861221d046
- Moved various header line printing into a single method
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- Fixed output for coverage above min depth
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2254 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-04 02:15:43 +00:00
c2017cc91b
PrintCoverageWalker functionality moved to DepthOfCoverageWalker. Added integration tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2247 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 17:23:59 +00:00
01cf5cc741
1. Merged CoverageHistogram into DepthOfCoverageWalker
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2. Fixed bug in histogram calculation for small intervals
3. Better output in DoCWalker
4. Comments added to code
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2245 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 17:01:53 +00:00
44b9f60735
PercentOfBasesCovered functionality moved to DepthOfCoverageWalker. Added integration tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2244 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 16:11:09 +00:00
b3bdcd0e60
make sure we close the error log stream in CommandLineProgram if it's opened; unit tests and clean-up for BasicVariation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2241 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 06:59:27 +00:00
a88202c3f6
Refactored DoCWalker to output in a more helpful and usable style. It now outputs in tabular format with 2 different sections: per locus and then per interval.
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I am now at a point where I can merge the functionality from other coverage walkers into this one.
Thanks to Andrew for input.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2239 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 05:28:21 +00:00
451a20ed55
commenting out some broken integration tests, to be uncommented if needed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2232 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 23:13:24 +00:00
9d598f1c82
some integration test clean-up
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2229 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 21:11:02 +00:00
0a2304eff8
- Rename minConfidenceScore in VariantEval to minPhredConfidenceScore
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- Moved validation walkers to new qc dir
- Killed unused test
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2218 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 17:59:19 +00:00
7055a3ea2d
- All annotations are now required to return their VCF INFO keys and descriptions
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- Renamed keys to fit with the standard naming
- FisherStrand is no longer standard
- Integration tests no longer test experimental annotations since they're not stable
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2216 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 17:24:06 +00:00
6231637615
fixes for VariantAnnotations and second bases. Misc. removal of failing (and unstable) integration tests that require rereview
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2213 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 15:41:35 +00:00
886c44303a
-Removing BTTJ integration test -- this broke a few revisions ago (2169) and it is unclear whether the resulting change was a correction to something that had previously been incorrect, or a true build-breaker. I'm currently investigating which case this is, but since Bamboo is back up I'm removing this _temporarily_ so that other testing can occur, and will make whatever changes to the test necessary to reflect the truth, then replace the test itself. Additional (and related) pileup tests are upcoming as well.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2210 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 05:37:15 +00:00
ba8a8febc6
Thanks to Steve Hershman for finding this bug:
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getNegLog10PError() does not equal the confidence score (you need to multiply by 10 as confidence is traditionally phred scaled). Probably we should change the method to be getNeg10Log10PError(). Anyone have strong feelings on this?
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2207 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 01:59:03 +00:00
3180fffd43
Eliminated unnecessary boxing of longs in RecalDatum. Changes to RecalDatum in preparation for new AnalyzeCovariates script. Updated TableRecalibrationWalker to make use of these changes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2199 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-01 16:49:05 +00:00
21a9a717e4
Some minor changes and test:
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- DepthOfCoverage is now by reference (so locus-by-locus output correctly reports zero-coverage bases)
- VariantsToVCF now lets you bind variants with any string except intervals and dbsnp (not just NA######)
- A PileupWalker integration test on a particularly nasty FHS site
- Two second-base annotation related integration tests on that same site
+ outputs were all hand-validated in matlab; within a certain tolerance for the annotations
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2197 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-01 15:15:54 +00:00
d8146ab23d
Changed the format of the recalibration csv file slightly so that it is easier to load the file into something like R and look at the values of the covariates.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2183 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-30 17:55:23 +00:00
af22ca1b47
Bug fixes for VariantEval. dbCoverage now reports dbSNP rate, not some wierd eval_snps_in_db as before. We now separate non-indel and non-snp db sites in dbcoverage. Some dbSNP records don't fit into these two categories. Also fixed a consistency issue where novel / known sites where being determined solely by whether dbSNP had a record there, rather than the stricter dbcoverage screen for isSNP().
