[med-svn] [sra-sdk] branch master updated (a246fc1 -> d9bf3d1)
Andreas Tille
tille at debian.org
Sun May 15 18:34:52 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository sra-sdk.
from a246fc1 Introduced EDAM annotation.
new 6881a00 Imported Upstream version 2.6.2
new 480e2b2 Merge tag 'upstream/2.6.2'
new d9bf3d1 New upstream version
The 3 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
debian/changelog | 6 +-
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 +-
380 files changed, 39540 insertions(+), 7257 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
create mode 100644 test/fastq-loader/expected/13.0.stdout
create mode 100644 test/fastq-loader/expected/13.1.stdout
create mode 100755 test/fastq-loader/expected/14.0.stdout
copy test/fastq-loader/input/{11.0.1.fasta => 13.0.fasta} (100%)
create mode 100644 test/fastq-loader/input/13.0.fastq
create mode 100644 test/fastq-loader/input/13.1.fastq
copy test/fastq-loader/input/{11.0.1.fasta => 14.0.fasta} (100%)
rename test/general-loader/{ => input}/column01 (91%)
rename test/general-loader/{ => input}/column02 (91%)
copy test/{align-info => kar}/Makefile (80%)
create mode 100644 test/kar/expected/1.0.stdout
create mode 100644 test/kar/input/1.0/1.md5
create mode 100644 test/kar/input/1.0/col/sub1/idx
create mode 100644 test/kar/input/1.0/col/sub1/idx0
create mode 100644 test/kar/input/1.0/col/sub1/idx1
create mode 100644 test/kar/input/1.0/col/sub1/idx2
create mode 100644 test/kar/input/1.0/col/sub1/idx3
create mode 100644 test/kar/input/1.0/idx/4a
create mode 100644 test/kar/input/1.0/idx/4b
create mode 100644 test/kar/input/1.0/idx/sub/4c
create mode 100644 test/kar/input/1.0/idx/sub/4d
create mode 100644 test/kar/input/1.0/md/cur
create mode 100644 test/kar/input/1.0/md5
create mode 100644 test/kar/input/1.0/sub1/col/sub1/idx
create mode 100644 test/kar/input/1.0/sub1/col/sub1/idx0
create mode 100644 test/kar/input/1.0/sub1/col/sub1/idx1
create mode 100644 test/kar/input/1.0/sub1/col/sub1/idx2
create mode 100644 test/kar/input/1.0/sub1/col/sub1/idx3
create mode 100644 test/kar/input/1.0/sub1/md/cur
create mode 100644 test/kar/input/1.0/sub1/sub2/col/sub1/idx
create mode 100644 test/kar/input/1.0/sub1/sub2/col/sub1/idx0
create mode 100644 test/kar/input/1.0/sub1/sub2/col/sub1/idx1
create mode 100644 test/kar/input/1.0/sub1/sub2/col/sub1/idx2
create mode 100644 test/kar/input/1.0/sub1/sub2/col/sub1/idx3
create mode 100755 test/kar/test-kar.sh
create mode 100644 test/kget/test_kget.py
copy test/{vcf-loader => pileup-stats}/Makefile (60%)
rename test/{ngs-pileup => pileup-stats}/valgrind.suppress (100%)
create mode 100644 test/ref-variation/expected/ref-variation.out
create mode 100644 test/ref-variation/expected/var-expand.out
create mode 100755 test/ref-variation/have-access.sh
create mode 100644 test/ref-variation/ref-variation.in
create mode 100755 test/ref-variation/ref-variation.sh
create mode 100755 test/samline/bx_tag_test.py
create mode 100755 test/samline/ca_test.py
create mode 100755 test/samline/reject_multi_refnames.sh
create mode 100644 test/samline/sam.py
create mode 100644 test/samline/sampart.c
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
create mode 100644 test/vdb-validate/db/sdc_pa_longer.csra
