v0.3.14

Fix to package generation

Full Changelog: v0.3.13...v0.3.14

v0.3.13

What's Changed

• fix(pipeline): fastqc rule uses the wrapper script by @alsmith151 in #273
• Ensure no special chars in viewpoints by @alsmith151 in #275
• fix(docs): update icen documentation by @alsmith151 in #276
• Docs update plotting documentation by @alsmith151 in #278
• chore: Remove duplicate entries in bedgraph files by @alsmith151 in #289
• feat(interactions-compare-summarise): improve speed and reduce complexity of code by @alsmith151 in #290
• Fix(polars) update drop method for compatibility by @alsmith151 in #300
• build(deps): Update pydantic requirement from <2.6.0,>2.4.0 to >2.4.0,<2.11.0 by @dependabot in #301
• build(deps): Update polars requirement from <=0.19.15 to <=1.6.0 by @dependabot in #297
• build(deps): Update pybedtools requirement from <=0.9.0 to <=0.9.1 by @dependabot in #256
• fix(genome_digest): update write_csv to use include_header by @alsmith151 in #306
• build(deps): Update pyranges requirement from <=0.0.129 to <=0.1.2 by @dependabot in #304
• build(deps): Update trackhub requirement from <=0.2.4 to <=1.0 by @dependabot in #302
• build(deps): Update cooler requirement from <=0.9.2 to <=0.10.3 by @dependabot in #303
• build(deps): Update ujson requirement from <=5.7.0 to <=5.8.0 by @dependabot in #245

Full Changelog: v0.3.12...v0.3.13

v0.3.12

What's Changed

• fix(packaging): Corrected some install errors
• chore(CI): update CI pipeline by @alsmith151 in #269
• feat(pipeline): Improve error reporting by @alsmith151 in #270

Full Changelog: v0.3.11...v0.3.12

CapCruncher v0.3.1 1 - Bugfix for genome digest

What's Changed

• chore(packaging): split requirements by @alsmith151 in #259
• fix(deps): PuLP<2.8.0 by @alsmith151 in #264
• fix: install "full" capcruncher package by @alsmith151 in #263
• chore(deps): Bumped minimum capcruncher-tools version by @alsmith151 in #262

Full Changelog: v0.3.10...v0.3.11

CapCruncher v0.3.10 - Bump dependencies

What's Changed

• Update requirements.txt with latest package by @alsmith151 in #252

Full Changelog: v0.3.9...v0.3.10

CapCruncher v0.3.9 - Bugfixes and Performance improvements

What's Changed

• build(deps): Update plotly requirement from <=5.17.0,>5.0.0 to >5.0.0,<=5.18.0 by @dependabot in #218
• chore: pyarrow minimum to 14.0.1 by @alsmith151 in #231
• fix(deduplicate-slices): Wrong Snakemake parameters supplied to script when empty input by @alsmith151 in #232
• Fixes UCSC hub generated when create == no by @alsmith151 in #230
• CCTrack file_type now accepts all cb tracks by @alsmith151 in #229
• fix(report): Use the active kernel for report generation by @alsmith151 in #233
• feat(utils): added make_chicago_map cli command by @alsmith151 in #228
• Reduce annotation memory usage by @alsmith151 in #236
• Feat enable aggregated track plotting by @alsmith151 in #235
• chore(deps): pinned polars by @alsmith151 in #240
• feat(pileup): added to_pyranges by @alsmith151 in #227
• fix(pipeline): using fastqc snakemake wrapper by @alsmith151 in #239
• fix(pipeline): Use recursion to format config dictionary by @alsmith151 in #242
• fix(ucsc-hub): Correct errors when generating the "Replicates" composite track by @alsmith151 in #243
• feat(pipeline): plotting logs moved by @alsmith151 in #238
• fix(cis-and-trans-stats): fixes OOM error by @alsmith151 in #250
• build(deps): Update pydantic requirement from <2.5.0,>2.4.0 to >2.4.0,<2.6.0 by @dependabot in #248
• build(deps): Update pyranges requirement from <=0.0.127 to <=0.0.129 by @dependabot in #247

Full Changelog: V0.3.8...v0.3.9

CapCruncher v0.3.8

What's Changed

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

New Contributors

• @mtekman made their first contribution in #224

Full Changelog: v0.3.7...V0.3.8

CapCruncher v0.3.7

• 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

CapCruncher v0.3.6

What's Changed

• fix: do not translate fastq names for fastqc by @alsmith151 in #210
• fix(pipeline): ignores viewpoint validation by @alsmith151 in #212
• build(deps): Update pandas requirement from <=2.0.1 to <=2.1.1 by @dependabot in #211
• build(deps): Update pysam requirement from <=0.19.1,>0.15.0 to >0.15.0,<=0.21.0 by @dependabot in #208
• build(deps): Update snakemake requirement from <=7.30.2 to <=7.32.4 by @dependabot in #206
• build(deps): Update pyarrow requirement from <12.0.0,>8.0.0 to >8.0.0,<14.0.0 by @dependabot in #205

Full Changelog: v0.3.5...v0.3.6

CapCruncher v0.3.5

What's Changed

• feat: enable pileups with multiple viewpoint bins by @alsmith151 in #202
• feat: add validation during pipeline run by @alsmith151 in #203
• fix: oom when counting by @alsmith151 in #204
• chore: clean-up repo by @alsmith151 in #196
• build(deps): Update plotly requirement from <=5.10.0,>5.0.0 to >5.0.0,<=5.17.0 by @dependabot in #209

Additional

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

Full Changelog: v0.3.4...v0.3.5