Mercurial > repos > iuc > stringtie
changeset 6:d0bb240d7525 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7
| author | iuc |
|---|---|
| date | Wed, 13 Jul 2016 14:48:26 -0400 |
| parents | f504b3b7e49d |
| children | e3f369973054 |
| files | macros.xml stringtie.xml stringtie_merge.xml test-data/e2t.ctab test-data/e_data.ctab test-data/i2t.ctab test-data/i_data.ctab test-data/stringtie_merge_in1.gtf test-data/stringtie_merge_in2.gtf test-data/stringtie_merge_in3.gtf test-data/stringtie_merge_out1.gtf test-data/stringtie_merge_out2.gtf test-data/stringtie_out1.gtf test-data/stringtie_out2.gtf test-data/stringtie_out3.gtf test-data/stringtie_out4.gtf test-data/stringtie_out5.gtf test-data/stringtie_out6.gtf test-data/stringtie_out7.gtf test-data/t_data.ctab tool_dependencies.xml |
| diffstat | 21 files changed, 609 insertions(+), 104 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Jul 13 14:48:26 2016 -0400 @@ -0,0 +1,22 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.2.3">stringtie</requirement> + <yield/> + </requirements> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1:" /> + </stdio> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1038/nbt.3122</citation> + <yield /> + </citations> + </xml> + <xml name="version_command"> + <version_command>stringtie --version</version_command> + </xml> +</macros> \ No newline at end of file
--- a/stringtie.xml Wed Oct 21 16:07:42 2015 -0400 +++ b/stringtie.xml Wed Jul 13 14:48:26 2016 -0400 @@ -1,38 +1,46 @@ -<tool id="stringtie" name="StringTie" version="1.1.0"> +<tool id="stringtie" name="StringTie" version="1.2.3"> <description>transcript assembly and quantification</description> - <requirements> - <requirement type="package" version="1.1.0">stringtie</requirement> - </requirements> - <command><![CDATA[ -stringtie "$input_bam" --o "$output_gtf" --p "\${GALAXY_SLOTS:-1}" -#if str($guide.use_guide) == 'yes': - -C "$coverage" -G "$guide.guide_gff" $guide.input_estimation - #if str($guide.output_ballgown) == '-b': - $guide.output_ballgown `pwd` - #end if -#end if -#if str($option_set.options) == 'advanced': - -l "$option_set.name_prefix" - -f "$option_set.fraction" - -m "$option_set.min_tlen" - -a "$option_set.min_anchor_len" - -j "$option_set.min_anchor_cov" - -c "$option_set.min_bundle_cov" - -g "$option_set.bdist" - -M "$option_set.bundle_fraction" $option_set.sensitive $option_set.disable_trimming - #if $option_set.A: - -A "$gene_abundance_estimation" - #end if - #if str($option_set.x).strip() != "": - -x "$option_set.x" - #end if -#end if -]]> -</command> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command> + <![CDATA[ + #if $input_bam.metadata.ftype == 'sam': + samtools sort -@ \${GALAXY_SLOTS:-1} "$input_bam" | stringtie + #else + stringtie "$input_bam" + #end if + -o "$output_gtf" + -p "\${GALAXY_SLOTS:-1}" + #if str($guide.use_guide) == 'yes': + -C "$coverage" -G "$guide.guide_gff" $guide.input_estimation + #if $guide.output_ballgown: + -b . + #end if + #end if + #if str($option_set.options) == 'advanced': + -l "$option_set.name_prefix" + -f "$option_set.fraction" + -m "$option_set.min_tlen" + -a "$option_set.min_anchor_len" + -j "$option_set.min_anchor_cov" + -c "$option_set.min_bundle_cov" + -g "$option_set.bdist" + -M "$option_set.bundle_fraction" $option_set.sensitive $option_set.disable_trimming $option_set.multi_mapping + #if $option_set.abundance_estimation: + -A "$gene_abundance_estimation" + #end if + #if str($option_set.omit_sequences).strip() != "": + -x "$option_set.omit_sequences" + #end if + #end if + ]]> + </command> <inputs> - <param format="bam" label="Mapped reads to assemble transcripts from" name="input_bam" type="data" /> + <param format="sam,bam" label="Mapped reads to assemble transcripts from" name="input_bam" type="data" /> <conditional name="guide"> <param label="Use GFF file to guide assembly" name="use_guide" type="select"> <option value="yes">Use GFF</option> @@ -40,37 +48,38 @@ </param> <when value="no" /> <when value="yes"> - <param format="gtf,gff3" help="-G" label="Reference annotation to use for guiding the assembly process" name="guide_gff" type="data" /> - <param falsevalue="" help="-e" label="Perform abundance estimation only of input transcripts" name="input_estimation" truevalue="-e" type="boolean" /> - <param falsevalue="" help="-b" label="Output additional files for use in Ballgown" name="output_ballgown" truevalue="-b" type="boolean" /> + <param argument="-G" format="gtf,gff3" help="" label="Reference annotation to use for guiding the assembly process" name="guide_gff" type="data" /> + <param argument="-e" falsevalue="" help="" label="Perform abundance estimation only of input transcripts" name="input_estimation" truevalue="-e" type="boolean" /> + <param argument="-b" falsevalue="" help="" label="Output additional files for use in Ballgown" name="output_ballgown" truevalue="-b" type="boolean" /> </when> </conditional> <conditional name="option_set"> - <param label="Options" name="options" type="select"> + <param help="" label="Options" name="options" type="select"> <option selected="True" value="default">Use defaults</option> <option value="advanced">Specify advanced options</option> </param> <when value="default" /> <when value="advanced"> - <param falsevalue="" help="-t" label="Disable trimming of predicted transcripts based on coverage" name="disable_trimming" truevalue="-t" type="boolean" /> - <param falsevalue="" help="-S" label="Increase sensitivity" name="sensitive" truevalue="-S" type="boolean" /> - <param help="-l" label="Name prefix for output transcripts" name="name_prefix" type="text" value="STRG" /> - <param help="-f" label="Minimum isoform fraction" max="1.0" min="0.0" name="fraction" type="float" value="0.15" /> - <param help="-m" label="Minimum assembled transcript length" name="min_tlen" type="integer" value="200" /> - <param help="-a" label="Minimum anchor length for junctions" name="min_anchor_len" type="integer" value="10" /> - <param help="-j" label="Minimum junction coverage" name="min_anchor_cov" type="integer" value="1" /> - <param help="-c" label="Minimum bundle reads per bp coverage to consider for assembly" name="min_bundle_cov" type="integer" value="2" /> - <param help="-g" label="Gap between read mappings triggering a new bundle" name="bdist" type="integer" value="50" /> - <param help="-M" label="Fraction of bundle allowed to be covered by multi-hit reads" name="bundle_fraction" type="float" value="0.95" /> - <param argument="-x" type="text" value="" label="Do not assemble any transcripts on these reference sequence(s)" help="e.g. chrM,chrX" /> - <param argument="-A" truevalue="-A" falsevalue="" type="boolean" help="" label="Additional gene abundance estimation output file" /> + <param argument="-t" falsevalue="" help="" label="Disable trimming of predicted transcripts based on coverage" name="disable_trimming" truevalue="-t" type="boolean" /> + <param argument="-S" falsevalue="" help="" label="Increase sensitivity" name="sensitive" truevalue="-S" type="boolean" /> + <param argument="-l" help="" label="Name prefix for output transcripts" name="name_prefix" type="text" value="STRG" /> + <param argument="-f" help="" label="Minimum isoform fraction" max="1.0" min="0.0" name="fraction" type="float" value="0.15" /> + <param argument="-m" help="" label="Minimum assembled transcript length" name="min_tlen" type="integer" value="200" /> + <param argument="-a" help="" label="Minimum anchor length for junctions" name="min_anchor_len" type="integer" value="10" /> + <param argument="-j" help="" label="Minimum junction coverage" name="min_anchor_cov" type="integer" value="1" /> + <param argument="-c" help="" label="Minimum bundle reads per bp coverage to consider for assembly" name="min_bundle_cov" type="integer" value="2" /> + <param argument="-g" help="" label="Gap between read mappings triggering a new bundle" name="bdist" type="integer" value="50" /> + <param argument="-M" help="" label="Fraction of bundle allowed to be covered by multi-hit reads" name="bundle_fraction" type="float" value="0.95" /> + <param argument="-x" help="e.g. chrM,chrX" label="Do not assemble any transcripts on these reference sequence(s)" name="omit_sequences" type="text" value="" /> + <param argument="-A" falsevalue="" help="" label="Additional gene abundance estimation output file" name="abundance_estimation" truevalue="-A" type="boolean" /> + <param argument="-u" falsevalue="" help="" label="Disable multi-mapping correction" name="multi_mapping" truevalue="-u" type="boolean" /> </when> </conditional> </inputs> <outputs> <data format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts" name="output_gtf" /> - <data format="tabular" label="${tool.name} on ${on_string}: Gene abundance estimates" name="gene_abundance_estimation"> - <filter>option_set['A']</filter> + <data format="gtf" label="${tool.name} on ${on_string}: Gene abundance estimates" name="gene_abundance_estimation"> + <filter>option_set['abundance_estimation']</filter> </data> <data format="gff3" label="${tool.name} on ${on_string}: Coverage" name="coverage"> <filter>guide['use_guide'] == "yes"</filter> @@ -96,21 +105,21 @@ <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> <param name="use_guide" value="no" /> <param name="options" value="default" /> - <output file="stringtie_out1.gtf" ftype="gtf" name="output_gtf" lines_diff="2" /> + <output file="stringtie_out1.gtf" ftype="gtf" lines_diff="2" name="output_gtf" /> </test> <test> <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> <param name="use_guide" value="no" /> <param name="options" value="advanced" /> <param name="fraction" value="0.17" /> - <output file="stringtie_out2.gtf" ftype="gtf" name="output_gtf" lines_diff="2" /> + <output file="stringtie_out2.gtf" ftype="gtf" lines_diff="2" name="output_gtf" /> </test> <test> <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> <param name="use_guide" value="yes" /> <param name="guide_gff" value="stringtie_in.gtf" /> <param name="options" value="default" /> - <output file="stringtie_out3.gtf" ftype="gtf" name="output_gtf" lines_diff="2" /> + <output file="stringtie_out3.gtf" ftype="gtf" lines_diff="2" name="output_gtf" /> </test> <test> <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> @@ -118,7 +127,7 @@ <param name="guide_gff" value="stringtie_in.gtf" /> <param name="options" value="advanced" /> <param name="fraction" value="0.17" /> - <output file="stringtie_out4.gtf" ftype="gtf" name="output_gtf" lines_diff="2" /> + <output