# HG changeset patch
# User iuc
# Date 1425573672 18000
# Node ID 9f80c71f1779c8d3193fe076ac28845bd5e528ac
# Parent  62d21219200212b7cecb98ab2bcc579b75b99b58
Uploaded updated tool wrapper for stringtie 1.0.1

diff -r 62d212192002 -r 9f80c71f1779 stringtie.xml
--- a/stringtie.xml	Thu Jul 03 18:38:02 2014 -0400
+++ b/stringtie.xml	Thu Mar 05 11:41:12 2015 -0500
@@ -1,19 +1,20 @@
-<?xml version="1.0"?>
-<tool name="StringTie" id="stringtie" version="1.0.0">
+<tool id="stringtie" name="StringTie" version="1.0.1">
     <description>RNA-Seq assembler</description>
     <requirements>
-        <requirement type="package" version="0.97">stringtie</requirement>
+        <requirement type="package" version="1.0.1">stringtie</requirement>
     </requirements>
-    <command>
-<![CDATA[
+    <command><![CDATA[
 stringtie "$input_bam"
 -o "$output_gtf"
 -p "\${GALAXY_SLOTS:-1}"
 #if str($guide.use_guide) == 'yes':
-    -G "$guide.guide_gff" $guide.input_estimation
-    -C "$coverage"
+    -C "$coverage" -G "$guide.guide_gff" $guide.input_estimation
+    #if str($guide.output_ballgown) == '-b':
+        $guide.output_ballgown `pwd`
+    #end if
 #end if
 #if str($option_set.options) == 'advanced':
+    -l "$option_set.name_prefix"
     -f "$option_set.fraction"
     -m "$option_set.min_tlen"
     -a "$option_set.min_anchor_len"
@@ -26,92 +27,142 @@
 ]]>
 </command>
     <inputs>
-        <param name="input_bam" type="data" format="bam" label="BAM file to assemble" />
+        <param format="bam" label="BAM file to assemble" name="input_bam" type="data" />
         <conditional name="guide">
-            <param name="use_guide" type="select" label="Use GFF file to guide assembly">
+            <param label="Use GFF file to guide assembly" name="use_guide" type="select">
                 <option value="yes">Use GFF</option>
-                <option value="no" selected="True">Do not use GFF</option>
+                <option selected="True" value="no">Do not use GFF</option>
             </param>
             <when value="no" />
             <when value="yes">
-                <param name="guide_gff" type="data" format="gtf,gff3" label="Reference annotation to use for guiding the assembly process" />
-                <param name="input_estimation" type="boolean" truevalue="-e" falsevalue="" label="Perform abundance estimation only of input transcripts" />
+                <param format="gtf,gff3" help="(-G)" label="Reference annotation to use for guiding the assembly process" name="guide_gff" type="data" />
+                <param falsevalue="" help="(-e)" label="Perform abundance estimation only of input transcripts" name="input_estimation" truevalue="-e" type="boolean" />
+                <param falsevalue="" help="(-b)" label="Output additional files for use in Ballgown" name="output_ballgown" truevalue="-b" type="boolean" />
             </when>
         </conditional>
         <conditional name="option_set">
-            <param name="options" type="select" label="Options">
-                <option value="default" selected="True">Use defaults</option>
+            <param label="Options" name="options" type="select">
+                <option selected="True" value="default">Use defaults</option>
                 <option value="advanced">Specify advanced options</option>
             </param>
             <when value="default" />
             <when value="advanced">
-                <param name="disable_trimming" type="boolean" falsevalue="" truevalue="-t" label="Disable trimming of predicted transcripts based on coverage" />
-                <param name="sensitive" type="boolean" truevalue="-S" falsevalue="" label="Increase sensitivity" />
-                <param name="label" type="text" value="STRG" label="Name prefix for output transcripts" />
-                <param name="fraction" type="float" value="0.15" min="0.0" max="1.0" label="Minimum isoform fraction" />
-                <param name="min_tlen" type="integer" value="200" label="Minimum assembled transcript length" />
-                <param name="min_anchor_len" type="integer" value="10" label="Minimum anchor length for junctions" />
-                <param name="min_anchor_cov" type="integer" value="1" label="Minimum junction coverage" />
-                <param name="min_bundle_cov" type="integer" value="2" label="Minimum bundle reads per bp coverage to consider for assembly" />
-                <param name="maxcov" type="integer" value="1000000" label="Coverage saturation threshold" />
-                <param name="bdist" type="integer" value="50" label="Gap between read mappings triggering a new bundle" />
-                <param name="bundle_fraction" type="float" value="0.95" label="Fraction of bundle allowed to be covered by multi-hit reads" />
-             </when>
+                <param falsevalue="" help="(-t)" label="Disable trimming of predicted transcripts based on coverage" name="disable_trimming" truevalue="-t" type="boolean" />
+                <param falsevalue="" help="(-S)" label="Increase sensitivity" name="sensitive" truevalue="-S" type="boolean" />
+                <param help="(-l)" label="Name prefix for output transcripts" name="name_prefix" type="text" value="STRG" />
+                <param help="(-f)" label="Minimum isoform fraction" max="1.0" min="0.0" name="fraction" type="float" value="0.15" />
+                <param help="(-m)" label="Minimum assembled transcript length" name="min_tlen" type="integer" value="200" />
+                <param help="(-a)" label="Minimum anchor length for junctions" name="min_anchor_len" type="integer" value="10" />
+                <param help="(-j)" label="Minimum junction coverage" name="min_anchor_cov" type="integer" value="1" />
+                <param help="(-c)" label="Minimum bundle reads per bp coverage to consider for assembly" name="min_bundle_cov" type="integer" value="2" />
+                <param help="(-s)" label="Coverage saturation threshold" name="maxcov" type="integer" value="1000000" />
+                <param help="(-g)" label="Gap between read mappings triggering a new bundle" name="bdist" type="integer" value="50" />
+                <param help="(-M)" label="Fraction of bundle allowed to be covered by multi-hit reads" name="bundle_fraction" type="float" value="0.95" />
+            </when>
         </conditional>
     </inputs>
