#!/usr/bin/bash
#sudeti homopolimer eilutes gale pagal log failus:

#https://stackoverflow.com/questions/3685970/check-if-a-bash-array-contains-a-value
function contains() {
    local n=$#
    local value=${!n}
    for ((i=1;i < $#;i++)) {
        if [ "${!i}" == "${value}" ]; then
            echo "y"
            return 0
        fi
    }
    echo "n"
    return 1
}
#example:
#A=("one" "two" "three four")
#if [ $(contains "${A[@]}" "one") == "y" ]; then
#    echo "contains one"
#fi


for file in *_Filtered/Variants/*/; do
        echo $file
        cd $file
        for log in homo*.log; do
                line=""
                while IFS='' read -r line || [[ -n "$line" ]]; do
                        ARRAY=()    
                        ARRAY+=($line)
                        for i in ${ARRAY[@]}; do echo $i; done
                done < $log
                #atitinkamas vcf failas yra kiekvienam log
                #kurio kieviena eilute skenuot del skaiciaus is log failo
                line=""
                chr=${log%.log}
                chr=${chr#homo}
                echo "SmallVariants.filtered_${chr}.vcf.recode_out2.vcf"
                while IFS='' read -r line || [[ -n "$line" ]]; do
                        #istraukti ID...
                        if [ $(contains "${ARRAY[@]}" "dummy") == "y" ]; then
                             #echo "contains dummy"
                        fi
                done < SmallVariants.filtered_${chr}.vcf.recode_out2.vcf
        done
        cd ~/SNP_Luko_0523/
done