75d4736600
Committing changes to comp overlap for indels. Passes all integration tests; minor changes to MVC walker.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3618 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-23 15:49:13 +00:00
9b8775180e
Turn on the memory improvement by default (assume the target interval list is sorted, since it is 99.9% of the time). Make the user throw a flag when it's specfically not sorted.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3617 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-23 15:44:55 +00:00
003dd4de3e
Rev Picard with performance enhancements.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3615 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-22 22:54:23 +00:00
0cafd3d642
clip VCF alleles for indels: only a single left base, and as many right bases as align before converting to variant context.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3614 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-22 22:42:38 +00:00
9872b65803
clip to the null allele on the reference string in VCF 4, instead of stopping to perserve one reference base.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3613 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-22 20:52:19 +00:00
b5df2705c9
-Remove Nway output option
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-Remove in-memory sorting
-Default to name-sorting (although we allow coordinate sorting with the --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe flag).
Cleaner, faster code. Wiki has been updated (including how to use FixMateInformation.jar from Picard). More changes coming soon.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3612 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-22 20:31:55 +00:00
30cf78fdc0
Refactoring for a first version of scatter gather api with basic shell script implementations.
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Modified build script so that queue is cleaned during "ant clean".
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3611 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-22 18:39:20 +00:00
a6d3e4bd47
Add code to allow reference alleles with 'N' in VariantContext, but not in the alternate allele(s). Also more updates to the VCF 4 code (fixed parsing for files without genotypes).
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This check-in will temperarly break the build (I need to see if Bamboo is correctly returning the log file for the failed builds).
Will be fixed once Bamboo starts building.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3609 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-22 18:26:37 +00:00
824c2bbac0
Finishing previous checkin
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3608 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-22 17:21:38 +00:00
4727bcda24
Removing Beagle output from UG. Use ProduceBeagleInput walker instead (since it can be run post-filtration and respects the FILTER column).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3607 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-22 16:56:37 +00:00
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
c38390eabb
Added option for min number of matches between reads and alleles required to consider reads.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3548 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 16:08:49 +00:00
4ab1f440c3
A new argument: --targetIntervalsSorted (boolean flag). If specified, the interval file is assumed to be sorted (duh!) and it is NOT slurped into the memory but instead traversed directly on disk as needed. If the file turns out to be unsorted, an exception will be thrown at the point where inconsistency occurs (can be late into the processing!).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3547 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 16:00:22 +00:00
671ac00748
A simple utility class that implements a merging Iterator<GenomeLoc> built over an interval or bed file (this is NOT a rod, but rather a direct line-by-line file reader that converts strings to genome locs on the fly and merges overlapping intervals)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3546 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 15:54:37 +00:00
f137bf8f85
now adaptor silently skips empty lines in the underlying string iterator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3545 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 15:35:07 +00:00
d8c963c91c
Remove PhaselikelihoodsWalker.java
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3544 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 15:21:43 +00:00
5704294f9d
HLA caller updated - now searches all (common and rare) alleles, more efficient read filtering and allele comparison runs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3543 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 15:14:40 +00:00
d51e6c45a7
a utility class; turns string iterator into GenomeLoc iterator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3542 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 14:07:44 +00:00
7b7d3341f0
trivial refactoring: isFile renamed to isIntervalFile and made public
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3541 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 14:02:23 +00:00
c3b68cc58d
Rethinking DownsamplingLocusIteratorByState with a flattened read structure. Samples are kept
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independent while processing, and only merged back in a priority queue if necessary in a special
variant of the ReadBackedPileup. This code is not live yet except in the case of naive deduping.
Downsampling by sample temporarily disabled, and the ReadBackedPileup variant is sketchy and
not well integrated with StratifiedAlignmentContext or the walkers. Cleanup to follow.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3540 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-13 01:47:02 +00:00
804facb0cc
Removing these utilities as part of a hostage negotation with Matt. Can I have my journal club paper now?!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3539 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-11 21:41:29 +00:00
e6d8faf293
making 'parseLocation' public static - as simple as the logic is, it's better kept in one place and I need it!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3537 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-11 18:19:59 +00:00
8c28be5933
Fixing a VCF bug for Sendu: we weren't emitting flags (booleans) correctly in VCF3.3 (rev'ed tribble for this).
