d323ef0461
As promised, VariantFiltration can now mask out sites within a user-specified window around the provided mask rod. By default the window is 0, but you can now use the --maskExtension argument to increase that value. Added integration tests to cover this new functionality.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6060 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-22 22:55:29 +00:00
26d837f59e
Factorial and log Factorial utilities avoiding overflow using the gamma function. Lots of unit tests. Everything is working great.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6058 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-22 22:55:20 +00:00
8d5b4af8ca
Binomial and Multinomial interfaces for probability and coefficients in log and real space. Passed all unit tests.
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BinomialCumulativeProbability was reformatted to follow the now standard parameter order.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6057 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-22 22:55:15 +00:00
4abb7c424b
implementation of the Gamma function and log10 Binomial / Multinomial coefficients. Unit tests for gamma and binomial passed with honors.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6056 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-22 22:55:09 +00:00
4f7a64a798
Fixing broken walker as per GS; adding integration test to cover it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6040 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-22 22:54:04 +00:00
0e057276ae
Changing the default behavior of the IndelRealigner to run without Smith-Waterman. Changed around the integration tests accordingly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6039 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-22 22:53:58 +00:00
53c089949e
Added integration test for -n parameter
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6032 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-22 22:53:22 +00:00
745935ffc2
No longer used - instead see the ConstrainedMateFixingManager class
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6030 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-22 19:38:17 +00:00
a1f8aa90c0
Added an integration test showing how to use LSF C API to get LSF parameters.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6025 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-21 22:54:55 +00:00
4c6d0e6143
Added stratification by discrete allele count, just like AF, but requiring genotypes so it can be exact. Added docs on wiki, and integrationtest using Kiran's very nice fundamental VCF
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VariantEvalWalker now passes a pointer to itself to the Stratefication setVariantEvalWalker (and assoc. get method) so that stratefications can look at VEWalker variables to obtain information necessary for their calculations, like the list of eval samples. This is a better interface, in my opinion, than the current approach of extending the base abstract Stratefication to include an initialize function that has all arguments necessarily for any Strat.
JEXL expressions now provide access to the VariantContext vc object itself, so you can write JEXL's that directly use VariantContext and associated functions from the command line.
ExomePostQC Queue script now creates a byAC eval using the new strat, and no longer produces a byAF file (as this was not exact, and lead to strange punctile behavior when actual AF quantization was out of sync with fix quantization of AF strat.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6015 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-19 03:11:00 +00:00
4e85416af1
[Foiled yet again when trying to do this in git] Slight modifications in the argument structure for the IndelRealigner. Instead of boolean flags -knownsOnly and -doNotUseSW, we now have an enum --consensusDeterminationModel which lets you specify knowns only, also use indels in reads, or also use SW. Please note that the default behavior of IR has not changed at all (and won't for a few more days) - that'll be done in GIT (fingers crossed).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6008 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-16 17:35:37 +00:00
4304fc4862
Fixed up md5s
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6007 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-16 16:20:41 +00:00
5be4f31515
Surprisingly, the TileCovariate was indeed covered in integration tests. Updated.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5997 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-14 17:40:23 +00:00
17e17d3c3c
Misc cleanup in VQSR.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5972 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-09 18:37:37 +00:00
ac3620839c
Very basic intergration tests for ReducedReads, to allow safe optimization of the code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5970 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-09 17:06:32 +00:00
895e86c544
Annotations used to build the 1000G consensus callsets are now standard annotations
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5969 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-09 17:03:39 +00:00
49b021d435
Changed the definition of degeneracy (it's at the site level - degeneracy of a position in a codon, not degeneracy of the amino acid itself like I initially thought. Added the ability to supply an ancestral allele track (available in /humgen/gsa-hpprojects/GATK/data/Ancestor/).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5963 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-08 15:07:31 +00:00
a331e13721
Slightly more extensive test includes a 0/0 site to genotype
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5961 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-08 14:48:55 +00:00
0f43b10c39
Optimization in CombineVariants when merging into a sites_only VCF
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VariantContextUtils now was a utility function that creates a sitesOnlyVariantContext from an input VC
Add complex merge test of SNPs and indels from the new batch merge wiki in :
http://www.broadinstitute.org/gsa/wiki/index.php/Merging_batched_call_sets
with multiple alleles for an indel. Created a BatchMergeIntegrationTest that uses GGA with the complex merged input alleles to genotype SNPs and Indels with multiple alleles simultaneously in NA12878. Looks great.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5959 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-08 14:31:46 +00:00
7e49e1668f
Finished changing md5's due to recent change in definition of mixed and indel vc's.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5948 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-05 00:40:51 +00:00
d534241f35
Major revamp of annotations for indels:
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a) All rank sum tests now work for indels including multiallelic sites. For the latter cases, rank sum test is REF vs most common allele
b) Redid computation of HaplotypeScore for indels. It's now trivially easy to do because we are already computing likelihoods of each read vs haplotypes in GL computation so we reuse that if available. For multiallelic case, we score against N haplotypes where N is total called alleles.
