changeset 2:fdf01b3c1841

Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output
author Jim Johnson <jj@umn.edu>
date Fri, 08 Nov 2013 14:54:01 -0600
parents ebb9a992508d
children f109453ecfa2
files cuffdiff_wrapper.py cuffdiff_wrapper.xml cummerbund_wrapper.py cummerbund_wrapper.xml test-data/cuffcompare_out5.gtf test-data/cuffdiff_in1.sam test-data/cuffdiff_in2.sam test-data/cuffdiff_out1.txt test-data/cuffdiff_out10.txt test-data/cuffdiff_out11.txt test-data/cuffdiff_out2.txt test-data/cuffdiff_out3.txt test-data/cuffdiff_out4.txt test-data/cuffdiff_out5.txt test-data/cuffdiff_out6.txt test-data/cuffdiff_out7.txt test-data/cuffdiff_out8.txt test-data/cuffdiff_out9.txt tool-data/sam_fa_indices.loc.sample tool_dependencies.xml
diffstat 20 files changed, 1808 insertions(+), 228 deletions(-) [+]
line wrap: on
line diff
--- a/cuffdiff_wrapper.py	Mon Feb 04 21:23:20 2013 -0600
+++ b/cuffdiff_wrapper.py	Fri Nov 08 14:54:01 2013 -0600
@@ -33,7 +33,7 @@
 
 def stop_err( msg ):
     sys.stderr.write( "%s\n" % msg )
-    sys.exit()
+    sys.exit(1)
     
 # Copied from sam_to_bam.py:
 def check_seq_file( dbkey, cached_seqs_pointer_file ):
@@ -62,6 +62,8 @@
     parser.add_option( '-c', '--min-alignment-count', dest='min_alignment_count', help='The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples. If no testing is performed, changes in the locus are deemed not signficant, and the locus\' observed changes don\'t contribute to correction for multiple testing. The default is 1,000 fragment alignments (up to 2,000 paired reads).' )
     parser.add_option( '--FDR', dest='FDR', help='The allowed false discovery rate. The default is 0.05.' )
     parser.add_option( '-u', '--multi-read-correct', dest='multi_read_correct', action="store_true", help='Tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome')
+    parser.add_option( '--library-norm-method', dest='library_norm_method' )
+    parser.add_option( '--dispersion-method', dest='dispersion_method' )
 
     # Advanced Options:	
     parser.add_option( '--num-importance-samples', dest='num_importance_samples', help='Sets the number of importance samples generated for each locus during abundance estimation. Default: 1000' )
@@ -98,12 +100,12 @@
     parser.add_option( "--genes_exp_output", dest="genes_exp_output" )
     parser.add_option( "--tss_groups_exp_output", dest="tss_groups_exp_output" )
     parser.add_option( "--cds_exp_fpkm_tracking_output", dest="cds_exp_fpkm_tracking_output" )
+    parser.add_option( "--cds_diff_output", dest="cds_diff_output" )
     parser.add_option( "--isoforms_count_tracking_output", dest="isoforms_count_tracking_output" )
     parser.add_option( "--genes_count_tracking_output", dest="genes_count_tracking_output" )
     parser.add_option( "--cds_count_tracking_output", dest="cds_count_tracking_output" )
     parser.add_option( "--tss_groups_count_tracking_output", dest="tss_groups_count_tracking_output" )
     parser.add_option( "--splicing_diff_output", dest="splicing_diff_output" )
-    parser.add_option( "--cds_diff_output", dest="cds_diff_output" )
     parser.add_option( "--promoters_diff_output", dest="promoters_diff_output" )
     parser.add_option( "--run_info_output", dest="run_info_output" )
     parser.add_option( "--read_groups_info_output", dest="read_groups_info_output" )
@@ -137,7 +139,6 @@
     if not os.path.exists( cuffdatadir ):
         os.makedirs( cuffdatadir )
     
-    
     # If doing bias correction, set/link to sequence file.
     if options.do_bias_correction:
         if options.ref_file != 'None':
@@ -162,6 +163,10 @@
     cmd = "cuffdiff --no-update-check -q"
     
     # Add options.
+    if options.library_norm_method:
+        cmd += ( " --library-norm-method %s" % options.library_norm_method )
+    if options.dispersion_method:
+        cmd += ( " --dispersion-method %s" % options.dispersion_method )
     if options.inner_dist_std_dev:
         cmd += ( " -s %i" % int ( options.inner_dist_std_dev ) )
     if options.num_threads:
@@ -188,7 +193,7 @@
     if options.groups:
         cmd += " --labels "
         for label in options.labels:
-            cmd += label + ","
+            cmd += '"%s",' % label
         cmd = cmd[:-1]
 
         cmd += " " + options.inputA + " "
--- a/cuffdiff_wrapper.xml	Mon Feb 04 21:23:20 2013 -0600
+++ b/cuffdiff_wrapper.xml	Fri Nov 08 14:54:01 2013 -0600
@@ -1,78 +1,30 @@
-<tool id="cuffdiff_cummerbund" name="Cuffdiff" version="0.0.6">
-    <!-- Wrapper supports Cuffdiff versions v1.3.0-v2.0 -->
+<tool id="cuffdiff_cummerbund" name="Cuffdiff for cummeRbund" version="0.0.7">
+    <!-- Wrapper supports Cuffdiff versions 2.1.0-2.1.1 -->
     <description>find significant changes in transcript expression, splicing, and promoter use</description>
     <requirements>
-        <requirement type="package">cufflinks</requirement>
+        <requirement type="package" version="2.1.1">cufflinks</requirement>
     </requirements>
-    <command interpreter="python">
-        #set sel_outputs = $output_sel.__str__.split(',')
-        cuffdiff_wrapper.py
+    <version_command>cuffdiff 2>&amp;1 | head -n 1</version_command>
+    <command>
+        cuffdiff
+            --no-update-check
             --FDR=$fdr
             --num-threads="4"
             --min-alignment-count=$min_alignment_count
-
-            #if 'cuffdata' in $sel_outputs or not $output_sel:
-                --cuffdatadir=$cuffdata.extra_files_path
-            #end if
-            #if 'cummeRbund_db' in $sel_outputs:
-                --cummeRbund_db=$cummeRbund_db
-            #end if
+            --library-norm-method=$library_norm_method
+            --dispersion-method=$dispersion_method
 
-            #if 'isoforms_fpkm_tracking' in $sel_outputs:
-                --isoforms_fpkm_tracking_output=$isoforms_fpkm_tracking
-            #end if
-            #if 'genes_fpkm_tracking' in $sel_outputs:
-                --genes_fpkm_tracking_output=$genes_fpkm_tracking
-            #end if
-            #if 'cds_fpkm_tracking' in $sel_outputs:
-                --cds_fpkm_tracking_output=$cds_fpkm_tracking
-            #end if
-            #if 'tss_groups_fpkm_tracking' in $sel_outputs:
-                --tss_groups_fpkm_tracking_output=$tss_groups_fpkm_tracking
-            #end if
-            #if 'isoforms_exp_diff' in $sel_outputs:
-                --isoforms_exp_output=$isoforms_exp_diff
-            #end if
-            #if 'genes_exp_diff' in $sel_outputs:
-                --genes_exp_output=$genes_exp_diff
-            #end if
-            #if 'tss_groups_exp_diff' in $sel_outputs:
-                --tss_groups_exp_output=$tss_groups_exp_diff
-            #end if
-            #if 'cds_exp_fpkm_tracking' in $sel_outputs:
-                --cds_exp_fpkm_tracking_output=$cds_exp_fpkm_tracking
-            #end if
-            #if 'splicing_diff' in $sel_outputs:
-                --splicing_diff_output=$splicing_diff
-            #end if
-            #if 'cds_diff' in $sel_outputs:
-                --cds_diff_output=$cds_diff
-            #end if
-            #if 'promoters_diff' in $sel_outputs:
-                --promoters_diff_output=$promoters_diff
-            #end if
-            #if 'cds_read_group_tracking' in $sel_outputs:
-                --cds_read_group_tracking=$cds_read_group_tracking
-            #end if
-            #if 'tss_groups_read_group_tracking' in $sel_outputs:
-                --tss_groups_read_group_tracking=$tss_groups_read_group_tracking
-            #end if
-            #if 'genes_read_group_tracking' in $sel_outputs:
-                --genes_read_group_tracking=$genes_read_group_tracking
-            #end if
-            #if 'isoforms_read_group_tracking' in $sel_outputs:
-                --isoforms_read_group_tracking=$isoforms_read_group_tracking
-            #end if
-            
             ## Set advanced data parameters?
             #if $additional.sAdditional == "Yes":
-                -m $additional.frag_mean_len
-                -s $additional.frag_len_std_dev
-            #end if
-
-            ## Normalization?
-            #if str($do_normalization) == "Yes":
-            -N
+                #if $additional.frag_mean_len:
+                    -m $additional.frag_mean_len
+                #end if
+                #if $additional.frag_len_std_dev:
+                    -s $additional.frag_len_std_dev
+                #end if
+                #if $additional.max_bundle_frags:
+                    --max-bundle-frags="$additional.max_bundle_frags"
+                #end if
             #end if
 
             ## Multi-read correct?
@@ -82,67 +34,77 @@
 
             ## Bias correction?
             #if $bias_correction.do_bias_correction == "Yes":
-	        -b
+               -b
                 #if $bias_correction.seq_source.index_source == "history":
-                    --ref_file=$bias_correction.seq_source.ref_file
+                    ## Custom genome from history.
+                    $bias_correction.seq_source.ref_file
                 #else:
-                    --ref_file="None"
+                    ## Built-in genome.
+                    ${__get_data_table_entry__('sam_fa_indexes', 'value', $gtf_input.dbkey, 'path')}
                 #end if
-                --dbkey=${gtf_input.metadata.dbkey}
-                --index_dir=${GALAXY_DATA_INDEX_DIR}
-            #end if
-                
-            ## Inputs.
-            --inputA=$gtf_input
-            #if $group_analysis.do_groups == "No":
-                --input1=$aligned_reads1
-                --input2=$aligned_reads2
-            #else:
-                ## Replicates.
-                --labels
-                #for $group in $group_analysis.groups
-                    ${group.group}
-                #end for
-                --files
-                #for $group in $group_analysis.groups
-                    #for $file in $group.files:
-                        ${file.file}
-                    #end for
-                    ,
-                #end for
             #end if
 
