From f2ea193149d56f0a743e80640110015089022047 Mon Sep 17 00:00:00 2001 From: ebanks Date: Fri, 22 May 2009 14:07:07 +0000 Subject: [PATCH] For some reason the apostraphes in the comments were throwing annoying compile-time warnings: "unmappable character for encoding UTF8" git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@792 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/PileupWalker.java | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java index 66d2cbf40..46981f5e3 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java @@ -18,15 +18,15 @@ import java.util.List; * consisting of chromosome name, coordinate, reference base, read bases, read qualities and alignment mapping * qualities. Information on match, mismatch, indel, strand, mapping quality and start and end of a read are all * encoded at the read base column. At this column, a dot stands for a match to the reference base on the forward strand, - * a comma for a match on the reverse strand, ÔACGTNÕ for a mismatch on the forward strand and ÔacgtnÕ for a mismatch on the + * a comma for a match on the reverse strand, 'ACGTN' for a mismatch on the forward strand and 'acgtn' for a mismatch on the * reverse strand. * - * A pattern Ô\+[0-9]+[ACGTNacgtn]+Õ indicates there is an insertion between this reference position and the next + * A pattern '\+[0-9]+[ACGTNacgtn]+' indicates there is an insertion between this reference position and the next * reference position. The length of the insertion is given by the integer in the pattern, followed by the inserted sequence. - * Similarly, a pattern Ô-[0-9]+[ACGTNacgtn]+Õ represents a deletion from the reference. - * Also at the read base column, a symbol Ô^Õ marks the start of a read segment which is a contiguous subsequence on the read - * separated by ÔN/S/HÕ CIGAR operations. The ASCII of the character following Ô^Õ minus 33 gives the mapping quality. - * A symbol Ô$Õ marks the end of a read segment. + * Similarly, a pattern '-[0-9]+[ACGTNacgtn]+' represents a deletion from the reference. + * Also at the read base column, a symbol '^' marks the start of a read segment which is a contiguous subsequence on the read + * separated by 'N/S/H' CIGAR operations. The ASCII of the character following '^' minus 33 gives the mapping quality. + * A symbol '$' marks the end of a read segment. */ public class PileupWalker extends LocusWalker implements TreeReducible { @Argument(fullName="alwaysShowSecondBase",doc="If true, prints dummy bases for the second bases in the BAM file where they are missing",required=false)