64c65c7751
New methods to generated compressed SQ quality elements in line with the SAM spec.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@699 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 16:50:31 +00:00
c3b2c66911
The GATK doesn't need the rest
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@698 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 16:20:45 +00:00
0215905bb6
Added an adapter class, that will adapt plain iterators and closeable iterators of SAMRecords into STingSAMIterators. Also unit tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@697 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 15:17:32 +00:00
5dda448ae0
1. Add printouts for the cleaner
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2. First pass at the entropy interval walker (still needs work)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@696 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 13:59:48 +00:00
80c13f7127
Added a getter for command-line arguments.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@695 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 13:55:52 +00:00
307c6e4ecf
Oops. Forgot to add new file to svn.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@694 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 00:52:30 +00:00
d14cab0be7
Added IterableLocusContextQueue and test. Cleaned up tests, adding BaseTest where it didn't exist. Enhanced test runner to run only classes ending in ...Test.java, so that utility classes can sit alongside the tests but won't be run by JUnit.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@693 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-13 21:32:05 +00:00
7b59f63f12
and don't forget to close sam writer after we are done...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@692 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-13 20:46:36 +00:00
de0cce87ea
new optional arg added that allows to specify a separate bam file to send all piles that fail to realign to; plus minor fixes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@691 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-13 20:24:23 +00:00
12ae3a22b6
Break locus context data access providers into modular components in preparation for traverse by loci.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@689 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-13 18:51:16 +00:00
7084ecdeb6
a few changes; checked in to allow debugging.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@688 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-13 15:50:48 +00:00
5b47c5ab6c
fixing kiran's busted build
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@686 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 21:29:04 +00:00
4f2c8bf0a3
Fixed an import statement that broke when all the files were moved to this directory.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@685 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 20:43:16 +00:00
cedc4c9ccb
Refactored into oblivion.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@684 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 20:33:07 +00:00
4e4767e5de
Moved to org.broadinstitute.sting.secondarybase
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@682 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 20:26:43 +00:00
219eb60716
Added newly-required documentation to arguments so that build can complete successfully.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@681 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 20:26:10 +00:00
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
c241d386a7
Beefed up command-line usage string.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@629 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 19:08:19 +00:00
5a6892900e
fixing oddities in duplicates
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@628 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 18:55:45 +00:00
4a26f35caa
new default syntax
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@627 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 18:16:53 +00:00
283a4d1b54
Fix some special-case cleaner issues.
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We now do the same as brute force in all examples to date.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@626 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 18:16:35 +00:00
93211c1cd8
template for windowmaker utility -- total non-functional
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@625 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 18:13:03 +00:00
2204be43eb
System for traversing duplicate reads, along with a walker to compute quality scores among duplicates and a smarter method to combine quality scores across duplicates -- v1
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@624 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 18:06:02 +00:00
71e8f47a6c
boundQual function for capping qual values
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@623 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 18:04:18 +00:00
e848f34896
countOccurances of char in string and max of a list of bytes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@622 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 18:03:49 +00:00
5a4bb76cc3
More capabilities for the pileup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@621 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 18:03:13 +00:00
89a26a7078
Utilities for handling duplicates
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@620 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 18:02:24 +00:00
4f85062004
Cleanup parsing method to make it less generic.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@619 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 16:21:17 +00:00
d725c6cf1c
Added unit tests for parsing failures that I encountered during integration testing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@618 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 14:01:54 +00:00
2f3ab53888
Oops. Arguments didn't load into applications with non-plugins (basically everything except the GATK).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@617 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 13:37:19 +00:00
4177560543
Mutually exclusive options.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@616 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 13:27:48 +00:00
752928df94
Switch to better mechanism for supplying a default.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@615 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 01:22:01 +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
9c0b81e946
Default flags to 'not required'.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@612 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 22:09:49 +00:00
072808858e
added COUNT_CUTOFF arg: it is nor possible to tell the code to try to realign all read piles over trains of nearby indels with at least one indel observed in COUNT_CUTOFF or more different alignments (set the arg to 1 to realign around all indels); also, some diagnostic printouts added to the output (time spent on loading the reference, time spent on scrolling through the input bam file, counts of discarded reads)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@611 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 21:59:33 +00:00
1fe8155111
Some critical fixes for cases where argument values directly abut argument names
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and for arguments with missing short names.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@610 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 21:47:34 +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
62e7e46754
Miscellaneous cleanup. Better display of help output. Better exception subtyping. More thought-out access routines.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@608 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 21:16:01 +00:00
5be75e0ae6
First version of indel cleaner walker that works on intervals
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@607 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 20:20:48 +00:00
98716138e9
Cleanup: add support for non-public fields. Track matches as state of parsing engine as well as definitions.
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Made fields of command-line argument system non-public by default.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@606 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 19:38:05 +00:00
f5eae98af2
Fixed a bug where we could ask for a read when there were none in the pool (that's a bad thing).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@605 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 18:40:55 +00:00
ef211f96b1
Remove old Apache CLI-based arg system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@604 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 18:37:51 +00:00
521aa40baa
Bring new command-line argument parsing system live.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@603 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 18:16:11 +00:00
98f4920739
Added BCEL and some basic instrumenation code to the test library.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@602 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 17:18:23 +00:00
bfd6dfe36c
Added real-world tests and tests for conditional validation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@601 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 13:38:46 +00:00
4ac9e72739
Migrate default and GATK arguments over to new attribute system in preparation for conversion.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@600 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-05 23:57:48 +00:00
2ee9374975
Check for proper error output in case of boolean args with parameter specified.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@599 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-05 23:08:48 +00:00
b0cdba8bb3
Acting on Kiran's suggestion to make the doc tag in the @Argument annotation required.x
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@598 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-05 22:43:40 +00:00
ec0261275b
Lots of command line argument validation. Catches all common validation problems, including missing required arguments, invalid arguments, and several types of misplaced argument value errors.
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Still pending:
- Help system.
- Mutually exclusive arguments.
- Design includes too many classes per file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@597 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-05 22:08:00 +00:00
70afda12c4
Cut the test time down
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@596 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-05 22:05:51 +00:00
kiran
aaron
ebanks
hanna
asivache
jmaguire
depristo
kcibul
andrewk