Fixing a bug in parsing of T0 tag #8185
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jamesemery
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Feb 13, 2023
| if ((probs[qualOfs-1])==(probs[qualOfs])){ | ||
| flowMatrix[1][flowIdx] = Math.max(flowMatrix[1][flowIdx], Math.max(probs[qualOfs-1],probs[qualOfs])); | ||
| } | ||
| flowMatrix[1][flowIdx] = Math.max(flowMatrix[1][flowIdx], Math.min(probs[qualOfs-1],probs[qualOfs])); |
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Can you provide a bit of context as to what the expectation is/was here?
| // instead of actually running the tests. Can be used with "./gradlew test -Dtest.single=HaplotypeCallerIntegrationTest" | ||
| // to update all of the exact-match tests at once. After you do this, you should look at the | ||
| // diffs in the new expected outputs in git to confirm that they are consistent with expectations. | ||
| public static final boolean UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS = false; |
| 322,0,0,.,.,.,.,. 0.9880 | ||
| 322,1,0,.,.,.,.,. 0.0010 | ||
| 322,0,0,.,.,.,.,. 0.8890 | ||
| 322,1,0,.,.,.,.,. 0.1000 |
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These seem like fairly small effects...
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Right. And from the beginning the effect is small. But the fix does seem to improve SNPs a tiny bit
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