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Author SHA1 Message Date
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