Mercurial > repos > devteam > cuffdiff
changeset 7:8da0eade1f59 draft
Uploaded
| author | devteam |
|---|---|
| date | Fri, 19 Dec 2014 11:57:43 -0500 |
| parents | 604fa75232a2 |
| children | 88fcac97c2a0 |
| files | cuff_macros.xml cuffdiff_wrapper.xml test-data/cuffdiff_out1.txt test-data/cuffdiff_out10.txt test-data/cuffdiff_out2.txt test-data/cuffdiff_out3.txt test-data/cuffdiff_out5.txt test-data/cuffdiff_out6.txt test-data/cuffdiff_out7.txt test-data/cuffdiff_out9.txt tool_dependencies.xml |
| diffstat | 11 files changed, 714 insertions(+), 533 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cuff_macros.xml Fri Dec 19 11:57:43 2014 -0500 @@ -0,0 +1,91 @@ +<macros> + <token name="@VERSION@">2.2.1</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="2.2.1">cufflinks</requirement> + <yield /> + </requirements> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1:" /> + <exit_code range=":-1" /> + <regex match="Error:" /> + <regex match="Exception:" /> + </stdio> + </xml> + <xml name="condition_inputs"> + <!-- DEFAULT : use BAM/SAM files --> + <conditional name="in_type"> + <param name="set_in_type" type="select" label="Input data type" + help="CuffNorm supports either CXB (from cuffquant) or SAM/BAM input files. Mixing is not supported. Default: SAM/BAM"> + <option value="BAM">SAM/BAM</option> + <option value="CXB">Cuffquant (CXB)</option> + <option value="CONDITION_LIST">List of single replicate conditions</option> + <option value="CONDITION_REPLICATE_LIST">List of multiple replicate conditions</option> + </param> + <when value="BAM"> + <repeat name="conditions" title="Condition" min="2"> + <param name="name" title="Condition name" type="text" label="Name"/> + <param name="samples" label="Replicates" type="data" format="sam,bam" multiple="true"/> + </repeat> + </when> + <when value="CXB"> + <repeat name="conditions" title="Condition" min="2"> + <param name="name" title="Condition name" type="text" label="Name"/> + <param name="samples" label="Replicates" type="data" format="cxb" multiple="true"/> + </repeat> + </when> + <when value="CONDITION_LIST"> + <param name="conditions" title="List of Conditions" type="data_collection" collection_type="list" /> + </when> + <when value="CONDITION_REPLICATE_LIST"> + <param name="conditions" title="List of Conditions" type="data_collection" collection_type="list:list" /> + </when> + </conditional> + </xml> + <token name="@CONDITION_SAMPLES@"> + #if $in_type.set_in_type in ['BAM', 'CXB'] + #for $condition in $in_type.conditions: + #set samples = ','.join( [ str( $sample ) for $sample in $condition.samples ] ) + $samples + #end for + #elif $in_type.set_in_type == 'CONDITION_LIST' + #for $sample in $in_type.conditions: + $sample + #end for + #elif $in_type.set_in_type == 'CONDITION_REPLICATE_LIST' + #for $condition_list in $in_type.conditions: + #set samples = ','.join( [ str( $sample ) for $sample in $condition_list ] ) + $samples + #end for + #end if + </token> + <token name="@CONDITION_LABELS@"> + #import re + #if $in_type.set_in_type in ['BAM', 'CXB'] + #set labels = '\'' + '\',\''.join( [ str( $condition.name ) for $condition in $in_type.conditions ] ) + '\'' + #elif $in_type.set_in_type in ['CONDITION_LIST', 'CONDITION_REPLICATE_LIST'] + #set labels = '\'' + '\',\''.join( map(lambda x: re.sub('[^\w\-_]', '_', x), $in_type.conditions.keys() ) ) + '\'' + #end if + --labels $labels + </token> + <xml name="cufflinks_gtf_inputs"> + <param format="gtf" name="inputs" type="data" label="GTF file(s) produced by Cufflinks" help="" multiple="true" /> + <repeat name="additional_inputs" title="Additional GTF Inputs (Lists)"> + <param format="gtf" name="additional_inputs" type="data_collection" label="GTF file(s) produced by Cufflinks" help="" /> + </repeat> + </xml> + <token name="@CUFFLINKS_GTF_INPUTS@"> + ## Inputs. + #for $input_file in $inputs: + "${input_file}" + #end for + #for $additional_input in $additional_inputs: + #for $input_file in $additional_input.additional_inputs: + "${input_file}" + #end for + #end for + </token> + <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token> +</macros> \ No newline at end of file
--- a/cuffdiff_wrapper.xml Thu Jan 16 13:13:52 2014 -0500 +++ b/cuffdiff_wrapper.xml Fri Dec 19 11:57:43 2014 -0500 @@ -1,9 +1,10 @@ -<tool id="cuffdiff" name="Cuffdiff" version="0.0.7"> - <!-- Wrapper supports Cuffdiff versions 2.1.0-2.1.1 --> +<tool id="cuffdiff" name="Cuffdiff" version="@VERSION@.0"> <description>find significant changes in transcript expression, splicing, and promoter use</description> - <requirements> - <requirement type="package" version="2.1.1">cufflinks</requirement> - </requirements> + <expand macro="requirements" /> + <expand macro="stdio" /> + <macros> + <import>cuff_macros.xml</import> + </macros> <version_command>cuffdiff 2>&1 | head -n 1</version_command> <command> cuffdiff @@ -14,15 +15,15 @@ --library-norm-method=$library_norm_method --dispersion-method=$dispersion_method - ## Set advanced data parameters? + ## Set advanced SE data parameters? #if $additional.sAdditional == "Yes": -m $additional.frag_mean_len -s $additional.frag_len_std_dev #end if ## Multi-read correct? - #if str($multiread_correct) == "Yes": - -u + #if $multiread_correct : + -u #end if ## Bias correction? @@ -33,30 +34,40 @@ $bias_correction.seq_source.ref_file #else: ## Built-in genome. - ${__get_data_table_entry__('fasta_indexes', 'value', $gtf_input.dbkey, 'path')} + "${ bias_correction.seq_source.index.fields.path }" #end if #end if - #set labels = '\'' + '\',\''.join( [ str( $condition.name ) for $condition in $conditions ] ) + '\'' - --labels $labels + @CONDITION_LABELS@ + + $length_correction + ## Set advanced parameters for cufflinks + #if $advanced_settings.sAdvanced == "Yes": + #if str($advanced_settings.library_type) != 'auto': + --library-type=$advanced_settings.library_type + #end if + #if $advanced_settings.mask_file: + --mask-file=$advanced_settings.mask_file + #end if + #if $advanced_settings.time_series: + --time-series + #end if + --max-mle-iterations=$advanced_settings.max_mle_iterations + $advanced_settings.hits_norm + --max-bundle-frags=$advanced_settings.max_bundle_frags + --num-frag-count-draws=$advanced_settings.num_frag_count_draws + --num-frag-assign-draws=$advanced_settings.num_frag_assign_draws + --min-reps-for-js-test=$advanced_settings.min_reps_for_js_test + #end if ## Inputs. $gtf_input - #for $condition in $conditions: - #set samples = ','.join( [ str( $sample.sample ) for $sample in $condition.samples ] ) - $samples - #end for + + @CONDITION_SAMPLES@ </command> <inputs> <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts" help="A transcript GFF3 or GTF file produced by cufflinks, cuffcompare, or other source."/> - - <repeat name="conditions" title="Condition" min="2"> - <param name="name" title="Condition name" type="text" label="Name"/> - <repeat name="samples" title="Replicate" min="1"> - <param name="sample" label="Add replicate" type="data" format="sam,bam"/> - </repeat> - </repeat> - + <expand macro="condition_inputs" /> <param name="library_norm_method" type="select" label="Library normalization method"> <option value="geometric" selected="True">geometric</option> <option value="classic-fpkm">classic-fpkm</option> @@ -67,19 +78,18 @@ <option value="pooled" selected="True">pooled</option> <option value="per-condition">per-condition</option> <option value="blind">blind</option> + <option value="poisson">poisson</option> </param> <param name="fdr" type="float" value="0.05" label="False Discovery Rate" help="The allowed false discovery rate."/> - - <param name="min_alignment_count" type="integer" value="10" label="Min Alignment Count" help="The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples."/> - - <param name="multiread_correct" type="select" label="Use multi-read correct" help="Tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome."> - <option value="No" selected="true">No</option> - <option value="Yes">Yes</option> - </param> + <param name="min_alignment_count" type="integer" value="10" label="Min Alignment Count" + help="The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples."/> + <param name="multiread_correct" type="boolean" label="Use multi-read correct" + help="Tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome." /> <conditional name="bias_correction"> - <param name="do_bias_correction" type="select" label="Perform Bias Correction" help="Bias detection and correction can significantly improve accuracy of transcript abundance estimates."> + <param name="do_bias_correction" type="select" label="Perform Bias Correction" + help="Bias detection and correction can significantly improve accuracy of transcript abundance estimates."> <option value="No">No</option> <option value="Yes">Yes</option> </param> @@ -109,10 +119,22 @@ <option value="No" selected="true">No</option> <option value="Yes">Yes</option> </param> + + <param name="include_count_files" type="select" label="Include Count Based output files" + help="Cuffdiff estimates the number of fragments that originated from each transcript, primary transcript, and gene in each sample. Primary transcript and gene counts are computed by summing the counts of transcripts in each primary transcript group or gene group."> + <option value="No" selected="true">No</option> + <option value="Yes">Yes</option> + </param> + + <param name="length_correction" type="select" label="apply length correction" help="mode of length normalization to transcript fpkm."> + <option value="" selected="true">cufflinks effective length correction</option> + <option value="--no-effective-length-correction">standard length correction</option> + <option value="--no-length-correction">no length correction at all (use raw counts)</option> + </param> <conditional name="additional"> - <param name="sAdditional" type="select" label="Set Additional Parameters? (not recommended for paired-end reads)"> - <option value="No">No</option> + <param name="sAdditional" type="select" label="Set Additional Parameters for single end reads? (not recommended for paired-end reads)"> + <option value="No" selected="True">No</option> <option value="Yes">Yes</option> </param> <when value="No"></when> @@ -121,40 +143,88 @@ <param name="frag_len_std_dev" type="integer" value="80" label="Fragment Length Standard Deviation"/> </when> </conditional> + + <conditional name="advanced_settings"> + <param name="sAdvanced" type="select" label="Set Advanced Cuffdiff parameters? "> + <option value="No" selected="True">No</option> + <option value="Yes">Yes</option> + </param> + <when value="No"></when> + <when value="Yes"> + <param type="select" name="library_type" label="Library prep used for input reads" help=""> + <option value="auto" selected="True">Auto Detect</option> + <option value="ff-firststrand">ff-firststrand</option> + <option value="ff-secondstrand">ff-secondstrand</option> + <option value="ff-unstranded">ff-unstranded</option> + <option value="fr-firststrand">fr-firststrand</option> + <option value="fr-secondstrand">fr-secondstrand</option> + <option value="fr-unstranded" >fr-unstranded</option> + <option value="transfrags">transfrags</option> + </param> + <param name="mask_file" type="data" format="gtf,gff3" label="Mask File" help="Ignore all alignment within transcripts in this file" optional="True" /> + <param name="time_series" type="boolean" label="Perform Time Series analysis" + help="Instructs Cuffdiff to analyze the provided samples as a time series, rather than testing for differences between all pairs of samples. Samples should be provided in increasing time order at the command line (e.g first time point SAM, second timepoint SAM, etc.)" /> + <param name="max_mle_iterations" value="5000" type="integer" label="Max MLE iterations" help="Maximum iterations allowed for Maximal Likelyhood Estimation calculations" /> + <param name="hits_norm" type="select" label="Hits included in normalization" help="All Hits: With this option, Cufflinks counts all fragments, including those not compatible with any reference transcript, towards the number of mapped fragments used in the FPKM denominator. Compatible Hits: With this option, Cufflinks counts only those fragments compatible with some reference transcript towards the number of mapped fragments used in the FPKM denominator. Using this mode is generally recommended in Cuffdiff to reduce certain types of bias caused by differential amounts of ribosomal reads which can create the impression of falsely differentially expressed genes. It is active by default." > + <option value="--compatible-hits-norm" selected="True">Compatible Hits</option> + <option value="--total-hits-norm">All Hits</option> + </param> + <param name="max_bundle_frags" type="integer" value="500000" label="Maximum number of fragments per locus" + help="Sets the maximum number of fragments a locus may have before being skipped. Skipped loci are listed in skipped.gtf. Default: 500,000" /> + <param name="num_frag_count_draws" type="integer" value="100" label="Number of fragment generation samples" + help="Cuffdiff will make this many draws from each transcript's predicted negative binomial random numbder generator. Each draw is a number of fragments that will be probabilistically assigned to the transcripts in the transcriptome. Used to estimate the variance-covariance matrix on assigned fragment counts. Default: 100."/> + <param name="num_frag_assign_draws" type="integer" value="50" label="Number of fragment assignment samples per generation" help="For each fragment drawn from a transcript, Cuffdiff will assign it this many times (probabilistically), thus estimating the assignment uncertainty for each transcript. Used to estimate the variance-covariance matrix on assigned fragment counts. Default: 50."/> + <param name="min_reps_for_js_test" type="integer" value="3" label="Minimal Replicates for isoform shift testing" help="Cuffdiff won't test genes for differential regulation unless the conditions in question have at least this many replicates. Default: 3." /> + </when> + </conditional> </inputs> - - <stdio> - <regex match="Error" source="both" level="fatal" description="Error"/> - <regex match=".*" source="both" level="log" description="tool progress"/> - </stdio> - <outputs> <!-- Optional read group datasets. --> <data format="tabular" name="isoforms_read_group" label="${tool.name} on ${on_string}: isoforms read group tracking" from_work_dir="isoforms.read_group_tracking" > - <filter>(params['include_read_group_files'] == 'Yes'</filter> + <filter>(include_read_group_files == 'Yes')</filter> </data> <data format="tabular" name="genes_read_group" label="${tool.name} on ${on_string}: genes read group tracking" from_work_dir="genes.read_group_tracking" > - <filter>(params['include_read_group_files'] == 'Yes'</filter> + <filter>(include_read_group_files == 'Yes')</filter> </data> <data format="tabular" name="cds_read_group" label="${tool.name} on ${on_string}: CDs read group tracking" from_work_dir="cds.read_group_tracking" > - <filter>(params['include_read_group_files'] == 'Yes'</filter> + <filter>(include_read_group_files == 'Yes')</filter> </data> <data format="tabular" name="tss_groups_read_group" label="${tool.name} on ${on_string}: TSS groups read group tracking" from_work_dir="tss_groups.read_group_tracking" > - <filter>(params['include_read_group_files'] == 'Yes'</filter> + <filter>(include_read_group_files == 'Yes')</filter> </data> - + <data format="text" name="read_group_info" label="${tool.name} on ${on_string}: read group info" from_work_dir="read_groups.info" > + <filter>(include_read_group_files == 'Yes')</filter> + </data> + <data format="text" name="run_info" label="${tool.name} on ${on_string}: run info" from_work_dir="run.info" > + <filter>(include_read_group_files == 'Yes')</filter> + </data> <!