v2.10.0 - Major release

CHANGES IN VERSION 2.10.0

NEW FEATURES

o New utility - hicpro2higlass.sh to convert HiC-Pro output into higlass .cool files

o HiC-Pro is now availabe as a Singularity container !

o hicpro2juicebox.sh utility now supports alof HiC-Pro format (< 2.7.5)

SIGNIFICANT USER-VISIBLE CHANGES

o N_CPU parameter is now correcly used for the mapping step. R1 and R2 reads are now mapped using N_CPU/2 CPUs

o add simple script for unit testing 'test-op'

o udpate R scripts to be compatible with the lastest ggplot2 version (>2.2.1) and fix graphical bugs in quality controls

o add new checks on input files and configuration files

o Only provide HindIII annotation files for Mouse and Human as examples.

BUG FIXES

o Remove the --user option during iced installation

o R sessions are no longer saved and restored

o hicpro2fithic - bug fix when no -o option specified

o Fix bug to avoid floating values in valid pair positions

o Fix bug in order of samtools sort parameter in bowtie_combine.sh

o Fix bug in output option of makeViewpoints

o fix bugs in plots of no trans interactions were detected

o fix bug in split_reads.py when -o is specified

o fix issue in hicpro2juicebox.sh. The first column was duplicated, and position are now 1-based

o fix bug in ice_norm.sh when HiC-Pro is run with -s ice_norm option