file="stringtie_out4.gtf" ftype="gtf" lines_diff="2" name="output_gtf" /> </test> <test> <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> @@ -131,7 +140,7 @@ <output file="ballgown/t_data.ctab" ftype="tabular" name="transcript_expression" /> <output file="ballgown/e2t.ctab" ftype="tabular" name="exon_transcript_mapping" /> <output file="ballgown/i2t.ctab" ftype="tabular" name="intron_transcript_mapping" /> - <output file="stringtie_out5.gtf" ftype="gtf" name="output_gtf" lines_diff="2" /> + <output file="stringtie_out5.gtf" ftype="gtf" lines_diff="2" name="output_gtf" /> <output file="stringtie_out_coverage.gtf" ftype="gff3" name="coverage" /> </test> <test> @@ -140,9 +149,9 @@ <param name="guide_gff" value="stringtie_in.gtf" /> <param name="options" value="advanced" /> <param name="fraction" value="0.17" /> - <param name="A" value="True" /> - <output file="stringtie_out4.gtf" ftype="gtf" name="output_gtf" lines_diff="2" /> - <output file="stringtie_out6.gtf" ftype="tabular" name="gene_abundance_estimation" /> + <param name="abundance_estimation" value="True" /> + <output file="stringtie_out4.gtf" ftype="gtf" lines_diff="2" name="output_gtf" /> + <output file="stringtie_out6.gtf" ftype="gtf" lines_diff="2" name="gene_abundance_estimation" /> </test> <test> <param ftype="bam" name="input_bam" value="stringtie_in1.bam" /> @@ -151,7 +160,7 @@ <param name="options" value="advanced" /> <param name="fraction" value="0.15" /> <param name="c" value="test_chromosome" /> - <output file="stringtie_out7.gtf" ftype="gtf" name="output_gtf" lines_diff="2" /> + <output file="stringtie_out7.gtf" ftype="gtf" lines_diff="2" name="output_gtf" /> </test> </tests> <help> @@ -182,18 +191,17 @@ -C output file with reference transcripts that are covered by reads -M fraction of bundle allowed to be covered by multi-hit reads (default:0.95) -p number of threads (CPUs) to use (default: 1) + -A gene abundance estimation output file -B enable output of Ballgown table files which will be created in the same directory as the output GTF (requires -G, -o recommended) -b enable output of Ballgown table files but these files will be created under the directory path given as <dir_path> -e only estimates the abundance of given reference transcripts (requires -G) - -A gene abundance estimation output file -x do not assemble any transcripts on these reference sequence(s) - + -u no multi-mapping correction default: false) ]]> </help> - <citations> - <citation type="doi">doi:10.1038/nbt.3122</citation> - </citations> + <expand macro="citations" /> </tool> + \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/stringtie_merge.xml Wed Jul 13 14:48:26 2016 -0400 @@ -0,0 +1,85 @@ +<tool id="stringtie_merge" name="StringTie" version="0.1.0"> + <description>merge transcripts</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command> + <![CDATA[ + stringtie --merge + -p \${GALAXY_SLOTS:-1} + #if str($guide_gff) != "": + -G "$guide_gff" + #end if + -m $min_len + -c $min_cov + -F $min_fpkm + -T $min_tpm + -f $min_iso + -g $gap_len + $keep_introns + #set inputs = '" "'.join(str($input_gtf).split(',')) + -o $out_gtf "$inputs" + ]]> + </command> + <inputs> + <param type="data" name="input_gtf" multiple="true" format="gtf,gff3" /> + <param type="data" name="guide_gff" optional="True" format="gtf,gff3" /> + <param argument="-m" type="integer" name="min_len" value="50" help="Minimum input transcript length to include in the merge" /> + <param argument="-c" type="integer" name="min_cov" value="0" help="Minimum input transcript coverage to include in the merge" /> + <param argument="-F" type="float" name="min_fpkm" value="1.0" help="Minimum input transcript FPKM to include in the merge" /> + <param argument="-T" type="float" name="min_tpm" value="1.0" help="Minimum input transcript TPM to include in the merge" /> + <param argument="-f" type="float" name="min_iso" value="0.01" help="Minimum isoform fraction" /> + <param argument="-g" type="integer" name="gap_len" value="250" help="Gap between transcripts to merge together" /> + <param argument="-i" type="boolean" truevalue="-i" falsevalue="" name="keep_introns" help="Keep merged transcripts with retained introns" /> + </inputs> + <outputs> + <data name="out_gtf" format="gtf" /> + </outputs> + <tests> + <test> + <param ftype="gtf" name="input_gtf" value="stringtie_out1.gtf,stringtie_out2.gtf,stringtie_out3.gtf,stringtie_out4.gtf" /> + <param ftype="gtf" name="guide_gff" value="stringtie_in.gtf" /> + <output file="stringtie_merge_out1.gtf" ftype="gtf" lines_diff="2" name="out_gtf" /> + </test> + <test> + <param ftype="gtf" name="input_gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf" /> + <param ftype="gtf" name="guide_gff" value="stringtie_merge_in3.gtf" /> + <output file="stringtie_merge_out2.gtf" ftype="gtf" lines_diff="2" name="out_gtf" /> + </test> + </tests> + <help><![CDATA[ + +**What it does?** + +This is a special usage mode of StringTie_, distinct from the assembly usage mode. In the merge mode, StringTie takes as input a list of GTF/GFF files and merges/assembles these transcripts into a non-redundant set of transcripts. This mode is used in the new differential analysis pipeline to generate a global, unified set of transcripts (isoforms) across multiple RNA-Seq samples. + +If a reference annotation is provided, StringTie will assemble the transfrags from the input GTF files with the reference transcripts. + +.. _StringTie: http://ccb.jhu.edu/software/stringtie/ + +------ + +StringTie --merge has the following options:: + + -G <guide_gff> reference annotation to include in the merging (GTF/GFF3) + -o <out_gtf> output file name for the merged transcripts GTF + (default: stdout) + -m <min_len> minimum input transcript length to include in the merge + (default: 50) + -c <min_cov> minimum input transcript coverage to include in the merge + (default: 0) + -F <min_fpkm> minimum input transcript FPKM to include in the merge + (default: 1.0) + -T <min_tpm> minimum input transcript TPM to include in the merge + (default: 1.0) + -f <min_iso> minimum isoform fraction (default: 0.01) + -g <gap_len> gap between transcripts to merge together (default: 250) + -i keep merged transcripts with retained introns; by default + these are not kept unless there is strong evidence for them + -l <label> name prefix for output transcripts (default: MSTRG) + ]]></help> + <expand macro="citations" /> +</tool> \ No newline at end of file
--- a/test-data/e2t.ctab Wed Oct 21 16:07:42 2015 -0400 +++ b/test-data/e2t.ctab Wed Jul 13 14:48:26 2016 -0400 @@ -1,4 +0,0 @@ -e_id t_id -1 1 -2 1 -3 1
--- a/test-data/e_data.ctab Wed Oct 21 16:07:42 2015 -0400 +++ b/test-data/e_data.ctab Wed Jul 13 14:48:26 2016 -0400 @@ -1,4 +0,0 @@ -e_id chr strand start end rcount ucount mrcount cov cov_sd mcov mcov_sd -1 test_chromosome + 53 250 158 158 158.00 49.7778 22.0747 49.7778 22.0747 -2 test_chromosome + 351 400 73 73 73.00 54.1600 6.1753 54.1600 6.1753 -3 test_chromosome + 501 550 38 38 38.00 21.6400 12.4350 21.6400 12.4350
--- a/test-data/i2t.ctab Wed Oct 21 16:07:42 2015 -0400 +++ b/test-data/i2t.ctab Wed Jul 13 14:48:26 2016 -0400 @@ -1,3 +0,0 @@ -i_id t_id -1 1 -2 1
--- a/test-data/i_data.ctab Wed Oct 21 16:07:42 2015 -0400 +++ b/test-data/i_data.ctab Wed Jul 13 14:48:26 2016 -0400 @@ -1,3 +0,0 @@ -i_id chr strand start end rcount ucount mrcount -1 test_chromosome + 251 350 49 49 49.00 -2 test_chromosome + 401 500 38 38 38.00
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stringtie_merge_in1.gtf Wed Jul 13 14:48:26 2016 -0400 @@ -0,0 +1,100 @@ +chr1 Cufflinks transcript 3111450 3111490 1000 . . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073"; +chr1 Cufflinks exon 3111450 3111490 1000 . . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073"; +chr1 Cufflinks transcript 3111546 3111576 1000 . . gene_id "CUFF.3"; transcript_id "CUFF.3.1"; FPKM "27.2556579354"; frac "1.000000"; conf_lo "0.000000"; conf_hi "65.800979"; cov "1.741935"; +chr1 Cufflinks exon 3111546 3111576 1000 . . gene_id "CUFF.3"; transcript_id "CUFF.3.1"; exon_number "1"; FPKM "27.2556579354"; frac "1.000000"; conf_lo "0.000000"; conf_hi "65.800979"; cov "1.741935"; +chr1 Cufflinks transcript 3200326 3200352 1000 . . gene_id "CUFF.5"; transcript_id "CUFF.5.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000"; +chr1 Cufflinks exon 3200326 3200352 1000 . . gene_id "CUFF.5"; transcript_id "CUFF.5.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000"; +chr1 Cufflinks transcript 3200023 3200191 1000 . . gene_id "CUFF.7"; transcript_id "CUFF.7.1"; FPKM "9.9991171124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "19.998234"; cov "0.639053"; +chr1 Cufflinks exon 3200023 3200191 1000 . . gene_id "CUFF.7"; transcript_id "CUFF.7.1"; exon_number "1"; FPKM "9.9991171124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "19.998234"; cov "0.639053"; +chr1 Cufflinks transcript 3201078 3201481 1000 . . gene_id "CUFF.9"; transcript_id "CUFF.9.1"; FPKM "17.7768957078"; frac "1.000000"; conf_lo "9.153835"; conf_hi "26.399957"; cov "1.136139"; +chr1 Cufflinks exon 3201078 3201481 1000 . . gene_id "CUFF.9"; transcript_id "CUFF.9.1"; exon_number "1"; FPKM "17.7768957078"; frac "1.000000"; conf_lo "9.153835"; conf_hi "26.399957"; cov "1.136139"; +chr1 Cufflinks transcript 3201673 3201699 1000 . . gene_id "CUFF.11"; transcript_id "CUFF.11.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000"; +chr1 Cufflinks exon 3201673 3201699 1000 . . gene_id "CUFF.11"; transcript_id "CUFF.11.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000"; +chr1 Cufflinks transcript 3204755 3204833 1000 . . gene_id "CUFF.13"; transcript_id "CUFF.13.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544"; +chr1 Cufflinks exon 3204755 3204833 1000 . . gene_id "CUFF.13"; transcript_id "CUFF.13.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544"; +chr1 Cufflinks transcript 3212214 3212292 1000 . . gene_id "CUFF.15"; transcript_id "CUFF.15.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544"; +chr1 Cufflinks exon 3212214 3212292 1000 . . gene_id "CUFF.15"; transcript_id "CUFF.15.