[med-svn] [sra-sdk] branch upstream updated (6881a00 -> a32a2f5)
Andreas Tille
tille at debian.org
Mon Jun 6 09:28:28 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 6881a00 Imported Upstream version 2.6.2
new a32a2f5 Imported Upstream version 2.6.3
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 | 13 ++
CHANGES.md | 12 ++
setup/package.prl | 2 +-
test/general-loader/expected/2.stderr | 4 +-
test/general-loader/expected/2packed.stderr | 4 +-
tools/align-info/align-info.vers | 2 +-
tools/align-info/align-info.vers.h | 2 +-
tools/bam-loader/Makefile | 20 ++
tools/bam-loader/alignment-writer.c | 26 ++-
tools/bam-loader/bam-load.vers | 2 +-
tools/bam-loader/bam.c | 235 +++++++++++++++------
tools/bam-loader/bam.h | 6 +-
tools/bam-loader/loader-imp.c | 129 ++++++++---
tools/bam-loader/reference-writer.c | 15 +-
tools/bam-loader/reference-writer.h | 2 +
tools/{util => bam-loader}/samview.c | 64 ++++--
.../bam-loader/samview.vers | 0
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/copycat.vers | 2 +-
tools/fastdump/fastdump.vers | 2 +-
tools/fastq-dump/fastq-dump.vers | 2 +-
tools/fastq-loader/latf-load.vers | 2 +-
tools/fastq-loader/latf-load.vers.h | 2 +-
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/general-loader.vers | 2 +-
tools/general-loader/general-loader.vers.h | 2 +-
tools/general-loader/libgeneral-writer.vers | 2 +-
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/kqsh/kqsh.vers | 2 +-
tools/nenctool/nenctest.vers | 2 +-
tools/nenctool/nenctool.vers | 2 +-
tools/nencvalid/nencvalid.vers | 2 +-
tools/pacbio-load/pacbio-load.vers | 2 +-
tools/pileup-stats/pileup-stats.vers | 2 +-
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/ref-variation.vers | 2 +-
tools/ref-variation/ref-variation.vers.h | 2 +-
tools/ref-variation/var-expand.vers | 2 +-
tools/ref-variation/var-expand.vers.h | 2 +-
tools/refseq-load/refseq-load.vers | 1 -
tools/sra-dump/abi-dump.vers | 2 +-
tools/sra-dump/abi-dump.vers.h | 2 +-
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-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/sam-dump.vers | 2 +-
tools/sra-pileup/sam-dump.vers.h | 2 +-
tools/sra-pileup/sam-dump2.vers | 2 +-
tools/sra-pileup/sra-pileup.vers | 2 +-
tools/sra-pileup/sra-pileup.vers.h | 2 +-
tools/sra-sort/sra-sort.vers | 2 +-
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/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/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.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/vdb-boot.vers | 2 +-
tools/vdb-dump/vdb-dump.vers | 2 +-
tools/vdb-dump/vdb-dump.vers.h | 2 +-
tools/vdb-validate/check-corrupt.vers | 2 +-
tools/vdb-validate/check-corrupt.vers.h | 2 +-
tools/vdb-validate/vdb-validate.vers | 2 +-
tools/vdb-validate/vdb-validate.vers.h | 2 +-
123 files changed, 500 insertions(+), 249 deletions(-)
copy tools/{util => bam-loader}/samview.c (59%)
copy test/network-test/network-test.vers => tools/bam-loader/samview.vers (100%)
delete mode 100644 tools/refseq-load/refseq-load.vers
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