gatk-3.8/public/java/test/org/broadinstitute/sting/gatk/walkers
Mark DePristo 8014178f2f Algorithmically faster version of DiffEngine
-- Now only includes leaf nodes in the summary, i.e., summaries of the form "*.*....*.X", which are really the most valuable to see.  This calculation can be accomplished in linear time for N differences, rather than the previous O(n^2) algorithm
-- Now computes the max number of elements to read correctly.  Counts now the size of the entire element tree, not just the count of the roots, which was painful because the trees vary by orders of magnitude in size.
-- Because of this we can enforce a meaningful, useful value for the max elements in MD5 or 100K, and this works well.
-- Added integration test for new leaf and old pairwise calculations
-- Bugfix for Utils.join(sep, int[]) that was eating the first element of the AD, PL fields
2012-06-14 16:42:30 -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 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 Algorithmically faster version of DiffEngine 2012-06-14 16:42:30 -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 Efficient Genotype object Intermediate commit 2012-06-14 16:42:24 -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 MD5DB for integrationtest management now writes out a md5mismatches files for clean analysis 2012-06-14 16:42:27 -04:00
variantutils No more makePrecisionFormatStringFromDenominatorValue 2012-06-14 16:42:30 -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