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544"; +chr1 Cufflinks transcript 3213096 3213192 1000 . . gene_id "CUFF.17"; transcript_id "CUFF.17.1"; FPKM "8.7105710927"; frac "1.000000"; conf_lo "0.000000"; conf_hi "21.029179"; cov "0.556701"; +chr1 Cufflinks exon 3213096 3213192 1000 . . gene_id "CUFF.17"; transcript_id "CUFF.17.1"; exon_number "1"; FPKM "8.7105710927"; frac "1.000000"; conf_lo "0.000000"; conf_hi "21.029179"; cov "0.556701"; +chr1 Cufflinks transcript 3212368 3212439 1000 . . gene_id "CUFF.19"; transcript_id "CUFF.19.1"; FPKM "29.3376873610"; frac "1.000000"; conf_lo "3.097262"; conf_hi "55.578113"; cov "1.875000"; +chr1 Cufflinks exon 3212368 3212439 1000 . . gene_id "CUFF.19"; transcript_id "CUFF.19.1"; exon_number "1"; FPKM "29.3376873610"; frac "1.000000"; conf_lo "3.097262"; conf_hi "55.578113"; cov "1.875000"; +chr1 Cufflinks transcript 3243019 3243079 1000 . . gene_id "CUFF.21"; transcript_id "CUFF.21.1"; FPKM "13.8512359999"; frac "1.000000"; conf_lo "0.000000"; conf_hi "33.439842"; cov "0.885246"; +chr1 Cufflinks exon 3243019 3243079 1000 . . gene_id "CUFF.21"; transcript_id "CUFF.21.1"; exon_number "1"; FPKM "13.8512359999"; frac "1.000000"; conf_lo "0.000000"; conf_hi "33.439842"; cov "0.885246"; +chr1 Cufflinks transcript 3243348 3243401 1000 . . gene_id "CUFF.23"; transcript_id "CUFF.23.1"; FPKM "23.4701498888"; frac "1.000000"; conf_lo "0.000000"; conf_hi "50.571145"; cov "1.500000"; +chr1 Cufflinks exon 3243348 3243401 1000 . . gene_id "CUFF.23"; transcript_id "CUFF.23.1"; exon_number "1"; FPKM "23.4701498888"; frac "1.000000"; conf_lo "0.000000"; conf_hi "50.571145"; cov "1.500000"; +chr1 Cufflinks transcript 3242634 3242923 1000 . . gene_id "CUFF.25"; transcript_id "CUFF.25.1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "5.354270"; conf_hi "23.781089"; cov "0.931034"; +chr1 Cufflinks exon 3242634 3242923 1000 . . gene_id "CUFF.25"; transcript_id "CUFF.25.1"; exon_number "1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "5.354270"; conf_hi "23.781089"; cov "0.931034"; +chr1 Cufflinks transcript 3256975 3257011 1000 . . gene_id "CUFF.27"; transcript_id "CUFF.27.1"; FPKM "34.2537322701"; frac "1.000000"; conf_lo "0.000000"; conf_hi "73.806535"; cov "2.189189"; +chr1 Cufflinks exon 3256975 3257011 1000 . . gene_id "CUFF.27"; transcript_id "CUFF.27.1"; exon_number "1"; FPKM "34.2537322701"; frac "1.000000"; conf_lo "0.000000"; conf_hi "73.806535"; cov "2.189189"; +chr1 Cufflinks transcript 3189900 3190041 1000 . . gene_id "CUFF.29"; transcript_id "CUFF.29.1"; FPKM "107.1032192108"; frac "1.000000"; conf_lo "71.402146"; conf_hi "142.804292"; cov "6.845070"; +chr1 Cufflinks exon 3189900 3190041 1000 . . gene_id "CUFF.29"; transcript_id "CUFF.29.1"; exon_number "1"; FPKM "107.1032192108"; frac "1.000000"; conf_lo "71.402146"; conf_hi "142.804292"; cov "6.845070"; +chr1 Cufflinks transcript 3190273 3190303 1000 . . gene_id "CUFF.31"; transcript_id "CUFF.31.1"; FPKM "122.6504607091"; frac "1.000000"; conf_lo "40.883487"; conf_hi "204.417435"; cov "7.838710"; +chr1 Cufflinks exon 3190273 3190303 1000 . . gene_id "CUFF.31"; transcript_id "CUFF.31.1"; exon_number "1"; FPKM "122.6504607091"; frac "1.000000"; conf_lo "40.883487"; conf_hi "204.417435"; cov "7.838710"; +chr1 Cufflinks transcript 3190455 3190481 1000 . . gene_id "CUFF.33"; transcript_id "CUFF.33.1"; FPKM "109.5273661476"; frac "1.000000"; conf_lo "26.732460"; conf_hi "192.322273"; cov "7.000000"; +chr1 Cufflinks exon 3190455 3190481 1000 . . gene_id "CUFF.33"; transcript_id "CUFF.33.1"; exon_number "1"; FPKM "109.5273661476"; frac "1.000000"; conf_lo "26.732460"; conf_hi "192.322273"; cov "7.000000"; +chr1 Cufflinks transcript 3191539 3191669 1000 . . gene_id "CUFF.35"; transcript_id "CUFF.35.1"; FPKM "96.7471827476"; frac "1.000000"; conf_lo "61.420107"; conf_hi "132.074259"; cov "6.183206"; +chr1 Cufflinks exon 3191539 3191669 1000 . . gene_id "CUFF.35"; transcript_id "CUFF.35.1"; exon_number "1"; FPKM "96.7471827476"; frac "1.000000"; conf_lo "61.420107"; conf_hi "132.074259"; cov "6.183206"; +chr1 Cufflinks transcript 3191877 3191945 1000 . . gene_id "CUFF.37"; transcript_id "CUFF.37.1"; FPKM "104.0850125502"; frac "1.000000"; conf_lo "53.596365"; conf_hi "154.573660"; cov "6.652174"; +chr1 Cufflinks exon 3191877 3191945 1000 . . gene_id "CUFF.37"; transcript_id "CUFF.37.1"; exon_number "1"; FPKM "104.0850125502"; frac "1.000000"; conf_lo "53.596365"; conf_hi "154.573660"; cov "6.652174"; +chr1 Cufflinks transcript 3192442 3192494 1000 . . gene_id "CUFF.39"; transcript_id "CUFF.39.1"; FPKM "23.9129829055"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.525317"; cov "1.528302"; +chr1 Cufflinks exon 3192442 3192494 1000 . . gene_id "CUFF.39"; transcript_id "CUFF.39.1"; exon_number "1"; FPKM "23.9129829055"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.525317"; cov "1.528302"; +chr1 Cufflinks transcript 3192551 3192629 1000 . . gene_id "CUFF.41"; transcript_id "CUFF.41.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544"; +chr1 Cufflinks exon 3192551 3192629 1000 . . gene_id "CUFF.41"; transcript_id "CUFF.41.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544"; +chr1 Cufflinks transcript 3192732 3192811 1000 . . gene_id "CUFF.43"; transcript_id "CUFF.43.1"; FPKM "10.5615674500"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.497879"; cov "0.675000"; +chr1 Cufflinks exon 3192732 3192811 1000 . . gene_id "CUFF.43"; transcript_id "CUFF.43.1"; exon_number "1"; FPKM "10.5615674500"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.497879"; cov "0.675000"; +chr1 Cufflinks transcript 3192941 3193042 1000 . . gene_id "CUFF.45"; transcript_id "CUFF.45.1"; FPKM "20.7089557842"; frac "1.000000"; conf_lo "2.186303"; conf_hi "39.231609"; cov "1.323529"; +chr1 Cufflinks exon 3192941 3193042 1000 . . gene_id "CUFF.45"; transcript_id "CUFF.45.1"; exon_number "1"; FPKM "20.7089557842"; frac "1.000000"; conf_lo "2.186303"; conf_hi "39.231609"; cov "1.323529"; +chr1 Cufflinks transcript 3194186 3194226 1000 . . gene_id "CUFF.47"; transcript_id "CUFF.47.1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073"; +chr1 Cufflinks exon 3194186 3194226 1000 . . gene_id "CUFF.47"; transcript_id "CUFF.47.1"; exon_number "1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073"; +chr1 Cufflinks transcript 3194303 3194329 1000 . . gene_id "CUFF.49"; transcript_id "CUFF.49.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000"; +chr1 Cufflinks exon 3194303 3194329 1000 . . gene_id "CUFF.49"; transcript_id "CUFF.49.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000"; +chr1 Cufflinks transcript 3195084 3195110 1000 . . gene_id "CUFF.51"; transcript_id "CUFF.51.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000"; +chr1 Cufflinks exon 3195084 3195110 1000 . . gene_id "CUFF.51"; transcript_id "CUFF.51.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000"; +chr1 Cufflinks transcript 3195451 3195477 1000 . . gene_id "CUFF.53"; transcript_id "CUFF.53.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000"; +chr1 Cufflinks exon 3195451 3195477 1000 . . gene_id "CUFF.53"; transcript_id "CUFF.53.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000"; +chr1 Cufflinks transcript 3197090 3197116 1000 . . gene_id "CUFF.55"; transcript_id "CUFF.55.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000"; +chr1 Cufflinks exon 3197090 3197116 1000 . . gene_id "CUFF.55"; transcript_id "CUFF.55.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000"; +chr1 Cufflinks transcript 3197247 3197273 1000 . . gene_id "CUFF.57"; transcript_id "CUFF.57.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000"; +chr1 Cufflinks exon 3197247 3197273 1000 . . gene_id "CUFF.57"; transcript_id "CUFF.57.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000"; +chr1 Cufflinks transcript 3197347 3197373 1000 . . gene_id "CUFF.59"; transcript_id "CUFF.59.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000"; +chr1 Cufflinks exon 3197347 3197373 1000 . . gene_id "CUFF.59"; transcript_id "CUFF.59.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000"; +chr1 Cufflinks transcript 3277191 3277218 1000 . . gene_id "CUFF.61"; transcript_id "CUFF.61.1"; FPKM "45.2638604998"; frac "1.000000"; conf_lo "0.000000"; conf_hi "97.530065"; cov "2.892857"; +chr1 Cufflinks exon 3277191 3277218 1000 . . gene_id "CUFF.61"; transcript_id "CUFF.61.1"; exon_number "1"; FPKM "45.2638604998"; frac "1.000000"; conf_lo "0.000000"; conf_hi "97.530065"; cov "2.892857"; +chr1 Cufflinks transcript 3278237 3278263 1000 . . gene_id "CUFF.63"; transcript_id "CUFF.63.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000"; +chr1 Cufflinks exon 3278237 3278263 1000 . . gene_id "CUFF.63"; transcript_id "CUFF.63.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000"; +chr1 Cufflinks transcript 3280687 3280741 1000 . . gene_id "CUFF.65"; transcript_id "CUFF.65.1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818"; +chr1 Cufflinks exon 3280687 3280741 1000 . . gene_id "CUFF.65"; transcript_id "CUFF.65.1"; exon_number "1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818"; +chr1 Cufflinks transcript 3290489 3290553 1000 . . gene_id "CUFF.67"; transcript_id "CUFF.67.1"; FPKM "12.9988522461"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.382005"; cov "0.830769"; +chr1 Cufflinks exon 3290489 3290553 1000 . . gene_id "CUFF.67"; transcript_id "CUFF.67.1"; exon_number "1"; FPKM "12.9988522461"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.382005"; cov "0.830769"; +chr1 Cufflinks transcript 3290940 3291023 1000 . . gene_id "CUFF.69"; transcript_id "CUFF.69.1"; FPKM "10.0586356666"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.283695"; cov "0.642857"; +chr1 Cufflinks exon 3290940 3291023 1000 . . gene_id "CUFF.69"; transcript_id "CUFF.69.1"; exon_number "1"; FPKM "10.0586356666"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.283695"; cov "0.642857"; +chr1 Cufflinks transcript 3291089 3291186 1000 . . gene_id "CUFF.71"; transcript_id "CUFF.71.1"; FPKM "8.6216877142"; frac "1.000000"; conf_lo "0.000000"; conf_hi "20.814595"; cov "0.551020"; +chr1 Cufflinks exon 3291089 3291186 1000 . . gene_id "CUFF.71"; transcript_id "CUFF.71.1"; exon_number "1"; FPKM "8.6216877142"; frac "1.000000"; conf_lo "0.000000"; conf_hi "20.814595"; cov "0.551020"; +chr1 Cufflinks transcript 3299610 3299664 1000 . . gene_id "CUFF.73"; transcript_id "CUFF.73.1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818"; +chr1 Cufflinks exon 3299610 3299664 1000 . . gene_id "CUFF.73"; transcript_id "CUFF.73.1"; exon_number "1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818"; +chr1 Cufflinks transcript 3300052 3300078 1000 . . gene_id "CUFF.75"; transcript_id "CUFF.75.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000"; +chr1 Cufflinks exon 3300052 3300078 1000 . . gene_id "CUFF.75"; transcript_id "CUFF.75.