0b1e243a7b
CountCovariates now sorts the list of standard covariate classes coming from PackageUtils.getClassesImplementingInterface(). As a result some of the integration tests now make use of -standard
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2817 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-10 15:52:20 +00:00
934d4b93a2
VariantContext to VCF converter. BeagleROD, and phasing of VCF calls. Integration tests galore :-)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2814 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-09 19:02:25 +00:00
94f892ad42
VCF->beagle and VCF phasing using beagle input. Appears to work fairly well. VariantContexts now support phased genotypes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2812 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-09 01:22:05 +00:00
935e76daa1
Minor changes to oneoff walkers. PlinkRod altered but still commented.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2808 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-08 18:49:56 +00:00
ca1917507f
Various improvements and fixes:
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In indel cleaner:
1. allow the user to specify that he wants to use Picardâs SAMFileWriter sorting on disk instead of having us sort in memory; this is useful if the input consists of long reads.
2. for N-way-out mode: output bams now use the original headers from the corresponding input bams - as opposed to the merged header. This entailed some reworking of the datasources code.
3. intermediate check-in of code that allows user to input known indels to be used as alternate consenses. Not done yet.
In UG: fix bug in beagle output for Jared.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2805 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-07 04:21:04 +00:00
3b1ab86d11
Added generic interfaces to RefMetaDataTracker to obtain VariantContext objects. More docs. Integration tests for VariantContexts using dbSNP and VCF. At this stage if you use dbSNP or VCF files only in your walkers, please move them over to the VariantContext, it's just nicer. If you've got RODs that implemented the old variation/genotype interfaces, and you want them to work in new walkers, please add an adaptor to VariantContextAdaptors in refdata package. It should be easy and will reduce burden in the long term when those interfaces are retired.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2803 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-06 16:26:06 +00:00
c7e006a996
Bug fixes for interval batching in sharding system. Sharding system now batches intervals and passes
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basic tests for small and large intervals and intervals that cross bin boundaries. Currently works
only with a single BAM file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2800 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-05 21:47:54 +00:00
be33d1852c
Reverting
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2792 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-05 15:57:09 +00:00
0d8d6e0a14
Ti/Tv module in VariantEval shows known and novel ratios if possible
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2790 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-05 15:37:40 +00:00
1494dc875f
fixing up tests. Moves are complete
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2789 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-05 14:24:00 +00:00
c6d86da4b8
almost managed to move things around perfectly in move go
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2788 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-05 14:18:26 +00:00
af7cd9cf58
some very old tests relied on cancer data that got moved. Reset one to use data in the validation directory, the other to the artificial sam utils (the best approach).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2767 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-02 23:13:10 +00:00
9dbdfff786
Moved VariantEval to core. Updated integration test md5s to reflect new Analysis class names.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2762 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-02 00:22:15 +00:00
e0808e6c37
Moved old EM model to archive
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2754 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-01 02:55:32 +00:00
f6da57dc79
1. For Matt: JIRA GSA-270. Other walkers needing to call into the Unified Genotyper now use static methods (e.g. runGenotyper()) instead of calling initialize and map.
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2. Set the default confidence cutoff to 50 (instead of 0).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2752 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-31 21:14:57 +00:00
62a80f2b6f
fixed out of date tests. Also, tests uncovered a subtle bug in new implementation that was also fixed
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2741 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-29 20:03:48 +00:00
e7f5c93fe5
Cleaning up the inheritance hierarchy from the previous commit.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2738 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-29 19:13:36 +00:00
5aaf4e6434
VariantFiltration now accepts any number of --name --filter expressions, and annotates the VCF file with each name that matches. Very useful
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2732 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-29 12:13:08 +00:00
3d922a019f
Basic support for very simple index-driven locus traversals. Interface has been changed to
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support batched intervals in a single shard, but intervals are not yet compressed into a single
shard.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2730 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-29 03:14:26 +00:00
476d6f3076
RealignerTargetCreator is officially live
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2697 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-27 03:41:52 +00:00
47440bc029
- Removed max_coverage argument from UG; Aaron will set it up so that we don't call when the GATK had to drop reads.
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- Reimplemented optimization in UG to not call when there are no non-ref bases.
- Compute reference confidence accurately in UG for ref calls.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2693 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-26 21:56:33 +00:00
a1054efe8a
Default platform and default read group are no longer set to values by default. The recalibrator throws an exception if needed values are empty in the bam file and the args weren't set by the user. This is done to make it more obvious to the user when the bam file is malformed. Similarly, the recalibrator now refuses to recalibrate any solid reads in which it can't find the color space information with an exception message explaining this. The recalibrator no longer maintains its own version number and instead uses the new global GATK version number.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2690 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-26 18:47:40 +00:00
c231547204
Refactoring and migration of new allele/variantcontext/genotype code into oneoffprojects. NOT FOR USE. PlinkRod commented out due to dependence on this new, rapidly changing interface.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2687 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-26 13:53:29 +00:00
d6b9b788a8
Renamed -- PlinkRodWithGenomeLoc --> PlinkRod
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Since binary files do not need encoded locus information in the SNP names there's no need to suggest that it is so in the name of the rod
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2671 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-23 18:19:28 +00:00
ac983e7a0b
Ran the rod on a binary plink file with indels and it just worked. Love it when that happens! Unit test to ensure this behaviour is maintained.