-- Standard datasets. --> <data format="tabular" name="splicing_diff" label="${tool.name} on ${on_string}: splicing differential expression testing" from_work_dir="splicing.diff" /> <data format="tabular" name="promoters_diff" label="${tool.name} on ${on_string}: promoters differential expression testing" from_work_dir="promoters.diff" /> <data format="tabular" name="cds_diff" label="${tool.name} on ${on_string}: CDS overloading diffential expression testing" from_work_dir="cds.diff" /> <data format="tabular" name="cds_exp_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM differential expression testing" from_work_dir="cds_exp.diff" /> <data format="tabular" name="cds_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM tracking" from_work_dir="cds.fpkm_tracking" /> + <data format="tabular" name="cds_count_tracking" label="${tool.name} on ${on_string}: CDS count tracking" from_work_dir="cds.count_tracking" > + <filter>(include_count_files == 'Yes')</filter> + </data> + <data format="tabular" name="tss_groups_exp" label="${tool.name} on ${on_string}: TSS groups differential expression testing" from_work_dir="tss_group_exp.diff" /> <data format="tabular" name="tss_groups_fpkm_tracking" label="${tool.name} on ${on_string}: TSS groups FPKM tracking" from_work_dir="tss_groups.fpkm_tracking" /> + <data format="tabular" name="tss_groups_count_tracking" label="${tool.name} on ${on_string}: TSS count FPKM tracking" from_work_dir="tss_groups.count_tracking" > + <filter>(include_count_files == 'Yes')</filter> + </data> + <data format="tabular" name="genes_exp" label="${tool.name} on ${on_string}: gene differential expression testing" from_work_dir="gene_exp.diff" /> <data format="tabular" name="genes_fpkm_tracking" label="${tool.name} on ${on_string}: gene FPKM tracking" from_work_dir="genes.fpkm_tracking" /> + <data format="tabular" name="genes_count_tracking" label="${tool.name} on ${on_string}: gene count tracking" from_work_dir="genes.count_tracking" > + <filter>(include_count_files == 'Yes')</filter> + </data> + <data format="tabular" name="isoforms_exp" label="${tool.name} on ${on_string}: transcript differential expression testing" from_work_dir="isoform_exp.diff" /> <data format="tabular" name="isoforms_fpkm_tracking" label="${tool.name} on ${on_string}: transcript FPKM tracking" from_work_dir="isoforms.fpkm_tracking" /> + <data format="tabular" name="isoforms_count_tracking" label="${tool.name} on ${on_string}: transcript count tracking" from_work_dir="isoforms.count_tracking" > + <filter>(include_count_files == 'Yes')</filter> + </data> </outputs> <tests> @@ -162,13 +232,22 @@ <!-- cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam --> - <!-- - NOTE: as of version 0.0.6 of the wrapper, tests cannot be run because multiple inputs to a repeat - element are not supported. <param name="gtf_input" value="cuffcompare_out5.gtf" ftype="gtf" /> - <param name="do_groups" value="No" /> - <param name="aligned_reads1" value="cuffdiff_in1.sam" ftype="sam" /> - <param name="aligned_reads2" value="cuffdiff_in2.sam" ftype="sam" /> + <conditional name="in_type"> + <param name="set_in_type" value="BAM" /> + <repeat name="conditions"> + <param name="name" value="q1" /> + <repeat name="samples"> + <param name="sample" value="cuffdiff_in1.sam" ftype="sam" /> + </repeat> + </repeat> + <repeat name="conditions"> + <param name="name" value="q2" /> + <repeat name="samples"> + <param name="sample" value="cuffdiff_in2.sam" ftype="sam" /> + </repeat> + </repeat> + </conditional> <param name="fdr" value="0.05" /> <param name="min_alignment_count" value="0" /> <param name="do_bias_correction" value="No" /> @@ -186,17 +265,15 @@ <output name="genes_fpkm_tracking" file="cuffdiff_out6.txt" lines_diff="200"/> <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="200"/> <output name="isoforms_fpkm_tracking" file="cuffdiff_out5.txt" lines_diff="200"/> - --> </test> </tests> - <help> **Cuffdiff Overview** Cuffdiff is part of Cufflinks_. Cuffdiff find significant changes in transcript expression, splicing, and promoter use. Please cite: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nature Biotechnology doi:10.1038/nbt.1621 -.. _Cufflinks: http://cufflinks.cbcb.umd.edu/ - +.. _Cufflinks: http://cole-trapnell-lab.github.io/cufflinks/ + ------ **Know what you are doing** @@ -205,7 +282,7 @@ There is no such thing (yet) as an automated gearshift in expression analysis. It is all like stick-shift driving in San Francisco. In other words, running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy. -.. __: http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff +.. __: http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/ ------ @@ -219,10 +296,10 @@ Cuffdiff produces many output files: -1. Transcript FPKM expression tracking. -2. Gene FPKM expression tracking; tracks the summed FPKM of transcripts sharing each gene_id -3. Primary transcript FPKM tracking; tracks the summed FPKM of transcripts sharing each tss_id -4. Coding sequence FPKM tracking; tracks the summed FPKM of transcripts sharing each p_id, independent of tss_id +1. Transcript FPKM (+count) expression tracking. +2. Gene FPKM (+count) expression tracking; tracks the summed FPKM of transcripts sharing each gene_id +3. Primary transcript FPKM (+count) tracking; tracks the summed FPKM of transcripts sharing each tss_id +4. Coding sequence FPKM (+count) tracking; tracks the summed FPKM of transcripts sharing each p_id, independent of tss_id 5. Transcript differential FPKM. 6. Gene differential FPKM. Tests difference sin the summed FPKM of transcripts sharing each gene_id 7. Primary transcript differential FPKM. Tests difference sin the summed FPKM of transcripts sharing each tss_id @@ -243,13 +320,28 @@ This is a list of implemented Cuffdiff options:: - -m INT Average fragement length; default 200 - -s INT Fragment legnth standard deviation; default 80 + -m INT Average fragment length (SE reads); default 200 + -s INT Fragment legnth standard deviation (SE reads); default 80 -c INT The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples. If no testing is performed, changes in the locus are deemed not significant, and the locus' observed changes don't contribute to correction for multiple testing. The default is 1,000 fragment alignments (up to 2,000 paired reads). --FDR FLOAT The allowed false discovery rate. The default is 0.05. - --num-importance-samples INT Sets the number of importance samples generated for each locus during abundance estimation. Default: 1000 --max-mle-iterations INT Sets the number of iterations allowed during maximum likelihood estimation of abundances. Default: 5000 - -N With this option, Cufflinks excludes the contribution of the top 25 percent most highly expressed genes from the number of mapped fragments used in the FPKM denominator. This can improve robustness of differential expression calls for less abundant genes and transcripts. - + --library-norm-method Library Normalization method : Geometric (default), classic-fpkm, quartile + --dispersion-method Dispersion estimation method : Pooled (default), per-condition, blind, poisson + -u Multi read correction tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome. + -b ref.fasta bias correction. Bias detection and correction can significantly improve accuracy of transcript abundance estimates. + --no-effective-length-correction Use standard length correction + --no-length-correction Disable all length correction. + --library-type ff-firststrand,ff-secondstrand,ff-unstranded,fr-firstrand,fr-secondstrand,fr-unstranded,transfrags + --mask-file (gff3/gtf) Ignore all alignment within transcripts in this file + --time-series Treat provided sam files as time series + --compatible-hits-norm With this option, Cufflinks counts only those fragments compatible with some reference transcript towards the number of mapped fragments used in the FPKM denominator. Using this mode is generally recommended in Cuffdiff to reduce certain types of bias caused by differential amounts of ribosomal reads which can create the impression of falsely differentially expressed genes. + --total-hits-norm With this option, Cufflinks counts all fragments, including those not compatible with any reference transcript, towards the number of mapped fragments used in the FPKM denominator + --max-bundle-frags Sets the maximum number of fragments a locus may have before being skipped. Skipped loci are listed in skipped.gtf. + --num-frag-count-draws Cuffdiff will make this many draws from each transcript's predicted negative binomial random numbder generator. Each draw is a number of fragments that will be probabilistically assigned to the transcripts in the transcriptome. Used to estimate the variance-covariance matrix on assigned fragment counts. + --num-frag-assign-draws For each fragment drawn from a transcript, Cuffdiff will assign it this many times (probabilistically), thus estimating the assignment uncertainty for each transcript. Used to estimate the variance-covariance matrix on assigned fragment counts. + --min-reps-for-js-test Cuffdiff won't test genes for differential regulation unless the conditions in question have at least this many replicates. </help> + <citations> + <citation type="doi">10.1038/nbt.1621</citation> + </citations> </tool>
--- a/test-data/cuffdiff_out1.txt Thu Jan 16 13:13:52 2014 -0500 +++ b/test-data/cuffdiff_out1.txt Fri Dec 19 11:57:43 2014 -0500 @@ -1,32 +1,32 @@ test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant -TCONS_00000001 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 OK 0 8.3103e+06 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TCONS_00000002 XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 2.1403e+08 1.79769e+308 1.79769e+308 0.158655 0.158655 no +TCONS_00000001 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 OK 0 9.45986e+06 inf -nan 0.01975 0.101571 no +TCONS_00000002 XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 2.43637e+08 inf -nan 0.12465 0.186975 no TCONS_00000003 XLOC_000003 - chr1:3111545-3111576 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000009 XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 5.68095e+07 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TCONS_00000010 XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 4.15515e+06 1.79769e+308 1.79769e+308 0.158655 0.158655 no +TCONS_00000009 XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 9.7002e+07 inf -nan 0.07975 0.186975 no +TCONS_00000010 XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 4.72993e+06 inf -nan 0.12465 0.186975 no TCONS_00000011 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000012 XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 6.02976e+06 1.79769e+308 1.79769e+308 0.0512352 0.150149 no -TCONS_00000013 XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 2.1403e+08 1.79769e+308 1.79769e+308 0.158655 0.158655 no +TCONS_00000012 XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 6.86386e+06 inf -nan 0.0612 0.186975 no +TCONS_00000013 XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 2.43637e+08 inf -nan 0.12465 0.186975 no TCONS_00000014 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 1 1 no TCONS_00000015 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 1 1 no TCONS_00000016 XLOC_000020 - chr1:3195450-3195477 q1 q2 NOTEST 0 0 0 0 1 1 no TCONS_00000017 XLOC_000021 - chr1:3197089-3197116 q1 q2 NOTEST 0 0 0 0 1 1 no TCONS_00000018 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 1 1 no TCONS_00000019 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000020 XLOC_000025 - chr1:3200022-3200191 q1 q2 NOTEST 959058 705514 -0.442943 0.376027 0.706897 1 no +TCONS_00000020 XLOC_000025 - chr1:3200022-3200191 q1 q2 OK 826392 803108 -0.0412311 -0.0180163 0.8625 0.887143 no TCONS_00000021 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000022 XLOC_000029 - chr1:3201077-3201481 q1 q2 NOTEST 77513.9 285108 1.87898 -1.76152 0.0781506 1 no +TCONS_00000022 XLOC_000029 - chr1:3201077-3201481 q1 q2 OK 66791.3 324548 2.2807 1.1905 0.3026 0.380545 no TCONS_00000023 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000024 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 OK 0 8.3103e+06 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TCONS_00000025 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 OK 0 2.4671e+07 1.79769e+308 1.79769e+308 0.0512352 0.150149 no -TCONS_00000026 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 NOTEST 3.99739e+06 1.82908e+06 -1.12794 0.781831 0.434314 1 no -TCONS_00000027 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 NOTEST 56312.4 372827 2.72698 -1.67622 0.0936947 1 no -TCONS_00000028 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 OK 0 2.66226e+07 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TCONS_00000029 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 OK 0 5.0951e+07 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TCONS_00000030 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 OK 0 2.06814e+09 1.79769e+308 1.79769e+308 0.0786496 0.150149 no +TCONS_00000024 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 OK 0 9.45986e+06 inf -nan 0.01975 0.101571 no +TCONS_00000025 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 OK 0 2.80837e+07 inf -nan 0.0612 0.186975 no +TCONS_00000026 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 OK 4.24463e+06 2.08209e+06 -1.0276 -0.36063 0.3844 0.435206 no +TCONS_00000027 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 OK 48522.7 424400 3.12869 1.23747 0.38685 0.435206 no +TCONS_00000028 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 OK 0 3.03053e+07 inf -nan 0.01975 0.101571 no +TCONS_00000029 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 OK 0 5.79991e+07 inf -nan 0.01975 0.101571 no +TCONS_00000030 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 OK 0 2.35423e+09 inf -nan 0.01975 0.101571 no TCONS_00000031 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000033 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 OK 0 2.29576e+07 1.79769e+308 1.79769e+308 0.158655 0.158655 no -TCONS_00000034 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 OK 0 9.79535e+06 1.79769e+308 1.79769e+308 0.158655 0.158655 no +TCONS_00000033 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 OK 0 2.61334e+07 inf -nan 0.12465 0.186975 no +TCONS_00000034 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 OK 0 1.11503e+07 inf -nan 0.12465 0.186975 no TCONS_00000037 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 1 1 no TCONS_00000038 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 1 1 no TCONS_00000039 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 1 1 no @@ -44,46 +44,46 @@ TCONS_00000051 XLOC_000004 - chr1:3174765-3174792 q1 q2 NOTEST 0 0 0 0 1 1 no TCONS_00000052 XLOC_000005 - chr1:3187401-3187428 q1 q2 NOTEST 0 0 0 0 1 1 no TCONS_00000053 XLOC_000006 - chr1:3188521-3188548 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000054 XLOC_000007 - chr1:3189810-3190789 q1 q2 NOTEST 368900 429265 0.21864 -0.483034 0.629072 1 no -TCONS_00000055 XLOC_000008 - chr1:3190858-3191434 q1 q2 NOTEST 404373 338500 -0.25653 0.342922 0.731657 1 no -TCONS_00000056 XLOC_000009 - chr1:3191512-3192077 q1 q2 NOTEST 402276 686974 0.772069 -1.24554 0.212932 1 no -TCONS_00000057 XLOC_000010 - chr1:3192250-3192336 q1 q2 NOTEST 3.994e+06 2.93812e+06 -0.442943 0.217099 0.828131 1 no +TCONS_00000054 XLOC_000007 - chr1:3189810-3190789 q1 q2 OK 358326 522345 0.543731 1.1445 0.1952 0.270969 no +TCONS_00000055 XLOC_000008 - chr1:3190858-3191434 q1 q2 OK 408511 420354 0.0412311 0.0469899 0.96715 0.96715 no +TCONS_00000056 XLOC_000009 - chr1:3191512-3192077 q1 q2 OK 433286 842157 0.958769 1.27887 0.20385 0.2718 no +TCONS_00000057 XLOC_000010 - chr1:3192250-3192336 q1 q2 OK 3.44151e+06 3.34455e+06 -0.0412311 -0.014084 0.67715 0.716982 no TCONS_00000058 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 1 1 no TCONS_00000059 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 1 1 no TCONS_00000060 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 1 