| .. |
|
EvalMapping.py
|
Move non-java code out of playground.
|
2009-03-23 19:31:38 +00:00 |
|
FastaQuals2Fastq.py
|
Move non-java code out of playground.
|
2009-03-23 19:31:38 +00:00 |
|
Geli2GFF.py
|
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.
|
2009-03-24 03:58:03 +00:00 |
|
LogRegression.py
|
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.
|
2009-04-28 00:37:48 +00:00 |
|
MergeBAMBatch.py
|
Actually has working version of the python script to merge multiple bam files
|
2009-04-24 19:15:55 +00:00 |
|
MergeEvalMapTabs.py
|
Move non-java code out of playground.
|
2009-03-23 19:31:38 +00:00 |
|
SAM.py
|
Move non-java code out of playground.
|
2009-03-23 19:31:38 +00:00 |
|
SamWalk.py
|
Move non-java code out of playground.
|
2009-03-23 19:31:38 +00:00 |
|
SamWalkTest.py
|
Move non-java code out of playground.
|
2009-03-23 19:31:38 +00:00 |
|
SimpleSAM.py
|
Move non-java code out of playground.
|
2009-03-23 19:31:38 +00:00 |
|
SimulateReads.py
|
Actually writes out a good header now
|
2009-05-18 13:34:52 +00:00 |
|
SpawnMapperJobs.py
|
Move non-java code out of playground.
|
2009-03-23 19:31:38 +00:00 |
|
SpawnValidationJobs.py
|
Move non-java code out of playground.
|
2009-03-23 19:31:38 +00:00 |
|
StressTestGATK.py
|
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.
|
2009-04-14 22:13:10 +00:00 |
|
ValidateGATK.py
|
Reference-ordered data relies on bugs in the old command-line argument system to work. Update the ROD system to from -B track1 type1 file1 track2 type2 file2 to -B track1,type1,file1 -B track2,type2,file2.
|
2009-05-08 15:28:19 +00:00 |
|
WalkLociTest.py
|
Move non-java code out of playground.
|
2009-03-23 19:31:38 +00:00 |
|
Walker.py
|
Move non-java code out of playground.
|
2009-03-23 19:31:38 +00:00 |
|
aln_file.nocvs.py
|
Move non-java code out of playground.
|
2009-03-23 19:31:38 +00:00 |
|
aln_file.py
|
Move non-java code out of playground.
|
2009-03-23 19:31:38 +00:00 |
|
compSNPCalls.py
|
Move non-java code out of playground.
|
2009-03-23 19:31:38 +00:00 |
|
countCoverageWithSamtools.py
|
Move non-java code out of playground.
|
2009-03-23 19:31:38 +00:00 |
|
farm_commands.py
|
Fixed potential bug with next() operation returning empty contexts when a read contains a large deletion. We can now use the look ahead safely...
|
2009-04-15 21:41:30 +00:00 |
|
fasta.py
|
Move non-java code out of playground.
|
2009-03-23 19:31:38 +00:00 |
|
memo.py
|
Move non-java code out of playground.
|
2009-03-23 19:31:38 +00:00 |
|
picard_utils.py
|
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.
|
2009-05-14 21:06:28 +00:00 |
|
pushback_file.py
|
Move non-java code out of playground.
|
2009-03-23 19:31:38 +00:00 |
|
qltout.py
|
Move non-java code out of playground.
|
2009-03-23 19:31:38 +00:00 |
|
samtooltest.sh
|
Move non-java code out of playground.
|
2009-03-23 19:31:38 +00:00 |
|
tgtc2sam.py
|
Move non-java code out of playground.
|
2009-03-23 19:31:38 +00:00 |
9dec783a82