BenLangmead / bowtie

An ultrafast memory-efficient short read aligner
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The -m option only results in some "many mapped" reads being supressed #94

Open Riptides opened 5 years ago

Riptides commented 5 years ago
bowtie \
    -v 0 \
    -a \
    -m 20 \
    --threads ${THREADS} \
    --max ${MANY} \
    -f \
    --un ${UNMAPPED} \
    ${REF} \
    ${FASTA} \
    > ${OUTFILE}

From my understanding, the above command should output all reads that align perfectly more than 20 times to ${MANY} and output all perfect alignments for reads that align 20 or fewer times to ${OUTFILE}. I am finding multiple instances, however, where a read will have over 20 perfect alignments reported in ${OUTFILE} and not be listed in ${MANY}.

Is this a bug or is my understanding of the flags incorrect?

Tested with both 1.2.2 and 1.2.3