Details
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Type:
Improvement
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: 9.0.2 Minor Release
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Labels:
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Story Points:2
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Sprint:Fall 2018 1, Fall 2018 Sprint 2
Description
Support newer VCF formats in IGB.
(User request)
Attachments
Issue Links
- relates to
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HELP-303 VCFv4 compatibility
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- Closed
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Activity
Merged into master
ann.loraine commented on pull request #623: IGBF-1380 Support VCF4.2
How is this more efficient? Does it reduce:
- processing time (less work per line of data)
- memory usage (how much?)
It seems to me that the main value of this change is it reduces complexity of the code, making it easier to understand and maintain.
_________________
You are right. "more efficient" was not the right phrase. "simpler" is better.
I reduced the comments that I added for the INFO and FORMAT sub-class definitions in VCF.java.
I made those changes, rebased onto upstream master, and created a pull request.
I think it will be best to talk through the code comments in person. Sneha and I can talk through this on Tuesday afternoon.
Notes from in-person review:
remove the code that was commented out in core/genometry/src/main/java/com/affymetrix/genometry/symloader/VCF.java
line 328
core/genometry/src/main/java/com/affymetrix/genometry/symloader/VCF.java
line 520
Otherwise, comments were addressed in discussion. No need for further testing. Remove the commented code and create pull request.
I think this is the file I will need to change, possibly the only file.
core/genometry/src/main/java/com/affymetrix/genometry/symloader/VCF.java
This post is helpful:
https://bioinformatics.stackexchange.com/questions/344/whats-the-difference-between-vcf-spec-versions-4-1-and-4-2
For reference, the PDF Samtools specification for VCF 4.1 (currently supported in IGB), 4.2 (not yet supported), and 4.3 (not yet supported)
https://samtools.github.io/hts-specs/VCFv4.1.pdf
https://samtools.github.io/hts-specs/VCFv4.2.pdf
https://samtools.github.io/hts-specs/VCFv4.3.pdf
My testing verifies that all VCF versions are now compatible with IGB and load as expected. There was no exception noted in the console during my testing and all other file formats are loading as expected, so this story will now be closed.