f2a05af356
Fixed layout problem with advanced arguments
2011-08-18 21:59:44 -04:00
d1892cd0d7
Bug fixes
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-- Sorting of ArgumentSources now done in GATKDoclet, not in the ParsingEngine, as the system depends on the LinkedTreeMap
-- Fixed broken exception throwing in the case where a file's type could not be determined
2011-08-18 21:58:36 -04:00
c5efb6f40e
Usability improvements to GATKDocs
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-- ArgumentSources are now sorted by case insensitive names, so arguments are shown in alphabetical order (Ryan)
-- @Advanced annotation can be used to indicate that an argument is an advanced option and should be visually deemphasized in the GATKs. There's now an advanced section. Mauricio or Ryan -- could you figure out how to make this section less prominent in the style.css?
2011-08-18 21:39:11 -04:00
cca0930517
Better formatting for GATKDocs
2011-08-18 21:24:23 -04:00
d94da0b1cf
Moved CG and SOAP codecs to private
2011-08-18 21:20:26 -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
6ef01e40b8
Complete rewrite of Hard Clipping (ReadClipper)
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Hard clipping is now completely independent from softclipping and plows through previously hard or soft clipped reads.
2011-08-18 18:35:45 -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
6ee54cce32
Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-18 15:29:13 -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
ce009bd4a4
Works without related data
2011-08-18 14:05:09 -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
5772766dd5
Improvements to GATKDocs
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-- Now supports a static list of root classes / interfaces that should receive docs. A complementary approach to documenting features to the DocumentedGATKFeature annotation
-- Tribble codecs are now documented!
-- No longer displayed sub and super classes
2011-08-18 14:00:09 -04:00
10d8033bcf
Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-18 12:58:16 -04:00
8b37a2d976
Could not get Khalid's DoC hack (for me) to play nicely with relative paths, although this somehow used to work. So, I made sure not to include paths in scattered commands. This would be a lot easier if DoC worked with Queue's Input/Output system. But, my long-term plan is still to write a new simpler DoC walker that will have less functionality but conform to the Queue model...
2011-08-18 12:39:52 -04:00
e03db30ca0
New uses DocumentedGATKFeatureObject instead of annotation directly
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-- Step 1 on the way to creating a static list of additional classes that we want to document.
2011-08-18 12:31:04 -04:00
3a6a206940
Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-18 12:23:32 -04:00
ff45fc9d5a
Output proper quality score string, slightly better insert size metrics
2011-08-18 11:58:34 -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
690f691ea9
Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-18 11:46:08 -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
ecfabd134f
Created a non destructive trim method for variable sites
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The trimToVariableSite now creates a new slidingReads (hard copy) that uses the SAMRecord's reference.
Renamed compressWindow to addToConsensus
2011-08-18 10:41:12 -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
de35bb2e4d
Update hard-coded path of CNV read-depth merging script. The design of this pipeline needs to be corrected in the next few months...
2011-08-18 00:10:12 -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
b75a1807e3
Adding integration test to cover sample exclusion
2011-08-17 22:40:09 -04:00
a7b70e6bb4
Adding feature for Khalid: ability to exclude particular samples.
2011-08-17 22:28:22 -04:00
ecf66b93ec
ILSS now outputs proper quality strings (should be phred-Q + 64, and capped at [2,40])
2011-08-17 22:23:21 -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
a9df365364
GenotypeAndValidate walker updated
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Updated the walker to comply with the new RodBinding system and the new GATKDocs. Will move it to public after writing integration tests.
2011-08-17 21:55:17 -04:00
fa1db3913b
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-17 21:49:25 -04:00
8e83b6646b
Bug fix for Chris: don't validate ref base for complex events.
2011-08-17 21:49:14 -04:00
Mark DePristo
Ryan Poplin
Mauricio Carneiro
Guillermo del Angel
Chris Hartl
Menachem Fromer
Eric Banks
Roger Zurawicki