Adding matching for deletions that have longer representations #89
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This patch fixes an issue that comes from the fact that deletions can have different REF but still be the same rsID:
Example from vcf file:
NC_000003.12 28891307 . CT C 306.593 . AB=0;TYPE=del;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:22:0,14:0:0:14:366:-32.988,-4.21442,0Same position from dbSNP:
NC_000003.12 28891307 rs34247537 CTTTT C,CT,CTT,CTTT,CTTTTT,CTTTTTT,CTTTTTTT,CTTTTTTTTTTTT . . RS=34247537;dbSNPBuildID=126Both represent the same deletion but due to the fact that the dbSNP contains other longer deletions dbSNP has to contain a longer slice of the reference. So will not match using SNPSifts earlier matching algorithm. This patch fixes this issue by appending the extended part of the reference ("TTT" in the example case) to the alt and to the REF then comparing again.
Like this:
"CT".concat("TTT") == "CTTTT" && "C".concat("TTT") == "CTTT"