lint

bpblanken · bpblanken · commit 8fe59fddc6e4 · 2024-03-13T14:13:43.000-04:00
diff --git a/v03_pipeline/lib/methods/sex_check.py b/v03_pipeline/lib/methods/sex_check.py
@@ -13,6 +13,7 @@
 
 AMBIGUOUS_THRESHOLD_PERC: float = 0.01  # Fraction of samples identified as "ambiguous_sex" above which an error will be thrown.
 AAF_THRESHOLD: float = 0.05  # Alternate allele frequency threshold for `hl.impute_sex`.
+BIALLELIC: int = 2
 XX_FSTAT_THRESHOLD: float = (
     0.5  # F-stat threshold below which a sample will be called XX
 )
@@ -25,7 +26,7 @@ def call_sex(mt: hl.MatrixTable) -> hl.Table:
     # Filter to SNVs and biallelics
     # NB: We should already have filtered biallelics, but just in case.
     mt = mt.filter_rows(
-        ((hl.len(mt.alleles) == 2) & hl.is_snp(mt.alleles[0], mt.alleles[1]))
+        (hl.len(mt.alleles) == BIALLELIC) & hl.is_snp(mt.alleles[0], mt.alleles[1]),
     )
 
     # Filter to PASS variants only (variants with empty or missing filter set)

Original file line number	Diff line number	Diff line change
`@@ -13,6 +13,7 @@`
`13`	`13`
`14`	`14`	`AMBIGUOUS_THRESHOLD_PERC: float = 0.01 # Fraction of samples identified as "ambiguous_sex" above which an error will be thrown.`
`15`	`15`	AAF_THRESHOLD: float = 0.05 # Alternate allele frequency threshold for `hl.impute_sex`.
	`16`	`+BIALLELIC: int = 2`
`16`	`17`	`XX_FSTAT_THRESHOLD: float = (`
`17`	`18`	`0.5 # F-stat threshold below which a sample will be called XX`
`18`	`19`	`)`
`@@ -25,7 +26,7 @@ def call_sex(mt: hl.MatrixTable) -> hl.Table:`
`25`	`26`	`# Filter to SNVs and biallelics`
`26`	`27`	`# NB: We should already have filtered biallelics, but just in case.`
`27`	`28`	`mt = mt.filter_rows(`
`28`		`- ((hl.len(mt.alleles) == 2) & hl.is_snp(mt.alleles[0], mt.alleles[1]))`
	`29`	`+ (hl.len(mt.alleles) == BIALLELIC) & hl.is_snp(mt.alleles[0], mt.alleles[1]),`
`29`	`30`	`)`
`30`	`31`
`31`	`32`	`# Filter to PASS variants only (variants with empty or missing filter set)`