gatk-3.8/protected/java/src/org/broadinstitute/sting/utils
Mauricio Carneiro 9bfa5eb70f Quick optimization to the PairHMM
Problem
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the logless HMM scale factor (to avoid double under-flows) was 10^300. Although this serves the purpose this value results in a complex mantissa that further complicates cpu calculations.

Solution
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initialize with 2^1020 (2^1023 is the max value), and adjust the scale factor accordingly.
2013-04-14 23:25:33 -04:00
..
haplotype Address reviewer comments 2013-04-08 12:48:20 -04:00
haplotypeBAMWriter Slightly improved Smith-Waterman parameter values for HaplotypeCaller Path comparisons 2013-04-11 18:22:55 -04:00
pairhmm Quick optimization to the PairHMM 2013-04-14 23:25:33 -04:00
recalibration Updating BQSR RecalibrationEngine to work correctly with empty BQSR tables. 2013-04-11 16:27:59 -04:00