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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk/walkers
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Roger Zurawicki b8b139841d DiagnoseTargets with working Q1,Median,Q3 
- Merged Roger's metrics with Mauricio's optimizations
 - Added Stats for DiagnoseTargets
     - now has functions to find the median depth, and upper/lower quartile
     - the REF_N callable status is implemented
 - The walker now runs efficiently
 - Diagnose Targets accepts overlapping intervals
 - Diagnose Targets now checks for bad mates
 - The read mates are checked in a memory efficient manner
 - The statistics thresholds have been consolidated and moved outside of the statistics classes and into the walker.
 - Fixed some bugs
 - Removed rod binding

Added more Unit tests

 - Test callable statuses on the locus level
 - Test bad mates

 - Changed NO_COVERAGE -> COVERAGE_GAPS to avoid confusion

Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
 		2012-05-29 10:16:45 -04:00
..
CNV GATK tests use public/testdata not /humgen/ as much as possible 2012-05-24 10:58:58 -04:00
annotator Made GQ an int, not a float. Updated VC code and lots of corresponding MD5s 2012-05-28 20:20:05 -04:00
beagle Missed one integration test 2012-05-29 07:23:24 -04:00
bqsr Removed old GATKReport code and moved the new stuff in its place. 2012-05-18 01:44:31 -04:00
coverage DoC now properly handles reference N bases + misc. additional cleanups 2012-02-25 11:32:50 -05:00
diagnostics DiagnoseTargets with working Q1,Median,Q3 2012-05-29 10:16:45 -04:00
diffengine Update MD5s to reflect new limited output of DiffObjectsWalkers 2012-05-27 11:20:47 -04:00
fasta Removing the legacy -L "interval1;interval2" syntax 2011-11-21 13:18:53 -05:00
filters Made GQ an int, not a float. Updated VC code and lots of corresponding MD5s 2012-05-28 20:20:05 -04:00
genotyper Made GQ an int, not a float. Updated VC code and lots of corresponding MD5s 2012-05-28 20:20:05 -04:00
indels GATK tests use public/testdata not /humgen/ as much as possible 2012-05-24 10:58:58 -04:00
phasing Made GQ an int, not a float. Updated VC code and lots of corresponding MD5s 2012-05-28 20:20:05 -04:00
qc First version of VariantContextBuilder 2011-11-18 11:06:15 -05:00
recalibration GATK tests use public/testdata not /humgen/ as much as possible 2012-05-24 10:58:58 -04:00
validation GATK tests use public/testdata not /humgen/ as much as possible 2012-05-24 10:58:58 -04:00
varianteval Final updates to integration tests for BCF2 2012-05-24 10:58:59 -04:00
variantrecalibration GATK tests use public/testdata not /humgen/ as much as possible 2012-05-24 10:58:58 -04:00
variantutils Made GQ an int, not a float. Updated VC code and lots of corresponding MD5s 2012-05-28 20:20:05 -04:00
BAQIntegrationTest.java merge master 2011-10-25 16:08:39 -04:00
ClipReadsWalkersIntegrationTest.java GATK tests use public/testdata not /humgen/ as much as possible 2012-05-24 10:58:58 -04:00
FlagStatIntegrationTest.java Adding integration test for Flag Stat 2012-04-10 22:40:38 -04:00
PileupWalkerIntegrationTest.java Had some free time, so I unplugged extended events from the walkers. Now they exist only in LocusIteratorByState, but ReadProperties.generateExtendedEvents() always returns false so that block is never actually executed anymore. I don't want to touch LIBS because I think David is in there right now. 2012-04-02 14:27:36 -04:00
PrintReadsIntegrationTest.java GATK tests use public/testdata not /humgen/ as much as possible 2012-05-24 10:58:58 -04:00
PrintReadsUnitTest.java Better location for the downsampling of reads in PrintReads 2012-01-14 14:06:09 -05:00