V3.1.3

Version 3.1.3

• Check third parties at the beginning of pipeline.
• Change output file names of hicstuff cutsite.
• Reverse reads if necessary in the hicstuff cutsite.
• Improve figures plot.

v3.1.2

• Add support for compressed genome
• Repare camembert plot
• Fix deprecation error form matplotlib 3.5.0
• correctly report when matrix rows do not match header in hics_flexible_loader
• Pin matplotlib version and docutils

Standardized help messages

• Improve dockerfile base layer to address compatibility bug with libcrypto.
• Standardize the format of default values in CLI help messages.
• Fix bug in distancelaw causing integer conversion of custom log bases

Use miniconda layer for docker and improved P(s) normalisation

• The docker image is now based on the miniconda3 layer, which greatly reduces build times.
• P(s) normalization factor is only computed based on P(s) values within xlim. Before that, all values above the lower bound were used. Because longer distances have much lower interaction values, this makes a small difference in practice.

More flexible view subcommand

New --min option in hicstuff view to set minimum colorscale value. Modify --max option to support raw values.

Safe concurrency

When indexing is required, hicstuff pipeline now generates the index in the run's temporary folder to avoid conflict between concurrent hicstuff pipeline instances. Index detection is more robust and edge cases are better handled.

Improved iteralign

• Make iteralign output name-sorted alignments
• Make replace all temporary SAM files from iteralign by BAM files
• Remove extraneous sorting step when using iteralign

v1.2.26: Fix PCR filter and improve scalogram CLI

• PCR filter now works as expected (removes all fragments with both reads at exact same coordinates except 1)
• scalogram now accepts genomic coordinates for range and index options

v1.2.25: Fix CLI bugs in view, correct bug in pipeline

• Fixed a bug that crashed hicstuff view when computing a matrix ratio without using -n and -l.
• Fixed a bug in hicstuff pipeline that caused some pairs not to be flipped correctly
• Added support for pairs files as input in hicstuff distancelaw

v1.2.22: Fix --region option in hicstuff view

Resolve bug that lost chromosome order when using hicstuff view --region if their names did not follow alphanumeric order.