post-processor for TopHat unmapped reads


tophat-recondition is a post-processor for TopHat unmapped reads (contained in unmapped.bam), making them compatible with downstream tools (e.g., the Picard suite, samtools, GATK) (TopHat issue #17). It also works around bugs in TopHat:

 * the "mate is unmapped" SAM flag is not set on any reads in the
   unmapped.bam file (TopHat issue #3)
 * the mapped mate of an unmapped read can be absent from
   accepted_hits.bam, creating a mismatch between the file and the unmapped
   read's flags (TopHat issue #16)

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