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Author SHA1 Message Date
ebanks 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. 
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
ebanks 3afa841a6a Fixing docs 
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
ebanks 6a6cdc1925 Adding minor usage docs 
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
ebanks 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. 
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
fromer 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 
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
ebanks 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. 
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
asivache 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... 
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
delangel 2ac938fe4e 1) 
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
rpoplin 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. 
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
ebanks 21256909bb Not supported. I'm checking this in for Ryan only. 
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
kshakir e21a66d876 Updated the Queue GATK generator and packaging to include more dependencies for fullCallingPipeline.q. 
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
aaron 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 
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
ebanks 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') 
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
asivache 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... 
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
aaron 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). 
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
hanna abc13d0a90 Temporary hack: force abort with an intelligent message suggesting that users 
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
ebanks d89e17ec8c Fare thee well, UGv1. Here come the days UGv2. 
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
fromer 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) 
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
ebanks 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. 
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
ebanks 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. 
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
ebanks ce051e4e9a Write to sdout when no -o is provided 
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
ebanks 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. 
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
ebanks 35b90d2295 Don't compute SB for ref calls 
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
ebanks 6934f83cc7 Two changes to CombineVariants. 
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
fromer d775192631 Check if MNP annotation of amino acid is dependent on the MNP, or could it be obtained through some single-base variant? 
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
rpoplin 0dd40c3684 Updating doc text 
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
rpoplin 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. 
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
fromer ca70ed611c Totally revamped the MNP annotation and put it in its own walker: AnnotateMNPsWalker 
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
depristo 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 
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
ebanks 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. 
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
ebanks caf2c21f61 Must close the writer to flush the cache 
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
ebanks 816c33c821 indel-related fixes to the strict validator 
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
delangel 9cdc341be5 Trivial update for data processing paper: change syntax of output argument for Beagle by depth walker to update to new GATK format. 
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
ebanks 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. 
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
aaron 53672361cc capture more details when something IO-related goes wrong in writing a Tribble index 
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
hanna 082073ca3c Stop RBP.getPileupBySample() from throwing a NullPointerException if the 
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
kshakir 787e5d85e9 Added the ability to test pipelines in dry or live mode via 'ant pipelinetest' and 'ant pipelinetest -Dpipeline.run=run'. 
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
hanna 8ca5edf89f Fix issue where non-required file inputs can throw a NullPointerException 
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
ebanks 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... 
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
ebanks cff7c6ddce These are user exceptions 
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
bthomas 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. 
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
kshakir c723db1f4b Added a -summary jexl argument to VariantEval similar to -validate. 
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
kshakir 79725f2d9c Excluding the QFunction log files from the set of files to delete on completion. 
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
depristo 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. 
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
depristo 8cba86a69d Trivial code organization for the haplotype score 
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
hanna 9f356b6cd0 Package all walkers in org/broadinstitute/sting/gatk/walkers directory in release. 
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
hanna 90711d445c Change the interface for RMDTrackBuilder, therefore always mandating the specification 
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
fromer 367cc9135f Use VariantContext and Genotype accessor methods for attributes that will return null for unparseable data 
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
fromer 2f3578182a Added VERY preliminary version for merging refseq annotations as SNPs are merged 
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
fromer e2f7f33ce7 Added getIntegerAttribute() 
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
