48c413fee8
Now throws an error when the mismatch fraction is too high
2011-09-20 21:28:31 -04:00
3b9314aecf
Max fraction of mismatch test for debugging
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-- Useful example for individuals who want to compute mismatches between a read and the reference.
2011-09-20 20:42:18 -04:00
b04d8eab55
Merged bug fix from Stable into Unstable
2011-09-20 17:24:14 -04:00
758ecf2d43
Bringing latest updates of ReduceReads to the master repository
2011-09-20 16:35:09 -04:00
d9ea764611
SnpEff annotator now adds OriginalSnpEffVersion and OriginalSnpEffCmd lines to the header of the VCF output file.
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This change is urgently required for production, which is why it's going into Stable+Unstable
instead of just Unstable.
The keys for the SnpEff version and command header lines in the VCF file output by
VariantAnnotator (OriginalSnpEffVersion and OriginalSnpEffCmd) are intentionally
different from the keys for those same lines in the SnpEff output file (SnpEffVersion
and SnpEffCmd), so that output files from VariantAnnotator won't be confused
with output files from SnpEff itself.
2011-09-20 16:30:55 -04:00
bffd3cca6f
Bug fix for reduced read; only adds regular bases for calculation
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-- No longer passes on deletions for genotyping
2011-09-20 15:07:06 -04:00
83bb91020f
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-20 14:52:54 -04:00
a97e039a62
Thanks to Chris for instructing me to use VCFExtractIntervals to get proper scattering of Variant Annotation
2011-09-20 14:29:39 -04:00
827c942c80
Rev tribble
2011-09-20 14:01:14 -04:00
a1b4cafe7a
Bug fix for NPE when timer wasn't initialized
2011-09-20 13:59:59 -04:00
08ffb18b96
Renaming datasets in the MDCP
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Making dataset names and files generated by the MDCP more uniform.
2011-09-20 11:02:51 -04:00
b7511c5ff3
Fixed long-standing bug in tribble index creation
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-- Previously, on the fly indices didn't have dictionary set on the fly, so the GATK would read, add dictionary, and rewrite the index. This is now fixed, so that the on the fly index contains the reference dictionary when first written, avoiding the unnecessary read and write
-- Added a GenomeAnalysisEngine and Walker function called getMasterSequenceDictionary() that fetches the reference sequence dictionary. This can be used conveniently everywhere, and is what's written into the Tribble index
-- Refactored tribble index utilities from RMDTrackBuilder into IndexDictionaryUtils
-- VCFWriter now requires the master sequence dictionary
-- Updated walkers that create VCFWriters to provide the master sequence dictionary
2011-09-20 10:53:18 -04:00
efce2ece9d
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-20 09:08:38 -04:00
5d0705acd6
Adding quality scores to the VCF records created by the Haplotype Caller
2011-09-20 09:07:28 -04:00
230e16d7c0
Merge branch 'master' into rodrewrite
2011-09-20 06:54:18 -04:00
b507bd946c
Merged bug fix from Stable into Unstable
2011-09-20 00:18:16 -04:00
61b89e236a
To work around potential problem with invalid javax.mail 1.4.1 in ivy cache, added explicit javax.mail 1.4.4 along with build.xml code to remove 1.4.1.
2011-09-20 00:14:35 -04:00
aa8afa3899
Merge
2011-09-19 21:16:47 -04:00
56106d54ed
Changing ReadUtils behavior to comply with GenomeLocParser
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Now the functions getRefCoordSoftUnclippedStart and getRefCoordSoftUnclippedEnd will return getUnclippedStart if the read is all contained within an insertion. Updated the contracts accordingly. This should give the same behavior as the GenomeLocParser now.
2011-09-19 14:00:00 -04:00
080c957547
Fixing contracts for SoftUnclippedEnd utils
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Now accepts reads that are entirely contained inside an insertion.
2011-09-19 13:53:53 -04:00
ba150570f3
Updating to use new rod system syntax plus name change for CountRODs
2011-09-19 13:30:32 -04:00
5e832254a4
Fixing ReadAndInterval overlap comments.