     <outputs>
-        <data name="output_gtf" format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts"/>
-        <data name="coverage" format="gff3" label="${tool.name} on ${on_string}: Coverage">
+        <data format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts" name="output_gtf" />
+        <data format="gff3" label="${tool.name} on ${on_string}: Coverage" name="coverage">
             <filter>guide['use_guide'] == "yes"</filter>
         </data>
+        <data format="tabular" from_work_dir="e_data.ctab" label="${tool.name} on ${on_string}: exon-level expression measurements" name="exon_expression">
+            <filter>guide['output_ballgown']</filter>
+        </data>
+        <data format="tabular" from_work_dir="i_data.ctab" label="${tool.name} on ${on_string}: intron-level expression measurements" name="intron_expression">
+            <filter>guide['output_ballgown']</filter>
+        </data>
+        <data format="tabular" from_work_dir="t_data.ctab" label="${tool.name} on ${on_string}: transcript-level expression measurements" name="transcript_expression">
+            <filter>guide['output_ballgown']</filter>
+        </data>
+        <data format="tabular" from_work_dir="e2t.ctab" label="${tool.name} on ${on_string}: exon to transcript mapping" name="exon_transcript_mapping">
+            <filter>guide['output_ballgown']</filter>
+        </data>
+        <data format="tabular" from_work_dir="i2t.ctab" label="${tool.name} on ${on_string}: intron to transcript mapping" name="intron_transcript_mapping">
+            <filter>guide['output_ballgown']</filter>
+        </data>
     </outputs>
     <tests>
         <test>
-            <param name="input_bam" value="stringtie_in1.bam" ftype="bam" />
+            <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
             <param name="use_guide" value="no" />
             <param name="options" value="default" />
-            <output name="output_gtf" file="stringtie_out1.gtf" ftype="gtf" />
+            <output file="stringtie_out1.gtf" ftype="gtf" name="output_gtf" />
         </test>
         <test>
-            <param name="input_bam" value="stringtie_in1.bam" ftype="bam" />
+            <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
             <param name="use_guide" value="no" />
             <param name="options" value="advanced" />
             <param name="fraction" value="0.17" />
-            <output name="output_gtf" file="stringtie_out2.gtf" ftype="gtf" />
+            <output file="stringtie_out2.gtf" ftype="gtf" name="output_gtf" />
+        </test>
+        <test>
+            <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
+            <param name="use_guide" value="yes" />
+            <param name="guide_gff" value="stringtie_in.gtf" />
+            <param name="options" value="default" />
+            <output file="stringtie_out3.gtf" ftype="gtf" name="output_gtf" />
+        </test>
+        <test>
+            <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
+            <param name="use_guide" value="yes" />
+            <param name="guide_gff" value="stringtie_in.gtf" />
+            <param name="options" value="advanced" />
+            <param name="fraction" value="0.17" />
+            <output file="stringtie_out4.gtf" ftype="gtf" name="output_gtf" />
+        </test>
+        <test>
+            <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
+            <param name="use_guide" value="yes" />
+            <param name="output_ballgown" value="yes" />
+            <param name="guide_gff" value="stringtie_in.gtf" />
+            <param name="options" value="default" />
+            <output file="ballgown/e_data.ctab" ftype="tabular" name="exon_expression" />
+            <output file="ballgown/i_data.ctab" ftype="tabular" name="intron_expression" />
+            <output file="ballgown/t_data.ctab" ftype="tabular" name="transcript_expression" />
+            <output file="ballgown/e2t.ctab" ftype="tabular" name="exon_transcript_mapping" />
+            <output file="ballgown/i2t.ctab" ftype="tabular" name="intron_transcript_mapping" />
+            <output file="stringtie_out5.gtf" ftype="gtf" name="output_gtf" />
+            <output file="stringtie_out_coverage.gtf" ftype="gff3" name="coverage" />
         </test>
     </tests>
     <help>
 <![CDATA[
-StringTie v0.97 usage::
-
-   stringtie <input.bam> [-G <guide_gff>] [-l <label>] [-o <out_gff>] [-p <cpus>]
-    [-v] [-a <min_anchor_len>] [-m <min_tlen>] [-j <min_anchor_cov>] [-n sens]
-    [-C <coverage_file_name>] [-s <maxcov>] [-c <min_bundle_cov>] [-g <bdist>]
-
-  Assemble RNA-Seq alignments into potential transcripts.
+StringTie v1.0.1 usage:
+ stringtie <input.bam> [-G <guide_gff>] [-l <label>] [-o <out_gtf>] [-p <cpus>]
+  [-v] [-a <min_anchor_len>] [-m <min_tlen>] [-j <min_anchor_cov>] [-n sens]
+  [-C <coverage_file_name>] [-s <maxcov>] [-c <min_bundle_cov>] [-g <bdist>]
+  {-B | -b <dir_path>} [-e]
 
-   Options:
-   -G  reference annotation to use for guiding the assembly process (GTF/GFF3)
-   -l  name prefix for output transcripts (default: STRG)
-   -f  minimum isoform fraction (default: 0.15)
-   -m  minimum assembled transcript length to report (default 200bp)
-   -o  output file with the assembled transcripts (default: stdout)
-   -a  minimum anchor length for junctions (default: 10)
-   -j  minimum junction coverage (default: 1)
-   -t  disable trimming of predicted transcripts based on coverage (default: trimming enabled)
-   -c  minimum bundle reads per bp coverage to consider for assembly (default: 2)
-   -s  coverage saturation threshold; further read alignments will be
-       ignored in a region where a local coverage depth of <maxcov>
-       is reached (default: 1,000,000);
-   -v  verbose (log bundle processing details)
-   -e  abundance estimation only of input transcripts (for -G option)
-   -g  gap between read mappings triggering a new bundle (default: 50)
-   -S  more sensitive run (default: no)
-   -C  output file with all transcripts in reference that are fully
-       covered by reads
-   -M  fraction of bundle allowed to be covered by multi-hit reads (default:0.95)
-   -p  number of threads (CPUs) to use (default: 1)
-
-]]>
-</help>
-</tool>
\ No newline at end of file
+Assemble RNA-Seq alignments into potential transcripts.
