# HG changeset patch
# User devteam
# Date 1433358259 14400
# Node ID 4e6f043995ff09d0c69f94b9278cfff2b9897bd0
# Parent  db57b46b05bf3b7af71ee38f28b2dde4328c76eb
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a

diff -r db57b46b05bf -r 4e6f043995ff cuffdiff_wrapper.xml
--- a/cuffdiff_wrapper.xml	Wed May 13 11:04:49 2015 -0400
+++ b/cuffdiff_wrapper.xml	Wed Jun 03 15:04:19 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="cuffdiff" name="Cuffdiff" version="@VERSION@.1">
+<tool id="cuffdiff" name="Cuffdiff" version="@VERSION@.2">
     <description>find significant changes in transcript expression, splicing, and promoter use</description>
     <requirements>
         <requirement type="set_environment">CUFFDIFF_SCRIPT_PATH</requirement>
@@ -68,12 +68,16 @@
             $gtf_input
 
             @CONDITION_SAMPLES@
-            &&
-            R --vanilla --no-save -f \$CUFFDIFF_SCRIPT_PATH/cummeRbund.R && mv cummeRbund.sqlite "${output_cummerbund}"
+            #if $generate_sqlite:
+                &&
+                R --vanilla --no-save -f \$CUFFDIFF_SCRIPT_PATH/cummeRbund.R && mv cummeRbund.sqlite "${output_cummerbund}"
+            #end if
             ]]>
     </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."/>
+        <param name="omit_tabular_output" type="boolean" truevalue="yes" falsevalue="no" label="Omit Tabular Datasets" help="Discard the tabular output." />
+        <param name="generate_sqlite" type="boolean" truevalue="yes" falsevalue="no" label="Generate SQLite" help="Generate a SQLite database for use with cummeRbund." />
         <expand macro="condition_inputs" />
         <param name="library_norm_method" type="select" label="Library normalization method">
             <option value="geometric" selected="True">geometric</option>
@@ -186,7 +190,77 @@
         </conditional>
     </inputs>
     <outputs>
-        <data format="sqlite" name="output_cummerbund" label="${tool.name} on ${on_string}: cummeRbund SQLite database" />
+        <!-- Optional read group datasets. -->
+        <data format="tabular" name="isoforms_read_group" label="${tool.name} on ${on_string}: isoforms read group tracking" from_work_dir="isoforms.read_group_tracking" >
+            <filter>(include_read_group_files == 'Yes') and not omit_tabular_output</filter>
+        </data>
+        <data format="tabular" name="genes_read_group" label="${tool.name} on ${on_string}: genes read group tracking" from_work_dir="genes.read_group_tracking" >
+            <filter>(include_read_group_files == 'Yes') and not omit_tabular_output</filter>
+        </data>
+        <data format="tabular" name="cds_read_group" label="${tool.name} on ${on_string}: CDs read group tracking" from_work_dir="cds.read_group_tracking" >
+            <filter>(include_read_group_files == 'Yes') and not omit_tabular_output</filter>
+        </data>
+        <data format="tabular" name="tss_groups_read_group" label="${tool.name} on ${on_string}: TSS groups read group tracking" from_work_dir="tss_groups.read_group_tracking" >
+            <filter>(include_read_group_files == 'Yes') and not omit_tabular_output</filter>
+        </data>
+        <data format="text" name="read_group_info" label="${tool.name} on ${on_string}: read group info" from_work_dir="read_groups.info" >
+            <filter>(include_read_group_files == 'Yes') and not omit_tabular_output</filter>
+        </data>
+        <data format="text" name="run_info" label="${tool.name} on ${on_string}: run info" from_work_dir="run.info" >
+            <filter>(include_read_group_files == 'Yes') and not omit_tabular_output</filter>
+        </data>
+        <!-- Standard datasets. -->
+        <data format="tabular" name="splicing_diff" label="${tool.name} on ${on_string}: splicing differential expression testing" from_work_dir="splicing.diff">
+                <filter>not omit_tabular_output</filter>
+        </data>
+        <data format="tabular" name="promoters_diff" label="${tool.name} on ${on_string}: promoters differential expression testing" from_work_dir="promoters.diff">
+                <filter>not omit_tabular_output</filter>
+        </data>
+        <data format="tabular" name="cds_diff" label="${tool.name} on ${on_string}: CDS overloading diffential expression testing" from_work_dir="cds.diff">
+                <filter>not omit_tabular_output</filter>
+        </data>
+        <data format="tabular" name="cds_exp_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM differential expression testing" from_work_dir="cds_exp.diff">
+                <filter>not omit_tabular_output</filter>
+        </data>
+        <data format="tabular" name="cds_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM tracking" from_work_dir="cds.fpkm_tracking">
+                <filter>not omit_tabular_output</filter>
+        </data>
+        <data format="tabular" name="cds_count_tracking" label="${tool.name} on ${on_string}: CDS count tracking" from_work_dir="cds.count_tracking" >
+                <filter>(include_count_files == 'Yes') and not omit_tabular_output</filter>
+        </data>
+
+        <data format="tabular" name="tss_groups_exp" label="${tool.name} on ${on_string}: TSS groups differential expression testing" from_work_dir="tss_group_exp.diff">
+                <filter>not omit_tabular_output</filter>
+        </data>
+        <data format="tabular" name="tss_groups_fpkm_tracking" label="${tool.name} on ${on_string}: TSS groups FPKM tracking" from_work_dir="tss_groups.fpkm_tracking">
+                <filter>not omit_tabular_output</filter>
+        </data>
+        <data format="tabular" name="tss_groups_count_tracking" label="${tool.name} on ${on_string}: TSS count FPKM tracking" from_work_dir="tss_groups.count_tracking" >
+                <filter>(include_count_files == 'Yes') and not omit_tabular_output</filter>
+        </data>
+
+        <data format="tabular" name="genes_exp" label="${tool.name} on ${on_string}: gene differential expression testing" from_work_dir="gene_exp.diff">
+                <filter>not omit_tabular_output</filter>
+        </data>
