[med-svn] [sra-sdk] branch master updated (5c5aaa0 -> 321e7d9)
Andreas Tille
tille at debian.org
Tue Jan 10 15:30:05 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository sra-sdk.
from 5c5aaa0 Upload to unstable
new 67dbdf6 Try to apply patches for new upstream version (not working yet)
new 06555f9 New upstream version 2.8.1
new 075ea1d Merge tag 'upstream/2.8.1'
new 321e7d9 New upstream version
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:
.github/ISSUE_TEMPLATE.md | 21 +
.github/PULL_REQUEST_TEMPLATE.md | 13 +
.gitignore | 41 +-
.travis.yml | 20 +
CHANGES | 127 -
CHANGES.md | 96 -
LICENSE | 66 -
Makefile | 187 -
README | 57 -
README-blastn | 133 -
README-vdb-config | 115 -
README.md | 143 +-
build.gradle | 227 +
build.xml | 62 +
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debian/patches/find_hdf5_serial.patch | 42 -
debian/patches/find_ncbi-vdb.patch | 20 +-
debian/patches/find_ngs-sdk.patch | 14 +-
debian/patches/hardening.patch | 9 +-
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gradle/wrapper/gradle-wrapper.jar | Bin 0 -> 53556 bytes
gradle/wrapper/gradle-wrapper.properties | 6 +
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scripts/explain_sam_flags.py | 65 +
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.../resources/htsjdk/samtools/cram/ce#2.2.1.cram | Bin 0 -> 10839 bytes
.../resources/htsjdk/samtools/cram/ce#2.3.0.cram | Bin 0 -> 988 bytes
src/test/resources/htsjdk/samtools/cram/ce#2.sam | 3 +
.../resources/htsjdk/samtools/cram/ce#5.2.1.cram | Bin 0 -> 11221 bytes
.../resources/htsjdk/samtools/cram/ce#5.3.0.cram | Bin 0 -> 1130 bytes
src/test/resources/htsjdk/samtools/cram/ce#5.sam | 11 +
.../resources/htsjdk/samtools/cram/ce#5b.2.1.cram | Bin 0 -> 12668 bytes
.../resources/htsjdk/samtools/cram/ce#5b.3.0.cram | Bin 0 -> 2669 bytes
src/test/resources/htsjdk/samtools/cram/ce#5b.sam | 12 +
.../htsjdk/samtools/cram/ce#large_seq.2.1.cram | Bin 0 -> 101355 bytes
.../htsjdk/samtools/cram/ce#large_seq.3.0.cram | Bin 0 -> 84800 bytes
.../htsjdk/samtools/cram/ce#large_seq.sam | 3 +
.../htsjdk/samtools/cram/ce#supp.2.1.cram | Bin 0 -> 10649 bytes
.../htsjdk/samtools/cram/ce#supp.3.0.cram | Bin 0 -> 809 bytes
.../resources/htsjdk/samtools/cram/ce#supp.sam | 6 +
.../htsjdk/samtools/cram/ce#tag_depadded.2.1.cram | Bin 0 -> 11114 bytes
.../htsjdk/samtools/cram/ce#tag_depadded.3.0.cram | Bin 0 -> 1258 bytes
.../htsjdk/samtools/cram/ce#tag_depadded.sam | 11 +
.../htsjdk/samtools/cram/ce#tag_padded.2.1.cram | Bin 0 -> 10922 bytes
.../htsjdk/samtools/cram/ce#tag_padded.3.0.cram | Bin 0 -> 1082 bytes
.../htsjdk/samtools/cram/ce#tag_padded.sam | 11 +
.../htsjdk/samtools/cram/ce#unmap.2.1.cram | Bin 0 -> 10503 bytes
.../htsjdk/samtools/cram/ce#unmap.3.0.cram | Bin 0 -> 601 bytes
.../resources/htsjdk/samtools/cram/ce#unmap.sam | 6 +
.../htsjdk/samtools/cram/ce#unmap1.2.1.cram | Bin 0 -> 11730 bytes
.../htsjdk/samtools/cram/ce#unmap1.3.0.cram | Bin 0 -> 1505 bytes
.../resources/htsjdk/samtools/cram/ce#unmap1.sam | 20 +
.../htsjdk/samtools/cram/ce#unmap2.2.1.cram | Bin 0 -> 12587 bytes
.../htsjdk/samtools/cram/ce#unmap2.3.0.cram | Bin 0 -> 2404 bytes
.../resources/htsjdk/samtools/cram/ce#unmap2.sam | 29 +
src/test/resources/htsjdk/samtools/cram/ce.fa | 20803 +++++++++++++
src/test/resources/htsjdk/samtools/cram/ce.fa.fai | 7 +
.../htsjdk/samtools/cram/cramQueryTest.cram | Bin 0 -> 2863 bytes
.../htsjdk/samtools/cram/cramQueryTest.cram.bai | Bin 0 -> 336 bytes
.../htsjdk/samtools/cram/cramQueryTestEmpty.cram | Bin 0 -> 2183 bytes
.../samtools/cram/cramQueryTestEmpty.cram.bai | Bin 0 -> 48 bytes
.../htsjdk/samtools/cram/cramQueryWithBAI.cram | Bin 0 -> 8947 bytes
.../htsjdk/samtools/cram/cramQueryWithBAI.cram.bai | Bin 0 -> 152 bytes
.../htsjdk/samtools/cram/cramQueryWithCRAI.cram | Bin 0 -> 4131 bytes
.../samtools/cram/cramQueryWithCRAI.cram.crai | Bin 0 -> 59 bytes
