# HG changeset patch
# User devteam
# Date 1419368131 18000
# Node ID 88fcac97c2a0adee36297b28a502b3af8a080a14
# Parent  8da0eade1f593775646acd6b2283046e88ec2296
Uploaded updated cuffdiff.

diff -r 8da0eade1f59 -r 88fcac97c2a0 cuffdiff_wrapper.xml
--- a/cuffdiff_wrapper.xml	Fri Dec 19 11:57:43 2014 -0500
+++ b/cuffdiff_wrapper.xml	Tue Dec 23 15:55:31 2014 -0500
@@ -1,12 +1,16 @@
-<tool id="cuffdiff" name="Cuffdiff" version="@VERSION@.0">
+<tool id="cuffdiff" name="Cuffdiff" version="@VERSION@.1">
     <description>find significant changes in transcript expression, splicing, and promoter use</description>
-    <expand macro="requirements" />
+    <requirements>
+        <requirement type="set_environment">CUFFDIFF_SCRIPT_PATH</requirement>
+        <requirement type="package" version="2.2.1">cufflinks</requirement>
+        <requirement type="package" version="2.8.2">cummeRbund</requirement>
+    </requirements>
     <expand macro="stdio" />
     <macros>
       <import>cuff_macros.xml</import>
     </macros>
     <version_command>cuffdiff 2>&amp;1 | head -n 1</version_command>
-    <command>
+    <command><![CDATA[
         cuffdiff
             --no-update-check
             --FDR=$fdr
@@ -64,6 +68,9 @@
             $gtf_input
 
             @CONDITION_SAMPLES@
+            &&
+            R --vanilla --no-save -f \$CUFFDIFF_SCRIPT_PATH/cummeRbund.R && mv cummeRbund.sqlite "${output_cummerbund}"
+            ]]>
     </command>
     <inputs>
         <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts" help="A transcript GFF3 or GTF file produced by cufflinks, cuffcompare, or other source."/>
@@ -179,52 +186,7 @@
         </conditional>
     </inputs>
     <outputs>
-        <!-- Optional read group datasets. -->
-        <data format="tabular" name="isoforms_read_group" label="${tool.name} on ${on_string}: isoforms read group tracking" from_work_dir="isoforms.read_group_tracking" >
-            <filter>(include_read_group_files == 'Yes')</filter>
-        </data>
-        <data format="tabular" name="genes_read_group" label="${tool.name} on ${on_string}: genes read group tracking" from_work_dir="genes.read_group_tracking" >
-            <filter>(include_read_group_files == 'Yes')</filter>
-        </data>
-        <data format="tabular" name="cds_read_group" label="${tool.name} on ${on_string}: CDs read group tracking" from_work_dir="cds.read_group_tracking" >
-            <filter>(include_read_group_files == 'Yes')</filter>
-        </data>
-        <data format="tabular" name="tss_groups_read_group" label="${tool.name} on ${on_string}: TSS groups read group tracking" from_work_dir="tss_groups.read_group_tracking" >
-            <filter>(include_read_group_files == 'Yes')</filter>
-        </data>
-        <data format="text" name="read_group_info" label="${tool.name} on ${on_string}: read group info" from_work_dir="read_groups.info" >
-            <filter>(include_read_group_files == 'Yes')</filter>
-        </data>
-        <data format="text" name="run_info" label="${tool.name} on ${on_string}: run info" from_work_dir="run.info" >
-            <filter>(include_read_group_files == 'Yes')</filter>
-        </data>
-        <!-- Standard datasets. -->
-        <data format="tabular" name="splicing_diff" label="${tool.name} on ${on_string}: splicing differential expression testing" from_work_dir="splicing.diff" />
-        <data format="tabular" name="promoters_diff" label="${tool.name} on ${on_string}: promoters differential expression testing" from_work_dir="promoters.diff" />
-        <data format="tabular" name="cds_diff" label="${tool.name} on ${on_string}: CDS overloading diffential expression testing" from_work_dir="cds.diff" />
-        <data format="tabular" name="cds_exp_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM differential expression testing" from_work_dir="cds_exp.diff" />
-        <data format="tabular" name="cds_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM tracking" from_work_dir="cds.fpkm_tracking" />
-        <data format="tabular" name="cds_count_tracking" label="${tool.name} on ${on_string}: CDS count tracking" from_work_dir="cds.count_tracking" >
-                <filter>(include_count_files == 'Yes')</filter>
-        </data>
-
-        <data format="tabular" name="tss_groups_exp" label="${tool.name} on ${on_string}: TSS groups differential expression testing" from_work_dir="tss_group_exp.diff" />
-        <data format="tabular" name="tss_groups_fpkm_tracking" label="${tool.name} on ${on_string}: TSS groups FPKM tracking" from_work_dir="tss_groups.fpkm_tracking" />
-        <data format="tabular" name="tss_groups_count_tracking" label="${tool.name} on ${on_string}: TSS count FPKM tracking" from_work_dir="tss_groups.count_tracking" >
-                <filter>(include_count_files == 'Yes')</filter>
-        </data>
-
-        <data format="tabular" name="genes_exp" label="${tool.name} on ${on_string}: gene differential expression testing" from_work_dir="gene_exp.diff" />
-        <data format="tabular" name="genes_fpkm_tracking" label="${tool.name} on ${on_string}: gene FPKM tracking" from_work_dir="genes.fpkm_tracking" />
-        <data format="tabular" name="genes_count_tracking" label="${tool.name} on ${on_string}: gene count tracking" from_work_dir="genes.count_tracking" >
-                <filter>(include_count_files == 'Yes')</filter>
-        </data>
-
-        <data format="tabular" name="isoforms_exp" label="${tool.name} on ${on_string}: transcript differential expression testing" from_work_dir="isoform_exp.diff" />
-        <data format="tabular" name="isoforms_fpkm_tracking" label="${tool.name} on ${on_string}: transcript FPKM tracking" from_work_dir="isoforms.fpkm_tracking" />
-        <data format="tabular" name="isoforms_count_tracking" label="${tool.name} on ${on_string}: transcript count tracking" from_work_dir="isoforms.count_tracking" >
-                <filter>(include_count_files == 'Yes')</filter>
-        </data>
+        <data format="sqlite" name="output_cummerbund" label="${tool.name} on ${on_string}: cummeRbund SQLite database" />
     </outputs>
 
     <tests>
@@ -254,17 +216,7 @@
                 <param name="do_normalization" value="No" />
                 <param name="multiread_correct" value="No"/>
                 <param name="sAdditional" value="No"/>
-                <output name="splicing_diff" file="cuffdiff_out9.txt"/>
-                <output name="promoters_diff" file="cuffdiff_out10.txt"/>
-                <output name="cds_diff" file="cuffdiff_out11.txt"/>
-                <output name="cds_exp_fpkm_tracking" file="cuffdiff_out4.txt"/>
-                <output name="cds_fpkm_tracking" file="cuffdiff_out8.txt"/>
-                <output name="tss_groups_exp" file="cuffdiff_out3.txt" lines_diff="200"/>
-                <output name="tss_groups_fpkm_tracking" file="cuffdiff_out7.txt"/>
-                <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="200"/>
-                <output name="genes_fpkm_tracking" file="cuffdiff_out6.txt" lines_diff="200"/>
-                <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="200"/>
-                <output name="isoforms_fpkm_tracking" file="cuffdiff_out5.txt" lines_diff="200"/>
+                <output name="output_cummerbund" ftype="sqlite" file="cuffdiff_out.sqlite"/>
         </test>
     </tests>
     <help>
diff -r 8da0eade1f59 -r 88fcac97c2a0 cummeRbund.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cummeRbund.R	Tue Dec 23 15:55:31 2014 -0500
@@ -0,0 +1,2 @@
+library("cummeRbund")
+cuff <- readCufflinks(dir = ".", dbFile = 'cummeRbund.sqlite')
\ No newline at end of file
diff -r 8da0eade1f59 -r 88fcac97c2a0 test-data/cuffdiff_out.sqlite
Binary file test-data/cuffdiff_out.sqlite has changed
diff -r 8da0eade1f59 -r 88fcac97c2a0 test-data/cuffdiff_out1.txt
--- a/test-data/cuffdiff_out1.txt	Fri Dec 19 11:57:43 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,91 +0,0 @@
-test_id	gene_id	gene	locus	sample_1	sample_2	status	value_1	value_2	log2(fold_change)	test_stat	p_value	q_value	significant
-TCONS_00000001	XLOC_000001	Xkr4	chr1:3204754-3204833	q1	q2	OK	0	9.45986e+06	inf	-nan	0.01975	0.101571	no
-TCONS_00000002	XLOC_000002	-	chr1:3111449-3111490	q1	q2	OK	0	2.43637e+08	inf	-nan	0.12465	0.186975	no
-TCONS_00000003	XLOC_000003	-	chr1:3111545-3111576	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000009	XLOC_000011	-	chr1:3192441-3192494	q1	q2	OK	0	9.7002e+07	inf	-nan	0.07975	0.186975	no
-TCONS_00000010	XLOC_000012	-	chr1:3192550-3192629	q1	q2	OK	0	4.72993e+06	inf	-nan	0.12465	0.186975	no
-TCONS_00000011	XLOC_000014	-	chr1:3192731-3192811	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000012	XLOC_000015	-	chr1:3192940-3193042	q1	q2	OK	0	6.86386e+06	inf	-nan	0.0612	0.186975	no
-TCONS_00000013	XLOC_000016	-	chr1:3194185-3194226	q1	q2	OK	0	2.43637e+08	inf	-nan	0.12465	0.186975	no
-TCONS_00000014	XLOC_000017	-	chr1:3194302-3194329	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000015	XLOC_000019	-	chr1:3195083-3195110	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000016	XLOC_000020	-	chr1:3195450-3195477	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000017	XLOC_000021	-	chr1:3197089-3197116	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000018	XLOC_000022	-	chr1:3197246-3197273	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000019	XLOC_000023	-	chr1:3197346-3197373	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000020	XLOC_000025	-	chr1:3200022-3200191	q1	q2	OK	826392	803108	-0.0412311	-0.0180163	0.8625	0.887143	no
-TCONS_00000021	XLOC_000026	-	chr1:3200325-3200352	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000022	XLOC_000029	-	chr1:3201077-3201481	q1	q2	OK	66791.3	324548	2.2807	1.1905	0.3026	0.380545	no
-TCONS_00000023	XLOC_000031	-	chr1:3201672-3201699	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000024	XLOC_000034	Xkr4	chr1:3212213-3212292	q1	q2	OK	0	9.45986e+06	inf	-nan	0.01975	0.101571	no
-TCONS_00000025	XLOC_000035	Xkr4	chr1:3212367-3212439	q1	q2	OK	0	2.80837e+07	inf	-nan	0.0612	0.186975	no