depristo d86ab2becb JEXL expressions now generate exceptions, not warnings. Tools should catch the runtime exception to handle correctly. Removed unncessary complexity from the JEXL contexts 
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
delangel 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: 
- 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
kshakir 01b721ab61 Passing ReviewedStingExceptions through the HMS. 
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
hanna 24ec35deaf - Reintroduce test dependency so that the tests passing / failing is not 
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
fromer 62f02bf30a Minor JAVA visibility updates 
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
ebanks f1b0f3bc49 Putting my changes from earlier in the day back in after someone (rhymes with 'Dark') trounced on them with his last commit... 
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
hanna 8ff4e4cb25 Cleanup testng listener configuration. 
- 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
rpoplin b677080858 Initial checkin of the ValidationGenotyper. Not intended to be used by anybody yet. Only here for archival purposes at this point. 
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
depristo 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 
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
hanna 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. 
- 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
ebanks 2af508ef83 Better docs, as requested by Matt 
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
depristo 62be55376b no longer useful 
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
ebanks 35382468ee Better error checking/output 
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
depristo 7a3a464959 Finally, the logic is right 
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
depristo 8d66637fc2 Bug fix for VariantsToTable with filtered records 
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
depristo d76b87d6e3 Useful debug file output 
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
ebanks 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. 
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
ebanks 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. 
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
kshakir 2fd816ac5f Updated ordering of integration tests. GVC > VR > AVC 
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
delangel 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. 
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
depristo 82f9327b5e Throw the right exception 
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 2010-11-13 22:18:42 +00:00
depristo 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 
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
kshakir 62a106ca5a Disabled VariantGaussianMixtureModelUnitTest 
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
kshakir 673fa841a4 Updated PluginManager so that during testing Queue can dynamically compile and load separately multiple class directories into the same class loader. 
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
depristo 42acc968b1 Unit tests 
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
ebanks b51762c279 When you commit code late at night you tend to make careless mistakes... like forgetting to update integration tests. 
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
depristo 988da428ae Bug fix for old style tranches file. ApplyVariantCuts moved over, and passes integration tests 
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
depristo c5f8c4dd0d VariantEval test for tranches file, plus cutting over VE to use the generic Tranches framework 
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
ebanks 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. 
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
depristo 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. 
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 ed6396ed43 No longer getting the inet, it seems to potentially hang the JVM 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4653 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-11 23:49:42 +00:00
ebanks 2f6666a988 Correcting traversal statistics 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4652 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-11 22:46:58 +00:00
depristo dbde721dd0 Bug fix for filtered records 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4651 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-11 18:54:51 +00:00
aaron 698e5cf345 for GATK style codecs, make sure we fill in their GenomeLocParser from the RMDIndexer 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4650 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-11 18:44:15 +00:00
delangel 2f3be24a00 Improvement in exact allele frequency calculation model (still under test, but this is definitely better than what I had before). Instead of approximating log(10^x+10^y) as max(x,y), approximate full Jacobian formula max(x,y)+log(1+10^-abs(x-y)) with static lookup table for the second term. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4647 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-11 01:22:35 +00:00
asivache 2e0296fef9 NWayOut logic slightly changed: 1) results.list file is gone; 2) now with -nWayOut one can specify either a) suffix to attach to every output file (i.e. cleaned reads from inputK.bam will be sent to inputK.suffix.bam) or b) *.map tab-separated file that must list <input_name> <output_name> mappings, one per line, for every input file. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4645 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-10 20:32:16 +00:00
asivache a1adfb91ce And now @Hidden tags are really in place :-/ 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4644 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-10 20:28:40 +00:00
asivache 68ce55148e (pseudo-)genotyping functionality added: force-emits calls (including REF) at specified locations. Currently @Hidden for testing. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4643 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-10 20:25:40 +00:00
hanna 8e36a07bea Convert GenomeLocParser into an instance variable. This change is required 
for anything that needs to be simultaneously aware of multiple references, eg
Queue's interval sharding code, liftover support, distributed GATK etc.  

