If novel_exons.gtf exists, still gets overwritten

[olgabot]

Description

With the --force flag, if novel_exons.gtf exists, then the exon finding step gets (correctly) skipped but then zero exons are written to novel_exons.gtf and whatever was there gets overwritten.

Steps to Reproduce

1. Interrupt outrigger index after creation of novel_exons.gtf file and re-runoutrigger index with the flag --resume Expected behavior: novel_exons.gtf to be read but not touched

Actual behavior: novel_exons.gtf was overwritten with an empty file.

2016-12-20 15:50:45     With the flag '--resume', Found an existing file containing novel exons,/home/obotvinnik/projects/singlecell_pnms/analysis/outrigger_v2/index/gtf/novel_exons.gtf, not re-calculating. To force overwriting, use the flag ''--force'.
2016-12-20 15:50:45     Writing 0 novel exons to /home/obotvinnik/projects/singlecell_pnms/analysis/outrigger_v2/index/gtf/novel_exons.gtf ...
2016-12-20 15:50:45             Done.

Versions

You can get this information from executing outrigger --version at the command line. Please include the OS (Operating System) and what version of the OS you're running.

$ outrigger --version
outrigger 1.0.0dev
$ uname --all
Linux tscc-login2.sdsc.edu 2.6.32-642.6.1.el6.x86_64 #1 SMP Wed Oct 5 00:36:12 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux