diff -Nru eigensoft-6.1.2+dfsg/bin/evec2pca-ped.perl eigensoft-6.1.3+dfsg/bin/evec2pca-ped.perl
--- eigensoft-6.1.2+dfsg/bin/evec2pca-ped.perl	1970-01-01 00:00:00.000000000 +0000
+++ eigensoft-6.1.3+dfsg/bin/evec2pca-ped.perl	2016-07-29 14:26:24.000000000 +0000
@@ -0,0 +1,79 @@
+#!/usr/bin/perl
+
+### translate .evec file to .pca file expected by eigenstrat program
+### Note: .evec file does not contain entries for outliers
+###       .pca  file does contain entries (set to all 0.0) for outliers
+
+# ----- This is a new version for PLINK input files.  It differs from the
+# ----- original in two ways.  (1) The indiv name is in the second column 
+# ----- of the .fam file, but the first of a .ind file.  (2) If the 
+# ----- indiv names are not found in the .evec file, try the 
+# ----- familyname:indivname combination.  
+
+$k = $ARGV[0];
+$evec = $ARGV[1]; 
+$ind = $ARGV[2];  
+$pca = $ARGV[3];  
+open(EVEC,$evec) || die("OOPS couldn't open file $evec for reading");
+open(PCA,">$pca") || die("OOPS couldn't open file $pca for writing");
+
+print PCA ("$k\n"); # number of output eigenvectors/eigenvalues
+$line = <EVEC>; chomp($line); # eigvals line
+my @array = split(/[\t ]+/,$line);
+for($x=0; $x<$k; $x++) { printf PCA ("%.04f\n",$array[$x+2]); } # x-th eval
+while($line = <EVEC>)
+{
+  chomp($line);
+  $line = " " . $line;
+  my @array = split(/[\t ]+/,$line);
+  $l = @array; 
+  unless($l == 3+$k) { die("OOPS #evec in $evec is different from $k"); }
+  $sample = $array[1];
+  for($x=0; $x<$k; $x++) { $evecarray{$sample}[$x] = $array[$x+2]; }
+  $found{$sample} = 1;
+}
+
+# ----- Figure out which name convention to use
+my $count1 = 0;
+my $count2 = 0;
+open(IND,$ind) || die("OOPS couldn't open indiv file $ind for reading");
+while ( my $line = <IND> )  {
+  chomp($line);
+  $line =~ s/^[\s]+//;     # remove leading white-space
+  my @E = split(/[\s]+/,$line);
+
+  my $s = $E[1];
+  my $t = $E[0] . ":" . $E[1];
+
+  if ( exists $found{$s} )  {
+    $count1++;
+  }
+  if ( exists $found{$t} )  {
+    $count2++;
+  }
+}
+close(IND);
+
+open(IND,$ind) || die("OOPS couldn't open indiv file $ind for reading");
+while($line = <IND>)
+{
+  chomp($line);
+  $line =~ s/^[\s]+//;
+  my @array = split(/[\s]+/,$line);
+  $sample = ($count1 >= $count2 ? $array[1] : $array[0] . ":" . $array[1]);
+  if($sample eq "") { $sample = $array[1]; }
+  unless($found{$sample})
+  {
+    for($x=0; $x<$k; $x++) { $evecarray{$sample}[$x] = 0.0; }
+  }
+  for($x=0; $x<$k; $x++)
+  {
+    printf PCA (" ");
+    if($evecarray{$sample}[$x] > 0) { printf PCA (" "); }
+    printf PCA ("%.04f",$evecarray{$sample}[$x]);
+  }
+  printf PCA ("\n");
+}
+
+
+
diff -Nru eigensoft-6.1.2+dfsg/bin/evec2pca-ped.pl eigensoft-6.1.3+dfsg/bin/evec2pca-ped.pl
--- eigensoft-6.1.2+dfsg/bin/evec2pca-ped.pl	2016-07-11 14:18:38.000000000 +0000
+++ eigensoft-6.1.3+dfsg/bin/evec2pca-ped.pl	1970-01-01 00:00:00.000000000 +0000
@@ -1,79 +0,0 @@
-#!/usr/bin/perl
-
-### translate .evec file to .pca file expected by eigenstrat program
-### Note: .evec file does not contain entries for outliers
-###       .pca  file does contain entries (set to all 0.0) for outliers
-
-# ----- This is a new version for PLINK input files.  It differs from the
-# ----- original in two ways.  (1) The indiv name is in the second column 
-# ----- of the .fam file, but the first of a .ind file.  (2) If the 
-# ----- indiv names are not found in the .evec file, try the 
-# ----- familyname:indivname combination.  
