Handling of empty alignment

katholt / srst2

Short Read Sequence Typing for Bacterial Pathogens

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Handling of empty alignment #98

Closed andreas-wilm closed 3 years ago

andreas-wilm commented 6 years ago

Hello,

SRST2 (0.2.0) fails in a non-graceful way when none of the input reads map. Bowtie reports for example " 0 (0.00%) aligned concordantly exactly 1 time" and eventually you get "[main_samview] truncated file.". This looks like an unhandled error. In case you are wondering: yes, these are fringe cases with few reads as input.

Thanks, Andreas

andreas-wilm commented 6 years ago

Just to add to this: What ultimately fails is samtools view right after running bowtieand sorting the BAM file