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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk/walkers
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Mark DePristo 68eed7b313 Optimizations for VCF and BCF2 
-- encodeTyped in BCF2Encoder now with specialized versions for int, float, and string, avoiding unnecessary intermediate list creation and dynamic type checking.  encodeTypedMissing also includes inline operations now instead of using Collections.emptyList() version.  Lots of contracts.  User code updated to use specialized versions where possible
-- Misc code refactoring
-- Updated VCF float formating to always include 3 sig digits for values < 1, and 2 for > 1.  Updating MD5s accordingly
-- Expanded testing of BCF2Decoder to really use all of the encodeTyped* operations
 		2012-06-14 16:42:39 -04:00
..
CNV Updating MD5s to latest version to reflect inclusion of contigs in headers 2012-06-14 16:42:36 -04:00
annotator Optimizations for VCF and BCF2 2012-06-14 16:42:39 -04:00
beagle Optimizations for VCF and BCF2 2012-06-14 16:42:39 -04:00
bqsr I hate these disabled unit tests, #2 2012-06-14 15:19:27 -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 Final support for variable length lists of strings in BCF2 2012-06-14 16:42:38 -04:00
fasta Removing the legacy -L "interval1;interval2" syntax 2011-11-21 13:18:53 -05:00
filters Updating MD5s to latest version to reflect inclusion of contigs in headers 2012-06-14 16:42:36 -04:00
genotyper Optimizations for VCF and BCF2 2012-06-14 16:42:39 -04:00
indels GATK tests use public/testdata not /humgen/ as much as possible 2012-05-24 10:58:58 -04:00
phasing Final support for variable length lists of strings in BCF2 2012-06-14 16:42:38 -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 Final support for variable length lists of strings in BCF2 2012-06-14 16:42:38 -04:00
varianteval Code cleanup and more documentation for BCFFieldWriters 2012-06-14 16:42:37 -04:00
variantrecalibration Final support for variable length lists of strings in BCF2 2012-06-14 16:42:38 -04:00
variantutils Optimizations for VCF and BCF2 2012-06-14 16:42:39 -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