Updated read counts to give information about aligment percent, and adapter percent.

[htsworkflow.git] / htswanalysis / scripts / CollectLibraries.pm

diff --git a/htswanalysis/scripts/CollectLibraries.pm b/htswanalysis/scripts/CollectLibraries.pm
index fcaa7928d348f8f15f19a934574fb7d869dc715d..5d1c214fba5625887f67ca771101d4f31af773a0 100755 (executable)
--- a/htswanalysis/scripts/CollectLibraries.pm
+++ b/htswanalysis/scripts/CollectLibraries.pm
@@ -14,8 +14,9 @@ for my $filename (@ARGV) {
   my($date,$flowcell,$lanes,$lib) = ($1,$2,$3,$4);
 
   open(COUNT,$filename.".count");
-  my $count = <COUNT>; chomp $count; $count =~ s/\s//g;
-  if(!defined($count)) { print STDERR $filename,"\n"; }
+  <COUNT>;
+  my $count_line = <COUNT>; chomp $count_line; my($all,$pf,$adapt,$align) = split(/\t/,$count_line);
+  if(!defined($align)) { print STDERR $filename," is badly formatted.\n"; }
   close(COUNT);
 
   if(!defined($lib)) {
@@ -24,7 +25,7 @@ for my $filename (@ARGV) {
   }
 
   if(!exists($libraries{$lib})) { my @a; $libraries{$lib} = \@a; }
-  push @{$libraries{$lib}}, "$flowcell\t$lanes\t$filename\t$count\t$date";
+  push @{$libraries{$lib}}, "$flowcell\t$lanes\t$filename\t$all\t$pf\t$adapt\t$align\t$date";
 }
 
   print "<?xml version=\"1.0\" ?>\n";
@@ -33,8 +34,8 @@ for my $filename (@ARGV) {
   for my $lib (sort {$a =~ /[sS][lL](\d+)/; my $a1 = $1; $b =~ /[sS][lL](\d+)/; my $b1 = $1; $a1 <=> $b1} keys %libraries) {
     print "<Library Name=\"$lib\">\n";
     for my $data (@{$libraries{$lib}}) {
-      my($f,$l,$fn,$N,$D) = split(/\t/,$data);
-      print "<Track Flowcell=\"$f\" Lane=\"$l\" Filename=\"$fn\" Count=\"$N\" Date=\"$D\" />\n";
+      my($f,$l,$fn,$all,$pf,$adapt,$align,$D) = split(/\t/,$data);
+      print "<Track Flowcell=\"$f\" Lane=\"$l\" Filename=\"$fn\" All=\"$all\" Pf=\"$pf\" Adapter=\"$adapt\" Align=\"$align\" Date=\"$D\" />\n";
     }
     print "</Library>\n";
   }