b5e843f8f0
Approaching the end for the new RodBinding system
...
-- support for explicit naming of bindings (-X:name,type x)
-- support for automatic naming of bindings in lists (-X:vcf foo.vcf -X:vcf bar.vcf will generate internal names X and X2)
-- ParserEngineUnitTest expanded to cover all of the Rodbinding cases
-- RodBindingUnitTest tests all of the low-level accessors
-- Parsing engine throws UserExceptions when bad bindings are provided on the command line
2011-08-02 22:00:06 -04:00
83891271b5
--variants throughout integrationtests
2011-08-02 20:28:47 -04:00
3a27a25cfc
Validates that the tribble binding provides the right object types at startup
...
Tests to ensure this remains working
2011-08-02 20:11:24 -04:00
e4a67f3df1
RefMetaDataTracker has complete set of get() functions for List<RodBinding<T>>
...
Including unit tests
2011-08-02 14:28:35 -04:00
03741fb640
Merge branch 'master' into rodRefactor
...
Conflicts:
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java
2011-08-02 14:21:58 -04:00
a366f9a18d
Updating tools to use the RodBinding<T> syntax
2011-08-02 14:05:51 -04:00
b9d0d2af22
Adding back temporarily removed integration test now that the file permissions have been fixed.
2011-08-02 12:39:11 -04:00
1c387848de
No more use of -D in the integration tests but instead stick with VCFs only. Since all of these tests were duplicated (one each for dbSNP format and for VCF), we don't actually lose coverage in the integration tests.
2011-08-02 10:39:50 -04:00
2c5e526eb7
Don't use the mismatch fraction by default in the RealignerTargetCreator (since it's only useful when using SW in the indel realigner). Also, no more use of -D but instead move over to using VCFs. One integration test is temporarily commented out while I wait for a VCF file to get fixed.
2011-08-02 10:34:46 -04:00
5626199bb6
The Unified Genotyper now does NOT emit SLOD/SB by default; to compute SB use --computeSLOD
2011-08-02 10:14:21 -04:00
8b1adb8c95
Removed getVariantContext() code
2011-08-01 13:41:09 -04:00
f69bff5dd6
Commented out, because these fail the now removed dbSNP conversion.
2011-08-01 13:34:25 -04:00
7b07c4e04e
RefMetaDataTracker now has get() methods accepting RodBindings
...
RodBinding no longer duplicates the get() methods in RMDT. This is just an object now that connects the command line system to the RMDT.
Updated programs to use new style
Added UnitTests for the RodBinding accessors.
2011-07-30 15:34:11 -04:00
3b799db61a
RefMetaDataTracker cleanup and unit tests
...
You know have to provide an explicit list of RODRecordLists upfront to the constructor. RefMetaDataTracker is now immutable. Changes in engine to incorporate these differences
Extensive UnitTests for RefMetaDataTracker now.
2011-07-29 13:23:17 -04:00
39b4e76fde
Continuing refactoring of RefMetaDataTracker.
...
On the path towards converging getVariantContext() and getValues() in tracker so that we can have a single approach to get values from RODs with the new RodBinding() types
2011-07-28 17:48:28 -04:00
7c5c656b46
Uncovered fundamental accounting bug in VariantEval. Will be fixed by dev. team
...
Problem is that Novelty sees multiple records at a site (SNP, INDEL) to calculate whether a site is novel, but VariantEvalWalker makes an arbitrary decision which to use for analysis and CompOverlap may not see a comp record of the same type as eval. So you get lines where the stratification is known but there are 10 novel sites!
2011-07-28 14:19:27 -04:00
33b32c4211
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-28 13:57:22 -04:00
7a2a65155f
Merged bug fix from Stable into Unstable
2011-07-28 13:56:43 -04:00
1afc49a297
There are some really 'interesting' (but apparently valid) records in the Mus musculus dbSNP file. Generalized the handling of complex cases in the dbSNP adaptor to handle it all. I just grabbed the actual Mus musculus dbSNP file as a test, ran it whole genome, and confirmed that we finally produce a valid VCF on it. Should be the last commit needed on this adaptor.
2011-07-28 13:55:58 -04:00
c83f9432eb
Cleaned up RefMetaDataTracker
...
