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gatk-3.8
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Optionally computes the error rate using the best base and a random base. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1991 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2009-11-08 16:47:34 +00:00
parent 567f5758d2
commit 95d381efe2
1 changed files with 9 additions and 2 deletions
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11
java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadErrorRateWalker.java
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@ -20,6 +20,7 @@ import java.util.Random;
public class ReadErrorRateWalker extends ReadWalker<boolean[], int[]> {
@Argument(fullName="printVisualHits", shortName="v", doc="print visual hits", required=false) public boolean printVisualHits = false;
@Argument(fullName="useNextBestBase", shortName="nb", doc="use next best base", required=false) public boolean useNextBestBase = false;
@Argument(fullName="useNonNextBestBase",shortName="nnb",doc="use nonnext best base",required=false) public boolean useNonNextBestBase = false;
@Argument(fullName="useNextRandomBase", shortName="nr", doc="use next random base", required=false) public boolean useNextRandomBase = false;
/**
@ -29,7 +30,7 @@ public class ReadErrorRateWalker extends ReadWalker<boolean[], int[]> {
* @return true if the read can be processed, false if it should be ignored
*/
public boolean filter(char[] ref, SAMRecord read) {
return (read.getCigar().numCigarElements() == 1 && read.getReadLength() <= ref.length);
return (read.getCigar().numCigarElements() == 1 && read.getReadLength() <= ref.length && (!useNonNextBestBase || read.getAttribute("SQ") != null));
}
/**
@ -68,10 +69,16 @@ public class ReadErrorRateWalker extends ReadWalker<boolean[], int[]> {
byte compBase = convertIUPACBaseToSimpleBase((byte)ref[cycle]);
if (compBase != '.') {
if (useNextBestBase || useNextRandomBase) {
if (useNextBestBase || useNextRandomBase || useNonNextBestBase) {
byte nextBestBase;
if (useNextBestBase) {
nextBestBase = (byte) BaseUtils.baseIndexToSimpleBase(QualityUtils.compressedQualityToBaseIndex(sq[cycle]));
} else if (useNonNextBestBase) {
nextBestBase = bases[cycle];
Random generator = new Random();
while (nextBestBase == bases[cycle] || nextBestBase == (byte) BaseUtils.baseIndexToSimpleBase(QualityUtils.compressedQualityToBaseIndex(sq[cycle]))) {
nextBestBase = (byte) BaseUtils.baseIndexToSimpleBase(generator.nextInt(4));
}
} else {
nextBestBase = bases[cycle];
Random generator = new Random();