GenomeLocParser instances must now be used to create/parse GenomeLocs.
GenomeLocParser instances are available in walkers by calling either

-getToolkit().getGenomeLocParser()
or
-refContext.getGenomeLocParser()

This is an intermediate change; GenomeLocParser will eventually be merged
with the reference, but we're not clear exactly how to do that yet.  This
will become clearer when contig aliasing is implemented.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4642 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-10 17:59:50 +00:00
depristo 5ef4b234d8 Updates for broken integration tests. Counting annotations (AC, AF) now work correctly for AC = 0 sites 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4640 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-09 19:43:43 +00:00
depristo 4759fdd2ac V1 of read and variant simulator and assessor. SimulateReadsForVariants generates BAM and VCF with given combinations of variant and read properties. AssessSimulatedPerformance produces a table suitable for analysis in R 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4637 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-08 21:01:33 +00:00
aaron 97db593efb making my last commit message actually true 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4636 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-07 18:26:23 +00:00
aaron be499fc986 making the reference optional (the GATK will set it on the first run if it's not included), and setting the seq index if they do supply it. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4635 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-07 18:15:31 +00:00
ebanks e05af54f3e Found the cause of 80% of our non-called FNs: an excess of filtered bases were causing us to choose the wrong alternate allele. More details to dev team. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4634 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-07 03:39:57 +00:00
aaron 2a8c97a4a7 better error catching, as well as allowing for default index naming, <filename>.idx 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4633 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-06 19:12:19 +00:00
aaron cb2e26a004 by request, an indexer tool to create Tribble style indexes outside of the GATK 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4632 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-06 18:59:06 +00:00
depristo bbb890dd6c Bug fix for variants in VCF header fetching to avoid null pointer when a VariantContext tribble codec doesn't have a header 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4630 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-05 12:43:25 +00:00
ebanks c9dbd8f80a Bug fix for Tim: all point events must be treated equally 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4629 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-05 03:42:51 +00:00
rpoplin 913db5d1ab Unfortunately when annotating sites with the UG the -G None option was wiping out the single annotations added by -A options 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4625 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-04 19:27:23 +00:00
ebanks 816c86776e Walker description was wrong and it was bothering me 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4624 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-04 02:17:09 +00:00
ebanks 87f6738d4c Deprecated 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4623 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-04 02:07:40 +00:00
chartl 42e9987e69 Bug fix to GenotypeConcordance. AC metrics get instantiated based on number of eval samples; if Comp has more samples, we can see AC indeces outside the bounds of the array. 
Bug fix to LiftoverVariants - no barfing at reference sites.

AlleleFrequencyComparison - local changes added to make sure parsing works properly

Added HammingDistance annotation. Mostly useless. But only mostly.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4622 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-03 19:23:03 +00:00
fromer 3d27defe93 Fixed output stats (percentage denominator) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4621 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-03 18:47:06 +00:00
ebanks 4e109f58bf In preparation for Ryan's jumping into SLOD: getting rid of bad hack to ensure P(AF=i) is calculated in the strand-specific cases. With Mark's recent changes this is no longer necessary and just makes the code slower. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4620 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-03 03:44:59 +00:00
fromer 22d64f77ff Added hidden --outputMultipleBaseCountsFile option to detect cases where a single read has more than one base at the same position 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4619 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-03 03:22:48 +00:00
hanna 8f9bf82aa7 Bamboo is correctly interpreting test fails. Reverting forced-fail test 
code.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4617 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-02 19:32:34 +00:00
hanna 1df166b76e Forcing a unit test fail to ensure that Bamboo is picking up on failed tests 
as well as successes.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4616 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-02 19:03:12 +00:00
fromer a885ecf046 When merging MNPs, the phased flag and the phase quality (PQ) are determined simultaneously 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4613 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-02 14:44:26 +00:00
hanna 861ee3e37a Changing testing framework from junit -> testng, for its enhanced configurability. 
Initial test to see how Bamboo will respond.  More detailed email to follow.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4609 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-01 21:31:44 +00:00
asivache fe3f78e1d3 make it full (absolute) path for the file names recorded in results.list 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4608 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-01 20:53:51 +00:00
asivache 2ac5e55130 typo 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4607 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-01 20:38:02 +00:00
asivache 0e6dd38936 In n-way-out mode, added printing names of all the output files into 'results.list' file 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4606 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-01 20:37:38 +00:00
fromer 64599d1074 Added debugging message 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4605 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-01 19:51:42 +00:00
fromer 639ecdc931 Noted in comment that using a single sample in MergePhasedSegregatingAlternateAllelesVCFWriter does NOT update any of the INFO fields, though this could be changed in the future... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4604 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-01 19:02:52 +00:00
fromer 8439f0aa61 Check for VCFConstants.MISSING_VALUE_v4 when retrieving INFO fields and consider such values as non-existent 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4603 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-01 17:51:35 +00:00
asivache aadd230636 N-Way-Out is back. Now uses SAMReadID to identify each read's source bam, so should be reliable. Interface is sort of ugly fo now: to generate output file names, .bam is stripped from input file names, then the value of -nWayOut argument is pasted on (and all the output files are written into the current dir). 
Unrelated change: in the sorted-target mode (when we read sorted target intervals one by on from a file), one can now specify multiple semicolon-separated interval files (all must be sorted). Not hugely useful probably, but makes --targetIntervals always process its values in exactly the same way, so we are consistent  (it has been already taking ;-separated args in unsorted mode)