+        <data format="tabular" name="genes_fpkm_tracking" label="${tool.name} on ${on_string}: gene FPKM tracking" from_work_dir="genes.fpkm_tracking">
+            <filter>not omit_tabular_output</filter>
+        </data>
+        <data format="tabular" name="genes_count_tracking" label="${tool.name} on ${on_string}: gene count tracking" from_work_dir="genes.count_tracking" >
+            <filter>(include_count_files == 'Yes') and not omit_tabular_output</filter>
+        </data>
+
+        <data format="tabular" name="isoforms_exp" label="${tool.name} on ${on_string}: transcript differential expression testing" from_work_dir="isoform_exp.diff">
+            <filter>not omit_tabular_output</filter>
+        </data>
+        <data format="tabular" name="isoforms_fpkm_tracking" label="${tool.name} on ${on_string}: transcript FPKM tracking" from_work_dir="isoforms.fpkm_tracking">
+            <filter>not omit_tabular_output</filter>
+        </data>
+        <data format="tabular" name="isoforms_count_tracking" label="${tool.name} on ${on_string}: transcript count tracking" from_work_dir="isoforms.count_tracking">
+            <filter>(include_count_files == 'Yes') and not omit_tabular_output</filter>
+        </data>
+        <data format="sqlite" name="output_cummerbund" label="${tool.name} on ${on_string}: cummeRbund SQLite database">
+            <filter>generate_sqlite</filter>
+        </data>
     </outputs>
 
     <tests>
@@ -194,7 +268,9 @@
                 <!--
                     cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam 
                 -->
-                <param name="gtf_input" value="cuffcompare_out5.gtf" ftype="gtf" />
+                <param name="gtf_input" value="cuffdiff_in1.gtf" ftype="gtf" />
+                <param name="generate_sqlite" value="yes" />
+                <param name="omit_tabular_output" value="yes" />
                 <conditional name="in_type">
                     <param name="set_in_type" value="BAM" />
                     <repeat name="conditions">
@@ -218,6 +294,45 @@
                 <param name="sAdditional" value="No"/>
                 <output name="output_cummerbund" ftype="sqlite" file="cuffdiff_out.sqlite"/>
         </test>
+        <test>
+                <!--
+                    cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam 
+                -->
+                <param name="gtf_input" value="cuffdiff_in1.gtf" ftype="gtf" />
+                <param name="omit_tabular_output" value="no" />
+                <conditional name="in_type">
+                    <param name="set_in_type" value="BAM" />
+                    <repeat name="conditions">
+                        <param name="name" value="q1" />
+                        <repeat name="samples">
+                            <param name="sample" value="cuffdiff_in1.sam" ftype="sam" />
+                        </repeat>
+                    </repeat>
+                    <repeat name="conditions">
+                        <param name="name" value="q2" />
+                        <repeat name="samples">
+                            <param name="sample" value="cuffdiff_in2.sam" ftype="sam" />
+                        </repeat>
+                    </repeat>
+                </conditional>
+                <param name="fdr" value="0.05" />
+                <param name="min_alignment_count" value="0" />
+                <param name="do_bias_correction" value="No" />
+                <param name="do_normalization" value="No" />
+                <param name="multiread_correct" value="No"/>
+                <param name="sAdditional" value="No"/>
+                <output name="splicing_diff" file="splicing.diff"/>
+                <output name="promoters_diff" file="promoters.diff"/>
+                <output name="cds_diff" file="cds.diff"/>
+                <output name="cds_exp_fpkm_tracking" file="cds.exp_fpkm_tracking"/>
+                <output name="cds_fpkm_tracking" file="cds.fpkm_tracking"/>
+                <output name="tss_groups_exp" file="tss.groups_exp" lines_diff="200"/>
+                <output name="tss_groups_fpkm_tracking" file="tss.groups_fpkm_tracking"/>
+                <output name="genes_exp" file="genes.exp" lines_diff="200"/>
+                <output name="genes_fpkm_tracking" file="genes.fpkm_tracking" lines_diff="200"/>
+                <output name="isoforms_exp" file="isoforms.exp" lines_diff="200"/>
+                <output name="isoforms_fpkm_tracking" file="isoforms.fpkm_tracking" lines_diff="200"/>
+        </test>
     </tests>
     <help>
 **Cuffdiff Overview**
diff -r db57b46b05bf -r 4e6f043995ff test-data/cds.diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cds.diff	Wed Jun 03 15:04:19 2015 -0400
@@ -0,0 +1,1 @@
+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 db57b46b05bf -r 4e6f043995ff test-data/cds.exp_fpkm_tracking
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cds.exp_fpkm_tracking	Wed Jun 03 15:04:19 2015 -0400
@@ -0,0 +1,1 @@
+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 db57b46b05bf -r 4e6f043995ff test-data/cds.fpkm_tracking
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cds.fpkm_tracking	Wed Jun 03 15:04:19 2015 -0400
@@ -0,0 +1,1 @@
+tracking_id	class_code	nearest_ref_id	gene_id	gene_short_name	tss_id	locus	length	coverage
diff -r db57b46b05bf -r 4e6f043995ff test-data/cuffcompare_out5.gtf
--- a/test-data/cuffcompare_out5.gtf	Wed May 13 11:04:49 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,90 +0,0 @@
-chr1	Cufflinks	exon	3204755	3204833	.	-	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.13.1"; nearest_ref "Xkr4"; class_code "c"; tss_id "TSS1";
-chr1	Cufflinks	exon	3111450	3111490	.	.	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "1"; oId "CUFF.1.1"; class_code "u"; tss_id "TSS2";
-chr1	Cufflinks	exon	3111546	3111576	.	.	.	gene_id "XLOC_000003"; transcript_id "TCONS_00000003"; exon_number "1"; oId "CUFF.3.1"; class_code "u"; tss_id "TSS3";
-chr1	Cufflinks	exon	3174766	3174792	.	.	.	gene_id "XLOC_000004"; transcript_id "TCONS_00000051"; exon_number "1"; oId "CUFF.1.1"; class_code "u"; tss_id "TSS4";