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2180 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-30 01:39:01 +00:00
75b61a3663
Updated, optimized REadBackedPileup. Updated test that was breaking the build -- it created a pileup from reads without bases...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2169 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-25 23:30:39 +00:00
d0f673f0c0
Use Math.abs so we don't get (inconsistent) -0's
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2160 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-25 19:08:34 +00:00
6ff8526592
Added arguments to the recalibration walkers so the user can specify the default read group id and platform to use when a read has no read group. There are also options to force every read group and every platform to be the specified values. Added integration tests that use a bam file with no read groups. Added comments to all the covariates to explain what each of the methods in the Covariate interface are used for.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2157 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-25 15:41:12 +00:00
e1e5b35b19
Don't have the spanning deletions argument be a hard cutoff, but instead be a percentage of the reads in the pileup. Default is now 5% of reads.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2155 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-25 04:54:44 +00:00
03342c1fdd
Restructuring and interface change to ReadBackedPileup. We now lower support the Pileup interface, the BasicPileup static methods, and the ReadBackedPileup class. Now everything is a ReadBackedPileup and all methods to manipulate pileups are off of it. Also provides the recommended iterable() interface of pileup elements so you can use the syntax for (PileupElement p : pileup) and access directly from p.getBase() and p.getQual() and p.getSecondBase(). Only a few straggler walkers use the old style interface -- but those walkers will be retired soon. Documentation coming in the AM. Please everyone use the new syntax, it's safer, and will be more efficient as soon as the LocusIteratorByState directly emits the ReadBackedPileup for the Alignment context, as opposed to the current interface. In the process of the change over, discovered several bugs in the second-best base code due to things getting out of sync, but these changes were resolved manually. All other integrationtests passed without modification.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2154 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-25 03:51:41 +00:00
c9ff5f209c
Added a CountCovariates integration test that uses a vcf file as the list of variant sites to skip over instead of the usual dbSNP rod.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2152 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 21:51:38 +00:00
3484f652e7
1. Variation is now passed to VariantAnnotator along with the List of Genotypes so non-genotype calls has access to all relevant info.
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2. Killed OnOffGenoype
3. SpanningDeletions is now SpanningDeletionFraction
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2151 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 21:47:20 +00:00
dffa46b380
BAM files created by TableRecalibration now have the version number and list of covariates used appended to their header with a new 'PG' tag. Eventually the entire list of command line args will be put in there as well. Big thanks to Matt and Aaron. The integration test uses the --no_pg_tag so that the md5 doesn't change every time the version number changes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2148 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 20:53:57 +00:00
8fbc0c8473
fix for bug GSA-234: fasta index files couldn't handle anything but letters, numbers, or spaces in the contig name
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2147 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 19:19:47 +00:00
b3f561710f
Optimizations:
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1. Only do calculations in UG for alternate allele with highest sum of quality scores (note that this also constitutes a bug fix for a precision problem we were having).
2. Avoid using Strings in DiploidGenotype when we can (it was taking 1.5% of my compute according to JProfiler)
UG now runs in half the time for JOINT_ESTIMATE model.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2141 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 16:27:39 +00:00
36d493e645
All standard annotations now inherit from StandardVariantAnnotation. Users can specify whether they want all annotations, just the standard annotations, or specific annotations. When calling in from another walker, the default is just the standard ones.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2134 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 03:55:12 +00:00
ee5093d2c6
-Added VariantFiltration integration tests
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-Added integration test for GLFs
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2133 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 02:36:27 +00:00
be6a549e7b
Added the capability to allow expressions in an integration test command (i.e. -filter 'foo') by escaping them in the command.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2132 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 02:34:48 +00:00
903342745d
Basic integration test for the aligner.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2131 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-23 23:08:05 +00:00
6a52ca3db6
Update to the UG integration test. Why I had to rm -rf my entire sting directory to get it to correctly fail we may never know.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2128 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-23 21:23:00 +00:00
23983b2fd8
New annotation: ResidualQuality
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Computes a metric for how much error is left that isn't explained by ref or snp bases. This is the sum of Q scores, weighted by the proportion of non-ref non-snp bases to non-snp bases. Reported in Log space.
Update to the integration test so bamboo doesn't look as though someone murdered it with a spork
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2124 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-23 20:04:01 +00:00
70059a0fc9
Refactored joint estimation model to allow subclasses to overload PofD calculation over all frequencies. Pooled model now takes only 20% of time that it used to.