+            #set labels = '\'' + '\',\''.join( [ str( $condition.name ) for $condition in $conditions ] ) + '\''
+            --labels $labels
+
+            ## Inputs.
+            $gtf_input
+            #for $condition in $conditions:
+                #set samples = ','.join( [ str( $sample.sample ) for $sample in $condition.samples ] )
+                $samples
+            #end for
+ 
+            ## If build cummerbund db
+            #if $build_cummerbund_db:
+                &amp;&amp; echo 'library(cummeRbund)' > cuffData.r 
+                #if $bias_correction.do_bias_correction == "Yes":
+                    #if $bias_correction.seq_source.index_source == "history":
+                        ## Custom genome from history.
+                        &amp;&amp; echo 'cuff&lt;-readCufflinks( dbFile = "cuffdata.db", gtfFile = "$gtf_input", genome = "$bias_correction.seq_source.ref_file", rebuild = T)' >> cuffData.r
+                    #else:
+                        ## Built-in genome.
+                        ${__get_data_table_entry__('sam_fa_indexes', 'value', $gtf_input.dbkey, 'path')}
+                        &amp;&amp; echo 'cuff&lt;-readCufflinks( dbFile = "cuffdata.db", gtfFile = "$gtf_input", genome = "${__get_data_table_entry__('sam_fa_indexes', 'value', $gtf_input.dbkey, 'path')}", rebuild = T)' >> cuffData.r
+                    #end if
+                #else 
+                    &amp;&amp; echo 'cuff&lt;-readCufflinks( dbFile = "cuffdata.db", rebuild = T)' >> cuffData.r
+                #end if
+                &amp;&amp; Rscript --vanilla cuffData.r
+                &amp;&amp; cp cuffdata.db $cummerbund_db
+            #end if
     </command>
     <inputs>
         <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts" help="A transcript GFF3 or GTF file produced by cufflinks, cuffcompare, or other source."/>
-        <conditional name="group_analysis"> 
-            <param name="do_groups" type="select" label="Perform replicate analysis" help="Perform cuffdiff with replicates in each group.">
-                <option value="No">No</option>
-                <option value="Yes">Yes</option>
-            </param>
-            <when value="Yes">
-                <repeat name="groups" title="Group">
-                    <param name="group" title="Group name" type="text" label="Group name (no spaces or commas)"/>
-                    <repeat name="files" title="Replicate">
-                        <param name="file" label="Add file" type="data" format="sam,bam"/>
-                    </repeat>
-                </repeat>
-            </when>
-            <when value="No">
-                <param format="sam,bam" name="aligned_reads1" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""/>
-                <param format="sam,bam" name="aligned_reads2" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""/>
-            </when>
-        </conditional>
+
+        <repeat name="conditions" title="Condition" min="2">
+            <param name="name" title="Condition name" type="text" label="Name"/>
+            <repeat name="samples" title="Replicate" min="1">
+                <param name="sample" label="Add replicate" type="data" format="sam,bam"/>
+            </repeat>
+        </repeat>
+        <param name="time_series" type="boolean" checked="false" truevalue="--time-series" falsevalue="" optional="true" label="treat samples as a time-series">
+            <help>
+            Instructs Cuffdiff to analyze the provided samples as a time series, rather than testing for differences between all pairs of samples. 
+            Samples should be provided in increasing time order at the command line (e.g first time point SAM, second timepoint SAM, etc.)
+            </help>
+        </param>
+
+        <param name="library_norm_method" type="select" label="Library normalization method">
+            <option value="geometric" selected="True">geometric</option>
+            <option value="classic-fpkm">classic-fpkm</option>
+            <option value="quartile">quartile</option>
+        </param>
+
+        <param name="dispersion_method" type="select" label="Dispersion estimation method" help="If using only one sample per condition, you must use 'blind.'">
+            <option value="pooled" selected="True">pooled</option>
+            <option value="per-condition">per-condition</option>
+            <option value="blind">blind</option>
+        </param>
 
         <param name="fdr" type="float" value="0.05" label="False Discovery Rate" help="The allowed false discovery rate."/>
 
         <param name="min_alignment_count" type="integer" value="10" label="Min Alignment Count" help="The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples."/>
 
-        <param name="do_normalization" type="select" label="Perform quartile normalization" help="Removes top 25% of genes from FPKM denominator to improve accuracy of differential expression calls for low abundance transcripts.">
-            <option value="No">No</option>
-            <option value="Yes">Yes</option>
-        </param>
-
         <param name="multiread_correct" type="select" label="Use multi-read correct" help="Tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome.">
             <option value="No" selected="true">No</option>
             <option value="Yes">Yes</option>
@@ -168,142 +130,95 @@
             <when value="No"></when>
         </conditional>
 
+        <param name="include_read_group_files" type="select" label="Include Read Group Datasets" help="Read group datasets provide information on replicates.">
+            <option value="No" selected="true">No</option>
+            <option value="Yes">Yes</option>
+        </param>
+        <param name="build_cummerbund_db" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Build cummeRbund database"/>
         <conditional name="additional">
-            <param name="sAdditional" type="select" label="Set Additional Parameters? (not recommended)">
+            <param name="sAdditional" type="select" label="Set Additional Parameters? (not recommended for paired-end reads)">
                 <option value="No">No</option>
                 <option value="Yes">Yes</option>
             </param>
             <when value="No"></when>
             <when value="Yes">
-                <param name="frag_mean_len" type="integer" value="200" label="Average Fragment Length"/>
-                <param name="frag_len_std_dev" type="integer" value="80" label="Fragment Length Standard Deviation"/>
+                <param name="frag_mean_len" type="integer" value="" optional="true" label="Average Fragment Length Default: 200">
+                    <help>
+                    Note: Cufflinks now learns the fragment length mean for each SAM file, 
+                    so using this option is no longer recommended with paired-end reads.
+                    </help>
+                </param>
+                <param name="frag_len_std_dev" type="integer" value="" optional="true" label="Fragment Length Standard Deviation Default: 80">
+                    <help>
+                    Note: Cufflinks now learns the fragment length mean for each SAM file, 
+                    so using this option is no longer recommended with paired-end reads.
+                    </help>
+                </param>
+                <param name="max_bundle_frags" type="integer" value="" optional="true" label="--max-bundle-frags">
+                    <help>
+                    Sets the maximum number of fragments a locus may have before being skipped. Skipped loci are listed in skipped.gtf. Default: 1000000
+                    </help>
+                    <validator type="in_range" message="Value greater than 0" min="1"/>
+                </param>
             </when>
         </conditional>
+    </inputs>
 
-        <param name="output_sel" type="select" multiple="true" display="checkboxes" force_select="true" label="Select outputs for history datasets">
-            <option value="cuffdata">cuffdata - html page with links to cuffdiff outputs</option>
-            <option value="cummeRbund_db">cummeRbund database</option>
-            <option value="run_info">run.info</option>
-            <option value="read_groups_info">read_groups.info</option>
-            <option value="splicing_diff">splicing.diff</option>
-            <option value="promoters_diff">promoters.diff</option>
-            <option value="genes_exp_diff">genes_exp.diff</option>
-            <option value="genes_fpkm_tracking">genes.fpkm_tracking</option>
-            <option value="genes_count_tracking">genes.count_tracking</option>
-            <option value="genes_read_group_tracking">genes.read_group_tracking</option>
-            <option value="isoforms_exp_diff">isoforms.exp_diff</option>
-            <option value="isoforms_fpkm_tracking">isoforms.fpkm_tracking</option>
-            <option value="isoforms_count_tracking">isoforms.count_tracking</option>
-            <option value="isoforms_read_group_tracking">isoforms.read_group_tracking</option>
-            <option value="cds_diff">cds.diff</option>
-            <option value="cds_exp_diff">cds_exp.diff</option>
-            <option value="cds_fpkm_tracking">cds.fpkm_tracking</option>
-            <option value="cds_count_tracking">cds.count_tracking</option>
-            <option value="cds_read_group_tracking">cds.read_group_tracking</option>
-            <option value="tss_groups_exp_diff">tss_groups_exp.diff</option>
-            <option value="tss_groups_fpkm_tracking">tss_groups.fpkm_tracking</option>
-            <option value="tss_groups_count_tracking">tss_groups.count_tracking</option>
-            <option value="tss_groups_read_group_tracking">tss_groups.read_group_tracking</option>
-        </param>
-        
-    </inputs>
+    <stdio>
+        <regex match="Error" source="both" level="fatal" description="Error"/>
+        <regex match=".*" source="both" level="log" description="tool progress"/>
+    </stdio>
 
