAM_FREAD2       128
+/*! @abstract not primary alignment */
+#define BAM_FSECONDARY   256
+/*! @abstract QC failure */
+#define BAM_FQCFAIL      512
+/*! @abstract optical or PCR duplicate */
+#define BAM_FDUP        1024
+/*! @abstract supplementary alignment */
+#define BAM_FSUPPLEMENTARY 2048
+
+/*************************
+ *** Alignment records ***
+ *************************/
+
+/*! @typedef
+ @abstract Structure for core alignment information.
+ @field  tid     chromosome ID, defined by bam_hdr_t
+ @field  pos     0-based leftmost coordinate
+ @field  bin     bin calculated by bam_reg2bin()
+ @field  qual    mapping quality
+ @field  l_qname length of the query name
+ @field  flag    bitwise flag
+ @field  n_cigar number of CIGAR operations
+ @field  l_qseq  length of the query sequence (read)
+ @field  mtid    chromosome ID of next read in template, defined by bam_hdr_t
+ @field  mpos    0-based leftmost coordinate of next read in template
+ */
+typedef struct {
+    int32_t tid;
+    int32_t pos;
+    uint32_t bin:16, qual:8, l_qname:8;
+    uint32_t flag:16, n_cigar:16;
+    int32_t l_qseq;
+    int32_t mtid;
+    int32_t mpos;
+    int32_t isize;
+} bam1_core_t;
+
+/*! @typedef
+ @abstract Structure for one alignment.
+ @field  core       core information about the alignment
+ @field  l_data     current length of bam1_t::data
+ @field  m_data     maximum length of bam1_t::data
+ @field  data       all variable-length data, concatenated; structure: qname-cigar-seq-qual-aux
+
+ @discussion Notes:
+
+ 1. qname is zero tailing and core.l_qname includes the tailing '\0'.
+ 2. l_qseq is calculated from the total length of an alignment block
+ on reading or from CIGAR.
+ 3. cigar data is encoded 4 bytes per CIGAR operation.
+ 4. seq is nybble-encoded according to bam_nt16_table.
+ */
+typedef struct {
+    bam1_core_t core;
+    int l_data, m_data;
+    uint8_t *data;
+#ifndef BAM_NO_ID
+    uint64_t id;
+#endif
+} bam1_t;
+
+/*! @function
+ @abstract  Get whether the query is on the reverse strand
+ @param  b  pointer to an alignment
+ @return    boolean true if query is on the reverse strand
+ */
+#define bam_is_rev(b) (((b)->core.flag&BAM_FREVERSE) != 0)
+/*! @function
+ @abstract  Get whether the query's mate is on the reverse strand
+ @param  b  pointer to an alignment
+ @return    boolean true if query's mate on the reverse strand
+ */
+#define bam_is_mrev(b) (((b)->core.flag&BAM_FMREVERSE) != 0)
+/*! @function
+ @abstract  Get the name of the query
+ @param  b  pointer to an alignment
+ @return    pointer to the name string, null terminated
+ */
+#define bam_get_qname(b) ((char*)(b)->data)
+/*! @function
+ @abstract  Get the CIGAR array
+ @param  b  pointer to an alignment
+ @return    pointer to the CIGAR array
+
+ @discussion In the CIGAR array, each element is a 32-bit integer. The
+ lower 4 bits gives a CIGAR operation and the higher 28 bits keep the
+ length of a CIGAR.
+ */
+#define bam_get_cigar(b) ((uint32_t*)((b)->data + (b)->core.l_qname))
+/*! @function
+ @abstract  Get query sequence
+ @param  b  pointer to an alignment
+ @return    pointer to sequence
+
+ @discussion Each base is encoded in 4 bits: 1 for A, 2 for C, 4 for G,
+ 8 for T and 15 for N. Two bases are packed in one byte with the base
+ at the higher 4 bits having smaller coordinate on the read. It is
+ recommended to use bam_seqi() macro to get the base.
+ */
+#define bam_get_seq(b)   ((b)->data + ((b)->core.n_cigar<<2) + (b)->core.l_qname)
+/*! @function
+ @abstract  Get query quality
+ @param  b  pointer to an alignment
+ @return    pointer to quality string
+ */
+#define bam_get_qual(b)  ((b)->data + ((b)->core.n_cigar<<2) + (b)->core.l_qname + (((b)->core.l_qseq + 1)>>1))
+/*! @function
+ @abstract  Get auxiliary data
+ @param  b  pointer to an alignment
+ @return    pointer to the concatenated auxiliary data
+ */
+#define bam_get_aux(b)   ((b)->data + ((b)->core.n_cigar<<2) + (b)->core.l_qname + (((b)->core.l_qseq + 1)>>1) + (b)->core.l_qseq)
+/*! @function
+ @abstract  Get length of auxiliary data
+ @param  b  pointer to an alignment
+ @return    length of the concatenated auxiliary data
+ */
+#define bam_get_l_aux(b) ((b)->l_data - ((b)->core.n_cigar<<2) - (b)->core.l_qname - (b)->core.l_qseq - (((b)->core.l_qseq + 1)>>1))
+/*! @function
+ @abstract  Get a base on read
+ @param  s  Query sequence returned by bam_get_seq()
+ @param  i  The i-th position, 0-based
+ @return    4-bit integer representing the base.
+ */
+#define bam_seqi(s, i) ((s)[(i)>>1] >> ((~(i)&1)<<2) & 0xf)
+
+/**************************
+ *** Exported functions ***
+ **************************/
+
+    /***************
+     *** BAM I/O ***
+     ***************/
+
+    bam_hdr_t *bam_hdr_init(void);
+    bam_hdr_t *bam_hdr_read(BGZF *fp);
+    int bam_hdr_write(BGZF *fp, const bam_hdr_t *h) HTS_RESULT_USED;
+    void bam_hdr_destroy(bam_hdr_t *h);
+    int bam_name2id(bam_hdr_t *h, const char *ref);
+    bam_hdr_t* bam_hdr_dup(const bam_hdr_t *h0);
+
+    bam1_t *bam_init1(void);
+    void bam_destroy1(bam1_t *b);
+    int bam_read1(BGZF *fp, bam1_t *b) HTS_RESULT_USED;
+    int bam_write1(BGZF *fp, const bam1_t *b) HTS_RESULT_USED;
+    bam1_t *bam_copy1(bam1_t *bdst, const bam1_t *bsrc);
+    bam1_t *bam_dup1(const bam1_t *bsrc);
+
+    int bam_cigar2qlen(int n_cigar, const uint32_t *cigar);
+    int bam_cigar2rlen(int n_cigar, const uint32_t *cigar);
+
+    /*!
+      @abstract Calculate the rightmost base position of an alignment on the
+      reference genome.
+
+      @param  b  pointer to an alignment
+      @return    the coordinate of the first base after the alignment, 0-based
+
+      @discussion For a mapped read, this is just b->core.pos + bam_cigar2rlen.
+      For an unmapped read (either according to its flags or if it has no cigar
+      string), we return b->core.pos + 1 by convention.
+    */
+    int32_t bam_endpos(const bam1_t *b);
+
+    int   bam_str2flag(const char *str);    /** returns negative value on error */
+    char *bam_flag2str(int flag);   /** The string must be freed by the user */
+
+    /*************************
+     *** BAM/CRAM indexing ***
+     *************************/
+
+    // These BAM iterator functions work only on BAM files.  To work with either
+    // BAM or CRAM files use the sam_index_load() & sam_itr_*() functions.
+    #define bam_itr_destroy(iter) hts_itr_destroy(iter)
+    #define bam_itr_queryi(idx, tid, beg, end) sam_itr_queryi(idx, tid, beg, end)
+    #define bam_itr_querys(idx, hdr, region) sam_itr_querys(idx, hdr, region)
+    #define bam_itr_next(htsfp, itr, r) hts_itr_next((htsfp)->fp.bgzf, (itr), (r), 0)
+
+// Load/build .csi or .bai BAM index file.  Does not work with CRAM.
+// It is recommended to use the sam_index_* functions below instead.
+#define bam_index_load(fn) hts_idx_load((fn), HTS_FMT_BAI)
+#define bam_index_build(fn, min_shift) (sam_index_build((fn), (min_shift)))
+
+/// Load a BAM (.csi or .bai) or CRAM (.crai) index file
+/** @param fp  File handle of the data file whose index is being opened
+    @param fn  BAM/CRAM/etc filename to search alongside for the index file
+    @return  The index, or NULL if an error occurred.
+*/
+hts_idx_t *sam_index_load(htsFile *fp, const char *fn);
+
+/// Load a specific BAM (.csi or .bai) or CRAM (.crai) index file
+/** @param fp     File handle of the data file whose index is being opened
+    @param fn     BAM/CRAM/etc data file filename
+    @param fnidx  Index filename, or NULL to search alongside @a fn
+    @return  The index, or NULL if an error occurred.
+*/
+hts_idx_t *sam_index_load2(htsFile *fp, const char *fn, const char *fnidx);
+
+/// Generate and save an index file
+/** @param fn        Input BAM/etc filename, to which .csi/etc will be added
+    @param min_shift Positive to generate CSI, or 0 to generate BAI
+    @return  0 if successful, or negative if an error occurred (usually -1; or
+             -2: opening fn failed; -3: format not indexable)
+*/
+int sam_index_build(const char *fn, int min_shift) HTS_RESULT_USED;
+
+/// Generate and save an index to a specific file
+/** @param fn        Input BAM/CRAM/etc filename
+    @param fnidx     Output filename, or NULL to add .bai/.csi/etc to @a fn
+    @param min_shift Positive to generate CSI, or 0 to generate BAI
+    @return  0 if successful, or negative if an error occurred.
+*/
+int sam_index_build2(const char *fn, const char *fnidx, int min_shift) HTS_RESULT_USED;
+
+    #define sam_itr_destroy(iter) hts_itr_destroy(iter)
+    hts_itr_t *sam_itr_queryi(const hts_idx_t *idx, int tid, int beg, int end);
+    hts_itr_t *sam_itr_querys(const hts_idx_t *idx, bam_hdr_t *hdr, const char *region);
+    #define sam_itr_next(htsfp, itr, r) hts_itr_next((htsfp)->fp.bgzf, (itr), (r), (htsfp))
+
+    /***************
+     *** SAM I/O ***
+     ***************/
+
+    #define sam_open(fn, mode) (hts_open((fn), (mode)))
+    #define sam_open_format(fn, mode, fmt) (hts_open_format((fn), (mode), (fmt)))
+    #define sam_close(fp) hts_close(fp)
+
+    int sam_open_mode(char *mode, const char *fn, const char *format);
+
+    // A version of sam_open_mode that can handle ,key=value options.
+    // The format string is allocated and returned, to be freed by the caller.
+    // Prefix should be "r" or "w",
+    char *sam_open_mode_opts(const char *fn,
+                             const char *mode,
+                             const char *format);
+
+    typedef htsFile samFile;
+    bam_hdr_t *sam_hdr_parse(int l_text, const char *text);
+    bam_hdr_t *sam_hdr_read(samFile *fp);
+    int sam_hdr_write(samFile *fp, const bam_hdr_t *h) HTS_RESULT_USED;
+
+    int sam_parse1(kstring_t *s, bam_hdr_t *h, bam1_t *b) HTS_RESULT_USED;
+    int sam_format1(const bam_hdr_t *h, const bam1_t *b, kstring_t *str) HTS_RESULT_USED;
+    int sam_read1(samFile *fp, bam_hdr_t *h, bam1_t *b) HTS_RESULT_USED;
+    int sam_write1(samFile *fp, const bam_hdr_t *h, const bam1_t *b) HTS_RESULT_USED;
+
+    /*************************************
+     *** Manipulating auxiliary fields ***
+     *************************************/
+
+    uint8_t *bam_aux_get(const bam1_t *b, const char tag[2]);
+    int32_t bam_aux2i(const uint8_t *s);
+    double bam_aux2f(const uint8_t *s);
+    char bam_aux2A(const uint8_t *s);
+    char *bam_aux2Z(const uint8_t *s);
+
+    void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *data);
+    int bam_aux_del(bam1_t *b, uint8_t *s);
+
+/**************************
+ *** Pileup and Mpileup ***
+ **************************/
+
+#if !defined(BAM_NO_PILEUP)
+
+/*! @typedef
+ @abstract Structure for one alignment covering the pileup position.
+ @field  b          pointer to the alignment
+ @field  qpos       position of the read base at the pileup site, 0-based
+ @field  indel      indel length; 0 for no indel, positive for ins and negative for del
+ @field  level      the level of the read in the "viewer" mode
+ @field  is_del     1 iff the base on the padded read is a deletion
+ @field  is_head    ???
+ @field  is_tail    ???
+ @field  is_refskip ???
+ @field  aux        ???
+
+ @discussion See also bam_plbuf_push() and bam_lplbuf_push(). The
+ difference between the two functions is that the former does not
+ set bam_pileup1_t::level, while the later does. Level helps the
+ implementation of alignment viewers, but calculating this has some
+ overhead.
+ */
+typedef struct {
+    bam1_t *b;
+    int32_t qpos;
+    int indel, level;
+    uint32_t is_del:1, is_head:1, is_tail:1, is_refskip:1, aux:28;
+} bam_pileup1_t;
+
+typedef int (*bam_plp_auto_f)(void *data, bam1_t *b);
+
+struct __bam_plp_t;
+typedef struct __bam_plp_t *bam_plp_t;
+
+struct __bam_mplp_t;
+typedef struct __bam_mplp_t *bam_mplp_t;
+
+    /**
+     *  bam_plp_init() - sets an iterator over multiple
+     *  @func:      see mplp_func in bam_plcmd.c in samtools for an example. Expected return
+     *              status: 0 on success, -1 on end, < -1 on non-recoverable errors
+     *  @data:      user data to pass to @func
+     */
+    bam_plp_t bam_plp_init(bam_plp_auto_f func, void *data);
+    void bam_plp_destroy(bam_plp_t iter);
+    int bam_plp_push(bam_plp_t iter, const bam1_t *b);
+    const bam_pileup1_t *bam_plp_next(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp);
+    const bam_pileup1_t *bam_plp_auto(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp);
+    void bam_plp_set_maxcnt(bam_plp_t iter, int maxcnt);
+    void bam_plp_reset(bam_plp_t iter);
+
+    bam_mplp_t bam_mplp_init(int n, bam_plp_auto_f func, void **data);
+    /**
+     *  bam_mplp_init_overlaps() - if called, mpileup will detect overlapping
+     *  read pairs and for each base pair set the base quality of the
+     *  lower-quality base to zero, thus effectively discarding it from
+     *  calling. If the two bases are identical, the quality of the other base
+     *  is increased to the sum of their qualities (capped at 200), otherwise
+     *  it is multiplied by 0.8.
+     */
+    void bam_mplp_init_overlaps(bam_mplp_t iter);
+    void bam_mplp_destroy(bam_mplp_t iter);
+    void bam_mplp_set_maxcnt(bam_mplp_t iter, int maxcnt);
+    int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp);
+
+#endif // ~!defined(BAM_NO_PILEUP)
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/htslib/htslib/synced_bcf_reader.h b/htslib/htslib/synced_bcf_reader.h
new file mode 100644
index 0000000..b746bc9
--- /dev/null
+++ b/htslib/htslib/synced_bcf_reader.h
@@ -0,0 +1,302 @@
+/*  synced_bcf_reader.h -- stream through multiple VCF files.
+
+    Copyright (C) 2012-2014 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3 at sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+/*
+    The synced_bcf_reader allows to keep multiple VCFs open and stream them
+    using the next_line iterator in a seamless matter without worrying about
+    chromosomes and synchronizing the sites. This is used by vcfcheck to
+    compare multiple VCFs simultaneously and is used also for merging,
+    creating intersections, etc.
+
+    The synced_bcf_reader also provides API for reading indexed BCF/VCF,
+    hiding differences in BCF/VCF opening, indexing and reading.
+
+
+    Example of usage:
+
+        bcf_srs_t *sr = bcf_sr_init();
+        for (i=0; i<nfiles; i++)
+            bcf_sr_add_reader(sr,files[i]);
+        while ( bcf_sr_next_line(sr) )
+        {
+            for (i=0; i<nfiles; i++)
+            {
+                bcf1_t *line = bcf_sr_get_line(sr,i);
+                ...
+            }
+        }
+        bcf_sr_destroy(sr);
+*/
+
+#ifndef HTSLIB_SYNCED_BCF_READER_H
+#define HTSLIB_SYNCED_BCF_READER_H
+
+#include "hts.h"
+#include "vcf.h"
+#include "tbx.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+// How should be treated sites with the same position but different alleles
+#define COLLAPSE_NONE   0   // require the exact same set of alleles in all files
+#define COLLAPSE_SNPS   1   // allow different alleles, as long as they all are SNPs
+#define COLLAPSE_INDELS 2   // the same as above, but with indels
+#define COLLAPSE_ANY    4   // any combination of alleles can be returned by bcf_sr_next_line()
+#define COLLAPSE_SOME   8   // at least some of the ALTs must match
+#define COLLAPSE_BOTH  (COLLAPSE_SNPS|COLLAPSE_INDELS)
+
+typedef struct _bcf_sr_regions_t
+{
+    // for reading from tabix-indexed file (big data)
+    tbx_t *tbx;             // tabix index
+    hts_itr_t *itr;         // tabix iterator
+    kstring_t line;         // holder of the current line, set only when reading from tabix-indexed files
+    htsFile *file;
+    char *fname;
+    int is_bin;             // is open in binary mode (tabix access)
+    char **als;             // parsed alleles if targets_als set and _regions_match_alleles called
+    kstring_t als_str;      // block of parsed alleles
+    int nals, mals;         // number of set alleles and the size of allocated array
+    int als_type;           // alleles type, currently VCF_SNP or VCF_INDEL
+
+    // user handler to deal with skipped regions without a counterpart in VCFs
+    void (*missed_reg_handler)(struct _bcf_sr_regions_t *, void *);
+    void *missed_reg_data;
+
+    // for in-memory regions (small data)
+    struct _region_t *regs; // the regions
+
+    // shared by both tabix-index and in-memory regions
+    void *seq_hash;         // keys: sequence names, values: index to seqs
+    char **seq_names;       // sequence names
+    int nseqs;              // number of sequences (chromosomes) in the file
+    int iseq;               // current position: chr name, index to snames
+    int start, end;         // current position: start, end of the region (0-based)
+    int prev_seq, prev_start;
+}
+bcf_sr_regions_t;
+
+typedef struct
+{
+    htsFile *file;
+    tbx_t *tbx_idx;
+    hts_idx_t *bcf_idx;
+    bcf_hdr_t *header;
+    hts_itr_t *itr;
+    char *fname;
+    bcf1_t **buffer;                // cached VCF records. First is the current record synced across the reader
+    int nbuffer, mbuffer;           // number of cached records (including the current record); number of allocated records
+    int nfilter_ids, *filter_ids;   // -1 for ".", otherwise filter id as returned by bcf_hdr_id2int
+    int *samples, n_smpl;   // list of columns in the order consistent with bcf_srs_t.samples
+}
+bcf_sr_t;
+
+typedef enum
+{
+    open_failed, not_bgzf, idx_load_failed, file_type_error, api_usage_error,
+    header_error, no_eof
+}
+bcf_sr_error;
+
+typedef struct
+{
+    // Parameters controlling the logic
+    int collapse;       // How should the duplicate sites be treated. One of the COLLAPSE_* types above.
+    char *apply_filters;    // If set, sites where none of the FILTER strings is listed
+                            // will be skipped. Active only at the time of
+                            // initialization, that is during the add_reader()
+                            // calls. Therefore, each reader can be initialized with different
+                            // filters.
+    int require_index;  // Some tools do not need random access
+    int max_unpack;     // When reading VCFs and knowing some fields will not be needed, boost performance of vcf_parse1
+    int *has_line;      // Corresponds to return value of bcf_sr_next_line but is not limited by sizeof(int). Use bcf_sr_has_line macro to query.
+    bcf_sr_error errnum;
+
+    // Auxiliary data
+    bcf_sr_t *readers;
+    int nreaders;
+    int streaming;      // reading mode: index-jumping or streaming
+    int explicit_regs;  // was the list of regions se by bcf_sr_set_regions or guessed from tabix index?
+    char **samples; // List of samples
+    bcf_sr_regions_t *regions, *targets;    // see bcf_sr_set_[targets|regions] for description
+    int targets_als;    // subset to targets not only by position but also by alleles?
+    int targets_exclude;
+    kstring_t tmps;
+    int n_smpl;
+}
+bcf_srs_t;
+
+/** Init bcf_srs_t struct */
+bcf_srs_t *bcf_sr_init(void);
+
+/** Destroy  bcf_srs_t struct */
+void bcf_sr_destroy(bcf_srs_t *readers);
+
+char *bcf_sr_strerror(int errnum);
+
+
+/**
+ *  bcf_sr_add_reader() - open new reader
+ *  @readers: holder of the open readers
+ *  @fname:   the VCF file
+ *
+ *  Returns 1 if the call succeeded, or 0 on error.
+ *
+ *  See also the bcf_srs_t data structure for parameters controlling
+ *  the reader's logic.
+ */
+int bcf_sr_add_reader(bcf_srs_t *readers, const char *fname);
+void bcf_sr_remove_reader(bcf_srs_t *files, int i);
+
+/**
+ * bcf_sr_next_line() - the iterator
+ * @readers:    holder of the open readers
+ *
+ * Returns the number of readers which have the current line
+ * (bcf_sr_t.buffer[0]) set at this position. Use the bcf_sr_has_line macro to
+ * determine which of the readers are set.
+ */
+int bcf_sr_next_line(bcf_srs_t *readers);
+#define bcf_sr_has_line(readers, i) (readers)->has_line[i]
+#define bcf_sr_get_line(_readers, i) ((_readers)->has_line[i] ? ((_readers)->readers[i].buffer[0]) : NULL)
+#define bcf_sr_swap_line(_readers, i, lieu) { bcf1_t *tmp = lieu; lieu = (_readers)->readers[i].buffer[0]; (_readers)->readers[i].buffer[0] = tmp; }
+#define bcf_sr_region_done(_readers,i) (!(_readers)->has_line[i] && !(_readers)->readers[i].nbuffer ? 1 : 0)
+#define bcf_sr_get_header(_readers, i) (_readers)->readers[i].header
+#define bcf_sr_get_reader(_readers, i) &((_readers)->readers[i])
+
+/**
+ *  bcf_sr_seek() - set all readers to selected position
+ *  @seq:  sequence name; NULL to seek to start
+ *  @pos:  0-based coordinate
+ */
+int bcf_sr_seek(bcf_srs_t *readers, const char *seq, int pos);
+
+/**
+ * bcf_sr_set_samples() - sets active samples
+ * @readers: holder of the open readers
+ * @samples: this can be one of: file name with one sample per line;
+ *           or column-separated list of samples; or '-' for a list of
+ *           samples shared by all files. If first character is the
+ *           exclamation mark, all but the listed samples are included.
+ * @is_file: 0: list of samples; 1: file with sample names
+ *
+ * Returns 1 if the call succeeded, or 0 on error.
+ */
+int bcf_sr_set_samples(bcf_srs_t *readers, const char *samples, int is_file);
+
+/**
+ *  bcf_sr_set_targets(), bcf_sr_set_regions() - init targets/regions
+ *  @readers:   holder of the open readers
+ *  @targets:   list of regions, one-based and inclusive.
+ *  @is_fname:  0: targets is a comma-separated list of regions (chr,chr:from-to)
+ *              1: targets is a tabix indexed file with a list of regions
+ *              (<chr,pos> or <chr,from,to>)
+ *
+ *  Returns 0 if the call succeeded, or -1 on error.
+ *
+ *  Both functions behave the same way, unlisted positions will be skipped by
+ *  bcf_sr_next_line(). However, there is an important difference: regions use
+ *  index to jump to desired positions while targets streams the whole files
+ *  and merely skip unlisted positions.
+ *
+ *  Moreover, bcf_sr_set_targets() accepts an optional parameter $alleles which
+ *  is intepreted as a 1-based column index in the tab-delimited file where
+ *  alleles are listed. This in principle enables to perform the COLLAPSE_*
+ *  logic also with tab-delimited files. However, the current implementation
+ *  considers the alleles merely as a suggestion for prioritizing one of possibly
+ *  duplicate VCF lines. It is up to the caller to examine targets->als if
+ *  perfect match is sought after. Note that the duplicate positions in targets
+ *  file are currently not supported.
+ *  Targets (but not regions) can be prefixed with "^" to request logical complement,
+ *  for example "^X,Y,MT" indicates that sequences X, Y and MT should be skipped.
+ */
+int bcf_sr_set_targets(bcf_srs_t *readers, const char *targets, int is_file, int alleles);
+int bcf_sr_set_regions(bcf_srs_t *readers, const char *regions, int is_file);
+
+
+
+/*
+ *  bcf_sr_regions_init()
+ *  @regions:   regions can be either a comma-separated list of regions
+ *              (chr|chr:pos|chr:from-to|chr:from-) or VCF, BED, or
+ *              tab-delimited file (the default). Uncompressed files
+ *              are stored in memory while bgzip-compressed and tabix-indexed
+ *              region files are streamed.
+ *  @is_file:   0: regions is a comma-separated list of regions
+ *                  (chr|chr:pos|chr:from-to|chr:from-)
+ *              1: VCF, BED or tab-delimited file
+ *  @chr, from, to:
+ *              Column indexes of chromosome, start position and end position
+ *              in the tab-delimited file. The positions are 1-based and
+ *              inclusive.
+ *              These parameters are ignored when reading from VCF, BED or
+ *              tabix-indexed files. When end position column is not present,
+ *              supply 'from' in place of 'to'. When 'to' is negative, first
+ *              abs(to) will be attempted and if that fails, 'from' will be used
+ *              instead.
+ */
+bcf_sr_regions_t *bcf_sr_regions_init(const char *regions, int is_file, int chr, int from, int to);
+void bcf_sr_regions_destroy(bcf_sr_regions_t *regions);
+
+/*
+ *  bcf_sr_regions_seek() - seek to the chromosome block
+ *
+ *  Returns 0 on success or -1 on failure. Sets reg->seq appropriately and
+ *  reg->start,reg->end to -1.
+ */
+int bcf_sr_regions_seek(bcf_sr_regions_t *regions, const char *chr);
+
+/*
+ *  bcf_sr_regions_next() - retrieves next region. Returns 0 on success and -1
+ *  when all regions have been read. The fields reg->seq, reg->start and
+ *  reg->end are filled with the genomic coordinates on succes or with
+ *  NULL,-1,-1 when no region is available. The coordinates are 0-based,
+ *  inclusive.
+ */
+int bcf_sr_regions_next(bcf_sr_regions_t *reg);
+
+/*
+ *  bcf_sr_regions_overlap() - checks if the interval <start,end> overlaps any of
+ *  the regions, the coordinates are 0-based, inclusive. The coordinate queries
+ *  must come in ascending order.
+ *
+ *  Returns 0 if the position is in regions; -1 if the position is not in the
+ *  regions and more regions exist; -2 if not in the regions and there are no more
+ *  regions left.
+ */
+int bcf_sr_regions_overlap(bcf_sr_regions_t *reg, const char *seq, int start, int end);
+
+/*
+ *  bcf_sr_regions_flush() - calls repeatedly regs->missed_reg_handler() until
+ *  all remaining records are processed.
+ */
+void bcf_sr_regions_flush(bcf_sr_regions_t *regs);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/htslib/htslib/tbx.h b/htslib/htslib/tbx.h
new file mode 100644
index 0000000..65243b9
--- /dev/null
+++ b/htslib/htslib/tbx.h
@@ -0,0 +1,79 @@
+/*  tbx.h -- tabix API functions.
+
+    Copyright (C) 2009, 2012-2015 Genome Research Ltd.
+    Copyright (C) 2010, 2012 Broad Institute.
+
+    Author: Heng Li <lh3 at sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#ifndef HTSLIB_TBX_H
+#define HTSLIB_TBX_H
+
+#include "hts.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+#define TBX_MAX_SHIFT 31
+
+#define TBX_GENERIC 0
+#define TBX_SAM     1
+#define TBX_VCF     2
+#define TBX_UCSC    0x10000
+
+typedef struct {
+    int32_t preset;
+    int32_t sc, bc, ec; // seq col., beg col. and end col.
+    int32_t meta_char, line_skip;
+} tbx_conf_t;
+
+typedef struct {
+    tbx_conf_t conf;
+    hts_idx_t *idx;
+    void *dict;
+} tbx_t;
+
+extern tbx_conf_t tbx_conf_gff, tbx_conf_bed, tbx_conf_psltbl, tbx_conf_sam, tbx_conf_vcf;
+
+    #define tbx_itr_destroy(iter) hts_itr_destroy(iter)
+    #define tbx_itr_queryi(tbx, tid, beg, end) hts_itr_query((tbx)->idx, (tid), (beg), (end), tbx_readrec)
+    #define tbx_itr_querys(tbx, s) hts_itr_querys((tbx)->idx, (s), (hts_name2id_f)(tbx_name2id), (tbx), hts_itr_query, tbx_readrec)
+    #define tbx_itr_next(htsfp, tbx, itr, r) hts_itr_next(hts_get_bgzfp(htsfp), (itr), (r), (tbx))
+    #define tbx_bgzf_itr_next(bgzfp, tbx, itr, r) hts_itr_next((bgzfp), (itr), (r), (tbx))
+
+    int tbx_name2id(tbx_t *tbx, const char *ss);
+
+    /* Internal helper function used by tbx_itr_next() */
+    BGZF *hts_get_bgzfp(htsFile *fp);
+    int tbx_readrec(BGZF *fp, void *tbxv, void *sv, int *tid, int *beg, int *end);
+
+    int tbx_index_build(const char *fn, int min_shift, const tbx_conf_t *conf);
+    int tbx_index_build2(const char *fn, const char *fnidx, int min_shift, const tbx_conf_t *conf);
+    tbx_t *tbx_index_load(const char *fn);
+    tbx_t *tbx_index_load2(const char *fn, const char *fnidx);
+    const char **tbx_seqnames(tbx_t *tbx, int *n);  // free the array but not the values
+    void tbx_destroy(tbx_t *tbx);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/htslib/htslib/vcf.h b/htslib/htslib/vcf.h
new file mode 100644
index 0000000..1838c27
--- /dev/null
+++ b/htslib/htslib/vcf.h
@@ -0,0 +1,914 @@
+/*  vcf.h -- VCF/BCF API functions.
+
+    Copyright (C) 2012, 2013 Broad Institute.
+    Copyright (C) 2012-2014 Genome Research Ltd.
+
+    Author: Heng Li <lh3 at sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+/*
+    todo:
+        - make the function names consistent
+        - provide calls to abstract away structs as much as possible
+ */
+
+#ifndef HTSLIB_VCF_H
+#define HTSLIB_VCF_H
+
+#include <stdint.h>
+#include <limits.h>
+#include <assert.h>
+#include "hts.h"
+#include "kstring.h"
+#include "hts_defs.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*****************
+ * Header struct *
+ *****************/
+
+#define BCF_HL_FLT  0 // header line
+#define BCF_HL_INFO 1
+#define BCF_HL_FMT  2
+#define BCF_HL_CTG  3
+#define BCF_HL_STR  4 // structured header line TAG=<A=..,B=..>
+#define BCF_HL_GEN  5 // generic header line
+
+#define BCF_HT_FLAG 0 // header type
+#define BCF_HT_INT  1
+#define BCF_HT_REAL 2
+#define BCF_HT_STR  3
+
+#define BCF_VL_FIXED 0 // variable length
+#define BCF_VL_VAR   1
+#define BCF_VL_A     2
+#define BCF_VL_G     3
+#define BCF_VL_R     4
+
+/* === Dictionary ===
+
+   The header keeps three dictonaries. The first keeps IDs in the
+   "FILTER/INFO/FORMAT" lines, the second keeps the sequence names and lengths
+   in the "contig" lines and the last keeps the sample names. bcf_hdr_t::dict[]
+   is the actual hash table, which is opaque to the end users. In the hash
+   table, the key is the ID or sample name as a C string and the value is a
+   bcf_idinfo_t struct. bcf_hdr_t::id[] points to key-value pairs in the hash
+   table in the order that they appear in the VCF header. bcf_hdr_t::n[] is the
+   size of the hash table or, equivalently, the length of the id[] arrays.
+*/
+
+#define BCF_DT_ID       0 // dictionary type
+#define BCF_DT_CTG      1
+#define BCF_DT_SAMPLE   2
+
+// Complete textual representation of a header line
+typedef struct {
+    int type;       // One of the BCF_HL_* type
+    char *key;      // The part before '=', i.e. FILTER/INFO/FORMAT/contig/fileformat etc.
+    char *value;    // Set only for generic lines, NULL for FILTER/INFO, etc.
+    int nkeys;              // Number of structured fields
+    char **keys, **vals;    // The key=value pairs
+} bcf_hrec_t;
+
+typedef struct {
+    uint32_t info[3];  // stores Number:20, var:4, Type:4, ColType:4 in info[0..2]
+                       // for BCF_HL_FLT,INFO,FMT and contig length in info[0] for BCF_HL_CTG
+    bcf_hrec_t *hrec[3];
+    int id;
+} bcf_idinfo_t;
+
+typedef struct {
+    const char *key;
+    const bcf_idinfo_t *val;
+} bcf_idpair_t;
+
+// Note that bcf_hdr_t structs must always be created via bcf_hdr_init()
+typedef struct {
+    int32_t n[3];           // n:the size of the dictionary block in use, (allocated size, m, is below to preserve ABI)
+    bcf_idpair_t *id[3];
+    void *dict[3];          // ID dictionary, contig dict and sample dict
+    char **samples;
+    bcf_hrec_t **hrec;
+    int nhrec, dirty;
+    int ntransl, *transl[2];    // for bcf_translate()
+    int nsamples_ori;           // for bcf_hdr_set_samples()
+    uint8_t *keep_samples;
+    kstring_t mem;
+    int32_t m[3];          // m: allocated size of the dictionary block in use (see n above)
+} bcf_hdr_t;
+
+extern uint8_t bcf_type_shift[];
+
+/**************
+ * VCF record *
+ **************/
+
+#define BCF_BT_NULL     0
+#define BCF_BT_INT8     1
+#define BCF_BT_INT16    2
+#define BCF_BT_INT32    3
+#define BCF_BT_FLOAT    5
+#define BCF_BT_CHAR     7
+
+#define VCF_REF   0
+#define VCF_SNP   1
+#define VCF_MNP   2
+#define VCF_INDEL 4
+#define VCF_OTHER 8
+
+typedef struct {
+    int type, n;    // variant type and the number of bases affected, negative for deletions
+} variant_t;
+
+typedef struct {
+    int id;             // id: numeric tag id, the corresponding string is bcf_hdr_t::id[BCF_DT_ID][$id].key
+    int n, size, type;  // n: number of values per-sample; size: number of bytes per-sample; type: one of BCF_BT_* types
+    uint8_t *p;         // same as vptr and vptr_* in bcf_info_t below
+    uint32_t p_len;
+    uint32_t p_off:31, p_free:1;
+} bcf_fmt_t;
+
+typedef struct {
+    int key;        // key: numeric tag id, the corresponding string is bcf_hdr_t::id[BCF_DT_ID][$key].key
+    int type, len;  // type: one of BCF_BT_* types; len: vector length, 1 for scalars
+    union {
+        int32_t i; // integer value
+        float f;   // float value
+    } v1; // only set if $len==1; for easier access
+    uint8_t *vptr;          // pointer to data array in bcf1_t->shared.s, excluding the size+type and tag id bytes
+    uint32_t vptr_len;      // length of the vptr block or, when set, of the vptr_mod block, excluding offset
+    uint32_t vptr_off:31,   // vptr offset, i.e., the size of the INFO key plus size+type bytes
+            vptr_free:1;    // indicates that vptr-vptr_off must be freed; set only when modified and the new
+                            //    data block is bigger than the original
+} bcf_info_t;
+
+
+#define BCF1_DIRTY_ID  1
+#define BCF1_DIRTY_ALS 2
+#define BCF1_DIRTY_FLT 4
+#define BCF1_DIRTY_INF 8
+
+typedef struct {
+    int m_fmt, m_info, m_id, m_als, m_allele, m_flt; // allocated size (high-water mark); do not change
+    int n_flt;  // Number of FILTER fields
+    int *flt;   // FILTER keys in the dictionary
+    char *id, *als;     // ID and REF+ALT block (\0-seperated)
+    char **allele;      // allele[0] is the REF (allele[] pointers to the als block); all null terminated
+    bcf_info_t *info;   // INFO
+    bcf_fmt_t *fmt;     // FORMAT and individual sample
+    variant_t *var;     // $var and $var_type set only when set_variant_types called
+    int n_var, var_type;
+    int shared_dirty;   // if set, shared.s must be recreated on BCF output
+    int indiv_dirty;    // if set, indiv.s must be recreated on BCF output
+} bcf_dec_t;
+
+
+#define BCF_ERR_CTG_UNDEF 1
+#define BCF_ERR_TAG_UNDEF 2
+#define BCF_ERR_NCOLS     4
+#define BCF_ERR_LIMITS    8
+#define BCF_ERR_CHAR     16
+#define BCF_ERR_CTG_INVALID   32
+#define BCF_ERR_TAG_INVALID   64
+
+/*
+    The bcf1_t structure corresponds to one VCF/BCF line. Reading from VCF file
+    is slower because the string is first to be parsed, packed into BCF line
+    (done in vcf_parse), then unpacked into internal bcf1_t structure. If it
+    is known in advance that some of the fields will not be required (notably
+    the sample columns), parsing of these can be skipped by setting max_unpack
+    appropriately.
+    Similarly, it is fast to output a BCF line because the columns (kept in
+    shared.s, indiv.s, etc.) are written directly by bcf_write, whereas a VCF
+    line must be formatted in vcf_format.
+ */
+typedef struct {
+    int32_t rid;  // CHROM
+    int32_t pos;  // POS
+    int32_t rlen; // length of REF
+    float qual;   // QUAL
+    uint32_t n_info:16, n_allele:16;
+    uint32_t n_fmt:8, n_sample:24;
+    kstring_t shared, indiv;
+    bcf_dec_t d; // lazy evaluation: $d is not generated by bcf_read(), but by explicitly calling bcf_unpack()
+    int max_unpack;         // Set to BCF_UN_STR, BCF_UN_FLT, or BCF_UN_INFO to boost performance of vcf_parse when some of the fields won't be needed
+    int unpacked;           // remember what has been unpacked to allow calling bcf_unpack() repeatedly without redoing the work
+    int unpack_size[3];     // the original block size of ID, REF+ALT and FILTER
+    int errcode;    // one of BCF_ERR_* codes
+} bcf1_t;
+
+/*******
+ * API *
+ *******/
+
+    /***********************************************************************
+     *  BCF and VCF I/O
+     *
+     *  A note about naming conventions: htslib internally represents VCF
+     *  records as bcf1_t data structures, therefore most functions are
+     *  prefixed with bcf_. There are a few exceptions where the functions must
+     *  be aware of both BCF and VCF worlds, such as bcf_parse vs vcf_parse. In
+     *  these cases, functions prefixed with bcf_ are more general and work
+     *  with both BCF and VCF.
+     *
+     ***********************************************************************/
+
+    /** These macros are defined only for consistency with other parts of htslib */
+    #define bcf_init1()         bcf_init()
+    #define bcf_read1(fp,h,v)   bcf_read((fp),(h),(v))
+    #define vcf_read1(fp,h,v)   vcf_read((fp),(h),(v))
+    #define bcf_write1(fp,h,v)  bcf_write((fp),(h),(v))
+    #define vcf_write1(fp,h,v)  vcf_write((fp),(h),(v))
+    #define bcf_destroy1(v)     bcf_destroy(v)
+    #define bcf_empty1(v)       bcf_empty(v)
+    #define vcf_parse1(s,h,v)   vcf_parse((s),(h),(v))
+    #define bcf_clear1(v)       bcf_clear(v)
+    #define vcf_format1(h,v,s)  vcf_format((h),(v),(s))
+
+    /**
+     *  bcf_hdr_init() - create an empty BCF header.
+     *  @param mode    "r" or "w"
+     *
+     *  When opened for writing, the mandatory fileFormat and
+     *  FILTER=PASS lines are added automatically.
+     */
+    bcf_hdr_t *bcf_hdr_init(const char *mode);
+
+    /** Destroy a BCF header struct */
+    void bcf_hdr_destroy(bcf_hdr_t *h);
+
+    /** Initialize a bcf1_t object; equivalent to calloc(1, sizeof(bcf1_t)) */
+    bcf1_t *bcf_init(void);
+
+    /** Deallocate a bcf1_t object */
+    void bcf_destroy(bcf1_t *v);
+
+    /**
+     *  Same as bcf_destroy() but frees only the memory allocated by bcf1_t,
+     *  not the bcf1_t object itself.
+     */
+    void bcf_empty(bcf1_t *v);
+
+    /**
+     *  Make the bcf1_t object ready for next read. Intended mostly for
+     *  internal use, the user should rarely need to call this function
+     *  directly.
+     */
+    void bcf_clear(bcf1_t *v);
+
+
+    /** bcf_open and vcf_open mode: please see hts_open() in hts.h */
+    typedef htsFile vcfFile;
+    #define bcf_open(fn, mode) hts_open((fn), (mode))
+    #define vcf_open(fn, mode) hts_open((fn), (mode))
+    #define bcf_close(fp) hts_close(fp)
+    #define vcf_close(fp) hts_close(fp)
+
+    /** Reads VCF or BCF header */
+    bcf_hdr_t *bcf_hdr_read(htsFile *fp);
+
+    /**
+     *  bcf_hdr_set_samples() - for more efficient VCF parsing when only one/few samples are needed
+     *  @samples: samples to include or exclude from file or as a comma-separated string.
+     *              LIST|FILE   .. select samples in list/file
+     *              ^LIST|FILE  .. exclude samples from list/file
+     *              -           .. include all samples
+     *              NULL        .. exclude all samples
+     *  @is_file: @samples is a file (1) or a comma-separated list (0)
+     *
+     *  The bottleneck of VCF reading is parsing of genotype fields. If the
+     *  reader knows in advance that only subset of samples is needed (possibly
+     *  no samples at all), the performance of bcf_read() can be significantly
+     *  improved by calling bcf_hdr_set_samples after bcf_hdr_read().
+     *  The function bcf_read() will subset the VCF/BCF records automatically
+     *  with the notable exception when reading records via bcf_itr_next().
+     *  In this case, bcf_subset_format() must be called explicitly, because
+     *  bcf_readrec() does not see the header.
+     *
+     *  Returns 0 on success, -1 on error or a positive integer if the list
+     *  contains samples not present in the VCF header. In such a case, the
+     *  return value is the index of the offending sample.
+     */
+    int bcf_hdr_set_samples(bcf_hdr_t *hdr, const char *samples, int is_file);
+    int bcf_subset_format(const bcf_hdr_t *hdr, bcf1_t *rec);
+
+
+    /** Writes VCF or BCF header */
+    int bcf_hdr_write(htsFile *fp, bcf_hdr_t *h);
+
+    /**
+     * Parse VCF line contained in kstring and populate the bcf1_t struct
+     * The line must not end with \n or \r characters.
+     */
+    int vcf_parse(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v);
+
+    /** The opposite of vcf_parse. It should rarely be called directly, see vcf_write */
+    int vcf_format(const bcf_hdr_t *h, const bcf1_t *v, kstring_t *s);
+
+    /**
+     *  bcf_read() - read next VCF or BCF record
+     *
+     *  Returns -1 on critical errors, 0 otherwise. On errors which are not
+     *  critical for reading, such as missing header definitions, v->errcode is
+     *  set to one of BCF_ERR* code and must be checked before calling
+     *  vcf_write().
+     */
+    int bcf_read(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v);
+
+    /**
+     *  bcf_unpack() - unpack/decode a BCF record (fills the bcf1_t::d field)
+     *
+     *  Note that bcf_unpack() must be called even when reading VCF. It is safe
+     *  to call the function repeatedly, it will not unpack the same field
+     *  twice.
+     */
+    #define BCF_UN_STR  1       // up to ALT inclusive
+    #define BCF_UN_FLT  2       // up to FILTER
+    #define BCF_UN_INFO 4       // up to INFO
+    #define BCF_UN_SHR  (BCF_UN_STR|BCF_UN_FLT|BCF_UN_INFO) // all shared information
+    #define BCF_UN_FMT  8                           // unpack format and each sample
+    #define BCF_UN_IND  BCF_UN_FMT                  // a synonymo of BCF_UN_FMT
+    #define BCF_UN_ALL  (BCF_UN_SHR|BCF_UN_FMT)     // everything
+    int bcf_unpack(bcf1_t *b, int which);
+
+    /*
+     *  bcf_dup() - create a copy of BCF record.
+     *
+     *  Note that bcf_unpack() must be called on the returned copy as if it was
+     *  obtained from bcf_read(). Also note that bcf_dup() calls bcf_sync1(src)
+     *  internally to reflect any changes made by bcf_update_* functions.
+     */
+    bcf1_t *bcf_dup(bcf1_t *src);
+    bcf1_t *bcf_copy(bcf1_t *dst, bcf1_t *src);
+
+    /**
+     *  bcf_write() - write one VCF or BCF record. The type is determined at the open() call.
+     */
+    int bcf_write(htsFile *fp, bcf_hdr_t *h, bcf1_t *v);
+
+    /**
+     *  The following functions work only with VCFs and should rarely be called
+     *  directly. Usually one wants to use their bcf_* alternatives, which work
+     *  transparently with both VCFs and BCFs.
+     */
+    bcf_hdr_t *vcf_hdr_read(htsFile *fp);
+    int vcf_hdr_write(htsFile *fp, const bcf_hdr_t *h);
+    int vcf_read(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v);
+    int vcf_write(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v);
+
+    /** Helper function for the bcf_itr_next() macro; internal use, ignore it */
+    int bcf_readrec(BGZF *fp, void *null, void *v, int *tid, int *beg, int *end);
+
+
+
+    /**************************************************************************
+     *  Header querying and manipulation routines
+     **************************************************************************/
+
+    /** Create a new header using the supplied template */
+    bcf_hdr_t *bcf_hdr_dup(const bcf_hdr_t *hdr);
+
+    /**
+     *  Copy header lines from src to dst if not already present in dst. See also bcf_translate().
+     *  Returns 0 on success or sets a bit on error:
+     *      1 .. conflicting definitions of tag length
+     *      // todo
+     */
+    int bcf_hdr_combine(bcf_hdr_t *dst, const bcf_hdr_t *src) HTS_DEPRECATED("Please use bcf_hdr_merge instead");
+
+    /**
+     *  bcf_hdr_merge() - copy header lines from src to dst, see also bcf_translate()
+     *  @param dst: the destination header to be merged into, NULL on the first pass
+     *  @param src: the source header
+     *
+     *  Notes:
+     *      - use as:
+     *          bcf_hdr_t *dst = NULL;
+     *          for (i=0; i<nsrc; i++) dst = bcf_hdr_merge(dst,src[i]);
+     *
+     *      - bcf_hdr_merge() replaces bcf_hdr_combine() which had a problem when
+     *      combining multiple BCF headers. The current bcf_hdr_combine()
+     *      does not have this problem, but became slow when used for many files.
+     */
+    bcf_hdr_t *bcf_hdr_merge(bcf_hdr_t *dst, const bcf_hdr_t *src);
+
+    /**
+     *  bcf_hdr_add_sample() - add a new sample.
+     *  @param sample:  sample name to be added
+     */
+    int bcf_hdr_add_sample(bcf_hdr_t *hdr, const char *sample);
+
+    /** Read VCF header from a file and update the header */
+    int bcf_hdr_set(bcf_hdr_t *hdr, const char *fname);
+
+    /** Returns formatted header (newly allocated string) and its length,
+     *  excluding the terminating \0. If is_bcf parameter is unset, IDX
+     *  fields are discarded.
+     */
+    char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len);
+
+    /** Append new VCF header line, returns 0 on success */
+    int bcf_hdr_append(bcf_hdr_t *h, const char *line);
+    int bcf_hdr_printf(bcf_hdr_t *h, const char *format, ...);
+
+    /** VCF version, e.g. VCFv4.2 */
+    const char *bcf_hdr_get_version(const bcf_hdr_t *hdr);
+    void bcf_hdr_set_version(bcf_hdr_t *hdr, const char *version);
+
+    /**
+     *  bcf_hdr_remove() - remove VCF header tag
+     *  @param type:      one of BCF_HL_*
+     *  @param key:       tag name or NULL to remove all tags of the given type
+     */
+    void bcf_hdr_remove(bcf_hdr_t *h, int type, const char *key);
+
+    /**
+     *  bcf_hdr_subset() - creates a new copy of the header removing unwanted samples
+     *  @param n:        number of samples to keep
+     *  @param samples:  names of the samples to keep
+     *  @param imap:     mapping from index in @samples to the sample index in the original file
+     *
+     *  Sample names not present in h0 are ignored. The number of unmatched samples can be checked
+     *  by comparing n and bcf_hdr_nsamples(out_hdr).
+     *  This function can be used to reorder samples.
+     *  See also bcf_subset() which subsets individual records.
+     */
+    bcf_hdr_t *bcf_hdr_subset(const bcf_hdr_t *h0, int n, char *const* samples, int *imap);
+
+    /** Creates a list of sequence names. It is up to the caller to free the list (but not the sequence names) */
+    const char **bcf_hdr_seqnames(const bcf_hdr_t *h, int *nseqs);
+
+    /** Get number of samples */
+    #define bcf_hdr_nsamples(hdr) (hdr)->n[BCF_DT_SAMPLE]
+
+
+    /** The following functions are for internal use and should rarely be called directly */
+    int bcf_hdr_parse(bcf_hdr_t *hdr, char *htxt);
+    int bcf_hdr_sync(bcf_hdr_t *h);
+    bcf_hrec_t *bcf_hdr_parse_line(const bcf_hdr_t *h, const char *line, int *len);
+    void bcf_hrec_format(const bcf_hrec_t *hrec, kstring_t *str);
+    int bcf_hdr_add_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec);
+    /**
+     *  bcf_hdr_get_hrec() - get header line info
+     *  @param type:  one of the BCF_HL_* types: FLT,INFO,FMT,CTG,STR,GEN
+     *  @param key:   the header key for generic lines (e.g. "fileformat"), any field
+     *                  for structured lines, typically "ID".
+     *  @param value: the value which pairs with key. Can be be NULL for BCF_HL_GEN
+     *  @param str_class: the class of BCF_HL_STR line (e.g. "ALT" or "SAMPLE"), otherwise NULL
+     */
+    bcf_hrec_t *bcf_hdr_get_hrec(const bcf_hdr_t *hdr, int type, const char *key, const char *value, const char *str_class);
+    bcf_hrec_t *bcf_hrec_dup(bcf_hrec_t *hrec);
+    void bcf_hrec_add_key(bcf_hrec_t *hrec, const char *str, int len);
+    void bcf_hrec_set_val(bcf_hrec_t *hrec, int i, const char *str, int len, int is_quoted);
+    int bcf_hrec_find_key(bcf_hrec_t *hrec, const char *key);
+    void hrec_add_idx(bcf_hrec_t *hrec, int idx);
+    void bcf_hrec_destroy(bcf_hrec_t *hrec);
+
+
+
+    /**************************************************************************
+     *  Individual record querying and manipulation routines
+     **************************************************************************/
+
+    /** See the description of bcf_hdr_subset() */
+    int bcf_subset(const bcf_hdr_t *h, bcf1_t *v, int n, int *imap);
+
+    /**
+     *  bcf_translate() - translate tags ids to be consistent with different header. This function
+     *                    is useful when lines from multiple VCF need to be combined.
+     *  @dst_hdr:   the destination header, to be used in bcf_write(), see also bcf_hdr_combine()
+     *  @src_hdr:   the source header, used in bcf_read()
+     *  @src_line:  line obtained by bcf_read()
+     */
+    int bcf_translate(const bcf_hdr_t *dst_hdr, bcf_hdr_t *src_hdr, bcf1_t *src_line);
+
+    /**
+     *  bcf_get_variant_type[s]()  - returns one of VCF_REF, VCF_SNP, etc
+     */
+    int bcf_get_variant_types(bcf1_t *rec);
+    int bcf_get_variant_type(bcf1_t *rec, int ith_allele);
+    int bcf_is_snp(bcf1_t *v);
+
+    /**
+     *  bcf_update_filter() - sets the FILTER column
+     *  @flt_ids:  The filter IDs to set, numeric IDs returned by bcf_hdr_id2int(hdr, BCF_DT_ID, "PASS")
+     *  @n:        Number of filters. If n==0, all filters are removed
+     */
+    int bcf_update_filter(const bcf_hdr_t *hdr, bcf1_t *line, int *flt_ids, int n);
+    /**
+     *  bcf_add_filter() - adds to the FILTER column
+     *  @flt_id:   filter ID to add, numeric ID returned by bcf_hdr_id2int(hdr, BCF_DT_ID, "PASS")
+     *
+     *  If flt_id is PASS, all existing filters are removed first. If other than PASS, existing PASS is removed.
+     */
+    int bcf_add_filter(const bcf_hdr_t *hdr, bcf1_t *line, int flt_id);
+    /**
+     *  bcf_remove_filter() - removes from the FILTER column
+     *  @flt_id:   filter ID to remove, numeric ID returned by bcf_hdr_id2int(hdr, BCF_DT_ID, "PASS")
+     *  @pass:     when set to 1 and no filters are present, set to PASS
+     */
+    int bcf_remove_filter(const bcf_hdr_t *hdr, bcf1_t *line, int flt_id, int pass);
+    /**
+     *  Returns 1 if present, 0 if absent, or -1 if filter does not exist. "PASS" and "." can be used interchangeably.
+     */
+    int bcf_has_filter(const bcf_hdr_t *hdr, bcf1_t *line, char *filter);
+    /**
+     *  bcf_update_alleles() and bcf_update_alleles_str() - update REF and ALLT column
+     *  @alleles:           Array of alleles
+     *  @nals:              Number of alleles
+     *  @alleles_string:    Comma-separated alleles, starting with the REF allele
+     */
+    int bcf_update_alleles(const bcf_hdr_t *hdr, bcf1_t *line, const char **alleles, int nals);
+    int bcf_update_alleles_str(const bcf_hdr_t *hdr, bcf1_t *line, const char *alleles_string);
+
+    /**
+      *  bcf_update_id() - sets new ID string
+      *  bcf_add_id() - adds to the ID string checking for duplicates
+      */
+    int bcf_update_id(const bcf_hdr_t *hdr, bcf1_t *line, const char *id);
+    int bcf_add_id(const bcf_hdr_t *hdr, bcf1_t *line, const char *id);
+
+    /*
+     *  bcf_update_info_*() - functions for updating INFO fields
+     *  @hdr:       the BCF header
+     *  @line:      VCF line to be edited
+     *  @key:       the INFO tag to be updated
+     *  @values:    pointer to the array of values. Pass NULL to remove the tag.
+     *  @n:         number of values in the array. When set to 0, the INFO tag is removed
+     *
+     *  The @string in bcf_update_info_flag() is optional, @n indicates whether
+     *  the flag is set or removed.
+     *
+     *  Returns 0 on success or negative value on error.
+     */
+    #define bcf_update_info_int32(hdr,line,key,values,n)   bcf_update_info((hdr),(line),(key),(values),(n),BCF_HT_INT)
+    #define bcf_update_info_float(hdr,line,key,values,n)   bcf_update_info((hdr),(line),(key),(values),(n),BCF_HT_REAL)
+    #define bcf_update_info_flag(hdr,line,key,string,n)    bcf_update_info((hdr),(line),(key),(string),(n),BCF_HT_FLAG)
+    #define bcf_update_info_string(hdr,line,key,string)    bcf_update_info((hdr),(line),(key),(string),1,BCF_HT_STR)
+    int bcf_update_info(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const void *values, int n, int type);
+
+    /*
+     *  bcf_update_format_*() - functions for updating FORMAT fields
+     *  @values:    pointer to the array of values, the same number of elements
+     *              is expected for each sample. Missing values must be padded
+     *              with bcf_*_missing or bcf_*_vector_end values.
+     *  @n:         number of values in the array. If n==0, existing tag is removed.
+     *
+     *  The function bcf_update_format_string() is a higher-level (slower) variant of
+     *  bcf_update_format_char(). The former accepts array of \0-terminated strings
+     *  whereas the latter requires that the strings are collapsed into a single array
+     *  of fixed-length strings. In case of strings with variable length, shorter strings
+     *  can be \0-padded. Note that the collapsed strings passed to bcf_update_format_char()
+     *  are not \0-terminated.
+     *
+     *  Returns 0 on success or negative value on error.
+     */
+    #define bcf_update_format_int32(hdr,line,key,values,n) bcf_update_format((hdr),(line),(key),(values),(n),BCF_HT_INT)
+    #define bcf_update_format_float(hdr,line,key,values,n) bcf_update_format((hdr),(line),(key),(values),(n),BCF_HT_REAL)
+    #define bcf_update_format_char(hdr,line,key,values,n) bcf_update_format((hdr),(line),(key),(values),(n),BCF_HT_STR)
+    #define bcf_update_genotypes(hdr,line,gts,n) bcf_update_format((hdr),(line),"GT",(gts),(n),BCF_HT_INT)     // See bcf_gt_ macros below
+    int bcf_update_format_string(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const char **values, int n);
+    int bcf_update_format(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const void *values, int n, int type);
+
+    // Macros for setting genotypes correctly, for use with bcf_update_genotypes only; idx corresponds
+    // to VCF's GT (1-based index to ALT or 0 for the reference allele) and val is the opposite, obtained
+    // from bcf_get_genotypes() below.
+    #define bcf_gt_phased(idx)      (((idx)+1)<<1|1)
+    #define bcf_gt_unphased(idx)    (((idx)+1)<<1)
+    #define bcf_gt_missing          0 
+    #define bcf_gt_is_missing(val)  ((val)>>1 ? 0 : 1)
+    #define bcf_gt_is_phased(idx)   ((idx)&1)
+    #define bcf_gt_allele(val)      (((val)>>1)-1)
+
+    /** Conversion between alleles indexes to Number=G genotype index (assuming diploid, all 0-based) */
+    #define bcf_alleles2gt(a,b) ((a)>(b)?((a)*((a)+1)/2+(b)):((b)*((b)+1)/2+(a)))
+    static inline void bcf_gt2alleles(int igt, int *a, int *b)
+    {
+        int k = 0, dk = 1;
+        while ( k<igt ) { dk++; k += dk; }
+        *b = dk - 1; *a = igt - k + *b;
+    }
+
+    /**
+     * bcf_get_fmt() - returns pointer to FORMAT's field data
+     * @header: for access to BCF_DT_ID dictionary
+     * @line:   VCF line obtained from vcf_parse1
+     * @fmt:    one of GT,PL,...
+     *
+     * Returns bcf_fmt_t* if the call succeeded, or returns NULL when the field
+     * is not available.
+     */
+    bcf_fmt_t *bcf_get_fmt(const bcf_hdr_t *hdr, bcf1_t *line, const char *key);
+    bcf_info_t *bcf_get_info(const bcf_hdr_t *hdr, bcf1_t *line, const char *key);
+
+    /**
+     * bcf_get_*_id() - returns pointer to FORMAT/INFO field data given the header index instead of the string ID
+     * @line: VCF line obtained from vcf_parse1
+     * @id:  The header index for the tag, obtained from bcf_hdr_id2int()
+     * 
+     * Returns bcf_fmt_t* / bcf_info_t*. These functions do not check if the index is valid 
+     * as their goal is to avoid the header lookup.
+     */
+    bcf_fmt_t *bcf_get_fmt_id(bcf1_t *line, const int id);
+    bcf_info_t *bcf_get_info_id(bcf1_t *line, const int id);
+
+    /**
+     *  bcf_get_info_*() - get INFO values, integers or floats
+     *  @hdr:       BCF header
+     *  @line:      BCF record
+     *  @tag:       INFO tag to retrieve
+     *  @dst:       *dst is pointer to a memory location, can point to NULL
+     *  @ndst:      pointer to the size of allocated memory
+     *
+     *  Returns negative value on error or the number of written values on
+     *  success. bcf_get_info_string() returns on success the number of
+     *  characters written excluding the null-terminating byte. bcf_get_info_flag()
+     *  returns 1 when flag is set or 0 if not.
+     *
+     *  List of return codes:
+     *      -1 .. no such INFO tag defined in the header
+     *      -2 .. clash between types defined in the header and encountered in the VCF record
+     *      -3 .. tag is not present in the VCF record
+     */
+    #define bcf_get_info_int32(hdr,line,tag,dst,ndst)  bcf_get_info_values(hdr,line,tag,(void**)(dst),ndst,BCF_HT_INT)
+    #define bcf_get_info_float(hdr,line,tag,dst,ndst)  bcf_get_info_values(hdr,line,tag,(void**)(dst),ndst,BCF_HT_REAL)
+    #define bcf_get_info_string(hdr,line,tag,dst,ndst) bcf_get_info_values(hdr,line,tag,(void**)(dst),ndst,BCF_HT_STR)
+    #define bcf_get_info_flag(hdr,line,tag,dst,ndst)   bcf_get_info_values(hdr,line,tag,(void**)(dst),ndst,BCF_HT_FLAG)
+    int bcf_get_info_values(const bcf_hdr_t *hdr, bcf1_t *line, const char *tag, void **dst, int *ndst, int type);
+
+    /**
+     *  bcf_get_format_*() - same as bcf_get_info*() above
+     *
+     *  The function bcf_get_format_string() is a higher-level (slower) variant of bcf_get_format_char().
+     *  see the description of bcf_update_format_string() and bcf_update_format_char() above.
+     *  Unlike other bcf_get_format__*() functions, bcf_get_format_string() allocates two arrays:
+     *  a single block of \0-terminated strings collapsed into a single array and an array of pointers
+     *  to these strings. Both arrays must be cleaned by the user.
+     *
+     *  Returns negative value on error or the number of written values on success.
+     *
+     *  Example:
+     *      int ndst = 0; char **dst = NULL;
+     *      if ( bcf_get_format_string(hdr, line, "XX", &dst, &ndst) > 0 )
+     *          for (i=0; i<bcf_hdr_nsamples(hdr); i++) printf("%s\n", dst[i]);
+     *      free(dst[0]); free(dst);
+     *
+     *  Example:
+     *      int ngt, *gt_arr = NULL, ngt_arr = 0;
+     *      ngt = bcf_get_genotypes(hdr, line, &gt_arr, &ngt_arr);
+     */
+    #define bcf_get_format_int32(hdr,line,tag,dst,ndst)  bcf_get_format_values(hdr,line,tag,(void**)(dst),ndst,BCF_HT_INT)
+    #define bcf_get_format_float(hdr,line,tag,dst,ndst)  bcf_get_format_values(hdr,line,tag,(void**)(dst),ndst,BCF_HT_REAL)
+    #define bcf_get_format_char(hdr,line,tag,dst,ndst)   bcf_get_format_values(hdr,line,tag,(void**)(dst),ndst,BCF_HT_STR)
+    #define bcf_get_genotypes(hdr,line,dst,ndst)         bcf_get_format_values(hdr,line,"GT",(void**)(dst),ndst,BCF_HT_INT)
+    int bcf_get_format_string(const bcf_hdr_t *hdr, bcf1_t *line, const char *tag, char ***dst, int *ndst);
+    int bcf_get_format_values(const bcf_hdr_t *hdr, bcf1_t *line, const char *tag, void **dst, int *ndst, int type);
+
+
+
+    /**************************************************************************
+     *  Helper functions
+     **************************************************************************/
+
+    /**
+     *  bcf_hdr_id2int() - Translates string into numeric ID
+     *  bcf_hdr_int2id() - Translates numeric ID into string
+     *  @type:     one of BCF_DT_ID, BCF_DT_CTG, BCF_DT_SAMPLE
+     *  @id:       tag name, such as: PL, DP, GT, etc.
+     *
+     *  Returns -1 if string is not in dictionary, otherwise numeric ID which identifies
+     *  fields in BCF records.
+     */
+    int bcf_hdr_id2int(const bcf_hdr_t *hdr, int type, const char *id);
+    #define bcf_hdr_int2id(hdr,type,int_id) ((hdr)->id[type][int_id].key)
+
+    /**
+     *  bcf_hdr_name2id() - Translates sequence names (chromosomes) into numeric ID
+     *  bcf_hdr_id2name() - Translates numeric ID to sequence name
+     */
+    static inline int bcf_hdr_name2id(const bcf_hdr_t *hdr, const char *id) { return bcf_hdr_id2int(hdr, BCF_DT_CTG, id); }
+    static inline const char *bcf_hdr_id2name(const bcf_hdr_t *hdr, int rid) { return hdr->id[BCF_DT_CTG][rid].key; }
+    static inline const char *bcf_seqname(const bcf_hdr_t *hdr, bcf1_t *rec) { return hdr->id[BCF_DT_CTG][rec->rid].key; }
+
+    /**
+     *  bcf_hdr_id2*() - Macros for accessing bcf_idinfo_t
+     *  @type:      one of BCF_HL_FLT, BCF_HL_INFO, BCF_HL_FMT
+     *  @int_id:    return value of bcf_hdr_id2int, must be >=0
+     *
+     *  The returned values are:
+     *     bcf_hdr_id2length   ..  whether the number of values is fixed or variable, one of BCF_VL_*
+     *     bcf_hdr_id2number   ..  the number of values, 0xfffff for variable length fields
+     *     bcf_hdr_id2type     ..  the field type, one of BCF_HT_*
+     *     bcf_hdr_id2coltype  ..  the column type, one of BCF_HL_*
+     *
+     *  Notes: Prior to using the macros, the presence of the info should be
+     *  tested with bcf_hdr_idinfo_exists().
+     */
+    #define bcf_hdr_id2length(hdr,type,int_id)  ((hdr)->id[BCF_DT_ID][int_id].val->info[type]>>8 & 0xf)
+    #define bcf_hdr_id2number(hdr,type,int_id)  ((hdr)->id[BCF_DT_ID][int_id].val->info[type]>>12)
+    #define bcf_hdr_id2type(hdr,type,int_id)    ((hdr)->id[BCF_DT_ID][int_id].val->info[type]>>4 & 0xf)
+    #define bcf_hdr_id2coltype(hdr,type,int_id) ((hdr)->id[BCF_DT_ID][int_id].val->info[type] & 0xf)
+    #define bcf_hdr_idinfo_exists(hdr,type,int_id)  ((int_id<0 || bcf_hdr_id2coltype(hdr,type,int_id)==0xf) ? 0 : 1)
+    #define bcf_hdr_id2hrec(hdr,dict_type,col_type,int_id)    ((hdr)->id[(dict_type)==BCF_DT_CTG?BCF_DT_CTG:BCF_DT_ID][int_id].val->hrec[(dict_type)==BCF_DT_CTG?0:(col_type)])
+
+    void bcf_fmt_array(kstring_t *s, int n, int type, void *data);
+    uint8_t *bcf_fmt_sized_array(kstring_t *s, uint8_t *ptr);
+
+    void bcf_enc_vchar(kstring_t *s, int l, const char *a);
+    void bcf_enc_vint(kstring_t *s, int n, int32_t *a, int wsize);
+    void bcf_enc_vfloat(kstring_t *s, int n, float *a);
+
+
+    /**************************************************************************
+     *  BCF index
+     *
+     *  Note that these functions work with BCFs only. See synced_bcf_reader.h
+     *  which provides (amongst other things) an API to work transparently with
+     *  both indexed BCFs and VCFs.
+     **************************************************************************/
+
+    #define bcf_itr_destroy(iter) hts_itr_destroy(iter)
+    #define bcf_itr_queryi(idx, tid, beg, end) hts_itr_query((idx), (tid), (beg), (end), bcf_readrec)
+    #define bcf_itr_querys(idx, hdr, s) hts_itr_querys((idx), (s), (hts_name2id_f)(bcf_hdr_name2id), (hdr), hts_itr_query, bcf_readrec)
+    #define bcf_itr_next(htsfp, itr, r) hts_itr_next((htsfp)->fp.bgzf, (itr), (r), 0)
+    #define bcf_index_load(fn) hts_idx_load(fn, HTS_FMT_CSI)
+    #define bcf_index_seqnames(idx, hdr, nptr) hts_idx_seqnames((idx),(nptr),(hts_id2name_f)(bcf_hdr_id2name),(hdr))
+
+    hts_idx_t *bcf_index_load2(const char *fn, const char *fnidx);
+    int bcf_index_build(const char *fn, int min_shift);
+    int bcf_index_build2(const char *fn, const char *fnidx, int min_shift);
+
+/*******************
+ * Typed value I/O *
+ *******************/
+
+/*
+    Note that in contrast with BCFv2.1 specification, HTSlib implementation
+    allows missing values in vectors. For integer types, the values 0x80,
+    0x8000, 0x80000000 are interpreted as missing values and 0x81, 0x8001,
+    0x80000001 as end-of-vector indicators.  Similarly for floats, the value of
+    0x7F800001 is interpreted as a missing value and 0x7F800002 as an
+    end-of-vector indicator.
+    Note that the end-of-vector byte is not part of the vector.
+
+    This trial BCF version (v2.2) is compatible with the VCF specification and
+    enables to handle correctly vectors with different ploidy in presence of
+    missing values.
+ */
+#define bcf_int8_vector_end  (INT8_MIN+1)
+#define bcf_int16_vector_end (INT16_MIN+1)
+#define bcf_int32_vector_end (INT32_MIN+1)
+#define bcf_str_vector_end   0
+#define bcf_int8_missing     INT8_MIN
+#define bcf_int16_missing    INT16_MIN
+#define bcf_int32_missing    INT32_MIN
+#define bcf_str_missing      0x07
+extern uint32_t bcf_float_vector_end;
+extern uint32_t bcf_float_missing;
+static inline void bcf_float_set(float *ptr, uint32_t value)
+{
+    union { uint32_t i; float f; } u;
+    u.i = value;
+    *ptr = u.f;
+}
+#define bcf_float_set_vector_end(x) bcf_float_set(&(x),bcf_float_vector_end)
+#define bcf_float_set_missing(x)    bcf_float_set(&(x),bcf_float_missing)
+static inline int bcf_float_is_missing(float f)
+{
+    union { uint32_t i; float f; } u;
+    u.f = f;
+    return u.i==bcf_float_missing ? 1 : 0;
+}
+static inline int bcf_float_is_vector_end(float f)
+{
+    union { uint32_t i; float f; } u;
+    u.f = f;
+    return u.i==bcf_float_vector_end ? 1 : 0;
+}
+
+static inline void bcf_format_gt(bcf_fmt_t *fmt, int isample, kstring_t *str)
+{
+    #define BRANCH(type_t, missing, vector_end) { \
+        type_t *ptr = (type_t*) (fmt->p + isample*fmt->size); \
+        int i; \
+        for (i=0; i<fmt->n && ptr[i]!=vector_end; i++) \
+        { \
+            if ( i ) kputc("/|"[ptr[i]&1], str); \
+            if ( !(ptr[i]>>1) ) kputc('.', str); \
+            else kputw((ptr[i]>>1) - 1, str); \
+        } \
+        if (i == 0) kputc('.', str); \
+    }
+    switch (fmt->type) {
+        case BCF_BT_INT8:  BRANCH(int8_t,  bcf_int8_missing, bcf_int8_vector_end); break;
+        case BCF_BT_INT16: BRANCH(int16_t, bcf_int16_missing, bcf_int16_vector_end); break;
+        case BCF_BT_INT32: BRANCH(int32_t, bcf_int32_missing, bcf_int32_vector_end); break;
+        case BCF_BT_NULL:  kputc('.', str); break;
+        default: fprintf(stderr,"FIXME: type %d in bcf_format_gt?\n", fmt->type); abort(); break;
+    }
+    #undef BRANCH
+}
+
+static inline void bcf_enc_size(kstring_t *s, int size, int type)
+{
+    if (size >= 15) {
+        kputc(15<<4|type, s);
+        if (size >= 128) {
+            if (size >= 32768) {
+                int32_t x = size;
+                kputc(1<<4|BCF_BT_INT32, s);
+                kputsn((char*)&x, 4, s);
+            } else {
+                int16_t x = size;
+                kputc(1<<4|BCF_BT_INT16, s);
+                kputsn((char*)&x, 2, s);
+            }
+        } else {
+            kputc(1<<4|BCF_BT_INT8, s);
+            kputc(size, s);
+        }
+    } else kputc(size<<4|type, s);
+}
+
+static inline int bcf_enc_inttype(long x)
+{
+    if (x <= INT8_MAX && x > bcf_int8_missing) return BCF_BT_INT8;
+    if (x <= INT16_MAX && x > bcf_int16_missing) return BCF_BT_INT16;
+    return BCF_BT_INT32;
+}
+
+static inline void bcf_enc_int1(kstring_t *s, int32_t x)
+{
+    if (x == bcf_int32_vector_end) {
+        bcf_enc_size(s, 1, BCF_BT_INT8);
+        kputc(bcf_int8_vector_end, s);
+    } else if (x == bcf_int32_missing) {
+        bcf_enc_size(s, 1, BCF_BT_INT8);
+        kputc(bcf_int8_missing, s);
+    } else if (x <= INT8_MAX && x > bcf_int8_missing) {
+        bcf_enc_size(s, 1, BCF_BT_INT8);
+        kputc(x, s);
+    } else if (x <= INT16_MAX && x > bcf_int16_missing) {
+        int16_t z = x;
+        bcf_enc_size(s, 1, BCF_BT_INT16);
+        kputsn((char*)&z, 2, s);
+    } else {
+        int32_t z = x;
+        bcf_enc_size(s, 1, BCF_BT_INT32);
+        kputsn((char*)&z, 4, s);
+    }
+}
+
+static inline int32_t bcf_dec_int1(const uint8_t *p, int type, uint8_t **q)
+{
+    if (type == BCF_BT_INT8) {
+        *q = (uint8_t*)p + 1;
+        return *(int8_t*)p;
+    } else if (type == BCF_BT_INT16) {
+        *q = (uint8_t*)p + 2;
+        return *(int16_t*)p;
+    } else {
+        *q = (uint8_t*)p + 4;
+        return *(int32_t*)p;
+    }
+}
+
+static inline int32_t bcf_dec_typed_int1(const uint8_t *p, uint8_t **q)
+{
+    return bcf_dec_int1(p + 1, *p&0xf, q);
+}
+
+static inline int32_t bcf_dec_size(const uint8_t *p, uint8_t **q, int *type)
+{
+    *type = *p & 0xf;
+    if (*p>>4 != 15) {
+        *q = (uint8_t*)p + 1;
+        return *p>>4;
+    } else return bcf_dec_typed_int1(p + 1, q);
+}
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/htslib/htslib/vcf_sweep.h b/htslib/htslib/vcf_sweep.h
new file mode 100644
index 0000000..82c9b03
--- /dev/null
+++ b/htslib/htslib/vcf_sweep.h
@@ -0,0 +1,47 @@
+/*  vcf_sweep.h -- forward/reverse sweep API.
+
+    Copyright (C) 2013 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3 at sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#ifndef HTSLIB_VCF_SWEEP_H
+#define HTSLIB_VCF_SWEEP_H
+
+#include "hts.h"
+#include "vcf.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+typedef struct _bcf_sweep_t bcf_sweep_t;
+
+bcf_sweep_t *bcf_sweep_init(const char *fname);
+void bcf_sweep_destroy(bcf_sweep_t *sw);
+bcf_hdr_t *bcf_sweep_hdr(bcf_sweep_t *sw);
+bcf1_t *bcf_sweep_fwd(bcf_sweep_t *sw);
+bcf1_t *bcf_sweep_bwd(bcf_sweep_t *sw);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/htslib/htslib/vcfutils.h b/htslib/htslib/vcfutils.h
new file mode 100644
index 0000000..82181b1
--- /dev/null
+++ b/htslib/htslib/vcfutils.h
@@ -0,0 +1,134 @@
+/*  vcfutils.h -- allele-related utility functions.
+
+    Copyright (C) 2012, 2013, 2015 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3 at sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#ifndef HTSLIB_VCFUTILS_H
+#define HTSLIB_VCFUTILS_H
+
+#include "vcf.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+struct kbitset_t;
+
+/**
+ *  bcf_trim_alleles() - remove ALT alleles unused in genotype fields
+ *  @header:  for access to BCF_DT_ID dictionary
+ *  @line:    VCF line obtain from vcf_parse1
+ *
+ *  Returns the number of removed alleles on success or negative
+ *  on error:
+ *      -1 .. some allele index is out of bounds
+ */
+int bcf_trim_alleles(const bcf_hdr_t *header, bcf1_t *line);
+
+/**
+ *  bcf_remove_alleles() - remove ALT alleles according to bitmask @mask
+ *  @header:  for access to BCF_DT_ID dictionary
+ *  @line:    VCF line obtained from vcf_parse1
+ *  @mask:    alleles to remove
+ * 
+ *  If you have more than 31 alleles, then the integer bit mask will
+ *  overflow, so use bcf_remove_allele_set instead
+ */
+void bcf_remove_alleles(const bcf_hdr_t *header, bcf1_t *line, int mask);
+
+/**
+ *  bcf_remove_allele_set() - remove ALT alleles according to bitset @rm_set
+ *  @header:  for access to BCF_DT_ID dictionary
+ *  @line:    VCF line obtained from vcf_parse1
+ *  @rm_set:  pointer to kbitset_t object with bits set for allele
+ *            indexes to remove
+ *  
+ *  Number=A,R,G INFO and FORMAT fields will be updated accordingly.
+ */
+void bcf_remove_allele_set(const bcf_hdr_t *header, bcf1_t *line, const struct kbitset_t *rm_set);
+
+/**
+ *  bcf_calc_ac() - calculate the number of REF and ALT alleles
+ *  @header:  for access to BCF_DT_ID dictionary
+ *  @line:    VCF line obtained from vcf_parse1
+ *  @ac:      array of length line->n_allele
+ *  @which:   determine if INFO/AN,AC and indv fields be used
+ *
+ *  Returns 1 if the call succeeded, or 0 if the value could not
+ *  be determined.
+ *
+ *  The value of @which determines if existing INFO/AC,AN can be
+ *  used (BCF_UN_INFO) and and if indv fields can be splitted
+ *  (BCF_UN_FMT).
+ */
+int bcf_calc_ac(const bcf_hdr_t *header, bcf1_t *line, int *ac, int which);
+
+
+/**
+ * bcf_gt_type() - determines type of the genotype
+ * @fmt_ptr:  the GT format field as set for example by set_fmt_ptr
+ * @isample:  sample index (starting from 0)
+ * @ial:      index of the 1st non-reference allele (starting from 1)
+ * @jal:      index of the 2nd non-reference allele (starting from 1)
+ *
+ * Returns the type of the genotype (one of GT_HOM_RR, GT_HET_RA,
+ * GT_HOM_AA, GT_HET_AA, GT_HAPL_R, GT_HAPL_A or GT_UNKN). If $ial
+ * is not NULL and the genotype has one or more non-reference
+ * alleles, $ial will be set. In case of GT_HET_AA, $ial is the
+ * position of the allele which appeared first in ALT. If $jal is
+ * not null and the genotype is GT_HET_AA, $jal will be set and is
+ * the position of the second allele in ALT.
+ */
+#define GT_HOM_RR 0 // note: the actual value of GT_* matters, used in dosage r2 calculation
+#define GT_HOM_AA 1
+#define GT_HET_RA 2
+#define GT_HET_AA 3
+#define GT_HAPL_R 4
+#define GT_HAPL_A 5
+#define GT_UNKN   6
+int bcf_gt_type(bcf_fmt_t *fmt_ptr, int isample, int *ial, int *jal);
+
+static inline int bcf_acgt2int(char c)
+{
+    if ( (int)c>96 ) c -= 32;
+    if ( c=='A' ) return 0;
+    if ( c=='C' ) return 1;
+    if ( c=='G' ) return 2;
+    if ( c=='T' ) return 3;
+    return -1;
+}
+
+#define bcf_int2acgt(i) "ACGT"[i]
+
+/**
+  * bcf_ij2G() - common task: allele indexes to Number=G index (diploid)
+  * @i,j:  allele indexes, 0-based, i<=j
+  *
+  * Returns index to the Number=G diploid array
+  */
+#define bcf_ij2G(i, j) ((j)*((j)+1)/2+(i))
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/htslib/htslib_vars.mk b/htslib/htslib_vars.mk
new file mode 100644
index 0000000..05a4906
--- /dev/null
+++ b/htslib/htslib_vars.mk
@@ -0,0 +1,49 @@
+# Makefile variables useful for third-party code using htslib's public API.
+#
+#    Copyright (C) 2013-2016 Genome Research Ltd.
+#
+#    Author: John Marshall <jm18 at sanger.ac.uk>
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+# DEALINGS IN THE SOFTWARE.
+
+# These variables can be used to express dependencies on htslib headers.
+# See htslib.mk for details.
+
+htslib_bgzf_h = $(HTSPREFIX)htslib/bgzf.h $(htslib_hts_defs_h)
+htslib_cram_h = $(HTSPREFIX)htslib/cram.h $(htslib_hts_h)
+htslib_faidx_h = $(HTSPREFIX)htslib/faidx.h $(htslib_hts_defs_h)
+htslib_hfile_h = $(HTSPREFIX)htslib/hfile.h $(htslib_hts_defs_h)
+htslib_hts_h = $(HTSPREFIX)htslib/hts.h $(htslib_hts_defs_h)
+htslib_hts_defs_h = $(HTSPREFIX)htslib/hts_defs.h
+htslib_kbitset_h = $(HTSPREFIX)htslib/kbitset.h
+htslib_kfunc_h = $(HTSPREFIX)htslib/kfunc.h
+htslib_khash_h = $(HTSPREFIX)htslib/khash.h
+htslib_khash_str2int_h = $(HTSPREFIX)htslib/khash_str2int.h $(htslib_khash_h)
+htslib_klist_h = $(HTSPREFIX)htslib/klist.h
+htslib_knetfile_h = $(HTSPREFIX)htslib/knetfile.h
+htslib_kseq_h = $(HTSPREFIX)htslib/kseq.h
+htslib_ksort_h = $(HTSPREFIX)htslib/ksort.h
+htslib_kstring_h = $(HTSPREFIX)htslib/kstring.h
+htslib_regidx_h = $(HTSPREFIX)htslib/regidx.h
+htslib_sam_h = $(HTSPREFIX)htslib/sam.h $(htslib_hts_h)
+htslib_synced_bcf_reader_h = $(HTSPREFIX)htslib/synced_bcf_reader.h $(htslib_hts_h) $(htslib_vcf_h) $(htslib_tbx_h)
+htslib_tbx_h = $(HTSPREFIX)htslib/tbx.h $(htslib_hts_h)
+htslib_vcf_h = $(HTSPREFIX)htslib/vcf.h $(htslib_hts_h) $(htslib_kstring_h) $(htslib_hts_defs_h)
+htslib_vcf_sweep_h = $(HTSPREFIX)htslib/vcf_sweep.h $(htslib_hts_h) $(htslib_vcf_h)
+htslib_vcfutils_h = $(HTSPREFIX)htslib/vcfutils.h $(htslib_vcf_h)
diff --git a/htslib/kfunc.c b/htslib/kfunc.c
new file mode 100644
index 0000000..323e70f
--- /dev/null
+++ b/htslib/kfunc.c
@@ -0,0 +1,282 @@
+/* The MIT License
+
+   Copyright (C) 2010, 2013 Genome Research Ltd.
+   Copyright (C) 2011 Attractive Chaos <attractor at live.co.uk>
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+
+#include <config.h>
+
+#include <math.h>
+#include <stdlib.h>
+#include "htslib/kfunc.h"
+
+/* Log gamma function
+ * \log{\Gamma(z)}
+ * AS245, 2nd algorithm, http://lib.stat.cmu.edu/apstat/245
+ */
+double kf_lgamma(double z)
+{
+	double x = 0;
+	x += 0.1659470187408462e-06 / (z+7);
+	x += 0.9934937113930748e-05 / (z+6);
+	x -= 0.1385710331296526     / (z+5);
+	x += 12.50734324009056      / (z+4);
+	x -= 176.6150291498386      / (z+3);
+	x += 771.3234287757674      / (z+2);
+	x -= 1259.139216722289      / (z+1);
+	x += 676.5203681218835      / z;
+	x += 0.9999999999995183;
+	return log(x) - 5.58106146679532777 - z + (z-0.5) * log(z+6.5);
+}
+
+/* complementary error function
+ * \frac{2}{\sqrt{\pi}} \int_x^{\infty} e^{-t^2} dt
+ * AS66, 2nd algorithm, http://lib.stat.cmu.edu/apstat/66
+ */
+double kf_erfc(double x)
+{
+	const double p0 = 220.2068679123761;
+	const double p1 = 221.2135961699311;
+	const double p2 = 112.0792914978709;
+	const double p3 = 33.912866078383;
+	const double p4 = 6.37396220353165;
+	const double p5 = .7003830644436881;
+	const double p6 = .03526249659989109;
+	const double q0 = 440.4137358247522;
+	const double q1 = 793.8265125199484;
+	const double q2 = 637.3336333788311;
+	const double q3 = 296.5642487796737;
+	const double q4 = 86.78073220294608;
+	const double q5 = 16.06417757920695;
+	const double q6 = 1.755667163182642;
+	const double q7 = .08838834764831844;
+	double expntl, z, p;
+	z = fabs(x) * M_SQRT2;
+	if (z > 37.) return x > 0.? 0. : 2.;
+	expntl = exp(z * z * - .5);
+	if (z < 10. / M_SQRT2) // for small z
+	    p = expntl * ((((((p6 * z + p5) * z + p4) * z + p3) * z + p2) * z + p1) * z + p0)
+			/ (((((((q7 * z + q6) * z + q5) * z + q4) * z + q3) * z + q2) * z + q1) * z + q0);
+	else p = expntl / 2.506628274631001 / (z + 1. / (z + 2. / (z + 3. / (z + 4. / (z + .65)))));
+	return x > 0.? 2. * p : 2. * (1. - p);
+}
+
+/* The following computes regularized incomplete gamma functions.
+ * Formulas are taken from Wiki, with additional input from Numerical
+ * Recipes in C (for modified Lentz's algorithm) and AS245
+ * (http://lib.stat.cmu.edu/apstat/245).
+ *
+ * A good online calculator is available at:
+ *
+ *   http://www.danielsoper.com/statcalc/calc23.aspx
+ *
+ * It calculates upper incomplete gamma function, which equals
+ * kf_gammaq(s,z)*tgamma(s).
+ */
+
+#define KF_GAMMA_EPS 1e-14
+#define KF_TINY 1e-290
+
+// regularized lower incomplete gamma function, by series expansion
+static double _kf_gammap(double s, double z)
+{
+	double sum, x;
+	int k;
+	for (k = 1, sum = x = 1.; k < 100; ++k) {
+		sum += (x *= z / (s + k));
+		if (x / sum < KF_GAMMA_EPS) break;
+	}
+	return exp(s * log(z) - z - kf_lgamma(s + 1.) + log(sum));
+}
+// regularized upper incomplete gamma function, by continued fraction
+static double _kf_gammaq(double s, double z)
+{
+	int j;
+	double C, D, f;
+	f = 1. + z - s; C = f; D = 0.;
+	// Modified Lentz's algorithm for computing continued fraction
+	// See Numerical Recipes in C, 2nd edition, section 5.2
+	for (j = 1; j < 100; ++j) {
+		double a = j * (s - j), b = (j<<1) + 1 + z - s, d;
+		D = b + a * D;
+		if (D < KF_TINY) D = KF_TINY;
+		C = b + a / C;
+		if (C < KF_TINY) C = KF_TINY;
+		D = 1. / D;
+		d = C * D;
+		f *= d;
+		if (fabs(d - 1.) < KF_GAMMA_EPS) break;
+	}
+	return exp(s * log(z) - z - kf_lgamma(s) - log(f));
+}
+
+double kf_gammap(double s, double z)
+{
+	return z <= 1. || z < s? _kf_gammap(s, z) : 1. - _kf_gammaq(s, z);
+}
+
+double kf_gammaq(double s, double z)
+{
+	return z <= 1. || z < s? 1. - _kf_gammap(s, z) : _kf_gammaq(s, z);
+}
+
+/* Regularized incomplete beta function. The method is taken from
+ * Numerical Recipe in C, 2nd edition, section 6.4. The following web
+ * page calculates the incomplete beta function, which equals
+ * kf_betai(a,b,x) * gamma(a) * gamma(b) / gamma(a+b):
+ *
+ *   http://www.danielsoper.com/statcalc/calc36.aspx
+ */
+static double kf_betai_aux(double a, double b, double x)
+{
+	double C, D, f;
+	int j;
+	if (x == 0.) return 0.;
+	if (x == 1.) return 1.;
+	f = 1.; C = f; D = 0.;
+	// Modified Lentz's algorithm for computing continued fraction
+	for (j = 1; j < 200; ++j) {
+		double aa, d;
+		int m = j>>1;
+		aa = (j&1)? -(a + m) * (a + b + m) * x / ((a + 2*m) * (a + 2*m + 1))
+			: m * (b - m) * x / ((a + 2*m - 1) * (a + 2*m));
+		D = 1. + aa * D;
+		if (D < KF_TINY) D = KF_TINY;
+		C = 1. + aa / C;
+		if (C < KF_TINY) C = KF_TINY;
+		D = 1. / D;
+		d = C * D;
+		f *= d;
+		if (fabs(d - 1.) < KF_GAMMA_EPS) break;
+	}
+	return exp(kf_lgamma(a+b) - kf_lgamma(a) - kf_lgamma(b) + a * log(x) + b * log(1.-x)) / a / f;
+}
+double kf_betai(double a, double b, double x)
+{
+	return x < (a + 1.) / (a + b + 2.)? kf_betai_aux(a, b, x) : 1. - kf_betai_aux(b, a, 1. - x);
+}
+
+#ifdef KF_MAIN
+#include <stdio.h>
+int main(int argc, char *argv[])
+{
+	double x = 5.5, y = 3;
+	double a, b;
+	printf("erfc(%lg): %lg, %lg\n", x, erfc(x), kf_erfc(x));
+	printf("upper-gamma(%lg,%lg): %lg\n", x, y, kf_gammaq(y, x)*tgamma(y));
+	a = 2; b = 2; x = 0.5;
+	printf("incomplete-beta(%lg,%lg,%lg): %lg\n", a, b, x, kf_betai(a, b, x) / exp(kf_lgamma(a+b) - kf_lgamma(a) - kf_lgamma(b)));
+	return 0;
+}
+#endif
+
+
+// log\binom{n}{k}
+static double lbinom(int n, int k)
+{
+    if (k == 0 || n == k) return 0;
+    return lgamma(n+1) - lgamma(k+1) - lgamma(n-k+1);
+}
+
+// n11  n12  | n1_
+// n21  n22  | n2_
+//-----------+----
+// n_1  n_2  | n
+
+// hypergeometric distribution
+static double hypergeo(int n11, int n1_, int n_1, int n)
+{
+    return exp(lbinom(n1_, n11) + lbinom(n-n1_, n_1-n11) - lbinom(n, n_1));
+}
+
+typedef struct {
+    int n11, n1_, n_1, n;
+    double p;
+} hgacc_t;
+
+// incremental version of hypergenometric distribution
+static double hypergeo_acc(int n11, int n1_, int n_1, int n, hgacc_t *aux)
+{
+    if (n1_ || n_1 || n) {
+        aux->n11 = n11; aux->n1_ = n1_; aux->n_1 = n_1; aux->n = n;
+    } else { // then only n11 changed; the rest fixed
+        if (n11%11 && n11 + aux->n - aux->n1_ - aux->n_1) {
+            if (n11 == aux->n11 + 1) { // incremental
+                aux->p *= (double)(aux->n1_ - aux->n11) / n11
+                    * (aux->n_1 - aux->n11) / (n11 + aux->n - aux->n1_ - aux->n_1);
+                aux->n11 = n11;
+                return aux->p;
+            }
+            if (n11 == aux->n11 - 1) { // incremental
+                aux->p *= (double)aux->n11 / (aux->n1_ - n11)
+                    * (aux->n11 + aux->n - aux->n1_ - aux->n_1) / (aux->n_1 - n11);
+                aux->n11 = n11;
+                return aux->p;
+            }
+        }
+        aux->n11 = n11;
+    }
+    aux->p = hypergeo(aux->n11, aux->n1_, aux->n_1, aux->n);
+    return aux->p;
+}
+
+double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two)
+{
+    int i, j, max, min;
+    double p, q, left, right;
+    hgacc_t aux;
+    int n1_, n_1, n;
+
+    n1_ = n11 + n12; n_1 = n11 + n21; n = n11 + n12 + n21 + n22; // calculate n1_, n_1 and n
+    max = (n_1 < n1_) ? n_1 : n1_; // max n11, for right tail
+    min = n1_ + n_1 - n;    // not sure why n11-n22 is used instead of min(n_1,n1_)
+    if (min < 0) min = 0; // min n11, for left tail
+    *two = *_left = *_right = 1.;
+    if (min == max) return 1.; // no need to do test
+    q = hypergeo_acc(n11, n1_, n_1, n, &aux); // the probability of the current table
+    // left tail
+    p = hypergeo_acc(min, 0, 0, 0, &aux);
+    for (left = 0., i = min + 1; p < 0.99999999 * q && i<=max; ++i) // loop until underflow
+        left += p, p = hypergeo_acc(i, 0, 0, 0, &aux);
+    --i;
+    if (p < 1.00000001 * q) left += p;
+    else --i;
+    // right tail
+    p = hypergeo_acc(max, 0, 0, 0, &aux);
+    for (right = 0., j = max - 1; p < 0.99999999 * q && j>=0; --j) // loop until underflow
+        right += p, p = hypergeo_acc(j, 0, 0, 0, &aux);
+    ++j;
+    if (p < 1.00000001 * q) right += p;
+    else ++j;
+    // two-tail
+    *two = left + right;
+    if (*two > 1.) *two = 1.;
+    // adjust left and right
+    if (abs(i - n11) < abs(j - n11)) right = 1. - left + q;
+    else left = 1.0 - right + q;
+    *_left = left; *_right = right;
+    return q;
+}
+
+
+
diff --git a/htslib/knetfile.c b/htslib/knetfile.c
new file mode 100644
index 0000000..aa28858
--- /dev/null
+++ b/htslib/knetfile.c
@@ -0,0 +1,634 @@
+/* The MIT License
+
+   Copyright (c) 2008 by Genome Research Ltd (GRL).
+                 2010 by Attractive Chaos <attractor at live.co.uk>
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+
+/* Probably I will not do socket programming in the next few years and
+   therefore I decide to heavily annotate this file, for Linux and
+   Windows as well.  -ac */
+
+#include <config.h>
+
+#include <time.h>
+#include <stdio.h>
+#include <ctype.h>
+#include <stdlib.h>
+#include <string.h>
+#include <errno.h>
+#include <unistd.h>
+#include <sys/types.h>
+
+#ifndef _WIN32
+#include <netdb.h>
+#include <arpa/inet.h>
+#include <sys/socket.h>
+#endif
+
+#include "htslib/knetfile.h"
+
+/* In winsock.h, the type of a socket is SOCKET, which is: "typedef
+ * u_int SOCKET". An invalid SOCKET is: "(SOCKET)(~0)", or signed
+ * integer -1. In knetfile.c, I use "int" for socket type
+ * throughout. This should be improved to avoid confusion.
+ *
+ * In Linux/Mac, recv() and read() do almost the same thing. You can see
+ * in the header file that netread() is simply an alias of read(). In
+ * Windows, however, they are different and using recv() is mandatory.
+ */
+
+/* This function tests if the file handler is ready for reading (or
+ * writing if is_read==0). */
+static int socket_wait(int fd, int is_read)
+{
+	fd_set fds, *fdr = 0, *fdw = 0;
+	struct timeval tv;
+	int ret;
+	tv.tv_sec = 5; tv.tv_usec = 0; // 5 seconds time out
+	FD_ZERO(&fds);
+	FD_SET(fd, &fds);
+	if (is_read) fdr = &fds;
+	else fdw = &fds;
+	ret = select(fd+1, fdr, fdw, 0, &tv);
+#ifndef _WIN32
+	if (ret == -1) perror("select");
+#else
+	if (ret == 0)
+		fprintf(stderr, "select time-out\n");
+	else if (ret == SOCKET_ERROR)
+		fprintf(stderr, "select: %d\n", WSAGetLastError());
+#endif
+	return ret;
+}
+
+#ifndef _WIN32
+/* This function does not work with Windows due to the lack of
+ * getaddrinfo() in winsock. It is addapted from an example in "Beej's
+ * Guide to Network Programming" (http://beej.us/guide/bgnet/). */
+static int socket_connect(const char *host, const char *port)
+{
+#define __err_connect(func) do { perror(func); freeaddrinfo(res); return -1; } while (0)
+
+	int ai_err, on = 1, fd;
+	struct linger lng = { 0, 0 };
+	struct addrinfo hints, *res = 0;
+	memset(&hints, 0, sizeof(struct addrinfo));
+	hints.ai_family = AF_UNSPEC;
+	hints.ai_socktype = SOCK_STREAM;
+	/* In Unix/Mac, getaddrinfo() is the most convenient way to get
+	 * server information. */
+	if ((ai_err = getaddrinfo(host, port, &hints, &res)) != 0) { fprintf(stderr, "can't resolve %s:%s: %s\n", host, port, gai_strerror(ai_err)); return -1; }
+	if ((fd = socket(res->ai_family, res->ai_socktype, res->ai_protocol)) == -1) __err_connect("socket");
+	/* The following two setsockopt() are used by ftplib
+	 * (http://nbpfaus.net/~pfau/ftplib/). I am not sure if they
+	 * necessary. */
+	if (setsockopt(fd, SOL_SOCKET, SO_REUSEADDR, &on, sizeof(on)) == -1) __err_connect("setsockopt");
+	if (setsockopt(fd, SOL_SOCKET, SO_LINGER, &lng, sizeof(lng)) == -1) __err_connect("setsockopt");
+	if (connect(fd, res->ai_addr, res->ai_addrlen) != 0) __err_connect("connect");
+	freeaddrinfo(res);
+	return fd;
+}
+#else
+/* MinGW's printf has problem with "%lld" */
+char *int64tostr(char *buf, int64_t x)
+{
+	int cnt;
+	int i = 0;
+	do {
+		buf[i++] = '0' + x % 10;
+		x /= 10;
+	} while (x);
+	buf[i] = 0;
+	for (cnt = i, i = 0; i < cnt/2; ++i) {
+		int c = buf[i]; buf[i] = buf[cnt-i-1]; buf[cnt-i-1] = c;
+	}
+	return buf;
+}
+
+int64_t strtoint64(const char *buf)
+{
+	int64_t x;
+	for (x = 0; *buf != '\0'; ++buf)
+		x = x * 10 + ((int64_t) *buf - 48);
+	return x;
+}
+/* In windows, the first thing is to establish the TCP connection. */
+int knet_win32_init()
+{
+	WSADATA wsaData;
+	return WSAStartup(MAKEWORD(2, 2), &wsaData);
+}
+void knet_win32_destroy()
+{
+	WSACleanup();
+}
+/* A slightly modfied version of the following function also works on
+ * Mac (and presummably Linux). However, this function is not stable on
+ * my Mac. It sometimes works fine but sometimes does not. Therefore for
+ * non-Windows OS, I do not use this one. */
+static SOCKET socket_connect(const char *host, const char *port)
+{
+#define __err_connect(func)										\
+	do {														\
+		fprintf(stderr, "%s: %d\n", func, WSAGetLastError());	\
+		return -1;												\
+	} while (0)
+
+	int on = 1;
+	SOCKET fd;
+	struct linger lng = { 0, 0 };
+	struct sockaddr_in server;
+	struct hostent *hp = 0;
+	// open socket
+	if ((fd = socket(AF_INET, SOCK_STREAM, IPPROTO_TCP)) == INVALID_SOCKET) __err_connect("socket");
+	if (setsockopt(fd, SOL_SOCKET, SO_REUSEADDR, (char*)&on, sizeof(on)) == -1) __err_connect("setsockopt");
+	if (setsockopt(fd, SOL_SOCKET, SO_LINGER, (char*)&lng, sizeof(lng)) == -1) __err_connect("setsockopt");
+	// get host info
+	if (isalpha(host[0])) hp = gethostbyname(host);
+	else {
+		struct in_addr addr;
+		addr.s_addr = inet_addr(host);
+		hp = gethostbyaddr((char*)&addr, 4, AF_INET);
+	}
+	if (hp == 0) __err_connect("gethost");
+	// connect
+	server.sin_addr.s_addr = *((unsigned long*)hp->h_addr);
+	server.sin_family= AF_INET;
+	server.sin_port = htons(atoi(port));
+	if (connect(fd, (struct sockaddr*)&server, sizeof(server)) != 0) __err_connect("connect");
+	// freehostent(hp); // strangely in MSDN, hp is NOT freed (memory leak?!)
+	return fd;
+}
+#endif
+
+static off_t my_netread(int fd, void *buf, off_t len)
+{
+	off_t rest = len, curr, l = 0;
+	/* recv() and read() may not read the required length of data with
+	 * one call. They have to be called repeatedly. */
+	while (rest) {
+		if (socket_wait(fd, 1) <= 0) break; // socket is not ready for reading
+		curr = netread(fd, (void*)((char*)buf + l), rest);
+		/* According to the glibc manual, section 13.2, a zero returned
+		 * value indicates end-of-file (EOF), which should mean that
+		 * read() will not return zero if EOF has not been met but data
+		 * are not immediately available. */
+		if (curr == 0) break;
+		l += curr; rest -= curr;
+	}
+	return l;
+}
+
+/*************************
+ * FTP specific routines *
+ *************************/
+
+static int kftp_get_response(knetFile *ftp)
+{
+#ifndef _WIN32
+	unsigned char c;
+#else
+	char c;
+#endif
+	int n = 0;
+	char *p;
+	if (socket_wait(ftp->ctrl_fd, 1) <= 0) return 0;
+	while (netread(ftp->ctrl_fd, &c, 1)) { // FIXME: this is *VERY BAD* for unbuffered I/O
+		//fputc(c, stderr);
+		if (n >= ftp->max_response) {
+			ftp->max_response = ftp->max_response? ftp->max_response<<1 : 256;
+			ftp->response = (char*)realloc(ftp->response, ftp->max_response);
+		}
+		ftp->response[n++] = c;
+		if (c == '\n') {
+			if (n >= 4 && isdigit(ftp->response[0]) && isdigit(ftp->response[1]) && isdigit(ftp->response[2])
+				&& ftp->response[3] != '-') break;
+			n = 0;
+			continue;
+		}
+	}
+	if (n < 2) return -1;
+	ftp->response[n-2] = 0;
+	return strtol(ftp->response, &p, 0);
+}
+
+static int kftp_send_cmd(knetFile *ftp, const char *cmd, int is_get)
+{
+	if (socket_wait(ftp->ctrl_fd, 0) <= 0) return -1; // socket is not ready for writing
+    int len = strlen(cmd);
+	if ( netwrite(ftp->ctrl_fd, cmd, len) != len ) return -1;
+	return is_get? kftp_get_response(ftp) : 0;
+}
+
+static int kftp_pasv_prep(knetFile *ftp)
+{
+	char *p;
+	int v[6];
+	kftp_send_cmd(ftp, "PASV\r\n", 1);
+	for (p = ftp->response; *p && *p != '('; ++p);
+	if (*p != '(') return -1;
+	++p;
+	sscanf(p, "%d,%d,%d,%d,%d,%d", &v[0], &v[1], &v[2], &v[3], &v[4], &v[5]);
+	memcpy(ftp->pasv_ip, v, 4 * sizeof(int));
+	ftp->pasv_port = (v[4]<<8&0xff00) + v[5];
+	return 0;
+}
+
+
+static int kftp_pasv_connect(knetFile *ftp)
+{
+	char host[80], port[10];
+	if (ftp->pasv_port == 0) {
+		fprintf(stderr, "[kftp_pasv_connect] kftp_pasv_prep() is not called before hand.\n");
+		return -1;
+	}
+	sprintf(host, "%d.%d.%d.%d", ftp->pasv_ip[0], ftp->pasv_ip[1], ftp->pasv_ip[2], ftp->pasv_ip[3]);
+	sprintf(port, "%d", ftp->pasv_port);
+	ftp->fd = socket_connect(host, port);
+	if (ftp->fd == -1) return -1;
+	return 0;
+}
+
+int kftp_connect(knetFile *ftp)
+{
+	ftp->ctrl_fd = socket_connect(ftp->host, ftp->port);
+	if (ftp->ctrl_fd == -1) return -1;
+	kftp_get_response(ftp);
+	kftp_send_cmd(ftp, "USER anonymous\r\n", 1);
+	kftp_send_cmd(ftp, "PASS kftp@\r\n", 1);
+	kftp_send_cmd(ftp, "TYPE I\r\n", 1);
+	return 0;
+}
+
+int kftp_reconnect(knetFile *ftp)
+{
+	if (ftp->ctrl_fd != -1) {
+		netclose(ftp->ctrl_fd);
+		ftp->ctrl_fd = -1;
+	}
+	netclose(ftp->fd);
+	ftp->fd = -1;
+	return kftp_connect(ftp);
+}
+
+// initialize ->type, ->host, ->retr and ->size
+knetFile *kftp_parse_url(const char *fn, const char *mode)
+{
+	knetFile *fp;
+	char *p;
+	int l;
+	if (strstr(fn, "ftp://") != fn) return 0;
+	for (p = (char*)fn + 6; *p && *p != '/'; ++p);
+	if (*p != '/') return 0;
+	l = p - fn - 6;
+	fp = (knetFile*)calloc(1, sizeof(knetFile));
+	fp->type = KNF_TYPE_FTP;
+	fp->fd = -1;
+	/* the Linux/Mac version of socket_connect() also recognizes a port
+	 * like "ftp", but the Windows version does not. */
+	fp->port = strdup("21");
+	fp->host = (char*)calloc(l + 1, 1);
+	if (strchr(mode, 'c')) fp->no_reconnect = 1;
+	strncpy(fp->host, fn + 6, l);
+	fp->retr = (char*)calloc(strlen(p) + 8, 1);
+	sprintf(fp->retr, "RETR %s\r\n", p);
+    fp->size_cmd = (char*)calloc(strlen(p) + 8, 1);
+    sprintf(fp->size_cmd, "SIZE %s\r\n", p);
+	fp->seek_offset = 0;
+	return fp;
+}
+// place ->fd at offset off
+int kftp_connect_file(knetFile *fp)
+{
+	int ret;
+	long long file_size;
+	if (fp->fd != -1) {
+		netclose(fp->fd);
+		if (fp->no_reconnect) kftp_get_response(fp);
+	}
+	kftp_pasv_prep(fp);
+    kftp_send_cmd(fp, fp->size_cmd, 1);
+#ifndef _WIN32
+    // If the file does not exist, the response will be "550 Could not get file
+    // size". Be silent on failure, hts_idx_load can be trying the existence of .csi or .tbi.
+    if ( sscanf(fp->response,"%*d %lld", &file_size) != 1 ) return -1;
+#else
+	const char *p = fp->response;
+	while (*p != ' ') ++p;
+	while (*p < '0' || *p > '9') ++p;
+	file_size = strtoint64(p);
+#endif
+	fp->file_size = file_size;
+	if (fp->offset>=0) {
+		char tmp[32];
+#ifndef _WIN32
+		sprintf(tmp, "REST %lld\r\n", (long long)fp->offset);
+#else
+		strcpy(tmp, "REST ");
+		int64tostr(tmp + 5, fp->offset);
+		strcat(tmp, "\r\n");
+#endif
+		kftp_send_cmd(fp, tmp, 1);
+	}
+	kftp_send_cmd(fp, fp->retr, 0);
+	kftp_pasv_connect(fp);
+	ret = kftp_get_response(fp);
+	if (ret != 150) {
+		fprintf(stderr, "[kftp_connect_file] %s\n", fp->response);
+		netclose(fp->fd);
+		fp->fd = -1;
+		return -1;
+	}
+	fp->is_ready = 1;
+	return 0;
+}
+
+
+/**************************
+ * HTTP specific routines *
+ **************************/
+
+knetFile *khttp_parse_url(const char *fn, const char *mode)
+{
+	knetFile *fp;
+	char *p, *proxy, *q;
+	int l;
+	if (strstr(fn, "http://") != fn) return 0;
+	// set ->http_host
+	for (p = (char*)fn + 7; *p && *p != '/'; ++p);
+	l = p - fn - 7;
+	fp = (knetFile*)calloc(1, sizeof(knetFile));
+	fp->http_host = (char*)calloc(l + 1, 1);
+	strncpy(fp->http_host, fn + 7, l);
+	fp->http_host[l] = 0;
+	for (q = fp->http_host; *q && *q != ':'; ++q);
+	if (*q == ':') *q++ = 0;
+	// get http_proxy
+	proxy = getenv("http_proxy");
+	// set ->host, ->port and ->path
+	if (proxy == 0) {
+		fp->host = strdup(fp->http_host); // when there is no proxy, server name is identical to http_host name.
+		fp->port = strdup(*q? q : "80");
+		fp->path = strdup(*p? p : "/");
+	} else {
+		fp->host = (strstr(proxy, "http://") == proxy)? strdup(proxy + 7) : strdup(proxy);
+		for (q = fp->host; *q && *q != ':'; ++q);
+		if (*q == ':') *q++ = 0; 
+		fp->port = strdup(*q? q : "80");
+		fp->path = strdup(fn);
+	}
+	fp->type = KNF_TYPE_HTTP;
+	fp->ctrl_fd = fp->fd = -1;
+	fp->seek_offset = 0;
+	return fp;
+}
+
+int khttp_connect_file(knetFile *fp)
+{
+	int ret, l = 0;
+	char *buf, *p;
+	if (fp->fd != -1) netclose(fp->fd);
+	fp->fd = socket_connect(fp->host, fp->port);
+	buf = (char*)calloc(0x10000, 1); // FIXME: I am lazy... But in principle, 64KB should be large enough.
+	l += sprintf(buf + l, "GET %s HTTP/1.0\r\nHost: %s\r\n", fp->path, fp->http_host);
+    l += sprintf(buf + l, "Range: bytes=%lld-\r\n", (long long)fp->offset);
+	l += sprintf(buf + l, "\r\n");
+	if ( netwrite(fp->fd, buf, l) != l ) { free(buf); return -1; }
+	l = 0;
+	while (netread(fp->fd, buf + l, 1)) { // read HTTP header; FIXME: bad efficiency
+		if (buf[l] == '\n' && l >= 3)
+			if (strncmp(buf + l - 3, "\r\n\r\n", 4) == 0) break;
+		++l;
+	}
+	buf[l] = 0;
+	if (l < 14) { // prematured header
+		free(buf);
+		netclose(fp->fd);
+		fp->fd = -1;
+		return -1;
+	}
+	ret = strtol(buf + 8, &p, 0); // HTTP return code
+	if (ret == 200 && fp->offset>0) { // 200 (complete result); then skip beginning of the file
+		off_t rest = fp->offset;
+		while (rest) {
+			off_t l = rest < 0x10000? rest : 0x10000;
+			rest -= my_netread(fp->fd, buf, l);
+		}
+	} else if (ret != 206 && ret != 200) {
+		// failed to open file
+		free(buf);
+		netclose(fp->fd);
+		switch (ret) {
+		case 401: errno = EPERM; break;
+		case 403: errno = EACCES; break;
+		case 404: errno = ENOENT; break;
+		case 407: errno = EPERM; break;
+		case 408: errno = ETIMEDOUT; break;
+		case 410: errno = ENOENT; break;
+		case 503: errno = EAGAIN; break;
+		case 504: errno = ETIMEDOUT; break;
+		default:  errno = (ret >= 400 && ret < 500)? EINVAL : EIO; break;
+		}
+		fp->fd = -1;
+		return -1;
+	}
+	free(buf);
+	fp->is_ready = 1;
+	return 0;
+}
+
+/********************
+ * Generic routines *
+ ********************/
+
+knetFile *knet_open(const char *fn, const char *mode)
+{
+	knetFile *fp = 0;
+	if (mode[0] != 'r') {
+		fprintf(stderr, "[kftp_open] only mode \"r\" is supported.\n");
+		return 0;
+	}
+	if (strstr(fn, "ftp://") == fn) {
+		fp = kftp_parse_url(fn, mode);
+		if (fp == 0) return 0;
+		if (kftp_connect(fp) == -1) {
+			knet_close(fp);
+			return 0;
+		}
+		kftp_connect_file(fp);
+	} else if (strstr(fn, "http://") == fn) {
+		fp = khttp_parse_url(fn, mode);
+		if (fp == 0) return 0;
+		khttp_connect_file(fp);
+	} else { // local file
+#ifdef _WIN32
+		/* In windows, O_BINARY is necessary. In Linux/Mac, O_BINARY may
+		 * be undefined on some systems, although it is defined on my
+		 * Mac and the Linux I have tested on. */
+		int fd = open(fn, O_RDONLY | O_BINARY);
+#else		
+		int fd = open(fn, O_RDONLY);
+#endif
+		if (fd == -1) {
+			perror("open");
+			return 0;
+		}
+		fp = (knetFile*)calloc(1, sizeof(knetFile));
+		fp->type = KNF_TYPE_LOCAL;
+		fp->fd = fd;
+		fp->ctrl_fd = -1;
+	}
+	if (fp && fp->fd == -1) {
+		knet_close(fp);
+		return 0;
+	}
+	return fp;
+}
+
+knetFile *knet_dopen(int fd, const char *mode)
+{
+	knetFile *fp = (knetFile*)calloc(1, sizeof(knetFile));
+	fp->type = KNF_TYPE_LOCAL;
+	fp->fd = fd;
+	return fp;
+}
+
+ssize_t knet_read(knetFile *fp, void *buf, size_t len)
+{
+	off_t l = 0;
+	if (fp->fd == -1) return 0;
+	if (fp->type == KNF_TYPE_FTP) {
+		if (fp->is_ready == 0) {
+			if (!fp->no_reconnect) kftp_reconnect(fp);
+			kftp_connect_file(fp);
+		}
+	} else if (fp->type == KNF_TYPE_HTTP) {
+		if (fp->is_ready == 0)
+			khttp_connect_file(fp);
+	}
+	if (fp->type == KNF_TYPE_LOCAL) { // on Windows, the following block is necessary; not on UNIX
+		size_t rest = len;
+		ssize_t curr;
+		while (rest) {
+			do {
+				curr = read(fp->fd, (void*)((char*)buf + l), rest);
+			} while (curr < 0 && EINTR == errno);
+			if (curr < 0) return -1;
+			if (curr == 0) break;
+			l += curr; rest -= curr;
+		}
+	} else l = my_netread(fp->fd, buf, len);
+	fp->offset += l;
+	return l;
+}
+
+off_t knet_seek(knetFile *fp, off_t off, int whence)
+{
+	if (whence == SEEK_SET && off == fp->offset) return 0;
+	if (fp->type == KNF_TYPE_LOCAL) {
+		/* Be aware that lseek() returns the offset after seeking, while fseek() returns zero on success. */
+		off_t offset = lseek(fp->fd, off, whence);
+		if (offset == -1) return -1;
+		fp->offset = offset;
+		return fp->offset;
+	} else if (fp->type == KNF_TYPE_FTP) {
+		if (whence == SEEK_CUR) fp->offset += off;
+		else if (whence == SEEK_SET) fp->offset = off;
+		else if (whence == SEEK_END) fp->offset = fp->file_size + off;
+		else return -1;
+		fp->is_ready = 0;
+		return fp->offset;
+	} else if (fp->type == KNF_TYPE_HTTP) {
+		if (whence == SEEK_END) { // FIXME: can we allow SEEK_END in future?
+			fprintf(stderr, "[knet_seek] SEEK_END is not supported for HTTP. Offset is unchanged.\n");
+			errno = ESPIPE;
+			return -1;
+		}
+		if (whence == SEEK_CUR) fp->offset += off;
+		else if (whence == SEEK_SET) fp->offset = off;
+		else return -1;
+		fp->is_ready = 0;
+		return fp->offset;
+	}
+	errno = EINVAL;
+	fprintf(stderr,"[knet_seek] %s\n", strerror(errno));
+	return -1;
+}
+
+int knet_close(knetFile *fp)
+{
+	if (fp == 0) return 0;
+	if (fp->ctrl_fd != -1) netclose(fp->ctrl_fd); // FTP specific
+	if (fp->fd != -1) {
+		/* On Linux/Mac, netclose() is an alias of close(), but on
+		 * Windows, it is an alias of closesocket(). */
+		if (fp->type == KNF_TYPE_LOCAL) close(fp->fd);
+		else netclose(fp->fd);
+	}
+	free(fp->host); free(fp->port);
+	free(fp->response); free(fp->retr); // FTP specific
+	free(fp->path); free(fp->http_host); // HTTP specific
+	free(fp);
+	return 0;
+}
+
+#ifdef KNETFILE_MAIN
+int main(void)
+{
+	char *buf;
+	knetFile *fp;
+	int type = 4, l;
+#ifdef _WIN32
+	knet_win32_init();
+#endif
+	buf = calloc(0x100000, 1);
+	if (type == 0) {
+		fp = knet_open("knetfile.c", "r");
+		knet_seek(fp, 1000, SEEK_SET);
+	} else if (type == 1) { // NCBI FTP, large file
+		fp = knet_open("ftp://ftp.ncbi.nih.gov/1000genomes/ftp/data/NA12878/alignment/NA12878.chrom6.SLX.SRP000032.2009_06.bam", "r");
+		knet_seek(fp, 2500000000ll, SEEK_SET);
+		l = knet_read(fp, buf, 255);
+	} else if (type == 2) {
+		fp = knet_open("ftp://ftp.sanger.ac.uk/pub4/treefam/tmp/index.shtml", "r");
+		knet_seek(fp, 1000, SEEK_SET);
+	} else if (type == 3) {
+		fp = knet_open("http://www.sanger.ac.uk/Users/lh3/index.shtml", "r");
+		knet_seek(fp, 1000, SEEK_SET);
+	} else if (type == 4) {
+		fp = knet_open("http://www.sanger.ac.uk/Users/lh3/ex1.bam", "r");
+		knet_read(fp, buf, 10000);
+		knet_seek(fp, 20000, SEEK_SET);
+		knet_seek(fp, 10000, SEEK_SET);
+		l = knet_read(fp, buf+10000, 10000000) + 10000;
+	}
+	if (type != 4 && type != 1) {
+		knet_read(fp, buf, 255);
+		buf[255] = 0;
+		printf("%s\n", buf);
+	} else write(fileno(stdout), buf, l);
+	knet_close(fp);
+	free(buf);
+	return 0;
+}
+#endif
diff --git a/htslib/kstring.c b/htslib/kstring.c
new file mode 100644
index 0000000..f43a982
--- /dev/null
+++ b/htslib/kstring.c
@@ -0,0 +1,276 @@
+/* The MIT License
+
+   Copyright (C) 2011 by Attractive Chaos <attractor at live.co.uk>
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+
+#include <config.h>
+
+#include <stdarg.h>
+#include <stdio.h>
+#include <ctype.h>
+#include <string.h>
+#include <stdint.h>
+#include "htslib/kstring.h"
+
+int kvsprintf(kstring_t *s, const char *fmt, va_list ap)
+{
+	va_list args;
+	int l;
+	va_copy(args, ap);
+	l = vsnprintf(s->s + s->l, s->m - s->l, fmt, args); // This line does not work with glibc 2.0. See `man snprintf'.
+	va_end(args);
+	if (l + 1 > s->m - s->l) {
+		s->m = s->l + l + 2;
+		kroundup32(s->m);
+		s->s = (char*)realloc(s->s, s->m);
+		va_copy(args, ap);
+		l = vsnprintf(s->s + s->l, s->m - s->l, fmt, args);
+		va_end(args);
+	}
+	s->l += l;
+	return l;
+}
+
+int ksprintf(kstring_t *s, const char *fmt, ...)
+{
+	va_list ap;
+	int l;
+	va_start(ap, fmt);
+	l = kvsprintf(s, fmt, ap);
+	va_end(ap);
+	return l;
+}
+
+char *kstrtok(const char *str, const char *sep, ks_tokaux_t *aux)
+{
+	const char *p, *start;
+	if (sep) { // set up the table
+		if (str == 0 && (aux->tab[0]&1)) return 0; // no need to set up if we have finished
+		aux->finished = 0;
+		if (sep[1]) {
+			aux->sep = -1;
+			aux->tab[0] = aux->tab[1] = aux->tab[2] = aux->tab[3] = 0;
+			for (p = sep; *p; ++p) aux->tab[*p>>6] |= 1ull<<(*p&0x3f);
+		} else aux->sep = sep[0];
+	}
+	if (aux->finished) return 0;
+	else if (str) aux->p = str - 1, aux->finished = 0;
+	if (aux->sep < 0) {
+		for (p = start = aux->p + 1; *p; ++p)
+			if (aux->tab[*p>>6]>>(*p&0x3f)&1) break;
+	} else {
+		for (p = start = aux->p + 1; *p; ++p)
+			if (*p == aux->sep) break;
+	}
+	aux->p = p; // end of token
+	if (*p == 0) aux->finished = 1; // no more tokens
+	return (char*)start;
+}
+
+// s MUST BE a null terminated string; l = strlen(s)
+int ksplit_core(char *s, int delimiter, int *_max, int **_offsets)
+{
+	int i, n, max, last_char, last_start, *offsets, l;
+	n = 0; max = *_max; offsets = *_offsets;
+	l = strlen(s);
+	
+#define __ksplit_aux do {						\
+		if (_offsets) {						\
+			s[i] = 0;					\
+			if (n == max) {					\
+				int *tmp;				\
+				max = max? max<<1 : 2;			\
+				if ((tmp = (int*)realloc(offsets, sizeof(int) * max))) {  \
+					offsets = tmp;			\
+				} else	{				\
+					free(offsets);			\
+					*_offsets = NULL;		\
+					return 0;			\
+				}					\
+			}						\
+			offsets[n++] = last_start;			\
+		} else ++n;						\
+	} while (0)
+
+	for (i = 0, last_char = last_start = 0; i <= l; ++i) {
+		if (delimiter == 0) {
+			if (isspace(s[i]) || s[i] == 0) {
+				if (isgraph(last_char)) __ksplit_aux; // the end of a field
+			} else {
+				if (isspace(last_char) || last_char == 0) last_start = i;
+			}
+		} else {
+			if (s[i] == delimiter || s[i] == 0) {
+				if (last_char != 0 && last_char != delimiter) __ksplit_aux; // the end of a field
+			} else {
+				if (last_char == delimiter || last_char == 0) last_start = i;
+			}
+		}
+		last_char = s[i];
+	}
+	*_max = max; *_offsets = offsets;
+	return n;
+}
+
+int kgetline(kstring_t *s, kgets_func *fgets_fn, void *fp)
+{
+	size_t l0 = s->l;
+
+	while (s->l == l0 || s->s[s->l-1] != '\n') {
+		if (s->m - s->l < 200) ks_resize(s, s->m + 200);
+		if (fgets_fn(s->s + s->l, s->m - s->l, fp) == NULL) break;
+		s->l += strlen(s->s + s->l);
+	}
+
+	if (s->l == l0) return EOF;
+
+	if (s->l > l0 && s->s[s->l-1] == '\n') {
+		s->l--;
+		if (s->l > l0 && s->s[s->l-1] == '\r') s->l--;
+	}
+	s->s[s->l] = '\0';
+	return 0;
+}
+
+/**********************
+ * Boyer-Moore search *
+ **********************/
+
+typedef unsigned char ubyte_t;
+
+// reference: http://www-igm.univ-mlv.fr/~lecroq/string/node14.html
+static int *ksBM_prep(const ubyte_t *pat, int m)
+{
+	int i, *suff, *prep, *bmGs, *bmBc;
+	prep = (int*)calloc(m + 256, sizeof(int));
+	bmGs = prep; bmBc = prep + m;
+	{ // preBmBc()
+		for (i = 0; i < 256; ++i) bmBc[i] = m;
+		for (i = 0; i < m - 1; ++i) bmBc[pat[i]] = m - i - 1;
+	}
+	suff = (int*)calloc(m, sizeof(int));
+	{ // suffixes()
+		int f = 0, g;
+		suff[m - 1] = m;
+		g = m - 1;
+		for (i = m - 2; i >= 0; --i) {
+			if (i > g && suff[i + m - 1 - f] < i - g)
+				suff[i] = suff[i + m - 1 - f];
+			else {
+				if (i < g) g = i;
+				f = i;
+				while (g >= 0 && pat[g] == pat[g + m - 1 - f]) --g;
+				suff[i] = f - g;
+			}
+		}
+	}
+	{ // preBmGs()
+		int j = 0;
+		for (i = 0; i < m; ++i) bmGs[i] = m;
+		for (i = m - 1; i >= 0; --i)
+			if (suff[i] == i + 1)
+				for (; j < m - 1 - i; ++j)
+					if (bmGs[j] == m)
+						bmGs[j] = m - 1 - i;
+		for (i = 0; i <= m - 2; ++i)
+			bmGs[m - 1 - suff[i]] = m - 1 - i;
+	}
+	free(suff);
+	return prep;
+}
+
+void *kmemmem(const void *_str, int n, const void *_pat, int m, int **_prep)
+{
+	int i, j, *prep = 0, *bmGs, *bmBc;
+	const ubyte_t *str, *pat;
+	str = (const ubyte_t*)_str; pat = (const ubyte_t*)_pat;
+	prep = (_prep == 0 || *_prep == 0)? ksBM_prep(pat, m) : *_prep;
+	if (_prep && *_prep == 0) *_prep = prep;
+	bmGs = prep; bmBc = prep + m;
+	j = 0;
+	while (j <= n - m) {
+		for (i = m - 1; i >= 0 && pat[i] == str[i+j]; --i);
+		if (i >= 0) {
+			int max = bmBc[str[i+j]] - m + 1 + i;
+			if (max < bmGs[i]) max = bmGs[i];
+			j += max;
+		} else return (void*)(str + j);
+	}
+	if (_prep == 0) free(prep);
+	return 0;
+}
+
+char *kstrstr(const char *str, const char *pat, int **_prep)
+{
+	return (char*)kmemmem(str, strlen(str), pat, strlen(pat), _prep);
+}
+
+char *kstrnstr(const char *str, const char *pat, int n, int **_prep)
+{
+	return (char*)kmemmem(str, n, pat, strlen(pat), _prep);
+}
+
+/***********************
+ * The main() function *
+ ***********************/
+
+#ifdef KSTRING_MAIN
+#include <stdio.h>
+int main()
+{
+	kstring_t *s;
+	int *fields, n, i;
+	ks_tokaux_t aux;
+	char *p;
+	s = (kstring_t*)calloc(1, sizeof(kstring_t));
+	// test ksprintf()
+	ksprintf(s, " abcdefg:    %d ", 100);
+	printf("'%s'\n", s->s);
+	// test ksplit()
+	fields = ksplit(s, 0, &n);
+	for (i = 0; i < n; ++i)
+		printf("field[%d] = '%s'\n", i, s->s + fields[i]);
+	// test kstrtok()
+	s->l = 0;
+	for (p = kstrtok("ab:cde:fg/hij::k", ":/", &aux); p; p = kstrtok(0, 0, &aux)) {
+		kputsn(p, aux.p - p, s);
+		kputc('\n', s);
+	}
+	printf("%s", s->s);
+	// free
+	free(s->s); free(s); free(fields);
+
+	{
+		static char *str = "abcdefgcdgcagtcakcdcd";
+		static char *pat = "cd";
+		char *ret, *s = str;
+		int *prep = 0;
+		while ((ret = kstrstr(s, pat, &prep)) != 0) {
+			printf("match: %s\n", ret);
+			s = ret + prep[0];
+		}
+		free(prep);
+	}
+	return 0;
+}
+#endif
diff --git a/htslib/md5.c b/htslib/md5.c
new file mode 100644
index 0000000..ddcfcdf
--- /dev/null
+++ b/htslib/md5.c
@@ -0,0 +1,386 @@
+/*
+ * Trivial amendments by James Bonfield <jkb at sanger.ac.uk> to provide an
+ * HTSlib interface. 2015.
+ *
+ * Externally our API uses an opaque hts_md5_context structure.
+ *
+ * Internally either this gets defined and used with the routines here
+ * or it remains incomplete and is cast to the OpenSSL MD5_CTX structure
+ * and used by routines from OpenSSL.
+ */
+
+/*
+ * This is an OpenSSL-compatible implementation of the RSA Data Security, Inc.
+ * MD5 Message-Digest Algorithm (RFC 1321).
+ *
+ * Homepage:
+ * http://openwall.info/wiki/people/solar/software/public-domain-source-code/md5
+ *
+ * Author:
+ * Alexander Peslyak, better known as Solar Designer <solar at openwall.com>
+ *
+ * This software was written by Alexander Peslyak in 2001.  No copyright is
+ * claimed, and the software is hereby placed in the public domain.
+ * In case this attempt to disclaim copyright and place the software in the
+ * public domain is deemed null and void, then the software is
+ * Copyright (c) 2001 Alexander Peslyak and it is hereby released to the
+ * general public under the following terms:
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted.
+ *
+ * There's ABSOLUTELY NO WARRANTY, express or implied.
+ *
+ * (This is a heavily cut-down "BSD license".)
+ *
+ * This differs from Colin Plumb's older public domain implementation in that
+ * no exactly 32-bit integer data type is required (any 32-bit or wider
+ * unsigned integer data type will do), there's no compile-time endianness
+ * configuration, and the function prototypes match OpenSSL's.  No code from
+ * Colin Plumb's implementation has been reused; this comment merely compares
+ * the properties of the two independent implementations.
+ *
+ * The primary goals of this implementation are portability and ease of use.
+ * It is meant to be fast, but not as fast as possible.  Some known
+ * optimizations are not included to reduce source code size and avoid
+ * compile-time configuration.
+ */
+
+#include <config.h>
+
+#include <stdlib.h>
+#include "htslib/hts.h"
+
+#ifndef HAVE_OPENSSL
+
+#include <string.h>
+
+/* Any 32-bit or wider unsigned integer data type will do */
+typedef unsigned int hts_md5_u32plus;
+
+struct hts_md5_context {
+	hts_md5_u32plus lo, hi;
+	hts_md5_u32plus a, b, c, d;
+	unsigned char buffer[64];
+	hts_md5_u32plus block[16];
+};
+
+/*
+ * The basic MD5 functions.
+ *
+ * F and G are optimized compared to their RFC 1321 definitions for
+ * architectures that lack an AND-NOT instruction, just like in Colin Plumb's
+ * implementation.
+ */
+#define F(x, y, z)			((z) ^ ((x) & ((y) ^ (z))))
+#define G(x, y, z)			((y) ^ ((z) & ((x) ^ (y))))
+#define H(x, y, z)			(((x) ^ (y)) ^ (z))
+#define H2(x, y, z)			((x) ^ ((y) ^ (z)))
+#define I(x, y, z)			((y) ^ ((x) | ~(z)))
+
+/*
+ * The MD5 transformation for all four rounds.
+ */
+#define STEP(f, a, b, c, d, x, t, s) \
+	(a) += f((b), (c), (d)) + (x) + (t); \
+	(a) = (((a) << (s)) | (((a) & 0xffffffff) >> (32 - (s)))); \
+	(a) += (b);
+
+/*
+ * SET reads 4 input bytes in little-endian byte order and stores them
+ * in a properly aligned word in host byte order.
+ *
+ * The check for little-endian architectures that tolerate unaligned
+ * memory accesses is just an optimization.  Nothing will break if it
+ * doesn't work.
+ */
+#if defined(__i386__) || defined(__x86_64__) || defined(__vax__)
+#define SET(n) \
+	(*(hts_md5_u32plus *)&ptr[(n) * 4])
+#define GET(n) \
+	SET(n)
+#else
+#define SET(n) \
+	(ctx->block[(n)] = \
+	(hts_md5_u32plus)ptr[(n) * 4] | \
+	((hts_md5_u32plus)ptr[(n) * 4 + 1] << 8) | \
+	((hts_md5_u32plus)ptr[(n) * 4 + 2] << 16) | \
+	((hts_md5_u32plus)ptr[(n) * 4 + 3] << 24))
+#define GET(n) \
+	(ctx->block[(n)])
+#endif
+
+/*
+ * This processes one or more 64-byte data blocks, but does NOT update
+ * the bit counters.  There are no alignment requirements.
+ */
+static const void *body(hts_md5_context *ctx, const void *data, unsigned long size)
+{
+	const unsigned char *ptr;
+	hts_md5_u32plus a, b, c, d;
+	hts_md5_u32plus saved_a, saved_b, saved_c, saved_d;
+
+	ptr = (const unsigned char *)data;
+
+	a = ctx->a;
+	b = ctx->b;
+	c = ctx->c;
+	d = ctx->d;
+
+	do {
+		saved_a = a;
+		saved_b = b;
+		saved_c = c;
+		saved_d = d;
+
+/* Round 1 */
+		STEP(F, a, b, c, d, SET(0), 0xd76aa478, 7)
+		STEP(F, d, a, b, c, SET(1), 0xe8c7b756, 12)
+		STEP(F, c, d, a, b, SET(2), 0x242070db, 17)
+		STEP(F, b, c, d, a, SET(3), 0xc1bdceee, 22)
+		STEP(F, a, b, c, d, SET(4), 0xf57c0faf, 7)
+		STEP(F, d, a, b, c, SET(5), 0x4787c62a, 12)
+		STEP(F, c, d, a, b, SET(6), 0xa8304613, 17)
+		STEP(F, b, c, d, a, SET(7), 0xfd469501, 22)
+		STEP(F, a, b, c, d, SET(8), 0x698098d8, 7)
+		STEP(F, d, a, b, c, SET(9), 0x8b44f7af, 12)
+		STEP(F, c, d, a, b, SET(10), 0xffff5bb1, 17)
+		STEP(F, b, c, d, a, SET(11), 0x895cd7be, 22)
+		STEP(F, a, b, c, d, SET(12), 0x6b901122, 7)
+		STEP(F, d, a, b, c, SET(13), 0xfd987193, 12)
+		STEP(F, c, d, a, b, SET(14), 0xa679438e, 17)
+		STEP(F, b, c, d, a, SET(15), 0x49b40821, 22)
+
+/* Round 2 */
+		STEP(G, a, b, c, d, GET(1), 0xf61e2562, 5)
+		STEP(G, d, a, b, c, GET(6), 0xc040b340, 9)
+		STEP(G, c, d, a, b, GET(11), 0x265e5a51, 14)
+		STEP(G, b, c, d, a, GET(0), 0xe9b6c7aa, 20)
+		STEP(G, a, b, c, d, GET(5), 0xd62f105d, 5)
+		STEP(G, d, a, b, c, GET(10), 0x02441453, 9)
+		STEP(G, c, d, a, b, GET(15), 0xd8a1e681, 14)
+		STEP(G, b, c, d, a, GET(4), 0xe7d3fbc8, 20)
+		STEP(G, a, b, c, d, GET(9), 0x21e1cde6, 5)
+		STEP(G, d, a, b, c, GET(14), 0xc33707d6, 9)
+		STEP(G, c, d, a, b, GET(3), 0xf4d50d87, 14)
+		STEP(G, b, c, d, a, GET(8), 0x455a14ed, 20)
+		STEP(G, a, b, c, d, GET(13), 0xa9e3e905, 5)
+		STEP(G, d, a, b, c, GET(2), 0xfcefa3f8, 9)
+		STEP(G, c, d, a, b, GET(7), 0x676f02d9, 14)
+		STEP(G, b, c, d, a, GET(12), 0x8d2a4c8a, 20)
+
+/* Round 3 */
+		STEP(H, a, b, c, d, GET(5), 0xfffa3942, 4)
+		STEP(H2, d, a, b, c, GET(8), 0x8771f681, 11)
+		STEP(H, c, d, a, b, GET(11), 0x6d9d6122, 16)
+		STEP(H2, b, c, d, a, GET(14), 0xfde5380c, 23)
+		STEP(H, a, b, c, d, GET(1), 0xa4beea44, 4)
+		STEP(H2, d, a, b, c, GET(4), 0x4bdecfa9, 11)
+		STEP(H, c, d, a, b, GET(7), 0xf6bb4b60, 16)
+		STEP(H2, b, c, d, a, GET(10), 0xbebfbc70, 23)
+		STEP(H, a, b, c, d, GET(13), 0x289b7ec6, 4)
+		STEP(H2, d, a, b, c, GET(0), 0xeaa127fa, 11)
+		STEP(H, c, d, a, b, GET(3), 0xd4ef3085, 16)
+		STEP(H2, b, c, d, a, GET(6), 0x04881d05, 23)
+		STEP(H, a, b, c, d, GET(9), 0xd9d4d039, 4)
+		STEP(H2, d, a, b, c, GET(12), 0xe6db99e5, 11)
+		STEP(H, c, d, a, b, GET(15), 0x1fa27cf8, 16)
+		STEP(H2, b, c, d, a, GET(2), 0xc4ac5665, 23)
+
+/* Round 4 */
+		STEP(I, a, b, c, d, GET(0), 0xf4292244, 6)
+		STEP(I, d, a, b, c, GET(7), 0x432aff97, 10)
+		STEP(I, c, d, a, b, GET(14), 0xab9423a7, 15)
+		STEP(I, b, c, d, a, GET(5), 0xfc93a039, 21)
+		STEP(I, a, b, c, d, GET(12), 0x655b59c3, 6)
+		STEP(I, d, a, b, c, GET(3), 0x8f0ccc92, 10)
+		STEP(I, c, d, a, b, GET(10), 0xffeff47d, 15)
+		STEP(I, b, c, d, a, GET(1), 0x85845dd1, 21)
+		STEP(I, a, b, c, d, GET(8), 0x6fa87e4f, 6)
+		STEP(I, d, a, b, c, GET(15), 0xfe2ce6e0, 10)
+		STEP(I, c, d, a, b, GET(6), 0xa3014314, 15)
+		STEP(I, b, c, d, a, GET(13), 0x4e0811a1, 21)
+		STEP(I, a, b, c, d, GET(4), 0xf7537e82, 6)
+		STEP(I, d, a, b, c, GET(11), 0xbd3af235, 10)
+		STEP(I, c, d, a, b, GET(2), 0x2ad7d2bb, 15)
+		STEP(I, b, c, d, a, GET(9), 0xeb86d391, 21)
+
+		a += saved_a;
+		b += saved_b;
+		c += saved_c;
+		d += saved_d;
+
+		ptr += 64;
+	} while (size -= 64);
+
+	ctx->a = a;
+	ctx->b = b;
+	ctx->c = c;
+	ctx->d = d;
+
+	return ptr;
+}
+
+void hts_md5_reset(hts_md5_context *ctx)
+{
+	ctx->a = 0x67452301;
+	ctx->b = 0xefcdab89;
+	ctx->c = 0x98badcfe;
+	ctx->d = 0x10325476;
+
+	ctx->lo = 0;
+	ctx->hi = 0;
+}
+
+void hts_md5_update(hts_md5_context *ctx, const void *data, unsigned long size)
+{
+	hts_md5_u32plus saved_lo;
+	unsigned long used, available;
+
+	saved_lo = ctx->lo;
+	if ((ctx->lo = (saved_lo + size) & 0x1fffffff) < saved_lo)
+		ctx->hi++;
+	ctx->hi += size >> 29;
+
+	used = saved_lo & 0x3f;
+
+	if (used) {
+		available = 64 - used;
+
+		if (size < available) {
+			memcpy(&ctx->buffer[used], data, size);
+			return;
+		}
+
+		memcpy(&ctx->buffer[used], data, available);
+		data = (const unsigned char *)data + available;
+		size -= available;
+		body(ctx, ctx->buffer, 64);
+	}
+
+	if (size >= 64) {
+		data = body(ctx, data, size & ~(unsigned long)0x3f);
+		size &= 0x3f;
+	}
+
+	memcpy(ctx->buffer, data, size);
+}
+
+void hts_md5_final(unsigned char *result, hts_md5_context *ctx)
+{
+	unsigned long used, available;
+
+	used = ctx->lo & 0x3f;
+
+	ctx->buffer[used++] = 0x80;
+
+	available = 64 - used;
+
+	if (available < 8) {
+		memset(&ctx->buffer[used], 0, available);
+		body(ctx, ctx->buffer, 64);
+		used = 0;
+		available = 64;
+	}
+
+	memset(&ctx->buffer[used], 0, available - 8);
+
+	ctx->lo <<= 3;
+	ctx->buffer[56] = ctx->lo;
+	ctx->buffer[57] = ctx->lo >> 8;
+	ctx->buffer[58] = ctx->lo >> 16;
+	ctx->buffer[59] = ctx->lo >> 24;
+	ctx->buffer[60] = ctx->hi;
+	ctx->buffer[61] = ctx->hi >> 8;
+	ctx->buffer[62] = ctx->hi >> 16;
+	ctx->buffer[63] = ctx->hi >> 24;
+
+	body(ctx, ctx->buffer, 64);
+
+	result[0] = ctx->a;
+	result[1] = ctx->a >> 8;
+	result[2] = ctx->a >> 16;
+	result[3] = ctx->a >> 24;
+	result[4] = ctx->b;
+	result[5] = ctx->b >> 8;
+	result[6] = ctx->b >> 16;
+	result[7] = ctx->b >> 24;
+	result[8] = ctx->c;
+	result[9] = ctx->c >> 8;
+	result[10] = ctx->c >> 16;
+	result[11] = ctx->c >> 24;
+	result[12] = ctx->d;
+	result[13] = ctx->d >> 8;
+	result[14] = ctx->d >> 16;
+	result[15] = ctx->d >> 24;
+
+	memset(ctx, 0, sizeof(*ctx));
+}
+
+
+hts_md5_context *hts_md5_init(void)
+{
+    hts_md5_context *ctx = malloc(sizeof(*ctx));
+    if (!ctx)
+        return NULL;
+
+    hts_md5_reset(ctx);
+    return ctx;
+}
+
+#else
+
+#include <openssl/md5.h>
+#include <assert.h>
+
+/*
+ * Wrappers around the OpenSSL libcrypto.so MD5 implementation.
+ *
+ * These are here to ensure they end up in the symbol table of the
+ * library regardless of the static inline in the headers.
+ */
+hts_md5_context *hts_md5_init(void)
+{
+    MD5_CTX *ctx = malloc(sizeof(*ctx));
+    if (!ctx)
+        return NULL;
+
+    MD5_Init(ctx);
+
+    return (hts_md5_context *)ctx;
+}
+
+void hts_md5_reset(hts_md5_context *ctx)
+{
+    MD5_Init((MD5_CTX *)ctx);
+}
+
+void hts_md5_update(hts_md5_context *ctx, const void *data, unsigned long size)
+{
+    MD5_Update((MD5_CTX *)ctx, data, size);
+}
+
+void hts_md5_final(unsigned char *result, hts_md5_context *ctx)
+{
+    MD5_Final(result, (MD5_CTX *)ctx);
+}
+
+#endif
+
+void hts_md5_destroy(hts_md5_context *ctx)
+{
+    if (!ctx)
+        return;
+
+    free(ctx);
+}
+
+void hts_md5_hex(char *hex, const unsigned char *digest)
+{
+    int i;
+    for (i = 0; i < 16; i++) {
+        hex[i*2+0] = "0123456789abcdef"[(digest[i]>>4)&0xf];
+        hex[i*2+1] = "0123456789abcdef"[digest[i]&0xf];
+    }
+    hex[32] = 0;
+}
diff --git a/htslib/plugin.c b/htslib/plugin.c
new file mode 100644
index 0000000..7525cc6
--- /dev/null
+++ b/htslib/plugin.c
@@ -0,0 +1,171 @@
+/*  plugin.c -- low-level path parsing and plugin functions.
+
+    Copyright (C) 2015 Genome Research Ltd.
+
+    Author: John Marshall <jm18 at sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <errno.h>
+
+#include <dirent.h>
+#include <dlfcn.h>
+
+#include "hts_internal.h"
+#include "htslib/kstring.h"
+
+#ifndef PLUGINPATH
+#define PLUGINPATH ""
+#endif
+
+#ifdef __APPLE__
+#define PLUGIN_EXT ".bundle"
+#define PLUGIN_EXT_LEN 7
+#else
+#define PLUGIN_EXT ".so"
+#define PLUGIN_EXT_LEN 3
+#endif
+
+static DIR *open_nextdir(struct hts_path_itr *itr)
+{
+    DIR *dir;
+
+    while (1) {
+        const char *colon = strchr(itr->pathdir, ':');
+        if (colon == NULL) return NULL;
+
+        itr->entry.l = 0;
+        kputsn(itr->pathdir, colon - itr->pathdir, &itr->entry);
+        itr->pathdir = &colon[1];
+        if (itr->entry.l == 0) continue;
+
+        dir = opendir(itr->entry.s);
+        if (dir) break;
+
+        if (hts_verbose >= 4)
+            fprintf(stderr,
+                    "[W::hts_path_itr] can't scan directory \"%s\": %s\n",
+                    itr->entry.s, strerror(errno));
+    }
+
+    if (itr->entry.s[itr->entry.l-1] != '/') kputc('/', &itr->entry);
+    itr->entry_dir_l = itr->entry.l;
+    return dir;
+}
+
+void hts_path_itr_setup(struct hts_path_itr *itr, const char *path,
+        const char *builtin_path, const char *prefix, size_t prefix_len,
+        const char *suffix, size_t suffix_len)
+{
+    itr->prefix = prefix;
+    itr->prefix_len = prefix_len;
+
+    if (suffix) itr->suffix = suffix, itr->suffix_len = suffix_len;
+    else itr->suffix = PLUGIN_EXT, itr->suffix_len = PLUGIN_EXT_LEN;
+
+    itr->path.l = itr->path.m = 0; itr->path.s = NULL;
+    itr->entry.l = itr->entry.m = 0; itr->entry.s = NULL;
+
+    if (! builtin_path) builtin_path = PLUGINPATH;
+    if (! path) {
+        path = getenv("HTS_PATH");
+        if (! path) path = "";
+    }
+
+    while (1) {
+        size_t len = strcspn(path, ":");
+        if (len == 0) kputs(builtin_path, &itr->path);
+        else kputsn(path, len, &itr->path);
+        kputc(':', &itr->path);
+
+        path += len;
+        if (*path == ':') path++;
+        else break;
+    }
+
+    // Note that ':' now terminates entries rather than separates them
+    itr->pathdir = itr->path.s;
+    itr->dirv = open_nextdir(itr);
+}
+
+const char *hts_path_itr_next(struct hts_path_itr *itr)
+{
+    while (itr->dirv) {
+        struct dirent *e;
+        while ((e = readdir((DIR *) itr->dirv)) != NULL) {
+            size_t d_name_len = strlen(e->d_name);
+            if (strncmp(e->d_name, itr->prefix, itr->prefix_len) == 0 &&
+                d_name_len >= itr->suffix_len &&
+                strncmp(e->d_name + d_name_len - itr->suffix_len, itr->suffix,
+                        itr->suffix_len) == 0) {
+                itr->entry.l = itr->entry_dir_l;
+                kputs(e->d_name, &itr->entry);
+                return itr->entry.s;
+            }
+        }
+
+        closedir((DIR *) itr->dirv);
+        itr->dirv = open_nextdir(itr);
+    }
+
+    itr->pathdir = NULL;
+    free(itr->path.s); itr->path.s = NULL;
+    free(itr->entry.s); itr->entry.s = NULL;
+    return NULL;
+}
+
+void *load_plugin(void **pluginp, const char *filename, const char *symbol)
+{
+    void *lib = dlopen(filename, RTLD_NOW | RTLD_LOCAL);
+    if (lib == NULL) goto error;
+
+    void *sym = dlsym(lib, symbol);
+    if (sym == NULL) goto error;
+
+    *pluginp = lib;
+    return sym;
+
+error:
+    if (hts_verbose >= 4)
+        fprintf(stderr, "[W::%s] can't load plugin \"%s\": %s\n",
+                __func__, filename, dlerror());
+    if (lib) dlclose(lib);
+    return NULL;
+}
+
+void *plugin_sym(void *plugin, const char *name, const char **errmsg)
+{
+    void *sym = dlsym(plugin, name);
+    if (sym == NULL) *errmsg = dlerror();
+    return sym;
+}
+
+void close_plugin(void *plugin)
+{
+    if (dlclose(plugin) != 0) {
+        if (hts_verbose >= 4)
+            fprintf(stderr, "[W::%s] dlclose() failed: %s\n",
+                    __func__, dlerror());
+    }
+}
diff --git a/htslib/regidx.c b/htslib/regidx.c
new file mode 100644
index 0000000..84f18b4
--- /dev/null
+++ b/htslib/regidx.c
@@ -0,0 +1,340 @@
+/* 
+    Copyright (C) 2014 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3 at sanger.ac.uk>
+
+    Permission is hereby granted, free of charge, to any person obtaining a copy
+    of this software and associated documentation files (the "Software"), to deal
+    in the Software without restriction, including without limitation the rights
+    to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+    copies of the Software, and to permit persons to whom the Software is
+    furnished to do so, subject to the following conditions:
+    
+    The above copyright notice and this permission notice shall be included in
+    all copies or substantial portions of the Software.
+    
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+    AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+    LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+    OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+    THE SOFTWARE.
+*/
+
+#include <config.h>
+
+#include "htslib/hts.h"
+#include "htslib/kstring.h"
+#include "htslib/kseq.h"
+#include "htslib/khash_str2int.h"
+#include "htslib/regidx.h"
+
+#define LIDX_SHIFT 13   // number of insignificant index bits
+
+// List of regions for one chromosome
+typedef struct
+{
+    int *idx, nidx;
+    int nregs, mregs;   // n:used, m:alloced
+    reg_t *regs;
+    void *payload;
+}
+reglist_t;
+
+// Container of all sequences
+struct _regidx_t
+{
+    int nseq, mseq;     // n:used, m:alloced
+    reglist_t *seq;     // regions for each sequence
+    void *seq2regs;     // hash for fast lookup from chr name to regions
+    char **seq_names;
+    regidx_free_f free;     // function to free any data allocated by regidx_parse_f
+    regidx_parse_f parse;   // parse one input line
+    void *usr;              // user data to pass to regidx_parse_f
+
+    // temporary data for index initialization
+    kstring_t str;
+    int rid_prev, start_prev, end_prev;
+    int payload_size;
+    void *payload;
+};
+
+int regidx_seq_nregs(regidx_t *idx, const char *seq)
+{
+    int iseq;
+    if ( khash_str2int_get(idx->seq2regs, seq, &iseq)!=0 ) return 0; // no such sequence
+    return idx->seq[iseq].nregs;
+}
+
+int regidx_nregs(regidx_t *idx)
+{
+    int i, nregs = 0;
+    for (i=0; i<idx->nseq; i++) nregs += idx->seq[i].nregs;
+    return nregs;
+}
+
+char **regidx_seq_names(regidx_t *idx, int *n)
+{
+    *n = idx->nseq;
+    return idx->seq_names;
+}
+
+int _regidx_build_index(regidx_t *idx)
+{
+    int iseq;
+    for (iseq=0; iseq<idx->nseq; iseq++)
+    {
+        reglist_t *list = &idx->seq[iseq];
+        int j,k, imax = 0;   // max index bin
+        for (j=0; j<list->nregs; j++)
+        {
+            int ibeg = list->regs[j].start >> LIDX_SHIFT;
+            int iend = list->regs[j].end >> LIDX_SHIFT;
+            if ( imax < iend + 1 )
+            {
+                int old_imax = imax; 
+                imax = iend + 1;
+                kroundup32(imax);
+                list->idx = (int*) realloc(list->idx, imax*sizeof(int));
+                for (k=old_imax; k<imax; k++) list->idx[k] = -1;
+            }
+            if ( ibeg==iend )
+            {
+                if ( list->idx[ibeg]<0 ) list->idx[ibeg] = j;
+            }
+            else
+            {
+                for (k=ibeg; k<=iend; k++)
+                    if ( list->idx[k]<0 ) list->idx[k] = j;
+            }
+            list->nidx = iend + 1;
+        }
+    }
+    return 0;
+}
+
+int regidx_insert(regidx_t *idx, char *line)
+{
+    if ( !line )
+        return _regidx_build_index(idx);
+
+    char *chr_from, *chr_to;
+    reg_t reg;
+    int ret = idx->parse(line,&chr_from,&chr_to,&reg,idx->payload,idx->usr);
+    if ( ret==-2 ) return -1;   // error
+    if ( ret==-1 ) return 0;    // skip the line
+
+    int rid;
+    idx->str.l = 0;
+    kputsn(chr_from, chr_to-chr_from+1, &idx->str);
+    if ( khash_str2int_get(idx->seq2regs, idx->str.s, &rid)!=0 )
+    {
+        idx->nseq++;
+        int m_prev = idx->mseq;
+        hts_expand0(reglist_t,idx->nseq,idx->mseq,idx->seq);
+        hts_expand0(char*,idx->nseq,m_prev,idx->seq_names);
+        idx->seq_names[idx->nseq-1] = strdup(idx->str.s);
+        rid = khash_str2int_inc(idx->seq2regs, idx->seq_names[idx->nseq-1]);
+    }
+
+    reglist_t *list = &idx->seq[rid];
+    list->nregs++;
+    int m_prev = list->mregs;
+    hts_expand(reg_t,list->nregs,list->mregs,list->regs);
+    list->regs[list->nregs-1] = reg;
+    if ( idx->payload_size )
+    {
+        if ( m_prev < list->mregs ) list->payload = realloc(list->payload,idx->payload_size*list->mregs);
+        memcpy(list->payload + idx->payload_size*(list->nregs-1), idx->payload, idx->payload_size);
+    }
+
+    if ( idx->rid_prev==rid )
+    {
+        if ( idx->start_prev > reg.start || (idx->start_prev==reg.start && idx->end_prev>reg.end) ) 
+        { 
+            fprintf(stderr,"The regions are not sorted: %s:%d-%d is before %s:%d-%d\n", 
+                idx->str.s,idx->start_prev+1,idx->end_prev+1,idx->str.s,reg.start+1,reg.end+1); 
+            return -1;
+        }
+    }
+    idx->rid_prev = rid;
+    idx->start_prev = reg.start;
+    idx->end_prev = reg.end;
+    return 0;
+}
+
+regidx_t *regidx_init(const char *fname, regidx_parse_f parser, regidx_free_f free_f, size_t payload_size, void *usr_dat)
+{
+    if ( !parser )
+    {
+        if ( !fname ) parser = regidx_parse_tab;
+        else
+        {
+            int len = strlen(fname);
+            if ( len>=7 && !strcasecmp(".bed.gz",fname+len-7) )
+                parser = regidx_parse_bed;
+            else if ( len>=8 && !strcasecmp(".bed.bgz",fname+len-8) )
+                parser = regidx_parse_bed;
+            else if ( len>=4 && !strcasecmp(".bed",fname+len-4) )
+                parser = regidx_parse_bed;
+            else
+                parser = regidx_parse_tab;
+        }
+    }
+
+    regidx_t *idx = (regidx_t*) calloc(1,sizeof(regidx_t));
+    idx->free  = free_f;
+    idx->parse = parser;
+    idx->usr   = usr_dat;
+    idx->seq2regs = khash_str2int_init();
+    idx->rid_prev   = -1;
+    idx->start_prev = -1;
+    idx->end_prev   = -1;
+    idx->payload_size = payload_size;
+    if ( payload_size ) idx->payload = malloc(payload_size);
+
+    if ( !fname ) return idx;
+    
+    kstring_t str = {0,0,0};
+
+    htsFile *fp = hts_open(fname,"r");
+    if ( !fp ) goto error;
+
+    while ( hts_getline(fp, KS_SEP_LINE, &str) > 0 )
+    {
+        if ( regidx_insert(idx, str.s) ) goto error;
+    }
+    regidx_insert(idx, NULL);
+    
+    free(str.s);
+    hts_close(fp);
+    return idx;
+
+error:
+    free(str.s);
+    if ( fp ) hts_close(fp);
+    regidx_destroy(idx);
+    return NULL;
+}
+
+void regidx_destroy(regidx_t *idx)
+{
+    int i, j;
+    for (i=0; i<idx->nseq; i++)
+    {
+        reglist_t *list = &idx->seq[i];
+        if ( idx->free )
+        {
+            for (j=0; j<list->nregs; j++)
+                idx->free(list->payload + idx->payload_size*j);
+        }
+        free(list->payload);
+        free(list->regs);
+        free(list->idx);
+    }
+    free(idx->seq_names);
+    free(idx->seq);
+    free(idx->str.s);
+    free(idx->payload);
+    khash_str2int_destroy_free(idx->seq2regs);
+    free(idx);
+}
+
+int regidx_overlap(regidx_t *idx, const char *chr, uint32_t from, uint32_t to, regitr_t *itr)
+{
+    if ( itr ) itr->i = itr->n = 0;
+
+    int iseq;
+    if ( khash_str2int_get(idx->seq2regs, chr, &iseq)!=0 ) return 0; // no such sequence
+
+    reglist_t *list = &idx->seq[iseq];
+    if ( !list->nregs ) return 0;
+
+    int i, ibeg = from>>LIDX_SHIFT; 
+    int ireg = ibeg < list->nidx ? list->idx[ibeg] : list->idx[ list->nidx - 1 ];
+    if ( ireg < 0 )
+    {
+        // linear search; if slow, replace with binary search
+        if ( ibeg > list->nidx ) ibeg = list->nidx;
+        for (i=ibeg - 1; i>=0; i--)
+            if ( list->idx[i] >=0 ) break;
+        ireg = i>=0 ? list->idx[i] : 0;
+    }
+    for (i=ireg; i<list->nregs; i++)
+    {
+        if ( list->regs[i].start > to ) return 0;   // no match
+        if ( list->regs[i].end >= from && list->regs[i].start <= to ) break; // found
+    }
+
+    if ( i>=list->nregs ) return 0;   // no match
+
+    if ( !itr ) return 1;
+
+    itr->i = 0;
+    itr->n = list->nregs - i;
+    itr->reg = &idx->seq[iseq].regs[i];
+    if ( idx->payload_size )
+        itr->payload = idx->seq[iseq].payload + i*idx->payload_size;
+    else
+        itr->payload = NULL;
+
+    return 1;
+}
+
+int regidx_parse_bed(const char *line, char **chr_beg, char **chr_end, reg_t *reg, void *payload, void *usr)
+{
+    char *ss = (char*) line;
+    while ( *ss && isspace(*ss) ) ss++;
+    if ( !*ss ) return -1;      // skip blank lines
+    if ( *ss=='#' ) return -1;  // skip comments
+    
+    char *se = ss;
+    while ( *se && !isspace(*se) ) se++;
+    if ( !*se ) { fprintf(stderr,"Could not parse bed line: %s\n", line); return -2; }
+
+    *chr_beg = ss;
+    *chr_end = se-1;
+
+    ss = se+1;
+    reg->start = hts_parse_decimal(ss, &se, 0);
+    if ( ss==se ) { fprintf(stderr,"Could not parse bed line: %s\n", line); return -2; }
+
+    ss = se+1;
+    reg->end = hts_parse_decimal(ss, &se, 0) - 1;
+    if ( ss==se ) { fprintf(stderr,"Could not parse bed line: %s\n", line); return -2; }
+    
+    return 0;
+}
+
+int regidx_parse_tab(const char *line, char **chr_beg, char **chr_end, reg_t *reg, void *payload, void *usr)
+{
+    char *ss = (char*) line;
+    while ( *ss && isspace(*ss) ) ss++;
+    if ( !*ss ) return -1;      // skip blank lines
+    if ( *ss=='#' ) return -1;  // skip comments
+    
+    char *se = ss;
+    while ( *se && !isspace(*se) ) se++;
+    if ( !*se ) { fprintf(stderr,"Could not parse bed line: %s\n", line); return -2; }
+
+    *chr_beg = ss;
+    *chr_end = se-1;
+
+    ss = se+1;
+    reg->start = hts_parse_decimal(ss, &se, 0) - 1;
+    if ( ss==se ) { fprintf(stderr,"Could not parse bed line: %s\n", line); return -2; }
+
+    if ( !se[0] || !se[1] )
+        reg->end = reg->start;
+    else
+    {
+        ss = se+1;
+        reg->end = hts_parse_decimal(ss, &se, 0);
+        if ( ss==se ) reg->end = reg->start;
+        else reg->end--;
+    }
+    
+    return 0;
+}
+
diff --git a/htslib/sam.c b/htslib/sam.c
new file mode 100644
index 0000000..66eeb2b
--- /dev/null
+++ b/htslib/sam.c
@@ -0,0 +1,2073 @@
+/*  sam.c -- SAM and BAM file I/O and manipulation.
+
+    Copyright (C) 2008-2010, 2012-2016 Genome Research Ltd.
+    Copyright (C) 2010, 2012, 2013 Broad Institute.
+
+    Author: Heng Li <lh3 at sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <errno.h>
+#include <ctype.h>
+#include <zlib.h>
+#include "htslib/sam.h"
+#include "htslib/bgzf.h"
+#include "cram/cram.h"
+#include "hts_internal.h"
+#include "htslib/hfile.h"
+
+#include "htslib/khash.h"
+KHASH_DECLARE(s2i, kh_cstr_t, int64_t)
+
+typedef khash_t(s2i) sdict_t;
+
+/**********************
+ *** BAM header I/O ***
+ **********************/
+
+bam_hdr_t *bam_hdr_init()
+{
+    return (bam_hdr_t*)calloc(1, sizeof(bam_hdr_t));
+}
+
+void bam_hdr_destroy(bam_hdr_t *h)
+{
+    int32_t i;
+    if (h == NULL) return;
+    if (h->target_name) {
+        for (i = 0; i < h->n_targets; ++i)
+            free(h->target_name[i]);
+        free(h->target_name);
+        free(h->target_len);
+    }
+    free(h->text); free(h->cigar_tab);
+    if (h->sdict) kh_destroy(s2i, (sdict_t*)h->sdict);
+    free(h);
+}
+
+bam_hdr_t *bam_hdr_dup(const bam_hdr_t *h0)
+{
+    if (h0 == NULL) return NULL;
+    bam_hdr_t *h;
+    if ((h = bam_hdr_init()) == NULL) return NULL;
+    // copy the simple data
+    h->n_targets = h0->n_targets;
+    h->ignore_sam_err = h0->ignore_sam_err;
+    h->l_text = h0->l_text;
+    // Then the pointery stuff
+    h->cigar_tab = NULL;
+    h->sdict = NULL;
+    // TODO Check for memory allocation failures
+    h->text = (char*)calloc(h->l_text + 1, 1);
+    memcpy(h->text, h0->text, h->l_text);
+    h->target_len = (uint32_t*)calloc(h->n_targets, sizeof(uint32_t));
+    h->target_name = (char**)calloc(h->n_targets, sizeof(char*));
+    int i;
+    for (i = 0; i < h->n_targets; ++i) {
+        h->target_len[i] = h0->target_len[i];
+        h->target_name[i] = strdup(h0->target_name[i]);
+    }
+    return h;
+}
+
+
+static bam_hdr_t *hdr_from_dict(sdict_t *d)
+{
+    bam_hdr_t *h;
+    khint_t k;
+    h = bam_hdr_init();
+    h->sdict = d;
+    h->n_targets = kh_size(d);
+    // TODO Check for memory allocation failures
+    h->target_len = (uint32_t*)malloc(sizeof(uint32_t) * h->n_targets);
+    h->target_name = (char**)malloc(sizeof(char*) * h->n_targets);
+    for (k = kh_begin(d); k != kh_end(d); ++k) {
+        if (!kh_exist(d, k)) continue;
+        h->target_name[kh_val(d, k)>>32] = (char*)kh_key(d, k);
+        h->target_len[kh_val(d, k)>>32]  = kh_val(d, k)<<32>>32;
+        kh_val(d, k) >>= 32;
+    }
+    return h;
+}
+
+bam_hdr_t *bam_hdr_read(BGZF *fp)
+{
+    bam_hdr_t *h;
+    char buf[4];
+    int magic_len, has_EOF;
+    int32_t i, name_len, num_names = 0;
+    size_t bufsize;
+    ssize_t bytes;
+    // check EOF
+    has_EOF = bgzf_check_EOF(fp);
+    if (has_EOF < 0) {
+        perror("[W::bam_hdr_read] bgzf_check_EOF");
+    } else if (has_EOF == 0 && hts_verbose >= 2)
+        fprintf(stderr, "[W::%s] EOF marker is absent. The input is probably truncated.\n", __func__);
+    // read "BAM1"
+    magic_len = bgzf_read(fp, buf, 4);
+    if (magic_len != 4 || strncmp(buf, "BAM\1", 4)) {
+        if (hts_verbose >= 1) fprintf(stderr, "[E::%s] invalid BAM binary header\n", __func__);
+        return 0;
+    }
+    h = bam_hdr_init();
+    if (!h) goto nomem;
+
+    // read plain text and the number of reference sequences
+    bytes = bgzf_read(fp, &h->l_text, 4);
+    if (bytes != 4) goto read_err;
+    if (fp->is_be) ed_swap_4p(&h->l_text);
+
+    bufsize = ((size_t) h->l_text) + 1;
+    if (bufsize < h->l_text) goto nomem; // so large that adding 1 overflowed
+    h->text = (char*)malloc(bufsize);
+    if (!h->text) goto nomem;
+    h->text[h->l_text] = 0; // make sure it is NULL terminated
+    bytes = bgzf_read(fp, h->text, h->l_text);
+    if (bytes != h->l_text) goto read_err;
+
+    bytes = bgzf_read(fp, &h->n_targets, 4);
+    if (bytes != 4) goto read_err;
+    if (fp->is_be) ed_swap_4p(&h->n_targets);
+
+    if (h->n_targets < 0) goto invalid;
+
+    // read reference sequence names and lengths
+    if (h->n_targets > 0) {
+        h->target_name = (char**)calloc(h->n_targets, sizeof(char*));
+        if (!h->target_name) goto nomem;
+        h->target_len = (uint32_t*)calloc(h->n_targets, sizeof(uint32_t));
+        if (!h->target_len) goto nomem;
+    }
+    else {
+        h->target_name = NULL;
+        h->target_len = NULL;
+    }
+
+    for (i = 0; i != h->n_targets; ++i) {
+        bytes = bgzf_read(fp, &name_len, 4);
+        if (bytes != 4) goto read_err;
+        if (fp->is_be) ed_swap_4p(&name_len);
+        if (name_len <= 0) goto invalid;
+
+        h->target_name[i] = (char*)malloc(name_len);
+        if (!h->target_name[i]) goto nomem;
+        num_names++;
+
+        bytes = bgzf_read(fp, h->target_name[i], name_len);
+        if (bytes != name_len) goto read_err;
+
+        if (h->target_name[i][name_len - 1] != '\0') {
+            /* Fix missing NUL-termination.  Is this being too nice?
+               We could alternatively bail out with an error. */
+            char *new_name;
+            if (name_len == INT32_MAX) goto invalid;
+            new_name = realloc(h->target_name[i], name_len + 1);
+            if (new_name == NULL) goto nomem;
+            h->target_name[i] = new_name;
+            h->target_name[i][name_len] = '\0';
+        }
+
+        bytes = bgzf_read(fp, &h->target_len[i], 4);
+        if (bytes != 4) goto read_err;
+        if (fp->is_be) ed_swap_4p(&h->target_len[i]);
+    }
+    return h;
+
+ nomem:
+    if (hts_verbose >= 1) fprintf(stderr, "[E::%s] out of memory\n", __func__);
+    goto clean;
+
+ read_err:
+    if (hts_verbose >= 1) {
+        if (bytes < 0) {
+            fprintf(stderr, "[E::%s] error reading BGZF stream\n", __func__);
+        } else {
+            fprintf(stderr, "[E::%s] truncated bam header\n", __func__);
+        }
+    }
+    goto clean;
+
+ invalid:
+    if (hts_verbose >= 1) {
+        fprintf(stderr, "[E::%s] invalid BAM binary header\n", __func__);
+    }
+
+ clean:
+    if (h != NULL) {
+        h->n_targets = num_names; // ensure we free only allocated target_names
+        bam_hdr_destroy(h);
+    }
+    return NULL;
+}
+
+int bam_hdr_write(BGZF *fp, const bam_hdr_t *h)
+{
+    char buf[4];
+    int32_t i, name_len, x;
+    // write "BAM1"
+    strncpy(buf, "BAM\1", 4);
+    if (bgzf_write(fp, buf, 4) < 0) return -1;
+    // write plain text and the number of reference sequences
+    if (fp->is_be) {
+        x = ed_swap_4(h->l_text);
+        if (bgzf_write(fp, &x, 4) < 0) return -1;
+        if (h->l_text) {
+            if (bgzf_write(fp, h->text, h->l_text) < 0) return -1;
+        }
+        x = ed_swap_4(h->n_targets);
+        if (bgzf_write(fp, &x, 4) < 0) return -1;
+    } else {
+        if (bgzf_write(fp, &h->l_text, 4) < 0) return -1;
+        if (h->l_text) {
+            if (bgzf_write(fp, h->text, h->l_text) < 0) return -1;
+        }
+        if (bgzf_write(fp, &h->n_targets, 4) < 0) return -1;
+    }
+    // write sequence names and lengths
+    for (i = 0; i != h->n_targets; ++i) {
+        char *p = h->target_name[i];
+        name_len = strlen(p) + 1;
+        if (fp->is_be) {
+            x = ed_swap_4(name_len);
+            if (bgzf_write(fp, &x, 4) < 0) return -1;
+        } else {
+            if (bgzf_write(fp, &name_len, 4) < 0) return -1;
+        }
+        if (bgzf_write(fp, p, name_len) < 0) return -1;
+        if (fp->is_be) {
+            x = ed_swap_4(h->target_len[i]);
+            if (bgzf_write(fp, &x, 4) < 0) return -1;
+        } else {
+            if (bgzf_write(fp, &h->target_len[i], 4) < 0) return -1;
+        }
+    }
+    if (bgzf_flush(fp) < 0) return -1;
+    return 0;
+}
+
+int bam_name2id(bam_hdr_t *h, const char *ref)
+{
+    sdict_t *d = (sdict_t*)h->sdict;
+    khint_t k;
+    if (h->sdict == 0) {
+        int i, absent;
+        d = kh_init(s2i);
+        for (i = 0; i < h->n_targets; ++i) {
+            k = kh_put(s2i, d, h->target_name[i], &absent);
+            kh_val(d, k) = i;
+        }
+        h->sdict = d;
+    }
+    k = kh_get(s2i, d, ref);
+    return k == kh_end(d)? -1 : kh_val(d, k);
+}
+
+/*************************
+ *** BAM alignment I/O ***
+ *************************/
+
+bam1_t *bam_init1()
+{
+    return (bam1_t*)calloc(1, sizeof(bam1_t));
+}
+
+void bam_destroy1(bam1_t *b)
+{
+    if (b == 0) return;
+    free(b->data); free(b);
+}
+
+bam1_t *bam_copy1(bam1_t *bdst, const bam1_t *bsrc)
+{
+    uint8_t *data = bdst->data;
+    int m_data = bdst->m_data;   // backup data and m_data
+    if (m_data < bsrc->l_data) { // double the capacity
+        m_data = bsrc->l_data; kroundup32(m_data);
+        data = (uint8_t*)realloc(data, m_data);
+    }
+    memcpy(data, bsrc->data, bsrc->l_data); // copy var-len data
+    *bdst = *bsrc; // copy the rest
+    // restore the backup
+    bdst->m_data = m_data;
+    bdst->data = data;
+    return bdst;
+}
+
+bam1_t *bam_dup1(const bam1_t *bsrc)
+{
+    if (bsrc == NULL) return NULL;
+    bam1_t *bdst = bam_init1();
+    if (bdst == NULL) return NULL;
+    return bam_copy1(bdst, bsrc);
+}
+
+int bam_cigar2qlen(int n_cigar, const uint32_t *cigar)
+{
+    int k, l;
+    for (k = l = 0; k < n_cigar; ++k)
+        if (bam_cigar_type(bam_cigar_op(cigar[k]))&1)
+            l += bam_cigar_oplen(cigar[k]);
+    return l;
+}
+
+int bam_cigar2rlen(int n_cigar, const uint32_t *cigar)
+{
+    int k, l;
+    for (k = l = 0; k < n_cigar; ++k)
+        if (bam_cigar_type(bam_cigar_op(cigar[k]))&2)
+            l += bam_cigar_oplen(cigar[k]);
+    return l;
+}
+
+int32_t bam_endpos(const bam1_t *b)
+{
+    if (!(b->core.flag & BAM_FUNMAP) && b->core.n_cigar > 0)
+        return b->core.pos + bam_cigar2rlen(b->core.n_cigar, bam_get_cigar(b));
