gatk-3.8

Author	SHA1	Message	Date
hanna	b19bb19f3d	First successful test of new sharding system prototype. Can traverse over reads from a single BAM file. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2587 348d0f76-0448-11de-a6fe-93d51630548a	2010-01-15 03:35:55 +00:00
hanna	7893aaefe9	Updates to chunk iteration. Includes the return of the dreaded *2.java files; hopefully I can find a way to kill these off before the Picard patch is ready. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2550 348d0f76-0448-11de-a6fe-93d51630548a	2010-01-08 20:20:56 +00:00
hanna	497ae700c4	A rethink of the existing BAM block extraction code: rather than working in chunk space directly, stream data in block space, converting to chunk space on demand. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2484 348d0f76-0448-11de-a6fe-93d51630548a	2009-12-30 18:19:51 +00:00
hanna	87ff2b15d4	First step in introducing a patch to Picard: create our ideal interface into the BAM file for sharding. This commit can iterate over the BAM file, pulling out information about the blocks in the file without actually loading or decompressing the reads. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2434 348d0f76-0448-11de-a6fe-93d51630548a	2009-12-23 21:35:08 +00:00