e19dba86a6
Merged bug fix from Stable into Unstable
2011-10-08 22:37:12 -04:00
0016c707a3
Codecs other than VCF accidentally bled into vcf.jar. Unfortunately, vcf.jar
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turned out to be the *only* home for these other codecs. This change pushes
them back into StingUtils.jar.
2011-10-08 22:24:35 -04:00
ec14a4a606
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-07 08:38:50 -07:00
6fbd41724a
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-07 11:20:00 -04:00
4514bc350f
More reliable way of finding the Tribble jar.
2011-10-07 11:19:29 -04:00
181c76750e
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-06 22:38:55 -04:00
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
f91b015e0e
Made the BaseTest.testDir absolute
2011-10-06 22:33:21 -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
d367945dec
Extending InsertSizeDistribution to compute stats by sample and by read group
2011-10-06 15:14:17 -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
6d9c210460
Updating MD5s for updated BAM with read groups
2011-10-06 12:15:48 -07:00
c528233578
Now uses exampleBAM and exampleFASTA instead of the misc. copies in validation_data
2011-10-06 12:03:45 -07:00
ab357ef900
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-06 10:50:02 -07:00
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
3961733590
Merged bug fix from Stable into Unstable
2011-10-06 12:54:52 -04:00
4fa5045e84
Abandoning classfileset/rootfileset approach due to difficulting managing
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classloading of bcel*.jar/ant-apache-bcel*.jar. Switching instead to manually
specifying a minimal set of packages/classes to include in the vcf.jar via
build.xml, and adding a unit test which creates a limited classloader
only aware of vcf.jar and tribble.jar and tries to use it to load the core
classes in the vcf jar.
Hopefully third time's the charm.
2011-10-06 12:49:51 -04:00
1dbe937396
Add in argument for downsampling threshold
2011-10-06 12:00:32 -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
4b5b9155a9
Fixed bad expected value in PedReaderUnitTest
2011-10-06 08:16:47 -07:00
daa5999489
Fixed typo in argument description
2011-10-06 08:16:25 -07:00
c649759978
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-06 10:10:46 -04:00
2f12bfaad5
Merged bug fix from Stable into Unstable
2011-10-06 10:10:00 -04:00
efca1fdfd8
Revert change until I figure out how to use classfileset/rootfileset
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with a vanilla ant install.
This reverts commit 4c9022872beec8dc0700a1320a267e3603c8212d.
2011-10-06 10:08:48 -04:00
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
a3c5a31686
Oops, forgot the PED test file
2011-10-05 21:09:08 -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
b945e97de1
Shouldn't have committed the non-fetching version by default
2011-10-05 17:12:48 -07:00
b068846407
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-05 17:12:09 -07:00
6d6149b9a2
Updated gsalib gsa.read.gatkreport to return all reports, even those beginning with '.'.
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In PreQC using geom_blank() so MEDIAN_INSERT_SIZE plot doesn't crash on facet_grid(scales='free') when data doesn't contain points for 'RF' or 'TANDEM'.
2011-10-05 18:30:40 -04:00
982983355f
Merged bug fix from Stable into Unstable
2011-10-05 18:27:29 -04:00
dd780dba5f
Rather than just picking a few classes to be the roots of the vcf jar and
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including all dependencies, use the entire codecs.vcf and variantcontext
packages as roots.
Fix for my fix for Jim Robinson.
2011-10-05 18:25:26 -04:00
a91509e7dd
Shouldn't be public
2011-10-05 15:22:57 -07:00
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
dc6d71dec5
Merged bug fix from Stable into Unstable
2011-10-05 16:53:32 -04:00
b732f740d2
Revert "Change vcf jar to use a classfileset to pull all dependencies. Should save"
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This reverts commit 441022c4c600624928da46419a6a289200700f3e.
2011-10-05 16:51:30 -04:00
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
Matt Hanna
Mark DePristo
Eric Banks
Khalid Shakir
Menachem Fromer
Guillermo del Angel
David Roazen