-TCONS_00000026	XLOC_000037	Xkr4	chr1:3213095-3213242	q1	q2	OK	4.24463e+06	2.08209e+06	-1.0276	-0.36063	0.3844	0.435206	no
-TCONS_00000027	XLOC_000040	Xkr4	chr1:3242633-3242923	q1	q2	OK	48522.7	424400	3.12869	1.23747	0.38685	0.435206	no
-TCONS_00000028	XLOC_000042	Xkr4	chr1:3243018-3243079	q1	q2	OK	0	3.03053e+07	inf	-nan	0.01975	0.101571	no
-TCONS_00000029	XLOC_000044	Xkr4	chr1:3243347-3243401	q1	q2	OK	0	5.79991e+07	inf	-nan	0.01975	0.101571	no
-TCONS_00000030	XLOC_000046	Xkr4	chr1:3256974-3257011	q1	q2	OK	0	2.35423e+09	inf	-nan	0.01975	0.101571	no
-TCONS_00000031	XLOC_000048	Xkr4	chr1:3277190-3277218	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000033	XLOC_000052	Xkr4	chr1:3280686-3280741	q1	q2	OK	0	2.61334e+07	inf	-nan	0.12465	0.186975	no
-TCONS_00000034	XLOC_000057	Xkr4	chr1:3290488-3290553	q1	q2	OK	0	1.11503e+07	inf	-nan	0.12465	0.186975	no
-TCONS_00000037	XLOC_000060	Xkr4	chr1:3299443-3299664	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000038	XLOC_000062	Xkr4	chr1:3300051-3300078	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000039	XLOC_000065	Xkr4	chr1:3318999-3319051	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000040	XLOC_000068	Xkr4	chr1:3355887-3356119	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000041	XLOC_000071	Xkr4	chr1:3363214-3363278	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000042	XLOC_000073	Xkr4	chr1:3363753-3363849	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000043	XLOC_000075	Xkr4	chr1:3367135-3367162	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000044	XLOC_000077	Xkr4	chr1:3367333-3367382	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000045	XLOC_000080	Xkr4	chr1:3377211-3377262	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000046	XLOC_000083	Xkr4	chr1:3391325-3391352	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000047	XLOC_000084	Xkr4	chr1:3435841-3435880	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000048	XLOC_000085	Xkr4	chr1:3447761-3447788	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000049	XLOC_000086	Xkr4	chr1:3450906-3450965	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000050	XLOC_000087	Xkr4	chr1:3451051-3451109	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000051	XLOC_000004	-	chr1:3174765-3174792	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000052	XLOC_000005	-	chr1:3187401-3187428	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000053	XLOC_000006	-	chr1:3188521-3188548	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000054	XLOC_000007	-	chr1:3189810-3190789	q1	q2	OK	358326	522345	0.543731	1.1445	0.1952	0.270969	no
-TCONS_00000055	XLOC_000008	-	chr1:3190858-3191434	q1	q2	OK	408511	420354	0.0412311	0.0469899	0.96715	0.96715	no
-TCONS_00000056	XLOC_000009	-	chr1:3191512-3192077	q1	q2	OK	433286	842157	0.958769	1.27887	0.20385	0.2718	no
-TCONS_00000057	XLOC_000010	-	chr1:3192250-3192336	q1	q2	OK	3.44151e+06	3.34455e+06	-0.0412311	-0.014084	0.67715	0.716982	no
-TCONS_00000058	XLOC_000013	-	chr1:3192649-3192676	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000059	XLOC_000018	-	chr1:3194706-3194733	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000060	XLOC_000024	-	chr1:3197425-3197452	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000062	XLOC_000027	-	chr1:3200430-3200457	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000063	XLOC_000028	-	chr1:3201007-3201039	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000065	XLOC_000030	-	chr1:3201596-3201666	q1	q2	OK	1.6359e+07	0	-inf	-nan	0.0148	0.101571	no
-TCONS_00000066	XLOC_000032	-	chr1:3201725-3201809	q1	q2	OK	1.5136e+07	0	-inf	-nan	0.06005	0.186975	no
-TCONS_00000067	XLOC_000033	Xkr4	chr1:3211521-3211561	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000068	XLOC_000036	Xkr4	chr1:3212717-3212801	q1	q2	OK	3.784e+06	0	-inf	-nan	0.12165	0.186975	no
-TCONS_00000069	XLOC_000037	Xkr4	chr1:3213095-3213242	q1	q2	OK	863189	0	-inf	-nan	0.1957	0.270969	no
-TCONS_00000070	XLOC_000038	Xkr4	chr1:3240606-3240633	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000071	XLOC_000039	Xkr4	chr1:3242479-3242512	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000072	XLOC_000041	Xkr4	chr1:3242924-3243005	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000073	XLOC_000043	Xkr4	chr1:3243108-3243154	q1	q2	OK	8.616e+07	0	-inf	-nan	0.12165	0.186975	no
-TCONS_00000074	XLOC_000045	Xkr4	chr1:3254079-3254106	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000075	XLOC_000047	Xkr4	chr1:3277155-3277182	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000076	XLOC_000049	Xkr4	chr1:3277913-3278390	q1	q2	OK	228872	47662.2	-2.26362	-1.16262	0.30655	0.380545	no
-TCONS_00000077	XLOC_000050	Xkr4	chr1:3280117-3280144	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000078	XLOC_000051	Xkr4	chr1:3280498-3280525	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000079	XLOC_000053	Xkr4	chr1:3282504-3282531	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000080	XLOC_000054	Xkr4	chr1:3282650-3282677	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000081	XLOC_000055	Xkr4	chr1:3282760-3282832	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000082	XLOC_000056	Xkr4	chr1:3284966-3284993	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000083	XLOC_000058	Xkr4	chr1:3290798-3290859	q1	q2	OK	1.55919e+07	0	-inf	-nan	0.12165	0.186975	no
-TCONS_00000084	XLOC_000059	Xkr4	chr1:3290919-3291273	q1	q2	OK	294879	85971.3	-1.7782	-0.902752	0.36915	0.435206	no
-TCONS_00000085	XLOC_000060	Xkr4	chr1:3299443-3299664	q1	q2	OK	807732	156995	-2.36316	-0.933704	0.4205	0.458727	no
-TCONS_00000086	XLOC_000061	Xkr4	chr1:3299691-3299733	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000087	XLOC_000063	Xkr4	chr1:3307748-3307775	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000088	XLOC_000064	Xkr4	chr1:3318620-3318647	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000089	XLOC_000066	Xkr4	chr1:3330527-3330554	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000090	XLOC_000067	Xkr4	chr1:3351240-3351311	q1	q2	OK	7.68169e+06	0	-inf	-nan	0.12165	0.186975	no
-TCONS_00000091	XLOC_000068	Xkr4	chr1:3355887-3356119	q1	q2	OK	504790	0	-inf	-nan	0.05945	0.186975	no
-TCONS_00000092	XLOC_000069	Xkr4	chr1:3356180-3356225	q1	q2	OK	1.02717e+08	0	-inf	-nan	0.12165	0.186975	no
-TCONS_00000093	XLOC_000070	Xkr4	chr1:3363076-3363176	q1	q2	OK	3.81001e+06	0	-inf	-nan	0.0148	0.101571	no
-TCONS_00000094	XLOC_000072	Xkr4	chr1:3363387-3363446	q1	q2	OK	5.53654e+07	0	-inf	-nan	0.0773	0.186975	no
-TCONS_00000095	XLOC_000074	Xkr4	chr1:3364871-3364919	q1	q2	OK	6.28966e+07	0	-inf	-nan	0.12165	0.186975	no
-TCONS_00000096	XLOC_000076	Xkr4	chr1:3367210-3367237	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000097	XLOC_000078	Xkr4	chr1:3369580-3369607	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000098	XLOC_000079	Xkr4	chr1:3375001-3375028	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000099	XLOC_000081	Xkr4	chr1:3379888-3379915	q1	q2	NOTEST	0	0	0	0	1	1	no
-TCONS_00000100	XLOC_000082	Xkr4	chr1:3386739-3386836	q1	q2	NOTEST	0	0	0	0	1	1	no
diff -r 8da0eade1f59 -r 88fcac97c2a0 test-data/cuffdiff_out10.txt
--- a/test-data/cuffdiff_out10.txt	Fri Dec 19 11:57:43 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,88 +0,0 @@
-test_id	gene_id	gene	locus	sample_1	sample_2	status	value_1	value_2	sqrt(JS)	test_stat	p_value	q_value	significant
-XLOC_000001	XLOC_000001	Xkr4	chr1:3204754-3204833	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000002	XLOC_000002	-	chr1:3111449-3111490	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000003	XLOC_000003	-	chr1:3111545-3111576	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000004	XLOC_000004	-	chr1:3174765-3174792	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000005	XLOC_000005	-	chr1:3187401-3187428	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000006	XLOC_000006	-	chr1:3188521-3188548	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000007	XLOC_000007	-	chr1:3189810-3190789	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000008	XLOC_000008	-	chr1:3190858-3191434	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000009	XLOC_000009	-	chr1:3191512-3192077	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000010	XLOC_000010	-	chr1:3192250-3192336	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000011	XLOC_000011	-	chr1:3192441-3192494	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000012	XLOC_000012	-	chr1:3192550-3192629	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000013	XLOC_000013	-	chr1:3192649-3192676	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000014	XLOC_000014	-	chr1:3192731-3192811	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000015	XLOC_000015	-	chr1:3192940-3193042	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000016	XLOC_000016	-	chr1:3194185-3194226	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000017	XLOC_000017	-	chr1:3194302-3194329	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000018	XLOC_000018	-	chr1:3194706-3194733	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000019	XLOC_000019	-	chr1:3195083-3195110	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000020	XLOC_000020	-	chr1:3195450-3195477	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000021	XLOC_000021	-	chr1:3197089-3197116	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000022	XLOC_000022	-	chr1:3197246-3197273	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000023	XLOC_000023	-	chr1:3197346-3197373	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000024	XLOC_000024	-	chr1:3197425-3197452	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000025	XLOC_000025	-	chr1:3200022-3200191	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000026	XLOC_000026	-	chr1:3200325-3200352	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000027	XLOC_000027	-	chr1:3200430-3200457	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000028	XLOC_000028	-	chr1:3201007-3201039	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000029	XLOC_000029	-	chr1:3201077-3201481	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000030	