Megalodon

Fix paths to 5mC model calibration files.

This a point release including new features:
* Add 5mC Rerio Model calibration files
* Add mapping trimming to summary file
* Optimized modified base aggregation

This point release includes some minor bug fixes and adds minor features and optimizations.

New features:
* Remove requirement for `per_read_mods` output when requesting `mod_mappings`
* Add script to output all motif hits to a BED file
* Optimize per-site threshold command (for training modified base models)
* Optimize standalone aggregation script when passing valid read IDs

Bug Fixes:
* Fix bug in per-site threshold `signal_mapping` output

This point release includes some minor bug fixes and adds minor features.

New features:
* New bedmethyl features (`megalodon_extras merge aggregated_modified_bases`)
* Expit-scaled modified base aggregation (potentially useful for 5hmC Rerio model; 47)
* More efficient per-site modified base annotation scripts.

Bug Fixes:
* Fix per-read text output commands (fixes 68)

This point release includes some minor bug fixes and adds minor features.

New features:
* Sequence variant calibration files for Rerio modified base models
* Improved documentation
* Add API example script (in `tests`)
* Optimize `megalodon_extras calibrate generate_variant_stats` command

Bug fixes:
* Fix signal coordinates in mapping summary file
* Fix alphabet printing bug

This a point release including a number of bug fixes and a few minor new features.

New features:
* Include raw signal endpoints in reference mapping summary file
* Add check for compatible Guppy and pyguppy versions
* Minor improvements to `megalodon_extra validate results` command

Bug fixes:
* Incorrect handling of `mod_mappings` output with `signal_mapping` options (Fixes 58)
* Fix error when no modified base scores are added to database
* Fix multiprocessing queues to correctly indicate full output queues
* Fix potential bottleneck for modified base data storage