CHANGELOG.md

Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

Unreleased

0.1.5

Fixed

• Fixed bug triggered by --case-insensitive option in find_seq tool.

0.1.4

Changed

• Dropped support for Python 3.6 and 3.7

Fixed

• Fixed bug triggered by --case-insensitive option in find_seq tool.

0.1.3

Fixed

• Cleaned dependencies, solved linting and packaging issues.

0.1.2

Fixed

• Bug in flagstats export.

0.1.1

Added

• find_seq option to locate needle sequence from FASTX files.
• Unit tests.
• BedWriter class for BED file output.
• Option for --simple-pattern in flag extraction.

Changed

• Script assert errors now reported through rich logging.

Fixed

• Empty output when output path is not in current working directory.
• Bug that caused log to crash script when extracting pattern matched no reads.

0.1.0

Added

• --split-by option to split output by flag during flag extraction.
• flag_filter script to apply quality filters after flag extraction.
• trim length to trim by length.
• trim quality to trim by quality.
• flag split to split file based on flag after flag extraction.
• flag stats to calculate flag stats after flag extraction.
• flag regex to filter flags based on regular expression after flag extraction.

Changed

• Using rich for richer logging.
• Removed default pattern. Switched with example pattern in help page.
• Moved trim by pattern as command of trim regex.
• Moved extract command as sub-command of flag.

Fixed

• Parallelization now working on Python 3.6+.
• Output compression now dependent only on output file extension.
• Logging proper number of reads passing flag quality filters.

0.0.1 - 2020-08-03