04e38929f0
Disabling parallelized version of VE integration tests. Still slow, but not
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deadlocking any more.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4580 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-27 02:47:03 +00:00
a7af1a164b
Updated MNP merging to merge VC records if any sample has a haplotype of ALT-ALT, since this could possibly change annotations. Note that, besides the "interesting" case of an ALT-ALT MNP in a pair of HET sites, this could even occur if two records are hom-var (irrespective of using phasing). Note also that this procedure may generate more than one ALT allele.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4577 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-27 01:50:36 +00:00
b085648141
Parallelized VariantEval. Refactored output to support parallel output style. Minor improvements to testing framework to enable easy executeTestParallel to run -nt 1 and -nt 4 by default.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4574 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-26 20:21:38 +00:00
c357ec775a
Trivially phases any hom site (since it is always correct to continue the previous haplotypes by appending the same allele onto both haplotypes)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4568 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-25 16:58:41 +00:00
9ba7269728
Fixed Integration Tests to output VCF files with -NO_HEADER
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4548 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-21 19:49:44 +00:00
b88cfd2939
Updated MD5s of VCFs, since the approximate command line arguments injected into the VCF headers now have a little more order to them thanks to changes in the ParsingEngine.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4538 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-21 03:07:40 +00:00
f76865abbc
ReadBackedPhasing now uses a SortedVCFWriter to simplify, and has the ability to merge phased SNPs into MNPs on the fly [turned off by default]; MergeSegregatingPolymorphismsWalker can also do this as a post-processing step; Integration tests for MergeSegregatingPolymorphismsWalker were also added
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4534 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-20 20:27:10 +00:00
7a291a8ff3
First pass at a VCF validator. Will test more tonight.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4524 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-19 19:55:49 +00:00
2bc5971ca1
Added - a tool to fix reference bases of a VCF. The OMNI had a couple of sites with incorrect reference bases (look to be legacy from other chips), and a few more that had ref and alt flipped. GAP should probably take care of it, but since I need results by monday, I'm doing it.
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Modified - SelectVariants: Hook up to VariantContextUtils to recalculate AC/AF/AN, which uses the accessor in VariantContext to do this. Somehow sites that were selected down to hom-ref genotypes only wound up getting positive AC.
**IMPORTANT** I kind of need input here. The header of a file used for an integration test specifies AC as being an integer. Recalculating it casts it into an integer list (which it should be, as it allows for alternate alleles). However this appears to clash with what the jexl expression is looking for? For now, the integration test itself needed to be changed -- it's unclear what to do when the header specifies AC of being one class, but recalculating it casts to another class, and I'm not sure what to do.
I'm committing my omni_qc pipeline because I'm almost certain 2 months down the road I'm going to wonder what the heck I did to generate my results.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4511 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-17 03:18:01 +00:00
7aa030a9a4
Hmm. Apparently variants can get lifted over to different chromosomes. Who knew? Reverting changes from a couple of days ago. The only way to do this correctly (without requiring lots of memory) is to turn off on-the-fly indexing for this walker. Integration tests cover this now.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4510 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-17 02:54:12 +00:00
954dd84f51
Adding an integration test (against hg18 this time) that requires on-the-fly sorting in order to work properly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4500 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-15 07:45:21 +00:00
9f54170dff
Hooking up the liftover tool to the new on-the-fly sorting VCF writer so that records can now get emitted in order.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4499 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-15 07:27:01 +00:00
7c9ef59d65
This is simultaneously a minor and major change to VariantEval, so take heed:
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The core walker has been modified so that when variant contexts (eval and comp) are subset to command-line-specified sample(s), the chromosome count annotations (AC/AN/AF) are altered to reflect the AC/AN/AF of only those samples involved in the comparison. No more getting AC500 when you're comparing a 10-sample overlap. Interestingly enough, this didn't break any integration tests.
GenotypeConcordance now has two additional tables: Allele Count Statistics, and Allele Count Summary Statistics. These work exactly identically to the Sample Statistics and Sample Summary Statistics tables, except that the partition being used is no longer the sample, but instead the allele count of the variant sites. These tables stratify by both eval and comp ACs, e.g.
evalAC0
evalAC1
evalAC2
compAC0
compAC1
compAC2
Differences with previous integration tests were verified to only be in the Allele Count tables (by grepping them out of the diff); a new test has been added for the simple case of an AC=1 site in the eval becoming an AC=2 site in the comp.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4491 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-13 22:26:15 +00:00
83b8676b69
Hack to fix mysterious disappearing read attributes. Ultimately caused
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by the fact that the GATKSAMRecord, by design, needs to both inherit from
SAMRecord and wrap a 'member' SAMRecord, and method calls that aren't
implemented as explicit passthroughs can compromise the content of the
SAMRecord in subtle ways.