XLOC_000030	-	chr1:3201596-3201666	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000031	XLOC_000031	-	chr1:3201672-3201699	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000032	XLOC_000032	-	chr1:3201725-3201809	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000033	XLOC_000033	Xkr4	chr1:3211521-3211561	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000034	XLOC_000034	Xkr4	chr1:3212213-3212292	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000035	XLOC_000035	Xkr4	chr1:3212367-3212439	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000036	XLOC_000036	Xkr4	chr1:3212717-3212801	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000037	XLOC_000037	Xkr4	chr1:3213095-3213242	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000038	XLOC_000038	Xkr4	chr1:3240606-3240633	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000039	XLOC_000039	Xkr4	chr1:3242479-3242512	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000040	XLOC_000040	Xkr4	chr1:3242633-3242923	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000041	XLOC_000041	Xkr4	chr1:3242924-3243005	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000042	XLOC_000042	Xkr4	chr1:3243018-3243079	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000043	XLOC_000043	Xkr4	chr1:3243108-3243154	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000044	XLOC_000044	Xkr4	chr1:3243347-3243401	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000045	XLOC_000045	Xkr4	chr1:3254079-3254106	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000046	XLOC_000046	Xkr4	chr1:3256974-3257011	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000047	XLOC_000047	Xkr4	chr1:3277155-3277182	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000048	XLOC_000048	Xkr4	chr1:3277190-3277218	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000049	XLOC_000049	Xkr4	chr1:3277913-3278390	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000050	XLOC_000050	Xkr4	chr1:3280117-3280144	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000051	XLOC_000051	Xkr4	chr1:3280498-3280525	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000052	XLOC_000052	Xkr4	chr1:3280686-3280741	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000053	XLOC_000053	Xkr4	chr1:3282504-3282531	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000054	XLOC_000054	Xkr4	chr1:3282650-3282677	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000055	XLOC_000055	Xkr4	chr1:3282760-3282832	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000056	XLOC_000056	Xkr4	chr1:3284966-3284993	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000057	XLOC_000057	Xkr4	chr1:3290488-3290553	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000058	XLOC_000058	Xkr4	chr1:3290798-3290859	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000059	XLOC_000059	Xkr4	chr1:3290919-3291273	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000060	XLOC_000060	Xkr4	chr1:3299443-3299664	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000061	XLOC_000061	Xkr4	chr1:3299691-3299733	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000062	XLOC_000062	Xkr4	chr1:3300051-3300078	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000063	XLOC_000063	Xkr4	chr1:3307748-3307775	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000064	XLOC_000064	Xkr4	chr1:3318620-3318647	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000065	XLOC_000065	Xkr4	chr1:3318999-3319051	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000066	XLOC_000066	Xkr4	chr1:3330527-3330554	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000067	XLOC_000067	Xkr4	chr1:3351240-3351311	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000068	XLOC_000068	Xkr4	chr1:3355887-3356119	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000069	XLOC_000069	Xkr4	chr1:3356180-3356225	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000070	XLOC_000070	Xkr4	chr1:3363076-3363176	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000071	XLOC_000071	Xkr4	chr1:3363214-3363278	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000072	XLOC_000072	Xkr4	chr1:3363387-3363446	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000073	XLOC_000073	Xkr4	chr1:3363753-3363849	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000074	XLOC_000074	Xkr4	chr1:3364871-3364919	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000075	XLOC_000075	Xkr4	chr1:3367135-3367162	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000076	XLOC_000076	Xkr4	chr1:3367210-3367237	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000077	XLOC_000077	Xkr4	chr1:3367333-3367382	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000078	XLOC_000078	Xkr4	chr1:3369580-3369607	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000079	XLOC_000079	Xkr4	chr1:3375001-3375028	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000080	XLOC_000080	Xkr4	chr1:3377211-3377262	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000081	XLOC_000081	Xkr4	chr1:3379888-3379915	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000082	XLOC_000082	Xkr4	chr1:3386739-3386836	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000083	XLOC_000083	Xkr4	chr1:3391325-3391352	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000084	XLOC_000084	Xkr4	chr1:3435841-3435880	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000085	XLOC_000085	Xkr4	chr1:3447761-3447788	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000086	XLOC_000086	Xkr4	chr1:3450906-3450965	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000087	XLOC_000087	Xkr4	chr1:3451051-3451109	q1	q2	NOTEST	0	0	0	0	1	1	no
diff -r 8da0eade1f59 -r 88fcac97c2a0 test-data/cuffdiff_out11.txt
--- a/test-data/cuffdiff_out11.txt	Fri Dec 19 11:57:43 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-test_id	gene_id	gene	locus	sample_1	sample_2	status	value_1	value_2	sqrt(JS)	test_stat	p_value	q_value	significant
diff -r 8da0eade1f59 -r 88fcac97c2a0 test-data/cuffdiff_out2.txt
--- a/test-data/cuffdiff_out2.txt	Fri Dec 19 11:57:43 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,88 +0,0 @@
-test_id	gene_id	gene	locus	sample_1	sample_2	status	value_1	value_2	log2(fold_change)	test_stat	p_value	q_value	significant
-XLOC_000001	XLOC_000001	Xkr4	chr1:3204754-3204833	q1	q2	OK	0	9.45986e+06	inf	-nan	0.01975	0.09875	no
-XLOC_000002	XLOC_000002	-	chr1:3111449-3111490	q1	q2	OK	0	2.43637e+08	inf	-nan	0.12465	0.181781	no
-XLOC_000003	XLOC_000003	-	chr1:3111545-3111576	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000004	XLOC_000004	-	chr1:3174765-3174792	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000005	XLOC_000005	-	chr1:3187401-3187428	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000006	XLOC_000006	-	chr1:3188521-3188548	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000007	XLOC_000007	-	chr1:3189810-3190789	q1	q2	OK	358326	522345	0.543731	1.1445	0.1952	0.27328	no
-XLOC_000008	XLOC_000008	-	chr1:3190858-3191434	q1	q2	OK	408511	420354	0.0412311	0.0469899	0.96715	0.96715	no
-XLOC_000009	XLOC_000009	-	chr1:3191512-3192077	q1	q2	OK	433286	842157	0.958769	1.27887	0.20385	0.274413	no
-XLOC_000010	XLOC_000010	-	chr1:3192250-3192336	q1	q2	OK	3.44151e+06	3.34455e+06	-0.0412311	-0.014084	0.67715	0.718189	no
-XLOC_000011	XLOC_000011	-	chr1:3192441-3192494	q1	q2	OK	0	9.7002e+07	inf	-nan	0.07975	0.181781	no
-XLOC_000012	XLOC_000012	-	chr1:3192550-3192629	q1	q2	OK	0	4.72993e+06	inf	-nan	0.12465	0.181781	no
-XLOC_000013	XLOC_000013	-	chr1:3192649-3192676	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000014	XLOC_000014	-	chr1:3192731-3192811	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000015	XLOC_000015	-	chr1:3192940-3193042	q1	q2	OK	0	6.86386e+06	inf	-nan	0.0612	0.181781	no
-XLOC_000016	XLOC_000016	-	chr1:3194185-3194226	q1	q2	OK	0	2.43637e+08	inf	-nan	0.12465	0.181781	no
-XLOC_000017	XLOC_000017	-	chr1:3194302-3194329	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000018	XLOC_000018	-	chr1:3194706-3194733	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000019	XLOC_000019	-	chr1:3195083-3195110	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000020	XLOC_000020	-	chr1:3195450-3195477	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000021	XLOC_000021	-	chr1:3197089-3197116	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000022	XLOC_000022	-	chr1:3197246-3197273	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000023	XLOC_000023	-	chr1:3197346-3197373	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000024	XLOC_000024	-	chr1:3197425-3197452	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000025	XLOC_000025	-	chr1:3200022-3200191	q1	q2	OK	826392	803108	-0.0412311	-0.0180163	0.8625	0.887868	no
-XLOC_000026	XLOC_000026	-	chr1:3200325-3200352	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000027	XLOC_000027	-	chr1:3200430-3200457	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000028	XLOC_000028	-	chr1:3201007-3201039	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000029	XLOC_000029	-	chr1:3201077-3201481	q1	q2	OK	66791.3	324548	2.2807	1.1905	0.3026	0.383188	no
-XLOC_000030	XLOC_000030	-	chr1:3201596-3201666	q1	q2	OK	1.6359e+07	0	-inf	-nan	0.0148	0.09875	no
-XLOC_000031	XLOC_000031	-	chr1:3201672-3201699	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000032	XLOC_000032	-	chr1:3201725-3201809	q1	q2	OK	1.5136e+07	0	-inf	-nan	0.06005	0.181781	no
-XLOC_000033	XLOC_000033	Xkr4	chr1:3211521-3211561	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000034	XLOC_000034	Xkr4	chr1:3212213-3212292	q1	q2	OK	0	9.45986e+06	inf	-nan	0.01975	0.09875	no
-XLOC_000035	XLOC_000035	Xkr4	chr1:3212367-3212439	q1	q2	OK	0	2.80837e+07	inf	-nan	0.0612	0.181781	no
-XLOC_000036	XLOC_000036	Xkr4	chr1:3212717-3212801	q1	q2	OK	3.784e+06	0	-inf	-nan	0.12165	0.181781	no
-XLOC_000037	XLOC_000037	Xkr4	chr1:3213095-3213242	q1	q2	OK	5.10781e+06	2.08209e+06	-1.29467	-0.482193	0.5916	0.647062	no
-XLOC_000038	XLOC_000038	Xkr4	chr1:3240606-3240633	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000039	XLOC_000039	Xkr4	chr1:3242479-3242512	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000040	XLOC_000040	Xkr4	chr1:3242633-3242923	q1	q2	OK	48522.7	424400	3.12869	1.23747	0.38685	0.450823	no
