Metadata-Version: 2.1
Name: capcruncher
Version: 0.2.2
Summary: An end-to-end solution for processing Capture-C, Tri-C and Tiled-C data
Home-page: https://github.com/sims-lab/CapCruncher.git
Author: asmith
Author-email: alastair.smith@ndcls.ox.ac.uk
License: GNU GENERAL PUBLIC LICENSE Version 3
Platform: UNKNOWN
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: POSIX :: Linux
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: Implementation :: CPython
Description-Content-Type: text/markdown
Provides-Extra: stats
Provides-Extra: plotting
License-File: LICENSE

# CapCruncher

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## Analysis software for Capture-C, Tri-C and Tiled-C data.

CapCruncher is a tool designed to automate the processing of Capture-C, Tri-C and Tiled-C data from FASTQ files, the package is written in python and  consists of an end-to-end data processing pipline together with a supporting command line interface to enable finer grained control. The pipeline provided is fast, robust and  scales from a laptop to a computational cluster. 

For further information see the [documentation](https://capcruncher.readthedocs.io/en/latest/)

## Changelog

### CapCruncher v[0.2.2](https://github.com/sims-lab/CapCruncher/compare/v0.2.0...v) (2022-03-03)

### Bug Fixes

* **alignment filtering:** Prevent cluster errors due to lack of allocated memory. ([#153](https://github.com/sims-lab/CapCruncher/issues/153)) ([c77c2fd](https://github.com/sims-lab/CapCruncher/commit/c77c2fd3c2374be5b5838c5b8e8e609f2debe201)), closes [#149](https://github.com/sims-lab/CapCruncher/issues/149) [#150](https://github.com/sims-lab/CapCruncher/issues/150) [#143](https://github.com/sims-lab/CapCruncher/issues/143) [#152](https://github.com/sims-lab/CapCruncher/issues/152) [#151](https://github.com/sims-lab/CapCruncher/issues/151)
* **alignment filtering:** Enabled max memory adjustment for alignment filtering ([#156](https://github.com/sims-lab/CapCruncher/issues/156)) ([05daf2d](https://github.com/sims-lab/CapCruncher/commit/05daf2da4bbecd38f0937431d050e40e1c5512ae))
* **packaging:** Fix issue with missing report text file ([#157](https://github.com/sims-lab/CapCruncher/issues/157)) ([b172c8b](https://github.com/sims-lab/CapCruncher/commit/b172c8b9d50d93a40f89475b768cf83da3437b08))
* **pipeline:** Fix dask client shutdown related errors ([#154](https://github.com/sims-lab/CapCruncher/issues/154)) ([80f1f1b](https://github.com/sims-lab/CapCruncher/commit/80f1f1bf3ff2550c8612a4e4d8f3e8b53c7268d3))
* **report:** Fixes error when generating a report for a single sample([#149](https://github.com/sims-lab/CapCruncher/issues/149)) ([3509c7c](https://github.com/sims-lab/CapCruncher/commit/3509c7c0f3d6d383216f0d5c8d1f06a63a4f811b))


### Features

* **alignment annotation:** Enabled biasing of duplicate removal towards trans reporters ([#151](https://github.com/sims-lab/CapCruncher/issues/151)) ([2de4e35](https://github.com/sims-lab/CapCruncher/commit/2de4e35e57f99711c2340f0b966c73eb59f30695)).
This effetively increases the proportion of cis interactions in comparison to trans.
* **preprocessing:** Reduced disk space required by fastq files ([#150](https://github.com/sims-lab/CapCruncher/issues/150)) ([b43dff2](https://github.com/sims-lab/CapCruncher/commit/b43dff2481e2978d920f4b3077f286722c5d34d3))
* **reporters compare:** Improved the utility of the reporters-compare CLI ([#145](https://github.com/sims-lab/CapCruncher/issues/145)) ([be0b8b0](https://github.com/sims-lab/CapCruncher/commit/be0b8b06d1841d3d1849ec20c4be033005c44e5f))
* **utilities:** Added CLI utility ti get viewpoint coordinates from capture oligos ([#144](https://github.com/sims-lab/CapCruncher/issues/144)) ([a7ffcaf](https://github.com/sims-lab/CapCruncher/commit/a7ffcaf785fde16f19deae46091b2eb754db16fd))





