[med-svn] [sra-sdk] branch upstream updated (82d7c33 -> 6881a00)

Andreas Tille tille at debian.org
Sun May 15 18:34:54 UTC 2016


This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch upstream
in repository sra-sdk.

      from  82d7c33   Imported Upstream version 2.5.7
       new  6881a00   Imported Upstream version 2.6.2

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 CHANGES                                            |    58 +-
 CHANGES.md                                         |    54 +
 Makefile                                           |    36 +-
 README                                             |     2 +
 README.md                                          |     5 +-
 build/.gitignore                                   |     3 +-
 ...mount-demo.vcxproj => dbgap-mount-tool.vcxproj} |     6 +-
 build/MSVC/2010/prefetch.vcxproj                   |     1 +
 build/MSVC/2010/test-align-info.vcxproj            |     5 +-
 build/MSVC/2010/test-fastq-loader.vcxproj          |     3 +-
 build/MSVC/2010/vdb-common.props                   |    10 +-
 build/MSVC/2010/vdb-dump.vcxproj                   |     2 +
 build/Makefile.deb                                 |   109 +
 build/Makefile.gcc                                 |    10 +-
 build/Makefile.install                             |    50 +-
 build/Makefile.linux                               |    13 +
 build/Makefile.rpm                                 |   165 +
 build/Makefile.shell                               |    14 +-
 build/Makefile.targets                             |    13 +
 build/Makefile.tools                               |    40 +
 build/ld.linux.exe.sh                              |     9 +-
 build/ld.linux.gcc.sh                              |     5 +-
 build/ld.mac.dlib.sh                               |     2 +-
 build/ld.mac.exe.sh                                |     2 +-
 build/ld.sh                                        |     9 +-
 {test/ngs-pileup => build}/valgrind.suppress       |     0
 setup/konfigure.perl                               |    44 +-
 setup/package.prl                                  |     2 +-
 test/Makefile                                      |     5 +
 test/align-cache/CSRA_file                         |   Bin 0 -> 154937 bytes
 test/{align-info => align-cache}/Makefile          |    24 +-
 .../valgrind.suppress                              |     0
 test/{align-info => copycat}/Makefile              |    26 +-
 test/copycat/input/1.xml                           |     5 +
 test/fastq-loader/Makefile                         |    22 +-
 test/fastq-loader/expected/1.1.stdout              |     3 +-
 test/fastq-loader/expected/1.2.stdout              |     3 +-
 test/fastq-loader/expected/1.4.stdout              |     6 +
 test/fastq-loader/expected/10.0.stdout             |     3 +-
 test/fastq-loader/expected/11.0.stdout             |     5 +-
 test/fastq-loader/expected/11.1.stdout             |     3 +-
 test/fastq-loader/expected/12.0.stdout             |     4 +
 test/fastq-loader/expected/12.1.stdout             |     4 +
 test/fastq-loader/expected/12.2.stdout             |     5 +-
 test/fastq-loader/expected/13.0.stdout             |    96 +
 test/fastq-loader/expected/13.1.stdout             |    96 +
 test/fastq-loader/expected/14.0.stdout             |    32 +
 test/fastq-loader/expected/2.1.1.stdout            |     4 +
 test/fastq-loader/expected/2.1.stdout              |     8 +-
 test/fastq-loader/expected/2.5.stdout              |     4 +
 test/fastq-loader/expected/2.6.stdout              |     3 +-
 test/fastq-loader/expected/2.7.stdout              |     3 +-
 test/fastq-loader/expected/2.8.1.stdout            |     8 +-
 test/fastq-loader/expected/2.8.stdout              |     8 +-
 test/fastq-loader/expected/3.1.stdout              |     8 +
 test/fastq-loader/expected/4.2.stdout              |     3 +-
 test/fastq-loader/expected/4.4.stdout              |     6 +
 test/fastq-loader/expected/4.6.stdout              |     3 +-
 test/fastq-loader/expected/5.0.stdout              |     3 +-
