changeset 4:dc97f71022e5 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
author iuc
date Tue, 16 Jun 2020 16:58:39 +0000
parents 47dccbe0516c
children 5e3670f94019
files cuff_macros.xml cuffnorm_wrapper.xml test-data/cds.count_table test-data/cds.fpkm_table test-data/cuffdiff_out1.txt test-data/cuffdiff_out10.txt test-data/cuffdiff_out11.txt test-data/cuffdiff_out2.txt test-data/cuffdiff_out3.txt test-data/cuffdiff_out4.txt test-data/cuffdiff_out5.txt test-data/cuffdiff_out6.txt test-data/cuffdiff_out7.txt test-data/cuffdiff_out8.txt test-data/cuffdiff_out9.txt test-data/genes.count_table test-data/genes.fpkm_table test-data/isoforms.count_table test-data/isoforms.fpkm_table test-data/tss_groups.count_table test-data/tss_groups.fpkm_table
diffstat 21 files changed, 580 insertions(+), 740 deletions(-) [+]
line wrap: on
line diff
--- a/cuff_macros.xml	Sun Feb 19 12:08:50 2017 -0500
+++ b/cuff_macros.xml	Tue Jun 16 16:58:39 2020 +0000
@@ -66,20 +66,26 @@
   </token>
   <xml name="cufflinks_gtf_inputs">
     <param format="gtf" name="inputs" type="data" label="GTF file(s) produced by Cufflinks" help="" multiple="true" />
-    <repeat name="additional_inputs" title="Additional GTF Inputs (Lists)">
-      <param format="gtf" name="additional_inputs" type="data_collection" label="GTF file(s) produced by Cufflinks" help="" />
-    </repeat>
   </xml>
+  <token name="@CUFFLINKS_LINK_GTF_INPUTS@"><![CDATA[
+            ## Inputs.
+            #for $i, $input_file in enumerate($inputs):
+                ln -s '${input_file}' input_$i &&
+            #end for
+  ]]></token>
   <token name="@CUFFLINKS_GTF_INPUTS@">
             ## Inputs.
-            #for $input_file in $inputs:
-                '${input_file}'
-            #end for
-            #for $additional_input in $additional_inputs:
-                #for $input_file in $additional_input.additional_inputs:
-                    '${input_file}'
-                #end for
+            #for $i, $input_file in enumerate($inputs):
+                'input_$i'
             #end for
   </token>
   <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token>
+
+  <xml name="citations">
+    <citations>
+        <citation type="doi">10.1038/nbt.1621</citation>
+        <yield/>
+    </citations>
+  </xml>
+
 </macros>
--- a/cuffnorm_wrapper.xml	Sun Feb 19 12:08:50 2017 -0500
+++ b/cuffnorm_wrapper.xml	Tue Jun 16 16:58:39 2020 +0000
@@ -4,8 +4,8 @@
       <import>cuff_macros.xml</import>
     </macros>
     <expand macro="requirements" />
-    <version_command>cuffnorm 2>&amp;1 | head -n 1</version_command>
-    <command detect_errors="aggressive">
+    <version_command><![CDATA[cuffnorm 2>&1 | head -n 1]]></version_command>
+    <command detect_errors="aggressive"><![CDATA[
         cuffnorm
             --no-update-check
             --num-threads="\${GALAXY_SLOTS:-4}"
@@ -22,10 +22,10 @@
                 $advanced_settings.hits_norm
             #end if
             ## Inputs.
-            $gtf_input
+            '$gtf_input'
 
             @CONDITION_SAMPLES@
-    </command>
+    ]]></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."/>
         <expand macro="condition_inputs" />
@@ -165,12 +165,28 @@
         </data>
     </outputs>
     <tests>
-        <!-- 
-        <test>
-                NOTE: as of version 0.0.6 of the wrapper, tests cannot be run because multiple inputs to a repeat
-                element are not supported.
+        <test expect_num_outputs="8">
+            <param name="gtf_input" value="cuffcompare_out5.gtf" ftype="gtf"/>
+            <conditional name="in_type">
+                <param name="set_in_type" value="BAM"/>
+                <repeat name="conditions">
+                    <param name="name" value="in1"/>
+                    <param name="samples" value="cuffdiff_in1.sam" ftype="sam"/>
+                </repeat>
+                <repeat name="conditions">
+                    <param name="name" value="in2"/>
+                    <param name="samples" value="cuffdiff_in2.sam" ftype="sam"/>
+                </repeat>
+            </conditional>
+            <output ftype="tabular" name="cds_fpkm_table" value="cds.fpkm_table"/>
+            <output ftype="tabular" name="cds_count_table" value="cds.count_table"/>
+            <output ftype="tabular" name="tss_groups_fpkm_table" value="tss_groups.fpkm_table"/>
+            <output ftype="tabular" name="tss_groups_count_table" value="tss_groups.count_table"/>
+            <output ftype="tabular" name="genes_fpkm_table" value="genes.fpkm_table"/>
+            <output ftype="tabular" name="genes_count_table" value="genes.count_table"/>
+            <output ftype="tabular" name="isoforms_fpkm_table" value="isoforms.fpkm_table"/>
+            <output ftype="tabular" name="isoforms_count_table" value="isoforms.count_table"/>
         </test>
-        -->
     </tests>
 
     <help>
@@ -222,7 +238,5 @@
   --compatible-hits-norm         With this option, Cufflinks counts only those fragments compatible with some reference transcript towards the number of mapped fragments used in the FPKM denominator. Using this mode is generally recommended in Cuffdiff to reduce certain types of bias caused by differential amounts of ribosomal reads which can create the impression of falsely differentially expressed genes.
   --total-hits-norm              With this option, Cufflinks counts all fragments, including those not compatible with any reference transcript, towards the number of mapped fragments used in the FPKM denominator
     </help>
-    <citations>
-        <citation type="doi">10.1038/nbt.1621</citation>
-    </citations>
+    <expand macro="citations"/>
 </tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cds.count_table	Tue Jun 16 16:58:39 2020 +0000
@@ -0,0 +1,1 @@
+tracking_id
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cds.fpkm_table	Tue Jun 16 16:58:39 2020 +0000
@@ -0,0 +1,1 @@
+tracking_id
\ No newline at end of file
--- a/test-data/cuffdiff_out1.txt	Sun Feb 19 12:08:50 2017 -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	8.3103e+06	1.79769e+308	1.79769e+308	0.0786496	0.150149	no
-TCONS_00000002	XLOC_000002	-	chr1:3111449-3111490	q1	q2	OK	0	2.1403e+08	1.79769e+308	1.79769e+308	0.158655	0.158655	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	5.68095e+07	1.79769e+308	1.79769e+308	0.0786496	0.150149	no
-TCONS_00000010	XLOC_000012	-	chr1:3192550-3192629	q1	q2	OK	0	4.15515e+06	1.79769e+308	1.79769e+308	0.158655	0.158655	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	6.02976e+06	1.79769e+308	1.79769e+308	0.0512352	0.150149	no
-TCONS_00000013	XLOC_000016	-	chr1:3194185-3194226	q1	q2	OK	0	2.1403e+08	1.79769e+308	1.79769e+308	0.158655	0.158655	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	NOTEST	959058	705514	-0.442943	0.376027	0.706897	1	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	NOTEST	77513.9	285108	1.87898	-1.76152	0.0781506	1	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	8.3103e+06	1.79769e+308	1.79769e+308	0.0786496	0.150149	no
-TCONS_00000025	XLOC_000035	Xkr4	chr1:3212367-3212439	q1	q2	OK	0	2.4671e+07	1.79769e+308	1.79769e+308	0.0512352	0.150149	no
-TCONS_00000026	XLOC_000037	Xkr4	chr1:3213095-3213242	q1	q2	NOTEST	3.99739e+06	1.82908e+06	-1.12794	0.781831	0.434314	1	no
-TCONS_00000027	XLOC_000040	Xkr4	chr1:3242633-3242923	q1	q2	NOTEST	56312.4	372827	2.72698	-1.67622	0.0936947	1	no
-TCONS_00000028	XLOC_000042	Xkr4	chr1:3243018-3243079	q1	q2	OK	0	2.66226e+07	1.79769e+308	1.79769e+308	0.0786496	0.150149	no
-TCONS_00000029	XLOC_000044	Xkr4	chr1:3243347-3243401	q1	q2	OK	0	5.0951e+07	1.79769e+308	1.79769e+308	0.0786496	0.150149	no
-TCONS_00000030	XLOC_000046	Xkr4	chr1:3256974-3257011	q1	q2	OK	0	2.06814e+09	1.79769e+308	1.79769e+308	0.0786496	0.150149	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	2.29576e+07	1.79769e+308	1.79769e+308	0.158655	0.158655	no
