ae83420637
Merged bug fix from Stable into Unstable
2011-10-11 12:26:08 -04:00
794f275871
SnpEff is now marked as a RodRequiringAnnotation instead of an ExperimentalAnnotation.
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Having SnpEff grouped with the Experimental annotations was proving problematic, since it
requires a rod. Placing it in its own group should improve the situation somewhat, making it
easier to request "all annotations except for SnpEff".
2011-10-11 12:08:56 -04:00
cfd0ac8410
Merged bug fix from Stable into Unstable
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Conflicts:
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
2011-10-11 12:03:51 -04:00
24b72334b3
UnifiedGenotyper now correctly initializes the VariantAnnotator engine.
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This allows the annotation classes to perform any necessary initialization/validation.
For example, it allows the SnpEff annotator to (among other things) validate its rod binding.
This will prevent a NullPointerException when SnpEff annotation is requested but no rod binding
is present.
Added an integration test to cover this case so that it doesn't break again.
2011-10-11 12:02:05 -04:00
0429b38021
Merged bug fix from Stable into Unstable
2011-10-11 11:19:38 -04:00
1c485d8b5e
Forgot that no matter how trivial a change it's a good idea to compile first
2011-10-11 11:18:41 -04:00
6418f4d69b
Merged bug fix from Stable into Unstable
2011-10-11 11:13:18 -04:00
1975de1b32
Second try: hide --do_indel_quality in AnalyzeCovariates
2011-10-11 11:11:29 -04:00
6506ea83e8
Revert "Hide --do_indel_quality argument in AnalyzeCovariates. This shouldn't be documented nor used by external users"... a hidden passenger change made it through.
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This reverts commit 70e10ccb1be90dcff8f4485ae6ee036db2d1ac86.
2011-10-11 11:03:12 -04:00
4c1d8c8d44
Hide --do_indel_quality argument in AnalyzeCovariates. This shouldn't be documented nor used by external users
2011-10-11 11:01:06 -04:00
77c983c5b5
No one claimed this walker and it doesn't have integration tests or GATKdocs so it doesn't belong in public.
2011-10-10 15:17:54 -04:00
fb72bcf732
DiffObjects no longer prints out the file name in the status so MD5 are stable
2011-10-10 15:10:57 -04:00
46e7370128
this.allele, getAlleles(), and getAltAlleles() now return List not set
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-- Changes associated code throughout the codebase
-- Updated necessary (but minimal) UnitTests to reflect new behavior
-- Much better makealleles() function in VC.java that enforces a lot of key constraints in VC
2011-10-09 11:45:55 -07:00
c67f6c076b
simpleMerge now preserves allele order
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-- UnitTests for dangerous PL merging cases in the multi-allelic case. The new behavior is correct
2011-10-08 17:39:53 -07:00
ec14a4a606
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-07 08:38:50 -07:00
ca9cd9b688
Minor fix for merging intervals which hadn't been necessary when only merging from the left to right. Added integration tests to cover the parallelization of RTC.
2011-10-06 22:38:44 -04:00
c7864c7256
Filter application order is now deterministic, in the order defined by the walker
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-- For no apparent reason we were using a HashSet to store the ReadFilters, so the order of operations was really arbitrarily applied. The order now is
(1) the order of the walker intrinsic filters
(2) read group black list (if provided)
(3) command line filters (if provided)
2011-10-06 18:51:40 -07:00
0b88af4af9
Counts of records failing filters are displayed sorted
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-- Stops random ordering of the output, as the counts are returned sorted by string name of the class
-- Deleted now unused sh*tty assessors in Utils
2011-10-06 18:42:26 -07:00
d1e70d6ec2
Removed Nx counting of reads in metrics with -nt > 1
2011-10-06 18:29:26 -07:00
c61804a450
Rename the long version of the argument name to more accurately reflect its purpose.
2011-10-06 16:14:04 -04:00
61a3dfae24
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-06 15:58:04 -04:00
6eb87bf58a
RTC now caches all intervals as GenomeLocs (which is expected to take < 1Gb whole genome based on back of the envelope calculations with Matt) so that 1) we don't have to worry about emitting outside of the leaves in the hierarchical reductions and 2) we can emit the intervals in sorted order which is a big performance plus for the realigner. Integration tests change only because intervals whose start=stop are now printed as chr:start instead of chr:start-stop.
2011-10-06 15:57:49 -04:00
1b0735f0a3
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-06 13:41:45 -04:00
c4dfc1fb8b
Temporary commit of parallelization support for RealignerTargetCreator. Tim begged us for this and I got assurances from Khalid/Matt that this would also be extremely helpful for the whole genome calling pipeline, so I spent a while working on this. Needs to be fixed up though because apparently only the leaves in the hierarchical reduce get their output aggregated. Worked out a better solution with Matt.
