Running HG38 and other bugs in the code

[vaksmaz]

Hi,

I am trying to run your code and am having too many issues. For many of the issues I am changing the code to run more smoothly. But there are a bunch of errors.

1. HG19 is hard-coded, can you make it accessible with HG38? - I am coding part of this in but it's better if you do this since you are more familiar with the code.
2. The chromosome:locus info does not match the test file. (you need a chr, which I added)
3. The output folders and data input folders don't match. To get it to work you have to place the bam files into the output folder, and some of the other files. In short, paths need to be fixed.
4. There are many more issues that I am recoding, including the actual comparison (the math). Can you check that the code is actually doing the comparison correctly. I will test if it translates to HG38 the same way, with the alt alignment HLA chrom.

Are you guys still up keeping the code?