-XLOC_000041	XLOC_000041	Xkr4	chr1:3242924-3243005	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000042	XLOC_000042	Xkr4	chr1:3243018-3243079	q1	q2	OK	0	3.03053e+07	inf	-nan	0.01975	0.09875	no
-XLOC_000043	XLOC_000043	Xkr4	chr1:3243108-3243154	q1	q2	OK	8.616e+07	0	-inf	-nan	0.12165	0.181781	no
-XLOC_000044	XLOC_000044	Xkr4	chr1:3243347-3243401	q1	q2	OK	0	5.79991e+07	inf	-nan	0.01975	0.09875	no
-XLOC_000045	XLOC_000045	Xkr4	chr1:3254079-3254106	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000046	XLOC_000046	Xkr4	chr1:3256974-3257011	q1	q2	OK	0	2.35423e+09	inf	-nan	0.01975	0.09875	no
-XLOC_000047	XLOC_000047	Xkr4	chr1:3277155-3277182	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000048	XLOC_000048	Xkr4	chr1:3277190-3277218	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000049	XLOC_000049	Xkr4	chr1:3277913-3278390	q1	q2	OK	228872	47662.2	-2.26362	-1.16262	0.30655	0.383188	no
-XLOC_000050	XLOC_000050	Xkr4	chr1:3280117-3280144	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000051	XLOC_000051	Xkr4	chr1:3280498-3280525	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000052	XLOC_000052	Xkr4	chr1:3280686-3280741	q1	q2	OK	0	2.61334e+07	inf	-nan	0.12465	0.181781	no
-XLOC_000053	XLOC_000053	Xkr4	chr1:3282504-3282531	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000054	XLOC_000054	Xkr4	chr1:3282650-3282677	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000055	XLOC_000055	Xkr4	chr1:3282760-3282832	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000056	XLOC_000056	Xkr4	chr1:3284966-3284993	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000057	XLOC_000057	Xkr4	chr1:3290488-3290553	q1	q2	OK	0	1.11503e+07	inf	-nan	0.12465	0.181781	no
-XLOC_000058	XLOC_000058	Xkr4	chr1:3290798-3290859	q1	q2	OK	1.55919e+07	0	-inf	-nan	0.12165	0.181781	no
-XLOC_000059	XLOC_000059	Xkr4	chr1:3290919-3291273	q1	q2	OK	294879	85971.3	-1.7782	-0.902752	0.36915	0.445526	no
-XLOC_000060	XLOC_000060	Xkr4	chr1:3299443-3299664	q1	q2	OK	807732	156995	-2.36316	-0.89463	0.3993	0.450823	no
-XLOC_000061	XLOC_000061	Xkr4	chr1:3299691-3299733	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000062	XLOC_000062	Xkr4	chr1:3300051-3300078	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000063	XLOC_000063	Xkr4	chr1:3307748-3307775	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000064	XLOC_000064	Xkr4	chr1:3318620-3318647	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000065	XLOC_000065	Xkr4	chr1:3318999-3319051	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000066	XLOC_000066	Xkr4	chr1:3330527-3330554	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000067	XLOC_000067	Xkr4	chr1:3351240-3351311	q1	q2	OK	7.68169e+06	0	-inf	-nan	0.12165	0.181781	no
-XLOC_000068	XLOC_000068	Xkr4	chr1:3355887-3356119	q1	q2	OK	504790	0	-inf	-nan	0.04565	0.181781	no
-XLOC_000069	XLOC_000069	Xkr4	chr1:3356180-3356225	q1	q2	OK	1.02717e+08	0	-inf	-nan	0.12165	0.181781	no
-XLOC_000070	XLOC_000070	Xkr4	chr1:3363076-3363176	q1	q2	OK	3.81001e+06	0	-inf	-nan	0.0148	0.09875	no
-XLOC_000071	XLOC_000071	Xkr4	chr1:3363214-3363278	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000072	XLOC_000072	Xkr4	chr1:3363387-3363446	q1	q2	OK	5.53654e+07	0	-inf	-nan	0.0773	0.181781	no
-XLOC_000073	XLOC_000073	Xkr4	chr1:3363753-3363849	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000074	XLOC_000074	Xkr4	chr1:3364871-3364919	q1	q2	OK	6.28966e+07	0	-inf	-nan	0.12165	0.181781	no
-XLOC_000075	XLOC_000075	Xkr4	chr1:3367135-3367162	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000076	XLOC_000076	Xkr4	chr1:3367210-3367237	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000077	XLOC_000077	Xkr4	chr1:3367333-3367382	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000078	XLOC_000078	Xkr4	chr1:3369580-3369607	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000079	XLOC_000079	Xkr4	chr1:3375001-3375028	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000080	XLOC_000080	Xkr4	chr1:3377211-3377262	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000081	XLOC_000081	Xkr4	chr1:3379888-3379915	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000082	XLOC_000082	Xkr4	chr1:3386739-3386836	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000083	XLOC_000083	Xkr4	chr1:3391325-3391352	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000084	XLOC_000084	Xkr4	chr1:3435841-3435880	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000085	XLOC_000085	Xkr4	chr1:3447761-3447788	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000086	XLOC_000086	Xkr4	chr1:3450906-3450965	q1	q2	NOTEST	0	0	0	0	1	1	no
-XLOC_000087	XLOC_000087	Xkr4	chr1:3451051-3451109	q1	q2	NOTEST	0	0	0	0	1	1	no
diff -r 8da0eade1f59 -r 88fcac97c2a0 test-data/cuffdiff_out3.txt
--- a/test-data/cuffdiff_out3.txt	Fri Dec 19 11:57:43 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,89 +0,0 @@
-test_id	gene_id	gene	locus	sample_1	sample_2	status	value_1	value_2	log2(fold_change)	test_stat	p_value	q_value	significant
-TSS1	XLOC_000001	Xkr4	chr1:3204754-3204833	q1	q2	OK	0	9.45986e+06	inf	-nan	0.01975	0.09875	no
-TSS10	XLOC_000008	-	chr1:3190858-3191434	q1	q2	OK	408511	420354	0.0412311	0.0469899	0.96715	0.96715	no
-TSS11	XLOC_000009	-	chr1:3191512-3192077	q1	q2	OK	433286	842157	0.958769	1.27887	0.20385	0.274413	no
-TSS13	XLOC_000010	-	chr1:3192250-3192336	q1	q2	OK	3.44151e+06	3.34455e+06	-0.0412311	-0.014084	0.67715	0.718189	no
-TSS14	XLOC_000011	-	chr1:3192441-3192494	q1	q2	OK	0	9.7002e+07	inf	-nan	0.07975	0.181781	no
-TSS15	XLOC_000012	-	chr1:3192550-3192629	q1	q2	OK	0	4.72993e+06	inf	-nan	0.12465	0.181781	no
-TSS16	XLOC_000013	-	chr1:3192649-3192676	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS17	XLOC_000014	-	chr1:3192731-3192811	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS18	XLOC_000015	-	chr1:3192940-3193042	q1	q2	OK	0	6.86386e+06	inf	-nan	0.0612	0.181781	no
-TSS19	XLOC_000016	-	chr1:3194185-3194226	q1	q2	OK	0	2.43637e+08	inf	-nan	0.12465	0.181781	no
-TSS2	XLOC_000002	-	chr1:3111449-3111490	q1	q2	OK	0	2.43637e+08	inf	-nan	0.12465	0.181781	no
-TSS20	XLOC_000017	-	chr1:3194302-3194329	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS21	XLOC_000018	-	chr1:3194706-3194733	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS22	XLOC_000019	-	chr1:3195083-3195110	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS23	XLOC_000020	-	chr1:3195450-3195477	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS24	XLOC_000021	-	chr1:3197089-3197116	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS25	XLOC_000022	-	chr1:3197246-3197273	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS26	XLOC_000023	-	chr1:3197346-3197373	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS27	XLOC_000024	-	chr1:3197425-3197452	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS28	XLOC_000025	-	chr1:3200022-3200191	q1	q2	OK	826392	803108	-0.0412311	-0.0180163	0.8625	0.887868	no
-TSS29	XLOC_000026	-	chr1:3200325-3200352	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS3	XLOC_000003	-	chr1:3111545-3111576	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS30	XLOC_000027	-	chr1:3200430-3200457	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS31	XLOC_000028	-	chr1:3201007-3201039	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS32	XLOC_000029	-	chr1:3201077-3201481	q1	q2	OK	66791.3	324548	2.2807	1.1905	0.3026	0.383188	no
-TSS33	XLOC_000030	-	chr1:3201596-3201666	q1	q2	OK	1.6359e+07	0	-inf	-nan	0.0148	0.09875	no
-TSS34	XLOC_000031	-	chr1:3201672-3201699	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS35	XLOC_000032	-	chr1:3201725-3201809	q1	q2	OK	1.5136e+07	0	-inf	-nan	0.06005	0.181781	no
-TSS36	XLOC_000033	Xkr4	chr1:3211521-3211561	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS37	XLOC_000034	Xkr4	chr1:3212213-3212292	q1	q2	OK	0	9.45986e+06	inf	-nan	0.01975	0.09875	no
-TSS38	XLOC_000035	Xkr4	chr1:3212367-3212439	q1	q2	OK	0	2.80837e+07	inf	-nan	0.0612	0.181781	no
-TSS39	XLOC_000036	Xkr4	chr1:3212717-3212801	q1	q2	OK	3.784e+06	0	-inf	-nan	0.12165	0.181781	no
-TSS4	XLOC_000004	-	chr1:3174765-3174792	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS40	XLOC_000037	Xkr4	chr1:3213095-3213242	q1	q2	OK	5.10781e+06	2.08209e+06	-1.29467	-0.482193	0.5916	0.647062	no
-TSS41	XLOC_000038	Xkr4	chr1:3240606-3240633	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS42	XLOC_000039	Xkr4	chr1:3242479-3242512	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS43	XLOC_000040	Xkr4	chr1:3242633-3242923	q1	q2	OK	48522.7	424400	3.12869	1.23747	0.38685	0.451325	no
-TSS44	XLOC_000041	Xkr4	chr1:3242924-3243005	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS45	XLOC_000042	Xkr4	chr1:3243018-3243079	q1	q2	OK	0	3.03053e+07	inf	-nan	0.01975	0.09875	no
-TSS46	XLOC_000043	Xkr4	chr1:3243108-3243154	q1	q2	OK	8.616e+07	0	-inf	-nan	0.12165	0.181781	no
-TSS47	XLOC_000044	Xkr4	chr1:3243347-3243401	q1	q2	OK	0	5.79991e+07	inf	-nan	0.01975	0.09875	no
-TSS48	XLOC_000045	Xkr4	chr1:3254079-3254106	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS49	XLOC_000046	Xkr4	chr1:3256974-3257011	q1	q2	OK	0	2.35423e+09	inf	-nan	0.01975	0.09875	no
-TSS5	XLOC_000005	-	chr1:3187401-3187428	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS50	XLOC_000047	Xkr4	chr1:3277155-3277182	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS51	XLOC_000048	Xkr4	chr1:3277190-3277218	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS52	XLOC_000049	Xkr4	chr1:3277913-3278390	q1	q2	OK	228872	47662.2	-2.26362	-1.16262	0.30655	0.383188	no
-TSS54	XLOC_000050	Xkr4	chr1:3280117-3280144	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS55	XLOC_000051	Xkr4	chr1:3280498-3280525	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS56	XLOC_000052	Xkr4	chr1:3280686-3280741	q1	q2	OK	0	2.61334e+07	inf	-nan	0.12465	0.181781	no
