Comments (2)
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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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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