Fix missing BAM indices

fix_bam_index.sh

# This quick script will check for big differences in a bams index and creation date and perform indexing.
for i in *.bam; do
    bam=${i}
    bai=${i}.bai
    bam_date=$(stat -c %Y ${bam})
    bai_date=$(stat -c %Y ${bai})
    diff=`expr ${bam_date} - ${bai_date}`
    if [ ${diff} -gt 100000 ]; then
        echo "${bam} ${diff}";
        sbatch --job-name=${bam} --partition=cpu --time=3:00:00 --cpus-per-task=32 --wrap "samtools index -@ 32 ${bam}"
    fi;
done;