Esempio n. 1
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 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 extractStrelkaIndelFeatures(vcfname, tag, self.chr_depth)
     else:
         features = ["CHROM", "POS", "REF", "ALT", "I.editDistance", "S.2.GT"]
     return GenericFeatures.collectFeatures(vcfname, tag, features, processor=StrelkaAdmixIndelFeatures.processValue)
Esempio n. 2
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 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 extractStrelkaIndelFeatures(vcfname, tag, self.chr_depth)
     else:
         features = ["CHROM", "POS", "REF", "ALT", "QUAL", "S.1.VT",
                     "I.T_ALT_RATE", "I.DP_normal", "I.DP_tumor", "I.tag", "I.count"]
     return GenericFeatures.collectFeatures(vcfname, tag, features, processor=StrelkaAdmixIndelFeatures.processValue)
Esempio n. 3
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 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 extractStrelkaIndelFeatures(vcfname, tag, self.chr_depth)
     else:
         features = [
             "CHROM", "POS", "REF", "ALT", "I.editDistance", "S.2.GT"
         ]
     return GenericFeatures.collectFeatures(
         vcfname,
         tag,
         features,
         processor=StrelkaAdmixIndelFeatures.processValue)
Esempio n. 4
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 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 extractStrelkaIndelFeatures(vcfname, tag, self.chr_depth)
     else:
         features = [
             "CHROM", "POS", "REF", "ALT", "QUAL", "S.1.VT", "I.T_ALT_RATE",
             "I.DP_normal", "I.DP_tumor", "I.tag", "I.count"
         ]
     return GenericFeatures.collectFeatures(
         vcfname,
         tag,
         features,
         processor=StrelkaAdmixIndelFeatures.processValue)