Corrupted output if decontaminating more than one sample using Python API

bede / hostile

Precise host read removal

MIT License

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Corrupted output if decontaminating more than one sample using Python API #25

Closed bede closed 1 year ago

bede commented 1 year ago

gen_clean_cmd() and gen_paired_clean_cmd() both mutate Aligner.cmd and Aligner.paired_cmd, and since Aligner is instantiated once, templating fails after processing the first fastq / pair of fastqs leading to corruption of the output of subsequent samples when using the Python API. Templating should not mutate Aligner instance. Needs tests for single and paired reads.

bede commented 1 year ago

Fixed in 50b9f531f93401c09fcbdbc79738999e5f684e22 / 0.1.0