Please discuss with Nowlan before working on this issue. I believe he may have some valuable input for this story.

From Ann:

Let's do this:

Let's draw in the insertion Glyph as a semi-transparent, pale triangle glyph, consistent with biology iconography for "insertion"
Color should be automatically chosen to contrast with the read color. You can find example code illustrating how to pick good contrasting colors somewhere in the code that draws the amino acid translation on top of Glyphs created from reading BED files.

The insertion Glyph needs to be semi-transarent so that the bases underneath can be read.
The triangle should point to the boundary between the two bases. Minus strand read triangles should point UP. Plus strand read triangles should point DOWN. (This will help people stay oriented.)
When users click on the triangle, the Selection Info should show information about the insertion, NOT the read.
Information should include:
insertion site (genomic coordinate)
sequence of the insertion (it should be something users can copy and paste)
Note that the inserted sequence will be always be less than the total length of the read

Right now we don't any glyph available for this and we might have to create a new glyph.

We need to change some things about how insertions (from BAM files) are shown, as follows:

1) When users select an insertion Glyph, Selection info should be listed as follows, from top to bottom:

feature type insertion
length [length of the inserted bases, e.g., number of residues inserted]
residues [whatever the inserted bases are]
strand [strand of the read]
start [start of the insertion]
end [end of the insertion]
id id

nothing else should be shown

3) Insertion Glyph should be black with white letters, not red with black letters

I need this for a class I'm teaching so it would be great to get it done soon

Insertion Glyph bases are not being shown. The Glyph is black, but the bases are either also black or not being drawn.

Bases neighboring the site of an insertion are not shown.

To repeat:

1) Visit S. lycopersicum (tomato) genome
2) Select chromosome chrC-NC_007898.3
3) Select a dataset from Plastid Resequencing folder (not Primers or Amplicon - choose one of the others)
4) Zoom in, load data
5) Zoom in further, look for black insertion Glyphs
6) Observe that bases are not being shown.

What should happen is that bases should be displayed on top of the black glyph.

While testing this issue I noticed that the Insertion bases are not being displayed on the black boxes, but I don't think they look as good as they could. The bases are slightly offset so that the left base is kind of bleeding into the nucleotide beside it. Because of this, I am moving it back to the To-Do column and assigning it to David.

This story is duplicated by IGBF-1057. Since IGBF-1057 is more recent and contains the information that is currently pertinent to the issue, I will close this story now since it is no longer needed.