Reads going out of bounds on the left aren't visible, while on the right they are cut off

[adamnovak]

I'm looking for a read, so I enter the read's start node into the tube map in node mode and hit go.

I don't see the read. It's because (I think) the read maps to the reverse strand. The tube map starts at the node I entered and heads locally right, while the read wanders off locally left.

But I don't even see the part of the read that visits the node I entered. I think we might only be collecting reads fully withing the graph.

Starting at the read's ending node gets it to show up.

[adamnovak]

I'm also having a related issue with reads that continue out of the viewport on the right side. Haplotypes are drawn leaving the final node and being cut off outside of the node, but reads that are cut off by the right side of the selected region appear to end inside the final node, so you can't tell that they continue out of the visible region.

They should, like the haplotypes, leave the final node and be cut off outside of it, to indicate that they continue on.

[wolfib]

Could it be that the missing reads are not part of the 'vg chunk' output?

The tube map is not aware of anything going on outside its window of view, so it cannot discern between reads which end at the last base of the final node or reads which continue off-screen. So believe that the only option would be to draw all reads which reach the right end to extend beyond that node (even though this might be incorrect for very few of them).

[adamnovak]

This definitely could be a result of vg chunk clipping the reads to the returned graph region, on the right side.

It could also just be neglecting to find them on the left side.

On Sat, Feb 3, 2018 at 10:09 AM, Wolfgang Beyer [email protected] wrote:

Could it be that the missing reads are not part of the 'vg chunk' output?

The tube map is not aware of anything going on outside its window of view, so it cannot discern between reads which end at the last base of the final node or reads which continue off-screen. So believe that the only option would be to draw all reads which reach the right end to extend beyond that node (even though this might be incorrect for very few of them).

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[adamnovak]

I think to fix this, we would make sure to not cut reads when doing vg chunk, but to instead include the pieces of them that touch nodes outside the chunk.

Then we would, in the tube map code, make sure we are detecting when a read wants to go to something not in the subgraph, and then draw it appropriately.