# HG changeset patch
# User iuc
# Date 1592326615 0
# Node ID 806c27c97df71c55e7ec0869fc901be9c14319d7
# Parent  5aac9b9d6f2a8feaf0692fae50bb6f66beede99d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffcompare commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"

diff -r 5aac9b9d6f2a -r 806c27c97df7 cuff_macros.xml
--- a/cuff_macros.xml	Sun Feb 19 12:11:14 2017 -0500
+++ b/cuff_macros.xml	Tue Jun 16 16:56:55 2020 +0000
@@ -66,20 +66,26 @@
   </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_LINK_GTF_INPUTS@"><![CDATA[
+            ## Inputs.
+            #for $i, $input_file in enumerate($inputs):
+                ln -s '${input_file}' input_$i &&
+            #end for
+  ]]></token>
   <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
+            #for $i, $input_file in enumerate($inputs):
+                'input_$i'
             #end for
   </token>
   <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token>
+
+  <xml name="citations">
+    <citations>
+        <citation type="doi">10.1038/nbt.1621</citation>
+        <yield/>
+    </citations>
+  </xml>
+
 </macros>
diff -r 5aac9b9d6f2a -r 806c27c97df7 cuffcompare_wrapper.py
--- a/cuffcompare_wrapper.py	Sun Feb 19 12:11:14 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,117 +0,0 @@
-#!/usr/bin/env python
-
-# Supports Cuffcompare versions v1.3.0 and newer.
-
-import optparse
-import os
-import shutil
-import subprocess
-import sys
-import tempfile
-
-
-def stop_err(msg):
-    sys.stderr.write('%s\n' % msg)
-    sys.exit()
-
-
-def __main__():
-    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()
-
-    # 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 the current 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
-
-    # Run command.
-    try:
-        with tempfile.NamedTemporaryFile(dir=".") as tmp_stderr:
-            returncode = subprocess.call(args=cmd, stderr=tmp_stderr, shell=True)
-
-            # Error checking.
-            if returncode != 0:
-                # Get stderr, allowing for case where it's very large.
-                buffsize = 1048576
-                stderr = ''
-                with open(tmp_stderr.name) as tmp_stderr2:
-                    try:
-                        while True:
-                            stderr += tmp_stderr2.read(buffsize)
-                            if not stderr or len(stderr) % buffsize != 0:
-                                break
-                    except OverflowError:
-                        pass
-                raise Exception(stderr)
-
-        # Copy outputs.
-        shutil.move("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).read().strip()) == 0:
-            raise Exception('The main output file is empty, there may be an error with your input file or settings.')
-    except Exception as e:
-        stop_err('Error running cuffcompare: %s' % e)
-
-
-if __name__ == "__main__":
-    __main__()
diff -r 5aac9b9d6f2a -r 806c27c97df7 cuffcompare_wrapper.xml
--- a/cuffcompare_wrapper.xml	Sun Feb 19 12:11:14 2017 -0500
+++ b/cuffcompare_wrapper.xml	Tue Jun 16 16:56:55 2020 +0000
@@ -1,31 +1,34 @@
-<tool id="cuffcompare" name="Cuffcompare" version="@VERSION@.1">
+<tool id="cuffcompare" name="Cuffcompare" version="@VERSION@.2">
     <description>compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments</description>
     <macros>
       <import>cuff_macros.xml</import>
     </macros>
     <expand macro="requirements" />
-    <version_command>cuffcompare 2>&amp;1 | head -n 1</version_command>
+    <version_command><![CDATA[
+cuffcompare 2>&1 | head -n 1
+    ]]></version_command>
     <command detect_errors="aggressive"><![CDATA[
-        python '$__tool_directory__/cuffcompare_wrapper.py'
+        @CUFFLINKS_LINK_GTF_INPUTS@
+        cuffcompare
+            -o output
             ## Use annotation reference?
             #if $annotation.use_ref_annotation == "Yes":
-                -r '$annotation.reference_annotation'
+            -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'
+                    '$seq_data.seq_source.ref_file'
                 #else:
-                    --index '${seq_data.seq_source.index.fields.path}'
+                    '${seq_data.seq_source.index.fields.path}'
                 #end if
             #end if
 
@@ -34,15 +37,10 @@
             -e $max_dist_exon
             -d $max_dist_group
 
-            #if $discard_intron_redundant_transfrags:
-                -F
-            #end if
-
-            ## Outputs.
