AmpliGone v0.4.2

Features

• allow the primer-search error rate to be set by the user (fddd94a)

AmpliGone v0.4.1

Bug Fixes

• don't report duplicate coordinates of same primer when ambiguity-primers are given (f5449e2)
• use Nonetypes instead of string "None" (f5449e2)

AmpliGone v0.4.0

Features

• find coordinates of primers with mismatches to reference (d6bf925)

Bug Fixes

• consistently remove reverse primers in end-to-end mode (0c4f621)
• Fix cutting too many bases (78bd9ea)
• Make number of iterations variable (62ac2d7)

Documentation

• update installation instructions and include primer-search changes (5fdc6fa)

AmpliGone v0.3.3

Bug Fixes

• solve preset-sampling crash when less than 3 input reads are provided (29d5624)
• solve reference before assignment error in end-to-mid mode (14c9d24)

AmpliGone v0.3.2

Bug Fixes

• report removed coordinates from all iterations (f726e9a)

AmpliGone v0.3.1

Bug Fixes

• Distinguish (mis)match and cut soft clips (d4132c1)

Performance Improvements

• Add minimap scoring to presets (11158e5)

AmpliGone v0.3.0

Features

• Use CIGAR strings to cut end-to-end (ebd2684)

Bug Fixes

• Fix typo in 75e792f (eca004b)
• only return data that got an alignment-hit (f9e64e8)

Performance Improvements

• Improved (fastq)data loading speed (9d1ae23)

Documentation

• Fix comment in cut_read function (b920738)
• update docs to match new primer removal process (035be92)
• update readme (95ff984)

AmpliGone v0.2.3

Bug Fixes

• set correct exit code when -to flag is given (5a93ff0)

AmpliGone v0.2.2

Bug Fixes

• add missing primer-orientation keywords (41a84e6)
• exit cleanly when primers aren't found (#11) (e927591)
• Exit cleanly with empty input (#12) (35aae65)

Documentation

• update user-guide to include newly added flag (4d28ac1)

AmpliGone v0.2.1

Documentation

• add changelog link (4b62a92)