asivache 240eb18564 fix a few related issues when not all the reads were written into the output files. now cleaned output still contains all reads either with modified alignments or untouched ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@444 348d0f76-0448-11de-a6fe-93d51630548a		2009-04-16 03:56:47 +00:00
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src/org/broadinstitute/sting	fix a few related issues when not all the reads were written into the output files. now cleaned output still contains all reads either with modified alignments or untouched	2009-04-16 03:56:47 +00:00
test/org/broadinstitute/sting	Changed interface from contig,pos,length to more common contig,start,stop interface.	2009-04-16 00:04:41 +00:00