changeset 0:d0d26169cc2a draft

Uploaded
author devteam
date Wed, 26 Nov 2014 13:54:44 -0500
parents
children 6d8ab54229a0
files cuff_macros.xml cuffcompare_wrapper.py cuffcompare_wrapper.xml shed_upload.tar.gz test-data/cuffcompare_in1.gtf test-data/cuffcompare_in1_liftover_mapped.bed test-data/cuffcompare_in1_liftover_unmapped.bed test-data/cuffcompare_in1_mult_liftover_mapped.bed test-data/cuffcompare_in1_mult_liftover_unmapped.bed test-data/cuffcompare_in2.gtf test-data/cuffcompare_in3.gtf test-data/cuffcompare_out1.tmap test-data/cuffcompare_out2.refmap test-data/cuffcompare_out3.tmap test-data/cuffcompare_out4.refmap test-data/cuffcompare_out5.gtf test-data/cuffcompare_out6.tracking test-data/cuffcompare_out7.txt test-data/cuffmerge_out1.gtf tool-data/fasta_indexes.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml
diffstat 22 files changed, 1443 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cuff_macros.xml	Wed Nov 26 13:54:44 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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cuffcompare_wrapper.py	Wed Nov 26 13:54:44 2014 -0500
@@ -0,0 +1,136 @@
+#!/usr/bin/env python
+
+# Supports Cuffcompare versions v1.3.0 and newer.
+
+import optparse, os, shutil, subprocess, sys, tempfile
+
+def stop_err( msg ):
+    sys.stderr.write( '%s\n' % msg )
+    sys.exit()
+
+def __main__():
+    #Parse Command Line
+    parser = optparse.OptionParser()
+    parser.add_option( '-r', dest='ref_annotation', help='An optional "reference" annotation GTF. Each sample is matched against this file, and sample isoforms are tagged as overlapping, matching, or novel where appropriate. See the refmap and tmap output file descriptions below.' )
+    parser.add_option( '-R', action="store_true", dest='ignore_nonoverlap_reference', help='If -r was specified, this option causes cuffcompare to ignore reference transcripts that are not overlapped by any transcript in one of cuff1.gtf,...,cuffN.gtf. Useful for ignoring annotated transcripts that are not present in your RNA-Seq samples and thus adjusting the "sensitivity" calculation in the accuracy report written in the transcripts accuracy file' )
+    parser.add_option( '-Q', action="store_true", dest='ignore_nonoverlap_transfrag', help='If -r was specified, this option causes cuffcompare to consider only the input transcripts that overlap any of the reference transcripts (Sp correction); Warning: this will discard all "novel" loci!)' )
+
+    parser.add_option( '-s', dest='use_seq_data', action="store_true", help='Causes cuffcompare to look into for fasta files with the underlying genomic sequences (one file per contig) against which your reads were aligned for some optional classification functions. For example, Cufflinks transcripts consisting mostly of lower-case bases are classified as repeats. Note that <seq_dir> must contain one fasta file per reference chromosome, and each file must be named after the chromosome, and have a .fa or .fasta extension.')
+    
+    parser.add_option( '-M', action="store_true", dest='discard_single_exon_all', help='discard (ignore) single-exon transfrags and reference transcript')
+    parser.add_option( '-N', action="store_true", dest='discard_single_exon_ref', help='discard (ignore) single-exon reference transcripts')
+    parser.add_option( '-e', dest='max_dist_exon', help='Max. Distance for assessing exon accuracy" help="max. distance (range) allowed from free ends of terminal exons of reference transcripts when assessing exon accuracy. Default: 100')
+    parser.add_option( '-d', dest='max_dist_group', help='Max.Distance for transcript grouping" help="max. distance (range) for grouping transcript start sites. Default: 100')
+    parser.add_option( '-F', action="store_true", dest='discard_redundant_intron_transfrags', help='Discard intron-redundant transfrags if they share the 5-prime end (if they differ only at the 3-prime end)')
+
+    # Wrapper / Galaxy options.
+    parser.add_option( '', '--index', dest='index', help='The path of the reference genome' )
+    parser.add_option( '', '--ref_file', dest='ref_file', help='The reference dataset from the history' )
+    
+    # Outputs.
+    parser.add_option( '', '--combined-transcripts', dest='combined_transcripts' )
+    
+    (options, args) = parser.parse_args()
+    
+    # output version # of tool
+    try:
+        tmp = tempfile.NamedTemporaryFile().name
+        tmp_stdout = open( tmp, 'wb' )
+        proc = subprocess.Popen( args='cuffcompare 2>&1', shell=True, stdout=tmp_stdout )
+        tmp_stdout.close()
+        returncode = proc.wait()
+        stdout = None
+        for line in open( tmp_stdout.name, 'rb' ):
+            if line.lower().find( 'cuffcompare v' ) >= 0:
+                stdout = line.strip()
+                break
+        if stdout:
+            sys.stdout.write( '%s\n' % stdout )
+        else:
+            raise Exception
+    except:
+        sys.stdout.write( 'Could not determine Cuffcompare version\n' )
+        
+    # Set/link to sequence file.
+    if options.use_seq_data:
+        if options.ref_file:
+            # Sequence data from history.
+            # Create symbolic link to ref_file so that index will be created in working directory.
+            seq_path = "ref.fa"
+            os.symlink( options.ref_file, seq_path  )
+        else:
+            if not os.path.exists( options.index ):
+                stop_err( 'Reference genome %s not present, request it by reporting this error.' % options.index )
+            seq_path = options.index
+    
+    # Build command.
+    
+    # Base.
+    cmd = "cuffcompare -o cc_output "
+    
+    # Add options.
+    if options.ref_annotation:
+        cmd += " -r %s " % options.ref_annotation
+    if options.ignore_nonoverlap_reference:
+        cmd += " -R "
+    if options.ignore_nonoverlap_transfrag:
+	cmd += " -Q "
+    if options.use_seq_data:
+        cmd += " -s %s " % seq_path
+    if options.discard_single_exon_all:
+	cmd += " -M "
+    if options.discard_single_exon_ref:
+	cmd += " -N "
+    if options.max_dist_exon:
+	cmd += " -e %i " % int( options.max_dist_exon )
+    if options.max_dist_group:
+	cmd += " -d %i " % int( options.max_dist_group )
+    if options.discard_redundant_intron_transfrags: 
+	cmd += " -F "
+    # Add input files.
+        
+    # Need to symlink inputs so that output files are written to temp directory.
+    for i, arg in enumerate( args ):
+        input_file_name = "./input%i" % ( i+1 )
+        os.symlink( arg, input_file_name )
+        cmd += "%s " % input_file_name
+
+    # Debugging.
+    print cmd
+    
+    # Run command.
+    try:        
+        tmp_name = tempfile.NamedTemporaryFile( dir="." ).name
+        tmp_stderr = open( tmp_name, 'wb' )
+        proc = subprocess.Popen( args=cmd, shell=True, stderr=tmp_stderr.fileno() )
+        returncode = proc.wait()
+        tmp_stderr.close()
+        
+        # Get stderr, allowing for case where it's very large.
+        tmp_stderr = open( tmp_name, 'rb' )
+        stderr = ''
+        buffsize = 1048576
+        try:
+            while True:
+                stderr += tmp_stderr.read( buffsize )
+                if not stderr or len( stderr ) % buffsize != 0:
+                    break
+        except OverflowError:
+            pass
+        tmp_stderr.close()
+        
+        # Error checking.
+        if returncode != 0:
+            raise Exception, stderr
+            
+        # Copy outputs.
+        shutil.copyfile( "cc_output.combined.gtf" , options.combined_transcripts )    
+            
+        # check that there are results in the output file
+        cc_output_fname = "cc_output.stats"
+        if len( open( cc_output_fname, 'rb' ).read().strip() ) == 0:
+            raise Exception, 'The main output file is empty, there may be an error with your input file or settings.'
+    except Exception, e:
+        stop_err( 'Error running cuffcompare. ' + str( e ) )
+        
+if __name__=="__main__": __main__()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cuffcompare_wrapper.xml	Wed Nov 26 13:54:44 2014 -0500
@@ -0,0 +1,253 @@
+<tool id="cuffcompare" name="Cuffcompare" version="2.2.1.0">
+    <description>compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments</description>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <macros>
+      <import>cuff_macros.xml</import>
+    </macros>
+    <version_command>cuffcompare 2>&amp;1 | head -n 1</version_command>
+    <command interpreter="python">
+        cuffcompare_wrapper.py 
+            ## Use annotation reference?
+            #if $annotation.use_ref_annotation == "Yes":
+                -r $annotation.reference_annotation
+                #if $annotation.ignore_nonoverlapping_reference:
+                    -R
+                #end if
+                #if $annotation.ignore_nonoverlapping_transfrags:
+                    -Q
+                #end if
+
+            #end if
+            
+            ## Use sequence data?
+            #if $seq_data.use_seq_data == "Yes":
+            -s
+                #if $seq_data.seq_source.index_source == "history":
+                    --ref_file=$seq_data.seq_source.ref_file
+                #else:
+                    --index=${seq_data.seq_source.index.fields.path}
+                #end if
+            #end if
+            
+            $discard_single_exon
+
+            -e $max_dist_exon
+            -d $max_dist_group
+
+            #if $discard_intron_redundant_transfrags:
+                -F
+            #end if 
+
+            ## Outputs.
+            --combined-transcripts=${transcripts_combined}
+
+            @CUFFLINKS_GTF_INPUTS@
+    </command>
+    <inputs>
+        <expand macro="cufflinks_gtf_inputs" />
+        <conditional name="annotation">
+            <param name="use_ref_annotation" type="select" label="Use Reference Annotation">
+                <option value="No">No</option>
+                <option value="Yes">Yes</option>
+            </param>
+            <when value="Yes">
+                <param format="gff3,gtf" name="reference_annotation" type="data" label="Reference Annotation" help="Requires an annotation file in GFF3 or GTF format."/>
+                <param name="ignore_nonoverlapping_reference" type="boolean" label="Ignore reference transcripts that are not overlapped by any input transfrags" help="consider only the reference transcripts that overlap any of the input transfrags (Sn correction)" />
+                <param name="ignore_nonoverlapping_transfrags" type="boolean" label="Ignore input transcripts that are not overlapped by any reference transcripts" help="consider only the input transcripts that overlap any of the reference transcripts (Sp correction). Warning: this will discard all 'novel' loci!" />
+            </when>
+            <when value="No">
+            </when>
+        </conditional>
+        <conditional name="seq_data">
+            <param name="use_seq_data" type="select" label="Use Sequence Data" 
+                help="Use sequence data for some optional classification functions, including the addition of the p_id attribute required by Cuffdiff.">
+                <option value="Yes">Yes</option>
+                <option value="No">No</option>
+            </param>
+            <when value="No"></when>
+            <when value="Yes">
+                <conditional name="seq_source">
+                  <param name="index_source" type="select" label="Choose the source for the reference list">
+                    <option value="cached">Locally cached</option>
+                    <option value="history">History</option>
+                  </param>
+                  <when value="cached">
+                    <param name="index" type="select" label="Using reference genome">
+                      <options from_data_table="fasta_indexes">
+                        <filter type="data_meta" ref="inputs" key="dbkey" column="1" />
+                        <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
+                      </options>
+                    </param>
+                  </when>
+                  <when value="history">
+                      <param name="ref_file" type="data" format="fasta" label="Using reference file" />
+                  </when>
+                </conditional>
+            </when>
+        </conditional>
+        <param type="select" name="discard_single_exon" label="discard (ignore) single-exon transcripts">
+                <option value="" selected="True">No</option>
+                <option value="-M">Discard single-exon transfrags and reference transcripts</option>
+                <option value="-N">Discard single-exon reference transcripts</option>
+        </param>
+        <param type="integer" name="max_dist_exon" value="100" label="Max. Distance for assessing exon accuracy" 
+            help="max. distance (range) allowed from free ends of terminal exons of reference transcripts when assessing exon accuracy. Default: 100" />
+        <param type="integer" name="max_dist_group" value="100" label="Max.Distance for transcript grouping" 
+            help="max. distance (range) for grouping transcript start sites. Default: 100" />
+        <param type="boolean" name="discard_intron_redundant_transfrags" label="discard intron-redundant transfrags sharing 5'" 
+            help="Discard intron-redundant transfrags if they share the 5' end (if they differ only at the 3' end)" />
+    </inputs>
+
+    <outputs>
+        <data format="txt" name="transcripts_accuracy" label="${tool.name} on ${on_string}: transcript accuracy" 
+            from_work_dir="cc_output.stats" />
+        <data format="tabular" name="input1_tmap" label="${tool.name} on ${on_string}: data ${inputs[0].hid} tmap file"
+            from_work_dir="cc_output.input1.tmap" />
+        <data format="tabular" name="input1_refmap" 
+              label="${tool.name} on ${on_string}: data ${inputs[0].hid} refmap file" 
+              from_work_dir="cc_output.input1.refmap">
+            <filter>annotation['use_ref_annotation'] == 'Yes'</filter>
+        </data>
+        <data format="tabular" name="input2_tmap" label="${tool.name} on ${on_string}: data ${inputs[1].hid} tmap file" from_work_dir="cc_output.input2.tmap">
+            <filter>@HAS_MULTIPLE_INPUTS@</filter>
+        </data>
+        <data format="tabular" name="input2_refmap" 
+              label="${tool.name} on ${on_string}: data ${inputs[1].hid} refmap file" 
+              from_work_dir="cc_output.input2.refmap">
+            <filter>annotation['use_ref_annotation'] == 'Yes' and @HAS_MULTIPLE_INPUTS@</filter>
+        </data>
+        <data format="tabular" name="transcripts_tracking" label="${tool.name} on ${on_string}: transcript tracking" from_work_dir="cc_output.tracking">
+            <filter>@HAS_MULTIPLE_INPUTS@</filter>
+        </data>
+        <data format="gtf" name="transcripts_combined" label="${tool.name} on ${on_string}: combined transcripts"/>
+    </outputs>
+
+    <tests>
+        <!-- 
+            cuffcompare -r cuffcompare_in3.gtf -R cuffcompare_in1.gtf cuffcompare_in2.gtf
+        -->
+        <test>
+            <param name="inputs" value="cuffcompare_in1.gtf,cuffcompare_in2.gtf" ftype="gtf"/>
+            <param name="use_ref_annotation" value="Yes"/>
+            <param name="reference_annotation" value="cuffcompare_in3.gtf" ftype="gtf"/>
+            <param name="ignore_nonoverlapping_reference" value="Yes"/>
+            <param name="ignore_nonoverlapping_transfrags" value="No"/>
+            <param name="use_seq_data" value="No"/>
+            <param name="discard_single_exon" value="" />
+            <param name="max_dist_exon" value="100" />
+            <param name="max_dist_group" value="100" />
+            <param name="discard_intron_redundant_transfrags" value="No" />
+            <!-- Line diffs are the result of different locations for input files; this cannot be fixed as cuffcompare outputs
+                full input path for each input. -->
+            <output name="transcripts_accuracy" file="cuffcompare_out7.txt" lines_diff="2"/>
+            <output name="input1_tmap" file="cuffcompare_out1.tmap"/>
+            <output name="input1_refmap" file="cuffcompare_out2.refmap"/>
+            <output name="input2_tmap" file="cuffcompare_out3.tmap"/>
+            <output name="input2_refmap" file="cuffcompare_out4.refmap"/>
+            <output name="transcripts_tracking" file="cuffcompare_out6.tracking"/>
+            <output name="transcripts_combined" file="cuffcompare_out5.gtf"/>
+        </test>
+    </tests>
+
+    <help>
+**Cuffcompare Overview**
+
+Cuffcompare is part of Cufflinks_. Cuffcompare helps you: (a) compare your assembled transcripts to a reference annotation and (b) track Cufflinks transcripts across multiple experiments (e.g. across a time course). 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/
+        
+------
+
+**Know what you are doing**
+
+.. class:: warningmark
+
+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#cuffcompare
+
+------
+
+**Input format**
+
+Cuffcompare takes Cufflinks' GTF output as input, and optionally can take a "reference" annotation (such as from Ensembl_)
+
+.. _Ensembl: http://www.ensembl.org 
+
+------
+
+**Outputs**
+
+Cuffcompare produces the following output files:
+
+Transcripts Accuracy File:
+
+Cuffcompare reports various statistics related to the "accuracy" of the transcripts in each sample when compared to the reference annotation data. The typical gene finding measures of "sensitivity" and "specificity" (as defined in Burset, M., Guigó, R. : Evaluation of gene structure prediction programs (1996) Genomics, 34 (3), pp. 353-367. doi: 10.1006/geno.1996.0298) are calculated at various levels (nucleotide, exon, intron, transcript, gene) for each input file and reported in this file. The Sn and Sp columns show specificity and sensitivity values at each level, while the fSn and fSp columns are "fuzzy" variants of these same accuracy calculations, allowing for a very small variation in exon boundaries to still be counted as a "match".
+
+Transcripts Combined File:
+
+Cuffcompare reports a GTF file containing the "union" of all transfrags in each sample. If a transfrag is present in both samples, it is thus reported once in the combined gtf. 
+
+Transcripts Tracking File:
+
+This file matches transcripts up between samples. Each row contains a transcript structure that is present in one or more input GTF files. Because the transcripts will generally have different IDs (unless you assembled your RNA-Seq reads against a reference transcriptome), cuffcompare examines the structure of each the transcripts, matching transcripts that agree on the coordinates and order of all of their introns, as well as strand. Matching transcripts are allowed to differ on the length of the first and last exons, since these lengths will naturally vary from sample to sample due to the random nature of sequencing.
+If you ran cuffcompare with the -r option, the first and second columns contain the closest matching reference transcript to the one described by each row.
+
+Here's an example of a line from the tracking file::
+
+  TCONS_00000045 XLOC_000023 Tcea|uc007afj.1        j        \
+     q1:exp.115|exp.115.0|100|3.061355|0.350242|0.350207 \
+     q2:60hr.292|60hr.292.0|100|4.094084|0.000000|0.000000
+
+In this example, a transcript present in the two input files, called exp.115.0 in the first and 60hr.292.0 in the second, doesn't match any reference transcript exactly, but shares exons with uc007afj.1, an isoform of the gene Tcea, as indicated by the class code j. The first three columns are as follows::
+
+  Column number   Column name               Example          Description
+  -----------------------------------------------------------------------
+  1               Cufflinks transfrag id    TCONS_00000045   A unique internal id for the transfrag
+  2               Cufflinks locus id        XLOC_000023      A unique internal id for the locus
+  3               Reference gene id         Tcea             The gene_name attribute of the reference GTF record for this transcript, or '-' if no reference transcript overlaps this Cufflinks transcript
+  4               Reference transcript id   uc007afj.1       The transcript_id attribute of the reference GTF record for this transcript, or '-' if no reference transcript overlaps this Cufflinks transcript
+  5               Class code                c                The type of match between the Cufflinks transcripts in column 6 and the reference transcript. See class codes
+  
+Each of the columns after the fifth have the following format:
+  qJ:gene_id|transcript_id|FMI|FPKM|conf_lo|conf_hi
+
+A transcript need be present in all samples to be reported in the tracking file. A sample not containing a transcript will have a "-" in its entry in the row for that transcript.
+
+Class Codes
+
+If you ran cuffcompare with the -r option, tracking rows will contain the following values. If you did not use -r, the rows will all contain "-" in their class code column::
+
+  Priority         Code           Description
+  ---------------------------------
+  1                 =               Match
+  2                 c               Contained        
+  3                 j               New isoform        
+  4                 e               A single exon transcript overlapping a reference exon and at least 10 bp of a reference intron, indicating a possible pre-mRNA fragment.        
+  5                 i               A single exon transcript falling entirely with a reference intron        
+  6                 r               Repeat. Currently determined by looking at the reference sequence and applied to transcripts where at least 50% of the bases are lower case        
+  7                 p               Possible polymerase run-on fragment        
+  8                 u               Unknown, intergenic transcript        
+  9                 o               Unknown, generic overlap with reference        
+  10             .               (.tracking file only, indicates multiple classifications)
+    
+-------
+
+**Settings**
+
+All of the options have a default value. You can change any of them. Most of the options in Cuffcompare have been implemented here.
+
+------
+
+**Cuffcompare parameter list**
+
+This is a list of implemented Cuffcompare options::
+
+  -r    An optional "reference" annotation GTF. Each sample is matched against this file, and sample isoforms are tagged as overlapping, matching, or novel where appropriate. See the refmap and tmap output file descriptions below.