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Added integration test for pooled model and updated other joint estimation tests to be more comprehensive now that they are faster.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2123 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-23 20:03:38 +00:00
7f947f6b60
Updated recalibrator integration tests to use all three platforms as well as a bam with multi-platform reads intermingled. CountCovariates v2.0.1: Once again uses a read filter to filter out zero mapping quality reads. Added --sorted_output option to output the table recalibration file in sorted order
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2122 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-23 19:51:36 +00:00
c299ca5f49
It would help if I copied the MD5s from the right integration test...
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I hate Mondays.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2121 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-23 17:21:36 +00:00
ff4797acbb
Forgot to check in integration test update
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2120 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-23 17:13:51 +00:00
1d46de6d34
The old recalibrator is replaced with the refactored recalibrator. Added a version message to the logger output. These walkers start at version 2.0.0
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2117 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-23 14:58:33 +00:00
bf935a6ab1
1. Fixed bug in PrimaryBaseSecondaryBaseSymmetry code (not checking for null before trying to access object's methods) which was causing Integration Tests to fail.
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2. Retired allele frequency range from UG, which wasn't very useful.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2113 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-23 01:31:48 +00:00
d84444200b
The Unified Genotyper now sorts the sample names in the vcf that it outputs.
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[There was no reason to enforce that every VCF being output from the GATK should have the samples sorted, since someone might want them ordered non-alphabetically]
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2102 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-20 16:13:18 +00:00
22aaf8c5e0
Added the old recalibrator integration tests to the refactored recalibrator sitting in playground.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2096 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-19 22:43:28 +00:00
306f4624c6
oops forgot to update the md5s
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2093 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-19 18:22:29 +00:00
6ba1f3321d
Fixed the sample mix-up bug Kiran discovered, and added a unit test in the VCF reader class (Thanks for the good example files Kiran). Also renamed the toStringRepresentation function to toStringEncoding, and added a matching method in VCFGenotypeRecord.
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Updated the integration tests that were failing to due to different ordering of genotyping entries in VCF, I'll check in the VCF diff tool I wrote when I get a cycle or two.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2092 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-19 18:17:47 +00:00
b4babb82eb
adding an extra bit of data to come out of CTT (number of chips with actual data)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2091 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-19 17:46:10 +00:00
b3872386c9
Test to ensure that ConcordanceTruthTable and those walkers which rely on it for tabulating pooled truth information from truth information of the individuals within the pool is doing that calculation correctly. Tests single het, single hom (with/without reference), together, together without reference, and a mix of everything.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2082 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-19 15:26:32 +00:00
90212c643b
more effective & efficient test for SecondBaseSkew
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2075 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-18 20:53:32 +00:00
0a35c8e0ba
1. The joint estimation model now constrains genotypes to be AA,AB,or BB only (i.e. to use a single alternate allele). Note that this doesn't work for the old models (point estimate or SSG) because calculations aren't divided by alternate allele.
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2. Allele frequency spectrum is not emitted for single samples (since it doesn't make sense).
3. If in pooled mode, throw an exception of pool size isn't set appropriately.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2072 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-18 17:43:15 +00:00
6fe1c337ff
Pileup cleanup; pooled caller v1
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2070 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-18 17:03:48 +00:00
be31d7f4cc
Added - a walker that outputs relevant information about false negatives given a bunch of hapmap individuals and corresponding integration tests for it.
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This will output for hapmap variant sites:
chromosome position ref allele variant allele number of variant alleles of the individuals depth of coverage power to detect singletons at lod 3 number of variant bases seen whether or not variant was called
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2068 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-18 15:47:52 +00:00
539f6f15e5
Added --
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Second base skew annotations and integration tests. Nothing need be given except -A SecondBaseSkew; the statistic it annotates calls with is a chi-square statistic given by the deviation of the observed proportion of reference second-best-bases from the expected 1/3. Future additions may be to ask that the deviation be instead from a given transition table.
A big note for all users: All IllegalStateExceptions from the variation ROD (e.g. the RodGeliText) are dealt with SILENTLY. I understand this isn't optimal, but I'd rather simply not annotate a non-bi-allelic site than fail completely (there are quite a few such sites even on the regions over which the integration test has been written).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2064 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-18 00:11:13 +00:00
4d9c826766
Integration tests actually run on real data now.
