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Merge pull request #269 from broadinstitute/rp_minor_pruning_function_name 

Minor changes to docs in the graph pruning.
This commit is contained in:
Ryan Poplin 2013-06-11 08:24:56 -07:00
parent c7836ec746 58e354176e
commit 210007cd09
1 changed files with 8 additions and 4 deletions
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12
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/LowWeightChainPruner.java
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@ -80,7 +80,7 @@ public class LowWeightChainPruner<V extends BaseVertex, E extends BaseEdge> {
final Set<E> edgesToKeep = new LinkedHashSet<>(); final Set<E> edgesToKeep = new LinkedHashSet<>();
for ( final Path<V,E> linearChain : getLinearChains(graph) ) { for ( final Path<V,E> linearChain : getLinearChains(graph) ) {
if( mustBeKeep(linearChain, pruneFactor) ) { if( mustBeKept(linearChain, pruneFactor) ) {
// we must keep edges in any path that contains a reference edge or an edge with weight > pruneFactor // we must keep edges in any path that contains a reference edge or an edge with weight > pruneFactor
edgesToKeep.addAll(linearChain.getEdges()); edgesToKeep.addAll(linearChain.getEdges());
} }
@ -96,10 +96,14 @@ public class LowWeightChainPruner<V extends BaseVertex, E extends BaseEdge> {
} }
/** /**
* Get the maximum pruning multiplicity seen on any edge in this graph * Traverse the edges in the path and determine if any are either ref edges or have weight above
* @return an integer > 0 * the pruning factor and should therefore not be pruned away.
*
* @param path the path in question
* @param pruneFactor the integer pruning factor
* @return true if any edge in the path must be kept
*/ */
private boolean mustBeKeep(final Path<V,E> path, final int pruneFactor) { private boolean mustBeKept(final Path<V, E> path, final int pruneFactor) {
for ( final E edge : path.getEdges() ) { for ( final E edge : path.getEdges() ) {
if ( edge.getPruningMultiplicity() >= pruneFactor || edge.isRef() ) if ( edge.getPruningMultiplicity() >= pruneFactor || edge.isRef() )
return true; return true;