+  -R    If -r was specified, this option causes cuffcompare to ignore reference transcripts that are not overlapped by any transcript in one of cuff1.gtf,...,cuffN.gtf. Useful for ignoring annotated transcripts that are not present in your RNA-Seq samples and thus adjusting the "sensitivity" calculation in the accuracy report written in the transcripts_accuracy file
+    </help>
+    <citations>
+        <citation type="doi">10.1038/nbt.1621</citation>
+    </citations>
+</tool>
Binary file shed_upload.tar.gz has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffcompare_in1.gtf	Wed Nov 26 13:54:44 2014 -0500
@@ -0,0 +1,100 @@
+chr1	Cufflinks	transcript	3111450	3111490	1000	.	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";
+chr1	Cufflinks	exon	3111450	3111490	1000	.	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";
+chr1	Cufflinks	transcript	3111546	3111576	1000	.	.	gene_id "CUFF.3"; transcript_id "CUFF.3.1"; FPKM "27.2556579354"; frac "1.000000"; conf_lo "0.000000"; conf_hi "65.800979"; cov "1.741935";
+chr1	Cufflinks	exon	3111546	3111576	1000	.	.	gene_id "CUFF.3"; transcript_id "CUFF.3.1"; exon_number "1"; FPKM "27.2556579354"; frac "1.000000"; conf_lo "0.000000"; conf_hi "65.800979"; cov "1.741935";
+chr1	Cufflinks	transcript	3200326	3200352	1000	.	.	gene_id "CUFF.5"; transcript_id "CUFF.5.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3200326	3200352	1000	.	.	gene_id "CUFF.5"; transcript_id "CUFF.5.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3200023	3200191	1000	.	.	gene_id "CUFF.7"; transcript_id "CUFF.7.1"; FPKM "9.9991171124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "19.998234"; cov "0.639053";
+chr1	Cufflinks	exon	3200023	3200191	1000	.	.	gene_id "CUFF.7"; transcript_id "CUFF.7.1"; exon_number "1"; FPKM "9.9991171124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "19.998234"; cov "0.639053";
+chr1	Cufflinks	transcript	3201078	3201481	1000	.	.	gene_id "CUFF.9"; transcript_id "CUFF.9.1"; FPKM "17.7768957078"; frac "1.000000"; conf_lo "9.153835"; conf_hi "26.399957"; cov "1.136139";
+chr1	Cufflinks	exon	3201078	3201481	1000	.	.	gene_id "CUFF.9"; transcript_id "CUFF.9.1"; exon_number "1"; FPKM "17.7768957078"; frac "1.000000"; conf_lo "9.153835"; conf_hi "26.399957"; cov "1.136139";
+chr1	Cufflinks	transcript	3201673	3201699	1000	.	.	gene_id "CUFF.11"; transcript_id "CUFF.11.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3201673	3201699	1000	.	.	gene_id "CUFF.11"; transcript_id "CUFF.11.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3204755	3204833	1000	.	.	gene_id "CUFF.13"; transcript_id "CUFF.13.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	exon	3204755	3204833	1000	.	.	gene_id "CUFF.13"; transcript_id "CUFF.13.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	transcript	3212214	3212292	1000	.	.	gene_id "CUFF.15"; transcript_id "CUFF.15.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	exon	3212214	3212292	1000	.	.	gene_id "CUFF.15"; transcript_id "CUFF.15.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	transcript	3213096	3213192	1000	.	.	gene_id "CUFF.17"; transcript_id "CUFF.17.1"; FPKM "8.7105710927"; frac "1.000000"; conf_lo "0.000000"; conf_hi "21.029179"; cov "0.556701";
+chr1	Cufflinks	exon	3213096	3213192	1000	.	.	gene_id "CUFF.17"; transcript_id "CUFF.17.1"; exon_number "1"; FPKM "8.7105710927"; frac "1.000000"; conf_lo "0.000000"; conf_hi "21.029179"; cov "0.556701";
+chr1	Cufflinks	transcript	3212368	3212439	1000	.	.	gene_id "CUFF.19"; transcript_id "CUFF.19.1"; FPKM "29.3376873610"; frac "1.000000"; conf_lo "3.097262"; conf_hi "55.578113"; cov "1.875000";
+chr1	Cufflinks	exon	3212368	3212439	1000	.	.	gene_id "CUFF.19"; transcript_id "CUFF.19.1"; exon_number "1"; FPKM "29.3376873610"; frac "1.000000"; conf_lo "3.097262"; conf_hi "55.578113"; cov "1.875000";
+chr1	Cufflinks	transcript	3243019	3243079	1000	.	.	gene_id "CUFF.21"; transcript_id "CUFF.21.1"; FPKM "13.8512359999"; frac "1.000000"; conf_lo "0.000000"; conf_hi "33.439842"; cov "0.885246";
+chr1	Cufflinks	exon	3243019	3243079	1000	.	.	gene_id "CUFF.21"; transcript_id "CUFF.21.1"; exon_number "1"; FPKM "13.8512359999"; frac "1.000000"; conf_lo "0.000000"; conf_hi "33.439842"; cov "0.885246";
+chr1	Cufflinks	transcript	3243348	3243401	1000	.	.	gene_id "CUFF.23"; transcript_id "CUFF.23.1"; FPKM "23.4701498888"; frac "1.000000"; conf_lo "0.000000"; conf_hi "50.571145"; cov "1.500000";
+chr1	Cufflinks	exon	3243348	3243401	1000	.	.	gene_id "CUFF.23"; transcript_id "CUFF.23.1"; exon_number "1"; FPKM "23.4701498888"; frac "1.000000"; conf_lo "0.000000"; conf_hi "50.571145"; cov "1.500000";
+chr1	Cufflinks	transcript	3242634	3242923	1000	.	.	gene_id "CUFF.25"; transcript_id "CUFF.25.1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "5.354270"; conf_hi "23.781089"; cov "0.931034";
+chr1	Cufflinks	exon	3242634	3242923	1000	.	.	gene_id "CUFF.25"; transcript_id "CUFF.25.1"; exon_number "1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "5.354270"; conf_hi "23.781089"; cov "0.931034";
+chr1	Cufflinks	transcript	3256975	3257011	1000	.	.	gene_id "CUFF.27"; transcript_id "CUFF.27.1"; FPKM "34.2537322701"; frac "1.000000"; conf_lo "0.000000"; conf_hi "73.806535"; cov "2.189189";
+chr1	Cufflinks	exon	3256975	3257011	1000	.	.	gene_id "CUFF.27"; transcript_id "CUFF.27.1"; exon_number "1"; FPKM "34.2537322701"; frac "1.000000"; conf_lo "0.000000"; conf_hi "73.806535"; cov "2.189189";
+chr1	Cufflinks	transcript	3189900	3190041	1000	.	.	gene_id "CUFF.29"; transcript_id "CUFF.29.1"; FPKM "107.1032192108"; frac "1.000000"; conf_lo "71.402146"; conf_hi "142.804292"; cov "6.845070";
+chr1	Cufflinks	exon	3189900	3190041	1000	.	.	gene_id "CUFF.29"; transcript_id "CUFF.29.1"; exon_number "1"; FPKM "107.1032192108"; frac "1.000000"; conf_lo "71.402146"; conf_hi "142.804292"; cov "6.845070";
+chr1	Cufflinks	transcript	3190273	3190303	1000	.	.	gene_id "CUFF.31"; transcript_id "CUFF.31.1"; FPKM "122.6504607091"; frac "1.000000"; conf_lo "40.883487"; conf_hi "204.417435"; cov "7.838710";
+chr1	Cufflinks	exon	3190273	3190303	1000	.	.	gene_id "CUFF.31"; transcript_id "CUFF.31.1"; exon_number "1"; FPKM "122.6504607091"; frac "1.000000"; conf_lo "40.883487"; conf_hi "204.417435"; cov "7.838710";
+chr1	Cufflinks	transcript	3190455	3190481	1000	.	.	gene_id "CUFF.33"; transcript_id "CUFF.33.1"; FPKM "109.5273661476"; frac "1.000000"; conf_lo "26.732460"; conf_hi "192.322273"; cov "7.000000";
+chr1	Cufflinks	exon	3190455	3190481	1000	.	.	gene_id "CUFF.33"; transcript_id "CUFF.33.1"; exon_number "1"; FPKM "109.5273661476"; frac "1.000000"; conf_lo "26.732460"; conf_hi "192.322273"; cov "7.000000";
+chr1	Cufflinks	transcript	3191539	3191669	1000	.	.	gene_id "CUFF.35"; transcript_id "CUFF.35.1"; FPKM "96.7471827476"; frac "1.000000"; conf_lo "61.420107"; conf_hi "132.074259"; cov "6.183206";
+chr1	Cufflinks	exon	3191539	3191669	1000	.	.	gene_id "CUFF.35"; transcript_id "CUFF.35.1"; exon_number "1"; FPKM "96.7471827476"; frac "1.000000"; conf_lo "61.420107"; conf_hi "132.074259"; cov "6.183206";
+chr1	Cufflinks	transcript	3191877	3191945	1000	.	.	gene_id "CUFF.37"; transcript_id "CUFF.37.1"; FPKM "104.0850125502"; frac "1.000000"; conf_lo "53.596365"; conf_hi "154.573660"; cov "6.652174";
+chr1	Cufflinks	exon	3191877	3191945	1000	.	.	gene_id "CUFF.37"; transcript_id "CUFF.37.1"; exon_number "1"; FPKM "104.0850125502"; frac "1.000000"; conf_lo "53.596365"; conf_hi "154.573660"; cov "6.652174";
+chr1	Cufflinks	transcript	3192442	3192494	1000	.	.	gene_id "CUFF.39"; transcript_id "CUFF.39.1"; FPKM "23.9129829055"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.525317"; cov "1.528302";
+chr1	Cufflinks	exon	3192442	3192494	1000	.	.	gene_id "CUFF.39"; transcript_id "CUFF.39.1"; exon_number "1"; FPKM "23.9129829055"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.525317"; cov "1.528302";
+chr1	Cufflinks	transcript	3192551	3192629	1000	.	.	gene_id "CUFF.41"; transcript_id "CUFF.41.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	exon	3192551	3192629	1000	.	.	gene_id "CUFF.41"; transcript_id "CUFF.41.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	transcript	3192732	3192811	1000	.	.	gene_id "CUFF.43"; transcript_id "CUFF.43.1"; FPKM "10.5615674500"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.497879"; cov "0.675000";
+chr1	Cufflinks	exon	3192732	3192811	1000	.	.	gene_id "CUFF.43"; transcript_id "CUFF.43.1"; exon_number "1"; FPKM "10.5615674500"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.497879"; cov "0.675000";
+chr1	Cufflinks	transcript	3192941	3193042	1000	.	.	gene_id "CUFF.45"; transcript_id "CUFF.45.1"; FPKM "20.7089557842"; frac "1.000000"; conf_lo "2.186303"; conf_hi "39.231609"; cov "1.323529";
+chr1	Cufflinks	exon	3192941	3193042	1000	.	.	gene_id "CUFF.45"; transcript_id "CUFF.45.1"; exon_number "1"; FPKM "20.7089557842"; frac "1.000000"; conf_lo "2.186303"; conf_hi "39.231609"; cov "1.323529";
+chr1	Cufflinks	transcript	3194186	3194226	1000	.	.	gene_id "CUFF.47"; transcript_id "CUFF.47.1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";
+chr1	Cufflinks	exon	3194186	3194226	1000	.	.	gene_id "CUFF.47"; transcript_id "CUFF.47.1"; exon_number "1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";
+chr1	Cufflinks	transcript	3194303	3194329	1000	.	.	gene_id "CUFF.49"; transcript_id "CUFF.49.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	exon	3194303	3194329	1000	.	.	gene_id "CUFF.49"; transcript_id "CUFF.49.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	transcript	3195084	3195110	1000	.	.	gene_id "CUFF.51"; transcript_id "CUFF.51.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3195084	3195110	1000	.	.	gene_id "CUFF.51"; transcript_id "CUFF.51.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3195451	3195477	1000	.	.	gene_id "CUFF.53"; transcript_id "CUFF.53.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3195451	3195477	1000	.	.	gene_id "CUFF.53"; transcript_id "CUFF.53.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3197090	3197116	1000	.	.	gene_id "CUFF.55"; transcript_id "CUFF.55.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3197090	3197116	1000	.	.	gene_id "CUFF.55"; transcript_id "CUFF.55.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3197247	3197273	1000	.	.	gene_id "CUFF.57"; transcript_id "CUFF.57.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	exon	3197247	3197273	1000	.	.	gene_id "CUFF.57"; transcript_id "CUFF.57.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	transcript	3197347	3197373	1000	.	.	gene_id "CUFF.59"; transcript_id "CUFF.59.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	exon	3197347	3197373	1000	.	.	gene_id "CUFF.59"; transcript_id "CUFF.59.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	transcript	3277191	3277218	1000	.	.	gene_id "CUFF.61"; transcript_id "CUFF.61.1"; FPKM "45.2638604998"; frac "1.000000"; conf_lo "0.000000"; conf_hi "97.530065"; cov "2.892857";
+chr1	Cufflinks	exon	3277191	3277218	1000	.	.	gene_id "CUFF.61"; transcript_id "CUFF.61.1"; exon_number "1"; FPKM "45.2638604998"; frac "1.000000"; conf_lo "0.000000"; conf_hi "97.530065"; cov "2.892857";
+chr1	Cufflinks	transcript	3278237	3278263	1000	.	.	gene_id "CUFF.63"; transcript_id "CUFF.63.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	exon	3278237	3278263	1000	.	.	gene_id "CUFF.63"; transcript_id "CUFF.63.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	transcript	3280687	3280741	1000	.	.	gene_id "CUFF.65"; transcript_id "CUFF.65.1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818";
+chr1	Cufflinks	exon	3280687	3280741	1000	.	.	gene_id "CUFF.65"; transcript_id "CUFF.65.1"; exon_number "1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818";
+chr1	Cufflinks	transcript	3290489	3290553	1000	.	.	gene_id "CUFF.67"; transcript_id "CUFF.67.1"; FPKM "12.9988522461"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.382005"; cov "0.830769";
+chr1	Cufflinks	exon	3290489	3290553	1000	.	.	gene_id "CUFF.67"; transcript_id "CUFF.67.1"; exon_number "1"; FPKM "12.9988522461"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.382005"; cov "0.830769";
+chr1	Cufflinks	transcript	3290940	3291023	1000	.	.	gene_id "CUFF.69"; transcript_id "CUFF.69.1"; FPKM "10.0586356666"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.283695"; cov "0.642857";
+chr1	Cufflinks	exon	3290940	3291023	1000	.	.	gene_id "CUFF.69"; transcript_id "CUFF.69.1"; exon_number "1"; FPKM "10.0586356666"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.283695"; cov "0.642857";
+chr1	Cufflinks	transcript	3291089	3291186	1000	.	.	gene_id "CUFF.71"; transcript_id "CUFF.71.1"; FPKM "8.6216877142"; frac "1.000000"; conf_lo "0.000000"; conf_hi "20.814595"; cov "0.551020";
+chr1	Cufflinks	exon	3291089	3291186	1000	.	.	gene_id "CUFF.71"; transcript_id "CUFF.71.1"; exon_number "1"; FPKM "8.6216877142"; frac "1.000000"; conf_lo "0.000000"; conf_hi "20.814595"; cov "0.551020";
+chr1	Cufflinks	transcript	3299610	3299664	1000	.	.	gene_id "CUFF.73"; transcript_id "CUFF.73.1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818";
+chr1	Cufflinks	exon	3299610	3299664	1000	.	.	gene_id "CUFF.73"; transcript_id "CUFF.73.1"; exon_number "1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818";
+chr1	Cufflinks	transcript	3300052	3300078	1000	.	.	gene_id "CUFF.75"; transcript_id "CUFF.75.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3300052	3300078	1000	.	.	gene_id "CUFF.75"; transcript_id "CUFF.75.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3319000	3319051	1000	.	.	gene_id "CUFF.77"; transcript_id "CUFF.77.1"; FPKM "16.2485653076"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.227507"; cov "1.038462";
+chr1	Cufflinks	exon	3319000	3319051	1000	.	.	gene_id "CUFF.77"; transcript_id "CUFF.77.1"; exon_number "1"; FPKM "16.2485653076"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.227507"; cov "1.038462";
+chr1	Cufflinks	transcript	3355888	3355914	1000	.	.	gene_id "CUFF.79"; transcript_id "CUFF.79.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3355888	3355914	1000	.	.	gene_id "CUFF.79"; transcript_id "CUFF.79.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3363215	3363278	1000	.	.	gene_id "CUFF.81"; transcript_id "CUFF.81.1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.872349"; cov "0.843750";
+chr1	Cufflinks	exon	3363215	3363278	1000	.	.	gene_id "CUFF.81"; transcript_id "CUFF.81.1"; exon_number "1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.872349"; cov "0.843750";
+chr1	Cufflinks	transcript	3363754	3363849	1000	.	.	gene_id "CUFF.83"; transcript_id "CUFF.83.1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "28.446269"; cov "0.843750";
+chr1	Cufflinks	exon	3363754	3363849	1000	.	.	gene_id "CUFF.83"; transcript_id "CUFF.83.1"; exon_number "1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "28.446269"; cov "0.843750";
+chr1	Cufflinks	transcript	3367136	3367162	1000	.	.	gene_id "CUFF.85"; transcript_id "CUFF.85.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3367136	3367162	1000	.	.	gene_id "CUFF.85"; transcript_id "CUFF.85.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3367334	3367382	1000	.	.	gene_id "CUFF.87"; transcript_id "CUFF.87.1"; FPKM "17.2433754285"; frac "1.000000"; conf_lo "0.000000"; conf_hi "41.629191"; cov "1.102041";
+chr1	Cufflinks	exon	3367334	3367382	1000	.	.	gene_id "CUFF.87"; transcript_id "CUFF.87.1"; exon_number "1"; FPKM "17.2433754285"; frac "1.000000"; conf_lo "0.000000"; conf_hi "41.629191"; cov "1.102041";
+chr1	Cufflinks	transcript	3377212	3377262	1000	.	.	gene_id "CUFF.89"; transcript_id "CUFF.89.1"; FPKM "16.5671646274"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.996674"; cov "1.058824";
+chr1	Cufflinks	exon	3377212	3377262	1000	.	.	gene_id "CUFF.89"; transcript_id "CUFF.89.1"; exon_number "1"; FPKM "16.5671646274"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.996674"; cov "1.058824";
+chr1	Cufflinks	transcript	3391326	3391352	1000	.	.	gene_id "CUFF.91"; transcript_id "CUFF.91.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3391326	3391352	1000	.	.	gene_id "CUFF.91"; transcript_id "CUFF.91.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3435842	3435880	1000	.	.	gene_id "CUFF.93"; transcript_id "CUFF.93.1"; FPKM "21.6647537435"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.303342"; cov "1.384615";
+chr1	Cufflinks	exon	3435842	3435880	1000	.	.	gene_id "CUFF.93"; transcript_id "CUFF.93.1"; exon_number "1"; FPKM "21.6647537435"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.303342"; cov "1.384615";
+chr1	Cufflinks	transcript	3447762	3447788	1000	.	.	gene_id "CUFF.95"; transcript_id "CUFF.95.1"; FPKM "46.9402997776"; frac "1.000000"; conf_lo "0.000000"; conf_hi "101.142289"; cov "3.000000";
+chr1	Cufflinks	exon	3447762	3447788	1000	.	.	gene_id "CUFF.95"; transcript_id "CUFF.95.1"; exon_number "1"; FPKM "46.9402997776"; frac "1.000000"; conf_lo "0.000000"; conf_hi "101.142289"; cov "3.000000";
+chr1	Cufflinks	transcript	3450907	3450965	1000	.	.	gene_id "CUFF.97"; transcript_id "CUFF.97.1"; FPKM "21.4811541355"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.285454"; cov "1.372881";
+chr1	Cufflinks	exon	3450907	3450965	1000	.	.	gene_id "CUFF.97"; transcript_id "CUFF.97.1"; exon_number "1"; FPKM "21.4811541355"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.285454"; cov "1.372881";
+chr1	Cufflinks	transcript	3451052	3451109	1000	.	.	gene_id "CUFF.99"; transcript_id "CUFF.99.1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.169489"; cov "0.931034";
+chr1	Cufflinks	exon	3451052	3451109	1000	.	.	gene_id "CUFF.99"; transcript_id "CUFF.99.1"; exon_number "1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.169489"; cov "0.931034";
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffcompare_in1_liftover_mapped.bed	Wed Nov 26 13:54:44 2014 -0500
@@ -0,0 +1,86 @@
+chr1	Cufflinks	transcript	3022555	3022596	1000	.	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";
+chr1	Cufflinks	exon	3022555	3022596	1000	.	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";
+chr1	Cufflinks	transcript	3117334	3117360	1000	.	.	gene_id "CUFF.5"; transcript_id "CUFF.5.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3117334	3117360	1000	.	.	gene_id "CUFF.5"; transcript_id "CUFF.5.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3117031	3117199	1000	.	.	gene_id "CUFF.7"; transcript_id "CUFF.7.1"; FPKM "9.9991171124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "19.998234"; cov "0.639053";
+chr1	Cufflinks	exon	3117031	3117199	1000	.	.	gene_id "CUFF.7"; transcript_id "CUFF.7.1"; exon_number "1"; FPKM "9.9991171124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "19.998234"; cov "0.639053";
+chr1	Cufflinks	transcript	3118118	3118521	1000	.	.	gene_id "CUFF.9"; transcript_id "CUFF.9.1"; FPKM "17.7768957078"; frac "1.000000"; conf_lo "9.153835"; conf_hi "26.399957"; cov "1.136139";
+chr1	Cufflinks	exon	3118118	3118521	1000	.	.	gene_id "CUFF.9"; transcript_id "CUFF.9.1"; exon_number "1"; FPKM "17.7768957078"; frac "1.000000"; conf_lo "9.153835"; conf_hi "26.399957"; cov "1.136139";