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<tries to hide sheepish grin>
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2061 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-17 21:04:14 +00:00
5e126875ea
temporarily disable (tests are broken)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2060 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-17 20:45:52 +00:00
a048f5cdf1
-Refactored JointEstimation code so that pooled calling will work
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-Use phred-scale for fisher strand test
-Use only 2N allele frequency estimation points
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2059 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-17 20:21:15 +00:00
aece7fa4c7
a convenience method to join a map into a single string, which I need for some VCF work. Added some documentation to the join method as well.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2057 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-17 16:50:01 +00:00
4558375575
Stage 1 of the VariantFiltration refactoring is now complete. There now exists a parallel tool called VariantAnnotator which simply takes variant calls and annotates them with the same type of data that we used to use for filtering (e.g. DoC, allele balance). The output is a VCF with the INFO field appropriately annotated.
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VariantAnnotator can be called as a standalone walker or by another walker, as it is by the UnifiedGenotyper. UG now no longer computes any of this meta data - it relegates the task completely to the annotator (assuming the output format accepts it).
This is a fairly all-encompassing check in. It involves changes to all of the UG code, bug fixes to much of the VCF code as things popped up, and other changes throughout. All integration tests pass and I've tediously confirmed that the annotation values are correct, but this framework could use some more rigorous testing.
Stage 2 of the process will happen later this week.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2053 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-16 02:41:20 +00:00
bf451873ff
1. Bug fix: check that AF=0 doesn't contain more probability than 1-fraction
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2. Fix for Kiran: allow UG to call SNPs at deletion sites; we'll add an annotation to the VariantAnotator for deletions at the locus (next week).
3. Added integration tests for joint estimation model
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2038 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-13 18:02:18 +00:00
7c386fa428
Another case of reordering of read groups blowing up checksums.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2030 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-13 00:07:35 +00:00
8145ed4672
Take 2, updating picard with bug fix for bam files containing no reads.
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Just stomped on the existing md5s because that's what Eric told me to do.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2029 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-12 22:52:08 +00:00
c3c001e02e
cleanup of the traversal output code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2026 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-12 06:18:10 +00:00
6a37090529
Output changes for VCF and UG:
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1. Don't cap q-scores at 99
2. Scale SLOD to allow more resolution in the output
3. UG outputs weighted allele balance (AB) and on-off genotype (OO) info fields for het genotype calls (works for joint estimation model and SSG)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2011 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-10 16:31:31 +00:00
d316cbad4c
VariantFilteration now accepts a VCF rod in addition to an input geli. It will then annotate this VCF file with filtering information in the INFO field too. --OnlyAnnotate will not write in filtering output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2008 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-10 13:24:58 +00:00
2ed423ed56
print the current location in read walkers (in addition to the number of reads processed), along with some refactoring to support the change.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2006 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-10 05:57:01 +00:00
c9c3cf477a
Based on feedback from Kiran, we know uniquify sample names as sample.rodName (instead of sample.1, sample.2, ...)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2005 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-10 02:41:37 +00:00
2fa2ae43ec
Enough people have found this useful, so...
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Moving Callset Concordance tool to core and adding integration test.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2003 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-09 20:59:18 +00:00
6fdfc97db6
Added optional field DP to VCF output for Mark.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1981 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-06 20:03:22 +00:00
aacd72854f
a fix for a bug Andrey discovered: in read-based interval traversals we're dupplicating reads in rare cases. The problem was that to accomidate a bug in SAM JDK indexing, we were forced to add one to the stop of our QueryOverlapping() calls to ensure we always got all of the overlapping reads.
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Added a PlusOneFixIterator that wraps other iterators, and eliminates reads that start outside of our intended interval (interval stop - 1). Updated and checked BamToFastqIntegrationTest MD5 sums.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1976 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-05 05:26:33 +00:00
11d950abe0
No longer allow the lod_threshold argument - use confidence instead.
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Have UG output qscores in all cases.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1968 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-03 16:18:51 +00:00
af6d0003f8
-Generalized the GenotypeConcordance module to deal with any number of individuals (although it will default to its old behavior if the -samples argument is left out).