1 no TCONS_00000062 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 1 1 no TCONS_00000063 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000065 XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 1.89853e+07 0 -1.79769e+308 -1.79769e+308 0.0786496 0.150149 no -TCONS_00000066 XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 1.31744e+07 0 -1.79769e+308 -1.79769e+308 0.0416323 0.150149 no +TCONS_00000065 XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 1.6359e+07 0 -inf -nan 0.0148 0.101571 no +TCONS_00000066 XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 1.5136e+07 0 -inf -nan 0.06005 0.186975 no TCONS_00000067 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000068 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 NOTEST 4.39147e+06 0 -1.79769e+308 -1.79769e+308 0.158655 1 no -TCONS_00000069 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 NOTEST 1.36901e+06 0 0 0 1 1 no +TCONS_00000068 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 OK 3.784e+06 0 -inf -nan 0.12165 0.186975 no +TCONS_00000069 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 OK 863189 0 -inf -nan 0.1957 0.270969 no TCONS_00000070 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 1 1 no TCONS_00000071 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 1 1 no TCONS_00000072 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000073 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 OK 9.99919e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no +TCONS_00000073 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 OK 8.616e+07 0 -inf -nan 0.12165 0.186975 no TCONS_00000074 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 1 1 no TCONS_00000075 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000076 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 NOTEST 265614 41870.3 -2.66534 2.48499 0.0129556 1 no +TCONS_00000076 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 OK 228872 47662.2 -2.26362 -1.16262 0.30655 0.380545 no TCONS_00000077 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 1 1 no TCONS_00000078 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 1 1 no TCONS_00000079 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 1 1 no TCONS_00000080 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 1 1 no TCONS_00000081 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 1 1 no TCONS_00000082 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000083 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 OK 1.8095e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no -TCONS_00000084 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 NOTEST 342218 75524 -2.17991 1.96162 0.049807 1 no -TCONS_00000085 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 937403 137917 -2.76487 1.66807 0.0953024 1 no +TCONS_00000083 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 OK 1.55919e+07 0 -inf -nan 0.12165 0.186975 no +TCONS_00000084 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 OK 294879 85971.3 -1.7782 -0.902752 0.36915 0.435206 no +TCONS_00000085 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 OK 807732 156995 -2.36316 -0.933704 0.4205 0.458727 no TCONS_00000086 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 1 1 no TCONS_00000087 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 1 1 no TCONS_00000088 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 1 1 no TCONS_00000089 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000090 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 OK 8.91489e+06 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no -TCONS_00000091 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 585828 0 -1.79769e+308 -1.79769e+308 0.0512352 1 no -TCONS_00000092 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 OK 1.19208e+08 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no -TCONS_00000093 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 NOTEST 4.42166e+06 0 -1.79769e+308 -1.79769e+308 0.0786496 1 no -TCONS_00000094 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 OK 4.28358e+07 0 -1.79769e+308 -1.79769e+308 0.0786496 0.150149 no -TCONS_00000095 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 OK 7.29939e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no +TCONS_00000090 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 OK 7.68169e+06 0 -inf -nan 0.12165 0.186975 no +TCONS_00000091 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 OK 504790 0 -inf -nan 0.05945 0.186975 no +TCONS_00000092 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 OK 1.02717e+08 0 -inf -nan 0.12165 0.186975 no +TCONS_00000093 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 OK 3.81001e+06 0 -inf -nan 0.0148 0.101571 no +TCONS_00000094 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 OK 5.53654e+07 0 -inf -nan 0.0773 0.186975 no +TCONS_00000095 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 OK 6.28966e+07 0 -inf -nan 0.12165 0.186975 no TCONS_00000096 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 1 1 no TCONS_00000097 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 NOTEST 0 0 0 0 1 1 no TCONS_00000098 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 NOTEST 0 0 0 0 1 1 no
--- a/test-data/cuffdiff_out10.txt Thu Jan 16 13:13:52 2014 -0500 +++ b/test-data/cuffdiff_out10.txt Fri Dec 19 11:57:43 2014 -0500 @@ -1,88 +1,88 @@ test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value q_value significant XLOC_000001 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000002 XLOC_000002 - chr1:3111449-3111490 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000003 XLOC_000003 - chr1:3111545-3111576 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000004 XLOC_000004 - chr1:3174765-3174792 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000005 XLOC_000005 - chr1:3187401-3187428 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000006 XLOC_000006 - chr1:3188521-3188548 q1 q2 LOWDATA 0 0 0 0 0 1 no +XLOC_000003 XLOC_000003 - chr1:3111545-3111576 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000004 XLOC_000004 - chr1:3174765-3174792 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000005 XLOC_000005 - chr1:3187401-3187428 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000006 XLOC_000006 - chr1:3188521-3188548 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000007 XLOC_000007 - chr1:3189810-3190789 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000008 XLOC_000008 - chr1:3190858-3191434 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000009 XLOC_000009 - chr1:3191512-3192077 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000010 XLOC_000010 - chr1:3192250-3192336 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000011 XLOC_000011 - chr1:3192441-3192494 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000012 XLOC_000012 - chr1:3192550-3192629 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000013 XLOC_000013 - chr1:3192649-3192676 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000014 XLOC_000014 - chr1:3192731-3192811 q1 q2 LOWDATA 0 0 0 0 0 1 no +XLOC_000013 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000014 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000015 XLOC_000015 - chr1:3192940-3193042 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000016 XLOC_000016 - chr1:3194185-3194226 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000017 XLOC_000017 - chr1:3194302-3194329 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000018 XLOC_000018 - chr1:3194706-3194733 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000019 XLOC_000019 - chr1:3195083-3195110 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000020 XLOC_000020 - chr1:3195450-3195477 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000021 XLOC_000021 - chr1:3197089-3197116 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000022 XLOC_000022 - chr1:3197246-3197273 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000023 XLOC_000023 - chr1:3197346-3197373 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000024 XLOC_000024 - chr1:3197425-3197452 q1 q2 LOWDATA 0 0 0 0 0 1 no +XLOC_000017 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000018 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000019 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000020 XLOC_000020 - chr1:3195450-3195477 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000021 XLOC_000021 - chr1:3197089-3197116 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000022 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000023 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000024 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000025 XLOC_000025 - chr1:3200022-3200191 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000026 XLOC_000026 - chr1:3200325-3200352 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000027 XLOC_000027 - chr1:3200430-3200457 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000028 XLOC_000028 - chr1:3201007-3201039 q1 q2 LOWDATA 0 0 0 0 0 1 no +XLOC_000026 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000027 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000028 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000029 XLOC_000029 - chr1:3201077-3201481 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000030 XLOC_000030 - chr1:3201596-3201666 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000031 XLOC_000031 - chr1:3201672-3201699 q1 q2 LOWDATA 0 0 0 0 0 1 no +XLOC_000031 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000032 XLOC_000032 - chr1:3201725-3201809 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000033 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 LOWDATA 0 0 0 0 0 1 no +XLOC_000033 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000034 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000035 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000036 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000037 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000038 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000039 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 LOWDATA 0 0 0 0 0 1 no +XLOC_000038 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000039 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000040 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000041 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 LOWDATA 0 0 0 0 0 1 no +XLOC_000041 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000042 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000043 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000044 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000045 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 LOWDATA 0 0 0 0 0 1 no +XLOC_000045 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000046 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000047 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000048 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 LOWDATA 0 0 0 0 0 1 no +XLOC_000047 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000048 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000049 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000050 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000051 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 LOWDATA 0 0 0 0 0 1 no +XLOC_000050 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000051 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000052 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000053 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000054 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000055 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000056 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 LOWDATA 0 0 0 0 0 1 no +XLOC_000053 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000054 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000055 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000056 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000057 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000058 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000059 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000060 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000061 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000062 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000063 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000064 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000065 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000066 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 LOWDATA 0 0 0 0 0 1 no +XLOC_000061 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000062 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000063 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000064 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000065 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000066 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000067 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000068 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000069 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000070 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000071 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 LOWDATA 0 0 0 0 0 1 no +XLOC_000071 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000072 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000073 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 LOWDATA 0 0 0 0 0 1 no +XLOC_000073 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000074 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000075 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000076 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000077 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000078 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000079 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000080 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000081 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000082 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000083 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000084 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000085 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000086 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000087 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 LOWDATA 0 0 0 0 0 1 no +XLOC_000075 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000076 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000077 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000078 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000079 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000080 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000081 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000082 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000083 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000084 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000085 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000086 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 NOTEST 0 0 0 0 1 1 no +XLOC_000087 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 NOTEST 0 0 0 0 1 1 no
