| .. |
|
annotator
|
Genotyper now is using bytes not chars. Passes all tests.
|
2010-05-20 21:02:44 +00:00 |
|
varianteval/multisample
|
Call out ROD types by there record type, instead of the codec type (which was clumsy). So instead of:
|
2010-05-28 14:52:44 +00:00 |
|
vcftools
|
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 |
|
AlignedReadsHistoWalker.java
|
Genotyper now is using bytes not chars. Passes all tests.
|
2010-05-20 21:02:44 +00:00 |
|
AlleleBalanceHistogramWalker.java
|
Call out ROD types by there record type, instead of the codec type (which was clumsy). So instead of:
|
2010-05-28 14:52:44 +00:00 |
|
AnnotationByAlleleFrequencyWalker.java
|
Bug fix to avoid build failure (class changed under me??)
|
2010-05-21 18:48:56 +00:00 |
|
BaseTransitionTableCalculatorJavaWalker.java
|
Genotyper now is using bytes not chars. Passes all tests.
|
2010-05-20 21:02:44 +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
|
updating the tribble library to include the reference dictionary reading / writing. We now check the dictionaries of any tracks that have them against the reference (all new tribble tracks and out-of-date tracks will have this). Also renamed some classes to be more reflective of their function.
|
2010-06-04 06:34:26 +00:00 |
|
DesignFileGeneratorWalker.java
|
VariantEvalWalker now takes indels if you throw the -dels flag. IndelLengthHistogram appears to be working properly, it is turned off by default (as it is experimental) but you can turn it on in your own repository.
|
2010-05-26 20:03:14 +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
|
VCF moved over to tribble.
|
2010-05-05 17:28:48 +00:00 |
|
IndelDBRateWalker.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 |
|
IndelErrorRateWalker.java
|
The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had
|
2010-04-20 15:26:32 +00:00 |
|
MendelianViolationClassifier.java
|
A quick commit before running home. This is a re-factored version of the OppositeHomozygoteClassifier which will work with deNovo violations as well. Some code still needs to be migrated from OHC which is wy that walker isn't yet deleted. This'll be up and running tonight.
|
2010-06-08 20:47:01 +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 |
|
OppositeHomozygoteClassifier.java
|
Initial commit of the opposite homozygote classifier. Currently does the following, given a trio vcf:
|
2010-06-08 03:56:07 +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
|
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 |
|
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
|
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 |
|
TestVariantContextWalker.java
|
The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had
|
2010-04-20 15:26:32 +00:00 |
|
VCF4ReaderTestWalker.java
|
Optimized, nearly complete VCF4 reader 2-4x faster than the previous implementation, along with a VCF4 reader performance testing walker that can read 3/4 files, useful for benchmarking
|
2010-06-04 18:11:38 +00:00 |
|
VCFReferenceFixerWalker.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 |
736098b58d