72fbfba97d
Added UnitTests for getFamilies() and getChildrenWithParents()
2011-12-09 15:57:07 +01:00
5a06170804
Corrected bug causing getChildrenWithParents() to not take the last family member into consideration.
2011-12-09 14:51:34 +01:00
1d5d200790
Cleaned up unused import statements
2011-11-30 15:30:30 +01:00
20bffe0430
Adapted for the new version of MendelianViolation
2011-11-30 14:46:38 +01:00
1cb5e9e149
Removed outdated (and unused) -familyStr commandline argument
2011-11-30 14:45:04 +01:00
9574be0394
Updated MendelianViolationEvaluator integration test
2011-11-30 14:44:15 +01:00
f49dc5c067
Added functionality to get all children that have both parents (useful when trios are needed)
2011-11-30 14:43:37 +01:00
a4606f9cfe
Merge branch 'MendelianViolation'
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Conflicts:
public/java/src/org/broadinstitute/sting/utils/MendelianViolation.java
2011-11-30 11:13:15 +01:00
b279ae4ead
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-30 10:10:21 +01:00
7d58db626e
Added MendelianViolationEvaluator integration test
2011-11-30 10:09:20 +01:00
91413cf0d9
Merged bug fix from Stable into Unstable
2011-11-29 14:01:23 -05:00
cb284eebde
Further updating VQSR tutorial wiki docs to reflect the bundle
2011-11-29 14:00:57 -05:00
dcb889665d
Merged bug fix from Stable into Unstable
2011-11-29 09:58:49 -05:00
447e9bff9e
Updating VQSR tutorial wiki docs to reflect the bundle
2011-11-29 09:57:45 -05:00
110298322c
Adding Transmission Disequilibrium Test annotation to VariantAnnotator and integration test to test it.
2011-11-29 09:29:18 -05:00
ab67011791
Corrected bug introduced in the last update and causing no families to be returned by getFamilies in case the samples were not specified
2011-11-29 11:18:15 +01:00
d7d8b8e380
Tribble v42 changes the Codec.canDecode method to take in a String instead of a File; this is something that Jim was adamant about (because Tribble can handle streams other than files). I didn't want the next person who needed to rev Tribble to deal with this change additionally, so I took care of updating the GATK now.
2011-11-28 14:18:28 -05:00
a09c01fcec
Removed walker argument FamilyStructure as this is now supported by the engine (ped file)
2011-11-28 17:18:11 +01:00
795c99d693
Adapted MendelianViolation to the new ped family representation. Adapted all classes using MendelianViolation too.
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MendelianViolationEvaluator was added a number of useful metrics on allele transmission and MVs
2011-11-28 17:13:14 +01:00
e877db8f42
Changed visibility of getSampleDB from protected to public as the sampleDB needs to be accessible from Annotators and Evaluators too.
2011-11-28 17:11:30 +01:00
5c2595701c
Added a function to get families only for a given list of samples.
2011-11-28 17:10:33 +01:00
436b4dc855
Updated docs
2011-11-28 08:59:48 -05:00
b1dd632d5d
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
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Conflicts:
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
2011-11-25 16:16:44 +01:00
e60272975a
Fix for changed MD5 in streaming VCF test
2011-11-23 19:01:33 -05:00
12f09d88f9
Removing references to SimpleMetricsByAC
2011-11-23 16:08:18 -05:00
fdd90825a1
Queue now outputs a GATK-like header with version number, build timestamp, etc.
2011-11-23 14:28:35 -05:00
e319079c32
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-23 13:02:11 -05:00
4107636144
VariantEval updates
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-- Performance optimizations
-- Tables now are cleanly formatted (floats are %.2f printed)
-- VariantSummary is a standard report now
-- Removed CompEvalGenotypes (it didn't do anything)
-- Deleted unused classes in GenotypeConcordance
-- Updates integration tests as appropriate
2011-11-23 13:02:07 -05:00
e5b85f0a78
A toString() method for IntervalBindings
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Necessary since we're currently writing things like this to our VCF headers:
intervals=[org.broadinstitute.sting.commandline.IntervalBinding@4ce66f56]
2011-11-23 11:56:12 -05:00
5a4856b82e
GATKReports now support a format field per column
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-- You can tell the table to format your object with "%.2f" for example.
2011-11-23 11:31:04 -05:00
c8bf7d2099
Check for null comment
2011-11-23 10:47:21 -05:00
c1ea53d088
Solve merge conflicts
2011-11-23 09:17:32 -05:00
d2499bcc33
Cleaning up and institutionalizing several local hacks to ValidationSiteSelector: add argument to ignore polymorphic status in VC (useful when we want to intentionally select monomorphic sites), add dummy NullSampleSelector class that should be used if we really don't want to do any sample selection, and enabled sampleMode=NONE for this purpose.
2011-11-23 09:14:10 -05:00
6c2555885c
Caching getSimpleName() in VariantEval is a big performance improvement
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-- Removed the SimpleMetricsByAC table, as one should just use the AlleleCount Stratefication and the upcoming VariantSummary table
2011-11-23 08:34:05 -05:00
32adbd614f
Solve merge conflict
2011-11-22 22:48:46 -05:00
941f3784dc
Solve merge conflict
2011-11-22 22:48:03 -05:00
75d93e6335
Another corner condition fix: skip likelihood computation in case we cut so many bases there's no haplotype or read left
2011-11-22 22:46:12 -05:00
a3aef8fa53
Final performance optimization for GenotypesContext
2011-11-22 17:19:30 -05:00
990c02e4de
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-22 17:19:11 -05:00
0fa50056eb
Reorganizing package structure for compression tools (incl. Reduce Reads)
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ReduceReads is no longer the only compression tool. Reorganizing the package structure to reflect that.
2011-11-22 15:03:31 -05:00
1a50d54c03
A walker that generates the distribution of quality scores
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Outputs a GATKReportTable that will be used as input to the Quantization walker. Eventually this functionality may be merged into ReduceReads or CountCovariates to avoid another traversal.
2011-11-22 14:49:28 -05:00
1614ca1115
Force use of LinkedList
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Disambiguating which collection I need to use for mapped reads.
2011-11-22 14:49:28 -05:00
38a90da92c
Fixed merge conflict to Unstable
2011-11-22 14:39:45 -05:00
32a77a8a56
Prevent out of bound error in case read span > reference context + indel length. Can happen in RNAseq reads with long N CIGAR operators in the middle.
2011-11-22 13:57:24 -05:00
5821c11fad
For BAM and Reviewed errors we now check the error message to see if it's actually a 'too many open files' problem and, if so, we generate a User Error instead.
2011-11-22 10:50:22 -05:00
5e7b9ae119
The NONE option is not supported yet (but the error message should mention this)
2011-11-22 10:48:38 -05:00
7087310373
Embarassing bug fixed
2011-11-22 10:16:36 -05:00
e484625594
GenotypesContext now updates cached data for add, set, replace operations when possible
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-- Involved separately managing the sample -> offset and sample sorted list operations. This should improve performance throughout the system
2011-11-22 08:40:48 -05:00
29ca24694a
UG now encoding NO_CALLs as ./. not ./.:.:4:0,0,0
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A few updated UGs integration tests
2011-11-22 08:22:32 -05:00
4ea74c42de
Including GENCODE BED argument, removing CAPTURE target
2011-11-21 19:18:43 -05:00
Laurent Francioli
Ryan Poplin
Eric Banks
Mark DePristo
David Roazen
Guillermo del Angel
Mauricio Carneiro