-            --combined-transcripts '${transcripts_combined}'
+            $discard_intron_redundant_transfrags
 
             @CUFFLINKS_GTF_INPUTS@
-    ]]></command>
+]]></command>
     <inputs>
         <expand macro="cufflinks_gtf_inputs" />
         <conditional name="annotation">
@@ -86,47 +84,48 @@
             </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>
+            <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'"
+            value="false" truevalue="-F" falsevalue=""
             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 ${on_string}: transcript accuracy"
-            from_work_dir="cc_output.stats" />
+            from_work_dir="output.stats" />
         <data format="tabular" name="input1_tmap" label="${tool.name} on ${on_string}: data ${inputs[0].hid} tmap file"
-            from_work_dir="cc_output.input1.tmap" />
+            from_work_dir="output.input_0.tmap" />
         <data format="tabular" name="input1_refmap"
               label="${tool.name} on ${on_string}: data ${inputs[0].hid} refmap file"
-              from_work_dir="cc_output.input1.refmap">
+              from_work_dir="output.input_0.refmap">
             <filter>annotation['use_ref_annotation'] == 'Yes'</filter>
         </data>
-        <data format="tabular" name="input2_tmap" label="${tool.name} on ${on_string}: data ${inputs[1].hid} tmap file" from_work_dir="cc_output.input2.tmap">
+        <data format="tabular" name="input2_tmap" label="${tool.name} on ${on_string}: data ${inputs[1].hid} tmap file" from_work_dir="output.input_1.tmap">
             <filter>@HAS_MULTIPLE_INPUTS@</filter>
         </data>
         <data format="tabular" name="input2_refmap"
               label="${tool.name} on ${on_string}: data ${inputs[1].hid} refmap file"
-              from_work_dir="cc_output.input2.refmap">
+              from_work_dir="output.input_1.refmap">
             <filter>annotation['use_ref_annotation'] == 'Yes' and @HAS_MULTIPLE_INPUTS@</filter>
         </data>
-        <data format="tabular" name="transcripts_tracking" label="${tool.name} on ${on_string}: transcript tracking" from_work_dir="cc_output.tracking">
+        <data format="tabular" name="transcripts_tracking" label="${tool.name} on ${on_string}: transcript tracking" from_work_dir="output.tracking">
             <filter>@HAS_MULTIPLE_INPUTS@</filter>
         </data>
-        <data format="gtf" name="transcripts_combined" label="${tool.name} on ${on_string}: combined transcripts"/>
+        <data format="gtf" name="transcripts_combined" label="${tool.name} on ${on_string}: combined transcripts" from_work_dir="output.combined.gtf"/>
     </outputs>
 
     <tests>
         <!--
             cuffcompare -r cuffcompare_in3.gtf -R cuffcompare_in1.gtf cuffcompare_in2.gtf
         -->
