refactored table writing in BasicSomaticValidator #6136
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Thanks so much for cleaning this up so quickly, @davidbenjamin! A few minor quibbles, OK to merge after.
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| import htsjdk.samtools.util.Locatable; | |||
| import htsjdk.variant.variantcontext.Allele; | |||
| import org.broadinstitute.hellbender.exceptions.UserException; | |||
| import org.broadinstitute.hellbender.tools.walkers.contamination.ContaminationRecord; | |||
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Optimize imports throughout.
| @@ -104,4 +118,112 @@ public String getFilters() { | |||
| public long getNumAltSupportingReadsInNormal() { | |||
| return numAltSupportingReadsInNormal; | |||
| } | |||
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| //----- The following two public static methods read and write files | |||
| public static void writeToFile(final List<BasicValidationResult> records, final File outputTable) { | |||
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I think just write and read as method names are fine, but up to you. Might also consider just file for the parameter names, or perhaps outputFile and inputFile (the distinction between the current outputTable and tableFile is not clear).
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| //----- The following two public static methods read and write files | ||
| public static void writeToFile(final List<BasicValidationResult> records, final File outputTable) { | ||
| try ( final BasicValidationResult.BasicValidationResultTableWriter writer = new BasicValidationResult.BasicValidationResultTableWriter(IOUtils.fileToPath(outputTable)) ) { |
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Some inconsistencies in white space here and in the try statement below.
| try ( final BasicValidationResult.BasicValidationResultTableWriter writer = new BasicValidationResult.BasicValidationResultTableWriter(IOUtils.fileToPath(outputTable)) ) { | ||
| writer.writeHeaderIfApplies(); | ||
| writer.writeAllRecords(records); | ||
| } catch (IOException e){ |
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Make the exception final here and below.
| } | ||
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| //-------- The following methods are boilerplate for reading and writing tables | ||
| private static class BasicValidationResultTableWriter extends TableWriter<BasicValidationResult> { |
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Reconsider the access modifiers of the below classes (and their constructors) and enum (and its COLUMNS field)---some inconsistencies here.
@samuelklee This is for you regarding #3884.