Will be automatically fixed when Picard moves to a lightweight SAMRecord
interface rather than the current heavyweight implementation. But in
the short-term, there's no obvious fix.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4489 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-13 19:06:54 +00:00
272ac2ae4a
more fixes for tests broken by indexing-on-the-fly; I think this should do it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4486 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-13 01:54:32 +00:00
ff0df1a2da
A fix for an integration test that was broken by on-the-fly indexing. Also, better reporting of Tribble exceptions in GATK integration tests. Trying to get the tests back up and running...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4483 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-12 18:39:56 +00:00
f348ca2976
Now processes VCF files with repeated loci without crashing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4481 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-12 04:36:07 +00:00
116309b3c3
More test cases for UG integration test. We currently fail doing multi-threaded gzip output, FYI
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4472 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-08 20:22:12 +00:00
38a67fed63
High performance version of standard vcf writer. New general static Tribble class for common constants, including general .idx constant and functions to get standard index name for a given file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4471 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-08 19:53:21 +00:00
bdd3a9752e
Changed min MQ and BQ to 20 (for phasing)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4469 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-08 19:27:45 +00:00
21ec44339d
Somewhat major update. Changes:
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- ProduceBeagleInputWalker
+ Now takes a validation ROD and a prior to give it, will use those genotypes in place of the variant genotypes if both are present
+ Takes a bootstrap argument -- can use some given %age of the validation sites
+ Optionally takes a bootstrap output argument -- re-prints the validation VCF, filtering those sites used as part of the bootstrap
-BeagleOutputToVCFWalker
+ Now filters sites where the genotypes have been reverted to hom ref
+ Now calls in to the new VCUtils to calculate AC/AN
-Queue
+ New pipeline libraries for easy qscript creation, still a work in progress, but this is a considerable prototype
+ full calling pipeline v2 uses the above libraries
+ minor changes to some of my own scripts
+ no more need for contig interval lists, these will be parsed out of your normal interval list when it is provided
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4459 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-08 13:30:28 +00:00
0a2e76e9dc
2nd step towards on the fly indexing. Also fixed parsing bug for headers with < symbols
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4454 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-07 21:38:46 +00:00
7bb9704592
Update the BeagleOutputToVCF integration test because of removing the source header line. Source headers are provided by the engine for all VCF files now.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4453 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-07 19:55:57 +00:00
0de658534d
Removed the qScale arguments in VariantRecalibrator. It is smarter about how it tries to find a cut so the arbitrary scale factor hopefully is no longer necessary. Now the recalibrated variant quality score more accurately reflects our believed lod of the call.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4451 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-07 18:04:57 +00:00
ee00dcb79d
1. Phasing now ignores bases without minimum base quality (BQ) and minimum mapping quality (MQ); 2. The probability of a non-called base is now divided by 3, to evenly split up the error probability over the non-called bases
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4450 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-07 17:40:59 +00:00
6205910f9f
updating integration test for Sarah Calvo
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4449 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-07 04:03:37 +00:00
652a3e8de5
Added integration tests for ReadBackedPhasing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4446 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-06 20:50:32 +00:00
ca5db821ce
Added the ability to Queue to run scala functions inside the JVM. NOTE: Extend from InProcessFunction instead of CommandLineFunction to use this functionality.
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Queue now submits new LSF jobs only after previous functions have completed successfully.
When the Queue process is shutdown (ex: via Control-C) sends a bkill command for any running jobs.
Ported commands like creating directories and scatter/gather interval list to scala functions.
Updates to LSF status tracking by porting the python to internally generated bash scripts.
Temporarily disabled job name submission to LSF. Plus side is that the full command is now available in "bjobs -w". TODO: Put back jobName passing to LSF based on an option?
Changed BaseTest to allow scala to access paths to references.
Changed the extension generator to default the analysis name to the walker "name".
