capcruncher 0.2.0

An end-to-end solution for processing Capture-C, Tri-C and Tiled-C data

CapCruncher

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

Changelog

CapCruncher v0.2.0 - (2022-02-07)

Bug Fixes

• CLI: Fixed help option not being displayed when running capcruncher pipeline (#129) (9f09093)
• Deduplication: Prevents excessive memory usage during duplicate removal (#136) (b175978)
• Packaging: Fixed bug after updating pyyaml to latest version (#122) (7d76b5f)
• Packaging: Added missing dependencies (seaborn and trackhub) to setup.cfg (550a882)
• Packaging: Fixed packaging long description. (#115) (6f716d1)
• Pipeline: Fixes issue with tasks going over their allotted number of cores. (#133) (27cd193)
• Pipeline: Fixes error during deduplication when using gzip compression (#134) (01ff56b)
• Pipeline: Re-partition reporter slices after filtering (#124) (db72c56)
• Reporter comparisons: Fixed an issue when no data exists for a viewpoint for a given sample (#139) (e720029)
• Storage: Fix link common cooler tables (#137) (4836fbe)

Features

• CLI: Enables pileup normalisation using a set of regions supplied as a bed file (#121) (9c587ff)
• Packaging: Moved all configuration from setup.py to setup.cfg. (#114) (4835da4)
• Pipeline: Expanded the number of viewpoints that can be processed (#128) (8fcb576)
• Pipeline: Capability to normalise pileups (bedgraphs/bigwigs) by a set of supplied regions. (#125) (bab07ea)
• Pipeline: Enable optional compression during fastq split and deduplicate (#131) (0c32b73)
• Pipeline: Enabled the use of custom filtering orders (#119) (b57ebe8)
• Pipeline: Reduced disk space required by pipeline by removing intermediate files (#135) (d6c4302)
• Pipeline:: Reporter counting now performed in parallel on separate partitions before collating. (#117) (aae5356)
• Pipeline: Reverted without_cluster for reporter comparisons (#140) (f847d28)
• Storage: Reduce disk space taken up by reporters (slices and counts) (#138) (7659a8c)