 test/fastq-loader/expected/6.0.stdout              |    26 +
 test/fastq-loader/expected/7.1.stdout              |     4 +
 test/fastq-loader/expected/7.2.stdout              |     4 +
 test/fastq-loader/expected/7.3.stdout              |     4 +
 test/fastq-loader/expected/8.0.stdout              |     3 +-
 test/fastq-loader/expected/9.0.stdout              |     4 +
 .../input/{11.0.1.fasta => 13.0.fasta}             |     0
 test/fastq-loader/input/13.0.fastq                 |    12 +
 test/fastq-loader/input/13.1.fastq                 |    12 +
 .../input/{11.0.1.fasta => 14.0.fasta}             |     0
 test/fastq-loader/wb-test-fastq.cpp                |    20 +
 test/general-loader/.gitignore                     |     1 -
 test/general-loader/Makefile                       |    13 +-
 test/general-loader/expected/2.stderr              |     4 +-
 test/general-loader/expected/2packed.stderr        |     4 +-
 test/general-loader/{ => input}/column01           |     5 +-
 test/general-loader/{ => input}/column02           |     5 +-
 test/general-loader/test-general-loader.cpp        |   304 +-
 test/general-loader/test-general-writer.cpp        |     4 +-
 test/{align-info => kar}/Makefile                  |    27 +-
 test/kar/expected/1.0.stdout                       |    35 +
 test/kar/input/1.0/1.md5                           |     0
 test/kar/input/1.0/col/sub1/idx                    |     0
 test/kar/input/1.0/col/sub1/idx0                   |     0
 test/kar/input/1.0/col/sub1/idx1                   |     0
 test/kar/input/1.0/col/sub1/idx2                   |     0
 test/kar/input/1.0/col/sub1/idx3                   |     0
 test/kar/input/1.0/idx/4a                          |     0
 test/kar/input/1.0/idx/4b                          |     0
 test/kar/input/1.0/idx/sub/4c                      |     0
 test/kar/input/1.0/idx/sub/4d                      |     0
 test/kar/input/1.0/md/cur                          |     0
 test/kar/input/1.0/md5                             |     0
 test/kar/input/1.0/sub1/col/sub1/idx               |     0
 test/kar/input/1.0/sub1/col/sub1/idx0              |     0
 test/kar/input/1.0/sub1/col/sub1/idx1              |     0
 test/kar/input/1.0/sub1/col/sub1/idx2              |     0
 test/kar/input/1.0/sub1/col/sub1/idx3              |     0
 test/kar/input/1.0/sub1/md/cur                     |     0
 test/kar/input/1.0/sub1/sub2/col/sub1/idx          |     0
 test/kar/input/1.0/sub1/sub2/col/sub1/idx0         |     0
 test/kar/input/1.0/sub1/sub2/col/sub1/idx1         |     0
 test/kar/input/1.0/sub1/sub2/col/sub1/idx2         |     0
 test/kar/input/1.0/sub1/sub2/col/sub1/idx3         |     0
 test/kar/test-kar.sh                               |    97 +
 test/kget/Makefile                                 |    10 +
 test/kget/test_kget.py                             |   175 +
 test/ngs-pileup/Makefile                           |     3 -
 test/{vcf-loader => pileup-stats}/Makefile         |    44 +-
 .../{ngs-pileup => pileup-stats}/valgrind.suppress |     0
 test/ref-variation/Makefile                        |    19 +-
 test/ref-variation/expected/ref-variation.out      |   192 +
 test/ref-variation/expected/var-expand.out         |     1 +
 test/ref-variation/have-access.sh                  |    25 +
 test/ref-variation/ref-variation.in                |     4 +
 test/ref-variation/ref-variation.sh                |    29 +
 test/samline/Makefile                              |    39 +-
 test/samline/alig-gen.c                            |   854 +-
 test/samline/bx_tag_test.py                        |    27 +
 test/samline/ca_test.py                            |    80 +
 test/samline/cigar.c                               |   628 +-
 test/samline/cigar.h                               |     4 +-
 test/samline/example.sh                            |    35 +-
 test/samline/refbases.c                            |   209 +-
 test/samline/refbases.h                            |     4 +-
 test/samline/reject_multi_refnames.sh              |    62 +
