Updated perl script

#! /usr/bin/perl

use warnings;
use strict;
use autodie;
use feature qw(say);
use File::Slurp qw(read_file);
use String::Util qw(trim);

my @lines=read_file('file');

my $grps=getGroups(\@lines);

processGroups(\@lines,$grps);

printLines(\@lines,$grps);


sub printLines {
  my ($lines,$grps) = @_;

  for my $grp (@$grps) {
    my $ind=$grp->{ind};
    my $line=$lines->[$ind->[0]];
    if (@$ind==1) {
      print $line;
    } else {
      my ($spc)=$line=~/^(\s+)/;
      $spc="" if ! defined $spc;
      my @fld=split(/(\s+)/,trim($line));
      $fld[2]=$grp->{min};
      $fld[4]=$grp->{max};
      $fld[8]=$grp->{score};
      $fld[10]=$grp->{strand};
      say $spc,join "",@fld;
    }
  }
}

sub processGroups {
  my ($lines,$grps) = @_;

  for my $grp (@$grps) {
    my $ind=$grp->{ind};
    if (@$ind==2) {
      my $gscore=0; my $gstrand;
      my $min=$ind->[0];
      my $max=$ind->[1];
      for ($min..$max) {
        my @fld=split(" ",$lines->[$_]);
        my ($score,$strand)=@fld[4,5];
        if ($score>$gscore) {
          $gscore=$score;
          $gstrand=$strand;
        }
      }
      my $gmin=@{[split(" ",$lines->[$min])]}[1];
      my $gmax=@{[split(" ",$lines->[$max])]}[2];
      $grp->{score}=$gscore;
      $grp->{strand}=$gstrand;
      $grp->{min}=$gmin;
      $grp->{max}=$gmax;
    }
  }
}

# Assume start and end columns are sorted.
sub getGroups {
  my ($lines) = @_;

  my @grps;
  my $grp=[];
  my $pstart=-1; my $pend=-1;
  my $start; my $end; my $gend=0;
  for my $i (0..$#$lines) {
    my @fld=split(" ",$lines->[$i]);
    if (@fld == 6) { #skip irrelevant lines.. e.g. starting with stars
      ($start,$end)=@fld[1,2];
      if ($pstart==-1) {
        $pstart=$start; $pend=$end;
        $grp=[$i];
      }
      #assert ( $start<$end)
      #assert ( $start>=$pstart)
      if ($start<=$pend) {
        $gend=$i;
      } else {
        push(@$grp,$gend) if $gend;
        push(@grps,{ind=>$grp});
        $grp=[$i]; $gend=0;
      }
      $pstart=$start; $pend=$end;
    }
  }
  return \@grps;
}