Issue with complement_map dict when using Broad GRCh38 reference

[jmlivingstone]

Hello,

I am having an issue running reditools.py with the Broad version of the GRCh38 fasta file.
I noticed that there are non-ACGT nucleotide symbols within this reference file, so the complement_map function throws an error when it encounters these symbols
Traceback (most recent call last):
File "/reditools2.0/src/cineca/reditools.py", line 1374, in
analyze(options)
File "/reditools2.0/src/cineca/reditools.py", line 1133, in analyze
column = get_column(pos_based_read_dictionary, reads, splice_positions, last_chr, omopolymeric_positions, target_positions, i)
File "/reditools2.0/src/cineca/reditools.py", line 289, in get_column
ref = complement(ref)
File "/reditools2.0/src/cineca/reditools.py", line 1190, in complement
return complement_map[b]
KeyError: 'R'

I believe the solution is to update the dictionary as such to map the non ACTG symbols to 'N'
complement_map = {"A":"T", "T":"A", "C":"G", "G":"C", "R":"N", "Y":"N", "K":"N", "M":"N", "S":"N", "W":"N", "B":"N"}

One specific co-ordinate you can test this failure on is chr17:489373

Thank you,
Julie