Shell Programming and Scripting

#! /bin/perl

open(IDX,"<Index") || die "Couldn't open index file";
@index=<IDX>;
close IDX;
$header{POSITION}="Position";
for($i=0;$i<$#ARGV+1;$i++)
{
$FH="F${i}";
open($FH,"< $ARGV[${i}]") || die "couldn't open $ARGV[${i}]";
$header{POSITION}="$header{POSITION} $ARGV[${i}]";
while(<$FH>){
chomp($_);
@array=split(/  */);
foreach $index (@index){
chomp($index);
if($index==$array[1]){
if((!$hash{$array[1]} || ($count{$array[1]}++ !=$i)) && $i){
$dem=($i-$count{$array[1]});
$tail="    "x$dem;
$hash{$array[1]}="$hash{$array[1]} $tail";
$count{$array[1]}++;
}
$hash{$index}="$hash{$index} $array[3] $array[5]";
#$count{$array[1]}++;
next;
}
}
}
close $FH;
}
print $header{POSITION}."\n";
foreach $item (keys %hash){
if($hash{$item}){
print "$item $hash{$item}"."\n";
}
}

FNR==1 {# Print the file key entry for another file and update the header lines.
        printf("File%03d is %s\n", ++fc, FILENAME)
        hdr1 = sprintf("%s\t --File%03d--", hdr1, fc)
        hdr2 = sprintf("%s\t Ref\t Alt", hdr2)
}

FNR==1 {# Update the header lines and the file count..
        ++fc
        if((dw = (14 - length(FILENAME)) / 2) > 0)
                ds = sprintf("%*.*s", dw, dw, "--------")
        else    ds = ""
        hdr1 = sprintf("%s\t%s%s%s", hdr1, ds, FILENAME, ds)
        hdr2 = sprintf("%s\t Ref\t Alt", hdr2)
}