merge

#!/bin/bash

# module init required when running on non-OSG resources, and has to sourced
# before set -e as sometimes it exits non-0 when a module environment is 
# already set up
. /cvmfs/oasis.opensciencegrid.org/osg/sw/module-init.sh

set -e

module load samtools/1.3.1
module load java/8u25

# 1 input file is possible, but samtools can't handle that
COUNT=`ls *.bam | wc -l`
if [ $COUNT = 1 ]; then
    echo "Only 1 input give. Ouput will be a copy of that one input"
    mv *.bam $1-merged.bam
    exit 0
fi

# remove "empty" inputs
for F in `ls *bam`; do
        SIZE=`du -sb $F | cut -f 1`
        if [ $SIZE -lt 50 ]; then
                echo "Removing $F due to it being empty"
                rm $F
        fi
done

echo
echo
ls -l
echo
echo

# no input files left
COUNT=`ls *.bam 2>/dev/null | wc -l`
if [ $COUNT = 0 ]; then
    echo "No bam files left - creating a new one"
    touch $1-merged.bam
    exit 0
fi

samtools merge $1-merged.bam *.bam