-TCONS_00000034	XLOC_000057	Xkr4	chr1:3290488-3290553	q1	q2	OK	0	9.79535e+06	1.79769e+308	1.79769e+308	0.158655	0.158655	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	NOTEST	368900	429265	0.21864	-0.483034	0.629072	1	no
-TCONS_00000055	XLOC_000008	-	chr1:3190858-3191434	q1	q2	NOTEST	404373	338500	-0.25653	0.342922	0.731657	1	no
-TCONS_00000056	XLOC_000009	-	chr1:3191512-3192077	q1	q2	NOTEST	402276	686974	0.772069	-1.24554	0.212932	1	no
-TCONS_00000057	XLOC_000010	-	chr1:3192250-3192336	q1	q2	NOTEST	3.994e+06	2.93812e+06	-0.442943	0.217099	0.828131	1	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	1.89853e+07	0	-1.79769e+308	-1.79769e+308	0.0786496	0.150149	no
-TCONS_00000066	XLOC_000032	-	chr1:3201725-3201809	q1	q2	OK	1.31744e+07	0	-1.79769e+308	-1.79769e+308	0.0416323	0.150149	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	NOTEST	4.39147e+06	0	-1.79769e+308	-1.79769e+308	0.158655	1	no
-TCONS_00000069	XLOC_000037	Xkr4	chr1:3213095-3213242	q1	q2	NOTEST	1.36901e+06	0	0	0	1	1	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	9.99919e+07	0	-1.79769e+308	-1.79769e+308	0.158655	0.158655	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	NOTEST	265614	41870.3	-2.66534	2.48499	0.0129556	1	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	1.8095e+07	0	-1.79769e+308	-1.79769e+308	0.158655	0.158655	no
-TCONS_00000084	XLOC_000059	Xkr4	chr1:3290919-3291273	q1	q2	NOTEST	342218	75524	-2.17991	1.96162	0.049807	1	no
-TCONS_00000085	XLOC_000060	Xkr4	chr1:3299443-3299664	q1	q2	NOTEST	937403	137917	-2.76487	1.66807	0.0953024	1	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	8.91489e+06	0	-1.79769e+308	-1.79769e+308	0.158655	0.158655	no
-TCONS_00000091	XLOC_000068	Xkr4	chr1:3355887-3356119	q1	q2	NOTEST	585828	0	-1.79769e+308	-1.79769e+308	0.0512352	1	no
-TCONS_00000092	XLOC_000069	Xkr4	chr1:3356180-3356225	q1	q2	OK	1.19208e+08	0	-1.79769e+308	-1.79769e+308	0.158655	0.158655	no
-TCONS_00000093	XLOC_000070	Xkr4	chr1:3363076-3363176	q1	q2	NOTEST	4.42166e+06	0	-1.79769e+308	-1.79769e+308	0.0786496	1	no
-TCONS_00000094	XLOC_000072	Xkr4	chr1:3363387-3363446	q1	q2	OK	4.28358e+07	0	-1.79769e+308	-1.79769e+308	0.0786496	0.150149	no
-TCONS_00000095	XLOC_000074	Xkr4	chr1:3364871-3364919	q1	q2	OK	7.29939e+07	0	-1.79769e+308	-1.79769e+308	0.158655	0.158655	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
--- a/test-data/cuffdiff_out10.txt	Sun Feb 19 12:08:50 2017 -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	LOWDATA	0	0	0	0	0	1	no
-XLOC_000004	XLOC_000004	-	chr1:3174765-3174792	q1	q2	LOWDATA	0	0	0	0	0	1	no
-XLOC_000005	XLOC_000005	-	chr1:3187401-3187428	q1	q2	LOWDATA	0	0	0	0	0	1	no
-XLOC_000006	XLOC_000006	-	chr1:3188521-3188548	q1	q2	LOWDATA	0	0	0	0	0	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	LOWDATA	0	0	0	0	0	1	no
-XLOC_000014	XLOC_000014	-	chr1:3192731-3192811	q1	q2	LOWDATA	0	0	0	0	0	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	LOWDATA	0	0	0	0	0	1	no
-XLOC_000018	XLOC_000018	-	chr1:3194706-3194733	q1	q2	LOWDATA	0	0	0	0	0	1	no
-XLOC_000019	XLOC_000019	-	chr1:3195083-3195110	q1	q2	LOWDATA	0	0	0	0	0	1	no
-XLOC_000020	XLOC_000020	-	chr1:3195450-3195477	q1	q2	LOWDATA	0	0	0	0	0	1	no
-XLOC_000021	XLOC_000021	-	chr1:3197089-3197116	q1	q2	LOWDATA	0	0	0	0	0	1	no
-XLOC_000022	XLOC_000022	-	chr1:3197246-3197273	q1	q2	LOWDATA	0	0	0	0	0	1	no
-XLOC_000023	XLOC_000023	-	chr1:3197346-3197373	q1	q2	LOWDATA	0	0	0	0	0	1	no
-XLOC_000024	XLOC_000024	-	chr1:3197425-3197452	q1	q2	LOWDATA	0	0	0	0	0	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	LOWDATA	0	0	0	0	0	1	no
-XLOC_000027	XLOC_000027	-	chr1:3200430-3200457	q1	q2	LOWDATA	0	0	0	0	0	1	no
-XLOC_000028	XLOC_000028	-	chr1:3201007-3201039	q1	q2	LOWDATA	0	0	0	0	0	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	LOWDATA	0	0	0	0	0	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	LOWDATA	0	0	0	0	0	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	LOWDATA	0	0	0	0	0	1	no
-XLOC_000039	XLOC_000039	Xkr4	chr1:3242479-3242512	q1	q2	LOWDATA	0	0	0	0	0	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	LOWDATA	0	0	0	0	0	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	LOWDATA	0	0	0	0	0	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	LOWDATA	0	0	0	0	0	1	no
-XLOC_000048	XLOC_000048	Xkr4	chr1:3277190-3277218	q1	q2	LOWDATA	0	0	0	0	0	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	LOWDATA	0	0	0	0	0	1	no
-XLOC_000051	XLOC_000051	Xkr4	chr1:3280498-3280525	q1	q2	LOWDATA	0	0	0	0	0	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	LOWDATA	0	0	0	0	0	1	no
-XLOC_000054	XLOC_000054	Xkr4	chr1:3282650-3282677	q1	q2	LOWDATA	0	0	0	0	0	1	no
-XLOC_000055	XLOC_000055	Xkr4	chr1:3282760-3282832	q1	q2	LOWDATA	0	0	0	0	0	1	no
-XLOC_000056	XLOC_000056	Xkr4	chr1:3284966-3284993	q1	q2	LOWDATA	0	0	0	0	0	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	LOWDATA	0	0	0	0	0	1	no
-XLOC_000062	XLOC_000062	Xkr4	chr1:3300051-3300078	q1	q2	LOWDATA	0	0	0	0	0	1	no
-XLOC_000063	XLOC_000063	Xkr4	chr1:3307748-3307775	q1	q2	LOWDATA	0	0	0	0	0	1	no
-XLOC_000064	XLOC_000064	Xkr4	chr1:3318620-3318647	q1	q2	LOWDATA	0	0	0	0	0	1	no
-XLOC_000065	XLOC_000065	Xkr4	chr1:3318999-3319051	q1	q2	LOWDATA	0	0	0	0	0	1	no
-XLOC_000066	XLOC_000066	Xkr4	chr1:3330527-3330554	q1	q2	LOWDATA	0	0	0	0	0	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	LOWDATA	0	0	0	0	0	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	LOWDATA	0	0	0	0	0	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	LOWDATA	0	0	0	0	0	1	no
-XLOC_000076	XLOC_000076	Xkr4	chr1:3367210-3367237	q1	q2	LOWDATA	0	0	0	0	0	1	no
-XLOC_000077	XLOC_000077	Xkr4	chr1:3367333-3367382	q1	q2	LOWDATA	0	0	0	0	0	1	no
-XLOC_000078	XLOC_000078	Xkr4	chr1:3369580-3369607	q1	q2	LOWDATA	0	0	0	0	0	1	no
-XLOC_000079	XLOC_000079	Xkr4	chr1:3375001-3375028	q1	q2	LOWDATA	0	0	0	0	0	1	no
-XLOC_000080	XLOC_000080	Xkr4	chr1:3377211-3377262	q1	q2	LOWDATA	0	0	0	0	0	1	no
-XLOC_000081	XLOC_000081	Xkr4	chr1:3379888-3379915	q1	q2	LOWDATA	0	0	0	0	0	1	no
-XLOC_000082	XLOC_000082	Xkr4	chr1:3386739-3386836	q1	q2	LOWDATA	0	0	0	0	0	1	no
-XLOC_000083	XLOC_000083	Xkr4	chr1:3391325-3391352	q1	q2	LOWDATA	0	0	0	0	0	1	no
-XLOC_000084	XLOC_000084	Xkr4	chr1:3435841-3435880	q1	q2	LOWDATA	0	0	0	0	0	1	no
-XLOC_000085	XLOC_000085	Xkr4	chr1:3447761-3447788	q1	q2	LOWDATA	0	0	0	0	0	1	no
-XLOC_000086	XLOC_000086	Xkr4	chr1:3450906-3450965	q1	q2	LOWDATA	0	0	0	0	0	1	no
-XLOC_000087	XLOC_000087	Xkr4	chr1:3451051-3451109	q1	q2	LOWDATA	0	0	0	0	0	1	no
--- a/test-data/cuffdiff_out11.txt	Sun Feb 19 12:08:50 2017 -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
--- a/test-data/cuffdiff_out2.txt	Sun Feb 19 12:08:50 2017 -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	8.3103e+06	1.79769e+308	1.79769e+308	0.0786496	0.157299	no
-XLOC_000002	XLOC_000002	-	chr1:3111449-3111490	q1	q2	OK	0	2.1403e+08	1.79769e+308	1.79769e+308	0.158655	0.16621	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	368900	429265	0.21864	-0.483034	0.629072	1	no
-XLOC_000008	XLOC_000008	-	chr1:3190858-3191434	q1	q2	NOTEST	404373	338500	-0.25653	0.342922	0.731657	1	no
-XLOC_000009	XLOC_000009	-	chr1:3191512-3192077	q1	q2	NOTEST	402276	686974	0.772069	-1.24554	0.212932	1	no
-XLOC_000010	XLOC_000010	-	chr1:3192250-3192336	q1	q2	NOTEST	3.994e+06	2.93812e+06	-0.442943	0.217099	0.828131	1	no
-XLOC_000011	XLOC_000011	-	chr1:3192441-3192494	q1	q2	OK	0	5.68095e+07	1.79769e+308	1.79769e+308	0.0786496	0.157299	no
-XLOC_000012	XLOC_000012	-	chr1:3192550-3192629	q1	q2	OK	0	4.15515e+06	1.79769e+308	1.79769e+308	0.158655	0.16621	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	6.02976e+06	1.79769e+308	1.79769e+308	0.0512352	0.157299	no
-XLOC_000016	XLOC_000016	-	chr1:3194185-3194226	q1	q2	OK	0	2.1403e+08	1.79769e+308	1.79769e+308	0.158655	0.16621	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	959058	705514	-0.442943	0.376027	0.706897	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	77513.9	285108	1.87898	-1.76152	0.0781506	1	no