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-Make rods return the appropriate type of Genotype calls from getGenotype().
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1954 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-01 05:35:47 +00:00
7d0ac7c6f2
Fix for long-term VariantEval bug plus new intergration test to catch it
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1951 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-31 00:00:33 +00:00
2b96b2e4e7
better multi-sample integration test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1933 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-29 13:51:51 +00:00
5cdbdd9e5b
now that the design is stable, pull the setReference and setLocation methods back out of Genotype and stick them into constructors of implementing classes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1931 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-29 13:27:37 +00:00
3091443dc7
Sweeping changes to the genotype output system, as per several discussions with Matt & Aaron.
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Some things still need to be changed, but it will entail some more design decisions first (which means I get to bug M&A again tomorrow!).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1930 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-29 03:46:41 +00:00
86573177d1
Reverting rod walkers to use underlying refwalker implementation while we work on ROD2 and reenable the system. Added some serious sparse file parsing to variant eval tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1929 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-29 01:04:37 +00:00
3fb3773098
a fix for traverse dupplicates bug: GSA-202. Also removed some debugging output from FastaAltRef walker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1912 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-26 20:18:55 +00:00
62c1001790
BTTJ is now correct. What a terrible waste of time, turns out I'd just reversed the header. Because of this the MD5 had to be updated in the tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1910 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-26 19:24:18 +00:00
ad1fc511b1
intermediate commit for some changes in the Variation system, so Eric can go ahead with his changes. Everything is pretty set, but the Variation interface could use a convenience method that joins all the alternate alleles.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1903 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-23 06:31:15 +00:00
a6dc8cd44e
BTTC is now Tree Reducible allowing for parallelization.
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Integration test comment changed to reflect actual date of last md5 update.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1901 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-22 23:19:29 +00:00
af761fb9bd
Base transition table now forces epsilon/3 (three-state) model for the unified genotyper. Verified to be identical with changing the default model to being epsilon/3. This of course changes the observed counts, so the integration test has been updated.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1897 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-21 21:18:26 +00:00
caa3187af8
Enabling correct high-performance ROD walker and moved VariantEval over to it. Performance improvements in variantEval in general. See wiki for full description
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1890 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-20 23:31:13 +00:00
4a8a6468be
Use read group as a condition for confusion tables. With an integration test.
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Changed BaseTransitionTable to comparable objects for consistent ordering of output
( e.g. so the integration test doesn't yell so much )
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1889 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-20 19:39:32 +00:00
3b1fabeff0
Major code refactoring:
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@ Pooled utils & power
- Removed two of the power walkers leaving only PowerBelowFrequency, added some additional
flags on PowerBelowFrequency to give it some of the behavior that PowerAndCoverage had
- Removed a number of PoolUtils variables and methods that were used in those walkers or simply
not used
- Removed AnalyzePowerWalker (un-necessary)
- Changed the location of Quad/Squad/ReadOffsetQuad into poolseq
@NQS
- Deleted all walkers but the minimum NQS walker, refactored not to use LocalMapType
@ BaseTransitionTable
- Added a slew of new integration tests for different flaggable and integral parameters
- (Scala) just a System.out that was added and commented out (no actual code change)
- (Java) changed a < to <= and a boolean formula
Chris
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1887 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-20 14:58:04 +00:00
449a6ba75a
Deleting lots of code as part of my cleanup. More classes tagged for removal. Many more walkers have their days numbered.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1885 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-20 12:23:36 +00:00
2a26bb42dd
Softclipping support in clip reads walker. Minor improvement to WalkerTest -- now can specify file extensions for tmp files. Matt -- I couldn't easily create non-presorted SAM file. The softclipper has an impact on this.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1878 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-19 21:54:53 +00:00
10bde9e77b
Integration test for BTT calculator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1876 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-19 18:21:55 +00:00
cfa86d52c2
ensure that in the indel case we don't allow identification as both an insertion and deletion at the same location in the VCF ROD
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1875 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-19 18:21:00 +00:00
bb180a23ef
Updated MD5
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1871 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-18 05:30:38 +00:00
b9e8867287
-push allele frequency and genotype likelihood variable definitions down into the subclasses so that they can use different data structures
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-use slightly more stringent stability metric
-better integration test
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1869 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-18 04:22:17 +00:00
d6385e0d88
simpleComplement function() in BaseUtils. Generic framework for clipping reads along with tests. Support for Q score based clipping, sequence-specific clipping (not1), and clipping of ranges of bases (cycles 1-5, 10-15 for example). Can write out clipped bases as Ns, quality scores as 0s, or in the future will support softclipping the bases themselves.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1868 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-16 22:29:35 +00:00
bdb34fcf38
Updated integration tests for VariantEval. Hooray for IT!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1866 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-16 20:00:29 +00:00
41a95cb3f0
fixing unified genotyper test for change: VCF output now emits no calls as ./.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1865 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-16 19:38:58 +00:00
8aacc43203
VCF output now emits no calls as ./.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1863 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-16 18:51:31 +00:00
07b134a124
Added some integration tests for multiple samples
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1861 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-16 15:22:10 +00:00
96972c3a5c
a fix for a bug Eric found: if your first call contains fewer samples than calls at other loci, your VCFHeader got setup incorrectly.
