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10 Commits (76efa757f0fe77bf2608541219afe3c8647efdc9)

Author SHA1 Message Date
hanna 76efa757f0 Switched over to reviewed version of Picard patch. In process, did some optimization to the IntervalSharder 
which improved startup time 5-10x when dynamically merging many BAMs.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3331 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-08 14:12:22 +00:00
hanna c1e53d407d The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had 
unicode quote characters embedded in it.  These characters were invisible inside
IntelliJ but cause compile warnings for Ryan and Aaron, who for whatever reason
have a different default charset.  Fixed.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3203 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 15:26:32 +00:00
hanna 1bc26f69e9 An attempt to cleanup the Utils directory. Email to follow. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3198 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-19 23:00:08 +00:00
hanna 400684542c Revisions to take into account finalization of Picard patch: naming changes, better definition 
of public interfaces.  This won't be the last Picard patch, but it should be the last big one.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3096 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-30 19:28:14 +00:00
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