Rev picard to get optimized tribble feature reads

-- The previous version of TribbleIndexedFeatureReader.query() would open a RandomAccessFile each time the GATK crossed a shard boundary.  When running with -L wex.intervals (or any time there were lots of intervals) we'd be opening and closing enormous numbers of files, radically slowing down the GATK.  With these patched versions of Tribble we see something like the following performance improvements:

SelectVariants with -L wex.intervals on my local machine against non-local file

pre-patch => 3 hours
post-patch => 30 seconds
This commit is contained in:
Mark DePristo 2013-08-02 09:16:50 -04:00
parent 9316a70d1e
commit d5dd3b23db
10 changed files with 8 additions and 8 deletions

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<ivy-module version="1.0">
<info organisation="net.sf" module="picard" revision="1.91.1453" status="release" />
</ivy-module>

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<ivy-module version="1.0">
<info organisation="net.sf" module="picard" revision="1.96.1515" status="release" />
</ivy-module>

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<ivy-module version="1.0">
<info organisation="net.sf" module="sam" revision="1.91.1453" status="release" />
</ivy-module>

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<ivy-module version="1.0">
<info organisation="net.sf" module="sam" revision="1.96.1515" status="release" />
</ivy-module>

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<ivy-module version="1.0">
<info organisation="org.broad" module="tribble" revision="1.91.1453" status="integration" />
<info organisation="org.broad" module="tribble" revision="1.96.1515" status="integration" />
</ivy-module>

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<ivy-module version="1.0">
<info organisation="org.broadinstitute" module="variant" revision="1.91.1453" status="integration" />
<info organisation="org.broadinstitute" module="variant" revision="1.96.1515" status="integration" />
</ivy-module>