--- a/test-data/cuffdiff_out2.txt Thu Jan 16 13:13:52 2014 -0500 +++ b/test-data/cuffdiff_out2.txt Fri Dec 19 11:57:43 2014 -0500 @@ -1,20 +1,20 @@ test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant -XLOC_000001 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 OK 0 8.3103e+06 1.79769e+308 1.79769e+308 0.0786496 0.157299 no -XLOC_000002 XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 2.1403e+08 1.79769e+308 1.79769e+308 0.158655 0.16621 no +XLOC_000001 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 OK 0 9.45986e+06 inf -nan 0.01975 0.09875 no +XLOC_000002 XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 2.43637e+08 inf -nan 0.12465 0.181781 no XLOC_000003 XLOC_000003 - chr1:3111545-3111576 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000004 XLOC_000004 - chr1:3174765-3174792 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000005 XLOC_000005 - chr1:3187401-3187428 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000006 XLOC_000006 - chr1:3188521-3188548 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000007 XLOC_000007 - chr1:3189810-3190789 q1 q2 NOTEST 368900 429265 0.21864 -0.483034 0.629072 1 no -XLOC_000008 XLOC_000008 - chr1:3190858-3191434 q1 q2 NOTEST 404373 338500 -0.25653 0.342922 0.731657 1 no -XLOC_000009 XLOC_000009 - chr1:3191512-3192077 q1 q2 NOTEST 402276 686974 0.772069 -1.24554 0.212932 1 no -XLOC_000010 XLOC_000010 - chr1:3192250-3192336 q1 q2 NOTEST 3.994e+06 2.93812e+06 -0.442943 0.217099 0.828131 1 no -XLOC_000011 XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 5.68095e+07 1.79769e+308 1.79769e+308 0.0786496 0.157299 no -XLOC_000012 XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 4.15515e+06 1.79769e+308 1.79769e+308 0.158655 0.16621 no +XLOC_000007 XLOC_000007 - chr1:3189810-3190789 q1 q2 OK 358326 522345 0.543731 1.1445 0.1952 0.27328 no +XLOC_000008 XLOC_000008 - chr1:3190858-3191434 q1 q2 OK 408511 420354 0.0412311 0.0469899 0.96715 0.96715 no +XLOC_000009 XLOC_000009 - chr1:3191512-3192077 q1 q2 OK 433286 842157 0.958769 1.27887 0.20385 0.274413 no +XLOC_000010 XLOC_000010 - chr1:3192250-3192336 q1 q2 OK 3.44151e+06 3.34455e+06 -0.0412311 -0.014084 0.67715 0.718189 no +XLOC_000011 XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 9.7002e+07 inf -nan 0.07975 0.181781 no +XLOC_000012 XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 4.72993e+06 inf -nan 0.12465 0.181781 no XLOC_000013 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000014 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000015 XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 6.02976e+06 1.79769e+308 1.79769e+308 0.0512352 0.157299 no -XLOC_000016 XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 2.1403e+08 1.79769e+308 1.79769e+308 0.158655 0.16621 no +XLOC_000015 XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 6.86386e+06 inf -nan 0.0612 0.181781 no +XLOC_000016 XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 2.43637e+08 inf -nan 0.12465 0.181781 no XLOC_000017 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000018 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000019 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 1 1 no @@ -23,56 +23,56 @@ XLOC_000022 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000023 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000024 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000025 XLOC_000025 - chr1:3200022-3200191 q1 q2 NOTEST 959058 705514 -0.442943 0.376027 0.706897 1 no +XLOC_000025 XLOC_000025 - chr1:3200022-3200191 q1 q2 OK 826392 803108 -0.0412311 -0.0180163 0.8625 0.887868 no XLOC_000026 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000027 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000028 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000029 XLOC_000029 - chr1:3201077-3201481 q1 q2 NOTEST 77513.9 285108 1.87898 -1.76152 0.0781506 1 no -XLOC_000030 XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 1.89853e+07 0 -1.79769e+308 -1.79769e+308 0.0786496 0.157299 no +XLOC_000029 XLOC_000029 - chr1:3201077-3201481 q1 q2 OK 66791.3 324548 2.2807 1.1905 0.3026 0.383188 no +XLOC_000030 XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 1.6359e+07 0 -inf -nan 0.0148 0.09875 no XLOC_000031 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000032 XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 1.31744e+07 0 -1.79769e+308 -1.79769e+308 0.0416323 0.157299 no +XLOC_000032 XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 1.5136e+07 0 -inf -nan 0.06005 0.181781 no XLOC_000033 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000034 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 OK 0 8.3103e+06 1.79769e+308 1.79769e+308 0.0786496 0.157299 no -XLOC_000035 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 OK 0 2.4671e+07 1.79769e+308 1.79769e+308 0.0512352 0.157299 no -XLOC_000036 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 NOTEST 4.39147e+06 0 -1.79769e+308 -1.79769e+308 0.158655 1 no -XLOC_000037 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 OK 5.3664e+06 1.82908e+06 -1.55284 0.839459 0.401212 0.401212 no +XLOC_000034 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 OK 0 9.45986e+06 inf -nan 0.01975 0.09875 no +XLOC_000035 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 OK 0 2.80837e+07 inf -nan 0.0612 0.181781 no +XLOC_000036 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 OK 3.784e+06 0 -inf -nan 0.12165 0.181781 no +XLOC_000037 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 OK 5.10781e+06 2.08209e+06 -1.29467 -0.482193 0.5916 0.647062 no XLOC_000038 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000039 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000040 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 NOTEST 56312.4 372827 2.72698 -1.67622 0.0936947 1 no +XLOC_000040 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 OK 48522.7 424400 3.12869 1.23747 0.38685 0.450823 no XLOC_000041 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000042 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 OK 0 2.66226e+07 1.79769e+308 1.79769e+308 0.0786496 0.157299 no -XLOC_000043 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 OK 9.99919e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.16621 no -XLOC_000044 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 OK 0 5.0951e+07 1.79769e+308 1.79769e+308 0.0786496 0.157299 no +XLOC_000042 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 OK 0 3.03053e+07 inf -nan 0.01975 0.09875 no +XLOC_000043 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 OK 8.616e+07 0 -inf -nan 0.12165 0.181781 no +XLOC_000044 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 OK 0 5.79991e+07 inf -nan 0.01975 0.09875 no XLOC_000045 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000046 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 OK 0 2.06814e+09 1.79769e+308 1.79769e+308 0.0786496 0.157299 no +XLOC_000046 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 OK 0 2.35423e+09 inf -nan 0.01975 0.09875 no XLOC_000047 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000048 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000049 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 NOTEST 265614 41870.3 -2.66534 2.48499 0.0129556 1 no +XLOC_000049 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 OK 228872 47662.2 -2.26362 -1.16262 0.30655 0.383188 no XLOC_000050 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000051 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000052 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 OK 0 2.29576e+07 1.79769e+308 1.79769e+308 0.158655 0.16621 no +XLOC_000052 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 OK 0 2.61334e+07 inf -nan 0.12465 0.181781 no XLOC_000053 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000054 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000055 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000056 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000057 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 OK 0 9.79535e+06 1.79769e+308 1.79769e+308 0.158655 0.16621 no -XLOC_000058 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 OK 1.8095e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.16621 no -XLOC_000059 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 NOTEST 342218 75524 -2.17991 1.96162 0.049807 1 no -XLOC_000060 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 937403 137917 -2.76487 1.66807 0.0953024 1 no +XLOC_000057 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 OK 0 1.11503e+07 inf -nan 0.12465 0.181781 no +XLOC_000058 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 OK 1.55919e+07 0 -inf -nan 0.12165 0.181781 no +XLOC_000059 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 OK 294879 85971.3 -1.7782 -0.902752 0.36915 0.445526 no +XLOC_000060 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 OK 807732 156995 -2.36316 -0.89463 0.3993 0.450823 no XLOC_000061 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000062 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000063 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000064 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000065 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000066 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000067 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 OK 8.91489e+06 0 -1.79769e+308 -1.79769e+308 0.158655 0.16621 no -XLOC_000068 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 585828 0 -1.79769e+308 -1.79769e+308 0.0512352 1 no -XLOC_000069 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 OK 1.19208e+08 0 -1.79769e+308 -1.79769e+308 0.158655 0.16621 no -XLOC_000070 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 NOTEST 4.42166e+06 0 -1.79769e+308 -1.79769e+308 0.0786496 1 no +XLOC_000067 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 OK 7.68169e+06 0 -inf -nan 0.12165 0.181781 no +XLOC_000068 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 OK 504790 0 -inf -nan 0.04565 0.181781 no +XLOC_000069 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 OK 1.02717e+08 0 -inf -nan 0.12165 0.181781 no +XLOC_000070 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 OK 3.81001e+06 0 -inf -nan 0.0148 0.09875 no XLOC_000071 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000072 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 OK 4.28358e+07 0 -1.79769e+308 -1.79769e+308 0.0786496 0.157299 no +XLOC_000072 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 OK 5.53654e+07 0 -inf -nan 0.0773 0.181781 no XLOC_000073 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000074 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 OK 7.29939e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.16621 no +XLOC_000074 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 OK 6.28966e+07 0 -inf -nan 0.12165 0.181781 no XLOC_000075 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000076 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 1 1 no XLOC_000077 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 NOTEST 0 0 0 0 1 1 no
--- a/test-data/cuffdiff_out3.txt Thu Jan 16 13:13:52 2014 -0500 +++ b/test-data/cuffdiff_out3.txt Fri Dec 19 11:57:43 2014 -0500 @@ -1,91 +1,89 @@ test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant -TSS1 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 OK 0 8.3103e+06 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TSS11 XLOC_000008 - chr1:3190858-3191434 q1 q2 NOTEST 404373 338500 -0.25653 0.342922 0.731657 1 no -TSS12 XLOC_000009 - chr1:3191512-3192077 q1 q2 NOTEST 402276 686974 0.772069 -1.24554 0.212932 1 no -TSS15 XLOC_000010 - chr1:3192250-3192336 q1 q2 NOTEST 3.994e+06 2.93812e+06 -0.442943 0.217099 0.828131 1 no -TSS16 XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 5.68095e+07 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TSS17 XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 4.15515e+06 1.79769e+308 1.79769e+308 0.158655 0.158655 no -TSS18 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS19 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS2 XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 2.1403e+08 1.79769e+308 1.79769e+308 0.158655 0.158655 no -TSS20 XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 6.02976e+06 1.79769e+308 1.79769e+308 0.0512352 0.150149 no -TSS21 XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 2.1403e+08 1.79769e+308 1.79769e+308 0.158655 0.158655 no -TSS22 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS23 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS24 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS25 XLOC_000020 - chr1:3195450-3195477 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS26 XLOC_000021 - chr1:3197089-3197116 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS27 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS28 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS29 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS1 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 OK 0 9.45986e+06 inf -nan 0.01975 0.09875 no +TSS10 XLOC_000008 - chr1:3190858-3191434 q1 q2 OK 408511 420354 0.0412311 0.0469899 0.96715 0.96715 no +TSS11 XLOC_000009 - chr1:3191512-3192077 q1 q2 OK 433286 842157 0.958769 1.27887 0.20385 0.274413 no +TSS13 XLOC_000010 - chr1:3192250-3192336 q1 q2 OK 3.44151e+06 3.34455e+06 -0.0412311 -0.014084 0.67715 0.718189 no +TSS14 XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 9.7002e+07 inf -nan 0.07975 0.181781 no +TSS15 XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 4.72993e+06 inf -nan 0.12465 0.181781 no +TSS16 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS17 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS18 XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 6.86386e+06 inf -nan 0.0612 0.181781 no +TSS19 XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 2.43637e+08 inf -nan 0.12465 0.181781 no +TSS2 XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 2.43637e+08 inf -nan 0.12465 0.181781 no +TSS20 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS21 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS22 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS23 XLOC_000020 - chr1:3195450-3195477 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS24 XLOC_000021 - chr1:3197089-3197116 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS25 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS26 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS27 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS28 XLOC_000025 - chr1:3200022-3200191 q1 q2 OK 826392 803108 -0.0412311 -0.0180163 0.8625 0.887868 no +TSS29 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 1 1 no TSS3 XLOC_000003 - chr1:3111545-3111576 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS30 XLOC_000025 - chr1:3200022-3200191 q1 q2 NOTEST 959058 705514 -0.442943 0.376027 0.706897 1 no -TSS32 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS33 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS34 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS35 XLOC_000029 - chr1:3201077-3201481 q1 q2 NOTEST 77513.9 285108 1.87898 -1.76152 0.0781506 1 no -TSS37 XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 1.89853e+07 0 -1.79769e+308 -1.79769e+308 0.0786496 0.150149 no -TSS38 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS39 XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 1.31744e+07 0 -1.79769e+308 -1.79769e+308 0.0416323 0.150149 no +TSS30 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS31 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS32 XLOC_000029 - chr1:3201077-3201481 q1 q2 OK 66791.3 324548 2.2807 1.1905 0.3026 0.383188 no +TSS33 XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 1.6359e+07 0 -inf -nan 0.0148 0.09875 no +TSS34 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS35 XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 1.5136e+07 0 -inf -nan 0.06005 0.181781 no +TSS36 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS37 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 OK 0 9.45986e+06 inf -nan 0.01975 0.09875 no +TSS38 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 OK 0 2.80837e+07 inf -nan 0.0612 0.181781 no +TSS39 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 OK 3.784e+06 0 -inf -nan 0.12165 0.181781 no TSS4 XLOC_000004 - chr1:3174765-3174792 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS40 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS41 