Pierre Lindenbaum

Thank you for the bug report. I think I found my error. Can you please test my latest commit please ?

> hard clipping seems incorrect @yliueagle well, I didn't want to count the hard+soft clipping in the count of bases. I've just added a new option `--clip` to count them....

@yliueagle i saw your mail. Sorry, I don't have the time to explore this for now.

@PAMorin I'm sorry I think I don't really understand the problem. How about using a regular expression like `(scaffold_1|scaffold_2|scaffold_3|scaffold_4|scaffold_5|scaffold_10)` ?

> E.g. same basic behaviour as with DNA alphabet reference and NGS input, but with a protein alphabet and peptide input. Hum I doubt it will work. jvarkit uses the...

> It can be fixed thank you for the bug report. Feel free to submit a pull request to fix this.

I wrote this for a colleagues years ago. As far as I understand my program only handled bases with one character only. Give me a few minutes, I'll update the...

@vicruiser i pushed https://github.com/lindenb/jvarkit/commit/c81f95bf192fd12ecc81a6b9ea159d419cd91caa , please tell me if that works. Please not for this kind of deletion T/TA I didn't look at the POS in the VCF. But in...

@vicruiser Hi again, Thanks for the report, I'll check this tomorrow (18H43 here)

handling DEL or INS is quite difficult for me now. There was a bug because I just use one character to get the reference allele. As a quick fix, The...