v0.3.10

Fixed

• stats_from_bam: handle cigar strings using = and X instead of M.

Changed

• Include mapping quality in stats_from_bam output.

Added

• Handling of LRA bams in which NM tag is number of matches rather than edit distance.
• Added an option (-y) to assess_assembly and mini_align to include supplementary alignments.
• Added an option (-d) to mini_align and assess_assembly to select minimap2 alignment preset.
• Added accumulation of errors over a number of chunks (-a option in summary_from_stats and assess_assembly) to get better stats.
• Use -L option for minimap2.
• Updated versions of minimap2, samtools, bcftools, bedtools, seqkit in Makefile to the most recent ones.