 test/samline/sam.py                                |   339 +
 test/samline/sampart.c                             |   304 +
 .../network-test.vers => samline/sampart.vers}     |     0
 test/samline/sec_align_problem.sh                  |    76 +
 test/vcf-loader/Makefile                           |     3 -
 test/{vcf-loader => vdb-validate}/Makefile         |    53 +-
 test/vdb-validate/db/blob-row-gap.kar              |   Bin 0 -> 3362642 bytes
 test/vdb-validate/db/sdc_len_mismatch.csra         |   Bin 0 -> 181017 bytes
 test/vdb-validate/db/sdc_pa_longer.csra            |   Bin 0 -> 183853 bytes
 test/vdb-validate/db/sdc_tmp_mismatch.csra         |   Bin 0 -> 170925 bytes
 test/vdb-validate/expected/ROW_GAP                 |    42 +
 test/vdb-validate/expected/no_sdc_checks           |    23 +
 test/vdb-validate/expected/sdc_len_mismatch_1      |    24 +
 test/vdb-validate/expected/sdc_len_mismatch_2      |    24 +
 test/vdb-validate/expected/sdc_pa_longer_1         |    26 +
 test/vdb-validate/expected/sdc_pa_longer_2         |    26 +
 test/vdb-validate/expected/sdc_pa_longer_3         |    26 +
 test/vdb-validate/expected/sdc_tmp_mismatch        |    16 +
 .../vdb-validate/runtestcase.sh                    |    64 +-
 test/vschema/Makefile                              |     2 +
 test/vschema/idx-text/checklookup.cpp              |    18 +-
 test/vschema/idx-text/expected/ci-1.stdout         |     6 +
 test/vschema/idx-text/expected/ci-5.stdout         |    15 +
 test/vschema/idx-text/expected/cs-3.stdout         |    18 +
 test/vschema/idx-text/makeinputs.cpp               |    40 +-
 tools/Makefile                                     |    12 +-
 tools/align-cache/Makefile                         |     1 -
 tools/align-info/align-info.vers                   |     2 +-
 tools/align-info/align-info.vers.h                 |     2 +-
 tools/bam-loader/Globals.h                         |    11 +-
 tools/bam-loader/Makefile                          |     3 +-
 tools/bam-loader/alignment-writer.h                |     2 +
 .../{util/samview.c => bam-loader/bam-alignment.h} |    97 +-
 tools/bam-loader/bam-load.vers                     |     2 +-
 tools/bam-loader/bam-loader.c                      |   395 +-
 tools/bam-loader/bam-priv.h                        |   196 +
 tools/bam-loader/bam.c                             |   531 +-
 tools/bam-loader/bam.h                             |    70 +-
 tools/bam-loader/loader-imp.c                      |  1573 +-
 tools/bam-loader/loader-imp.h                      |     3 +-
 .../low-match-count.cpp}                           |    59 +-
 .../directory.h => bam-loader/low-match-count.h}   |    13 +-
 tools/bam-loader/reference-writer.c                |    57 +-
 tools/bam-loader/reference-writer.h                |     2 +-
 tools/bam-loader/sequence-writer.c                 |   478 +-
 tools/bam-loader/sequence-writer.h                 |    23 +-
 tools/cache-mgr/cache-mgr.vers                     |     2 +-
 tools/cache-mgr/cache-mgr.vers.h                   |     2 +-
 tools/ccextract/ccextract.vers                     |     2 +-
 tools/cg-load/cg-load.vers                         |     2 +-
 tools/copycat/Makefile                             |     1 +
 tools/copycat/ccfileformat.c                       |    42 +-
 tools/copycat/copycat.vers                         |     2 +-
 tools/copycat/magic                                | 18398 +++++++++++++++++++
 tools/dbgap-mount/Makefile                         |    37 +-
 tools/dbgap-mount/dbgap-mount-tool.c               |   565 +
 .../dbgap-mount-tool.h}                            |    61 +-
 .../{demo.vers => dbgap-mount-tool.vers}           |     0
 tools/dbgap-mount/dbgap-mount-tool.vers.h          |     1 +
 tools/dbgap-mount/demo.c                           |    14 +-
 .../column_match.c => dbgap-mount/unix/wrap.c}     |    21 +-
 tools/dbgap-mount/win/wrap.c                       |   344 +
 tools/fastdump/.gitignore                          |     3 +