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4442 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-06 18:29:56 +00:00
69485d6a7a
Added command line argument for the max value of the allele count prior in VariantRecalibrator (--max_ac_prior). Default value increased to 0.99 from 0.95.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4436 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-06 14:00:53 +00:00
b5e148140b
Officially fixed the UG priors; updated the default min MQ/BQs to pipeline values of q20 and min calling threshold to Q50
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4431 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-05 18:35:36 +00:00
6448753cf7
Removed the SequenomValidationConvertor and renamed it VariantValidationAssessor since it no longer handles ped/sequenom files (but instead works on vcfs/variantcontexts). Updated all of the wiki docs, including adding instructions on how to convert ped files to vcf, a la Shaun Purcell. We now officially no longer support ped files everyone. Other misc cleanup in the code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4419 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-04 02:11:38 +00:00
4ea73bcfb1
Basic unit tests for WalkerManager.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4394 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-30 19:27:41 +00:00
78343be52c
At some time in the recent past, we lost our ability to process the '-L all'
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argument. Brought it back, and added an integrationtest to make sure it
stays around.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4390 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-30 15:58:43 +00:00
e80742e72f
Use -o as argument for output file in ProduceBeagleInputWalker, to be consistent with other walkers (you're welcome, chartl :)).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4386 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-29 22:46:39 +00:00
a6c7de95c8
By using the AC info field instead of parsing the genotypes we cut 78% off the runtime of VariantRecalibrator. There is a new argument to force the parsing of genotypes if necessary. Various other optimizations throughout.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4383 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-29 18:56:50 +00:00
862c94c8ce
Small change for Matt -- output partition types in lexicographic order.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4365 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-28 20:08:03 +00:00
96cccafb0d
Adding a few helper methods for accessing sample metadata, and associated unit tests. These are motivated by discussion with Ryan about how he'll use sample metadata in VariantEvalwalker - hopefully will make it easier for him. Methods are:
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-- getToolkit().subContextFromSampleProperty(): filters a VariantContext to genotypes that come from samples that have a given property value
-- getToolkit().getSamplesWithProperty(): gets all samples with a given property
-- getToolkit().getSamplesFromVariantContext(): sample objects that are referenced by name in a VariantContext
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4361 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-28 02:16:25 +00:00
edaa278edd
Removed cases where various toolkit functions were accessing GenomeAnalysisEngine.instance.
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This will allow other programs like Queue to reuse the functionality.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4351 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-25 02:49:30 +00:00
497bcbcbb7
Recent changes to the build system make the build system complain loudly about
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pieces of core that depend on playground. Most of these have been eliminated by
(temporarily) promoting Aaron's report system to core in this checkin. I'll
follow up with other changes in separately.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4350 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-24 22:09:12 +00:00
745b8cc6d3
GATK now detects and UserExceptions when human lexicographically sorted data is provided
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4343 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-24 15:19:48 +00:00
1931b2e1bd
Three fixes for VariantFiltrationWalker: Trying to filter an empty VCF file will produce a well-formed VCF file with zero records instead of a blank file, needed for pipelines. The first record's genotype info fields are now in the same order as all the others. The VCF header lines are pulled from just the input variant rod instead of from all rods.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4341 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-24 13:52:56 +00:00
4ed9f437e9
Sliced the GAE in half like a gordian knot to avoid the constant merge conflicts.
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The GAE half has all the walker specific code. The new "Abstract" GAE has the rest of the logic.
More refactoring to come, with the end goal of having a tool that other java analysis programs (Queue, etc.) can use to read in genomic data.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4339 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-23 23:28:55 +00:00
8f75d88519
Fix for GATK run report ids:
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mOVsxGfDiiSMxVs2PPTVjzYTVbizlD6e
f9kUHUADFsZ0LiTGxRL5zPmq9kZcA4cQ
8eGHWJFAlBVmgxwPi3sMd1RmiN2PwHOf
iLhvHWveypKb2F8vKS5irHylc3pYvlOb
HDttXKUMEVoPrvVeWrH7E0htxYyNydMx
plus a bit of cleanup of custom exceptions in the sharding system.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4330 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-22 19:49:25 +00:00
20b38b38f3
Updated from SnakeYAML 1.6 to 1.7.
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Added a pipeline java bean and YAML utility to serialize java beans.
Added a getFirehosePipelineYaml.sh that can pull firehose data into the pipeline yaml file format.
