log.txt

#08/25/2017
First release

#09/02/2017
Updated the ReadMe.txt files

#11/28/2017
Added the combine_multiple_replicates.pl script.
If there are multiple replicates and generated multiple *.F_GC_MAP.bed and *.perREfragStats files, then this script 
will combine all the *.F_GC_MAP.bed and *.perREfragStats files and generate a single "Sample.combined.F_GC_MAP.bed" 
and "Sample.combined.perREfragStats". Use these combined files to run the next scripts under CNV_calling folder.

Added "genome_wide_copy_number.r" script. This script will generate genome wide copy number plot. "hg19" is the
default plot paprameter.

#02/03/2018
Added exampleData folder under Read_coverage_generation. exampleData folder contains an output example file of forward and reverse read
mapped bam files from HiC-Pro pipeline. This is a MCF7 HiC data (GSE66733), subsampled to generate bam files within size limits.
run.sh file contains the commands to process the data in order to generate the *.perREfragStats and *.F_GC_MAP.bed files.
This subsampled bam files are provided to show how the input files looks like to generate the *.perREfragStats and *.F_GC_MAP.bed files for further analysis.

#04/26/2018
Fixed the bug in "kde_hmm_segmentation.r" script which sometimes tends to crash the program while running a diploid chromosome segmentation part