coverage_file documentation

[multimeric]

Hi, I'm just a trying to understand the --coverage_file parameter. I suppose that it sets the parameters of the distribution defined by --coverage, but I don't understand the format of the file. I suppose each line will relate to one genome?

In addition, I'm interested if InSilicoSeq can handle something like a BED file of regions so that I can customize the coverage on a per-region basis within one single genome.

[cilliannolan]

I am also interested in using InSilicoSeq to simulate genomes with coverage dependent on the region, and would like to know more about the --coverage_file parameter.

[multimeric]

I've had a dig into the source code, which says:

InSilicoSeq/iss/abundance.py

Lines 16 to 19 in 52ad1fb

	The abundance/coverage file is a flat file of the format
	"genome_id<TAB>abundance"
	or
	"genome_id<TAB>coverage"

So if you have only one genome, you will have a file such as:

some_genome    50

[HadrienG]

Hi folks!

using a bed file is a good idea, but I don't have much time to add new functionality at the moment. I'll definitely put it on the wishlist though!

Concerning the --coverage_file option, I tried to clarify how it works in the documantation.

Best,
Hadrien

[multimeric]

Thanks for documenting this! Since the issue was about documentation I'll close it now. Unfortunately I don't think I have time to add the per-region coverage feature either, but it certainly would be nice at some point.