+chr1	Cufflinks	transcript	3118713	3118739	1000	.	.	gene_id "CUFF.11"; transcript_id "CUFF.11.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3118713	3118739	1000	.	.	gene_id "CUFF.11"; transcript_id "CUFF.11.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3121789	3121867	1000	.	.	gene_id "CUFF.13"; transcript_id "CUFF.13.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	exon	3121789	3121867	1000	.	.	gene_id "CUFF.13"; transcript_id "CUFF.13.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	transcript	3128503	3128581	1000	.	.	gene_id "CUFF.15"; transcript_id "CUFF.15.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	exon	3128503	3128581	1000	.	.	gene_id "CUFF.15"; transcript_id "CUFF.15.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	transcript	3129386	3129482	1000	.	.	gene_id "CUFF.17"; transcript_id "CUFF.17.1"; FPKM "8.7105710927"; frac "1.000000"; conf_lo "0.000000"; conf_hi "21.029179"; cov "0.556701";
+chr1	Cufflinks	exon	3129386	3129482	1000	.	.	gene_id "CUFF.17"; transcript_id "CUFF.17.1"; exon_number "1"; FPKM "8.7105710927"; frac "1.000000"; conf_lo "0.000000"; conf_hi "21.029179"; cov "0.556701";
+chr1	Cufflinks	transcript	3128657	3128728	1000	.	.	gene_id "CUFF.19"; transcript_id "CUFF.19.1"; FPKM "29.3376873610"; frac "1.000000"; conf_lo "3.097262"; conf_hi "55.578113"; cov "1.875000";
+chr1	Cufflinks	exon	3128657	3128728	1000	.	.	gene_id "CUFF.19"; transcript_id "CUFF.19.1"; exon_number "1"; FPKM "29.3376873610"; frac "1.000000"; conf_lo "3.097262"; conf_hi "55.578113"; cov "1.875000";
+chr1	Cufflinks	transcript	3162445	3162500	1000	.	.	gene_id "CUFF.23"; transcript_id "CUFF.23.1"; FPKM "23.4701498888"; frac "1.000000"; conf_lo "0.000000"; conf_hi "50.571145"; cov "1.500000";
+chr1	Cufflinks	exon	3162445	3162500	1000	.	.	gene_id "CUFF.23"; transcript_id "CUFF.23.1"; exon_number "1"; FPKM "23.4701498888"; frac "1.000000"; conf_lo "0.000000"; conf_hi "50.571145"; cov "1.500000";
+chr1	Cufflinks	transcript	3176998	3177034	1000	.	.	gene_id "CUFF.27"; transcript_id "CUFF.27.1"; FPKM "34.2537322701"; frac "1.000000"; conf_lo "0.000000"; conf_hi "73.806535"; cov "2.189189";
+chr1	Cufflinks	exon	3176998	3177034	1000	.	.	gene_id "CUFF.27"; transcript_id "CUFF.27.1"; exon_number "1"; FPKM "34.2537322701"; frac "1.000000"; conf_lo "0.000000"; conf_hi "73.806535"; cov "2.189189";
+chr1	Cufflinks	transcript	3107191	3107612	1000	.	.	gene_id "CUFF.29"; transcript_id "CUFF.29.1"; FPKM "107.1032192108"; frac "1.000000"; conf_lo "71.402146"; conf_hi "142.804292"; cov "6.845070";
+chr1	Cufflinks	exon	3107191	3107612	1000	.	.	gene_id "CUFF.29"; transcript_id "CUFF.29.1"; exon_number "1"; FPKM "107.1032192108"; frac "1.000000"; conf_lo "71.402146"; conf_hi "142.804292"; cov "6.845070";
+chr1	Cufflinks	transcript	3107844	3107874	1000	.	.	gene_id "CUFF.31"; transcript_id "CUFF.31.1"; FPKM "122.6504607091"; frac "1.000000"; conf_lo "40.883487"; conf_hi "204.417435"; cov "7.838710";
+chr1	Cufflinks	exon	3107844	3107874	1000	.	.	gene_id "CUFF.31"; transcript_id "CUFF.31.1"; exon_number "1"; FPKM "122.6504607091"; frac "1.000000"; conf_lo "40.883487"; conf_hi "204.417435"; cov "7.838710";
+chr1	Cufflinks	transcript	3108025	3108051	1000	.	.	gene_id "CUFF.33"; transcript_id "CUFF.33.1"; FPKM "109.5273661476"; frac "1.000000"; conf_lo "26.732460"; conf_hi "192.322273"; cov "7.000000";
+chr1	Cufflinks	exon	3108025	3108051	1000	.	.	gene_id "CUFF.33"; transcript_id "CUFF.33.1"; exon_number "1"; FPKM "109.5273661476"; frac "1.000000"; conf_lo "26.732460"; conf_hi "192.322273"; cov "7.000000";
+chr1	Cufflinks	transcript	3109111	3109241	1000	.	.	gene_id "CUFF.35"; transcript_id "CUFF.35.1"; FPKM "96.7471827476"; frac "1.000000"; conf_lo "61.420107"; conf_hi "132.074259"; cov "6.183206";
+chr1	Cufflinks	exon	3109111	3109241	1000	.	.	gene_id "CUFF.35"; transcript_id "CUFF.35.1"; exon_number "1"; FPKM "96.7471827476"; frac "1.000000"; conf_lo "61.420107"; conf_hi "132.074259"; cov "6.183206";
+chr1	Cufflinks	transcript	3109989	3110041	1000	.	.	gene_id "CUFF.39"; transcript_id "CUFF.39.1"; FPKM "23.9129829055"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.525317"; cov "1.528302";
+chr1	Cufflinks	exon	3109989	3110041	1000	.	.	gene_id "CUFF.39"; transcript_id "CUFF.39.1"; exon_number "1"; FPKM "23.9129829055"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.525317"; cov "1.528302";
+chr1	Cufflinks	transcript	3110098	3110176	1000	.	.	gene_id "CUFF.41"; transcript_id "CUFF.41.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	exon	3110098	3110176	1000	.	.	gene_id "CUFF.41"; transcript_id "CUFF.41.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	transcript	3110280	3110358	1000	.	.	gene_id "CUFF.43"; transcript_id "CUFF.43.1"; FPKM "10.5615674500"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.497879"; cov "0.675000";
+chr1	Cufflinks	exon	3110280	3110358	1000	.	.	gene_id "CUFF.43"; transcript_id "CUFF.43.1"; exon_number "1"; FPKM "10.5615674500"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.497879"; cov "0.675000";
+chr1	Cufflinks	transcript	3110488	3110589	1000	.	.	gene_id "CUFF.45"; transcript_id "CUFF.45.1"; FPKM "20.7089557842"; frac "1.000000"; conf_lo "2.186303"; conf_hi "39.231609"; cov "1.323529";
+chr1	Cufflinks	exon	3110488	3110589	1000	.	.	gene_id "CUFF.45"; transcript_id "CUFF.45.1"; exon_number "1"; FPKM "20.7089557842"; frac "1.000000"; conf_lo "2.186303"; conf_hi "39.231609"; cov "1.323529";
+chr1	Cufflinks	transcript	3111332	3111358	1000	.	.	gene_id "CUFF.49"; transcript_id "CUFF.49.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	exon	3111332	3111358	1000	.	.	gene_id "CUFF.49"; transcript_id "CUFF.49.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	transcript	3112113	3112139	1000	.	.	gene_id "CUFF.51"; transcript_id "CUFF.51.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3112113	3112139	1000	.	.	gene_id "CUFF.51"; transcript_id "CUFF.51.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3112479	3112505	1000	.	.	gene_id "CUFF.53"; transcript_id "CUFF.53.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3112479	3112505	1000	.	.	gene_id "CUFF.53"; transcript_id "CUFF.53.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3114116	3114142	1000	.	.	gene_id "CUFF.55"; transcript_id "CUFF.55.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3114116	3114142	1000	.	.	gene_id "CUFF.55"; transcript_id "CUFF.55.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3114273	3114299	1000	.	.	gene_id "CUFF.57"; transcript_id "CUFF.57.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	exon	3114273	3114299	1000	.	.	gene_id "CUFF.57"; transcript_id "CUFF.57.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	transcript	3114373	3114399	1000	.	.	gene_id "CUFF.59"; transcript_id "CUFF.59.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	exon	3114373	3114399	1000	.	.	gene_id "CUFF.59"; transcript_id "CUFF.59.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	transcript	3201794	3201848	1000	.	.	gene_id "CUFF.65"; transcript_id "CUFF.65.1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818";
+chr1	Cufflinks	exon	3201794	3201848	1000	.	.	gene_id "CUFF.65"; transcript_id "CUFF.65.1"; exon_number "1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818";
+chr1	Cufflinks	transcript	3211077	3211141	1000	.	.	gene_id "CUFF.67"; transcript_id "CUFF.67.1"; FPKM "12.9988522461"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.382005"; cov "0.830769";
+chr1	Cufflinks	exon	3211077	3211141	1000	.	.	gene_id "CUFF.67"; transcript_id "CUFF.67.1"; exon_number "1"; FPKM "12.9988522461"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.382005"; cov "0.830769";
+chr1	Cufflinks	transcript	3211528	3211611	1000	.	.	gene_id "CUFF.69"; transcript_id "CUFF.69.1"; FPKM "10.0586356666"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.283695"; cov "0.642857";
+chr1	Cufflinks	exon	3211528	3211611	1000	.	.	gene_id "CUFF.69"; transcript_id "CUFF.69.1"; exon_number "1"; FPKM "10.0586356666"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.283695"; cov "0.642857";
+chr1	Cufflinks	transcript	3211677	3211774	1000	.	.	gene_id "CUFF.71"; transcript_id "CUFF.71.1"; FPKM "8.6216877142"; frac "1.000000"; conf_lo "0.000000"; conf_hi "20.814595"; cov "0.551020";
+chr1	Cufflinks	exon	3211677	3211774	1000	.	.	gene_id "CUFF.71"; transcript_id "CUFF.71.1"; exon_number "1"; FPKM "8.6216877142"; frac "1.000000"; conf_lo "0.000000"; conf_hi "20.814595"; cov "0.551020";
+chr1	Cufflinks	transcript	3220199	3220253	1000	.	.	gene_id "CUFF.73"; transcript_id "CUFF.73.1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818";
+chr1	Cufflinks	exon	3220199	3220253	1000	.	.	gene_id "CUFF.73"; transcript_id "CUFF.73.1"; exon_number "1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818";
+chr1	Cufflinks	transcript	3220641	3220667	1000	.	.	gene_id "CUFF.75"; transcript_id "CUFF.75.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3220641	3220667	1000	.	.	gene_id "CUFF.75"; transcript_id "CUFF.75.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3240464	3240515	1000	.	.	gene_id "CUFF.77"; transcript_id "CUFF.77.1"; FPKM "16.2485653076"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.227507"; cov "1.038462";
+chr1	Cufflinks	exon	3240464	3240515	1000	.	.	gene_id "CUFF.77"; transcript_id "CUFF.77.1"; exon_number "1"; FPKM "16.2485653076"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.227507"; cov "1.038462";
+chr1	Cufflinks	transcript	3277601	3277627	1000	.	.	gene_id "CUFF.79"; transcript_id "CUFF.79.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3277601	3277627	1000	.	.	gene_id "CUFF.79"; transcript_id "CUFF.79.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3285318	3285381	1000	.	.	gene_id "CUFF.81"; transcript_id "CUFF.81.1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.872349"; cov "0.843750";
+chr1	Cufflinks	exon	3285318	3285381	1000	.	.	gene_id "CUFF.81"; transcript_id "CUFF.81.1"; exon_number "1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.872349"; cov "0.843750";
+chr1	Cufflinks	transcript	3285858	3285953	1000	.	.	gene_id "CUFF.83"; transcript_id "CUFF.83.1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "28.446269"; cov "0.843750";
+chr1	Cufflinks	exon	3285858	3285953	1000	.	.	gene_id "CUFF.83"; transcript_id "CUFF.83.1"; exon_number "1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "28.446269"; cov "0.843750";
+chr1	Cufflinks	transcript	3289268	3289294	1000	.	.	gene_id "CUFF.85"; transcript_id "CUFF.85.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3289268	3289294	1000	.	.	gene_id "CUFF.85"; transcript_id "CUFF.85.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3289466	3289514	1000	.	.	gene_id "CUFF.87"; transcript_id "CUFF.87.1"; FPKM "17.2433754285"; frac "1.000000"; conf_lo "0.000000"; conf_hi "41.629191"; cov "1.102041";
+chr1	Cufflinks	exon	3289466	3289514	1000	.	.	gene_id "CUFF.87"; transcript_id "CUFF.87.1"; exon_number "1"; FPKM "17.2433754285"; frac "1.000000"; conf_lo "0.000000"; conf_hi "41.629191"; cov "1.102041";
+chr1	Cufflinks	transcript	3300382	3300432	1000	.	.	gene_id "CUFF.89"; transcript_id "CUFF.89.1"; FPKM "16.5671646274"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.996674"; cov "1.058824";
+chr1	Cufflinks	exon	3300382	3300432	1000	.	.	gene_id "CUFF.89"; transcript_id "CUFF.89.1"; exon_number "1"; FPKM "16.5671646274"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.996674"; cov "1.058824";
+chr1	Cufflinks	transcript	3317446	3317472	1000	.	.	gene_id "CUFF.91"; transcript_id "CUFF.91.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3317446	3317472	1000	.	.	gene_id "CUFF.91"; transcript_id "CUFF.91.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3365246	3365284	1000	.	.	gene_id "CUFF.93"; transcript_id "CUFF.93.1"; FPKM "21.6647537435"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.303342"; cov "1.384615";
+chr1	Cufflinks	exon	3365246	3365284	1000	.	.	gene_id "CUFF.93"; transcript_id "CUFF.93.1"; exon_number "1"; FPKM "21.6647537435"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.303342"; cov "1.384615";
+chr1	Cufflinks	transcript	3377607	3377633	1000	.	.	gene_id "CUFF.95"; transcript_id "CUFF.95.1"; FPKM "46.9402997776"; frac "1.000000"; conf_lo "0.000000"; conf_hi "101.142289"; cov "3.000000";
+chr1	Cufflinks	exon	3377607	3377633	1000	.	.	gene_id "CUFF.95"; transcript_id "CUFF.95.1"; exon_number "1"; FPKM "46.9402997776"; frac "1.000000"; conf_lo "0.000000"; conf_hi "101.142289"; cov "3.000000";
+chr1	Cufflinks	transcript	3381259	3381317	1000	.	.	gene_id "CUFF.97"; transcript_id "CUFF.97.1"; FPKM "21.4811541355"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.285454"; cov "1.372881";
+chr1	Cufflinks	exon	3381259	3381317	1000	.	.	gene_id "CUFF.97"; transcript_id "CUFF.97.1"; exon_number "1"; FPKM "21.4811541355"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.285454"; cov "1.372881";
+chr1	Cufflinks	transcript	3381404	3381474	1000	.	.	gene_id "CUFF.99"; transcript_id "CUFF.99.1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.169489"; cov "0.931034";
+chr1	Cufflinks	exon	3381404	3381474	1000	.	.	gene_id "CUFF.99"; transcript_id "CUFF.99.1"; exon_number "1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.169489"; cov "0.931034";
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffcompare_in1_liftover_unmapped.bed	Wed Nov 26 13:54:44 2014 -0500
@@ -0,0 +1,28 @@
+# Deleted in new
+chr1	Cufflinks	transcript	3111546	3111576	1000	.	.	gene_id "CUFF.3"; transcript_id "CUFF.3.1"; FPKM "27.2556579354"; frac "1.000000"; conf_lo "0.000000"; conf_hi "65.800979"; cov "1.741935";
+# Deleted in new
+chr1	Cufflinks	exon	3111546	3111576	1000	.	.	gene_id "CUFF.3"; transcript_id "CUFF.3.1"; exon_number "1"; FPKM "27.2556579354"; frac "1.000000"; conf_lo "0.000000"; conf_hi "65.800979"; cov "1.741935";
+# Partially deleted in new
+chr1	Cufflinks	transcript	3243019	3243079	1000	.	.	gene_id "CUFF.21"; transcript_id "CUFF.21.1"; FPKM "13.8512359999"; frac "1.000000"; conf_lo "0.000000"; conf_hi "33.439842"; cov "0.885246";
+# Partially deleted in new
+chr1	Cufflinks	exon	3243019	3243079	1000	.	.	gene_id "CUFF.21"; transcript_id "CUFF.21.1"; exon_number "1"; FPKM "13.8512359999"; frac "1.000000"; conf_lo "0.000000"; conf_hi "33.439842"; cov "0.885246";
+# Partially deleted in new
+chr1	Cufflinks	transcript	3242634	3242923	1000	.	.	gene_id "CUFF.25"; transcript_id "CUFF.25.1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "5.354270"; conf_hi "23.781089"; cov "0.931034";
+# Partially deleted in new
+chr1	Cufflinks	exon	3242634	3242923	1000	.	.	gene_id "CUFF.25"; transcript_id "CUFF.25.1"; exon_number "1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "5.354270"; conf_hi "23.781089"; cov "0.931034";
+# Partially deleted in new
+chr1	Cufflinks	transcript	3191877	3191945	1000	.	.	gene_id "CUFF.37"; transcript_id "CUFF.37.1"; FPKM "104.0850125502"; frac "1.000000"; conf_lo "53.596365"; conf_hi "154.573660"; cov "6.652174";
+# Partially deleted in new
+chr1	Cufflinks	exon	3191877	3191945	1000	.	.	gene_id "CUFF.37"; transcript_id "CUFF.37.1"; exon_number "1"; FPKM "104.0850125502"; frac "1.000000"; conf_lo "53.596365"; conf_hi "154.573660"; cov "6.652174";
+# Partially deleted in new
+chr1	Cufflinks	transcript	3194186	3194226	1000	.	.	gene_id "CUFF.47"; transcript_id "CUFF.47.1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";
+# Partially deleted in new
+chr1	Cufflinks	exon	3194186	3194226	1000	.	.	gene_id "CUFF.47"; transcript_id "CUFF.47.1"; exon_number "1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";
+# Deleted in new
+chr1	Cufflinks	transcript	3277191	3277218	1000	.	.	gene_id "CUFF.61"; transcript_id "CUFF.61.1"; FPKM "45.2638604998"; frac "1.000000"; conf_lo "0.000000"; conf_hi "97.530065"; cov "2.892857";
+# Deleted in new
+chr1	Cufflinks	exon	3277191	3277218	1000	.	.	gene_id "CUFF.61"; transcript_id "CUFF.61.1"; exon_number "1"; FPKM "45.2638604998"; frac "1.000000"; conf_lo "0.000000"; conf_hi "97.530065"; cov "2.892857";
+# Deleted in new
+chr1	Cufflinks	transcript	3278237	3278263	1000	.	.	gene_id "CUFF.63"; transcript_id "CUFF.63.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+# Deleted in new
+chr1	Cufflinks	exon	3278237	3278263	1000	.	.	gene_id "CUFF.63"; transcript_id "CUFF.63.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffcompare_in1_mult_liftover_mapped.bed	Wed Nov 26 13:54:44 2014 -0500
@@ -0,0 +1,92 @@
+chr1	Cufflinks	transcript	3022555	3022596	1000	.	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";
+chr1	Cufflinks	exon	3022555	3022596	1000	.	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";
+chr1	Cufflinks	transcript	3117334	3117360	1000	.	.	gene_id "CUFF.5"; transcript_id "CUFF.5.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3117334	3117360	1000	.	.	gene_id "CUFF.5"; transcript_id "CUFF.5.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3117031	3117199	1000	.	.	gene_id "CUFF.7"; transcript_id "CUFF.7.1"; FPKM "9.9991171124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "19.998234"; cov "0.639053";
+chr1	Cufflinks	exon	3117031	3117199	1000	.	.	gene_id "CUFF.7"; transcript_id "CUFF.7.1"; exon_number "1"; FPKM "9.9991171124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "19.998234"; cov "0.639053";
+chr1	Cufflinks	transcript	3118118	3118521	1000	.	.	gene_id "CUFF.9"; transcript_id "CUFF.9.1"; FPKM "17.7768957078"; frac "1.000000"; conf_lo "9.153835"; conf_hi "26.399957"; cov "1.136139";
+chr1	Cufflinks	exon	3118118	3118521	1000	.	.	gene_id "CUFF.9"; transcript_id "CUFF.9.1"; exon_number "1"; FPKM "17.7768957078"; frac "1.000000"; conf_lo "9.153835"; conf_hi "26.399957"; cov "1.136139";
+chr1	Cufflinks	transcript	3118713	3118739	1000	.	.	gene_id "CUFF.11"; transcript_id "CUFF.11.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3118713	3118739	1000	.	.	gene_id "CUFF.11"; transcript_id "CUFF.11.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3121789	3121867	1000	.	.	gene_id "CUFF.13"; transcript_id "CUFF.13.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	exon	3121789	3121867	1000	.	.	gene_id "CUFF.13"; transcript_id "CUFF.13.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	transcript	3128503	3128581	1000	.	.	gene_id "CUFF.15"; transcript_id "CUFF.15.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	exon	3128503	3128581	1000	.	.	gene_id "CUFF.15"; transcript_id "CUFF.15.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	transcript	3129386	3129482	1000	.	.	gene_id "CUFF.17"; transcript_id "CUFF.17.1"; FPKM "8.7105710927"; frac "1.000000"; conf_lo "0.000000"; conf_hi "21.029179"; cov "0.556701";
+chr1	Cufflinks	exon	3129386	3129482	1000	.	.	gene_id "CUFF.17"; transcript_id "CUFF.17.1"; exon_number "1"; FPKM "8.7105710927"; frac "1.000000"; conf_lo "0.000000"; conf_hi "21.029179"; cov "0.556701";
+chr1	Cufflinks	transcript	3128657	3128728	1000	.	.	gene_id "CUFF.19"; transcript_id "CUFF.19.1"; FPKM "29.3376873610"; frac "1.000000"; conf_lo "3.097262"; conf_hi "55.578113"; cov "1.875000";
+chr1	Cufflinks	exon	3128657	3128728	1000	.	.	gene_id "CUFF.19"; transcript_id "CUFF.19.1"; exon_number "1"; FPKM "29.3376873610"; frac "1.000000"; conf_lo "3.097262"; conf_hi "55.578113"; cov "1.875000";
