Removed redundant IOUtil.openFileForWriting() calls for the fastq writers.
Moved the test for duplicate @PD.IDs into AbstractAlignmentMerger to avoid opening the unmapped SAM file twice.
Merge pull request #66 from broadinstitute/tf_streaming_mergebam

Moved the test for duplicate @PD.IDs into AbstractAlignmentMerger to avo...
Merge pull request #65 from broadinstitute/tf_samtofastq_singleopen

Removed redundant IOUtil.openFileForWriting() calls for the fastq writer...