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)