[med-svn] [rsem] branch master updated (3582100 -> d1e06e1)
Michael Crusoe
misterc-guest at moszumanska.debian.org
Sun May 15 16:34:31 UTC 2016
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a change to branch master
in repository rsem.
from 3582100 enable full hardening
adds 4e68d2a Imported Upstream version 1.2.27+dfsg
adds 1f68569 Imported Upstream version 1.2.28+dfsg
adds d11ea60 Imported Upstream version 1.2.30+dfsg
adds c64e5ae Merge tag 'upstream/1.2.30+dfsg'
adds d1e06e1 adapt to new upstream layout
No new revisions were added by this update.
Summary of changes:
.gitignore | 6 +-
BamConverter.h | 191 +-
BamWriter.h | 130 +-
EBSeq/Makefile | 7 +-
EBSeq/calcClusteringInfo.cpp | 2 -
EBSeq/install | 7 +-
EBSeq/rsem-for-ebseq-find-DE | 4 +-
EM.cpp | 29 +-
FOR_CYGWIN_USERS | 1 -
GTFItem.h | 74 +-
Gibbs.cpp | 4 +-
Makefile | 235 +-
PairedEndModel.h | 17 +-
PairedEndQModel.h | 17 +-
README.md | 102 +-
Refs.h | 2 +-
SamHeader.cpp | 111 +
SamHeader.hpp | 71 +
SamParser.h | 352 +-
SingleModel.h | 19 +-
SingleQModel.h | 20 +-
Transcript.h | 6 +-
Transcripts.h | 2 +-
WHAT_IS_NEW | 34 +
bam2wig.cpp | 4 +-
bc_aux.h | 8 +-
buildReadIndex.cpp | 2 +
calcCI.cpp | 2 +
convert-sam-for-rsem | 87 +-
debian/changelog | 10 +
debian/clean | 1 +
debian/control | 9 +-
debian/copyright | 62 +-
debian/patches/add-descriptions | 80 -
debian/patches/fix-boost | 64 -
debian/patches/fix-for-g++-6 | 13 -
debian/patches/fix-sam-includes | 126 -
debian/patches/hardening | 20 +
debian/patches/ignore-sam | 108 -
debian/patches/series | 8 +-
debian/patches/spelling | 49 -
debian/patches/use-flags | 119 -
debian/rsem.lintian-overrides | 5 +-
debian/rules | 16 +-
extract-transcript-to-gene-map-from-trinity | 8 +-
extractRef.cpp | 71 +-
getUnique.cpp | 41 +-
parseIt.cpp | 44 +-
preRef.cpp | 2 +
rsem-calculate-expression | 484 +-
rsem-control-fdr | 4 +
rsem-gen-transcript-plots | 210 +-
rsem-generate-ngvector | 6 +-
rsem-gff3-to-gtf | 18 +-
rsem-plot-transcript-wiggles | 28 +-
rsem-prepare-reference | 8 +-
rsem-run-ebseq | 12 +-
rsem_perl_utils.pm | 10 +-
samValidator.cpp | 173 +-
sam_rsem_aux.h | 48 -
sam_rsem_cvt.h | 92 -
sam_utils.h | 210 +
samtools-1.3/AUTHORS | 18 +
samtools-1.3/ChangeLog.old | 3875 ++++
samtools-1.3/INSTALL | 123 +
samtools-1.3/LICENSE | 33 +
samtools-1.3/Makefile | 314 +
samtools-1.3/Makefile.cygwin | 314 +
samtools-1.3/Makefile.mingw | 63 +
samtools-1.3/NEWS | 979 +
samtools-1.3/README | 55 +
samtools-1.3/aclocal.m4 | 674 +
samtools-1.3/bam.c | 235 +
samtools-1.3/bam.h | 577 +
samtools-1.3/bam2bcf.c | 841 +
samtools-1.3/bam2bcf.h | 139 +
samtools-1.3/bam2bcf_indel.c | 531 +
samtools-1.3/bam2depth.c | 301 +
samtools-1.3/bam_addrprg.c | 476 +
samtools-1.3/bam_aux.c | 79 +
samtools-1.3/bam_cat.c | 558 +
samtools-1.3/bam_color.c | 169 +
samtools-1.3/bam_endian.h | 66 +
samtools-1.3/bam_flags.c | 68 +
samtools-1.3/bam_import.c | 63 +
samtools-1.3/bam_index.c | 121 +
samtools-1.3/bam_lpileup.c | 223 +
samtools-1.3/bam_lpileup.h | 57 +
samtools-1.3/bam_mate.c | 362 +
samtools-1.3/bam_md.c | 441 +
samtools-1.3/bam_plbuf.c | 66 +
samtools-1.3/bam_plbuf.h | 55 +
samtools-1.3/bam_plcmd.c | 1028 +
samtools-1.3/bam_quickcheck.c | 134 +
samtools-1.3/bam_reheader.c | 482 +
samtools-1.3/bam_rmdup.c | 261 +
samtools-1.3/bam_rmdupse.c | 187 +
samtools-1.3/bam_sort.c | 1839 ++
samtools-1.3/bam_split.c | 567 +
samtools-1.3/bam_stat.c | 177 +
samtools-1.3/bam_tview.c | 439 +
samtools-1.3/bam_tview.h | 105 +
samtools-1.3/bam_tview_curses.c | 352 +
samtools-1.3/bam_tview_html.c | 375 +
samtools-1.3/bamshuf.c | 213 +
samtools-1.3/bamtk.c | 227 +
samtools-1.3/bedcov.c | 177 +
samtools-1.3/bedidx.c | 258 +
samtools-1.3/config.h.in | 39 +
samtools-1.3/config.mk.in | 52 +
samtools-1.3/configure | 5146 +++++
samtools-1.3/configure.ac | 101 +
samtools-1.3/cut_target.c | 242 +
samtools-1.3/dict.c | 151 +
samtools-1.3/errmod.c | 192 +
samtools-1.3/errmod.h | 49 +
samtools-1.3/examples/00README.txt | 41 +
samtools-1.3/examples/ex1.fa | 56 +
samtools-1.3/examples/ex1.sam.gz | Bin 0 -> 114565 bytes
