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CHANGELOG
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CHANGELOG
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0.9.28
- Fix Biopython import (#182), thanks @rlowe-altoslabs!
0.9.27
- Fixed an issue with Colorbar.draw_all in recent versions of Matplotlib
0.9.26
- Fixed issue #135 where insulation scores were NaN when using geometric mean
- Fixed issue #136 that prevented the use of -r parameter in fanc insulation
- Added option to ignore sambamba when using sam_sort or auto
- Fixed an issue with Juicer fieles when normalisation info is missing
- Fix issue #163 where boundaries might be reported multiple times in rare cases
0.9.25
- Fixed an issue with plotting insulation scores using fancplot
- Fixed an issue with aggregate plots and float coordinates
0.9.24
- Fixed an issue recognising quality cutoffs in fanc map when splitting FASTQ files
- Support for bwa-mem2
- Fixed an issue with fancplot --window-size
- Fixed an issue with fanc expected where the plot did not respect the -N parameter
0.9.23
- Fixed compatibility with Juicer v9 hic files
- Fixed issue with loop strength calculation caused by out-of-bounds regions
0.9.22
- to-fanc function consolidates matrix conversion to FAN-C
- speed up 4D nucleome pairs file loading
- reduce downsample memory consumption (thanks @wangfuzhou110)
0.9.21
- Help text improvements
- Minor plotting fixes
0.9.20
- Fixed an issue retrieving out of bounds matrices with Juicer files
- Fixed an issue in Juicer files with missing normalisation vectors for small chromosomes
- Improved EV orientation using GC content by ignoring (but warning about) missing chromosome sequences
0.9.19
- Copy read filtering stats when merging pairs files
- Fix missing normalisation vector info that affects some Juicer files
0.9.18
- Fix LinePlot color handling
- Fix hanging of fanc map in some cluster setups
0.9.17
- Fix boundaries command so it works on all region-based files (BED, GFF, BigWig, ...)
0.9.16
- Fix Matplotlib error due to existing default colormaps
0.9.15
- Option to plot aggregate loops below or above matrix diagonal
- Warn, but no longer crash on too small chromosomes in compartments EV calculation
0.9.14
- Fixed a multiprocessing issue with fanc map
0.9.13
- Fix bug with retrieving off-diagonal, lower triangular matrices from Cooler
0.9.12
- Fix Cooler problem with Virtual4CPlot
0.9.11
- Fix Juicer expected value vector length
- Fix pairs import issue due to missing multiprocessing manager
0.9.10
- Restore ability to bin regions on the fly in LinePlot and BarPlot
0.9.9
- Report number of pairs as total in stats and split stats plot in alignment and pairs plots
- Fix Cooler bias vector compatibility (fixes expected values)
- Fix Cooler attributes list
0.9.8
- Fix mode parameter for matrix comparisons
- Fix explicit Cooler weight query
- Speed up region and edge iterators in Cooler objects
0.9.7
- NumExpr logging fix
0.9.6
- Fix from-cooler output file
0.9.5
- Option in fancplot and in config file to export txt in PDFs as actual text, not as paths
- Properly raise exception in main thread if SAM file is unsorted
- Fix error with uncorrected Cooler matrices
0.9.4
- Fix Cooler to FAN-C conversion
0.9.3
- Improved performance for possible values calculation, especially for matrices with sparse mappability
- Fix API read pairs merge
0.9.2
- Add a parameter for fanc auto to choose RE distance cutoff manually
0.9.1
- Fix issue where ICE would fail for chromosomes without signal
0.9.0
- Support for VC and SQRT_VC normalisations using --norm-method
- Support for choosing Juicer normalisation method on the command line using "@" notation
- Convenience function for saddle plot in Python API
- Convenience function for aggregate plot in Python API
- Updated function for distance decay in Python API
- Fix PCA plot axis labels
- Fix bug when enabling imputation of contacts in insulation score calculation
- Fix x axis limits in LinePlot
- Increased slice size in loops annotation for efficiency
- Fix Cooler out of bounds error
- Added support for expected value caching in Cooler files
- Fix expected values return value when requesting only a single chromosome
- Fix random freezing of multiprocessing workers by using "spawn" context
0.8.39
- Fix for wrong barplot alignment
0.8.38
- Fix for using fanc pca without -r argument
0.8.37
- Fix for --split-fastq command in fanc map
0.8.36
- Fix crash due to multiprocessing / threading incompatibility
- Fix ICE balancing bias vector
- Fix axis label for Hi-C stats plot
0.8.35
- Fix genome partitioning for integer input
0.8.34
- Fix fanc fragments bug where it would not work with bin sizes
- Fix Juicer issue with missing normalisation information
- Add support for using multiple regions in PCA analysis
0.8.33
- Do not raise exception when when no contacts between specific chromosomes are found in Juicer file
0.8.32
- Fix for 4D nucleome pairs format import
- Error when subsetting on files other than FAN-C
0.8.31
- Remove qname_ix references left over from legacy code
- Force recalculation of aggregate matrices in tad strength
0.8.30
- Fix a bug in Cooler file expected value calculation
0.8.29
- ensure juicer tools can be found when running to-juicer
- Fix a bug when manually specifying juicer resolutions
0.8.28
- Remove unsorted BAM files produced by auto
- Fix an issue with difference matrices where regions were incorrectly masked
0.8.27
- Fix an issue where cooler files could not be generated for highly sparse matrices
- Fix help text display for fanc map
0.8.26
- Faster edge iterators with speedups up to 10-15x
- Option to deep-copy a Hi-C (or related) matrix in fanc hic
- O/E transformation of individual edges is now possible, not just whole matrices
- Startup and cleanup commands for fanc auto --run-with sge
- TAD, loop, and compartment strength functions
0.8.25
- Improved subsetting that maintains uncorrected matrix version
- Removed redundant calculation of expected values when retrieving bias vector
- Fixed msgpack 1.0.0 compatibility
- Improved chimeric read resolution
0.8.24
- Silence divide by zero warning in compartment analysis
- Fix AB domain reporting
0.8.23
- Fix a bug where plotting a gene panel to PDF would crash
- Optimised file handling for pairs generation
0.8.22
- Juicer compatibility improvements
- Fix for a bug in fanc dump which ignored expected value normalisation in some cases
- Improved compartments help text
0.8.21
- Temporary file support for Juicer and Cooler files
0.8.20
- Added support for multiple restriction enzymes in fanc fragments, pairs, map, and auto
- Optimised binning for large number of very small contigs
0.8.19
- Fixed issue # 9 where BED files were not loaded correctly as genome files
0.8.18
- Fix for an index bug that could lead to table write errors in some settings
- add from-txt capability to fanc
- Support for loading gzipped FASTA files as genome. Closes issues #1 and #2
- Updated fanc fragments. Note that the --chromosomes argument now requires a comma-separated list as input. Closes issue #4
- Support for multi-threaded SAM/BAM sorting with sambamba. Closes issue #5
- Check for equal bin sizes before combining matrix for split plot. Fixes issue #7
0.8.17
- Renamed --tads-flyamer to --tads-imakaev in fanc aggregate
- option for strings passed to max_dist in triangular matrix plot API