 tools/{kget => fastdump}/Makefile                  |    22 +-
 tools/fastdump/cmn_iter.c                          |   287 +
 .../vdb-copy-includes.h => fastdump/cmn_iter.h}    |    91 +-
 tools/fastdump/fastdump.c                          |   432 +
 .../fastdump/fastdump.vers                         |     0
 tools/fastdump/fastq_iter.c                        |    97 +
 .../{vdb-dump/vdb_info.h => fastdump/fastq_iter.h} |    37 +-
 tools/fastdump/file_printer.c                      |   130 +
 .../vdb-dump-fastq.h => fastdump/file_printer.h}   |    23 +-
 tools/fastdump/helper.c                            |   685 +
 tools/fastdump/helper.h                            |   141 +
 tools/fastdump/index.c                             |   335 +
 .../ref_exclude.h => fastdump/index.h}             |    48 +-
 tools/fastdump/join.c                              |   543 +
 .../spot_position.h => fastdump/join.h}            |    56 +-
 tools/fastdump/line_iter.c                         |   199 +
 .../vdb-dump-fastq.h => fastdump/line_iter.h}      |    27 +-
 tools/fastdump/lookup_reader.c                     |   331 +
 .../lookup_reader.h}                               |    84 +-
 tools/fastdump/lookup_writer.c                     |   138 +
 .../ref_exclude.h => fastdump/lookup_writer.h}     |    46 +-
 tools/fastdump/merge_sorter.c                      |   173 +
 .../vdb-dump-fastq.h => fastdump/merge_sorter.h}   |   113 +-
 tools/fastdump/raw_read_iter.c                     |   100 +
 .../vdb_info.h => fastdump/raw_read_iter.h}        |    36 +-
 tools/fastdump/readme.txt                          |    92 +
 tools/fastdump/sorter.c                            |   538 +
 .../spot_position.h => fastdump/sorter.h}          |    55 +-
 tools/fastdump/special_iter.c                      |    98 +
 .../spot_position.h => fastdump/special_iter.h}    |    44 +-
 tools/fastdump/todo.txt                            |     3 +
 tools/fastdump/verify.sh                           |    60 +
 tools/fastq-dump/fastq-dump.vers                   |     2 +-
 tools/fastq-loader/Makefile                        |     2 +-
 tools/fastq-loader/fastq-grammar.c                 |   480 +-
 tools/fastq-loader/fastq-grammar.y                 |    37 +-
 tools/fastq-loader/fastq-lex.c                     |   453 +-
 tools/fastq-loader/fastq-lex.l                     |     1 +
 tools/fastq-loader/fastq-loader.c                  |     7 +-
 tools/fastq-loader/fastq-tokens.h                  |    21 +-
 tools/fastq-loader/latf-load.vers                  |     2 +-
 tools/fastq-loader/latf-load.vers.h                |     2 +-
 tools/fuse/remote-cache.c                          |   631 +-
 tools/fuse/remote-cache.h                          |     4 +-
 tools/fuse/remote-file.c                           |    24 +-
 tools/fuse/remote-fuser.vers                       |     2 +-
 tools/fuse/sra-fuser-test.vers                     |     2 +-
 tools/fuse/sra-fuser-test.vers.h                   |     2 +-
 tools/fuse/sra-fuser.vers                          |     2 +-
 tools/fuse/sra-makeidx.vers                        |     2 +-
 tools/general-loader/database-loader.cpp           |     3 +-
 tools/general-loader/general-loader.vers           |     2 +-
 tools/general-loader/general-loader.vers.h         |     2 +-
 tools/general-loader/libgeneral-writer.vers        |     2 +-
 tools/kar/kar.c                                    |    70 +-
 tools/kar/kar.vers                                 |     2 +-
 tools/kar/kar.vers.h                               |     2 +-
 tools/kar/sra-kar.vers                             |     2 +-
 tools/kar/sra-kar.vers.h                           |     2 +-
 tools/keyring-srv/keyring-srv.vers                 |     2 +-
 tools/kget/examples.sh                             |    62 +
 tools/kget/kget.c                                  |   739 +-
 tools/kget/kget.vers                               |     2 +-
 tools/kqsh/kqsh.vers                               |     2 +-
 tools/nenctool/nenctest.vers                       |     2 +-
