ecbc38aff0
If no comp rod is specified, specify the dummy name none so that we still get counts.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5211 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-07 19:24:52 +00:00
698096dc5a
Moving VariantsToVCF to the proper directory; removing the oneoffs CG indel converter in preparation for a ligitimate CG variant Feature class in the works.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5207 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-07 05:21:01 +00:00
35c688ac67
Updated md5 for testVCFStreamingChain to reflect latest changes to VariantEval.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5206 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-06 21:22:05 +00:00
1085bbf303
Fixed issue where all comp tracks were being treated as known tracks. Fixed issue where multiple JEXL expressions were causing an exception because the underlying object did not implement the Comparable interface. Fixed issue where variants being compared to the known track were not being checked for equality of variation type. Fixed issue where functional annotations were not being iterated over properly. Refactored a lot of helper methods into a separate VariantEvalUtils utility class. Significantly expanded the test suite using a small VCF with SNPs, indels, and non-variant loci which makes it much easier to see what the proper answer should be, and included the appropriate grep and awk commands in the comments to confirm the values.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5204 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-06 19:19:20 +00:00
9ddc95c833
NewEvaluationContext needs to be generated in the inner loop. Otherwise, multiple comp tracks end up getting routed to the same row of the output table. Added test to cover multiple comp tracks.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5181 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-03 07:04:53 +00:00
cb6454bf98
Multiple eval tracks should be bound with different names, rather than just 'eval'. Added tests to cover usage with multiple tracks.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5177 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-02 22:33:50 +00:00
2732c839d4
Restored parallelism and associated tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5170 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-02 02:04:03 +00:00
fd8dd8fb9b
Fixed an issue where a no-call in the eval track would prevent a site from a comparison track from being loaded. Added a new test to cover the use case.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5169 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-02 01:47:53 +00:00
06b63d8336
Pulled out CpG stratification in test results at Kiran's suggestion.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5165 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 18:36:09 +00:00
91297c138b
Update VCFStreamingIntegrationTest to use new variant eval command-line
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arguments, output format.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5162 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 15:40:43 +00:00
7d89ce820b
Got tired of waiting for Kiran to fix the build: updated NewVariantEval ->
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VariantEval.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5161 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 15:32:39 +00:00
96241c6637
More testng fallout: fixing another seemingly 'random' issue arising from an
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alternate test ordering.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5160 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-01 15:25:50 +00:00
401feca90d
Updates to VariantEval 3.0 integration test.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5140 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 17:45:06 +00:00
d406d9b3fc
There's no reason to special case no-calls if they already have PLs associated with them. Just use the PLs!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5136 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-31 15:05:45 +00:00
04d66a7d0d
Updated integration test's MD5s reflect the fact that assay sequences were previously designed incorrectly for indels, the bug is now fixed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5120 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 23:00:22 +00:00
2182b8c7e2
Better query start / stop function that directly parses the cigar string, unlike the previous version. Now properly handles H (hard-clipped) reads. Added -baq OFF and -baq RECALCULATE integration tests on all three 1KG technologies. Please let me know if this new code somehow fails.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5108 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 15:08:21 +00:00
9cb1ae384c
Constant precision for floating point numbers. Added integration test - carries over tests from VariantEval with the necessary modifications to command-line arguments and md5s. Disabled use of 'synchronized' keyword because I clearly don't get how that keyword is supposed to work yet...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5107 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-28 05:19:18 +00:00
4a33cdacde
Some basic integration tests detecting breakage in OTF BAM index generation.
