v0.3.3

Added

• Deprecation warning. Update sam->bam in readme.

v0.3.2

Added

• Update to dorado_stereo.sh, do not create directories when using -n flag (dry run).

v0.3.1

Added

• wrapper for a prototype stereo-calling pipeline dorado_stereo.sh that does 2-stage stereo calling.

v0.3.0

Changed

• update fastx iteration in split_pairs to be compatible with pyfastx>=0.9.0.

Fixed

• Bug where split_pairs would raise a StopIteration if dataset has < 5k reads.

v0.2.20

Added

• split_pairs a tool to recover non-split reads into their template/complement parts.

v0.2.19

Fixed

• Bug where approximate start times led to incorrectly rejecting candidate duplex pairs.

v0.2.17

Fixed

• Bug where an incorrect tag was used to get sequence lengths from .bam files (for dorado)

Changed

• ProcessPoolExecutor -> ThreadPoolExecutor in filter_pairs for faster filtering
• Reporting duplex rate in duplex_tools pair

v0.2.15

Fixed

• Bug where template/complement pairs with small negative time between them would not be chosen (rounding error).

Added

• Option to set --no_end_penalties in filter_pairs. This option favours partial matches and avoids unbounded negative pairing scores

v0.2.14

Fixed

• Bug where template/complement pairs with no time between them would not be chosen

v0.2.13

Added

• Option to set --threads in filter_pairs

Updated

• Updated defaults in readme for duplex basecalling (chunks_per_runner 16 -> 416)