 tools/nenctool/nenctool.vers                       |     2 +-
 tools/nencvalid/nencvalid.vers                     |     2 +-
 tools/pacbio-load/pacbio-load.c                    |    81 +-
 tools/pacbio-load/pacbio-load.vers                 |     2 +-
 tools/pileup-stats/pileup-stats.cpp                |   187 +-
 tools/pileup-stats/pileup-stats.vers               |     2 +-
 tools/prefetch/prefetch.c                          |   186 +-
 tools/prefetch/prefetch.vers                       |     2 +-
 tools/prefetch/prefetch.vers.h                     |     2 +-
 tools/qual-recalib-stat/qual-recalib-stat.vers     |     2 +-
 tools/qual-recalib-stat/qual-recalib-stat.vers.h   |     2 +-
 tools/rd-filter-redact/rd-filter-redact.vers       |     2 +-
 tools/rd-filter-redact/read-filter-redact.vers     |     2 +-
 tools/rd-filter-redact/read-filter-redact.vers.h   |     2 +-
 tools/rd-filter-redact/test-read-write-cursor.vers |     2 +-
 tools/ref-variation/common.cpp                     |     5 +-
 tools/ref-variation/common.h                       |     3 +-
 tools/ref-variation/helper.cpp                     |   176 +-
 tools/ref-variation/helper.h                       |    34 +-
 tools/ref-variation/ref-variation.cpp              |    79 +-
 tools/ref-variation/ref-variation.vers             |     2 +-
 tools/ref-variation/ref-variation.vers.h           |     2 +-
 tools/ref-variation/var-expand.cpp                 |   171 +-
 tools/ref-variation/var-expand.vers                |     2 +-
 tools/ref-variation/var-expand.vers.h              |     2 +-
 tools/refseq-load/refseq-load.vers                 |     2 +-
 tools/sra-dump/abi-dump.vers                       |     2 +-
 tools/sra-dump/abi-dump.vers.h                     |     2 +-
 tools/sra-dump/core.c                              |     4 +-
 tools/sra-dump/fastq-dump.vers                     |     2 +-
 tools/sra-dump/fastq-dump.vers.h                   |     2 +-
 tools/sra-dump/illumina-dump.vers                  |     2 +-
 tools/sra-dump/illumina-dump.vers.h                |     2 +-
 tools/sra-dump/sff-dump.vers                       |     2 +-
 tools/sra-dump/sff-dump.vers.h                     |     2 +-
 tools/sra-dump/sra-dump.vers                       |     2 +-
 tools/sra-load/abi-load.vers                       |     2 +-
 tools/sra-load/fastq-fmt.c                         |     2 +-
 tools/sra-load/fastq-load.vers                     |     2 +-
 tools/sra-load/helicos-load.vers                   |     2 +-
 tools/sra-load/illumina-load.vers                  |     2 +-
 tools/sra-load/pacbio-loadxml.vers                 |     2 +-
 tools/sra-load/sff-load.vers                       |     2 +-
 tools/sra-load/srf-load.vers                       |     2 +-
 tools/sra-pileup/read_fkt.c                        |   882 +-
 tools/sra-pileup/sam-aligned.c                     |   231 +-
 tools/sra-pileup/sam-dump.vers                     |     2 +-
 tools/sra-pileup/sam-dump.vers.h                   |     2 +-
 tools/sra-pileup/sam-dump2.vers                    |     2 +-
 tools/sra-pileup/sam-hdr1.c                        |  1055 +-
 tools/sra-pileup/sam-unaligned.c                   |    68 +-
 tools/sra-pileup/sra-pileup.vers                   |     2 +-
 tools/sra-pileup/sra-pileup.vers.h                 |     2 +-
 tools/sra-sort/buff-writer.c                       |    16 +-
 tools/sra-sort/col-pair.c                          |     4 +-
 tools/sra-sort/csra-pair.c                         |    36 +-
 tools/sra-sort/csra-pair.h                         |     3 +
 tools/sra-sort/csra-tbl.c                          |    31 +-
 tools/sra-sort/sra-sort.vers                       |     2 +-
 tools/sra-sort/xcheck-ref-align.c                  |     9 +-
 tools/sra-stat/sra-stat.c                          |   107 +-
 tools/sra-stat/sra-stat.vers                       |     2 +-
 tools/sra-stat/sra-stat.vers.h                     |     2 +-
 tools/sra/table-vers.vers                          |     2 +-
 tools/srapath/srapath.vers                         |     2 +-
