# HG changeset patch
# User iuc
# Date 1424277401 18000
# Node ID 1903b1fe70fcdc31754e4eab4e5f5eb6bfab718a
# Parent  a711b92d85c1c836fe017650e7890bed9c90946b
Uploaded

diff -r a711b92d85c1 -r 1903b1fe70fc prepStar.sh
--- a/prepStar.sh	Wed Mar 05 19:06:51 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-# automate rnastar index generation
-# from existing fasta genomes using limited ram - cut genomeChrbinNbits down to 13, genomeSAindexNbases 12 genomeSAsparseD 1
-
-INDEXROOT=/mnt/galaxyIndices/genomes
-# fix that, the list of genomes below and SOURCE below to suit your needs. This is for GVL august 2013
-for genome in Arabidopsis_thaliana_TAIR9  ce10  danRer7  dm3  hg19  hg_g1k_v37  mm9  phiX  rn5  sacCer2  sacCer3  xenTro2
-do
-  SOURCE=${INDEXROOT}/${genome}/seq/
-  TARGET=${INDEXROOT}/${genome}/rnastar
-  mkdir -p $TARGET
-  cd $TARGET
-/mnt/galaxy/tools/rnastar/2.3.0e/fubar/rgrnastar_203e/9425706f4e97/bin/STAR --runMode genomeGenerate --genomeDir $TARGET --genomeFastaFiles ${SOURCE}/${genome}.fa --runThreadN 2 genomeLoad=NoSharedMemory --genomeChrBinNbits 13 genomeSAindexNbases 12 genomeSAsparseD 1
-done
-
-echo "#add these lines TABS not spaces please to rnastar_indexes.loc in tool-data" > rnastar_indexes.loc
-for genome in Arabidopsis_thaliana_TAIR9  ce10  danRer7  dm3  hg19  hg_g1k_v37  mm9  phiX  rn5  sacCer2  sacCer3  xenTro2
-do
-  SOURCE=${INDEXROOT}/${genome}/seq/
-  TARGET=${INDEXROOT}/${genome}/rnastar
-  echo ${genome}'\t'${genome}'\t'${genome}'\t'/mnt/galaxyIndices/genomes/${genome}/rnastar >> rnastar_indexes.loc
-done
diff -r a711b92d85c1 -r 1903b1fe70fc rg_rnaStar.xml
--- a/rg_rnaStar.xml	Wed Mar 05 19:06:51 2014 -0500
+++ b/rg_rnaStar.xml	Wed Feb 18 11:36:41 2015 -0500
@@ -1,49 +1,60 @@
-<tool id="rna_star" name="RNA-STAR" version="0.23">
+<tool id="rna_star" name="rnastar" version="2.4.0d">
     <description>Gapped-read mapper for RNA-seq data</description>
     <requirements>
-        <requirement type="package" version="2.3.1z">rnastar</requirement>
+        <requirement type="package" version="2.4.0d">rnastar</requirement>
         <requirement type="package" version="0.1.19">samtools</requirement>
     </requirements>
     <command>
     ##
     ## Run STAR.
     ##
-
-        STAR
+    #if str($refGenomeSource.genomeSource) == 'history':
+       mkdir -p tempstargenomedir; STAR --runMode genomeGenerate --genomeDir "tempstargenomedir" --genomeFastaFiles "$refGenomeSource.ownFile" --runThreadN 2
+        #if str($refGenomeSource.geneModel) != 'None':
+          --sjdbOverhang "100" --sjdbGTFfile "$refGenomeSource.geneModel"
+          #if str($refGenomeSource.geneModel.ext) == 'gff3':
+            --sjdbGTFtagExonParentTranscript Parent
+          #end if
+        #end if
+        ;
