688358190c
Moved secondary base stuff out of playground for the purpose of making it a core utility. Modified package names and imports such that things would build properly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@680 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 20:24:18 +00:00
8079acb1d3
basic step0 implementation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@679 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 19:49:39 +00:00
57ecb7fbf1
Nicer reporting functions.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@678 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 19:48:30 +00:00
ee99320c83
Removed at Mark's request.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@677 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 19:48:21 +00:00
f1de3d6366
Minor tweaks to how probs are supplied.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@676 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 19:47:41 +00:00
095dacd154
Experimental refactoring.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@675 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 19:46:50 +00:00
758f8aa89b
Experimental refactoring.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@674 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 19:46:34 +00:00
1518f8f9bf
Update training data creation in CovariateCounterWalker to output much smaller files by counting the number of occurences of each data point combination rather than outputting a line for each data point (i.e. each base). Also fixed bug in LogisticRecalibrationWalker where a null SAMHeader was being pulled from a function that is now marked deprecated.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@673 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 19:23:14 +00:00
4c12df372c
Dumb, dumb bug.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@672 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 19:21:33 +00:00
6e69193e3c
Deprecated calls to getSamReader on both the GenomeAnalysisEngine and the TraversalEngine. This call fails in the new style traversals, but it won't disapear until the cut-over to the new traversals is complete.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@671 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 18:52:42 +00:00
630066cc0a
1. Merge LocusWindows whose reads overlap.
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2. Fix bug (we weren't clearing the "to emit" list)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@670 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 17:33:23 +00:00
9f942fdfa0
Added code to correct the violation of the parsing interface. Now the analysis type resides in the command line arg, but is stored into the argument collection before it's passed to the genomeAnalysisEngine.
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Also fixed a bug where we'd exception-out if we didn't provide a interval region.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@669 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 15:33:55 +00:00
c4d89997ca
put in a dummy sample_name so it'll compile
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@668 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 15:12:42 +00:00
c8d7223789
do pooled calling properly for 1kg
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@667 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 15:12:13 +00:00
313a6d0fb5
lots of changes to facilitate calling indels and 1kG
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@666 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 15:11:42 +00:00
add7b6cf65
add sample_name to constructor, misc bug fixes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@665 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 15:10:17 +00:00
0267ccae7f
add code for computing indel genotype likelihoods
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make reference lods negative
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@664 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 15:09:29 +00:00
11723fbcc2
added method indelPileup. Generates a pileup of indel alleles given reads and ofsets (as from a locus walker).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@663 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 15:08:24 +00:00
ee9077fc69
LocusIterator iterated through LocusContexts, which was fine until now when we need something
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that iterates through loci (GenomeLocs). Rename LocusIterator to LocusContextIterator.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@662 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 13:54:57 +00:00
608948210c
Check for a reference before extraction.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@661 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 13:29:44 +00:00
32696b13f5
Fixed method override issue with old-style traversals.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@660 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 01:22:18 +00:00
862b8a6787
intervals_file + genome_loc => intervals.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@659 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 01:04:18 +00:00
0bca588629
Botched some boolean logic.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@658 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-11 22:53:52 +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
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
ff1b92acc4
Switch over to the GenomeAnalysisEngine/CommandLineGATK system from the GenomeAnalysisTK code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@655 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-11 22:05:58 +00:00
009e71fcd9
We need to sort cleaned reads ourselves (instead of letting SAMFileWriter
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do it) because the SAM headers are often screwed up and claim to be
"unsorted". While here, I broke off the module from the SortSamIterator
in case someone else wants to use it.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@654 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-11 15:43:42 +00:00
c735e1f627
small javadoc cleanup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@653 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-11 03:44:21 +00:00
e8b8ab5985
Added code to extend Matt's getReferenceBases out to the read walkers, so they can see the corresponding reference for each read.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@652 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-11 03:42:38 +00:00
4ce3feba4d
my move ended up being a copy, so this is to delete dupplicate files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@651 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-11 02:10:26 +00:00
898f65547e
Added code to split GenomeAnalysisTK.java into an object concerned with loading command line args, and one that runs the engines. This will allow us to run the GATK from other tools (like Matlab). Also some cleanup to seperate out the legacy traversals and the new style traversals. This is not live yet, and any modifications you need should be made to GenomeAnalysisTK.java for now.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@650 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-11 02:07:20 +00:00
8d43ec3d7e
a fix for a situation where a chromosome on the reference file contains no reads, and doesn't align to the bam file. This came up using reference 18, which has chomosomes like chr1_random that aren't in all BAM files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@649 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-11 01:39:25 +00:00
ee02b61068
added support for the argument collections code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@648 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-09 07:07:33 +00:00
742840017b
added the argument collection annotation for situations where fields in a command line args have embedded fields that should be checked for command line args
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@647 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-09 06:59:17 +00:00
55c1b688bd
Fix mediocre javadoc.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@646 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 22:31:16 +00:00
522f8b58be
Added second method for getting large sequences of the reference for use in reads traversals.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@645 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 22:18:04 +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
ee777c89de
Change the default mechanism for adding ROD bindings to the new system. TODO: create a new object type for these triplets.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@642 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 18:43:00 +00:00
3aabc144c6
Added functionality to allow for a contract between LocusWindowTraversalEngine and LocusWindowWalker which allows the Walker to act upon reads outside of the provided intervals.
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(Really, all we want to do is spit out all reads, but this allows the Walker to do other things with the reads if it wants)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@641 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 17:28:16 +00:00
de1c282e62
Reference-ordered data relies on bugs in the old command-line argument system to work. Update the ROD system to from -B track1 type1 file1 track2 type2 file2 to -B track1,type1,file1 -B track2,type2,file2.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@640 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 15:28:19 +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
a5154d99a3
Haven't heard any complaints, so I'm deleting the original implementation of TraverseByLociByReference. All TbyLbyR's will now go through the new sharding code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@637 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 13:37:00 +00:00
bae4256574
Started the process to make the GATK engine into a runnable object so we can call it from other processes. Step 1: make a configuration object that can serialize to and from an XML file. This way we can store the information everyone uses shell scripts for. Also we can now pull the list of params out of the GenomeAnalysisTK.java. More to come...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@636 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 01:25:26 +00:00
226edbdef6
Hypen-style xml output. Much sexier.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@635 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 01:04:40 +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
21536df308
Change the sample XML marshalling code over to simple XML, and take out the castor lines in the ivy.xml
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@633 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 00:08:25 +00:00
7f8850a8a2
Argument validation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@631 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 20:28:56 +00:00
a3d8febbf2
Error message cleanup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@630 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 19:31:32 +00:00
kiran
kcibul
hanna
andrewk
ebanks
aaron
jmaguire