 tools/srapath/srapath.vers.h                       |     2 +-
 tools/update-schema/vdb-update-schema.vers         |     2 +-
 tools/util/Makefile                                |    17 +-
 tools/util/kdb-index.vers                          |     2 +-
 tools/util/kdbmeta.vers                            |     2 +-
 tools/util/kdbmeta.vers.h                          |     2 +-
 tools/util/md5cp.vers                              |     2 +-
 tools/util/md5cp.vers.h                            |     2 +-
 tools/util/pacbio-correct.vers                     |     2 +-
 tools/util/pseudo-aligner.cpp                      |   515 +
 tools/util/rcexplain.vers                          |     2 +-
 tools/util/rcexplain.vers.h                        |     2 +-
 tools/util/rowwritetest.vers                       |     2 +-
 tools/util/schema-replace.vers                     |     2 +-
 tools/util/schema-replace.vers.h                   |     2 +-
 tools/util/test-sra.vers                           |     2 +-
 tools/util/test-sra.vers.h                         |     2 +-
 tools/util/testld.vers                             |     2 +-
 tools/util/txt2kdb.vers                            |     2 +-
 tools/util/vdb-lock.vers                           |     2 +-
 tools/util/vdb-lock.vers.h                         |     2 +-
 tools/util/vdb-passwd.vers                         |     2 +-
 tools/util/vdb-passwd.vers.h                       |     2 +-
 tools/util/vdb-unlock.vers                         |     2 +-
 tools/util/vdb-unlock.vers.h                       |     2 +-
 tools/vcf-loader/vcf-load.vers                     |     2 +-
 tools/vdb-config/vdb-config.c                      |    51 +-
 tools/vdb-config/vdb-config.vers                   |     2 +-
 tools/vdb-config/vdb-config.vers.h                 |     2 +-
 tools/vdb-copy/vdb-copy.vers                       |     2 +-
 tools/vdb-copy/vdb-copy.vers.h                     |     2 +-
 tools/vdb-decrypt/vdb-decrypt.vers                 |     2 +-
 tools/vdb-decrypt/vdb-decrypt.vers.h               |     2 +-
 tools/vdb-decrypt/vdb-encrypt.vers                 |     2 +-
 tools/vdb-decrypt/vdb-encrypt.vers.h               |     2 +-
 tools/vdb-dump/Makefile                            |     3 +
 tools/vdb-dump/vdb-boot.vers                       |     2 +-
 tools/vdb-dump/vdb-dump-context.c                  |   109 +-
 tools/vdb-dump/vdb-dump-context.h                  |    30 +-
 tools/vdb-dump/vdb-dump-fastq.c                    |  1379 +-
 tools/vdb-dump/vdb-dump-formats.c                  |    12 +-
 tools/vdb-dump/vdb-dump-helper.c                   |   512 +-
 tools/vdb-dump/vdb-dump-helper.h                   |    22 +-
 tools/vdb-dump/vdb-dump-interact.c                 |   265 +
 .../{vdb-dump-fastq.h => vdb-dump-interact.h}      |    13 +-
 tools/vdb-dump/vdb-dump-print.c                    |   895 +-
 tools/vdb-dump/vdb-dump-print.h                    |    15 +-
 tools/vdb-dump/vdb-dump-repo.c                     |   281 +
 .../vdb-dump/vdb-dump-repo.h                       |    88 +-
 tools/vdb-dump/vdb-dump-str.c                      |    96 +-
 tools/vdb-dump/vdb-dump.c                          |  1150 +-
 tools/vdb-dump/vdb-dump.vers                       |     2 +-
 tools/vdb-dump/vdb-dump.vers.h                     |     2 +-
 tools/vdb-dump/vdb_info.c                          |   547 +-
 tools/vdb-validate/Makefile                        |    21 +-
 tools/vdb-validate/check-corrupt.cpp               |   644 +
 tools/vdb-validate/check-corrupt.vers              |     1 +
 tools/vdb-validate/check-corrupt.vers.h            |     1 +
 tools/vdb-validate/vdb-validate.c                  |   677 +-
 tools/vdb-validate/vdb-validate.vers               |     2 +-
 tools/vdb-validate/vdb-validate.vers.h             |     2 +-
 379 files changed, 39537 insertions(+), 7254 deletions(-)
 create mode 100644 CHANGES.md
 copy build/MSVC/2010/{dbgap-mount-demo.vcxproj => dbgap-mount-tool.vcxproj} (81%)
 create mode 100644 build/Makefile.deb