Drawback is that all cases need information contained in likelihood table that stores likelihood for each pileup element, for each allele. If this table is not available we dont annotate, so we can only fully annotate indels right now when running UG but not when running VariantAnnotator alone.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5947 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-04 15:34:24 +00:00
1448a1f155
Change md5 because conversion of a tri-allelic dbsnp indel record is now legit
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5946 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-04 11:24:16 +00:00
53667ce8fa
Disabled test that checks whether output is the same whether in Genotype Given Alleles mode or not - it won't as long as extended events are finally removed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5945 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-04 00:52:54 +00:00
35df80de14
Updated md5 due to changes to changes in QUAL field when in Genotype given alleles mode w/indels when in insertions.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5944 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-03 23:52:38 +00:00
b93829e505
The underlying bam file for this test was busted for many reasons preventing Picard folks from making unrelated changes, so I needed to fix it. Updating md5s accordingly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5943 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-03 22:26:06 +00:00
cd293f145b
More stable reduced reads representation. Bug fixes throughout. No diffs by <1% of sites in an exome, and the majority of these differences are filtered out, or are obvious artifacts. UnitTests for BaseCounts. BaseCounts extended to handle indels, but not yet enabled in the consensus reads.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5939 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-03 20:11:31 +00:00
420d8feff6
No one should be calling the createHeader method(s) directly, but instead should be going through the full readHeader method (because it first sets the version); therefore I made them package protected and merged them. Updated the various unit tests that were using createHeader and were dangerously assuming that the header version was defaulting to 4.0 (which it no longer does).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5934 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-03 02:17:37 +00:00
86df10ec09
UnitTests for ConsensusSpan infrastructure
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5929 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-02 22:44:52 +00:00
dd6d61c031
Adding integration test to cover the case of a read that only covers an insertion (i.e. no M in the CIGAR string).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5923 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-02 21:02:47 +00:00
84c2c5d7e6
Stop running away from my commits, test modules.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5919 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-02 13:05:53 +00:00
092952db44
After verifying that the changes to these tests were all in the RankSum annotations, I'm commiting fixes to the test md5s.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5918 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-02 13:01:18 +00:00
511cd48d7a
There is an edge case ( |Set1| = 5, |Set2| = 4) where the exact p-value exceeds the range of the normal distribution we want to invert. For the edge cases, this happens exactly at the mean, and so this can be safely replaced with a z value of 0.0
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5915 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-01 17:30:09 +00:00
a79967d9af
After extensive testing of MannWhitneyU:
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- Verified that exact calculations do agree with R's dwilcox()
- Verified that exact calculations do not agree with R's wilcox.test
+ This is because R does a correction, and calculates CDFs rather than PDFs (e.g. sums over dwilcox() values)
- Can now specify MWU to calculate cumulative exact tests, rather than point probabilities
- Z-scores are now calculated properly for exact tests
+ Previously, z-values calculated by inverting normal CDF from U-statistic PDF
+ Now both inversions are done, with a smart heuristic (biased variance) to make the point-calculated Z-value more accurate
+ Additional tests
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5911 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-01 15:51:27 +00:00
2b5683909e
Updated VQSR integration tests because of the new Omni file. Fixed overflow condition in FisherStrand when the depth is too high.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5910 348d0f76-0448-11de-a6fe-93d51630548a
2011-06-01 14:20:37 +00:00
44cb7e4980
Renaming to make grepping through the output less confusing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5908 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-31 19:54:44 +00:00
9e834391fe
We now skip over all covering RODs in the BQSR as intended instead of just those which can be converted into a VariantContext. All the integration tests change because of subtleties in how certain dbsnp rod records are being converted into VCs. Added integration test which uses a bed file as the list of known polymorphic sites.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5892 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-27 16:32:17 +00:00
8ed82e5a08
The previous version of the UG was always creating BAQ'd pileups for the underlying site QUAL calculation. This resulted in some slowdown in the code. But as far as I can tell, the code actually didn't apply the BAQ'd base quality anywhere when the BAQ field wasn't in the read, so this just saves us 20% of the runtime when BAQ isn't enabled from heading into the BAQ subsystem when we don't actually want to get the BAQ'd base qualities.
