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

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

diff --git a/htswanalysis/scripts/SummarizeLibrary.pm b/htswanalysis/scripts/SummarizeLibrary.pm
index 4a62e3df45e78063b5dba737f51749a8bd829505..889fc9c5d0ef750cd0f2e7c04a4ec2c6a43a4dfb 100755 (executable)
--- a/htswanalysis/scripts/SummarizeLibrary.pm
+++ b/htswanalysis/scripts/SummarizeLibrary.pm
@@ -56,7 +56,7 @@ sub SummarizeLibrary {
       $filename =~ /^(\d+)_(.+?)_s(\d+)_(.+?)_$lib.align/;
       ($date,$fc,$lane,$desc) = ($1,$2,$3,$4);
       $num_lanes += length($lane);
-      $num_reads += $xml->{Library}->[$i]->{Track}->[$t]->{Count};
+      $num_reads += $xml->{Library}->[$i]->{Track}->[$t]->{Align};
       if(!defined($start_date)) {
         $start_date = $date;
         $end_date = $date;