-        <test>
+        <test expect_num_outputs="7">
             <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"/>
@@ -136,10 +135,10 @@
             <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" />
+            <param name="discard_intron_redundant_transfrags" value="false" />
             <!-- 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="transcripts_accuracy" file="cuffcompare_out7.txt" lines_diff="6"/>
             <output name="input1_tmap" file="cuffcompare_out1.tmap"/>
             <output name="input1_refmap" file="cuffcompare_out2.refmap"/>
             <output name="input2_tmap" file="cuffcompare_out3.tmap"/>
@@ -248,7 +247,5 @@
   -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>
+    <expand macro="citations"/>
 </tool>
diff -r 5aac9b9d6f2a -r 806c27c97df7 test-data/cuffcompare_out7.txt
--- a/test-data/cuffcompare_out7.txt	Sun Feb 19 12:11:14 2017 -0500
+++ b/test-data/cuffcompare_out7.txt	Tue Jun 16 16:56:55 2020 +0000
@@ -1,8 +1,8 @@
 # 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
+#cuffcompare -o output -r /tmp/tmpt36dzh0b/files/7/5/1/dataset_75119a58-1488-40cb-bd1d-4e92052062f5.dat -R -e 100 -d 100 /tmp/tmpt36dzh0b/files/1/c/9/dataset_1c9fee4e-77d4-48eb-95ec-43841c5b63b1.dat /tmp/tmpt36dzh0b/files/0/d/d/dataset_0ddbc5aa-4094-447c-ae9e-f30a1f7af6a9.dat
 #
 
-#= Summary for dataset: ./input1 :
+#= Summary for dataset: /tmp/tmpt36dzh0b/files/1/c/9/dataset_1c9fee4e-77d4-48eb-95ec-43841c5b63b1.dat :
 #     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)
@@ -24,7 +24,7 @@
            Missed loci:       0/1	(  0.0%)
             Novel loci:      49/50	( 98.0%)
 
-#= Summary for dataset: ./input2 :
+#= Summary for dataset: /tmp/tmpt36dzh0b/files/0/d/d/dataset_0ddbc5aa-4094-447c-ae9e-f30a1f7af6a9.dat :
 #     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)
diff -r 5aac9b9d6f2a -r 806c27c97df7 test-data/output.combined.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.combined.gtf	Tue Jun 16 16:56:55 2020 +0000
@@ -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";
diff -r 5aac9b9d6f2a -r 806c27c97df7 test-data/output.cuffcompare_in1.gtf.refmap
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.cuffcompare_in1.gtf.refmap	Tue Jun 16 16:56:55 2020 +0000
@@ -0,0 +1,2 @@
+ref_gene_id	ref_id	class_code	cuff_id_list
+Xkr4	Xkr4	c	CUFF.13|CUFF.13.1
diff -r 5aac9b9d6f2a -r 806c27c97df7 test-data/output.cuffcompare_in1.gtf.tmap
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.cuffcompare_in1.gtf.tmap	Tue Jun 16 16:56:55 2020 +0000
@@ -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
diff -r 5aac9b9d6f2a -r 806c27c97df7 test-data/output.cuffcompare_in2.gtf.refmap
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.cuffcompare_in2.gtf.refmap	Tue Jun 16 16:56:55 2020 +0000
@@ -0,0 +1,1 @@
