Ben J Woodcroft

Thanks for the interest. Those are 2 definitions which don't rely on mapping though. Can't you just use mean or trimmed mean coverage as already implemented? Seems like mapping or...

I'm reasonably sure that is the same thing as mean coverage, if you are only counting the bits of the reads which map. The genome size isn't actually needed as...

Thanks Alex, much appreciated for the bug and the kind words. I think this is really an issue with count, not with non-mean methods, agree? What would be a good...

Hi, Sure, it is just based on NM tags plus lengths of the read etc. The cigar string cannot be reliably used for %ID because mapping software often does not...

Hi, Thanks for the kind words. I keep finding little things to fix. At a minimum, would want to update the bird tool utils dep and so change to newest...

Hi @jianshu93 right, I agree. I had considered this, but I had thought that the opening of the BAM file could not be done multiple times? This is especially true...

Thanks both, yeh gene-wise abundance is tracked in https://github.com/wwood/CoverM/issues/16 but there hasn't been much movement there for a while, it seems. @rhysnewell do you have some sense of how fast...

Hi, > When testing I looked a bit at samples with low mapping% and noticed that setting --min-covered-fraction 0 changed % reads mapped from 17% to 45% when using coverm...

Hi, I'm afraid there's not enough information here to know what the problem might be (other than what the error is suggesting). What command line did you use?

Hi, At the bottom of the log it suggests a pair of files have different numbers of reads to each other, when it is expecting the same number in each....