.../resources/htsjdk/samtools/cram/fieldarith.sam | 15 +
.../samtools/cram/human_g1k_v37.20.21.1-100.dict | 3 +
.../samtools/cram/human_g1k_v37.20.21.1-100.fasta | 11 +
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.../cram/human_g1k_v37.20.21.10M-10M200k.dict | 3 +
.../cram/human_g1k_v37.20.21.10M-10M200k.fasta | 5002 +++
.../cram/human_g1k_v37.20.21.10M-10M200k.fasta.fai | 2 +
.../htsjdk/samtools/cram/io/bzip2-test.bz2 | Bin 0 -> 56 bytes
src/test/resources/htsjdk/samtools/cram/test.cram | Bin 0 -> 3433 bytes
.../resources/htsjdk/samtools/cram/test.cram.bai | Bin 0 -> 96 bytes
src/test/resources/htsjdk/samtools/cram/test.dict | 2 +
src/test/resources/htsjdk/samtools/cram/test.fa | 2 +
.../resources/htsjdk/samtools/cram/test.fa.fai | 1 +
src/test/resources/htsjdk/samtools/cram/test2.cram | Bin 0 -> 3433 bytes
src/test/resources/htsjdk/samtools/cram/test2.dict | 2 +
src/test/resources/htsjdk/samtools/cram/test2.fa | 2 +
.../resources/htsjdk/samtools/cram/test2.fa.fai | 1 +
.../htsjdk/samtools/cram/xx#blank.2.1.cram | Bin 0 -> 10080 bytes
.../htsjdk/samtools/cram/xx#blank.3.0.cram | Bin 0 -> 140 bytes
.../resources/htsjdk/samtools/cram/xx#blank.sam | 0
.../htsjdk/samtools/cram/xx#large_aux.2.1.cram | Bin 0 -> 35824 bytes
.../htsjdk/samtools/cram/xx#large_aux.3.0.cram | Bin 0 -> 20418 bytes
.../htsjdk/samtools/cram/xx#large_aux.sam | 4 +
.../htsjdk/samtools/cram/xx#large_aux2.2.1.cram | Bin 0 -> 10868 bytes
.../htsjdk/samtools/cram/xx#large_aux2.3.0.cram | Bin 0 -> 1008 bytes
.../htsjdk/samtools/cram/xx#large_aux2.sam | 11 +
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.../htsjdk/samtools/cram/xx#minimal.3.0.cram | Bin 0 -> 1096 bytes
.../resources/htsjdk/samtools/cram/xx#minimal.sam | 10 +
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.../resources/htsjdk/samtools/cram/xx#pair.sam | 7 +
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.../resources/htsjdk/samtools/cram/xx#rg.3.0.cram | Bin 0 -> 794 bytes
src/test/resources/htsjdk/samtools/cram/xx#rg.sam | 13 +
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.../htsjdk/samtools/cram/xx#tlen2.2.1.cram | Bin 0 -> 11380 bytes
.../htsjdk/samtools/cram/xx#tlen2.3.0.cram | Bin 0 -> 1359 bytes
.../htsjdk/samtools/cram/xx#triplet.2.1.cram | Bin 0 -> 10853 bytes
.../htsjdk/samtools/cram/xx#triplet.3.0.cram | Bin 0 -> 950 bytes
.../resources/htsjdk/samtools/cram/xx#triplet.sam | 7 +
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.../htsjdk/samtools/cram/xx#unsorted.3.0.cram | Bin 0 -> 1262 bytes
.../resources/htsjdk/samtools/cram/xx#unsorted.sam | 8 +
src/test/resources/htsjdk/samtools/cram/xx.fa | 5 +
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.../htsjdk/samtools/cram_query_sorted.cram | Bin 0 -> 13266 bytes
.../htsjdk/samtools/cram_query_sorted.fasta | 40 +
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src/test/resources/htsjdk/samtools/cram_tlen.fasta | 41 +
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.../htsjdk/samtools/cram_with_crai_index.cram | Bin 0 -> 4213 bytes
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src/test/resources/htsjdk/samtools/empty.bai | Bin 0 -> 8 bytes
src/test/resources/htsjdk/samtools/empty.bam | Bin 0 -> 90 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 +
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.../reference_with_trailing_whitespace.dict | 3 +
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src/test/resources/htsjdk/samtools/roundtrip.sam | 16 +
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src/test/resources/htsjdk/samtools/unsorted.sam | 15 +
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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 +
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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.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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