Examples with SequenceDictionary org.bdgenomics.adam.models.SequenceDictionary used on opensource projects

Example 1 with SequenceDictionary

use of org.bdgenomics.adam.models.SequenceDictionary in project gatk by broadinstitute.

the class ReadsSparkSink method writeReadsADAM.

private static void writeReadsADAM(final JavaSparkContext ctx, final String outputFile, final JavaRDD<SAMRecord> reads, final SAMFileHeader header) throws IOException {
    final SequenceDictionary seqDict = SequenceDictionary.fromSAMSequenceDictionary(header.getSequenceDictionary());
    final RecordGroupDictionary readGroups = RecordGroupDictionary.fromSAMHeader(header);
    final JavaPairRDD<Void, AlignmentRecord> rddAlignmentRecords = reads.map(read -> {
        read.setHeaderStrict(header);
        AlignmentRecord alignmentRecord = GATKReadToBDGAlignmentRecordConverter.convert(read, seqDict, readGroups);
        read.setHeaderStrict(null);
        return alignmentRecord;
    }).mapToPair(alignmentRecord -> new Tuple2<>(null, alignmentRecord));
    // instantiating a Job is necessary here in order to set the Hadoop Configuration...
    final Job job = Job.getInstance(ctx.hadoopConfiguration());
    // ...here, which sets a config property that the AvroParquetOutputFormat needs when writing data. Specifically,
    // we are writing the Avro schema to the Configuration as a JSON string. The AvroParquetOutputFormat class knows
    // how to translate objects in the Avro data model to the Parquet primitives that get written.
    AvroParquetOutputFormat.setSchema(job, AlignmentRecord.getClassSchema());
    deleteHadoopFile(outputFile, ctx.hadoopConfiguration());
    rddAlignmentRecords.saveAsNewAPIHadoopFile(outputFile, Void.class, AlignmentRecord.class, AvroParquetOutputFormat.class, job.getConfiguration());
}

Example 2 with SequenceDictionary

use of org.bdgenomics.adam.models.SequenceDictionary in project gatk by broadinstitute.

the class GATKReadToBDGAlignmentRecordConverter method convert.

public static AlignmentRecord convert(final GATKRead gatkRead, final SAMFileHeader header) {
    SequenceDictionary dict = SequenceDictionary.fromSAMSequenceDictionary(header.getSequenceDictionary());
    RecordGroupDictionary readGroups = RecordGroupDictionary.fromSAMHeader(header);
    return GATKReadToBDGAlignmentRecordConverter.convert(gatkRead, header, dict, readGroups);
}