+    else
+        return b->core.pos + 1;
+}
+
+static inline int aux_type2size(uint8_t type)
+{
+    switch (type) {
+    case 'A': case 'c': case 'C':
+        return 1;
+    case 's': case 'S':
+        return 2;
+    case 'i': case 'I': case 'f':
+        return 4;
+    case 'd':
+        return 8;
+    case 'Z': case 'H': case 'B':
+        return type;
+    default:
+        return 0;
+    }
+}
+
+static void swap_data(const bam1_core_t *c, int l_data, uint8_t *data, int is_host)
+{
+    uint8_t *s;
+    uint32_t *cigar = (uint32_t*)(data + c->l_qname);
+    uint32_t i, n;
+    s = data + c->n_cigar*4 + c->l_qname + c->l_qseq + (c->l_qseq + 1)/2;
+    for (i = 0; i < c->n_cigar; ++i) ed_swap_4p(&cigar[i]);
+    while (s < data + l_data) {
+        int size;
+        s += 2; // skip key
+        size = aux_type2size(*s); ++s; // skip type
+        switch (size) {
+        case 1: ++s; break;
+        case 2: ed_swap_2p(s); s += 2; break;
+        case 4: ed_swap_4p(s); s += 4; break;
+        case 8: ed_swap_8p(s); s += 8; break;
+        case 'Z':
+        case 'H':
+            while (*s) ++s;
+            ++s;
+            break;
+        case 'B':
+            size = aux_type2size(*s); ++s;
+            if (is_host) memcpy(&n, s, 4), ed_swap_4p(s);
+            else ed_swap_4p(s), memcpy(&n, s, 4);
+            s += 4;
+            switch (size) {
+            case 1: s += n; break;
+            case 2: for (i = 0; i < n; ++i, s += 2) ed_swap_2p(s); break;
+            case 4: for (i = 0; i < n; ++i, s += 4) ed_swap_4p(s); break;
+            case 8: for (i = 0; i < n; ++i, s += 8) ed_swap_8p(s); break;
+            }
+            break;
+        }
+    }
+}
+
+int bam_read1(BGZF *fp, bam1_t *b)
+{
+    bam1_core_t *c = &b->core;
+    int32_t block_len, ret, i;
+    uint32_t x[8];
+    if ((ret = bgzf_read(fp, &block_len, 4)) != 4) {
+        if (ret == 0) return -1; // normal end-of-file
+        else return -2; // truncated
+    }
+    if (bgzf_read(fp, x, 32) != 32) return -3;
+    if (fp->is_be) {
+        ed_swap_4p(&block_len);
+        for (i = 0; i < 8; ++i) ed_swap_4p(x + i);
+    }
+    c->tid = x[0]; c->pos = x[1];
+    c->bin = x[2]>>16; c->qual = x[2]>>8&0xff; c->l_qname = x[2]&0xff;
+    c->flag = x[3]>>16; c->n_cigar = x[3]&0xffff;
+    c->l_qseq = x[4];
+    c->mtid = x[5]; c->mpos = x[6]; c->isize = x[7];
+    b->l_data = block_len - 32;
+    if (b->l_data < 0 || c->l_qseq < 0 || c->l_qname < 1) return -4;
+    if ((char *)bam_get_aux(b) - (char *)b->data > b->l_data)
+        return -4;
+    if (b->m_data < b->l_data) {
+        b->m_data = b->l_data;
+        kroundup32(b->m_data);
+        b->data = (uint8_t*)realloc(b->data, b->m_data);
+        if (!b->data)
+            return -4;
+    }
+    if (bgzf_read(fp, b->data, b->l_data) != b->l_data) return -4;
+    //b->l_aux = b->l_data - c->n_cigar * 4 - c->l_qname - c->l_qseq - (c->l_qseq+1)/2;
+    if (fp->is_be) swap_data(c, b->l_data, b->data, 0);
+    return 4 + block_len;
+}
+
+int bam_write1(BGZF *fp, const bam1_t *b)
+{
+    const bam1_core_t *c = &b->core;
+    uint32_t x[8], block_len = b->l_data + 32, y;
+    int i, ok;
+    x[0] = c->tid;
+    x[1] = c->pos;
+    x[2] = (uint32_t)c->bin<<16 | c->qual<<8 | c->l_qname;
+    x[3] = (uint32_t)c->flag<<16 | c->n_cigar;
+    x[4] = c->l_qseq;
+    x[5] = c->mtid;
+    x[6] = c->mpos;
+    x[7] = c->isize;
+    ok = (bgzf_flush_try(fp, 4 + block_len) >= 0);
+    if (fp->is_be) {
+        for (i = 0; i < 8; ++i) ed_swap_4p(x + i);
+        y = block_len;
+        if (ok) ok = (bgzf_write(fp, ed_swap_4p(&y), 4) >= 0);
+        swap_data(c, b->l_data, b->data, 1);
+    } else {
+        if (ok) ok = (bgzf_write(fp, &block_len, 4) >= 0);
+    }
+    if (ok) ok = (bgzf_write(fp, x, 32) >= 0);
+    if (ok) ok = (bgzf_write(fp, b->data, b->l_data) >= 0);
+    if (fp->is_be) swap_data(c, b->l_data, b->data, 0);
+    return ok? 4 + block_len : -1;
+}
+
+/********************
+ *** BAM indexing ***
+ ********************/
+
+static hts_idx_t *bam_index(BGZF *fp, int min_shift)
+{
+    int n_lvls, i, fmt, ret;
+    bam1_t *b;
+    hts_idx_t *idx;
+    bam_hdr_t *h;
+    h = bam_hdr_read(fp);
+    if (h == NULL) return NULL;
+    if (min_shift > 0) {
+        int64_t max_len = 0, s;
+        for (i = 0; i < h->n_targets; ++i)
+            if (max_len < h->target_len[i]) max_len = h->target_len[i];
+        max_len += 256;
+        for (n_lvls = 0, s = 1<<min_shift; max_len > s; ++n_lvls, s <<= 3);
+        fmt = HTS_FMT_CSI;
+    } else min_shift = 14, n_lvls = 5, fmt = HTS_FMT_BAI;
+    idx = hts_idx_init(h->n_targets, fmt, bgzf_tell(fp), min_shift, n_lvls);
+    bam_hdr_destroy(h);
+    b = bam_init1();
+    while ((ret = bam_read1(fp, b)) >= 0) {
+        ret = hts_idx_push(idx, b->core.tid, b->core.pos, bam_endpos(b), bgzf_tell(fp), !(b->core.flag&BAM_FUNMAP));
+        if (ret < 0) goto err; // unsorted
+    }
+    if (ret < -1) goto err; // corrupted BAM file
+
+    hts_idx_finish(idx, bgzf_tell(fp));
+    bam_destroy1(b);
+    return idx;
+
+err:
+    bam_destroy1(b);
+    hts_idx_destroy(idx);
+    return NULL;
+}
+
+int sam_index_build2(const char *fn, const char *fnidx, int min_shift)
+{
+    hts_idx_t *idx;
+    htsFile *fp;
+    int ret = 0;
+
+    if ((fp = hts_open(fn, "r")) == 0) return -2;
+    switch (fp->format.format) {
+    case cram:
+        ret = cram_index_build(fp->fp.cram, fn, fnidx);
+        break;
+
+    case bam:
+        idx = bam_index(fp->fp.bgzf, min_shift);
+        if (idx) {
+            ret = hts_idx_save_as(idx, fn, fnidx, (min_shift > 0)? HTS_FMT_CSI : HTS_FMT_BAI);
+            hts_idx_destroy(idx);
+        }
+        else ret = -1;
+        break;
+
+    default:
+        ret = -3;
+        break;
+    }
+    hts_close(fp);
+
+    return ret;
+}
+
+int sam_index_build(const char *fn, int min_shift)
+{
+    return sam_index_build2(fn, NULL, min_shift);
+}
+
+// Provide bam_index_build() symbol for binary compability with earlier HTSlib
+#undef bam_index_build
+int bam_index_build(const char *fn, int min_shift)
+{
+    return sam_index_build2(fn, NULL, min_shift);
+}
+
+static int bam_readrec(BGZF *fp, void *ignored, void *bv, int *tid, int *beg, int *end)
+{
+    bam1_t *b = bv;
+    int ret;
+    if ((ret = bam_read1(fp, b)) >= 0) {
+        *tid = b->core.tid;
+        *beg = b->core.pos;
+        *end = bam_endpos(b);
+    }
+    return ret;
+}
+
+// This is used only with read_rest=1 iterators, so need not set tid/beg/end.
+static int cram_readrec(BGZF *ignored, void *fpv, void *bv, int *tid, int *beg, int *end)
+{
+    htsFile *fp = fpv;
+    bam1_t *b = bv;
+    return cram_get_bam_seq(fp->fp.cram, &b);
+}
+
+// This is used only with read_rest=1 iterators, so need not set tid/beg/end.
+static int sam_bam_cram_readrec(BGZF *bgzfp, void *fpv, void *bv, int *tid, int *beg, int *end)
+{
+    htsFile *fp = fpv;
+    bam1_t *b = bv;
+    switch (fp->format.format) {
+    case bam:   return bam_read1(bgzfp, b);
+    case cram:  return cram_get_bam_seq(fp->fp.cram, &b);
+    default:
+        // TODO Need headers available to implement this for SAM files
+        fprintf(stderr, "[sam_bam_cram_readrec] Not implemented for SAM files -- Exiting\n");
+        abort();
+    }
+}
+
+hts_idx_t *sam_index_load2(htsFile *fp, const char *fn, const char *fnidx)
+{
+    switch (fp->format.format) {
+    case bam:
+        return fnidx? hts_idx_load2(fn, fnidx) : hts_idx_load(fn, HTS_FMT_BAI);
+
+    case cram: {
+        if (cram_index_load(fp->fp.cram, fn, fnidx) < 0) return NULL;
+        // Cons up a fake "index" just pointing at the associated cram_fd:
+        hts_cram_idx_t *idx = malloc(sizeof (hts_cram_idx_t));
+        if (idx == NULL) return NULL;
+        idx->fmt = HTS_FMT_CRAI;
+        idx->cram = fp->fp.cram;
+        return (hts_idx_t *) idx;
+        }
+
+    default:
+        return NULL; // TODO Would use tbx_index_load if it returned hts_idx_t
+    }
+}
+
+hts_idx_t *sam_index_load(htsFile *fp, const char *fn)
+{
+    return sam_index_load2(fp, fn, NULL);
+}
+
+static hts_itr_t *cram_itr_query(const hts_idx_t *idx, int tid, int beg, int end, hts_readrec_func *readrec)
+{
+    const hts_cram_idx_t *cidx = (const hts_cram_idx_t *) idx;
+    hts_itr_t *iter = (hts_itr_t *) calloc(1, sizeof(hts_itr_t));
+    if (iter == NULL) return NULL;
+
+    // Cons up a dummy iterator for which hts_itr_next() will simply invoke
+    // the readrec function:
+    iter->read_rest = 1;
+    iter->off = NULL;
+    iter->bins.a = NULL;
+    iter->readrec = readrec;
+
+    if (tid >= 0 || tid == HTS_IDX_NOCOOR) {
+        cram_range r = { tid == HTS_IDX_NOCOOR ? -1 : tid, beg+1, end };
+        int ret = cram_set_option(cidx->cram, CRAM_OPT_RANGE, &r);
+
+        iter->curr_off = 0;
+        // The following fields are not required by hts_itr_next(), but are
+        // filled in in case user code wants to look at them.
+        iter->tid = tid;
+        iter->beg = beg;
+        iter->end = end;
+
+        switch (ret) {
+        case 0:
+            break;
+
+        case -2:
+            // No data vs this ref, so mark iterator as completed.
+            // Same as HTS_IDX_NONE.
+            iter->finished = 1;
+            break;
+
+        default:
+            free(iter);
+            return NULL;
+        }
+    }
+    else switch (tid) {
+    case HTS_IDX_REST:
+        iter->curr_off = 0;
+        break;
+    case HTS_IDX_NONE:
+        iter->curr_off = 0;
+        iter->finished = 1;
+        break;
+    default:
+        fprintf(stderr, "[cram_itr_query] tid=%d not implemented for CRAM files -- Exiting\n", tid);
+        abort();
+        break;
+    }
+
+    return iter;
+}
+
+hts_itr_t *sam_itr_queryi(const hts_idx_t *idx, int tid, int beg, int end)
+{
+    const hts_cram_idx_t *cidx = (const hts_cram_idx_t *) idx;
+    if (idx == NULL)
+        return hts_itr_query(NULL, tid, beg, end, sam_bam_cram_readrec);
+    else if (cidx->fmt == HTS_FMT_CRAI)
+        return cram_itr_query(idx, tid, beg, end, cram_readrec);
+    else
+        return hts_itr_query(idx, tid, beg, end, bam_readrec);
+}
+
+static int cram_name2id(void *fdv, const char *ref)
+{
+    cram_fd *fd = (cram_fd *) fdv;
+    return sam_hdr_name2ref(fd->header, ref);
+}
+
+hts_itr_t *sam_itr_querys(const hts_idx_t *idx, bam_hdr_t *hdr, const char *region)
+{
+    const hts_cram_idx_t *cidx = (const hts_cram_idx_t *) idx;
+    if (cidx->fmt == HTS_FMT_CRAI)
+        return hts_itr_querys(idx, region, cram_name2id, cidx->cram, cram_itr_query, cram_readrec);
+    else
+        return hts_itr_querys(idx, region, (hts_name2id_f)(bam_name2id), hdr, hts_itr_query, bam_readrec);
+}
+
+/**********************
+ *** SAM header I/O ***
+ **********************/
+
+#include "htslib/kseq.h"
+#include "htslib/kstring.h"
+
+bam_hdr_t *sam_hdr_parse(int l_text, const char *text)
+{
+    const char *q, *r, *p;
+    khash_t(s2i) *d;
+    d = kh_init(s2i);
+    for (p = text; *p; ++p) {
+        if (strncmp(p, "@SQ\t", 4) == 0) {
+            char *sn = 0;
+            int ln = -1;
+            for (q = p + 4;; ++q) {
+                if (strncmp(q, "SN:", 3) == 0) {
+                    q += 3;
+                    for (r = q; *r != '\t' && *r != '\n' && *r != '\0'; ++r);
+                    sn = (char*)calloc(r - q + 1, 1);
+                    strncpy(sn, q, r - q);
+                    q = r;
+                } else if (strncmp(q, "LN:", 3) == 0)
+                    ln = strtol(q + 3, (char**)&q, 10);
+                while (*q != '\t' && *q != '\n' && *q != '\0') ++q;
+                if (*q == '\0' || *q == '\n') break;
+            }
+            p = q;
+            if (sn && ln >= 0) {
+                khint_t k;
+                int absent;
+                k = kh_put(s2i, d, sn, &absent);
+                if (!absent) {
+                    if (hts_verbose >= 2)
+                        fprintf(stderr, "[W::%s] duplicated sequence '%s'\n", __func__, sn);
+                    free(sn);
+                } else kh_val(d, k) = (int64_t)(kh_size(d) - 1)<<32 | ln;
+            }
+        }
+        while (*p != '\0' && *p != '\n') ++p;
+    }
+    return hdr_from_dict(d);
+}
+
+bam_hdr_t *sam_hdr_read(htsFile *fp)
+{
+    switch (fp->format.format) {
+    case bam:
+        return bam_hdr_read(fp->fp.bgzf);
+
+    case cram:
+        return cram_header_to_bam(fp->fp.cram->header);
+
+    case sam: {
+        kstring_t str;
+        bam_hdr_t *h;
+        int has_SQ = 0;
+        str.l = str.m = 0; str.s = 0;
+        while (hts_getline(fp, KS_SEP_LINE, &fp->line) >= 0) {
+            if (fp->line.s[0] != '@') break;
+            if (fp->line.l > 3 && strncmp(fp->line.s,"@SQ",3) == 0) has_SQ = 1;
+            kputsn(fp->line.s, fp->line.l, &str);
+            kputc('\n', &str);
+        }
+        if (! has_SQ && fp->fn_aux) {
+            char line[2048];
+            FILE *f = fopen(fp->fn_aux, "r");
+            if (f == NULL) return NULL;
+            while (fgets(line, sizeof line, f)) {
+                const char *name = strtok(line, "\t");
+                const char *length = strtok(NULL, "\t");
+                ksprintf(&str, "@SQ\tSN:%s\tLN:%s\n", name, length);
+            }
+            fclose(f);
+        }
+        if (str.l == 0) kputsn("", 0, &str);
+        h = sam_hdr_parse(str.l, str.s);
+        h->l_text = str.l; h->text = str.s;
+        return h;
+        }
+
+    default:
+        abort();
+    }
+}
+
+int sam_hdr_write(htsFile *fp, const bam_hdr_t *h)
+{
+    switch (fp->format.format) {
+    case binary_format:
+        fp->format.category = sequence_data;
+        fp->format.format = bam;
+        /* fall-through */
+    case bam:
+        if (bam_hdr_write(fp->fp.bgzf, h) < 0) return -1;
+        break;
+
+    case cram: {
+        cram_fd *fd = fp->fp.cram;
+        SAM_hdr *hdr = bam_header_to_cram((bam_hdr_t *)h);
+        if (! hdr) return -1;
+        if (cram_set_header(fd, hdr) < 0) return -1;
+        if (fp->fn_aux)
+            cram_load_reference(fd, fp->fn_aux);
+        if (cram_write_SAM_hdr(fd, fd->header) < 0) return -1;
+        }
+        break;
+
+    case text_format:
+        fp->format.category = sequence_data;
+        fp->format.format = sam;
+        /* fall-through */
+    case sam: {
+        char *p;
+        hputs(h->text, fp->fp.hfile);
+        p = strstr(h->text, "@SQ\t"); // FIXME: we need a loop to make sure "@SQ\t" does not match something unwanted!!!
+        if (p == 0) {
+            int i;
+            for (i = 0; i < h->n_targets; ++i) {
+                fp->line.l = 0;
+                kputsn("@SQ\tSN:", 7, &fp->line); kputs(h->target_name[i], &fp->line);
+                kputsn("\tLN:", 4, &fp->line); kputw(h->target_len[i], &fp->line); kputc('\n', &fp->line);
+                if ( hwrite(fp->fp.hfile, fp->line.s, fp->line.l) != fp->line.l ) return -1;
+            }
+        }
+        if ( hflush(fp->fp.hfile) != 0 ) return -1;
+        }
+        break;
+
+    default:
+        abort();
+    }
+    return 0;
+}
+
+/**********************
+ *** SAM record I/O ***
+ **********************/
+
+int sam_parse1(kstring_t *s, bam_hdr_t *h, bam1_t *b)
+{
+#define _read_token(_p) (_p); for (; *(_p) && *(_p) != '\t'; ++(_p)); if (*(_p) != '\t') goto err_ret; *(_p)++ = 0
+#define _read_token_aux(_p) (_p); for (; *(_p) && *(_p) != '\t'; ++(_p)); *(_p)++ = 0 // this is different in that it does not test *(_p)=='\t'
+#define _get_mem(type_t, _x, _s, _l) ks_resize((_s), (_s)->l + (_l)); *(_x) = (type_t*)((_s)->s + (_s)->l); (_s)->l += (_l)
+#define _parse_err(cond, msg) do { if ((cond) && hts_verbose >= 1) { fprintf(stderr, "[E::%s] " msg "\n", __func__); goto err_ret; } } while (0)
+#define _parse_warn(cond, msg) if ((cond) && hts_verbose >= 2) fprintf(stderr, "[W::%s] " msg "\n", __func__)
+
+    uint8_t *t;
+    char *p = s->s, *q;
+    int i;
+    kstring_t str;
+    bam1_core_t *c = &b->core;
+
+    str.l = b->l_data = 0;
+    str.s = (char*)b->data; str.m = b->m_data;
+    memset(c, 0, 32);
+    if (h->cigar_tab == 0) {
+        h->cigar_tab = (int8_t*) malloc(128);
+        for (i = 0; i < 128; ++i)
+            h->cigar_tab[i] = -1;
+        for (i = 0; BAM_CIGAR_STR[i]; ++i)
+            h->cigar_tab[(int)BAM_CIGAR_STR[i]] = i;
+    }
+    // qname
+    q = _read_token(p);
+    _parse_warn(p - q <= 1, "empty query name");
+    _parse_err(p - q > 255, "query name too long");
+    kputsn_(q, p - q, &str);
+    c->l_qname = p - q;
+    // flag
+    c->flag = strtol(p, &p, 0);
+    if (*p++ != '\t') goto err_ret; // malformated flag
+    // chr
+    q = _read_token(p);
+    if (strcmp(q, "*")) {
+        _parse_err(h->n_targets == 0, "missing SAM header");
+        c->tid = bam_name2id(h, q);
+        _parse_warn(c->tid < 0, "urecognized reference name; treated as unmapped");
+    } else c->tid = -1;
+    // pos
+    c->pos = strtol(p, &p, 10) - 1;
+    if (*p++ != '\t') goto err_ret;
+    if (c->pos < 0 && c->tid >= 0) {
+        _parse_warn(1, "mapped query cannot have zero coordinate; treated as unmapped");
+        c->tid = -1;
+    }
+    if (c->tid < 0) c->flag |= BAM_FUNMAP;
+    // mapq
+    c->qual = strtol(p, &p, 10);
+    if (*p++ != '\t') goto err_ret;
+    // cigar
+    if (*p != '*') {
+        uint32_t *cigar;
+        size_t n_cigar = 0;
+        for (q = p; *p && *p != '\t'; ++p)
+            if (!isdigit(*p)) ++n_cigar;
+        if (*p++ != '\t') goto err_ret;
+        _parse_err(n_cigar == 0, "no CIGAR operations");
+        _parse_err(n_cigar >= 65536, "too many CIGAR operations");
+        c->n_cigar = n_cigar;
+        _get_mem(uint32_t, &cigar, &str, c->n_cigar * sizeof(uint32_t));
+        for (i = 0; i < c->n_cigar; ++i, ++q) {
+            int op;
+            cigar[i] = strtol(q, &q, 10)<<BAM_CIGAR_SHIFT;
+            op = (uint8_t)*q >= 128? -1 : h->cigar_tab[(int)*q];
+            _parse_err(op < 0, "unrecognized CIGAR operator");
+            cigar[i] |= op;
+        }
+        // can't use bam_endpos() directly as some fields not yet set up
+        i = (!(c->flag&BAM_FUNMAP))? bam_cigar2rlen(c->n_cigar, cigar) : 1;
+    } else {
+        _parse_warn(!(c->flag&BAM_FUNMAP), "mapped query must have a CIGAR; treated as unmapped");
+        c->flag |= BAM_FUNMAP;
+        q = _read_token(p);
+        i = 1;
+    }
+    c->bin = hts_reg2bin(c->pos, c->pos + i, 14, 5);
+    // mate chr
+    q = _read_token(p);
+    if (strcmp(q, "=") == 0) {
+        c->mtid = c->tid;
+    } else if (strcmp(q, "*") == 0) {
+        c->mtid = -1;
+    } else {
+        c->mtid = bam_name2id(h, q);
+        _parse_warn(c->mtid < 0, "urecognized mate reference name; treated as unmapped");
+    }
+    // mpos
+    c->mpos = strtol(p, &p, 10) - 1;
+    if (*p++ != '\t') goto err_ret;
+    if (c->mpos < 0 && c->mtid >= 0) {
+        _parse_warn(1, "mapped mate cannot have zero coordinate; treated as unmapped");
+        c->mtid = -1;
+    }
+    // tlen
+    c->isize = strtol(p, &p, 10);
+    if (*p++ != '\t') goto err_ret;
+    // seq
+    q = _read_token(p);
+    if (strcmp(q, "*")) {
+        c->l_qseq = p - q - 1;
+        i = bam_cigar2qlen(c->n_cigar, (uint32_t*)(str.s + c->l_qname));
+        _parse_err(c->n_cigar && i != c->l_qseq, "CIGAR and query sequence are of different length");
+        i = (c->l_qseq + 1) >> 1;
+        _get_mem(uint8_t, &t, &str, i);
+        memset(t, 0, i);
+        for (i = 0; i < c->l_qseq; ++i)
+            t[i>>1] |= seq_nt16_table[(int)q[i]] << ((~i&1)<<2);
+    } else c->l_qseq = 0;
+    // qual
+    q = _read_token_aux(p);
+    _get_mem(uint8_t, &t, &str, c->l_qseq);
+    if (strcmp(q, "*")) {
+        _parse_err(p - q - 1 != c->l_qseq, "SEQ and QUAL are of different length");
+        for (i = 0; i < c->l_qseq; ++i) t[i] = q[i] - 33;
+    } else memset(t, 0xff, c->l_qseq);
+    // aux
+    // Note that (like the bam1_core_t fields) this aux data in b->data is
+    // stored in host endianness; so there is no byte swapping needed here.
+    while (p < s->s + s->l) {
+        uint8_t type;
+        q = _read_token_aux(p); // FIXME: can be accelerated for long 'B' arrays
+        _parse_err(p - q - 1 < 6, "incomplete aux field");
+        kputsn_(q, 2, &str);
+        q += 3; type = *q++; ++q; // q points to value
+        if (type == 'A' || type == 'a' || type == 'c' || type == 'C') {
+            kputc_('A', &str);
+            kputc_(*q, &str);
+        } else if (type == 'i' || type == 'I') {
+            if (*q == '-') {
+                long x = strtol(q, &q, 10);
+                if (x >= INT8_MIN) {
+                    kputc_('c', &str); kputc_(x, &str);
+                } else if (x >= INT16_MIN) {
+                    int16_t y = x;
+                    kputc_('s', &str); kputsn_((char*)&y, 2, &str);
+                } else {
+                    int32_t y = x;
+                    kputc_('i', &str); kputsn_(&y, 4, &str);
+                }
+            } else {
+                unsigned long x = strtoul(q, &q, 10);
+                if (x <= UINT8_MAX) {
+                    kputc_('C', &str); kputc_(x, &str);
+                } else if (x <= UINT16_MAX) {
+                    uint16_t y = x;
+                    kputc_('S', &str); kputsn_(&y, 2, &str);
+                } else {
+                    uint32_t y = x;
+                    kputc_('I', &str); kputsn_(&y, 4, &str);
+                }
+            }
+        } else if (type == 'f') {
+            float x;
+            x = strtod(q, &q);
+            kputc_('f', &str); kputsn_(&x, 4, &str);
+        } else if (type == 'd') {
+            double x;
+            x = strtod(q, &q);
+            kputc_('d', &str); kputsn_(&x, 8, &str);
+        } else if (type == 'Z' || type == 'H') {
+            kputc_(type, &str);kputsn_(q, p - q, &str); // note that this include the trailing NULL
+        } else if (type == 'B') {
+            int32_t n;
+            char *r;
+            _parse_err(p - q - 1 < 3, "incomplete B-typed aux field");
+            type = *q++; // q points to the first ',' following the typing byte
+            for (r = q, n = 0; *r; ++r)
+                if (*r == ',') ++n;
+            kputc_('B', &str); kputc_(type, &str); kputsn_(&n, 4, &str);
+            // FIXME: to evaluate which is faster: a) aligned array and then memmove(); b) unaligned array; c) kputsn_()
+            if (type == 'c')      while (q + 1 < p) { int8_t   x = strtol(q + 1, &q, 0); kputc_(x, &str); }
+            else if (type == 'C') while (q + 1 < p) { uint8_t  x = strtoul(q + 1, &q, 0); kputc_(x, &str); }
+            else if (type == 's') while (q + 1 < p) { int16_t  x = strtol(q + 1, &q, 0); kputsn_(&x, 2, &str); }
+            else if (type == 'S') while (q + 1 < p) { uint16_t x = strtoul(q + 1, &q, 0); kputsn_(&x, 2, &str); }
+            else if (type == 'i') while (q + 1 < p) { int32_t  x = strtol(q + 1, &q, 0); kputsn_(&x, 4, &str); }
+            else if (type == 'I') while (q + 1 < p) { uint32_t x = strtoul(q + 1, &q, 0); kputsn_(&x, 4, &str); }
+            else if (type == 'f') while (q + 1 < p) { float    x = strtod(q + 1, &q);    kputsn_(&x, 4, &str); }
+            else _parse_err(1, "unrecognized type");
+        } else _parse_err(1, "unrecognized type");
+    }
+    b->data = (uint8_t*)str.s; b->l_data = str.l; b->m_data = str.m;
+    return 0;
+
+#undef _parse_warn
+#undef _parse_err
+#undef _get_mem
+#undef _read_token_aux
+#undef _read_token
+err_ret:
+    b->data = (uint8_t*)str.s; b->l_data = str.l; b->m_data = str.m;
+    return -2;
+}
+
+int sam_read1(htsFile *fp, bam_hdr_t *h, bam1_t *b)
+{
+    switch (fp->format.format) {
+    case bam: {
+        int r = bam_read1(fp->fp.bgzf, b);
+        if (r >= 0) {
+            if (b->core.tid  >= h->n_targets || b->core.tid  < -1 ||
+                b->core.mtid >= h->n_targets || b->core.mtid < -1)
+                return -3;
+        }
+        return r;
+        }
+
+    case cram: {
+        int ret = cram_get_bam_seq(fp->fp.cram, &b);
+        return ret >= 0
+            ? ret
+            : (cram_eof(fp->fp.cram) ? -1 : -2);
+    }
+
+    case sam: {
+        int ret;
+err_recover:
+        if (fp->line.l == 0) {
+            ret = hts_getline(fp, KS_SEP_LINE, &fp->line);
+            if (ret < 0) return -1;
+        }
+        ret = sam_parse1(&fp->line, h, b);
+        fp->line.l = 0;
+        if (ret < 0) {
+            if (hts_verbose >= 1)
+                fprintf(stderr, "[W::%s] parse error at line %lld\n", __func__, (long long)fp->lineno);
+            if (h->ignore_sam_err) goto err_recover;
+        }
+        return ret;
+        }
+
+    default:
+        abort();
+    }
+}
+
+int sam_format1(const bam_hdr_t *h, const bam1_t *b, kstring_t *str)
+{
+    int i;
+    uint8_t *s;
+    const bam1_core_t *c = &b->core;
+
+    str->l = 0;
+    kputsn(bam_get_qname(b), c->l_qname-1, str); kputc('\t', str); // query name
+    kputw(c->flag, str); kputc('\t', str); // flag
+    if (c->tid >= 0) { // chr
+        kputs(h->target_name[c->tid] , str);
+        kputc('\t', str);
+    } else kputsn("*\t", 2, str);
+    kputw(c->pos + 1, str); kputc('\t', str); // pos
+    kputw(c->qual, str); kputc('\t', str); // qual
+    if (c->n_cigar) { // cigar
+        uint32_t *cigar = bam_get_cigar(b);
+        for (i = 0; i < c->n_cigar; ++i) {
+            kputw(bam_cigar_oplen(cigar[i]), str);
+            kputc(bam_cigar_opchr(cigar[i]), str);
+        }
+    } else kputc('*', str);
+    kputc('\t', str);
+    if (c->mtid < 0) kputsn("*\t", 2, str); // mate chr
+    else if (c->mtid == c->tid) kputsn("=\t", 2, str);
+    else {
+        kputs(h->target_name[c->mtid], str);
+        kputc('\t', str);
+    }
+    kputw(c->mpos + 1, str); kputc('\t', str); // mate pos
+    kputw(c->isize, str); kputc('\t', str); // template len
+    if (c->l_qseq) { // seq and qual
+        uint8_t *s = bam_get_seq(b);
+        for (i = 0; i < c->l_qseq; ++i) kputc("=ACMGRSVTWYHKDBN"[bam_seqi(s, i)], str);
+        kputc('\t', str);
+        s = bam_get_qual(b);
+        if (s[0] == 0xff) kputc('*', str);
+        else for (i = 0; i < c->l_qseq; ++i) kputc(s[i] + 33, str);
+    } else kputsn("*\t*", 3, str);
+
+    // FIXME change "s+N <= b->data+b->l_data" to "b->data+b->l_data - s >= N"
+    // (or equivalent) everywhere to avoid looking past the end of the array
+    s = bam_get_aux(b); // aux
+    while (s+4 <= b->data + b->l_data) {
+        uint8_t type, key[2];
+        key[0] = s[0]; key[1] = s[1];
+        s += 2; type = *s++;
+        kputc('\t', str); kputsn((char*)key, 2, str); kputc(':', str);
+        if (type == 'A') {
+            kputsn("A:", 2, str);
+            kputc(*s, str);
+            ++s;
+        } else if (type == 'C') {
+            kputsn("i:", 2, str);
+            kputw(*s, str);
+            ++s;
+        } else if (type == 'c') {
+            kputsn("i:", 2, str);
+            kputw(*(int8_t*)s, str);
+            ++s;
+        } else if (type == 'S') {
+            if (s+2 <= b->data + b->l_data) {
+                kputsn("i:", 2, str);
+                kputw(*(uint16_t*)s, str);
+                s += 2;
+            } else return -1;
+        } else if (type == 's') {
+            if (s+2 <= b->data + b->l_data) {
+                kputsn("i:", 2, str);
+                kputw(*(int16_t*)s, str);
+                s += 2;
+            } else return -1;
+        } else if (type == 'I') {
+            if (s+4 <= b->data + b->l_data) {
+                kputsn("i:", 2, str);
+                kputuw(*(uint32_t*)s, str);
+                s += 4;
+            } else return -1;
+        } else if (type == 'i') {
+            if (s+4 <= b->data + b->l_data) {
+                kputsn("i:", 2, str);
+                kputw(*(int32_t*)s, str);
+                s += 4;
+            } else return -1;
+        } else if (type == 'f') {
+            if (s+4 <= b->data + b->l_data) {
+                ksprintf(str, "f:%g", *(float*)s);
+                s += 4;
+            } else return -1;
+
+        } else if (type == 'd') {
+            if (s+8 <= b->data + b->l_data) {
+                ksprintf(str, "d:%g", *(double*)s);
+                s += 8;
+            } else return -1;
+        } else if (type == 'Z' || type == 'H') {
+            kputc(type, str); kputc(':', str);
+            while (s < b->data + b->l_data && *s) kputc(*s++, str);
+            if (s >= b->data + b->l_data)
+                return -1;
+            ++s;
+        } else if (type == 'B') {
+            uint8_t sub_type = *(s++);
+            int sub_type_size = aux_type2size(sub_type);
+            uint32_t n;
+            if (sub_type_size == 0 || b->data + b->l_data - s < 4)
+                return -1;
+            memcpy(&n, s, 4);
+            s += 4; // now points to the start of the array
+            if ((b->data + b->l_data - s) / sub_type_size < n)
+                return -1;
+            kputsn("B:", 2, str); kputc(sub_type, str); // write the typing
+            for (i = 0; i < n; ++i) { // FIXME: for better performance, put the loop after "if"
+                kputc(',', str);
+                if ('c' == sub_type)      { kputw(*(int8_t*)s, str); ++s; }
+                else if ('C' == sub_type) { kputw(*(uint8_t*)s, str); ++s; }
+                else if ('s' == sub_type) { kputw(*(int16_t*)s, str); s += 2; }
+                else if ('S' == sub_type) { kputw(*(uint16_t*)s, str); s += 2; }
+                else if ('i' == sub_type) { kputw(*(int32_t*)s, str); s += 4; }
+                else if ('I' == sub_type) { kputuw(*(uint32_t*)s, str); s += 4; }
+                else if ('f' == sub_type) { ksprintf(str, "%g", *(float*)s); s += 4; }
+                else return -1;
+            }
+        }
+    }
+    return str->l;
+}
+
+int sam_write1(htsFile *fp, const bam_hdr_t *h, const bam1_t *b)
+{
+    switch (fp->format.format) {
+    case binary_format:
+        fp->format.category = sequence_data;
+        fp->format.format = bam;
+        /* fall-through */
+    case bam:
+        return bam_write1(fp->fp.bgzf, b);
+
+    case cram:
+        return cram_put_bam_seq(fp->fp.cram, (bam1_t *)b);
+
+    case text_format:
+        fp->format.category = sequence_data;
+        fp->format.format = sam;
+        /* fall-through */
+    case sam:
+        if (sam_format1(h, b, &fp->line) < 0) return -1;
+        kputc('\n', &fp->line);
+        if ( hwrite(fp->fp.hfile, fp->line.s, fp->line.l) != fp->line.l ) return -1;
+        return fp->line.l;
+
+    default:
+        abort();
+    }
+}
+
+/************************
+ *** Auxiliary fields ***
+ ************************/
+
+void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *data)
+{
+    int ori_len = b->l_data;
+    b->l_data += 3 + len;
+    if (b->m_data < b->l_data) {
+        b->m_data = b->l_data;
+        kroundup32(b->m_data);
+        b->data = (uint8_t*)realloc(b->data, b->m_data);
+    }
+    b->data[ori_len] = tag[0]; b->data[ori_len + 1] = tag[1];
+    b->data[ori_len + 2] = type;
+    memcpy(b->data + ori_len + 3, data, len);
+}
+
+static inline uint8_t *skip_aux(uint8_t *s)
+{
+    int size = aux_type2size(*s); ++s; // skip type
+    uint32_t n;
+    switch (size) {
+    case 'Z':
+    case 'H':
+        while (*s) ++s;
+        return s + 1;
+    case 'B':
+        size = aux_type2size(*s); ++s;
+        memcpy(&n, s, 4); s += 4;
+        return s + size * n;
+    case 0:
+        abort();
+        break;
+    default:
+        return s + size;
+    }
+}
+
+uint8_t *bam_aux_get(const bam1_t *b, const char tag[2])
+{
+    uint8_t *s;
+    int y = tag[0]<<8 | tag[1];
+    s = bam_get_aux(b);
+    while (s < b->data + b->l_data) {
+        int x = (int)s[0]<<8 | s[1];
+        s += 2;
+        if (x == y) return s;
+        s = skip_aux(s);
+    }
+    return 0;
+}
+// s MUST BE returned by bam_aux_get()
+int bam_aux_del(bam1_t *b, uint8_t *s)
+{
+    uint8_t *p, *aux;
+    int l_aux = bam_get_l_aux(b);
+    aux = bam_get_aux(b);
+    p = s - 2;
+    s = skip_aux(s);
+    memmove(p, s, l_aux - (s - aux));
+    b->l_data -= s - p;
+    return 0;
+}
+
+int32_t bam_aux2i(const uint8_t *s)
+{
+    int type;
+    type = *s++;
+    if (type == 'c') return (int32_t)*(int8_t*)s;
+    else if (type == 'C') return (int32_t)*(uint8_t*)s;
+    else if (type == 's') return (int32_t)*(int16_t*)s;
+    else if (type == 'S') return (int32_t)*(uint16_t*)s;
+    else if (type == 'i' || type == 'I') return *(int32_t*)s;
+    else return 0;
+}
+
+double bam_aux2f(const uint8_t *s)
+{
+    int type;
+    type = *s++;
+    if (type == 'd') return *(double*)s;
+    else if (type == 'f') return *(float*)s;
+    else return 0.0;
+}
+
+char bam_aux2A(const uint8_t *s)
+{
+    int type;
+    type = *s++;
+    if (type == 'A') return *(char*)s;
+    else return 0;
+}
+
+char *bam_aux2Z(const uint8_t *s)
+{
+    int type;
+    type = *s++;
+    if (type == 'Z' || type == 'H') return (char*)s;
+    else return 0;
+}
+
+int sam_open_mode(char *mode, const char *fn, const char *format)
+{
+    // TODO Parse "bam5" etc for compression level
+    if (format == NULL) {
+        // Try to pick a format based on the filename extension
+        const char *ext = fn? strrchr(fn, '.') : NULL;
+        if (ext == NULL || strchr(ext, '/')) return -1;
+        return sam_open_mode(mode, fn, ext+1);
+    }
+    else if (strcmp(format, "bam") == 0) strcpy(mode, "b");
+    else if (strcmp(format, "cram") == 0) strcpy(mode, "c");
+    else if (strcmp(format, "sam") == 0) strcpy(mode, "");
+    else return -1;
+
+    return 0;
+}
+
+// A version of sam_open_mode that can handle ,key=value options.
+// The format string is allocated and returned, to be freed by the caller.
+// Prefix should be "r" or "w",
+char *sam_open_mode_opts(const char *fn,
+                         const char *mode,
+                         const char *format)
+{
+    char *mode_opts = malloc((format ? strlen(format) : 1) +
+                             (mode   ? strlen(mode)   : 1) + 12);
+    char *opts, *cp;
+    int format_len;
+
+    if (!mode_opts)
+        return NULL;
+
+    strcpy(mode_opts, mode ? mode : "r");
+    cp = mode_opts + strlen(mode_opts);
+
+    if (format == NULL) {
+        // Try to pick a format based on the filename extension
+        const char *ext = fn? strrchr(fn, '.') : NULL;
+        if (ext == NULL || strchr(ext, '/')) {
+            free(mode_opts);
+            return NULL;
+        }
+        return sam_open_mode(cp, fn, ext+1)
+            ? (free(mode_opts), NULL)
+            : mode_opts;
+    }
+
+    if ((opts = strchr(format, ','))) {
+        format_len = opts-format;
+    } else {
+        opts="";
+        format_len = strlen(format);
+    }
+
+    if (strncmp(format, "bam", format_len) == 0) {
+        *cp++ = 'b';
+    } else if (strncmp(format, "cram", format_len) == 0) {
+        *cp++ = 'c';
+    } else if (strncmp(format, "cram2", format_len) == 0) {
+        *cp++ = 'c';
+        strcpy(cp, ",VERSION=2.1");
+        cp += 12;
+    } else if (strncmp(format, "cram3", format_len) == 0) {
+        *cp++ = 'c';
+        strcpy(cp, ",VERSION=3.0");
+        cp += 12;
+    } else if (strncmp(format, "sam", format_len) == 0) {
+        ; // format mode=""
+    } else {
+        free(mode_opts);
+        return NULL;
+    }
+
+    strcpy(cp, opts);
+
+    return mode_opts;
+}
+
+#define STRNCMP(a,b,n) (strncasecmp((a),(b),(n)) || strlen(a)!=(n))
+int bam_str2flag(const char *str)
+{
+    char *end, *beg = (char*) str;
+    long int flag = strtol(str, &end, 0);
+    if ( end!=str ) return flag;    // the conversion was successful
+    flag = 0;
+    while ( *str )
+    {
+        end = beg;
+        while ( *end && *end!=',' ) end++;
+        if ( !STRNCMP("PAIRED",beg,end-beg) ) flag |= BAM_FPAIRED;
+        else if ( !STRNCMP("PROPER_PAIR",beg,end-beg) ) flag |= BAM_FPROPER_PAIR;
+        else if ( !STRNCMP("UNMAP",beg,end-beg) ) flag |= BAM_FUNMAP;
+        else if ( !STRNCMP("MUNMAP",beg,end-beg) ) flag |= BAM_FMUNMAP;
+        else if ( !STRNCMP("REVERSE",beg,end-beg) ) flag |= BAM_FREVERSE;
+        else if ( !STRNCMP("MREVERSE",beg,end-beg) ) flag |= BAM_FMREVERSE;
+        else if ( !STRNCMP("READ1",beg,end-beg) ) flag |= BAM_FREAD1;
+        else if ( !STRNCMP("READ2",beg,end-beg) ) flag |= BAM_FREAD2;
+        else if ( !STRNCMP("SECONDARY",beg,end-beg) ) flag |= BAM_FSECONDARY;
+        else if ( !STRNCMP("QCFAIL",beg,end-beg) ) flag |= BAM_FQCFAIL;
+        else if ( !STRNCMP("DUP",beg,end-beg) ) flag |= BAM_FDUP;
+        else if ( !STRNCMP("SUPPLEMENTARY",beg,end-beg) ) flag |= BAM_FSUPPLEMENTARY;
+        else return -1;
+        if ( !*end ) break;
+        beg = end + 1;
+    }
+    return flag;
+}
+
+char *bam_flag2str(int flag)
+{
+    kstring_t str = {0,0,0};
+    if ( flag&BAM_FPAIRED ) ksprintf(&str,"%s%s", str.l?",":"","PAIRED");
+    if ( flag&BAM_FPROPER_PAIR ) ksprintf(&str,"%s%s", str.l?",":"","PROPER_PAIR");
+    if ( flag&BAM_FUNMAP ) ksprintf(&str,"%s%s", str.l?",":"","UNMAP");
+    if ( flag&BAM_FMUNMAP ) ksprintf(&str,"%s%s", str.l?",":"","MUNMAP");
+    if ( flag&BAM_FREVERSE ) ksprintf(&str,"%s%s", str.l?",":"","REVERSE");
+    if ( flag&BAM_FMREVERSE ) ksprintf(&str,"%s%s", str.l?",":"","MREVERSE");
+    if ( flag&BAM_FREAD1 ) ksprintf(&str,"%s%s", str.l?",":"","READ1");
+    if ( flag&BAM_FREAD2 ) ksprintf(&str,"%s%s", str.l?",":"","READ2");
+    if ( flag&BAM_FSECONDARY ) ksprintf(&str,"%s%s", str.l?",":"","SECONDARY");
+    if ( flag&BAM_FQCFAIL ) ksprintf(&str,"%s%s", str.l?",":"","QCFAIL");
+    if ( flag&BAM_FDUP ) ksprintf(&str,"%s%s", str.l?",":"","DUP");
+    if ( flag&BAM_FSUPPLEMENTARY ) ksprintf(&str,"%s%s", str.l?",":"","SUPPLEMENTARY");
+    if ( str.l == 0 ) kputsn("", 0, &str);
+    return str.s;
+}
+
+
+/**************************
+ *** Pileup and Mpileup ***
+ **************************/
+
+#if !defined(BAM_NO_PILEUP)
+
+#include <assert.h>
+
+/*******************
+ *** Memory pool ***
+ *******************/
+
+typedef struct {
+    int k, x, y, end;
+} cstate_t;
+
+static cstate_t g_cstate_null = { -1, 0, 0, 0 };
+
+typedef struct __linkbuf_t {
+    bam1_t b;
+    int32_t beg, end;
+    cstate_t s;
+    struct __linkbuf_t *next;
+} lbnode_t;
+
+typedef struct {
+    int cnt, n, max;
+    lbnode_t **buf;
+} mempool_t;
+
+static mempool_t *mp_init(void)
+{
+    mempool_t *mp;
+    mp = (mempool_t*)calloc(1, sizeof(mempool_t));
+    return mp;
+}
+static void mp_destroy(mempool_t *mp)
+{
+    int k;
+    for (k = 0; k < mp->n; ++k) {
+        free(mp->buf[k]->b.data);
+        free(mp->buf[k]);
+    }
+    free(mp->buf);
+    free(mp);
+}
+static inline lbnode_t *mp_alloc(mempool_t *mp)
+{
+    ++mp->cnt;
+    if (mp->n == 0) return (lbnode_t*)calloc(1, sizeof(lbnode_t));
+    else return mp->buf[--mp->n];
+}
+static inline void mp_free(mempool_t *mp, lbnode_t *p)
+{
+    --mp->cnt; p->next = 0; // clear lbnode_t::next here
+    if (mp->n == mp->max) {
+        mp->max = mp->max? mp->max<<1 : 256;
+        mp->buf = (lbnode_t**)realloc(mp->buf, sizeof(lbnode_t*) * mp->max);
+    }
+    mp->buf[mp->n++] = p;
+}
+
+/**********************
+ *** CIGAR resolver ***
+ **********************/
+
+/* s->k: the index of the CIGAR operator that has just been processed.
+   s->x: the reference coordinate of the start of s->k
+   s->y: the query coordiante of the start of s->k
+ */
+static inline int resolve_cigar2(bam_pileup1_t *p, int32_t pos, cstate_t *s)
+{
+#define _cop(c) ((c)&BAM_CIGAR_MASK)
+#define _cln(c) ((c)>>BAM_CIGAR_SHIFT)
+
+    bam1_t *b = p->b;
+    bam1_core_t *c = &b->core;
+    uint32_t *cigar = bam_get_cigar(b);
+    int k;
+    // determine the current CIGAR operation
+//  fprintf(stderr, "%s\tpos=%d\tend=%d\t(%d,%d,%d)\n", bam_get_qname(b), pos, s->end, s->k, s->x, s->y);
+    if (s->k == -1) { // never processed
+        if (c->n_cigar == 1) { // just one operation, save a loop
+          if (_cop(cigar[0]) == BAM_CMATCH || _cop(cigar[0]) == BAM_CEQUAL || _cop(cigar[0]) == BAM_CDIFF) s->k = 0, s->x = c->pos, s->y = 0;
+        } else { // find the first match or deletion
+            for (k = 0, s->x = c->pos, s->y = 0; k < c->n_cigar; ++k) {
+                int op = _cop(cigar[k]);
+                int l = _cln(cigar[k]);
+                if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CEQUAL || op == BAM_CDIFF) break;
+                else if (op == BAM_CREF_SKIP) s->x += l;
+                else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) s->y += l;
+            }
+            assert(k < c->n_cigar);
+            s->k = k;
+        }
+    } else { // the read has been processed before
+        int op, l = _cln(cigar[s->k]);
+        if (pos - s->x >= l) { // jump to the next operation
+            assert(s->k < c->n_cigar); // otherwise a bug: this function should not be called in this case
+            op = _cop(cigar[s->k+1]);
+            if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP || op == BAM_CEQUAL || op == BAM_CDIFF) { // jump to the next without a loop
+              if (_cop(cigar[s->k]) == BAM_CMATCH|| _cop(cigar[s->k]) == BAM_CEQUAL || _cop(cigar[s->k]) == BAM_CDIFF) s->y += l;
+                s->x += l;
+                ++s->k;
+            } else { // find the next M/D/N/=/X
+              if (_cop(cigar[s->k]) == BAM_CMATCH|| _cop(cigar[s->k]) == BAM_CEQUAL || _cop(cigar[s->k]) == BAM_CDIFF) s->y += l;
+                s->x += l;
+                for (k = s->k + 1; k < c->n_cigar; ++k) {
+                    op = _cop(cigar[k]), l = _cln(cigar[k]);
+                    if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP || op == BAM_CEQUAL || op == BAM_CDIFF) break;
+                    else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) s->y += l;
+                }
+                s->k = k;
+            }
+            assert(s->k < c->n_cigar); // otherwise a bug
+        } // else, do nothing
+    }
+    { // collect pileup information
+        int op, l;
+        op = _cop(cigar[s->k]); l = _cln(cigar[s->k]);
+        p->is_del = p->indel = p->is_refskip = 0;
+        if (s->x + l - 1 == pos && s->k + 1 < c->n_cigar) { // peek the next operation
+            int op2 = _cop(cigar[s->k+1]);
+            int l2 = _cln(cigar[s->k+1]);
+            if (op2 == BAM_CDEL) p->indel = -(int)l2;
+            else if (op2 == BAM_CINS) p->indel = l2;
+            else if (op2 == BAM_CPAD && s->k + 2 < c->n_cigar) { // no working for adjacent padding
+                int l3 = 0;
+                for (k = s->k + 2; k < c->n_cigar; ++k) {
+                    op2 = _cop(cigar[k]); l2 = _cln(cigar[k]);
+                    if (op2 == BAM_CINS) l3 += l2;
+                    else if (op2 == BAM_CDEL || op2 == BAM_CMATCH || op2 == BAM_CREF_SKIP || op2 == BAM_CEQUAL || op2 == BAM_CDIFF) break;
+                }
+                if (l3 > 0) p->indel = l3;
+            }
+        }
+        if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
+            p->qpos = s->y + (pos - s->x);
+        } else if (op == BAM_CDEL || op == BAM_CREF_SKIP) {
+            p->is_del = 1; p->qpos = s->y; // FIXME: distinguish D and N!!!!!
+            p->is_refskip = (op == BAM_CREF_SKIP);
+        } // cannot be other operations; otherwise a bug
+        p->is_head = (pos == c->pos); p->is_tail = (pos == s->end);
+    }
+    return 1;
+}
+
+/***********************
+ *** Pileup iterator ***
+ ***********************/
+
+// Dictionary of overlapping reads
+KHASH_MAP_INIT_STR(olap_hash, lbnode_t *)
+typedef khash_t(olap_hash) olap_hash_t;
+
+struct __bam_plp_t {
+    mempool_t *mp;
+    lbnode_t *head, *tail;
+    int32_t tid, pos, max_tid, max_pos;
+    int is_eof, max_plp, error, maxcnt;
+    uint64_t id;
+    bam_pileup1_t *plp;
+    // for the "auto" interface only
+    bam1_t *b;
+    bam_plp_auto_f func;
+    void *data;
+    olap_hash_t *overlaps;
+};
+
+bam_plp_t bam_plp_init(bam_plp_auto_f func, void *data)
+{
+    bam_plp_t iter;
+    iter = (bam_plp_t)calloc(1, sizeof(struct __bam_plp_t));
+    iter->mp = mp_init();
+    iter->head = iter->tail = mp_alloc(iter->mp);
+    iter->max_tid = iter->max_pos = -1;
+    iter->maxcnt = 8000;
+    if (func) {
+        iter->func = func;
+        iter->data = data;
+        iter->b = bam_init1();
+    }
+    return iter;
+}
+
+void bam_plp_init_overlaps(bam_plp_t iter)
+{
+    iter->overlaps = kh_init(olap_hash);  // hash for tweaking quality of bases in overlapping reads
+}
+
+void bam_plp_destroy(bam_plp_t iter)
+{
+    lbnode_t *p, *pnext;
+    if ( iter->overlaps ) kh_destroy(olap_hash, iter->overlaps);
+    for (p = iter->head; p != NULL; p = pnext) {
+        pnext = p->next;
+        mp_free(iter->mp, p);
+    }
+    mp_destroy(iter->mp);
+    if (iter->b) bam_destroy1(iter->b);
+    free(iter->plp);
+    free(iter);
+}
+
+
+//---------------------------------
+//---  Tweak overlapping reads
+//---------------------------------
+
+/**
+ *  cigar_iref2iseq_set()  - find the first CMATCH setting the ref and the read index
+ *  cigar_iref2iseq_next() - get the next CMATCH base
+ *  @cigar:       pointer to current cigar block (rw)
+ *  @cigar_max:   pointer just beyond the last cigar block
+ *  @icig:        position within the current cigar block (rw)
+ *  @iseq:        position in the sequence (rw)
+ *  @iref:        position with respect to the beginning of the read (iref_pos - b->core.pos) (rw)
+ *
+ *  Returns BAM_CMATCH or -1 when there is no more cigar to process or the requested position is not covered.
+ */
+static inline int cigar_iref2iseq_set(uint32_t **cigar, uint32_t *cigar_max, int *icig, int *iseq, int *iref)
+{
+    int pos = *iref;
+    if ( pos < 0 ) return -1;
+    *icig = 0;
+    *iseq = 0;
+    *iref = 0;
+    while ( *cigar<cigar_max )
+    {
+        int cig  = (**cigar) & BAM_CIGAR_MASK;
+        int ncig = (**cigar) >> BAM_CIGAR_SHIFT;
+
+        if ( cig==BAM_CSOFT_CLIP ) { (*cigar)++; *iseq += ncig; *icig = 0; continue; }
+        if ( cig==BAM_CHARD_CLIP || cig==BAM_CPAD ) { (*cigar)++; *icig = 0; continue; }
+        if ( cig==BAM_CMATCH || cig==BAM_CEQUAL || cig==BAM_CDIFF )
+        {
+            pos -= ncig;
+            if ( pos < 0 ) { *icig = ncig + pos; *iseq += *icig; *iref += *icig; return BAM_CMATCH; }
+            (*cigar)++; *iseq += ncig; *icig = 0; *iref += ncig;
+            continue;
+        }
+        if ( cig==BAM_CINS ) { (*cigar)++; *iseq += ncig; *icig = 0; continue; }
+        if ( cig==BAM_CDEL || cig==BAM_CREF_SKIP )
+        {
+            pos -= ncig;
+            if ( pos<0 ) pos = 0;
+            (*cigar)++; *icig = 0; *iref += ncig;
+            continue;
+        }
+        fprintf(stderr,"todo: cigar %d\n", cig);
+        assert(0);
+    }
+    *iseq = -1;
+    return -1;
+}
+static inline int cigar_iref2iseq_next(uint32_t **cigar, uint32_t *cigar_max, int *icig, int *iseq, int *iref)
+{
+    while ( *cigar < cigar_max )
+    {
+        int cig  = (**cigar) & BAM_CIGAR_MASK;
+        int ncig = (**cigar) >> BAM_CIGAR_SHIFT;
+
+        if ( cig==BAM_CMATCH || cig==BAM_CEQUAL || cig==BAM_CDIFF )
+        {
+            if ( *icig >= ncig - 1 ) { *icig = 0;  (*cigar)++; continue; }
+            (*iseq)++; (*icig)++; (*iref)++;
+            return BAM_CMATCH;
+        }
+        if ( cig==BAM_CDEL || cig==BAM_CREF_SKIP ) { (*cigar)++; (*iref) += ncig; *icig = 0; continue; }
+        if ( cig==BAM_CINS ) { (*cigar)++; *iseq += ncig; *icig = 0; continue; }
+        if ( cig==BAM_CSOFT_CLIP ) { (*cigar)++; *iseq += ncig; *icig = 0; continue; }
+        if ( cig==BAM_CHARD_CLIP || cig==BAM_CPAD ) { (*cigar)++; *icig = 0; continue; }
+        fprintf(stderr,"todo: cigar %d\n", cig);
+        assert(0);
+    }
+    *iseq = -1;
+    *iref = -1;
+    return -1;
+}
+
+static void tweak_overlap_quality(bam1_t *a, bam1_t *b)
+{
+    uint32_t *a_cigar = bam_get_cigar(a), *a_cigar_max = a_cigar + a->core.n_cigar;
+    uint32_t *b_cigar = bam_get_cigar(b), *b_cigar_max = b_cigar + b->core.n_cigar;
+    int a_icig = 0, a_iseq = 0;
+    int b_icig = 0, b_iseq = 0;
+    uint8_t *a_qual = bam_get_qual(a), *b_qual = bam_get_qual(b);
+    uint8_t *a_seq  = bam_get_seq(a), *b_seq = bam_get_seq(b);
+
+    int iref   = b->core.pos;
+    int a_iref = iref - a->core.pos;
+    int b_iref = iref - b->core.pos;
+    int a_ret = cigar_iref2iseq_set(&a_cigar, a_cigar_max, &a_icig, &a_iseq, &a_iref);
+    if ( a_ret<0 ) return;  // no overlap
+    int b_ret = cigar_iref2iseq_set(&b_cigar, b_cigar_max, &b_icig, &b_iseq, &b_iref);
+    if ( b_ret<0 ) return;  // no overlap
+
+    #if DBG
+        fprintf(stderr,"tweak %s  n_cigar=%d %d  .. %d-%d vs %d-%d\n", bam_get_qname(a), a->core.n_cigar, b->core.n_cigar,
+            a->core.pos+1,a->core.pos+bam_cigar2rlen(a->core.n_cigar,bam_get_cigar(a)), b->core.pos+1, b->core.pos+bam_cigar2rlen(b->core.n_cigar,bam_get_cigar(b)));
+    #endif
+
+    while ( 1 )
+    {
+        // Increment reference position
+        while ( a_iref>=0 && a_iref < iref - a->core.pos )
+            a_ret = cigar_iref2iseq_next(&a_cigar, a_cigar_max, &a_icig, &a_iseq, &a_iref);
+        if ( a_ret<0 ) break;   // done
+        if ( iref < a_iref + a->core.pos ) iref = a_iref + a->core.pos;
+
+        while ( b_iref>=0 && b_iref < iref - b->core.pos )
+            b_ret = cigar_iref2iseq_next(&b_cigar, b_cigar_max, &b_icig, &b_iseq, &b_iref);
+        if ( b_ret<0 ) break;   // done
+        if ( iref < b_iref + b->core.pos ) iref = b_iref + b->core.pos;
+
+        iref++;
+        if ( a_iref+a->core.pos != b_iref+b->core.pos ) continue;   // only CMATCH positions, don't know what to do with indels
+
+        if ( bam_seqi(a_seq,a_iseq) == bam_seqi(b_seq,b_iseq) )
+        {
+            #if DBG
+                fprintf(stderr,"%c",seq_nt16_str[bam_seqi(a_seq,a_iseq)]);
+            #endif
+            // we are very confident about this base
+            int qual = a_qual[a_iseq] + b_qual[b_iseq];
+            a_qual[a_iseq] = qual>200 ? 200 : qual;
+            b_qual[b_iseq] = 0;
+        }
+        else
+        {
+            if ( a_qual[a_iseq] >= b_qual[b_iseq] )
+            {
+                #if DBG
+                    fprintf(stderr,"[%c/%c]",seq_nt16_str[bam_seqi(a_seq,a_iseq)],tolower(seq_nt16_str[bam_seqi(b_seq,b_iseq)]));
+                #endif
+                a_qual[a_iseq] = 0.8 * a_qual[a_iseq];  // not so confident about a_qual anymore given the mismatch
+                b_qual[b_iseq] = 0;
+            }
+            else
+            {
+                #if DBG
+                    fprintf(stderr,"[%c/%c]",tolower(seq_nt16_str[bam_seqi(a_seq,a_iseq)]),seq_nt16_str[bam_seqi(b_seq,b_iseq)]);
+                #endif
+                b_qual[b_iseq] = 0.8 * b_qual[b_iseq];
+                a_qual[a_iseq] = 0;
+            }
+        }
+    }
+    #if DBG
+        fprintf(stderr,"\n");
+    #endif
+}
+
+// Fix overlapping reads. Simple soft-clipping did not give good results.
+// Lowering qualities of unwanted bases is more selective and works better.
+//
+static void overlap_push(bam_plp_t iter, lbnode_t *node)
+{
+    if ( !iter->overlaps ) return;
+
+    // mapped mates and paired reads only
+    if ( node->b.core.flag&BAM_FMUNMAP || !(node->b.core.flag&BAM_FPROPER_PAIR) ) return;
+
+    // no overlap possible, unless some wild cigar
+    if ( abs(node->b.core.isize) >= 2*node->b.core.l_qseq ) return;
+
+    khiter_t kitr = kh_get(olap_hash, iter->overlaps, bam_get_qname(&node->b));
+    if ( kitr==kh_end(iter->overlaps) )
+    {
+        int ret;
+        kitr = kh_put(olap_hash, iter->overlaps, bam_get_qname(&node->b), &ret);
+        kh_value(iter->overlaps, kitr) = node;
+    }
+    else
+    {
+        lbnode_t *a = kh_value(iter->overlaps, kitr);
+        tweak_overlap_quality(&a->b, &node->b);
+        kh_del(olap_hash, iter->overlaps, kitr);
+        assert(a->end-1 == a->s.end);
+        a->end = bam_endpos(&a->b);
+        a->s.end = a->end - 1;
+    }
+}
+
+static void overlap_remove(bam_plp_t iter, const bam1_t *b)
+{
+    if ( !iter->overlaps ) return;
+
+    khiter_t kitr;
+    if ( b )
+    {
+        kitr = kh_get(olap_hash, iter->overlaps, bam_get_qname(b));
+        if ( kitr!=kh_end(iter->overlaps) )
+            kh_del(olap_hash, iter->overlaps, kitr);
+    }
+    else
+    {
+        // remove all
+        for (kitr = kh_begin(iter->overlaps); kitr<kh_end(iter->overlaps); kitr++)
+            if ( kh_exist(iter->overlaps, kitr) ) kh_del(olap_hash, iter->overlaps, kitr);
+    }
+}
+
+
+
+// Prepares next pileup position in bam records collected by bam_plp_auto -> user func -> bam_plp_push. Returns
+// pointer to the piled records if next position is ready or NULL if there is not enough records in the
+// buffer yet (the current position is still the maximum position across all buffered reads).
+const bam_pileup1_t *bam_plp_next(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp)
+{
+    if (iter->error) { *_n_plp = -1; return 0; }
+    *_n_plp = 0;
+    if (iter->is_eof && iter->head == iter->tail) return 0;
+    while (iter->is_eof || iter->max_tid > iter->tid || (iter->max_tid == iter->tid && iter->max_pos > iter->pos)) {
+        int n_plp = 0;
+        // write iter->plp at iter->pos
+        lbnode_t **pptr = &iter->head;
+        while (*pptr != iter->tail) {
+            lbnode_t *p = *pptr;
+            if (p->b.core.tid < iter->tid || (p->b.core.tid == iter->tid && p->end <= iter->pos)) { // then remove
+                overlap_remove(iter, &p->b);
+                *pptr = p->next; mp_free(iter->mp, p);
+            }
+            else {
+                if (p->b.core.tid == iter->tid && p->beg <= iter->pos) { // here: p->end > pos; then add to pileup
+                    if (n_plp == iter->max_plp) { // then double the capacity
+                        iter->max_plp = iter->max_plp? iter->max_plp<<1 : 256;
+                        iter->plp = (bam_pileup1_t*)realloc(iter->plp, sizeof(bam_pileup1_t) * iter->max_plp);
+                    }
+                    iter->plp[n_plp].b = &p->b;
+                    if (resolve_cigar2(iter->plp + n_plp, iter->pos, &p->s)) ++n_plp; // actually always true...
+                }
+                pptr = &(*pptr)->next;
+            }
+        }
+        *_n_plp = n_plp; *_tid = iter->tid; *_pos = iter->pos;
+        // update iter->tid and iter->pos
+        if (iter->head != iter->tail) {
+            if (iter->tid > iter->head->b.core.tid) {
+                fprintf(stderr, "[%s] unsorted input. Pileup aborts.\n", __func__);
+                iter->error = 1;
+                *_n_plp = -1;
+                return 0;
+            }
+        }
+        if (iter->tid < iter->head->b.core.tid) { // come to a new reference sequence
+            iter->tid = iter->head->b.core.tid; iter->pos = iter->head->beg; // jump to the next reference
+        } else if (iter->pos < iter->head->beg) { // here: tid == head->b.core.tid
+            iter->pos = iter->head->beg; // jump to the next position
+        } else ++iter->pos; // scan contiguously
+        // return
+        if (n_plp) return iter->plp;
+        if (iter->is_eof && iter->head == iter->tail) break;
+    }
+    return 0;
+}
+
+int bam_plp_push(bam_plp_t iter, const bam1_t *b)
+{
+    if (iter->error) return -1;
+    if (b) {
+        if (b->core.tid < 0) { overlap_remove(iter, b); return 0; }
+        // Skip only unmapped reads here, any additional filtering must be done in iter->func
+        if (b->core.flag & BAM_FUNMAP) { overlap_remove(iter, b); return 0; }
+        if (iter->tid == b->core.tid && iter->pos == b->core.pos && iter->mp->cnt > iter->maxcnt)
+        {
+            overlap_remove(iter, b);
+            return 0;
+        }
+        bam_copy1(&iter->tail->b, b);
+        overlap_push(iter, iter->tail);
+#ifndef BAM_NO_ID
+        iter->tail->b.id = iter->id++;
+#endif
+        iter->tail->beg = b->core.pos;
+        iter->tail->end = bam_endpos(b);
+        iter->tail->s = g_cstate_null; iter->tail->s.end = iter->tail->end - 1; // initialize cstate_t
+        if (b->core.tid < iter->max_tid) {
+            fprintf(stderr, "[bam_pileup_core] the input is not sorted (chromosomes out of order)\n");
+            iter->error = 1;
+            return -1;
+        }
+        if ((b->core.tid == iter->max_tid) && (iter->tail->beg < iter->max_pos)) {
+            fprintf(stderr, "[bam_pileup_core] the input is not sorted (reads out of order)\n");
+            iter->error = 1;
+            return -1;
+        }
+        iter->max_tid = b->core.tid; iter->max_pos = iter->tail->beg;
+        if (iter->tail->end > iter->pos || iter->tail->b.core.tid > iter->tid) {
+            iter->tail->next = mp_alloc(iter->mp);
+            iter->tail = iter->tail->next;
+        }
+    } else iter->is_eof = 1;
+    return 0;
+}
+
+const bam_pileup1_t *bam_plp_auto(bam_plp_t iter, int *_tid, int *_pos, int *_n_plp)
+{
+    const bam_pileup1_t *plp;
+    if (iter->func == 0 || iter->error) { *_n_plp = -1; return 0; }
+    if ((plp = bam_plp_next(iter, _tid, _pos, _n_plp)) != 0) return plp;
+    else { // no pileup line can be obtained; read alignments
+        *_n_plp = 0;
+        if (iter->is_eof) return 0;
+        int ret;
+        while ( (ret=iter->func(iter->data, iter->b)) >= 0) {
+            if (bam_plp_push(iter, iter->b) < 0) {
+                *_n_plp = -1;
+                return 0;
+            }
+            if ((plp = bam_plp_next(iter, _tid, _pos, _n_plp)) != 0) return plp;
+            // otherwise no pileup line can be returned; read the next alignment.
+        }
+        if ( ret < -1 ) { iter->error = ret; *_n_plp = -1; return 0; }
+        bam_plp_push(iter, 0);
+        if ((plp = bam_plp_next(iter, _tid, _pos, _n_plp)) != 0) return plp;
+        return 0;
+    }
+}
+
+void bam_plp_reset(bam_plp_t iter)
+{
+    overlap_remove(iter, NULL);
+    iter->max_tid = iter->max_pos = -1;
+    iter->tid = iter->pos = 0;
+    iter->is_eof = 0;
+    while (iter->head != iter->tail) {
+        lbnode_t *p = iter->head;
+        iter->head = p->next;
+        mp_free(iter->mp, p);
+    }
+}
+
+void bam_plp_set_maxcnt(bam_plp_t iter, int maxcnt)
+{
+    iter->maxcnt = maxcnt;
+}
+
+/************************
+ *** Mpileup iterator ***
+ ************************/
+
+struct __bam_mplp_t {
+    int n;
+    uint64_t min, *pos;
+    bam_plp_t *iter;
+    int *n_plp;
+    const bam_pileup1_t **plp;
+};
+
+bam_mplp_t bam_mplp_init(int n, bam_plp_auto_f func, void **data)
+{
+    int i;
+    bam_mplp_t iter;
+    iter = (bam_mplp_t)calloc(1, sizeof(struct __bam_mplp_t));
+    iter->pos = (uint64_t*)calloc(n, sizeof(uint64_t));
+    iter->n_plp = (int*)calloc(n, sizeof(int));
+    iter->plp = (const bam_pileup1_t**)calloc(n, sizeof(bam_pileup1_t*));
+    iter->iter = (bam_plp_t*)calloc(n, sizeof(bam_plp_t));
+    iter->n = n;
+    iter->min = (uint64_t)-1;
+    for (i = 0; i < n; ++i) {
+        iter->iter[i] = bam_plp_init(func, data[i]);
+        iter->pos[i] = iter->min;
+    }
+    return iter;
+}
+
+void bam_mplp_init_overlaps(bam_mplp_t iter)
+{
+    int i;
+    for (i = 0; i < iter->n; ++i)
+        bam_plp_init_overlaps(iter->iter[i]);
+}
+
+void bam_mplp_set_maxcnt(bam_mplp_t iter, int maxcnt)
+{
+    int i;
+    for (i = 0; i < iter->n; ++i)
+        iter->iter[i]->maxcnt = maxcnt;
+}
+
+void bam_mplp_destroy(bam_mplp_t iter)
+{
+    int i;
+    for (i = 0; i < iter->n; ++i) bam_plp_destroy(iter->iter[i]);
+    free(iter->iter); free(iter->pos); free(iter->n_plp); free(iter->plp);
+    free(iter);
+}
+
+int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_pileup1_t **plp)
+{
+    int i, ret = 0;
+    uint64_t new_min = (uint64_t)-1;
+    for (i = 0; i < iter->n; ++i) {
+        if (iter->pos[i] == iter->min) {
+            int tid, pos;
+            iter->plp[i] = bam_plp_auto(iter->iter[i], &tid, &pos, &iter->n_plp[i]);
+            if ( iter->iter[i]->error ) return -1;
+            iter->pos[i] = iter->plp[i] ? (uint64_t)tid<<32 | pos : 0;
+        }
+        if (iter->plp[i] && iter->pos[i] < new_min) new_min = iter->pos[i];
+    }
+    iter->min = new_min;
+    if (new_min == (uint64_t)-1) return 0;
+    *_tid = new_min>>32; *_pos = (uint32_t)new_min;
+    for (i = 0; i < iter->n; ++i) {
+        if (iter->pos[i] == iter->min) { // FIXME: valgrind reports "uninitialised value(s) at this line"
+            n_plp[i] = iter->n_plp[i], plp[i] = iter->plp[i];
+            ++ret;
+        } else n_plp[i] = 0, plp[i] = 0;
+    }
+    return ret;
+}
+
+#endif // ~!defined(BAM_NO_PILEUP)
diff --git a/htslib/synced_bcf_reader.c b/htslib/synced_bcf_reader.c
new file mode 100644
index 0000000..1e70fc6
--- /dev/null
+++ b/htslib/synced_bcf_reader.c
@@ -0,0 +1,1284 @@
+/*  synced_bcf_reader.c -- stream through multiple VCF files.
+
+    Copyright (C) 2012-2014 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3 at sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdio.h>
+#include <unistd.h>
+#include <string.h>
+#include <limits.h>
+#include <errno.h>
+#include <ctype.h>
+#include <sys/stat.h>
+#include "htslib/synced_bcf_reader.h"
+#include "htslib/kseq.h"
+#include "htslib/khash_str2int.h"
+#include "htslib/bgzf.h"
+
+#define MAX_CSI_COOR 0x7fffffff     // maximum indexable coordinate of .csi
+
+typedef struct
+{
+    uint32_t start, end;
+}
+region1_t;
+
+typedef struct _region_t
+{
+    region1_t *regs;
+    int nregs, mregs, creg;
+}
+region_t;
+
+static void _regions_add(bcf_sr_regions_t *reg, const char *chr, int start, int end);
+static bcf_sr_regions_t *_regions_init_string(const char *str);
+static int _regions_match_alleles(bcf_sr_regions_t *reg, int als_idx, bcf1_t *rec);
+
+char *bcf_sr_strerror(int errnum)
+{
+    switch (errnum)
+    {
+        case open_failed: 
+            return strerror(errno); break;
+        case not_bgzf:
+            return "not compressed with bgzip"; break;
+        case idx_load_failed:
+            return "could not load index"; break;
+        case file_type_error:
+            return "unknown file type"; break;
+        case api_usage_error:
+            return "API usage error"; break;
+        case header_error:
+            return "could not parse header"; break;
+        case no_eof:
+            return "no BGZF EOF marker; file may be truncated"; break;
+        default: return ""; 
+    }
+}
+
+static int *init_filters(bcf_hdr_t *hdr, const char *filters, int *nfilters)
+{
+    kstring_t str = {0,0,0};
+    const char *tmp = filters, *prev = filters;
+    int nout = 0, *out = NULL;
+    while ( 1 )
+    {
+        if ( *tmp==',' || !*tmp )
+        {
+            out = (int*) realloc(out, (nout+1)*sizeof(int));
+            if ( tmp-prev==1 && *prev=='.' )
+            {
+                out[nout] = -1;
+                nout++;
+            }
+            else
+            {
+                str.l = 0;
+                kputsn(prev, tmp-prev, &str);
+                out[nout] = bcf_hdr_id2int(hdr, BCF_DT_ID, str.s);
+                if ( out[nout]>=0 ) nout++;
+            }
+            if ( !*tmp ) break;
+            prev = tmp+1;
+        }
+        tmp++;
+    }
+    if ( str.m ) free(str.s);
+    *nfilters = nout;
+    return out;
+}
+
+int bcf_sr_set_regions(bcf_srs_t *readers, const char *regions, int is_file)
+{
+    assert( !readers->regions );
+    if ( readers->nreaders )
+    {
+        fprintf(stderr,"[%s:%d %s] Error: bcf_sr_set_regions() must be called before bcf_sr_add_reader()\n", __FILE__,__LINE__,__FUNCTION__);
+        return -1;
+    }
+    readers->regions = bcf_sr_regions_init(regions,is_file,0,1,-2);
+    if ( !readers->regions ) return -1;
+    readers->explicit_regs = 1;
+    readers->require_index = 1;
+    return 0;
+}
+int bcf_sr_set_targets(bcf_srs_t *readers, const char *targets, int is_file, int alleles)
+{
+    assert( !readers->targets );
+    if ( targets[0]=='^' )
+    {
+        readers->targets_exclude = 1;
+        targets++;
+    }
+    readers->targets = bcf_sr_regions_init(targets,is_file,0,1,-2);
+    if ( !readers->targets ) return -1;
+    readers->targets_als = alleles;
+    return 0;
+}
+
+int bcf_sr_add_reader(bcf_srs_t *files, const char *fname)
+{
+    htsFile* file_ptr = hts_open(fname, "r");
+    if ( ! file_ptr ) {
+        files->errnum = open_failed;
+        return 0;
+    }
+
+    files->has_line = (int*) realloc(files->has_line, sizeof(int)*(files->nreaders+1));
+    files->has_line[files->nreaders] = 0;
+    files->readers  = (bcf_sr_t*) realloc(files->readers, sizeof(bcf_sr_t)*(files->nreaders+1));
+    bcf_sr_t *reader = &files->readers[files->nreaders++];
+    memset(reader,0,sizeof(bcf_sr_t));
+
+    reader->file = file_ptr;
+
+    files->errnum = 0;
+
+    if ( reader->file->format.compression==bgzf )
+    {
+        BGZF *bgzf = hts_get_bgzfp(reader->file);
+        if ( bgzf && bgzf_check_EOF(bgzf) == 0 ) {
+            files->errnum = no_eof;
+            fprintf(stderr,"[%s] Warning: no BGZF EOF marker; file may be truncated.\n", fname);
+        }
+    }
+
+    if ( files->require_index )
+    {
+        if ( reader->file->format.format==vcf )
+        {
+            if ( reader->file->format.compression!=bgzf )
+            {
+                files->errnum = not_bgzf;
+                return 0;
+            }
+
+            reader->tbx_idx = tbx_index_load(fname);
+            if ( !reader->tbx_idx )
+            {
+                files->errnum = idx_load_failed;
+                return 0;
+            }
+
+            reader->header = bcf_hdr_read(reader->file);
+        }
+        else if ( reader->file->format.format==bcf )
+        {
+            if ( reader->file->format.compression!=bgzf )
+            {
+                files->errnum = not_bgzf;
+                return 0;
+            }
+
+            reader->header = bcf_hdr_read(reader->file);
+
+            reader->bcf_idx = bcf_index_load(fname);
+            if ( !reader->bcf_idx )
+            {
+                files->errnum = idx_load_failed;
+                return 0;
+            }
+        }
+        else
+        {
+            files->errnum = file_type_error;
+            return 0;
+        }
+    }
+    else
+    {
+        if ( reader->file->format.format==bcf || reader->file->format.format==vcf )
+        {
+            reader->header = bcf_hdr_read(reader->file);
+        }
+        else
+        {
+            files->errnum = file_type_error;
+            return 0;
+        }
+        files->streaming = 1;
+    }
+    if ( files->streaming && files->nreaders>1 )
+    {
+        files->errnum = api_usage_error;
+        fprintf(stderr,"[%s:%d %s] Error: %d readers, yet require_index not set\n", __FILE__,__LINE__,__FUNCTION__,files->nreaders);
+        return 0;
+    }
+    if ( files->streaming && files->regions )
+    {
+        files->errnum = api_usage_error;
+        fprintf(stderr,"[%s:%d %s] Error: cannot tabix-jump in streaming mode\n", __FILE__,__LINE__,__FUNCTION__);
+        return 0;
+    }
+    if ( !reader->header )
+    {
+        files->errnum = header_error;
+        return 0;
+    }
+
+    reader->fname = strdup(fname);
+    if ( files->apply_filters )
+        reader->filter_ids = init_filters(reader->header, files->apply_filters, &reader->nfilter_ids);
+
+    // Update list of chromosomes
+    if ( !files->explicit_regs && !files->streaming )
+    {
+        int n,i;
+        const char **names = reader->tbx_idx ? tbx_seqnames(reader->tbx_idx, &n) : bcf_hdr_seqnames(reader->header, &n);
+        for (i=0; i<n; i++)
+        {
+            if ( !files->regions )
+                files->regions = _regions_init_string(names[i]);
+            else
+                _regions_add(files->regions, names[i], -1, -1);
+        }
+        free(names);
+    }
+
+    return 1;
+}
+
+bcf_srs_t *bcf_sr_init(void)
+{
+    bcf_srs_t *files = (bcf_srs_t*) calloc(1,sizeof(bcf_srs_t));
+    return files;
+}
+
+static void bcf_sr_destroy1(bcf_sr_t *reader)
+{
+    free(reader->fname);
+    if ( reader->tbx_idx ) tbx_destroy(reader->tbx_idx);
+    if ( reader->bcf_idx ) hts_idx_destroy(reader->bcf_idx);
+    bcf_hdr_destroy(reader->header);
+    hts_close(reader->file);
+    if ( reader->itr ) tbx_itr_destroy(reader->itr);
+    int j;
+    for (j=0; j<reader->mbuffer; j++)
+        bcf_destroy1(reader->buffer[j]);
+    free(reader->buffer);
+    free(reader->samples);
+    free(reader->filter_ids);
+}
+void bcf_sr_destroy(bcf_srs_t *files)
+{
+    int i;
+    for (i=0; i<files->nreaders; i++)
+        bcf_sr_destroy1(&files->readers[i]);
+    free(files->has_line);
+    free(files->readers);
+    for (i=0; i<files->n_smpl; i++) free(files->samples[i]);
+    free(files->samples);
+    if (files->targets) bcf_sr_regions_destroy(files->targets);
+    if (files->regions) bcf_sr_regions_destroy(files->regions);
+    if ( files->tmps.m ) free(files->tmps.s);
+    free(files);
+}
+
+void bcf_sr_remove_reader(bcf_srs_t *files, int i)
+{
+    assert( !files->samples );  // not ready for this yet
+    bcf_sr_destroy1(&files->readers[i]);
+    if ( i+1 < files->nreaders )
+    {
+        memmove(&files->readers[i], &files->readers[i+1], (files->nreaders-i-1)*sizeof(bcf_sr_t));
+        memmove(&files->has_line[i], &files->has_line[i+1], (files->nreaders-i-1)*sizeof(int));
+    }
+    files->nreaders--;
+}
+
+
+/*
+   Removes duplicate records from the buffer. The meaning of "duplicate" is
+   controlled by the $collapse variable, which can cause that from multiple
+   <indel|snp|any> lines only the first is considered and the rest is ignored.
+   The removal is done by setting the redundant lines' positions to -1 and
+   moving these lines at the end of the buffer.
+ */
+static void collapse_buffer(bcf_srs_t *files, bcf_sr_t *reader)
+{
+    int irec,jrec, has_snp=0, has_indel=0, has_any=0;
+    for (irec=1; irec<=reader->nbuffer; irec++)
+    {
+        bcf1_t *line = reader->buffer[irec];
+        if ( line->pos != reader->buffer[1]->pos ) break;
+        if ( files->collapse&COLLAPSE_ANY )
+        {
+            if ( !has_any ) has_any = 1;
+            else line->pos = -1;
+        }
+        int line_type = bcf_get_variant_types(line);
+        if ( files->collapse&COLLAPSE_SNPS && line_type&(VCF_SNP|VCF_MNP) )
+        {
+            if ( !has_snp ) has_snp = 1;
+            else line->pos = -1;
+        }
+        if ( files->collapse&COLLAPSE_INDELS && line_type&VCF_INDEL )
+        {
+            if ( !has_indel ) has_indel = 1;
+            else line->pos = -1;
+        }
+    }
+    bcf1_t *tmp;
+    irec = jrec = 1;
+    while ( irec<=reader->nbuffer && jrec<=reader->nbuffer )
+    {
+        if ( reader->buffer[irec]->pos != -1 ) { irec++; continue; }
+        if ( jrec<=irec ) jrec = irec+1;
+        while ( jrec<=reader->nbuffer && reader->buffer[jrec]->pos==-1 ) jrec++;
+        if ( jrec<=reader->nbuffer )
+        {
+            tmp = reader->buffer[irec]; reader->buffer[irec] = reader->buffer[jrec]; reader->buffer[jrec] = tmp;
+        }
+    }
+    reader->nbuffer = irec - 1;
+}
+
+void debug_buffer(FILE *fp, bcf_sr_t *reader)
+{
+    int j;
+    for (j=0; j<=reader->nbuffer; j++)
+    {
+        bcf1_t *line = reader->buffer[j];
+        fprintf(fp,"\t%p\t%s%s\t%s:%d\t%s ", line,reader->fname,j==0?"*":" ",reader->header->id[BCF_DT_CTG][line->rid].key,line->pos+1,line->n_allele?line->d.allele[0]:"");
+        int k;
+        for (k=1; k<line->n_allele; k++) fprintf(fp," %s", line->d.allele[k]);
+        fprintf(fp,"\n");
+    }
+}
+
+void debug_buffers(FILE *fp, bcf_srs_t *files)
+{
+    int i;
+    for (i=0; i<files->nreaders; i++)
+    {
+        fprintf(fp, "has_line: %d\t%s\n", bcf_sr_has_line(files,i),files->readers[i].fname);
+        debug_buffer(fp, &files->readers[i]);
+    }
+    fprintf(fp,"\n");
+}
+
+static inline int has_filter(bcf_sr_t *reader, bcf1_t *line)
+{
+    int i, j;
+    if ( !line->d.n_flt )
+    {
+        for (j=0; j<reader->nfilter_ids; j++)
+            if ( reader->filter_ids[j]<0 ) return 1;
+        return 0;
+    }
+    for (i=0; i<line->d.n_flt; i++)
+    {
+        for (j=0; j<reader->nfilter_ids; j++)
+            if ( line->d.flt[i]==reader->filter_ids[j] ) return 1;
+    }
+    return 0;
+}
+
+static int _reader_seek(bcf_sr_t *reader, const char *seq, int start, int end)
+{
+    if ( end>=MAX_CSI_COOR )
+    {
+        fprintf(stderr,"The coordinate is out of csi index limit: %d\n", end+1);
+        exit(1);
+    }
+    if ( reader->itr )
+    {
+        hts_itr_destroy(reader->itr);
+        reader->itr = NULL;
+    }
+    reader->nbuffer = 0;
+    if ( reader->tbx_idx )
+    {
+        int tid = tbx_name2id(reader->tbx_idx, seq);
+        if ( tid==-1 ) return -1;    // the sequence not present in this file
+        reader->itr = tbx_itr_queryi(reader->tbx_idx,tid,start,end+1);
+    }
+    else
+    {
+        int tid = bcf_hdr_name2id(reader->header, seq);
+        if ( tid==-1 ) return -1;    // the sequence not present in this file
+        reader->itr = bcf_itr_queryi(reader->bcf_idx,tid,start,end+1);
+    }
+    if ( !reader->itr ) fprintf(stderr,"Could not seek: %s:%d-%d\n",seq,start+1,end+1);
+    assert(reader->itr);
+    return 0;
+}
+
+/*
+ *  _readers_next_region() - jumps to next region if necessary
+ *  Returns 0 on success or -1 when there are no more regions left
+ */
+static int _readers_next_region(bcf_srs_t *files)
+{
+    // Need to open new chromosome? Check number of lines in all readers' buffers
+    int i, eos = 0;
+    for (i=0; i<files->nreaders; i++)
+        if ( !files->readers[i].itr && !files->readers[i].nbuffer ) eos++;
+
+    if ( eos!=files->nreaders )
+    {
+        // Some of the readers still has buffered lines
+        return 0;
+    }
+
+    // No lines in the buffer, need to open new region or quit
+    if ( bcf_sr_regions_next(files->regions)<0 ) return -1;
+
+    for (i=0; i<files->nreaders; i++)
+        _reader_seek(&files->readers[i],files->regions->seq_names[files->regions->iseq],files->regions->start,files->regions->end);
+
+    return 0;
+}
+
+/*
+ *  _reader_fill_buffer() - buffers all records with the same coordinate
+ */
+static void _reader_fill_buffer(bcf_srs_t *files, bcf_sr_t *reader)
+{
+    // Return if the buffer is full: the coordinate of the last buffered record differs
+    if ( reader->nbuffer && reader->buffer[reader->nbuffer]->pos != reader->buffer[1]->pos ) return;
+
+    // No iterator (sequence not present in this file) and not streaming
+    if ( !reader->itr && !files->streaming ) return;
+
+    // Fill the buffer with records starting at the same position
+    int i, ret = 0;
+    while (1)
+    {
+        if ( reader->nbuffer+1 >= reader->mbuffer )
+        {
+            // Increase buffer size
+            reader->mbuffer += 8;
+            reader->buffer = (bcf1_t**) realloc(reader->buffer, sizeof(bcf1_t*)*reader->mbuffer);
+            for (i=8; i>0; i--)     // initialize
+            {
+                reader->buffer[reader->mbuffer-i] = bcf_init1();
+                reader->buffer[reader->mbuffer-i]->max_unpack = files->max_unpack;
+                reader->buffer[reader->mbuffer-i]->pos = -1;    // for rare cases when VCF starts from 1
+            }
+        }
+        if ( files->streaming )
+        {
+            if ( reader->file->format.format==vcf )
+            {
+                if ( (ret=hts_getline(reader->file, KS_SEP_LINE, &files->tmps)) < 0 ) break;   // no more lines
+                int ret = vcf_parse1(&files->tmps, reader->header, reader->buffer[reader->nbuffer+1]);
+                if ( ret<0 ) break;
+            }
+            else if ( reader->file->format.format==bcf )
+            {
+                if ( (ret=bcf_read1(reader->file, reader->header, reader->buffer[reader->nbuffer+1])) < 0 ) break; // no more lines
+            }
+            else
+            {
+                fprintf(stderr,"[%s:%d %s] fixme: not ready for this\n", __FILE__,__LINE__,__FUNCTION__);
+                exit(1);
+            }
+        }
+        else if ( reader->tbx_idx )
+        {
+            if ( (ret=tbx_itr_next(reader->file, reader->tbx_idx, reader->itr, &files->tmps)) < 0 ) break;  // no more lines
+            vcf_parse1(&files->tmps, reader->header, reader->buffer[reader->nbuffer+1]);
+        }
+        else
+        {
+            if ( (ret=bcf_itr_next(reader->file, reader->itr, reader->buffer[reader->nbuffer+1])) < 0 ) break; // no more lines
+            bcf_subset_format(reader->header,reader->buffer[reader->nbuffer+1]);
+        }
+
+        // apply filter
+        if ( !reader->nfilter_ids )
+            bcf_unpack(reader->buffer[reader->nbuffer+1], BCF_UN_STR);
+        else
+        {
+            bcf_unpack(reader->buffer[reader->nbuffer+1], BCF_UN_STR|BCF_UN_FLT);
+            if ( !has_filter(reader, reader->buffer[reader->nbuffer+1]) ) continue;
+        }
+        reader->nbuffer++;
+
+        if ( reader->buffer[reader->nbuffer]->pos != reader->buffer[1]->pos ) break;    // the buffer is full
+    }
+    if ( ret<0 )
+    {
+        // done for this region
+        tbx_itr_destroy(reader->itr);
+        reader->itr = NULL;
+    }
+    if ( files->collapse && reader->nbuffer>=2 && reader->buffer[1]->pos==reader->buffer[2]->pos )
+        collapse_buffer(files, reader);
+}
+
+/*
+ *  _readers_shift_buffer() - removes the first line and all subsequent lines with the same position
+ */
+static void _reader_shift_buffer(bcf_sr_t *reader)
+{
+    int i;
+    for (i=2; i<=reader->nbuffer; i++)
+        if ( reader->buffer[i]->pos!=reader->buffer[1]->pos ) break;
+    if ( i<=reader->nbuffer )
+    {
+        // A record with a different position follows, swap it. Because of the reader's logic,
+        // only one such line can be present.
+        bcf1_t *tmp = reader->buffer[1]; reader->buffer[1] = reader->buffer[i]; reader->buffer[i] = tmp;
+        reader->nbuffer = 1;
+    }
+    else
+        reader->nbuffer = 0;    // no other line
+}
+
+/*
+ *  _reader_match_alleles() - from multiple buffered lines selects the one which
+ *  corresponds best to the template line. The logic is controlled by COLLAPSE_*
+ *  Returns 0 on success or -1 when no good matching line is found.
+ */
+static int _reader_match_alleles(bcf_srs_t *files, bcf_sr_t *reader, bcf1_t *tmpl)
+{
+    int i, irec = -1;
+
+    // if no template given, use the first available record
+    if ( !tmpl )
+        irec = 1;
+    else
+    {
+        int tmpl_type = bcf_get_variant_types(tmpl);
+        for (i=1; i<=reader->nbuffer; i++)
+        {
+            bcf1_t *line = reader->buffer[i];
+            if ( line->pos != reader->buffer[1]->pos ) break;  // done with this reader
+
+            // Easiest case: matching by position only
+            if ( files->collapse&COLLAPSE_ANY ) { irec=i; break; }
+
+            int line_type = bcf_get_variant_types(line);
+
+            // No matter what the alleles are, as long as they are both SNPs
+            if ( files->collapse&COLLAPSE_SNPS && tmpl_type&VCF_SNP && line_type&VCF_SNP ) { irec=i; break; }
+            // ... or indels
+            if ( files->collapse&COLLAPSE_INDELS && tmpl_type&VCF_INDEL && line_type&VCF_INDEL ) { irec=i; break; }
+
+            // More thorough checking: REFs must match
+            if ( tmpl->rlen != line->rlen ) continue;  // different length
+            if ( !tmpl->d.allele || !line->d.allele ) continue;   // one of the lines is empty, someone is swapped buffered lines?!
+            if ( strcmp(tmpl->d.allele[0], line->d.allele[0]) ) continue; // the strings do not match
+
+            int ial,jal;
+            if ( files->collapse==COLLAPSE_NONE )
+            {
+                // Exact match, all alleles must be identical
+                if ( tmpl->n_allele!=line->n_allele ) continue;   // different number of alleles, skip
+
+                int nmatch = 1; // REF has been already checked
+                for (ial=1; ial<tmpl->n_allele; ial++)
+                {
+                    for (jal=1; jal<line->n_allele; jal++)
+                        if ( !strcmp(tmpl->d.allele[ial], line->d.allele[jal]) ) { nmatch++; break; }
+                }
+                if ( nmatch==tmpl->n_allele ) { irec=i; break; }    // found: exact match
+                continue;
+            }
+
+            if ( line->n_allele==1 && tmpl->n_allele==1 ) { irec=i; break; }    // both sites are non-variant
+
+            // COLLAPSE_SOME: at least some ALTs must match
+            for (ial=1; ial<tmpl->n_allele; ial++)
+            {
+                for (jal=1; jal<line->n_allele; jal++)
+                    if ( !strcmp(tmpl->d.allele[ial], line->d.allele[jal]) ) { irec=i; break; }
+                if ( irec>=1 ) break;
+            }
+            if ( irec>=1 ) break;
+        }
+        if ( irec==-1 ) return -1;  // no matching line was found
+    }
+
+    // Set the selected line (irec) as active: set it to buffer[0], move the remaining lines forward
+    // and put the old bcf1_t record at the end.
+    bcf1_t *tmp = reader->buffer[0];
+    reader->buffer[0] = reader->buffer[irec];
+    for (i=irec+1; i<=reader->nbuffer; i++) reader->buffer[i-1] = reader->buffer[i];
+    reader->buffer[ reader->nbuffer ] = tmp;
+    reader->nbuffer--;
+
+    return 0;
+}
+
+int _reader_next_line(bcf_srs_t *files)
+{
+    int i, min_pos = INT_MAX;
+
+    // Loop until next suitable line is found or all readers have finished
+    while ( 1 )
+    {
+        // Get all readers ready for the next region.
+        if ( files->regions && _readers_next_region(files)<0 ) break;
+
+        // Fill buffers
+        const char *chr = NULL;
+        for (i=0; i<files->nreaders; i++)
+        {
+            _reader_fill_buffer(files, &files->readers[i]);
+
+            // Update the minimum coordinate
+            if ( !files->readers[i].nbuffer ) continue;
+            if ( min_pos > files->readers[i].buffer[1]->pos )
+            {
+                min_pos = files->readers[i].buffer[1]->pos;
+                chr = bcf_seqname(files->readers[i].header, files->readers[i].buffer[1]);
+            }
+        }
+        if ( min_pos==INT_MAX )
+        {
+            if ( !files->regions ) break;
+            continue;
+        }
+
+        // Skip this position if not present in targets
+        if ( files->targets )
+        {
+            int ret = bcf_sr_regions_overlap(files->targets, chr, min_pos, min_pos);
+            if ( (!files->targets_exclude && ret<0) || (files->targets_exclude && !ret) )
+            {
+                // Remove all lines with this position from the buffer
+                for (i=0; i<files->nreaders; i++)
+                    if ( files->readers[i].nbuffer && files->readers[i].buffer[1]->pos==min_pos )
+                        _reader_shift_buffer(&files->readers[i]);
+                min_pos = INT_MAX;
+                continue;
+            }
+        }
+
+        break;  // done: min_pos is set
+    }
+
+    // There can be records with duplicate positions. Set the active line intelligently so that
+    // the alleles match.
+    int nret = 0;   // number of readers sharing the position
+    bcf1_t *first = NULL;   // record which will be used for allele matching
+    for (i=0; i<files->nreaders; i++)
+    {
+        files->has_line[i] = 0;
+
+        // Skip readers with no records at this position
+        if ( !files->readers[i].nbuffer || files->readers[i].buffer[1]->pos!=min_pos ) continue;
+
+        // Until now buffer[0] of all reader was empty and the lines started at buffer[1].
+        // Now lines which are ready to be output will be moved to buffer[0].
+        if ( _reader_match_alleles(files, &files->readers[i], first) < 0 ) continue;
+        if ( !first ) first = files->readers[i].buffer[0];
+
+        nret++;
+        files->has_line[i] = 1;
+    }
+    return nret;
+}
+
+int bcf_sr_next_line(bcf_srs_t *files)
+{
+    if ( !files->targets_als )
+        return _reader_next_line(files);
+
+    while (1)
+    {
+        int i, ret = _reader_next_line(files);
+        if ( !ret ) return ret;
+
+        for (i=0; i<files->nreaders; i++)
+            if ( files->has_line[i] ) break;
+
+        if ( _regions_match_alleles(files->targets, files->targets_als-1, files->readers[i].buffer[0]) ) return ret;
+
+        // Check if there are more duplicate lines in the buffers. If not, return this line as if it
+        // matched the targets, even if there is a type mismatch
+        for (i=0; i<files->nreaders; i++)
+        {
+            if ( !files->has_line[i] ) continue;
+            if ( files->readers[i].nbuffer==0 || files->readers[i].buffer[1]->pos!=files->readers[i].buffer[0]->pos ) continue;
+            break;
+        }
+        if ( i==files->nreaders ) return ret;   // no more lines left, output even if target alleles are not of the same type
+    }
+}
+
+static void bcf_sr_seek_start(bcf_srs_t *readers)
+{
+    bcf_sr_regions_t *reg = readers->regions;
+    int i;
+    for (i=0; i<reg->nseqs; i++)
+        reg->regs[i].creg = -1;
+    reg->iseq = 0;
+}
+
+
+int bcf_sr_seek(bcf_srs_t *readers, const char *seq, int pos)
+{
+    if ( !readers->regions ) return 0;
+    if ( !seq && !pos )
+    {
+        // seek to start
+        bcf_sr_seek_start(readers);
+        return 0;
+    }
+    bcf_sr_regions_overlap(readers->regions, seq, pos, pos);
+    int i, nret = 0;
+    for (i=0; i<readers->nreaders; i++)
+    {
+        nret += _reader_seek(&readers->readers[i],seq,pos,MAX_CSI_COOR-1);
+    }
+    return nret;
+}
+
+int bcf_sr_set_samples(bcf_srs_t *files, const char *fname, int is_file)
+{
+    int i, j, nsmpl, free_smpl = 0;
+    char **smpl = NULL;
+
+    void *exclude = (fname[0]=='^') ? khash_str2int_init() : NULL;
+    if ( exclude || strcmp("-",fname) ) // "-" stands for all samples
+    {
+        smpl = hts_readlist(fname, is_file, &nsmpl);
+        if ( !smpl )
+        {
+            fprintf(stderr,"Could not read the file: \"%s\"\n", fname);
+            return 0;
+        }
+        if ( exclude )
+        {
+            for (i=0; i<nsmpl; i++)
+                khash_str2int_inc(exclude, smpl[i]);
+        }
+        free_smpl = 1;
+    }
+    if ( !smpl )
+    {
+        smpl  = files->readers[0].header->samples;   // intersection of all samples
+        nsmpl = bcf_hdr_nsamples(files->readers[0].header);
+    }
+
+    files->samples = NULL;
+    files->n_smpl  = 0;
+    for (i=0; i<nsmpl; i++)
+    {
+        if ( exclude && khash_str2int_has_key(exclude,smpl[i])  ) continue;
+
+        int n_isec = 0;
+        for (j=0; j<files->nreaders; j++)
+        {
+            if ( bcf_hdr_id2int(files->readers[j].header, BCF_DT_SAMPLE, smpl[i])<0 ) break;
+            n_isec++;
+        }
+        if ( n_isec!=files->nreaders )
+        {
+            fprintf(stderr,"Warning: The sample \"%s\" was not found in %s, skipping\n", smpl[i], files->readers[n_isec].fname);
+            continue;
+        }
+
+        files->samples = (char**) realloc(files->samples, (files->n_smpl+1)*sizeof(const char*));
+        files->samples[files->n_smpl++] = strdup(smpl[i]);
+    }
+
+    if ( exclude ) khash_str2int_destroy(exclude);
+    if ( free_smpl )
+    {
+        for (i=0; i<nsmpl; i++) free(smpl[i]);
+        free(smpl);
+    }
+
+    if ( !files->n_smpl )
+    {
+        if ( files->nreaders>1 )
+            fprintf(stderr,"No samples in common.\n");
+        return 0;
+    }
+    for (i=0; i<files->nreaders; i++)
+    {
+        bcf_sr_t *reader = &files->readers[i];
+        reader->samples  = (int*) malloc(sizeof(int)*files->n_smpl);
+        reader->n_smpl   = files->n_smpl;
+        for (j=0; j<files->n_smpl; j++)
+            reader->samples[j] = bcf_hdr_id2int(reader->header, BCF_DT_SAMPLE, files->samples[j]);
+    }
+    return 1;
+}
+
+// Add a new region into a list sorted by start,end. On input the coordinates
+// are 1-based, stored 0-based, inclusive.
+static void _regions_add(bcf_sr_regions_t *reg, const char *chr, int start, int end)
+{
+    if ( start==-1 && end==-1 )
+    {
+        start = 0; end = MAX_CSI_COOR-1;
+    }
+    else
+    {
+        start--; end--; // store 0-based coordinates
+    }
+
+    if ( !reg->seq_hash )
+         reg->seq_hash = khash_str2int_init();
+
+    int iseq;
+    if ( khash_str2int_get(reg->seq_hash, chr, &iseq)<0 )
+    {
+        // the chromosome block does not exist
+        iseq = reg->nseqs++;
+        reg->seq_names = (char**) realloc(reg->seq_names,sizeof(char*)*reg->nseqs);
+        reg->regs = (region_t*) realloc(reg->regs,sizeof(region_t)*reg->nseqs);
+        memset(&reg->regs[reg->nseqs-1],0,sizeof(region_t));
+        reg->seq_names[iseq] = strdup(chr);
+        reg->regs[iseq].creg = -1;
+        khash_str2int_set(reg->seq_hash,reg->seq_names[iseq],iseq);
+    }
+
+    region_t *creg = &reg->regs[iseq];
+
+    // the regions may not be sorted on input: binary search
+    int i, min = 0, max = creg->nregs - 1;
+    while ( min<=max )
+    {
+        i = (max+min)/2;
+        if ( start < creg->regs[i].start ) max = i - 1;
+        else if ( start > creg->regs[i].start ) min = i + 1;
+        else break;
+    }
+    if ( min>max || creg->regs[i].start!=start || creg->regs[i].end!=end )
+    {
+        // no such region, insert a new one just after max
+        hts_expand(region1_t,creg->nregs+1,creg->mregs,creg->regs);
+        if ( ++max < creg->nregs )
+            memmove(&creg->regs[max+1],&creg->regs[max],(creg->nregs - max)*sizeof(region1_t));
+        creg->regs[max].start = start;
+        creg->regs[max].end   = end;
+        creg->nregs++;
+    }
+}
+
+// File name or a list of genomic locations. If file name, NULL is returned.
+static bcf_sr_regions_t *_regions_init_string(const char *str)
+{
+    bcf_sr_regions_t *reg = (bcf_sr_regions_t *) calloc(1, sizeof(bcf_sr_regions_t));
+    reg->start = reg->end = -1;
+    reg->prev_start = reg->prev_seq = -1;
+
+    kstring_t tmp = {0,0,0};
+    const char *sp = str, *ep = str;
+    int from, to;
+    while ( 1 )
+    {
+        while ( *ep && *ep!=',' && *ep!=':' ) ep++;
+        tmp.l = 0;
+        kputsn(sp,ep-sp,&tmp);
+        if ( *ep==':' )
+        {
+            sp = ep+1;
+            from = hts_parse_decimal(sp,(char**)&ep,0);
+            if ( sp==ep )
+            {
+                fprintf(stderr,"[%s:%d %s] Could not parse the region(s): %s\n", __FILE__,__LINE__,__FUNCTION__,str);
+                free(reg); free(tmp.s); return NULL;
+            }
+            if ( !*ep || *ep==',' )
+            {
+                _regions_add(reg, tmp.s, from, from);
+                sp = ep;
+                continue;
+            }
+            if ( *ep!='-' )
+            {
+                fprintf(stderr,"[%s:%d %s] Could not parse the region(s): %s\n", __FILE__,__LINE__,__FUNCTION__,str);
+                free(reg); free(tmp.s); return NULL;
+            }
+            ep++;
+            sp = ep;
+            to = hts_parse_decimal(sp,(char**)&ep,0);
+            if ( *ep && *ep!=',' )
+            {
+                fprintf(stderr,"[%s:%d %s] Could not parse the region(s): %s\n", __FILE__,__LINE__,__FUNCTION__,str);
+                free(reg); free(tmp.s); return NULL;
+            }
+            if ( sp==ep ) to = MAX_CSI_COOR-1;
+            _regions_add(reg, tmp.s, from, to);
+            if ( !*ep ) break;
+            sp = ep;
+        }
+        else
+        {
+            if ( tmp.l ) _regions_add(reg, tmp.s, -1, -1);
+            if ( !*ep ) break;
+            sp = ++ep;
+        }
+    }
+    free(tmp.s);
+    return reg;
+}
+
+// ichr,ifrom,ito are 0-based;
+// returns -1 on error, 0 if the line is a comment line, 1 on success
+static int _regions_parse_line(char *line, int ichr,int ifrom,int ito, char **chr,char **chr_end,int *from,int *to)
+{
+    *chr_end = NULL;
+
+    if ( line[0]=='#' ) return 0;
+
+    int k,l;    // index of the start and end column of the tab-delimited file
+    if ( ifrom <= ito )
+        k = ifrom, l = ito;
+    else
+        l = ifrom, k = ito;
+
+    int i;
+    char *se = line, *ss = NULL; // start and end
+    char *tmp;
+    for (i=0; i<=k && *se; i++)
+    {
+        ss = i==0 ? se++ : ++se;
+        while (*se && *se!='\t') se++;
+    }
+    if ( i<=k ) return -1;
+    if ( k==l )
+    {
+        *from = *to = hts_parse_decimal(ss, &tmp, 0);
+        if ( tmp==ss ) return -1;
+    }
+    else
+    {
+        if ( k==ifrom )
+            *from = hts_parse_decimal(ss, &tmp, 0);
+        else
+            *to = hts_parse_decimal(ss, &tmp, 0);
+        if ( ss==tmp ) return -1;
+
+        for (i=k; i<l && *se; i++)
+        {
+            ss = ++se;
+            while (*se && *se!='\t') se++;
+        }
+        if ( i<l ) return -1;
+        if ( k==ifrom )
+            *to = hts_parse_decimal(ss, &tmp, 0);
+        else
+            *from = hts_parse_decimal(ss, &tmp, 0);
+        if ( ss==tmp ) return -1;
+    }
+
+    ss = se = line;
+    for (i=0; i<=ichr && *se; i++)
+    {
+        if ( i>0 ) ss = ++se;
+        while (*se && *se!='\t') se++;
+    }
+    if ( i<=ichr ) return -1;
+    *chr_end = se;
+    *chr = ss;
+    return 1;
+}
+
+bcf_sr_regions_t *bcf_sr_regions_init(const char *regions, int is_file, int ichr, int ifrom, int ito)
+{
+    bcf_sr_regions_t *reg;
+    if ( !is_file ) return _regions_init_string(regions);
+
+    reg = (bcf_sr_regions_t *) calloc(1, sizeof(bcf_sr_regions_t));
+    reg->start = reg->end = -1;
+    reg->prev_start = reg->prev_seq = -1;
+
+    reg->file = hts_open(regions, "rb");
+    if ( !reg->file )
+    {
+        fprintf(stderr,"[%s:%d %s] Could not open file: %s\n", __FILE__,__LINE__,__FUNCTION__,regions);
+        free(reg);
+        return NULL;
+    }
+
+    reg->tbx = tbx_index_load(regions);
+    if ( !reg->tbx )
+    {
+        int len = strlen(regions);
+        int is_bed  = strcasecmp(".bed",regions+len-4) ? 0 : 1;
+        if ( !is_bed && !strcasecmp(".bed.gz",regions+len-7) ) is_bed = 1;
+
+        if ( reg->file->format.format==vcf ) ito = 1;
+
+        // read the whole file, tabix index is not present
+        while ( hts_getline(reg->file, KS_SEP_LINE, &reg->line) > 0 )
+        {
+            char *chr, *chr_end;
+            int from, to, ret;
+            ret = _regions_parse_line(reg->line.s, ichr,ifrom,abs(ito), &chr,&chr_end,&from,&to);
+            if ( ret < 0 )
+            {
+                if ( ito<0 )
+                    ret = _regions_parse_line(reg->line.s, ichr,ifrom,ifrom, &chr,&chr_end,&from,&to);
+                if ( ret<0 )
+                {
+                    fprintf(stderr,"[%s:%d] Could not parse the file %s, using the columns %d,%d[,%d]\n", __FILE__,__LINE__,regions,ichr+1,ifrom+1,ito+1);
+                    hts_close(reg->file); reg->file = NULL; free(reg);
+                    return NULL;
+                }
+            }
+            if ( !ret ) continue;
+            if ( is_bed ) from++;
+            *chr_end = 0;
+            _regions_add(reg, chr, from, to);
+            *chr_end = '\t';
+        }
+        hts_close(reg->file); reg->file = NULL;
+        if ( !reg->nseqs ) { free(reg); return NULL; }
+        return reg;
+    }
+
+    reg->seq_names = (char**) tbx_seqnames(reg->tbx, &reg->nseqs);
+    if ( !reg->seq_hash )
+        reg->seq_hash = khash_str2int_init();
+    int i;
+    for (i=0; i<reg->nseqs; i++)
+    {
+        khash_str2int_set(reg->seq_hash,reg->seq_names[i],i);
+    }
+    reg->fname  = strdup(regions);
+    reg->is_bin = 1;
+    return reg;
+}
+
+void bcf_sr_regions_destroy(bcf_sr_regions_t *reg)
+{
+    int i;
+    free(reg->fname);
+    if ( reg->itr ) tbx_itr_destroy(reg->itr);
+    if ( reg->tbx ) tbx_destroy(reg->tbx);
+    if ( reg->file ) hts_close(reg->file);
+    if ( reg->als ) free(reg->als);
+    if ( reg->als_str.s ) free(reg->als_str.s);
+    free(reg->line.s);
+    if ( reg->regs )
+    {
+         // free only in-memory names, tbx names are const
+        for (i=0; i<reg->nseqs; i++)
+        {
+            free(reg->seq_names[i]);
+            free(reg->regs[i].regs);
+        }
+    }
+    free(reg->regs);
+    free(reg->seq_names);
+    khash_str2int_destroy(reg->seq_hash);
+    free(reg);
+}
+
+int bcf_sr_regions_seek(bcf_sr_regions_t *reg, const char *seq)
+{
+    reg->iseq = reg->start = reg->end = -1;
+    if ( khash_str2int_get(reg->seq_hash, seq, &reg->iseq) < 0 ) return -1;  // sequence seq not in regions
+
+    // using in-memory regions
+    if ( reg->regs )
+    {
+        reg->regs[reg->iseq].creg = -1;
+        return 0;
+    }
+
+    // reading regions from tabix
+    if ( reg->itr ) tbx_itr_destroy(reg->itr);
+    reg->itr = tbx_itr_querys(reg->tbx, seq);
+    if ( reg->itr ) return 0;
+
+    return -1;
+}
+
+int bcf_sr_regions_next(bcf_sr_regions_t *reg)
+{
+    if ( reg->iseq<0 ) return -1;
+    reg->start = reg->end = -1;
+    reg->nals = 0;
+
+    // using in-memory regions
+    if ( reg->regs )
+    {
+        while ( reg->iseq < reg->nseqs )
+        {
+            reg->regs[reg->iseq].creg++;
+            if ( reg->regs[reg->iseq].creg < reg->regs[reg->iseq].nregs ) break;
+            reg->iseq++;
+        }
+        if ( reg->iseq >= reg->nseqs ) { reg->iseq = -1; return -1; } // no more regions left
+        region1_t *creg = &reg->regs[reg->iseq].regs[reg->regs[reg->iseq].creg];
+        reg->start = creg->start;
+        reg->end   = creg->end;
+        return 0;
+    }
+
+    // reading from tabix
+    char *chr, *chr_end;
+    int ichr = 0, ifrom = 1, ito = 2, is_bed = 0, from, to;
+    if ( reg->tbx )
+    {
+        ichr   = reg->tbx->conf.sc-1;
+        ifrom  = reg->tbx->conf.bc-1;
+        ito    = reg->tbx->conf.ec-1;
+        if ( ito<0 ) ito = ifrom;
+        is_bed = reg->tbx->conf.preset==TBX_UCSC ? 1 : 0;
+    }
+
+    int ret = 0;
+    while ( !ret )
+    {
+        if ( reg->itr )
+        {
+            // tabix index present, reading a chromosome block
+            ret = tbx_itr_next(reg->file, reg->tbx, reg->itr, &reg->line);
+            if ( ret<0 ) { reg->iseq = -1; return -1; }
+        }
+        else
+        {
+            if ( reg->is_bin )
+            {
+                // Waited for seek which never came. Reopen in text mode and stream
+                // through the regions, otherwise hts_getline would fail
+                hts_close(reg->file);
+                reg->file = hts_open(reg->fname, "r");
+                if ( !reg->file )
+                {
+                    fprintf(stderr,"[%s:%d %s] Could not open file: %s\n", __FILE__,__LINE__,__FUNCTION__,reg->fname);
+                    reg->file = NULL;
+                    bcf_sr_regions_destroy(reg);
+                    return -1;
+                }
+                reg->is_bin = 0;
+            }
+
+            // tabix index absent, reading the whole file
+            ret = hts_getline(reg->file, KS_SEP_LINE, &reg->line);
+            if ( ret<0 ) { reg->iseq = -1; return -1; }
+        }
+        ret = _regions_parse_line(reg->line.s, ichr,ifrom,ito, &chr,&chr_end,&from,&to);
+        if ( ret<0 )
+        {
+            fprintf(stderr,"[%s:%d] Could not parse the file %s, using the columns %d,%d,%d\n", __FILE__,__LINE__,reg->fname,ichr+1,ifrom+1,ito+1);
+            return -1;
+        }
+    }
+    if ( is_bed ) from++;
+
+    *chr_end = 0;
+    if ( khash_str2int_get(reg->seq_hash, chr, &reg->iseq)<0 )
+    {
+        fprintf(stderr,"Broken tabix index? The sequence \"%s\" not in dictionary [%s]\n", chr,reg->line.s);
+        exit(1);
+    }
+    *chr_end = '\t';
+
+    reg->start = from - 1;
+    reg->end   = to - 1;
+    return 0;
+}
+
+static int _regions_match_alleles(bcf_sr_regions_t *reg, int als_idx, bcf1_t *rec)
+{
+    if ( reg->regs )
+    {
+        // payload is not supported for in-memory regions, switch to regidx instead in future
+        fprintf(stderr,"Error: Compressed and indexed targets file is required\n");
+        exit(1);
+    }
+
+    int i = 0, max_len = 0;
+    if ( !reg->nals )
+    {
+        char *ss = reg->line.s;
+        while ( i<als_idx && *ss )
+        {
+            if ( *ss=='\t' ) i++;
+            ss++;
+        }
+        char *se = ss;
+        reg->nals = 1;
+        while ( *se && *se!='\t' )
+        {
+            if ( *se==',' ) reg->nals++;
+            se++;
+        }
+        ks_resize(&reg->als_str, se-ss+1+reg->nals);
+        reg->als_str.l = 0;
+        hts_expand(char*,reg->nals,reg->mals,reg->als);
+        reg->nals = 0;
+
+        se = ss;
+        while ( *(++se) )
+        {
+            if ( *se=='\t' ) break;
+            if ( *se!=',' ) continue;
+            reg->als[reg->nals] = &reg->als_str.s[reg->als_str.l];
+            kputsn(ss,se-ss,&reg->als_str);
+            if ( &reg->als_str.s[reg->als_str.l] - reg->als[reg->nals] > max_len ) max_len = &reg->als_str.s[reg->als_str.l] - reg->als[reg->nals];
+            reg->als_str.l++;
+            reg->nals++;
+            ss = ++se;
+        }
+        reg->als[reg->nals] = &reg->als_str.s[reg->als_str.l];
+        kputsn(ss,se-ss,&reg->als_str);
+        if ( &reg->als_str.s[reg->als_str.l] - reg->als[reg->nals] > max_len ) max_len = &reg->als_str.s[reg->als_str.l] - reg->als[reg->nals];
+        reg->nals++;
+        reg->als_type = max_len > 1 ? VCF_INDEL : VCF_SNP;  // this is a simplified check, see vcf.c:bcf_set_variant_types
+    }
+    int type = bcf_get_variant_types(rec);
+    if ( reg->als_type & VCF_INDEL )
+        return type & VCF_INDEL ? 1 : 0;
+    return !(type & VCF_INDEL) ? 1 : 0;
+}
+
+int bcf_sr_regions_overlap(bcf_sr_regions_t *reg, const char *seq, int start, int end)
+{
+    int iseq;
+    if ( khash_str2int_get(reg->seq_hash, seq, &iseq)<0 ) return -1;    // no such sequence
+
+    if ( reg->prev_seq==-1 || iseq!=reg->prev_seq || reg->prev_start > start ) // new chromosome or after a seek
+    {
+        // flush regions left on previous chromosome
+        if ( reg->missed_reg_handler && reg->prev_seq!=-1 && reg->iseq!=-1 )
+            bcf_sr_regions_flush(reg);
+
+        bcf_sr_regions_seek(reg, seq);
+        reg->start = reg->end = -1;
+    }
+    if ( reg->prev_seq==iseq && reg->iseq!=iseq ) return -2;    // no more regions on this chromosome
+    reg->prev_seq = reg->iseq;
+    reg->prev_start = start;
+
+    while ( iseq==reg->iseq && reg->end < start )
+    {
+        if ( bcf_sr_regions_next(reg) < 0 ) return -2;  // no more regions left
+        if ( reg->iseq != iseq ) return -1; // does not overlap any regions
+        if ( reg->missed_reg_handler && reg->end < start ) reg->missed_reg_handler(reg, reg->missed_reg_data);
+    }
+    if ( reg->start <= end ) return 0;    // region overlap
+    return -1;  // no overlap
+}
+
+void bcf_sr_regions_flush(bcf_sr_regions_t *reg)
+{
+    if ( !reg->missed_reg_handler || reg->prev_seq==-1 ) return;
+    while ( !bcf_sr_regions_next(reg) ) reg->missed_reg_handler(reg, reg->missed_reg_data);
+    return;
+}
+
diff --git a/htslib/tabix.c b/htslib/tabix.c
new file mode 100644
index 0000000..8bd65e7
--- /dev/null
+++ b/htslib/tabix.c
@@ -0,0 +1,544 @@
+/*  tabix.c -- Generic indexer for TAB-delimited genome position files.
+
+    Copyright (C) 2009-2011 Broad Institute.
+    Copyright (C) 2010-2012, 2014-2016 Genome Research Ltd.
+
+    Author: Heng Li <lh3 at sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <string.h>
+#include <getopt.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <errno.h>
+#include "htslib/tbx.h"
+#include "htslib/sam.h"
+#include "htslib/vcf.h"
+#include "htslib/kseq.h"
+#include "htslib/bgzf.h"
+#include "htslib/hts.h"
+#include "htslib/regidx.h"
+
+typedef struct
+{
+    char *regions_fname, *targets_fname;
+    int print_header, header_only;
+}
+args_t;
+
+static void error(const char *format, ...)
+{
+    va_list ap;
+    va_start(ap, format);
+    vfprintf(stderr, format, ap);
+    va_end(ap);
+    exit(EXIT_FAILURE);
+}
+
+#define IS_GFF  (1<<0)
+#define IS_BED  (1<<1)
+#define IS_SAM  (1<<2)
+#define IS_VCF  (1<<3)
+#define IS_BCF  (1<<4)
+#define IS_BAM  (1<<5)
+#define IS_CRAM (1<<6)
+#define IS_TXT  (IS_GFF|IS_BED|IS_SAM|IS_VCF)
+
+int file_type(const char *fname)
+{
+    int l = strlen(fname);
+    int strcasecmp(const char *s1, const char *s2);
+    if (l>=7 && strcasecmp(fname+l-7, ".gff.gz") == 0) return IS_GFF;
+    else if (l>=7 && strcasecmp(fname+l-7, ".bed.gz") == 0) return IS_BED;
+    else if (l>=7 && strcasecmp(fname+l-7, ".sam.gz") == 0) return IS_SAM;
+    else if (l>=7 && strcasecmp(fname+l-7, ".vcf.gz") == 0) return IS_VCF;
+    else if (l>=4 && strcasecmp(fname+l-4, ".bcf") == 0) return IS_BCF;
+    else if (l>=4 && strcasecmp(fname+l-4, ".bam") == 0) return IS_BAM;
+    else if (l>=4 && strcasecmp(fname+l-5, ".cram") == 0) return IS_CRAM;
+
+    htsFile *fp = hts_open(fname,"r");
+    enum htsExactFormat format = fp->format.format;
+    hts_close(fp);
+    if ( format == bcf ) return IS_BCF;
+    if ( format == bam ) return IS_BAM;
+    if ( format == cram ) return IS_CRAM;
+    if ( format == vcf ) return IS_VCF;
+
+    return 0;
+}
+
+static char **parse_regions(char *regions_fname, char **argv, int argc, int *nregs)
+{
+    kstring_t str = {0,0,0};
+    int iseq = 0, ireg = 0;
+    char **regs = NULL;
+    *nregs = argc;
+
+    if ( regions_fname )
+    {
+        // improve me: this is a too heavy machinery for parsing regions...
+
+        regidx_t *idx = regidx_init(regions_fname, NULL, NULL, 0, NULL);
+        if ( !idx ) error("Could not read %s\n", regions_fname);
+
+        (*nregs) += regidx_nregs(idx);
+        regs = (char**) malloc(sizeof(char*)*(*nregs));
+
+        int nseq;
+        char **seqs = regidx_seq_names(idx, &nseq);
+        for (iseq=0; iseq<nseq; iseq++)
+        {
+            regitr_t itr;
+            regidx_overlap(idx, seqs[iseq], 0, UINT32_MAX, &itr);
+            while ( itr.i < itr.n )
+            {
+                str.l = 0;
+                ksprintf(&str, "%s:%d-%d", seqs[iseq], REGITR_START(itr)+1, REGITR_END(itr)+1);
+                regs[ireg++] = strdup(str.s);
+                itr.i++;
+            }
+        }
+        regidx_destroy(idx);
+    }
+    free(str.s);
+
+    if ( !ireg )
+    {
+        if ( argc )
+            regs = (char**) malloc(sizeof(char*)*argc);
+        else
+        {
+            regs = (char**) malloc(sizeof(char*));
+            regs[0] = strdup(".");
+            *nregs = 1;
+        }
+    }
+
+    for (iseq=0; iseq<argc; iseq++) regs[ireg++] = strdup(argv[iseq]);
+    return regs;
+}
+static int query_regions(args_t *args, char *fname, char **regs, int nregs)
+{
+    int i;
+    htsFile *fp = hts_open(fname,"r");
+    if ( !fp ) error("Could not read %s\n", fname);
+    enum htsExactFormat format = hts_get_format(fp)->format;
+
+    regidx_t *reg_idx = NULL;
+    if ( args->targets_fname )
+    {
+        reg_idx = regidx_init(args->targets_fname, NULL, NULL, 0, NULL);
+        if ( !reg_idx ) error("Could not read %s\n", args->targets_fname);
+    }
+
+    if ( format == bcf )
+    {
+        htsFile *out = hts_open("-","w");
+        if ( !out ) error("Could not open stdout\n", fname);
+        hts_idx_t *idx = bcf_index_load(fname);
+        if ( !idx ) error("Could not load .csi index of %s\n", fname);
+        bcf_hdr_t *hdr = bcf_hdr_read(fp);
+        if ( !hdr ) error("Could not read the header: %s\n", fname);
+        if ( args->print_header )
+            bcf_hdr_write(out,hdr);
+        if ( !args->header_only )
+        {
+            bcf1_t *rec = bcf_init();
+            for (i=0; i<nregs; i++)
+            {
+                hts_itr_t *itr = bcf_itr_querys(idx,hdr,regs[i]);
+                while ( bcf_itr_next(fp, itr, rec) >=0 )
+                {
+                    if ( reg_idx && !regidx_overlap(reg_idx, bcf_seqname(hdr,rec),rec->pos,rec->pos+rec->rlen-1, NULL) ) continue; 
+                    bcf_write(out,hdr,rec);
+                }
+                tbx_itr_destroy(itr);
+            }
+            bcf_destroy(rec);
+        }
+        if ( hts_close(out) ) error("hts_close returned non-zero status for stdout\n");
+        bcf_hdr_destroy(hdr);
+        hts_idx_destroy(idx);
+    }
+    else if ( format==vcf || format==sam || format==unknown_format )
+    {
+        tbx_t *tbx = tbx_index_load(fname);
+        if ( !tbx ) error("Could not load .tbi/.csi index of %s\n", fname);
+        kstring_t str = {0,0,0};
+        if ( args->print_header )
+        {
+            while ( hts_getline(fp, KS_SEP_LINE, &str) >= 0 )
+            {
+                if ( !str.l || str.s[0]!=tbx->conf.meta_char ) break;
+                puts(str.s);
+            }
+        }
+        if ( !args->header_only )
+        {
+            int nseq;
+            const char **seq = NULL;
+            if ( reg_idx ) seq = tbx_seqnames(tbx, &nseq);
+            for (i=0; i<nregs; i++)
+            {
+                hts_itr_t *itr = tbx_itr_querys(tbx, regs[i]);
+                if ( !itr ) continue;
+                while (tbx_itr_next(fp, tbx, itr, &str) >= 0)
+                {
+                    if ( reg_idx && !regidx_overlap(reg_idx,seq[itr->curr_tid],itr->curr_beg,itr->curr_end, NULL) ) continue;
+                    puts(str.s);
+                }
+                tbx_itr_destroy(itr);
+            }
+            free(seq);
+        }
+        free(str.s);
+        tbx_destroy(tbx);
+    }
+    else if ( format==bam )
+        error("Please use \"samtools view\" for querying BAM files.\n");
+
+    if ( reg_idx ) regidx_destroy(reg_idx);
+    if ( hts_close(fp) ) error("hts_close returned non-zero status: %s\n", fname);
+
+    for (i=0; i<nregs; i++) free(regs[i]);
+    free(regs);
+    return 0;
+}
+static int query_chroms(char *fname)
+{
+    const char **seq;
+    int i, nseq, ftype = file_type(fname);
+    if ( ftype & IS_TXT || !ftype )
+    {
+        tbx_t *tbx = tbx_index_load(fname);
+        if ( !tbx ) error("Could not load .tbi index of %s\n", fname);
+        seq = tbx_seqnames(tbx, &nseq);
+        for (i=0; i<nseq; i++)
+            printf("%s\n", seq[i]);
+        free(seq);
+        tbx_destroy(tbx);
+    }
+    else if ( ftype==IS_BCF )
+    {
+        htsFile *fp = hts_open(fname,"r");
+        if ( !fp ) error("Could not read %s\n", fname);
+        bcf_hdr_t *hdr = bcf_hdr_read(fp);
+        if ( !hdr ) error("Could not read the header: %s\n", fname);
+        hts_close(fp);
+        hts_idx_t *idx = bcf_index_load(fname);
+        if ( !idx ) error("Could not load .csi index of %s\n", fname);
+        seq = bcf_index_seqnames(idx, hdr, &nseq);
+        for (i=0; i<nseq; i++)
+            printf("%s\n", seq[i]);
+        free(seq);
+        bcf_hdr_destroy(hdr);
+        hts_idx_destroy(idx);
+    }
+    else if ( ftype==IS_BAM )   // todo: BAM
+        error("BAM: todo\n");
+    return 0;
+}
+
+int reheader_file(const char *fname, const char *header, int ftype, tbx_conf_t *conf)
+{
+    if ( ftype & IS_TXT || !ftype )
+    {
+        BGZF *fp = bgzf_open(fname,"r");
+        if ( !fp || bgzf_read_block(fp) != 0 || !fp->block_length ) return -1;
+
+        char *buffer = fp->uncompressed_block;
+        int skip_until = 0;
+
+        // Skip the header: find out the position of the data block
+        if ( buffer[0]==conf->meta_char )
+        {
+            skip_until = 1;
+            while (1)
+            {
+                if ( buffer[skip_until]=='\n' )
+                {
+                    skip_until++;
+                    if ( skip_until>=fp->block_length )
+                    {
+                        if ( bgzf_read_block(fp) != 0 || !fp->block_length ) error("FIXME: No body in the file: %s\n", fname);
+                        skip_until = 0;
+                    }
+                    // The header has finished
+                    if ( buffer[skip_until]!=conf->meta_char ) break;
+                }
+                skip_until++;
+                if ( skip_until>=fp->block_length )
+                {
+                    if (bgzf_read_block(fp) != 0 || !fp->block_length) error("FIXME: No body in the file: %s\n", fname);
+                    skip_until = 0;
+                }
+            }
+        }
+
+        // Output the new header
+        FILE *hdr  = fopen(header,"r");
+        if ( !hdr ) error("%s: %s", header,strerror(errno));
+        const size_t page_size = 32768;
+        char *buf = malloc(page_size);
+        BGZF *bgzf_out = bgzf_open("-", "w");
+        ssize_t nread;
+        while ( (nread=fread(buf,1,page_size-1,hdr))>0 )
+        {
+            if ( nread<page_size-1 && buf[nread-1]!='\n' ) buf[nread++] = '\n';
+            if (bgzf_write(bgzf_out, buf, nread) < 0) error("Error: %d\n",bgzf_out->errcode);
+        }
+        if ( fclose(hdr) ) error("close failed: %s\n", header);
+
+        // Output all remainig data read with the header block
+        if ( fp->block_length - skip_until > 0 )
+        {
+            if (bgzf_write(bgzf_out, buffer+skip_until, fp->block_length-skip_until) < 0) error("Error: %d\n",fp->errcode);
+        }
+        if (bgzf_flush(bgzf_out) < 0) error("Error: %d\n",bgzf_out->errcode);
+
+        while (1)
+        {
+            nread = bgzf_raw_read(fp, buf, page_size);
+            if ( nread<=0 ) break;
+
+            int count = bgzf_raw_write(bgzf_out, buf, nread);
+            if (count != nread) error("Write failed, wrote %d instead of %d bytes.\n", count,(int)nread);
+        }
+        if (bgzf_close(bgzf_out) < 0) error("Error: %d\n",bgzf_out->errcode);
+        if (bgzf_close(fp) < 0) error("Error: %d\n",fp->errcode);
+        free(buf);
+    }
+    else
+        error("todo: reheader BCF, BAM\n");  // BCF is difficult, records contain pointers to the header.
+    return 0;
+}
+
+static int usage(void)
+{
+    fprintf(stderr, "\n");
+    fprintf(stderr, "Version: %s\n", hts_version());
+    fprintf(stderr, "Usage:   tabix [OPTIONS] [FILE] [REGION [...]]\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "Indexing Options:\n");
+    fprintf(stderr, "   -0, --zero-based           coordinates are zero-based\n");
+    fprintf(stderr, "   -b, --begin INT            column number for region start [4]\n");
+    fprintf(stderr, "   -c, --comment CHAR         skip comment lines starting with CHAR [null]\n");
+    fprintf(stderr, "   -C, --csi                  generate CSI index for VCF (default is TBI)\n");
+    fprintf(stderr, "   -e, --end INT              column number for region end (if no end, set INT to -b) [5]\n");
+    fprintf(stderr, "   -f, --force                overwrite existing index without asking\n");
+    fprintf(stderr, "   -m, --min-shift INT        set minimal interval size for CSI indices to 2^INT [14]\n");
+    fprintf(stderr, "   -p, --preset STR           gff, bed, sam, vcf\n");
+    fprintf(stderr, "   -s, --sequence INT         column number for sequence names (suppressed by -p) [1]\n");
+    fprintf(stderr, "   -S, --skip-lines INT       skip first INT lines [0]\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "Querying and other options:\n");
+    fprintf(stderr, "   -h, --print-header         print also the header lines\n");
+    fprintf(stderr, "   -H, --only-header          print only the header lines\n");
+    fprintf(stderr, "   -l, --list-chroms          list chromosome names\n");
+    fprintf(stderr, "   -r, --reheader FILE        replace the header with the content of FILE\n");
+    fprintf(stderr, "   -R, --regions FILE         restrict to regions listed in the file\n");
+    fprintf(stderr, "   -T, --targets FILE         similar to -R but streams rather than index-jumps\n");
+    fprintf(stderr, "\n");
+    return 1;
+}
+
+int main(int argc, char *argv[])
+{
+    int c, min_shift = 0, is_force = 0, list_chroms = 0, do_csi = 0;
+    tbx_conf_t conf = tbx_conf_gff, *conf_ptr = NULL;
+    char *reheader = NULL;
+    args_t args;
+    memset(&args,0,sizeof(args_t));
+
+    static const struct option loptions[] =
+    {
+        {"help", no_argument, NULL, 'h'},
+        {"regions", required_argument, NULL, 'R'},
+        {"targets", required_argument, NULL, 'T'},
+        {"csi", no_argument, NULL, 'C'},
+        {"zero-based", no_argument, NULL, '0'},
+        {"print-header", no_argument, NULL, 'h'},
+        {"only-header", no_argument, NULL, 'H'},
+        {"begin", required_argument, NULL, 'b'},
+        {"comment", required_argument, NULL, 'c'},
+        {"end", required_argument, NULL, 'e'},
+        {"force", no_argument, NULL, 'f'},
+        {"preset", required_argument, NULL, 'p'},
+        {"sequence", required_argument, NULL, 's'},
+        {"skip-lines", required_argument, NULL, 'S'},
+        {"list-chroms", no_argument, NULL, 'l'},
+        {"reheader", required_argument, NULL, 'r'},
+        {"version", no_argument, NULL, 1},
+        {NULL, 0, NULL, 0}
+    };
+
+    char *tmp;
+    while ((c = getopt_long(argc, argv, "hH?0b:c:e:fm:p:s:S:lr:CR:T:", loptions,NULL)) >= 0)
+    {
+        switch (c)
+        {
+            case 'R': args.regions_fname = optarg; break;
+            case 'T': args.targets_fname = optarg; break;
+            case 'C': do_csi = 1; break;
+            case 'r': reheader = optarg; break;
+            case 'h': args.print_header = 1; break;
+            case 'H': args.print_header = 1; args.header_only = 1; break;
+            case 'l': list_chroms = 1; break;
+            case '0': conf.preset |= TBX_UCSC; break;
+            case 'b':
+                conf.bc = strtol(optarg,&tmp,10);
+                if ( *tmp ) error("Could not parse argument: -b %s\n", optarg);
+                break;
+            case 'e':
+                conf.ec = strtol(optarg,&tmp,10);
+                if ( *tmp ) error("Could not parse argument: -e %s\n", optarg);
+                break;
+            case 'c': conf.meta_char = *optarg; break;
+            case 'f': is_force = 1; break;
+            case 'm':
+                min_shift = strtol(optarg,&tmp,10);
+                if ( *tmp ) error("Could not parse argument: -m %s\n", optarg);
+                break;
+            case 'p':
+                      if (strcmp(optarg, "gff") == 0) conf_ptr = &tbx_conf_gff;
+                      else if (strcmp(optarg, "bed") == 0) conf_ptr = &tbx_conf_bed;
+                      else if (strcmp(optarg, "sam") == 0) conf_ptr = &tbx_conf_sam;
+                      else if (strcmp(optarg, "vcf") == 0) conf_ptr = &tbx_conf_vcf;
+                      else if (strcmp(optarg, "bcf") == 0) ;    // bcf is autodetected, preset is not needed
+                      else if (strcmp(optarg, "bam") == 0) ;    // same as bcf
+                      else error("The preset string not recognised: '%s'\n", optarg);
+                      break;
+            case 's':
+                conf.sc = strtol(optarg,&tmp,10);
+                if ( *tmp ) error("Could not parse argument: -s %s\n", optarg);
+                break;
+            case 'S':
+                conf.line_skip = strtol(optarg,&tmp,10);
+                if ( *tmp ) error("Could not parse argument: -S %s\n", optarg);
+                break;
+            case 1:
+                printf(
+"tabix (htslib) %s\n"
+"Copyright (C) 2016 Genome Research Ltd.\n", hts_version());
+                return EXIT_SUCCESS;
+            default: return usage();
+        }
+    }
+
+    if ( optind==argc ) return usage();
+
+    if ( list_chroms )
+        return query_chroms(argv[optind]);
+
+    if ( argc > optind+1 || args.header_only || args.regions_fname || args.targets_fname )
+    {
+        int nregs = 0;
+        char **regs = NULL;
+        if ( !args.header_only )
+            regs = parse_regions(args.regions_fname, argv+optind+1, argc-optind-1, &nregs);
+        return query_regions(&args, argv[optind], regs, nregs);
+    }
+
+    char *fname = argv[optind];
+    int ftype = file_type(fname);
+    if ( !conf_ptr )    // no preset given
+    {
+        if ( ftype==IS_GFF ) conf_ptr = &tbx_conf_gff;
+        else if ( ftype==IS_BED ) conf_ptr = &tbx_conf_bed;
+        else if ( ftype==IS_SAM ) conf_ptr = &tbx_conf_sam;
+        else if ( ftype==IS_VCF )
+        {
+            conf_ptr = &tbx_conf_vcf;
+            if ( !min_shift && do_csi ) min_shift = 14;
+        }
+        else if ( ftype==IS_BCF )
+        {
+            if ( !min_shift ) min_shift = 14;
+        }
+        else if ( ftype==IS_BAM )
+        {
+            if ( !min_shift ) min_shift = 14;
+        }
+    }
+    if ( do_csi )
+    {
+        if ( !min_shift ) min_shift = 14;
+        min_shift *= do_csi;  // positive for CSIv2, negative for CSIv1
+    }
+    if ( min_shift!=0 && !do_csi ) do_csi = 1;
+
+    if ( reheader )
+        return reheader_file(fname, reheader, ftype, conf_ptr);
+
+    if ( conf_ptr )
+        conf = *conf_ptr;
+
+    char *suffix = ".tbi";
+    if ( do_csi ) suffix = ".csi";
+    else if ( ftype==IS_BAM ) suffix = ".bai";
+    else if ( ftype==IS_CRAM ) suffix = ".crai";
+
+    char *idx_fname = calloc(strlen(fname) + 5, 1);
+    strcat(strcpy(idx_fname, fname), suffix);
+
+    struct stat stat_tbi, stat_file;
+    if ( !is_force && stat(idx_fname, &stat_tbi)==0 )
+    {
+        // Before complaining about existing index, check if the VCF file isn't
+        // newer. This is a common source of errors, people tend not to notice
+        // that tabix failed
+        stat(fname, &stat_file);
+        if ( stat_file.st_mtime <= stat_tbi.st_mtime )
+            error("[tabix] the index file exists. Please use '-f' to overwrite.\n");
+    }
+    free(idx_fname);
+
+    if ( ftype==IS_CRAM )
+    {
+        if ( bam_index_build(fname, min_shift)!=0 ) error("bam_index_build failed: %s\n", fname);
+        return 0;
+    }
+    else if ( do_csi )
+    {
+        if ( ftype==IS_BCF )
+        {
+            if ( bcf_index_build(fname, min_shift)!=0 ) error("bcf_index_build failed: %s\n", fname);
+            return 0;
+        }
+        if ( ftype==IS_BAM )
+        {
+            if ( bam_index_build(fname, min_shift)!=0 ) error("bam_index_build failed: %s\n", fname);
+            return 0;
+        }
+        if ( tbx_index_build(fname, min_shift, &conf)!=0 ) error("tbx_index_build failed: %s\n", fname);
+        return 0;
+    }
+    else    // TBI index
+    {
+        if ( tbx_index_build(fname, min_shift, &conf) ) error("tbx_index_build failed: %s\n", fname);
+        return 0;
+    }
+    return 0;
+}
diff --git a/htslib/tbx.c b/htslib/tbx.c
new file mode 100644
index 0000000..7b74ea4
--- /dev/null
+++ b/htslib/tbx.c
@@ -0,0 +1,333 @@
+/*  tbx.c -- tabix API functions.
+
+    Copyright (C) 2009, 2010, 2012-2015 Genome Research Ltd.
+    Copyright (C) 2010-2012 Broad Institute.
+
+    Author: Heng Li <lh3 at sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdlib.h>
+#include <string.h>
+#include <ctype.h>
+#include <stdio.h>
+#include <assert.h>
+#include "htslib/tbx.h"
+#include "htslib/bgzf.h"
+
+#include "htslib/khash.h"
+KHASH_DECLARE(s2i, kh_cstr_t, int64_t)
+
+tbx_conf_t tbx_conf_gff = { 0, 1, 4, 5, '#', 0 };
+tbx_conf_t tbx_conf_bed = { TBX_UCSC, 1, 2, 3, '#', 0 };
+tbx_conf_t tbx_conf_psltbl = { TBX_UCSC, 15, 17, 18, '#', 0 };
+tbx_conf_t tbx_conf_sam = { TBX_SAM, 3, 4, 0, '@', 0 };
+tbx_conf_t tbx_conf_vcf = { TBX_VCF, 1, 2, 0, '#', 0 };
+
+typedef struct {
+    int64_t beg, end;
+    char *ss, *se;
+    int tid;
+} tbx_intv_t;
+
+static inline int get_tid(tbx_t *tbx, const char *ss, int is_add)
+{
+    khint_t k;
+    khash_t(s2i) *d;
+    if (tbx->dict == 0) tbx->dict = kh_init(s2i);
+    d = (khash_t(s2i)*)tbx->dict;
+    if (is_add) {
+        int absent;
+        k = kh_put(s2i, d, ss, &absent);
+        if (absent) {
+            kh_key(d, k) = strdup(ss);
+            kh_val(d, k) = kh_size(d) - 1;
+        }
+    } else k = kh_get(s2i, d, ss);
+    return k == kh_end(d)? -1 : kh_val(d, k);
+}
+
+int tbx_name2id(tbx_t *tbx, const char *ss)
+{
+    return get_tid(tbx, ss, 0);
+}
+
+int tbx_parse1(const tbx_conf_t *conf, int len, char *line, tbx_intv_t *intv)
+{
+    int i, b = 0, id = 1, ncols = 0;
+    char *s;
+    intv->ss = intv->se = 0; intv->beg = intv->end = -1;
+    for (i = 0; i <= len; ++i) {
+        if (line[i] == '\t' || line[i] == 0) {
+            ++ncols;
+            if (id == conf->sc) {
+                intv->ss = line + b; intv->se = line + i;
+            } else if (id == conf->bc) {
+                // here ->beg is 0-based.
+                intv->beg = intv->end = strtol(line + b, &s, 0);
+                if ( s==line+b ) return -1; // expected int
+                if (!(conf->preset&TBX_UCSC)) --intv->beg;
+                else ++intv->end;
+                if (intv->beg < 0) intv->beg = 0;
+                if (intv->end < 1) intv->end = 1;
+            } else {
+                if ((conf->preset&0xffff) == TBX_GENERIC) {
+                    if (id == conf->ec)
+                    {
+                        intv->end = strtol(line + b, &s, 0);
+                        if ( s==line+b ) return -1; // expected int
+                    }
+                } else if ((conf->preset&0xffff) == TBX_SAM) {
+                    if (id == 6) { // CIGAR
+                        int l = 0, op;
+                        char *t;
+                        for (s = line + b; s < line + i;) {
+                            long x = strtol(s, &t, 10);
+                            op = toupper(*t);
+                            if (op == 'M' || op == 'D' || op == 'N') l += x;
+                            s = t + 1;
+                        }
+                        if (l == 0) l = 1;
+                        intv->end = intv->beg + l;
+                    }
+                } else if ((conf->preset&0xffff) == TBX_VCF) {
+                    if (id == 4) {
+                        if (b < i) intv->end = intv->beg + (i - b);
+                    } else if (id == 8) { // look for "END="
+                        int c = line[i];
+                        line[i] = 0;
+                        s = strstr(line + b, "END=");
+                        if (s == line + b) s += 4;
+                        else if (s) {
+                            s = strstr(line + b, ";END=");
+                            if (s) s += 5;
+                        }
+                        if (s) intv->end = strtol(s, &s, 0);
+                        line[i] = c;
+                    }
+                }
+            }
+            b = i + 1;
+            ++id;
+        }
+    }
+    if (intv->ss == 0 || intv->se == 0 || intv->beg < 0 || intv->end < 0) return -1;
+    return 0;
+}
+
+static inline int get_intv(tbx_t *tbx, kstring_t *str, tbx_intv_t *intv, int is_add)
+{
+    if (tbx_parse1(&tbx->conf, str->l, str->s, intv) == 0) {
+        int c = *intv->se;
+        *intv->se = '\0'; intv->tid = get_tid(tbx, intv->ss, is_add); *intv->se = c;
+        return (intv->tid >= 0 && intv->beg >= 0 && intv->end >= 0)? 0 : -1;
+    } else {
+        char *type = NULL;
+        switch (tbx->conf.preset&0xffff)
+        {
+            case TBX_SAM: type = "TBX_SAM"; break;
+            case TBX_VCF: type = "TBX_VCF"; break;
+            case TBX_UCSC: type = "TBX_UCSC"; break;
+            default: type = "TBX_GENERIC"; break;
+        }
+        fprintf(stderr, "[E::%s] failed to parse %s, was wrong -p [type] used?\nThe offending line was: \"%s\"\n", __func__, type, str->s);
+        return -1;
+    }
+}
+
+int tbx_readrec(BGZF *fp, void *tbxv, void *sv, int *tid, int *beg, int *end)
+{
+    tbx_t *tbx = (tbx_t *) tbxv;
+    kstring_t *s = (kstring_t *) sv;
+    int ret;
+    if ((ret = bgzf_getline(fp, '\n', s)) >= 0) {
+        tbx_intv_t intv;
+        get_intv(tbx, s, &intv, 0);
+        *tid = intv.tid; *beg = intv.beg; *end = intv.end;
+    }
+    return ret;
+}
+
+void tbx_set_meta(tbx_t *tbx)
+{
+    int i, l = 0, l_nm;
+    uint32_t x[7];
+    char **name;
+    uint8_t *meta;
+    khint_t k;
+    khash_t(s2i) *d = (khash_t(s2i)*)tbx->dict;
+
+    memcpy(x, &tbx->conf, 24);
+    name = (char**)malloc(sizeof(char*) * kh_size(d));
+    for (k = kh_begin(d), l = 0; k != kh_end(d); ++k) {
+        if (!kh_exist(d, k)) continue;
+        name[kh_val(d, k)] = (char*)kh_key(d, k);
+        l += strlen(kh_key(d, k)) + 1; // +1 to include '\0'
+    }
+    l_nm = x[6] = l;
+    meta = (uint8_t*)malloc(l_nm + 28);
+    if (ed_is_big())
+        for (i = 0; i < 7; ++i)
+            x[i] = ed_swap_4(x[i]);
+    memcpy(meta, x, 28);
+    for (l = 28, i = 0; i < (int)kh_size(d); ++i) {
+        int x = strlen(name[i]) + 1;
+        memcpy(meta + l, name[i], x);
+        l += x;
+    }
+    free(name);
+    hts_idx_set_meta(tbx->idx, l, meta, 0);
+}
+
+tbx_t *tbx_index(BGZF *fp, int min_shift, const tbx_conf_t *conf)
+{
+    tbx_t *tbx;
+    kstring_t str;
+    int ret, first = 0, n_lvls, fmt;
+    int64_t lineno = 0;
+    uint64_t last_off = 0;
+    tbx_intv_t intv;
+
+    str.s = 0; str.l = str.m = 0;
+    tbx = (tbx_t*)calloc(1, sizeof(tbx_t));
+    tbx->conf = *conf;
+    if (min_shift > 0) n_lvls = (TBX_MAX_SHIFT - min_shift + 2) / 3, fmt = HTS_FMT_CSI;
+    else min_shift = 14, n_lvls = 5, fmt = HTS_FMT_TBI;
+    while ((ret = bgzf_getline(fp, '\n', &str)) >= 0) {
+        ++lineno;
+        if (lineno <= tbx->conf.line_skip || str.s[0] == tbx->conf.meta_char) {
+            last_off = bgzf_tell(fp);
+            continue;
+        }
+        if (first == 0) {
+            tbx->idx = hts_idx_init(0, fmt, last_off, min_shift, n_lvls);
+            first = 1;
+        }
+        get_intv(tbx, &str, &intv, 1);
+        ret = hts_idx_push(tbx->idx, intv.tid, intv.beg, intv.end, bgzf_tell(fp), 1);
+        if (ret < 0)
+        {
+            free(str.s);
+            tbx_destroy(tbx);
+            return NULL;
+        }
+    }
+    if ( !tbx->idx ) tbx->idx = hts_idx_init(0, fmt, last_off, min_shift, n_lvls);   // empty file
+    if ( !tbx->dict ) tbx->dict = kh_init(s2i);
+    hts_idx_finish(tbx->idx, bgzf_tell(fp));
+    tbx_set_meta(tbx);
+    free(str.s);
+    return tbx;
+}
+
+void tbx_destroy(tbx_t *tbx)
+{
+    khash_t(s2i) *d = (khash_t(s2i)*)tbx->dict;
+    if (d != NULL)
+    {
+        khint_t k;
+        for (k = kh_begin(d); k != kh_end(d); ++k)
+            if (kh_exist(d, k)) free((char*)kh_key(d, k));
+    }
+    hts_idx_destroy(tbx->idx);
+    kh_destroy(s2i, d);
+    free(tbx);
+}
+
+int tbx_index_build2(const char *fn, const char *fnidx, int min_shift, const tbx_conf_t *conf)
+{
+    tbx_t *tbx;
+    BGZF *fp;
+    int ret;
+    if ( bgzf_is_bgzf(fn)!=1 ) { fprintf(stderr,"Not a BGZF file: %s\n", fn); return -1; }
+    if ((fp = bgzf_open(fn, "r")) == 0) return -1;
+    if ( !fp->is_compressed ) { bgzf_close(fp); return -1; }
+    tbx = tbx_index(fp, min_shift, conf);
+    bgzf_close(fp);
+    if ( !tbx ) return -1;
+    ret = hts_idx_save_as(tbx->idx, fn, fnidx, min_shift > 0? HTS_FMT_CSI : HTS_FMT_TBI);
+    tbx_destroy(tbx);
+    return ret;
+}
+
+int tbx_index_build(const char *fn, int min_shift, const tbx_conf_t *conf)
+{
+    return tbx_index_build2(fn, NULL, min_shift, conf);
+}
+
+tbx_t *tbx_index_load2(const char *fn, const char *fnidx)
+{
+    tbx_t *tbx;
+    uint8_t *meta;
+    char *nm, *p;
+    uint32_t x[7];
+    int l_meta, l_nm;
+    tbx = (tbx_t*)calloc(1, sizeof(tbx_t));
+    tbx->idx = fnidx? hts_idx_load2(fn, fnidx) : hts_idx_load(fn, HTS_FMT_TBI);
+    if ( !tbx->idx )
+    {
+        free(tbx);
+        return NULL;
+    }
+    meta = hts_idx_get_meta(tbx->idx, &l_meta);
+    if ( !meta )
+    {
+        free(tbx);
+        return NULL;
+    }
+    memcpy(x, meta, 28);
+    memcpy(&tbx->conf, x, 24);
+    p = nm = (char*)meta + 28;
+    l_nm = x[6];
+    for (; p - nm < l_nm; p += strlen(p) + 1) get_tid(tbx, p, 1);
+    return tbx;
+}
+
+tbx_t *tbx_index_load(const char *fn)
+{
+    return tbx_index_load2(fn, NULL);
+}
+
+const char **tbx_seqnames(tbx_t *tbx, int *n)
+{
+    khash_t(s2i) *d = (khash_t(s2i)*)tbx->dict;
+    if (d == NULL)
+    {
+        *n = 0;
+        return NULL;
+    }
+    int tid, m = kh_size(d);
+    const char **names = (const char**) calloc(m,sizeof(const char*));
+    khint_t k;
+    for (k=kh_begin(d); k<kh_end(d); k++)
+    {
+        if ( !kh_exist(d,k) ) continue;
+        tid = kh_val(d,k);
+        assert( tid<m );
+        names[tid] = kh_key(d,k);
+    }
+    // sanity check: there should be no gaps
+    for (tid=0; tid<m; tid++)
+        assert(names[tid]);
+    *n = m;
+    return names;
+}
+
diff --git a/htslib/vcf.c b/htslib/vcf.c
new file mode 100644
index 0000000..3602e14
--- /dev/null
+++ b/htslib/vcf.c
@@ -0,0 +1,3483 @@
+/*  vcf.c -- VCF/BCF API functions.
+
+    Copyright (C) 2012, 2013 Broad Institute.
+    Copyright (C) 2012-2016 Genome Research Ltd.
+    Portions copyright (C) 2014 Intel Corporation.
+
+    Author: Heng Li <lh3 at sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <zlib.h>
+#include <stdio.h>
+#include <ctype.h>
+#include <assert.h>
+#include <string.h>
+#include <stdlib.h>
+#include <limits.h>
+#include "htslib/kstring.h"
+#include "htslib/bgzf.h"
+#include "htslib/vcf.h"
+#include "htslib/tbx.h"
+#include "htslib/hfile.h"
+#include "htslib/khash_str2int.h"
+#include "hts_internal.h"
+
+#include "htslib/khash.h"
+KHASH_MAP_INIT_STR(vdict, bcf_idinfo_t)
+typedef khash_t(vdict) vdict_t;
+
+#include "htslib/kseq.h"
+KSTREAM_DECLARE(gzFile, gzread)
+
+uint32_t bcf_float_missing    = 0x7F800001;
+uint32_t bcf_float_vector_end = 0x7F800002;
+uint8_t bcf_type_shift[] = { 0, 0, 1, 2, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 };
+static bcf_idinfo_t bcf_idinfo_def = { .info = { 15, 15, 15 }, .hrec = { NULL, NULL, NULL}, .id = -1 };
+
+static const char *dump_char(char *buffer, char c)
+{
+    switch (c) {
+    case '\n': strcpy(buffer, "\\n"); break;
+    case '\r': strcpy(buffer, "\\r"); break;
+    case '\t': strcpy(buffer, "\\t"); break;
+    case '\'':
+    case '\"':
+    case '\\':
+        sprintf(buffer, "\\%c", c);
+        break;
+    default:
+        if (isprint_c(c)) sprintf(buffer, "%c", c);
+        else sprintf(buffer, "\\x%02X", (unsigned char) c);
+        break;
+    }
+    return buffer;
+}
+
+/*************************
+ *** VCF header parser ***
+ *************************/
+
+int bcf_hdr_add_sample(bcf_hdr_t *h, const char *s)
+{
+    if ( !s ) return 0;
+
+    const char *ss = s;
+    while ( !*ss && isspace(*ss) ) ss++;
+    if ( !*ss )
+    {
+        fprintf(stderr,"[E::%s] Empty sample name: trailing spaces/tabs in the header line?\n", __func__);
+        abort();
+    }
+
+    vdict_t *d = (vdict_t*)h->dict[BCF_DT_SAMPLE];
+    int ret;
+    char *sdup = strdup(s);
+    int k = kh_put(vdict, d, sdup, &ret);
+    if (ret) { // absent
+        kh_val(d, k) = bcf_idinfo_def;
+        kh_val(d, k).id = kh_size(d) - 1;
+    } else {
+        if (hts_verbose >= 2)
+        {
+            fprintf(stderr, "[E::%s] Duplicated sample name '%s'\n", __func__, s);
+            abort();
+        }
+        free(sdup);
+        return -1;
+    }
+    int n = kh_size(d);
+    h->samples = (char**) realloc(h->samples,sizeof(char*)*n);
+    h->samples[n-1] = sdup;
+    h->dirty = 1;
+    return 0;
+}
+
+int bcf_hdr_parse_sample_line(bcf_hdr_t *h, const char *str)
+{
+    int ret = 0;
+    int i = 0;
+    const char *p, *q;
+    // add samples
+    for (p = q = str;; ++q) {
+        if (*q != '\t' && *q != 0 && *q != '\n') continue;
+        if (++i > 9) {
+            char *s = (char*)malloc(q - p + 1);
+            strncpy(s, p, q - p);
+            s[q - p] = 0;
+            if ( bcf_hdr_add_sample(h,s) < 0 ) ret = -1;
+            free(s);
+        }
+        if (*q == 0 || *q == '\n') break;
+        p = q + 1;
+    }
+    bcf_hdr_add_sample(h,NULL);
+    return ret;
+}
+
+int bcf_hdr_sync(bcf_hdr_t *h)
+{
+    int i;
+    for (i = 0; i < 3; i++)
+    {
+        vdict_t *d = (vdict_t*)h->dict[i];
+        khint_t k;
+        if ( h->n[i] < kh_size(d) )
+        {
+            // this should be true only for i=2, BCF_DT_SAMPLE
+            h->n[i] = kh_size(d);
+            h->id[i] = (bcf_idpair_t*) realloc(h->id[i], kh_size(d)*sizeof(bcf_idpair_t));
+        }
+        for (k=kh_begin(d); k<kh_end(d); k++)
+        {
+            if (!kh_exist(d,k)) continue;
+            h->id[i][kh_val(d,k).id].key = kh_key(d,k);
+            h->id[i][kh_val(d,k).id].val = &kh_val(d,k);
+        }
+    }
+    h->dirty = 0;
+    return 0;
+}
+
+void bcf_hrec_destroy(bcf_hrec_t *hrec)
+{
+    free(hrec->key);
+    if ( hrec->value ) free(hrec->value);
+    int i;
+    for (i=0; i<hrec->nkeys; i++)
+    {
+        free(hrec->keys[i]);
+        free(hrec->vals[i]);
+    }
+    free(hrec->keys);
+    free(hrec->vals);
+    free(hrec);
+}
+
+// Copies all fields except IDX.
+bcf_hrec_t *bcf_hrec_dup(bcf_hrec_t *hrec)
+{
+    bcf_hrec_t *out = (bcf_hrec_t*) calloc(1,sizeof(bcf_hrec_t));
+    out->type = hrec->type;
+    if ( hrec->key ) out->key = strdup(hrec->key);
+    if ( hrec->value ) out->value = strdup(hrec->value);
+    out->nkeys = hrec->nkeys;
+    out->keys = (char**) malloc(sizeof(char*)*hrec->nkeys);
+    out->vals = (char**) malloc(sizeof(char*)*hrec->nkeys);
+    int i, j = 0;
+    for (i=0; i<hrec->nkeys; i++)
+    {
+        if ( hrec->keys[i] && !strcmp("IDX",hrec->keys[i]) ) continue;
+        if ( hrec->keys[i] ) out->keys[j] = strdup(hrec->keys[i]);
+        if ( hrec->vals[i] ) out->vals[j] = strdup(hrec->vals[i]);
+        j++;
+    }
+    if ( i!=j ) out->nkeys -= i-j;   // IDX was omitted
+    return out;
+}
+
+void bcf_hrec_debug(FILE *fp, bcf_hrec_t *hrec)
+{
+    fprintf(fp, "key=[%s] value=[%s]", hrec->key, hrec->value?hrec->value:"");
+    int i;
+    for (i=0; i<hrec->nkeys; i++)
+        fprintf(fp, "\t[%s]=[%s]", hrec->keys[i],hrec->vals[i]);
+    fprintf(fp, "\n");
+}
+
+void bcf_header_debug(bcf_hdr_t *hdr)
+{
+    int i, j;
+    for (i=0; i<hdr->nhrec; i++)
+    {
+        if ( !hdr->hrec[i]->value )
+        {
+            fprintf(stderr, "##%s=<", hdr->hrec[i]->key);
+            fprintf(stderr,"%s=%s", hdr->hrec[i]->keys[0], hdr->hrec[i]->vals[0]);
+            for (j=1; j<hdr->hrec[i]->nkeys; j++)
+                fprintf(stderr,",%s=%s", hdr->hrec[i]->keys[j], hdr->hrec[i]->vals[j]);
+            fprintf(stderr,">\n");
+        }
+        else
+            fprintf(stderr,"##%s=%s\n", hdr->hrec[i]->key,hdr->hrec[i]->value);
+    }
+}
+
+void bcf_hrec_add_key(bcf_hrec_t *hrec, const char *str, int len)
+{
+    int n = ++hrec->nkeys;
+    hrec->keys = (char**) realloc(hrec->keys, sizeof(char*)*n);
+    hrec->vals = (char**) realloc(hrec->vals, sizeof(char*)*n);
+    assert( len );
+    hrec->keys[n-1] = (char*) malloc((len+1)*sizeof(char));
+    memcpy(hrec->keys[n-1],str,len);
+    hrec->keys[n-1][len] = 0;
+    hrec->vals[n-1] = NULL;
+}
+
+void bcf_hrec_set_val(bcf_hrec_t *hrec, int i, const char *str, int len, int is_quoted)
+{
+    if ( !str ) { hrec->vals[i] = NULL; return; }
+    if ( hrec->vals[i] ) free(hrec->vals[i]);
+    if ( is_quoted )
+    {
+        hrec->vals[i] = (char*) malloc((len+3)*sizeof(char));
+        hrec->vals[i][0] = '"';
+        memcpy(&hrec->vals[i][1],str,len);
+        hrec->vals[i][len+1] = '"';
+        hrec->vals[i][len+2] = 0;
+    }
+    else
+    {
+        hrec->vals[i] = (char*) malloc((len+1)*sizeof(char));
+        memcpy(hrec->vals[i],str,len);
+        hrec->vals[i][len] = 0;
+    }
+}
+
+void hrec_add_idx(bcf_hrec_t *hrec, int idx)
+{
+    int n = ++hrec->nkeys;
+    hrec->keys = (char**) realloc(hrec->keys, sizeof(char*)*n);
+    hrec->vals = (char**) realloc(hrec->vals, sizeof(char*)*n);
+    hrec->keys[n-1] = strdup("IDX");
+    kstring_t str = {0,0,0};
+    kputw(idx, &str);
+    hrec->vals[n-1] = str.s;
+}
+
+int bcf_hrec_find_key(bcf_hrec_t *hrec, const char *key)
+{
+    int i;
+    for (i=0; i<hrec->nkeys; i++)
+        if ( !strcasecmp(key,hrec->keys[i]) ) return i;
+    return -1;
+}
+
+static inline int is_escaped(const char *min, const char *str)
+{
+    int n = 0;
+    while ( --str>=min && *str=='\\' ) n++;
+    return n%2;
+}
+
+bcf_hrec_t *bcf_hdr_parse_line(const bcf_hdr_t *h, const char *line, int *len)
+{
+    const char *p = line;
+    if (p[0] != '#' || p[1] != '#') { *len = 0; return NULL; }
+    p += 2;
+
+    const char *q = p;
+    while ( *q && *q!='=' ) q++;
+    int n = q-p;
+    if ( *q!='=' || !n ) { *len = q-line+1; return NULL; } // wrong format
+
+    bcf_hrec_t *hrec = (bcf_hrec_t*) calloc(1,sizeof(bcf_hrec_t));
+    hrec->key = (char*) malloc(sizeof(char)*(n+1));
+    memcpy(hrec->key,p,n);
+    hrec->key[n] = 0;
+
+    p = ++q;
+    if ( *p!='<' ) // generic field, e.g. ##samtoolsVersion=0.1.18-r579
+    {
+        while ( *q && *q!='\n' ) q++;
+        hrec->value = (char*) malloc((q-p+1)*sizeof(char));
+        memcpy(hrec->value, p, q-p);
+        hrec->value[q-p] = 0;
+        *len = q-line+1;
+        return hrec;
+    }
+
+    // structured line, e.g.
+    // ##INFO=<ID=PV1,Number=1,Type=Float,Description="P-value for baseQ bias">
+    // ##PEDIGREE=<Name_0=G0-ID,Name_1=G1-ID,Name_3=GN-ID>
+    int nopen = 1;
+    while ( *q && *q!='\n' && nopen>0 )
+    {
+        p = ++q;
+        while ( *q && *q==' ' ) { p++; q++; }
+        // ^[A-Za-z_][0-9A-Za-z_.]*$
+        if (p==q && *q && (isalpha(*q) || *q=='_'))
+        {
+            q++;
+            while ( *q && (isalnum(*q) || *q=='_' || *q=='.') ) q++;
+        }
+        n = q-p;
+        int m = 0;
+        while ( *q && *q==' ' ) { q++; m++; }
+        if ( *q!='=' || !n )
+        {
+            // wrong format
+            while ( *q && *q!='\n' ) q++;
+            kstring_t tmp = {0,0,0};
+            kputsn(line,q-line,&tmp);
+            fprintf(stderr,"Could not parse the header line: \"%s\"\n", tmp.s);
+            free(tmp.s);
+            *len = q-line+1;
+            bcf_hrec_destroy(hrec);
+            return NULL;
+        }
+        bcf_hrec_add_key(hrec, p, q-p-m);
+        p = ++q;
+        while ( *q && *q==' ' ) { p++; q++; }
+        int quoted = *p=='"' ? 1 : 0;
+        if ( quoted ) p++, q++;
+        while ( *q && *q != '\n' )
+        {
+            if ( quoted ) { if ( *q=='"' && !is_escaped(p,q) ) break; }
+            else
+            {
+                if ( *q=='<' ) nopen++;
+                if ( *q=='>' ) nopen--;
+                if ( !nopen ) break;
+                if ( *q==',' && nopen==1 ) break;
+            }
+            q++;
+        }
+        const char *r = q;
+        while ( r > p && r[-1] == ' ' ) r--;
+        bcf_hrec_set_val(hrec, hrec->nkeys-1, p, r-p, quoted);
+        if ( quoted && *q=='"' ) q++;
+        if ( *q=='>' ) { nopen--; q++; }
+    }
+
+    // Skip trailing spaces
+    while ( *q && *q==' ' ) { q++; }
+
+    *len = q-line+1;
+    return hrec;
+}
+
+static int bcf_hdr_set_idx(bcf_hdr_t *hdr, int dict_type, const char *tag, bcf_idinfo_t *idinfo)
+{
+    // If available, preserve existing IDX
+    if ( idinfo->id==-1 )
+        idinfo->id = hdr->n[dict_type]++;
+    else if ( idinfo->id < hdr->n[dict_type] && hdr->id[dict_type][idinfo->id].key )
+    {
+        fprintf(stderr,"[%s:%d %s] Conflicting IDX=%d lines in the header dictionary, the new tag is %s\n", __FILE__,__LINE__,__FUNCTION__, idinfo->id, tag);
+        exit(1);
+    }
+
+    if ( idinfo->id >= hdr->n[dict_type] ) hdr->n[dict_type] = idinfo->id+1;
