gatk-3.8/public
Mark DePristo 8b01969762 More code cleanup and optimizations to BCF2 writer
-- Cleanup a few contracts
-- BCF2FieldManager uses new VCFHeader accessors for specific info and format fields
-- A few simple optimizations
    -- VCF header samples stored in String[] in the writer for fast access
    -- getCalledChrCount() uses emptySet instead of allocating over and over empty hashset
    -- VariantContextWriterStorage now creates a 1MB buffered output writer, which results in 3x performance boost when writing BCF2 files
-- A few editorial comments in VCFHeader
2012-06-14 16:42:38 -04:00
..
R Bugfix for R 2.15 not including reshape 2012-06-14 16:42:29 -04:00
c At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings. 2012-01-17 14:47:53 -05:00
chainFiles
doc
java More code cleanup and optimizations to BCF2 writer 2012-06-14 16:42:38 -04:00
keys Public-key authorization scheme to restrict use of NO_ET 2012-03-06 00:09:43 -05:00
packages Temporary fake release directories for Bamboo testing purposes 2012-05-31 16:04:07 -04:00
perl
scala MD5DB for integrationtest management now writes out a md5mismatches files for clean analysis 2012-06-14 16:42:27 -04:00
testdata More testdata test files 2012-06-14 16:42:35 -04:00