ernfrid
commented
8 years ago @IgorFobia – I'm going to leave this open. I think the request is reasonable and, while I can't say when I might get to it, I'd like to document it as a feature request.
Open IgorFobia opened 9 years ago
ernfrid
commented
8 years ago @IgorFobia – I'm going to leave this open. I think the request is reasonable and, while I can't say when I might get to it, I'd like to document it as a feature request.
IgorFobia
commented
8 years ago To be honest this was probably just my fault, not a bug. To check if it was really a bug, somebody should try to replicate it.
af8
commented
8 years ago I have the same issue. I would support the fact that it would be a great enhancement to be able to have all positions reported. This dramatically simplifies downstream analysis when you have several files containing information about these positions of interest. It's apparently a samtools feature (see https://github.com/samtools/samtools/issues/374) , samtools is not reporting positions with zero coverage.
It could be enough to have a switch like -a (--all) to specify that user wants a report on all positions he submitted.
jml96
commented
8 years ago Hi, I posted this issue in biostar today but then I realised that it was already reported here. Are you planning to add this option to the script? Thanks you!
iranmdl
commented
7 years ago Hello! Any update on this?
Hello,
I gave as an additional input a list of regions, each of those made by just one position (therefore start=end). I see the output does not include all those positions; I checked a missing one and I saw that there were no alignments mapping it. If this is the issue, I guess it should be still present in the output but with depth=0.
Thank you!