721e8cb679
VariantsToTable now supports wildcard captures. -F PREFIX* now captures all fields that begin with PREFIX, output as a comma-separated list of unique values. Added integration test for VariantsToTable since I find it so useful.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4706 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-18 18:54:59 +00:00
8cba86a69d
Trivial code organization for the haplotype score
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4703 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-18 12:32:55 +00:00
9f356b6cd0
Package all walkers in org/broadinstitute/sting/gatk/walkers directory in release.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4702 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-18 02:33:45 +00:00
90711d445c
Change the interface for RMDTrackBuilder, therefore always mandating the specification
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of a sequence dictionary and related info. This will hopefully eliminate the cases in
which the refseq track depends a sequence dictionary / contig parser that hasn't been
specified.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4700 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-17 19:00:17 +00:00
367cc9135f
Use VariantContext and Genotype accessor methods for attributes that will return null for unparseable data
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4699 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-17 18:19:56 +00:00
2f3578182a
Added VERY preliminary version for merging refseq annotations as SNPs are merged
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4698 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-17 16:49:12 +00:00
e2f7f33ce7
Added getIntegerAttribute()
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4697 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-17 16:33:07 +00:00
d86ab2becb
JEXL expressions now generate exceptions, not warnings. Tools should catch the runtime exception to handle correctly. Removed unncessary complexity from the JEXL contexts
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4695 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-17 16:08:16 +00:00
539651de30
Initial version of Indel Statistics module for Variant Eval - not for general use yet, needs more verification and more work. Older IndelHistogram module will be obsolete with this new walker. Right now, for each sample (and for all samples), the following are computed:
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- Number of insertions
- Number of deletions
- Length distribution for indels.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4694 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-17 15:52:01 +00:00
01b721ab61
Passing ReviewedStingExceptions through the HMS.
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Added a @Hidden experimental argument -validate to VariantEval that allows external JEXL assertions that must evaluate to true will throw an exception.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4692 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-16 21:50:42 +00:00
24ec35deaf
- Reintroduce test dependency so that the tests passing / failing is not
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dependent on the contents of the integrationtest directory. Will figure
out how to better manage the integrationtest directory at some point in
the future.
- Up the max heap size for tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4691 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-16 19:55:20 +00:00
62f02bf30a
Minor JAVA visibility updates
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4690 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-16 15:28:58 +00:00
f1b0f3bc49
Putting my changes from earlier in the day back in after someone (rhymes with 'Dark') trounced on them with his last commit...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4687 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-16 01:55:50 +00:00
8ff4e4cb25
Cleanup testng listener configuration.
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- Add StingTextReporter, which provides a text dump of the errors to the
console. Had to create our own reporter (inheriting from the standard
TestNG TextReporter) to work around a configuration issue with the
TextReporter. In an ideal world, I'd report this on the TestNG mailing
list and help them resolve the issue, but this solution is relatively
robust at the moment and life is too short.
- Added back the failed test listener, which generates the testng-failed.xml
file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4686 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 23:43:14 +00:00
b677080858
Initial checkin of the ValidationGenotyper. Not intended to be used by anybody yet. Only here for archival purposes at this point.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4685 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 22:33:49 +00:00
ef2f6d90d2
VQSR now operates on LOD scores in the INFO field directly, and doesn't adjust the QUAL field. New format for tranches file uses LOD score. Old file format no longer supported. log10sumlog10() function, a very useful utility in MathUtils. No more ExtendedPileupElement! Robust math calculations in GMM so that no infinities are generated! HaplotypeScore refactored to enable use of filtered context. Not yet enabled... InferredContext getDouble and getInteger arguments now parse values from Strings if necessary
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4684 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 22:19:22 +00:00
5b83942cee
- Fix DepthOfCoverage so that, when it abuses the ROD system by instantiating a track in onTraversalDone, it also supplies the correct sequence dictionary and parser.
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- Changed RMDTrackBuilder to use SequenceDictionaryUtils.validateDictionaries for ref <-> ROD sequence dictionary validation.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4683 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 20:34:04 +00:00
2af508ef83
Better docs, as requested by Matt
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4681 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 18:24:15 +00:00
62be55376b
no longer useful
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4677 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 17:53:33 +00:00
35382468ee
Better error checking/output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4676 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 16:36:34 +00:00
7a3a464959
Finally, the logic is right
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4674 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 14:02:09 +00:00
8d66637fc2
Bug fix for VariantsToTable with filtered records
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4673 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 13:49:16 +00:00
d76b87d6e3
Useful debug file output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4672 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 13:36:52 +00:00
28142408ff
Refactoring so that all counting in UGv2 is done on the filtered context. In particular, tests for empty pileups and too many spanning deletions now use the correct counts. Also, -all_bases mode now trumps all; this one is for you, chartl.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4671 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 05:01:12 +00:00
c7229abbf7
Get rid of 'meaningless and random values' that prevent Sendu from merging PG lines. I have to admit that he did have a good point there.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4670 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-15 03:35:12 +00:00
2fd816ac5f
Updated ordering of integration tests. GVC > VR > AVC
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4669 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-14 06:33:28 +00:00
cb1e8ad43a
Temp bug fix for indel genotyper: if there are two or more variant contexts at a site, just choose the first one containing an indel and genotype that. There might be cases where IGv2 emits 2 indel variant contexts in at the same ref location which made us fail there. A better solution will be to form underlying haplotypes supported by reads and compute likelihoods of that.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4667 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-14 00:21:54 +00:00
82f9327b5e
Throw the right exception
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4666 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-13 22:18:42 +00:00
44d0cb6cde
New version of cutting routines for VQSR. Old code removed. Working unit tests. Best practice with testng integration test (everyone look at it). Walker test now allows you to not specify no. input files, if it can infer input counts from MD5s
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4664 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-13 16:19:56 +00:00
62a106ca5a
Disabled VariantGaussianMixtureModelUnitTest
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4663 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-13 03:53:33 +00:00
673fa841a4
Updated PluginManager so that during testing Queue can dynamically compile and load separately multiple class directories into the same class loader.
