SAM reader complains about SAM file with sequences not matching reference

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

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SAM reader complains about SAM file with sequences not matching reference #13

Closed mateiz closed 4 years ago

mateiz commented 12 years ago

This should be disabled when using a SAM for input to the aligner, because sometimes you want to pass an already-aligned database through SNAP, for example, to align the reads that didn't match the original DB.