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Updated dbsnp/hapmap membership info fields to be flags now instead of ints.
While I was there, I added the change in the Annotator for Jan to force reads to be from a specific sample.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3536 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-11 16:42:06 +00:00
22620ba95c
Adding "abi_solid" to the list of known platforms.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3534 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-11 13:37:19 +00:00
63ad71cca6
Fix busted code. Note for all:
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String.valueOf(byte[]) doesn't work. You must use new String(byte[]).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3533 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-11 05:01:48 +00:00
338bb9adf4
CommandLineProgram for measuring java I/O speeds for large plain-text or gzipped files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3532 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-10 21:34:37 +00:00
06fc5eecf8
Implemented TreeReducible - if num threads > 1, the output will be accumulated in memory and written to a vcf file at the end - in onTraveralDone(..). If num threads == 1, things will work as before - where vcf records are written to disk as soon as they are computed with map(..).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3530 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-10 20:57:23 +00:00
3b375cb237
Sped up parseGenomeLoc(..) by replacing regexp with String.indexOf(..) - attempt 2
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3529 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-10 20:54:36 +00:00
99b684ea89
Adding new support for reference data. ReferenceDataSource is a new class that manages reference data, and allows IndexedFastaSequenceFile to be a simple reader. This checkin also includes FastaSequenceIndexBuilder, which reads a fasta file and creates an index, like samtools faidx. Right now this is not enabled, because we are still working out thread safety. So the only new UI change is that GATK can be run without a fai file. Soon, we will enable 1) GATK to be run without a dict file too, and 2) both dict and fai files will be saved on disk for future program executions. For more info, see ReferenceDataSource.java
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3527 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-10 20:10:23 +00:00
f55f32d4ee
Bug fix.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3526 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-10 01:53:26 +00:00
ca4eab1d23
Now annotations that require reads return null if there's no alignment context, so that running without reads adds annotations only for the appropriate fields.
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Added an integration test for the read-less case.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3525 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 20:36:46 +00:00
6941c81bfa
reverting revision 3522 to the old code until we fix the tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3524 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 19:25:02 +00:00
dbee21a50f
Bugfixes for the case when no read groups / no samples are available.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3523 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 18:47:05 +00:00
adc4c4e577
Sped up parseGenomeLoc(..) by replacing regexp with String.indexOf(..)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3522 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 18:11:43 +00:00
20167fd411
Final changes to MVC -- associates variants with regions of homozygosity in child and parents, corrects for genotype errors, and prints out a separate file with informationf or each region of homozygosity.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3521 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 18:05:37 +00:00
fdded73861
Improved error reporting
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3520 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 17:52:48 +00:00
4f00e265a8
quick update for a change I implemented for Ryan
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3519 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 17:23:31 +00:00
ad98512f6c
adding changes so that we look at the headers already loaded by the engine for samples and other VCF utils, and not create readers for each file to get them (this caused Tribble to regerenate indices if the index file can't be written to disk).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3518 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 17:21:12 +00:00
c1b7bcc786
Fixed handling of mitochondrial genes - added special cases such as ATT being a start codon in mitochondria. Added warning if a gene doesn't start with Met or end in a stop codon
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3517 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 17:15:47 +00:00
4f1181974b
Added toString() method
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3516 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 17:12:57 +00:00
9b2fcc4711
Refactoring of the annotation system:
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1. VA is now a ROD walker so it no longer requires reads (needs a little more testing)
2. Annotations can now represent multiple INFO fields (i.e. sets of key/value pairs)
3. The chromosome count annotations have been pulled out of UG and the VCF writer code and into VA where they belong. Fixed the headers too.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3513 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 17:05:51 +00:00
84563b37e5
Partial flattening of the hanger data structure. Hanger data structure is
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not currently as flat as it could / should be, but it's already comparable
to the speed of the reference implementation.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3512 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 16:28:49 +00:00
8f9e3e8ad7
Commit for Kiran; but this is now working, barring little exceptions that I've yet to run across...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3511 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 14:21:19 +00:00
6d5556939d
updating Tribble with a couple of important Tabix fixes, and updating the variant eval integration tests to run each test with both plain vcf and gzipped tabix (added the tabix version
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to the vlidation directory), using the same md5sum.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3509 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-09 01:47:04 +00:00
c2858c8988
Minor performance enhancement. Checkpoint commit before major performance
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overhaul.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3504 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-08 21:39:39 +00:00
5ed2818ffb
Forgot to commit code i relied upon
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3503 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-08 21:01:35 +00:00
736098b58d
A quick commit before running home. This is a re-factored version of the OppositeHomozygoteClassifier which will work with deNovo violations as well. Some code still needs to be migrated from OHC which is wy that walker isn't yet deleted. This'll be up and running tonight.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3502 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-08 20:47:01 +00:00
de134c226d
Removed ability of users to specify annotations to recompute, cleanups.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3501 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-08 19:17:59 +00:00
4d1a6b3d99
quick changes for G
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3500 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-08 16:33:27 +00:00
907931c902
a) Update annotations when creating new vcf with Beagle's imputed data. Since genotypes may (will) change based on imputation, several annotations need to be updated. By default, AC, AF, AN and AB will be updated. User can force extra annotaqtions to be updated with -A <annotation> argument.
