v0.2.5

Fixes

• [extract] Only emit mapped reads when --region is provided, but still emit unmapped bases in those reads unless --mapped-only is passed.
• [extract] Performance improvement due to better tracking of interval boundaries.
• [repair] Updates the MN tag on repaired records.

Adds

• [dmr, single-site] Refactor dmr pair without regions (i.e. single site analysis) to increase performance.
• [dmr, single-site] Add estimated MAP-based p-value to output.
• [all] Allows BED3 input for all options that use --include-bed. Strand will be assumed to be BOTH (equivalent to '.').
• [extract] Increases the kmer size limit to 50.