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Example 16 with GATKVariant

use of org.broadinstitute.hellbender.utils.variant.GATKVariant in project gatk by broadinstitute.

the class ReadContextData method toString.

@Override
public String toString() {
    StringBuilder builder = new StringBuilder();
    builder.append("<");
    for (GATKVariant v : variants) {
        builder.append(v).append(",");
    }
    builder.append(">");
    return "ReadContextData{" + "referenceBases=" + referenceBases.toString() + ", variants=" + builder.toString() + '}';
}
Also used : GATKVariant(org.broadinstitute.hellbender.utils.variant.GATKVariant)

Aggregations

GATKVariant (org.broadinstitute.hellbender.utils.variant.GATKVariant)16 GATKRead (org.broadinstitute.hellbender.utils.read.GATKRead)10 ReadContextData (org.broadinstitute.hellbender.engine.ReadContextData)7 SimpleInterval (org.broadinstitute.hellbender.utils.SimpleInterval)7 JavaSparkContext (org.apache.spark.api.java.JavaSparkContext)6 ReferenceBases (org.broadinstitute.hellbender.utils.reference.ReferenceBases)5 BaseTest (org.broadinstitute.hellbender.utils.test.BaseTest)4 Test (org.testng.annotations.Test)4 SAMSequenceDictionary (htsjdk.samtools.SAMSequenceDictionary)3 ArrayList (java.util.ArrayList)3 ReferenceMultiSource (org.broadinstitute.hellbender.engine.datasources.ReferenceMultiSource)3 ReadFilter (org.broadinstitute.hellbender.engine.filters.ReadFilter)3 VariantsSparkSource (org.broadinstitute.hellbender.engine.spark.datasources.VariantsSparkSource)3 IntervalsSkipList (org.broadinstitute.hellbender.utils.collections.IntervalsSkipList)3 RecalibrationReport (org.broadinstitute.hellbender.utils.recalibration.RecalibrationReport)3 Tuple2 (scala.Tuple2)3 IOException (java.io.IOException)2 JavaPairRDD (org.apache.spark.api.java.JavaPairRDD)2 JavaRDD (org.apache.spark.api.java.JavaRDD)2 ContextShard (org.broadinstitute.hellbender.engine.ContextShard)2