# HG changeset patch
# User iuc
# Date 1473152121 14400
# Node ID 93704f98f56e2aae463a21d3ee57415a5db847eb

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2

diff -r 000000000000 -r 93704f98f56e star_fusion.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/star_fusion.xml	Tue Sep 06 04:55:21 2016 -0400
@@ -0,0 +1,249 @@
+<tool id="star_fusion" name="STAR-Fusion" version="0.5.4-2" profile="16.07">
+    <description>detect fusion genes in RNA-Seq data</description>
+    <requirements>
+        <!-- Bio-conda -->
+        <requirement type="package" version="0.5.4">star-fusion</requirement>
+    </requirements>
+
+    <stdio>
+        <regex match="command not found" source="stderr" level="fatal"/>
+        <regex match="EXITING because of INPUT ERROR" source="stderr" level="fatal"/>
+        <regex match="FATAL ERROR" source="stderr" level="fatal"/>
+        
+        <regex match="Warning:" source="stderr" level="warning"/>
+        <regex match="CMD:" source="stderr" level="warning"/>
+        
+        <regex match="-done creating index file:" source="stderr" level="warning"/>
+        <regex match="-parsing GTF file:" source="stderr" level="warning"/>
+        <regex match="-building interval tree" source="stderr" level="warning"/>
+        <regex match="-parsing fusion evidence:" source="stderr" level="warning"/>
+        <regex match="-mapping reads to genes" source="stderr" level="warning"/>
+        <regex match="-outputting fusion candidates to file:" source="stderr" level="warning"/>
+        
+        <regex match="Process complete" source="stderr" level="warning"/>
+    </stdio>
+
+    <version_command>STAR-Fusion --version  2>&amp;1 | grep version | grep -o -E "software version.*?"</version_command>
+
+    <command><![CDATA[
+        ## 1. ensure the blastn file is provided as *.gz
+        if file --mime-type '${blast_pairs}' | grep -q /gzip\$; then
+            gzip_suffix='' ;
+        else
+            ## Older versions of gzip do not support the -k option to keep
+            ## the original file - this should be an universion solution
+            
+            gzip -1 -c -- '${blast_pairs}' > '${blast_pairs}.gz' &&
+            gzip_suffix='.gz' ;
+        fi &&
+        
+        ## 2. create reference index - using \$(pwd) is necessary, probably because the perl script changes work directory
+        ## - @todo once write a decent STAR and STAR Fusion data manager
+        prep_genome_lib.pl
+            --genome_fa '${fasta_type.ownFile}'
+            --gtf '${geneModel}'
+            --blast_pairs "${blast_pairs}\$gzip_suffix"
+            --CPU \${GALAXY_SLOTS:-1}
+            --output_dir "\$(pwd)/tmp_star_fusion_genome_dir"
+        &&
+        
+        ## 3. Run STAR-Fusion
+        STAR-Fusion
+            #if str($input_params.input_source) == "use_chimeric":
+                --chimeric_junction '${input_params.chimeric_junction}'
+            #else:
+                --left_fq '${input_params.left_fq}'
+                #if $input_params.right_fq:
+                    --right_fq '${input_params.right_fq}'
+                #end if
+            #end if
+
+            --genome_lib_dir "\$(pwd)/tmp_star_fusion_genome_dir"
+
+        #if str($params.settingsType) == "full":
+            --min_junction_reads $params.min_junction_reads
+            --min_sum_frags $params.min_sum_frags
+            --max_promiscuity $params.max_promiscuity
+            --min_novel_junction_support $params.min_novel_junction_support
+            --min_alt_pct_junction $params.min_alt_pct_junction
+            --aggregate_novel_junction_dist $params.aggregate_novel_junction_dist
+            --E $params.E
+        #end if
+    ]]></command>
+
+    <inputs>
+        <conditional name="input_params">
+            <param name="input_source"
+                   type="select"
+                   label="Use output from earlier STAR run or let STAR Fusion control running STAR">
+                <option value="use_chimeric">Use output from earlier STAR</option>
+                <option value="use_fastq">Let STAR Fusion control running STAR</option>
+            </param>
+            <when value="use_chimeric">
