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Maybe one code bug with GATK 3.7

ZexuanZexuan JiangsuChinaMember

@valentin @Geraldine_VdAuwera
I had transform some code from JAVA to C in HaplotypeCaller step 2 ;
CommonSuffixSplitter.java
before
if ( prefixV == null ) {
// this node is entirely explained by suffix
incomingTarget = suffixV;
} else {
incomingTarget = prefixV;
graph.addVertex(prefixV);
graph.addEdge(prefixV, suffixV, new BaseEdge(out.isRef(), 1));
edgesToRemove.add(out);
}
after
if ( prefixV == null ) {
// this node is entirely explained by suffix
incomingTarget = suffixV;
edgesToRemove.add(out);
} else {
incomingTarget = prefixV;
graph.addVertex(prefixV);
graph.addEdge(prefixV, suffixV, new BaseEdge(out.isRef(), 1));
edgesToRemove.add(out);
}
right ?

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