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
bf69b5fa21
"!=" != "=="
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4297 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-16 19:15:37 +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
c1720cc8f5
Now compiles.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4295 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-16 18:49:53 +00:00
c581bd2d84
Minor modifications to fCP
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4294 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-16 18:29:24 +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
c604ed9440
Several improvements to new indel genotyper (more to come soon):
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a) Turns out previous change of centering haplotype around indel was a bad idea. Context to the left of indel is important but not as important as right one, because by definition all alleles start at the same location, so haplotype is the same to the left of indel regardless of allele. So, go back to having a constant size window to the left of event.
b) Expand reference context so we can test larger haplotypes.
c) Optimize computation of read likelihoods by doing them in linear array instead of in a matrix - no difference in biallelic sites but could be significantly faster in multiallelic sites.
d) Bug fix: read alignment wasn't being computed correctly if, a) we were at an insertion, b) read started right at the insertion, c) read CIGAR didn't include insertion - more of these corner conditions are lurking, so a revamped computation of how reads align to candidate haplotypes is in the works.
e) Add debug option not to use prior haplotype likelihoods.
f) Don't hard-code NA12878 for genotyping, now sample name is a required input argument.
g) Bug fix: if there are no reads covering a candidate indel event, just output NO_CALL (didn't notice this in HiSeq, but in P1 data it happens all the time). I need to add a confidence threshold for calling later on.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4291 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-15 21:53:08 +00:00
fb6d7d19f9
Better window size error message
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4290 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-15 20:40:56 +00:00
b5d2e299d2
Make it more clear what is going on with the by-hapmap validation status in the dbSNP rod
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4289 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-15 17:29:31 +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
d7b5baf8e5
Now uses tagging of -I arguments. Multiple -I options (merging) is now allowed. In somatic mode 'tumor' and 'normal' tags are required for each input bam, the order does not matter anymore (since we use tags!)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4286 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-15 13:58:51 +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
6dcbf04378
Added gsa-firehose2
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4284 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-15 02:24:04 +00:00
dd23f204ab
Making the UG args that allow users to proceed with insufficient bam headers (no SM or PL tags) @Hidden; removed them from wiki.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4283 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-15 01:54:50 +00:00
514b28210e
Have VF write to sdout when no -o is supplied
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4282 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-15 01:48:33 +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
b57a0a0310
improvements to the report code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4280 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-15 00:45:13 +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
74d4f124b1
Bug fixes to allow us to generate GATKRunReports for very early errors that leave the engine in a corrupt state. Vastly better error handling of common command line problems. Analysis output now notes whether an exception is a a UserException or a StingException
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4278 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-14 22:45:15 +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
6d07181dc9
When processing Beagle output and creating new vcf, output the filtered records in the original input vcf as is, so that we don't lose the information on them when we run Beagle.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4276 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-14 19:18:45 +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
dbb641280e
CycleCovariate now tolerates SOLEXA as machine type. Also, exception handling is now written to stderr.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4274 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-14 12:35:57 +00:00
71d2d69b41
Better error message
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4273 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-14 05:04:26 +00:00
248cc308b2
ReadBackedPhasing silently ignores sites with ploidy != 2
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4272 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-13 21:14:17 +00:00
528f6344af
Moved ReadBackedPhasingWalker to phasing sub-directory
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4271 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-13 19:36:41 +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
81c82ce134
Fix for Queue
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4268 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-12 15:18:08 +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
bccebf8899
Newly placed StingException
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4264 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-12 14:38:46 +00:00
3964e02fb6
Newly placed StingException
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4263 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-12 14:38:32 +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
8c16babe91
continuing improvements to the queueStatus helper script
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4261 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-12 14:04:59 +00:00
3c5b8730d5
More Queue scripts for analysis
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4260 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-12 14:04:10 +00:00
5de1124997
more useful reports
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4259 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-12 14:03:44 +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
da2e879bbc
Miscellaneous improvements to indel genotyper:
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- Add a simple calculation model for Pr(R|H) that doesn't rely on Dindel's HMM model. MUCH faster, at a cost of slightly worse performance since we're more sensitive to bad reads coming from sequencing artifacts (add -simple to command line to activate).
- Add debug option to calculation model so that we can optionally output useful info on current read being evaluated. (add -debugout to commandline).
- Small performance improvement: instead of evaluating haplotype to the right of indel (just with a 5 base addition to the left), it seems better to center the indel and to add context evenly around event.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4257 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-12 13:50:28 +00:00
61d511f601
Small memory performance improvement: remove the mapping from the hash instead of setting the value to null (i.e. remove the key too)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4256 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-12 05:19:09 +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
87aca64716
Jumped the gun a bit on bam on-the-fly indexing -- Tim says it's not ready yet.
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Turned it off by default and added a property to turn it back on.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4254 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-10 21:16:03 +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
8f1a32acae
All exceptions thrown by the GATK have been reviewed and UserErrors replaced where appropriate. Shazam. Another check-in will remove the GATKException and restore the StingException.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4252 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-10 15:25:30 +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
ebanks
bthomas
rpoplin
kshakir
chartl
aaron
delangel
depristo
asivache
hanna
fromer