-XLOC_000030	XLOC_000030	-	chr1:3201596-3201666	q1	q2	OK	1.89853e+07	0	-1.79769e+308	-1.79769e+308	0.0786496	0.157299	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	1.31744e+07	0	-1.79769e+308	-1.79769e+308	0.0416323	0.157299	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	8.3103e+06	1.79769e+308	1.79769e+308	0.0786496	0.157299	no
-XLOC_000035	XLOC_000035	Xkr4	chr1:3212367-3212439	q1	q2	OK	0	2.4671e+07	1.79769e+308	1.79769e+308	0.0512352	0.157299	no
-XLOC_000036	XLOC_000036	Xkr4	chr1:3212717-3212801	q1	q2	NOTEST	4.39147e+06	0	-1.79769e+308	-1.79769e+308	0.158655	1	no
-XLOC_000037	XLOC_000037	Xkr4	chr1:3213095-3213242	q1	q2	OK	5.3664e+06	1.82908e+06	-1.55284	0.839459	0.401212	0.401212	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	56312.4	372827	2.72698	-1.67622	0.0936947	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	OK	0	2.66226e+07	1.79769e+308	1.79769e+308	0.0786496	0.157299	no
-XLOC_000043	XLOC_000043	Xkr4	chr1:3243108-3243154	q1	q2	OK	9.99919e+07	0	-1.79769e+308	-1.79769e+308	0.158655	0.16621	no
-XLOC_000044	XLOC_000044	Xkr4	chr1:3243347-3243401	q1	q2	OK	0	5.0951e+07	1.79769e+308	1.79769e+308	0.0786496	0.157299	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	2.06814e+09	1.79769e+308	1.79769e+308	0.0786496	0.157299	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	265614	41870.3	-2.66534	2.48499	0.0129556	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	OK	0	2.29576e+07	1.79769e+308	1.79769e+308	0.158655	0.16621	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	9.79535e+06	1.79769e+308	1.79769e+308	0.158655	0.16621	no
-XLOC_000058	XLOC_000058	Xkr4	chr1:3290798-3290859	q1	q2	OK	1.8095e+07	0	-1.79769e+308	-1.79769e+308	0.158655	0.16621	no
-XLOC_000059	XLOC_000059	Xkr4	chr1:3290919-3291273	q1	q2	NOTEST	342218	75524	-2.17991	1.96162	0.049807	1	no
-XLOC_000060	XLOC_000060	Xkr4	chr1:3299443-3299664	q1	q2	NOTEST	937403	137917	-2.76487	1.66807	0.0953024	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	OK	8.91489e+06	0	-1.79769e+308	-1.79769e+308	0.158655	0.16621	no
-XLOC_000068	XLOC_000068	Xkr4	chr1:3355887-3356119	q1	q2	NOTEST	585828	0	-1.79769e+308	-1.79769e+308	0.0512352	1	no
-XLOC_000069	XLOC_000069	Xkr4	chr1:3356180-3356225	q1	q2	OK	1.19208e+08	0	-1.79769e+308	-1.79769e+308	0.158655	0.16621	no
-XLOC_000070	XLOC_000070	Xkr4	chr1:3363076-3363176	q1	q2	NOTEST	4.42166e+06	0	-1.79769e+308	-1.79769e+308	0.0786496	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	OK	4.28358e+07	0	-1.79769e+308	-1.79769e+308	0.0786496	0.157299	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	7.29939e+07	0	-1.79769e+308	-1.79769e+308	0.158655	0.16621	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
--- a/test-data/cuffdiff_out3.txt	Sun Feb 19 12:08:50 2017 -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
-TSS1	XLOC_000001	Xkr4	chr1:3204754-3204833	q1	q2	OK	0	8.3103e+06	1.79769e+308	1.79769e+308	0.0786496	0.150149	no
-TSS11	XLOC_000008	-	chr1:3190858-3191434	q1	q2	NOTEST	404373	338500	-0.25653	0.342922	0.731657	1	no
-TSS12	XLOC_000009	-	chr1:3191512-3192077	q1	q2	NOTEST	402276	686974	0.772069	-1.24554	0.212932	1	no
-TSS15	XLOC_000010	-	chr1:3192250-3192336	q1	q2	NOTEST	3.994e+06	2.93812e+06	-0.442943	0.217099	0.828131	1	no
-TSS16	XLOC_000011	-	chr1:3192441-3192494	q1	q2	OK	0	5.68095e+07	1.79769e+308	1.79769e+308	0.0786496	0.150149	no
-TSS17	XLOC_000012	-	chr1:3192550-3192629	q1	q2	OK	0	4.15515e+06	1.79769e+308	1.79769e+308	0.158655	0.158655	no
-TSS18	XLOC_000013	-	chr1:3192649-3192676	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS19	XLOC_000014	-	chr1:3192731-3192811	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS2	XLOC_000002	-	chr1:3111449-3111490	q1	q2	OK	0	2.1403e+08	1.79769e+308	1.79769e+308	0.158655	0.158655	no
-TSS20	XLOC_000015	-	chr1:3192940-3193042	q1	q2	OK	0	6.02976e+06	1.79769e+308	1.79769e+308	0.0512352	0.150149	no
-TSS21	XLOC_000016	-	chr1:3194185-3194226	q1	q2	OK	0	2.1403e+08	1.79769e+308	1.79769e+308	0.158655	0.158655	no
-TSS22	XLOC_000017	-	chr1:3194302-3194329	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS23	XLOC_000018	-	chr1:3194706-3194733	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS24	XLOC_000019	-	chr1:3195083-3195110	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS25	XLOC_000020	-	chr1:3195450-3195477	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS26	XLOC_000021	-	chr1:3197089-3197116	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS27	XLOC_000022	-	chr1:3197246-3197273	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS28	XLOC_000023	-	chr1:3197346-3197373	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS29	XLOC_000024	-	chr1:3197425-3197452	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_000025	-	chr1:3200022-3200191	q1	q2	NOTEST	959058	705514	-0.442943	0.376027	0.706897	1	no
-TSS32	XLOC_000026	-	chr1:3200325-3200352	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS33	XLOC_000027	-	chr1:3200430-3200457	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS34	XLOC_000028	-	chr1:3201007-3201039	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS35	XLOC_000029	-	chr1:3201077-3201481	q1	q2	NOTEST	77513.9	285108	1.87898	-1.76152	0.0781506	1	no
-TSS37	XLOC_000030	-	chr1:3201596-3201666	q1	q2	OK	1.89853e+07	0	-1.79769e+308	-1.79769e+308	0.0786496	0.150149	no
-TSS38	XLOC_000031	-	chr1:3201672-3201699	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS39	XLOC_000032	-	chr1:3201725-3201809	q1	q2	OK	1.31744e+07	0	-1.79769e+308	-1.79769e+308	0.0416323	0.150149	no
-TSS4	XLOC_000004	-	chr1:3174765-3174792	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS40	XLOC_000033	Xkr4	chr1:3211521-3211561	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS41	XLOC_000034	Xkr4	chr1:3212213-3212292	q1	q2	OK	0	8.3103e+06	1.79769e+308	1.79769e+308	0.0786496	0.150149	no
-TSS42	XLOC_000035	Xkr4	chr1:3212367-3212439	q1	q2	OK	0	2.4671e+07	1.79769e+308	1.79769e+308	0.0512352	0.150149	no
-TSS43	XLOC_000036	Xkr4	chr1:3212717-3212801	q1	q2	NOTEST	4.39147e+06	0	-1.79769e+308	-1.79769e+308	0.158655	1	no
-TSS44	XLOC_000037	Xkr4	chr1:3213095-3213242	q1	q2	NOTEST	3.99739e+06	1.82908e+06	-1.12794	0.489836	0.62425	1	no
-TSS45	XLOC_000037	Xkr4	chr1:3213095-3213242	q1	q2	NOTEST	1.36901e+06	0	0	0	1	1	no
-TSS46	XLOC_000038	Xkr4	chr1:3240606-3240633	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS47	XLOC_000039	Xkr4	chr1:3242479-3242512	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS48	XLOC_000040	Xkr4	chr1:3242633-3242923	q1	q2	NOTEST	56312.4	372827	2.72698	-1.67622	0.0936947	1	no
-TSS49	XLOC_000041	Xkr4	chr1:3242924-3243005	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_000042	Xkr4	chr1:3243018-3243079	q1	q2	OK	0	2.66226e+07	1.79769e+308	1.79769e+308	0.0786496	0.150149	no
-TSS51	XLOC_000043	Xkr4	chr1:3243108-3243154	q1	q2	OK	9.99919e+07	0	-1.79769e+308	-1.79769e+308	0.158655	0.158655	no
-TSS52	XLOC_000044	Xkr4	chr1:3243347-3243401	q1	q2	OK	0	5.0951e+07	1.79769e+308	1.79769e+308	0.0786496	0.150149	no
-TSS53	XLOC_000045	Xkr4	chr1:3254079-3254106	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS54	XLOC_000046	Xkr4	chr1:3256974-3257011	q1	q2	OK	0	2.06814e+09	1.79769e+308	1.79769e+308	0.0786496	0.150149	no
-TSS55	XLOC_000047	Xkr4	chr1:3277155-3277182	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS56	XLOC_000048	Xkr4	chr1:3277190-3277218	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS57	XLOC_000049	Xkr4	chr1:3277913-3278390	q1	q2	NOTEST	265614	41870.3	-2.66534	2.48499	0.0129556	1	no
-TSS59	XLOC_000050	Xkr4	chr1:3280117-3280144	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_000051	Xkr4	chr1:3280498-3280525	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS61	XLOC_000052	Xkr4	chr1:3280686-3280741	q1	q2	OK	0	2.29576e+07	1.79769e+308	1.79769e+308	0.158655	0.158655	no
-TSS62	XLOC_000053	Xkr4	chr1:3282504-3282531	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS63	XLOC_000054	Xkr4	chr1:3282650-3282677	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS64	XLOC_000055	Xkr4	chr1:3282760-3282832	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS65	XLOC_000056	Xkr4	chr1:3284966-3284993	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS66	XLOC_000057	Xkr4	chr1:3290488-3290553	q1	q2	OK	0	9.79535e+06	1.79769e+308	1.79769e+308	0.158655	0.158655	no