+    #end if
+    STAR
     ## Can adjust this as appropriate for the system.
     --genomeLoad NoSharedMemory
-
-    --genomeDir ${refGenomeSource.index.fields.path} 
-    --readFilesIn $input1 
-    #if $singlePaired.sPaired == "paired"
+    #if str($refGenomeSource.genomeSource) == 'history':
+        --genomeDir "tempstargenomedir"
+    #else
+        --genomeDir $refGenomeSource.index.fields.pathls 
+    #end if
+    --readFilesIn $singlePaired.input1 
+    #if str($singlePaired.sPaired) == "paired"
             $singlePaired.input2
-        #end if
+    #end if
         --runThreadN 4
-    #if $params.settingsType == "full":
+    #if str($params.settingsType) == "full":
         --chimSegmentMin $params.chim_segment_min
         --chimScoreMin $params.chim_score_min
     #end if
 
     ## may or may not need to generate SAM tags and handle non-canonicals for Cufflinks tools.
-    ${outSAMstrandField} ${outFilterIntronMotifs} ${outSAMattributes}
+    $outSAMstrandField $outFilterIntronMotifs $outSAMattributes
 
     ;
-
     ##
     ## BAM conversion.
     ##
 
     ## Convert aligned reads.
-    samtools view -Shb Aligned.out.sam | samtools sort - Aligned.out
+    samtools view -Shb Aligned.out.sam | samtools sort - AlignedSorted 2&gt;/dev/null 
 
     ## Convert chimeric reads.
-    #if $params.settingsType == "full" and $params.chim_segment_min > 0:
-        ; samtools view -Shb Chimeric.out.sam | samtools sort - Chimeric.out
+    #if str($params.settingsType) == "full" and $params.chim_segment_min > 0:
+        ; samtools view -Shb Chimeric.out.sam | samtools sort - ChimericSorted 2&gt;/dev/null 
     #end if
     </command>
 
     <stdio>
-        <regex match=".*" source="both" level="warning" description="generic stdout/err chatter"/>
+        <regex match=".*" source="both" level="warning" description="Some stderr/stdout text"/>
     </stdio>
 
     <inputs>
@@ -63,20 +74,22 @@
                 <param format="fastqsanger,fastq,fasta" name="input1" type="data" label="RNA-Seq FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33"/>
             </when>
             <when value="paired">
-                <param format="fastqsanger,fastq,fasta" name="input1" type="data" label="RNA-Seq FASTQ file, forward reads" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
-                <param format="fastqsanger,fastq,fasta" name="input2" type="data" label="RNA-Seq FASTQ file, reverse reads" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
+                <param format="fastqsanger,fastq,fasta" name="input1" type="data" label="RNA-Seq FASTQ file, forward reads" 
+            help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
+                <param format="fastqsanger,fastq,fasta" name="input2" type="data" label="RNA-Seq FASTQ file, reverse reads"
+            help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
             </when>
         </conditional>
 
         <!-- Genome source. -->
         <conditional name="refGenomeSource">
             <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
-                <option value="indexed">Use a built-in index</option>
-                <option value="history">Use one from the history</option>
+                <option value="indexed" selected="True">Use a built-in index</option>
+                <option value="history">Index and use a genome fasta file from my current history</option>
             </param>
             <when value="indexed">
             <param name="index" type="select" label="Select a reference genome">
-                <options from_data_table="rnastar_indexes">
+                <options from_data_table="rnastar_index">
                     <filter type="sort_by" column="2"/>
                     <validator type="no_options" message="No indexes are available for the selected input dataset"/>
                 </options>
@@ -84,6 +97,8 @@
             </when>
             <when value="history">
                 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
+                <param name="geneModel" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions. Leave blank for none"
+                optional="true" help="Optional. If supplied, the index file will retain exon junction information for mapping splices" />
             </when>
         </conditional>
             <param name="outSAMattributes" type="select" label="Include extra sam attributes for downstream processing">
@@ -116,14 +131,14 @@
     </inputs>
 
     <outputs>
-       <data format="txt" name="output_log" label="${on_string}_{jobName}.log" from_work_dir="Log.final.out"/>
-       <data format="interval" name="chimeric_junctions" label="${on_string}_{jobName}_starchimjunc.bed" from_work_dir="Chimeric.out.junction">
+       <data format="txt" name="output_log" label="${jobName}.log" from_work_dir="Log.final.out"/>