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b) Several cleanups and beautifications.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3499 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-08 15:12:04 +00:00
933133ee28
Initial commit of the opposite homozygote classifier. Currently does the following, given a trio vcf:
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+ Identifies opposite homozygote sites
+ Identifies the parent from whom it is expected that a null allele was inherited (or whether it was a putative genotype error; e.g. mom=homref, dad=homref, child=homvar)
+ Labels each opposite homozygote with its homozygous region in the child (e.g. region 1, region 2)
+ Labels each opposite homozygote with the size of the homozygous region in which it was found, the number of child homozygotes in the region, and the number of opposite homozygote violations within that region
To come:
+ Classification of sites as likely tri-allelic
Note that this is very experimental
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3498 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-08 03:56:07 +00:00
199e4208cd
Bug fixes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3497 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-08 00:30:33 +00:00
52ab9f2417
Feature parity between LocusIteratorByState, DownsamplingLocusIteratorByState, including pushing mrl /
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the LocusOverflowTracker into LocusIteratorByState. Note that the 'Matt Hanna exception', is still enabled
because I haven't yet validated the performance of the DownsamplingLocusIteratorByState when running
without downsampling.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3496 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-07 22:58:21 +00:00
5c4d070566
Push Mark's changes in LocusIteratorByState into DownsamplingLocusIteratorByState
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in preparation for merging the two into one.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3495 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-07 17:29:30 +00:00
6eeb1693ca
JEXL2 upgrade. Improvements to JEXL processing including dynamically resolving variable -> value bindings instead of up front adding them to a map. Performance improvements and code cleanup throughout.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3494 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-07 00:33:02 +00:00
c1ecf75dd5
Update to the latest rev of the picard sharding patch. Includes updates reflecting
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the imminent move of IlluminaUtil into picard public.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3493 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-06 20:33:21 +00:00
c503f01dcf
More cleanup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3492 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-06 17:41:38 +00:00
d4c66d6191
a) Small cleanup
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b) Fix major issue with Beagle likelihood converter: if likelihood triplets from UG end up being too low, then Beagle input file will be produced with 0.00,0.00,0.00 triplet. If all samples at a marker have this issue, Beagle will effectively produce junk. To fix, likelihoods are renormalized before converting to linear space.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3491 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-06 17:31:59 +00:00
cfa18f6743
Fixing missed update with new Allele in it
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3490 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-04 23:56:34 +00:00
3ea506fe52
No more new Allele() -- must use create. Allelel simple alleles are now cached for efficiency reasons. VCF4 codec optimizations -- 4x performance in general. Now working in general but hooked up to the ROD system now as VCF4. WARNING -- does not actually work with indels, genotype filters, etc.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3489 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-04 23:03:55 +00:00
ef47a69c50
a) First fully functional (sort of) version of walker that parses Beagle imputation output files and produce a vcf with imputed genotypes.
