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Now handle the case where we don't actually SEE all of the positions. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@248 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
jmaguire 2009-04-01 19:50:07 +00:00
parent 675505646d
commit 4faacac315
1 changed files with 11 additions and 3 deletions
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14
java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java
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@ -356,6 +356,7 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
private String confident_ref_interval_start = ""; private String confident_ref_interval_start = "";
private double confident_ref_interval_LOD_sum = 0; private double confident_ref_interval_LOD_sum = 0;
private double confident_ref_interval_length = 0; private double confident_ref_interval_length = 0;
private int last_position_considered = -1;
private boolean inside_confident_ref_interval = false; private boolean inside_confident_ref_interval = false;
public String reduceInit() public String reduceInit()
@ -363,6 +364,7 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
confident_ref_interval_start = ""; confident_ref_interval_start = "";
confident_ref_interval_LOD_sum = 0; confident_ref_interval_LOD_sum = 0;
confident_ref_interval_length = 0; confident_ref_interval_length = 0;
last_position_considered = -1;
inside_confident_ref_interval = false; inside_confident_ref_interval = false;
return ""; return "";
} }
@ -371,17 +373,21 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
{ {
// Print RESULT data for confident calls // Print RESULT data for confident calls
if (inside_confident_ref_interval && (alleleFreq.lodVsRef > -5.0)) String[] tokens;
tokens = alleleFreq.location.split(":");
int current_offset = Integer.parseInt(tokens[1]);
if (inside_confident_ref_interval &&
((alleleFreq.lodVsRef > -5.0) || (current_offset != last_position_considered + 1)))
{ {
// No longer hom-ref, so output a ref line. // No longer hom-ref, so output a ref line.
String[] tokens;
tokens = confident_ref_interval_start.split(":"); tokens = confident_ref_interval_start.split(":");
String contig = tokens[0]; String contig = tokens[0];
int start = Integer.parseInt(tokens[1]); int start = Integer.parseInt(tokens[1]);
tokens = alleleFreq.location.split(":"); tokens = alleleFreq.location.split(":");
int end = Integer.parseInt(tokens[1])-1; int end = last_position_considered;
double lod = confident_ref_interval_LOD_sum / confident_ref_interval_length; double lod = confident_ref_interval_LOD_sum / confident_ref_interval_length;
@ -412,6 +418,8 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
confident_ref_interval_length = 1; confident_ref_interval_length = 1;
inside_confident_ref_interval = true; inside_confident_ref_interval = true;
} }
last_position_considered = current_offset;
if (alleleFreq.lodVsRef >= 5) { this.output.print(alleleFreq.asGFFString()); } if (alleleFreq.lodVsRef >= 5) { this.output.print(alleleFreq.asGFFString()); }
return ""; return "";