samtools-1.3/examples/toy.fa | 4 +
samtools-1.3/examples/toy.sam | 14 +
samtools-1.3/faidx.c | 95 +
samtools-1.3/htslib-1.3/INSTALL | 102 +
samtools-1.3/htslib-1.3/LICENSE | 69 +
samtools-1.3/htslib-1.3/Makefile | 426 +
samtools-1.3/htslib-1.3/NEWS | 74 +
samtools-1.3/htslib-1.3/README | 5 +
samtools-1.3/htslib-1.3/bgzf.c | 1125 +
samtools-1.3/htslib-1.3/bgzip.c | 297 +
samtools-1.3/htslib-1.3/config.h.in | 27 +
samtools-1.3/htslib-1.3/config.mk.in | 111 +
samtools-1.3/htslib-1.3/configure | 5267 +++++
samtools-1.3/htslib-1.3/configure.ac | 192 +
samtools-1.3/htslib-1.3/cram/cram.h | 61 +
samtools-1.3/htslib-1.3/cram/cram_codecs.c | 1949 ++
samtools-1.3/htslib-1.3/cram/cram_codecs.h | 194 +
samtools-1.3/htslib-1.3/cram/cram_decode.c | 3143 +++
samtools-1.3/htslib-1.3/cram/cram_decode.h | 112 +
samtools-1.3/htslib-1.3/cram/cram_encode.c | 3094 +++
samtools-1.3/htslib-1.3/cram/cram_encode.h | 105 +
samtools-1.3/htslib-1.3/cram/cram_external.c | 377 +
samtools-1.3/htslib-1.3/cram/cram_index.c | 582 +
samtools-1.3/htslib-1.3/cram/cram_index.h | 99 +
samtools-1.3/htslib-1.3/cram/cram_io.c | 4555 ++++
samtools-1.3/htslib-1.3/cram/cram_io.h | 669 +
samtools-1.3/htslib-1.3/cram/cram_samtools.c | 149 +
samtools-1.3/htslib-1.3/cram/cram_samtools.h | 105 +
samtools-1.3/htslib-1.3/cram/cram_stats.c | 448 +
samtools-1.3/htslib-1.3/cram/cram_stats.h | 59 +
samtools-1.3/htslib-1.3/cram/cram_structs.h | 816 +
samtools-1.3/htslib-1.3/cram/files.c | 74 +
samtools-1.3/htslib-1.3/cram/mFILE.c | 694 +
samtools-1.3/htslib-1.3/cram/mFILE.h | 89 +
samtools-1.3/htslib-1.3/cram/misc.h | 110 +
samtools-1.3/htslib-1.3/cram/open_trace_file.c | 414 +
samtools-1.3/htslib-1.3/cram/open_trace_file.h | 125 +
samtools-1.3/htslib-1.3/cram/os.h | 308 +
samtools-1.3/htslib-1.3/cram/pooled_alloc.c | 188 +
samtools-1.3/htslib-1.3/cram/pooled_alloc.h | 64 +
samtools-1.3/htslib-1.3/cram/rANS_byte.h | 336 +
samtools-1.3/htslib-1.3/cram/rANS_static.c | 868 +
samtools-1.3/htslib-1.3/cram/rANS_static.h | 51 +
samtools-1.3/htslib-1.3/cram/sam_header.c | 1268 ++
samtools-1.3/htslib-1.3/cram/sam_header.h | 459 +
samtools-1.3/htslib-1.3/cram/string_alloc.c | 155 +
samtools-1.3/htslib-1.3/cram/string_alloc.h | 68 +
samtools-1.3/htslib-1.3/cram/thread_pool.c | 813 +
samtools-1.3/htslib-1.3/cram/thread_pool.h | 218 +
samtools-1.3/htslib-1.3/cram/vlen.c | 430 +
samtools-1.3/htslib-1.3/cram/vlen.h | 48 +
samtools-1.3/htslib-1.3/cram/zfio.c | 183 +
samtools-1.3/htslib-1.3/cram/zfio.h | 62 +
samtools-1.3/htslib-1.3/faidx.5 | 146 +
samtools-1.3/htslib-1.3/faidx.c | 484 +
samtools-1.3/htslib-1.3/hfile.c | 744 +
samtools-1.3/htslib-1.3/hfile_internal.h | 139 +
samtools-1.3/htslib-1.3/hfile_irods.c | 259 +
samtools-1.3/htslib-1.3/hfile_libcurl.c | 919 +
samtools-1.3/htslib-1.3/hfile_net.c | 112 +
samtools-1.3/htslib-1.3/hts.c | 2055 ++
samtools-1.3/htslib-1.3/hts_internal.h | 69 +
samtools-1.3/htslib-1.3/htsfile.1 | 75 +
samtools-1.3/htslib-1.3/htsfile.c | 234 +
samtools-1.3/htslib-1.3/htslib.mk | 163 +
samtools-1.3/htslib-1.3/htslib.pc.in | 10 +
samtools-1.3/htslib-1.3/htslib/bgzf.h | 329 +
samtools-1.3/htslib-1.3/htslib/cram.h | 492 +
samtools-1.3/htslib-1.3/htslib/faidx.h | 137 +
samtools-1.3/htslib-1.3/htslib/hfile.h | 215 +
samtools-1.3/htslib-1.3/htslib/hts.h | 637 +
samtools-1.3/htslib-1.3/htslib/hts_defs.h | 72 +
samtools-1.3/htslib-1.3/htslib/kbitset.h | 160 +
samtools-1.3/htslib-1.3/htslib/kfunc.h | 83 +
samtools-1.3/htslib-1.3/htslib/khash.h | 627 +
samtools-1.3/htslib-1.3/htslib/khash_str2int.h | 133 +
samtools-1.3/htslib-1.3/htslib/klist.h | 135 +
samtools-1.3/htslib-1.3/htslib/knetfile.h | 101 +
samtools-1.3/htslib-1.3/htslib/kseq.h | 253 +
samtools-1.3/htslib-1.3/htslib/ksort.h | 285 +
samtools-1.3/htslib-1.3/htslib/kstring.h | 277 +
samtools-1.3/htslib-1.3/htslib/regidx.h | 154 +
samtools-1.3/htslib-1.3/htslib/sam.h | 454 +
samtools-1.3/htslib-1.3/htslib/synced_bcf_reader.h | 302 +
samtools-1.3/htslib-1.3/htslib/tbx.h | 79 +
samtools-1.3/htslib-1.3/htslib/vcf.h | 907 +