+    hts_expand0(bcf_idpair_t,hdr->n[dict_type],hdr->m[dict_type],hdr->id[dict_type]);
+
+    // NB: the next kh_put call can invalidate the idinfo pointer, therefore
+    // we leave it unassigned here. It myst be set explicitly in bcf_hdr_sync.
+    hdr->id[dict_type][idinfo->id].key = tag;
+
+    return 0;
+}
+
+// returns: 1 when hdr needs to be synced, 0 otherwise
+int bcf_hdr_register_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec)
+{
+    // contig
+    int i,j, ret;
+    khint_t k;
+    char *str;
+    if ( !strcmp(hrec->key, "contig") )
+    {
+        hrec->type = BCF_HL_CTG;
+
+        // Get the contig ID ($str) and length ($j)
+        i = bcf_hrec_find_key(hrec,"length");
+        if ( i<0 ) j = 0;
+        else if ( sscanf(hrec->vals[i],"%d",&j)!=1 ) return 0;
+
+        i = bcf_hrec_find_key(hrec,"ID");
+        if ( i<0 ) return 0;
+        str = strdup(hrec->vals[i]);
+
+        // Register in the dictionary
+        vdict_t *d = (vdict_t*)hdr->dict[BCF_DT_CTG];
+        khint_t k = kh_get(vdict, d, str);
+        if ( k != kh_end(d) ) { free(str); return 0; }    // already present
+        k = kh_put(vdict, d, str, &ret);
+
+        int idx = bcf_hrec_find_key(hrec,"IDX");
+        if ( idx!=-1 )
+        {
+            char *tmp = hrec->vals[idx];
+            idx = strtol(hrec->vals[idx], &tmp, 10);
+            if ( *tmp || idx < 0 )
+            {
+                fprintf(stderr,"[%s:%d %s] Error parsing the IDX tag, skipping.\n", __FILE__,__LINE__,__FUNCTION__);
+                return 0;
+            }
+        }
+
+        kh_val(d, k) = bcf_idinfo_def;
+        kh_val(d, k).id = idx;
+        kh_val(d, k).info[0] = j;
+        kh_val(d, k).hrec[0] = hrec;
+        bcf_hdr_set_idx(hdr, BCF_DT_CTG, kh_key(d,k), &kh_val(d,k));
+        if ( idx==-1 ) hrec_add_idx(hrec, kh_val(d,k).id);
+
+        return 1;
+    }
+
+    if ( !strcmp(hrec->key, "INFO") ) hrec->type = BCF_HL_INFO;
+    else if ( !strcmp(hrec->key, "FILTER") ) hrec->type = BCF_HL_FLT;
+    else if ( !strcmp(hrec->key, "FORMAT") ) hrec->type = BCF_HL_FMT;
+    else if ( hrec->nkeys>0 ) { hrec->type = BCF_HL_STR; return 1; }
+    else return 0;
+
+    // INFO/FILTER/FORMAT
+    char *id = NULL;
+    int type = -1, num = -1, var = -1, idx = -1;
+    for (i=0; i<hrec->nkeys; i++)
+    {
+        if ( !strcmp(hrec->keys[i], "ID") ) id = hrec->vals[i];
+        else if ( !strcmp(hrec->keys[i], "IDX") )
+        {
+            char *tmp = hrec->vals[i];
+            idx = strtol(hrec->vals[i], &tmp, 10);
+            if ( *tmp || idx < 0 )
+            {
+                fprintf(stderr,"[%s:%d %s] Error parsing the IDX tag, skipping.\n", __FILE__,__LINE__,__FUNCTION__);
+                return 0;
+            }
+        }
+        else if ( !strcmp(hrec->keys[i], "Type") )
+        {
+            if ( !strcmp(hrec->vals[i], "Integer") ) type = BCF_HT_INT;
+            else if ( !strcmp(hrec->vals[i], "Float") ) type = BCF_HT_REAL;
+            else if ( !strcmp(hrec->vals[i], "String") ) type = BCF_HT_STR;
+            else if ( !strcmp(hrec->vals[i], "Character") ) type = BCF_HT_STR;
+            else if ( !strcmp(hrec->vals[i], "Flag") ) type = BCF_HT_FLAG;
+            else
+            {
+                if (hts_verbose >= 2) fprintf(stderr, "[E::%s] The type \"%s\" is not supported, assuming \"String\"\n", __func__, hrec->vals[i]);
+                type = BCF_HT_STR;
+            }
+        }
+        else if ( !strcmp(hrec->keys[i], "Number") )
+        {
+            if ( !strcmp(hrec->vals[i],"A") ) var = BCF_VL_A;
+            else if ( !strcmp(hrec->vals[i],"R") ) var = BCF_VL_R;
+            else if ( !strcmp(hrec->vals[i],"G") ) var = BCF_VL_G;
+            else if ( !strcmp(hrec->vals[i],".") ) var = BCF_VL_VAR;
+            else
+            {
+                sscanf(hrec->vals[i],"%d",&num);
+                var = BCF_VL_FIXED;
+            }
+            if (var != BCF_VL_FIXED) num = 0xfffff;
+        }
+    }
+    uint32_t info = (uint32_t)num<<12 | var<<8 | type<<4 | hrec->type;
+
+    if ( !id ) return 0;
+    str = strdup(id);
+
+    vdict_t *d = (vdict_t*)hdr->dict[BCF_DT_ID];
+    k = kh_get(vdict, d, str);
+    if ( k != kh_end(d) ) 
+    {
+        // already present
+        free(str);
+        if ( kh_val(d, k).hrec[info&0xf] ) return 0;
+        kh_val(d, k).info[info&0xf] = info;
+        kh_val(d, k).hrec[info&0xf] = hrec;
+        if ( idx==-1 ) hrec_add_idx(hrec, kh_val(d, k).id);
+        return 1;
+    }
+    k = kh_put(vdict, d, str, &ret);
+    kh_val(d, k) = bcf_idinfo_def;
+    kh_val(d, k).info[info&0xf] = info;
+    kh_val(d, k).hrec[info&0xf] = hrec;
+    kh_val(d, k).id = idx;
+    bcf_hdr_set_idx(hdr, BCF_DT_ID, kh_key(d,k), &kh_val(d,k));
+    if ( idx==-1 ) hrec_add_idx(hrec, kh_val(d,k).id);
+
+    return 1;
+}
+
+int bcf_hdr_add_hrec(bcf_hdr_t *hdr, bcf_hrec_t *hrec)
+{
+    if ( !hrec ) return 0;
+
+    hrec->type = BCF_HL_GEN;
+    if ( !bcf_hdr_register_hrec(hdr,hrec) )
+    {
+        // If one of the hashed field, then it is already present
+        if ( hrec->type != BCF_HL_GEN )
+        {
+            bcf_hrec_destroy(hrec);
+            return 0;
+        }
+
+        // Is one of the generic fields and already present?
+        int i;
+        for (i=0; i<hdr->nhrec; i++)
+        {
+            if ( hdr->hrec[i]->type!=BCF_HL_GEN ) continue;
+            if ( !strcmp(hdr->hrec[i]->key,hrec->key) && !strcmp(hrec->key,"fileformat") ) break;
+            if ( !strcmp(hdr->hrec[i]->key,hrec->key) && !strcmp(hdr->hrec[i]->value,hrec->value) ) break;
+        }
+        if ( i<hdr->nhrec )
+        {
+            bcf_hrec_destroy(hrec);
+            return 0;
+        }
+    }
+
+    // New record, needs to be added
+    int n = ++hdr->nhrec;
+    hdr->hrec = (bcf_hrec_t**) realloc(hdr->hrec, n*sizeof(bcf_hrec_t*));
+    hdr->hrec[n-1] = hrec;
+    hdr->dirty = 1;
+
+    return hrec->type==BCF_HL_GEN ? 0 : 1;
+}
+
+/*
+ *  Note that while querying of FLT,INFO,FMT,CTG lines is fast (the keys are hashed),
+ *  the STR,GEN lines are searched for linearly in a linked list of all header lines.
+ *  This may become a problem for VCFs with huge headers, we might need to build a
+ *  dictionary for these lines as well.
+ */
+bcf_hrec_t *bcf_hdr_get_hrec(const bcf_hdr_t *hdr, int type, const char *key, const char *value, const char *str_class)
+{
+    int i;
+    if ( type==BCF_HL_GEN )
+    {
+        for (i=0; i<hdr->nhrec; i++)
+        {
+            if ( hdr->hrec[i]->type!=type ) continue;
+            if ( strcmp(hdr->hrec[i]->key,key) ) continue;
+            if ( !value || !strcmp(hdr->hrec[i]->value,value) ) return hdr->hrec[i];
+        }
+        return NULL;
+    }
+    else if ( type==BCF_HL_STR )
+    {
+        for (i=0; i<hdr->nhrec; i++)
+        {
+            if ( hdr->hrec[i]->type!=type ) continue;
+            if ( strcmp(hdr->hrec[i]->key,str_class) ) continue;
+            int j = bcf_hrec_find_key(hdr->hrec[i],key);
+            if ( j>=0 && !strcmp(hdr->hrec[i]->vals[j],value) ) return hdr->hrec[i];
+        }
+        return NULL;
+    }
+    vdict_t *d = type==BCF_HL_CTG ? (vdict_t*)hdr->dict[BCF_DT_CTG] : (vdict_t*)hdr->dict[BCF_DT_ID];
+    khint_t k = kh_get(vdict, d, value);
+    if ( k == kh_end(d) ) return NULL;
+    return kh_val(d, k).hrec[type==BCF_HL_CTG?0:type];
+}
+
+void bcf_hdr_check_sanity(bcf_hdr_t *hdr)
+{
+    static int PL_warned = 0, GL_warned = 0;
+
+    if ( !PL_warned )
+    {
+        int id = bcf_hdr_id2int(hdr, BCF_DT_ID, "PL");
+        if ( bcf_hdr_idinfo_exists(hdr,BCF_HL_FMT,id) && bcf_hdr_id2length(hdr,BCF_HL_FMT,id)!=BCF_VL_G )
+        {
+            if (hts_verbose >= 2) fprintf(stderr,"[W::%s] PL should be declared as Number=G\n", __func__);
+            PL_warned = 1;
+        }
+    }
+    if ( !GL_warned )
+    {
+        int id = bcf_hdr_id2int(hdr, BCF_DT_ID, "GL");
+        if ( bcf_hdr_idinfo_exists(hdr,BCF_HL_FMT,id) && bcf_hdr_id2length(hdr,BCF_HL_FMT,id)!=BCF_VL_G )
+        {
+            if (hts_verbose >= 2) fprintf(stderr,"[W::%s] GL should be declared as Number=G\n", __func__);
+            GL_warned = 1;
+        }
+    }
+}
+
+int bcf_hdr_parse(bcf_hdr_t *hdr, char *htxt)
+{
+    int len, needs_sync = 0;
+    char *p = htxt;
+
+    // Check sanity: "fileformat" string must come as first
+    bcf_hrec_t *hrec = bcf_hdr_parse_line(hdr,p,&len);
+    if ( !hrec || !hrec->key || strcasecmp(hrec->key,"fileformat") )
+        fprintf(stderr, "[W::%s] The first line should be ##fileformat; is the VCF/BCF header broken?\n", __func__);
+    needs_sync += bcf_hdr_add_hrec(hdr, hrec);
+
+    // The filter PASS must appear first in the dictionary
+    hrec = bcf_hdr_parse_line(hdr,"##FILTER=<ID=PASS,Description=\"All filters passed\">",&len);
+    needs_sync += bcf_hdr_add_hrec(hdr, hrec);
+
+    // Parse the whole header
+    while ( (hrec=bcf_hdr_parse_line(hdr,p,&len)) )
+    {
+        needs_sync += bcf_hdr_add_hrec(hdr, hrec);
+        p += len;
+    }
+    int ret = bcf_hdr_parse_sample_line(hdr,p);
+    bcf_hdr_sync(hdr);
+    bcf_hdr_check_sanity(hdr);
+    return ret;
+}
+
+int bcf_hdr_append(bcf_hdr_t *hdr, const char *line)
+{
+    int len;
+    bcf_hrec_t *hrec = bcf_hdr_parse_line(hdr, (char*) line, &len);
+    if ( !hrec ) return -1;
+    bcf_hdr_add_hrec(hdr, hrec);
+    return 0;
+}
+
+void bcf_hdr_remove(bcf_hdr_t *hdr, int type, const char *key)
+{
+    int i = 0;
+    bcf_hrec_t *hrec;
+    if ( !key )
+    {
+        while ( i<hdr->nhrec )
+        {
+            if ( hdr->hrec[i]->type!=type ) { i++; continue; }
+            hrec = hdr->hrec[i];
+
+            if ( type==BCF_HL_FLT || type==BCF_HL_INFO || type==BCF_HL_FMT || type== BCF_HL_CTG )
+            {
+                int j = bcf_hrec_find_key(hdr->hrec[i], "ID");
+                if ( j>0 )
+                {
+                    vdict_t *d = type==BCF_HL_CTG ? (vdict_t*)hdr->dict[BCF_DT_CTG] : (vdict_t*)hdr->dict[BCF_DT_ID];
+                    khint_t k = kh_get(vdict, d, hdr->hrec[i]->vals[j]);
+                    kh_val(d, k).hrec[type==BCF_HL_CTG?0:type] = NULL;
+                }
+            }
+
+            hdr->dirty = 1;
+            hdr->nhrec--;
+            if ( i < hdr->nhrec )
+                memmove(&hdr->hrec[i],&hdr->hrec[i+1],(hdr->nhrec-i)*sizeof(bcf_hrec_t*));
+            bcf_hrec_destroy(hrec);
+        }
+        return;
+    }
+    while (1)
+    {
+        if ( type==BCF_HL_FLT || type==BCF_HL_INFO || type==BCF_HL_FMT || type== BCF_HL_CTG )
+        {
+            hrec = bcf_hdr_get_hrec(hdr, type, "ID", key, NULL);
+            if ( !hrec ) return;
+
+            for (i=0; i<hdr->nhrec; i++)
+                if ( hdr->hrec[i]==hrec ) break;
+            assert( i<hdr->nhrec );
+
+            vdict_t *d = type==BCF_HL_CTG ? (vdict_t*)hdr->dict[BCF_DT_CTG] : (vdict_t*)hdr->dict[BCF_DT_ID];
+            khint_t k = kh_get(vdict, d, key);
+            kh_val(d, k).hrec[type==BCF_HL_CTG?0:type] = NULL;
+        }
+        else
+        {
+            for (i=0; i<hdr->nhrec; i++)
+            {
+                if ( hdr->hrec[i]->type!=type ) continue;
+                if ( type==BCF_HL_GEN )
+                {
+                    if ( !strcmp(hdr->hrec[i]->key,key) ) break;
+                }
+                else
+                {
+                    // not all structured lines have ID, we could be more sophisticated as in bcf_hdr_get_hrec()
+                    int j = bcf_hrec_find_key(hdr->hrec[i], "ID");
+                    if ( j>=0 && !strcmp(hdr->hrec[i]->vals[j],key) ) break;
+                }
+            }
+            if ( i==hdr->nhrec ) return;
+            hrec = hdr->hrec[i];
+        }
+
+        hdr->nhrec--;
+        if ( i < hdr->nhrec )
+            memmove(&hdr->hrec[i],&hdr->hrec[i+1],(hdr->nhrec-i)*sizeof(bcf_hrec_t*));
+        bcf_hrec_destroy(hrec);
+        hdr->dirty = 1;
+    }
+}
+
+int bcf_hdr_printf(bcf_hdr_t *hdr, const char *fmt, ...)
+{
+    va_list ap;
+    va_start(ap, fmt);
+    int n = vsnprintf(NULL, 0, fmt, ap) + 2;
+    va_end(ap);
+
+    char *line = (char*)malloc(n);
+    va_start(ap, fmt);
+    vsnprintf(line, n, fmt, ap);
+    va_end(ap);
+
+    int ret = bcf_hdr_append(hdr, line);
+
+    free(line);
+    return ret;
+}
+
+
+/**********************
+ *** BCF header I/O ***
+ **********************/
+
+const char *bcf_hdr_get_version(const bcf_hdr_t *hdr)
+{
+    bcf_hrec_t *hrec = bcf_hdr_get_hrec(hdr, BCF_HL_GEN, "fileformat", NULL, NULL);
+    if ( !hrec )
+    {
+        fprintf(stderr,"No version string found, assuming VCFv4.2\n");
+        return "VCFv4.2";
+    }
+    return hrec->value;
+}
+
+void bcf_hdr_set_version(bcf_hdr_t *hdr, const char *version)
+{
+    bcf_hrec_t *hrec = bcf_hdr_get_hrec(hdr, BCF_HL_GEN, "fileformat", NULL, NULL);
+    if ( !hrec )
+    {
+        int len;
+        kstring_t str = {0,0,0};
+        ksprintf(&str,"##fileformat=%s", version);
+        hrec = bcf_hdr_parse_line(hdr, str.s, &len);
+        free(str.s);
+    }
+    else
+    {
+        free(hrec->value);
+        hrec->value = strdup(version);
+    }
+    hdr->dirty = 1;
+}
+
+bcf_hdr_t *bcf_hdr_init(const char *mode)
+{
+    int i;
+    bcf_hdr_t *h;
+    h = (bcf_hdr_t*)calloc(1, sizeof(bcf_hdr_t));
+    if (!h) return NULL;
+    for (i = 0; i < 3; ++i)
+        if ((h->dict[i] = kh_init(vdict)) == NULL) goto fail;
+    if ( strchr(mode,'w') )
+    {
+        bcf_hdr_append(h, "##fileformat=VCFv4.2");
+        // The filter PASS must appear first in the dictionary
+        bcf_hdr_append(h, "##FILTER=<ID=PASS,Description=\"All filters passed\">");
+    }
+    return h;
+
+ fail:
+    for (i = 0; i < 3; ++i)
+        kh_destroy(vdict, h->dict[i]);
+    free(h);
+    return NULL;
+}
+
+void bcf_hdr_destroy(bcf_hdr_t *h)
+{
+    int i;
+    khint_t k;
+    for (i = 0; i < 3; ++i) {
+        vdict_t *d = (vdict_t*)h->dict[i];
+        if (d == 0) continue;
+        for (k = kh_begin(d); k != kh_end(d); ++k)
+            if (kh_exist(d, k)) free((char*)kh_key(d, k));
+        kh_destroy(vdict, d);
+        free(h->id[i]);
+    }
+    for (i=0; i<h->nhrec; i++)
+        bcf_hrec_destroy(h->hrec[i]);
+    if (h->nhrec) free(h->hrec);
+    if (h->samples) free(h->samples);
+    free(h->keep_samples);
+    free(h->transl[0]); free(h->transl[1]);
+    free(h->mem.s);
+    free(h);
+}
+
+bcf_hdr_t *bcf_hdr_read(htsFile *hfp)
+{
+    if (hfp->format.format == vcf)
+        return vcf_hdr_read(hfp);
+
+    BGZF *fp = hfp->fp.bgzf;
+    uint8_t magic[5];
+    bcf_hdr_t *h;
+    h = bcf_hdr_init("r");
+    if (!h) {
+        fprintf(stderr, "[E::%s] failed to allocate bcf header\n", __func__);
+        return NULL;
+    }
+    if (bgzf_read(fp, magic, 5) != 5)
+    {
+        fprintf(stderr,"[%s:%d %s] Failed to read the header (reading BCF in text mode?)\n", __FILE__,__LINE__,__FUNCTION__);
+        bcf_hdr_destroy(h);
+        return NULL;
+    }
+    if (strncmp((char*)magic, "BCF\2\2", 5) != 0)
+    {
+        if (!strncmp((char*)magic, "BCF", 3))
+            fprintf(stderr,"[%s:%d %s] invalid BCF2 magic string: only BCFv2.2 is supported.\n", __FILE__,__LINE__,__FUNCTION__);
+        else if (hts_verbose >= 2)
+            fprintf(stderr, "[E::%s] invalid BCF2 magic string\n", __func__);
+        bcf_hdr_destroy(h);
+        return NULL;
+    }
+    int hlen;
+    char *htxt = NULL;
+    if (bgzf_read(fp, &hlen, 4) != 4) goto fail;
+    htxt = (char*)malloc(hlen);
+    if (!htxt) goto fail;
+    if (bgzf_read(fp, htxt, hlen) != hlen) goto fail;
+    bcf_hdr_parse(h, htxt);  // FIXME: Does this return anything meaningful?
+    free(htxt);
+    return h;
+ fail:
+    if (hts_verbose >= 2) {
+        fprintf(stderr, "[E::%s] failed to read BCF header\n", __func__);
+    }
+    free(htxt);
+    bcf_hdr_destroy(h);
+    return NULL;
+}
+
+int bcf_hdr_write(htsFile *hfp, bcf_hdr_t *h)
+{
+    if ( h->dirty ) bcf_hdr_sync(h);
+    if (hfp->format.format == vcf || hfp->format.format == text_format)
+        return vcf_hdr_write(hfp, h);
+
+    int hlen;
+    char *htxt = bcf_hdr_fmt_text(h, 1, &hlen);
+    hlen++; // include the \0 byte
+
+    BGZF *fp = hfp->fp.bgzf;
+    if ( bgzf_write(fp, "BCF\2\2", 5) !=5 ) return -1;
+    if ( bgzf_write(fp, &hlen, 4) !=4 ) return -1;
+    if ( bgzf_write(fp, htxt, hlen) != hlen ) return -1;
+
+    free(htxt);
+    return 0;
+}
+
+/********************
+ *** BCF site I/O ***
+ ********************/
+
+bcf1_t *bcf_init()
+{
+    bcf1_t *v;
+    v = (bcf1_t*)calloc(1, sizeof(bcf1_t));
+    return v;
+}
+
+void bcf_clear(bcf1_t *v)
+{
+    int i;
+    for (i=0; i<v->d.m_info; i++)
+    {
+        if ( v->d.info[i].vptr_free )
+        {
+            free(v->d.info[i].vptr - v->d.info[i].vptr_off);
+            v->d.info[i].vptr_free = 0;
+        }
+    }
+    for (i=0; i<v->d.m_fmt; i++)
+    {
+        if ( v->d.fmt[i].p_free )
+        {
+            free(v->d.fmt[i].p - v->d.fmt[i].p_off);
+            v->d.fmt[i].p_free = 0;
+        }
+    }
+    v->rid = v->pos = v->rlen = v->unpacked = 0;
+    bcf_float_set_missing(v->qual);
+    v->n_info = v->n_allele = v->n_fmt = v->n_sample = 0;
+    v->shared.l = v->indiv.l = 0;
+    v->d.var_type = -1;
+    v->d.shared_dirty = 0;
+    v->d.indiv_dirty  = 0;
+    v->d.n_flt = 0;
+    v->errcode = 0;
+    if (v->d.m_als) v->d.als[0] = 0;
+    if (v->d.m_id) v->d.id[0] = 0;
+}
+
+void bcf_empty(bcf1_t *v)
+{
+    bcf_clear1(v);
+    free(v->d.id);
+    free(v->d.als);
+    free(v->d.allele); free(v->d.flt); free(v->d.info); free(v->d.fmt);
+    if (v->d.var ) free(v->d.var);
+    free(v->shared.s); free(v->indiv.s);
+}
+
+void bcf_destroy(bcf1_t *v)
+{
+    bcf_empty1(v);
+    free(v);
+}
+
+static inline int bcf_read1_core(BGZF *fp, bcf1_t *v)
+{
+    uint32_t x[8];
+    int ret;
+    if ((ret = bgzf_read(fp, x, 32)) != 32) {
+        if (ret == 0) return -1;
+        return -2;
+    }
+    bcf_clear1(v);
+    x[0] -= 24; // to exclude six 32-bit integers
+    ks_resize(&v->shared, x[0]);
+    ks_resize(&v->indiv, x[1]);
+    memcpy(v, x + 2, 16);
+    v->n_allele = x[6]>>16; v->n_info = x[6]&0xffff;
+    v->n_fmt = x[7]>>24; v->n_sample = x[7]&0xffffff;
+    v->shared.l = x[0], v->indiv.l = x[1];
+    // silent fix of broken BCFs produced by earlier versions of bcf_subset, prior to and including bd6ed8b4
+    if ( (!v->indiv.l || !v->n_sample) && v->n_fmt ) v->n_fmt = 0;
+
+    if (bgzf_read(fp, v->shared.s, v->shared.l) != v->shared.l) return -1;
+    if (bgzf_read(fp, v->indiv.s, v->indiv.l) != v->indiv.l) return -1;
+    return 0;
+}
+
+#define bit_array_size(n) ((n)/8+1)
+#define bit_array_set(a,i)   ((a)[(i)/8] |=   1 << ((i)%8))
+#define bit_array_clear(a,i) ((a)[(i)/8] &= ~(1 << ((i)%8)))
+#define bit_array_test(a,i)  ((a)[(i)/8] &   (1 << ((i)%8)))
+
+static inline uint8_t *bcf_unpack_fmt_core1(uint8_t *ptr, int n_sample, bcf_fmt_t *fmt);
+int bcf_subset_format(const bcf_hdr_t *hdr, bcf1_t *rec)
+{
+    if ( !hdr->keep_samples ) return 0;
+    if ( !bcf_hdr_nsamples(hdr) )
+    {
+        rec->indiv.l = rec->n_sample = 0;
+        return 0;
+    }
+
+    int i, j;
+    uint8_t *ptr = (uint8_t*)rec->indiv.s, *dst = NULL, *src;
+    bcf_dec_t *dec = &rec->d;
+    hts_expand(bcf_fmt_t, rec->n_fmt, dec->m_fmt, dec->fmt);
+    for (i=0; i<dec->m_fmt; ++i) dec->fmt[i].p_free = 0;
+
+    for (i=0; i<rec->n_fmt; i++)
+    {
+        ptr = bcf_unpack_fmt_core1(ptr, rec->n_sample, &dec->fmt[i]);
+        src = dec->fmt[i].p - dec->fmt[i].size;
+        if ( dst )
+        {
+            memmove(dec->fmt[i-1].p + dec->fmt[i-1].p_len, dec->fmt[i].p - dec->fmt[i].p_off, dec->fmt[i].p_off);
+            dec->fmt[i].p = dec->fmt[i-1].p + dec->fmt[i-1].p_len + dec->fmt[i].p_off;
+        }
+        dst = dec->fmt[i].p;
+        for (j=0; j<hdr->nsamples_ori; j++)
+        {
+            src += dec->fmt[i].size;
+            if ( !bit_array_test(hdr->keep_samples,j) ) continue;
+            memmove(dst, src, dec->fmt[i].size);
+            dst += dec->fmt[i].size;
+        }
+        rec->indiv.l -= dec->fmt[i].p_len - (dst - dec->fmt[i].p);
+        dec->fmt[i].p_len = dst - dec->fmt[i].p;
+    }
+    rec->unpacked |= BCF_UN_FMT;
+
+    rec->n_sample = bcf_hdr_nsamples(hdr);
+    return 0;
+}
+
+int bcf_read(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v)
+{
+    if (fp->format.format == vcf) return vcf_read(fp,h,v);
+    int ret = bcf_read1_core(fp->fp.bgzf, v);
+    if ( ret!=0 || !h->keep_samples ) return ret;
+    return bcf_subset_format(h,v);
+}
+
+int bcf_readrec(BGZF *fp, void *null, void *vv, int *tid, int *beg, int *end)
+{
+    bcf1_t *v = (bcf1_t *) vv;
+    int ret;
+    if ((ret = bcf_read1_core(fp, v)) >= 0)
+        *tid = v->rid, *beg = v->pos, *end = v->pos + v->rlen;
+    return ret;
+}
+
+static inline void bcf1_sync_id(bcf1_t *line, kstring_t *str)
+{
+    // single typed string
+    if ( line->d.id && strcmp(line->d.id, ".") ) bcf_enc_vchar(str, strlen(line->d.id), line->d.id);
+    else bcf_enc_size(str, 0, BCF_BT_CHAR);
+}
+static inline void bcf1_sync_alleles(bcf1_t *line, kstring_t *str)
+{
+    // list of typed strings
+    int i;
+    for (i=0; i<line->n_allele; i++)
+        bcf_enc_vchar(str, strlen(line->d.allele[i]), line->d.allele[i]);
+    if ( !line->rlen && line->n_allele ) line->rlen = strlen(line->d.allele[0]);
+}
+static inline void bcf1_sync_filter(bcf1_t *line, kstring_t *str)
+{
+    // typed vector of integers
+    if ( line->d.n_flt ) bcf_enc_vint(str, line->d.n_flt, line->d.flt, -1);
+    else bcf_enc_vint(str, 0, 0, -1);
+}
+
+static inline void bcf1_sync_info(bcf1_t *line, kstring_t *str)
+{
+    // pairs of typed vectors
+    int i, irm = -1;
+    for (i=0; i<line->n_info; i++)
+    {
+        bcf_info_t *info = &line->d.info[i];
+        if ( !info->vptr )
+        {
+            // marked for removal
+            if ( irm < 0 ) irm = i;
+            continue;
+        }
+        kputsn_(info->vptr - info->vptr_off, info->vptr_len + info->vptr_off, str);
+        if ( irm >=0 )
+        {
+            bcf_info_t tmp = line->d.info[irm]; line->d.info[irm] = line->d.info[i]; line->d.info[i] = tmp;
+            while ( irm<=i && line->d.info[irm].vptr ) irm++;
+        }
+    }
+    if ( irm>=0 ) line->n_info = irm;
+}
+
+static int bcf1_sync(bcf1_t *line)
+{
+    char *shared_ori = line->shared.s;
+    size_t prev_len;
+
+    kstring_t tmp = {0,0,0};
+    if ( !line->shared.l )
+    {
+        // New line created via API, BCF data blocks do not exist. Get it ready for BCF output
+        tmp = line->shared;
+        bcf1_sync_id(line, &tmp);
+        line->unpack_size[0] = tmp.l; prev_len = tmp.l;
+
+        bcf1_sync_alleles(line, &tmp);
+        line->unpack_size[1] = tmp.l - prev_len; prev_len = tmp.l;
+
+        bcf1_sync_filter(line, &tmp);
+        line->unpack_size[2] = tmp.l - prev_len;
+
+        bcf1_sync_info(line, &tmp);
+        line->shared = tmp;
+    }
+    else if ( line->d.shared_dirty )
+    {
+        // The line was edited, update the BCF data block.
+        
+        if ( !(line->unpacked & BCF_UN_STR) ) bcf_unpack(line,BCF_UN_STR);
+        
+        // ptr_ori points to the original unchanged BCF data.
+        uint8_t *ptr_ori = (uint8_t *) line->shared.s;
+
+        // ID: single typed string
+        if ( line->d.shared_dirty & BCF1_DIRTY_ID )
+            bcf1_sync_id(line, &tmp);
+        else
+            kputsn_(ptr_ori, line->unpack_size[0], &tmp);
+        ptr_ori += line->unpack_size[0];
+        line->unpack_size[0] = tmp.l; prev_len = tmp.l;
+
+        // REF+ALT: list of typed strings
+        if ( line->d.shared_dirty & BCF1_DIRTY_ALS )
+            bcf1_sync_alleles(line, &tmp);
+        else
+        {
+            kputsn_(ptr_ori, line->unpack_size[1], &tmp);
+            if ( !line->rlen && line->n_allele ) line->rlen = strlen(line->d.allele[0]);
+        }
+        ptr_ori += line->unpack_size[1];
+        line->unpack_size[1] = tmp.l - prev_len; prev_len = tmp.l;
+
+        if ( line->unpacked & BCF_UN_FLT )
+        {
+            // FILTER: typed vector of integers
+            if ( line->d.shared_dirty & BCF1_DIRTY_FLT )
+                bcf1_sync_filter(line, &tmp);
+            else if ( line->d.n_flt )
+                kputsn_(ptr_ori, line->unpack_size[2], &tmp);
+            else
+                bcf_enc_vint(&tmp, 0, 0, -1);
+            ptr_ori += line->unpack_size[2];
+            line->unpack_size[2] = tmp.l - prev_len;
+
+            if ( line->unpacked & BCF_UN_INFO )
+            {
+                // INFO: pairs of typed vectors
+                if ( line->d.shared_dirty & BCF1_DIRTY_INF )
+                {
+                    bcf1_sync_info(line, &tmp);
+                    ptr_ori = (uint8_t*)line->shared.s + line->shared.l;
+                }
+            }
+        }
+
+        int size = line->shared.l - (size_t)ptr_ori + (size_t)line->shared.s;
+        if ( size ) kputsn_(ptr_ori, size, &tmp);
+
+        free(line->shared.s);
+        line->shared = tmp;
+    }
+    if ( line->shared.s != shared_ori && line->unpacked & BCF_UN_INFO )
+    {
+        // Reallocated line->shared.s block invalidated line->d.info[].vptr pointers
+        size_t off_new = line->unpack_size[0] + line->unpack_size[1] + line->unpack_size[2];
+        int i;
+        for (i=0; i<line->n_info; i++)
+        {
+            uint8_t *vptr_free = line->d.info[i].vptr_free ? line->d.info[i].vptr - line->d.info[i].vptr_off : NULL;
+            line->d.info[i].vptr = (uint8_t*) line->shared.s + off_new + line->d.info[i].vptr_off;
+            off_new += line->d.info[i].vptr_len + line->d.info[i].vptr_off;
+            if ( vptr_free )
+            {
+                free(vptr_free);
+                line->d.info[i].vptr_free = 0;
+            }
+        }
+    }
+
+    if ( line->n_sample && line->n_fmt && (!line->indiv.l || line->d.indiv_dirty) )
+    {
+        // The genotype fields changed or are not present
+        tmp.l = tmp.m = 0; tmp.s = NULL;
+        int i, irm = -1;
+        for (i=0; i<line->n_fmt; i++)
+        {
+            bcf_fmt_t *fmt = &line->d.fmt[i];
+            if ( !fmt->p )
+            {
+                // marked for removal
+                if ( irm < 0 ) irm = i;
+                continue;
+            }
+            kputsn_(fmt->p - fmt->p_off, fmt->p_len + fmt->p_off, &tmp);
+            if ( irm >=0 )
+            {
+                bcf_fmt_t tfmt = line->d.fmt[irm]; line->d.fmt[irm] = line->d.fmt[i]; line->d.fmt[i] = tfmt;
+                while ( irm<=i && line->d.fmt[irm].p ) irm++;
+            }
+
+        }
+        if ( irm>=0 ) line->n_fmt = irm;
+        free(line->indiv.s);
+        line->indiv = tmp;
+
+        // Reallocated line->indiv.s block invalidated line->d.fmt[].p pointers
+        size_t off_new = 0;
+        for (i=0; i<line->n_fmt; i++)
+        {
+            uint8_t *p_free = line->d.fmt[i].p_free ? line->d.fmt[i].p - line->d.fmt[i].p_off : NULL;
+            line->d.fmt[i].p = (uint8_t*) line->indiv.s + off_new + line->d.fmt[i].p_off;
+            off_new += line->d.fmt[i].p_len + line->d.fmt[i].p_off;
+            if ( p_free )
+            {
+                free(p_free);
+                line->d.fmt[i].p_free = 0;
+            }
+        }
+    }
+    if ( !line->n_sample ) line->n_fmt = 0;
+    line->d.shared_dirty = line->d.indiv_dirty = 0;
+    return 0;
+}
+
+bcf1_t *bcf_copy(bcf1_t *dst, bcf1_t *src)
+{
+    bcf1_sync(src);
+
+    bcf_clear(dst);
+    dst->rid  = src->rid;
+    dst->pos  = src->pos;
+    dst->rlen = src->rlen;
+    dst->qual = src->qual;
+    dst->n_info = src->n_info; dst->n_allele = src->n_allele;
+    dst->n_fmt = src->n_fmt; dst->n_sample = src->n_sample;
+
+    dst->shared.m = dst->shared.l = src->shared.l;
+    dst->shared.s = (char*) malloc(dst->shared.l);
+    memcpy(dst->shared.s,src->shared.s,dst->shared.l);
+
+    dst->indiv.m = dst->indiv.l = src->indiv.l;
+    dst->indiv.s = (char*) malloc(dst->indiv.l);
+    memcpy(dst->indiv.s,src->indiv.s,dst->indiv.l);
+
+    return dst;
+}
+bcf1_t *bcf_dup(bcf1_t *src)
+{
+    bcf1_t *out = bcf_init1();
+    return bcf_copy(out, src);
+}
+
+int bcf_write(htsFile *hfp, bcf_hdr_t *h, bcf1_t *v)
+{
+    if ( h->dirty ) bcf_hdr_sync(h);
+    if ( bcf_hdr_nsamples(h)!=v->n_sample )
+    {
+        fprintf(stderr,"[%s:%d %s] Broken VCF record, the number of columns at %s:%d does not match the number of samples (%d vs %d).\n",
+                __FILE__,__LINE__,__FUNCTION__,bcf_seqname(h,v),v->pos+1, v->n_sample,bcf_hdr_nsamples(h));
+        return -1;
+    }
+
+    if ( hfp->format.format == vcf || hfp->format.format == text_format )
+        return vcf_write(hfp,h,v);
+
+    if ( v->errcode )
+    {
+        // vcf_parse1() encountered a new contig or tag, undeclared in the
+        // header.  At this point, the header must have been printed,
+        // proceeding would lead to a broken BCF file. Errors must be checked
+        // and cleared by the caller before we can proceed.
+        fprintf(stderr,"[%s:%d %s] Unchecked error (%d), exiting.\n", __FILE__,__LINE__,__FUNCTION__,v->errcode);
+        exit(1);
+    }
+    bcf1_sync(v);   // check if the BCF record was modified
+
+    BGZF *fp = hfp->fp.bgzf;
+    uint32_t x[8];
+    x[0] = v->shared.l + 24; // to include six 32-bit integers
+    x[1] = v->indiv.l;
+    memcpy(x + 2, v, 16);
+    x[6] = (uint32_t)v->n_allele<<16 | v->n_info;
+    x[7] = (uint32_t)v->n_fmt<<24 | v->n_sample;
+    if ( bgzf_write(fp, x, 32) != 32 ) return -1;
+    if ( bgzf_write(fp, v->shared.s, v->shared.l) != v->shared.l ) return -1;
+    if ( bgzf_write(fp, v->indiv.s, v->indiv.l) != v->indiv.l ) return -1;
+    return 0;
+}
+
+/**********************
+ *** VCF header I/O ***
+ **********************/
+
+bcf_hdr_t *vcf_hdr_read(htsFile *fp)
+{
+    kstring_t txt, *s = &fp->line;
+    bcf_hdr_t *h;
+    h = bcf_hdr_init("r");
+    if (!h) {
+        fprintf(stderr, "[E::%s] failed to allocate bcf header\n", __func__);
+        return NULL;
+    }
+    txt.l = txt.m = 0; txt.s = 0;
+    while (hts_getline(fp, KS_SEP_LINE, s) >= 0) {
+        if (s->l == 0) continue;
+        if (s->s[0] != '#') {
+            if (hts_verbose >= 2)
+                fprintf(stderr, "[E::%s] no sample line\n", __func__);
+            free(txt.s);
+            bcf_hdr_destroy(h);
+            return NULL;
+        }
+        if (s->s[1] != '#' && fp->fn_aux) { // insert contigs here
+            int dret;
+            gzFile f;
+            kstream_t *ks;
+            kstring_t tmp;
+            tmp.l = tmp.m = 0; tmp.s = 0;
+            f = gzopen(fp->fn_aux, "r");
+            ks = ks_init(f);
+            while (ks_getuntil(ks, 0, &tmp, &dret) >= 0) {
+                int c;
+                kputs("##contig=<ID=", &txt); kputs(tmp.s, &txt);
+                ks_getuntil(ks, 0, &tmp, &dret);
+                kputs(",length=", &txt); kputw(atol(tmp.s), &txt);
+                kputsn(">\n", 2, &txt);
+                if (dret != '\n')
+                    while ((c = ks_getc(ks)) != '\n' && c != -1); // skip the rest of the line
+            }
+            free(tmp.s);
+            ks_destroy(ks);
+            gzclose(f);
+        }
+        kputsn(s->s, s->l, &txt);
+        kputc('\n', &txt);
+        if (s->s[1] != '#') break;
+    }
+    if ( !txt.s )
+    {
+        fprintf(stderr,"[%s:%d %s] Could not read the header\n", __FILE__,__LINE__,__FUNCTION__);
+        return NULL;
+    }
+    bcf_hdr_parse(h, txt.s);
+
+    // check tabix index, are all contigs listed in the header? add the missing ones
+    tbx_t *idx = tbx_index_load(fp->fn);
+    if ( idx )
+    {
+        int i, n, need_sync = 0;
+        const char **names = tbx_seqnames(idx, &n);
+        for (i=0; i<n; i++)
+        {
+            bcf_hrec_t *hrec = bcf_hdr_get_hrec(h, BCF_HL_CTG, "ID", (char*) names[i], NULL);
+            if ( hrec ) continue;
+            hrec = (bcf_hrec_t*) calloc(1,sizeof(bcf_hrec_t));
+            hrec->key = strdup("contig");
+            bcf_hrec_add_key(hrec, "ID", strlen("ID"));
+            bcf_hrec_set_val(hrec, hrec->nkeys-1, (char*) names[i], strlen(names[i]), 0);
+            bcf_hdr_add_hrec(h, hrec);
+            need_sync = 1;
+        }
+        free(names);
+        tbx_destroy(idx);
+        if ( need_sync )
+            bcf_hdr_sync(h);
+    }
+    free(txt.s);
+    return h;
+}
+
+int bcf_hdr_set(bcf_hdr_t *hdr, const char *fname)
+{
+    int i, n;
+    char **lines = hts_readlines(fname, &n);
+    if ( !lines ) return 1;
+    for (i=0; i<n-1; i++)
+    {
+        int k;
+        bcf_hrec_t *hrec = bcf_hdr_parse_line(hdr,lines[i],&k);
+        if ( hrec ) bcf_hdr_add_hrec(hdr, hrec);
+        free(lines[i]);
+    }
+    bcf_hdr_parse_sample_line(hdr,lines[n-1]);
+    free(lines[n-1]);
+    free(lines);
+    bcf_hdr_sync(hdr);
+    return 0;
+}
+
+static void _bcf_hrec_format(const bcf_hrec_t *hrec, int is_bcf, kstring_t *str)
+{
+    if ( !hrec->value )
+    {
+        int j, nout = 0;
+        ksprintf(str, "##%s=<", hrec->key);
+        for (j=0; j<hrec->nkeys; j++)
+        {
+            // do not output IDX if output is VCF
+            if ( !is_bcf && !strcmp("IDX",hrec->keys[j]) ) continue;
+            if ( nout ) kputc(',',str);
+            ksprintf(str,"%s=%s", hrec->keys[j], hrec->vals[j]);
+            nout++;
+        }
+        ksprintf(str,">\n");
+    }
+    else
+        ksprintf(str,"##%s=%s\n", hrec->key,hrec->value);
+}
+
+void bcf_hrec_format(const bcf_hrec_t *hrec, kstring_t *str)
+{
+    _bcf_hrec_format(hrec,0,str);
+}
+char *bcf_hdr_fmt_text(const bcf_hdr_t *hdr, int is_bcf, int *len)
+{
+    int i;
+    kstring_t txt = {0,0,0};
+    for (i=0; i<hdr->nhrec; i++)
+        _bcf_hrec_format(hdr->hrec[i], is_bcf, &txt);
+
+    ksprintf(&txt,"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO");
+    if ( bcf_hdr_nsamples(hdr) )
+    {
+        ksprintf(&txt,"\tFORMAT");
+        for (i=0; i<bcf_hdr_nsamples(hdr); i++)
+            ksprintf(&txt,"\t%s", hdr->samples[i]);
+    }
+    ksprintf(&txt,"\n");
+
+    if ( len ) *len = txt.l;
+    return txt.s;
+}
+
+const char **bcf_hdr_seqnames(const bcf_hdr_t *h, int *n)
+{
+    vdict_t *d = (vdict_t*)h->dict[BCF_DT_CTG];
+    int tid, m = kh_size(d);
+    const char **names = (const char**) calloc(m,sizeof(const char*));
+    khint_t k;
+    for (k=kh_begin(d); k<kh_end(d); k++)
+    {
+        if ( !kh_exist(d,k) ) continue;
+        tid = kh_val(d,k).id;
+        assert( tid<m );
+        names[tid] = kh_key(d,k);
+    }
+    // sanity check: there should be no gaps
+    for (tid=0; tid<m; tid++)
+        assert(names[tid]);
+    *n = m;
+    return names;
+}
+
+int vcf_hdr_write(htsFile *fp, const bcf_hdr_t *h)
+{
+    int hlen;
+    char *htxt = bcf_hdr_fmt_text(h, 0, &hlen);
+    while (hlen && htxt[hlen-1] == 0) --hlen; // kill trailing zeros
+    int ret;
+    if ( fp->format.compression!=no_compression )
+        ret = bgzf_write(fp->fp.bgzf, htxt, hlen);
+    else
+        ret = hwrite(fp->fp.hfile, htxt, hlen);
+    free(htxt);
+    return ret<0 ? -1 : 0;
+}
+
+/***********************
+ *** Typed value I/O ***
+ ***********************/
+
+void bcf_enc_vint(kstring_t *s, int n, int32_t *a, int wsize)
+{
+    int32_t max = INT32_MIN + 1, min = INT32_MAX;
+    int i;
+    if (n == 0) bcf_enc_size(s, 0, BCF_BT_NULL);
+    else if (n == 1) bcf_enc_int1(s, a[0]);
+    else {
+        if (wsize <= 0) wsize = n;
+        for (i = 0; i < n; ++i) {
+            if (a[i] == bcf_int32_missing || a[i] == bcf_int32_vector_end ) continue;
+            if (max < a[i]) max = a[i];
+            if (min > a[i]) min = a[i];
+        }
+        if (max <= INT8_MAX && min > bcf_int8_vector_end) {
+            bcf_enc_size(s, wsize, BCF_BT_INT8);
+            for (i = 0; i < n; ++i)
+                if ( a[i]==bcf_int32_vector_end ) kputc(bcf_int8_vector_end, s);
+                else if ( a[i]==bcf_int32_missing ) kputc(bcf_int8_missing, s);
+                else kputc(a[i], s);
+        } else if (max <= INT16_MAX && min > bcf_int16_vector_end) {
+            bcf_enc_size(s, wsize, BCF_BT_INT16);
+            for (i = 0; i < n; ++i)
+            {
+                int16_t x;
+                if ( a[i]==bcf_int32_vector_end ) x = bcf_int16_vector_end;
+                else if ( a[i]==bcf_int32_missing ) x = bcf_int16_missing;
+                else x = a[i];
+                kputsn((char*)&x, 2, s);
+            }
+        } else {
+            bcf_enc_size(s, wsize, BCF_BT_INT32);
+            for (i = 0; i < n; ++i) {
+                int32_t x = a[i];
+                kputsn((char*)&x, 4, s);
+            }
+        }
+    }
+}
+
+void bcf_enc_vfloat(kstring_t *s, int n, float *a)
+{
+    bcf_enc_size(s, n, BCF_BT_FLOAT);
+    kputsn((char*)a, n << 2, s);
+}
+
+void bcf_enc_vchar(kstring_t *s, int l, const char *a)
+{
+    bcf_enc_size(s, l, BCF_BT_CHAR);
+    kputsn(a, l, s);
+}
+
+void bcf_fmt_array(kstring_t *s, int n, int type, void *data)
+{
+    int j = 0;
+    if (n == 0) {
+        kputc('.', s);
+        return;
+    }
+    if (type == BCF_BT_CHAR)
+    {
+        char *p = (char*)data;
+        for (j = 0; j < n && *p; ++j, ++p)
+        {
+            if ( *p==bcf_str_missing ) kputc('.', s);
+            else kputc(*p, s);
+        }
+    }
+    else
+    {
+        #define BRANCH(type_t, is_missing, is_vector_end, kprint) { \
+            type_t *p = (type_t *) data; \
+            for (j=0; j<n; j++) \
+            { \
+                if ( is_vector_end ) break; \
+                if ( j ) kputc(',', s); \
+                if ( is_missing ) kputc('.', s); \
+                else kprint; \
+            } \
+        }
+        switch (type) {
+            case BCF_BT_INT8:  BRANCH(int8_t,  p[j]==bcf_int8_missing,  p[j]==bcf_int8_vector_end,  kputw(p[j], s)); break;
+            case BCF_BT_INT16: BRANCH(int16_t, p[j]==bcf_int16_missing, p[j]==bcf_int16_vector_end, kputw(p[j], s)); break;
+            case BCF_BT_INT32: BRANCH(int32_t, p[j]==bcf_int32_missing, p[j]==bcf_int32_vector_end, kputw(p[j], s)); break;
+            case BCF_BT_FLOAT: BRANCH(float,   bcf_float_is_missing(p[j]), bcf_float_is_vector_end(p[j]), ksprintf(s, "%g", p[j])); break;
+            default: fprintf(stderr,"todo: type %d\n", type); exit(1); break;
+        }
+        #undef BRANCH
+    }
+}
+
+uint8_t *bcf_fmt_sized_array(kstring_t *s, uint8_t *ptr)
+{
+    int x, type;
+    x = bcf_dec_size(ptr, &ptr, &type);
+    bcf_fmt_array(s, x, type, ptr);
+    return ptr + (x << bcf_type_shift[type]);
+}
+
+/********************
+ *** VCF site I/O ***
+ ********************/
+
+typedef struct {
+    int key, max_m, size, offset;
+    uint64_t is_gt:1, max_g:31, max_l:32;
+    uint32_t y;
+    uint8_t *buf;
+} fmt_aux_t;
+
+static inline void align_mem(kstring_t *s)
+{
+    if (s->l&7) {
+        uint64_t zero = 0;
+        int l = ((s->l + 7)>>3<<3) - s->l;
+        kputsn((char*)&zero, l, s);
+    }
+}
+
+// p,q is the start and the end of the FORMAT field
+#define MAX_N_FMT 255   /* Limited by size of bcf1_t n_fmt field */
+static int vcf_parse_format(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v, char *p, char *q)
+{
+    if ( !bcf_hdr_nsamples(h) ) return 0;
+
+    char *r, *t;
+    int j, l, m, g;
+    khint_t k;
+    ks_tokaux_t aux1;
+    vdict_t *d = (vdict_t*)h->dict[BCF_DT_ID];
+    kstring_t *mem = (kstring_t*)&h->mem;
+    fmt_aux_t fmt[MAX_N_FMT];
+    mem->l = 0;
+
+    char *end = s->s + s->l;
+    if ( q>=end )
+    {
+        fprintf(stderr,"[%s:%d %s] Error: FORMAT column with no sample columns starting at %s:%d\n", __FILE__,__LINE__,__FUNCTION__,s->s,v->pos+1);
+        return -1;
+    }
+
+    // get format information from the dictionary
+    v->n_fmt = 0;
+    for (j = 0, t = kstrtok(p, ":", &aux1); t; t = kstrtok(0, 0, &aux1), ++j) {
+        if (j >= MAX_N_FMT) {
+            v->errcode |= BCF_ERR_LIMITS;
+            fprintf(stderr,"[E::%s] Error: FORMAT column at %s:%d lists more identifiers than htslib can handle.\n", __func__, bcf_seqname(h,v), v->pos+1);
+            return -1;
+        }
+
+        *(char*)aux1.p = 0;
+        k = kh_get(vdict, d, t);
+        if (k == kh_end(d) || kh_val(d, k).info[BCF_HL_FMT] == 15) {
+            if (hts_verbose >= 2) fprintf(stderr, "[W::%s] FORMAT '%s' is not defined in the header, assuming Type=String\n", __func__, t);
+            kstring_t tmp = {0,0,0};
+            int l;
+            ksprintf(&tmp, "##FORMAT=<ID=%s,Number=1,Type=String,Description=\"Dummy\">", t);
+            bcf_hrec_t *hrec = bcf_hdr_parse_line(h,tmp.s,&l);
+            free(tmp.s);
+            if ( bcf_hdr_add_hrec((bcf_hdr_t*)h, hrec) ) bcf_hdr_sync((bcf_hdr_t*)h);
+            k = kh_get(vdict, d, t);
+            v->errcode = BCF_ERR_TAG_UNDEF;
+            if (k == kh_end(d)) {
+                fprintf(stderr, "[E::%s] Could not add dummy header for FORMAT '%s'\n", __func__, t);
+                v->errcode |= BCF_ERR_TAG_INVALID;
+                return -1;
+            }
+        }
+        fmt[j].max_l = fmt[j].max_m = fmt[j].max_g = 0;
+        fmt[j].key = kh_val(d, k).id;
+        fmt[j].is_gt = !strcmp(t, "GT");
+        fmt[j].y = h->id[0][fmt[j].key].val->info[BCF_HL_FMT];
+        v->n_fmt++;
+    }
+    // compute max
+    int n_sample_ori = -1;
+    r = q + 1;  // r: position in the format string
+    l = 0, m = g = 1, v->n_sample = 0;  // m: max vector size, l: max field len, g: max number of alleles
+    while ( r<end )
+    {
+        // can we skip some samples?
+        if ( h->keep_samples )
+        {
+            n_sample_ori++;
+            if ( !bit_array_test(h->keep_samples,n_sample_ori) )
+            {
+                while ( *r!='\t' && r<end ) r++;
+                if ( *r=='\t' ) { *r = 0; r++; }
+                continue;
+            }
+        }
+
+        // collect fmt stats: max vector size, length, number of alleles
+        j = 0;  // j-th format field
+        for (;;)
+        {
+            if ( *r == '\t' ) *r = 0;
+            if ( *r == ':' || !*r )  // end of field or end of sample
+            {
+                if (fmt[j].max_m < m) fmt[j].max_m = m;
+                if (fmt[j].max_l < l) fmt[j].max_l = l;
+                if (fmt[j].is_gt && fmt[j].max_g < g) fmt[j].max_g = g;
+                l = 0, m = g = 1;
+                if ( *r==':' ) 
+                {
+                    j++;
+                    if ( j>=v->n_fmt ) 
+                    { 
+                        fprintf(stderr,"Incorrect number of FORMAT fields at %s:%d\n", h->id[BCF_DT_CTG][v->rid].key,v->pos+1);
+                        exit(1); 
+                    }
+                }
+                else break;
+            }
+            else if ( *r== ',' ) m++;
+            else if ( fmt[j].is_gt && (*r == '|' || *r == '/') ) g++;
+            if ( r>=end ) break;
+            r++; l++;
+        }
+        v->n_sample++;
+        if ( v->n_sample == bcf_hdr_nsamples(h) ) break;
+        r++;
+    }
+
+    // allocate memory for arrays
+    for (j = 0; j < v->n_fmt; ++j) {
+        fmt_aux_t *f = &fmt[j];
+        if ( !f->max_m ) f->max_m = 1;  // omitted trailing format field
+        if ((f->y>>4&0xf) == BCF_HT_STR) {
+            f->size = f->is_gt? f->max_g << 2 : f->max_l;
+        } else if ((f->y>>4&0xf) == BCF_HT_REAL || (f->y>>4&0xf) == BCF_HT_INT) {
+            f->size = f->max_m << 2;
+        } else
+        {
+            fprintf(stderr, "[E::%s] the format type %d currently not supported\n", __func__, f->y>>4&0xf);
+            abort(); // I do not know how to do with Flag in the genotype fields
+        }
+        align_mem(mem);
+        f->offset = mem->l;
+        ks_resize(mem, mem->l + v->n_sample * f->size);
+        mem->l += v->n_sample * f->size;
+    }
+    for (j = 0; j < v->n_fmt; ++j)
+        fmt[j].buf = (uint8_t*)mem->s + fmt[j].offset;
+    // fill the sample fields; at beginning of the loop, t points to the first char of a format
+    n_sample_ori = -1;
+    t = q + 1; m = 0;   // m: sample id
+    while ( t<end )
+    {
+        // can we skip some samples?
+        if ( h->keep_samples )
+        {
+            n_sample_ori++;
+            if ( !bit_array_test(h->keep_samples,n_sample_ori) )
+            {
+                while ( *t && t<end ) t++;
+                t++;
+                continue;
+            }
+        }
+        if ( m == bcf_hdr_nsamples(h) ) break;
+
+        j = 0; // j-th format field, m-th sample
+        while ( t < end )
+        {
+            fmt_aux_t *z = &fmt[j++];
+            if ((z->y>>4&0xf) == BCF_HT_STR) {
+                if (z->is_gt) { // genotypes
+                    int32_t is_phased = 0, *x = (int32_t*)(z->buf + z->size * m);
+                    for (l = 0;; ++t) {
+                        if (*t == '.') ++t, x[l++] = is_phased;
+                        else x[l++] = (strtol(t, &t, 10) + 1) << 1 | is_phased;
+#if THOROUGH_SANITY_CHECKS
+                        assert( 0 );    // success of strtol,strtod not checked
+#endif
+                        is_phased = (*t == '|');
+                        if (*t != '|' && *t != '/') break;
+                    }
+                    if ( !l ) x[l++] = 0;   // An empty field, insert missing value
+                    for (; l < z->size>>2; ++l) x[l] = bcf_int32_vector_end;
+                } else {
+                    char *x = (char*)z->buf + z->size * m;
+                    for (r = t, l = 0; *t != ':' && *t; ++t) x[l++] = *t;
+                    for (; l < z->size; ++l) x[l] = 0;
+                }
+            } else if ((z->y>>4&0xf) == BCF_HT_INT) {
+                int32_t *x = (int32_t*)(z->buf + z->size * m);
+                for (l = 0;; ++t) {
+                    if (*t == '.') x[l++] = bcf_int32_missing, ++t; // ++t to skip "."
+                    else x[l++] = strtol(t, &t, 10);
+                    if (*t != ',') break;
+                }
+                if ( !l ) x[l++] = bcf_int32_missing;
+                for (; l < z->size>>2; ++l) x[l] = bcf_int32_vector_end;
+            } else if ((z->y>>4&0xf) == BCF_HT_REAL) {
+                float *x = (float*)(z->buf + z->size * m);
+                for (l = 0;; ++t) {
+                    if (*t == '.' && !isdigit(t[1])) bcf_float_set_missing(x[l++]), ++t; // ++t to skip "."
+                    else x[l++] = strtod(t, &t);
+                    if (*t != ',') break;
+                }
+                if ( !l ) bcf_float_set_missing(x[l++]);    // An empty field, insert missing value
+                for (; l < z->size>>2; ++l) bcf_float_set_vector_end(x[l]);
+            } else abort();
+
+            if (*t == '\0') {
+                break;
+            }
+            else if (*t == ':') {
+                t++;
+            }
+            else {
+                char buffer[8];
+                fprintf(stderr,"[E::%s] Invalid character '%s' in '%s' FORMAT field at %s:%d\n", __FUNCTION__, dump_char(buffer, *t), h->id[BCF_DT_ID][z->key].key, bcf_seqname(h,v), v->pos+1);
+                v->errcode |= BCF_ERR_CHAR;
+                return -1;
+            }
+        }
+
+        for (; j < v->n_fmt; ++j) { // fill end-of-vector values
+            fmt_aux_t *z = &fmt[j];
+            if ((z->y>>4&0xf) == BCF_HT_STR) {
+                if (z->is_gt) {
+                    int32_t *x = (int32_t*)(z->buf + z->size * m);
+                    if (z->size) x[0] = bcf_int32_missing;
+                    for (l = 1; l < z->size>>2; ++l) x[l] = bcf_int32_vector_end;
+                } else {
+                    char *x = (char*)z->buf + z->size * m;
+                    if ( z->size ) x[0] = '.';
+                    for (l = 1; l < z->size; ++l) x[l] = 0;
+                }
+            } else if ((z->y>>4&0xf) == BCF_HT_INT) {
+                int32_t *x = (int32_t*)(z->buf + z->size * m);
+                x[0] = bcf_int32_missing;
+                for (l = 1; l < z->size>>2; ++l) x[l] = bcf_int32_vector_end;
+            } else if ((z->y>>4&0xf) == BCF_HT_REAL) {
+                float *x = (float*)(z->buf + z->size * m);
+                bcf_float_set_missing(x[0]);
+                for (l = 1; l < z->size>>2; ++l) bcf_float_set_vector_end(x[l]);
+            }
+        }
+
+        m++; t++;
+    }
+
+    // write individual genotype information
+    kstring_t *str = &v->indiv;
+    int i;
+    if (v->n_sample > 0) {
+        for (i = 0; i < v->n_fmt; ++i) {
+            fmt_aux_t *z = &fmt[i];
+            bcf_enc_int1(str, z->key);
+            if ((z->y>>4&0xf) == BCF_HT_STR && !z->is_gt) {
+                bcf_enc_size(str, z->size, BCF_BT_CHAR);
+                kputsn((char*)z->buf, z->size * v->n_sample, str);
+            } else if ((z->y>>4&0xf) == BCF_HT_INT || z->is_gt) {
+                bcf_enc_vint(str, (z->size>>2) * v->n_sample, (int32_t*)z->buf, z->size>>2);
+            } else {
+                bcf_enc_size(str, z->size>>2, BCF_BT_FLOAT);
+                kputsn((char*)z->buf, z->size * v->n_sample, str);
+            }
+        }
+    }
+
+    if ( v->n_sample!=bcf_hdr_nsamples(h) )
+    {
+        fprintf(stderr,"[%s:%d %s] Number of columns at %s:%d does not match the number of samples (%d vs %d).\n",
+                __FILE__,__LINE__,__FUNCTION__,bcf_seqname(h,v),v->pos+1, v->n_sample,bcf_hdr_nsamples(h));
+        v->errcode |= BCF_ERR_NCOLS;
+        return -1;
+    }
+    if ( v->indiv.l > 0xffffffff )
+    {
+        fprintf(stderr,"[%s:%d %s] The FORMAT at %s:%d is too long...\n",
+                __FILE__,__LINE__,__FUNCTION__,bcf_seqname(h,v),v->pos+1);
+        v->errcode |= BCF_ERR_LIMITS;
+
+        // Error recovery: return -1 if this is a critical error or 0 if we want to ignore the FORMAT and proceed
+        v->n_fmt = 0;
+        return -1;
+    }
+
+    return 0;
+}
+
+int vcf_parse(kstring_t *s, const bcf_hdr_t *h, bcf1_t *v)
+{
+    int i = 0;
+    char *p, *q, *r, *t;
+    kstring_t *str;
+    khint_t k;
+    ks_tokaux_t aux;
+
+    bcf_clear1(v);
+    str = &v->shared;
+    memset(&aux, 0, sizeof(ks_tokaux_t));
+    for (p = kstrtok(s->s, "\t", &aux), i = 0; p; p = kstrtok(0, 0, &aux), ++i) {
+        q = (char*)aux.p;
+        *q = 0;
+        if (i == 0) { // CHROM
+            vdict_t *d = (vdict_t*)h->dict[BCF_DT_CTG];
+            k = kh_get(vdict, d, p);
+            if (k == kh_end(d))
+            {
+                // Simple error recovery for chromosomes not defined in the header. It will not help when VCF header has
+                // been already printed, but will enable tools like vcfcheck to proceed.
+                if (hts_verbose >= 2) fprintf(stderr, "[W::%s] contig '%s' is not defined in the header. (Quick workaround: index the file with tabix.)\n", __func__, p);
+                kstring_t tmp = {0,0,0};
+                int l;
+                ksprintf(&tmp, "##contig=<ID=%s>", p);
+                bcf_hrec_t *hrec = bcf_hdr_parse_line(h,tmp.s,&l);
+                free(tmp.s);
+                if ( bcf_hdr_add_hrec((bcf_hdr_t*)h, hrec) ) bcf_hdr_sync((bcf_hdr_t*)h);
+                k = kh_get(vdict, d, p);
+                v->errcode = BCF_ERR_CTG_UNDEF;
+                if (k == kh_end(d)) {
+                    fprintf(stderr, "[E::%s] Could not add dummy header for contig '%s'\n", __func__, p);
+                    v->errcode |= BCF_ERR_CTG_INVALID;
+                    return -1;
+                }
+            }
+            v->rid = kh_val(d, k).id;
+        } else if (i == 1) { // POS
+            v->pos = atoi(p) - 1;
+        } else if (i == 2) { // ID
+            if (strcmp(p, ".")) bcf_enc_vchar(str, q - p, p);
+            else bcf_enc_size(str, 0, BCF_BT_CHAR);
+        } else if (i == 3) { // REF
+            bcf_enc_vchar(str, q - p, p);
+            v->n_allele = 1, v->rlen = q - p;
+        } else if (i == 4) { // ALT
+            if (strcmp(p, ".")) {
+                for (r = t = p;; ++r) {
+                    if (*r == ',' || *r == 0) {
+                        bcf_enc_vchar(str, r - t, t);
+                        t = r + 1;
+                        ++v->n_allele;
+                    }
+                    if (r == q) break;
+                }
+            }
+        } else if (i == 5) { // QUAL
+            if (strcmp(p, ".")) v->qual = atof(p);
+            else memcpy(&v->qual, &bcf_float_missing, 4);
+            if ( v->max_unpack && !(v->max_unpack>>1) ) return 0; // BCF_UN_STR
+        } else if (i == 6) { // FILTER
+            if (strcmp(p, ".")) {
+                int32_t *a;
+                int n_flt = 1, i;
+                ks_tokaux_t aux1;
+                vdict_t *d = (vdict_t*)h->dict[BCF_DT_ID];
+                // count the number of filters
+                if (*(q-1) == ';') *(q-1) = 0;
+                for (r = p; *r; ++r)
+                    if (*r == ';') ++n_flt;
+                a = (int32_t*)alloca(n_flt * sizeof(int32_t));
+                // add filters
+                for (t = kstrtok(p, ";", &aux1), i = 0; t; t = kstrtok(0, 0, &aux1)) {
+                    *(char*)aux1.p = 0;
+                    k = kh_get(vdict, d, t);
+                    if (k == kh_end(d))
+                    {
+                        // Simple error recovery for FILTERs not defined in the header. It will not help when VCF header has
+                        // been already printed, but will enable tools like vcfcheck to proceed.
+                        if (hts_verbose >= 2) fprintf(stderr, "[W::%s] FILTER '%s' is not defined in the header\n", __func__, t);
+                        kstring_t tmp = {0,0,0};
+                        int l;
+                        ksprintf(&tmp, "##FILTER=<ID=%s,Description=\"Dummy\">", t);
+                        bcf_hrec_t *hrec = bcf_hdr_parse_line(h,tmp.s,&l);
+                        free(tmp.s);
+                        if ( bcf_hdr_add_hrec((bcf_hdr_t*)h, hrec) ) bcf_hdr_sync((bcf_hdr_t*)h);
+                        k = kh_get(vdict, d, t);
+                        v->errcode = BCF_ERR_TAG_UNDEF;
+                        if (k == kh_end(d)) {
+                            fprintf(stderr, "[E::%s] Could not add dummy header for FILTER '%s'\n", __func__, t);
+                            v->errcode |= BCF_ERR_TAG_INVALID;
+                            return -1;
+                        }
+                    }
+                    a[i++] = kh_val(d, k).id;
+                }
+                n_flt = i;
+                bcf_enc_vint(str, n_flt, a, -1);
+            } else bcf_enc_vint(str, 0, 0, -1);
+            if ( v->max_unpack && !(v->max_unpack>>2) ) return 0;    // BCF_UN_FLT
+        } else if (i == 7) { // INFO
+            char *key;
+            vdict_t *d = (vdict_t*)h->dict[BCF_DT_ID];
+            v->n_info = 0;
+            if (strcmp(p, ".")) {
+                if (*(q-1) == ';') *(q-1) = 0;
+                for (r = key = p;; ++r) {
+                    int c;
+                    char *val, *end;
+                    if (*r != ';' && *r != '=' && *r != 0) continue;
+                    val = end = 0;
+                    c = *r; *r = 0;
+                    if (c == '=') {
+                        val = r + 1;
+                        for (end = val; *end != ';' && *end != 0; ++end);
+                        c = *end; *end = 0;
+                    } else end = r;
+                    if ( !*key ) { if (c==0) break; r = end; key = r + 1; continue; }  // faulty VCF, ";;" in the INFO
+                    k = kh_get(vdict, d, key);
+                    if (k == kh_end(d) || kh_val(d, k).info[BCF_HL_INFO] == 15)
+                    {
+                        if (hts_verbose >= 2) fprintf(stderr, "[W::%s] INFO '%s' is not defined in the header, assuming Type=String\n", __func__, key);
+                        kstring_t tmp = {0,0,0};
+                        int l;
+                        ksprintf(&tmp, "##INFO=<ID=%s,Number=1,Type=String,Description=\"Dummy\">", key);
+                        bcf_hrec_t *hrec = bcf_hdr_parse_line(h,tmp.s,&l);
+                        free(tmp.s);
+                        if ( bcf_hdr_add_hrec((bcf_hdr_t*)h, hrec) ) bcf_hdr_sync((bcf_hdr_t*)h);
+                        k = kh_get(vdict, d, key);
+                        v->errcode = BCF_ERR_TAG_UNDEF;
+                        if (k == kh_end(d)) {
+                            fprintf(stderr, "[E::%s] Could not add dummy header for INFO '%s'\n", __func__, key);
+                            v->errcode |= BCF_ERR_TAG_INVALID;
+                            return -1;
+                        }
+                    }
+                    uint32_t y = kh_val(d, k).info[BCF_HL_INFO];
+                    ++v->n_info;
+                    bcf_enc_int1(str, kh_val(d, k).id);
+                    if (val == 0) {
+                        bcf_enc_size(str, 0, BCF_BT_NULL);
+                    } else if ((y>>4&0xf) == BCF_HT_FLAG || (y>>4&0xf) == BCF_HT_STR) { // if Flag has a value, treat it as a string
+                        bcf_enc_vchar(str, end - val, val);
+                    } else { // int/float value/array
+                        int i, n_val;
+                        char *t, *te;
+                        for (t = val, n_val = 1; *t; ++t) // count the number of values
+                            if (*t == ',') ++n_val;
+                        if ((y>>4&0xf) == BCF_HT_INT) {
+                            int32_t *z;
+                            z = (int32_t*)alloca(n_val * sizeof(int32_t));
+                            for (i = 0, t = val; i < n_val; ++i, ++t)
+                            {
+                                z[i] = strtol(t, &te, 10);
+                                if ( te==t ) // conversion failed
+                                {
+                                    z[i] = bcf_int32_missing;
+                                    while ( *te && *te!=',' ) te++;
+                                }
+                                t = te;
+                            }
+                            bcf_enc_vint(str, n_val, z, -1);
+                            if (strcmp(key, "END") == 0) v->rlen = z[0] - v->pos;
+                        } else if ((y>>4&0xf) == BCF_HT_REAL) {
+                            float *z;
+                            z = (float*)alloca(n_val * sizeof(float));
+                            for (i = 0, t = val; i < n_val; ++i, ++t)
+                            {
+                                z[i] = strtod(t, &te);
+                                if ( te==t ) // conversion failed
+                                {
+                                    bcf_float_set_missing(z[i]);
+                                    while ( *te && *te!=',' ) te++;
+                                }
+                                t = te;
+                            }
+                            bcf_enc_vfloat(str, n_val, z);
+                        }
+                    }
+                    if (c == 0) break;
+                    r = end;
+                    key = r + 1;
+                }
+            }
+            if ( v->max_unpack && !(v->max_unpack>>3) ) return 0;
+        } else if (i == 8) // FORMAT
+            return vcf_parse_format(s, h, v, p, q);
+    }
+    return 0;
+}
+
+int vcf_read(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v)
+{
+    int ret;
+    ret = hts_getline(fp, KS_SEP_LINE, &fp->line);
+    if (ret < 0) return -1;
+    return vcf_parse1(&fp->line, h, v);
+}
+
+static inline uint8_t *bcf_unpack_fmt_core1(uint8_t *ptr, int n_sample, bcf_fmt_t *fmt)
+{
+    uint8_t *ptr_start = ptr;
+    fmt->id = bcf_dec_typed_int1(ptr, &ptr);
+    fmt->n = bcf_dec_size(ptr, &ptr, &fmt->type);
+    fmt->size = fmt->n << bcf_type_shift[fmt->type];
+    fmt->p = ptr;
+    fmt->p_off  = ptr - ptr_start;
+    fmt->p_free = 0;
+    ptr += n_sample * fmt->size;
+    fmt->p_len = ptr - fmt->p;
+    return ptr;
+}
+
+static inline uint8_t *bcf_unpack_info_core1(uint8_t *ptr, bcf_info_t *info)
+{
+    uint8_t *ptr_start = ptr;
+    info->key = bcf_dec_typed_int1(ptr, &ptr);
+    info->len = bcf_dec_size(ptr, &ptr, &info->type);
+    info->vptr = ptr;
+    info->vptr_off  = ptr - ptr_start;
+    info->vptr_free = 0;
+    info->v1.i = 0;
+    if (info->len == 1) {
+        if (info->type == BCF_BT_INT8 || info->type == BCF_BT_CHAR) info->v1.i = *(int8_t*)ptr;
+        else if (info->type == BCF_BT_INT32) info->v1.i = *(int32_t*)ptr;
+        else if (info->type == BCF_BT_FLOAT) info->v1.f = *(float*)ptr;
+        else if (info->type == BCF_BT_INT16) info->v1.i = *(int16_t*)ptr;
+    }
+    ptr += info->len << bcf_type_shift[info->type];
+    info->vptr_len = ptr - info->vptr;
+    return ptr;
+}
+
+int bcf_unpack(bcf1_t *b, int which)
+{
+    if ( !b->shared.l ) return 0; // Building a new BCF record from scratch
+    uint8_t *ptr = (uint8_t*)b->shared.s, *ptr_ori;
+    int *offset, i;
+    bcf_dec_t *d = &b->d;
+    if (which & BCF_UN_FLT) which |= BCF_UN_STR;
+    if (which & BCF_UN_INFO) which |= BCF_UN_SHR;
+    if ((which&BCF_UN_STR) && !(b->unpacked&BCF_UN_STR))
+    {
+        kstring_t tmp;
+
+        // ID
+        tmp.l = 0; tmp.s = d->id; tmp.m = d->m_id;
+        ptr_ori = ptr;
+        ptr = bcf_fmt_sized_array(&tmp, ptr);
+        b->unpack_size[0] = ptr - ptr_ori;
+        kputc('\0', &tmp);
+        d->id = tmp.s; d->m_id = tmp.m;
+
+        // REF and ALT are in a single block (d->als) and d->alleles are pointers into this block
+        tmp.l = 0; tmp.s = d->als; tmp.m = d->m_als;
+        offset = (int*)alloca(b->n_allele * sizeof(int));
+        ptr_ori = ptr;
+        for (i = 0; i < b->n_allele; ++i) {
+            offset[i] = tmp.l;
+            ptr = bcf_fmt_sized_array(&tmp, ptr);
+            kputc('\0', &tmp);
+        }
+        b->unpack_size[1] = ptr - ptr_ori;
+        d->als = tmp.s; d->m_als = tmp.m;
+
+        hts_expand(char*, b->n_allele, d->m_allele, d->allele); // NM: hts_expand() is a macro
+        for (i = 0; i < b->n_allele; ++i)
+            d->allele[i] = d->als + offset[i];
+        b->unpacked |= BCF_UN_STR;
+    }
+    if ((which&BCF_UN_FLT) && !(b->unpacked&BCF_UN_FLT)) { // FILTER
+        ptr = (uint8_t*)b->shared.s + b->unpack_size[0] + b->unpack_size[1];
+        ptr_ori = ptr;
+        if (*ptr>>4) {
+            int type;
+            d->n_flt = bcf_dec_size(ptr, &ptr, &type);
+            hts_expand(int, d->n_flt, d->m_flt, d->flt);
+            for (i = 0; i < d->n_flt; ++i)
+                d->flt[i] = bcf_dec_int1(ptr, type, &ptr);
+        } else ++ptr, d->n_flt = 0;
+        b->unpack_size[2] = ptr - ptr_ori;
+        b->unpacked |= BCF_UN_FLT;
+    }
+    if ((which&BCF_UN_INFO) && !(b->unpacked&BCF_UN_INFO)) { // INFO
+        ptr = (uint8_t*)b->shared.s + b->unpack_size[0] + b->unpack_size[1] + b->unpack_size[2];
+        hts_expand(bcf_info_t, b->n_info, d->m_info, d->info);
+        for (i = 0; i < d->m_info; ++i) d->info[i].vptr_free = 0;
+        for (i = 0; i < b->n_info; ++i)
+            ptr = bcf_unpack_info_core1(ptr, &d->info[i]);
+        b->unpacked |= BCF_UN_INFO;
+    }
+    if ((which&BCF_UN_FMT) && b->n_sample && !(b->unpacked&BCF_UN_FMT)) { // FORMAT
+        ptr = (uint8_t*)b->indiv.s;
+        hts_expand(bcf_fmt_t, b->n_fmt, d->m_fmt, d->fmt);
+        for (i = 0; i < d->m_fmt; ++i) d->fmt[i].p_free = 0;
+        for (i = 0; i < b->n_fmt; ++i)
+            ptr = bcf_unpack_fmt_core1(ptr, b->n_sample, &d->fmt[i]);
+        b->unpacked |= BCF_UN_FMT;
+    }
+    return 0;
+}
+
+int vcf_format(const bcf_hdr_t *h, const bcf1_t *v, kstring_t *s)
+{
+    int i;
+    bcf_unpack((bcf1_t*)v, BCF_UN_ALL);
+    kputs(h->id[BCF_DT_CTG][v->rid].key, s); // CHROM
+    kputc('\t', s); kputw(v->pos + 1, s); // POS
+    kputc('\t', s); kputs(v->d.id ? v->d.id : ".", s); // ID
+    kputc('\t', s); // REF
+    if (v->n_allele > 0) kputs(v->d.allele[0], s);
+    else kputc('.', s);
+    kputc('\t', s); // ALT
+    if (v->n_allele > 1) {
+        for (i = 1; i < v->n_allele; ++i) {
+            if (i > 1) kputc(',', s);
+            kputs(v->d.allele[i], s);
+        }
+    } else kputc('.', s);
+    kputc('\t', s); // QUAL
+    if ( bcf_float_is_missing(v->qual) ) kputc('.', s); // QUAL
+    else ksprintf(s, "%g", v->qual);
+    kputc('\t', s); // FILTER
+    if (v->d.n_flt) {
+        for (i = 0; i < v->d.n_flt; ++i) {
+            if (i) kputc(';', s);
+            kputs(h->id[BCF_DT_ID][v->d.flt[i]].key, s);
+        }
+    } else kputc('.', s);
+    kputc('\t', s); // INFO
+    if (v->n_info) {
+        int first = 1;
+        for (i = 0; i < v->n_info; ++i) {
+            bcf_info_t *z = &v->d.info[i];
+            if ( !z->vptr ) continue;
+            if ( !first ) kputc(';', s);
+            first = 0;
+            kputs(h->id[BCF_DT_ID][z->key].key, s);
+            if (z->len <= 0) continue;
+            kputc('=', s);
+            if (z->len == 1) 
+            {
+                switch (z->type) 
+                {
+                    case BCF_BT_INT8:  if ( z->v1.i==bcf_int8_missing ) kputc('.', s); else kputw(z->v1.i, s); break;
+                    case BCF_BT_INT16: if ( z->v1.i==bcf_int16_missing ) kputc('.', s); else kputw(z->v1.i, s); break;
+                    case BCF_BT_INT32: if ( z->v1.i==bcf_int32_missing ) kputc('.', s); else kputw(z->v1.i, s); break;
+                    case BCF_BT_FLOAT: if ( bcf_float_is_missing(z->v1.f) ) kputc('.', s); else ksprintf(s, "%g", z->v1.f); break;
+                    case BCF_BT_CHAR:  kputc(z->v1.i, s); break;
+                    default: fprintf(stderr,"todo: type %d\n", z->type); exit(1); break;
+                }
+            }
+            else bcf_fmt_array(s, z->len, z->type, z->vptr);
+        }
+        if ( first ) kputc('.', s);
+    } else kputc('.', s);
+    // FORMAT and individual information
+    if (v->n_sample)
+    {
+        int i,j;
+        if ( v->n_fmt)
+        {
+            int gt_i = -1;
+            bcf_fmt_t *fmt = v->d.fmt;
+            int first = 1;
+            for (i = 0; i < (int)v->n_fmt; ++i) {
+                if ( !fmt[i].p ) continue;
+                kputc(!first ? ':' : '\t', s); first = 0;
+                if ( fmt[i].id<0 ) //!bcf_hdr_idinfo_exists(h,BCF_HL_FMT,fmt[i].id) )
+                {
+                    fprintf(stderr, "[E::%s] invalid BCF, the FORMAT tag id=%d not present in the header.\n", __func__, fmt[i].id);
+                    abort();
+                }
+                kputs(h->id[BCF_DT_ID][fmt[i].id].key, s);
+                if (strcmp(h->id[BCF_DT_ID][fmt[i].id].key, "GT") == 0) gt_i = i;
+            }
+            if ( first ) kputs("\t.", s);
+            for (j = 0; j < v->n_sample; ++j) {
+                kputc('\t', s);
+                first = 1;
+                for (i = 0; i < (int)v->n_fmt; ++i) {
+                    bcf_fmt_t *f = &fmt[i];
+                    if ( !f->p ) continue;
+                    if (!first) kputc(':', s);
+                    first = 0;
+                    if (gt_i == i)
+                        bcf_format_gt(f,j,s);
+                    else
+                        bcf_fmt_array(s, f->n, f->type, f->p + j * f->size);
+                }
+                if ( first ) kputc('.', s);
+            }
+        }
+        else
+            for (j=0; j<=v->n_sample; j++)
+                kputs("\t.", s);
+    }
+    kputc('\n', s);
+    return 0;
+}
+
+int vcf_write_line(htsFile *fp, kstring_t *line)
+{
+    int ret;
+    if ( line->s[line->l-1]!='\n' ) kputc('\n',line);
+    if ( fp->format.compression!=no_compression )
+        ret = bgzf_write(fp->fp.bgzf, line->s, line->l);
+    else
+        ret = hwrite(fp->fp.hfile, line->s, line->l);
+    return ret==line->l ? 0 : -1;
+}
+
+int vcf_write(htsFile *fp, const bcf_hdr_t *h, bcf1_t *v)
+{
+    int ret;
+    fp->line.l = 0;
+    vcf_format1(h, v, &fp->line);
+    if ( fp->format.compression!=no_compression )
+        ret = bgzf_write(fp->fp.bgzf, fp->line.s, fp->line.l);
+    else
+        ret = hwrite(fp->fp.hfile, fp->line.s, fp->line.l);
+    return ret==fp->line.l ? 0 : -1;
+}
+
+/************************
+ * Data access routines *
+ ************************/
+
+int bcf_hdr_id2int(const bcf_hdr_t *h, int which, const char *id)
+{
+    khint_t k;
+    vdict_t *d = (vdict_t*)h->dict[which];
+    k = kh_get(vdict, d, id);
+    return k == kh_end(d)? -1 : kh_val(d, k).id;
+}
+
+
+/********************
+ *** BCF indexing ***
+ ********************/
+
+hts_idx_t *bcf_index(htsFile *fp, int min_shift)
+{
+    int n_lvls, i;
+    bcf1_t *b;
+    hts_idx_t *idx;
+    bcf_hdr_t *h;
+    int64_t max_len = 0, s;
+    h = bcf_hdr_read(fp);
+    if ( !h ) return NULL;
+    int nids = 0;
+    for (i = 0; i < h->n[BCF_DT_CTG]; ++i)
+    {
+        if ( !h->id[BCF_DT_CTG][i].val ) continue;
+        if ( max_len < h->id[BCF_DT_CTG][i].val->info[0] ) max_len = h->id[BCF_DT_CTG][i].val->info[0];
+        nids++;
+    }
+    if ( !max_len ) max_len = ((int64_t)1<<31) - 1;  // In case contig line is broken.
+    max_len += 256;
+    for (n_lvls = 0, s = 1<<min_shift; max_len > s; ++n_lvls, s <<= 3);
+    idx = hts_idx_init(nids, HTS_FMT_CSI, bgzf_tell(fp->fp.bgzf), min_shift, n_lvls);
+    b = bcf_init1();
+    while (bcf_read1(fp,h, b) >= 0) {
+        int ret;
+        ret = hts_idx_push(idx, b->rid, b->pos, b->pos + b->rlen, bgzf_tell(fp->fp.bgzf), 1);
+        if (ret < 0)
+        {
+            bcf_destroy1(b);
+            hts_idx_destroy(idx);
+            return NULL;
+        }
+    }
+    hts_idx_finish(idx, bgzf_tell(fp->fp.bgzf));
+    bcf_destroy1(b);
+    bcf_hdr_destroy(h);
+    return idx;
+}
+
+hts_idx_t *bcf_index_load2(const char *fn, const char *fnidx)
+{
+    return fnidx? hts_idx_load2(fn, fnidx) : bcf_index_load(fn);
+}
+
+int bcf_index_build2(const char *fn, const char *fnidx, int min_shift)
+{
+    htsFile *fp;
+    hts_idx_t *idx;
+    int ret;
+    if ((fp = hts_open(fn, "rb")) == 0) return -1;
+    if ( fp->format.compression!=bgzf ) { hts_close(fp); return -1; }
+    idx = bcf_index(fp, min_shift);
+    hts_close(fp);
+    if ( !idx ) return -1;
+    ret = hts_idx_save_as(idx, fn, fnidx, HTS_FMT_CSI);
+    hts_idx_destroy(idx);
+    return ret;
+}
+
+int bcf_index_build(const char *fn, int min_shift)
+{
+    return bcf_index_build2(fn, NULL, min_shift);
+}
+
+/*****************
+ *** Utilities ***
+ *****************/
+
+int bcf_hdr_combine(bcf_hdr_t *dst, const bcf_hdr_t *src)
+{
+    int i, ndst_ori = dst->nhrec, need_sync = 0, ret = 0;
+    for (i=0; i<src->nhrec; i++)
+    {
+        if ( src->hrec[i]->type==BCF_HL_GEN && src->hrec[i]->value )
+        {
+            int j;
+            for (j=0; j<ndst_ori; j++)
+            {
+                if ( dst->hrec[j]->type!=BCF_HL_GEN ) continue;
+
+                // Checking only the key part of generic lines, otherwise
+                // the VCFs are too verbose. Should we perhaps add a flag
+                // to bcf_hdr_combine() and make this optional?
+                if ( !strcmp(src->hrec[i]->key,dst->hrec[j]->key) ) break;
+            }
+            if ( j>=ndst_ori )
+                need_sync += bcf_hdr_add_hrec(dst, bcf_hrec_dup(src->hrec[i]));
+        }
+        else if ( src->hrec[i]->type==BCF_HL_STR )
+        {
+            // NB: we are ignoring fields without ID
+            int j = bcf_hrec_find_key(src->hrec[i],"ID");
+            if ( j>=0 )
+            {
+                bcf_hrec_t *rec = bcf_hdr_get_hrec(dst, src->hrec[i]->type, "ID", src->hrec[i]->vals[j], src->hrec[i]->key);
+                if ( !rec )
+                    need_sync += bcf_hdr_add_hrec(dst, bcf_hrec_dup(src->hrec[i]));
+            }
+        }
+        else
+        {
+            int j = bcf_hrec_find_key(src->hrec[i],"ID");
+            assert( j>=0 ); // this should always be true for valid VCFs
+
+            bcf_hrec_t *rec = bcf_hdr_get_hrec(dst, src->hrec[i]->type, "ID", src->hrec[i]->vals[j], NULL);
+            if ( !rec )
+                need_sync += bcf_hdr_add_hrec(dst, bcf_hrec_dup(src->hrec[i]));
+            else if ( src->hrec[i]->type==BCF_HL_INFO || src->hrec[i]->type==BCF_HL_FMT )
+            {
+                // Check that both records are of the same type. The bcf_hdr_id2length
+                // macro cannot be used here because dst header is not synced yet.
+                vdict_t *d_src = (vdict_t*)src->dict[BCF_DT_ID];
+                vdict_t *d_dst = (vdict_t*)dst->dict[BCF_DT_ID];
+                khint_t k_src  = kh_get(vdict, d_src, src->hrec[i]->vals[0]);
+                khint_t k_dst  = kh_get(vdict, d_dst, src->hrec[i]->vals[0]);
+                if ( (kh_val(d_src,k_src).info[rec->type]>>8 & 0xf) != (kh_val(d_dst,k_dst).info[rec->type]>>8 & 0xf) )
+                {
+                    fprintf(stderr,"Warning: trying to combine \"%s\" tag definitions of different lengths\n", src->hrec[i]->vals[0]);
+                    ret |= 1;
+                }
+                if ( (kh_val(d_src,k_src).info[rec->type]>>4 & 0xf) != (kh_val(d_dst,k_dst).info[rec->type]>>4 & 0xf) )
+                {
+                    fprintf(stderr,"Warning: trying to combine \"%s\" tag definitions of different types\n", src->hrec[i]->vals[0]);
+                    ret |= 1;
+                }
+            }
+        }
+    }
+    if ( need_sync ) bcf_hdr_sync(dst);
+    return ret;
+}
+
+bcf_hdr_t *bcf_hdr_merge(bcf_hdr_t *dst, const bcf_hdr_t *src)
+{
+    if ( !dst )
+    {
+        // this will effectively strip existing IDX attributes from src to become dst
+        dst = bcf_hdr_init("r");
+        char *htxt = bcf_hdr_fmt_text(src, 0, NULL);
+        bcf_hdr_parse(dst, htxt);
+        free(htxt);
+        return dst;
+    }
+
+    int i, ndst_ori = dst->nhrec, need_sync = 0, ret = 0;
+    for (i=0; i<src->nhrec; i++)
+    {
+        if ( src->hrec[i]->type==BCF_HL_GEN && src->hrec[i]->value )
+        {
+            int j;
+            for (j=0; j<ndst_ori; j++)
+            {
+                if ( dst->hrec[j]->type!=BCF_HL_GEN ) continue;
+
+                // Checking only the key part of generic lines, otherwise
+                // the VCFs are too verbose. Should we perhaps add a flag
+                // to bcf_hdr_combine() and make this optional?
+                if ( !strcmp(src->hrec[i]->key,dst->hrec[j]->key) ) break;
+            }
+            if ( j>=ndst_ori )
+                need_sync += bcf_hdr_add_hrec(dst, bcf_hrec_dup(src->hrec[i]));
+        }
+        else if ( src->hrec[i]->type==BCF_HL_STR )
+        {
+            // NB: we are ignoring fields without ID
+            int j = bcf_hrec_find_key(src->hrec[i],"ID");
+            if ( j>=0 )
+            {
+                bcf_hrec_t *rec = bcf_hdr_get_hrec(dst, src->hrec[i]->type, "ID", src->hrec[i]->vals[j], src->hrec[i]->key);
+                if ( !rec )
+                    need_sync += bcf_hdr_add_hrec(dst, bcf_hrec_dup(src->hrec[i]));
+            }
+        }
+        else
+        {
+            int j = bcf_hrec_find_key(src->hrec[i],"ID");
+            assert( j>=0 ); // this should always be true for valid VCFs
+
+            bcf_hrec_t *rec = bcf_hdr_get_hrec(dst, src->hrec[i]->type, "ID", src->hrec[i]->vals[j], NULL);
+            if ( !rec )
+                need_sync += bcf_hdr_add_hrec(dst, bcf_hrec_dup(src->hrec[i]));
+            else if ( src->hrec[i]->type==BCF_HL_INFO || src->hrec[i]->type==BCF_HL_FMT )
+            {
+                // Check that both records are of the same type. The bcf_hdr_id2length
+                // macro cannot be used here because dst header is not synced yet.
+                vdict_t *d_src = (vdict_t*)src->dict[BCF_DT_ID];
+                vdict_t *d_dst = (vdict_t*)dst->dict[BCF_DT_ID];
+                khint_t k_src  = kh_get(vdict, d_src, src->hrec[i]->vals[0]);
+                khint_t k_dst  = kh_get(vdict, d_dst, src->hrec[i]->vals[0]);
+                if ( (kh_val(d_src,k_src).info[rec->type]>>8 & 0xf) != (kh_val(d_dst,k_dst).info[rec->type]>>8 & 0xf) )
+                {
+                    fprintf(stderr,"Warning: trying to combine \"%s\" tag definitions of different lengths\n", src->hrec[i]->vals[0]);
+                    ret |= 1;
+                }
+                if ( (kh_val(d_src,k_src).info[rec->type]>>4 & 0xf) != (kh_val(d_dst,k_dst).info[rec->type]>>4 & 0xf) )
+                {
+                    fprintf(stderr,"Warning: trying to combine \"%s\" tag definitions of different types\n", src->hrec[i]->vals[0]);
+                    ret |= 1;
+                }
+            }
+        }
+    }
+    if ( need_sync ) bcf_hdr_sync(dst);
+    return dst;
+}
+int bcf_translate(const bcf_hdr_t *dst_hdr, bcf_hdr_t *src_hdr, bcf1_t *line)
+{
+    int i;
+    if ( line->errcode )
+    {
+        fprintf(stderr,"[%s:%d %s] Unchecked error (%d), exiting.\n", __FILE__,__LINE__,__FUNCTION__,line->errcode);
+        exit(1);
+    }
+    if ( src_hdr->ntransl==-1 ) return 0;    // no need to translate, all tags have the same id
+    if ( !src_hdr->ntransl )  // called for the first time, see what needs translating
+    {
+        int dict;
+        for (dict=0; dict<2; dict++)    // BCF_DT_ID and BCF_DT_CTG
+        {
+            src_hdr->transl[dict] = (int*) malloc(src_hdr->n[dict]*sizeof(int));
+            for (i=0; i<src_hdr->n[dict]; i++)
+            {
+                if ( !src_hdr->id[dict][i].key ) // gap left after removed BCF header lines
+                {
+                    src_hdr->transl[dict][i] = -1;
+                    continue;
+                }
+                src_hdr->transl[dict][i] = bcf_hdr_id2int(dst_hdr,dict,src_hdr->id[dict][i].key);
+                if ( src_hdr->transl[dict][i]!=-1 && i!=src_hdr->transl[dict][i] ) src_hdr->ntransl++;
+            }
+        }
+        if ( !src_hdr->ntransl )
+        {
+            free(src_hdr->transl[0]); src_hdr->transl[0] = NULL;
+            free(src_hdr->transl[1]); src_hdr->transl[1] = NULL;
+            src_hdr->ntransl = -1;
+        }
+        if ( src_hdr->ntransl==-1 ) return 0;
+    }
+    bcf_unpack(line,BCF_UN_ALL);
+
+    // CHROM
+    if ( src_hdr->transl[BCF_DT_CTG][line->rid] >=0 ) line->rid = src_hdr->transl[BCF_DT_CTG][line->rid];
+
+    // FILTER
+    for (i=0; i<line->d.n_flt; i++)
+    {
+        int src_id = line->d.flt[i];
+        if ( src_hdr->transl[BCF_DT_ID][src_id] >=0 )
+            line->d.flt[i] = src_hdr->transl[BCF_DT_ID][src_id];
+        line->d.shared_dirty |= BCF1_DIRTY_FLT;
+    }
+
+    // INFO
+    for (i=0; i<line->n_info; i++)
+    {
+        int src_id = line->d.info[i].key;
+        int dst_id = src_hdr->transl[BCF_DT_ID][src_id];
+        if ( dst_id<0 ) continue;
+        int src_size = src_id>>7 ? ( src_id>>15 ? BCF_BT_INT32 : BCF_BT_INT16) : BCF_BT_INT8;
+        int dst_size = dst_id>>7 ? ( dst_id>>15 ? BCF_BT_INT32 : BCF_BT_INT16) : BCF_BT_INT8;
+        if ( src_size==dst_size )   // can overwrite
+        {
+            line->d.info[i].key = dst_id;
+            uint8_t *vptr = line->d.info[i].vptr - line->d.info[i].vptr_off;
+            if ( dst_size==BCF_BT_INT8 ) { vptr[1] = (uint8_t)dst_id; }
+            else if ( dst_size==BCF_BT_INT16 ) { *(uint16_t*)vptr = (uint16_t)dst_id; }
+            else { *(uint32_t*)vptr = (uint32_t)dst_id; }
+        }
+        else    // must realloc
+        {
+            bcf_info_t *info = &line->d.info[i];
+            assert( !info->vptr_free );
+            kstring_t str = {0,0,0};
+            bcf_enc_int1(&str, dst_id);
+            bcf_enc_size(&str, info->len,info->type);
+            info->vptr_off = str.l;
+            kputsn((char*)info->vptr, info->vptr_len, &str);
+            info->vptr = (uint8_t*)str.s + info->vptr_off;
+            info->vptr_free = 1;
+            info->key = dst_id;
+            line->d.shared_dirty |= BCF1_DIRTY_INF;
+        }
+    }
+
+    // FORMAT
+    for (i=0; i<line->n_fmt; i++)
+    {
+        int src_id = line->d.fmt[i].id;
+        int dst_id = src_hdr->transl[BCF_DT_ID][src_id];
+        if ( dst_id<0 ) continue;
+        int src_size = src_id>>7 ? ( src_id>>15 ? BCF_BT_INT32 : BCF_BT_INT16) : BCF_BT_INT8;
+        int dst_size = dst_id>>7 ? ( dst_id>>15 ? BCF_BT_INT32 : BCF_BT_INT16) : BCF_BT_INT8;
+        if ( src_size==dst_size )   // can overwrite
+        {
+            line->d.fmt[i].id = dst_id;
+            uint8_t *p = line->d.fmt[i].p - line->d.fmt[i].p_off;    // pointer to the vector size (4bits) and BT type (4bits)
+            if ( dst_size==BCF_BT_INT8 ) { p[1] = dst_id; }
+            else if ( dst_size==BCF_BT_INT16 ) { uint8_t *x = (uint8_t*) &dst_id; p[1] = x[0]; p[2] = x[1]; }
+            else { uint8_t *x = (uint8_t*) &dst_id; p[1] = x[0]; p[2] = x[1]; p[3] = x[2]; p[4] = x[3]; }
+        }
+        else    // must realloc
+        {
+            bcf_fmt_t *fmt = &line->d.fmt[i];
+            assert( !fmt->p_free );
+            kstring_t str = {0,0,0};
+            bcf_enc_int1(&str, dst_id);
+            bcf_enc_size(&str, fmt->n, fmt->type);
+            fmt->p_off = str.l;
+            kputsn((char*)fmt->p, fmt->p_len, &str);
+            fmt->p = (uint8_t*)str.s + fmt->p_off;
+            fmt->p_free = 1;
+            fmt->id = dst_id;
+            line->d.indiv_dirty = 1;
+        }
+    }
+    return 0;
+}
+
+bcf_hdr_t *bcf_hdr_dup(const bcf_hdr_t *hdr)
+{
+    bcf_hdr_t *hout = bcf_hdr_init("r");
+    char *htxt = bcf_hdr_fmt_text(hdr, 1, NULL);
+    if (!hout) {
+        fprintf(stderr, "[E::%s] failed to allocate bcf header\n", __func__);
+        free(htxt);
+        return NULL;
+    }
+    bcf_hdr_parse(hout, htxt);
+    free(htxt);
+    return hout;
+}
+
+bcf_hdr_t *bcf_hdr_subset(const bcf_hdr_t *h0, int n, char *const* samples, int *imap)
+{
+    int hlen;
+    void *names_hash = khash_str2int_init();
+    char *htxt = bcf_hdr_fmt_text(h0, 1, &hlen);
+    kstring_t str;
+    bcf_hdr_t *h;
+    str.l = str.m = 0; str.s = 0;
+    h = bcf_hdr_init("w");
+    if (!h) {
+        fprintf(stderr, "[E::%s] failed to allocate bcf header\n", __func__);
+        free(htxt);
+        return NULL;
+    }
+    bcf_hdr_set_version(h,bcf_hdr_get_version(h0));
+    int j;
+    for (j=0; j<n; j++) imap[j] = -1;
+    if ( bcf_hdr_nsamples(h0) > 0) {
+        char *p;
+        int i = 0, end = n? 8 : 7;
+        while ((p = strstr(htxt, "#CHROM\t")) != 0)
+            if (p > htxt && *(p-1) == '\n') break;
+        while ((p = strchr(p, '\t')) != 0 && i < end) ++i, ++p;
+        if (i != end) {
+            free(h); free(str.s);
+            return 0; // malformated header
+        }
+        kputsn(htxt, p - htxt, &str);
+        for (i = 0; i < n; ++i) {
+            if ( khash_str2int_has_key(names_hash,samples[i]) )
+            {
+                fprintf(stderr,"[E::bcf_hdr_subset] Duplicate sample name \"%s\".\n", samples[i]);
+                free(str.s);
+                free(htxt);
+                khash_str2int_destroy(names_hash);
+                bcf_hdr_destroy(h);
+                return NULL;
+            }
+            imap[i] = bcf_hdr_id2int(h0, BCF_DT_SAMPLE, samples[i]);
+            if (imap[i] < 0) continue;
+            kputc('\t', &str);
+            kputs(samples[i], &str);
+            khash_str2int_inc(names_hash,samples[i]);
+        }
+    } else kputsn(htxt, hlen, &str);
+    while (str.l && (!str.s[str.l-1] || str.s[str.l-1]=='\n') ) str.l--; // kill trailing zeros and newlines
+    kputc('\n',&str);
+    bcf_hdr_parse(h, str.s);
+    free(str.s);
+    free(htxt);
+    khash_str2int_destroy(names_hash);
+    return h;
+}
+
+int bcf_hdr_set_samples(bcf_hdr_t *hdr, const char *samples, int is_file)
+{
+    if ( samples && !strcmp("-",samples) ) return 0;            // keep all samples
+
+    hdr->nsamples_ori = bcf_hdr_nsamples(hdr);
+    if ( !samples ) { bcf_hdr_nsamples(hdr) = 0; return 0; }    // exclude all samples
+
+    int i, narr = bit_array_size(bcf_hdr_nsamples(hdr));
+    hdr->keep_samples = (uint8_t*) calloc(narr,1);
+    if ( samples[0]=='^' )
+        for (i=0; i<bcf_hdr_nsamples(hdr); i++) bit_array_set(hdr->keep_samples,i);
+
+    int idx, n, ret = 0;
+    char **smpls = hts_readlist(samples[0]=='^'?samples+1:samples, is_file, &n);
+    if ( !smpls ) return -1;
+    for (i=0; i<n; i++)
+    {
+        idx = bcf_hdr_id2int(hdr,BCF_DT_SAMPLE,smpls[i]);
+        if ( idx<0 )
+        {
+            if ( !ret ) ret = i+1;
+            continue;
+        }
+        assert( idx<bcf_hdr_nsamples(hdr) );
+        if (  samples[0]=='^' )
+            bit_array_clear(hdr->keep_samples, idx);
+        else
+            bit_array_set(hdr->keep_samples, idx);
+    }
+    for (i=0; i<n; i++) free(smpls[i]);
+    free(smpls);
+
+    bcf_hdr_nsamples(hdr) = 0;
+    for (i=0; i<hdr->nsamples_ori; i++)
+        if ( bit_array_test(hdr->keep_samples,i) ) bcf_hdr_nsamples(hdr)++;
+    if ( !bcf_hdr_nsamples(hdr) ) { free(hdr->keep_samples); hdr->keep_samples=NULL; }
+    else
+    {
+        char **samples = (char**) malloc(sizeof(char*)*bcf_hdr_nsamples(hdr));
+        idx = 0;
+        for (i=0; i<hdr->nsamples_ori; i++)
+            if ( bit_array_test(hdr->keep_samples,i) ) samples[idx++] = strdup(hdr->samples[i]);
+        free(hdr->samples);
+        hdr->samples = samples;
+
+        // delete original samples from the dictionary
+        vdict_t *d = (vdict_t*)hdr->dict[BCF_DT_SAMPLE];
+        int k;
+        for (k = kh_begin(d); k != kh_end(d); ++k)
+            if (kh_exist(d, k)) free((char*)kh_key(d, k));
+        kh_destroy(vdict, d);
+
+        // add the subset back
+        hdr->dict[BCF_DT_SAMPLE] = d = kh_init(vdict);
+        for (i=0; i<bcf_hdr_nsamples(hdr); i++)
+        {
+            int ignore, k = kh_put(vdict, d, hdr->samples[i], &ignore);
+            kh_val(d, k) = bcf_idinfo_def;
+            kh_val(d, k).id = kh_size(d) - 1;
+        }
+        bcf_hdr_sync(hdr);
+    }
+
+    return ret;
+}
+
+int bcf_subset(const bcf_hdr_t *h, bcf1_t *v, int n, int *imap)
+{
+    kstring_t ind;
+    ind.s = 0; ind.l = ind.m = 0;
+    if (n) {
+        bcf_fmt_t *fmt;
+        int i, j;
+        fmt = (bcf_fmt_t*)alloca(v->n_fmt * sizeof(bcf_fmt_t));
+        uint8_t *ptr = (uint8_t*)v->indiv.s;
+        for (i = 0; i < v->n_fmt; ++i)
+            ptr = bcf_unpack_fmt_core1(ptr, v->n_sample, &fmt[i]);
+        for (i = 0; i < (int)v->n_fmt; ++i) {
+            bcf_fmt_t *f = &fmt[i];
+            bcf_enc_int1(&ind, f->id);
+            bcf_enc_size(&ind, f->n, f->type);
+            for (j = 0; j < n; ++j)
+                if (imap[j] >= 0) kputsn((char*)(f->p + imap[j] * f->size), f->size, &ind);
+        }
+        for (i = j = 0; j < n; ++j) if (imap[j] >= 0) ++i;
+        v->n_sample = i;
+    } else v->n_sample = 0;
+    if ( !v->n_sample ) v->n_fmt = 0;
+    free(v->indiv.s);
+    v->indiv = ind;
+    v->unpacked &= ~BCF_UN_FMT;    // only BCF is ready for output, VCF will need to unpack again
+    return 0;
+}
+
+int bcf_is_snp(bcf1_t *v)
+{
+    int i;
+    bcf_unpack(v, BCF_UN_STR);
+    for (i = 0; i < v->n_allele; ++i)
+    {
+        if ( v->d.allele[i][1]==0 ) continue;
+
+        // mpileup's <X> allele, see also below. This is not completely satisfactory,
+        // a general library is here narrowly tailored to fit samtools.
+        if ( v->d.allele[i][0]=='<' && v->d.allele[i][1]=='X' && v->d.allele[i][2]=='>' ) continue;
+        if ( v->d.allele[i][0]=='<' && v->d.allele[i][1]=='*' && v->d.allele[i][2]=='>' ) continue;
+
+        break;
+    }
+    return i == v->n_allele;
+}
+
+static void bcf_set_variant_type(const char *ref, const char *alt, variant_t *var)
+{
+    // The most frequent case
+    if ( !ref[1] && !alt[1] )
+    {
+        if ( *alt == '.' || *ref==*alt ) { var->n = 0; var->type = VCF_REF; return; }
+        if ( *alt == 'X' ) { var->n = 0; var->type = VCF_REF; return; }  // mpileup's X allele shouldn't be treated as variant
+        if ( *alt == '*' ) { var->n = 0; var->type = VCF_REF; return; } 
+        var->n = 1; var->type = VCF_SNP; return;
+    }
+    if ( alt[0]=='<' )
+    {
+        if ( alt[1]=='X' && alt[2]=='>' ) { var->n = 0; var->type = VCF_REF; return; }  // mpileup's X allele shouldn't be treated as variant
+        if ( alt[1]=='*' && alt[2]=='>' ) { var->n = 0; var->type = VCF_REF; return; }
+        var->type = VCF_OTHER;
+        return;
+    }
+
+    const char *r = ref, *a = alt;
+    while (*r && *a && toupper(*r)==toupper(*a) ) { r++; a++; }     // unfortunately, matching REF,ALT case is not guaranteed
+
+    if ( *a && !*r )
+    {
+        while ( *a ) a++;
+        var->n = (a-alt)-(r-ref); var->type = VCF_INDEL; return;
+    }
+    else if ( *r && !*a )
+    {
+        while ( *r ) r++;
+        var->n = (a-alt)-(r-ref); var->type = VCF_INDEL; return;
+    }
+    else if ( !*r && !*a )
+    {
+        var->n = 0; var->type = VCF_REF; return;
+    }
+
+    const char *re = r, *ae = a;
+    while ( re[1] ) re++;
+    while ( ae[1] ) ae++;
+    while ( re>r && ae>a && toupper(*re)==toupper(*ae) ) { re--; ae--; }
+    if ( ae==a )
+    {
+        if ( re==r ) { var->n = 1; var->type = VCF_SNP; return; }
+        var->n = -(re-r);
+        if ( toupper(*re)==toupper(*ae) ) { var->type = VCF_INDEL; return; }
+        var->type = VCF_OTHER; return;
+    }
+    else if ( re==r )
+    {
+        var->n = ae-a;
+        if ( toupper(*re)==toupper(*ae) ) { var->type = VCF_INDEL; return; }
+        var->type = VCF_OTHER; return;
+    }
+
+    var->type = ( re-r == ae-a ) ? VCF_MNP : VCF_OTHER;
+    var->n = ( re-r > ae-a ) ? -(re-r+1) : ae-a+1;
+
+    // should do also complex events, SVs, etc...
+}
+
+static void bcf_set_variant_types(bcf1_t *b)
+{
+    if ( !(b->unpacked & BCF_UN_STR) ) bcf_unpack(b, BCF_UN_STR);
+    bcf_dec_t *d = &b->d;
+    if ( d->n_var < b->n_allele )
+    {
+        d->var = (variant_t *) realloc(d->var, sizeof(variant_t)*b->n_allele);
+        d->n_var = b->n_allele;
+    }
+    int i;
+    b->d.var_type = 0;
+    for (i=1; i<b->n_allele; i++)
+    {
+        bcf_set_variant_type(d->allele[0],d->allele[i], &d->var[i]);
+        b->d.var_type |= d->var[i].type;
+        //fprintf(stderr,"[set_variant_type] %d   %s %s -> %d %d .. %d\n", b->pos+1,d->allele[0],d->allele[i],d->var[i].type,d->var[i].n, b->d.var_type);
+    }
+}
+
+int bcf_get_variant_types(bcf1_t *rec)
+{
+    if ( rec->d.var_type==-1 ) bcf_set_variant_types(rec);
+    return rec->d.var_type;
+}
+int bcf_get_variant_type(bcf1_t *rec, int ith_allele)
+{
+    if ( rec->d.var_type==-1 ) bcf_set_variant_types(rec);
+    return rec->d.var[ith_allele].type;
+}
+
+int bcf_update_info(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const void *values, int n, int type)
+{
+    // Is the field already present?
+    int i, inf_id = bcf_hdr_id2int(hdr,BCF_DT_ID,key);
+    if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_INFO,inf_id) ) return -1;    // No such INFO field in the header
+    if ( !(line->unpacked & BCF_UN_INFO) ) bcf_unpack(line, BCF_UN_INFO);
+
+    for (i=0; i<line->n_info; i++)
+        if ( inf_id==line->d.info[i].key ) break;
+    bcf_info_t *inf = i==line->n_info ? NULL : &line->d.info[i];
+
+    if ( !n || (type==BCF_HT_STR && !values) )
+    {
+        if ( n==0 && !strcmp("END",key) )
+            line->rlen = line->n_allele ? strlen(line->d.allele[0]) : 0;
+        if ( inf )
+        {
+            // Mark the tag for removal, free existing memory if necessary
+            if ( inf->vptr_free )
+            {
+                free(inf->vptr - inf->vptr_off);
+                inf->vptr_free = 0;
+            }
+            line->d.shared_dirty |= BCF1_DIRTY_INF;
+            inf->vptr = NULL;
+        }
+        return 0;
+    }
+
+    // Encode the values and determine the size required to accommodate the values
+    kstring_t str = {0,0,0};
+    bcf_enc_int1(&str, inf_id);
+    if ( type==BCF_HT_INT )
+        bcf_enc_vint(&str, n, (int32_t*)values, -1);
+    else if ( type==BCF_HT_REAL )
+        bcf_enc_vfloat(&str, n, (float*)values);
+    else if ( type==BCF_HT_FLAG || type==BCF_HT_STR )
+    {
+        if ( values==NULL )
+            bcf_enc_size(&str, 0, BCF_BT_NULL);
+        else
+            bcf_enc_vchar(&str, strlen((char*)values), (char*)values);
+    }
+    else
+    {
+        fprintf(stderr, "[E::%s] the type %d not implemented yet\n", __func__, type);
+        abort();
+    }
+
+    // Is the INFO tag already present
+    if ( inf )
+    {
+        // Is it big enough to accommodate new block?
+        if ( str.l <= inf->vptr_len + inf->vptr_off )
+        {
+            if ( str.l != inf->vptr_len + inf->vptr_off ) line->d.shared_dirty |= BCF1_DIRTY_INF;
+            uint8_t *ptr = inf->vptr - inf->vptr_off;
+            memcpy(ptr, str.s, str.l);
+            free(str.s);
+            int vptr_free = inf->vptr_free;
+            bcf_unpack_info_core1(ptr, inf);
+            inf->vptr_free = vptr_free;
+        }
+        else
+        {
+            assert( !inf->vptr_free );  // fix the caller or improve here: this has been modified before
+            bcf_unpack_info_core1((uint8_t*)str.s, inf);
+            inf->vptr_free = 1;
+            line->d.shared_dirty |= BCF1_DIRTY_INF;
+        }
+    }
+    else
+    {
+        // The tag is not present, create new one
+        line->n_info++;
+        hts_expand0(bcf_info_t, line->n_info, line->d.m_info , line->d.info);
+        inf = &line->d.info[line->n_info-1];
+        bcf_unpack_info_core1((uint8_t*)str.s, inf);
+        inf->vptr_free = 1;
+        line->d.shared_dirty |= BCF1_DIRTY_INF;
+    }
+    line->unpacked |= BCF_UN_INFO;
+
+    if ( n==1 && !strcmp("END",key) ) line->rlen = ((int32_t*)values)[0] - line->pos;
+    return 0;
+}
+
+int bcf_update_format_string(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const char **values, int n)
+{
+    if ( !n )
+        return bcf_update_format(hdr,line,key,NULL,0,BCF_HT_STR);
+
+    int i, max_len = 0;
+    for (i=0; i<n; i++)
+    {
+        int len = strlen(values[i]);
+        if ( len > max_len ) max_len = len;
+    }
+    char *out = (char*) malloc(max_len*n);
+    if ( !out ) return -2;
+    for (i=0; i<n; i++)
+    {
+        char *dst = out+i*max_len;
+        const char *src = values[i];
+        int j = 0;
+        while ( src[j] ) { dst[j] = src[j]; j++; }
+        for (; j<max_len; j++) dst[j] = 0;
+    }
+    int ret = bcf_update_format(hdr,line,key,out,max_len*n,BCF_HT_STR);
+    free(out);
+    return ret;
+}
+
+int bcf_update_format(const bcf_hdr_t *hdr, bcf1_t *line, const char *key, const void *values, int n, int type)
+{
+    // Is the field already present?
+    int i, fmt_id = bcf_hdr_id2int(hdr,BCF_DT_ID,key);
+    if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_FMT,fmt_id) )
+    {
+        if ( !n ) return 0;
+        return -1;  // the key not present in the header
+    }
+
+    if ( !(line->unpacked & BCF_UN_FMT) ) bcf_unpack(line, BCF_UN_FMT);
+
+    for (i=0; i<line->n_fmt; i++)
+        if ( line->d.fmt[i].id==fmt_id ) break;
+    bcf_fmt_t *fmt = i==line->n_fmt ? NULL : &line->d.fmt[i];
+
+    if ( !n )
+    {
+        if ( fmt )
+        {
+            // Mark the tag for removal, free existing memory if necessary
+            if ( fmt->p_free )
+            {
+                free(fmt->p - fmt->p_off);
+                fmt->p_free = 0;
+            }
+            line->d.indiv_dirty = 1;
+            fmt->p = NULL;
+        }
+        return 0;
+    }
+
+    line->n_sample = bcf_hdr_nsamples(hdr);
+    int nps = n / line->n_sample;  // number of values per sample
+    assert( nps && nps*line->n_sample==n );     // must be divisible by n_sample
+
+    // Encode the values and determine the size required to accommodate the values
+    kstring_t str = {0,0,0};
+    bcf_enc_int1(&str, fmt_id);
+    if ( type==BCF_HT_INT )
+        bcf_enc_vint(&str, n, (int32_t*)values, nps);
+    else if ( type==BCF_HT_REAL )
+    {
+        bcf_enc_size(&str, nps, BCF_BT_FLOAT);
+        kputsn((char*)values, nps*line->n_sample*sizeof(float), &str);
+    }
+    else if ( type==BCF_HT_STR )
+    {
+        bcf_enc_size(&str, nps, BCF_BT_CHAR);
+        kputsn((char*)values, nps*line->n_sample, &str);
+    }
+    else
+    {
+        fprintf(stderr, "[E::%s] the type %d not implemented yet\n", __func__, type);
+        abort();
+    }
+
+    if ( !fmt )
+    {
+        // Not present, new format field
+        line->n_fmt++;
+        hts_expand0(bcf_fmt_t, line->n_fmt, line->d.m_fmt, line->d.fmt);
+
+        // Special case: VCF specification requires that GT is always first
+        if ( line->n_fmt > 1 && key[0]=='G' && key[1]=='T' && !key[2] )
+        {
+            for (i=line->n_fmt-1; i>0; i--)
+                line->d.fmt[i] = line->d.fmt[i-1];
+            fmt = &line->d.fmt[0];
+        }
+        else
+            fmt = &line->d.fmt[line->n_fmt-1];
+        bcf_unpack_fmt_core1((uint8_t*)str.s, line->n_sample, fmt);
+        line->d.indiv_dirty = 1;
+        fmt->p_free = 1;
+    }
+    else
+    {
+        // The tag is already present, check if it is big enough to accomodate the new block
+        if ( str.l <= fmt->p_len + fmt->p_off )
+        {
+            // good, the block is big enough
+            if ( str.l != fmt->p_len + fmt->p_off ) line->d.indiv_dirty = 1;
+            uint8_t *ptr = fmt->p - fmt->p_off;
+            memcpy(ptr, str.s, str.l);
+            free(str.s);
+            int p_free = fmt->p_free;
+            bcf_unpack_fmt_core1(ptr, line->n_sample, fmt);
+            fmt->p_free = p_free;
+        }
+        else
+        {
+            assert( !fmt->p_free );  // fix the caller or improve here: this has been modified before
+            bcf_unpack_fmt_core1((uint8_t*)str.s, line->n_sample, fmt);
+            fmt->p_free = 1;
+            line->d.indiv_dirty = 1;
+        }
+    }
+    line->unpacked |= BCF_UN_FMT;
+    return 0;
+}
+
+
+int bcf_update_filter(const bcf_hdr_t *hdr, bcf1_t *line, int *flt_ids, int n)
+{
+    if ( !(line->unpacked & BCF_UN_FLT) ) bcf_unpack(line, BCF_UN_FLT);
+    line->d.shared_dirty |= BCF1_DIRTY_FLT;
+    line->d.n_flt = n;
+    if ( !n ) return 0;
+    hts_expand(int, line->d.n_flt, line->d.m_flt, line->d.flt);
+    int i;
+    for (i=0; i<n; i++)
+        line->d.flt[i] = flt_ids[i];
+    return 0;
+}
+
+int bcf_add_filter(const bcf_hdr_t *hdr, bcf1_t *line, int flt_id)
+{
+    if ( !(line->unpacked & BCF_UN_FLT) ) bcf_unpack(line, BCF_UN_FLT);
+    int i;
+    for (i=0; i<line->d.n_flt; i++)
+        if ( flt_id==line->d.flt[i] ) break;
+    if ( i<line->d.n_flt ) return 0;    // this filter is already set
+    line->d.shared_dirty |= BCF1_DIRTY_FLT;
+    if ( flt_id==0 )    // set to PASS
+        line->d.n_flt = 1;
+    else if ( line->d.n_flt==1 && line->d.flt[0]==0 )
+        line->d.n_flt = 1;
+    else
+        line->d.n_flt++;
+    hts_expand(int, line->d.n_flt, line->d.m_flt, line->d.flt);
+    line->d.flt[line->d.n_flt-1] = flt_id;
+    return 1;
+}
+int bcf_remove_filter(const bcf_hdr_t *hdr, bcf1_t *line, int flt_id, int pass)
+{
+    if ( !(line->unpacked & BCF_UN_FLT) ) bcf_unpack(line, BCF_UN_FLT);
+    int i;
+    for (i=0; i<line->d.n_flt; i++)
+        if ( flt_id==line->d.flt[i] ) break;
+    if ( i==line->d.n_flt ) return 0;   // the filter is not present
+    line->d.shared_dirty |= BCF1_DIRTY_FLT;
+    if ( i!=line->d.n_flt-1 ) memmove(line->d.flt+i,line->d.flt+i+1,(line->d.n_flt-i-1)*sizeof(*line->d.flt));
+    line->d.n_flt--;
+    if ( !line->d.n_flt && pass ) bcf_add_filter(hdr,line,0);
+    return 0;
+}
+
+int bcf_has_filter(const bcf_hdr_t *hdr, bcf1_t *line, char *filter)
+{
+    if ( filter[0]=='.' && !filter[1] ) filter = "PASS";
+    int id = bcf_hdr_id2int(hdr, BCF_DT_ID, filter);
+    if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_FLT,id) ) return -1;  // not defined in the header
+
+    if ( !(line->unpacked & BCF_UN_FLT) ) bcf_unpack(line, BCF_UN_FLT);
+    if ( id==0 && !line->d.n_flt) return 1; // PASS
+
+    int i;
+    for (i=0; i<line->d.n_flt; i++)
+        if ( line->d.flt[i]==id ) return 1;
+    return 0;
+}
+
+static inline int _bcf1_sync_alleles(const bcf_hdr_t *hdr, bcf1_t *line, int nals)
+{
+    line->d.shared_dirty |= BCF1_DIRTY_ALS;
+
+    line->n_allele = nals;
+    hts_expand(char*, line->n_allele, line->d.m_allele, line->d.allele);
+
+    char *als = line->d.als;
+    int n = 0;
+    while (n<nals)
+    {
+        line->d.allele[n] = als;
+        while ( *als ) als++;
+        als++;
+        n++;
+    }
+
+    // Update REF length
+    bcf_info_t *end_info = bcf_get_info(hdr,line,"END");
+    line->rlen = end_info ? end_info->v1.i : strlen(line->d.allele[0]);
+
+    return 0;
+}
+int bcf_update_alleles(const bcf_hdr_t *hdr, bcf1_t *line, const char **alleles, int nals)
+{
+    kstring_t tmp = {0,0,0};
+    char *free_old = NULL;
+
+    // If the supplied alleles are not pointers to line->d.als, the existing block can be reused.
+    int i;
+    for (i=0; i<nals; i++)
+        if ( alleles[i]>=line->d.als && alleles[i]<line->d.als+line->d.m_als ) break;
+    if ( i==nals )
+    {
+        // all alleles point elsewhere, reuse the existing block
+        tmp.l = 0; tmp.s = line->d.als; tmp.m = line->d.m_als;
+    }
+    else
+        free_old = line->d.als;
+
+    for (i=0; i<nals; i++)
+    {
+        kputs(alleles[i], &tmp);
+        kputc(0, &tmp);
+    }
+    line->d.als = tmp.s; line->d.m_als = tmp.m;
+    free(free_old);
+    return _bcf1_sync_alleles(hdr,line,nals);
+}
+
+int bcf_update_alleles_str(const bcf_hdr_t *hdr, bcf1_t *line, const char *alleles_string)
+{
+    kstring_t tmp;
+    tmp.l = 0; tmp.s = line->d.als; tmp.m = line->d.m_als;
+    kputs(alleles_string, &tmp);
+    line->d.als = tmp.s; line->d.m_als = tmp.m;
+
+    int nals = 1;
+    char *t = line->d.als;
+    while (*t)
+    {
+        if ( *t==',' ) { *t = 0; nals++; }
+        t++;
+    }
+    return _bcf1_sync_alleles(hdr, line, nals);
+}
+
+int bcf_update_id(const bcf_hdr_t *hdr, bcf1_t *line, const char *id)
+{
+    kstring_t tmp;
+    tmp.l = 0; tmp.s = line->d.id; tmp.m = line->d.m_id;
+    if ( id )
+        kputs(id, &tmp);
+    else
+        kputs(".", &tmp);
+    line->d.id = tmp.s; line->d.m_id = tmp.m;
+    line->d.shared_dirty |= BCF1_DIRTY_ID;
+    return 0;
+}
+
+int bcf_add_id(const bcf_hdr_t *hdr, bcf1_t *line, const char *id)
+{
+    if ( !id ) return 0;
+
+    kstring_t tmp;
+    tmp.l = 0; tmp.s = line->d.id; tmp.m = line->d.m_id;
+
+    int len = strlen(id);
+    char *dst = line->d.id;
+    while ( *dst && (dst=strstr(dst,id)) )
+    {
+        if ( dst[len]!=0 && dst[len]!=';' ) dst++;              // a prefix, not a match
+        else if ( dst==line->d.id || dst[-1]==';' ) return 0;   // already present
+        dst++;  // a suffix, not a match
+    }
+    if ( line->d.id && (line->d.id[0]!='.' || line->d.id[1]) )
+    {
+        tmp.l = strlen(line->d.id);
+        kputc(';',&tmp);
+    }
+    kputs(id,&tmp);
+
+    line->d.id = tmp.s; line->d.m_id = tmp.m;
+    line->d.shared_dirty |= BCF1_DIRTY_ID;
+    return 0;
+
+}
+
+bcf_fmt_t *bcf_get_fmt(const bcf_hdr_t *hdr, bcf1_t *line, const char *key)
+{
+    int id = bcf_hdr_id2int(hdr, BCF_DT_ID, key);
+    if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_FMT,id) ) return NULL;   // no such FMT field in the header
+    return bcf_get_fmt_id(line, id);
+}
+
+bcf_info_t *bcf_get_info(const bcf_hdr_t *hdr, bcf1_t *line, const char *key)
+{
+    int id = bcf_hdr_id2int(hdr, BCF_DT_ID, key);
+    if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_INFO,id) ) return NULL;   // no such INFO field in the header
+    return bcf_get_info_id(line, id);
+}
+
+bcf_fmt_t *bcf_get_fmt_id(bcf1_t *line, const int id) 
+{
+    int i;
+    if ( !(line->unpacked & BCF_UN_FMT) ) bcf_unpack(line, BCF_UN_FMT);
+    for (i=0; i<line->n_fmt; i++)
+    {
+        if ( line->d.fmt[i].id==id ) return &line->d.fmt[i];
+    }
+    return NULL;
+}
+
+bcf_info_t *bcf_get_info_id(bcf1_t *line, const int id) 
+{
+    int i;
+    if ( !(line->unpacked & BCF_UN_INFO) ) bcf_unpack(line, BCF_UN_INFO);
+    for (i=0; i<line->n_info; i++)
+    {
+        if ( line->d.info[i].key==id ) return &line->d.info[i];
+    }
+    return NULL;
+}
+
+
+int bcf_get_info_values(const bcf_hdr_t *hdr, bcf1_t *line, const char *tag, void **dst, int *ndst, int type)
+{
+    int i,j, tag_id = bcf_hdr_id2int(hdr, BCF_DT_ID, tag);
+    if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_INFO,tag_id) ) return -1;    // no such INFO field in the header
+    if ( bcf_hdr_id2type(hdr,BCF_HL_INFO,tag_id)!=type ) return -2;     // expected different type
+
+    if ( !(line->unpacked & BCF_UN_INFO) ) bcf_unpack(line, BCF_UN_INFO);
+
+    for (i=0; i<line->n_info; i++)
+        if ( line->d.info[i].key==tag_id ) break;
+    if ( i==line->n_info ) return ( type==BCF_HT_FLAG ) ? 0 : -3;       // the tag is not present in this record
+    if ( type==BCF_HT_FLAG ) return 1;
+
+    bcf_info_t *info = &line->d.info[i];
+    if ( !info->vptr ) return -3;           // the tag was marked for removal
+    if ( type==BCF_HT_STR )
+    {
+        if ( *ndst < info->len+1 )
+        {
+            *ndst = info->len + 1;
+            *dst  = realloc(*dst, *ndst);
+        }
+        memcpy(*dst,info->vptr,info->len);
+        ((uint8_t*)*dst)[info->len] = 0;
+        return info->len;
+    }
+
+    // Make sure the buffer is big enough
+    int size1 = type==BCF_HT_INT ? sizeof(int32_t) : sizeof(float);
+    if ( *ndst < info->len )
+    {
+        *ndst = info->len;
+        *dst  = realloc(*dst, *ndst * size1);
+    }
+
+    if ( info->len == 1 )
+    {
+        if ( info->type==BCF_BT_FLOAT ) *((float*)*dst) = info->v1.f;
+        else 
+        {
+            #define BRANCH(type_t, missing) { \
+                if ( info->v1.i==missing ) *((int32_t*)*dst) = bcf_int32_missing; \
+                else *((int32_t*)*dst) = info->v1.i; \
+            }
+            switch (info->type)
+            {
+                case BCF_BT_INT8:  BRANCH(int8_t,  bcf_int8_missing ); break;
+                case BCF_BT_INT16: BRANCH(int16_t, bcf_int16_missing); break;
+                case BCF_BT_INT32: BRANCH(int32_t, bcf_int32_missing); break;
+            }
+            #undef BRANCH
+        }
+        return 1;
+    }
+
+    #define BRANCH(type_t, is_missing, is_vector_end, set_missing, out_type_t) { \
+        out_type_t *tmp = (out_type_t *) *dst; \
+        type_t *p = (type_t *) info->vptr; \
+        for (j=0; j<info->len; j++) \
+        { \
+            if ( is_vector_end ) return j; \
+            if ( is_missing ) set_missing; \
+            else *tmp = p[j]; \
+            tmp++; \
+        } \
+        return j; \
+    }
+    switch (info->type) {
+        case BCF_BT_INT8:  BRANCH(int8_t,  p[j]==bcf_int8_missing,  p[j]==bcf_int8_vector_end,  *tmp=bcf_int32_missing, int32_t); break;
+        case BCF_BT_INT16: BRANCH(int16_t, p[j]==bcf_int16_missing, p[j]==bcf_int16_vector_end, *tmp=bcf_int32_missing, int32_t); break;
+        case BCF_BT_INT32: BRANCH(int32_t, p[j]==bcf_int32_missing, p[j]==bcf_int32_vector_end, *tmp=bcf_int32_missing, int32_t); break;
+        case BCF_BT_FLOAT: BRANCH(float,   bcf_float_is_missing(p[j]), bcf_float_is_vector_end(p[j]), bcf_float_set_missing(*tmp), float); break;
+        default: fprintf(stderr,"TODO: %s:%d .. info->type=%d\n", __FILE__,__LINE__, info->type); exit(1);
+    }
+    #undef BRANCH
+    return -4;  // this can never happen
+}
+
+int bcf_get_format_string(const bcf_hdr_t *hdr, bcf1_t *line, const char *tag, char ***dst, int *ndst)
+{
+    int i,tag_id = bcf_hdr_id2int(hdr, BCF_DT_ID, tag);
+    if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_FMT,tag_id) ) return -1;    // no such FORMAT field in the header
+    if ( bcf_hdr_id2type(hdr,BCF_HL_FMT,tag_id)!=BCF_HT_STR ) return -2;     // expected different type
+
+    if ( !(line->unpacked & BCF_UN_FMT) ) bcf_unpack(line, BCF_UN_FMT);
+
+    for (i=0; i<line->n_fmt; i++)
+        if ( line->d.fmt[i].id==tag_id ) break;
+    if ( i==line->n_fmt ) return -3;                               // the tag is not present in this record
+    bcf_fmt_t *fmt = &line->d.fmt[i];
+    if ( !fmt->p ) return -3;                                      // the tag was marked for removal
+
+    int nsmpl = bcf_hdr_nsamples(hdr);
+    if ( !*dst )
+    {
+        *dst = (char**) malloc(sizeof(char*)*nsmpl);
+        if ( !*dst ) return -4;     // could not alloc
+        (*dst)[0] = NULL;
+    }
+    int n = (fmt->n+1)*nsmpl;
+    if ( *ndst < n )
+    {
+        (*dst)[0] = realloc((*dst)[0], n);
+        if ( !(*dst)[0] ) return -4;    // could not alloc
+        *ndst = n;
+    }
+    for (i=0; i<nsmpl; i++)
+    {
+        uint8_t *src = fmt->p + i*fmt->n;
+        uint8_t *tmp = (uint8_t*)(*dst)[0] + i*(fmt->n+1);
+        memcpy(tmp,src,fmt->n);
+        tmp[fmt->n] = 0;
+        (*dst)[i] = (char*) tmp;
+    }
+    return n;
+}
+
+int bcf_get_format_values(const bcf_hdr_t *hdr, bcf1_t *line, const char *tag, void **dst, int *ndst, int type)
+{
+    int i,j, tag_id = bcf_hdr_id2int(hdr, BCF_DT_ID, tag);
+    if ( !bcf_hdr_idinfo_exists(hdr,BCF_HL_FMT,tag_id) ) return -1;    // no such FORMAT field in the header
+    if ( tag[0]=='G' && tag[1]=='T' && tag[2]==0 )
+    {
+        // Ugly: GT field is considered to be a string by the VCF header but BCF represents it as INT.
+        if ( bcf_hdr_id2type(hdr,BCF_HL_FMT,tag_id)!=BCF_HT_STR ) return -2;
+    }
+    else if ( bcf_hdr_id2type(hdr,BCF_HL_FMT,tag_id)!=type ) return -2;     // expected different type
+
+    if ( !(line->unpacked & BCF_UN_FMT) ) bcf_unpack(line, BCF_UN_FMT);
+
+    for (i=0; i<line->n_fmt; i++)
+        if ( line->d.fmt[i].id==tag_id ) break;
+    if ( i==line->n_fmt ) return -3;                               // the tag is not present in this record
+    bcf_fmt_t *fmt = &line->d.fmt[i];
+    if ( !fmt->p ) return -3;                                      // the tag was marked for removal
+
+    if ( type==BCF_HT_STR )
+    {
+        int n = fmt->n*bcf_hdr_nsamples(hdr);
+        if ( *ndst < n )
+        {
+            *dst  = realloc(*dst, n);
+            if ( !*dst ) return -4;     // could not alloc
+            *ndst = n;
+        }
+        memcpy(*dst,fmt->p,n);
+        return n;
+    }
+
+    // Make sure the buffer is big enough
+    int nsmpl = bcf_hdr_nsamples(hdr);
+    int size1 = type==BCF_HT_INT ? sizeof(int32_t) : sizeof(float);
+    if ( *ndst < fmt->n*nsmpl )
+    {
+        *ndst = fmt->n*nsmpl;
+        *dst  = realloc(*dst, *ndst*size1);
+        if ( !dst ) return -4;     // could not alloc
+    }
+
+    #define BRANCH(type_t, is_missing, is_vector_end, set_missing, set_vector_end, out_type_t) { \
+        out_type_t *tmp = (out_type_t *) *dst; \
+        type_t *p = (type_t*) fmt->p; \
+        for (i=0; i<nsmpl; i++) \
+        { \
+            for (j=0; j<fmt->n; j++) \
+            { \
+                if ( is_missing ) set_missing; \
+                else if ( is_vector_end ) { set_vector_end; break; } \
+                else *tmp = p[j]; \
+                tmp++; \
+            } \
+            for (; j<fmt->n; j++) { set_vector_end; tmp++; } \
+            p = (type_t *)((char *)p + fmt->size); \
+        } \
+    }
+    switch (fmt->type) {
+        case BCF_BT_INT8:  BRANCH(int8_t,  p[j]==bcf_int8_missing,  p[j]==bcf_int8_vector_end,  *tmp=bcf_int32_missing, *tmp=bcf_int32_vector_end, int32_t); break;
+        case BCF_BT_INT16: BRANCH(int16_t, p[j]==bcf_int16_missing, p[j]==bcf_int16_vector_end, *tmp=bcf_int32_missing, *tmp=bcf_int32_vector_end, int32_t); break;
+        case BCF_BT_INT32: BRANCH(int32_t, p[j]==bcf_int32_missing, p[j]==bcf_int32_vector_end, *tmp=bcf_int32_missing, *tmp=bcf_int32_vector_end, int32_t); break;
+        case BCF_BT_FLOAT: BRANCH(float,   bcf_float_is_missing(p[j]), bcf_float_is_vector_end(p[j]), bcf_float_set_missing(*tmp), bcf_float_set_vector_end(*tmp), float); break;
+        default: fprintf(stderr,"TODO: %s:%d .. fmt->type=%d\n", __FILE__,__LINE__, fmt->type); exit(1);
+    }
+    #undef BRANCH
+    return nsmpl*fmt->n;
+}
+
diff --git a/htslib/vcf_sweep.c b/htslib/vcf_sweep.c
new file mode 100644
index 0000000..38e384f
--- /dev/null
+++ b/htslib/vcf_sweep.c
@@ -0,0 +1,183 @@
+/*  vcf_sweep.c -- forward/reverse sweep API.
+
+    Copyright (C) 2013 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3 at sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include "htslib/vcf_sweep.h"
+#include "htslib/bgzf.h"
+
+#define SW_FWD 0
+#define SW_BWD 1
+
+struct _bcf_sweep_t
+{
+    htsFile *file;
+    bcf_hdr_t *hdr;
+    BGZF *fp;
+
+    int direction;          // to tell if the direction has changed
+    int block_size;         // the size of uncompressed data to hold in memory
+    bcf1_t *rec;            // bcf buffer
+    int nrec, mrec;         // number of used records; total size of the buffer
+    int lrid, lpos, lnals, lals_len, mlals;   // to check uniqueness of a record
+    char *lals;
+
+    uint64_t *idx;          // uncompressed offsets of VCF/BCF records
+    int iidx, nidx, midx;   // i: current offset; n: used; m: allocated
+    int idx_done;           // the index is built during the first pass
+};
+
+BGZF *hts_get_bgzfp(htsFile *fp);
+int hts_useek(htsFile *file, long uoffset, int where);
+long hts_utell(htsFile *file);
+
+static inline int sw_rec_equal(bcf_sweep_t *sw, bcf1_t *rec)
+{
+    if ( sw->lrid!=rec->rid ) return 0;
+    if ( sw->lpos!=rec->pos ) return 0;
+    if ( sw->lnals!=rec->n_allele ) return 0;
+
+    char *t = rec->d.allele[sw->lnals-1];
+    int len = t - rec->d.allele[0] + 1;
+    while ( *t ) { t++; len++; }
+    if ( sw->lals_len!=len ) return 0;
+    if ( memcmp(sw->lals,rec->d.allele[0],len) ) return 0;
+    return 1;
+}
+
+static void sw_rec_save(bcf_sweep_t *sw, bcf1_t *rec)
+{
+    sw->lrid  = rec->rid;
+    sw->lpos  = rec->pos;
+    sw->lnals = rec->n_allele;
+
+    char *t = rec->d.allele[sw->lnals-1];
+    int len = t - rec->d.allele[0] + 1;
+    while ( *t ) { t++; len++; }
+    sw->lals_len = len;
+    hts_expand(char, len, sw->mlals, sw->lals);
+    memcpy(sw->lals, rec->d.allele[0], len);
+}
+
+static void sw_fill_buffer(bcf_sweep_t *sw)
+{
+    if ( !sw->iidx ) return;
+    sw->iidx--;
+
+    int ret = hts_useek(sw->file, sw->idx[sw->iidx], 0);
+    assert( ret==0 );
+
+    sw->nrec = 0;
+    bcf1_t *rec = &sw->rec[sw->nrec];
+    while ( (ret=bcf_read1(sw->file, sw->hdr, rec))==0 )
+    {
+        bcf_unpack(rec, BCF_UN_STR);
+
+        // if not in the last block, stop at the saved record
+        if ( sw->iidx+1 < sw->nidx && sw_rec_equal(sw,rec) ) break;
+
+        sw->nrec++;
+        hts_expand0(bcf1_t, sw->nrec+1, sw->mrec, sw->rec);
+        rec = &sw->rec[sw->nrec];
+    }
+    sw_rec_save(sw, &sw->rec[0]);
+}
+
+bcf_sweep_t *bcf_sweep_init(const char *fname)
+{
+    bcf_sweep_t *sw = (bcf_sweep_t*) calloc(1,sizeof(bcf_sweep_t));
+    sw->file = hts_open(fname, "r");
+    sw->fp   = hts_get_bgzfp(sw->file);
+    bgzf_index_build_init(sw->fp);
+    sw->hdr  = bcf_hdr_read(sw->file);
+    sw->mrec = 1;
+    sw->rec  = (bcf1_t*) calloc(sw->mrec,(sizeof(bcf1_t)));
+    sw->block_size = 1024*1024*3;
+    sw->direction = SW_FWD;
+    return sw;
+}
+
+void bcf_sweep_destroy(bcf_sweep_t *sw)
+{
+    int i;
+    for (i=0; i<sw->mrec; i++) bcf_empty1(&sw->rec[i]);
+    free(sw->idx);
+    free(sw->rec);
+    free(sw->lals);
+    bcf_hdr_destroy(sw->hdr);
+    hts_close(sw->file);
+    free(sw);
+}
+
+static void sw_seek(bcf_sweep_t *sw, int direction)
+{
+    sw->direction = direction;
+    if ( direction==SW_FWD )
+        hts_useek(sw->file, sw->idx[0], 0);
+    else
+    {
+        sw->iidx = sw->nidx;
+        sw->nrec = 0;
+    }
+}
+
+bcf1_t *bcf_sweep_fwd(bcf_sweep_t *sw)
+{
+    if ( sw->direction==SW_BWD ) sw_seek(sw, SW_FWD);
+
+    long pos = hts_utell(sw->file);
+
+    bcf1_t *rec = &sw->rec[0];
+    int ret = bcf_read1(sw->file, sw->hdr, rec);
+
+    if ( ret!=0 )   // last record, get ready for sweeping backwards
+    {
+        sw->idx_done = 1;
+        sw->fp->idx_build_otf = 0;
+        sw_seek(sw, SW_BWD);
+        return NULL;
+    }
+
+    if ( !sw->idx_done )
+    {
+        if ( !sw->nidx || pos - sw->idx[sw->nidx-1] > sw->block_size )
+        {
+            sw->nidx++;
+            hts_expand(uint64_t, sw->nidx, sw->midx, sw->idx);
+            sw->idx[sw->nidx-1] = pos;
+        }
+    }
+    return rec;
+}
+
+bcf1_t *bcf_sweep_bwd(bcf_sweep_t *sw)
+{
+    if ( sw->direction==SW_FWD ) sw_seek(sw, SW_BWD);
+    if ( !sw->nrec ) sw_fill_buffer(sw);
+    if ( !sw->nrec ) return NULL;
+    return &sw->rec[ --sw->nrec ];
+}
+
+bcf_hdr_t *bcf_sweep_hdr(bcf_sweep_t *sw) { return sw->hdr; }
+
diff --git a/htslib/vcfutils.c b/htslib/vcfutils.c
new file mode 100644
index 0000000..141fe0e
--- /dev/null
+++ b/htslib/vcfutils.c
@@ -0,0 +1,691 @@
+/*  vcfutils.c -- allele-related utility functions.
+
+    Copyright (C) 2012-2015 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3 at sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include "htslib/vcfutils.h"
+#include "htslib/kbitset.h"
+
+int bcf_calc_ac(const bcf_hdr_t *header, bcf1_t *line, int *ac, int which)
+{
+    int i;
+    for (i=0; i<line->n_allele; i++) ac[i]=0;
+
+    // Use INFO/AC,AN field only when asked
+    if ( which&BCF_UN_INFO )
+    {
+        bcf_unpack(line, BCF_UN_INFO);
+        int an_id = bcf_hdr_id2int(header, BCF_DT_ID, "AN");
+        int ac_id = bcf_hdr_id2int(header, BCF_DT_ID, "AC");
+        int i, an=-1, ac_len=0, ac_type=0;
+        uint8_t *ac_ptr=NULL;
+        if ( an_id>=0 && ac_id>=0 )
+        {
+            for (i=0; i<line->n_info; i++)
+            {
+                bcf_info_t *z = &line->d.info[i];
+                if ( z->key == an_id ) an = z->v1.i;
+                else if ( z->key == ac_id ) { ac_ptr = z->vptr; ac_len = z->len; ac_type = z->type; }
+            }
+        }
+        if ( an>=0 && ac_ptr )
+        {
+            int nac = 0;
+            #define BRANCH_INT(type_t) {        \
+                type_t *p = (type_t *) ac_ptr;  \
+                for (i=0; i<ac_len; i++)        \
+                {                               \
+                    ac[i+1] = p[i];             \
+                    nac += p[i];                \
+                }                               \
+            }
+            switch (ac_type) {
+                case BCF_BT_INT8:  BRANCH_INT(int8_t); break;
+                case BCF_BT_INT16: BRANCH_INT(int16_t); break;
+                case BCF_BT_INT32: BRANCH_INT(int32_t); break;
+                default: fprintf(stderr, "[E::%s] todo: %d at %s:%d\n", __func__, ac_type, header->id[BCF_DT_CTG][line->rid].key, line->pos+1); exit(1); break;
+            }
+            #undef BRANCH_INT
+            if ( an<nac )
+            {
+                fprintf(stderr,"[E::%s] Incorrect AN/AC counts at %s:%d\n", __func__,header->id[BCF_DT_CTG][line->rid].key, line->pos+1); 
+                exit(1); 
+            }
+            ac[0] = an - nac;
+            return 1;
+        }
+    }
+
+    // Split genotype fields only when asked
+    if ( which&BCF_UN_FMT )
+    {
+        int i, gt_id = bcf_hdr_id2int(header,BCF_DT_ID,"GT");
+        if ( gt_id<0 ) return 0;
+        bcf_unpack(line, BCF_UN_FMT);
+        bcf_fmt_t *fmt_gt = NULL;
+        for (i=0; i<(int)line->n_fmt; i++)
+            if ( line->d.fmt[i].id==gt_id ) { fmt_gt = &line->d.fmt[i]; break; }
+        if ( !fmt_gt ) return 0;
+        #define BRANCH_INT(type_t,vector_end) { \
+            for (i=0; i<line->n_sample; i++) \
+            { \
+                type_t *p = (type_t*) (fmt_gt->p + i*fmt_gt->size); \
+                int ial; \
+                for (ial=0; ial<fmt_gt->n; ial++) \
+                { \
+                    if ( p[ial]==vector_end ) break; /* smaller ploidy */ \
+                    if ( bcf_gt_is_missing(p[ial]) ) continue; /* missing allele */ \
+                    if ( p[ial]>>1 > line->n_allele ) \
+                    { \
+                        fprintf(stderr,"[E::%s] Incorrect allele (\"%d\") in %s at %s:%d\n", __func__,(p[ial]>>1)-1, header->samples[i],header->id[BCF_DT_CTG][line->rid].key, line->pos+1); \
+                        exit(1); \
+                    } \
+                    ac[(p[ial]>>1)-1]++; \
+                } \
+            } \
+        }
+        switch (fmt_gt->type) {
+            case BCF_BT_INT8:  BRANCH_INT(int8_t,  bcf_int8_vector_end); break;
+            case BCF_BT_INT16: BRANCH_INT(int16_t, bcf_int16_vector_end); break;
+            case BCF_BT_INT32: BRANCH_INT(int32_t, bcf_int32_vector_end); break;
+            default: fprintf(stderr, "[E::%s] todo: %d at %s:%d\n", __func__, fmt_gt->type, header->id[BCF_DT_CTG][line->rid].key, line->pos+1); exit(1); break;
+        }
+        #undef BRANCH_INT
+        return 1;
+    }
+    return 0;
+}
+
+int bcf_gt_type(bcf_fmt_t *fmt_ptr, int isample, int *_ial, int *_jal)
+{
+    int i, nals = 0, has_ref = 0, has_alt = 0, ial = 0, jal = 0;
+    #define BRANCH_INT(type_t,vector_end) { \
+        type_t *p = (type_t*) (fmt_ptr->p + isample*fmt_ptr->size); \
+        for (i=0; i<fmt_ptr->n; i++) \
+        { \
+            if ( p[i] == vector_end ) break; /* smaller ploidy */ \
+            if ( bcf_gt_is_missing(p[i]) ) return GT_UNKN; /* missing allele */ \
+            int tmp = p[i]>>1; \
+            if ( tmp>1 ) \
+            { \
+                if ( !ial ) { ial = tmp; has_alt = 1; } \
+                else if ( tmp!=ial ) \
+                { \
+                    if ( tmp<ial ) \
+                    { \
+                        jal = ial; \
+                        ial = tmp; \
+                    } \
+                    else \
+                    { \
+                        jal = tmp; \
+                    } \
+                    has_alt = 2; \
+                } \
+            } \
+            else has_ref = 1; \
+            nals++; \
+        } \
+    }
+    switch (fmt_ptr->type) {
+        case BCF_BT_INT8:  BRANCH_INT(int8_t,  bcf_int8_vector_end); break;
+        case BCF_BT_INT16: BRANCH_INT(int16_t, bcf_int16_vector_end); break;
+        case BCF_BT_INT32: BRANCH_INT(int32_t, bcf_int32_vector_end); break;
+        default: fprintf(stderr, "[E::%s] todo: fmt_type %d\n", __func__, fmt_ptr->type); exit(1); break;
+    }
+    #undef BRANCH_INT
+
+    if ( _ial ) *_ial = ial>0 ? ial-1 : ial;
+    if ( _jal ) *_jal = jal>0 ? jal-1 : jal;
+    if ( !nals ) return GT_UNKN;
+    if ( nals==1 )
+        return has_ref ? GT_HAPL_R : GT_HAPL_A;
+    if ( !has_ref )
+        return has_alt==1 ? GT_HOM_AA : GT_HET_AA;
+    if ( !has_alt )
+        return GT_HOM_RR;
+    return GT_HET_RA;
+}
+
+int bcf_trim_alleles(const bcf_hdr_t *header, bcf1_t *line)
+{
+    int i;
+    bcf_fmt_t *gt = bcf_get_fmt(header, line, "GT");
+    if ( !gt ) return 0;
+
+    int *ac = (int*) calloc(line->n_allele,sizeof(int));
+
+    // check if all alleles are populated
+    #define BRANCH(type_t,vector_end) { \
+        for (i=0; i<line->n_sample; i++) \
+        { \
+            type_t *p = (type_t*) (gt->p + i*gt->size); \
+            int ial; \
+            for (ial=0; ial<gt->n; ial++) \
+            { \
+                if ( p[ial]==vector_end ) break; /* smaller ploidy */ \
+                if ( bcf_gt_is_missing(p[ial]) ) continue; /* missing allele */ \
+                if ( (p[ial]>>1)-1 >= line->n_allele ) { free(ac); return -1; } \
+                ac[(p[ial]>>1)-1]++; \
+            } \
+        } \
+    }
+    switch (gt->type) {
+        case BCF_BT_INT8:  BRANCH(int8_t,  bcf_int8_vector_end); break;
+        case BCF_BT_INT16: BRANCH(int16_t, bcf_int16_vector_end); break;
+        case BCF_BT_INT32: BRANCH(int32_t, bcf_int32_vector_end); break;
+        default: fprintf(stderr, "[E::%s] todo: %d at %s:%d\n", __func__, gt->type, header->id[BCF_DT_CTG][line->rid].key, line->pos+1); exit(1); break;
+    }
+    #undef BRANCH
+
+    int nrm = 0;
+    kbitset_t *rm_set = kbs_init(line->n_allele);
+    for (i=1; i<line->n_allele; i++)
+    {
+        if ( !ac[i] ) { kbs_insert(rm_set, i); nrm++; }
+    }
+    free(ac);
+
+    if ( nrm ) bcf_remove_allele_set(header, line, rm_set);
+    kbs_destroy(rm_set);
+    return nrm;
+}
+
+void bcf_remove_alleles(const bcf_hdr_t *header, bcf1_t *line, int rm_mask)
+{
+    int i;
+    kbitset_t *rm_set = kbs_init(line->n_allele);
+    for (i=1; i<line->n_allele; i++)
+        if ( rm_mask & 1<<i ) kbs_insert(rm_set, i);
+
+    bcf_remove_allele_set(header, line, rm_set);
+    kbs_destroy(rm_set);
+}
+
+void bcf_remove_allele_set(const bcf_hdr_t *header, bcf1_t *line, const struct kbitset_t *rm_set)
+{
+    int *map = (int*) calloc(line->n_allele, sizeof(int));
+
+    // create map of indexes from old to new ALT numbering and modify ALT
+    kstring_t str = {0,0,0};
+    kputs(line->d.allele[0], &str);
+
+    int nrm = 0, i,j;  // i: ori alleles, j: new alleles
+    for (i=1, j=1; i<line->n_allele; i++)
+    {
+        if ( kbs_exists(rm_set, i) )
+        {
+            // remove this allele
+            line->d.allele[i] = NULL;
+            nrm++;
+            continue;
+        }
+        kputc(',', &str);
+        kputs(line->d.allele[i], &str);
+        map[i] = j;
+        j++;
+    }
+    if ( !nrm ) { free(map); free(str.s); return; }
+
+    int nR_ori = line->n_allele;
+    int nR_new = line->n_allele-nrm;
+    assert(nR_new > 0); // should not be able to remove reference allele
+    int nA_ori = nR_ori-1;
+    int nA_new = nR_new-1;
+
+    int nG_ori = nR_ori*(nR_ori + 1)/2;
+    int nG_new = nR_new*(nR_new + 1)/2;
+
+    bcf_update_alleles_str(header, line, str.s);
+
+    // remove from Number=G, Number=R and Number=A INFO fields.
+    uint8_t *dat = NULL;
+    int mdat = 0, ndat = 0, mdat_bytes = 0, nret;
+    for (i=0; i<line->n_info; i++)
+    {
+        bcf_info_t *info = &line->d.info[i];
+        int vlen = bcf_hdr_id2length(header,BCF_HL_INFO,info->key);
+
+        if ( vlen!=BCF_VL_A && vlen!=BCF_VL_G && vlen!=BCF_VL_R ) continue; // no need to change
+
+        int type = bcf_hdr_id2type(header,BCF_HL_INFO,info->key);
+        if ( type==BCF_HT_FLAG ) continue;
+        int size = 1;
+        if ( type==BCF_HT_REAL || type==BCF_HT_INT ) size = 4;
+
+        mdat = mdat_bytes / size;
+        nret = bcf_get_info_values(header, line, bcf_hdr_int2id(header,BCF_DT_ID,info->key), (void**)&dat, &mdat, type);
+        mdat_bytes = mdat * size;
+        if ( nret<0 )
+        {
+            fprintf(stderr,"[%s:%d %s] Could not access INFO/%s at %s:%d [%d]\n", __FILE__,__LINE__,__FUNCTION__,
+                bcf_hdr_int2id(header,BCF_DT_ID,info->key), bcf_seqname(header,line), line->pos+1, nret);
+            exit(1);
+        }
+        if ( type==BCF_HT_STR )
+        {
+            str.l = 0;
+            char *ss = (char*) dat, *se = (char*) dat;
+            if ( vlen==BCF_VL_A || vlen==BCF_VL_R )
+            {
+                int nexp, inc = 0;
+                if ( vlen==BCF_VL_A )
+                {
+                    nexp = nA_ori;
+                    inc  = 1;
+                }
+                else
+                    nexp = nR_ori;
+                for (j=0; j<nexp; j++)
+                {
+                    if ( !*se ) break;
+                    while ( *se && *se!=',' ) se++;
+                    if ( kbs_exists(rm_set, j+inc) )
+                    {
+                        if ( *se ) se++;
+                        ss = se;
+                        continue;
+                    }
+                    if ( str.l ) kputc(',',&str);
+                    kputsn(ss,se-ss,&str);
+                    if ( *se ) se++;
+                    ss = se;
+                }
+                assert( j==nexp );
+            }
+            else    // Number=G, assuming diploid genotype
+            {
+                int k = 0, n = 0;
+                for (j=0; j<nR_ori; j++)
+                {
+                    for (k=0; k<=j; k++)
+                    {
+                        if ( !*se ) break;
+                        while ( *se && *se!=',' ) se++;
+                        n++;
+                        if ( kbs_exists(rm_set, j) || kbs_exists(rm_set, k) )
+                        {
+                            if ( *se ) se++;
+                            ss = se;
+                            continue;
+                        }
+                        if ( str.l ) kputc(',',&str);
+                        kputsn(ss,se-ss,&str);
+                        if ( *se ) se++;
+                        ss = se;
+                    }
+                    if ( !*se ) break;
+                }
+                assert( n==nG_ori );
+            }
+
+            nret = bcf_update_info(header, line, bcf_hdr_int2id(header,BCF_DT_ID,info->key), (void*)str.s, str.l, type);
+            if ( nret<0 )
+            {
+                fprintf(stderr,"[%s:%d %s] Could not update INFO/%s at %s:%d [%d]\n", __FILE__,__LINE__,__FUNCTION__,
+                        bcf_hdr_int2id(header,BCF_DT_ID,info->key), bcf_seqname(header,line), line->pos+1, nret);
+                exit(1);
+            }
+            continue;
+        }
+
+        if ( vlen==BCF_VL_A || vlen==BCF_VL_R )
+        {
+            int inc = 0, ntop;
+            if ( vlen==BCF_VL_A )
+            {
+                assert( nret==nA_ori );
+                ntop = nA_ori;
+                ndat = nA_new;
+                inc  = 1;
+            }
+            else
+            {
+                assert( nret==nR_ori );
+                ntop = nR_ori;
+                ndat = nR_new;
+            }
+            int k = 0;
+
+            #define BRANCH(type_t,is_vector_end) \
+            { \
+                type_t *ptr = (type_t*) dat; \
+                int size = sizeof(type_t); \
+                for (j=0; j<ntop; j++) /* j:ori, k:new */ \
+                { \
+                    if ( is_vector_end ) { memcpy(dat+k*size, dat+j*size, size); break; } \
+                    if ( kbs_exists(rm_set, j+inc) ) continue; \
+                    if ( j!=k ) memcpy(dat+k*size, dat+j*size, size); \
+                    k++; \
+                } \
+            }
+            switch (type)
+            {
+                case BCF_HT_INT:  BRANCH(int32_t,ptr[j]==bcf_int32_vector_end); break;
+                case BCF_HT_REAL: BRANCH(float,bcf_float_is_vector_end(ptr[j])); break;
+            }
+            #undef BRANCH
+        }
+        else    // Number=G
+        {
+            assert( nret==nG_ori );
+            int k, l_ori = -1, l_new = 0;
+            ndat = nG_new;
+
+            #define BRANCH(type_t,is_vector_end) \
+            { \
+                type_t *ptr = (type_t*) dat; \
+                int size = sizeof(type_t); \
+                for (j=0; j<nR_ori; j++) \
+                { \
+                    for (k=0; k<=j; k++) \
+                    { \
+                        l_ori++; \
+                        if ( is_vector_end ) { memcpy(dat+l_new*size, dat+l_ori*size, size); break; } \
+                        if ( kbs_exists(rm_set, j) || kbs_exists(rm_set, k) ) continue; \
+                        if ( l_ori!=l_new ) memcpy(dat+l_new*size, dat+l_ori*size, size); \
+                        l_new++; \
+                    } \
+                } \
+            }
+            switch (type)
+            {
+                case BCF_HT_INT:  BRANCH(int32_t,ptr[l_ori]==bcf_int32_vector_end); break;
+                case BCF_HT_REAL: BRANCH(float,bcf_float_is_vector_end(ptr[l_ori])); break;
+            }
+            #undef BRANCH
+        }
+
+        nret = bcf_update_info(header, line, bcf_hdr_int2id(header,BCF_DT_ID,info->key), (void*)dat, ndat, type);
+        if ( nret<0 )
+        {
+            fprintf(stderr,"[%s:%d %s] Could not update INFO/%s at %s:%d [%d]\n", __FILE__,__LINE__,__FUNCTION__,
+                    bcf_hdr_int2id(header,BCF_DT_ID,info->key), bcf_seqname(header,line), line->pos+1, nret);
+            exit(1);
+        }
+    }
+
+    // Update GT fields, the allele indexes might have changed
+    for (i=1; i<line->n_allele; i++) if ( map[i]!=i ) break;
+    if ( i<line->n_allele )
+    {
+        mdat = mdat_bytes / 4;  // sizeof(int32_t)
+        nret = bcf_get_genotypes(header,line,(void**)&dat,&mdat);
+        mdat_bytes = mdat * 4;
+        if ( nret>0 )
+        {
+            nret /= line->n_sample;
+            int32_t *ptr = (int32_t*) dat;
+            for (i=0; i<line->n_sample; i++)
+            {
+                for (j=0; j<nret; j++)
+                {
+                    if ( bcf_gt_is_missing(ptr[j]) ) continue;
+                    if ( ptr[j]==bcf_int32_vector_end ) break;
+                    int al = bcf_gt_allele(ptr[j]);
+                    assert( al<nR_ori && map[al]>=0 );
+                    ptr[j] = (map[al]+1)<<1 | (ptr[j]&1);
+                }
+                ptr += nret;
+            }
+            bcf_update_genotypes(header, line, (void*)dat, nret*line->n_sample);
+        }
+    }
+
+    // Remove from Number=G, Number=R and Number=A FORMAT fields.
+    // Assuming haploid or diploid GTs
+    for (i=0; i<line->n_fmt; i++)
+    {
+        bcf_fmt_t *fmt = &line->d.fmt[i];
+        int vlen = bcf_hdr_id2length(header,BCF_HL_FMT,fmt->id);
+
+        if ( vlen!=BCF_VL_A && vlen!=BCF_VL_G && vlen!=BCF_VL_R ) continue; // no need to change
+
+        int type = bcf_hdr_id2type(header,BCF_HL_FMT,fmt->id);
+        if ( type==BCF_HT_FLAG ) continue;
+
+        int size = 1;
+        if ( type==BCF_HT_REAL || type==BCF_HT_INT ) size = 4;
+
+        mdat = mdat_bytes / size;
+        nret = bcf_get_format_values(header, line, bcf_hdr_int2id(header,BCF_DT_ID,fmt->id), (void**)&dat, &mdat, type);
+        mdat_bytes = mdat * size;
+        if ( nret<0 )
+        {
+            fprintf(stderr,"[%s:%d %s] Could not access FORMAT/%s at %s:%d [%d]\n", __FILE__,__LINE__,__FUNCTION__,
+                    bcf_hdr_int2id(header,BCF_DT_ID,fmt->id), bcf_seqname(header,line), line->pos+1, nret);
+            exit(1);
+        }
+
+        if ( type==BCF_HT_STR )
+        {
+            int size = nret/line->n_sample;     // number of bytes per sample
+            str.l = 0;
+            if ( vlen==BCF_VL_A || vlen==BCF_VL_R )
+            {
+                int nexp, inc = 0;
+                if ( vlen==BCF_VL_A )
+                {
+                    nexp = nA_ori;
+                    inc  = 1;
+                }
+                else
+                    nexp = nR_ori;
+                for (j=0; j<line->n_sample; j++)
+                {
+                    char *ss = ((char*)dat) + j*size, *se = ss + size, *ptr = ss;
+                    int k_src = 0, k_dst = 0, l = str.l;
+                    for (k_src=0; k_src<nexp; k_src++)
+                    {
+                        if ( ptr>=se || !*ptr) break;
+                        while ( ptr<se && *ptr && *ptr!=',' ) ptr++;
+                        if ( kbs_exists(rm_set, k_src+inc) )
+                        {
+                            ss = ++ptr;
+                            continue;
+                        }
+                        if ( k_dst ) kputc(',',&str);
+                        kputsn(ss,ptr-ss,&str);
+                        ss = ++ptr;
+                        k_dst++;
+                    }
+                    assert( k_src==nexp );
+                    l = str.l - l;
+                    for (; l<size; l++) kputc(0, &str);
+                }
+            }
+            else    // Number=G, diploid or haploid
+            {
+                for (j=0; j<line->n_sample; j++)
+                {
+                    char *ss = ((char*)dat) + j*size, *se = ss + size, *ptr = ss;
+                    int k_src = 0, k_dst = 0, l = str.l;
+                    int nexp = 0; // diploid or haploid?
+                    while ( ptr<se )
+                    {
+                        if ( !*ptr ) break;
+                        if ( *ptr==',' ) nexp++;
+                        ptr++;
+                    }
+                    if ( ptr!=ss ) nexp++;
+                    assert( nexp==nG_ori || nexp==nR_ori );
+                    ptr = ss;
+                    if ( nexp==nG_ori ) // diploid
+                    {
+                        int ia, ib;
+                        for (ia=0; ia<nR_ori; ia++)
+                        {
+                            for (ib=0; ib<=ia; ib++)
+                            {
+                                if ( ptr>=se || !*ptr ) break;
+                                while ( ptr<se && *ptr && *ptr!=',' ) ptr++;
+                                if ( kbs_exists(rm_set, ia) || kbs_exists(rm_set, ib) )
+                                {
+                                    ss = ++ptr;
+                                    continue;
+                                }
+                                if ( k_dst ) kputc(',',&str);
+                                kputsn(ss,ptr-ss,&str);
+                                ss = ++ptr;
+                                k_dst++;
+                            }
+                            if ( ptr>=se || !*ptr ) break;
+                        }
+                    }
+                    else    // haploid
+                    {
+                        for (k_src=0; k_src<nR_ori; k_src++)
+                        {
+                            if ( ptr>=se || !*ptr ) break;
+                            while ( ptr<se && *ptr && *ptr!=',' ) ptr++;
+                            if ( kbs_exists(rm_set, k_src) )
+                            {
+                                ss = ++ptr;
+                                continue;
+                            }
+                            if ( k_dst ) kputc(',',&str);
+                            kputsn(ss,ptr-ss,&str);
+                            ss = ++ptr;
+                            k_dst++;
+                        }
+                        assert( k_src==nR_ori );
+                        l = str.l - l;
+                        for (; l<size; l++) kputc(0, &str);
+                    }
+                }
+            }
+            nret = bcf_update_format(header, line, bcf_hdr_int2id(header,BCF_DT_ID,fmt->id), (void*)str.s, str.l, type);
+            if ( nret<0 )
+            {
+                fprintf(stderr,"[%s:%d %s] Could not update FORMAT/%s at %s:%d [%d]\n", __FILE__,__LINE__,__FUNCTION__,
+                        bcf_hdr_int2id(header,BCF_DT_ID,fmt->id), bcf_seqname(header,line), line->pos+1, nret);
+                exit(1);
+            }
+            continue;
+        }
+
+        int nori = nret / line->n_sample;
+        if ( vlen==BCF_VL_A || vlen==BCF_VL_R || (vlen==BCF_VL_G && nori==nR_ori) ) // Number=A, R or haploid Number=G
+        {
+            int inc = 0, nnew;
+            if ( vlen==BCF_VL_A )
+            {
+                assert( nori==nA_ori );     // todo: will fail if all values are missing
+                ndat = nA_new*line->n_sample;
+                nnew = nA_new;
+                inc  = 1;
+            }
+            else
+            {
+                assert( nori==nR_ori );     // todo: will fail if all values are missing
+                ndat = nR_new*line->n_sample;
+                nnew = nR_new;
+            }
+
+            #define BRANCH(type_t,is_vector_end) \
+            { \
+                for (j=0; j<line->n_sample; j++) \
+                { \
+                    type_t *ptr_src = ((type_t*)dat) + j*nori; \
+                    type_t *ptr_dst = ((type_t*)dat) + j*nnew; \
+                    int size = sizeof(type_t); \
+                    int k_src, k_dst = 0; \
+                    for (k_src=0; k_src<nori; k_src++) \
+                    { \
+                        if ( is_vector_end ) { memcpy(ptr_dst+k_dst, ptr_src+k_src, size); break; } \
+                        if ( kbs_exists(rm_set, k_src+inc) ) continue; \
+                        memcpy(ptr_dst+k_dst, ptr_src+k_src, size); \
+                        k_dst++; \
+                    } \
+                } \
+            }
+            switch (type)
+            {
+                case BCF_HT_INT:  BRANCH(int32_t,ptr_src[k_src]==bcf_int32_vector_end); break;
+                case BCF_HT_REAL: BRANCH(float,bcf_float_is_vector_end(ptr_src[k_src])); break;
+            }
+            #undef BRANCH
+        }
+        else    // Number=G, diploid or mixture of haploid+diploid
+        {
+            assert( nori==nG_ori );
+            ndat = nG_new*line->n_sample;
+
+            #define BRANCH(type_t,is_vector_end) \
+            { \
+                for (j=0; j<line->n_sample; j++) \
+                { \
+                    type_t *ptr_src = ((type_t*)dat) + j*nori; \
+                    type_t *ptr_dst = ((type_t*)dat) + j*nG_new; \
+                    int size = sizeof(type_t); \
+                    int ia, ib, k_dst = 0, k_src; \
+                    int nset = 0;   /* haploid or diploid? */ \
+                    for (k_src=0; k_src<nG_ori; k_src++) { if ( is_vector_end ) break; nset++; } \
+                    if ( nset==nR_ori ) /* haploid */ \
+                    { \
+                        for (k_src=0; k_src<nR_ori; k_src++) \
+                        { \
+                            if ( kbs_exists(rm_set, k_src) ) continue; \
+                            memcpy(ptr_dst+k_dst, ptr_src+k_src, size); \
+                            k_dst++; \
+                        } \
+                        memcpy(ptr_dst+k_dst, ptr_src+k_src, size); \
+                    } \
+                    else /* diploid */ \
+                    { \
+                        k_src = -1; \
+                        for (ia=0; ia<nR_ori; ia++) \
+                        { \
+                            for (ib=0; ib<=ia; ib++) \
+                            { \
+                                k_src++; \
+                                if ( is_vector_end ) { memcpy(ptr_dst+k_dst, ptr_src+k_src, size); ia = nR_ori; break; }  \
+                                if ( kbs_exists(rm_set, ia) || kbs_exists(rm_set, ib) ) continue; \
+                                memcpy(ptr_dst+k_dst, ptr_src+k_src, size); \
+                                k_dst++; \
+                            } \
+                        } \
+                    } \
+                } \
+            }
+            switch (type)
+            {
+                case BCF_HT_INT:  BRANCH(int32_t,ptr_src[k_src]==bcf_int32_vector_end); break;
+                case BCF_HT_REAL: BRANCH(float,bcf_float_is_vector_end(ptr_src[k_src])); break;
+            }
+            #undef BRANCH
+        }
+        nret = bcf_update_format(header, line, bcf_hdr_int2id(header,BCF_DT_ID,fmt->id), (void*)dat, ndat, type);
+        if ( nret<0 )
+        {
+            fprintf(stderr,"[%s:%d %s] Could not update FORMAT/%s at %s:%d [%d]\n", __FILE__,__LINE__,__FUNCTION__,
+                    bcf_hdr_int2id(header,BCF_DT_ID,fmt->id), bcf_seqname(header,line), line->pos+1, nret);
+            exit(1);
+        }
+    }
+    free(dat);
+    free(str.s);
+    free(map);
+}
+
diff --git a/scripts/ref_map.pl b/scripts/ref_map.pl
index 18ec64b..83dd103 100755
--- a/scripts/ref_map.pl
+++ b/scripts/ref_map.pl
@@ -872,7 +872,7 @@ sub usage {
     version();
 
