32f324a009
incremental changes to the VCF4 codec, including allele clipping down to the minimum reference allele; adding unit testing for certain aspects of the parsing. Not ready for prime-time yet.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3604 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-22 06:31:05 +00:00
de9f1f575f
Fixing command line parsing to accept negative number arguments. Command line definitions must now start with a letter or underscore; previously, they could start with a digit.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3603 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-21 21:54:31 +00:00
9d6a341d15
Fixing the error messages thrown with bad interval arguments. I simplified the exception handling and made the messages more verbose.
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Note: the -L argument takes both interval strings and filenames. If you specify an interval string that is also a file, an error will be thrown to move the file: ie. if you have a file "chr1" in the parent directory, GATK will ask you to move/delete it. But, this only happens with interval string arguments, NOT with intervals that are contained in files, which is a majority of the use case.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3602 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-21 21:49:41 +00:00
300a18b85f
Updating the way reference data is processed, so GATK creates the .fasta.fai and .dict files automatically. If either (or both) don't exist, GATK will create them in the same folder as the fasta file. If it can't write the file, GATK will fail with a message to create them manually.
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Note that this functionality will only work if the directory with the fasta is writeable. GATK will fail if directory is read only and and either the .fasta.fai or .dict files don't exist. In the future, we could have these references be created in memory, but we decided against it this time.
Locking was also added to ReferenceDataSource so no issues come up while running multiple GATKs on the same reference: we don't want one process to be half-finished and another try to read it. So, you could see error messages related to locking. See ReferenceDataSource.java for explanation of the locking strategy.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3601 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-21 21:42:42 +00:00
df1cadc4c9
Fix NullPointerException when priority list is left out
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3600 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-21 13:46:54 +00:00
c806ffba5f
Switching over DownsamplingLocusIteratorByState -> LocusIteratorByState. Some operations
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will not be as fast as they could be because the workflow is currently merge sam records (sharding)
-> split sam records (LocusIteratorByState) -> merge records (LocusIteraotorByState) -> split
records (StratifiedAlignmentContext), but this will be fixed when StratifiedAlignmentContext
is updated to take advantage of the new functionality in ReadBackedPileup.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3599 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-21 02:11:42 +00:00
1d50fc7087
Misc bug fixes: fix tracking of nInsertions with sample-split pileup constructor. Fix performance
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issue building up pileups from pileups of individual sample data.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3598 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-20 20:32:27 +00:00
f18ac069e2
A refactoring / unification of ReadBackedPileup and ReadBackedExtendedEventPileup.
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Provides a cleaner interface with extended events inheriting all of the basic RBP
functionality. Implementation is still slightly messy, but should allow users to
provide separate implementations of methods for sample split pileups and unsplit
pileups for efficiency's sake.
Methods not covered by unit/integration tests have not been sufficiently tested yet.
Unit tests will follow this week.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3597 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-20 04:42:26 +00:00
57a13805da
GATK now uses a optimized indexing scheme in Tribble. 5x or more performance gain on files with many genotypes. Updated integrationtest that was failing and was clearly wrong. DB=; isn't a valid annotation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3596 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-19 21:36:41 +00:00
8ff93f77e6
Added evaluation module to count functional classes (missense, nonsense, etc.). At the moment, it only understands Cancer's MAF annotations. Added integration test for the functional class counting. Added better description for VariantEval.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3595 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-18 21:51:40 +00:00
1e06d2bf68
Initial HLA Caller integration tests. Kind of painful, but will improve with code refactoring.
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This baby is now officially ours.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3593 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-18 20:35:27 +00:00
f44d8b150f
Mendelian Violation Classifier now filters violations on the fly via command line arguments; and closes unterminated homozygous regions at the end of a chromosome (so we see arms falling off in the file, rather than in the log)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3592 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-18 19:32:24 +00:00
aa1852575e
Add -noVerbose flag to stop output of INFO data.
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Cuts runtime by 30% and output from 65Mb to 1Kb.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3591 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-18 18:53:35 +00:00
724affc3cc
Major bug fixes for the Variant Recalibrator. Covariance matrix values are now allowed to be negative. When probabilities are multiplied together the calculation is done in log space, normalized, then converted back to real valued probabilities. Clustering weights have been changed to only use HapMap and by-1000genomes sites. The -nI argument was removed and now clustering simply runs until convergence. Test cases seem to work best when using just two annotations (QD and SB). More changes are in the works and are being evaluated. Misc fixes to walkers that use RScript due to CentOS changes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3590 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-18 17:37:11 +00:00
c3434493b0
fixed integration test for VCF Header changes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3589 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-18 16:31:48 +00:00
52477bd9e6
Add some missing methods to the pileup architecture.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3588 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-18 15:03:08 +00:00
5050b19457
We're unable to make the naive deduper more worldly, so we're killing it instead.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3587 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-18 13:54:27 +00:00
42e7ff4f28
forgot to update a test, the md5sum of the underlying file changed (which is recorded in the ROD tests).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3586 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-18 13:27:56 +00:00
b978d5946b
adding changes for VCF 4, mostly in the way we handle VCF headers. The header fields are now aware of the differences between different VCF formats. There was also a bunch of clean-up of out-of-spec VCF used in the tests (mismatched VCF file format fields, etc), and updates to the associated integration tests. Also some logging statements for BTI.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3584 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-18 08:23:23 +00:00
e26a273ef5
Turned the test back on
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3582 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-17 22:57:42 +00:00
48cbc5ce37
Merging the sharding-specific inherited classes down into the base.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3581 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-17 22:36:13 +00:00
612c3fdd9d
First pass at eliminating the old sharding system. Classes required for the original sharding system
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are gone where I could identify them, but hierarchies that split to support two sharding systems have
not yet been taken apart.
