[med-svn] [ncbi-vdb] branch master updated (65a9516 -> 1ee3605)
Andreas Tille
tille at debian.org
Tue Jan 10 15:28:56 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository ncbi-vdb.
from 65a9516 Adjust dependencies from other development packages
new ea6b76a New upstream version 2.8.1
new 1ee3605 Merge tag 'upstream/2.8.1'
The 2 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:
.github/ISSUE_TEMPLATE.md | 21 +
.github/PULL_REQUEST_TEMPLATE.md | 13 +
.gitignore | 49 +-
.travis.yml | 20 +
CHANGES.md | 52 -
LICENSE | 77 -
Makefile | 159 -
README.md | 114 +-
build.gradle | 227 +
build.xml | 62 +
build/.gitignore | 10 -
build/Makefile.cc | 67 -
build/Makefile.clang | 80 -
build/Makefile.env | 373 -
build/Makefile.gcc | 88 -
build/Makefile.icc | 77 -
build/Makefile.install | 151 -
build/Makefile.linux | 84 -
build/Makefile.rules | 111 -
build/Makefile.scm | 94 -
build/Makefile.shell | 176 -
build/Makefile.targets | 117 -
build/Makefile.vers | 26 -
build/abspath.sh | 31 -
build/cc.sh | 129 -
build/cp.sh | 32 -
build/gprof2dot.py | 2763 --
build/increment-release.sh | 44 -
build/ld.linux.cmn.sh | 158 -
build/ld.linux.dlib.sh | 308 -
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build/scm-collect.sh | 42 -
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build/scm.txt | 117 -
build/sra-dflt-schema.sh | 163 -
build/tag-module.sh | 213 -
build/valgrind.suppress | 21 -
build/wait_for_file.sh | 65 -
configure | 45 -
gradle/wrapper/gradle-wrapper.jar | Bin 0 -> 53556 bytes
gradle/wrapper/gradle-wrapper.properties | 6 +
gradlew | 164 +
interfaces/align/align-access.h | 350 -
interfaces/align/align.h | 70 -
interfaces/align/align.vschema | 1610 -
interfaces/align/alignsrc.h | 71 -
interfaces/align/bam.h | 836 -
interfaces/align/dna-reverse-cmpl.h | 43 -
interfaces/align/extern.h | 41 -
interfaces/align/iterator.h | 610 -
interfaces/align/iterator_examples.txt | 148 -
interfaces/align/manager.h | 69 -
interfaces/align/mate-cache.vschema | 99 -
interfaces/align/pileup-stats.vschema | 120 -
interfaces/align/qstat.vschema | 87 -
interfaces/align/quality-quantizer.h | 49 -
interfaces/align/reader-refseq.h | 72 -
interfaces/align/reference.h | 150 -
interfaces/align/refseq-mgr.h | 88 -
interfaces/align/refseq.vschema | 100 -
interfaces/align/seq.vschema | 300 -
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interfaces/align/writer-cmn.h | 46 -
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interfaces/align/writer-refseq.h | 89 -
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src/main/java/htsjdk/samtools/SAMLineParser.java | 487 +
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src/main/java/htsjdk/samtools/SAMRecord.java | 2378 ++
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src/main/java/htsjdk/samtools/SAMRecordUtil.java | 77 +
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src/main/java/htsjdk/samtools/SAMTag.java | 82 +
src/main/java/htsjdk/samtools/SAMTagUtil.java | 122 +
src/main/java/htsjdk/samtools/SAMTestUtil.java | 128 +
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src/main/java/htsjdk/samtools/SAMTextReader.java | 253 +
src/main/java/htsjdk/samtools/SAMTextWriter.java | 221 +
src/main/java/htsjdk/samtools/SAMTools.java | 119 +
src/main/java/htsjdk/samtools/SAMUtils.java | 1226 +
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src/main/java/htsjdk/samtools/SQTagUtil.java | 154 +
src/main/java/htsjdk/samtools/SRAFileReader.java | 309 +
src/main/java/htsjdk/samtools/SRAIndex.java | 257 +
src/main/java/htsjdk/samtools/SRAIterator.java | 256 +
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src/main/java/htsjdk/samtools/SamFiles.java | 98 +
src/main/java/htsjdk/samtools/SamFlagField.java | 203 +
src/main/java/htsjdk/samtools/SamIndexes.java | 94 +
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src/main/java/htsjdk/samtools/SamPairUtil.java | 510 +
src/main/java/htsjdk/samtools/SamReader.java | 621 +
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src/main/java/htsjdk/samtools/SamStreams.java | 164 +
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src/main/java/htsjdk/samtools/TextCigarCodec.java | 91 +
src/main/java/htsjdk/samtools/TextTagCodec.java | 331 +
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src/main/java/htsjdk/samtools/cram/CRAIEntry.java | 195 +
src/main/java/htsjdk/samtools/cram/CRAIIndex.java | 267 +
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src/main/java/htsjdk/samtools/cram/io/CramInt.java | 78 +
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src/main/java/htsjdk/samtools/cram/io/ITF8.java | 186 +