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More doc/info to follow shortly. Issues still to be solved:
a) Walker changes all genotypes based on Beagle data, but annotations on the original VCF are unchanged. They should in theory be recomputed based on new genotypes.
b) Current implementation is ugly, dirty unwieldy and will necessitate a refactoring soon so I can keep my pride. Most aesthetically affronting issue right now is that we read the full Beagle files at initialization and keep them in memory, but a more delicate implementation would just read from files on a marker by marker basis. Issue that currently prevents this is that BufferedReader() instances don't seem to play nice when called from the map() function.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3488 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-04 20:37:25 +00:00
b811e61ae1
Optimized, nearly complete VCF4 reader 2-4x faster than the previous implementation, along with a VCF4 reader performance testing walker that can read 3/4 files, useful for benchmarking
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3487 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-04 18:11:38 +00:00
6482b87741
adding the super experimental, half-broken, generally crippled, awkwardly commented, header ignoring vcf4 code. Don't use this, unless you're a developer for VCF4. If so, remove the exception from the constructor so that it won't always exception out.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3486 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-04 07:38:46 +00:00
0b03e28b60
updating the tribble library to include the reference dictionary reading / writing. We now check the dictionaries of any tracks that have them against the reference (all new tribble tracks and out-of-date tracks will have this). Also renamed some classes to be more reflective of their function.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3485 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-04 06:34:26 +00:00
3d055e3d16
Fail fast if users try to parallelize a read walker.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3484 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-03 18:14:33 +00:00
7d79848f40
Better error message when bam file / list file with wrong extension is
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supplied.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3483 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-03 17:52:48 +00:00
597b3744ab
Always use phasing info when converting genotypes to strings
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3482 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-03 17:50:50 +00:00
e2b41082af
GATK now does automatic adaptor filtering in locus iterators (but not expt. downsampling iterator). General support for LocusIteratorFilters just like read filters but only applying at particular bases. Updated tools with new MD5 sums due to adaptor bases in their integrationtest data. Not that as a side effect here reads close to each other with odd orientations are also filtered out. Updated minor argument to VariantRecalibrator to change the qStep value on the command line
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3481 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-02 22:26:32 +00:00
8ec091d6d2
re-enabling regeneration of the tribble index if it's out of date. Also moved the class that can detect text in the log4j stream (useful in testing to make sure appropriate messages are generated).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3480 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-02 17:45:51 +00:00
f0c379dde8
Unconsequential changes in report formatting
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3479 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-02 17:43:25 +00:00
3ab936181c
Supports the join feature of GenomicAnnotator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3478 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-02 16:29:57 +00:00
f5f7217413
Implemented joins
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3477 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-02 16:28:53 +00:00
09c3b15af3
Implemented joins
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3476 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-02 16:28:06 +00:00
e14ae471a0
Refactored some of the small utility methods
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3475 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-02 16:26:00 +00:00
898a78e97d
Added toString()
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3474 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-02 16:24:25 +00:00
12c3e3ecda
Added back the check for values.size() != header.size(). Now exception will be thrown if number of columns in a record doesn't equal number of columns in the header
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3473 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-02 16:23:05 +00:00
290771a8c2
Automatic cutting of recalibrated variant calls using ApplyVariantCuts. VariantRecalibrator produces the tranches plot alongside the optimization curve. Specify the levels using -tranche 1.0 -tranche 5.0 etc
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3472 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-02 15:03:00 +00:00
4a555827aa
Removing more toUpperCase sanity checks
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3471 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-02 14:38:39 +00:00
56e504789a
trivial change: toUpperCase no longer necessary
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3470 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-02 14:00:47 +00:00
87fe60fe4f
Fix for Sendu. new Process and p.waitFor() don't seem to work on his farm. Throws an IOException. This was a problem way back with AnalyzeCovariates too.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3469 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-02 11:37:10 +00:00
7f0c638653
Fix for the indel cleaner: I forgot to "unclip" the cigar string (even though the clipped bases were removed) before using it as an alternate consensus in a particular instance.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3468 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-01 02:07:20 +00:00
21427211c0
Personal MD5 database system now live. WalkerTest now maintains a database of result files associated with MD5 results in integrationtest/, and provides command lines for diff-ing expected to current md5 results when encountering failed intergration tests. The suite currently takes 200Mb to store. Update and run intergrationtest to build your very own expectation database for future development work.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3466 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-31 16:06:16 +00:00
2b02324587
Support for detecting and automatically excluding reads reading into the adaptor sequence and, if desired, also only showing the first pair when two reads overlap in the fragment. Not enabled, an intermediate check in before updating and verifying the impact on locus walkers everywhere.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3465 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-30 18:00:12 +00:00
eb25e41111
minor update to new tribble name
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3462 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-28 20:23:25 +00:00
ffeb3fd80d
Thanks to Guillermo, I found a bug in the Unified Genotyper output: GL was posteriors instead of likelihoods. Not a huge deal because the
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priors were flat, but fixed nonetheless.