Renamed many functions to more clearly state what they are actually doing
Removed unnecessary / unused functionality, reducing interface complexity
Updated all uses of this code in GATK
Added generic, type-safe accessors to RefMetaDataTracker such as public <T> List<T> getValues(final String name, Class<T> clazz)
Added standard refMetaDataTracker accessors to RodBinding, so you can do everything you can for generic rods with the tracker directly with with the RodBinding
2011-07-27 23:25:52 -04:00
1865211b6d
Merged bug fix from Stable into Unstable
2011-07-27 22:52:06 -04:00
6230315ff2
Along with my half-written commit message from earlier, I also forgot to commit the integration test updates. This is what happens when you try to do things 30 seconds before you leave for the day. To finish up from before: complex events weren't being padded with the reference base as per the VCF spec. They are now.
2011-07-27 22:51:21 -04:00
f3ad4ec94b
Removed annoying FastaSequenceIndexBuilderProgressListener infrastructure that was just a boolean switch on whether to print progress or not.
2011-07-27 22:06:23 -04:00
ff31fa7990
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-27 16:15:23 -04:00
15be383d5b
Merge branch 'master' into rodRefactor
2011-07-27 15:36:49 -04:00
38a2518668
Merge branch 'master' into rodRefactor
2011-07-27 15:34:54 -04:00
405e521d44
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-26 17:56:48 -04:00
92a11ed8dc
Updated MD5 for PhaseByTransmissionIntegrationTest
2011-07-26 17:52:25 -04:00
f6a5e0e36a
Go for global integrationtest path first, if possible.
2011-07-26 17:35:30 -04:00
a53aeb75ab
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-25 15:10:35 -04:00
a29554e565
Removing the Genomic Annotator and its supporting classes
2011-07-25 15:10:25 -04:00
3afcb3415d
Max of 1000 records will be loaded and compared to avoid heap size problem.
2011-07-25 14:58:31 -04:00
2a51543693
Actually should have been gone...
2011-07-25 13:27:42 -04:00
ebfd8df06c
Restoring accidentially deleted unit test
2011-07-25 13:25:30 -04:00
f3049fba63
refdata directory cleanup
...
Removing unused files RODRecordIterator, ReferenceOrderedData, QueryableTrack, RMDTrackCreationException, GATKFeatureIterator, ReferenceOrderedDataUnitTest
Refactored dbSNP and refseq utilities to be closer to the other files implementing these features
2011-07-25 13:21:52 -04:00
bbb8473f03
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-25 10:59:00 -04:00
1d3bcce2c4
Merge branch 'master' into NoDistributedGATK
2011-07-23 20:04:50 -04:00
0b36b6540f
Merge branch 'laptop'
2011-07-23 01:44:54 -04:00
e23cb27451
Modified MD5 to account for the triple hets that shouldn't be phased
2011-07-23 01:44:44 -04:00
f366124778
Merge branch 'laptop'
2011-07-23 01:25:36 -04:00
45f2ca8d99
Changed MD5 to reflect latest changes to PhaseByTransmission.
2011-07-23 01:21:07 -04:00
b5deff48e6
Merge branch 'laptop'
2011-07-23 00:56:50 -04:00
5638017137
Removed the nofilters argument specification in the integrationtest
2011-07-23 00:56:23 -04:00
ffa361f57f
Merge branch 'laptop'
2011-07-23 00:50:38 -04:00
9417ba8c2c
Modified to accept multi-sample VCFs, removed the application of filters, and changed transmission probability field to be a genotype field rather than an INFO field.
2011-07-23 00:48:26 -04:00
f50145b872
Reinitialize random seed in the bwa bindings from the fixed seed stored in the
...
BWA support files every time the support files are loaded.
2011-07-22 13:41:53 -04:00
172b35372b
Moved all of the distributed GATK code to archive.
2011-07-22 09:20:32 -04:00
8b8f121cfb
Merge branch 'master' of ssh://gsa3.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-21 23:01:11 -04:00
59eb1f4663
Memory limits changed from Int to Double.
...
Updated LSF calls to read memory units from config along with tweaks to select hosts.
Moved some common code from GridEngine and LSF to super classes.
2011-07-21 22:57:18 -04:00
7054c5342f
When using the BWA bindings, you have to explicitly call close() to get the
...
bindings to release memory.
It may or may not be possible to implicitly close triggered by the GC; I'll add a JIRA.
2011-07-21 12:13:29 -04:00
Mark DePristo
Eric Banks
Kiran V Garimella
Matt Hanna
Khalid Shakir