230e16d7c0
Merge branch 'master' into rodrewrite
2011-09-20 06:54:18 -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
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
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
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
b2e8e11128
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-16 00:52:27 -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
d78e00e5b2
Renaming VariantAnnotator SnpEff keys
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This is to head off potential confusion with the output from the SnpEff tool itself,
which also uses a key named EFF.
2011-09-15 17:42:15 -04:00
1971fb35d7
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-15 16:55:33 -04:00
9dc6354130
Oops didn't mean to touch this test before
2011-09-15 16:55:24 -04:00
2a8b8efd2f
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-15 16:26:35 -04:00
2f58fdb369
Adding expected output doc to CountCovariates
2011-09-15 16:26:11 -04:00
fd1831b4a5
Updating docs to include more details
2011-09-15 16:25:03 -04:00
6d02a34bfb
Updating docs to include output
2011-09-15 16:17:54 -04:00
4ef6a4598c
Updating docs to include output
2011-09-15 16:10:34 -04:00
fe474b77f8
Updating docs so printing looks nicer
2011-09-15 16:05:39 -04:00
f04e51c6c2
Adding docs from Andrey since his repo was all screwed up.
2011-09-15 15:38:56 -04:00
86480b2e13
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-15 15:31:07 -04:00
d369d10593
Adding documentation before the release for GATK wiki page
2011-09-15 13:56:23 -04:00
202405b1a1
Updating the FunctionalClass stratification in VariantEval to handle the snpEff annotations; this change really needs to be in before the release so that the pipeline can output semi-meaningful plots. This commit maintains backwards compatibility with the crappy Genomic Annotator output. However, I did clean up the code a bit so that we now use an Enum instead of hard-coded values (so it's now much easier to change things if we choose to do so in the future). I do not see this as the final commit on this topic - I think we need to make some changes to the snpEff annotator to preferentially choose certain annotations within effect classes; Mark, let's chat about this for a bit when you get back next week. Also, for the record, I should be blamed for David's temporary commit the other day because I gave him the green light (since when do you care about backwards compatibility anyways?). In any case, at least now we have something that works for both the old and new annotations.
2011-09-15 13:52:31 -04:00
1e682deb26
Minor html-formatting-related documentation fix to the SnpEff class.
2011-09-15 13:07:50 -04:00
a942fa38ef
Refine the way we merge records in CombineVariants of different types. As of before, two records of different types were not combined and were kept separate. This is still the case, except when the alleles of one record are a strict subset of alleles of another record. For example, a SNP with alleles {A*,T} and a mixed record with alleles {A*,T, AAT} are now combined when start position matches.
2011-09-15 10:22:28 -04:00
3db457ed01
Revert "Modified VariantEval FunctionalClass stratification to remove hardcoded GenomicAnnotator keynames"
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After discussing this with Mark, it seems clear that the old version of the
VariantEval FunctionalClass stratification is preferable to this version.
By reverting, we maintain backwards compatibility with legacy output files
from the old GenomicAnnotator, and can add SnpEff support later without
breaking that backwards compatibility.
This reverts commit b44acd1abd9ab6eec37111a19fa797f9e2ca3326.
2011-09-14 10:47:28 -04:00
e0c8c0ddcb
Modified VariantEval FunctionalClass stratification to remove hardcoded GenomicAnnotator keynames
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This is a temporary and hopefully short-lived solution. I've modified
the FunctionalClass stratification to stratify by effect impact as
defined by SnpEff annotations (high, moderate, and low impact) rather
than by the silent/missense/nonsense categories.
If we want to bring back the silent/missense/nonsense stratification,
we should probably take the approach of asking the SnpEff author
to add it as a feature to SnpEff rather than coding it ourselves,
since the whole point of moving to SnpEff was to outsource genomic
annotation.
2011-09-14 07:09:47 -04:00
1213b2f8c6
SnpEff 2.0.2 support
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-Rewrote SnpEff support in VariantAnnotator to support the latest SnpEff release (version 2.0.2)
-Removed support for SnpEff 1.9.6 (and associated tribble codec)
-Will refuse to parse SnpEff output files produced by unsupported versions (or without a version tag)
-Correctly matches ref/alt alleles before annotating a record, unlike the previous version
-Correctly handles indels (again, unlike the previous version
2011-09-14 07:09:47 -04:00
5b1bf6e244
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-09-13 17:04:43 -04:00
c6672f2397
Intermediate (but necessary) fix for Beagle walkers: if a marker is absent in the Beagle output files, but present in the input vcf, there's no reason why it should be omitted in the output vcf. Rather, the vc is written as is from the input vcf
2011-09-13 16:57:37 -04:00
edf29d0616
Explicit info message about uploading S3 log
2011-09-12 22:16:52 -04:00
2316b6aad3
Trying to fix problems with S3 uploading behind firewalls
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-- Cannot reproduce the very long waits reported by some users.
-- Fixed problem that exception might result in an undeleted file, which is now fixed with deleteOnExit()
2011-09-12 22:02:42 -04:00
64707c33bb
Merged bug fix from Stable into Unstable
2011-09-12 21:54:11 -04:00
e63d9d8f8e
Mauricio pointed out to me that dynamic merging the unmapped regions of multiple BAMs ('-L unmapped' with a BAM list)
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was completely broken. Sorry about this! Fixed.
2011-09-12 21:50:59 -04:00
ec4b30de6d
Patch from Laurent: typo leads to bad error messages.
2011-09-12 14:45:53 -04:00
9d9d438bc4
New VariantAnnotatorEngine capability: an initialize() method for all annotation classes.
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All VariantAnnotator annotation classes may now have an (optional) initialize() method
that gets called by the VariantAnnotatorEngine ONCE before annotation starts.
As an example of how this can be used, the SnpEff annotation class will use the initialize()
method to check whether the SnpEff version number stored in the vcf header is a supported
version, and also to verify that its required RodBinding is present.
2011-09-12 13:00:53 -04:00
981b78ea50
Changing the VQSR command line syntax back to the parsed tags approach. This cleans up the code and makes sure we won't be parsing the same rod file multiple times. I've tried to update the appropriate qscripts.
2011-09-12 12:17:43 -04:00
60ebe68aff
Fixing issue in VariantEval in which insertion and deletion events weren't treated symmetrically. Added new option to require strict allele matching.
2011-09-12 09:43:23 -04:00
Mark DePristo
Mauricio Carneiro
Christopher Hartl
Guillermo del Angel
Menachem Fromer
David Roazen
Eric Banks
Ryan Poplin
Matt Hanna