1eab9be35d
Now with accurate javadoc
2011-08-22 17:25:15 -04:00
f93a554b01
updating exome specific parameters in MDCP
2011-08-21 10:25:36 -04:00
dbff84c54e
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-21 10:09:19 -04:00
a8cbced71b
Bug fix for Ryan: check for no context
2011-08-20 22:49:51 -04:00
0ccd173967
Fixing the recent SelectVariants fix
2011-08-20 21:30:08 -04:00
b008676878
fixing the previous fix
2011-08-20 21:21:55 -04:00
782453235a
Updated VariantEvalIntegrationTest since there's a new column separating nMixed and nComplex in CountVariants
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Misc updates to WholeGenomeIndelCalling.scala
Bug fix in VariantEval (may be temporary, need more investigation): if -disc option is used in sites-only vcf's then a null pointer exception is produced, caused by recent introduction of -xl_sf options.
2011-08-20 12:24:22 -04:00
539e157ecd
Fixing misc parameters in MDCP. The pipeline now does VariantEval of output by default. Fix for NaN vqslod values in VQSR
2011-08-20 11:28:48 -04:00
4939648fd4
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-20 08:50:43 -04:00
ddb5045e14
Updating the methods development calling pipeline for the new rod binding syntax and the new best practices.
2011-08-19 19:29:51 -04:00
b08d63a6b8
Documentation and code cleanup for ClipReads, CallableLoci, and VariantsToTable
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-- Swapped -o [summary] and -ob [bam] for more standard -o [bam] and -os [summary] arguments.
-- @Advanced arguments
2011-08-19 15:06:37 -04:00
49e831a13b
Should have checked in
2011-08-19 14:35:16 -04:00
7b5fa4486d
GenotypeAndValidate - Added docs to the @Arguments
2011-08-19 13:35:11 -04:00
0f25167efd
minor fix in VariantEval docs
2011-08-19 11:01:04 -04:00
269ed1206c
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-19 09:32:20 -04:00
40e67cff1b
I like the @Advanced annotation
2011-08-18 22:27:34 -04:00
2457c7b8f5
Merge branch 'master' into help
2011-08-18 22:20:43 -04:00
77fa2c1546
Renaming read filters with a superfluous 'Read' in their names. Kept the ones that made sense to have it (e.g. MalformedReadFilter).
2011-08-18 22:01:33 -04:00
1d3799ddf7
Merge branch 'master' into help
2011-08-18 22:00:29 -04:00
f7414e39bc
Improvements to GATKDocs
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-- Allowed values for RodBinding<T> are displayed in the GATKDocs
-- Longest name up to 30 characters is chosen for main argument list (suggested by Ryan/Mauricio)
-- Features are listed in alphabetical order
-- Moved useful getParameterizedType() function to JVMUtils
-- Tests of these features in the Documentation Test
2011-08-18 21:20:09 -04:00
09d099cada
Added GATKDocs to the UnifiedGenotyper.
2011-08-18 20:57:02 -04:00
626cbf9411
Bug fixes and cleanups for IndelStatistics
2011-08-18 16:28:40 -04:00
58560a6d50
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-18 16:17:52 -04:00
3dfb60a46e
Fixing up and refactoring usage of indel categories. On a variant context, isInsertion() and isDeletion() are now removed because behavior before was wrong in case of multiallelic sites. Now, methods isSimpleInsertion() and isSimpleDeletion() will return true only if sites are biallelic. For multiallelic sites, isComplex() will return true in all cases.
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VariantEval module CountVariants is corrected and an additional column is added so that we log mixed events and complex indels separately (before they were being conflated).
VariantEval module IndelStatistics is considerably simplified as the sample stratification was wrong and redundant, now it should work with the VE-generic Sample stratification. Several columns are renamed or removed since they're not really useful
2011-08-18 16:17:38 -04:00
6b256a8ac5
Merge branch 'master' of ssh://gsa2/humgen/gsa-scr1/chartl/dev/git
2011-08-18 15:29:24 -04:00
a8935c99fc
dding docs for DepthOfCoverage and ValidationAmplicons
2011-08-18 15:28:35 -04:00
f2f51e35e3
Merge branch 'master' into help
2011-08-18 14:05:33 -04:00
faa3f8b6f6
Only concrete classes are now documented
2011-08-18 14:04:47 -04:00
7c4ce6d969
Added GATKDocs for the VQSR walkers.
2011-08-18 14:00:39 -04:00
d4511807ed
Merge branch 'master' into help
2011-08-18 11:53:37 -04:00
c787fd0b70
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-18 11:52:45 -04:00
c797616c65
If you have one sample in your BAM, getToolkit().getSamples().size() == 2
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Also deleted double initializationm, where a line of code was duplicated in creating the GATK engine.
