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
...
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
...
-- 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
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
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
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
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
c193f52e5d
Fixed up examples: pasting from wiki still had old rod syntax
2011-08-17 16:29:45 -04:00
2b2a4e0795
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/stable
2011-08-17 16:26:45 -04:00
297c9e513c
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable into unstable
2011-08-17 16:24:02 -04:00
a210a62ab9
Merged bug fix from Stable into Unstable
2011-08-17 16:23:31 -04:00
d59e6ed274
Fix for RefSeqCodec bug and better error messages
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-- RefSeqCodec bug: getFeatureClass() returned RefSeqCodec.class, not RefSeqFeature.class. Really should change this in Tribble to require Class<T extends Feature> to get compile time type checking
-- Better error messages that actually list the available tribble types, when there's a type error
2011-08-17 16:22:07 -04:00
d170187896
Disable optimization that increases marginal speed of the GATK slightly but
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can produce data loss in a narrow corner case where the BGZF block(s) locations
and offsets in the last index bucket of contig n overlap exactly with the BGZF
block locations and offset in the last index bucket of contig n+1.
A proper fix that keeps the optimization has already been introduced into
unstable, but disabling the optimization is a low risk way to make sure that
users of stable experience no data loss.
2011-08-17 16:16:05 -04:00
53006da9a5
Improved descriptions for the SnpEff annotations in the VCF header
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(based on Eric's feedback).
2011-08-17 16:09:10 -04:00
784fb148b9
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-17 15:47:01 -04:00
671330950d
Updated Beagle walker for gatkdocs format. Pushed unsupported, undocumented arguments to @Hidden
2011-08-17 15:46:31 -04:00
0af68e052a
Merge branch 'master' of ssh://cga1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-17 15:17:47 -04:00
a423546cdd
fix: RefSeq contains records with zero coding length and the refsec codec/feature used to crash on those; now such records are ignored, with warning printed (once)
2011-08-17 15:17:31 -04:00
710d34633e
now the reads that are too long are truly ignored (fix of the fix)
2011-08-17 15:16:23 -04:00
2f19046f0c
Adding docs to the 2 beasts. Saved the worst for last.
2011-08-17 14:19:14 -04:00
069554efe5
somatic indel detector does not die on reads that are too long (likely contain a huge deletion) anymore; instead print a warning and ignore the read
2011-08-17 14:05:19 -04:00
c405a75f54
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-17 13:28:25 -04:00
575303ae6b
Renaming for consistency and bringing up to speed with new rod system
2011-08-17 13:28:19 -04:00
6d629c176c
Adding docs
2011-08-17 13:27:36 -04:00
a21e193a9e
Adding docs to 3 more walkers
2011-08-17 12:35:08 -04:00
98acb546a9
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-17 12:22:29 -04:00
d1bb302d12
Added GatkDocs documentation
2011-08-17 12:21:37 -04:00
3da71a9bb6
Clean up summary
2011-08-17 12:04:45 -04:00
c6fb215faf
GATKDocs for VariantsToTable
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-- Made a previously required argument optional, as this was a long-standing bug
2011-08-17 12:02:41 -04:00
5f794d16a7
Fixed bad character in documentation
2011-08-17 12:01:08 -04:00
9d1d5bd27a
Revert "Fixed bad character in documentation"
...
This reverts commit a1f50c82d3cb25e5e83d36e9054d74cdee957d87.
2011-08-17 11:57:31 -04:00
78deb3f195
Fixed bad character in documentation
2011-08-17 11:57:00 -04:00
79dcfca25f
Fixed bad character in documentation
2011-08-17 11:56:51 -04:00
b3b5d608ca
Adding docs to yet more walkers
2011-08-17 09:57:19 -04:00
fadcbf68fd
Adding docs to QC walkers
2011-08-17 09:39:33 -04:00
5d6a6fab98
Renamed softUnclipped functions to refCoord*
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These functions return reference coordinates, so they should be named accordingly.
2011-08-16 18:56:28 -04:00
ed8f769dce
Fixed index for getSoftUnclippedEnd()
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Unclipped end can be calculated simply by looking at the last cigar element and adding it's length in case it's a soft clip.
2011-08-16 18:54:28 -04:00
5f3f46aad1
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-16 16:26:33 -04:00
946f5c53fe
Adding docs to more walkers
2011-08-16 16:26:26 -04:00
6e828260a0
Removed -B support. Now explodes with error if -B provided.
2011-08-16 16:13:47 -04:00
2d5bbecd9e
Merged bug fix from Stable into Unstable
2011-08-16 14:19:04 -04:00
07c1e113cd
Fixed interval traversal for previously hard clipped reads.
...
If a read was hard clipped for being low quality and no does not overlap the interval anymore, this read will now be discarded instead of treated as an error by the GATK traversal engine.
