cd /BLUES/eric/ONT_WGBS/Allele_analysis/summary_plots_analysis

cat \
/BLUES/eric/ONT_WGBS/Allele_analysis/window_delta_prime/prime_windows_1000bp_delta_gt_0.5.tsv \
/BLUES/eric/ONT_WGBS/Allele_analysis/window_delta_prime/prime_windows_1000bp_delta_lt_-0.5.tsv \
| awk 'BEGIN{FS=OFS="\t"}
NR>1 {

    gsub(/"/,"",$1)

    if($1 !~ /^chr/)
        next

    s=int($2)
    e=int($3)

    if(s<e)
        print $1,s,e
}' \
| sort -u \
> prime_all_clean.bed


cat \
/BLUES/eric/ONT_WGBS/Allele_analysis/window_delta_naive_d0.5_cpg5_meancov5/naive_windows_1000bp_delta_ge_0.5_cpg5_meancov5.tsv \
/BLUES/eric/ONT_WGBS/Allele_analysis/window_delta_naive_d0.5_cpg5_meancov5/naive_windows_1000bp_delta_le_-0.5_cpg5_meancov5.tsv \
| awk 'BEGIN{FS=OFS="\t"}
NR>1 && $1 ~ /^chr/ {

    gsub(/"/,"",$1)

    s=int($2)
    e=int($3)

    if(s<e)
        print $1,s,e
}' \
| sort -u \
> naive_all_clean.bed



cat \
/BLUES/eric/ONT_WGBS/Allele_analysis/window_delta_TSC_d0.5_cpg5_meancov5/TSC_windows_1000bp_delta_ge.tsv \
/BLUES/eric/ONT_WGBS/Allele_analysis/window_delta_TSC_d0.5_cpg5_meancov5/TSC_windows_1000bp_delta_le.tsv \
| awk 'BEGIN{FS=OFS="\t"}
NR>1 && $1 ~ /^chr/ {

    gsub(/"/,"",$1)

    s=int($2)
    e=int($3)

    if(s<e)
        print $1,s,e
}' \
| sort -u \
> TSC_all_clean.bed