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Can now optionally print the read and the alignment region of the reference. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@423 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-04-15 04:10:30 +00:00
parent d4aaa1bef4
commit d0b8d311e6
1 changed files with 31 additions and 3 deletions
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34
java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadErrorRateWalker.java
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@ -20,6 +20,9 @@ public class ReadErrorRateWalker extends ReadWalker<boolean[], int[]> {
@Argument(fullName="useNextBestBase",required=false,defaultValue="false")
public boolean useNextBestBase;
@Argument(fullName="printVisualHits",required=false,defaultValue="false")
public boolean printVisualHits;
/**
* Ignore reads with indels or clipping
*
@ -28,7 +31,7 @@ public class ReadErrorRateWalker extends ReadWalker<boolean[], int[]> {
* @return true if the read can be processed, false if it should be ignored
*/
public boolean filter(LocusContext context, SAMRecord read) {
return (read.getCigar().numCigarElements() == 1);
return (read.getCigar().numCigarElements() == 1 && read.getAlignmentStart() + read.getReadLength() < context.getReferenceContig().length());
}
/**
@ -50,9 +53,34 @@ public class ReadErrorRateWalker extends ReadWalker<boolean[], int[]> {
byte[] contig = context.getReferenceContig().getBases();
byte[] sq = (byte[]) read.getAttribute("SQ");
int totalMismatches = 0;
if (printVisualHits) {
System.out.println(read.getReadName());
for (int cycle = 0; cycle < bases.length; cycle++) {
System.out.print((char) bases[cycle]);
}
System.out.println();
for (int cycle = 0, offset = (int) context.getPosition(); cycle < bases.length; cycle++, offset++) {
for (int cycle = 0, offset = (int) context.getPosition() - 1; cycle < bases.length; cycle++, offset++) {
byte compBase;
switch (contig[offset]) {
case 'A':
case 'a': compBase = 'A'; break;
case 'C':
case 'c': compBase = 'C'; break;
case 'G':
case 'g': compBase = 'G'; break;
case 'T':
case 't': compBase = 'T'; break;
default: compBase = '.'; break;
}
System.out.print((char) compBase);
}
System.out.println("\n");
}
for (int cycle = 0, offset = (int) context.getPosition() - 1; cycle < bases.length; cycle++, offset++) {
byte compBase;
switch (contig[offset]) {