NwayIntervalMergingIterator: reads in multiple sorted GenomeLoc input streams (iterators) and presents them as a single sorted and merged stream

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4602 348d0f76-0448-11de-a6fe-93d51630548a
 2010-11-01 16:06:51 +00:00
depristo 23cb399a88 Reasonable first pass at a correct SB calculation. Simple utilities to support it. VariantsToTable no longer prints filtered sites by default. New non-standard variant eval module to print comp sites not present in eval (FN finder) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4601 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-31 12:41:52 +00:00
delangel 30fae5cf18 Major redo of exact AF computation for UnifiedGenotyperV2. Fact of life is, there's no way we can compute an exact QUAL field and keep performing the AF computation in linear probability space. In good sites with lots of samples, the ratio of Pr(AC=K*|D) to Pr(AC=0|D) can be 10^1500 or some ridiculous large number like that, which no double can represent. So, we abandon probablity space and work now in log likelihood space, which has several major repercussions: 
a) Sites were numerically well behaved now, but another hard fact of life is that the AF iteration is defined in linear Pr space, not in log likelihood space, and the math doesn't work out in log space. So, we need to convert back and forth from lin to log space.
b) As a consequence of a), the code got a major slowdown, and calling the 629 samples was about 15 times slower than before (sic).
c) To solve b), log10 of integers are now cached at init, and numerical approximations are now made. Most importantly, I'm using the approximation that log(exp(a) + exp(b)) ~= max(a,b) which seems almost inconsequential in practical performance but reduces computation time to what it was before. More detailes analyses are forthcoming. This approximation can be refined further on to avoid expensive log-exp conversions if further profiling and analysis deems it necessary.

