Mercurial > repos > ryotas > count_reads

changeset 7:b4f110c177f9 default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
commit
author ryotas <yamanaka@genome.rcast.u-tokyo.ac.jp>
date Tue, 01 Mar 2016 01:41:39 +0900
parents c98e9654bd29
children
files count_reads.pl
diffstat 1 files changed, 7 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/count_reads.pl	Sun Jan 17 23:41:30 2016 +0900
+++ b/count_reads.pl	Tue Mar 01 01:41:39 2016 +0900
@@ -22,9 +22,13 @@
 system "mkdir bedgraph";
 
 # Get number of total reads
-#$stat = `samtools flagstat $tmp`;
-#if ($stat =~ /([0-9]+) \+ [0-9]+ in total .*/) { $reads_total = $1; }
-#print "Total Reads: $reads_total\n";
+system "echo $divide";
+if ($divide == 1) {
+  system "echo $bam";
+  $stat = `samtools flagstat $tmp`;
+  if ($stat =~ /([0-9]+) \+ [0-9]+ in total .*/) { $reads_total = $1; }
+  print "Total Reads: $reads_total\n";
+}
 
 while ($line = <GENELIST>) {
   print $line;