Bam reads are cutoff

[jfear]

Hey guys, sorry to bug you again.

When loading a BAM file the reads appear to get cutoff. This happens with default setting, and I have played with the display_mode, height, maxRows, and samplingDepth parameters which do not fix the problem.

thanks Justin

[jrobinso]

Thanks for the report, we'll look into it.

[jrobinso]

BTW, keep bugging us.

On Thu, Oct 27, 2016 at 10:05 AM, Justin Fear notifications@github.com wrote:

Hey guys, sorry to bug you again.

When loading a BAM file the reads appear to get cutoff. This happens with default setting, and I have played with the display_mode, height, maxRows, and samplingDepth parameters which do not fix the problem.

[image: screen shot 2016-10-27 at 1 02 29 pm] https://cloud.githubusercontent.com/assets/1240432/19777371/e9b87136-9c45-11e6-9267-554e64ce9bd3.png

thanks Justin

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[jfear]

I think I have narrowed the problem down. If I change the height attribute on the canvas it seems to look as expected.

Before the change:

After the change:

Don't know if there is an attribute I should change when making the IGV object or the BAM track, or if this is a bug.

[turner]

Justin that's helpful. I'm looking at this now.

[jrobinso]

Thanks for the info, I think its a bug on our side, you shouldn't have to do that. You should see a scrollbar when the alignments are "cut off", and also you should be able to control the height of the track in the properties.

On Thu, Oct 27, 2016 at 11:47 AM, Justin Fear notifications@github.com wrote:

I think I have narrowed the problem down. If I change the height attribute on the canvas it seems to look as expected.

Before the change:

[image: screen shot 2016-10-27 at 2 39 37 pm] https://cloud.githubusercontent.com/assets/1240432/19780541/74c7d7e6-9c53-11e6-820a-be3752b6480a.png

After the change:

[image: screen shot 2016-10-27 at 2 37 00 pm] https://cloud.githubusercontent.com/assets/1240432/19780549/7b62a8ba-9c53-11e6-931f-0f8bdcef636a.png

Don't know if there is an attribute I should change when making the IGV object or the BAM track, or if this is a bug.

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[turner]

I can not reproduce this issues. Are you seeing this with the examples as well. Try "BAM Example.ipynb"

[jfear]

Sorry, just saw that you had replied.

I still get the same thing using the example notebook. I will play with it on some different computers and see if I can figure out if there is something specific to my setup. Nothing in the javascript console jumps out, so it maybe a chrome/osx thing. I will keep you posted.

[jrobinso]

To be clear the "cut off" alignments are normal, what's not normal is the absence of a scrollbar in the track. Also, setting track height should work (it does for us).

On Wed, Nov 2, 2016 at 10:56 AM, Justin Fear notifications@github.com wrote:

Sorry, just saw that you had replied.

I still get the same thing using the example notebook. I will play with it on some different computers and see if I can figure out if there is something specific to my setup. Nothing in the javascript console jumps out, so it maybe a chrome/osx thing. I will keep you posted.

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[jfear]

Just to clarify. There is a scroll bar, but the bams are cutoff half way through the read. I can scroll down, but it is just white.

I tried messing with the height and maxHeight parameters but they appear to do nothing.

When I get a chance I will test on different browsers/machines and see if there is something strange with my set up.

[a-slide]

I believe this is solved in the last version of the package