+ref_gene_id	ref_id	class_code	cuff_id_list
diff -r 5aac9b9d6f2a -r 806c27c97df7 test-data/output.cuffcompare_in2.gtf.tmap
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.cuffcompare_in2.gtf.tmap	Tue Jun 16 16:56:55 2020 +0000
@@ -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
diff -r 5aac9b9d6f2a -r 806c27c97df7 test-data/output.loci
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.loci	Tue Jun 16 16:56:55 2020 +0000
@@ -0,0 +1,87 @@
+XLOC_000001	chr1[-]3204563-3661579	Xkr4|Xkr4	CUFF.13.1	-
+XLOC_000002	chr1[.]3111450-3111490	-	CUFF.1.1	-
+XLOC_000003	chr1[.]3111546-3111576	-	CUFF.3.1	-
+XLOC_000004	chr1[.]3174766-3174792	-	-	CUFF.1.1
+XLOC_000005	chr1[.]3187402-3187428	-	-	CUFF.3.1
+XLOC_000006	chr1[.]3188522-3188548	-	-	CUFF.5.1
+XLOC_000007	chr1[.]3189811-3190789	-	CUFF.31.1,CUFF.33.1,CUFF.29.1	CUFF.11.1
+XLOC_000008	chr1[.]3190859-3191434	-	-	CUFF.7.1
+XLOC_000009	chr1[.]3191513-3192077	-	CUFF.35.1,CUFF.37.1	CUFF.9.1
+XLOC_000010	chr1[.]3192251-3192336	-	-	CUFF.13.1
+XLOC_000011	chr1[.]3192442-3192494	-	CUFF.39.1	-
+XLOC_000012	chr1[.]3192551-3192629	-	CUFF.41.1	-
+XLOC_000013	chr1[.]3192650-3192676	-	-	CUFF.15.1
+XLOC_000014	chr1[.]3192732-3192811	-	CUFF.43.1	-
+XLOC_000015	chr1[.]3192941-3193042	-	CUFF.45.1	-
+XLOC_000016	chr1[.]3194186-3194226	-	CUFF.47.1	-
+XLOC_000017	chr1[.]3194303-3194329	-	CUFF.49.1	-
+XLOC_000018	chr1[.]3194707-3194733	-	-	CUFF.17.1
+XLOC_000019	chr1[.]3195084-3195110	-	CUFF.51.1	-
+XLOC_000020	chr1[.]3195451-3195477	-	CUFF.53.1	-
+XLOC_000021	chr1[.]3197090-3197116	-	CUFF.55.1	-
+XLOC_000022	chr1[.]3197247-3197273	-	CUFF.57.1	-
+XLOC_000023	chr1[.]3197347-3197373	-	CUFF.59.1	-
+XLOC_000024	chr1[.]3197426-3197452	-	-	CUFF.19.1
+XLOC_000025	chr1[.]3200023-3200191	-	CUFF.7.1	CUFF.23.1
+XLOC_000026	chr1[.]3200326-3200352	-	CUFF.5.1	-
+XLOC_000027	chr1[.]3200431-3200457	-	-	CUFF.21.1
+XLOC_000028	chr1[.]3201008-3201039	-	-	CUFF.26.1
+XLOC_000029	chr1[.]3201078-3201481	-	CUFF.9.1	CUFF.25.1
+XLOC_000030	chr1[.]3201597-3201666	-	-	CUFF.29.1
+XLOC_000031	chr1[.]3201673-3201699	-	CUFF.11.1	-
+XLOC_000032	chr1[.]3201726-3201809	-	-	CUFF.31.1
+XLOC_000033	chr1[.]3211522-3211561	-	-	CUFF.33.1
+XLOC_000034	chr1[.]3212214-3212292	-	CUFF.15.1	-
+XLOC_000035	chr1[.]3212368-3212439	-	CUFF.19.1	-
+XLOC_000036	chr1[.]3212718-3212801	-	-	CUFF.35.1
+XLOC_000037	chr1[.]3213096-3213242	-	CUFF.17.1	CUFF.37.1
+XLOC_000038	chr1[.]3240607-3240633	-	-	CUFF.39.1
+XLOC_000039	chr1[.]3242480-3242512	-	-	CUFF.41.1
+XLOC_000040	chr1[.]3242634-3242923	-	CUFF.25.1	-
+XLOC_000041	chr1[.]3242925-3243005	-	-	CUFF.43.1
+XLOC_000042	chr1[.]3243019-3243079	-	CUFF.21.1	-
+XLOC_000043	chr1[.]3243109-3243154	-	-	CUFF.45.1
+XLOC_000044	chr1[.]3243348-3243401	-	CUFF.23.1	-
+XLOC_000045	chr1[.]3254080-3254106	-	-	CUFF.47.1
+XLOC_000046	chr1[.]3256975-3257011	-	CUFF.27.1	-