-
-$k = $ARGV[0];
-$evec = $ARGV[1]; 
-$ind = $ARGV[2];  
-$pca = $ARGV[3];  
-open(EVEC,$evec) || die("OOPS couldn't open file $evec for reading");
-open(PCA,">$pca") || die("OOPS couldn't open file $pca for writing");
-
-print PCA ("$k\n"); # number of output eigenvectors/eigenvalues
-$line = <EVEC>; chomp($line); # eigvals line
-my @array = split(/[\t ]+/,$line);
-for($x=0; $x<$k; $x++) { printf PCA ("%.04f\n",$array[$x+2]); } # x-th eval
-while($line = <EVEC>)
-{
-  chomp($line);
-  $line = " " . $line;
-  my @array = split(/[\t ]+/,$line);
-  $l = @array; 
-  unless($l == 3+$k) { die("OOPS #evec in $evec is different from $k"); }
-  $sample = $array[1];
-  for($x=0; $x<$k; $x++) { $evecarray{$sample}[$x] = $array[$x+2]; }
-  $found{$sample} = 1;
-}
-
-# ----- Figure out which name convention to use
-my $count1 = 0;
-my $count2 = 0;
-open(IND,$ind) || die("OOPS couldn't open indiv file $ind for reading");
-while ( my $line = <IND> )  {
-  chomp($line);
-  $line =~ s/^[\s]+//;     # remove leading white-space
-  my @E = split(/[\s]+/,$line);
-
-  my $s = $E[1];
-  my $t = $E[0] . ":" . $E[1];
-
-  if ( exists $found{$s} )  {
-    $count1++;
-  }
-  if ( exists $found{$t} )  {
-    $count2++;
-  }
-}
-close(IND);
-
-open(IND,$ind) || die("OOPS couldn't open indiv file $ind for reading");
-while($line = <IND>)
-{
-  chomp($line);
-  $line =~ s/^[\s]+//;
-  my @array = split(/[\s]+/,$line);
-  $sample = ($count1 >= $count2 ? $array[1] : $array[0] . ":" . $array[1]);
-  if($sample eq "") { $sample = $array[1]; }
-  unless($found{$sample})
-  {
-    for($x=0; $x<$k; $x++) { $evecarray{$sample}[$x] = 0.0; }
-  }
-  for($x=0; $x<$k; $x++)
-  {
-    printf PCA (" ");
-    if($evecarray{$sample}[$x] > 0) { printf PCA (" "); }
-    printf PCA ("%.04f",$evecarray{$sample}[$x]);
-  }
-  printf PCA ("\n");
-}
-
-
-
diff -Nru eigensoft-6.1.2+dfsg/bin/evec2pca.perl eigensoft-6.1.3+dfsg/bin/evec2pca.perl
--- eigensoft-6.1.2+dfsg/bin/evec2pca.perl	1970-01-01 00:00:00.000000000 +0000
+++ eigensoft-6.1.3+dfsg/bin/evec2pca.perl	2016-07-29 14:26:24.000000000 +0000
@@ -0,0 +1,52 @@
+#!/usr/bin/perl
+
+### translate .evec file to .pca file expected by eigenstrat program
+### Note: .evec file does not contain entries for outliers
+###       .pca  file does contain entries (set to all 0.0) for outliers
+
+$k = $ARGV[0];
+$evec = $ARGV[1]; 
+$ind = $ARGV[2];  
+$pca = $ARGV[3];  
+
+open(EVEC,$evec) || die("OOPS couldn't open file $evec for reading");
+open(IND,$ind) || die("OOPS couldn't open indiv file $ind for reading");
+open(PCA,">$pca") || die("OOPS couldn't open file $pca for writing");
+
+print PCA ("$k\n"); # number of output eigenvectors/eigenvalues
+$line = <EVEC>; chomp($line); # eigvals line
+my @array = split(/[\t ]+/,$line);
+for($x=0; $x<$k; $x++) { printf PCA ("%.04f\n",$array[$x+2]); } # x-th eval
+while($line = <EVEC>)
+{
+  chomp($line);
+  $line = " " . $line;
+  my @array = split(/[\t ]+/,$line);
+  $l = @array; 
+  unless($l == 3+$k) { die("OOPS #evec in $evec is different from $k"); }
+  $sample = $array[1];
+  for($x=0; $x<$k; $x++) { $evecarray{$sample}[$x] = $array[$x+2]; }
+  $found{$sample} = 1;
+}
+
+while($line = <IND>)
+{
+  chomp($line);
+  my @array = split(/[\t ]+/,$line);
+  $sample = $array[0];
+  if($sample eq "") { $sample = $array[1]; }
+  unless($found{$sample})
+  {
+    for($x=0; $x<$k; $x++) { $evecarray{$sample}[$x] = 0.0; }
+  }
+  for($x=0; $x<$k; $x++)
+  {
+    printf PCA (" ");
+    if($evecarray{$sample}[$x] > 0) { printf PCA (" "); }
+    printf PCA ("%.04f",$evecarray{$sample}[$x]);
+  }
+  printf PCA ("\n");
+}
+
+
+
diff -Nru eigensoft-6.1.2+dfsg/bin/evec2pca.pl eigensoft-6.1.3+dfsg/bin/evec2pca.pl
--- eigensoft-6.1.2+dfsg/bin/evec2pca.pl	2016-07-11 14:18:38.000000000 +0000
+++ eigensoft-6.1.3+dfsg/bin/evec2pca.pl	1970-01-01 00:00:00.000000000 +0000
@@ -1,52 +0,0 @@
-#!/usr/bin/perl
-
-### translate .evec file to .pca file expected by eigenstrat program
-### Note: .evec file does not contain entries for outliers
-###       .pca  file does contain entries (set to all 0.0) for outliers
-
-$k = $ARGV[0];
-$evec = $ARGV[1]; 
-$ind = $ARGV[2];  
-$pca = $ARGV[3];  
-
