6e394490cb1666c0d0f92ce2958c8c6dbb648d85,java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsTest.java,TraverseReadsTest,testUnmappedReadCount,#,192
Before Change
readSize);
SAMDataSource dataSource = null;
try {
dataSource = new SAMDataSource(TraversalEngine.unpackReads(bamList));
dataSource.viewUnmappedReads(true);
//dataSource.viewUnmappedReads(false);
}
After Change
ShardStrategy shardStrategy = ShardStrategyFactory.shatter(ShardStrategyFactory.SHATTER_STRATEGY.READS,
ref.getSequenceDictionary(),
readSize);
List<File> unpackedReads = null;
try {
unpackedReads = TraversalEngine.unpackReads(bamList);
}
catch (FileNotFoundException ex) {
throw new RuntimeException(ex);
}
SAMDataSource dataSource = new SAMDataSource(unpackedReads);
dataSource.viewUnmappedReads(true);
countReadWalker.initialize();