ebanks ca1917507f Various improvements and fixes: ... In indel cleaner: 1. allow the user to specify that he wants to use Picard’s SAMFileWriter sorting on disk instead of having us sort in memory; this is useful if the input consists of long reads. 2. for N-way-out mode: output bams now use the original headers from the corresponding input bams - as opposed to the merged header. This entailed some reworking of the datasources code. 3. intermediate check-in of code that allows user to input known indels to be used as alternate consenses. Not done yet. In UG: fix bug in beagle output for Jared. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2805 348d0f76-0448-11de-a6fe-93d51630548a		2010-02-07 04:21:04 +00:00
..
broadinstitute/sting	Various improvements and fixes:	2010-02-07 04:21:04 +00:00