2011-10-06 13:41:36 -04:00
73f9d1f217
GATK read group requirement iron hand
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-- The GATK will now throw a user exception if it opens a SAM/BAM file that doesn't have at least one RG defined
-- LIBS again throws an error if the complete list of samples isn't provided
-- Updating ExmpleCountLociPipeline test to use the well-formated versions of the exampleBAM and exampleFASTA files in testdata, instead of the old broken ones in validation_data.
-- Convenience constructors for UserExceptions.MalformedBAM
2011-10-06 08:40:35 -07:00
23845ac798
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-06 08:17:08 -07:00
daa5999489
Fixed typo in argument description
2011-10-06 08:16:25 -07:00
8a474e38ff
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-06 10:08:39 -04:00
93f7e632bd
Minor fix/enhancement for VariantEval: if a vcf has symbolic alleles, program would crash ungracefully - now we'll just skip record without processing. This is a big issue since we can't process 1000G integration files with code as is.
2011-10-06 10:07:46 -04:00
190be4d0d1
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-05 21:27:11 -07:00
8e6845806a
Allowing empty samples list in LIBS
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-- Right now we cannot process BAM files without read groups because we enforce the samples list to not be empty when there's a SAM record. Now if there are reads and there are no samples we add the "null" sample so that LIBS walks the reads properly
2011-10-05 21:26:21 -07:00
180c8f286f
Merged bug fix from Stable into Unstable
2011-10-05 20:37:43 -04:00
55b9f06527
Ensure that IndelRealigner n-way out option supports MD5 generation.
2011-10-05 20:36:28 -04:00
be2d29ce69
Final PED documentation
2011-10-05 15:17:41 -07:00
3226d5dc0d
Merge branch 'master' into ped
2011-10-05 15:03:09 -07:00
6a573437af
Details documentation arguments for -ped
2011-10-05 15:00:58 -07:00
e7c80f7c45
Renaming quantitative trait to OtherPhenotype which is now a String not a double
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-- we can now use PED file to represent population data or other arbitrary phenotype data, not just doubles
2011-10-05 12:26:33 -07:00
51ecc20867
getFamily() and associated methods implemented and tested
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-- Sample no longer serializable
-- Sample now implements Comparable
2011-10-05 09:55:05 -07:00
a45d985818
TODO method stubs
2011-10-04 15:54:09 -07:00
fee89e47ff
Only throws an error when there are no samples but there are reads
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-- Handles the case when you are running a ROD traversal and yet the LIBS is still used to return null everywhere.
2011-10-04 06:50:54 -07:00
f552aede42
Only provide the sample names in the BAM file for efficiency
2011-10-04 06:50:12 -07:00
a27641e1fc
Cleaned up imports
2011-10-04 06:28:36 -07:00
b20689ff55
No longer supports extraProperties
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-- the underlying data structure is still present, but until I decide what to do for the extensible system I've completely disabled the subsystem
-- Added code to merge Samples, so that a mostly full record can be merged with a consistent empty record. If the two records are inconsistent, an error is thrown
-- addSample() in Sample.class now invokes mergeSample() when appropriate
-- Validation types are now only STRICT or SILENT
-- Validation code implemented in SampleDBBuilder
-- Extensive unit tests for SampleDBBuilder
2011-10-03 19:20:33 -07:00
3837aa45b4
Fixing conflicts
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Conflicts:
public/java/test/org/broadinstitute/sting/utils/clipreads/ReadClipperUnitTest.java
2011-10-03 19:07:59 -07:00
2e3dc52088
Minor function renaming
2011-10-03 14:41:13 -07:00
dd71884b0c
On path to SampleDB engine integration
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-- PedReader tag parser
-- Separation of SampleDBBuilder from SampleDB (now immutable)
-- Removed old sample engine arguments
2011-10-03 12:08:07 -07:00
c3eff7451a
Found a small inefficiency while profiling: we were still using String.split instead of ParsingUtils.split to break up array values in the INFO field. There was a noticeable (albeit not big) difference in the change when reading sites only files.
2011-10-03 14:20:39 -04:00
8ee0f91904
Remove residual processing tracker arguments
2011-10-03 09:50:01 -07:00
89ac50e86e
SampleDataSource -> SampleDB
2011-10-03 09:33:30 -07:00
93fba06cb5
Support for whitespace only lines
2011-10-03 09:30:10 -07:00
David Roazen
Guillermo del Angel
Eric Banks
Mark DePristo
Matt Hanna
Mauricio Carneiro