+                <param name="chimeric_junction"
+                       type="data"
+                       format="interval"
+                       argument="--chimeric_junction"
+                       label="Chimeric junction file from STAR (with STAR-Fusion settings)"/>
+            </when>
+            <when value="use_fastq">
+                <param name="left_fq"
+                       type="data"
+                       format="fastqsanger"
+                       argument="--left_fq"
+                       label="left.fq file"/>
+                <param name="right_fq"
+                       type="data"
+                       format="fastqsanger"
+                       optional="true"
+                       argument="--right_fq"
+                       label="right.fq file (actually optional, but highly recommended)"/>
+            </when>
+        </conditional>
+
+        <!-- Genome source. -->
+        <conditional name="fasta_type">
+            <param name="fasta_type_selector" type="select" label="Source for sequence to search">
+                <option value="cached">Locally Cached sequences</option>
+                <option value="history" selected="true">Sequences from your history</option>
+            </param>
+            <when value="cached">
+                <param name="ownFile"
+                       type="select" label="Genome to search">
+                    <options from_data_table="all_fasta">
+                        <column name="dbkey" index="1"/>
+                        <column name="name" index="2"/>
+                        <column name="value" index="3"/>
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <param name="ownFile"
+                       type="data"
+                       format="fasta"
+                       metadata_name="dbkey"
+                       label="Select the reference genome (FASTA file)"/>
+            </when>
+        </conditional>
+        
+        <param name="geneModel"
+               type="data"
+               format="gff3,gtf"
+               label="Gene model (gff3,gtf) file for splice junctions and fusion gene detection"/>
+        <param name="blast_pairs"
+               type="data"
+               format="tabular"
+               label="Result of BLAST+-blastn of the reference fasta sequence with itself"
+               help="Run blastn with '-outputfmt 6' or choose 'Tabular (standard 12 columns)' in the Galaxy wrapper. For human data it is recommended to obtain it from here: https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/"/>
+        
+        <conditional name="params">
+            <param name="settingsType" type="select" label="Settings to use" help="You can use the default settings or set custom values for any STAR Fusion parameter.">
+                <option value="default" selected="true">Use Defaults</option>
+                <option value="full">Full parameter list</option>
+            </param>
+            <when value="default" />
+            <when value="full"><!-- Full/advanced params. -->
+                <param name="min_junction_reads"
+                       type="integer" value="1"
+                       label="minimum number of junction-spanning reads required."
+                       argument="--min_junction_reads"/>
+                <param name="min_sum_frags"
+                       type="integer"
+                       value="2"
+                       label="minimum fusion support = (#junction_reads + #spanning_frags)"
+                       argument="--min_sum_frags"/>
+                <param name="max_promiscuity"
+                       type="integer"
+                       value="3"
+                       label="maximum number of partners allowed for a given fusion"
+                       argument="--max_promiscuity"/>
+                <param name="min_novel_junction_support"
+                       type="integer"
+                       value="3"
+                       label="minimum of 3 junction reads required if breakpoint lacks involvement of only reference junctions"
+                       argument="--min_novel_junction_support"/>
