gfa view subgraph radius definition

[ggonnella]

Dear Heng Li,
I recently tried the gfa view command with options -l <SEGMENT_NAME> -r <RADIUS>.

However, the results are not the one which I would expect. Since the tools do not have a very clear documentation yet, I am not sure if I maybe misunderstood completely the commands - or if there is some kind of bug instead.

E.g. when I use the test file included in the repository (MT.gfa). This is the file displayed using my gfaviz tool. I gave a different color to each of what I would expect to be the definition of different radius.

I would expect to extract, when using -l MTh0 -r <radius> the following:

• r=0 --> red segment only
• r=1 --> red segment & blue segments and links between them
• r=2 --> ...& yellow
• r=3 --> ...& magenta
• r>=4 --> whole graph.

What I actually get is:

• r=0 => as expected
• r=1 => as expected
• r=2 => as expected
• r=3 => as expected, BUT:
• r=4 => same result as r=2, which I do not understand...
• r=5 => same result as r=3 (unexpected)

[lh3]

Thanks. I have also noticed some weird behavior of subgraph extraction, but I haven't gone into that.

[lh3]

Sorry for coming back to this so late. Before 53eca7a, gfatools was using DFS to extract subgraphs. The extraction depends on which node is visited first. I don't understand its behavior sometimes, either. I have changed DFS to BFS. It should match the expectation better.

By the way, what command-line were you using to produce the graph layout? Thanks.

CC @snurk on #8

[lh3]

Never mind about my question. It is gfaviz. Nice visualization. Would you provide precompiled binaries?

[ggonnella]

Hi Heng Li. I am looking back at some old projects and I see that I never answered this comment, because I actually did not notice it. Sorry for that. Anyway gfaviz is in my Github https://github.com/ggonnella/gfaviz