+chr1	Cufflinks	transcript	3162123	3162179	1000	.	.	gene_id "CUFF.21"; transcript_id "CUFF.21.1"; FPKM "13.8512359999"; frac "1.000000"; conf_lo "0.000000"; conf_hi "33.439842"; cov "0.885246";
+chr1	Cufflinks	exon	3162123	3162179	1000	.	.	gene_id "CUFF.21"; transcript_id "CUFF.21.1"; exon_number "1"; FPKM "13.8512359999"; frac "1.000000"; conf_lo "0.000000"; conf_hi "33.439842"; cov "0.885246";
+chr1	Cufflinks	transcript	3162445	3162500	1000	.	.	gene_id "CUFF.23"; transcript_id "CUFF.23.1"; FPKM "23.4701498888"; frac "1.000000"; conf_lo "0.000000"; conf_hi "50.571145"; cov "1.500000";
+chr1	Cufflinks	exon	3162445	3162500	1000	.	.	gene_id "CUFF.23"; transcript_id "CUFF.23.1"; exon_number "1"; FPKM "23.4701498888"; frac "1.000000"; conf_lo "0.000000"; conf_hi "50.571145"; cov "1.500000";
+chr1	Cufflinks	transcript	3161752	3162025	1000	.	.	gene_id "CUFF.25"; transcript_id "CUFF.25.1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "5.354270"; conf_hi "23.781089"; cov "0.931034";
+chr1	Cufflinks	exon	3161752	3162025	1000	.	.	gene_id "CUFF.25"; transcript_id "CUFF.25.1"; exon_number "1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "5.354270"; conf_hi "23.781089"; cov "0.931034";
+chr1	Cufflinks	transcript	3176998	3177034	1000	.	.	gene_id "CUFF.27"; transcript_id "CUFF.27.1"; FPKM "34.2537322701"; frac "1.000000"; conf_lo "0.000000"; conf_hi "73.806535"; cov "2.189189";
+chr1	Cufflinks	exon	3176998	3177034	1000	.	.	gene_id "CUFF.27"; transcript_id "CUFF.27.1"; exon_number "1"; FPKM "34.2537322701"; frac "1.000000"; conf_lo "0.000000"; conf_hi "73.806535"; cov "2.189189";
+chr1	Cufflinks	transcript	3107191	3107612	1000	.	.	gene_id "CUFF.29"; transcript_id "CUFF.29.1"; FPKM "107.1032192108"; frac "1.000000"; conf_lo "71.402146"; conf_hi "142.804292"; cov "6.845070";
+chr1	Cufflinks	exon	3107191	3107612	1000	.	.	gene_id "CUFF.29"; transcript_id "CUFF.29.1"; exon_number "1"; FPKM "107.1032192108"; frac "1.000000"; conf_lo "71.402146"; conf_hi "142.804292"; cov "6.845070";
+chr1	Cufflinks	transcript	3107844	3107874	1000	.	.	gene_id "CUFF.31"; transcript_id "CUFF.31.1"; FPKM "122.6504607091"; frac "1.000000"; conf_lo "40.883487"; conf_hi "204.417435"; cov "7.838710";
+chr1	Cufflinks	exon	3107844	3107874	1000	.	.	gene_id "CUFF.31"; transcript_id "CUFF.31.1"; exon_number "1"; FPKM "122.6504607091"; frac "1.000000"; conf_lo "40.883487"; conf_hi "204.417435"; cov "7.838710";
+chr1	Cufflinks	transcript	3108025	3108051	1000	.	.	gene_id "CUFF.33"; transcript_id "CUFF.33.1"; FPKM "109.5273661476"; frac "1.000000"; conf_lo "26.732460"; conf_hi "192.322273"; cov "7.000000";
+chr1	Cufflinks	exon	3108025	3108051	1000	.	.	gene_id "CUFF.33"; transcript_id "CUFF.33.1"; exon_number "1"; FPKM "109.5273661476"; frac "1.000000"; conf_lo "26.732460"; conf_hi "192.322273"; cov "7.000000";
+chr1	Cufflinks	transcript	3109111	3109241	1000	.	.	gene_id "CUFF.35"; transcript_id "CUFF.35.1"; FPKM "96.7471827476"; frac "1.000000"; conf_lo "61.420107"; conf_hi "132.074259"; cov "6.183206";
+chr1	Cufflinks	exon	3109111	3109241	1000	.	.	gene_id "CUFF.35"; transcript_id "CUFF.35.1"; exon_number "1"; FPKM "96.7471827476"; frac "1.000000"; conf_lo "61.420107"; conf_hi "132.074259"; cov "6.183206";
+chr1	Cufflinks	transcript	3109449	3109512	1000	.	.	gene_id "CUFF.37"; transcript_id "CUFF.37.1"; FPKM "104.0850125502"; frac "1.000000"; conf_lo "53.596365"; conf_hi "154.573660"; cov "6.652174";
+chr1	Cufflinks	exon	3109449	3109512	1000	.	.	gene_id "CUFF.37"; transcript_id "CUFF.37.1"; exon_number "1"; FPKM "104.0850125502"; frac "1.000000"; conf_lo "53.596365"; conf_hi "154.573660"; cov "6.652174";
+chr1	Cufflinks	transcript	3109989	3110041	1000	.	.	gene_id "CUFF.39"; transcript_id "CUFF.39.1"; FPKM "23.9129829055"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.525317"; cov "1.528302";
+chr1	Cufflinks	exon	3109989	3110041	1000	.	.	gene_id "CUFF.39"; transcript_id "CUFF.39.1"; exon_number "1"; FPKM "23.9129829055"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.525317"; cov "1.528302";
+chr1	Cufflinks	transcript	3110098	3110176	1000	.	.	gene_id "CUFF.41"; transcript_id "CUFF.41.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	exon	3110098	3110176	1000	.	.	gene_id "CUFF.41"; transcript_id "CUFF.41.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";
+chr1	Cufflinks	transcript	3110280	3110358	1000	.	.	gene_id "CUFF.43"; transcript_id "CUFF.43.1"; FPKM "10.5615674500"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.497879"; cov "0.675000";
+chr1	Cufflinks	exon	3110280	3110358	1000	.	.	gene_id "CUFF.43"; transcript_id "CUFF.43.1"; exon_number "1"; FPKM "10.5615674500"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.497879"; cov "0.675000";
+chr1	Cufflinks	transcript	3110488	3110589	1000	.	.	gene_id "CUFF.45"; transcript_id "CUFF.45.1"; FPKM "20.7089557842"; frac "1.000000"; conf_lo "2.186303"; conf_hi "39.231609"; cov "1.323529";
+chr1	Cufflinks	exon	3110488	3110589	1000	.	.	gene_id "CUFF.45"; transcript_id "CUFF.45.1"; exon_number "1"; FPKM "20.7089557842"; frac "1.000000"; conf_lo "2.186303"; conf_hi "39.231609"; cov "1.323529";
+chr1	Cufflinks	transcript	3111332	3111358	1000	.	.	gene_id "CUFF.49"; transcript_id "CUFF.49.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	exon	3111332	3111358	1000	.	.	gene_id "CUFF.49"; transcript_id "CUFF.49.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	transcript	3112113	3112139	1000	.	.	gene_id "CUFF.51"; transcript_id "CUFF.51.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3112113	3112139	1000	.	.	gene_id "CUFF.51"; transcript_id "CUFF.51.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3112479	3112505	1000	.	.	gene_id "CUFF.53"; transcript_id "CUFF.53.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3112479	3112505	1000	.	.	gene_id "CUFF.53"; transcript_id "CUFF.53.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3114116	3114142	1000	.	.	gene_id "CUFF.55"; transcript_id "CUFF.55.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3114116	3114142	1000	.	.	gene_id "CUFF.55"; transcript_id "CUFF.55.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3114273	3114299	1000	.	.	gene_id "CUFF.57"; transcript_id "CUFF.57.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	exon	3114273	3114299	1000	.	.	gene_id "CUFF.57"; transcript_id "CUFF.57.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	transcript	3114373	3114399	1000	.	.	gene_id "CUFF.59"; transcript_id "CUFF.59.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	exon	3114373	3114399	1000	.	.	gene_id "CUFF.59"; transcript_id "CUFF.59.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+chr1	Cufflinks	transcript	3201794	3201848	1000	.	.	gene_id "CUFF.65"; transcript_id "CUFF.65.1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818";
+chr1	Cufflinks	exon	3201794	3201848	1000	.	.	gene_id "CUFF.65"; transcript_id "CUFF.65.1"; exon_number "1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818";
+chr1	Cufflinks	transcript	3211077	3211141	1000	.	.	gene_id "CUFF.67"; transcript_id "CUFF.67.1"; FPKM "12.9988522461"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.382005"; cov "0.830769";
+chr1	Cufflinks	exon	3211077	3211141	1000	.	.	gene_id "CUFF.67"; transcript_id "CUFF.67.1"; exon_number "1"; FPKM "12.9988522461"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.382005"; cov "0.830769";
+chr1	Cufflinks	transcript	3211528	3211611	1000	.	.	gene_id "CUFF.69"; transcript_id "CUFF.69.1"; FPKM "10.0586356666"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.283695"; cov "0.642857";
+chr1	Cufflinks	exon	3211528	3211611	1000	.	.	gene_id "CUFF.69"; transcript_id "CUFF.69.1"; exon_number "1"; FPKM "10.0586356666"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.283695"; cov "0.642857";
+chr1	Cufflinks	transcript	3211677	3211774	1000	.	.	gene_id "CUFF.71"; transcript_id "CUFF.71.1"; FPKM "8.6216877142"; frac "1.000000"; conf_lo "0.000000"; conf_hi "20.814595"; cov "0.551020";
+chr1	Cufflinks	exon	3211677	3211774	1000	.	.	gene_id "CUFF.71"; transcript_id "CUFF.71.1"; exon_number "1"; FPKM "8.6216877142"; frac "1.000000"; conf_lo "0.000000"; conf_hi "20.814595"; cov "0.551020";
+chr1	Cufflinks	transcript	3220199	3220253	1000	.	.	gene_id "CUFF.73"; transcript_id "CUFF.73.1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818";
+chr1	Cufflinks	exon	3220199	3220253	1000	.	.	gene_id "CUFF.73"; transcript_id "CUFF.73.1"; exon_number "1"; FPKM "15.3622799272"; frac "1.000000"; conf_lo "0.000000"; conf_hi "37.087825"; cov "0.981818";
+chr1	Cufflinks	transcript	3220641	3220667	1000	.	.	gene_id "CUFF.75"; transcript_id "CUFF.75.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3220641	3220667	1000	.	.	gene_id "CUFF.75"; transcript_id "CUFF.75.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3240464	3240515	1000	.	.	gene_id "CUFF.77"; transcript_id "CUFF.77.1"; FPKM "16.2485653076"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.227507"; cov "1.038462";
+chr1	Cufflinks	exon	3240464	3240515	1000	.	.	gene_id "CUFF.77"; transcript_id "CUFF.77.1"; exon_number "1"; FPKM "16.2485653076"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.227507"; cov "1.038462";
+chr1	Cufflinks	transcript	3277601	3277627	1000	.	.	gene_id "CUFF.79"; transcript_id "CUFF.79.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3277601	3277627	1000	.	.	gene_id "CUFF.79"; transcript_id "CUFF.79.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3285318	3285381	1000	.	.	gene_id "CUFF.81"; transcript_id "CUFF.81.1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.872349"; cov "0.843750";
+chr1	Cufflinks	exon	3285318	3285381	1000	.	.	gene_id "CUFF.81"; transcript_id "CUFF.81.1"; exon_number "1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.872349"; cov "0.843750";
+chr1	Cufflinks	transcript	3285858	3285953	1000	.	.	gene_id "CUFF.83"; transcript_id "CUFF.83.1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "28.446269"; cov "0.843750";
+chr1	Cufflinks	exon	3285858	3285953	1000	.	.	gene_id "CUFF.83"; transcript_id "CUFF.83.1"; exon_number "1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "28.446269"; cov "0.843750";
+chr1	Cufflinks	transcript	3289268	3289294	1000	.	.	gene_id "CUFF.85"; transcript_id "CUFF.85.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3289268	3289294	1000	.	.	gene_id "CUFF.85"; transcript_id "CUFF.85.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3289466	3289514	1000	.	.	gene_id "CUFF.87"; transcript_id "CUFF.87.1"; FPKM "17.2433754285"; frac "1.000000"; conf_lo "0.000000"; conf_hi "41.629191"; cov "1.102041";
+chr1	Cufflinks	exon	3289466	3289514	1000	.	.	gene_id "CUFF.87"; transcript_id "CUFF.87.1"; exon_number "1"; FPKM "17.2433754285"; frac "1.000000"; conf_lo "0.000000"; conf_hi "41.629191"; cov "1.102041";
+chr1	Cufflinks	transcript	3300382	3300432	1000	.	.	gene_id "CUFF.89"; transcript_id "CUFF.89.1"; FPKM "16.5671646274"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.996674"; cov "1.058824";
+chr1	Cufflinks	exon	3300382	3300432	1000	.	.	gene_id "CUFF.89"; transcript_id "CUFF.89.1"; exon_number "1"; FPKM "16.5671646274"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.996674"; cov "1.058824";
+chr1	Cufflinks	transcript	3317446	3317472	1000	.	.	gene_id "CUFF.91"; transcript_id "CUFF.91.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	exon	3317446	3317472	1000	.	.	gene_id "CUFF.91"; transcript_id "CUFF.91.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";
+chr1	Cufflinks	transcript	3365246	3365284	1000	.	.	gene_id "CUFF.93"; transcript_id "CUFF.93.1"; FPKM "21.6647537435"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.303342"; cov "1.384615";
+chr1	Cufflinks	exon	3365246	3365284	1000	.	.	gene_id "CUFF.93"; transcript_id "CUFF.93.1"; exon_number "1"; FPKM "21.6647537435"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.303342"; cov "1.384615";
+chr1	Cufflinks	transcript	3377607	3377633	1000	.	.	gene_id "CUFF.95"; transcript_id "CUFF.95.1"; FPKM "46.9402997776"; frac "1.000000"; conf_lo "0.000000"; conf_hi "101.142289"; cov "3.000000";
+chr1	Cufflinks	exon	3377607	3377633	1000	.	.	gene_id "CUFF.95"; transcript_id "CUFF.95.1"; exon_number "1"; FPKM "46.9402997776"; frac "1.000000"; conf_lo "0.000000"; conf_hi "101.142289"; cov "3.000000";
+chr1	Cufflinks	transcript	3381259	3381317	1000	.	.	gene_id "CUFF.97"; transcript_id "CUFF.97.1"; FPKM "21.4811541355"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.285454"; cov "1.372881";
+chr1	Cufflinks	exon	3381259	3381317	1000	.	.	gene_id "CUFF.97"; transcript_id "CUFF.97.1"; exon_number "1"; FPKM "21.4811541355"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.285454"; cov "1.372881";
+chr1	Cufflinks	transcript	3381404	3381474	1000	.	.	gene_id "CUFF.99"; transcript_id "CUFF.99.1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.169489"; cov "0.931034";
+chr1	Cufflinks	exon	3381404	3381474	1000	.	.	gene_id "CUFF.99"; transcript_id "CUFF.99.1"; exon_number "1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.169489"; cov "0.931034";
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffcompare_in1_mult_liftover_unmapped.bed	Wed Nov 26 13:54:44 2014 -0500
@@ -0,0 +1,16 @@
+# Deleted in new
+chr1	Cufflinks	transcript	3111546	3111576	1000	.	.	gene_id "CUFF.3"; transcript_id "CUFF.3.1"; FPKM "27.2556579354"; frac "1.000000"; conf_lo "0.000000"; conf_hi "65.800979"; cov "1.741935";
+# Deleted in new
+chr1	Cufflinks	exon	3111546	3111576	1000	.	.	gene_id "CUFF.3"; transcript_id "CUFF.3.1"; exon_number "1"; FPKM "27.2556579354"; frac "1.000000"; conf_lo "0.000000"; conf_hi "65.800979"; cov "1.741935";
+# Partially deleted in new
+chr1	Cufflinks	transcript	3194186	3194226	1000	.	.	gene_id "CUFF.47"; transcript_id "CUFF.47.1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";
+# Partially deleted in new
+chr1	Cufflinks	exon	3194186	3194226	1000	.	.	gene_id "CUFF.47"; transcript_id "CUFF.47.1"; exon_number "1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";
+# Deleted in new
+chr1	Cufflinks	transcript	3277191	3277218	1000	.	.	gene_id "CUFF.61"; transcript_id "CUFF.61.1"; FPKM "45.2638604998"; frac "1.000000"; conf_lo "0.000000"; conf_hi "97.530065"; cov "2.892857";
+# Deleted in new
+chr1	Cufflinks	exon	3277191	3277218	1000	.	.	gene_id "CUFF.61"; transcript_id "CUFF.61.1"; exon_number "1"; FPKM "45.2638604998"; frac "1.000000"; conf_lo "0.000000"; conf_hi "97.530065"; cov "2.892857";
+# Deleted in new
+chr1	Cufflinks	transcript	3278237	3278263	1000	.	.	gene_id "CUFF.63"; transcript_id "CUFF.63.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
+# Deleted in new
+chr1	Cufflinks	exon	3278237	3278263	1000	.	.	gene_id "CUFF.63"; transcript_id "CUFF.63.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000";
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffcompare_in2.gtf	Wed Nov 26 13:54:44 2014 -0500
@@ -0,0 +1,100 @@
+chr1	Cufflinks	transcript	3174766	3174792	1000	.	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	exon	3174766	3174792	1000	.	.	gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	transcript	3187402	3187428	1000	.	.	gene_id "CUFF.3"; transcript_id "CUFF.3.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	exon	3187402	3187428	1000	.	.	gene_id "CUFF.3"; transcript_id "CUFF.3.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	transcript	3188522	3188548	1000	.	.	gene_id "CUFF.5"; transcript_id "CUFF.5.1"; FPKM "21.2266273824"; frac "1.000000"; conf_lo "0.000000"; conf_hi "59.889707"; cov "1.205672";
+chr1	Cufflinks	exon	3188522	3188548	1000	.	.	gene_id "CUFF.5"; transcript_id "CUFF.5.1"; exon_number "1"; FPKM "21.2266273824"; frac "1.000000"; conf_lo "0.000000"; conf_hi "59.889707"; cov "1.205672";
+chr1	Cufflinks	transcript	3190859	3191434	1000	.	.	gene_id "CUFF.7"; transcript_id "CUFF.7.1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "19.806349"; conf_hi "39.612698"; cov "1.687500";
+chr1	Cufflinks	exon	3190859	3191434	1000	.	.	gene_id "CUFF.7"; transcript_id "CUFF.7.1"; exon_number "1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "19.806349"; conf_hi "39.612698"; cov "1.687500";
+chr1	Cufflinks	transcript	3191513	3192077	1000	.	.	gene_id "CUFF.9"; transcript_id "CUFF.9.1"; FPKM "34.0729325807"; frac "1.000000"; conf_lo "23.364686"; conf_hi "44.781179"; cov "1.935341";
+chr1	Cufflinks	exon	3191513	3192077	1000	.	.	gene_id "CUFF.9"; transcript_id "CUFF.9.1"; exon_number "1"; FPKM "34.0729325807"; frac "1.000000"; conf_lo "23.364686"; conf_hi "44.781179"; cov "1.935341";
+chr1	Cufflinks	transcript	3189811	3190789	1000	.	.	gene_id "CUFF.11"; transcript_id "CUFF.11.1"; FPKM "32.5317765567"; frac "1.000000"; conf_lo "24.582998"; conf_hi "40.480555"; cov "1.847804";
+chr1	Cufflinks	exon	3189811	3190789	1000	.	.	gene_id "CUFF.11"; transcript_id "CUFF.11.1"; exon_number "1"; FPKM "32.5317765567"; frac "1.000000"; conf_lo "24.582998"; conf_hi "40.480555"; cov "1.847804";
+chr1	Cufflinks	transcript	3192251	3192336	1000	.	.	gene_id "CUFF.13"; transcript_id "CUFF.13.1"; FPKM "16.5820596576"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.729373"; cov "0.941860";
+chr1	Cufflinks	exon	3192251	3192336	1000	.	.	gene_id "CUFF.13"; transcript_id "CUFF.13.1"; exon_number "1"; FPKM "16.5820596576"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.729373"; cov "0.941860";
+chr1	Cufflinks	transcript	3192650	3192676	1000	.	.	gene_id "CUFF.15"; transcript_id "CUFF.15.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	exon	3192650	3192676	1000	.	.	gene_id "CUFF.15"; transcript_id "CUFF.15.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	transcript	3194707	3194733	1000	.	.	gene_id "CUFF.17"; transcript_id "CUFF.17.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	exon	3194707	3194733	1000	.	.	gene_id "CUFF.17"; transcript_id "CUFF.17.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	transcript	3197426	3197452	1000	.	.	gene_id "CUFF.19"; transcript_id "CUFF.19.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	exon	3197426	3197452	1000	.	.	gene_id "CUFF.19"; transcript_id "CUFF.19.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	transcript	3200431	3200457	1000	.	.	gene_id "CUFF.21"; transcript_id "CUFF.21.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	exon	3200431	3200457	1000	.	.	gene_id "CUFF.21"; transcript_id "CUFF.21.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	transcript	3200057	3200144	1000	.	.	gene_id "CUFF.23"; transcript_id "CUFF.23.1"; FPKM "16.2051946653"; frac "1.000000"; conf_lo "0.000000"; conf_hi "34.917342"; cov "0.920455";
+chr1	Cufflinks	exon	3200057	3200144	1000	.	.	gene_id "CUFF.23"; transcript_id "CUFF.23.1"; exon_number "1"; FPKM "16.2051946653"; frac "1.000000"; conf_lo "0.000000"; conf_hi "34.917342"; cov "0.920455";
+chr1	Cufflinks	transcript	3201161	3201187	1000	.	.	gene_id "CUFF.25"; transcript_id "CUFF.25.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	exon	3201161	3201187	1000	.	.	gene_id "CUFF.25"; transcript_id "CUFF.25.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	transcript	3201008	3201039	1000	.	.	gene_id "CUFF.26"; transcript_id "CUFF.26.1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "0.000000"; conf_hi "71.725135"; cov "1.687500";