samtools-1.3/htslib-1.3/htslib/vcf_sweep.h | 47 +
samtools-1.3/htslib-1.3/htslib/vcfutils.h | 134 +
samtools-1.3/htslib-1.3/htslib_vars.mk | 49 +
samtools-1.3/htslib-1.3/kfunc.c | 280 +
samtools-1.3/htslib-1.3/knetfile.c | 632 +
samtools-1.3/htslib-1.3/kstring.c | 274 +
samtools-1.3/htslib-1.3/md5.c | 386 +
samtools-1.3/htslib-1.3/plugin.c | 171 +
samtools-1.3/htslib-1.3/regidx.c | 340 +
samtools-1.3/htslib-1.3/sam.5 | 68 +
samtools-1.3/htslib-1.3/sam.c | 2059 ++
samtools-1.3/htslib-1.3/synced_bcf_reader.c | 1284 ++
samtools-1.3/htslib-1.3/tabix.1 | 177 +
samtools-1.3/htslib-1.3/tabix.c | 538 +
samtools-1.3/htslib-1.3/tbx.c | 333 +
samtools-1.3/htslib-1.3/test/auxf#values.sam | 5 +
samtools-1.3/htslib-1.3/test/auxf.fa | 2 +
samtools-1.3/htslib-1.3/test/auxf.fa.fai | 1 +
samtools-1.3/htslib-1.3/test/c1#bounds.sam | 4 +
samtools-1.3/htslib-1.3/test/c1#clip.sam | 8 +
samtools-1.3/htslib-1.3/test/c1#noseq.sam | 10 +
samtools-1.3/htslib-1.3/test/c1#pad1.sam | 10 +
samtools-1.3/htslib-1.3/test/c1#pad2.sam | 14 +
samtools-1.3/htslib-1.3/test/c1#pad3.sam | 14 +
samtools-1.3/htslib-1.3/test/c1#unknown.sam | 9 +
samtools-1.3/htslib-1.3/test/c1.fa | 2 +
samtools-1.3/htslib-1.3/test/c1.fa.fai | 1 +
samtools-1.3/htslib-1.3/test/c2#pad.sam | 26 +
samtools-1.3/htslib-1.3/test/c2.fa | 2 +
samtools-1.3/htslib-1.3/test/c2.fa.fai | 1 +
samtools-1.3/htslib-1.3/test/ce#1.sam | 2 +
samtools-1.3/htslib-1.3/test/ce#2.sam | 3 +
samtools-1.3/htslib-1.3/test/ce#5.sam | 11 +
samtools-1.3/htslib-1.3/test/ce#5b.sam | 12 +
samtools-1.3/htslib-1.3/test/ce#large_seq.sam | 3 +
samtools-1.3/htslib-1.3/test/ce#supp.sam | 6 +
samtools-1.3/htslib-1.3/test/ce#tag_depadded.sam | 11 +
samtools-1.3/htslib-1.3/test/ce#tag_padded.sam | 11 +
samtools-1.3/htslib-1.3/test/ce#unmap.sam | 6 +
samtools-1.3/htslib-1.3/test/ce#unmap1.sam | 20 +
samtools-1.3/htslib-1.3/test/ce#unmap2.sam | 29 +
samtools-1.3/htslib-1.3/test/ce.fa | 20803 +++++++++++++++++++
samtools-1.3/htslib-1.3/test/ce.fa.fai | 7 +
samtools-1.3/htslib-1.3/test/compare_sam.pl | 194 +
samtools-1.3/htslib-1.3/test/cross_validate.sh | 126 +
samtools-1.3/htslib-1.3/test/faidx.fa | 17 +
samtools-1.3/htslib-1.3/test/fieldarith.c | 72 +
samtools-1.3/htslib-1.3/test/fieldarith.sam | 15 +
samtools-1.3/htslib-1.3/test/hfile.c | 204 +
samtools-1.3/htslib-1.3/test/sam.c | 208 +
samtools-1.3/htslib-1.3/test/test-regidx.c | 116 +
samtools-1.3/htslib-1.3/test/test-vcf-api.c | 282 +
samtools-1.3/htslib-1.3/test/test-vcf-api.out | 28 +
samtools-1.3/htslib-1.3/test/test-vcf-hdr-in.vcf | 25 +
samtools-1.3/htslib-1.3/test/test-vcf-hdr.out | 16 +
samtools-1.3/htslib-1.3/test/test-vcf-sweep.c | 112 +
samtools-1.3/htslib-1.3/test/test-vcf-sweep.out | 4 +
samtools-1.3/htslib-1.3/test/test.pl | 227 +
samtools-1.3/htslib-1.3/test/test_view.c | 194 +
samtools-1.3/htslib-1.3/test/test_view.pl | 93 +
samtools-1.3/htslib-1.3/test/xx#blank.sam | 0
samtools-1.3/htslib-1.3/test/xx#large_aux.sam | 4 +
samtools-1.3/htslib-1.3/test/xx#large_aux2.sam | 11 +
samtools-1.3/htslib-1.3/test/xx#minimal.sam | 10 +
samtools-1.3/htslib-1.3/test/xx#pair.sam | 7 +
samtools-1.3/htslib-1.3/test/xx#rg.sam | 13 +
samtools-1.3/htslib-1.3/test/xx#tlen.sam | 34 +
samtools-1.3/htslib-1.3/test/xx#tlen2.sam | 36 +
samtools-1.3/htslib-1.3/test/xx#triplet.sam | 7 +
samtools-1.3/htslib-1.3/test/xx#unsorted.sam | 8 +
samtools-1.3/htslib-1.3/test/xx.fa | 5 +
samtools-1.3/htslib-1.3/test/xx.fa.fai | 2 +
samtools-1.3/htslib-1.3/vcf.5 | 120 +
samtools-1.3/htslib-1.3/vcf.c | 3389 +++
samtools-1.3/htslib-1.3/vcf_sweep.c | 183 +
samtools-1.3/htslib-1.3/vcfutils.c | 691 +
samtools-1.3/install-sh | 501 +
samtools-1.3/kprobaln.c | 280 +
samtools-1.3/kprobaln.h | 49 +
samtools-1.3/misc/HmmGlocal.java | 202 +
samtools-1.3/misc/ace2sam.c | 249 +
samtools-1.3/misc/blast2sam.pl | 178 +
samtools-1.3/misc/bowtie2sam.pl | 111 +
samtools-1.3/misc/export2sam.pl | 545 +
samtools-1.3/misc/interpolate_sam.pl | 149 +
samtools-1.3/misc/maq2sam.c | 197 +
samtools-1.3/misc/md5fa.c | 89 +
samtools-1.3/misc/md5sum-lite.c | 61 +
