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Removed outdated (and unused) -familyStr commandline argument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
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
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
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
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
2b51c01df4
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-21 19:16:06 -05:00
5443d3634a
Again, fixing the add call when we really mean replace
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-- Updating MD5s for UG to reflect that what was previously called ./.:.:10:0,0,0 is now just ./. Eric will fix long-standing bug in QD observed from this change
-- VFW MD5s restored to their old correct values. There was a bug in my implementation to caused the genotypes to not be parsed from the lazy output even through the header was incorrect.
2011-11-21 19:15:56 -05:00
5ad3dfcd62
BugFix: byte overflow in SyntheticRead compressed base counts
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* fixed and added unit test
2011-11-21 17:11:50 -05:00
9ea7b70a02
Added decode method to LazyGenotypesContext
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-- AbstractVCFCodec calls this if the samples are not sorted. Previously called getGenotypes() which didn't actually trigger the decode
2011-11-21 16:21:23 -05:00
ab2efe3bd3
Reverting bad exact model changes
2011-11-21 16:14:40 -05:00
44554b2bfd
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-11-21 15:01:45 -05:00
022832bd74
Very bad use of the == operator with Strings was ensuring that validating GenomeLocs was very inefficient. This fix resulted in a significant speedup for a simple RodWalker.
2011-11-21 14:49:47 -05:00
1561af22af
Exact model code cleanup
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-- Fixed up code when fixing a bug detected by aggressive contracts in GenotypesContext.
2011-11-21 14:35:15 -05:00
Laurent Francioli
Ryan Poplin
Eric Banks
Mark DePristo
David Roazen
Guillermo del Angel
Mauricio Carneiro