 create mode 100644 build/Makefile.rpm
 create mode 100644 build/Makefile.tools
 copy {test/ngs-pileup => build}/valgrind.suppress (100%)
 create mode 100644 test/align-cache/CSRA_file
 copy test/{align-info => align-cache}/Makefile (73%)
 rename test/{ref-variation => align-cache}/valgrind.suppress (100%)
 copy test/{align-info => copycat}/Makefile (73%)
 create mode 100644 test/copycat/input/1.xml
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 copy test/fastq-loader/input/{11.0.1.fasta => 13.0.fasta} (100%)
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 copy test/fastq-loader/input/{11.0.1.fasta => 14.0.fasta} (100%)
 rename test/general-loader/{ => input}/column01 (91%)
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 copy test/{align-info => kar}/Makefile (80%)
 create mode 100644 test/kar/expected/1.0.stdout
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 copy test/{vcf-loader => pileup-stats}/Makefile (60%)
 rename test/{ngs-pileup => pileup-stats}/valgrind.suppress (100%)
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 copy test/{network-test/network-test.vers => samline/sampart.vers} (100%)
 create mode 100755 test/samline/sec_align_problem.sh
 copy test/{vcf-loader => vdb-validate}/Makefile (56%)
 create mode 100644 test/vdb-validate/db/blob-row-gap.kar
 create mode 100644 test/vdb-validate/db/sdc_len_mismatch.csra
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 create mode 100644 test/vschema/idx-text/expected/ci-5.stdout
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 copy tools/{util/samview.c => bam-loader/bam-alignment.h} (53%)
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 copy tools/{fastq-loader/fastq-reader.h => bam-loader/low-match-count.cpp} (57%)
 copy tools/{fuse/directory.h => bam-loader/low-match-count.h} (79%)
 create mode 100644 tools/copycat/magic
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 copy tools/dbgap-mount/{demo.vers => dbgap-mount-tool.vers} (100%)
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 copy tools/{vdb-copy/column_match.c => dbgap-mount/unix/wrap.c} (78%)
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 copy tools/{kget => fastdump}/Makefile (91%)
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 copy tools/{vdb-copy/vdb-copy-includes.h => fastdump/cmn_iter.h} (58%)
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 copy tools/{qual-recalib-stat/spot_position.h => fastdump/join.h} (67%)
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 copy tools/{vdb-dump/vdb-dump-fastq.h => fastdump/line_iter.h} (71%)
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 copy tools/{vdb-copy/vdb-copy-includes.h => fastdump/lookup_reader.h} (57%)
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 copy tools/{qual-recalib-stat/ref_exclude.h => fastdump/lookup_writer.h} (64%)
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 copy tools/{vdb-dump/vdb-dump-fastq.h => fastdump/merge_sorter.h} (66%)
 create mode 100644 tools/fastdump/raw_read_iter.c
 copy tools/{vdb-dump/vdb_info.h => fastdump/raw_read_iter.h} (68%)
 create mode 100644 tools/fastdump/readme.txt
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 copy tools/{qual-recalib-stat/spot_position.h => fastdump/sorter.h} (66%)
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 copy tools/{qual-recalib-stat/spot_position.h => fastdump/special_iter.h} (68%)
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 create mode 100755 tools/fastdump/verify.sh
 create mode 100755 tools/kget/examples.sh
 create mode 100644 tools/util/pseudo-aligner.cpp
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 copy tools/vdb-dump/{vdb-dump-fastq.h => vdb-dump-interact.h} (87%)
 create mode 100644 tools/vdb-dump/vdb-dump-repo.c
 copy test/network-test/network-testing.h => tools/vdb-dump/vdb-dump-repo.h (88%)
 create mode 100644 tools/vdb-validate/check-corrupt.cpp
 create mode 100644 tools/vdb-validate/check-corrupt.vers
 create mode 100644 tools/vdb-validate/check-corrupt.vers.h

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