diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java index cd0165b1a..fb01a51d2 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java @@ -11,11 +11,8 @@ import java.util.Arrays; import net.sf.samtools.SAMRecord; /** - * Created by IntelliJ IDEA. - * User: hanna - * Date: 13 Apr, 2009 - * Time: 11:23:14 AM - * To change this template use File | Settings | File Templates. + * Diagnostics analysis. At each locus in the input data set, prints the reference base, genomic location, and + * all aligning reads in a compact but human-readable form. */ public class PrintLocusContextWalker extends LocusWalker implements TreeReducible { public AlignmentContext map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java index f44dbc75f..59dc30070 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java @@ -37,12 +37,9 @@ import java.util.ArrayList; */ /** - * - * @author aaron - * - * Class ReadValidationWalker - * - * A descriptions should go here. Blame aaron if it's missing. + * Diagnostics analysis. Checks all reads passed through the system to ensure that + * the same read is not passed to the walker multiple consecutive times. + * @author aaron */ public class ReadValidationWalker extends ReadWalker { diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java index e86a1f358..eb077dbb4 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java @@ -14,11 +14,9 @@ import org.broadinstitute.sting.utils.StingException; import java.util.Arrays; /** - * Created by IntelliJ IDEA. - * User: mdepristo - * Date: Feb 22, 2009 - * Time: 3:22:14 PM - * To change this template use File | Settings | File Templates. + * Diagnostics analysis. At every locus in the input set, compares the pileup data (reference base, aligned base from + * each overlapping read, and quality score) to the reference pileup data generated by samtools. Samtools' pileup data + * should be specified using the command-line argument '-B pileup,SAMPileup,'. */ @Requires(value={DataSource.READS,DataSource.REFERENCE},referenceMetaData=@RMD(name="pileup",type=rodSAMPileup.class)) public class ValidatingPileupWalker extends LocusWalker implements TreeReducible {