feat: a default base quality may be provided in consensus callers whe… #1032
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…n base qualities are missing
nh13
commented
Feb 20, 2025
| @@ -113,6 +113,7 @@ class CallDuplexConsensusReads | |||
| val maxReadsPerStrand: Option[Int] = None, | |||
| @arg(doc="The number of threads to use while consensus calling.") val threads: Int = 1, | |||
| @arg(doc="Consensus call overlapping bases in mapped paired end reads") val consensusCallOverlappingBases: Boolean = true, | |||
| @arg(doc = "The phred-scaled base quality to use when base qualities are missing in the input") val missingBaseQuality: Option[PhredScore] = None, | |||
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Suggested change
| @arg(doc = "The phred-scaled base quality to use when base qualities are missing in the input") val missingBaseQuality: Option[PhredScore] = None, | |
| @arg(doc="The phred-scaled base quality to use when base qualities are missing in the input") val missingBaseQuality: Option[PhredScore] = None, |
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #1032 +/- ##
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Coverage 95.68% 95.68%
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Files 126 126
Lines 7410 7415 +5
Branches 500 524 +24
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+ Hits 7090 7095 +5
Misses 320 320
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…n base qualities are missing.
Fixes: #1031
This has the following improvements:
ArrayIndexOutOfBoundsExceptionwith on mention of which read.--missing-base-qualityis not given, then the exception occurs (no change in current behavior)--missing-base-qualityis given, then it is used (gracefully)My only question is if we should have a non-None value by default. See #1031 for a discussion on why that might be a bad idea.