-TSS67	XLOC_000058	Xkr4	chr1:3290798-3290859	q1	q2	OK	1.8095e+07	0	-1.79769e+308	-1.79769e+308	0.158655	0.158655	no
-TSS68	XLOC_000059	Xkr4	chr1:3290919-3291273	q1	q2	NOTEST	342218	75524	-2.17991	1.96162	0.049807	1	no
-TSS7	XLOC_000007	-	chr1:3189810-3190789	q1	q2	NOTEST	368900	429265	0.21864	-0.483034	0.629072	1	no
-TSS70	XLOC_000060	Xkr4	chr1:3299443-3299664	q1	q2	NOTEST	937403	137917	-2.76487	1.66807	0.0953024	1	no
-TSS71	XLOC_000060	Xkr4	chr1:3299443-3299664	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS72	XLOC_000061	Xkr4	chr1:3299691-3299733	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS73	XLOC_000062	Xkr4	chr1:3300051-3300078	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS74	XLOC_000063	Xkr4	chr1:3307748-3307775	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS75	XLOC_000064	Xkr4	chr1:3318620-3318647	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS76	XLOC_000065	Xkr4	chr1:3318999-3319051	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS77	XLOC_000066	Xkr4	chr1:3330527-3330554	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS78	XLOC_000067	Xkr4	chr1:3351240-3351311	q1	q2	OK	8.91489e+06	0	-1.79769e+308	-1.79769e+308	0.158655	0.158655	no
-TSS79	XLOC_000068	Xkr4	chr1:3355887-3356119	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS80	XLOC_000068	Xkr4	chr1:3355887-3356119	q1	q2	NOTEST	585828	0	-1.79769e+308	-1.79769e+308	0.0512352	1	no
-TSS81	XLOC_000069	Xkr4	chr1:3356180-3356225	q1	q2	OK	1.19208e+08	0	-1.79769e+308	-1.79769e+308	0.158655	0.158655	no
-TSS82	XLOC_000070	Xkr4	chr1:3363076-3363176	q1	q2	NOTEST	4.42166e+06	0	-1.79769e+308	-1.79769e+308	0.0786496	1	no
-TSS83	XLOC_000071	Xkr4	chr1:3363214-3363278	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS84	XLOC_000072	Xkr4	chr1:3363387-3363446	q1	q2	OK	4.28358e+07	0	-1.79769e+308	-1.79769e+308	0.0786496	0.150149	no
-TSS85	XLOC_000073	Xkr4	chr1:3363753-3363849	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS86	XLOC_000074	Xkr4	chr1:3364871-3364919	q1	q2	OK	7.29939e+07	0	-1.79769e+308	-1.79769e+308	0.158655	0.158655	no
-TSS87	XLOC_000075	Xkr4	chr1:3367135-3367162	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS88	XLOC_000076	Xkr4	chr1:3367210-3367237	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS89	XLOC_000077	Xkr4	chr1:3367333-3367382	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS90	XLOC_000078	Xkr4	chr1:3369580-3369607	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS91	XLOC_000079	Xkr4	chr1:3375001-3375028	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS92	XLOC_000080	Xkr4	chr1:3377211-3377262	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS93	XLOC_000081	Xkr4	chr1:3379888-3379915	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS94	XLOC_000082	Xkr4	chr1:3386739-3386836	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS95	XLOC_000083	Xkr4	chr1:3391325-3391352	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS96	XLOC_000084	Xkr4	chr1:3435841-3435880	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS97	XLOC_000085	Xkr4	chr1:3447761-3447788	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS98	XLOC_000086	Xkr4	chr1:3450906-3450965	q1	q2	NOTEST	0	0	0	0	1	1	no
-TSS99	XLOC_000087	Xkr4	chr1:3451051-3451109	q1	q2	NOTEST	0	0	0	0	1	1	no
--- a/test-data/cuffdiff_out4.txt	Sun Feb 19 12:08:50 2017 -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
--- a/test-data/cuffdiff_out5.txt	Sun Feb 19 12:08:50 2017 -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	8.3103e+06	0	2.00628e+07	OK
-TCONS_00000002	-	-	XLOC_000002	-	TSS2	chr1:3111449-3111490	41	-	0	0	0	OK	2.1403e+08	0	6.42089e+08	OK
-TCONS_00000003	-	-	XLOC_000003	-	TSS3	chr1:3111545-3111576	31	-	0	0	0	OK	0	0	0	OK
-TCONS_00000009	-	-	XLOC_000011	-	TSS16	chr1:3192441-3192494	53	-	0	0	0	OK	5.68095e+07	0	1.3715e+08	OK
-TCONS_00000010	-	-	XLOC_000012	-	TSS17	chr1:3192550-3192629	79	-	0	0	0	OK	4.15515e+06	0	1.24654e+07	OK
-TCONS_00000011	-	-	XLOC_000014	-	TSS19	chr1:3192731-3192811	80	-	0	0	0	OK	0	0	0	OK
-TCONS_00000012	-	-	XLOC_000015	-	TSS20	chr1:3192940-3193042	102	-	0	0	0	OK	6.02976e+06	0	1.34147e+07	OK
-TCONS_00000013	-	-	XLOC_000016	-	TSS21	chr1:3194185-3194226	41	-	0	0	0	OK	2.1403e+08	0	6.42089e+08	OK
-TCONS_00000014	-	-	XLOC_000017	-	TSS22	chr1:3194302-3194329	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000015	-	-	XLOC_000019	-	TSS24	chr1:3195083-3195110	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000016	-	-	XLOC_000020	-	TSS25	chr1:3195450-3195477	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000017	-	-	XLOC_000021	-	TSS26	chr1:3197089-3197116	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000018	-	-	XLOC_000022	-	TSS27	chr1:3197246-3197273	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000019	-	-	XLOC_000023	-	TSS28	chr1:3197346-3197373	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000020	-	-	XLOC_000025	-	TSS30	chr1:3200022-3200191	169	-	959058	0	2.06648e+06	OK	705514	0	1.52017e+06	OK
-TCONS_00000021	-	-	XLOC_000026	-	TSS32	chr1:3200325-3200352	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000022	-	-	XLOC_000029	-	TSS35	chr1:3201077-3201481	404	-	77513.9	0	167019	OK	285108	21736.5	548480	OK
-TCONS_00000023	-	-	XLOC_000031	-	TSS38	chr1:3201672-3201699	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000024	i	Xkr4	XLOC_000034	Xkr4	TSS41	chr1:3212213-3212292	79	-	0	0	0	OK	8.3103e+06	0	2.00628e+07	OK
-TCONS_00000025	i	Xkr4	XLOC_000035	Xkr4	TSS42	chr1:3212367-3212439	72	-	0	0	0	OK	2.4671e+07	0	5.48867e+07	OK
-TCONS_00000026	i	Xkr4	XLOC_000037	Xkr4	TSS44	chr1:3213095-3213242	97	-	3.99739e+06	3.99339e+06	4.00139e+06	LOWDATA	1.82908e+06	0	5.48723e+06	OK
-TCONS_00000027	i	Xkr4	XLOC_000040	Xkr4	TSS48	chr1:3242633-3242923	290	-	56312.4	0	168937	OK	372827	0	761430	OK
-TCONS_00000028	i	Xkr4	XLOC_000042	Xkr4	TSS50	chr1:3243018-3243079	61	-	0	0	0	OK	2.66226e+07	0	6.42725e+07	OK
-TCONS_00000029	i	Xkr4	XLOC_000044	Xkr4	TSS52	chr1:3243347-3243401	54	-	0	0	0	OK	5.0951e+07	0	1.23007e+08	OK
-TCONS_00000030	i	Xkr4	XLOC_000046	Xkr4	TSS54	chr1:3256974-3257011	37	-	0	0	0	OK	2.06814e+09	0	4.99293e+09	OK
-TCONS_00000031	i	Xkr4	XLOC_000048	Xkr4	TSS56	chr1:3277190-3277218	28	-	0	0	0	OK	0	0	0	OK
-TCONS_00000033	i	Xkr4	XLOC_000052	Xkr4	TSS61	chr1:3280686-3280741	55	-	0	0	0	OK	2.29576e+07	0	6.88728e+07	OK
-TCONS_00000034	i	Xkr4	XLOC_000057	Xkr4	TSS66	chr1:3290488-3290553	65	-	0	0	0	OK	9.79535e+06	0	2.9386e+07	OK
-TCONS_00000037	i	Xkr4	XLOC_000060	Xkr4	TSS71	chr1:3299443-3299664	55	-	0	0	0	OK	0	0	0	OK
-TCONS_00000038	i	Xkr4	XLOC_000062	Xkr4	TSS73	chr1:3300051-3300078	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000039	i	Xkr4	XLOC_000065	Xkr4	TSS76	chr1:3318999-3319051	52	-	0	0	0	OK	0	0	0	OK
-TCONS_00000040	i	Xkr4	XLOC_000068	Xkr4	TSS79	chr1:3355887-3356119	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000041	i	Xkr4	XLOC_000071	Xkr4	TSS83	chr1:3363214-3363278	64	-	0	0	0	OK	0	0	0	OK
-TCONS_00000042	i	Xkr4	XLOC_000073	Xkr4	TSS85	chr1:3363753-3363849	96	-	0	0	0	OK	0	0	0	OK
-TCONS_00000043	i	Xkr4	XLOC_000075	Xkr4	TSS87	chr1:3367135-3367162	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000044	i	Xkr4	XLOC_000077	Xkr4	TSS89	chr1:3367333-3367382	49	-	0	0	0	OK	0	0	0	OK
-TCONS_00000045	i	Xkr4	XLOC_000080	Xkr4	TSS92	chr1:3377211-3377262	51	-	0	0	0	OK	0	0	0	OK
-TCONS_00000046	i	Xkr4	XLOC_000083	Xkr4	TSS95	chr1:3391325-3391352	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000047	i	Xkr4	XLOC_000084	Xkr4	TSS96	chr1:3435841-3435880	39	-	0	0	0	OK	0	0	0	OK
-TCONS_00000048	i	Xkr4	XLOC_000085	Xkr4	TSS97	chr1:3447761-3447788	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000049	i	Xkr4	XLOC_000086	Xkr4	TSS98	chr1:3450906-3450965	59	-	0	0	0	OK	0	0	0	OK
-TCONS_00000050	i	Xkr4	XLOC_000087	Xkr4	TSS99	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	-	368900	151353	586447	OK	429265	337221	521309	OK
