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new template for minimap2 alignment, with optional post-alignment filtering of secondary and supplementary alignments, and minimap2_F_value parameter to allow non-default insert size to be specified (-F flag)
subsampling of 10K reads (fastq produced by samtools view -s SEED.FRAC) and production of fastqcheck files added to stage1 and stage2 analyses (nchs, single-/paired-end)
add lane-level samtools stats to stage1
spatial filter application moved to stage2 from stage1
amend spatial_filter input/output file names for easier identification
empty edge entries recognised as noop - filter in viv.pl, ignore in visualisation, do not apply VTFILE
prefixes when there are no to and from attributes