This repository has been archived by the owner on Dec 16, 2022. It is now read-only.
-
Notifications
You must be signed in to change notification settings - Fork 13
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Fix handling of vector end values by Genotype::operator[]
Vector end values were not passing through to the caller when accessing alleles via operator[] in the Genotype class.
- Loading branch information
Showing
3 changed files
with
38 additions
and
4 deletions.
There are no files selected for viewing
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
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
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
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,19 @@ | ||
##fileformat=VCFv4.1 | ||
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed"> | ||
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> | ||
##INFO=<ID=VALIDATED,Number=0,Type=Flag,Description="Validated By Follow-up Experiment"> | ||
##INFO=<ID=DESC,Number=.,Type=String,Description="Custom Description"> | ||
##FILTER=<ID=PASS,Description=All filters passed> | ||
##FILTER=<ID=LOW_QUAL,Description=Low quality call> | ||
##FILTER=<ID=MISSED,Description=Missed by the variant caller> | ||
##FILTER=<ID=NOT_DEFINED,Description=Undefined filter> | ||
##contig=<ID=1,Length=300000000,Description=the first chromosome> | ||
##contig=<ID=20,Length=64000000> | ||
##contig=<ID=22,Length=120000000> | ||
##FORMAT=<ID=GT,Number=1,Type=String,Description=Genotype> | ||
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=Genotype quality> | ||
##FORMAT=<ID=PL,Number=G,Type=Integer,Description=Phred scaled relative Likelihoods of the genotypes> | ||
##FORMAT=<ID=AF,Number=2,Type=Float,Description=Arbitrary float field with 2 values (test purposes only)> | ||
##FORMAT=<ID=AS,Number=1,Type=String,Description=Arbitrary string field with 1 value (test purposes only)> | ||
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 NA12891 NA12892 | ||
1 10000000 db2342 T C 80 PASS AF=0.5;AN=6;VALIDATED;DESC=Test1,Test2 GT:GQ:PL:AF:AS 0/1:25:10,0,100:3.1,2.2:ABA 0:12:0,10,1000:3.1,2.2:CA 1:650:10,100,0:3.1,2.2:XISPAFORRO |