--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/sRNAPipe/resize.pm	Mon Jan 28 11:57:15 2019 -0500
@@ -0,0 +1,101 @@
+package sRNAPipe::resize;
+
+use strict;
+use warnings;
+
+use FindBin;
+use lib "$FindBin::Bin/../lib";
+use sRNAPipe::Rcall qw ( histogram );
+
+use Exporter;
+our @ISA = qw( Exporter );
+our @EXPORT_OK = qw( &size_distribution );
+
+sub size_distribution
+{
+    my ( $fastq, $fastq_out, $dir, $min, $max ) = @_;
+
+    my ( %fragments_size, %duplicates ) ;
+    my $num = size($min, $max, $fastq, $fastq_out, \%fragments_size, \%duplicates);
+
+    my $png = $dir.'histogram.png';
+    histogram(\%fragments_size, $png, $num);
+    
+    my $size = $dir.'reads_size.txt';
+    
+
+    my $pourcentage;
+    open    my $o, '>', $size || die "cannot open $size $!\n";
+    print $o "size\tnumber\tpercentage\n";
+    foreach my    $k (sort { $a <=> $b } keys %fragments_size )
+    {
+        $pourcentage = $fragments_size{$k} / $num * 100;
+        
+        print $o "$k\t$fragments_size{$k}\t";
+        printf $o "%.2f\n",$pourcentage;
+    }
+    close $o;
+    
+    my $dup = $dir.'duplicates.txt' ;
+    open $o, '>', $dup || die "cannot open $size $!\n";
+    print $o "size\tnumber\n";
+    foreach my    $k (sort { $duplicates{$b} <=> $duplicates{$a} } keys %duplicates )
+    {
+        print $o "$k\t$duplicates{$k}\n";
+    }
+    close $o;
+}
+
+sub size
+{
+    my ($min, $max, $in_file, $out_file, $sizeHashR, $duplicateHashR) = @_;
+    my ($numreads, $size, $cmp, $ok, $line) = (0, 0, 0, 0);
+    my @fastq;
+    open (my $in, $in_file) || die "cannot open $in_file $!\n";
+    open (my $out, ">".$out_file)    || die "cannot create $out_file $!\n";
+    while(<$in>)
+    {
+        chomp $_;
+        $cmp++; $line++;
+        if ($cmp == 1)
+        {
+            die "file do not contain a @ at line $line\n" unless ($_ =~ /^\@/ );
+            $ok = 0; @fastq = ();
+            push(@fastq,$_);
+        }
+        elsif ($cmp == 2)
+        {
+            #die "unrecognized symbol at line $line\n" unless ($_ =~ /[atcgATCGnN]+/ || $_ =~ /^$/ );
+            push(@fastq,$_);
+            $size = length($_);
+            if ($size >= $min && $size <= $max)
+            {
+                $numreads++;
+                ${$sizeHashR}{$size}+=1;
+                ${$duplicateHashR}{$_}+=1 if (defined($duplicateHashR));
+                $ok = 1;
+            }
+        }
+        elsif ($cmp == 3 )
+        {
+            die "file do not contain a + at line $line\n" unless $_ =~ /^\+/;
+            push(@fastq,$_);
+        }
+        elsif ($cmp == 4 )
+        {
+            push(@fastq,$_);
+            $cmp = 0;
+            if ($ok == 1)
+            {
+                foreach my $t (@fastq)
+                {
+                    print $out $t."\n";
+                }
+            }
+        }
+    }
+    close $in; close $out;
+    return $numreads;
+}
+
+1;