aaron 78b7fb25c7 allow contig names to have spaces in the fai. This is not yet supported by samtools fai generator (which truncates at the first space), but we might as well fix it on our side. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1022 348d0f76-0448-11de-a6fe-93d51630548a		2009-06-16 22:23:12 +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/org/broadinstitute/sting	allow contig names to have spaces in the fai. This is not yet supported by samtools fai generator (which truncates at the first space), but we might as well fix it on our side.	2009-06-16 22:23:12 +00:00
test/org/broadinstitute/sting	added changes to support alec toUnmappedRead seek. Huge improvements (orders of magnitude) in unmapped read performance.	2009-06-16 22:15:56 +00:00