From 5847b85c09db8c9cc76ccaec3333de6ddb13c131 Mon Sep 17 00:00:00 2001
From: earonesty <erik@q32.com>
Date: Thu, 12 Dec 2013 12:48:32 -0500
Subject: [PATCH] Update Local.pm

If the variable_length_reads flag is set, then the files should not be checked for the same size.
---
 lib/RUM/Platform/Local.pm | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/lib/RUM/Platform/Local.pm b/lib/RUM/Platform/Local.pm
index 897dc2b..997d56d 100644
--- a/lib/RUM/Platform/Local.pm
+++ b/lib/RUM/Platform/Local.pm
@@ -204,7 +204,9 @@ sub _check_read_file_pair {
     my @reads = $self->config->reads;
 
     if (@reads == 2) {
-        if ($reads[0] !~ /\.gz$/ && 
+        if ($self->config->variable_length_reads) {
+            $self->say("Working with variable length reads; skipping check to make sure files are the same size.");
+        } elsif ($reads[0] !~ /\.gz$/ && 
             $reads[1] !~ /\.gz$/) {
             $self->_check_read_files_same_size();
         }