samtools-1.3/misc/novo2sam.pl | 281 +
samtools-1.3/misc/plot-bamstats | 1398 ++
samtools-1.3/misc/psl2sam.pl | 85 +
samtools-1.3/misc/r2plot.lua | 83 +
samtools-1.3/misc/sam2vcf.pl | 289 +
samtools-1.3/misc/samtools.pl | 552 +
samtools-1.3/misc/seq_cache_populate.pl | 322 +
samtools-1.3/misc/soap2sam.pl | 128 +
samtools-1.3/misc/varfilter.py | 227 +
samtools-1.3/misc/vcfutils.lua | 694 +
samtools-1.3/misc/wgsim.1 | 55 +
samtools-1.3/misc/wgsim.c | 466 +
samtools-1.3/misc/wgsim_eval.pl | 339 +
samtools-1.3/misc/zoom2sam.pl | 116 +
samtools-1.3/padding.c | 604 +
samtools-1.3/phase.c | 744 +
samtools-1.3/sam.c | 133 +
samtools-1.3/sam.h | 145 +
samtools-1.3/sam_header.c | 834 +
samtools-1.3/sam_header.h | 72 +
samtools-1.3/sam_opts.c | 153 +
samtools-1.3/sam_opts.h | 99 +
samtools-1.3/sam_view.c | 1030 +
samtools-1.3/sample.c | 132 +
samtools-1.3/sample.h | 41 +
samtools-1.3/samtools.1 | 1957 ++
samtools-1.3/samtools.h | 39 +
samtools-1.3/stats.c | 1728 ++
samtools-1.3/stats_isize.c | 219 +
samtools-1.3/stats_isize.h | 83 +
samtools-1.3/test/addrprg/1_fixup.sam | 30 +
samtools-1.3/test/addrprg/1_fixup.sam.expected | 30 +
samtools-1.3/test/addrprg/1_fixup.sam.expected.err | 0
samtools-1.3/test/addrprg/2_fixup_orphan.sam | 30 +
.../test/addrprg/2_fixup_orphan.sam.expected | 30 +
.../test/addrprg/2_fixup_orphan.sam.expected.err | 0
samtools-1.3/test/addrprg/3_fixup.sam.expected | 0
samtools-1.3/test/addrprg/3_fixup.sam.expected.err | 1 +
samtools-1.3/test/addrprg/4_fixup_norg.sam | 29 +
.../test/addrprg/4_fixup_norg.sam.expected | 30 +
.../test/addrprg/4_fixup_norg.sam.expected.err | 0
samtools-1.3/test/bam2fq/1.1.fq.expected | 72 +
samtools-1.3/test/bam2fq/1.2.fq.expected | 72 +
samtools-1.3/test/bam2fq/1.stdout.expected | 0
samtools-1.3/test/bam2fq/2.1.fq.expected | 72 +
samtools-1.3/test/bam2fq/2.2.fq.expected | 72 +
samtools-1.3/test/bam2fq/2.s.fq.expected | 0
samtools-1.3/test/bam2fq/2.stdout.expected | 0
samtools-1.3/test/bam2fq/3.1.fq.expected | 72 +
samtools-1.3/test/bam2fq/3.2.fq.expected | 72 +
samtools-1.3/test/bam2fq/3.s.fq.expected | 4 +
samtools-1.3/test/bam2fq/3.stdout.expected | 0
samtools-1.3/test/bam2fq/4.1.fq.expected | 68 +
samtools-1.3/test/bam2fq/4.2.fq.expected | 68 +
samtools-1.3/test/bam2fq/4.s.fq.expected | 8 +
samtools-1.3/test/bam2fq/4.stdout.expected | 0
samtools-1.3/test/dat/bam2fq.001.sam | 65 +
samtools-1.3/test/dat/bam2fq.002.sam | 66 +
samtools-1.3/test/dat/bam2fq.003.sam | 65 +
samtools-1.3/test/dat/cat.hdr | 25 +
.../dat/cram_md5/08c04d512d4797d9ba2a156c1daba468 | 1 +
.../dat/cram_md5/7c35feac7036c1cdef3bee0cc4b21437 | 1 +
.../dat/cram_md5/89b96de7acc5918c2858ef92710be7d4 | 1 +
.../dat/cram_md5/8a3d8deb9edd4ce3346b6061fcee6d0b | 1 +
samtools-1.3/test/dat/depad.001.fa | 2 +
samtools-1.3/test/dat/depad.001.fa.fai | 1 +
samtools-1.3/test/dat/depad.001p.sam | 138 +
samtools-1.3/test/dat/depad.001u.sam | 138 +
samtools-1.3/test/dat/dict.fa | 46 +
samtools-1.3/test/dat/dict.out | 10 +
samtools-1.3/test/dat/empty.expected | 0
samtools-1.3/test/dat/large_chrom.out | 6 +
samtools-1.3/test/dat/large_chrom.sam | 63 +
samtools-1.3/test/dat/large_chrom_bai_index.err | 1 +
samtools-1.3/test/dat/mpileup.1.sam | 1016 +
samtools-1.3/test/dat/mpileup.2.sam | 248 +
samtools-1.3/test/dat/mpileup.3.sam | 250 +
samtools-1.3/test/dat/mpileup.err.1 | 2 +
samtools-1.3/test/dat/mpileup.out.1 | 51 +
samtools-1.3/test/dat/mpileup.out.2 | 523 +
samtools-1.3/test/dat/mpileup.out.3 | 11 +
samtools-1.3/test/dat/mpileup.out.4 | 527 +
samtools-1.3/test/dat/mpileup.ref.fa | 71 +
samtools-1.3/test/dat/mpileup.ref.fa.fai | 1 +
samtools-1.3/test/dat/test_input_1_a.bam | Bin 0 -> 759 bytes
.../test/dat/test_input_1_a.bam.bai.expected | Bin 0 -> 264 bytes
samtools-1.3/test/dat/test_input_1_a.sam | 28 +
samtools-1.3/test/dat/test_input_1_a_regex.sam | 28 +
samtools-1.3/test/dat/test_input_1_b.bam | Bin 0 -> 686 bytes
samtools-1.3/test/dat/test_input_1_b.sam | 24 +
samtools-1.3/test/dat/test_input_1_b_regex.sam | 24 +
