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766 Commits (7b452ea2b9ad2d2f3e8bbfcbfb0e818f0a87f18d)

Author SHA1 Message Date
droazen 7b452ea2b9 Fix for bug GSA-430: Can't specify same BAM file twice on the command line. An ArgumentException with an appropriate error message and a list of the duplicate BAMs is now thrown in this case. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5542 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-30 22:23:24 +00:00
rpoplin 5ddc0e464a Under guidance from Matt added ability to use key-value tags with ROD binding command line arguments, so now one can say -B:hapmap,VCF,known=false,training=true,truth=true,prior=12.0 hapmap.vcf and get the tags in a walker. Look at ContrastiveRecalibrator for an example of how to use the new ReferenceOrderedDataSource.getTags(). Removed references to FDR in tranches since we are only using truth sensitivity. Finally fixed long standing bug where tranche filters weren't set appropriately. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5536 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-29 21:04:09 +00:00
depristo cd8321cdc9 Removed the completely unused generic but extremely expensive infrastructure for dynamic LocusIteratorFilters. Now the one, and probably only useful one, is called directly in the LocusIteratorByState itself to filter adaptor bases from reads. This shaves 10% off the runtime of all walkers, apparently. Has the additional benefit of eliminating a lot of complex infrastructure that resulted ultimately in only a single function call. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5525 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-27 20:48:24 +00:00
depristo 3bcd4c5d75 --simplifyBAM is now in the SAMFileWriterArgumentTypeDescriptor, as suggested by map. PrintReads has an integrationtest now that writes out a 1 MB bit of HiSeq normally, with compress 0, and with simplifyBAM on. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5521 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-26 14:57:18 +00:00
ebanks 69646ff840 ... and the corresponding integration test update 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5496 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-23 01:58:07 +00:00
ebanks 1c95208e26 Finally found the bug that everyone is reporting on GS. Iterators on PriorityQueues aren't guaranteed to return elements in sorted order (a pretty stupid contract) - so we were passing items to the constrained writer out of order. Just do a Collections.sort instead (1 line of code). Happy father's day! 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5476 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-18 21:28:19 +00:00
depristo 3e3ec85807 Checked for consistency with the previous integration tests, and updated the walker and test to use the new I/O system (always prints 4 digits on floats. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5433 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-13 15:24:22 +00:00
depristo ee8f2871f7 A better output for Genotype Concordance summary. Now does only % comp hom-ref called hom-ref, het called het, and hom-var called hom-var, which are the quantities we typically show in slides. Updated intergration tests to reflect this change. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5429 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-12 02:03:48 +00:00
ebanks 3596c56602 New attempt at the constrained movement version of the indel realigner (I've kept around the old writer for now). The new contract is that the realigner must ask permission before trying to clean an area; permission will be denied by the CM-Manager if it was required to flush its cache of reads because of too much depth within a distance of maxInsertSizeForMovingReadPairs. Added integration tests to cover different max cache sizes, including an expected exception when too small a value is chosen. The actual logic changes were fairly minor - much of this commit is really just some cleanup. I'd like to throw 1000G Phase I at it, but will respectfully wait for Ryan to hit his deadline before doing so. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5414 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-10 02:48:29 +00:00
rpoplin ff7edc4493 Minor bug fix in empiricalMu prior calculation in VQSR. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5412 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-10 00:42:38 +00:00
rpoplin 509daac9f7 Minor bug fix in k-means implementation. Updating VQSR integration tests in preparation for VQSRv2 by removing some unused features such as VariantDatum.weight and ti/tv cutting. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5410 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-09 00:26:28 +00:00
delangel 00ac51acc8 Added several integration tests for UG indel caller: 
- Basic
- Multiple technology
- Test minIndelCnt parameter