     print STDERR <<EOQ; 
-ref_map.pl -p path -r path [-s path] -o path [-t] [-m min_cov] [-M mismatches] [-n mismatches] [-T num_threads] [-A type] [-O popmap] [-B db -b batch_id -D "desc"] [-S -i num] [-e path] [-d] [-h]
+ref_map.pl -p path -r path [-s path] -o path [-t] [-m min_cov] [-M mismatches] [-T num_threads] [-A type] [-O popmap] [-B db -b batch_id -D "desc"] [-S -i num] [-e path] [-d] [-h]
     b: batch ID representing this dataset (an integer, e.g. 1, 2, 3).
     o: path to write pipeline output files.
     O: if analyzing one or more populations, specify a pOpulation map.
diff --git a/src/BamI.h b/src/BamI.h
index a769089..5e2a9cf 100644
--- a/src/BamI.h
+++ b/src/BamI.h
@@ -29,11 +29,12 @@
 #ifdef HAVE_BAM
 
 #include "input.h"
-#include "bam.h"
+#include "sam.h"
 
 class Bam: public Input {
-    bamFile  bam_fh;
-    bam1_t  *aln;
+    htsFile   *bam_fh;
+    bam_hdr_t *bamh;
+    bam1_t    *aln;
 
     map<uint, string> chrs;
 
@@ -47,13 +48,14 @@ class Bam: public Input {
  public:
     Bam(const char *path) : Input() {
 	this->path   = string(path);
-	this->bam_fh = bam_open(path, "r");
+	this->bam_fh = hts_open(path, "r");
 	this->aln    = bam_init1();
 
 	this->parse_header();
     };
     ~Bam() {
-	bam_close(this->bam_fh);
+	hts_close(this->bam_fh);
+        bam_hdr_destroy(this->bamh);
 	bam_destroy1(this->aln);
     };
     Seq *next_seq();
@@ -63,18 +65,16 @@ class Bam: public Input {
 int
 Bam::parse_header()
 {
-    bam_header_t *bamh = bam_header_init();
-    bamh = bam_header_read(this->bam_fh);
+    this->bamh = bam_hdr_init();
+    this->bamh = sam_hdr_read(this->bam_fh);
 
-    for (uint j = 0; j < (uint) bamh->n_targets; j++) {
+    for (uint j = 0; j < (uint) this->bamh->n_targets; j++) {
 	//
 	// Record the mapping from integer ID to chromosome name that we will see in BAM records.
 	//
-	this->chrs[j] = string(bamh->target_name[j]);
+	this->chrs[j] = string(this->bamh->target_name[j]);
     }
 
-    bam_header_destroy(bamh);
-
     return 0;
 }
 
@@ -88,7 +88,7 @@ Bam::next_seq()
     // Read a record from the file, skipping unmapped reads,  and place it in a Seq object.
     //
     do {
-	bytes_read = bam_read1(this->bam_fh, this->aln);
+	bytes_read = sam_read1(this->bam_fh, this->bamh, this->aln);
 
         if (bytes_read <= 0)
             return NULL;
@@ -122,8 +122,11 @@ Bam::next_seq()
     //
     string  seq;
     uint8_t j;
+
+    seq.reserve(this->aln->core.l_qseq);
+    
     for (int i = 0; i < this->aln->core.l_qseq; i++) {
-	j = bam1_seqi(bam1_seq(this->aln), i);
+	j = bam_seqi(bam_get_seq(this->aln), i);
 	switch(j) {
 	case 1:
 	    seq += 'A';
@@ -147,15 +150,15 @@ Bam::next_seq()
     // Fetch the quality score.
     //
     string   qual;
-    uint8_t *q = bam1_qual(this->aln);
+    uint8_t *q = bam_get_qual(this->aln);
     for (int i = 0; i < this->aln->core.l_qseq; i++) {
 	qual += char(int(q[i]) + 33);
     }
 
     string chr = this->chrs[this->aln->core.tid];
 
-    Seq *s = new Seq((const char *) bam1_qname(this->aln), seq.c_str(), qual.c_str(),
-		     chr.c_str(), bp, flag ? minus : plus);
+    Seq *s = new Seq((const char *) bam_get_qname(this->aln), seq.c_str(), qual.c_str(),
+		     chr.c_str(), bp, flag ? strand_minus : strand_plus);
 
     if (cigar.size() > 0)
     	this->edit_gaps(cigar, s->seq);
@@ -168,7 +171,7 @@ Bam::parse_bam_cigar(vector<pair<char, uint> > &cigar, bool orientation)
 {
     int  op, len;
     char c;
-    uint32_t *cgr = bam1_cigar(this->aln);
+    uint32_t *cgr = bam_get_cigar(this->aln);
 
     for (int k = 0; k < this->aln->core.n_cigar; k++) {
 	op  = cgr[k] &  BAM_CIGAR_MASK;
@@ -202,7 +205,7 @@ Bam::parse_bam_cigar(vector<pair<char, uint> > &cigar, bool orientation)
 	// If aligned to the negative strand, sequence has been reverse complemented and 
 	// CIGAR string should be interpreted in reverse.
 	//
-	if (orientation == plus)
+	if (orientation == strand_plus)
 	    cigar.push_back(make_pair(c, len));
 	else
 	    cigar.insert(cigar.begin(), make_pair(c, len));
@@ -235,7 +238,7 @@ Bam::parse_cigar(const char *cigar_str, vector<pair<char, uint> > &cigar, bool o
 	// If aligned to the negative strand, sequence has been reverse complemented and 
 	// CIGAR string should be interpreted in reverse.
 	//
-	if (orientation == plus)
+	if (orientation == strand_plus)
 	    cigar.push_back(make_pair(*q, dist));
 	else
 	    cigar.insert(cigar.begin(), make_pair(*q, dist));
diff --git a/src/BamUnalignedI.h b/src/BamUnalignedI.h
index b6224b8..73f8496 100644
--- a/src/BamUnalignedI.h
+++ b/src/BamUnalignedI.h
@@ -29,11 +29,12 @@
 #ifdef HAVE_BAM
 
 #include "input.h"
-#include "bam.h"
+#include "sam.h"
 
 class BamUnAln: public Input {
-    bamFile  bam_fh;
-    bam1_t  *aln;
+    htsFile   *bam_fh;
+    bam_hdr_t *bamh;
+    bam1_t    *aln;
 
     map<uint, string> chrs;
 
@@ -42,20 +43,21 @@ class BamUnAln: public Input {
  public:
     BamUnAln(const char *path) : Input() {
 	this->path   = string(path);
-	this->bam_fh = bam_open(path, "r");
+	this->bam_fh = hts_open(path, "r");
 	this->aln    = bam_init1();
 
 	this->parse_header();
     };
     BamUnAln(string path) : Input() {
 	this->path   = path;
-	this->bam_fh = bam_open(path.c_str(), "r");
+	this->bam_fh = hts_open(path.c_str(), "r");
 	this->aln    = bam_init1();
 
 	this->parse_header();
     };
     ~BamUnAln() {
-	bam_close(this->bam_fh);
+	hts_close(this->bam_fh);
+        bam_hdr_destroy(this->bamh);
 	bam_destroy1(this->aln);
     };
     Seq *next_seq();
@@ -65,18 +67,16 @@ class BamUnAln: public Input {
 int
 BamUnAln::parse_header()
 {
-    bam_header_t *bamh = bam_header_init();
-    bamh = bam_header_read(this->bam_fh);
+    this->bamh = bam_hdr_init();
+    this->bamh = sam_hdr_read(this->bam_fh);
 
-    for (uint j = 0; j < (uint) bamh->n_targets; j++) {
+    for (uint j = 0; j < (uint) this->bamh->n_targets; j++) {
 	//
 	// Record the mapping from integer ID to chromosome name that we will see in BAM records.
 	//
-	this->chrs[j] = string(bamh->target_name[j]);
+	this->chrs[j] = string(this->bamh->target_name[j]);
     }
 
-    bam_header_destroy(bamh);
-
     return 0;
 }
 
@@ -88,7 +88,7 @@ BamUnAln::next_seq()
     //
     // Read a record from the file and place it in a Seq object.
     //
-    bytes_read = bam_read1(this->bam_fh, this->aln);
+    bytes_read = sam_read1(this->bam_fh, this->bamh, this->aln);
 
     if (bytes_read <= 0)
 	return NULL;
@@ -98,8 +98,11 @@ BamUnAln::next_seq()
     //
     string  seq;
     uint8_t j;
+
+    seq.reserve(this->aln->core.l_qseq);
+    
     for (int i = 0; i < this->aln->core.l_qseq; i++) {
-	j = bam1_seqi(bam1_seq(this->aln), i);
+	j = bam_seqi(bam_get_seq(this->aln), i);
 	switch(j) {
 	case 1:
 	    seq += 'A';
@@ -123,7 +126,7 @@ BamUnAln::next_seq()
     // Fetch the quality score.
     //
     string   qual;
-    uint8_t *q = bam1_qual(this->aln);
+    uint8_t *q = bam_get_qual(this->aln);
     for (int i = 0; i < this->aln->core.l_qseq; i++) {
 	qual += char(int(q[i]) + 33);
     }
@@ -134,7 +137,7 @@ BamUnAln::next_seq()
     // Attempt to parse the query name for this read.
     //
 
-    Seq *s = new Seq((const char *) bam1_qname(this->aln), seq.c_str(), qual.c_str());
+    Seq *s = new Seq((const char *) bam_get_qname(this->aln), seq.c_str(), qual.c_str());
 
     return s;
 }
diff --git a/src/BowtieI.h b/src/BowtieI.h
index 5501846..2d30c18 100644
--- a/src/BowtieI.h
+++ b/src/BowtieI.h
@@ -55,14 +55,14 @@ Seq *Bowtie::next_seq() {
 
     parse_tsv(this->line, parts);
 
-    strand_type strand = parts[1] == "+" ? plus : minus;
+    strand_type strand = parts[1] == "+" ? strand_plus : strand_minus;
 
     //
     // If the read was aligned on the reverse strand (and is therefore reverse complemented)
     // alter the start point of the alignment to reflect the right-side of the read, at the
     // end of the RAD cut site.
     //
-    int bp = strand == plus ? atoi(parts[3].c_str()) : atoi(parts[3].c_str()) + parts[4].length();
+    int bp = strand == strand_plus ? atoi(parts[3].c_str()) : atoi(parts[3].c_str()) + parts[4].length();
 
     Seq *s = new Seq(parts[0].c_str(), parts[4].c_str(), parts[5].c_str(), 
 		     parts[2].c_str(), bp, strand);
diff --git a/src/GappedAln.h b/src/GappedAln.h
index fc05ab0..af42ba4 100644
--- a/src/GappedAln.h
+++ b/src/GappedAln.h
@@ -125,7 +125,7 @@ GappedAln::GappedAln(int len_1, int len_2)
 
 GappedAln::~GappedAln()
 {
-    for (int i = 0; i < this->_m; i++) {
+    for (uint i = 0; i < this->_m; i++) {
         delete [] this->matrix[i];
         delete [] this->path[i];
     }
@@ -139,8 +139,8 @@ GappedAln::init(int size_1, int size_2)
     //
     // Resize the underlying matrix and path arrays, if necessary.
     //
-    if ((size_1 + 1) > this->_m_size || (size_2 + 1) > this->_n_size) {
-	for (int i = 0; i < this->_m_size; i++) {
+    if ((size_1 + 1) > (int)_m_size || (size_2 + 1) > (int)_n_size) {
+	for (uint i = 0; i < this->_m_size; i++) {
 	    delete [] this->matrix[i];
 	    delete [] this->path[i];
 	}
diff --git a/src/MetaPopInfo.cc b/src/MetaPopInfo.cc
new file mode 100644
index 0000000..0ec5799
--- /dev/null
+++ b/src/MetaPopInfo.cc
@@ -0,0 +1,347 @@
+#include <fstream>
+#include <dirent.h>
+#include <iostream>
+#include <algorithm>
+#include <cstring>
+#include <vector>
+
+#include "config.h"
+#include "constants.h"
+#include "input.h"
+
+#include "MetaPopInfo.h"
+
+using std::ifstream;
+using std::cerr;
+using std::exception;
+
+const string MetaPopInfo::Pop::default_name = "defaultpop";
+const string MetaPopInfo::Group::default_name = "defaultgrp";
+
+void MetaPopInfo::reset_sample_map() {
+    sample_indexes_.clear();
+    for (size_t i = 0; i < samples_.size(); ++i)
+        sample_indexes_.insert( {samples_[i].name, i} );
+}
+
+void MetaPopInfo::reset_pop_map() {
+    pop_indexes_.clear();
+    for (size_t i = 0; i < pops_.size(); ++i)
+        pop_indexes_.insert( {pops_[i].name, i} );
+}
+
+void MetaPopInfo::reset_group_map() {
+    group_indexes_.clear();
+    for (size_t i = 0; i < groups_.size(); ++i)
+        group_indexes_.insert( {groups_[i].name, i} );
+}
+
+bool MetaPopInfo::init_popmap(const string& pmap_path) {
+
+    ifstream fh(pmap_path.c_str(), ifstream::in);
+    if (fh.fail())
+        return false;
+
+    size_t p = 0; // pop index counter
+    size_t g = 0; // group index counter
+
+    char line[max_len];
+    memset(line, '\0', max_len);
+    vector<string> parts;
+    while (fh.getline(line, max_len)) {
+        size_t len = strlen(line);
+
+        // Skip empty lines and comments
+        if (len == 0 || line[0] == '#')
+            continue;
+
+        // Check for Windows line endings
+        if (line[len - 1] == '\r') {
+            line[len - 1] = '\0';
+            len -= 1;
+        }
+
+        //
+        // Parse the contents, we expect:
+        // <file name> tab <population string> [tab <group string>]
+        //
+
+        parse_tsv(line, parts);
+
+        if (parts.size() < 2
+            || parts.size() > 3
+            || parts[0].empty()
+            || parts[1].empty()) {
+            cerr << "Error: Malformed population map -- expected 'SAMPLE\\tPOP[\\tGROUP]'. In file '" << pmap_path << "', line :\n" << line << "\n";
+            throw exception();
+        }
+
+        //
+        // Process the sample name.
+        //
+
+        samples_.push_back(Sample(parts[0]));
+
+        //
+        // Process the population field.
+        //
+
+        pair<map<string,size_t>::iterator, bool> pop_ins = pop_indexes_.insert( {parts[1], p} );
+        size_t pop_index = pop_ins.first->second;
+
+        samples_.back().pop = pop_index; // Set the sample's population index.
+        if (pop_ins.second) {
+            // Unknown pop
+            pops_.push_back(Pop(parts[1]));
+            ++p;
+        }
+
+        //
+        // Process the group field, if any
+        //
+
+        if (parts.size() == 3 && ! parts[2].empty()) {
+            // Get the index of this group -- create it if necessary.
+            pair<map<string,size_t>::iterator, bool> grp_ins = group_indexes_.insert( {parts[2], g} );
+            if (grp_ins.second) {
+                groups_.push_back(Group(parts[2]));
+                ++g;
+            }
+            size_t grp_index = grp_ins.first->second;
+
+            if (pops_[pop_index].group != size_t(-1)) {
+                // The current pop already has a group, check that it is the same.
+                if (pops_[pop_index].group != grp_index) {
+                    cerr << "Error: In population map file '"
+                         << pmap_path << "': population '"
+                         << pops_[pop_index].name << "' belongs to two groups, '"
+                         << groups_[pops_[pop_index].group].name << "' and '"
+                         << groups_[grp_index].name << "'\n.";
+                    throw exception();
+                }
+            } else {
+                pops_[pop_index].group = grp_index;
+                groups_[grp_index].pops.push_back(pop_index);
+            }
+        }
+    }
+    if (samples_.empty())
+        // Empty population map.
+        return false;
+
+    //
+    // Check that all the populations are in a group. Put
+    // populations that do not have a group in a default
+    // one.
+    //
+
+    bool missing_group = false;
+    if (not groups_.empty()) {
+        for (vector<Pop>::iterator p = pops_.begin(); p != pops_.end(); ++p) {
+            if (p->group == size_t(-1)) {
+                cerr << "Warning: Population '" << p->name
+                << "' did not have a group, adding it to '"
+                << Group::default_name << "'.\n";
+                missing_group = true;
+            }
+        }
+    } else {
+        missing_group = true;
+    }
+    if (missing_group) {
+        groups_.push_back(Group(Group::default_name));
+        g = groups_.size()-1;
+        group_indexes_.insert( {Group::default_name, g} );
+        for (size_t p = 0; p < pops_.size(); ++p) {
+            if (pops_[p].group == size_t(-1)) {
+                pops_[p].group = g;
+                groups_[g].pops.push_back(p);
+            }
+        }
+    }
+
+    //
+    // Sort the samples. Determine the first/last indexes for each population.
+    //
+
+    sort(samples_.begin(), samples_.end());
+    reset_sample_map();
+
+    size_t curr_pop = 0;
+    pops_[curr_pop].first_sample = 0;
+    for (size_t s = 1; s < samples_.size(); ++s) {
+        if (samples_[s].pop != curr_pop) {
+            pops_[curr_pop].last_sample = s-1;
+            ++curr_pop;
+            pops_[curr_pop].first_sample = s;
+        }
+    }
+    pops_[curr_pop].last_sample = samples_.size()-1;
+
+    return true;
+}
+
+bool MetaPopInfo::init_names(const vector<string>& sample_names) {
+    if(sample_names.empty())
+        return false;
+
+    // Create the samples
+    for (vector<string>::const_iterator s=sample_names.begin(); s!= sample_names.end(); ++s) {
+        samples_.push_back(Sample(*s));
+        samples_.back().pop = 0;
+    }
+    sort(samples_.begin(), samples_.end());
+
+    // Create a default population
+    pops_.push_back(Pop(Pop::default_name));
+    pops_[0].first_sample = 0;
+    pops_[0].last_sample = samples_.size()-1;
+    pops_[0].group = 0;
+
+    // Create a default group
+    groups_.push_back(Group(Group::default_name));
+    groups_[0].pops.push_back(0);
+
+    // Set the support members.
+    reset_sample_map();
+    reset_pop_map();
+    reset_group_map();
+
+    return true;
+}
+
+bool MetaPopInfo::init_directory(const string& dir_path) {
+
+    //
+    // Find all sample names.
+    //
+
+    vector<string> sample_names;
+    DIR* dir = opendir(dir_path.c_str());
+    if (dir == NULL) {
+        cerr << "Unable to open directory '" << dir_path << "' for reading.\n";
+        throw exception();
+    }
+    dirent *direntry;
+    while ((direntry = readdir(dir)) != NULL) {
+        string filename = direntry->d_name;
+
+        if (filename == "." || filename == ".." || filename.substr(0, 6) == "batch_")
+            continue;
+
+        size_t pos = filename.rfind(".tags.tsv");
+        if (pos == string::npos)
+            pos = filename.rfind(".tags.tsv.gz");
+
+        if (pos != string::npos)
+            sample_names.push_back(filename.substr(0, pos));
+    }
+    closedir(dir);
+
+    //
+    // Initialize the MetaPopInfo
+    //
+
+    return init_names(sample_names);
+}
+
+void MetaPopInfo::delete_samples(const vector<size_t>& rm_samples) {
+
+    // Remove these samples from [samples_].
+    for (vector<size_t>::const_iterator s = rm_samples.begin(); s != rm_samples.end(); ++s) {
+        samples_.at(*s).name.clear(); // Mark the sample for removal.
+    }
+    samples_.erase(
+            remove_if(samples_.begin(), samples_.end(),
+                    [] (Sample& s) {return s.name.empty();} ),
+            samples_.end());
+
+    // Update the indexes of the populations.
+    for (vector<Pop>::iterator p = pops_.begin(); p != pops_.end(); ++p) {
+        for (vector<size_t>::const_reverse_iterator rm_sample = rm_samples.rbegin(); rm_sample != rm_samples.rend(); ++rm_sample) {
+            if (p->first_sample > *rm_sample) // n.b. ">"
+                --p->first_sample;
+            if (p->last_sample >= *rm_sample) // n.b. ">=". Thus if the population becomes
+                                              // empty, [first_sample] will be past [last_sample].
+                                              // n.b. If removing the first pop, last_sample=size_t(-1).
+                --p->last_sample;
+        }
+    }
+
+    auto pop_is_empty = [] (Pop& p) {return (p.first_sample > p.last_sample || p.last_sample == size_t(-1));};
+
+    // Remove the empty populations from [groups_].
+    for(vector<Group>::iterator group = groups_.begin(); group != groups_.end(); ++group)
+        group->pops.erase(
+                remove_if(group->pops.begin(), group->pops.end(),
+                        [this,&pop_is_empty] (size_t p) {return pop_is_empty(pops_[p]);}),
+                group->pops.end());
+
+    // Remove the empty populations from [pops_].
+    pops_.erase(
+            remove_if(pops_.begin(), pops_.end(), pop_is_empty),
+            pops_.end());
+
+    // Remove empty groups from [groups_].
+    groups_.erase(
+            remove_if(groups_.begin(), groups_.end(),
+                    [] (Group& g) {return g.pops.empty();}),
+            groups_.end());
+
+    // Update the support members.
+    reset_sample_map();
+    reset_pop_map();
+    reset_group_map();
+    reset_sample_id_map();
+}
+
+void MetaPopInfo::reset_sample_id_map() {
+    sample_indexes_by_id_.clear();
+    for (size_t i = 0; i < samples_.size(); ++i)
+        sample_indexes_by_id_[samples_[i].id] = i;
+}
+
+void MetaPopInfo::fill_files(vector<pair<int, string> >& files) const {
+    files.clear();
+    for (vector<Sample>::const_iterator sample = samples_.begin(); sample != samples_.end(); ++sample)
+        files.push_back( {sample->pop, sample->name} );
+}
+
+void MetaPopInfo::fill_sample_ids(vector<int>& sample_ids) const {
+    sample_ids.clear();
+    for (vector<Sample>::const_iterator sample = samples_.begin(); sample != samples_.end(); ++sample)
+        sample_ids.push_back(sample->id);
+}
+
+void MetaPopInfo::fill_samples(map<int, string>& samples) const {
+    samples.clear();
+    for (vector<Sample>::const_iterator sample = samples_.begin(); sample != samples_.end(); ++sample)
+        samples.insert({sample->id, sample->name});
+}
+
+void MetaPopInfo::fill_pop_key(map<int, string>& pop_key) const {
+    pop_key.clear();
+    for (size_t i = 0; i < pops_.size(); ++i)
+        pop_key.insert( {i, pops_[i].name} );
+}
+
+void MetaPopInfo::fill_pop_indexes(map<int, pair<int, int> >& pop_indexes) const {
+    pop_indexes.clear();
+    for (size_t i = 0; i < pops_.size(); ++i)
+        pop_indexes.insert( {i, {pops_[i].first_sample, pops_[i].last_sample}} );
+}
+
+void MetaPopInfo::fill_grp_key(map<int, string>& grp_key) const {
+    grp_key.clear();
+    for (size_t i = 0; i < groups_.size(); ++i)
+        grp_key.insert({i, groups_[i].name});
+}
+
+void MetaPopInfo::fill_grp_members(map<int, vector<int> >& grp_members) const {
+    grp_members.clear();
+    for (size_t i = 0; i < groups_.size(); ++i) {
+        vector<int>& pop_ids = grp_members.insert( {i, vector<int>()} ).first->second;
+        for(vector<size_t>::const_iterator p = groups_[i].pops.begin(); p != groups_[i].pops.end(); ++p)
+            pop_ids.push_back(*p);
+    }
+}
diff --git a/src/MetaPopInfo.h b/src/MetaPopInfo.h
new file mode 100644
index 0000000..57d6f6f
--- /dev/null
+++ b/src/MetaPopInfo.h
@@ -0,0 +1,111 @@
+#ifndef METAPOPINFO_H
+#define METAPOPINFO_H
+
+#include <string>
+#include <vector>
+#include <map>
+
+using std::size_t;
+using std::pair;
+using std::vector;
+using std::string;
+using std::map;
+
+/*
+ * MetaPopInfo
+ * Class for reprensenting a metapopulation : its samples, populations,
+ * groups of populations, and associated information.
+ */
+class MetaPopInfo {
+public:
+    struct Sample {
+        string name;
+        size_t pop;
+        size_t id; // optional, deprecated
+
+        Sample(const string& n) : name(n), pop(-1), id(-1) {}
+        inline bool operator<(const Sample& other) const;
+    };
+    struct Pop {
+        string name;
+        size_t first_sample;
+        size_t last_sample;
+        size_t group;
+
+        Pop(const string& n) : name(n), first_sample(-1), last_sample(-1), group(-1) {}
+        static const string default_name;
+    };
+    struct Group {
+        string name;
+        vector<size_t> pops;
+
+        Group(const string& n) : name(n), pops() {}
+        static const string default_name;
+    };
+
+private:
+    vector<Sample> samples_; //n.b. Samples are sorted primarily by population index, and secondarily by name.
+    vector<Pop> pops_;
+    vector<Group> groups_;
+
+    map<string,size_t> sample_indexes_; // Links a name with an index in [samples_].
+    map<string,size_t> pop_indexes_;
+    map<string,size_t> group_indexes_;
+    void reset_sample_map(); // Resets [sample_indexes_].
+    void reset_pop_map();
+    void reset_group_map();
+
+    map<size_t,size_t> sample_indexes_by_id_; // Links a sample ID with an index in [samples_].
+    void reset_sample_id_map();
+
+public:
+    // Create the representation :
+    // -- from a population map file.
+    // -- from just a vector of sample names.
+    // -- or by looking for "*.tags.tsv(.gz)" files in a directory.
+    bool init_popmap(const string& popmap_path);
+    bool init_names(const vector<string>& sample_names);
+    bool init_directory(const string& dir_path);
+
+    // Delete samples from the metapopulation.
+    // (As samples, populations or groups may be deleted, the indexes of
+    // the remaining ones change, but the order in which they appear
+    // is preserved.)
+    void delete_samples(const vector<size_t>& rm_samples);
+
+    // Retrieve information.
+    const vector<Sample>& samples() const {return samples_;}
+    const vector<Pop>& pops() const {return pops_;}
+    const vector<Group>& groups() const {return groups_;}
+
+    size_t get_sample_index(const string& name) const {return sample_indexes_.at(name);}
+    size_t get_pop_index(const string& name) const {return pop_indexes_.at(name);}
+    size_t get_group_index(const string& name) const {return group_indexes_.at(name);}
+
+    // Work with sample IDs. (IDs unicity is not enforced.)
+    void set_sample_id(size_t index, size_t id) {samples_.at(index).id = id; sample_indexes_by_id_[id] = index;}
+    size_t get_sample_index(const size_t& id) const {return sample_indexes_by_id_.at(id);}
+
+    /*
+     * Methods for backwards compatibility
+     */
+
+    // Fill former globals.
+    void fill_files(vector<pair<int, string> >&) const;
+    void fill_sample_ids(vector<int>&) const;
+    void fill_samples(map<int, string>&) const;
+    void fill_pop_key(map<int, string>&) const;
+    void fill_pop_indexes(map<int, pair<int, int> >&) const;
+    void fill_grp_key(map<int, string>&) const;
+    void fill_grp_members(map<int, vector<int> >&) const;
+};
+
+inline
+bool MetaPopInfo::Sample::operator<(const Sample& other) const {
+    if (pop == other.pop)
+        return name < other.name;
+    else
+        return pop < other.pop;
+}
+
+#endif // METAPOPINFO_H
diff --git a/src/PopMap.h b/src/PopMap.h
index 495d42a..5172f2c 100644
--- a/src/PopMap.h
+++ b/src/PopMap.h
@@ -21,7 +21,9 @@
 #ifndef __POPMAP_H__
 #define __POPMAP_H__
 
-#include <string.h>
+#include <exception>
+using std::exception;
+#include <cstring>
 #include <string>
 using std::string;
 #include <vector>
@@ -30,6 +32,8 @@ using std::vector;
 using std::map;
 #include <set>
 using std::set;
+#include <numeric>
+using std::accumulate;
 #include <algorithm>
 #include <utility>
 using std::pair;
@@ -38,6 +42,8 @@ using std::make_pair;
 #include "stacks.h"
 #include "locus.h"
 #include "aln_utils.h"
+#include "MetaPopInfo.h"
+#include "Vcf.h"
 
 class Datum {
 public:
@@ -53,8 +59,9 @@ public:
     char          *cigar;         // CIGAR string describing how the datum aligns to the catalog locus.
     double         lnl;           // Log likelihood of this locus.
     vector<char *> obshap;        // Observed Haplotypes
-    vector<SNP *>  snps;
+    vector<SNP *>  snps;          // All calls for this sample for this locus. size() is [len].
     Datum()  {
+        this->id            = -1;
         this->corrected     = false;
         this->gtype         = NULL;
         this->trans_gtype   = NULL;
@@ -97,57 +104,69 @@ public:
 
 template<class LocusT=Locus>
 class PopMap {
-    set<pair<int, int> > blacklist;
+    const MetaPopInfo& metapopinfo;
     int      num_loci;
-    int      num_samples;
+    set<pair<int, int> > blacklist;
     Datum ***data;
     map<int, int> locus_order;  // LocusID => ArrayIndex; map catalog IDs to their first dimension 
                                 // position in the Datum array.
     map<int, int> rev_locus_order;
-    map<int, int> sample_order; // SampleID => ArrayIndex; map defining at what position in 
-                                // the second dimension of the datum array each sample is stored.
-    map<int, int> rev_sample_order;
 
 public:
     map<string, vector<LocusT *> > ordered_loci; // Loci ordered by genomic position
 
-    PopMap(int, int);
+    PopMap(const MetaPopInfo& mpopi, int n_loci);
     ~PopMap();
 
-    int populate(vector<int> &, map<int, LocusT*> &, vector<vector<CatMatch *> > &);
-    int order_loci(map<int, LocusT*> &);
-    int prune(set<int> &);
+    // Populates the PopMap based on sstack matches files.
+    // The catalog is modified (LocusT must be CSLocus, and
+    // members [cnt, hcnt, confounded_cnt] are modified).
+    int populate(map<int, LocusT*>& catalog, const vector<vector<CatMatch *> >& matches);
+
+    // Populates the PopMap based on VCF (SNP) records.
+    // The catalog is modified (LocusT must be CSLocus, and
+    // members [cnt, hcnt] are modified).
+    // N.B. The IDs of the loci in the catalog MUST be the same
+    // as the indexes in the records vector.
+    int populate(map<int, LocusT*>& catalog, const vector<VcfRecord>& records, const VcfHeader& header);
+
+    int order_loci(const map<int, LocusT*>& catalog);
+    int prune(set<int>& loc_ids);
 
-    int loci_cnt() { return this->num_loci; }
-    int rev_locus_index(int index) { if (this->rev_locus_order.count(index) == 0) return -1; return this->rev_locus_order[index]; }
-    int sample_cnt() { return this->num_samples; }
-    int sample_index(int index) { if (this->sample_order.count(index) == 0) return -1; return this->sample_order[index]; }
-    int rev_sample_index(int index) { if (this->rev_sample_order.count(index) == 0) return -1; return this->rev_sample_order[index]; }
+    int loci_cnt() const { return this->num_loci; }
+    int locus_index(int id) const {return locus_order.at(id);}
+    int rev_locus_index(int index) const {try {return rev_locus_order.at(index);} catch(exception&) {return -1;}}
 
-    Datum **locus(int);
-    Datum  *datum(int, int);
-    bool    blacklisted(int, int);
+    int sample_cnt() const { return metapopinfo.samples().size(); }
+    int sample_index(int id) const {try {return metapopinfo.get_sample_index(id);} catch (exception&) {return -1;}}
+    int rev_sample_index(int index) const {return metapopinfo.samples().at(index).id;}
+
+    Datum **locus(int id);
+    Datum  *datum(int loc_id, int sample_id);
+
+    bool    blacklisted(int loc_id, int sample_id);
 };
 
 template<class LocusT>
-PopMap<LocusT>::PopMap(int num_samples, int num_loci) {
+PopMap<LocusT>::PopMap(const MetaPopInfo& mpopi, int num_loci)
+: metapopinfo(mpopi)
+{
     this->data = new Datum **[num_loci];
 
     for (int i = 0; i < num_loci; i++) {
-        this->data[i] = new Datum *[num_samples];
+        this->data[i] = new Datum *[metapopinfo.samples().size()];
 
-        for (int j = 0; j < num_samples; j++)
+        for (size_t j = 0; j < metapopinfo.samples().size(); j++)
             this->data[i][j] = NULL;
     }
 
-    this->num_samples = num_samples;
     this->num_loci    = num_loci;
 }
 
 template<class LocusT>
 PopMap<LocusT>::~PopMap() {
     for (int i = 0; i < this->num_loci; i++) {
-        for (int j = 0; j < this->num_samples; j++)
+        for (int j = 0; j < metapopinfo.samples().size(); j++)
             delete this->data[i][j];
         delete [] this->data[i];
     }
@@ -155,22 +174,13 @@ PopMap<LocusT>::~PopMap() {
 }
 
 template<class LocusT>
-int PopMap<LocusT>::populate(vector<int> &sample_ids,
-                             map<int, LocusT*> &catalog,
-                             vector<vector<CatMatch *> > &matches) {
-    //
-    // Record the array position of each sample that we will load.
-    //
-    for (uint i = 0; i < sample_ids.size(); i++) {
-        this->sample_order[sample_ids[i]] = i;
-        this->rev_sample_order[i]         = sample_ids[i];
-    }
-
+int PopMap<LocusT>::populate(map<int, LocusT*> &catalog,
+                             const vector<vector<CatMatch *> > &matches) {
     //
     // Create an index showing what position each catalog locus is stored at in the datum 
     // array. Create a second index allowing ordering of Loci by genomic position.
     //
-    typename std::map<int, LocusT*>::iterator it;
+    typename std::map<int, LocusT*>::const_iterator it;
     uint i = 0;
     for (it = catalog.begin(); it != catalog.end(); it++) {
         this->locus_order[it->first] = i;
@@ -191,7 +201,7 @@ int PopMap<LocusT>::populate(vector<int> &sample_ids,
 
     for (i = 0; i < matches.size(); i++) {
         for (uint j = 0; j < matches[i].size(); j++) {
-            sample = this->sample_order[matches[i][j]->sample_id];
+            sample = metapopinfo.get_sample_index(matches[i][j]->sample_id);
 
             if (this->locus_order.count(matches[i][j]->cat_id) == 0)
                 continue;
@@ -260,11 +270,154 @@ int PopMap<LocusT>::populate(vector<int> &sample_ids,
 }
 
 template<class LocusT>
-int PopMap<LocusT>::order_loci(map<int, LocusT*> &catalog) 
+int PopMap<LocusT>::populate(map<int, LocusT*>& catalog,
+             const vector<VcfRecord>& records,
+             const VcfHeader& header) {
+
+    // Initalize [locus_order], [rev_locus_order].
+    size_t loc_index = 0;
+    for (typename map<int, LocusT*>::iterator
+            l = catalog.begin();
+            l != catalog.end();
+            ++l) {
+        locus_order[l->first] = loc_index;
+        rev_locus_order[loc_index] = l->first;
+        ++loc_index;
+    }
+
+    // Initialize [ordered_loci].
+    order_loci(catalog);
+
+    /*
+     * Fill the PopMap.
+     *
+     * We observe the following rules to create the Datums :
+     * [id] is the locus id.
+     * [len] is the locus length (expected to be one, for a SNP)
+     * [model] "E" or "O" according to the SAMPLE/GT field, or
+     *     "U" if the GT field is absent.
+     * [obshap] the nucleotide(s) observed for this SNP for this individual.
+     *     If one of a sample's VCF alleles is missing ('.') or has an index
+     *     corresponding to the special '*' allele, the Datum* is left to NULL.
+     *
+     * When no depth information is available, [tot_depth] and the [depths]
+     * of all alleles are set to 0.
+     * (n.b. the parsing of depth information in VCF is not implemented as
+     * of Mar 21, 2016.)
+     *
+     * When no likelihood information is available, [lnl] is set to 0.
+     * (n.b. the parsing of depth information in VCF is not implemented as
+     * of Mar 21, 2016.)
+     *
+     * The following members are left unset, on the premise that
+     * "populations" does not use them :
+     * corrected, genotype, trans_genotype
+     *
+     * [merge_partner] is set later by [merge_datums()] (in populations.cc).
+     * [snps] is only used by [write_vcf()] and [write_vcf_strict()], which
+     *     first call [populate_snp_calls()] then use the SNP data in the
+     *     datum.
+     */
+
+    loc_index = 0;
+    for (typename map<int, LocusT*>::iterator
+            l = catalog.begin();
+            l != catalog.end();
+            ++l) {
+        LocusT* loc = l->second;
+
+        const VcfRecord& rec = records[loc->id]; // n.b. assumes locus ID == record index.
+        int ad_index;
+        try {
+            ad_index = rec.index_of_gt_subfield("AD");
+        } catch (exception& e) {
+            ad_index = -1;
+        }
+
+        for (size_t s = 0; s < metapopinfo.samples().size(); ++s) {
+            size_t vcf_index = header.sample_indexes().at(metapopinfo.samples()[s].name);
+            const string& sample = rec.samples.at(vcf_index);
+
+            pair<int, int> gt = rec.parse_genotype(sample);
+            if (gt.first < 0
+                    || gt.second < 0
+                    || rec.alleles[gt.first]=="*"
+                    || rec.alleles[gt.second]=="*")
+                // Missing or incomplete genotype.
+                continue;
+
+            vector<int> ad;
+            if (ad_index != -1) {
+                string ad_str = rec.parse_gt_subfield(sample, ad_index);
+                size_t start = 0;
+                size_t coma;
+                try {
+                     while ((coma = ad_str.find(',', start)) != string::npos) {
+                         ad.push_back(std::stoi(ad_str.substr(start,coma)));
+                         if (ad.back() < 0)
+                             throw exception();
+                         start=coma+1;
+                     }
+                     ad.push_back(std::stoi(ad_str.substr(start)));
+                     if (ad.size() != rec.alleles.size())
+                         throw exception();
+                 } catch (exception& e) {
+                     cerr << "Warning: Badly formatted AD string '" << ad_str
+                          << "' at VCF record '" << rec.chrom << ":" << rec.pos << "'.\n";
+                     ad = vector<int>(rec.alleles.size(), 0);
+                 }
+            }
+
+            Datum* d = new Datum();
+            data[loc_index][s] = d;
+            ++loc->cnt;
+            ++loc->hcnt;
+
+            // id, len, lnl
+            d->id = loc->id;
+            d->len = loc->len;
+            d->lnl = 0;
+
+            // model, obshap, depth
+            d->model = new char[2];
+            if (gt.first == gt.second) {
+                strcpy(d->model, "O");
+                const string& allele = rec.alleles[gt.first];
+                d->obshap.push_back(new char[allele.size()+1]);
+                strcpy(d->obshap[0], allele.c_str());
+                if (ad_index != -1)
+                    d->depth = { ad[gt.first] };
+                else
+                    d->depth = {0};
+            } else {
+                strcpy(d->model, "E");
+                const string& allele1 = rec.alleles[gt.first];
+                const string& allele2 = rec.alleles[gt.second];
+                d->obshap.push_back(new char[allele1.size()+1]);
+                d->obshap.push_back(new char[allele2.size()+1]);
+                strcpy(d->obshap[0], allele1.c_str());
+                strcpy(d->obshap[1], allele2.c_str());
+                if (ad_index != -1)
+                    d->depth = {ad[gt.first], ad[gt.second]};
+                else
+                    d->depth = {0, 0};
+            }
+
+            // tot_depth
+            d->tot_depth = std::accumulate(d->depth.begin(), d->depth.end(), 0);
+        }
+        ++loc_index;
+    }
+
+    return 0;
+}
+
+template<class LocusT>
+int PopMap<LocusT>::order_loci(const map<int, LocusT*> &catalog)
 {
     this->ordered_loci.clear();
 
-    typename std::map<int, LocusT*>::iterator it;
+    typename std::map<int, LocusT*>::const_iterator it;
 
     for (it = catalog.begin(); it != catalog.end(); it++) {
         if (strlen(it->second->loc.chr) > 0)
@@ -294,20 +447,16 @@ int PopMap<LocusT>::prune(set<int> &remove_ids) {
 
         loc_id = this->rev_locus_order[i];
 
-        //
-        // Keep this locus.
-        //
         if (remove_ids.count(loc_id) == 0) {
+            // Keep this locus.
             d[j] = this->data[i];
             new_loc_order[loc_id] = j;
             new_rev_loc_order[j] = loc_id;
             j++;
 
         } else {
-            //
             // Remove this locus.
-            //
-            for (int k = 0; k < this->num_samples; k++)
+            for (size_t k = 0; k < metapopinfo.samples().size(); k++)
                 delete this->data[i][k];
             delete [] this->data[i];
         }
@@ -345,13 +494,13 @@ int PopMap<LocusT>::prune(set<int> &remove_ids) {
 }
 
 template<class LocusT>
-Datum **PopMap<LocusT>::locus(int locus) {
-    return this->data[this->locus_order[locus]];
+Datum **PopMap<LocusT>::locus(int id) {
+    return this->data[this->locus_order[id]];
 }
 
 template<class LocusT>
-Datum  *PopMap<LocusT>::datum(int locus, int sample) {
-    return this->data[this->locus_order[locus]][this->sample_order[sample]];
+Datum  *PopMap<LocusT>::datum(int loc_id, int sample_id) {
+    return this->data[this->locus_order[loc_id]][metapopinfo.get_sample_index(sample_id)];
 }
 
 template<class LocusT>
diff --git a/src/PopSum.h b/src/PopSum.h
index 9b53c3e..d8d491f 100644
--- a/src/PopSum.h
+++ b/src/PopSum.h
@@ -38,10 +38,12 @@ using std::make_pair;
 #include <math.h>
 
 #include "stacks.h"
+#include "locus.h"
+#include "PopMap.h"
+#include "MetaPopInfo.h"
 
 extern bool   log_fst_comp;
 extern double minor_allele_freq;
-extern map<int, string> pop_key;
 const  uint   PopStatSize = 5;
 
 class PopStat {
@@ -84,6 +86,7 @@ public:
 
     HapStat(): PopStat() {
         comp = NULL;
+        popcnt = uint(-1);
     }
     ~HapStat() {
         if (this->comp != NULL)
@@ -249,36 +252,29 @@ public:
 //
 template<class LocusT=Locus>
 class PopSum {
-    int           num_loci;
-    int           num_pops;
+    const PopMap<LocusT>& popmap;
+    const MetaPopInfo& metapopinfo;
     LocSum     ***data;
     LocTally    **loc_tally;
-    map<int, int> locus_order;  // LocusID => ArrayIndex; map catalog IDs to their first dimension 
-                                // position in the LocSum array.
-    map<int, int> rev_locus_order;
-    map<int, int> pop_order;    // PopulationID => ArrayIndex; map defining at what position in 
-                                // the second dimension of the LocSum array each population is stored.
-    map<int, int> rev_pop_order;
-    map<int, int> pop_sizes;    // The maximum size of each separate population.
 
 public:
-    PopSum(int, int);
+    PopSum(const PopMap<LocusT>& pmap, const MetaPopInfo& mpopi);
     ~PopSum();
 
     int initialize(PopMap<LocusT> *);
-    int add_population(map<int, LocusT *> &, PopMap<LocusT> *, uint, uint, uint, bool, ofstream &);
+    int add_population(map<int, LocusT *> &, PopMap<LocusT> *, size_t, bool, ofstream &);
     int tally(map<int, LocusT *> &);
 
-    int loci_cnt() { return this->num_loci; }
-    int rev_locus_index(int index) { return this->rev_locus_order[index]; }
-    int pop_cnt()  { return this->num_pops; }
-    int pop_index(int index)     { return this->pop_order[index]; }
-    int rev_pop_index(int index) { return this->rev_pop_order[index]; }
-    int pop_size(int pop_id)     { return this->pop_sizes[pop_id]; }
+    int loci_cnt() const {return popmap.loci_cnt();}
+    int rev_locus_index(int index) const {return popmap.rev_locus_index(index);}
+    int pop_cnt() const {return metapopinfo.pops().size();}
+    int pop_size(size_t pop_index) const {
+        return metapopinfo.pops().at(pop_index).last_sample - metapopinfo.pops().at(pop_index).first_sample + 1;
+    }
 
-    LocSum  **locus(int);
-    LocSum   *pop(int, int);
-    LocTally *locus_tally(int);
+    LocSum  **locus(int locus_id);
+    LocSum   *pop(int locus_id, size_t pop_index);
+    LocTally *locus_tally(int locus_id);
     PopPair  *Fst(int, int, int, int);
     int       fishers_exact_test(PopPair *, double, double, double, double);
 
@@ -292,25 +288,24 @@ private:
 };
 
 template<class LocusT>
-PopSum<LocusT>::PopSum(int num_loci, int num_populations) {
-    this->loc_tally = new LocTally *[num_loci];
-    this->data      = new LocSum  **[num_loci];
+PopSum<LocusT>::PopSum(const PopMap<LocusT>& pmap, const MetaPopInfo& mpopi)
+: popmap(pmap), metapopinfo(mpopi)
+{
+    this->loc_tally = new LocTally*[popmap.loci_cnt()];
+    this->data      = new LocSum**[popmap.loci_cnt()];
 
-    for (int i = 0; i < num_loci; i++) {
-        this->data[i] = new LocSum *[num_populations];
+    for (int i = 0; i < popmap.loci_cnt(); i++) {
+        this->data[i] = new LocSum *[metapopinfo.pops().size()];
 
-        for (int j = 0; j < num_populations; j++)
+        for (size_t j = 0; j < metapopinfo.pops().size(); j++)
             this->data[i][j] = NULL;
     }
-
-    this->num_pops = num_populations;
-    this->num_loci = num_loci;
 }
 
 template<class LocusT>
 PopSum<LocusT>::~PopSum() {
-    for (int i = 0; i < this->num_loci; i++) {
-        for (int j = 0; j < this->num_pops; j++)
+    for (int i = 0; i < loci_cnt(); i++) {
+        for (int j = 0; j < pop_cnt(); j++)
             delete this->data[i][j];
         delete [] this->data[i];
         delete this->loc_tally[i];
@@ -321,30 +316,21 @@ PopSum<LocusT>::~PopSum() {
 
 template<class LocusT>
 int PopSum<LocusT>::initialize(PopMap<LocusT> *pmap) {
-    int locus_id;
-
-    for (int i = 0; i < this->num_loci; i++) {
-        locus_id = pmap->rev_locus_index(i);
-        this->locus_order[locus_id] = i;
-        this->rev_locus_order[i]    = locus_id;
-    }
-
     return 0;
 }
 
 template<class LocusT>
 int PopSum<LocusT>::add_population(map<int, LocusT *> &catalog,
-                                   PopMap<LocusT> *pmap, 
-                                   uint population_id,
-                                   uint start_index, uint end_index, 
-                                   bool verbose, ofstream &log_fh) {
+                                   PopMap<LocusT> *pmap,
+                                   size_t pop_index,
+                                   bool verbose,
+                                   ofstream &log_fh) {
     LocusT  *loc;
     Datum  **d;
     LocSum **s;
     uint locus_id, len;
     int res;
     set<int> snp_cols;
-
     int incompatible_loci = 0;
 
     if (verbose)
@@ -352,20 +338,10 @@ int PopSum<LocusT>::add_population(map<int, LocusT *> &catalog,
                << "#\n"
                << "# Level\tAction\tLocus ID\tChr\tBP\tColumn\tPopID\n#\n";
 
-    //
-    // Determine the index for this population
-    //
-    uint pop_index = this->pop_order.size() == 0 ? 0 : this->pop_order.size();
-    this->pop_order[population_id] = pop_index;
-    this->rev_pop_order[pop_index] = population_id;
-
-    //
-    // Record the maximal size of this population.
-    //
-    this->pop_sizes[population_id] = end_index - start_index + 1;
+    const MetaPopInfo::Pop& pop = metapopinfo.pops().at(pop_index);
 
-    for (int i = 0; i < this->num_loci; i++) {
-        locus_id = pmap->rev_locus_index(i);
+    for (int i = 0; i < loci_cnt(); i++) {
+        locus_id = rev_locus_index(i);
         d   = pmap->locus(locus_id);
         s   = this->locus(locus_id);
         loc = catalog[locus_id];
@@ -379,8 +355,9 @@ int PopSum<LocusT>::add_population(map<int, LocusT *> &catalog,
         // Check if this locus has already been filtered and is NULL in all individuals.
         //
         bool filtered = true;
-        for (uint k = start_index; k <= end_index; k++) {
-            if (d[k] != NULL) filtered = false;
+        for (uint k = pop.first_sample; k <= pop.last_sample; k++) {
+            if (d[k] != NULL)
+                filtered = false;
         }
         if (filtered == true) {
             for (uint k = 0; k < len; k++) {
@@ -394,8 +371,8 @@ int PopSum<LocusT>::add_population(map<int, LocusT *> &catalog,
         // calculate observed genotype frequencies, allele frequencies, and expected genotype frequencies.
         //
         for (uint k = 0; k < loc->snps.size(); k++) {
-            res = this->tally_heterozygous_pos(loc, d, s[pop_index], 
-                                               loc->snps[k]->col, k, start_index, end_index);
+            res = this->tally_heterozygous_pos(loc, d, s[pop_index],
+                                               loc->snps[k]->col, k, pop.first_sample, pop.last_sample);
             //
             // If site is incompatible (too many alleles present), log it.
             //
@@ -408,9 +385,9 @@ int PopSum<LocusT>::add_population(map<int, LocusT *> &catalog,
                            << "incompatible_locus\t"
                            << loc->id << "\t"
                            << loc->loc.chr << "\t"
-                           << loc->sort_bp(loc->snps[k]->col) << "\t"
+                           << loc->sort_bp(loc->snps[k]->col) +1 << "\t"
                            << loc->snps[k]->col << "\t" 
-                           << pop_key[population_id] << "\n";
+                           << pop.name << "\n";
             }
 
             snp_cols.insert(loc->snps[k]->col);
@@ -420,15 +397,15 @@ int PopSum<LocusT>::add_population(map<int, LocusT *> &catalog,
         //
         for (uint k = 0; k < len; k++) {
             if (snp_cols.count(k)) continue;
-            this->tally_fixed_pos(loc, d, s[pop_index], 
-                                  k, start_index, end_index);
+            this->tally_fixed_pos(loc, d, s[pop_index],
+                                  k, pop.first_sample, pop.last_sample);
         }
 
         snp_cols.clear();
     }
 
-    cerr << "Population '" << pop_key[population_id] << "' contained " << incompatible_loci << " incompatible loci -- more than two alleles present.\n";
-    log_fh <<  "Population " << population_id << " contained " << incompatible_loci << " incompatible loci -- more than two alleles present.\n";
+    cerr << "Population '" << pop.name << "' contained " << incompatible_loci << " incompatible loci -- more than two alleles present.\n";
+    log_fh <<  "Population " << pop.name << " contained " << incompatible_loci << " incompatible loci -- more than two alleles present.\n";
 
     return 0;
 }
@@ -442,7 +419,7 @@ int PopSum<LocusT>::tally(map<int, LocusT *> &catalog)
     int       locus_id, variable_pop;
     uint16_t  p_cnt, q_cnt, len, col;
 
-    for (int n = 0; n < this->num_loci; n++) {
+    for (int n = 0; n < loci_cnt(); n++) {
         locus_id = this->rev_locus_index(n);
         loc      = catalog[locus_id];
         s        = this->locus(locus_id);
@@ -471,7 +448,7 @@ int PopSum<LocusT>::tally(map<int, LocusT *> &catalog)
             if (ltally->nucs[col].allele_cnt > 1)
                 ltally->nucs[col].fixed = false;
             
-            for (int j = 0; j < this->num_pops; j++) {
+            for (int j = 0; j < pop_cnt(); j++) {
                 //
                 // Sum the number of individuals examined at this locus across populations.
                 //
@@ -479,7 +456,7 @@ int PopSum<LocusT>::tally(map<int, LocusT *> &catalog)
                 ltally->nucs[col].pop_cnt  += s[j]->nucs[col].num_indv > 0 ? 1 : 0;
             }
 
-            for (int j = 0; j < this->num_pops; j++) {
+            for (int j = 0; j < pop_cnt(); j++) {
                 //
                 // Sum the most frequent allele across populations.
                 //
@@ -499,6 +476,7 @@ int PopSum<LocusT>::tally(map<int, LocusT *> &catalog)
             //
             // We want to report the most frequent allele as the P allele. Reorder the alleles 
             // if necessary.
+            // XXX Possibly unstable for p_freq ~ 0.5. @Nick (July 2016)
             //
             if (ltally->nucs[col].p_freq < 0.5) {
                 char a = ltally->nucs[col].p_allele;
@@ -518,12 +496,12 @@ int PopSum<LocusT>::tally(map<int, LocusT *> &catalog)
             variable_pop = -1;
 
             if (p_cnt == 1 && q_cnt > 1) {
-                for (int j = 0; j < this->num_pops; j++)
+                for (int j = 0; j < pop_cnt(); j++)
                     if (s[j]->nucs[col].p_nuc == ltally->nucs[col].p_allele ||
                         s[j]->nucs[col].q_nuc == ltally->nucs[col].p_allele)
                         variable_pop = j;
             } else if (p_cnt > 1 && q_cnt == 1) {
-                for (int j = 0; j < this->num_pops; j++)
+                for (int j = 0; j < pop_cnt(); j++)
                     if (s[j]->nucs[col].p_nuc == ltally->nucs[col].q_allele ||
                         s[j]->nucs[col].q_nuc == ltally->nucs[col].q_allele)
                         variable_pop = j;
@@ -548,7 +526,7 @@ int PopSum<LocusT>::tally_ref_alleles(LocSum **s, int snp_index,
     q_allele   = 0;
     allele_cnt = 0;
 
-    for (int j = 0; j < this->num_pops; j++) {
+    for (int j = 0; j < pop_cnt(); j++) {
         nuc[0] = 0;
         nuc[1] = 0;
         nuc[0] = s[j]->nucs[snp_index].p_nuc;
@@ -636,7 +614,7 @@ int PopSum<LocusT>::tally_ref_alleles(LocSum **s, int snp_index,
     p_cnt = 0;
     q_cnt = 0;
 
-    for (int j = 0; j < this->num_pops; j++) {
+    for (int j = 0; j < pop_cnt(); j++) {
         nuc[0] = 0;
         nuc[1] = 0;
         nuc[0] = s[j]->nucs[snp_index].p_nuc;
@@ -653,10 +631,10 @@ int PopSum<LocusT>::tally_ref_alleles(LocSum **s, int snp_index,
 }
 
 template<class LocusT>
-PopPair *PopSum<LocusT>::Fst(int locus, int pop_1, int pop_2, int pos) 
+PopPair *PopSum<LocusT>::Fst(int locus_id, int pop_1, int pop_2, int pos)
 {
-    LocSum  *s_1  = this->pop(locus, pop_1);  /////// SLOW!
-    LocSum  *s_2  = this->pop(locus, pop_2);
+    LocSum  *s_1  = pop(locus_id, pop_1);  /////// SLOW!
+    LocSum  *s_2  = pop(locus_id, pop_2);
     PopPair *pair = new PopPair();
 
     //
@@ -1346,21 +1324,21 @@ double PopSum<LocusT>::binomial_coeff(double n, double k)
 }
 
 template<class LocusT>
-LocSum **PopSum<LocusT>::locus(int locus) 
+LocSum **PopSum<LocusT>::locus(int locus_id)
 {
-    return this->data[this->locus_order[locus]];
+    return this->data[popmap.locus_index(locus_id)];
 }
 
 template<class LocusT>
-LocSum  *PopSum<LocusT>::pop(int locus, int pop_id) 
+LocSum  *PopSum<LocusT>::pop(int locus_id, size_t pop_index)
 {
-    return this->data[this->locus_order[locus]][this->pop_order[pop_id]];
+    return this->data[popmap.locus_index(locus_id)][pop_index];
 }
 
 template<class LocusT>
-LocTally *PopSum<LocusT>::locus_tally(int locus) 
+LocTally *PopSum<LocusT>::locus_tally(int locus_id)
 {
-    return this->loc_tally[this->locus_order[locus]];
+    return this->loc_tally[popmap.locus_index(locus_id)];
 }
 
 #endif // __POPSUM_H__
diff --git a/src/SamI.h b/src/SamI.h
index 8bab0d1..74ab51c 100644
--- a/src/SamI.h
+++ b/src/SamI.h
@@ -106,7 +106,7 @@ Sam::next_seq()
     bp--;
 
     Seq *s = new Seq(parts[0].c_str(), parts[9].c_str(), parts[10].c_str(), // Read ID, Sequence, Quality
-		     parts[2].c_str(), bp, flag ? minus : plus);            // Chr, BasePair, Strand
+		     parts[2].c_str(), bp, flag ? strand_minus : strand_plus);            // Chr, BasePair, Strand
 
     if (cigar.size() > 0)
 	this->edit_gaps(cigar, s->seq);
@@ -138,7 +138,7 @@ Sam::parse_cigar(const char *cigar_str, vector<pair<char, uint> > &cigar, bool o
 	// If aligned to the negative strand, sequence has been reverse complemented and 
 	// CIGAR string should be interpreted in reverse.
 	//
-	if (orientation == plus)
+	if (orientation == strand_plus)
 	    cigar.push_back(make_pair(*q, dist));
 	else
 	    cigar.insert(cigar.begin(), make_pair(*q, dist));
diff --git a/src/Tsv.h b/src/Tsv.h
index 435d97b..f94d94d 100644
--- a/src/Tsv.h
+++ b/src/Tsv.h
@@ -56,7 +56,7 @@ Seq *Tsv::next_seq() {
 
     string id = parts[0] + "_" + parts[1];
 
-    Seq *s = new Seq(id.c_str(), parts[2].c_str(), parts[3].c_str(), parts[0].c_str(), atoi(parts[1].c_str()), plus);
+    Seq *s = new Seq(id.c_str(), parts[2].c_str(), parts[3].c_str(), parts[0].c_str(), atoi(parts[1].c_str()), strand_plus);
 
     return s;
 }
diff --git a/src/Vcf.cc b/src/Vcf.cc
new file mode 100644
index 0000000..32e63c3
--- /dev/null
+++ b/src/Vcf.cc
@@ -0,0 +1,506 @@
+#include <algorithm>
+#include <ctime>
+#include <iomanip>
+#include <sstream>
+
+#include "Vcf.h"
+
+using namespace std;
+
+const map<string, VcfMeta> VcfMeta::predefined = {
+        {"INFO/NS", VcfMeta("INFO","<ID=NS,Number=1,Type=Integer,Description=\"Number of Samples With Data\">")},
+        {"INFO/AF", VcfMeta("INFO","<ID=AF,Number=.,Type=Float,Description=\"Allele Frequency\">")},
+        {"FORMAT/GT", VcfMeta("FORMAT","<ID=GT,Number=1,Type=String,Description=\"Genotype\">")},
+        {"FORMAT/DP", VcfMeta("FORMAT","<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">")},
+        {"FORMAT/AD", VcfMeta("FORMAT","<ID=AD,Number=1,Type=Integer,Description=\"Allele Depth\">")},
+        {"FORMAT/GL", VcfMeta("FORMAT","<ID=GL,Number=.,Type=Float,Description=\"Genotype Likelihood\">")},
+    };
+
+void VcfHeader::init_meta(const string& fileformat) {
+    add_meta(VcfMeta("fileformat", fileformat));
+
+    time_t t;
+    time(&t);
+    char date[9];
+    strftime(date, 9, "%Y%m%d", localtime(&t));
+    add_meta(VcfMeta("fileDate", date));
+
+    add_meta(VcfMeta("source", string("\"Stacks v") + VERSION + "\""));
+}
+
+VcfAbstractParser::VcfAbstractParser(const string& path)
+: path_(path), header_(), line_number_(0), eol_(true), eof_(false), tabs_(), bounds_(), sample_index_(-1)
+{
+    memset(line_, '\0', Vcf::line_buf_size);
+}
+
+void
+VcfAbstractParser::read_header()
+{
+    auto malformed = [this] () {
+        cerr << "Error: Malformed header."
+             << " At line " << line_number_ << " in file '" << path_ << "'.\n";
+        throw exception();
+    };
+
+    while(true) {
+        getline(line_, Vcf::line_buf_size);
+        ++line_number_;
+        if(eof_)
+            malformed();
+
+        if (line_[0] != '#')
+            malformed();
+
+        if(line_[1] == '#') {
+            // Meta header line.
+
+            char* equal = strchr(line_, '=');
+            if(equal == NULL) {
+                // (Notice: Skipping missing '=')
+                tabs_.clear();
+                tabs_.push_back(line_+strlen(line_));
+                check_eol();
+                read_to_eol();
+                continue;
+            }
+            char* end = equal + strlen(equal);
+
+            // Check the length of the line (discard lines that don't fit in the buffer).
+            tabs_.clear();
+            tabs_.push_back(end);
+            check_eol();
+            if(!eol_) {
+                // (Notice: Skipping long line)
+                read_to_eol();
+                continue;
+            }
+
+            string key = string(line_+2, equal);
+            transform(key.begin(), key.end(), key.begin(), ::toupper);
+            header_.add_meta(VcfMeta(key, string(equal+1, end)));
+
+            continue;
+        }
+        break;
+    }
+
+    // Final header line.
+
+    if(strncmp(line_, Vcf::base_fields.c_str(), Vcf::base_fields.length()) != 0)
+        malformed();
+
+    // Get tabs.
+    tabs_.clear();
+    tabs_.push_back(strchr(line_, '\t')); //rem. one tab guaranteed
+    while (tabs_.back())
+        tabs_.push_back(strchr(tabs_.back()+1, '\t'));
+    tabs_.pop_back();
+    tabs_.push_back(tabs_.back() + strlen(tabs_.back())); // final '\0'
+    check_eol();
+
+    // Check the number of tabs.
+    if(!(tabs_.size() == Vcf::base_fields_no or tabs_.size() >= Vcf::base_fields_no+2))
+        malformed();
+
+    // Check windows line endings.
+    if(*(tabs_.back()-1) == '\r') {
+        tabs_.back() = tabs_.back()-1;
+        *tabs_.back() = '\0';
+    }
+
+    // Parse sample names.
+    if(tabs_.size() >= Vcf::base_fields_no+2) {
+        for(size_t i=Vcf::first_sample-1; i < tabs_.size()-2; ++i)
+            header_.add_sample(string(tabs_[i]+1, tabs_[i+1]));
+
+        while(!eol_){
+            // Buffer wasn't long enough : parse until eol is found.
+            // Copy the truncated name at the beginning of the buffer.
+            size_t last_field_len = tabs_.back() - *(tabs_.end()-2);
+            *line_ = '\t';
+            strcpy(line_+1, *(tabs_.end()-2)+1);
+
+            getline(line_+last_field_len, Vcf::line_buf_size-last_field_len);
+            if(eof_)
+                malformed();
+
+            // Get tabs.
+            tabs_.clear();
+            tabs_.push_back(line_);
+            while (tabs_.back())
+                tabs_.push_back(strchr(tabs_.back()+1, '\t'));
+            tabs_.pop_back();
+            tabs_.push_back(tabs_.back() + strlen(tabs_.back()));
+            check_eol();
+
+            // Check windows line endings.
+            if(*(tabs_.back()-1) == '\r') {
+                tabs_.back() = tabs_.back()-1;
+                *tabs_.back() = '\0';
+            }
+
+            for(size_t i = 0; i<tabs_.size()-2;++i)
+                header_.add_sample(string(tabs_[i]+1, tabs_[i+1]));
+        }
+        header_.add_sample(string(*(tabs_.end()-2)+1, tabs_.back()));
+    }
+
+    return;
+}
+
+#ifdef HAVE_LIBZ
+VcfGzParser::VcfGzParser(const string& path)
+: VcfAbstractParser(path), file_(NULL)
+{
+    file_ = gzopen(path_.c_str(), "rb");
+#if ZLIB_VERNUM >= 0x1240
+    gzbuffer(file_, libz_buffer_size);
+#endif
+}
+
+#endif // HAVE_LIBZ
+
+VcfAbstractParser*
+Vcf::adaptive_open(const string& path)
+{
+    VcfAbstractParser* parser = NULL;
+    if (path.length() >= 4 && path.substr(path.length()-4) == ".vcf") {
+        parser = new VcfParser(path);
+        if (parser->fail()) {
+            // Opening failed
+            delete parser;
+            parser = NULL;
+        }
+#ifdef HAVE_LIBZ
+    } else if (path.length() >= 7 && path.substr(path.length()-7) == ".vcf.gz") {
+        parser = new VcfGzParser(path);
+        if (parser->fail()) {
+            delete parser;
+            parser = NULL;
+        }
+#endif
+    } else {
+        cerr << "Error: File '" << path << "' : expected '.vcf(.gz)' suffix.";
+        throw exception();
+    }
+
+    return parser;
+}
+
+bool
+VcfAbstractParser::next_record(VcfRecord& record)
+{
+    getline(line_, Vcf::line_buf_size);
+    if(eof_)
+        return false;
+    ++line_number_;
+
+    record.clear();
+
+    // Get tabs.
+    tabs_.clear();
+    tabs_.push_back(strchr(line_, '\t'));
+    while(tabs_.back())
+        tabs_.push_back(strchr(tabs_.back()+1, '\t'));
+    tabs_.pop_back();
+    if(tabs_.size() > 0)
+        tabs_.push_back(tabs_.back() + strlen(tabs_.back()));
+    else
+        tabs_.push_back(line_ + strlen(line_));
+    check_eol();
+
+    /* Check the number of fields (should be ==8 or >=10 depending on the
+     * presence of samples) :
+     * If the line fits in the buffer but the number of fields is wrong,
+     * raise an error.
+     * If the fixed fields don't fit in the buffer, return a null record. */
+    if(eol_) {
+        if(tabs_.size() < Vcf::base_fields_no + (header_.samples().empty() ? 0 : 2)) {
+            cerr << "Error: malformed VCF record line (at least "
+                    << Vcf::base_fields_no + (header_.samples().empty() ? 0 : 2)
+                    << " fields required).\nLine " << line_number_ << " in file '" << path_ << "'.\n";
+            throw exception ();
+        }
+    } else {
+        if(header_.samples().empty() || tabs_.size() < Vcf::base_fields_no + 2) {
+            cerr << "Warning: In file '" << path_ << "': skipping the very long record at line "
+                 << line_number_ << ".\n";
+            read_to_eol();
+            return true;
+        }
+    }
+
+    // Check windows line endings.
+    if(*(tabs_.back()-1) == '\r') {
+        tabs_.back() = tabs_.back()-1;
+        *tabs_.back() = '\0';
+    }
+
+    // Separate all substrings (replace \t's with \0's).
+    for(size_t i = 0; i<tabs_.size()-1;++i)
+        *tabs_[i] = '\0';
+
+    // CHROM
+    if(line_ == tabs_[Vcf::chrom]) {
+        cerr << "Warning: Skipping malformed VCF record (missing CHROM value)."
+                << " Line " << line_number_ << " in file '" << path_ << "'.\n";
+        // Skip this record.
+        // ([record.type] is still [null].)
+        return true;
+    }
+    record.chrom.assign(line_, tabs_[Vcf::chrom]);
+
+    // POS
+    if(tabs_[Vcf::pos-1]+1 == tabs_[Vcf::pos]
+        || *(tabs_[Vcf::pos-1]+1) == '.' ){
+        cerr << "Warning: Skipping malformed VCF record (missing POS value)."
+                << " Line " << line_number_ << " in file '" << path_ << "'.\n";
+        // Skip this record.
+        // ([record.type] is still [null].)
+        return true;
+    }
+    record.pos = stoi(tabs_[Vcf::pos-1]+1) -1 ; // VCF is 1-based
+
+    // ID
+    if(tabs_[Vcf::id-1]+1 == tabs_[Vcf::id])
+        cerr << "Notice: Empty ID field should be marked by a dot."
+                << " Line " << line_number_ << " in file '" << path_ << "'.\n";
+    if(*(tabs_[Vcf::id-1]+1) != '.')
+        record.id.assign(tabs_[Vcf::id-1]+1, tabs_[Vcf::id]);
+
+    // REF
+    if(tabs_[Vcf::ref-1]+1 == tabs_[Vcf::ref]
+        || *(tabs_[Vcf::ref-1]+1) == '.' ) {
+        cerr << "Warning: malformed VCF record (missing REF value)."
+                << " Line " << line_number_ << " in file '" << path_ << "'.\n";
+        // Skip this record.
+        // ([record.type] is still [null].)
+        return true;
+    }
+    record.alleles.push_back(string(tabs_[Vcf::ref-1]+1, tabs_[Vcf::ref]));
+
+    // ALT & determine the type of the record
+    if(tabs_[Vcf::alt-1]+1 == tabs_[Vcf::alt]) {
+        cerr << "Warning: Skipping malformed VCF record (expected ALT field to be marked by a dot)."
+                << " Line " << line_number_ << " in file '" << path_ << "'.\n";
+        // Skip this record.
+        // ([record.type] is still [null].)
+        return true;
+    } else if(*(tabs_[Vcf::alt-1]+1) == '.') {
+        record.type = Vcf::RType::invariant;
+    } else {
+        get_bounds(bounds_, tabs_[Vcf::alt-1], tabs_[Vcf::alt], ',');
+        for (size_t i = 0; i < bounds_.size()-1; ++i ) {
+            record.alleles.push_back(string(bounds_.at(i)+1, bounds_.at(i+1)));
+            if (record.alleles.back().empty()) {
+                record.alleles.pop_back();
+                cerr << "Warning: Skipping malformed VCF record (malformed ALT field)."
+                     << " Line " << line_number_ << " in file '" << path_ << "'.\n";
+                // Skip this record.
+                // ([record.type] is still [null].)
+                return true;
+            }
+        }
+
+        if (strchr(tabs_[Vcf::alt-1]+1, '[') || strchr(tabs_[Vcf::alt-1]+1, ']'))
+            record.type = Vcf::RType::breakend;
+        else if (strchr(tabs_[Vcf::alt-1]+1, '<'))
+            record.type = Vcf::RType::symbolic;
+        else
+            record.type = Vcf::RType::expl;
+    }
+
+    // Do not parse symbolic & breakend records.
+    if (record.type == Vcf::RType::symbolic || record.type == Vcf::RType::breakend) {
+        read_to_eol();
+        return true;
+    }
+
+    // QUAL
+    if(tabs_[Vcf::qual-1]+1 == tabs_[Vcf::qual])
+        cerr << "Notice: Empty QUAL field should be marked by a dot."
+             << " Line " << line_number_ << " in file '" << path_ << "'.\n";
+    if(*(tabs_[Vcf::qual-1]+1) != '.')
+        record.qual.assign(tabs_[Vcf::qual-1]+1, tabs_[Vcf::qual]);
+
+    // FILTER
+    if(tabs_[Vcf::filter-1]+1 == tabs_[Vcf::filter])
+        cerr << "Notice: Empty FILTER field should be marked by a dot."
+             << " Line " << line_number_ << " in file '" << path_ << "'.\n";
+    if(*(tabs_[Vcf::filter-1]+1) != '.') {
+        get_bounds(bounds_, tabs_[Vcf::filter-1], tabs_[Vcf::filter],';');
+        for(size_t i = 0; i < bounds_.size()-1; ++i )
+            record.filter.push_back(string(bounds_.at(i)+1, bounds_.at(i+1)));
+    }
+
+    // INFO
+    if(tabs_[Vcf::info-1]+1 == tabs_[Vcf::info])
+        cerr << "Notice: Empty INFO field should be marked by a dot."
+             << " Line " << line_number_ << " in file '" << path_ << "'.\n";
+    if(*(tabs_[Vcf::info-1]+1) != '.') {
+        get_bounds(bounds_, tabs_[Vcf::info-1], tabs_[Vcf::info], ';');
+        for(size_t i = 0; i < bounds_.size()-1; ++i ) {
+            char* equal = strchr(bounds_[i]+1, '=');
+            if(equal == NULL or bounds_[i+1] - equal < 0)
+                record.info.push_back(pair<string,string>(string(bounds_[i]+1, bounds_[i+1]),string()));
+            else
+                record.info.push_back(pair<string,string>(string(bounds_[i]+1, equal),string(equal+1,bounds_[i+1])));
+        }
+    }
+
+    // FORMAT
+    if (!header_.samples().empty() && *(tabs_[Vcf::format-1]+1) != '.') {
+        if(tabs_[Vcf::format-1]+1 == tabs_[Vcf::format])
+            cerr << "Notice: Empty FORMAT field should be marked by a dot."
+                 << " Line " << line_number_ << " in file '" << path_ << "'.\n";
+
+        get_bounds(bounds_, tabs_[Vcf::format-1], tabs_[Vcf::format],':');
+        for(size_t i = 0; i < bounds_.size()-1; ++i )
+            record.format.push_back(string(bounds_.at(i)+1, bounds_.at(i+1)));
+
+        // SAMPLES
+        sample_index_ = 0;
+        for (size_t s = Vcf::base_fields_no; s < tabs_.size()-2; ++s) //n.b. -2
+            add_sample(record, tabs_[s], tabs_[s+1]);
+
+        // If the record line was not read entirely, copy the trucated sample field
+        // to the beggining of the buffer and read some more.
+        while (!eol_) {
+            size_t lastfieldlen = tabs_.back() - *(tabs_.end()-2);
+            *line_ = '\t';
+            strcpy(line_+1, *(tabs_.end()-2)+1);
+
+            getline(line_+lastfieldlen, Vcf::line_buf_size-lastfieldlen);
+            if(eof_) {
+                cerr << "Warning: Encountered end of file while reading a record.\n";
+                record.type = Vcf::RType::null;
+                return false;
+            }
+
+            // Get tabs.
+            tabs_.clear();
+            tabs_.push_back(line_);
+            while (tabs_.back())
+                tabs_.push_back(strchr(tabs_.back()+1, '\t'));
+            tabs_.pop_back();
+            tabs_.push_back(tabs_.back() + strlen(tabs_.back()));
+            check_eol();
+
+            // Windows line endings.
+            if(*(tabs_.back()-1) == '\r') {
+                tabs_.back() = tabs_.back()-1;
+                *tabs_.back() = '\0';
+            }
+            for(size_t i = 0; i<tabs_.size()-2;++i) {
+                *tabs_[i+1] = '\0';
+                add_sample(record, tabs_[i], tabs_[i+1]);
+            }
+        }
+        //the actual last sample
+        add_sample(record, *(tabs_.end()-2), tabs_.back());
+
+        if(sample_index_ != header_.samples().size()) {
+            cerr << "Error: malformed VCF record ("
+                 << header_.samples().size() << " SAMPLE fields expected, "
+                 << sample_index_ <<  " found). File '" << path_ << "', line "
+                 << line_number_ << ".\n";
+            throw exception();
+        }
+    }
+
+    return true;
+}
+
+void VcfWriter::write_header(const VcfHeader& header) {
+    for(const VcfMeta& m : header.meta())
+        file_ << "##" << m.key() << "=" << m.value() << "\n";
+
+    file_ << Vcf::base_header;
+    if(not header.samples().empty())
+        file_ << "\tFORMAT";
+    for(const string& s : header.samples())
+        file_ << "\t" << s;
+    file_ << "\n";
+}
+
+void VcfWriter::write_record(const VcfRecord& r, const VcfHeader& h) {
+
+    if (r.type != Vcf::RType::expl)
+        // This is not implemented.
+        throw exception();
+
+    file_ << r.chrom
+          << "\t" << r.pos
+          << "\t" << (r.id.empty() ? "." : r.id)
+          << "\t" << r.alleles.at(0);
+
+    //ALT
+    file_ << "\t";
+    if (r.alleles.size() == 1) {
+        file_ << ".";
+    } else {
+        auto allele = r.alleles.begin()+1;
+        file_ << *allele;
+        ++allele;
+        while(allele != r.alleles.end()) {
+            file_ << "," << *allele;
+            ++allele;
+        }
+    }
+
+    file_ << "\t" << (r.qual.empty() ? "." : r.qual);
+
+    //FILTER
+    file_ << "\t";
+    if (r.filter.empty()) {
+        file_ << "\t.";
+    } else {
+        auto filter = r.filter.begin();
+        file_ << *filter;
+        ++filter;
+        while(filter != r.filter.end()) {
+            file_ << ";" << *filter;
+            ++filter;
+        }
+    }
+
+    //INFO
+    file_ << "\t";
+    if (r.info.empty()) {
+        file_ << ".";
+    } else {
+        auto i = r.info.begin();
+        file_ << i->first << "=" << i->second;
+        ++i;
+        while(i != r.info.end()) {
+            file_ << ";" << i->first << "=" << i->second;
+            ++i;
+        }
+    }
+
+    if (not h.samples().empty()) {
+        //FORMAT
+        file_ << "\t";
+        if (r.format.empty()) {
+            file_ << ".";
+        } else {
+            auto f = r.format.begin();
+            file_ << *f;
+            ++f;
+            while(f != r.format.end()) {
+                file_ << ":" << *f;
+                ++f;
+            }
+        }
+
+        //SAMPLES
+        if (r.samples.size() != h.samples().size())
+            throw exception();
+
+        for (const string& s : r.samples)
+            file_ << "\t" << s;
+    }
+
+    file_ << "\n";
+}
diff --git a/src/Vcf.h b/src/Vcf.h
new file mode 100644
index 0000000..5c2eb35
--- /dev/null
+++ b/src/Vcf.h
@@ -0,0 +1,467 @@
+// -*-mode:c++; c-style:k&r; c-basic-offset:4;-*-
+//
+// Copyright 2010-2015, Julian Catchen <jcatchen at uoregon.edu>
+//
+// This file is part of Stacks.
+//
+// Stacks is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// Stacks is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU General Public License for more details.
+//
+// You should have received a copy of the GNU General Public License
+// along with Stacks.  If not, see <http://www.gnu.org/licenses/>.
+//
+
+#ifndef __VCF_H__
+#define __VCF_H__
+
+#include "config.h"
+
+#include <fstream>
+#include <iostream>
+#include <exception>
+#include <stdexcept>
+#include <utility>
+#include <cstring>
+#include <cstdlib>
+#include <string>
+#include <vector>
+#include <set>
+#include <map>
+
+#ifdef HAVE_LIBZ
+#include <zlib.h>
+#endif
+
+#include "constants.h"
+
+using std::size_t;
+using std::pair;
+using std::vector;
+using std::string;
+using std::set;
+using std::map;
+using std::ifstream;
+using std::ofstream;
+using std::cerr;
+
+using std::exception;
+using std::out_of_range;
+
+class VcfAbstractParser;
+class VcfHeader;
+
+namespace Vcf {
+
+const size_t base_fields_no = 8; // CHROM POS ID REF ALT QUAL FILTER INFO [FORMAT SAMPLE ...]]
+const string base_fields = "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO";
+const size_t chrom = 0;
+const size_t pos = 1;
+const size_t id = 2;
+const size_t ref = 3;
+const size_t alt = 4;
+const size_t qual = 5;
+const size_t filter = 6;
+const size_t info = 7;
+const size_t format = 8;
+const size_t first_sample = 9;
+
+const string base_header = "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO";
+
+// enum for record types
+enum class RType {
+    null,
+    expl,      // Record with explicitly written alleles, e.g. SNPs, small indels or entirely defined haplotypes
+    invariant, // ALT is empty
+    symbolic,  // ALT is e.g. "<DUP:TANDEM>"
+    breakend   // ALT is e.g. "G]17:198982]"
+};
+
+// Constants for the parser.
+const size_t line_buf_size = 4096;
+
+// Open the given VCF file using VcfParser or VcfGzParser, depending on the
+// suffix of the file. Return NULL if the opening failed.
+// (The pointee is dynamically allocated and should be deleted.)
+VcfAbstractParser* adaptive_open(const string& path);
+
+} //namespace Vcf
+
+/*
+ * VcfRecord
+ * ==========
+ * Datastructure to store VCF records
+ */
+struct VcfRecord {
+    string chrom; // required
+    size_t pos; // required
+    string id;
+    vector<string> alleles; // allele 0 is REF and is required ; case insensitive
+    string qual;
+    vector<string> filter;
+    vector<pair<string, string> > info;
+    vector<string> format;
+    vector<string> samples;
+
+    Vcf::RType type;
+
+    //map<string, size_t> allele_indexes;
+    //void refresh_allele_indexes();
+
+    VcfRecord()
+    : chrom(), pos(-1), id(), alleles(), qual(), filter(), info(), format(),
+      samples(), type(Vcf::RType::null)
+    {}
+
+    // Clears all the members.
+    inline void clear();
+
+    inline size_t index_of_gt_subfield(const string& key) const;
+    inline string parse_gt_subfield(const string& sample, size_t index) const;
+
+    // Returns (first allele, second allele), '-1' meaning no data.
+    inline pair<int, int> parse_genotype(const string& sample) const;
+
+    inline bool is_snp() const;
+};
+
+/*
+ * VcfMeta
+ * ==========
+ * Represents one line of VCF metainformation.
+ */
+class VcfMeta {
+    string key_;
+    string value_;
+public:
+    VcfMeta(const string& k, const string& p) : key_(k), value_(p) {}
+
+    const string& key() const {return key_;}
+    const string& value() const {return value_;}
+
+    static const map<string, VcfMeta> predefined;
+};
+//class Info : public Meta {...};
+
+/*
+ * VcfHeader
+ * ==========
+ * Stores the contents of a VCF header.
+ */
+class VcfHeader {
+    vector<string> samples_;
+    vector<VcfMeta> meta_;
+
+    map<string, size_t> sample_indexes_;
+    // map<string, vector<size_t> > meta_indexes;
+public:
+    VcfHeader() : samples_(), meta_() {}
+
+    const vector<VcfMeta>& meta() const {return meta_;}
+    const vector<string>& samples() const {return samples_;}
+    const map<string, size_t>& sample_indexes() const {return sample_indexes_;}
+
+    // Adds the meta lines VERSION, FILEDATE and SOURCE
+    void init_meta(const string& fileformat = "VCFv4.2");
+    void add_meta(const VcfMeta& m) {meta_.push_back(m);}
+    void add_sample(const string& s) {samples_.push_back(s); sample_indexes_.insert({s, samples_.size()-1});}
+};
+
+/*
+ * VcfAbstractParser
+ * ==========
+ *
+ * Main class for parsing VCF. The derived non-abstract classes
+ * VcfParser and VcfGzParser only add the file_ attribute and
+ * implement the getline(), eof() and check_eol() methods.
+ *
+ * At present, the parser does not handle :
+ * -- records for which the fixed fields (CHROM to FORMAT) do not
+ *    fit in the buffer. Such records usually correspond to large
+ *    indels with several alleles. In these cases, the record
+ *    passed to next_record() will be empty and have the default
+ *    type 'null'.
+ * -- records describing symbolic or breakends alleles. In these
+ *    cases the record passed to next_record() will be of type
+ *    'symbolic' or 'breakend', with only the fields CHROM, POS,
+ *    ID and REF filled in.
+ */
+class VcfAbstractParser {
+protected:
+    const string path_;
+    VcfHeader header_;
+
+    size_t line_number_;
+    char line_[Vcf::line_buf_size];
+    bool eol_; // Set by check_eol(). True if the buffer reaches the end of the currently parsed line.
+    bool eof_; // Set by getline(). True if EOF was reached.
+    vector<char*> tabs_; // Vector of pointers to {first_tab, second_tab, ..., \0 } in [line_].
+    vector<char*> bounds_; // Vector of pointers to {leading_tab, first_sep, second_sep, ..., (trailing \t or \0) } in [line_].
+    size_t sample_index_; // Index of the current (next) sample.
+
+    virtual void getline(char* ptr, size_t n) =0;
+    virtual void check_eol() =0; // rem. The implementation in gzparser relies on [tabs_] to access the end of the string in [line_].
+    inline void read_to_eol(); // Reads while [eol_] is false.
+
+    // Add a sample to [record.samples_] if [samples_to_keep_.at(sample_index_)] is true.
+    inline void add_sample(VcfRecord& record, char* tab1, char* tab2);
+
+public:
+    VcfAbstractParser(const string& path);
+    virtual ~VcfAbstractParser() {}
+
+    // Assess the state of the underlying file.
+    virtual bool fail() =0;
+
+    // Getters.
+    const string& path() const {return path_;};
+    const VcfHeader& header() const {return header_;};
+    size_t line_number() const {return line_number_;}
+
+    // Parse the header.
+    void read_header();
+
+    // Read a record. Returns false on EOF, true otherwise.
+    bool next_record(VcfRecord& record);
+};
+
+/*
+ * VcfParser
+ * =========
+ * Implements VcfAbstractParser for plain text files.
+ */
+class VcfParser : public VcfAbstractParser {
+    ifstream file_;
+    inline void getline(char* ptr, size_t n);
+    void check_eol() {eol_ = ! file_.fail(); file_.clear();}
+public:
+    VcfParser(const string& path) : VcfAbstractParser(path), file_(path) {}
+    bool fail() {return file_.fail();}
+};
+
+#ifdef HAVE_LIBZ
+/*
+ * VcfGzParser
+ * ==========
+ * Implements VcfAbstractParser for gzipped files.
+ */
+class VcfGzParser : public VcfAbstractParser {
+    gzFile file_;
+    inline void getline(char* ptr, size_t n);
+    inline void check_eol();
+
+    VcfGzParser(VcfGzParser& p) = delete; // No copy constructor.
+    VcfGzParser& operator=(VcfGzParser& p) = delete;
+public:
+    VcfGzParser(const string& path);
+    ~VcfGzParser() {if(file_) gzclose(file_);}
+    bool fail() {return file_ == NULL;}
+};
+#endif // HAVE_LIBZ
+
+/*
+ * VcfWriter
+ * ==========
+ */
+class VcfWriter {
+private:
+    const string path_;
+    ofstream file_;
+
+public:
+    VcfWriter(const string& path) : path_(path), file_(path) {}
+    bool fail() {return file_.fail();}
+
+    void write_header(const VcfHeader& h);
+    void write_record(const VcfRecord& r, const VcfHeader& h);
+};
+
+/*
+ * Inline methods.
+ * ==========
+ */
+
+inline void
+get_bounds(vector<char*>& bounds, char* tab1, char* tab2, char sep)
+{
+    bounds.clear();
+    bounds.push_back(tab1);
+    do {
+        bounds.push_back(strchr(bounds.back()+1, sep)); // this is last+1 if tab1==tab2
+    } while (bounds.back());
+    bounds.pop_back();
+    bounds.push_back(tab2);
+}
+
+inline
+void VcfRecord::clear() {
+    pos = -1;
+    chrom.clear();
+    id.clear();
+    alleles.clear();
+    qual.clear();
+    filter.clear();
+    info.clear();
+    format.clear();
+    samples.clear();
+    type = Vcf::RType::null;
+}
+
+inline
+size_t VcfRecord::index_of_gt_subfield(const string& key) const {
+    size_t i = 0;
+    for (const string& f : format) {
+        if (f == key)
+            return i;
+        ++i;
+    }
+
+    throw out_of_range(key);
+}
+
+inline
+string VcfRecord::parse_gt_subfield(const string& sample, size_t index) const {
+    string subf;
+
+    // Skip the first [index] colons.
+    const char* first = sample.c_str();
+    for(size_t i=0; i<index; ++i) {
+        first = strchr(first, ':');
+        if (first == NULL)
+            // The requested field is not explicitly written, return the empty string.
+            return subf;
+        else
+            first += 1;
+    }
+
+    const char* last = strchr(first, ':');
+    subf = last == NULL ? string(first) : string(first, last);
+    return subf;
+}
+
+inline
+pair<int, int> VcfRecord::parse_genotype(const string& sample) const {
+
+    pair<int, int> genotype = {-1,-1};
+
+    if (format.empty()
+            || format[0] != "GT"
+            || sample.empty()
+            || sample[0] == '.') {
+        return genotype;
+    }
+    const char* first = sample.c_str();
+    const char* slash = strchr(first, '/');
+    if (slash == NULL) {
+        slash = strchr(first, '|');
+        if (slash == NULL) {
+            cerr << "Error: Malformed VCF genotype field '" << sample
+                    << "', at marker '" << chrom << ":" << pos
+                    << "'.\n";
+            throw exception();
+        }
+    }
+    if (*(slash+1) == '.') {
+        static bool printed = false;
+        if (not printed) {
+            // Print the warning once.
+            cerr << "Notice: Treating incomplete genotypes (e.g. '1/.') as missing.\n";
+            printed = true;
+        }
+        return genotype;
+    }
+
+    const char* colon = strchr(slash, ':');
+    try {
+        genotype.first = std::stoi(string(first, slash));
+        genotype.second = std::stoi(colon==NULL ? string(slash+1) : string(slash+1, colon));
+        if (genotype.first < 0
+            || genotype.first >= int(alleles.size())
+            || genotype.second < 0
+            || genotype.second >= int(alleles.size()))
+            throw exception();
+    } catch (exception& e) {
+        cerr << "Error: Malformed VCF genotype '" << sample
+             << "', at marker '" << chrom << ":" << pos
+             << "'.\n";
+        throw e;
+    }
+
+    return genotype;
+}
+
+inline
+bool VcfRecord::is_snp() const {
+    if (type != Vcf::RType::expl)
+        return false;
+
+    for (const string& a : alleles)
+        if (a.length() > 1)
+            return false;
+
+    return true;
+}
+
+inline
+void VcfAbstractParser::read_to_eol()
+{
+    while(!eol_) {
+        getline(line_, Vcf::line_buf_size);
+        if(eof_) {
+            eol_=true;
+        } else {
+            tabs_.clear();
+            tabs_.push_back(line_+strlen(line_));
+            check_eol();
+        }
+    }
+}
+
+inline
+void VcfAbstractParser::add_sample(VcfRecord& record, char* tab1, char* tab2)
+{
+    if(tab2 == tab1+1)
+        cerr << "Warning: malformed VCF record line (empty SAMPLE field should be marked by a dot)."
+             << " Line " << line_number_ << " in file " << path_ << "'.\n";
+
+    record.samples.push_back(string(tab1+1, tab2));
+
+    ++sample_index_;
+}
+
+inline
+void VcfParser::getline(char* ptr, size_t n) {
+    file_.getline(ptr, n);
+    if(file_.eof()) {
+        eof_=file_.fail();
+        if(!eof_)
+            cerr << "Notice: File '" << path_ << "' does not end with a newline.\n";
+    }
+}
+
+#ifdef HAVE_LIBZ
+inline
+void VcfGzParser::getline(char* buf, size_t n) {
+    if (gzgets(file_, buf, n) == NULL)
+        eof_ = true;
+}
+
+inline
+void VcfGzParser::check_eol() {
+    if(*(tabs_.back()-1) == '\n') { // rem. safe, gzgets returns NULL on EOF
+        eol_ = true;
+        tabs_.back() = tabs_.back()-1;
+        *tabs_.back() = '\0';
+    } else {
+        eol_= false;
+    }
+}
+#endif // HAVE_LIBZ
+
+#endif // __VCF_H__
diff --git a/src/aln_utils.cc b/src/aln_utils.cc
index baf00a4..24107a5 100644
--- a/src/aln_utils.cc
+++ b/src/aln_utils.cc
@@ -182,9 +182,8 @@ apply_cigar_to_seq(char *seq, uint seq_len, const char *old_seq, vector<pair<cha
 {
     uint   size = cigar.size();
     char   op;
-    uint   dist, bp, seq_bp, oldseq_len, stop;
+    uint   dist, bp, seq_bp, stop;
 
