Banded alignment bug fix and multi-alignment

[jeizenga]

I believe this resolves #485, which was caused by an edge condition across node boundaries that I hadn't thought of. I have created a new unit test for this case. The PR also includes my multi-alignment code for the banded aligner, which I guess I hadn't PR'ed yet.

[jeizenga]

Actually, I did PR this #461. I don't know why those commits are showing up again. I probably Githubbed something wrong.

[ekg]

It may be because of the squash merge commit. I am not going to do that
more. To resolve it make sure to do a git rebase on master before branching
off again.

On Mon, Sep 26, 2016, 14:11 jeizenga notifications@github.com wrote:

Actually, I did PR this #461 #461. I
don't know why those commits are showing up again. I probably Githubbed
something wrong.

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[ekg]

There are still problems.

For instance, try "CAATTT" against this graph:

{"node": [{"sequence": "TA", "id": 72571}, {"sequence": "A", "id": 72572}, {"sequence": "G", "id": 72573}, {"sequence": "TTTG", "id": 72574}], "edge": [{"from": 72571, "to": 72572}, {"from": 72571, "to": 72573}, {"from": 72572, "to": 72574}, {"from": 72573, "to": 72574}]}

[ekg]

When aligning with bandwidth 1. I'll write a test case.

[ekg]

I get this error:

error:[BandedGlobalAligner] traceback stuck in insert row matrix interior
vg: src/banded_global_aligner.cpp:906: void vg::BandedGlobalAligner::BAMatrix::traceback_internal(vg::BandedGlobalAligner::BABuilder&, vg::BandedGlobalAligner::AltTracebackStack&, int64_t, int64_t, vg::BandedGlobalAligner::matrix_t, bool, int8_t*, int8_t*, int8_t, int8_t, bool, int8_t): Assertion `0' failed.

But, I can't seem to trigger it during tests. It looks like a problem with my use, or some invalid memory access? I'm confused.

[jeizenga]

Definitely not a problem with your use. That code should never execute if the aligner is working correctly. If it's non-deterministic, then I'd say the usual culprits: uninitialized variables, invalid memory access, bad thread syncing. Probably not the last option in this case. Can you give me the invocation that you see it on?