-open(EVEC,$evec) || die("OOPS couldn't open file $evec for reading");
-open(IND,$ind) || die("OOPS couldn't open indiv file $ind for reading");
-open(PCA,">$pca") || die("OOPS couldn't open file $pca for writing");
-
-print PCA ("$k\n"); # number of output eigenvectors/eigenvalues
-$line = <EVEC>; chomp($line); # eigvals line
-my @array = split(/[\t ]+/,$line);
-for($x=0; $x<$k; $x++) { printf PCA ("%.04f\n",$array[$x+2]); } # x-th eval
-while($line = <EVEC>)
-{
-  chomp($line);
-  $line = " " . $line;
-  my @array = split(/[\t ]+/,$line);
-  $l = @array; 
-  unless($l == 3+$k) { die("OOPS #evec in $evec is different from $k"); }
-  $sample = $array[1];
-  for($x=0; $x<$k; $x++) { $evecarray{$sample}[$x] = $array[$x+2]; }
-  $found{$sample} = 1;
-}
-
-while($line = <IND>)
-{
-  chomp($line);
-  my @array = split(/[\t ]+/,$line);
-  $sample = $array[0];
-  if($sample eq "") { $sample = $array[1]; }
-  unless($found{$sample})
-  {
-    for($x=0; $x<$k; $x++) { $evecarray{$sample}[$x] = 0.0; }
-  }
-  for($x=0; $x<$k; $x++)
-  {
-    printf PCA (" ");
-    if($evecarray{$sample}[$x] > 0) { printf PCA (" "); }
-    printf PCA ("%.04f",$evecarray{$sample}[$x]);
-  }
-  printf PCA ("\n");
-}
-
-
-
diff -Nru eigensoft-6.1.2+dfsg/bin/gc.perl eigensoft-6.1.3+dfsg/bin/gc.perl
--- eigensoft-6.1.2+dfsg/bin/gc.perl	1970-01-01 00:00:00.000000000 +0000
+++ eigensoft-6.1.3+dfsg/bin/gc.perl	2016-07-29 14:26:24.000000000 +0000
@@ -0,0 +1,76 @@
+#!/usr/bin/perl
+
+$P = $ARGV[0];
+$out = $ARGV[1];
+
+# get data
+$m=0;
+open(P,"$P") || die("COF");
+while($line = <P>) { if($line =~ /Chisq/) { last; } } # header lines
+while($line = <P>)
+{
+  chomp($line);
+  if($line =~ /NA/) 
+  {
+    $chisq1[$m] = -100;
+    $chisq2[$m] = -100;
+    $m++;  
+    next;
+  }
+  my @array = split(/[\t ]+/,$line);
+  $chisq1[$m] = $array[0]; # Chisq
+  $chisq2[$m] = $array[1]; # EIGENSTRAT
+  $m++; 
+  $mvalid++;
+}
+close(P);
+$nSNP = $m;
+$nSNPvalid = $mvalid;
+
+# compute $lambda1 (Chisq)
+$CHISQTHRESH = 0.456;
+$step = 0.25;
+$oktoreducestep = 0;
+for($iter=0; $iter<20; $iter++)
+{
+  $mm = 0;
+  for($m=0; $m<$nSNP; $m++) 
+  { 
+    if($chisq1[$m] > $CHISQTHRESH) { $mm++; } 
+  }
+  $frac = $mm/$nSNPvalid; # frac of SNPs exceeding CHISQTHRESH
+  if($frac > 0.5) { $CHISQTHRESH += $step; }
+  else { $CHISQTHRESH -= $step; $oktoreducestep = 1; }
+  if($oktoreducestep) { $step *= 0.5; }
+}
+$lambda1 = $CHISQTHRESH/0.456; # 0.456 is median if no inflation
+if($lambda1 < 1) { $lambda1 = 1; } # not allowed to be less than 1
+
+# compute $lambda2 (EIGENSTRAT)
+$CHISQTHRESH = 0.456;
+$step = 0.25;
+$oktoreducestep = 1;
+for($iter=0; $iter<20; $iter++)
+{
+  $mm = 0;
+  for($m=0; $m<$nSNP; $m++) 
+  { 
+    if($chisq2[$m] > $CHISQTHRESH) { $mm++; } 
+  }
+  $frac = $mm/$nSNPvalid; # frac of SNPs exceeding CHISQTHRESH
+  if($frac > 0.5) { $CHISQTHRESH += $step; }
+  else { $CHISQTHRESH -= $step; $oktoreducestep = 1; }
+  if($oktoreducestep) { $step *= 0.5; }
+}
+$lambda2 = $CHISQTHRESH/0.456; # 0.456 is median if no inflation
+if($lambda2 < 1) { $lambda2 = 1; } # not allowed to be less than 1
+
+# output
+open(OUT,">$out") || die("COF");
+print OUT ("Chisq EIGENSTRAT\n");
+printf OUT ("lambda=%.03f lambda=%.03f\n",$lambda1,$lambda2);
+for($m=0; $m<$nSNP; $m++)
+{
+  if($chisq1[$m] < 0) { print OUT ("NA NA\n"); next; }
+  printf OUT ("%.04f %.04f\n",$chisq1[$m]/$lambda1,$chisq2[$m]/$lambda2);
+}
diff -Nru eigensoft-6.1.2+dfsg/bin/gc.pl eigensoft-6.1.3+dfsg/bin/gc.pl
--- eigensoft-6.1.2+dfsg/bin/gc.pl	2016-07-11 14:18:38.000000000 +0000
+++ eigensoft-6.1.3+dfsg/bin/gc.pl	1970-01-01 00:00:00.000000000 +0000
@@ -1,76 +0,0 @@
-#!/usr/bin/perl
-
-$P = $ARGV[0];
-$out = $ARGV[1];
-
-# get data
-$m=0;
-open(P,"$P") || die("COF");
-while($line = <P>) { if($line =~ /Chisq/) { last; } } # header lines
-while($line = <P>)
-{
-  chomp($line);
-  if($line =~ /NA/) 
-  {
-    $chisq1[$m] = -100;
-    $chisq2[$m] = -100;
-    $m++;  
-    next;
-  }
-  my @array = split(/[\t ]+/,$line);
-  $chisq1[$m] = $array[0]; # Chisq
-  $chisq2[$m] = $array[1]; # EIGENSTRAT
-  $m++; 
-  $mvalid++;
-}
-close(P);
-$nSNP = $m;
-$nSNPvalid = $mvalid;
-
-# compute $lambda1 (Chisq)
-$CHISQTHRESH = 0.456;
