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Active regions that don't contain any usable reads should just be ski…

…pped over instead of throwing an IllegalStateException.
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1 parent 2a7af43 commit 069759477867237557a873f2f744e8fe8cb6e2f1 @rpoplin rpoplin committed Mar 4, 2013
@@ -136,7 +136,7 @@ protected void createDeBruijnGraphs( final List<GATKSAMRecord> reads, final Hapl
graphs.clear();
final int maxKmer = ReadUtils.getMaxReadLength(reads) - KMER_OVERLAP - 1;
- if( maxKmer < MIN_KMER ) { throw new IllegalStateException("Reads are too small for use in assembly."); }
+ if( maxKmer < MIN_KMER ) { return; } // Reads are too small for assembly so don't try to create any assembly graphs
// create the graph for each possible kmer
for( int kmer = maxKmer; kmer >= MIN_KMER; kmer -= GRAPH_KMER_STEP ) {

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