# HG changeset patch
# User iuc
# Date 1404427082 14400
# Node ID 62d21219200212b7cecb98ab2bcc579b75b99b58

Imported from capsule None

diff -r 000000000000 -r 62d212192002 stringtie.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/stringtie.xml	Thu Jul 03 18:38:02 2014 -0400
@@ -0,0 +1,117 @@
+<?xml version="1.0"?>
+<tool name="StringTie" id="stringtie" version="1.0.0">
+    <description>RNA-Seq assembler</description>
+    <requirements>
+        <requirement type="package" version="0.97">stringtie</requirement>
+    </requirements>
+    <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"
+#end if
+#if str($option_set.options) == 'advanced':
+    -f "$option_set.fraction"
+    -m "$option_set.min_tlen"
+    -a "$option_set.min_anchor_len"
+    -j "$option_set.min_anchor_cov"
+    -c "$option_set.min_bundle_cov"
+    -s "$option_set.maxcov"
+    -g "$option_set.bdist"    
+    -M "$option_set.bundle_fraction" $option_set.sensitive $option_set.disable_trimming
+#end if
+]]>
+</command>
+    <inputs>
+        <param name="input_bam" type="data" format="bam" label="BAM file to assemble" />
+        <conditional name="guide">
+            <param name="use_guide" type="select" label="Use GFF file to guide assembly">
+                <option value="yes">Use GFF</option>
+                <option value="no" selected="True">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" />
+            </when>
+        </conditional>
+        <conditional name="option_set">
+            <param name="options" type="select" label="Options">
+                <option value="default" selected="True">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>
+        </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">
+            <filter>guide['use_guide'] == "yes"</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_bam" value="stringtie_in1.bam" ftype="bam" />
+            <param name="use_guide" value="no" />
+            <param name="options" value="default" />
+            <output name="output_gtf" file="stringtie_out1.gtf" ftype="gtf" />
+        </test>
+        <test>
+            <param name="input_bam" value="stringtie_in1.bam" ftype="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" />
+        </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.
+
+   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
diff -r 000000000000 -r 62d212192002 test-data/._stringtie_in1.bam
Binary file test-data/._stringtie_in1.bam has changed
diff -r 000000000000 -r 62d212192002 test-data/._stringtie_out2.gtf
Binary file test-data/._stringtie_out2.gtf has changed
diff -r 000000000000 -r 62d212192002 test-data/stringtie_in1.bam
Binary file test-data/stringtie_in1.bam has changed
diff -r 000000000000 -r 62d212192002 test-data/stringtie_out1.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/stringtie_out1.gtf	Thu Jul 03 18:38:02 2014 -0400
@@ -0,0 +1,154 @@
+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";
diff -r 000000000000 -r 62d212192002 test-data/stringtie_out2.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/stringtie_out2.gtf	Thu Jul 03 18:38:02 2014 -0400
@@ -0,0 +1,145 @@
+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";
diff -r 000000000000 -r 62d212192002 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Jul 03 18:38:02 2014 -0400
@@ -0,0 +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>
+</tool_dependency>