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)