+ 
+ Options:
+ -G reference annotation to use for guiding the assembly process (GTF/GFF3)
+ -l name prefix for output transcripts (default: STRG)
+ -f minimum isoform fraction (default: 0.1)
+ -m minimum assembled transcript length to report (default 200bp)
+ -o output path/file name for the assembled transcripts GTF (default: stdout)
+ -a minimum anchor length for junctions (default: 10)
+ -j minimum junction coverage (default: 1)
+ -t disable trimming of predicted transcripts based on coverage
+    (default: coverage trimming is enabled)
+ -c minimum reads per bp coverage to consider for transcript assembly (default: 2.5)
+ -s coverage saturation threshold; further read alignments will be
+    ignored in a region where a local coverage depth of <maxcov> 
+    is reached (default: 1,000,000);
+ -v verbose (log bundle processing details)
+ -g gap between read mappings triggering a new bundle (default: 50)
+ -C output file with reference transcripts that are covered by reads
+ -M fraction of bundle allowed to be covered by multi-hit reads (default:0.95)
+ -p number of threads (CPUs) to use (default: 1)
+ -B enable output of Ballgown table files which will be created in the
+    same directory as the output GTF (requires -G, -o recommended)
+ -b enable output of Ballgown table files but these files will be 
+    created under the directory path given as <dir_path>
+ -e only estimates the abundance of given reference transcripts (requires -G)
+ ]]>
+    </help>
+    <citations>
+        <citation type="doi">doi:10.1038/nbt.3122</citation>
+    </citations>
+</tool>
diff -r 62d212192002 -r 9f80c71f1779 test-data/._stringtie_in1.bam
Binary file test-data/._stringtie_in1.bam has changed
diff -r 62d212192002 -r 9f80c71f1779 test-data/._stringtie_out2.gtf
Binary file test-data/._stringtie_out2.gtf has changed
diff -r 62d212192002 -r 9f80c71f1779 test-data/ballgown/e2t.ctab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ballgown/e2t.ctab	Thu Mar 05 11:41:12 2015 -0500
@@ -0,0 +1,4 @@
+e_id	t_id
+1	1
+2	1
+3	1
diff -r 62d212192002 -r 9f80c71f1779 test-data/ballgown/e_data.ctab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ballgown/e_data.ctab	Thu Mar 05 11:41:12 2015 -0500
@@ -0,0 +1,4 @@
+e_id	chr	strand	start	end	rcount	ucount	mrcount	cov	cov_sd	mcov	mcov_sd
+1	test_chromosome	+	53	250	154	154	154.00	49.7778	22.0747	49.7778	22.0747
+2	test_chromosome	+	351	400	73	73	73.00	54.1600	6.1753	54.1600	6.1753
+3	test_chromosome	+	501	550	38	38	38.00	21.6400	12.4350	21.6400	12.4350
diff -r 62d212192002 -r 9f80c71f1779 test-data/ballgown/i2t.ctab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ballgown/i2t.ctab	Thu Mar 05 11:41:12 2015 -0500
@@ -0,0 +1,3 @@
+i_id	t_id
+1	1
+2	1
diff -r 62d212192002 -r 9f80c71f1779 test-data/ballgown/i_data.ctab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ballgown/i_data.ctab	Thu Mar 05 11:41:12 2015 -0500
@@ -0,0 +1,3 @@
+i_id	chr	strand	start	end	rcount	ucount	mrcount
+1	test_chromosome	+	251	350	49	49	49.00
+2	test_chromosome	+	401	500	38	38	38.00
diff -r 62d212192002 -r 9f80c71f1779 test-data/ballgown/t_data.ctab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ballgown/t_data.ctab	Thu Mar 05 11:41:12 2015 -0500
@@ -0,0 +1,2 @@
+t_id	chr	strand	start	end	t_name	num_exons	length	gene_id	gene_name	cov	FPKM
+1	test_chromosome	+	53	550	CUFF.1.1	3	298	CUFF.1	.	44.724823	3276543.750000
diff -r 62d212192002 -r 9f80c71f1779 test-data/stringtie_in.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/stringtie_in.gtf	Thu Mar 05 11:41:12 2015 -0500
@@ -0,0 +1,4 @@
+test_chromosome	Cufflinks	transcript	53	550	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8542701.791788"; conf_hi "12815567.020892"; cov "145.770185";
+test_chromosome	Cufflinks	exon	53	250	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8542701.791788"; conf_hi "12815567.020892"; cov "145.770185";
+test_chromosome	Cufflinks	exon	351	400	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "2"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8542701.791788"; conf_hi "12815567.020892"; cov "145.770185";
+test_chromosome	Cufflinks	exon	501	550	1000	+	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "3"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8542701.791788"; conf_hi "12815567.020892"; cov "145.770185";
diff -r 62d212192002 -r 9f80c71f1779 test-data/stringtie_in1.bam
Binary file test-data/stringtie_in1.bam has changed
diff -r 62d212192002 -r 9f80c71f1779 test-data/stringtie_out1.gtf
--- a/test-data/stringtie_out1.gtf	Thu Jul 03 18:38:02 2014 -0400
+++ b/test-data/stringtie_out1.gtf	Thu Mar 05 11:41:12 2015 -0500
@@ -1,154 +1,4 @@
-chr19	StringTie	transcript	3052907	3062360	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "883.073547";FPKM "189664.171875";
-chr19	StringTie	exon	3052907	3054038	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "966.177673";
-chr19	StringTie	exon	3054118	3054192	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "1301.127930";
-chr19	StringTie	exon	3055662	3055724	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "1990.478271";
-chr19	StringTie	exon	3056310	3056354	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "4"; cov "942.796082";
-chr19	StringTie	exon	3057677	3057740	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "5"; cov "351.962616";
-chr19	StringTie	exon	3061158	3061255	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "6"; cov "1122.192017";
-chr19	StringTie	exon	3062172	3062360	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "7"; cov "214.494049";
-chr19	StringTie	transcript	3052907	3063089	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.2"; cov "168.800812";FPKM "36254.585938";
-chr19	StringTie	exon	3052907	3054038	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "1"; cov "220.181381";
-chr19	StringTie	exon	3054118	3054192	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "2"; cov "258.932983";
-chr19	StringTie	exon	3055662	3055724	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "3"; cov "176.962967";
-chr19	StringTie	exon	3056310	3056354	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "4"; cov "118.451096";
-chr19	StringTie	exon	3057677	3057740	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "5"; cov "254.885681";
-chr19	StringTie	exon	3061158	3061255	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "6"; cov "78.436821";
-chr19	StringTie	exon	3062698	3063089	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "7"; cov "16.186066";
-chr19	StringTie	transcript	2997664	3015854	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; cov "115.851471";FPKM "24882.267578";
-chr19	StringTie	exon	2997664	2997953	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "1"; cov "110.703667";
-chr19	StringTie	exon	3000645	3000721	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "2"; cov "207.771072";
-chr19	StringTie	exon	3002351	3002501	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "3"; cov "114.276024";
-chr19	StringTie	exon	3005435	3005582	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "4"; cov "120.278976";
-chr19	StringTie	exon	3005719	3005966	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "5"; cov "78.667053";
-chr19	StringTie	exon	3006418	3006667	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "6"; cov "48.566441";
-chr19	StringTie	exon	3008867	3008943	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "7"; cov "66.379005";
-chr19	StringTie	exon	3009540	3009700	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "8"; cov "62.793331";