-$step = 0.25;
-$oktoreducestep = 0;
-for($iter=0; $iter<20; $iter++)
-{
-  $mm = 0;
-  for($m=0; $m<$nSNP; $m++) 
-  { 
-    if($chisq1[$m] > $CHISQTHRESH) { $mm++; } 
-  }
-  $frac = $mm/$nSNPvalid; # frac of SNPs exceeding CHISQTHRESH
-  if($frac > 0.5) { $CHISQTHRESH += $step; }
-  else { $CHISQTHRESH -= $step; $oktoreducestep = 1; }
-  if($oktoreducestep) { $step *= 0.5; }
-}
-$lambda1 = $CHISQTHRESH/0.456; # 0.456 is median if no inflation
-if($lambda1 < 1) { $lambda1 = 1; } # not allowed to be less than 1
-
-# compute $lambda2 (EIGENSTRAT)
-$CHISQTHRESH = 0.456;
-$step = 0.25;
-$oktoreducestep = 1;
-for($iter=0; $iter<20; $iter++)
-{
-  $mm = 0;
-  for($m=0; $m<$nSNP; $m++) 
-  { 
-    if($chisq2[$m] > $CHISQTHRESH) { $mm++; } 
-  }
-  $frac = $mm/$nSNPvalid; # frac of SNPs exceeding CHISQTHRESH
-  if($frac > 0.5) { $CHISQTHRESH += $step; }
-  else { $CHISQTHRESH -= $step; $oktoreducestep = 1; }
-  if($oktoreducestep) { $step *= 0.5; }
-}
-$lambda2 = $CHISQTHRESH/0.456; # 0.456 is median if no inflation
-if($lambda2 < 1) { $lambda2 = 1; } # not allowed to be less than 1
-
-# output
-open(OUT,">$out") || die("COF");
-print OUT ("Chisq EIGENSTRAT\n");
-printf OUT ("lambda=%.03f lambda=%.03f\n",$lambda1,$lambda2);
-for($m=0; $m<$nSNP; $m++)
-{
-  if($chisq1[$m] < 0) { print OUT ("NA NA\n"); next; }
-  printf OUT ("%.04f %.04f\n",$chisq1[$m]/$lambda1,$chisq2[$m]/$lambda2);
-}
diff -Nru eigensoft-6.1.2+dfsg/bin/smarteigenstrat.perl eigensoft-6.1.3+dfsg/bin/smarteigenstrat.perl
--- eigensoft-6.1.2+dfsg/bin/smarteigenstrat.perl	1970-01-01 00:00:00.000000000 +0000
+++ eigensoft-6.1.3+dfsg/bin/smarteigenstrat.perl	2016-07-29 14:26:24.000000000 +0000
@@ -0,0 +1,76 @@
+#!/usr/bin/perl
+
+# perl wrapper for smarteigenstrat program.  Run smarteigenstrat.perl with no options for usage
+
+use Getopt::Std;
+
+my @flaglist = ("i","a","b","o","p","q","l","k");
+$x = @ARGV;
+for($n=0;$n<$x;$n++)  {
+  foreach $flag (@flaglist)  {
+    if ($ARGV[$n] eq "-$flag")  {
+      $specified{$flag} = 1;
+    }
+  }
+}
+
+# check for mandatory options
+foreach $flag ("i","a","b","p","o","l")  {
+  unless ($specified{$flag})  {
+    usage();
+    die("Error:  -$flag not specified");
+  }
+}
+
+# get opts from hash
+getopts('i:a:b:p:o:q:k:l:', \%opts);
+$genofilename = $opts{"i"};
+$indfilename  = $opts{"b"};
+$snpfilename  = $opts{"a"};
+$pcafilename  = $opts{"p"};
+$outfilename  = $opts{"o"};
+$logfilename  = $opts{"l"};
+$qtmode = "NO";
+if ( $specified{"q"} )  {
+  $qtmode = $opts{"q"};
+}
+$k = 1;
+if ( $specified{"k"} )  {
+  $k = $opts{"k"};
+}
+
+# write parameter file
+open(PAR, ">$outfilename.par") || die("Error:  unable to open $outfilename.par\n");
+print PAR "genotypename:  $genofilename\n";
+print PAR "snpname:       $snpfilename\n";
+print PAR "indivname:     $indfilename\n";
+print PAR "pcaname:       $pcafilename\n";
+print PAR "outputname:    $outfilename\n";
+print PAR "numpc:         $k\n";
+print PAR "qtmode:        $qtmode\n";
+close(PAR);
+
+# run smarteigenstrat
+$cmd = "smarteigenstrat -p $outfilename.par >$logfilename";
+print "$cmd\n";
+system($cmd);
+
+sub usage  {
+  print "smarteigenstrat.perl -i <genotypefile>  -a <indivfile>  -b <snpfile>  -p <pcafile>   -o <outputfile>  ";
+  print "    -l <logfile>  -k <numpca>  -q <qtlmode>";
+  print "\n";
+  print "-i  genotype file (PED, PACKEDPED, EIGENSTRAT, ANCESTRYMAP or PACKEDANCESTRYMAP format)";
+  print "-o  output file (chisq)\n"; 
+  print "-l  logfile (screen output,including error messages)\n";
+  print "-q  YES for quantitative phenotype or NO otherwise\n";
+  print "\n";
+  print "For quantitative phenotype, sixth column of .ped file or third column of EIGENSTRAT .ind file\n";
+  print "should be real numbers.  For non-quantitative phenotype, sixth column of .ped or third column\n";
+  print "should be 'Case' or 'Control'\n";
+}
+
+
+
+
+
+
diff -Nru eigensoft-6.1.2+dfsg/bin/smarteigenstrat.pl eigensoft-6.1.3+dfsg/bin/smarteigenstrat.pl
--- eigensoft-6.1.2+dfsg/bin/smarteigenstrat.pl	2016-07-11 14:18:38.000000000 +0000
+++ eigensoft-6.1.3+dfsg/bin/smarteigenstrat.pl	1970-01-01 00:00:00.000000000 +0000
@@ -1,76 +0,0 @@
-#!/usr/bin/perl