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 OK 0 8.3103e+06 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TSS42 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 OK 0 2.4671e+07 1.79769e+308 1.79769e+308 0.0512352 0.150149 no -TSS43 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 NOTEST 4.39147e+06 0 -1.79769e+308 -1.79769e+308 0.158655 1 no -TSS44 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 NOTEST 3.99739e+06 1.82908e+06 -1.12794 0.489836 0.62425 1 no -TSS45 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 NOTEST 1.36901e+06 0 0 0 1 1 no -TSS46 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS47 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS48 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 NOTEST 56312.4 372827 2.72698 -1.67622 0.0936947 1 no -TSS49 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS40 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 OK 5.10781e+06 2.08209e+06 -1.29467 -0.482193 0.5916 0.647062 no +TSS41 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS42 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS43 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 OK 48522.7 424400 3.12869 1.23747 0.38685 0.451325 no +TSS44 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS45 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 OK 0 3.03053e+07 inf -nan 0.01975 0.09875 no +TSS46 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 OK 8.616e+07 0 -inf -nan 0.12165 0.181781 no +TSS47 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 OK 0 5.79991e+07 inf -nan 0.01975 0.09875 no +TSS48 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS49 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 OK 0 2.35423e+09 inf -nan 0.01975 0.09875 no TSS5 XLOC_000005 - chr1:3187401-3187428 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS50 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 OK 0 2.66226e+07 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TSS51 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 OK 9.99919e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no -TSS52 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 OK 0 5.0951e+07 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TSS53 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS54 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 OK 0 2.06814e+09 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TSS55 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS56 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS57 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 NOTEST 265614 41870.3 -2.66534 2.48499 0.0129556 1 no -TSS59 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS50 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS51 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS52 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 OK 228872 47662.2 -2.26362 -1.16262 0.30655 0.383188 no +TSS54 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS55 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS56 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 OK 0 2.61334e+07 inf -nan 0.12465 0.181781 no +TSS57 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS58 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS59 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 1 1 no TSS6 XLOC_000006 - chr1:3188521-3188548 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS60 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS61 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 OK 0 2.29576e+07 1.79769e+308 1.79769e+308 0.158655 0.158655 no -TSS62 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS63 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS64 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS65 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS66 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 OK 0 9.79535e+06 1.79769e+308 1.79769e+308 0.158655 0.158655 no -TSS67 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 OK 1.8095e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no -TSS68 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 NOTEST 342218 75524 -2.17991 1.96162 0.049807 1 no -TSS7 XLOC_000007 - chr1:3189810-3190789 q1 q2 NOTEST 368900 429265 0.21864 -0.483034 0.629072 1 no -TSS70 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 937403 137917 -2.76487 1.66807 0.0953024 1 no -TSS71 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS72 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS73 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS74 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS75 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS76 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS77 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS78 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 OK 8.91489e+06 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no -TSS79 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS80 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 585828 0 -1.79769e+308 -1.79769e+308 0.0512352 1 no -TSS81 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 OK 1.19208e+08 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no -TSS82 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 NOTEST 4.42166e+06 0 -1.79769e+308 -1.79769e+308 0.0786496 1 no -TSS83 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS84 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 OK 4.28358e+07 0 -1.79769e+308 -1.79769e+308 0.0786496 0.150149 no -TSS85 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS86 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 OK 7.29939e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no -TSS87 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS88 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS89 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS90 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS91 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS92 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS93 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS94 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS95 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS96 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS97 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS98 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS99 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS60 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS61 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 OK 0 1.11503e+07 inf -nan 0.12465 0.181781 no +TSS62 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 OK 1.55919e+07 0 -inf -nan 0.12165 0.181781 no +TSS63 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 OK 294879 85971.3 -1.7782 -0.902752 0.36915 0.445526 no +TSS65 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 OK 807732 156995 -2.36316 -0.933704 0.4205 0.474758 no +TSS66 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS67 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS68 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS69 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS7 XLOC_000007 - chr1:3189810-3190789 q1 q2 OK 358326 522345 0.543731 1.1445 0.1952 0.27328 no +TSS70 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS71 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS72 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS73 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 OK 7.68169e+06 0 -inf -nan 0.12165 0.181781 no +TSS74 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 OK 504790 0 -inf -nan 0.04565 0.181781 no +TSS75 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 OK 1.02717e+08 0 -inf -nan 0.12165 0.181781 no +TSS76 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 OK 3.81001e+06 0 -inf -nan 0.0148 0.09875 no +TSS77 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS78 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 OK 5.53654e+07 0 -inf -nan 0.0773 0.181781 no +TSS79 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS80 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 OK 6.28966e+07 0 -inf -nan 0.12165 0.181781 no +TSS81 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS82 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS83 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS84 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS85 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS86 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS87 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS88 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS89 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS90 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS91 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS92 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS93 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 NOTEST 0 0 0 0 1 1 no
--- a/test-data/cuffdiff_out5.txt Thu Jan 16 13:13:52 2014 -0500 +++ b/test-data/cuffdiff_out5.txt Fri Dec 19 11:57:43 2014 -0500 @@ -1,91 +1,91 @@ tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage q1_FPKM q1_conf_lo q1_conf_hi q1_status q2_FPKM q2_conf_lo q2_conf_hi q2_status -TCONS_00000001 c Xkr4 XLOC_000001 Xkr4 TSS1 chr1:3204754-3204833 79 - 0 0 0 OK 8.3103e+06 0 2.00628e+07 OK -TCONS_00000002 - - XLOC_000002 - TSS2 chr1:3111449-3111490 41 - 0 0 0 OK 2.1403e+08 0 6.42089e+08 OK +TCONS_00000001 c Xkr4 XLOC_000001 Xkr4 TSS1 chr1:3204754-3204833 79 - 0 0 0 OK 9.45986e+06 0 3.33035e+07 OK +TCONS_00000002 - - XLOC_000002 - TSS2 chr1:3111449-3111490 41 - 0 0 0 OK 2.43637e+08 0 9.52723e+08 OK TCONS_00000003 - - XLOC_000003 - TSS3 chr1:3111545-3111576 31 - 0 0 0 OK 0 0 0 OK -TCONS_00000009 - - XLOC_000011 - TSS16 chr1:3192441-3192494 53 - 0 0 0 OK 5.68095e+07 0 1.3715e+08 OK -TCONS_00000010 - - XLOC_000012 - TSS17 chr1:3192550-3192629 79 - 0 0 0 OK 4.15515e+06 0 1.24654e+07 OK -TCONS_00000011 - - XLOC_000014 - TSS19 chr1:3192731-3192811 80 - 0 0 0 OK 0 0 0 OK -TCONS_00000012 - - XLOC_000015 - TSS20 chr1:3192940-3193042 102 - 0 0 0 OK 6.02976e+06 0 1.34147e+07 OK -TCONS_00000013 - - XLOC_000016 - TSS21 chr1:3194185-3194226 41 - 0 0 0 OK 2.1403e+08 0 6.42089e+08 OK -TCONS_00000014 - - XLOC_000017 - TSS22 chr1:3194302-3194329 27 - 0 0 0 OK 0 0 0 OK -TCONS_00000015 - - XLOC_000019 - TSS24 chr1:3195083-3195110 27 - 0 0 0 OK 0 0 0 OK -TCONS_00000016 - - XLOC_000020 - TSS25 chr1:3195450-3195477 27 - 0 0 0 OK 0 0 0 OK -TCONS_00000017 - - XLOC_000021 - TSS26 chr1:3197089-3197116 27 - 0 0 0 OK 0 0 0 OK -TCONS_00000018 - - XLOC_000022 - TSS27 chr1:3197246-3197273 27 - 0 0 0 OK 0 0 0 OK -TCONS_00000019 - - XLOC_000023 - TSS28 chr1:3197346-3197373 27 - 0 0 0 OK 0 0 0 OK -TCONS_00000020 - - XLOC_000025 - TSS30 chr1:3200022-3200191 169 - 959058 0 2.06648e+06 OK 705514 0 1.52017e+06 OK -TCONS_00000021 - - XLOC_000026 - TSS32 chr1:3200325-3200352 27 - 0 0 0 OK 0 0 0 OK -TCONS_00000022 - - XLOC_000029 - TSS35 chr1:3201077-3201481 404 - 77513.9 0 167019 OK 285108 21736.5 548480 OK -TCONS_00000023 - - XLOC_000031 - TSS38 chr1:3201672-3201699 27 - 0 0 0 OK 0 0 0 OK -TCONS_00000024 i Xkr4 XLOC_000034 Xkr4 TSS41 chr1:3212213-3212292 79 - 0 0 0 OK 8.3103e+06 0 2.00628e+07 OK -TCONS_00000025 i Xkr4 XLOC_000035 Xkr4 TSS42 chr1:3212367-3212439 72 - 0 0 0 OK 2.4671e+07 0 5.48867e+07 OK -TCONS_00000026 i Xkr4 XLOC_000037 Xkr4 TSS44 chr1:3213095-3213242 97 - 3.99739e+06 3.99339e+06 4.00139e+06 LOWDATA 1.82908e+06 0 5.48723e+06 OK -TCONS_00000027 i Xkr4 XLOC_000040 Xkr4 TSS48 chr1:3242633-3242923 290 - 56312.4 0 168937 OK 372827 0 761430 OK -TCONS_00000028 i Xkr4 XLOC_000042 Xkr4 TSS50 chr1:3243018-3243079 61 - 0 0 0 OK 2.66226e+07 0 6.42725e+07 OK -TCONS_00000029 i Xkr4 XLOC_000044 Xkr4 TSS52 chr1:3243347-3243401 54 - 0 0 0 OK 5.0951e+07 0 1.23007e+08 OK -TCONS_00000030 i Xkr4 XLOC_000046 Xkr4 TSS54 chr1:3256974-3257011 37 - 0 0 0 OK 2.06814e+09 0 4.99293e+09 OK -TCONS_00000031 i Xkr4 XLOC_000048 Xkr4 TSS56 chr1:3277190-3277218 28 - 0 0 0 OK 0 0 0 OK -TCONS_00000033 i Xkr4 XLOC_000052 Xkr4 TSS61 chr1:3280686-3280741 55 - 0 0 0 OK 2.29576e+07 0 6.88728e+07 OK -TCONS_00000034 i Xkr4 XLOC_000057 Xkr4 TSS66 chr1:3290488-3290553 65 - 0 0 0 OK 9.79535e+06 0 2.9386e+07 OK -TCONS_00000037 i Xkr4 XLOC_000060 Xkr4 TSS71 chr1:3299443-3299664 55 - 0 0 0 OK 0 0 0 OK -TCONS_00000038 i Xkr4 XLOC_000062 Xkr4 TSS73 chr1:3300051-3300078 27 - 0 0 0 OK 0 0 0 OK -TCONS_00000039 i Xkr4 XLOC_000065 Xkr4 TSS76 chr1:3318999-3319051 52 - 0 0 0 OK 0 0 0 OK -TCONS_00000040 i Xkr4 XLOC_000068 Xkr4 TSS79 chr1:3355887-3356119 27 - 0 0 0 OK 0 0 0 OK -TCONS_00000041 i Xkr4 XLOC_000071 Xkr4 TSS83 chr1:3363214-3363278 64 - 0 0 0 OK 0 0 0 OK -TCONS_00000042 i Xkr4 XLOC_000073 Xkr4 TSS85 chr1:3363753-3363849 96 - 0 0 0 OK 0 0 0 OK -TCONS_00000043 i Xkr4 XLOC_000075 Xkr4 TSS87 chr1:3367135-3367162 27 - 0 0 0 OK 0 0 0 OK -TCONS_00000044 i Xkr4 XLOC_000077 Xkr4 TSS89 chr1:3367333-3367382 49 - 0 0 0 OK 0 0 0 OK -TCONS_00000045 i Xkr4 XLOC_000080 Xkr4 TSS92 chr1:3377211-3377262 51 - 0 0 0 OK 0 0 0 OK -TCONS_00000046 i Xkr4 XLOC_000083 Xkr4 TSS95 chr1:3391325-3391352 27 - 0 0 0 OK 0 0 0 OK -TCONS_00000047 i Xkr4 XLOC_000084 Xkr4 TSS96 chr1:3435841-3435880 39 - 0 0 0 OK 0 0 0 OK -TCONS_00000048 i Xkr4 XLOC_000085 Xkr4 TSS97 chr1:3447761-3447788 27 - 0 0 0 OK 0 0 0 OK -TCONS_00000049 i Xkr4 XLOC_000086 Xkr4 TSS98 chr1:3450906-3450965 59 - 0 0 0 OK 0 0 0 OK -TCONS_00000050 i Xkr4 XLOC_000087 Xkr4 TSS99 chr1:3451051-3451109 58 - 0 0 0 OK 0 0 0 OK +TCONS_00000009 - - XLOC_000011 - TSS14 chr1:3192441-3192494 53 - 0 0 0 OK 9.7002e+07 0 3.17699e+08 OK +TCONS_00000010 - - XLOC_000012 - TSS15 chr1:3192550-3192629 79 - 0 0 0 OK 4.72993e+06 0 1.84961e+07 OK +TCONS_00000011 - - XLOC_000014 - TSS17 chr1:3192731-3192811 80 - 0 0 0 OK 0 0 0 OK +TCONS_00000012 - - XLOC_000015 - TSS18 chr1:3192940-3193042 102 - 0 0 0 OK 6.86386e+06 0 2.14243e+07 OK +TCONS_00000013 - - XLOC_000016 - TSS19 chr1:3194185-3194226 41 - 0 0 0 OK 2.43637e+08 0 9.52723e+08 OK +TCONS_00000014 - - XLOC_000017 - TSS20 chr1:3194302-3194329 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000015 - - XLOC_000019 - TSS22 chr1:3195083-3195110 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000016 - - XLOC_000020 - TSS23 chr1:3195450-3195477 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000017 - - XLOC_000021 - TSS24 chr1:3197089-3197116 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000018 - - XLOC_000022 - TSS25 chr1:3197246-3197273 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000019 - - XLOC_000023 - TSS26 chr1:3197346-3197373 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000020 - - XLOC_000025 - TSS28 chr1:3200022-3200191 169 - 826392 0 2.65361e+06 OK 803108 0 2.63033e+06 OK +TCONS_00000021 - - XLOC_000026 - TSS29 chr1:3200325-3200352 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000022 - - XLOC_000029 - TSS32 chr1:3201077-3201481 404 - 66791.3 0 214473 OK 324548 0 802006 OK +TCONS_00000023 - - XLOC_000031 - TSS34 chr1:3201672-3201699 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000024 i Xkr4 XLOC_000034 Xkr4 TSS37 chr1:3212213-3212292 79 - 0 0 0 OK 9.45986e+06 0 3.33035e+07 OK +TCONS_00000025 i Xkr4 XLOC_000035 Xkr4 TSS38 chr1:3212367-3212439 72 - 0 0 0 OK 2.80837e+07 0 8.76584e+07 OK +TCONS_00000026 i Xkr4 XLOC_000037 Xkr4 TSS40 chr1:3213095-3213242 97 - 4.24463e+06 0 1.55814e+07 OK 2.08209e+06 0 8.14187e+06 OK +TCONS_00000027 i Xkr4 XLOC_000040 Xkr4 TSS43 chr1:3242633-3242923 290 - 48522.7 0 185766 OK 424400 0 1.30289e+06 OK +TCONS_00000028 i Xkr4 XLOC_000042 Xkr4 TSS45 chr1:3243018-3243079 61 - 0 0 0 OK 3.03053e+07 0 1.0669e+08 OK +TCONS_00000029 i Xkr4 XLOC_000044 Xkr4 TSS47 chr1:3243347-3243401 54 - 0 0 0 OK 5.79991e+07 0 2.04186e+08 OK +TCONS_00000030 i Xkr4 XLOC_000046 Xkr4 TSS49 chr1:3256974-3257011 37 - 0 0 0 OK 2.35423e+09 0 8.28806e+09 OK +TCONS_00000031 i Xkr4 