-chr19	StringTie	exon	3011020	3011158	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "9"; cov "219.519562";
-chr19	StringTie	exon	3013667	3013816	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "10"; cov "172.405579";
-chr19	StringTie	exon	3014568	3014612	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "11"; cov "342.860687";
-chr19	StringTie	exon	3015651	3015854	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "12"; cov "119.223740";
-chr19	StringTie	transcript	3018960	3029141	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; cov "18.253860";FPKM "3920.515381";
-chr19	StringTie	exon	3018960	3019461	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "1"; cov "10.802196";
-chr19	StringTie	exon	3019697	3019771	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "2"; cov "23.808632";
-chr19	StringTie	exon	3025018	3025080	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "3"; cov "33.401360";
-chr19	StringTie	exon	3027827	3027871	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "4"; cov "41.172310";
-chr19	StringTie	exon	3028317	3028380	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "5"; cov "42.650341";
-chr19	StringTie	exon	3028704	3028801	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "6"; cov "32.359097";
-chr19	StringTie	exon	3028879	3029141	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "7"; cov "12.150498";
-chr19	StringTie	transcript	3018960	3029141	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.3"; cov "5.218285";FPKM "1120.769287";
-chr19	StringTie	exon	3018960	3019464	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.3"; exon_number "1"; cov "4.017776";
-chr19	StringTie	exon	3019697	3019771	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.3"; exon_number "2"; cov "15.457561";
-chr19	StringTie	exon	3025018	3025080	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.3"; exon_number "3"; cov "1.183362";
-chr19	StringTie	exon	3027827	3027871	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.3"; exon_number "4"; cov "3.434842";
-chr19	StringTie	exon	3028317	3028380	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.3"; exon_number "5"; cov "20.437429";
-chr19	StringTie	exon	3028704	3028801	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.3"; exon_number "6"; cov "6.825138";
-chr19	StringTie	exon	3028879	3029141	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.3"; exon_number "7"; cov "1.572921";
-chr19	StringTie	transcript	3094613	3119121	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; cov "80.540161";FPKM "17298.201172";
-chr19	StringTie	exon	3094613	3094785	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "1"; cov "67.409538";
-chr19	StringTie	exon	3110147	3110331	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "2"; cov "102.204170";
-chr19	StringTie	exon	3113328	3113482	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "3"; cov "108.144516";
-chr19	StringTie	exon	3114942	3115070	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "4"; cov "63.896484";
-chr19	StringTie	exon	3118922	3119121	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "5"; cov "61.832138";
-chr19	StringTie	transcript	3119186	3123995	1000	+	.	gene_id "STRG.4"; transcript_id "STRG.4.1"; cov "69.395134";FPKM "14904.501953";
-chr19	StringTie	exon	3119186	3119357	1000	+	.	gene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "1"; cov "71.938263";
-chr19	StringTie	exon	3120987	3123995	1000	+	.	gene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "2"; cov "69.249763";
-chr19	StringTie	transcript	3136149	3163782	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; cov "13.414832";FPKM "2881.201660";
-chr19	StringTie	exon	3136149	3136593	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "1"; cov "2.243525";
-chr19	StringTie	exon	3148589	3148773	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "2"; cov "6.817567";
-chr19	StringTie	exon	3150129	3150283	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "3"; cov "12.169776";
-chr19	StringTie	exon	3151705	3151833	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "4"; cov "5.409668";
-chr19	StringTie	exon	3155821	3155950	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "5"; cov "22.124674";
-chr19	StringTie	exon	3157726	3157879	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "6"; cov "16.131796";
-chr19	StringTie	exon	3162791	3163782	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "7"; cov "19.328829";
-chr19	StringTie	transcript	3176651	3177191	1000	.	.	gene_id "STRG.6"; transcript_id "STRG.6.1"; cov "2.218115";FPKM "476.400818";
-chr19	StringTie	exon	3176651	3177191	1000	.	.	gene_id "STRG.6"; transcript_id "STRG.6.1"; exon_number "1"; cov "2.218115";
-chr19	StringTie	transcript	3178008	3178218	1000	.	.	gene_id "STRG.7"; transcript_id "STRG.7.1"; cov "2.132701";FPKM "458.055786";
-chr19	StringTie	exon	3178008	3178218	1000	.	.	gene_id "STRG.7"; transcript_id "STRG.7.1"; exon_number "1"; cov "2.132701";
-chr19	StringTie	transcript	3178290	3182254	1000	.	.	gene_id "STRG.8"; transcript_id "STRG.8.1"; cov "25.143421";FPKM "5400.236816";
-chr19	StringTie	exon	3178290	3182254	1000	.	.	gene_id "STRG.8"; transcript_id "STRG.8.1"; exon_number "1"; cov "25.143421";
-chr19	StringTie	transcript	3182964	3183191	1000	.	.	gene_id "STRG.9"; transcript_id "STRG.9.1"; cov "3.289474";FPKM "706.504456";
-chr19	StringTie	exon	3182964	3183191	1000	.	.	gene_id "STRG.9"; transcript_id "STRG.9.1"; exon_number "1"; cov "3.289474";
-chr19	StringTie	transcript	3183534	3184980	1000	.	.	gene_id "STRG.10"; transcript_id "STRG.10.1"; cov "10.234969";FPKM "2198.239258";
-chr19	StringTie	exon	3183534	3184980	1000	.	.	gene_id "STRG.10"; transcript_id "STRG.10.1"; exon_number "1"; cov "10.234969";
-chr19	StringTie	transcript	3185059	3185762	1000	.	.	gene_id "STRG.11"; transcript_id "STRG.11.1"; cov "4.474432";FPKM "961.006531";
-chr19	StringTie	exon	3185059	3185762	1000	.	.	gene_id "STRG.11"; transcript_id "STRG.11.1"; exon_number "1"; cov "4.474432";
-chr19	StringTie	transcript	3185993	3209570	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.1"; cov "46.485111";FPKM "9983.947266";
-chr19	StringTie	exon	3185993	3186212	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.1"; exon_number "1"; cov "9.429298";
-chr19	StringTie	exon	3192468	3192658	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.1"; exon_number "2"; cov "21.059887";
-chr19	StringTie	exon	3193282	3193426	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.1"; exon_number "3"; cov "39.715225";
-chr19	StringTie	exon	3196181	3196275	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.1"; exon_number "4"; cov "37.911308";
-chr19	StringTie	exon	3198815	3198895	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.1"; exon_number "5"; cov "51.996696";
-chr19	StringTie	exon	3201521	3201624	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.1"; exon_number "6"; cov "31.073275";
-chr19	StringTie	exon	3203754	3203842	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.1"; exon_number "7"; cov "55.852036";
-chr19	StringTie	exon	3204003	3204142	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.1"; exon_number "8"; cov "30.771446";
-chr19	StringTie	exon	3204571	3204749	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.1"; exon_number "9"; cov "34.595020";
-chr19	StringTie	exon	3205937	3206024	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.1"; exon_number "10"; cov "43.030930";
-chr19	StringTie	exon	3206150	3206188	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.1"; exon_number "11"; cov "59.276905";
