80f32712dc
Tiny bug fix
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4793 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-05 18:48:33 +00:00
44feb4a362
Improved BAQ implementation. Now supports adding BAQ tags to reads on the fly with ADD_TAG_ONLY option. Caching fasta reader implementation, and changes throughout the system to enable this. Many performance improvements throughout the system due to better reference access patterns.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4792 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-05 18:29:39 +00:00
8901e63879
Cheap optimization: don't keep calculating the log of a constant. (How did I not catch this before?)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4791 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-05 04:36:21 +00:00
bef48e7a42
For Chris, to make his life easier: iterate over all VCF records passed in looking for one with an ALT allele defined instead of assuming all records have one.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4789 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-05 02:23:38 +00:00
97c94176c0
Immediate, obvious bug fix to avoid blowing up on unmapped reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4788 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-04 20:43:39 +00:00
a5b3aac864
Engine-level BAQ calculation now available in the GATK [totally experimental right now]. -baq argument to disable (NONE), to only use the tags in the BAM (USE_TAG_ONLY), use the tag when present but calculate on the fly as necessary (CALCULATE_AS_NECESSARY), and to always recalculate (RECALCULATE_ALWAYS). BAQ.java contains the complete implementation, for those interested. ValidateBAQWalker is a useful QC tool for verifying the BAQ is correct. BAQSamIterator applies BAQ to reads, as needed, in the engine. Let me know if you encounter any problems. Before prime-time, needs a caching implementation of IndexedFastaReader to avoid loading *lots* of reference data all of the time
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4787 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-04 20:23:06 +00:00
b12cec4302
Added emitOnlyMNPs flag
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4785 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-03 20:34:17 +00:00
6d4ec7f9e7
Remove RefSeq INFO from MNPs since annotating them properly
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4784 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-03 19:03:35 +00:00
4719bbc772
Changed dontRequireSomeSampleHasDoubleAltAllele parameter to mean that merging should only start at a polymorphic site
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4783 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-03 17:52:56 +00:00
ec174dc0ba
As per Menachem's last commit, there's a minimally more efficient way of doing the MQ cap.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4782 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-03 16:37:08 +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
237ab1d489
1. As discussed in group meeting today, because we cap BQ by MQ, if MQ < minBQ then we filter the read.
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2. Update to UGCalcLikelihoods for Chris: require a vcf bound to 'allele' to be provided so that we know exactly which alternate allele we should be calculating GLs for at each site. The user is warned when the VC is not biallelic or there are multiple records at a site.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4780 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-03 05:57:06 +00:00
da6a07ad3b
First round of critical fixes to indel genotyper (more to come tomorrow):
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a) Avoid complete crash of caller that broke due to a recent refactoring by someone who must not be named <cough>EB<cough>... an integration test to avoid this in the future coming soon.
b) Fixed up strand bias computation for indels
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4779 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-03 02:48:09 +00:00
e09d6ee56b
write non-MNP VariantContexts records only once (where they start)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4777 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-02 22:14:26 +00:00
1515bf6de9
Merged common VCF writing logic into phasing/WriteVCF.java
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4776 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-02 22:03:02 +00:00
4e62de4213
Added method getOriginalReadGroupId(): takes merged (in case of collision) read group id as reported by a read coming from the merged stream and returns this read's read group id as it was listed in the original input bam file.
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IndelRealigner now uses this functionality to correctly un-mangle read group id's in --nWayOut mode (i.e. when we need to write reads into separate output bams with headers matching the original inputs).
Some hidden changes to IndelRealigner: purely testing and development, transparent to the users (hidden option added)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4775 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-02 21:41:52 +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
99b942b0b4
Removing duplicated header args
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4770 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-01 20:16:53 +00:00
9ac0f98d0d
Fixed bug in retaining proper RefSeq records
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4768 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-01 18:39:02 +00:00
7caf666f48
For Sendu: add a hidden option to allow bams to come out unsorted. We've agreed to let him deal with sorting these puppies on his own.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4767 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-01 17:56:13 +00:00
3afa841a6a
Fixing docs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4766 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-01 17:36:47 +00:00
6a6cdc1925
Adding minor usage docs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4765 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-01 17:34:33 +00:00
0d1c905df3
Adding UGCalcLikelihoods and UGCallVariants so that GSA members can break up the calling process into separate steps (calculate the GLs and then call off of those) - useful for Chris's new batch merger. As the docs say, these are absolutely not supported or recommended for public use.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4764 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-01 17:32:26 +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
0892daddb0
Improvement for the TGEN folks: when running in the solid recal mode of SET_Q_ZERO_BASE_N, update the NM tag if one was present in the read to reflect the new N's in the read.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4761 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-01 04:36:44 +00:00
a22b1b04e6
SW-turbo. Kind of. This implementation is presumably equivalent to the old one (mathematically), but runs ~10 times faster: inner loops eliminated completely. The author of the original implementation should be sentenced to the galleys. Oh, that would be me...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4760 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-01 00:08:47 +00:00
2ac938fe4e
1)
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Minor fixes to avoid crashes vs CG indel files:
- Add count for complex events, not just insertions and deletions
- Handle correctly cases of large indels falling out of bounds of histogram array: added a count of indels ouf of bounds and avoid exceptions.
