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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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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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Better version of MergeBAMBatch -- more options for creating the file
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2009-05-21 22:26:19 +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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2009-03-23 19:31:38 +00:00 |
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SamWalkTest.py
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2009-03-23 19:31:38 +00:00 |
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SimpleSAM.py
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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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2009-03-23 19:31:38 +00:00 |
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SpawnValidationJobs.py
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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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2009-03-23 19:31:38 +00:00 |
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aln_file.nocvs.py
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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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Better version of MergeBAMBatch -- more options for creating the file
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2009-05-21 22:26:19 +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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Revised ROD system. Split the system in Basic type and interface. Enabled more control over rod accessing, including an initialize() function to fetch headers and other options from the file. Added general tabular rod, which has a named columns and supports a map<String,String> interface. Comes with shiny new Junit system for RODs. Also, added simple python script for accessing picard data.
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2009-05-14 21:06:28 +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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