2011-08-16 14:18:05 -04:00
9d4add3268
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2011-08-16 14:18:03 -04:00
170d1ff7b6
Fix in UG for trying to call indels at IUPAC code bases when in EMIT_ALL_SITES mode
2011-08-16 14:17:46 -04:00
b135565183
Added low quality clipping
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Clips both tails of a read if the tails are below a given quality threshold (default Q2).
*Added special treatment for reads that get completely clipped.
2011-08-16 13:51:25 -04:00
9f3328db53
fixing read group name collision: before writing the read into respective stream in nway-out mode we now retrieve the original rg, not the merged/modified one
2011-08-16 13:45:40 -04:00
ab0b56ed11
Minor doc fixes
2011-08-16 12:55:45 -04:00
125ad0bcfa
Added docs to RTC
2011-08-16 12:46:48 -04:00
ef9216011e
Added docs to IR
2011-08-16 12:24:53 -04:00
ab1e3d6a98
Use the right set of sample names
2011-08-16 01:03:05 -04:00
36c7f83208
Refactoring VE stratifications so that they don't pass around bulky data; instead just pull needed data from the VE parent. This allows us stop using deprecated features of the rod system.
2011-08-15 16:31:57 -04:00
1246b89049
Forgot to initialize variants on the merge
2011-08-15 16:00:43 -04:00
993ecb85da
Added Hard Clipping Tail Ends
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Added functionality to hard clip the low quality tail ends of reads (lowQual <= 2)
2011-08-15 15:22:54 -04:00
045e8a045e
Updating random walkers to new rod system; removing unused GenotypeAndValidateWalker
2011-08-15 14:05:23 -04:00
fc2c21433b
Updating random walkers to new rod system
2011-08-15 13:29:31 -04:00
3d56bbf087
Resolving merge conflicts
2011-08-15 12:28:05 -04:00
9ddbfdcb9f
Check filtered status before applying to alt reference
2011-08-15 12:25:23 -04:00
0d976d6211
Fixed second time clipping
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When a read is clipped once, and then in the second operation, because of indels, it doesn't reach the coordinate initially set for hard clipping, the indices were wrong. This should fix it.
2011-08-15 12:04:53 -04:00
489c15b99d
Fixed indexing issue in coordinate conversion
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When a read had been previously soft clipped, the UnclippedEnd could not be used directly as Reference Coordinate for clipping , because the read does not go that far.
2011-08-15 01:42:34 -04:00
c7b69a4574
Fixed integration tests
2011-08-14 16:38:20 -04:00
6ae3f9e322
Wrapped clipping op information
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The clipping op extra information being kept by this walker was specific to the walker, not to the read clipper. Created a wrapper ReadClipperWithData class that keeps the extra information and leaves the ReadClipper slim.
(this is a quick commit to unbreak the build, performing integration tests and will make further commits if necessary)
2011-08-14 15:44:48 -04:00
8a51732049
Fixes to ReadClipper and added Reference Coordinate clipping.
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* Added reference coordinate based hard clipping functions. This allows you to set a hard cut on where you need the read to be trimmed despite indels.
* soft clipping was messing up cigar string if there was already a hard clip at the beginning of the read. Fixed.
* hard clipping now works with previously hard clipped reads.
2011-08-14 14:54:33 -04:00
291d8c7596
Fixed HardClipping and Interval containment
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* Hard clipping was wrongfully hard clipping unmapped reads while soft clipping then hard clipping mapped reads. Now we throw exception if we try to hard/soft clip unmapped reads and use the soft->hard clip procedure fore every mapped read.
* Interval containment needed a <= and >= to make sure it caught the borders right.
2011-08-14 14:54:33 -04:00
0be1dacddb
Refactored interval clipping utility
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reads are clipped in map() and now we cover almost all cases. Left behind the case where the read stretches through two intervals. This will need special treatment later.
2011-08-14 14:54:33 -04:00
9d2cda3d41
Removed a public -> private dependency in our test suite.
2011-08-12 17:29:10 -04:00
bb4ced3201
SnpEff-related fixes.
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-To correctly handle indels and MNPs, only consider features that start at the current locus,
rather than features that span the current locus, when selecting the most significant effect.
-Throw a UserException when a SnpEff rodbinding is not provided instead of simply not adding
any annotations and silently returning.
2011-08-12 15:26:24 -04:00
10e873d9c6
Merge branch 'repval'
2011-08-12 15:24:31 -04:00
31dc831531
Merged bug fix from Stable into Unstable
2011-08-12 13:26:41 -04:00
9121b8ed65
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-12 12:24:19 -04:00
7ed120361d
Fixed bug that required symbolic alleles to be padded with reference base and added integration test to test parsing and output of symbolic alleles
2011-08-12 12:23:44 -04:00
7ea9196321
Better error message for name/type clashes.
2011-08-12 11:18:14 -04:00
27f0748b33
Renaming the HapMap codec and feature to RawHapMap so that we don't get esoteric errors when trying to bind a rod with the name 'hapmap' (since it was also a feature).