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Removed obsolete usages of PackageUtils with updated PluginManager.
Ported Queue interval utilities written in scala over to Sting's java IntervalUtils.
Added a very basic intergration test to ensure that the fullCallingPipeline.q compiles.
Added options to specify the temporary directories without having to use -Djava.io.tmpdir (useful during the above integration test).
While adding tempDir added options to specify the run directory from the command line, for example "-runDir v1".
Upgraded to scala 2.8.1 and updated calls to deprecated functions.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4661 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-12 20:14:28 +00:00
42acc968b1
Unit tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4660 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-12 20:09:39 +00:00
b51762c279
When you commit code late at night you tend to make careless mistakes... like forgetting to update integration tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4658 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-12 14:41:10 +00:00
988da428ae
Bug fix for old style tranches file. ApplyVariantCuts moved over, and passes integration tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4657 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-12 14:38:26 +00:00
c5f8c4dd0d
VariantEval test for tranches file, plus cutting over VE to use the generic Tranches framework
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4656 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-12 13:52:40 +00:00
69de3e51bf
Better precision for the calculated AF value. Now looks at the total number of samples to determine how much precision is necessary. Also, changing default min BQ used for calling in UGv2 to Q17.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4655 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-12 08:31:40 +00:00
ec83a4b765
Initial commit, without any tool changes, of a new infrastructure for determining tranches. This new version walker up from the lowest quality snps and determines Ti/Tv. This is marginally more stable than moving in the other direction when there are few novel variants (exomes). Can make a substantial difference in the size of the call set (10-20%). I'll hook it into the main system now. Includes an new class Tranche, isolated read/writing utilities that are now testing in TestVariantRecalibrator, which should be moved to UnitTest as soon as I can figure out how to do this on my mac.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4654 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-11 23:52:49 +00:00
ed6396ed43
No longer getting the inet, it seems to potentially hang the JVM
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4653 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-11 23:49:42 +00:00
2f6666a988
Correcting traversal statistics
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4652 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-11 22:46:58 +00:00
dbde721dd0
Bug fix for filtered records
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4651 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-11 18:54:51 +00:00
698e5cf345
for GATK style codecs, make sure we fill in their GenomeLocParser from the RMDIndexer
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4650 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-11 18:44:15 +00:00
2f3be24a00
Improvement in exact allele frequency calculation model (still under test, but this is definitely better than what I had before). Instead of approximating log(10^x+10^y) as max(x,y), approximate full Jacobian formula max(x,y)+log(1+10^-abs(x-y)) with static lookup table for the second term.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4647 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-11 01:22:35 +00:00
2e0296fef9
NWayOut logic slightly changed: 1) results.list file is gone; 2) now with -nWayOut one can specify either a) suffix to attach to every output file (i.e. cleaned reads from inputK.bam will be sent to inputK.suffix.bam) or b) *.map tab-separated file that must list <input_name> <output_name> mappings, one per line, for every input file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4645 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-10 20:32:16 +00:00
a1adfb91ce
And now @Hidden tags are really in place :-/
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4644 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-10 20:28:40 +00:00
68ce55148e
(pseudo-)genotyping functionality added: force-emits calls (including REF) at specified locations. Currently @Hidden for testing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4643 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-10 20:25:40 +00:00
8e36a07bea
Convert GenomeLocParser into an instance variable. This change is required
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for anything that needs to be simultaneously aware of multiple references, eg
Queue's interval sharding code, liftover support, distributed GATK etc.
GenomeLocParser instances must now be used to create/parse GenomeLocs.
GenomeLocParser instances are available in walkers by calling either
-getToolkit().getGenomeLocParser()
or
-refContext.getGenomeLocParser()
This is an intermediate change; GenomeLocParser will eventually be merged
with the reference, but we're not clear exactly how to do that yet. This
will become clearer when contig aliasing is implemented.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4642 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-10 17:59:50 +00:00
5ef4b234d8
Updates for broken integration tests. Counting annotations (AC, AF) now work correctly for AC = 0 sites
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4640 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-09 19:43:43 +00:00
4759fdd2ac
V1 of read and variant simulator and assessor. SimulateReadsForVariants generates BAM and VCF with given combinations of variant and read properties. AssessSimulatedPerformance produces a table suitable for analysis in R
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4637 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-08 21:01:33 +00:00
97db593efb
making my last commit message actually true
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4636 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-07 18:26:23 +00:00
be499fc986
making the reference optional (the GATK will set it on the first run if it's not included), and setting the seq index if they do supply it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4635 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-07 18:15:31 +00:00
depristo
hanna
fromer
delangel
kshakir
ebanks
rpoplin
aaron
asivache