Note: I manually edited the first record in the file for demo purposes. For testing, use second record.

The code for this is on this branch of the IGBquickload repository (branch name is parse_XML_AWS_bams)
https://bitbucket.org/lorainelab/igbquickload/branch/parse_XML_AWS_bams

The color was being converted from 8-digit hex to 6-digit hex. This was something of a headache because most color functions I use don't account for an 8-digit hex option, and the documentation about the 8-digit format is unclear about when it aRGB or RGBA. Having documentation from BAR about how they formatted their color string might be helpful in the future. In the mean time, it looks like all of the colors start with 0x, so (assuming that's the transparency field) it doesn't actually change the color.
We have made changes to how IGB limits the colors it will accept (it will accept a 6-digit string with or without a # in front). I think those changes may have changed how IGB handles the 8-digit string. I was quite sure IGB would only take a 6-digit hex, but it seems to be working now with the unchanged 8-digit hex as well. And obviously the best option would be to pass the color directly as it comes as long as that doesn't break anything. We should test this further.

I added the new attributes but I made a point to keep those in a separate commit so we might cherry pick around that.
For the max_depth and show2tracks, I think those values are already the defaults, so there is very little value in hard-coding them.
I don't think direction_type=arrow is a default---and for good reason, its ugly. I think that setting is ok for gene models, but RNA-Seq reads are so short that they look weird with arrows, and all the introns look like a stack of barbed wire. ...my opinion.

• Yes, please change "direction_type" to a setting that does not show the "barbed wire" look but does not color by strand.
• For foreground color, stick with hex convention used in our other annots.xml's - e.g., "FFFFFF" for black and "FF0000" for red, etc.
• Yes, it is fine to leave out the "show2tracks" setting.

I rolled back the last two commits. So the this branch what I think we have decided is ideal. The colors using this annots file look like the colors on http://bar.utoronto.ca/eFP-Seq_Browser/
branch parse_XML_AWS_bams
https://bitbucket.org/lorainelab/igbquickload/branch/parse_XML_AWS_bams

I made a new branch that still has the two extra commits, just so you can see them on bitbucket in case you want to consider them.
After reviewing this issue, if we don't want to use them, we should delete that branch to avoid confusion later.
branch otherOptions
http://bar.utoronto.ca/eFP-Seq_Browser/

I'm moving to Needs first level review and assigning it to Ann.

Merge to master & send AL new annots.xml

done and done.

I'm moving this to needs testing and assigning it to Ann.

Deployed and live on http://lorainelab-quickload.scidas.org/bar/
To test:

• Visit BAR page http://bar.utoronto.ca/eFP-Seq_Browser/
• Click LOAD DATA
• Scroll up & down to view coverage graphs
• Load corresponding data sets into IGB
• Note whether colors match
• Note whether data set names from Details column match IGB track labels

During my testing, I reviewed the following items:

-Colors from images on BAR site match the corresponding tracks from the BAR data source in IGB
-Track names in IGB correspond to the details column from the BAR site. The track label is in the form: "carpels SRR1207194". This is one of the details seen in the details column of the BAR site, although there are many other details included.

Since this story meets all expectations and there seem to be no side effects as a result of this cahnge, I am now marking this story as resolved.