2) Cosmetic fix for R script assessing UG calling performance: draw red y=x line on top of Simulated vs Estimated AC to get a better view of under/over-estimation of AC.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4758 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-30 21:08:25 +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
21256909bb
Not supported. I'm checking this in for Ryan only.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4756 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-30 16:59:18 +00:00
e21a66d876
Updated the Queue GATK generator and packaging to include more dependencies for fullCallingPipeline.q.
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Set the -bigMemQueue in the FullCallingPipelineTest to GSA to avoid waiting for the week queue when it is busy.
Fixed the package definition of PipelineTest so that scalac won't recompile it every time.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4755 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-30 15:29:40 +00:00
7f2ded0706
belated special case fix for Menachem; if the results of a BTI and BTIMR produce an empty interval list, exception out. This would be solved long term with better handling or empty and / or null interval lists. I'll add a JIRA
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4754 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-30 05:49:20 +00:00
a181680814
We no longer require dbSNP files to be of the dbsnp rod-type; VCFs will do (provided they are bound to the name 'dbsnp')
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4753 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-30 03:25:18 +00:00
8ffea42b75
about 10% improvement in SW alignment (and hence IndelRealigner!) speed by using c-style linearized array representation for matrices instead of java 2D arrays...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4751 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-30 00:06:50 +00:00
b03ac61e9d
consolidating the checking of the RMD sequence dictionary against the reference into a single function, and adding an integration test to test that empty VCFs pass (both the indexing and the seq dictionary validation).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4750 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-30 00:01:56 +00:00
abc13d0a90
Temporary hack: force abort with an intelligent message suggesting that users
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specify -B:dbsnp,vcf <filename> if the filename passed if the --DBSNP argument
value contains 'vcf'. We'll replace this functionality once dbSNP 132 starts
playing nicely with the tagging system.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4749 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-29 23:37:30 +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
727dac7b7a
Added MNP annotation of the number of AA changes occuring in the SAME RefSeq entry (numAAchanges), and if this number is > 1 for any of the alt alleles (alleleHasMultAAchanges)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4746 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-29 21:24:30 +00:00
222cd42ceb
Have the UG engine take care of the GL to PL conversion. Note that we still use GLs for calling (since we are losing precision in high-pass and, even worse, it can affect QD), but we emit PLs in all cases. This means that calculating the GLs, emitting them to VCF, and then calling off of them (a la samtools) is absolutely, positively not ideal.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4745 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-29 20:28:16 +00:00
102c8b1f59
Large refactoring of the UGv2 engine so that it is now truly separated into 2 distict phases: GL calculation and AF calculation, where each can be done independently. This is not yet enabled in UGv2 itself though because I need to work out one last issue or two. Tested on 1Mb of 1000G Aug allPops low-pass and results are identical as before. Also, making BQ capping by MQ mandatory.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4744 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-28 21:36:33 +00:00
ce051e4e9a
Write to sdout when no -o is provided
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4743 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-28 06:19:26 +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
35b90d2295
Don't compute SB for ref calls
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4735 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-26 03:54:26 +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
d775192631
Check if MNP annotation of amino acid is dependent on the MNP, or could it be obtained through some single-base variant?
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4733 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-24 22:38:33 +00:00
0dd40c3684
Updating doc text
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4732 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-24 21:34:14 +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
ca70ed611c
Totally revamped the MNP annotation and put it in its own walker: AnnotateMNPsWalker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4730 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-24 18:05:10 +00:00
8768e1a240
Useful profiling tool that reads in a single rod and evalutes the time it takes to read the file by byte, by line, into pieces, just the sites of the vcf, and finally the full vcf. Emits a useful table for plotting with the associated R script that can be run like Rscript R/analyzeRodProfile.R table.txt table.pdf titleString
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4728 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-24 14:59:16 +00:00
7a8b85dd15
Catch the JEXL exception when trying to match a variable that's not in the context - and don't filter in these cases. Now everyone can happily go back to using the stupid (and hopefully temporary) AlleleBalance filter.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4727 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-24 05:00:41 +00:00
caf2c21f61
Must close the writer to flush the cache
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4726 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-24 04:33:08 +00:00
816c33c821
indel-related fixes to the strict validator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4725 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-24 04:08:34 +00:00
9cdc341be5
Trivial update for data processing paper: change syntax of output argument for Beagle by depth walker to update to new GATK format.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4724 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-24 01:45:44 +00:00
ea6e2218c1
1. dbsnp has some massive indels which my left-aligner was barfing on because there isn't enough reference context; fixed. 2. Lower default calling threshold to Q30 for UGv2.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4722 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-23 19:28:33 +00:00
53672361cc
capture more details when something IO-related goes wrong in writing a Tribble index
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4720 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-23 17:06:28 +00:00
082073ca3c
Stop RBP.getPileupBySample() from throwing a NullPointerException if the
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sample doesn't exist -- now returns null.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4719 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-23 05:17:06 +00:00
787e5d85e9
Added the ability to test pipelines in dry or live mode via 'ant pipelinetest' and 'ant pipelinetest -Dpipeline.run=run'.
