a1e8a532ad
Support for initialize() and onTraversalDone() output from parallelized walkers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1911 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-26 20:18:31 +00:00
b69eb208a6
Always create output files, even if no output was written to them.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1627 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-15 17:58:14 +00:00
ccdb4a0313
General-purpose management of output streams.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1454 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-23 00:56:02 +00:00
5429b4d4a8
A bit of reorganization to help with more flexible output streams. Pushed construction of data
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sources and post-construction validation back into the GATKEngine, leaving the MicroScheduler
to just microschedule.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1336 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-29 23:00:15 +00:00
7a13647c35
Support for specifying SAMFileReaders and SAMFileWriters as @Arguments directly. *Very*
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rough initial implementation, but should provide enough support so that people can stop
creating SAMFileWriters in reduceInit.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1332 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-29 16:11:45 +00:00
a361e7b342
SAMDataSource is now exposed by GATK engine; SamFileHeaderMerger is exposed from Resources all the way up to SAMDataSource, so now we can see underlying individual readers should we need them; GATK engine has new methods getSamplesByReaders(), getLibrariesByReaders(), and getMergedReadGroupsByReaders(): each of these methods returns a list of sets, with each element (set) holding, respectively, samples, libraries, or (merged) read groups coming from an individual input bam file (so now when using multiple -I options we can still find out which of the input bams each read comes from)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1315 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-24 22:59:49 +00:00
99f9cd84ed
Warning for possibly mismatched reads / reference was very aggressive. Relax
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the criteria a bit.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1234 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-14 16:21:22 +00:00
0f6bfaaf73
Skip validation in case of no reads aligning.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1230 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-14 02:03:36 +00:00
b18caa2052
Fix for GSA-90: System isn't failing with an error when you use the wrong reference.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1225 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-13 20:42:12 +00:00
d86717db93
Refactoring of the traversal engine base class, I removed a lot of old code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1209 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-09 21:57:00 +00:00
5e26770634
Hack the MicroScheduler to be tolerant of RefWalkers. We need to implement a longer-term solution to make it easier for datasources to report problems they've encountered along the way (GSA-103).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1205 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-09 17:26:59 +00:00
5735c87581
Basic infrastructure for filtering malformed reads.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1178 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-06 22:50:22 +00:00
491ed70b44
TraverseByLocusWindow -- asstd bug fixes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1109 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 22:51:38 +00:00
5b1c23a7f2
changes to fix and test the interval based traversals
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1095 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 17:54:15 +00:00
8b4d0412ca
Changed the duplicate traversal over to the new style of traversal and plumbed into the genome analysis engine. Also added a CountDuplicates walker, to validate the engine.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1072 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-22 21:11:18 +00:00
bcb64d92e9
Aaron: 1, GenomeLoc: 0. I changed our GenomeLoc class, seperating the creation of a genome loc (with the reference setup) to a parser class. GenomeLoc now just represents the actual genomic postion. The constructors are now package-protected (to enforce using the parser), but we may want to expose some constructors in the future.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1069 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-22 14:39:41 +00:00
cba9025983
More package-level documentation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1030 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 16:28:45 +00:00
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.
