gatk-3.8

Author	SHA1	Message	Date
carneiro	7598f5f6a7	forgot to remove a debug line. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5246 348d0f76-0448-11de-a6fe-93d51630548a	2011-02-15 16:25:48 +00:00
carneiro	e45b699ac0	standardizing the name of the scripts and fixing some bugs with the remapping. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5245 348d0f76-0448-11de-a6fe-93d51630548a	2011-02-15 16:19:58 +00:00
carneiro	50c2fa3c3a	this -1 made ALL the difference in the world. Minor bug fix. Regular updates to the pbCalling pipeline. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5232 348d0f76-0448-11de-a6fe-93d51630548a	2011-02-11 19:25:09 +00:00
carneiro	e7d38247bb	chunkIntervals.lua creates 1Mb interval chunks out of any .intervals file. Useful for methods development pipeline datasets. remapAmplicons.lua takes a sam file with reads aligned to amplicon references, a reference genome , and an amplicon reference mapping table, and rewrites the sam file with mappings to the reference sequence. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5230 348d0f76-0448-11de-a6fe-93d51630548a	2011-02-11 18:21:31 +00:00