v0.1.9

Changes

• [pileup] When estimating the pass-threshold only use base modification probabilities if the read base is aligned to the reference (don't use soft-clipped and inserts). Use --include-unmapped to use all base modification probabilities.
• [adjust-mods] requires --ignore, --convert, or --edge-filter.

Adds

• [pileup, extract, sample-probs, summary] Allow narrowing of analysis to specific sites with --include-bed.
• [summary, sample-probs] Add --only-mapped flag that will only report on base modification probabilities if they are mapped to the reference.
• [pileup] Allow partitioning counts to separate bedMethyl files based on SAM tags with --partition-tag option.

Fixes

• [adjust-mods, update-tags, call-mods] Panic when failure to parse SAM header, fixes #29.