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#!/bin/bash
awk '
FNR==1 && FNR == NR{
FILES[1] = FILENAME
}
FNR==1 && FNR!=NR {
FILES[length(FILES) +1] = FILENAME
}
{
if(arr[$1,$2,$3,$4]){
arr[$1,$2,$3,$4]++
} else {
arr[$1,$2,$3,$4] = 1
}
line[FILENAME,$1,$2,$3,$4] = $0
}
END {
num_files = ARGC -1
printf "REGION\tPOS\tREF\tALT\t"
ORS="\t"
for(k in FILES){
print "REF_DP_" FILES[k] "\tREF_RV_" FILES[k] "\tREF_QUAL_" FILES[k] "\tALT_DP_" FILES[k] "\tALT_RV_" FILES[k] "\tALT_QUAL_" FILES[k] "\tALT_FREQ_" FILES[k] "\tTOTAL_DP_" FILES[k] "\tPVAL_" FILES[k] "\tPASS_" FILES[k]
}
ORS="\n"
printf "\n"
for ( key in arr ) {
if ( arr[key] < num_files ) { continue }
split(line[FILES[1],key], line_arr, "\t")
if (line_arr[ 1 ] == "REGION") { continue }
printf "%s\t", line[FILES[1],key]
for(f = 2; f <= length(FILES); f++){
# printf "KEY: %s\nFILE: %s\nLINE: %s\n", key, FILES[f], line[FILES[f],key]
split(line[FILES[f],key], line_arr, "\t")
for ( i = 5; i <= length( line_arr ); i++ ) {
printf "%s\t", line_arr[ i ]
}
}
printf "\n"
}
}
' "$@"
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