kmer.annotate.cits.sh hard-codes path to reference genome

[AmandaBirmingham]

The kmer.annotate.cits.sh script usage information states:

# The script requires two input arguments: 
# 1.) the bed file of truncations to work on 
# 2.) the fasta file of the genome used for alignment. This fasta file needs to be indexed with a "genome.fasta.fai" index file in the same directory. 
# Example usage: kmer.annotate.cits.sh my.truncations.bed genomes/genome.fasta

However, there are locations in the script (e.g., https://github.com/jaffreylab/miCLIP_MiMB_2016/blob/master/kmer.annotate.cits.sh#L15 , https://github.com/jaffreylab/miCLIP_MiMB_2016/blob/master/kmer.annotate.cits.sh#L19 ) at which the script ignores the input genome information and instead attempts to access a hard-coded path: /home/shareowner/genomes/human/all_chrom.fa . As one might imagine, this causes errors.

[jaffreylab]

Thanks for filing this! We indeed missed to update the hard-coded genome paths at these positions. Should be fixed now.