     <outputs>
-        <data format="text" name="run_info" label="${tool.name} on ${on_string}: run.info">
-            <filter>output_sel and 'run_info' in output_sel</filter>
-        </data>
-        <data format="tabular" name="read_groups_info" label="${tool.name} on ${on_string}: read_groups.info">
-            <filter>output_sel and 'read_groups_info' in output_sel</filter>
-        </data>
-        <data format="tabular" name="splicing_diff" label="${tool.name} on ${on_string}: splicing differential expression testing">
-            <filter>output_sel and 'splicing_diff' in output_sel</filter>
-        </data>
-        <data format="tabular" name="promoters_diff" label="${tool.name} on ${on_string}: promoters differential expression testing">
-            <filter>output_sel and 'promoters_diff' in output_sel</filter>
-        </data>
-        <data format="tabular" name="cds_diff" label="${tool.name} on ${on_string}: CDS overloading diffential expression testing">
-            <filter>output_sel and 'cds_diff' in output_sel</filter>
-        </data>
-        <data format="tabular" name="cds_exp_diff" label="${tool.name} on ${on_string}: CDS differential expression testing">
-            <filter>output_sel and 'cds_exp_diff' in output_sel</filter>
+        <!-- Optional read group datasets. -->
+        <data format="cuffdatadb" name="cummerbund_db" label="${tool.name} on ${on_string}: cummeRbund sqlite Database" >
+            <filter>build_cummerbund_db</filter>
         </data>
-        <data format="tabular" name="cds_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM tracking">
-            <filter>output_sel and 'cds_fpkm_tracking' in output_sel</filter>
-        </data>
-        <data format="tabular" name="cds_count_tracking" label="${tool.name} on ${on_string}: CDS counts">
-            <filter>output_sel and 'cds_count_tracking' in output_sel</filter>
-        </data>
-        <data format="tabular" name="cds_read_group_tracking" label="${tool.name} on ${on_string}: CDS Read Group tracking">
-            <filter>output_sel and 'cds_read_group_tracking' in output_sel</filter>
+        <data format="tabular" name="isoforms_read_group" label="${tool.name} on ${on_string}: isoforms read group tracking" from_work_dir="isoforms.read_group_tracking" >
+            <filter>(params['include_read_group_files'] == 'Yes'</filter>
         </data>
-        <data format="tabular" name="tss_groups_exp_diff" label="${tool.name} on ${on_string}: TSS groups differential expression testing">
-            <filter>output_sel and 'tss_groups_exp_diff' in output_sel</filter>
+        <data format="tabular" name="genes_read_group" label="${tool.name} on ${on_string}: genes read group tracking" from_work_dir="genes.read_group_tracking" >
+            <filter>(params['include_read_group_files'] == 'Yes'</filter>
         </data>
-        <data format="tabular" name="tss_groups_fpkm_tracking" label="${tool.name} on ${on_string}: TSS groups FPKM tracking">
-            <filter>output_sel and 'tss_groups_fpkm_tracking' in output_sel</filter>
-        </data>
-        <data format="tabular" name="tss_groups_count_tracking" label="${tool.name} on ${on_string}: TSS groups counts">
-            <filter>output_sel and 'tss_groups_count_tracking' in output_sel</filter>
+        <data format="tabular" name="cds_read_group" label="${tool.name} on ${on_string}: CDs read group tracking" from_work_dir="cds.read_group_tracking" >
+            <filter>(params['include_read_group_files'] == 'Yes'</filter>
         </data>
-        <data format="tabular" name="tss_groups_read_group_tracking" label="${tool.name} on ${on_string}: TSS groups Read Group tracking">
-            <filter>output_sel and 'tss_groups_read_group_tracking' in output_sel</filter>
-        </data>
-        <data format="tabular" name="isoforms_exp_diff" label="${tool.name} on ${on_string}: transcript differential expression testing">
-            <filter>output_sel and 'isoforms_exp_diff' in output_sel</filter>
-        </data>
-        <data format="tabular" name="isoforms_fpkm_tracking" label="${tool.name} on ${on_string}: transcript FPKM tracking">
-            <filter>output_sel and 'isoforms_fpkm_tracking' in output_sel</filter>
-        </data>
-        <data format="tabular" name="isoforms_count_tracking" label="${tool.name} on ${on_string}: transcript counts">
-            <filter>output_sel and 'isoforms_count_tracking' in output_sel</filter>
-        </data>
-        <data format="tabular" name="isoforms_read_group_tracking" label="${tool.name} on ${on_string}: transcript Read Group tracking">
-            <filter>output_sel and 'isoforms_read_group_tracking' in output_sel</filter>
-        </data>
-        <data format="tabular" name="genes_exp_diff" label="${tool.name} on ${on_string}: gene differential expression testing">
-            <filter>output_sel and 'genes_exp_diff' in output_sel</filter>
+        <data format="tabular" name="tss_groups_read_group" label="${tool.name} on ${on_string}: TSS groups read group tracking" from_work_dir="tss_groups.read_group_tracking" >
+            <filter>(params['include_read_group_files'] == 'Yes'</filter>
         </data>
-        <data format="tabular" name="genes_fpkm_tracking" label="${tool.name} on ${on_string}: gene FPKM tracking">
-            <filter>output_sel and 'genes_fpkm_tracking' in output_sel</filter>
-        </data>
-        <data format="tabular" name="genes_count_tracking" label="${tool.name} on ${on_string}: gene counts">
-            <filter>output_sel and 'genes_count_tracking' in output_sel</filter>
-        </data>
-        <data format="tabular" name="genes_read_group_tracking" label="${tool.name} on ${on_string}: gene Read Group tracking">
-            <filter>output_sel and 'genes_read_group_tracking' in output_sel</filter>
-        </data>
-        <data format="cuffdata" name="cuffdata" label="${tool.name} on ${on_string}: cuffdata" >
-            <filter>not output_sel or output_sel and 'cuffdata' in output_sel</filter>
-        </data>
-        <data format="cuffdatadb" name="cummeRbund_db" label="${tool.name} on ${on_string}: cummeRbund sqlite Database" >
-            <filter>output_sel and 'cummeRbund_db' in output_sel</filter>
-        </data>
+
+        <!-- Standard datasets. -->
+        <data format="tabular" name="splicing_diff" label="${tool.name} on ${on_string}: splicing differential expression testing" from_work_dir="splicing.diff" />
+        <data format="tabular" name="promoters_diff" label="${tool.name} on ${on_string}: promoters differential expression testing" from_work_dir="promoters.diff" />
+        <data format="tabular" name="cds_diff" label="${tool.name} on ${on_string}: CDS overloading diffential expression testing" from_work_dir="cds.diff" />
+        <data format="tabular" name="cds_exp_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM differential expression testing" from_work_dir="cds_exp.diff" />
+        <data format="tabular" name="cds_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM tracking" from_work_dir="cds.fpkm_tracking" />
+        <data format="tabular" name="tss_groups_exp" label="${tool.name} on ${on_string}: TSS groups differential expression testing" from_work_dir="tss_group_exp.diff" />
+        <data format="tabular" name="tss_groups_fpkm_tracking" label="${tool.name} on ${on_string}: TSS groups FPKM tracking" from_work_dir="tss_groups.fpkm_tracking" />
+        <data format="tabular" name="genes_exp" label="${tool.name} on ${on_string}: gene differential expression testing" from_work_dir="gene_exp.diff" />
+        <data format="tabular" name="genes_fpkm_tracking" label="${tool.name} on ${on_string}: gene FPKM tracking" from_work_dir="genes.fpkm_tracking" />
+        <data format="tabular" name="isoforms_exp" label="${tool.name} on ${on_string}: transcript differential expression testing" from_work_dir="isoform_exp.diff" />
+        <data format="tabular" name="isoforms_fpkm_tracking" label="${tool.name} on ${on_string}: transcript FPKM tracking" from_work_dir="isoforms.fpkm_tracking" />
     </outputs>
-    <stdio>
-        <exit_code range="1:"  level="fatal"   description="Cufflinks Err" />
-    </stdio>
-
 
     <tests>
         <test>
                 <!--
                     cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam 
                 -->
+                <!-- 
+                    NOTE: as of version 0.0.6 of the wrapper, tests cannot be run because multiple inputs to a repeat
+                    element are not supported.
                 <param name="gtf_input" value="cuffcompare_out5.gtf" ftype="gtf" />
                 <param name="do_groups" value="No" />
                 <param name="aligned_reads1" value="cuffdiff_in1.sam" ftype="sam" />
                 <param name="aligned_reads2" value="cuffdiff_in2.sam" ftype="sam" />
-                <!-- Defaults. -->
                 <param name="fdr" value="0.05" />
                 <param name="min_alignment_count" value="0" />
                 <param name="do_bias_correction" value="No" />
                 <param name="do_normalization" value="No" />
                 <param name="multiread_correct" value="No"/>
                 <param name="sAdditional" value="No"/>
-                <!-- 
-                    Line diffs are needed because cuffdiff does not produce deterministic output.
-                    TODO: can we find datasets that lead to deterministic behavior?
-                -->
                 <output name="splicing_diff" file="cuffdiff_out9.txt"/>
                 <output name="promoters_diff" file="cuffdiff_out10.txt"/>
                 <output name="cds_diff" file="cuffdiff_out11.txt"/>
@@ -315,6 +230,7 @@
                 <output name="genes_fpkm_tracking" file="cuffdiff_out6.txt" lines_diff="200"/>
                 <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="200"/>
                 <output name="isoforms_fpkm_tracking" file="cuffdiff_out5.txt" lines_diff="200"/>
+                -->
         </test>
     </tests>
 
--- a/cummerbund_wrapper.py	Mon Feb 04 21:23:20 2013 -0600
+++ b/cummerbund_wrapper.py	Fri Nov 08 14:54:01 2013 -0600
@@ -13,8 +13,10 @@
 def html_report_from_directory( html_out, dir ):
     html_out.write( '<html>\n<head>\n<title>Galaxy - cummeRbund Output</title>\n</head>\n<body>\n<p/>\n<ul>\n' )
     for fname in sorted( os.listdir( dir ) ):
-        # html_out.write(  '<li><a href="%s">%s</a></li>\n' % ( fname, fname ) )
-        html_out.write(  '<li><a href="%s"><img src="%s" alt="" height="80" width="80">%s</a></li>\n' % ( fname, fname , fname ) )
+        if fname.endswith(".txt"):
+            html_out.write(  '<li><a href="%s">%s</a></li>\n' % ( fname, fname ) )
+        else:
+            html_out.write(  '<li><a href="%s"><img src="%s" alt="" height="80" width="80">%s</a></li>\n' % ( fname, fname , fname ) )
     html_out.write( '</ul>\n</body>\n</html>\n' )
 
 def __main__():
--- a/cummerbund_wrapper.xml	Mon Feb 04 21:23:20 2013 -0600
+++ b/cummerbund_wrapper.xml	Fri Nov 08 14:54:01 2013 -0600
@@ -1,5 +1,4 @@
-<tool id="cummerbund" name="cummeRbund" version="0.0.6">
-    
+<tool id="cummerbund" name="cummeRbund" version="0.0.7">
     <description>R package designed to aid and simplify the task of analyzing Cufflinks RNA-Seq output</description>
     
     <command interpreter="python">
@@ -64,8 +63,12 @@
 					<param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Replicates?"/>
 				</when>
 				<when value="maplot">
-					<param name="x" type="text" label="Sample name 1"/>
-					<param name="y" type="text" label="Sample name 2"/>
+					<param name="x" type="text" label="Sample name 1" help="Condition1 name used in cuffdiff">
+                                        <validator type="empty_field" message="A Condition name from the cuffdiff run is required"/>
+                                        </param>
+					<param name="y" type="text" label="Sample name 2" help="Condition2 name used in cuffdiff">
+                                        <validator type="empty_field" message="A Condition name from the cuffdiff run is required"/>
+                                        </param>
 					<param name="use_count" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Use Count?"/>
 				</when>
 				<when value="dendrogram">
@@ -185,7 +188,7 @@
         <exit_code range="1:"  level="fatal"   description="CummerBund Error" />
     </stdio>
     <outputs>
-        <data format="data" name="output_database" label="${tool.name} on ${on_string}: Database File (sqlite)">
+        <data format="cuffdatadb" name="output_database" label="${tool.name} on ${on_string}: Database File (sqlite)">
             <filter>backend_database_source['backend_database_selector'] == "cuffdiff_output"</filter>
         </data>
     	<data format="html" name="output_html" label="${tool.name} on ${on_string} (HTML)"/>
@@ -244,6 +247,18 @@
                          rebuild = F)
 #end if
 
