A question about index-genome

luckyzzr commented 4 years ago

I'm just getting into gene editing, and I'm interested in the tools you're developing. I ran into a problem when running the' index-genome 'function.

terminate called after throwing an instance of 'std::out_of_range' what(): basic_string::substr: __pos (which is 1) > this->size() (which is 0)

I checked the source suspected a problem here. https://github.com/pinellolab/CRISPRitz/blob/master/sourceCode/CRISPR-Cas-Tree/aho-Corasick.cpp

if ((i - (pamlimit - 1)) <= (l - (pamlen + max_bulges)))  //save the pam position only if possible for a guide to attach that position(avoid out of bound)
{
    indices_private.push_back(-(i - (pamlimit - 1)));
}

But I'm not so sure, so ask.

luckyzzr commented 4 years ago

Ok, so I've seen the effect of the minus sign. I'm not sure why it went wrong.

luckyzzr commented 4 years ago

I found the problem because the jupyter automatically creates a hidden folder under /hg38_ref.

pinellolab / CRISPRitz

A question about index-genome #2