#!/bin/sh -e

##########################################################################
#   Script description:
#       Test bowtie2 on examples provided
#       http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
#       
#   History:
#   Date        Name        Modification
#   2019-03-17  Jason Bacon Begin
##########################################################################

usage()
{
    printf "Usage: $0 \n"
    exit 1
}


##########################################################################
#   Main
##########################################################################

if [ $# != 0 ]; then
    usage
fi

##########################################################################
#   Function description:
#       Pause until user presses return
##########################################################################

pause()
{
    local junk
    
    printf "Press return to continue..."
    read junk
}

cat << EOM

This script follows the bowtie2 "Getting Started" section of the manual:

http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml

EOM
pause

examples_dir=%%EXAMPLESDIR%%
bowtie2-build $examples_dir/reference/lambda_virus.fa \
    lambda_virus
printf "Done indexing...\n"
pause

bowtie2 -x lambda_virus -U $examples_dir/reads/reads_1.fq -S eg1.sam
printf "Done with alignment.\n"
pause
more eg1.sam

bowtie2 -x lambda_virus -1 $examples_dir/reads/reads_1.fq -2 $examples_dir/reads/reads_2.fq -S eg2.sam
printf "Done with paired end example.\n"
pause
more eg2.sam

bowtie2 --local -x lambda_virus -U $examples_dir/reads/longreads.fq -S eg3.sam
printf "Done with local alignment example.\n"
pause
more eg3.sam