Examples with VariantContextWritable org.seqdoop.hadoop_bam.VariantContextWritable used on opensource projects

Example 1 with VariantContextWritable

use of org.seqdoop.hadoop_bam.VariantContextWritable in project gatk by broadinstitute.

the class VariantsSparkSource method getParallelVariantContexts.

/**
     * Loads variants in parallel using Hadoop-BAM for vcfs and bcfs.
     * @param vcf file to load variants from.
     * @param intervals intervals of variants to include, or null if all should be included.
     * @return JavaRDD<VariantContext> of variants from all files.
     */
public JavaRDD<VariantContext> getParallelVariantContexts(final String vcf, final List<SimpleInterval> intervals) {
    Configuration conf = new Configuration();
    conf.setStrings("io.compression.codecs", BGZFEnhancedGzipCodec.class.getCanonicalName(), BGZFCodec.class.getCanonicalName());
    if (intervals != null && !intervals.isEmpty()) {
        VCFInputFormat.setIntervals(conf, intervals);
    }
    final JavaPairRDD<LongWritable, VariantContextWritable> rdd2 = ctx.newAPIHadoopFile(vcf, VCFInputFormat.class, LongWritable.class, VariantContextWritable.class, conf);
    return rdd2.map(v1 -> v1._2().get());
}

Example 2 with VariantContextWritable

use of org.seqdoop.hadoop_bam.VariantContextWritable in project gatk by broadinstitute.

the class VariantsSparkSink method pairVariantsWithVariantContextWritables.

private static JavaPairRDD<VariantContext, VariantContextWritable> pairVariantsWithVariantContextWritables(JavaRDD<VariantContext> records) {
    return records.mapToPair(variantContext -> {
        final VariantContextWritable variantContextWritable = new VariantContextWritable();
        variantContextWritable.set(variantContext);
        return new Tuple2<>(variantContext, variantContextWritable);
    });
}