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Also moved a buch of Lists over to Sets for consistancy.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1859 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-16 04:57:50 +00:00
a69ea9b57c
Cleaning up the VCF code, adding lots of tests for a variety of edge cases. Two issues are still outstanding: updating the no call string with the standard 1000g decided on today, and fixing Eric's issue where not all the VCF sample names are present initially.
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also: their, I hope your happy Eric, from now on I'll try not to flout my awesomest grammer in the future accept when I need to illicit a strong response :-)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1858 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-16 04:11:34 +00:00
eb90e5c4d7
changes to VCF output, and updated MD5's in the integration tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1836 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-14 18:42:48 +00:00
d89bc2c796
This class no longer outputs in sequenom format
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1832 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-14 17:16:36 +00:00
0c06bf9dbc
Explicitly set output to GELI now that default is VCF
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1824 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-13 22:12:03 +00:00
32d55eb2ff
Fix issue Eric was seeing with java.lang.Error in unmap0.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1804 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-09 17:46:56 +00:00
f4b6afb42c
JVM issue id 5092131 ( http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=5092131 )
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was causing OOM issues with the new mmapping fasta file reader during large jobs.
Temporarily reverting the reader until a workaround can be found.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1801 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-09 04:45:46 +00:00
98e3a0bf1a
VCF can now be emitted from SSG. The basic's are there (the genotype, read depth, our error estimate), but more fields need to be added for each record as nessasary.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1797 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 19:50:04 +00:00
df8ea8f437
UG integration test. This was the old SSG test with MD5s updated.
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I'll need to add some multi-sample tests in a bit...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1791 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 17:43:58 +00:00
008455915a
One way of making the integration test stop failing is to remove it...
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[waiting for Matt to cringe...]
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1789 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 17:08:41 +00:00
04fe50cadd
*** We no longer have a separate model for the single-sample case. ***
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For now, a single sample input will be special-cased in the EM model - but that will change when the EM model degenerates to the single sample output with a single sample as input. For now, the EM code for multi-samples isn't finished; I'm planning on checking that in soon.
The SingleSampleIntegrationTest now uses the UnifiedCaller instead of SSG, and so should all of you. More on that in a separate email.
Other minor cleanups added too.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1785 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 14:08:57 +00:00
fcb6a992c8
Switched IndexedFastaSequenceFile over to use memory mapping to load data rather than
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the loop-with-small block size. Performance improvements in loading refs are extreme;
segments can be loaded in <1ms. chr1 in its entirety can be loaded in 1.5sec (down
from 30sec).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1781 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 00:07:15 +00:00
f9a0eefe4b
GELI_BINARY is now functional, and can be used as a variant type in SSG (-vf=GELI_BINARY). Also fixed the max mapping quality column in both GELI output formats, we haven't been correctly outputing up until now.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1774 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-07 18:20:34 +00:00
3aec76136f
Removing the AllelicVariant interface, which is replaced by the Variation interface.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1770 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-06 17:44:24 +00:00
66fc8ea444
GSA-182: Adding support for BED interval files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1767 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-06 02:45:31 +00:00
7fc4472e6d
A big fix for MergingSamRecordIterator, where we weren't correctly handling the comparisons of SAMRecords correctly (we weren't applying the new reference index first, so sometimes the MT contig would be ID 23, sometimes 24 in different records).
