show-snps can't handle whitespace in delta file path
not-a-feature opened this issue · 0 comments
not-a-feature commented
Problem
If the delta-file, created with nucmer, contains a whitespace in the reference path, show-snps will throw the error
ERROR: Could not parse delta file, /path/with/a/white space/out.delta
error no: 400
and abort.
The header of the delta file looks as follows:
/path/with/a/white space/Pseudomonas_aeruginosa_PAO1.fasta /path/with/a/white space/scaffolds.5000.fasta
NUCMER
>gi|110645304|ref|NC_002516.2| NODE_1_length_2076507_cov_34.010685 6264404 2076507
[...]
Workaround
Move everything to a path without a whitespace.
This is somehow related to #70