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Fix small check_filter bug
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artic/vcf_filter.py

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -56,7 +56,7 @@ def check_filter(self, v, min_depth):
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depth = v.INFO["DP"]
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except KeyError:
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depth = v.format("DP")[0][0]
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if depth < min_depth:
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return False
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@@ -107,7 +107,7 @@ def go(args):
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indx = "%s-%s" % (v.CHROM, v.POS)
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if len(group_variants[indx]) > 1:
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for check_variant in group_variants[indx]:
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if filter.check_filter(check_variant):
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if filter.check_filter(check_variant, args.min_depth):
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variant_passes = True
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if not variant_passes:

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