map_kmers doesn't appear to be working on my branch and I'm out of ideas.
https://github.com/rarichards/bgwas3/blob/master/bgwas3/bgwas3.py#L480
It should output two files per iid: "_maps.tsv" and "_gene_info.tsv". Every gene info file output is empty. No error messages.
I think this command in map_kmers.py may be the problem. https://github.com/rarichards/bgwas3/blob/master/bgwas3/python/map_kmers.py#L202
e.g.
bedtools intersect -a results/AT_new_query.bed -b annotations/S02.bed -wb > results/AT_new_genes_in
There is the possibility that this is caused by an issue with input files (from ref2bed, bwa_index or annotate). I'll look more into that.
map_kmersdoesn't appear to be working on my branch and I'm out of ideas.https://github.com/rarichards/bgwas3/blob/master/bgwas3/bgwas3.py#L480
It should output two files per iid: "_maps.tsv" and "_gene_info.tsv". Every gene info file output is empty. No error messages.
I think this command in map_kmers.py may be the problem. https://github.com/rarichards/bgwas3/blob/master/bgwas3/python/map_kmers.py#L202
e.g.
There is the possibility that this is caused by an issue with input files (from
ref2bed,bwa_indexorannotate). I'll look more into that.