Mark DePristo 9e28d1e347 Cleanup and unit tests for QualityUtils ... -- Fixed a few conversion bugs with edge case quals (ones that were very high) -- Fixed a critical bug in the conversion of quals that was causing near capped quals to fall below their actual value. Will undoubtedly need to fix md5s -- More precise prob -> qual calculations for very high confidence events in phredScaleCorrectRate, trueProbToQual, and errorProbToQual. Very likely to improve accuracy of many calculations in the GATK -- Added errorProbToQual and trueProbToQual calculations that accept an integer cap, and perform the (tricky) conversion from int to byte correctly. -- Full docs and unit tests for phredScaleCorrectRate and phredScaleErrorRate. -- Renamed probToQual to trueProbToQual -- Added goodProbability and log10OneMinusX to MathUtils -- Went through the GATK and cleaned up many uses of QualityUtils -- Cleanup constants in QualityUtils -- Added full docs for all of the constants -- Rename MAX_QUAL_SCORE to MAX_SAM_QUAL_SCORE for clarity -- Moved MAX_GATK_USABLE_Q_SCORE to RecalDatum, as it's s BQSR specific feature -- Convert uses of QualityUtils.errorProbToQual(1-x) to QualityUtils.trueProbToQual(x) -- Cleanup duplicate quality score routines in MathUtils. Moved and renamed MathUtils.log10ProbabilityToPhredScale => QualityUtils.phredScaleLog10ErrorRate. Removed 3 routines from MathUtils, and remapped their usages into the better routines in QualityUtils		2013-02-16 07:31:37 -08:00
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net/sf	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
org/broadinstitute/sting	Cleanup and unit tests for QualityUtils	2013-02-16 07:31:37 -08:00