+       <data format="interval" name="chimeric_junctions" label="${jobName}_starchimjunc.bed" from_work_dir="Chimeric.out.junction">
           <filter>(params['settingsType'] == 'full' and params['chim_segment_min'] > 0)</filter>
           <actions>
              <conditional name="refGenomeSource.genomeSource">
              <when value="indexed">
                <action type="metadata" name="dbkey">
-                <option type="from_data_table" name="star_indexes" column="1" offset="0">
+                <option type="from_data_table" name="rnastar_index" column="1" offset="0">
                  <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
                   <filter type="param_value" ref="refGenomeSource.index" column="0"/>
                 </option>
@@ -137,14 +152,14 @@
              </conditional>
           </actions>
        </data>
-       <data format="bam" name="chimeric_reads" label="${on_string}_${jobName}_starmappedchim.bam" 
-                    from_work_dir="Chimeric.out.bam">
+       <data format="bam" name="chimeric_reads" label="${jobName}_starmappedchim.bam" 
+                    from_work_dir="ChimericSorted.bam">
          <filter>(params['settingsType'] == 'full' and params['chim_segment_min'] > 0)</filter>
           <actions>
              <conditional name="refGenomeSource.genomeSource">
              <when value="indexed">
                <action type="metadata" name="dbkey">
-                <option type="from_data_table" name="star_indexes" column="1" offset="0">
+                <option type="from_data_table" name="rnastar_index" column="1" offset="0">
                  <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
                   <filter type="param_value" ref="refGenomeSource.index" column="0"/>
                 </option>
@@ -158,13 +173,13 @@
              </conditional>
           </actions>
         </data>
-        <data format="interval" name="splice_junctions" label="${on_string}_${jobName}_starsplicejunct.bed" 
+        <data format="interval" name="splice_junctions" label="${jobName}_starsplicejunct.bed" 
                    from_work_dir="SJ.out.tab">
           <actions>
              <conditional name="refGenomeSource.genomeSource">
              <when value="indexed">
                <action type="metadata" name="dbkey">
-                <option type="from_data_table" name="star_indexes" column="1" offset="0">
+                <option type="from_data_table" name="rnastar_index" column="1" offset="0">
                  <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
                   <filter type="param_value" ref="refGenomeSource.index" column="0"/>
                 </option>
@@ -178,13 +193,13 @@
              </conditional>
           </actions>
         </data>
-        <data format="bam" name="mapped_reads" label="${on_string}_${jobName}_starmapped.bam" 
-                    from_work_dir="Aligned.out.bam">
+        <data format="bam" name="mapped_reads" label="${jobName}_starmapped.bam" 
+                    from_work_dir="AlignedSorted.bam">
           <actions>
              <conditional name="refGenomeSource.genomeSource">
              <when value="indexed">
                <action type="metadata" name="dbkey">
-                <option type="from_data_table" name="star_indexes" column="1" offset="0">
+                <option type="from_data_table" name="rnastar_index" column="1" offset="0">
                  <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
                   <filter type="param_value" ref="refGenomeSource.index" column="0"/>
                 </option>
@@ -199,6 +214,21 @@
           </actions>
         </data>
     </outputs>
+    <tests>
+        <test>
+ <param name='input1' value='tophat_in2.fastqsanger' ftype='fastqsanger' />
+ <param name='jobName' value='rnastar_test' />
+ <param name='genomeSource' value='history' />
+ <param name='ownFile' value='tophat_test.fa' />
+ <param name='sPaired' value='single' />
+ <param name='outSAMattributes' value='--outSAMattributes All' />
+ <param name='outSAMstrandField' value='--outSAMstrandField intronMotif' />
+ <param name='outFilterIntronMotifs' value='--outFilterIntronMotifs RemoveNoncanonical' />
+ <output name='output_log' file='rnastar_test.log' compare='diff' lines_diff = '10'/>
+ <output name='splice_junctions' file="rnastar_test_splicejunctions.bed" compare="sim_size" delta="200"/>
+ <output name='mapped_reads' file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="200" />
+        </test>
+    </tests>
 <help>
 
 **What it does**
@@ -243,10 +273,10 @@
 
 If you have stranded RNA-seq data, you do not need to use any specific STAR options. Instead, you need
 to run Cufflinks with the library option --library-type options. For example, cufflinks with
-library-type fr-firststrand should be used for the “standard” dUTP protocol.
-This option has to be used only for Cufflinks runs and not for STAR runs.