-TSS57	XLOC_000053	Xkr4	chr1:3282504-3282531	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS58	XLOC_000054	Xkr4	chr1:3282650-3282677	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS59	XLOC_000055	Xkr4	chr1:3282760-3282832	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS6	XLOC_000006	-	chr1:3188521-3188548	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS60	XLOC_000056	Xkr4	chr1:3284966-3284993	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS61	XLOC_000057	Xkr4	chr1:3290488-3290553	q1	q2	OK	0	1.11503e+07	inf	-nan	0.12465	0.181781	no
-TSS62	XLOC_000058	Xkr4	chr1:3290798-3290859	q1	q2	OK	1.55919e+07	0	-inf	-nan	0.12165	0.181781	no
-TSS63	XLOC_000059	Xkr4	chr1:3290919-3291273	q1	q2	OK	294879	85971.3	-1.7782	-0.902752	0.36915	0.445526	no
-TSS65	XLOC_000060	Xkr4	chr1:3299443-3299664	q1	q2	OK	807732	156995	-2.36316	-0.933704	0.4205	0.474758	no
-TSS66	XLOC_000060	Xkr4	chr1:3299443-3299664	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS67	XLOC_000061	Xkr4	chr1:3299691-3299733	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS68	XLOC_000062	Xkr4	chr1:3300051-3300078	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS69	XLOC_000063	Xkr4	chr1:3307748-3307775	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS7	XLOC_000007	-	chr1:3189810-3190789	q1	q2	OK	358326	522345	0.543731	1.1445	0.1952	0.27328	no
-TSS70	XLOC_000064	Xkr4	chr1:3318620-3318647	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS71	XLOC_000065	Xkr4	chr1:3318999-3319051	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS72	XLOC_000066	Xkr4	chr1:3330527-3330554	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS73	XLOC_000067	Xkr4	chr1:3351240-3351311	q1	q2	OK	7.68169e+06	0	-inf	-nan	0.12165	0.181781	no
-TSS74	XLOC_000068	Xkr4	chr1:3355887-3356119	q1	q2	OK	504790	0	-inf	-nan	0.04565	0.181781	no
-TSS75	XLOC_000069	Xkr4	chr1:3356180-3356225	q1	q2	OK	1.02717e+08	0	-inf	-nan	0.12165	0.181781	no
-TSS76	XLOC_000070	Xkr4	chr1:3363076-3363176	q1	q2	OK	3.81001e+06	0	-inf	-nan	0.0148	0.09875	no
-TSS77	XLOC_000071	Xkr4	chr1:3363214-3363278	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS78	XLOC_000072	Xkr4	chr1:3363387-3363446	q1	q2	OK	5.53654e+07	0	-inf	-nan	0.0773	0.181781	no
-TSS79	XLOC_000073	Xkr4	chr1:3363753-3363849	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS80	XLOC_000074	Xkr4	chr1:3364871-3364919	q1	q2	OK	6.28966e+07	0	-inf	-nan	0.12165	0.181781	no
-TSS81	XLOC_000075	Xkr4	chr1:3367135-3367162	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS82	XLOC_000076	Xkr4	chr1:3367210-3367237	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS83	XLOC_000077	Xkr4	chr1:3367333-3367382	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS84	XLOC_000078	Xkr4	chr1:3369580-3369607	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS85	XLOC_000079	Xkr4	chr1:3375001-3375028	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS86	XLOC_000080	Xkr4	chr1:3377211-3377262	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS87	XLOC_000081	Xkr4	chr1:3379888-3379915	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS88	XLOC_000082	Xkr4	chr1:3386739-3386836	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS89	XLOC_000083	Xkr4	chr1:3391325-3391352	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS90	XLOC_000084	Xkr4	chr1:3435841-3435880	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS91	XLOC_000085	Xkr4	chr1:3447761-3447788	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS92	XLOC_000086	Xkr4	chr1:3450906-3450965	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS93	XLOC_000087	Xkr4	chr1:3451051-3451109	q1	q2	NOTEST	0	0	0	0	1	1	no
diff -r 8da0eade1f59 -r 88fcac97c2a0 test-data/cuffdiff_out4.txt
--- a/test-data/cuffdiff_out4.txt	Fri Dec 19 11:57:43 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-test_id	gene_id	gene	locus	sample_1	sample_2	status	value_1	value_2	log2(fold_change)	test_stat	p_value	q_value	significant
diff -r 8da0eade1f59 -r 88fcac97c2a0 test-data/cuffdiff_out5.txt
--- a/test-data/cuffdiff_out5.txt	Fri Dec 19 11:57:43 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,91 +0,0 @@
-tracking_id	class_code	nearest_ref_id	gene_id	gene_short_name	tss_id	locus	length	coverage	q1_FPKM	q1_conf_lo	q1_conf_hi	q1_status	q2_FPKM	q2_conf_lo	q2_conf_hi	q2_status
-TCONS_00000001	c	Xkr4	XLOC_000001	Xkr4	TSS1	chr1:3204754-3204833	79	-	0	0	0	OK	9.45986e+06	0	3.33035e+07	OK
-TCONS_00000002	-	-	XLOC_000002	-	TSS2	chr1:3111449-3111490	41	-	0	0	0	OK	2.43637e+08	0	9.52723e+08	OK
-TCONS_00000003	-	-	XLOC_000003	-	TSS3	chr1:3111545-3111576	31	-	0	0	0	OK	0	0	0	OK
-TCONS_00000009	-	-	XLOC_000011	-	TSS14	chr1:3192441-3192494	53	-	0	0	0	OK	9.7002e+07	0	3.17699e+08	OK
-TCONS_00000010	-	-	XLOC_000012	-	TSS15	chr1:3192550-3192629	79	-	0	0	0	OK	4.72993e+06	0	1.84961e+07	OK
-TCONS_00000011	-	-	XLOC_000014	-	TSS17	chr1:3192731-3192811	80	-	0	0	0	OK	0	0	0	OK
-TCONS_00000012	-	-	XLOC_000015	-	TSS18	chr1:3192940-3193042	102	-	0	0	0	OK	6.86386e+06	0	2.14243e+07	OK
-TCONS_00000013	-	-	XLOC_000016	-	TSS19	chr1:3194185-3194226	41	-	0	0	0	OK	2.43637e+08	0	9.52723e+08	OK
-TCONS_00000014	-	-	XLOC_000017	-	TSS20	chr1:3194302-3194329	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000015	-	-	XLOC_000019	-	TSS22	chr1:3195083-3195110	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000016	-	-	XLOC_000020	-	TSS23	chr1:3195450-3195477	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000017	-	-	XLOC_000021	-	TSS24	chr1:3197089-3197116	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000018	-	-	XLOC_000022	-	TSS25	chr1:3197246-3197273	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000019	-	-	XLOC_000023	-	TSS26	chr1:3197346-3197373	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000020	-	-	XLOC_000025	-	TSS28	chr1:3200022-3200191	169	-	826392	0	2.65361e+06	OK	803108	0	2.63033e+06	OK
-TCONS_00000021	-	-	XLOC_000026	-	TSS29	chr1:3200325-3200352	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000022	-	-	XLOC_000029	-	TSS32	chr1:3201077-3201481	404	-	66791.3	0	214473	OK	324548	0	802006	OK
-TCONS_00000023	-	-	XLOC_000031	-	TSS34	chr1:3201672-3201699	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000024	i	Xkr4	XLOC_000034	Xkr4	TSS37	chr1:3212213-3212292	79	-	0	0	0	OK	9.45986e+06	0	3.33035e+07	OK
-TCONS_00000025	i	Xkr4	XLOC_000035	Xkr4	TSS38	chr1:3212367-3212439	72	-	0	0	0	OK	2.80837e+07	0	8.76584e+07	OK
-TCONS_00000026	i	Xkr4	XLOC_000037	Xkr4	TSS40	chr1:3213095-3213242	97	-	4.24463e+06	0	1.55814e+07	OK	2.08209e+06	0	8.14187e+06	OK
-TCONS_00000027	i	Xkr4	XLOC_000040	Xkr4	TSS43	chr1:3242633-3242923	290	-	48522.7	0	185766	OK	424400	0	1.30289e+06	OK
-TCONS_00000028	i	Xkr4	XLOC_000042	Xkr4	TSS45	chr1:3243018-3243079	61	-	0	0	0	OK	3.03053e+07	0	1.0669e+08	OK
-TCONS_00000029	i	Xkr4	XLOC_000044	Xkr4	TSS47	chr1:3243347-3243401	54	-	0	0	0	OK	5.79991e+07	0	2.04186e+08	OK
-TCONS_00000030	i	Xkr4	XLOC_000046	Xkr4	TSS49	chr1:3256974-3257011	37	-	0	0	0	OK	2.35423e+09	0	8.28806e+09	OK
-TCONS_00000031	i	Xkr4	XLOC_000048	Xkr4	TSS51	chr1:3277190-3277218	28	-	0	0	0	OK	0	0	0	OK
-TCONS_00000033	i	Xkr4	XLOC_000052	Xkr4	TSS56	chr1:3280686-3280741	55	-	0	0	0	OK	2.61334e+07	0	1.02193e+08	OK
-TCONS_00000034	i	Xkr4	XLOC_000057	Xkr4	TSS61	chr1:3290488-3290553	65	-	0	0	0	OK	1.11503e+07	0	4.36026e+07	OK
-TCONS_00000037	i	Xkr4	XLOC_000060	Xkr4	TSS66	chr1:3299443-3299664	55	-	0	0	163195	OK	0	0	163195	OK
-TCONS_00000038	i	Xkr4	XLOC_000062	Xkr4	TSS68	chr1:3300051-3300078	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000039	i	Xkr4	XLOC_000065	Xkr4	TSS71	chr1:3318999-3319051	52	-	0	0	0	OK	0	0	0	OK
-TCONS_00000040	i	Xkr4	XLOC_000068	Xkr4	TSS74	chr1:3355887-3356119	27	-	0	0	332434	OK	0	0	0	OK
-TCONS_00000041	i	Xkr4	XLOC_000071	Xkr4	TSS77	chr1:3363214-3363278	64	-	0	0	0	OK	0	0	0	OK
-TCONS_00000042	i	Xkr4	XLOC_000073	Xkr4	TSS79	chr1:3363753-3363849	96	-	0	0	0	OK	0	0	0	OK
-TCONS_00000043	i	Xkr4	XLOC_000075	Xkr4	TSS81	chr1:3367135-3367162	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000044	i	Xkr4	XLOC_000077	Xkr4	TSS83	chr1:3367333-3367382	49	-	0	0	0	OK	0	0	0	OK
-TCONS_00000045	i	Xkr4	XLOC_000080	Xkr4	TSS86	chr1:3377211-3377262	51	-	0	0	0	OK	0	0	0	OK
-TCONS_00000046	i	Xkr4	XLOC_000083	Xkr4	TSS89	chr1:3391325-3391352	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000047	i	Xkr4	XLOC_000084	Xkr4	TSS90	chr1:3435841-3435880	39	-	0	0	0	OK	0	0	0	OK
-TCONS_00000048	i	Xkr4	XLOC_000085	Xkr4	TSS91	chr1:3447761-3447788	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000049	i	Xkr4	XLOC_000086	Xkr4	TSS92	chr1:3450906-3450965	59	-	0	0	0	OK	0	0	0	OK
-TCONS_00000050	i	Xkr4	XLOC_000087	Xkr4	TSS93	chr1:3451051-3451109	58	-	0	0	0	OK	0	0	0	OK
-TCONS_00000051	-	-	XLOC_000004	-	TSS4	chr1:3174765-3174792	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000052	-	-	XLOC_000005	-	TSS5	chr1:3187401-3187428	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000053	-	-	XLOC_000006	-	TSS6	chr1:3188521-3188548	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000054	-	-	XLOC_000007	-	TSS7	chr1:3189810-3190789	979	-	358326	135086	581565	OK	522345	410780	633911	OK
-TCONS_00000055	-	-	XLOC_000008	-	TSS10	chr1:3190858-3191434	576	-	408511	54526.1	762496	OK	420354	61509.1	779200	OK
-TCONS_00000056	-	-	XLOC_000009	-	TSS11	chr1:3191512-3192077	565	-	433286	63552.3	803020	OK	842157	342520	1.34179e+06	OK
-TCONS_00000057	-	-	XLOC_000010	-	TSS13	chr1:3192250-3192336	86	-	3.44151e+06	0	1.31756e+07	OK	3.34455e+06	0	1.30786e+07	OK
-TCONS_00000058	-	-	XLOC_000013	-	TSS16	chr1:3192649-3192676	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000059	-	-	XLOC_000018	-	TSS21	chr1:3194706-3194733	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000060	-	-	XLOC_000024	-	TSS27	chr1:3197425-3197452	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000062	-	-	XLOC_000027	-	TSS30	chr1:3200430-3200457	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000063	-	-	XLOC_000028	-	TSS31	chr1:3201007-3201039	32	-	0	0	0	OK	0	0	0	OK
-TCONS_00000065	-	-	XLOC_000030	-	TSS33	chr1:3201596-3201666	70	-	1.6359e+07	0	5.96409e+07	OK	0	0	0	OK
-TCONS_00000066	-	-	XLOC_000032	-	TSS35	chr1:3201725-3201809	84	-	1.5136e+07	0	4.63396e+07	OK	0	0	0	OK
-TCONS_00000067	i	Xkr4	XLOC_000033	Xkr4	TSS36	chr1:3211521-3211561	40	-	0	0	0	OK	0	0	0	OK
-TCONS_00000068	i	Xkr4	XLOC_000036	Xkr4	TSS39	chr1:3212717-3212801	84	-	3.784e+06	0	1.44868e+07	OK	0	0	0	OK