+                <param name="min_alt_pct_junction"
+                       type="float"
+                       value="10"
+                       label="10% of the dominant isoform junction support"
+                       argument="--min_alt_pct_junction"/>
+                <param name="aggregate_novel_junction_dist"
+                       type="integer"
+                       value="5"
+                       label="non-ref junctions within 5 are merged into single calls"
+                       argument="--aggregate_novel_junction_dist"/>
+                <param name="E"
+                       type="float"
+                       value="0.001"
+                       label="E-value threshold for blast searches"
+                       argument="-E"/>
+            </when>
+        </conditional>
+    </inputs>
+
+    <outputs>
+        <data format="tabular" name="output_final" label="${tool.name} on ${on_string}: fusion_candidates.final" from_work_dir="star-fusion.fusion_candidates.final"/>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input_source" value="use_chimeric" />
+            <param name="chimeric_junction" ftype="interval" value="test1.tabular" />
+            <param name="fasta_type_selector" value="history" />
+            <param name="ownFile" ftype="fasta" value="test1.fa" />
+            <param name="geneModel" ftype="gtf" value="test1.gtf" />
+            <param name="blast_pairs" ftype="tabular" value="test1-test1.blastn.tabular" />
+            <param name="settingsType" value="default" />
+            
+            <!-- Last column of the results contains data in a random order so exact matching is not feasible -->
+            <output name="output_final">
+                <assert_contents>
+                    <has_line line="#fusion_name&#009;JunctionReads&#009;SpanningFrags&#009;Splice_type&#009;LeftGene&#009;LeftBreakpoint&#009;RightGene&#009;RightBreakpoint&#009;JunctionReads&#009;SpanningFrags" />
+                    <has_text text="GENE1--GENE2&#009;24&#009;0&#009;INCL_NON_REF_SPLICE&#009;GENE1^GENE1&#009;chr1:240:+&#009;GENE2^GENE2&#009;chr2:241:+" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_source" value="use_fastq" />
+            <param name="left_fq" ftype="fastqsanger" value="test1.fastqsanger"/>
+            <param name="fasta_type_selector" value="history" />
+            <param name="ownFile" ftype="fasta" value="test1.fa" />
+            <param name="geneModel" ftype="gtf" value="test1.gtf" />
+            <param name="blast_pairs" ftype="tabular" value="test1-test1.blastn.tabular" />
+            <param name="settingsType" value="default" />
+            
+            <!-- Last column of the results contains data in a random order so exact matching is not feasible -->
+            <output name="output_final">
+                <assert_contents>
+                    <has_line line="#fusion_name&#009;JunctionReads&#009;SpanningFrags&#009;Splice_type&#009;LeftGene&#009;LeftBreakpoint&#009;RightGene&#009;RightBreakpoint&#009;JunctionReads&#009;SpanningFrags" />
+                    <has_text text="GENE1--GENE2&#009;24&#009;0&#009;INCL_NON_REF_SPLICE&#009;GENE1^GENE1&#009;chr1:240:+&#009;GENE2^GENE2&#009;chr2:241:+" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+STAR-Fusion is a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT). STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads. STAR-Fusion further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set.
+
+**Input: files required to run STAR-Fusion**
+ - A genome reference sequence (FASTA-format)
+ - A corresponding protein-coding gene annotation set (GTF/GFF Format)
+ - A last-matching gene pairs file - in Galaxy you can create such files with the *ncbi_blast_plus* tool suite containing *blastn*: https://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus
+ - A STAR chimeric/junction output file - this is optional as STAR Fusion can control running STAR as well.
+
+The authors of STAR Fusion have made some of these files avaialble at: https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/. The gene annotations in each case are restricted to the protein-coding and lincRNA transcripts.