+## Print out info
+print(cuff)
+sink("cuffdb_info.txt")
+print(cuff)
+print("SAMPLES:")
+samples(cuff)
+print("REPLICATES:")
+replicates(cuff)
+print("FEATURES:")
+print(annotation(genes(cuff)))
+sink()
+
 #for $i, $p in enumerate($plots, start=1):
 	#set $filename = "plot%02d-%s.png" % ($i, $p.plot['type'])
 png(filename = "${filename}", width = ${p.width}, height = ${p.height})
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffcompare_out5.gtf	Fri Nov 08 14:54:01 2013 -0600
@@ -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 "u"; 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_00000062"; 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_00000063"; 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 "u"; tss_id "TSS32";
+chr1	Cufflinks	exon	3201597	3201666	.	.	.	gene_id "XLOC_000030"; transcript_id "TCONS_00000065"; 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_00000066"; 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_00000067"; 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_00000068"; 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_00000069"; 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_00000070"; 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_00000071"; 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_00000072"; 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_00000073"; 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_00000074"; 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_00000075"; 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_00000076"; 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_00000077"; 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_00000078"; 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_00000079"; 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_00000080"; 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_00000081"; 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_00000082"; 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_00000083"; 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_00000084"; 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_00000085"; 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_00000086"; 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_00000087"; 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_00000088"; 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_00000089"; 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_00000090"; 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_00000091"; 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_00000092"; 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_00000093"; 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_00000094"; 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_00000095"; 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_00000096"; 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_00000097"; 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_00000098"; 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_00000099"; 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_00000100"; 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/cuffdiff_in1.sam	Fri Nov 08 14:54:01 2013 -0600
@@ -0,0 +1,400 @@
+EAS38_8_212_338_985	0	chr1	3004981	0	35M	*	0	0	CCAATGGGCCTCTATTTGCAGTGATGGGCGAGTAG	hhhhhhhhhhhhhEhhhhYhhhhUhhh@Ih?BZ?e	NM:i:2
+EAS38_8_8_215_414	0	chr1	3035356	0	35M	*	0	0	TACCCCATAAAAGCCCCTGGCTTTCGCGCCTCGTG	hhhhhhhhhhhhhhhhhhhhhhh`GI>PPIQPBOH	NM:i:1
+EAS38_8_8_622_393	16	chr1	3065512	0	35M	*	0	0	AAAAAAAAAAAAACAAAAAAAAAAAAAACAGCGAG	hhHhhhhhhhhhhMhhhhhhhhhhhhhhhhhhhhh	NM:i:2
+EAS38_8_53_557_326	16	chr1	3075162	0	35M	*	0	0	TAGAGAAATGGATACAGAAAGTGTGGTAATTTACA	Ihehhhhh]hhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:2
+EAS38_8_259_911_538	0	chr1	3099409	0	35M	*	0	0	TTTGGCTGGGAGACAATTAATGACTGCTTTTTTTT	hhhhhhhhhhhh_hhhhhNhhP\hhaEhhHhNhhh	NM:i:2
+EAS38_8_284_729_569	16	chr1	3113004	255	35M	*	0	0	CTATCTGTTGCAAAGAGAACTTTCCTTGGTGTAAG	EIIEKhRh@K_hahhhhhhh`ehhhhhhhhhhhhh	NM:i:0
+EAS38_8_27_537_242	0	chr1	3118613	255	35M	*	0	0	AGGACTCACATTCCCTTACTTTGTTTACAAAATGA	hhh`hhhhhhhhhhhhhhhhhhhhhh]hhYXOhD`	NM:i:0
+EAS38_8_38_947_12	0	chr1	3131368	0	35M	*	0	0	TATTAGTCCCCTATCANATTTAGGATTGTTAATAA	hhhhhhh_bchhhhUh;\hhhhh`EXcIVhNJZ]P	NM:i:2
+EAS38_8_205_433_879	16	chr1	3136988	0	35M	*	0	0	CATATCAATTGAACGGAACTAAAGTCTGTGACAGT	hhhhchhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_155_191_162	16	chr1	3136999	0	35M	*	0	0	AACGGAACTAAAGTCTGTGACAGTGGACATAGCTG	hh_h\hhYhhhhhMhfhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_216_635_828	0	chr1	3137063	0	35M	*	0	0	ATCTGGAATTATGTGATTATAATTTTCTTAGCATT	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_317_949_784	0	chr1	3137063	0	35M	*	0	0	ATCTGGAATTATGTGATTATAATTTTCTTAGCATT	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhNchh	NM:i:0
+EAS38_8_278_281_786	16	chr1	3137078	0	35M	*	0	0	ATTATAATTTTCTTAGCATTTTCTTTGTAAAAAAA	AhhhQhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_228_462_705	0	chr1	3137133	0	35M	*	0	0	GTTGGTGTATAGTAAAAAGTAAAGAAATTCTGAGA	hhhhhhhhhhhhhhhhhhh_hghhWhYh`LhhKbY	NM:i:0
+EAS38_8_299_582_840	0	chr1	3137133	0	35M	*	0	0	GTTGGTGTATAGTAAAAAGTAAAGAAATTCTGAGA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhWhhhhh	NM:i:0
+EAS38_8_125_742_683	16	chr1	3137135	0	35M	*	0	0	TGGTGTATAGTAAAAAGTAAAGAAATTCTGAGAGG	GJCZSShchhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_208_212_874	0	chr1	3137137	0	35M	*	0	0	GTGTATAGTAAAAAGTAAAGAAATTCTGAGAGGAG	hhhhhhhhhhhhhhhhhhhhhhhhh[hhhhhhh`h	NM:i:0
+EAS38_8_241_424_62	16	chr1	3137137	0	35M	*	0	0	GTGTATAGTAAAAAGTAAAGAAATTCTGAGAGGAG	hhhhhhhhehhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_245_195_910	16	chr1	3137137	0	35M	*	0	0	GTGTATAGTAAAAAGTAAAGAAATTCTGAGAGGAG	Bhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_234_890_706	0	chr1	3137138	0	35M	*	0	0	TGTATAGTAAAAAGTAAAGAAATTCTGAGAGGAGT	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhUhh	NM:i:0
+EAS38_8_317_909_810	16	chr1	3137175	0	35M	*	0	0	TATTTTAGGATAATACATATATACATATGCAGTGT	hhhhhhhaThhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_111_444_456	0	chr1	3137180	0	35M	*	0	0	TAGGTTAATACATATATACATATGCAGTGTGTGTG	hhhhhhhhhhhhhhhhhhhahhhhhhhhgehhhhH	NM:i:1
+EAS38_8_134_193_731	0	chr1	3137180	0	35M	*	0	0	TAGGATAATACATATATACATATGCAGTGTGTGTG	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_138_869_374	0	chr1	3137180	0	35M	*	0	0	TAGGATAATACATATATACATATGCAGTGTGTGTG	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_36_257_907	0	chr1	3137192	0	35M	*	0	0	TATATACATATGCAGTGTGTGTGCCAGTGGTGTTA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhNJDhS	NM:i:0
+EAS38_8_50_322_852	0	chr1	3137192	0	35M	*	0	0	TATATACATATGCAGTGTGTGTGCCAGTGGTGTTA	hhhhhhhhhhhhhhhhhhhhhhhRcZhhhhVhShY	NM:i:0
+EAS38_8_207_430_640	16	chr1	3146524	0	35M	*	0	0	AAAAAACATCGGCACAACAATCAAAAAAAAAAAAA	VE_AhhhhFhhhhh]hhhhhhhhhhhhhhhhhhhh	NM:i:2
+EAS38_8_289_914_684	0	chr1	3154024	255	35M	*	0	0	TCACAGAAGGCTCACTTCCTTTCTGTCTGTGTCAA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhdhhMGT	NM:i:0