+XLOC_000047	chr1[.]3277156-3277182	-	-	CUFF.49.1
+XLOC_000048	chr1[.]3277191-3277218	-	CUFF.61.1	-
+XLOC_000049	chr1[.]3277914-3278390	-	CUFF.63.1	CUFF.51.1
+XLOC_000050	chr1[.]3280118-3280144	-	-	CUFF.53.1
+XLOC_000051	chr1[.]3280499-3280525	-	-	CUFF.55.1
+XLOC_000052	chr1[.]3280687-3280741	-	CUFF.65.1	-
+XLOC_000053	chr1[.]3282505-3282531	-	-	CUFF.57.1
+XLOC_000054	chr1[.]3282651-3282677	-	-	CUFF.59.1
+XLOC_000055	chr1[.]3282761-3282832	-	-	CUFF.61.1
+XLOC_000056	chr1[.]3284967-3284993	-	-	CUFF.63.1
+XLOC_000057	chr1[.]3290489-3290553	-	CUFF.67.1	-
+XLOC_000058	chr1[.]3290799-3290859	-	-	CUFF.65.1
+XLOC_000059	chr1[.]3290920-3291273	-	CUFF.69.1,CUFF.71.1	CUFF.69.1
+XLOC_000060	chr1[.]3299444-3299664	-	CUFF.73.1	CUFF.67.1
+XLOC_000061	chr1[.]3299692-3299733	-	-	CUFF.71.1
+XLOC_000062	chr1[.]3300052-3300078	-	CUFF.75.1	-
+XLOC_000063	chr1[.]3307749-3307775	-	-	CUFF.73.1
+XLOC_000064	chr1[.]3318621-3318647	-	-	CUFF.75.1
+XLOC_000065	chr1[.]3319000-3319051	-	CUFF.77.1	-
+XLOC_000066	chr1[.]3330528-3330554	-	-	CUFF.77.1
+XLOC_000067	chr1[.]3351241-3351311	-	-	CUFF.79.1
+XLOC_000068	chr1[.]3355888-3356119	-	CUFF.79.1	CUFF.81.1
+XLOC_000069	chr1[.]3356181-3356225	-	-	CUFF.83.1
+XLOC_000070	chr1[.]3363077-3363176	-	-	CUFF.85.1
+XLOC_000071	chr1[.]3363215-3363278	-	CUFF.81.1	-
+XLOC_000072	chr1[.]3363388-3363446	-	-	CUFF.87.1
+XLOC_000073	chr1[.]3363754-3363849	-	CUFF.83.1	-
+XLOC_000074	chr1[.]3364872-3364919	-	-	CUFF.89.1
+XLOC_000075	chr1[.]3367136-3367162	-	CUFF.85.1	-
+XLOC_000076	chr1[.]3367211-3367237	-	-	CUFF.91.1
+XLOC_000077	chr1[.]3367334-3367382	-	CUFF.87.1	-
+XLOC_000078	chr1[.]3369581-3369607	-	-	CUFF.93.1
+XLOC_000079	chr1[.]3375002-3375028	-	-	CUFF.95.1
+XLOC_000080	chr1[.]3377212-3377262	-	CUFF.89.1	-
+XLOC_000081	chr1[.]3379889-3379915	-	-	CUFF.97.1
+XLOC_000082	chr1[.]3386740-3386836	-	-	CUFF.99.1
+XLOC_000083	chr1[.]3391326-3391352	-	CUFF.91.1	-
+XLOC_000084	chr1[.]3435842-3435880	-	CUFF.93.1	-
+XLOC_000085	chr1[.]3447762-3447788	-	CUFF.95.1	-
+XLOC_000086	chr1[.]3450907-3450965	-	CUFF.97.1	-
+XLOC_000087	chr1[.]3451052-3451109	-	CUFF.99.1	-
diff -r 5aac9b9d6f2a -r 806c27c97df7 test-data/output.stats
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.stats	Tue Jun 16 16:56:55 2020 +0000
@@ -0,0 +1,33 @@
+# Cuffcompare v2.2.1 | Command line was:
+#cuffcompare -o output -r cuffcompare_in3.gtf -R -e 100 -d 100 cuffcompare_in1.gtf cuffcompare_in2.gtf
+#
+
+#= Summary for dataset: cuffcompare_in1.gtf :
+#     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: cuffcompare_in2.gtf :
+#     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)
diff -r 5aac9b9d6f2a -r 806c27c97df7 test-data/output.tracking
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.tracking	Tue Jun 16 16:56:55 2020 +0000
@@ -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|-