LaraFuhrmann
LaraFuhrmann
Thank you very much for your response. Would you agree that our best course of action would be to provide our end-users with the caveat that ``` - In the...
> What you describe is NOT what bcftools consensus does. Are you referring to our first or second point? > The program takes the first variant and uses that. Just...
> The record that comes first in the VCF is always applied, regardless of coverage. By record you are referring to the rows of the vcf-file? If there are two...
Seems like it is in the master. I was not aware of that.
Tested VILOCA on the hiv-tutorial data `CAP188 4` using the following config files to test uniform-tiling strategy and amplicon tiling strategy. ``` general: virus_base_config: "" aligner: bwa snv_caller: viloca input:...
I added a README to this branch for the global haplotype reconstruction study. This should not cause any problems.
I added clearer links to the tutorials, and made a subsection Tutorials as requested by the reviewer.
I see - thanks a lot for the explanation :) I was able to implement a custom version of `np.put_along_axis` using the index update operators as you suggested. Thanks again!
As there is some interest in this custom version that I am using for my problem, I am sharing the code here: (Happy to any suggestions on how to solve...
Now we are adding the smallgenomeutilities scritp to merge the paried-end reads into one read. This is since viloca can then be applied to the merged reads with longer local...