-    oldseq_len = strlen(old_seq);
     bp         = 0;
     seq_bp     = 0;
 
@@ -235,9 +234,8 @@ apply_cigar_to_model_seq(char *seq, uint seq_len, const char *model, vector<pair
 {
     uint   size = cigar.size();
     char   op;
-    uint   dist, model_bp, seq_bp, model_len, stop;
+    uint   dist, model_bp, seq_bp, stop;
 
-    model_len = strlen(model);
     model_bp  = 0;
     seq_bp    = 0;
 
@@ -429,7 +427,6 @@ remove_snps_from_gaps(vector<pair<char, uint> > &cigar, Locus *loc)
     uint   size = cigar.size();
     char   op;
     uint   dist, bp, new_bp, stop, snp_cnt;
-    SNP   *s;
 
     bp      = 0;
     new_bp  = 0;
diff --git a/src/catalog_utils.cc b/src/catalog_utils.cc
index 61d666d..09374cc 100644
--- a/src/catalog_utils.cc
+++ b/src/catalog_utils.cc
@@ -28,7 +28,7 @@
 #include "catalog_utils.h"
 
 int 
-reduce_catalog(map<int, CSLocus *> &catalog, set<int> &whitelist, set<int> &blacklist) 
+reduce_catalog(map<int, CSLocus *> &catalog, set<int> &whitelist, set<int> &blacklist)
 {
     map<int, CSLocus *> list;
     map<int, CSLocus *>::iterator it;
@@ -204,7 +204,7 @@ check_whitelist_integrity(map<int, CSLocus *> &catalog, map<int, set<int> > &whi
 }
 
 int 
-reduce_catalog(map<int, CSLocus *> &catalog, map<int, set<int> > &whitelist, set<int> &blacklist) 
+reduce_catalog(map<int, CSLocus *> &catalog, map<int, set<int> > &whitelist, set<int> &blacklist)
 {
     map<int, CSLocus *> list;
     map<int, CSLocus *>::iterator it;
@@ -339,3 +339,57 @@ reduce_catalog_snps(map<int, CSLocus *> &catalog, map<int, set<int> > &whitelist
 
     return 0;
 }
+
+map<int, CSLocus*> create_catalog(const vector<VcfRecord>& records) {
+    map<int, CSLocus*> catalog;
+
+    for (size_t i = 0; i < records.size(); ++i) {
+        const VcfRecord& rec = records[i];
+
+        CSLocus* loc = catalog.insert(make_pair(i, new CSLocus())).first->second;
+        loc->sample_id = 0;
+        loc->id = i;
+        loc->len = 1;
+        loc->con = new char[2];
+        strcpy(loc->con, rec.alleles[0].c_str());
+        loc->loc.set(rec.chrom.c_str(), (uint)rec.pos, strand_plus);
+        for (const string& a : rec.alleles) {
+            if (a=="*")
+                continue;
+            loc->alleles.insert({a, 0});
+        }
+        loc->depth = 0;
+        loc->lnl = 0;
+
+        loc->snps.push_back(new SNP());
+        SNP& snp = *loc->snps.back();
+        snp.col = 0;
+        vector<char*> snp_alleles = {&snp.rank_1, &snp.rank_2, &snp.rank_3, &snp.rank_4};
+        try {
+            size_t s=0;
+            for (const string& a : rec.alleles) {
+                if (a=="*")
+                    continue;
+                *snp_alleles.at(s) = a.at(0);
+                ++s;
+            }
+        } catch (out_of_range& e) {
+            cerr << "Warning: Skipping malformed VCF SNP record '"
+                 << rec.chrom << ":" << rec.pos << "'."
+                 << " Alleles were:";
+            for (const string& a : rec.alleles)
+                cerr << " '" << a << "';";
+            cerr << ".\n";
+            delete loc->snps[0];
+            delete loc->con;
+            delete loc;
+            catalog.erase(i);
+            continue;
+        }
+        snp.type = *snp_alleles[2] == 0 ? snp_type_hom : snp_type_het;
+
+        loc->populate_alleles();
+    }
+
+    return catalog;
+}
diff --git a/src/catalog_utils.h b/src/catalog_utils.h
index e0520f1..a68f0ee 100644
--- a/src/catalog_utils.h
+++ b/src/catalog_utils.h
@@ -31,6 +31,7 @@ using std::set;
 #include "locus.h"
 #include "PopMap.h"
 #include "PopSum.h"
+#include "Vcf.h"
 
 int check_whitelist_integrity(map<int, CSLocus *> &, map<int, set<int> > &);
 int reduce_catalog(map<int, CSLocus *> &, set<int> &, set<int> &);
@@ -39,4 +40,47 @@ int reduce_catalog_snps(map<int, CSLocus *> &, map<int, set<int> > &, PopMap<CSL
 int implement_single_snp_whitelist(map<int, CSLocus *> &, PopSum<CSLocus> *, map<int, set<int> > &);
 int implement_random_snp_whitelist(map<int, CSLocus *> &, PopSum<CSLocus> *, map<int, set<int> > &);
 
+/*
+ * create_catalog(vector<VcfRecord>&):
+ * Creates a catalog based on VCF SNP records.
+ *
+ * We observe the following rules to create the catalog loci :
+ * [sample_id] (batch number) Always set to 0.
+ * [id] VCF records do not intrinsically have locus ids; we use the SNP records indexes.
+ * [len] Always set to 1.
+ * [con] We use the reference nucleotide as the consensus.
+ * [loc] Use the chromosome and position given by each record (n.b. the
+ *       VCF format requires these field), and strand "strand_plus".
+ * [snps] Use the ref+alt alleles.
+ *     [col] Always set to 0 (first nucleotide in the consensus).
+ *     [type] "snp_type_het" if the alt field is not empty, otherwise "snp_type_hom".
+ *     [lratio] Always set to 0.
+ *     [rank_1] The ref allele.
+ *     [rank_2], [rank_3], [rank_4] The alt allele(s).
+ * [alleles] Use the ref+alt alleles in the order they appear, skipping
+ *     the special '*' allele ('variant is irrelevant in certain context
+ *     because of an neighboring structural polymorphism') if present.
+ * [strings] We fill this by calling Locus::populate_alleles().
+ * [cnt] Set to the approriate value when filling the PopMap.
+ * [hcnt] (Same as above.)
+ * [confounded_cnt] (Same as above.)
+ * [gmap] This is filled by tabulate_haplotypes() (in "populations.cc").
+ * [gcnt] (Same as above.)
+ * [marker] (Same as above.)
+ *
+ * When no depth information is available, the [depth] and the depths
+ * of the [alleles] are set to 0. (n.b. the parsing of depth information in
+ * VCF is not implemented as of Mar 21, 2016.)
+ *
+ * When no likelihood information is available, [lnl] is set to 0. (n.b.
+ * the parsing of likelihood information in VCF is not implemented as of
+ * Mar 21, 2016.)
+ *
+ * The following members are left unset, on the premise that
+ * "populations" does not use them :
+ * model, blacklisted, deleveraged, lumberjack, components, reads, comp_cnt,
+ * comp_type, annotation, uncor_marker, hap_cnts, f, trans_gcnt, chisq.
+ */
+map<int, CSLocus*> create_catalog(const vector<VcfRecord>& vcf_records);
+
 #endif // __CATALOG_UTILS_H__
diff --git a/src/clone_filter.cc b/src/clone_filter.cc
index 9a3b2fc..fd3de72 100644
--- a/src/clone_filter.cc
+++ b/src/clone_filter.cc
@@ -1,6 +1,6 @@
 // -*-mode:c++; c-style:k&r; c-basic-offset:4;-*-
 //
-// Copyright 2011-2015, Julian Catchen <jcatchen at illinois.edu>
+// Copyright 2011-2016, Julian Catchen <jcatchen at illinois.edu>
 //
 // This file is part of Stacks.
 //
@@ -73,47 +73,47 @@ int main (int argc, char* argv[]) {
     // If input files are gzipped, output gziped files, unless the user chooses an output type.
     //
     if (out_file_type == FileT::unknown) {
-	if (in_file_type == FileT::gzfastq || in_file_type == FileT::bam)
-	    out_file_type = FileT::gzfastq;
-	else
-	    out_file_type = FileT::fastq;
+        if (in_file_type == FileT::gzfastq || in_file_type == FileT::bam)
+            out_file_type = FileT::gzfastq;
+        else
+            out_file_type = FileT::fastq;
     }
 
     if (paired)
-	cerr << "Processing paired-end data.\n";
+        cerr << "Processing paired-end data.\n";
     else
-	cerr << "Processing single-end data.\n";
+        cerr << "Processing single-end data.\n";
 
     switch(barcode_type) {
     case null_null:
-	cerr << "No oligo sequence specified, will use single and paired-end reads to determine clones.\n";
-	break;
+        cerr << "No oligo sequence specified, will use single and paired-end reads to determine clones.\n";
+        break;
     case null_index:
-	cerr << "Searching for index oligo (i7 Illumina read).\n";
-	break;
+        cerr << "Searching for index oligo (i7 Illumina read).\n";
+        break;
     case index_null:
-	cerr << "Searching for index oligo (i5 Illumina read).\n";
-	break;
+        cerr << "Searching for index oligo (i5 Illumina read).\n";
+        break;
     case inline_null:
-	cerr << "Searching for inline oligo on single-end read.\n";
-	break;
+        cerr << "Searching for inline oligo on single-end read.\n";
+        break;
     case index_index:
-	cerr << "Searching for index oligos (i5 and i7 Illumina reads).\n";
-	break;
+        cerr << "Searching for index oligos (i5 and i7 Illumina reads).\n";
+        break;
     case inline_inline:
-	cerr << "Searching for inline oligos on single and paired-end read.\n";
-	break;
+        cerr << "Searching for inline oligos on single and paired-end read.\n";
+        break;
     case inline_index:
-	cerr << "Searching for inline oligo on single-end read and index oligo (i5 or i7 Illumina read).\n";
-	break;
+        cerr << "Searching for inline oligo on single-end read and index oligo (i5 or i7 Illumina read).\n";
+        break;
     case index_inline:
-	if (paired)
-	    cerr << "Searching for inline oligo on paired-end read and index oligo (i5 or i7 Illumina read).\n";
-	else
-	    cerr << "Searching for inline oligo on single-end read and index oligo (i5 or i7 Illumina read).\n";
-	break;
+        if (paired)
+            cerr << "Searching for inline oligo on paired-end read and index oligo (i5 or i7 Illumina read).\n";
+        else
+            cerr << "Searching for inline oligo on single-end read and index oligo (i5 or i7 Illumina read).\n";
+        break;
     }
-	
+        
     map<string, long> counters;
     counters["total"] = 0;
     counters["red_reads"] = 0;
@@ -130,38 +130,38 @@ int main (int argc, char* argv[]) {
 
     int result = 1;
     for (uint i = 0; i < files.size(); i++) {
-	cerr << "Processing file " << i+1 << " of " << files.size() << " [" << files[i].first.c_str() << "]\n";
-
-	result = 1;
-	if (paired) {
-	    if (barcode_type == null_null)
-		result = process_paired_reads_by_sequence(files[i].first, files[i].second, counters, clone_map, clone_map_keys);
-	    else
-		result = process_paired_reads(files[i].first, files[i].second, counters, oligo_map);
-
-	} else {
-	    result = process_reads(files[i].first, counters, oligo_map);
-	}
-
-	if (!result) {
-	    cerr << "Error processing reads.\n";
-	    break;
-	}
+        cerr << "Processing file " << i+1 << " of " << files.size() << " [" << files[i].first.c_str() << "]\n";
+
+        result = 1;
+        if (paired) {
+            if (barcode_type == null_null)
+                result = process_paired_reads_by_sequence(files[i].first, files[i].second, counters, clone_map, clone_map_keys);
+            else
+                result = process_paired_reads(files[i].first, files[i].second, counters, oligo_map);
+
+        } else {
+            result = process_reads(files[i].first, counters, oligo_map);
+        }
+
+        if (!result) {
+            cerr << "Error processing reads.\n";
+            break;
+        }
     }
 
     if (barcode_type == null_null && result) {
-	write_clonereduced_sequence(files[0].first, files[0].second, clone_map, clone_dist, counters);
+        write_clonereduced_sequence(files[0].first, files[0].second, clone_map, clone_dist, counters);
 
     } else {
-	for (OligoHash::iterator i = oligo_map.begin(); i != oligo_map.end(); i++)
-	    for (map<string, uint16_t>::iterator j = i->second.begin(); j != i->second.end(); j++)
-		clone_dist[j->second]++;
+        for (OligoHash::iterator i = oligo_map.begin(); i != oligo_map.end(); i++)
+            for (map<string, uint16_t>::iterator j = i->second.begin(); j != i->second.end(); j++)
+                clone_dist[j->second]++;
     }
 
     if (clone_map_keys.size() > 0) {
-	cerr << "Freeing hash key memory...";
-	free_hash(clone_map_keys);
-	cerr << "done.\n";
+        cerr << "Freeing hash key memory...";
+        free_hash(clone_map_keys);
+        cerr << "done.\n";
     }
 
     //
@@ -172,24 +172,24 @@ int main (int argc, char* argv[]) {
     vector<int> bins;
     map<int, int>::iterator it;
     for (it = clone_dist.begin(); it != clone_dist.end(); it++)
-	bins.push_back(it->first);
+        bins.push_back(it->first);
     sort(bins.begin(), bins.end());
     cout << "Num Clones\tCount\n";
     for (uint i = 0; i < bins.size(); i++)
-	cout << bins[i] << "\t" << clone_dist[bins[i]] << "\n";
+        cout << bins[i] << "\t" << clone_dist[bins[i]] << "\n";
 
     char buf[32];
     sprintf(buf, "%0.2f%%", ((double) (counters["total"] - counters["red_reads"]) / (double) counters["total"]) * 100);
     cerr << counters["total"] << " pairs of reads input. "
-	 << counters["red_reads"] << " pairs of reads output, discarded "
-	 << counters["dis_reads"] << " pairs of reads, " << buf << " clone reads.\n";
+         << counters["red_reads"] << " pairs of reads output, discarded "
+         << counters["dis_reads"] << " pairs of reads, " << buf << " clone reads.\n";
 
     return 0;
 }
 
 int 
 process_paired_reads_by_sequence(string prefix_1, string prefix_2, map<string, long> &counters,
-				 CloneHash &clone_map, vector<char *> &clone_map_keys)
+                                 CloneHash &clone_map, vector<char *> &clone_map_keys)
 {
     Input *fh_1, *fh_2;
 
@@ -199,37 +199,37 @@ process_paired_reads_by_sequence(string prefix_1, string prefix_2, map<string, l
     string path_2 = in_path_2 + prefix_2;
 
     cerr << "Reading data from:\n  " 
-	 << path_1 << " and\n  " 
-	 << path_2 << "\n";
+         << path_1 << " and\n  " 
+         << path_2 << "\n";
 
     switch (in_file_type) {
     case FileT::fastq:
         fh_1 = new Fastq(path_1);
-	fh_2 = interleaved ? fh_1 : new Fastq(path_2);
-	break;
+        fh_2 = interleaved ? fh_1 : new Fastq(path_2);
+        break;
     case FileT::gzfastq:
         fh_1 = new GzFastq(path_1);
-	fh_2 = interleaved ? fh_1 : new GzFastq(path_2);
-	break;
+        fh_2 = interleaved ? fh_1 : new GzFastq(path_2);
+        break;
     case FileT::fasta:
         fh_1 = new Fasta(path_1);
-	fh_2 = interleaved ? fh_1 : new Fasta(path_2);
-	break;
+        fh_2 = interleaved ? fh_1 : new Fasta(path_2);
+        break;
     case FileT::gzfasta:
         fh_1 = new GzFasta(path_1);
-	fh_2 = interleaved ? fh_1 : new GzFasta(path_2);
-	break;
+        fh_2 = interleaved ? fh_1 : new GzFasta(path_2);
+        break;
     case FileT::bam:
         fh_1 = new BamUnAln(path_1);
-	fh_2 = fh_1;
-	break;
+        fh_2 = fh_1;
+        break;
     case FileT::bustard:
         fh_1 = new Bustard(path_1);
         fh_2 = interleaved ? fh_1 : new Bustard(path_2);
     default:
         fh_1 = NULL;
         fh_2 = NULL;
-	break;
+        break;
     }
 
     //
@@ -238,8 +238,8 @@ process_paired_reads_by_sequence(string prefix_1, string prefix_2, map<string, l
     Seq *s_1 = fh_1->next_seq();
     Seq *s_2 = fh_2->next_seq();
     if (s_1 == NULL || s_2 == NULL) {
-	cerr << "Unable to allocate Seq object.\n";
-	return 0;
+        cerr << "Unable to allocate Seq object.\n";
+        return 0;
     }
 
     long  i = 1;
@@ -250,31 +250,31 @@ process_paired_reads_by_sequence(string prefix_1, string prefix_2, map<string, l
     do {
         if (i % 10000 == 0) cerr << "Processing short read " << i << "       \r";
 
-	counters["total"]++;
+        counters["total"]++;
 
-	exists = clone_map.count(s_1->seq) == 0 ? false : true;
+        exists = clone_map.count(s_1->seq) == 0 ? false : true;
 
-	if (exists) {
-	    hash_key = s_1->seq;
-	} else {
-	    hash_key = new char [seq_len + 1];
-	    strcpy(hash_key, s_1->seq);
-	    clone_map_keys.push_back(hash_key);
-	}
+        if (exists) {
+            hash_key = s_1->seq;
+        } else {
+            hash_key = new char [seq_len + 1];
+            strcpy(hash_key, s_1->seq);
+            clone_map_keys.push_back(hash_key);
+        }
 
-	if (out_file_type == FileT::fastq ||
+        if (out_file_type == FileT::fastq ||
             out_file_type == FileT::gzfastq)
- 	    clone_map[hash_key][s_2->seq].push_back(Pair(s_1->id, s_2->id, s_1->qual, s_2->qual));
-	else if (out_file_type == FileT::fasta ||
+            clone_map[hash_key][s_2->seq].push_back(Pair(s_1->id, s_2->id, s_1->qual, s_2->qual));
+        else if (out_file_type == FileT::fasta ||
                  out_file_type == FileT::gzfasta)
-	    clone_map[hash_key][s_2->seq].push_back(Pair(s_1->id, s_2->id));
+            clone_map[hash_key][s_2->seq].push_back(Pair(s_1->id, s_2->id));
 
-	delete s_1;
-	delete s_2;
+        delete s_1;
+        delete s_2;
 
-	i++;
+        i++;
     } while ((s_1 = fh_1->next_seq()) != NULL && 
-	     (s_2 = fh_2->next_seq()) != NULL);
+             (s_2 = fh_2->next_seq()) != NULL);
 
     cerr << "\n";
 
@@ -286,8 +286,8 @@ process_paired_reads_by_sequence(string prefix_1, string prefix_2, map<string, l
 
 int
 write_clonereduced_sequence(string prefix_1, string prefix_2,
-			    CloneHash &clone_map, map<int, int> &clone_dist,
-			    map<string, long> &counters)
+                            CloneHash &clone_map, map<int, int> &clone_dist,
+                            map<string, long> &counters)
 {
     ofstream  out_fh_1,   out_fh_2, discard_fh_1, discard_fh_2;
     gzFile    out_gzfh_1, out_gzfh_2, discard_gzfh_1, discard_gzfh_2;
@@ -306,56 +306,56 @@ write_clonereduced_sequence(string prefix_1, string prefix_2,
     string suffix_1, suffix_2;
     
     if (out_file_type == FileT::gzfastq) {
-	suffix_1 = ".1.fq.gz";
-	suffix_2 = ".2.fq.gz";
+        suffix_1 = ".1.fq.gz";
+        suffix_2 = ".2.fq.gz";
     } else if (out_file_type == FileT::fastq) {
-	suffix_1 = ".1.fq";
-	suffix_2 = ".2.fq";
+        suffix_1 = ".1.fq";
+        suffix_2 = ".2.fq";
     } else if (out_file_type == FileT::gzfasta) {
-	suffix_1 = ".1.fa.gz";
-	suffix_2 = ".2.fa.gz";
+        suffix_1 = ".1.fa.gz";
+        suffix_2 = ".2.fa.gz";
     } else if (out_file_type == FileT::fasta) {
-	suffix_1 = ".1.fa";
-	suffix_2 = ".2.fa";
+        suffix_1 = ".1.fa";
+        suffix_2 = ".2.fa";
     }
 
     string file_1 = remove_suffix(in_file_type, prefix_1);
     path_1 = out_path + file_1 + suffix_1;
     if (out_file_type == FileT::gzfastq || out_file_type == FileT::gzfasta) {
-	out_gzfh_1 = gzopen(path_1.c_str(), "wb");
-	if (!(out_gzfh_1)) {
-	    cerr << "Error opening output file '" << path_1 << "'\n";
-	    return -1;
-	}
-    } else {	    
-	out_fh_1.open(path_1.c_str(), ifstream::out);
-	if (out_fh_1.fail()) {
-	    cerr << "Error opening output file '" << path_1 << "'\n";
-	    return -1;
-	}
+        out_gzfh_1 = gzopen(path_1.c_str(), "wb");
+        if (!(out_gzfh_1)) {
+            cerr << "Error opening output file '" << path_1 << "'\n";
+            return -1;
+        }
+    } else {        
+        out_fh_1.open(path_1.c_str(), ifstream::out);
+        if (out_fh_1.fail()) {
+            cerr << "Error opening output file '" << path_1 << "'\n";
+            return -1;
+        }
     }
 
     string file_2 = remove_suffix(in_file_type, prefix_2);
     path_2 = out_path + file_2 + suffix_2;
     if (out_file_type == FileT::gzfastq || out_file_type == FileT::gzfasta) {
-	out_gzfh_2 = gzopen(path_2.c_str(), "wb");
-	if (!(out_gzfh_2)) {
-	    cerr << "Error opening output file '" << path_2 << "'\n";
-	    return -1;
-	}
-    } else {	    
-	out_fh_2.open(path_2.c_str(), ifstream::out);
-	if (out_fh_2.fail()) {
-	    cerr << "Error opening output file '" << path_2 << "'\n";
-	    return -1;
-	}
+        out_gzfh_2 = gzopen(path_2.c_str(), "wb");
+        if (!(out_gzfh_2)) {
+            cerr << "Error opening output file '" << path_2 << "'\n";
+            return -1;
+        }
+    } else {        
+        out_fh_2.open(path_2.c_str(), ifstream::out);
+        if (out_fh_2.fail()) {
+            cerr << "Error opening output file '" << path_2 << "'\n";
+            return -1;
+        }
     }
 
     //
     // Open files for recording discarded reads.
     //
     if (discards) {
-	path_1 = out_path + file_1 + ".discards" + suffix_1;
+        path_1 = out_path + file_1 + ".discards" + suffix_1;
         if (out_file_type == FileT::gzfastq || out_file_type == FileT::gzfasta) {
             discard_gzfh_1 = gzopen(path_1.c_str(), "wb");
             if (!(discard_gzfh_1)) {
@@ -370,7 +370,7 @@ write_clonereduced_sequence(string prefix_1, string prefix_2,
             }
         }
 
-	path_2 = out_path + file_2 + ".discards" + suffix_2;
+        path_2 = out_path + file_2 + ".discards" + suffix_2;
         if (out_file_type == FileT::gzfastq || out_file_type == FileT::gzfasta) {
             discard_gzfh_2 = gzopen(path_2.c_str(), "wb");
             if (!(discard_gzfh_2)) {
@@ -394,7 +394,7 @@ write_clonereduced_sequence(string prefix_1, string prefix_2,
 
     for (hash_it = clone_map.begin(); hash_it != clone_map.end(); hash_it++) {
 
-	for (map_it = hash_it->second.begin(); map_it != hash_it->second.end(); map_it++) {
+        for (map_it = hash_it->second.begin(); map_it != hash_it->second.end(); map_it++) {
             sstr_1.str("");
             sstr_2.str("");
 
@@ -408,33 +408,33 @@ write_clonereduced_sequence(string prefix_1, string prefix_2,
                        << "+\n"
                        << map_it->second[0].p2_qual << "\n";
             } else {
-		sstr_1 << ">" << map_it->second[0].p1_id << "\n"
+                sstr_1 << ">" << map_it->second[0].p1_id << "\n"
                        << hash_it->first << "\n";
-		sstr_2 << ">" << map_it->second[0].p2_id << "\n"
+                sstr_2 << ">" << map_it->second[0].p2_id << "\n"
                        << map_it->first << "\n";
             }
 
             switch(out_file_type) {
             case FileT::gzfastq:
             case FileT::gzfasta:
-		gzputs(out_gzfh_1, sstr_1.str().c_str());
-		gzputs(out_gzfh_2, sstr_2.str().c_str());
+                gzputs(out_gzfh_1, sstr_1.str().c_str());
+                gzputs(out_gzfh_2, sstr_2.str().c_str());
                 break;
             case FileT::fastq:
             case FileT::fasta:
             default:
-		out_fh_1 << sstr_2.str();
-		out_fh_2 << sstr_2.str();
+                out_fh_1 << sstr_1.str();
+                out_fh_2 << sstr_2.str();
             }
             
-	    counters["dis_reads"] += map_it->second.size() - 1;
-	    clone_dist[map_it->second.size()]++;
-
-	    //
-	    // Write cloned read pairs that we are discarding
-	    //
-	    if (discards) {
-		for (uint i = 1; i < map_it->second.size(); i++) {
+            counters["dis_reads"] += map_it->second.size() - 1;
+            clone_dist[map_it->second.size()]++;
+
+            //
+            // Write cloned read pairs that we are discarding
+            //
+            if (discards) {
+                for (uint i = 1; i < map_it->second.size(); i++) {
                     sstr_1.str("");
                     sstr_2.str("");
 
@@ -463,27 +463,27 @@ write_clonereduced_sequence(string prefix_1, string prefix_2,
                     case FileT::fastq:
                     case FileT::fasta:
                     default:
-                        discard_fh_1 << sstr_2.str();
+                        discard_fh_1 << sstr_1.str();
                         discard_fh_2 << sstr_2.str();
                     }
-		}
+                }
             }
-	    counters["red_reads"]++;
-	}
+            counters["red_reads"]++;
+        }
     }
 
     cerr << "done.\n";
 
     if (out_file_type == FileT::gzfastq || out_file_type == FileT::gzfasta) {
-	gzclose(out_gzfh_1);
-	gzclose(out_gzfh_2);
-	if (discards) {
-	    gzclose(discard_gzfh_1);
-	    gzclose(discard_gzfh_2);
-	}
+        gzclose(out_gzfh_1);
+        gzclose(out_gzfh_2);
+        if (discards) {
+            gzclose(discard_gzfh_1);
+            gzclose(discard_gzfh_2);
+        }
     } else {
-	out_fh_1.close();
-	out_fh_2.close();
+        out_fh_1.close();
+        out_fh_2.close();
         if (discards) {
             discard_fh_1.close();
             discard_fh_2.close();
@@ -509,38 +509,38 @@ process_paired_reads(string prefix_1, string prefix_2, map<string, long> &counte
     string path_2 = in_path_2 + prefix_2;
 
     if (interleaved)
-	cerr << "  Reading data from:\n  " << path_1 << "\n";
+        cerr << "  Reading data from:\n  " << path_1 << "\n";
     else
-	cerr << "  Reading data from:\n  " << path_1 << " and\n  " << path_2 << "\n";
+        cerr << "  Reading data from:\n  " << path_1 << " and\n  " << path_2 << "\n";
 
     switch (in_file_type) {
     case FileT::fastq:
         fh_1 = new Fastq(path_1);
-	fh_2 = interleaved ? fh_1 : new Fastq(path_2);
-	break;
+        fh_2 = interleaved ? fh_1 : new Fastq(path_2);
+        break;
     case FileT::gzfastq:
         fh_1 = new GzFastq(path_1);
-	fh_2 = interleaved ? fh_1 : new GzFastq(path_2);
-	break;
+        fh_2 = interleaved ? fh_1 : new GzFastq(path_2);
+        break;
     case FileT::fasta:
         fh_1 = new Fasta(path_1);
-	fh_2 = interleaved ? fh_1 : new Fasta(path_2);
-	break;
+        fh_2 = interleaved ? fh_1 : new Fasta(path_2);
+        break;
     case FileT::gzfasta:
         fh_1 = new GzFasta(path_1);
-	fh_2 = interleaved ? fh_1 : new GzFasta(path_2);
-	break;
+        fh_2 = interleaved ? fh_1 : new GzFasta(path_2);
+        break;
     case FileT::bam:
         fh_1 = new BamUnAln(path_1);
-	fh_2 = fh_1;
-	break;
+        fh_2 = fh_1;
+        break;
     case FileT::bustard:
         fh_1 = new Bustard(path_1);
         fh_2 = interleaved ? fh_1 : new Bustard(path_2);
     default:
         fh_1 = NULL;
         fh_2 = NULL;
-	break;
+        break;
     }
 
     //
@@ -549,86 +549,86 @@ process_paired_reads(string prefix_1, string prefix_2, map<string, long> &counte
     string suffix_1, suffix_2;
     
     if (out_file_type == FileT::gzfastq) {
-	suffix_1 = ".1.fq.gz";
-	suffix_2 = ".2.fq.gz";
+        suffix_1 = ".1.fq.gz";
+        suffix_2 = ".2.fq.gz";
     } else if (out_file_type == FileT::fastq) {
-	suffix_1 = ".1.fq";
-	suffix_2 = ".2.fq";
+        suffix_1 = ".1.fq";
+        suffix_2 = ".2.fq";
     } else if (out_file_type == FileT::gzfasta) {
-	suffix_1 = ".1.fa.gz";
-	suffix_2 = ".2.fa.gz";
+        suffix_1 = ".1.fa.gz";
+        suffix_2 = ".2.fa.gz";
     } else if (out_file_type == FileT::fasta) {
-	suffix_1 = ".1.fa";
-	suffix_2 = ".2.fa";
+        suffix_1 = ".1.fa";
+        suffix_2 = ".2.fa";
     }
 
     string file_1 = remove_suffix(in_file_type, prefix_1);
     path_1 = out_path + file_1 + suffix_1;
     if (in_file_type == FileT::gzfastq || in_file_type == FileT::gzfasta) {
-	out_gzfh_1 = gzopen(path_1.c_str(), "wb");
-	if (!(out_gzfh_1)) {
-	    cerr << "Error opening output file '" << path_1 << "'\n";
-	    return -1;
-	}
-    } else {	    
-	out_fh_1.open(path_1.c_str(), ifstream::out);
-	if (out_fh_1.fail()) {
-	    cerr << "Error opening output file '" << path_1 << "'\n";
-	    return -1;
-	}
+        out_gzfh_1 = gzopen(path_1.c_str(), "wb");
+        if (!(out_gzfh_1)) {
+            cerr << "Error opening output file '" << path_1 << "'\n";
+            return -1;
+        }
+    } else {        
+        out_fh_1.open(path_1.c_str(), ifstream::out);
+        if (out_fh_1.fail()) {
+            cerr << "Error opening output file '" << path_1 << "'\n";
+            return -1;
+        }
     }
 
     string file_2 = remove_suffix(in_file_type, prefix_2);
     path_2 = out_path + file_2 + suffix_2;
     if (in_file_type == FileT::gzfastq || in_file_type == FileT::gzfasta) {
-	out_gzfh_2 = gzopen(path_2.c_str(), "wb");
-	if (!(out_gzfh_2)) {
-	    cerr << "Error opening output file '" << path_2 << "'\n";
-	    return -1;
-	}
-    } else {	    
-	out_fh_2.open(path_2.c_str(), ifstream::out);
-	if (out_fh_2.fail()) {
-	    cerr << "Error opening output file '" << path_2 << "'\n";
-	    return -1;
-	}
+        out_gzfh_2 = gzopen(path_2.c_str(), "wb");
+        if (!(out_gzfh_2)) {
+            cerr << "Error opening output file '" << path_2 << "'\n";
+            return -1;
+        }
+    } else {        
+        out_fh_2.open(path_2.c_str(), ifstream::out);
+        if (out_fh_2.fail()) {
+            cerr << "Error opening output file '" << path_2 << "'\n";
+            return -1;
+        }
     }
 
     //
     // Open files for recording discarded reads.
     //
     if (discards) {
-	path_1 = out_path + file_1 + ".discards" + suffix_1;
-
-	if (in_file_type == FileT::gzfastq || in_file_type == FileT::gzfasta) {
-	    discard_gzfh_1 = gzopen(path_1.c_str(), "wb");
-	    if (!(discard_gzfh_1)) {
-		cerr << "Error opening discard file '" << path_1 << "'\n";
-		return -1;
-	    }
-	} else {	    
-	    discard_fh_1.open(path_1.c_str(), ifstream::out);
-	    if (discard_fh_1.fail()) {
-		cerr << "Error opening discard file '" << path_1 << "'\n";
-		return -1;
-	    }
-	}
-
-	path_2 = out_path + file_2 + ".discards" + suffix_2;
-
-	if (in_file_type == FileT::gzfastq || in_file_type == FileT::gzfasta) {
-	    discard_gzfh_2 = gzopen(path_2.c_str(), "wb");
-	    if (!(discard_gzfh_2)) {
-		cerr << "Error opening discard file '" << path_2 << "'\n";
-		return -1;
-	    }
-	} else {	    
-	    discard_fh_2.open(path_2.c_str(), ifstream::out);
-	    if (discard_fh_2.fail()) {
-		cerr << "Error opening discard file '" << path_2 << "'\n";
-		return -1;
-	    }
-	}
+        path_1 = out_path + file_1 + ".discards" + suffix_1;
+
+        if (in_file_type == FileT::gzfastq || in_file_type == FileT::gzfasta) {
+            discard_gzfh_1 = gzopen(path_1.c_str(), "wb");
+            if (!(discard_gzfh_1)) {
+                cerr << "Error opening discard file '" << path_1 << "'\n";
+                return -1;
+            }
+        } else {            
+            discard_fh_1.open(path_1.c_str(), ifstream::out);
+            if (discard_fh_1.fail()) {
+                cerr << "Error opening discard file '" << path_1 << "'\n";
+                return -1;
+            }
+        }
+
+        path_2 = out_path + file_2 + ".discards" + suffix_2;
+
+        if (in_file_type == FileT::gzfastq || in_file_type == FileT::gzfasta) {
+            discard_gzfh_2 = gzopen(path_2.c_str(), "wb");
+            if (!(discard_gzfh_2)) {
+                cerr << "Error opening discard file '" << path_2 << "'\n";
+                return -1;
+            }
+        } else {            
+            discard_fh_2.open(path_2.c_str(), ifstream::out);
+            if (discard_fh_2.fail()) {
+                cerr << "Error opening discard file '" << path_2 << "'\n";
+                return -1;
+            }
+        }
     }
 
     //
@@ -638,27 +638,27 @@ process_paired_reads(string prefix_1, string prefix_2, map<string, long> &counte
     switch (barcode_type) {
     case inline_null:
     case inline_index:
-	offset_1 = oligo_len_1;
-	offset_2 = 0;
-	break;
+        offset_1 = oligo_len_1;
+        offset_2 = 0;
+        break;
     case index_null:
     case null_index:
     case index_index:
-	offset_1 = 0;
-	offset_2 = 0;
-	break;
+        offset_1 = 0;
+        offset_2 = 0;
+        break;
     case inline_inline:
-	offset_1 = oligo_len_1;
-	offset_2 = oligo_len_2;
-	break;
+        offset_1 = oligo_len_1;
+        offset_2 = oligo_len_2;
+        break;
     case index_inline:
-	offset_1 = 0;
-	offset_2 = oligo_len_2;
+        offset_1 = 0;
+        offset_2 = oligo_len_2;
     default:
-	break;
+        break;
     }
 
-		
+                
     //
     // Read in the first record, initializing the Seq object s. Then 
     // initialize the Read object r, then loop, using the same objects.
@@ -666,9 +666,9 @@ process_paired_reads(string prefix_1, string prefix_2, map<string, long> &counte
     Seq *s_1 = fh_1->next_seq();
     Seq *s_2 = fh_2->next_seq();
     if (s_1 == NULL || s_2 == NULL) {
-    	cerr << "Attempting to read first pair of input records, unable to allocate " 
-	     << "Seq object (Was the correct input type specified?).\n";
-	exit(1);
+        cerr << "Attempting to read first pair of input records, unable to allocate " 
+             << "Seq object (Was the correct input type specified?).\n";
+        exit(1);
     }
 
     r_1 = new Read(strlen(s_1->seq), 1, min_bc_size_1, win_size);
@@ -683,146 +683,146 @@ process_paired_reads(string prefix_1, string prefix_2, map<string, long> &counte
     do {
         if (i % 10000 == 0) cerr << "  Processing RAD-Tag " << i << "       \r";
 
-	parse_input_record(s_1, r_1);
-	parse_input_record(s_2, r_2);
-	counters["total"]++;
-
-	result_1 = 1;
-	result_2 = 1;
-	clone    = false;
-
-	//
-	// Fetch the randomized oligo sequence from the proper position in the reads.
-	//
-	switch (barcode_type) {
-	case inline_null:
-	    oligo_1 = r_1->inline_bc;
-	    break;
-	case index_null:
-	    oligo_1 = r_1->index_bc;
-	    break;
-	case null_index:
-	    oligo_1 = r_2->index_bc;
-	    break;
+        parse_input_record(s_1, r_1);
+        parse_input_record(s_2, r_2);
+        counters["total"]++;
+
+        result_1 = 1;
+        result_2 = 1;
+        clone    = false;
+
+        //
+        // Fetch the randomized oligo sequence from the proper position in the reads.
+        //
+        switch (barcode_type) {
+        case inline_null:
+            oligo_1 = r_1->inline_bc;
+            break;
+        case index_null:
+            oligo_1 = r_1->index_bc;
+            break;
+        case null_index:
+            oligo_1 = r_2->index_bc;
+            break;
         case inline_inline:
-	    oligo_1 = r_1->inline_bc;
-	    oligo_2 = r_2->inline_bc;
-	    break;
-	case index_index:
-	    oligo_1 = r_1->index_bc;
-	    oligo_2 = r_2->index_bc;
-	    break;
-	case inline_index:
-	    oligo_1 = r_1->inline_bc;
-	    oligo_2 = r_2->index_bc;
-	    break;
-	case index_inline:
-	    oligo_1 = r_1->index_bc;
-	    oligo_2 = r_2->inline_bc;
-	default:
-	    break;
-	}
-
-	//
-	// Have we seen this combination of oligos before for this read?
-	//
-	oligo = oligo_1 + oligo_2;
-	key   = string(s_1->seq + offset_1) + string(s_2->seq + offset_2);
-
-	// cerr << "Oligo: '" << oligo << "'\n"
-	//      << "Seq: '" << s_1->seq << "'\n"
-	//      << "Key: '" << key << "'\n";
-
-	if (oligo_map.count(key) == 0)
-	    oligo_map[key] = map<string, uint16_t>();
-
-	if (oligo_map[key].count(oligo) == 0) {
-	    oligo_map[key][oligo] = 1;
-	    clone = false;
-	} else {
-	    oligo_map[key][oligo]++;
-	    clone = true;
-	}
-
-	if (clone == false) {
-	    counters["red_reads"]++;
-
-	    switch (out_file_type) {
-	    case FileT::fastq:
-		result_1 = write_fastq(&out_fh_1, s_1, retain_oligo ? 0 : offset_1);
-		result_2 = write_fastq(&out_fh_2, s_2, retain_oligo ? 0 : offset_2);
-		break;
-	    case FileT::gzfastq:
-		result_1 = write_fastq(&out_gzfh_1, s_1, retain_oligo ? 0 : offset_1);
-		result_2 = write_fastq(&out_gzfh_2, s_2, retain_oligo ? 0 : offset_2);
-		break;
-	    case FileT::fasta:
-		result_1 = write_fasta(&out_fh_1, s_1, retain_oligo ? 0 : offset_1);
-		result_2 = write_fasta(&out_fh_2, s_2, retain_oligo ? 0 : offset_2);
-		break;
-	    case FileT::gzfasta:
-		result_1 = write_fasta(&out_gzfh_1, s_1, retain_oligo ? 0 : offset_1);
-		result_2 = write_fasta(&out_gzfh_2, s_2, retain_oligo ? 0 : offset_2);
-	    default:
-		break;
-	    }
-
-	    if (!result_1 || !result_2) {
-	    	cerr << "Error writing to output file for '" << file_1 << " / " << file_2 << "'\n";
-	    	return_val = -1;
-	    	break;
-	    }
-	} else if (clone == true && discards) {
-	    counters["dis_reads"]++;
-
-	    switch (out_file_type) {
-	    case FileT::fastq:
-		result_1 = write_fastq(&discard_fh_1,   s_1);
-		result_2 = write_fastq(&discard_fh_2,   s_2);
-		break;
-	    case FileT::gzfastq:
-		result_1 = write_fastq(&discard_gzfh_1, s_1);
-		result_2 = write_fastq(&discard_gzfh_2, s_2);
-		break;
-	    case FileT::fasta:
-		result_1 = write_fasta(&discard_fh_1,   s_1);
-		result_2 = write_fasta(&discard_fh_2,   s_2);
-		break;
-	    case FileT::gzfasta:
-		result_1 = write_fasta(&discard_gzfh_1, s_1);
-		result_2 = write_fasta(&discard_gzfh_2, s_2);
-	    default:
-		break;
-	    }
-
-	    if (!result_1 || !result_2) {
-		cerr << "Error writing to discard file for '" << file_1 << " / " << file_2 << "'\n";
-		return_val = -1;
-		break;
-	    }
-	}
-	
-	delete s_1;
-	delete s_2;
-
-	i++;
+            oligo_1 = r_1->inline_bc;
+            oligo_2 = r_2->inline_bc;
+            break;
+        case index_index:
+            oligo_1 = r_1->index_bc;
+            oligo_2 = r_2->index_bc;
+            break;
+        case inline_index:
+            oligo_1 = r_1->inline_bc;
+            oligo_2 = r_2->index_bc;
+            break;
+        case index_inline:
+            oligo_1 = r_1->index_bc;
+            oligo_2 = r_2->inline_bc;
+        default:
+            break;
+        }
+
+        //
+        // Have we seen this combination of oligos before for this read?
+        //
+        oligo = oligo_1 + oligo_2;
+        key   = string(s_1->seq + offset_1) + string(s_2->seq + offset_2);
+
+        // cerr << "Oligo: '" << oligo << "'\n"
+        //      << "Seq: '" << s_1->seq << "'\n"
+        //      << "Key: '" << key << "'\n";
+
+        if (oligo_map.count(key) == 0)
+            oligo_map[key] = map<string, uint16_t>();
+
+        if (oligo_map[key].count(oligo) == 0) {
+            oligo_map[key][oligo] = 1;
+            clone = false;
+        } else {
+            oligo_map[key][oligo]++;
+            clone = true;
+        }
+
+        if (clone == false) {
+            counters["red_reads"]++;
+
+            switch (out_file_type) {
+            case FileT::fastq:
+                result_1 = write_fastq(&out_fh_1, s_1, retain_oligo ? 0 : offset_1);
+                result_2 = write_fastq(&out_fh_2, s_2, retain_oligo ? 0 : offset_2);
+                break;
+            case FileT::gzfastq:
+                result_1 = write_fastq(&out_gzfh_1, s_1, retain_oligo ? 0 : offset_1);
+                result_2 = write_fastq(&out_gzfh_2, s_2, retain_oligo ? 0 : offset_2);
+                break;
+            case FileT::fasta:
+                result_1 = write_fasta(&out_fh_1, s_1, retain_oligo ? 0 : offset_1);
+                result_2 = write_fasta(&out_fh_2, s_2, retain_oligo ? 0 : offset_2);
+                break;
+            case FileT::gzfasta:
+                result_1 = write_fasta(&out_gzfh_1, s_1, retain_oligo ? 0 : offset_1);
+                result_2 = write_fasta(&out_gzfh_2, s_2, retain_oligo ? 0 : offset_2);
+            default:
+                break;
+            }
+
+            if (!result_1 || !result_2) {
+                cerr << "Error writing to output file for '" << file_1 << " / " << file_2 << "'\n";
+                return_val = -1;
+                break;
+            }
+        } else if (clone == true && discards) {
+            counters["dis_reads"]++;
+
+            switch (out_file_type) {
+            case FileT::fastq:
+                result_1 = write_fastq(&discard_fh_1,   s_1);
+                result_2 = write_fastq(&discard_fh_2,   s_2);
+                break;
+            case FileT::gzfastq:
+                result_1 = write_fastq(&discard_gzfh_1, s_1);
+                result_2 = write_fastq(&discard_gzfh_2, s_2);
+                break;
+            case FileT::fasta:
+                result_1 = write_fasta(&discard_fh_1,   s_1);
+                result_2 = write_fasta(&discard_fh_2,   s_2);
+                break;
+            case FileT::gzfasta:
+                result_1 = write_fasta(&discard_gzfh_1, s_1);
+                result_2 = write_fasta(&discard_gzfh_2, s_2);
+            default:
+                break;
+            }
+
+            if (!result_1 || !result_2) {
+                cerr << "Error writing to discard file for '" << file_1 << " / " << file_2 << "'\n";
+                return_val = -1;
+                break;
+            }
+        }
+        
+        delete s_1;
+        delete s_2;
+
+        i++;
     } while ((s_1 = fh_1->next_seq()) != NULL && 
-	     (s_2 = fh_2->next_seq()) != NULL);
+             (s_2 = fh_2->next_seq()) != NULL);
 
     if (out_file_type == FileT::gzfastq || out_file_type == FileT::gzfasta) {
-	gzclose(out_gzfh_1);
-	gzclose(out_gzfh_2);
-	if (discards) {
-	    gzclose(discard_gzfh_1);
-	    gzclose(discard_gzfh_2);
-	}
+        gzclose(out_gzfh_1);
+        gzclose(out_gzfh_2);
+        if (discards) {
+            gzclose(discard_gzfh_1);
+            gzclose(discard_gzfh_2);
+        }
     } else {
-	out_fh_1.close();
-	out_fh_2.close();
-	if (discards) {
-	    discard_fh_1.close();
-	    discard_fh_2.close();
-	}
+        out_fh_1.close();
+        out_fh_2.close();
+        if (discards) {
+            discard_fh_1.close();
+            discard_fh_2.close();
+        }
     }
     
     delete fh_1;
@@ -853,24 +853,24 @@ process_reads(string prefix_1, map<string, long> &counters, OligoHash &oligo_map
 
     switch(in_file_type) {
     case FileT::fastq:
-	fh_1 = new Fastq(path_1);
-	break;
+        fh_1 = new Fastq(path_1);
+        break;
     case FileT::gzfastq:
         fh_1 = new GzFastq(path_1.c_str());
-	break;
+        break;
     case FileT::fasta:
-        fh_1 = new Fasta(path_1);	
-	break;
+        fh_1 = new Fasta(path_1);       
+        break;
     case FileT::gzfasta: 
         fh_1 = new GzFasta(path_1);
-	break;
+        break;
     case FileT::bam:
         fh_1 = new BamUnAln(path_1);
-	break;
+        break;
     case FileT::bustard:
         fh_1 = new Bustard(path_1);
     default:
-	break;
+        break;
     }
 
     //
@@ -879,55 +879,55 @@ process_reads(string prefix_1, map<string, long> &counters, OligoHash &oligo_map
     string suffix_1;
     
     if (out_file_type == FileT::gzfastq)
-	suffix_1 = ".fq.gz";
+        suffix_1 = ".fq.gz";
     else if (out_file_type == FileT::fastq)
-	suffix_1 = ".fq";
+        suffix_1 = ".fq";
     else if (out_file_type == FileT::gzfasta)
-	suffix_1 = ".fa.gz";
+        suffix_1 = ".fa.gz";
     else if (out_file_type == FileT::fasta)
-	suffix_1 = ".fa";
+        suffix_1 = ".fa";
 
     string file_1 = prefix_1;
     int    pos    = file_1.find_last_of(".");
     if ((in_file_type == FileT::gzfastq || in_file_type == FileT::gzfasta) && 
-	file_1.substr(pos) == ".gz") {
-	file_1 = file_1.substr(0, pos);
-	pos    = file_1.find_last_of(".");
+        file_1.substr(pos) == ".gz") {
+        file_1 = file_1.substr(0, pos);
+        pos    = file_1.find_last_of(".");
     }
     path_1 = out_path + file_1.substr(0, pos) + suffix_1;
     if (in_file_type == FileT::gzfastq || in_file_type == FileT::gzfasta) {
-	out_gzfh_1 = gzopen(path_1.c_str(), "wb");
-	if (!(out_gzfh_1)) {
-	    cerr << "Error opening output file '" << path_1 << "'\n";
-	    return -1;
-	}
-    } else {	    
-	out_fh_1.open(path_1.c_str(), ifstream::out);
-	if (out_fh_1.fail()) {
-	    cerr << "Error opening output file '" << path_1 << "'\n";
-	    return -1;
-	}
+        out_gzfh_1 = gzopen(path_1.c_str(), "wb");
+        if (!(out_gzfh_1)) {
+            cerr << "Error opening output file '" << path_1 << "'\n";
+            return -1;
+        }
+    } else {        
+        out_fh_1.open(path_1.c_str(), ifstream::out);
+        if (out_fh_1.fail()) {
+            cerr << "Error opening output file '" << path_1 << "'\n";
+            return -1;
+        }
     }
 
     //
     // Open files for recording discarded reads.
     //
     if (discards) {
-	path_1 = out_path + file_1 + ".discards" + suffix_1;
-
-	if (in_file_type == FileT::gzfastq || in_file_type == FileT::gzfasta) {
-	    discard_gzfh_1 = gzopen(path_1.c_str(), "wb");
-	    if (!(discard_gzfh_1)) {
-		cerr << "Error opening discard file '" << path_1 << "'\n";
-		return -1;
-	    }
-	} else {	    
-	    discard_fh_1.open(path_1.c_str(), ifstream::out);
-	    if (discard_fh_1.fail()) {
-		cerr << "Error opening discard file '" << path_1 << "'\n";
-		return -1;
-	    }
-	}
+        path_1 = out_path + file_1 + ".discards" + suffix_1;
+
+        if (in_file_type == FileT::gzfastq || in_file_type == FileT::gzfasta) {
+            discard_gzfh_1 = gzopen(path_1.c_str(), "wb");
+            if (!(discard_gzfh_1)) {
+                cerr << "Error opening discard file '" << path_1 << "'\n";
+                return -1;
+            }
+        } else {            
+            discard_fh_1.open(path_1.c_str(), ifstream::out);
+            if (discard_fh_1.fail()) {
+                cerr << "Error opening discard file '" << path_1 << "'\n";
+                return -1;
+            }
+        }
     }
 
     //
@@ -938,22 +938,22 @@ process_reads(string prefix_1, map<string, long> &counters, OligoHash &oligo_map
     case inline_null:
     case inline_index:
     case index_inline:
-	offset_1 = oligo_len_1;
-	break;
+        offset_1 = oligo_len_1;
+        break;
     default:
-	offset_1 = 0;
-	break;
+        offset_1 = 0;
+        break;
     }
-		
+                
     //
     // Read in the first record, initializing the Seq object s. Then 
     // initialize the Read object r, then loop, using the same objects.
     //
     Seq *s_1 = fh_1->next_seq();
     if (s_1 == NULL) {
-    	cerr << "Attempting to read first pair of input records, unable to allocate " 
-	     << "Seq object (Was the correct input type specified?).\n";
-	exit(1);
+        cerr << "Attempting to read first pair of input records, unable to allocate " 
+             << "Seq object (Was the correct input type specified?).\n";
+        exit(1);
     }
 
     r_1 = new Read(strlen(s_1->seq), 1, min_bc_size_1, win_size);
@@ -966,97 +966,97 @@ process_reads(string prefix_1, map<string, long> &counters, OligoHash &oligo_map
     do {
         if (i % 10000 == 0) cerr << "  Processing RAD-Tag " << i << "       \r";
 
-	parse_input_record(s_1, r_1);
-	counters["total"]++;
-
-	result_1 = 1;
-	clone    = false;
-
-	//
-	// Fetch the randomized oligo sequence from the proper position in the reads.
-	//
-	if (barcode_type == inline_null)
-	    oligo_1 = r_1->inline_bc;
-	else if (barcode_type == index_null)
-	    oligo_1 = r_1->index_bc;
-
-	//
-	// Have we seen this combination of oligos before for this read?
-	//
-	key = string(s_1->seq + offset_1);
-
-	if (oligo_map.count(key) == 0)
-	    oligo_map[key] = map<string, uint16_t>();
-
-	if (oligo_map[key].count(oligo_1) == 0) {
-	    oligo_map[key][oligo_1] = 1;
-	    clone = false;
-	} else {
-	    oligo_map[key][oligo_1]++;
-	    clone = true;
-	}
-
-	if (clone == false) {
-	    counters["red_reads"]++;
-
-	    switch (out_file_type) {
-	    case FileT::fastq:
-		result_1 = write_fastq(&out_fh_1,   s_1, retain_oligo ? 0 : offset_1);
-		break;
-	    case FileT::gzfastq:
-		result_1 = write_fastq(&out_gzfh_1, s_1, retain_oligo ? 0 : offset_1);
-		break;
-	    case FileT::fasta:
-		result_1 = write_fasta(&out_fh_1,   s_1, retain_oligo ? 0 : offset_1);
-		break;
-	    case FileT::gzfasta:
-		result_1 = write_fasta(&out_gzfh_1, s_1, retain_oligo ? 0 : offset_1);
-	    default:
-		break;
-	    }
-	    
-	    if (!result_1) {
-	    	cerr << "Error writing to output file for '" << file_1 << "'\n";
-	    	return_val = -1;
-	    	break;
-	    }
-	} else if (clone == true && discards) {
-	    counters["dis_reads"]++;
-
-	    switch (out_file_type) {
-	    case FileT::fastq:
-		result_1 = write_fastq(&discard_fh_1,   s_1);
-		break;
-	    case FileT::gzfastq:
-		result_1 = write_fastq(&discard_gzfh_1, s_1);
-		break;
-	    case FileT::fasta:
-		result_1 = write_fasta(&discard_fh_1,   s_1);
-		break;
-	    case FileT::gzfasta:
-		result_1 = write_fasta(&discard_gzfh_1, s_1);
-	    default:
-		break;
-	    }
-
-	    if (!result_1) {
-		cerr << "Error writing to discard file for '" << file_1 << "'\n";
-		return_val = -1;
-		break;
-	    }
-	}
-
-	delete s_1;
-
-	i++;
+        parse_input_record(s_1, r_1);
+        counters["total"]++;
+
+        result_1 = 1;
+        clone    = false;
+
+        //
+        // Fetch the randomized oligo sequence from the proper position in the reads.
+        //
+        if (barcode_type == inline_null)
+            oligo_1 = r_1->inline_bc;
+        else if (barcode_type == index_null)
+            oligo_1 = r_1->index_bc;
+
+        //
+        // Have we seen this combination of oligos before for this read?
+        //
+        key = string(s_1->seq + offset_1);
+
+        if (oligo_map.count(key) == 0)
+            oligo_map[key] = map<string, uint16_t>();
+
+        if (oligo_map[key].count(oligo_1) == 0) {
+            oligo_map[key][oligo_1] = 1;
+            clone = false;
+        } else {
+            oligo_map[key][oligo_1]++;
+            clone = true;
+        }
+
+        if (clone == false) {
+            counters["red_reads"]++;
+
+            switch (out_file_type) {
+            case FileT::fastq:
+                result_1 = write_fastq(&out_fh_1,   s_1, retain_oligo ? 0 : offset_1);
+                break;
+            case FileT::gzfastq:
+                result_1 = write_fastq(&out_gzfh_1, s_1, retain_oligo ? 0 : offset_1);
+                break;
+            case FileT::fasta:
+                result_1 = write_fasta(&out_fh_1,   s_1, retain_oligo ? 0 : offset_1);
+                break;
+            case FileT::gzfasta:
+                result_1 = write_fasta(&out_gzfh_1, s_1, retain_oligo ? 0 : offset_1);
+            default:
+                break;
+            }
+            
+            if (!result_1) {
+                cerr << "Error writing to output file for '" << file_1 << "'\n";
+                return_val = -1;
+                break;
+            }
+        } else if (clone == true && discards) {
+            counters["dis_reads"]++;
+
+            switch (out_file_type) {
+            case FileT::fastq:
+                result_1 = write_fastq(&discard_fh_1,   s_1);
+                break;
+            case FileT::gzfastq:
+                result_1 = write_fastq(&discard_gzfh_1, s_1);
+                break;
+            case FileT::fasta:
+                result_1 = write_fasta(&discard_fh_1,   s_1);
+                break;
+            case FileT::gzfasta:
+                result_1 = write_fasta(&discard_gzfh_1, s_1);
+            default:
+                break;
+            }
+
+            if (!result_1) {
+                cerr << "Error writing to discard file for '" << file_1 << "'\n";
+                return_val = -1;
+                break;
+            }
+        }
+
+        delete s_1;
+
+        i++;
     } while ((s_1 = fh_1->next_seq()) != NULL);
 
     if (out_file_type == FileT::gzfastq || out_file_type == FileT::gzfasta) {
-	gzclose(out_gzfh_1);
-	if (discards) gzclose(discard_gzfh_1);
+        gzclose(out_gzfh_1);
+        if (discards) gzclose(discard_gzfh_1);
     } else {
-	out_fh_1.close();
-	if (discards) discard_fh_1.close();
+        out_fh_1.close();
+        if (discards) discard_fh_1.close();
     }
     
     delete fh_1;
@@ -1070,7 +1070,7 @@ int
 free_hash(vector<char *> &keys) 
 {
     for (uint i = 0; i < keys.size(); i++) {
-	delete [] keys[i];
+        delete [] keys[i];
     }
     keys.clear();
 
@@ -1082,182 +1082,182 @@ int parse_command_line(int argc, char* argv[]) {
     int   c;
 
     while (1) {
-	static struct option long_options[] = {
-	    {"help",          no_argument,       NULL, 'h'},
+        static struct option long_options[] = {
+            {"help",          no_argument,       NULL, 'h'},
             {"version",       no_argument,       NULL, 'v'},
-	    {"discards",      no_argument,       NULL, 'D'},
-	    {"paired",        no_argument,       NULL, 'P'},
-	    {"null_index",    no_argument,       NULL, 'U'},
-	    {"index_null",    no_argument,       NULL, 'u'},
-	    {"inline_null",   no_argument,       NULL, 'V'},
-	    {"index_index",   no_argument,       NULL, 'W'},
-	    {"inline_inline", no_argument,       NULL, 'x'},
-	    {"index_inline",  no_argument,       NULL, 'Y'},
-	    {"inline_index",  no_argument,       NULL, 'Z'},
-	    {"infile_type",   required_argument, NULL, 'i'},
-	    {"outfile_type",  required_argument, NULL, 'y'},
-	    {"file",          required_argument, NULL, 'f'},
-	    {"path",          required_argument, NULL, 'p'},
-	    {"file_p1",       required_argument, NULL, '1'},
-	    {"file_p2",       required_argument, NULL, '2'},
-	    {"outpath",       required_argument, NULL, 'o'},
-	    {"oligo_len_1",   required_argument, NULL, 'O'},
-	    {"oligo_len_2",   required_argument, NULL, 'L'},
-	    {"retain_oligo",  required_argument, NULL, 'R'},
-	    {0, 0, 0, 0}
-	};
-	
-	// getopt_long stores the option index here.
-	int option_index = 0;
-
-	c = getopt_long(argc, argv, "hvDPuUVWxYZi:y:f:p:1:2:o:O:L:R:", long_options, &option_index);
-
-	// Detect the end of the options.
-	if (c == -1)
-	    break;
-
-	switch (c) {
-	case 'h':
-	    help();
-	    break;
-     	case 'i':
+            {"discards",      no_argument,       NULL, 'D'},
+            {"paired",        no_argument,       NULL, 'P'},
+            {"null_index",    no_argument,       NULL, 'U'},
+            {"index_null",    no_argument,       NULL, 'u'},
+            {"inline_null",   no_argument,       NULL, 'V'},
+            {"index_index",   no_argument,       NULL, 'W'},
+            {"inline_inline", no_argument,       NULL, 'x'},
+            {"index_inline",  no_argument,       NULL, 'Y'},
+            {"inline_index",  no_argument,       NULL, 'Z'},
+            {"infile_type",   required_argument, NULL, 'i'},
+            {"outfile_type",  required_argument, NULL, 'y'},
+            {"file",          required_argument, NULL, 'f'},
+            {"path",          required_argument, NULL, 'p'},
+            {"file_p1",       required_argument, NULL, '1'},
+            {"file_p2",       required_argument, NULL, '2'},
+            {"outpath",       required_argument, NULL, 'o'},
+            {"oligo_len_1",   required_argument, NULL, 'O'},
+            {"oligo_len_2",   required_argument, NULL, 'L'},
+            {"retain_oligo",  required_argument, NULL, 'R'},
+            {0, 0, 0, 0}
+        };
+        
+        // getopt_long stores the option index here.
+        int option_index = 0;
+
+        c = getopt_long(argc, argv, "hvDPuUVWxYZi:y:f:p:1:2:o:O:L:R:", long_options, &option_index);
+
+        // Detect the end of the options.
+        if (c == -1)
+            break;
+
+        switch (c) {
+        case 'h':
+            help();
+            break;
+        case 'i':
             if (strcasecmp(optarg, "bustard") == 0)
                 in_file_type = FileT::bustard;
-	    else if (strcasecmp(optarg, "fasta") == 0)
+            else if (strcasecmp(optarg, "fasta") == 0)
                 in_file_type = FileT::fasta;
-	     else if (strcasecmp(optarg, "gzfasta") == 0)
-		 in_file_type = FileT::gzfasta;
-	     else if (strcasecmp(optarg, "gzfastq") == 0)
-		 in_file_type = FileT::gzfastq;
-	     else
-		 in_file_type = FileT::fastq;
-	    break;
-     	case 'y':
-	    if (strcasecmp(optarg, "fastq") == 0)
-		out_file_type = FileT::fastq;
+             else if (strcasecmp(optarg, "gzfasta") == 0)
+                 in_file_type = FileT::gzfasta;
+             else if (strcasecmp(optarg, "gzfastq") == 0)
+                 in_file_type = FileT::gzfastq;
+             else
+                 in_file_type = FileT::fastq;
+            break;
+        case 'y':
+            if (strcasecmp(optarg, "fastq") == 0)
+                out_file_type = FileT::fastq;
             else if (strcasecmp(optarg, "gzfastq") == 0)
-		out_file_type = FileT::gzfastq;
+                out_file_type = FileT::gzfastq;
             else if (strcasecmp(optarg, "fasta") == 0)
                 out_file_type = FileT::fasta;
             else if (strcasecmp(optarg, "gzfasta") == 0)
-		out_file_type = FileT::gzfasta;
-	    break;
-	case 'D':
-	    discards = true;
-	    break;
-     	case 'f':
-	    in_file = optarg;
-	    ftype   = FileT::fastq;
-	    break;
-	case 'p':
-	    in_path_1 = optarg;
-	    in_path_2 = in_path_1;
-	    ftype     = FileT::fastq;
-	    break;
-	case '1':
-	    paired     = true;
-	    in_file_p1 = optarg;
-	    ftype      = FileT::fastq;
-	    break;
-	case '2':
-	    paired     = true;
-	    in_file_p2 = optarg;
-	    ftype      = FileT::fastq;
-	    break;
-	case 'P':
-	    paired = true;
-	    break;
-	case 'o':
-	    out_path = optarg;
-	    break;
-	case 'U':
-	    barcode_type = null_index;
-	    break;
-	case 'u':
-	    barcode_type = index_null;
-	    break;
-	case 'V':
-	    barcode_type = inline_null;
-	    break;
-	case 'W':
-	    barcode_type = index_index;
-	    break;
-	case 'x':
-	    barcode_type = inline_inline;
-	    break;
-	case 'Y':
-	    barcode_type = index_inline;
-	    break;
-	case 'Z':
-	    barcode_type = inline_index;
-	    break;
-	case 'O':
-	    oligo_len_1 = is_integer(optarg);
-	    break;
-	case 'L':
-	    oligo_len_2 = is_integer(optarg);
-	    break;
-	case 'R':
-	    retain_oligo = true;
-	    break;
+                out_file_type = FileT::gzfasta;
+            break;
+        case 'D':
+            discards = true;
+            break;
+        case 'f':
+            in_file = optarg;
+            ftype   = FileT::fastq;
+            break;
+        case 'p':
+            in_path_1 = optarg;
+            in_path_2 = in_path_1;
+            ftype     = FileT::fastq;
+            break;
+        case '1':
+            paired     = true;
+            in_file_p1 = optarg;
+            ftype      = FileT::fastq;
+            break;
+        case '2':
+            paired     = true;
+            in_file_p2 = optarg;
+            ftype      = FileT::fastq;
+            break;
+        case 'P':
+            paired = true;
+            break;
+        case 'o':
+            out_path = optarg;
+            break;
+        case 'U':
+            barcode_type = null_index;
+            break;
+        case 'u':
+            barcode_type = index_null;
+            break;
+        case 'V':
+            barcode_type = inline_null;
+            break;
+        case 'W':
+            barcode_type = index_index;
+            break;
+        case 'x':
+            barcode_type = inline_inline;
+            break;
+        case 'Y':
+            barcode_type = index_inline;
+            break;
+        case 'Z':
+            barcode_type = inline_index;
+            break;
+        case 'O':
+            oligo_len_1 = is_integer(optarg);
+            break;
+        case 'L':
+            oligo_len_2 = is_integer(optarg);
+            break;
+        case 'R':
+            retain_oligo = true;
+            break;
         case 'v':
             version();
             break;
-	case '?':
-	    // getopt_long already printed an error message.
-	    help();
-	    break;
+        case '?':
+            // getopt_long already printed an error message.
+            help();
+            break;
      
-	default:
-	    cerr << "Unknown command line option '" << (char) c << "'\n";
-	    help();
-	    abort();
-	}
+        default:
+            cerr << "Unknown command line option '" << (char) c << "'\n";
+            help();
+            abort();
+        }
     }
 
     if (in_file.length() == 0 && in_path_1.length() == 0 && in_file_p1.length() == 0) {
-	cerr << "You must specify an input file of a directory path to a set of input files.\n";
-	help();
+        cerr << "You must specify an input file of a directory path to a set of input files.\n";
+        help();
     }
 
     if (in_file.length() > 0 && in_path_1.length() > 0) {
-	cerr << "You must specify either a single input file (-f) or a directory path (-p), not both.\n";
-	help();
+        cerr << "You must specify either a single input file (-f) or a directory path (-p), not both.\n";
+        help();
     }
 
     if (in_file.length() > 0 && (in_file_p1.length() > 0 || in_file_p2.length() > 0)) {
-	cerr << "You must specify either a single input file (-f) or a set of paired files (-1, -2), not both.\n";
-	help();
+        cerr << "You must specify either a single input file (-f) or a set of paired files (-1, -2), not both.\n";
+        help();
     }
 
     if (in_path_1.length() > 0 && (in_file_p1.length() > 0 || in_file_p2.length() > 0)) {
-	cerr << "You must specify either a file path (-p) or a set of paired files (-1, -2), not both.\n";
-	help();
+        cerr << "You must specify either a file path (-p) or a set of paired files (-1, -2), not both.\n";
+        help();
     }
 
     if (in_path_1.length() > 0 && in_path_1.at(in_path_1.length() - 1) != '/') 
-	in_path_1 += "/";
+        in_path_1 += "/";
 
     if (in_path_2.length() > 0 && in_path_2.at(in_path_2.length() - 1) != '/') 
-	in_path_2 += "/";
+        in_path_2 += "/";
 
     if (out_path.length() == 0) 
-	out_path = ".";
+        out_path = ".";
 
     if (out_path.at(out_path.length() - 1) != '/') 
-	out_path += "/";
+        out_path += "/";
 
     if (in_file_type == FileT::unknown)
-	in_file_type = ftype;
+        in_file_type = ftype;
 
     if (paired == false && barcode_type == null_null) {
-	cerr << "You must specify paired-end data if you do not have oligo sequences to differentiate cloned reads.\n";
-	help();
+        cerr << "You must specify paired-end data if you do not have oligo sequences to differentiate cloned reads.\n";
+        help();
     }
 
     if (barcode_type != null_null && oligo_len_1 == 0 && oligo_len_2 == 0) {
-	cerr << "You must specify the length of the oligo sequences (--oligo_len_1 / --oligo_len_2).\n";
-	help();
+        cerr << "You must specify the length of the oligo sequences (--oligo_len_1 / --oligo_len_2).\n";
+        help();
     }
     
     return 0;
@@ -1272,27 +1272,27 @@ void version() {
 void help() {
     std::cerr << "clone_filter " << VERSION << "\n"
               << "clone_filter [-f in_file | -p in_dir [-P] [-I] | -1 pair_1 -2 pair_2] -o out_dir [-i type] [-y type] [-D] [-h]\n"
-	      << "  f: path to the input file if processing single-end sequences.\n"
-	      << "  p: path to a directory of files.\n"
-	      << "  P: files contained within directory specified by '-p' are paired.\n"
-	      << "  1: first input file in a set of paired-end sequences.\n"
-	      << "  2: second input file in a set of paired-end sequences.\n"
-	      << "  i: input file type, either 'bustard', 'fastq', 'fasta', 'gzfasta', or 'gzfastq' (default 'fastq').\n"
-	      << "  o: path to output the processed files.\n"
-	      << "  y: output type, either 'fastq', 'fasta', 'gzfasta', or 'gzfastq' (default same as input type).\n"
-	      << "  D: capture discarded reads to a file.\n"
-	      << "  h: display this help messsage.\n"
-	      << "  --oligo_len_1 len: length of the single-end oligo sequence in data set.\n"
-	      << "  --oligo_len_2 len: length of the paired-end oligo sequence in data set.\n"
-	      << "  --retain_oligo: do not trim off the random oligo sequence (if oligo is inline).\n\n"
-	      << "  Oligo sequence options:\n"
-	      << "    --inline_null:   random oligo is inline with sequence, occurs only on single-end read (default).\n"
-	      << "    --null_index:    random oligo is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided).\n"
-	      << "    --index_null:    random oligo is provded in FASTQ header (Illumina i5 or i7 read).\n"
-	      << "    --inline_inline: random oligo is inline with sequence, occurs on single and paired-end read.\n"
-	      << "    --index_index:   random oligo is provded in FASTQ header (Illumina i5 and i7 read).\n"
-	      << "    --inline_index:  random oligo is inline with sequence on single-end read and second oligo occurs in FASTQ header.\n"
-	      << "    --index_inline:  random oligo occurs in FASTQ header (Illumina i5 or i7 read) and is inline with sequence on single-end read (if single read data) or paired-end read (if paired data).\n\n";
+              << "  f: path to the input file if processing single-end sequences.\n"
+              << "  p: path to a directory of files.\n"
+              << "  P: files contained within directory specified by '-p' are paired.\n"
+              << "  1: first input file in a set of paired-end sequences.\n"
+              << "  2: second input file in a set of paired-end sequences.\n"
+              << "  i: input file type, either 'bustard', 'fastq', 'fasta', 'gzfasta', or 'gzfastq' (default 'fastq').\n"
+              << "  o: path to output the processed files.\n"
+              << "  y: output type, either 'fastq', 'fasta', 'gzfasta', or 'gzfastq' (default same as input type).\n"
+              << "  D: capture discarded reads to a file.\n"
+              << "  h: display this help messsage.\n"
+              << "  --oligo_len_1 len: length of the single-end oligo sequence in data set.\n"
+              << "  --oligo_len_2 len: length of the paired-end oligo sequence in data set.\n"
+              << "  --retain_oligo: do not trim off the random oligo sequence (if oligo is inline).\n\n"
+              << "  Oligo sequence options:\n"
+              << "    --inline_null:   random oligo is inline with sequence, occurs only on single-end read (default).\n"
+              << "    --null_index:    random oligo is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided).\n"
+              << "    --index_null:    random oligo is provded in FASTQ header (Illumina i5 or i7 read).\n"
+              << "    --inline_inline: random oligo is inline with sequence, occurs on single and paired-end read.\n"
+              << "    --index_index:   random oligo is provded in FASTQ header (Illumina i5 and i7 read).\n"
+              << "    --inline_index:  random oligo is inline with sequence on single-end read and second oligo occurs in FASTQ header.\n"
+              << "    --index_inline:  random oligo occurs in FASTQ header (Illumina i5 or i7 read) and is inline with sequence on single-end read (if single read data) or paired-end read (if paired data).\n\n";
 
     exit(0);
 }
diff --git a/src/cstacks.cc b/src/cstacks.cc
index 7bf608c..010b7be 100644
--- a/src/cstacks.cc
+++ b/src/cstacks.cc
@@ -48,8 +48,11 @@ int main (int argc, char* argv[]) {
 
     uint sample_cnt = samples.size();
 
-    cerr << "Number of mismatches allowed between stacks: " << ctag_dist << "\n"
-	 << "Loci matched based on " << (search_type == sequence ? "sequence identity" : "genomic location") << ".\n"
+    cerr << "cstacks paramters selected:\n"
+	 << "  Loci matched based on " << (search_type == sequence ? "sequence identity" : "genomic location") << ".\n";
+    if (search_type == sequence)
+        cerr << "  Number of mismatches allowed between stacks: " << ctag_dist << "\n";
+    cerr << "  Gapped alignments: " << (gapped_alignments ? "enabled" : "disabled") << "\n"
 	 << "Constructing catalog from " << sample_cnt << " samples.\n";
 
     //
@@ -173,7 +176,7 @@ int update_catalog_index(map<int, CLocus *> &catalog, map<string, int> &cat_inde
 	snprintf(id, id_len - 1, "%s|%d|%c", 
 		 j->second->loc.chr, 
 		 j->second->loc.bp, 
-		 j->second->loc.strand == plus ? '+' : '-');
+		 j->second->loc.strand == strand_plus ? '+' : '-');
 
 	if (cat_index.count(id) == 0) {
 	    cat_index[id] = j->first;
@@ -249,7 +252,7 @@ merge_matches(map<int, CLocus *> &catalog, map<int, QLocus *> &sample, pair<int,
     CLocus *ctag;
     QLocus *qtag;
     string  cseq, qseq, cigar_str;
-    int     cseq_len, qseq_len, match_index;
+    int     cseq_len, match_index;
     vector<pair<char, uint> > cigar;
 
     GappedAln *aln = new GappedAln();
@@ -324,7 +327,7 @@ merge_matches(map<int, CLocus *> &catalog, map<int, QLocus *> &sample, pair<int,
         cigar_str = "";
 
         for (uint k = 0; k < qtag->matches.size(); k++)
-            if (qtag->matches[k]->cat_id == min_cat_id) {
+            if ((int)qtag->matches[k]->cat_id == min_cat_id) {
                 cigar_str   = qtag->matches[k]->cigar;
                 match_index = k;
                 break;
@@ -335,7 +338,7 @@ merge_matches(map<int, CLocus *> &catalog, map<int, QLocus *> &sample, pair<int,
         // sample, we must re-align the sequences in case changes have been made to the
         // sequence by the previous matching sequence.
         //
-        if (ctag->match_cnt > 0) {
+        if (gapped_alignments && ctag->match_cnt > 0) {
             string query_allele, query_seq, cat_allele, cat_seq;
             // cerr << "    Warning: Catalog locus " << ctag->id
             //      << ", Sample " << qtag->sample_id << ", locus " << qtag->id
@@ -367,7 +370,6 @@ merge_matches(map<int, CLocus *> &catalog, map<int, QLocus *> &sample, pair<int,
         // Adjust the postition of any SNPs that were shifted down sequence due to a gap.
         //
         if (gapped_aln) {
-            qseq_len  = parse_cigar(cigar_str.c_str(), cigar);
             qseq      = apply_cigar_to_seq(qtag->con, cigar);
             adjust_snps_for_gaps(cigar, qtag);
 
@@ -380,7 +382,7 @@ merge_matches(map<int, CLocus *> &catalog, map<int, QLocus *> &sample, pair<int,
             // If the alignment modified the catalog locus, record it so we can re-align
             // any other matching sequences from this sample.
             //
-            if (cseq_len > ctag->len)
+            if ((uint)cseq_len > ctag->len)
                 ctag->match_cnt++;
 
             //
@@ -547,7 +549,7 @@ int find_kmer_matches_by_sequence(map<int, CLocus *> &catalog, map<int, QLocus *
 		// generate, multiple, spurious hits in sequences with multiple copies of the same kmer.
 		//
 		uniq_kmers.clear();
-                for (uint j = 0; j < num_kmers; j++)
+                for (int j = 0; j < num_kmers; j++)
 		    uniq_kmers.insert(kmers[j]);
 
 		hits.clear();
@@ -586,7 +588,7 @@ int find_kmer_matches_by_sequence(map<int, CLocus *> &catalog, map<int, QLocus *
 		    hit_cnt   = 0;
 		    allele_id = prev_id;
 
-		    while (hits[index] == prev_id) {
+		    while ((uint)hits[index] == prev_id) {
 			hit_cnt++;
 			index++;
 		    }
@@ -594,7 +596,7 @@ int find_kmer_matches_by_sequence(map<int, CLocus *> &catalog, map<int, QLocus *
 		    if (index < hits_size)
 			prev_id = hits[index];
 
-		    if (hit_cnt >= min_hits)
+		    if (hit_cnt >= (uint)min_hits)
 			ordered_hits.push_back(make_pair(allele_id, hit_cnt));
 
         	} while (index < hits_size);
@@ -725,7 +727,7 @@ search_for_gaps(map<int, CLocus *> &catalog, map<int, QLocus *> &sample, double
 		// generate, multiple, spurious hits in sequences with multiple copies of the same kmer.
 		//
 		uniq_kmers.clear();
-                for (uint j = 0; j < num_kmers; j++)
+                for (int j = 0; j < num_kmers; j++)
 		    uniq_kmers.insert(kmers[j]);
 
                 hits.clear();
@@ -764,7 +766,7 @@ search_for_gaps(map<int, CLocus *> &catalog, map<int, QLocus *> &sample, double
 		    hit_cnt   = 0;
 		    allele_id = prev_id;
 
-		    while (hits[index] == prev_id) {
+		    while ((uint)hits[index] == prev_id) {
 			hit_cnt++;
 			index++;
 		    }
@@ -772,7 +774,7 @@ search_for_gaps(map<int, CLocus *> &catalog, map<int, QLocus *> &sample, double
 		    if (index < hits_size)
 			prev_id = hits[index];
 
-		    if (hit_cnt >= min_hits)
+		    if (hit_cnt >= (uint)min_hits)
 			ordered_hits.push_back(make_pair(allele_id, hit_cnt));
 
         	} while (index < hits_size);
@@ -791,7 +793,7 @@ search_for_gaps(map<int, CLocus *> &catalog, map<int, QLocus *> &sample, double
 		top_hit = ordered_hits[0].second;
                 stop    = 1;
 		for (uint j = 1; j < ordered_hits.size(); j++)
-		    if (ordered_hits[j].second < top_hit) {
+		    if ((uint)ordered_hits[j].second < top_hit) {
 			stop = j;
 			break;
 		    }
@@ -932,7 +934,7 @@ int find_matches_by_genomic_loc(map<string, int> &cat_index, map<int, QLocus *>
 	    snprintf(id, id_len - 1, "%s|%d|%c", 
 		     i->second->loc.chr, 
 		     i->second->loc.bp, 
-		     i->second->loc.strand == plus ? '+' : '-');
+		     i->second->loc.strand == strand_plus ? '+' : '-');
 
 	    if (cat_index.count(id) > 0)
 		i->second->add_match(cat_index[id], "", "", 0);
@@ -1536,7 +1538,7 @@ write_simple_output(CLocus *tag, ofstream &cat_file, ofstream &snp_file, ofstrea
 	tag->id      << "\t" <<
         tag->loc.chr << "\t" <<
         tag->loc.bp  << "\t" <<
-        (tag->loc.strand == plus ? "+" : "-") << "\t" <<
+        (tag->loc.strand == strand_plus ? "+" : "-") << "\t" <<
 	"consensus"  << "\t" <<
 	"0"          << "\t" <<
 	sources      << "\t" <<
@@ -1613,7 +1615,7 @@ write_gzip_output(CLocus *tag, gzFile &cat_file, gzFile &snp_file, gzFile &all_f
 	tag->id      << "\t" <<
         tag->loc.chr << "\t" <<
         tag->loc.bp  << "\t" <<
-        (tag->loc.strand == plus ? "+" : "-") << "\t" <<
+        (tag->loc.strand == strand_plus ? "+" : "-") << "\t" <<
 	"consensus"  << "\t" <<
 	"0"          << "\t" <<
 	sources      << "\t" <<
diff --git a/src/export_formats.cc b/src/export_formats.cc
new file mode 100644
index 0000000..6397f57
--- /dev/null
+++ b/src/export_formats.cc
@@ -0,0 +1,3333 @@
+#include <algorithm>
+#include <vector>
+
+#include "ordered.h"
+#include "sql_utilities.h"
+#include "MetaPopInfo.h"
+
+#include "export_formats.h"
+
+using namespace std;
+
+extern InputMode input_mode;
+extern int batch_id;
+extern string in_path;
+extern string out_path;
+extern string out_prefix;
+extern bool phylip_var;
+extern bool loci_ordered;
+extern bool merge_sites;
+extern string enz;
+extern set<string> debug_flags;
+
+extern MetaPopInfo mpopi;
+extern map<string, int> renz_olap;
+
+int 
+write_sql(map<int, CSLocus *> &catalog, PopMap<CSLocus> *pmap) 
+{
+    string file = out_path + out_prefix + ".markers.tsv";
+
+    cerr << "Writing SQL markers file to '" << file << "'\n";
+
+    ofstream fh(file.c_str(), ofstream::out);
+    if (fh.fail()) {
+        cerr << "Error opening markers SQL file '" << file << "'\n";
+        exit(1);
+    }
+    fh.precision(fieldw);
+    fh.setf(std::ios::fixed);
+
+    fh << "# SQL ID"            << "\t" 
+       << "Batch ID"            << "\t" 
+       << "Catalog Locus ID"    << "\t" 
+       << "\t"
+       << "Total Genotypes"     << "\t"
+       << "Max"                 << "\t"
+       << "Genotype Freqs"      << "\t"
+       << "F"                   << "\t"
+       << "Mean Log Likelihood" << "\t"
+       << "Genotype Map"        << "\t"
+       << "\n";
+
+    map<int, CSLocus *>::iterator it;
+    CSLocus *loc;
+    stringstream gtype_map;
+
+    for (it = catalog.begin(); it != catalog.end(); it++) {
+        loc = it->second;
+
+        string freq  = "";
+        double max   = 0.0;
+        int    total = 0;
+        gtype_map.str("");
+
+        if (loc->marker.length() > 0) {
+            tally_haplotype_freq(loc, pmap, total, max, freq);
+
+            //
+            // Record the haplotype to genotype map.
+            //
+            map<string, string>::iterator j;
+            for (j = loc->gmap.begin(); j != loc->gmap.end(); j++)
+                gtype_map << j->first << ":" << j->second << ";";
+        }
+
+        fh << 0 << "\t" 
+           << batch_id << "\t" 
+           << loc->id  << "\t" 
+           << "\t"              // Marker
+           << total    << "\t"
+           << max      << "\t"
+           << freq     << "\t"
+           << loc->f   << "\t"
+           << loc->lnl << "\t"
+           << gtype_map.str() << "\t"
+           << "\n";
+    }
+
+    fh.close();
+
+    return 0;
+}
+
+int 
+write_fasta(map<int, CSLocus *> &catalog, PopMap<CSLocus> *pmap)
+{
+    //
+    // Write a FASTA file containing each allele from each locus from 
+    // each sample in the population.
+    //
+    string file = out_path + out_prefix + ".fa";
+
+    cerr << "Writing population alleles to FASTA file '" << file << "'\n";
+
+    ofstream fh(file.c_str(), ofstream::out);
+
+    if (fh.fail()) {
+        cerr << "Error opening FASTA file '" << file << "'\n";
+        exit(1);
+    }
+
+    map<string, vector<CSLocus *> >::iterator it;
+    CSLocus *loc;
+    Datum  **d;
+    char    *seq;
+
+    for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
+        for (uint pos = 0; pos < it->second.size(); pos++) {
+            loc = it->second[pos];
+            d   = pmap->locus(loc->id);
+            seq = new char[loc->len + 1];
+            strcpy(seq, loc->con);
+
+            for (int j = 0; j < pmap->sample_cnt(); j++) {
+                if (d[j] == NULL) 
+                    continue;
+
+                for (uint k = 0; k < d[j]->obshap.size(); k++) {
+
+                    for (uint i = 0; i < loc->snps.size(); i++) {
+                        uint col = loc->snps[i]->col;
+                        seq[col] = col < loc->len ? d[j]->obshap[k][i] : loc->con[col];
+                    }
+
+                    fh << ">CLocus_" << loc->id 
+                       << "_Sample_" << pmap->rev_sample_index(j)
+                       << "_Locus_"  << d[j]->id 
+                       << "_Allele_" << k
+                       << " ["       << mpopi.samples()[j].name;
+
+                    if (strcmp(loc->loc.chr, "un") != 0)
+                        fh << "; " << loc->loc.chr << ", " << loc->sort_bp() + 1 << ", " << (loc->loc.strand == strand_plus ? "+" : "-");
+                    fh << "]\n"
+                       << seq << "\n";
+                }
+            }
+            delete [] seq;
+        }
+    }
+
+    fh.close();
+
+    return 0;
+}
+
+int 
+write_strict_fasta(map<int, CSLocus *> &catalog, PopMap<CSLocus> *pmap)
+{
+    //
+    // Write a FASTA file containing each allele from each locus from 
+    // each sample in the population.
+    //
+    string file = out_path + out_prefix + ".strict.fa";
+
+    cerr << "Writing strict population alleles to FASTA file '" << file << "'\n";
+
+    ofstream fh(file.c_str(), ofstream::out);
+
+    if (fh.fail()) {
+        cerr << "Error opening strict FASTA file '" << file << "'\n";
+        exit(1);
+    }
+
+    map<string, vector<CSLocus *> >::iterator it;
+    CSLocus *loc;
+    Datum  **d;
+    char    *seq;
+
+    for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
+        for (uint pos = 0; pos < it->second.size(); pos++) {
+            loc = it->second[pos];
+            d   = pmap->locus(loc->id);
+            seq = new char[loc->len + 1];
+            strcpy(seq, loc->con);
+
+            for (int j = 0; j < pmap->sample_cnt(); j++) {
+                if (d[j] == NULL) 
+                    continue;
+                if (d[j]->obshap.size() > 2) 
+                    continue;
+
+                if (d[j]->obshap.size() == 1) {
+
+                    for (uint i = 0; i < loc->snps.size(); i++) {
+                        uint col = loc->snps[i]->col;
+                        seq[col] = col < loc->len ? d[j]->obshap[0][i] : loc->con[col];
+                    }
+
+                    fh << ">CLocus_" << loc->id 
+                       << "_Sample_" << pmap->rev_sample_index(j)
+                       << "_Locus_"  << d[j]->id 
+                       << "_Allele_" << 0
+                       << " ["       << mpopi.samples()[j].name;
+                    if (strcmp(loc->loc.chr, "un") != 0)
+                        fh << "; " << loc->loc.chr << ", " << loc->sort_bp() + 1 << ", " << (loc->loc.strand == strand_plus ? "+" : "-");
+                    fh << "]\n"
+                       << seq << "\n";
+
+                    fh << ">CLocus_" << loc->id 
+                       << "_Sample_" << pmap->rev_sample_index(j)
+                       << "_Locus_"  << d[j]->id 
+                       << "_Allele_" << 1
+                       << " ["       << mpopi.samples()[j].name;
+                    if (strcmp(loc->loc.chr, "un") != 0)
+                        fh << "; " << loc->loc.chr << ", " << loc->sort_bp() + 1 << ", " << (loc->loc.strand == strand_plus ? "+" : "-");
+                    fh << "]\n"
+                       << seq << "\n";
+
+                } else {
+                    for (uint k = 0; k < d[j]->obshap.size(); k++) {
+                        for (uint i = 0; i < loc->snps.size(); i++) {
+                            uint col = loc->snps[i]->col;
+                            seq[col] = col < loc->len ? d[j]->obshap[k][i] : loc->con[col];
+                        }
+
+                        fh << ">CLocus_" << loc->id 
+                           << "_Sample_" <<  mpopi.samples()[j].id
+                           << "_Locus_"  << d[j]->id 
+                           << "_Allele_" << k
+                           << " ["       <<  mpopi.samples()[j].name;
+                        if (strcmp(loc->loc.chr, "un") != 0)
+                            fh << "; " << loc->loc.chr << ", " << loc->sort_bp() + 1 << ", " << (loc->loc.strand == strand_plus ? "+" : "-");
+                        fh << "]\n"
+                           << seq << "\n";
+                    }
+                }
+            }
+
+            delete [] seq;
+        }
+    }
+
+    fh.close();
+
+    return 0;
+}
+
+int 
+write_vcf_ordered(map<int, CSLocus *> &catalog, 
+                  PopMap<CSLocus> *pmap, PopSum<CSLocus> *psum, 
+                  map<int, pair<merget, int> > &merge_map, ofstream &log_fh) 
+{
+    //
+    // Write a VCF file as defined here: http://www.1000genomes.org/node/101
+    // Order SNPs by genomic position (and handle overlapping loci).
+    //
+
+    string file = out_path + out_prefix + ".vcf";
+    cerr << "Writing ordered population data to VCF file '" << file << "'\n";
+    log_fh << "\n#\n# Generating SNP-based VCF export.\n#\n";
+    VcfWriter writer (file);
+    if (writer.fail()) {
+        cerr << "Error opening VCF file '" << file << "'\n";
+        exit(-1);
+    }
+
+    bool gl = false; // Whether to include the GL genotype subfield.
+    if (input_mode == InputMode::stacks
+            && !debug_flags.count("VCFCOMP")) {
+        gl=true;
+        // Load SNP data so that model likelihoods can be output to VCF file.
+        cerr << "In preparation for VCF export, loading SNP data for " <<  mpopi.samples().size() << " samples.\n";
+        populate_snp_calls(catalog, pmap, merge_map);
+    }
+
+    //
+    // Obtain the current date.
+    //
+    time_t     rawtime;
+    struct tm *timeinfo;
+    char       date[32];
+    time(&rawtime);
+    timeinfo = localtime(&rawtime);
+    strftime(date, 32, "%Y%m%d", timeinfo);
+
+    VcfHeader header;
+    header.init_meta();
+    header.add_meta(VcfMeta::predefined.at("INFO/NS"));
+    header.add_meta(VcfMeta::predefined.at("INFO/AF"));
+    header.add_meta(VcfMeta::predefined.at("FORMAT/GT"));
+    header.add_meta(VcfMeta::predefined.at("FORMAT/DP"));
+    header.add_meta(VcfMeta::predefined.at("FORMAT/AD"));
+    header.add_meta(VcfMeta::predefined.at("FORMAT/GL"));
+    for(auto& s : mpopi.samples()) {
+        header.add_sample(s.name);
+    }
+    writer.write_header(header);
+
+    // We need to order the SNPs taking into account overlapping loci.
+    OLocTally<NucTally> *ord = new OLocTally<NucTally>(psum, log_fh);
+
+    for (auto it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
+        vector<NucTally *> sites;
+        ord->order(sites, it->second);
+
+        for (uint pos = 0; pos < sites.size(); pos++) {
+            if (catalog.count(sites[pos]->loc_id) == 0) {
+                cerr << "Unable to find locus id " << sites[pos]->loc_id << "\n";
+                continue;
+            }
+            CSLocus* loc = catalog[sites[pos]->loc_id];
+            uint16_t col = sites[pos]->col;
+            int snp_index = loc->snp_index(col);
+            if (snp_index < 0) {
+                cerr << "Warning: unable to locate SNP call in column " << col << " for catalog locus " << loc->id << "\n";
+                continue;
+            }
+            Datum** d = pmap->locus(loc->id);
+
+
+            const char ref = sites[pos]->p_allele;
+            const char alt = sites[pos]->q_allele;
+            char freq_alt[32];
+            sprintf(freq_alt, "%0.3f", 1 - sites[pos]->p_freq);
+
+            VcfRecord rec;
+            rec.type = Vcf::RType::expl;
+            rec.chrom = loc->loc.chr;
+            rec.pos = loc->sort_bp(col) + 1;
+            rec.id = to_string(loc->id) + "_" + to_string(col);
+            rec.alleles.push_back(string(1, loc->loc.strand == strand_plus ? ref : reverse(ref)));
+            rec.alleles.push_back(string(1, loc->loc.strand == strand_plus ? alt : reverse(alt)));
+            rec.qual = ".";
+            rec.filter.push_back("PASS");
+            rec.info.push_back({"NS",to_string(sites[pos]->num_indv)});
+            rec.info.push_back({"AF",freq_alt});
+            rec.format.push_back("GT");
+            rec.format.push_back("DP");
+            rec.format.push_back("AD");
+            if (gl)
+                rec.format.push_back("GL");
+
+            for (int j = 0; j < pmap->sample_cnt(); j++) {
+                stringstream sample;
+
+                if (d[j] == NULL || col >= d[j]->len) {
+                    // Data does not exist.
+                    sample << "./.:0:.,.";
+                    if (gl)
+                        sample << ":.,.,.";
+                } else if (d[j]->model[col] == 'U') {
+                    // Data exists, but the model call was uncertain.
+                    sample << "./.:" << d[j]->tot_depth << ":.,.";
+                    if (gl)
+                        sample << ":.,.,.";
+                } else {
+                    char allele1, allele2;
+                    tally_observed_haplotypes(d[j]->obshap, snp_index, allele1, allele2);
+
+                    if (allele1 == 0) {
+                        // More than two alleles in this sample
+                        sample << "./.:" << d[j]->tot_depth << ":.,.";
+                        if (gl)
+                            sample << ":.,.,.";
+                    } else {
+                        // Write the genotype.
+
+                        int dp1, dp2;
+                        find_datum_allele_depths(d[j], snp_index, allele1, allele2, dp1, dp2);
+
+                        if(gl && col >= d[j]->snps.size())
+                            cerr << "Warning, unable to locate SNP call in column " << col << " for catalog locus " << loc->id << ", tag ID " << d[j]->id << "\n";
+
+                        if (allele2 == 0) {
+                            // homozygote
+                            if (allele1 == ref) {
+                                sample << "0/0:" << d[j]->tot_depth << ":" << dp1 << "," << dp2;
+                                if (gl)
+                                    sample << ":" << - d[j]->snps[col]->lratio << ",.,.";
+                            } else {
+                                sample << "1/1:" << d[j]->tot_depth << ":" << dp2 << "," << dp1;
+                                if (gl)
+                                    sample << ":.,.," << - d[j]->snps[col]->lratio;
+                            }
+                        } else {
+                            // heterozygote
+                            sample << "0/1:" << d[j]->tot_depth
+                                   << ":" << (allele1 == ref ? dp1 : dp2) << "," << (allele1 == ref ? dp2 : dp1);
+                            if (gl)
+                                sample << ":.," << - d[j]->snps[col]->lratio << ",.";
+                        }
+                    }
+                }
+                rec.samples.push_back(sample.str());
+            }
+            writer.write_record(rec, header);
+        }
+    }
+
+    return 0;
+}
+
+int 
+write_vcf(map<int, CSLocus *> &catalog, 
+          PopMap<CSLocus> *pmap, PopSum<CSLocus> *psum, 
+          map<int, pair<merget, int> > &merge_map) 
+{
+    //
+    // Write a VCF file as defined here: http://www.1000genomes.org/node/101
+    //
+
+    string file = out_path + out_prefix + ".vcf";
+    cerr << "Writing population data to VCF file '" << file << "'\n";
+    VcfWriter writer (file);
+    if (writer.fail()) {
+        cerr << "Error opening VCF file '" << file << "'\n";
+        exit(-1);
+    }
+
+    bool gl = false; // Whether to include the GL genotype subfield.
+    if (input_mode == InputMode::stacks
+            && !debug_flags.count("VCFCOMP")) {
+        gl=true;
+        // Load SNP data so that model likelihoods can be output to VCF file.
+        cerr << "In preparation for VCF export, loading SNP data for " << mpopi.samples().size() << " samples.\n";
+        populate_snp_calls(catalog, pmap, merge_map);
+    }
+
+    //
+    // Output the header.
+    //
+
+    // Obtain the current date.
+    time_t     rawtime;
+    struct tm *timeinfo;
+    char       date[32];
+    time(&rawtime);
+    timeinfo = localtime(&rawtime);
+    strftime(date, 32, "%Y%m%d", timeinfo);
+
+    VcfHeader header;
+    header.init_meta();
+    header.add_meta(VcfMeta::predefined.at("INFO/NS"));
+    header.add_meta(VcfMeta::predefined.at("INFO/AF"));
+    header.add_meta(VcfMeta::predefined.at("FORMAT/GT"));
+    header.add_meta(VcfMeta::predefined.at("FORMAT/DP"));
+    header.add_meta(VcfMeta::predefined.at("FORMAT/AD"));
+    header.add_meta(VcfMeta::predefined.at("FORMAT/GL"));
+    for(auto& s : mpopi.samples()) {
+        header.add_sample(s.name);
+    }
+    writer.write_header(header);
+
+    map<string, vector<CSLocus *> >::iterator it;
+    CSLocus *loc;
+    Datum   **d;
+    LocTally *t;
+
+    for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
+
+        // We need to order the SNPs so negative and positive strand SNPs are properly ordered.
+        vector<GenPos> ordered_loci;
+        for (uint pos = 0; pos < it->second.size(); pos++) {
+            loc = it->second[pos];
+            t   = psum->locus_tally(loc->id);
+
+            for (uint i = 0; i < loc->snps.size(); i++) {
+                uint16_t col = loc->snps[i]->col;
+                if (t->nucs[col].allele_cnt == 2)
+                    ordered_loci.push_back(GenPos(loc->id, i, loc->sort_bp(col)));
+            }
+        }
+        sort(ordered_loci.begin(), ordered_loci.end());
+
+        for (uint pos = 0; pos < ordered_loci.size(); pos++) {
+            loc = catalog[ordered_loci[pos].id];
+            uint16_t col = loc->snps[ordered_loci[pos].snp_index]->col;
+            int snp_index = loc->snp_index(col);
+            if (snp_index < 0) {
+                cerr << "Warning: unable to locate SNP call in column " << col << " for locus #" << loc->id << "\n";
+                continue;
+            }
+            t   = psum->locus_tally(loc->id);
+            d = pmap->locus(loc->id);
+
+            const char ref = t->nucs[col].p_allele;
+            const char alt = t->nucs[col].q_allele;
+            char freq_alt[32];
+            sprintf(freq_alt, "%0.3f", 1 - t->nucs[col].p_freq);
+
+            VcfRecord rec;
+            rec.type = Vcf::RType::expl;
+            rec.chrom = loc->loc.chr;
+            rec.pos = loc->sort_bp(col) + 1;
+            rec.id = to_string(loc->id) + "_" + to_string(col);
+            rec.alleles.push_back(string(1, loc->loc.strand == strand_plus ? ref : reverse(ref)));
+            rec.alleles.push_back(string(1, loc->loc.strand == strand_plus ? alt : reverse(alt)));
+            rec.qual = ".";
+            rec.filter.push_back("PASS");
+            rec.info.push_back({"NS",to_string(t->nucs[col].num_indv)});
+            rec.info.push_back({"AF",freq_alt});
+            rec.format.push_back("GT");
+            rec.format.push_back("DP");
+            rec.format.push_back("AD");
+            if (gl)
+                rec.format.push_back("GL");
+
+            for (int j = 0; j < pmap->sample_cnt(); j++) {
+                stringstream sample;
+
+                if (d[j] == NULL || col >= uint(d[j]->len)) {
+                    // Data does not exist.
+                    sample << "./.:0:.,.";
+                    if (gl)
+                        sample << ":.,.,.";
+                } else if (d[j]->model[col] == 'U') {
+                    // Data exists, but the model call was uncertain.
+                    sample << "./.:" << d[j]->tot_depth << ":.,.";
+                    if (gl)
+                        sample << ":.,.,.";
+                } else {
+                    char allele1, allele2;
+                    tally_observed_haplotypes(d[j]->obshap, ordered_loci[pos].snp_index, allele1, allele2);
+
+                    if (allele1 == 0) {
+                        // More than two alleles in this sample
+                        sample << "./.:" << d[j]->tot_depth << ":.,.";
+                        if (gl)
+                            sample << ":.,.,.";
+                    } else {
+                        // Write the genotype.
+
+                        int dp1, dp2;
+                        find_datum_allele_depths(d[j], snp_index, allele1, allele2, dp1, dp2);
+
+                        if (allele2 == 0) {
+                            // homozygote
+                            if (allele1 == ref) {
+                                sample << "0/0:" << d[j]->tot_depth << ":" << dp1 << "," << dp2;
+                                if (gl)
+                                    sample << ":" << - d[j]->snps[col]->lratio << ",.,.";
+                            } else {
+                                sample << "1/1:" << d[j]->tot_depth << ":" << dp2 << "," << dp1;
+                                if (gl)
+                                    sample << ":.,.," << - d[j]->snps[col]->lratio;
+                            }
+                        } else {
+                            // heterozygote
+                            sample << "0/1:" << d[j]->tot_depth
+                                   << ":" << (allele1 == ref ? dp1 : dp2) << "," << (allele1 == ref ? dp2 : dp1);
+                            if (gl)
+                                sample << ":.," << - d[j]->snps[col]->lratio << ",.";
+                        }
+                    }
+                }
+                rec.samples.push_back(sample.str());
+            }
+            writer.write_record(rec, header);
+        }
+    }
+
+    return 0;
+}
+
+int 
+write_vcf_haplotypes(map<int, CSLocus *> &catalog, 
+                     PopMap<CSLocus> *pmap,
+                     PopSum<CSLocus> *psum)
+{
+    //
+    // Write a VCF file as defined here: http://samtools.github.io/hts-specs/
+    //XXX Datum::obshap *is not* ordered, I think. See Bitbucket. @Nick (June 2016)
+    //
+
+    string file = out_path + out_prefix + ".haplotypes.vcf";
+    cerr << "Writing population data haplotypes to VCF file '" << file << "'\n";
+    VcfWriter writer (file);
+    if (writer.fail()) {
+        cerr << "Error opening VCF file '" << file << "'\n";
+        exit(-1);
+    }
+
+    //
+    // Obtain the current date.
+    //
+    time_t     rawtime;
+    struct tm *timeinfo;
+    char       date[32];
+    time(&rawtime);
+    timeinfo = localtime(&rawtime);
+    strftime(date, 32, "%Y%m%d", timeinfo);
+
+    VcfHeader header;
+    header.init_meta();
+    header.add_meta(VcfMeta::predefined.at("INFO/NS"));
+    header.add_meta(VcfMeta::predefined.at("INFO/AF"));
+    header.add_meta(VcfMeta::predefined.at("FORMAT/GT"));
+    header.add_meta(VcfMeta::predefined.at("FORMAT/DP"));
+    for(auto& s : mpopi.samples()) {
+        header.add_sample(s.name);
+    }
+    writer.write_header(header);
+
+    CSLocus  *loc;
+    Datum   **d;
+    char      allele[id_len];
+
+    for (auto chr = pmap->ordered_loci.begin(); chr != pmap->ordered_loci.end(); chr++) {
+        for (uint pos = 0; pos < chr->second.size(); pos++) {
+            loc = chr->second[pos];
+            d   = pmap->locus(loc->id);
+
+            map<string, double> hap_freq;
+            const double n_alleles = count_haplotypes_at_locus(0, pmap->sample_cnt() - 1, d, hap_freq);
+            if (hap_freq.size() <= 1)
+                // Monomorphic locus.
+                // XXX What does [hap_freq.size()==1] mean ? @Nick (July 2016)
+                continue;
+            for(auto& h : hap_freq)
+                // Convert counts to freqs.
+                h.second /= n_alleles;
+
+            //
+            // Order the haplotypes according to most frequent. Record the ordered position or each 
+            // haplotype and convert them from counts to frequencies.
+            //
+
+            VcfRecord rec;
+            rec.type = Vcf::RType::expl;
+            rec.chrom = loc->loc.chr;
+            rec.pos = loc->sort_bp() + 1;
+            rec.id = to_string(loc->id);
+
+            //alleles
+            vector<pair<string, double> > ordered_hap (hap_freq.begin(), hap_freq.end());
+            sort(ordered_hap.begin(), ordered_hap.end(), compare_pair_haplotype);
+            map<string, int> hap_index;
+            for (size_t i = 0; i < ordered_hap.size(); i++) {
+                string h = ordered_hap[i].first;
+                rec.alleles.push_back(loc->loc.strand == strand_plus ? h : string(rev_comp(h.c_str())));
+                hap_index[h] = i;
+            }
+
+            rec.qual = ".";
+            rec.filter.push_back("PASS");
+
+            //info
+            stringstream ss;
+            ss << n_alleles/2;
+            rec.info.push_back({"NS",ss.str()});
+            rec.info.push_back({"AF",string()});
+            string& af=rec.info.back().second;
+            sprintf(allele, "%0.3f", ordered_hap[1].second); //NB. hap_freq.size() >= 2
+            af += allele;
+            for (auto h=ordered_hap.begin()+2; h!=ordered_hap.end(); ++h) {
+                sprintf(allele, "%0.3f", h->second);
+                af += string(",") + allele;
+            }
+
+            //format
+            rec.format.push_back("GT");
+            rec.format.push_back("DP");
+
+            for (int j = 0; j < pmap->sample_cnt(); j++) {
+                stringstream sample;
+
+                if (d[j] == NULL) {
+                    // Data does not exist.
+                    sample << "./.:0";
+                } else if (d[j]->obshap.size() > 2) {
+                    // More than two alleles in this sample
+                    sample << "./.:" << d[j]->tot_depth;
+                } else if (d[j]->obshap.size() == 1) {
+                    // Homozygote.
+                    char* h = d[j]->obshap[0];
+                    int i = uncalled_haplotype(h) ? -1 : hap_index.at(h);
+                    if(i >= 0)
+                        sample << i << "/" << i << ":" << d[j]->tot_depth;
+                    else
+                        sample << "./.:" << d[j]->tot_depth;
+                } else {
+                    // Heterozygote.
+                    char* h1 = d[j]->obshap[0];
+                    char* h2 = d[j]->obshap[1];
+                    int i1 = uncalled_haplotype(h1) ? -1 : hap_index.at(h1);
+                    int i2 = uncalled_haplotype(h2) ? -1 : hap_index.at(h2);
+                    if(i1 >= 0 && i2 >= 0)
+                        sample << (i1 < i2 ? i1 : i2) << "/" << (i1 < i2 ? i2 : i1) << ":" << d[j]->tot_depth;
+                    else if (i1 >= 0)
+                        sample << i1 << "/.:" << d[j]->tot_depth;
+                    else if (i2 >= 0)
+                        sample << i2 << "/.:" << d[j]->tot_depth;
+                }
+                rec.samples.push_back(sample.str());
+            }
+            writer.write_record(rec, header);
+        }
+    }
+    return 0;
+}
+
+int 
+write_genepop(map<int, CSLocus *> &catalog, 
+              PopMap<CSLocus> *pmap, 
+              PopSum<CSLocus> *psum)
+{
+    //
+    // Write a GenePop file as defined here: http://kimura.univ-montp2.fr/~rousset/Genepop.htm
+    //
+    string file = out_path + out_prefix + ".genepop";
+
+    cerr << "Writing population data to GenePop file '" << file << "'\n";
+
+    ofstream fh(file.c_str(), ofstream::out);
+
+    if (fh.fail()) {
+        cerr << "Error opening GenePop file '" << file << "'\n";
+        exit(1);
+    }
+
+    //
+    // Obtain the current date.
+    //
+    time_t     rawtime;
+    struct tm *timeinfo;
+    char       date[32];
+    time(&rawtime);
+    timeinfo = localtime(&rawtime);
+    strftime(date, 32, "%B %d, %Y", timeinfo);
+
+    //
+    // Output the header line.
+    //
+    fh << "Stacks version " << VERSION << "; Genepop version 4.1.3; " << date << "\n";
+
+    map<int, CSLocus *>::iterator it;
+    CSLocus  *loc;
+    Datum   **d;
+    LocSum  **s;
+    LocTally *t;
+    int      col;
+    char     p_allele, q_allele;
+
+    //
+    // Determine how many loci will be output, then output all the loci on the second line, comma-separated.
+    //
+    uint cnt = 0;
+    for (it = catalog.begin(); it != catalog.end(); it++) {
+        loc = it->second;
+        for (uint j = 0; j < loc->snps.size(); j++) {
+            col = loc->snps[j]->col;
+            t   = psum->locus_tally(loc->id);
+
+            if (t->nucs[col].allele_cnt != 2) 
+                continue;
+            cnt++;
+        }
+    }
+
+    uint i = 0;
+    for (it = catalog.begin(); it != catalog.end(); it++) {
+        loc = it->second;
+        for (uint j = 0; j < loc->snps.size(); j++) {
+            col = loc->snps[j]->col;
+            t   = psum->locus_tally(loc->id);
+
+            // 
+            // If this site is fixed in all populations or has too many alleles don't output it.
+            //
+            if (t->nucs[col].allele_cnt != 2) 
+                continue;
+            i++;
+            fh << loc->id << "_" << col;
+            if (i <  cnt) fh << ",";
+        }
+    }
+    fh << "\n";
+
+    map<char, string> nuc_map;
+    nuc_map['A'] = "01";
+    nuc_map['C'] = "02";
+    nuc_map['G'] = "03";
+    nuc_map['T'] = "04";
+
+    for (size_t p=0; p<mpopi.pops().size(); ++p) {
+        const MetaPopInfo::Pop& pop = mpopi.pops()[p];
+
+        fh << "pop\n";
+
+        for (size_t j = pop.first_sample; j <= pop.last_sample; j++) {
+
+            fh << mpopi.samples()[j].name << ",";
+
+            for (it = catalog.begin(); it != catalog.end(); it++) {
+                loc = it->second;
+                d   = pmap->locus(loc->id);
+                s   = psum->locus(loc->id);
+                t   = psum->locus_tally(loc->id);
+
+                for (i = 0; i < loc->snps.size(); i++) {
+                    uint col = loc->snps[i]->col;
+
+                    if (t->nucs[col].allele_cnt != 2) 
+                        continue;
+
+                    if (s[p]->nucs[col].incompatible_site ||
+                        s[p]->nucs[col].filtered_site) {
+                        //
+                        // This site contains more than two alleles in this population or was filtered
+                        // due to a minor allele frequency that is too low.
+                        //
+                        fh << "\t0000";
+                    } else if (d[j] == NULL || col >= uint(d[j]->len)) {
+                        //
+                        // Data does not exist.
+                        //
+                        fh << "\t0000";
+                    } else if (d[j]->model[col] == 'U') {
+                        //
+                        // Data exists, but the model call was uncertain.
+                        //
+                        fh << "\t0000";
+                    } else {
+                        //
+                        // Tally up the nucleotide calls.
+                        //
+                        tally_observed_haplotypes(d[j]->obshap, i, p_allele, q_allele);
+
+                        if (p_allele == 0 && q_allele == 0) {
+                            // More than two potential alleles.
+                            fh << "\t0000";
+                        } else if (p_allele == 0) {
+                            fh << "\t" << nuc_map[q_allele] << nuc_map[q_allele];
+
+                        } else if (q_allele == 0) {
+                            fh << "\t" << nuc_map[p_allele] << nuc_map[p_allele];
+
+                        } else {
+                            fh << "\t" << nuc_map[p_allele] << nuc_map[q_allele];
+                        }
+                    }
+                }
+            }
+            fh << "\n";
+        }
+    }
+
+    fh.close();
+
+    return 0;
+}
+
+int 
+write_genepop_ordered(map<int, CSLocus *> &catalog, 
+                      PopMap<CSLocus> *pmap, 
+                      PopSum<CSLocus> *psum, 
+                      ofstream &log_fh)
+{
+    //
+    // Write a GenePop file as defined here: http://kimura.univ-montp2.fr/~rousset/Genepop.htm
+    //
+    string file = out_path + out_prefix + ".genepop";
+
+    cerr << "Writing population data to GenePop file '" << file << "'\n";
+
+    ofstream fh(file.c_str(), ofstream::out);
+
+    if (fh.fail()) {
+        cerr << "Error opening GenePop file '" << file << "'\n";
+        exit(1);
+    }
+
+    //
+    // Obtain the current date.
+    //
+    time_t     rawtime;
+    struct tm *timeinfo;
+    char       date[32];
+    time(&rawtime);
+    timeinfo = localtime(&rawtime);
+    strftime(date, 32, "%B %d, %Y", timeinfo);
+
+    //
+    // Output the header line.
+    //
+    fh << "Stacks version " << VERSION << "; Genepop version 4.1.3; " << date << "\n";
+
+    map<string, vector<NucTally *> > genome_sites;
+    map<string, vector<CSLocus *> >::iterator it;
+    CSLocus  *loc;
+    Datum   **d;
+    LocSum  **s;
+    uint     col, snp_index;
+    char     p_allele, q_allele;
+
+    //
+    // We need to order the SNPs to take into account overlapping loci.
+    //
+    OLocTally<NucTally> *ord = new OLocTally<NucTally>(psum, log_fh);
+
+    //
+    // Output all the loci on the second line, comma-separated.
+    //
+    int chrs = pmap->ordered_loci.size();
+    int cnt  = 0;
+    for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
+        vector<NucTally *> &sites = genome_sites[it->first];
+        ord->order(sites, it->second);
+        cnt++;
+
+        for (uint pos = 0; pos < sites.size(); pos++) {
+            fh << sites[pos]->loc_id << "_" << sites[pos]->col;
+            if (cnt < chrs || pos < sites.size() - 1) fh << ",";
+        }
+    }
+    fh << "\n";
+
+    map<char, string> nuc_map;
+    nuc_map['A'] = "01";
+    nuc_map['C'] = "02";
+    nuc_map['G'] = "03";
+    nuc_map['T'] = "04";
+
+    for (size_t p=0; p<mpopi.pops().size(); ++p) {
+        const MetaPopInfo::Pop& pop = mpopi.pops()[p];
+
+        fh << "pop\n";
+        for (size_t j = pop.first_sample; j <= pop.last_sample; j++) {
+
+            fh << mpopi.samples()[j].name << ",";
+
+            for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
+                vector<NucTally *> &sites = genome_sites[it->first];
+
+                for (uint pos = 0; pos < sites.size(); pos++) {
+                    loc = catalog[sites[pos]->loc_id];
+                    s   = psum->locus(loc->id);
+                    d   = pmap->locus(loc->id);
+                    col = sites[pos]->col;
+
+                    if (s[p]->nucs[col].incompatible_site ||
+                        s[p]->nucs[col].filtered_site) {
+                        //
+                        // This site contains more than two alleles in this population or was filtered
+                        // due to a minor allele frequency that is too low.
+                        //
+                        fh << "\t0000";
+                    } else if (d[j] == NULL || col >= uint(d[j]->len)) {
+                        //
+                        // Data does not exist.
+                        //
+                        fh << "\t0000";
+                    } else if (d[j]->model[col] == 'U') {
+                        //
+                        // Data exists, but the model call was uncertain.
+                        //
+                        fh << "\t0000";
+                    } else {
+                        snp_index = loc->snp_index(col);
+                        //
+                        // Tally up the nucleotide calls.
+                        //
+                        tally_observed_haplotypes(d[j]->obshap, snp_index, p_allele, q_allele);
+
+                        if (p_allele == 0 && q_allele == 0) {
+                            // More than two potential alleles.
+                            fh << "\t0000";
+                        } else if (p_allele == 0) {
+                            fh << "\t" << nuc_map[q_allele] << nuc_map[q_allele];
+
+                        } else if (q_allele == 0) {
+                            fh << "\t" << nuc_map[p_allele] << nuc_map[p_allele];
+
+                        } else {
+                            fh << "\t" << nuc_map[p_allele] << nuc_map[q_allele];
+                        }
+                    }
+                }
+            }
+            fh << "\n";
+        }
+    }
+
+    fh.close();
+
+    return 0;
+}
+
+int 
+write_structure(map<int, CSLocus *> &catalog, 
+                PopMap<CSLocus> *pmap, 
+                PopSum<CSLocus> *psum)
+{
+    //
+    // Write a Structure file as defined here: http://pritch.bsd.uchicago.edu/structure.html
+    //
+    // To avoid linked SNPs (which Structure can't handle), we will only output the first
+    // SNP from each variable locus.
+    //
+    string file = out_path + out_prefix + ".structure.tsv";
+
+    cerr << "Writing population data to Structure file '" << file << "'...";
+
+    ofstream fh(file.c_str(), ofstream::out);
+
+    if (fh.fail()) {
+        cerr << "Error opening Structure file '" << file << "'\n";
+        exit(1);
+    }
+
+    //
+    // Obtain the current date.
+    //
+    time_t     rawtime;
+    struct tm *timeinfo;
+    char       date[32];
+    time(&rawtime);
+    timeinfo = localtime(&rawtime);
+    strftime(date, 32, "%B %d, %Y", timeinfo);
+
+    //
+    // Output the header.
+    //
+    fh << "# Stacks v" << VERSION << "; " << " Structure v2.3; " << date << "\n";
+
+    map<string, vector<CSLocus *> >::iterator it;
+    CSLocus  *loc;
+    Datum   **d;
+    LocSum  **s;
+    LocTally *t;
+
+    for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
+        for (uint pos = 0; pos < it->second.size(); pos++) {
+            loc = it->second[pos];
+            t   = psum->locus_tally(loc->id);
+
+            for (uint i = 0; i < loc->snps.size(); i++) {
+                uint col = loc->snps[i]->col;
+                if (t->nucs[col].allele_cnt == 2)
+                    fh << "\t" << loc->id << "_" << col;
+            }
+        }
+    }
+    fh << "\n";
+
+    map<char, string> nuc_map;
+    nuc_map['A'] = "1";
+    nuc_map['C'] = "2";
+    nuc_map['G'] = "3";
+    nuc_map['T'] = "4";
+
+    char      p_allele, q_allele;
+
+    for (size_t p=0; p<mpopi.pops().size(); ++p) {
+        const MetaPopInfo::Pop& pop = mpopi.pops()[p];
+
+        for (size_t j = pop.first_sample; j <= pop.last_sample; j++) {
+            //
+            // Output all the loci for this sample, printing only the p allele
+            //
+            fh << mpopi.samples()[j].name << "\t" << pop.name;
+
+            for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
+                for (uint pos = 0; pos < it->second.size(); pos++) {
+                    loc = it->second[pos];
+
+                    s = psum->locus(loc->id);
+                    d = pmap->locus(loc->id);
+                    t = psum->locus_tally(loc->id);
+
+                    for (uint i = 0; i < loc->snps.size(); i++) {
+                        uint col = loc->snps[i]->col;
+
+                        // 
+                        // If this site is fixed in all populations or has too many alleles don't output it.
+                        //
+                        if (t->nucs[col].allele_cnt != 2) 
+                            continue;
+
+                        if (s[p]->nucs[col].incompatible_site ||
+                            s[p]->nucs[col].filtered_site) {
+                            //
+                            // This site contains more than two alleles in this population or was filtered
+                            // due to a minor allele frequency that is too low.
+                            //
+                            fh << "\t" << "0";
+                        } else if (d[j] == NULL || col >= uint(d[j]->len)) {
+                            //
+                            // Data does not exist.
+                            //
+                            fh << "\t" << "0";
+                        } else if (d[j]->model[col] == 'U') {
+                            //
+                            // Data exists, but the model call was uncertain.
+                            //
+                            fh << "\t" << "0";
+                        } else {
+                            //
+                            // Tally up the nucleotide calls.
+                            //
+                            tally_observed_haplotypes(d[j]->obshap, i, p_allele, q_allele);
+
+                            if (p_allele == 0 && q_allele == 0)
+                                fh << "\t" << "0";
+                            else if (p_allele == 0)
+                                fh << "\t" << nuc_map[q_allele];
+                            else
+                                fh << "\t" << nuc_map[p_allele];
+                        }
+                    }
+                }
+            }
+            fh << "\n";
+
+            //
+            // Output all the loci for this sample again, now for the q allele
+            //
+            fh << mpopi.samples()[j].name << "\t" << pop.name;
+
+            for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
+                for (uint pos = 0; pos < it->second.size(); pos++) {
+                    loc = it->second[pos];
+
+                    s = psum->locus(loc->id);
+                    d = pmap->locus(loc->id);
+                    t = psum->locus_tally(loc->id);
+
+                    for (uint i = 0; i < loc->snps.size(); i++) {
+                        uint col = loc->snps[i]->col;
+
+                        if (t->nucs[col].allele_cnt != 2) 
+                            continue;
+
+                        if (s[p]->nucs[col].incompatible_site ||
+                            s[p]->nucs[col].filtered_site) {
+                            fh << "\t" << "0";
+                        } else if (d[j] == NULL || col >= uint(d[j]->len)) {
+                            fh << "\t" << "0";
+                        } else if (d[j]->model[col] == 'U') {
+                            fh << "\t" << "0";
+                        } else {
+                            tally_observed_haplotypes(d[j]->obshap, i, p_allele, q_allele);
+
+                            if (p_allele == 0 && q_allele == 0)
+                                fh << "\t" << "0";
+                            else if (q_allele == 0)
+                                fh << "\t" << nuc_map[p_allele];
+                            else
+                                fh << "\t" << nuc_map[q_allele];
+                        }
+                    }
+                }
+            }
+            fh << "\n";
+        }
+    }
+
+    fh.close();
+
+    cerr << "done.\n";
+
+    return 0;
+}
+
+int 
+write_structure_ordered(map<int, CSLocus *> &catalog, 
+                        PopMap<CSLocus> *pmap, 
+                        PopSum<CSLocus> *psum, 
+                        ofstream &log_fh)
+{
+    //
+    // Write a Structure file as defined here: http://pritch.bsd.uchicago.edu/structure.html
+    //
+    // To avoid linked SNPs (which Structure can't handle), we will only output the first
+    // SNP from each variable locus.
+    //
+    string file = out_path + out_prefix + ".structure.tsv";
+
+    cerr << "Writing population data to Structure file '" << file << "'...";
+
+    ofstream fh(file.c_str(), ofstream::out);
+
+    if (fh.fail()) {
+        cerr << "Error opening Structure file '" << file << "'\n";
+        exit(1);
+    }
+
+    //
+    // Obtain the current date.
+    //
+    time_t     rawtime;
+    struct tm *timeinfo;
+    char       date[32];
+    time(&rawtime);
+    timeinfo = localtime(&rawtime);
+    strftime(date, 32, "%B %d, %Y", timeinfo);
+
+    //
+    // Output the header.
+    //
+    fh << "# Stacks v" << VERSION << "; " << " Structure v2.3; " << date << "\n";
+
+    map<string, vector<NucTally *> > genome_sites;
+    map<string, vector<CSLocus *> >::iterator it;
+    CSLocus  *loc;
+    Datum   **d;
+    LocSum  **s;
+
+    //
+    // We need to order the SNPs to take into account overlapping loci.
+    //
+    OLocTally<NucTally> *ord = new OLocTally<NucTally>(psum, log_fh);
+
+    for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
+        vector<NucTally *> &sites = genome_sites[it->first];
+        ord->order(sites, it->second);
+
+        for (uint pos = 0; pos < sites.size(); pos++)
+            fh << "\t" << sites[pos]->loc_id << "_" << sites[pos]->col;
+    }
+    fh << "\n";
+
+    map<char, string> nuc_map;
+    nuc_map['A'] = "1";
+    nuc_map['C'] = "2";
+    nuc_map['G'] = "3";
+    nuc_map['T'] = "4";
+
+    char      p_allele, q_allele;
+    uint      col, snp_index;
+
+    for (size_t p=0; p<mpopi.pops().size(); ++p) {
+        const MetaPopInfo::Pop& pop = mpopi.pops()[p];
+
+        for (size_t j = pop.first_sample; j <= pop.last_sample; j++) {
+            //
+            // Output all the loci for this sample, printing only the p allele
+            //
+            fh << mpopi.samples()[j].name << "\t" << pop.name;
+
+            for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
+                vector<NucTally *> &sites = genome_sites[it->first];
+
+                for (uint pos = 0; pos < sites.size(); pos++) {
+                    loc = catalog[sites[pos]->loc_id];
+                    s   = psum->locus(loc->id);
+                    d   = pmap->locus(loc->id);
+                    col = sites[pos]->col;
+
+                    if (s[p]->nucs[col].incompatible_site ||
+                        s[p]->nucs[col].filtered_site) {
+                        //
+                        // This site contains more than two alleles in this population or was filtered
+                        // due to a minor allele frequency that is too low.
+                        //
+                        fh << "\t" << "0";
+                    } else if (d[j] == NULL || col >= uint(d[j]->len)) {
+                        //
+                        // Data does not exist.
+                        //
+                        fh << "\t" << "0";
+                    } else if (d[j]->model[col] == 'U') {
+                        //
+                        // Data exists, but the model call was uncertain.
+                        //
+                        fh << "\t" << "0";
+                    } else {
+                        snp_index = loc->snp_index(col);
+                        //
+                        // Tally up the nucleotide calls.
+                        //
+                        tally_observed_haplotypes(d[j]->obshap, snp_index, p_allele, q_allele);
+
+                        if (p_allele == 0 && q_allele == 0)
+                            fh << "\t" << "0";
+                        else if (p_allele == 0)
+                            fh << "\t" << nuc_map[q_allele];
+                        else
+                            fh << "\t" << nuc_map[p_allele];
+                    }
+                }
+            }
+            fh << "\n";
+
+            //
+            // Output all the loci for this sample again, now for the q allele
+            //
+            fh << mpopi.samples()[j].name << "\t" << pop.name;
+
+            for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
+                vector<NucTally *> &sites = genome_sites[it->first];
+
+                for (uint pos = 0; pos < sites.size(); pos++) {
+                    loc = catalog[sites[pos]->loc_id];
+                    s   = psum->locus(loc->id);
+                    d   = pmap->locus(loc->id);
+                    col = sites[pos]->col;
+
+                    if (s[p]->nucs[col].incompatible_site ||
+                        s[p]->nucs[col].filtered_site) {
+                        fh << "\t" << "0";
+                    } else if (d[j] == NULL || col >= uint(d[j]->len)) {
+                        fh << "\t" << "0";
+                    } else if (d[j]->model[col] == 'U') {
+                        fh << "\t" << "0";
+                    } else {
+                        snp_index = loc->snp_index(col);
+                        tally_observed_haplotypes(d[j]->obshap, snp_index, p_allele, q_allele);
+
+                        if (p_allele == 0 && q_allele == 0)
+                            fh << "\t" << "0";
+                        else if (q_allele == 0)
+                            fh << "\t" << nuc_map[p_allele];
+                        else
+                            fh << "\t" << nuc_map[q_allele];
+                    }
+                }
+            }
+            fh << "\n";
+        }
+    }
+
+    fh.close();
+
+    cerr << "done.\n";
+
+    return 0;
+}
+
+int 
+write_hzar(map<int, CSLocus *> &catalog, 
+           PopMap<CSLocus> *pmap, 
+           PopSum<CSLocus> *psum)
+{
+    //
+    // Write a Hybrid Zone Analysis using R (HZAR) file as defined here: 
+    //    http://cran.r-project.org/web/packages/hzar/hzar.pdf
+    //
+    string file = out_path + out_prefix + ".hzar.csv";
+
+    cerr << "Writing population data to HZAR file '" << file << "'...";
+
+    ofstream fh(file.c_str(), ofstream::out);
+
+    if (fh.fail()) {
+        cerr << "Error opening HZAR file '" << file << "'\n";
+        exit(1);
+    }
+
+    //
+    // Obtain the current date.
+    //
+    time_t     rawtime;
+    struct tm *timeinfo;
+    char       date[32];
+    time(&rawtime);
+    timeinfo = localtime(&rawtime);
+    strftime(date, 32, "%B %d, %Y", timeinfo);
+
+    //
+    // Output the header.
+    //
+    fh << "# Stacks v" << VERSION << "; " << " HZAR v0.2-5; " << date << "\n"
+       << "Population" << "," << "Distance";
+
+    map<string, vector<CSLocus *> >::iterator it;
+    CSLocus  *loc;
+    LocSum  **s;
+    LocTally *t;
+
+    for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
+        for (uint pos = 0; pos < it->second.size(); pos++) {
+            loc = it->second[pos];
+            s   = psum->locus(loc->id);
+            t   = psum->locus_tally(loc->id);
+
+            for (uint i = 0; i < loc->snps.size(); i++) {
+                uint col = loc->snps[i]->col;
+                if (t->nucs[col].allele_cnt == 2) {
+                    fh << "," << loc->id << "_" << col << ".A"
+                       << "," << loc->id << "_" << col << ".B"
+                       << "," << loc->id << "_" << col << ".N";
+                }
+            }
+        }
+    }
+    fh << "\n";
+
+    for (size_t p=0; p<mpopi.pops().size(); ++p) {
+        const MetaPopInfo::Pop& pop = mpopi.pops()[p];
+
+        fh << pop.name << ",";
+
+        for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
+            for (uint pos = 0; pos < it->second.size(); pos++) {
+                loc = it->second[pos];
+
+                s = psum->locus(loc->id);
+                t = psum->locus_tally(loc->id);
+
+                for (uint i = 0; i < loc->snps.size(); i++) {
+                    uint col = loc->snps[i]->col;
+
+                    // 
+                    // If this site is fixed in all populations or has too many alleles don't output it.
+                    //
+                    if (t->nucs[col].allele_cnt != 2) 
+                        continue;
+
+                    if (s[p]->nucs[col].num_indv == 0 ||
+                        s[p]->nucs[col].incompatible_site ||
+                        s[p]->nucs[col].filtered_site) {
+                        fh << ",0,0,0";
+                        continue;
+                    }
+                    
+                    if (t->nucs[col].p_allele == s[p]->nucs[col].p_nuc)
+                        fh << "," << s[p]->nucs[col].p << "," << 1 - s[p]->nucs[col].p << ",";
+                    else
+                        fh << "," << 1 - s[p]->nucs[col].p << "," << s[p]->nucs[col].p << ",";
+
+                    fh << s[p]->nucs[col].num_indv * 2;
+                }
+            }
+        }
+        fh << "\n";
+    }
+
+    fh.close();
+
+    cerr << "done.\n";
+
+    return 0;
+}
+
+int 
+write_treemix(map<int, CSLocus *> &catalog, 
+              PopMap<CSLocus> *pmap, 
+              PopSum<CSLocus> *psum)
+{
+    //
+    // Write a TreeMix file (Pickrell and Pritchard, 2012 PLoS Genetics)
+    //    https://bitbucket.org/nygcresearch/treemix/wiki/Home
+    //
+    string file = out_path + out_prefix + ".treemix";
+
+    cerr << "Writing population data to TreeMix file '" << file << "'; ";
+
+    ofstream fh(file.c_str(), ofstream::out);
+
+    if (fh.fail()) {
+        cerr << "Error opening TreeMix file '" << file << "'\n";
+        exit(1);
+    }
+
+    file += ".log";
+
+    cerr << "logging nucleotide positions to '" << file << "'...";
+
+    ofstream log_fh(file.c_str(), ofstream::out);
+
+    if (log_fh.fail()) {
+        cerr << "Error opening Phylip Log file '" << file << "'\n";
+        exit(1);
+    }
+
+    //
+    // Obtain the current date.
+    //
+    time_t     rawtime;
+    struct tm *timeinfo;
+    char       date[32];
+    time(&rawtime);
+    timeinfo = localtime(&rawtime);
+    strftime(date, 32, "%B %d, %Y", timeinfo);
+
+    log_fh << "# Stacks v" << VERSION << "; " << " TreeMix v1.1; " << date << "\n"
+           << "# Line\tLocus ID\tColumn\tChr\tBasepair\n";
+
+    //
+    // Output the header.
+    //
+    fh << "# Stacks v" << VERSION << "; " << " TreeMix v1.1; " << date << "\n";
+
+    map<string, vector<CSLocus *> >::iterator it;
+    CSLocus  *loc;
+    LocSum  **s;
+    LocTally *t;
+
+    //
+    // Output a space-separated list of the populations on the first line.
+    //
+    stringstream sstr;
+    for (auto& pop : mpopi.pops())
+        sstr << pop.name << " ";
+    
+    fh << sstr.str().substr(0, sstr.str().length() - 1) << "\n";
+
+    double p_freq, p_cnt, q_cnt, allele_cnt;
+    long int line = 1;
+    
+    for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
+        for (uint pos = 0; pos < it->second.size(); pos++) {
+            loc = it->second[pos];
+
+            s = psum->locus(loc->id);
+            t = psum->locus_tally(loc->id);
+                
+            for (uint i = 0; i < loc->snps.size(); i++) {
+                uint col = loc->snps[i]->col;
+
+                sstr.str("");
+
+                // 
+                // If this site is fixed in all populations or has too many alleles don't output it.
+                //
+                if (t->nucs[col].allele_cnt != 2) 
+                    continue;
+
+                for (size_t p=0; p<mpopi.pops().size(); ++p) {
+
+                    if (s[p]->nucs[col].num_indv == 0 ||
+                        s[p]->nucs[col].incompatible_site ||
+                        s[p]->nucs[col].filtered_site) {
+                        sstr << "0,0 ";
+                        continue;
+                    }
+                    
+                    p_freq = (t->nucs[col].p_allele == s[p]->nucs[col].p_nuc) ?
+                        s[p]->nucs[col].p :
+                        1 - s[p]->nucs[col].p;
+                    
+                    allele_cnt = s[p]->nucs[col].num_indv * 2;
+                    p_cnt      = round(allele_cnt * p_freq);
+                    q_cnt      = allele_cnt - p_cnt;
+                    sstr << (int) p_cnt << "," << (int) q_cnt << " ";
+                }
+
+                if (sstr.str().length() == 0)
+                    continue;
+
+                fh << sstr.str().substr(0, sstr.str().length() - 1) << "\n";
+                log_fh << line << "\t" << loc->id << "\t" << col << "\t" << loc->loc.chr << "\t" << loc->sort_bp(col) + 1 << "\n";
+                line++;
+            }
+        }
+    }
+
+    fh.close();
+    log_fh.close();
+    
+    cerr << "done.\n";
+
+    return 0;
+}
+
+int 
+write_fastphase(map<int, CSLocus *> &catalog, 
+                PopMap<CSLocus> *pmap, 
+                PopSum<CSLocus> *psum)
+{
+    //
+    // Write a fastPHASE file as defined here: http://stephenslab.uchicago.edu/software.html
+    //
+    // Data will be written as independent, bi-allelic SNPs. We will write one file per chromosome.
+    //
+    cerr << "Writing population data to fastPHASE files...";
+
+    map<string, vector<CSLocus *> >::iterator it;
+    CSLocus  *loc;
+    Datum   **d;
+    LocSum  **s;
+    LocTally *t;
+
+    for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
+
+        string file = out_path + out_prefix + "." + it->first + ".fastphase.inp";
+
+        ofstream fh(file.c_str(), ofstream::out);
+
+        if (fh.fail()) {
+            cerr << "Error opening fastPHASE file '" << file << "'\n";
+            exit(1);
+        }
+
+        //
+        // Tally up the number of sites
+        //
+        int  total_sites = 0;
+        uint col;
+        for (uint pos = 0; pos < it->second.size(); pos++) {
+            loc = it->second[pos];
+            t   = psum->locus_tally(loc->id);
+
+            for (uint i = 0; i < loc->snps.size(); i++) {
+                col = loc->snps[i]->col;
+                if (t->nucs[col].allele_cnt == 2)
+                    total_sites++;
+            }
+        }
+
+        //
+        // Output the total number of SNP sites and the number of individuals.
+        //
+        fh << mpopi.samples().size() << "\n"
+           << total_sites    << "\n";
+
+        //
+        // We need to determine an ordering that can take into account overlapping RAD sites.
+        //
+        vector<GenPos> ordered_loci;
+        for (uint pos = 0; pos < it->second.size(); pos++) {
+            loc = it->second[pos];
+            t   = psum->locus_tally(loc->id);
+
+            for (uint i = 0; i < loc->snps.size(); i++) {
+                col = loc->snps[i]->col;
+                if (t->nucs[col].allele_cnt == 2)
+                    ordered_loci.push_back(GenPos(loc->id, i, loc->sort_bp(col)));
+            }
+        }
+        sort(ordered_loci.begin(), ordered_loci.end());
+
+        //
+        // Output the position of each site according to its basepair.
+        //
+        fh << "P";
+        for (uint pos = 0; pos < ordered_loci.size(); pos++) {
+            loc = catalog[ordered_loci[pos].id];
+            col = loc->snps[ordered_loci[pos].snp_index]->col;
+            fh << " " << ordered_loci[pos].bp +1;
+        }
+        fh << "\n";
+
+        //
+        // Output a line of 'S' characters, one per site, indicating that these are SNP markers.
+        //
+        string snp_markers, gtypes_str;
+        snp_markers.assign(total_sites, 'S');
+        fh << snp_markers << '\n';          
+
+        //
+        // Now output each sample name followed by a new line, then all of the genotypes for that sample
+        // on two lines.
+        //
+
+        char         p_allele, q_allele;
+        stringstream gtypes;
+
+        for (size_t p=0; p<mpopi.pops().size(); ++p) {
+            const MetaPopInfo::Pop& pop = mpopi.pops()[p];
+
+            for (size_t j = pop.first_sample; j <= pop.last_sample; j++) {
+                //
+                // Output all the loci for this sample, printing only the p allele
+                //
+                fh << mpopi.samples()[j].name << "\n";
+
+                gtypes.str("");
+                for (uint pos = 0; pos < ordered_loci.size(); pos++) {
+                    loc = catalog[ordered_loci[pos].id];
+                    col = loc->snps[ordered_loci[pos].snp_index]->col;
+
+                    s = psum->locus(loc->id);
+                    d = pmap->locus(loc->id);
+                    t = psum->locus_tally(loc->id);
+
+                    // 
+                    // If this site is fixed in all populations or has too many alleles don't output it.
+                    //
+                    if (t->nucs[col].allele_cnt != 2) 
+                        continue;
+
+                    if (s[p]->nucs[col].incompatible_site ||
+                        s[p]->nucs[col].filtered_site) {
+                        //
+                        // This site contains more than two alleles in this population or was filtered
+                        // due to a minor allele frequency that is too low.
+                        //
+                        gtypes << "? ";
+
+                    } else if (d[j] == NULL || col >= uint(d[j]->len)) {
+                        //
+                        // Data does not exist.
+                        //
+                        gtypes << "? ";
+                    } else if (d[j]->model[col] == 'U') {
+                        //
+                        // Data exists, but the model call was uncertain.
+                        //
+                        gtypes << "? ";
+                    } else {
+                        //
+                        // Tally up the nucleotide calls.
+                        //
+                        tally_observed_haplotypes(d[j]->obshap, ordered_loci[pos].snp_index, p_allele, q_allele);
+
+                        if (p_allele == 0 && q_allele == 0)
+                            gtypes << "? ";
+                        else if (p_allele == 0)
+                            gtypes << q_allele << " ";
+                        else
+                            gtypes << p_allele << " ";
+                    }
+                }
+                gtypes_str = gtypes.str();
+                fh << gtypes_str.substr(0, gtypes_str.length() - 1) << "\n";
+
+                //
+                // Output all the loci for this sample again, now for the q allele
+                //
+                gtypes.str("");
+                for (uint pos = 0; pos < ordered_loci.size(); pos++) {
+                    loc = catalog[ordered_loci[pos].id];
+                    col = loc->snps[ordered_loci[pos].snp_index]->col;
+
+
+                    s = psum->locus(loc->id);
+                    d = pmap->locus(loc->id);
+                    t = psum->locus_tally(loc->id);
+
+                    if (t->nucs[col].allele_cnt != 2) 
+                        continue;
+
+                    if (s[p]->nucs[col].incompatible_site ||
+                        s[p]->nucs[col].filtered_site) {
+                        gtypes << "? ";
+
+                    } else if (d[j] == NULL || col >= uint(d[j]->len)) {
+                        gtypes << "? ";
+
+                    } else if (d[j]->model[col] == 'U') {
+                        gtypes << "? ";
+
+                    } else {
+                        tally_observed_haplotypes(d[j]->obshap, ordered_loci[pos].snp_index, p_allele, q_allele);
+
+                        if (p_allele == 0 && q_allele == 0)
+                            gtypes << "? ";
+                        else if (q_allele == 0)
+                            gtypes << p_allele << " ";
+                        else
+                            gtypes << q_allele << " ";
+                    }
+                }
+                gtypes_str = gtypes.str();
+                fh << gtypes_str.substr(0, gtypes_str.length() - 1) << "\n";
+            }
+        }
+
+        fh.close();
+    }
+
+    cerr << "done.\n";
+
+    return 0;
+}
+
+int 
+write_phase(map<int, CSLocus *> &catalog, 
+            PopMap<CSLocus> *pmap, 
+            PopSum<CSLocus> *psum)
+{
+    //
+    // Write a PHASE file as defined here: http://stephenslab.uchicago.edu/software.html
+    //
+    // Data will be written as mixture of multiple allele, linked RAD sites 
+    // (SNPs within a single RAD locus are already phased), and bi-allelic SNPs. We 
+    // will write one file per chromosome.
+    //
+    cerr << "Writing population data to PHASE files...";
+
+    map<string, vector<CSLocus *> >::iterator it;
+    CSLocus  *loc;
+    Datum   **d;
+    LocSum  **s;
+    LocTally *t;
+
+    for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
+
+        string file = out_path + out_prefix + "." + it->first + ".phase.inp";
+
+        ofstream fh(file.c_str(), ofstream::out);
+
+        if (fh.fail()) {
+            cerr << "Error opening PHASE file '" << file << "'\n";
+            exit(1);
+        }
+
+        //
+        // We need to determine an ordering for all legitimate loci/SNPs.
+        //
+        uint           col;
+        vector<GenPos> ordered_loci;
+        for (uint pos = 0; pos < it->second.size(); pos++) {
+            loc = it->second[pos];
+            t   = psum->locus_tally(loc->id);
+
+            if (loc->snps.size() == 0) continue;
+
+            //
+            // Will we output this locus as a haplotype or as a SNP?
+            //
+            if (loc->snps.size() > 1) {
+                //
+                // Check that there aren't too many haplotypes (PHASE has a max of 50).
+                //
+                if (loc->alleles.size() > 40) continue;
+
+                //
+                // Iterate over the population to determine that this subset of the population
+                // has data at this locus.
+                //
+                d = pmap->locus(loc->id);
+                for (int j = 0; j < pmap->sample_cnt(); j++) {
+                    if (d[j] != NULL &&
+                        d[j]->obshap.size() > 0 && 
+                        d[j]->obshap.size() <= 2) {
+                        //
+                        // Data exists, and there are the correct number of haplotypes.
+                        //
+                        ordered_loci.push_back(GenPos(loc->id, 0, loc->sort_bp(), haplotype));
+                        break;
+                    }
+                }
+            } else {
+                col = loc->snps[0]->col;
+
+                if (t->nucs[col].allele_cnt == 2)
+                    ordered_loci.push_back(GenPos(loc->id, 0, loc->sort_bp(col), snp));
+            }
+        }
+        sort(ordered_loci.begin(), ordered_loci.end());
+
+        //
+        // Output the total number of SNP sites and the number of individuals.
+        //
+        fh << mpopi.samples().size()      << "\n"
+           << ordered_loci.size() << "\n";
+
+        //
+        // Output the position of each site according to its basepair.
+        //
+        fh << "P";
+        for (uint pos = 0; pos < ordered_loci.size(); pos++)
+            fh << " " << ordered_loci[pos].bp +1;
+        fh << "\n";
+
+        //
+        // Output a line of 'S' characters for SNP markers, 'M' characters for multiallelic haplotypes.
+        //
+        for (uint pos = 0; pos < ordered_loci.size(); pos++) {
+            if (pos > 0) fh << " ";
+            fh << (ordered_loci[pos].type == snp ? "S" : "M");
+        }
+        fh << "\n";
+
+        //
+        // Now output each sample name followed by a new line, then all of the genotypes for that sample
+        // on two lines.
+        //
+
+        string       gtypes_str;
+        bool         found;
+        char         p_allele, q_allele;
+        stringstream gtypes;
+
+        for (size_t p=0; p<mpopi.pops().size(); ++p) {
+            const MetaPopInfo::Pop& pop = mpopi.pops()[p];
+
+            for (size_t j = pop.first_sample; j <= pop.last_sample; j++) {
+                //
+                // Output all the loci for this sample, printing only the p allele
+                //
+                fh << mpopi.samples()[j].name << "\n";
+                
+                gtypes.str("");
+                for (uint pos = 0; pos < ordered_loci.size(); pos++) {
+                    loc = catalog[ordered_loci[pos].id];
+
+                    s = psum->locus(loc->id);
+                    d = pmap->locus(loc->id);
+                    t = psum->locus_tally(loc->id);
+
+                    //
+                    // Will we output this locus as a haplotype or as a SNP?
+                    //
+                    if (ordered_loci[pos].type == haplotype) {
+                        if (d[j] == NULL) {
+                            //
+                            // Data does not exist.
+                            //
+                            gtypes << "-1 ";
+                        } else {
+                            //
+                            // Data exists, output the first haplotype. We will assume the haplotypes are 
+                            // numbered by their position in the loc->strings vector.
+                            //
+                            if (d[j]->obshap.size() > 2)  {
+                                // cerr << "Warning: too many haplotypes, catalog locus: " << loc->id << "\n";
+                                gtypes << "-1 ";
+                            } else {
+                                found = false;
+                                for (uint k = 0; k < loc->strings.size(); k++)
+                                    if (d[j]->obshap[0] == loc->strings[k].first) {
+                                        found = true;
+                                        gtypes << k + 1 << " ";
+                                    }
+                                if (found == false)
+                                    cerr << "Unable to find haplotype " << d[j]->obshap[0] << " from individual " 
+                                         << mpopi.samples()[j].name << "; catalog locus: " << loc->id << "\n";
+                            }
+                        }
+                    } else {
+                        col = loc->snps[ordered_loci[pos].snp_index]->col;
+
+                        if (s[p]->nucs[col].incompatible_site ||
+                            s[p]->nucs[col].filtered_site) {
+                            //
+                            // This site contains more than two alleles in this population or was filtered
+                            // due to a minor allele frequency that is too low.
+                            //
+                            gtypes << "? ";
+
+                        } else if (d[j] == NULL || col >= uint(d[j]->len)) {
+                            //
+                            // Data does not exist.
+                            //
+                            gtypes << "? ";
+                        } else if (d[j]->model[col] == 'U') {
+                            //
+                            // Data exists, but the model call was uncertain.
+                            //
+                            gtypes << "? ";
+                        } else {
+                            //
+                            // Tally up the nucleotide calls.
+                            //
+                            tally_observed_haplotypes(d[j]->obshap, ordered_loci[pos].snp_index, p_allele, q_allele);
+
+                            if (p_allele == 0 && q_allele == 0)
+                                gtypes << "? ";
+                            else if (p_allele == 0)
+                                gtypes << q_allele << " ";
+                            else
+                                gtypes << p_allele << " ";
+                        }
+                    }
+                }
+                gtypes_str = gtypes.str();
+                fh << gtypes_str.substr(0, gtypes_str.length() - 1) << "\n";
+
+                //
+                // Output all the loci for this sample again, now for the q allele
+                //
+                gtypes.str("");
+                for (uint pos = 0; pos < ordered_loci.size(); pos++) {
+                    loc = catalog[ordered_loci[pos].id];
+
+                    s = psum->locus(loc->id);
+                    d = pmap->locus(loc->id);
+                    t = psum->locus_tally(loc->id);
+
+                    //
+                    // Will we output this locus as a haplotype or as a SNP?
+                    //
+                    if (ordered_loci[pos].type == haplotype) {
+                        if (d[j] == NULL) {
+                            //
+                            // Data does not exist.
+                            //
+                            gtypes << "-1 ";
+                        } else {
+                            //
+                            // Data exists, output the second haplotype. We will assume the haplotypes are 
+                            // numbered by their position in the loc->strings vector.
+                            //
+                            if (d[j]->obshap.size() > 2)  {
+                                // cerr << "Warning: too many haplotypes, catalog locus: " << loc->id << "\n";
+                                gtypes << "-1 ";
+                            } else if (d[j]->obshap.size() > 1)  {
+                                found = false;
+                                for (uint k = 0; k < loc->strings.size(); k++)
+                                    if (d[j]->obshap[1] == loc->strings[k].first) {
+                                        found = true;
+                                        gtypes << k + 1 << " ";
+                                    }
+                                if (found == false)
+                                    cerr << "Unable to find haplotype " << d[j]->obshap[1] << " from individual " 
+                                         << mpopi.samples()[j].name << "; catalog locus: " << loc->id << "\n";
+                            } else {
+                                found = false;
+                                for (uint k = 0; k < loc->strings.size(); k++)
+                                    if (d[j]->obshap[0] == loc->strings[k].first) {
+                                        found = true;
+                                        gtypes << k + 1 << " ";
+                                    }
+                                if (found == false)
+                                    cerr << "Unable to find haplotype " << d[j]->obshap[0] << " from individual " 
+                                         << mpopi.samples()[j].name << "; catalog locus: " << loc->id << "\n";
+                            }
+                        }
+                    } else {
+                        col = loc->snps[ordered_loci[pos].snp_index]->col;
+
+                        if (s[p]->nucs[col].incompatible_site ||
+                            s[p]->nucs[col].filtered_site) {
+                            gtypes << "? ";
+
+                        } else if (d[j] == NULL || col >= uint(d[j]->len)) {
+                            gtypes << "? ";
+
+                        } else if (d[j]->model[col] == 'U') {
+                            gtypes << "? ";
+
+                        } else {
+                            tally_observed_haplotypes(d[j]->obshap, ordered_loci[pos].snp_index, p_allele, q_allele);
+
+                            if (p_allele == 0 && q_allele == 0)
+                                gtypes << "? ";
+                            else if (q_allele == 0)
+                                gtypes << p_allele << " ";
+                            else
+                                gtypes << q_allele << " ";
+                        }
+                    }
+                }
+                gtypes_str = gtypes.str();
+                fh << gtypes_str.substr(0, gtypes_str.length() - 1) << "\n";
+            }
+        }
+
+        fh.close();
+    }
+
+    cerr << "done.\n";
+
+    return 0;
+}
+
+int 
+write_plink(map<int, CSLocus *> &catalog, 
+            PopMap<CSLocus> *pmap, 
+            PopSum<CSLocus> *psum)
+{
+    //
+    // Write a PLINK file as defined here: http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml
+    //
+    // We will write one file per chromosome.
+    //
+    cerr << "Writing population data to PLINK files...";
+
+    //
+    // Obtain the current date.
+    //
+    time_t     rawtime;
+    struct tm *timeinfo;
+    char       date[32];
+    time(&rawtime);
+    timeinfo = localtime(&rawtime);
+    strftime(date, 32, "%B %d, %Y", timeinfo);
+
+    map<string, vector<CSLocus *> >::iterator it;
+    CSLocus  *loc;
+    Datum   **d;
+    LocSum  **s;
+    LocTally *t;
+    string    chr;
+
+    //
+    // First, write a markers file containing each marker, the chromosome it falls on,
+    // an empty centiMorgan field, and finally its genomic position in basepairs.
+    //
+    string file = out_path + out_prefix + ".plink.map";
+
+    ofstream fh(file.c_str(), ofstream::out);
+
+    if (fh.fail()) {
+        cerr << "Error opening PLINK markers file '" << file << "'\n";
+        exit(1);
+    }
+
+    //
+    // Output the header.
+    //
+    fh << "# Stacks v" << VERSION << "; " << " PLINK v1.07; " << date << "\n";
+
+    for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
+        chr = it->first;
+
+        for (uint pos = 0; pos < it->second.size(); pos++) {
+            loc = it->second[pos];
+            t   = psum->locus_tally(loc->id);
+
+            for (uint i = 0; i < loc->snps.size(); i++) {
+                uint col = loc->snps[i]->col;
+                if (t->nucs[col].allele_cnt == 2)
+                    fh << chr << "\t"
+                       << loc->id << "_" << col << "\t"
+                       << "0\t" 
+                       << loc->sort_bp(col) +1 << "\n";
+            }
+        }
+    }
+    fh.close();
+
+    //
+    // Now output the genotypes in a separate file.
+    //
+    file = out_path + out_prefix + ".plink.ped";
+
+    fh.open(file.c_str(), ofstream::out);
+
+    if (fh.fail()) {
+        cerr << "Error opening PLINK markers file '" << file << "'\n";
+        exit(1);
+    }
+
+    fh << "# Stacks v" << VERSION << "; " << " PLINK v1.07; " << date << "\n";
+
+    char p_allele, q_allele;
+
+    //
+    //  marker, output the genotypes for each sample in two successive columns.
+    //
+    for (size_t p=0; p<mpopi.pops().size(); ++p) {
+        const MetaPopInfo::Pop& pop = mpopi.pops()[p];
+
+        for (size_t j = pop.first_sample; j <= pop.last_sample; j++) {
+
+            fh << pop.name << "\t"
+               << mpopi.samples()[j].name << "\t"
+               << "0\t"  // Paternal ID
+               << "0\t"  // Maternal ID
+               << "0\t"  // Sex
+               << "0";   // Phenotype
+
+            for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
+                for (uint pos = 0; pos < it->second.size(); pos++) {
+                    loc = it->second[pos];
+
+                    s = psum->locus(loc->id);
+                    d = pmap->locus(loc->id);
+                    t = psum->locus_tally(loc->id);
+ 
+                    for (uint i = 0; i < loc->snps.size(); i++) {
+                        uint col = loc->snps[i]->col;
+
+                        // 
+                        // If this site is fixed in all populations or has too many alleles don't output it.
+                        //
+                        if (t->nucs[col].allele_cnt != 2) 
+                            continue;
+                        //
+                        // Output the p and q alleles
+                        //
+                        if (s[p]->nucs[col].incompatible_site ||
+                            s[p]->nucs[col].filtered_site) {
+                            //
+                            // This site contains more than two alleles in this population or was filtered
+                            // due to a minor allele frequency that is too low.
+                            //
+                            fh << "\t" << "0" << "\t" << "0";
+                        } else if (d[j] == NULL || col >= uint(d[j]->len)) {
+                            //
+                            // Data does not exist.
+                            //
+                            fh << "\t" << "0" << "\t" << "0";
+                        } else if (d[j]->model[col] == 'U') {
+                            //
+                            // Data exists, but the model call was uncertain.
+                            //
+                            fh << "\t" << "0" << "\t" << "0";
+                        } else {
+                            //
+                            // Tally up the nucleotide calls.
+                            //
+                            tally_observed_haplotypes(d[j]->obshap, i, p_allele, q_allele);
+
+                            if (p_allele == 0 && q_allele == 0)
+                                fh << "\t" << "0" << "\t" << "0";
+                            else if (p_allele == 0)
+                                fh << "\t" << q_allele << "\t" << q_allele;
+                            else if (q_allele == 0)
+                                fh << "\t" << p_allele << "\t" << p_allele;
+                            else
+                                fh << "\t" << p_allele << "\t" << q_allele;
+                        }
+                    }
+                }
+            }
+            fh << "\n";
+        }
+    }
+
+    fh.close();
+
+    cerr << "done.\n";
+
+    return 0;
+}
+
+int 
+write_beagle(map<int, CSLocus *> &catalog, 
+            PopMap<CSLocus> *pmap, 
+            PopSum<CSLocus> *psum)
+{
+    //
+    // Write a Beagle file as defined here: http://faculty.washington.edu/browning/beagle/beagle.html
+    //
+    // We will write one file per chromosome, per population.
+    //
+    cerr << "Writing population data to unphased Beagle files...";
+
+    //
+    // Obtain the current date.
+    //
+    time_t     rawtime;
+    struct tm *timeinfo;
+    char       date[32];
+    time(&rawtime);
+    timeinfo = localtime(&rawtime);
+    strftime(date, 32, "%B %d, %Y", timeinfo);
+
+    map<string, vector<CSLocus *> >::iterator it;
+    CSLocus  *loc;
+    Datum   **d;
+    LocSum  **s;
+    LocTally *t;
+    uint      col;
+
+    stringstream pop_name;
+    string       file;
+
+    for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
+
+        //
+        // We need to determine an ordering that can take into account overlapping RAD sites.
+        //
+        vector<GenPos> ordered_loci;
+        for (uint pos = 0; pos < it->second.size(); pos++) {
+            loc = it->second[pos];
+            t   = psum->locus_tally(loc->id);
+
+            for (uint i = 0; i < loc->snps.size(); i++) {
+                col = loc->snps[i]->col;
+                if (t->nucs[col].allele_cnt == 2)
+                    ordered_loci.push_back(GenPos(loc->id, i, loc->sort_bp(col)));
+            }
+        }
+        sort(ordered_loci.begin(), ordered_loci.end());
+
+        //
+        // Now output the genotypes in a separate file for each population.
+        //
+        for (size_t p=0; p<mpopi.pops().size(); ++p) {
+            const MetaPopInfo::Pop& pop = mpopi.pops()[p];
+
+            //
+            // Open a markers file containing each marker, its genomic position in basepairs
+            // and the two alternative alleles at this position.
+            //
+            file = out_path + out_prefix + "." + pop.name + "-" + it->first + ".unphased.bgl.markers";
+
+            ofstream mfh(file.c_str(), ofstream::out);
+            if (mfh.fail()) {
+                cerr << "Error opening Beagle markers file '" << file << "'\n";
+                exit(1);
+            }
+            mfh << "# Stacks v" << VERSION << "; " << " Beagle v3.3; " << date << "\n";
+
+            //
+            // Open the genotypes file.
+            //
+            file = out_path + out_prefix + "." + pop.name + "-" + it->first + ".unphased.bgl";
+
+            ofstream fh(file.c_str(), ofstream::out);
+            if (fh.fail()) {
+                cerr << "Error opening Beagle genotypes file '" << file << "'\n";
+                exit(1);
+            }
+            fh << "# Stacks v" << VERSION << "; " << " Beagle v3.3; " << date << "\n";
+
+            char p_allele, q_allele;
+            //
+            // Output a list of all the samples in this population.
+            //
+            fh << "I\tid";
+            for (size_t j = pop.first_sample; j <= pop.last_sample; j++)
+                fh << "\t" << mpopi.samples()[j].name << "\t" << mpopi.samples()[j].name;
+            fh << "\n";
+
+            //
+            // Output population IDs for each sample.
+            //
+            fh << "S\tid";
+            for (size_t j = pop.first_sample; j <= pop.last_sample; j++)
+                fh << "\t" << pop.name << "\t" << pop.name;
+            fh << "\n";
+
+            //
+            // For each marker, output the genotypes for each sample in two successive columns.
+            //
+            for (uint pos = 0; pos < ordered_loci.size(); pos++) {
+                loc = catalog[ordered_loci[pos].id];
+
+                s   = psum->locus(loc->id);
+                d   = pmap->locus(loc->id);
+                t   = psum->locus_tally(loc->id);
+                col = loc->snps[ordered_loci[pos].snp_index]->col;
+
+                // 
+                // If this site is fixed in all populations or has too many alleles don't output it.
+                //
+                if (t->nucs[col].allele_cnt != 2) 
+                    continue;
+
+                //
+                // If this site is monomorphic in this population don't output it.
+                //
+                if (s[p]->nucs[col].pi == 0.0)
+                    continue;
+
+                //
+                // Output this locus to the markers file.
+                //
+                mfh << loc->id << "_" << col << "\t" 
+                    << loc->sort_bp(col) +1  << "\t"
+                    << t->nucs[col].p_allele << "\t" 
+                    << t->nucs[col].q_allele << "\n";
+
+                fh << "M" << "\t" << loc->id << "_" << col;
+
+                for (size_t j = pop.first_sample; j <= pop.last_sample; j++) {
+                    //
+                    // Output the p allele
+                    //
+                    if (s[p]->nucs[col].incompatible_site ||
+                        s[p]->nucs[col].filtered_site) {
+                        //
+                        // This site contains more than two alleles in this population or was filtered
+                        // due to a minor allele frequency that is too low.
+                        //
+                        fh << "\t" << "?";
+
+                    } else if (d[j] == NULL || col >= uint(d[j]->len)) {
+                        //
+                        // Data does not exist.
+                        //
+                        fh << "\t" << "?";
+                    } else if (d[j]->model[col] == 'U') {
+                        //
+                        // Data exists, but the model call was uncertain.
+                        //
+                        fh << "\t" << "?";
+                    } else {
+                        //
+                        // Tally up the nucleotide calls.
+                        //
+                        tally_observed_haplotypes(d[j]->obshap, ordered_loci[pos].snp_index, p_allele, q_allele);
+
+                        if (p_allele == 0 && q_allele == 0)
+                            fh << "\t" << "?";
+                        else if (p_allele == 0)
+                            fh << "\t" << q_allele;
+                        else
+                            fh << "\t" << p_allele;
+                    }
+
+                    //
+                    // Now output the q allele
+                    //
+                    if (s[p]->nucs[col].incompatible_site ||
+                        s[p]->nucs[col].filtered_site) {
+                        fh << "\t" << "?";
+
+                    } else if (d[j] == NULL || col >= uint(d[j]->len)) {
+                        fh << "\t" << "?";
+
+                    } else if (d[j]->model[col] == 'U') {
+                        fh << "\t" << "?";
+
+                    } else {
+                        if (p_allele == 0 && q_allele == 0)
+                            fh << "\t" << "?";
+                        else if (q_allele == 0)
+                            fh << "\t" << p_allele;
+                        else
+                            fh << "\t" << q_allele;
+                    }
+                }
+                fh << "\n";
+            }
+
+            fh.close();
+            mfh.close();
+        }
+    }
+
+    cerr << "done.\n";
+
+    return 0;
+}
+
+int 
+write_beagle_phased(map<int, CSLocus *> &catalog, 
+                    PopMap<CSLocus> *pmap, 
+                    PopSum<CSLocus> *psum)
+{
+    //
+    // Write a Beagle file as a set of haplotpyes as defined here: 
+    //   http://faculty.washington.edu/browning/beagle/beagle.html
+    //
+    // We will write one file per chromosome.
+    //
+    cerr << "Writing population data to phased Beagle files...";
+
+    //
+    // Obtain the current date.
+    //
+    time_t     rawtime;
+    struct tm *timeinfo;
+    char       date[32];
+    time(&rawtime);
+    timeinfo = localtime(&rawtime);
+    strftime(date, 32, "%B %d, %Y", timeinfo);
+
+    map<string, vector<CSLocus *> >::iterator it;
+    CSLocus  *loc;
+    Datum   **d;
+
+    stringstream pop_name;
+    string       file;
+
+    for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
+
+        //
+        // We need to determine an ordering for all legitimate loci/SNPs.
+        //
+        vector<GenPos> ordered_loci;
+        for (uint pos = 0; pos < it->second.size(); pos++) {
+            loc = it->second[pos];
+
+            if (loc->snps.size() == 0) continue;
+
+            //
+            // Check that there aren't too many haplotypes (PHASE has a max of 50).
+            //
+            if (loc->alleles.size() > 40) continue;
+
+            //
+            // Iterate over the population to determine that this subset of the population
+            // has data at this locus.
+            //
+            d = pmap->locus(loc->id);
+            for (int j = 0; j < pmap->sample_cnt(); j++) {
+                if (d[j] != NULL &&
+                    d[j]->obshap.size() > 0 && 
+                    d[j]->obshap.size() <= 2) {
+                    //
+                    // Data exists, and their are the corrent number of haplotypes.
+                    //
+                    ordered_loci.push_back(GenPos(loc->id, 0, loc->sort_bp(), haplotype));
+                    break;
+                }
+            }
+        }
+        sort(ordered_loci.begin(), ordered_loci.end());
+
+        //
+        // Now output the genotypes in a separate file for each population.
+        //
+
+        for (size_t i_pop=0; i_pop<mpopi.pops().size(); ++i_pop) {
+            const MetaPopInfo::Pop& pop = mpopi.pops()[i_pop];
+
+            //
+            // Open a file for writing the markers: their genomic position in basepairs
+            // and the two alternative alleles at this position.
+            //
+            file = out_path + out_prefix + "." + pop.name + "-" + it->first + ".phased.bgl.markers";
+
+            ofstream mfh(file.c_str(), ofstream::out);
+            if (mfh.fail()) {
+                cerr << "Error opening Beagle markers file '" << file << "'\n";
+                exit(1);
+            }
+            mfh << "# Stacks v" << VERSION << "; " << " Beagle v3.3; " << date << "\n";
+
+            //
+            // Now output the haplotypes in a separate file.
+            //
+            file = out_path + out_prefix + "." + pop.name + "-" + it->first + ".phased.bgl";
+
+            ofstream fh(file.c_str(), ofstream::out);
+            if (fh.fail()) {
+                cerr << "Error opening Beagle markers file '" << file << "'\n";
+                exit(1);
+            }
+            fh << "# Stacks v" << VERSION << "; " << " Beagle v3.3; " << date << "\n";
+
+            //
+            // Output a list of all the samples in the data set.
+            //
+            fh << "I\tid";
+            for (size_t j = pop.first_sample; j <= pop.last_sample; j++)
+                fh << "\t" << mpopi.samples()[j].name << "\t" << mpopi.samples()[j].name;
+            fh << "\n";
+
+            //
+            // Output population IDs for each sample.
+            //
+            fh << "S\tid";
+            for (size_t j = pop.first_sample; j <= pop.last_sample; j++)
+                fh << "\t" << pop.name << "\t" << pop.name;
+            fh << "\n";
+
+            for (uint pos = 0; pos < ordered_loci.size(); pos++) {
+                loc = catalog[ordered_loci[pos].id];
+                d   = pmap->locus(loc->id);
+
+                //
+                // If this locus is monomorphic in this population don't output it.
+                //
+                set<string> haplotypes;
+                for (size_t j = pop.first_sample; j <= pop.last_sample; j++) {
+                    if (d[j] == NULL) continue;
+
+                    if (d[j]->obshap.size() == 2) {
+                        haplotypes.insert(d[j]->obshap[0]);
+                        haplotypes.insert(d[j]->obshap[1]);
+                    } else {
+                        haplotypes.insert(d[j]->obshap[0]);
+                    }
+                }
+                if (haplotypes.size() == 1) continue;
+
+                //
+                // Output this locus to the markers file.
+                //
+                mfh << loc->id << "\t" 
+                    << loc->sort_bp() +1;
+                for (uint j = 0; j < loc->strings.size(); j++)
+                    mfh << "\t" << loc->strings[j].first;
+                mfh << "\n";
+
+                //
+                // For each marker, output the genotypes for each sample in two successive columns.
+                //
+                fh << "M" << "\t" << loc->id;
+
+                for (size_t j = pop.first_sample; j <= pop.last_sample; j++) {
+                    //
+                    // Output the p and the q haplotype
+                    //
+                    if (d[j] == NULL) {
+                        //
+                        // Data does not exist.
+                        //
+                        fh << "\t" << "?" << "\t" << "?";
+                    } else {
+                        //
+                        // Data exists, output the first haplotype. We will assume the haplotypes are 
+                        // numbered by their position in the loc->strings vector.
+                        //
+                        if (d[j]->obshap.size() > 2)
+                            fh << "\t" << "?" << "\t" << "?";
+                        else if (d[j]->obshap.size() == 2)
+                            fh << "\t" << d[j]->obshap[0] << "\t" << d[j]->obshap[1];
+                        else
+                            fh << "\t" << d[j]->obshap[0] << "\t" << d[j]->obshap[0];
+                    }
+                }
+                fh << "\n";
+            }
+            fh.close();
+            mfh.close();
+        }
+    }   
+
+    cerr << "done.\n";
+
+    return 0;
+}
+
+int 
+write_phylip(map<int, CSLocus *> &catalog, 
+             PopMap<CSLocus> *pmap, 
+             PopSum<CSLocus> *psum)
+{
+    //
+    // We want to find loci where each locus is fixed within a population but variable between populations.
+    //
+    // We will write those loci to a Phylip file as defined here: 
+    //     http://evolution.genetics.washington.edu/phylip/doc/main.html#inputfiles
+    //
+    string file = out_path + out_prefix + ".phylip";
+
+    cerr << "Writing population data to Phylip file '" << file << "'; ";
+
+    ofstream fh(file.c_str(), ofstream::out);
+
+    if (fh.fail()) {
+        cerr << "Error opening Phylip file '" << file << "'\n";
+        exit(1);
+    }
+
+    file += ".log";
+
+    cerr << "logging nucleotide positions to '" << file << "'...";
+
+    ofstream log_fh(file.c_str(), ofstream::out);
+
+    if (log_fh.fail()) {
+        cerr << "Error opening Phylip Log file '" << file << "'\n";
+        exit(1);
+    }
+
+    //
+    // Obtain the current date.
+    //
+    time_t     rawtime;
+    struct tm *timeinfo;
+    char       date[32];
+    time(&rawtime);
+    timeinfo = localtime(&rawtime);
+    strftime(date, 32, "%B %d, %Y", timeinfo);
+
+    log_fh << "# Stacks v" << VERSION << "; " << " Phylip sequential; " << date << "\n"
+           << "# Seq Pos\tLocus ID\tColumn\tPopulation\n";
+
+    map<string, vector<CSLocus *> >::iterator it;
+    CSLocus  *loc;
+    LocSum  **s;
+    LocTally *t;
+
+    int  pop_cnt = psum->pop_cnt();
+    char nuc;
+
+    //
+    // A map storing, for each population, the concatenated list of interspecific nucleotides.
+    //
+    map<int, string> interspecific_nucs;
+
+    int index = 0;
+    for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
+        for (uint pos = 0; pos < it->second.size(); pos++) {
+            loc = it->second[pos];
+
+            s = psum->locus(loc->id);
+            t = psum->locus_tally(loc->id);
+
+            for (uint i = 0; i < loc->snps.size(); i++) {
+                uint col = loc->snps[i]->col;
+
+                if (phylip_var == false) {
+                    //
+                    // We are looking for loci that are fixed within each population, but are 
+                    // variable between one or more populations.
+                    //
+                    if (t->nucs[col].fixed == true || t->nucs[col].allele_cnt != 2 || t->nucs[col].pop_cnt < 2)
+                        continue;
+
+                    bool fixed_within = true;
+                    for (int j = 0; j < pop_cnt; j++) {
+                        if (s[j]->nucs[col].num_indv == 0)
+                            continue;
+                        if (s[j]->nucs[col].fixed == false) {
+                            fixed_within = false;
+                            break;
+                        }
+                    }
+                    if (fixed_within == false) continue;
+
+                    log_fh << index << "\t" << loc->id << "\t" << col << "\t";
+
+                    for (int p=0; p<pop_cnt; p++) {
+                        if (s[p]->nucs[col].num_indv > 0) {
+                            interspecific_nucs[p] += s[p]->nucs[col].p_nuc;
+                            log_fh << mpopi.pops()[p].name << ":" << s[p]->nucs[col].p_nuc << ",";
+                        } else {
+                            interspecific_nucs[p] += 'N';
+                            log_fh << mpopi.pops()[p].name << ":N" << ",";
+                        }
+                    }
+                    log_fh << "\n";
+                    index++;
+
+                } else {
+                    //
+                    // Encode SNPs that are variable within a population as well, using IUPAC notation:
+                    //     http://en.wikipedia.org/wiki/Nucleic_acid_notation#IUPAC_notation
+                    //
+                    if (t->nucs[col].allele_cnt != 2)
+                        continue;
+
+                    log_fh << index << "\t" << loc->id << "\t" << col << "\t";
+
+                    for (int j=0; j<pop_cnt; j++) {
+
+                        switch(s[j]->nucs[col].p_nuc) {
+                        case 0:
+                            nuc = 'N';
+                            break;
+                        case 'A':
+                            switch(s[j]->nucs[col].q_nuc) {
+                            case 'C':
+                                nuc = 'M';
+                                break;
+                            case 'G':
+                                nuc = 'R';
+                                break;
+                            case 'T':
+                                nuc = 'W';
+                                break;
+                            case 0:
+                                nuc = 'A';
+                                break;
+                            }
+                            break;
+                        case 'C':
+                            switch(s[j]->nucs[col].q_nuc) {
+                            case 'A':
+                                nuc = 'M';
+                                break;
+                            case 'G':
+                                nuc = 'S';
+                                break;
+                            case 'T':
+                                nuc = 'Y';
+                                break;
+                            case 0:
+                                nuc = 'C';
+                                break;
+                            }
+                            break;
+                        case 'G':
+                            switch(s[j]->nucs[col].q_nuc) {
+                            case 'A':
+                                nuc = 'R';
+                                break;
+                            case 'C':
+                                nuc = 'S';
+                                break;
+                            case 'T':
+                                nuc = 'K';
+                                break;
+                            case 0:
+                                nuc = 'G';
+                                break;
+                            }
+                            break;
+                        case 'T':
+                            switch(s[j]->nucs[col].q_nuc) {
+                            case 'A':
+                                nuc = 'W';
+                                break;
+                            case 'C':
+                                nuc = 'Y';
+                                break;
+                            case 'G':
+                                nuc = 'K';
+                                break;
+                            case 0:
+                                nuc = 'T';
+                                break;
+                            }
+                            break;
+                        }
+                        interspecific_nucs[j] += nuc;
+                        log_fh << mpopi.pops()[j].name << ":" << nuc << ",";
+
+                    }
+                    log_fh << "\n";
+                    index++;
+                }
+            }
+        }
+    }
+
+    if (interspecific_nucs.size() == 0) {
+        cerr << "  No data is available to write to the Phylip file.\n";
+        return 0;
+    }
+
+    fh << mpopi.pops().size() << "    " << interspecific_nucs.begin()->second.length() << "\n";
+    for (size_t i_pop=0; i_pop<mpopi.pops().size(); ++i_pop) {
+        const MetaPopInfo::Pop& pop = mpopi.pops()[i_pop];
+
+        char id_str[id_len];
+        sprintf(id_str, "%s", pop.name.c_str());
+        uint len = strlen(id_str);
+        for (uint j = len; j < 10; j++)
+            id_str[j] = ' ';
+        id_str[9] = '\0';
+
+        fh << id_str << " " << interspecific_nucs[i_pop] << "\n";
+    }
+
+    //
+    // Output the header.
+    //
+    fh << "# Stacks v" << VERSION << "; " << " Phylip sequential; " << date << "\n";
+
+    fh.close();
+    log_fh.close();
+
+    cerr << "done.\n";
+
+    return 0;
+}
+
+int 
+write_fullseq_phylip(map<int, CSLocus *> &catalog, 
+                     PopMap<CSLocus> *pmap, 
+                     PopSum<CSLocus> *psum)
+{
+    //
+    // We want to write all variable loci in Phylip interleaved format. Polymorphic positions
+    // will be encoded using IUPAC notation.
+    //
+    // We will write those loci to a Phylip file as defined here: 
+    //     http://evolution.genetics.washington.edu/phylip/doc/main.html#inputfiles
+    //
+    string file = out_path + out_prefix + ".fullseq.phylip";
+
+    cerr << "Writing full sequence population data to Phylip file '" << file << "'; ";
+
+    ofstream fh(file.c_str(), ofstream::out);
+
+    if (fh.fail()) {
+        cerr << "Error opening Phylip file '" << file << "'\n";
+        exit(1);
+    }
+
+    //
+    // We will also write a file that allows us to specify each RAD locus as a separate partition
+    // for use in phylogenetics programs.
+    //
+    file = out_path + out_prefix + ".fullseq.partitions.phylip";
+
+    ofstream par_fh(file.c_str(), ofstream::out);
+
+    if (par_fh.fail()) {
+        cerr << "Error opening Phylip partitions file '" << file << "'\n";
+        exit(1);
+    }
+
+    file = out_path + out_prefix + ".fullseq.phylip.log";
+    cerr << "logging nucleotide positions to '" << file << "'...";
+
+    ofstream log_fh(file.c_str(), ofstream::out);
+
+    if (log_fh.fail()) {
+        cerr << "Error opening Phylip Log file '" << file << "'\n";
+        exit(1);
+    }
+
+    //
+    // Obtain the current date.
+    //
+    time_t     rawtime;
+    struct tm *timeinfo;
+    char       date[32];
+    time(&rawtime);
+    timeinfo = localtime(&rawtime);
+    strftime(date, 32, "%B %d, %Y", timeinfo);
+
+    log_fh << "# Stacks v" << VERSION << "; " << " Phylip interleaved; " << date << "\n"
+           << "# Locus ID\tLine Number";
+    if (loci_ordered) log_fh << "\tChr\tBasepair";
+    log_fh << "\n";
+
+    map<string, vector<CSLocus *> >::iterator it;
+    CSLocus  *loc;
+    LocSum  **s;
+    LocTally *t;
+
+    int  pop_cnt = psum->pop_cnt();
+    char nuc = '\0';
+
+    bool include;
+    uint len = 0;
+
+    //
+    // Determine the length of sequence we will output.
+    //
+    for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
+        for (uint pos = 0; pos < it->second.size(); pos++) {
+            loc = it->second[pos];
+
+            t = psum->locus_tally(loc->id);
+
+            include = true;
+            for (uint i = 0; i < loc->snps.size(); i++) {
+                uint col = loc->snps[i]->col;
+
+                if (t->nucs[col].allele_cnt != 2)
+                    include = false;
+            }
+
+            if (include)
+                len += strlen(loc->con);
+        }
+    }
+
+    map<int, string> outstrs;
+    fh << mpopi.pops().size() << "    " << len << "\n";
+    for (size_t i_pop=0; i_pop<mpopi.pops().size(); ++i_pop) {
+        const MetaPopInfo::Pop& pop = mpopi.pops()[i_pop];
+
+        char id_str[id_len];
+        sprintf(id_str, "%s", pop.name.c_str());
+        len = strlen(id_str);
+        for (uint j = len; j < 10; j++)
+            id_str[j] = ' ';
+        id_str[9] = '\0'; 
+
+        outstrs[i_pop] = string(id_str) + " ";
+    }
+
+    char *seq;
+    int   line  = 1;
+    int   index = 1;
+    int   cnt   = 1;
+    
+    for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
+        for (uint pos = 0; pos < it->second.size(); pos++) {
+            loc = it->second[pos];
+
+            s = psum->locus(loc->id);
+            t = psum->locus_tally(loc->id);
+
+            include = true;
+            for (uint i = 0; i < loc->snps.size(); i++) {
+                uint col = loc->snps[i]->col;
+
+                if (t->nucs[col].allele_cnt != 2)
+                    include = false;
+            }
+
+            if (!include)
+                continue;
+
+            seq = new char[loc->len + 1];
+            strcpy(seq, loc->con);
+
+            for (int j = 0; j < pop_cnt; j++) {
+                for (uint i = 0; i < loc->snps.size(); i++) {
+                    uint col = loc->snps[i]->col;
+
+                    //
+                    // Encode SNPs that are variable within a population using IUPAC notation:
+                    //     http://en.wikipedia.org/wiki/Nucleic_acid_notation#IUPAC_notation
+                    //
+                    switch(s[j]->nucs[col].p_nuc) {
+                    case 0:
+                        nuc = 'N';
+                        break;
+                    case 'A':
+                        switch(s[j]->nucs[col].q_nuc) {
+                        case 'C':
+                            nuc = 'M';
+                            break;
+                        case 'G':
+                            nuc = 'R';
+                            break;
+                        case 'T':
+                            nuc = 'W';
+                            break;
+                        case 0:
+                            nuc = 'A';
+                            break;
+                        }
+                        break;
+                    case 'C':
+                        switch(s[j]->nucs[col].q_nuc) {
+                        case 'A':
+                            nuc = 'M';
+                            break;
+                        case 'G':
+                            nuc = 'S';
+                            break;
+                        case 'T':
+                            nuc = 'Y';
+                            break;
+                        case 0:
+                            nuc = 'C';
+                            break;
+                        }
+                        break;
+                    case 'G':
+                        switch(s[j]->nucs[col].q_nuc) {
+                        case 'A':
+                            nuc = 'R';
+                            break;
+                        case 'C':
+                            nuc = 'S';
+                            break;
+                        case 'T':
+                            nuc = 'K';
+                            break;
+                        case 0:
+                            nuc = 'G';
+                            break;
+                        }
+                        break;
+                    case 'T':
+                        switch(s[j]->nucs[col].q_nuc) {
+                        case 'A':
+                            nuc = 'W';
+                            break;
+                        case 'C':
+                            nuc = 'Y';
+                            break;
+                        case 'G':
+                            nuc = 'K';
+                            break;
+                        case 0:
+                            nuc = 'T';
+                            break;
+                        }
+                        break;
+                    }
+
+                    seq[col] = nuc;
+                }
+                
+                outstrs[j] += string(seq);
+            }
+            delete [] seq;
+
+            log_fh << line << "\t" << loc->id;
+            if (loci_ordered) log_fh << "\t" << loc->loc.chr << "\t" << loc->sort_bp() + 1;
+            log_fh << "\n";
+
+            for (size_t i_pop=0; i_pop<mpopi.pops().size(); ++i_pop) {
+                fh << outstrs[i_pop] << "\n";
+                outstrs[i_pop] = "";
+                line++;
+            }
+            fh << "\n";
+            line++;
+
+            par_fh << "DNA, p" << cnt << "=" << index << "-" << index + loc->len - 1 << "\n";
+            index += loc->len;
+            cnt++;
+        }
+    }
+
+    //
+    // Output the header.
+    //
+    fh << "# Stacks v" << VERSION << "; " << " Phylip interleaved; " << date << "\n";
+
+    fh.close();
+    par_fh.close();
+    log_fh.close();
+
+    cerr << "done.\n";
+
+    return 0;
+}
+
+int
+populate_snp_calls(map<int, CSLocus *> &catalog,
+                   PopMap<CSLocus> *pmap,
+                   map<int, pair<merget, int> > &merge_map)
+{
+    map<int, CSLocus *>::iterator cit;
+    map<int, SNPRes *>::iterator sit;
+    CSLocus *loc;
+    Datum   *datum;
+    SNPRes  *snpr;
+    SNP     *snp;
+
+    for (uint i = 0; i < mpopi.samples().size(); i++) {
+        map<int, SNPRes *> snpres;
+        load_snp_calls(in_path + mpopi.samples()[i].name, snpres);
+
+        for (cit = catalog.begin(); cit != catalog.end(); cit++) {
+            loc = cit->second;
+            datum = pmap->datum(loc->id, mpopi.samples()[i].id);
+
+            if (datum != NULL && snpres.count(datum->id)) {
+
+                if (merge_sites && merge_map.count(loc->id)) {
+                    datum_adjust_snp_positions(merge_map, loc, datum, snpres);
+                } else {
+                    //
+                    // Deep copy the SNP objects.
+                    //
+                    snpr = snpres[datum->id];
+                    for (uint j = 0; j < snpr->snps.size(); j++) {
+                        snp         = new SNP;
+                        snp->col    = snpr->snps[j]->col;
+                        snp->lratio = snpr->snps[j]->lratio;
+                        snp->rank_1 = snpr->snps[j]->rank_1;
+                        snp->rank_2 = snpr->snps[j]->rank_2;
+                        snp->rank_3 = snpr->snps[j]->rank_3;
+                        snp->rank_4 = snpr->snps[j]->rank_4;
+
+                        datum->snps.push_back(snp);
+                    }
+                }
+            }
+        }
+
+        for (sit = snpres.begin(); sit != snpres.end(); sit++)
+            delete sit->second;
+    }
+
+    return 0;
+}
+
+/*
+ * Calculate the SNP-wise allelic depths by adding up the haplotype depths.
+ */
+int
+find_datum_allele_depths(Datum *d, int snp_index, char allele1, char allele2, int &dp1, int &dp2)
+{
+    dp1 = 0;
+    dp2 = 0;
+
+    for(uint i = 0; i < d->obshap.size(); i++) {
+        char nt = d->obshap[i][snp_index];
+        if(nt == allele1)
+            dp1 += d->depth[i];
+        else if(nt == allele2)
+            dp2 += d->depth[i];
+        else
+            throw std::exception();
+    }
+
+    return 0;
+}
+
+int
+tally_observed_haplotypes(vector<char *> &obshap, int snp_index, char &p_allele, char &q_allele)
+{
+    int  nucs[4] = {0};
+    char nuc;
+
+    //
+    // Pull each allele for this SNP from the observed haplotype.
+    //
+    for (uint j = 0; j < obshap.size(); j++) {
+        nuc = obshap[j][snp_index];
+
+        switch(nuc) {
+        case 'A':
+        case 'a':
+            nucs[0]++;
+            break;
+        case 'C':
+        case 'c':
+            nucs[1]++;
+            break;
+        case 'G':
+        case 'g':
+            nucs[2]++;
+            break;
+        case 'T':
+        case 't':
+            nucs[3]++;
+            break;
+        }
+    }
+
+    //
+    // Determine how many alleles are present at this position in this population.
+    // We cannot deal with more than two alternative alleles, if there are more than two
+    // in a single population, print a warning and exclude this nucleotide position.
+    //
+    int i;
+    int allele_cnt = 0;
+    for (i = 0; i < 4; i++)
+        if (nucs[i] > 0) allele_cnt++;
+
+    if (allele_cnt > 2) {
+        p_allele = 0;
+        q_allele = 0;
+        return -1;
+    }
+
+    //
+    // Record which nucleotide is the P allele and which is the Q allele.
+    // (The P allele is the first one alphabetically, and the Q allele the second
+    // one, if any.)
+    //
+    p_allele = 0;
+    q_allele = 0;
+
+    i = 0;
+    while (p_allele == 0 && i < 4) {
+        if (nucs[i] > 0) {
+            switch(i) {
+            case 0:
+                p_allele = 'A';
+                break;
+            case 1:
+                p_allele = 'C';
+                break;
+            case 2:
+                p_allele = 'G';
+                break;
+            case 3:
+                p_allele = 'T';
+                break;
+            }
+        }
+        i++;
+    }
+    while (q_allele == 0 && i < 4) {
+        if (nucs[i] > 0) {
+            switch(i) {
+            case 1:
+                q_allele = 'C';
+                break;
+            case 2:
+                q_allele = 'G';
+                break;
+            case 3:
+                q_allele = 'T';
+                break;
+            }
+        }
+        i++;
+    }
+
+    return 0;
+}
+
+int tally_haplotype_freq(CSLocus *locus, PopMap<CSLocus> *pmap,
+                         int &total, double &max, string &freq_str) {
+
+    map<string, double> freq;
+    Datum **d = pmap->locus(locus->id);
+
+    total = 0;
+    max   = 0;
+
+    for (int i = 0; i < pmap->sample_cnt(); i++) {
+        if (d[i] == NULL)
+            continue;
+
+        if (d[i]->gtype[0] != '-') {
+            freq[d[i]->gtype]++;
+            total++;
+        }
+    }
+
+    if (total == 0)
+        return 0;
+
+    double frac;
+    stringstream s;
+    char   f[id_len];
+    map<string, double>::iterator it;
+    for (it = freq.begin(); it != freq.end(); it++) {
+        frac = (double) it->second / (double) total * 100;
+        if (frac > max) max = frac;
+        sprintf(f, "(%0.1f%%);", frac);
+        s << it->first << ":" << it->second << f;
+    }
+
+    freq_str = s.str();
+
+    return 0;
+}
+
+int
+datum_adjust_snp_positions(map<int, pair<merget, int> > &merge_map,
+                           CSLocus *loc, Datum *datum,
+                           map<int, SNPRes *> &snpres)
+{
+    //
+    // We will start with the 'sink' locus, which was originally on the negative strand:
+    //   1. If the locus was shorter than the catalog locus, pad the difference.
+    //   2. Convert to positive strand: Reverse the order, complement the alleles,
+    //      alter the internal column position.
+    //
+    SNP    *snp;
+    SNPRes *snpr     = snpres[datum->id];
+    int     index    = 0;
+    int     stop_pos = renz_olap[enz] - 1;
+
+    //
+    // We know the catalog was padded since we already padded hte model call string
+    // if it was necessary when originally merging.
+    //
+    while (datum->model[index] == 'N') {
+        snp         = new SNP;
+        snp->col    = index;
+        snp->lratio = 0.0;
+        snp->rank_1 = 'N';
+        snp->type   = snp_type_unk;
+        datum->snps.push_back(snp);
+        index++;
+    }
+
+    for (int j = snpr->snps.size() - 1; j > stop_pos; j--) {
+        snp         = new SNP;
+        snp->col    = index;
+        snp->lratio = snpr->snps[j]->lratio;
+        snp->rank_1 = reverse(snpr->snps[j]->rank_1);
+        snp->rank_2 = reverse(snpr->snps[j]->rank_2);
+        snp->rank_3 = reverse(snpr->snps[j]->rank_3);
+        snp->rank_4 = reverse(snpr->snps[j]->rank_4);
+        datum->snps.push_back(snp);
+        index++;
+    }
+
+    //
+    // Now we fetch the former locus, the 'src', which was originally on the positive strand.
+    // All we have to do is adjust the column position of each SNP.
+    //
+    snpr = snpres[datum->merge_partner];
+
+    for (uint j = 0; j < snpres[datum->id]->snps.size(); j++) {
+        snp         = new SNP;
+        snp->col    = index;
+        snp->lratio = snpr->snps[j]->lratio;
+        snp->rank_1 = snpr->snps[j]->rank_1;
+        snp->rank_2 = snpr->snps[j]->rank_2;
+        snp->rank_3 = snpr->snps[j]->rank_3;
+        snp->rank_4 = snpr->snps[j]->rank_4;
+        datum->snps.push_back(snp);
+        index++;
+    }
+
+    return 0;
+}
diff --git a/src/export_formats.h b/src/export_formats.h
new file mode 100644
index 0000000..c867c68
--- /dev/null
+++ b/src/export_formats.h
@@ -0,0 +1,70 @@
+#ifndef EXPORT_FORMATS_H
+#define EXPORT_FORMATS_H
+
+#include <iostream>
+#include <utility>
+#include <map>
+
+#include "locus.h"
+#include "PopMap.h"
+#include "PopSum.h"
+#include "ordered.h" // for "snp"
+#include "populations.h" // for "merget", "InputMode", "uncalled_haplotype()", "count_haplotypes_at_locus()"
+
+using std::ofstream;
+using std::pair;
+using std::map;
+
+class GenPos {
+public:
+    uint     id;
+    uint     bp;
+    uint     snp_index;
+    loc_type type;
+
+    GenPos(int id, int snp_index, int bp) {
+    this->id        = id;
+    this->snp_index = snp_index;
+    this->bp        = bp;
+    this->type      = snp;
+    }
+    GenPos(int id, int snp_index, int bp, loc_type type) {
+    this->id        = id;
+    this->snp_index = snp_index;
+    this->bp        = bp;
+    this->type      = type;
+    }
+
+    bool operator<(const GenPos& other) const {return bp < other.bp;}
+};
+
+int write_sql(map<int, CSLocus *> &, PopMap<CSLocus> *);
+int write_fst_stats(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *, ofstream &);
+int write_generic(map<int, CSLocus *> &, PopMap<CSLocus> *, bool);
+int write_genomic(map<int, CSLocus *> &, PopMap<CSLocus> *);
+int write_fasta(map<int, CSLocus *> &, PopMap<CSLocus> *);
+int write_strict_fasta(map<int, CSLocus *> &, PopMap<CSLocus> *);
+int write_vcf(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *, map<int, pair<merget, int> > &);
+int write_vcf_ordered(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *, map<int, pair<merget, int> > &, ofstream &);
+int write_vcf_haplotypes(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *);
+int write_genepop(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *);
+int write_genepop_ordered(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *, ofstream &);
+int write_structure(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *);
+int write_structure_ordered(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *, ofstream &);
+int write_phase(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *);
+int write_fastphase(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *);
+int write_beagle(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *);
+int write_beagle_phased(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *);
+int write_plink(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *);
+int write_hzar(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *);
+int write_treemix(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *);
+int write_phylip(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *);
+int write_fullseq_phylip(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *);
+
+int populate_snp_calls(map<int, CSLocus *> &, PopMap<CSLocus> *, map<int, pair<merget, int> > &);
+int find_datum_allele_depths(Datum *, int, char, char, int &, int &);
+int tally_observed_haplotypes(vector<char *> &, int, char &, char &);
+int tally_haplotype_freq(CSLocus *, PopMap<CSLocus> *, int &, double &, string &);
+int datum_adjust_snp_positions(map<int, pair<merget, int> > &, CSLocus *, Datum *, map<int, SNPRes *> &);
+
+#endif // EXPORT_FORMATS_H
diff --git a/src/file_io.cc b/src/file_io.cc
index d297a92..3631769 100644
--- a/src/file_io.cc
+++ b/src/file_io.cc
@@ -772,13 +772,14 @@ load_barcodes(string barcode_file, vector<BarcodePair> &barcodes,
 		switch (*q) {
 		case '-':
 		case '_':
+                case '.':
 		    break;
 		case '\r':
 		case '\t':
 		    *q = '\0';
 		    break;
 		default:
-		    cerr << "Invalid filename on line " << line_num << ": '" << s << "' (filenames can consist of letters, numbers, '-' and '_').\n";
+		    cerr << "Invalid filename on line " << line_num << ": '" << s << "' (filenames can consist of letters, numbers, '.', '-' and '_').\n";
 		    exit(1);
 		}
 	    }
diff --git a/src/genotype_dictionaries.h b/src/genotype_dictionaries.cc
similarity index 75%
copy from src/genotype_dictionaries.h
copy to src/genotype_dictionaries.cc
index d90ece3..6c6b4ca 100644
--- a/src/genotype_dictionaries.h
+++ b/src/genotype_dictionaries.cc
@@ -1,31 +1,17 @@
-// -*-mode:c++; c-style:k&r; c-basic-offset:4;-*-
-//
-// Copyright 2011-2014, Julian Catchen <jcatchen at uoregon.edu>
-//
-// This file is part of Stacks.
-//
-// Stacks is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// (at your option) any later version.
-//
-// Stacks is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-// GNU General Public License for more details.
-//
-// You should have received a copy of the GNU General Public License
-// along with Stacks.  If not, see <http://www.gnu.org/licenses/>.
-//
-
-#ifndef __GENOTYPE_DICTIONARIES_H__
-#define __GENOTYPE_DICTIONARIES_H__
-
-enum map_types {unk, none, gen, dh, cp, bc1, f2};
-enum out_types {rqtl, joinmap, onemap, genomic};
-
-void 
-initialize_dictionaries(map<string, map<string, string> > &global_dictionary) 
+#include "genotype_dictionaries.h"
+
+int
+encoded_gtypes[4][4] =
+{
+  // A  C  G   T
+    {1, 2, 3,  4}, // A
+    {2, 5, 6,  7}, // C
+    {3, 6, 8,  9}, // G
+    {4, 7, 9, 10}  // T
+};
+
+void
+initialize_dictionaries(map<string, map<string, string> > &global_dictionary)
 {
     global_dictionary["ab/--"]["a"]  = "aa";
     global_dictionary["ab/--"]["b"]  = "bb";
@@ -82,9 +68,9 @@ initialize_dictionaries(map<string, map<string, string> > &global_dictionary)
     global_dictionary["ab/ab"]["ab"] = "ab";
 }
 