XLOC_000048 Xkr4 TSS51 chr1:3277190-3277218 28 - 0 0 0 OK 0 0 0 OK +TCONS_00000033 i Xkr4 XLOC_000052 Xkr4 TSS56 chr1:3280686-3280741 55 - 0 0 0 OK 2.61334e+07 0 1.02193e+08 OK +TCONS_00000034 i Xkr4 XLOC_000057 Xkr4 TSS61 chr1:3290488-3290553 65 - 0 0 0 OK 1.11503e+07 0 4.36026e+07 OK +TCONS_00000037 i Xkr4 XLOC_000060 Xkr4 TSS66 chr1:3299443-3299664 55 - 0 0 163195 OK 0 0 163195 OK +TCONS_00000038 i Xkr4 XLOC_000062 Xkr4 TSS68 chr1:3300051-3300078 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000039 i Xkr4 XLOC_000065 Xkr4 TSS71 chr1:3318999-3319051 52 - 0 0 0 OK 0 0 0 OK +TCONS_00000040 i Xkr4 XLOC_000068 Xkr4 TSS74 chr1:3355887-3356119 27 - 0 0 332434 OK 0 0 0 OK +TCONS_00000041 i Xkr4 XLOC_000071 Xkr4 TSS77 chr1:3363214-3363278 64 - 0 0 0 OK 0 0 0 OK +TCONS_00000042 i Xkr4 XLOC_000073 Xkr4 TSS79 chr1:3363753-3363849 96 - 0 0 0 OK 0 0 0 OK +TCONS_00000043 i Xkr4 XLOC_000075 Xkr4 TSS81 chr1:3367135-3367162 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000044 i Xkr4 XLOC_000077 Xkr4 TSS83 chr1:3367333-3367382 49 - 0 0 0 OK 0 0 0 OK +TCONS_00000045 i Xkr4 XLOC_000080 Xkr4 TSS86 chr1:3377211-3377262 51 - 0 0 0 OK 0 0 0 OK +TCONS_00000046 i Xkr4 XLOC_000083 Xkr4 TSS89 chr1:3391325-3391352 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000047 i Xkr4 XLOC_000084 Xkr4 TSS90 chr1:3435841-3435880 39 - 0 0 0 OK 0 0 0 OK +TCONS_00000048 i Xkr4 XLOC_000085 Xkr4 TSS91 chr1:3447761-3447788 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000049 i Xkr4 XLOC_000086 Xkr4 TSS92 chr1:3450906-3450965 59 - 0 0 0 OK 0 0 0 OK +TCONS_00000050 i Xkr4 XLOC_000087 Xkr4 TSS93 chr1:3451051-3451109 58 - 0 0 0 OK 0 0 0 OK TCONS_00000051 - - XLOC_000004 - TSS4 chr1:3174765-3174792 27 - 0 0 0 OK 0 0 0 OK TCONS_00000052 - - XLOC_000005 - TSS5 chr1:3187401-3187428 27 - 0 0 0 OK 0 0 0 OK TCONS_00000053 - - XLOC_000006 - TSS6 chr1:3188521-3188548 27 - 0 0 0 OK 0 0 0 OK -TCONS_00000054 - - XLOC_000007 - TSS7 chr1:3189810-3190789 979 - 368900 151353 586447 OK 429265 337221 521309 OK -TCONS_00000055 - - XLOC_000008 - TSS11 chr1:3190858-3191434 576 - 404373 101434 707312 OK 338500 95761.5 581239 OK -TCONS_00000056 - - XLOC_000009 - TSS12 chr1:3191512-3192077 565 - 402276 96829.4 707722 OK 686974 410563 963384 OK -TCONS_00000057 - - XLOC_000010 - TSS15 chr1:3192250-3192336 86 - 3.994e+06 0 1.1982e+07 OK 2.93812e+06 0 8.81435e+06 OK -TCONS_00000058 - - XLOC_000013 - TSS18 chr1:3192649-3192676 27 - 0 0 0 OK 0 0 0 OK -TCONS_00000059 - - XLOC_000018 - TSS23 chr1:3194706-3194733 27 - 0 0 0 OK 0 0 0 OK -TCONS_00000060 - - XLOC_000024 - TSS29 chr1:3197425-3197452 27 - 0 0 0 OK 0 0 0 OK -TCONS_00000062 - - XLOC_000027 - TSS33 chr1:3200430-3200457 27 - 0 0 0 OK 0 0 0 OK -TCONS_00000063 - - XLOC_000028 - TSS34 chr1:3201007-3201039 32 - 0 0 0 OK 0 0 0 OK -TCONS_00000065 - - XLOC_000030 - TSS37 chr1:3201596-3201666 70 - 1.89853e+07 0 4.58345e+07 OK 0 0 0 OK -TCONS_00000066 - - XLOC_000032 - TSS39 chr1:3201725-3201809 84 - 1.31744e+07 0 2.83869e+07 OK 0 0 0 OK -TCONS_00000067 i Xkr4 XLOC_000033 Xkr4 TSS40 chr1:3211521-3211561 40 - 0 0 0 OK 0 0 0 OK -TCONS_00000068 i Xkr4 XLOC_000036 Xkr4 TSS43 chr1:3212717-3212801 84 - 4.39147e+06 0 1.31744e+07 OK 0 0 0 OK -TCONS_00000069 i Xkr4 XLOC_000037 Xkr4 TSS45 chr1:3213095-3213242 124 - 1.36901e+06 1.36667e+06 1.37135e+06 LOWDATA 0 0 0 OK -TCONS_00000070 i Xkr4 XLOC_000038 Xkr4 TSS46 chr1:3240606-3240633 27 - 0 0 0 OK 0 0 0 OK -TCONS_00000071 i Xkr4 XLOC_000039 Xkr4 TSS47 chr1:3242479-3242512 33 - 0 0 0 OK 0 0 0 OK -TCONS_00000072 i Xkr4 XLOC_000041 Xkr4 TSS49 chr1:3242924-3243005 81 - 0 0 0 OK 0 0 0 OK -TCONS_00000073 i Xkr4 XLOC_000043 Xkr4 TSS51 chr1:3243108-3243154 46 - 9.99919e+07 0 2.99976e+08 OK 0 0 0 OK -TCONS_00000074 i Xkr4 XLOC_000045 Xkr4 TSS53 chr1:3254079-3254106 27 - 0 0 0 OK 0 0 0 OK -TCONS_00000075 i Xkr4 XLOC_000047 Xkr4 TSS55 chr1:3277155-3277182 27 - 0 0 0 OK 0 0 0 OK -TCONS_00000076 i Xkr4 XLOC_000049 Xkr4 TSS57 chr1:3277913-3278390 477 - 265614 16793 514436 OK 41870.3 0 90217.9 OK -TCONS_00000077 i Xkr4 XLOC_000050 Xkr4 TSS59 chr1:3280117-3280144 27 - 0 0 0 OK 0 0 0 OK -TCONS_00000078 i Xkr4 XLOC_000051 Xkr4 TSS60 chr1:3280498-3280525 27 - 0 0 0 OK 0 0 0 OK -TCONS_00000079 i Xkr4 XLOC_000053 Xkr4 TSS62 chr1:3282504-3282531 27 - 0 0 0 OK 0 0 0 OK -TCONS_00000080 i Xkr4 XLOC_000054 Xkr4 TSS63 chr1:3282650-3282677 27 - 0 0 0 OK 0 0 0 OK -TCONS_00000081 i Xkr4 XLOC_000055 Xkr4 TSS64 chr1:3282760-3282832 72 - 0 0 0 OK 0 0 0 OK -TCONS_00000082 i Xkr4 XLOC_000056 Xkr4 TSS65 chr1:3284966-3284993 27 - 0 0 0 OK 0 0 0 OK -TCONS_00000083 i Xkr4 XLOC_000058 Xkr4 TSS67 chr1:3290798-3290859 61 - 1.8095e+07 0 5.4285e+07 OK 0 0 0 OK -TCONS_00000084 i Xkr4 XLOC_000059 Xkr4 TSS68 chr1:3290919-3291273 354 - 342218 0 691214 OK 75524 0 162732 OK -TCONS_00000085 i Xkr4 XLOC_000060 Xkr4 TSS70 chr1:3299443-3299664 197 - 937403 0 1.99795e+06 OK 137917 0 413751 OK -TCONS_00000086 i Xkr4 XLOC_000061 Xkr4 TSS72 chr1:3299691-3299733 42 - 0 0 0 OK 0 0 0 OK -TCONS_00000087 i Xkr4 XLOC_000063 Xkr4 TSS74 chr1:3307748-3307775 27 - 0 0 0 OK 0 0 0 OK -TCONS_00000088 i Xkr4 XLOC_000064 Xkr4 TSS75 chr1:3318620-3318647 27 - 0 0 0 OK 0 0 0 OK -TCONS_00000089 i Xkr4 XLOC_000066 Xkr4 TSS77 chr1:3330527-3330554 27 - 0 0 0 OK 0 0 0 OK -TCONS_00000090 i Xkr4 XLOC_000067 Xkr4 TSS78 chr1:3351240-3351311 71 - 8.91489e+06 0 2.67447e+07 OK 0 0 0 OK -TCONS_00000091 i Xkr4 XLOC_000068 Xkr4 TSS80 chr1:3355887-3356119 212 - 585828 0 1.30332e+06 OK 0 0 0 OK -TCONS_00000092 i Xkr4 XLOC_000069 Xkr4 TSS81 chr1:3356180-3356225 45 - 1.19208e+08 0 3.57623e+08 OK 0 0 0 OK -TCONS_00000093 i Xkr4 XLOC_000070 Xkr4 TSS82 chr1:3363076-3363176 100 - 4.42166e+06 0 1.06748e+07 OK 0 0 0 OK -TCONS_00000094 i Xkr4 XLOC_000072 Xkr4 TSS84 chr1:3363387-3363446 59 - 4.28358e+07 0 1.03415e+08 OK 0 0 0 OK -TCONS_00000095 i Xkr4 XLOC_000074 Xkr4 TSS86 chr1:3364871-3364919 48 - 7.29939e+07 0 2.18982e+08 OK 0 0 0 OK -TCONS_00000096 i Xkr4 XLOC_000076 Xkr4 TSS88 chr1:3367210-3367237 27 - 0 0 0 OK 0 0 0 OK -TCONS_00000097 i Xkr4 XLOC_000078 Xkr4 TSS90 chr1:3369580-3369607 27 - 0 0 0 OK 0 0 0 OK -TCONS_00000098 i Xkr4 XLOC_000079 Xkr4 TSS91 chr1:3375001-3375028 27 - 0 0 0 OK 0 0 0 OK -TCONS_00000099 i Xkr4 XLOC_000081 Xkr4 TSS93 chr1:3379888-3379915 27 - 0 0 0 OK 0 0 0 OK -TCONS_00000100 i Xkr4 XLOC_000082 Xkr4 TSS94 chr1:3386739-3386836 97 - 0 0 0 OK 0 0 0 OK +TCONS_00000054 - - XLOC_000007 - TSS7 chr1:3189810-3190789 979 - 358326 135086 581565 OK 522345 410780 633911 OK +TCONS_00000055 - - XLOC_000008 - TSS10 chr1:3190858-3191434 576 - 408511 54526.1 762496 OK 420354 61509.1 779200 OK +TCONS_00000056 - - XLOC_000009 - TSS11 chr1:3191512-3192077 565 - 433286 63552.3 803020 OK 842157 342520 1.34179e+06 OK +TCONS_00000057 - - XLOC_000010 - TSS13 chr1:3192250-3192336 86 - 3.44151e+06 0 1.31756e+07 OK 3.34455e+06 0 1.30786e+07 OK +TCONS_00000058 - - XLOC_000013 - TSS16 chr1:3192649-3192676 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000059 - - XLOC_000018 - TSS21 chr1:3194706-3194733 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000060 - - XLOC_000024 - TSS27 chr1:3197425-3197452 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000062 - - XLOC_000027 - TSS30 chr1:3200430-3200457 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000063 - - XLOC_000028 - TSS31 chr1:3201007-3201039 32 - 0 0 0 OK 0 0 0 OK +TCONS_00000065 - - XLOC_000030 - TSS33 chr1:3201596-3201666 70 - 1.6359e+07 0 5.96409e+07 OK 0 0 0 OK +TCONS_00000066 - - XLOC_000032 - TSS35 chr1:3201725-3201809 84 - 1.5136e+07 0 4.63396e+07 OK 0 0 0 OK +TCONS_00000067 i Xkr4 XLOC_000033 Xkr4 TSS36 chr1:3211521-3211561 40 - 0 0 0 OK 0 0 0 OK +TCONS_00000068 i Xkr4 XLOC_000036 Xkr4 TSS39 chr1:3212717-3212801 84 - 3.784e+06 0 1.44868e+07 OK 0 0 0 OK +TCONS_00000069 i Xkr4 XLOC_000037 Xkr4 TSS40 chr1:3213095-3213242 124 - 863189 0 4.25222e+06 OK 0 0 72384.9 OK +TCONS_00000070 i Xkr4 XLOC_000038 Xkr4 TSS41 chr1:3240606-3240633 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000071 i Xkr4 XLOC_000039 Xkr4 TSS42 chr1:3242479-3242512 33 - 0 0 0 OK 0 0 0 OK +TCONS_00000072 i Xkr4 XLOC_000041 Xkr4 TSS44 chr1:3242924-3243005 81 - 0 0 0 OK 0 0 0 OK +TCONS_00000073 i Xkr4 XLOC_000043 Xkr4 TSS46 chr1:3243108-3243154 46 - 8.616e+07 0 3.29857e+08 OK 0 0 0 OK +TCONS_00000074 i Xkr4 XLOC_000045 Xkr4 TSS48 chr1:3254079-3254106 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000075 i Xkr4 XLOC_000047 Xkr4 TSS50 chr1:3277155-3277182 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000076 i Xkr4 XLOC_000049 Xkr4 TSS52 chr1:3277913-3278390 477 - 228872 0 561229 OK 47662.2 0 156103 OK +TCONS_00000077 i Xkr4 XLOC_000050 Xkr4 TSS54 chr1:3280117-3280144 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000078 i Xkr4 XLOC_000051 Xkr4 TSS55 chr1:3280498-3280525 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000079 i Xkr4 XLOC_000053 Xkr4 TSS57 chr1:3282504-3282531 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000080 i Xkr4 XLOC_000054 Xkr4 TSS58 chr1:3282650-3282677 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000081 i Xkr4 XLOC_000055 Xkr4 TSS59 chr1:3282760-3282832 72 - 0 0 0 OK 0 0 0 OK +TCONS_00000082 i Xkr4 XLOC_000056 Xkr4 TSS60 chr1:3284966-3284993 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000083 i Xkr4 XLOC_000058 Xkr4 TSS62 chr1:3290798-3290859 61 - 1.55919e+07 0 5.96926e+07 OK 0 0 0 OK +TCONS_00000084 i Xkr4 XLOC_000059 Xkr4 TSS63 chr1:3290919-3291273 354 - 294879 0 740137 OK 85971.3 0 281572 OK +TCONS_00000085 i Xkr4 XLOC_000060 Xkr4 TSS65 chr1:3299443-3299664 197 - 807732 0 2.39056e+06 OK 156995 0 613917 OK +TCONS_00000086 i Xkr4 XLOC_000061 Xkr4 TSS67 chr1:3299691-3299733 42 - 0 0 0 OK 0 0 0 OK +TCONS_00000087 i Xkr4 XLOC_000063 Xkr4 TSS69 chr1:3307748-3307775 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000088 i Xkr4 XLOC_000064 Xkr4 TSS70 chr1:3318620-3318647 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000089 i Xkr4 XLOC_000066 Xkr4 TSS72 chr1:3330527-3330554 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000090 i Xkr4 XLOC_000067 Xkr4 TSS73 chr1:3351240-3351311 71 - 7.68169e+06 0 2.94088e+07 OK 0 0 0 OK +TCONS_00000091 i Xkr4 XLOC_000068 Xkr4 TSS74 chr1:3355887-3356119 212 - 504790 0 1.54544e+06 OK 0 0 0 OK +TCONS_00000092 i Xkr4 XLOC_000069 Xkr4 TSS75 chr1:3356180-3356225 45 - 1.02717e+08 0 3.93246e+08 OK 0 0 0 OK +TCONS_00000093 i Xkr4 XLOC_000070 Xkr4 TSS76 chr1:3363076-3363176 100 - 3.81001e+06 0 1.38903e+07 OK 0 0 0 OK +TCONS_00000094 i Xkr4 XLOC_000072 Xkr4 TSS78 chr1:3363387-3363446 59 - 5.53654e+07 0 1.77783e+08 OK 0 0 0 OK +TCONS_00000095 i Xkr4 XLOC_000074 Xkr4 TSS80 chr1:3364871-3364919 48 - 6.28966e+07 0 2.40795e+08 OK 0 0 0 OK +TCONS_00000096 i Xkr4 XLOC_000076 Xkr4 TSS82 chr1:3367210-3367237 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000097 i Xkr4 XLOC_000078 Xkr4 TSS84 chr1:3369580-3369607 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000098 i Xkr4 XLOC_000079 Xkr4 TSS85 chr1:3375001-3375028 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000099 i Xkr4 XLOC_000081 Xkr4 TSS87 chr1:3379888-3379915 27 - 0 0 0 OK 0 0 0 OK +TCONS_00000100 i Xkr4 XLOC_000082 Xkr4 TSS88 chr1:3386739-3386836 97 - 0 0 0 OK 0 0 0 OK
--- a/test-data/cuffdiff_out6.txt Thu Jan 16 13:13:52 2014 -0500 +++ b/test-data/cuffdiff_out6.txt Fri Dec 19 11:57:43 2014 -0500 @@ -1,88 +1,88 @@ tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage q1_FPKM q1_conf_lo q1_conf_hi q1_status q2_FPKM q2_conf_lo q2_conf_hi q2_status -XLOC_000001 - - XLOC_000001 Xkr4 TSS1 chr1:3204754-3204833 - - 0 0 0 OK 8.3103e+06 0 2.00628e+07 OK -XLOC_000002 - - XLOC_000002 - TSS2 chr1:3111449-3111490 - - 0 0 0 OK 2.1403e+08 0 6.42089e+08 OK +XLOC_000001 - - XLOC_000001 Xkr4 TSS1 chr1:3204754-3204833 - - 0 0 0 OK 9.45986e+06 0 3.33035e+07 OK +XLOC_000002 - - XLOC_000002 - TSS2 chr1:3111449-3111490 - - 0 0 0 OK 2.43637e+08 0 9.52723e+08 OK XLOC_000003 - - XLOC_000003 - TSS3 chr1:3111545-3111576 - - 0 0 0 OK 0 0 0 OK XLOC_000004 - - XLOC_000004 - TSS4 chr1:3174765-3174792 - - 0 0 0 OK 0 0 0 OK XLOC_000005 - - XLOC_000005 - TSS5 chr1:3187401-3187428 - - 0 0 0 OK 0 0 0 OK XLOC_000006 - - XLOC_000006 - TSS6 chr1:3188521-3188548 - - 0 0 0 OK 0 0 0 OK -XLOC_000007 - - XLOC_000007 - TSS7 chr1:3189810-3190789 - - 368900 151353 586447 OK 429265 337221 521309 OK -XLOC_000008 - - XLOC_000008 - TSS11 chr1:3190858-3191434 - - 404373 101434 707312 OK 338500 95761.5 581239 OK -XLOC_000009 - - XLOC_000009 - TSS12 chr1:3191512-3192077 - - 402276 96829.4 707722 OK 686974 410563 963384 OK -XLOC_000010 - - XLOC_000010 - TSS15 chr1:3192250-3192336 - - 3.994e+06 0 1.1982e+07 OK 2.93812e+06 0 8.81435e+06 OK -XLOC_000011 - - XLOC_000011 - TSS16 chr1:3192441-3192494 - - 0 0 0 OK 5.68095e+07 0 1.3715e+08 OK -XLOC_000012 - - XLOC_000012 - TSS17 chr1:3192550-3192629 - - 0 0 0 OK 4.15515e+06 0 1.24654e+07 OK -XLOC_000013 - - XLOC_000013 - TSS18 chr1:3192649-3192676 - - 0 0 0 OK 0 0 0 OK -XLOC_000014 - - XLOC_000014 - TSS19 chr1:3192731-3192811 - - 0 0 0 OK 0 0 0 OK -XLOC_000015 - - XLOC_000015 - TSS20 chr1:3192940-3193042 - - 0 0 0 OK 6.02976e+06 0 1.34147e+07 OK -XLOC_000016 - - XLOC_000016 - TSS21 chr1:3194185-3194226 - - 0 0 0 OK 2.1403e+08 0 6.42089e+08 OK -XLOC_000017 - - XLOC_000017 - TSS22 chr1:3194302-3194329 - - 0 0 0 OK 0 0 0 OK -XLOC_000018 - - XLOC_000018 - TSS23 chr1:3194706-3194733 - - 0 0 0 OK 0 0 0 OK -XLOC_000019 - - XLOC_000019 - TSS24 chr1:3195083-3195110 - - 0 0 0 OK 0 0 0 OK -XLOC_000020 - - XLOC_000020 - TSS25 chr1:3195450-3195477 - - 0 0 0 OK 0 0 0 OK -XLOC_000021 - - XLOC_000021 - TSS26 chr1:3197089-3197116 - - 0 0 0 OK 0 0 0 OK -XLOC_000022 - - XLOC_000022 - TSS27 chr1:3197246-3197273 - - 0 0 0 OK 0 0 0 OK -XLOC_000023 - - XLOC_000023 - TSS28 chr1:3197346-3197373 - - 0 0 0 OK 0 0 0 OK -XLOC_000024 - - XLOC_000024 - TSS29 chr1:3197425-3197452 - - 0 0 0 OK 0 0 0 OK -XLOC_000025 - - XLOC_000025 - TSS30 chr1:3200022-3200191 - - 959058 0 2.06648e+06 OK 705514 0 1.52017e+06 OK -XLOC_000026 - - XLOC_000026 - TSS32 chr1:3200325-3200352 - - 0 0 0 OK 0 0 0 OK -XLOC_000027 - - XLOC_000027 - TSS33 chr1:3200430-3200457 - - 0 0 0 OK 0 0 0 OK -XLOC_000028 - - XLOC_000028 - TSS34 chr1:3201007-3201039 - - 0 0 0 OK 0 0 0 OK -XLOC_000029 - - XLOC_000029 - TSS35 chr1:3201077-3201481 - - 77513.9 0 167019 OK 285108 21736.5 548480 OK -XLOC_000030 - - XLOC_000030 - TSS37 chr1:3201596-3201666 - - 1.89853e+07 0 4.58345e+07 OK 0 0 0 OK -XLOC_000031 - - XLOC_000031 - TSS38 chr1:3201672-3201699 - - 0 0 0 OK 0 0 0 OK -XLOC_000032 - - XLOC_000032 - TSS39 chr1:3201725-3201809 - - 1.31744e+07 0 2.83869e+07 OK 0 0 0 OK -XLOC_000033 - - XLOC_000033 Xkr4 TSS40 chr1:3211521-3211561 - - 0 0 0 OK 0 0 0 OK -XLOC_000034 - - XLOC_000034 Xkr4 TSS41 chr1:3212213-3212292 - - 0 0 0 OK 8.3103e+06 0 2.00628e+07 OK -XLOC_000035 - - XLOC_000035 Xkr4 TSS42 chr1:3212367-3212439 - - 0 0 0 OK 2.4671e+07 0 5.48867e+07 OK -XLOC_000036 - - XLOC_000036 Xkr4 TSS43 chr1:3212717-3212801 - - 4.39147e+06 0 1.31744e+07 OK 0 0 0 OK -XLOC_000037 - - XLOC_000037 Xkr4 TSS44,TSS45 chr1:3213095-3213242 - - 5.3664e+06 0 1.39795e+07 LOWDATA 1.82908e+06 0 5.48723e+06 OK -XLOC_000038 - - XLOC_000038 Xkr4 TSS46 chr1:3240606-3240633 - - 0 0 0 OK 0 0 0 OK -XLOC_000039 - - XLOC_000039 Xkr4 TSS47 chr1:3242479-3242512 - - 0 0 0 OK 0 0 0 OK -XLOC_000040 - - XLOC_000040 Xkr4 TSS48 chr1:3242633-3242923 - - 56312.4 0 168937 OK 372827 0 761430 OK -XLOC_000041 - - XLOC_000041 Xkr4 TSS49 chr1:3242924-3243005 - - 0 0 0 OK 0 0 0 OK -XLOC_000042 - - XLOC_000042 Xkr4 TSS50 chr1:3243018-3243079 - - 0 0 0 OK 2.66226e+07 0 6.42725e+07 OK -XLOC_000043 - - XLOC_000043 Xkr4 TSS51 chr1:3243108-3243154 - - 9.99919e+07 0 2.99976e+08 OK 0 0 0 OK -XLOC_000044 - - XLOC_000044 Xkr4 TSS52 chr1:3243347-3243401 - - 0 0 0 OK 5.0951e+07 0 1.23007e+08 OK -XLOC_000045 - - XLOC_000045 Xkr4 TSS53 chr1:3254079-3254106 - - 0 0 0 OK 0 0 0 OK -XLOC_000046 - - XLOC_000046 Xkr4 TSS54 chr1:3256974-3257011 - - 0 0 0 OK 2.06814e+09 0 4.99293e+09 OK -XLOC_000047 - - XLOC_000047 Xkr4 TSS55 chr1:3277155-3277182 - - 0 0 0 OK 0 0 0 OK -XLOC_000048 - - XLOC_000048 