com.google.cloud.genomics.dataflow.utils.VariantFunctions Maven / Gradle / Ivy
/*
* Copyright (C) 2015 Google Inc.
*
* Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except
* in compliance with the License. You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software distributed under the License
* is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express
* or implied. See the License for the specific language governing permissions and limitations under
* the License.
*/
package com.google.cloud.genomics.dataflow.utils;
import java.util.regex.Pattern;
import com.google.cloud.dataflow.sdk.transforms.SerializableFunction;
import com.google.cloud.genomics.utils.grpc.VariantUtils;
/**
* Utility methods for working with genetic variant data.
*/
public class VariantFunctions {
/**
* Determines whether a variant is called according to the provided filtering, using the notation
* required by the VCF 4.2 standard. This means that the filter field of the variant must
* contain either only "PASS" or ".".
*/
public static final SerializableFunction IS_PASSING
= new SerializableFunction() {
@Override
public Boolean apply(com.google.genomics.v1.Variant v) {
return (v.getFilterCount() == 1) && (v.getFilter(0).equalsIgnoreCase("PASS")
|| v.getFilter(0).equalsIgnoreCase("."));
}
};
/**
* Determines whether a Variant is from a chromosome.
*/
public static final SerializableFunction IS_ON_CHROMOSOME
= new SerializableFunction() {
@Override
public Boolean apply(com.google.genomics.v1.Variant v) {
return Pattern.compile("^(chr)?(X|Y|([12]?\\d))$")
.matcher(v.getReferenceName())
.matches();
}
};
/**
* Determines whether a Variant's quality is the lowest level (Phred score 0).
*/
public static final SerializableFunction
IS_NOT_LOW_QUALITY = new SerializableFunction() {
@Override
public Boolean apply(com.google.genomics.v1.Variant v) {
return (v.getQuality() != 0.0);
}
};
/**
* Determines whether a Variant is a SNP with a single alternative base.
*
* To the output of @link{VariantRatios.IsSnpFn} we add the condition that
* the variant has exactly one alternative base.
*/
public static final SerializableFunction
IS_SINGLE_ALTERNATE_SNP = new SerializableFunction(){
@Override
public Boolean apply(com.google.genomics.v1.Variant v) {
return (v.getAlternateBasesList().size() == 1) && VariantUtils.IS_SNP.apply(v);
}
};
}