-
-# perl wrapper for smarteigenstrat program.  Run smarteigenstrat.perl with no options for usage
-
-use Getopt::Std;
-
-my @flaglist = ("i","a","b","o","p","q","l","k");
-$x = @ARGV;
-for($n=0;$n<$x;$n++)  {
-  foreach $flag (@flaglist)  {
-    if ($ARGV[$n] eq "-$flag")  {
-      $specified{$flag} = 1;
-    }
-  }
-}
-
-# check for mandatory options
-foreach $flag ("i","a","b","p","o","l")  {
-  unless ($specified{$flag})  {
-    usage();
-    die("Error:  -$flag not specified");
-  }
-}
-
-# get opts from hash
-getopts('i:a:b:p:o:q:k:l:', \%opts);
-$genofilename = $opts{"i"};
-$indfilename  = $opts{"b"};
-$snpfilename  = $opts{"a"};
-$pcafilename  = $opts{"p"};
-$outfilename  = $opts{"o"};
-$logfilename  = $opts{"l"};
-$qtmode = "NO";
-if ( $specified{"q"} )  {
-  $qtmode = $opts{"q"};
-}
-$k = 1;
-if ( $specified{"k"} )  {
-  $k = $opts{"k"};
-}
-
-# write parameter file
-open(PAR, ">$outfilename.par") || die("Error:  unable to open $outfilename.par\n");
-print PAR "genotypename:  $genofilename\n";
-print PAR "snpname:       $snpfilename\n";
-print PAR "indivname:     $indfilename\n";
-print PAR "pcaname:       $pcafilename\n";
-print PAR "outputname:    $outfilename\n";
-print PAR "numpc:         $k\n";
-print PAR "qtmode:        $qtmode\n";
-close(PAR);
-
-# run smarteigenstrat
-$cmd = "smarteigenstrat -p $outfilename.par >$logfilename";
-print "$cmd\n";
-system($cmd);
-
-sub usage  {
-  print "smarteigenstrat.perl -i <genotypefile>  -a <indivfile>  -b <snpfile>  -p <pcafile>   -o <outputfile>  ";
-  print "    -l <logfile>  -k <numpca>  -q <qtlmode>";
-  print "\n";
-  print "-i  genotype file (PED, PACKEDPED, EIGENSTRAT, ANCESTRYMAP or PACKEDANCESTRYMAP format)";
-  print "-o  output file (chisq)\n"; 
-  print "-l  logfile (screen output,including error messages)\n";
-  print "-q  YES for quantitative phenotype or NO otherwise\n";
-  print "\n";
-  print "For quantitative phenotype, sixth column of .ped file or third column of EIGENSTRAT .ind file\n";
-  print "should be real numbers.  For non-quantitative phenotype, sixth column of .ped or third column\n";
-  print "should be 'Case' or 'Control'\n";
-}
-
-
-
-
-
-
diff -Nru eigensoft-6.1.2+dfsg/bin/smartpca.perl eigensoft-6.1.3+dfsg/bin/smartpca.perl
--- eigensoft-6.1.2+dfsg/bin/smartpca.perl	1970-01-01 00:00:00.000000000 +0000
+++ eigensoft-6.1.3+dfsg/bin/smartpca.perl	2016-07-29 14:26:24.000000000 +0000
@@ -0,0 +1,156 @@
+#!/usr/bin/perl
+
+use Getopt::Std ;
+use File::Basename ;
+
+### process flags
+# -w poplist is compute eigenvectors using populations in poplist, then project
+# -y poplistplot is use populations in poplistplot for plot
+# -z badsnpfile is use badsnpname: badsnpfile in call to smartpca
+my @flaglist = ("i","a","b","k","o","p","e","l","m","q","t","s","w","y","z");
+$x = @ARGV;
+for($n=0; $n<$x; $n++)
+{
+  foreach $flag (@flaglist) 
+  {
+    if($ARGV[$n] eq "-$flag") { $specified{$flag} = 1; }
+  }
+}
+foreach $flag ("i","a","b","o","p","e","l")
+{
+  unless($specified{$flag}) { die("OOPS -$flag flag not specified"); }
+}
+getopts('i:a:b:k:o:p:e:l:m:t:s:w:y:z:q:',\%opts);
+$i = $opts{"i"}; 
+$a = $opts{"a"}; 
+$b = $opts{"b"}; 
+$k = 10; if($specified{"k"}) { $k = $opts{"k"}; }
+$o = $opts{"o"}; 
+$q = 0; if($specified{"q"}) { $q = $opts{"q"}; }
+$p = $opts{"p"}; 
+$e = $opts{"e"}; 
+$l = $opts{"l"}; 
+$m = 5; if($specified{"m"}) { $m = $opts{"m"}; }
+$t = 10; if($specified{"t"}) { $t = $opts{"t"}; }
+$s = 6.0; if($specified{"s"}) { $s = $opts{"s"}; }
+if($specified{"w"}) { $w = $opts{"w"}; }
+if($specified{"y"}) { $y = $opts{"y"}; }
+if($specified{"z"}) { $z = $opts{"z"}; }
+
+### run smartpca
+$parfile = "$o.par"; 
+$evec = "$o.evec";
+open(PARFILE,">$parfile") || die("OOPS couldn't open file $parfile for writing");
+print PARFILE ("genotypename: $i\n");
+print PARFILE ("snpname: $a\n");
+print PARFILE ("indivname: $b\n");
+print PARFILE ("evecoutname: $evec\n");
+print PARFILE ("evaloutname: $e\n");
+print PARFILE ("altnormstyle: NO\n");
+print PARFILE ("numoutevec: $k\n");
+print PARFILE ("numoutlieriter: $m\n");
+print PARFILE ("numoutlierevec: $t\n");
+print PARFILE ("outliersigmathresh: $s\n");
+print PARFILE ("qtmode: $q\n");