-chr1	Cufflinks	exon	3187402	3187428	.	.	.	gene_id "XLOC_000005"; transcript_id "TCONS_00000052"; exon_number "1"; oId "CUFF.3.1"; class_code "u"; tss_id "TSS5";
-chr1	Cufflinks	exon	3188522	3188548	.	.	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000053"; exon_number "1"; oId "CUFF.5.1"; class_code "u"; tss_id "TSS6";
-chr1	Cufflinks	exon	3189811	3190789	.	.	.	gene_id "XLOC_000007"; transcript_id "TCONS_00000054"; exon_number "1"; oId "CUFF.11.1"; class_code "u"; tss_id "TSS7";
-chr1	Cufflinks	exon	3190859	3191434	.	.	.	gene_id "XLOC_000008"; transcript_id "TCONS_00000055"; exon_number "1"; oId "CUFF.7.1"; class_code "u"; tss_id "TSS10";
-chr1	Cufflinks	exon	3191513	3192077	.	.	.	gene_id "XLOC_000009"; transcript_id "TCONS_00000056"; exon_number "1"; oId "CUFF.9.1"; class_code "u"; tss_id "TSS11";
-chr1	Cufflinks	exon	3192251	3192336	.	.	.	gene_id "XLOC_000010"; transcript_id "TCONS_00000057"; exon_number "1"; oId "CUFF.13.1"; class_code "u"; tss_id "TSS13";
-chr1	Cufflinks	exon	3192442	3192494	.	.	.	gene_id "XLOC_000011"; transcript_id "TCONS_00000009"; exon_number "1"; oId "CUFF.39.1"; class_code "u"; tss_id "TSS14";
-chr1	Cufflinks	exon	3192551	3192629	.	.	.	gene_id "XLOC_000012"; transcript_id "TCONS_00000010"; exon_number "1"; oId "CUFF.41.1"; class_code "u"; tss_id "TSS15";
-chr1	Cufflinks	exon	3192650	3192676	.	.	.	gene_id "XLOC_000013"; transcript_id "TCONS_00000058"; exon_number "1"; oId "CUFF.15.1"; class_code "u"; tss_id "TSS16";
-chr1	Cufflinks	exon	3192732	3192811	.	.	.	gene_id "XLOC_000014"; transcript_id "TCONS_00000011"; exon_number "1"; oId "CUFF.43.1"; class_code "u"; tss_id "TSS17";
-chr1	Cufflinks	exon	3192941	3193042	.	.	.	gene_id "XLOC_000015"; transcript_id "TCONS_00000012"; exon_number "1"; oId "CUFF.45.1"; class_code "u"; tss_id "TSS18";
-chr1	Cufflinks	exon	3194186	3194226	.	.	.	gene_id "XLOC_000016"; transcript_id "TCONS_00000013"; exon_number "1"; oId "CUFF.47.1"; class_code "u"; tss_id "TSS19";
-chr1	Cufflinks	exon	3194303	3194329	.	.	.	gene_id "XLOC_000017"; transcript_id "TCONS_00000014"; exon_number "1"; oId "CUFF.49.1"; class_code "u"; tss_id "TSS20";
-chr1	Cufflinks	exon	3194707	3194733	.	.	.	gene_id "XLOC_000018"; transcript_id "TCONS_00000059"; exon_number "1"; oId "CUFF.17.1"; class_code "u"; tss_id "TSS21";
-chr1	Cufflinks	exon	3195084	3195110	.	.	.	gene_id "XLOC_000019"; transcript_id "TCONS_00000015"; exon_number "1"; oId "CUFF.51.1"; class_code "u"; tss_id "TSS22";
-chr1	Cufflinks	exon	3195451	3195477	.	.	.	gene_id "XLOC_000020"; transcript_id "TCONS_00000016"; exon_number "1"; oId "CUFF.53.1"; class_code "u"; tss_id "TSS23";
-chr1	Cufflinks	exon	3197090	3197116	.	.	.	gene_id "XLOC_000021"; transcript_id "TCONS_00000017"; exon_number "1"; oId "CUFF.55.1"; class_code "u"; tss_id "TSS24";
-chr1	Cufflinks	exon	3197247	3197273	.	.	.	gene_id "XLOC_000022"; transcript_id "TCONS_00000018"; exon_number "1"; oId "CUFF.57.1"; class_code "u"; tss_id "TSS25";
-chr1	Cufflinks	exon	3197347	3197373	.	.	.	gene_id "XLOC_000023"; transcript_id "TCONS_00000019"; exon_number "1"; oId "CUFF.59.1"; class_code "u"; tss_id "TSS26";
-chr1	Cufflinks	exon	3197426	3197452	.	.	.	gene_id "XLOC_000024"; transcript_id "TCONS_00000060"; exon_number "1"; oId "CUFF.19.1"; class_code "u"; tss_id "TSS27";
-chr1	Cufflinks	exon	3200023	3200191	.	.	.	gene_id "XLOC_000025"; transcript_id "TCONS_00000020"; exon_number "1"; oId "CUFF.7.1"; class_code "u"; tss_id "TSS28";
-chr1	Cufflinks	exon	3200326	3200352	.	.	.	gene_id "XLOC_000026"; transcript_id "TCONS_00000021"; exon_number "1"; oId "CUFF.5.1"; class_code "u"; tss_id "TSS29";
-chr1	Cufflinks	exon	3200431	3200457	.	.	.	gene_id "XLOC_000027"; transcript_id "TCONS_00000062"; exon_number "1"; oId "CUFF.21.1"; class_code "u"; tss_id "TSS30";
-chr1	Cufflinks	exon	3201008	3201039	.	.	.	gene_id "XLOC_000028"; transcript_id "TCONS_00000063"; exon_number "1"; oId "CUFF.26.1"; class_code "u"; tss_id "TSS31";
-chr1	Cufflinks	exon	3201078	3201481	.	.	.	gene_id "XLOC_000029"; transcript_id "TCONS_00000022"; exon_number "1"; oId "CUFF.9.1"; class_code "u"; tss_id "TSS32";
-chr1	Cufflinks	exon	3201597	3201666	.	.	.	gene_id "XLOC_000030"; transcript_id "TCONS_00000065"; exon_number "1"; oId "CUFF.29.1"; class_code "u"; tss_id "TSS33";
-chr1	Cufflinks	exon	3201673	3201699	.	.	.	gene_id "XLOC_000031"; transcript_id "TCONS_00000023"; exon_number "1"; oId "CUFF.11.1"; class_code "u"; tss_id "TSS34";
-chr1	Cufflinks	exon	3201726	3201809	.	.	.	gene_id "XLOC_000032"; transcript_id "TCONS_00000066"; exon_number "1"; oId "CUFF.31.1"; class_code "u"; tss_id "TSS35";
-chr1	Cufflinks	exon	3211522	3211561	.	.	.	gene_id "XLOC_000033"; transcript_id "TCONS_00000067"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.33.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS36";
-chr1	Cufflinks	exon	3212214	3212292	.	.	.	gene_id "XLOC_000034"; transcript_id "TCONS_00000024"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.15.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS37";
-chr1	Cufflinks	exon	3212368	3212439	.	.	.	gene_id "XLOC_000035"; transcript_id "TCONS_00000025"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.19.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS38";
-chr1	Cufflinks	exon	3212718	3212801	.	.	.	gene_id "XLOC_000036"; transcript_id "TCONS_00000068"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.35.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS39";
-chr1	Cufflinks	exon	3213096	3213192	.	.	.	gene_id "XLOC_000037"; transcript_id "TCONS_00000026"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.17.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS40";
-chr1	Cufflinks	exon	3213119	3213242	.	.	.	gene_id "XLOC_000037"; transcript_id "TCONS_00000069"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.37.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS40";
-chr1	Cufflinks	exon	3240607	3240633	.	.	.	gene_id "XLOC_000038"; transcript_id "TCONS_00000070"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.39.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS41";