-chr19	StringTie	exon	3206260	3206423	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.1"; exon_number "12"; cov "46.387093";
-chr19	StringTie	exon	3207196	3207249	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.1"; exon_number "13"; cov "63.118416";
-chr19	StringTie	exon	3207389	3207467	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.1"; exon_number "14"; cov "65.674583";
-chr19	StringTie	exon	3207627	3209570	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.1"; exon_number "15"; cov "54.248878";
-chr19	StringTie	transcript	3195437	3209570	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.2"; cov "17.133051";FPKM "3679.790771";
-chr19	StringTie	exon	3195437	3196275	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.2"; exon_number "1"; cov "10.562823";
-chr19	StringTie	exon	3198815	3198895	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.2"; exon_number "2"; cov "17.045162";
-chr19	StringTie	exon	3201521	3201624	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.2"; exon_number "3"; cov "9.639905";
-chr19	StringTie	exon	3203754	3203842	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.2"; exon_number "4"; cov "14.507616";
-chr19	StringTie	exon	3204003	3204142	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.2"; exon_number "5"; cov "5.000354";
-chr19	StringTie	exon	3204571	3204749	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.2"; exon_number "6"; cov "10.209009";
-chr19	StringTie	exon	3205937	3206024	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.2"; exon_number "7"; cov "16.365309";
-chr19	StringTie	exon	3206150	3206188	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.2"; exon_number "8"; cov "25.572968";
-chr19	StringTie	exon	3206263	3206423	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.2"; exon_number "9"; cov "19.185726";
-chr19	StringTie	exon	3207196	3207249	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.2"; exon_number "10"; cov "38.189373";
-chr19	StringTie	exon	3207389	3207467	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.2"; exon_number "11"; cov "31.688845";
-chr19	StringTie	exon	3207627	3209570	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.2"; exon_number "12"; cov "20.523384";
-chr19	StringTie	transcript	3203443	3209570	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.3"; cov "7.056122";FPKM "1515.494995";
-chr19	StringTie	exon	3203443	3203842	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.3"; exon_number "1"; cov "2.242009";
-chr19	StringTie	exon	3204003	3204142	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.3"; exon_number "2"; cov "3.895410";
-chr19	StringTie	exon	3204571	3204749	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.3"; exon_number "3"; cov "6.615313";
-chr19	StringTie	exon	3205937	3206024	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.3"; exon_number "4"; cov "10.143439";
-chr19	StringTie	exon	3206150	3206188	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.3"; exon_number "5"; cov "11.954673";
-chr19	StringTie	exon	3206260	3207249	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.3"; exon_number "6"; cov "3.642324";
-chr19	StringTie	exon	3207389	3207467	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.3"; exon_number "7"; cov "5.884272";
-chr19	StringTie	exon	3207627	3209570	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.3"; exon_number "8"; cov "9.862993";
-chr19	StringTie	transcript	3363620	3364229	1000	.	.	gene_id "STRG.13"; transcript_id "STRG.13.1"; cov "2.622951";FPKM "563.350403";
-chr19	StringTie	exon	3363620	3364229	1000	.	.	gene_id "STRG.13"; transcript_id "STRG.13.1"; exon_number "1"; cov "2.622951";
-chr19	StringTie	transcript	3366538	3469274	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.1"; cov "71.175430";FPKM "15286.868164";
-chr19	StringTie	exon	3366538	3366664	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.1"; exon_number "1"; cov "11.686789";
-chr19	StringTie	exon	3381710	3382241	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.1"; exon_number "2"; cov "56.353500";
-chr19	StringTie	exon	3425104	3425175	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.1"; exon_number "3"; cov "74.173615";
-chr19	StringTie	exon	3433516	3433590	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.1"; exon_number "4"; cov "65.354446";
-chr19	StringTie	exon	3434275	3434398	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.1"; exon_number "5"; cov "80.448212";
-chr19	StringTie	exon	3435081	3435205	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.1"; exon_number "6"; cov "71.471077";
-chr19	StringTie	exon	3449012	3449137	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.1"; exon_number "7"; cov "107.203087";
-chr19	StringTie	exon	3452480	3452664	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.1"; exon_number "8"; cov "71.914742";
-chr19	StringTie	exon	3453761	3453914	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.1"; exon_number "9"; cov "30.357872";
-chr19	StringTie	exon	3456548	3456633	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.1"; exon_number "10"; cov "40.561024";
-chr19	StringTie	exon	3462750	3469274	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.1"; exon_number "11"; cov "74.051750";
-chr19	StringTie	transcript	3366538	3469274	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.2"; cov "18.338432";FPKM "3938.679688";
-chr19	StringTie	exon	3366538	3366664	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "1"; cov "3.412646";
-chr19	StringTie	exon	3381710	3382241	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "2"; cov "15.545184";
-chr19	StringTie	exon	3425104	3425175	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "3"; cov "21.998638";
-chr19	StringTie	exon	3433516	3433590	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "4"; cov "17.916565";
-chr19	StringTie	exon	3434275	3434398	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "5"; cov "24.749645";
-chr19	StringTie	exon	3435081	3435205	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "6"; cov "20.192204";
-chr19	StringTie	exon	3449012	3449137	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "7"; cov "19.043257";
-chr19	StringTie	exon	3452480	3452664	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "8"; cov "32.998787";
-chr19	StringTie	exon	3462750	3469274	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "9"; cov "18.234524";
-chr19	StringTie	transcript	3472911	3473297	1000	.	.	gene_id "STRG.15"; transcript_id "STRG.15.1"; cov "2.842377";FPKM "610.478088";
-chr19	StringTie	exon	3472911	3473297	1000	.	.	gene_id "STRG.15"; transcript_id "STRG.15.1"; exon_number "1"; cov "2.842377";
-chr19	StringTie	transcript	3473383	3473585	1000	.	.	gene_id "STRG.16"; transcript_id "STRG.16.1"; cov "2.216749";FPKM "476.107422";
-chr19	StringTie	exon	3473383	3473585	1000	.	.	gene_id "STRG.16"; transcript_id "STRG.16.1"; exon_number "1"; cov "2.216749";
-chr19	StringTie	transcript	3473881	3474130	1000	.	.	gene_id "STRG.17"; transcript_id "STRG.17.1"; cov "5.800000";FPKM "1245.708496";
-chr19	StringTie	exon	3473881	3474130	1000	.	.	gene_id "STRG.17"; transcript_id "STRG.17.1"; exon_number "1"; cov "5.800000";
-chr19	StringTie	transcript	3474201	3474891	1000	.	.	gene_id "STRG.18"; transcript_id "STRG.18.1"; cov "6.512301";FPKM "1398.694580";
-chr19	StringTie	exon	3474201	3474891	1000	.	.	gene_id "STRG.18"; transcript_id "STRG.18.1"; exon_number "1"; cov "6.512301";
-chr19	StringTie	transcript	3475786	3476529	1000	.	.	gene_id "STRG.19"; transcript_id "STRG.19.1"; cov "4.166667";FPKM "894.905579";
