Mikhail Karasikov

Please apply [.clang-format](https://github.com/ratschlab/metagraph/blob/master/metagraph/.clang-format) or make it more or less consistent with the code style in the rest of the codebase.

Hi Moustafa, There is a package with a snakemake workflow for constructing annotated graphs. https://metagraph.ethz.ch/static/docs/workflows.html Hope that helps. Let me know if you have any questions regarding it.

Ah, yeah. The Snakemake scripts were indeed written before we added indexing of counts. I recommend using the main tool for the time being. You can find many useful example...

Exactly, this is done in this step: https://github.com/ratschlab/counting_dbg/blob/master/scripts.md#prepare-and-build-graph 1. Build sample (weighted) graphs 2. Extract contigs from each 3. Build a joint graph from all these contigs (build canonical ->...

Hi Joe, can you try again? Sometimes the download limit on Google Drive is exceeded and then it recovers in a day or so. Hope it helps.

Hi Pierre, As we've already briefly discussed this on e-mail, I'm just going to summarize the answer here. The graph itself can be constructed from multiple files -- simply pipe...

Is this ready for review?

Could you add a test where it builds one graph, kills the process, so it fails to build to the end. Then it does the same thing for a different...

It's better to have non-deterministic tests than no tests. The expected result is well determined. The second run of metagraph started after a previous run that was killed, must construct...

> A test that sometimes passes and sometimes not is harmful. I agree that we should never write such tests. But I don't get what does it have to do...