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src/main/java/htsjdk/samtools/cram/io/LTF8.java | 193 +
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src/main/java/htsjdk/samtools/liftover/Chain.java | 414 +
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src/main/java/htsjdk/samtools/metrics/Header.java | 43 +
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src/main/java/htsjdk/samtools/sra/SRAUtils.java | 83 +
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src/main/java/htsjdk/samtools/util/CigarUtil.java | 294 +
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src/main/java/htsjdk/samtools/util/CloserUtil.java | 81 +
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src/main/java/htsjdk/samtools/util/CoordMath.java | 76 +
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src/main/java/htsjdk/samtools/util/DateParser.java | 337 +
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src/main/java/htsjdk/samtools/util/FormatUtil.java | 203 +
src/main/java/htsjdk/samtools/util/Histogram.java | 567 +
src/main/java/htsjdk/samtools/util/HttpUtils.java | 80 +
src/main/java/htsjdk/samtools/util/IOUtil.java | 946 +
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src/main/java/htsjdk/samtools/util/Log.java | 214 +
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src/main/java/htsjdk/samtools/util/StopWatch.java | 76 +
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src/main/java/htsjdk/samtools/util/StringUtil.java | 603 +
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src/main/java/htsjdk/samtools/util/TestUtil.java | 98 +
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src/main/java/htsjdk/samtools/util/Tuple.java | 41 +
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.../ValidateSamFileTest/mate_cigar_and_no_oqs.sam | 4 +
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.../htsjdk/samtools/ValidateSamFileTest/valid.sam | 21 +
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src/test/resources/htsjdk/samtools/compressed.bam | Bin 0 -> 307 bytes
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.../cram/CRAMException/testContigNotInRef.dict | 2 +
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src/test/resources/htsjdk/samtools/cram/c1.fa | 2 +
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src/test/resources/htsjdk/samtools/cram/ce#1.sam | 2 +
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src/test/resources/htsjdk/samtools/cram/ce#2.sam | 3 +
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src/test/resources/htsjdk/samtools/cram/ce#5.sam | 11 +
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src/test/resources/htsjdk/samtools/cram/ce#5b.sam | 12 +
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.../htsjdk/samtools/cram/ce#tag_padded.sam | 11 +
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.../htsjdk/samtools/cram/ce#unmap.3.0.cram | Bin 0 -> 601 bytes
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.../resources/htsjdk/samtools/cram/ce#unmap1.sam | 20 +
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src/test/resources/htsjdk/samtools/cram/ce.fa | 20803 +++++++++++++
src/test/resources/htsjdk/samtools/cram/ce.fa.fai | 7 +
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.../cram/human_g1k_v37.20.21.10M-10M200k.fasta | 5002 +++
.../cram/human_g1k_v37.20.21.10M-10M200k.fasta.fai | 2 +
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src/test/resources/htsjdk/samtools/cram/test.dict | 2 +
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src/test/resources/htsjdk/samtools/cram/test2.dict | 2 +
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src/test/resources/htsjdk/samtools/cram/xx#rg.sam | 13 +
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.../htsjdk/samtools/cram_query_sorted.fasta | 40 +
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src/test/resources/htsjdk/samtools/cram_tlen.fasta | 41 +
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src/test/resources/htsjdk/samtools/empty.bai | Bin 0 -> 8 bytes
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src/test/resources/htsjdk/samtools/hg19mini.dict | 5 +
src/test/resources/htsjdk/samtools/hg19mini.fasta | 804 +
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src/test/resources/htsjdk/samtools/inttest.bam | Bin 0 -> 329 bytes
src/test/resources/htsjdk/samtools/inttest.sam | 26 +
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.../htsjdk/samtools/liftover/hg18ToHg19.over.chain | 30850 +++++++++++++++++++
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.../reference/Homo_sapiens_assembly18.trimmed.dict | 3 +