+if($specified{"w"}) { print PARFILE ("poplistname: $w\n"); }
+if($specified{"z"}) { print PARFILE ("badsnpname: $z\n"); }
+close(PARFILE);
+$command = "smartpca";          # MUST put bin directory in path
+$command .= " -p $parfile >$l";
+print("$command\n");
+system("$command");
+
+### make string of populations for ploteig
+$popstring = "";
+open(EVEC,$evec) || die("OOPS couldn't open file $evec for reading");
+while($line = <EVEC>)
+{
+  chomp($line);
+  my @array = split(/[\t ]+/,$line);
+  $x = @array;
+  if($array[1] =~ /eigvals/) { next; } # eigvals header line
+  $pop = $array[$x-1];
+  if($popfound{$pop}) { next; }
+  $popstring = $popstring . "$pop:";
+  $popfound{$pop} = 1;
+}
+close(EVEC);
+chop($popstring); # remove last ":"
+
+if($specified{"y"}) 
+{
+  ### make string of populations for ploteig based on -y flag input
+  $popstring = "";
+  open(Y,$y) || die("COF");
+  while($line = <Y>)
+  {
+    chomp($line);
+    $popstring .= "$line:";
+  }
+  chop($popstring);
+}
+
+### cax ploteig
+$command = "ploteig";           # MUST put bin directory in path
+$command .= " -i $evec";
+$command .= " -c 1:2 ";
+$command .= " -p $popstring ";
+$command .= " -x ";
+$command .= " -y ";
+$command .= " -o $p.xtxt "; # must end in .xtxt
+print("$command\n");
+system("$command");
+
+### translate .evec file to .pca file expected by eigenstrat program
+### Note: .evec file does not contain entries for outliers 
+###       .pca  file does contain entries (set to all 0.0) for outliers
+
+# ----- If this looks like a PLINK run, call the PLINK kludge
+if ( $i =~ m/\.ped$/ || $i =~ m/\.PED/ )  {
+  $command = "evec2pca-ped.perl $k $evec $b $o";
+}
+else  {
+  $command = "evec2pca.perl $k $evec $b $o";
+}
+print("$command\n");
+system("$command");
+
+### If labels are Case and Control only, compute correlations between
+### Case/Control status and each eigenvector.  Append to logfile.
+if(($popstring eq "Case:Control") || ($popstring eq "Control:Case"))
+{
+  open(LOG,">>$l") || die("OOPS couldn't open file $l for appending");
+  print LOG ("\n");
+  for($x=0; $x<$k; $x++) # compute correlation for evec $x
+  {
+    open(EVEC,$evec) || die("OOPS couldn't open file $evec for reading");
+    $sum1=0; $sumx=0; $sumxx=0; $sumy=0; $sumyy=0; $sumxy=0;
+    $line = <EVEC>; chomp($line); # eigvals line
+    while($line = <EVEC>)
+    {
+      chomp($line);
+      my @array = split(/[\t ]+/,$line);
+      $this = $array[2+$x];
+      $sumy += $this;
+      $sumyy += $this*$this;
+      $sum1 += 1;
+      if($line =~ /Case/) # Case is 1, Control is 0
+      {
+        $sumx += 1;
+        $sumxx += 1;
+        $sumxy += $this;
+      }
+    }
+    close(EVEC);
+    $meanx = $sumx/$sum1;
+    $meany = $sumy/$sum1;
+    if($sum1 == 0) { next; }
+    $sdevx = sqrt($sumxx/$sum1 - $meanx*$meanx);
+    $sdevy = sqrt($sumyy/$sum1 - $meany*$meany);
+    if($sdevx * $sdevy == 0) { next; }
+    $corr = ($sumxy/$sum1) / ($sdevx*$sdevy);
+    $x1 = $x+1;
+    printf LOG ("Correlation between eigenvector $x1 (of $k) and Case/Control status is %.03f\n",$corr);
+  }
+  close(LOG);
+}
diff -Nru eigensoft-6.1.2+dfsg/bin/smartpca.pl eigensoft-6.1.3+dfsg/bin/smartpca.pl
--- eigensoft-6.1.2+dfsg/bin/smartpca.pl	2016-07-11 14:18:38.000000000 +0000
+++ eigensoft-6.1.3+dfsg/bin/smartpca.pl	1970-01-01 00:00:00.000000000 +0000
@@ -1,156 +0,0 @@
-#!/usr/bin/perl
-
-use Getopt::Std ;
-use File::Basename ;
-
-### process flags
-# -w poplist is compute eigenvectors using populations in poplist, then project
-# -y poplistplot is use populations in poplistplot for plot
-# -z badsnpfile is use badsnpname: badsnpfile in call to smartpca
-my @flaglist = ("i","a","b","k","o","p","e","l","m","q","t","s","w","y","z");
-$x = @ARGV;
-for($n=0; $n<$x; $n++)
-{
-  foreach $flag (@flaglist) 
-  {
-    if($ARGV[$n] eq "-$flag") { $specified{$flag} = 1; }
-  }
-}
-foreach $flag ("i","a","b","o","p","e","l")
-{
-  unless($specified{$flag}) { die("OOPS -$flag flag not specified"); }
-}
-getopts('i:a:b:k:o:p:e:l:m:t:s:w:y:z:q:',\%opts);
-$i = $opts{"i"}; 
-$a = $opts{"a"}; 
-$b = $opts{"b"}; 
-$k = 10; if($specified{"k"}) { $k = $opts{"k"}; }
-$o = $opts{"o"}; 
