fixed contamination calculation, added error bars to output #3385
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Codecov Report
@@ Coverage Diff @@
## master #3385 +/- ##
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- Coverage 80.475% 80.468% -0.007%
- Complexity 17507 17508 +1
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Files 1173 1173
Lines 63376 63384 +8
Branches 9878 9878
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+ Hits 51002 51004 +2
- Misses 8426 8432 +6
Partials 3948 3948
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takutosato
approved these changes
Jul 31, 2017
| final double proportionRefReads = (double) contaminationRefCount / totalReadCount; | ||
| final double proportionOfContaminatingReadsThatAreRef = homAltSites.stream().mapToDouble(PileupSummary::getRefFrequency).average().getAsDouble(); | ||
| final double contamination = proportionRefReads / proportionOfContaminatingReadsThatAreRef; | ||
| final double totalDepthWeightedByRefFraction = homAltSites.stream() |
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totalDepthWeightedByRefFrequency instead of RefFraction
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Eh fraction is probably just as good. You use fraction in the docs. Your call
| "Therefore, we estimate a contamination of %.3f", proportionRefReads, proportionOfContaminatingReadsThatAreRef, contamination)); | ||
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| return contamination; | ||
| logger.info(String.format("Based on population data, we would expect %d reference reads in a contaminant with the same depths at these sites.", (long) totalDepthWeightedByRefFraction)); |
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as* these sites? Alternatively, maybe we can say that totalDepthWeightedByRefFraction is the expected number of ref reads if we had 100% contamination
This was referenced Jul 31, 2017
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@takutosato This corrects the math error you pointed out in your code review of the docs. While we're at it, it also outputs the error bars according to the formula given in the docs. I have tested it on an in silico contamination series and it improves results slightly.