#
# Strelka - Small Variant Caller
# Copyright (c) 2009-2018 Illumina, Inc.
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <http://www.gnu.org/licenses/>.
#
#

from VcfFeatureSet import VcfFeatureSet


@VcfFeatureSet.register("germline.indel")
class GermlineSNVFeatures(VcfFeatureSet):
    """Collect germline INDEL features from VCF"""

    def collect(self, vcfname):
        """ Return a data frame with features collected from the
            given VCF"""

        return self.collectCore(vcfname,"germline_indel_scoring_features")


    def trainingfeatures(self):
        """ Return a list of columns that are features to
            use for EVS training

            Any change here must be done together with changing
            src/c++/lib/applications/starling/germlineVariantEmpiricalScoringFeatures.hh
        """
        return [
            "GenotypeCategory",
            "SampleIndelRepeatCount",
            "SampleIndelRepeatUnitSize",
            "SampleIndelAlleleBiasLower",
            "SampleIndelAlleleBias",
            "SampleProxyRMSMappingQuality",
            "RelativeTotalLocusDepth",
            "SamplePrimaryAltAlleleDepthFraction",
            "ConservativeGenotypeQuality",
            "InterruptedHomopolymerLength",
            "ContextCompressability",
            "IndelCategory",
            "NormalizedAltHaplotypeCountRatio",
            "SampleAlleleCountStrandBias"]