2011-08-12 11:11:56 -04:00
005bd71be3
Working too quickly earlier. Fixing syntax.
2011-08-12 10:29:36 -04:00
c7ca33cbff
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-12 10:12:09 -04:00
639a01f382
Updating integration test now that VE has been updated
2011-08-12 07:15:08 -04:00
41f3da75d7
Implementation in VE was confusing 'variant' status vs. 'polymorphic' status. This led to issues because we now match types of eval and comp; specifically, subsetting a VC to a monomorphic sample can't change the 'variant' status of the VC (it's still a variant site or otherwise we'll never match the comps, which breaks GenotypeConcordance). CountVariants really got this wrong. Fixed. VE now passes all integration tests.
2011-08-12 02:22:44 -04:00
45f973ab1f
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-12 00:40:18 -04:00
eba316621d
Finish moving VE over to new rod system and fixing up the type inconsistency between eval and comp rods. Now the novel count is always 0 under the known stratification. :)
2011-08-12 00:40:08 -04:00
9de06560df
Update to new RodBinding system
2011-08-11 17:54:16 -04:00
f1d1252be2
Fixing syntax of BQSR and UG performance tests.
2011-08-11 17:04:09 -04:00
902eb0c61e
Adding dbsnp annotation back into the UG integration tests
2011-08-11 13:55:03 -04:00
90771b74b4
When matching eval to comps, try to choose the one with the same alt allele.
2011-08-11 13:55:01 -04:00
200f73b008
No reason to warn the user anymore because it's no longer possible for them to specify a dbsnp file on the command-line.
2011-08-11 13:44:07 -04:00
e93538cdf7
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-11 13:39:36 -04:00
265c3d744b
Fixing VariantEval logic and having it use the new rod system.
2011-08-11 13:39:34 -04:00
b705d9cf15
Oops, these VariantAnnotator input bindings aren't needed during the UG
2011-08-11 13:17:16 -04:00
7fade88070
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-11 11:02:47 -04:00
c7b9a9ef0a
Updating UnifiedGenotyper to use the new rod binding system.
2011-08-11 11:02:11 -04:00
418a4d541f
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-11 11:01:38 -04:00
e71255d3c2
GATKDocsExample walker
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-- Shows the best practice for documentating a walker with the GATKdocs
-- See http://www.broadinstitute.org/gsa/wiki/index.php/GATKdocs#Writing_GATKdocs_for_your_walkers for a brief discussion
2011-08-11 11:01:21 -04:00
79c86e211f
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-11 09:59:20 -04:00
ea42ee4a95
Updating BQSR for the new rod binding system.
2011-08-11 09:58:42 -04:00
8cdc0cbd9c
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-11 08:58:49 -04:00
40e06f9afb
Fixed broken RodBinding defaults.
...
-- Verified now to be correct at runtime
-- UnitTest covers this
-- createTypeDefault now takes a Type, not a Class, so that parameterized classes can have their parameter fetched in the defaults.
2011-08-11 08:58:30 -04:00
dd5fe8291d
Fixing up some comments in the BQSR
2011-08-11 08:36:00 -04:00
f1b09db39e
Fixes for rod bindings
2011-08-10 23:08:47 -04:00
75985c2fa0
Resolving merge conflicts
2011-08-10 22:45:11 -04:00
bdb1da30fd
Better interface for getting RodBindings to the VariantAnnotatorEngine and its annotations: pass around an AnnotatorCompatibleWalker (interface) object. Updating VA to use the new rod system.
2011-08-10 22:43:08 -04:00
0086e27741
makeUnbound now package protected
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-- Removed references to it in the codebase
-- Fixed documentation I saw that had the summary + body style
2011-08-10 22:29:32 -04:00
cb6cf25bb0
Updating SelectVariants documentation to reflect best practice
2011-08-10 22:24:18 -04:00
00b4d6ec57
Updated the best practice on documenting a field
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-- Best practice is now to skip the summary, as this is the @annotation doc value.
2011-08-10 22:21:12 -04:00
2007d2fcad
Better documentation for default value fields
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-- DocString function for types that create default outputs "stdout"
-- RodBinding now creates a makeUnbound default value automatically for you if your RodBinding isn't required
-- Removed warning about sparse help from TextFormattingUtils
2011-08-10 22:16:22 -04:00
bb557266ca
Merge branches to get new RodBinding framework
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Conflicts:
private/java/src/org/broadinstitute/sting/gatk/walkers/replication_validation/ReplicationValidationWalker.java
2011-08-10 18:23:01 -04:00
8325cb8c26
Fixing up apparent source control/merge snafu: fix to correctly output PL ordering in multi-allelic sites by UG was only half-committed and hence not working. This completes fix
2011-08-10 15:31:49 -04:00
07ad8c78a9
More tools moved over. Fixed the VariantContextIntegrationTest which was not useful because the md5s were all removed. In the future, instead of removing md5s (putting it in 'parameterization' mode), you should instead use @Test{enabled=false} since it's easier to track.
