Capcruncher

What's Changed
* fix(annotation): Corrects only null values for "get" intersections by alsmith151 in https://github.com/sims-lab/CapCruncher/pull/222
* build(deps): Update pyarrow requirement from <14.0.0,>8.0.0 to >8.0.0,<15.0.0 by dependabot in https://github.com/sims-lab/CapCruncher/pull/216
* chore(CI): Run workflow on PRs by alsmith151 in https://github.com/sims-lab/CapCruncher/pull/225
* Fix to sorting on chromosomes with non-integer names (e.g. 'X') by mtekman in https://github.com/sims-lab/CapCruncher/pull/224
* feat(pipeline): regenerate fastq from capcruncher results by alsmith151 in https://github.com/sims-lab/CapCruncher/pull/226

New Contributors
* mtekman made their first contribution in https://github.com/sims-lab/CapCruncher/pull/224

**Full Changelog**: https://github.com/sims-lab/CapCruncher/compare/v0.3.7...V0.3.8

* Altered the stats report to better include trimming and FLASh stats.
* Updated how statistics are stored for the pipeline run. This should enable greater flexibility to add additional stats later.
* Fixed bug in alignment_filtering causing a freeze in the pipeline. This appears to be an issue with duckdb
* Pinned additional requirements to try and avoid similar errors.
* Additional bug fixes and improvements

What's Changed
* fix: do not translate fastq names for fastqc by alsmith151 in https://github.com/sims-lab/CapCruncher/pull/210
* fix(pipeline): ignores viewpoint validation by alsmith151 in https://github.com/sims-lab/CapCruncher/pull/212
* build(deps): Update pandas requirement from <=2.0.1 to <=2.1.1 by dependabot in https://github.com/sims-lab/CapCruncher/pull/211
* build(deps): Update pysam requirement from <=0.19.1,>0.15.0 to >0.15.0,<=0.21.0 by dependabot in https://github.com/sims-lab/CapCruncher/pull/208
* build(deps): Update snakemake requirement from <=7.30.2 to <=7.32.4 by dependabot in https://github.com/sims-lab/CapCruncher/pull/206
* build(deps): Update pyarrow requirement from <12.0.0,>8.0.0 to >8.0.0,<14.0.0 by dependabot in https://github.com/sims-lab/CapCruncher/pull/205


**Full Changelog**: https://github.com/sims-lab/CapCruncher/compare/v0.3.5...v0.3.6

What's Changed
* feat: enable pileups with multiple viewpoint bins by alsmith151 in https://github.com/sims-lab/CapCruncher/pull/202
* feat: add validation during pipeline run by alsmith151 in https://github.com/sims-lab/CapCruncher/pull/203
* fix: oom when counting by alsmith151 in https://github.com/sims-lab/CapCruncher/pull/204
* chore: clean-up repo by alsmith151 in https://github.com/sims-lab/CapCruncher/pull/196
* build(deps): Update plotly requirement from <=5.10.0,>5.0.0 to >5.0.0,<=5.17.0 by dependabot in https://github.com/sims-lab/CapCruncher/pull/209

Additional

* capcruncher-tools now no longer an optional dependency. Full integration into the package has been performed


**Full Changelog**: https://github.com/sims-lab/CapCruncher/compare/v0.3.4...v0.3.5

What's Changed
* fix: converted all viewpoint names to strings by alsmith151 in https://github.com/sims-lab/CapCruncher/pull/197
* feat: reduce io memory during pipeline run alsmith151 in https://github.com/sims-lab/CapCruncher/pull/198
* feat: capcruncher utilities dump cli added. by alsmith151 in https://github.com/sims-lab/CapCruncher/pull/199
* fix(pipeline): corrected under counting by alsmith151 in https://github.com/sims-lab/CapCruncher/pull/200


**Full Changelog**: https://github.com/sims-lab/CapCruncher/compare/v0.3.3...v0.3.4

What's Changed
* fix: cis-and-trans stats by alsmith151 in https://github.com/sims-lab/CapCruncher/pull/195 - Viewpoint region was excluded from number of cis interactions in tiled-c mode. Now corrected.


**Full Changelog**: https://github.com/sims-lab/CapCruncher/compare/v0.3.2...v0.3.3