From 9d09230c26ff832f48d0c7ee289971a2ca5d2168 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Wed, 15 Aug 2012 21:55:08 -0400 Subject: [PATCH] Better docs for verbose output of Pileup --- .../org/broadinstitute/sting/gatk/walkers/Pileup.java | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/Pileup.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/Pileup.java index 0eb3a628d..2a6ecdb8c 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/Pileup.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/Pileup.java @@ -64,9 +64,17 @@ import java.util.List; */ @DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} ) public class Pileup extends LocusWalker implements TreeReducible { + + private static final String verboseDelimiter = "@"; // it's ugly to use "@" but it's literally the only usable character not allowed in read names + @Output 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") public boolean SHOW_VERBOSE = false; @@ -116,8 +124,6 @@ public class Pileup extends LocusWalker implements TreeReducib 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) { final StringBuilder sb = new StringBuilder(); boolean isFirst = true;