#!/bin/bash

# Path to the input .bam file
BAM_FILE="/data/images/proton/DKlab/mr/parclip/shrimp/IFN-15mMm.bam.md.bam"

# Path to the fasta file containing the reference genome (the same as the one used for alignment)
REF_FILE="/data/results/reference/mmu/mm9/shrimp/shrimp-15mMm/mm9-stranded-mRNA.fa"

# Chosen name for the experiment (the produced files will contain this name)
SAMPLE_NAME="IFN"

# Path of the folder where the output will be saved (a new folder will be created if it does not exist already)
WORK_FOLDER="/data/images/proton/DKlab/mr/parclip/bmix/BMix-master/test/IFNb"

# Minimum coverage to consider (default is 5)
COV_MIN=5

# The tails of the binding sites with coverage lower than this value will be trimmed (default is 1)
REFINE_COV=1

# Threshold for the posterior probability used to classify substitutions (default is 0.95)
CONFIDENCE_PER=0.95

# Indicator variable which tells BMix to learn the parameters of the model independently for both strands (1), or not (0)
SEPARATE_STRANDS=0