-chr1	Cufflinks	exon	3242480	3242512	.	.	.	gene_id "XLOC_000039"; transcript_id "TCONS_00000071"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.41.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS42";
-chr1	Cufflinks	exon	3242634	3242923	.	.	.	gene_id "XLOC_000040"; transcript_id "TCONS_00000027"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.25.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS43";
-chr1	Cufflinks	exon	3242925	3243005	.	.	.	gene_id "XLOC_000041"; transcript_id "TCONS_00000072"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.43.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS44";
-chr1	Cufflinks	exon	3243019	3243079	.	.	.	gene_id "XLOC_000042"; transcript_id "TCONS_00000028"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.21.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS45";
-chr1	Cufflinks	exon	3243109	3243154	.	.	.	gene_id "XLOC_000043"; transcript_id "TCONS_00000073"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.45.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS46";
-chr1	Cufflinks	exon	3243348	3243401	.	.	.	gene_id "XLOC_000044"; transcript_id "TCONS_00000029"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.23.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS47";
-chr1	Cufflinks	exon	3254080	3254106	.	.	.	gene_id "XLOC_000045"; transcript_id "TCONS_00000074"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.47.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS48";
-chr1	Cufflinks	exon	3256975	3257011	.	.	.	gene_id "XLOC_000046"; transcript_id "TCONS_00000030"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.27.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS49";
-chr1	Cufflinks	exon	3277156	3277182	.	.	.	gene_id "XLOC_000047"; transcript_id "TCONS_00000075"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.49.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS50";
-chr1	Cufflinks	exon	3277191	3277218	.	.	.	gene_id "XLOC_000048"; transcript_id "TCONS_00000031"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.61.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS51";
-chr1	Cufflinks	exon	3277914	3278390	.	.	.	gene_id "XLOC_000049"; transcript_id "TCONS_00000076"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.51.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS52";
-chr1	Cufflinks	exon	3280118	3280144	.	.	.	gene_id "XLOC_000050"; transcript_id "TCONS_00000077"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.53.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS54";
-chr1	Cufflinks	exon	3280499	3280525	.	.	.	gene_id "XLOC_000051"; transcript_id "TCONS_00000078"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.55.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS55";
-chr1	Cufflinks	exon	3280687	3280741	.	.	.	gene_id "XLOC_000052"; transcript_id "TCONS_00000033"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.65.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS56";
-chr1	Cufflinks	exon	3282505	3282531	.	.	.	gene_id "XLOC_000053"; transcript_id "TCONS_00000079"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.57.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS57";
-chr1	Cufflinks	exon	3282651	3282677	.	.	.	gene_id "XLOC_000054"; transcript_id "TCONS_00000080"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.59.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS58";
-chr1	Cufflinks	exon	3282761	3282832	.	.	.	gene_id "XLOC_000055"; transcript_id "TCONS_00000081"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.61.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS59";
-chr1	Cufflinks	exon	3284967	3284993	.	.	.	gene_id "XLOC_000056"; transcript_id "TCONS_00000082"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.63.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS60";
-chr1	Cufflinks	exon	3290489	3290553	.	.	.	gene_id "XLOC_000057"; transcript_id "TCONS_00000034"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.67.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS61";
-chr1	Cufflinks	exon	3290799	3290859	.	.	.	gene_id "XLOC_000058"; transcript_id "TCONS_00000083"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.65.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS62";
-chr1	Cufflinks	exon	3290920	3291273	.	.	.	gene_id "XLOC_000059"; transcript_id "TCONS_00000084"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.69.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS63";
-chr1	Cufflinks	exon	3299444	3299640	.	.	.	gene_id "XLOC_000060"; transcript_id "TCONS_00000085"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.67.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS65";
-chr1	Cufflinks	exon	3299610	3299664	.	.	.	gene_id "XLOC_000060"; transcript_id "TCONS_00000037"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.73.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS66";
-chr1	Cufflinks	exon	3299692	3299733	.	.	.	gene_id "XLOC_000061"; transcript_id "TCONS_00000086"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.71.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS67";
-chr1	Cufflinks	exon	3300052	3300078	.	.	.	gene_id "XLOC_000062"; transcript_id "TCONS_00000038"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.75.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS68";
-chr1	Cufflinks	exon	3307749	3307775	.	.	.	gene_id "XLOC_000063"; transcript_id "TCONS_00000087"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.73.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS69";
-chr1	Cufflinks	exon	3318621	3318647	.	.	.	gene_id "XLOC_000064"; transcript_id "TCONS_00000088"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.75.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS70";
-chr1	Cufflinks	exon	3319000	3319051	.	.	.	gene_id "XLOC_000065"; transcript_id "TCONS_00000039"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.77.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS71";
-chr1	Cufflinks	exon	3330528	3330554	.	.	.	gene_id "XLOC_000066"; transcript_id "TCONS_00000089"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.77.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS72";