-TCONS_00000055	-	-	XLOC_000008	-	TSS11	chr1:3190858-3191434	576	-	404373	101434	707312	OK	338500	95761.5	581239	OK
-TCONS_00000056	-	-	XLOC_000009	-	TSS12	chr1:3191512-3192077	565	-	402276	96829.4	707722	OK	686974	410563	963384	OK
-TCONS_00000057	-	-	XLOC_000010	-	TSS15	chr1:3192250-3192336	86	-	3.994e+06	0	1.1982e+07	OK	2.93812e+06	0	8.81435e+06	OK
-TCONS_00000058	-	-	XLOC_000013	-	TSS18	chr1:3192649-3192676	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000059	-	-	XLOC_000018	-	TSS23	chr1:3194706-3194733	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000060	-	-	XLOC_000024	-	TSS29	chr1:3197425-3197452	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000062	-	-	XLOC_000027	-	TSS33	chr1:3200430-3200457	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000063	-	-	XLOC_000028	-	TSS34	chr1:3201007-3201039	32	-	0	0	0	OK	0	0	0	OK
-TCONS_00000065	-	-	XLOC_000030	-	TSS37	chr1:3201596-3201666	70	-	1.89853e+07	0	4.58345e+07	OK	0	0	0	OK
-TCONS_00000066	-	-	XLOC_000032	-	TSS39	chr1:3201725-3201809	84	-	1.31744e+07	0	2.83869e+07	OK	0	0	0	OK
-TCONS_00000067	i	Xkr4	XLOC_000033	Xkr4	TSS40	chr1:3211521-3211561	40	-	0	0	0	OK	0	0	0	OK
-TCONS_00000068	i	Xkr4	XLOC_000036	Xkr4	TSS43	chr1:3212717-3212801	84	-	4.39147e+06	0	1.31744e+07	OK	0	0	0	OK
-TCONS_00000069	i	Xkr4	XLOC_000037	Xkr4	TSS45	chr1:3213095-3213242	124	-	1.36901e+06	1.36667e+06	1.37135e+06	LOWDATA	0	0	0	OK
-TCONS_00000070	i	Xkr4	XLOC_000038	Xkr4	TSS46	chr1:3240606-3240633	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000071	i	Xkr4	XLOC_000039	Xkr4	TSS47	chr1:3242479-3242512	33	-	0	0	0	OK	0	0	0	OK
-TCONS_00000072	i	Xkr4	XLOC_000041	Xkr4	TSS49	chr1:3242924-3243005	81	-	0	0	0	OK	0	0	0	OK
-TCONS_00000073	i	Xkr4	XLOC_000043	Xkr4	TSS51	chr1:3243108-3243154	46	-	9.99919e+07	0	2.99976e+08	OK	0	0	0	OK
-TCONS_00000074	i	Xkr4	XLOC_000045	Xkr4	TSS53	chr1:3254079-3254106	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000075	i	Xkr4	XLOC_000047	Xkr4	TSS55	chr1:3277155-3277182	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000076	i	Xkr4	XLOC_000049	Xkr4	TSS57	chr1:3277913-3278390	477	-	265614	16793	514436	OK	41870.3	0	90217.9	OK
-TCONS_00000077	i	Xkr4	XLOC_000050	Xkr4	TSS59	chr1:3280117-3280144	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000078	i	Xkr4	XLOC_000051	Xkr4	TSS60	chr1:3280498-3280525	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000079	i	Xkr4	XLOC_000053	Xkr4	TSS62	chr1:3282504-3282531	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000080	i	Xkr4	XLOC_000054	Xkr4	TSS63	chr1:3282650-3282677	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000081	i	Xkr4	XLOC_000055	Xkr4	TSS64	chr1:3282760-3282832	72	-	0	0	0	OK	0	0	0	OK
-TCONS_00000082	i	Xkr4	XLOC_000056	Xkr4	TSS65	chr1:3284966-3284993	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000083	i	Xkr4	XLOC_000058	Xkr4	TSS67	chr1:3290798-3290859	61	-	1.8095e+07	0	5.4285e+07	OK	0	0	0	OK
-TCONS_00000084	i	Xkr4	XLOC_000059	Xkr4	TSS68	chr1:3290919-3291273	354	-	342218	0	691214	OK	75524	0	162732	OK
-TCONS_00000085	i	Xkr4	XLOC_000060	Xkr4	TSS70	chr1:3299443-3299664	197	-	937403	0	1.99795e+06	OK	137917	0	413751	OK
-TCONS_00000086	i	Xkr4	XLOC_000061	Xkr4	TSS72	chr1:3299691-3299733	42	-	0	0	0	OK	0	0	0	OK
-TCONS_00000087	i	Xkr4	XLOC_000063	Xkr4	TSS74	chr1:3307748-3307775	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000088	i	Xkr4	XLOC_000064	Xkr4	TSS75	chr1:3318620-3318647	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000089	i	Xkr4	XLOC_000066	Xkr4	TSS77	chr1:3330527-3330554	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000090	i	Xkr4	XLOC_000067	Xkr4	TSS78	chr1:3351240-3351311	71	-	8.91489e+06	0	2.67447e+07	OK	0	0	0	OK
-TCONS_00000091	i	Xkr4	XLOC_000068	Xkr4	TSS80	chr1:3355887-3356119	212	-	585828	0	1.30332e+06	OK	0	0	0	OK
-TCONS_00000092	i	Xkr4	XLOC_000069	Xkr4	TSS81	chr1:3356180-3356225	45	-	1.19208e+08	0	3.57623e+08	OK	0	0	0	OK
-TCONS_00000093	i	Xkr4	XLOC_000070	Xkr4	TSS82	chr1:3363076-3363176	100	-	4.42166e+06	0	1.06748e+07	OK	0	0	0	OK
-TCONS_00000094	i	Xkr4	XLOC_000072	Xkr4	TSS84	chr1:3363387-3363446	59	-	4.28358e+07	0	1.03415e+08	OK	0	0	0	OK
-TCONS_00000095	i	Xkr4	XLOC_000074	Xkr4	TSS86	chr1:3364871-3364919	48	-	7.29939e+07	0	2.18982e+08	OK	0	0	0	OK
-TCONS_00000096	i	Xkr4	XLOC_000076	Xkr4	TSS88	chr1:3367210-3367237	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000097	i	Xkr4	XLOC_000078	Xkr4	TSS90	chr1:3369580-3369607	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000098	i	Xkr4	XLOC_000079	Xkr4	TSS91	chr1:3375001-3375028	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000099	i	Xkr4	XLOC_000081	Xkr4	TSS93	chr1:3379888-3379915	27	-	0	0	0	OK	0	0	0	OK
-TCONS_00000100	i	Xkr4	XLOC_000082	Xkr4	TSS94	chr1:3386739-3386836	97	-	0	0	0	OK	0	0	0	OK
--- a/test-data/cuffdiff_out6.txt	Sun Feb 19 12:08:50 2017 -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	8.3103e+06	0	2.00628e+07	OK
-XLOC_000002	-	-	XLOC_000002	-	TSS2	chr1:3111449-3111490	-	-	0	0	0	OK	2.1403e+08	0	6.42089e+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	-	-	368900	151353	586447	OK	429265	337221	521309	OK
-XLOC_000008	-	-	XLOC_000008	-	TSS11	chr1:3190858-3191434	-	-	404373	101434	707312	OK	338500	95761.5	581239	OK
-XLOC_000009	-	-	XLOC_000009	-	TSS12	chr1:3191512-3192077	-	-	402276	96829.4	707722	OK	686974	410563	963384	OK
-XLOC_000010	-	-	XLOC_000010	-	TSS15	chr1:3192250-3192336	-	-	3.994e+06	0	1.1982e+07	OK	2.93812e+06	0	8.81435e+06	OK
-XLOC_000011	-	-	XLOC_000011	-	TSS16	chr1:3192441-3192494	-	-	0	0	0	OK	5.68095e+07	0	1.3715e+08	OK
-XLOC_000012	-	-	XLOC_000012	-	TSS17	chr1:3192550-3192629	-	-	0	0	0	OK	4.15515e+06	0	1.24654e+07	OK
-XLOC_000013	-	-	XLOC_000013	-	TSS18	chr1:3192649-3192676	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000014	-	-	XLOC_000014	-	TSS19	chr1:3192731-3192811	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000015	-	-	XLOC_000015	-	TSS20	chr1:3192940-3193042	-	-	0	0	0	OK	6.02976e+06	0	1.34147e+07	OK
-XLOC_000016	-	-	XLOC_000016	-	TSS21	chr1:3194185-3194226	-	-	0	0	0	OK	2.1403e+08	0	6.42089e+08	OK
-XLOC_000017	-	-	XLOC_000017	-	TSS22	chr1:3194302-3194329	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000018	-	-	XLOC_000018	-	TSS23	chr1:3194706-3194733	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000019	-	-	XLOC_000019	-	TSS24	chr1:3195083-3195110	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000020	-	-	XLOC_000020	-	TSS25	chr1:3195450-3195477	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000021	-	-	XLOC_000021	-	TSS26	chr1:3197089-3197116	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000022	-	-	XLOC_000022	-	TSS27	chr1:3197246-3197273	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000023	-	-	XLOC_000023	-	TSS28	chr1:3197346-3197373	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000024	-	-	XLOC_000024	-	TSS29	chr1:3197425-3197452	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000025	-	-	XLOC_000025	-	TSS30	chr1:3200022-3200191	-	-	959058	0	2.06648e+06	OK	705514	0	1.52017e+06	OK
-XLOC_000026	-	-	XLOC_000026	-	TSS32	chr1:3200325-3200352	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000027	-	-	XLOC_000027	-	TSS33	chr1:3200430-3200457	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000028	-	-	XLOC_000028	-	TSS34	chr1:3201007-3201039	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000029	-	-	XLOC_000029	-	TSS35	chr1:3201077-3201481	-	-	77513.9	0	167019	OK	285108	21736.5	548480	OK
-XLOC_000030	-	-	XLOC_000030	-	TSS37	chr1:3201596-3201666	-	-	1.89853e+07	0	4.58345e+07	OK	0	0	0	OK
-XLOC_000031	-	-	XLOC_000031	-	TSS38	chr1:3201672-3201699	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000032	-	-	XLOC_000032	-	TSS39	chr1:3201725-3201809	-	-	1.31744e+07	0	2.83869e+07	OK	0	0	0	OK
-XLOC_000033	-	-	XLOC_000033	Xkr4	TSS40	chr1:3211521-3211561	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000034	-	-	XLOC_000034	Xkr4	TSS41	chr1:3212213-3212292	-	-	0	0	0	OK	8.3103e+06	0	2.00628e+07	OK
-XLOC_000035	-	-	XLOC_000035	Xkr4	TSS42	chr1:3212367-3212439	-	-	0	0	0	OK	2.4671e+07	0	5.48867e+07	OK