-TCONS_00000069	i	Xkr4	XLOC_000037	Xkr4	TSS40	chr1:3213095-3213242	124	-	863189	0	4.25222e+06	OK	0	0	72384.9	OK
-TCONS_00000070	i	Xkr4	XLOC_000038	Xkr4	TSS41	chr1:3240606-3240633	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000071	i	Xkr4	XLOC_000039	Xkr4	TSS42	chr1:3242479-3242512	33	-	0	0	0	OK	0	0	0	OK
-TCONS_00000072	i	Xkr4	XLOC_000041	Xkr4	TSS44	chr1:3242924-3243005	81	-	0	0	0	OK	0	0	0	OK
-TCONS_00000073	i	Xkr4	XLOC_000043	Xkr4	TSS46	chr1:3243108-3243154	46	-	8.616e+07	0	3.29857e+08	OK	0	0	0	OK
-TCONS_00000074	i	Xkr4	XLOC_000045	Xkr4	TSS48	chr1:3254079-3254106	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000075	i	Xkr4	XLOC_000047	Xkr4	TSS50	chr1:3277155-3277182	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000076	i	Xkr4	XLOC_000049	Xkr4	TSS52	chr1:3277913-3278390	477	-	228872	0	561229	OK	47662.2	0	156103	OK
-TCONS_00000077	i	Xkr4	XLOC_000050	Xkr4	TSS54	chr1:3280117-3280144	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000078	i	Xkr4	XLOC_000051	Xkr4	TSS55	chr1:3280498-3280525	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000079	i	Xkr4	XLOC_000053	Xkr4	TSS57	chr1:3282504-3282531	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000080	i	Xkr4	XLOC_000054	Xkr4	TSS58	chr1:3282650-3282677	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000081	i	Xkr4	XLOC_000055	Xkr4	TSS59	chr1:3282760-3282832	72	-	0	0	0	OK	0	0	0	OK
-TCONS_00000082	i	Xkr4	XLOC_000056	Xkr4	TSS60	chr1:3284966-3284993	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000083	i	Xkr4	XLOC_000058	Xkr4	TSS62	chr1:3290798-3290859	61	-	1.55919e+07	0	5.96926e+07	OK	0	0	0	OK
-TCONS_00000084	i	Xkr4	XLOC_000059	Xkr4	TSS63	chr1:3290919-3291273	354	-	294879	0	740137	OK	85971.3	0	281572	OK
-TCONS_00000085	i	Xkr4	XLOC_000060	Xkr4	TSS65	chr1:3299443-3299664	197	-	807732	0	2.39056e+06	OK	156995	0	613917	OK
-TCONS_00000086	i	Xkr4	XLOC_000061	Xkr4	TSS67	chr1:3299691-3299733	42	-	0	0	0	OK	0	0	0	OK
-TCONS_00000087	i	Xkr4	XLOC_000063	Xkr4	TSS69	chr1:3307748-3307775	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000088	i	Xkr4	XLOC_000064	Xkr4	TSS70	chr1:3318620-3318647	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000089	i	Xkr4	XLOC_000066	Xkr4	TSS72	chr1:3330527-3330554	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000090	i	Xkr4	XLOC_000067	Xkr4	TSS73	chr1:3351240-3351311	71	-	7.68169e+06	0	2.94088e+07	OK	0	0	0	OK
-TCONS_00000091	i	Xkr4	XLOC_000068	Xkr4	TSS74	chr1:3355887-3356119	212	-	504790	0	1.54544e+06	OK	0	0	0	OK
-TCONS_00000092	i	Xkr4	XLOC_000069	Xkr4	TSS75	chr1:3356180-3356225	45	-	1.02717e+08	0	3.93246e+08	OK	0	0	0	OK
-TCONS_00000093	i	Xkr4	XLOC_000070	Xkr4	TSS76	chr1:3363076-3363176	100	-	3.81001e+06	0	1.38903e+07	OK	0	0	0	OK
-TCONS_00000094	i	Xkr4	XLOC_000072	Xkr4	TSS78	chr1:3363387-3363446	59	-	5.53654e+07	0	1.77783e+08	OK	0	0	0	OK
-TCONS_00000095	i	Xkr4	XLOC_000074	Xkr4	TSS80	chr1:3364871-3364919	48	-	6.28966e+07	0	2.40795e+08	OK	0	0	0	OK
-TCONS_00000096	i	Xkr4	XLOC_000076	Xkr4	TSS82	chr1:3367210-3367237	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000097	i	Xkr4	XLOC_000078	Xkr4	TSS84	chr1:3369580-3369607	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000098	i	Xkr4	XLOC_000079	Xkr4	TSS85	chr1:3375001-3375028	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000099	i	Xkr4	XLOC_000081	Xkr4	TSS87	chr1:3379888-3379915	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000100	i	Xkr4	XLOC_000082	Xkr4	TSS88	chr1:3386739-3386836	97	-	0	0	0	OK	0	0	0	OK
diff -r 8da0eade1f59 -r 88fcac97c2a0 test-data/cuffdiff_out6.txt
--- a/test-data/cuffdiff_out6.txt	Fri Dec 19 11:57:43 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,88 +0,0 @@
-tracking_id	class_code	nearest_ref_id	gene_id	gene_short_name	tss_id	locus	length	coverage	q1_FPKM	q1_conf_lo	q1_conf_hi	q1_status	q2_FPKM	q2_conf_lo	q2_conf_hi	q2_status
-XLOC_000001	-	-	XLOC_000001	Xkr4	TSS1	chr1:3204754-3204833	-	-	0	0	0	OK	9.45986e+06	0	3.33035e+07	OK
-XLOC_000002	-	-	XLOC_000002	-	TSS2	chr1:3111449-3111490	-	-	0	0	0	OK	2.43637e+08	0	9.52723e+08	OK
-XLOC_000003	-	-	XLOC_000003	-	TSS3	chr1:3111545-3111576	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000004	-	-	XLOC_000004	-	TSS4	chr1:3174765-3174792	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000005	-	-	XLOC_000005	-	TSS5	chr1:3187401-3187428	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000006	-	-	XLOC_000006	-	TSS6	chr1:3188521-3188548	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000007	-	-	XLOC_000007	-	TSS7	chr1:3189810-3190789	-	-	358326	135086	581565	OK	522345	410780	633911	OK
-XLOC_000008	-	-	XLOC_000008	-	TSS10	chr1:3190858-3191434	-	-	408511	54526.1	762496	OK	420354	61509.1	779200	OK
-XLOC_000009	-	-	XLOC_000009	-	TSS11	chr1:3191512-3192077	-	-	433286	63552.3	803020	OK	842157	342520	1.34179e+06	OK
-XLOC_000010	-	-	XLOC_000010	-	TSS13	chr1:3192250-3192336	-	-	3.44151e+06	0	1.31756e+07	OK	3.34455e+06	0	1.30786e+07	OK
-XLOC_000011	-	-	XLOC_000011	-	TSS14	chr1:3192441-3192494	-	-	0	0	0	OK	9.7002e+07	0	3.17699e+08	OK
-XLOC_000012	-	-	XLOC_000012	-	TSS15	chr1:3192550-3192629	-	-	0	0	0	OK	4.72993e+06	0	1.84961e+07	OK
-XLOC_000013	-	-	XLOC_000013	-	TSS16	chr1:3192649-3192676	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000014	-	-	XLOC_000014	-	TSS17	chr1:3192731-3192811	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000015	-	-	XLOC_000015	-	TSS18	chr1:3192940-3193042	-	-	0	0	0	OK	6.86386e+06	0	2.14243e+07	OK
-XLOC_000016	-	-	XLOC_000016	-	TSS19	chr1:3194185-3194226	-	-	0	0	0	OK	2.43637e+08	0	9.52723e+08	OK
-XLOC_000017	-	-	XLOC_000017	-	TSS20	chr1:3194302-3194329	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000018	-	-	XLOC_000018	-	TSS21	chr1:3194706-3194733	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000019	-	-	XLOC_000019	-	TSS22	chr1:3195083-3195110	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000020	-	-	XLOC_000020	-	TSS23	chr1:3195450-3195477	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000021	-	-	XLOC_000021	-	TSS24	chr1:3197089-3197116	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000022	-	-	XLOC_000022	-	TSS25	chr1:3197246-3197273	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000023	-	-	XLOC_000023	-	TSS26	chr1:3197346-3197373	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000024	-	-	XLOC_000024	-	TSS27	chr1:3197425-3197452	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000025	-	-	XLOC_000025	-	TSS28	chr1:3200022-3200191	-	-	826392	0	2.65361e+06	OK	803108	0	2.63033e+06	OK
-XLOC_000026	-	-	XLOC_000026	-	TSS29	chr1:3200325-3200352	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000027	-	-	XLOC_000027	-	TSS30	chr1:3200430-3200457	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000028	-	-	XLOC_000028	-	TSS31	chr1:3201007-3201039	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000029	-	-	XLOC_000029	-	TSS32	chr1:3201077-3201481	-	-	66791.3	0	214473	OK	324548	0	802006	OK
-XLOC_000030	-	-	XLOC_000030	-	TSS33	chr1:3201596-3201666	-	-	1.6359e+07	0	5.96409e+07	OK	0	0	0	OK
-XLOC_000031	-	-	XLOC_000031	-	TSS34	chr1:3201672-3201699	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000032	-	-	XLOC_000032	-	TSS35	chr1:3201725-3201809	-	-	1.5136e+07	0	4.63396e+07	OK	0	0	0	OK
-XLOC_000033	-	-	XLOC_000033	Xkr4	TSS36	chr1:3211521-3211561	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000034	-	-	XLOC_000034	Xkr4	TSS37	chr1:3212213-3212292	-	-	0	0	0	OK	9.45986e+06	0	3.33035e+07	OK
-XLOC_000035	-	-	XLOC_000035	Xkr4	TSS38	chr1:3212367-3212439	-	-	0	0	0	OK	2.80837e+07	0	8.76584e+07	OK
-XLOC_000036	-	-	XLOC_000036	Xkr4	TSS39	chr1:3212717-3212801	-	-	3.784e+06	0	1.44868e+07	OK	0	0	0	OK
-XLOC_000037	-	-	XLOC_000037	Xkr4	TSS40	chr1:3213095-3213242	-	-	5.10781e+06	0	1.69588e+07	OK	2.08209e+06	0	8.1421e+06	OK
-XLOC_000038	-	-	XLOC_000038	Xkr4	TSS41	chr1:3240606-3240633	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000039	-	-	XLOC_000039	Xkr4	TSS42	chr1:3242479-3242512	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000040	-	-	XLOC_000040	Xkr4	TSS43	chr1:3242633-3242923	-	-	48522.7	0	185766	OK	424400	0	1.30289e+06	OK
-XLOC_000041	-	-	XLOC_000041	Xkr4	TSS44	chr1:3242924-3243005	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000042	-	-	XLOC_000042	Xkr4	TSS45	chr1:3243018-3243079	-	-	0	0	0	OK	3.03053e+07	0	1.0669e+08	OK
-XLOC_000043	-	-	XLOC_000043	Xkr4	TSS46	chr1:3243108-3243154	-	-	8.616e+07	0	3.29857e+08	OK	0	0	0	OK
-XLOC_000044	-	-	XLOC_000044	Xkr4	TSS47	chr1:3243347-3243401	-	-	0	0	0	OK	5.79991e+07	0	2.04186e+08	OK
-XLOC_000045	-	-	XLOC_000045	Xkr4	TSS48	chr1:3254079-3254106	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000046	-	-	XLOC_000046	Xkr4	TSS49	chr1:3256974-3257011	-	-	0	0	0	OK	2.35423e+09	0	8.28806e+09	OK
-XLOC_000047	-	-	XLOC_000047	Xkr4	TSS50	chr1:3277155-3277182	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000048	-	-	XLOC_000048	Xkr4	TSS51	chr1:3277190-3277218	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000049	-	-	XLOC_000049	Xkr4	TSS52	chr1:3277913-3278390	-	-	228872	0	561229	OK	47662.2	0	156103	OK
-XLOC_000050	-	-	XLOC_000050	Xkr4	TSS54	chr1:3280117-3280144	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000051	-	-	XLOC_000051	Xkr4	TSS55	chr1:3280498-3280525	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000052	-	-	XLOC_000052	Xkr4	TSS56	chr1:3280686-3280741	-	-	0	0	0	OK	2.61334e+07	0	1.02193e+08	OK
-XLOC_000053	-	-	XLOC_000053	Xkr4	TSS57	chr1:3282504-3282531	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000054	-	-	XLOC_000054	Xkr4	TSS58	chr1:3282650-3282677	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000055	-	-	XLOC_000055	Xkr4	TSS59	chr1:3282760-3282832	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000056	-	-	XLOC_000056	Xkr4	TSS60	chr1:3284966-3284993	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000057	-	-	XLOC_000057	Xkr4	TSS61	chr1:3290488-3290553	-	-	0	0	0	OK	1.11503e+07	0	4.36026e+07	OK
-XLOC_000058	-	-	XLOC_000058	Xkr4	TSS62	chr1:3290798-3290859	-	-	1.55919e+07	0	5.96926e+07	OK	0	0	0	OK
-XLOC_000059	-	-	XLOC_000059	Xkr4	TSS63	chr1:3290919-3291273	-	-	294879	0	740137	OK	85971.3	0	281572	OK
-XLOC_000060	-	-	XLOC_000060	Xkr4	TSS65,TSS66	chr1:3299443-3299664	-	-	807732	0	2.39786e+06	OK	156995	0	641748	OK
