Umi-tools

UMI-tools output is now deterministic with `--random-seed`
Many users have had issues with making UMI-tools deterministic, which previously relied upon both `--random-seed` and the enivornmental variable `PYTHONHASHSEED` being set. From `v1.1.6` only `--random seed` is required.

Please note that in some cases the implemented solution may make the output from v.1.1.6 different to previous versions, even if `--random-seed` is set to the same value. The differences will be very slight and the different outputs represent equally sensible UMI grouping/deduplication since they relate only to how ties are broken.

Thank you TyberiusPrime, christianbioinf and others for their suggestions for how to remove the dependency on `PYTHONHASHSEED` for deterministic output.

New features
* umi_tools is now deterministic when using --random-seed - TomSmithCGAT in https://github.com/CGATOxford/UMI-tools/pull/550
* Option to extract barcode from read2 only - TomSmithCGAT in https://github.com/CGATOxford/UMI-tools/pull/630
* Adds support for python 3.12 - IanSudbery in https://github.com/CGATOxford/UMI-tools/pull/657

Bugfix
* Avoids switching matplotlib backend - sshen8 in https://github.com/CGATOxford/UMI-tools/pull/640
* count_tab now correctly reads UMI and cell barcodes - eachanjohnson in https://github.com/CGATOxford/UMI-tools/pull/654
* count_tab now writes out strings not bytes - eachanjohnson in https://github.com/CGATOxford/UMI-tools/pull/654
* Installation with < python 3 prevented - IanSudbery in https://github.com/CGATOxford/UMI-tools/pull/644

Documentation
* FAQ entry regarding identification of possible duplicates reads/pairs - TomSmithCGAT in https://github.com/CGATOxford/UMI-tools/pull/631
* Improved docs regarding chimeric/unmapped/unpaired read pairs - TomSmithCGAT in https://github.com/CGATOxford/UMI-tools/pull/629

Other

* Add issue templates - TomSmithCGAT in https://github.com/CGATOxford/UMI-tools/pull/632
* Update testing suite to pytest - eachanjohnson in https://github.com/CGATOxford/UMI-tools/pull/655

New Contributors
* sshen8 made their first contribution in https://github.com/CGATOxford/UMI-tools/pull/640
* eachanjohnson made their first contribution in https://github.com/CGATOxford/UMI-tools/pull/654

**Full Changelog**: https://github.com/CGATOxford/UMI-tools/compare/1.1.5...v1.1.6

New features
- Enables read suffixes to be removed from single end data: IanSudbery in https://github.com/CGATOxford/UMI-tools/pull/591. See https://github.com/CGATOxford/UMI-tools/issues/580 for motivating issue
- Adds a script to prepare `umi_tools dedup` output for use with `RSEM`: IanSudbery in https://github.com/CGATOxford/UMI-tools/pull/609. See https://github.com/CGATOxford/UMI-tools/issues/465 and https://github.com/CGATOxford/UMI-tools/issues/607 for motivating issues

Bugfix
- Fix lack of help messages in 1.1.4 by IanSudbery in https://github.com/CGATOxford/UMI-tools/pull/586
- Fixes read suffix line end: IanSudbery in https://github.com/CGATOxford/UMI-tools/pull/611

Documentation
- Fixed docs for dedup stats filenames: msto in https://github.com/CGATOxford/UMI-tools/pull/604

New Contributors
- msto made their first contribution in https://github.com/CGATOxford/UMI-tools/pull/604


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**Full Changelog**: https://github.com/CGATOxford/UMI-tools/compare/1.1.4...1.1.5

Debug to support `python 3.11`. Thank you sjaenick for bringing this to our attention and testing (563)

New features
- Adds '--umi-separator' option to `umi_tools extract` to specify UMI separator. Thanks opplatek (548)

Optimisation
- Speeds up read pair mate writing. Significant benefit for transcriptome alignments (543)

Bugfix
- Handles `umi_tools group` output to tsv with `--per-contig` when no gene tags are present. Thanks mfansler & akmorrow13 (577)
- Fixes syntax warning in extract.py. Thanks rajivnarayan (558)
- Improves error message for incorrect command line input. Thanks epruesse (506 & 537)

**Bugfix**
- `whitelist --filtered-out` with SE reads threw an unassigned error. Thanks yech1990 for rectifying this (453)

Also includes a very minor update of syntax (455)

Updates requirements for pysam version to `>0.16.0.1`. Thanks sunnymouse25 (444)