-XLOC_000036	-	-	XLOC_000036	Xkr4	TSS43	chr1:3212717-3212801	-	-	4.39147e+06	0	1.31744e+07	OK	0	0	0	OK
-XLOC_000037	-	-	XLOC_000037	Xkr4	TSS44,TSS45	chr1:3213095-3213242	-	-	5.3664e+06	0	1.39795e+07	LOWDATA	1.82908e+06	0	5.48723e+06	OK
-XLOC_000038	-	-	XLOC_000038	Xkr4	TSS46	chr1:3240606-3240633	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000039	-	-	XLOC_000039	Xkr4	TSS47	chr1:3242479-3242512	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000040	-	-	XLOC_000040	Xkr4	TSS48	chr1:3242633-3242923	-	-	56312.4	0	168937	OK	372827	0	761430	OK
-XLOC_000041	-	-	XLOC_000041	Xkr4	TSS49	chr1:3242924-3243005	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000042	-	-	XLOC_000042	Xkr4	TSS50	chr1:3243018-3243079	-	-	0	0	0	OK	2.66226e+07	0	6.42725e+07	OK
-XLOC_000043	-	-	XLOC_000043	Xkr4	TSS51	chr1:3243108-3243154	-	-	9.99919e+07	0	2.99976e+08	OK	0	0	0	OK
-XLOC_000044	-	-	XLOC_000044	Xkr4	TSS52	chr1:3243347-3243401	-	-	0	0	0	OK	5.0951e+07	0	1.23007e+08	OK
-XLOC_000045	-	-	XLOC_000045	Xkr4	TSS53	chr1:3254079-3254106	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000046	-	-	XLOC_000046	Xkr4	TSS54	chr1:3256974-3257011	-	-	0	0	0	OK	2.06814e+09	0	4.99293e+09	OK
-XLOC_000047	-	-	XLOC_000047	Xkr4	TSS55	chr1:3277155-3277182	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000048	-	-	XLOC_000048	Xkr4	TSS56	chr1:3277190-3277218	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000049	-	-	XLOC_000049	Xkr4	TSS57	chr1:3277913-3278390	-	-	265614	16793	514436	OK	41870.3	0	90217.9	OK
-XLOC_000050	-	-	XLOC_000050	Xkr4	TSS59	chr1:3280117-3280144	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000051	-	-	XLOC_000051	Xkr4	TSS60	chr1:3280498-3280525	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000052	-	-	XLOC_000052	Xkr4	TSS61	chr1:3280686-3280741	-	-	0	0	0	OK	2.29576e+07	0	6.88728e+07	OK
-XLOC_000053	-	-	XLOC_000053	Xkr4	TSS62	chr1:3282504-3282531	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000054	-	-	XLOC_000054	Xkr4	TSS63	chr1:3282650-3282677	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000055	-	-	XLOC_000055	Xkr4	TSS64	chr1:3282760-3282832	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000056	-	-	XLOC_000056	Xkr4	TSS65	chr1:3284966-3284993	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000057	-	-	XLOC_000057	Xkr4	TSS66	chr1:3290488-3290553	-	-	0	0	0	OK	9.79535e+06	0	2.9386e+07	OK
-XLOC_000058	-	-	XLOC_000058	Xkr4	TSS67	chr1:3290798-3290859	-	-	1.8095e+07	0	5.4285e+07	OK	0	0	0	OK
-XLOC_000059	-	-	XLOC_000059	Xkr4	TSS68	chr1:3290919-3291273	-	-	342218	0	691214	OK	75524	0	162732	OK
-XLOC_000060	-	-	XLOC_000060	Xkr4	TSS70,TSS71	chr1:3299443-3299664	-	-	937403	0	1.99795e+06	OK	137917	0	413751	OK
-XLOC_000061	-	-	XLOC_000061	Xkr4	TSS72	chr1:3299691-3299733	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000062	-	-	XLOC_000062	Xkr4	TSS73	chr1:3300051-3300078	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000063	-	-	XLOC_000063	Xkr4	TSS74	chr1:3307748-3307775	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000064	-	-	XLOC_000064	Xkr4	TSS75	chr1:3318620-3318647	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000065	-	-	XLOC_000065	Xkr4	TSS76	chr1:3318999-3319051	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000066	-	-	XLOC_000066	Xkr4	TSS77	chr1:3330527-3330554	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000067	-	-	XLOC_000067	Xkr4	TSS78	chr1:3351240-3351311	-	-	8.91489e+06	0	2.67447e+07	OK	0	0	0	OK
-XLOC_000068	-	-	XLOC_000068	Xkr4	TSS79,TSS80	chr1:3355887-3356119	-	-	585828	0	1.30332e+06	OK	0	0	0	OK
-XLOC_000069	-	-	XLOC_000069	Xkr4	TSS81	chr1:3356180-3356225	-	-	1.19208e+08	0	3.57623e+08	OK	0	0	0	OK
-XLOC_000070	-	-	XLOC_000070	Xkr4	TSS82	chr1:3363076-3363176	-	-	4.42166e+06	0	1.06748e+07	OK	0	0	0	OK
-XLOC_000071	-	-	XLOC_000071	Xkr4	TSS83	chr1:3363214-3363278	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000072	-	-	XLOC_000072	Xkr4	TSS84	chr1:3363387-3363446	-	-	4.28358e+07	0	1.03415e+08	OK	0	0	0	OK
-XLOC_000073	-	-	XLOC_000073	Xkr4	TSS85	chr1:3363753-3363849	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000074	-	-	XLOC_000074	Xkr4	TSS86	chr1:3364871-3364919	-	-	7.29939e+07	0	2.18982e+08	OK	0	0	0	OK
-XLOC_000075	-	-	XLOC_000075	Xkr4	TSS87	chr1:3367135-3367162	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000076	-	-	XLOC_000076	Xkr4	TSS88	chr1:3367210-3367237	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000077	-	-	XLOC_000077	Xkr4	TSS89	chr1:3367333-3367382	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000078	-	-	XLOC_000078	Xkr4	TSS90	chr1:3369580-3369607	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000079	-	-	XLOC_000079	Xkr4	TSS91	chr1:3375001-3375028	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000080	-	-	XLOC_000080	Xkr4	TSS92	chr1:3377211-3377262	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000081	-	-	XLOC_000081	Xkr4	TSS93	chr1:3379888-3379915	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000082	-	-	XLOC_000082	Xkr4	TSS94	chr1:3386739-3386836	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000083	-	-	XLOC_000083	Xkr4	TSS95	chr1:3391325-3391352	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000084	-	-	XLOC_000084	Xkr4	TSS96	chr1:3435841-3435880	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000085	-	-	XLOC_000085	Xkr4	TSS97	chr1:3447761-3447788	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000086	-	-	XLOC_000086	Xkr4	TSS98	chr1:3450906-3450965	-	-	0	0	0	OK	0	0	0	OK
-XLOC_000087	-	-	XLOC_000087	Xkr4	TSS99	chr1:3451051-3451109	-	-	0	0	0	OK	0	0	0	OK
--- a/test-data/cuffdiff_out7.txt	Sun Feb 19 12:08:50 2017 -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	5.42247e+06	0	1.83844e+07	OK
-TSS10	-	-	XLOC_000008	-	TSS10	chr1:3190858-3191434	-	-	227564	0	483427	OK	240951	0	505030	OK
-TSS11	-	-	XLOC_000009	-	TSS11	chr1:3191512-3192077	-	-	241366	0	509259	OK	482731	109420	856042	OK
-TSS13	-	-	XLOC_000010	-	TSS13	chr1:3192250-3192336	-	-	1.91712e+06	0	7.66198e+06	OK	1.91712e+06	0	7.66198e+06	OK
-TSS14	-	-	XLOC_000011	-	TSS14	chr1:3192441-3192494	-	-	0	0	0	OK	5.56023e+07	0	1.86077e+08	OK
-TSS15	-	-	XLOC_000012	-	TSS15	chr1:3192550-3192629	-	-	0	0	0	OK	2.71123e+06	0	1.08357e+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	3.93442e+06	0	1.25021e+07	OK
-TSS19	-	-	XLOC_000016	-	TSS19	chr1:3194185-3194226	-	-	0	0	0	OK	1.39654e+08	0	5.58144e+08	OK
-TSS2	-	-	XLOC_000002	-	TSS2	chr1:3111449-3111490	-	-	0	0	0	OK	1.39654e+08	0	5.58144e+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	-	-	460348	0	1.54058e+06	OK	460348	0	1.54058e+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	-	-	37206.6	0	124514	OK	186033	0	476912	OK
-TSS33	-	-	XLOC_000030	-	TSS33	chr1:3201596-3201666	-	-	9.11292e+06	0	3.08965e+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	-	-	8.43162e+06	0	2.67925e+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	5.42247e+06	0	1.83844e+07	OK
-TSS38	-	-	XLOC_000035	Xkr4	TSS38	chr1:3212367-3212439	-	-	0	0	0	OK	1.60978e+07	0	5.11527e+07	OK
-TSS39	-	-	XLOC_000036	Xkr4	TSS39	chr1:3212717-3212801	-	-	2.10791e+06	0	8.42447e+06	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	-	-	2.84535e+06	0	1.07397e+07	OK	1.19347e+06	0	5.96736e+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	-	-	27029.9	0	108028	OK	243269	0	681799	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	1.73712e+07	0	5.88955e+07	OK
-TSS46	-	-	XLOC_000043	Xkr4	TSS46	chr1:3243108-3243154	-	-	4.79961e+07	0	1.91822e+08	OK	0	0	0	OK
-TSS47	-	-	XLOC_000044	Xkr4	TSS47	chr1:3243347-3243401	-	-	0	0	0	OK	3.32455e+07	0	1.12716e+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	1.34946e+09	0	4.57522e+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	-	-	127495	0	331348	OK	27320.3	0	91429.2	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	1.49798e+07	0	5.98686e+07	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	6.39146e+06	0	2.55442e+07	OK
-TSS62	-	-	XLOC_000058	Xkr4	TSS62	chr1:3290798-3290859	-	-	8.68561e+06	0	3.4713e+07	OK	0	0	0	OK
