hanna 56bc4fa21a Fixed bug where not all alignments were returned if read aligned to multiple locations. Enhanced test suite to validate all alignments. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1762 348d0f76-0448-11de-a6fe-93d51630548a		2009-10-04 18:20:20 +00:00
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bwa	Fixed bug where not all alignments were returned if read aligned to multiple locations. Enhanced test suite to validate all alignments.	2009-10-04 18:20:20 +00:00
Aligner.java	Unidirectional alignments with mismatches now working. Significant refactoring will be required.	2009-09-22 19:05:10 +00:00
Alignment.java	Indels supported. Variable gap penalties are not yet taken into account.	2009-09-24 21:03:02 +00:00