Functions

function	type	input files	main output file(s)
qc_report	QC	1 or more BAM	summary report with figures & table for read length, mapping quality, basecall quality, etc.
plot_browser	visualization	1 or more BAM	single-molecule browser as html or pdf; aggregate browser plots and coverage
plot_enrichment	visualization	1 or more BAM, 1 or more BED	barplot of fraction modified bases within region(s) defined by BED(s)
plot_enrichment_profile	visualization	1 or more BAM, 1 or more BED	profile, single molecule plots, base abundance; option to overlay if input multiple BAM/BED
parse_bam	data formatting	1 BAM	sql database (to allow for custom visualization)