Xkr4 TSS56 chr1:3277190-3277218 - - 0 0 0 OK 0 0 0 OK -XLOC_000049 - - XLOC_000049 Xkr4 TSS57 chr1:3277913-3278390 - - 265614 16793 514436 OK 41870.3 0 90217.9 OK -XLOC_000050 - - XLOC_000050 Xkr4 TSS59 chr1:3280117-3280144 - - 0 0 0 OK 0 0 0 OK -XLOC_000051 - - XLOC_000051 Xkr4 TSS60 chr1:3280498-3280525 - - 0 0 0 OK 0 0 0 OK -XLOC_000052 - - XLOC_000052 Xkr4 TSS61 chr1:3280686-3280741 - - 0 0 0 OK 2.29576e+07 0 6.88728e+07 OK -XLOC_000053 - - XLOC_000053 Xkr4 TSS62 chr1:3282504-3282531 - - 0 0 0 OK 0 0 0 OK -XLOC_000054 - - XLOC_000054 Xkr4 TSS63 chr1:3282650-3282677 - - 0 0 0 OK 0 0 0 OK -XLOC_000055 - - XLOC_000055 Xkr4 TSS64 chr1:3282760-3282832 - - 0 0 0 OK 0 0 0 OK -XLOC_000056 - - XLOC_000056 Xkr4 TSS65 chr1:3284966-3284993 - - 0 0 0 OK 0 0 0 OK -XLOC_000057 - - XLOC_000057 Xkr4 TSS66 chr1:3290488-3290553 - - 0 0 0 OK 9.79535e+06 0 2.9386e+07 OK -XLOC_000058 - - XLOC_000058 Xkr4 TSS67 chr1:3290798-3290859 - - 1.8095e+07 0 5.4285e+07 OK 0 0 0 OK -XLOC_000059 - - XLOC_000059 Xkr4 TSS68 chr1:3290919-3291273 - - 342218 0 691214 OK 75524 0 162732 OK -XLOC_000060 - - XLOC_000060 Xkr4 TSS70,TSS71 chr1:3299443-3299664 - - 937403 0 1.99795e+06 OK 137917 0 413751 OK -XLOC_000061 - - XLOC_000061 Xkr4 TSS72 chr1:3299691-3299733 - - 0 0 0 OK 0 0 0 OK -XLOC_000062 - - XLOC_000062 Xkr4 TSS73 chr1:3300051-3300078 - - 0 0 0 OK 0 0 0 OK -XLOC_000063 - - XLOC_000063 Xkr4 TSS74 chr1:3307748-3307775 - - 0 0 0 OK 0 0 0 OK -XLOC_000064 - - XLOC_000064 Xkr4 TSS75 chr1:3318620-3318647 - - 0 0 0 OK 0 0 0 OK -XLOC_000065 - - XLOC_000065 Xkr4 TSS76 chr1:3318999-3319051 - - 0 0 0 OK 0 0 0 OK -XLOC_000066 - - XLOC_000066 Xkr4 TSS77 chr1:3330527-3330554 - - 0 0 0 OK 0 0 0 OK -XLOC_000067 - - XLOC_000067 Xkr4 TSS78 chr1:3351240-3351311 - - 8.91489e+06 0 2.67447e+07 OK 0 0 0 OK -XLOC_000068 - - XLOC_000068 Xkr4 TSS79,TSS80 chr1:3355887-3356119 - - 585828 0 1.30332e+06 OK 0 0 0 OK -XLOC_000069 - - XLOC_000069 Xkr4 TSS81 chr1:3356180-3356225 - - 1.19208e+08 0 3.57623e+08 OK 0 0 0 OK -XLOC_000070 - - XLOC_000070 Xkr4 TSS82 chr1:3363076-3363176 - - 4.42166e+06 0 1.06748e+07 OK 0 0 0 OK -XLOC_000071 - - XLOC_000071 Xkr4 TSS83 chr1:3363214-3363278 - - 0 0 0 OK 0 0 0 OK -XLOC_000072 - - XLOC_000072 Xkr4 TSS84 chr1:3363387-3363446 - - 4.28358e+07 0 1.03415e+08 OK 0 0 0 OK -XLOC_000073 - - XLOC_000073 Xkr4 TSS85 chr1:3363753-3363849 - - 0 0 0 OK 0 0 0 OK -XLOC_000074 - - XLOC_000074 Xkr4 TSS86 chr1:3364871-3364919 - - 7.29939e+07 0 2.18982e+08 OK 0 0 0 OK -XLOC_000075 - - XLOC_000075 Xkr4 TSS87 chr1:3367135-3367162 - - 0 0 0 OK 0 0 0 OK -XLOC_000076 - - XLOC_000076 Xkr4 TSS88 chr1:3367210-3367237 - - 0 0 0 OK 0 0 0 OK -XLOC_000077 - - XLOC_000077 Xkr4 TSS89 chr1:3367333-3367382 - - 0 0 0 OK 0 0 0 OK -XLOC_000078 - - XLOC_000078 Xkr4 TSS90 chr1:3369580-3369607 - - 0 0 0 OK 0 0 0 OK -XLOC_000079 - - XLOC_000079 Xkr4 TSS91 chr1:3375001-3375028 - - 0 0 0 OK 0 0 0 OK -XLOC_000080 - - XLOC_000080 Xkr4 TSS92 chr1:3377211-3377262 - - 0 0 0 OK 0 0 0 OK -XLOC_000081 - - XLOC_000081 Xkr4 TSS93 chr1:3379888-3379915 - - 0 0 0 OK 0 0 0 OK -XLOC_000082 - - XLOC_000082 Xkr4 TSS94 chr1:3386739-3386836 - - 0 0 0 OK 0 0 0 OK -XLOC_000083 - - XLOC_000083 Xkr4 TSS95 chr1:3391325-3391352 - - 0 0 0 OK 0 0 0 OK -XLOC_000084 - - XLOC_000084 Xkr4 TSS96 chr1:3435841-3435880 - - 0 0 0 OK 0 0 0 OK -XLOC_000085 - - XLOC_000085 Xkr4 TSS97 chr1:3447761-3447788 - - 0 0 0 OK 0 0 0 OK -XLOC_000086 - - XLOC_000086 Xkr4 TSS98 chr1:3450906-3450965 - - 0 0 0 OK 0 0 0 OK -XLOC_000087 - - XLOC_000087 Xkr4 TSS99 chr1:3451051-3451109 - - 0 0 0 OK 0 0 0 OK +XLOC_000007 - - XLOC_000007 - TSS7 chr1:3189810-3190789 - - 358326 135086 581565 OK 522345 410780 633911 OK +XLOC_000008 - - XLOC_000008 - TSS10 chr1:3190858-3191434 - - 408511 54526.1 762496 OK 420354 61509.1 779200 OK +XLOC_000009 - - XLOC_000009 - TSS11 chr1:3191512-3192077 - - 433286 63552.3 803020 OK 842157 342520 1.34179e+06 OK +XLOC_000010 - - XLOC_000010 - TSS13 chr1:3192250-3192336 - - 3.44151e+06 0 1.31756e+07 OK 3.34455e+06 0 1.30786e+07 OK +XLOC_000011 - - XLOC_000011 - TSS14 chr1:3192441-3192494 - - 0 0 0 OK 9.7002e+07 0 3.17699e+08 OK +XLOC_000012 - - XLOC_000012 - TSS15 chr1:3192550-3192629 - - 0 0 0 OK 4.72993e+06 0 1.84961e+07 OK +XLOC_000013 - - XLOC_000013 - TSS16 chr1:3192649-3192676 - - 0 0 0 OK 0 0 0 OK +XLOC_000014 - - XLOC_000014 - TSS17 chr1:3192731-3192811 - - 0 0 0 OK 0 0 0 OK +XLOC_000015 - - XLOC_000015 - TSS18 chr1:3192940-3193042 - - 0 0 0 OK 6.86386e+06 0 2.14243e+07 OK +XLOC_000016 - - XLOC_000016 - TSS19 chr1:3194185-3194226 - - 0 0 0 OK 2.43637e+08 0 9.52723e+08 OK +XLOC_000017 - - XLOC_000017 - TSS20 chr1:3194302-3194329 - - 0 0 0 OK 0 0 0 OK +XLOC_000018 - - XLOC_000018 - TSS21 chr1:3194706-3194733 - - 0 0 0 OK 0 0 0 OK +XLOC_000019 - - XLOC_000019 - TSS22 chr1:3195083-3195110 - - 0 0 0 OK 0 0 0 OK +XLOC_000020 - - XLOC_000020 - TSS23 chr1:3195450-3195477 - - 0 0 0 OK 0 0 0 OK +XLOC_000021 - - XLOC_000021 - TSS24 chr1:3197089-3197116 - - 0 0 0 OK 0 0 0 OK +XLOC_000022 - - XLOC_000022 - TSS25 chr1:3197246-3197273 - - 0 0 0 OK 0 0 0 OK +XLOC_000023 - - XLOC_000023 - TSS26 chr1:3197346-3197373 - - 0 0 0 OK 0 0 0 OK +XLOC_000024 - - XLOC_000024 - TSS27 chr1:3197425-3197452 - - 0 0 0 OK 0 0 0 OK +XLOC_000025 - - XLOC_000025 - TSS28 chr1:3200022-3200191 - - 826392 0 2.65361e+06 OK 803108 0 2.63033e+06 OK +XLOC_000026 - - XLOC_000026 - TSS29 chr1:3200325-3200352 - - 0 0 0 OK 0 0 0 OK +XLOC_000027 - - XLOC_000027 - TSS30 chr1:3200430-3200457 - - 0 0 0 OK 0 0 0 OK +XLOC_000028 - - XLOC_000028 - TSS31 chr1:3201007-3201039 - - 0 0 0 OK 0 0 0 OK +XLOC_000029 - - XLOC_000029 - TSS32 chr1:3201077-3201481 - - 66791.3 0 214473 OK 324548 0 802006 OK +XLOC_000030 - - XLOC_000030 - TSS33 chr1:3201596-3201666 - - 1.6359e+07 0 5.96409e+07 OK 0 0 0 OK +XLOC_000031 - - XLOC_000031 - TSS34 chr1:3201672-3201699 - - 0 0 0 OK 0 0 0 OK +XLOC_000032 - - XLOC_000032 - TSS35 chr1:3201725-3201809 - - 1.5136e+07 0 4.63396e+07 OK 0 0 0 OK +XLOC_000033 - - XLOC_000033 Xkr4 TSS36 chr1:3211521-3211561 - - 0 0 0 OK 0 0 0 OK +XLOC_000034 - - XLOC_000034 Xkr4 TSS37 chr1:3212213-3212292 - - 0 0 0 OK 9.45986e+06 0 3.33035e+07 OK +XLOC_000035 - - XLOC_000035 Xkr4 TSS38 chr1:3212367-3212439 - - 0 0 0 OK 2.80837e+07 0 8.76584e+07 OK +XLOC_000036 - - XLOC_000036 Xkr4 TSS39 chr1:3212717-3212801 - - 3.784e+06 0 1.44868e+07 OK 0 0 0 OK +XLOC_000037 - - XLOC_000037 Xkr4 TSS40 chr1:3213095-3213242 - - 5.10781e+06 0 1.69588e+07 OK 2.08209e+06 0 8.1421e+06 OK +XLOC_000038 - - XLOC_000038 Xkr4 TSS41 chr1:3240606-3240633 - - 0 0 0 OK 0 0 0 OK +XLOC_000039 - - XLOC_000039 Xkr4 TSS42 chr1:3242479-3242512 - - 0 0 0 OK 0 0 0 OK +XLOC_000040 - - XLOC_000040 Xkr4 TSS43 chr1:3242633-3242923 - - 48522.7 0 185766 OK 424400 0 1.30289e+06 OK +XLOC_000041 - - XLOC_000041 Xkr4 TSS44 chr1:3242924-3243005 - - 0 0 0 OK 0 0 0 OK +XLOC_000042 - - XLOC_000042 Xkr4 TSS45 chr1:3243018-3243079 - - 0 0 0 OK 3.03053e+07 0 1.0669e+08 OK +XLOC_000043 - - XLOC_000043 Xkr4 TSS46 chr1:3243108-3243154 - - 8.616e+07 0 3.29857e+08 OK 0 0 0 OK +XLOC_000044 - - XLOC_000044 Xkr4 TSS47 chr1:3243347-3243401 - - 0 0 0 OK 5.79991e+07 0 2.04186e+08 OK +XLOC_000045 - - XLOC_000045 Xkr4 TSS48 chr1:3254079-3254106 - - 0 0 0 OK 0 0 0 OK +XLOC_000046 - - XLOC_000046 Xkr4 TSS49 chr1:3256974-3257011 - - 0 0 0 OK 2.35423e+09 0 8.28806e+09 OK +XLOC_000047 - - XLOC_000047 Xkr4 TSS50 chr1:3277155-3277182 - - 0 0 0 OK 0 0 0 OK +XLOC_000048 - - XLOC_000048 Xkr4 TSS51 chr1:3277190-3277218 - - 0 0 0 OK 0 0 0 OK +XLOC_000049 - - XLOC_000049 Xkr4 TSS52 chr1:3277913-3278390 - - 228872 0 561229 OK 47662.2 0 156103 OK +XLOC_000050 - - XLOC_000050 Xkr4 TSS54 chr1:3280117-3280144 - - 0 0 0 OK 0 0 0 OK +XLOC_000051 - - XLOC_000051 Xkr4 TSS55 chr1:3280498-3280525 - - 0 0 0 OK 0 0 0 OK +XLOC_000052 - - XLOC_000052 Xkr4 TSS56 chr1:3280686-3280741 - - 0 0 0 OK 2.61334e+07 0 1.02193e+08 OK +XLOC_000053 - - XLOC_000053 Xkr4 TSS57 chr1:3282504-3282531 - - 0 0 0 OK 0 0 0 OK +XLOC_000054 - - XLOC_000054 Xkr4 TSS58 chr1:3282650-3282677 - - 0 0 0 OK 0 0 0 OK +XLOC_000055 - - XLOC_000055 Xkr4 TSS59 chr1:3282760-3282832 - - 0 0 0 OK 0 0 0 OK +XLOC_000056 - - XLOC_000056 Xkr4 TSS60 chr1:3284966-3284993 - - 0 0 0 OK 0 0 0 OK +XLOC_000057 - - XLOC_000057 Xkr4 TSS61 chr1:3290488-3290553 - - 0 0 0 OK 1.11503e+07 0 4.36026e+07 OK +XLOC_000058 - - XLOC_000058 Xkr4 TSS62 chr1:3290798-3290859 - - 1.55919e+07 0 5.96926e+07 OK 0 0 0 OK +XLOC_000059 - - XLOC_000059 Xkr4 TSS63 chr1:3290919-3291273 - - 294879 0 740137 OK 85971.3 0 281572 OK +XLOC_000060 - - XLOC_000060 Xkr4 TSS65,TSS66 chr1:3299443-3299664 - - 807732 0 2.39786e+06 OK 156995 0 641748 OK +XLOC_000061 - - XLOC_000061 Xkr4 TSS67 chr1:3299691-3299733 - - 0 0 0 OK 0 0 0 OK +XLOC_000062 - - XLOC_000062 Xkr4 TSS68 chr1:3300051-3300078 - - 0 0 0 OK 0 0 0 OK +XLOC_000063 - - XLOC_000063 Xkr4 TSS69 chr1:3307748-3307775 - - 0 0 0 OK 0 0 0 OK +XLOC_000064 - - XLOC_000064 Xkr4 TSS70 chr1:3318620-3318647 - - 0 0 0 OK 0 0 0 OK +XLOC_000065 - - XLOC_000065 Xkr4 TSS71 chr1:3318999-3319051 - - 0 0 0 OK 0 0 0 OK +XLOC_000066 - - XLOC_000066 Xkr4 TSS72 chr1:3330527-3330554 - - 0 0 0 OK 0 0 0 OK +XLOC_000067 - - XLOC_000067 Xkr4 TSS73 chr1:3351240-3351311 - - 7.68169e+06 0 2.94088e+07 OK 0 0 0 OK +XLOC_000068 - - XLOC_000068 Xkr4 TSS74 chr1:3355887-3356119 - - 504790 0 1.59712e+06 OK 0 0 0 OK +XLOC_000069 - - XLOC_000069 Xkr4 TSS75 chr1:3356180-3356225 - - 1.02717e+08 0 3.93246e+08 OK 0 0 0 OK +XLOC_000070 - - XLOC_000070 Xkr4 TSS76 chr1:3363076-3363176 - - 3.81001e+06 0 1.38903e+07 OK 0 0 0 OK +XLOC_000071 - - XLOC_000071 Xkr4 TSS77 chr1:3363214-3363278 - - 0 0 0 OK 0 0 0 OK +XLOC_000072 - - XLOC_000072 Xkr4 TSS78 chr1:3363387-3363446 - - 5.53654e+07 0 1.77783e+08 OK 0 0 0 OK +XLOC_000073 - - XLOC_000073 Xkr4 TSS79 chr1:3363753-3363849 - - 0 0 0 OK 0 0 0 OK +XLOC_000074 - - XLOC_000074 Xkr4 TSS80 chr1:3364871-3364919 - - 6.28966e+07 0 2.40795e+08 OK 0 0 0 OK +XLOC_000075 - - XLOC_000075 Xkr4 TSS81 chr1:3367135-3367162 - - 0 0 0 OK 0 0 0 OK +XLOC_000076 - - XLOC_000076 Xkr4 TSS82 chr1:3367210-3367237 - - 0 0 0 OK 0 0 0 OK +XLOC_000077 - - XLOC_000077 Xkr4 TSS83 chr1:3367333-3367382 - - 0 0 0 OK 0 0 0 OK +XLOC_000078 - - XLOC_000078 Xkr4 TSS84 chr1:3369580-3369607 - - 0 0 0 OK 0 0 0 OK +XLOC_000079 - - XLOC_000079 Xkr4 TSS85 chr1:3375001-3375028 - - 0 0 0 OK 0 0 0 OK +XLOC_000080 - - XLOC_000080 Xkr4 TSS86 chr1:3377211-3377262 - - 0 0 0 OK 0 0 0 OK +XLOC_000081 - - XLOC_000081 Xkr4 TSS87 chr1:3379888-3379915 - - 0 0 0 OK 0 0 0 OK +XLOC_000082 - - XLOC_000082 Xkr4 TSS88 chr1:3386739-3386836 - - 0 0 0 OK 0 0 0 OK +XLOC_000083 - - XLOC_000083 Xkr4 TSS89 chr1:3391325-3391352 - - 0 0 0 OK 0 0 0 OK +XLOC_000084 - - XLOC_000084 Xkr4 TSS90 chr1:3435841-3435880 - - 0 0 0 OK 0 0 0 OK +XLOC_000085 - - XLOC_000085 Xkr4 TSS91 chr1:3447761-3447788 - - 0 0 0 OK 0 0 0 OK +XLOC_000086 - - XLOC_000086 Xkr4 TSS92 chr1:3450906-3450965 - - 0 0 0 OK 0 0 0 OK +XLOC_000087 - - XLOC_000087 Xkr4 TSS93 chr1:3451051-3451109 - - 0 0 0 OK 0 0 0 OK
--- a/test-data/cuffdiff_out7.txt Thu Jan 16 13:13:52 2014 -0500 +++ b/test-data/cuffdiff_out7.txt Fri Dec 19 11:57:43 2014 -0500 @@ -1,15 +1,15 @@ tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage q1_FPKM q1_conf_lo q1_conf_hi q1_status q2_FPKM q2_conf_lo q2_conf_hi q2_status -TSS1 - - XLOC_000001 Xkr4 TSS1 chr1:3204754-3204833 - - 0 0 0 OK 5.42247e+06 0 1.83844e+07 OK -TSS10 - - XLOC_000008 - TSS10 chr1:3190858-3191434 - - 227564 0 483427 OK 240951 0 505030 OK -TSS11 - - XLOC_000009 - TSS11 chr1:3191512-3192077 - - 241366 0 509259 OK 482731 109420 856042 OK -TSS13 - - XLOC_000010 - TSS13 chr1:3192250-3192336 - - 1.91712e+06 0 7.66198e+06 OK 1.91712e+06 0 7.66198e+06 OK -TSS14 - - XLOC_000011 - TSS14 chr1:3192441-3192494 - - 0 0 0 OK 5.56023e+07 0 1.86077e+08 OK -TSS15 - - XLOC_000012 - TSS15 chr1:3192550-3192629 - - 0 0 0 OK 2.71123e+06 0 1.08357e+07 OK +TSS1 - - XLOC_000001 Xkr4 TSS1 chr1:3204754-3204833 - - 0 0 0 OK 9.45986e+06 0 3.33035e+07 OK +TSS10 - - XLOC_000008 - TSS10 chr1:3190858-3191434 - - 408511 54526.1 762496 OK 420354 61509.1 779200 OK +TSS11 - - XLOC_000009 - TSS11 chr1:3191512-3192077 - - 433286 63552.3 803020 OK 842157 342520 1.34179e+06 OK +TSS13 - - XLOC_000010 - TSS13 chr1:3192250-3192336 - - 3.44151e+06 0 1.31756e+07 OK 3.34455e+06 0 1.30786e+07 OK +TSS14 - - XLOC_000011 - TSS14 chr1:3192441-3192494 - - 0 0 0 OK 9.7002e+07 0 3.17699e+08 OK +TSS15 - - XLOC_000012 - TSS15 chr1:3192550-3192629 - - 0 0 0 OK 4.72993e+06 0 1.84961e+07 OK TSS16 - - XLOC_000013 - TSS16 chr1:3192649-3192676 - - 0 0 0 OK 0 0 0 OK TSS17 - - XLOC_000014 - TSS17 chr1:3192731-3192811 - - 0 0 0 OK 0 0 0 OK -TSS18 - - XLOC_000015 - TSS18 chr1:3192940-3193042 - - 0 0 0 OK 3.93442e+06 0 1.25021e+07 OK -TSS19 - - XLOC_000016 - TSS19 chr1:3194185-3194226 - - 0 0 0 OK 1.39654e+08 0 5.58144e+08 OK -TSS2 - - XLOC_000002 - TSS2 chr1:3111449-3111490 - - 0 0 0 OK 1.39654e+08 0 5.58144e+08 OK +TSS18 - - XLOC_000015 - TSS18 chr1:3192940-3193042 - - 0 0 0 OK 6.86386e+06 0 2.14243e+07 OK +TSS19 - - XLOC_000016 - TSS19 chr1:3194185-3194226 - - 0 0 0 OK 2.43637e+08 0 9.52723e+08 OK +TSS2 - - XLOC_000002 - TSS2 chr1:3111449-3111490 - - 0 0 0 OK 2.43637e+08 0 9.52723e+08 OK TSS20 - - XLOC_000017 - TSS20 chr1:3194302-3194329 - - 0 0 0 OK 0 0 0 OK TSS21 - - XLOC_000018 - TSS21 chr1:3194706-3194733 - - 0 0 0 OK 0 0 0 OK TSS22 - - XLOC_000019 - TSS22 chr1:3195083-3195110 - - 0 0 0 OK 0 0 0 OK @@ -18,62 +18,62 @@ TSS25 - - XLOC_000022 - TSS25 chr1:3197246-3197273 - - 0 0 0 OK 0 0 0 OK TSS26 - - XLOC_000023 - TSS26 chr1:3197346-3197373 - - 0 0 0 OK 0 0 0 OK TSS27 - - XLOC_000024 - TSS27 chr1:3197425-3197452 - - 0 0 0 OK 0 0 0 OK -TSS28 - - XLOC_000025 - TSS28 chr1:3200022-3200191 - - 460348 0 1.54058e+06 OK 460348 0 1.54058e+06 OK +TSS28 - - XLOC_000025 - TSS28 chr1:3200022-3200191 - - 826392 0 2.65361e+06 OK 803108 0 2.63033e+06 OK TSS29 - - XLOC_000026 - TSS29 chr1:3200325-3200352 - - 0 0 0 OK 0 0 0 OK TSS3 - - XLOC_000003 - TSS3 chr1:3111545-3111576 - - 0 0 0 OK 0 0 0 OK TSS30 - - XLOC_000027 - TSS30 chr1:3200430-3200457 - - 0 0 0 OK 0 0 0 OK TSS31 - - XLOC_000028 - TSS31 chr1:3201007-3201039 - - 0 0 0 OK 0 0 0 OK -TSS32 - - XLOC_000029 - TSS32 chr1:3201077-3201481 - - 37206.6 0 124514 OK 186033 0 476912 OK -TSS33 - - XLOC_000030 - TSS33 chr1:3201596-3201666 - - 9.11292e+06 0 3.08965e+07 OK 0 0 0 OK +TSS32 - - XLOC_000029 - TSS32 chr1:3201077-3201481 - - 66791.3 0 214473 OK 324548 0 802006 OK +TSS33 - - XLOC_000030 - TSS33 chr1:3201596-3201666 - - 1.6359e+07 0 5.96409e+07 OK 0 0 0 OK TSS34 - - XLOC_000031 - TSS34 chr1:3201672-3201699 - - 0 0 0 OK 0 0 0 OK -TSS35 - - XLOC_000032 - TSS35 chr1:3201725-3201809 - - 8.43162e+06 0 2.67925e+07 OK 0 0 0 OK +TSS35 - - XLOC_000032 - TSS35 chr1:3201725-3201809 - - 1.5136e+07 0 4.63396e+07 OK 0 0 0 OK TSS36 - - XLOC_000033 Xkr4 TSS36 chr1:3211521-3211561 - - 0 0 0 OK 0 0 0 OK -TSS37 - - XLOC_000034 Xkr4 TSS37 chr1:3212213-3212292 - - 0 0 0 OK 5.42247e+06 0 1.83844e+07 OK -TSS38 - - XLOC_000035 Xkr4 TSS38 chr1:3212367-3212439 - - 0 0 0 OK 1.60978e+07 0 5.11527e+07 OK -TSS39 - - XLOC_000036 Xkr4 TSS39 chr1:3212717-3212801 - - 2.10791e+06 0 8.42447e+06 OK 0 0 0 OK +TSS37 - - XLOC_000034 Xkr4 TSS37 chr1:3212213-3212292 - - 0 0 0 OK 9.45986e+06 0 3.33035e+07 OK +TSS38 - - XLOC_000035 Xkr4 TSS38 chr1:3212367-3212439 - - 0 0 0 OK 2.80837e+07 0 8.76584e+07 OK +TSS39 - - XLOC_000036 Xkr4 TSS39 chr1:3212717-3212801 - - 3.784e+06 0 1.44868e+07 OK 0 0 0 OK TSS4 - - XLOC_000004 - TSS4 chr1:3174765-3174792 - - 0 0 0 OK 0 0 0 OK -TSS40 - - XLOC_000037 Xkr4 TSS40 chr1:3213095-3213242 - - 2.84535e+06 0 1.07397e+07 OK 1.19347e+06 0 5.96736e+06 OK +TSS40 - - XLOC_000037 Xkr4 TSS40 chr1:3213095-3213242 - - 5.10781e+06 0 1.69588e+07 OK 2.08209e+06 0 8.1421e+06 OK TSS41 - - XLOC_000038 Xkr4 TSS41 chr1:3240606-3240633 - - 0 0 0 OK 0 0 0 OK TSS42 - - XLOC_000039 Xkr4 TSS42 chr1:3242479-3242512 - - 0 0 0 OK 0 0 0 OK -TSS43 - - XLOC_000040 Xkr4 TSS43 chr1:3242633-3242923 - - 27029.9 0 108028 OK 243269 0 681799 OK +TSS43 - - XLOC_000040 Xkr4 TSS43 