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better validation when saving paired fastqs #830

Merged
merged 1 commit into from
Sep 27, 2015
Merged

better validation when saving paired fastqs #830

merged 1 commit into from
Sep 27, 2015

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ryan-williams
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  • logError for LENIENT
  • throw for `STRICT

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Test PASSed.
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https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/926/
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fnothaft
fnothaft reviewed Sep 25, 2015
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adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDDFunctions.scala
readNameOccurrencesMap.map({
case (numOccurrences, numReadNames) => s"${numOccurrences}x:\t$numReadNames"
}).take(100).mkString("\t", "\n\t", ""),
"",
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Nit: if we have more than 100 improperly paired reads, then I would think we should print an ellipsis at the end of the message.

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ha yea I meant to add that and forgot, thanks, will add

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Other than the small nit, LGTM!

@ryan-williams
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nit should be fixed

@fnothaft
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Thanks @ryan-williams! I'll leave this open for comments, but if we don't hear from anyone else tomorrow, I'll merge.

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Test PASSed.
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https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/931/
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@fnothaft fnothaft merged commit aea329e into bigdatagenomics:master Sep 27, 2015
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Thanks @ryan-williams!

@fnothaft fnothaft mentioned this pull request Nov 10, 2015
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3 participants
@ryan-williams @AmplabJenkins @fnothaft