From acbc070a66833e6bc83f30ddbfb540e84f35021f Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Wed, 27 Oct 2010 17:59:07 -0400
Subject: [PATCH] More tweaking to try to get Cuffdiff to pass functional
 tests. The problem is that Cuffdiff's output is not deterministic, so
 lines_diff needs to be large enough (but no larger than needed) to accomodate
 small differences in output.

---
 tools/ngs_rna/cuffdiff_wrapper.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/ngs_rna/cuffdiff_wrapper.xml b/tools/ngs_rna/cuffdiff_wrapper.xml
index 4591b62a113..0037c1ef8ac 100644
--- a/tools/ngs_rna/cuffdiff_wrapper.xml
+++ b/tools/ngs_rna/cuffdiff_wrapper.xml
@@ -77,7 +77,7 @@
                     Line diffs are needed because cuffdiff does not produce deterministic output.
                     TODO: can we find datasets that lead to deterministic behavior?
                 -->
-                <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="8"/>
+                <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="14"/>
                 <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="4"/>
                 <output name="tss_groups_exp" file="cuffdiff_out3.txt"/>
                 <output name="cds_exp_fpkm_tracking" file="cuffdiff_out4.txt"/>