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parameterized a bit more 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@877 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kcibul 2009-06-02 17:58:26 +00:00
parent 587d07da00
commit ad5b057140
1 changed files with 19 additions and 14 deletions
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33
java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticMutationWalker.java
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@ -65,6 +65,20 @@ public class SomaticMutationWalker extends LocusWalker<Integer, Integer> {
@Argument(fullName = "normal_sample_name", shortName = "s2", required = true, doc="Name of the normal sample")
public String normalSampleName;
@Argument(fullName = "tumor_lod", required = false, doc = "LOD threshold for calling tumor variant")
public float TUMOR_LOD_THRESHOLD = 6.3f;
@Argument(fullName = "normal_lod", required = false, doc = "LOD threshold for calling normal non-variant")
public float NORMAL_LOD_THRESHOLD = 2.3f;
@Argument(fullName = "min_mutant_sum", required = false, doc = "threshold for sum of mutant allele quality scores")
public int MIN_MUTANT_SUM = 100;
@Argument(fullName = "output_failures", required = false, doc="produce output for failed sites")
public boolean OUTPUT_FAILURES = false;
public boolean bedOutput = true;
public void initialize() {
@ -79,18 +93,9 @@ public class SomaticMutationWalker extends LocusWalker<Integer, Integer> {
public static int MAX_INSERT_SIZE = 10000;
public static int MIN_MUTANT_SUM_PRETEST = 60;
public static int MIN_MUTANT_SUM = 100;
public static int MIN_QSCORE = 13;
// public static double TUMOR_LOD = 6.3d;
public static double TUMOR_LOD = 4.0d;
public static double NORMAL_LOD = 2.3d;
private String cachedContigName;
private byte[] cachedContig;
private boolean outputFailures = true;
private static class LocusReadPile {
private char refBase;
@ -257,7 +262,7 @@ public class SomaticMutationWalker extends LocusWalker<Integer, Integer> {
int mutantSum = tumorReadPile.qualitySums.get(altAllele);
int refSum = tumorReadPile.qualitySums.get(ref);
if (tumorReadPile.getAltVsRef(altAllele) >= TUMOR_LOD
if (tumorReadPile.getAltVsRef(altAllele) >= TUMOR_LOD_THRESHOLD
// ||
// (mutantSum >= MIN_MUTANT_SUM && (float)mutantSum / (float) refSum >= 0.05f)
) {
@ -299,8 +304,8 @@ public class SomaticMutationWalker extends LocusWalker<Integer, Integer> {
// at least 100 or the LOD score for mutant:ref + mutant:mutant vs ref:ref must
// be at least 6.3;
double tumorLod = t2.getAltVsRef(altAllele);
if (t2.qualitySums.get(altAllele) < MIN_MUTANT_SUM && tumorLod < TUMOR_LOD) {
if (outputFailures) {
if (t2.qualitySums.get(altAllele) < MIN_MUTANT_SUM && tumorLod < TUMOR_LOD_THRESHOLD) {
if (OUTPUT_FAILURES) {
System.out.println("FAILED " + context.getContig() + ":" + context.getPosition() + " due to MAX MM QSCORE TEST." +
" LOD was " + tumorReadPile.getAltVsRef(altAllele) +
" LOD is now " + t2.getAltVsRef(altAllele) +
@ -316,7 +321,7 @@ public class SomaticMutationWalker extends LocusWalker<Integer, Integer> {
disaligner(context.getPosition(), tumorReadPile, StringUtil.bytesToString(refSeq.getBases()), refStart);
if (shouldDisalign) {
if (outputFailures) {
if (OUTPUT_FAILURES) {
System.out.println("FAILED " + context.getContig() + ":" + context.getPosition() + " due to DISALIGNMENT TEST.");
}
continue;
@ -330,7 +335,7 @@ public class SomaticMutationWalker extends LocusWalker<Integer, Integer> {
// (ii) the quality score sum for the mutant base in the normal must be < 50 and the
// LOD score for ref:ref vs mutant:ref + mutant:mutant must be at least 2.3.
double normalLod = normalReadPile.getRefVsAlt(altAllele);
if ( normalReadPile.qualitySums.get(altAllele) > 50 || normalLod < NORMAL_LOD ) {
if ( normalReadPile.qualitySums.get(altAllele) > 50 || normalLod < NORMAL_LOD_THRESHOLD) {
continue;
}