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pushing up to test on unix box 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1101 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kcibul 2009-06-25 19:00:48 +00:00
parent 0d9041380d
commit 11d83ac7d0
1 changed files with 7 additions and 6 deletions
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13
java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticMutationWalker.java
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@ -81,7 +81,7 @@ public class SomaticMutationWalker extends LocusWalker<Integer, Integer> {
@Argument(fullName = "mode", required = false, doc="Mode of operation (detect, full)") @Argument(fullName = "mode", required = false, doc="Mode of operation (detect, full)")
public String mode = "full"; public String mode = "full";
public float SKEW_LOD_THRESHOLD = 1.0f; public float SKEW_LOD_THRESHOLD = 1.5f;
// @Argument(fullName = "output_failures", required = false, doc="produce output for failed sites") // @Argument(fullName = "output_failures", required = false, doc="produce output for failed sites")
public boolean OUTPUT_FAILURES = true; public boolean OUTPUT_FAILURES = true;
@ -432,8 +432,8 @@ public class SomaticMutationWalker extends LocusWalker<Integer, Integer> {
if (mode.equals("full") && failureReason.first != null) { if (mode.equals("full") && failureReason.first != null) {
if (OUTPUT_FAILURES) { if (OUTPUT_FAILURES) {
String msg = "FAILED due to " + failureReason.first.name() + String msg = "FAILED due to " + failureReason.first.name() +
"mutAllele_" + altAllele + "_" + " mutAllele " + altAllele + "_" +
"maxSkewLod_" + failureReason.second " maxSkewLod " + failureReason.second
; ;
out.println( out.println(
@ -534,13 +534,14 @@ public class SomaticMutationWalker extends LocusWalker<Integer, Integer> {
//chr17:4979257 //chr17:4979257
// are the two alleles distributed differently // are the two alleles distributed differently
//fixme: calculate this range properly
//fixme: this seems to degrade as you lose reads? //fixme: this seems to degrade as you lose reads?
//fixme: what should the threshold be here? //fixme: what should the threshold be here?
SortedMap<Integer, Double> skewLodOffsets = new TreeMap<Integer, Double>(); SortedMap<Integer, Double> skewLodOffsets = new TreeMap<Integer, Double>();
double maxSkewLod = 0; double maxSkewLod = 0;
for(int offset=-76; offset<76; offset++) { //fixme: calculate this range properly
int MAX_OFFSET_DISTANCE = 60;
for(int offset=-1 * MAX_OFFSET_DISTANCE; offset<MAX_OFFSET_DISTANCE; offset++) {
// allow for doubletons // allow for doubletons
if (offset >= -1 && offset <= 1 ) { continue; } if (offset >= -1 && offset <= 1 ) { continue; }
@ -555,6 +556,7 @@ public class SomaticMutationWalker extends LocusWalker<Integer, Integer> {
double skewLod = Math.log10( (1-J) / J); double skewLod = Math.log10( (1-J) / J);
// fixme: is it legit to require that we see it in at least 2 reads each?
int mutantReadCounts = mutantPile.getLocusBases(offset).length(); int mutantReadCounts = mutantPile.getLocusBases(offset).length();
int otherReadCounts = refPile.getLocusBases(offset).length(); int otherReadCounts = refPile.getLocusBases(offset).length();
if (mutantReadCounts >= 2 && otherReadCounts >= 2) { if (mutantReadCounts >= 2 && otherReadCounts >= 2) {
@ -562,7 +564,6 @@ public class SomaticMutationWalker extends LocusWalker<Integer, Integer> {
if (skewLod > maxSkewLod) { maxSkewLod = skewLod; } if (skewLod > maxSkewLod) { maxSkewLod = skewLod; }
if (skewLod > SKEW_LOD_THRESHOLD) { if (skewLod > SKEW_LOD_THRESHOLD) {
// fixme: is it legit to require that we see it in at least 2 reads each?
// System.out.println( "Offset: " + offset + // System.out.println( "Offset: " + offset +
// " mutant_reads: " + mutantReadCounts + // " mutant_reads: " + mutantReadCounts +
// " mutant bases: " + mutantPile.getLocusBases(offset) + // " mutant bases: " + mutantPile.getLocusBases(offset) +