Additional flow space features

[nh13]

I have added additional features:

1. Base shading can be done by flow signal deviation from the read or reference. If the read has a signal of 232 and a base call of 2, then the deviation is 2 (= 232 - 100*(2)). Similarly for the reference.
2. The base shading is now a sub-menu, given the increased number of options (none, quality, flow-dev-read, flow-dev-ref).
3. Add the ability to copy the flow signal distribution across bases at a given genomic position. The output is in JSON format.

commit fa6c3bc

[jsilter]

Some of this has already been discussed via email, but I'll restate. In general we want to accept this but not yet.

• We're going to be redesigning the context menu (basically changing it to a "tool" window), so the context menu entries will need to be changed. Since we haven't done that redesign yet, it's gotta wait.
• Since this is applicable only to specific data, we want to make sure these options only show up when the appropriate data is loaded.
• IGV 2.1 will be coming out soon (sometime in March), we're holding off on major changes until after that release.

Re: 3., why JSON for copying to clipboard? Could you post an example of what a typical string would look like?

I'll leave this request open for now, feel free to update the branch (or if you'd like to close it that's fine too).

[nh13]

I will keep my fork update until you ready to start work on the new context menu, as well as ready to discuss on-demand options.

Re:3, JSON is a very convenient and readable format for this type of data. We could make this a preference too!

A dummy example would be:

{
"198" : "12",
"199" : "14",
"200" : "52",
"201" : "23",
"202" " "15"
}

where there are key-value pairs, keys being the flow signal, values be the observed counts.

[jsilter]

I'm a huge fan of JSON when the other option is XML, I'm just wondering if it will include extra characters that we don't really need. Most of our copy-to-clipboard is basically a table format, so in your example it might be:

198 : 12
199 : 14
200 : 52
201 : 23
202 : 15

I don't quite know what the use case for this is; are you grabbing small snippets to put in a text file and eyeball, or are people going to be making big data files and looking at them in excel? You're the user, so you know better than I do.

[nh13]

I think from IGV, folks may look at them in excel, R, or whatever language they choose. Sure we have extra characters, but that's JSON.

[jsilter]

Well I'll defer to you for now. But if anybody else complains it's on you ;-).

[nh13]

I'll just add a dropdown list in the preferences bar...

[nh13]

Any news on the switch over to this GIT repository, and when I should start developing on the new UI?

[jsilter]

Talking to other devs, may happen soon. You don't have to wait for the switch, we can always copy changes in via patch. Is the functionality the same as in the original pull request, or have you added more?

GitHub is saying this branch can't be auto-merged (likely my fault, small mistakes when using git svn can force one to rewrite the git history on push). Don't worry about that now because we may not try to do a git merge for this patch anyway, just thought I'd let you know.