def collect(self, vcfname, tag):
""" Return a data frame with features collected from the given VCF, tagged by given type """
if tag not in ["TP", "FN"]:
return extractStrelkaSNVFeatures(vcfname, tag, self.chr_depth)
else:
features = ["CHROM", "POS", "REF", "ALT", "I.editDistance", "S.2.GT"]
return GenericFeatures.collectFeatures(vcfname, tag, features, processor=StrelkaAdmixSNVFeatures.processValue)
def collect(self, vcfname, tag):
""" Return a data frame with features collected from the given VCF, tagged by given type """
if tag not in ["TP", "FN"]:
return extractStrelkaSNVFeatures(vcfname, tag, self.chr_depth)
else:
features = ["CHROM", "POS", "REF", "ALT", "QUAL",
"I.T_ALT_RATE", "I.DP_normal", "I.DP_tumor", "I.tag", "I.count"]
return GenericFeatures.collectFeatures(vcfname, tag, features, processor=StrelkaAdmixSNVFeatures.processValue)
def collect(self, vcfname, tag):
""" Return a data frame with features collected from the given VCF, tagged by given type """
if tag not in ["TP", "FN"]:
return extractStrelkaSNVFeatures(vcfname, tag, self.chr_depth)
else:
features = [
"CHROM", "POS", "REF", "ALT", "I.editDistance", "S.2.GT"
]
return GenericFeatures.collectFeatures(
vcfname,
tag,
features,
processor=StrelkaAdmixSNVFeatures.processValue)
def collect(self, vcfname, tag):
""" Return a data frame with features collected from the given VCF, tagged by given type """
if tag not in ["TP", "FN"]:
return extractStrelkaSNVFeatures(vcfname, tag, self.chr_depth)
else:
features = [
"CHROM", "POS", "REF", "ALT", "QUAL", "I.T_ALT_RATE",
"I.DP_normal", "I.DP_tumor", "I.tag", "I.count"
]
return GenericFeatures.collectFeatures(
vcfname,
tag,
features,
processor=StrelkaAdmixSNVFeatures.processValue)