gatk-3.8/public
Mark DePristo c97a361b5d Added realistic BandPassFilterUnitTest that ensures quality results for 1000G phase I VCF and NA12878 VCF
-- Helped ID more bugs in the ActivityProfile, necessitating a new algorithm for popping off active regions.  This new algorithm requires that at least maxRegionSize + prob. propagation distance states have been examined.  This ensures that the incremental results are the same as you get reading in an entire profile and running getRegions on the full profile
-- TODO is to remove incremental search start algorithm, as this is no longer necessary, and nicely eliminates a state variable I was always uncomfortable with
2013-01-27 14:10:08 -05:00
..
R Fix a nasty bug in reading GATK reports with a single line 2012-09-10 20:14:13 -04:00
c
chainFiles
doc
java Added realistic BandPassFilterUnitTest that ensures quality results for 1000G phase I VCF and NA12878 VCF 2013-01-27 14:10:08 -05:00
keys
packages Remove DepthOfCoverage.java because it is no longer public 2013-01-10 11:45:38 -05:00
perl Split out contig names from Reference .fai file on white space (to support the GATK resource bundle's file human_g1k_v37.fasta.fai.gz, which does not use tab delimiters) 2012-06-07 16:56:32 -04:00
scala Making metrics a required parameter in MarkDuplicates 2013-01-25 17:49:49 -05:00
testdata Reverting move of BQSR tests to public, as per DR's email 2012-07-19 10:02:05 -04:00