Updates including fix for roi on counts-nano output and move to strict SAM as assumed in format command - #299
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…d and only keeping track of the fundamental counts; this is so the db will be in normal form
…rinted and only keeping track of the fundamental counts; this is so the db will be in normal form
…pth_covered and sites_covered_fraction
…s_covered_frac to match the colname in the view in methbase db
…strict SAM format
…tput, which is useful for current counts format output by counts-nano
…nor change to a tag in the output of levels. Might break.
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This includes changes to the way summary stats are accumulated for uniq, bsrate and levels, with a change to one of the tags for levels output which might break some downstream processing that requires an exact tag