09811b9f34
Now that we always output the VCF header, make sure that we correctly handle the situation where there are no records in the file. Added unit tests as well.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2333 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 19:51:05 +00:00
2ea7632b76
The SNP genotype concordance module is now more comprehensive.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2330 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 18:34:33 +00:00
2de7e1a178
Move VariantAnnotator over to use a StratifiedAlignmentContext split by sample.
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The only major difference is that we are now able to get accurate allele balance ratios.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2321 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 05:28:28 +00:00
e6f541fdca
Forgot to update integration test last night
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2308 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 12:57:10 +00:00
ee691b8899
Added a whole bunch of unit tests for VCF reading.
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We could still use more, but this is a good start.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2303 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 03:31:23 +00:00
f7c44ad019
- Read in arguments for the header based on reflection
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- Hook up Variation and Genotype in SSG
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2300 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-09 21:35:33 +00:00
40c2d7a4bc
Fix all-bases-mode and genotype-mode in the UG and add integration tests for them.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2295 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-09 17:41:30 +00:00
4e54b91ce4
UG now outputs the FORMAT header fields when there's genotype data.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2294 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-09 16:31:07 +00:00
fb900b12e1
VariantFiltration now details the filters it has used in the header of the VCF it produces.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2292 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-09 15:36:15 +00:00
8a1c876104
Weird. I thought I had updated these md5s...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2289 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-09 03:31:41 +00:00
717eb1de96
- Depth annotation now includes MQ0 reads
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- Removed MQ0 annotation
- Updated RMS MQ annotation to use new pileup
- UG now outputs all of its arguments as key/value pairs in the header (for VCF)
- Cleaned up VCFGenotypeWriterAdapter interface a bit
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2288 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-09 02:53:00 +00:00
e8822a3fb4
Stage 3 of Variation refactoring:
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We are now VCF3.3 compliant.
(Only a few more stages left. Sigh.)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2287 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-08 21:43:28 +00:00
9e2f831206
A bit of cleanup in preparation for Picard patch.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2286 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-08 16:09:04 +00:00
1d5b9883db
Added --solid_recal_mode argument to experiment with different ways of dealing with solid reference bias. Currently the default option is DO_NOTHING which means use the same behavior as the old recalibrator. Eventually the new methods in RecalDataManager will be moved over to a SolidUtils class. Added transition and transversion methods to BaseUtils that work like simpleComplement, used with the color space in my solid methods. Also, initial check-in of HomopolymerCovariate.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2276 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-07 14:26:27 +00:00
8f461d3c40
Critical bug fix for VariantEval dbSNP calculations. Moved the system over to the new improved ROD iterators, resulting in dbSNP rates jumping 5% or so, due to masking of true SNPs by preceding indels.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2274 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-07 03:36:38 +00:00
c0528cd88e
Updated the CallsetConcordance classes to use new VCF Variation code... and uncovered a whole bunch of VCF bugs in the process. I'm not convinced that I got them all, so I'll unit test like crazy when the refactoring is done.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2272 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-06 11:43:40 +00:00
b6f8e33f4c
Stage 2 of Variation refactoring:
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VCFRecord now implements Variation, VCFGenotypeRecord now implements Genotype.
Because of this change, RodVCF is now just a wrapper around the VCFRecord and does nothing else. Also, one can call toVariation on the VCFGenotypeRecord and it returns the VCFRecord.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2271 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-06 06:48:03 +00:00
08f2214f14
Stage 1 of massive Variation/Genotype refactoring.
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This stage consists only of the code originating in the Genotyper and flowing through to the genotype writers. I haven't finished refactoring the writers and haven't even touched the readers at all.
The major changes here are that
1. Variations which are BackedByGenotypes are now correctly associated with those Genotypes
2. Genotypes which have an associated Variation can actually be associated with it (and then return it when toVariation() is called).
The only integration tests which need to be updated are MSG-related (because the refactoring now made it easy for me to prevent MSG from emitting tri-allelic sites).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2269 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-06 03:12:41 +00:00
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
aaron
ebanks
hanna
rpoplin
depristo
chartl