v2.11.1 - Major Release

CHANGES IN VERSION 2.11.1

SIGNIFICANT USER-VISIBLE CHANGES

o Update ice_mod source organization

BUG FIXES

o Fix bug in mapping_2hic_fragments.py. 'dist' was not defined for filtered pairs (issue #185)

CHANGES IN VERSION 2.11.0

NEW FEATURES

o Improved capture-Hi-C analysis

o Add MultiQC support for HiC-Pro (issue #144)

o New utils: split_sparse.py allowing to split a genome-wide matrix into per-chromosome sparse matrices

SIGNIFICANT USER-VISIBLE CHANGES

o Filtered pairs based on min/max insert/fragment size are now distinguished from the dumped pairs

o Reads are now reported based on the 5' end and not on their middle position

o _allValidPairs extension is now changed to .allValidpairs

o Defulat MAPQ filter in the configuration file is now set to 10

o Update log reports

o Stats file per sample are not put in hic_results/stats for clarity reasons

o GET_PROCESS_SAM now generates a bam file, instead of a sam file

o FORMAT variable in the configuration is now deprecated as currently all sequencing data are encoded in phred33

o Only one BED file is now generated by build_matrix (issue #158)

o Update of Singularity image

o Small changes during installation process to deal with --user

o Update layout of quality control plots

o hicpro2juicebox - add temporary folder for sorting, and update juicer path variable (issue#147)

BUG FIXES

o Fix bug when RM_SINGLETON=0

o Fix bug in hicpro2higlass.sh - added option --balance if normalization is specified

o Fix bug in read name when merging SAM files (issue #153)

o Fix inversion between cis/long range contacts in plot_hic_contacts.R

o Fix bug in mapped_2hic_fragments.py (issue #134)

o Fix shebang in make_viewpoints.py