Mercurial > repos > estrain > sum_fastqc

changeset 7:b769c810924e draft default tip

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Added option for multiple Q scores
author estrain
date Wed, 17 Oct 2018 07:11:51 -0400
parents 9a9fdfef8b90
children
files sum_fastqc.pl
diffstat 1 files changed, 12 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/sum_fastqc.pl	Wed Oct 17 07:11:24 2018 -0400
+++ b/sum_fastqc.pl	Wed Oct 17 07:11:51 2018 -0400
@@ -13,8 +13,14 @@
 
 my($inname)=shift(@ARGV);
 my($qscore)=shift(@ARGV);
+$qscore=~s/\s+//g;
+my(@qlist)=split(/\,/,$qscore);
 
-print "Input\tFile\tFastQC\tPass-Fail\tReads\tPoor_Reads\tGC\tQ".$qscore."\n";
+print "Input\tFile\tFastQC\tPass-Fail\tReads\tPoor_Reads\tGC";
+foreach(@qlist) {
+  print "\tQ".$_;
+}
+print "\n";
 
 foreach (@ARGV) {
   print_stats($_);
@@ -47,8 +53,11 @@
   print $pass[1]."\t";
   print $nreads[1]."\t";
   print $npoor[1]."\t";
-  print $gc[1]."\t";
-  print qcal($nreads[1],$qscore,\@qlines);
+  print $gc[1];
+  foreach $qs (@qlist) {
+    print "\t";
+    print qcal($nreads[1],$qs,\@qlines);
+  }
   print "\n";
 }