-XLOC_000061	-	-	XLOC_000061	Xkr4	TSS67	chr1:3299691-3299733	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000062	-	-	XLOC_000062	Xkr4	TSS68	chr1:3300051-3300078	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000063	-	-	XLOC_000063	Xkr4	TSS69	chr1:3307748-3307775	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000064	-	-	XLOC_000064	Xkr4	TSS70	chr1:3318620-3318647	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000065	-	-	XLOC_000065	Xkr4	TSS71	chr1:3318999-3319051	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000066	-	-	XLOC_000066	Xkr4	TSS72	chr1:3330527-3330554	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000067	-	-	XLOC_000067	Xkr4	TSS73	chr1:3351240-3351311	-	-	7.68169e+06	0	2.94088e+07	OK	0	0	0	OK
-XLOC_000068	-	-	XLOC_000068	Xkr4	TSS74	chr1:3355887-3356119	-	-	504790	0	1.59712e+06	OK	0	0	0	OK
-XLOC_000069	-	-	XLOC_000069	Xkr4	TSS75	chr1:3356180-3356225	-	-	1.02717e+08	0	3.93246e+08	OK	0	0	0	OK
-XLOC_000070	-	-	XLOC_000070	Xkr4	TSS76	chr1:3363076-3363176	-	-	3.81001e+06	0	1.38903e+07	OK	0	0	0	OK
-XLOC_000071	-	-	XLOC_000071	Xkr4	TSS77	chr1:3363214-3363278	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000072	-	-	XLOC_000072	Xkr4	TSS78	chr1:3363387-3363446	-	-	5.53654e+07	0	1.77783e+08	OK	0	0	0	OK
-XLOC_000073	-	-	XLOC_000073	Xkr4	TSS79	chr1:3363753-3363849	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000074	-	-	XLOC_000074	Xkr4	TSS80	chr1:3364871-3364919	-	-	6.28966e+07	0	2.40795e+08	OK	0	0	0	OK
-XLOC_000075	-	-	XLOC_000075	Xkr4	TSS81	chr1:3367135-3367162	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000076	-	-	XLOC_000076	Xkr4	TSS82	chr1:3367210-3367237	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000077	-	-	XLOC_000077	Xkr4	TSS83	chr1:3367333-3367382	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000078	-	-	XLOC_000078	Xkr4	TSS84	chr1:3369580-3369607	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000079	-	-	XLOC_000079	Xkr4	TSS85	chr1:3375001-3375028	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000080	-	-	XLOC_000080	Xkr4	TSS86	chr1:3377211-3377262	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000081	-	-	XLOC_000081	Xkr4	TSS87	chr1:3379888-3379915	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000082	-	-	XLOC_000082	Xkr4	TSS88	chr1:3386739-3386836	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000083	-	-	XLOC_000083	Xkr4	TSS89	chr1:3391325-3391352	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000084	-	-	XLOC_000084	Xkr4	TSS90	chr1:3435841-3435880	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000085	-	-	XLOC_000085	Xkr4	TSS91	chr1:3447761-3447788	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000086	-	-	XLOC_000086	Xkr4	TSS92	chr1:3450906-3450965	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000087	-	-	XLOC_000087	Xkr4	TSS93	chr1:3451051-3451109	-	-	0	0	0	OK	0	0	0	OK
diff -r 8da0eade1f59 -r 88fcac97c2a0 test-data/cuffdiff_out7.txt
--- a/test-data/cuffdiff_out7.txt	Fri Dec 19 11:57:43 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,89 +0,0 @@
-tracking_id	class_code	nearest_ref_id	gene_id	gene_short_name	tss_id	locus	length	coverage	q1_FPKM	q1_conf_lo	q1_conf_hi	q1_status	q2_FPKM	q2_conf_lo	q2_conf_hi	q2_status
-TSS1	-	-	XLOC_000001	Xkr4	TSS1	chr1:3204754-3204833	-	-	0	0	0	OK	9.45986e+06	0	3.33035e+07	OK
-TSS10	-	-	XLOC_000008	-	TSS10	chr1:3190858-3191434	-	-	408511	54526.1	762496	OK	420354	61509.1	779200	OK
-TSS11	-	-	XLOC_000009	-	TSS11	chr1:3191512-3192077	-	-	433286	63552.3	803020	OK	842157	342520	1.34179e+06	OK
-TSS13	-	-	XLOC_000010	-	TSS13	chr1:3192250-3192336	-	-	3.44151e+06	0	1.31756e+07	OK	3.34455e+06	0	1.30786e+07	OK
-TSS14	-	-	XLOC_000011	-	TSS14	chr1:3192441-3192494	-	-	0	0	0	OK	9.7002e+07	0	3.17699e+08	OK
-TSS15	-	-	XLOC_000012	-	TSS15	chr1:3192550-3192629	-	-	0	0	0	OK	4.72993e+06	0	1.84961e+07	OK
-TSS16	-	-	XLOC_000013	-	TSS16	chr1:3192649-3192676	-	-	0	0	0	OK	0	0	0	OK
-TSS17	-	-	XLOC_000014	-	TSS17	chr1:3192731-3192811	-	-	0	0	0	OK	0	0	0	OK
-TSS18	-	-	XLOC_000015	-	TSS18	chr1:3192940-3193042	-	-	0	0	0	OK	6.86386e+06	0	2.14243e+07	OK
-TSS19	-	-	XLOC_000016	-	TSS19	chr1:3194185-3194226	-	-	0	0	0	OK	2.43637e+08	0	9.52723e+08	OK
-TSS2	-	-	XLOC_000002	-	TSS2	chr1:3111449-3111490	-	-	0	0	0	OK	2.43637e+08	0	9.52723e+08	OK
-TSS20	-	-	XLOC_000017	-	TSS20	chr1:3194302-3194329	-	-	0	0	0	OK	0	0	0	OK
-TSS21	-	-	XLOC_000018	-	TSS21	chr1:3194706-3194733	-	-	0	0	0	OK	0	0	0	OK
-TSS22	-	-	XLOC_000019	-	TSS22	chr1:3195083-3195110	-	-	0	0	0	OK	0	0	0	OK
-TSS23	-	-	XLOC_000020	-	TSS23	chr1:3195450-3195477	-	-	0	0	0	OK	0	0	0	OK
-TSS24	-	-	XLOC_000021	-	TSS24	chr1:3197089-3197116	-	-	0	0	0	OK	0	0	0	OK
-TSS25	-	-	XLOC_000022	-	TSS25	chr1:3197246-3197273	-	-	0	0	0	OK	0	0	0	OK
-TSS26	-	-	XLOC_000023	-	TSS26	chr1:3197346-3197373	-	-	0	0	0	OK	0	0	0	OK
-TSS27	-	-	XLOC_000024	-	TSS27	chr1:3197425-3197452	-	-	0	0	0	OK	0	0	0	OK
-TSS28	-	-	XLOC_000025	-	TSS28	chr1:3200022-3200191	-	-	826392	0	2.65361e+06	OK	803108	0	2.63033e+06	OK
-TSS29	-	-	XLOC_000026	-	TSS29	chr1:3200325-3200352	-	-	0	0	0	OK	0	0	0	OK
-TSS3	-	-	XLOC_000003	-	TSS3	chr1:3111545-3111576	-	-	0	0	0	OK	0	0	0	OK
-TSS30	-	-	XLOC_000027	-	TSS30	chr1:3200430-3200457	-	-	0	0	0	OK	0	0	0	OK
-TSS31	-	-	XLOC_000028	-	TSS31	chr1:3201007-3201039	-	-	0	0	0	OK	0	0	0	OK
-TSS32	-	-	XLOC_000029	-	TSS32	chr1:3201077-3201481	-	-	66791.3	0	214473	OK	324548	0	802006	OK
-TSS33	-	-	XLOC_000030	-	TSS33	chr1:3201596-3201666	-	-	1.6359e+07	0	5.96409e+07	OK	0	0	0	OK
-TSS34	-	-	XLOC_000031	-	TSS34	chr1:3201672-3201699	-	-	0	0	0	OK	0	0	0	OK
-TSS35	-	-	XLOC_000032	-	TSS35	chr1:3201725-3201809	-	-	1.5136e+07	0	4.63396e+07	OK	0	0	0	OK
-TSS36	-	-	XLOC_000033	Xkr4	TSS36	chr1:3211521-3211561	-	-	0	0	0	OK	0	0	0	OK
-TSS37	-	-	XLOC_000034	Xkr4	TSS37	chr1:3212213-3212292	-	-	0	0	0	OK	9.45986e+06	0	3.33035e+07	OK
-TSS38	-	-	XLOC_000035	Xkr4	TSS38	chr1:3212367-3212439	-	-	0	0	0	OK	2.80837e+07	0	8.76584e+07	OK
-TSS39	-	-	XLOC_000036	Xkr4	TSS39	chr1:3212717-3212801	-	-	3.784e+06	0	1.44868e+07	OK	0	0	0	OK
-TSS4	-	-	XLOC_000004	-	TSS4	chr1:3174765-3174792	-	-	0	0	0	OK	0	0	0	OK
-TSS40	-	-	XLOC_000037	Xkr4	TSS40	chr1:3213095-3213242	-	-	5.10781e+06	0	1.69588e+07	OK	2.08209e+06	0	8.1421e+06	OK
-TSS41	-	-	XLOC_000038	Xkr4	TSS41	chr1:3240606-3240633	-	-	0	0	0	OK	0	0	0	OK
-TSS42	-	-	XLOC_000039	Xkr4	TSS42	chr1:3242479-3242512	-	-	0	0	0	OK	0	0	0	OK
-TSS43	-	-	XLOC_000040	Xkr4	TSS43	chr1:3242633-3242923	-	-	48522.7	0	185766	OK	424400	0	1.30289e+06	OK
-TSS44	-	-	XLOC_000041	Xkr4	TSS44	chr1:3242924-3243005	-	-	0	0	0	OK	0	0	0	OK
-TSS45	-	-	XLOC_000042	Xkr4	TSS45	chr1:3243018-3243079	-	-	0	0	0	OK	3.03053e+07	0	1.0669e+08	OK
-TSS46	-	-	XLOC_000043	Xkr4	TSS46	chr1:3243108-3243154	-	-	8.616e+07	0	3.29857e+08	OK	0	0	0	OK
-TSS47	-	-	XLOC_000044	Xkr4	TSS47	chr1:3243347-3243401	-	-	0	0	0	OK	5.79991e+07	0	2.04186e+08	OK
-TSS48	-	-	XLOC_000045	Xkr4	TSS48	chr1:3254079-3254106	-	-	0	0	0	OK	0	0	0	OK
-TSS49	-	-	XLOC_000046	Xkr4	TSS49	chr1:3256974-3257011	-	-	0	0	0	OK	2.35423e+09	0	8.28806e+09	OK
-TSS5	-	-	XLOC_000005	-	TSS5	chr1:3187401-3187428	-	-	0	0	0	OK	0	0	0	OK
-TSS50	-	-	XLOC_000047	Xkr4	TSS50	chr1:3277155-3277182	-	-	0	0	0	OK	0	0	0	OK
-TSS51	-	-	XLOC_000048	Xkr4	TSS51	chr1:3277190-3277218	-	-	0	0	0	OK	0	0	0	OK
-TSS52	-	-	XLOC_000049	Xkr4	TSS52	chr1:3277913-3278390	-	-	228872	0	561229	OK	47662.2	0	156103	OK
-TSS54	-	-	XLOC_000050	Xkr4	TSS54	chr1:3280117-3280144	-	-	0	0	0	OK	0	0	0	OK
-TSS55	-	-	XLOC_000051	Xkr4	TSS55	chr1:3280498-3280525	-	-	0	0	0	OK	0	0	0	OK
-TSS56	-	-	XLOC_000052	Xkr4	TSS56	chr1:3280686-3280741	-	-	0	0	0	OK	2.61334e+07	0	1.02193e+08	OK
-TSS57	-	-	XLOC_000053	Xkr4	TSS57	chr1:3282504-3282531	-	-	0	0	0	OK	0	0	0	OK
-TSS58	-	-	XLOC_000054	Xkr4	TSS58	chr1:3282650-3282677	-	-	0	0	0	OK	0	0	0	OK
-TSS59	-	-	XLOC_000055	Xkr4	TSS59	chr1:3282760-3282832	-	-	0	0	0	OK	0	0	0	OK
-TSS6	-	-	XLOC_000006	-	TSS6	chr1:3188521-3188548	-	-	0	0	0	OK	0	0	0	OK
-TSS60	-	-	XLOC_000056	Xkr4	TSS60	chr1:3284966-3284993	-	-	0	0	0	OK	0	0	0	OK
-TSS61	-	-	XLOC_000057	Xkr4	TSS61	chr1:3290488-3290553	-	-	0	0	0	OK	1.11503e+07	0	4.36026e+07	OK
-TSS62	-	-	XLOC_000058	Xkr4	TSS62	chr1:3290798-3290859	-	-	1.55919e+07	0	5.96926e+07	OK	0	0	0	OK
-TSS63	-	-	XLOC_000059	Xkr4	TSS63	chr1:3290919-3291273	-	-	294879	0	740137	OK	85971.3	0	281572	OK
-TSS65	-	-	XLOC_000060	Xkr4	TSS65	chr1:3299443-3299664	-	-	807732	0	2.39056e+06	OK	156995	0	613917	OK
-TSS66	-	-	XLOC_000060	Xkr4	TSS66	chr1:3299443-3299664	-	-	0	0	0	OK	0	0	0	OK
-TSS67	-	-	XLOC_000061	Xkr4	TSS67	chr1:3299691-3299733	-	-	0	0	0	OK	0	0	0	OK
-TSS68	-	-	XLOC_000062	Xkr4	TSS68	chr1:3300051-3300078	-	-	0	0	0	OK	0	0	0	OK
-TSS69	-	-	XLOC_000063	Xkr4	TSS69	chr1:3307748-3307775	-	-	0	0	0	OK	0	0	0	OK
-TSS7	-	-	XLOC_000007	-	TSS7	chr1:3189810-3190789	-	-	358326	135086	581565	OK	522345	410780	633911	OK
-TSS70	-	-	XLOC_000064	Xkr4	TSS70	chr1:3318620-3318647	-	-	0	0	0	OK	0	0	0	OK
-TSS71	-	-	XLOC_000065	Xkr4	TSS71	chr1:3318999-3319051	-	-	0	0	0	OK	0	0	0	OK
-TSS72	-	-	XLOC_000066	Xkr4	TSS72	chr1:3330527-3330554	-	-	0	0	0	OK	0	0	0	OK
-TSS73	-	-	XLOC_000067	Xkr4	TSS73	chr1:3351240-3351311	-	-	7.68169e+06	0	2.94088e+07	OK	0	0	0	OK
-TSS74	-	-	XLOC_000068	Xkr4	TSS74	chr1:3355887-3356119	-	-	504790	0	1.59712e+06	OK	0	0	0	OK
-TSS75	-	-	XLOC_000069	Xkr4	TSS75	chr1:3356180-3356225	-	-	1.02717e+08	0	3.93246e+08	OK	0	0	0	OK
-TSS76	-	-	XLOC_000070	Xkr4	TSS76	chr1:3363076-3363176	-	-	3.81001e+06	0	1.38903e+07	OK	0	0	0	OK
-TSS77	-	-	XLOC_000071	Xkr4	TSS77	chr1:3363214-3363278	-	-	0	0	0	OK	0	0	0	OK
-TSS78	-	-	XLOC_000072	Xkr4	TSS78	chr1:3363387-3363446	-	-	5.53654e+07	0	1.77783e+08	OK	0	0	0	OK
-TSS79	-	-	XLOC_000073	Xkr4	TSS79	chr1:3363753-3363849	-	-	0	0	0	OK	0	0	0	OK
-TSS80	-	-	XLOC_000074	Xkr4	TSS80	chr1:3364871-3364919	-	-	6.28966e+07	0	2.40795e+08	OK	0	0	0	OK
-TSS81	-	-	XLOC_000075	Xkr4	TSS81	chr1:3367135-3367162	-	-	0	0	0	OK	0	0	0	OK
-TSS82	-	-	XLOC_000076	Xkr4	TSS82	chr1:3367210-3367237	-	-	0	0	0	OK	0	0	0	OK
-TSS83	-	-	XLOC_000077	Xkr4	TSS83	chr1:3367333-3367382	-	-	0	0	0	OK	0	0	0	OK
-TSS84	-	-	XLOC_000078	Xkr4	TSS84	chr1:3369580-3369607	-	-	0	0	0	OK	0	0	0	OK
-TSS85	-	-	XLOC_000079	Xkr4	TSS85	chr1:3375001-3375028	-	-	0	0	0	OK	0	0	0	OK
-TSS86	-	-	XLOC_000080	Xkr4	TSS86	chr1:3377211-3377262	-	-	0	0	0	OK	0	0	0	OK
