Filter M2 calls that are near other filtered calls on the same haplotype #5092
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LeeTL1220
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Aug 7, 2018
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@davidbenjamin Minor stuff. Feel free to merge after you address the comments.
| * will not exceed the requested false positive rate | ||
| * | ||
| * @param posteriors A list of posterior probabilities, which gets sorted | ||
| * @param requestedFPR We set the filtering threshold such that the FPR doesn't exceed this value |
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Since this is a public static method, please document and have checks for requestedFPR. For example, can it be negative?
| import java.io.IOException; | ||
| import java.util.*; | ||
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| public class FilteringFirstPass { |
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Could you add some class javadoc? Would like to know how this fits in the grand scheme of things...
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Codecov Report
@@ Coverage Diff @@
## master #5092 +/- ##
===============================================
+ Coverage 86.478% 86.485% +0.006%
- Complexity 29155 29168 +13
===============================================
Files 1813 1813
Lines 135228 135256 +28
Branches 15023 15027 +4
===============================================
+ Hits 116943 116976 +33
+ Misses 12825 12818 -7
- Partials 5460 5462 +2
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@LeeTL1220 This gets rid of a bunch of false positives with no effect on sensitivity. It also does some useful refactoring of the filtering engine in order to exploit Takuto's two-pass formalism for more filters than just OB.