Updated the fullCallingPipeline.q to begin using the pipeline yaml file format for bams and reference.
More changes to come as this code gets tested out in the fullCallingPipeline.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4329 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-22 19:47:49 +00:00
fb5d595ef0
Disable VCF header output in the Beagle integrationtest.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4327 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-22 16:50:03 +00:00
0c99c97685
The engine now automatically adds the command-line arguments to the header of every VCF, unless -NO_HEADER is specified.
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Changed integration tests, adding the -NO_HEADER argument, for walkers that previously did not include the command-line
arg headers.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4326 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-22 15:27:58 +00:00
1af9ca6d45
enabling tests that now pass with the conitg length validation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4325 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-21 22:20:50 +00:00
3938d53738
one broken build short of the hat trick. Fixing the unix test which expects the sequence dictionary of the Tribble track to equal the reference; we actually return the sequence dictionary of the track iself, with each contig set to the length of the sequence dictionary contig entry.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4322 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-21 18:47:20 +00:00
b968af5db5
The tribble indexes are now updated with correct sequence lengths for each contig they have in their sequence dictionary. Also clean-up in the RMD track builder.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4321 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-21 18:21:22 +00:00
2586f0a1ca
fix for the build I broke - the original file got corrupted, which I replaced with a version that didn't have the header stripped off. Other integration tests passed, but this test relied on the header being stripped off.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4320 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-21 15:35:25 +00:00
547763b230
Better error message for Petr's null pointer exception. Also added an exception integration test because I'm certain this used to work.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4319 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-21 13:44:40 +00:00
f5a30d0248
I just spoke to Andrey & Kiran (the original authors of these tools), and they voted to kill these in favor of Picard
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4313 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-20 13:27:35 +00:00
7e58d8ed61
CombineVariants now outputs the command line in the VCF header. Added a new hidden argument to VR walkers called --NoByHapMapValidationStatus to turn off the by-hapmap dbsnp rod behavior. Very useful for experimenting with which sets to use as training data.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4307 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-18 16:06:50 +00:00
c6c6d32b46
Quickly adding a new convenience method for retreiving a group of samples. The method is getSamples(Collection<String>) and returns a set of sample objects. There's also a test there.
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Ryan is using this to modify VCF code today...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4303 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-17 15:55:17 +00:00
a10b2a00a5
Moving the util VariantContext 'modifying' routines into VC itself (as opposed to VCUtils) so that we can pass the genotype data directly into it and are no longer forced to decode the genotypes for no reason. This means that any walker that takes in a VCF and modifies the records without touching the genotypes never have to decode them. I've hooked this into the other two Variant Recalibrator walkers for Ryan. One side effect, though, is that we no longer can sort the sample names in the VCF (i.e. if the input VCF doesn't have samples in alphabetical order, then we used to sort them when writing a new VCF but no longer do that), because if we don't decode then we can't re-order the genotypes. I don't think this is a big concern given that the Unified Genotyper does emit sorted samples and that's the main source for most of the VCFs we use.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4300 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-17 07:09:58 +00:00
f66ef4626e
Fixing two minor issues: 1) adding a new error message if the user adds a fasta file in a directory that doesn't exist; 2) renaming my sample unit tests so they actually run.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4299 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-16 20:45:51 +00:00
3a400e3dc0
Added CountCovariates integration test to ensure that it throws an exception if a variant mask isn't provided.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4298 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-16 19:18:38 +00:00
de56568ce4
Adding the appropriate DbSNP file to the performance tests so they don't exception out.
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The exception: "org.broadinstitute.sting.utils.exceptions.UserException$CommandLineException: Invalid command line: This calculation is critically dependent on being able to skip over known variant sites. Please provide a dbSNP ROD or a VCF file containing known sites of genetic variation."
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4293 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-16 16:30:54 +00:00
782e0018e4
removal of most of the old GATK ROD system; also a fix for -Dsingle so we can again run just a single unit or integration test (single tests in tribble can be run with the -DsingleTest option now). More to come.
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*** Three integration tests had to change: ***
RecalibarationWalkersIntegrationTest:
One of the tests was using the interval as the snp track, and wasn't supplying a DbSNP track (for CountCovariates)
SequenomValidationConverterIntegrationTest:
relies on Plink ROD which we've removed.