-chr1	Cufflinks	exon	3351241	3351311	.	.	.	gene_id "XLOC_000067"; transcript_id "TCONS_00000090"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.79.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS73";
-chr1	Cufflinks	exon	3355888	3355914	.	.	.	gene_id "XLOC_000068"; transcript_id "TCONS_00000040"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.79.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS74";
-chr1	Cufflinks	exon	3355908	3356119	.	.	.	gene_id "XLOC_000068"; transcript_id "TCONS_00000091"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.81.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS74";
-chr1	Cufflinks	exon	3356181	3356225	.	.	.	gene_id "XLOC_000069"; transcript_id "TCONS_00000092"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.83.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS75";
-chr1	Cufflinks	exon	3363077	3363176	.	.	.	gene_id "XLOC_000070"; transcript_id "TCONS_00000093"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.85.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS76";
-chr1	Cufflinks	exon	3363215	3363278	.	.	.	gene_id "XLOC_000071"; transcript_id "TCONS_00000041"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.81.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS77";
-chr1	Cufflinks	exon	3363388	3363446	.	.	.	gene_id "XLOC_000072"; transcript_id "TCONS_00000094"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.87.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS78";
-chr1	Cufflinks	exon	3363754	3363849	.	.	.	gene_id "XLOC_000073"; transcript_id "TCONS_00000042"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.83.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS79";
-chr1	Cufflinks	exon	3364872	3364919	.	.	.	gene_id "XLOC_000074"; transcript_id "TCONS_00000095"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.89.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS80";
-chr1	Cufflinks	exon	3367136	3367162	.	.	.	gene_id "XLOC_000075"; transcript_id "TCONS_00000043"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.85.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS81";
-chr1	Cufflinks	exon	3367211	3367237	.	.	.	gene_id "XLOC_000076"; transcript_id "TCONS_00000096"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.91.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS82";
-chr1	Cufflinks	exon	3367334	3367382	.	.	.	gene_id "XLOC_000077"; transcript_id "TCONS_00000044"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.87.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS83";
-chr1	Cufflinks	exon	3369581	3369607	.	.	.	gene_id "XLOC_000078"; transcript_id "TCONS_00000097"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.93.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS84";
-chr1	Cufflinks	exon	3375002	3375028	.	.	.	gene_id "XLOC_000079"; transcript_id "TCONS_00000098"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.95.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS85";
-chr1	Cufflinks	exon	3377212	3377262	.	.	.	gene_id "XLOC_000080"; transcript_id "TCONS_00000045"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.89.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS86";
-chr1	Cufflinks	exon	3379889	3379915	.	.	.	gene_id "XLOC_000081"; transcript_id "TCONS_00000099"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.97.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS87";
-chr1	Cufflinks	exon	3386740	3386836	.	.	.	gene_id "XLOC_000082"; transcript_id "TCONS_00000100"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.99.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS88";
-chr1	Cufflinks	exon	3391326	3391352	.	.	.	gene_id "XLOC_000083"; transcript_id "TCONS_00000046"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.91.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS89";
-chr1	Cufflinks	exon	3435842	3435880	.	.	.	gene_id "XLOC_000084"; transcript_id "TCONS_00000047"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.93.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS90";
-chr1	Cufflinks	exon	3447762	3447788	.	.	.	gene_id "XLOC_000085"; transcript_id "TCONS_00000048"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.95.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS91";
-chr1	Cufflinks	exon	3450907	3450965	.	.	.	gene_id "XLOC_000086"; transcript_id "TCONS_00000049"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.97.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS92";
-chr1	Cufflinks	exon	3451052	3451109	.	.	.	gene_id "XLOC_000087"; transcript_id "TCONS_00000050"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.99.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS93";
diff -r db57b46b05bf -r 4e6f043995ff test-data/cuffdiff_in1.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffdiff_in1.gtf	Wed Jun 03 15:04:19 2015 -0400
@@ -0,0 +1,90 @@
+chr1	Cufflinks	exon	3204755	3204833	.	-	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.13.1"; nearest_ref "Xkr4"; class_code "c"; tss_id "TSS1";
+chr1	Cufflinks	exon	3111450	3111490	.	.	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "1"; oId "CUFF.1.1"; class_code "u"; tss_id "TSS2";
+chr1	Cufflinks	exon	3111546	3111576	.	.	.	gene_id "XLOC_000003"; transcript_id "TCONS_00000003"; exon_number "1"; oId "CUFF.3.1"; class_code "u"; tss_id "TSS3";
+chr1	Cufflinks	exon	3174766	3174792	.	.	.	gene_id "XLOC_000004"; transcript_id "TCONS_00000051"; exon_number "1"; oId "CUFF.1.1"; class_code "u"; tss_id "TSS4";
+chr1	Cufflinks	exon	3187402	3187428	.	.	.	gene_id "XLOC_000005"; transcript_id "TCONS_00000052"; exon_number "1"; oId "CUFF.3.1"; class_code "u"; tss_id "TSS5";
+chr1	Cufflinks	exon	3188522	3188548	.	.	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000053"; exon_number "1"; oId "CUFF.5.1"; class_code "u"; tss_id "TSS6";
+chr1	Cufflinks	exon	3189811	3190789	.	.	.	gene_id "XLOC_000007"; transcript_id "TCONS_00000054"; exon_number "1"; oId "CUFF.11.1"; class_code "u"; tss_id "TSS7";
+chr1	Cufflinks	exon	3190859	3191434	.	.	.	gene_id "XLOC_000008"; transcript_id "TCONS_00000055"; exon_number "1"; oId "CUFF.7.1"; class_code "u"; tss_id "TSS10";
+chr1	Cufflinks	exon	3191513	3192077	.	.	.	gene_id "XLOC_000009"; transcript_id "TCONS_00000056"; exon_number "1"; oId "CUFF.9.1"; class_code "u"; tss_id "TSS11";
