com.google.cloud.genomics.dataflow.functions.pca.ExtractSimilarCallsets.java Source code

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Here is the source code for com.google.cloud.genomics.dataflow.functions.pca.ExtractSimilarCallsets.java

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/*
 * Copyright (C) 2014 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.functions.pca;

import com.google.cloud.dataflow.sdk.transforms.DoFn;
import com.google.cloud.dataflow.sdk.values.KV;
import com.google.cloud.genomics.dataflow.utils.CallFilters;
import com.google.cloud.genomics.dataflow.utils.PairGenerator;
import com.google.common.base.Function;
import com.google.common.collect.FluentIterable;
import com.google.common.collect.ImmutableList;
import com.google.common.collect.ImmutableMultiset;
import com.google.common.collect.Iterables;
import com.google.common.collect.Multiset;
import com.google.common.collect.Ordering;
import com.google.genomics.v1.Variant;
import com.google.genomics.v1.VariantCall;

/**
 * Emits a callset pair every time they share a variant.
 */
public class ExtractSimilarCallsets extends DoFn<Variant, KV<KV<String, String>, Long>> {

    private ImmutableMultiset.Builder<KV<String, String>> accumulator;

    @Override
    public void startBundle(Context c) {
        accumulator = ImmutableMultiset.builder();
    }

    @Override
    public void processElement(ProcessContext context) {
        FluentIterable<KV<String, String>> pairs = PairGenerator.WITH_REPLACEMENT
                .allPairs(getSamplesWithVariant(context.element()), Ordering.natural());
        for (KV<String, String> pair : pairs) {
            accumulator.add(pair);
        }
    }

    @Override
    public void finishBundle(Context context) {
        for (Multiset.Entry<KV<String, String>> entry : accumulator.build().entrySet()) {
            context.output(KV.of(entry.getElement(), Long.valueOf(entry.getCount())));
        }
    }

    protected ImmutableList<String> getSamplesWithVariant(Variant variant) {
        return ImmutableList.copyOf(Iterables.transform(CallFilters.getSamplesWithVariantOfMinGenotype(variant, 1),
                new Function<VariantCall, String>() {

                    @Override
                    public String apply(VariantCall call) {
                        return call.getCallSetName();
                    }

                }));
    }
}