Mercurial > repos > estrain > sum_fastqc

changeset 3:5e1f199bd289 draft

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Uploaded
author estrain
date Tue, 16 Oct 2018 18:59:58 -0400
parents 226ce8aaa97a
children d1090415088b
files sum_fastqc.pl
diffstat 1 files changed, 2 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/sum_fastqc.pl	Tue Oct 16 18:59:44 2018 -0400
+++ b/sum_fastqc.pl	Tue Oct 16 18:59:58 2018 -0400
@@ -12,7 +12,6 @@
 #################################################### 
 
 $infile=@ARGV[0];
-$galfile=@ARGV[1];
 
 # First 10 lines of raw FASTQC contain basic overview
 @sumlines=`head -n 10 $infile`;
@@ -33,16 +32,15 @@
 shift(@sumlines);
 @gc = split(/\t/,shift(@sumlines));
 
-print "Input Data\tFile\tFastQC\tPass-Fail\tReads\tPoor_Reads\tGC\tQ30\n";
+print "File\tFastQC\tPass-Fail\tReads\tPoor_Reads\tGC\tQ30\n";
 
-print $galfile."\t";
 print $fn[1]."\t";
 print $fastqc[1]."\t";
 print $pass[1]."\t";
 print $nreads[1]."\t";
 print $npoor[1]."\t";
 print $gc[1]."\t";
-print qcal($nreads[1],30,\@qlines)."\t";
+print qcal($nreads[1],30,\@qlines);
 print "\n";
 
 # Sum reads w/ Q scores > cutoff and divide by number of reads