[med-svn] [sra-sdk] branch master updated (d9bf3d1 -> d94cb58)
Andreas Tille
tille at debian.org
Mon Jun 6 09:28:27 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 d9bf3d1 New upstream version
new dec61ff Try to call non-standard configure script properly
new bb4e6ee New upstream version
new a32a2f5 Imported Upstream version 2.6.3
new d94cb58 Merge tag 'upstream/2.6.3'
The 4 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 ++
debian/changelog | 4 +-
debian/rules | 4 +-
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 +-
125 files changed, 505 insertions(+), 252 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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