supp_align_query.sh

#!/bin/bash

REGION="$1"
WORKDIR="$2"

for f in "$WORKDIR"/*.bam;
do
    if [ -f "$f.bai" ]
    then
        #echo "File: $f"
        with_sa="$(samtools view "$f" "$REGION" -@8 | awk '$21 ~ /chr[0-9MSID,+]*;/ {print $1, $6, $21}')"
        while read -r read_data
        do
            SAs="$(echo "$read_data" | grep -o 'chr[0-9MSID,+]*;')"
            [[ -z "$SAs" ]] && continue
            #echo "Read: $(echo "$read_data" | cut -d' ' -f1)"

            while read -r sa
            do
                start_pos="$(echo "$sa" | cut -d, -f2)"
                chrom="$(echo "$sa" | cut -d, -f1)"
                cigar="$(echo "$sa" | cut -d, -f4)"
                quality="$(echo "$sa" | cut -d, -f5)"
                echo "$cigar" | grep -Eo '[0-9]+[MSID]' | while read -r cig
                do
                    len="${cig::-1}"
                    case "${cig:(-1)}" in
                        M)
                            echo "Matches at $chrom:$start_pos-$((start_pos+len)) (length:$len, quality:$quality)"
                            break
                        ;;
                        S)
                            ((start_pos+=len))
                        ;;
                        I)
                        ;;
                    esac
                done
            done <<< "$SAs"
        done <<< "$with_sa"
    fi
done