[med-svn] [sra-sdk] 02/03: Merge tag 'upstream/2.6.2'
Andreas Tille
tille at debian.org
Sun May 15 18:34:53 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository sra-sdk.
commit 480e2b2af9ac5d2ca998163746a38786aafa916a
Merge: a246fc1 6881a00
Author: Andreas Tille <tille at debian.org>
Date: Sun May 15 20:18:08 2016 +0200
Merge tag 'upstream/2.6.2'
Upstream version 2.6.2
CHANGES | 58 +-
CHANGES.md | 54 +
Makefile | 36 +-
README | 2 +
README.md | 5 +-
build/.gitignore | 3 +-
.../{prefetch.vcxproj => dbgap-mount-tool.vcxproj} | 20 +-
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/{kget => align-cache}/Makefile | 36 +-
.../valgrind.suppress | 0
test/{vcf-loader => copycat}/Makefile | 47 +-
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 +
test/fastq-loader/input/13.0.fasta | 2 +
test/fastq-loader/input/13.0.fastq | 12 +
test/fastq-loader/input/13.1.fastq | 12 +
test/fastq-loader/input/14.0.fasta | 2 +
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/{kget => kar}/Makefile | 35 +-
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 +
tools/kget/kget.vers => test/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 | 59 +-
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 +
tools/bam-loader/bam-alignment.h | 74 +
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 +-
.../{loader-imp.h => low-match-count.cpp} | 49 +-
.../bam-loader/{loader-imp.h => low-match-count.h} | 10 +-
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} | 49 +-
.../dbgap-mount-tool.vers} | 0
tools/dbgap-mount/dbgap-mount-tool.vers.h | 1 +
tools/dbgap-mount/demo.c | 14 +-
.../refbases.h => tools/dbgap-mount/unix/wrap.c | 31 +-
tools/dbgap-mount/win/wrap.c | 344 +
tools/fastdump/.gitignore | 3 +
{test/samline => tools/fastdump}/Makefile | 25 +-
tools/fastdump/cmn_iter.c | 287 +
test/samline/cigar.h => tools/fastdump/cmn_iter.h | 51 +-
tools/fastdump/fastdump.c | 432 +
tools/{kget/kget.vers => fastdump/fastdump.vers} | 0
tools/fastdump/fastq_iter.c | 97 +
.../refbases.h => tools/fastdump/fastq_iter.h | 35 +-
tools/fastdump/file_printer.c | 130 +
.../refbases.h => tools/fastdump/file_printer.h | 23 +-
tools/fastdump/helper.c | 685 +
tools/fastdump/helper.h | 141 +
tools/fastdump/index.c | 335 +
test/samline/cigar.h => tools/fastdump/index.h | 38 +-
tools/fastdump/join.c | 543 +
test/samline/refbases.h => tools/fastdump/join.h | 43 +-
tools/fastdump/line_iter.c | 199 +
.../refbases.h => tools/fastdump/line_iter.h | 27 +-
tools/fastdump/lookup_reader.c | 331 +
.../cigar.h => tools/fastdump/lookup_reader.h | 46 +-
tools/fastdump/lookup_writer.c | 138 +
.../cigar.h => tools/fastdump/lookup_writer.h | 38 +-
tools/fastdump/merge_sorter.c | 173 +
.../refbases.h => tools/fastdump/merge_sorter.h | 107 +-
tools/fastdump/raw_read_iter.c | 100 +
.../refbases.h => tools/fastdump/raw_read_iter.h | 34 +-
tools/fastdump/readme.txt | 92 +
tools/fastdump/sorter.c | 538 +
test/samline/cigar.h => tools/fastdump/sorter.h | 46 +-
tools/fastdump/special_iter.c | 98 +
.../refbases.h => tools/fastdump/special_iter.h | 35 +-
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 +-
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tools/kqsh/kqsh.vers | 2 +-
tools/nenctool/nenctest.vers | 2 +-
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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/vdb-dump-interact.h | 17 +-
tools/vdb-dump/vdb-dump-print.c | 895 +-
tools/vdb-dump/vdb-dump-print.h | 15 +-
tools/vdb-dump/vdb-dump-repo.c | 281 +
.../refbases.h => tools/vdb-dump/vdb-dump-repo.h | 87 +-
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, 39662 insertions(+), 7014 deletions(-)
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