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000"; +chr1 Cufflinks transcript 3319000 3319051 1000 . . gene_id "CUFF.77"; transcript_id "CUFF.77.1"; FPKM "16.2485653076"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.227507"; cov "1.038462"; +chr1 Cufflinks exon 3319000 3319051 1000 . . gene_id "CUFF.77"; transcript_id "CUFF.77.1"; exon_number "1"; FPKM "16.2485653076"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.227507"; cov "1.038462"; +chr1 Cufflinks transcript 3355888 3355914 1000 . . gene_id "CUFF.79"; transcript_id "CUFF.79.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000"; +chr1 Cufflinks exon 3355888 3355914 1000 . . gene_id "CUFF.79"; transcript_id "CUFF.79.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000"; +chr1 Cufflinks transcript 3363215 3363278 1000 . . gene_id "CUFF.81"; transcript_id "CUFF.81.1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.872349"; cov "0.843750"; +chr1 Cufflinks exon 3363215 3363278 1000 . . gene_id "CUFF.81"; transcript_id "CUFF.81.1"; exon_number "1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.872349"; cov "0.843750"; +chr1 Cufflinks transcript 3363754 3363849 1000 . . gene_id "CUFF.83"; transcript_id "CUFF.83.1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "28.446269"; cov "0.843750"; +chr1 Cufflinks exon 3363754 3363849 1000 . . gene_id "CUFF.83"; transcript_id "CUFF.83.1"; exon_number "1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "28.446269"; cov "0.843750"; +chr1 Cufflinks transcript 3367136 3367162 1000 . . gene_id "CUFF.85"; transcript_id "CUFF.85.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000"; +chr1 Cufflinks exon 3367136 3367162 1000 . . gene_id "CUFF.85"; transcript_id "CUFF.85.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000"; +chr1 Cufflinks transcript 3367334 3367382 1000 . . gene_id "CUFF.87"; transcript_id "CUFF.87.1"; FPKM "17.2433754285"; frac "1.000000"; conf_lo "0.000000"; conf_hi "41.629191"; cov "1.102041"; +chr1 Cufflinks exon 3367334 3367382 1000 . . gene_id "CUFF.87"; transcript_id "CUFF.87.1"; exon_number "1"; FPKM "17.2433754285"; frac "1.000000"; conf_lo "0.000000"; conf_hi "41.629191"; cov "1.102041"; +chr1 Cufflinks transcript 3377212 3377262 1000 . . gene_id "CUFF.89"; transcript_id "CUFF.89.1"; FPKM "16.5671646274"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.996674"; cov "1.058824"; +chr1 Cufflinks exon 3377212 3377262 1000 . . gene_id "CUFF.89"; transcript_id "CUFF.89.1"; exon_number "1"; FPKM "16.5671646274"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.996674"; cov "1.058824"; +chr1 Cufflinks transcript 3391326 3391352 1000 . . gene_id "CUFF.91"; transcript_id "CUFF.91.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000"; +chr1 Cufflinks exon 3391326 3391352 1000 . . gene_id "CUFF.91"; transcript_id "CUFF.91.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000"; +chr1 Cufflinks transcript 3435842 3435880 1000 . . gene_id "CUFF.93"; transcript_id "CUFF.93.1"; FPKM "21.6647537435"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.303342"; cov "1.384615"; +chr1 Cufflinks exon 3435842 3435880 1000 . . gene_id "CUFF.93"; transcript_id "CUFF.93.1"; exon_number "1"; FPKM "21.6647537435"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.303342"; cov "1.384615"; +chr1 Cufflinks transcript 3447762 3447788 1000 . . gene_id "CUFF.95"; transcript_id "CUFF.95.1"; FPKM "46.9402997776"; frac "1.000000"; conf_lo "0.000000"; conf_hi "101.142289"; cov "3.000000"; +chr1 Cufflinks exon 3447762 3447788 1000 . . gene_id "CUFF.95"; transcript_id "CUFF.95.1"; exon_number "1"; FPKM "46.9402997776"; frac "1.000000"; conf_lo "0.000000"; conf_hi "101.142289"; cov "3.000000"; +chr1 Cufflinks transcript 3450907 3450965 1000 . . gene_id "CUFF.97"; transcript_id "CUFF.97.1"; FPKM "21.4811541355"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.285454"; cov "1.372881"; +chr1 Cufflinks exon 3450907 3450965 1000 . . gene_id "CUFF.97"; transcript_id "CUFF.97.1"; exon_number "1"; FPKM "21.4811541355"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.285454"; cov "1.372881"; +chr1 Cufflinks transcript 3451052 3451109 1000 . . gene_id "CUFF.99"; transcript_id "CUFF.99.1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.169489"; cov "0.931034"; +chr1 Cufflinks exon 3451052 3451109 1000 . . gene_id "CUFF.99"; transcript_id "CUFF.99.1"; exon_number "1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.169489"; cov "0.931034";
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stringtie_merge_in2.gtf Wed Jul 13 14:48:26 2016 -0400 @@ -0,0 +1,100 @@ +chr1 Cufflinks transcript 3174766 3174792 1000 . . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks exon 3174766 3174792 1000 . . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks transcript 3187402 3187428 1000 . . gene_id "CUFF.3"; transcript_id "CUFF.3.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks exon 3187402 3187428 1000 . . gene_id "CUFF.3"; transcript_id "CUFF.3.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks transcript 3188522 3188548 1000 . . gene_id "CUFF.5"; transcript_id "CUFF.5.1"; FPKM "21.2266273824"; frac "1.000000"; conf_lo "0.000000"; conf_hi "59.889707"; cov "1.205672"; +chr1 Cufflinks exon 3188522 3188548 1000 . . gene_id "CUFF.5"; transcript_id "CUFF.5.1"; exon_number "1"; FPKM "21.2266273824"; frac "1.000000"; conf_lo "0.000000"; conf_hi "59.889707"; cov "1.205672"; +chr1 Cufflinks transcript 3190859 3191434 1000 . . gene_id "CUFF.7"; transcript_id "CUFF.7.1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "19.806349"; conf_hi "39.612698"; cov "1.687500"; +chr1 Cufflinks exon 3190859 3191434 1000 . . gene_id "CUFF.7"; transcript_id "CUFF.7.1"; exon_number "1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "19.806349"; conf_hi "39.612698"; cov "1.687500"; +chr1 Cufflinks transcript 3191513 3192077 1000 . . gene_id "CUFF.9"; transcript_id "CUFF.9.1"; FPKM "34.0729325807"; frac "1.000000"; conf_lo "23.364686"; conf_hi "44.781179"; cov "1.935341"; +chr1 Cufflinks exon 3191513 3192077 1000 . . gene_id "CUFF.9"; transcript_id "CUFF.9.1"; exon_number "1"; FPKM "34.0729325807"; frac "1.000000"; conf_lo "23.364686"; conf_hi "44.781179"; cov "1.935341"; +chr1 Cufflinks transcript 3189811 3190789 1000 . . gene_id "CUFF.11"; transcript_id "CUFF.11.1"; FPKM "32.5317765567"; frac "1.000000"; conf_lo "24.582998"; conf_hi "40.480555"; cov "1.847804"; +chr1 Cufflinks exon 3189811 3190789 1000 . . gene_id "CUFF.11"; transcript_id "CUFF.11.1"; exon_number "1"; FPKM "32.5317765567"; frac "1.000000"; conf_lo "24.582998"; conf_hi "40.480555"; cov "1.847804"; +chr1 Cufflinks transcript 3192251 3192336 1000 . . gene_id "CUFF.13"; transcript_id "CUFF.13.1"; FPKM "16.5820596576"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.729373"; cov "0.941860"; +chr1 Cufflinks exon 3192251 3192336 1000 . . gene_id "CUFF.13"; transcript_id "CUFF.13.1"; exon_number "1"; FPKM "16.5820596576"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.729373"; cov "0.941860"; +chr1 Cufflinks transcript 3192650 3192676 1000 . . gene_id "CUFF.15"; transcript_id "CUFF.15.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks exon 3192650 3192676 1000 . . gene_id "CUFF.15"; transcript_id "CUFF.15.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks transcript 3194707 3194733 1000 . . gene_id "CUFF.17"; transcript_id "CUFF.17.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks exon 3194707 3194733 1000 . . gene_id "CUFF.17"; transcript_id "CUFF.17.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks transcript 3197426 3197452 1000 . . gene_id "CUFF.19"; transcript_id "CUFF.19.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks exon 3197426 3197452 1000 . . gene_id "CUFF.19"; transcript_id "CUFF.19.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks transcript 3200431 3200457 1000 . . gene_id "CUFF.21"; transcript_id "CUFF.21.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks exon 3200431 3200457 1000 . . gene_id "CUFF.21"; transcript_id "CUFF.21.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks transcript 3200057 3200144 1000 . . gene_id "CUFF.23"; transcript_id "CUFF.23.1"; FPKM "16.2051946653"; frac "1.000000"; conf_lo "0.000000"; conf_hi "34.917342"; cov "0.920455"; +chr1 Cufflinks exon 3200057 3200144 1000 . . gene_id "CUFF.23"; transcript_id "CUFF.23.1"; exon_number "1"; FPKM "16.2051946653"; frac "1.000000"; conf_lo "0.000000"; conf_hi "34.917342"; cov "0.920455"; +chr1 Cufflinks transcript 3201161 3201187 1000 . . gene_id "CUFF.25"; transcript_id "CUFF.25.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks exon 3201161 3201187 1000 . . gene_id "CUFF.25"; transcript_id "CUFF.25.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks transcript 3201008 3201039 1000 . . gene_id "CUFF.26"; transcript_id "CUFF.26.1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "0.000000"; conf_hi "71.725135"; cov "1.687500"; +chr1 Cufflinks exon 3201008 3201039 1000 . . gene_id "CUFF.26"; transcript_id "CUFF.26.1"; exon_number "1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "0.000000"; conf_hi "71.725135"; cov "1.687500"; +chr1 Cufflinks transcript 3201597 3201666 1000 . . gene_id "CUFF.29"; transcript_id "CUFF.29.1"; FPKM "13.5814964814"; frac "1.000000"; conf_lo "0.000000"; conf_hi "32.788633"; cov "0.771429"; +chr1 Cufflinks exon 3201597 3201666 1000 . . gene_id "CUFF.29"; transcript_id "CUFF.29.1"; exon_number "1"; FPKM "13.5814964814"; frac "1.000000"; conf_lo "0.000000"; conf_hi "32.788633"; cov "0.771429"; +chr1 Cufflinks transcript 3201726 3201809 1000 . . gene_id "CUFF.31"; transcript_id "CUFF.31.1"; FPKM "22.6358274691"; frac "1.000000"; conf_lo "0.000000"; conf_hi "45.271655"; cov "1.285714"; +chr1 Cufflinks exon 3201726 3201809 1000 . . gene_id "CUFF.31"; transcript_id "CUFF.31.1"; exon_number "1"; FPKM "22.6358274691"; frac "1.000000"; conf_lo "0.000000"; conf_hi "45.271655"; cov "1.285714"; +chr1 Cufflinks transcript 3211522 3211561 1000 . . gene_id "CUFF.33"; transcript_id "CUFF.33.1"; FPKM "23.7676188425"; frac "1.000000"; conf_lo "0.000000"; conf_hi "57.380108"; cov "1.350000"; +chr1 Cufflinks exon 3211522 3211561 1000 . . gene_id "CUFF.33"; transcript_id "CUFF.33.1"; exon_number "1"; FPKM "23.7676188425"; frac "1.000000"; conf_lo "0.000000"; conf_hi "57.380108"; cov "1.350000"; +chr1 Cufflinks transcript 3212718 3212801 1000 . . gene_id "CUFF.35"; transcript_id "CUFF.35.1"; FPKM "11.3179137345"; frac "1.000000"; conf_lo "0.000000"; conf_hi "27.323861"; cov "0.642857"; +chr1 Cufflinks exon 3212718 3212801 1000 . . gene_id "CUFF.35"; transcript_id "CUFF.35.1"; exon_number "1"; FPKM "11.3179137345"; frac "1.000000"; conf_lo "0.000000"; conf_hi "27.323861"; cov "0.642857"; +chr1 Cufflinks transcript 3213119 3213242 1000 . . gene_id "CUFF.37"; transcript_id "CUFF.37.1"; FPKM "11.5004607302"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.780049"; cov "0.653226"; +chr1 Cufflinks exon 3213119 3213242 1000 . . gene_id "CUFF.37"; transcript_id "CUFF.37.1"; exon_number "1"; FPKM "11.5004607302"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.780049"; cov "0.653226"; +chr1 Cufflinks transcript 3240607 3240633 1000 . . gene_id "CUFF.39"; transcript_id "CUFF.39.1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000"; +chr1 Cufflinks exon 3240607 3240633 1000 . . gene_id "CUFF.39"; transcript_id "CUFF.39.1"; exon_number "1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000"; +chr1 Cufflinks transcript 3242480 3242512 1000 . . gene_id "CUFF.41"; transcript_id "CUFF.41.1"; FPKM "43.2138524409"; frac "1.000000"; conf_lo "0.000000"; conf_hi "93.112911"; cov "2.454545"; +chr1 Cufflinks exon 3242480 3242512 1000 . . gene_id "CUFF.41"; transcript_id "CUFF.41.1"; exon_number "1"; FPKM "43.2138524409"; frac "1.000000"; conf_lo "0.000000"; conf_hi "93.112911"; cov "2.454545"; +chr1 Cufflinks transcript 3242925 3243005 1000 . . gene_id "CUFF.43"; transcript_id "CUFF.43.1"; FPKM "23.4741914494"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.948383"; cov "1.333333"; +chr1 Cufflinks exon 3242925 3243005 1000 . . gene_id "CUFF.43"; transcript_id "CUFF.43.1"; exon_number "1"; FPKM "23.4741914494"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.948383"; cov "1.333333"; +chr1 Cufflinks transcript 3243109 3243154 1000 . . gene_id "CUFF.45"; transcript_id "CUFF.45.1"; FPKM "20.6674946457"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.895746"; cov "1.173913"; +chr1 Cufflinks exon 3243109 3243154 1000 . . gene_id "CUFF.45"; transcript_id "CUFF.45.1"; exon_number "1"; FPKM "20.6674946457"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.895746"; cov "1.173913"; +chr1 Cufflinks transcript 3254080 3254106 1000 . . gene_id "CUFF.47"; transcript_id "CUFF.47.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks exon 3254080 3254106 1000 . . gene_id "CUFF.47"; transcript_id "CUFF.47.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks transcript 3277156 3277182 1000 . . gene_id "CUFF.49"; transcript_id "CUFF.49.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks exon 3277156 3277182 1000 . . gene_id "CUFF.49"; transcript_id "CUFF.49.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks transcript 3277914 3278390 1000 . . gene_id "CUFF.51"; transcript_id "CUFF.51.1"; FPKM "14.9481879513"; frac "1.000000"; conf_lo "7.228977"; conf_hi "22.667399"; cov "0.849057"; +chr1 Cufflinks exon 3277914 3278390 1000 . . gene_id "CUFF.51"; transcript_id "CUFF.51.1"; exon_number "1"; FPKM "14.9481879513"; frac "1.000000"; conf_lo "7.228977"; conf_hi "22.667399"; cov "0.849057"; +chr1 Cufflinks transcript 3280118 3280144 1000 . . gene_id "CUFF.53"; transcript_id "CUFF.53.1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000"; +chr1 Cufflinks exon 3280118 3280144 1000 . . gene_id "CUFF.53"; transcript_id "CUFF.53.1"; exon_number "1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000"; +chr1 Cufflinks transcript 3280499 3280525 1000 . . gene_id "CUFF.55"; transcript_id "CUFF.55.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks exon 3280499 3280525 1000 . . gene_id "CUFF.55"; transcript_id "CUFF.55.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks transcript 3282505 3282531 1000 . . gene_id "CUFF.57"; transcript_id "CUFF.57.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks exon 3282505 3282531 1000 . . gene_id "CUFF.57"; transcript_id "CUFF.57.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks transcript 3282651 3282677 1000 . . gene_id "CUFF.59"; transcript_id "CUFF.59.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks exon 3282651 3282677 1000 . . gene_id "CUFF.59"; transcript_id "CUFF.59.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks transcript 3282761 3282832 1000 . . gene_id "CUFF.61"; transcript_id "CUFF.61.1"; FPKM "13.2042326903"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.877838"; cov "0.750000"; +chr1 Cufflinks exon 3282761 3282832 1000 . . gene_id "CUFF.61"; transcript_id "CUFF.61.1"; exon_number "1"; FPKM "13.2042326903"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.877838"; cov "0.750000"; +chr1 Cufflinks transcript 3284967 3284993 1000 . . gene_id "CUFF.63"; transcript_id "CUFF.63.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks exon 3284967 3284993 1000 . . gene_id "CUFF.63"; transcript_id "CUFF.63.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks transcript 3290799 3290859 1000 . . gene_id "CUFF.65"; transcript_id "CUFF.65.1"; FPKM "31.1706476623"; frac "1.000000"; conf_lo "0.000000"; conf_hi "62.341295"; cov "1.770492"; +chr1 Cufflinks exon 3290799 3290859 1000 . . gene_id "CUFF.65"; transcript_id "CUFF.65.1"; exon_number "1"; FPKM "31.1706476623"; frac "1.000000"; conf_lo "0.000000"; conf_hi "62.341295"; cov "1.770492"; +chr1 Cufflinks transcript 3299444 3299640 1000 . . gene_id "CUFF.67"; transcript_id "CUFF.67.1"; FPKM "15.6813507371"; frac "1.000000"; conf_lo "3.378764"; conf_hi "27.983938"; cov "0.890700"; +chr1 Cufflinks exon 3299444 3299640 1000 . . gene_id "CUFF.67"; transcript_id "CUFF.67.1"; exon_number "1"; FPKM "15.6813507371"; frac "1.000000"; conf_lo "3.378764"; conf_hi "27.983938"; cov "0.890700"; +chr1 Cufflinks transcript 3290920 3291273 1000 . . gene_id "CUFF.69"; transcript_id "CUFF.69.1"; FPKM "18.7992465421"; frac "1.000000"; conf_lo "8.750627"; conf_hi "28.847866"; cov "1.067797"; +chr1 Cufflinks exon 3290920 3291273 1000 . . gene_id "CUFF.69"; transcript_id "CUFF.69.1"; exon_number "1"; FPKM "18.7992465421"; frac "1.000000"; conf_lo "8.750627"; conf_hi "28.847866"; cov "1.067797"; +chr1 Cufflinks transcript 3299692 3299733 1000 . . gene_id "CUFF.71"; transcript_id "CUFF.71.1"; FPKM "22.6358274691"; frac "1.000000"; conf_lo "0.000000"; conf_hi "54.647722"; cov "1.285714"; +chr1 Cufflinks exon 3299692 3299733 1000 . . gene_id "CUFF.71"; transcript_id "CUFF.71.1"; exon_number "1"; FPKM "22.6358274691"; frac "1.000000"; conf_lo "0.000000"; conf_hi "54.647722"; cov "1.285714"; +chr1 Cufflinks transcript 3307749 3307775 1000 . . gene_id "CUFF.73"; transcript_id "CUFF.73.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks exon 3307749 3307775 1000 . . gene_id "CUFF.73"; transcript_id "CUFF.73.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks transcript 3318621 3318647 1000 . . gene_id "CUFF.75"; transcript_id "CUFF.75.1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000"; +chr1 Cufflinks exon 3318621 3318647 1000 . . gene_id "CUFF.75"; transcript_id "CUFF.75.1"; exon_number "1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000"; +chr1 Cufflinks transcript 3330528 3330554 1000 . . gene_id "CUFF.77"; transcript_id "CUFF.77.1"; FPKM "17.6056435870"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.816931"; cov "1.000000"; +chr1 Cufflinks exon 3330528 3330554 1000 . . gene_id "CUFF.77"; transcript_id "CUFF.77.1"; exon_number "1"; FPKM "17.6056435870"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.816931"; cov "1.000000"; +chr1 Cufflinks transcript 3351241 3351311 1000 . . gene_id "CUFF.79"; transcript_id "CUFF.79.1"; FPKM "13.3902077986"; frac "1.000000"; conf_lo "0.000000"; conf_hi "32.326821"; cov "0.760563"; +chr1 Cufflinks exon 3351241 3351311 1000 . . gene_id "CUFF.79"; transcript_id "CUFF.79.1"; exon_number "1"; FPKM "13.3902077986"; frac "1.000000"; conf_lo "0.000000"; conf_hi "32.326821"; cov "0.760563"; +chr1 Cufflinks transcript 3355908 3356119 1000 . . gene_id "CUFF.81"; transcript_id "CUFF.81.1"; FPKM "11.2111409634"; frac "1.000000"; conf_lo "1.183592"; conf_hi "21.238690"; cov "0.636792"; +chr1 Cufflinks exon 3355908 3356119 1000 . . gene_id "CUFF.81"; transcript_id "CUFF.81.1"; exon_number "1"; FPKM "11.2111409634"; frac "1.000000"; conf_lo "1.183592"; conf_hi "21.238690"; cov "0.636792"; +chr1 Cufflinks transcript 3356181 3356225 1000 . . gene_id "CUFF.83"; transcript_id "CUFF.83.1"; FPKM "21.1267723045"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.004540"; cov "1.200000"; +chr1 Cufflinks exon 3356181 3356225 1000 . . gene_id "CUFF.83"; transcript_id "CUFF.83.1"; exon_number "1"; FPKM "21.1267723045"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.004540"; cov "1.200000"; +chr1 Cufflinks transcript 3363077 3363176 1000 . . gene_id "CUFF.85"; transcript_id "CUFF.85.1"; FPKM "19.0140950740"; frac "1.000000"; conf_lo "0.000000"; conf_hi "38.028190"; cov "1.080000"; +chr1 Cufflinks exon 3363077 3363176 1000 . . gene_id "CUFF.85"; transcript_id "CUFF.85.1"; exon_number "1"; FPKM "19.0140950740"; frac "1.000000"; conf_lo "0.000000"; conf_hi "38.028190"; cov "1.080000"; +chr1 Cufflinks transcript 3363388 3363446 1000 . . gene_id "CUFF.87"; transcript_id "CUFF.87.1"; FPKM "24.1704598398"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.080103"; cov "1.372881"; +chr1 Cufflinks exon 3363388 3363446 1000 . . gene_id "CUFF.87"; transcript_id "CUFF.87.1"; exon_number "1"; FPKM "24.1704598398"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.080103"; cov "1.372881"; +chr1 Cufflinks transcript 3364872 3364919 1000 . . gene_id "CUFF.89"; transcript_id "CUFF.89.1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "0.000000"; conf_hi "64.015126"; cov "1.687500"; +chr1 Cufflinks exon 3364872 3364919 1000 . . gene_id "CUFF.89"; transcript_id "CUFF.89.1"; exon_number "1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "0.000000"; conf_hi "64.015126"; cov "1.687500"; +chr1 Cufflinks transcript 3367211 3367237 1000 . . gene_id "CUFF.91"; transcript_id "CUFF.91.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks exon 3367211 3367237 1000 . . gene_id "CUFF.91"; transcript_id "CUFF.91.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks transcript 3369581 3369607 1000 . . gene_id "CUFF.93"; transcript_id "CUFF.93.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks exon 3369581 3369607 1000 . . gene_id "CUFF.93"; transcript_id "CUFF.93.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks transcript 3375002 3375028 1000 . . gene_id "CUFF.95"; transcript_id "CUFF.95.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks exon 3375002 3375028 1000 . . gene_id "CUFF.95"; transcript_id "CUFF.95.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks transcript 3379889 3379915 1000 . . gene_id "CUFF.97"; transcript_id "CUFF.97.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks exon 3379889 3379915 1000 . . gene_id "CUFF.97"; transcript_id "CUFF.97.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; +chr1 Cufflinks transcript 3386740 3386836 1000 . . gene_id "CUFF.99"; transcript_id "CUFF.99.1"; FPKM "19.6021598701"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.204320"; cov "1.113402"; +chr1 Cufflinks exon 3386740 3386836 1000 . . gene_id "CUFF.99"; transcript_id "CUFF.99.1"; exon_number "1"; FPKM "19.6021598701"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.204320"; cov "1.113402";