Also, needed to update Tribble.
Minor updates to the Beagle input maker.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3461 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-28 19:28:26 +00:00
4e268ef6ac
Removing the Variant Recalibration Performance test because it isn't ready yet.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3460 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-28 18:27:25 +00:00
522dd7a5b2
Adding the variantrecalibration classes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3459 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-28 18:21:27 +00:00
2014837f8a
VariantOptimizer package is moved to core, renamed as VariantRecalibration, and added to the binary release package. VariantOptimizer walker is renamed to GenerateVariantClustersWalker and ApplyVariantClustersWalker renamed to VariantRecalibrator. Integration tests added, performance tests still to be done.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3458 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-28 18:20:18 +00:00
871cf0f4f6
Call out ROD types by there record type, instead of the codec type (which was clumsy). So instead of:
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@Requires(value={},referenceMetaData=@RMD(name="eval",type= VCFCodec.class))
you'd say:
@Requires(value={},referenceMetaData=@RMD(name="eval",type= VCFRecord.class))
Which is more in-line with what was done before. All instances in the existing codebase should be switched over.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3457 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-28 14:52:44 +00:00
cc2bf549c8
Removing my unnecessary optimization. 10 lines later in the code the same optimization was applied. A monumental waste of time.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3455 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-28 14:10:48 +00:00
a4d834cc01
fixing the test I broke
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3454 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-28 02:06:20 +00:00
6485e8383d
Trivial change to retrigger broken build that really isn't broken
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3453 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-27 23:33:46 +00:00
f2e7582cfc
Reorganization of SW code for clarity. Totally failure at raw optimization. Discovered that ~50% of reads being cleaned were perfect reference matches. New code comes with flag to look at NM field and not clean perfect matches. Can we turned off with command line option (needed for 1KG bams with bad NM fields). Going to rerun cleaning jobs due to accidentally rebuilding of stable codebase and loss of 2 days of runtime.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3452 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-27 23:16:00 +00:00
e1b0aefb29
fix for parallelism bug
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3451 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-27 22:16:14 +00:00
cded9ec985
adding a command line option, -etd (enable threaded debugging), that uses a custom thread pool class to catch exceptions thrown inside of a thread.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3450 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-27 21:57:56 +00:00
e2674671e7
The liftover code needs to *hard filter* records whose reference changes (since they no longer adhere to the VCF spec as they don't match the new reference - and can't be converted to VariantContext).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3448 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-27 19:22:47 +00:00
ff4a0764df
Read error rate is now parallelizable
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3447 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-27 19:00:09 +00:00
dfc36c1e95
Restructuring of the mandatory read filters for traversals. Now everything uses ReadFilters, even for the required filters like being mapped for LocusWalkers. Statistics now tracked for each read filter used during the traversal and info emitted in INFO at the end.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3445 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-26 22:12:25 +00:00
3873dccb35
First fully functional (though preliminary) version of walker that takes an input VCF and outputs a Beagle .bgl file that can be used for missing genotype calls/haplotype imputation. For now, only supported input format is likelihood format for unrelated individuals.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3444 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-26 21:03:23 +00:00
f9efc1248c
VariantEvalWalker now takes indels if you throw the -dels flag. IndelLengthHistogram appears to be working properly, it is turned off by default (as it is experimental) but you can turn it on in your own repository.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3443 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-26 20:03:14 +00:00
058441fa39
Trivial renaming of test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3441 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-26 16:56:42 +00:00
chartl
ebanks
hanna
aaron
kshakir
bthomas
depristo
kiran
rpoplin
weisburd
delangel
asivache
sjia