2011-08-10 14:24:40 -04:00
8d14d32a62
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-10 13:42:37 -04:00
749c8bfbcd
Moving more tools over to the new rod system
2011-08-10 13:42:35 -04:00
0497170bc9
SnpEffCodec now implements SelfScopingFeatureCodec so that we no longer have to specify the codec name on the command line for SnpEff files.
2011-08-10 13:12:09 -04:00
577f861f69
Pass the rodBindings into the VariantAnnotator engine, and from there to the
...
annotation classes themselves.
2011-08-10 13:11:57 -04:00
480e7a7984
Correctly initialize the optional SnpEff rod binding in VariantAnnotator using
...
RodBinding.makeUnbound()
2011-08-10 12:25:26 -04:00
a42f90db11
Moving more tools over to use the standard VC arg collection. Also, while I'm in there, I removed all of the empty references to @Requires given that it's no longer relevant.
2011-08-10 12:20:18 -04:00
c884b6bf1f
Fixed comment
2011-08-10 12:07:43 -04:00
06cdc4d5f9
Added a StandardVariantContextInputArgumentCollection that is now used for consistency by many of the core tools.
2011-08-10 12:00:56 -04:00
bc125f104a
TrainingSets class is obsolete now.
2011-08-10 10:23:33 -04:00
c60cf52f73
Updating VQSR for new RodBinding syntax. Cleaning up indel specific parts of VQSR.
2011-08-10 10:20:37 -04:00
1ea5ec276b
Minor cleanup
2011-08-09 23:28:59 -04:00
bc2d4f554d
Bringing Indel Realigner up to speed with the new rod binding syntax; now use -known to specify the known indels track.
2011-08-09 23:21:17 -04:00
b8f572b571
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-09 23:19:51 -04:00
08631546c8
Partial commit for David so he can see what I want to do with the VariantAnnotator. Added a DbsnpArgumentCollection that people can use in their walkers to ensure that we have a standard syntax whenever allowing dbsnp rods. Added it to UG, but didn't hook it up. Maybe we should do the same for the 'variant' rod?
2011-08-09 23:19:40 -04:00
86afe878a7
ReducedRead optimization: single pass likelihood calculation
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-- Low level add() now takes a nObs argument and rather than += likelihood now does += nObs * likelihood
2011-08-09 20:55:15 -04:00
489e5cffc1
Missed a few 'variants'
2011-08-09 14:29:15 -04:00
b20c4d5286
Thanks to Mark for agreeing to transition from 'variants' back to 'variant'. I think I got them all but I've been jumping all around the code, so there might be a straggler or two.
2011-08-09 12:04:55 -04:00
78aa6db076
added the 'reference' header line too. We are now header-compliant for vcf4.1.
2011-08-09 11:45:54 -04:00
ec76bf6d4a
VCF headers now include 'contig' lines describing the name, length, and assembly (when easily parsable) for each contig in the reference.
2011-08-09 11:24:48 -04:00
7afb5c9f1c
More updates to be consistent with the new rod syntax.
2011-08-09 10:11:37 -04:00
1e490e0dec
Bringing up to speed with new syntax
2011-08-09 09:26:06 -04:00
70b3daf689
VariantsToVCF is up and running again; integration tests are reenabled (and added one for dbSNP).ant
2011-08-09 03:03:43 -04:00
d15852be0a
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-09 00:04:59 -04:00
2db6225c53
A read filter that sets all mapping qualities to a given value
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Pacbio has decided to assign 255 to the MQ of all their reads since they claim their aligner does not produce a number equivalent to a mapping quality. Despite much back and forth, they are dead set on not using this field, so if we want to use their bams, we will need to override that. This filter does just that. Replacing all values with a given one. Default is 60.
2011-08-09 00:04:42 -04:00
2efa376619
Made the necessary changes to get SnpEff support working with the new rodbinding system.
2011-08-08 23:29:39 -04:00
b180a1311a
Merge branch 'snpEff'
2011-08-08 22:12:14 -04:00
28d8c8fcbc
Modified the SnpEff integration test to run on a much smaller interval.
2011-08-08 21:51:16 -04:00
a13bc7b929
Added an integration test for the SnpEff annotation support, as well as some extra safety checks and comments.
2011-08-08 20:01:24 -04:00
80924d24de
Single positional arguments are now treated as names unless they actually match a tribble feature
2011-08-08 19:26:27 -04:00
f8a56bc64b
Merge branch 'master' into rodRefactor
2011-08-08 16:58:18 -04:00
f8ad91b16f
Reverting a bunch of bad -B type drops
2011-08-08 16:57:38 -04:00
5e288136e0
Added unit tests for the SnpEff codec, and made minor adjustments to the codec itself.