samtools-1.3/test/dat/test_input_1_c.bam | Bin 0 -> 692 bytes
samtools-1.3/test/dat/test_input_1_c.sam | 23 +
samtools-1.3/test/dat/view.001.01.bed | 27 +
samtools-1.3/test/dat/view.001.02.bed | 22 +
samtools-1.3/test/dat/view.001.fa | 4 +
samtools-1.3/test/dat/view.001.fa.fai | 2 +
samtools-1.3/test/dat/view.001.sam | 62 +
samtools-1.3/test/dat/view.002.01.bed | 25 +
samtools-1.3/test/dat/view.002.02.bed | 30 +
samtools-1.3/test/dat/view.002.fa | 2 +
samtools-1.3/test/dat/view.002.fa.fai | 1 +
samtools-1.3/test/dat/view.002.sam | 83 +
samtools-1.3/test/dat/view.003.expected.sam | 39 +
samtools-1.3/test/dat/view.003.sam | 39 +
samtools-1.3/test/fixmate/1_coord_sort.sam | 16 +
.../test/fixmate/1_coord_sort.sam.expected | 0
.../test/fixmate/1_coord_sort.sam.expected.err | 2 +
samtools-1.3/test/fixmate/2_isize_overflow.sam | 18 +
.../test/fixmate/2_isize_overflow.sam.expected | 18 +
samtools-1.3/test/fixmate/3_reverse_read_pp_lt.sam | 5 +
.../test/fixmate/3_reverse_read_pp_lt.sam.expected | 5 +
.../test/fixmate/4_reverse_read_pp_equal.sam | 5 +
.../fixmate/4_reverse_read_pp_equal.sam.expected | 5 +
samtools-1.3/test/fixmate/5_ct.sam | 5 +
samtools-1.3/test/fixmate/5_ct.sam.expected | 5 +
samtools-1.3/test/fixmate/6_ct_replace.sam | 5 +
.../test/fixmate/6_ct_replace.sam.expected | 5 +
.../test/idxstats/test_input_1_a.bam.expected | 5 +
.../test/idxstats/test_input_1_a.bam.expected.err | 0
samtools-1.3/test/merge/2.merge.expected.bam | Bin 0 -> 1228 bytes
samtools-1.3/test/merge/3.merge.expected.bam | Bin 0 -> 1233 bytes
samtools-1.3/test/merge/3.merge.expected.err | 1 +
samtools-1.3/test/merge/4.merge.expected.bam | Bin 0 -> 689 bytes
samtools-1.3/test/merge/5.merge.expected.bam | Bin 0 -> 1115 bytes
samtools-1.3/test/merge/5.merge.expected.sam | 61 +
samtools-1.3/test/merge/6.merge.expected.bam | Bin 0 -> 899 bytes
samtools-1.3/test/merge/7.merge.expected.bam | Bin 0 -> 1056 bytes
samtools-1.3/test/merge/test_3.fofn | 2 +
samtools-1.3/test/merge/test_bam_translate.c | 596 +
samtools-1.3/test/merge/test_header.sam | 11 +
samtools-1.3/test/merge/test_rtrans_build.c | 118 +
samtools-1.3/test/merge/test_trans_tbl_init.c | 574 +
samtools-1.3/test/mpileup/1read.bam | Bin 0 -> 525 bytes
samtools-1.3/test/mpileup/1read.sam | 1 +
samtools-1.3/test/mpileup/anomalous.sam | 6 +
samtools-1.3/test/mpileup/c1#ID.bam | Bin 0 -> 293 bytes
samtools-1.3/test/mpileup/c1#ID2.bam | Bin 0 -> 377 bytes
samtools-1.3/test/mpileup/c1#clip.bam | Bin 0 -> 265 bytes
samtools-1.3/test/mpileup/c1#pad1.bam | Bin 0 -> 299 bytes
samtools-1.3/test/mpileup/c1#pad2.bam | Bin 0 -> 349 bytes
samtools-1.3/test/mpileup/c1#pad3.bam | Bin 0 -> 382 bytes
samtools-1.3/test/mpileup/c1.fa | 4 +
samtools-1.3/test/mpileup/c1.fa.fai | 2 +
samtools-1.3/test/mpileup/ce#5b.bam | Bin 0 -> 557 bytes
samtools-1.3/test/mpileup/ce#5b.bam.bai | Bin 0 -> 416 bytes
samtools-1.3/test/mpileup/ce#5b.cram | Bin 0 -> 13183 bytes
samtools-1.3/test/mpileup/ce#5b.cram.crai | Bin 0 -> 75 bytes
samtools-1.3/test/mpileup/ce#5b.sam | 12 +
samtools-1.3/test/mpileup/ce#large_seq.bam | Bin 0 -> 345315 bytes
samtools-1.3/test/mpileup/ce#unmap.bam | Bin 0 -> 233 bytes
samtools-1.3/test/mpileup/ce#unmap1.bam | Bin 0 -> 896 bytes
samtools-1.3/test/mpileup/ce#unmap2.bam | Bin 0 -> 1344 bytes
samtools-1.3/test/mpileup/ce.fa | 20803 +++++++++++++++++++
samtools-1.3/test/mpileup/ce.fa.fai | 7 +
samtools-1.3/test/mpileup/deep.sam | 9001 ++++++++
samtools-1.3/test/mpileup/depth.reg | 39 +
samtools-1.3/test/mpileup/expected/1.out.f3-6.gz | Bin 0 -> 596114 bytes
samtools-1.3/test/mpileup/expected/10.out | 40 +
samtools-1.3/test/mpileup/expected/11.out | 9 +
samtools-1.3/test/mpileup/expected/12.out | 9 +
samtools-1.3/test/mpileup/expected/13.out | 4101 ++++
samtools-1.3/test/mpileup/expected/14.out | 4101 ++++
samtools-1.3/test/mpileup/expected/15.out | 4101 ++++
samtools-1.3/test/mpileup/expected/16.out | 4101 ++++
samtools-1.3/test/mpileup/expected/17.out | 4101 ++++
samtools-1.3/test/mpileup/expected/18.out | 4101 ++++
samtools-1.3/test/mpileup/expected/19.out | 4101 ++++
