Rename full reference in BAM file

gistfile1.sh

mv "$input" "$input.tmp"
samtools view -h "$input.tmp" \
    | awk -F '\t' -v OFS='\t' '
    /^@SQ/ {
        $2 = "SN:chr" substr($2, 4, match($2, " ") - 4)
        print
    }

    /^@/ && !/^@SQ/ { print }

    !/^@/ {
        $3 = "chr" substr($3, 0, match($3, " "))
        print
    }' \
    | samtools view -Sb - \
    > "$output"
rm "$input.tmp"