Summer 2020 release bug fix 1

• patch hicCorrelate
• hicBuildMatrix: Better help text
• patch for hicPlotMatrix if matrix does not start at 0 and --region is used
• bug fix for remove option in hicAdjustMatrix

Summer 2020 release

• Major update for hicDetectLoops: Results are now closer to HiCCUPS, it is faster and needs less memory.
• hicHyperoptDetectLoops: New tool to compute the best parameter setting if the number of expected loops is given and a protein boundary file (e.g. CTCF on mammals) is provided
• hicHyperoptDetectLoopsHiCCUPS: New tool to compute the best parameter setting for Juicers HiCCUPS. HiCCUPS and all its dependencies are not part of HiCExplorer and must be provided by the user. Number of expected loops and a protein boundary file (e.g. CTCF on mammals) must be provided.
• hicMergeDomains: New tool to compute a merge of TADs computed on different resolutions. Moreover it provides a cleaning of the boundaries with the help of a protein peak file, and the hierarchical dependencies of TADs can be plotted. This tool is the result of the Bachelor thesis from Sarah Domogalla (@SarahMaria27). Thanks for your contribution!
• hicDifferentialTAD: New tool to compute differential TADs between two samples
• Bug fix for hicFindTADs: The format of the intermediate z-score matrices are now depending on the format of the input Hi-C matrix
• Bug fix for chic*-modules: Fixate range is now correct applied.
• Bug fix for hicPlotMatrix:
  • multiple bigwig tracks in the vertical setting are now supported
  • correct plot of bigwig if the given matrix does not start at the beginning of the chromosome
  • new parameters 'increaseFigureWidth' and 'increaseFigureHeight' to add more space to the plot if multiple bigwigs are plotted. Adjust this parameter to correct the plot of the heatmap which may be not quadratic anymore.
  • restriction of the loop regions to the user given range. This effects especially SVGs that will now contain less objects as before.
• New feature for hicBuildMatrix:
  • multiple restriction cut sequences, dangling ends and restriction cut sites files are now supported
  • restriction cut sequences, dangling ends and restriction cut sites files are now mandatory parameters. This is now enforced to guarantee a correct detection of self ligations and self circles
• hicPrepareQCreport: New support for multiple dangling ends
• hicQuickQC: restriction cut sequences, dangling ends and restriction cut sites files are now mandatory parameters
• hicFindRestSite: gz support for fasta file
• hicAggregate: interactions between two bed files by comparing every row in the first bed file with its corresponding row in the second file. (issue #390)
• hicAdjustMatrix: fix #341, 454
  • fixed --action remove: it actually remove the part from the matrix previously was masking it
  • the case where the end of the chromosome need to be removed.
• New Azure testing for the general test cases, the trivial ones run on travis. Makes it faster, maybe around half an hour to 45 mins instead of multiple hours of CI

Mid-Winter release 2020 bug fix 3

• Fixing the wrong p-value computation in for chicViewpoint. New method is more accurate for floating points.
• Fixing a bug in chicViewpointBackgroundModel and chicQualityControl if an non-existing reference point was used.
• Improving all chic* modules with a capturing of errors in sub-processes. It is now guaranteed that the computation will terminate. Either successfull or by error.
• Add option 'truncateZero' to chicViewpointBackgroundModel: This removes all zero values for the distributions before fitting to fight over dispersion.
• Add option 'decimalPlaces' to chicViewpoint to adjust the decimal places in the output for all floating values. Helpful for really small p-values
• Add option 'truncateZeroPvalues' to chicSignificantInteractions to set all p-values which are 0 to 1 and are therefore ignored.
• Add option 'truncateZeroPvalues' to chicPlotViewpoint to set all p-values which are 0 to 1 and do not disturb the presentation of real p-values

Mid-Winter release 2020 bug fix 2

• Improving the documentation
• hicPlotMatrix: add three options: change font size, change rotation of X label and change rotation of Y labels
• hicDetectLoops: add option to apply a parallelization within each chromosome
• hicPlotAverageRegions: Fixing the plotting. Thanks @lldelisle
• chic*-modules: change output from .bed to .txt

Mid-Winter release 2020 bug fix 1

This release fixes a bug in chicViewpoint that caused a crash if the data to be averaged is less than the window size.

