CHANGELOG

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