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Also a fix to the GLF tests, and a correction to PrintReadsWalker to remove the close() on the output source, the source handles that itself (and you get a double close).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1758 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-02 19:35:35 +00:00
7249fade05
updated
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1756 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-02 18:10:34 +00:00
e885cc4b21
changes for corrected GLF likelihood output, along with better tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1754 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-01 20:45:05 +00:00
2e4949c4d6
Rev'ing Picard, which includes the update to get all the reads in the query region (GSA-173). With it come a bunch of fixes, including retiring the FourBaseRecaller code, and updated md5 for some walker tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1751 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-30 20:37:59 +00:00
70e1aef550
Better integrate the @ArgumentCollection into the command-line argument parser. Walkers can now specify their own @ArgumentCollections. Also cleaned up a bit of the CommandLineProgram template method pattern to minimize duplicate code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1746 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-29 22:23:19 +00:00
5662a88ee1
Cosmetic change to list sampling functions: the typical usage of n and k were reversed. No change in functionality of the classes has been made and unit tests still pass.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1736 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-28 18:12:32 +00:00
130a01a40a
delete the integration test temp files when the test is over
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1727 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-25 16:34:08 +00:00
d262cbd41c
changes to add VCF to the rod system, fix VCF output in VariantsToVCF, and some other minor changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1715 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-24 15:16:11 +00:00
eeb14ec717
a couple of light changes to GenomeLocSortedSet.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1708 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-23 20:38:53 +00:00
11c32b588f
fixing VariantEvalWalkerIntegrationTest md5 sums, a couple comment changes, and a little bit of cleanup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1690 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-22 20:54:47 +00:00
b0fa19a0b2
Fixed recal integration test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1689 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-22 20:22:32 +00:00
6780476fb5
updated to deal with new dbSNP rod
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1687 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-22 19:46:32 +00:00
83a9eebcc4
fixed a bug I checked in that Eric found, for intervals with no start or stop coordinate. Now I owe Eric a cookie, and Milk Street is so far away. Damn.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1679 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-22 04:34:18 +00:00
7bfb5fad27
fixing the dbSNP test. Also removing unnessasary comments from the GenomeLocParser, added some tests, and commented out the performance test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1676 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-21 23:32:24 +00:00
39a47491a9
changes to make GenomeLoc string parsing 25% faster
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1675 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-21 22:37:47 +00:00
a6bd509593
Changing the carpet under your feet!! New incremental update to th eROD system has arrived.
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all the updated classes now make use of new SeekableRodIterator instead of RODIterator. RODIterator class deleted. This batch makes only trivial updates to tests dictated by the change in the ROD system interface. Few less trivial updates to follow. This is a partial commit; a few walkers also still need to be updated, hold on...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1667 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-21 16:55:22 +00:00
b6d7d6acc6
fix for the eval tests, and a change to the backedbygenotypes interface, more changes to come
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1661 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-18 22:25:16 +00:00
7b39aa4966
Adding the VCF ROD. Also changed the VCF objects to much more user friendly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1658 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-18 20:19:34 +00:00
01a9b1c63b
Fix for problem where err stream remapped to output stream in certain cases, (hopefully) completing Matt's hat trick of fail. Thanks, unit tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1634 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-16 08:33:56 +00:00
eedf55e94d
temp fix for a broken test, we'll fix the test tomorrow. We promise, we're engineers, we love our tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1633 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-16 04:36:42 +00:00
542d817688
more cleanup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1631 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-15 21:42:03 +00:00
b401929e41
incremental clean-up and changes for VariantEval, moved DiploidGenotype to a better home, and fixed a spelling error.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1624 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-15 04:48:42 +00:00
6783fda42a
Updated unit test to reflect changes to vcf output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1623 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-15 01:56:08 +00:00
e03fccb223
Changes to switch Variant Eval over to the new Variation system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1611 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-14 05:34:33 +00:00
5b41ef5f70
rod DBSNP had a bug where the reference wasn't calculated correctly under certain conditions. Fixed getRefBasesFWD and getRefSnpFWD so that they were more in line with getAltBasesFWD and getAltSnpFWD. Also updated Variant Eval tests to reflect this change.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1609 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-13 23:48:58 +00:00
6e13a36059
Framework for ROD walkers -- totally experiment and not working right now
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1600 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-12 19:13:15 +00:00
17ab1d8b25
General purpose merging iterator implementation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1593 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-12 19:06:15 +00:00
e24c8d00d5
So, the VCF spec allows for an optional meta field in the header representing the date. However, using this field means that integration tests run on the vcf file will fail the MD5 test (which is what happened to the VariantFiltration test this morning after working just fine yesterday).
