3dc78855fd
Command-line argument tagging is in, and the ROD system is hacked slightly to support the new syntax
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(-B:name,type file) as well as the old syntax. Also, a bonus feature: BAMs can now be tagged at the
command-line, which should allow us to get rid of some of the hackier calls in GenomeAnalysisEngine.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4105 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-25 03:47:57 +00:00
fa36731faf
fixes for VariantEval integration tests affected by the spaces to underscores change.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4070 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-19 22:43:20 +00:00
340bd0e2c1
Removed hard-coded pointers to references
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3934 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-04 17:59:37 +00:00
2307bed742
VariantEval now uses the "standard" modules only by default. You can add other modules with the -E argument and not use all of the standard ones with -noStandard (they can be added back individually with -E).
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Generalized some of the packaging code from VariantAnnotator. Matt might want to take a look to make this nicer...?
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3925 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-03 16:51:10 +00:00
c6ad26e04f
1) When quals/GQs are really integers (x.00), strip off the floating points.
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2) Keep track of whether vcf records are unfiltered vs. pass filters in the variant context so we can regenerate the records on output.
3) No more "ID" hard-coded all over the code to set the VariantContext ID. Use a static variable instead.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3840 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-20 18:01:45 +00:00
b29eda83bb
Parallelized CountCovarites! percent_ref_called_var now a standard genotype concordance module (for validation!). Really much smarter merging of headers for combineVariants. VCF codecs now actually look at the file version and blow up if they are the wrong versions. setHeaderVersion() in VCFHeaderLine.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3802 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-16 14:10:18 +00:00
460283f6d2
No more manually converting VariantContexts to VCFRecords. You should be utilizing VCs and not VCFRecords.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3787 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-14 05:21:28 +00:00
8ff93f77e6
Added evaluation module to count functional classes (missense, nonsense, etc.). At the moment, it only understands Cancer's MAF annotations. Added integration test for the functional class counting. Added better description for VariantEval.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3595 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-18 21:51:40 +00:00
7a91dbd490
Renamed some of the column names in Ti/Tv and Concordance modules so that they are clearer. Removed ValidationRate module (it was busted).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3564 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-16 15:53:06 +00:00
6d5556939d
updating Tribble with a couple of important Tabix fixes, and updating the variant eval integration tests to run each test with both plain vcf and gzipped tabix (added the tabix version
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to the vlidation directory), using the same md5sum.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3509 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 01:47:04 +00:00
6eeb1693ca
JEXL2 upgrade. Improvements to JEXL processing including dynamically resolving variable -> value bindings instead of up front adding them to a map. Performance improvements and code cleanup throughout.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3494 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-07 00:33:02 +00:00
57f254b13a
VE integration test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3324 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-07 13:58:25 +00:00
5dce16a8f1
Better genotype concordance module. Code refactoring for clarity (please see below/after for educational purposes). Now reports variant sensitivity, concordance, and genotype error rate by default. Also aggregates this data across all samples, so you get a per sample and overall stats for each of these in the allSamples row.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3265 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-28 13:10:11 +00:00
7f4d5d9973
Ti/Tv by AC
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3252 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 17:56:29 +00:00
e7c0ded40e
Fixed long-standing bug in GenotypeConcordance module of VariantEval which caused incorrect numbers to be displayed in the concordance table. The format of the concordance table has changed. Added a concordance summary table which gives overall genotype concordance summary stats by sample. None of the VE integration tests contained genotype information so I added a comp track with genotypes to one of the tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3247 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 15:48:41 +00:00
e9e844fbf5
1. Reverting: dbsnp automatically is a comp
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2. Fixing logic for min Qscore calculation
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3230 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 18:51:35 +00:00
4abd3b0b7b
Fixing known/novel calc now that dbsnp isn't a default comp track
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3223 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 05:43:59 +00:00
3b5673d967
1. Removed -all; by default all modules are used; use -none for no modules.
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2. Don't make dbsnp track be a comp by default (to cut back on output). Please let me know if someone wants this back for some reason.
3. Cleaned up dbsnp module output to print the right numbers.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3220 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 02:46:42 +00:00
7adff5b81a
Renaming for consistency
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3180 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 20:36:19 +00:00
e702bea99f
Moving VE2 to core; calling it "VariantEval" (one more checkin coming)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3179 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 20:25:47 +00:00
ac9dc0b4b4
Removing VariantEval (v1); everyone should be using VE2 now. Docs coming ASAP.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3177 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 19:53:02 +00:00
9f6377f7fb
added a performance test build option (for the upcoming performance test suite), and added a sample performance test for VariantEval.
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IMPORTANT: it was really redundant that we had -Dsingle and -Dsingleintegration to run single unit tests and integration tests, now you can just use -Dsingle to run a single test for performance, unit, and integration tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3136 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-08 15:37:15 +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
be33d1852c
Reverting
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2792 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-05 15:57:09 +00:00
0d8d6e0a14
Ti/Tv module in VariantEval shows known and novel ratios if possible
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2790 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-05 15:37:40 +00:00
9dbdfff786
Moved VariantEval to core. Updated integration test md5s to reflect new Analysis class names.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2762 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-02 00:22:15 +00:00
hanna
aaron
ebanks
depristo
kiran
rpoplin