Better docs for verbose output of Pileup
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@ -64,9 +64,17 @@ import java.util.List;
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*/
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@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
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public class Pileup extends LocusWalker<Integer, Integer> implements TreeReducible<Integer> {
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private static final String verboseDelimiter = "@"; // it's ugly to use "@" but it's literally the only usable character not allowed in read names
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@Output
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PrintStream out;
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/**
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* In addition to the standard pileup output, adds 'verbose' output too. The verbose output contains the number of spanning deletions,
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* and for each read in the pileup it has the read name, offset in the base string, read length, and read mapping quality. These per
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* read items are delimited with an '@' character.
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*/
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@Argument(fullName="showVerbose",shortName="verbose",doc="Add an extra verbose section to the pileup output")
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public boolean SHOW_VERBOSE = false;
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@ -116,8 +124,6 @@ public class Pileup extends LocusWalker<Integer, Integer> implements TreeReducib
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return rodString;
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}
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private static final String verboseDelimiter = "@"; // it's ugly to use "@" but it's literally the only usable character not allowed in read names
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private static String createVerboseOutput(final ReadBackedPileup pileup) {
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final StringBuilder sb = new StringBuilder();
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boolean isFirst = true;
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