Currently, assemble_refbased reports reference_genome_length based on inspection of the mapped bam file used in plot_coverage however in the event zero reads map, the reference length is reported as zero. This commit reports the actual length of the sequence in the reference fasta provided to assemble_refbased, as the first Int output of the scattered calls to assembly.align_reads (and exposes the value, which was already obtained but not output, in align_reads)
dpark01
commented
3 months ago
Currently, assemble_refbased reports reference_genome_length based on inspection of the mapped bam file used in plot_coverage however in the event zero reads map, the reference length is reported as zero. This commit reports the actual length of the sequence in the reference fasta provided to assemble_refbased, as the first Int output of the scattered calls to assembly.align_reads (and exposes the value, which was already obtained but not output, in align_reads)