gatk-3.8

Author	SHA1	Message	Date
kiran	6c5fbb988b	Now basecalls an entire read (both ends of the pair, barcode... everything) at once. After, RawRead and FourProbRead can be asked to return a specified subset (corresponding to the ranges specified for each end of the read. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@754 348d0f76-0448-11de-a6fe-93d51630548a	2009-05-20 00:09:20 +00:00
kiran	5858f20902	Documentation. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@712 348d0f76-0448-11de-a6fe-93d51630548a	2009-05-14 18:58:43 +00:00
kiran	e4770885fd	The four-probs for all bases in a single read. Some utility functions for generating the primary and secondary base strings, as well as generating the SQ tag byte array in a manner that's consistent with the Bustard base calls (meaning the primary Bustard call and the secondary Four-Prob call are not permitted to be the same). git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@704 348d0f76-0448-11de-a6fe-93d51630548a	2009-05-14 16:55:49 +00:00