-$q = 0; if($specified{"q"}) { $q = $opts{"q"}; }
-$p = $opts{"p"}; 
-$e = $opts{"e"}; 
-$l = $opts{"l"}; 
-$m = 5; if($specified{"m"}) { $m = $opts{"m"}; }
-$t = 10; if($specified{"t"}) { $t = $opts{"t"}; }
-$s = 6.0; if($specified{"s"}) { $s = $opts{"s"}; }
-if($specified{"w"}) { $w = $opts{"w"}; }
-if($specified{"y"}) { $y = $opts{"y"}; }
-if($specified{"z"}) { $z = $opts{"z"}; }
-
-### run smartpca
-$parfile = "$o.par"; 
-$evec = "$o.evec";
-open(PARFILE,">$parfile") || die("OOPS couldn't open file $parfile for writing");
-print PARFILE ("genotypename: $i\n");
-print PARFILE ("snpname: $a\n");
-print PARFILE ("indivname: $b\n");
-print PARFILE ("evecoutname: $evec\n");
-print PARFILE ("evaloutname: $e\n");
-print PARFILE ("altnormstyle: NO\n");
-print PARFILE ("numoutevec: $k\n");
-print PARFILE ("numoutlieriter: $m\n");
-print PARFILE ("numoutlierevec: $t\n");
-print PARFILE ("outliersigmathresh: $s\n");
-print PARFILE ("qtmode: $q\n");
-if($specified{"w"}) { print PARFILE ("poplistname: $w\n"); }
-if($specified{"z"}) { print PARFILE ("badsnpname: $z\n"); }
-close(PARFILE);
-$command = "smartpca";          # MUST put bin directory in path
-$command .= " -p $parfile >$l";
-print("$command\n");
-system("$command");
-
-### make string of populations for ploteig
-$popstring = "";
-open(EVEC,$evec) || die("OOPS couldn't open file $evec for reading");
-while($line = <EVEC>)
-{
-  chomp($line);
-  my @array = split(/[\t ]+/,$line);
-  $x = @array;
-  if($array[1] =~ /eigvals/) { next; } # eigvals header line
-  $pop = $array[$x-1];
-  if($popfound{$pop}) { next; }
-  $popstring = $popstring . "$pop:";
-  $popfound{$pop} = 1;
-}
-close(EVEC);
-chop($popstring); # remove last ":"
-
-if($specified{"y"}) 
-{
-  ### make string of populations for ploteig based on -y flag input
-  $popstring = "";
-  open(Y,$y) || die("COF");
-  while($line = <Y>)
-  {
-    chomp($line);
-    $popstring .= "$line:";
-  }
-  chop($popstring);
-}
-
-### cax ploteig
-$command = "ploteig";           # MUST put bin directory in path
-$command .= " -i $evec";
-$command .= " -c 1:2 ";
-$command .= " -p $popstring ";
-$command .= " -x ";
-$command .= " -y ";
-$command .= " -o $p.xtxt "; # must end in .xtxt
-print("$command\n");
-system("$command");
-
-### translate .evec file to .pca file expected by eigenstrat program
-### Note: .evec file does not contain entries for outliers 
-###       .pca  file does contain entries (set to all 0.0) for outliers
-
-# ----- If this looks like a PLINK run, call the PLINK kludge
-if ( $i =~ m/\.ped$/ || $i =~ m/\.PED/ )  {
-  $command = "evec2pca-ped.perl $k $evec $b $o";
-}
-else  {
-  $command = "evec2pca.perl $k $evec $b $o";
-}
-print("$command\n");
-system("$command");
-
-### If labels are Case and Control only, compute correlations between
-### Case/Control status and each eigenvector.  Append to logfile.
-if(($popstring eq "Case:Control") || ($popstring eq "Control:Case"))
-{
-  open(LOG,">>$l") || die("OOPS couldn't open file $l for appending");
-  print LOG ("\n");
-  for($x=0; $x<$k; $x++) # compute correlation for evec $x
-  {
-    open(EVEC,$evec) || die("OOPS couldn't open file $evec for reading");
-    $sum1=0; $sumx=0; $sumxx=0; $sumy=0; $sumyy=0; $sumxy=0;
-    $line = <EVEC>; chomp($line); # eigvals line
-    while($line = <EVEC>)
-    {
-      chomp($line);
-      my @array = split(/[\t ]+/,$line);
-      $this = $array[2+$x];
-      $sumy += $this;
-      $sumyy += $this*$this;
-      $sum1 += 1;
-      if($line =~ /Case/) # Case is 1, Control is 0
-      {
-        $sumx += 1;
-        $sumxx += 1;
-        $sumxy += $this;
-      }
-    }
-    close(EVEC);
-    $meanx = $sumx/$sum1;
-    $meany = $sumy/$sum1;
-    if($sum1 == 0) { next; }
-    $sdevx = sqrt($sumxx/$sum1 - $meanx*$meanx);
-    $sdevy = sqrt($sumyy/$sum1 - $meany*$meany);
-    if($sdevx * $sdevy == 0) { next; }
-    $corr = ($sumxy/$sum1) / ($sdevx*$sdevy);
-    $x1 = $x+1;
-    printf LOG ("Correlation between eigenvector $x1 (of $k) and Case/Control status is %.03f\n",$corr);
-  }
-  close(LOG);
-}
diff -Nru eigensoft-6.1.2+dfsg/debian/changelog eigensoft-6.1.3+dfsg/debian/changelog
