Shaun Jackman

> Gziped SAM files are supported, but without piping. Good to know!

Gzipped BAM file? 😈 (just kidding, please don't)

Actually a little-known fact that I've actually found really useful is that a BAM file *is* a gzip file. You can `gunzip -c` a BAM file to get an uncompressed...

This Canu unitigs graph reproduces the segmentation fault: [canu.unitigs.gfa.gz](https://github.com/lh3/gfa1/files/2295658/canu.unitigs.gfa.gz)

Backtrace ``` 0 gfaview 0x000000010377f3f6 gfa_arc_rm + 102 (gfa.c:587) 1 gfaview 0x000000010377eea5 gfa_cleanup + 21 (gfa.c:600) 2 gfaview 0x000000010377ea76 gfa_read + 854 (gfa.c:11) 3 gfaview 0x0000000103783111 main + 609 (gfaview.c:91)...

This segmentation fault is caused by an overlap that is larger than the adjacent segment size. I've opened PR #5 to fix this issue.

Yeah, I look into circlator too, and came to the same conclusion. I checked and my genome does not start with a coding gene, a tRNA I think (I could...

The last time `sjackman/prokka` was built was [over a year ago](https://hub.docker.com/r/sjackman/prokka/builds/). I'll rebuild it now. That should hopefully fix your issue, since it's already resolved in the parent image.

One fix is to upload a copy of the tarball, if you can find one, to some other server (like Bintray) and edit the formula to use that mirror.

It looks like `infernal` has moved to http://eddylab.org/software/infernal/infernal-1.1.1.tar.gz