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Doing it manually for the moment so that there's at least something testing
this capability; will followup eventually with Mark to see whether we can
shape the VCF index generation code in such a way that it supports BAM index
testing as well.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5093 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-26 23:48:04 +00:00
dfc5a3d1f3
added integration test for --sites_only option
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5082 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-26 14:58:15 +00:00
2d4bcb60a1
Don't print out alt alleles for ref calls
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5060 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-23 06:33:31 +00:00
2bbcc9275a
Committing the fragment-based calling code. Results look great in all datasets (will show this at 1000G this week with Ryan). Note that this is an intermediate commit. The code needs to be cleaned up and the fragmentation code needs to be moved up into LocusIteratorByState. This should all happen later this week, but I don't want Ryan to have to keep running from my own personal Sting directory. The current crappy implementation adds ~10% to the runtime, but that should all go away in the next iteration.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5058 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-23 05:04:17 +00:00
aea121a9d5
<key>=<value> tagging support for command-line arguments. Unfortunately, still
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very hard to validate and still very hard to use (requires core hacking to
support additional tags).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5038 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-21 00:22:42 +00:00
8831ec3dce
Some refactoring and cleanup around the area of my sleep-deprived integration
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test typo, which Khalid already fixed for me. Sorry, Khalid!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5035 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-20 15:03:14 +00:00
3022f4dfa0
Fixed missing space character in testSimpleVCFStreaming.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5034 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-20 14:49:38 +00:00
7087c2f422
Very simple integration tests for basic VCF streaming functionality.
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Rather than try to fork the integration test process to get a pipe source
and sink, creates a new named pipe by Runtime.exec()ing the 'mkfifo' shell
command. We'll see whether this proves to be a reliable method for testing
streaming.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5028 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-20 04:38:54 +00:00
ce3d226183
Reverting back to the old definition of QD because it works better with large numbers of samples. The new QD is relegated to a new annotation: sumGLbyD. Tweaks to the new HaplotypeScore based on evaluation with better QD calculation. The default qual threshold in GenerateVariantClusters is updated to be in line with the variant quality scores coming from the exact model.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4984 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 14:12:30 +00:00
23dbc5ccf3
HaplotypeScore is revamped. It now uses reads' Cigar strings when building the haplotype blocks to skip over soft-clipped bases and factor in insertions and deletions. The statistic now uses only the reads from the filtered context to build the haplotypes but it scores all reads against the two best haplotypes. The score is now computed individually for each sample's reads and then averaged together. Bug fixes throughout. The math for the base quality and mapping quality rank sum tests is fixed. The annotations remain as ExperimentalAnnotations pending more investigation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4934 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-05 00:28:05 +00:00
848977678d
No reason to convert the GLs to a String for formatting when they're just going to be converted to PLs later. That was 5% of the UG runtime...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4913 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-29 22:06:19 +00:00
8a0c07b865
Support for indels in hapmap. This was non-trivial because not only does hapmap not tell you whether the allele is an insertion or deletion, but it also has a completely different positioning strategy (rightmost base). I'll send out an email tomorrow when the new HapMap3.3 VCF is ready.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4908 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-27 07:37:46 +00:00
5c0b66cb7c
3 big changes that all kill the integration tests: 1. Don't cap the PLs by 255 anymore. 2. Move over to the 3state model as the only available base model for UG (no more base transition tables). 3. New QD implementation when GLs/PLs are available.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4846 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-15 16:24:28 +00:00
5a27d231fa
Rename it so that nobody else falls into the trap laid out (the test is VariantToTable, the walker is Variant[s]ToTable)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4844 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-15 11:43:00 +00:00
5e27e9162f
Huh? I thought we parsed out comma-separated command line arguments into list automatically...just change the syntax of the integration test, no need to update the md5
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4843 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-15 11:40:27 +00:00
01323447c6
Removed LibBat.SUB2_BSUB_BLOCK since the use of it exits the JVM.
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Fixed integration tests to wait on their own for the job to run instead of using SUB2_BSUB_BLOCK.