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Added an initial test for genotyping chr20 on ten 1000G bams.
Since tribble needs logging support too, for now setting the logging level and appending the console logger to the root logger, not just to "org.broadinstitute.sting".
Updated IntervalUtilsUnitTest to output to a temp directory and not the SVN controlled testdata directory.
Added refseq tables and dbsnps to validation data in BaseTest.
Now waiting up to two minutes for gather parts to propagate over NFS before attempting to merge the files.
Setting scatter/gather directories relative to the -run directory instead of the current directory that queue is running.
Fixed a bug where escaping test expressions didn't handle delimiters at the beginning or end of the String.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4717 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-22 22:59:42 +00:00
8ca5edf89f
Fix issue where non-required file inputs can throw a NullPointerException
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rather than a UserException when an the input argument is specified without
an argument value.
The magnitude of code required to fix this points to a need to give the
command-line argument system a good spring cleaning.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4714 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-22 01:49:17 +00:00
b9a59ea54f
Adding Het/Hom ratio to the temp per sample metrics. Because I'm in a generous mood tonight, I'm going ahead and fixing the paths for the classes I'm touching...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4713 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-21 04:24:42 +00:00
cff7c6ddce
These are user exceptions
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4712 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-21 02:08:11 +00:00
374c0deba2
Updating the core LocusWalker tools to include the Sample infrastructure that I added last month. This commit touches a lot of files, but only significantly changes a few: LocusIteratorByState and ReadBackedPileup and associated classes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4711 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-19 19:59:05 +00:00
c723db1f4b
Added a -summary jexl argument to VariantEval similar to -validate.
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Updated the package of ValidationGenotyper to match the file location.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4710 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-19 04:42:46 +00:00
79725f2d9c
Excluding the QFunction log files from the set of files to delete on completion.
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When a QGraph is empty displaying a warning instead of crashing with an JGraph internal assertion error.
Cleaned up code using the Log4J root logger and explicitly talking to a logger for Sting.
When integration tests are run detecting that the logger has already been setup so that messages aren't logged twice.
Updated from Ivy 2.2.0-rc1 to 2.2.0.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4707 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-18 20:22:01 +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
8cba86a69d
Trivial code organization for the haplotype score
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4703 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-18 12:32:55 +00:00
9f356b6cd0
Package all walkers in org/broadinstitute/sting/gatk/walkers directory in release.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4702 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-18 02:33:45 +00:00
90711d445c
Change the interface for RMDTrackBuilder, therefore always mandating the specification
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of a sequence dictionary and related info. This will hopefully eliminate the cases in
which the refseq track depends a sequence dictionary / contig parser that hasn't been
specified.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4700 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-17 19:00:17 +00:00
367cc9135f
Use VariantContext and Genotype accessor methods for attributes that will return null for unparseable data
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4699 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-17 18:19:56 +00:00
2f3578182a
Added VERY preliminary version for merging refseq annotations as SNPs are merged
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4698 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-17 16:49:12 +00:00
e2f7f33ce7
Added getIntegerAttribute()
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4697 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-17 16:33:07 +00:00
d86ab2becb
JEXL expressions now generate exceptions, not warnings. Tools should catch the runtime exception to handle correctly. Removed unncessary complexity from the JEXL contexts
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4695 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-17 16:08:16 +00:00
539651de30
Initial version of Indel Statistics module for Variant Eval - not for general use yet, needs more verification and more work. Older IndelHistogram module will be obsolete with this new walker. Right now, for each sample (and for all samples), the following are computed:
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- Number of insertions
- Number of deletions
- Length distribution for indels.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4694 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-17 15:52:01 +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
62f02bf30a
Minor JAVA visibility updates
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4690 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-16 15:28:58 +00:00
f1b0f3bc49
Putting my changes from earlier in the day back in after someone (rhymes with 'Dark') trounced on them with his last commit...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4687 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-16 01:55:50 +00:00
8ff4e4cb25
Cleanup testng listener configuration.