samtools-1.3/test/mpileup/expected/2.out | 0
samtools-1.3/test/mpileup/expected/20.out | 4101 ++++
samtools-1.3/test/mpileup/expected/21.out | 4101 ++++
samtools-1.3/test/mpileup/expected/22.out | 4101 ++++
samtools-1.3/test/mpileup/expected/23.out | 150 +
samtools-1.3/test/mpileup/expected/24.out | 150 +
samtools-1.3/test/mpileup/expected/25.out | 150 +
samtools-1.3/test/mpileup/expected/26.out | 100 +
samtools-1.3/test/mpileup/expected/27.out | 100 +
samtools-1.3/test/mpileup/expected/28.out | 4101 ++++
samtools-1.3/test/mpileup/expected/29.out | 0
samtools-1.3/test/mpileup/expected/3.out | 0
samtools-1.3/test/mpileup/expected/30.out | 100 +
samtools-1.3/test/mpileup/expected/31.out | 100 +
samtools-1.3/test/mpileup/expected/32.out | 100 +
samtools-1.3/test/mpileup/expected/33.out | 12 +
samtools-1.3/test/mpileup/expected/34.out | 12 +
samtools-1.3/test/mpileup/expected/35.out | 3397 +++
samtools-1.3/test/mpileup/expected/37.out | 4101 ++++
samtools-1.3/test/mpileup/expected/38.out | 102 +
samtools-1.3/test/mpileup/expected/39.out | 11 +
samtools-1.3/test/mpileup/expected/4.out | 101 +
samtools-1.3/test/mpileup/expected/40.out | 84 +
samtools-1.3/test/mpileup/expected/41.out | 21 +
samtools-1.3/test/mpileup/expected/42.out | 0
samtools-1.3/test/mpileup/expected/43.out | 3893 ++++
samtools-1.3/test/mpileup/expected/44.out | 3893 ++++
samtools-1.3/test/mpileup/expected/45.out | 4097 ++++
samtools-1.3/test/mpileup/expected/46.out | 4097 ++++
samtools-1.3/test/mpileup/expected/47.out | 1 +
samtools-1.3/test/mpileup/expected/48.out | 4104 ++++
samtools-1.3/test/mpileup/expected/49.out | 4104 ++++
samtools-1.3/test/mpileup/expected/5.out | 10 +
samtools-1.3/test/mpileup/expected/50.out | 4104 ++++
samtools-1.3/test/mpileup/expected/51.out | 4104 ++++
samtools-1.3/test/mpileup/expected/52.out | 4208 ++++
samtools-1.3/test/mpileup/expected/53.out | 1 +
samtools-1.3/test/mpileup/expected/54.out | 1 +
samtools-1.3/test/mpileup/expected/55.out | 1 +
samtools-1.3/test/mpileup/expected/56.out | 1 +
samtools-1.3/test/mpileup/expected/57.out | 1 +
samtools-1.3/test/mpileup/expected/58.out | 1 +
samtools-1.3/test/mpileup/expected/59.out | 1 +
samtools-1.3/test/mpileup/expected/6.out | 10 +
samtools-1.3/test/mpileup/expected/60.out | 0
samtools-1.3/test/mpileup/expected/61.out | 1 +
samtools-1.3/test/mpileup/expected/62.out | 0
samtools-1.3/test/mpileup/expected/63.out | 1 +
samtools-1.3/test/mpileup/expected/64.out | 0
samtools-1.3/test/mpileup/expected/65.out | 1 +
samtools-1.3/test/mpileup/expected/66.out | 0
samtools-1.3/test/mpileup/expected/67.out | 1 +
samtools-1.3/test/mpileup/expected/68.out | 0
samtools-1.3/test/mpileup/expected/69.out | 0
samtools-1.3/test/mpileup/expected/7.out | 10 +
samtools-1.3/test/mpileup/expected/70.out | 1 +
samtools-1.3/test/mpileup/expected/71.out | 1 +
samtools-1.3/test/mpileup/expected/72.out | 0
samtools-1.3/test/mpileup/expected/73.out | 1 +
samtools-1.3/test/mpileup/expected/74.out | 0
samtools-1.3/test/mpileup/expected/75.out | 1 +
samtools-1.3/test/mpileup/expected/76.out | 4101 ++++
samtools-1.3/test/mpileup/expected/77.out | 4101 ++++
samtools-1.3/test/mpileup/expected/8.out | 5 +
samtools-1.3/test/mpileup/expected/9.out | 10 +
samtools-1.3/test/mpileup/expected/d1_1.out | 6 +
samtools-1.3/test/mpileup/expected/d1_12.out | 9 +
samtools-1.3/test/mpileup/expected/d1_2.out | 6 +
samtools-1.3/test/mpileup/expected/d2_12r.out | 5 +
samtools-1.3/test/mpileup/expected/d3_12.out | 20 +
samtools-1.3/test/mpileup/expected/d3_12r1a.out | 12 +
samtools-1.3/test/mpileup/expected/d3_12r2a.out | 6 +
samtools-1.3/test/mpileup/expected/d4_12.out | 60 +
samtools-1.3/test/mpileup/expected/d4_12b.out | 17 +
samtools-1.3/test/mpileup/expected/d4_12r.out | 12 +
samtools-1.3/test/mpileup/indels.sam | 9 +
.../mpileup/md5/02099b2aad2cfe707759353724fb40ae | 1 +
.../mpileup/md5/0d4dfc45807d6a11439e858605cb364d | 1 +
.../mpileup/md5/351f64d4f4f9ddd45b35336ad97aa6de | 1 +
.../mpileup/md5/6ec590eb82c361a61e6baabce20109bc | 1 +