Updated VariantRecalibrationIntegrationTests MD5s which were knocked out of sync whele SUB2_BSUB_BLOCK was exiting in the middle of integration tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4840 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-14 19:57:20 +00:00
abd6ce1c77
A TiTv-free approach for cutting variants! Apparently much better than previous approach, and will work for indels and SV will truly minor modifications to the code. Will discuss with methods group on Monday.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4822 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-11 23:08:13 +00:00
f1f01610f8
Remove the extra trailing tab at the end of the VCF ## header line. Unfortunately, this meant updating every freaking integration test.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4806 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-08 17:22:29 +00:00
92cf7744a6
Set minMQ = max(minMQ, minBQ) for phasing since anyway we cap BQ by MQ; also, lowered MIN_BASE_QUALITY_SCORE for phasing to 17 (was previously 20)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4781 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-03 16:31:13 +00:00
e5282742f9
Bug fix in CountCovariates, skip over indel records as well as SNPs in the dbsnp file. CountCovariates is now called CountCovariatesWalker. I've always hated that the name was swapped.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4774 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-02 18:43:24 +00:00
0adf505b53
We no longer look at by-hapmap validation status in the VQSR because using the HapMap VCF file is higher quality. As a side effect we now support the dbsnp 132 vcf file. ApplyVariantCuts now requires that the input VCF rod bindings begin with input, matching the other VQSR walkers. Wiki updated with information about how to obtain the hapmap and 1kg truth sets.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4772 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-02 15:38:45 +00:00
b4ef716aaf
As per Eric and Mark's suggestions, separated the segregating MNP merger (MergeMNPs) from the more general merger employed for annotation purposes (MergeSegregatingAlternateAlleles). Both use the same core MergePhasedSegregatingAlternateAllelesVCFWriter
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4763 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-01 16:42:08 +00:00
af84462f3e
The dev team has decided to change the filter that is added to records that are set to monomorphic by Beagle. It no longer lists the reference allele. Added those filters to the header of the output VCF file. Finally, we no longer use R2=NaN values coming from Beagle.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4757 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-30 17:19:54 +00:00
d89e17ec8c
Fare thee well, UGv1. Here come the days UGv2.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4747 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-29 21:51:19 +00:00
e3e6d176df
Looking over the daily error log email made me realize that there were 2 implementations of vc.modifyLocation() - the correct one in VC that didn't require lazy loading the genotype data and the bad one in VCUtils that did. Removing the implementation in VCUtils and updating the code accordingly. Also, removing createPotentiallyInvalidGenomeLoc() since no one uses it anymore.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4736 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-26 18:40:34 +00:00
6934f83cc7
Two changes to CombineVariants.
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1. Fix: VCs were padded before the merge, but they were never unpadded afterwards. This leaves us with a VC that doesn't meet our spec.
2. Update: instead of running the merged VC through every standard annotation (which seems really wrong, since this isn't the annotator tool), just update the chromosome count annotations (AC,AF,AN) through VCUtils.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4734 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-25 04:52:12 +00:00
ed08899abc
Overwhelming evidence that maxQ = 50 is now a better default than maxQ = 40 in the base quality score recalibrator, especially when combined with dbsnp build 132. Also, added option in ProduceBeagleInputWalker for Beagle-ing chromosome X calls with male samples which sets the genotype likelihood for the AB allele to zero for those samples.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4731 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-24 21:32:26 +00:00
721e8cb679
VariantsToTable now supports wildcard captures. -F PREFIX* now captures all fields that begin with PREFIX, output as a comma-separated list of unique values. Added integration test for VariantsToTable since I find it so useful.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4706 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-18 18:54:59 +00:00
01b721ab61
Passing ReviewedStingExceptions through the HMS.
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Added a @Hidden experimental argument -validate to VariantEval that allows external JEXL assertions that must evaluate to true will throw an exception.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4692 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-16 21:50:42 +00:00
24ec35deaf
- Reintroduce test dependency so that the tests passing / failing is not
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dependent on the contents of the integrationtest directory. Will figure
out how to better manage the integrationtest directory at some point in
the future.
- Up the max heap size for tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4691 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-16 19:55:20 +00:00
ef2f6d90d2
VQSR now operates on LOD scores in the INFO field directly, and doesn't adjust the QUAL field. New format for tranches file uses LOD score. Old file format no longer supported. log10sumlog10() function, a very useful utility in MathUtils. No more ExtendedPileupElement! Robust math calculations in GMM so that no infinities are generated! HaplotypeScore refactored to enable use of filtered context. Not yet enabled... InferredContext getDouble and getInteger arguments now parse values from Strings if necessary
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4684 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 22:19:22 +00:00
2fd816ac5f
Updated ordering of integration tests. GVC > VR > AVC
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4669 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-14 06:33:28 +00:00
44d0cb6cde
New version of cutting routines for VQSR. Old code removed. Working unit tests. Best practice with testng integration test (everyone look at it). Walker test now allows you to not specify no. input files, if it can infer input counts from MD5s
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4664 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-13 16:19:56 +00:00
kiran
ebanks
hanna
asivache
depristo
kshakir
rpoplin
chartl
fromer