SW implementation is command line argument in FilterAlignmentArtifacts #7105
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Closes #7162. |
| @@ -135,10 +131,15 @@ | |||
| @Argument(fullName= AssemblyBasedCallerArgumentCollection.BAM_OUTPUT_LONG_NAME, shortName= AssemblyBasedCallerArgumentCollection.BAM_OUTPUT_SHORT_NAME, doc="File to which assembled haplotypes should be written", optional = true) | |||
| public String bamOutputPath = null; | |||
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| @Advanced | |||
| @Argument(fullName = AssemblyBasedCallerArgumentCollection.SMITH_WATERMAN_LONG_NAME, doc = "Which Smith-Waterman implementation to use, generally FASTEST_AVAILABLE is the right choice", optional = true) | |||
| public SmithWatermanAligner.Implementation smithWatermanImplementation = SmithWatermanAligner.Implementation.JAVA; | |||
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You want the default here to be JAVA, not FASTEST_AVAILABLE? If so, might be helpful to update the doc for this arg to say that JAVA is the preferred implementation. (And possibly leave a comment somewhere to the issue causing you to choose the JAVA implementation if that exists somewhere.)
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I switched it to fastest available.
| import org.broadinstitute.barclay.argparser.ArgumentCollection; | ||
| import org.broadinstitute.barclay.argparser.CommandLineProgramProperties; | ||
| import org.broadinstitute.barclay.argparser.ExperimentalFeature; | ||
| import org.broadinstitute.barclay.argparser.*; |
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I think we want to use explicit imports
| @@ -135,10 +131,15 @@ | |||
| @Argument(fullName= AssemblyBasedCallerArgumentCollection.BAM_OUTPUT_LONG_NAME, shortName= AssemblyBasedCallerArgumentCollection.BAM_OUTPUT_SHORT_NAME, doc="File to which assembled haplotypes should be written", optional = true) | |||
| public String bamOutputPath = null; | |||
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| @Advanced | |||
| @Argument(fullName = AssemblyBasedCallerArgumentCollection.SMITH_WATERMAN_LONG_NAME, doc = "Which Smith-Waterman implementation to use, generally FASTEST_AVAILABLE is the right choice", optional = true) | |||
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I think the word "Which" is unnecessary here.
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@davidbenjamin Sorry, I reviewed this sometime ago, but didn't push the button to submit the review :( |
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@davidbenjamin Oops, I shouldn't approve changes that break the tests. |
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The broken test seems to be accidental removed the import for |
Closes #7087. @fleharty can you review this?