Added also 2 disabled tests:
- Parallelization: issue w/code right now is that if -nt > 1, filter field shows "PASS" instead to ".", cause TBD
- Genotype given alleles mode: code not working yet.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5404 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-08 16:21:21 +00:00
kiran d0598c7a04 Somehow missed this test when I was updating the md5s 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5400 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-07 23:53:42 +00:00
kiran b6339967f8 Updated GenomicAnnotator integration tests to include the -NO_HEADER argument so that they tests op yelling about trtrivial differences 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5398 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-07 23:07:01 +00:00
kiran 43056d0188 Fixed integration test to reflect changes regarding when comp tracks got subset to fewer samples and whether no-call sites would get pulled in for comp tracks. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5393 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-07 20:25:57 +00:00
kshakir dc33fbed7c Switched the CVUnitTest broken info from an Integer to a String since as of r5383 Integers are no longer broken when converted to Floats. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5390 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-07 16:33:14 +00:00
depristo af71576a07 CalculateChromosomeCounts() now only calculates AC, AF, and AN when there are genotypes. Can now combine variants with headers that differ in only whether a field is a integer or a float. Updated CombineVariants integrationtest, as incorrect AC values where being calculated in the previous GS outputs. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5383 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-06 19:25:52 +00:00
kiran 1861ca90fc A change to the definition of CpG sites (is now, from 5' to 3' a CG dinucleotide in the reference, and the CpG site is at the C, rather than either at the C or a G). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5373 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-04 15:36:07 +00:00
hanna 7a22f19366 More descriptive error when VerifyingSamIterator hits an inconsistent alignment. Also updated 
case UserException.MalformedBAM to match case of UserExceptio.MissortedBAM for consistency and
ease-of-use.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5364 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-03 03:55:24 +00:00
ebanks bb969cd3a2 EMIT_ALL_SITES now does exactly that - even when there's no coverage or too many deletions 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5343 348d0f76-0448-11de-a6fe-93d51630548a
 2011-03-01 05:05:00 +00:00
ebanks 5ac9af472c Adding performance test for case with very high coverage (> 600,000x) over an interval 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5336 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-28 19:48:56 +00:00
hanna 600f73cbd6 A checkpoint commit of two BAM reading projects going on simultaneously. These two projects 
are works in progress, and this checkin will provide a baseline against which to gauge 
improvements to both projects.

Low-memory BAM protoshards (disabled by default):
- Currently passing ValidatingPileupIntegrationTest.
- Gets progressively slower throughout the traversal, but should run at least as fast as original implementation.
- Uses 10+ file handles per BAM, but should use 3.

BAM performance microbenchmark test system:
- Currently tests performance of BAM reading using SAM-JDK vs. GATK
- Tests do not hit all GATK performance hotspots.
- New tests that require input data in a slightly different form are hard to implement.
- Output of test results is not easily parseable (investigating Google Caliper for possible improvements).



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5317 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-25 17:50:32 +00:00
ebanks cba88a8861 Elegant solution to the determinism problem: force testNG to run tests in the order that I want it to. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5312 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-24 21:32:35 +00:00
ebanks 15dfac6bf7 Updating integration test to be in sync with previous commit 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5309 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-24 20:21:58 +00:00
ebanks 06e3c34e7f Updating performance test to be in sync with previous commit 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5308 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-24 20:13:35 +00:00
chartl 97e1a5262e -ct x no longer includes coverage in the previous bin 
BatchMerge - additional support for indels (can't just test the alternate allele when it's an extended event, must also specify that you want to use the dindel model when you actually test the allele)



