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@akikuno akikuno released this 04 Oct 02:35
· 36 commits to main since this release
1.0.3
a5a46f1
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Learn about vigilant mode.

New feature

  • None

Maintenance

  • Fixed a bug in the RD calculation
    • For instance, in the case of ["=C-g", "=C"], the correct approach is to separate the REF's CG and C to calculate RD (initially RD=1, next RD=1). However, since it was counting all the Cs (RD=2), it has been modified to calculate them separately.
import cstag

cs_tags = [
    '=A*cg=GTAC',
    '=AC-g=TAC',
    '=ACGT+ggAC',
    ]
chroms = ["chr1", "chr1", "chr1"]
positions = [10, 10, 10]

x = cstag.to_vcf(cs_tags, chroms, positions)
print(x)

#####################
# Before:
#####################
chr1	11	.	CG	C	.	.	DP=4;RD=3;AD=1;VAF=0.25
chr1	11	.	C	G	.	.	DP=4;RD=3;AD=1;VAF=0.25
chr1	13	.	T	TGG	.	.	DP=3;RD=2;AD=1;VAF=0.333

#####################
# After:
#####################
chr1	11	.	CG	C	.	.	DP=2;RD=1;AD=1;VAF=0.5
chr1	11	.	C	G	.	.	DP=3;RD=2;AD=1;VAF=0.333
chr1	13	.	T	TGG	.	.	DP=3;RD=2;AD=1;VAF=0.333
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