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
3c40db260d
Added REFERENCE_BASES required annotation for performance
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1047 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 21:03:57 +00:00
11aa715630
added capability for filtering by platform
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1011 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-15 19:19:50 +00:00
8f4bc8cb6e
Move filtering functionality into the PrintReadsWalker. More to come.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1010 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-15 16:38:08 +00:00
bf6190b471
cleaned up the PrintReadsWalker, and added a lot of documentation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@952 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 14:28:32 +00:00
36fb6ca3c5
Allow user to specify the compression to be used when writing out BAM files.
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Updated most of the walkers to reflect this change.
Now it won't take forever to write BAMs!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@909 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-05 08:48:34 +00:00
0219d33e10
QualityUtils: added reverse function to reverse an array of bytes (and not complement it), BaseUtils: split qualToProb into itself and qualToErrProb, CovariateCounterWalker and LogisticRecalibrationWalker: several changes including a properly acocunting (only partly complete) for reversing AND complementing bases that are negative strand, PrintReadsWalker: created option to output reads to a BAM file rather than just to the sceern (useful for creating a downsampled BAM file)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@770 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 18:30:45 +00:00
23e9e29964
Changed reads traversals from providing a LocusContext from which the reference sequence
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could be extracted to a char[] containing the reference bases.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@657 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-11 22:45:11 +00:00
4a6be896b9
Provide out and err PrintStreams to the walkers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@213 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-27 15:03:32 +00:00
5f9010116a
Collapse the walker hierarchy, in preparation for in-walker output streams less hokey walker args.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@201 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-26 16:22:35 +00:00
63cd1fe201
Push core / playground lower into the tree.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@160 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-23 23:19:54 +00:00
hanna
depristo
ebanks
aaron
andrewk