+chr1	Cufflinks	exon	3192251	3192336	.	.	.	gene_id "XLOC_000010"; transcript_id "TCONS_00000057"; exon_number "1"; oId "CUFF.13.1"; class_code "u"; tss_id "TSS13";
+chr1	Cufflinks	exon	3192442	3192494	.	.	.	gene_id "XLOC_000011"; transcript_id "TCONS_00000009"; exon_number "1"; oId "CUFF.39.1"; class_code "u"; tss_id "TSS14";
+chr1	Cufflinks	exon	3192551	3192629	.	.	.	gene_id "XLOC_000012"; transcript_id "TCONS_00000010"; exon_number "1"; oId "CUFF.41.1"; class_code "u"; tss_id "TSS15";
+chr1	Cufflinks	exon	3192650	3192676	.	.	.	gene_id "XLOC_000013"; transcript_id "TCONS_00000058"; exon_number "1"; oId "CUFF.15.1"; class_code "u"; tss_id "TSS16";
+chr1	Cufflinks	exon	3192732	3192811	.	.	.	gene_id "XLOC_000014"; transcript_id "TCONS_00000011"; exon_number "1"; oId "CUFF.43.1"; class_code "u"; tss_id "TSS17";
+chr1	Cufflinks	exon	3192941	3193042	.	.	.	gene_id "XLOC_000015"; transcript_id "TCONS_00000012"; exon_number "1"; oId "CUFF.45.1"; class_code "u"; tss_id "TSS18";
+chr1	Cufflinks	exon	3194186	3194226	.	.	.	gene_id "XLOC_000016"; transcript_id "TCONS_00000013"; exon_number "1"; oId "CUFF.47.1"; class_code "u"; tss_id "TSS19";
+chr1	Cufflinks	exon	3194303	3194329	.	.	.	gene_id "XLOC_000017"; transcript_id "TCONS_00000014"; exon_number "1"; oId "CUFF.49.1"; class_code "u"; tss_id "TSS20";
+chr1	Cufflinks	exon	3194707	3194733	.	.	.	gene_id "XLOC_000018"; transcript_id "TCONS_00000059"; exon_number "1"; oId "CUFF.17.1"; class_code "u"; tss_id "TSS21";
+chr1	Cufflinks	exon	3195084	3195110	.	.	.	gene_id "XLOC_000019"; transcript_id "TCONS_00000015"; exon_number "1"; oId "CUFF.51.1"; class_code "u"; tss_id "TSS22";
+chr1	Cufflinks	exon	3195451	3195477	.	.	.	gene_id "XLOC_000020"; transcript_id "TCONS_00000016"; exon_number "1"; oId "CUFF.53.1"; class_code "u"; tss_id "TSS23";
+chr1	Cufflinks	exon	3197090	3197116	.	.	.	gene_id "XLOC_000021"; transcript_id "TCONS_00000017"; exon_number "1"; oId "CUFF.55.1"; class_code "u"; tss_id "TSS24";
+chr1	Cufflinks	exon	3197247	3197273	.	.	.	gene_id "XLOC_000022"; transcript_id "TCONS_00000018"; exon_number "1"; oId "CUFF.57.1"; class_code "u"; tss_id "TSS25";
+chr1	Cufflinks	exon	3197347	3197373	.	.	.	gene_id "XLOC_000023"; transcript_id "TCONS_00000019"; exon_number "1"; oId "CUFF.59.1"; class_code "u"; tss_id "TSS26";
+chr1	Cufflinks	exon	3197426	3197452	.	.	.	gene_id "XLOC_000024"; transcript_id "TCONS_00000060"; exon_number "1"; oId "CUFF.19.1"; class_code "u"; tss_id "TSS27";
+chr1	Cufflinks	exon	3200023	3200191	.	.	.	gene_id "XLOC_000025"; transcript_id "TCONS_00000020"; exon_number "1"; oId "CUFF.7.1"; class_code "u"; tss_id "TSS28";
+chr1	Cufflinks	exon	3200326	3200352	.	.	.	gene_id "XLOC_000026"; transcript_id "TCONS_00000021"; exon_number "1"; oId "CUFF.5.1"; class_code "u"; tss_id "TSS29";
+chr1	Cufflinks	exon	3200431	3200457	.	.	.	gene_id "XLOC_000027"; transcript_id "TCONS_00000062"; exon_number "1"; oId "CUFF.21.1"; class_code "u"; tss_id "TSS30";
+chr1	Cufflinks	exon	3201008	3201039	.	.	.	gene_id "XLOC_000028"; transcript_id "TCONS_00000063"; exon_number "1"; oId "CUFF.26.1"; class_code "u"; tss_id "TSS31";
+chr1	Cufflinks	exon	3201078	3201481	.	.	.	gene_id "XLOC_000029"; transcript_id "TCONS_00000022"; exon_number "1"; oId "CUFF.9.1"; class_code "u"; tss_id "TSS32";
+chr1	Cufflinks	exon	3201597	3201666	.	.	.	gene_id "XLOC_000030"; transcript_id "TCONS_00000065"; exon_number "1"; oId "CUFF.29.1"; class_code "u"; tss_id "TSS33";
+chr1	Cufflinks	exon	3201673	3201699	.	.	.	gene_id "XLOC_000031"; transcript_id "TCONS_00000023"; exon_number "1"; oId "CUFF.11.1"; class_code "u"; tss_id "TSS34";
+chr1	Cufflinks	exon	3201726	3201809	.	.	.	gene_id "XLOC_000032"; transcript_id "TCONS_00000066"; exon_number "1"; oId "CUFF.31.1"; class_code "u"; tss_id "TSS35";
+chr1	Cufflinks	exon	3211522	3211561	.	.	.	gene_id "XLOC_000033"; transcript_id "TCONS_00000067"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.33.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS36";
+chr1	Cufflinks	exon	3212214	3212292	.	.	.	gene_id "XLOC_000034"; transcript_id "TCONS_00000024"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.15.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS37";
+chr1	Cufflinks	exon	3212368	3212439	.	.	.	gene_id "XLOC_000035"; transcript_id "TCONS_00000025"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.19.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS38";
+chr1	Cufflinks	exon	3212718	3212801	.	.	.	gene_id "XLOC_000036"; transcript_id "TCONS_00000068"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.35.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS39";
+chr1	Cufflinks	exon	3213096	3213192	.	.	.	gene_id "XLOC_000037"; transcript_id "TCONS_00000026"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.17.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS40";
+chr1	Cufflinks	exon	3213119	3213242	.	.	.	gene_id "XLOC_000037"; transcript_id "TCONS_00000069"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.37.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS40";
+chr1	Cufflinks	exon	3240607	3240633	.	.	.	gene_id "XLOC_000038"; transcript_id "TCONS_00000070"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.39.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS41";
+chr1	Cufflinks	exon	3242480	3242512	.	.	.	gene_id "XLOC_000039"; transcript_id "TCONS_00000071"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.41.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS42";
+chr1	Cufflinks	exon	3242634	3242923	.	.	.	gene_id "XLOC_000040"; transcript_id "TCONS_00000027"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.25.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS43";
+chr1	Cufflinks	exon	3242925	3243005	.	.	.	gene_id "XLOC_000041"; transcript_id "TCONS_00000072"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.43.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS44";
+chr1	Cufflinks	exon	3243019	3243079	.	.	.	gene_id "XLOC_000042"; transcript_id "TCONS_00000028"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.21.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS45";