-void 
-load_cp_dictionary(map<string, string> &types, 
-		   map<string, map<string, string> > &dictionary)
+void
+load_cp_dictionary(map<string, string> &types,
+           map<string, map<string, string> > &dictionary)
 {
     types["ab/--"] = "ab/--";
     types["--/ab"] = "--/ab";
@@ -144,9 +130,9 @@ load_cp_dictionary(map<string, string> &types,
     return;
 }
 
-void 
-load_joinmap_cp_dictionary(map<string, string> &types, 
-			   map<string, map<string, string> > &dictionary)
+void
+load_joinmap_cp_dictionary(map<string, string> &types,
+               map<string, map<string, string> > &dictionary)
 {
     types["ab/--"] = "lmx--";
     types["--/ab"] = "--xnp";
@@ -198,8 +184,8 @@ load_joinmap_cp_dictionary(map<string, string> &types,
     return;
 }
 
-void 
-load_onemap_cp_dictionary(map<string, string> &types, map<string, map<string, string> > &dictionary) 
+void
+load_onemap_cp_dictionary(map<string, string> &types, map<string, map<string, string> > &dictionary)
 {
     types["ab/--"] = "abxoo";
     types["--/ab"] = "ooxab";
@@ -252,9 +238,9 @@ load_onemap_cp_dictionary(map<string, string> &types, map<string, map<string, st
     return;
 }
 
-void 
-load_bc_dictionary(map<string, string> &types, 
-		   map<string, map<string, string> > &dictionary)
+void
+load_bc_dictionary(map<string, string> &types,
+           map<string, map<string, string> > &dictionary)
 {
     types["aa/bb"] = "aa/bb";
     types["bb/aa"] = "bb/aa";
@@ -286,9 +272,9 @@ load_bc_dictionary(map<string, string> &types,
     dictionary["cc/ab"]["bb"] = "bb";
 }
 
-void 
-load_f2_dictionary(map<string, string> &types, 
-		   map<string, map<string, string> > &dictionary)
+void
+load_f2_dictionary(map<string, string> &types,
+           map<string, map<string, string> > &dictionary)
 {
     types["aa/bb"] = "aa/bb";
     types["ab/cd"] = "ab/cd";
@@ -341,9 +327,9 @@ load_f2_dictionary(map<string, string> &types,
     dictionary["cc/ab"]["--"] = "--";
 }
 
-void 
-load_mm_bc_dictionary(map<string, string> &types, 
-		      map<string, map<string, string> > &dictionary)
+void
+load_mm_bc_dictionary(map<string, string> &types,
+              map<string, map<string, string> > &dictionary)
 {
     types["aa/bb"] = "aaxbb";
     types["bb/aa"] = "bbxaa";
@@ -375,9 +361,9 @@ load_mm_bc_dictionary(map<string, string> &types,
     dictionary["ccxab"]["bb"] = "a";
 }
 
-void 
-load_mm_f2_dictionary(map<string, string> &types, 
-		      map<string, map<string, string> > &dictionary)
+void
+load_mm_f2_dictionary(map<string, string> &types,
+              map<string, map<string, string> > &dictionary)
 {
     types["aa/bb"] = "aaxbb";
     types["ab/cd"] = "abxcd";
@@ -430,9 +416,9 @@ load_mm_f2_dictionary(map<string, string> &types,
     dictionary["ccxab"]["--"] = "-";
 }
 
-void 
-load_dh_dictionary(map<string, string> &types, 
-		   map<string, map<string, string> > &dictionary)
+void
+load_dh_dictionary(map<string, string> &types,
+           map<string, map<string, string> > &dictionary)
 {
     types["ab/--"] = "ab/--";
     types["--/ab"] = "--/ab";
@@ -446,9 +432,9 @@ load_dh_dictionary(map<string, string> &types,
     dictionary["--/ab"]["--"] = "--";
 }
 
-void 
-load_mm_dh_dictionary(map<string, string> &types, 
-		      map<string, map<string, string> > &dictionary)
+void
+load_mm_dh_dictionary(map<string, string> &types,
+              map<string, map<string, string> > &dictionary)
 {
     types["ab/--"] = "abx--";
     types["--/ab"] = "--xab";
@@ -462,111 +448,81 @@ load_mm_dh_dictionary(map<string, string> &types,
     dictionary["--xab"]["--"] = "-";
 }
 
-void 
-load_segregation_ratios(map_types type, map<string, map<string, double> > &segregation_ratios) 
+void
+load_segregation_ratios(map_types type, map<string, map<string, double> > &segregation_ratios)
 {
     switch(type) {
     case cp:
-	segregation_ratios["ab/--"]["aa"] = 0.50;
-	segregation_ratios["ab/--"]["ab"] = 0.50;
+    segregation_ratios["ab/--"]["aa"] = 0.50;
+    segregation_ratios["ab/--"]["ab"] = 0.50;
 
-	segregation_ratios["--/ab"]["aa"] = 0.50;
-	segregation_ratios["--/ab"]["ab"] = 0.50;
+    segregation_ratios["--/ab"]["aa"] = 0.50;
+    segregation_ratios["--/ab"]["ab"] = 0.50;
 
-	segregation_ratios["ab/aa"]["aa"] = 0.50;
-	segregation_ratios["ab/aa"]["ab"] = 0.50;
+    segregation_ratios["ab/aa"]["aa"] = 0.50;
+    segregation_ratios["ab/aa"]["ab"] = 0.50;
 
-	segregation_ratios["aa/ab"]["aa"] = 0.50;
-	segregation_ratios["aa/ab"]["ab"] = 0.50;
+    segregation_ratios["aa/ab"]["aa"] = 0.50;
+    segregation_ratios["aa/ab"]["ab"] = 0.50;
 
-	segregation_ratios["ab/ab"]["ab"] = 0.50;
-	segregation_ratios["ab/ab"]["aa"] = 0.25;
-	segregation_ratios["ab/ab"]["bb"] = 0.25;
+    segregation_ratios["ab/ab"]["ab"] = 0.50;
+    segregation_ratios["ab/ab"]["aa"] = 0.25;
+    segregation_ratios["ab/ab"]["bb"] = 0.25;
 
-	segregation_ratios["ab/ac"]["ab"] = 0.25;
-	segregation_ratios["ab/ac"]["ac"] = 0.25;
-	segregation_ratios["ab/ac"]["bc"] = 0.25;
-	segregation_ratios["ab/ac"]["aa"] = 0.25;
+    segregation_ratios["ab/ac"]["ab"] = 0.25;
+    segregation_ratios["ab/ac"]["ac"] = 0.25;
+    segregation_ratios["ab/ac"]["bc"] = 0.25;
+    segregation_ratios["ab/ac"]["aa"] = 0.25;
 
-	segregation_ratios["ab/cd"]["ac"] = 0.25;
-	segregation_ratios["ab/cd"]["ad"] = 0.25;
-	segregation_ratios["ab/cd"]["bc"] = 0.25;
-	segregation_ratios["ab/cd"]["bd"] = 0.25;
-	break;
+    segregation_ratios["ab/cd"]["ac"] = 0.25;
+    segregation_ratios["ab/cd"]["ad"] = 0.25;
+    segregation_ratios["ab/cd"]["bc"] = 0.25;
+    segregation_ratios["ab/cd"]["bd"] = 0.25;
+    break;
     case f2:
-	segregation_ratios["aaxbb"]["a"] = 0.25;
-	segregation_ratios["aaxbb"]["b"] = 0.25;
-	segregation_ratios["aaxbb"]["h"] = 0.50;
+    segregation_ratios["aaxbb"]["a"] = 0.25;
+    segregation_ratios["aaxbb"]["b"] = 0.25;
+    segregation_ratios["aaxbb"]["h"] = 0.50;
 
-	segregation_ratios["abxcd"]["a"] = 0.25;
-	segregation_ratios["abxcd"]["b"] = 0.25;
-	segregation_ratios["abxcd"]["h"] = 0.50;
+    segregation_ratios["abxcd"]["a"] = 0.25;
+    segregation_ratios["abxcd"]["b"] = 0.25;
+    segregation_ratios["abxcd"]["h"] = 0.50;
 
-	segregation_ratios["abxaa"]["a"] = 1.00;
+    segregation_ratios["abxaa"]["a"] = 1.00;
 
-	segregation_ratios["aaxab"]["b"] = 1.00;
+    segregation_ratios["aaxab"]["b"] = 1.00;
 
-	segregation_ratios["abxcc"]["a"] = 0.50;
-	segregation_ratios["abxcc"]["b"] = 0.50;
+    segregation_ratios["abxcc"]["a"] = 0.50;
+    segregation_ratios["abxcc"]["b"] = 0.50;
 
-	segregation_ratios["ccxab"]["b"] = 0.50;
-	segregation_ratios["ccxab"]["a"] = 0.50;
-	break;
+    segregation_ratios["ccxab"]["b"] = 0.50;
+    segregation_ratios["ccxab"]["a"] = 0.50;
+    break;
     case bc1:
-	segregation_ratios["aaxbb"]["h"] = 0.50;
-	segregation_ratios["aaxbb"]["b"] = 0.50;
+    segregation_ratios["aaxbb"]["h"] = 0.50;
+    segregation_ratios["aaxbb"]["b"] = 0.50;
 
-	segregation_ratios["bbxaa"]["h"] = 0.50;
-	segregation_ratios["bbxaa"]["a"] = 0.50;
+    segregation_ratios["bbxaa"]["h"] = 0.50;
+    segregation_ratios["bbxaa"]["a"] = 0.50;
 
-	segregation_ratios["abxcc"]["h"] = 0.50;
-	segregation_ratios["abxcc"]["b"] = 0.50;
+    segregation_ratios["abxcc"]["h"] = 0.50;
+    segregation_ratios["abxcc"]["b"] = 0.50;
 
-	segregation_ratios["ccxab"]["h"] = 0.50;
-	segregation_ratios["ccxab"]["a"] = 0.50;
-	break;
+    segregation_ratios["ccxab"]["h"] = 0.50;
+    segregation_ratios["ccxab"]["a"] = 0.50;
+    break;
     case dh:
-	segregation_ratios["ab/--"]["a"] = 0.50;
-	segregation_ratios["ab/--"]["b"] = 0.50;
+    segregation_ratios["ab/--"]["a"] = 0.50;
+    segregation_ratios["ab/--"]["b"] = 0.50;
 
-	segregation_ratios["--/ab"]["a"] = 0.50;
-	segregation_ratios["--/ab"]["b"] = 0.50;
-	break;
+    segregation_ratios["--/ab"]["a"] = 0.50;
+    segregation_ratios["--/ab"]["b"] = 0.50;
+    break;
     case gen:
     case none:
     case unk:
-	break;
+    break;
     }
 
     return;
 }
-
-inline
-int 
-encode_gtype(char a) 
-{ 
-    switch (a) {
-    case 'A':
-	return 0;
-    case 'C':
-	return 1;
-    case 'G':
-	return 2;
-    case 'T':
-	return 3;
-    }
-
-    return -1;
-}
-
-int 
-encoded_gtypes[4][4] = 
-{
-  // A  C  G   T
-    {1, 2, 3,  4}, // A
-    {2, 5, 6,  7}, // C
-    {3, 6, 8,  9}, // G
-    {4, 7, 9, 10}  // T
-};
-
-#endif // __GENOTYPE_DICTIONARIES_H__
diff --git a/src/genotype_dictionaries.h b/src/genotype_dictionaries.h
index d90ece3..a174bb8 100644
--- a/src/genotype_dictionaries.h
+++ b/src/genotype_dictionaries.h
@@ -21,552 +21,42 @@
 #ifndef __GENOTYPE_DICTIONARIES_H__
 #define __GENOTYPE_DICTIONARIES_H__
 
-enum map_types {unk, none, gen, dh, cp, bc1, f2};
-enum out_types {rqtl, joinmap, onemap, genomic};
-
-void 
-initialize_dictionaries(map<string, map<string, string> > &global_dictionary) 
-{
-    global_dictionary["ab/--"]["a"]  = "aa";
-    global_dictionary["ab/--"]["b"]  = "bb";
-
-    global_dictionary["--/ab"]["a"]  = "aa";
-    global_dictionary["--/ab"]["b"]  = "bb";
-
-    global_dictionary["aa/bb"]["a"]  = "aa";
-    global_dictionary["aa/bb"]["ab"] = "ab";
-    global_dictionary["aa/bb"]["b"]  = "bb";
-
-    global_dictionary["ab/ac"]["a"]  = "aa";
-    global_dictionary["ab/ac"]["ab"] = "ab";
-    global_dictionary["ab/ac"]["b"]  = "bb";
-    global_dictionary["ab/ac"]["ac"] = "ac";
-    global_dictionary["ab/ac"]["c"]  = "cc";
-    global_dictionary["ab/ac"]["bc"] = "bc";
-
-    global_dictionary["ab/cd"]["a"]  = "aa";
-    global_dictionary["ab/cd"]["ab"] = "ab";
-    global_dictionary["ab/cd"]["b"]  = "bb";
-    global_dictionary["ab/cd"]["c"]  = "cc";
-    global_dictionary["ab/cd"]["cd"] = "cd";
-    global_dictionary["ab/cd"]["d"]  = "dd";
-    global_dictionary["ab/cd"]["ac"] = "ac";
-    global_dictionary["ab/cd"]["ad"] = "ad";
-    global_dictionary["ab/cd"]["bc"] = "bc";
-    global_dictionary["ab/cd"]["bd"] = "bd";
-
-    global_dictionary["ab/aa"]["a"]  = "aa";
-    global_dictionary["ab/aa"]["ab"] = "ab";
-    global_dictionary["ab/aa"]["b"]  = "bb";
-
-    global_dictionary["aa/ab"]["a"]  = "aa";
-    global_dictionary["aa/ab"]["ab"] = "ab";
-    global_dictionary["aa/ab"]["b"]  = "bb";
-
-    global_dictionary["ab/cc"]["a"]  = "aa";
-    global_dictionary["ab/cc"]["ab"] = "ab";
-    global_dictionary["ab/cc"]["b"]  = "bb";
-    global_dictionary["ab/cc"]["c"]  = "cc";
-    global_dictionary["ab/cc"]["ac"] = "ac";
-    global_dictionary["ab/cc"]["bc"] = "bc";
-
-    global_dictionary["cc/ab"]["a"]  = "aa";
-    global_dictionary["cc/ab"]["ab"] = "ab";
-    global_dictionary["cc/ab"]["b"]  = "bb";
-    global_dictionary["cc/ab"]["c"]  = "cc";
-    global_dictionary["cc/ab"]["ac"] = "ac";
-    global_dictionary["cc/ab"]["bc"] = "bc";
-
-    global_dictionary["ab/ab"]["a"]  = "aa";
-    global_dictionary["ab/ab"]["b"]  = "bb";
-    global_dictionary["ab/ab"]["ab"] = "ab";
-}
-
-void 
-load_cp_dictionary(map<string, string> &types, 
-		   map<string, map<string, string> > &dictionary)
-{
-    types["ab/--"] = "ab/--";
-    types["--/ab"] = "--/ab";
-    types["ab/aa"] = "ab/aa";
-    types["aa/ab"] = "aa/ab";
-    types["ab/a-"] = "ab/--";
-    types["-a/ab"] = "--/ab";
-    types["ab/c-"] = "ab/cd";
-    types["-c/ab"] = "ab/cd";
-    types["ab/cc"] = "ab/--";
-    types["cc/ab"] = "--/ab";
-    types["ab/ab"] = "ab/ab";
-    types["ab/ac"] = "ab/ac";
-    types["ab/cd"] = "ab/cd";
-    types["-a/bb"] = "ab/--";
-    types["aa/b-"] = "--/ab";
-
-    dictionary["ab/--"]["--"] = "--";
-    dictionary["ab/--"]["aa"] = "aa";
-    dictionary["ab/--"]["ab"] = "ab";
-    dictionary["ab/--"]["bb"] = "ab";
-    dictionary["ab/--"]["ac"] = "aa";
-    dictionary["ab/--"]["bc"] = "ab";
-
-    dictionary["--/ab"]["--"] = "--";
-    dictionary["--/ab"]["aa"] = "aa";
-    dictionary["--/ab"]["ab"] = "ab";
-    dictionary["--/ab"]["bb"] = "ab";
-    dictionary["--/ab"]["ac"] = "aa";
-    dictionary["--/ab"]["bc"] = "ab";
-
-    dictionary["ab/aa"]["--"] = "--";
-    dictionary["ab/aa"]["aa"] = "aa";
-    dictionary["ab/aa"]["ab"] = "ab";
-
-    dictionary["aa/ab"]["--"] = "--";
-    dictionary["aa/ab"]["aa"] = "aa";
-    dictionary["aa/ab"]["ab"] = "ab";
-
-    dictionary["ab/ab"]["--"] = "--";
-    dictionary["ab/ab"]["ab"] = "ab";
-    dictionary["ab/ab"]["aa"] = "aa";
-    dictionary["ab/ab"]["bb"] = "bb";
-
-    dictionary["ab/ac"]["--"] = "--";
-    dictionary["ab/ac"]["ab"] = "ab";
-    dictionary["ab/ac"]["ac"] = "ac";
-    dictionary["ab/ac"]["bc"] = "bc";
-    dictionary["ab/ac"]["aa"] = "aa";
-
-    dictionary["ab/cd"]["--"] = "--";
-    dictionary["ab/cd"]["ac"] = "ac";
-    dictionary["ab/cd"]["ad"] = "ad";
-    dictionary["ab/cd"]["bc"] = "bc";
-    dictionary["ab/cd"]["bd"] = "bd";
-
-    return;
-}
-
-void 
-load_joinmap_cp_dictionary(map<string, string> &types, 
-			   map<string, map<string, string> > &dictionary)
-{
-    types["ab/--"] = "lmx--";
-    types["--/ab"] = "--xnp";
-    types["ab/aa"] = "lmxll";
-    types["aa/ab"] = "nnxnp";
-    types["ab/ab"] = "hkxhk";
-    types["ab/ac"] = "efxeg";
-    types["ab/cd"] = "abxcd";
-
-    dictionary["lmx--"]["--"] = "--";
-    dictionary["lmx--"]["aa"] = "ll";
-    dictionary["lmx--"]["ab"] = "lm";
-    dictionary["lmx--"]["bb"] = "lm";
-    dictionary["lmx--"]["ac"] = "ll";
-    dictionary["lmx--"]["bc"] = "lm";
-
-    dictionary["--xnp"]["--"] = "--";
-    dictionary["--xnp"]["aa"] = "nn";
-    dictionary["--xnp"]["ab"] = "np";
-    dictionary["--xnp"]["bb"] = "np";
-    dictionary["--xnp"]["ac"] = "nn";
-    dictionary["--xnp"]["bc"] = "np";
-
-    dictionary["lmxll"]["--"] = "--";
-    dictionary["lmxll"]["aa"] = "ll";
-    dictionary["lmxll"]["ab"] = "lm";
-
-    dictionary["nnxnp"]["--"] = "--";
-    dictionary["nnxnp"]["aa"] = "nn";
-    dictionary["nnxnp"]["ab"] = "np";
-
-    dictionary["hkxhk"]["--"] = "--";
-    dictionary["hkxhk"]["ab"] = "hk";
-    dictionary["hkxhk"]["aa"] = "hh";
-    dictionary["hkxhk"]["bb"] = "kk";
-
-    dictionary["efxeg"]["--"] = "--";
-    dictionary["efxeg"]["ab"] = "ef";
-    dictionary["efxeg"]["ac"] = "eg";
-    dictionary["efxeg"]["bc"] = "fg";
-    dictionary["efxeg"]["aa"] = "ee";
-
-    dictionary["abxcd"]["--"] = "--";
-    dictionary["abxcd"]["ac"] = "ac";
-    dictionary["abxcd"]["ad"] = "ad";
-    dictionary["abxcd"]["bc"] = "bc";
-    dictionary["abxcd"]["bd"] = "bd";
-
-    return;
-}
-
-void 
-load_onemap_cp_dictionary(map<string, string> &types, map<string, map<string, string> > &dictionary) 
-{
-    types["ab/--"] = "abxoo";
-    types["--/ab"] = "ooxab";
-    types["ab/aa"] = "abxaa";
-    types["aa/ab"] = "aaxab";
-    types["ab/ab"] = "abxab";
-    types["ab/ac"] = "abxac";
-    types["ab/cd"] = "abxcd";
-
-    // D1.11
-    dictionary["abxoo"]["--"] = "-";
-    dictionary["abxoo"]["aa"] = "a";
-    dictionary["abxoo"]["bb"] = "b";
-
-    // D2.16
-    dictionary["ooxab"]["--"] = "-";
-    dictionary["ooxab"]["aa"] = "a";
-    dictionary["ooxab"]["bb"] = "b";
-
-    // D1.10
-    dictionary["abxaa"]["--"] = "-";
-    dictionary["abxaa"]["aa"] = "a";
-    dictionary["abxaa"]["ab"] = "ab";
-
-    // D2.15
-    dictionary["aaxab"]["--"] = "-";
-    dictionary["aaxab"]["aa"] = "a";
-    dictionary["aaxab"]["ab"] = "ab";
-
-    // B3.7
-    dictionary["abxab"]["--"] = "-";
-    dictionary["abxab"]["ab"] = "ab";
-    dictionary["abxab"]["aa"] = "a";
-    dictionary["abxab"]["bb"] = "b";
-
-    // A.2
-    dictionary["abxac"]["--"] = "-";
-    dictionary["abxac"]["ab"] = "ba";
-    dictionary["abxac"]["ac"] = "ac";
-    dictionary["abxac"]["bc"] = "bc";
-    dictionary["abxac"]["aa"] = "a";
-
-    // A.1
-    dictionary["abxcd"]["--"] = "-";
-    dictionary["abxcd"]["ac"] = "ac";
-    dictionary["abxcd"]["ad"] = "ad";
-    dictionary["abxcd"]["bc"] = "bc";
-    dictionary["abxcd"]["bd"] = "bd";
-
-    return;
-}
-
-void 
-load_bc_dictionary(map<string, string> &types, 
-		   map<string, map<string, string> > &dictionary)
-{
-    types["aa/bb"] = "aa/bb";
-    types["bb/aa"] = "bb/aa";
-    types["ab/cc"] = "ab/cc";
-    types["cc/ab"] = "cc/ab";
-
-    dictionary["aa/bb"]["--"] = "--";
-    dictionary["aa/bb"]["aa"] = "aa";
-    dictionary["aa/bb"]["ab"] = "ab";
-    dictionary["aa/bb"]["bb"] = "bb";
-
-    dictionary["bb/aa"]["--"] = "--";
-    dictionary["bb/aa"]["aa"] = "aa";
-    dictionary["bb/aa"]["ab"] = "ab";
-    dictionary["bb/aa"]["bb"] = "bb";
-
-    dictionary["ab/cc"]["--"] = "--";
-    dictionary["ab/cc"]["ac"] = "ac";
-    dictionary["ab/cc"]["bc"] = "bc";
-    dictionary["ab/cc"]["ab"] = "ab";
-    dictionary["ab/cc"]["aa"] = "aa";
-    dictionary["ab/cc"]["bb"] = "bb";
-
-    dictionary["cc/ab"]["--"] = "--";
-    dictionary["cc/ab"]["ac"] = "ac";
-    dictionary["cc/ab"]["bc"] = "bc";
-    dictionary["cc/ab"]["ab"] = "ab";
-    dictionary["cc/ab"]["aa"] = "aa";
-    dictionary["cc/ab"]["bb"] = "bb";
-}
-
-void 
-load_f2_dictionary(map<string, string> &types, 
-		   map<string, map<string, string> > &dictionary)
-{
-    types["aa/bb"] = "aa/bb";
-    types["ab/cd"] = "ab/cd";
-    types["ab/aa"] = "ab/aa";
-    types["aa/ab"] = "aa/ab";
-    types["ab/cc"] = "ab/cc";
-    types["cc/ab"] = "cc/ab";
+#include <string>
+#include <map>
 
-    dictionary["aa/bb"]["aa"] = "aa";
-    dictionary["aa/bb"]["ab"] = "ab";
-    dictionary["aa/bb"]["bb"] = "bb";
-    dictionary["aa/bb"]["--"] = "--";
+using std::string;
+using std::map;
 
-    dictionary["ab/cd"]["aa"] = "aa";
-    dictionary["ab/cd"]["ab"] = "ab";
-    dictionary["ab/cd"]["bb"] = "bb";
-    dictionary["ab/cd"]["cc"] = "cc";
-    dictionary["ab/cd"]["cd"] = "cd";
-    dictionary["ab/cd"]["dd"] = "dd";
-    dictionary["ab/cd"]["ac"] = "ac";
-    dictionary["ab/cd"]["ad"] = "ad";
-    dictionary["ab/cd"]["bc"] = "bc";
-    dictionary["ab/cd"]["bd"] = "bd";
-    dictionary["ab/cd"]["--"] = "--";
-
-    dictionary["ab/aa"]["aa"] = "--";
-    dictionary["ab/aa"]["ab"] = "--";
-    dictionary["ab/aa"]["bb"] = "bb";
-    dictionary["ab/aa"]["--"] = "--";
-
-    dictionary["aa/ab"]["aa"] = "--";
-    dictionary["aa/ab"]["ab"] = "--";
-    dictionary["aa/ab"]["bb"] = "bb";
-    dictionary["aa/ab"]["--"] = "--";
-
-    dictionary["ab/cc"]["aa"] = "aa";
-    dictionary["ab/cc"]["ab"] = "ab";
-    dictionary["ab/cc"]["bb"] = "bb";
-    dictionary["ab/cc"]["cc"] = "cc";
-    dictionary["ab/cc"]["ac"] = "--";
-    dictionary["ab/cc"]["bc"] = "--";
-    dictionary["ab/cc"]["--"] = "--";
-
-    dictionary["cc/ab"]["aa"] = "aa";
-    dictionary["cc/ab"]["ab"] = "ab";
-    dictionary["cc/ab"]["bb"] = "bb";
-    dictionary["cc/ab"]["cc"] = "cc";
-    dictionary["cc/ab"]["ac"] = "--";
-    dictionary["cc/ab"]["bc"] = "--";
-    dictionary["cc/ab"]["--"] = "--";
-}
-
-void 
-load_mm_bc_dictionary(map<string, string> &types, 
-		      map<string, map<string, string> > &dictionary)
-{
-    types["aa/bb"] = "aaxbb";
-    types["bb/aa"] = "bbxaa";
-    types["ab/cc"] = "abxcc";
-    types["cc/ab"] = "ccxab";
-
-    dictionary["aaxbb"]["--"] = "-";
-    dictionary["aaxbb"]["aa"] = "b";
-    dictionary["aaxbb"]["ab"] = "h";
-    dictionary["aaxbb"]["bb"] = "h";
-
-    dictionary["bbxaa"]["--"] = "-";
-    dictionary["bbxaa"]["aa"] = "h";
-    dictionary["bbxaa"]["ab"] = "h";
-    dictionary["bbxaa"]["bb"] = "a";
-
-    dictionary["abxcc"]["--"] = "-";
-    dictionary["abxcc"]["ac"] = "h";
-    dictionary["abxcc"]["bc"] = "h";
-    dictionary["abxcc"]["ab"] = "b";
-    dictionary["abxcc"]["aa"] = "b";
-    dictionary["abxcc"]["bb"] = "b";
-
-    dictionary["ccxab"]["--"] = "-";
-    dictionary["ccxab"]["ac"] = "h";
-    dictionary["ccxab"]["bc"] = "h";
-    dictionary["ccxab"]["ab"] = "a";
-    dictionary["ccxab"]["aa"] = "a";
-    dictionary["ccxab"]["bb"] = "a";
-}
-
-void 
-load_mm_f2_dictionary(map<string, string> &types, 
-		      map<string, map<string, string> > &dictionary)
-{
-    types["aa/bb"] = "aaxbb";
-    types["ab/cd"] = "abxcd";
-    types["ab/aa"] = "abxaa";
-    types["aa/ab"] = "aaxab";
-    types["ab/cc"] = "abxcc";
-    types["cc/ab"] = "ccxab";
-
-    dictionary["aaxbb"]["aa"] = "a";
-    dictionary["aaxbb"]["ab"] = "h";
-    dictionary["aaxbb"]["bb"] = "b";
-    dictionary["aaxbb"]["--"] = "-";
-
-    dictionary["abxcd"]["aa"] = "a";
-    dictionary["abxcd"]["ab"] = "a";
-    dictionary["abxcd"]["bb"] = "a";
-    dictionary["abxcd"]["cc"] = "b";
-    dictionary["abxcd"]["cd"] = "b";
-    dictionary["abxcd"]["dd"] = "b";
-    dictionary["abxcd"]["ac"] = "h";
-    dictionary["abxcd"]["ad"] = "h";
-    dictionary["abxcd"]["bc"] = "h";
-    dictionary["abxcd"]["bd"] = "h";
-    dictionary["abxcd"]["--"] = "-";
-
-    dictionary["abxaa"]["aa"] = "-";
-    dictionary["abxaa"]["ab"] = "-";
-    dictionary["abxaa"]["bb"] = "a";
-    dictionary["abxaa"]["--"] = "-";
-
-    dictionary["aaxab"]["aa"] = "-";
-    dictionary["aaxab"]["ab"] = "-";
-    dictionary["aaxab"]["bb"] = "b";
-    dictionary["aaxab"]["--"] = "-";
-
-    dictionary["abxcc"]["aa"] = "a";
-    dictionary["abxcc"]["ab"] = "a";
-    dictionary["abxcc"]["bb"] = "a";
-    dictionary["abxcc"]["cc"] = "b";
-    dictionary["abxcc"]["ac"] = "-";
-    dictionary["abxcc"]["bc"] = "-";
-    dictionary["abxcc"]["--"] = "-";
-
-    dictionary["ccxab"]["aa"] = "b";
-    dictionary["ccxab"]["ab"] = "b";
-    dictionary["ccxab"]["bb"] = "b";
-    dictionary["ccxab"]["cc"] = "a";
-    dictionary["ccxab"]["ac"] = "-";
-    dictionary["ccxab"]["bc"] = "-";
-    dictionary["ccxab"]["--"] = "-";
-}
-
-void 
-load_dh_dictionary(map<string, string> &types, 
-		   map<string, map<string, string> > &dictionary)
-{
-    types["ab/--"] = "ab/--";
-    types["--/ab"] = "--/ab";
-
-    dictionary["ab/--"]["aa"] = "aa";
-    dictionary["ab/--"]["bb"] = "bb";
-    dictionary["ab/--"]["--"] = "--";
-
-    dictionary["--/ab"]["aa"] = "aa";
-    dictionary["--/ab"]["bb"] = "bb";
-    dictionary["--/ab"]["--"] = "--";
-}
-
-void 
-load_mm_dh_dictionary(map<string, string> &types, 
-		      map<string, map<string, string> > &dictionary)
-{
-    types["ab/--"] = "abx--";
-    types["--/ab"] = "--xab";
-
-    dictionary["abx--"]["aa"] = "a";
-    dictionary["abx--"]["bb"] = "b";
-    dictionary["abx--"]["--"] = "-";
-
-    dictionary["--xab"]["aa"] = "a";
-    dictionary["--xab"]["bb"] = "b";
-    dictionary["--xab"]["--"] = "-";
-}
-
-void 
-load_segregation_ratios(map_types type, map<string, map<string, double> > &segregation_ratios) 
-{
-    switch(type) {
-    case cp:
-	segregation_ratios["ab/--"]["aa"] = 0.50;
-	segregation_ratios["ab/--"]["ab"] = 0.50;
-
-	segregation_ratios["--/ab"]["aa"] = 0.50;
-	segregation_ratios["--/ab"]["ab"] = 0.50;
-
-	segregation_ratios["ab/aa"]["aa"] = 0.50;
-	segregation_ratios["ab/aa"]["ab"] = 0.50;
-
-	segregation_ratios["aa/ab"]["aa"] = 0.50;
-	segregation_ratios["aa/ab"]["ab"] = 0.50;
-
-	segregation_ratios["ab/ab"]["ab"] = 0.50;
-	segregation_ratios["ab/ab"]["aa"] = 0.25;
-	segregation_ratios["ab/ab"]["bb"] = 0.25;
-
-	segregation_ratios["ab/ac"]["ab"] = 0.25;
-	segregation_ratios["ab/ac"]["ac"] = 0.25;
-	segregation_ratios["ab/ac"]["bc"] = 0.25;
-	segregation_ratios["ab/ac"]["aa"] = 0.25;
-
-	segregation_ratios["ab/cd"]["ac"] = 0.25;
-	segregation_ratios["ab/cd"]["ad"] = 0.25;
-	segregation_ratios["ab/cd"]["bc"] = 0.25;
-	segregation_ratios["ab/cd"]["bd"] = 0.25;
-	break;
-    case f2:
-	segregation_ratios["aaxbb"]["a"] = 0.25;
-	segregation_ratios["aaxbb"]["b"] = 0.25;
-	segregation_ratios["aaxbb"]["h"] = 0.50;
-
-	segregation_ratios["abxcd"]["a"] = 0.25;
-	segregation_ratios["abxcd"]["b"] = 0.25;
-	segregation_ratios["abxcd"]["h"] = 0.50;
-
-	segregation_ratios["abxaa"]["a"] = 1.00;
-
-	segregation_ratios["aaxab"]["b"] = 1.00;
-
-	segregation_ratios["abxcc"]["a"] = 0.50;
-	segregation_ratios["abxcc"]["b"] = 0.50;
-
-	segregation_ratios["ccxab"]["b"] = 0.50;
-	segregation_ratios["ccxab"]["a"] = 0.50;
-	break;
-    case bc1:
-	segregation_ratios["aaxbb"]["h"] = 0.50;
-	segregation_ratios["aaxbb"]["b"] = 0.50;
-
-	segregation_ratios["bbxaa"]["h"] = 0.50;
-	segregation_ratios["bbxaa"]["a"] = 0.50;
-
-	segregation_ratios["abxcc"]["h"] = 0.50;
-	segregation_ratios["abxcc"]["b"] = 0.50;
-
-	segregation_ratios["ccxab"]["h"] = 0.50;
-	segregation_ratios["ccxab"]["a"] = 0.50;
-	break;
-    case dh:
-	segregation_ratios["ab/--"]["a"] = 0.50;
-	segregation_ratios["ab/--"]["b"] = 0.50;
-
-	segregation_ratios["--/ab"]["a"] = 0.50;
-	segregation_ratios["--/ab"]["b"] = 0.50;
-	break;
-    case gen:
-    case none:
-    case unk:
-	break;
-    }
+enum map_types {unk, none, gen, dh, cp, bc1, f2};
+enum out_types {rqtl, joinmap, onemap, genomic};
 
-    return;
-}
+void initialize_dictionaries(map<string, map<string, string> > &global_dictionary);
+void load_cp_dictionary(map<string, string> &types, map<string, map<string, string> > &dictionary);
+void load_joinmap_cp_dictionary(map<string, string> &types, map<string, map<string, string> > &dictionary);
+void load_onemap_cp_dictionary(map<string, string> &types, map<string, map<string, string> > &dictionary);
+void load_bc_dictionary(map<string, string> &types, map<string, map<string, string> > &dictionary);
+void load_f2_dictionary(map<string, string> &types, map<string, map<string, string> > &dictionary);
+void load_mm_bc_dictionary(map<string, string> &types, map<string, map<string, string> > &dictionary);
+void load_mm_f2_dictionary(map<string, string> &types, map<string, map<string, string> > &dictionary);
+void load_dh_dictionary(map<string, string> &types, map<string, map<string, string> > &dictionary);
+void load_mm_dh_dictionary(map<string, string> &types, map<string, map<string, string> > &dictionary);
+void load_segregation_ratios(map_types type, map<string, map<string, double> > &segregation_ratios);
 
 inline
-int 
-encode_gtype(char a) 
-{ 
+int
+encode_gtype(char a)
+{
     switch (a) {
     case 'A':
-	return 0;
+        return 0;
     case 'C':
-	return 1;
+        return 1;
     case 'G':
-	return 2;
+        return 2;
     case 'T':
-	return 3;
+        return 3;
     }
-
     return -1;
 }
 
-int 
-encoded_gtypes[4][4] = 
-{
-  // A  C  G   T
-    {1, 2, 3,  4}, // A
-    {2, 5, 6,  7}, // C
-    {3, 6, 8,  9}, // G
-    {4, 7, 9, 10}  // T
-};
-
 #endif // __GENOTYPE_DICTIONARIES_H__
diff --git a/src/genotypes.cc b/src/genotypes.cc
index 9d0180e..d160159 100644
--- a/src/genotypes.cc
+++ b/src/genotypes.cc
@@ -26,8 +26,12 @@
 // University of Oregon
 //
 
+#include "MetaPopInfo.h"
+
 #include "genotypes.h"
 
+extern int **encoded_gtypes;
+
 // Global variables to hold command-line options.
 int       num_threads =  1;
 int       batch_id    = -1;
@@ -82,8 +86,12 @@ int main (int argc, char* argv[]) {
 
     initialize_dictionaries(global_dictionary);
 
-    vector<string> files;
-    build_file_list(files);
+    MetaPopInfo mpopi;
+    mpopi.init_directory(in_path);
+    if (mpopi.samples().empty()) {
+        cerr << "Error: Failed to find sample files in directory '" << in_path << "'.\n";
+        return -1;
+    }
 
     if (wl_file.length() > 0) {
 	load_marker_list(wl_file, whitelist);
@@ -116,33 +124,58 @@ int main (int argc, char* argv[]) {
     // Load matches to the catalog
     //
     vector<vector<CatMatch *> > catalog_matches;
-    map<int, string>            samples;
-    vector<int>                 sample_ids;
-    for (uint i = 0; i < files.size(); i++) {
-	vector<CatMatch *> m;
-	load_catalog_matches(in_path + files[i], m);
-
-	if (m.size() == 0) {
-	    cerr << "Warning: unable to find any matches in file '" << files[i] << "', excluding this sample from genotypes analysis.\n";
-	    continue;
-	}
+    vector<size_t> samples_to_remove;
+    set<size_t> seen_samples;
+    for (size_t i=0; i<mpopi.samples().size(); ++i) {
+        catalog_matches.push_back(vector<CatMatch*>());
+        vector<CatMatch *>& m = catalog_matches.back();
+
+        const MetaPopInfo::Sample& sample = mpopi.samples()[i];
+        load_catalog_matches(in_path + sample.name, m);
+
+        if (m.size() == 0) {
+            cerr << "Warning: Absent or malformed matches file '"
+                 << sample.name << ".matches.tsv(.gz)"
+                 <<"', excluding this sample from population analysis.\n";
+            samples_to_remove.push_back(i);
+            catalog_matches.pop_back(); // n.b. Index shift will be resolved by the call to MetaPopInfo::delete_samples().
+            continue;
+        }
 
-	catalog_matches.push_back(m);
- 	samples[m[0]->sample_id] = files[i];
-	sample_ids.push_back(m[0]->sample_id);
+        size_t sample_id = m[0]->sample_id;
+        if (seen_samples.count(sample_id) > 0) {
+            cerr << "Error: sample ID " << sample_id << " occurs twice in this data set, likely the pipeline was run incorrectly.\n";
+            return -1;
+        }
+        seen_samples.insert(sample_id);
+        mpopi.set_sample_id(i, sample_id);
+    }
+    mpopi.delete_samples(samples_to_remove);
+    if (mpopi.samples().size() == 0) {
+        cerr << "Error: Couln't find any matches files.\n";
+        return -1;
     }
+    // [mpopi] is definitive.
+    cerr << "Working on " << mpopi.samples().size() << " samples.\n";
 
-    sort(sample_ids.begin(), sample_ids.end());
+    // Set the deprecated [samples] variable to the value it should have
+    map<int, string> samples; // map of {sample_id, sample_name}
+    mpopi.fill_samples(samples);
 
+    // Retrieve the IDs of the parents
+    vector<int> sample_ids;
+    for (auto& sample : mpopi.samples())
+        sample_ids.push_back(sample.id);
+    sort(sample_ids.begin(), sample_ids.end());
     set<int> parent_ids;
     identify_parental_ids(catalog, sample_ids, parent_ids);
 
     //
     // Create the population map
     //
-    cerr << "Populating observed haplotypes for " << sample_ids.size() << " samples, " << catalog.size() << " loci.\n";
-    PopMap<CSLocus> *pmap = new PopMap<CSLocus>(sample_ids.size(), catalog.size());
-    pmap->populate(sample_ids, catalog, catalog_matches);
+    cerr << "Populating observed haplotypes for " << mpopi.samples().size() << " samples, " << catalog.size() << " loci.\n";
+    PopMap<CSLocus> *pmap = new PopMap<CSLocus>(mpopi, catalog.size());
+    pmap->populate(catalog, catalog_matches);
 
     apply_locus_constraints(catalog, pmap);
 
@@ -2677,45 +2710,6 @@ int load_marker_list(string path, set<int> &list) {
     return 0;
 }
 
-int build_file_list(vector<string> &files) {
-    uint   pos;
-    string file;
-    struct dirent *direntry;
-
-    DIR *dir = opendir(in_path.c_str());
-
-    if (dir == NULL) {
-	cerr << "Unable to open directory '" << in_path << "' for reading.\n";
-	exit(1);
-    }
-
-    while ((direntry = readdir(dir)) != NULL) {
-	file = direntry->d_name;
-
-	if (file == "." || file == "..")
-	    continue;
-
-	if (file.substr(0, 6) == "batch_")
-	    continue;
-
-	pos = file.rfind(".tags.tsv");
-	if (pos < file.length())
-	    files.push_back(file.substr(0, pos));
-    }
-
-    closedir(dir);
-
-    sort(files.begin(), files.end());
-
-    if (files.size() == 0) {
-	cerr << "Unable to locate any input files to process within '" << in_path << "'\n";
-    }
-
-    cerr << "Found " << files.size() << " input file(s).\n";
-
-    return 0;
-}
-
 bool hap_compare(pair<string, int> a, pair<string, int> b) {
     return (a.second > b.second);
 }
diff --git a/src/input.cc b/src/input.cc
index 3834e06..d58b6a6 100644
--- a/src/input.cc
+++ b/src/input.cc
@@ -67,12 +67,12 @@ Seq::Seq(const char *id, const char *seq, const char *qual, const char *chr, uin
     strcpy(this->qual, qual);
     this->loc.set(chr, bp, strand);
 
-    sprintf(this->loc_str, "%s|%d|%c", chr, bp, strand == plus ? '+' : '-');
+    sprintf(this->loc_str, "%s|%d|%c", chr, bp, strand == strand_plus ? '+' : '-');
 
     //
     // Reverse complement sequences from the negative strand 
     //
-    if (strand == plus) {
+    if (strand == strand_plus) {
 	this->seq = new char[strlen(seq)  + 1];
 	strcpy(this->seq, seq);
     } else {
diff --git a/src/kmers.cc b/src/kmers.cc
index 60bf0c5..d1bff17 100644
--- a/src/kmers.cc
+++ b/src/kmers.cc
@@ -98,7 +98,7 @@ generate_kmers_lazily(const char *seq, uint kmer_len, uint num_kmers, vector<cha
     if (num_kmers > kmers.size()) {
 	int new_kmers = num_kmers - kmers.size();
 
-        for (uint i = 0; i < new_kmers; i++) {
+        for (int i = 0; i < new_kmers; i++) {
 	    kmer = new char[kmer_len + 1];
 	    kmers.push_back(kmer);
 	}
diff --git a/src/locus.cc b/src/locus.cc
index 67ffea9..7daee85 100644
--- a/src/locus.cc
+++ b/src/locus.cc
@@ -26,7 +26,7 @@
 uint 
 Locus::sort_bp(uint k) 
 {
-    if (this->loc.strand == plus)
+    if (this->loc.strand == strand_plus)
         return this->loc.bp + k;
     else
         return (k == 0 ? this->loc.bp - this->len + 1 : this->loc.bp - k);
diff --git a/src/mstack.cc b/src/mstack.cc
index 32127bc..8d7054f 100644
--- a/src/mstack.cc
+++ b/src/mstack.cc
@@ -194,10 +194,10 @@ MergedStack::calc_likelihood()
         //
         // Don't invoke the model within gaps.
         //
-        if (cur_gap < this->gaps.size() && col == this->gaps[cur_gap].start) {
+        if (cur_gap < gaps.size() && col == (int)gaps[cur_gap].start) {
             do {
                 col++;
-            } while (col < this->gaps[cur_gap].end && col < length);
+            } while (col < (int)gaps[cur_gap].end && col < length);
             col--;
             continue;
         }
diff --git a/src/ordered.h b/src/ordered.h
index 6d74a86..e3455f8 100644
--- a/src/ordered.h
+++ b/src/ordered.h
@@ -21,6 +21,7 @@
 #ifndef __ORDERED_H__
 #define __ORDERED_H__
 
+#include <iostream>
 #include <fstream>
 using std::ifstream;
 using std::ofstream;
@@ -34,8 +35,11 @@ using std::map;
 #include <set>
 using std::set;
 
+#include "MetaPopInfo.h"
 #include "PopSum.h"
 
+extern MetaPopInfo mpopi;
+
 enum loc_type {haplotype, snp};
 
 template<class StatT>
@@ -263,10 +267,10 @@ OPopPair<StatT>::order(vector<StatT *> &sites, map<uint, uint> &sites_key, vecto
 				<< "incompatible_locus\t"
 				<< loc->id << "\t"
 				<< loc->loc.chr << "\t"
-				<< loc->sort_bp(k) << "\t"
+				<< loc->sort_bp(k) +1 << "\t"
 				<< k << "\t" 
-				<< pop_1 << "\t" 
-				<< pop_2 << "\n";
+				<< mpopi.pops()[pop_1].name << "\t"
+				<< mpopi.pops()[pop_2].name << "\n";
 		delete pair;
 		continue;
 	    }
@@ -292,10 +296,10 @@ OPopPair<StatT>::order(vector<StatT *> &sites, map<uint, uint> &sites_key, vecto
 				<< "multiple_locus\t"
 				<< loc->id << "\t"
 				<< loc->loc.chr << "\t"
-				<< pair->bp << "\t"
+				<< pair->bp +1 << "\t"
 				<< k << "\t" 
-				<< pop_key[pop_1] << "\t" 
-				<< pop_key[pop_2] << "\n";
+				<< mpopi.pops()[pop_1].name << "\t"
+				<< mpopi.pops()[pop_2].name << "\n";
 		delete pair;
 		continue;
 	    }
@@ -346,7 +350,7 @@ OSumStat<StatT>::order(vector<StatT *> &sites, vector<CSLocus *> &sorted_loci, i
 	    if (lsum->nucs[k].num_indv == 0) continue;
 
 	    if (sites_key.count(lsum->nucs[k].bp) == 0) {
-		cerr << "Error: locus " << lsum->nucs[k].loc_id << " at " << lsum->nucs[k].bp << "bp is not defined in the sites map.\n";
+		cerr << "Error: locus " << lsum->nucs[k].loc_id << " at " << lsum->nucs[k].bp +1 << "bp is not defined in the sites map.\n";
 
 	    } else if (sites[sites_key[lsum->nucs[k].bp]] == NULL) {
 		sites[sites_key[lsum->nucs[k].bp]] = &(lsum->nucs[k]);
@@ -357,9 +361,9 @@ OSumStat<StatT>::order(vector<StatT *> &sites, vector<CSLocus *> &sorted_loci, i
 				<< "multiple_locus\t"
 				<< loc->id << "\t"
 				<< loc->loc.chr << "\t"
-				<< lsum->nucs[k].bp << "\t"
+				<< lsum->nucs[k].bp +1 << "\t"
 				<< k << "\t" 
-				<< pop_id << "\t"
+				<< mpopi.pops()[pop_id].name << "\t"
 				<< "conflicts with locus " << sites[sites_key[lsum->nucs[k].bp]]->loc_id << "\n";
 	    }
 	}
@@ -407,7 +411,7 @@ OLocTally<StatT>::order(vector<StatT *> &sites, vector<CSLocus *> &sorted_loci)
 	    if (ltally->nucs[k].allele_cnt != 2) continue;
 
 	    if (sites_key.count(ltally->nucs[k].bp) == 0) {
-		cerr << "Error: locus " << ltally->nucs[k].loc_id << " at " << ltally->nucs[k].bp << "bp is not defined in the sites map.\n";
+		cerr << "Error: locus " << ltally->nucs[k].loc_id << " at " << ltally->nucs[k].bp +1 << "bp is not defined in the sites map.\n";
 
 	    } else if (sites[sites_key[ltally->nucs[k].bp]] == NULL) {
 		sites[sites_key[ltally->nucs[k].bp]] = &(ltally->nucs[k]);
@@ -418,7 +422,7 @@ OLocTally<StatT>::order(vector<StatT *> &sites, vector<CSLocus *> &sorted_loci)
 				<< "multiple_locus\t"
 				<< loc->id << "\t"
 				<< loc->loc.chr << "\t"
-				<< ltally->nucs[k].bp << "\t"
+				<< ltally->nucs[k].bp +1 << "\t"
 				<< k << "\t" 
 				<< "conflicts with locus " << sites[sites_key[ltally->nucs[k].bp]]->loc_id << "\n";
 	    }
diff --git a/src/populations.cc b/src/populations.cc
index 97bbfa5..072c494 100644
--- a/src/populations.cc
+++ b/src/populations.cc
@@ -23,14 +23,30 @@
 // haplotypes in a population context.
 //
 
+#include <dirent.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+
+#include "MetaPopInfo.h"
+#include "export_formats.h"
+
 #include "populations.h"
 
+using namespace std;
+
+typedef MetaPopInfo::Sample Sample;
+typedef MetaPopInfo::Pop Pop;
+typedef MetaPopInfo::Group Group;
+
+extern int **encoded_gtypes;
+
 // Global variables to hold command-line options.
+InputMode input_mode  = InputMode::stacks;
 int       num_threads =  1;
 int       batch_id    = -1;
 string    in_path;
+string    in_vcf_path;
 string    out_path;
-string    out_file;
 string    pmap_path;
 string    bl_file;
 string    wl_file;
@@ -83,10 +99,11 @@ double    minor_allele_freq = 0.0;
 double    max_obs_het       = 1.0;
 double    p_value_cutoff    = 0.05;
 corr_type fst_correction    = no_correction;
+set<string> debug_flags;
+
+string    out_prefix;
 
-map<int, string>          pop_key, grp_key;
-map<int, pair<int, int> > pop_indexes;
-map<int, vector<int> >    grp_members;
+MetaPopInfo mpopi;
 
 set<int> blacklist, bootstraplist;
 map<int, set<int> > whitelist;
@@ -101,9 +118,20 @@ map<string, int>           renz_olap;
 
 int main (int argc, char* argv[]) {
 
+#ifndef HAVE_LIBZ
+    cerr << "Stacks was compiled without zlib, and will refuse to parse compressed files.\n";
+#endif
+
+    //
+    // Initialize the globals that need it.
+    //
     initialize_renz(renz, renz_cnt, renz_len);
     initialize_renz_olap(renz_olap);
+    srandom(time(NULL));
 
+    //
+    // Parse the command line.
+    //
     parse_command_line(argc, argv);
 
     cerr
@@ -137,128 +165,321 @@ int main (int argc, char* argv[]) {
     }
 
     //
+    // Open and initialize the log file.
+    //
+    struct stat path_stat;
+    if (stat(out_path.c_str(), &path_stat) == 0) {
+        // Path exists, check that it is a directory
+        DIR* d = opendir(out_path.c_str());
+        if (d == NULL) {
+            cerr << "Error: Failed to open '" << out_path << "' as a directory.\n";
+            return -1;
+        }
+        closedir(d);
+    } else if (mkdir(out_path.c_str(), ACCESSPERMS) != 0) {
+        // Failed to create the directory.
+        cerr << "Error: Failed to create directory '" << out_path << "'.\n";
+        return -1;
+    }
+    string log_path = out_path + out_prefix + ".populations.log";
+    ofstream log_fh(log_path.c_str(), ofstream::out);
+    if (log_fh.fail()) {
+        cerr << "Error opening log file '" << log_path << "'\n";
+        return -1;
+    }
+    init_log(log_fh, argc, argv);
+    log_fh << flush;
+
+    //
     // Set the number of OpenMP parallel threads to execute.
     //
+
     #ifdef _OPENMP
     omp_set_num_threads(num_threads);
     #endif
 
     //
-    // Seed the random number generator
+    // Initialize the catalog and the MetaPopInfo
     //
-    srandom(time(NULL));
 
-    vector<pair<int, string> > files;
-    if (!build_file_list(files, pop_indexes, grp_members))
-        exit(1);
+    map<int, CSLocus *> catalog;
 
-    if (wl_file.length() > 0) {
-        load_marker_column_list(wl_file, whitelist);
-        cerr << "Loaded " << whitelist.size() << " whitelisted markers.\n";
+    // We need some objects in the main scope for each mode.
+    vector<vector<CatMatch *> > catalog_matches;
+    VcfHeader                  *vcf_header  = NULL;
+    vector<VcfRecord>          *vcf_records = NULL;
+
+    // Read the population map file, if any.
+    if (not pmap_path.empty()) {
+        cerr << "Parsing population map...\n";
+        mpopi.init_popmap(pmap_path);
+        if (mpopi.samples().empty()) {
+            cerr << "Error: Failed to open or parse population map file '" << pmap_path << "'.\n";
+            return -1;
+        }
+        cerr << "The population map contained " << mpopi.samples().size() << " samples, "
+             << mpopi.pops().size() << " population(s), " << mpopi.groups().size() << " group(s).\n";
+    }
+
+    if (input_mode == InputMode::stacks) {
+        //
+        // Stacks mode
+        //
+        if (pmap_path.empty()) {
+            cerr << "No population map specified, building file list...\n";
+            mpopi.init_directory(in_path);
+            if (mpopi.samples().empty()) {
+                cerr << "Error: Failed to find sample files in directory '" << in_path << "'.\n";
+                return -1;
+            }
+        }
+
+        // Check that at least one sample file exists in the directory.
+        bool dir_good = false;
+        for (vector<Sample>::const_iterator s=mpopi.samples().begin(); s!=mpopi.samples().end(); ++s) {
+            ifstream f;
+            string path = in_path + s->name + ".matches.tsv";
+            f.open(path);
+            if (f.is_open()) {
+                dir_good = true;
+                break;
+            }
+#if HAVE_LIBZ
+            path += ".gz";
+            gzFile g = gzopen(path.c_str(), "rb");
+            if (g != NULL) {
+                dir_good = true;
+                gzclose(g);
+                break;
+            }
+#endif
+        }
+        if (!dir_good) {
+            cerr << "Error: Unable to locate any file in input directory '" << in_path << "'.\n";
+            return -1;
+        }
+
+        //
+        // Load the catalog
+        //
+        cerr << "Reading the catalog...\n";
+        string catalog_prefix = in_path + "batch_" + to_string(batch_id) + ".catalog";
+        bool   compressed     = false;
+        int    res = load_loci(catalog_prefix, catalog, false, false, compressed);
+        if (res == 0) {
+            cerr << "Unable to load the catalog '" << catalog_prefix << "'\n";
+            return -1;
+        }
+
+        //
+        // Load the matches
+        //
+        cerr << "Reading matches to the catalog...\n";
+        vector<size_t> samples_to_remove;
+        set<size_t>    seen_samples;
+        for (size_t i = 0; i < mpopi.samples().size(); ++i) {
+            catalog_matches.push_back(vector<CatMatch*>());
+            vector<CatMatch *>& m = catalog_matches.back();
+            load_catalog_matches(in_path + mpopi.samples().at(i).name, m);
+
+            if (m.size() == 0) {
+                cerr << "Warning: Absent or malformed matches file '"
+                     << mpopi.samples()[i].name << ".matches.tsv(.gz)"
+                     <<"', excluding this sample from population analysis.\n";
+                samples_to_remove.push_back(i);
+                catalog_matches.pop_back(); // This introduces an index shift between catalog_matches and [i]/[mpopi],
+                                            // which will be resolved by a call to MetaPopInfo::delete_samples().
+                continue;
+            }
+
+            size_t sample_id = m[0]->sample_id;
+            if (seen_samples.count(sample_id) > 0) {
+                cerr << "Error: sample ID " << sample_id << " occurs twice in this data set, likely the pipeline was run incorrectly.\n";
+                exit(0);
+            }
+            seen_samples.insert(sample_id);
+            mpopi.set_sample_id(i, sample_id);
+        }
+
+        mpopi.delete_samples(samples_to_remove);
+        if (mpopi.samples().size() == 0) {
+            cerr << "Error: Couln't find any matches files.\n";
+            return -1;
+        }
+        // [mpopi] is definitive.
+
+    } else if (input_mode == InputMode::vcf) {
+
+        //
+        // VCF mode
+        //
+
+        // Open the VCF file
+        cerr << "Opening the VCF file...\n";
+        VcfAbstractParser* parser = Vcf::adaptive_open(in_vcf_path);
+        if (parser == NULL) {
+            cerr << "Error: Unable to open VCF file '" << in_vcf_path << "'.\n";
+            return -1;
+        }
+
+        parser->read_header();
+        if (parser->header().samples().empty()) {
+            cerr << "Error: No samples in VCF file '" << in_vcf_path << "'.\n";
+            return -1;
+        }
+
+        // Reconsider the MetaPopInfo in light of the VCF header.
+        if (pmap_path.empty()) {
+            cerr << "No population map specified, creating one from the VCF header...\n";
+            mpopi.init_names(parser->header().samples());
+        } else {
+            // Intersect the samples present in the population map and the VCF.
+            vector<size_t> samples_to_discard;
+            for (size_t i=0; i<mpopi.samples().size(); ++i)
+                if (not parser->header().sample_indexes().count(mpopi.samples()[i].name))
+                    samples_to_discard.push_back(i);
+            if (not samples_to_discard.empty()) {
+                if (samples_to_discard.size() == mpopi.samples().size()) {
+                    cerr << "Error: No common samples between the population map and VCF header.\n";
+                    return -1;
+                }
+                cerr << "Warning: of the samples listed in the population map, "
+                     << samples_to_discard.size() << " could not be found in the VCF :";
+                for (const size_t& s : samples_to_discard)
+                    cerr << " " << mpopi.samples()[s].name;
+                cerr << "\n";
+                mpopi.delete_samples(samples_to_discard);
+            }
+
+            // Create arbitrary sample IDs.
+            for (size_t i = 0; i < mpopi.samples().size(); ++i)
+                mpopi.set_sample_id(i, i+1); //id=i+1
+
+            // [mpopi] is definitive.
+        }
+
+        // Read the SNP records
+        cerr << "Reading the VCF records...\n";
+        vcf_records = new vector<VcfRecord>();
+        vector<size_t> skipped_notsnp;
+        vector<size_t> skipped_filter;
+
+        vcf_records->push_back(VcfRecord());
+        VcfRecord* rec = & vcf_records->back();
+        while (parser->next_record(*rec)) {
+            // Check for a SNP.
+            if (not rec->is_snp()) {
+                skipped_notsnp.push_back(parser->line_number());
+                continue;
+            }
+
+            // Check for a filtered-out SNP
+            if (not rec->filter.empty() && rec->filter[0] != "PASS") {
+                skipped_filter.push_back(parser->line_number());
+                continue;
+            }
+
+            // Save the SNP.
+            vcf_records->push_back(VcfRecord());
+            rec = & vcf_records->back();
+        }
+        vcf_records->pop_back();
+
+        cerr << "Found " << vcf_records->size() << " SNP records in file '" << in_vcf_path
+             << "'. (Skipped " << skipped_filter.size() << " already filtered-out SNPs and "
+             << skipped_notsnp.size() << " non-SNP records ; more with --verbose.)\n";
+        if (verbose && not skipped_notsnp.empty()) {
+            log_fh << "The following VCF record lines were determined not to be SNPs and skipped :";
+            for (vector<size_t>::const_iterator l=skipped_notsnp.begin(); l!=skipped_notsnp.end(); ++l)
+                log_fh << " " << *l;
+            log_fh << "\n";
+        }
+        if (vcf_records->size() == 0) {
+            cerr << "Error: No records.\n";
+            return -1;
+        }
+
+        catalog = create_catalog(*vcf_records);
+        vcf_header = new VcfHeader(parser->header());
+        delete parser;
     }
+
+    //
+    // Read the blacklist, the whitelist, and the bootstrap-whitelist.
+    //
     if (bl_file.length() > 0) {
         load_marker_list(bl_file, blacklist);
         cerr << "Loaded " << blacklist.size() << " blacklisted markers.\n";
     }
+    if (wl_file.length() > 0) {
+        load_marker_column_list(wl_file, whitelist);
+        cerr << "Loaded " << whitelist.size() << " whitelisted markers.\n";
+        check_whitelist_integrity(catalog, whitelist);
+    }
     if (bs_wl_file.length() > 0) {
         load_marker_list(bs_wl_file, bootstraplist);
         cerr << "Loaded " << bootstraplist.size() << " markers to include when bootstrapping.\n";
     }
 
     //
-    // Open the log file.
+    // Reduce the catalog accordingly, and retrieve the genomic order of loci.
     //
-    stringstream log;
-    log << "batch_" << batch_id << ".populations.log";
-    string log_path = in_path + log.str();
-    ofstream log_fh(log_path.c_str(), ofstream::out);
-    if (log_fh.fail()) {
-        cerr << "Error opening log file '" << log_path << "'\n";
-        exit(1);
-    }
-    init_log(log_fh, argc, argv);
+    reduce_catalog(catalog, whitelist, blacklist);
+    loci_ordered = order_unordered_loci(catalog);
 
-    //
-    // Load the catalog
-    //
-    stringstream catalog_file;
-    map<int, CSLocus *> catalog;
-    bool compressed = false;
-    int  res;
-    catalog_file << in_path << "batch_" << batch_id << ".catalog";
-    if ((res = load_loci(catalog_file.str(), catalog, false, false, compressed)) == 0) {
-        cerr << "Unable to load the catalog '" << catalog_file.str() << "'\n";
-        return 0;
+    // Report information on the MetaPopInfo.
+    cerr << "Working on " << mpopi.samples().size() << " samples.\n";
+    cerr << "Working on " << mpopi.pops().size() << " population(s):\n";
+    for (vector<Pop>::const_iterator p = mpopi.pops().begin(); p != mpopi.pops().end(); p++) {
+        cerr << "    " << p->name << ": ";
+        for (size_t s = p->first_sample; s < p->last_sample; ++s) {
+            cerr << mpopi.samples()[s].name << ", ";
+        }
+        cerr << mpopi.samples()[p->last_sample].name << "\n";
+    }
+    cerr << "Working on " << mpopi.groups().size() << " group(s) of populations:\n";
+    for (vector<Group>::const_iterator g = mpopi.groups().begin(); g != mpopi.groups().end(); g++) {
+        cerr << "    " << g->name << ": ";
+        for (vector<size_t>::const_iterator p = g->pops.begin(); p != g->pops.end() -1; ++p) {
+            //rem. end()-1 and back() are safe, there's always at least one pop
+            cerr << mpopi.pops()[*p].name << ", ";
+        }
+        cerr << mpopi.pops()[g->pops.back()].name << "\n";
     }
 
-    //
-    // Check the whitelist.
-    //
-    check_whitelist_integrity(catalog, whitelist);
-
-    //
-    // Implement the black/white list
-    //
-    reduce_catalog(catalog, whitelist, blacklist);
+    if (size_t(population_limit) > mpopi.pops().size()) {
+        cerr << "Notice: Population limit (" << population_limit << ")"
+             << " larger than number of popualtions present, adjusting parameter to "
+             << mpopi.pops().size() << "\n";
+        population_limit = mpopi.pops().size();
+    }
 
     //
-    // If the catalog is not reference aligned, assign an arbitrary ordering to catalog loci.
+    // Initialize the PopMap
     //
-    loci_ordered = order_unordered_loci(catalog);
 
-    //
-    // Load matches to the catalog
-    //
-    vector<vector<CatMatch *> > catalog_matches;
-    map<int, string>            samples;
-    vector<int>                 sample_ids;
-    uint                        removed_cnt = 0;
+    cerr << "Populating observed haplotypes for " << mpopi.samples().size() << " samples, " << catalog.size() << " loci.\n";
+    PopMap<CSLocus> *pmap = new PopMap<CSLocus>(mpopi, catalog.size());
 
-    for (int i = 0; i < (int) files.size(); i++) {
-        vector<CatMatch *> m;
-        load_catalog_matches(in_path + files[i].second, m);
+    if (input_mode == InputMode::stacks) {
+        // Using SStacks matches files...
+        pmap->populate(catalog, catalog_matches);
 
-        if (m.size() == 0) {
-            cerr << "    Warning: unable to find any matches in file '" << files[i].second << "', excluding this sample from population analysis.\n";
-            //
-            // This case is generated by an existing, but empty file.
-            // Remove this sample from the population index which was built from 
-            // existing files, but we couldn't yet check for empty files.
-            //
-            uint index = i - removed_cnt;
-            for (map<int, pair<int, int> >::iterator pit = pop_indexes.begin(); pit != pop_indexes.end(); pit++)
-                if ((index >= pit->second.first && index <= pit->second.second)) {
-                    pit->second.second--;
-                    removed_cnt++;
-                    pit++;
-                    while (pit != pop_indexes.end()) {
-                        pit->second.first--;
-                        pit->second.second--;
-                        pit++;
-                    }
-                    break;
-                }
-            continue;
-        }
+        for(vector<vector<CatMatch *> >::iterator sample = catalog_matches.begin(); sample != catalog_matches.end(); ++sample)
+            for(vector<CatMatch*>::iterator match = sample->begin(); match != sample->end(); ++match)
+                delete *match;
+        catalog_matches.clear();
 
-        catalog_matches.push_back(m);
-        if (samples.count(m[0]->sample_id) == 0) {
-            samples[m[0]->sample_id] = files[i].second;
-            sample_ids.push_back(m[0]->sample_id);
-        } else {
-            cerr << "Fatal error: sample ID " << m[0]->sample_id << " occurs twice in this data set, likely the pipeline was run incorrectly.\n";
-            exit(0);
-        }
+    } else if (input_mode == InputMode::vcf) {
+        // ...or using VCF records.
+        pmap->populate(catalog, *vcf_records, *vcf_header);
+        delete vcf_records;
+        delete vcf_header;
+        vcf_records = NULL;
+        vcf_header = NULL;
     }
 
     //
-    // Create the population map
-    // 
-    cerr << "Populating observed haplotypes for " << sample_ids.size() << " samples, " << catalog.size() << " loci.\n";
-    PopMap<CSLocus> *pmap = new PopMap<CSLocus>(sample_ids.size(), catalog.size());
-    pmap->populate(sample_ids, catalog, catalog_matches);
-
-    //
     // Tabulate haplotypes present and in what combinations.
     //
     tabulate_haplotypes(catalog, pmap);
@@ -272,64 +493,61 @@ int main (int argc, char* argv[]) {
     log_fh << "# Distribution of population loci.\n";
     log_haplotype_cnts(catalog, log_fh);
 
-    apply_locus_constraints(catalog, pmap, pop_indexes, log_fh);
+    apply_locus_constraints(catalog, pmap, log_fh);
 
     log_fh << "# Distribution of population loci after applying locus constraints.\n";
     log_haplotype_cnts(catalog, log_fh);
 
-    cerr << "Loading model outputs for " << sample_ids.size() << " samples, " << catalog.size() << " loci.\n";
-    map<int, CSLocus *>::iterator it;
-    map<int, ModRes *>::iterator mit;
-    Datum   *d;
-    CSLocus *loc;
+    if (input_mode == InputMode::stacks) {
+        //
+        // Load the output from the SNP calling model (hOm/hEt/Unk) for
+        // each individual at each locus.
+        //
 
-    //
-    // Load the output from the SNP calling model for each individual at each locus. This
-    // model output string looks like this:
-    //   OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOEOOOOOOEOOOOOOOOOOOOOOOOOOOOOOOOOOOOOUOOOOUOOOOOO
-    // and records model calls for each nucleotide: O (hOmozygous), E (hEterozygous), U (Unknown)
-    //
-    for (uint i = 0; i < sample_ids.size(); i++) {
-        map<int, ModRes *> modres;
-        load_model_results(in_path + samples[sample_ids[i]], modres);
+        cerr << "Loading model outputs for " << mpopi.samples().size() << " samples, " << catalog.size() << " loci.\n";
 
-        if (modres.size() == 0) {
-            cerr << "    Warning: unable to find any model results in file '" << samples[sample_ids[i]] << "', excluding this sample from population analysis.\n";
-            continue;
-        }
+        map<int, CSLocus *>::iterator it;
+        map<int, ModRes *>::iterator mit;
+        Datum   *d;
+        CSLocus *loc;
 
-        for (it = catalog.begin(); it != catalog.end(); it++) {
-            loc = it->second;
-            d = pmap->datum(loc->id, sample_ids[i]);
-
-            if (d != NULL) {
-                if (modres.count(d->id) == 0) {
-                    cerr << "Fatal error: Unable to find model data for catalog locus " << loc->id 
-                         << ", sample ID " << sample_ids[i] << ", sample locus " << d->id 
-                         << "; likely IDs were mismatched when running pipeline.\n";
-                    exit(0);
+        for (uint i = 0; i < mpopi.samples().size(); i++) {
+            map<int, ModRes *> modres;
+            load_model_results(in_path + mpopi.samples()[i].name, modres);
+
+            if (modres.size() == 0) {
+                cerr << "    Warning: unable to find any model results in file '" << mpopi.samples()[i].name << ".models.tsv(.gz)', excluding this sample from population analysis.\n";
+                continue;
+            }
+
+            for (it = catalog.begin(); it != catalog.end(); it++) {
+                loc = it->second;
+                d = pmap->datum(loc->id, mpopi.samples()[i].id);
+
+                if (d != NULL) {
+                    if (modres.count(d->id) == 0) {
+                        cerr << "Fatal error: Unable to find model data for catalog locus " << loc->id
+                             << ", sample ID " << mpopi.samples()[i].id << ", sample locus " << d->id
+                             << "; likely IDs were mismatched when running pipeline.\n";
+                        exit(0);
+                    }
+                    d->add_model(modres[d->id]->model);
                 }
-                d->add_model(modres[d->id]->model);
             }
+            for (mit = modres.begin(); mit != modres.end(); mit++)
+                delete mit->second;
+            modres.clear();
         }
-
-        for (mit = modres.begin(); mit != modres.end(); mit++)
-            delete mit->second;
-        modres.clear();
     }
 
-    uint pop_id, start_index, end_index;
-    map<int, pair<int, int> >::iterator pit;
-
-    PopSum<CSLocus> *psum = new PopSum<CSLocus>(pmap->loci_cnt(), pop_indexes.size());
-    psum->initialize(pmap);
+    //
+    // Create the PopSum object and compute the summary statistics.
+    //
 
-    for (pit = pop_indexes.begin(); pit != pop_indexes.end(); pit++) {
-        start_index = pit->second.first;
-        end_index   = pit->second.second;
-        pop_id      = pit->first;
-        cerr << "Generating nucleotide-level summary statistics for population '" << pop_key[pop_id] << "'\n";
-        psum->add_population(catalog, pmap, pop_id, start_index, end_index, verbose, log_fh);
+    PopSum<CSLocus> *psum = new PopSum<CSLocus>(*pmap, mpopi);
+    for (size_t i=0; i<mpopi.pops().size(); ++i) {
+        cerr << "Generating nucleotide-level summary statistics for population '" << mpopi.pops()[i].name << "'\n";
+        psum->add_population(catalog, pmap, i, verbose, log_fh);
     }
 
     cerr << "Tallying loci across populations...";
@@ -342,12 +560,9 @@ int main (int argc, char* argv[]) {
     // frequency threshold (-a). In these cases we will remove the SNP, but keep the locus.
     //
     blacklist.clear();
-    int pruned_snps = prune_polymorphic_sites(catalog, pmap, psum, pop_indexes, whitelist, blacklist, log_fh);
-    cerr << "Pruned " << pruned_snps << " variant sites due to filter constraints.\n";
+    int pruned_snps = prune_polymorphic_sites(catalog, pmap, psum, whitelist, blacklist, log_fh);
+    cerr << "Pruned " << pruned_snps << " variant sites due to filter constraints (more with --verbose).\n";
 
-    if (!verbose)
-        cerr << "  (enable the --verbose flag to record the reason why each site was filtered in the batch_X.populations.log file.)\n";
-    
     //
     // Create an artificial whitelist if the user requested only the first or a random SNP per locus.
     //
@@ -376,105 +591,107 @@ int main (int argc, char* argv[]) {
     //
     // Regenerate summary statistics after pruning SNPs and  merging loci.
     //
+
+    if (debug_flags.count("VCFCOMP"))
+        vcfcomp_simplify_pmap(catalog, pmap);
+
     delete psum;
-    psum = new PopSum<CSLocus>(pmap->loci_cnt(), pop_indexes.size());
-    psum->initialize(pmap);
-    for (pit = pop_indexes.begin(); pit != pop_indexes.end(); pit++) {
-        start_index = pit->second.first;
-        end_index   = pit->second.second;
-        pop_id      = pit->first;
-        cerr << "Regenerating nucleotide-level summary statistics for population '" << pop_key[pop_id] << "'\n";
-        psum->add_population(catalog, pmap, pop_id, start_index, end_index, verbose, log_fh);
+    psum = new PopSum<CSLocus>(*pmap, mpopi);
+    for (size_t i=0; i<mpopi.pops().size(); ++i) {
+        cerr << "Regenerating nucleotide-level summary statistics for population '" << mpopi.pops()[i].name << "'\n";
+        psum->add_population(catalog, pmap, i, verbose, log_fh);
     }
     cerr << "Re-tallying loci across populations...";
     psum->tally(catalog);
     cerr << "done.\n";
 
-    for (pit = pop_indexes.begin(); pit != pop_indexes.end(); pit++) {
-        pop_id = pit->first;
-        if (kernel_smoothed && loci_ordered) {
-            cerr << "  Generating kernel-smoothed population statistics...\n";
-            kernel_smoothed_popstats(catalog, pmap, psum, pop_id, log_fh);
+    if (kernel_smoothed) {
+        if (loci_ordered) {
+            for (size_t i=0; i<mpopi.pops().size(); ++i) {
+                cerr << "  Generating kernel-smoothed population statistics for population '" << mpopi.pops()[i].name << "'...\n";
+                kernel_smoothed_popstats(catalog, pmap, psum, i, log_fh);
+            }
+        } else {
+            cerr << "Notice: Smoothing was requested (-k), but will not be performed as the loci are not ordered.\n";
         }
     }
 
-    calculate_haplotype_stats(files, pop_indexes, catalog, pmap, psum);
+    calculate_haplotype_stats(catalog, pmap, psum);
 
     if (calc_fstats) {
-        calculate_haplotype_divergence(files, pop_indexes, grp_members, catalog, pmap, psum);
-
-        calculate_haplotype_divergence_pairwise(files, pop_indexes, grp_members, catalog, pmap, psum);
+        calculate_haplotype_divergence(catalog, pmap, psum);
+        calculate_haplotype_divergence_pairwise(catalog, pmap, psum);
     }
 
     //
     // Calculate and output the locus-level summary statistics.
     //
-    calculate_summary_stats(files, pop_indexes, catalog, pmap, psum);
+    calculate_summary_stats(catalog, pmap, psum);
 
     //
     // Output the observed haplotypes.
     //
-    write_generic(catalog, pmap, samples, false);
+    write_generic(catalog, pmap, false);
 
     //
     // Output data in requested formats
     //
     if (fasta_out)
-        write_fasta(catalog, pmap, samples, sample_ids);
+        write_fasta(catalog, pmap);
 
     if (fasta_strict_out)
-        write_strict_fasta(catalog, pmap, samples, sample_ids);
+        write_strict_fasta(catalog, pmap);
 
     if (genepop_out && ordered_export)
-        write_genepop_ordered(catalog, pmap, psum, pop_indexes, samples, log_fh);
+        write_genepop_ordered(catalog, pmap, psum, log_fh);
     else if (genepop_out)
-        write_genepop(catalog, pmap, psum, pop_indexes, samples);
+        write_genepop(catalog, pmap, psum);
 
     if (structure_out && ordered_export)
-        write_structure_ordered(catalog, pmap, psum, pop_indexes, samples, log_fh);
+        write_structure_ordered(catalog, pmap, psum, log_fh);
     else if (structure_out) 
-        write_structure(catalog, pmap, psum, pop_indexes, samples);
+        write_structure(catalog, pmap, psum);
 
     if (fastphase_out)
-        write_fastphase(catalog, pmap, psum, pop_indexes, samples);
+        write_fastphase(catalog, pmap, psum);
 
     if (phase_out)
-        write_phase(catalog, pmap, psum, pop_indexes, samples);
+        write_phase(catalog, pmap, psum);
 
     if (beagle_out)
-        write_beagle(catalog, pmap, psum, pop_indexes, samples);
+        write_beagle(catalog, pmap, psum);
 
     if (beagle_phased_out)
-        write_beagle_phased(catalog, pmap, psum, pop_indexes, samples);
+        write_beagle_phased(catalog, pmap, psum);
 
     if (plink_out)
-        write_plink(catalog, pmap, psum, pop_indexes, samples);
+        write_plink(catalog, pmap, psum);
 
     if (hzar_out)
-        write_hzar(catalog, pmap, psum, pop_indexes, samples);
+        write_hzar(catalog, pmap, psum);
 
     if (treemix_out)
-        write_treemix(catalog, pmap, psum, pop_indexes, samples);
+        write_treemix(catalog, pmap, psum);
     
     if (phylip_out || phylip_var)
-        write_phylip(catalog, pmap, psum, pop_indexes, samples);
+        write_phylip(catalog, pmap, psum);
 
     if (phylip_var_all)
-        write_fullseq_phylip(catalog, pmap, psum, pop_indexes, samples);
+        write_fullseq_phylip(catalog, pmap, psum);
 
     if (vcf_haplo_out)
-        write_vcf_haplotypes(catalog, pmap, psum, samples, sample_ids);
+        write_vcf_haplotypes(catalog, pmap, psum);
 
     if (vcf_out && ordered_export)
-        write_vcf_ordered(catalog, pmap, psum, samples, sample_ids, merge_map, log_fh);
+        write_vcf_ordered(catalog, pmap, psum, merge_map, log_fh);
     else if (vcf_out)
-        write_vcf(catalog, pmap, psum, samples, sample_ids, merge_map);
+        write_vcf(catalog, pmap, psum, merge_map);
 
     //
     // Calculate and write Fst.
     //
     if (calc_fstats)
-        write_fst_stats(files, pop_indexes, catalog, pmap, psum, log_fh);
+        write_fst_stats(catalog, pmap, psum, log_fh);
 
     //
     // Output nucleotide-level genotype calls for each individual.
@@ -484,16 +701,105 @@ int main (int argc, char* argv[]) {
 
     log_fh.close();
 
+    cerr << "Populations is done.\n";
     return 0;
 }
 
+void vcfcomp_simplify_pmap (map<int, CSLocus*>& catalog, PopMap<CSLocus>* pmap) {
+
+    cerr << "DEBUG Deleting information from the pmap & catalog so that they resemble what can be retrieved from a VCF.\n";
+    // n.b. In this configuration we only have one SNP per locus so we don't have
+    // to worry about what U's imply regarding haplotypes.
+    size_t n_deleted = 0;
+    size_t n_loci = pmap->loci_cnt();
+    size_t n_samples = pmap->sample_cnt();
+    for (size_t l=0; l<n_loci; ++l) {
+        CSLocus* loc = catalog.at(pmap->rev_locus_index(l));
+        if (loc->snps.empty())
+            continue;
+        if (loc->snps.size() > 1) {
+            cerr << "Error: This requires --write_single_snp.\n";
+            throw exception();
+        }
+        size_t col = loc->snps.at(0)->col;
+        Datum** datums = pmap->locus(loc->id);
+        for (size_t s=0; s<n_samples; ++s) {
+            if (datums[s] == NULL)
+                continue;
+            if (size_t(datums[s]->len) <= col
+                    || datums[s]->model[col] == 'U'
+                    || datums[s]->obshap.empty()
+                    || strcmp(datums[s]->obshap[0], "N") == 0
+                    ) {
+                delete datums[s];
+                datums[s] = NULL;
+                --loc->cnt;
+                --loc->hcnt;
+                ++n_deleted;
+            }
+        }
+    }
+    cerr << "? Deleted " << n_deleted << " 'Datums'.\n";
+
+    set<int> myblacklist;
+    // All NULL.
+    for (auto& l : catalog) {
+        Datum** data = pmap->locus(l.second->id);
+        size_t non_null = 0;
+        for (size_t i=0; i < size_t(pmap->sample_cnt()); ++i)
+            if (data[i]!=NULL)
+                ++non_null;
+        if (non_null == 0)
+            myblacklist.insert(l.second->id);
+    }
+    // Not two alleles.
+    for (auto& l : catalog) {
+        if (l.second->snps.empty()
+                || l.second->snps[0]->rank_2 == 0
+                || l.second->snps[0]->rank_3 != 0
+                || l.second->alleles.size() != 2) {
+            myblacklist.insert(l.second->id);
+        } else {
+            // Check the actual number of alleles
+            Datum** data = pmap->locus(l.second->id);
+            set<char> seen_alleles;
+            for (size_t i=0; i<size_t(pmap->sample_cnt()); ++i) {
+                Datum* d = data[i];
+                if (d != NULL)
+                    for(char* hapl : d->obshap)
+                        seen_alleles.insert(hapl[0]);
+            }
+            if ((int((seen_alleles.count('A') || seen_alleles.count('a')))
+                    + (seen_alleles.count('C') || seen_alleles.count('c'))
+                    + (seen_alleles.count('T') || seen_alleles.count('t'))
+                    + (seen_alleles.count('G') || seen_alleles.count('g')))
+                    != 2)
+                myblacklist.insert(l.second->id);
+        }
+    }
+    // Same SNP in different loci.
+    for (auto& chr : pmap->ordered_loci) {
+        map<size_t,vector<size_t> > seen_bp0; // (bp, [loc_id's])
+        for (CSLocus* loc : chr.second)
+            if (not loc->snps.empty())
+                seen_bp0[loc->sort_bp(loc->snps[0]->col)].push_back(loc->id);
+        for (auto& bp : seen_bp0)
+            if (bp.second.size() > 1)
+                for (size_t loc_id : bp.second)
+                    myblacklist.insert(loc_id);
+    }
+    set<int> empty;
+    reduce_catalog(catalog, empty, myblacklist);
+    pmap->prune(myblacklist);
+    cerr << "? Now working on " << catalog.size() << " loci (deleted " << myblacklist.size() << " loci).\n";
+}
+
 int
 apply_locus_constraints(map<int, CSLocus *> &catalog, 
                         PopMap<CSLocus> *pmap, 
-                        map<int, pair<int, int> > &pop_indexes, 
                         ofstream &log_fh)
 {
-    uint pop_id, start_index, end_index;
+    uint pop_sthg;
     CSLocus *loc;
     Datum  **d;
 
@@ -504,9 +810,8 @@ apply_locus_constraints(map<int, CSLocus *> &catalog,
                << "# Action\tLocus ID\tChr\tBP\tColumn\tReason\n";
 
     map<int, CSLocus *>::iterator it;
-    map<int, pair<int, int> >::iterator pit;
 
-    uint pop_cnt   = pop_indexes.size();
+    uint pop_cnt   = mpopi.pops().size();
     int *pop_order = new int [pop_cnt];
 
     // Which population each sample belongs to.
@@ -518,18 +823,17 @@ apply_locus_constraints(map<int, CSLocus *> &catalog,
     // The total number of samples in each population.
     int *pop_tot   = new int [pop_cnt];
 
-    pop_id = 0;
-    for (pit = pop_indexes.begin(); pit != pop_indexes.end(); pit++) {
-        start_index = pit->second.first;
-        end_index   = pit->second.second;
-        pop_tot[pop_id]  = 0;
+    pop_sthg = 0;
+    for (size_t i_pop=0; i_pop<mpopi.pops().size(); ++i_pop) {
+        const Pop& pop = mpopi.pops()[i_pop];
+        pop_tot[pop_sthg]  = 0;
 
-        for (uint i = start_index; i <= end_index; i++) {
-            samples[i] = pop_id;
-            pop_tot[pop_id]++;
+        for (uint i = pop.first_sample; i <= pop.last_sample; i++) {
+            samples[i] = pop_sthg;
+            pop_tot[pop_sthg]++;
         }
-        pop_order[pop_id] = pit->first;
-        pop_id++;
+        pop_order[pop_sthg] = i_pop;
+        pop_sthg++;
     }
 
     for (uint i = 0; i < pop_cnt; i++)
@@ -585,14 +889,13 @@ apply_locus_constraints(map<int, CSLocus *> &catalog,
         // the members of that population.
         //
         for (uint i = 0; i < pop_cnt; i++) {
-            pct = (double) pop_cnts[i] / (double) pop_tot[i];
+            const Pop& pop = mpopi.pops()[pop_order[i]];
 
+            pct = (double) pop_cnts[i] / (double) pop_tot[i];
+            
             if (pop_cnts[i] > 0 && pct < sample_limit) {
                 //cerr << "Removing population " << pop_order[i] << " at locus: " << loc->id << "; below sample limit: " << pct << "\n";
-                start_index = pop_indexes[pop_order[i]].first;
-                end_index   = pop_indexes[pop_order[i]].second;
-
-                for (uint j  = start_index; j <= end_index; j++) {
+                for (uint j  = pop.first_sample; j <= pop.last_sample; j++) {
                     if (d[j] != NULL) {
                         delete d[j];
                         d[j] = NULL;
@@ -620,7 +923,7 @@ apply_locus_constraints(map<int, CSLocus *> &catalog,
                 log_fh << "removed_locus\t"
                        << loc->id << "\t"
                        << loc->loc.chr << "\t"
-                       << loc->sort_bp() << "\t"
+                       << loc->sort_bp() +1 << "\t"
                        << 0 << "\tfailed_population_limit\n";
         }
 
@@ -658,7 +961,6 @@ int
 prune_polymorphic_sites(map<int, CSLocus *> &catalog, 
                         PopMap<CSLocus> *pmap,
                         PopSum<CSLocus> *psum,
-                        map<int, pair<int, int> > &pop_indexes, 
                         map<int, set<int> > &whitelist, set<int> &blacklist,
                         ofstream &log_fh)
 {
@@ -670,8 +972,7 @@ prune_polymorphic_sites(map<int, CSLocus *> &catalog,
     Datum   **d;
     bool      sample_prune, maf_prune, het_prune, inc_prune;
     int       size, pruned = 0;
-    uint      pop_id, start_index, end_index;
-    
+
     if (verbose)
         log_fh << "\n#\n# List of pruned nucleotide sites\n#\n"
                << "# Action\tLocus ID\tChr\tBP\tColumn\tReason\n";
@@ -721,32 +1022,29 @@ prune_polymorphic_sites(map<int, CSLocus *> &catalog,
                 inc_prune    = false;
                 pop_prune_list.clear();
                 
-                for (int j = 0; j < psum->pop_cnt(); j++) {
-                    pop_id = psum->rev_pop_index(j);
-
-                    if (s[j]->nucs[loc->snps[i]->col].incompatible_site)
+                for (size_t p=0; p<mpopi.pops().size(); ++p) {
+                    if (s[p]->nucs[loc->snps[i]->col].incompatible_site)
                         inc_prune = true;
 
-                    else if (s[j]->nucs[loc->snps[i]->col].num_indv == 0 ||
-                             (double) s[j]->nucs[loc->snps[i]->col].num_indv / (double) psum->pop_size(pop_id) < sample_limit)
-                        pop_prune_list.push_back(pop_id);
+                    else if (s[p]->nucs[loc->snps[i]->col].num_indv == 0 ||
+                             (double) s[p]->nucs[loc->snps[i]->col].num_indv / (double) psum->pop_size(p) < sample_limit)
+                        pop_prune_list.push_back(p);
                 }
 
                 //
                 // Check how many populations have to be pruned out due to sample limit. If less than
                 // population limit, prune them; if more than population limit, mark locus for deletion.
                 //
-                if ((psum->pop_cnt() - pop_prune_list.size()) < (uint) population_limit) {
+                if ((mpopi.pops().size() - pop_prune_list.size()) < (uint) population_limit) {
                     sample_prune = true;
                 } else {
-                    for (uint j = 0; j < pop_prune_list.size(); j++) {
-                        if (s[psum->pop_index(pop_prune_list[j])]->nucs[loc->snps[i]->col].num_indv == 0) continue;
-
-                        start_index = pop_indexes[pop_prune_list[j]].first;
-                        end_index   = pop_indexes[pop_prune_list[j]].second;
-                        d           = pmap->locus(loc->id);
+                    for (size_t p : pop_prune_list) {
+                        if (s[p]->nucs[loc->snps[i]->col].num_indv == 0)
+                            continue;
 
-                        for (uint k = start_index; k <= end_index; k++) {
+                        d = pmap->locus(loc->id);
+                        const Pop& pop = mpopi.pops()[p];
+                        for (uint k = pop.first_sample; k <= pop.last_sample; k++) {
                             if (d[k] == NULL || loc->snps[i]->col >= (uint) d[k]->len) 
                                 continue;
                             if (d[k]->model != NULL) {
@@ -777,7 +1075,7 @@ prune_polymorphic_sites(map<int, CSLocus *> &catalog,
                         log_fh << "pruned_polymorphic_site\t"
                                << loc->id << "\t"
                                << loc->loc.chr << "\t"
-                               << loc->sort_bp(loc->snps[i]->col) << "\t"
+                               << loc->sort_bp(loc->snps[i]->col) +1 << "\t"
                                << loc->snps[i]->col << "\t"; 
                         if (inc_prune)
                             log_fh << "incompatible_site\n";
@@ -801,7 +1099,7 @@ prune_polymorphic_sites(map<int, CSLocus *> &catalog,
                     log_fh << "removed_locus\t"
                            << loc->id << "\t"
                            << loc->loc.chr << "\t"
-                           << loc->sort_bp() << "\t"
+                           << loc->sort_bp() +1 << "\t"
                            << 0 << "\tno_snps_remaining\n";
                 blacklist.insert(loc->id);
             }
@@ -840,14 +1138,12 @@ prune_polymorphic_sites(map<int, CSLocus *> &catalog,
                 inc_prune    = false;
                 pop_prune_list.clear();
                 
-                for (int j = 0; j < psum->pop_cnt(); j++) {
-                    pop_id = psum->rev_pop_index(j);
-
-                    if (s[j]->nucs[loc->snps[i]->col].incompatible_site)
+                for (size_t p = 0; p < mpopi.pops().size(); p++) {
+                    if (s[p]->nucs[loc->snps[i]->col].incompatible_site)
                         inc_prune = true;
-                    else if (s[j]->nucs[loc->snps[i]->col].num_indv == 0 ||
-                             (double) s[j]->nucs[loc->snps[i]->col].num_indv / (double) psum->pop_size(pop_id) < sample_limit)
-                        pop_prune_list.push_back(pop_id);
+                    else if (s[p]->nucs[loc->snps[i]->col].num_indv == 0 ||
+                             (double) s[p]->nucs[loc->snps[i]->col].num_indv / (double) psum->pop_size(p) < sample_limit)
+                        pop_prune_list.push_back(p);
                 }
 
                 //
@@ -857,14 +1153,13 @@ prune_polymorphic_sites(map<int, CSLocus *> &catalog,
                 if ((psum->pop_cnt() - pop_prune_list.size()) < (uint) population_limit) {
                     sample_prune = true;
                 } else {
-                    for (uint j = 0; j < pop_prune_list.size(); j++) {
-                        if (s[psum->pop_index(pop_prune_list[j])]->nucs[loc->snps[i]->col].num_indv == 0) continue;
-                        
-                        start_index = pop_indexes[pop_prune_list[j]].first;
-                        end_index   = pop_indexes[pop_prune_list[j]].second;
-                        d           = pmap->locus(loc->id);
-
-                        for (uint k = start_index; k <= end_index; k++) {
+                    for (size_t p : pop_prune_list) {
+                        if (s[p]->nucs[loc->snps[i]->col].num_indv == 0)
+                            continue;
+
+                        d = pmap->locus(loc->id);
+                        const Pop& pop = mpopi.pops()[p];
+                        for (uint k = pop.first_sample; k <= pop.last_sample; k++) {
                             if (d[k] == NULL || loc->snps[i]->col >= (uint) d[k]->len) 
                                 continue;
                             if (d[k]->model != NULL) {
@@ -895,7 +1190,7 @@ prune_polymorphic_sites(map<int, CSLocus *> &catalog,
                         log_fh << "pruned_polymorphic_site\t"
                                << loc->id << "\t"
                                << loc->loc.chr << "\t"
-                               << loc->sort_bp(loc->snps[i]->col) << "\t"
+                               << loc->sort_bp(loc->snps[i]->col) +1 << "\t"
                                << loc->snps[i]->col << "\t";
                         if (inc_prune)
                             log_fh << "incompatible_site\n";
@@ -919,7 +1214,7 @@ prune_polymorphic_sites(map<int, CSLocus *> &catalog,
                     log_fh << "removed_locus\t"
                            << loc->id << "\t"
                            << loc->loc.chr << "\t"
-                           << loc->sort_bp() << "\t"
+                           << loc->sort_bp() +1 << "\t"
                            << 0 << "\tno_snps_remaining\n";
                 blacklist.insert(loc->id);
             }
@@ -1104,9 +1399,9 @@ merge_shared_cutsite_loci(map<int, CSLocus *> &catalog,
             //   +Must occur on opposite strands
             //   +Must overlap according to the length of the cutsite.
             //
-            if (((cur->loc.strand == minus && next->loc.strand == plus) &&
+            if (((cur->loc.strand == strand_minus && next->loc.strand == strand_plus) &&
                  ((int) (cur->loc.bp  - next->loc.bp + 1) == renz_olap[enz])) ||
-                ((cur->loc.strand == plus  && next->loc.strand == minus) &&
+                ((cur->loc.strand == strand_plus  && next->loc.strand == strand_minus) &&
                  ((int) (next->loc.bp - cur->loc.bp  + 1) == renz_olap[enz]))) {
                 overlap++;
 
@@ -1476,7 +1771,7 @@ merge_csloci(CSLocus *sink, CSLocus *src, set<string> &phased_haplotypes)
     //
     uint bp = sink->sort_bp();
     sink->loc.bp     = bp;
-    sink->loc.strand = plus;
+    sink->loc.strand = strand_plus;
 
     //
     // 5. Adjust the length of the sequence.
@@ -1505,7 +1800,7 @@ merge_csloci(CSLocus *sink, CSLocus *src, set<string> &phased_haplotypes)
         sink->alleles[*it] = 0;
 
     // cerr << "CSLocus " << sink->id << ":\n"
-    //   << "Length: " << sink->len << "; Chr: " << sink->loc.chr << "; BP: " << sink->sort_bp() << "; strand: " << (sink->loc.strand == plus ? "+" : "-") << "\n"
+    //   << "Length: " << sink->len << "; Chr: " << sink->loc.chr << "; BP: " << sink->sort_bp() << "; strand: " << (sink->loc.strand == strand_plus ? "+" : "-") << "\n"
     //   << "  SNPs:\n";
     // for (uint j = 0; j < sink->snps.size(); j++) 
     //  cerr << "    Col: " << sink->snps[j]->col 
@@ -1727,69 +2022,6 @@ merge_datums(int sample_cnt,
     return 1;
 }
 
-int
-datum_adjust_snp_positions(map<int, pair<merget, int> > &merge_map, 
-                           CSLocus *loc, Datum *datum, 
-                           map<int, SNPRes *> &snpres)
-{
-    //
-    // We will start with the 'sink' locus, which was originally on the negative strand:
-    //   1. If the locus was shorter than the catalog locus, pad the difference.
-    //   2. Convert to positive strand: Reverse the order, complement the alleles,
-    //      alter the internal column position.
-    //
-    SNP    *snp;
-    SNPRes *snpr     = snpres[datum->id];
-    int     index    = 0;
-    int     stop_pos = renz_olap[enz] - 1;
-
-    //
-    // We know the catalog was padded since we already padded hte model call string
-    // if it was necessary when originally merging.
-    //
-    while (datum->model[index] == 'N') {
-        snp         = new SNP;
-        snp->col    = index;
-        snp->lratio = 0.0;
-        snp->rank_1 = 'N';
-        snp->type   = snp_type_unk;
-        datum->snps.push_back(snp);
-        index++;
-    }
-
-    for (int j = snpr->snps.size() - 1; j > stop_pos; j--) {
-        snp         = new SNP;
-        snp->col    = index;
-        snp->lratio = snpr->snps[j]->lratio;
-        snp->rank_1 = reverse(snpr->snps[j]->rank_1);
-        snp->rank_2 = reverse(snpr->snps[j]->rank_2);
-        snp->rank_3 = reverse(snpr->snps[j]->rank_3);
-        snp->rank_4 = reverse(snpr->snps[j]->rank_4);
-        datum->snps.push_back(snp);
-        index++;
-    }
-
-    //
-    // Now we fetch the former locus, the 'src', which was originally on the positive strand.
-    // All we have to do is adjust the column position of each SNP.
-    //
-    snpr = snpres[datum->merge_partner];
-
-    for (uint j = 0; j < snpres[datum->id]->snps.size(); j++) {
-        snp         = new SNP;
-        snp->col    = index;
-        snp->lratio = snpr->snps[j]->lratio;
-        snp->rank_1 = snpr->snps[j]->rank_1;
-        snp->rank_2 = snpr->snps[j]->rank_2;
-        snp->rank_3 = snpr->snps[j]->rank_3;
-        snp->rank_4 = snpr->snps[j]->rank_4;
-        datum->snps.push_back(snp);
-        index++;
-    }
-
-    return 0;
-}
-
 int 
 create_genotype_map(CSLocus *locus, PopMap<CSLocus> *pmap) 
 {
@@ -1892,51 +2124,8 @@ int call_population_genotypes(CSLocus *locus,
     return 0;
 }
 
-int tally_haplotype_freq(CSLocus *locus, PopMap<CSLocus> *pmap,
-                         int &total, double &max, string &freq_str) {
-
-    map<string, double> freq;
-    Datum **d = pmap->locus(locus->id);
-
-    total = 0;
-    max   = 0;
-
-    //cerr << "Examining marker: " << locus->id << "\n";
-
-    for (int i = 0; i < pmap->sample_cnt(); i++) {
-        if (d[i] == NULL) continue;
-
-        //cerr << "  Sample: " << i << "; Haplotype: " << d[i]->obshap[0] << "; Genotype: " << d[i]->gtype << "\n";
-        if (d[i]->gtype[0] != '-') {
-            freq[d[i]->gtype]++;
-            total++;
-        }
-    }
-
-    if (total == 0)
-        return 0;
-
-    double frac;
-    stringstream s;
-    char   f[id_len];
-    map<string, double>::iterator it;
-    for (it = freq.begin(); it != freq.end(); it++) {
-        frac = (double) it->second / (double) total * 100;
-        if (frac > max) max = frac;
-        sprintf(f, "(%0.1f%%);", frac);
-        s << it->first << ":" << it->second << f;
-    }
-
-    freq_str = s.str();
-
-    return 0;
-}
-
 int write_genomic(map<int, CSLocus *> &catalog, PopMap<CSLocus> *pmap) {
-    stringstream pop_name;
-    pop_name << "batch_" << batch_id << ".genomic.tsv";
-
-    string file = in_path + pop_name.str();
+    string file = out_path + out_prefix + ".genomic.tsv";
 
     ofstream fh(file.c_str(), ofstream::out);
 
@@ -2003,7 +2192,7 @@ int write_genomic(map<int, CSLocus *> &catalog, PopMap<CSLocus> *pmap) {
 
             uint k = 0;
             for (uint n = start; n < end; n++) {
-                fh << loc->id << "\t" << loc->loc.chr << "\t" << loc->sort_bp(n);
+                fh << loc->id << "\t" << loc->loc.chr << "\t" << loc->sort_bp(n) +1;
 
                 if (snp_locs.count(n) == 0) {
                     for (int j = 0; j < pmap->sample_cnt(); j++) {
@@ -2045,8 +2234,7 @@ int write_genomic(map<int, CSLocus *> &catalog, PopMap<CSLocus> *pmap) {
 }
 
 int 
-calculate_haplotype_stats(vector<pair<int, string> > &files, map<int, pair<int, int> > &pop_indexes, 
-                          map<int, CSLocus *> &catalog, PopMap<CSLocus> *pmap, PopSum<CSLocus> *psum) 
+calculate_haplotype_stats(map<int, CSLocus *> &catalog, PopMap<CSLocus> *pmap, PopSum<CSLocus> *psum)
 {
     map<string, vector<CSLocus *> >::iterator it;
     CSLocus  *loc;
@@ -2067,9 +2255,7 @@ calculate_haplotype_stats(vector<pair<int, string> > &files, map<int, pair<int,
     //
     // Open output file and print header.
     //
-    stringstream pop_name;
-    pop_name << "batch_" << batch_id << ".hapstats" << ".tsv";
-    string file = in_path + pop_name.str();
+    string file = out_path + out_prefix + ".hapstats.tsv";
 
     ofstream fh(file.c_str(), ofstream::out);
     if (fh.fail()) {
@@ -2079,19 +2265,15 @@ calculate_haplotype_stats(vector<pair<int, string> > &files, map<int, pair<int,
     fh.precision(fieldw);
     fh.setf(std::ios::fixed);
 
-    map<int, pair<int, int> >::iterator pit;
-    int start, end, pop_id;
-
     //
     // Write the population members.
     //
-    for (pit = pop_indexes.begin(); pit != pop_indexes.end(); pit++) {
-        start = pit->second.first;
-        end   = pit->second.second;
-        fh << "# " << pop_key[pit->first] << "\t";
-        for (int i = start; i <= end; i++) {
-            fh << files[i].second;
-            if (i < end) fh << ",";
+    for (auto& pop : mpopi.pops()) {
+        fh << "# " << pop.name << "\t";
+        for (size_t i = pop.first_sample; i <= pop.last_sample; i++) {
+            fh << mpopi.samples()[i].name;
+            if (i < pop.last_sample)
+                fh << ",";
         }
         fh << "\n";
     }
@@ -2114,12 +2296,9 @@ calculate_haplotype_stats(vector<pair<int, string> > &files, map<int, pair<int,
     //
     // Iterate over the members of each population.
     //
-    for (pit = pop_indexes.begin(); pit != pop_indexes.end(); pit++) {
-        start     = pit->second.first;
-        end       = pit->second.second;
-        pop_id    = pit->first;
+    for (auto& pop : mpopi.pops()) {
 
-        cerr << "Generating haplotype-level summary statistics for population '" << pop_key[pop_id] << "'\n";
+        cerr << "Generating haplotype-level summary statistics for population '" << pop.name << "'\n";
         map<string, vector<LocStat *> > genome_locstats;
 
         for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
@@ -2140,7 +2319,7 @@ calculate_haplotype_stats(vector<pair<int, string> > &files, map<int, pair<int,
 
                 // cerr << "Looking at locus " << loc->id << "\n";
 
-                l = haplotype_diversity(start, end, d);
+                l = haplotype_diversity(pop.first_sample, pop.last_sample, d);
 
                 if (l != NULL) {
                     l->loc_id = loc->id;
@@ -2175,7 +2354,7 @@ calculate_haplotype_stats(vector<pair<int, string> > &files, map<int, pair<int,
                    << l->loc_id        << "\t"
                    << it->first        << "\t"
                    << l->bp + 1        << "\t"
-                   << pop_key[pop_id]  << "\t"
+                   << pop.name         << "\t"
                    << (int) l->alleles << "\t"
                    << l->hap_cnt       << "\t"
                    << l->stat[0]       << "\t"
@@ -2303,10 +2482,7 @@ nuc_substitution_identity_max(map<string, int> &hap_index, double **hdists)
 }
 
 int 
-calculate_haplotype_divergence(vector<pair<int, string> > &files, 
-                               map<int, pair<int, int> > &pop_indexes, 
-                               map<int, vector<int> > &master_grp_members,
-                               map<int, CSLocus *> &catalog, PopMap<CSLocus> *pmap, PopSum<CSLocus> *psum) 
+calculate_haplotype_divergence(map<int, CSLocus *> &catalog, PopMap<CSLocus> *pmap, PopSum<CSLocus> *psum)
 {
     map<string, vector<CSLocus *> >::iterator it;
 