Also, two other issues were solved:
a) Strand bias computation was actually wrong in the case where the optimal AC was bigger than max(forward reads,reverse reads). Now the code is exactly as buggy as the grid search model (all bugs are equal, but some are more equal than others)
b) Genotype likelihoods are now computed in a better way and if a likelihood < 0 we don't just cap to 0 but do something a bit smarter.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4600 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-31 01:26:04 +00:00
hanna d492621122 The TraversalEngine's habit of hanging onto old ROD states seems to have a bad 
interaction with Tribble.  In Tribble, keeping these references in memory until
the shard is flushed means keeping one 512K character buffer per object in
memory.  Fixed by purging the reference to the object at the end of the 
shard traversal.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4599 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-29 17:09:58 +00:00
ebanks 1c056ea791 Users can now use VariantAnnotator to add annotations from one VCF to another. For example, if you want to annotate your target VCF with the AC field value from the rod bound to CEU1kg, you can specify -E CEU1kg.AC and records will be annotated with CEU1kg.AC=N when a record exists in that rod at the given position. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4598 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-29 16:38:31 +00:00
ebanks 1b3fc8ddd2 Doing things too quickly is also naughty. Thanks, Andrey. Now, we're even. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4597 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-29 14:50:04 +00:00
ebanks 58f7b4c595 Naughty use of assertions means that malformed records are not caught. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4596 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-29 14:41:38 +00:00
delangel 9a60e72364 Trivial change to LeftAlignVariants: make walker return number of aligned variants on map(), and print out the # of aligned variants at the end of the traversal. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4595 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-29 02:03:36 +00:00
hanna 2f8057bf24 Cleanup for multithreading memory leak during integration tests...unregister MXBean at end 
of traversal to avoid holding a reference to the microscheduler, which holds a reference to
the engine, which in turn holds a reference to the walker, which itself holds a reference to
all the data aggregated during the course of the traversal.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4594 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-28 18:37:42 +00:00
depristo 860de05a7c Bug fix for PL vs. GL in header. PL now truly default output for UGv2 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4592 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-28 12:39:18 +00:00
depristo 9782dde3dd Bug fix for PL vs. GL in header. PL now truly default output for UGv2 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4591 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-28 12:38:48 +00:00
ebanks fe3cfb067c very minor cleanup 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4590 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-28 02:11:33 +00:00
depristo cbce3e3c83 General support for both GL (log10) and PL (phred-scaled) genotype likelihoods. All walkers now use the Tribble GenotypeLikelihoods object for parsing VCFs with genotype likelihood fields. Please use GenotypeLikelihoods object from now on for seamless support for GL and PL tags. UGv2 now uses PL by default. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4589 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-28 01:48:47 +00:00
fromer 15183ed778 Reduced header to single sample when useSingleSample arg is given (to prevent lots of pointless no-calls) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4588 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-27 23:02:10 +00:00
fromer 34538bf2b3 Added ability to focus only on a single sample and/or emit only merged records in MNP merger 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4587 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-27 20:41:05 +00:00
kshakir 5cdd7a7ba4 There's no such thing as a sam index, so the GATK extension generator doesn't need to add an @Input for them. 
Updated a call to swapExt to specify the directory.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4586 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-27 20:39:03 +00:00
hanna 4c23b1fe9c Get rid of the static cache of ArgumentTypeDescriptors by making them an integral part of the 
parsing engine.  Hugely lowers our memory footprint in integrationtests, but not yet enough to 
run Mark's new parallelized VariantEvalIntegrationTests.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4585 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-27 19:44:55 +00:00
ebanks e112df20df Use a sorting VCF writer because records can flip positions during left-alignment 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4583 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-27 06:33:03 +00:00
ebanks 708e973911 Adding a walker to left-align indels in a VCF file (was able to reuse code from AlignmentUtils to do the hard part). The code correctly updates the alleles if they change. This makes it much easier to compare our indel calls to e.g. CG or dbSNP. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4582 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-27 06:08:26 +00:00
ebanks ec442086ec Minor refactoring of the cleaner allows me to add a trivial walker that left aligns the indels present in reads. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4581 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-27 03:39:10 +00:00
hanna 04e38929f0 Disabling parallelized version of VE integration tests. Still slow, but not 
deadlocking any more.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4580 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-27 02:47:03 +00:00
ebanks ffc0ed2b32 Renamed getName() to getSource() in VariantContext to be more accurate 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4579 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-27 02:21:41 +00:00
ebanks 52fc023d80 Added convenience methods to check/get the ID of the VariantContext 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4578 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-27 01:56:58 +00:00
fromer a7af1a164b Updated MNP merging to merge VC records if any sample has a haplotype of ALT-ALT, since this could possibly change annotations. Note that, besides the "interesting" case of an ALT-ALT MNP in a pair of HET sites, this could even occur if two records are hom-var (irrespective of using phasing). Note also that this procedure may generate more than one ALT allele. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4577 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-27 01:50:36 +00:00
