4995950d04
IndexedFastaSequenceFile is now in Picard; transitioning to that implementation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3701 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-01 04:40:31 +00:00
96662d8d1b
Moving from GATK dependencies on isolated classes checked into the GATK
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codebase to a dependency on a jar file compiled from my private picard branch.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3034 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-18 17:43:42 +00:00
a7fe07c404
A few stopgap fixes to get the GATK to the point where the old sharding
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infrastructure can be torn down:
1) New sharding system emulates old MonolithicSharding mechanism.
2) Better awareness of differences between fasta and BAM files when creating
shards.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2948 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-07 21:01:25 +00:00
1ef1091f7c
Cleanup and simplification of read interval sharding.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2944 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-05 23:34:38 +00:00
023654696e
First pass at handling SAMFileReaders using a SAMReaderID. This allows us to firewall
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GATK users from the readers, which they could abuse in ways that could destabilize the GATK.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2923 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-04 00:59:32 +00:00
104f4f7383
Mediocre implementation of reader pooling within the SAM data source. Will fix this week.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2915 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-02 22:35:02 +00:00
30eb28886b
Basic functionality for intervaled reads in new sharding system. Not currently filtering out cruft, so
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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
1017a38f38
Initial refactoring of read traversal to make it easier to drop in intervalled reads traversal.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2894 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-26 15:09:09 +00:00
88d0677379
Misc correctness enhancements: develop the bin selector into a recursive algorithm and return a shard when reads are missing. Also improve the performance of the read filter that clips reads not actually present in the shard.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2870 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-22 22:19:06 +00:00
cc09f48cd8
Correctness fix: index can concat chunks around shard edges, and my code didn't account for that.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2861 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-19 21:44:33 +00:00
71f18e941f
Significant performance improvements made by subtracting out the contents of the prior highest-level bin.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2859 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-19 16:46:16 +00:00
232d884578
Got back most of the performance lost when I fixed the dropped reads problem.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2835 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-12 19:59:56 +00:00
77af5822d4
Correcting my incomplete understanding of how the BAM file index actually works.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2833 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-12 16:15:19 +00:00
34e566c90d
Fixed bug where new sharding system wasn't grabbing the reads that start at the end of a bin. Caused by what I currently believe to be a bug in Picard -- will verify with Alec.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2826 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-11 17:00:04 +00:00
dc885ba386
Fix for some correctness bugs found during early performance testing, phase 1.
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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
0250338ce7
Basic use cases for merging BAM files with the new sharding system work.
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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
57b8c9a53c
Supporting infrastructure for merging SAM files. Not yet integrated into the datasource.
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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
e53432d54d
Checkpoint for combining adjacent intervals into the same shard.
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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
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.
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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
668c7da33d
Bug fix in custom override of queryOverlapping.
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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
e7f5c93fe5
Cleaning up the inheritance hierarchy from the previous commit.
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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
3d922a019f
Basic support for very simple index-driven locus traversals. Interface has been changed to
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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
b19bb19f3d
First successful test of new sharding system prototype. Can traverse over reads from a single
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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
7893aaefe9
Updates to chunk iteration. Includes the return of the dreaded *2.java files;
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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
497ae700c4
A rethink of the existing BAM block extraction code: rather than working in
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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
87ff2b15d4
First step in introducing a patch to Picard: create our ideal interface into the BAM file for sharding.
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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
hanna