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stringtie_merge_in3.gtf Wed Jul 13 14:48:26 2016 -0400 @@ -0,0 +1,100 @@ +chr1 mm9_refFlat stop_codon 3206103 3206105 0.000000 - . gene_id "Xkr4"; transcript_id "Xkr4"; +chr1 mm9_refFlat CDS 3206106 3207049 0.000000 - 2 gene_id "Xkr4"; transcript_id "Xkr4"; +chr1 mm9_refFlat exon 3204563 3207049 0.000000 - . gene_id "Xkr4"; transcript_id "Xkr4"; +chr1 mm9_refFlat CDS 3411783 3411982 0.000000 - 1 gene_id "Xkr4"; transcript_id "Xkr4"; +chr1 mm9_refFlat exon 3411783 3411982 0.000000 - . gene_id "Xkr4"; transcript_id "Xkr4"; +chr1 mm9_refFlat CDS 3660633 3661429 0.000000 - 0 gene_id "Xkr4"; transcript_id "Xkr4"; +chr1 mm9_refFlat start_codon 3661427 3661429 0.000000 - . gene_id "Xkr4"; transcript_id "Xkr4"; +chr1 mm9_refFlat exon 3660633 3661579 0.000000 - . gene_id "Xkr4"; transcript_id "Xkr4"; +chr1 mm9_refFlat stop_codon 4334681 4334683 0.000000 - . gene_id "Rp1"; transcript_id "Rp1"; +chr1 mm9_refFlat CDS 4334684 4340172 0.000000 - 2 gene_id "Rp1"; transcript_id "Rp1"; +chr1 mm9_refFlat exon 4334224 4340172 0.000000 - . gene_id "Rp1"; transcript_id "Rp1"; +chr1 mm9_refFlat CDS 4341991 4342162 0.000000 - 0 gene_id "Rp1"; transcript_id "Rp1"; +chr1 mm9_refFlat exon 4341991 4342162 0.000000 - . gene_id "Rp1"; transcript_id "Rp1"; +chr1 mm9_refFlat CDS 4342283 4342906 0.000000 - 0 gene_id "Rp1"; transcript_id "Rp1"; +chr1 mm9_refFlat start_codon 4342904 4342906 0.000000 - . gene_id "Rp1"; transcript_id "Rp1"; +chr1 mm9_refFlat exon 4342283 4342918 0.000000 - . gene_id "Rp1"; transcript_id "Rp1"; +chr1 mm9_refFlat exon 4350281 4350473 0.000000 - . gene_id "Rp1"; transcript_id "Rp1"; +chr1 mm9_refFlat stop_codon 4481797 4481799 0.000000 - . gene_id "Sox17"; transcript_id "Sox17"; +chr1 mm9_refFlat CDS 4481800 4482749 0.000000 - 2 gene_id "Sox17"; transcript_id "Sox17"; +chr1 mm9_refFlat exon 4481009 4482749 0.000000 - . gene_id "Sox17"; transcript_id "Sox17"; +chr1 mm9_refFlat CDS 4483181 4483487 0.000000 - 0 gene_id "Sox17"; transcript_id "Sox17"; +chr1 mm9_refFlat start_codon 4483485 4483487 0.000000 - . gene_id "Sox17"; transcript_id "Sox17"; +chr1 mm9_refFlat exon 4483181 4483547 0.000000 - . gene_id "Sox17"; transcript_id "Sox17"; +chr1 mm9_refFlat exon 4483853 4483944 0.000000 - . gene_id "Sox17"; transcript_id "Sox17"; +chr1 mm9_refFlat exon 4485217 4486023 0.000000 - . gene_id "Sox17"; transcript_id "Sox17"; +chr1 mm9_refFlat exon 4486372 4486494 0.000000 - . gene_id "Sox17"; transcript_id "Sox17"; +chr1 mm9_refFlat stop_codon 4766545 4766547 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; +chr1 mm9_refFlat CDS 4766548 4766882 0.000000 - 2 gene_id "Mrpl15"; transcript_id "Mrpl15"; +chr1 mm9_refFlat exon 4763279 4766882 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; +chr1 mm9_refFlat CDS 4767606 4767729 0.000000 - 0 gene_id "Mrpl15"; transcript_id "Mrpl15"; +chr1 mm9_refFlat exon 4767606 4767729 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; +chr1 mm9_refFlat CDS 4772649 4772814 0.000000 - 1 gene_id "Mrpl15"; transcript_id "Mrpl15"; +chr1 mm9_refFlat exon 4772649 4772814 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; +chr1 mm9_refFlat CDS 4774032 4774186 0.000000 - 0 gene_id "Mrpl15"; transcript_id "Mrpl15"; +chr1 mm9_refFlat exon 4774032 4774186 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; +chr1 mm9_refFlat CDS 4775654 4775758 0.000000 - 0 gene_id "Mrpl15"; transcript_id "Mrpl15"; +chr1 mm9_refFlat start_codon 4775756 4775758 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; +chr1 mm9_refFlat exon 4775654 4775807 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; +chr1 mm9_refFlat stop_codon 4764533 4764535 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; +chr1 mm9_refFlat CDS 4764536 4764597 0.000000 - 2 gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; +chr1 mm9_refFlat exon 4763279 4764597 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; +chr1 mm9_refFlat CDS 4767606 4767729 0.000000 - 0 gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; +chr1 mm9_refFlat exon 4767606 4767729 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; +chr1 mm9_refFlat CDS 4772649 4772814 0.000000 - 1 gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; +chr1 mm9_refFlat exon 4772649 4772814 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; +chr1 mm9_refFlat CDS 4774032 4774186 0.000000 - 0 gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; +chr1 mm9_refFlat exon 4774032 4774186 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; +chr1 mm9_refFlat CDS 4775654 4775758 0.000000 - 0 gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; +chr1 mm9_refFlat start_codon 4775756 4775758 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; +chr1 mm9_refFlat exon 4775654 4775807 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; +chr1 mm9_refFlat exon 4763279 4764597 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; +chr1 mm9_refFlat exon 4767606 4767729 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; +chr1 mm9_refFlat exon 4772649 4772814 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; +chr1 mm9_refFlat exon 4775654 4775807 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; +chr1 mm9_refFlat start_codon 4797995 4797997 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat CDS 4797995 4798063 0.000000 + 0 gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat exon 4797974 4798063 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat CDS 4798536 4798567 0.000000 + 0 gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat exon 4798536 4798567 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat CDS 4818665 4818730 0.000000 + 1 gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat exon 4818665 4818730 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat CDS 4820349 4820396 0.000000 + 1 gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat exon 4820349 4820396 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat CDS 4822392 4822462 0.000000 + 1 gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat exon 4822392 4822462 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat CDS 4827082 4827155 0.000000 + 2 gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat exon 4827082 4827155 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat CDS 4829468 4829569 0.000000 + 0 gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat exon 4829468 4829569 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat CDS 4831037 4831213 0.000000 + 0 gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat exon 4831037 4831213 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat CDS 4835044 4835094 0.000000 + 0 gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat stop_codon 4835095 4835097 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat exon 4835044 4836816 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; +chr1 mm9_refFlat start_codon 4847995 4847997 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat CDS 4847995 4848057 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat exon 4847775 4848057 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat CDS 4857551 4857613 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat exon 4857551 4857613 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat CDS 4868108 4868213 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat exon 4868108 4868213 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat CDS 4876825 4876912 0.000000 + 2 gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat exon 4876825 4876912 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat CDS 4879538 4879683 0.000000 + 1 gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat exon 4879538 4879683 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat CDS 4880821 4880877 0.000000 + 2 gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat exon 4880821 4880877 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat CDS 4881996 4882150 0.000000 + 2 gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat exon 4881996 4882150 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat CDS 4883498 4883644 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat exon 4883498 4883644 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat CDS 4885015 4885086 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat exon 4885015 4885086 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat CDS 4886437 4886442 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat stop_codon 4886443 4886445 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat exon 4886437 4887987 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; +chr1 mm9_refFlat start_codon 4847995 4847997 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1_dup1"; +chr1 mm9_refFlat CDS 4847995 4848057 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1_dup1"; +chr1 mm9_refFlat exon 4847775 4848057 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1_dup1"; +chr1 mm9_refFlat CDS 4857551 4857613 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1_dup1";
