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
55b9f06527
Ensure that IndelRealigner n-way out option supports MD5 generation.
2011-10-05 20:36:28 -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
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
d1d39943d0
Updating MD5 for BAMs that I added a read group to, part 2
2011-10-04 21:00:15 -07:00
941317167e
Updating MD5 for BAMs that I added a read group to
2011-10-04 14:08:00 -07:00
88c2fad64f
Change vcf jar to use a classfileset to pull all dependencies. Should save
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Jim Robinson some detective work in the long run.
2011-10-04 13:14:39 -04:00
0acaf2df65
Fix an embarrassing issue where a specific configuration of minimal coverage
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over small intervals could cause reads to be dropped from the pileup. Nothing
to see here...
2011-09-28 21:23:01 -04:00
a5006831d7
Shows "" not empty space when default string value is ""
2011-09-28 11:35:52 -04:00
1e32281a15
Fix to not show -null when missing short name argument
2011-09-28 11:31:20 -04:00
43b0c98298
Fix docs
2011-09-27 20:34:46 -04:00
b090751f62
Fixed Ant / PluginManager issue where reflections was picking up all class files under current working directory due to "." in jar manifest classpaths.
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Updates to HybridSelectionPipeline:
- Added annotations back via snpEff
- Minor updates to VQSR paths and lowered memory
2011-09-27 14:33:57 -04:00
6478681c0c
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/stable
2011-09-26 15:12:52 -04:00
059cdcb1be
Changing packaging system path for GATK-only Tribble codecs.
2011-09-26 14:58:19 -04:00
317b95fa57
Fixing some annotator docs
2011-09-26 11:46:45 -05:00
6804ab6d2f
Bug fix for NPE in very short GATK runs
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-- Was already in unstable, but not stable...
2011-09-24 09:25:29 -04:00
8ceb93b8ac
Fixed an integration test which crashed on the out of date LSF DRMAA library when run against the obsolete LSF dotkit instead of .combined_LSF_SGE
2011-09-23 21:03:22 -04:00
fbe3c1e0b3
Adding warning on HardClipping
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Hard Clipping is still under heavy development and should not be used by anyone less prepared than MacGyver.
2011-09-23 19:00:19 -04:00
e1cb5f6459
SnpEff annotator now assigns a functional class to each effect and distinguishes between actual effects and mere modifiers.
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-We now assign a functional class (nonsense, missense, silent, or none) to each SnpEff effect, and add a
SNPEFF_FUNCTIONAL_CLASS annotation to the INFO field of the output VCF.
-Effects are now prioritized according to both biological impact and functional class, instead of impact only.
-Many of SnpEff's "low-impact" effects are now classified as "modifiers" with lower priority than every
other effect. This includes such "effects" as DOWNSTREAM, UPSTREAM, INTRON, GENE, EXON, and others that
really describe the location of the variant rather than its biological effect.
This code will be short-lived (likely 1.2-only), as the next version of SnpEff will include most of these
features directly.
Checking this change into Stable+Unstable instead of Unstable because the current functional class stratification
in VariantEval is basically broken and urgently needs to be fixed for production purposes.
2011-09-23 16:06:52 -04:00
bcecc61715
Fixing md5 because file changed on disk
2011-09-23 10:56:16 -04:00
2bb77a7978
Docs for all VariantAnnotator annotations
2011-09-23 09:04:16 -04:00
68d5544ec9
Accurate docs for IOCrusher
2011-09-23 09:03:50 -04:00
dd65ba5bae
@Hidden for DocumentationTest and GATKDocsExample
2011-09-23 09:03:37 -04:00
dfce301beb
Looks for @Hidden annotation on all classes and excludes them from the docs
2011-09-23 09:03:04 -04:00
15a410b24b
Updating md5 for fixed file
2011-09-22 13:15:41 -04:00
5e06a45628
Fix the AnalayzeCovariates packaging.
2011-09-22 11:55:40 -04:00
f81a41b889
Updating MD5s for CombineVariants
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-- Old version had broken RSIDs, new version is fixed. No longer see rs1234,. as it is now just rs1234
2011-09-22 10:30:25 -04:00
2585fc3d6c
Updating Rscript path doc text for Broad users
2011-09-21 15:22:26 -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
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
a91ac0c5db
Intermediate commit of bugfixes to CombineVariants
2011-09-21 10:15:05 -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
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
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
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
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
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
Matt Hanna
David Roazen
Mark DePristo
Eric Banks
Khalid Shakir
Mauricio Carneiro
Ryan Poplin
Christopher Hartl