+EAS38_8_35_737_747	16	chr1	3174758	255	35M	*	0	0	TTTTGGGTGAGATGGAATCTCAGAGTAGTTATTTT	[hghdhMhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_75_492_572	16	chr1	3174758	255	35M	*	0	0	TTTTGGGTGAGATGGAATCTCAGAGTAGTTATTTT	[Vhhh^hhhhhhhhhhhdhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_187_160_172	16	chr1	3175562	255	35M	*	0	0	TAGTCTGGTCTGTGGCTTCAGCGGTAGGATGGCCT	BT\JAGMQVRN[QhYZGchhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_56_600_894	0	chr1	3175828	255	35M	*	0	0	GAGAAAGAGGTGGGAAGGGAAAGAGAGAGAGAAGA	hhhhhhhhhhhhhhhhhhhhhhhhhhhShChDKhI	NM:i:0
+EAS38_8_106_467_709	16	chr1	3181781	255	35M	*	0	0	CTTTAGTACAGGTTACATTCCATACCTATAGCAAG	hhhhhhhhhhh`hhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_199_476_527	16	chr1	3181781	255	35M	*	0	0	CTTTAGTACAGGTTACATTCCATACCTATAGCAAG	E[dbhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_116_967_124	16	chr1	3187134	255	35M	*	0	0	ATAGCTCTTCATCTAGGGGTGGGACTTTTGAGATT	hghYhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_182_44_990	16	chr1	3187394	255	35M	*	0	0	GAAATGCTCATTCTCATAGAGAAGAGATTGCCTAG	EhhhaKhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_203_996_132	16	chr1	3187394	255	35M	*	0	0	GAAATGATCATTCTCATAGAGAAGAGATTGCCTAG	JXJ`_eFVVhhhhhchhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_318_612_118	0	chr1	3188522	255	35M	*	0	0	GTATTCTTAATCTATTGTGTTTTGTTTGTTCTTTG	hhhhhhhhhhhhhhhhhhShhhhIhhhWhh_hYhC	NM:i:1
+EAS38_8_52_573_715	16	chr1	3188914	255	35M	*	0	0	TTTGGAAGATAGTTTTCATTTCAGGACTGTCATTA	hh]hDhh\hhhghhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_82_668_114	16	chr1	3189123	255	35M	*	0	0	TAGATTCTGTTGAAAGCTGCTTGTGTAGGTGCTGG	Jhfheh@_Nh`hhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_229_732_980	16	chr1	3189293	255	35M	*	0	0	ATATGTAGAAAAAGAAAGCAATTAGATGTATCATA	hhhhWhhOhhhhhghhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_49_685_15	0	chr1	3189811	255	35M	*	0	0	CTTTTAAAATGACCACAGTGTACTTTATTTAATTA	hhhhhhhhhhhhhhhhhhhhhhhhhh]hhhPahZQ	NM:i:2
+EAS38_8_228_500_937	0	chr1	3189812	255	35M	*	0	0	TTTTAAAATGACCACAGTGTACTTTATTTAATGAT	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhLh	NM:i:1
+EAS38_8_8_865_653	0	chr1	3189812	255	35M	*	0	0	TTTTAAAATGACCACAGTGTACTTTATTTAATGAT	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_284_550_449	0	chr1	3189815	255	35M	*	0	0	TGAAATGACCACAGTGTACTTTATTTAATGATTTT	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhPhhhh	NM:i:1
+EAS38_8_44_493_707	0	chr1	3189839	255	35M	*	0	0	TTAATGATTTTTGTACTTTGTGTTGCAATAAAATA	hhhhhhhhhhhhhhhhhhhhhhhhRhhhhhhhhhh	NM:i:0
+EAS38_8_173_339_743	0	chr1	3189847	255	35M	*	0	0	TTTTGTACTTTGTGTTGCAATAAAATAAAAAAAAA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhZhhhf	NM:i:0
+EAS38_8_69_320_425	16	chr1	3189862	255	35M	*	0	0	TGAAATAAAAAAAAAAAAAAATCTACAAAATTCAA	_OahhShhhhAhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:2
+EAS38_8_253_215_784	0	chr1	3189882	255	35M	*	0	0	ATCTACAAAATTCAAATATATAAAATTTCAAGTTT	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_254_492_492	0	chr1	3189882	255	35M	*	0	0	ATCTACAAAATTCAAATATATAAAATTTCAAGTTT	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhchhhhh	NM:i:0
+EAS38_8_164_969_744	0	chr1	3189884	255	35M	*	0	0	CTACAAAATTCAAATATATAAAATTTCAAGTTTTC	hhhhhhhhhhhhhhhhhhhhhVhhWhTNchDhhgA	NM:i:0
+EAS38_8_76_118_672	0	chr1	3189938	255	35M	*	0	0	AGAAAAAAAATCAGATAACCGAGGAAAATTATTCA	hhhhhhhhhhhhhhhhhhhhhhhh]hhhhhThhR]	NM:i:0
+EAS38_8_322_903_184	16	chr1	3189967	255	35M	*	0	0	TATTCATTATGAAGTACTACTTTCCACTTCATTTC	O[ENehNVh`ahh]hhhhhhWhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_122_863_114	16	chr1	3189975	255	35M	*	0	0	ATGAAGTACTACTTTCCACTTCATTTCATCACAAA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_328_905_544	0	chr1	3189975	255	35M	*	0	0	ATGAAGTACTACTTTCCACTTCATTTCATCACAAA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhXhO	NM:i:0
+EAS38_8_49_611_982	16	chr1	3189991	255	35M	*	0	0	CACTTCATTTCATCACAAATTGTAACTTACTTAAC	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_149_471_590	0	chr1	3189993	255	35M	*	0	0	CTTCATTTCATCACAAATTGTAACTTACTTAACTG	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhc	NM:i:0
+EAS38_8_176_471_461	0	chr1	3189993	255	35M	*	0	0	CTTCATTTCATCACAAATTGTAACTTACTTAACTG	hhhhhhhhhhhhhhhhhhhhhhchhh`hhh[hhhO	NM:i:0
+EAS38_8_330_91_472	16	chr1	3189999	255	35M	*	0	0	TTAATCACAAATTGTAACTTACTTAACTGACCAAA	hhOhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_330_964_788	16	chr1	3189999	255	35M	*	0	0	TTCATCACAAATTGTAACTTACTTAACTGACCAAA	aIhhhh`hhhhhhhhhhhhhBhhhhhhhchhhhhh	NM:i:0
+EAS38_8_281_200_582	16	chr1	3190038	255	35M	*	0	0	CTATGGTACTGCAGTATAGAAAATACTCCACACAC	ONK[MhhhdhhQhhhhhhhMhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_241_125_175	16	chr1	3190056	255	35M	*	0	0	GAAAATAATCCACACACTGTGCTTTGAGCTAGAGC	HhhhhShIhhShhhhhhhhhhhhhhhhhhhhhhhh	NM:i:2
+EAS38_8_274_895_968	0	chr1	3190074	255	35M	*	0	0	GTGCTTTGAGCTAGAGCACTTGGAGTCACTGCACA	hhhhhhhhhhhhhhhhPhOhhhhPhhMTMXhLBMC	NM:i:1
+EAS38_8_274_589_297	16	chr1	3190081	255	35M	*	0	0	GAGCTAGAGCACTGGGAGTCACTGCCCAGGGCAGC	]W_IHUh_hh^WZDhhhhKhhh[hhhhhhhhhhhh	NM:i:1
+EAS38_8_11_418_433	0	chr1	3190094	255	35M	*	0	0	TGGAGTCACTGCCCAGGGCAGCAGCCTCCAACCAA	hhhhhhhhhhhhhhhhhhbCchhb`PUPhJWIOGA	NM:i:0
+EAS38_8_324_436_604	16	chr1	3190136	255	35M	*	0	0	ACACTTACAAGTTGAATTCTAAAGGAAGGTCTGGT	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_131_262_425	16	chr1	3190137	255	35M	*	0	0	CACGTACAAGTTGAATTCTAAAGGAAGGTCTGGTT	dVKEhhhhhhhWhhhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_5_661_318	16	chr1	3190137	255	35M	*	0	0	CACTTACAAGTTGAATTCTAAAGGAAGGTCTGGTT	F^O_ZhhhhhAhhhhhMh`hhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_109_581_805	0	chr1	3190144	255	35M	*	0	0	AAGTTGAATTCTAAAGGAAGGTCTGGTTATGTGGG	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_279_908_963	0	chr1	3190154	255	35M	*	0	0	CTAAAGGAAGGTCTGGTTATGTGGGGTTGGAATAT	hhhhhhhhhhhhhhhhhhhhhhhhhhDhhhRDEhH	NM:i:0
+EAS38_8_207_793_649	16	chr1	3190155	255	35M	*	0	0	TAAAGGAAGGTCTGGTTATGTGGGGTTGGAATATG	FThTO[ZcIHRhhShhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_249_136_550	0	chr1	3190167	255	35M	*	0	0	TGGTTATGTGGGGTTGGAATATGTATATCTATATA	hhhhhhhhhhhhhhhhhghhhhhhhhhhhhDhJhh	NM:i:0
+EAS38_8_197_214_431	16	chr1	3190168	255	35M	*	0	0	GGTTATGTGGGGTTGGAATATGTATATCTATATAT	EUEU@QhJhhVgFUhhhhPhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_124_625_963	16	chr1	3190174	255	35M	*	0	0	GTGGGGTTGGAATATGTATATCTATATATCTCTAT	]hdTChhhXhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_314_668_328	16	chr1	3190176	255	35M	*	0	0	GGGGTTGGAATATGTATATCTATATATCTCTATAT	hhhh]]hhhhOh_hhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_8_247_406	16	chr1	3190176	255	35M	*	0	0	GGGGTTGGAATATGTATATCTATATATCTCTATAT	fY]NUFQQhhVcRhhhhhhehhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_45_380_957	16	chr1	3190191	255	35M	*	0	0	ATATCTATATATCTCTATATATATTTACATCAAAG	hhhVhbhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_224_453_647	16	chr1	3190214	255	35M	*	0	0	TTTACATCAAAGAATTTAATAACTCATTTAAATTT	hKhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_120_914_892	0	chr1	3190236	255	35M	*	0	0	CTCATTTAAATTTTTGTTTCAAATAAAATTCCAAA	hhhhhhhhhhhhhhhhhhhhhhhhhhfhhhLWh]K	NM:i:0
+EAS38_8_8_442_670	0	chr1	3190258	255	35M	*	0	0	ATAAAATTCCAAATACATTTGTACAATGTTTACAA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhRhhTe_\	NM:i:0
+EAS38_8_245_767_298	16	chr1	3190284	255	35M	*	0	0	TGTTTACAAAGTAAGAGACAGGACTGGCAGGTTTG	WOF`hhhhhhhbhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_94_374_121	16	chr1	3190284	255	35M	*	0	0	TGTTTACAAAGTAAGAGACAGGACTGGCAGGTTTG	Shh`hhRhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_256_414_787	0	chr1	3190333	255	35M	*	0	0	CACCGTGATGTCCGGGTGATATATCTTCACGTTGC	hhhhhhhhhhhhhhhhdhchhhhh`hhJRBhfhhJ	NM:i:0