2011-08-08 16:51:43 -04:00
d7813db217
Combine Variants was actually outputting invalid VCFs in cases where it was combining Variant Contexts with different alternate alleles: if any of the genotypes had PLs they were no longer valid/correct. Added a check for such cases (the combined VC has more alleles than an original VC) and strip out the PLs when triggered; added integration test to cover it. I also added the check to Select Variants, although it currently doesn't remove unused alleles so it should never trigger. Is there any reason not to strip out unused alleles after a select?
2011-08-08 16:25:35 -04:00
383bb6f0e0
Merge branch 'master' into rodRefactor
2011-08-08 15:25:55 -04:00
4f8fc0f2f1
VCF3 now dynamically determined
2011-08-08 15:05:47 -04:00
ba7353c561
Updated IntegrationTests to use the new type free format for VCF files
2011-08-08 15:04:38 -04:00
0810c42309
GATK now does dynamic type determination for VCF files
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Added UnitTests covering all of the cases.
2011-08-08 14:45:46 -04:00
e36994e36b
Refactored a FeatureManager class from RMDTrackBuilder
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New class handles (vastly more cleanly) the db of tribble codecs, features, and names for use throughout the GATK.
Added SelfScopingFeatureCodec interface that allows a FeatureCodec to examine a file and determine if the file can be parsed. This is the first step towards allowing the GATK to dynamically determine the type of a RodBinding.
2011-08-08 14:04:46 -04:00
197169e47b
Submitting patch from Larry Singh to make MathUtils compatible with java 1.7
2011-08-08 13:34:04 -04:00
dd974040af
When finding the highest-impact effect at a locus, all effects that are not within a
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non-coding gene are now considered higher impact than all effects that are within a
non-coding gene.
2011-08-08 13:29:54 -04:00
c1061e994c
Initial support for adding genomic annotations through VariantAnnotator using
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the output from the SnpEff tool, which replaces the old Genomic Annotator.
2011-08-08 13:29:53 -04:00
0db79207e8
Refactored dependancy from CommandLineGATK from javadocs
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This allows us to run the GATK again in environments without Javadoc loading by default in the classpath
2011-08-08 12:27:13 -04:00
e5fde0d16b
Merge branch 'master' into rodRefactor
2011-08-08 10:08:43 -04:00
526b524c3c
CombineVariants with new RodBinding. Bugfix
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-- CombineVariants now uses the new RodBinding syntax, -V / --variants. Passed all integration tests on first run
-- Exposed gapping bug in the List<RodBinding<T>> system now fixed. ParserEngine now has a addRodBinding() that is called by RodBindingArgumentTypeDescriptor when it encounters each RodBinding. This allows the system to work with collection types that are recursively parsed by the system.
2011-08-07 20:16:51 -04:00
6693407bd8
Merged bug fix from Stable into Unstable
2011-08-07 17:39:03 -04:00
5f8bc3aa8a
Documenting classes, and name cleanup
2011-08-07 15:17:50 -04:00
1c63d43176
Help now points to GATKDocs instead of spitting out full, garbled description
2011-08-07 15:02:46 -04:00
1d8b1bae0a
Need to rename the integration test argument -mask to -maskName
2011-08-07 13:32:26 -04:00
ece8f0db5e
Added b37dbSNP129, needed for Queue
2011-08-07 11:26:07 -04:00
b0e91f85cf
fix merge from Khalid's Queue fix
2011-08-07 10:33:20 -04:00
4d88e72958
Merge remote-tracking branch 'remotes/khalid/rodRefactor' into rodRefactor
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Conflicts:
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
public/java/test/org/broadinstitute/sting/BaseTest.java
2011-08-07 10:32:27 -04:00
f049461120
Changed @Argument to @Input on input RodBindings.
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Changed shortname collision with longname.
Restored scala builds.
Updated HSP to use new syntax.
2011-08-06 20:44:19 -04:00
573700d18d
Adding missing import
2011-08-04 21:57:00 -04:00
14e43c3382
Final fix to RodBindingUnitTest to reset global counter variable
2011-08-04 21:52:39 -04:00
d7f98e5c2a
Fixed merge conflict deleting a {
2011-08-04 18:48:34 -04:00
75632abf88
Merge branch 'master' into rodRefactor
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Conflicts:
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java
public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
2011-08-04 18:44:14 -04:00
f21f7f6335
SelectVariants fully documented, now the shining example of the new RodBinding system.
2011-08-04 18:28:59 -04:00
9308fbe3fb
VariantEval Integration Test parameterized for new novelty stratification
2011-08-04 18:08:47 -04:00
9be1ee59cc
TODO comments for Eric
2011-08-04 18:07:50 -04:00
b22a3d6508
Functional VCF output.
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It is outputting a VCF with the 'second best guess' for the alternate allele correctly. Annotations are added at the pool level, but may get overwritten at the lane and site level. Still need to implement the merging of the the annotations at higher levels.