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After consulting our resident expert (Aaron), we're going to (temporarily) remove the date from the vcf output until we can come up with a better solution. However, this shouldn't cause any short-term problems because the data truly is optional.
VF test's MD5s are updated.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1580 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-10 14:28:43 +00:00
5a64a80ab5
changes to the variation class, updates to SSG, updated tests based on changes to the SSGenotypeCall, and added the ability to run a single integration test from using the build script.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1577 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-10 04:31:33 +00:00
1362a56227
Added fasta tests and small fix to cleaner test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1575 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-10 03:13:11 +00:00
8ca89279aa
Added a test for VariantFiltration and the VECs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1574 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-10 02:21:14 +00:00
bed646e4f6
Adding cleaner test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1561 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 16:05:56 +00:00
d9588e6083
bug fixes to LIBS and LIBH following ultra-aggressive regression testing across 454, solid, and solexa
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1558 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 15:36:12 +00:00
0df6a9da5c
-Seperating out normal (unit) tests and integration tests. From now on if your test are more of an integration test (i.e. you're testing a walker and all the subunits it relies on) please name the test "______IntegrationTest.java" instead of "______Test.java".
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-Bamboo will now run the integration tests once a day, and the normal units tests on each check-in.
-Also added a bunch of unit tests for VariantEval walker
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1555 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 15:01:40 +00:00
eeb9b6eb13
GenotypeLikelhoods now support a cache per subclass, avoiding genotyping clashes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1554 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 10:39:14 +00:00
0cc219c0df
-Added unit test for walkers dealing with intervals for cleaning
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-I also uncovered a corner case in the cleaner that for some reason was commented out but shouldn't have been. Hooray for unit tests!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1553 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 02:35:17 +00:00
ec0f6f23c7
LocusIterationByState is now the system deafult. Fixed Aaron's build problem
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1552 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 01:28:05 +00:00
ea6ffd3796
initial VariantEvalWalker test. More to be added soon...
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Also fixed the case where MD5 sums had leading zero's clipped off
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1551 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 01:02:04 +00:00
1c3d67f0f3
Improvements to the CountCovariates and TableRecablirator, as well as regression tests for SLX and 454 data
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1539 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-04 22:26:57 +00:00
2b0d1c52b2
General WalkerTest framework. Includes some minor changes to GATK core to enable creation of true command-line like GATK modules in the code. Extensive first-pass tests for SSG
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1538 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-04 19:13:37 +00:00
0cc634ed5d
-Renamed rodVariants to RodGeliText
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-Remove KGenomesSNPROD
-Remove rodFLT
-Renamed rodGFF to RodGenotypeChipAsGFF
-Fixed a problem in SSGenotypeCall
-Added basic SSGenotype Test class
-Make VCFHeader constructors public
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1536 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-04 18:40:43 +00:00
a08c68362e
Renaming error to getNegLog10PError(); added Cached clearing method to GL; SSG now has a CallResult that counts calls; No more Adding class to System.out, now to logger.info; First major testing piece (and general approach too) to unit testing of a walker -- SingleSampleGenotyper now knows how many calls to make on a particular 1mb region on NA12878 for each call type and counts the number of calls *AND* the compares the geli MD5 sum to the expected one!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1530 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-04 12:39:06 +00:00
49a7babb2c
Better organization of Genotype likelihood calculations. NewHotness is now just GenotypeLikelihoods. There are 1, 3, and empirical base error models available as subclasses, along with a simple way to make this (see the factory).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1481 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-30 19:16:30 +00:00
ebanks
aaron
depristo
chartl
rpoplin
hanna
andrewk
asivache