Closed jtarraga closed 7 years ago
The command line should offer some basic filters (e.g., region filter, mapping quality filter,...) and take into account some important Parquet parameters (e.g. page size, row group size), and parameters to compress de SAM sequences and qualities
./hpg-bigdata.sh alignment convert -i .... -o .... --to {avro | parquet} [--from {bam|sam|cram||avro}] --compression {deflate | snappy | ...} [--page-size ...] [--row-group-size ...] [--skip-sequence] [--bin-qualities] [--region ....] [--region-file ....] [--mapping-qual ....]
The command line should offer some basic filters (e.g., region filter, mapping quality filter,...) and take into account some important Parquet parameters (e.g. page size, row group size), and parameters to compress de SAM sequences and qualities
./hpg-bigdata.sh alignment convert -i .... -o .... --to {avro | parquet} [--from {bam|sam|cram||avro}] --compression {deflate | snappy | ...} [--page-size ...] [--row-group-size ...] [--skip-sequence] [--bin-qualities] [--region ....] [--region-file ....] [--mapping-qual ....]