depristo e02aac0743 No longer print out 0 reads were filtered out... message when there were no reads scene at all 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4575 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-26 20:22:16 +00:00
depristo b085648141 Parallelized VariantEval. Refactored output to support parallel output style. Minor improvements to testing framework to enable easy executeTestParallel to run -nt 1 and -nt 4 by default. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4574 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-26 20:21:38 +00:00
kshakir 8211cee0b2 Queue UI Improvements: 
- Forcing user to set the temp directory via -Djava.io.tmpdir to avoid filling up /tmp.
- By default deleting job outputs tagged as intermediate.
- Defaulting pipeline to scatter count 1 (no reads deleted).
- Cleaning up temp classes even when scripting fails.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4573 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-26 19:49:08 +00:00
ebanks cedceb33cd My only experience with getting external groups (GAP,dbSNP) to use VCF has been painful at best, so I'm not holding my breath to get indels for CG in VCF. To that extent, here's a oneoffs walker to convert from CG format to VCF for all 'del' & 'ins' types (but not 'sub' types, since they're too complex to code up in VCF and I don't care about them for now). rs ids are included. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4572 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-26 17:53:14 +00:00
ebanks 071799453c More complete fix to previous commit 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4571 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-25 20:47:37 +00:00
ebanks 67a776d53c Yikes! VariantEval was always loading genotypes unnecessarily when no sample list was provided because the order of the checks in the if statement wasn't optimal. This results in a massive performance penalty when running with many-sample VCFs. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4570 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-25 20:30:23 +00:00
ebanks 0d97394c4f Add capability to liftover to do the right thing when sections of the genome are reverse complemented. This does not work for indels (we don't try to reverse complement) because we need to figure out what the hell to do about the fact that the 'base to the left' that we automatically add on will be wrong because the location of the indel actually changes when reverse complemented. Sheesh. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4569 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-25 20:03:03 +00:00
fromer c357ec775a Trivially phases any hom site (since it is always correct to continue the previous haplotypes by appending the same allele onto both haplotypes) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4568 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-25 16:58:41 +00:00
rpoplin da64183854 Fix for the case of the truth VCF file having multiple SNPs at the same locus. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4567 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-25 15:04:50 +00:00
hanna 3039c0de3c Retire old ROD syntax. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4564 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-22 23:52:11 +00:00
depristo 78e71c4167 Fisher exact makes a return. Seems to be working properly. Current tagged as a work in progress. Needs to take the filtered context to be truly correct. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4561 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-22 20:35:44 +00:00
fromer f06f955e06 Added count of number of mergeable records (within specified distance cutoff) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4560 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-22 20:11:15 +00:00
depristo 84b6d2926b Useful walker that creates a new interval list with only the interval overlapping input sites list. Really a one-off walker 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4559 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-22 19:55:04 +00:00
depristo 78b4a1c240 VariantsToTable now supports the virtual TRANSITION field 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4558 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-22 19:53:46 +00:00
hanna e6d61197e6 Disable OTF indexing when writing indices for temporary VCFs when running 
with -nt option.  When last I checked in, Ryan was seeing a ~25% speedup 
per shard by not indexing.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4556 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-22 17:40:37 +00:00
depristo e6b008f87c Fixed >= vs. > test leading to failure to tolerate dynamic indexes that are created at *exactly* the instant the output VCF is closed too 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4555 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-22 16:11:14 +00:00
ebanks 72c5b75460 Tribble exceptions can be generated outside of the normal codec parsing code because we now lazy load the VCF genotype fields. I'm not sure how else to account for this (to make sure they show up as user errors and not GATK system errors) besides catching them here. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4554 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-22 15:22:17 +00:00
delangel e24f7fec47 Fixed indel genotyper which broke yet again because we can't just call context.getBasePileup() without checking again for its existence in the first place. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4553 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-22 15:17:11 +00:00
ebanks c0b4317311 Er, here's the right fix 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4552 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-22 15:08:25 +00:00
ebanks 181f901126 Fix for Ryan: don't pull reference sequence for the portions of reads that extend beyond the contig boundaries 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4551 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-22 14:38:26 +00:00
ebanks 9f76aed515 Fix for IDs 5zP7jJeffK2sdPH1BH4JBVSrQztVEDKP and nX0cuBjoqBW4NQFpM6dE13KpkCuYFpZu 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4550 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-22 14:05:27 +00:00
hanna d4feb99d9a For parallel ROD traversals, simplified reference sharding. Will replace 
with a more sensible strategy for sharding w/o BAMs at some point after
ASHG.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4549 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-22 05:08:15 +00:00
fromer 9ba7269728 Fixed Integration Tests to output VCF files with -NO_HEADER 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4548 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-21 19:49:44 +00:00
