Closed tsnowlan closed 4 years ago
For the sake of completeness, from example/conf.toml
:
using bad_conf.txt (github doesn't like .toml extension)
~/vcfanno$ vcfanno -base-path example -lua custom.lua example/bad_conf.txt example/query.vcf.gz
=============================================
vcfanno version 0.3.2 [built with go1.13.1]
see: https://github.com/brentp/vcfanno
=============================================
ERROR: can't find query file: example/example/query.vcf.gz
closed in #119
Related to: #82
Config and files used are arbitrary, just make a typo in the path for
file
in config toml and-base-path
.When attempting to open a Source file, the basepath is prepended twice. The first time in Sources, the next time in Flatten. This causes the error string to be
[Flatten] unable to open file: basepath/basepath/filename in basepath
. which implies that the basepath string was doubled somewhere rather thanbasepath/filename
also not existing.PR incoming with proposed fix.
If you have encountered an error, please include: