Version 3.2.4

BUG FIXES:

• two submodules were imported as hcs

Full Changelog: v3.2.3...v3.2.4

v3.2.3

NEW FEATURE(S):

• Add stats subcommand to CLI

BUG FIXES:

• Fix changes in pairtools 1.1.0 (explicitly specify chrom1, chrom2, pair_type ... in pairtools sort)

Full Changelog: v3.2.2...v3.2.3

Version 3.2.2

NEW FEATURE(S):

• Add stats module to report statistics on Hi-C library processing

CHANGES:

• zcat no longer needed

BUG FIXES:

• avoid removesuffix

Version 3.2.1

NEW FEATURE(S):

• Final pairs file is now sorted and gzipped with pairtools

CHANGES:

• Docker now uses micromamba base image

BUG FIXES:

• cases when exclude is specified
• cheking number of reads in fastq

Version 3.2.0

CHANGES:

• --mat_fmt=cool by default

NEW FEATURE(S):

• by default, an un-binned .cool file is generated
• if the end user provides a --binning=INT in pipeline, a balanced .mcool file binned at multiple resolutions will be automatically generated
• specify --zoomify=False to only generate a single-resolution binned .cool
• balancing arguments can be specified with --balancing_args "..."
• --exclude=STR in pipeline to remove chromosomes from the final matrix

BUG FIXES:

• check that provided fastq/bam files have the same length before starting
• cutsite doc is fixed

Version 3.1.7

• Add --binning, --zoomify and --balancing arguments to pipeline by @js2264 in #76
• Fixed deprecated SeqUtils.GC
• cooler is a strict dependency

Full Changelog: v3.1.6...v3.1.7

Version 3.1.6

• Use local alignment for the iterative mapping mode with bowtie2
• Update deprecated sklearn pypi package requirement
• Update the docs

Version 3.1.5

• Fix file extension in hicstuff rebin.
• Fix incompatibility between lines and trim in hicstuff view.
• More flexible binning suffix support.
• Update commands.py and fix pandas >= 1.5, accordingly.

Version 3.1.4

• Correct build to make it work.
• Correct hicstuff rebin fragments size issue.

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.