5298e3a942
Making the outputDir optional. Default = ./
2011-07-05 16:30:41 -04:00
7d3dfdfdf2
Updating the MDCP to use the classpath for the GATK jar, removing -gatk parameter.
2011-07-05 16:30:10 -04:00
5faf40b79d
Moving AnalyzeAnnotations into the archive because it has outlived its usefulness.
2011-07-02 10:39:53 -04:00
b6bc64a0c8
Cleanup of the utils.broad package.
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Using Picard IoUtils on sample names.
2011-07-01 20:47:03 -04:00
444eae316c
Moving these supported perl scripts to public
2011-07-01 17:26:25 -04:00
546e7777fa
Re-fixing paths in pipeline tests after example qscripts got moved.
2011-07-01 16:39:10 -04:00
e9030a7bfd
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-07-01 16:19:35 -04:00
b0fb63e20a
moving the example scala scripts to the qscripts package.
2011-07-01 16:14:59 -04:00
d647ea4fdc
Long-delayed change to CachingIndexedFastaSequenceFile. Made the cache
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non-static to avoid problems when multiple references are used within the same
thread (eg., during integration tests). This should kill the intermittent
IndelRealignerIntegrationTest failures.
2011-07-01 16:04:30 -04:00
d19351f71a
Added capability of running multiple bam files in the same directory.
2011-07-01 16:02:28 -04:00
11d4af0e75
Path-related fixes to the private queue pipeline tests.
2011-07-01 13:41:34 -04:00
9644f104c4
Fixes to the queue pipeline tests to account for the new directory structure.
2011-07-01 13:13:24 -04:00
4b17f34640
Fixes to the packaging system to work with the new directory structure.
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Also added a few R scripts to the list of files to include in the resources
directory of the binary distribution, at Ryan's request.
2011-06-30 18:27:17 -04:00
5786b51bcf
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-06-30 15:26:28 -04:00
761347b8d5
The VariantContext utility method used by SelectVariants wasn't checking the filter status (unfiltered vs. passing filters) and always returned a VC that was passing filters. This is fixed and the md5 from the VCF Streaming test has been re-updated.
2011-06-30 15:26:09 -04:00
64048a67e8
cleaning up ghost scala scripts. Deleting clearly unused one and moving others to qscripts.archive
2011-06-30 15:20:43 -04:00
867056af51
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-06-30 15:03:18 -04:00
defa3cfe85
Moved around private walkers into appropriate directories in private gatk.walkers. Moved a few public walkers into private qc package, and some private qc walkers into the public directory. Removed several obviously broken and/or unused walkers.
2011-06-30 14:59:58 -04:00
75f93882c7
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-06-30 14:59:10 -04:00
2cb1376ed0
VCFStreaming was failing integration tests because now select variants outputs the samples in alphabetical order, instead of random as before. Fixed the MD5.
2011-06-30 14:55:39 -04:00
f4ae6edb92
Moving some of the released R scripts into public from private
2011-06-30 14:55:25 -04:00
197b7141c1
Added an optional argument -bt <num_threads> for BWA to run multithreaded.
2011-06-30 14:41:57 -04:00
f4463d38ca
BWA requires pair ended reads to be sorted by read names when operating over BAM files, but Picard sorts by coordinate, so in case we use BWA in pair ended reads, the pipeline now resorts the BAM in read name order, realigns it then sorts it in coordinate order.
2011-06-30 14:29:21 -04:00
bb6b1d615b
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-06-30 13:50:16 -04:00
804d5f22d5
Reverting previous change, as promised.
2011-06-30 13:18:30 -04:00
9e234cf5d6
This is a temporary commit for Picard. It will absolutely break integration tests, but I'm going to revert it in 1 minute. Because we don't want them in unstable, I need to push this into stable.
2011-06-30 13:17:14 -04:00
352c38fc0b
Updated to reflect dbsnp conversion fix
2011-06-30 11:55:56 -04:00
efd99c3c11
new home for the core qscripts
2011-06-30 11:32:06 -04:00
f18fffd625
Fixing broken paths to the testdata directory throughout the codebase.
2011-06-29 17:36:47 -04:00
2ad4d2f0bb
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-06-29 16:06:14 -04:00
1085df8b7b
Making the BQSR pipeline publicly available and supported.
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this is for all the Pacbio validation that is going on right no in the cancer group. They are all using this script, and I'm happy to support it.
2011-06-29 16:05:32 -04:00
70ba851478
Might as well check for the illegal state and throw an exception
2011-06-29 15:59:10 -04:00
1f19afe1d9
Fixed bug in the IndelRealigner: now that variants are correctly typed in VariantContext, it is possible that a variant can be an indel but neither an insertion or a deletion; added a isComplexIndel() method and now we check for such an event in the realigner (we don't use them to generate alternate consenses). Also, added a isMNP() method while I was there so that it would be consistent with other variant types.
2011-06-29 15:54:09 -04:00
33c67a139c
Wrong package; this should have been moved when VC got moved in from Tribble
2011-06-29 14:56:02 -04:00
dee10140dd
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-06-29 13:58:04 -04:00
8586c86bc4
My commit from last week to fix the old dbsnp rod conversion only worked for locus traversals. Updated now to work for all traversals.
2011-06-29 13:56:37 -04:00
f736a1d61b
Updated md5's from previous checkin
2011-06-29 13:37:15 -04:00
5b6d279a2e
Two bug fixes:
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a) Modified the way clipped bases are dealt with in ReadPosRankSumTest when annotating indels. Cigar string cannot be trusted because BWA can clip good high quality bases and some sites get incorrect ReadPos annotations if BWA systematically clips at an indel breakpoint.
b) PL header needs to specify "." as length. Otherwise we fail VCF validation if multiallelic sites are present.
2011-06-29 10:21:27 -04:00
139c6b84a1
Modified build.xml and the help extractor doclet to use the output of "git
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describe" as an absolute version number (if the repository has at least one
tag), using the raw SHA-1 hash value as a fallback version number in the case
where there are no tags.
2011-06-28 08:37:05 -04:00
3c9497788e
Reorganized the codebase beneath top-level public and private directories,
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removing the playground and oneoffprojects directories in the process. Updated
build.xml accordingly.
2011-06-28 06:55:19 -04:00
Mauricio Carneiro
Ryan Poplin
Khalid Shakir
Eric Banks
David Roazen
Mark A. DePristo
Guillermo del Angel