fromer 60f88866dd Uses VCFConstants instead of hard-coded constants 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4547 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-21 19:49:01 +00:00
fromer 883b8ff80e Removed flush() method from VCFWriter interface; added takeOwnershipOfInner parameter in constructor of wrapper VCFWriters to designate if the Writer should close the inner Writer it receives on construction 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4546 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-21 19:48:00 +00:00
fromer 1ea43be976 Removed flush() method from VCFWriter interface 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4545 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-21 19:46:42 +00:00
chartl 3566ad2146 Wrong if statement. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4544 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-21 17:37:45 +00:00
chartl bf17f92b64 Do not look for samples in dbsnp binding 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4543 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-21 17:36:38 +00:00
ebanks 225cf49128 Implementing reference confidence estimate in UGv2 as per UGv1 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4542 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-21 16:57:59 +00:00
delangel cf9c9ae241 Three important updates for Dindel genotyper: 
a) Fix it up because it broke with a recent checkin to annotate vcf with unfiltered depth.
b) Printout of ref/alt alleles in output vcf was incorrect because the start/stop positions of associated GenomeLoc were incorrectly computed in case of a deletion.
c) Redid Beagle input/output walkers as not assume that ref was a single base, not to assume that variant was a vcf and generalized it to be indel-capable, so now the Beagle walkers can be used for indels as well.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4541 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-21 16:00:16 +00:00
kshakir b88cfd2939 Updated MD5s of VCFs, since the approximate command line arguments injected into the VCF headers now have a little more order to them thanks to changes in the ParsingEngine. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4538 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-21 03:07:40 +00:00
ebanks 8f38ebf98e Throw a user exception when using the clustered SNP filter in the presence of ref calls. It's unfortunate, but until we get a windowed ROD context this is just too much of a headache to support. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4537 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-21 02:44:10 +00:00
kshakir 88a0d77433 Changed parsing engine to store the order the argument bindings based on their definition in the class, moving "-T" to the front of Queue command lines. 
Queue GATK generated .intervals is now a List(File) again removing special case handling in the generator.
Instead of using @Scatter annotation, using ScatterFunction instance to determine if a job can be scattered.
Implemented special VcfGatherFunction which only uses the header from the first file, even if the other files differ in their headers.
Added a -deleteIntermediates to Queue to delete the outputs from intermediate commands after a successful run.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4536 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-20 21:43:52 +00:00
ebanks 91049269c2 Optimizations across the board, with help from Guillermo, Matt, and JProfiler. Too tired to give details now. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4535 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-20 20:47:41 +00:00
fromer f76865abbc ReadBackedPhasing now uses a SortedVCFWriter to simplify, and has the ability to merge phased SNPs into MNPs on the fly [turned off by default]; MergeSegregatingPolymorphismsWalker can also do this as a post-processing step; Integration tests for MergeSegregatingPolymorphismsWalker were also added 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4534 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-20 20:27:10 +00:00
fromer e8079399ac Added flush() method to VCFWriters 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4533 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-20 20:23:22 +00:00
fromer 00726b6c4b Added mergeIntoMNPs to merge successive VCF records into a single MNP VCF [if possible] 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4532 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-20 19:40:26 +00:00
fromer 55230ce5f3 Added startsBefore, startsAfter, and minDistance [calculates distance between any pair of bases in the two GenomeLocs] 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4531 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-20 19:12:34 +00:00
ebanks 4f77581087 More optimizations for HaplotypeScore: pulling final constants out of loops 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4530 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-20 17:40:57 +00:00
hanna 20fac43521 Add extra logging to the GATK run report at the start of metrics aggregation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4529 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-20 17:32:51 +00:00
ebanks a205900eff Naughty use of Strings in HaplotypeScore literally double the runtime of Unified Genotyper. Moved over to bytes and no longer allow Strings in the Haplotype util class. New round of profiling on tap for tomorrow. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4528 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-20 03:32:21 +00:00
depristo f9541b78d3 Timing of traversal now starts at the start of the traversal, so the rate is reasonable right off the bat. For example, we now see: INFO 22:45:02,476 TraversalEngine - [TRAVERSAL STARTING]; INFO 22:45:32,484 TraversalEngine - [PROGRESS] Traversed to 2:50850686, processing 18,646 sites in 30.05 secs (1611.50 secs per 1M sites) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4527 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-20 02:47:34 +00:00
depristo f7ce18553e GenotypeConcordance now prints interesting sites more nicely. RMDTrackBuilder is now uses the root class FeatureSource not BasicFeatureSource. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4525 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-20 00:29:02 +00:00
ebanks 7a291a8ff3 First pass at a VCF validator. Will test more tonight. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4524 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-19 19:55:49 +00:00
chartl 341e93ee12 The reference fixer seems to have munged the OMNI rather than making it better. Looks like some sites need to only have the ref and alt bases swapped, and others need to have the genotypes swapped as well? E.g. 
some subset need
A  C  1/1   -->  C  A  0/0

