FitHiChIP major release

This version contains a major upgrade of both methodology and configuration parameters:

1. implements a novel bias regression technique, in addition to original distance decay modeling, to find out the statistical significant interactions.
2. Supports both coverage specific bias normalization, as well as normalization using ICE.
3. Implements a novel peak to peak background specific interaction detection, and applies it specifically for peak to all (default) interaction modeling. The proposed background modeling is found to significantly reduce the number of false positive interactions.
4. Supports overwriting existing FitHiChIP outputs (if user wants to overwrite the existing output files with a new execution)

FitHiChIP + HiCPro - Release 3.0

Changes done in this release:

1. Main executable is modified for more stringent checking of the input paramters, HiC-Pro installation directory.
2. Minor changes of the source code of merging nearby interactions.
3. Updating sample configuration file and sample test scripts.
4. Bedtools latest version (2.26) support and corresponding adjustment in the code

FitHiChIP_HiCPro - 2nd release

Updated code with the following modifications:

1. Updated bias correction routines with peak and non-peak specific bias values.
2. Added an optional routine of merging the nearby interactions. If user opts this option, interactions whose both ends are very close (within a bin) are represented as a single interaction.
3. Minor bug fix regarding the distance threshold settings.

FitHiChIP_HiCPro - 1st release

Software to analyze HiChIP data, by getting the statistical significant interactions using FitHiC.
The input paired end reads are provided from the HiC-Pro package.
The pipeline creates the interaction matrix, considers CIS interactions within a specified distance range, applies FitHIC on the raw contact count, and also generates filtered interactions using a bias correction method.