+chr1	Cufflinks	exon	3201008	3201039	1000	.	.	gene_id "CUFF.26"; transcript_id "CUFF.26.1"; exon_number "1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "0.000000"; conf_hi "71.725135"; cov "1.687500";
+chr1	Cufflinks	transcript	3201597	3201666	1000	.	.	gene_id "CUFF.29"; transcript_id "CUFF.29.1"; FPKM "13.5814964814"; frac "1.000000"; conf_lo "0.000000"; conf_hi "32.788633"; cov "0.771429";
+chr1	Cufflinks	exon	3201597	3201666	1000	.	.	gene_id "CUFF.29"; transcript_id "CUFF.29.1"; exon_number "1"; FPKM "13.5814964814"; frac "1.000000"; conf_lo "0.000000"; conf_hi "32.788633"; cov "0.771429";
+chr1	Cufflinks	transcript	3201726	3201809	1000	.	.	gene_id "CUFF.31"; transcript_id "CUFF.31.1"; FPKM "22.6358274691"; frac "1.000000"; conf_lo "0.000000"; conf_hi "45.271655"; cov "1.285714";
+chr1	Cufflinks	exon	3201726	3201809	1000	.	.	gene_id "CUFF.31"; transcript_id "CUFF.31.1"; exon_number "1"; FPKM "22.6358274691"; frac "1.000000"; conf_lo "0.000000"; conf_hi "45.271655"; cov "1.285714";
+chr1	Cufflinks	transcript	3211522	3211561	1000	.	.	gene_id "CUFF.33"; transcript_id "CUFF.33.1"; FPKM "23.7676188425"; frac "1.000000"; conf_lo "0.000000"; conf_hi "57.380108"; cov "1.350000";
+chr1	Cufflinks	exon	3211522	3211561	1000	.	.	gene_id "CUFF.33"; transcript_id "CUFF.33.1"; exon_number "1"; FPKM "23.7676188425"; frac "1.000000"; conf_lo "0.000000"; conf_hi "57.380108"; cov "1.350000";
+chr1	Cufflinks	transcript	3212718	3212801	1000	.	.	gene_id "CUFF.35"; transcript_id "CUFF.35.1"; FPKM "11.3179137345"; frac "1.000000"; conf_lo "0.000000"; conf_hi "27.323861"; cov "0.642857";
+chr1	Cufflinks	exon	3212718	3212801	1000	.	.	gene_id "CUFF.35"; transcript_id "CUFF.35.1"; exon_number "1"; FPKM "11.3179137345"; frac "1.000000"; conf_lo "0.000000"; conf_hi "27.323861"; cov "0.642857";
+chr1	Cufflinks	transcript	3213119	3213242	1000	.	.	gene_id "CUFF.37"; transcript_id "CUFF.37.1"; FPKM "11.5004607302"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.780049"; cov "0.653226";
+chr1	Cufflinks	exon	3213119	3213242	1000	.	.	gene_id "CUFF.37"; transcript_id "CUFF.37.1"; exon_number "1"; FPKM "11.5004607302"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.780049"; cov "0.653226";
+chr1	Cufflinks	transcript	3240607	3240633	1000	.	.	gene_id "CUFF.39"; transcript_id "CUFF.39.1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000";
+chr1	Cufflinks	exon	3240607	3240633	1000	.	.	gene_id "CUFF.39"; transcript_id "CUFF.39.1"; exon_number "1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000";
+chr1	Cufflinks	transcript	3242480	3242512	1000	.	.	gene_id "CUFF.41"; transcript_id "CUFF.41.1"; FPKM "43.2138524409"; frac "1.000000"; conf_lo "0.000000"; conf_hi "93.112911"; cov "2.454545";
+chr1	Cufflinks	exon	3242480	3242512	1000	.	.	gene_id "CUFF.41"; transcript_id "CUFF.41.1"; exon_number "1"; FPKM "43.2138524409"; frac "1.000000"; conf_lo "0.000000"; conf_hi "93.112911"; cov "2.454545";
+chr1	Cufflinks	transcript	3242925	3243005	1000	.	.	gene_id "CUFF.43"; transcript_id "CUFF.43.1"; FPKM "23.4741914494"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.948383"; cov "1.333333";
+chr1	Cufflinks	exon	3242925	3243005	1000	.	.	gene_id "CUFF.43"; transcript_id "CUFF.43.1"; exon_number "1"; FPKM "23.4741914494"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.948383"; cov "1.333333";
+chr1	Cufflinks	transcript	3243109	3243154	1000	.	.	gene_id "CUFF.45"; transcript_id "CUFF.45.1"; FPKM "20.6674946457"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.895746"; cov "1.173913";
+chr1	Cufflinks	exon	3243109	3243154	1000	.	.	gene_id "CUFF.45"; transcript_id "CUFF.45.1"; exon_number "1"; FPKM "20.6674946457"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.895746"; cov "1.173913";
+chr1	Cufflinks	transcript	3254080	3254106	1000	.	.	gene_id "CUFF.47"; transcript_id "CUFF.47.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	exon	3254080	3254106	1000	.	.	gene_id "CUFF.47"; transcript_id "CUFF.47.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	transcript	3277156	3277182	1000	.	.	gene_id "CUFF.49"; transcript_id "CUFF.49.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	exon	3277156	3277182	1000	.	.	gene_id "CUFF.49"; transcript_id "CUFF.49.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	transcript	3277914	3278390	1000	.	.	gene_id "CUFF.51"; transcript_id "CUFF.51.1"; FPKM "14.9481879513"; frac "1.000000"; conf_lo "7.228977"; conf_hi "22.667399"; cov "0.849057";
+chr1	Cufflinks	exon	3277914	3278390	1000	.	.	gene_id "CUFF.51"; transcript_id "CUFF.51.1"; exon_number "1"; FPKM "14.9481879513"; frac "1.000000"; conf_lo "7.228977"; conf_hi "22.667399"; cov "0.849057";
+chr1	Cufflinks	transcript	3280118	3280144	1000	.	.	gene_id "CUFF.53"; transcript_id "CUFF.53.1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000";
+chr1	Cufflinks	exon	3280118	3280144	1000	.	.	gene_id "CUFF.53"; transcript_id "CUFF.53.1"; exon_number "1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000";
+chr1	Cufflinks	transcript	3280499	3280525	1000	.	.	gene_id "CUFF.55"; transcript_id "CUFF.55.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	exon	3280499	3280525	1000	.	.	gene_id "CUFF.55"; transcript_id "CUFF.55.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	transcript	3282505	3282531	1000	.	.	gene_id "CUFF.57"; transcript_id "CUFF.57.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	exon	3282505	3282531	1000	.	.	gene_id "CUFF.57"; transcript_id "CUFF.57.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	transcript	3282651	3282677	1000	.	.	gene_id "CUFF.59"; transcript_id "CUFF.59.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	exon	3282651	3282677	1000	.	.	gene_id "CUFF.59"; transcript_id "CUFF.59.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	transcript	3282761	3282832	1000	.	.	gene_id "CUFF.61"; transcript_id "CUFF.61.1"; FPKM "13.2042326903"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.877838"; cov "0.750000";
+chr1	Cufflinks	exon	3282761	3282832	1000	.	.	gene_id "CUFF.61"; transcript_id "CUFF.61.1"; exon_number "1"; FPKM "13.2042326903"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.877838"; cov "0.750000";
+chr1	Cufflinks	transcript	3284967	3284993	1000	.	.	gene_id "CUFF.63"; transcript_id "CUFF.63.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	exon	3284967	3284993	1000	.	.	gene_id "CUFF.63"; transcript_id "CUFF.63.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	transcript	3290799	3290859	1000	.	.	gene_id "CUFF.65"; transcript_id "CUFF.65.1"; FPKM "31.1706476623"; frac "1.000000"; conf_lo "0.000000"; conf_hi "62.341295"; cov "1.770492";
+chr1	Cufflinks	exon	3290799	3290859	1000	.	.	gene_id "CUFF.65"; transcript_id "CUFF.65.1"; exon_number "1"; FPKM "31.1706476623"; frac "1.000000"; conf_lo "0.000000"; conf_hi "62.341295"; cov "1.770492";
+chr1	Cufflinks	transcript	3299444	3299640	1000	.	.	gene_id "CUFF.67"; transcript_id "CUFF.67.1"; FPKM "15.6813507371"; frac "1.000000"; conf_lo "3.378764"; conf_hi "27.983938"; cov "0.890700";
+chr1	Cufflinks	exon	3299444	3299640	1000	.	.	gene_id "CUFF.67"; transcript_id "CUFF.67.1"; exon_number "1"; FPKM "15.6813507371"; frac "1.000000"; conf_lo "3.378764"; conf_hi "27.983938"; cov "0.890700";
+chr1	Cufflinks	transcript	3290920	3291273	1000	.	.	gene_id "CUFF.69"; transcript_id "CUFF.69.1"; FPKM "18.7992465421"; frac "1.000000"; conf_lo "8.750627"; conf_hi "28.847866"; cov "1.067797";
+chr1	Cufflinks	exon	3290920	3291273	1000	.	.	gene_id "CUFF.69"; transcript_id "CUFF.69.1"; exon_number "1"; FPKM "18.7992465421"; frac "1.000000"; conf_lo "8.750627"; conf_hi "28.847866"; cov "1.067797";
+chr1	Cufflinks	transcript	3299692	3299733	1000	.	.	gene_id "CUFF.71"; transcript_id "CUFF.71.1"; FPKM "22.6358274691"; frac "1.000000"; conf_lo "0.000000"; conf_hi "54.647722"; cov "1.285714";
+chr1	Cufflinks	exon	3299692	3299733	1000	.	.	gene_id "CUFF.71"; transcript_id "CUFF.71.1"; exon_number "1"; FPKM "22.6358274691"; frac "1.000000"; conf_lo "0.000000"; conf_hi "54.647722"; cov "1.285714";
+chr1	Cufflinks	transcript	3307749	3307775	1000	.	.	gene_id "CUFF.73"; transcript_id "CUFF.73.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	exon	3307749	3307775	1000	.	.	gene_id "CUFF.73"; transcript_id "CUFF.73.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	transcript	3318621	3318647	1000	.	.	gene_id "CUFF.75"; transcript_id "CUFF.75.1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000";
+chr1	Cufflinks	exon	3318621	3318647	1000	.	.	gene_id "CUFF.75"; transcript_id "CUFF.75.1"; exon_number "1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000";
+chr1	Cufflinks	transcript	3330528	3330554	1000	.	.	gene_id "CUFF.77"; transcript_id "CUFF.77.1"; FPKM "17.6056435870"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.816931"; cov "1.000000";
+chr1	Cufflinks	exon	3330528	3330554	1000	.	.	gene_id "CUFF.77"; transcript_id "CUFF.77.1"; exon_number "1"; FPKM "17.6056435870"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.816931"; cov "1.000000";
+chr1	Cufflinks	transcript	3351241	3351311	1000	.	.	gene_id "CUFF.79"; transcript_id "CUFF.79.1"; FPKM "13.3902077986"; frac "1.000000"; conf_lo "0.000000"; conf_hi "32.326821"; cov "0.760563";
+chr1	Cufflinks	exon	3351241	3351311	1000	.	.	gene_id "CUFF.79"; transcript_id "CUFF.79.1"; exon_number "1"; FPKM "13.3902077986"; frac "1.000000"; conf_lo "0.000000"; conf_hi "32.326821"; cov "0.760563";
+chr1	Cufflinks	transcript	3355908	3356119	1000	.	.	gene_id "CUFF.81"; transcript_id "CUFF.81.1"; FPKM "11.2111409634"; frac "1.000000"; conf_lo "1.183592"; conf_hi "21.238690"; cov "0.636792";
+chr1	Cufflinks	exon	3355908	3356119	1000	.	.	gene_id "CUFF.81"; transcript_id "CUFF.81.1"; exon_number "1"; FPKM "11.2111409634"; frac "1.000000"; conf_lo "1.183592"; conf_hi "21.238690"; cov "0.636792";
+chr1	Cufflinks	transcript	3356181	3356225	1000	.	.	gene_id "CUFF.83"; transcript_id "CUFF.83.1"; FPKM "21.1267723045"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.004540"; cov "1.200000";
+chr1	Cufflinks	exon	3356181	3356225	1000	.	.	gene_id "CUFF.83"; transcript_id "CUFF.83.1"; exon_number "1"; FPKM "21.1267723045"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.004540"; cov "1.200000";
+chr1	Cufflinks	transcript	3363077	3363176	1000	.	.	gene_id "CUFF.85"; transcript_id "CUFF.85.1"; FPKM "19.0140950740"; frac "1.000000"; conf_lo "0.000000"; conf_hi "38.028190"; cov "1.080000";
+chr1	Cufflinks	exon	3363077	3363176	1000	.	.	gene_id "CUFF.85"; transcript_id "CUFF.85.1"; exon_number "1"; FPKM "19.0140950740"; frac "1.000000"; conf_lo "0.000000"; conf_hi "38.028190"; cov "1.080000";
+chr1	Cufflinks	transcript	3363388	3363446	1000	.	.	gene_id "CUFF.87"; transcript_id "CUFF.87.1"; FPKM "24.1704598398"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.080103"; cov "1.372881";
+chr1	Cufflinks	exon	3363388	3363446	1000	.	.	gene_id "CUFF.87"; transcript_id "CUFF.87.1"; exon_number "1"; FPKM "24.1704598398"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.080103"; cov "1.372881";
+chr1	Cufflinks	transcript	3364872	3364919	1000	.	.	gene_id "CUFF.89"; transcript_id "CUFF.89.1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "0.000000"; conf_hi "64.015126"; cov "1.687500";
+chr1	Cufflinks	exon	3364872	3364919	1000	.	.	gene_id "CUFF.89"; transcript_id "CUFF.89.1"; exon_number "1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "0.000000"; conf_hi "64.015126"; cov "1.687500";
+chr1	Cufflinks	transcript	3367211	3367237	1000	.	.	gene_id "CUFF.91"; transcript_id "CUFF.91.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	exon	3367211	3367237	1000	.	.	gene_id "CUFF.91"; transcript_id "CUFF.91.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	transcript	3369581	3369607	1000	.	.	gene_id "CUFF.93"; transcript_id "CUFF.93.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	exon	3369581	3369607	1000	.	.	gene_id "CUFF.93"; transcript_id "CUFF.93.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	transcript	3375002	3375028	1000	.	.	gene_id "CUFF.95"; transcript_id "CUFF.95.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	exon	3375002	3375028	1000	.	.	gene_id "CUFF.95"; transcript_id "CUFF.95.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	transcript	3379889	3379915	1000	.	.	gene_id "CUFF.97"; transcript_id "CUFF.97.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	exon	3379889	3379915	1000	.	.	gene_id "CUFF.97"; transcript_id "CUFF.97.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";
+chr1	Cufflinks	transcript	3386740	3386836	1000	.	.	gene_id "CUFF.99"; transcript_id "CUFF.99.1"; FPKM "19.6021598701"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.204320"; cov "1.113402";
+chr1	Cufflinks	exon	3386740	3386836	1000	.	.	gene_id "CUFF.99"; transcript_id "CUFF.99.1"; exon_number "1"; FPKM "19.6021598701"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.204320"; cov "1.113402";
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffcompare_in3.gtf	Wed Nov 26 13:54:44 2014 -0500
@@ -0,0 +1,100 @@
+chr1	mm9_refFlat	stop_codon	3206103	3206105	0.000000	-	.	gene_id "Xkr4"; transcript_id "Xkr4"; 
+chr1	mm9_refFlat	CDS	3206106	3207049	0.000000	-	2	gene_id "Xkr4"; transcript_id "Xkr4"; 
+chr1	mm9_refFlat	exon	3204563	3207049	0.000000	-	.	gene_id "Xkr4"; transcript_id "Xkr4"; 
+chr1	mm9_refFlat	CDS	3411783	3411982	0.000000	-	1	gene_id "Xkr4"; transcript_id "Xkr4"; 
+chr1	mm9_refFlat	exon	3411783	3411982	0.000000	-	.	gene_id "Xkr4"; transcript_id "Xkr4"; 
+chr1	mm9_refFlat	CDS	3660633	3661429	0.000000	-	0	gene_id "Xkr4"; transcript_id "Xkr4"; 
+chr1	mm9_refFlat	start_codon	3661427	3661429	0.000000	-	.	gene_id "Xkr4"; transcript_id "Xkr4"; 
+chr1	mm9_refFlat	exon	3660633	3661579	0.000000	-	.	gene_id "Xkr4"; transcript_id "Xkr4"; 
+chr1	mm9_refFlat	stop_codon	4334681	4334683	0.000000	-	.	gene_id "Rp1"; transcript_id "Rp1"; 
+chr1	mm9_refFlat	CDS	4334684	4340172	0.000000	-	2	gene_id "Rp1"; transcript_id "Rp1"; 
+chr1	mm9_refFlat	exon	4334224	4340172	0.000000	-	.	gene_id "Rp1"; transcript_id "Rp1"; 
+chr1	mm9_refFlat	CDS	4341991	4342162	0.000000	-	0	gene_id "Rp1"; transcript_id "Rp1"; 
+chr1	mm9_refFlat	exon	4341991	4342162	0.000000	-	.	gene_id "Rp1"; transcript_id "Rp1"; 
+chr1	mm9_refFlat	CDS	4342283	4342906	0.000000	-	0	gene_id "Rp1"; transcript_id "Rp1"; 
+chr1	mm9_refFlat	start_codon	4342904	4342906	0.000000	-	.	gene_id "Rp1"; transcript_id "Rp1"; 
+chr1	mm9_refFlat	exon	4342283	4342918	0.000000	-	.	gene_id "Rp1"; transcript_id "Rp1"; 
+chr1	mm9_refFlat	exon	4350281	4350473	0.000000	-	.	gene_id "Rp1"; transcript_id "Rp1"; 
+chr1	mm9_refFlat	stop_codon	4481797	4481799	0.000000	-	.	gene_id "Sox17"; transcript_id "Sox17"; 
+chr1	mm9_refFlat	CDS	4481800	4482749	0.000000	-	2	gene_id "Sox17"; transcript_id "Sox17"; 
+chr1	mm9_refFlat	exon	4481009	4482749	0.000000	-	.	gene_id "Sox17"; transcript_id "Sox17"; 
+chr1	mm9_refFlat	CDS	4483181	4483487	0.000000	-	0	gene_id "Sox17"; transcript_id "Sox17"; 
+chr1	mm9_refFlat	start_codon	4483485	4483487	0.000000	-	.	gene_id "Sox17"; transcript_id "Sox17"; 
+chr1	mm9_refFlat	exon	4483181	4483547	0.000000	-	.	gene_id "Sox17"; transcript_id "Sox17"; 
+chr1	mm9_refFlat	exon	4483853	4483944	0.000000	-	.	gene_id "Sox17"; transcript_id "Sox17"; 
+chr1	mm9_refFlat	exon	4485217	4486023	0.000000	-	.	gene_id "Sox17"; transcript_id "Sox17"; 
+chr1	mm9_refFlat	exon	4486372	4486494	0.000000	-	.	gene_id "Sox17"; transcript_id "Sox17"; 
+chr1	mm9_refFlat	stop_codon	4766545	4766547	0.000000	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; 
+chr1	mm9_refFlat	CDS	4766548	4766882	0.000000	-	2	gene_id "Mrpl15"; transcript_id "Mrpl15"; 
+chr1	mm9_refFlat	exon	4763279	4766882	0.000000	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; 
+chr1	mm9_refFlat	CDS	4767606	4767729	0.000000	-	0	gene_id "Mrpl15"; transcript_id "Mrpl15"; 
+chr1	mm9_refFlat	exon	4767606	4767729	0.000000	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; 
+chr1	mm9_refFlat	CDS	4772649	4772814	0.000000	-	1	gene_id "Mrpl15"; transcript_id "Mrpl15"; 
+chr1	mm9_refFlat	exon	4772649	4772814	0.000000	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; 
+chr1	mm9_refFlat	CDS	4774032	4774186	0.000000	-	0	gene_id "Mrpl15"; transcript_id "Mrpl15"; 
+chr1	mm9_refFlat	exon	4774032	4774186	0.000000	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; 
+chr1	mm9_refFlat	CDS	4775654	4775758	0.000000	-	0	gene_id "Mrpl15"; transcript_id "Mrpl15"; 
+chr1	mm9_refFlat	start_codon	4775756	4775758	0.000000	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; 
+chr1	mm9_refFlat	exon	4775654	4775807	0.000000	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15"; 
+chr1	mm9_refFlat	stop_codon	4764533	4764535	0.000000	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; 
+chr1	mm9_refFlat	CDS	4764536	4764597	0.000000	-	2	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; 
+chr1	mm9_refFlat	exon	4763279	4764597	0.000000	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; 
+chr1	mm9_refFlat	CDS	4767606	4767729	0.000000	-	0	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; 
+chr1	mm9_refFlat	exon	4767606	4767729	0.000000	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; 
+chr1	mm9_refFlat	CDS	4772649	4772814	0.000000	-	1	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; 
+chr1	mm9_refFlat	exon	4772649	4772814	0.000000	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; 
+chr1	mm9_refFlat	CDS	4774032	4774186	0.000000	-	0	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; 
+chr1	mm9_refFlat	exon	4774032	4774186	0.000000	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; 
+chr1	mm9_refFlat	CDS	4775654	4775758	0.000000	-	0	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; 
+chr1	mm9_refFlat	start_codon	4775756	4775758	0.000000	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; 
+chr1	mm9_refFlat	exon	4775654	4775807	0.000000	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; 
+chr1	mm9_refFlat	exon	4763279	4764597	0.000000	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; 
+chr1	mm9_refFlat	exon	4767606	4767729	0.000000	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; 
+chr1	mm9_refFlat	exon	4772649	4772814	0.000000	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; 
+chr1	mm9_refFlat	exon	4775654	4775807	0.000000	-	.	gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; 