while another subset need
A  C  1/1   -->  C  A  1/1

it's unclear how big these subsets are (or even if one is empty). What I do know is, doing the first one totally screws up concordance metrics for the 421-sample chip. So either something else needs to be done, or there's a bug in this walker. Until I know for sure, I've added an initialize exception to disable this thing...



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4523 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-19 12:50:24 +00:00
ebanks 5251f49a90 Including Marian Thieme's BaseCounts class (with some modifications) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4522 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-19 03:07:30 +00:00
hanna c5f105d050 Fix boneheaded mistake in the new interval filtering code I added on Sunday. 
Sorry everyone.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4521 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-19 01:20:12 +00:00
ebanks 524cb8257c Renaming for accuracy 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4519 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-18 18:11:07 +00:00
ebanks 0fe504b748 Use filtered depth for Exact model (just like grid search) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4518 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-18 18:08:31 +00:00
ebanks d54d9880d7 Now that G's new genotyping algorithm is live, I've cleaned up the code to completely separate the grid search from the exact model. AlleleFrequencyCalculationModel is now completely abstract. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4517 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-18 18:04:06 +00:00
ebanks 80e5ac65b4 CAP_BASE_QUALITY needs to be included in the clone() method for it to be usable in UG 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4516 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-18 03:11:03 +00:00
hanna 6af9532090 Fix for GATK slowdowns at the ends of intervals. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4514 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-17 23:21:23 +00:00
chartl 5889138f4a *facepalm* 
forgot to add the samples to the header. How could the VCFWriter let me get away with something so boneheaded?!



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4513 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-17 05:36:29 +00:00
chartl 2bc5971ca1 Added - a tool to fix reference bases of a VCF. The OMNI had a couple of sites with incorrect reference bases (look to be legacy from other chips), and a few more that had ref and alt flipped. GAP should probably take care of it, but since I need results by monday, I'm doing it. 
Modified - SelectVariants: Hook up to VariantContextUtils to recalculate AC/AF/AN, which uses the accessor in VariantContext to do this. Somehow sites that were selected down to hom-ref genotypes only wound up getting positive AC. 

**IMPORTANT** I kind of need input here. The header of a file used for an integration test specifies AC as being an integer. Recalculating it casts it into an integer list (which it should be, as it allows for alternate alleles). However this appears to clash with what the jexl expression is looking for? For now, the integration test itself needed to be changed -- it's unclear what to do when the header specifies AC of being one class, but recalculating it casts to another class, and I'm not sure what to do.

I'm committing my omni_qc pipeline because I'm almost certain 2 months down the road I'm going to wonder what the heck I did to generate my results.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4511 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-17 03:18:01 +00:00
ebanks 7aa030a9a4 Hmm. Apparently variants can get lifted over to different chromosomes. Who knew? Reverting changes from a couple of days ago. The only way to do this correctly (without requiring lots of memory) is to turn off on-the-fly indexing for this walker. Integration tests cover this now. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4510 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-17 02:54:12 +00:00
chartl 8b2d387643 Added in an eval module that calculates the dispersion histograms between eval and comp (e.g. M_{i,j} = # of times eval observed to have AC i, comp AC j -- for af it's i/100 vs j/100 ) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4507 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-15 19:07:43 +00:00
ebanks f78ff08e2b This is less correct than my previous change but it's what UGv1 does and now is not the right time to start mucking with things. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4506 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-15 18:56:45 +00:00
ebanks 471c18054f Fix for SB calculation: the best overall AF might not have any mass when just looking at reads from a single strand. We need to compute the best AF for each stratification. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4505 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-15 17:51:18 +00:00
asivache 42c3d74432 bug fix 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4503 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-15 16:27:40 +00:00
chartl c9d473edee More changes to Variant Eval and Genotype Concordance (passes all integration tests): 
1: -sample can now include a file, which will be parsed for sample-name entries
2: If you request a sample to run analysis on, but it is not present in any of your RODs, VEW will exception out
3: Change added to parse Integer, String, and List<Integer> type Allele Count annotations (error otherwise)
4 [slightly problematic]: The count objects now maintain row-keys in order, as the keys were taking an inordinate amount of time in onTraversalDone (multiple calls to getRowKeys(), so many multiple sorts of the same underlying unsorted object, very bad)

There is a legacy comparison object which is unused which I will strip out soon.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4502 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-15 12:40:36 +00:00
ebanks 954dd84f51 Adding an integration test (against hg18 this time) that requires on-the-fly sorting in order to work properly. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4500 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-15 07:45:21 +00:00