.../mpileup/md5/6f60cdf4c739651ae72d53e2e94825c1 | 1 +
.../mpileup/md5/73d180d5cb3860a2713927b6812eab0e | 1 +
samtools-1.3/test/mpileup/mpileup-E.bam | Bin 0 -> 280 bytes
samtools-1.3/test/mpileup/mpileup.1.bam | Bin 0 -> 71637 bytes
samtools-1.3/test/mpileup/mpileup.1.bam.bai | Bin 0 -> 776 bytes
samtools-1.3/test/mpileup/mpileup.2.bam | Bin 0 -> 31556 bytes
samtools-1.3/test/mpileup/mpileup.3.bam | Bin 0 -> 31216 bytes
samtools-1.3/test/mpileup/mpileup.ref.fa | 71 +
samtools-1.3/test/mpileup/mpileup.ref.fa.fai | 1 +
samtools-1.3/test/mpileup/mpileup.reg | 144 +
samtools-1.3/test/mpileup/overlap50.sam | 5 +
samtools-1.3/test/mpileup/overlapIllumina.bam | Bin 0 -> 583 bytes
samtools-1.3/test/mpileup/regions | 10 +
samtools-1.3/test/mpileup/regression.sh | 158 +
samtools-1.3/test/mpileup/xx#depth1.sam | 6 +
samtools-1.3/test/mpileup/xx#depth2.sam | 6 +
samtools-1.3/test/mpileup/xx#minimal.bam | Bin 0 -> 215 bytes
samtools-1.3/test/mpileup/xx#triplet.bam | Bin 0 -> 247 bytes
samtools-1.3/test/mpileup/xx.bed | 2 +
samtools-1.3/test/mpileup/xx.bed2 | 1 +
samtools-1.3/test/mpileup/xx.fa | 5 +
samtools-1.3/test/mpileup/xx.fa.fai | 2 +
.../test/quickcheck/1.quickcheck.badeof.bam | Bin 0 -> 1228 bytes
.../test/quickcheck/2.quickcheck.badheader.bam | Bin 0 -> 1233 bytes
samtools-1.3/test/quickcheck/3.quickcheck.ok.bam | Bin 0 -> 1228 bytes
samtools-1.3/test/quickcheck/4.quickcheck.ok.bam | Bin 0 -> 1233 bytes
samtools-1.3/test/quickcheck/all.expected | 2 +
samtools-1.3/test/reheader/1_view1.sam.expected | 63 +
.../test/reheader/1_view1.sam.expected.err | 0
samtools-1.3/test/reheader/2_view1.sam.expected | 63 +
.../test/reheader/2_view1.sam.expected.err | 0
samtools-1.3/test/reheader/3_view1.sam.expected | 63 +
.../test/reheader/3_view1.sam.expected.err | 0
samtools-1.3/test/reheader/hdr.sam | 28 +
samtools-1.3/test/split/test_count_rg.c | 123 +
.../test/split/test_expand_format_string.c | 123 +
samtools-1.3/test/split/test_filter_header_rg.c | 192 +
samtools-1.3/test/split/test_parse_args.c | 215 +
samtools-1.3/test/stat/1.stats.expected | 302 +
samtools-1.3/test/stat/10.stats.expected | 302 +
samtools-1.3/test/stat/10_map_cigar.sam | 8 +
.../stat/10_map_cigar.sam_s1_a_1.expected.bamstat | 302 +
.../stat/10_map_cigar.sam_s1_b_1.expected.bamstat | 302 +
samtools-1.3/test/stat/1_map_cigar.sam | 5 +
.../stat/1_map_cigar.sam_s1_a_1.expected.bamstat | 302 +
samtools-1.3/test/stat/2.stats.expected | 302 +
samtools-1.3/test/stat/2_equal_cigar_full_seq.sam | 5 +
samtools-1.3/test/stat/3.stats.expected | 265 +
samtools-1.3/test/stat/3_map_cigar_equal_seq.sam | 5 +
samtools-1.3/test/stat/4.stats.expected | 302 +
samtools-1.3/test/stat/4_X_cigar_full_seq.sam | 5 +
samtools-1.3/test/stat/5.stats.expected | 304 +
samtools-1.3/test/stat/5_insert_cigar.sam | 5 +
samtools-1.3/test/stat/6.stats.expected | 304 +
samtools-1.3/test/stat/7.stats.expected | 305 +
samtools-1.3/test/stat/7_supp.sam | 6 +
samtools-1.3/test/stat/8.stats.expected | 304 +
samtools-1.3/test/stat/8_secondary.sam | 6 +
samtools-1.3/test/stat/9.stats.expected | 302 +
samtools-1.3/test/stat/test.fa | 3 +
samtools-1.3/test/stat/test.fa.fai | 1 +
samtools-1.3/test/test.c | 53 +
samtools-1.3/test/test.h | 35 +
samtools-1.3/test/test.pl | 2448 +++
samtools-1.3/test/tview/test_get_rg_sample.c | 81 +
samtools-1.3/test/vcf-miniview.c | 115 +
samtools-1.3/win32/xcurses.h | 1377 ++
samtools-1.3/win32/zconf.h | 332 +
samtools-1.3/win32/zlib.h | 1357 ++
scanForPairedEndReads.cpp | 150 +-
simulation.cpp | 2 +
synthesisRef.cpp | 49 +-
tbam2gbam.cpp | 11 +-
utils.h | 11 +-
wiggle.cpp | 107 +-
616 files changed, 265139 insertions(+), 2083 deletions(-)
delete mode 100644 FOR_CYGWIN_USERS
create mode 100644 SamHeader.cpp
create mode 100644 SamHeader.hpp
delete mode 100644 debian/patches/add-descriptions
delete mode 100644 debian/patches/fix-boost
delete mode 100644 debian/patches/fix-for-g++-6
delete mode 100644 debian/patches/fix-sam-includes
create mode 100644 debian/patches/hardening