@@ -2316,22 +2492,11 @@ calculate_haplotype_divergence(vector<pair<int, string> > &files,
         cerr << "Calculating haplotype F statistics across all populations/groups...\n";
 
     //
-    // Create a list of all the groups we have.
-    //
-    map<int, vector<int> >::iterator git;
-    map<int, int> pop_grp_key;
-    for (git = master_grp_members.begin(); git != master_grp_members.end(); git++)
-        for (uint i = 0; i < git->second.size(); i++)
-            pop_grp_key[git->second[i]] = git->first;
-
-    //
     // Create a list of all the populations we have.
     //
     vector<int> pop_ids;
-
-    map<int, pair<int, int> >::iterator pit;
-    for (pit = pop_indexes.begin(); pit != pop_indexes.end(); pit++)
-        pop_ids.push_back(pit->first);
+    for (size_t i=0; i<mpopi.pops().size(); ++i)
+        pop_ids.push_back(i);
 
     //
     // Instantiate the kernel smoothing object and associated ordering object if requested.
@@ -2379,16 +2544,16 @@ calculate_haplotype_divergence(vector<pair<int, string> > &files,
                 // If this locus only appears in one population or there is only a single haplotype,
                 // do not calculate haplotype F stats.
                 //
-                if (fixed_locus(pop_indexes, d, pop_ids))
+                if (fixed_locus(d, pop_ids))
                     continue;
 
                 cnt++;
                 // cerr << "Processing locus " << loc->id << "\n";
 
-                h = haplotype_amova(pop_grp_key, pop_indexes, d, s, pop_ids);
+                h = haplotype_amova(d, s, pop_ids);
 
                 if (h != NULL) {
-                    h->stat[4] = haplotype_d_est(pop_indexes, d, s, pop_ids);
+                    h->stat[4] = haplotype_d_est(d, s, pop_ids);
 
                     h->loc_id = loc->id;
                     h->bp     = loc->sort_bp();
@@ -2429,10 +2594,7 @@ calculate_haplotype_divergence(vector<pair<int, string> > &files,
 
     cerr << "Writing haplotype F statistics... ";
 
-    stringstream pop_name;
-    pop_name << "batch_" << batch_id << ".phistats" << ".tsv";
-
-    string file = in_path + pop_name.str();
+    string file = out_path + out_prefix + ".phistats.tsv";
 
     ofstream fh(file.c_str(), ofstream::out);
     if (fh.fail()) {
@@ -2445,14 +2607,12 @@ calculate_haplotype_divergence(vector<pair<int, string> > &files,
     //
     // Write the population members.
     //
-    int start, end;
-    for (pit = pop_indexes.begin(); pit != pop_indexes.end(); pit++) {
-        start = pit->second.first;
-        end   = pit->second.second;
-        fh << "# Population " << pop_key[pit->first] << "\t";
-        for (int k = start; k <= end; k++) {
-            fh << files[k].second;
-            if (k < end) fh << ",";
+    for (auto& pop : mpopi.pops()) {
+        fh << "# Population " << pop.name << "\t";
+        for (size_t k = pop.first_sample; k <= pop.last_sample; k++) {
+            fh << mpopi.samples()[k].name;
+            if (k < pop.last_sample)
+                fh << ",";
         }
         fh << "\n";
     }
@@ -2460,12 +2620,12 @@ calculate_haplotype_divergence(vector<pair<int, string> > &files,
     //
     // Write the group members.
     //
-    for (git = grp_members.begin(); git != grp_members.end(); git++) {
-        end = git->second.size();
-        fh << "# Group " << grp_key[git->first] << "\t";
-        for (int k = 0; k < end; k++) {
-            fh << pop_key[git->second[k]];
-            if (k < end - 1) fh << ",";
+    for (auto& group : mpopi.groups()) {
+        fh << "# Group " << group.name << "\t";
+        for (size_t i_pop : group.pops) {
+            fh << mpopi.pops()[i_pop].name;
+            if (i_pop != group.pops.back())
+                fh << ",";
         }
         fh << "\n";
     }
@@ -2518,7 +2678,7 @@ calculate_haplotype_divergence(vector<pair<int, string> > &files,
             fh << batch_id            << "\t"
                << hapstats[k]->loc_id << "\t"
                << chr                 << "\t"
-               << hapstats[k]->bp     << "\t"
+               << hapstats[k]->bp +1  << "\t"
                << hapstats[k]->popcnt << "\t";
             if (log_fst_comp)
                 fh << hapstats[k]->comp[0]  << "\t"
@@ -2564,10 +2724,7 @@ calculate_haplotype_divergence(vector<pair<int, string> > &files,
 }
 
 int 
-calculate_haplotype_divergence_pairwise(vector<pair<int, string> > &files, 
-                                        map<int, pair<int, int> > &pop_indexes, 
-                                        map<int, vector<int> > &master_grp_members,
-                                        map<int, CSLocus *> &catalog, PopMap<CSLocus> *pmap, PopSum<CSLocus> *psum) 
+calculate_haplotype_divergence_pairwise(map<int, CSLocus *> &catalog, PopMap<CSLocus> *pmap, PopSum<CSLocus> *psum)
 {
     map<string, vector<CSLocus *> >::iterator it;
 
@@ -2579,16 +2736,9 @@ calculate_haplotype_divergence_pairwise(vector<pair<int, string> > &files,
     //
     // Assign all individuals to one group for the pairwise calculations.
     //
-    map<int, vector<int> >::iterator git;
-    map<int, int> pop_grp_key;
-    for (git = master_grp_members.begin(); git != master_grp_members.end(); git++)
-        for (uint i = 0; i < git->second.size(); i++)
-            pop_grp_key[git->second[i]] = 1;
-
-    map<int, pair<int, int> >::iterator pit;
     vector<int> pop_ids;
-    for (pit = pop_indexes.begin(); pit != pop_indexes.end(); pit++)
-        pop_ids.push_back(pit->first);
+    for (size_t i=0; i<mpopi.pops().size(); ++i)
+        pop_ids.push_back(i);
 
     //
     // Instantiate the kernel smoothing object if requested.
@@ -2601,19 +2751,20 @@ calculate_haplotype_divergence_pairwise(vector<pair<int, string> > &files,
         ord = new OHaplotypes<HapStat>();
     }
 
-    for (uint i = 0; i < pop_ids.size(); i++) {
-        for (uint j = i + 1; j < pop_ids.size(); j++) {
+    for (uint i = 0; i < mpopi.pops().size(); ++i) {
+        const Pop& pop_i = mpopi.pops()[i];
+        for (uint j = i + 1; j < mpopi.pops().size(); ++j) {
+            const Pop& pop_j = mpopi.pops()[j];
+            vector<int> subpop_ids;
+            subpop_ids.push_back(i);
+            subpop_ids.push_back(j);
 
             if (bootstrap_phist)
                 bs = new Bootstrap<HapStat>(5);
 
             map<string, vector<HapStat *> > genome_hapstats;
-            vector<int> subpop_ids;
-
-            subpop_ids.push_back(pop_ids[i]);
-            subpop_ids.push_back(pop_ids[j]);
 
-            cerr << "  Processing populations '" << pop_key[pop_ids[i]] << "' and '" << pop_key[pop_ids[j]] << "'\n";
+            cerr << "  Processing populations '" << pop_i.name << "' and '" << pop_j.name << "'\n";
 
             uint cnt = 0;
             for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
@@ -2645,16 +2796,16 @@ calculate_haplotype_divergence_pairwise(vector<pair<int, string> > &files,
                         // If this locus only appears in one population or there is only a single haplotype,
                         // do not calculate haplotype F stats.
                         //
-                        if (fixed_locus(pop_indexes, d, subpop_ids))
+                        if (fixed_locus(d, subpop_ids))
                             continue;
 
                         cnt++;
                         // cerr << "Processing locus " << loc->id << "\n";
 
-                        h = haplotype_amova(pop_grp_key, pop_indexes, d, s, subpop_ids);
+                        h = haplotype_amova(d, s, subpop_ids);
 
                         if (h != NULL) {
-                            h->stat[4] = haplotype_d_est(pop_indexes, d, s, subpop_ids);
+                            h->stat[4] = haplotype_d_est(d, s, subpop_ids);
 
                             h->loc_id = loc->id;
                             h->bp     = loc->sort_bp();
@@ -2690,10 +2841,7 @@ calculate_haplotype_divergence_pairwise(vector<pair<int, string> > &files,
 
             cerr << "Writing haplotype F statistics... ";
 
-            stringstream pop_name;
-            pop_name << "batch_" << batch_id << ".phistats_" << pop_key[pop_ids[i]] << "-" << pop_key[pop_ids[j]] << ".tsv";
-
-            string file = in_path + pop_name.str();
+            string file = out_path + out_prefix + ".phistats_" + pop_i.name + "-" + pop_j.name + ".tsv";
 
             ofstream fh(file.c_str(), ofstream::out);
             if (fh.fail()) {
@@ -2706,14 +2854,13 @@ calculate_haplotype_divergence_pairwise(vector<pair<int, string> > &files,
             //
             // Write the population members.
             //
-            int start, end;
-            for (uint k = 0; k < subpop_ids.size(); k++) {
-                start = pop_indexes[subpop_ids[k]].first;
-                end   = pop_indexes[subpop_ids[k]].second;
-                fh << "# Population " << pop_key[subpop_ids[k]] << "\t";
-                for (int n = start; n <= end; n++) {
-                    fh << files[n].second;
-                    if (n < end) fh << ",";
+            for (int k : subpop_ids) {
+                const Pop& pop_k = mpopi.pops()[k]; // This is [pop_i], then [pop_j].
+                fh << "# Population " << pop_k.name << "\t";
+                for (size_t n = pop_k.first_sample; n <= pop_k.last_sample; n++) {
+                    fh << mpopi.samples()[n].name;
+                    if (n < pop_k.last_sample)
+                        fh << ",";
                 }
                 fh << "\n";
             }
@@ -2760,10 +2907,10 @@ calculate_haplotype_divergence_pairwise(vector<pair<int, string> > &files,
 
                     fh << batch_id            << "\t"
                        << hapstats[k]->loc_id << "\t"
-                       << pop_key[pop_ids[i]] << "\t"
-                       << pop_key[pop_ids[j]] << "\t"
+                       << pop_i.name          << "\t"
+                       << pop_j.name          << "\t"
                        << chr                 << "\t"
-                       << hapstats[k]->bp     << "\t";
+                       << hapstats[k]->bp +1  << "\t";
                     if (log_fst_comp)
                         fh << hapstats[k]->comp[0]  << "\t"
                            << hapstats[k]->comp[1]  << "\t"
@@ -2809,19 +2956,14 @@ calculate_haplotype_divergence_pairwise(vector<pair<int, string> > &files,
 }
 
 bool
-fixed_locus(map<int, pair<int, int> > &pop_indexes, Datum **d, vector<int> &pop_ids)
+fixed_locus(Datum **d, vector<int> &pop_ids)
 {
     set<string>               loc_haplotypes;
     map<int, vector<string> > pop_haplotypes;
-    int start, end, pop_id;
-    int pop_cnt = pop_ids.size();
-
-    for (int p = 0; p < pop_cnt; p++) {
-        start  = pop_indexes[pop_ids[p]].first;
-        end    = pop_indexes[pop_ids[p]].second;
-        pop_id = pop_ids[p];
 
-        for (int i = start; i <= end; i++) {
+    for (int pop_id : pop_ids) {
+        const Pop& pop = mpopi.pops()[pop_id];
+        for (size_t i = pop.first_sample; i <= pop.last_sample; i++) {
             if (d[i] == NULL) continue;
 
             if (d[i]->obshap.size() > 2) { 
@@ -2846,10 +2988,8 @@ fixed_locus(map<int, pair<int, int> > &pop_indexes, Datum **d, vector<int> &pop_
 
     uint valid_pops = 0;
 
-    for (int p = 0; p < pop_cnt; p++) {
-        pop_id = pop_ids[p];
-
-        if (pop_haplotypes[pop_id].size() > 0) 
+    for (int pop_id : pop_ids) {
+        if (pop_haplotypes[pop_id].size() > 0)
             valid_pops++;
     }
 
@@ -2868,55 +3008,17 @@ fixed_locus(map<int, pair<int, int> > &pop_indexes, Datum **d, vector<int> &pop_
     return false;
 }
 
-inline bool
-uncalled_haplotype(const char *haplotype)
-{
-    for (const char *p = haplotype; *p != '\0'; p++)
-        if (*p == 'N' || *p == 'n')
-            return true;
-    return false;
-}
-
-inline double
-count_haplotypes_at_locus(int start, int end, Datum **d, map<string, double> &hap_cnts)
+LocStat *
+haplotype_diversity(int start, int end, Datum **d)
 {
-    double n = 0.0;
-
-    for (int i = start; i <= end; i++) {
-        if (d[i] == NULL) continue;
-
-        if (d[i]->obshap.size() > 2) { 
-            continue;
-
-        } else if (d[i]->obshap.size() == 1) {
-            if(!uncalled_haplotype(d[i]->obshap[0])) {
-                n += 2;
-                hap_cnts[d[i]->obshap[0]] += 2;
-            }
-        } else {
-            for (uint j = 0; j < d[i]->obshap.size(); j++) {
-                if(!uncalled_haplotype(d[i]->obshap[0])) {
-                    n++;
-                    hap_cnts[d[i]->obshap[j]]++;
-                }
-            }
-        }
-    }
-    
-    return n;
-}
-
-LocStat *
-haplotype_diversity(int start, int end, Datum **d)
-{
-    map<string, double>::iterator hit;
-    vector<string>      haplotypes;
-    map<string, double> hap_freq;
-    map<string, int>    hap_index;
-    double   n              = 0.0;
-    double   gene_diversity = 0.0;
-    double   hapl_diversity = 0.0;
-    LocStat *lstat;
+    map<string, double>::iterator hit;
+    vector<string>      haplotypes;
+    map<string, double> hap_freq;
+    map<string, int>    hap_index;
+    double   n              = 0.0;
+    double   gene_diversity = 0.0;
+    double   hapl_diversity = 0.0;
+    LocStat *lstat;
 
     //
     // Tabulate the haplotypes in this population.
@@ -3006,8 +3108,7 @@ haplotype_diversity(int start, int end, Datum **d)
 }
 
 HapStat *
-haplotype_amova(map<int, int> &pop_grp_key, map<int, pair<int, int> > &pop_indexes, 
-                Datum **d, LocSum **s, vector<int> &pop_ids)
+haplotype_amova(Datum **d, LocSum **s, vector<int> &pop_ids)
 {
     map<string, int>          loc_hap_index;
     vector<string>            loc_haplotypes;
@@ -3016,21 +3117,15 @@ haplotype_amova(map<int, int> &pop_grp_key, map<int, pair<int, int> > &pop_index
     vector<int>               grps;
 
     map<string, int>::iterator hit, hit_2;
-    map<int, pair<int, int> >::iterator pit;
-    int start, end, pop_id, pop_id_1;
 
     HapStat  *h;
-    int pop_cnt = pop_ids.size();
 
     //
     // Tabulate the occurences of haplotypes at this locus.
     //
-    for (int p = 0; p < pop_cnt; p++) {
-        start  = pop_indexes[pop_ids[p]].first;
-        end    = pop_indexes[pop_ids[p]].second;
-        pop_id = pop_ids[p];
-
-        for (int i = start; i <= end; i++) {
+    for (int pop_id : pop_ids) {
+        const Pop& pop = mpopi.pops()[pop_id];
+        for (size_t i = pop.first_sample; i <= pop.last_sample; i++) {
             if (d[i] == NULL) continue;
 
             if (d[i]->obshap.size() > 2) { 
@@ -3060,8 +3155,7 @@ haplotype_amova(map<int, int> &pop_grp_key, map<int, pair<int, int> > &pop_index
     // What is the total number of populations that had valid haplotypes.
     //
     double valid_pop_cnt = 0.0;
-    for (int p = 0; p < pop_cnt; p++) {
-        pop_id = pop_ids[p];
+    for (int pop_id : pop_ids) {
         if (pop_haplotypes[pop_id].size() > 0)
             valid_pop_cnt++;
     }
@@ -3071,12 +3165,11 @@ haplotype_amova(map<int, int> &pop_grp_key, map<int, pair<int, int> > &pop_index
     // representative present in each group.
     //
     set<int> uniq_grps;
-    for (pit = pop_indexes.begin(); pit != pop_indexes.end(); pit++) {
-        pop_id = pit->first;
-
+    for (size_t pop_id=0; pop_id<mpopi.pops().size(); ++pop_id) {
+        const Pop& pop = mpopi.pops()[pop_id];
         if (pop_haplotypes.count(pop_id) > 0) {
-            uniq_grps.insert(pop_grp_key[pop_id]);
-            grp_members[pop_grp_key[pop_id]].push_back(pop_id);
+            uniq_grps.insert(pop.group);
+            grp_members[pop.group].push_back(pop_id);
         }
     }
     set<int>::iterator uit;
@@ -3147,20 +3240,20 @@ haplotype_amova(map<int, int> &pop_grp_key, map<int, pair<int, int> > &pop_index
 
     for (uint g = 0; g < num_grps; g++) {
         for (uint r = 0; r < grp_members[grps[g]].size(); r++) {
-            pop_id_1 = grp_members[grps[g]][r];
+            int pop_id_1 = grp_members[grps[g]][r];
             tot_cnt += (double) pop_haplotypes[pop_id_1].size();
         }
     }
     for (uint g = 0; g < num_grps; g++) {
         grp_cnt = 0.0;
         for (uint r = 0; r < grp_members[grps[g]].size(); r++) {
-            pop_id_1 = grp_members[grps[g]][r];
+            int pop_id_1 = grp_members[grps[g]][r];
             grp_cnt += (double) pop_haplotypes[pop_id_1].size();
         }
 
         a = 0.0;
         for (uint r = 0; r < grp_members[grps[g]].size(); r++) {
-            pop_id_1 = grp_members[grps[g]][r];
+            int pop_id_1 = grp_members[grps[g]][r];
             a += (double) (pop_haplotypes[pop_id_1].size() * pop_haplotypes[pop_id_1].size()) / grp_cnt;
         }
         s_g += a;
@@ -3176,7 +3269,7 @@ haplotype_amova(map<int, int> &pop_grp_key, map<int, pair<int, int> > &pop_index
         a = 0.0;
         for (uint g = 0; g < num_grps; g++) {
             for (uint r = 0; r < grp_members[grps[g]].size(); r++) {
-                pop_id_1 = grp_members[grps[g]][r];
+                int pop_id_1 = grp_members[grps[g]][r];
                 a += ((double) (pop_haplotypes[pop_id_1].size() * pop_haplotypes[pop_id_1].size()) / tot_cnt);
             }
         }
@@ -3190,7 +3283,7 @@ haplotype_amova(map<int, int> &pop_grp_key, map<int, pair<int, int> > &pop_index
         for (uint g = 0; g < num_grps; g++) {
             a = 0.0;
             for (uint r = 0; r < grp_members[grps[g]].size(); r++) {
-                pop_id_1 = grp_members[grps[g]][r];
+                int pop_id_1 = grp_members[grps[g]][r];
                 a += pop_haplotypes[pop_id_1].size();
             }
             b += ((a * a) / tot_cnt);
@@ -3492,7 +3585,7 @@ amova_ssd_ag(vector<int> &grps, map<int, vector<int> > &grp_members,
 }
 
 double
-haplotype_d_est(map<int, pair<int, int> > &pop_indexes, Datum **d, LocSum **s, vector<int> &pop_ids)
+haplotype_d_est(Datum **d, LocSum **s, vector<int> &pop_ids)
 {
     //
     // Calculate D_est, fixation index, as described by 
@@ -3507,24 +3600,19 @@ haplotype_d_est(map<int, pair<int, int> > &pop_indexes, Datum **d, LocSum **s, v
     map<int, double>               pop_totals;
 
     map<string, double>::iterator it;
-    int start, end, pop_id;
 
     uint pop_cnt = pop_ids.size();
 
     //
     // Tabulate the occurences of haplotypes at this locus.
     //
-    for (uint p = 0; p < pop_cnt; p++) {
-        start  = pop_indexes[pop_ids[p]].first;
-        end    = pop_indexes[pop_ids[p]].second;
-        pop_id = pop_ids[p];
-
-        for (int i = start; i <= end; i++) {
-            if (d[i] == NULL) continue;
-
-            if (d[i]->obshap.size() > 2) { 
+    for (int pop_id : pop_ids) {
+        const Pop& pop = mpopi.pops()[pop_id];
+        for (size_t i = pop.first_sample; i <= pop.last_sample; i++) {
+            if (d[i] == NULL) {
+                continue;
+            } else if (d[i]->obshap.size() > 2) {
                 continue;
-
             } else if (d[i]->obshap.size() == 1) {
                 loc_haplotypes[d[i]->obshap[0]]         += 2;
                 pop_haplotypes[pop_id][d[i]->obshap[0]] += 2;
@@ -3547,8 +3635,7 @@ haplotype_d_est(map<int, pair<int, int> > &pop_indexes, Datum **d, LocSum **s, v
 
         double freq_sum_sq = 0.0;
         double freq_sq_sum = 0.0;
-        for (uint p = 0; p < pop_cnt; p++) {
-            pop_id = pop_ids[p];
+        for (int pop_id : pop_ids) {
             freq_sum_sq += (pop_haplotypes[pop_id][it->first] / pop_totals[pop_id]);
             freq_sq_sum += pow((pop_haplotypes[pop_id][it->first] / pop_totals[pop_id]), 2);
         }
@@ -3560,9 +3647,7 @@ haplotype_d_est(map<int, pair<int, int> > &pop_indexes, Datum **d, LocSum **s, v
     double y = 0.0;
 
     for (it = loc_haplotypes.begin(); it != loc_haplotypes.end(); it++) {
-        for (uint p = 0; p < pop_cnt; p++) {
-            pop_id = pop_ids[p];
-
+        for (int pop_id : pop_ids) {
             y += (pop_haplotypes[pop_id][it->first] * (pop_haplotypes[pop_id][it->first] - 1)) /
                 (pop_totals[pop_id] * (pop_totals[pop_id] - 1));
         }
@@ -3574,8 +3659,7 @@ haplotype_d_est(map<int, pair<int, int> > &pop_indexes, Datum **d, LocSum **s, v
 }
 
 int 
-calculate_summary_stats(vector<pair<int, string> > &files, map<int, pair<int, int> > &pop_indexes, 
-                        map<int, CSLocus *> &catalog, PopMap<CSLocus> *pmap, PopSum<CSLocus> *psum) 
+calculate_summary_stats(map<int, CSLocus *> &catalog, PopMap<CSLocus> *pmap, PopSum<CSLocus> *psum)
 {
     map<string, vector<CSLocus *> >::iterator it;
     CSLocus  *loc;
@@ -3755,10 +3839,7 @@ calculate_summary_stats(vector<pair<int, string> > &files, map<int, pair<int, in
         fis_mean_all[j]      = fis_mean_all[j]      / n_all[j];
     }
 
-    stringstream pop_name;
-    pop_name << "batch_" << batch_id << ".sumstats" << ".tsv";
-
-    string file = in_path + pop_name.str();
+    string file = out_path + out_prefix + ".sumstats.tsv";
 
     ofstream fh(file.c_str(), ofstream::out);
     if (fh.fail()) {
@@ -3769,18 +3850,15 @@ calculate_summary_stats(vector<pair<int, string> > &files, map<int, pair<int, in
     fh.setf(std::ios::fixed);
 
     double p_freq;
-    int start, end;
     //
     // Write the population members.
     //
-    map<int, pair<int, int> >::iterator pit;
-    for (pit = pop_indexes.begin(); pit != pop_indexes.end(); pit++) {
-        start = pit->second.first;
-        end   = pit->second.second;
-        fh << "# " << pit->first << "\t";
-        for (int i = start; i <= end; i++) {
-            fh << files[i].second;
-            if (i < end) fh << ",";
+    for (auto& pop : mpopi.pops()) {
+        fh << "# " << pop.name << "\t";
+        for (size_t i = pop.first_sample; i <= pop.last_sample; i++) {
+            fh << mpopi.samples()[i].name;
+            if (i < pop.last_sample)
+                fh << ",";
         }
         fh << "\n";
     }
@@ -3827,14 +3905,15 @@ calculate_summary_stats(vector<pair<int, string> > &files, map<int, pair<int, in
 
                     for (int j = 0; j < pop_cnt; j++) {
 
-                        if (s[j]->nucs[i].num_indv == 0) continue;
+                        if (s[j]->nucs[i].num_indv == 0)
+                            continue;
 
                         fh << batch_id << "\t"
                            << loc->id << "\t"
                            << loc->loc.chr << "\t"
                            << loc->sort_bp(i) + 1 << "\t"
                            << i << "\t"
-                           << pop_key[psum->rev_pop_index(j)] << "\t";
+                           << mpopi.pops()[j].name << "\t";
 
                         //
                         // Output the p and q alleles in the same order in each population.
@@ -3932,10 +4011,7 @@ calculate_summary_stats(vector<pair<int, string> > &files, map<int, pair<int, in
 
     fh.close();
 
-    pop_name.str("");
-    pop_name << "batch_" << batch_id << ".sumstats_summary" << ".tsv";
-
-    file = in_path + pop_name.str();
+    file = out_path + out_prefix + ".sumstats_summary.tsv";
 
     fh.open(file.c_str(), ofstream::out);
 
@@ -3984,7 +4060,7 @@ calculate_summary_stats(vector<pair<int, string> > &files, map<int, pair<int, in
     }
 
     for (int j = 0; j < pop_cnt; j++)
-        fh << pop_key[psum->rev_pop_index(j)] << "\t" 
+        fh << mpopi.pops()[j].name << "\t"
            << private_cnt[j]         << "\t"
            << num_indv_mean[j]       << "\t"
            << num_indv_var[j]        << "\t"
@@ -4044,7 +4120,7 @@ calculate_summary_stats(vector<pair<int, string> > &files, map<int, pair<int, in
        << "StdErr\n";
 
     for (int j = 0; j < pop_cnt; j++) {
-        fh << pop_key[psum->rev_pop_index(j)] << "\t" 
+        fh << mpopi.pops()[j].name << "\t"
            << private_cnt[j]             << "\t"
            << n_all[j]                   << "\t"
            << n[j]                       << "\t"
@@ -4122,20 +4198,16 @@ calculate_summary_stats(vector<pair<int, string> > &files, map<int, pair<int, in
 }
 
 int 
-write_fst_stats(vector<pair<int, string> > &files, map<int, pair<int, int> > &pop_indexes, 
-                map<int, CSLocus *> &catalog, PopMap<CSLocus> *pmap, PopSum<CSLocus> *psum, ofstream &log_fh) 
+write_fst_stats(map<int, CSLocus *> &catalog, PopMap<CSLocus> *pmap, PopSum<CSLocus> *psum, ofstream &log_fh)
 {
     //
     // We want to iterate over each pair of populations and calculate Fst at each 
     // nucleotide of each locus.
     //
-    vector<double> means;
-    vector<int>    pops;
-    map<int, pair<int, int> >::iterator pit;
-    for (pit = pop_indexes.begin(); pit != pop_indexes.end(); pit++)
-        pops.push_back(pit->first);
+    if (mpopi.pops().size() == 1)
+        return 0;
 
-    if (pops.size() == 1) return 0;
+    vector<double> means;
 
     //
     // Instantiate the kernel smoothing object if requested.
@@ -4143,22 +4215,20 @@ write_fst_stats(vector<pair<int, string> > &files, map<int, pair<int, int> > &po
     OPopPair<PopPair>  *ord = new OPopPair<PopPair>(psum, log_fh);
     KSmooth<PopPair>   *ks;
     Bootstrap<PopPair> *bs;
-    if (kernel_smoothed && loci_ordered)
+    if (kernel_smoothed && loci_ordered) {
+        cerr << "Instantiating the kernel smoothing window, using sigma = " << sigma << " with a sliding window size of " << 6 * sigma << "\n";
         ks  = new KSmooth<PopPair>(2);
+    }
 
-    for (uint i = 0; i < pops.size(); i++) {
-
-        for (uint j = i + 1; j < pops.size(); j++) {
-            int pop_1 = pops[i];
-            int pop_2 = pops[j];
+    for (uint pop_1 = 0; pop_1 < mpopi.pops().size(); pop_1++) {
+        const Pop& pop_1p = mpopi.pops()[pop_1];
+        for (uint pop_2 = pop_1 + 1; pop_2 < mpopi.pops().size(); pop_2++) {
+            const Pop& pop_2p = mpopi.pops()[pop_2];
 
             double sum = 0.0;
             double cnt = 0.0;
 
-            stringstream pop_name;
-            pop_name << "batch_" << batch_id << ".fst_" << pop_key[pop_1] << "-" << pop_key[pop_2] << ".tsv";
-
-            string   file = in_path + pop_name.str();
+            string file = out_path + out_prefix + ".fst_" + pop_1p.name + "-" + pop_2p.name + ".tsv";
             ofstream fh(file.c_str(), ofstream::out);
             if (fh.fail()) {
                 cerr << "Error opening Fst output file '" << file << "'\n";
@@ -4167,7 +4237,7 @@ write_fst_stats(vector<pair<int, string> > &files, map<int, pair<int, int> > &po
             fh.precision(fieldw);
             fh.setf(std::ios::fixed);
 
-            cerr << "Calculating Fst for populations '" << pop_key[pop_1] << "' and '" << pop_key[pop_2] << "' and writing it to file, '" << file << "'\n";
+            cerr << "Calculating Fst for populations '" << pop_1p.name << "' and '" << pop_2p.name << "' and writing it to file, '" << file << "'\n";
 
             fh << "# Batch ID" << "\t"
                << "Locus ID"   << "\t"
@@ -4323,10 +4393,10 @@ write_fst_stats(vector<pair<int, string> > &files, map<int, pair<int, int> > &po
 
                     fh << batch_id          << "\t"
                        << pairs[i]->loc_id  << "\t"
-                       << pop_key[pop_1]    << "\t"
-                       << pop_key[pop_2]    << "\t"
+                       << pop_1p.name       << "\t"
+                       << pop_2p.name       << "\t"
                        << chr               << "\t"
-                       << pairs[i]->bp      << "\t"
+                       << pairs[i]->bp +1   << "\t"
                        << pairs[i]->col     << "\t"
                        << pairs[i]->pi      << "\t"
                        << pairs[i]->fst     << "\t"
@@ -4372,10 +4442,10 @@ write_fst_stats(vector<pair<int, string> > &files, map<int, pair<int, int> > &po
                     delete pairs[i];
                 }
             }
-            cerr << "Pop 1: " << pop_key[pop_1] << "; Pop 2: " << pop_key[pop_2] << "; mean Fst: " << (sum / cnt) << "\n";
+            cerr << "Pop 1: " << pop_1p.name << "; Pop 2: " << pop_2p.name << "; mean Fst: " << (sum / cnt) << "\n";
             means.push_back(sum / cnt);
 
-            cerr << "Pooled populations '" << pop_key[pop_1] << "' and '" << pop_key[pop_2] << "' contained: " << ord->incompatible_loci << " incompatible loci; " 
+            cerr << "Pooled populations '" << pop_1p.name << "' and '" << pop_2p.name << "' contained: " << ord->incompatible_loci << " incompatible loci; "
                  << ord->multiple_loci << " nucleotides covered by more than one RAD locus.\n";
             fh.close();
 
@@ -4387,10 +4457,7 @@ write_fst_stats(vector<pair<int, string> > &files, map<int, pair<int, int> > &po
     //
     // Write out the mean Fst measure of each pair of populations.
     //
-    stringstream pop_name;
-    pop_name << "batch_" << batch_id << ".fst_summary.tsv";
-
-    string file = in_path + pop_name.str();
+    string file = out_path + out_prefix + ".fst_summary.tsv";
     ofstream fh(file.c_str(), ofstream::out);
 
     if (fh.fail()) {
@@ -4401,18 +4468,18 @@ write_fst_stats(vector<pair<int, string> > &files, map<int, pair<int, int> > &po
     //
     // Write out X-axis header.
     //
-    for (uint i = 0; i < pops.size(); i++)
-        fh << "\t" << pop_key[pops[i]];
+    for (auto& pop : mpopi.pops())
+        fh << "\t" << pop.name;
     fh << "\n";
 
     uint n = 0;
-    for (uint i = 0; i < pops.size() - 1; i++) {
-        fh << pop_key[pops[i]];
+    for (uint i = 0; i < mpopi.pops().size() - 1; i++) {
+        fh << mpopi.pops()[i].name;
 
         for (uint k = 0; k <= i; k++)
             fh << "\t";
 
-        for (uint j = i + 1; j < pops.size(); j++) {
+        for (uint j = i + 1; j < mpopi.pops().size(); j++) {
             fh << "\t" << means[n];
             n++;
         }
@@ -4506,7 +4573,7 @@ kernel_smoothed_popstats(map<int, CSLocus *> &catalog, PopMap<CSLocus> *pmap, Po
         if (bootstrap_pifis) bs->add_data(sites);
     }
 
-    cerr << "    Population '" << pop_key[pop_id] << "' contained " << ord->multiple_loci << " nucleotides covered by more than one RAD locus.\n";
+    cerr << "    Population '" << mpopi.pops()[pop_id].name << "' contained " << ord->multiple_loci << " nucleotides covered by more than one RAD locus.\n";
 
     for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
         if (bootstrap_pifis)
@@ -4875,17 +4942,9 @@ bootstrap_approximate_pval(int snp_cnt, double stat, map<int, vector<double> > &
 }
 
 int
-write_generic(map<int, CSLocus *> &catalog, PopMap<CSLocus> *pmap, 
-              map<int, string> &samples, bool write_gtypes)
+write_generic(map<int, CSLocus *> &catalog, PopMap<CSLocus> *pmap, bool write_gtypes)
 {
-    stringstream pop_name;
-    pop_name << "batch_" << batch_id;
-    if (write_gtypes)
-        pop_name << ".genotypes.tsv";
-    else 
-        pop_name << ".haplotypes.tsv";
-
-    string file = in_path + pop_name.str();
+    string file = out_path + out_prefix + (write_gtypes ? ".genotypes.tsv" : ".haplotypes.tsv");
 
     ofstream fh(file.c_str(), ofstream::out);
 
@@ -4914,7 +4973,7 @@ write_generic(map<int, CSLocus *> &catalog, PopMap<CSLocus> *pmap,
     fh << "Cnt\t";
 
     for (int i = 0; i < pmap->sample_cnt(); i++) {
-        fh << samples[pmap->rev_sample_index(i)];
+        fh << mpopi.samples()[i].name;
         if (i < pmap->sample_cnt() - 1) 
             fh << "\t";
     }
@@ -4936,7 +4995,7 @@ write_generic(map<int, CSLocus *> &catalog, PopMap<CSLocus> *pmap,
             if (loc->annotation.length() > 0)
                 id << "\t" << loc->id << "\t" << loc->annotation;
             else if (strlen(loc->loc.chr) > 0)
-                id << "\t" << loc->id << "\t" << loc->loc.chr << "_" << loc->loc.bp;
+                id << "\t" << loc->id << "\t" << loc->loc.chr << "_" << loc->loc.bp +1;
             else
                 id << "\t" << loc->id << "\t";
         }
@@ -4954,7 +5013,7 @@ write_generic(map<int, CSLocus *> &catalog, PopMap<CSLocus> *pmap,
 
             if (d[i] == NULL)
                 fh << "-";
-            else
+            else {
                 if (write_gtypes) {
                     fh << d[i]->gtype;
                 } else {
@@ -4964,6 +5023,7 @@ write_generic(map<int, CSLocus *> &catalog, PopMap<CSLocus> *pmap,
                     obshap = obshap.substr(0, obshap.length()-1);
                     fh << obshap;
                 }
+            }
         }
 
         fh << "\n";
@@ -4974,3863 +5034,129 @@ write_generic(map<int, CSLocus *> &catalog, PopMap<CSLocus> *pmap,
     return 0;
 }
 
-int 
-write_sql(map<int, CSLocus *> &catalog, PopMap<CSLocus> *pmap) 
-{
-    stringstream pop_name;
-    pop_name << "batch_" << batch_id << ".markers.tsv";
-    string file = in_path + pop_name.str();
-
-    cerr << "Writing SQL markers file to '" << file << "'\n";
+int load_marker_list(string path, set<int> &list) {
+    char     line[id_len];
+    ifstream fh(path.c_str(), ifstream::in);
 
-    ofstream fh(file.c_str(), ofstream::out);
     if (fh.fail()) {
-        cerr << "Error opening markers SQL file '" << file << "'\n";
+        cerr << "Error opening white/black list file '" << path << "'\n";
         exit(1);
     }
-    fh.precision(fieldw);
-    fh.setf(std::ios::fixed);
-
-    fh << "# SQL ID"            << "\t" 
-       << "Batch ID"            << "\t" 
-       << "Catalog Locus ID"    << "\t" 
-       << "\t"
-       << "Total Genotypes"     << "\t"
-       << "Max"                 << "\t"
-       << "Genotype Freqs"      << "\t"
-       << "F"                   << "\t"
-       << "Mean Log Likelihood" << "\t"
-       << "Genotype Map"        << "\t"
-       << "\n";
 
-    map<int, CSLocus *>::iterator it;
-    CSLocus *loc;
-    stringstream gtype_map;
+    int   marker;
+    char *p, *e;
 
-    for (it = catalog.begin(); it != catalog.end(); it++) {
-        loc = it->second;
+    while (fh.good()) {
+        fh.getline(line, id_len);
 
-        string freq  = "";
-        double max   = 0.0;
-        int    total = 0;
-        gtype_map.str("");
+        if (strlen(line) == 0) continue;
 
-        if (loc->marker.length() > 0) {
-            tally_haplotype_freq(loc, pmap, total, max, freq);
+        //
+        // Skip commented lines.
+        //
+        for (p = line; isspace(*p) && *p != '\0'; p++);
+        if (*p == '#') continue;
 
-            //
-            // Record the haplotype to genotype map.
-            //
-            map<string, string>::iterator j;
-            for (j = loc->gmap.begin(); j != loc->gmap.end(); j++)
-                gtype_map << j->first << ":" << j->second << ";";
-        }
+        marker = (int) strtol(line, &e, 10);
 
-        fh << 0 << "\t" 
-           << batch_id << "\t" 
-           << loc->id  << "\t" 
-           << "\t"              // Marker
-           << total    << "\t"
-           << max      << "\t"
-           << freq     << "\t"
-           << loc->f   << "\t"
-           << loc->lnl << "\t"
-           << gtype_map.str() << "\t"
-           << "\n";
+        if (*e == '\0')
+            list.insert(marker);
     }
 
     fh.close();
 
-    return 0;
-}
-
-int 
-write_fasta(map<int, CSLocus *> &catalog, PopMap<CSLocus> *pmap, map<int, string> &samples, vector<int> &sample_ids) 
-{
-    //
-    // Write a FASTA file containing each allele from each locus from 
-    // each sample in the population.
-    //
-    stringstream pop_name;
-    pop_name << "batch_" << batch_id << ".fa";
-    string file = in_path + pop_name.str();
-
-    cerr << "Writing population alleles to FASTA file '" << file << "'\n";
-
-    ofstream fh(file.c_str(), ofstream::out);
-
-    if (fh.fail()) {
-        cerr << "Error opening FASTA file '" << file << "'\n";
+    if (list.size() == 0) {
+        cerr << "Unable to load any markers from '" << path << "'\n";
         exit(1);
     }
 
-    map<string, vector<CSLocus *> >::iterator it;
-    CSLocus *loc;
-    Datum  **d;
-    char    *seq;
-
-    for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
-        for (uint pos = 0; pos < it->second.size(); pos++) {
-            loc = it->second[pos];
-            d   = pmap->locus(loc->id);
-            seq = new char[loc->len + 1];
-            strcpy(seq, loc->con);
-
-            for (int j = 0; j < pmap->sample_cnt(); j++) {
-                if (d[j] == NULL) 
-                    continue;
-
-                for (uint k = 0; k < d[j]->obshap.size(); k++) {
-
-                    for (uint i = 0; i < loc->snps.size(); i++) {
-                        uint col = loc->snps[i]->col;
-                        seq[col] = col < loc->len ? d[j]->obshap[k][i] : loc->con[col];
-                    }
-
-                    fh << ">CLocus_" << loc->id 
-                       << "_Sample_" << pmap->rev_sample_index(j)
-                       << "_Locus_"  << d[j]->id 
-                       << "_Allele_" << k
-                       << " ["       << samples[pmap->rev_sample_index(j)];
-
-                    if (strcmp(loc->loc.chr, "un") != 0)
-                        fh << "; " << loc->loc.chr << ", " << loc->sort_bp() + 1 << ", " << (loc->loc.strand == plus ? "+" : "-");
-                    fh << "]\n"
-                       << seq << "\n";
-                }
-            }
-            delete [] seq;
-        }
-    }
-
-    fh.close();
-
     return 0;
 }
 
-int 
-write_strict_fasta(map<int, CSLocus *> &catalog, PopMap<CSLocus> *pmap, map<int, string> &samples, vector<int> &sample_ids) 
-{
-    //
-    // Write a FASTA file containing each allele from each locus from 
-    // each sample in the population.
-    //
-    stringstream pop_name;
-    pop_name << "batch_" << batch_id << ".strict.fa";
-    string file = in_path + pop_name.str();
-
-    cerr << "Writing strict population alleles to FASTA file '" << file << "'\n";
-
-    ofstream fh(file.c_str(), ofstream::out);
+int load_marker_column_list(string path, map<int, set<int> > &list) {
+    char     line[id_len];
+    ifstream fh(path.c_str(), ifstream::in);
 
     if (fh.fail()) {
-        cerr << "Error opening strict FASTA file '" << file << "'\n";
+        cerr << "Error opening white/black list file '" << path << "'\n";
         exit(1);
     }
 
-    map<string, vector<CSLocus *> >::iterator it;
-    CSLocus *loc;
-    Datum  **d;
-    char    *seq;
-
-    for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
-        for (uint pos = 0; pos < it->second.size(); pos++) {
-            loc = it->second[pos];
-            d   = pmap->locus(loc->id);
-            seq = new char[loc->len + 1];
-            strcpy(seq, loc->con);
+    vector<string> parts;
+    uint  marker, col;
+    char *p, *e;
 
-            for (int j = 0; j < pmap->sample_cnt(); j++) {
-                if (d[j] == NULL) 
-                    continue;
-                if (d[j]->obshap.size() > 2) 
-                    continue;
+    uint line_num = 1;
+    while (fh.good()) {
+        fh.getline(line, id_len);
 
-                if (d[j]->obshap.size() == 1) {
+        if (strlen(line) == 0) continue;
 
-                    for (uint i = 0; i < loc->snps.size(); i++) {
-                        uint col = loc->snps[i]->col;
-                        seq[col] = col < loc->len ? d[j]->obshap[0][i] : loc->con[col];
-                    }
+        //
+        // Skip commented lines.
+        //
+        for (p = line; isspace(*p) && *p != '\0'; p++);
+        if (*p == '#') continue;
 
-                    fh << ">CLocus_" << loc->id 
-                       << "_Sample_" << pmap->rev_sample_index(j)
-                       << "_Locus_"  << d[j]->id 
-                       << "_Allele_" << 0
-                       << " ["       << samples[pmap->rev_sample_index(j)];
-                    if (strcmp(loc->loc.chr, "un") != 0)
-                        fh << "; " << loc->loc.chr << ", " << loc->sort_bp() + 1 << ", " << (loc->loc.strand == plus ? "+" : "-");
-                    fh << "]\n"
-                       << seq << "\n";
-
-                    fh << ">CLocus_" << loc->id 
-                       << "_Sample_" << pmap->rev_sample_index(j)
-                       << "_Locus_"  << d[j]->id 
-                       << "_Allele_" << 1
-                       << " ["       << samples[pmap->rev_sample_index(j)];
-                    if (strcmp(loc->loc.chr, "un") != 0)
-                        fh << "; " << loc->loc.chr << ", " << loc->sort_bp() + 1 << ", " << (loc->loc.strand == plus ? "+" : "-");
-                    fh << "]\n"
-                       << seq << "\n";
+        //
+        // Parse the whitelist, we expect:
+        // <marker>[<tab><snp column>]
+        //
+        parse_tsv(line, parts);
 
-                } else {
-                    for (uint k = 0; k < d[j]->obshap.size(); k++) {
-                        for (uint i = 0; i < loc->snps.size(); i++) {
-                            uint col = loc->snps[i]->col;
-                            seq[col] = col < loc->len ? d[j]->obshap[k][i] : loc->con[col];
-                        }
+        if (parts.size() > 2) {
+            cerr << "Too many columns in whitelist " << path << "' at line " << line_num << "\n";
+            exit(1);
 
-                        fh << ">CLocus_" << loc->id 
-                           << "_Sample_" << pmap->rev_sample_index(j)
-                           << "_Locus_"  << d[j]->id 
-                           << "_Allele_" << k
-                           << " ["       << samples[pmap->rev_sample_index(j)];
-                        if (strcmp(loc->loc.chr, "un") != 0)
-                            fh << "; " << loc->loc.chr << ", " << loc->sort_bp() + 1 << ", " << (loc->loc.strand == plus ? "+" : "-");
-                        fh << "]\n"
-                           << seq << "\n";
-                    }
-                }
+        } else if (parts.size() == 2) {
+            marker = (int) strtol(parts[0].c_str(), &e, 10);
+            if (*e != '\0') {
+                cerr << "Unable to parse whitelist, '" << path << "' at line " << line_num << "\n";
+                exit(1);
+            }
+            col = (int) strtol(parts[1].c_str(), &e, 10);
+            if (*e != '\0') {
+                cerr << "Unable to parse whitelist, '" << path << "' at line " << line_num << "\n";
+                exit(1);
             }
+            list[marker].insert(col);
 
-            delete [] seq;
+        } else {
+            marker = (int) strtol(parts[0].c_str(), &e, 10);
+            if (*e != '\0') {
+                cerr << "Unable to parse whitelist, '" << path << "' at line " << line << "\n";
+                exit(1);
+            }
+            list.insert(make_pair(marker, std::set<int>()));
         }
+
+        line_num++;
     }
 
     fh.close();
 
-    return 0;
-}
-
-int 
-write_vcf_ordered(map<int, CSLocus *> &catalog, 
-                  PopMap<CSLocus> *pmap, PopSum<CSLocus> *psum, 
-                  map<int, string> &samples, vector<int> &sample_ids,
-                  map<int, pair<merget, int> > &merge_map, ofstream &log_fh) 
-{
-    //
-    // Write a VCF file as defined here: http://www.1000genomes.org/node/101
-    //
-    stringstream pop_name;
-    pop_name << "batch_" << batch_id << ".vcf";
-    string file = in_path + pop_name.str();
-
-    ofstream fh(file.c_str(), ofstream::out);
-
-    if (fh.fail()) {
-        cerr << "Error opening VCF file '" << file << "'\n";
-        exit(1);
+    if (list.size() == 0) {
+        cerr << "Unable to load any markers from '" << path << "'\n";
+        help();
     }
 
-    //
-    // Load SNP data so that model likelihoods can be output to VCF file.
-    //
-    cerr << "In preparation for VCF export, loading SNP data for " << samples.size() << " samples.\n";
-
-    populate_snp_calls(catalog, pmap, samples, sample_ids, merge_map);
-
-    cerr << "Writing population data to VCF file '" << file << "'\n";
-
-    log_fh << "\n#\n# Generating SNP-based VCF export.\n#\n";
-
-    //
-    // Obtain the current date.
-    //
-    time_t     rawtime;
-    struct tm *timeinfo;
-    char       date[32];
-    time(&rawtime);
-    timeinfo = localtime(&rawtime);
-    strftime(date, 32, "%Y%m%d", timeinfo);
-
-    //
-    // Output the header.
-    //
-    fh << "##fileformat=VCFv4.0\n"
-       << "##fileDate=" << date << "\n"
-       << "##source=\"Stacks v" << VERSION << "\"\n"
-       << "##INFO=<ID=NS,Number=1,Type=Integer,Description=\"Number of Samples With Data\">\n"
-       << "##INFO=<ID=AF,Number=.,Type=Float,Description=\"Allele Frequency\">\n"
-       << "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n"
-       << "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\n"
-       << "##FORMAT=<ID=AD,Number=1,Type=Integer,Description=\"Allele Depth\">\n"
-       << "##FORMAT=<ID=GL,Number=.,Type=Float,Description=\"Genotype Likelihood\">\n"
-       << "#CHROM" << "\t" << "POS" << "\t" << "ID" << "\t" << "REF" << "\t" << "ALT" << "\t" 
-       << "QUAL" << "\t" << "FILTER" << "\t" << "INFO" << "\t" << "FORMAT";
-
-    for (int i = 0; i < pmap->sample_cnt(); i++)
-        fh << "\t" << samples[pmap->rev_sample_index(i)];
-    fh << "\n";    
-
-    map<string, vector<CSLocus *> >::iterator it;
-    CSLocus *loc;
-    Datum  **d;
-    int      gt_1, gt_2, dp_1, dp_2;
-    char     p_allele, q_allele, p_str[32], q_str[32];
-    uint16_t col;
-    int      snp_index;
-
-    //
-    // We need to order the SNPs taking into account overlapping loci.
-    //
-    OLocTally<NucTally> *ord = new OLocTally<NucTally>(psum, log_fh);
-
-    for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
-        vector<NucTally *> sites;
-        ord->order(sites, it->second);
-
-        for (uint pos = 0; pos < sites.size(); pos++) {
-            if (catalog.count(sites[pos]->loc_id) == 0) {
-                cerr << "Unable to find locus id " << sites[pos]->loc_id << "\n";
-                continue;
-            }
-            loc = catalog[sites[pos]->loc_id];
-            col = sites[pos]->col;
-
-            sprintf(p_str, "%0.3f", sites[pos]->p_freq);
-            sprintf(q_str, "%0.3f", 1 - sites[pos]->p_freq);
-
-            //
-            // If on the negative strand, complement the alleles.
-            //
-            p_allele = loc->loc.strand == minus ? reverse(sites[pos]->p_allele) : sites[pos]->p_allele;
-            q_allele = loc->loc.strand == minus ? reverse(sites[pos]->q_allele) : sites[pos]->q_allele;
-
-            fh << loc->loc.chr << "\t" 
-               << loc->sort_bp(col) + 1 << "\t" 
-               << loc->id    << "\t"
-               << p_allele   << "\t"            // REFerence allele
-               << q_allele   << "\t"            // ALTernate allele
-               << "."        << "\t"            // QUAL
-               << "PASS"     << "\t"            // FILTER
-               << "NS="      << sites[pos]->num_indv << ";"   // INFO
-               << "AF="      << p_str << "," << q_str << "\t" // INFO
-               << "GT:DP:AD:GL";                // FORMAT
-
-            snp_index = loc->snp_index(col);
-            if (snp_index < 0) {
-                cerr << "Warning, unable to locate SNP call in column " << col << " for catalog locus " << loc->id << "\n";
-                fh << "\n";
-                continue;
-            }
+    return 0;
+}
 
-            d = pmap->locus(loc->id);
 
-            for (int j = 0; j < pmap->sample_cnt(); j++) {
-                fh << "\t";
+bool hap_compare(pair<string, int> a, pair<string, int> b) {
+    return (a.second > b.second);
+}
 
-                if (d[j] == NULL || col >= d[j]->len) {
-                    //
-                    // Data does not exist.
-                    //
-                    fh << "./.:0:.,.:.,.,.";
-                } else if (d[j]->model[col] == 'U') {
-                    //
-                    // Data exists, but the model call was uncertain.
-                    //
-                    fh << "./.:" << d[j]->tot_depth << ":.,.:.,.,.";
-                } else {
-                    //
-                    // Tally up the nucleotide calls.
-                    //
-                    tally_observed_haplotypes(d[j]->obshap, snp_index, p_allele, q_allele);
+int parse_command_line(int argc, char* argv[]) {
 
-                    if (p_allele == 0 && q_allele == 0) {
-                        // More than two potential alleles.
-                        fh << "./.:" << d[j]->tot_depth << ":.,.:.,.,.";
-                    } else {
-                        find_datum_allele_depths(d[j], snp_index, sites[pos]->p_allele, sites[pos]->q_allele, p_allele+q_allele, dp_1, dp_2);
-
-                        if (p_allele == 0) {
-                            gt_1 = q_allele == sites[pos]->p_allele ? 0 : 1;
-                            fh << gt_1 << "/" << gt_1 << ":" << d[j]->tot_depth << ":" << dp_1 << "," << dp_2;
-                        } else if (q_allele == 0) {
-                            gt_1 = p_allele == sites[pos]->p_allele ? 0 : 1;
-                            fh << gt_1 << "/" << gt_1 << ":" << d[j]->tot_depth << ":" << dp_1 << "," << dp_2;
-                        } else {
-                            gt_1 = p_allele == sites[pos]->p_allele ? 0 : 1;
-                            gt_2 = q_allele == sites[pos]->p_allele ? 0 : 1;
-                            fh << gt_1 << "/" << gt_2 << ":" << d[j]->tot_depth << ":" << dp_1 << "," << dp_2;
-                        }
-                        //
-                        // Output the likelihood for this model call.
-                        //
-                        if (col < d[j]->snps.size()) {
-                            fh << ":.," << d[j]->snps[col]->lratio << ",.";
-                        } else {
-                            cerr << "Warning, unable to locate SNP call in column " << col << " for catalog locus " << loc->id << ", tag ID " << d[j]->id << "\n";
-                            fh << ":.,.,.";
-                        }
-                    }
-                }
-            }
-            fh << "\n";
-        }
-    }
-    fh.close();
-
-    return 0;
-}
-
-int 
-write_vcf(map<int, CSLocus *> &catalog, 
-          PopMap<CSLocus> *pmap, PopSum<CSLocus> *psum, 
-          map<int, string> &samples, vector<int> &sample_ids,
-          map<int, pair<merget, int> > &merge_map) 
-{
-    //
-    // Write a VCF file as defined here: http://www.1000genomes.org/node/101
-    //
-    stringstream pop_name;
-    pop_name << "batch_" << batch_id << ".vcf";
-    string file = in_path + pop_name.str();
-
-    ofstream fh(file.c_str(), ofstream::out);
-
-    if (fh.fail()) {
-        cerr << "Error opening VCF file '" << file << "'\n";
-        exit(1);
-    }
-
-    cerr << "In preparation for VCF export, loading SNP data for " << samples.size() << " samples.\n";
-    //
-    // Load SNP data so that model likelihoods can be output to VCF file.
-    //
-    populate_snp_calls(catalog, pmap, samples, sample_ids, merge_map);
-
-    //
-    // Obtain the current date.
-    //
-    time_t     rawtime;
-    struct tm *timeinfo;
-    char       date[32];
-    time(&rawtime);
-    timeinfo = localtime(&rawtime);
-    strftime(date, 32, "%Y%m%d", timeinfo);
-
-    cerr << "Writing population data to VCF file '" << file << "'\n";
-
-    //
-    // Output the header.
-    //
-    fh << "##fileformat=VCFv4.0\n"
-       << "##fileDate=" << date << "\n"
-       << "##source=\"Stacks v" << VERSION << "\"\n"
-       << "##INFO=<ID=NS,Number=1,Type=Integer,Description=\"Number of Samples With Data\">\n"
-       << "##INFO=<ID=AF,Number=.,Type=Float,Description=\"Allele Frequency\">\n"
-       << "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n"
-       << "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\n"
-       << "##FORMAT=<ID=AD,Number=1,Type=Integer,Description=\"Allele Depth\">\n"
-       << "##FORMAT=<ID=GL,Number=.,Type=Float,Description=\"Genotype Likelihood\">\n"
-       << "#CHROM" << "\t" << "POS" << "\t" << "ID" << "\t" << "REF" << "\t" << "ALT" << "\t" 
-       << "QUAL" << "\t" << "FILTER" << "\t" << "INFO" << "\t" << "FORMAT";
-
-    for (int i = 0; i < pmap->sample_cnt(); i++)
-        fh << "\t" << samples[pmap->rev_sample_index(i)];
-    fh << "\n";    
-
-    map<string, vector<CSLocus *> >::iterator it;
-    CSLocus *loc;
-    Datum   **d;
-    LocTally *t;
-    int       gt_1, gt_2, dp_1, dp_2;
-    double    num_indv;
-    char      p_allele, q_allele, p_str[32], q_str[32];
-    int       snp_index;
-
-    for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
-
-        //
-        // We need to order the SNPs so negative and positive strand SNPs are properly ordered.
-        //
-        vector<GenPos> ordered_loci;
-        uint           col;
-        for (uint pos = 0; pos < it->second.size(); pos++) {
-            loc = it->second[pos];
-            t   = psum->locus_tally(loc->id);
-
-            for (uint i = 0; i < loc->snps.size(); i++) {
-                col = loc->snps[i]->col;
-                if (t->nucs[col].allele_cnt == 2)
-                    ordered_loci.push_back(GenPos(loc->id, i, loc->sort_bp(col)));
-            }
-        }
-        sort(ordered_loci.begin(), ordered_loci.end(), compare_genpos);
-
-        for (uint pos = 0; pos < ordered_loci.size(); pos++) {
-            loc = catalog[ordered_loci[pos].id];
-            col = loc->snps[ordered_loci[pos].snp_index]->col;
-            t   = psum->locus_tally(loc->id);
-
-            num_indv = (double) t->nucs[col].num_indv;
-
-            sprintf(p_str, "%0.3f", t->nucs[col].p_freq);
-            sprintf(q_str, "%0.3f", 1 - t->nucs[col].p_freq);
-
-            //
-            // If on the negative strand, complement the alleles.
-            //
-            p_allele = loc->loc.strand == minus ? reverse(t->nucs[col].p_allele) : t->nucs[col].p_allele;
-            q_allele = loc->loc.strand == minus ? reverse(t->nucs[col].q_allele) : t->nucs[col].q_allele;
-
-            fh << loc->loc.chr << "\t" 
-               << loc->sort_bp(col) + 1 << "\t" 
-               << loc->id << "\t"
-               << p_allele << "\t"              // REFerence allele
-               << q_allele << "\t"              // ALTernate allele
-               << "."        << "\t"            // QUAL
-               << "PASS"     << "\t"            // FILTER
-               << "NS="      << num_indv << ";" // INFO
-               << "AF="      << p_str << "," << q_str << "\t" // INFO
-               << "GT:DP:AD:GL";                // FORMAT
-
-            snp_index = loc->snp_index(col);
-            if (snp_index < 0) {
-                cerr << "Warning, unable to locate SNP call in column " << col << " for catalog locus " << loc->id << "\n";
-                fh << "\n";
-                continue;
-            }
-
-            d = pmap->locus(loc->id);
-
-            for (int j = 0; j < pmap->sample_cnt(); j++) {
-                fh << "\t";
-
-                if (d[j] == NULL || col >= d[j]->len) {
-                    //
-                    // Data does not exist.
-                    //
-                    fh << "./.:0:.,.:.,.,.";
-                } else if (d[j]->model[col] == 'U') {
-                    //
-                    // Data exists, but the model call was uncertain.
-                    //
-                    fh << "./.:" << d[j]->tot_depth << ":.,.:.,.,.";
-                } else {
-                    //
-                    // Tally up the nucleotide calls.
-                    //
-                    tally_observed_haplotypes(d[j]->obshap, ordered_loci[pos].snp_index, p_allele, q_allele);
-
-                    if (p_allele == 0 && q_allele == 0) {
-                        // More than two potential alleles.
-                        fh << "./.:" << d[j]->tot_depth << ":.,.:.,.,.";
-                    } else {
-                        find_datum_allele_depths(d[j], snp_index, t->nucs[col].p_allele, t->nucs[col].q_allele, p_allele+q_allele, dp_1, dp_2);
-
-                        if (p_allele == 0) {
-                            gt_1 = q_allele == t->nucs[col].p_allele ? 0 : 1;
-                            fh << gt_1 << "/" << gt_1 << ":" << d[j]->tot_depth << ":" << dp_1 << "," << dp_2;
-                        } else if (q_allele == 0) {
-                            gt_1 = p_allele == t->nucs[col].p_allele ? 0 : 1;
-                            fh << gt_1 << "/" << gt_1 << ":" << d[j]->tot_depth << ":" << dp_1 << "," << dp_2;
-                        } else {
-                            gt_1 = p_allele == t->nucs[col].p_allele ? 0 : 1;
-                            gt_2 = q_allele == t->nucs[col].p_allele ? 0 : 1;
-                            fh << gt_1 << "/" << gt_2 << ":" << d[j]->tot_depth << ":" << dp_1 << "," << dp_2;
-                        }
-                        //
-                        // Output the likelihood measure for this model call.
-                        //
-                        if (snp_index >= 0) {
-                            fh << ":.," << d[j]->snps[snp_index]->lratio << ",.";
-                        } else {
-                            cerr << "Warning, unable to locate SNP call in column " << col << " for catalog locus " << loc->id << ", tag ID " << d[j]->id << "\n";
-                            fh << ":.,.,.";
-                        }
-                    }
-                }
-            }
-            fh << "\n";
-        }
-    }
-    fh.close();
-
-    return 0;
-}
-
-int
-populate_snp_calls(map<int, CSLocus *> &catalog, PopMap<CSLocus> *pmap,
-                   map<int, string> &samples, vector<int> &sample_ids,
-                   map<int, pair<merget, int> > &merge_map)
-{
-    map<int, CSLocus *>::iterator cit;
-    map<int, SNPRes *>::iterator sit;
-    CSLocus *loc;
-    Datum   *datum;
-    SNPRes  *snpr;
-    SNP     *snp;
-
-    for (uint i = 0; i < sample_ids.size(); i++) {
-        map<int, SNPRes *> snpres;
-        load_snp_calls(in_path + samples[sample_ids[i]], snpres);
-
-        for (cit = catalog.begin(); cit != catalog.end(); cit++) {
-            loc = cit->second;
-            datum = pmap->datum(loc->id, sample_ids[i]);
-
-            if (datum != NULL && snpres.count(datum->id)) {
-
-                if (merge_sites && merge_map.count(loc->id)) { 
-                    datum_adjust_snp_positions(merge_map, loc, datum, snpres);
-                } else {
-                    //
-                    // Deep copy the SNP objects.
-                    //
-                    snpr = snpres[datum->id];
-                    for (uint j = 0; j < snpr->snps.size(); j++) {
-                        snp         = new SNP;
-                        snp->col    = snpr->snps[j]->col;
-                        snp->lratio = snpr->snps[j]->lratio;
-                        snp->rank_1 = snpr->snps[j]->rank_1;
-                        snp->rank_2 = snpr->snps[j]->rank_2;
-                        snp->rank_3 = snpr->snps[j]->rank_3;
-                        snp->rank_4 = snpr->snps[j]->rank_4;
-
-                        datum->snps.push_back(snp);
-                    }
-                }
-            }
-        }
-
-        for (sit = snpres.begin(); sit != snpres.end(); sit++)
-            delete sit->second;
-    }
-
-    return 0;
-}
-
-int
-find_datum_allele_depths(Datum *d, int snp_index, char p_allele, char q_allele, int allele_cnt, int &dp_1, int &dp_2)
-{
-    dp_1 = 0;
-    dp_2 = 0;
-
-    if (allele_cnt == 1) {
-
-        //
-        // There is a single observed haplotype for this locus, e.g. GA.
-        //
-        if (d->obshap.size() == 1) {
-            if (d->obshap[0][snp_index] == p_allele) {
-                dp_1 = d->depth[0];
-                dp_2 = 0;
-            } else {
-                dp_1 = 0;
-                dp_2 = d->depth[0];
-            }
-        } else {
-            //
-            // This SNP position is homozygous, but the locus is heterozygous, so there is more
-            // than one observed haplotype, e.g. GA / TA.
-            //
-            if (d->obshap[0][snp_index] == p_allele) {
-                dp_1 = d->tot_depth;
-                dp_2 = 0;
-            } else  {
-                dp_1 = 0;
-                dp_2 = d->tot_depth;
-            }
-        }
-
-    } else {
-        //
-        // This SNP position is heterozygous.
-        //
-        for (uint i = 0; i < d->obshap.size(); i++) {
-            if (d->obshap[i][snp_index] == p_allele)
-                dp_1 = d->depth[i];
-            else if (d->obshap[i][snp_index] == q_allele)
-                dp_2 = d->depth[i];
-        }
-    }
-
-    if (dp_1 == 0 && dp_2 == 0)
-        cerr << "Warning: Unable to find allele depths for datum " << d->id << "\n";
-
-    return 0;
-}
-
-int 
-write_vcf_haplotypes(map<int, CSLocus *> &catalog, 
-                     PopMap<CSLocus> *pmap, PopSum<CSLocus> *psum, 
-                     map<int, string> &samples, vector<int> &sample_ids) 
-{
-    //
-    // Write a VCF file as defined here: http://samtools.github.io/hts-specs/
-    //
-    stringstream pop_name;
-    pop_name << "batch_" << batch_id << ".haplotypes.vcf";
-    string file = in_path + pop_name.str();
-
-    cerr << "Writing population data haplotypes to VCF file '" << file << "'\n";
-
-    ofstream fh(file.c_str(), ofstream::out);
-
-    if (fh.fail()) {
-        cerr << "Error opening VCF file '" << file << "'\n";
-        exit(1);
-    }
-
-    //
-    // Obtain the current date.
-    //
-    time_t     rawtime;
-    struct tm *timeinfo;
-    char       date[32];
-    time(&rawtime);
-    timeinfo = localtime(&rawtime);
-    strftime(date, 32, "%Y%m%d", timeinfo);
-
-    //
-    // Output the header.
-    //
-    fh << "##fileformat=VCFv4.2\n"
-       << "##fileDate=" << date << "\n"
-       << "##source=\"Stacks v" << VERSION << "\"\n"
-       << "##INFO=<ID=NS,Number=1,Type=Integer,Description=\"Number of Samples With Data\">\n"
-       << "##INFO=<ID=AF,Number=.,Type=Float,Description=\"Allele Frequency\">\n"
-       << "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n"
-       << "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\n"
-       << "#CHROM" << "\t" << "POS" << "\t" << "ID" << "\t" << "REF" << "\t" << "ALT" << "\t" 
-       << "QUAL" << "\t" << "FILTER" << "\t" << "INFO" << "\t" << "FORMAT";
-
-    for (int i = 0; i < pmap->sample_cnt(); i++)
-        fh << "\t" << samples[pmap->rev_sample_index(i)];
-    fh << "\n";    
-
-    map<string, vector<CSLocus *> >::iterator it;
-    map<string, double>::iterator hit;
-    map<string, double> hap_freq;
-    map<string, int>    hap_index;
-    vector<pair<string, int> > ordered_hap;
-    CSLocus  *loc;
-    Datum   **d;
-    double    num_indv, num_hap;
-    char      allele[id_len];
-
-    for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
-        for (uint pos = 0; pos < it->second.size(); pos++) {
-            loc = it->second[pos];
-            d   = pmap->locus(loc->id);
-
-            hap_freq.clear();
-            hap_index.clear();
-            ordered_hap.clear();
-
-            num_hap = count_haplotypes_at_locus(0, pmap->sample_cnt() - 1, d, hap_freq);
-
-            if (num_hap == 0 || hap_freq.size() == 1) 
-                continue;
-
-            num_indv = num_hap / 2.0;
-
-            //
-            // Order the haplotypes according to most frequent. Record the ordered position or each 
-            // haplotype and convert them from counts to frequencies.
-            //
-            for (hit = hap_freq.begin(); hit != hap_freq.end(); hit++) {
-                ordered_hap.push_back(make_pair(hit->first, hit->second));
-                hit->second = hit->second / num_hap;
-            }
-            sort(ordered_hap.begin(), ordered_hap.end(), compare_pair_haplotype);
-            for (uint i = 0; i < ordered_hap.size(); i++)
-                hap_index[ordered_hap[i].first] = i;
-
-            string alt_str, freq_str;
-            for (uint i = 1; i < ordered_hap.size(); i++) {
-                alt_str  += ordered_hap[i].first;
-                sprintf(allele, "%0.3f", hap_freq[ordered_hap[i].first]);
-                freq_str += allele;
-                if (i < ordered_hap.size() - 1) {
-                    alt_str  += ",";
-                    freq_str += ",";
-                }
-            }
-
-            fh << loc->loc.chr         << "\t" 
-               << loc->sort_bp() + 1   << "\t" 
-               << loc->id              << "\t"
-               << ordered_hap[0].first << "\t"       // REFerence haplotypes
-               << alt_str        << "\t"             // ALTernate haplotypes
-               << "."            << "\t"             // QUAL
-               << "PASS"         << "\t"             // FILTER
-               << "NS="          << num_indv << ";"  // INFO
-               << "AF="          << freq_str << "\t" // INFO
-               << "GT:DP";                           // FORMAT
-
-            for (int j = 0; j < pmap->sample_cnt(); j++) {
-                fh << "\t";
-
-                if (d[j] == NULL) {
-                    //
-                    // Data does not exist.
-                    //
-                    fh << "./.:0";
-
-                } else if (d[j]->obshap.size() > 2) { 
-                    fh << "./.:" << d[j]->tot_depth;
-
-                } else if (d[j]->obshap.size() == 1) {
-                    if(uncalled_haplotype(d[j]->obshap[0]))
-                        fh << "./.:" << d[j]->tot_depth;
-                    else
-                        fh << hap_index[d[j]->obshap[0]] << "/" << hap_index[d[j]->obshap[0]] << ":" << d[j]->tot_depth;
-                } else {
-                    if(!uncalled_haplotype(d[j]->obshap[0]) &&
-                       !uncalled_haplotype(d[j]->obshap[1]))
-                        fh << hap_index[d[j]->obshap[0]] << "/" << hap_index[d[j]->obshap[1]] << ":" << d[j]->tot_depth;
-                    else if (!uncalled_haplotype(d[j]->obshap[0]))
-                        fh << hap_index[d[j]->obshap[0]] << "/" << "." << ":" << d[j]->tot_depth;
-                    else if (!uncalled_haplotype(d[j]->obshap[1]))
-                        fh << "." << "/" << hap_index[d[j]->obshap[1]] << ":" << d[j]->tot_depth;
-                }
-            }
-            fh << "\n";
-        }
-    }
-
-    fh.close();
-
-    return 0;
-}
-
-int 
-write_genepop(map<int, CSLocus *> &catalog, 
-              PopMap<CSLocus> *pmap, 
-              PopSum<CSLocus> *psum, 
-              map<int, pair<int, int> > &pop_indexes, 
-              map<int, string> &samples) 
-{
-    //
-    // Write a GenePop file as defined here: http://kimura.univ-montp2.fr/~rousset/Genepop.htm
-    //
-    stringstream pop_name;
-    pop_name << "batch_" << batch_id << ".genepop";
-    string file = in_path + pop_name.str();
-
-    cerr << "Writing population data to GenePop file '" << file << "'\n";
-
-    ofstream fh(file.c_str(), ofstream::out);
-
-    if (fh.fail()) {
-        cerr << "Error opening GenePop file '" << file << "'\n";
-        exit(1);
-    }
-
-    //
-    // Obtain the current date.
-    //
-    time_t     rawtime;
-    struct tm *timeinfo;
-    char       date[32];
-    time(&rawtime);
-    timeinfo = localtime(&rawtime);
-    strftime(date, 32, "%B %d, %Y", timeinfo);
-
-    //
-    // Output the header line.
-    //
-    fh << "Stacks version " << VERSION << "; Genepop version 4.1.3; " << date << "\n";
-
-    map<int, pair<int, int> >::iterator pit;
-    map<int, CSLocus *>::iterator it;
-    CSLocus  *loc;
-    Datum   **d;
-    LocSum  **s;
-    LocTally *t;
-    int      start_index, end_index, col, pop_id;
-    char     p_allele, q_allele;
-
-    //
-    // Determine how many loci will be output, then output all the loci on the second line, comma-separated.
-    //
-    uint cnt = 0;
-    for (it = catalog.begin(); it != catalog.end(); it++) {
-        loc = it->second;
-        for (uint j = 0; j < loc->snps.size(); j++) {
-            col = loc->snps[j]->col;
-            t   = psum->locus_tally(loc->id);
-
-            if (t->nucs[col].allele_cnt != 2) 
-                continue;
-            cnt++;
-        }
-    }
-
-    uint i = 0;
-    for (it = catalog.begin(); it != catalog.end(); it++) {
-        loc = it->second;
-        for (uint j = 0; j < loc->snps.size(); j++) {
-            col = loc->snps[j]->col;
-            t   = psum->locus_tally(loc->id);
-
-            // 
-            // If this site is fixed in all populations or has too many alleles don't output it.
-            //
-            if (t->nucs[col].allele_cnt != 2) 
-                continue;
-            i++;
-            fh << loc->id << "_" << col;
-            if (i <  cnt) fh << ",";
-        }
-    }
-    fh << "\n";
-
-    map<char, string> nuc_map;
-    nuc_map['A'] = "01";
-    nuc_map['C'] = "02";
-    nuc_map['G'] = "03";
-    nuc_map['T'] = "04";
-
-    for (pit = pop_indexes.begin(); pit != pop_indexes.end(); pit++) {
-        pop_id      = psum->pop_index(pit->first);
-        start_index = pit->second.first;
-        end_index   = pit->second.second;
-
-        fh << "pop\n";
-
-        for (int j = start_index; j <= end_index; j++) {
-
-            fh << samples[pmap->rev_sample_index(j)] << ",";
-
-            for (it = catalog.begin(); it != catalog.end(); it++) {
-                loc = it->second;
-                d   = pmap->locus(loc->id);
-                s   = psum->locus(loc->id);
-                t   = psum->locus_tally(loc->id);
-
-                for (i = 0; i < loc->snps.size(); i++) {
-                    uint col = loc->snps[i]->col;
-
-                    if (t->nucs[col].allele_cnt != 2) 
-                        continue;
-
-                    if (s[pop_id]->nucs[col].incompatible_site ||
-                        s[pop_id]->nucs[col].filtered_site) {
-                        //
-                        // This site contains more than two alleles in this population or was filtered
-                        // due to a minor allele frequency that is too low.
-                        //
-                        fh << "\t0000";
-                    } else if (d[j] == NULL || col >= d[j]->len) {
-                        //
-                        // Data does not exist.
-                        //
-                        fh << "\t0000";
-                    } else if (d[j]->model[col] == 'U') {
-                        //
-                        // Data exists, but the model call was uncertain.
-                        //
-                        fh << "\t0000";
-                    } else {
-                        //
-                        // Tally up the nucleotide calls.
-                        //
-                        tally_observed_haplotypes(d[j]->obshap, i, p_allele, q_allele);
-
-                        if (p_allele == 0 && q_allele == 0) {
-                            // More than two potential alleles.
-                            fh << "\t0000";
-                        } else if (p_allele == 0) {
-                            fh << "\t" << nuc_map[q_allele] << nuc_map[q_allele];
-
-                        } else if (q_allele == 0) {
-                            fh << "\t" << nuc_map[p_allele] << nuc_map[p_allele];
-
-                        } else {
-                            fh << "\t" << nuc_map[p_allele] << nuc_map[q_allele];
-                        }
-                    }
-                }
-            }
-            fh << "\n";
-        }
-    }
-
-    fh.close();
-
-    return 0;
-}
-
-int 
-write_genepop_ordered(map<int, CSLocus *> &catalog, 
-                      PopMap<CSLocus> *pmap, 
-                      PopSum<CSLocus> *psum, 
-                      map<int, pair<int, int> > &pop_indexes, 
-                      map<int, string> &samples, ofstream &log_fh) 
-{
-    //
-    // Write a GenePop file as defined here: http://kimura.univ-montp2.fr/~rousset/Genepop.htm
-    //
-    stringstream pop_name;
-    pop_name << "batch_" << batch_id << ".genepop";
-    string file = in_path + pop_name.str();
-
-    cerr << "Writing population data to GenePop file '" << file << "'\n";
-
-    ofstream fh(file.c_str(), ofstream::out);
-
-    if (fh.fail()) {
-        cerr << "Error opening GenePop file '" << file << "'\n";
-        exit(1);
-    }
-
-    //
-    // Obtain the current date.
-    //
-    time_t     rawtime;
-    struct tm *timeinfo;
-    char       date[32];
-    time(&rawtime);
-    timeinfo = localtime(&rawtime);
-    strftime(date, 32, "%B %d, %Y", timeinfo);
-
-    //
-    // Output the header line.
-    //
-    fh << "Stacks version " << VERSION << "; Genepop version 4.1.3; " << date << "\n";
-
-    map<string, vector<NucTally *> > genome_sites;
-    map<int, pair<int, int> >::iterator pit;
-    map<string, vector<CSLocus *> >::iterator it;
-    CSLocus  *loc;
-    Datum   **d;
-    LocSum  **s;
-    int      start_index, end_index, pop_id;
-    uint     col, snp_index;
-    char     p_allele, q_allele;
-
-    //
-    // We need to order the SNPs to take into account overlapping loci.
-    //
-    OLocTally<NucTally> *ord = new OLocTally<NucTally>(psum, log_fh);
-
-    //
-    // Output all the loci on the second line, comma-separated.
-    //
-    int chrs = pmap->ordered_loci.size();
-    int cnt  = 0;
-    for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
-        vector<NucTally *> &sites = genome_sites[it->first];
-        ord->order(sites, it->second);
-        cnt++;
-
-        for (uint pos = 0; pos < sites.size(); pos++) {
-            fh << sites[pos]->loc_id << "_" << sites[pos]->col;
-            if (cnt < chrs || pos < sites.size() - 1) fh << ",";
-        }
-    }
-    fh << "\n";
-
-    map<char, string> nuc_map;
-    nuc_map['A'] = "01";
-    nuc_map['C'] = "02";
-    nuc_map['G'] = "03";
-    nuc_map['T'] = "04";
-
-    for (pit = pop_indexes.begin(); pit != pop_indexes.end(); pit++) {
-        pop_id      = psum->pop_index(pit->first);
-        start_index = pit->second.first;
-        end_index   = pit->second.second;
-
-        fh << "pop\n";
-
-        for (int j = start_index; j <= end_index; j++) {
-
-            fh << samples[pmap->rev_sample_index(j)] << ",";
-
-            for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
-                vector<NucTally *> &sites = genome_sites[it->first];
-
-                for (uint pos = 0; pos < sites.size(); pos++) {
-                    loc = catalog[sites[pos]->loc_id];
-                    s   = psum->locus(loc->id);
-                    d   = pmap->locus(loc->id);
-                    col = sites[pos]->col;
-
-                    if (s[pop_id]->nucs[col].incompatible_site ||
-                        s[pop_id]->nucs[col].filtered_site) {
-                        //
-                        // This site contains more than two alleles in this population or was filtered
-                        // due to a minor allele frequency that is too low.
-                        //
-                        fh << "\t0000";
-                    } else if (d[j] == NULL || col >= d[j]->len) {
-                        //
-                        // Data does not exist.
-                        //
-                        fh << "\t0000";
-                    } else if (d[j]->model[col] == 'U') {
-                        //
-                        // Data exists, but the model call was uncertain.
-                        //
-                        fh << "\t0000";
-                    } else {
-                        snp_index = loc->snp_index(col);
-                        //
-                        // Tally up the nucleotide calls.
-                        //
-                        tally_observed_haplotypes(d[j]->obshap, snp_index, p_allele, q_allele);
-
-                        if (p_allele == 0 && q_allele == 0) {
-                            // More than two potential alleles.
-                            fh << "\t0000";
-                        } else if (p_allele == 0) {
-                            fh << "\t" << nuc_map[q_allele] << nuc_map[q_allele];
-
-                        } else if (q_allele == 0) {
-                            fh << "\t" << nuc_map[p_allele] << nuc_map[p_allele];
-
-                        } else {
-                            fh << "\t" << nuc_map[p_allele] << nuc_map[q_allele];
-                        }
-                    }
-                }
-            }
-            fh << "\n";
-        }
-    }
-
-    fh.close();
-
-    return 0;
-}
-
-int 
-write_structure(map<int, CSLocus *> &catalog, 
-                PopMap<CSLocus> *pmap, 
-                PopSum<CSLocus> *psum, 
-                map<int, pair<int, int> > &pop_indexes, 
-                map<int, string> &samples) 
-{
-    //
-    // Write a Structure file as defined here: http://pritch.bsd.uchicago.edu/structure.html
-    //
-    // To avoid linked SNPs (which Structure can't handle), we will only output the first
-    // SNP from each variable locus.
-    //
-    stringstream pop_name;
-    pop_name << "batch_" << batch_id << ".structure.tsv";
-    string file = in_path + pop_name.str();
-
-    cerr << "Writing population data to Structure file '" << file << "'...";
-
-    ofstream fh(file.c_str(), ofstream::out);
-
-    if (fh.fail()) {
-        cerr << "Error opening Structure file '" << file << "'\n";
-        exit(1);
-    }
-
-    //
-    // Obtain the current date.
-    //
-    time_t     rawtime;
-    struct tm *timeinfo;
-    char       date[32];
-    time(&rawtime);
-    timeinfo = localtime(&rawtime);
-    strftime(date, 32, "%B %d, %Y", timeinfo);
-
-    //
-    // Output the header.
-    //
-    fh << "# Stacks v" << VERSION << "; " << " Structure v2.3; " << date << "\n";
-
-    map<string, vector<CSLocus *> >::iterator it;
-    CSLocus  *loc;
-    Datum   **d;
-    LocSum  **s;
-    LocTally *t;
-
-    for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
-        for (uint pos = 0; pos < it->second.size(); pos++) {
-            loc = it->second[pos];
-            t   = psum->locus_tally(loc->id);
-
-            for (uint i = 0; i < loc->snps.size(); i++) {
-                uint col = loc->snps[i]->col;
-                if (t->nucs[col].allele_cnt == 2)
-                    fh << "\t" << loc->id << "_" << col;
-            }
-        }
-    }
-    fh << "\n";
-
-    map<char, string> nuc_map;
-    nuc_map['A'] = "1";
-    nuc_map['C'] = "2";
-    nuc_map['G'] = "3";
-    nuc_map['T'] = "4";
-
-    map<int, pair<int, int> >::iterator pit;
-    int       start_index, end_index, pop_id, p;
-    char      p_allele, q_allele;
-
-    for (pit = pop_indexes.begin(); pit != pop_indexes.end(); pit++) {
-        p           = psum->pop_index(pit->first);
-        pop_id      = pit->first;
-        start_index = pit->second.first;
-        end_index   = pit->second.second;
-
-        for (int j = start_index; j <= end_index; j++) {
-            //
-            // Output all the loci for this sample, printing only the p allele
-            //
-            fh << samples[pmap->rev_sample_index(j)] << "\t" << pop_id;
-
-            for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
-                for (uint pos = 0; pos < it->second.size(); pos++) {
-                    loc = it->second[pos];
-
-                    s = psum->locus(loc->id);
-                    d = pmap->locus(loc->id);
-                    t = psum->locus_tally(loc->id);
-
-                    for (uint i = 0; i < loc->snps.size(); i++) {
-                        uint col = loc->snps[i]->col;
-
-                        // 
-                        // If this site is fixed in all populations or has too many alleles don't output it.
-                        //
-                        if (t->nucs[col].allele_cnt != 2) 
-                            continue;
-
-                        if (s[p]->nucs[col].incompatible_site ||
-                            s[p]->nucs[col].filtered_site) {
-                            //
-                            // This site contains more than two alleles in this population or was filtered
-                            // due to a minor allele frequency that is too low.
-                            //
-                            fh << "\t" << "0";
-                        } else if (d[j] == NULL || col >= d[j]->len) {
-                            //
-                            // Data does not exist.
-                            //
-                            fh << "\t" << "0";
-                        } else if (d[j]->model[col] == 'U') {
-                            //
-                            // Data exists, but the model call was uncertain.
-                            //
-                            fh << "\t" << "0";
-                        } else {
-                            //
-                            // Tally up the nucleotide calls.
-                            //
-                            tally_observed_haplotypes(d[j]->obshap, i, p_allele, q_allele);
-
-                            if (p_allele == 0 && q_allele == 0)
-                                fh << "\t" << "0";
-                            else if (p_allele == 0)
-                                fh << "\t" << nuc_map[q_allele];
-                            else
-                                fh << "\t" << nuc_map[p_allele];
-                        }
-                    }
-                }
-            }
-            fh << "\n";
-
-            //
-            // Output all the loci for this sample again, now for the q allele
-            //
-            fh << samples[pmap->rev_sample_index(j)] << "\t" << pop_id;
-
-            for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
-                for (uint pos = 0; pos < it->second.size(); pos++) {
-                    loc = it->second[pos];
-
-                    s = psum->locus(loc->id);
-                    d = pmap->locus(loc->id);
-                    t = psum->locus_tally(loc->id);
-
-                    for (uint i = 0; i < loc->snps.size(); i++) {
-                        uint col = loc->snps[i]->col;
-
-                        if (t->nucs[col].allele_cnt != 2) 
-                            continue;
-
-                        if (s[p]->nucs[col].incompatible_site ||
-                            s[p]->nucs[col].filtered_site) {
-                            fh << "\t" << "0";
-                        } else if (d[j] == NULL || col >= d[j]->len) {
-                            fh << "\t" << "0";
-                        } else if (d[j]->model[col] == 'U') {
-                            fh << "\t" << "0";
-                        } else {
-                            tally_observed_haplotypes(d[j]->obshap, i, p_allele, q_allele);
-
-                            if (p_allele == 0 && q_allele == 0)
-                                fh << "\t" << "0";
-                            else if (q_allele == 0)
-                                fh << "\t" << nuc_map[p_allele];
-                            else
-                                fh << "\t" << nuc_map[q_allele];
-                        }
-                    }
-                }
-            }
-            fh << "\n";
-        }
-    }
-
-    fh.close();
-
-    cerr << "done.\n";
-
-    return 0;
-}
-
-int 
-write_structure_ordered(map<int, CSLocus *> &catalog, 
-                        PopMap<CSLocus> *pmap, 
-                        PopSum<CSLocus> *psum, 
-                        map<int, pair<int, int> > &pop_indexes, 
-                        map<int, string> &samples, ofstream &log_fh) 
-{
-    //
-    // Write a Structure file as defined here: http://pritch.bsd.uchicago.edu/structure.html
-    //
-    // To avoid linked SNPs (which Structure can't handle), we will only output the first
-    // SNP from each variable locus.
-    //
-    stringstream pop_name;
-    pop_name << "batch_" << batch_id << ".structure.tsv";
-    string file = in_path + pop_name.str();
-
-    cerr << "Writing population data to Structure file '" << file << "'...";
-
-    ofstream fh(file.c_str(), ofstream::out);
-
-    if (fh.fail()) {
-        cerr << "Error opening Structure file '" << file << "'\n";
-        exit(1);
-    }
-
-    //
-    // Obtain the current date.
-    //
-    time_t     rawtime;
-    struct tm *timeinfo;
-    char       date[32];
-    time(&rawtime);
-    timeinfo = localtime(&rawtime);
-    strftime(date, 32, "%B %d, %Y", timeinfo);
-
-    //
-    // Output the header.
-    //
-    fh << "# Stacks v" << VERSION << "; " << " Structure v2.3; " << date << "\n";
-
-    map<string, vector<NucTally *> > genome_sites;
-    map<string, vector<CSLocus *> >::iterator it;
-    CSLocus  *loc;
-    Datum   **d;
-    LocSum  **s;
-
-    //
-    // We need to order the SNPs to take into account overlapping loci.
-    //
-    OLocTally<NucTally> *ord = new OLocTally<NucTally>(psum, log_fh);
-
-    for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
-        vector<NucTally *> &sites = genome_sites[it->first];
-        ord->order(sites, it->second);
-
-        for (uint pos = 0; pos < sites.size(); pos++)
-            fh << "\t" << sites[pos]->loc_id << "_" << sites[pos]->col;
-    }
-    fh << "\n";
-
-    map<char, string> nuc_map;
-    nuc_map['A'] = "1";
-    nuc_map['C'] = "2";
-    nuc_map['G'] = "3";
-    nuc_map['T'] = "4";
-
-    map<int, pair<int, int> >::iterator pit;
-    int       start_index, end_index, pop_id, p;
-    char      p_allele, q_allele;
-    uint      col, snp_index;
-
-    for (pit = pop_indexes.begin(); pit != pop_indexes.end(); pit++) {
-        p           = psum->pop_index(pit->first);
-        pop_id      = pit->first;
-        start_index = pit->second.first;
-        end_index   = pit->second.second;
-
-        for (int j = start_index; j <= end_index; j++) {
-            //
-            // Output all the loci for this sample, printing only the p allele
-            //
-            fh << samples[pmap->rev_sample_index(j)] << "\t" << pop_id;
-
-            for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
-                vector<NucTally *> &sites = genome_sites[it->first];
-
-                for (uint pos = 0; pos < sites.size(); pos++) {
-                    loc = catalog[sites[pos]->loc_id];
-                    s   = psum->locus(loc->id);
-                    d   = pmap->locus(loc->id);
-                    col = sites[pos]->col;
-
-                    if (s[p]->nucs[col].incompatible_site ||
-                        s[p]->nucs[col].filtered_site) {
-                        //
-                        // This site contains more than two alleles in this population or was filtered
-                        // due to a minor allele frequency that is too low.
-                        //
-                        fh << "\t" << "0";
-                    } else if (d[j] == NULL || col >= d[j]->len) {
-                        //
-                        // Data does not exist.
-                        //
-                        fh << "\t" << "0";
-                    } else if (d[j]->model[col] == 'U') {
-                        //
-                        // Data exists, but the model call was uncertain.
-                        //
-                        fh << "\t" << "0";
-                    } else {
-                        snp_index = loc->snp_index(col);
-                        //
-                        // Tally up the nucleotide calls.
-                        //
-                        tally_observed_haplotypes(d[j]->obshap, snp_index, p_allele, q_allele);
-
-                        if (p_allele == 0 && q_allele == 0)
-                            fh << "\t" << "0";
-                        else if (p_allele == 0)
-                            fh << "\t" << nuc_map[q_allele];
-                        else
-                            fh << "\t" << nuc_map[p_allele];
-                    }
-                }
-            }
-            fh << "\n";
-
-            //
-            // Output all the loci for this sample again, now for the q allele
-            //
-            fh << samples[pmap->rev_sample_index(j)] << "\t" << pop_id;
-
-            for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
-                vector<NucTally *> &sites = genome_sites[it->first];
-
-                for (uint pos = 0; pos < sites.size(); pos++) {
-                    loc = catalog[sites[pos]->loc_id];
-                    s   = psum->locus(loc->id);
-                    d   = pmap->locus(loc->id);
-                    col = sites[pos]->col;
-
-                    if (s[p]->nucs[col].incompatible_site ||
-                        s[p]->nucs[col].filtered_site) {
-                        fh << "\t" << "0";
-                    } else if (d[j] == NULL || col >= d[j]->len) {
-                        fh << "\t" << "0";
-                    } else if (d[j]->model[col] == 'U') {
-                        fh << "\t" << "0";
-                    } else {
-                        snp_index = loc->snp_index(col);
-                        tally_observed_haplotypes(d[j]->obshap, snp_index, p_allele, q_allele);
-
-                        if (p_allele == 0 && q_allele == 0)
-                            fh << "\t" << "0";
-                        else if (q_allele == 0)
-                            fh << "\t" << nuc_map[p_allele];
-                        else
-                            fh << "\t" << nuc_map[q_allele];
-                    }
-                }
-            }
-            fh << "\n";
-        }
-    }
-
-    fh.close();
-
-    cerr << "done.\n";
-
-    return 0;
-}
-
-int 
-write_hzar(map<int, CSLocus *> &catalog, 
-           PopMap<CSLocus> *pmap, 
-           PopSum<CSLocus> *psum, 
-           map<int, pair<int, int> > &pop_indexes, 
-           map<int, string> &samples) 
-{
-    //
-    // Write a Hybrid Zone Analysis using R (HZAR) file as defined here: 
-    //    http://cran.r-project.org/web/packages/hzar/hzar.pdf
-    //
-    stringstream pop_name;
-    pop_name << "batch_" << batch_id << ".hzar.csv";
-    string file = in_path + pop_name.str();
-
-    cerr << "Writing population data to HZAR file '" << file << "'...";
-
-    ofstream fh(file.c_str(), ofstream::out);
-
-    if (fh.fail()) {
-        cerr << "Error opening HZAR file '" << file << "'\n";
-        exit(1);
-    }
-
-    //
-    // Obtain the current date.
-    //
-    time_t     rawtime;
-    struct tm *timeinfo;
-    char       date[32];
-    time(&rawtime);
-    timeinfo = localtime(&rawtime);
-    strftime(date, 32, "%B %d, %Y", timeinfo);
-
-    //
-    // Output the header.
-    //
-    fh << "# Stacks v" << VERSION << "; " << " HZAR v0.2-5; " << date << "\n"
-       << "Population" << "," << "Distance";
-
-    map<string, vector<CSLocus *> >::iterator it;
-    CSLocus  *loc;
-    LocSum  **s;
-    LocTally *t;
-
-    for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
-        for (uint pos = 0; pos < it->second.size(); pos++) {
-            loc = it->second[pos];
-            s   = psum->locus(loc->id);
-            t   = psum->locus_tally(loc->id);
-
-            for (uint i = 0; i < loc->snps.size(); i++) {
-                uint col = loc->snps[i]->col;
-                if (t->nucs[col].allele_cnt == 2) {
-                    fh << "," << loc->id << "_" << col << ".A"
-                       << "," << loc->id << "_" << col << ".B"
-                       << "," << loc->id << "_" << col << ".N";
-                }
-            }
-        }
-    }
-    fh << "\n";
-
-    map<int, pair<int, int> >::iterator pit;
-    int pop_id, p;
-
-    for (pit = pop_indexes.begin(); pit != pop_indexes.end(); pit++) {
-        p      = psum->pop_index(pit->first);
-        pop_id = pit->first;
-
-        fh << pop_key[pop_id] << ",";
-
-        for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
-            for (uint pos = 0; pos < it->second.size(); pos++) {
-                loc = it->second[pos];
-
-                s = psum->locus(loc->id);
-                t = psum->locus_tally(loc->id);
-
-                for (uint i = 0; i < loc->snps.size(); i++) {
-                    uint col = loc->snps[i]->col;
-
-                    // 
-                    // If this site is fixed in all populations or has too many alleles don't output it.
-                    //
-                    if (t->nucs[col].allele_cnt != 2) 
-                        continue;
-
-                    if (s[p]->nucs[col].num_indv == 0 ||
-                        s[p]->nucs[col].incompatible_site ||
-                        s[p]->nucs[col].filtered_site) {
-                        fh << ",0,0,0";
-                        continue;
-                    }
-                    
-                    if (t->nucs[col].p_allele == s[p]->nucs[col].p_nuc)
-                        fh << "," << s[p]->nucs[col].p << "," << 1 - s[p]->nucs[col].p << ",";
-                    else
-                        fh << "," << 1 - s[p]->nucs[col].p << "," << s[p]->nucs[col].p << ",";
-
-                    fh << s[p]->nucs[col].num_indv * 2;
-                }
-            }
-        }
-        fh << "\n";
-    }
-
-    fh.close();
-
-    cerr << "done.\n";
-
-    return 0;
-}
-
-int 
-write_treemix(map<int, CSLocus *> &catalog, 
-              PopMap<CSLocus> *pmap, 
-              PopSum<CSLocus> *psum, 
-              map<int, pair<int, int> > &pop_indexes, 
-              map<int, string> &samples) 
-{
-    //
-    // Write a TreeMix file (Pickrell and Pritchard, 2012 PLoS Genetics)
-    //    https://bitbucket.org/nygcresearch/treemix/wiki/Home
-    //
-    stringstream pop_name;
-    pop_name << "batch_" << batch_id << ".treemix";
-    string file = in_path + pop_name.str();
-
-    cerr << "Writing population data to TreeMix file '" << file << "'; ";
-
-    ofstream fh(file.c_str(), ofstream::out);
-
-    if (fh.fail()) {
-        cerr << "Error opening TreeMix file '" << file << "'\n";
-        exit(1);
-    }
-
-    pop_name << ".log";
-    file = in_path + pop_name.str();
-
-    cerr << "logging nucleotide positions to '" << file << "'...";
-
-    ofstream log_fh(file.c_str(), ofstream::out);
-
-    if (log_fh.fail()) {
-        cerr << "Error opening Phylip Log file '" << file << "'\n";
-        exit(1);
-    }
-
-    //
-    // Obtain the current date.
-    //
-    time_t     rawtime;
-    struct tm *timeinfo;
-    char       date[32];
-    time(&rawtime);
-    timeinfo = localtime(&rawtime);
-    strftime(date, 32, "%B %d, %Y", timeinfo);
-
-    log_fh << "# Stacks v" << VERSION << "; " << " TreeMix v1.1; " << date << "\n"
-           << "# Line\tLocus ID\tColumn\tChr\tBasepair\n";
-
-    //
-    // Output the header.
-    //
-    fh << "# Stacks v" << VERSION << "; " << " TreeMix v1.1; " << date << "\n";
-
-    map<string, vector<CSLocus *> >::iterator it;
-    map<int, pair<int, int> >::iterator pit;
-    CSLocus  *loc;
-    LocSum  **s;
-    LocTally *t;
-    int       p;
-
-    //
-    // Output a space-separated list of the populations on the first line.
-    //
-    stringstream sstr;
-    for (pit = pop_indexes.begin(); pit != pop_indexes.end(); pit++)
-        sstr << pop_key[pit->first] << " ";
-    
-    fh << sstr.str().substr(0, sstr.str().length() - 1) << "\n";
-
-    double p_freq, p_cnt, q_cnt, allele_cnt;
-    long int line = 1;
-    
-    for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
-        for (uint pos = 0; pos < it->second.size(); pos++) {
-            loc = it->second[pos];
-
-            s = psum->locus(loc->id);
-            t = psum->locus_tally(loc->id);
-                
-            for (uint i = 0; i < loc->snps.size(); i++) {
-                uint col = loc->snps[i]->col;
-
-                sstr.str("");
-
-                // 
-                // If this site is fixed in all populations or has too many alleles don't output it.
-                //
-                if (t->nucs[col].allele_cnt != 2) 
-                    continue;
-
-                for (pit = pop_indexes.begin(); pit != pop_indexes.end(); pit++) {
-                    p = psum->pop_index(pit->first);
-
-                    if (s[p]->nucs[col].num_indv == 0 ||
-                        s[p]->nucs[col].incompatible_site ||
-                        s[p]->nucs[col].filtered_site) {
-                        sstr << "0,0 ";
-                        continue;
-                    }
-                    
-                    p_freq = (t->nucs[col].p_allele == s[p]->nucs[col].p_nuc) ? 
-                        s[p]->nucs[col].p :
-                        1 - s[p]->nucs[col].p;
-                    
-                    allele_cnt = s[p]->nucs[col].num_indv * 2;
-                    p_cnt      = round(allele_cnt * p_freq);
-                    q_cnt      = allele_cnt - p_cnt;
-                    sstr << (int) p_cnt << "," << (int) q_cnt << " ";
-                }
-
-                if (sstr.str().length() == 0)
-                    continue;
-
-                fh << sstr.str().substr(0, sstr.str().length() - 1) << "\n";
-                log_fh << line << "\t" << loc->id << "\t" << col << "\t" << loc->loc.chr << "\t" << loc->sort_bp(col) + 1 << "\n";
-                line++;
-            }
-        }
-    }
-
-    fh.close();
-    log_fh.close();
-    
-    cerr << "done.\n";
-
-    return 0;
-}
-
-int 
-write_fastphase(map<int, CSLocus *> &catalog, 
-                PopMap<CSLocus> *pmap, 
-                PopSum<CSLocus> *psum, 
-                map<int, pair<int, int> > &pop_indexes, 
-                map<int, string> &samples) 
-{
-    //
-    // Write a fastPHASE file as defined here: http://stephenslab.uchicago.edu/software.html
-    //
-    // Data will be written as independent, bi-allelic SNPs. We will write one file per chromosome.
-    //
-    cerr << "Writing population data to fastPHASE files...";
-
-    map<string, vector<CSLocus *> >::iterator it;
-    CSLocus  *loc;
-    Datum   **d;
-    LocSum  **s;
-    LocTally *t;
-
-    for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
-
-        stringstream pop_name;
-        pop_name << "batch_" << batch_id << "." << it->first << ".fastphase.inp";
-        string file = in_path + pop_name.str();
-
-        ofstream fh(file.c_str(), ofstream::out);
-
-        if (fh.fail()) {
-            cerr << "Error opening fastPHASE file '" << file << "'\n";
-            exit(1);
-        }
-
-        //
-        // Tally up the number of sites
-        //
-        int  total_sites = 0;
-        uint col;
-        for (uint pos = 0; pos < it->second.size(); pos++) {
-            loc = it->second[pos];
-            t   = psum->locus_tally(loc->id);
-
-            for (uint i = 0; i < loc->snps.size(); i++) {
-                col = loc->snps[i]->col;
-                if (t->nucs[col].allele_cnt == 2)
-                    total_sites++;
-            }
-        }
-
-        //
-        // Output the total number of SNP sites and the number of individuals.
-        //
-        fh << samples.size() << "\n"
-           << total_sites    << "\n";
-
-        //
-        // We need to determine an ordering that can take into account overlapping RAD sites.
-        //
-        vector<GenPos> ordered_loci;
-        for (uint pos = 0; pos < it->second.size(); pos++) {
-            loc = it->second[pos];
-            t   = psum->locus_tally(loc->id);
-
-            for (uint i = 0; i < loc->snps.size(); i++) {
-                col = loc->snps[i]->col;
-                if (t->nucs[col].allele_cnt == 2)
-                    ordered_loci.push_back(GenPos(loc->id, i, loc->sort_bp(col)));
-            }
-        }
-        sort(ordered_loci.begin(), ordered_loci.end(), compare_genpos);
-
-        //
-        // Output the position of each site according to its basepair.
-        //
-        fh << "P";
-        for (uint pos = 0; pos < ordered_loci.size(); pos++) {
-            loc = catalog[ordered_loci[pos].id];
-            col = loc->snps[ordered_loci[pos].snp_index]->col;
-            fh << " " << ordered_loci[pos].bp;
-        }
-        fh << "\n";
-
-        //
-        // Output a line of 'S' characters, one per site, indicating that these are SNP markers.
-        //
-        string snp_markers, gtypes_str;
-        snp_markers.assign(total_sites, 'S');
-        fh << snp_markers << '\n';          
-
-        //
-        // Now output each sample name followed by a new line, then all of the genotypes for that sample
-        // on two lines.
-        //
-
-        map<int, pair<int, int> >::iterator pit;
-        int          start_index, end_index, pop_id;
-        char         p_allele, q_allele;
-        stringstream gtypes;
-
-        for (pit = pop_indexes.begin(); pit != pop_indexes.end(); pit++) {
-            pop_id      = psum->pop_index(pit->first);
-            start_index = pit->second.first;
-            end_index   = pit->second.second;
-
-            for (int j = start_index; j <= end_index; j++) {
-                //
-                // Output all the loci for this sample, printing only the p allele
-                //
-                fh << samples[pmap->rev_sample_index(j)] << "\n";
-                
-                gtypes.str("");
-                for (uint pos = 0; pos < ordered_loci.size(); pos++) {
-                    loc = catalog[ordered_loci[pos].id];
-                    col = loc->snps[ordered_loci[pos].snp_index]->col;
-
-                    s = psum->locus(loc->id);
-                    d = pmap->locus(loc->id);
-                    t = psum->locus_tally(loc->id);
-
-                    // 
-                    // If this site is fixed in all populations or has too many alleles don't output it.
-                    //
-                    if (t->nucs[col].allele_cnt != 2) 
-                        continue;
-
-                    if (s[pop_id]->nucs[col].incompatible_site ||
-                        s[pop_id]->nucs[col].filtered_site) {
-                        //
-                        // This site contains more than two alleles in this population or was filtered
-                        // due to a minor allele frequency that is too low.
-                        //
-                        gtypes << "? ";
-
-                    } else if (d[j] == NULL || col >= d[j]->len) {
-                        //
-                        // Data does not exist.
-                        //
-                        gtypes << "? ";
-                    } else if (d[j]->model[col] == 'U') {
-                        //
-                        // Data exists, but the model call was uncertain.
-                        //
-                        gtypes << "? ";
-                    } else {
-                        //
-                        // Tally up the nucleotide calls.
-                        //
-                        tally_observed_haplotypes(d[j]->obshap, ordered_loci[pos].snp_index, p_allele, q_allele);
-
-                        if (p_allele == 0 && q_allele == 0)
-                            gtypes << "? ";
-                        else if (p_allele == 0)
-                            gtypes << q_allele << " ";
-                        else
-                            gtypes << p_allele << " ";
-                    }
-                }
-                gtypes_str = gtypes.str();
-                fh << gtypes_str.substr(0, gtypes_str.length() - 1) << "\n";
-
-                //
-                // Output all the loci for this sample again, now for the q allele
-                //
-                gtypes.str("");
-                for (uint pos = 0; pos < ordered_loci.size(); pos++) {
-                    loc = catalog[ordered_loci[pos].id];
-                    col = loc->snps[ordered_loci[pos].snp_index]->col;
-
-
-                    s = psum->locus(loc->id);
-                    d = pmap->locus(loc->id);
-                    t = psum->locus_tally(loc->id);
-
-                    if (t->nucs[col].allele_cnt != 2) 
-                        continue;
-
-                    if (s[pop_id]->nucs[col].incompatible_site ||
-                        s[pop_id]->nucs[col].filtered_site) {
-                        gtypes << "? ";
-
-                    } else if (d[j] == NULL || col >= d[j]->len) {
-                        gtypes << "? ";
-
-                    } else if (d[j]->model[col] == 'U') {
-                        gtypes << "? ";
-
-                    } else {
-                        tally_observed_haplotypes(d[j]->obshap, ordered_loci[pos].snp_index, p_allele, q_allele);
-
-                        if (p_allele == 0 && q_allele == 0)
-                            gtypes << "? ";
-                        else if (q_allele == 0)
-                            gtypes << p_allele << " ";
-                        else
-                            gtypes << q_allele << " ";
-                    }
-                }
-                gtypes_str = gtypes.str();
-                fh << gtypes_str.substr(0, gtypes_str.length() - 1) << "\n";
-            }
-        }
-
-        fh.close();
-    }
-
-    cerr << "done.\n";
-
-    return 0;
-}
-
-int 
-write_phase(map<int, CSLocus *> &catalog, 
-            PopMap<CSLocus> *pmap, 
-            PopSum<CSLocus> *psum, 
-            map<int, pair<int, int> > &pop_indexes, 
-            map<int, string> &samples) 
-{
-    //
-    // Write a PHASE file as defined here: http://stephenslab.uchicago.edu/software.html
-    //
-    // Data will be written as mixture of multiple allele, linked RAD sites 
-    // (SNPs within a single RAD locus are already phased), and bi-allelic SNPs. We 
-    // will write one file per chromosome.
-    //
-    cerr << "Writing population data to PHASE files...";
-
-    map<string, vector<CSLocus *> >::iterator it;
-    CSLocus  *loc;
-    Datum   **d;
-    LocSum  **s;
-    LocTally *t;
-
-    for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
-
-        stringstream pop_name;
-        pop_name << "batch_" << batch_id << "." << it->first << ".phase.inp";
-        string file = in_path + pop_name.str();
-
-        ofstream fh(file.c_str(), ofstream::out);
-
-        if (fh.fail()) {
-            cerr << "Error opening PHASE file '" << file << "'\n";
-            exit(1);
-        }
-
-        //
-        // We need to determine an ordering for all legitimate loci/SNPs.
-        //
-        uint           col;
-        vector<GenPos> ordered_loci;
-        for (uint pos = 0; pos < it->second.size(); pos++) {
-            loc = it->second[pos];
-            t   = psum->locus_tally(loc->id);
-
-            if (loc->snps.size() == 0) continue;
-
-            //
-            // Will we output this locus as a haplotype or as a SNP?
-            //
-            if (loc->snps.size() > 1) {
-                //
-                // Check that there aren't too many haplotypes (PHASE has a max of 50).
-                //
-                if (loc->alleles.size() > 40) continue;
-
-                //
-                // Iterate over the population to determine that this subset of the population
-                // has data at this locus.
-                //
-                d = pmap->locus(loc->id);
-                for (int j = 0; j < pmap->sample_cnt(); j++) {
-                    if (d[j] != NULL &&
-                        d[j]->obshap.size() > 0 && 
-                        d[j]->obshap.size() <= 2) {
-                        //
-                        // Data exists, and there are the correct number of haplotypes.
-                        //
-                        ordered_loci.push_back(GenPos(loc->id, 0, loc->sort_bp(), haplotype));
-                        break;
-                    }
-                }
-            } else {
-                col = loc->snps[0]->col;
-
-                if (t->nucs[col].allele_cnt == 2)
-                    ordered_loci.push_back(GenPos(loc->id, 0, loc->sort_bp(col), snp));
-            }
-        }
-        sort(ordered_loci.begin(), ordered_loci.end(), compare_genpos);
-
-        //
-        // Output the total number of SNP sites and the number of individuals.
-        //
-        fh << samples.size()      << "\n"
-           << ordered_loci.size() << "\n";
-
-        //
-        // Output the position of each site according to its basepair.
-        //
-        fh << "P";
-        for (uint pos = 0; pos < ordered_loci.size(); pos++)
-            fh << " " << ordered_loci[pos].bp;
-        fh << "\n";
-
-        //
-        // Output a line of 'S' characters for SNP markers, 'M' characters for multiallelic haplotypes.
-        //
-        for (uint pos = 0; pos < ordered_loci.size(); pos++) {
-            if (pos > 0) fh << " ";
-            fh << (ordered_loci[pos].type == snp ? "S" : "M");
-        }
-        fh << "\n";
-
-        //
-        // Now output each sample name followed by a new line, then all of the genotypes for that sample
-        // on two lines.
-        //
-
-        map<int, pair<int, int> >::iterator pit;
-        string       gtypes_str;
-        bool         found;
-        int          start_index, end_index, pop_id;
-        char         p_allele, q_allele;
-        stringstream gtypes;
-
-        for (pit = pop_indexes.begin(); pit != pop_indexes.end(); pit++) {
-            pop_id      = psum->pop_index(pit->first);
-            start_index = pit->second.first;
-            end_index   = pit->second.second;
-
-            for (int j = start_index; j <= end_index; j++) {
-                //
-                // Output all the loci for this sample, printing only the p allele
-                //
-                fh << samples[pmap->rev_sample_index(j)] << "\n";
-                
-                gtypes.str("");
-                for (uint pos = 0; pos < ordered_loci.size(); pos++) {
-                    loc = catalog[ordered_loci[pos].id];
-
-                    s = psum->locus(loc->id);
-                    d = pmap->locus(loc->id);
-                    t = psum->locus_tally(loc->id);
-
-                    //
-                    // Will we output this locus as a haplotype or as a SNP?
-                    //
-                    if (ordered_loci[pos].type == haplotype) {
-                        if (d[j] == NULL) {
-                            //
-                            // Data does not exist.
-                            //
-                            gtypes << "-1 ";
-                        } else {
-                            //
-                            // Data exists, output the first haplotype. We will assume the haplotypes are 
-                            // numbered by their position in the loc->strings vector.
-                            //
-                            if (d[j]->obshap.size() > 2)  {
-                                // cerr << "Warning: too many haplotypes, catalog locus: " << loc->id << "\n";
-                                gtypes << "-1 ";
-                            } else {
-                                found = false;
-                                for (uint k = 0; k < loc->strings.size(); k++)
-                                    if (d[j]->obshap[0] == loc->strings[k].first) {
-                                        found = true;
-                                        gtypes << k + 1 << " ";
-                                    }
-                                if (found == false)
-                                    cerr << "Unable to find haplotype " << d[j]->obshap[0] << " from individual " 
-                                         << samples[pmap->rev_sample_index(j)] << "; catalog locus: " << loc->id << "\n";
-                            }
-                        }
-                    } else {
-                        col = loc->snps[ordered_loci[pos].snp_index]->col;
-
-                        if (s[pop_id]->nucs[col].incompatible_site ||
-                            s[pop_id]->nucs[col].filtered_site) {
-                            //
-                            // This site contains more than two alleles in this population or was filtered
-                            // due to a minor allele frequency that is too low.
-                            //
-                            gtypes << "? ";
-
-                        } else if (d[j] == NULL || col >= d[j]->len) {
-                            //
-                            // Data does not exist.
-                            //
-                            gtypes << "? ";
-                        } else if (d[j]->model[col] == 'U') {
-                            //
-                            // Data exists, but the model call was uncertain.
-                            //
-                            gtypes << "? ";
-                        } else {
-                            //
-                            // Tally up the nucleotide calls.
-                            //
-                            tally_observed_haplotypes(d[j]->obshap, ordered_loci[pos].snp_index, p_allele, q_allele);
-
-                            if (p_allele == 0 && q_allele == 0)
-                                gtypes << "? ";
-                            else if (p_allele == 0)
-                                gtypes << q_allele << " ";
-                            else
-                                gtypes << p_allele << " ";
-                        }
-                    }
-                }
-                gtypes_str = gtypes.str();
-                fh << gtypes_str.substr(0, gtypes_str.length() - 1) << "\n";
-
-                //
-                // Output all the loci for this sample again, now for the q allele
-                //
-                gtypes.str("");
-                for (uint pos = 0; pos < ordered_loci.size(); pos++) {
-                    loc = catalog[ordered_loci[pos].id];
-
-                    s = psum->locus(loc->id);
-                    d = pmap->locus(loc->id);
-                    t = psum->locus_tally(loc->id);
-
-                    //
-                    // Will we output this locus as a haplotype or as a SNP?
-                    //
-                    if (ordered_loci[pos].type == haplotype) {
-                        if (d[j] == NULL) {
-                            //
-                            // Data does not exist.
-                            //
-                            gtypes << "-1 ";
-                        } else {
-                            //
-                            // Data exists, output the second haplotype. We will assume the haplotypes are 
-                            // numbered by their position in the loc->strings vector.
-                            //
-                            if (d[j]->obshap.size() > 2)  {
-                                // cerr << "Warning: too many haplotypes, catalog locus: " << loc->id << "\n";
-                                gtypes << "-1 ";
-                            } else if (d[j]->obshap.size() > 1)  {
-                                found = false;
-                                for (uint k = 0; k < loc->strings.size(); k++)
-                                    if (d[j]->obshap[1] == loc->strings[k].first) {
-                                        found = true;
-                                        gtypes << k + 1 << " ";
-                                    }
-                                if (found == false)
-                                    cerr << "Unable to find haplotype " << d[j]->obshap[1] << " from individual " 
-                                         << samples[pmap->rev_sample_index(j)] << "; catalog locus: " << loc->id << "\n";
-                            } else {
-                                found = false;
-                                for (uint k = 0; k < loc->strings.size(); k++)
-                                    if (d[j]->obshap[0] == loc->strings[k].first) {
-                                        found = true;
-                                        gtypes << k + 1 << " ";
-                                    }
-                                if (found == false)
-                                    cerr << "Unable to find haplotype " << d[j]->obshap[0] << " from individual " 
-                                         << samples[pmap->rev_sample_index(j)] << "; catalog locus: " << loc->id << "\n";
-                            }
-                        }
-                    } else {
-                        col = loc->snps[ordered_loci[pos].snp_index]->col;
-
-                        if (s[pop_id]->nucs[col].incompatible_site ||
-                            s[pop_id]->nucs[col].filtered_site) {
-                            gtypes << "? ";
-
-                        } else if (d[j] == NULL || col >= d[j]->len) {
-                            gtypes << "? ";
-
-                        } else if (d[j]->model[col] == 'U') {
-                            gtypes << "? ";
-
-                        } else {
-                            tally_observed_haplotypes(d[j]->obshap, ordered_loci[pos].snp_index, p_allele, q_allele);
-
-                            if (p_allele == 0 && q_allele == 0)
-                                gtypes << "? ";
-                            else if (q_allele == 0)
-                                gtypes << p_allele << " ";
-                            else
-                                gtypes << q_allele << " ";
-                        }
-                    }
-                }
-                gtypes_str = gtypes.str();
-                fh << gtypes_str.substr(0, gtypes_str.length() - 1) << "\n";
-            }
-        }
-
-        fh.close();
-    }
-
-    cerr << "done.\n";
-
-    return 0;
-}
-
-int 
-write_plink(map<int, CSLocus *> &catalog, 
-            PopMap<CSLocus> *pmap, 
-            PopSum<CSLocus> *psum, 
-            map<int, pair<int, int> > &pop_indexes, 
-            map<int, string> &samples) 
-{
-    //
-    // Write a PLINK file as defined here: http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml
-    //
-    // We will write one file per chromosome.
-    //
-    cerr << "Writing population data to PLINK files...";
-
-    //
-    // Obtain the current date.
-    //
-    time_t     rawtime;
-    struct tm *timeinfo;
-    char       date[32];
-    time(&rawtime);
-    timeinfo = localtime(&rawtime);
-    strftime(date, 32, "%B %d, %Y", timeinfo);
-
-    map<string, vector<CSLocus *> >::iterator it;
-    CSLocus  *loc;
-    Datum   **d;
-    LocSum  **s;
-    LocTally *t;
-    string    chr;
-
-    //
-    // First, write a markers file containing each marker, the chromosome it falls on,
-    // an empty centiMorgan field, and finally its genomic position in basepairs.
-    //
-    stringstream pop_name;
-    pop_name << "batch_" << batch_id << ".plink.map";
-    string file = in_path + pop_name.str();
-
-    ofstream fh(file.c_str(), ofstream::out);
-
-    if (fh.fail()) {
-        cerr << "Error opening PLINK markers file '" << file << "'\n";
-        exit(1);
-    }
-
-    //
-    // Output the header.
-    //
-    fh << "# Stacks v" << VERSION << "; " << " PLINK v1.07; " << date << "\n";
-
-    for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
-        chr = it->first;
-
-        for (uint pos = 0; pos < it->second.size(); pos++) {
-            loc = it->second[pos];
-            t   = psum->locus_tally(loc->id);
-
-            for (uint i = 0; i < loc->snps.size(); i++) {
-                uint col = loc->snps[i]->col;
-                if (t->nucs[col].allele_cnt == 2)
-                    fh << chr << "\t"
-                       << loc->id << "_" << col << "\t"
-                       << "0\t" 
-                       << loc->sort_bp(col) << "\n";
-            }
-        }
-    }
-    fh.close();
-
-    //
-    // Now output the genotypes in a separate file.
-    //
-    pop_name.str("");
-    pop_name << "batch_" << batch_id << ".plink.ped";
-    file = in_path + pop_name.str();
-
-    fh.open(file.c_str(), ofstream::out);
-
-    if (fh.fail()) {
-        cerr << "Error opening PLINK markers file '" << file << "'\n";
-        exit(1);
-    }
-
-    fh << "# Stacks v" << VERSION << "; " << " PLINK v1.07; " << date << "\n";
-
-    map<int, pair<int, int> >::iterator pit;
-    int  start_index, end_index, pop_id;
-    char p_allele, q_allele;
-
-    //
-    //  marker, output the genotypes for each sample in two successive columns.
-    //
-    for (pit = pop_indexes.begin(); pit != pop_indexes.end(); pit++) {
-        pop_id      = psum->pop_index(pit->first);
-        start_index = pit->second.first;
-        end_index   = pit->second.second;
-
-        for (int j = start_index; j <= end_index; j++) {
-
-            fh << pit->first << "\t"
-               << samples[pmap->rev_sample_index(j)] << "\t"
-               << "0\t"  // Paternal ID
-               << "0\t"  // Maternal ID
-               << "0\t"  // Sex
-               << "0";   // Phenotype
-
-            for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
-                for (uint pos = 0; pos < it->second.size(); pos++) {
-                    loc = it->second[pos];
-
-                    s = psum->locus(loc->id);
-                    d = pmap->locus(loc->id);
-                    t = psum->locus_tally(loc->id);
- 
-                    for (uint i = 0; i < loc->snps.size(); i++) {
-                        uint col = loc->snps[i]->col;
-
-                        // 
-                        // If this site is fixed in all populations or has too many alleles don't output it.
-                        //
-                        if (t->nucs[col].allele_cnt != 2) 
-                            continue;
-                        //
-                        // Output the p and q alleles
-                        //
-                        if (s[pop_id]->nucs[col].incompatible_site ||
-                            s[pop_id]->nucs[col].filtered_site) {
-                            //
-                            // This site contains more than two alleles in this population or was filtered
-                            // due to a minor allele frequency that is too low.
-                            //
-                            fh << "\t" << "0" << "\t" << "0";
-                        } else if (d[j] == NULL || col >= d[j]->len) {
-                            //
-                            // Data does not exist.
-                            //
-                            fh << "\t" << "0" << "\t" << "0";
-                        } else if (d[j]->model[col] == 'U') {
-                            //
-                            // Data exists, but the model call was uncertain.
-                            //
-                            fh << "\t" << "0" << "\t" << "0";
-                        } else {
-                            //
-                            // Tally up the nucleotide calls.
-                            //
-                            tally_observed_haplotypes(d[j]->obshap, i, p_allele, q_allele);
-
-                            if (p_allele == 0 && q_allele == 0)
-                                fh << "\t" << "0" << "\t" << "0";
-                            else if (p_allele == 0)
-                                fh << "\t" << q_allele << "\t" << q_allele;
-                            else if (q_allele == 0)
-                                fh << "\t" << p_allele << "\t" << p_allele;
-                            else
-                                fh << "\t" << p_allele << "\t" << q_allele;
-                        }
-                    }
-                }
-            }
-            fh << "\n";
-        }
-    }
-
-    fh.close();
-
-    cerr << "done.\n";
-
-    return 0;
-}
-
-int 
-write_beagle(map<int, CSLocus *> &catalog, 
-            PopMap<CSLocus> *pmap, 
-            PopSum<CSLocus> *psum, 
-            map<int, pair<int, int> > &pop_indexes, 
-            map<int, string> &samples) 
-{
-    //
-    // Write a Beagle file as defined here: http://faculty.washington.edu/browning/beagle/beagle.html
-    //
-    // We will write one file per chromosome, per population.
-    //
-    cerr << "Writing population data to unphased Beagle files...";
-
-    //
-    // Obtain the current date.
-    //
-    time_t     rawtime;
-    struct tm *timeinfo;
-    char       date[32];
-    time(&rawtime);
-    timeinfo = localtime(&rawtime);
-    strftime(date, 32, "%B %d, %Y", timeinfo);
-
-    map<string, vector<CSLocus *> >::iterator it;
-    CSLocus  *loc;
-    Datum   **d;
-    LocSum  **s;
-    LocTally *t;
-    uint      col;
-
-    stringstream pop_name;
-    string       file;
-
-    for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
-
-        //
-        // We need to determine an ordering that can take into account overlapping RAD sites.
-        //
-        vector<GenPos> ordered_loci;
-        for (uint pos = 0; pos < it->second.size(); pos++) {
-            loc = it->second[pos];
-            t   = psum->locus_tally(loc->id);
-
-            for (uint i = 0; i < loc->snps.size(); i++) {
-                col = loc->snps[i]->col;
-                if (t->nucs[col].allele_cnt == 2)
-                    ordered_loci.push_back(GenPos(loc->id, i, loc->sort_bp(col)));
-            }
-        }
-        sort(ordered_loci.begin(), ordered_loci.end(), compare_genpos);
-
-        //
-        // Now output the genotypes in a separate file for each population.
-        //
-        map<int, pair<int, int> >::iterator pit;
-        int  start_index, end_index, pop_id;
-
-        for (pit = pop_indexes.begin(); pit != pop_indexes.end(); pit++) {
-            pop_id      = psum->pop_index(pit->first);
-            start_index = pit->second.first;
-            end_index   = pit->second.second;
-
-            //
-            // Open a markers file containing each marker, its genomic position in basepairs
-            // and the two alternative alleles at this position.
-            //
-            pop_name.str("");
-            pop_name << "batch_" << batch_id << "." << pop_key[pit->first] << "-" << it->first << ".unphased.bgl.markers";
-            file = in_path + pop_name.str();
-
-            ofstream mfh(file.c_str(), ofstream::out);
-            if (mfh.fail()) {
-                cerr << "Error opening Beagle markers file '" << file << "'\n";
-                exit(1);
-            }
-            mfh << "# Stacks v" << VERSION << "; " << " Beagle v3.3; " << date << "\n";
-
-            //
-            // Open the genotypes file.
-            //
-            pop_name.str("");
-            pop_name << "batch_" << batch_id << "." << pop_key[pit->first] << "-" << it->first << ".unphased.bgl";
-            file = in_path + pop_name.str();
-
-            ofstream fh(file.c_str(), ofstream::out);
-            if (fh.fail()) {
-                cerr << "Error opening Beagle genotypes file '" << file << "'\n";
-                exit(1);
-            }
-            fh << "# Stacks v" << VERSION << "; " << " Beagle v3.3; " << date << "\n";
-
-            char p_allele, q_allele;
-            //
-            // Output a list of all the samples in this population.
-            //
-            fh << "I\tid";
-            for (int j = start_index; j <= end_index; j++)
-                fh << "\t" << samples[pmap->rev_sample_index(j)] << "\t" << samples[pmap->rev_sample_index(j)];
-            fh << "\n";
-
-            //
-            // Output population IDs for each sample.
-            //
-            fh << "S\tid";
-            for (int j = start_index; j <= end_index; j++)
-                fh << "\t" << pit->first << "\t" << pit->first;
-            fh << "\n";
-
-            //
-            // For each marker, output the genotypes for each sample in two successive columns.
-            //
-            for (uint pos = 0; pos < ordered_loci.size(); pos++) {
-                loc = catalog[ordered_loci[pos].id];
-
-                s   = psum->locus(loc->id);
-                d   = pmap->locus(loc->id);
-                t   = psum->locus_tally(loc->id);
-                col = loc->snps[ordered_loci[pos].snp_index]->col;
-
-                // 
-                // If this site is fixed in all populations or has too many alleles don't output it.
-                //
-                if (t->nucs[col].allele_cnt != 2) 
-                    continue;
-
-                //
-                // If this site is monomorphic in this population don't output it.
-                //
-                if (s[pop_id]->nucs[col].pi == 0.0)
-                    continue;
-
-                //
-                // Output this locus to the markers file.
-                //
-                mfh << loc->id << "_" << col << "\t" 
-                    << loc->sort_bp(col)     << "\t" 
-                    << t->nucs[col].p_allele << "\t" 
-                    << t->nucs[col].q_allele << "\n";
-
-                fh << "M" << "\t" << loc->id << "_" << col;
-
-                for (int j = start_index; j <= end_index; j++) {
-                    //
-                    // Output the p allele
-                    //
-                    if (s[pop_id]->nucs[col].incompatible_site ||
-                        s[pop_id]->nucs[col].filtered_site) {
-                        //
-                        // This site contains more than two alleles in this population or was filtered
-                        // due to a minor allele frequency that is too low.
-                        //
-                        fh << "\t" << "?";
-
-                    } else if (d[j] == NULL || col >= d[j]->len) {
-                        //
-                        // Data does not exist.
-                        //
-                        fh << "\t" << "?";
-                    } else if (d[j]->model[col] == 'U') {
-                        //
-                        // Data exists, but the model call was uncertain.
-                        //
-                        fh << "\t" << "?";
-                    } else {
-                        //
-                        // Tally up the nucleotide calls.
-                        //
-                        tally_observed_haplotypes(d[j]->obshap, ordered_loci[pos].snp_index, p_allele, q_allele);
-
-                        if (p_allele == 0 && q_allele == 0)
-                            fh << "\t" << "?";
-                        else if (p_allele == 0)
-                            fh << "\t" << q_allele;
-                        else
-                            fh << "\t" << p_allele;
-                    }
-
-                    //
-                    // Now output the q allele
-                    //
-                    if (s[pop_id]->nucs[col].incompatible_site ||
-                        s[pop_id]->nucs[col].filtered_site) {
-                        fh << "\t" << "?";
-
-                    } else if (d[j] == NULL || col >= d[j]->len) {
-                        fh << "\t" << "?";
-
-                    } else if (d[j]->model[col] == 'U') {
-                        fh << "\t" << "?";
-
-                    } else {
-                        if (p_allele == 0 && q_allele == 0)
-                            fh << "\t" << "?";
-                        else if (q_allele == 0)
-                            fh << "\t" << p_allele;
-                        else
-                            fh << "\t" << q_allele;
-                    }
-                }
-                fh << "\n";
-            }
-
-            fh.close();
-            mfh.close();
-        }
-    }
-
-    cerr << "done.\n";
-
-    return 0;
-}
-
-int 
-write_beagle_phased(map<int, CSLocus *> &catalog, 
-                    PopMap<CSLocus> *pmap, 
-                    PopSum<CSLocus> *psum, 
-                    map<int, pair<int, int> > &pop_indexes, 
-                    map<int, string> &samples) 
-{
-    //
-    // Write a Beagle file as a set of haplotpyes as defined here: 
-    //   http://faculty.washington.edu/browning/beagle/beagle.html
-    //
-    // We will write one file per chromosome.
-    //
-    cerr << "Writing population data to phased Beagle files...";
-
-    //
-    // Obtain the current date.
-    //
-    time_t     rawtime;
-    struct tm *timeinfo;
-    char       date[32];
-    time(&rawtime);
-    timeinfo = localtime(&rawtime);
-    strftime(date, 32, "%B %d, %Y", timeinfo);
-
-    map<string, vector<CSLocus *> >::iterator it;
-    CSLocus  *loc;
-    Datum   **d;
-
-    stringstream pop_name;
-    string       file;
-
-    for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
-
-        //
-        // We need to determine an ordering for all legitimate loci/SNPs.
-        //
-        vector<GenPos> ordered_loci;
-        for (uint pos = 0; pos < it->second.size(); pos++) {
-            loc = it->second[pos];
-
-            if (loc->snps.size() == 0) continue;
-
-            //
-            // Check that there aren't too many haplotypes (PHASE has a max of 50).
-            //
-            if (loc->alleles.size() > 40) continue;
-
-            //
-            // Iterate over the population to determine that this subset of the population
-            // has data at this locus.
-            //
-            d = pmap->locus(loc->id);
-            for (int j = 0; j < pmap->sample_cnt(); j++) {
-                if (d[j] != NULL &&
-                    d[j]->obshap.size() > 0 && 
-                    d[j]->obshap.size() <= 2) {
-                    //
-                    // Data exists, and their are the corrent number of haplotypes.
-                    //
-                    ordered_loci.push_back(GenPos(loc->id, 0, loc->sort_bp(), haplotype));
-                    break;
-                }
-            }
-        }
-        sort(ordered_loci.begin(), ordered_loci.end(), compare_genpos);
-
-        //
-        // Now output the genotypes in a separate file for each population.
-        //
-        map<int, pair<int, int> >::iterator pit;
-        int  start_index, end_index, pop_id;
-
-        for (pit = pop_indexes.begin(); pit != pop_indexes.end(); pit++) {
-            pop_id      = psum->pop_index(pit->first);
-            start_index = pit->second.first;
-            end_index   = pit->second.second;
-
-            //
-            // Open a file for writing the markers: their genomic position in basepairs
-            // and the two alternative alleles at this position.
-            //
-            pop_name.str("");
-            pop_name << "batch_" << batch_id << "." << pop_key[pit->first] << "-" << it->first << ".phased.bgl.markers";
-            file = in_path + pop_name.str();
-
-            ofstream mfh(file.c_str(), ofstream::out);
-            if (mfh.fail()) {
-                cerr << "Error opening Beagle markers file '" << file << "'\n";
-                exit(1);
-            }
-            mfh << "# Stacks v" << VERSION << "; " << " Beagle v3.3; " << date << "\n";
-
-            //
-            // Now output the haplotypes in a separate file.
-            //
-            pop_name.str("");
-            pop_name << "batch_" << batch_id << "." << pop_key[pit->first] << "-" << it->first << ".phased.bgl";
-            file = in_path + pop_name.str();
-
-            ofstream fh(file.c_str(), ofstream::out);
-            if (fh.fail()) {
-                cerr << "Error opening Beagle markers file '" << file << "'\n";
-                exit(1);
-            }
-            fh << "# Stacks v" << VERSION << "; " << " Beagle v3.3; " << date << "\n";
-
-            //
-            // Output a list of all the samples in the data set.
-            //
-            fh << "I\tid";
-            for (int j = start_index; j <= end_index; j++)
-                fh << "\t" << samples[pmap->rev_sample_index(j)] << "\t" << samples[pmap->rev_sample_index(j)];
-            fh << "\n";
-
-            //
-            // Output population IDs for each sample.
-            //
-            fh << "S\tid";
-            for (int j = start_index; j <= end_index; j++)
-                fh << "\t" << pop_id << "\t" << pop_id;
-            fh << "\n";
-
-            for (uint pos = 0; pos < ordered_loci.size(); pos++) {
-                loc = catalog[ordered_loci[pos].id];
-                d   = pmap->locus(loc->id);
-
-                //
-                // If this locus is monomorphic in this population don't output it.
-                //
-                set<string> haplotypes;
-                for (int j = start_index; j <= end_index; j++) {
-                    if (d[j] == NULL) continue;
-
-                    if (d[j]->obshap.size() == 2) {
-                        haplotypes.insert(d[j]->obshap[0]);
-                        haplotypes.insert(d[j]->obshap[1]);
-                    } else {
-                        haplotypes.insert(d[j]->obshap[0]);
-                    }
-                }
-                if (haplotypes.size() == 1) continue;
-
-                //
-                // Output this locus to the markers file.
-                //
-                mfh << loc->id << "\t" 
-                    << loc->sort_bp();
-                for (uint j = 0; j < loc->strings.size(); j++)
-                    mfh << "\t" << loc->strings[j].first;
-                mfh << "\n";
-
-                //
-                // For each marker, output the genotypes for each sample in two successive columns.
-                //
-                fh << "M" << "\t" << loc->id;
-
-                for (int j = start_index; j <= end_index; j++) {
-                    //
-                    // Output the p and the q haplotype
-                    //
-                    if (d[j] == NULL) {
-                        //
-                        // Data does not exist.
-                        //
-                        fh << "\t" << "?" << "\t" << "?";
-                    } else {
-                        //
-                        // Data exists, output the first haplotype. We will assume the haplotypes are 
-                        // numbered by their position in the loc->strings vector.
-                        //
-                        if (d[j]->obshap.size() > 2)
-                            fh << "\t" << "?" << "\t" << "?";
-                        else if (d[j]->obshap.size() == 2)
-                            fh << "\t" << d[j]->obshap[0] << "\t" << d[j]->obshap[1];
-                        else
-                            fh << "\t" << d[j]->obshap[0] << "\t" << d[j]->obshap[0];
-                    }
-                }
-                fh << "\n";
-            }
-            fh.close();
-            mfh.close();
-        }
-    }   
-
-    cerr << "done.\n";
-
-    return 0;
-}
-
-int 
-write_phylip(map<int, CSLocus *> &catalog, 
-             PopMap<CSLocus> *pmap, 
-             PopSum<CSLocus> *psum, 
-             map<int, pair<int, int> > &pop_indexes, 
-             map<int, string> &samples) 
-{
-    //
-    // We want to find loci where each locus is fixed within a population but variable between populations.
-    //
-    // We will write those loci to a Phylip file as defined here: 
-    //     http://evolution.genetics.washington.edu/phylip/doc/main.html#inputfiles
-    //
-    stringstream pop_name;
-    pop_name << "batch_" << batch_id << ".phylip";
-    string file = in_path + pop_name.str();
-
-    cerr << "Writing population data to Phylip file '" << file << "'; ";
-
-    ofstream fh(file.c_str(), ofstream::out);
-
-    if (fh.fail()) {
-        cerr << "Error opening Phylip file '" << file << "'\n";
-        exit(1);
-    }
-
-    pop_name << ".log";
-    file = in_path + pop_name.str();
-
-    cerr << "logging nucleotide positions to '" << file << "'...";
-
-    ofstream log_fh(file.c_str(), ofstream::out);
-
-    if (log_fh.fail()) {
-        cerr << "Error opening Phylip Log file '" << file << "'\n";
-        exit(1);
-    }
-
-    //
-    // Obtain the current date.
-    //
-    time_t     rawtime;
-    struct tm *timeinfo;
-    char       date[32];
-    time(&rawtime);
-    timeinfo = localtime(&rawtime);
-    strftime(date, 32, "%B %d, %Y", timeinfo);
-
-    log_fh << "# Stacks v" << VERSION << "; " << " Phylip sequential; " << date << "\n"
-           << "# Seq Pos\tLocus ID\tColumn\tPopulation\n";
-
-    map<string, vector<CSLocus *> >::iterator it;
-    CSLocus  *loc;
-    LocSum  **s;
-    LocTally *t;
-
-    map<int, pair<int, int> >::iterator pit;
-    int  pop_cnt = psum->pop_cnt();
-    int  pop_id;
-    char nuc;
-
-    //
-    // A map storing, for each population, the concatenated list of interspecific nucleotides.
-    //
-    map<int, string> interspecific_nucs;
-
-    int index = 0;
-    for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
-        for (uint pos = 0; pos < it->second.size(); pos++) {
-            loc = it->second[pos];
-
-            s = psum->locus(loc->id);
-            t = psum->locus_tally(loc->id);
-
-            for (uint i = 0; i < loc->snps.size(); i++) {
-                uint col = loc->snps[i]->col;
-
-                if (phylip_var == false) {
-                    //
-                    // We are looking for loci that are fixed within each population, but are 
-                    // variable between one or more populations.
-                    //
-                    if (t->nucs[col].fixed == true || t->nucs[col].allele_cnt != 2 || t->nucs[col].pop_cnt < 2)
-                        continue;
-
-                    bool fixed_within = true;
-                    for (int j = 0; j < pop_cnt; j++) {
-                        if (s[j]->nucs[col].num_indv == 0)
-                            continue;
-                        if (s[j]->nucs[col].fixed == false) {
-                            fixed_within = false;
-                            break;
-                        }
-                    }
-                    if (fixed_within == false) continue;
-
-                    log_fh << index << "\t" << loc->id << "\t" << col << "\t";
-
-                    for (int j = 0; j < pop_cnt; j++) {
-                        pop_id = psum->rev_pop_index(j);
-
-                        if (s[j]->nucs[col].num_indv > 0) {
-                            interspecific_nucs[pop_id] += s[j]->nucs[col].p_nuc;
-                            log_fh << pop_key[pop_id] << ":" << s[j]->nucs[col].p_nuc << ",";
-                        } else {
-                            interspecific_nucs[pop_id] += 'N';
-                            log_fh << pop_key[pop_id] << ":N" << ",";
-                        }
-                    }
-                    log_fh << "\n";
-                    index++;
-
-                } else {
-                    //
-                    // Encode SNPs that are variable within a population as well, using IUPAC notation:
-                    //     http://en.wikipedia.org/wiki/Nucleic_acid_notation#IUPAC_notation
-                    //
-                    if (t->nucs[col].allele_cnt != 2)
-                        continue;
-
-                    log_fh << index << "\t" << loc->id << "\t" << col << "\t";
-
-                    for (int j = 0; j < pop_cnt; j++) {
-                        pop_id = psum->rev_pop_index(j);
-
-                        switch(s[j]->nucs[col].p_nuc) {
-                        case 0:
-                            nuc = 'N';
-                            break;
-                        case 'A':
-                            switch(s[j]->nucs[col].q_nuc) {
-                            case 'C':
-                                nuc = 'M';
-                                break;
-                            case 'G':
-                                nuc = 'R';
-                                break;
-                            case 'T':
-                                nuc = 'W';
-                                break;
-                            case 0:
-                                nuc = 'A';
-                                break;
-                            }
-                            break;
-                        case 'C':
-                            switch(s[j]->nucs[col].q_nuc) {
-                            case 'A':
-                                nuc = 'M';
-                                break;
-                            case 'G':
-                                nuc = 'S';
-                                break;
-                            case 'T':
-                                nuc = 'Y';
-                                break;
-                            case 0:
-                                nuc = 'C';
-                                break;
-                            }
-                            break;
-                        case 'G':
-                            switch(s[j]->nucs[col].q_nuc) {
-                            case 'A':
-                                nuc = 'R';
-                                break;
-                            case 'C':
-                                nuc = 'S';
-                                break;
-                            case 'T':
-                                nuc = 'K';
-                                break;
-                            case 0:
-                                nuc = 'G';
-                                break;
-                            }
-                            break;
-                        case 'T':
-                            switch(s[j]->nucs[col].q_nuc) {
-                            case 'A':
-                                nuc = 'W';
-                                break;
-                            case 'C':
-                                nuc = 'Y';
-                                break;
-                            case 'G':
-                                nuc = 'K';
-                                break;
-                            case 0:
-                                nuc = 'T';
-                                break;
-                            }
-                            break;
-                        }
-                        interspecific_nucs[pop_id] += nuc;
-                        log_fh << pop_key[pop_id] << ":" << nuc << ",";
-
-                    }
-                    log_fh << "\n";
-                    index++;
-                }
-            }
-        }
-    }
-
-    if (interspecific_nucs.size() == 0) {
-        cerr << "  No data is available to write to the Phylip file.\n";
-        return 0;
-    }
-
-    char id_str[id_len];
-    uint len;
-
-    fh << pop_indexes.size() << "    " << interspecific_nucs.begin()->second.length() << "\n";
-    for (pit = pop_indexes.begin(); pit != pop_indexes.end(); pit++) {
-        pop_id = pit->first;
-
-        sprintf(id_str, "%s", pop_key[pop_id].c_str());
-        len = strlen(id_str);
-        for (uint j = len; j < 10; j++)
-            id_str[j] = ' ';
-        id_str[9] = '\0'; 
-
-        fh << id_str << " " << interspecific_nucs[pop_id] << "\n";
-    }
-
-    //
-    // Output the header.
-    //
-    fh << "# Stacks v" << VERSION << "; " << " Phylip sequential; " << date << "\n";
-
-    fh.close();
-    log_fh.close();
-
-    cerr << "done.\n";
-
-    return 0;
-}
-
-int 
-write_fullseq_phylip(map<int, CSLocus *> &catalog, 
-                     PopMap<CSLocus> *pmap, 
-                     PopSum<CSLocus> *psum, 
-                     map<int, pair<int, int> > &pop_indexes, 
-                     map<int, string> &samples) 
-{
-    //
-    // We want to write all variable loci in Phylip interleaved format. Polymorphic positions
-    // will be encoded using IUPAC notation.
-    //
-    // We will write those loci to a Phylip file as defined here: 
-    //     http://evolution.genetics.washington.edu/phylip/doc/main.html#inputfiles
-    //
-    stringstream pop_name;
-    pop_name << "batch_" << batch_id << ".fullseq.phylip";
-    string file = in_path + pop_name.str();
-
-    cerr << "Writing full sequence population data to Phylip file '" << file << "'; ";
-
-    ofstream fh(file.c_str(), ofstream::out);
-
-    if (fh.fail()) {
-        cerr << "Error opening Phylip file '" << file << "'\n";
-        exit(1);
-    }
-
-    //
-    // We will also write a file that allows us to specify each RAD locus as a separate partition
-    // for use in phylogenetics programs.
-    //
-    pop_name.str("");
-    pop_name << "batch_" << batch_id << ".fullseq.partitions.phylip";
-    file = in_path + pop_name.str();
-
-    ofstream par_fh(file.c_str(), ofstream::out);
-
-    if (par_fh.fail()) {
-        cerr << "Error opening Phylip partitions file '" << file << "'\n";
-        exit(1);
-    }
-
-    pop_name.str("");
-    pop_name << "batch_" << batch_id << "fullseq.phylip.log";
-    file = in_path + pop_name.str();
-
-    cerr << "logging nucleotide positions to '" << file << "'...";
-
-    ofstream log_fh(file.c_str(), ofstream::out);
-
-    if (log_fh.fail()) {
-        cerr << "Error opening Phylip Log file '" << file << "'\n";
-        exit(1);
-    }
-
-        //
-    // Obtain the current date.
-    //
-    time_t     rawtime;
-    struct tm *timeinfo;
-    char       date[32];
-    time(&rawtime);
-    timeinfo = localtime(&rawtime);
-    strftime(date, 32, "%B %d, %Y", timeinfo);
-
-    log_fh << "# Stacks v" << VERSION << "; " << " Phylip interleaved; " << date << "\n"
-           << "# Locus ID\tLine Number";
-    if (loci_ordered) log_fh << "\tChr\tBasepair";
-    log_fh << "\n";
-
-    map<string, vector<CSLocus *> >::iterator it;
-    CSLocus  *loc;
-    LocSum  **s;
-    LocTally *t;
-
-    map<int, pair<int, int> >::iterator pit;
-    int  pop_cnt = psum->pop_cnt();
-    int  pop_id;
-    char nuc;
-
-    bool include;
-    char id_str[id_len];
-    uint len = 0;
-
-    //
-    // Determine the length of sequence we will output.
-    //
-    for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
-        for (uint pos = 0; pos < it->second.size(); pos++) {
-            loc = it->second[pos];
-
-            t = psum->locus_tally(loc->id);
-
-            include = true;
-            for (uint i = 0; i < loc->snps.size(); i++) {
-                uint col = loc->snps[i]->col;
-
-                if (t->nucs[col].allele_cnt != 2)
-                    include = false;
-            }
-
-            if (include)
-                len += strlen(loc->con);
-        }
-    }
-
-    map<int, string> outstrs;
-    
-    fh << pop_indexes.size() << "    " << len << "\n";
-
-    for (pit = pop_indexes.begin(); pit != pop_indexes.end(); pit++) {
-        pop_id = pit->first;
-
-        outstrs[pop_id] = "";
-        sprintf(id_str, "%s", pop_key[pop_id].c_str());
-        len = strlen(id_str);
-        for (uint j = len; j < 10; j++)
-            id_str[j] = ' ';
-        id_str[9] = '\0'; 
-
-        outstrs[pop_id] += string(id_str) + " ";
-    }
-
-    char *seq;
-    int   line  = 1;
-    int   index = 1;
-    int   cnt   = 1;
-    
-    for (it = pmap->ordered_loci.begin(); it != pmap->ordered_loci.end(); it++) {
-        for (uint pos = 0; pos < it->second.size(); pos++) {
-            loc = it->second[pos];
-
-            s = psum->locus(loc->id);
-            t = psum->locus_tally(loc->id);
-
-            include = true;
-            for (uint i = 0; i < loc->snps.size(); i++) {
-                uint col = loc->snps[i]->col;
-
-                if (t->nucs[col].allele_cnt != 2)
-                    include = false;
-            }
-
-            if (!include)
-                continue;
-
-            seq = new char[loc->len + 1];
-            strcpy(seq, loc->con);
-
-            for (int j = 0; j < pop_cnt; j++) {
-                pop_id = psum->rev_pop_index(j);
-
-                for (uint i = 0; i < loc->snps.size(); i++) {
-                    uint col = loc->snps[i]->col;
-
-                    //
-                    // Encode SNPs that are variable within a population using IUPAC notation:
-                    //     http://en.wikipedia.org/wiki/Nucleic_acid_notation#IUPAC_notation
-                    //
-                    switch(s[j]->nucs[col].p_nuc) {
-                    case 0:
-                        nuc = 'N';
-                        break;
-                    case 'A':
-                        switch(s[j]->nucs[col].q_nuc) {
-                        case 'C':
-                            nuc = 'M';
-                            break;
-                        case 'G':
-                            nuc = 'R';
-                            break;
-                        case 'T':
-                            nuc = 'W';
-                            break;
-                        case 0:
-                            nuc = 'A';
-                            break;
-                        }
-                        break;
-                    case 'C':
-                        switch(s[j]->nucs[col].q_nuc) {
-                        case 'A':
-                            nuc = 'M';
-                            break;
-                        case 'G':
-                            nuc = 'S';
-                            break;
-                        case 'T':
-                            nuc = 'Y';
-                            break;
-                        case 0:
-                            nuc = 'C';
-                            break;
-                        }
-                        break;
-                    case 'G':
-                        switch(s[j]->nucs[col].q_nuc) {
-                        case 'A':
-                            nuc = 'R';
-                            break;
-                        case 'C':
-                            nuc = 'S';
-                            break;
-                        case 'T':
-                            nuc = 'K';
-                            break;
-                        case 0:
-                            nuc = 'G';
-                            break;
-                        }
-                        break;
-                    case 'T':
-                        switch(s[j]->nucs[col].q_nuc) {
-                        case 'A':
-                            nuc = 'W';
-                            break;
-                        case 'C':
-                            nuc = 'Y';
-                            break;
-                        case 'G':
-                            nuc = 'K';
-                            break;
-                        case 0:
-                            nuc = 'T';
-                            break;
-                        }
-                        break;
-                    }
-
-                    seq[col] = nuc;
-                }
-                
-                outstrs[pop_id] += string(seq);
-            }
-            delete [] seq;
-
-            log_fh << line << "\t" << loc->id;
-            if (loci_ordered) log_fh << "\t" << loc->loc.chr << "\t" << loc->sort_bp() + 1;
-            log_fh << "\n";
-            
-            for (pit = pop_indexes.begin(); pit != pop_indexes.end(); pit++) {
-                pop_id = pit->first;
-                fh << outstrs[pop_id] << "\n";
-                outstrs[pop_id] = "";
-                line++;
-            }
-            fh << "\n";
-            line++;
-
-            par_fh << "DNA, p" << cnt << "=" << index << "-" << index + loc->len - 1 << "\n";
-            index += loc->len;
-            cnt++;
-        }
-    }
-
-    //
-    // Output the header.
-    //
-    fh << "# Stacks v" << VERSION << "; " << " Phylip interleaved; " << date << "\n";
-
-    fh.close();
-    par_fh.close();
-    log_fh.close();
-
-    cerr << "done.\n";
-
-    return 0;
-}
-
-int 
-tally_ref_alleles(LocSum **s, int pop_cnt, int snp_index, char &p_allele, char &q_allele) 
-{
-    int  nucs[4] = {0};
-    char nuc[2];
-
-    for (int j = 0; j < pop_cnt; j++) {
-        nuc[0] = 0;
-        nuc[1] = 0;
-        nuc[0] = s[j]->nucs[snp_index].p_nuc;
-        nuc[1] = s[j]->nucs[snp_index].q_nuc;
-
-        for (uint k = 0; k < 2; k++) 
-            switch(nuc[k]) {
-            case 'A':
-            case 'a':
-                nucs[0]++;
-                break;
-            case 'C':
-            case 'c':
-                nucs[1]++;
-                break;
-            case 'G':
-            case 'g':
-                nucs[2]++;
-                break;
-            case 'T':
-            case 't':
-                nucs[3]++;
-                break;
-            }
-    }
-
-    //
-    // Determine how many alleles are present at this position in this population.
-    // We cannot deal with more than two alternative alleles, if there are more than two
-    // in a single population, print a warning and exclude this nucleotide position.
-    //
-    int i;
-    int allele_cnt = 0;
-    for (i = 0; i < 4; i++)
-        if (nucs[i] > 0) allele_cnt++;
-
-    if (allele_cnt > 2) {
-        p_allele = 0;
-        q_allele = 0;
-        return 0;
-    }
-
-    //
-    // Record which nucleotide is the P allele and which is the Q allele.
-    //
-    p_allele = 0;
-    q_allele = 0;
-
-    i = 0;
-    while (p_allele == 0 && i < 4) {
-        if (nucs[i] > 0) {
-            switch(i) {
-            case 0:
-                p_allele = 'A';
-                break;
-            case 1:
-                p_allele = 'C';
-                break;
-            case 2:
-                p_allele = 'G';
-                break;
-            case 3:
-                p_allele = 'T';
-                break;
-            }
-        }
-        i++;
-    }
-    while (q_allele == 0 && i < 4) {
-        if (nucs[i] > 0) {
-            switch(i) {
-            case 1:
-                q_allele = 'C';
-                break;
-            case 2:
-                q_allele = 'G';
-                break;
-            case 3:
-                q_allele = 'T';
-                break;
-            }
-        }
-        i++;
-    }
-
-    return 1;
-}
-
-int 
-tally_observed_haplotypes(vector<char *> &obshap, int snp_index, char &p_allele, char &q_allele) 
-{
-    int  nucs[4] = {0};
-    char nuc;
-
-    //
-    // Pull each allele for this SNP from the observed haplotype.
-    //
-    for (uint j = 0; j < obshap.size(); j++) {
-        nuc = obshap[j][snp_index];
-
-        switch(nuc) {
-        case 'A':
-        case 'a':
-            nucs[0]++;
-            break;
-        case 'C':
-        case 'c':
-            nucs[1]++;
-            break;
-        case 'G':
-        case 'g':
-            nucs[2]++;
-            break;
-        case 'T':
-        case 't':
-            nucs[3]++;
-            break;
-        }
-    }
-
-    //
-    // Determine how many alleles are present at this position in this population.
-    // We cannot deal with more than two alternative alleles, if there are more than two
-    // in a single population, print a warning and exclude this nucleotide position.
-    //
-    int i;
-    int allele_cnt = 0;
-    for (i = 0; i < 4; i++)
-        if (nucs[i] > 0) allele_cnt++;
-
-    if (allele_cnt > 2) {
-        p_allele = 0;
-        q_allele = 0;
-        return -1;
-    }
-
-    //
-    // Record which nucleotide is the P allele and which is the Q allele.
-    //
-    p_allele = 0;
-    q_allele = 0;
-
-    i = 0;
-    while (p_allele == 0 && i < 4) {
-        if (nucs[i] > 0) {
-            switch(i) {
-            case 0:
-                p_allele = 'A';
-                break;
-            case 1:
-                p_allele = 'C';
-                break;
-            case 2:
-                p_allele = 'G';
-                break;
-            case 3:
-                p_allele = 'T';
-                break;
-            }
-        }
-        i++;
-    }
-    while (q_allele == 0 && i < 4) {
-        if (nucs[i] > 0) {
-            switch(i) {
-            case 1:
-                q_allele = 'C';
-                break;
-            case 2:
-                q_allele = 'G';
-                break;
-            case 3:
-                q_allele = 'T';
-                break;
-            }
-        }
-        i++;
-    }
-
-    return 0;
-}
-
-int load_marker_list(string path, set<int> &list) {
-    char     line[id_len];
-    ifstream fh(path.c_str(), ifstream::in);
-
-    if (fh.fail()) {
-        cerr << "Error opening white/black list file '" << path << "'\n";
-        exit(1);
-    }
-
-    int   marker;
-    char *p, *e;
-
-    while (fh.good()) {
-        fh.getline(line, id_len);
-
-        if (strlen(line) == 0) continue;
-
-        //
-        // Skip commented lines.
-        //
-        for (p = line; isspace(*p) && *p != '\0'; p++);
-        if (*p == '#') continue;
-
-        marker = (int) strtol(line, &e, 10);
-
-        if (*e == '\0')
-            list.insert(marker);
-    }
-
-    fh.close();
-
-    if (list.size() == 0) {
-        cerr << "Unable to load any markers from '" << path << "'\n";
-        exit(1);
-    }
-
-    return 0;
-}
-
-int load_marker_column_list(string path, map<int, set<int> > &list) {
-    char     line[id_len];
-    ifstream fh(path.c_str(), ifstream::in);
-
-    if (fh.fail()) {
-        cerr << "Error opening white/black list file '" << path << "'\n";
-        exit(1);
-    }
-
-    vector<string> parts;
-    uint  marker, col;
-    char *p, *e;
-
-    uint line_num = 1;
-    while (fh.good()) {
-        fh.getline(line, id_len);
-
-        if (strlen(line) == 0) continue;
-
-        //
-        // Skip commented lines.
-        //
-        for (p = line; isspace(*p) && *p != '\0'; p++);
-        if (*p == '#') continue;
-
-        //
-        // Parse the whitelist, we expect:
-        // <marker>[<tab><snp column>]
-        //
-        parse_tsv(line, parts);
-
-        if (parts.size() > 2) {
-            cerr << "Too many columns in whitelist " << path << "' at line " << line_num << "\n";
-            exit(1);
-
-        } else if (parts.size() == 2) {
-            marker = (int) strtol(parts[0].c_str(), &e, 10);
-            if (*e != '\0') {
-                cerr << "Unable to parse whitelist, '" << path << "' at line " << line_num << "\n";
-                exit(1);
-            }
-            col = (int) strtol(parts[1].c_str(), &e, 10);
-            if (*e != '\0') {
-                cerr << "Unable to parse whitelist, '" << path << "' at line " << line_num << "\n";
-                exit(1);
-            }
-            list[marker].insert(col);
-
-        } else {
-            marker = (int) strtol(parts[0].c_str(), &e, 10);
-            if (*e != '\0') {
-                cerr << "Unable to parse whitelist, '" << path << "' at line " << line << "\n";
-                exit(1);
-            }
-            list.insert(make_pair(marker, std::set<int>()));
-        }
-
-        line_num++;
-    }
-
-    fh.close();
-
-    if (list.size() == 0) {
-        cerr << "Unable to load any markers from '" << path << "'\n";
-        help();
-    }
-
-    return 0;
-}
-
-int 
-build_file_list(vector<pair<int, string> > &files, 
-                map<int, pair<int, int> > &pop_indexes, 
-                map<int, vector<int> > &grp_members) 
-{
-    char             line[max_len];
-    vector<string>   parts;
-    map<string, int> pop_key_rev, grp_key_rev;
-    set<string>      pop_names, grp_names;
-    string f;
-    uint   len;
-
-    if (pmap_path.length() > 0) {
-        cerr << "Parsing population map.\n";
-
-        ifstream fh(pmap_path.c_str(), ifstream::in);
-
-        if (fh.fail()) {
-            cerr << "Error opening population map '" << pmap_path << "'\n";
-            return 0;
-        }
-
-        uint pop_id = 0;
-        uint grp_id = 0;
-
-        while (fh.good()) {
-            fh.getline(line, max_len);
-
-            len = strlen(line);
-            if (len == 0) continue;
-
-            //
-            // Check that there is no carraige return in the buffer.
-            //
-            if (line[len - 1] == '\r') line[len - 1] = '\0';
-
-            //
-            // Ignore comments
-            //
-            if (line[0] == '#') continue;
-
-            //
-            // Parse the population map, we expect:
-            // <file name><tab><population string>[<tab><group string>]
-            //
-            parse_tsv(line, parts);
-
-            if (parts.size() < 2 || parts.size() > 3) {
-                cerr << "Population map is not formated correctly: expecting two or three, tab separated columns, found " << parts.size() << ".\n";
-                return 0;
-            }
-
-            //
-            // Have we seen this population or group before?
-            //
-            if (pop_names.count(parts[1]) == 0) {
-                pop_names.insert(parts[1]);
-                pop_id++;
-                pop_key[pop_id]       = parts[1];
-                pop_key_rev[parts[1]] = pop_id;
-
-                //
-                // If this is the first time we have seen this population, but not the
-                // first time we have seen this group, add the population to the group list.
-                //
-                if (parts.size() == 3 && grp_key_rev.count(parts[2]) > 0)
-                    grp_members[grp_key_rev[parts[2]]].push_back(pop_id);
-            }
-            if (parts.size() == 3 && grp_names.count(parts[2]) == 0) {
-                grp_names.insert(parts[2]);
-                grp_id++;
-                grp_key[grp_id] = parts[2];
-                grp_key_rev[parts[2]] = grp_id;
-
-                //
-                // Associate the current population with the group.
-                //
-                grp_members[grp_id].push_back(pop_id);
-            }
-
-            //
-            // Test that file exists before adding to list.
-            //
-            ifstream test_fh;
-            gzFile   gz_test_fh;
-
-            f = in_path.c_str() + parts[0] + ".matches.tsv";
-            test_fh.open(f.c_str());
-
-            if (test_fh.fail()) {
-                //
-                // Test for a gzipped file.
-                //
-                f = in_path.c_str() + parts[0] + ".matches.tsv.gz";
-                gz_test_fh = gzopen(f.c_str(), "rb");
-                if (!gz_test_fh) {
-                    cerr << " Unable to find " << f.c_str() << ", excluding it from the analysis.\n";
-                } else {
-                    gzclose(gz_test_fh);
-                    files.push_back(make_pair(pop_key_rev[parts[1]], parts[0]));
-                }
-            } else {
-                test_fh.close();
-                files.push_back(make_pair(pop_key_rev[parts[1]], parts[0]));
-            }
-        }
-
-        fh.close();
-    } else {
-        cerr << "No population map specified, building file list.\n";
-
-        //
-        // If no population map is specified, read all the files from the Stacks directory.
-        //
-        uint   pos;
-        string file;
-        struct dirent *direntry;
-
-        DIR *dir = opendir(in_path.c_str());
-
-        if (dir == NULL) {
-            cerr << "Unable to open directory '" << in_path << "' for reading.\n";
-            exit(1);
-        }
-
-        while ((direntry = readdir(dir)) != NULL) {
-            file = direntry->d_name;
-
-            if (file == "." || file == "..")
-                continue;
-
-            if (file.substr(0, 6) == "batch_")
-                continue;
-
-            pos = file.rfind(".tags.tsv");
-            if (pos < file.length()) {
-                files.push_back(make_pair(1, file.substr(0, pos)));
-            } else {
-                pos = file.rfind(".tags.tsv.gz");
-                if (pos < file.length())
-                    files.push_back(make_pair(1, file.substr(0, pos)));
-            }
-        }
-
-        pop_key[1] = "1";
-
-        closedir(dir);
-    }
-
-    if (files.size() == 0) {
-        cerr << "Unable to locate any input files to process within '" << in_path << "'\n";
-        return 0;
-    }
-
-    //
-    // Sort the files according to population ID.
-    //
-    sort(files.begin(), files.end(), compare_pop_map);
-
-    cerr << "Found " << files.size() << " input file(s).\n";
-
-    //
-    // Determine the start/end index for each population in the files array.
-    //
-    int start  = 0;
-    int end    = 0;
-    int pop_id = files[0].first;
-
-    do {
-        end++;
-        if (pop_id != files[end].first) {
-            pop_indexes[pop_id] = make_pair(start, end - 1);
-            start  = end;
-            pop_id = files[end].first;
-        }
-    } while (end < (int) files.size());
-
-    pop_indexes.size() == 1 ?
-        cerr << "  " << pop_indexes.size() << " population found\n" :
-        cerr << "  " << pop_indexes.size() << " populations found\n";
-
-    if (population_limit > (int) pop_indexes.size()) {
-        cerr << "Population limit (" 
-             << population_limit 
-             << ") larger than number of popualtions present, adjusting parameter to " 
-             << pop_indexes.size() << "\n";
-        population_limit = pop_indexes.size();
-    }
-
-    map<int, pair<int, int> >::iterator it;
-    for (it = pop_indexes.begin(); it != pop_indexes.end(); it++) {
-        start = it->second.first;
-        end   = it->second.second;
-        cerr << "    " << pop_key[it->first] << ": ";
-        for (int i = start; i <= end; i++) {
-            cerr << files[i].second;
-            if (i < end) cerr << ", ";
-        }
-        cerr << "\n";
-    }
-
-    //
-    // If no group membership is specified in the population map, create a default 
-    // group with each population ID as a member.
-    //
-    if (grp_members.size() == 0) {
-        for (it = pop_indexes.begin(); it != pop_indexes.end(); it++)
-            grp_members[1].push_back(it->first);
-        grp_key[1] = "1";
-    }
-
-    grp_members.size() == 1 ?
-        cerr << "  " << grp_members.size() << " group of populations found\n" :
-        cerr << "  " << grp_members.size() << " groups of populations found\n";
-    map<int, vector<int> >::iterator git;
-    for (git = grp_members.begin(); git != grp_members.end(); git++) {
-        cerr << "    " << grp_key[git->first] << ": ";
-        for (uint i = 0; i < git->second.size(); i++) {
-            cerr << pop_key[git->second[i]];
-            if (i < git->second.size() - 1) cerr << ", ";
-        }
-        cerr << "\n";
-    }
-
-    return 1;
-}
-
-bool compare_pop_map(pair<int, string> a, pair<int, string> b) {
-    if (a.first == b.first)
-        return (a.second < b.second);
-    return (a.first < b.first);
-}
-
-bool hap_compare(pair<string, int> a, pair<string, int> b) {
-    return (a.second > b.second);
-}
-
-bool compare_genpos(GenPos a, GenPos b) {
-    return (a.bp < b.bp);
-}
-
-int parse_command_line(int argc, char* argv[]) {
-    int c;
-     
     while (1) {
         static struct option long_options[] = {
             {"help",           no_argument,       NULL, 'h'},
             {"version",        no_argument,       NULL, 'v'},
             {"verbose",        no_argument,       NULL, 'd'},
             {"sql",            no_argument,       NULL, 's'},
-            {"vcf",            no_argument,       NULL, 'V'},
+            {"vcf",            no_argument,       NULL, 1004},
             {"vcf_haplotypes", no_argument,       NULL, 'n'},
             {"fasta",          no_argument,       NULL, 'F'},
             {"fasta_strict",   no_argument,       NULL, 'J'},
@@ -8849,23 +5175,25 @@ int parse_command_line(int argc, char* argv[]) {
             {"treemix",        no_argument,       NULL, 'U'},
             {"merge_sites",    no_argument,       NULL, 'D'},
             {"window_size",    required_argument, NULL, 'w'},
-            {"num_threads",    required_argument, NULL, 't'},
+            {"threads",    required_argument, NULL, 't'},
             {"batch_id",       required_argument, NULL, 'b'},
             {"in_path",        required_argument, NULL, 'P'},
+            {"out_path",       required_argument, NULL, 'O'},
+            {"in_vcf",         required_argument, NULL, 'V'},
             {"progeny",        required_argument, NULL, 'r'},
             {"min_depth",      required_argument, NULL, 'm'},
             {"renz",           required_argument, NULL, 'e'},
-            {"pop_map",        required_argument, NULL, 'M'},
+            {"popmap",         required_argument, NULL, 'M'},
             {"whitelist",      required_argument, NULL, 'W'},
             {"blacklist",      required_argument, NULL, 'B'},
             {"write_single_snp",  no_argument,       NULL, 'I'},
             {"write_random_snp",  no_argument,       NULL, 'j'},
-            {"ordered_export",    no_argument,       NULL, 'N'},
+            {"ordered_export",    no_argument,       NULL, 1002},
             {"kernel_smoothed",   no_argument,       NULL, 'k'},
             {"fstats",            no_argument,       NULL, '6'},
             {"log_fst_comp",      no_argument,       NULL, 'l'},
-            {"bootstrap_type",    required_argument, NULL, 'O'},
-            {"bootstrap_reps",    required_argument, NULL, 'R'},
+            {"bootstrap_type",    required_argument, NULL, 1001},
+            {"bootstrap_reps",    required_argument, NULL, 1003},
             {"bootstrap_wl",      required_argument, NULL, 'Q'},
             {"bootstrap",         no_argument,       NULL, '1'},
             {"bootstrap_fst",     no_argument,       NULL, '2'},
@@ -8879,13 +5207,12 @@ int parse_command_line(int argc, char* argv[]) {
             {"merge_prune_lim",   required_argument, NULL, 'i'},
             {"fst_correction",    required_argument, NULL, 'f'},
             {"p_value_cutoff",    required_argument, NULL, 'u'},
+            {"debug_flags",    required_argument, NULL, 1000},
             {0, 0, 0, 0}
         };
         