+More info: https://github.com/STAR-Fusion/STAR-Fusion/wiki
+
+    </help>
+
+    <citations>
+        <citation type="bibtex">
+           @unpublished{star_fusion,
+              author = {Brian Haas and Nicolas Stransky and Daniel Nicorici}, 
+              title  = {STAR-Fusion},
+              url    = {https://github.com/STAR-Fusion/STAR-Fusion}
+            }
+        </citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 93704f98f56e test-data/test1-test1.blastn.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test1-test1.blastn.tabular	Tue Sep 06 04:55:21 2016 -0400
@@ -0,0 +1,2 @@
+chr1	chr1	100.00	480	0	0	1	480	1	480	0.0	866
+chr2	chr2	100.00	480	0	0	1	480	1	480	0.0	866
diff -r 000000000000 -r 93704f98f56e test-data/test1.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test1.fa	Tue Sep 06 04:55:21 2016 -0400
@@ -0,0 +1,18 @@
+>chr1
+GACGGACGTATTCCTCTGGCCTCAACGGTTCCTGCTTTCGCTGGGATCCAAGATTGGCAG
+CTGAAACCGCCTTTCCAAAGTGAGTCCTTCGTCTGTGACTAACTGTGCCAAATCGTCTTG
+CAAACTCCTGATCCAGTTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATC
+ATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCG
+GTGCAGCCGATTAGGACCATCTAATGCACTTGTTACAAGACTTCTTTTAAATACTTTCTT
+CCTGCCCAGTAGCGGATGATAATGGTTGTTGCCAGCCGGTGTGGAAGGTAACAGCACCGG
+TGCGAGCCTAATGTGCCGTCTCCACCAACACAAGGCTATCCGGTCGTATAATAGGATTCC
+GCAATGGGGTTAGCAAATGGCAGCCTAAACGATATCGGGGACTTGCGATGTACATGCTTT
+>chr2
+TCAACAATAAGCGCTTTTTGTAGGCAGGGGCACCCCCTATCAGTGGCTGCGCCAAAACAT
+CTTCGGATCCCCTTGTCCAATCAAATTGATCGAATTCTTTCATTTAAGACCCTAATATGA
+CATCATTAGTGATTAAATGCCACTCCCAAAATTCTGCCTAGAAATGTTTAAGTTCGCTCC
+ACTAAAGTTGTTTAAAACGACTACTAAATCCGCGTGATAGGGGATTTCATATTTAATCTT
+TTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCG
+CGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAACGGGCGATTCTATAAGA
+TTGCACATTGCGTCTACTTATAAGATGTCTCAACGGCATGCGCAACTTGTGAAGTGCCTA
+CTATCCTTAAACGCATATCTCGCACAGTAACTCCCCAATATGTGAGCATCTGATGTTGCC
diff -r 000000000000 -r 93704f98f56e test-data/test1.fastqsanger
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test1.fastqsanger	Tue Sep 06 04:55:21 2016 -0400
@@ -0,0 +1,332 @@
+@test_chimeric_mRNA_0
+CAAACTCCTGATCCAGTTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_2
+AACTCCTGATCCAGTTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_4
+CTCCTGATCCAGTTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_6
+CCTGATCCAGTTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_8
+TGATCCAGTTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_10
+ATCCAGTTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_12
+CCAGTTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_14
+AGTTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_16
+TTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_18
+TAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_20
+ACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_22
+TCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_24
+ACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_26
+CAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_28
+AATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_30
+TTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_32
+ATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_34
+AGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_36
+CCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_38
+ATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_40
+ACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_42
+AGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_44
+ACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_46
+CCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_48
+AAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_50
+ATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_52
+TTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_54
+TAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_56
+AATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_58
+TCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_60
+ATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_62
+ATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_64
+CACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_66
+CGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_68
+CGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_70
+ACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_72
+TAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_74
+GCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_76
+CTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_78
+CTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_80
+GCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_82
+TTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_84
+AATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_86
+TTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_88
+TCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_90
+TGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_92
+TGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_94
+CTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_96
+CAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_98
+AGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_100
+GGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_102
+TTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_104
+TTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_106
+GGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_108
+TCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_110
+CGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_112
+CCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_114
+CGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_116
+AGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_118
+CGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_120
+TTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_122
+ATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_124
+CGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_126
+TAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_128
+AGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_130
+GAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_132
+ACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_134
+AGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_136
+CCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_138
+GATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_140
+TCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACAC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_142
+TTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_144
+AATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_146
+TGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_148
+GATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_150
+TGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAACG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_152
+GCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAACGGG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_154
+CGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAACGGGCG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_156
+CAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAACGGGCGAT
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_158
+GGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAACGGGCGATTC
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_160
+TGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAACGGGCGATTCTA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_162
+GTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAACGGGCGATTCTATA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
+@test_chimeric_mRNA_164
+ATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAACGGGCGATTCTATAAG
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
diff -r 000000000000 -r 93704f98f56e test-data/test1.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test1.gtf	Tue Sep 06 04:55:21 2016 -0400
@@ -0,0 +1,8 @@
+chr1	test	gene	140	363	.	+	.	gene_id "GENE1"; gene_name "GENE1"; transcript_id "GENE1_t1";
+chr1	test	transcript	150	353	.	+	.	gene_id "GENE1"; gene_name "GENE1"; transcript_id "GENE1_t1";
+chr1	test	exon	150	353	.	+	.	gene_id "GENE1"; transcript_id "GENE1_t1"; exon_number "1"; gene_name "GENE1";
+chr1	test	CDS	153	350	.	+	.	gene_id "GENE1"; transcript_id "GENE1_t1"; exon_number "1"; gene_name "GENE1";
+chr2	test	gene	140	363	.	+	.	gene_id "GENE2"; gene_name "GENE2"; transcript_id "GENE2_t1";
+chr2	test	transcript	150	353	.	+	.	gene_id "GENE2"; gene_name "GENE2"; transcript_id "GENE2_t1";
+chr2	test	exon	150	353	.	+	.	gene_id "GENE2"; transcript_id "GENE2_t1"; exon_number "1"; gene_name "GENE2";
+chr2	test	CDS	153	350	.	+	.	gene_id "GENE2"; transcript_id "GENE2_t1"; exon_number "1"; gene_name "GENE2";
diff -r 000000000000 -r 93704f98f56e test-data/test1.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test1.tabular	Tue Sep 06 04:55:21 2016 -0400
@@ -0,0 +1,24 @@
+chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_60	181	60M15S	241	60S15M
+chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_62	183	58M17S	241	58S17M
+chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_64	185	56M19S	241	56S19M
+chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_66	187	54M21S	241	54S21M
+chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_68	189	52M23S	241	52S23M
+chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_70	191	50M25S	241	50S25M
+chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_72	193	48M27S	241	48S27M
+chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_74	195	46M29S	241	46S29M
+chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_76	197	44M31S	241	44S31M
+chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_78	199	42M33S	241	42S33M
+chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_80	201	40M35S	241	40S35M
+chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_82	203	38M37S	241	38S37M
+chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_84	205	36M39S	241	36S39M
+chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_86	207	34M41S	241	34S41M
+chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_88	209	32M43S	241	32S43M
+chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_90	211	30M45S	241	30S45M
+chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_92	213	28M47S	241	28S47M
+chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_94	215	26M49S	241	26S49M
+chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_96	217	24M51S	241	24S51M
+chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_98	219	22M53S	241	22S53M
+chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_100	221	20M55S	241	20S55M
+chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_102	223	18M57S	241	18S57M
+chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_104	225	16M59S	241	16S59M
+chr1	241	+	chr2	240	+	0	0	0	test_chimeric_mRNA_106	227	14M61S	241	14S61M
diff -r 000000000000 -r 93704f98f56e tool-data/all_fasta.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_fasta.loc.sample	Tue Sep 06 04:55:21 2016 -0400
@@ -0,0 +1,18 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_build_id>	<dbkey>	<display_name>	<file_path>
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3	/path/to/genome/apiMel3/apiMel3.fa
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/path/to/genome/hg19/hg19canon.fa
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#
diff -r 000000000000 -r 93704f98f56e tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Tue Sep 06 04:55:21 2016 -0400
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of all fasta files under genome directory -->
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/all_fasta.loc" />
+    </table>
+</tables>
diff -r 000000000000 -r 93704f98f56e tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Sep 06 04:55:21 2016 -0400
@@ -0,0 +1,3 @@
+<?xml version="1.0"?>
+<tool_dependency>
+</tool_dependency>