b39b5edca8
Bug fix in variant eval 2. Preliminary (slow and buggy) support for -XL exclude lists.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2991 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-12 19:23:12 +00:00
1eb5f97255
fixed dropping single base intervals from deleteRegion, moving onto performance fixes.
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(stop - start is length-1 on closed intervals, so we need to check greater than OR equals to zero)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2990 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-12 19:14:21 +00:00
661a043cef
adding methods to get RODs by name or type in read traversals, performance improvements to RODs for Reads in general, and some more Tribble infrastructure.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2984 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-11 21:13:39 +00:00
a7ba88e649
Rework the way the MicroScheduler handles locus shards to handle intervals that span shards
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with less memory consumption.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2981 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-11 18:40:31 +00:00
dde9fd8a15
some rods-for-reads cleaning and performance improvements.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2979 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-10 22:54:58 +00:00
4f4555c80f
PPV and Sensitivity added to validation tool output; support for arbitrary -sample arguments to subset variant contexts by sample
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2978 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-10 22:28:31 +00:00
40d305bc7e
Added test of Nway cleaning for Matt; thanks to Aaron for the help.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2977 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-10 21:00:41 +00:00
486bef9318
Support for validationRate calculation in variant eval 2; better error messages for failed genome loc parsing; tolerance to odd whitespace in plinkrod, and fix for monomorphic sites in vcf2variantcontext.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2976 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-10 16:25:16 +00:00
7ddd45d059
Hmm. I thought I removed this already.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2973 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-10 03:09:13 +00:00
1a576525e9
misc improvements
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2972 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-10 03:00:28 +00:00
6e855809e1
Renaming and moving relevant tools into a sequenom directory
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2971 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-10 02:31:10 +00:00
0a49dffa8f
Row/Column names are now R-friendly
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2966 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-09 19:01:03 +00:00
e5475a7ba9
re-enabling PlinkToVCF integration tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2964 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-09 17:35:49 +00:00
5a20bf0e64
3 changes to UG which break integration tests:
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1. emit AA,AB,BB likelihoods in the FORMAT field for Mark
2. remove constraint that genotype alleles (in the GT field) need to be lexigraphically sorted.
3. Add bam file(s) used by genotyper to header for Kiran
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2963 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-09 17:16:47 +00:00
9f3b99c11b
Moving UnifiedGenotyper and VariantAnnotator over to VariantContext system.
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Removing obsolete genotyping classes.
First stage of removing dependence on old Genotype class.
More changes to come.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2960 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-09 03:41:07 +00:00
bca9bdcc68
Add integration test for quartiles overflowing on interval reduce
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2957 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-08 16:18:45 +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
dd6122f682
Fixed another bug in the original sharding system. Updated integration tests
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as appropriate.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2947 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-07 15:32:18 +00:00
ee2ec7ced9
Fix off-by-one error in original implementation of read sharding. Tested by
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awking output of BamToFastq vs. samtools until the outputs matched exactly.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2945 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-06 18:52:53 +00:00
ee913eca07
Forgot to check in fix this morning
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2943 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-05 21:07:19 +00:00
8738c544f1
Minor refactoring of CoverageStatistics to allow simultaneous output of per-sample and per-read group statistics.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2940 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-05 17:06:52 +00:00
7104a3a96c
Fix for accumulator exception when running reduce by interval walkers without
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intervals.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2935 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-05 01:04:08 +00:00
366771d5a6
another test-with-multiple outputs fix
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2934 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-04 22:46:15 +00:00
706d49d84c
Commit for Aaron
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2932 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-04 21:29:07 +00:00
54f04dc541
forgot to uncomment the auto-deletion of temp files...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2930 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-04 20:29:42 +00:00
80cc6bbeb4
add a way to test files generated by a walker that aren't command-line arguments; added some example code in CoverageStatisticsIntegrationTest for Chris.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2929 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-04 20:20:58 +00:00
0dd65461a1
Various improvements to plink, variant context, and VCF code.