+chr1	Cufflinks	exon	3243109	3243154	.	.	.	gene_id "XLOC_000043"; transcript_id "TCONS_00000073"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.45.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS46";
+chr1	Cufflinks	exon	3243348	3243401	.	.	.	gene_id "XLOC_000044"; transcript_id "TCONS_00000029"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.23.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS47";
+chr1	Cufflinks	exon	3254080	3254106	.	.	.	gene_id "XLOC_000045"; transcript_id "TCONS_00000074"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.47.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS48";
+chr1	Cufflinks	exon	3256975	3257011	.	.	.	gene_id "XLOC_000046"; transcript_id "TCONS_00000030"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.27.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS49";
+chr1	Cufflinks	exon	3277156	3277182	.	.	.	gene_id "XLOC_000047"; transcript_id "TCONS_00000075"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.49.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS50";
+chr1	Cufflinks	exon	3277191	3277218	.	.	.	gene_id "XLOC_000048"; transcript_id "TCONS_00000031"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.61.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS51";
+chr1	Cufflinks	exon	3277914	3278390	.	.	.	gene_id "XLOC_000049"; transcript_id "TCONS_00000076"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.51.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS52";
+chr1	Cufflinks	exon	3280118	3280144	.	.	.	gene_id "XLOC_000050"; transcript_id "TCONS_00000077"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.53.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS54";
+chr1	Cufflinks	exon	3280499	3280525	.	.	.	gene_id "XLOC_000051"; transcript_id "TCONS_00000078"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.55.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS55";
+chr1	Cufflinks	exon	3280687	3280741	.	.	.	gene_id "XLOC_000052"; transcript_id "TCONS_00000033"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.65.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS56";
+chr1	Cufflinks	exon	3282505	3282531	.	.	.	gene_id "XLOC_000053"; transcript_id "TCONS_00000079"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.57.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS57";
+chr1	Cufflinks	exon	3282651	3282677	.	.	.	gene_id "XLOC_000054"; transcript_id "TCONS_00000080"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.59.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS58";
+chr1	Cufflinks	exon	3282761	3282832	.	.	.	gene_id "XLOC_000055"; transcript_id "TCONS_00000081"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.61.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS59";
+chr1	Cufflinks	exon	3284967	3284993	.	.	.	gene_id "XLOC_000056"; transcript_id "TCONS_00000082"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.63.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS60";
+chr1	Cufflinks	exon	3290489	3290553	.	.	.	gene_id "XLOC_000057"; transcript_id "TCONS_00000034"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.67.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS61";
+chr1	Cufflinks	exon	3290799	3290859	.	.	.	gene_id "XLOC_000058"; transcript_id "TCONS_00000083"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.65.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS62";
+chr1	Cufflinks	exon	3290920	3291273	.	.	.	gene_id "XLOC_000059"; transcript_id "TCONS_00000084"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.69.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS63";
+chr1	Cufflinks	exon	3299444	3299640	.	.	.	gene_id "XLOC_000060"; transcript_id "TCONS_00000085"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.67.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS65";
+chr1	Cufflinks	exon	3299610	3299664	.	.	.	gene_id "XLOC_000060"; transcript_id "TCONS_00000037"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.73.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS66";
+chr1	Cufflinks	exon	3299692	3299733	.	.	.	gene_id "XLOC_000061"; transcript_id "TCONS_00000086"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.71.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS67";
+chr1	Cufflinks	exon	3300052	3300078	.	.	.	gene_id "XLOC_000062"; transcript_id "TCONS_00000038"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.75.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS68";
+chr1	Cufflinks	exon	3307749	3307775	.	.	.	gene_id "XLOC_000063"; transcript_id "TCONS_00000087"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.73.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS69";
+chr1	Cufflinks	exon	3318621	3318647	.	.	.	gene_id "XLOC_000064"; transcript_id "TCONS_00000088"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.75.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS70";
+chr1	Cufflinks	exon	3319000	3319051	.	.	.	gene_id "XLOC_000065"; transcript_id "TCONS_00000039"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.77.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS71";
+chr1	Cufflinks	exon	3330528	3330554	.	.	.	gene_id "XLOC_000066"; transcript_id "TCONS_00000089"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.77.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS72";
+chr1	Cufflinks	exon	3351241	3351311	.	.	.	gene_id "XLOC_000067"; transcript_id "TCONS_00000090"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.79.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS73";
+chr1	Cufflinks	exon	3355888	3355914	.	.	.	gene_id "XLOC_000068"; transcript_id "TCONS_00000040"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.79.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS74";
+chr1	Cufflinks	exon	3355908	3356119	.	.	.	gene_id "XLOC_000068"; transcript_id "TCONS_00000091"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.81.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS74";
+chr1	Cufflinks	exon	3356181	3356225	.	.	.	gene_id "XLOC_000069"; transcript_id "TCONS_00000092"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.83.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS75";