+EAS38_8_215_417_539	16	chr1	3190353	255	35M	*	0	0	ATATCTTCACGTTGCCTGCACACACCTTATTTCTG	VAHGh@XhBhhhRhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_167_839_349	0	chr1	3190379	255	35M	*	0	0	TTATTTCTGAAATGGAGAGAGAAACTCAAGAATGT	hhhhhhhhhhhhhhhhhhhhhdhhhhhPhhDhhCh	NM:i:0
+EAS38_8_235_344_488	0	chr1	3190402	255	35M	*	0	0	ACTCAAGAATGTCACCGACTATGCATCAGAATACT	hhhhhhhhhhhhhhhhhLhhhhbfhGUILPJQQPL	NM:i:0
+EAS38_8_287_803_220	0	chr1	3190402	255	35M	*	0	0	ACTCAAGAATGTCACCGACTATGCATCAGAATACT	hhhhhhhhhhhhhhhhhhhhhhhhdhgTMVEh\^N	NM:i:0
+EAS38_8_23_488_181	16	chr1	3190434	255	35M	*	0	0	ACTATGTACAGTTGAAGTTAGGGAGCTGAGAACCT	hChhhhOhhhhgUhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_137_662_459	16	chr1	3190469	255	35M	*	0	0	AGTGTTCTGTTCTCTTCTGGTTTGTCTTCATCTAC	eOKeGUhIhVhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_228_762_237	16	chr1	3190469	255	35M	*	0	0	AGTGGTCTGTTCTCTTCTGGTTTGTCTTCATCTAC	ZhMhbWK\hgShShhhh^hhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_65_836_536	16	chr1	3190469	255	35M	*	0	0	AGTGTTCTGTTCTCTTCTGGTTTGTCTTCATCTAC	ahYhThhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_100_122_849	0	chr1	3190545	255	35M	*	0	0	CAAACATTGGAAAGAGGAAGGAGAAAAACACAAAA	hhhhhhhhhhhhhhhhhhhhhXhhhhhhCdM[TUh	NM:i:1
+EAS38_8_172_157_846	16	chr1	3190553	255	35M	*	0	0	GGAAAGAGGAAGGAGAAAAGTACAAAATATTTAAG	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_166_123_980	16	chr1	3190565	255	35M	*	0	0	GAGAAAAGCACAAAATATTTAAGGCAAATTAAGCA	FhThhhhLhhhhhhhhhhhhhhhbhhhhhhhhhhh	NM:i:0
+EAS38_8_202_25_949	16	chr1	3190601	255	35M	*	0	0	ATATGTATAGTCTCTTTGTGCCAGGAGGATGTGAC	OKTX@[hhdGVhVhhhhMhdhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_135_382_764	0	chr1	3190604	255	35M	*	0	0	TGTACAGTCTCTTTGTGCCAGGAGGATGTGACTTT	hhhhhhhhhhhhhhhhhhhhhhhhhOhhhhYHhhh	NM:i:0
+EAS38_8_256_748_407	16	chr1	3190604	255	35M	*	0	0	TGTACAGTCTCTTTGTGCCAGGAGGATGTGACTTT	RWEhhhhZhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_328_369_595	0	chr1	3190604	255	35M	*	0	0	TGTACAGTCTCTTTGTGCCAGGAGGATGTGACTTT	hhhhhhhhhhhhhhhhhhhhhhhhhFahJORXhhh	NM:i:0
+EAS38_8_13_985_934	16	chr1	3190609	255	35M	*	0	0	AGTCTCTTTGTGCCAGGAGGATGTGACTTTCTTTT	STZhQhhUhcdhhhhdSh^Zhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_13_657_254	0	chr1	3190659	255	35M	*	0	0	GCTTTAAAAAATTCAAATAAAGCAAGTCTGGTGTG	hhhhhhhhhhhhhhhhhhhhhhhhZhhhhhYh]h\	NM:i:0
+EAS38_8_97_368_634	0	chr1	3190659	255	35M	*	0	0	GCTTTAAAAAATTCAAATAAAGCAAGTCTGGTGTG	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_158_637_333	0	chr1	3190697	255	35M	*	0	0	TGGGTTGCTTGTGTTGTTTTAATTTTTTTTGAAAA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh@ZMhQ	NM:i:0
+EAS38_8_7_431_889	0	chr1	3190697	255	35M	*	0	0	TGGGTTGCTTGTGTTGTTTTAATTTTTTTTGAAAA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_129_799_390	0	chr1	3190859	255	35M	*	0	0	TAAAATAATGAGAGAATGGAGAACCAATGTAAGGA	hhhhhhhhhhhhbhQMhhhXhJgFNJVKJLT>BI?	NM:i:0
+EAS38_8_186_234_660	16	chr1	3190910	255	35M	*	0	0	TCTGGAAGCAGGCTCACCAAGTATGATGGTTTCAT	bb\hhhhhhhhdhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_99_392_34	16	chr1	3190940	255	35M	*	0	0	TTCATACACAGAAAAACATTTGTTCTTTTGGATGC	`dAhhhEUMhhhhhhhhhhThhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_141_299_800	0	chr1	3190964	255	35M	*	0	0	CTTTTGGATGCCATTAGTTCAGCCAGTGTCAACAT	hhhhhhhhhhhhhhhhhhhhhhhhahhhhhhhQh]	NM:i:0
+EAS38_8_41_30_673	0	chr1	3190983	255	35M	*	0	0	CAGCCAGTGTCAACATGACTAGTGGTTTCCCCAGC	hhhhhhhhhhhhhhhhhhQhhhhhhJhh>SWHLEM	NM:i:1
+EAS38_8_270_818_467	16	chr1	3191047	255	35M	*	0	0	CTGCTTTCCAGGCTTCTCATCTATAGATAGAGAAG	YADUL]DhhhhYhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_295_700_520	0	chr1	3191049	255	35M	*	0	0	GCTTTCCAGGCTTCTCATCTATAGATAGAGAAGAC	hhhhhhhhhhhhhhhhhhhhRhhhhhhah`IhRXG	NM:i:0
+EAS38_8_326_937_869	0	chr1	3191049	255	35M	*	0	0	GCTTTCCAGGCTTCTCATCTATAGATAGAGAAGAA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhQMhFG?	NM:i:1
+EAS38_8_156_546_203	0	chr1	3191080	255	35M	*	0	0	AGACTTTTACAAGGTGTATGTATTGAATCCATTAT	hhhhhhhhhhhhhhhhhhhfhhhhDhhVhhRhhPh	NM:i:1
+EAS38_8_226_788_95	0	chr1	3191080	255	35M	*	0	0	AGACTTTTACAAGGTGTATGTATTTAAGCCATTAT	hhhhhhhhhhhhhhhhhhhhhhhhPhhSghchhhh	NM:i:1
+EAS38_8_206_454_499	16	chr1	3191117	255	35M	*	0	0	AAAATGACATTATTTATCATTATTAGAAATTCCAA	hhhhZhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_126_432_418	0	chr1	3191141	255	35M	*	0	0	AGAAATTCCAACCCTAGTTATGAAAGATTGAGGGA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhYhchR	NM:i:0
+EAS38_8_255_473_525	0	chr1	3191143	255	35M	*	0	0	AAATTCCAACCCTAGTTATGAAAGATTGAGGGAAA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhWhhhafh	NM:i:0
+EAS38_8_293_908_459	16	chr1	3191160	255	35M	*	0	0	ATGAAAGATTGAGGGAAAGTGATAAAGAACAAAAG	hhehhhhhhYhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_126_512_733	0	chr1	3191163	255	35M	*	0	0	AAAGATTGAGGGAAAGTGATAAAGAACAAAAGGGA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhN	NM:i:0
+EAS38_8_132_357_350	0	chr1	3191163	255	35M	*	0	0	AAAGATTGAGGGAAAGTGATAAAGAACAAAAGGGA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh^hL	NM:i:0
+EAS38_8_225_963_686	16	chr1	3191186	255	35M	*	0	0	GAACAAAAGGGAGGGATATTATTCTCTCATTTTTA	UchhhhfhhhahNhahhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_91_183_721	0	chr1	3191203	255	35M	*	0	0	ATTATTCTCTCATTTTTAACAGCATATTTGTCTTA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh[	NM:i:0
+EAS38_8_91_184_720	0	chr1	3191203	255	35M	*	0	0	ATTATTCTCTCATTTTTAACAGCATATTTGTCTTA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhX	NM:i:0
+EAS38_8_37_742_366	16	chr1	3191253	255	35M	*	0	0	TACTGTGTGGCTTCAAAGAAGATAGTCATCTCTGG	h]hQhhB_hhRhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_164_833_223	16	chr1	3191267	255	35M	*	0	0	AAAGAAGATAGTCATCTCTGGTTCTCTTACTGAGA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_20_3_646	16	chr1	3191299	255	35M	*	0	0	AGAATAGAAAGTCTCTCCTTACTGAGAATAGGAAG	hVhh_hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_305_336_434	16	chr1	3191299	255	35M	*	0	0	AGAATAGAAAGTCTCTCCTTACTGAGAATAGGAAG	hhhhhhhhhhhUhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_133_876_487	16	chr1	3191301	255	35M	*	0	0	AATAGAAAGTCTCTCCTTACTGAGAATAGGAAGCC	hhGhThhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_58_243_264	16	chr1	3191305	255	35M	*	0	0	GAAAGTCTCTAATTACTGAGAATAGGAAGCCATCT	hhhhh?UQLOIAhhhWhhhhhhhhhhhhhhhhhhh	NM:i:2
+EAS38_8_158_87_484	16	chr1	3191325	255	35M	*	0	0	AATAGGAAGCCATCTTCATACCTGTCCCTCTGCAT	gh@hChhhh`LhFhhghhRhhhhhghhhhhhhhhh	NM:i:0
+EAS38_8_49_289_587	16	chr1	3191360	255	35M	*	0	0	TTATTCTTGAGGTTACTGAGCCATCTGGCTACAGA	hhh^XhKUhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_226_316_409	0	chr1	3191368	255	35M	*	0	0	GAGGTTACTGAGCCATCTGGCTACAGAGAAGAAAA	hhhhhhhhhhhhhhhhhhahhhah_UOhDENhC[G	NM:i:0