+chr1	mm9_refFlat	start_codon	4797995	4797997	0.000000	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	CDS	4797995	4798063	0.000000	+	0	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	exon	4797974	4798063	0.000000	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	CDS	4798536	4798567	0.000000	+	0	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	exon	4798536	4798567	0.000000	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	CDS	4818665	4818730	0.000000	+	1	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	exon	4818665	4818730	0.000000	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	CDS	4820349	4820396	0.000000	+	1	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	exon	4820349	4820396	0.000000	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	CDS	4822392	4822462	0.000000	+	1	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	exon	4822392	4822462	0.000000	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	CDS	4827082	4827155	0.000000	+	2	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	exon	4827082	4827155	0.000000	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	CDS	4829468	4829569	0.000000	+	0	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	exon	4829468	4829569	0.000000	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	CDS	4831037	4831213	0.000000	+	0	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	exon	4831037	4831213	0.000000	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	CDS	4835044	4835094	0.000000	+	0	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	stop_codon	4835095	4835097	0.000000	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	exon	4835044	4836816	0.000000	+	.	gene_id "Lypla1"; transcript_id "Lypla1"; 
+chr1	mm9_refFlat	start_codon	4847995	4847997	0.000000	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	CDS	4847995	4848057	0.000000	+	0	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	exon	4847775	4848057	0.000000	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	CDS	4857551	4857613	0.000000	+	0	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	exon	4857551	4857613	0.000000	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	CDS	4868108	4868213	0.000000	+	0	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	exon	4868108	4868213	0.000000	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	CDS	4876825	4876912	0.000000	+	2	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	exon	4876825	4876912	0.000000	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	CDS	4879538	4879683	0.000000	+	1	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	exon	4879538	4879683	0.000000	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	CDS	4880821	4880877	0.000000	+	2	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	exon	4880821	4880877	0.000000	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	CDS	4881996	4882150	0.000000	+	2	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	exon	4881996	4882150	0.000000	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	CDS	4883498	4883644	0.000000	+	0	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	exon	4883498	4883644	0.000000	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	CDS	4885015	4885086	0.000000	+	0	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	exon	4885015	4885086	0.000000	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	CDS	4886437	4886442	0.000000	+	0	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	stop_codon	4886443	4886445	0.000000	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	exon	4886437	4887987	0.000000	+	.	gene_id "Tcea1"; transcript_id "Tcea1"; 
+chr1	mm9_refFlat	start_codon	4847995	4847997	0.000000	+	.	gene_id "Tcea1"; transcript_id "Tcea1_dup1"; 
+chr1	mm9_refFlat	CDS	4847995	4848057	0.000000	+	0	gene_id "Tcea1"; transcript_id "Tcea1_dup1"; 
+chr1	mm9_refFlat	exon	4847775	4848057	0.000000	+	.	gene_id "Tcea1"; transcript_id "Tcea1_dup1"; 
+chr1	mm9_refFlat	CDS	4857551	4857613	0.000000	+	0	gene_id "Tcea1"; transcript_id "Tcea1_dup1"; 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffcompare_out1.tmap	Wed Nov 26 13:54:44 2014 -0500
@@ -0,0 +1,51 @@
+ref_gene_id	ref_id	class_code	cuff_gene_id	cuff_id	FMI	FPKM	FPKM_conf_lo	FPKM_conf_hi	cov	len	major_iso_id	ref_match_len
+-	-	u	CUFF.1	CUFF.1.1	100	20.607936	0.000000	49.751960	1.317073	41	CUFF.1.1	-
+-	-	u	CUFF.3	CUFF.3.1	100	27.255658	0.000000	65.800979	1.741935	31	CUFF.3.1	-
+-	-	u	CUFF.5	CUFF.5.1	100	31.293533	0.000000	75.549272	2.000000	27	CUFF.5.1	-
+-	-	u	CUFF.7	CUFF.7.1	100	9.999117	0.000000	19.998234	0.639053	169	CUFF.7.1	-
+-	-	u	CUFF.9	CUFF.9.1	100	17.776896	9.153835	26.399957	1.136139	404	CUFF.9.1	-
+-	-	u	CUFF.11	CUFF.11.1	100	31.293533	0.000000	75.549272	2.000000	27	CUFF.11.1	-
+Xkr4	Xkr4	c	CUFF.13	CUFF.13.1	100	10.695258	0.000000	25.820637	0.683544	79	CUFF.13.1	3634
+Xkr4	Xkr4	i	CUFF.15	CUFF.15.1	100	10.695258	0.000000	25.820637	0.683544	79	CUFF.15.1	3634
+Xkr4	Xkr4	i	CUFF.17	CUFF.17.1	100	8.710571	0.000000	21.029179	0.556701	97	CUFF.17.1	3634
+Xkr4	Xkr4	i	CUFF.19	CUFF.19.1	100	29.337687	3.097262	55.578113	1.875000	72	CUFF.19.1	3634
+Xkr4	Xkr4	i	CUFF.21	CUFF.21.1	100	13.851236	0.000000	33.439842	0.885246	61	CUFF.21.1	3634
+Xkr4	Xkr4	i	CUFF.23	CUFF.23.1	100	23.470150	0.000000	50.571145	1.500000	54	CUFF.23.1	3634
+Xkr4	Xkr4	i	CUFF.25	CUFF.25.1	100	14.567679	5.354270	23.781089	0.931034	290	CUFF.25.1	3634
+Xkr4	Xkr4	i	CUFF.27	CUFF.27.1	100	34.253732	0.000000	73.806535	2.189189	37	CUFF.27.1	3634
+-	-	u	CUFF.29	CUFF.29.1	100	107.103219	71.402146	142.804292	6.845070	142	CUFF.29.1	-
+-	-	u	CUFF.31	CUFF.31.1	100	122.650461	40.883487	204.417435	7.838710	31	CUFF.31.1	-
+-	-	u	CUFF.33	CUFF.33.1	100	109.527366	26.732460	192.322273	7.000000	27	CUFF.33.1	-
+-	-	u	CUFF.35	CUFF.35.1	100	96.747183	61.420107	132.074259	6.183206	131	CUFF.35.1	-
+-	-	u	CUFF.37	CUFF.37.1	100	104.085013	53.596365	154.573660	6.652174	69	CUFF.37.1	-
+-	-	u	CUFF.39	CUFF.39.1	100	23.912983	0.000000	51.525317	1.528302	53	CUFF.39.1	-
+-	-	u	CUFF.41	CUFF.41.1	100	10.695258	0.000000	25.820637	0.683544	79	CUFF.41.1	-
+-	-	u	CUFF.43	CUFF.43.1	100	10.561567	0.000000	25.497879	0.675000	80	CUFF.43.1	-
+-	-	u	CUFF.45	CUFF.45.1	100	20.708956	2.186303	39.231609	1.323529	102	CUFF.45.1	-
+-	-	u	CUFF.47	CUFF.47.1	100	20.607936	0.000000	49.751960	1.317073	41	CUFF.47.1	-
+-	-	u	CUFF.49	CUFF.49.1	100	15.646767	0.000000	46.940300	1.000000	27	CUFF.49.1	-
+-	-	u	CUFF.51	CUFF.51.1	100	31.293533	0.000000	75.549272	2.000000	27	CUFF.51.1	-
+-	-	u	CUFF.53	CUFF.53.1	100	31.293533	0.000000	75.549272	2.000000	27	CUFF.53.1	-
+-	-	u	CUFF.55	CUFF.55.1	100	31.293533	0.000000	75.549272	2.000000	27	CUFF.55.1	-
+-	-	u	CUFF.57	CUFF.57.1	100	15.646767	0.000000	46.940300	1.000000	27	CUFF.57.1	-
+-	-	u	CUFF.59	CUFF.59.1	100	15.646767	0.000000	46.940300	1.000000	27	CUFF.59.1	-
+Xkr4	Xkr4	i	CUFF.61	CUFF.61.1	100	45.263860	0.000000	97.530065	2.892857	28	CUFF.61.1	3634
+Xkr4	Xkr4	i	CUFF.63	CUFF.63.1	100	15.646767	0.000000	46.940300	1.000000	27	CUFF.63.1	3634
+Xkr4	Xkr4	i	CUFF.65	CUFF.65.1	100	15.362280	0.000000	37.087825	0.981818	55	CUFF.65.1	3634
+Xkr4	Xkr4	i	CUFF.67	CUFF.67.1	100	12.998852	0.000000	31.382005	0.830769	65	CUFF.67.1	3634
+Xkr4	Xkr4	i	CUFF.69	CUFF.69.1	100	10.058636	0.000000	24.283695	0.642857	84	CUFF.69.1	3634
+Xkr4	Xkr4	i	CUFF.71	CUFF.71.1	100	8.621688	0.000000	20.814595	0.551020	98	CUFF.71.1	3634
+Xkr4	Xkr4	i	CUFF.73	CUFF.73.1	100	15.362280	0.000000	37.087825	0.981818	55	CUFF.73.1	3634
+Xkr4	Xkr4	i	CUFF.75	CUFF.75.1	100	31.293533	0.000000	75.549272	2.000000	27	CUFF.75.1	3634
+Xkr4	Xkr4	i	CUFF.77	CUFF.77.1	100	16.248565	0.000000	39.227507	1.038462	52	CUFF.77.1	3634
+Xkr4	Xkr4	i	CUFF.79	CUFF.79.1	100	31.293533	0.000000	75.549272	2.000000	27	CUFF.79.1	3634
+Xkr4	Xkr4	i	CUFF.81	CUFF.81.1	100	13.201959	0.000000	31.872349	0.843750	64	CUFF.81.1	3634
+Xkr4	Xkr4	i	CUFF.83	CUFF.83.1	100	13.201959	0.000000	28.446269	0.843750	96	CUFF.83.1	3634
+Xkr4	Xkr4	i	CUFF.85	CUFF.85.1	100	31.293533	0.000000	75.549272	2.000000	27	CUFF.85.1	3634
+Xkr4	Xkr4	i	CUFF.87	CUFF.87.1	100	17.243375	0.000000	41.629191	1.102041	49	CUFF.87.1	3634
+Xkr4	Xkr4	i	CUFF.89	CUFF.89.1	100	16.567165	0.000000	39.996674	1.058824	51	CUFF.89.1	3634
+Xkr4	Xkr4	i	CUFF.91	CUFF.91.1	100	31.293533	0.000000	75.549272	2.000000	27	CUFF.91.1	3634
+Xkr4	Xkr4	i	CUFF.93	CUFF.93.1	100	21.664754	0.000000	52.303342	1.384615	39	CUFF.93.1	3634
+Xkr4	Xkr4	i	CUFF.95	CUFF.95.1	100	46.940300	0.000000	101.142289	3.000000	27	CUFF.95.1	3634
+Xkr4	Xkr4	i	CUFF.97	CUFF.97.1	100	21.481154	0.000000	46.285454	1.372881	59	CUFF.97.1	3634
+Xkr4	Xkr4	i	CUFF.99	CUFF.99.1	100	14.567679	0.000000	35.169489	0.931034	58	CUFF.99.1	3634
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffcompare_out2.refmap	Wed Nov 26 13:54:44 2014 -0500
@@ -0,0 +1,2 @@
+ref_gene_id	ref_id	class_code	cuff_id_list
+Xkr4	Xkr4	c	CUFF.13|CUFF.13.1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffcompare_out3.tmap	Wed Nov 26 13:54:44 2014 -0500
@@ -0,0 +1,51 @@
+ref_gene_id	ref_id	class_code	cuff_gene_id	cuff_id	FMI	FPKM	FPKM_conf_lo	FPKM_conf_hi	cov	len	major_iso_id	ref_match_len
+-	-	u	CUFF.1	CUFF.1.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.1.1	-
+-	-	u	CUFF.3	CUFF.3.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.3.1	-
+-	-	u	CUFF.5	CUFF.5.1	100	21.226627	0.000000	59.889707	1.205672	27	CUFF.5.1	-
+-	-	u	CUFF.7	CUFF.7.1	100	29.709524	19.806349	39.612698	1.687500	576	CUFF.7.1	-
+-	-	u	CUFF.9	CUFF.9.1	100	34.072933	23.364686	44.781179	1.935341	565	CUFF.9.1	-
+-	-	u	CUFF.11	CUFF.11.1	100	32.531777	24.582998	40.480555	1.847804	979	CUFF.11.1	-
+-	-	u	CUFF.13	CUFF.13.1	100	16.582060	0.000000	35.729373	0.941860	86	CUFF.13.1	-
+-	-	u	CUFF.15	CUFF.15.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.15.1	-
+-	-	u	CUFF.17	CUFF.17.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.17.1	-
+-	-	u	CUFF.19	CUFF.19.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.19.1	-
+-	-	u	CUFF.21	CUFF.21.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.21.1	-
+-	-	u	CUFF.23	CUFF.23.1	100	16.205195	0.000000	34.917342	0.920455	88	CUFF.23.1	-
+-	-	u	CUFF.25	CUFF.25.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.25.1	-
+-	-	u	CUFF.26	CUFF.26.1	100	29.709524	0.000000	71.725135	1.687500	32	CUFF.26.1	-
+-	-	u	CUFF.29	CUFF.29.1	100	13.581496	0.000000	32.788633	0.771429	70	CUFF.29.1	-
+-	-	u	CUFF.31	CUFF.31.1	100	22.635827	0.000000	45.271655	1.285714	84	CUFF.31.1	-
+Xkr4	Xkr4	i	CUFF.33	CUFF.33.1	100	23.767619	0.000000	57.380108	1.350000	40	CUFF.33.1	3634
+Xkr4	Xkr4	i	CUFF.35	CUFF.35.1	100	11.317914	0.000000	27.323861	0.642857	84	CUFF.35.1	3634
+Xkr4	Xkr4	i	CUFF.37	CUFF.37.1	100	11.500461	0.000000	24.780049	0.653226	124	CUFF.37.1	3634
+Xkr4	Xkr4	i	CUFF.39	CUFF.39.1	100	52.816931	0.000000	113.804669	3.000000	27	CUFF.39.1	3634
+Xkr4	Xkr4	i	CUFF.41	CUFF.41.1	100	43.213852	0.000000	93.112911	2.454545	33	CUFF.41.1	3634
+Xkr4	Xkr4	i	CUFF.43	CUFF.43.1	100	23.474191	0.000000	46.948383	1.333333	81	CUFF.43.1	3634
+Xkr4	Xkr4	i	CUFF.45	CUFF.45.1	100	20.667495	0.000000	49.895746	1.173913	46	CUFF.45.1	3634
+Xkr4	Xkr4	i	CUFF.47	CUFF.47.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.47.1	3634
+Xkr4	Xkr4	i	CUFF.49	CUFF.49.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.49.1	3634
+Xkr4	Xkr4	i	CUFF.51	CUFF.51.1	100	14.948188	7.228977	22.667399	0.849057	477	CUFF.51.1	3634
+Xkr4	Xkr4	i	CUFF.53	CUFF.53.1	100	52.816931	0.000000	113.804669	3.000000	27	CUFF.53.1	3634
+Xkr4	Xkr4	i	CUFF.55	CUFF.55.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.55.1	3634
+Xkr4	Xkr4	i	CUFF.57	CUFF.57.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.57.1	3634
+Xkr4	Xkr4	i	CUFF.59	CUFF.59.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.59.1	3634
+Xkr4	Xkr4	i	CUFF.61	CUFF.61.1	100	13.204233	0.000000	31.877838	0.750000	72	CUFF.61.1	3634
+Xkr4	Xkr4	i	CUFF.63	CUFF.63.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.63.1	3634
+Xkr4	Xkr4	i	CUFF.65	CUFF.65.1	100	31.170648	0.000000	62.341295	1.770492	61	CUFF.65.1	3634
+Xkr4	Xkr4	i	CUFF.67	CUFF.67.1	100	15.681351	3.378764	27.983938	0.890700	197	CUFF.67.1	3634
+Xkr4	Xkr4	i	CUFF.69	CUFF.69.1	100	18.799247	8.750627	28.847866	1.067797	354	CUFF.69.1	3634
+Xkr4	Xkr4	i	CUFF.71	CUFF.71.1	100	22.635827	0.000000	54.647722	1.285714	42	CUFF.71.1	3634
+Xkr4	Xkr4	i	CUFF.73	CUFF.73.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.73.1	3634
+Xkr4	Xkr4	i	CUFF.75	CUFF.75.1	100	52.816931	0.000000	113.804669	3.000000	27	CUFF.75.1	3634
+Xkr4	Xkr4	i	CUFF.77	CUFF.77.1	100	17.605644	0.000000	52.816931	1.000000	27	CUFF.77.1	3634
+Xkr4	Xkr4	i	CUFF.79	CUFF.79.1	100	13.390208	0.000000	32.326821	0.760563	71	CUFF.79.1	3634
+Xkr4	Xkr4	i	CUFF.81	CUFF.81.1	100	11.211141	1.183592	21.238690	0.636792	212	CUFF.81.1	3634
+Xkr4	Xkr4	i	CUFF.83	CUFF.83.1	100	21.126772	0.000000	51.004540	1.200000	45	CUFF.83.1	3634
+Xkr4	Xkr4	i	CUFF.85	CUFF.85.1	100	19.014095	0.000000	38.028190	1.080000	100	CUFF.85.1	3634
+Xkr4	Xkr4	i	CUFF.87	CUFF.87.1	100	24.170460	0.000000	52.080103	1.372881	59	CUFF.87.1	3634
+Xkr4	Xkr4	i	CUFF.89	CUFF.89.1	100	29.709524	0.000000	64.015126	1.687500	48	CUFF.89.1	3634
+Xkr4	Xkr4	i	CUFF.91	CUFF.91.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.91.1	3634
+Xkr4	Xkr4	i	CUFF.93	CUFF.93.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.93.1	3634
+Xkr4	Xkr4	i	CUFF.95	CUFF.95.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.95.1	3634
+Xkr4	Xkr4	i	CUFF.97	CUFF.97.1	100	35.211287	0.000000	85.007567	2.000000	27	CUFF.97.1	3634
+Xkr4	Xkr4	i	CUFF.99	CUFF.99.1	100	19.602160	0.000000	39.204320	1.113402	97	CUFF.99.1	3634
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffcompare_out4.refmap	Wed Nov 26 13:54:44 2014 -0500
@@ -0,0 +1,1 @@
+ref_gene_id	ref_id	class_code	cuff_id_list
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffcompare_out5.gtf	Wed Nov 26 13:54:44 2014 -0500
@@ -0,0 +1,90 @@
+chr1	Cufflinks	exon	3204755	3204833	.	-	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.13.1"; nearest_ref "Xkr4"; class_code "c"; tss_id "TSS1";
+chr1	Cufflinks	exon	3111450	3111490	.	.	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "1"; oId "CUFF.1.1"; class_code "u"; tss_id "TSS2";
+chr1	Cufflinks	exon	3111546	3111576	.	.	.	gene_id "XLOC_000003"; transcript_id "TCONS_00000003"; exon_number "1"; oId "CUFF.3.1"; class_code "u"; tss_id "TSS3";
+chr1	Cufflinks	exon	3174766	3174792	.	.	.	gene_id "XLOC_000004"; transcript_id "TCONS_00000051"; exon_number "1"; oId "CUFF.1.1"; class_code "u"; tss_id "TSS4";
+chr1	Cufflinks	exon	3187402	3187428	.	.	.	gene_id "XLOC_000005"; transcript_id "TCONS_00000052"; exon_number "1"; oId "CUFF.3.1"; class_code "u"; tss_id "TSS5";
+chr1	Cufflinks	exon	3188522	3188548	.	.	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000053"; exon_number "1"; oId "CUFF.5.1"; class_code "u"; tss_id "TSS6";
+chr1	Cufflinks	exon	3189811	3190789	.	.	.	gene_id "XLOC_000007"; transcript_id "TCONS_00000054"; exon_number "1"; oId "CUFF.11.1"; class_code "u"; tss_id "TSS7";
+chr1	Cufflinks	exon	3190859	3191434	.	.	.	gene_id "XLOC_000008"; transcript_id "TCONS_00000055"; exon_number "1"; oId "CUFF.7.1"; class_code "u"; tss_id "TSS10";
+chr1	Cufflinks	exon	3191513	3192077	.	.	.	gene_id "XLOC_000009"; transcript_id "TCONS_00000056"; exon_number "1"; oId "CUFF.9.1"; class_code "u"; tss_id "TSS11";
+chr1	Cufflinks	exon	3192251	3192336	.	.	.	gene_id "XLOC_000010"; transcript_id "TCONS_00000057"; exon_number "1"; oId "CUFF.13.1"; class_code "u"; tss_id "TSS13";
+chr1	Cufflinks	exon	3192442	3192494	.	.	.	gene_id "XLOC_000011"; transcript_id "TCONS_00000009"; exon_number "1"; oId "CUFF.39.1"; class_code "u"; tss_id "TSS14";
+chr1	Cufflinks	exon	3192551	3192629	.	.	.	gene_id "XLOC_000012"; transcript_id "TCONS_00000010"; exon_number "1"; oId "CUFF.41.1"; class_code "u"; tss_id "TSS15";
+chr1	Cufflinks	exon	3192650	3192676	.	.	.	gene_id "XLOC_000013"; transcript_id "TCONS_00000058"; exon_number "1"; oId "CUFF.15.1"; class_code "u"; tss_id "TSS16";
+chr1	Cufflinks	exon	3192732	3192811	.	.	.	gene_id "XLOC_000014"; transcript_id "TCONS_00000011"; exon_number "1"; oId "CUFF.43.1"; class_code "u"; tss_id "TSS17";
+chr1	Cufflinks	exon	3192941	3193042	.	.	.	gene_id "XLOC_000015"; transcript_id "TCONS_00000012"; exon_number "1"; oId "CUFF.45.1"; class_code "u"; tss_id "TSS18";
+chr1	Cufflinks	exon	3194186	3194226	.	.	.	gene_id "XLOC_000016"; transcript_id "TCONS_00000013"; exon_number "1"; oId "CUFF.47.1"; class_code "u"; tss_id "TSS19";
+chr1	Cufflinks	exon	3194303	3194329	.	.	.	gene_id "XLOC_000017"; transcript_id "TCONS_00000014"; exon_number "1"; oId "CUFF.49.1"; class_code "u"; tss_id "TSS20";
+chr1	Cufflinks	exon	3194707	3194733	.	.	.	gene_id "XLOC_000018"; transcript_id "TCONS_00000059"; exon_number "1"; oId "CUFF.17.1"; class_code "u"; tss_id "TSS21";
+chr1	Cufflinks	exon	3195084	3195110	.	.	.	gene_id "XLOC_000019"; transcript_id "TCONS_00000015"; exon_number "1"; oId "CUFF.51.1"; class_code "u"; tss_id "TSS22";
+chr1	Cufflinks	exon	3195451	3195477	.	.	.	gene_id "XLOC_000020"; transcript_id "TCONS_00000016"; exon_number "1"; oId "CUFF.53.1"; class_code "u"; tss_id "TSS23";
+chr1	Cufflinks	exon	3197090	3197116	.	.	.	gene_id "XLOC_000021"; transcript_id "TCONS_00000017"; exon_number "1"; oId "CUFF.55.1"; class_code "u"; tss_id "TSS24";
+chr1	Cufflinks	exon	3197247	3197273	.	.	.	gene_id "XLOC_000022"; transcript_id "TCONS_00000018"; exon_number "1"; oId "CUFF.57.1"; class_code "u"; tss_id "TSS25";
+chr1	Cufflinks	exon	3197347	3197373	.	.	.	gene_id "XLOC_000023"; transcript_id "TCONS_00000019"; exon_number "1"; oId "CUFF.59.1"; class_code "u"; tss_id "TSS26";
+chr1	Cufflinks	exon	3197426	3197452	.	.	.	gene_id "XLOC_000024"; transcript_id "TCONS_00000060"; exon_number "1"; oId "CUFF.19.1"; class_code "u"; tss_id "TSS27";
+chr1	Cufflinks	exon	3200023	3200191	.	.	.	gene_id "XLOC_000025"; transcript_id "TCONS_00000020"; exon_number "1"; oId "CUFF.7.1"; class_code "."; tss_id "TSS28";
+chr1	Cufflinks	exon	3200326	3200352	.	.	.	gene_id "XLOC_000026"; transcript_id "TCONS_00000021"; exon_number "1"; oId "CUFF.5.1"; class_code "u"; tss_id "TSS29";
+chr1	Cufflinks	exon	3200431	3200457	.	.	.	gene_id "XLOC_000027"; transcript_id "TCONS_00000061"; exon_number "1"; oId "CUFF.21.1"; class_code "u"; tss_id "TSS30";
+chr1	Cufflinks	exon	3201008	3201039	.	.	.	gene_id "XLOC_000028"; transcript_id "TCONS_00000062"; exon_number "1"; oId "CUFF.26.1"; class_code "u"; tss_id "TSS31";
+chr1	Cufflinks	exon	3201078	3201481	.	.	.	gene_id "XLOC_000029"; transcript_id "TCONS_00000022"; exon_number "1"; oId "CUFF.9.1"; class_code "."; tss_id "TSS32";
+chr1	Cufflinks	exon	3201597	3201666	.	.	.	gene_id "XLOC_000030"; transcript_id "TCONS_00000063"; exon_number "1"; oId "CUFF.29.1"; class_code "u"; tss_id "TSS33";
+chr1	Cufflinks	exon	3201673	3201699	.	.	.	gene_id "XLOC_000031"; transcript_id "TCONS_00000023"; exon_number "1"; oId "CUFF.11.1"; class_code "u"; tss_id "TSS34";
+chr1	Cufflinks	exon	3201726	3201809	.	.	.	gene_id "XLOC_000032"; transcript_id "TCONS_00000064"; exon_number "1"; oId "CUFF.31.1"; class_code "u"; tss_id "TSS35";
+chr1	Cufflinks	exon	3211522	3211561	.	.	.	gene_id "XLOC_000033"; transcript_id "TCONS_00000065"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.33.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS36";
+chr1	Cufflinks	exon	3212214	3212292	.	.	.	gene_id "XLOC_000034"; transcript_id "TCONS_00000024"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.15.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS37";
+chr1	Cufflinks	exon	3212368	3212439	.	.	.	gene_id "XLOC_000035"; transcript_id "TCONS_00000025"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.19.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS38";
+chr1	Cufflinks	exon	3212718	3212801	.	.	.	gene_id "XLOC_000036"; transcript_id "TCONS_00000066"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.35.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS39";
