Currently, the alignment convert command line expects a BAM file as input file, then to covert to Avro or Parquet. This command line should support the Avro to Parquet conversion too. An optional --from parameter should indicate the input file format. Valid values are bam and avro; by default, bam. E.g.:
Currently, the alignment convert command line expects a BAM file as input file, then to covert to Avro or Parquet. This command line should support the Avro to Parquet conversion too. An optional --from parameter should indicate the input file format. Valid values are bam and avro; by default, bam. E.g.:
./build/bin/hpg-bigdata-local.sh alignment convert --i test.avro --o test.parquet --from avro --to parquet