gatk-3.8

History

Alec Wysoker bccc9d79e5 Clear ReduceReads name cache after each set of reads produced by ReduceReadsStash. Name cache was filling up with names of all reads in entire file, which for large file eventually consumes all of memory. Only keep read name cache for the reads that are together in one variant region, so that a pair of reads within the same variant region will still be joined via read name. Otherwise the ability to connect a read to its mate is lost. Update MD5s in integration test to reflect altered output. Add new integration test that confirms that pair within variant region is joined by read name.	2013-03-19 14:12:33 -04:00
..
java	Clear ReduceReads name cache after each set of reads produced by ReduceReadsStash.	2013-03-19 14:12:33 -04:00
scala/test/org/broadinstitute/sting/queue/pipeline/examples	Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest	2013-02-27 04:45:53 -05:00

Alec Wysoker bccc9d79e5 Clear ReduceReads name cache after each set of reads produced by ReduceReadsStash.

Name cache was filling up with names of all reads in entire file, which for large file eventually
consumes all of memory.  Only keep read name cache for the reads that are together in one variant
region, so that a pair of reads within the same variant region will still be joined via read name.
Otherwise the ability to connect a read to its mate is lost.

Update MD5s in integration test to reflect altered output.
Add new integration test that confirms that pair within variant region is joined by read name.

2013-03-19 14:12:33 -04:00

java

Clear ReduceReads name cache after each set of reads produced by ReduceReadsStash.

2013-03-19 14:12:33 -04:00

scala/test/org/broadinstitute/sting/queue/pipeline/examples

Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest

2013-02-27 04:45:53 -05:00