6 Commits (b00d2bf2bcc97a5c18977360bed0532381cb61ec)

Author	SHA1	Message	Date
hanna	1f451e17e5	Changing preloaded index to only "preload" reference sequences on demand. ... Results in drastic lowering of startup cost when multiple BAM files are merged. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3066 348d0f76-0448-11de-a6fe-93d51630548a	2010-03-23 22:02:28 +00:00
hanna	c0eb5c27ea	Lower memory support for merged sharding. Merged sharding is still not available. ... WARNING: If you update frequently, you might have to rm -rf ~/.ant/cache -- this is an unfortunate side effect of the way we distribute picard-private.jar. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3050 348d0f76-0448-11de-a6fe-93d51630548a	2010-03-19 22:03:47 +00:00
hanna	30eb28886b	Basic functionality for intervaled reads in new sharding system. Not currently filtering out cruft, so ... the mode of operation is currently queryOverlapping rather than queryContained. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2899 348d0f76-0448-11de-a6fe-93d51630548a	2010-02-26 21:41:55 +00:00
hanna	0250338ce7	Basic use cases for merging BAM files with the new sharding system work. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2815 348d0f76-0448-11de-a6fe-93d51630548a	2010-02-09 22:14:37 +00:00
hanna	e53432d54d	Checkpoint for combining adjacent intervals into the same shard. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2782 348d0f76-0448-11de-a6fe-93d51630548a	2010-02-05 02:48:02 +00:00
hanna	3f35e181d5	Add an alternate implementation of the BAM file reader that keeps the entire index in memory. Initial revision of BAMFileStat, a tool to inspect BAM file BGZF blocks and index entries. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2769 348d0f76-0448-11de-a6fe-93d51630548a	2010-02-03 19:48:15 +00:00