Bug in read generation with paired-end and coverage.
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#13 Bug in read generation with paired-end and coverage.
Hi.
I'm currently using grinder to do a benchmark of genome assemblies algorithms. And the generation of pairend-end reads (with a coverage of 10) sometimes bug, with a last read without it's mate (x/1 without x/2).
And this is not supported by some genome assemblies algo. I wrote a script in python to correct this if it appear, so it's not an hurry.
I think it's come from the coverage option: it check if the coverage is ok, and stop if it's the case, but don't check if their is the mate of the last read.
Expecting it's just an option I did not notice.
Have a nice day.
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Anonymous
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"Expecting it's just an option I did not notice."
Expecting it's NOT just an option I did not notice. ^^
Hi there!
Thanks a lot, I did not think about this potential issue before. This is now fixed in Grinder 0.5.4 and Grinder will always return complete mate pairs, no matter what -total_reads or -fold_coverage values were used.
Cheers, Florent