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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
a8a2d0eab9
added support for the -M option in traversals.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@935 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-08 15:12:24 +00:00
109bef6c08
We're no longer in the read-dropping business.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@901 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 22:37:51 +00:00
fc7320133c
Cleaned up error when fasta index is missing. Code still throws an exception, but the message is more direct (no more 'error while micromanaging') and tells the user to run 'samtools faidx' to fix the issue.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@867 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-01 15:34:38 +00:00
c04b67c969
Basic instrumentation support for the hierarchical microscheduler.x
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@862 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-29 22:19:27 +00:00
a1edb898ef
Make criteria for determining whether to stop and merge inputs more sane.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@855 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-29 18:08:18 +00:00
5e8c08ee63
Update to latest version of picard. Change imports in all classes dependent on picard public from import edu.mit.broad.picard... to import net.sf.picard...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@849 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-28 20:13:01 +00:00
3c3cd5bb64
Moving some of the data sharding around. A new shard catagory now exits, INTERVAL. This saved a lot of code that was mirroring the same approach in both the read and locus shard strategies.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@840 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 18:24:31 +00:00
864a1e81e3
Delete stale class from previous rethink of the traversal engine.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@828 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 13:52:03 +00:00
a488d2dbb2
Lazy creation of output streams. Only create output streams when absolutely necessary.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@824 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 21:56:57 +00:00
d994544c47
Added back end code support for Sharding based on genomic location for reads. Changed the sharding
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code to take GenomeLocSortedSet instead of a list<GenomeLoc>, and added a bunch of much simplier
and cleaner test cases.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@816 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 20:57:46 +00:00
34413362fd
Bugfix: handle case where queue is empty.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@808 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 21:45:22 +00:00
ec2e8d5726
Fixes for getting ValidatingPileup running in parallel.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@807 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 21:20:24 +00:00
d61a5261c1
Better integration of reference-ordered data into the data sharding system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@779 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 20:09:32 +00:00
01a3cb27c7
@Required / @Allows flags for main arguments.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@751 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-19 23:26:17 +00:00
ff798fe483
Reintroduce support for interval-based traversals.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@749 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-18 22:54:18 +00:00
c10741e9f5
Rename TraverseLociByReference to TraverseLoci to represent its new function.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@743 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-18 01:31:57 +00:00
2c4de7b5c5
Switch TraverseByLoci over to new sharding system, and cleanup some code in passing read files along
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the pathway from command line to traversal engine.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@727 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-15 21:02:12 +00:00
99d4ebc26d
Added functionality to return the final accumulator of a traversal, so external tools can get the result of a walker.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@724 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-15 20:20:27 +00:00
052819bed5
Switched dependencies of GenomeAnalysisTK to depend on GenomeAnalysisEngine.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@656 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-11 22:33:00 +00:00
517f27f331
Added sharding strat. code that picks the right kind of shard, based on the traversal engine
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@644 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 21:55:10 +00:00
6e394490cb
Cleanup in preparation for ByLoci traversal. Also did some work minimizing unit tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@643 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 21:27:54 +00:00
483a58627b
More cleanup -- pushing shared functions down into the traversal engine.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@639 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 14:12:45 +00:00
7a9cfe1f75
Push reduceInit down a level so that the walker can call into it without weird casts.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@638 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 13:46:28 +00:00
4c269b8496
Cleanup LinearMicroScheduler in preparation for TraverseByLoci inclusion.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@634 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 00:58:37 +00:00
dc944ec69b
First stage of ROD plumbing for MicroScheduler.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@614 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 23:26:21 +00:00
5136724884
Added code to the schedulers, one step closer to turning on the new reads traversals
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@613 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 22:36:25 +00:00
0aba688e6f
Added a interface that all our SAMRecord iterators should try to code to. This is in the effort to keep our code generic
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@609 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 21:40:41 +00:00
6e38966349
Rename some key classes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@587 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 22:01:04 +00:00
5bdf653919
Cleanup: prepare for better output handling.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@586 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 21:40:46 +00:00
9f5f6f9bc7
N-way parallelism. Works for small test cases. Untested for large test cases.
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-Needs more comprehensive unit testing.
-Needs some basic refactoring.
-Needs rethink of interface boundaries.
-Needs to play more nicely in the /tmp sandbox.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@583 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 19:34:09 +00:00
63403d32cd
Changes to the interface to the simple data source rippled out to a bunch of files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@572 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-30 20:35:56 +00:00
ba9a0b5da8
Break out some of the weird inner classes out of the HierachicalMicroScheduler.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@566 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-29 21:07:07 +00:00
hanna
asivache
aaron