What does TopHat do with discordantly mapping PE reads?

[krobison]

What does TopHat do with discordantly mapping paired end reads -- either one read fails to align or the two cannot be aligned in a manner compatible with appropriate constraints (different chromosomes, wrong orientation on same chromosome, too far apart for intron size constraint)?

Also, a feature request: it would be useful if TopHat dumped a FASTQ file of reads it couldn't align. But, that's lazy me talking -- I'm writing an unaligned puller right now.