v0.2.3

Adds

• [dmr, multi] Allow site-level scoring by omitting the --regions argument. Sites will be collected from the input bedMethyl files.
• [dmr] Friendlier handling of missing files and when regions aren't found in the bedMethyl input files.
• [dmr] allow filtering on valid coverage without changing input
• [extract] output "read calls" extract table, a TSV with the base modification calls for every modified position in every read using the same thresholding algorithm as pileup
• [extract] allow filtering of calls by reference motif (like in pileup) as well as BED regions (and exclude regions)

Fixes

• [extract] Improve performance, especially on longer reads.
• [extract] Improve performance with long reads (actually a bug fix)
• [extract] num_soft_clipped_start and num_soft_clipped_end were incorrect on some reverse-mapped reads