Mark DePristo 2996693c9f FisherStrand now computed with and without filtering low-qual bases, and least significant pvalue is kept ... -- Old way (filtering for Q > 17 bases) resulted in biased FS when the site was good but there was a systematic shift in the QUAL of REF and ALT between strands of the reads (sometimes happens) -- New way (taking all bases) was consistent with BaseQualRankSum and other tests, but there can be a lot of low qual reference bases on one strand in some techs (ION/PROTON/PACBIO) because of the preference for introducing an indel vs. a mismatch. -- This implementation allows us to have our cake and eat it to by computing both p-values, and taking the maximum one (i.e., least significant). -- No integration tests updated yet -- still exploring the consequences of this change		2012-08-28 08:06:47 -04:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	FisherStrand now computed with and without filtering low-qual bases, and least significant pvalue is kept	2012-08-28 08:06:47 -04:00
test	Ensure thread-safety of CachingIndexedFastaSequenceFile	2012-08-27 12:11:54 -04:00