delete mode 100644 debian/patches/ignore-sam
delete mode 100644 debian/patches/spelling
delete mode 100644 debian/patches/use-flags
delete mode 100644 sam_rsem_aux.h
delete mode 100644 sam_rsem_cvt.h
create mode 100644 sam_utils.h
create mode 100644 samtools-1.3/AUTHORS
create mode 100644 samtools-1.3/ChangeLog.old
create mode 100644 samtools-1.3/INSTALL
create mode 100644 samtools-1.3/LICENSE
create mode 100644 samtools-1.3/Makefile
create mode 100644 samtools-1.3/Makefile.cygwin
create mode 100644 samtools-1.3/Makefile.mingw
create mode 100644 samtools-1.3/NEWS
create mode 100644 samtools-1.3/README
create mode 100644 samtools-1.3/aclocal.m4
create mode 100644 samtools-1.3/bam.c
create mode 100644 samtools-1.3/bam.h
create mode 100644 samtools-1.3/bam2bcf.c
create mode 100644 samtools-1.3/bam2bcf.h
create mode 100644 samtools-1.3/bam2bcf_indel.c
create mode 100644 samtools-1.3/bam2depth.c
create mode 100644 samtools-1.3/bam_addrprg.c
create mode 100644 samtools-1.3/bam_aux.c
create mode 100644 samtools-1.3/bam_cat.c
create mode 100644 samtools-1.3/bam_color.c
create mode 100644 samtools-1.3/bam_endian.h
create mode 100644 samtools-1.3/bam_flags.c
create mode 100644 samtools-1.3/bam_import.c
create mode 100644 samtools-1.3/bam_index.c
create mode 100644 samtools-1.3/bam_lpileup.c
create mode 100644 samtools-1.3/bam_lpileup.h
create mode 100644 samtools-1.3/bam_mate.c
create mode 100644 samtools-1.3/bam_md.c
create mode 100644 samtools-1.3/bam_plbuf.c
create mode 100644 samtools-1.3/bam_plbuf.h
create mode 100644 samtools-1.3/bam_plcmd.c
create mode 100644 samtools-1.3/bam_quickcheck.c
create mode 100644 samtools-1.3/bam_reheader.c
create mode 100644 samtools-1.3/bam_rmdup.c
create mode 100644 samtools-1.3/bam_rmdupse.c
create mode 100644 samtools-1.3/bam_sort.c
create mode 100644 samtools-1.3/bam_split.c
create mode 100644 samtools-1.3/bam_stat.c
create mode 100644 samtools-1.3/bam_tview.c
create mode 100644 samtools-1.3/bam_tview.h
create mode 100644 samtools-1.3/bam_tview_curses.c
create mode 100644 samtools-1.3/bam_tview_html.c
create mode 100644 samtools-1.3/bamshuf.c
create mode 100644 samtools-1.3/bamtk.c
create mode 100644 samtools-1.3/bedcov.c
create mode 100644 samtools-1.3/bedidx.c
create mode 100644 samtools-1.3/config.h.in
create mode 100644 samtools-1.3/config.mk.in
create mode 100755 samtools-1.3/configure
create mode 100644 samtools-1.3/configure.ac
create mode 100644 samtools-1.3/cut_target.c
create mode 100644 samtools-1.3/dict.c
create mode 100644 samtools-1.3/errmod.c
create mode 100644 samtools-1.3/errmod.h
create mode 100644 samtools-1.3/examples/00README.txt
create mode 100644 samtools-1.3/examples/ex1.fa
create mode 100644 samtools-1.3/examples/ex1.sam.gz
create mode 100644 samtools-1.3/examples/toy.fa
create mode 100644 samtools-1.3/examples/toy.sam
create mode 100644 samtools-1.3/faidx.c
create mode 100644 samtools-1.3/htslib-1.3/INSTALL
create mode 100644 samtools-1.3/htslib-1.3/LICENSE
create mode 100644 samtools-1.3/htslib-1.3/Makefile
create mode 100644 samtools-1.3/htslib-1.3/NEWS
create mode 100644 samtools-1.3/htslib-1.3/README
create mode 100644 samtools-1.3/htslib-1.3/bgzf.c
create mode 100644 samtools-1.3/htslib-1.3/bgzip.c
create mode 100644 samtools-1.3/htslib-1.3/config.h.in
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create mode 100755 samtools-1.3/htslib-1.3/configure
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create mode 100644 samtools-1.3/htslib-1.3/cram/cram_codecs.c
create mode 100644 samtools-1.3/htslib-1.3/cram/cram_codecs.h
create mode 100644 samtools-1.3/htslib-1.3/cram/cram_decode.c
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create mode 100644 samtools-1.3/htslib-1.3/cram/cram_encode.c
create mode 100644 samtools-1.3/htslib-1.3/cram/cram_encode.h
create mode 100644 samtools-1.3/htslib-1.3/cram/cram_external.c
create mode 100644 samtools-1.3/htslib-1.3/cram/cram_index.c
create mode 100644 samtools-1.3/htslib-1.3/cram/cram_index.h
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