tophat-recondition - 1.4-3 main

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)