depristo 5cca100aea Eliminated the redundant StratifiedAlignmentContext, which previously just held a ReadBackedPileup, and made all of the class methods here just static functions. Far more logical organization, and avoided O(N) endless copying of data for the COMPLETE context. Many tools have been trivially reorganized to take an alignment context now. Everything passes integration tests. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5562 348d0f76-0448-11de-a6fe-93d51630548a		2011-04-03 14:20:43 +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	Eliminated the redundant StratifiedAlignmentContext, which previously just held a ReadBackedPileup, and made all of the class methods here just static functions. Far more logical organization, and avoided O(N) endless copying of data for the COMPLETE context. Many tools have been trivially reorganized to take an alignment context now. Everything passes integration tests.	2011-04-03 14:20:43 +00:00
test	Fix for bug GSA-441: BAM file list with blank lines gives a confusing error	2011-04-01 15:04:35 +00:00