Re-organizes and completes build-index options to support a decoy genome
Adds support for decoy genomes
Changes the SA index structure to support more genome sequences (chrom., decoy, ALT...): the CHROM table contains 16-bit values instead of 8-bit values
Improves CAL manager, in terms of speed, when handling a large number of genome sequences (chrom., decoy, ALT,...)
Implements a second improvement for the CAL manager, in terms of speed, to handle a large number of genome sequences (chrom., decoy, ALT,...)
Adds the optional field: XD:Z:<decoy_sequence_name> for decoy mappings
Adds decoy genome for GRCh38, and updates options to build index