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****** PLINK ROD IS NOW READY TO GO ********
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2670 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-23 18:13:05 +00:00
ae22d35212
PlinkRod now correctly parses binary files without indels; unit test added for this behavior.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2669 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-23 17:34:06 +00:00
94dc09c865
PlinkRod now successfully instantiates on the binary ped file trio (.bim, .bam, .fam) for non-indel files.
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Upcoming: Test that the instantiation is correct, do it for indel-containing files.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2668 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-23 16:13:24 +00:00
01db93299c
PlinkRodWithGenomeLoc now properly handels indels.
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There is now a DELETION_REFERENCE allele type to allow for the storage of multi-base references rather than point-mutation references.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2667 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-23 07:34:52 +00:00
42fb85e7f3
PlinkRodWithGenomeLoc now properly parses text plink files. Unit test added to test this functionality. Indels and binary files to come.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2666 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-23 06:19:26 +00:00
2ea768d902
ant clean is your friend....fixed test code dependent on an interface change.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2660 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-22 20:07:46 +00:00
c1e09efb23
- Fixed output for beagle header
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- Better description for QualByDepth annotation
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2655 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-21 21:25:56 +00:00
9c7b281b4f
Set default value for max_coverage to be 100K (since 10K is too small).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2646 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-20 20:15:25 +00:00
8d1d37302c
a quick change to GLF to keep as much precision in our likelihoods as long as possible, before we put it into byte space. Sanger was doing a diff at low coverage and noticed our calls didn't contain as much precision as theirs. Updated the MD5 for unified genotyper output.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2644 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-20 19:36:49 +00:00
a1b4cc4baf
changes to intelligently log overflowing locus pile-ups.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2640 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-20 08:09:48 +00:00
4ac9eb7cb2
- Smarter strand bias calculation
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- Better debug/verbose printing
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2639 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-20 03:01:26 +00:00
c98df0a862
Updated solid_recal_modes to work with bfast aligned data. Added an integration test that uses the BFAST file provided by TGen.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2630 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-19 21:18:02 +00:00
12453fa163
Misc cleanup of UG args
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2620 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-17 04:38:52 +00:00
b911b7df82
Fixing the AC annotation to be in line with the VCF spec
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2593 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 18:28:52 +00:00
f2e539c52f
As per discussions with Tim we are reverting the previous change regarding PairedReadOrderCovariate. The CycleCovariate now differentiates between first and second of pair by multiplying the cycle by -1. PairedReadOrderCovariate has been removed completely.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2592 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 18:18:59 +00:00
df998041a8
Minor change to solid warning message. Added note for a future solid recalibration integration test when we get the required data file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2590 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 16:31:25 +00:00
b19bb19f3d
First successful test of new sharding system prototype. Can traverse over reads from a single
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BAM file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2587 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 03:35:55 +00:00
db9570ae29
Looks bigger than it is:
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* Moved GATKArgumentCollection into gatk.arguments folder to clean up the main folder, also added some associated argument classes (most of the changes).
* Added code the argument parsing system for default enums, we needed this so we could preserve the current unsafe flag, and at the same time allow finer grained control of unsafe operations. You can now specify:
"-U" (for all unsafe operations), "-U ALLOW_UNINDEXED_BAM" (only allow unindexed BAMs), "-U NO_READ_ORDER_VERIFICATION", etc.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2586 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 00:14:35 +00:00
9bf0d7250a
Fixing the testOtherOutput UG integration test so it will run.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2580 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-14 13:40:14 +00:00
f96b2b211e
My last checkin updating R code broke an unrelated UnifiedGenotyper integration test. Eric says that I should take out the verbose test.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2576 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-13 22:28:10 +00:00
49c44e7b36
PairedReadOrderCovariate is now a standard covariate and because of this CycleCovariate no longer multiplies by negative one for second of pair reads. Added PairedReadOrderCovariate to some of the integration tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2574 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-13 20:09:10 +00:00
f99586f91b
Added integration test for beagle and verbose output in UG.
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Minor cleanup of VCFRecord code.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2570 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-13 03:55:24 +00:00
189829841b
The recalibrator now uses all input RODs when looking for known polymorphic sites not just the one named dbsnp. Added an integration test which uses both dbsnp and an input vcf file and skips over the union of the two.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2564 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-12 18:50:39 +00:00
16777e3875
more fixes for the empty interval list problem; you can now run LocusWindow traversals with an empty interval list, but the GATK will give you a warning (unless you're running in unsafe mode).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2563 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-12 18:47:43 +00:00
03b7d5f5c7
1. Fixed small but embarrassing bug in weighted Allele Balance annotation calculation.
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2. Made RankSumTest abstract; added 2 subclasses: BaseQualityRST and MappingQualityRST (the latter based on a suggestion from Mark Daly). Untested so they're still experimental.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2561 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-12 18:33:53 +00:00
42aff1d2c3
Annotator in general should be able to annotate monomorphic or tri-allelic sites.
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It's up to the individual annotations to decide whether they want to annotate or not.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2556 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-11 19:52:18 +00:00
rpoplin
depristo
chartl
ebanks
hanna
aaron