         // getopt_long stores the option index here.
-        int option_index = 0;
-     
-        c = getopt_long(argc, argv, "ACDEFGHJKLNSTUVYZ123456dghjklnsva:b:c:e:f:i:m:o:p:q:r:t:u:w:B:I:M:O:P:R:Q:W:", long_options, &option_index);
+        int c = getopt_long(argc, argv, "ACDEFGHJKLNSTUVYZ123456dghjklnsva:b:c:e:f:i:m:o:p:q:r:t:u:w:B:I:M:O:P:R:Q:W:", long_options, NULL);
 
         // Detect the end of the options.
         if (c == -1)
@@ -8903,6 +5230,16 @@ int parse_command_line(int argc, char* argv[]) {
             break;
         case 'P':
             in_path = optarg;
+            if (!in_path.empty() && in_path.back() != '/')
+                in_path += "/";
+            break;
+        case 'O':
+            out_path = optarg;
+            if (!out_path.empty() && out_path.back() != '/')
+                out_path += "/";
+            break;
+        case 'V':
+            in_vcf_path = optarg;
             break;
         case 'M':
             pmap_path = optarg;
@@ -8912,9 +5249,23 @@ int parse_command_line(int argc, char* argv[]) {
             break;
         case 'i':
             merge_prune_lim = is_double(optarg);
+            if (merge_prune_lim > 1.0)
+                merge_prune_lim = merge_prune_lim / 100;
+
+            if (merge_prune_lim < 0 || merge_prune_lim > 1.0) {
+                cerr << "Unable to parse the merge sites pruning limit.\n";
+                help();
+            }
             break;
         case 'q':
             max_obs_het = is_double(optarg);
+            if (max_obs_het > 1)
+                max_obs_het = max_obs_het / 100;
+
+            if (max_obs_het < 0 || max_obs_het > 1.0) {
+                cerr << "Unable to parse the maximum observed heterozygosity.\n";
+                help();
+            }
             break;
         case 'b':
             batch_id = is_integer(optarg);
@@ -8925,6 +5276,13 @@ int parse_command_line(int argc, char* argv[]) {
             break;
         case 'r':
             sample_limit = atof(optarg);
+            if (sample_limit > 1)
+                sample_limit = sample_limit / 100;
+
+            if (sample_limit > 1.0) {
+                cerr << "Unable to parse the sample limit frequency\n";
+                help();
+            }
             break;
         case 'p':
             population_limit = atoi(optarg);
@@ -8958,7 +5316,7 @@ int parse_command_line(int argc, char* argv[]) {
         case '5':
             bootstrap_pifis = true;
             break;
-        case 'O':
+        case 1001:
             if (strcasecmp(optarg, "exact") == 0)
                 bootstrap_type = bs_exact;
             else if (strcasecmp(optarg, "approx") == 0)
@@ -8968,7 +5326,7 @@ int parse_command_line(int argc, char* argv[]) {
                 help();
             }
             break;
-        case 'R':
+        case 1003:
             bootstrap_reps = atoi(optarg);
             break;
         case 'Q':
@@ -8985,13 +5343,13 @@ int parse_command_line(int argc, char* argv[]) {
         case 'j':
             write_random_snp = true;
             break;
-        case 'N':
+        case 1002:
             ordered_export = true;
             break;
         case 's':
             sql_out = true;
             break;
-        case 'V':
+        case 1004:
             vcf_out = true;
             break;
         case 'n':
@@ -9053,6 +5411,13 @@ int parse_command_line(int argc, char* argv[]) {
             break;
         case 'a':
             minor_allele_freq = atof(optarg);
+            if (minor_allele_freq > 1)
+                minor_allele_freq = minor_allele_freq / 100;
+
+            if (minor_allele_freq < 0 || minor_allele_freq > 0.5) {
+                cerr << "Unable to parse the minor allele frequency.\n";
+                help();
+            }
             break;
         case 'f':
             if (strcasecmp(optarg, "p_value") == 0)
@@ -9071,17 +5436,44 @@ int parse_command_line(int argc, char* argv[]) {
             break;
         case 'e':
             enz = optarg;
+            if (renz.count(enz) == 0) {
+                cerr << "Unrecognized restriction enzyme specified: '" << enz.c_str() << "'.\n";
+                help();
+            }
             break;
         case 'w':
             sigma = atof(optarg);
             break;
         case 'v':
             version();
+            exit(0);
             break;
         case '?':
             // getopt_long already printed an error message.
             help();
             break;
+        case 1000:
+        {
+            static const set<string> known_debug_flags = {"VCFCOMP"};
+            stringstream ss (optarg);
+            string s;
+            while (std::getline(ss, s, ',')) {
+                if (known_debug_flags.count(s)) {
+                    debug_flags.insert(s);
+                } else {
+                    cerr << "DEBUG> Error: Unknown error flag '" << s << "'.\n";
+                    return -1;
+                }
+            }
+            cerr << "DEBUG> Debug flag(s) : '" << optarg << "'.\n";
+
+            if (debug_flags.count("VCFCOMP") && not write_random_snp) {
+                write_single_snp = true;
+                cerr << "DEBUG> Added --write_single_snp.\n";
+            }
+
+            break;
+        }
         default:
             cerr << "Unknown command line option: '" << (char) c << "'\n";
             help();
@@ -9089,68 +5481,57 @@ int parse_command_line(int argc, char* argv[]) {
         }
     }
 
-    if (in_path.length() == 0) {
-        cerr << "You must specify a path to the directory containing Stacks output files.\n";
-        help();
-    }
-
-    if (in_path.at(in_path.length() - 1) != '/') 
-        in_path += "/";
-
-    if (pmap_path.length() == 0) {
-        cerr << "A population map was not specified, all samples will be read from '" << in_path << "' as a single popultaion.\n";
-    }
+    //
+    // Check argument constrains.
+    //
 
-    if (batch_id < 0) {
-        cerr << "You must specify a batch ID.\n";
+    if (not in_path.empty() && not in_vcf_path.empty()) {
+        cerr << "Error: Please specify either '-P' or '--in_vcf', not both.\n";
         help();
-    }
-
-    if (enz.length() > 0 && renz.count(enz) == 0) {
-        cerr << "Unrecognized restriction enzyme specified: '" << enz.c_str() << "'.\n";
+    } else if (not in_path.empty()) {
+        input_mode = InputMode::stacks;
+    } else if (not in_vcf_path.empty()) {
+        input_mode = InputMode::vcf;
+    } else {
+        cerr << "Error: One of '--in_path' or '--in_vcf' is required.\n";
         help();
     }
 
-    if (merge_prune_lim != 1.0) {
-        if (merge_prune_lim > 1.0)
-            merge_prune_lim = merge_prune_lim / 100;
-
-        if (merge_prune_lim < 0 || merge_prune_lim > 1.0) {
-            cerr << "Unable to parse the merge sites pruning limit.\n";
-            help();
-        }
-    }
+    if (input_mode == InputMode::stacks) {
 
-    if (minor_allele_freq > 0) {
-        if (minor_allele_freq > 1)
-            minor_allele_freq = minor_allele_freq / 100;
+        if (pmap_path.empty())
+            cerr << "A population map was not specified, all samples will be read from '" << in_path << "' as a single popultaion.\n";
 
-        if (minor_allele_freq > 0.5) {
-            cerr << "Unable to parse the minor allele frequency.\n";
+        if (batch_id < 0) {
+            cerr << "You must specify a batch ID.\n";
             help();
         }
-    }
 
-    if (max_obs_het != 1.0) {
-        if (max_obs_het > 1)
-            max_obs_het = max_obs_het / 100;
+        if (out_path.empty())
+            out_path = in_path;
 
-        if (max_obs_het < 0 || max_obs_het > 1.0) {
-            cerr << "Unable to parse the maximum observed heterozygosity.\n";
-            help();
-        }
-    }
+        out_prefix = string("batch_") + to_string(batch_id);
 
-    if (sample_limit > 0) {
-        if (sample_limit > 1)
-            sample_limit = sample_limit / 100;
+    } else if (input_mode == InputMode::vcf) {
 
-        if (sample_limit > 1.0) {
-            cerr << "Unable to parse the sample limit frequency\n";
+        if (out_path.empty()) {
+            cerr << "Error: Malformed arguments: input mode 'vcf' requires an output directory (--out_path).\n";
             help();
         }
+
+        // Determine out_prefix
+        string fname = in_vcf_path;
+        if (in_vcf_path.find_last_of('/') != string::npos && in_vcf_path.back() != '/')
+            fname = in_vcf_path.substr(in_vcf_path.find_last_of('/')+1);
+        size_t trim = 0;
+        if (fname.length() > 4 && fname.substr(fname.length()-4) == ".vcf")
+            trim = 4;
+        else if (fname.length() > 7 && fname.substr(fname.length()-7) == ".vcf.gz")
+            trim = 7;
+        out_prefix = fname.substr(0, fname.length()-trim);
     }
 
+    // Other
     if (write_single_snp && write_random_snp) {
         cerr << "Please specify either '--write_single_snp' or '--write_random_snp', not both.\n";
         help();
@@ -9165,74 +5546,83 @@ int parse_command_line(int argc, char* argv[]) {
 }
 
 void version() {
-    std::cerr << "populations " << VERSION << "\n\n";
-
-    exit(0);
+    cerr << "populations " << VERSION << "\n\n";
 }
 
 void help() {
-    std::cerr << "populations " << VERSION << "\n"
-              << "populations -b batch_id -P path -M path [-r min] [-m min] [-B blacklist] [-W whitelist] [-s] [-e renz] [-t threads] [-v] [-h]" << "\n"
-              << "  b: Batch ID to examine when exporting from the catalog.\n"
-              << "  P: path to the Stacks output files.\n"
-              << "  M: path to the population map, a tab separated file describing which individuals belong in which population.\n"
-              << "  s: output a file to import results into an SQL database.\n"
-              << "  B: specify a file containing Blacklisted markers to be excluded from the export.\n"
-              << "  W: specify a file containing Whitelisted markers to include in the export.\n"
-              << "  e: restriction enzyme, required if generating 'genomic' output.\n"
-              << "  t: number of threads to run in parallel sections of code.\n"
-              << "  v: print program version." << "\n"
-              << "  h: display this help messsage." << "\n\n"
-              << "  Merging and Phasing:\n"
-              << "    --merge_sites: merge loci that were produced from the same restriction enzyme cutsite (requires reference-aligned data).\n"
-              << "    --merge_prune_lim: when merging adjacent loci, if at least X% samples posses both loci prune the remaining samples out of the analysis.\n"
-              << "  Data Filtering:\n"
-              << "    r: minimum percentage of individuals in a population required to process a locus for that population.\n"
-              << "    p: minimum number of populations a locus must be present in to process a locus.\n"
-              << "    m: specify a minimum stack depth required for individuals at a locus.\n"
-              << "    f: specify a correction to be applied to Fst values: 'p_value', 'bonferroni_win', or 'bonferroni_gen'.\n"
-              << "    --min_maf: specify a minimum minor allele frequency required to process a nucleotide site at a locus (0 < min_maf < 0.5).\n"
-              << "    --max_obs_het: specify a maximum observed heterozygosity required to process a nucleotide site at a locus.\n"
-              << "    --p_value_cutoff [num]: required p-value to keep an Fst measurement (0.05 by default). Also used as base for Bonferroni correction.\n"
-              << "    --lnl_lim [num]: filter loci with log likelihood values below this threshold.\n"
-              << "    --write_single_snp: restrict data analysis to only the first SNP per locus.\n"
-              << "    --write_random_snp: restrict data analysis to one random SNP per locus.\n\n"
-              << "  Fstats:\n"
-              << "    --fstats: enable SNP and haplotype-based F statistics.\n\n"
-              << "  Kernel-smoothing algorithm:\n" 
-              << "    k: enable kernel-smoothed Pi, Fis, Fst, Fst', and Phi_st calculations.\n"
-              << "    --window_size [num]: distance over which to average values (sigma, default 150,000bp; window is 3sigma in length).\n\n"
-              << "  Bootstrap Resampling:\n" 
-              << "    --bootstrap: turn on boostrap resampling for all smoothed statistics.\n"
-              << "    --bootstrap_pifis: turn on boostrap resampling for smoothed SNP-based Pi and Fis calculations.\n"
-              << "    --bootstrap_fst: turn on boostrap resampling for smoothed Fst calculations based on pairwise population comparison of SNPs.\n"
-              << "    --bootstrap_div: turn on boostrap resampling for smoothed haplotype diveristy and gene diversity calculations based on haplotypes.\n"
-              << "    --bootstrap_phist: turn on boostrap resampling for smoothed Phi_st calculations based on haplotypes.\n"
-              << "    --bootstrap_reps [num]: number of bootstrap resamplings to calculate (default 100).\n"
-              << "    --bootstrap_wl [path]: only bootstrap loci contained in this whitelist.\n\n"
-              << "  File ouput options:\n"
-              << "    --ordered_export: if data is reference aligned, exports will be ordered; only a single representative of each overlapping site.\n"
-              << "    --genomic: output each nucleotide position (fixed or polymorphic) in all population members to a file.\n"
-              << "    --fasta: output full sequence for each unique haplotype, from each sample locus in FASTA format, regardless of plausibility.\n"
-              << "    --fasta_strict: output full sequence for each haplotype, from each sample locus in FASTA format, only for biologically plausible loci.\n"
-              << "    --vcf: output SNPs in Variant Call Format (VCF).\n"
-              << "    --vcf_haplotypes: output haplotypes in Variant Call Format (VCF).\n"
-              << "    --genepop: output results in GenePop format.\n"
-              << "    --structure: output results in Structure format.\n"
-              << "    --phase: output genotypes in PHASE format.\n"
-              << "    --fastphase: output genotypes in fastPHASE format.\n"
-              << "    --beagle: output genotypes in Beagle format.\n"
-              << "    --beagle_phased: output haplotypes in Beagle format.\n"
-              << "    --plink: output genotypes in PLINK format.\n"
-              << "    --hzar: output genotypes in Hybrid Zone Analysis using R (HZAR) format.\n"
-              << "    --phylip: output nucleotides that are fixed-within, and variant among populations in Phylip format for phylogenetic tree construction.\n"
-              << "    --phylip_var: include variable sites in the phylip output encoded using IUPAC notation.\n"
-              << "    --phylip_var_all: include all sequence as well as variable sites in the phylip output encoded using IUPAC notation.\n"
-              << "    --treemix: output SNPs in a format useable for the TreeMix program (Pickrell and Pritchard).\n\n"
-              << "  Debugging:\n"
-              << "    --verbose: turn on additional logging.\n"
-              << "    --log_fst_comp: log components of Fst/Phi_st calculations to a file.\n";
-    // << "    --bootstrap_type [exact|approx]: enable bootstrap resampling for population statistics (reference genome required).\n"
+    cerr << "populations " << VERSION << "\n"
+         << "Usage:\n"
+              << "populations -P dir -b batch_id [-O dir] [-M popmap] (filters) [--fstats] [-k [--window_size=150000] [--bootstrap [-N 100]]] (output formats)\n"
+              << "populations -V vcf -O dir [-M popmap] (filters) [--fstats] [-k [--window_size=150000] [--bootstrap [-N 100]]] (output formats)\n"
+              << "\n"
+              << "  -P,--in_path: path to the directory containing the Stacks files.\n"
+              << "  -b,--batch_id: Batch ID to examine when exporting from the catalog (required by -P).\n"
+              << "  -V,--in_vcf: path to an input VCF file.\n"
+              << "  -O,--out_path: path to a directory where to white the output files. (Required by -V; otherwise defaults to value of -P.)\n"
+              << "  -M,--popmap: path to a population map. (Format is 'SAMPLE1\tPOP1\\n...'.)\n"
+              << "  -t,--threads: number of threads to run in parallel sections of code.\n"
+              << "  -s,--sql_out: output a file to import results into an SQL database.\n"
+              << "\n"
+              << "Data Filtering:\n"
+              << "  -p [int]: minimum number of populations a locus must be present in to process a locus.\n"
+              << "  -r [float]: minimum percentage of individuals in a population required to process a locus for that population.\n"
+              << "  --min_maf [float]: specify a minimum minor allele frequency required to process a nucleotide site at a locus (0 < min_maf < 0.5).\n"
+              << "  --max_obs_het [float]: specify a maximum observed heterozygosity required to process a nucleotide site at a locus.\n"
+              << "  -m [int]: specify a minimum stack depth required for individuals at a locus.\n"
+              << "  --lnl_lim [float]: filter loci with log likelihood values below this threshold.\n"
+              << "  --write_single_snp: restrict data analysis to only the first SNP per locus.\n"
+              << "  --write_random_snp: restrict data analysis to one random SNP per locus.\n"
+              << "  -B: path to a file containing Blacklisted markers to be excluded from the export.\n"
+              << "  -W: path to a file containing Whitelisted markers to include in the export.\n"
+              << "\n"
+              << "Merging and Phasing:\n"
+              << "  -e,--renz: restriction enzyme name.\n"
+              << "  --merge_sites: merge loci that were produced from the same restriction enzyme cutsite (requires reference-aligned data).\n"
+              << "  --merge_prune_lim: when merging adjacent loci, if at least X% samples posses both loci prune the remaining samples out of the analysis.\n"
+              << "\n"
+              << "Fstats:\n"
+              << "  --fstats: enable SNP and haplotype-based F statistics.\n"
+              << "  --fst_correction: specify a correction to be applied to Fst values: 'p_value', 'bonferroni_win', or 'bonferroni_gen'. Default: off.\n"
+              << "  --p_value_cutoff [float]: maximum p-value to keep an Fst measurement. Default: 0.05. (Also used as base for Bonferroni correction.)\n"
+              << "\n"
+              << "Kernel-smoothing algorithm:\n"
+              << "  -k,--kernel_smoothed: enable kernel-smoothed Pi, Fis, Fst, Fst', and Phi_st calculations.\n"
+              << "  --sigma [int]: standard deviation of the kernel smoothing weight distribution. Default 150kb.\n"
+              << "  --bootstrap: turn on boostrap resampling for all smoothed statistics.\n"
+              << "  -N,--bootstrap_reps [int]: number of bootstrap resamplings to calculate (default 100).\n"
+              << "  --bootstrap_pifis: turn on boostrap resampling for smoothed SNP-based Pi and Fis calculations.\n"
+              << "  --bootstrap_fst: turn on boostrap resampling for smoothed Fst calculations based on pairwise population comparison of SNPs.\n"
+              << "  --bootstrap_div: turn on boostrap resampling for smoothed haplotype diveristy and gene diversity calculations based on haplotypes.\n"
+              << "  --bootstrap_phist: turn on boostrap resampling for smoothed Phi_st calculations based on haplotypes.\n"
+              << "  --bootstrap_wl [path]: only bootstrap loci contained in this whitelist.\n"
+              << "\n"
+              << "File output options:\n"
+              << "  --ordered_export: if data is reference aligned, exports will be ordered; only a single representative of each overlapping site.\n"
+              << "  --genomic: output each nucleotide position (fixed or polymorphic) in all population members to a file (requires --renz).\n"
+              << "  --fasta: output full sequence for each unique haplotype, from each sample locus in FASTA format, regardless of plausibility.\n"
+              << "  --fasta_strict: output full sequence for each haplotype, from each sample locus in FASTA format, only for biologically plausible loci.\n"
+              << "  --vcf: output SNPs in Variant Call Format (VCF).\n"
+              << "  --vcf_haplotypes: output haplotypes in Variant Call Format (VCF).\n"
+              << "  --genepop: output results in GenePop format.\n"
+              << "  --structure: output results in Structure format.\n"
+              << "  --phase: output genotypes in PHASE format.\n"
+              << "  --fastphase: output genotypes in fastPHASE format.\n"
+              << "  --beagle: output genotypes in Beagle format.\n"
+              << "  --beagle_phased: output haplotypes in Beagle format.\n"
+              << "  --plink: output genotypes in PLINK format.\n"
+              << "  --hzar: output genotypes in Hybrid Zone Analysis using R (HZAR) format.\n"
+              << "  --phylip: output nucleotides that are fixed-within, and variant among populations in Phylip format for phylogenetic tree construction.\n"
+              << "  --phylip_var: include variable sites in the phylip output encoded using IUPAC notation.\n"
+              << "  --phylip_var_all: include all sequence as well as variable sites in the phylip output encoded using IUPAC notation.\n"
+              << "  --treemix: output SNPs in a format useable for the TreeMix program (Pickrell and Pritchard).\n"
+              << "\n"
+              << "Additional options:\n"
+              << "  -h,--help: display this help messsage.\n"
+              << "  -v,--version: print program version.\n"
+              << "  --verbose: turn on additional logging.\n"
+              << ("  --log_fst_comp: log components of Fst/Phi_st calculations to a file.\n");
+
+              // << "    --bootstrap_type [exact|approx]: enable bootstrap resampling for population statistics (reference genome required).\n"
 
     exit(0);
 }
diff --git a/src/populations.h b/src/populations.h
index b10a831..38dbb56 100644
--- a/src/populations.h
+++ b/src/populations.h
@@ -75,108 +75,103 @@ enum corr_type {p_value, bonferroni_win, bonferroni_gen, no_correction};
 enum bs_type   {bs_exact, bs_approx, bs_none};
 enum merget    {merge_sink, merge_src};
 enum phaset    {merge_failure, simple_merge, complex_phase, nomapping_fail, multimapping_fail, multiple_fails};
+enum class InputMode {stacks, vcf};
 
 const int max_snp_dist = 500;
 
-class GenPos {
-public:
-    uint     id;
-    uint     bp;
-    uint     snp_index;
-    loc_type type;
-
-    GenPos(int id, int snp_index, int bp) {
-	this->id        = id;
-	this->snp_index = snp_index;
-	this->bp        = bp;
-	this->type      = snp;
-    }
-    GenPos(int id, int snp_index, int bp, loc_type type) {
-	this->id        = id;
-	this->snp_index = snp_index;
-	this->bp        = bp;
-	this->type      = type;
-    }
-};
-
 void    help( void );
 void    version( void );
 int     parse_command_line(int, char**);
-int     build_file_list(vector<pair<int, string> > &, map<int, pair<int, int> > &, map<int, vector<int> > &);
+int     build_file_list();
 int     load_marker_list(string, set<int> &);
 int     load_marker_column_list(string, map<int, set<int> > &);
-int     apply_locus_constraints(map<int, CSLocus *> &, PopMap<CSLocus> *, map<int, pair<int, int> > &, ofstream &);
-int     prune_polymorphic_sites(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *, map<int, pair<int, int> > &, map<int, set<int> > &, set<int> &, ofstream &);
+int     apply_locus_constraints(map<int, CSLocus *> &, PopMap<CSLocus> *, ofstream &);
+int     prune_polymorphic_sites(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *, map<int, set<int> > &, set<int> &, ofstream &);
 int     log_haplotype_cnts(map<int, CSLocus *> &, ofstream &);
 bool    order_unordered_loci(map<int, CSLocus *> &);
 int     merge_shared_cutsite_loci(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *, map<int, pair<merget, int> > &, ofstream &);
 phaset  merge_and_phase_loci(PopMap<CSLocus> *, CSLocus *, CSLocus *, set<int> &, ofstream &);
 int     merge_datums(int, int, Datum **, Datum **, set<string> &, int);
 int     merge_csloci(CSLocus *, CSLocus *, set<string> &);
-int     datum_adjust_snp_positions(map<int, pair<merget, int> > &, CSLocus *, Datum *, map<int, SNPRes *> &);
 int     tabulate_haplotypes(map<int, CSLocus *> &, PopMap<CSLocus> *);
 int     create_genotype_map(CSLocus *, PopMap<CSLocus> *);
 int     call_population_genotypes(CSLocus *, PopMap<CSLocus> *);
-int     tally_haplotype_freq(CSLocus *, PopMap<CSLocus> *, int &, double &, string &);
-int     translate_genotypes(map<string, string> &, map<string, map<string, string> > &, map<int, CSLocus *> &, PopMap<CSLocus> *, map<int, string> &, set<int> &);
+int     translate_genotypes(map<string, string> &, map<string, map<string, string> > &, map<int, CSLocus *> &, PopMap<CSLocus> *, map<int, string> &, set<int> &); // This function doesn't exist (March 24, 2016)
 int     correct_fst_bonferroni_win(vector<PopPair *> &);
-int     bootstrap_fst_approximate_dist(vector<double> &, vector<int>  &, double *, int *, map<int, vector<double> > &);
+int     bootstrap_fst_approximate_dist(vector<double> &, vector<int>  &, double *, int *, map<int, vector<double> > &); // not used (March 23, 2016)
 int     kernel_smoothed_popstats(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *, int, ofstream &);
-int     bootstrap_popstats_approximate_dist(vector<double> &, vector<double> &, vector<int>  &, double *, int *, int, map<int, vector<double> > &, map<int, vector<double> > &);
+int     bootstrap_popstats_approximate_dist(vector<double> &, vector<double> &, vector<int>  &, double *, int *, int, map<int, vector<double> > &, map<int, vector<double> > &); // not used (March 23, 2016)
 double  bootstrap_approximate_pval(int, double, map<int, vector<double> > &);
 
-int      calculate_summary_stats(vector<pair<int, string> > &, map<int, pair<int, int> > &, map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *);
-int      calculate_haplotype_stats(vector<pair<int, string> > &, map<int, pair<int, int> > &, map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *);
+int      calculate_summary_stats(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *);
+int      calculate_haplotype_stats(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *);
 int      kernel_smoothed_hapstats(vector<CSLocus *> &, PopSum<CSLocus> *, int, double *);
-int      calculate_haplotype_divergence(vector<pair<int, string> > &, map<int, pair<int, int> > &, map<int, vector<int> > &, map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *);
-int      calculate_haplotype_divergence_pairwise(vector<pair<int, string> > &, map<int, pair<int, int> > &, map<int, vector<int> > &, map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *);
-double   count_haplotypes_at_locus(int, int, Datum **, map<string, double> &);
-bool     fixed_locus(map<int, pair<int, int> > &, Datum **, vector<int> &);
-bool     uncalled_haplotype(const char *);
+int      calculate_haplotype_divergence(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *);
+int      calculate_haplotype_divergence_pairwise(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *);
+bool     fixed_locus(Datum **, vector<int> &);
 
 int      nuc_substitution_dist(map<string, int> &, double **);
 int      nuc_substitution_identity(map<string, int> &, double **);
 int      nuc_substitution_identity_max(map<string, int> &, double **);
 
-HapStat *haplotype_amova(map<int, int> &, map<int, pair<int, int> > &, Datum **, LocSum **, vector<int> &);
+HapStat *haplotype_amova(Datum **, LocSum **, vector<int> &);
 double   amova_ssd_total(vector<string> &, map<string, int> &, double **);
 double   amova_ssd_wp(vector<int> &, map<int, vector<int> > &, map<string, int> &, map<int, vector<string> > &, double **);
 double   amova_ssd_ap_wg(vector<int> &, map<int, vector<int> > &, map<string, int> &, map<int, vector<string> > &, double **, double **);
 double   amova_ssd_ag(vector<int> &, map<int, vector<int> > &, map<string, int> &, map<int, vector<string> > &, double **, double);
 
-double   haplotype_d_est(map<int, pair<int, int> > &, Datum **, LocSum **, vector<int> &);
+double   haplotype_d_est(Datum **, LocSum **, vector<int> &);
 LocStat *haplotype_diversity(int, int, Datum **);
+double   count_haplotypes_at_locus(int, int, Datum**, map<string, double>&);
 
-int  write_sql(map<int, CSLocus *> &, PopMap<CSLocus> *);
-int  write_fst_stats(vector<pair<int, string> > &, map<int, pair<int, int> > &, map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *, ofstream &);
-int  write_generic(map<int, CSLocus *> &, PopMap<CSLocus> *, map<int, string> &, bool);
-int  write_genomic(map<int, CSLocus *> &, PopMap<CSLocus> *);
-int  write_fasta(map<int, CSLocus *> &, PopMap<CSLocus> *, map<int, string> &, vector<int> &);
-int  write_strict_fasta(map<int, CSLocus *> &, PopMap<CSLocus> *, map<int, string> &, vector<int> &);
-int  write_vcf(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *, map<int, string> &, vector<int> &, map<int, pair<merget, int> > &);
-int  write_vcf_ordered(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *, map<int, string> &, vector<int> &, map<int, pair<merget, int> > &, ofstream &);
-int  write_vcf_haplotypes(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *, map<int, string> &, vector<int> &);
-int  populate_snp_calls(map<int, CSLocus *> &, PopMap<CSLocus> *, map<int, string> &, vector<int> &, map<int, pair<merget, int> > &);
-int  find_datum_allele_depths(Datum *, int, char, char, int, int &, int &);
-int  write_genepop(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *, map<int, pair<int, int> > &, map<int, string> &);
-int  write_genepop_ordered(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *, map<int, pair<int, int> > &, map<int, string> &, ofstream &);
-int  write_structure(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *, map<int, pair<int, int> > &, map<int, string> &);
-int  write_structure_ordered(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *, map<int, pair<int, int> > &, map<int, string> &, ofstream &);
-int  write_phase(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *, map<int, pair<int, int> > &, map<int, string> &);
-int  write_fastphase(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *, map<int, pair<int, int> > &, map<int, string> &);
-int  write_beagle(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *, map<int, pair<int, int> > &, map<int, string> &);
-int  write_beagle_phased(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *, map<int, pair<int, int> > &, map<int, string> &);
-int  write_plink(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *, map<int, pair<int, int> > &, map<int, string> &);
-int  write_hzar(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *, map<int, pair<int, int> > &, map<int, string> &);
-int  write_treemix(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *, map<int, pair<int, int> > &, map<int, string> &);
-int  write_phylip(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *, map<int, pair<int, int> > &, map<int, string> &);
-int  write_fullseq_phylip(map<int, CSLocus *> &, PopMap<CSLocus> *, PopSum<CSLocus> *, map<int, pair<int, int> > &, map<int, string> &);
-int  tally_observed_haplotypes(vector<char *> &, int, char &, char &);
-int  tally_ref_alleles(LocSum **, int, int, char &, char &);
-int  load_snp_calls(string,  PopMap<CSLocus> *);
-
-bool compare_pop_map(pair<int, string>, pair<int, string>);
+//int  tally_ref_alleles(LocSum **, int, int, char &, char &); //unused; also commented out in the .cc
+//int  load_snp_calls(string,  PopMap<CSLocus> *); //no implementation
+
+//bool compare_pop_map(pair<int, string>, pair<int, string>); //no implementation; the function is in [sql_utilities.h]
 bool hap_compare(pair<string, int>, pair<string, int>);
-bool compare_genpos(GenPos, GenPos);
+
+void vcfcomp_simplify_pmap (map<int, CSLocus*>& catalog, PopMap<CSLocus>* pmap);
+
+inline
+bool uncalled_haplotype(const char *haplotype)
+{
+    for (const char *p = haplotype; *p != '\0'; p++)
+        if (*p == 'N' || *p == 'n')
+            return true;
+    return false;
+}
+
+inline
+double count_haplotypes_at_locus(int start, int end, Datum **d, map<string, double> &hap_cnts)
+{
+    double n = 0.0;
+
+    for (int i = start; i <= end; i++) {
+        if (d[i] == NULL)
+            // No data, ignore this sample.
+            continue;
+
+        const vector<char*>& haps = d[i]->obshap;
+        if (haps.size() > 2) {
+            // Too many haplotypes, ignore this sample.
+            continue;
+        } else if (haps.size() == 1) {
+            // Homozygote.
+            if(!uncalled_haplotype(d[i]->obshap[0])) {
+                n += 2;
+                hap_cnts[d[i]->obshap[0]] += 2;
+            }
+        } else {
+            // Heterozygote.
+            for (uint j = 0; j < d[i]->obshap.size(); j++) {
+                if(!uncalled_haplotype(d[i]->obshap[0])) {
+                    n++;
+                    hap_cnts[d[i]->obshap[j]]++;
+                }
+            }
+        }
+    }
+    return n;
+}
 
 #endif // __POPULATIONS_H__
diff --git a/src/pstacks.cc b/src/pstacks.cc
index 45d3159..11bb13b 100644
--- a/src/pstacks.cc
+++ b/src/pstacks.cc
@@ -52,17 +52,17 @@ int main (int argc, char* argv[]) {
     parse_command_line(argc, argv);
 
     cerr << "Min depth of coverage to report a stack: " << min_stack_cov << "\n"
-	 << "Model type: ";
+         << "Model type: ";
     switch (model_type) {
     case snp:
-	cerr << "SNP\n";
-	break;
+        cerr << "SNP\n";
+        break;
     case fixed: 
-	cerr << "Fixed\n";
-	break;
+        cerr << "Fixed\n";
+        break;
     case bounded:
-	cerr << "Bounded; lower epsilon bound: " << bound_low << "; upper bound: " << bound_high << "\n";
-	break;
+        cerr << "Bounded; lower epsilon bound: " << bound_low << "; upper bound: " << bound_high << "\n";
+        break;
     }
     cerr << "Alpha significance level for model: " << alpha << "\n";
 
@@ -72,17 +72,17 @@ int main (int argc, char* argv[]) {
     //   http://en.wikipedia.org/wiki/Chi-squared_distribution#Table_of_.CF.872_value_vs_p-value
     //
     if (alpha == 0.1) {
-	heterozygote_limit = -2.71;
-	homozygote_limit   =  2.71;
+        heterozygote_limit = -2.71;
+        homozygote_limit   =  2.71;
     } else if (alpha == 0.05) {
-	heterozygote_limit = -3.84;
-	homozygote_limit   =  3.84;
+        heterozygote_limit = -3.84;
+        homozygote_limit   =  3.84;
     } else if (alpha == 0.01) {
-	heterozygote_limit = -6.64;
-	homozygote_limit   =  6.64;
+        heterozygote_limit = -6.64;
+        homozygote_limit   =  6.64;
     } else if (alpha == 0.001) {
-	heterozygote_limit = -10.83;
-	homozygote_limit   =  10.83;
+        heterozygote_limit = -10.83;
+        homozygote_limit   =  10.83;
     }
 
     //
@@ -132,30 +132,30 @@ int call_alleles(MergedStack *mtag, vector<DNANSeq *> &reads) {
     DNANSeq *d;
 
     for (row = 0; row < height; row++) {
-	allele.clear();
+        allele.clear();
 
-	uint snp_cnt = 0;
+        uint snp_cnt = 0;
 
-	for (snp = mtag->snps.begin(); snp != mtag->snps.end(); snp++) {
-	    if ((*snp)->type != snp_type_het) continue;
+        for (snp = mtag->snps.begin(); snp != mtag->snps.end(); snp++) {
+            if ((*snp)->type != snp_type_het) continue;
 
-	    snp_cnt++;
+            snp_cnt++;
 
             d    = reads[row];
-	    base = (*d)[(*snp)->col];
-
-	    //
-	    // Check to make sure the nucleotide at the location of this SNP is
-	    // of one of the two possible states the multinomial model called.
-	    //
-	    if (base == (*snp)->rank_1 || base == (*snp)->rank_2) 
-		allele += base;
-	    else
-		break;
-	}
-
-	if (snp_cnt > 0 && allele.length() == snp_cnt)
-	    mtag->alleles[allele]++;
+            base = (*d)[(*snp)->col];
+
+            //
+            // Check to make sure the nucleotide at the location of this SNP is
+            // of one of the two possible states the multinomial model called.
+            //
+            if (base == (*snp)->rank_1 || base == (*snp)->rank_2) 
+                allele += base;
+            else
+                break;
+        }
+
+        if (snp_cnt > 0 && allele.length() == snp_cnt)
+            mtag->alleles[allele]++;
     }
 
     return 0;
@@ -169,90 +169,90 @@ int call_consensus(map<int, MergedStack *> &merged, map<int, PStack *> &unique,
     map<int, MergedStack *>::iterator it;
     vector<int> keys;
     for (it = merged.begin(); it != merged.end(); it++) 
-	keys.push_back(it->first);
+        keys.push_back(it->first);
 
     int i;
     #pragma omp parallel private(i)
     { 
         #pragma omp for schedule(dynamic) 
-	for (i = 0; i < (int) keys.size(); i++) {
-	    MergedStack *mtag;
-	    PStack *utag;
-
-	    mtag = merged[keys[i]];
-
-	    //
-	    // Create a two-dimensional array, each row containing one read. For
-	    // each unique tag that has been merged together, add the sequence for
-	    // that tag into our array as many times as it originally occurred. 
-	    //
-	    vector<int>::iterator j;
-	    vector<DNANSeq *> reads;
-
-	    for (j = mtag->utags.begin(); j != mtag->utags.end(); j++) {
-		utag = unique[*j];
-
-		for (uint k = 0; k < utag->count; k++) {
-		    reads.push_back(utag->seq);
-		}
-	    }
-
-	    //
-	    // Iterate over each column of the array and call the consensus base.
-	    //
-	    int row, col;
-	    int length = reads[0]->size();
-	    int height = reads.size();
-	    string con;
-	    map<char, int> nuc;
-	    map<char, int>::iterator max, n;
-	    DNANSeq *d;
-
-	    for (col = 0; col < length; col++) {
-		nuc['A'] = 0;
-		nuc['C'] = 0;
-		nuc['G'] = 0;
-		nuc['T'] = 0;
-		nuc['N'] = 0;
-
-		for (row = 0; row < height; row++) {
-    		    d = reads[row];
-		    if (nuc.count((*d)[col]))
-			nuc[(*d)[col]]++;
-		}
-
-		//
-		// Find the base with a plurality of occurances and call it.
-		//
-		max = nuc.end();
-
-		for (n = nuc.begin(); n != nuc.end(); n++) {
-		    if (n->first == 'N') 
-			continue;
-		    if (max == nuc.end() || n->second > max->second)
-			max = n;
-		}
-		con += max->second == 0 ? 'N' : max->first;
-
-		//
-		// Search this column for the presence of a SNP
-		//
-		if (invoke_model)
-		    switch(model_type) {
-		    case snp:
+        for (i = 0; i < (int) keys.size(); i++) {
+            MergedStack *mtag;
+            PStack *utag;
+
+            mtag = merged[keys[i]];
+
+            //
+            // Create a two-dimensional array, each row containing one read. For
+            // each unique tag that has been merged together, add the sequence for
+            // that tag into our array as many times as it originally occurred. 
+            //
+            vector<int>::iterator j;
+            vector<DNANSeq *> reads;
+
+            for (j = mtag->utags.begin(); j != mtag->utags.end(); j++) {
+                utag = unique[*j];
+
+                for (uint k = 0; k < utag->count; k++) {
+                    reads.push_back(utag->seq);
+                }
+            }
+
+            //
+            // Iterate over each column of the array and call the consensus base.
+            //
+            int row, col;
+            int length = reads[0]->size();
+            int height = reads.size();
+            string con;
+            map<char, int> nuc;
+            map<char, int>::iterator max, n;
+            DNANSeq *d;
+
+            for (col = 0; col < length; col++) {
+                nuc['A'] = 0;
+                nuc['C'] = 0;
+                nuc['G'] = 0;
+                nuc['T'] = 0;
+                nuc['N'] = 0;
+
+                for (row = 0; row < height; row++) {
+                    d = reads[row];
+                    if (nuc.count((*d)[col]))
+                        nuc[(*d)[col]]++;
+                }
+
+                //
+                // Find the base with a plurality of occurances and call it.
+                //
+                max = nuc.end();
+
+                for (n = nuc.begin(); n != nuc.end(); n++) {
+                    if (n->first == 'N') 
+                        continue;
+                    if (max == nuc.end() || n->second > max->second)
+                        max = n;
+                }
+                con += max->second == 0 ? 'N' : max->first;
+
+                //
+                // Search this column for the presence of a SNP
+                //
+                if (invoke_model)
+                    switch(model_type) {
+                    case snp:
                         call_multinomial_snp(mtag, col, nuc, true);
-			break;
-		    case bounded:
-			call_bounded_multinomial_snp(mtag, col, nuc, true);
-			break;
-		    case fixed:
+                        break;
+                    case bounded:
+                        call_bounded_multinomial_snp(mtag, col, nuc, true);
+                        break;
+                    case fixed:
                         call_multinomial_fixed(mtag, col, nuc);
-			break;
-		    }
-	    }
+                        break;
+                    }
+            }
 
-	    if (invoke_model) {
-		call_alleles(mtag, reads);
+            if (invoke_model) {
+                call_alleles(mtag, reads);
 
                 if (model_type == fixed) {
                     //
@@ -260,27 +260,27 @@ int call_consensus(map<int, MergedStack *> &merged, map<int, PStack *> &unique,
                     //
                     vector<SNP *>::iterator s;
                     for (s = mtag->snps.begin(); s != mtag->snps.end(); s++) {
-			if ((*s)->type == snp_type_unk)
-			    con.replace((*s)->col, 1, "N");
+                        if ((*s)->type == snp_type_unk)
+                            con.replace((*s)->col, 1, "N");
                     }
                 }
             }
 
-	    mtag->add_consensus(con.c_str());
-
-	    //
-	    // If SNPs were called at this locus but no alleles could be determined,
-	    // blacklist this tag. This can occur if there are two many uncalled bases
-	    // in the locus (Ns), such that haplotypes can't be consistently read
-	    // due to the presence of the Ns in the reads.
-	    //
- 	    if (mtag->alleles.empty())
-		for (uint j = 0; j < mtag->snps.size(); j++)
-		    if (mtag->snps[j]->type == snp_type_het) {
-			mtag->blacklisted = 1;
-			break;
-		    }
-	}
+            mtag->add_consensus(con.c_str());
+
+            //
+            // If SNPs were called at this locus but no alleles could be determined,
+            // blacklist this tag. This can occur if there are two many uncalled bases
+            // in the locus (Ns), such that haplotypes can't be consistently read
+            // due to the presence of the Ns in the reads.
+            //
+            if (mtag->alleles.empty())
+                for (uint j = 0; j < mtag->snps.size(); j++)
+                    if (mtag->snps[j]->type == snp_type_het) {
+                        mtag->blacklisted = 1;
+                        break;
+                    }
+        }
     }
 
     return 0;
@@ -298,19 +298,19 @@ double calc_coverage_distribution(map<int, PStack *> &unique, map<int, MergedSta
     double  stdev = 0.0;
 
     for (it = merged.begin(); it != merged.end(); it++) {
-	depth = 0.0;
-	for (k = it->second->utags.begin(); k != it->second->utags.end(); k++) {
-	    tag    = unique[*k];
-	    depth += tag->count;
-	}
-
-	if (depth < min_stack_cov)
-	    continue;
-	if (depth > max) 
-	    max = depth;
-
-	sum += depth;
-	total++;
+        depth = 0.0;
+        for (k = it->second->utags.begin(); k != it->second->utags.end(); k++) {
+            tag    = unique[*k];
+            depth += tag->count;
+        }
+
+        if (depth < min_stack_cov)
+            continue;
+        if (depth > max) 
+            max = depth;
+
+        sum += depth;
+        total++;
     }
 
     mean = sum / total;
@@ -319,16 +319,16 @@ double calc_coverage_distribution(map<int, PStack *> &unique, map<int, MergedSta
     // Calculate the standard deviation
     //
     for (it = merged.begin(); it != merged.end(); it++) {
-	depth = 0.0;
-	for (k = it->second->utags.begin(); k != it->second->utags.end(); k++) {
-	    tag    = unique[*k];
-	    depth += tag->count;
-	}
+        depth = 0.0;
+        for (k = it->second->utags.begin(); k != it->second->utags.end(); k++) {
+            tag    = unique[*k];
+            depth += tag->count;
+        }
 
-	if (depth < min_stack_cov)
-	    continue;
+        if (depth < min_stack_cov)
+            continue;
 
-	sum += pow((depth - mean), 2);
+        sum += pow((depth - mean), 2);
     }
 
     stdev = sqrt(sum / (total - 1));
@@ -345,10 +345,10 @@ int count_raw_reads(map<int, PStack *> &unique, map<int, MergedStack *> &merged)
     long int m = 0;
 
     for (it = merged.begin(); it != merged.end(); it++) {
-	for (k = it->second->utags.begin(); k != it->second->utags.end(); k++) {
-	    tag  = unique[*k];
-	    m   += tag->count;
-	}
+        for (k = it->second->utags.begin(); k != it->second->utags.end(); k++) {
+            tag  = unique[*k];
+            m   += tag->count;
+        }
         m += it->second->remtags.size();
     }
 
@@ -380,9 +380,9 @@ int write_results(map<int, MergedStack *> &m, map<int, PStack *> &u) {
     string mod_file = out_path + in_file.substr(pos_1 + 1, (pos_2 - pos_1 - 1)) + ".models.tsv";
     
     if (gzip) {
-	tag_file += ".gz";
-	snp_file += ".gz";
-	all_file += ".gz";
+        tag_file += ".gz";
+        snp_file += ".gz";
+        all_file += ".gz";
         mod_file += ".gz";
     }
 
@@ -392,14 +392,14 @@ int write_results(map<int, MergedStack *> &m, map<int, PStack *> &u) {
     gzFile   gz_tags, gz_snps, gz_alle, gz_mods;
     ofstream tags, snps, alle, mods;
     if (gzip) {
-	gz_tags = gzopen(tag_file.c_str(), "wb");
-	if (!gz_tags) {
-	    cerr << "Error: Unable to open gzipped tag file '" << tag_file << "': " << strerror(errno) << ".\n";
-	    exit(1);
-	}
+        gz_tags = gzopen(tag_file.c_str(), "wb");
+        if (!gz_tags) {
+            cerr << "Error: Unable to open gzipped tag file '" << tag_file << "': " << strerror(errno) << ".\n";
+            exit(1);
+        }
         #if ZLIB_VERNUM >= 0x1240
-	gzbuffer(gz_tags, libz_buffer_size);
-	#endif
+        gzbuffer(gz_tags, libz_buffer_size);
+        #endif
         gz_mods = gzopen(mod_file.c_str(), "wb");
         if (!gz_mods) {
             cerr << "Error: Unable to open gzipped tag file '" << tag_file << "': " << strerror(errno) << ".\n";
@@ -408,43 +408,43 @@ int write_results(map<int, MergedStack *> &m, map<int, PStack *> &u) {
         #if ZLIB_VERNUM >= 0x1240
         gzbuffer(gz_mods, libz_buffer_size);
         #endif
-	gz_snps = gzopen(snp_file.c_str(), "wb");
-	if (!gz_snps) {
-	    cerr << "Error: Unable to open gzipped snps file '" << snp_file << "': " << strerror(errno) << ".\n";
-	    exit(1);
-	}
+        gz_snps = gzopen(snp_file.c_str(), "wb");
+        if (!gz_snps) {
+            cerr << "Error: Unable to open gzipped snps file '" << snp_file << "': " << strerror(errno) << ".\n";
+            exit(1);
+        }
         #if ZLIB_VERNUM >= 0x1240
-	gzbuffer(gz_snps, libz_buffer_size);
-	#endif
-	gz_alle = gzopen(all_file.c_str(), "wb");
-	if (!gz_alle) {
-	    cerr << "Error: Unable to open gzipped alleles file '" << all_file << "': " << strerror(errno) << ".\n";
-	    exit(1);
-	}
+        gzbuffer(gz_snps, libz_buffer_size);
+        #endif
+        gz_alle = gzopen(all_file.c_str(), "wb");
+        if (!gz_alle) {
+            cerr << "Error: Unable to open gzipped alleles file '" << all_file << "': " << strerror(errno) << ".\n";
+            exit(1);
+        }
         #if ZLIB_VERNUM >= 0x1240
-	gzbuffer(gz_alle, libz_buffer_size);
-	#endif
+        gzbuffer(gz_alle, libz_buffer_size);
+        #endif
     } else {
-	tags.open(tag_file.c_str());
-	if (tags.fail()) {
-	    cerr << "Error: Unable to open tag file for writing.\n";
-	    exit(1);
-	}
+        tags.open(tag_file.c_str());
+        if (tags.fail()) {
+            cerr << "Error: Unable to open tag file for writing.\n";
+            exit(1);
+        }
         mods.open(mod_file.c_str());
         if (mods.fail()) {
             cerr << "Error: Unable to open tag file for writing.\n";
             exit(1);
         }
-	snps.open(snp_file.c_str());
-	if (snps.fail()) {
-	    cerr << "Error: Unable to open SNPs file for writing.\n";
-	    exit(1);
-	}
-	alle.open(all_file.c_str());
-	if (alle.fail()) {
-	    cerr << "Error: Unable to open allele file for writing.\n";
-	    exit(1);
-	}
+        snps.open(snp_file.c_str());
+        if (snps.fail()) {
+            cerr << "Error: Unable to open SNPs file for writing.\n";
+            exit(1);
+        }
+        alle.open(all_file.c_str());
+        if (alle.fail()) {
+            cerr << "Error: Unable to open allele file for writing.\n";
+            exit(1);
+        }
     }
 
     //
@@ -468,8 +468,8 @@ int write_results(map<int, MergedStack *> &m, map<int, PStack *> &u) {
     } else {
         tags << log.str();
         mods << log.str();
-	snps << log.str();
-	alle << log.str();
+        snps << log.str();
+        alle << log.str();
     }
 
     int id;
@@ -480,147 +480,147 @@ int write_results(map<int, MergedStack *> &m, map<int, PStack *> &u) {
     int   blacklisted = 0;
 
     for (i = m.begin(); i != m.end(); i++) {
-	tag_1 = i->second;
+        tag_1 = i->second;
 
-	float total = 0;
-	for (k = tag_1->utags.begin(); k != tag_1->utags.end(); k++)
- 	    total += u[*k]->count;
+        float total = 0;
+        for (k = tag_1->utags.begin(); k != tag_1->utags.end(); k++)
+            total += u[*k]->count;
 
-	if (total < min_stack_cov) {
-	    excluded++;
-	    continue;
-	}
+        if (total < min_stack_cov) {
+            excluded++;
+            continue;
+        }
 
-	//
-	// Calculate the log likelihood of this merged stack.
-	//
-	tag_1->gen_matrix(u);
-	tag_1->calc_likelihood();
+        //
+        // Calculate the log likelihood of this merged stack.
+        //
+        tag_1->gen_matrix(u);
+        tag_1->calc_likelihood();
 
-	wrote++;
+        wrote++;
 
-	if (tag_1->blacklisted) blacklisted++;
+        if (tag_1->blacklisted) blacklisted++;
 
-	// First write the consensus sequence
-	sstr << "0" << "\t" 
-	     << sql_id << "\t" 
-	     << tag_1->id << "\t" 
+        // First write the consensus sequence
+        sstr << "0" << "\t" 
+             << sql_id << "\t" 
+             << tag_1->id << "\t" 
              << tag_1->loc.chr << "\t"
              << tag_1->loc.bp << "\t"
-             << (tag_1->loc.strand == plus ? "+" : "-") << "\t"
-	     << "consensus\t" << "\t\t" 
-	     << tag_1->con << "\t" 
-	     << tag_1->deleveraged << "\t" 
-	     << tag_1->blacklisted << "\t"
-	     << tag_1->lumberjackstack << "\t"
-	     << tag_1->lnl << "\n";
-
-	//
-	// Write a sequence recording the output of the SNP model for each nucleotide.
-	//
-	sstr << "0" << "\t" 
-	     << sql_id << "\t" 
-	     << tag_1->id << "\t" 
+             << (tag_1->loc.strand == strand_plus ? "+" : "-") << "\t"
+             << "consensus\t" << "\t\t" 
+             << tag_1->con << "\t" 
+             << tag_1->deleveraged << "\t" 
+             << tag_1->blacklisted << "\t"
+             << tag_1->lumberjackstack << "\t"
+             << tag_1->lnl << "\n";
+
+        //
+        // Write a sequence recording the output of the SNP model for each nucleotide.
+        //
+        sstr << "0" << "\t" 
+             << sql_id << "\t" 
+             << tag_1->id << "\t" 
+             << "\t"
+             << "\t"
+             << "\t"
+             << "model\t" << "\t"
+             << "\t";
+        for (s = tag_1->snps.begin(); s != tag_1->snps.end(); s++) {
+            switch((*s)->type) {
+            case snp_type_het:
+                sstr << "E";
+                break;
+            case snp_type_hom:
+                sstr << "O";
+                break;
+            default:
+                sstr << "U";
+                break;
+            }
+        }
+        sstr << "\t"
              << "\t"
              << "\t"
              << "\t"
-	     << "model\t" << "\t"
-	     << "\t";
-	for (s = tag_1->snps.begin(); s != tag_1->snps.end(); s++) {
-	    switch((*s)->type) {
-	    case snp_type_het:
-		sstr << "E";
-		break;
-	    case snp_type_hom:
-		sstr << "O";
-		break;
-	    default:
-		sstr << "U";
-		break;
-	    }
-	}
-	sstr << "\t"
-	     << "\t"
-	     << "\t"
-	     << "\t"
-	     << "\n";
-	
-	if (gzip) gzputs(gz_tags, sstr.str().c_str()); else tags << sstr.str();
+             << "\n";
+        
+        if (gzip) gzputs(gz_tags, sstr.str().c_str()); else tags << sstr.str();
         if (gzip) gzputs(gz_mods, sstr.str().c_str()); else mods << sstr.str();
-	sstr.str("");
-
-	// Now write out the components of each unique tag merged into this one.
-	id = 0;
-	for (k = tag_1->utags.begin(); k != tag_1->utags.end(); k++) {
-	    tag_2  = u[*k];
-	    buf = tag_2->seq->seq();
-
-	    for (j = tag_2->map.begin(); j != tag_2->map.end(); j++) {
-		sstr << "0" << "\t" << sql_id << "\t" << tag_1->id << "\t\t\t\t" << "primary\t" << id << "\t" << *j << "\t" << buf << "\t\t\t\t\n";
-		if (gzip) gzputs(gz_tags, sstr.str().c_str()); else tags << sstr.str();
-		sstr.str("");
-	    }
-	    id++;
-	    delete [] buf;
-	}
-
-	//
-	// Write out the model calls for each nucleotide in this locus.
-	//
-	for (s = tag_1->snps.begin(); s != tag_1->snps.end(); s++) {
-	    sstr << "0"          << "\t" 
-		 << sql_id       << "\t" 
-		 << tag_1->id    << "\t" 
-		 << (*s)->col    << "\t";
-
-	    switch((*s)->type) {
-	    case snp_type_het:
-		sstr << "E\t";
-		break;
-	    case snp_type_hom:
-		sstr << "O\t";
-		break;
-	    default:
-		sstr << "U\t";
-		break;
-	    }
-
-	    sstr << std::fixed   << std::setprecision(2)
-		 << (*s)->lratio << "\t" 
-		 << (*s)->rank_1 << "\t" 
-		 << (*s)->rank_2 << "\t\t\n";
-	}
-
-	if (gzip) gzputs(gz_snps, sstr.str().c_str()); else snps << sstr.str();
-	sstr.str("");
-
-	// Write the expressed alleles seen for the recorded SNPs and
-	// the percentage of tags a particular allele occupies.
-	//
+        sstr.str("");
+
+        // Now write out the components of each unique tag merged into this one.
+        id = 0;
+        for (k = tag_1->utags.begin(); k != tag_1->utags.end(); k++) {
+            tag_2  = u[*k];
+            buf = tag_2->seq->seq();
+
+            for (j = tag_2->map.begin(); j != tag_2->map.end(); j++) {
+                sstr << "0" << "\t" << sql_id << "\t" << tag_1->id << "\t\t\t\t" << "primary\t" << id << "\t" << *j << "\t" << buf << "\t\t\t\t\n";
+                if (gzip) gzputs(gz_tags, sstr.str().c_str()); else tags << sstr.str();
+                sstr.str("");
+            }
+            id++;
+            delete [] buf;
+        }
+
+        //
+        // Write out the model calls for each nucleotide in this locus.
+        //
+        for (s = tag_1->snps.begin(); s != tag_1->snps.end(); s++) {
+            sstr << "0"          << "\t" 
+                 << sql_id       << "\t" 
+                 << tag_1->id    << "\t" 
+                 << (*s)->col    << "\t";
+
+            switch((*s)->type) {
+            case snp_type_het:
+                sstr << "E\t";
+                break;
+            case snp_type_hom:
+                sstr << "O\t";
+                break;
+            default:
+                sstr << "U\t";
+                break;
+            }
+
+            sstr << std::fixed   << std::setprecision(2)
+                 << (*s)->lratio << "\t" 
+                 << (*s)->rank_1 << "\t" 
+                 << (*s)->rank_2 << "\t\t\n";
+        }
+
+        if (gzip) gzputs(gz_snps, sstr.str().c_str()); else snps << sstr.str();
+        sstr.str("");
+
+        // Write the expressed alleles seen for the recorded SNPs and
+        // the percentage of tags a particular allele occupies.
+        //
         char pct[id_len];
-	for (t = tag_1->alleles.begin(); t != tag_1->alleles.end(); t++) {
+        for (t = tag_1->alleles.begin(); t != tag_1->alleles.end(); t++) {
             sprintf(pct, "%.2f", ((t->second/total) * 100));
-	    sstr << "0"       << "\t" 
-		 << sql_id    << "\t" 
-		 << tag_1->id << "\t" 
-		 << t->first  << "\t" 
-		 << pct       << "\t" 
-		 << t->second << "\n";
-	}
-	if (gzip) gzputs(gz_alle, sstr.str().c_str()); else alle << sstr.str();
-	sstr.str("");
+            sstr << "0"       << "\t" 
+                 << sql_id    << "\t" 
+                 << tag_1->id << "\t" 
+                 << t->first  << "\t" 
+                 << pct       << "\t" 
+                 << t->second << "\n";
+        }
+        if (gzip) gzputs(gz_alle, sstr.str().c_str()); else alle << sstr.str();
+        sstr.str("");
     }
 
     if (gzip) {
-	gzclose(gz_tags);
+        gzclose(gz_tags);
         gzclose(gz_mods);
-	gzclose(gz_snps);
-	gzclose(gz_alle);
+        gzclose(gz_snps);
+        gzclose(gz_alle);
     } else {
-	tags.close();
+        tags.close();
         mods.close();
-	snps.close();
-	alle.close();
+        snps.close();
+        alle.close();
     }
 
     cerr << "  Wrote " << wrote << " loci, excluded " << excluded << " loci due to insuffient depth of coverage; blacklisted " << blacklisted << " loci.\n";
@@ -644,23 +644,23 @@ int populate_merged_tags(map<int, PStack *> &unique, map<int, MergedStack *> &me
     //
     for (i = unique.begin(); i != unique.end(); i++) {
         snprintf(id, id_len - 1, "%s|%d|%s", 
-		 i->second->loc.chr, 
-		 i->second->loc.bp, 
-		 i->second->loc.strand == plus ? "+" : "-");
+                 i->second->loc.chr, 
+                 i->second->loc.bp, 
+                 i->second->loc.strand == strand_plus ? "+" : "-");
         locations[id].insert(i->second->id);
     }
 
     it_old = merged.begin();
 
     for (k = locations.begin(); k != locations.end(); k++) {
-	m = new MergedStack;
-	m->id = global_id;
+        m = new MergedStack;
+        m->id = global_id;
 
         // 
         // Record the consensus and physical location for this stack.
         //
         s = k->second.begin();
-	m->add_consensus(unique[*s]->seq);
+        m->add_consensus(unique[*s]->seq);
         m->loc.set(unique[*s]->loc.chr, unique[*s]->loc.bp, unique[*s]->loc.strand);
 
         //
@@ -672,13 +672,13 @@ int populate_merged_tags(map<int, PStack *> &unique, map<int, MergedStack *> &me
             m->utags.push_back(u->id);
         }
 
-	//
-	// Insert the new MergedStack giving a hint as to which position
-	// to insert it at.
-	//
-	it_new = merged.insert(it_old, pair<int, MergedStack *>(global_id, m));
-	it_old = it_new;
-	global_id++;
+        //
+        // Insert the new MergedStack giving a hint as to which position
+        // to insert it at.
+        //
+        it_new = merged.insert(it_old, pair<int, MergedStack *>(global_id, m));
+        it_old = it_new;
+        global_id++;
     }
 
     cerr << "  Merged " << unique.size() << " unique Stacks into " << merged.size() << " loci.\n";
@@ -732,6 +732,8 @@ int reduce_radtags(HashMap &radtags, map<int, PStack *> &unique) {
         }
     }
 
+    cerr << "  " << radtags.size() << " unique stacks were aligned to " << unique.size() << " genomic locations.\n";
+    
     return 0;
 }
 
@@ -757,9 +759,9 @@ int load_radtags(string in_file, HashMap &radtags) {
     int i = 1;
     while ((c = fh->next_seq()) != NULL) {
         if (i % 10000 == 0) cerr << "Loading aligned sequence " << i << "       \r";
-	// cerr << "Loading aligned sequence " << i << "       \n";
+        // cerr << "Loading aligned sequence " << i << "       \n";
 
-	radtags[c->seq].push_back(c);
+        radtags[c->seq].push_back(c);
         i++;
     }
 
@@ -788,14 +790,14 @@ int dump_stacks(map<int, PStack *> &u) {
 
     for (it = u.begin(); it != u.end(); it++) {
 
-	cerr << "Stack ID: " << (*it).second->id << "\n"
-	     << "  Seq:    " << (*it).second->seq->seq() << "\n"
-	     << "  IDs:    "; 
+        cerr << "Stack ID: " << (*it).second->id << "\n"
+             << "  Seq:    " << (*it).second->seq->seq() << "\n"
+             << "  IDs:    "; 
 
-	for (fit = (*it).second->map.begin(); fit != (*it).second->map.end(); fit++)
-	    cerr << *fit << " ";
+        for (fit = (*it).second->map.begin(); fit != (*it).second->map.end(); fit++)
+            cerr << *fit << " ";
 
-	cerr << "\n\n";
+        cerr << "\n\n";
     }
 
     return 0;
@@ -808,24 +810,24 @@ int dump_merged_stacks(map<int, MergedStack *> &m) {
 
     for (it = m.begin(); it != m.end(); it++) {
 
-	cerr << "MergedStack ID: " << it->second->id << "\n"
-	     << "  Consensus:  ";
-	if (it->second->con != NULL)
-	    cerr << it->second->con << "\n";
-	else 
-	    cerr << "\n";
-	cerr << "  IDs:        "; 
+        cerr << "MergedStack ID: " << it->second->id << "\n"
+             << "  Consensus:  ";
+        if (it->second->con != NULL)
+            cerr << it->second->con << "\n";
+        else 
+            cerr << "\n";
+        cerr << "  IDs:        "; 
 
-	for (fit = it->second->utags.begin(); fit != it->second->utags.end(); fit++)
-	    cerr << (*fit) << " ";
+        for (fit = it->second->utags.begin(); fit != it->second->utags.end(); fit++)
+            cerr << (*fit) << " ";
 
-	cerr << "\n"
-	     << "  Distances: ";
+        cerr << "\n"
+             << "  Distances: ";
 
-	for (pit = it->second->dist.begin(); pit != it->second->dist.end(); pit++)
-	    cerr << (*pit).first << ": " << (*pit).second << ", ";
+        for (pit = it->second->dist.begin(); pit != it->second->dist.end(); pit++)
+            cerr << (*pit).first << ": " << (*pit).second << ", ";
 
-	cerr << "\n\n";
+        cerr << "\n\n";
     }
 
     return 0;
@@ -835,38 +837,38 @@ int parse_command_line(int argc, char* argv[]) {
     int c;
 
     while (1) {
-	static struct option long_options[] = {
-	    {"help",         no_argument,       NULL, 'h'},
+        static struct option long_options[] = {
+            {"help",         no_argument,       NULL, 'h'},
             {"version",      no_argument,       NULL, 'v'},
-	    {"infile_type",  required_argument, NULL, 't'},
-	    {"outfile_type", required_argument, NULL, 'y'},
-	    {"file",         required_argument, NULL, 'f'},
-	    {"outpath",      required_argument, NULL, 'o'},
-	    {"id",           required_argument, NULL, 'i'},
-	    {"min_cov",      required_argument, NULL, 'm'},
-	    {"num_threads",  required_argument, NULL, 'p'},
-	    {"bc_err_freq",  required_argument, NULL, 'e'},
-	    {"model_type",   required_argument, NULL, 'T'},
-	    {"bound_low",    required_argument, NULL, 'L'},
-	    {"bound_high",   required_argument, NULL, 'U'},
-	    {"alpha",        required_argument, NULL, 'A'},
-	    {0, 0, 0, 0}
-	};
-
-	// getopt_long stores the option index here.
-	int option_index = 0;
-
-	c = getopt_long(argc, argv, "hvOT:A:L:U:f:o:i:e:p:m:s:f:t:y:", long_options, &option_index);
-
-	// Detect the end of the options.
-	if (c == -1)
-	    break;
-
-	switch (c) {
-	case 'h':
-	    help();
-	    break;
-     	case 't':
+            {"infile_type",  required_argument, NULL, 't'},
+            {"outfile_type", required_argument, NULL, 'y'},
+            {"file",         required_argument, NULL, 'f'},
+            {"outpath",      required_argument, NULL, 'o'},
+            {"id",           required_argument, NULL, 'i'},
+            {"min_cov",      required_argument, NULL, 'm'},
+            {"num_threads",  required_argument, NULL, 'p'},
+            {"bc_err_freq",  required_argument, NULL, 'e'},
+            {"model_type",   required_argument, NULL, 'T'},
+            {"bound_low",    required_argument, NULL, 'L'},
+            {"bound_high",   required_argument, NULL, 'U'},
+            {"alpha",        required_argument, NULL, 'A'},
+            {0, 0, 0, 0}
+        };
+
+        // getopt_long stores the option index here.
+        int option_index = 0;
+
+        c = getopt_long(argc, argv, "hvOT:A:L:U:f:o:i:e:p:m:s:f:t:y:", long_options, &option_index);
+
+        // Detect the end of the options.
+        if (c == -1)
+            break;
+
+        switch (c) {
+        case 'h':
+            help();
+            break;
+        case 't':
             if (strcmp(optarg, "bowtie") == 0)
                 in_file_type = FileT::bowtie;
             else if (strcmp(optarg, "sam") == 0)
@@ -877,33 +879,33 @@ int parse_command_line(int argc, char* argv[]) {
                 in_file_type = FileT::tsv;
             else
                 in_file_type = FileT::unknown;
-	    break;
-     	case 'y':
+            break;
+        case 'y':
             if (strcmp(optarg, "sam") == 0)
                 out_file_type = FileT::sam;
             else
                 out_file_type = FileT::sql;
-	    break;
-     	case 'f':
-	    in_file = optarg;
-	    break;
-	case 'o':
-	    out_path = optarg;
-	    break;
-	case 'i':
-	    sql_id = is_integer(optarg);
-	    if (sql_id < 0) {
-		cerr << "SQL ID (-i) must be an integer, e.g. 1, 2, 3\n";
-		help();
-	    }
-	    break;
-	case 'm':
-	    min_stack_cov = atoi(optarg);
-	    break;
-	case 'e':
-	    barcode_err_freq = atof(optarg);
-	    break;
-     	case 'T':
+            break;
+        case 'f':
+            in_file = optarg;
+            break;
+        case 'o':
+            out_path = optarg;
+            break;
+        case 'i':
+            sql_id = is_integer(optarg);
+            if (sql_id < 0) {
+                cerr << "SQL ID (-i) must be an integer, e.g. 1, 2, 3\n";
+                help();
+            }
+            break;
+        case 'm':
+            min_stack_cov = atoi(optarg);
+            break;
+        case 'e':
+            barcode_err_freq = atof(optarg);
+            break;
+        case 'T':
             if (strcmp(optarg, "snp") == 0) {
                 model_type = snp;
             } else if (strcmp(optarg, "fixed") == 0) {
@@ -914,66 +916,66 @@ int parse_command_line(int argc, char* argv[]) {
                 cerr << "Unknown model type specified '" << optarg << "'\n";
                 help();
             }
-	case 'L':
-	    bound_low  = atof(optarg);
-	    break;
-	case 'U':
-	    bound_high = atof(optarg);
-	    break;
-	case 'A':
-	    alpha = atof(optarg);
-	    break;
-	case 'p':
-	    num_threads = atoi(optarg);
-	    break;
+        case 'L':
+            bound_low  = atof(optarg);
+            break;
+        case 'U':
+            bound_high = atof(optarg);
+            break;
+        case 'A':
+            alpha = atof(optarg);
+            break;
+        case 'p':
+            num_threads = atoi(optarg);
+            break;
         case 'v':
             version();
             break;
-	case '?':
-	    // getopt_long already printed an error message.
-	    help();
-	    break;
+        case '?':
+            // getopt_long already printed an error message.
+            help();
+            break;
      
-	default:
-	    cerr << "Unknown command line option '" << (char) c << "'\n";
-	    help();
-	    abort();
-	}
+        default:
+            cerr << "Unknown command line option '" << (char) c << "'\n";
+            help();
+            abort();
+        }
     }
 
     if (alpha != 0.1 && alpha != 0.05 && alpha != 0.01 && alpha != 0.001) {
-	cerr << "SNP model alpha significance level must be either 0.1, 0.05, 0.01, or 0.001.\n";
-	help();
+        cerr << "SNP model alpha significance level must be either 0.1, 0.05, 0.01, or 0.001.\n";
+        help();
     }
 
     if (bound_low != 0 && (bound_low < 0 || bound_low >= 1.0)) {
-	cerr << "SNP model lower bound must be between 0.0 and 1.0.\n";
-	help();
+        cerr << "SNP model lower bound must be between 0.0 and 1.0.\n";
+        help();
     }
 
     if (bound_high != 1 && (bound_high <= 0 || bound_high > 1.0)) {
-	cerr << "SNP model upper bound must be between 0.0 and 1.0.\n";
-	help();
+        cerr << "SNP model upper bound must be between 0.0 and 1.0.\n";
+        help();
     }
 
     if (bound_low > 0 || bound_high < 1.0) {
-	model_type = bounded;
+        model_type = bounded;
     }
 
     if (in_file.length() == 0 || in_file_type == FileT::unknown) {
-	cerr << "You must specify an input file of a supported type.\n";
-	help();
+        cerr << "You must specify an input file of a supported type.\n";
+        help();
     }
 
     if (out_path.length() == 0) 
-	out_path = ".";
+        out_path = ".";
 
     if (out_path.at(out_path.length() - 1) != '/') 
-	out_path += "/";
+        out_path += "/";
 
     if (model_type == fixed && barcode_err_freq == 0) {
-	cerr << "You must specify the barcode error frequency.\n";
-	help();
+        cerr << "You must specify the barcode error frequency.\n";
+        help();
     }
 
     return 0;
@@ -988,22 +990,22 @@ void version() {
 void help() {
     std::cerr << "pstacks " << VERSION << "\n"
               << "pstacks -t file_type -f file_path [-o path] [-i id] [-m min_cov] [-p num_threads] [-h]" << "\n"
-	      << "  t: input file Type. Supported types: bowtie, sam, or bam.\n"
+              << "  t: input file Type. Supported types: bowtie, sam, or bam.\n"
               << "  f: input file path.\n"
-	      << "  o: output path to write results.\n"
-	      << "  i: SQL ID to insert into the output to identify this sample.\n"
-	      << "  m: minimum depth of coverage to report a stack (default 1).\n"
+              << "  o: output path to write results.\n"
+              << "  i: SQL ID to insert into the output to identify this sample.\n"
+              << "  m: minimum depth of coverage to report a stack (default 1).\n"
               << "  p: enable parallel execution with num_threads threads.\n"
-	      << "  h: display this help messsage.\n"
-	      << "  Model options:\n" 
-	      << "    --model_type <type>: either 'snp' (default), 'bounded', or 'fixed'\n"
-	      << "    For the SNP or Bounded SNP model:\n"
-	      << "      --alpha <num>: chi square significance level required to call a heterozygote or homozygote, either 0.1, 0.05 (default), 0.01, or 0.001.\n"
-	      << "    For the Bounded SNP model:\n"
-	      << "      --bound_low <num>: lower bound for epsilon, the error rate, between 0 and 1.0 (default 0).\n"
-	      << "      --bound_high <num>: upper bound for epsilon, the error rate, between 0 and 1.0 (default 1).\n"
-	      << "    For the Fixed model:\n"
-	      << "      --bc_err_freq <num>: specify the barcode error frequency, between 0 and 1.0.\n";
+              << "  h: display this help messsage.\n"
+              << "  Model options:\n" 
+              << "    --model_type <type>: either 'snp' (default), 'bounded', or 'fixed'\n"
+              << "    For the SNP or Bounded SNP model:\n"
+              << "      --alpha <num>: chi square significance level required to call a heterozygote or homozygote, either 0.1, 0.05 (default), 0.01, or 0.001.\n"
+              << "    For the Bounded SNP model:\n"
+              << "      --bound_low <num>: lower bound for epsilon, the error rate, between 0 and 1.0 (default 0).\n"
+              << "      --bound_high <num>: upper bound for epsilon, the error rate, between 0 and 1.0 (default 1).\n"
+              << "    For the Fixed model:\n"
+              << "      --bc_err_freq <num>: specify the barcode error frequency, between 0 and 1.0.\n";
 
     exit(0);
 }
diff --git a/src/renz.h b/src/renz.cc
similarity index 80%
copy from src/renz.h
copy to src/renz.cc
index b009c52..c153069 100644
--- a/src/renz.h
+++ b/src/renz.cc
@@ -1,31 +1,11 @@
-// -*-mode:c++; c-style:k&r; c-basic-offset:4;-*-
-//
-// Copyright 2011-2015, Julian Catchen <jcatchen at uoregon.edu>
-//
-// This file is part of Stacks.
-//
-// Stacks is free software: you can redistribute it and/or modify
-// it under the terms of the GNU General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// (at your option) any later version.
-//
-// Stacks is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-// GNU General Public License for more details.
-//
-// You should have received a copy of the GNU General Public License
-// along with Stacks.  If not, see <http://www.gnu.org/licenses/>.
-//
-
-#ifndef __RENZ_H__
-#define __RENZ_H__
+#include "renz.h"
 
-#include <map>
-using std::map;
-#include <string>
-using std::string;
+using namespace std;
 
+//
+// First line of static array contains each enzyme's cut sites. Second
+// line is the reverse complement of each cut site.
+//
 const char *aciI[]    = {"CGC", "CGG",        // C/CGC, AciI
                          "GCG", "CCG"};
 const char *ageI[]    = {"CCGGT",             // A/CCGGT, AgeI
@@ -33,81 +13,89 @@ const char *ageI[]    = {"CCGGT",             // A/CCGGT, AgeI
 const char *aluI[]    = {"CT",                // AG/CT, AluI
                          "AG"};
 const char *apeKI[]   = {"CAGC", "CTGC",      // G/CWGC, ApeKI; W=A or T
- 			 "GTCG", "GACG"};
+             "GTCG", "GACG"};
 const char *apoI[]    = {"AATTC", "AATTT",    // R/AATTY, ApoI  (also known as XapI)
                          "GAATT", "AAATT"};
 const char *aseI[]    = {"TAAT",              // AT/TAAT, AseI
                          "ATTA"};
 const char *bamHI[]   = {"GATCC",             // G/GATCC, BamHI
-			 "GGATC"};
+             "GGATC"};
 const char *bfaI[]    = {"TAG",               // C/TAG, BfaI
                          "CTA"};
 const char *bgIII[]   = {"GATCT",             // A/GATCT, BgIII
-			 "AGATC"};
+             "AGATC"};
+const char *bsaHI[]   = {"CGCC", "CGTC",      // GR/CGYC, BsaHI
+                         "GGCG", "GACG"};
 const char *bspDI[]   = {"CGAT",              // AT/CGAT, BspDI
-			 "ATCG"};
+             "ATCG"};
 const char *bstYI[]   = {"GATCC", "GATCT",    // R/GATCY, BstYI (also known as PsuI)
                          "GGATC", "AGATC"};
 const char *claI[]    = {"CGAT",              // AT/CGAT, ClaI
                          "ATCG"};
+const char *csp6I[]   = {"TAC",               // G/TAC, Csp6I
+                         "GTA"};
 const char *ddeI[]    = {"TAAG", "TCAG", "TGAG", "TTAG", // C/TNAG, DdeI
-			 "CTTA", "CTGA", "CTCA", "CTAA"};
+             "CTTA", "CTGA", "CTCA", "CTAA"};
 const char *dpnII[]   = {"GATC",              // GATC, DpnII
-			 "GATC"};
+             "GATC"};
 const char *eaeI[]    = {"GGCCA", "GGCCG",    // Y/GGCCR, EaeI
-			 "TGGCC", "CGGCC"};
+             "TGGCC", "CGGCC"};
 const char *ecoRI[]   = {"AATTC",             // G/AATTC, EcoRI
-			 "GAATT"};
+             "GAATT"};
 const char *ecoRV[]   = {"ATC",               // GAT/ATC, EcoRV
-			 "GAT"};
+             "GAT"};
 const char *ecoT22I[] = {"TGCAT",             // A/TGCAT, EcoT22I
-			 "ATGCA"};
+             "ATGCA"};
 const char *hindIII[] = {"AGCTT",             // A/AGCTT, HindIII
-			 "TCGAA"};
+             "TCGAA"};
+const char *hpaII[]   = {"CGG",               // C/CGG, HpaII
+                         "CCG"};
 const char *kpnI[]    = {"GTACC",             // C/CATGG, KpnI
-			 "GGTAC"};
+             "GGTAC"};
 const char *mluCI[]   = {"AATT",              // AATT, MluCI
-			 "AATT"};
+             "AATT"};
 const char *mseI[]    = {"TAA",               // T/TAA, MseI
- 			 "TTA"};
+             "TTA"};
 const char *mspI[]    = {"CGG",               // C/CGG, MspI
-			 "CCG"};
-const char *ndeI[]    = {"TA",                // CA/TATG, NdeI
-			 "TA"};
+             "CCG"};
+const char *ncoI[]    = {"CATGG",             // C/CATGG, NcoI
+                         "CCATG"};
+const char *ndeI[]    = {"TATG",              // CA/TATG, NdeI
+                         "CATA"};
 const char *nheI[]    = {"CTAGC",             // G/CTAGC, NheI
                          "GCTAG"};
 const char *nlaIII[]  = {"CATG",              // CATG, NlaIII
-			 "CATG"};
+             "CATG"};
 const char *notI[]    = {"GGCCGC",            // GC/GGCCGC, NotI
-			 "GCGGCC"};
+             "GCGGCC"};
 const char *nsiI[]    = {"TGCAT",             // ATGCA/T, NsiI
-			 "ATGCA"};
+             "ATGCA"};
 const char *pstI[]    = {"TGCAG",             // CTGCA/G, PstI
-			 "CTGCA"};
+             "CTGCA"};
 const char *rsaI[]    = {"AC",                // GT/AC, RsaI
                          "GT"};
 const char *sacI[]    = {"AGCTC",             // GAGCT/C, SacI
-			 "GAGCT"};
+             "GAGCT"};
 const char *sau3AI[]  = {"GATC",              // GATC, Sau3AI
-			 "GATC"};
+             "GATC"};
 const char *sbfI[]    = {"TGCAGG",            // CCTGCA/GG, SbfI
-			 "CCTGCA"};
+             "CCTGCA"};
 const char *sexAI[]   = {"CCAGGT", "CCTGGT",  // A/CCWGGT, SexAI; W=A or T
-			 "ACCTGG", "ACCAGG"};
+             "ACCTGG", "ACCAGG"};
 const char *sgrAI[]   = {"CCGGCG", "CCGGTG",  // CR/CCGGYG, SgrAI; R=A or G; Y=C or T
-			 "CGCCGG", "CACCGG"};
+             "CGCCGG", "CACCGG"};
 const char *speI[]    = {"CTAGT",             // A/CTAGT, SpeI
                          "ACTAG"};
 const char *sphI[]    = {"CATGC",             // GCATG/C, SphI
-			 "GCATG"};
+             "GCATG"};
 const char *taqI[]    = {"CGA",               // T/CGA, TaqI
-			 "TCG"};
+             "TCG"};
 const char *xbaI[]    = {"CTAGA",             // T/CTAGA, XbaI
-			 "TCTAG"};
+             "TCTAG"};
 const char *xhoI[]    = {"TCGAG",             // C/TCGAG, XhoI
                          "CTCGA"};
 
-void 
+void
 initialize_renz(map<string, const char **> &renz, map<string, int> &renz_cnt, map<string, int> &renz_len) {
 
     renz["sbfI"]    = sbfI;    // CCTGCA/GG, SbfI
@@ -150,7 +138,11 @@ initialize_renz(map<string, const char **> &renz, map<string, int> &renz_cnt, ma
     renz["bfaI"]    = bfaI;    // C/TAG, BfaI
     renz["aseI"]    = aseI;    // AT/TAAT, AseI
     renz["bspDI"]   = bspDI;   // AT/CGAT, BspDI
-    
+    renz["csp6I"]   = csp6I;   // G/TAC, Csp6I
+    renz["bsaHI"]   = bsaHI;   // GR/CGYC, BsaHI
+    renz["hpaII"]   = hpaII;   // C/CGG, HpaII
+    renz["ncoI"]    = ncoI;    // C/CATGG, NcoI
+
     renz_cnt["sbfI"]    = 1;
     renz_cnt["pstI"]    = 1;
     renz_cnt["notI"]    = 1;
@@ -191,6 +183,10 @@ initialize_renz(map<string, const char **> &renz, map<string, int> &renz_cnt, ma
     renz_cnt["bfaI"]    = 1;
     renz_cnt["aseI"]    = 1;
     renz_cnt["bspDI"]   = 1;
+    renz_cnt["csp6I"]   = 1;
+    renz_cnt["bsaHI"]   = 2;
+    renz_cnt["hpaII"]   = 1;
+    renz_cnt["ncoI"]    = 1;
 
     renz_len["sbfI"]    = 6;
     renz_len["pstI"]    = 5;
@@ -204,7 +200,7 @@ initialize_renz(map<string, const char **> &renz, map<string, int> &renz_cnt, ma
     renz_len["nlaIII"]  = 4;
     renz_len["mluCI"]   = 4;
     renz_len["ecoT22I"] = 5;
-    renz_len["ndeI"]    = 2;
+    renz_len["ndeI"]    = 4;
     renz_len["nsiI"]    = 5;
     renz_len["mseI"]    = 3;
     renz_len["mspI"]    = 3;
@@ -232,11 +228,14 @@ initialize_renz(map<string, const char **> &renz, map<string, int> &renz_cnt, ma
     renz_len["bfaI"]    = 3;
     renz_len["aseI"]    = 4;
     renz_len["bspDI"]   = 4;
+    renz_len["csp6I"]   = 3;
+    renz_len["bsaHI"]   = 4;
+    renz_len["hpaII"]   = 3;
+    renz_len["ncoI"]    = 5;
 }
 
-void 
+void
 initialize_renz_olap(map<string, int> &renz_olap) {
     renz_olap["sbfI"]   = 4;
 }
 
-#endif // __RENZ_H__
diff --git a/src/renz.h b/src/renz.h
index b009c52..63bc8c4 100644
--- a/src/renz.h
+++ b/src/renz.h
@@ -1,6 +1,6 @@
 // -*-mode:c++; c-style:k&r; c-basic-offset:4;-*-
 //
-// Copyright 2011-2015, Julian Catchen <jcatchen at uoregon.edu>
+// Copyright 2011-2016, Julian Catchen <jcatchen at illinois.edu>
 //
 // This file is part of Stacks.
 //
@@ -22,221 +22,12 @@
 #define __RENZ_H__
 
 #include <map>
-using std::map;
 #include <string>
-using std::string;
-
-const char *aciI[]    = {"CGC", "CGG",        // C/CGC, AciI
-                         "GCG", "CCG"};
-const char *ageI[]    = {"CCGGT",             // A/CCGGT, AgeI
-                         "ACCGG"};
-const char *aluI[]    = {"CT",                // AG/CT, AluI
-                         "AG"};
-const char *apeKI[]   = {"CAGC", "CTGC",      // G/CWGC, ApeKI; W=A or T
- 			 "GTCG", "GACG"};
-const char *apoI[]    = {"AATTC", "AATTT",    // R/AATTY, ApoI  (also known as XapI)
-                         "GAATT", "AAATT"};
-const char *aseI[]    = {"TAAT",              // AT/TAAT, AseI
-                         "ATTA"};
-const char *bamHI[]   = {"GATCC",             // G/GATCC, BamHI
-			 "GGATC"};
-const char *bfaI[]    = {"TAG",               // C/TAG, BfaI
-                         "CTA"};
-const char *bgIII[]   = {"GATCT",             // A/GATCT, BgIII
-			 "AGATC"};
-const char *bspDI[]   = {"CGAT",              // AT/CGAT, BspDI
-			 "ATCG"};
-const char *bstYI[]   = {"GATCC", "GATCT",    // R/GATCY, BstYI (also known as PsuI)
-                         "GGATC", "AGATC"};
-const char *claI[]    = {"CGAT",              // AT/CGAT, ClaI
-                         "ATCG"};
-const char *ddeI[]    = {"TAAG", "TCAG", "TGAG", "TTAG", // C/TNAG, DdeI
-			 "CTTA", "CTGA", "CTCA", "CTAA"};
-const char *dpnII[]   = {"GATC",              // GATC, DpnII
-			 "GATC"};
-const char *eaeI[]    = {"GGCCA", "GGCCG",    // Y/GGCCR, EaeI
-			 "TGGCC", "CGGCC"};
-const char *ecoRI[]   = {"AATTC",             // G/AATTC, EcoRI
-			 "GAATT"};
-const char *ecoRV[]   = {"ATC",               // GAT/ATC, EcoRV
-			 "GAT"};
-const char *ecoT22I[] = {"TGCAT",             // A/TGCAT, EcoT22I
-			 "ATGCA"};
-const char *hindIII[] = {"AGCTT",             // A/AGCTT, HindIII
-			 "TCGAA"};
-const char *kpnI[]    = {"GTACC",             // C/CATGG, KpnI
-			 "GGTAC"};
-const char *mluCI[]   = {"AATT",              // AATT, MluCI
-			 "AATT"};
-const char *mseI[]    = {"TAA",               // T/TAA, MseI
- 			 "TTA"};
-const char *mspI[]    = {"CGG",               // C/CGG, MspI
-			 "CCG"};
-const char *ndeI[]    = {"TA",                // CA/TATG, NdeI
-			 "TA"};
-const char *nheI[]    = {"CTAGC",             // G/CTAGC, NheI
-                         "GCTAG"};
-const char *nlaIII[]  = {"CATG",              // CATG, NlaIII
-			 "CATG"};
-const char *notI[]    = {"GGCCGC",            // GC/GGCCGC, NotI
-			 "GCGGCC"};
-const char *nsiI[]    = {"TGCAT",             // ATGCA/T, NsiI
-			 "ATGCA"};
-const char *pstI[]    = {"TGCAG",             // CTGCA/G, PstI
-			 "CTGCA"};
-const char *rsaI[]    = {"AC",                // GT/AC, RsaI
-                         "GT"};
-const char *sacI[]    = {"AGCTC",             // GAGCT/C, SacI
-			 "GAGCT"};
-const char *sau3AI[]  = {"GATC",              // GATC, Sau3AI
-			 "GATC"};
-const char *sbfI[]    = {"TGCAGG",            // CCTGCA/GG, SbfI
-			 "CCTGCA"};
-const char *sexAI[]   = {"CCAGGT", "CCTGGT",  // A/CCWGGT, SexAI; W=A or T
-			 "ACCTGG", "ACCAGG"};
-const char *sgrAI[]   = {"CCGGCG", "CCGGTG",  // CR/CCGGYG, SgrAI; R=A or G; Y=C or T
-			 "CGCCGG", "CACCGG"};
-const char *speI[]    = {"CTAGT",             // A/CTAGT, SpeI
-                         "ACTAG"};
-const char *sphI[]    = {"CATGC",             // GCATG/C, SphI
-			 "GCATG"};
-const char *taqI[]    = {"CGA",               // T/CGA, TaqI
-			 "TCG"};
-const char *xbaI[]    = {"CTAGA",             // T/CTAGA, XbaI
-			 "TCTAG"};
-const char *xhoI[]    = {"TCGAG",             // C/TCGAG, XhoI
-                         "CTCGA"};
-
-void 
-initialize_renz(map<string, const char **> &renz, map<string, int> &renz_cnt, map<string, int> &renz_len) {
 
-    renz["sbfI"]    = sbfI;    // CCTGCA/GG, SbfI
-    renz["pstI"]    = pstI;    // CTGCA/G, PstI
-    renz["notI"]    = notI;    // GC/GGCCGC, NotI
-    renz["ecoRI"]   = ecoRI;   // G/AATTC, EcoRI
-    renz["sgrAI"]   = sgrAI;   // CR/CCGGYG, SgrAI; R=A or G; Y=C or T
-    renz["apeKI"]   = apeKI;   // G/CWGC, ApeKI; W=A or T
-    renz["hindIII"] = hindIII; // A/AGCTT, HindIII
-    renz["dpnII"]   = dpnII;   // GATC, DpnII
-    renz["sphI"]    = sphI;    // GCATG/C, SphI
-    renz["nlaIII"]  = nlaIII;  // CATG, NlaIII
-    renz["mluCI"]   = mluCI;   // AATT, MluCI
-    renz["ecoT22I"] = ecoT22I; // A/TGCAT, EcoT22I
-    renz["ndeI"]    = ndeI;    // CA/TATG, NdeI
-    renz["nsiI"]    = nsiI;    // ATGCA/T, NsiI
-    renz["mseI"]    = mseI;    // T/TAA, MseI
-    renz["mspI"]    = mspI;    // C/CGG, MspI
-    renz["sexAI"]   = sexAI;   // A/CCWGGT, SexAI; W=A or T
-    renz["sau3AI"]  = sau3AI;  // GATC, Sau3AI
-    renz["bamHI"]   = bamHI;   // G/GATCC, BamHI
-    renz["xbaI"]    = xbaI;    // T/CTAGA, XbaI
-    renz["eaeI"]    = eaeI;    // Y/GGCCR, EaeI
-    renz["taqI"]    = taqI;    // T/CGA, TaqI
-    renz["claI"]    = claI;    // AT/CGAT, ClaI
-    renz["nheI"]    = nheI;    // G/CTAGC, NheI
-    renz["speI"]    = speI;    // A/CTAGT, SpeI
-    renz["apoI"]    = apoI;    // R/AATTY, ApoI, XapI
-    renz["bstYI"]   = bstYI;   // R/GATCY, BstYI, PsuI
-    renz["xhoI"]    = xhoI;    // C/TCGAG, XhoI
-    renz["sacI"]    = sacI;    // GAGCT/C, SacI
-    renz["bgIII"]   = bgIII;   // A/GATCT, BgIII
-    renz["ecoRV"]   = ecoRV;   // GAT/ATC, EcoRV
-    renz["kpnI"]    = kpnI;    // C/CATGG, KpnI
-    renz["ddeI"]    = ddeI;    // C/TNAG, DdeI
-    renz["aluI"]    = aluI;    // AG/CT, AluI
-    renz["ageI"]    = ageI;    // A/CCGGT, AgeI
-    renz["rsaI"]    = rsaI;    // GT/AC, RsaI
-    renz["aciI"]    = aciI;    // C/CGC, AciI
-    renz["bfaI"]    = bfaI;    // C/TAG, BfaI
-    renz["aseI"]    = aseI;    // AT/TAAT, AseI
-    renz["bspDI"]   = bspDI;   // AT/CGAT, BspDI
-    
-    renz_cnt["sbfI"]    = 1;
-    renz_cnt["pstI"]    = 1;
-    renz_cnt["notI"]    = 1;
-    renz_cnt["ecoRI"]   = 1;
-    renz_cnt["sgrAI"]   = 2;
-    renz_cnt["apeKI"]   = 2;
-    renz_cnt["hindIII"] = 1;
-    renz_cnt["dpnII"]   = 1;
-    renz_cnt["sphI"]    = 1;
-    renz_cnt["nlaIII"]  = 1;
-    renz_cnt["mluCI"]   = 1;
-    renz_cnt["ecoT22I"] = 1;
-    renz_cnt["ndeI"]    = 1;
-    renz_cnt["nsiI"]    = 1;
-    renz_cnt["mseI"]    = 1;
-    renz_cnt["mspI"]    = 1;
-    renz_cnt["sexAI"]   = 2;
-    renz_cnt["sau3AI"]  = 1;
-    renz_cnt["bamHI"]   = 1;
-    renz_cnt["xbaI"]    = 1;
-    renz_cnt["eaeI"]    = 2;
-    renz_cnt["taqI"]    = 1;
-    renz_cnt["claI"]    = 1;
-    renz_cnt["nheI"]    = 1;
-    renz_cnt["speI"]    = 1;
-    renz_cnt["apoI"]    = 2;
-    renz_cnt["bstYI"]   = 2;
-    renz_cnt["xhoI"]    = 1;
-    renz_cnt["sacI"]    = 1;
-    renz_cnt["bgIII"]   = 1;
-    renz_cnt["ecoRV"]   = 1;
-    renz_cnt["kpnI"]    = 1;
-    renz_cnt["ddeI"]    = 4;
-    renz_cnt["aluI"]    = 1;
-    renz_cnt["ageI"]    = 1;
-    renz_cnt["rsaI"]    = 1;
-    renz_cnt["aciI"]    = 2;
-    renz_cnt["bfaI"]    = 1;
-    renz_cnt["aseI"]    = 1;
-    renz_cnt["bspDI"]   = 1;
-
-    renz_len["sbfI"]    = 6;
-    renz_len["pstI"]    = 5;
-    renz_len["notI"]    = 6;
-    renz_len["ecoRI"]   = 5;
-    renz_len["sgrAI"]   = 6;
-    renz_len["apeKI"]   = 4;
-    renz_len["hindIII"] = 5;
-    renz_len["dpnII"]   = 4;
-    renz_len["sphI"]    = 5;
-    renz_len["nlaIII"]  = 4;
-    renz_len["mluCI"]   = 4;
-    renz_len["ecoT22I"] = 5;
-    renz_len["ndeI"]    = 2;
-    renz_len["nsiI"]    = 5;
-    renz_len["mseI"]    = 3;
-    renz_len["mspI"]    = 3;
-    renz_len["sexAI"]   = 6;
-    renz_len["sau3AI"]  = 4;
-    renz_len["bamHI"]   = 5;
-    renz_len["xbaI"]    = 5;
-    renz_len["eaeI"]    = 5;
-    renz_len["taqI"]    = 3;
-    renz_len["claI"]    = 4;
-    renz_len["nheI"]    = 5;
-    renz_len["speI"]    = 5;
-    renz_len["apoI"]    = 5;
-    renz_len["bstYI"]   = 5;
-    renz_len["xhoI"]    = 5;
-    renz_len["sacI"]    = 5;
-    renz_len["bgIII"]   = 5;
-    renz_len["ecoRV"]   = 3;
-    renz_len["kpnI"]    = 5;
-    renz_len["ddeI"]    = 4;
-    renz_len["aluI"]    = 2;
-    renz_len["ageI"]    = 5;
-    renz_len["rsaI"]    = 2;
-    renz_len["aciI"]    = 3;
-    renz_len["bfaI"]    = 3;
-    renz_len["aseI"]    = 4;
-    renz_len["bspDI"]   = 4;
-}
+using std::map;
+using std::string;
 
-void 
-initialize_renz_olap(map<string, int> &renz_olap) {
-    renz_olap["sbfI"]   = 4;
-}
+void initialize_renz_olap(map<string, int> &renz_olap);
+void initialize_renz(map<string, const char **> &renz, map<string, int> &renz_cnt, map<string, int> &renz_len);
 
 #endif // __RENZ_H__
diff --git a/src/rxstacks.cc b/src/rxstacks.cc
index 3ca8781..b800df1 100644
--- a/src/rxstacks.cc
+++ b/src/rxstacks.cc
@@ -23,8 +23,12 @@
 // across a population of samples.
 //
 
+#include "MetaPopInfo.h"
+
 #include "rxstacks.h"
 
+typedef MetaPopInfo::Sample Sample;
+
 // Global variables to hold command-line options.
 int    num_threads = 1;
 int    batch_id    = 0;
@@ -89,9 +93,12 @@ int main (int argc, char* argv[]) {
     omp_set_num_threads(num_threads);
     #endif
 
-    vector<pair<int, string> > files;
-    if (!build_file_list(files))
-	exit(1);
+    MetaPopInfo mpopi;
+    mpopi.init_directory(in_path);
+    if (mpopi.samples().empty()) {
+        cerr << "Error: Failed to find sample files in directory '" << in_path << "'.\n";
+        return -1;
+    }
 
     //
     // Open and initialize the log files.
@@ -124,33 +131,46 @@ int main (int argc, char* argv[]) {
     // Load matches to the catalog
     //
     vector<vector<CatMatch *> > catalog_matches;
-    map<int, string>            samples;
-    vector<int>                 sample_ids;
-    for (uint i = 0; i < files.size(); i++) {
-	vector<CatMatch *> m;
-	load_catalog_matches(in_path + files[i].second, m);
-
-	if (m.size() == 0) {
-	    cerr << "Warning: unable to find any matches in file '" << files[i].second << "', excluding this sample from population analysis.\n";
-	    continue;
-	}
+    vector<size_t> samples_to_remove;
+    set<size_t> seen_samples;
+    for (size_t i=0; i<mpopi.samples().size(); ++i) {
+        catalog_matches.push_back(vector<CatMatch*>());
+        vector<CatMatch *>& m = catalog_matches.back();
+
+        const Sample& sample = mpopi.samples()[i];
+        load_catalog_matches(in_path + sample.name, m);
+
+        if (m.size() == 0) {
+            cerr << "Warning: Absent or malformed matches file '"
+                 << sample.name << ".matches.tsv(.gz)"
+                 <<"', excluding this sample from population analysis.\n";
+            samples_to_remove.push_back(i);
+            catalog_matches.pop_back(); // n.b. Index shift will be resolved by the call to MetaPopInfo::delete_samples().
+            continue;
+        }
 
-	catalog_matches.push_back(m);
-	if (samples.count(m[0]->sample_id) == 0) {
-	    samples[m[0]->sample_id] = files[i].second;
-	    sample_ids.push_back(m[0]->sample_id);
-	} else {
-	    cerr << "Fatal error: sample ID " << m[0]->sample_id << " occurs twice in this data set, likely the pipeline was run incorrectly.\n";
-	    exit(0);
-	}
+        size_t sample_id = m[0]->sample_id;
+        if (seen_samples.count(sample_id) > 0) {
+            cerr << "Error: sample ID " << sample_id << " occurs twice in this data set, likely the pipeline was run incorrectly.\n";
+            return -1;
+        }
+        seen_samples.insert(sample_id);
+        mpopi.set_sample_id(i, sample_id);
+    }
+    mpopi.delete_samples(samples_to_remove);
+    if (mpopi.samples().size() == 0) {
+        cerr << "Error: Couln't find any matches files.\n";
+        return -1;
     }
+    // [mpopi] is definitive.
+    cerr << "Working on " << mpopi.samples().size() << " samples.\n";
 
     //
     // Create the population map
     // 
-    cerr << "Populating observed haplotypes for " << sample_ids.size() << " samples, " << catalog.size() << " loci.\n";
-    PopMap<CSLocus> *pmap = new PopMap<CSLocus>(sample_ids.size(), catalog.size());
-    pmap->populate(sample_ids, catalog, catalog_matches);
+    cerr << "Populating observed haplotypes for " << mpopi.samples().size() << " samples, " << catalog.size() << " loci.\n";
+    PopMap<CSLocus> *pmap = new PopMap<CSLocus>(mpopi, catalog.size());
+    pmap->populate(catalog, catalog_matches);
 
     //
     // Sum haplotype counts across the population for each catalog locus.
@@ -162,17 +182,15 @@ int main (int argc, char* argv[]) {
     //
     calc_lnl_means(catalog, pmap);
 
-    int    catalog_id, sample_id, tag_id;
-    string file;
+    int    catalog_id, tag_id;
 
     //
     // Process samples matched to the catalog, one by one.
     //
-    for (uint i = 0; i < catalog_matches.size(); i++) {
-	sample_id = catalog_matches[i][0]->sample_id;
-	file      = samples[sample_id];
+    for (uint i = 0; i < mpopi.samples().size(); i++) {
+        const Sample& sample = mpopi.samples()[i];
 
-	cerr << "Loading stacks from sample " << file << " [" << i+1 << " of " << catalog_matches.size() << "]...\n";
+	cerr << "Loading stacks from sample " << sample.name << " [" << i+1 << " of " << mpopi.samples().size() << "]...\n";
 
 	//////
 	//////
@@ -182,12 +200,12 @@ int main (int argc, char* argv[]) {
 
 	map<int, Locus *> stacks;
 	int res;
-	if ((res = load_loci(in_path + file, stacks, true, true, compressed)) == 0) {
-	    cerr << "Unable to load sample file '" << file << "'\n";
+	if ((res = load_loci(in_path + sample.name, stacks, true, true, compressed)) == 0) {
+	    cerr << "Unable to load sample file '" << sample.name << "'\n";
 	    continue;
 	}
 
-	cerr << "Making corrections to sample " << file << "...";
+	cerr << "Making corrections to sample " << sample.name << "...";
 	
 	set<pair<int, int> >           uniq_matches;
 	set<pair<int, int> >::iterator it;
@@ -262,7 +280,7 @@ int main (int argc, char* argv[]) {
 		    continue;
 		}
 
-		d = pmap->datum(catalog_id, sample_id);
+		d = pmap->datum(catalog_id, sample.id);
 
 		if (d == NULL) continue;
 
@@ -350,7 +368,7 @@ int main (int argc, char* argv[]) {
 	     << "Blacklisted: " << lnl_cnt            << " loci due to log likelihoods below threshold.\n"
 	     << "Blacklisted: " << conf_loci_cnt      << " confounded loci.\n";
 
-	log_fh << file           << "\t"
+	log_fh << sample.name           << "\t"
 	       << nuc_cnt        << "\t"
 	       << total          << "\t"
 	       << unk_hom_cnt    << "\t"
@@ -370,7 +388,7 @@ int main (int argc, char* argv[]) {
 	//
 	// Rewrite stacks, model outputs, and haplotypes.
 	//
-	write_results(file, stacks);
+	write_results(sample.name, stacks);
 
 	//
 	// Free up memory
@@ -1300,7 +1318,7 @@ write_results(string file, map<int, Locus *> &m)
 	     << tag_1->id << "\t" 
              << tag_1->loc.chr << "\t"
              << tag_1->loc.bp << "\t"
-             << (tag_1->loc.strand == plus ? "+" : "-") << "\t"
+             << (tag_1->loc.strand == strand_plus ? "+" : "-") << "\t"
 	     << "consensus" << "\t" 
 	     << "\t"
 	     << "\t" 
@@ -1430,50 +1448,6 @@ write_results(string file, map<int, Locus *> &m)
     return 0;
 }
 
-int build_file_list(vector<pair<int, string> > &files) {
-    vector<string> parts;
-    string f;
-
-    //
-    // Read all the files from the Stacks directory.
-    //
-    uint   pos;
-    string file;
-    struct dirent *direntry;
-
-    DIR *dir = opendir(in_path.c_str());
-
-    if (dir == NULL) {
-	cerr << "Unable to open directory '" << in_path << "' for reading.\n";
-	exit(1);
-    }
-
-    while ((direntry = readdir(dir)) != NULL) {
-	file = direntry->d_name;
-
-	if (file == "." || file == "..")
-	    continue;
-
-	if (file.substr(0, 6) == "batch_")
-	    continue;
-
-	pos = file.rfind(".tags.tsv");
-	if (pos < file.length())
-	    files.push_back(make_pair(1, file.substr(0, pos)));
-    }
-
-    closedir(dir);
-
-    if (files.size() == 0) {
-	cerr << "Unable to locate any input files to process within '" << in_path << "'\n";
-	return 0;
-    }
-
-    cerr << "Found " << files.size() << " input file(s).\n";
-
-    return 1;
-}
-
 int
 fill_catalog_snps(map<int, CSLocus *> &catalog)
 {
diff --git a/src/smoothing.h b/src/smoothing.h
index 7c95913..b0ce73f 100644
--- a/src/smoothing.h
+++ b/src/smoothing.h
@@ -60,7 +60,8 @@ KSmooth<StatT>::smooth(vector<StatT *> &popstats)
     // By default, sigma = 150Kb, for computational efficiency, only calculate average out to 3sigma.
     //
     #pragma omp parallel
-    { 
+    {
+        int      limit = 3 * sigma;
 	int      dist;
 	uint     pos_l, pos_u;
 	double   sum, final_weight;
@@ -94,16 +95,16 @@ KSmooth<StatT>::smooth(vector<StatT *> &popstats)
 		    #pragma omp critical
 		    {
 			cerr << "ERROR: current basepair is out of the sliding window.\n"
-			     << "  Calculating sliding window; start position: " << pos_l << ", " << (popstats[pos_l] == NULL ? -1 : popstats[pos_l]->bp) << "bp; end position: " 
-			     << pos_u << ", " << (popstats[pos_u] == NULL ? -1 : popstats[pos_u]->bp) << "bp; center: " 
-			     << pos_c << ", " << popstats[pos_c]->bp << "bp\n"
-			     << "  Current position: " << pos_p << ", " << popstats[pos_p]->bp << "; Dist: " << dist << "\n"
+			     << "  Calculating sliding window; start position: " << pos_l << ", " << (popstats[pos_l] == NULL ? -1 : popstats[pos_l]->bp +1) << "bp; end position: "
+			     << pos_u << ", " << (popstats[pos_u] == NULL ? -1 : popstats[pos_u]->bp +1) << "bp; center: "
+			     << pos_c << ", " << popstats[pos_c]->bp +1 << "bp\n"
+			     << "  Current position: " << pos_p << ", " << popstats[pos_p]->bp +1 << "; Dist: " << dist << "\n"
 			     << "  Window positions:\n";
 
 			for (uint j = pos_l; j < pos_u; j++) {
 			    p = popstats[j];
 			    if (p == NULL) continue;
-			    cerr << "    Position: " << j << "; " << p->bp << "bp\n";
+			    cerr << "    Position: " << j << "; " << p->bp +1 << "bp\n";
 			}
 			//exit(0);
 		    }
diff --git a/src/smoothing_utils.h b/src/smoothing_utils.h
index 86b09e6..685e20d 100644
--- a/src/smoothing_utils.h
+++ b/src/smoothing_utils.h
@@ -26,8 +26,8 @@
 using std::vector;
 
 extern double sigma;
-int limit = 3 * sigma;
 
+inline
 double *
 calc_weights() 
 {
@@ -38,6 +38,7 @@ calc_weights()
     // genetic statistic at position p to the region average was weighted by the Gaussian function:
     //   exp( (-1 * (p - c)^2) / (2 * sigma^2))
     //
+    int     limit   = 3 * sigma;
     double *weights = new double[limit + 1];
 
     for (int i = 0; i <= limit; i++)
@@ -50,6 +51,7 @@ template<class StatT>
 inline int
 determine_window_limits(vector<StatT *> &sites, uint center_bp, uint &pos_l, uint &pos_u)
 {
+    int limit   = 3 * sigma;
     int limit_l = center_bp - limit > 0 ? center_bp - limit : 0;
     int limit_u = center_bp + limit;
 
diff --git a/src/sql_utilities.cc b/src/sql_utilities.cc
new file mode 100644
index 0000000..3143f2c
--- /dev/null
+++ b/src/sql_utilities.cc
@@ -0,0 +1,299 @@
+#include "sql_utilities.h"
+
+using namespace std;
+
+int load_catalog_matches(string sample,  vector<CatMatch *> &matches) {
+    CatMatch      *m;
+    string         f;
+    vector<string> parts;
+    long int       line_num;
+    ifstream       fh;
+    gzFile         gz_fh;
+
+    char *line      = (char *) malloc(sizeof(char) * max_len);
+    int   size      = max_len;
+    int   cnt       = 0;
+    bool  gzip      = false;
+    int   fh_status = 1;
+
+    f = sample + ".matches.tsv";
+    fh.open(f.c_str(), ifstream::in);
+    if (fh.fail()) {
+        //
+        // Test for a gzipped file.
+        //
+        f = sample + ".matches.tsv.gz";
+        gz_fh = gzopen(f.c_str(), "rb");
+        if (!gz_fh)
+            return 0;
+
+        #if ZLIB_VERNUM >= 0x1240
+        gzbuffer(gz_fh, libz_buffer_size);
+        #endif
+        gzip = true;
+    }
+    cerr << "  Parsing " << f.c_str() << "\n";
+
+    line_num = 1;
+    while (fh_status) {
+        fh_status = (gzip == true) ? read_gzip_line(gz_fh, &line, &size) : read_line(fh, &line, &size);
+        line_num++;
+
+        if (!fh_status && strlen(line) == 0)
+            continue;
+
+        if (is_comment(line)) continue;
+
+        parse_tsv(line, parts);
+
+        cnt = parts.size();
+
+        if (cnt != num_matches_fields && cnt != num_matches_fields - 1) {
+            cerr << "Error parsing " << f.c_str() << " at line: " << line_num << ". (" << parts.size() << " fields).\n";
+            return 0;
+        }
+
+        m = new CatMatch;
+        m->batch_id  = atoi(parts[1].c_str());
+        m->cat_id    = atoi(parts[2].c_str());
+        m->sample_id = atoi(parts[3].c_str());
+        m->tag_id    = atoi(parts[4].c_str());
+        m->haplotype = new char[parts[5].length() + 1];
+        strcpy(m->haplotype, parts[5].c_str());
+        m->depth     = atoi(parts[6].c_str());
+        m->lnl       = is_double(parts[7].c_str());
+
+        if (cnt == num_matches_fields && parts[8].length() > 0) {
+            m->cigar = new char[parts[8].length() + 1];
+            strcpy(m->cigar, parts[8].c_str());
+        }
+
+        matches.push_back(m);
+    }
+
+    if (gzip)
+        gzclose(gz_fh);
+    else
+        fh.close();
+
+    return 0;
+}
+
+int load_model_results(string sample,  map<int, ModRes *> &modres) {
+    string         f;
+    vector<string> parts;
+    long int       line_num;
+    ifstream       fh;
+    gzFile   gz_fh;
+
+    char *line      = (char *) malloc(sizeof(char) * max_len);
+    int   size      = max_len;
+    bool  gzip      = false;
+    bool  open_fail  = false;
+    int   fh_status = 1;
+
+    //
+    // Parse the models file (if it exists), otherwise parse the tag file to
+    // pull in the model calls for each locus.
+    //
+    gzip      = false;
+    fh_status = 1;
+    line_num  = 1;
+
+    f = sample + ".models.tsv";
+    fh.open(f.c_str(), ifstream::in);
+    if (fh.fail())
+        open_fail = true;
+
+    if (open_fail) {
+        //
+        // Test for a gzipped MODELs file.
+        //
+        f = sample + ".models.tsv.gz";
+        gz_fh = gzopen(f.c_str(), "rb");
+        if (!gz_fh) {
+            open_fail = true;
+        } else {
+            open_fail = false;
+            #if ZLIB_VERNUM >= 0x1240
+            gzbuffer(gz_fh, libz_buffer_size);
+            #endif
+            gzip = true;
+        }
+    }
+
+    if (open_fail) {
+        //
+        // Test for a TAGs file.
+        //
+        f = sample + ".tags.tsv";
+        fh.open(f.c_str(), ifstream::in);
+        if (fh.fail())
+            open_fail = true;
+        else
+            open_fail = false;
+    }
+
+    if (open_fail) {
+        //
+        // Test for a gzipped TAGs file.
+        //
+        f = sample + ".tags.tsv.gz";
+        gz_fh = gzopen(f.c_str(), "rb");
+        if (!gz_fh) {
+            open_fail = true;
+        } else {
+            open_fail = false;
+            #if ZLIB_VERNUM >= 0x1240
+            gzbuffer(gz_fh, libz_buffer_size);
+            #endif
+            gzip = true;
+        }
+    }
+
+    if (open_fail) {
+        cerr << " Unable to open '" << sample << "'\n";
+        return 0;
+    }
+
+    cerr << "  Parsing " << f.c_str() << "\n";
+
+    ModRes *mod;
+    uint    tag_id, samp_id;
+
+    while (fh_status) {
+        fh_status = (gzip == true) ? read_gzip_line(gz_fh, &line, &size) : read_line(fh, &line, &size);
+        line_num++;
+
+        if (!fh_status && strlen(line) == 0)
+            continue;
+        if (is_comment(line)) continue;
+
+        parse_tsv(line, parts);
+
+        if (parts.size() != num_tags_fields) {
+            cerr << "Error parsing " << f.c_str() << " at line: " << line_num << ". (" << parts.size() << " fields).\n";
+            return 0;
+        }
+
+        //
+        // Read the model sequence, a series of letters specifying if the model called a
+        // homozygous base (O), a heterozygous base (E), or if the base type was unknown (U).
+        //
+        if (parts[6] != "model") continue;
+
+        samp_id = atoi(parts[1].c_str());
+        tag_id  = atoi(parts[2].c_str());
+        mod     = new ModRes(samp_id, tag_id, parts[9].c_str());
+
+        modres[tag_id] = mod;
+    }
+
+    if (gzip)
+        gzclose(gz_fh);
+    else
+        fh.close();
+
+    delete [] line;
+
+    return 1;
+}
+
+int load_snp_calls(string sample,  map<int, SNPRes *> &snpres) {
+    string         f;
+    int id, samp_id;
+    vector<string> parts;
+    long int       line_num;
+    SNP           *snp;
+    SNPRes        *snpr;
+    ifstream       fh;
+    gzFile   gz_fh;
+
+    char *line      = (char *) malloc(sizeof(char) * max_len);
+    int   size      = max_len;
+    bool  gzip      = false;
+    int   fh_status = 1;
+
+    //
+    // Parse the SNP file
+    //
+    f = sample + ".snps.tsv";
+    fh.open(f.c_str(), ifstream::in);
+    if (fh.fail()) {
+        //
+        // Test for a gzipped file.
+        //
+        f = sample + ".snps.tsv.gz";
+        gz_fh = gzopen(f.c_str(), "rb");
+        if (!gz_fh) {
+            cerr << " Unable to open '" << sample << "'\n";
+            return 0;
+        }
+        #if ZLIB_VERNUM >= 0x1240
+        gzbuffer(gz_fh, libz_buffer_size);
+        #endif
+        gzip = true;
+    }
+    cerr << "  Parsing " << f.c_str() << "\n";
+
+    line_num = 1;
+    while (fh_status) {
+        fh_status = (gzip == true) ? read_gzip_line(gz_fh, &line, &size) : read_line(fh, &line, &size);
+
+        if (!fh_status && strlen(line) == 0)
+            continue;
+        if (is_comment(line)) continue;
+
+        parse_tsv(line, parts);
+
+        if (parts.size() != num_snps_fields && parts.size() != num_snps_fields - 2) {
+            cerr << "Error parsing " << f.c_str() << " at line: " << line_num << ". (" << parts.size() << " fields).\n";
+            return 0;
+        }
+
+        samp_id = atoi(parts[1].c_str());
+        id      = atoi(parts[2].c_str());
+
+        snp         = new SNP;
+        snp->col    = atoi(parts[3].c_str());
+
+        if (parts[4] == "O")
+            snp->type = snp_type_hom;
+        else if (parts[4] == "E")
+            snp->type = snp_type_het;
+        else
+            snp->type = snp_type_unk;
+
+        snp->lratio = atof(parts[5].c_str());
+        snp->rank_1 = parts[6].at(0);
+        snp->rank_2 = parts[7].at(0) == '-' ? 0 : parts[7].at(0);
+
+        if (parts.size() == 10) {
+            if (parts[8].length() == 0 || parts[8].at(0) == '-')
+                snp->rank_3 = 0;
+            else
+                snp->rank_3 = parts[8].at(0);
+            if (parts[9].length() == 0 || parts[9].at(0) == '-')
+                snp->rank_4 = 0;
+            else
+                snp->rank_4 = parts[9].at(0);
+        }
+
+        if (snpres.count(id) == 0) {
+            snpr = new SNPRes(samp_id, id);
+            snpres[id] = snpr;
+        }
+        snpres[id]->snps.push_back(snp);
+
+        line_num++;
+    }
+
+    if (gzip)
+        gzclose(gz_fh);
+    else
+        fh.close();
+
+    delete [] line;
+
+    return 1;
+}
diff --git a/src/sql_utilities.h b/src/sql_utilities.h
index 8fc23d1..9b92b8f 100644
--- a/src/sql_utilities.h
+++ b/src/sql_utilities.h
@@ -35,6 +35,10 @@ const uint num_snps_fields    = 10;
 const uint num_alleles_fields =  6;
 const uint num_matches_fields =  9;
 
+int load_catalog_matches(string sample,  vector<CatMatch *> &matches);
+int load_model_results(string sample,  map<int, ModRes *> &modres);
+int load_snp_calls(string sample,  map<int, SNPRes *> &snpres);
+
 template <class LocusT>
 int 
 load_loci(string sample,  map<int, LocusT *> &loci, bool store_reads, bool load_all_model_calls, bool &compressed) 
@@ -221,7 +225,7 @@ load_loci(string sample,  map<int, LocusT *> &loci, bool store_reads, bool load_
         //
         // Parse the physical genome location of this locus.
         //
-        c->loc.set(parts[3].c_str(), atoi(parts[4].c_str()), (parts[5] == "+" ? plus : minus));
+        c->loc.set(parts[3].c_str(), atoi(parts[4].c_str()), (parts[5] == "+" ? strand_plus : strand_minus));
 
         //
         // Parse the components of this stack (either the Illumina ID, or the catalog constituents)
@@ -423,7 +427,7 @@ int dump_loci(map<int, LocusT *> &u) {
 
         cerr << "Locus ID:    " << i->second->id << "\n"
              << "  Consensus: " << i->second->con << "\n"
-             << "  Genomic Location: " << i->second->loc.chr << "; " << i->second->loc.bp << "bp\n"
+             << "  Genomic Location: " << i->second->loc.chr << "; " << i->second->loc.bp +1 << "bp\n"
              << "  SNPs:\n";
 
         for (s = i->second->snps.begin(); s != i->second->snps.end(); s++)
@@ -435,301 +439,4 @@ int dump_loci(map<int, LocusT *> &u) {
     return 0;
 }
 
-int load_catalog_matches(string sample,  vector<CatMatch *> &matches) {
-    CatMatch      *m;
-    string         f;
-    vector<string> parts;
-    long int       line_num;
-    ifstream       fh;
-    gzFile         gz_fh;
-
-    char *line      = (char *) malloc(sizeof(char) * max_len);
-    int   size      = max_len;
-    int   cnt       = 0;
-    bool  gzip      = false;
-    int   fh_status = 1;
-
-    f = sample + ".matches.tsv";
-    fh.open(f.c_str(), ifstream::in);
-    if (fh.fail()) {
-        //
-        // Test for a gzipped file.
-        //
-        f = sample + ".matches.tsv.gz";
-        gz_fh = gzopen(f.c_str(), "rb");
-        if (!gz_fh) {
-            cerr << " Unable to open '" << sample << "'\n";
-            return 0;
-        }
-        #if ZLIB_VERNUM >= 0x1240
-        gzbuffer(gz_fh, libz_buffer_size);
-        #endif
-        gzip = true;
-    }
-    cerr << "  Parsing " << f.c_str() << "\n";
-
-    line_num = 1;
-    while (fh_status) {
-        fh_status = (gzip == true) ? read_gzip_line(gz_fh, &line, &size) : read_line(fh, &line, &size);
-        line_num++;
-
-        if (!fh_status && strlen(line) == 0)
-            continue;
-
-        if (is_comment(line)) continue;
-
-        parse_tsv(line, parts);
-
-        cnt = parts.size();
-
-        if (cnt != num_matches_fields && cnt != num_matches_fields - 1) {
-            cerr << "Error parsing " << f.c_str() << " at line: " << line_num << ". (" << parts.size() << " fields).\n";
-            return 0;
-        }
-
-        m = new CatMatch;
-        m->batch_id  = atoi(parts[1].c_str());
-        m->cat_id    = atoi(parts[2].c_str());
-        m->sample_id = atoi(parts[3].c_str());
-        m->tag_id    = atoi(parts[4].c_str());
-        m->haplotype = new char[parts[5].length() + 1];
-        strcpy(m->haplotype, parts[5].c_str());
-        m->depth     = atoi(parts[6].c_str());
-        m->lnl       = is_double(parts[7].c_str());
-
-        if (cnt == num_matches_fields && parts[8].length() > 0) {
-            m->cigar = new char[parts[8].length() + 1];
-            strcpy(m->cigar, parts[8].c_str());
-        }
-
-        matches.push_back(m);
-    }
-
-    if (gzip)
-        gzclose(gz_fh);
-    else
-        fh.close();
-
-    return 0;
-}
-
-int load_model_results(string sample,  map<int, ModRes *> &modres) {
-    string         f;
-    vector<string> parts;
-    long int       line_num;
-    ifstream       fh;
-    gzFile   gz_fh;
-
-    char *line      = (char *) malloc(sizeof(char) * max_len);
-    int   size      = max_len;
-    bool  gzip      = false;
-    bool  open_fail  = false;
-    int   fh_status = 1;
-
-    // 
-    // Parse the models file (if it exists), otherwise parse the tag file to
-    // pull in the model calls for each locus.
-    //
-    gzip      = false;
-    fh_status = 1;
-    line_num  = 1;
-
-    f = sample + ".models.tsv";
-    fh.open(f.c_str(), ifstream::in);
-    if (fh.fail())
-        open_fail = true;
-
-    if (open_fail) {
-        //
-        // Test for a gzipped MODELs file.
-        //
-        f = sample + ".models.tsv.gz";
-        gz_fh = gzopen(f.c_str(), "rb");
-        if (!gz_fh) {
-            open_fail = true;
-        } else {
-            open_fail = false;
-            #if ZLIB_VERNUM >= 0x1240
-            gzbuffer(gz_fh, libz_buffer_size);
-            #endif
-            gzip = true;
-        }
-    }
-
-    if (open_fail) {
-        //
-        // Test for a TAGs file.
-        //
-        f = sample + ".tags.tsv";
-        fh.open(f.c_str(), ifstream::in);
-        if (fh.fail())
-            open_fail = true;
-        else
-            open_fail = false;
-    }
-
-    if (open_fail) {
-        //
-        // Test for a gzipped TAGs file.
-        //
-        f = sample + ".tags.tsv.gz";
-        gz_fh = gzopen(f.c_str(), "rb");
-        if (!gz_fh) {
-            open_fail = true;
-        } else {
-            open_fail = false;
-            #if ZLIB_VERNUM >= 0x1240
-            gzbuffer(gz_fh, libz_buffer_size);
-            #endif
-            gzip = true;
-        }
-    }
-
-    if (open_fail) {
-        cerr << " Unable to open '" << sample << "'\n";
-        return 0;
-    }
-
-    cerr << "  Parsing " << f.c_str() << "\n";
-
-    ModRes *mod;
-    uint    tag_id, samp_id;
-
-    while (fh_status) {
-        fh_status = (gzip == true) ? read_gzip_line(gz_fh, &line, &size) : read_line(fh, &line, &size);
-        line_num++;
-
-        if (!fh_status && strlen(line) == 0)
-            continue;
-        if (is_comment(line)) continue;
-
-        parse_tsv(line, parts);
-
-        if (parts.size() != num_tags_fields) {
-            cerr << "Error parsing " << f.c_str() << " at line: " << line_num << ". (" << parts.size() << " fields).\n";
-            return 0;
-        }
-
-        //
-        // Read the model sequence, a series of letters specifying if the model called a
-        // homozygous base (O), a heterozygous base (E), or if the base type was unknown (U).
-        //
-        if (parts[6] != "model") continue;
-
-        samp_id = atoi(parts[1].c_str()); 
-        tag_id  = atoi(parts[2].c_str());
-        mod     = new ModRes(samp_id, tag_id, parts[9].c_str());
-
-        modres[tag_id] = mod;
-    }
-
-    if (gzip)
-        gzclose(gz_fh);
-    else
-        fh.close();
-
-    delete [] line;
-
-    return 1;
-}
-
-int load_snp_calls(string sample,  map<int, SNPRes *> &snpres) {
-    string         f;
-    int id, samp_id;
-    vector<string> parts;
-    long int       line_num;
-    SNP           *snp;
-    SNPRes        *snpr;
-    ifstream       fh;
-    gzFile   gz_fh;
-
-    char *line      = (char *) malloc(sizeof(char) * max_len);
-    int   size      = max_len;
-    bool  gzip      = false;
-    int   fh_status = 1;
-
-    // 
-    // Parse the SNP file
-    //
-    f = sample + ".snps.tsv";
-    fh.open(f.c_str(), ifstream::in);
-    if (fh.fail()) {
-        //
-        // Test for a gzipped file.
-        //
-        f = sample + ".snps.tsv.gz";
-        gz_fh = gzopen(f.c_str(), "rb");
-        if (!gz_fh) {
-            cerr << " Unable to open '" << sample << "'\n";
-            return 0;
-        }
-        #if ZLIB_VERNUM >= 0x1240
-        gzbuffer(gz_fh, libz_buffer_size);
-        #endif
-        gzip = true;
-    }
-    cerr << "  Parsing " << f.c_str() << "\n";
-
-    line_num = 1;
-    while (fh_status) {
-        fh_status = (gzip == true) ? read_gzip_line(gz_fh, &line, &size) : read_line(fh, &line, &size);
-
-        if (!fh_status && strlen(line) == 0)
-            continue;
-        if (is_comment(line)) continue;
-
-        parse_tsv(line, parts);
-
-        if (parts.size() != num_snps_fields && parts.size() != num_snps_fields - 2) {
-            cerr << "Error parsing " << f.c_str() << " at line: " << line_num << ". (" << parts.size() << " fields).\n";
-            return 0;
-        }
-
-        samp_id = atoi(parts[1].c_str()); 
-        id      = atoi(parts[2].c_str());
-
-        snp         = new SNP;
-        snp->col    = atoi(parts[3].c_str());
-
-        if (parts[4] == "O")
-            snp->type = snp_type_hom;
-        else if (parts[4] == "E")
-            snp->type = snp_type_het;
-        else
-            snp->type = snp_type_unk;
-
-        snp->lratio = atof(parts[5].c_str());
-        snp->rank_1 = parts[6].at(0);
-        snp->rank_2 = parts[7].at(0) == '-' ? 0 : parts[7].at(0);
-
-        if (parts.size() == 10) {
-            if (parts[8].length() == 0 || parts[8].at(0) == '-')
-                snp->rank_3 = 0;
-            else 
-                snp->rank_3 = parts[8].at(0);
-            if (parts[9].length() == 0 || parts[9].at(0) == '-')
-                snp->rank_4 = 0;
-            else 
-                snp->rank_4 = parts[9].at(0);
-        }
-
-        if (snpres.count(id) == 0) {
-            snpr = new SNPRes(samp_id, id);
-            snpres[id] = snpr;
-        }
-        snpres[id]->snps.push_back(snp);
-
-        line_num++;
-    }
-
-    if (gzip)
-        gzclose(gz_fh);
-    else
-        fh.close();
-
-    delete [] line;
-
-    return 1;
-}
-
 #endif // __SQL_UTILITIES_H__
diff --git a/src/sstacks.cc b/src/sstacks.cc
index 3b10560..d51331f 100644
--- a/src/sstacks.cc
+++ b/src/sstacks.cc
@@ -167,7 +167,7 @@ find_matches_by_genomic_loc(map<int, Locus *> &sample_1, map<int, QLocus *> &sam
         snprintf(id, id_len - 1, "%s|%d|%c", 
 		 j->second->loc.chr, 
 		 j->second->loc.bp, 
-		 j->second->loc.strand == plus ? '+' : '-');
+		 j->second->loc.strand == strand_plus ? '+' : '-');
         locations[id].insert(j->second->id);
     }
 
@@ -198,7 +198,7 @@ find_matches_by_genomic_loc(map<int, Locus *> &sample_1, map<int, QLocus *> &sam
 	    snprintf(id, id_len - 1, "%s|%d|%c", 
 		     i->second->loc.chr, 
 		     i->second->loc.bp, 
-		     i->second->loc.strand == plus ? '+' : '-');
+		     i->second->loc.strand == strand_plus ? '+' : '-');
 
 	    if (locations.count(id) > 0) {
 		Locus *tag;
@@ -830,7 +830,7 @@ search_for_gaps(map<int, Locus *> &catalog, map<int, QLocus *> &sample,
 		// generate, multiple, spurious hits in sequences with multiple copies of the same kmer.
 		//
 		uniq_kmers.clear();
-                for (uint j = 0; j < num_kmers; j++)
+                for (int j = 0; j < num_kmers; j++)
 		    uniq_kmers.insert(kmers[j]);
 
 		hits.clear();
@@ -869,7 +869,7 @@ search_for_gaps(map<int, Locus *> &catalog, map<int, QLocus *> &sample,
 		    hit_cnt   = 0;
 		    allele_id = prev_id;
 
-		    while (hits[index] == prev_id) {
+		    while ((uint)hits[index] == prev_id) {
 			hit_cnt++;
 			index++;
 		    }
@@ -877,7 +877,7 @@ search_for_gaps(map<int, Locus *> &catalog, map<int, QLocus *> &sample,
 		    if (index < hits_size)
 			prev_id = hits[index];
 
-		    if (hit_cnt >= min_hits)
+		    if (hit_cnt >= (uint)min_hits)
 			ordered_hits.push_back(make_pair(allele_id, hit_cnt));
 
         	} while (index < hits_size);
@@ -896,7 +896,7 @@ search_for_gaps(map<int, Locus *> &catalog, map<int, QLocus *> &sample,
 		top_hit = ordered_hits[0].second;
                 stop    = 1;
 		for (uint j = 1; j < ordered_hits.size(); j++)
-		    if (ordered_hits[j].second < top_hit) {
+		    if ((uint)ordered_hits[j].second < top_hit) {
 			stop = j;
 			break;
 		    }
@@ -1025,7 +1025,7 @@ verify_gapped_match(map<int, Locus *> &catalog, QLocus *query,
     qseq = apply_cigar_to_seq(query->con, cigar);
     query->add_consensus(qseq.c_str());
 
-    int min_tag_len = query_len > cat->len ? query_len : cat->len;
+    int min_tag_len = (uint)query_len > cat->len ? query_len : cat->len;
 
     vector<SNP *>::iterator i, j;
     bool found;
@@ -1035,7 +1035,7 @@ verify_gapped_match(map<int, Locus *> &catalog, QLocus *query,
 	//
 	// SNP occurs in a column that is beyond the length of the catalog
 	//
-	if ((*i)->col > min_tag_len - 1)
+	if ((int)(*i)->col > min_tag_len - 1)
 	    continue;
 
 	for (j = cat->snps.begin(); j != cat->snps.end(); j++) {
diff --git a/src/stacks.h b/src/stacks.h
index dc9958d..d9b0ba0 100644
--- a/src/stacks.h
+++ b/src/stacks.h
@@ -49,7 +49,7 @@ typedef string allele_type;
 
 enum snp_type    {snp_type_het, snp_type_hom, snp_type_unk};
 enum read_type   {primary, secondary};
-enum strand_type {plus, minus};
+enum strand_type {strand_plus, strand_minus};
 enum searcht     {sequence, genomic_loc};
 
 class PhyLoc {
@@ -69,12 +69,12 @@ public:
     PhyLoc() {
         chr    = NULL;
         bp     = 0;
-        strand = plus;
+        strand = strand_plus;
     }
     PhyLoc(const char *chr, uint bp) {
         this->chr    = new char[strlen(chr)  + 1];
         this->bp     = bp;
-        this->strand = plus;
+        this->strand = strand_plus;
         strcpy(this->chr,  chr);
     }
     PhyLoc(const char *chr, uint bp, strand_type strnd) {
diff --git a/src/ustacks.cc b/src/ustacks.cc
index b0bd7ae..f46d584 100644
--- a/src/ustacks.cc
+++ b/src/ustacks.cc
@@ -246,7 +246,7 @@ merge_gapped_alns(map<int, Stack *> &unique, map<int, Rem *> &rem, map<int, Merg
 	if (tag_2->alns.size() > 1 && tag_2->alns[0].pct_id == tag_2->alns[1].pct_id)
             continue;
 
-        if (tag_1->id != tag_2->alns[0].id)
+        if (tag_1->id != (int)tag_2->alns[0].id)
             continue;
 
 	cigar_1 = invert_cigar(tag_1->alns[0].cigar);
@@ -557,7 +557,7 @@ search_for_gaps(map<int, MergedStack *> &merged, double min_match_len)
         //
         // Free the k-mers we generated for this query.
         //
-        for (int j = 0; j < query_kmers.size(); j++)
+        for (uint j = 0; j < query_kmers.size(); j++)
             delete [] query_kmers[j];
         query_kmers.clear();
 
@@ -633,7 +633,7 @@ merge_remainders(map<int, MergedStack *> &merged, map<int, Rem *> &rem)
             //
             // Lookup the occurances of each remainder k-mer in the MergedStack k-mer map
             //
-            for (uint k = 0; k < num_kmers; k++) {
+            for (int k = 0; k < num_kmers; k++) {
                 h = kmer_map.find(rem_kmers[k]);
 
                 if (h != kmer_map.end())
@@ -1591,7 +1591,7 @@ int calc_kmer_distance(map<int, MergedStack *> &merged, int utag_dist) {
 	//
 	// Free the k-mers we generated for this query
 	//
-	for (int j = 0; j < query_kmers.size(); j++)
+	for (uint j = 0; j < query_kmers.size(); j++)
 	    delete [] query_kmers[j];
     }
 

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/stacks.git