+library-type fr-firststrand should be used for the b
 
-It is recommended to remove the non-canonical junctions for Cufflinks runs using –
+It is recommended to remove the non-canonical junctions for Cufflinks runs using b
+
 
 --outFilterIntronMotifs RemoveNoncanonical
 filter out alignments that contain non-canonical junctions
@@ -284,4 +314,8 @@
 .. _Galaxy: http://getgalaxy.org
 
 </help>
+<citations>
+    <citation type="doi">doi: 10.1093/bioinformatics/bts635</citation>
+</citations>
 </tool>
+
diff -r a711b92d85c1 -r 1903b1fe70fc test-data/rnastar_test_mapped_reads.bam
Binary file test-data/rnastar_test_mapped_reads.bam has changed
diff -r a711b92d85c1 -r 1903b1fe70fc test-data/rnastar_test_splicejunctions.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnastar_test_splicejunctions.bed	Wed Feb 18 11:36:41 2015 -0500
@@ -0,0 +1,2 @@
+test_chromosome	251	350	1	1	0	27	0	37
+test_chromosome	401	500	1	1	0	25	0	36
diff -r a711b92d85c1 -r 1903b1fe70fc test-data/tophat_in2.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tophat_in2.fastqsanger	Wed Feb 18 11:36:41 2015 -0500
@@ -0,0 +1,400 @@
+@test_mRNA_150_290_0/1
+TCCTAAAAAGTCCGCCTCGGTCTCAGTCTCAAGTAGAAAAAGTCCCGTTGGCGATCCGTCTACGTCCGAGTAAGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_8_197_1/1
+TCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGACACTACGGGGATGGCGACTAGGACTACGGACGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_82_255_2/1
+GAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAATATAGTAAAGTAATAGTGGCGTATCGCAAGCTCGACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_96_238_3/1
+GATCCGTCTACGTCCGCGTAAGATAATAAAGTACTAGTAGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_72_258_4/1
+GTAGAAAAAGTCCCGTTGCCCATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_107_286_5/1
+AAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_122_299_6/1
+CAAGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGCTCCGTCTACGTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_58_234_7/1
+AGTCTACGTCCGAGTCAGATAATAAACTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_57_231_8/1
+GGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCACCGACTGGACTATTTAGGACGATCGGACTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_8_155_9/1
+TACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTACAGTCGCTGCATCTGACGCTCGAAGTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_51_237_a/1
+ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_89_230_b/1
+TACGTCCGAGTGAGTTAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_105_276_c/1
+CCTCGATCCCAGTCTCAAGTAGAAAAAGCCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_111_268_d/1
+CCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAATAATAGTGGCGTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_151_286_e/1
+ACGTATTTGGCGCGCGGCCGTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_118_297_f/1
+AGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_16_194_10/1
+TCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_28_188_11/1
+TTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGAACGGACTTAGAGCGTCAGATGCAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_36_218_12/1
+GAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGCCTTAGAGCGTCAGATGCAGCGACTGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_105_266_13/1
+AGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGGATCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_51_248_14/1
+ACTACGGGGATGACGACGAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGAACTTTTTAGGACGATC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_89_245_15/1
+AGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_58_218_16/1
+AGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_46_195_17/1
+ATCCCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGACAAATATGTAGCGTCCTACTGCCCTCCTCAGTCCAATCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_126_282_18/1
+AGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_53_212_19/1
+TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGAATATTTAGGACGATCGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_11_190_1a/1
+GACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_52_261_1b/1
+CTACGGGAATGACGACTAGGGCTACGGAGGGACTTACAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_104_274_1c/1
+TCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_151_297_1d/1
+ACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_44_225_1e/1
+CCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCATATACGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_28_206_1f/1
+TTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGACGCAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_48_249_20/1
+GTCCCGTTGCCGATCCGTCTCCGTCCGAGTAAGATAGTAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_75_235_21/1
+ACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGCACGATCGGACTGAGGAGGGCAGTAGAACGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_110_267_22/1
+CAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_69_229_23/1
+ACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTAGACGCTCAGCCGTAGGGCCGCGCGCCAAAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_21_208_24/1
+GTAATAGTGGCGTATCGCAAGCTCGACGCTCAGGCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_42_209_25/1
+GGACGTGCCACTACGTGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_97_275_26/1
+ATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_36_146_27/1