+chr1	Cufflinks	exon	3213096	3213192	.	.	.	gene_id "XLOC_000037"; transcript_id "TCONS_00000026"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.17.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS40";
+chr1	Cufflinks	exon	3213119	3213242	.	.	.	gene_id "XLOC_000037"; transcript_id "TCONS_00000067"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.37.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS40";
+chr1	Cufflinks	exon	3240607	3240633	.	.	.	gene_id "XLOC_000038"; transcript_id "TCONS_00000068"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.39.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS41";
+chr1	Cufflinks	exon	3242480	3242512	.	.	.	gene_id "XLOC_000039"; transcript_id "TCONS_00000069"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.41.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS42";
+chr1	Cufflinks	exon	3242634	3242923	.	.	.	gene_id "XLOC_000040"; transcript_id "TCONS_00000027"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.25.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS43";
+chr1	Cufflinks	exon	3242925	3243005	.	.	.	gene_id "XLOC_000041"; transcript_id "TCONS_00000070"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.43.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS44";
+chr1	Cufflinks	exon	3243019	3243079	.	.	.	gene_id "XLOC_000042"; transcript_id "TCONS_00000028"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.21.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS45";
+chr1	Cufflinks	exon	3243109	3243154	.	.	.	gene_id "XLOC_000043"; transcript_id "TCONS_00000071"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.45.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS46";
+chr1	Cufflinks	exon	3243348	3243401	.	.	.	gene_id "XLOC_000044"; transcript_id "TCONS_00000029"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.23.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS47";
+chr1	Cufflinks	exon	3254080	3254106	.	.	.	gene_id "XLOC_000045"; transcript_id "TCONS_00000072"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.47.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS48";
+chr1	Cufflinks	exon	3256975	3257011	.	.	.	gene_id "XLOC_000046"; transcript_id "TCONS_00000030"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.27.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS49";
+chr1	Cufflinks	exon	3277156	3277182	.	.	.	gene_id "XLOC_000047"; transcript_id "TCONS_00000073"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.49.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS50";
+chr1	Cufflinks	exon	3277191	3277218	.	.	.	gene_id "XLOC_000048"; transcript_id "TCONS_00000031"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.61.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS51";
+chr1	Cufflinks	exon	3277914	3278390	.	.	.	gene_id "XLOC_000049"; transcript_id "TCONS_00000074"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.51.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS52";
+chr1	Cufflinks	exon	3280118	3280144	.	.	.	gene_id "XLOC_000050"; transcript_id "TCONS_00000075"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.53.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS54";
+chr1	Cufflinks	exon	3280499	3280525	.	.	.	gene_id "XLOC_000051"; transcript_id "TCONS_00000076"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.55.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS55";
+chr1	Cufflinks	exon	3280687	3280741	.	.	.	gene_id "XLOC_000052"; transcript_id "TCONS_00000033"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.65.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS56";
+chr1	Cufflinks	exon	3282505	3282531	.	.	.	gene_id "XLOC_000053"; transcript_id "TCONS_00000077"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.57.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS57";
+chr1	Cufflinks	exon	3282651	3282677	.	.	.	gene_id "XLOC_000054"; transcript_id "TCONS_00000078"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.59.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS58";
+chr1	Cufflinks	exon	3282761	3282832	.	.	.	gene_id "XLOC_000055"; transcript_id "TCONS_00000079"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.61.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS59";
+chr1	Cufflinks	exon	3284967	3284993	.	.	.	gene_id "XLOC_000056"; transcript_id "TCONS_00000080"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.63.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS60";
+chr1	Cufflinks	exon	3290489	3290553	.	.	.	gene_id "XLOC_000057"; transcript_id "TCONS_00000034"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.67.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS61";
+chr1	Cufflinks	exon	3290799	3290859	.	.	.	gene_id "XLOC_000058"; transcript_id "TCONS_00000081"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.65.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS62";
+chr1	Cufflinks	exon	3290920	3291273	.	.	.	gene_id "XLOC_000059"; transcript_id "TCONS_00000082"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.69.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS63";
+chr1	Cufflinks	exon	3299444	3299640	.	.	.	gene_id "XLOC_000060"; transcript_id "TCONS_00000083"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.67.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS65";
+chr1	Cufflinks	exon	3299610	3299664	.	.	.	gene_id "XLOC_000060"; transcript_id "TCONS_00000037"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.73.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS66";
+chr1	Cufflinks	exon	3299692	3299733	.	.	.	gene_id "XLOC_000061"; transcript_id "TCONS_00000084"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.71.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS67";
+chr1	Cufflinks	exon	3300052	3300078	.	.	.	gene_id "XLOC_000062"; transcript_id "TCONS_00000038"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.75.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS68";
+chr1	Cufflinks	exon	3307749	3307775	.	.	.	gene_id "XLOC_000063"; transcript_id "TCONS_00000085"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.73.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS69";
+chr1	Cufflinks	exon	3318621	3318647	.	.	.	gene_id "XLOC_000064"; transcript_id "TCONS_00000086"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.75.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS70";
+chr1	Cufflinks	exon	3319000	3319051	.	.	.	gene_id "XLOC_000065"; transcript_id "TCONS_00000039"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.77.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS71";
+chr1	Cufflinks	exon	3330528	3330554	.	.	.	gene_id "XLOC_000066"; transcript_id "TCONS_00000087"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.77.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS72";
+chr1	Cufflinks	exon	3351241	3351311	.	.	.	gene_id "XLOC_000067"; transcript_id "TCONS_00000088"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.79.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS73";
+chr1	Cufflinks	exon	3355888	3355914	.	.	.	gene_id "XLOC_000068"; transcript_id "TCONS_00000040"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.79.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS74";
+chr1	Cufflinks	exon	3355908	3356119	.	.	.	gene_id "XLOC_000068"; transcript_id "TCONS_00000089"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.81.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS74";
+chr1	Cufflinks	exon	3356181	3356225	.	.	.	gene_id "XLOC_000069"; transcript_id "TCONS_00000090"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.83.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS75";
+chr1	Cufflinks	exon	3363077	3363176	.	.	.	gene_id "XLOC_000070"; transcript_id "TCONS_00000091"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.85.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS76";
+chr1	Cufflinks	exon	3363215	3363278	.	.	.	gene_id "XLOC_000071"; transcript_id "TCONS_00000041"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.81.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS77";
+chr1	Cufflinks	exon	3363388	3363446	.	.	.	gene_id "XLOC_000072"; transcript_id "TCONS_00000092"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.87.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS78";
+chr1	Cufflinks	exon	3363754	3363849	.	.	.	gene_id "XLOC_000073"; transcript_id "TCONS_00000042"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.83.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS79";
+chr1	Cufflinks	exon	3364872	3364919	.	.	.	gene_id "XLOC_000074"; transcript_id "TCONS_00000093"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.89.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS80";
+chr1	Cufflinks	exon	3367136	3367162	.	.	.	gene_id "XLOC_000075"; transcript_id "TCONS_00000043"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.85.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS81";
+chr1	Cufflinks	exon	3367211	3367237	.	.	.	gene_id "XLOC_000076"; transcript_id "TCONS_00000094"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.91.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS82";
+chr1	Cufflinks	exon	3367334	3367382	.	.	.	gene_id "XLOC_000077"; transcript_id "TCONS_00000044"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.87.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS83";
+chr1	Cufflinks	exon	3369581	3369607	.	.	.	gene_id "XLOC_000078"; transcript_id "TCONS_00000095"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.93.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS84";
+chr1	Cufflinks	exon	3375002	3375028	.	.	.	gene_id "XLOC_000079"; transcript_id "TCONS_00000096"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.95.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS85";
+chr1	Cufflinks	exon	3377212	3377262	.	.	.	gene_id "XLOC_000080"; transcript_id "TCONS_00000045"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.89.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS86";
+chr1	Cufflinks	exon	3379889	3379915	.	.	.	gene_id "XLOC_000081"; transcript_id "TCONS_00000097"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.97.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS87";
+chr1	Cufflinks	exon	3386740	3386836	.	.	.	gene_id "XLOC_000082"; transcript_id "TCONS_00000098"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.99.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS88";
+chr1	Cufflinks	exon	3391326	3391352	.	.	.	gene_id "XLOC_000083"; transcript_id "TCONS_00000046"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.91.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS89";
+chr1	Cufflinks	exon	3435842	3435880	.	.	.	gene_id "XLOC_000084"; transcript_id "TCONS_00000047"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.93.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS90";
+chr1	Cufflinks	exon	3447762	3447788	.	.	.	gene_id "XLOC_000085"; transcript_id "TCONS_00000048"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.95.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS91";
+chr1	Cufflinks	exon	3450907	3450965	.	.	.	gene_id "XLOC_000086"; transcript_id "TCONS_00000049"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.97.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS92";
+chr1	Cufflinks	exon	3451052	3451109	.	.	.	gene_id "XLOC_000087"; transcript_id "TCONS_00000050"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.99.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS93";
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffcompare_out6.tracking	Wed Nov 26 13:54:44 2014 -0500
@@ -0,0 +1,98 @@
+TCONS_00000001	XLOC_000001	Xkr4|Xkr4	c	q1:CUFF.13|CUFF.13.1|100|10.695258|0.000000|25.820637|0.683544|-	-
+TCONS_00000002	XLOC_000002	-	u	q1:CUFF.1|CUFF.1.1|100|20.607936|0.000000|49.751960|1.317073|-	-
+TCONS_00000003	XLOC_000003	-	u	q1:CUFF.3|CUFF.3.1|100|27.255658|0.000000|65.800979|1.741935|-	-
+TCONS_00000004	XLOC_000007	-	u	q1:CUFF.29|CUFF.29.1|100|107.103219|71.402146|142.804292|6.845070|-	-
+TCONS_00000005	XLOC_000007	-	u	q1:CUFF.31|CUFF.31.1|100|122.650461|40.883487|204.417435|7.838710|-	-
+TCONS_00000006	XLOC_000007	-	u	q1:CUFF.33|CUFF.33.1|100|109.527366|26.732460|192.322273|7.000000|-	-
+TCONS_00000007	XLOC_000009	-	u	q1:CUFF.35|CUFF.35.1|100|96.747183|61.420107|132.074259|6.183206|-	-
+TCONS_00000008	XLOC_000009	-	u	q1:CUFF.37|CUFF.37.1|100|104.085013|53.596365|154.573660|6.652174|-	-
+TCONS_00000009	XLOC_000011	-	u	q1:CUFF.39|CUFF.39.1|100|23.912983|0.000000|51.525317|1.528302|-	-
+TCONS_00000010	XLOC_000012	-	u	q1:CUFF.41|CUFF.41.1|100|10.695258|0.000000|25.820637|0.683544|-	-
+TCONS_00000011	XLOC_000014	-	u	q1:CUFF.43|CUFF.43.1|100|10.561567|0.000000|25.497879|0.675000|-	-
+TCONS_00000012	XLOC_000015	-	u	q1:CUFF.45|CUFF.45.1|100|20.708956|2.186303|39.231609|1.323529|-	-
+TCONS_00000013	XLOC_000016	-	u	q1:CUFF.47|CUFF.47.1|100|20.607936|0.000000|49.751960|1.317073|-	-
+TCONS_00000014	XLOC_000017	-	u	q1:CUFF.49|CUFF.49.1|100|15.646767|0.000000|46.940300|1.000000|-	-
+TCONS_00000015	XLOC_000019	-	u	q1:CUFF.51|CUFF.51.1|100|31.293533|0.000000|75.549272|2.000000|-	-
+TCONS_00000016	XLOC_000020	-	u	q1:CUFF.53|CUFF.53.1|100|31.293533|0.000000|75.549272|2.000000|-	-
+TCONS_00000017	XLOC_000021	-	u	q1:CUFF.55|CUFF.55.1|100|31.293533|0.000000|75.549272|2.000000|-	-
+TCONS_00000018	XLOC_000022	-	u	q1:CUFF.57|CUFF.57.1|100|15.646767|0.000000|46.940300|1.000000|-	-
+TCONS_00000019	XLOC_000023	-	u	q1:CUFF.59|CUFF.59.1|100|15.646767|0.000000|46.940300|1.000000|-	-
+TCONS_00000020	XLOC_000025	-	.	q1:CUFF.7|CUFF.7.1|100|9.999117|0.000000|19.998234|0.639053|169	q2:CUFF.23|CUFF.23.1|100|16.205195|0.000000|34.917342|0.920455|88
+TCONS_00000021	XLOC_000026	-	u	q1:CUFF.5|CUFF.5.1|100|31.293533|0.000000|75.549272|2.000000|-	-
+TCONS_00000022	XLOC_000029	-	.	q1:CUFF.9|CUFF.9.1|100|17.776896|9.153835|26.399957|1.136139|404	q2:CUFF.25|CUFF.25.1|100|35.211287|0.000000|85.007567|2.000000|27
+TCONS_00000023	XLOC_000031	-	u	q1:CUFF.11|CUFF.11.1|100|31.293533|0.000000|75.549272|2.000000|-	-
+TCONS_00000024	XLOC_000034	Xkr4|Xkr4	i	q1:CUFF.15|CUFF.15.1|100|10.695258|0.000000|25.820637|0.683544|-	-
+TCONS_00000025	XLOC_000035	Xkr4|Xkr4	i	q1:CUFF.19|CUFF.19.1|100|29.337687|3.097262|55.578113|1.875000|-	-
+TCONS_00000026	XLOC_000037	Xkr4|Xkr4	i	q1:CUFF.17|CUFF.17.1|100|8.710571|0.000000|21.029179|0.556701|-	-
+TCONS_00000027	XLOC_000040	Xkr4|Xkr4	i	q1:CUFF.25|CUFF.25.1|100|14.567679|5.354270|23.781089|0.931034|-	-
+TCONS_00000028	XLOC_000042	Xkr4|Xkr4	i	q1:CUFF.21|CUFF.21.1|100|13.851236|0.000000|33.439842|0.885246|-	-
+TCONS_00000029	XLOC_000044	Xkr4|Xkr4	i	q1:CUFF.23|CUFF.23.1|100|23.470150|0.000000|50.571145|1.500000|-	-
+TCONS_00000030	XLOC_000046	Xkr4|Xkr4	i	q1:CUFF.27|CUFF.27.1|100|34.253732|0.000000|73.806535|2.189189|-	-
+TCONS_00000031	XLOC_000048	Xkr4|Xkr4	i	q1:CUFF.61|CUFF.61.1|100|45.263860|0.000000|97.530065|2.892857|-	-
+TCONS_00000032	XLOC_000049	Xkr4|Xkr4	i	q1:CUFF.63|CUFF.63.1|100|15.646767|0.000000|46.940300|1.000000|-	-
+TCONS_00000033	XLOC_000052	Xkr4|Xkr4	i	q1:CUFF.65|CUFF.65.1|100|15.362280|0.000000|37.087825|0.981818|-	-
+TCONS_00000034	XLOC_000057	Xkr4|Xkr4	i	q1:CUFF.67|CUFF.67.1|100|12.998852|0.000000|31.382005|0.830769|-	-
+TCONS_00000035	XLOC_000059	Xkr4|Xkr4	i	q1:CUFF.69|CUFF.69.1|100|10.058636|0.000000|24.283695|0.642857|-	-
+TCONS_00000036	XLOC_000059	Xkr4|Xkr4	i	q1:CUFF.71|CUFF.71.1|100|8.621688|0.000000|20.814595|0.551020|-	-
+TCONS_00000037	XLOC_000060	Xkr4|Xkr4	i	q1:CUFF.73|CUFF.73.1|100|15.362280|0.000000|37.087825|0.981818|-	-
+TCONS_00000038	XLOC_000062	Xkr4|Xkr4	i	q1:CUFF.75|CUFF.75.1|100|31.293533|0.000000|75.549272|2.000000|-	-
+TCONS_00000039	XLOC_000065	Xkr4|Xkr4	i	q1:CUFF.77|CUFF.77.1|100|16.248565|0.000000|39.227507|1.038462|-	-
+TCONS_00000040	XLOC_000068	Xkr4|Xkr4	i	q1:CUFF.79|CUFF.79.1|100|31.293533|0.000000|75.549272|2.000000|-	-
+TCONS_00000041	XLOC_000071	Xkr4|Xkr4	i	q1:CUFF.81|CUFF.81.1|100|13.201959|0.000000|31.872349|0.843750|-	-
+TCONS_00000042	XLOC_000073	Xkr4|Xkr4	i	q1:CUFF.83|CUFF.83.1|100|13.201959|0.000000|28.446269|0.843750|-	-
+TCONS_00000043	XLOC_000075	Xkr4|Xkr4	i	q1:CUFF.85|CUFF.85.1|100|31.293533|0.000000|75.549272|2.000000|-	-
+TCONS_00000044	XLOC_000077	Xkr4|Xkr4	i	q1:CUFF.87|CUFF.87.1|100|17.243375|0.000000|41.629191|1.102041|-	-
+TCONS_00000045	XLOC_000080	Xkr4|Xkr4	i	q1:CUFF.89|CUFF.89.1|100|16.567165|0.000000|39.996674|1.058824|-	-
+TCONS_00000046	XLOC_000083	Xkr4|Xkr4	i	q1:CUFF.91|CUFF.91.1|100|31.293533|0.000000|75.549272|2.000000|-	-
+TCONS_00000047	XLOC_000084	Xkr4|Xkr4	i	q1:CUFF.93|CUFF.93.1|100|21.664754|0.000000|52.303342|1.384615|-	-
+TCONS_00000048	XLOC_000085	Xkr4|Xkr4	i	q1:CUFF.95|CUFF.95.1|100|46.940300|0.000000|101.142289|3.000000|-	-
+TCONS_00000049	XLOC_000086	Xkr4|Xkr4	i	q1:CUFF.97|CUFF.97.1|100|21.481154|0.000000|46.285454|1.372881|-	-
+TCONS_00000050	XLOC_000087	Xkr4|Xkr4	i	q1:CUFF.99|CUFF.99.1|100|14.567679|0.000000|35.169489|0.931034|-	-
+TCONS_00000051	XLOC_000004	-	u	-	q2:CUFF.1|CUFF.1.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000052	XLOC_000005	-	u	-	q2:CUFF.3|CUFF.3.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000053	XLOC_000006	-	u	-	q2:CUFF.5|CUFF.5.1|100|21.226627|0.000000|59.889707|1.205672|-
+TCONS_00000054	XLOC_000007	-	u	-	q2:CUFF.11|CUFF.11.1|100|32.531777|24.582998|40.480555|1.847804|-
+TCONS_00000055	XLOC_000008	-	u	-	q2:CUFF.7|CUFF.7.1|100|29.709524|19.806349|39.612698|1.687500|-
+TCONS_00000056	XLOC_000009	-	u	-	q2:CUFF.9|CUFF.9.1|100|34.072933|23.364686|44.781179|1.935341|-
+TCONS_00000057	XLOC_000010	-	u	-	q2:CUFF.13|CUFF.13.1|100|16.582060|0.000000|35.729373|0.941860|-
+TCONS_00000058	XLOC_000013	-	u	-	q2:CUFF.15|CUFF.15.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000059	XLOC_000018	-	u	-	q2:CUFF.17|CUFF.17.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000060	XLOC_000024	-	u	-	q2:CUFF.19|CUFF.19.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000061	XLOC_000027	-	u	-	q2:CUFF.21|CUFF.21.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000062	XLOC_000028	-	u	-	q2:CUFF.26|CUFF.26.1|100|29.709524|0.000000|71.725135|1.687500|-
+TCONS_00000063	XLOC_000030	-	u	-	q2:CUFF.29|CUFF.29.1|100|13.581496|0.000000|32.788633|0.771429|-
+TCONS_00000064	XLOC_000032	-	u	-	q2:CUFF.31|CUFF.31.1|100|22.635827|0.000000|45.271655|1.285714|-
+TCONS_00000065	XLOC_000033	Xkr4|Xkr4	i	-	q2:CUFF.33|CUFF.33.1|100|23.767619|0.000000|57.380108|1.350000|-
+TCONS_00000066	XLOC_000036	Xkr4|Xkr4	i	-	q2:CUFF.35|CUFF.35.1|100|11.317914|0.000000|27.323861|0.642857|-
+TCONS_00000067	XLOC_000037	Xkr4|Xkr4	i	-	q2:CUFF.37|CUFF.37.1|100|11.500461|0.000000|24.780049|0.653226|-
+TCONS_00000068	XLOC_000038	Xkr4|Xkr4	i	-	q2:CUFF.39|CUFF.39.1|100|52.816931|0.000000|113.804669|3.000000|-
+TCONS_00000069	XLOC_000039	Xkr4|Xkr4	i	-	q2:CUFF.41|CUFF.41.1|100|43.213852|0.000000|93.112911|2.454545|-
+TCONS_00000070	XLOC_000041	Xkr4|Xkr4	i	-	q2:CUFF.43|CUFF.43.1|100|23.474191|0.000000|46.948383|1.333333|-
+TCONS_00000071	XLOC_000043	Xkr4|Xkr4	i	-	q2:CUFF.45|CUFF.45.1|100|20.667495|0.000000|49.895746|1.173913|-
+TCONS_00000072	XLOC_000045	Xkr4|Xkr4	i	-	q2:CUFF.47|CUFF.47.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000073	XLOC_000047	Xkr4|Xkr4	i	-	q2:CUFF.49|CUFF.49.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000074	XLOC_000049	Xkr4|Xkr4	i	-	q2:CUFF.51|CUFF.51.1|100|14.948188|7.228977|22.667399|0.849057|-