PileupWalkerIntegrationTest:
we no longer have implicit interval tracks, so there isn't a rod name over the specified region. Otherwise the same result.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4292 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-15 22:54:49 +00:00
0a06fbdb94
Adding header lines to output of VR walkers to settle validator warnings. Command lines are added to the VCF header. GATK version numbers will be added to the header lines by Matt.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4288 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-15 16:45:03 +00:00
41fa323e63
Added iterator for tribble, fixing GS bug report. Removed unnecessary tabix double wrapping. Intergation tests to ensure the BTI works with both vcfs and vcf.gz
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4287 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-15 16:38:04 +00:00
e5f81d25d4
Adding the --sample-metadata (-SM) command line argument and associated functionality. This is something Matt and I have been working on for a while. Basically, it allows you to integrate sample metadata into an analysis, by including a sample file. More detailed documentation is on the wiki: http://www.broadinstitute.org/gsa/wiki/index.php/Adding_Sample_data_to_an_analysis
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This commit adds two important classes: Sample, which contains data about one sample; and SampleDataSource, which manages sample data a la ReferenceDataSource and ReadsDataSource.
This code should be stable, but it has not been integrated with existing walkers yet. That's the next commit.
In the meantime, feel free to experiment with the code - there are two basic example walkers in the playground.sample package. And PLEASE let me know if you see any errors/inconsistencies.
Note that this also adds a new dependency on SnakeYaml, a YAML parser.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4285 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-15 11:50:22 +00:00
1901e3208e
Oops, ran integration tests before Guillermo committed his change to the Beagle code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4281 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-15 01:41:02 +00:00
4e83ba411f
We now do lazy loading for the genotype data in VCF. Practically, almost all walkers end of loading the genotype data because we need to be smarter about transfering the unparsed genotype string when modifying VariantContexts; however, this does solve the problem for VR's piece to generate clusters (shaved off 75% of runtime for Ryan's large case). That further optimization will happen later.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4279 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-15 00:18:17 +00:00
2be5e862f1
forgot to commit change to MD5
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4277 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-14 19:28:03 +00:00
7fa6b2135b
Added a back door so that integration tests can reset the sequence dictionary
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in the reference. Reset routine is not accessible to any class outside
GenomeLocParser's package.
We'll have to do something more intelligent with this when the GATK goes
distributed.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4275 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-14 18:58:08 +00:00
fa3be2209f
Improvements to the error display code to print out the SVN number in all messages. Fixes to CallableLoci and tests to check for that case
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4270 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-13 18:36:45 +00:00
4d0ff336c2
Missed update input
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4269 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-12 15:46:13 +00:00
7880863eb7
Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4267 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-12 15:07:38 +00:00
7ad8fbdd5a
Moved GATKException to exceptions
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4266 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-12 14:47:19 +00:00
1876c9856a
Moved stingexception
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4265 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-12 14:39:22 +00:00
595907e98e
Moving StingException
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4262 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-12 14:34:15 +00:00
40e6179911
Penultimate step in exception system overhaul. UserError is now UserException. This class should be used for all communication with the USER for problems with their inputs. Engine now validates sequence dictionaries for compatibility, detecting not only lack of overlap but now inconsistent headers (b36 ref with v37 BAM, for example) as well as ref / bam order inconsistency. New -U option to allow users to tolerate dangerous seq dict issues. WalkerTest system now supports testing for exceptions (see email and wiki for docs). Tests for vcf and bam vs. ref incompatibility. Waiting on Tribble seq dict improvements to detect b36 VCF with b37 ref (currently cannot tell this is wrong.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4258 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-12 14:02:43 +00:00
a0231f073f
Damnit. Enabling the Picard code to recalculate all of the relevant SAMRecord attribute tags means that I need to have reference bases over all read bases even after realignment (and there are some big indels in dbsnp). Fortunately, I have my trusty IndexedFastaSequenceFile reader handy! Re-enabling the previously broken performance test.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4255 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-12 05:06:37 +00:00
7b113a4886
Truncate the floating point numbers coming out of the variant recalibration walkers. Integration tests now work with both 1.6.0_16-b01 and 1.6.0_21-b06
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4253 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-10 18:37:49 +00:00
cf33614ddc
remove the test that's failing the performance tests, please don't release until this is figured out
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4251 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-10 06:30:40 +00:00
4adb07683d
all fixed..thanks Matt!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4250 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-10 06:18:59 +00:00
bd4bc84abd
comment out the broken aligner test again - I'll take a crack at fixing it tomorrow. Each software engineer is going to take a pass at fixing it, and we'll see who can do it with the most style.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4249 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-10 05:22:24 +00:00
61e848c4f0
It's clear from Sendu's calling and my own calling that -qScale 100.0 is a much better default value for low pass data.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4248 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-10 01:47:21 +00:00
e183b6598c
- Fix our private repository of bwa reference support files.
