search

amplab / snap

Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data
https://www.microsoft.com/en-us/research/project/snap/
Apache License 2.0
288 stars 66 forks source link

TLEN should be 0 for paired reads where the ends map cross-chromosome #17

Closed bolosky closed 12 years ago

bolosky commented 12 years ago

The SAM spec limits the max value of TLEN, plus it doesn't really make sense to do what we're doing, since in the real world the genome isn't in a single address space, that's just internal to SNAP.

bolosky commented 12 years ago

This is fixed in 0.13.6 When read ends map to different chromosomes, TLEN will be 0 for both ends.