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EvalMapping.py
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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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FastaQuals2Fastq.py
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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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Geli2GFF.py
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Added Hapmap data track (using rodGFF class for GFF file format) to toolkit as a command line option, Hapmap metrics to AlleleFrequencyMetricsWalker, and a python Geli2GFF file converter.
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2009-03-24 03:58:03 +00:00 |
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Gelis2PopSNPs.py
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Improving, yet again, the merging of bam files
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2009-06-02 13:31:12 +00:00 |
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LogRegression.py
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Several changes to CovariateCounter walker to print more tables (called vs. observed Q scores), bug fixes to LogisticRecalibrationWalker and LogisticRegressor, and print string functionality added to Pair.
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2009-04-28 00:37:48 +00:00 |
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MergeBAMBatch.py
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Improving, yet again, the merging of bam files
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2009-06-02 13:31:12 +00:00 |
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MergeBAMsUtils.py
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Improving, yet again, the merging of bam files
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2009-06-02 13:31:12 +00:00 |
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MergeBamsByKey.py
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Improving, yet again, the merging of bam files
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2009-06-02 13:31:12 +00:00 |
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MergeEvalMapTabs.py
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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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SAM.py
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Better merge support
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2009-05-18 21:18:51 +00:00 |
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SamWalk.py
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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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SamWalkTest.py
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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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SimpleSAM.py
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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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SimulateReads.py
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Actually writes out a good header now
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2009-05-18 13:34:52 +00:00 |
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SpawnMapperJobs.py
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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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SpawnValidationJobs.py
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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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StressTestGATK.py
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General purpose pileup code -- you can use these features to obtain detailed pileup data from reads and offsets. Useful for all pileup based walkers. Expanded support for rodSAMPileup to enable the new ValidatingPileupWalker, which takes a samtools pileup output and checks that GATK gives identical output as samtools on a per base and per qual pileup. It's going to be a very useful validation tool.
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2009-04-14 22:13:10 +00:00 |
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ValidateGATK.py
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Slightly improved interface to merging utility for multiple bam files
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2009-05-20 12:54:41 +00:00 |
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WalkLociTest.py
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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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Walker.py
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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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aln_file.nocvs.py
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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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aln_file.py
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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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compSNPCalls.py
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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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countCoverageWithSamtools.py
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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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farm_commands.py
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now returns the farm id when submitting a job!
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2009-05-26 22:23:24 +00:00 |
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fasta.py
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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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memo.py
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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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picard_utils.py
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Now supports automatic merging by population
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2009-05-31 15:28:44 +00:00 |
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pushback_file.py
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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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qltout.py
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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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samtooltest.sh
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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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tgtc2sam.py
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Move non-java code out of playground.
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2009-03-23 19:31:38 +00:00 |
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