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Permit retrieval of read names for debugging purposes 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5011 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
fromer 2011-01-18 16:09:34 +00:00
parent f8ba76d87c
commit 4bec93e3e4
1 changed files with 8 additions and 5 deletions
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13
java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/ReadBasedPhasingValidationWalker.java
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@ -175,9 +175,12 @@ public class ReadBasedPhasingValidationWalker extends RodWalker<Integer, Integer
buildReads.updateBases(1, readBases); buildReads.updateBases(1, readBases);
List<PhasingRead> reads = new LinkedList<PhasingRead>(); List<PhasingRead> reads = new LinkedList<PhasingRead>();
for (PhasingRead rd : buildReads) { for (Map.Entry<String, PhasingRead> readEntry : buildReads.entrySet()) {
if (rd.getNonNullIndices().length == NUM_IN_PAIR) // only want reads with BOTH bases called [possibly as deleted ("D")] PhasingRead rd = readEntry.getValue();
if (rd.getNonNullIndices().length == NUM_IN_PAIR) { // only want reads with BOTH bases called [possibly as deleted ("D")]
reads.add(rd); reads.add(rd);
logger.debug("Read name: " + readEntry.getKey() + "\trd: " + rd);
}
} }
// Count the occurence of each "haplotype": // Count the occurence of each "haplotype":
@ -339,7 +342,7 @@ class SiteGenotypeAndReads {
} }
} }
class PhasingReadList implements Iterable<PhasingRead> { class PhasingReadList {
private Map<String, PhasingRead> readsAtSites = null; private Map<String, PhasingRead> readsAtSites = null;
private int numSites; private int numSites;
@ -366,8 +369,8 @@ class PhasingReadList implements Iterable<PhasingRead> {
} }
} }
public Iterator<PhasingRead> iterator() { public Set<Map.Entry<String, PhasingRead>> entrySet() {
return readsAtSites.values().iterator(); return readsAtSites.entrySet();
} }
public int size() { public int size() {