+TCONS_00000075	XLOC_000050	Xkr4|Xkr4	i	-	q2:CUFF.53|CUFF.53.1|100|52.816931|0.000000|113.804669|3.000000|-
+TCONS_00000076	XLOC_000051	Xkr4|Xkr4	i	-	q2:CUFF.55|CUFF.55.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000077	XLOC_000053	Xkr4|Xkr4	i	-	q2:CUFF.57|CUFF.57.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000078	XLOC_000054	Xkr4|Xkr4	i	-	q2:CUFF.59|CUFF.59.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000079	XLOC_000055	Xkr4|Xkr4	i	-	q2:CUFF.61|CUFF.61.1|100|13.204233|0.000000|31.877838|0.750000|-
+TCONS_00000080	XLOC_000056	Xkr4|Xkr4	i	-	q2:CUFF.63|CUFF.63.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000081	XLOC_000058	Xkr4|Xkr4	i	-	q2:CUFF.65|CUFF.65.1|100|31.170648|0.000000|62.341295|1.770492|-
+TCONS_00000082	XLOC_000059	Xkr4|Xkr4	i	-	q2:CUFF.69|CUFF.69.1|100|18.799247|8.750627|28.847866|1.067797|-
+TCONS_00000083	XLOC_000060	Xkr4|Xkr4	i	-	q2:CUFF.67|CUFF.67.1|100|15.681351|3.378764|27.983938|0.890700|-
+TCONS_00000084	XLOC_000061	Xkr4|Xkr4	i	-	q2:CUFF.71|CUFF.71.1|100|22.635827|0.000000|54.647722|1.285714|-
+TCONS_00000085	XLOC_000063	Xkr4|Xkr4	i	-	q2:CUFF.73|CUFF.73.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000086	XLOC_000064	Xkr4|Xkr4	i	-	q2:CUFF.75|CUFF.75.1|100|52.816931|0.000000|113.804669|3.000000|-
+TCONS_00000087	XLOC_000066	Xkr4|Xkr4	i	-	q2:CUFF.77|CUFF.77.1|100|17.605644|0.000000|52.816931|1.000000|-
+TCONS_00000088	XLOC_000067	Xkr4|Xkr4	i	-	q2:CUFF.79|CUFF.79.1|100|13.390208|0.000000|32.326821|0.760563|-
+TCONS_00000089	XLOC_000068	Xkr4|Xkr4	i	-	q2:CUFF.81|CUFF.81.1|100|11.211141|1.183592|21.238690|0.636792|-
+TCONS_00000090	XLOC_000069	Xkr4|Xkr4	i	-	q2:CUFF.83|CUFF.83.1|100|21.126772|0.000000|51.004540|1.200000|-
+TCONS_00000091	XLOC_000070	Xkr4|Xkr4	i	-	q2:CUFF.85|CUFF.85.1|100|19.014095|0.000000|38.028190|1.080000|-
+TCONS_00000092	XLOC_000072	Xkr4|Xkr4	i	-	q2:CUFF.87|CUFF.87.1|100|24.170460|0.000000|52.080103|1.372881|-
+TCONS_00000093	XLOC_000074	Xkr4|Xkr4	i	-	q2:CUFF.89|CUFF.89.1|100|29.709524|0.000000|64.015126|1.687500|-
+TCONS_00000094	XLOC_000076	Xkr4|Xkr4	i	-	q2:CUFF.91|CUFF.91.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000095	XLOC_000078	Xkr4|Xkr4	i	-	q2:CUFF.93|CUFF.93.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000096	XLOC_000079	Xkr4|Xkr4	i	-	q2:CUFF.95|CUFF.95.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000097	XLOC_000081	Xkr4|Xkr4	i	-	q2:CUFF.97|CUFF.97.1|100|35.211287|0.000000|85.007567|2.000000|-
+TCONS_00000098	XLOC_000082	Xkr4|Xkr4	i	-	q2:CUFF.99|CUFF.99.1|100|19.602160|0.000000|39.204320|1.113402|-
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffcompare_out7.txt	Wed Nov 26 13:54:44 2014 -0500
@@ -0,0 +1,33 @@
+# Cuffcompare v2.2.1 | Command line was:
+#cuffcompare -o cc_output -r /tmp/tmpZ9KXPVfiles/000/dataset_3.dat -R -e 100 -d 100 ./input1 ./input2
+#
+
+#= Summary for dataset: ./input1 :
+#     Query mRNAs :      50 in      50 loci  (0 multi-exon transcripts)
+#            (0 multi-transcript loci, ~1.0 transcripts per locus)
+# Reference mRNAs :       1 in       1 loci  (1 multi-exon)
+# Super-loci w/ reference transcripts:        1
+#--------------------|   Sn   |  Sp   |  fSn |  fSp  
+        Base level: 	  2.2	  2.3	  - 	  - 
+        Exon level: 	  0.0	  0.0	  0.0	  0.0
+      Intron level: 	  0.0	 -nan	  0.0	 -nan
+Intron chain level: 	  0.0	 -nan	  0.0	 -nan
+  Transcript level: 	  0.0	  0.0	  0.0	  0.0
+       Locus level: 	  0.0	  0.0	  0.0	  0.0
+
+     Matching intron chains:       0
+              Matching loci:       0
+
+          Missed exons:       2/3	( 66.7%)
+           Novel exons:      49/50	( 98.0%)
+        Missed introns:       2/2	(100.0%)
+           Missed loci:       0/1	(  0.0%)
+            Novel loci:      49/50	( 98.0%)
+
+#= Summary for dataset: ./input2 :
+#     Query mRNAs :      50 in      50 loci  (0 multi-exon transcripts)
+#            (0 multi-transcript loci, ~1.0 transcripts per locus)
+# Reference mRNAs :       0 in       0 loci  (0 multi-exon)
+
+ Total union super-loci across all input datasets: 87 
+  (0 multi-transcript, ~1.1 transcripts per locus)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffmerge_out1.gtf	Wed Nov 26 13:54:44 2014 -0500
@@ -0,0 +1,74 @@
+chr1	Cufflinks	exon	4797974	4798063	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";
+chr1	Cufflinks	exon	4798536	4798567	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "2"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";
+chr1	Cufflinks	exon	4818665	4818730	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "3"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";
+chr1	Cufflinks	exon	4820349	4820396	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "4"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";
+chr1	Cufflinks	exon	4822392	4822462	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "5"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";
+chr1	Cufflinks	exon	4827082	4827155	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "6"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";
+chr1	Cufflinks	exon	4829468	4829569	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "7"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";
+chr1	Cufflinks	exon	4831037	4831213	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "8"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";
+chr1	Cufflinks	exon	4835044	4836816	.	+	.	gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "9"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";
+chr1	Cufflinks	exon	4847775	4848057	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "1"; gene_name "Tcea1"; oId "Tcea1_dup1"; contained_in "TCONS_00000003"; nearest_ref "Tcea1_dup1"; class_code "="; tss_id "TSS2";
+chr1	Cufflinks	exon	4857551	4857613	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "2"; gene_name "Tcea1"; oId "Tcea1_dup1"; contained_in "TCONS_00000003"; nearest_ref "Tcea1_dup1"; class_code "="; tss_id "TSS2";
+chr1	Cufflinks	exon	4847775	4848057	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "1"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
+chr1	Cufflinks	exon	4857551	4857613	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "2"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
+chr1	Cufflinks	exon	4868108	4868213	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "3"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
+chr1	Cufflinks	exon	4876825	4876912	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "4"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
+chr1	Cufflinks	exon	4879538	4879683	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "5"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
+chr1	Cufflinks	exon	4880821	4880877	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "6"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
+chr1	Cufflinks	exon	4881996	4882150	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "7"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
+chr1	Cufflinks	exon	4883498	4883644	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "8"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
+chr1	Cufflinks	exon	4885015	4885086	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "9"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
+chr1	Cufflinks	exon	4886437	4887987	.	+	.	gene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "10"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";
+chr1	Cufflinks	exon	3204563	3207049	.	-	.	gene_id "XLOC_000003"; transcript_id "TCONS_00000004"; exon_number "1"; gene_name "Xkr4"; oId "Xkr4"; nearest_ref "Xkr4"; class_code "="; tss_id "TSS3";
+chr1	Cufflinks	exon	3411783	3411982	.	-	.	gene_id "XLOC_000003"; transcript_id "TCONS_00000004"; exon_number "2"; gene_name "Xkr4"; oId "Xkr4"; nearest_ref "Xkr4"; class_code "="; tss_id "TSS3";
+chr1	Cufflinks	exon	3660633	3661579	.	-	.	gene_id "XLOC_000003"; transcript_id "TCONS_00000004"; exon_number "3"; gene_name "Xkr4"; oId "Xkr4"; nearest_ref "Xkr4"; class_code "="; tss_id "TSS3";
+chr1	Cufflinks	exon	4334224	4340172	.	-	.	gene_id "XLOC_000004"; transcript_id "TCONS_00000005"; exon_number "1"; gene_name "Rp1"; oId "Rp1"; nearest_ref "Rp1"; class_code "="; tss_id "TSS4";
+chr1	Cufflinks	exon	4341991	4342162	.	-	.	gene_id "XLOC_000004"; transcript_id "TCONS_00000005"; exon_number "2"; gene_name "Rp1"; oId "Rp1"; nearest_ref "Rp1"; class_code "="; tss_id "TSS4";
+chr1	Cufflinks	exon	4342283	4342918	.	-	.	gene_id "XLOC_000004"; transcript_id "TCONS_00000005"; exon_number "3"; gene_name "Rp1"; oId "Rp1"; nearest_ref "Rp1"; class_code "="; tss_id "TSS4";
+chr1	Cufflinks	exon	4350281	4350473	.	-	.	gene_id "XLOC_000004"; transcript_id "TCONS_00000005"; exon_number "4"; gene_name "Rp1"; oId "Rp1"; nearest_ref "Rp1"; class_code "="; tss_id "TSS4";
+chr1	Cufflinks	exon	4481009	4482749	.	-	.	gene_id "XLOC_000005"; transcript_id "TCONS_00000006"; exon_number "1"; gene_name "Sox17"; oId "Sox17"; nearest_ref "Sox17"; class_code "="; tss_id "TSS5";
+chr1	Cufflinks	exon	4483181	4483547	.	-	.	gene_id "XLOC_000005"; transcript_id "TCONS_00000006"; exon_number "2"; gene_name "Sox17"; oId "Sox17"; nearest_ref "Sox17"; class_code "="; tss_id "TSS5";
+chr1	Cufflinks	exon	4483853	4483944	.	-	.	gene_id "XLOC_000005"; transcript_id "TCONS_00000006"; exon_number "3"; gene_name "Sox17"; oId "Sox17"; nearest_ref "Sox17"; class_code "="; tss_id "TSS5";
+chr1	Cufflinks	exon	4485217	4486023	.	-	.	gene_id "XLOC_000005"; transcript_id "TCONS_00000006"; exon_number "4"; gene_name "Sox17"; oId "Sox17"; nearest_ref "Sox17"; class_code "="; tss_id "TSS5";
+chr1	Cufflinks	exon	4486372	4486494	.	-	.	gene_id "XLOC_000005"; transcript_id "TCONS_00000006"; exon_number "5"; gene_name "Sox17"; oId "Sox17"; nearest_ref "Sox17"; class_code "="; tss_id "TSS5";
+chr1	Cufflinks	exon	4763279	4764597	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000009"; exon_number "1"; gene_name "Mrpl15"; oId "Mrpl15_dup2"; nearest_ref "Mrpl15_dup2"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4767606	4767729	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000009"; exon_number "2"; gene_name "Mrpl15"; oId "Mrpl15_dup2"; nearest_ref "Mrpl15_dup2"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4772649	4772814	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000009"; exon_number "3"; gene_name "Mrpl15"; oId "Mrpl15_dup2"; nearest_ref "Mrpl15_dup2"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4775654	4775807	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000009"; exon_number "4"; gene_name "Mrpl15"; oId "Mrpl15_dup2"; nearest_ref "Mrpl15_dup2"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4763279	4764597	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000008"; exon_number "1"; gene_name "Mrpl15"; oId "Mrpl15_dup1"; nearest_ref "Mrpl15_dup1"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4767606	4767729	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000008"; exon_number "2"; gene_name "Mrpl15"; oId "Mrpl15_dup1"; nearest_ref "Mrpl15_dup1"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4772649	4772814	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000008"; exon_number "3"; gene_name "Mrpl15"; oId "Mrpl15_dup1"; nearest_ref "Mrpl15_dup1"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4774032	4774186	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000008"; exon_number "4"; gene_name "Mrpl15"; oId "Mrpl15_dup1"; nearest_ref "Mrpl15_dup1"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4775654	4775807	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000008"; exon_number "5"; gene_name "Mrpl15"; oId "Mrpl15_dup1"; nearest_ref "Mrpl15_dup1"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4763279	4766882	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000007"; exon_number "1"; gene_name "Mrpl15"; oId "Mrpl15"; nearest_ref "Mrpl15"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4767606	4767729	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000007"; exon_number "2"; gene_name "Mrpl15"; oId "Mrpl15"; nearest_ref "Mrpl15"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4772649	4772814	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000007"; exon_number "3"; gene_name "Mrpl15"; oId "Mrpl15"; nearest_ref "Mrpl15"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4774032	4774186	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000007"; exon_number "4"; gene_name "Mrpl15"; oId "Mrpl15"; nearest_ref "Mrpl15"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	4775654	4775807	.	-	.	gene_id "XLOC_000006"; transcript_id "TCONS_00000007"; exon_number "5"; gene_name "Mrpl15"; oId "Mrpl15"; nearest_ref "Mrpl15"; class_code "="; tss_id "TSS6";
+chr1	Cufflinks	exon	3111450	3111490	.	.	.	gene_id "XLOC_000007"; transcript_id "TCONS_00000010"; exon_number "1"; oId "CUFF.1.1"; class_code "u"; tss_id "TSS7";
+chr1	Cufflinks	exon	3111546	3111576	.	.	.	gene_id "XLOC_000008"; transcript_id "TCONS_00000011"; exon_number "1"; oId "CUFF.2.1"; class_code "u"; tss_id "TSS8";
+chr1	Cufflinks	exon	3174766	3174792	.	.	.	gene_id "XLOC_000009"; transcript_id "TCONS_00000012"; exon_number "1"; oId "CUFF.3.1"; class_code "u"; tss_id "TSS9";
+chr1	Cufflinks	exon	3187402	3187428	.	.	.	gene_id "XLOC_000010"; transcript_id "TCONS_00000013"; exon_number "1"; oId "CUFF.4.1"; class_code "u"; tss_id "TSS10";
+chr1	Cufflinks	exon	3188522	3188548	.	.	.	gene_id "XLOC_000011"; transcript_id "TCONS_00000014"; exon_number "1"; oId "CUFF.5.1"; class_code "u"; tss_id "TSS11";
+chr1	Cufflinks	exon	3189811	3190789	.	.	.	gene_id "XLOC_000012"; transcript_id "TCONS_00000015"; exon_number "1"; oId "CUFF.6.1"; class_code "u"; tss_id "TSS12";
+chr1	Cufflinks	exon	3190859	3191434	.	.	.	gene_id "XLOC_000013"; transcript_id "TCONS_00000016"; exon_number "1"; oId "CUFF.7.1"; class_code "u"; tss_id "TSS13";
+chr1	Cufflinks	exon	3191513	3192077	.	.	.	gene_id "XLOC_000014"; transcript_id "TCONS_00000017"; exon_number "1"; oId "CUFF.8.1"; class_code "u"; tss_id "TSS14";
+chr1	Cufflinks	exon	3192251	3192336	.	.	.	gene_id "XLOC_000015"; transcript_id "TCONS_00000018"; exon_number "1"; oId "CUFF.9.1"; class_code "u"; tss_id "TSS15";
+chr1	Cufflinks	exon	3192442	3192494	.	.	.	gene_id "XLOC_000016"; transcript_id "TCONS_00000019"; exon_number "1"; oId "CUFF.10.1"; class_code "u"; tss_id "TSS16";
+chr1	Cufflinks	exon	3192551	3192676	.	.	.	gene_id "XLOC_000017"; transcript_id "TCONS_00000020"; exon_number "1"; oId "CUFF.11.1"; class_code "u"; tss_id "TSS17";
+chr1	Cufflinks	exon	3192732	3192811	.	.	.	gene_id "XLOC_000018"; transcript_id "TCONS_00000021"; exon_number "1"; oId "CUFF.12.1"; class_code "u"; tss_id "TSS18";
+chr1	Cufflinks	exon	3192941	3193042	.	.	.	gene_id "XLOC_000019"; transcript_id "TCONS_00000022"; exon_number "1"; oId "CUFF.13.1"; class_code "u"; tss_id "TSS19";
+chr1	Cufflinks	exon	3194186	3194226	.	.	.	gene_id "XLOC_000020"; transcript_id "TCONS_00000023"; exon_number "1"; oId "CUFF.14.1"; class_code "u"; tss_id "TSS20";
+chr1	Cufflinks	exon	3194303	3194329	.	.	.	gene_id "XLOC_000021"; transcript_id "TCONS_00000024"; exon_number "1"; oId "CUFF.15.1"; class_code "u"; tss_id "TSS21";
+chr1	Cufflinks	exon	3194707	3194733	.	.	.	gene_id "XLOC_000022"; transcript_id "TCONS_00000025"; exon_number "1"; oId "CUFF.16.1"; class_code "u"; tss_id "TSS22";
+chr1	Cufflinks	exon	3195084	3195110	.	.	.	gene_id "XLOC_000023"; transcript_id "TCONS_00000026"; exon_number "1"; oId "CUFF.17.1"; class_code "u"; tss_id "TSS23";
+chr1	Cufflinks	exon	3195451	3195477	.	.	.	gene_id "XLOC_000024"; transcript_id "TCONS_00000027"; exon_number "1"; oId "CUFF.18.1"; class_code "u"; tss_id "TSS24";
+chr1	Cufflinks	exon	3197090	3197116	.	.	.	gene_id "XLOC_000025"; transcript_id "TCONS_00000028"; exon_number "1"; oId "CUFF.19.1"; class_code "u"; tss_id "TSS25";
+chr1	Cufflinks	exon	3197247	3197273	.	.	.	gene_id "XLOC_000026"; transcript_id "TCONS_00000029"; exon_number "1"; oId "CUFF.20.1"; class_code "u"; tss_id "TSS26";
+chr1	Cufflinks	exon	3197347	3197373	.	.	.	gene_id "XLOC_000027"; transcript_id "TCONS_00000030"; exon_number "1"; oId "CUFF.21.1"; class_code "u"; tss_id "TSS27";
+chr1	Cufflinks	exon	3197426	3197452	.	.	.	gene_id "XLOC_000028"; transcript_id "TCONS_00000031"; exon_number "1"; oId "CUFF.22.1"; class_code "u"; tss_id "TSS28";
+chr1	Cufflinks	exon	3200023	3200191	.	.	.	gene_id "XLOC_000029"; transcript_id "TCONS_00000032"; exon_number "1"; oId "CUFF.23.1"; class_code "u"; tss_id "TSS29";
+chr1	Cufflinks	exon	3200326	3200352	.	.	.	gene_id "XLOC_000030"; transcript_id "TCONS_00000033"; exon_number "1"; oId "CUFF.24.1"; class_code "u"; tss_id "TSS30";
+chr1	Cufflinks	exon	3200431	3200457	.	.	.	gene_id "XLOC_000031"; transcript_id "TCONS_00000034"; exon_number "1"; oId "CUFF.25.1"; class_code "u"; tss_id "TSS31";
+chr1	Cufflinks	exon	3201008	3201481	.	.	.	gene_id "XLOC_000032"; transcript_id "TCONS_00000035"; exon_number "1"; oId "CUFF.26.1"; class_code "u"; tss_id "TSS32";
+chr1	Cufflinks	exon	3201597	3201809	.	.	.	gene_id "XLOC_000033"; transcript_id "TCONS_00000036"; exon_number "1"; oId "CUFF.27.1"; class_code "u"; tss_id "TSS33";
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/fasta_indexes.loc.sample	Wed Nov 26 13:54:44 2014 -0500
@@ -0,0 +1,29 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Samtools indexed sequences data files.  You will need
+#to create these data files and then create a fasta_indexes.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The fasta_indexes.loc
+#file has this format (white space characters are TAB characters):
+#
+# <unique_build_id>	<dbkey>	<display_name>	<file_base_path>
+#
+#So, for example, if you had hg19 Canonical indexed stored in
+#
+# /depot/data2/galaxy/hg19/sam/,
+#
+#then the fasta_indexes.loc entry would look like this:
+#
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
+#
+#and your /depot/data2/galaxy/hg19/sam/ directory
+#would contain hg19canon.fa and hg19canon.fa.fai files.
+#
+#Your fasta_indexes.loc file should include an entry per line for
+#each index set you have stored.  The file in the path does actually
+#exist, but it should never be directly used. Instead, the name serves
+#as a prefix for the index file.  For example:
+#
+#hg18canon	hg18	Human (Homo sapiens): hg18 Canonical	/depot/data2/galaxy/hg18/sam/hg18canon.fa
+#hg18full	hg18	Human (Homo sapiens): hg18 Full	/depot/data2/galaxy/hg18/sam/hg18full.fa
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/depot/data2/galaxy/hg19/sam/hg19full.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Wed Nov 26 13:54:44 2014 -0500
@@ -0,0 +1,6 @@
+<tables>
+    <table name="fasta_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/fasta_indexes.loc" />
+    </table>
+</tables>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Nov 26 13:54:44 2014 -0500
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="cufflinks" version="2.2.1">
+        <repository changeset_revision="8f755957b6a1" name="package_cufflinks_2_2_1" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>