-TSS63	-	-	XLOC_000059	Xkr4	TSS63	chr1:3290919-3291273	-	-	164265	0	453103	OK	49279.4	0	164917	OK
-TSS65	-	-	XLOC_000060	Xkr4	TSS65	chr1:3299443-3299664	-	-	449954	0	1.56567e+06	OK	89990.7	0	449954	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	-	-	199608	33901.5	365315	OK	299412	183619	415206	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	-	-	4.27915e+06	0	1.71021e+07	OK	0	0	0	OK
-TSS74	-	-	XLOC_000068	Xkr4	TSS74	chr1:3355887-3356119	-	-	281197	0	1.06014e+06	OK	0	0	0	OK
-TSS75	-	-	XLOC_000069	Xkr4	TSS75	chr1:3356180-3356225	-	-	5.72196e+07	0	2.28684e+08	OK	0	0	0	OK
-TSS76	-	-	XLOC_000070	Xkr4	TSS76	chr1:3363076-3363176	-	-	2.1224e+06	0	7.19579e+06	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	-	-	3.08417e+07	0	1.03214e+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	-	-	3.50371e+07	0	1.40029e+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
--- a/test-data/cuffdiff_out8.txt	Sun Feb 19 12:08:50 2017 -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
--- a/test-data/cuffdiff_out9.txt	Sun Feb 19 12:08:50 2017 -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	LOWDATA	0	0	0	0	0	1	no
-TSS17	XLOC_000014	-	chr1:3192731-3192811	q1	q2	LOWDATA	0	0	0	0	0	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	LOWDATA	0	0	0	0	0	1	no
-TSS21	XLOC_000018	-	chr1:3194706-3194733	q1	q2	LOWDATA	0	0	0	0	0	1	no
-TSS22	XLOC_000019	-	chr1:3195083-3195110	q1	q2	LOWDATA	0	0	0	0	0	1	no
-TSS23	XLOC_000020	-	chr1:3195450-3195477	q1	q2	LOWDATA	0	0	0	0	0	1	no
-TSS24	XLOC_000021	-	chr1:3197089-3197116	q1	q2	LOWDATA	0	0	0	0	0	1	no
-TSS25	XLOC_000022	-	chr1:3197246-3197273	q1	q2	LOWDATA	0	0	0	0	0	1	no
-TSS26	XLOC_000023	-	chr1:3197346-3197373	q1	q2	LOWDATA	0	0	0	0	0	1	no
-TSS27	XLOC_000024	-	chr1:3197425-3197452	q1	q2	LOWDATA	0	0	0	0	0	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	LOWDATA	0	0	0	0	0	1	no
-TSS3	XLOC_000003	-	chr1:3111545-3111576	q1	q2	LOWDATA	0	0	0	0	0	1	no
-TSS30	XLOC_000027	-	chr1:3200430-3200457	q1	q2	LOWDATA	0	0	0	0	0	1	no
-TSS31	XLOC_000028	-	chr1:3201007-3201039	q1	q2	LOWDATA	0	0	0	0	0	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	LOWDATA	0	0	0	0	0	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	LOWDATA	0	0	0	0	0	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	LOWDATA	0	0	0	0	0	1	no
-TSS40	XLOC_000037	Xkr4	chr1:3213095-3213242	q1	q2	NOTEST	0	0	0.249947	0	0.557805	1	no
-TSS41	XLOC_000038	Xkr4	chr1:3240606-3240633	q1	q2	LOWDATA	0	0	0	0	0	1	no
-TSS42	XLOC_000039	Xkr4	chr1:3242479-3242512	q1	q2	LOWDATA	0	0	0	0	0	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	LOWDATA	0	0	0	0	0	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	LOWDATA	0	0	0	0	0	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	LOWDATA	0	0	0	0	0	1	no
-TSS50	XLOC_000047	Xkr4	chr1:3277155-3277182	q1	q2	LOWDATA	0	0	0	0	0	1	no
-TSS51	XLOC_000048	Xkr4	chr1:3277190-3277218	q1	q2	LOWDATA	0	0	0	0	0	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	LOWDATA	0	0	0	0	0	1	no
-TSS55	XLOC_000051	Xkr4	chr1:3280498-3280525	q1	q2	LOWDATA	0	0	0	0	0	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	LOWDATA	0	0	0	0	0	1	no
-TSS58	XLOC_000054	Xkr4	chr1:3282650-3282677	q1	q2	LOWDATA	0	0	0	0	0	1	no
-TSS59	XLOC_000055	Xkr4	chr1:3282760-3282832	q1	q2	LOWDATA	0	0	0	0	0	1	no
-TSS6	XLOC_000006	-	chr1:3188521-3188548	q1	q2	LOWDATA	0	0	0	0	0	1	no
-TSS60	XLOC_000056	Xkr4	chr1:3284966-3284993	q1	q2	LOWDATA	0	0	0	0	0	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	LOWDATA	0	0	0	0	0	1	no
-TSS67	XLOC_000061	Xkr4	chr1:3299691-3299733	q1	q2	LOWDATA	0	0	0	0	0	1	no
-TSS68	XLOC_000062	Xkr4	chr1:3300051-3300078	q1	q2	LOWDATA	0	0	0	0	0	1	no
-TSS69	XLOC_000063	Xkr4	chr1:3307748-3307775	q1	q2	LOWDATA	0	0	0	0	0	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	LOWDATA	0	0	0	0	0	1	no
-TSS71	XLOC_000065	Xkr4	chr1:3318999-3319051	q1	q2	LOWDATA	0	0	0	0	0	1	no
-TSS72	XLOC_000066	Xkr4	chr1:3330527-3330554	q1	q2	LOWDATA	0	0	0	0	0	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	LOWDATA	0	0	0	0	0	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	LOWDATA	0	0	0	0	0	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	LOWDATA	0	0	0	0	0	1	no
-TSS82	XLOC_000076	Xkr4	chr1:3367210-3367237	q1	q2	LOWDATA	0	0	0	0	0	1	no
-TSS83	XLOC_000077	Xkr4	chr1:3367333-3367382	q1	q2	LOWDATA	0	0	0	0	0	1	no
-TSS84	XLOC_000078	Xkr4	chr1:3369580-3369607	q1	q2	LOWDATA	0	0	0	0	0	1	no
-TSS85	XLOC_000079	Xkr4	chr1:3375001-3375028	q1	q2	LOWDATA	0	0	0	0	0	1	no
-TSS86	XLOC_000080	Xkr4	chr1:3377211-3377262	q1	q2	LOWDATA	0	0	0	0	0	1	no
-TSS87	XLOC_000081	Xkr4	chr1:3379888-3379915	q1	q2	LOWDATA	0	0	0	0	0	1	no
-TSS88	XLOC_000082	Xkr4	chr1:3386739-3386836	q1	q2	LOWDATA	0	0	0	0	0	1	no
-TSS89	XLOC_000083	Xkr4	chr1:3391325-3391352	q1	q2	LOWDATA	0	0	0	0	0	1	no
-TSS90	XLOC_000084	Xkr4	chr1:3435841-3435880	q1	q2	LOWDATA	0	0	0	0	0	1	no
-TSS91	XLOC_000085	Xkr4	chr1:3447761-3447788	q1	q2	LOWDATA	0	0	0	0	0	1	no
-TSS92	XLOC_000086	Xkr4	chr1:3450906-3450965	q1	q2	LOWDATA	0	0	0	0	0	1	no
-TSS93	XLOC_000087	Xkr4	chr1:3451051-3451109	q1	q2	LOWDATA	0	0	0	0	0	1	no
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genes.count_table	Tue Jun 16 16:58:39 2020 +0000
@@ -0,0 +1,88 @@
+tracking_id	in1_0	in2_0
+XLOC_000001	0	1.94365
+XLOC_000002	0	0.971825
+XLOC_000003	0	0
+XLOC_000004	0	0
+XLOC_000005	0	0
+XLOC_000006	0	0
+XLOC_000007	62	90.3798
+XLOC_000008	34	34.9857
+XLOC_000009	35	68.0278
+XLOC_000010	1	0.971825
+XLOC_000011	0	2.91548
+XLOC_000012	0	0.971825
+XLOC_000013	0	0
+XLOC_000014	0	0
+XLOC_000015	0	3.8873
+XLOC_000016	0	0.971825
+XLOC_000017	0	0
+XLOC_000018	0	0
+XLOC_000019	0	0
+XLOC_000020	0	0
+XLOC_000021	0	0
+XLOC_000022	0	0
+XLOC_000023	0	0
+XLOC_000024	0	0
+XLOC_000025	3	2.91548
+XLOC_000026	0	0
+XLOC_000027	0	0
+XLOC_000028	0	0
+XLOC_000029	3	14.5774
+XLOC_000030	2	0
+XLOC_000031	0	0
+XLOC_000032	4	0
+XLOC_000033	0	0
+XLOC_000034	0	1.94365
+XLOC_000035	0	3.8873
+XLOC_000036	1	0
+XLOC_000037	3	0.971825
+XLOC_000038	0	0
+XLOC_000039	0	0
+XLOC_000040	1	8.74643
+XLOC_000041	0	0
+XLOC_000042	0	1.94365
+XLOC_000043	1	0
+XLOC_000044	0	1.94365
+XLOC_000045	0	0
+XLOC_000046	0	1.94365
+XLOC_000047	0	0
+XLOC_000048	0	0
+XLOC_000049	14	2.91548
+XLOC_000050	0	0
+XLOC_000051	0	0
+XLOC_000052	0	0.971825
+XLOC_000053	0	0
+XLOC_000054	0	0
+XLOC_000055	0	0
+XLOC_000056	0	0
+XLOC_000057	0	0.971825
+XLOC_000058	1	0
+XLOC_000059	10	2.91548
+XLOC_000060	5	0.971825
+XLOC_000061	0	0
+XLOC_000062	0	0
+XLOC_000063	0	0
+XLOC_000064	0	0
+XLOC_000065	0	0
+XLOC_000066	0	0
+XLOC_000067	1	0
+XLOC_000068	4	0
+XLOC_000069	1	0
+XLOC_000070	2	0
+XLOC_000071	0	0
+XLOC_000072	3	0
+XLOC_000073	0	0
+XLOC_000074	1	0
+XLOC_000075	0	0
+XLOC_000076	0	0
+XLOC_000077	0	0
+XLOC_000078	0	0
+XLOC_000079	0	0
+XLOC_000080	0	0
+XLOC_000081	0	0
+XLOC_000082	0	0
+XLOC_000083	0	0
+XLOC_000084	0	0
+XLOC_000085	0	0
+XLOC_000086	0	0
+XLOC_000087	0	0
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genes.fpkm_table	Tue Jun 16 16:58:39 2020 +0000
@@ -0,0 +1,88 @@
+tracking_id	in1_0	in2_0
+XLOC_000001	0	9.45986e+06
+XLOC_000002	0	2.43637e+08
+XLOC_000003	0	0
+XLOC_000004	0	0
+XLOC_000005	0	0
+XLOC_000006	0	0
+XLOC_000007	358326	522345
+XLOC_000008	408511	420354
+XLOC_000009	433286	842157
+XLOC_000010	3.44151e+06	3.34455e+06
+XLOC_000011	0	9.7002e+07
+XLOC_000012	0	4.72993e+06
+XLOC_000013	0	0
+XLOC_000014	0	0
+XLOC_000015	0	6.86386e+06
+XLOC_000016	0	2.43637e+08
+XLOC_000017	0	0
+XLOC_000018	0	0
+XLOC_000019	0	0
+XLOC_000020	0	0
+XLOC_000021	0	0
+XLOC_000022	0	0
+XLOC_000023	0	0
+XLOC_000024	0	0
+XLOC_000025	826392	803108
+XLOC_000026	0	0
+XLOC_000027	0	0
+XLOC_000028	0	0
+XLOC_000029	66791.3	324548
+XLOC_000030	1.6359e+07	0
+XLOC_000031	0	0
+XLOC_000032	1.5136e+07	0
+XLOC_000033	0	0
+XLOC_000034	0	9.45986e+06
+XLOC_000035	0	2.80837e+07
+XLOC_000036	3.784e+06	0
+XLOC_000037	5.10781e+06	2.08209e+06
+XLOC_000038	0	0
+XLOC_000039	0	0
+XLOC_000040	48522.7	424400
+XLOC_000041	0	0
+XLOC_000042	0	3.03053e+07
+XLOC_000043	8.616e+07	0
+XLOC_000044	0	5.79991e+07
+XLOC_000045	0	0
+XLOC_000046	0	2.35423e+09
+XLOC_000047	0	0
+XLOC_000048	0	0
