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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fourbasecaller	Intermediate commit. Refactored some simple base manipulation stuff into BaseUtils.java. Generalized some likelihood computation logic to make future possible EM-ing easier.	2009-04-15 04:18:07 +00:00
gatk	* added some error checking for read groups	2009-04-16 03:22:49 +00:00
illumina	Make output type identical to the bustard parser so the values can be easily swapped for one another.	2009-04-09 20:49:34 +00:00
indels	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
samples	Added a sample xml marshaller / unmarshaller.	2009-04-07 22:28:16 +00:00
utils	Commented out a debugging line	2009-04-14 20:15:11 +00:00
ValidateSAM.java	generic declarations added here and there to eliminate a few annoying warnings; no consequential changes	2009-04-02 20:53:01 +00:00