chr1:3242633-3242923 - - 48522.7 0 185766 OK 424400 0 1.30289e+06 OK TSS44 - - XLOC_000041 Xkr4 TSS44 chr1:3242924-3243005 - - 0 0 0 OK 0 0 0 OK -TSS45 - - XLOC_000042 Xkr4 TSS45 chr1:3243018-3243079 - - 0 0 0 OK 1.73712e+07 0 5.88955e+07 OK -TSS46 - - XLOC_000043 Xkr4 TSS46 chr1:3243108-3243154 - - 4.79961e+07 0 1.91822e+08 OK 0 0 0 OK -TSS47 - - XLOC_000044 Xkr4 TSS47 chr1:3243347-3243401 - - 0 0 0 OK 3.32455e+07 0 1.12716e+08 OK +TSS45 - - XLOC_000042 Xkr4 TSS45 chr1:3243018-3243079 - - 0 0 0 OK 3.03053e+07 0 1.0669e+08 OK +TSS46 - - XLOC_000043 Xkr4 TSS46 chr1:3243108-3243154 - - 8.616e+07 0 3.29857e+08 OK 0 0 0 OK +TSS47 - - XLOC_000044 Xkr4 TSS47 chr1:3243347-3243401 - - 0 0 0 OK 5.79991e+07 0 2.04186e+08 OK TSS48 - - XLOC_000045 Xkr4 TSS48 chr1:3254079-3254106 - - 0 0 0 OK 0 0 0 OK -TSS49 - - XLOC_000046 Xkr4 TSS49 chr1:3256974-3257011 - - 0 0 0 OK 1.34946e+09 0 4.57522e+09 OK +TSS49 - - XLOC_000046 Xkr4 TSS49 chr1:3256974-3257011 - - 0 0 0 OK 2.35423e+09 0 8.28806e+09 OK TSS5 - - XLOC_000005 - TSS5 chr1:3187401-3187428 - - 0 0 0 OK 0 0 0 OK TSS50 - - XLOC_000047 Xkr4 TSS50 chr1:3277155-3277182 - - 0 0 0 OK 0 0 0 OK TSS51 - - XLOC_000048 Xkr4 TSS51 chr1:3277190-3277218 - - 0 0 0 OK 0 0 0 OK -TSS52 - - XLOC_000049 Xkr4 TSS52 chr1:3277913-3278390 - - 127495 0 331348 OK 27320.3 0 91429.2 OK +TSS52 - - XLOC_000049 Xkr4 TSS52 chr1:3277913-3278390 - - 228872 0 561229 OK 47662.2 0 156103 OK TSS54 - - XLOC_000050 Xkr4 TSS54 chr1:3280117-3280144 - - 0 0 0 OK 0 0 0 OK TSS55 - - XLOC_000051 Xkr4 TSS55 chr1:3280498-3280525 - - 0 0 0 OK 0 0 0 OK -TSS56 - - XLOC_000052 Xkr4 TSS56 chr1:3280686-3280741 - - 0 0 0 OK 1.49798e+07 0 5.98686e+07 OK +TSS56 - - XLOC_000052 Xkr4 TSS56 chr1:3280686-3280741 - - 0 0 0 OK 2.61334e+07 0 1.02193e+08 OK TSS57 - - XLOC_000053 Xkr4 TSS57 chr1:3282504-3282531 - - 0 0 0 OK 0 0 0 OK TSS58 - - XLOC_000054 Xkr4 TSS58 chr1:3282650-3282677 - - 0 0 0 OK 0 0 0 OK TSS59 - - XLOC_000055 Xkr4 TSS59 chr1:3282760-3282832 - - 0 0 0 OK 0 0 0 OK TSS6 - - XLOC_000006 - TSS6 chr1:3188521-3188548 - - 0 0 0 OK 0 0 0 OK TSS60 - - XLOC_000056 Xkr4 TSS60 chr1:3284966-3284993 - - 0 0 0 OK 0 0 0 OK -TSS61 - - XLOC_000057 Xkr4 TSS61 chr1:3290488-3290553 - - 0 0 0 OK 6.39146e+06 0 2.55442e+07 OK -TSS62 - - XLOC_000058 Xkr4 TSS62 chr1:3290798-3290859 - - 8.68561e+06 0 3.4713e+07 OK 0 0 0 OK -TSS63 - - XLOC_000059 Xkr4 TSS63 chr1:3290919-3291273 - - 164265 0 453103 OK 49279.4 0 164917 OK -TSS65 - - XLOC_000060 Xkr4 TSS65 chr1:3299443-3299664 - - 449954 0 1.56567e+06 OK 89990.7 0 449954 OK +TSS61 - - XLOC_000057 Xkr4 TSS61 chr1:3290488-3290553 - - 0 0 0 OK 1.11503e+07 0 4.36026e+07 OK +TSS62 - - XLOC_000058 Xkr4 TSS62 chr1:3290798-3290859 - - 1.55919e+07 0 5.96926e+07 OK 0 0 0 OK +TSS63 - - XLOC_000059 Xkr4 TSS63 chr1:3290919-3291273 - - 294879 0 740137 OK 85971.3 0 281572 OK +TSS65 - - XLOC_000060 Xkr4 TSS65 chr1:3299443-3299664 - - 807732 0 2.39056e+06 OK 156995 0 613917 OK TSS66 - - XLOC_000060 Xkr4 TSS66 chr1:3299443-3299664 - - 0 0 0 OK 0 0 0 OK TSS67 - - XLOC_000061 Xkr4 TSS67 chr1:3299691-3299733 - - 0 0 0 OK 0 0 0 OK TSS68 - - XLOC_000062 Xkr4 TSS68 chr1:3300051-3300078 - - 0 0 0 OK 0 0 0 OK TSS69 - - XLOC_000063 Xkr4 TSS69 chr1:3307748-3307775 - - 0 0 0 OK 0 0 0 OK -TSS7 - - XLOC_000007 - TSS7 chr1:3189810-3190789 - - 199608 33901.5 365315 OK 299412 183619 415206 OK +TSS7 - - XLOC_000007 - TSS7 chr1:3189810-3190789 - - 358326 135086 581565 OK 522345 410780 633911 OK TSS70 - - XLOC_000064 Xkr4 TSS70 chr1:3318620-3318647 - - 0 0 0 OK 0 0 0 OK TSS71 - - XLOC_000065 Xkr4 TSS71 chr1:3318999-3319051 - - 0 0 0 OK 0 0 0 OK TSS72 - - XLOC_000066 Xkr4 TSS72 chr1:3330527-3330554 - - 0 0 0 OK 0 0 0 OK -TSS73 - - XLOC_000067 Xkr4 TSS73 chr1:3351240-3351311 - - 4.27915e+06 0 1.71021e+07 OK 0 0 0 OK -TSS74 - - XLOC_000068 Xkr4 TSS74 chr1:3355887-3356119 - - 281197 0 1.06014e+06 OK 0 0 0 OK -TSS75 - - XLOC_000069 Xkr4 TSS75 chr1:3356180-3356225 - - 5.72196e+07 0 2.28684e+08 OK 0 0 0 OK -TSS76 - - XLOC_000070 Xkr4 TSS76 chr1:3363076-3363176 - - 2.1224e+06 0 7.19579e+06 OK 0 0 0 OK +TSS73 - - XLOC_000067 Xkr4 TSS73 chr1:3351240-3351311 - - 7.68169e+06 0 2.94088e+07 OK 0 0 0 OK +TSS74 - - XLOC_000068 Xkr4 TSS74 chr1:3355887-3356119 - - 504790 0 1.59712e+06 OK 0 0 0 OK +TSS75 - - XLOC_000069 Xkr4 TSS75 chr1:3356180-3356225 - - 1.02717e+08 0 3.93246e+08 OK 0 0 0 OK +TSS76 - - XLOC_000070 Xkr4 TSS76 chr1:3363076-3363176 - - 3.81001e+06 0 1.38903e+07 OK 0 0 0 OK TSS77 - - XLOC_000071 Xkr4 TSS77 chr1:3363214-3363278 - - 0 0 0 OK 0 0 0 OK -TSS78 - - XLOC_000072 Xkr4 TSS78 chr1:3363387-3363446 - - 3.08417e+07 0 1.03214e+08 OK 0 0 0 OK +TSS78 - - XLOC_000072 Xkr4 TSS78 chr1:3363387-3363446 - - 5.53654e+07 0 1.77783e+08 OK 0 0 0 OK TSS79 - - XLOC_000073 Xkr4 TSS79 chr1:3363753-3363849 - - 0 0 0 OK 0 0 0 OK -TSS80 - - XLOC_000074 Xkr4 TSS80 chr1:3364871-3364919 - - 3.50371e+07 0 1.40029e+08 OK 0 0 0 OK +TSS80 - - XLOC_000074 Xkr4 TSS80 chr1:3364871-3364919 - - 6.28966e+07 0 2.40795e+08 OK 0 0 0 OK TSS81 - - XLOC_000075 Xkr4 TSS81 chr1:3367135-3367162 - - 0 0 0 OK 0 0 0 OK TSS82 - - XLOC_000076 Xkr4 TSS82 chr1:3367210-3367237 - - 0 0 0 OK 0 0 0 OK TSS83 - - XLOC_000077 Xkr4 TSS83 chr1:3367333-3367382 - - 0 0 0 OK 0 0 0 OK
--- a/test-data/cuffdiff_out9.txt Thu Jan 16 13:13:52 2014 -0500 +++ b/test-data/cuffdiff_out9.txt Fri Dec 19 11:57:43 2014 -0500 @@ -5,85 +5,85 @@ TSS13 XLOC_000010 - chr1:3192250-3192336 q1 q2 NOTEST 0 0 0 0 1 1 no TSS14 XLOC_000011 - chr1:3192441-3192494 q1 q2 NOTEST 0 0 0 0 1 1 no TSS15 XLOC_000012 - chr1:3192550-3192629 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS16 XLOC_000013 - chr1:3192649-3192676 q1 q2 LOWDATA 0 0 0 0 0 1 no -TSS17 XLOC_000014 - chr1:3192731-3192811 q1 q2 LOWDATA 0 0 0 0 0 1 no +TSS16 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS17 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 1 1 no TSS18 XLOC_000015 - chr1:3192940-3193042 q1 q2 NOTEST 0 0 0 0 1 1 no TSS19 XLOC_000016 - chr1:3194185-3194226 q1 q2 NOTEST 0 0 0 0 1 1 no TSS2 XLOC_000002 - chr1:3111449-3111490 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS20 XLOC_000017 - chr1:3194302-3194329 q1 q2 LOWDATA 0 0 0 0 0 1 no -TSS21 XLOC_000018 - chr1:3194706-3194733 q1 q2 LOWDATA 0 0 0 0 0 1 no -TSS22 XLOC_000019 - chr1:3195083-3195110 q1 q2 LOWDATA 0 0 0 0 0 1 no -TSS23 XLOC_000020 - chr1:3195450-3195477 q1 q2 LOWDATA 0 0 0 0 0 1 no -TSS24 XLOC_000021 - chr1:3197089-3197116 q1 q2 LOWDATA 0 0 0 0 0 1 no -TSS25 XLOC_000022 - chr1:3197246-3197273 q1 q2 LOWDATA 0 0 0 0 0 1 no -TSS26 XLOC_000023 - chr1:3197346-3197373 q1 q2 LOWDATA 0 0 0 0 0 1 no -TSS27 XLOC_000024 - chr1:3197425-3197452 q1 q2 LOWDATA 0 0 0 0 0 1 no +TSS20 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS21 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS22 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS23 XLOC_000020 - chr1:3195450-3195477 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS24 XLOC_000021 - chr1:3197089-3197116 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS25 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS26 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS27 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 1 1 no TSS28 XLOC_000025 - chr1:3200022-3200191 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS29 XLOC_000026 - chr1:3200325-3200352 q1 q2 LOWDATA 0 0 0 0 0 1 no -TSS3 XLOC_000003 - chr1:3111545-3111576 q1 q2 LOWDATA 0 0 0 0 0 1 no -TSS30 XLOC_000027 - chr1:3200430-3200457 q1 q2 LOWDATA 0 0 0 0 0 1 no -TSS31 XLOC_000028 - chr1:3201007-3201039 q1 q2 LOWDATA 0 0 0 0 0 1 no +TSS29 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS3 XLOC_000003 - chr1:3111545-3111576 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS30 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS31 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 1 1 no TSS32 XLOC_000029 - chr1:3201077-3201481 q1 q2 NOTEST 0 0 0 0 1 1 no TSS33 XLOC_000030 - chr1:3201596-3201666 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS34 XLOC_000031 - chr1:3201672-3201699 q1 q2 LOWDATA 0 0 0 0 0 1 no +TSS34 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 1 1 no TSS35 XLOC_000032 - chr1:3201725-3201809 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS36 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 LOWDATA 0 0 0 0 0 1 no +TSS36 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 1 1 no TSS37 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 NOTEST 0 0 0 0 1 1 no TSS38 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 NOTEST 0 0 0 0 1 1 no TSS39 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS4 XLOC_000004 - chr1:3174765-3174792 q1 q2 LOWDATA 0 0 0 0 0 1 no -TSS40 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 NOTEST 0 0 0.249947 0 0.557805 1 no -TSS41 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 LOWDATA 0 0 0 0 0 1 no -TSS42 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 LOWDATA 0 0 0 0 0 1 no +TSS4 XLOC_000004 - chr1:3174765-3174792 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS40 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 NOTEST 0 0 0.249947 0 0.5526 1 no +TSS41 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS42 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 1 1 no TSS43 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS44 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 LOWDATA 0 0 0 0 0 1 no +TSS44 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 1 1 no TSS45 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 NOTEST 0 0 0 0 1 1 no TSS46 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 NOTEST 0 0 0 0 1 1 no TSS47 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS48 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 LOWDATA 0 0 0 0 0 1 no +TSS48 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 1 1 no TSS49 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS5 XLOC_000005 - chr1:3187401-3187428 q1 q2 LOWDATA 0 0 0 0 0 1 no -TSS50 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 LOWDATA 0 0 0 0 0 1 no -TSS51 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 LOWDATA 0 0 0 0 0 1 no +TSS5 XLOC_000005 - chr1:3187401-3187428 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS50 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS51 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 1 1 no TSS52 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS54 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 LOWDATA 0 0 0 0 0 1 no -TSS55 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 LOWDATA 0 0 0 0 0 1 no +TSS54 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS55 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 1 1 no TSS56 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS57 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 LOWDATA 0 0 0 0 0 1 no -TSS58 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 LOWDATA 0 0 0 0 0 1 no -TSS59 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 LOWDATA 0 0 0 0 0 1 no -TSS6 XLOC_000006 - chr1:3188521-3188548 q1 q2 LOWDATA 0 0 0 0 0 1 no -TSS60 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 LOWDATA 0 0 0 0 0 1 no +TSS57 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS58 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS59 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS6 XLOC_000006 - chr1:3188521-3188548 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS60 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 1 1 no TSS61 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 NOTEST 0 0 0 0 1 1 no TSS62 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 NOTEST 0 0 0 0 1 1 no TSS63 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 NOTEST 0 0 0 0 1 1 no TSS65 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS66 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 LOWDATA 0 0 0 0 0 1 no -TSS67 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 LOWDATA 0 0 0 0 0 1 no -TSS68 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 LOWDATA 0 0 0 0 0 1 no -TSS69 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 LOWDATA 0 0 0 0 0 1 no +TSS66 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS67 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS68 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS69 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 1 1 no TSS7 XLOC_000007 - chr1:3189810-3190789 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS70 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 LOWDATA 0 0 0 0 0 1 no -TSS71 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 LOWDATA 0 0 0 0 0 1 no -TSS72 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 LOWDATA 0 0 0 0 0 1 no +TSS70 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS71 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS72 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 1 1 no TSS73 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 NOTEST 0 0 0 0 1 1 no TSS74 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 0 0 0 0 1 1 no TSS75 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 NOTEST 0 0 0 0 1 1 no TSS76 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS77 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 LOWDATA 0 0 0 0 0 1 no +TSS77 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 NOTEST 0 0 0 0 1 1 no TSS78 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS79 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 LOWDATA 0 0 0 0 0 1 no +TSS79 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 NOTEST 0 0 0 0 1 1 no TSS80 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS81 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 LOWDATA 0 0 0 0 0 1 no -TSS82 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 LOWDATA 0 0 0 0 0 1 no -TSS83 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 LOWDATA 0 0 0 0 0 1 no -TSS84 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 LOWDATA 0 0 0 0 0 1 no -TSS85 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 LOWDATA 0 0 0 0 0 1 no -TSS86 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 LOWDATA 0 0 0 0 0 1 no -TSS87 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 LOWDATA 0 0 0 0 0 1 no -TSS88 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 LOWDATA 0 0 0 0 0 1 no -TSS89 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 LOWDATA 0 0 0 0 0 1 no -TSS90 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 LOWDATA 0 0 0 0 0 1 no -TSS91 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 LOWDATA 0 0 0 0 0 1 no -TSS92 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 LOWDATA 0 0 0 0 0 1 no -TSS93 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 LOWDATA 0 0 0 0 0 1 no +TSS81 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS82 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS83 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS84 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS85 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS86 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS87 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS88 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS89 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS90 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS91 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS92 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 NOTEST 0 0 0 0 1 1 no +TSS93 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 NOTEST 0 0 0 0 1 1 no
--- a/tool_dependencies.xml Thu Jan 16 13:13:52 2014 -0500 +++ b/tool_dependencies.xml Fri Dec 19 11:57:43 2014 -0500 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="cufflinks" version="2.1.1"> - <repository changeset_revision="394b13717223" name="package_cufflinks_2_1_1" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + <package name="cufflinks" version="2.2.1"> + <repository changeset_revision="899067a260d1" name="package_cufflinks_2_2_1" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>