@Eric: ~4k lines.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3580 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-17 20:17:31 +00:00
b694ca9633
Cleanup: Don't require likelihood ROD in Beagle parameters when generating output VCF. Likelihoods file is only an input to Beagle but the Walker that generates a VCF doesn't need it, so it's silly to ask for it and it's error-prone.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3579 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-17 17:45:48 +00:00
c1595a383a
More bugfixes for cases where no sample name is present.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3578 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-17 16:46:02 +00:00
3d049204ed
some refactoring for the variant eval output system
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3576 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-17 05:34:31 +00:00
db1383d0b2
Rev the latest version of Picard.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3575 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-16 23:55:07 +00:00
5b370ffc62
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3574 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-16 20:42:58 +00:00
5972ad1199
Fixes to mrl integration.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3573 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-16 20:40:10 +00:00
b75ded61b8
Removing obsolete rod; no longer needed given previous addition to SampleUtils.
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JIRA GSA-318
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3572 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-16 20:03:14 +00:00
c671864228
Re-allowing blacklist by read group id.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3571 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-16 19:45:44 +00:00
f003703912
Allow specification of particular rods for pulling out sample names.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3570 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-16 19:37:09 +00:00
01ffa307c2
When going NWay out in the cleaner, use the new *merged* header (instead of the original one) for each bam file so that it matches the new uniquified read group ids in the reads.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3569 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-16 19:36:36 +00:00
05c2f96bb4
Small update to the command line docs for read_group_black_list.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3568 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-16 19:23:34 +00:00
d7f3102c3f
Fixed read group blacklist filter to look only at readgroups (and not the read's themselves). Otherwise, it fails when attribute tags with different meanings show up in both places (e.g. SM). Added performance improvement.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3567 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-16 19:14:37 +00:00
e77f76f8e1
Reenabled downsampling by sample after basic sanity testing and fixes of the
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new implementation. Hard testing and performance enhancements are still
pending.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3566 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-16 17:23:27 +00:00
c44fd05aa1
Fix for a reflection issue with generic types.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3565 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-16 15:58:38 +00:00
7a91dbd490
Renamed some of the column names in Ti/Tv and Concordance modules so that they are clearer. Removed ValidationRate module (it was busted).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3564 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-16 15:53:06 +00:00
8cb16a1d45
a) Cleanup, remove -input argument from BeagleOutputToVCFWalker since it's not needed.
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b) Added back old Beagle ROD to maintain backward compatibility (does anyone even use this???)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3563 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-16 02:13:08 +00:00
d319a28be7
Complete rewrite of the Beagle functionality to read from Beagle output files and produce VCF with modified genotypes. Now, a new ROD system using Tribble is in place. Beagle inputs are set using -B beagleType,Beagle,pathToBeagleFile, where beagleType can be either beagleR2, beagleLike, beaglePhased or beagleR2 (BeagleOutputToVCFWalker requires all of the above). Only pending items: -input argument is now unused and can be removed, will be cleaned later. Wiki will be updated with new usage shortly.
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We can now run with a reduced memory footprint, and output VCF is exactly identical to previous version. Drawback is increased runtime because Tribble has to create an index for all the Beagle files when starting if the idx files are missing.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3562 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-16 02:01:35 +00:00
d265397bf6
removing a reference to a unused internal Sun class
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3560 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-15 15:27:57 +00:00
42b8a8f295
slight change in output format
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3559 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-15 14:52:04 +00:00
32fc221ffe
Replaced pattern matched pipeline spec with annotated objects.
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Old version is no longer available.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3558 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-15 04:43:46 +00:00
b99a5e06f3
Added option to only consider alleles of > specific allele frequency.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3557 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-15 02:09:35 +00:00
8a895f481f
Proper exception chaining for troubleshooting Sendu's issue.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3556 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-15 01:38:36 +00:00
8defb30796
Documentation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3555 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 21:31:01 +00:00
c1046653a2
Fixed handling of records where gene-names are identical (eg. as in refseq NR_030638 in chr20)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3554 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 20:00:49 +00:00
1e42984a16
Improved buffer-size arg handling
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3553 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 19:59:15 +00:00
b3c3023c3c
Allows callers to handle HLA reference files as input (rather than hard-coded paths)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3552 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 18:56:08 +00:00
9666d47d17
ooops, debug print now removed
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3550 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 18:07:12 +00:00
abdc8521ea
Added debug options for FindClosestHLAWalker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3549 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 17:52:03 +00:00
aaron
bthomas
ebanks
hanna
depristo
kiran
chartl
rpoplin
weisburd
delangel
kshakir
asivache
sjia