Missing tmap and refmap files

gpertea / gffcompare

classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF

MIT License

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Missing tmap and refmap files #43

Closed fgypas closed 4 years ago

fgypas commented 4 years ago

I tried version 0.11.2 (from anaconda) and 0.11.4 (precompiled binary) as following:

gffcompare \
-r reference.gtf \
-s .genome.fa \
-o prefix \
merged_annotation.gtf

where merged_annotation.gtf is the output of stringtie merge. After this run I get the following files:

.tracking
.annotated.gtf
.loci
.stats

but I am missing the .tmap and .refmap

Am I doing something wrong?

Thank you in advance Foivos

fgypas commented 4 years ago

OK, I just saw #8

gpertea commented 4 years ago

Indeed, that was the problem - I cannot guarantee the uniqueness of the per-sample output files when multiple "query" samples are provided, unless I write them into their original directories..

Also, please use the latest binary precompiled version (or compile the latest released version from source, if you prefer) as there could be sometimes bugs that I fix and then I immediately release the new version, while the anaconda version usually lags behind and could be the "buggy" one that I just fixed (duh).