+chr1	Cufflinks	exon	3363077	3363176	.	.	.	gene_id "XLOC_000070"; transcript_id "TCONS_00000093"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.85.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS76";
+chr1	Cufflinks	exon	3363215	3363278	.	.	.	gene_id "XLOC_000071"; transcript_id "TCONS_00000041"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.81.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS77";
+chr1	Cufflinks	exon	3363388	3363446	.	.	.	gene_id "XLOC_000072"; transcript_id "TCONS_00000094"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.87.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS78";
+chr1	Cufflinks	exon	3363754	3363849	.	.	.	gene_id "XLOC_000073"; transcript_id "TCONS_00000042"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.83.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS79";
+chr1	Cufflinks	exon	3364872	3364919	.	.	.	gene_id "XLOC_000074"; transcript_id "TCONS_00000095"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.89.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS80";
+chr1	Cufflinks	exon	3367136	3367162	.	.	.	gene_id "XLOC_000075"; transcript_id "TCONS_00000043"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.85.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS81";
+chr1	Cufflinks	exon	3367211	3367237	.	.	.	gene_id "XLOC_000076"; transcript_id "TCONS_00000096"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.91.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS82";
+chr1	Cufflinks	exon	3367334	3367382	.	.	.	gene_id "XLOC_000077"; transcript_id "TCONS_00000044"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.87.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS83";
+chr1	Cufflinks	exon	3369581	3369607	.	.	.	gene_id "XLOC_000078"; transcript_id "TCONS_00000097"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.93.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS84";
+chr1	Cufflinks	exon	3375002	3375028	.	.	.	gene_id "XLOC_000079"; transcript_id "TCONS_00000098"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.95.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS85";
+chr1	Cufflinks	exon	3377212	3377262	.	.	.	gene_id "XLOC_000080"; transcript_id "TCONS_00000045"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.89.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS86";
+chr1	Cufflinks	exon	3379889	3379915	.	.	.	gene_id "XLOC_000081"; transcript_id "TCONS_00000099"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.97.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS87";
+chr1	Cufflinks	exon	3386740	3386836	.	.	.	gene_id "XLOC_000082"; transcript_id "TCONS_00000100"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.99.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS88";
+chr1	Cufflinks	exon	3391326	3391352	.	.	.	gene_id "XLOC_000083"; transcript_id "TCONS_00000046"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.91.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS89";
+chr1	Cufflinks	exon	3435842	3435880	.	.	.	gene_id "XLOC_000084"; transcript_id "TCONS_00000047"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.93.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS90";
+chr1	Cufflinks	exon	3447762	3447788	.	.	.	gene_id "XLOC_000085"; transcript_id "TCONS_00000048"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.95.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS91";
+chr1	Cufflinks	exon	3450907	3450965	.	.	.	gene_id "XLOC_000086"; transcript_id "TCONS_00000049"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.97.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS92";
+chr1	Cufflinks	exon	3451052	3451109	.	.	.	gene_id "XLOC_000087"; transcript_id "TCONS_00000050"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.99.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS93";
diff -r db57b46b05bf -r 4e6f043995ff test-data/genes.exp
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genes.exp	Wed Jun 03 15:04:19 2015 -0400
@@ -0,0 +1,88 @@
+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 db57b46b05bf -r 4e6f043995ff test-data/genes.fpkm_tracking
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genes.fpkm_tracking	Wed Jun 03 15:04:19 2015 -0400
@@ -0,0 +1,88 @@
+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 db57b46b05bf -r 4e6f043995ff test-data/isoforms.exp
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/isoforms.exp	Wed Jun 03 15:04:19 2015 -0400
@@ -0,0 +1,91 @@
+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 db57b46b05bf -r 4e6f043995ff test-data/isoforms.fpkm_tracking
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/isoforms.fpkm_tracking	Wed Jun 03 15:04:19 2015 -0400
@@ -0,0 +1,91 @@
+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 db57b46b05bf -r 4e6f043995ff test-data/promoters.diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/promoters.diff	Wed Jun 03 15:04:19 2015 -0400
@@ -0,0 +1,88 @@
+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 db57b46b05bf -r 4e6f043995ff test-data/splicing.diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/splicing.diff	Wed Jun 03 15:04:19 2015 -0400
@@ -0,0 +1,89 @@
+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 db57b46b05bf -r 4e6f043995ff test-data/tss.groups_exp
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tss.groups_exp	Wed Jun 03 15:04:19 2015 -0400
@@ -0,0 +1,89 @@
+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 db57b46b05bf -r 4e6f043995ff test-data/tss.groups_fpkm_tracking
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tss.groups_fpkm_tracking	Wed Jun 03 15:04:19 2015 -0400
@@ -0,0 +1,89 @@
+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 db57b46b05bf -r 4e6f043995ff tool_dependencies.xml
--- a/tool_dependencies.xml	Wed May 13 11:04:49 2015 -0400
+++ b/tool_dependencies.xml	Wed Jun 03 15:04:19 2015 -0400
@@ -7,6 +7,6 @@
         <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="d9d166e54a21" name="package_cummerbund_2_8_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="f18bcdb8c6c5" name="package_cummerbund_2_8_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>