f9cdc119af
Added a method to ReadUtils that converts reads of the form 10S20M10S to 40M (just unclips the soft-clips).
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Be careful when using this - if you're writing a bam file it will be potentially written out of order (since the previous alignment start was at the M, not the S).
2011-09-21 18:16:42 -04:00
faff6e4019
Failed to commit changes to the GATKReport required for more easy access when using the files as data sources (read: histograms) for walkers
2011-09-21 18:15:23 -04:00
1b47dcb1b5
Removing old intron loss genotyper (though all of the development tree got rebased away, I hope); committing a new version of the likelihood calculation model and the genotyper, as well as the sequence simulator (and a QualityScoreHisotgramWalker to help with the simulation of read qualities). RFA will remain local for now.
2011-09-21 16:55:09 -04:00
ef05827c7b
Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-21 16:40:47 -04:00
3b51d9106a
Adding in likelihood calculations for mendelian violations. Also fixing a minor and rare bug in SelectVariants when specifying family structure on the command line.
2011-09-21 16:40:29 -04:00
04968c88b3
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-21 15:43:25 -04:00
c6ba944719
Adding bgzip vcf file for unit tests
2011-09-21 15:39:45 -04:00
6bcfce225f
Fix for dynamic type determination for bgzip files
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-- GZipInputStream handles bgzip files under linux, but not mac
-- Added BlockCompressedInputStream test as well, which works properly on bgzip files
2011-09-21 15:39:19 -04:00
9f6f0c443c
Marginally cleaner isVCFStream() function
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-- cleanup trying to debug minor bug. Failed to fix the bug, but the code is nicer now
2011-09-21 15:25:01 -04:00
5fef6dc5d0
Merged bug fix from Stable into Unstable
2011-09-21 15:23:06 -04:00
2585fc3d6c
Updating Rscript path doc text for Broad users
2011-09-21 15:22:26 -04:00
74f9ccf6dd
Merge
2011-09-21 11:30:11 -04:00
6592972f82
Putative fix for BAQ array out of bounds
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-- Old code required qual to be <64, which isn't strictly necessary. Now uses the Picard SAMUtils.MAX_PHRED_SCORE constant
-- Unittest to enforce this behavior
2011-09-21 11:25:08 -04:00
174859fc68
Don't allow whitespace in the INFO field
2011-09-21 11:14:54 -04:00
ecc7f34774
Putative fix for BAQ problem.
2011-09-21 11:09:54 -04:00
7d11f93b82
Final bugfix for CombineVariants
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-- Now handles multiple records at a site, so that you don't see records like set=dbsnp-dbsnp-dbsnp when combining something with dbsnp
-- Proper handling of ids. If you are merging files with multiple ids for the same record, the ids are merged into a comma separated list
2011-09-21 10:58:32 -04:00
b36d396c16
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-21 10:16:24 -04:00
34f435565c
Accidentally committed unclean tribble jar to repo
2011-09-21 10:16:17 -04:00
a91ac0c5db
Intermediate commit of bugfixes to CombineVariants
2011-09-21 10:15:05 -04:00
ac4f2d6d34
Fixing choppy consensus reads
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When the consensus read had holes in the middle, the consensus was being finalized but not properly reinitialized. It was restarting with the old coordinates of the finalized consensus, misaligning following bases.
2011-09-21 00:49:50 -04:00
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
Christopher Hartl
Christopher Hartl
Mark DePristo
Ryan Poplin
Eric Banks
Mauricio Carneiro
David Roazen
Menachem Fromer
Khalid Shakir