Dario Beraldi

@marcelm Ok, thanks for replying. In principle, I would prefer tabular data to have complete rows - I think it makes processing neater also if one wants to load the...

Hi- thanks for reporting the issue. I'm pretty sure this is due to tabix index failing with chromosomes larger than 512MB. One should work with CSI indexes instead for both...

Hi- There may be something odd with your alignments. First thing I would try to do is to reindex the bam files with e.g. `samtools index bamsource/2A/16NASWI0308.bam` It may be...

Hi- Thanks for your interest and for the PR! Indeed, the main problem here is that the message is cleared shortly after it is printed. It's no big deal, but...

Hello- A couple of things... For looping over a number of regions consider using the `-b/--batch` option, see an example [here] (ttp://asciigenome.readthedocs.io/en/latest/examples.html#batch-and-non-interactive-mode). This is faster than re-starting ASCIIGenome from scratch...

Hi again- you can separate commands with the `&&` syntax (like in Unix), e.g.: ``` ASCIIGenome -x 'orderTracks PEO1 PEO4 && colorTrack blue PEO1 && trackHeight 10 DMF' ... ```...

Hi- thanks for feedback! The list of sequence names can be printed with `showGenome`, from there you can copy & paste the desired chromosome. The autocompletion is possible but I'm...

Hi- `fastaRegexFinder` uses the standard [re](https://docs.python.org/3/library/re.html) package for parsing regular expressions and I don't think it supports fuzzy matches. However, I may have a look at replacing the re package...

Hi- See if this helps https://github.com/mskcc/facets/issues/66 About the workings of facets package, you may get better answers by asking at https://github.com/mskcc/facets. My program, `cnv_facets.R`, is just a convenient wrapper around...

Thanks - I'll keep this in mind but for now I may leave it to the user to prepare the desired file for IGV.