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ch4rr0 avatar ch4rr0 commented on July 28, 2024

Hello @dominik-handler,

I committed an issue that I think fixes the issue. Here's the output from my test runs:

./bowtie-align-s -x indexes/e_coli reads/e_coli_1000.fq -m1 --best -S
# reads processed: 1000
# reads with at least one alignment: 699 (69.90%)
# reads that failed to align: 301 (30.10%)
# reads with alignments suppressed due to -m: 22 (2.20%)
Reported 677 alignments

./bowtie-align-s -x indexes/e_coli reads/e_coli_1000.fq -M1 --best -S
# reads processed: 1000
# reads with at least one alignment: 699 (69.90%)
# reads that failed to align: 301 (30.10%)
# reads with alignments sampled due to -M: 22 (2.20%)
Reported 699 alignments

Please let me know your thoughts on this.

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ch4rr0 avatar ch4rr0 commented on July 28, 2024

This change is now available in our latest release, v1.3.1. Feel free to reopen the issue if you feel like it has not been properly addressed.

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