.../Homo_sapiens_assembly18.trimmed.fasta | 16946 ++++++++++
.../Homo_sapiens_assembly18.trimmed.fasta.fai | 2 +
.../Homo_sapiens_assembly18.trimmed.nodict.fasta | 16946 ++++++++++
...omo_sapiens_assembly18.trimmed.nodict.fasta.fai | 2 +
.../Homo_sapiens_assembly18.trimmed.noindex.fasta | 16946 ++++++++++
.../reference_with_trailing_whitespace.dict | 3 +
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.../htsjdk/samtools/reference/testing.fai | 7 +
src/test/resources/htsjdk/samtools/roundtrip.sam | 16 +
src/test/resources/htsjdk/samtools/samFilter01.js | 2 +
src/test/resources/htsjdk/samtools/samFilter02.js | 9 +
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src/test/resources/htsjdk/samtools/unsorted.sam | 15 +
.../5k-30BB2AAXX.3.aligned.sam.fastq | 19808 ++++++++++++
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src/test/resources/htsjdk/tribble/Tb.vcf.idx | Bin 0 -> 998966 bytes
src/test/resources/htsjdk/tribble/basicDbSNP.dbsnp | 43 +
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src/test/resources/htsjdk/tribble/gwas/smallp.gwas | 20 +
.../htsjdk/tribble/index/chrY_Y4_small.bed | 5000 +++
src/test/resources/htsjdk/tribble/large.txt | 165 +
src/test/resources/htsjdk/tribble/sites.bed | 1000 +
src/test/resources/htsjdk/tribble/soapsnp.txt | 24 +
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src/test/resources/htsjdk/tribble/test.bed | 9 +
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src/test/resources/htsjdk/tribble/test.vcf | 24 +
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src/test/resources/htsjdk/tribble/testGeliText.txt | 50 +
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src/test/resources/htsjdk/tribble/trio.vcf | 100 +
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src/test/resources/htsjdk/tribble/trioDup.vcf | 75 +
src/test/resources/htsjdk/tribble/vcfexample.vcf | 12 +
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src/test/resources/htsjdk/variant/HiSeq.10000.vcf | 10001 ++++++
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src/test/resources/htsjdk/variant/breakpoint.vcf | 6 +
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src/test/resources/htsjdk/variant/ex2.vcf | 23 +
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.../htsjdk/variant/structuralvariants.vcf | 22 +
.../Homo_sapiens_assembly18.trimmed.dict | 3 +
.../Homo_sapiens_assembly18.trimmed.fasta | 16946 ++++++++++
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delete mode 100644 vdb3/itf/kfc/fd.hpp
delete mode 100644 vdb3/itf/kfc/fdmgr.hpp
delete mode 100644 vdb3/itf/kfc/integer.hpp
delete mode 100644 vdb3/itf/kfc/log.hpp
delete mode 100644 vdb3/itf/kfc/memmgr.hpp
delete mode 100644 vdb3/itf/kfc/memory.hpp
delete mode 100644 vdb3/itf/kfc/ptr.hpp
delete mode 100644 vdb3/itf/kfc/ref.hpp
delete mode 100644 vdb3/itf/kfc/refcount.hpp
delete mode 100644 vdb3/itf/kfc/rsrc.hpp
delete mode 100644 vdb3/itf/kfc/stream.hpp
delete mode 100644 vdb3/itf/kfc/string.hpp
delete mode 100644 vdb3/itf/kfc/syserr.hpp
delete mode 100644 vdb3/itf/kfc/task-impl.hpp
delete mode 100644 vdb3/itf/kfc/task.hpp
delete mode 100644 vdb3/itf/kfc/time.hpp
delete mode 100644 vdb3/itf/kfc/timemgr.hpp
delete mode 100644 vdb3/itf/kfc/vers.hpp
delete mode 100644 vdb3/src/kfc/Makefile
delete mode 100644 vdb3/src/kfc/array.cpp
delete mode 100644 vdb3/src/kfc/callstk.cpp
delete mode 100644 vdb3/src/kfc/except.cpp
delete mode 100644 vdb3/src/kfc/fd.cpp
delete mode 100644 vdb3/src/kfc/fdmgr.cpp
delete mode 100644 vdb3/src/kfc/integer.cpp
delete mode 100644 vdb3/src/kfc/log.cpp
delete mode 100644 vdb3/src/kfc/memmgr.cpp
delete mode 100644 vdb3/src/kfc/memory.cpp
delete mode 100644 vdb3/src/kfc/pfdmgr.cpp
delete mode 100644 vdb3/src/kfc/pfdmgr.hpp
delete mode 100644 vdb3/src/kfc/plogger.cpp
delete mode 100644 vdb3/src/kfc/plogger.hpp
delete mode 100644 vdb3/src/kfc/pmemmgr.cpp
delete mode 100644 vdb3/src/kfc/pmemmgr.hpp
delete mode 100644 vdb3/src/kfc/ptimemgr.cpp
delete mode 100644 vdb3/src/kfc/ptimemgr.hpp
delete mode 100644 vdb3/src/kfc/ptr.cpp
delete mode 100644 vdb3/src/kfc/ref.cpp
delete mode 100644 vdb3/src/kfc/refcount.cpp
delete mode 100644 vdb3/src/kfc/rsrc.cpp
delete mode 100644 vdb3/src/kfc/stream.cpp
delete mode 100644 vdb3/src/kfc/string.cpp
delete mode 100644 vdb3/src/kfc/syserr.cpp
delete mode 100644 vdb3/src/kfc/task-impl.cpp
delete mode 100644 vdb3/src/kfc/task.cpp
delete mode 100644 vdb3/src/kfc/time.cpp
delete mode 100644 vdb3/src/kfc/timemgr.cpp
delete mode 100644 vdb3/src/kfc/vers.cpp
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