aaron ab5c4064ed quick bug fix for variant context utils: only calculate the max AC if we're using the mergeInfoWithMaxAC flag, and if so deal with sites that have multiple alternate alleles correctly. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5582 348d0f76-0448-11de-a6fe-93d51630548a		2011-04-06 05:36:52 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src	quick bug fix for variant context utils: only calculate the max AC if we're using the mergeInfoWithMaxAC flag, and if so deal with sites that have multiple alternate alleles correctly.	2011-04-06 05:36:52 +00:00
test	Only store a read in the mate hash if it could possibly be moved. This reduces memory consumption especially when dealing with a case of tons of unmapped reads at the end of the bam; however, it's only mildly helpful for chr1 of the Papuans (there's a truly massive pileup 120Mb into it; more thought needed at a later point). Integration tests changed only because some of the reads in the original bam were busted to begin with (it's an old pilot 1000G bam).	2011-04-05 22:20:09 +00:00