2011-08-04 17:49:08 -04:00
a8eb8c27f0
a) Minor changes to indel consensus scripts to better reflect good default values, b) Fixed up Mills/Devine codec so it always produces correct ref padded bases, and added option to VariantsToVCF to fix reference base
2011-08-04 15:34:49 -04:00
98a96f07c1
Updated standard deviation parameter in VQSR to our current recommended value
2011-08-04 14:06:26 -04:00
58a60d4901
Merge branch 'master' into rodRefactor
2011-08-04 12:48:56 -04:00
e48492f3c3
Validate that the reference padding base for indels is correct.
2011-08-04 12:48:56 -04:00
d2078f09b2
Minor fixes to ITs
2011-08-04 12:47:55 -04:00
f10588420c
Fixing path to dbSNP file as the other one was replaced
2011-08-04 12:36:24 -04:00
f0d798d47c
Bug fix: call RodBinding.resetNameCounter() in new ParsingEngine() so that we don't magically misnumber arguments in the integration tests where the GATK is only instantiated once.
2011-08-04 12:06:10 -04:00
490ca475fc
Replacing hardcoded dbsnp129 with BaseTest variable
2011-08-03 22:15:22 -04:00
a831af1166
Another misprint when removing the references to -D
2011-08-03 21:29:21 -04:00
d0279bb28c
RodBinding names are now defaulting to the ArgumentTypeDescriptor fullname
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Nearly all of the tools are passing integrationtests
2011-08-03 20:48:11 -04:00
d8f1ebf8c6
Parameterized RecalibrationWalkers with clean unstable database
2011-08-03 20:06:00 -04:00
41b3840d26
Took latest VEIT and updated to use dbsnp132 vcf
2011-08-03 18:40:32 -04:00
0ef85647f7
A working version of a GATKReportDiffableReader for the diffEngine!
2011-08-03 18:21:18 -04:00
acbd3d0922
Fixing up integration tests so more
2011-08-03 17:26:35 -04:00
8f696c7731
Continuing progress towards RodBinding 1.0
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-- Cleaning up old interface to RMDT, docs and contracts added
-- Proper type checking for RodBinding for cases where the Tribble type isn't found or is the wrong type
2011-08-03 17:19:28 -04:00
800bb97f0b
Removed getFeaturesAsGATKFeature and created createGenomeLoc(Feature) in genomeLocParser
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Updated all walkers that used the now deleted methods.
2011-08-03 16:04:51 -04:00
f6563c0f9f
Removed support for RMD in @Requires and @Allows
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Merge as well
Conflicts:
private/java/src/org/broadinstitute/sting/gatk/walkers/qc/TestVariantContextWalker.java
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java
public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java
public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java
2011-08-03 15:36:55 -04:00
79e4a8f6d3
Merge
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Conflicts:
private/java/src/org/broadinstitute/sting/gatk/walkers/qc/TestVariantContextWalker.java
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java
public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
public/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java
public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java
2011-08-03 15:09:47 -04:00
38efd3066c
Bug fix for mask RodBinding
2011-08-03 14:58:18 -04:00
f62f47d476
Not sure why this didn't fail before, but bringing VE up to date with previous changes
2011-08-03 14:27:07 -04:00
b25140db83
Contracts and documentation for some of RefMetaDataTracker
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Continuing to fix integration tests that don't pass / run
2011-08-03 13:34:20 -04:00
3de10b1ef8
Fixing misprint from Ryan's commit
2011-08-03 12:37:50 -04:00
db2e0aaa1a
Darn, forgot to update unit tests.
2011-08-03 12:31:08 -04:00
020b2408a8
Adding integration test for left alignment of indels
2011-08-03 12:19:44 -04:00
f6648e0144
Don't left-align complex indels because it's too complicated.
2011-08-03 12:03:50 -04:00
85c67e9891
Contracts and documentation for Rodbinding
2011-08-03 11:16:06 -04:00
5dc324ff35
Dealing with merge confict
2011-08-03 11:03:47 -04:00
7c89fe01b3
Instead of having the padded reference base be some hackish attribute it is now an actual variable in the Variant Context class. More importantly, we now always require that it be present when padding is necessary - and validate as such upon construction of the VC. This cleans up the interface significantly because we no longer require that a reference base be passed in when writing a VC/VCF record.
2011-08-03 11:00:36 -04:00
d9bc673ff2
Fixed bad constructor in RMDTUnitTest
2011-08-03 09:42:43 -04:00
5dcac7b064
GATKReport v0.2:
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- Floating point column widths are measured correctly
- Using fixed width columns instead of white space separated which allows spaces embedded in cell values
- Legacy support for parsing white space separated v0.1 tables where the columns may not be fixed width
- Enforcing that table descriptions do not contain newlines so that tables can be parsed correctly
Replaced GATKReportTableParser with existing functionality in GATKReport
2011-08-03 00:24:47 -04:00
2874835997
Bug fix for type checking RodBindings
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Now compares the feature class not the codec class.