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5300 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-24 15:52:04 +00:00
ebanks ee6f112556 Phase 3: constrained movement is now the only option available in the realigner (so I guess technically it's not really an option). Several command-line options are deprecated. Code cleaned up. Wiki updated. Release coming. One phase left... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5299 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-24 14:59:48 +00:00
ebanks 93888e570b Phase 2: after hours of testing, confirming that constrained mode looks good so moving the integration tests over to use it. Some cleanup. More cleanup coming in Phase 3. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5298 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-24 06:23:41 +00:00
ebanks c59c8b9872 Phase I of my promise to Mark: fleshed out integration tests for Indel Realigner 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5297 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-23 21:05:20 +00:00
ebanks 318035c147 Fixing up the output system of the Unified Genotyper. Deprecating the -all_bases and -genotype arguments. Adding instead the --output_mode (EMIT_VARIANTS_ONLY, EMIT_ALL_CONFIDENT_SITES, EMIT_ALL_SITES) and --genotyping_mode (DISCOVERY, GENOTYPE_GIVEN_ALLELES) arguments. UG now does the correct thing when passed alleles (bound to the 'alleles' rod) to use for genotyping; added several integration tests to cover this case. This commit will break the batched calls merging script, but Chris knows this and is ready for it... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5288 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-22 06:07:18 +00:00
kiran 52f860c9b2 Modified MD5s to account for Andrey's new MNP column in CountVariants. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5274 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-18 13:13:58 +00:00
kiran cb95e68fc0 CpG is no longer a standard stratification. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5273 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-18 07:17:35 +00:00
kiran 9ddee96f93 When subsetting by sample, need to take extra care that hom-ref sites don't accidentally get treated as variant sites in CompOverlap. Renamed convenience method for creating command-lines in integration tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5272 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-18 06:26:38 +00:00
kiran 92c82200c9 Fixed an issue where an eval module with TableType objects would get an extra, empty table in the output, screwing up the parse in R. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5267 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-17 23:03:46 +00:00
kiran d3660aa00e Very basic functionality for annotating indels (specifies whether the indel is frameshift, inframe, or non-coding). Does not attempt to recalculate the variant codon, variant amino acid, or whether the site falls within a splice region. Added a convenience method to WalkerTest for building command-line arguments with the proper spacing (so that I stop getting annoyed when I've gotten it wrong and the test system yells at me. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5235 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-13 17:58:20 +00:00
ebanks 9554df1a7c Adding integration test for indels in VF 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5227 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-11 16:58:57 +00:00
hanna b992abb6eb A few more unit tests plus some extra 
functionality for BAM index visualization.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5222 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-09 01:51:34 +00:00
kiran ecbc38aff0 If no comp rod is specified, specify the dummy name none so that we still get counts. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5211 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-07 19:24:52 +00:00
ebanks 698096dc5a Moving VariantsToVCF to the proper directory; removing the oneoffs CG indel converter in preparation for a ligitimate CG variant Feature class in the works. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5207 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-07 05:21:01 +00:00
kiran 35c688ac67 Updated md5 for testVCFStreamingChain to reflect latest changes to VariantEval. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5206 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-06 21:22:05 +00:00
kiran 1085bbf303 Fixed issue where all comp tracks were being treated as known tracks. Fixed issue where multiple JEXL expressions were causing an exception because the underlying object did not implement the Comparable interface. Fixed issue where variants being compared to the known track were not being checked for equality of variation type. Fixed issue where functional annotations were not being iterated over properly. Refactored a lot of helper methods into a separate VariantEvalUtils utility class. Significantly expanded the test suite using a small VCF with SNPs, indels, and non-variant loci which makes it much easier to see what the proper answer should be, and included the appropriate grep and awk commands in the comments to confirm the values. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5204 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-06 19:19:20 +00:00
hanna 5c3198520c A few minor modifications masquerading as significant changes according to 
svn's logs:
- Copied BAM indexing engine from Picard back into the GATK anticipating
  shard merging algorithm.  Tried to leave most of the building blocks in
  Picard.  If this turns into a logistical nightmare, I'll merge the building
  blocks into the GATK as well.
- Reorganized the org.broadinstitute.sting.gatk.datasources package, giving
  better separation of query and management functionality for reads, ref, rmd,
  and samples.  
- Merged Shard building blocks into org.broadinstitute.sting.gatk.datasources.
  reads package, indicating it's current strong relationship with the reads,
  rather than the general unifying element I wish this would be.
- Collapsed BAMFormatAwareShard into Shard.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5184 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-03 17:59:19 +00:00
kiran 9ddc95c833 NewEvaluationContext needs to be generated in the inner loop. Otherwise, multiple comp tracks end up getting routed to the same row of the output table. Added test to cover multiple comp tracks. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5181 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-03 07:04:53 +00:00
kiran cb6454bf98 Multiple eval tracks should be bound with different names, rather than just 'eval'. Added tests to cover usage with multiple tracks. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5177 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-02 22:33:50 +00:00
kiran 2732c839d4 Restored parallelism and associated tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5170 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-02 02:04:03 +00:00
kiran fd8dd8fb9b Fixed an issue where a no-call in the eval track would prevent a site from a comparison track from being loaded. Added a new test to cover the use case. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5169 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-02 01:47:53 +00:00
hanna 06b63d8336 Pulled out CpG stratification in test results at Kiran's suggestion. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5165 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-01 18:36:09 +00:00
hanna 91297c138b Update VCFStreamingIntegrationTest to use new variant eval command-line 
arguments, output format.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5162 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-01 15:40:43 +00:00
hanna 7d89ce820b Got tired of waiting for Kiran to fix the build: updated NewVariantEval -> 
VariantEval.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5161 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-01 15:32:39 +00:00
hanna 96241c6637 More testng fallout: fixing another seemingly 'random' issue arising from an 
alternate test ordering.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5160 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-01 15:25:50 +00:00