+ACCTACTGCACTCCTCAGTCCGATCGTCCTAAATAGTCCAGTCGCTGCATCTGACGCTCTAAGTCCGTCCGTAGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_110_271_28/1
+ACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_38_199_29/1
+GCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_103_284_2a/1
+AAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_116_271_2b/1
+ATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCTGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_77_256_2c/1
+GGACGGACTTAGAGCATCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_50_224_2d/1
+CGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_65_238_2e/1
+GACTAGGACTACGGACGGACTTAGAGCGTCAGAAGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_46_232_2f/1
+GTGCCACTACGGGGATGACGACTAGGACTACGGCCGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_26_189_30/1
+AGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTACCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_79_256_31/1
+AGAAAAAGTCCCGTTGCCGATCCGGCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATGGCAAGCTCGAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_89_267_32/1
+CAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGAAAGATAATAAAGTAATAGTGCCGTATC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_131_260_33/1
+GAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_73_240_34/1
+CTACGGACGGACTTAGAGCGTCAGATGCAGCGAATGGACTATTTAGGACGCTCGGACTGAGGAGGGCAGTAGGAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_44_197_35/1
+ACGTGCAACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_128_252_36/1
+ACTGAGGAGGGCAGTAGGACGCTACGCATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATAGGCCAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_145_300_37/1
+GCAAGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTTCCGATCCGTCTACGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_85_275_38/1
+TTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGAAGCTACGTCTTTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_48_207_39/1
+GCCCCTACGGGGATGACGACTAGGACTACGGACGGATTTAGACCGTCAGATGCAGCGACTGGACTATTTAGGACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_81_228_3a/1
+CCTACGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCATAGGGCCGCGCGCCAAATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_75_277_3b/1
+ACGGACGGACTTAAAGCTTCAGATGCAGCGACAGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_30_231_3c/1
+CTACGTGCGAGTAAGATATTAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTTAGCCGTAGGGCCGCGCGCCAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_58_220_3d/1
+GAAGATAATAAAGTAATAGTGGCGTATCGCAACCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_104_278_3e/1
+CGCCTCGATTCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_44_193_3f/1
+ACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGTCTATTTAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_94_291_40/1
+CAGATGCAGCGACTGTACTATTTAGGACGACCTGACTGAGGAGGGTAGTAGGACGCTACGTATTTGGCGCGCGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_91_256_41/1
+CGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_23_186_42/1
+TCGACGCTCAGTCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTTCTGCCCTCCTCCGTCCGATCGTCCTAAATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_92_266_43/1
+GTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTCAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_92_250_44/1
+GTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_106_253_45/1
+AAAAGTCCCGTTGCCGATCCGTTTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_5_197_46/1
+CTATCTGACTAGACTCGAGGCGCTTGCGTCTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_51_194_47/1
+TCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_125_280_48/1
+CGGACTGAGGAGGGCAGTAGGACGCTATGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGAAACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_51_194_49/1
+ACTACGGGGATGACGACTAGGCCTACGGATGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_33_189_4a/1
+AGCCCGACGCTCAGCCGTAGGGCCGCGCGCCAAATAGGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_78_276_4b/1
+GACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGGCGCTAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_63_229_4c/1
+ACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACACTCAGCCGTAGGGCCGCGCGCCAAAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_81_245_4d/1
+CGTTGCCGATCCGTCTACGTCCGAGTAAGATTATAAAGTAATAGTGGCGTATCGCAACCTCGACGCTCAGCCGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_33_223_4e/1
+ACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_172_294_4f/1
+ACGGATGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTCCTCGGACGTAGACGGATCGCCAACGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_88_257_50/1
+TAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_3_187_51/1
+TACTATTTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTCGGACTACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_9_179_52/1
+TCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATGGTCCAGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_85_268_53/1
+TTAGTGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_75_204_54/1
+ACGGACGGACTTCGAGCCTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_41_236_55/1
+AGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGAATATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_56_183_56/1
+GGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTGGGACGATCGGACT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_87_250_57/1
+AGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_82_271_58/1
+GACTTAGAGCGTCAGTTGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_6_182_59/1
+TATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCAGTACGGGGATGACGACTAGGACTACGGAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_53_272_5a/1
+GATCCCAGTGTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_114_277_5b/1
+GCCTCGATCCCAGTCTCAAGCAGAAAAAGTCCCGTTGCCGTTCCGTCTACCTCCGAGTAAGATAATAAAGTAATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_39_219_5c/1
+CTAGGACGTCCCACTATGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGGCTGGACTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_4_191_5d/1
+CAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGTGTCCTACTGCCCTACTCAGTCCGATCGTCCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_73_259_5e/1
+CTACGGACGGACTTAGAGCGTCAGATGCTGCGACTGGACTATTTGGGACGATCGGACTGAGGAGGGCAGTAGGAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_87_279_5f/1
+CCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_125_293_60/1
+CCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_111_297_61/1
+AGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCGGATCCGTCTACGTCCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_22_173_62/1
+AGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_116_295_63/1
+TCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
diff -r a711b92d85c1 -r 1903b1fe70fc test-data/tophat_in3.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tophat_in3.fastqsanger	Wed Feb 18 11:36:41 2015 -0500
@@ -0,0 +1,400 @@
+@test_mRNA_150_290_0/2
+TACGTATTTGTCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATCCGCCACTATTACTTTATTATCTTACTCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_8_197_1/2
+GTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_82_255_2/2
+GACTTAGAGCGTCAGATGCAGCGACTGGACTTTTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_96_238_3/2
+GATGCAGCGACTGGACTATTTAGGACGATCGGACGGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGACC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_72_258_4/2
+ACTACGGACGGACTTAGAGCGTCAGATGCAGCAACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_107_286_5/2
+TGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGCATTTGGCGCGCGGCCCTACGGCTGAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_122_299_6/2
+GATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_58_234_7/2
+GGATGACGCCTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_57_231_8/2
+CTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCCTAGGGCCGCGCGCCAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_8_155_9/2
+TGTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_51_237_a/2
+ATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_89_230_b/2
+AGCGTCAGGTGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_105_276_c/2
+ACTGGACTATTTAGGACGATCGGACTGAGGAAGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_111_268_d/2
+CTATTTAAGACGTTCCGCCTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_151_286_e/2
+AAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGATAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_118_297_f/2
+GGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_16_194_10/2
+GACTGGATGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTCGGACTACGGACGGACTTAAAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_28_188_11/2
+GCTCGACGCTCAGCCGTAGGGCCTCGCGCCAAATACGAAGCGTCCTACTGCCTTCCTCAGTCCGATCGTCCTAAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_36_218_12/2
+AGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_105_266_13/2
+ACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_51_248_14/2
+TCCCGTTGCCGTTCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_89_245_15/2
+CGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAGAGAAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_58_218_16/2
+GGATGACGACTAGGACTACGGACGGACTTAGAACGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_46_195_17/2
+GTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_126_282_18/2
+GGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_53_212_19/2
+TAAAGAAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_11_190_1a/2
+AAGCTCGACGCTCAGCCGTAGGGCCACGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCCATCGACCTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_52_261_1b/2
+CAAGTAGAAAAAGTCCCGTTGCCGATCCTTCTACGTCCGAGTAAGATAATTAAGTAATAGTGGCGTATCGCAAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_104_274_1c/2
+GAGTGTACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATGTGCCGCGCGGCCCTACGGCTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_151_297_1d/2
+AGTCCCGTCCTAAAATGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_44_225_1e/2
+ACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCGGGTGCAGCGACTGGACTATTTAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_28_206_1f/2
+AATAGTGGCTTATCGCAAGCTCGACTCTCAGCCGTAGGGCCGCGCGCCAAATACGTGGCGTCCTACTGCCCTCCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_48_249_20/2
+GCCACTACGGGGATGACGACTAGGACGACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_75_235_21/2
+CCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCAACGCTCAGCCGTAGGGCCGTGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_110_267_22/2
+ACTAGTTAGGGCGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAGTTGGCGCGCGGCCCTACGACTGAGCGTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_69_229_23/2
+AGGACTACGGACGGACTTATAGGGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_21_208_24/2
+GAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_42_209_25/2
+AGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_97_275_26/2
+CTCGATCCCAGTCTCAAGTAGAAAGAGTCCCGTTTCCGATCCGTCTACGTCCGACTAAGATAATAAAGTAATAGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_36_146_27/2
+GCGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACAGACGGACTTAGAGCGTCAGATGCAGCGACTGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_110_271_28/2
+ATCCCAGTCTCAAGTAGAAAAAGCCCCGTTGCCGATCCGTCTTCGTCCGAGTAAGATAATAAAGTAATAGTGGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_38_199_29/2
+GCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_103_284_2a/2
+CGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_116_271_2b/2
+TAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_77_256_2c/2
+AGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_50_224_2d/2
+CACTACGAGGATGACGTCTAGGACTACGGACGGACTTAGAGCGTCAGACGCAGCGACTGGACTATTTAGGACGAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_65_238_2e/2
+GATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCGCAGCCGTAGGGCCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_46_232_2f/2
+TCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_26_189_30/2
+GCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_79_256_31/2
+ACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_89_267_32/2
+AGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGAGTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_131_260_33/2
+AAGTAAAAAAAGTCCCGTGGCCGATCCGTTTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCACAAGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_73_240_34/2
+CCGATCCGTCTACGTCCGAGAAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_44_197_35/2
+GTATCGCAAGCTCGACGATCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_128_252_36/2
+AAAGTCCCGTTCCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_145_300_37/2
+GACGCTACGTATTTGGCGCGGGGCCCTATGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTAGTATATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_85_275_38/2
+CTCGATCCCAGTCTCAAGTAGTAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAAGAGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_48_207_39/2
+TAAGAGTGGCGTATCGCAAGATCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTTCCCTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_81_228_3a/2
+GGACTGAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGTAGTAGGACGCTACGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_75_277_3b/2
+GCCTCGATCCCAGTCTCAGGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_30_231_3c/2
+GCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_58_220_3d/2
+GGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_104_278_3e/2
+GACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTTTTTGGCGCGCGGCCCTACGGCTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_44_193_3f/2
+CGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCTCTCCCCAGTCCGATCGTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_94_291_40/2
+GTCCCAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAATGTCGCGTTGCCGATCCGTCTACGTCCCAGGAAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_91_256_41/2
+AGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_23_186_42/2
+GGCGCTTGTGACTGAGCTAGGACGTGCCACTACGGGGATGAAGACTAGGACTACGGACGGACTTAGAGCGTCAGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_92_266_43/2
+GGTCTCAAGTAGAAAAAGTCCCGTTGCCGCTCCGTCTACGTCCGAGTAAGATAAGAAAGTAATAGTGGCGTATCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_92_250_44/2
+AGTCCCGTACCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_106_253_45/2
+CTGGACTATTTAGGTCGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_5_197_46/2
+GTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCCCGCCAAATACGTAGCGTCCTACTGCCCTCCTCCGTCCGAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_51_194_47/2
+ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_125_280_48/2
+TCCGCCTCGCTCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCAGAGTAAGATAATAAAGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_51_194_49/2
+CCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTGGCGTCCTACTGCCCTCCTCAGTCCGAACGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_33_189_4a/2
+ACTGAGCTAGGACGTGCCACTACGGGGATTACCACTAGGGCTACGGACGGACTTAGAGCGTCAGATGCAGCGACT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_78_276_4b/2
+CCTCGATCCTAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_63_229_4c/2
+ACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGGGACTGGACTATTTAGGACGATCGGACTGAGGAGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_81_245_4d/2
+GGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGATGAGGGCAGTAGGACGCTACGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_33_223_4e/2
+GAGTTAGATAATAAAGTAATAGTGGCTTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACCTAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_172_294_4f/2
+CCCGTCCTAAAACGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGCTGCCGACCCGTCTACGTCCGAGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_88_257_50/2
+GAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_3_187_51/2
+CTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_9_179_52/2
+CTGACTAGACTGGAGGCGCTCGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_85_268_53/2
+CCAGTCTCAAGTAGAAAAAGTCCCGTTGACGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_75_204_54/2
+TCGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_41_236_55/2
+TCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_56_183_56/2
+ACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_87_250_57/2
+AGAGCGTCAGATGCAGAGACTGGACTATTTAGGACGATCGGACTGAGGAGTGCAGTAGGACGCTACGTATTTGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_82_271_58/2
+ATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATGCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_6_182_59/2
+CGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_53_272_5a/2
+TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_114_277_5b/2
+TTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGCCTGAGCGTCGAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_39_219_5c/2
+AAGATAATAAAGTAATAGTGGCGTATCGCAAGCTGGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_4_191_5d/2
+ACTATCTGACGAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTACCATTACGCGGATGACGACTAGGACTACGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_73_259_5e/2
+AGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATACAGTAATAGTGGCGTATCGCAAGCTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_87_279_5f/2
+AGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACCGAGGAGGGCAGTAGGACGCTACGTATTTGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_125_293_60/2
+CGGACTGAGGAGGGCAGTAGGACGCTATGTATTTGGCGCGCGGCCCTACGGCTGAGCTTCGAGGTTGCGATACGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_111_297_61/2
+CTATTTAGGACGATCGGACTGGGGAGGGCAGTAGGACGCTACGGATTTGGCGCGCGGCCCTACGGCTGAGCGTCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_22_173_62/2
+GTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTCCAGTCGCTGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_mRNA_116_295_63/2
+TAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
diff -r a711b92d85c1 -r 1903b1fe70fc test-data/tophat_test.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tophat_test.fa	Wed Feb 18 11:36:41 2015 -0500
@@ -0,0 +1,14 @@
+>test_chromosome
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+ACTACTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCC
+ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGC
+AGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCT
+ACGTATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCC
+GTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG
+ACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACT
+GTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG
+TTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
diff -r a711b92d85c1 -r 1903b1fe70fc tool-data/rnastar_index.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/rnastar_index.loc.sample	Wed Feb 18 11:36:41 2015 -0500
@@ -0,0 +1,11 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of rna-star indexed sequences data files. You will
+#need to create these data files and then create a bowtie_indices.loc
+#file similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The bowtie2_indices.loc
+#file has this format (longer white space characters are TAB characters):
+#
+#<unique_build_id>   <dbkey>   <display_name>   <file_base_path>
+#
+#hg19   hg19    hg19 full   /mnt/galaxyIndices/genomes/hg19/rnastar
+
diff -r a711b92d85c1 -r 1903b1fe70fc tool-data/rnastar_indices.loc.sample
--- a/tool-data/rnastar_indices.loc.sample	Wed Mar 05 19:06:51 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
-#This is a sample file distributed with Galaxy that enables tools
-#to use a directory of rna-star indexed sequences data files. You will
-#need to create these data files and then create a bowtie_indices.loc
-#file similar to this one (store it in this directory) that points to
-#the directories in which those files are stored. The bowtie2_indices.loc
-#file has this format (longer white space characters are TAB characters):
-#
-#<unique_build_id>   <dbkey>   <display_name>   <file_base_path>
-#
-#hg19   hg19    hg19 full   /mnt/galaxyIndices/genomes/hg19/rnastar
-
diff -r a711b92d85c1 -r 1903b1fe70fc tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Wed Mar 05 19:06:51 2014 -0500
+++ b/tool_data_table_conf.xml.sample	Wed Feb 18 11:36:41 2015 -0500
@@ -1,7 +1,7 @@
 <!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
 <tables>
-    <table name="rnastar_indexes" comment_char="#">
+    <table name="rnastar_index" comment_char="#">
         <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/rnastar_indices.loc" />
+        <file path="tool-data/rnastar_index.loc" />
     </table>
 </tables>
diff -r a711b92d85c1 -r 1903b1fe70fc tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Mar 05 19:06:51 2014 -0500
+++ b/tool_dependencies.xml	Wed Feb 18 11:36:41 2015 -0500
@@ -1,10 +1,10 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="rnastar" version="2.3.1z">
-        <repository changeset_revision="0fa7feb9b4a8" name="package_rnastar_2_3_1z" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+    <package name="rnastar" version="2.4.0d">
+        <repository changeset_revision="2ab1b6182b63" name="package_rnastar_240d" owner="fubar" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="samtools" version="0.1.19">
-        <repository changeset_revision="54195f1d4b0f" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
+        <repository changeset_revision="8b98841b6b2f" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 
     <readme>