UnitTests improvements
integrationtests on their way to actually running
2011-08-02 22:25:41 -04:00
b5e843f8f0
Approaching the end for the new RodBinding system
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-- support for explicit naming of bindings (-X:name,type x)
-- support for automatic naming of bindings in lists (-X:vcf foo.vcf -X:vcf bar.vcf will generate internal names X and X2)
-- ParserEngineUnitTest expanded to cover all of the Rodbinding cases
-- RodBindingUnitTest tests all of the low-level accessors
-- Parsing engine throws UserExceptions when bad bindings are provided on the command line
2011-08-02 22:00:06 -04:00
d3437e62da
Added a simple utility method Utils.optimumHashSize() to calculate the optimum
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initial size for a Java hash table (HashMap, HashSet, etc.) given an expected
maximum number of elements. The optimum size is the smallest size that's
guaranteed not to result in any rehash / table-resize operations.
Example Usage:
Map<String, Object> hash = new HashMap<String, Object>(Utils.optimumHashSize(expectedMaxElements));
I think we're paying way too heavy a price in unnecessary rehash operations across
the GATK. If you don't specify an initial size, you get a table of size 16 that gets
completely rehashed and doubles in size every time it becomes 75% full. This means you
do at least twice as much work as you need to in order to populate your table:
(n + n/2 + n/4 + ... 16 ~= (1 + 1/2 + 1/4...) * n ~= 2 * n
2011-08-02 21:59:06 -04:00
83891271b5
--variants throughout integrationtests
2011-08-02 20:28:47 -04:00
3a27a25cfc
Validates that the tribble binding provides the right object types at startup
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Tests to ensure this remains working
2011-08-02 20:11:24 -04:00
df37716857
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-02 18:27:13 -04:00
b2cde87378
Removing --DBSNP syntax from BQSR integration tests
2011-08-02 15:34:38 -04:00
e4a67f3df1
RefMetaDataTracker has complete set of get() functions for List<RodBinding<T>>
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Including unit tests
2011-08-02 14:28:35 -04:00
03741fb640
Merge branch 'master' into rodRefactor
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Conflicts:
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java
2011-08-02 14:21:58 -04:00
a366f9a18d
Updating tools to use the RodBinding<T> syntax
2011-08-02 14:05:51 -04:00
c0653514b3
minor update to comment in UG
2011-08-02 13:34:48 -04:00
2ba57bb502
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-02 13:30:46 -04:00
38e4ae4176
minor update to comment in UG
2011-08-02 13:30:38 -04:00
821bbfa9e0
Bug fixes and enhancements to run whole-genome indel VQSR, removed old chr20-only code and cleanup
2011-08-02 13:17:20 -04:00
65c5d55b72
Not sure how I missed these. These lines are now superfluous.
2011-08-02 12:48:36 -04:00
b9d0d2af22
Adding back temporarily removed integration test now that the file permissions have been fixed.
2011-08-02 12:39:11 -04:00
1c387848de
No more use of -D in the integration tests but instead stick with VCFs only. Since all of these tests were duplicated (one each for dbSNP format and for VCF), we don't actually lose coverage in the integration tests.
2011-08-02 10:39:50 -04:00
2c5e526eb7
Don't use the mismatch fraction by default in the RealignerTargetCreator (since it's only useful when using SW in the indel realigner). Also, no more use of -D but instead move over to using VCFs. One integration test is temporarily commented out while I wait for a VCF file to get fixed.
2011-08-02 10:34:46 -04:00
5626199bb6
The Unified Genotyper now does NOT emit SLOD/SB by default; to compute SB use --computeSLOD
2011-08-02 10:14:21 -04:00
184030dd56
RefMetaDataTracker no longer automagically converts inputs to VariantContexts
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This was no longer working properly given that DBSNP indels needed to be moved around. The adaptor system is being refactored and you will need to convert files from X -> VCF for many tools to work.
2011-08-01 15:21:16 -04:00
8b1adb8c95
Removed getVariantContext() code
2011-08-01 13:41:09 -04:00
f69bff5dd6
Commented out, because these fail the now removed dbSNP conversion.
2011-08-01 13:34:25 -04:00
3a9b6eacdf
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-08-01 11:23:18 -04:00
7b07c4e04e
RefMetaDataTracker now has get() methods accepting RodBindings
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RodBinding no longer duplicates the get() methods in RMDT. This is just an object now that connects the command line system to the RMDT.
Updated programs to use new style
Added UnitTests for the RodBinding accessors.
2011-07-30 15:34:11 -04:00
a6691ab2fd
List<RodBinding<T>> now working (sort of).
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At least the argument parsing system tolerates it.
2011-07-29 16:11:22 -04:00
6acb4aad3b
RodBinding<T> are properly generic now.
