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Scala class to convert to adam file
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| import org.bdgenomics.formats.avro.AlignmentRecord | |
| import org.bdgenomics.adam.rdd.ADAMContext._ | |
| import org.bdgenomics.adam.projections.{ AlignmentRecordField, Projection } | |
| import org.apache.spark.rdd.RDD | |
| import org.bdgenomics.adam.rdd.ReferencePartitioner | |
| import org.bdgenomics.adam.models.ReferenceRegion | |
| val bamFile = "/user/nikhilrp/ENCFF000QJB.bam" | |
| val reads = sc.loadBam(bamFile) | |
| val sd = reads.adamGetSequenceDictionary() | |
| val mappedReads = reads.filter(read => read.getReadMapped) | |
| val referencePartitions = mappedReads.keyBy(read => ReferenceRegion(read)).repartitionAndSortWithinPartitions(ReferencePartitioner(sd)) |
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