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annotator
A brief implementation of a QD calculation that is not quite so bimodal for known variants (multiplicatively penalizes QD by (n variant samples)/(n variant alleles) ). Not sure how helpful this will be (which is why it is in oneoffs). Seems nice on MCKD1, but I'm still playing with the optimization.
2010-08-13 15:42:37 +00:00
varianteval
Occasionally if a JEXL expression results in no variants being captured (like "QD > 20.0" on filtered variants) the per-sample mapping from samples to eval objects can be empty. This semi-hacky fix prevents null pointer exceptions in setting up the resulting empty table (by jumping straight to it in this case)
2010-08-13 15:37:45 +00:00
AlignedReadsHistoWalker.java
Genotyper now is using bytes not chars. Passes all tests.
2010-05-20 21:02:44 +00:00
AlleleBalanceHistogramWalker.java
VariantContext has now moved over to Tribble, and the VCF4 parser is now the only VCF parser in town. Other changes include:
2010-08-05 18:47:53 +00:00
AnnotationByAlleleFrequencyWalker.java
VariantContext has now moved over to Tribble, and the VCF4 parser is now the only VCF parser in town. Other changes include:
2010-08-05 18:47:53 +00:00
BaseTransitionTableCalculatorJavaWalker.java
Genotyper now is using bytes not chars. Passes all tests.
2010-05-20 21:02:44 +00:00
BeagleOutputByDepthWalker.java
VariantContext has now moved over to Tribble, and the VCF4 parser is now the only VCF parser in town. Other changes include:
2010-08-05 18:47:53 +00:00
CountIntervals.java
Minor modification: adding an argument to make slightly more general.
2010-07-30 05:20:20 +00:00
CreateTiTvTrack.java
VariantContext has now moved over to Tribble, and the VCF4 parser is now the only VCF parser in town. Other changes include:
2010-08-05 18:47:53 +00:00
DSBWalkerV3.java
Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK
2010-05-19 23:27:55 +00:00
DbSNPWindowCounter.java
The first step in integrating Jim's tree based index scheme:
2010-07-19 04:49:27 +00:00
DesignFileGeneratorWalker.java
Two fixes together:
2010-06-24 22:17:03 +00:00
DownsamplingValidationWalker.java
A downsampling validator. Compares the generated pileup passed in from the alignment context to the reads,
2010-05-23 21:49:54 +00:00
ErrorRatePerReadPosition.java
Can now threshold results based on minimum base and/or mapping quality.
2010-05-10 19:58:07 +00:00
GCCalculatorWalker.java
Added a GCCalculatorWalker for a oneoff analysis for Mark Daly (GC content of agilent 1.1 targets)
2010-05-19 18:49:51 +00:00
IOCrusherWalker.java
Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK
2010-05-19 23:27:55 +00:00
IndelAnnotator.java
Getting rid of GenotypeWriter interface. Of note:
2010-08-13 16:33:22 +00:00
IndelConsistencyReadCounter.java
Useful tool for calculating the perentage of misaligned reads at homozygous non-ref indel sites
2010-08-11 17:57:44 +00:00
IndelDBRateWalker.java
Getting rid of GenotypeWriter interface. Of note:
2010-08-13 16:33:22 +00:00
IndelErrorRateWalker.java
A refactoring / unification of ReadBackedPileup and ReadBackedExtendedEventPileup.
2010-06-20 04:42:26 +00:00
MendelianViolationClassifier.java
Getting rid of GenotypeWriter interface. Of note:
2010-08-13 16:33:22 +00:00
MismatchCounterWalker.java
Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK
2010-05-19 23:27:55 +00:00
MismatchHistoWalker.java
Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK
2010-05-19 23:27:55 +00:00
NeighborhoodQualityWalker.java
Yet more walkers moved to oneoffprojects.
2009-12-01 21:29:12 +00:00
PairedQualityScoreCountsWalker.java
BaseUtils has more clear distinction between byte and char routines. All char routines are @Depreciated now. Please use bytes. Better organization of reverse(), now in Utils not BaseUtils.
2010-05-20 14:05:13 +00:00
QualityScoreByStrandWalker.java
The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had
2010-04-20 15:26:32 +00:00
ReadErrorRateWalker.java
Read error rate is now parallelizable
2010-05-27 19:00:09 +00:00
ReadQualityScoreWalker.java
Knocking out some quick findBugs.
2010-07-27 14:10:59 +00:00
RealignedReadCounter.java
VariantContext has now moved over to Tribble, and the VCF4 parser is now the only VCF parser in town. Other changes include:
2010-08-05 18:47:53 +00:00
ReplaceQuals.java
Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK
2010-05-19 23:27:55 +00:00
TestReadFishingWalker.java
IndexedFastaSequenceFile is now in Picard; transitioning to that implementation.
2010-07-01 04:40:31 +00:00
TestVariantContextWalker.java
Getting rid of GenotypeWriter interface. Of note:
2010-08-13 16:33:22 +00:00
VCF4WriterTestWalker.java
Getting rid of GenotypeWriter interface. Of note:
2010-08-13 16:33:22 +00:00
ValidateRODForReads.java
fixing a bug that Eric found with RODs for reads, where some records could be omitted. Sorry Eric!
2010-06-29 21:38:55 +00:00
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