+EAS38_8_27_871_685	16	chr1	3191375	255	35M	*	0	0	CAGAGCCATCTGGCTACAGAGAAGAAAAGCAAGAG	gAhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_323_782_711	16	chr1	3191375	255	35M	*	0	0	CTGAGCCATCTGGCTACAGAGAAGAAAAGCAAGAG	hGdhZhghhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_138_990_817	16	chr1	3191399	255	35M	*	0	0	AAAAGCAAGAGTTGTTTTTTTATTTTTATTTTATT	hhhhKhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_185_443_369	16	chr1	3191399	255	35M	*	0	0	AAAAGCAAGAGTTGTTTTTTTATTTTTATTTTATT	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_16_393_343	16	chr1	3191400	255	35M	*	0	0	AAAGCAAGAGTTGTTTTTTTATTTTTATTTTATTT	hhhhVhhhhhI]hPJhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_50_691_313	16	chr1	3191400	255	35M	*	0	0	AAAGCAAGAGTTGTTTTTTTATTTTTATTTTATTT	hhhhhhhhhhhhhXhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_189_168_310	16	chr1	3191408	255	35M	*	0	0	AGTTGTTTTTTTATTTTTATTTTATTTTTATTTTT	hhWWhhh[hh_hhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_247_520_310	16	chr1	3191408	255	35M	*	0	0	AGTTGTTTTTTTATTTTTATTTTATTTTTATTTTT	hhTRhhh]hhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_8_620_387	0	chr1	3191411	3	35M	*	0	0	TTTTTTTTTATTTTTATTTTATTTTTATTTTTTTA	hhhhhhhhhhhhhhh`hhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_264_985_305	0	chr1	3191415	1	35M	*	0	0	TTTTTATTTTTATTTTATTTTTATTTTTTTAATTA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhOhh	NM:i:1
+EAS38_8_290_750_320	16	chr1	3191505	255	35M	*	0	0	CAGACAATGGCTTTAAGTGGGGCCTATATGAACTG	BaFA>PbShGXfXhh_hJhh[hhhhhhhhhhhhhh	NM:i:1
+EAS38_8_220_527_228	16	chr1	3191562	255	35M	*	0	0	CGGTTTTGTGAAGGTAATATATCAGTAATATGGTT	E[gYhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_181_540_123	0	chr1	3191572	255	35M	*	0	0	AAGGTAATATATCAGTAATATGGTTGACATAAATA	hhhhhhhhhhhhhhhhhhhhhhhhhOfhPhhEZDS	NM:i:0
+EAS38_8_28_698_660	0	chr1	3191572	255	35M	*	0	0	AAGGTAATATATCAGTAATATGGTTGACATAAATA	hhhhhhhhhhhhhhhhhhhhhhhhhheRchhHhGh	NM:i:0
+EAS38_8_304_298_316	0	chr1	3191572	255	35M	*	0	0	AAGGTAATATATCAGTAATATGTTTGACATAAATA	hhhhhhhhhhhhhhhhhhhhhhhhhhbchhhTchh	NM:i:1
+EAS38_8_146_777_942	0	chr1	3191575	255	35M	*	0	0	GTAATATATCAGTAATATGGTTGACATAAATAAGC	hhhhhhhhhhhhhhhhhhhhhhhhahhhhhhhhhG	NM:i:0
+EAS38_8_206_582_659	0	chr1	3191575	255	35M	*	0	0	GTAATATATCAGTAATATGGTTGACATAAATAAAC	hhhhhhhhhhhhhhhhhhhhhhhhhhhhgh[hh@T	NM:i:1
+EAS38_8_113_379_524	0	chr1	3191576	255	35M	*	0	0	TAATATATCAGTAATATGGTTGACATAAATAAGCT	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhIh	NM:i:0
+EAS38_8_197_772_581	16	chr1	3191611	255	35M	*	0	0	GGGAAATAGTTCTTTTAGGAAGTAGAAGATTTTTC	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_256_457_159	16	chr1	3191611	255	35M	*	0	0	GGGAAATAGTTCTTTTAGGAAGTAGAAGATTTTTC	hhhhhhUhhhgPhhghhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_315_836_955	0	chr1	3191675	255	35M	*	0	0	TGAAAAGAATGTTAGTTGGCTGTAACCATAAAATT	hhhhhhhhhhhhhhhhhhhLhhHhhhEMhghJhUW	NM:i:0
+EAS38_8_255_763_380	16	chr1	3191702	255	35M	*	0	0	ATAAAATGGGCAGTTGTATTTACAAATAATCACAT	hhhhhhhBhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_279_818_155	0	chr1	3191716	255	35M	*	0	0	TGTATTTACAAATAATCACATATATGATGCTTACA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhT^G	NM:i:0
+EAS38_8_48_883_242	16	chr1	3191719	255	35M	*	0	0	ATTTAAAAATAATCACATATATGATGCTTACAGAA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_78_140_97	0	chr1	3191764	255	35M	*	0	0	ATTTCTAAATAATCACATATGCTAAAAGCTAGTTT	hhhhhhhhhhhhhhhhhhhhPhhh\ThGhhDILh]	NM:i:1
+EAS38_8_322_980_805	16	chr1	3191782	255	35M	*	0	0	ATGCTAAAAGCTAGGTTTTTCTAATACACTTTTAT	hSYhhhhhh\hhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_319_99_291	16	chr1	3191786	255	35M	*	0	0	TAAAAGCTAGGTTTTTCTAATACACTTTTACTTTC	hhhhhhhdhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_64_224_620	0	chr1	3191811	255	35M	*	0	0	TTTTATTTTCATGGAGGGCTCTAGAGGTTTCCACG	hhhhhhhhhhhhhPhhhhhhhhhhZh]>hhCPJQJ	NM:i:1
+EAS38_8_108_348_710	0	chr1	3191850	255	35M	*	0	0	ATAGAAACCACTGAAAAGAGACTCAACTCTTTTTC	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh\	NM:i:0
+EAS38_8_231_364_552	0	chr1	3191864	255	35M	*	0	0	AAAGAGACTCAACTCTTTTTCCCCCCAGCAATATT	hhhhhhhhhhhhhhhhhhhhhhhhhhfhhhRhEhh	NM:i:0
+EAS38_8_116_293_619	0	chr1	3191865	255	35M	*	0	0	AAGAGACTCAACTCTTTTTCCCCCCAGCAATATTA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhchhhhX	NM:i:0
+EAS38_8_145_345_869	0	chr1	3191865	255	35M	*	0	0	AAGAGACTCAACTCTTTTTCCCCCCAGCAATATTA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhchhXhhh	NM:i:0
+EAS38_8_275_299_203	0	chr1	3191865	255	35M	*	0	0	AAGAGACTCAACTCTTTTTCCCCCCAGCAATATTA	hhhhhhhhhhhhhhhhhhhhhhhhhHBhhBhXh^\	NM:i:0
+EAS38_8_14_653_187	16	chr1	3191901	255	35M	*	0	0	GTTGCTCTGGGCTGCTCTATGCATATGGCATGTTG	NQKhhRTYh@hNdhhWMhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_123_560_667	16	chr1	3191909	255	35M	*	0	0	GTGCTGCTCTATGCATATGGCATGTTGTTGGTACC	eThh]hhfhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_158_848_347	16	chr1	3191913	255	35M	*	0	0	GGCTCTATGCATATGGCATGTTGTTGGTACCTGTA	@U\EWWhRbhhhhbhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_259_577_716	0	chr1	3191933	255	35M	*	0	0	TTGTTGGTACCTGTACCATTCTCTTCCATTGAGAA	hhhhhhhhhhhhhhhRhhhhhhhhh]hhhhhKhhh	NM:i:0
+EAS38_8_37_266_444	16	chr1	3191981	255	35M	*	0	0	GGTGGAGGAGCTGTTCAGCTCTCTCTAACCTATTT	EfQhWOhh`hhWhhhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_298_155_843	16	chr1	3191988	255	35M	*	0	0	GAGCTGTTCAGCTCTCTCTAACCTATTTAGATTTT	Lhh`hhh[hhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_171_911_326	16	chr1	3192010	255	35M	*	0	0	CTATTTAGATTTTATCTTTCACTTTGTGATAGAAT	[hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_213_546_978	16	chr1	3192010	255	35M	*	0	0	CTATTTAGATTTTATCTTTCACTTTGTGATAGAAT	afhhhhh\hhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_165_431_451	0	chr1	3192012	255	35M	*	0	0	ATTTAGATTTTATCTTTCACTTTGTGATAGAATCT	hhhhhhhhhhhhhhhhhhhhhhhhhhhhh]Chhhh	NM:i:0
+EAS38_8_130_352_184	16	chr1	3192020	255	35M	*	0	0	TTTATCTTTCACTTTGTGATAGAATCTCTCTATAG	hfdhhYhhhghJhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_303_420_658	16	chr1	3192025	255	35M	*	0	0	CTTTCACTTTGTGATAGAATCTCTCTATAGAATGT	hKhhhUhhhhhhhhhhhhh]hhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_11_860_892	16	chr1	3192043	255	35M	*	0	0	ATCTCTCTATAGAATGTTCTCTCCACCACCTCCTG	LLhXhchhhh^@hhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_166_250_850	16	chr1	3192043	255	35M	*	0	0	ACCTCTCTATAGAATGTTCTCTCCACCACCTCCTG	M@X?CGhhhhhLhhhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_41_436_855	0	chr1	3192251	255	35M	*	0	0	TACCTTTTACCCACTTACTGTTCTTACATGACCTG	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhbAhhh	NM:i:0
+EAS38_8_1_614_740	0	chr1	3192310	255	35M	*	0	0	GCACTGTAGATATTTTTGAGGAGTCACATAATTTT	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_1_615_739	0	chr1	3192310	255	35M	*	0	0	GCACTGTAGATATTTTTGAGGAGTCACATAATTTT	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_11_667_100	0	chr1	3192520	255	35M	*	0	0	CTCCTCAAGGGAAAATTTGGAAAGTATTTCATATT	hhhhhhhhhhhhhhhhhhh\hhhHhhhhhhhhhhh	NM:i:0
+EAS38_8_142_397_982	16	chr1	3192642	255	35M	*	0	0	CTGTTAGCACAGTTCAATGATACATTCTTATTTTA	hVShThOhhhhGhhhhhhhAhFhhhhhhhhhhhhh	NM:i:2
+EAS38_8_201_45_850	16	chr1	3192642	255	35M	*	0	0	CTGTTAGCACAGTTCAATGGTGCATTCTTATTTTA	hfMfYhhhVhh[hhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_198_171_959	0	chr1	3192730	255	35M	*	0	0	TAGTCATTTAGGCAAGGAAATAGACATTGTTTTGA	hhhhhhhhhhhhhhhhhhhhhhhfZhhhhhhhhTR	NM:i:0
+EAS38_8_300_863_946	16	chr1	3193601	255	35M	*	0	0	ATTCCTTTCTTCTTTGTTGCTATCATTGAACCACA	BGbhah[IhhhhhhfOhh^hhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_311_818_593	0	chr1	3193885	255	35M	*	0	0	CACAGATGCACAGATTGATGATCTCTAGGAAAAAG	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhZ]hh	NM:i:0
+EAS38_8_126_604_962	0	chr1	3194707	255	35M	*	0	0	TGGATCAAACAATTTAAACAACTTTAGCTTTACAA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhKWh	NM:i:1
