The run-depth-compiler.sh and run-genotype-compiler.sh scripts create TSV files that look something like this:
VIC10508
100 1
3292 1
101 1
The first row in this file consists of a tab followed by a column name. The column name is based on the name of another file. The code removes the suffix (".depth.tab" or ".filt.tab") from the other filename and uses that for a column name. For example VIC10508.depth.tab would be converted to VIC10508.
The run-depth-compiler.sh and run-genotype-compiler.sh scripts create TSV files that look something like this:
The first row in this file consists of a tab followed by a column name. The column name is based on the name of another file. The code removes the suffix (".depth.tab" or ".filt.tab") from the other filename and uses that for a column name. For example
VIC10508.depth.tab
would be converted toVIC10508
.While working on changes for issue https://github.com/wodanaz/Assembling_viruses/issues/25#issuecomment-788233739 I noticed that this code does not strip the trailing path. So a path like
/data/jpb/tmp.68LzubWRvd/VIC10508.depth.tab
would be converted to/data/jpb/tmp.68LzubWRvd/VIC10508
.Should we remove the directory from this column name as well?
Code that removes suffixes
https://github.com/wodanaz/Assembling_viruses/blob/a5dd984b82dca5da538210b64cfcf1a8fa912a10/scripts/run-depth-compiler.sh#L13
https://github.com/wodanaz/Assembling_viruses/blob/a5dd984b82dca5da538210b64cfcf1a8fa912a10/scripts/run-genotype-compiler.sh#L13