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Fixed IndexOutOfBounds error associated with tail merging. 

Don't expand out source nodes for tail merging, since that's a head merging action only.
This shows up as a bug only because we now allow merging tails against non-reference paths.
This commit is contained in:
Eric Banks 2014-07-16 23:14:33 -04:00 committed by David Roazen
parent 799071b520
commit 98d88eb07e
2 changed files with 8 additions and 6 deletions
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8
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/DanglingChainMergingGraph.java
View File

@ -448,18 +448,18 @@ public abstract class DanglingChainMergingGraph extends BaseGraph<MultiDeBruijnV
* The base sequence for the given path.
*
* @param path the list of vertexes that make up the path
* @param reverseIfSource if true and if we encounter a source node, then reverse the character sequence for that node
* @param expandSource if true and if we encounter a source node, then expand (and reverse) the character sequence for that node
* @return non-null sequence of bases corresponding to the given path
*/
@Ensures({"result != null"})
public byte[] getBasesForPath(final List<MultiDeBruijnVertex> path, final boolean reverseIfSource) {
public byte[] getBasesForPath(final List<MultiDeBruijnVertex> path, final boolean expandSource) {
if ( path == null ) throw new IllegalArgumentException("Path cannot be null");
final StringBuilder sb = new StringBuilder();
for ( final MultiDeBruijnVertex v : path ) {
if ( isSource(v) ) {
if ( expandSource && isSource(v) ) {
final String seq = v.getSequenceString();
sb.append(reverseIfSource ? new StringBuilder(seq).reverse().toString() : seq);
sb.append(new StringBuilder(seq).reverse().toString());
} else {
sb.append((char)v.getSuffix());
}

6
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/readthreading/DanglingChainMergingGraphUnitTest.java
View File

@ -174,8 +174,10 @@ public class DanglingChainMergingGraphUnitTest extends BaseTest {
v = graph.getNextReferenceVertex(v);
}
final String result = new String(graph.getBasesForPath(vertexes, false));
Assert.assertEquals(result, testString);
final String resultForTails = new String(graph.getBasesForPath(vertexes, false));
Assert.assertEquals(resultForTails, testString.substring(kmerSize-1));
final String resultForHeads = new String(graph.getBasesForPath(vertexes, true));
Assert.assertEquals(resultForHeads, "GTAAGGGCAATACTA"); // because the source node will be reversed
}
@DataProvider(name = "DanglingHeads")