aaron 8d43ec3d7e a fix for a situation where a chromosome on the reference file contains no reads, and doesn't align to the bam file. This came up using reference 18, which has chomosomes like chr1_random that aren't in all BAM files. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@649 348d0f76-0448-11de-a6fe-93d51630548a		2009-05-11 01:39:25 +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	a fix for a situation where a chromosome on the reference file contains no reads, and doesn't align to the bam file. This came up using reference 18, which has chomosomes like chr1_random that aren't in all BAM files.	2009-05-11 01:39:25 +00:00
test/org/broadinstitute/sting	Cleanup in preparation for ByLoci traversal. Also did some work minimizing unit tests.	2009-05-08 21:27:54 +00:00