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12 Commits (96fee7cf7aea84e25b41a1c6c61fa0414d830ffe)

Author SHA1 Message Date
hanna dc885ba386 Fix for some correctness bugs found during early performance testing, phase 1. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2822 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-10 22:32:25 +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 57b8c9a53c Supporting infrastructure for merging SAM files. Not yet integrated into the datasource. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2810 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-08 23:59:38 +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
hanna 668c7da33d Bug fix in custom override of queryOverlapping. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2743 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-29 21:35:59 +00:00
hanna e7f5c93fe5 Cleaning up the inheritance hierarchy from the previous commit. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2738 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-29 19:13:36 +00:00
hanna 3d922a019f Basic support for very simple index-driven locus traversals. Interface has been changed to 
support batched intervals in a single shard, but intervals are not yet compressed into a single
shard.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2730 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-29 03:14:26 +00:00
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