Merge pull request #914 from deeptools/micro-c

Micro-c build matrix support

Author: joachimwolff

README.rst

@@ -16,8 +16,8 @@
 HiCExplorer
 ===========
 
-Set of programs to process, analyze and visualize Hi-C and cHi-C data
----------------------------------------------------------------------
+Set of programs to process, analyze and visualize Hi-C, Micro-C and cHi-C data
+------------------------------------------------------------------------------
 
 Sequencing techniques that probe the 3D organization of the genome generate large amounts of data whose processing,
 analysis and visualization is challenging. Here, we present HiCExplorer, a set of tools for the analysis and
@@ -26,7 +26,7 @@ of contacts, TAD detection, A/B compartments, merging, reordering or chromosomes
 `cooler <https://github.com/mirnylab/cooler>`_ and detection of long-range contacts. Moreover, it allows the visualization of
 multiple contact matrices along with other types of data like genes, compartments, ChIP-seq coverage tracks (and in general
 any type of genomic scores), long range contacts and the visualization of viewpoints.
-
+With version 3.7.6 we introduce the support for Micro-C data for the build of matrices.
 
 Single-cell Hi-C data
 ---------------------

azure-pipelines.yml

@@ -15,7 +15,10 @@ jobs:
         python.version: '3.9'
       Python310:
         python.version: '3.10'
-
+      Python311:
+        python.version: '3.11'
+      Python312:
+        python.version: '3.12'
 
   steps:
   - bash: |
@@ -66,6 +69,11 @@ jobs:
         python.version: '3.9'
       Python310:
         python.version: '3.10'
+      Python311:
+        python.version: '3.11'
+      Python312:
+        python.version: '3.12'
+
 
   steps:
   - bash: |

bin/hicBuildMatrixMicroC

@@ -0,0 +1,7 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+from hicexplorer.hicBuildMatrixMicroC import main
+
+if __name__ == "__main__":
+    main()

docs/content/News.rst

@@ -1,6 +1,14 @@
 News and Developments
 =====================
 
+Release 3.7.6
+-------------
+**27 November 2024**
+
+- Add a new hicBuildMatrixMicroC script to build matrices from Micro-C data. It is the same as hicBuildMatrix but without the enforcement of the restriction cut site file, restriction sequence and dangling end since this is not necessary for Micro-C data.
+- Update to include support for Python 3.11 and 3.12
+
+
 Release 3.7.5
 -------------
 **June 2024**

docs/content/list-of-tools.rst

@@ -8,6 +8,7 @@ Tools for Hi-C data pre-processing
 
     tools/hicFindRestSite
     tools/hicBuildMatrix
+    tools/hicBuildMatrixMicroC
     tools/hicSumMatrices
     tools/hicMergeMatrixBins
     tools/hicCorrectMatrix
@@ -98,6 +99,8 @@ For single-cell Hi-C data analysis please use `scHiCExplorer <https://schicexplo
 +--------------------------------------+------------------+-----------------------------------+---------------------------------------------+-----------------------------------------------------------------------------------+
 |:ref:`hicBuildMatrix`                 | preprocessing    | 2 BAM/SAM files                   | hicMatrix object                            | Creates a Hi-C matrix using the aligned BAM files of the Hi-C sequencing reads    |
 +--------------------------------------+------------------+-----------------------------------+---------------------------------------------+-----------------------------------------------------------------------------------+
+|:ref:`hicBuildMatrixMicroC`           | preprocessing    | 2 BAM/SAM files                   | hicMatrix object                            | Creates a Hi-C matrix using the aligned BAM files of the Hi-C sequencing reads    |
++--------------------------------------+------------------+-----------------------------------+---------------------------------------------+-----------------------------------------------------------------------------------+
 |:ref:`hicCorrectMatrix`               | preprocessing    | hicMatrix object                  | normalized hicMatrix object                 | Uses iterative correction or Knight-Ruiz to remove biases from a Hi-C matrix      |
 +--------------------------------------+------------------+-----------------------------------+---------------------------------------------+-----------------------------------------------------------------------------------+
 |:ref:`hicMergeMatrixBins`             | preprocessing    | hicMatrix object                  | hicMatrix object                            | Merges consecutive bins on a Hi-C matrix to reduce resolution                     |

hicexplorer/_version.py

@@ -2,4 +2,4 @@
 # This file is originally generated from Git information by running 'setup.py
 # version'. Distribution tarballs contain a pre-generated copy of this file.
 
-__version__ = '3.7.5'
+__version__ = '3.7.6'