2011-09-19 13:28:41 -04:00
ecb8466662
Merged bug fix from Stable into Unstable
2011-09-19 12:32:08 -04:00
8143def292
Fix the -T argument in the DepthOfCoverage docs
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Add documentation for the RefSeqCodec, pointing users to the wiki page describing how to create the file
2011-09-19 12:31:47 -04:00
095f75ff7d
Merge branch 'master' of ssh://gsa1.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-19 12:24:12 -04:00
85626e7a5d
We no longer want people to use the August 2010 Dindel calls for indel realignment but instead Guillermo's new whole genome bi-allelic indel calls; updating the bundle accordingly. Also, there was some confusion by the 1000G data processing folks as to exactly what these indel files are, so I've renamed them so that it's clear. Wiki updated too.
2011-09-19 12:24:05 -04:00
034b868588
Revert "Fix the -T argument in the DepthOfCoverage docs"
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This reverts commit 0994efda998cf3a41b1a43696dbc852a441d5316.
2011-09-19 12:16:07 -04:00
cfde0e674b
Merge branch 'sgintervals'
2011-09-19 12:02:41 -04:00
3e93f246f7
Support for sample sets in AssignSomaticStatus
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-- Also cleaned up SampleUtils.getSamplesFromCommandLine() to return a set, not a list, and trim the sample names.
2011-09-19 11:40:45 -04:00
41ffb25b74
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-19 10:55:18 -04:00
ca1b30e4a4
Fix the -T argument in the DepthOfCoverage docs
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Add documentation for the RefSeqCodec, pointing users to the wiki page describing how to create the file
2011-09-19 10:29:06 -04:00
4ad330008d
Final intervals cleanup
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-- No functional changes (my algorithm wouldn't work)
-- Major structural cleanup (returning more basic data structures that allow us to development new algorithm)
-- Unit tests for the efficiency of interval partitioning
2011-09-19 10:19:10 -04:00
6ea57bf036
Merge branch 'master' into sgintervals
2011-09-19 09:50:19 -04:00
6bd42c053d
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-18 20:18:39 -04:00
bed78b47e0
Marginally better formating, with hours the default time
2011-09-18 20:18:18 -04:00
091c7197cd
Fixed memory leak and bug with deletions in clipping
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The ClippingOp clip cigar function would run into a endless loop if the parameter were out of the reads range, I stopped the bug.
* There is no check to make sure the read coordinate are covered by the read though
When Hard clipping to interval, I added a check for deletions.
NOTE: method works for NA12878 WEx but needs to be more thoroughly tested/optimized
2011-09-18 19:21:51 -04:00
67cca5196c
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-18 12:13:01 -04:00
cb4a50b147
Adding ability to try both small and large kmer lengths. Highest likelihood wins.
2011-09-17 16:42:49 -04:00
7fa1e237d9
Forgot to git stash pop new MD5's for CombineVariants integration test
2011-09-16 12:53:54 -04:00
e7b9a009b7
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-16 12:48:30 -04:00
42f3b7ba32
Merged bug fix from Stable into Unstable
2011-09-16 12:46:38 -04:00
33967a4e0c
Fixed issue reported by chartl where cloned functions lost tags on @Inputs.
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Updated ExampleUnifiedGenotyper.scala with new syntax.
2011-09-16 12:46:07 -04:00
92f7db3228
Can now optionally suppress the use of all annotations and then add back in specific annotations/groups. This was necessary, since using all annotations for VariantAnnotator NOW includes SNPeff, which (annoyingly) requires a SNPeff VCF...
2011-09-16 02:40:24 -04:00
b2e8e11128
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-16 00:52:27 -04:00
3cd9f3fe81
Merge remote-tracking branch 'unstable/master'
2011-09-15 21:14:17 -04:00
57b3efa2e2
Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-15 21:06:38 -04:00
939babc820
Updating formating for ValidationAmplicons GATK docs
2011-09-15 21:05:51 -04:00
9fdf1f8eb6
Fix some doc formatting for Depth of Coverage
2011-09-15 21:05:22 -04:00
e6e9b08c9a
Must provide alleles VCF to UGCallVariants
2011-09-15 18:51:09 -04:00
1960bcabb8
Updated to use new ROD-binding system
2011-09-15 18:07:32 -04:00
Mark DePristo
David Roazen
Mauricio Carneiro
Menachem Fromer
Ryan Poplin
Khalid Shakir
Eric Banks
Christopher Hartl
Roger Zurawicki
Guillermo del Angel