Checks if the bam index files in a directory are newer than their corresponding bam files.

bam_index.sh

#!/bin/bash

# Directory of the directory you want to scan
DIR="ENTER DIRECTORY HERE"

TOTALBAMS=0
OLDINDEX=0
UNINDEXED=0

for file in $DIR*.bam; do # Iterate over all bam files in given directory
    ((TOTALBAMS++)) #Count the bam
    if [ -f "$file.bai" ]; then # If index exists then check if its newer than bam
        if [ "$file" -nt "$file.bai" ]; then 
            ((OLDINDEX++)) # If bam is newer then increment old index counter
        fi
    else
        ((UNINDEXED++)) # If index doesn't exist then increment unindexed
    fi
done

printf "Total bams in directory: $TOTALBAMS\n"
printf "Old bams: $OLDINDEX\n"
printf "Unindexed bams: $UNINDEXED\n"