Test fail but example runs

[Xavster838]

Hello, I was able to install your cactus-gfa-tools after upgrading my gcc to 10+. Make successfully ran and I added the directory to my $PATH. I also have all the dependencies requires (minimap2, gfatools, minigraph).

When I run the make test however, it is failing all tests, getting these errors:

not ok 2 - validator accepts minimap2 output because there are indels and no snps not ok 3 - reverse strand clip 1 produces valid paf not ok 4 - reverse strand clip 2 produces valid paf not ok 5 - validator accepts minimap2 output because there are indels and no snps not ok 6 - reverse strand clip 1 produces valid paf not ok 7 - reverse strand clip 2 produces valid pa Failed 6/7 subtests

However, when I run the example within the test subdirectory: making a gfa with minigraph, aligning an hg38 sequence and then generating a paf with mzgaf2paf, I'm not getting any errors. Can I trust this process. My goal is to produce a reliable PAF file from a GFA.

Thanks!

Some session info info:
minigraph version: 0.14-r415
gfatools version: 0.4-r179-dirty
minimap2 version: 2.24-r1122

[glennhickey]

Hard to say what's happening, though likely a problem with the tests rather than tools (all tests pass for me for what it's worth).

For the tests to run, you need cactus-gfa-tools in your PATH, and also you need to be able to run test/verify_matches.py -- so if you're python doesn't have the modules to run that, many tests will fail.