-chr19	StringTie	exon	3475786	3476529	1000	.	.	gene_id "STRG.19"; transcript_id "STRG.19.1"; exon_number "1"; cov "4.166667";
-chr19	StringTie	transcript	3474957	3475188	1000	-	.	gene_id "STRG.20"; transcript_id "STRG.20.1"; cov "3.719828";FPKM "798.934692";
-chr19	StringTie	exon	3474957	3475188	1000	-	.	gene_id "STRG.20"; transcript_id "STRG.20.1"; exon_number "1"; cov "3.719828";
-chr19	StringTie	transcript	3490820	3500661	1000	-	.	gene_id "STRG.21"; transcript_id "STRG.21.1"; cov "38.885868";FPKM "8351.802734";
-chr19	StringTie	exon	3490820	3491809	1000	-	.	gene_id "STRG.21"; transcript_id "STRG.21.1"; exon_number "1"; cov "49.893391";
-chr19	StringTie	exon	3492260	3492497	1000	-	.	gene_id "STRG.21"; transcript_id "STRG.21.1"; exon_number "2"; cov "14.960925";
-chr19	StringTie	exon	3494026	3494102	1000	-	.	gene_id "STRG.21"; transcript_id "STRG.21.1"; exon_number "3"; cov "22.457817";
-chr19	StringTie	exon	3496539	3496884	1000	-	.	gene_id "STRG.21"; transcript_id "STRG.21.1"; exon_number "4"; cov "35.878857";
-chr19	StringTie	exon	3500559	3500661	1000	-	.	gene_id "STRG.21"; transcript_id "STRG.21.1"; exon_number "5"; cov "10.650763";
+test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "44.724823";FPKM "3276543.750000";
+test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "49.011967";
+test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "51.382565";
+test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "21.090000";
diff -r 62d212192002 -r 9f80c71f1779 test-data/stringtie_out2.gtf
--- a/test-data/stringtie_out2.gtf	Thu Jul 03 18:38:02 2014 -0400
+++ b/test-data/stringtie_out2.gtf	Thu Mar 05 11:41:12 2015 -0500
@@ -1,145 +1,4 @@
-chr19	StringTie	transcript	3052907	3062360	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "883.073547";FPKM "189664.171875";
-chr19	StringTie	exon	3052907	3054038	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "966.177673";
-chr19	StringTie	exon	3054118	3054192	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "1301.127930";
-chr19	StringTie	exon	3055662	3055724	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "1990.478271";
-chr19	StringTie	exon	3056310	3056354	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "4"; cov "942.796082";
-chr19	StringTie	exon	3057677	3057740	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "5"; cov "351.962616";
-chr19	StringTie	exon	3061158	3061255	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "6"; cov "1122.192017";
-chr19	StringTie	exon	3062172	3062360	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "7"; cov "214.494049";
-chr19	StringTie	transcript	3052907	3063089	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.2"; cov "168.800812";FPKM "36254.585938";
-chr19	StringTie	exon	3052907	3054038	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "1"; cov "220.181381";
-chr19	StringTie	exon	3054118	3054192	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "2"; cov "258.932983";
-chr19	StringTie	exon	3055662	3055724	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "3"; cov "176.962967";
-chr19	StringTie	exon	3056310	3056354	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "4"; cov "118.451096";
-chr19	StringTie	exon	3057677	3057740	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "5"; cov "254.885681";
-chr19	StringTie	exon	3061158	3061255	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "6"; cov "78.436821";
-chr19	StringTie	exon	3062698	3063089	1000	-	.	gene_id "STRG.1"; transcript_id "STRG.1.2"; exon_number "7"; cov "16.186066";
-chr19	StringTie	transcript	2997664	3015854	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; cov "115.851471";FPKM "24882.267578";
-chr19	StringTie	exon	2997664	2997953	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "1"; cov "110.703667";
-chr19	StringTie	exon	3000645	3000721	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "2"; cov "207.771072";
-chr19	StringTie	exon	3002351	3002501	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "3"; cov "114.276024";
-chr19	StringTie	exon	3005435	3005582	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "4"; cov "120.278976";
-chr19	StringTie	exon	3005719	3005966	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "5"; cov "78.667053";
-chr19	StringTie	exon	3006418	3006667	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "6"; cov "48.566441";
-chr19	StringTie	exon	3008867	3008943	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "7"; cov "66.379005";
-chr19	StringTie	exon	3009540	3009700	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "8"; cov "62.793331";
-chr19	StringTie	exon	3011020	3011158	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "9"; cov "219.519562";
-chr19	StringTie	exon	3013667	3013816	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "10"; cov "172.405579";
-chr19	StringTie	exon	3014568	3014612	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "11"; cov "342.860687";
-chr19	StringTie	exon	3015651	3015854	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "12"; cov "119.223740";
-chr19	StringTie	transcript	3018960	3029141	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; cov "18.253860";FPKM "3920.515381";
-chr19	StringTie	exon	3018960	3019461	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "1"; cov "10.802196";
-chr19	StringTie	exon	3019697	3019771	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "2"; cov "23.808632";
-chr19	StringTie	exon	3025018	3025080	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "3"; cov "33.401360";
-chr19	StringTie	exon	3027827	3027871	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "4"; cov "41.172310";
-chr19	StringTie	exon	3028317	3028380	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "5"; cov "42.650341";
-chr19	StringTie	exon	3028704	3028801	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "6"; cov "32.359097";
-chr19	StringTie	exon	3028879	3029141	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "7"; cov "12.150498";
-chr19	StringTie	transcript	3018960	3029141	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.3"; cov "5.218285";FPKM "1120.769287";
-chr19	StringTie	exon	3018960	3019464	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.3"; exon_number "1"; cov "4.017776";
-chr19	StringTie	exon	3019697	3019771	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.3"; exon_number "2"; cov "15.457561";
-chr19	StringTie	exon	3025018	3025080	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.3"; exon_number "3"; cov "1.183362";
-chr19	StringTie	exon	3027827	3027871	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.3"; exon_number "4"; cov "3.434842";
-chr19	StringTie	exon	3028317	3028380	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.3"; exon_number "5"; cov "20.437429";
-chr19	StringTie	exon	3028704	3028801	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.3"; exon_number "6"; cov "6.825138";
-chr19	StringTie	exon	3028879	3029141	1000	-	.	gene_id "STRG.2"; transcript_id "STRG.2.3"; exon_number "7"; cov "1.572921";
-chr19	StringTie	transcript	3094613	3119121	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; cov "80.540161";FPKM "17298.201172";
-chr19	StringTie	exon	3094613	3094785	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "1"; cov "67.409538";
-chr19	StringTie	exon	3110147	3110331	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "2"; cov "102.204170";
-chr19	StringTie	exon	3113328	3113482	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "3"; cov "108.144516";
-chr19	StringTie	exon	3114942	3115070	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "4"; cov "63.896484";
