v0.6.2

Fixes

• [docs] Fixes transparent background making it difficult to view images thank you @SuhasSrinivasan
• [pileup] Fix "typo" that ignored Mm tags
• [pileup, bedRmod] Allow DS tag to fail parsing or be missing

Adds

• [pileup] Allow optional usage of non-primary alignments with --allow-non-primary flag
• [extract] Adds extract read-stats command to make tables of read-level modification counts

Changes

• [modbam, sample-probs] Refactor algorithm to decrease memory usage when sampling from the whole modBAM and decrease run time
• [dmr] Allow single modification to be run is isolation. This makes tests "mod" vs "unmodified or other mod".
• [modbam, summary] Refactor to use same mechanism as sample-probs. Allow summary at --matched-only sites.