--- eigensoft-6.1.2+dfsg/debian/changelog	2016-07-21 06:49:12.000000000 +0000
+++ eigensoft-6.1.3+dfsg/debian/changelog	2016-08-05 21:40:38.000000000 +0000
@@ -1,3 +1,10 @@
+eigensoft (6.1.3+dfsg-1) unstable; urgency=medium
+
+  * New upstream version
+  * Upstream has changed extensions from .pl to .perl
+
+ -- Andreas Tille <tille@debian.org>  Fri, 05 Aug 2016 23:40:38 +0200
+
 eigensoft (6.1.2+dfsg-1) unstable; urgency=medium
 
   [ Andreas Tille ]
diff -Nru eigensoft-6.1.2+dfsg/debian/install eigensoft-6.1.3+dfsg/debian/install
--- eigensoft-6.1.2+dfsg/debian/install	2016-07-21 06:49:12.000000000 +0000
+++ eigensoft-6.1.3+dfsg/debian/install	2016-08-05 21:40:38.000000000 +0000
@@ -1,6 +1,6 @@
 bin/smarteigenstrat	usr/lib/eigensoft
 bin/smartpca		usr/lib/eigensoft
-bin/gc.pl		usr/lib/debian-med/bin
+bin/gc.perl		usr/lib/debian-med/bin
 bin/*       		usr/bin
 CONVERTF    		usr/share/eigensoft
 EIGENSTRAT  		usr/share/eigensoft
diff -Nru eigensoft-6.1.2+dfsg/debian/links eigensoft-6.1.3+dfsg/debian/links
--- eigensoft-6.1.2+dfsg/debian/links	2016-07-21 06:49:12.000000000 +0000
+++ eigensoft-6.1.3+dfsg/debian/links	2016-08-05 21:40:38.000000000 +0000
@@ -1 +1 @@
-usr/lib/debian-med/bin/gc.pl	usr/bin/gc-eigensoft
+usr/lib/debian-med/bin/gc.perl	usr/bin/gc-eigensoft
diff -Nru eigensoft-6.1.2+dfsg/debian/rules eigensoft-6.1.3+dfsg/debian/rules
--- eigensoft-6.1.2+dfsg/debian/rules	2016-07-21 06:49:12.000000000 +0000
+++ eigensoft-6.1.3+dfsg/debian/rules	2016-08-05 21:40:38.000000000 +0000
@@ -28,7 +28,7 @@
 	find debian/eigensoft/usr/share/ -type f -empty -delete
 	# file consists only from single line with wrong interpreter
 	find debian/eigensoft/usr/share/ -type f -name HGDP.X.perl -delete
-	# Fix wrappers and drop *.pl extension in /usr/bin while keeping
+	# Fix wrappers and drop *.perl extension in /usr/bin while keeping
 	# the original name in /usr/lib/debian-med/bin
 	mkdir -p debian/$(DEBPKGNAME)/usr/lib/debian-med/bin
 	for pl in $(WRAPPERS) ; do \
@@ -38,11 +38,11 @@
                 -e "s?\(cmd[[:space:]]*=[[:space:]]*\"\)\($${pl}\)?\1/usr/lib/$(DEBPKGNAME)/\2?" \
                 -e "s?\(cmd[[:space:]]*=[[:space:]]*\"\)\(evec2pca.*\)\.perl?\1?" \
                 -e "s?\($${pl}\)\.perl?\1?" \
-	        debian/$(DEBPKGNAME)/usr/bin/$${pl}.pl ; \
-	    cp -a debian/$(DEBPKGNAME)/usr/bin/$${pl}.pl debian/$(DEBPKGNAME)/usr/bin/$${pl} ; \
-	    mv debian/$(DEBPKGNAME)/usr/bin/$${pl}.pl debian/$(DEBPKGNAME)/usr/lib/debian-med/bin ; \
+	        debian/$(DEBPKGNAME)/usr/bin/$${pl}.perl ; \
+	    cp -a debian/$(DEBPKGNAME)/usr/bin/$${pl}.perl debian/$(DEBPKGNAME)/usr/bin/$${pl} ; \
+	    mv debian/$(DEBPKGNAME)/usr/bin/$${pl}.perl debian/$(DEBPKGNAME)/usr/lib/debian-med/bin ; \
 	done
-	rm debian/$(DEBPKGNAME)/usr/bin/gc.pl
+	rm debian/$(DEBPKGNAME)/usr/bin/gc.perl
 
 override_dh_fixperms:
 	dh_fixperms
diff -Nru eigensoft-6.1.2+dfsg/.gitignore eigensoft-6.1.3+dfsg/.gitignore
--- eigensoft-6.1.2+dfsg/.gitignore	1970-01-01 00:00:00.000000000 +0000
+++ eigensoft-6.1.3+dfsg/.gitignore	2016-07-29 14:26:24.000000000 +0000
@@ -0,0 +1,32 @@
+# Object files
+*.o
+*.ko
+*.obj
+*.elf
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Libraries
+*.lib
+*.a
+*.la
+*.lo
+
+# Shared objects (inc. Windows DLLs)
+*.dll
+*.so
+*.so.*
+*.dylib
+
+# Executables
+*.exe
+*.out
+*.app
+*.i*86
+*.x86_64
+*.hex
+
+# Debug files
+*.dSYM/
diff -Nru eigensoft-6.1.2+dfsg/README eigensoft-6.1.3+dfsg/README
--- eigensoft-6.1.2+dfsg/README	2016-07-11 14:18:38.000000000 +0000
+++ eigensoft-6.1.3+dfsg/README	2016-07-29 14:26:24.000000000 +0000
@@ -1,10 +1,13 @@
-EIGENSOFT version 6.1.2, 6/27/16 (for Linux only)
+EIGENSOFT version 6.1.3, 7/29/16 (for Linux only)
 
 The EIGENSOFT package implements methods from the following 3 papers:
 Patterson et al. 2006 PLoS Genet (population structure)
 Price et al. 2006 Nat Genet (EIGENSTRAT stratification correction)
 Galinsky et al. 2016 Am J Hum Genet (FastPCA and PC-based selection statistic)
 
+NEW features of EIGENSOFT version 6.1.3 include:
+-- Restored script file extensions to .perl instead of .pl
+
 NEW features of EIGENSOFT version 6.1.2 include:
 -- Updated license info to be GPL compliant required by linking the GSL