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stringtie_merge_out1.gtf Wed Jul 13 14:48:26 2016 -0400 @@ -0,0 +1,6 @@ +# stringtie --merge -p 1 -G /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_5.dat -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 250 -o /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_6.dat /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_1.dat /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_2.dat /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_3.dat /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_4.dat +# StringTie version 1.2.3 +test_chromosome StringTie transcript 53 550 1000 + . gene_id "MSTRG.1"; transcript_id "CUFF.1.1"; ref_gene_id "CUFF.1"; +test_chromosome StringTie exon 53 250 1000 + . gene_id "MSTRG.1"; transcript_id "CUFF.1.1"; exon_number "1"; ref_gene_id "CUFF.1"; +test_chromosome StringTie exon 351 400 1000 + . gene_id "MSTRG.1"; transcript_id "CUFF.1.1"; exon_number "2"; ref_gene_id "CUFF.1"; +test_chromosome StringTie exon 501 550 1000 + . gene_id "MSTRG.1"; transcript_id "CUFF.1.1"; exon_number "3"; ref_gene_id "CUFF.1";
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stringtie_merge_out2.gtf Wed Jul 13 14:48:26 2016 -0400 @@ -0,0 +1,100 @@ +# stringtie --merge -p 1 -G /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_9.dat -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 250 -o /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_10.dat /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_7.dat /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_8.dat +# StringTie version 1.2.3 +chr1 StringTie transcript 3189811 3193042 1000 . . gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; +chr1 StringTie exon 3189811 3193042 1000 . . gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; exon_number "1"; +chr1 StringTie transcript 3200023 3200191 1000 . . gene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; +chr1 StringTie exon 3200023 3200191 1000 . . gene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; exon_number "1"; +chr1 StringTie transcript 3201078 3201809 1000 . . gene_id "MSTRG.3"; transcript_id "MSTRG.3.1"; +chr1 StringTie exon 3201078 3201809 1000 . . gene_id "MSTRG.3"; transcript_id "MSTRG.3.1"; exon_number "1"; +chr1 StringTie transcript 3204563 3661579 1000 - . gene_id "MSTRG.4"; transcript_id "Xkr4"; ref_gene_id "Xkr4"; +chr1 StringTie exon 3204563 3207049 1000 - . gene_id "MSTRG.4"; transcript_id "Xkr4"; exon_number "1"; ref_gene_id "Xkr4"; +chr1 StringTie exon 3411783 3411982 1000 - . gene_id "MSTRG.4"; transcript_id "Xkr4"; exon_number "2"; ref_gene_id "Xkr4"; +chr1 StringTie exon 3660633 3661579 1000 - . gene_id "MSTRG.4"; transcript_id "Xkr4"; exon_number "3"; ref_gene_id "Xkr4"; +chr1 StringTie transcript 3212214 3212439 1000 . . gene_id "MSTRG.5"; transcript_id "MSTRG.5.1"; +chr1 StringTie exon 3212214 3212439 1000 . . gene_id "MSTRG.5"; transcript_id "MSTRG.5.1"; exon_number "1"; +chr1 StringTie transcript 3212718 3212801 1000 . . gene_id "MSTRG.6"; transcript_id "MSTRG.6.1"; +chr1 StringTie exon 3212718 3212801 1000 . . gene_id "MSTRG.6"; transcript_id "MSTRG.6.1"; exon_number "1"; +chr1 StringTie transcript 3213096 3213242 1000 . . gene_id "MSTRG.7"; transcript_id "MSTRG.7.1"; +chr1 StringTie exon 3213096 3213242 1000 . . gene_id "MSTRG.7"; transcript_id "MSTRG.7.1"; exon_number "1"; +chr1 StringTie transcript 3242634 3243079 1000 . . gene_id "MSTRG.8"; transcript_id "MSTRG.8.1"; +chr1 StringTie exon 3242634 3243079 1000 . . gene_id "MSTRG.8"; transcript_id "MSTRG.8.1"; exon_number "1"; +chr1 StringTie transcript 3243348 3243401 1000 . . gene_id "MSTRG.9"; transcript_id "MSTRG.9.1"; +chr1 StringTie exon 3243348 3243401 1000 . . gene_id "MSTRG.9"; transcript_id "MSTRG.9.1"; exon_number "1"; +chr1 StringTie transcript 3277914 3278390 1000 . . gene_id "MSTRG.10"; transcript_id "MSTRG.10.1"; +chr1 StringTie exon 3277914 3278390 1000 . . gene_id "MSTRG.10"; transcript_id "MSTRG.10.1"; exon_number "1"; +chr1 StringTie transcript 3280687 3280741 1000 . . gene_id "MSTRG.11"; transcript_id "MSTRG.11.1"; +chr1 StringTie exon 3280687 3280741 1000 . . gene_id "MSTRG.11"; transcript_id "MSTRG.11.1"; exon_number "1"; +chr1 StringTie transcript 3282761 3282832 1000 . . gene_id "MSTRG.12"; transcript_id "MSTRG.12.1"; +chr1 StringTie exon 3282761 3282832 1000 . . gene_id "MSTRG.12"; transcript_id "MSTRG.12.1"; exon_number "1"; +chr1 StringTie transcript 3290489 3291273 1000 . . gene_id "MSTRG.13"; transcript_id "MSTRG.13.1"; +chr1 StringTie exon 3290489 3291273 1000 . . gene_id "MSTRG.13"; transcript_id "MSTRG.13.1"; exon_number "1"; +chr1 StringTie transcript 3299444 3299664 1000 . . gene_id "MSTRG.14"; transcript_id "MSTRG.14.1"; +chr1 StringTie exon 3299444 3299664 1000 . . gene_id "MSTRG.14"; transcript_id "MSTRG.14.1"; exon_number "1"; +chr1 StringTie transcript 3319000 3319051 1000 . . gene_id "MSTRG.15"; transcript_id "MSTRG.15.1"; +chr1 StringTie exon 3319000 3319051 1000 . . gene_id "MSTRG.15"; transcript_id "MSTRG.15.1"; exon_number "1"; +chr1 StringTie transcript 3351241 3351311 1000 . . gene_id "MSTRG.16"; transcript_id "MSTRG.16.1"; +chr1 StringTie exon 3351241 3351311 1000 . . gene_id "MSTRG.16"; transcript_id "MSTRG.16.1"; exon_number "1"; +chr1 StringTie transcript 3355908 3356119 1000 . . gene_id "MSTRG.17"; transcript_id "MSTRG.17.1"; +chr1 StringTie exon 3355908 3356119 1000 . . gene_id "MSTRG.17"; transcript_id "MSTRG.17.1"; exon_number "1"; +chr1 StringTie transcript 3363077 3363446 1000 . . gene_id "MSTRG.18"; transcript_id "MSTRG.18.1"; +chr1 StringTie exon 3363077 3363446 1000 . . gene_id "MSTRG.18"; transcript_id "MSTRG.18.1"; exon_number "1"; +chr1 StringTie transcript 3363754 3363849 1000 . . gene_id "MSTRG.19"; transcript_id "MSTRG.19.1"; +chr1 StringTie exon 3363754 3363849 1000 . . gene_id "MSTRG.19"; transcript_id "MSTRG.19.1"; exon_number "1"; +chr1 StringTie transcript 3377212 3377262 1000 . . gene_id "MSTRG.20"; transcript_id "MSTRG.20.1"; +chr1 StringTie exon 3377212 3377262 1000 . . gene_id "MSTRG.20"; transcript_id "MSTRG.20.1"; exon_number "1"; +chr1 StringTie transcript 3386740 3386836 1000 . . gene_id "MSTRG.21"; transcript_id "MSTRG.21.1"; +chr1 StringTie exon 3386740 3386836 1000 . . gene_id "MSTRG.21"; transcript_id "MSTRG.21.1"; exon_number "1"; +chr1 StringTie transcript 3450907 3451109 1000 . . gene_id "MSTRG.22"; transcript_id "MSTRG.22.1"; +chr1 StringTie exon 3450907 3451109 1000 . . gene_id "MSTRG.22"; transcript_id "MSTRG.22.1"; exon_number "1"; +chr1 mm9_refFlat transcript 4334224 4350473 . - . gene_id "Rp1"; transcript_id "Rp1"; ref_gene_id "Rp1"; +chr1 mm9_refFlat exon 4334224 4340172 . - . gene_id "Rp1"; transcript_id "Rp1"; exon_number "1"; ref_gene_id "Rp1"; +chr1 mm9_refFlat exon 4341991 4342162 . - . gene_id "Rp1"; transcript_id "Rp1"; exon_number "2"; ref_gene_id "Rp1"; +chr1 mm9_refFlat exon 4342283 4342918 . - . gene_id "Rp1"; transcript_id "Rp1"; exon_number "3"; ref_gene_id "Rp1"; +chr1 mm9_refFlat exon 4350281 4350473 . - . gene_id "Rp1"; transcript_id "Rp1"; exon_number "4"; ref_gene_id "Rp1"; +chr1 mm9_refFlat transcript 4481009 4486494 . - . gene_id "Sox17"; transcript_id "Sox17"; ref_gene_id "Sox17"; +chr1 mm9_refFlat exon 4481009 4482749 . - . gene_id "Sox17"; transcript_id "Sox17"; exon_number "1"; ref_gene_id "Sox17"; +chr1 mm9_refFlat exon 4483181 4483547 . - . gene_id "Sox17"; transcript_id "Sox17"; exon_number "2"; ref_gene_id "Sox17"; +chr1 mm9_refFlat exon 4483853 4483944 . - . gene_id "Sox17"; transcript_id "Sox17"; exon_number "3"; ref_gene_id "Sox17"; +chr1 mm9_refFlat exon 4485217 4486023 . - . gene_id "Sox17"; transcript_id "Sox17"; exon_number "4"; ref_gene_id "Sox17"; +chr1 mm9_refFlat exon 4486372 4486494 . - . gene_id "Sox17"; transcript_id "Sox17"; exon_number "5"; ref_gene_id "Sox17"; +chr1 mm9_refFlat transcript 4763279 4775807 . - . gene_id "Mrpl15"; transcript_id "Mrpl15"; ref_gene_id "Mrpl15"; +chr1 mm9_refFlat exon 4763279 4766882 . - . gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "1"; ref_gene_id "Mrpl15"; +chr1 mm9_refFlat exon 4767606 4767729 . - . gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "2"; ref_gene_id "Mrpl15"; +chr1 mm9_refFlat exon 4772649 4772814 . - . gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "3"; ref_gene_id "Mrpl15"; +chr1 mm9_refFlat exon 4774032 4774186 . - . gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "4"; ref_gene_id "Mrpl15"; +chr1 mm9_refFlat exon 4775654 4775807 . - . gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "5"; ref_gene_id "Mrpl15"; +chr1 mm9_refFlat transcript 4763279 4775807 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; ref_gene_id "Mrpl15"; +chr1 mm9_refFlat exon 4763279 4764597 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "1"; ref_gene_id "Mrpl15"; +chr1 mm9_refFlat exon 4767606 4767729 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "2"; ref_gene_id "Mrpl15"; +chr1 mm9_refFlat exon 4772649 4772814 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "3"; ref_gene_id "Mrpl15"; +chr1 mm9_refFlat exon 4774032 4774186 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "4"; ref_gene_id "Mrpl15"; +chr1 mm9_refFlat exon 4775654 4775807 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "5"; ref_gene_id "Mrpl15"; +chr1 mm9_refFlat transcript 4763279 4775807 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; ref_gene_id "Mrpl15"; +chr1 mm9_refFlat exon 4763279 4764597 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "1"; ref_gene_id "Mrpl15"; +chr1 mm9_refFlat exon 4767606 4767729 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "2"; ref_gene_id "Mrpl15"; +chr1 mm9_refFlat exon 4772649 4772814 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "3"; ref_gene_id "Mrpl15"; +chr1 mm9_refFlat exon 4775654 4775807 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "4"; ref_gene_id "Mrpl15"; +chr1 mm9_refFlat transcript 4797974 4836816 . + . gene_id "Lypla1"; transcript_id "Lypla1"; ref_gene_id "Lypla1"; +chr1 mm9_refFlat exon 4797974 4798063 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "1"; ref_gene_id "Lypla1"; +chr1 mm9_refFlat exon 4798536 4798567 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "2"; ref_gene_id "Lypla1"; +chr1 mm9_refFlat exon 4818665 4818730 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "3"; ref_gene_id "Lypla1"; +chr1 mm9_refFlat exon 4820349 4820396 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "4"; ref_gene_id "Lypla1"; +chr1 mm9_refFlat exon 4822392 4822462 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "5"; ref_gene_id "Lypla1"; +chr1 mm9_refFlat exon 4827082 4827155 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "6"; ref_gene_id "Lypla1"; +chr1 mm9_refFlat exon 4829468 4829569 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "7"; ref_gene_id "Lypla1"; +chr1 mm9_refFlat exon 4831037 4831213 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "8"; ref_gene_id "Lypla1"; +chr1 mm9_refFlat exon 4835044 4836816 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "9"; ref_gene_id "Lypla1"; +chr1 mm9_refFlat transcript 4847775 4857613 . + . gene_id "Tcea1"; transcript_id "Tcea1_dup1"; ref_gene_id "Tcea1"; +chr1 mm9_refFlat exon 4847775 4848057 . + . gene_id "Tcea1"; transcript_id "Tcea1_dup1"; exon_number "1"; ref_gene_id "Tcea1"; +chr1 mm9_refFlat exon 4857551 4857613 . + . gene_id "Tcea1"; transcript_id "Tcea1_dup1"; exon_number "2"; ref_gene_id "Tcea1"; +chr1 mm9_refFlat transcript 4847775 4887987 . + . gene_id "Tcea1"; transcript_id "Tcea1"; ref_gene_id "Tcea1"; +chr1 mm9_refFlat exon 4847775 4848057 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "1"; ref_gene_id "Tcea1"; +chr1 mm9_refFlat exon 4857551 4857613 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "2"; ref_gene_id "Tcea1"; +chr1 mm9_refFlat exon 4868108 4868213 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "3"; ref_gene_id "Tcea1"; +chr1 mm9_refFlat exon 4876825 4876912 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "4"; ref_gene_id "Tcea1"; +chr1 mm9_refFlat exon 4879538 4879683 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "5"; ref_gene_id "Tcea1"; +chr1 mm9_refFlat exon 4880821 4880877 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "6"; ref_gene_id "Tcea1"; +chr1 mm9_refFlat exon 4881996 4882150 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "7"; ref_gene_id "Tcea1"; +chr1 mm9_refFlat exon 4883498 4883644 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "8"; ref_gene_id "Tcea1"; +chr1 mm9_refFlat exon 4885015 4885086 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "9"; ref_gene_id "Tcea1"; +chr1 mm9_refFlat exon 4886437 4887987 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "10"; ref_gene_id "Tcea1";
--- a/test-data/stringtie_out1.gtf Wed Oct 21 16:07:42 2015 -0400 +++ b/test-data/stringtie_out1.gtf Wed Jul 13 14:48:26 2016 -0400 @@ -1,6 +1,6 @@ -# stringtie /tmp/tmpoOYb63/files/000/dataset_1.dat -o /tmp/tmpoOYb63/files/000/dataset_2.dat -p 1 -# StringTie version 1.1.0 -test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "44.682419"; FPKM "3273437.500000"; TPM "995243.375000"; +# stringtie /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_1.dat -o /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_2.dat -p 1 +# StringTie version 1.2.3 +test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "44.682419"; FPKM "3273437.500000"; TPM "975770.250000"; test_chromosome StringTie exon 53 250 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "48.948147"; test_chromosome StringTie exon 351 400 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "51.382565"; test_chromosome StringTie exon 501 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "21.090000";
--- a/test-data/stringtie_out2.gtf Wed Oct 21 16:07:42 2015 -0400 +++ b/test-data/stringtie_out2.gtf Wed Jul 13 14:48:26 2016 -0400 @@ -1,6 +1,6 @@ -# stringtie /tmp/tmpoOYb63/files/000/dataset_9.dat -o /tmp/tmpoOYb63/files/000/dataset_10.dat -p 1 -l STRG -f 0.17 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 -# StringTie version 1.1.0 -test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "44.682419"; FPKM "3273437.500000"; TPM "995243.375000"; +# stringtie /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_9.dat -o /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_10.dat -p 1 -l STRG -f 0.17 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 +# StringTie version 1.2.3 +test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "44.682419"; FPKM "3273437.500000"; TPM "975770.250000"; test_chromosome StringTie exon 53 250 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "48.948147"; test_chromosome StringTie exon 351 400 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "51.382565"; test_chromosome StringTie exon 501 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "21.090000";
--- a/test-data/stringtie_out3.gtf Wed Oct 21 16:07:42 2015 -0400 +++ b/test-data/stringtie_out3.gtf Wed Jul 13 14:48:26 2016 -0400 @@ -1,6 +1,6 @@ -# stringtie /tmp/tmpoOYb63/files/000/dataset_16.dat -o /tmp/tmpoOYb63/files/000/dataset_18.dat -p 1 -C /tmp/tmpoOYb63/files/000/dataset_20.dat -G /tmp/tmpoOYb63/files/000/dataset_17.dat -# StringTie version 1.1.0 -test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "44.724823"; FPKM "3276543.750000"; TPM "996187.875000"; +# stringtie /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_16.dat -o /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_18.dat -p 1 -C /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_20.dat -G /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_17.dat +# StringTie version 1.2.3 +test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "44.724823"; FPKM "3276543.750000"; TPM "976696.312500"; test_chromosome StringTie exon 53 250 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "49.011967"; test_chromosome StringTie exon 351 400 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "51.382565"; test_chromosome StringTie exon 501 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "21.090000";
--- a/test-data/stringtie_out4.gtf Wed Oct 21 16:07:42 2015 -0400 +++ b/test-data/stringtie_out4.gtf Wed Jul 13 14:48:26 2016 -0400 @@ -1,6 +1,6 @@ -# stringtie /tmp/tmpoOYb63/files/000/dataset_35.dat -o /tmp/tmpoOYb63/files/000/dataset_37.dat -p 1 -C /tmp/tmpoOYb63/files/000/dataset_39.dat -G /tmp/tmpoOYb63/files/000/dataset_36.dat -l STRG -f 0.17 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 -A /tmp/tmpoOYb63/files/000/dataset_38.dat -# StringTie version 1.1.0 -test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "44.724823"; FPKM "3276543.750000"; TPM "996187.875000"; +# stringtie /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpv7zmop/files/000/dataset_1.dat -o /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpv7zmop/files/000/dataset_3.dat -p 1 -C /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpv7zmop/files/000/dataset_5.dat -G /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpv7zmop/files/000/dataset_2.dat -l STRG -f 0.17 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 -A /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpv7zmop/files/000/dataset_4.dat +# StringTie version 1.2.3 +test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "44.724823"; FPKM "3276543.750000"; TPM "976696.312500"; test_chromosome StringTie exon 53 250 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "49.011967"; test_chromosome StringTie exon 351 400 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "51.382565"; test_chromosome StringTie exon 501 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "21.090000";
--- a/test-data/stringtie_out5.gtf Wed Oct 21 16:07:42 2015 -0400 +++ b/test-data/stringtie_out5.gtf Wed Jul 13 14:48:26 2016 -0400 @@ -1,6 +1,6 @@ -# stringtie /tmp/tmpoOYb63/files/000/dataset_25.dat -o /tmp/tmpoOYb63/files/000/dataset_27.dat -p 1 -C /tmp/tmpoOYb63/files/000/dataset_29.dat -G /tmp/tmpoOYb63/files/000/dataset_26.dat -b /tmp/tmpoOYb63/job_working_directory/000/13 -# StringTie version 1.1.0 -test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "44.724823"; FPKM "3276543.750000"; TPM "996187.875000"; +# stringtie /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_25.dat -o /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_27.dat -p 1 -C /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_29.dat -G /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_26.dat -B +# StringTie version 1.2.3 +test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "44.724823"; FPKM "3276543.750000"; TPM "976696.312500"; test_chromosome StringTie exon 53 250 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "49.011967"; test_chromosome StringTie exon 351 400 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "51.382565"; test_chromosome StringTie exon 501 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "21.090000";
--- a/test-data/stringtie_out6.gtf Wed Oct 21 16:07:42 2015 -0400 +++ b/test-data/stringtie_out6.gtf Wed Jul 13 14:48:26 2016 -0400 @@ -1,3 +1,3 @@ -Gene ID Gene Name Strand Start End Length Coverage FPKM TPM -CUFF.1 - + 53 550 298 44.895973 3289082.250000 1000000.000000 -STRG.1 - + 53 550 298 44.895973 3289082.250000 1000000.000000 +Gene ID Gene Name Reference Strand Start End Coverage FPKM TPM +CUFF.1 - test_chromosome + 53 550 45.791946 3354721.250000 1000000.062500 +STRG.1 - test_chromosome + 53 550 45.791946 3354721.250000 1000000.062500
--- a/test-data/stringtie_out7.gtf Wed Oct 21 16:07:42 2015 -0400 +++ b/test-data/stringtie_out7.gtf Wed Jul 13 14:48:26 2016 -0400 @@ -1,6 +1,6 @@ -# stringtie /tmp/tmpoOYb63/files/000/dataset_40.dat -o /tmp/tmpoOYb63/files/000/dataset_42.dat -p 1 -C /tmp/tmpoOYb63/files/000/dataset_43.dat -G /tmp/tmpoOYb63/files/000/dataset_41.dat -l STRG -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 -# StringTie version 1.1.0 -test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "44.724823"; FPKM "3276543.750000"; TPM "996187.875000"; +# stringtie /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_39.dat -o /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_41.dat -p 1 -C /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_42.dat -G /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_40.dat -l STRG -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 +# StringTie version 1.2.3 +test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "44.724823"; FPKM "3276543.750000"; TPM "976696.312500"; test_chromosome StringTie exon 53 250 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "49.011967"; test_chromosome StringTie exon 351 400 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "51.382565"; test_chromosome StringTie exon 501 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "21.090000";
--- a/test-data/t_data.ctab Wed Oct 21 16:07:42 2015 -0400 +++ b/test-data/t_data.ctab Wed Jul 13 14:48:26 2016 -0400 @@ -1,2 +0,0 @@ -t_id chr strand start end t_name num_exons length gene_id gene_name cov FPKM -1 test_chromosome + 53 550 CUFF.1.1 3 298 CUFF.1 . 44.724823 3276543.750000
--- a/tool_dependencies.xml Wed Oct 21 16:07:42 2015 -0400 +++ b/tool_dependencies.xml Wed Jul 13 14:48:26 2016 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="stringtie" version="1.1.0"> - <repository changeset_revision="62a98ebf406f" name="package_stringtie_1_1_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="stringtie" version="1.2.3"> + <repository changeset_revision="ee804c6f3b97" name="package_stringtie_1_2_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>