-chr19	StringTie	exon	3118922	3119121	1000	+	.	gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "5"; cov "61.832138";
-chr19	StringTie	transcript	3119186	3123995	1000	+	.	gene_id "STRG.4"; transcript_id "STRG.4.1"; cov "69.395134";FPKM "14904.501953";
-chr19	StringTie	exon	3119186	3119357	1000	+	.	gene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "1"; cov "71.938263";
-chr19	StringTie	exon	3120987	3123995	1000	+	.	gene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "2"; cov "69.249763";
-chr19	StringTie	transcript	3136149	3163782	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; cov "13.414832";FPKM "2881.201660";
-chr19	StringTie	exon	3136149	3136593	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "1"; cov "2.243525";
-chr19	StringTie	exon	3148589	3148773	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "2"; cov "6.817567";
-chr19	StringTie	exon	3150129	3150283	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "3"; cov "12.169776";
-chr19	StringTie	exon	3151705	3151833	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "4"; cov "5.409668";
-chr19	StringTie	exon	3155821	3155950	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "5"; cov "22.124674";
-chr19	StringTie	exon	3157726	3157879	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "6"; cov "16.131796";
-chr19	StringTie	exon	3162791	3163782	1000	+	.	gene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "7"; cov "19.328829";
-chr19	StringTie	transcript	3176651	3177191	1000	.	.	gene_id "STRG.6"; transcript_id "STRG.6.1"; cov "2.218115";FPKM "476.400818";
-chr19	StringTie	exon	3176651	3177191	1000	.	.	gene_id "STRG.6"; transcript_id "STRG.6.1"; exon_number "1"; cov "2.218115";
-chr19	StringTie	transcript	3178008	3178218	1000	.	.	gene_id "STRG.7"; transcript_id "STRG.7.1"; cov "2.132701";FPKM "458.055786";
-chr19	StringTie	exon	3178008	3178218	1000	.	.	gene_id "STRG.7"; transcript_id "STRG.7.1"; exon_number "1"; cov "2.132701";
-chr19	StringTie	transcript	3178290	3182254	1000	.	.	gene_id "STRG.8"; transcript_id "STRG.8.1"; cov "25.143421";FPKM "5400.236816";
-chr19	StringTie	exon	3178290	3182254	1000	.	.	gene_id "STRG.8"; transcript_id "STRG.8.1"; exon_number "1"; cov "25.143421";
-chr19	StringTie	transcript	3182964	3183191	1000	.	.	gene_id "STRG.9"; transcript_id "STRG.9.1"; cov "3.289474";FPKM "706.504456";
-chr19	StringTie	exon	3182964	3183191	1000	.	.	gene_id "STRG.9"; transcript_id "STRG.9.1"; exon_number "1"; cov "3.289474";
-chr19	StringTie	transcript	3183534	3184980	1000	.	.	gene_id "STRG.10"; transcript_id "STRG.10.1"; cov "10.234969";FPKM "2198.239258";
-chr19	StringTie	exon	3183534	3184980	1000	.	.	gene_id "STRG.10"; transcript_id "STRG.10.1"; exon_number "1"; cov "10.234969";
-chr19	StringTie	transcript	3185059	3185762	1000	.	.	gene_id "STRG.11"; transcript_id "STRG.11.1"; cov "4.474432";FPKM "961.006531";
-chr19	StringTie	exon	3185059	3185762	1000	.	.	gene_id "STRG.11"; transcript_id "STRG.11.1"; exon_number "1"; cov "4.474432";
-chr19	StringTie	transcript	3185993	3209570	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.1"; cov "46.485111";FPKM "9983.947266";
-chr19	StringTie	exon	3185993	3186212	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.1"; exon_number "1"; cov "9.429298";
-chr19	StringTie	exon	3192468	3192658	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.1"; exon_number "2"; cov "21.059887";
-chr19	StringTie	exon	3193282	3193426	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.1"; exon_number "3"; cov "39.715225";
-chr19	StringTie	exon	3196181	3196275	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.1"; exon_number "4"; cov "37.911308";
-chr19	StringTie	exon	3198815	3198895	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.1"; exon_number "5"; cov "51.996696";
-chr19	StringTie	exon	3201521	3201624	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.1"; exon_number "6"; cov "31.073275";
-chr19	StringTie	exon	3203754	3203842	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.1"; exon_number "7"; cov "55.852036";
-chr19	StringTie	exon	3204003	3204142	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.1"; exon_number "8"; cov "30.771446";
-chr19	StringTie	exon	3204571	3204749	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.1"; exon_number "9"; cov "34.595020";
-chr19	StringTie	exon	3205937	3206024	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.1"; exon_number "10"; cov "43.030930";
-chr19	StringTie	exon	3206150	3206188	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.1"; exon_number "11"; cov "59.276905";
-chr19	StringTie	exon	3206260	3206423	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.1"; exon_number "12"; cov "46.387093";
-chr19	StringTie	exon	3207196	3207249	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.1"; exon_number "13"; cov "63.118416";
-chr19	StringTie	exon	3207389	3207467	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.1"; exon_number "14"; cov "65.674583";
-chr19	StringTie	exon	3207627	3209570	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.1"; exon_number "15"; cov "54.248878";
-chr19	StringTie	transcript	3195437	3209570	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.2"; cov "17.133051";FPKM "3679.790771";
-chr19	StringTie	exon	3195437	3196275	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.2"; exon_number "1"; cov "10.562823";
-chr19	StringTie	exon	3198815	3198895	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.2"; exon_number "2"; cov "17.045162";
-chr19	StringTie	exon	3201521	3201624	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.2"; exon_number "3"; cov "9.639905";
-chr19	StringTie	exon	3203754	3203842	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.2"; exon_number "4"; cov "14.507616";
-chr19	StringTie	exon	3204003	3204142	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.2"; exon_number "5"; cov "5.000354";
-chr19	StringTie	exon	3204571	3204749	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.2"; exon_number "6"; cov "10.209009";
-chr19	StringTie	exon	3205937	3206024	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.2"; exon_number "7"; cov "16.365309";
-chr19	StringTie	exon	3206150	3206188	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.2"; exon_number "8"; cov "25.572968";
-chr19	StringTie	exon	3206263	3206423	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.2"; exon_number "9"; cov "19.185726";
-chr19	StringTie	exon	3207196	3207249	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.2"; exon_number "10"; cov "38.189373";
-chr19	StringTie	exon	3207389	3207467	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.2"; exon_number "11"; cov "31.688845";
-chr19	StringTie	exon	3207627	3209570	1000	+	.	gene_id "STRG.12"; transcript_id "STRG.12.2"; exon_number "12"; cov "20.523384";
-chr19	StringTie	transcript	3363620	3364229	1000	.	.	gene_id "STRG.13"; transcript_id "STRG.13.1"; cov "2.622951";FPKM "563.350403";
-chr19	StringTie	exon	3363620	3364229	1000	.	.	gene_id "STRG.13"; transcript_id "STRG.13.1"; exon_number "1"; cov "2.622951";
-chr19	StringTie	transcript	3366538	3469274	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.1"; cov "71.175430";FPKM "15286.868164";
-chr19	StringTie	exon	3366538	3366664	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.1"; exon_number "1"; cov "11.686789";
-chr19	StringTie	exon	3381710	3382241	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.1"; exon_number "2"; cov "56.353500";
-chr19	StringTie	exon	3425104	3425175	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.1"; exon_number "3"; cov "74.173615";
