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Better docs for verbose output of Pileup

This commit is contained in:
Eric Banks 2012-08-15 21:55:08 -04:00
parent 3556c36668
commit 9d09230c26
1 changed files with 8 additions and 2 deletions
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10
public/java/src/org/broadinstitute/sting/gatk/walkers/Pileup.java
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@ -64,9 +64,17 @@ import java.util.List;
*/ */
@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} ) @DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
public class Pileup extends LocusWalker<Integer, Integer> implements TreeReducible<Integer> { public class Pileup extends LocusWalker<Integer, Integer> implements TreeReducible<Integer> {
private static final String verboseDelimiter = "@"; // it's ugly to use "@" but it's literally the only usable character not allowed in read names
@Output @Output
PrintStream out; PrintStream out;
/**
* In addition to the standard pileup output, adds 'verbose' output too. The verbose output contains the number of spanning deletions,
* 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
* read items are delimited with an '@' character.
*/
@Argument(fullName="showVerbose",shortName="verbose",doc="Add an extra verbose section to the pileup output") @Argument(fullName="showVerbose",shortName="verbose",doc="Add an extra verbose section to the pileup output")
public boolean SHOW_VERBOSE = false; public boolean SHOW_VERBOSE = false;
@ -116,8 +124,6 @@ public class Pileup extends LocusWalker<Integer, Integer> implements TreeReducib
return rodString; return rodString;
} }
private static final String verboseDelimiter = "@"; // it's ugly to use "@" but it's literally the only usable character not allowed in read names
private static String createVerboseOutput(final ReadBackedPileup pileup) { private static String createVerboseOutput(final ReadBackedPileup pileup) {
final StringBuilder sb = new StringBuilder(); final StringBuilder sb = new StringBuilder();
boolean isFirst = true; boolean isFirst = true;