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We almost completely support indels. Not yet done with plink stuff.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2926 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-04 17:58:01 +00:00
c8077b7a22
Waypoint check-in: a couple of changes to for Tribble, and adding some options to the integration test for passing in auxillary files that aren’t “%s” command line options.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2925 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-04 16:02:21 +00:00
ca2cd9d4f5
a little clean-up: move setting the bases of generated reads into Artificial SAM Utils now that the clean read injector test is gone.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2919 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-03 16:31:45 +00:00
790d2a7776
adding the initial ROD for Reads support; more convenience methods in ReadMetaDataTracker to come.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2918 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-03 15:56:44 +00:00
0e9a6826b0
Update to VCF code to get it up to spec.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2917 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-03 06:12:42 +00:00
74a5223b11
oops - didn't mean to check this in
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2914 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-02 20:28:22 +00:00
5f3c80d9aa
1. To make indel calls, we need to get rid of the SNP-centricity of our code. First step is to have the reference be a String, not a char in the Genotype. Note that this is just a temporary patch until the genotype code is ported over to use VariantContext.
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2. Significant refactoring of Plink code to work in the rods and use VariantContext. More coming.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2913 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-02 20:26:40 +00:00
d8fedd59be
docs, cleanup, and some improvements to the iterators.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2901 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-26 22:36:04 +00:00
87f8fb7282
Quick commit in advance of Aaron's. Just a bunch of refactoring (private classes separated out, put in proper package). Also support added for coverage by read group rather than sample.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2897 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-26 16:39:47 +00:00
9a6b384adb
Support for no qual fields in VCF; better support for Mendelian violation calculations
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2893 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-26 00:29:17 +00:00
246fa28386
RODs for reads phase 2: modified RODRecordList to implement List<ReferenceOrderedDatum> so I could stub it out for testing, added a FlashBackIterator which is needed to prevent the ResourcePool from opening infinity+1 iterators, and some other interfaces to make unit testing much smoother.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2892 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-25 22:48:55 +00:00
3d92e5a737
Initial commit of integration test(s) for CoverageStatistics, currently in progress [midway commit is for Matt]
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Modifications to CoverageStatistics - now includes and extends much of the behavior of DepthOfCoverage (per-base output, per-target output).
Additional functionality (coverage without deletions, base counts, by read group instead of by sample) is upcoming.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2888 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-25 20:25:07 +00:00
553d39bb00
Clean up the code a bit following the introduction of reduceByInterval.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2887 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-25 01:20:22 +00:00
199b43fcf2
Reduce by interval alterations to interface with new sharding system. This checkin with be followed by a
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simplification of some of the locus traversal code.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2886 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-25 00:16:50 +00:00
fef1154fc8
starting on RODs for Reads: made RODRecordList implement list<RODatum> (so we can sub in fake lists during testing), and removed unnecessary generic-ness. Removed BrokenRODSimulator, which isn't being used.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2884 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-24 22:11:53 +00:00
5546aa4416
adding code to deal with the off-spec situation where our minimum likelihood is above the GLF max of 255.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2871 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-22 22:27:39 +00:00
8b555ff17c
Killed the old cleaner code. Bye bye.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2868 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-22 20:49:58 +00:00
3e0e7aad2d
Removing debug statement. oops.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2858 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-19 15:26:22 +00:00
7f19ff1fa1
Added a new option in the recalibrator to be used by people who have SOLiD data in which only a few of the reads have no-calls in the color space. These reads will be skipped over and left in the bam file untouched.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2857 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-19 15:25:23 +00:00
b1a4e6d840
removing non-ascii characters from my Copyright and from VariantEval2Walker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2856 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-18 18:54:36 +00:00
33ae256186
a start to some of the infrastructure for Tribble, including dynamic detection of new RMD; not nearly wired in or complete yet.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2855 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-18 18:43:52 +00:00
79ab7affda
- Change sortOnDisk option to sortInMemory
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- Fix horrible cleaner bug
- Trivial optimizations to cleaner code - more significant ones coming soon.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2850 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-17 20:52:57 +00:00
653f70efa2
added methods to validate an interval before you try to make a GenomeLoc: boolean validGenomeLoc().
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2846 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-16 20:35:35 +00:00
8072e9aed5
should never commit without running intergration tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2838 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-12 23:42:37 +00:00
depristo
aaron
hanna
ebanks
chartl
rpoplin