This PR replaces the existing read_bed_file function in vcftagprimersites.py with one which tries to make primer scheme processing more robust to format errors.
This assumes primer schemes conform to the format used in the nCov scheme. This is basically the standard BED format fields 1-4, plus a 5th field which is used for PoolName.
Main changes:
primer schemes now read into pandas dataframe
only the first five columns are read - replacing the old switch between old/new bed file format detection
type checks for fields, checks for null fields, checks for duplicate primer IDs
This PR replaces the existing
read_bed_filefunction invcftagprimersites.pywith one which tries to make primer scheme processing more robust to format errors.This assumes primer schemes conform to the format used in the nCov scheme. This is basically the standard BED format fields 1-4, plus a 5th field which is used for
PoolName.Main changes: