5 Commits (199b43fcf2abb365a7dc5bf9907f49b749a784e5)

Author	SHA1	Message	Date
hanna	199b43fcf2	Reduce by interval alterations to interface with new sharding system. This checkin with be followed by a ... simplification of some of the locus traversal code. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2886 348d0f76-0448-11de-a6fe-93d51630548a	2010-02-25 00:16:50 +00:00
aaron	7fc4472e6d	A big fix for MergingSamRecordIterator, where we weren't correctly handling the comparisons of SAMRecords correctly (we weren't applying the new reference index first, so sometimes the MT contig would be ID 23, sometimes 24 in different records). ... Also a fix to the GLF tests, and a correction to PrintReadsWalker to remove the close() on the output source, the source handles that itself (and you get a double close). git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1758 348d0f76-0448-11de-a6fe-93d51630548a	2009-10-02 19:35:35 +00:00
aaron	63b5c12cbd	Changed dataSources to datasources, to be consistant with the rest of our package names. Also, this makes me champion in the largest check-in contest. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@985 348d0f76-0448-11de-a6fe-93d51630548a	2009-06-11 18:13:22 +00:00
aaron	195b4ea7b4	a rename for consistancy of Sam to SAM, creating a genotype utils dir, and moving the GLF code into it. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@984 348d0f76-0448-11de-a6fe-93d51630548a	2009-06-11 17:46:06 +00:00
aaron	36c98b9d6c	added tools to test read based traversals using the artificial in-memory SAM file tools, and testing of the PrintReadsWalker ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@957 348d0f76-0448-11de-a6fe-93d51630548a	2009-06-10 01:52:25 +00:00