create mode 100644 test/vdb-validate/db/sdc_tmp_mismatch.csra
create mode 100644 test/vdb-validate/expected/ROW_GAP
create mode 100644 test/vdb-validate/expected/no_sdc_checks
create mode 100644 test/vdb-validate/expected/sdc_len_mismatch_1
create mode 100644 test/vdb-validate/expected/sdc_len_mismatch_2
create mode 100644 test/vdb-validate/expected/sdc_pa_longer_1
create mode 100644 test/vdb-validate/expected/sdc_pa_longer_2
create mode 100644 test/vdb-validate/expected/sdc_pa_longer_3
create mode 100644 test/vdb-validate/expected/sdc_tmp_mismatch
copy build/wait_for_file.sh => test/vdb-validate/runtestcase.sh (63%)
create mode 100644 test/vschema/idx-text/expected/ci-5.stdout
create mode 100644 test/vschema/idx-text/expected/cs-3.stdout
copy tools/{util/samview.c => bam-loader/bam-alignment.h} (53%)
create mode 100644 tools/bam-loader/bam-priv.h
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
create mode 100644 tools/dbgap-mount/dbgap-mount-tool.c
copy tools/{fastq-loader/fastq-reader.h => dbgap-mount/dbgap-mount-tool.h} (54%)
copy tools/dbgap-mount/{demo.vers => dbgap-mount-tool.vers} (100%)
create mode 100644 tools/dbgap-mount/dbgap-mount-tool.vers.h
copy tools/{vdb-copy/column_match.c => dbgap-mount/unix/wrap.c} (78%)
create mode 100644 tools/dbgap-mount/win/wrap.c
create mode 100644 tools/fastdump/.gitignore
copy tools/{kget => fastdump}/Makefile (91%)
create mode 100644 tools/fastdump/cmn_iter.c
copy tools/{vdb-copy/vdb-copy-includes.h => fastdump/cmn_iter.h} (58%)
create mode 100644 tools/fastdump/fastdump.c
copy test/network-test/network-test.vers => tools/fastdump/fastdump.vers (100%)
create mode 100644 tools/fastdump/fastq_iter.c
copy tools/{vdb-dump/vdb_info.h => fastdump/fastq_iter.h} (69%)
create mode 100644 tools/fastdump/file_printer.c
copy tools/{vdb-dump/vdb-dump-fastq.h => fastdump/file_printer.h} (75%)
create mode 100644 tools/fastdump/helper.c
create mode 100644 tools/fastdump/helper.h
create mode 100644 tools/fastdump/index.c
copy tools/{qual-recalib-stat/ref_exclude.h => fastdump/index.h} (61%)
create mode 100644 tools/fastdump/join.c
copy tools/{qual-recalib-stat/spot_position.h => fastdump/join.h} (67%)
create mode 100644 tools/fastdump/line_iter.c
copy tools/{vdb-dump/vdb-dump-fastq.h => fastdump/line_iter.h} (71%)
create mode 100644 tools/fastdump/lookup_reader.c
copy tools/{vdb-copy/vdb-copy-includes.h => fastdump/lookup_reader.h} (57%)
create mode 100644 tools/fastdump/lookup_writer.c
copy tools/{qual-recalib-stat/ref_exclude.h => fastdump/lookup_writer.h} (64%)
create mode 100644 tools/fastdump/merge_sorter.c
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
create mode 100644 tools/fastdump/sorter.c
copy tools/{qual-recalib-stat/spot_position.h => fastdump/sorter.h} (66%)
create mode 100644 tools/fastdump/special_iter.c
copy tools/{qual-recalib-stat/spot_position.h => fastdump/special_iter.h} (68%)
create mode 100644 tools/fastdump/todo.txt
create mode 100755 tools/fastdump/verify.sh
create mode 100755 tools/kget/examples.sh
create mode 100644 tools/util/pseudo-aligner.cpp
create mode 100644 tools/vdb-dump/vdb-dump-interact.c
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
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/sra-sdk.git
More information about the debian-med-commit
mailing list