hammerlab/guacamole — pull request #147 by arahuja (2014-08-20 19:04:25+00:00)
Title: Optimize Somatic SNV LogOdds Caller

After the updates and optimizations here we can do full WGS variant calling on tumor normal pair in ~11 - 17 min (latest run with new cluster launch script was 11:21, but I saw 17 min early, will test more to pin down and have another optimization related to #141 coming next)

Major updates:
- Removed check for correlated (nearby) SNVs from caller - moved this to a second pass over genotypes in some window
- Added new CalledGenotype and CalledSomaticGenotype (and Kryo serializers) to save more intermediate variant calling information used for filtering
- Changed all bases to be saved as Seq[Byte] instead of Array[Byte] to allow for easy element comparison
- Changed BayesianCaller and LogOdds caller to save alleles and sequences as Seq[Byte] to save conversion costs back and forth to strings
- Dropped filterLociWhoseContigsHaveNoRegions - this is useful if the file the user is running on 1) the user misspecifies loci by including loci not in the file or 2) loci are not specified the sequence dictionary has more sequences than actually in the file. These are easily solved by the user either specifying loci or using the flag to get loci from reads instead of the sequence dictionary. Otherwise has ~4-5min overhead on every run. Closes #140