-TSS87	-	-	XLOC_000081	Xkr4	TSS87	chr1:3379888-3379915	-	-	0	0	0	OK	0	0	0	OK
-TSS88	-	-	XLOC_000082	Xkr4	TSS88	chr1:3386739-3386836	-	-	0	0	0	OK	0	0	0	OK
-TSS89	-	-	XLOC_000083	Xkr4	TSS89	chr1:3391325-3391352	-	-	0	0	0	OK	0	0	0	OK
-TSS90	-	-	XLOC_000084	Xkr4	TSS90	chr1:3435841-3435880	-	-	0	0	0	OK	0	0	0	OK
-TSS91	-	-	XLOC_000085	Xkr4	TSS91	chr1:3447761-3447788	-	-	0	0	0	OK	0	0	0	OK
-TSS92	-	-	XLOC_000086	Xkr4	TSS92	chr1:3450906-3450965	-	-	0	0	0	OK	0	0	0	OK
-TSS93	-	-	XLOC_000087	Xkr4	TSS93	chr1:3451051-3451109	-	-	0	0	0	OK	0	0	0	OK
diff -r 8da0eade1f59 -r 88fcac97c2a0 test-data/cuffdiff_out8.txt
--- a/test-data/cuffdiff_out8.txt	Fri Dec 19 11:57:43 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-tracking_id	class_code	nearest_ref_id	gene_id	gene_short_name	tss_id	locus	length	coverage
diff -r 8da0eade1f59 -r 88fcac97c2a0 test-data/cuffdiff_out9.txt
--- a/test-data/cuffdiff_out9.txt	Fri Dec 19 11:57:43 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,89 +0,0 @@
-test_id	gene_id	gene	locus	sample_1	sample_2	status	value_1	value_2	sqrt(JS)	test_stat	p_value	q_value	significant
-TSS1	XLOC_000001	Xkr4	chr1:3204754-3204833	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS10	XLOC_000008	-	chr1:3190858-3191434	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS11	XLOC_000009	-	chr1:3191512-3192077	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS13	XLOC_000010	-	chr1:3192250-3192336	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS14	XLOC_000011	-	chr1:3192441-3192494	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS15	XLOC_000012	-	chr1:3192550-3192629	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS16	XLOC_000013	-	chr1:3192649-3192676	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS17	XLOC_000014	-	chr1:3192731-3192811	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS18	XLOC_000015	-	chr1:3192940-3193042	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS19	XLOC_000016	-	chr1:3194185-3194226	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS2	XLOC_000002	-	chr1:3111449-3111490	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS20	XLOC_000017	-	chr1:3194302-3194329	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS21	XLOC_000018	-	chr1:3194706-3194733	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS22	XLOC_000019	-	chr1:3195083-3195110	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS23	XLOC_000020	-	chr1:3195450-3195477	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS24	XLOC_000021	-	chr1:3197089-3197116	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS25	XLOC_000022	-	chr1:3197246-3197273	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS26	XLOC_000023	-	chr1:3197346-3197373	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS27	XLOC_000024	-	chr1:3197425-3197452	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS28	XLOC_000025	-	chr1:3200022-3200191	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS29	XLOC_000026	-	chr1:3200325-3200352	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS3	XLOC_000003	-	chr1:3111545-3111576	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS30	XLOC_000027	-	chr1:3200430-3200457	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS31	XLOC_000028	-	chr1:3201007-3201039	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS32	XLOC_000029	-	chr1:3201077-3201481	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS33	XLOC_000030	-	chr1:3201596-3201666	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS34	XLOC_000031	-	chr1:3201672-3201699	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS35	XLOC_000032	-	chr1:3201725-3201809	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS36	XLOC_000033	Xkr4	chr1:3211521-3211561	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS37	XLOC_000034	Xkr4	chr1:3212213-3212292	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS38	XLOC_000035	Xkr4	chr1:3212367-3212439	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS39	XLOC_000036	Xkr4	chr1:3212717-3212801	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS4	XLOC_000004	-	chr1:3174765-3174792	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS40	XLOC_000037	Xkr4	chr1:3213095-3213242	q1	q2	NOTEST	0	0	0.249947	0	0.5526	1	no
-TSS41	XLOC_000038	Xkr4	chr1:3240606-3240633	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS42	XLOC_000039	Xkr4	chr1:3242479-3242512	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS43	XLOC_000040	Xkr4	chr1:3242633-3242923	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS44	XLOC_000041	Xkr4	chr1:3242924-3243005	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS45	XLOC_000042	Xkr4	chr1:3243018-3243079	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS46	XLOC_000043	Xkr4	chr1:3243108-3243154	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS47	XLOC_000044	Xkr4	chr1:3243347-3243401	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS48	XLOC_000045	Xkr4	chr1:3254079-3254106	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS49	XLOC_000046	Xkr4	chr1:3256974-3257011	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS5	XLOC_000005	-	chr1:3187401-3187428	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS50	XLOC_000047	Xkr4	chr1:3277155-3277182	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS51	XLOC_000048	Xkr4	chr1:3277190-3277218	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS52	XLOC_000049	Xkr4	chr1:3277913-3278390	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS54	XLOC_000050	Xkr4	chr1:3280117-3280144	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS55	XLOC_000051	Xkr4	chr1:3280498-3280525	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS56	XLOC_000052	Xkr4	chr1:3280686-3280741	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS57	XLOC_000053	Xkr4	chr1:3282504-3282531	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS58	XLOC_000054	Xkr4	chr1:3282650-3282677	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS59	XLOC_000055	Xkr4	chr1:3282760-3282832	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS6	XLOC_000006	-	chr1:3188521-3188548	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS60	XLOC_000056	Xkr4	chr1:3284966-3284993	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS61	XLOC_000057	Xkr4	chr1:3290488-3290553	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS62	XLOC_000058	Xkr4	chr1:3290798-3290859	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS63	XLOC_000059	Xkr4	chr1:3290919-3291273	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS65	XLOC_000060	Xkr4	chr1:3299443-3299664	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS66	XLOC_000060	Xkr4	chr1:3299443-3299664	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS67	XLOC_000061	Xkr4	chr1:3299691-3299733	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS68	XLOC_000062	Xkr4	chr1:3300051-3300078	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS69	XLOC_000063	Xkr4	chr1:3307748-3307775	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS7	XLOC_000007	-	chr1:3189810-3190789	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS70	XLOC_000064	Xkr4	chr1:3318620-3318647	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS71	XLOC_000065	Xkr4	chr1:3318999-3319051	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS72	XLOC_000066	Xkr4	chr1:3330527-3330554	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS73	XLOC_000067	Xkr4	chr1:3351240-3351311	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS74	XLOC_000068	Xkr4	chr1:3355887-3356119	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS75	XLOC_000069	Xkr4	chr1:3356180-3356225	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS76	XLOC_000070	Xkr4	chr1:3363076-3363176	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS77	XLOC_000071	Xkr4	chr1:3363214-3363278	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS78	XLOC_000072	Xkr4	chr1:3363387-3363446	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS79	XLOC_000073	Xkr4	chr1:3363753-3363849	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS80	XLOC_000074	Xkr4	chr1:3364871-3364919	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS81	XLOC_000075	Xkr4	chr1:3367135-3367162	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS82	XLOC_000076	Xkr4	chr1:3367210-3367237	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS83	XLOC_000077	Xkr4	chr1:3367333-3367382	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS84	XLOC_000078	Xkr4	chr1:3369580-3369607	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS85	XLOC_000079	Xkr4	chr1:3375001-3375028	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS86	XLOC_000080	Xkr4	chr1:3377211-3377262	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS87	XLOC_000081	Xkr4	chr1:3379888-3379915	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS88	XLOC_000082	Xkr4	chr1:3386739-3386836	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS89	XLOC_000083	Xkr4	chr1:3391325-3391352	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS90	XLOC_000084	Xkr4	chr1:3435841-3435880	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS91	XLOC_000085	Xkr4	chr1:3447761-3447788	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS92	XLOC_000086	Xkr4	chr1:3450906-3450965	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS93	XLOC_000087	Xkr4	chr1:3451051-3451109	q1	q2	NOTEST	0	0	0	0	1	1	no
diff -r 8da0eade1f59 -r 88fcac97c2a0 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Dec 19 11:57:43 2014 -0500
+++ b/tool_dependencies.xml	Tue Dec 23 15:55:31 2014 -0500
@@ -1,6 +1,12 @@
 <?xml version="1.0"?>
 <tool_dependency>
+    <set_environment version="1.0">
+        <environment_variable action="set_to" name="CUFFDIFF_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
+    </set_environment>
     <package name="cufflinks" version="2.2.1">
         <repository changeset_revision="899067a260d1" name="package_cufflinks_2_2_1" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
+    <package name="cummeRbund" version="2.8.2">
+        <repository changeset_revision="5aacc6d160ed" name="package_cummerbund_2_8_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
 </tool_dependency>