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Fixed minor problem with WalkerTest for "" (for parameterization) md5s.
Added an explicit integrationtest for BAQ NONE
Now only creates the BAQ'd pileup, if the useBAQPileup parameter is provide in initializeAlternateAllele.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5891 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-27 14:00:52 +00:00
136c8c7900
ClipReads now supports HARDCLIP_BASES, though in fact this turned out to be not necessary for my desired tests. In the process of developing the HARDCLIP mode, I added some proper ReadUtils unit tests, which would ideally be expanded to include other ReadUtil functions, as added
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5890 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-27 11:42:22 +00:00
f7298f4a7f
First of many baby steps to redo way in which we trigger events for indel calling and to eliminate extended events: get rid of SpanningDeletions annotation for indels. It's completely useless, and even more so once we no longer trigger at extended events (because we'll trigger by definition a base before a deletion starts, so deletions present in the current pileup are not informative).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5876 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-26 00:49:23 +00:00
1bd1404aa9
Sometimes md5s can be null
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5867 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-24 19:17:18 +00:00
e582a92af6
WalkerTest now checks for valid md5s in the integrationtests themselves, so no more stray whitespace errors. Added a WalkerTestTest to ensure tha t bad MD5s are detected and an error thrown
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5865 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-24 14:34:55 +00:00
06486c134a
Kill extra space in the md5.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5863 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-24 12:00:31 +00:00
57e4693e4c
Slightly better error message when failing to create the index on the fly
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5861 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-24 11:04:08 +00:00
cf3dbfee97
Renamed variantMergeOptions to filteredRecordsMergeType, as this is really what it does. Cleaned up the wiki so that it's clear what this does, as well as included an example of how to create an intersection with CombineVariants and SelectVariants. Added integrationtests of CombineVariants with OMNI and HapMap that deal with the two ways to merge fitlered/unfiltered records at the same site.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5860 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-24 01:54:29 +00:00
4bfec4c55b
Reenabling E.coli ValidatingPileup with MV1994 realigned using the BWA/C bindings.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5856 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-23 21:32:53 +00:00
5dca1e4d2e
Make IntervalIntegrationTest aware of the new alignments in the MV1994.bam
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testset.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5852 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-23 19:59:47 +00:00
7ff5375493
Removing build-killing dependency on a private package.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5851 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-23 18:13:15 +00:00
0b07373909
Incorporating old feedback from eric: @deprecated methods should not be @deprecated, but rather protected, and the test's package moved to where it can access those test methods.
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Also allows for the slightly more awesome name "MWUnitTest"
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5850 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-23 18:06:05 +00:00
480859db50
Contractified version of MannWhitneyU. Some behavior has been changed:
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- Running a test when there are no observations of at least one of the sets now breaks the MWU contract
+ MWU returns Pair(Double.NaN,Double.NaN) in these instances to maintain the contract of never returning null
+ No more Double.Infinity values will appear
- RankSumTests now probe the return values for NaNs, and don't annotate if they appear
- For small sets where the probability is calculated recursively, the z-value is now the inversion of the error function
and not the approximate z-value
- UG and Annotator integration tests updated to reflect changes
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5845 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-23 13:57:15 +00:00
a18b0152df
Contracts for SimpleTimer, as well as UnitTests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5841 348d0f76-0448-11de-a6fe-93d51630548a
2011-05-22 19:45:31 +00:00
droazen
ebanks
kshakir
depristo
rpoplin
kiran
delangel
chartl
hanna