Releases: nservant/HiC-Pro
v3.1.0 - Major Release
v3.0.0 - Major Release
CHANGES IN VERSION 3.0.0
NEW FEATURES
- vcf file can be zipped in vcf.gz
- Add a Dockerfile for automatic Docker build on DockerHub
- Set up Travis continuous testing
- iced has been removed from HiC-Pro and is now an independant module
- Add a environment.yml file for installation with conda
- HiC-Pro is now based on python3. /!\ Python2 is no longer maintained /!\
SIGNIFICANT USER-VISIBLE CHANGES
- SORT_RAM is not divided by N_CPU for samtools (#369)
- Fix bug in make_viewpoints.py if multiple viewpoints are specified in the bed file
- Add '--float' option for hicpro2higlass to manage normalized Hi-C data
- Update of the Singularity image
v.2.11.4 - Minor Release
CHANGES IN VERSION 2.11.4
BUG FIXES
o Fix major bug in parallel mode from 2.11.3
CHANGES IN VERSION 2.11.3
NEW FEATURES
o 'N' is now support in the digest_genome.py utility
o 'N' is now supported in the ligation motif (for Arima Hi-C kit)
SIGNIFICANT USER-VISIBLE CHANGES
o Update ice usage. Pull request from NVaroquaux (#323)
o Update of the sparse2dense.py utils to include insulation score (Crane et al.) format
o Update of Singularity image
o Update hicpro2juicebox.sh script for memory issue (#246)
o Update hicpro2higlass.sh script (#254)
BUG FIXES
o Check if annotation files are readable (#282)
o If RM_DUP is unset, the duplicates are not filtered (#256)
o Support both .fastq.gz and .fq.gz files (#311)
o Bug in R plots legends (#257, #250, #240)
o Fix small printing bugs in mapped_2hic_fragments.py
o N_CPU for LSF usage (#250) and bowtie2 (#262)
o Update doc (#307, #273)
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
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
v2.9.0 - Major release
CHANGES IN VERSION 2.9.0
NEW FEATURES
o update iced_0.4.2
SIGNIFICANT USER-VISIBLE CHANGES
o Fix issues with floating values in hicpro2fithic.py (F. Ay)
o Update hicpro2fithic.py script. New '-r' option to set up the data resolution (F. Ay)
o samtools >1.0 is now required
o The -s build_contact_maps option now directly creates matrix files from .allValidPairs file. It does not merge the .validPairs anymore. Please use -s merge_persample to merge .validPairs files and remove duplicates.
o Update manual and correct errors
BUG FIXES
o Fix bug for SLURM support
o Fix python path in merge_valid_interaction.sh
o Fix bug in hicpro2juicebox when chromosome names have "_"
o Fix a bug in detection of religation events
o Fix some issue with sort -T. This option is no longer used and replaced by setting the TMPDIR variable
v2.8.0 - Major release
CHANGES IN VERSION 2.8.0
NEW FEATURES
o Return bias vector after IC normalization
o New utils hicpro2fithic.py to convert HiC-Pro output into fitHiC input
SIGNIFICANT USER-VISIBLE CHANGES
o Update iced version (-> 0.4.0). This version includes a major changes on matrix filtering before iced normalization
o sparseToDense.py utils. Create output file in the current folder by default
BUG FIXES
o Fix bug in the help message of digest_genome.py
CHANGES IN VERSION 2.7.9
NEW FEATURES
o Update for capture Hi-C. New variable CAPTURE_TARGET allowing to restrict the analysis to the captured region(s)
SIGNIFICANT USER-VISIBLE CHANGES
o Update iced version (-> 0.3.0)
o Exit with an error if the restriction fragment file is set but not found. In the previous version, HiC-Pro automatically switched to DNAse mode.
o Optimisation of python scripts
v2.7.8 - Major release
CHANGES IN VERSION 2.7.8
NEW FEATURES
o Religation are now discarded and considered as invalid pairs. Religation are defined as FR read pairs involving contiguous restriction fragments
SIGNIFICANT USER-VISIBLE CHANGES
o Installation process has been changed ! Please read the manual !
o Update of sparseTodense utils. It now provides a ---perchr option to generate intrachromosomal dense contact maps
o Clean hicpro2juicebox.sh utils
BUG FIXES
o Update script allowing to check the python version
o Bug fix in R code in case of NA values
v2.7.6 - Major release
CHANGES IN VERSION 2.7.6
NEW FEATURES
o New utils : hicpro2juicebox. HiC-Pro results can now be converted into Juicebox input for visualization (A. Barrera, N. Servant)
o New utils : make_viewpoints.py. Allows to generate viewpoint from the list of valid interaction products. Initially developed for capture-C analysis
SIGNIFICANT USER-VISIBLE CHANGES
o validPairs output format was updated for Juicebox compatibility. New columns were added with restriction fragment names and mapping quality
BUG FIXES
o Fix bug in hic_inc.sh for numeric comparison
o Fix bug in bam/sam extension removal
v2.7.4 - Major release
CHANGES IN VERSION 2.7.4
NEW FEATURES
o Support for LSF scheduler thanks to J. Phlipps-Cremins
o HiC-Pro is now compatible with the HiCPlotter viewer (see https://github.com/kcakdemir/HiCPlotter)
o Add support for the SLURM scheduler thanks to A. D'Ippolito !
o Add support for the SGE scheduler thanks to G. Li !
SIGNIFICANT USER-VISIBLE CHANGES
o Update singleton reporting in pairing mode (pull request N. Varoquaux, F. Ai)
o Additional checks on input files to report more "user-friendly" errors
o Update python access in utils (pull request D. Vanichkina)
o Update iced version (0.2.1 official release)
o be careful - configuration files for installing and running HiC-Pro have been updated to manage multiple schedulers !
BUG FIXES
o Fix bugs in singleton and multiple hits reporting
o Fix bug when fastq.gz files are processed without parallel mode but using a cluster
o Bug fixed if space in the configuration file
o Bug fixed in plot_pairing_portion.R (pull request M. Blum)
o Update samtools sort for compatibility with version >1.1