Read length is not restricted to the set limit

[schmeing]

I run the simulation using the following commands:

./generate_reads.py -d -r ref.fa -a abundance.txt -o uniform-reads -t 18000000  -l 100 -i 164 -s 30
./trim_reads.pl -i reads1.fastq -f uniform-reads.1.fasta -o bear1.fq -r dri_read1.txt.per -q reads1.fastq.err.qual -m reads2.fastq.err.matr
./trim_reads.pl -i reads2.fastq -f uniform-reads.2.fasta -o bear2.fq -r dri_read2.txt.per -q reads2.fastq.err.qual -m reads2.fastq.err.matr

Looking at the cigar string of the mappings, the reason seems to be InDels that are inserted after the sequence was cut to the desired length:

66M1D33M
89M1I11M

If it helps I can supply the input files, but I assume this is general and not limited to those.

[sej917]

Oof, yes, this needs to be fixed. Back when I wrote BEAR, a million years ago, non-uniform read length distributions were a lot more common (at least with the folks I was working with), so this specific behaviour wouldn't really be noticeable. Clearly not the case these days.

if you wouldn't mind, could you supply the input files? Let's just limit it to the files for your second command. Your diagnosis is almost certainly correct, but I'd like to be 100% certain.

[schmeing]

Can you send me an email here, so I can reply with the download link, please?