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VariantContextRodBinding removed, as RodBinding<VariantContext> is the right style now.
2011-07-29 14:37:12 -04:00
3b799db61a
RefMetaDataTracker cleanup and unit tests
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You know have to provide an explicit list of RODRecordLists upfront to the constructor. RefMetaDataTracker is now immutable. Changes in engine to incorporate these differences
Extensive UnitTests for RefMetaDataTracker now.
2011-07-29 13:23:17 -04:00
b06deac9ea
Merged bug fix from Stable into Unstable
2011-07-29 10:02:36 -04:00
c0d4110ffd
Correcting redundant warning text.
2011-07-29 10:01:11 -04:00
a58ddab93b
minQual and minPower filters added. VCF output added.
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Calls are now made based on the likelihood AC model. Two filters are applied: minQual and minPower. Output is now a VCF file with the variant context. It's now called the gatk's PoolCaller, no longer Replication Validation framework. Lots of testing ensue....
2011-07-28 18:58:36 -04:00
39b4e76fde
Continuing refactoring of RefMetaDataTracker.
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On the path towards converging getVariantContext() and getValues() in tracker so that we can have a single approach to get values from RODs with the new RodBinding() types
2011-07-28 17:48:28 -04:00
7c5c656b46
Uncovered fundamental accounting bug in VariantEval. Will be fixed by dev. team
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Problem is that Novelty sees multiple records at a site (SNP, INDEL) to calculate whether a site is novel, but VariantEvalWalker makes an arbitrary decision which to use for analysis and CompOverlap may not see a comp record of the same type as eval. So you get lines where the stratification is known but there are 10 novel sites!
2011-07-28 14:19:27 -04:00
33b32c4211
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-28 13:57:22 -04:00
7a2a65155f
Merged bug fix from Stable into Unstable
2011-07-28 13:56:43 -04:00
1afc49a297
There are some really 'interesting' (but apparently valid) records in the Mus musculus dbSNP file. Generalized the handling of complex cases in the dbSNP adaptor to handle it all. I just grabbed the actual Mus musculus dbSNP file as a test, ran it whole genome, and confirmed that we finally produce a valid VCF on it. Should be the last commit needed on this adaptor.
2011-07-28 13:55:58 -04:00
f7a126722b
Cleaned up VariantContext accessors in RefMetaDataTracker
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It's no longer possible to provided allowed types, as this was a very rarely used feature in the engine. These get methods have been removed and local uses replaced with tests directly in their code. This simplified the RefMetaDataTracker significantly
VariantContextRodBinding now forwards along all of the RefMetaDataTracker methods, so it is possible to create a full equivalent VariantContextRodBinding now as a walker field variable.
All walkers updated to the new RefMetaDataTracker function call style
2011-07-28 00:16:34 -04:00
c83f9432eb
Cleaned up RefMetaDataTracker
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Renamed many functions to more clearly state what they are actually doing
Removed unnecessary / unused functionality, reducing interface complexity
Updated all uses of this code in GATK
Added generic, type-safe accessors to RefMetaDataTracker such as public <T> List<T> getValues(final String name, Class<T> clazz)
Added standard refMetaDataTracker accessors to RodBinding, so you can do everything you can for generic rods with the tracker directly with with the RodBinding
2011-07-27 23:25:52 -04:00
1865211b6d
Merged bug fix from Stable into Unstable
2011-07-27 22:52:06 -04:00
6230315ff2
Along with my half-written commit message from earlier, I also forgot to commit the integration test updates. This is what happens when you try to do things 30 seconds before you leave for the day. To finish up from before: complex events weren't being padded with the reference base as per the VCF spec. They are now.
2011-07-27 22:51:21 -04:00
f3ad4ec94b
Removed annoying FastaSequenceIndexBuilderProgressListener infrastructure that was just a boolean switch on whether to print progress or not.
2011-07-27 22:06:23 -04:00
ff31fa7990
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-07-27 16:15:23 -04:00
5809a61b20
Merged bug fix from Stable into Unstable
2011-07-27 16:14:59 -04:00
64aad67b5f
Fixing dbSNP adaptor for complex indels (wasn)
2011-07-27 16:13:45 -04:00
15be383d5b
Merge branch 'master' into rodRefactor
2011-07-27 15:36:49 -04:00
38a2518668
Merge branch 'master' into rodRefactor
2011-07-27 15:34:54 -04:00
60db6cc836
Warnings for old ROD system use.
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Removed unused class GATKRODFeature
2011-07-27 12:39:12 -04:00
097828a466
ParsingEngine now maintains the list of rodBindings
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No longer try to reparser objects to find the right fields
Direct support in RodBinding for getTags()
2011-07-27 11:36:53 -04:00
Mark DePristo
Eric Banks
Mauricio Carneiro
Matt Hanna
Guillermo del Angel
David Roazen
Andrey Sivachenko
Menachem Fromer
Ryan Poplin
Khalid Shakir