-chr19	StringTie	exon	3433516	3433590	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.1"; exon_number "4"; cov "65.354446";
-chr19	StringTie	exon	3434275	3434398	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.1"; exon_number "5"; cov "80.448212";
-chr19	StringTie	exon	3435081	3435205	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.1"; exon_number "6"; cov "71.471077";
-chr19	StringTie	exon	3449012	3449137	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.1"; exon_number "7"; cov "107.203087";
-chr19	StringTie	exon	3452480	3452664	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.1"; exon_number "8"; cov "71.914742";
-chr19	StringTie	exon	3453761	3453914	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.1"; exon_number "9"; cov "30.357872";
-chr19	StringTie	exon	3456548	3456633	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.1"; exon_number "10"; cov "40.561024";
-chr19	StringTie	exon	3462750	3469274	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.1"; exon_number "11"; cov "74.051750";
-chr19	StringTie	transcript	3366538	3469274	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.2"; cov "18.338432";FPKM "3938.679688";
-chr19	StringTie	exon	3366538	3366664	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "1"; cov "3.412646";
-chr19	StringTie	exon	3381710	3382241	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "2"; cov "15.545184";
-chr19	StringTie	exon	3425104	3425175	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "3"; cov "21.998638";
-chr19	StringTie	exon	3433516	3433590	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "4"; cov "17.916565";
-chr19	StringTie	exon	3434275	3434398	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "5"; cov "24.749645";
-chr19	StringTie	exon	3435081	3435205	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "6"; cov "20.192204";
-chr19	StringTie	exon	3449012	3449137	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "7"; cov "19.043257";
-chr19	StringTie	exon	3452480	3452664	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "8"; cov "32.998787";
-chr19	StringTie	exon	3462750	3469274	1000	+	.	gene_id "STRG.14"; transcript_id "STRG.14.2"; exon_number "9"; cov "18.234524";
-chr19	StringTie	transcript	3472911	3473297	1000	.	.	gene_id "STRG.15"; transcript_id "STRG.15.1"; cov "2.842377";FPKM "610.478088";
-chr19	StringTie	exon	3472911	3473297	1000	.	.	gene_id "STRG.15"; transcript_id "STRG.15.1"; exon_number "1"; cov "2.842377";
-chr19	StringTie	transcript	3473383	3473585	1000	.	.	gene_id "STRG.16"; transcript_id "STRG.16.1"; cov "2.216749";FPKM "476.107422";
-chr19	StringTie	exon	3473383	3473585	1000	.	.	gene_id "STRG.16"; transcript_id "STRG.16.1"; exon_number "1"; cov "2.216749";
-chr19	StringTie	transcript	3473881	3474130	1000	.	.	gene_id "STRG.17"; transcript_id "STRG.17.1"; cov "5.800000";FPKM "1245.708496";
-chr19	StringTie	exon	3473881	3474130	1000	.	.	gene_id "STRG.17"; transcript_id "STRG.17.1"; exon_number "1"; cov "5.800000";
-chr19	StringTie	transcript	3474201	3474891	1000	.	.	gene_id "STRG.18"; transcript_id "STRG.18.1"; cov "6.512301";FPKM "1398.694580";
-chr19	StringTie	exon	3474201	3474891	1000	.	.	gene_id "STRG.18"; transcript_id "STRG.18.1"; exon_number "1"; cov "6.512301";
-chr19	StringTie	transcript	3475786	3476529	1000	.	.	gene_id "STRG.19"; transcript_id "STRG.19.1"; cov "4.166667";FPKM "894.905579";
-chr19	StringTie	exon	3475786	3476529	1000	.	.	gene_id "STRG.19"; transcript_id "STRG.19.1"; exon_number "1"; cov "4.166667";
-chr19	StringTie	transcript	3474957	3475188	1000	-	.	gene_id "STRG.20"; transcript_id "STRG.20.1"; cov "3.719828";FPKM "798.934692";
-chr19	StringTie	exon	3474957	3475188	1000	-	.	gene_id "STRG.20"; transcript_id "STRG.20.1"; exon_number "1"; cov "3.719828";
-chr19	StringTie	transcript	3490820	3500661	1000	-	.	gene_id "STRG.21"; transcript_id "STRG.21.1"; cov "38.885868";FPKM "8351.802734";
-chr19	StringTie	exon	3490820	3491809	1000	-	.	gene_id "STRG.21"; transcript_id "STRG.21.1"; exon_number "1"; cov "49.893391";
-chr19	StringTie	exon	3492260	3492497	1000	-	.	gene_id "STRG.21"; transcript_id "STRG.21.1"; exon_number "2"; cov "14.960925";
-chr19	StringTie	exon	3494026	3494102	1000	-	.	gene_id "STRG.21"; transcript_id "STRG.21.1"; exon_number "3"; cov "22.457817";
-chr19	StringTie	exon	3496539	3496884	1000	-	.	gene_id "STRG.21"; transcript_id "STRG.21.1"; exon_number "4"; cov "35.878857";
-chr19	StringTie	exon	3500559	3500661	1000	-	.	gene_id "STRG.21"; transcript_id "STRG.21.1"; exon_number "5"; cov "10.650763";
+test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "44.724823";FPKM "3276543.750000";
+test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "49.011967";
+test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "51.382565";
+test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "21.090000";
diff -r 62d212192002 -r 9f80c71f1779 test-data/stringtie_out3.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/stringtie_out3.gtf	Thu Mar 05 11:41:12 2015 -0500
@@ -0,0 +1,4 @@
+test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; cov "44.724823";FPKM "3276543.750000";
+test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; cov "49.011967";
+test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; cov "51.382565";
+test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; cov "21.090000";
diff -r 62d212192002 -r 9f80c71f1779 test-data/stringtie_out4.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/stringtie_out4.gtf	Thu Mar 05 11:41:12 2015 -0500
@@ -0,0 +1,4 @@
+test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; cov "44.724823";FPKM "3276543.750000";
+test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; cov "49.011967";
+test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; cov "51.382565";
+test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; cov "21.090000";
diff -r 62d212192002 -r 9f80c71f1779 test-data/stringtie_out5.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/stringtie_out5.gtf	Thu Mar 05 11:41:12 2015 -0500
@@ -0,0 +1,4 @@
+test_chromosome	StringTie	transcript	53	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; cov "44.724823";FPKM "3276543.750000";
+test_chromosome	StringTie	exon	53	250	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; cov "49.011967";
+test_chromosome	StringTie	exon	351	400	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; cov "51.382565";
+test_chromosome	StringTie	exon	501	550	1000	+	.	gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; cov "21.090000";
diff -r 62d212192002 -r 9f80c71f1779 test-data/stringtie_out_coverage.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/stringtie_out_coverage.gtf	Thu Mar 05 11:41:12 2015 -0500
@@ -0,0 +1,4 @@
+test_chromosome	Cufflinks	transcript	53	550	1000.00	+	.	ID=CUFF.1.1;geneID=CUFF.1
+test_chromosome	Cufflinks	exon	53	250	1000.00	+	.	Parent=CUFF.1.1
+test_chromosome	Cufflinks	exon	351	400	1000.00	+	.	Parent=CUFF.1.1
+test_chromosome	Cufflinks	exon	501	550	1000.00	+	.	Parent=CUFF.1.1
diff -r 62d212192002 -r 9f80c71f1779 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Jul 03 18:38:02 2014 -0400
+++ b/tool_dependencies.xml	Thu Mar 05 11:41:12 2015 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="stringtie" version="0.97">
-      <repository changeset_revision="bbcdfb50d3f0" name="package_stringtie_0_97" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+  <package name="stringtie" version="1.0.1">
+      <repository changeset_revision="cd94bd10219b" name="package_stringtie_1_0_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>