Mid-Winter release 2020

Release 3.4 of HiCExplorer comes with improvements in the documentation and smaller bug fixes:

• Fixing a bug in hicAdjustMatrix: keep option had a bug concerning the cutting before the end of a chromosome or the start position was not from the beginning of the chromosome
• hicCompartmentPolarization was renamed to hicCompartmentalization and got some bug fixes:
  • set an offset to remove diagonals to help with the artifact they may generate
  • Removed the last quantile from the polarization calculation
  • sum devides by count at the end of the loop and only affects the final output
• Extending the option on how the observed vs. Expected matrix is computed and adding the parameter --ligation_factor to achieve a rescale behaviour of the values as it is implemented in Homer. The same changes are applied to hicTransform
• Improved the documentation
• Adding an option in hicAverageRegions to select start, end, center or start_end as start index for up/downstream range.
• hicBuildMatrix: Removed default value of binSize to enable mutually exclusive group error if not one of them is set. Behaviour so far was that the binSize was taken.
• hicPlotSVL: adding xlegend to plot of SVL ratios to indicate the data points per boxplots are the chromosome ratios
• hicQuickQC: Removed binSize option of hicQuickQC because it does not matter for QC calculation and adding a sentence to recommend the usage of restriction enzyme and dangling end sequence. Fixing bug issue #464
• hicNormalize: Adding option in hicNormalize to remove values after the normalization if values are smaller than a given threshold
• Capture Hi-C modules: Change background model distribution assumption from negative binomial to continuous negative binomial by using Gamma functions as a replacement for the binomial coefficient. Source: https://stats.stackexchange.com/questions/310676/continuous-generalization-of-the-negative-binomial-distribution/311927
• hicInfo: Implementing feature request #456. The length of chromosomes is now show in the information too

Early autumn 2019 bug fix 1

• Bug fix labels chicPlotViewpoint concerning the MB value range
• Add option to chicViewpoint to pre-compute an x-fold of value for the p-values per relative distance

Early autumn 2019

• Fixing many bugs:
  • A bug in hicDetectLoops if a sub-matrix was very small
  • A bug in hicPlotMatrix if the region defined by --region was only a chromosome and loops should be plotted too
  • A bug in hicPlotMatrix if a loop region should be plotted and chromosomeOrder argument was used too
  • A bug in hicAggregateContacts (issue #405) if chromosomes were present in the matrix but not in the bed file
  • A bug in hicAdjustMatrix concerning a bed file and consecutive regions, see issue #343
  • A bug in hicAdjustMatrix if a chromosome is present in the matrix but not in the bed file, see issue #397
  • A bug in hicCompartmentsPolarization concerning the arguments 'quantile' and 'outliers' were interpreted as strings but should be integers
  • A bug in hicAdjustMatrix concerning the 'keep' option and how matrices are reordered internally. Thanks @LeilyR

Added features as requested:

• hicPCA ignores now masked bins, see issue #342

• chicPlotViewpoint:

  • Better legend handling on x-axis
  • Peaks are now display with their fill width
  • Add option --pValueSignificantLevels to categorize the p-values in x levels (e.g. 0.001 0.05 0.1)

• chicViewpoint:

  • adding sorting via viewpoints and not by samples option (--allViewpointsList)

• Adding an option to hicNormalize to normalize via multiplication and a user defined value (see issues #385, #424)

• Restructure source code of hicAdjustMatrix to have a better accessibility to its functions from outside of main

• Improving the documentation and fixing grammar / spelling mistakes. Thanks @simonbray

• New script: hicPlotSVL to investigate short range vs long range ratios.

Late summer 2019 release

• Adding the new captured Hi-C module. Viewpoint analysis based on a background model, significant interaction detection and differential analysis are provided. Thanks to @rgilsbach and @DonStephano .
• Adding documentation for captured Hi-C module and a tutorial on how to use it.
• Adding a module to be able to detect quite fast the quality of a Hi-C data set: hicQuickQC.
• Adding a tool to merge loops of different resolutions.
• Improving validation of locations: Presorting is no longer necessary; adding feature to add 'chr' prefix to loop or protein chromosome name
• Change loop detection slightly to improve results and fixed bugs:
  • preselection p-value was ignored and only p-value was used
  • adding additional test to the peak region test to decrease false discoveries
  • exchanging pThreshold / ln(distance) to remove too low values by a share of the maximum value of the distance. New parameter 'maximumInteractionPercentageThreshold'
• Removal of the folder 'scripts' and its content. These were outdated scripts and will maybe part of regular Hi-C tools in the future.

Summer 2019

This new release updates HiCExplorer to version 3.1:

• Improved memory handling for hicCorrectMatrix with KR algorithm
• Adding a script to validate loop locations with protein peak locations
• Adding a script to compute the global compartmentalization signal
• Typos and documentation improvements.