problem with chromosome mapping in vcf #549
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…o '20', but was to '0')
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Great catch @piotr-gawron! One small question, other then that looks great! Thank you for your contribution.
src/main/data/vcf.js
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| @@ -152,8 +152,8 @@ class ImmediateVcfFile { | |||
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| var contigMap = {}; | |||
| contigs.forEach(contig => { | |||
| if (contig.slice(0, 3) == 'chr') { | |||
| contigMap[contig.slice(4)] = contig; | |||
| if (contig.slice(0, 3) === 'chr') { | |||
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Why did you change to strict equality here?
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I did it probably out of habit. I never use == in JavaScript. There are too many pitfalls. My IDE also complains about == most of the time.
Probably in this case it does not matter so please revert. I did not want to interfere with your code style.
Another thing. I'm currently working on two features for pileup:
- support for tabix index in vcf file. So you would be able to visualize huge vcf files without network performance issue. There is a javascript library that deals with tabix indexes (https://github.com/GMOD/tabix-js). I'm just in a process of making it work in browserify (there are some dependencies that must be fixed).
- support for custom track visualization - in a project I'm working on there is need for visualization of project-related data. I can fork from pileup and modify the code (in fact I already have it working). However, I was thinking about making it more generic, so user would be able to plug in to canvas drawing of his own track.
I hope the functionalities could be introduced in the main pileup.
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This is great @piotr-gawron! Please let me know if there is anything I can do to help with these features.
I am curious, what custom track visualizations have you built? Do you think any of them would be useful for bringing into pileup.js?
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We have a lot of variant data and the idea is to allow developer to implement filtering and custom visualization of the data together with crosslinks to annotations. I'm not even sure what the biologist would require from me at this point, I have only general overview of the requirements.
This is very had to generalize because every researcher is looking at the data differently and not everything is standardized. Therefore I wanted to open the possibility to customize it and not be forced to modify pileup with every tiny change request.
I will probably create a PR with tabix support as soon as the following pull requests will be pushed into npm:
- when library is browserified the code does not work in browser GMOD/generic-filehandle#79
- Fix browserify issue GMOD/bgzf-filehandle#42
I already have it working locally so it's just a matter of cleaning the code and fixing dependencies.
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Great! Very excited to see this @piotr-gawron!
moved === to ==
This PR address small issue with mapping chromosomes ids to numbers. When vcf file contained chromosomes like
chr20the id was mapped to0instead of20.There is also a unit test showing the issue.