Andrea Telatin

Good to know :) Thanks for the prompt reply!

To clarify, you would need a `--extendReads INT` that will artificially count the read coverage from the read starting base to INT base downstream?

As an experimental feature, I added `--extendRead INT` in bamtocov today, that will artificially set the end of an alignment at (alignment start + INT) nucleotides (or the end of...

Generally speaking, the algorithm counts each read with the strand it is reported in the BAM file. There's no general reason to do otherwise, as some pair-ends might behave differently....

Hi @BharatRaviIyengar, thanks for the feedback. Can you provide a minimal example of the desired output and your `bedtools coverage` command to be able to test how that would work...

Is this related to #6, and specifically, are you interested in read counts (counting the number of reads mapped) in both issues rather than nucleotide coverage?

Ok, consider that `bamtocov` computes nucleotide coverage, while `bamtocounts` focuses on read counts on a target, and it has some options for normalization already built-in.

Nice, didn't notice that flag: ``` Traceback (most recent call last) /local/src/covtobed2.nim(254) covtobed2 /local/src/covtobed2.nim(229) main /root/.nimble/pkgs/hts-0.3.11/hts/bam.nim(373) open SIGILL: Illegal operation. ```

I'm sorry, gdb seems too complicated for me. `cov2bed2` is basically an empty script to read a BAM file, as I never tried htslib in the past (I was used...

Thanks for the quick reply. I used PyFastx 0.8.4. I tried both on `Python 3.6.9 |Anaconda, Inc.| (default, Jul 30 2019, 19:07:31), [GCC 7.3.0] on linux` under `Ubuntu 16.04.4 LTS`,...