2011-08-18 11:51:53 -04:00
cbec69a130
Merge branch 'master' into help
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Conflicts:
public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java
2011-08-18 11:33:27 -04:00
aa21fc7c9c
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-18 11:30:59 -04:00
f5d7cabb20
Fix for reintroducing an already solved problem.
2011-08-18 11:20:12 -04:00
a45498150a
Remove non-ascii char
2011-08-18 11:18:29 -04:00
c08a9964d4
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-18 10:58:04 -04:00
bb79d3edae
Added GATKDocs for the BQSR walkers.
2011-08-18 10:57:48 -04:00
47bbddb724
Now provides type-specific user feedback
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For RodBinding<VariantContext> error messages now list only the Tribble types that produce VariantContexts
2011-08-18 10:47:16 -04:00
2d41ba15a4
Vastly better Tribble help message
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Here's a new example:
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 1.1-520-g76495cd):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
##### ERROR
##### ERROR MESSAGE: Invalid command line: Failed to parse value /humgen/gsa-hpprojects/GATK/data/refGene_b37.filtered.sorted.txt for argument refSeqRodBinding. Message: Invalid command line: No tribble type was provided on the command line and the type of the file could not be determined dynamically. Please add an explicit type tag :TYPE listing the correct type from among the supported types:
##### ERROR Name FeatureType Documentation
##### ERROR BEAGLE BeagleFeature http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_beagle_BeagleCodec.html
##### ERROR BED BEDFeature http://www.broadinstitute.org/gsa/gatkdocs/release/org_broad_tribble_bed_BEDCodec.html
##### ERROR BEDTABLE TableFeature http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_table_BedTableCodec.html
##### ERROR CGVAR VariantContext http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_completegenomics_CGVarCodec.html
##### ERROR DBSNP DbSNPFeature http://www.broadinstitute.org/gsa/gatkdocs/release/org_broad_tribble_dbsnp_DbSNPCodec.html
##### ERROR GELITEXT GeliTextFeature http://www.broadinstitute.org/gsa/gatkdocs/release/org_broad_tribble_gelitext_GeliTextCodec.html
##### ERROR MAF MafFeature http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_gatk_features_maf_MafCodec.html
##### ERROR MILLSDEVINE VariantContext http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_MillsDevineCodec.html
##### ERROR RAWHAPMAP RawHapMapFeature http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_hapmap_RawHapMapCodec.html
##### ERROR REFSEQ RefSeqFeature http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_refseq_RefSeqCodec.html
##### ERROR SAMPILEUP SAMPileupFeature http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_sampileup_SAMPileupCodec.html
##### ERROR SAMREAD SAMReadFeature http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_samread_SAMReadCodec.html
##### ERROR SNPEFF SnpEffFeature http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_snpEff_SnpEffCodec.html
##### ERROR SOAPSNP VariantContext http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_soapsnp_SoapSNPCodec.html
##### ERROR TABLE TableFeature http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_table_TableCodec.html
##### ERROR VCF VariantContext http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_vcf_VCFCodec.html
##### ERROR VCF3 VariantContext http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_utils_codecs_vcf_VCF3Codec.html
##### ERROR ------------------------------------------------------------------------------------------
2011-08-18 10:31:32 -04:00
c2287c93d7
Cleanup of codec locations. No more dbSNPHelper
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-- refdata/features now in utils/codecs with the other codecs
-- Deleted dbsnpHelper. rsID function now in VCFutils. Remaining code either deleted or put into VariantContextAdaptors
-- Many associated import updates due to code move
2011-08-18 10:02:46 -04:00
9c17d54cb6
getFeatureClass() now returns Class<T> not Class to avoid yesterday's runtime error
2011-08-18 09:39:20 -04:00
c30e1db744
Better location for help utils
2011-08-18 09:38:51 -04:00
4da42d9f39
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-18 09:32:57 -04:00
c91a442be1
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-17 22:40:16 -04:00
a7b70e6bb4
Adding feature for Khalid: ability to exclude particular samples.
2011-08-17 22:28:22 -04:00
cc3df8f11a
Moving GAV walker to public
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Walker is updated to the new RodBinding system and has the new GATKDocs layout.
2011-08-17 21:55:17 -04:00
c104dd7a09
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-17 16:59:12 -04:00
81a792afeb
Reverting optimization disable in unstable.
2011-08-17 16:58:24 -04:00
2e35592295
GATKDocs for CallableLoci
2011-08-17 16:32:01 -04:00
Mark DePristo
Ryan Poplin
Eric Banks
Guillermo del Angel
Mauricio Carneiro
Chris Hartl
Matt Hanna