unmapped.bam lacks BAM flag 0x8 for read pairs where both mates are unmapped

[cbrueffer]

TopHat up to version 2.0.14 doesn't set the 0x8 (mate unmapped) flag for read pairs where both mates are unmapped. This causes downstream software, e.g., samtools merge to error on the data.

The bug can be reproduced by running TopHat on the test_data set from the TopHat tutorial (http://ccb.jhu.edu/software/tophat/downloads/test_data.tar.gz)

samtools view -f 0x8 unmapped.bam returns no output, where it should yield 16 reads with this bit set.

Running the tophat-recondition script from https://github.com/cbrueffer/tophat-recondition restores the missing flags.