e322e71c2f
Restored SVN history for phasing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4373 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-29 00:02:02 +00:00
720aaca8a0
Trying to restore SVN history for phasing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4372 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-28 23:50:28 +00:00
bf88117ead
Trying to restore SVN history for phasing directory
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4371 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-28 23:48:24 +00:00
dfb5143a41
Restore folder
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4370 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-28 23:46:07 +00:00
7c909bef82
Moved phasing classes out of playground! The code is still under production, though...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4369 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-28 23:21:28 +00:00
8d8980e8eb
Fixed phasing algorithm to: 1. More correctly weed out irrelevant reads and sites; 2. Crudely flag sites with large phase discrepancies betweens reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4368 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-28 23:02:53 +00:00
5a5c72c80d
Accidentally commited some debug output to PackageUtils, reverting change.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4367 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-28 21:58:42 +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
7ad87d328d
Make sure to uppercase ref bases since they aren't coming from the engine
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4364 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-28 19:05:46 +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
1034853a84
Adding 'solexa' to list of known/supported platforms
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4357 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-27 02:38:38 +00:00
70f03a7113
first pass of well-formatted tribble exceptions
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4352 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-25 03:29:33 +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
6ebca5d219
Enhancements to build external projects for walker sharing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4348 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-24 21:17:16 +00:00
eb1fa4bff3
changes an argument to an output so I can use it to track dependencies in queue
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4347 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-24 21:07:09 +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
0c9fabb06f
Fix in AnalyzeAnnotations, somebody changed it look for ID in the vc's info field. This dinosaur desperately needs integration tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4338 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-23 19:48:44 +00:00
0c781968fb
Tried to do a bit of pre-commit refactoring and screwed it up. Fixed.
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Thanks to Ryan for identifying the problem.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4336 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-23 18:17:29 +00:00
d081b9b352
Improvements to error messages about @Requires and @Allows
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4334 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-23 12:08:27 +00:00
7841b301c4
Added more diagnostics so that I have some idea of what a 'general' exception
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is. Required to fix bug ZjhCJAdwhtFq1x54ZlmlN8pFNcbrRpdJ and similar. We
might want to change this particular case to a ReviewedStingException after
we gain a bit more experience with it.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4333 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-22 21:32:01 +00:00
44ccfc3531
Updated Phasing algorithm + evaluation module to properly implement haplotypes [including homozygous genotypes]; Implemented dynamic window phasing model for LARGE increase in efficiency
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4332 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-22 21:29:58 +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
522830fb01
Support for --assume-single-sample in UG, better malformated bam exceptions, and ignoring out of order contigs in seqdictutils. All for the CG bam file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4323 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-21 20:33:34 +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
8719dde59d
Now prints out PASS when a variant is unfiltered
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4318 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-21 13:16:41 +00:00
205fc0b636
Cleanup: Use Tribble's version of createVariantContextWithPaddedAlleles (no real functional difference) to avoid duplicated code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4315 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-20 19:53:30 +00:00
a10cfe213b
Small bug fix in simple indel genotyper: Likelihood of case where best haplotype pair was (REF,REF) was not computed correctly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4314 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-20 17:04:39 +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
f64b6fddc1
Major changes/improvements to indel genotyper:
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a) Redid way to compute path metrics in indel error model. Paper formulation where we have an anchor point in the alignemt between read and haplotype won't work in practice except in nice data sets that are perfectly indel-realigned and that are well mapped by aligner. New formulation doesn't assume this, and it's actually simpler and uses less code. It now resembles more a classic SW dynamic programming formulation but it still preserves the HMM probabilistic formulation.
b) Added a programmable call threshold, set by command line.
c) Use now sample name from BAM file, remove -sampleName argument.
d) Simplify loop to compute read-haplotype likelihoods.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4311 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-19 23:47:31 +00:00
c6351a11d6
Clearer logger output when not using by-hapmap
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4308 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-18 16:10:42 +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
a3f31e5df0
When QScript writers use the RodBind, then the File version of the same argument should be optional, i.e. should not always try to output the file, which when unpopulated will be null.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4305 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-17 18:22:07 +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
a898908918
The output BAM file optional arguments of compression and whether to write an index are not outputs themselves.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4302 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-17 15:35:54 +00:00
bc12055fcf
Quick patch to fix the sample code. It wasn't actually initializing the sample data source, so I added a call to initializeSampleDataSource() in GenomeAnalysisEngine. I think there was just an error resolving the versions of GenomeAnalysisEngine
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Also added a new error message that I thought would be helpful...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4301 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-17 14:05:26 +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
2eb5d9b2d2
CountCovariates makes sure that it sees a rod type that it expects for use as a variant mask (accepted types are dbsnp, vcf, and bed)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4296 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-16 18:53:42 +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
fromer
chartl
ebanks
bthomas
aaron
kshakir
hanna
corin
depristo
rpoplin
delangel