#!/bin/bash

READDIR="/home/reads/" # Directory all reads are stored in
GENOME="/home/ref_chr_17.dat" # reference genome
JUMP="ref_chr17.hg.19.mosaikh15" # Mosaik jump database
THREADS="24" # no. of threads available
NETWORKPE="MOSAIK/networkFile/2.1.26.pe.100.0065.ann" # Mosaik pe neural network file
NETWORKSE="MOSAIK/networkFile/2.1.26.se.100.005.ann" # Mosaik se neural network file
# Output must be converted to SAM/BAM with MosaikText


for file in $READDIR*; do prefix=${file##$READDIR}; prefix=${prefix%%.fastq}; MosaikAligner -in $file -out $prefix.dat -ia $GENOME -p $THREADS -j $JUMP -annpe $NETWORKPE -annse $NETWORKSE;done

