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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
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ebanks 2009-05-22 14:07:07 +00:00
parent 9902ce8073
commit f2ea193149
1 changed files with 6 additions and 6 deletions
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12
java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
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@ -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<Integer, Integer> implements TreeReducible<Integer> {
@Argument(fullName="alwaysShowSecondBase",doc="If true, prints dummy bases for the second bases in the BAM file where they are missing",required=false)