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- Add StingTextReporter, which provides a text dump of the errors to the
console. Had to create our own reporter (inheriting from the standard
TestNG TextReporter) to work around a configuration issue with the
TextReporter. In an ideal world, I'd report this on the TestNG mailing
list and help them resolve the issue, but this solution is relatively
robust at the moment and life is too short.
- Added back the failed test listener, which generates the testng-failed.xml
file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4686 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 23:43:14 +00:00
b677080858
Initial checkin of the ValidationGenotyper. Not intended to be used by anybody yet. Only here for archival purposes at this point.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4685 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 22:33:49 +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
5b83942cee
- Fix DepthOfCoverage so that, when it abuses the ROD system by instantiating a track in onTraversalDone, it also supplies the correct sequence dictionary and parser.
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- Changed RMDTrackBuilder to use SequenceDictionaryUtils.validateDictionaries for ref <-> ROD sequence dictionary validation.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4683 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 20:34:04 +00:00
2af508ef83
Better docs, as requested by Matt
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4681 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 18:24:15 +00:00
62be55376b
no longer useful
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4677 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 17:53:33 +00:00
35382468ee
Better error checking/output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4676 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 16:36:34 +00:00
7a3a464959
Finally, the logic is right
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4674 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 14:02:09 +00:00
8d66637fc2
Bug fix for VariantsToTable with filtered records
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4673 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 13:49:16 +00:00
d76b87d6e3
Useful debug file output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4672 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 13:36:52 +00:00
28142408ff
Refactoring so that all counting in UGv2 is done on the filtered context. In particular, tests for empty pileups and too many spanning deletions now use the correct counts. Also, -all_bases mode now trumps all; this one is for you, chartl.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4671 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 05:01:12 +00:00
c7229abbf7
Get rid of 'meaningless and random values' that prevent Sendu from merging PG lines. I have to admit that he did have a good point there.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4670 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 03:35:12 +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
cb1e8ad43a
Temp bug fix for indel genotyper: if there are two or more variant contexts at a site, just choose the first one containing an indel and genotype that. There might be cases where IGv2 emits 2 indel variant contexts in at the same ref location which made us fail there. A better solution will be to form underlying haplotypes supported by reads and compute likelihoods of that.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4667 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-14 00:21:54 +00:00
82f9327b5e
Throw the right exception
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4666 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-13 22:18:42 +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
62a106ca5a
Disabled VariantGaussianMixtureModelUnitTest
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4663 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-13 03:53:33 +00:00
673fa841a4
Updated PluginManager so that during testing Queue can dynamically compile and load separately multiple class directories into the same class loader.
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Removed obsolete usages of PackageUtils with updated PluginManager.
Ported Queue interval utilities written in scala over to Sting's java IntervalUtils.
Added a very basic intergration test to ensure that the fullCallingPipeline.q compiles.
Added options to specify the temporary directories without having to use -Djava.io.tmpdir (useful during the above integration test).
While adding tempDir added options to specify the run directory from the command line, for example "-runDir v1".
Upgraded to scala 2.8.1 and updated calls to deprecated functions.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4661 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-12 20:14:28 +00:00
42acc968b1
Unit tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4660 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-12 20:09:39 +00:00
b51762c279
When you commit code late at night you tend to make careless mistakes... like forgetting to update integration tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4658 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-12 14:41:10 +00:00
988da428ae
Bug fix for old style tranches file. ApplyVariantCuts moved over, and passes integration tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4657 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-12 14:38:26 +00:00
c5f8c4dd0d
VariantEval test for tranches file, plus cutting over VE to use the generic Tranches framework
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4656 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-12 13:52:40 +00:00
69de3e51bf
Better precision for the calculated AF value. Now looks at the total number of samples to determine how much precision is necessary. Also, changing default min BQ used for calling in UGv2 to Q17.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4655 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-12 08:31:40 +00:00
ec83a4b765
Initial commit, without any tool changes, of a new infrastructure for determining tranches. This new version walker up from the lowest quality snps and determines Ti/Tv. This is marginally more stable than moving in the other direction when there are few novel variants (exomes). Can make a substantial difference in the size of the call set (10-20%). I'll hook it into the main system now. Includes an new class Tranche, isolated read/writing utilities that are now testing in TestVariantRecalibrator, which should be moved to UnitTest as soon as I can figure out how to do this on my mac.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4654 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-11 23:52:49 +00:00
depristo
ebanks
fromer
delangel
asivache
rpoplin
kshakir
aaron
hanna
bthomas