+XLOC_000049	228872	47662.2
+XLOC_000050	0	0
+XLOC_000051	0	0
+XLOC_000052	0	2.61334e+07
+XLOC_000053	0	0
+XLOC_000054	0	0
+XLOC_000055	0	0
+XLOC_000056	0	0
+XLOC_000057	0	1.11503e+07
+XLOC_000058	1.55919e+07	0
+XLOC_000059	294879	85971.3
+XLOC_000060	807732	156995
+XLOC_000061	0	0
+XLOC_000062	0	0
+XLOC_000063	0	0
+XLOC_000064	0	0
+XLOC_000065	0	0
+XLOC_000066	0	0
+XLOC_000067	7.68169e+06	0
+XLOC_000068	504790	0
+XLOC_000069	1.02717e+08	0
+XLOC_000070	3.81001e+06	0
+XLOC_000071	0	0
+XLOC_000072	5.53654e+07	0
+XLOC_000073	0	0
+XLOC_000074	6.28966e+07	0
+XLOC_000075	0	0
+XLOC_000076	0	0
+XLOC_000077	0	0
+XLOC_000078	0	0
+XLOC_000079	0	0
+XLOC_000080	0	0
+XLOC_000081	0	0
+XLOC_000082	0	0
+XLOC_000083	0	0
+XLOC_000084	0	0
+XLOC_000085	0	0
+XLOC_000086	0	0
+XLOC_000087	0	0
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/isoforms.count_table	Tue Jun 16 16:58:39 2020 +0000
@@ -0,0 +1,91 @@
+tracking_id	in1_0	in2_0
+TCONS_00000001	0	1.94365
+TCONS_00000002	0	0.971825
+TCONS_00000003	0	0
+TCONS_00000009	0	2.91548
+TCONS_00000010	0	0.971825
+TCONS_00000011	0	0
+TCONS_00000012	0	3.8873
+TCONS_00000013	0	0.971825
+TCONS_00000014	0	0
+TCONS_00000015	0	0
+TCONS_00000016	0	0
+TCONS_00000017	0	0
+TCONS_00000018	0	0
+TCONS_00000019	0	0
+TCONS_00000020	3	2.91548
+TCONS_00000021	0	0
+TCONS_00000022	3	14.5774
+TCONS_00000023	0	0
+TCONS_00000024	0	1.94365
+TCONS_00000025	0	3.8873
+TCONS_00000026	1.9812	0.971825
+TCONS_00000027	1	8.74643
+TCONS_00000028	0	1.94365
+TCONS_00000029	0	1.94365
+TCONS_00000030	0	1.94365
+TCONS_00000031	0	0
+TCONS_00000033	0	0.971825
+TCONS_00000034	0	0.971825
+TCONS_00000037	0	0
+TCONS_00000038	0	0
+TCONS_00000039	0	0
+TCONS_00000040	0	0
+TCONS_00000041	0	0
+TCONS_00000042	0	0
+TCONS_00000043	0	0
+TCONS_00000044	0	0
+TCONS_00000045	0	0
+TCONS_00000046	0	0
+TCONS_00000047	0	0
+TCONS_00000048	0	0
+TCONS_00000049	0	0
+TCONS_00000050	0	0
+TCONS_00000051	0	0
+TCONS_00000052	0	0
+TCONS_00000053	0	0
+TCONS_00000054	62	90.3798
+TCONS_00000055	34	34.9857
+TCONS_00000056	35	68.0278
+TCONS_00000057	1	0.971825
+TCONS_00000058	0	0
+TCONS_00000059	0	0
+TCONS_00000060	0	0
+TCONS_00000062	0	0
+TCONS_00000063	0	0
+TCONS_00000065	2	0
+TCONS_00000066	4	0
+TCONS_00000067	0	0
+TCONS_00000068	1	0
+TCONS_00000069	1.0188	0
+TCONS_00000070	0	0
+TCONS_00000071	0	0
+TCONS_00000072	0	0
+TCONS_00000073	1	0
+TCONS_00000074	0	0
+TCONS_00000075	0	0
+TCONS_00000076	14	2.91548
+TCONS_00000077	0	0
+TCONS_00000078	0	0
+TCONS_00000079	0	0
+TCONS_00000080	0	0
+TCONS_00000081	0	0
+TCONS_00000082	0	0
+TCONS_00000083	1	0
+TCONS_00000084	10	2.91548
+TCONS_00000085	5	0.971825
+TCONS_00000086	0	0
+TCONS_00000087	0	0
+TCONS_00000088	0	0
+TCONS_00000089	0	0
+TCONS_00000090	1	0
+TCONS_00000091	4	0
+TCONS_00000092	1	0
+TCONS_00000093	2	0
+TCONS_00000094	3	0
+TCONS_00000095	1	0
+TCONS_00000096	0	0
+TCONS_00000097	0	0
+TCONS_00000098	0	0
+TCONS_00000099	0	0
+TCONS_00000100	0	0
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/isoforms.fpkm_table	Tue Jun 16 16:58:39 2020 +0000
@@ -0,0 +1,91 @@
+tracking_id	in1_0	in2_0
+TCONS_00000001	0	9.45986e+06
+TCONS_00000002	0	2.43637e+08
+TCONS_00000003	0	0
+TCONS_00000009	0	9.7002e+07
+TCONS_00000010	0	4.72993e+06
+TCONS_00000011	0	0
+TCONS_00000012	0	6.86386e+06
+TCONS_00000013	0	2.43637e+08
+TCONS_00000014	0	0
+TCONS_00000015	0	0
+TCONS_00000016	0	0
+TCONS_00000017	0	0
+TCONS_00000018	0	0
+TCONS_00000019	0	0
+TCONS_00000020	826392	803108
+TCONS_00000021	0	0
+TCONS_00000022	66791.3	324548
+TCONS_00000023	0	0
+TCONS_00000024	0	9.45986e+06
+TCONS_00000025	0	2.80837e+07
+TCONS_00000026	4.24463e+06	2.08209e+06
+TCONS_00000027	48522.7	424400
+TCONS_00000028	0	3.03053e+07
+TCONS_00000029	0	5.79991e+07
+TCONS_00000030	0	2.35423e+09
+TCONS_00000031	0	0
+TCONS_00000033	0	2.61334e+07
+TCONS_00000034	0	1.11503e+07
+TCONS_00000037	0	0
+TCONS_00000038	0	0
+TCONS_00000039	0	0
+TCONS_00000040	0	0
+TCONS_00000041	0	0
+TCONS_00000042	0	0
+TCONS_00000043	0	0
+TCONS_00000044	0	0
+TCONS_00000045	0	0
+TCONS_00000046	0	0
+TCONS_00000047	0	0
+TCONS_00000048	0	0
+TCONS_00000049	0	0
+TCONS_00000050	0	0
+TCONS_00000051	0	0
+TCONS_00000052	0	0
+TCONS_00000053	0	0
+TCONS_00000054	358326	522345
+TCONS_00000055	408511	420354
+TCONS_00000056	433286	842157
+TCONS_00000057	3.44151e+06	3.34455e+06
+TCONS_00000058	0	0
+TCONS_00000059	0	0
+TCONS_00000060	0	0
+TCONS_00000062	0	0
+TCONS_00000063	0	0
+TCONS_00000065	1.6359e+07	0
+TCONS_00000066	1.5136e+07	0
+TCONS_00000067	0	0
+TCONS_00000068	3.784e+06	0
+TCONS_00000069	863189	0
+TCONS_00000070	0	0
+TCONS_00000071	0	0
+TCONS_00000072	0	0
+TCONS_00000073	8.616e+07	0
+TCONS_00000074	0	0
+TCONS_00000075	0	0
+TCONS_00000076	228872	47662.2
+TCONS_00000077	0	0
+TCONS_00000078	0	0
+TCONS_00000079	0	0
+TCONS_00000080	0	0
+TCONS_00000081	0	0
+TCONS_00000082	0	0
+TCONS_00000083	1.55919e+07	0
+TCONS_00000084	294879	85971.3
+TCONS_00000085	807732	156995
+TCONS_00000086	0	0
+TCONS_00000087	0	0
+TCONS_00000088	0	0
+TCONS_00000089	0	0
+TCONS_00000090	7.68169e+06	0
+TCONS_00000091	504790	0
+TCONS_00000092	1.02717e+08	0
+TCONS_00000093	3.81001e+06	0
+TCONS_00000094	5.53654e+07	0
+TCONS_00000095	6.28966e+07	0
+TCONS_00000096	0	0
+TCONS_00000097	0	0
+TCONS_00000098	0	0
+TCONS_00000099	0	0
+TCONS_00000100	0	0
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tss_groups.count_table	Tue Jun 16 16:58:39 2020 +0000
@@ -0,0 +1,89 @@
+tracking_id	in1_0	in2_0
+TSS1	0	1.94365
+TSS10	34	34.9857
+TSS11	35	68.0278
+TSS13	1	0.971825
+TSS14	0	2.91548
+TSS15	0	0.971825
+TSS16	0	0
+TSS17	0	0
+TSS18	0	3.8873
+TSS19	0	0.971825
+TSS2	0	0.971825
+TSS20	0	0
+TSS21	0	0
+TSS22	0	0
+TSS23	0	0
+TSS24	0	0
+TSS25	0	0
+TSS26	0	0
+TSS27	0	0
+TSS28	3	2.91548
+TSS29	0	0
+TSS3	0	0
+TSS30	0	0
+TSS31	0	0
+TSS32	3	14.5774
+TSS33	2	0
+TSS34	0	0
+TSS35	4	0
+TSS36	0	0
+TSS37	0	1.94365
+TSS38	0	3.8873
+TSS39	1	0
+TSS4	0	0
+TSS40	3	0.971825
+TSS41	0	0
+TSS42	0	0
+TSS43	1	8.74643
+TSS44	0	0
+TSS45	0	1.94365
+TSS46	1	0
+TSS47	0	1.94365
+TSS48	0	0
+TSS49	0	1.94365
+TSS5	0	0
+TSS50	0	0
+TSS51	0	0
+TSS52	14	2.91548
+TSS54	0	0
+TSS55	0	0
+TSS56	0	0.971825
+TSS57	0	0
+TSS58	0	0
+TSS59	0	0
+TSS6	0	0
+TSS60	0	0
+TSS61	0	0.971825
+TSS62	1	0
+TSS63	10	2.91548
+TSS65	5	0.971825
+TSS66	0	0
+TSS67	0	0
+TSS68	0	0
+TSS69	0	0
+TSS7	62	90.3798
+TSS70	0	0
+TSS71	0	0
+TSS72	0	0
+TSS73	1	0
+TSS74	4	0
+TSS75	1	0
+TSS76	2	0
+TSS77	0	0
+TSS78	3	0
+TSS79	0	0
+TSS80	1	0
+TSS81	0	0
+TSS82	0	0
+TSS83	0	0
+TSS84	0	0
+TSS85	0	0
+TSS86	0	0
+TSS87	0	0
+TSS88	0	0
+TSS89	0	0
+TSS90	0	0
+TSS91	0	0
+TSS92	0	0
+TSS93	0	0
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tss_groups.fpkm_table	Tue Jun 16 16:58:39 2020 +0000
@@ -0,0 +1,89 @@
+tracking_id	in1_0	in2_0
+TSS1	0	9.45986e+06
+TSS10	408511	420354
+TSS11	433286	842157
+TSS13	3.44151e+06	3.34455e+06
+TSS14	0	9.7002e+07
+TSS15	0	4.72993e+06
+TSS16	0	0
+TSS17	0	0
+TSS18	0	6.86386e+06
+TSS19	0	2.43637e+08
+TSS2	0	2.43637e+08
+TSS20	0	0
+TSS21	0	0
+TSS22	0	0
+TSS23	0	0
+TSS24	0	0
+TSS25	0	0
+TSS26	0	0
+TSS27	0	0
+TSS28	826392	803108
+TSS29	0	0
+TSS3	0	0
+TSS30	0	0
+TSS31	0	0
+TSS32	66791.3	324548
+TSS33	1.6359e+07	0
+TSS34	0	0
+TSS35	1.5136e+07	0
+TSS36	0	0
+TSS37	0	9.45986e+06
+TSS38	0	2.80837e+07
+TSS39	3.784e+06	0
+TSS4	0	0
+TSS40	5.10781e+06	2.08209e+06
+TSS41	0	0
+TSS42	0	0
+TSS43	48522.7	424400
+TSS44	0	0
+TSS45	0	3.03053e+07
+TSS46	8.616e+07	0
+TSS47	0	5.79991e+07
+TSS48	0	0
+TSS49	0	2.35423e+09
+TSS5	0	0
+TSS50	0	0
+TSS51	0	0
+TSS52	228872	47662.2
+TSS54	0	0
+TSS55	0	0
+TSS56	0	2.61334e+07
+TSS57	0	0
+TSS58	0	0
+TSS59	0	0
+TSS6	0	0
+TSS60	0	0
+TSS61	0	1.11503e+07
+TSS62	1.55919e+07	0
+TSS63	294879	85971.3
+TSS65	807732	156995
+TSS66	0	0
+TSS67	0	0
+TSS68	0	0
+TSS69	0	0
+TSS7	358326	522345
+TSS70	0	0
+TSS71	0	0
+TSS72	0	0
+TSS73	7.68169e+06	0
+TSS74	504790	0
+TSS75	1.02717e+08	0
+TSS76	3.81001e+06	0
+TSS77	0	0
+TSS78	5.53654e+07	0
+TSS79	0	0
+TSS80	6.28966e+07	0
+TSS81	0	0
+TSS82	0	0
+TSS83	0	0
+TSS84	0	0
+TSS85	0	0
+TSS86	0	0
+TSS87	0	0
+TSS88	0	0
+TSS89	0	0
+TSS90	0	0
+TSS91	0	0
+TSS92	0	0
+TSS93	0	0
\ No newline at end of file