Torsten Seemann

Some relevant discussion here? https://bioinformatics.stackexchange.com/questions/5427/double-counting-coverage-of-overlapped-read-pairs

> And if they do overlap, this further support the fact that these reads come from the same > template. Including both reads in the counts does not make biological...

What happens if there is a SNP in the overlapping section ie. a disagreement at one position ?

In the meantime, I have written a simple but useful standalone Perl script (core only) https://github.com/tseemann/samclip ``` SYNOPSIS Filter SAM file for soft & hard clipped alignments AUTHOR Torsten Seemann...

@eoziolor there might be some bugs with edge effects; I currently allow soft clipping at contig boundaries?

FIrstly, I am not an expert here, but I notice your interval `536881483..536881484` is only 2 bp long. I also notice `samtools index -c` has an option `-m` to do...

Can this be detected with the `getrlimit` system call? http://man7.org/linux/man-pages/man2/setrlimit.2.html ``` RLIMIT_NOFILE Specifies a value one greater than the maximum file descriptor number that can be opened by this process....

This may also be a problem for the threads `-@ N` option. Last night I helped a student whose supercomputer head node had a really low "number of processes" limit...

I've just realised Finch does something like this already https://github.com/onecodex/finch-rs

Why do you say "whereas I should have 0.295981" ? Perhaps try `fastANI`? https://github.com/ParBLiSS/FastANI ``` % seqkit stat genome?.txt file format type num_seqs sum_len min_len avg_len max_len genome1.txt FASTA DNA...