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- Update the test to point to our repository.
- Update the md5 to reflect new Picard tag ordering.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4247 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-10 00:29:26 +00:00
4183e8805a
Fixed reference (via busted symlink) /broad/1KG
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4245 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-09 20:34:51 +00:00
aeb897db7f
VR walkers look at by-hapmap validation status by default. Eric will be updating the syntax to allow for more flexibility here.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4242 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-09 15:40:56 +00:00
d7f55574e2
Re-enabling aligner integration test now that we're back to having more than 1 or 2GB memory.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4241 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-09 15:09:48 +00:00
d625186796
I think the VR integration tests are fine.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4240 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-09 15:00:41 +00:00
6a30617a60
Initial implementation of UserError exceptions and error message overhaul. UserErrors and their subclasses UserError.MalFormedBam for example should be used when the GATK detects errors on part of the user. The output for errors is now much clearer and hopefully will reduce GS posts. Please start using UserError and its subclasses in your code. I've replace some, but not all, of the StingExceptions in the GATK with UserError where appropriate.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4239 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-09 11:32:20 +00:00
65edbced36
Addition for Tim: recalculate the NM and UQ tags after realignment. Also, don't fix the insert size calculation, since that's done by fix mate information.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4227 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-08 04:02:14 +00:00
e3962c0d13
VR integration tests are longer but much more useful.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4210 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-03 15:50:19 +00:00
b59d62927e
Fix busted performance test (-outputBam has been deprecated in the BQ recalibrator in favor of -o)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4201 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-03 12:51:53 +00:00
70bb480939
The battle is over. Picard is revved.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4200 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-03 05:28:01 +00:00
0bb05fb472
Bug fix in VariantRecalibrator. Only add sample names from the input rod bindings, not from all rod bindings.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4194 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-02 21:12:09 +00:00
dc5f858d29
Replaced placeholder support for splitting by read group with read support (sorry everyone), and added relatively comprehensive unit tests to ensure that splitting by read group works.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4190 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-01 22:24:50 +00:00
b28f63a948
Base recalibrator now uses -o and deprecates -outputBam
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4189 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-01 22:13:50 +00:00
33400074fa
Updated tribble BED parsing code to use the official UCSC spec, and updated tests to match expected results.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4188 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-01 21:49:06 +00:00
469bbaa240
Added more integration tests for the variant quality score recalibrator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4181 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-01 15:31:24 +00:00
8c4009ee18
Oops, don't enable reporting in integration tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4179 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-31 22:56:18 +00:00
3d6c4fc55f
Removing the obsolete --hapmap and --hapmap_chip options
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4172 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-31 16:57:05 +00:00
b33873206a
GATKRunReport now has an ID (random 32 char string) that uniquely identifies the JOB run and can be used to find a run in the run repository
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4171 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-31 16:18:57 +00:00
3fd2392090
Improved interface to getting command line options. Now fully traverses all objects to get all internal argument collections. Preliminary (but disabled version) of phoning home (see -et argument for more information). Captures correct and erroring out runs and writes out gzipped, xml report with lots of useful information. Needs a bit more information but is approximately working. Reports going to /humgen/gsa-hpprojects/GATK/reports/ in submitted directory that will be collated by some external tool. Only operating if -et STANDARD or -et STDOUT are provided currently and REPORT_DIR contains a file called ENABLE. WalkerTest now adds -et NO_ET to tests to avoid populating the reports with tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4155 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-28 22:53:32 +00:00
9c3f403307
Add the calculated lod value to the info field of each recalibrated VCF record.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4153 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-27 21:33:58 +00:00
bfcac33e80
Cleaning up playground utils and tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4136 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-27 01:25:47 +00:00
hanna
fromer
depristo
kshakir
ebanks
chartl
aaron
kiran
rpoplin
delangel
bthomas