+EAS38_8_95_901_210	0	chr1	3194707	255	35M	*	0	0	TGGATCAAACAATTTAAACAACTTTAGCTTTACAA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_145_407_869	16	chr1	3195051	255	35M	*	0	0	TAGGTTGCAGTTGCTCTATGTGATGTATTTCTCTT	ShP?MhHhhZhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_111_861_260	16	chr1	3196449	255	35M	*	0	0	TTTTTTCCTGGAGTGCATAATGGATACATTTGATG	\OhfhMhhShhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_167_257_42	16	chr1	3197418	255	35M	*	0	0	AATTAAGGCATCAGTGTTCTGAACTGTGTGATAGC	hhhAhhhhUhVhhhbhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_233_573_175	16	chr1	3197418	255	35M	*	0	0	AATTAAGGCATAAGTGTTCTGAACTGTGTGATAGC	hhDIhhhh[h_BhhVhhhdhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_305_871_204	16	chr1	3199438	255	35M	*	0	0	AGTTGCTCACTTTCATGAGTAGCTTTGACTAATTA	hXGMDTVdhhYhZhhPhhhhhhhhchhhhhhhhhh	NM:i:0
+EAS38_8_231_724_560	0	chr1	3200057	255	35M	*	0	0	TACAGCAATAACACATGGCAAATTCTTAATAATGA	hhhhhhhhhhhhhhhhhhhhQhhhhhgJhShQeAA	NM:i:0
+EAS38_8_203_543_728	0	chr1	3200118	255	35M	*	0	0	CCACAAGGAAATCTATAGGCAAACAAAATAACCAA	hhhhhhhhhhhhhhhhhhhhhhh^Xhhh_hh\@Ch	NM:i:0
+EAS38_8_229_849_498	0	chr1	3200118	255	35M	*	0	0	CCACAAGGAAATCTATAGGCAAACAAAATAACTAA	hhhhhhhhhhhhhhhhhhhbhfhhY`hQcaK?hBV	NM:i:1
+EAS38_8_119_995_590	0	chr1	3200431	255	35M	*	0	0	CTTATTTCTGTGGGCACATGGCTGGTTGCCACTTC	hhhhhhhhhhhhhhhhhhhhhhhhDVhEEJICIh@	NM:i:1
+EAS38_8_253_690_533	0	chr1	3200431	255	35M	*	0	0	CTTATTTCTGTGGGCACATGGCTGCTTGCCCCTTC	hhhhhhhhhhhhhhhhhhhhhhhhIhRHM@GQMR?	NM:i:1
+EAS38_8_2_361_608	16	chr1	3200848	255	35M	*	0	0	CAAATGTTGGGTAGCAGATTGGTGTCATAAGTCAA	G^h^PNLLKh@hhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_19_443_443	16	chr1	3201005	255	35M	*	0	0	GGTCCACCTTGGTCCTGCTGTGCTGTCAGCTTCTG	N\MhhAVhQYhh]hhShhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_240_860_321	0	chr1	3201008	255	35M	*	0	0	CCACCTTGGTCCTGCTGTGCTGTCAGCTTTTGTCT	hhhhhhhhhhhhhhhhhhehhhhSGhHhP@YI`CL	NM:i:1
+EAS38_8_159_889_369	16	chr1	3201153	255	35M	*	0	0	TATATAGAAATAGTCGTGGCTAATGGCAAAGATAT	Nh`hPhhhhhhhhNhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_6_649_343	16	chr1	3201153	255	35M	*	0	0	TATATAGAAATAGTCGTGGCTAATGGCAAAGATAT	hhhhhhhhhhhhhhhhhhhZhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_159_13_859	16	chr1	3201231	255	35M	*	0	0	CATTAGAAAAAATTCACAGGATTCTTGTCTAAACA	hhghhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_206_389_817	0	chr1	3201597	255	35M	*	0	0	CATGCATTTCTAAGTTTATCTCTGTGTAGATGCAT	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhZhahhh	NM:i:0
+EAS38_8_8_834_910	16	chr1	3201632	255	35M	*	0	0	GTAAGAGAGTCAGTCTTTCTGTCTGTCTGTTTCTG	KTEPRY\hhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_193_381_989	0	chr1	3201726	255	35M	*	0	0	GGCAAATCTGTAGAAATTGATATCTCTTTATGTTA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_218_286_583	16	chr1	3201770	255	35M	*	0	0	CAGGGATCAAATTCAGGTCAAGTTTGCATCTTTTT	hh[a\h\hhhh^hhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_231_842_613	16	chr1	3201775	255	35M	*	0	0	ATCAAGTTCAGGTCAAGTTTGCATCTTTTTTCAGT	hahhhOhbhhhKhhhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_69_697_617	16	chr1	3201775	255	35M	*	0	0	ATCAAATTCAGGTCAAGTTTGCATCTTTTTTCAGT	heghhhOhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_315_783_294	16	chr1	3205321	255	35M	*	0	0	CTAAAAGTAAAAACAAATCCTGAAATATGTAGAAA	ERhhhhhXhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_208_943_432	16	chr1	3206163	255	35M	*	0	0	CCTTGGAGGAGATGGGGAACATTCAAAAGCTAAAA	bVQHbOhahhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_17_380_277	0	chr1	3209126	255	35M	*	0	0	TTGGTGTGCTTATCCGACACTGTAGGTAGAAACCA	hhhhhhhhhhhhhhhh]hPh\NhhJQhEKCEOJhG	NM:i:1
+EAS38_8_156_409_184	16	chr1	3211514	255	35M	*	0	0	CAAGAAAGATTGATGAGACACAGTTGATAGAGGGA	HKhThhhhhhOhhghhhhLhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_189_963_938	0	chr1	3211535	255	35M	*	0	0	AGTTGATAGAGGGATGATAAATAATCCTTTCCTTT	hhhhhhhhhhhhhhhhahhh^hhdSGTTZ`>D[XR	NM:i:0
+EAS38_8_194_593_290	0	chr1	3212718	255	35M	*	0	0	GCTTAAGACACTTTGCATCCCTCTTTTGTAACATT	hhhhhhhhhhhhhhhhhhhhhhhhhhhWhRK^Jhb	NM:i:0
+EAS38_8_54_951_1001	0	chr1	3212775	255	35M	*	0	0	ACTTTCCTTTTCAGGAAAAAAAATGTATATAATAT	hhhhhhhhhhhhhhhhhhh[hhhhhIHhhdbaSOJ	NM:i:0
+EAS38_8_55_222_593	16	chr1	3213111	255	35M	*	0	0	CTCACTGCCTCCCTCTTAGGACTCTTACACTGAAA	h>hPhf`ZhYhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_192_865_198	16	chr1	3213157	255	35M	*	0	0	AGTCAATGCAAGAAAGCAGATGCTTCCATCTTGCT	_JHhOhFhBhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_257_284_263	16	chr1	3213208	255	35M	*	0	0	AAAAAAAACAAAACAAATCTCCACTTTTTGTAAAT	hXhMhhhhOhhhhIhhhfhPhQhhhhhhhhhhhhh	NM:i:2
+EAS38_8_14_341_452	0	chr1	3234830	255	35M	*	0	0	CCTTGATGTCTTGATGGTTGAAATAGGTTACATTT	hhhhhhhhhhhhhhhhhhhh`hhh^IhhhN`Lhhh	NM:i:0
+EAS38_8_171_140_943	0	chr1	3239649	255	35M	*	0	0	TCCCTGTTAGATTCAAATGTTACTTTATAGTTAAA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh^h	NM:i:0
+EAS38_8_98_123_525	16	chr1	3240599	255	35M	*	0	0	ACATCCCTCCCTAAATAAACCACAATCCACCCCCA	hdhLDhEMhhfhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_178_873_141	16	chr1	3242478	255	35M	*	0	0	TTTTTTTTTTTTTTTAAACAAGATTTTTAGTTTTT	OVhhRhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_215_180_235	16	chr1	3242478	255	35M	*	0	0	TGTTTTTTTTTTTTTAAACAAGATTTTTAGTTTTT	hThhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_7_814_774	16	chr1	3242478	255	35M	*	0	0	TTTTTTTTTTTTTTTAAACAAGATTTTTAGTTTTT	Jhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_315_926_983	16	chr1	3242791	255	35M	*	0	0	ACCTCCTCCTATAGCTTCTAGAGACAACAGACCTT	@<BEAZIMRhHhIdhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_163_191_986	16	chr1	3242917	255	35M	*	0	0	AATCATATTTTGACCTCAATTAGCCTTGGGGTTGA	hhTRhSaeh\UAThhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_173_800_35	16	chr1	3242917	255	35M	*	0	0	AATAATATTTTGACCTCAATTAGCCTTGGGGTTGA	hh=FhRhVhOhShGhcZhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_25_295_514	0	chr1	3242979	255	35M	*	0	0	GCTCTTCTGTCAAGAGTACCTGAAATTTATCTGTG	hhhhhhhhhhhhhhhhhhhhhhhehhhhhhZhhhc	NM:i:0
+EAS38_8_260_745_595	0	chr1	3242979	255	35M	*	0	0	GCTCTTCTGTCAAGAGTACCTGAAATTTATCTGTG	hhhhhhhhhhhhhhhhhhhhhhLhhhhhhhhhhfM	NM:i:0
+EAS38_8_162_854_426	16	chr1	3243101	255	35M	*	0	0	GAAAAAACCTGTCTTGGTCTGAGGTCTGGGCCACT	>hhhhhPhhU_XhXZhhhhehhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_120_168_509	16	chr1	3243120	255	35M	*	0	0	TGAGGTCTGGGCCACTGTTATTCAGAGTGAACAAC	AZc^hCcMhhhWhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_219_315_931	16	chr1	3243676	255	35M	*	0	0	TTTGTTGAAGGAGAACACAATGAGAGGTGCATATT	]OhYhhchhahhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_180_247_88	16	chr1	3244868	255	35M	*	0	0	GCATACTTAAAATTAGGCTGCAATCAGTCTTCCTT	_@hhhCJhhhhhhIhhhhShhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_144_513_481	0	chr1	3252847	255	35M	*	0	0	AATGGCATTCAGTTAGCTTTAGTGACTGATCCCAA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhBC	NM:i:0
+EAS38_8_125_631_236	0	chr1	3253217	255	35M	*	0	0	TGAGGCATGACCTCCTTTCACTGAATCTTAGTCTT	hhhhhhhhhhhhhhhhhhhhhhhhehhhhhLChhh	NM:i:1
+EAS38_8_312_169_822	16	chr1	3253312	255	35M	*	0	0	AAGGCTAAAATTGCTGTTACCAGCTGCTATGCTTG	[JNDIONDhWhhhhhhIhhhhhhhhhhhhhhhhhh	NM:i:2
+EAS38_8_10_227_417	0	chr1	3253759	255	35M	*	0	0	CAAATTTTAGCTCCTTTCCCAGTTTCCCTCTGGAA	hYhhhhhhhhhhhhhhhh`hG_heh\V^hXhUBH?	NM:i:0
+EAS38_8_144_231_566	0	chr1	3253759	255	35M	*	0	0	CAAATTTTAGCTCCTTTCCCAGTTTCCCTCTGGAA	hhhhhhhhhhhhhhhhhhXhghhhhROZWKbU\MM	NM:i:0
+EAS38_8_208_276_857	16	chr1	3254072	255	35M	*	0	0	TCAACTTCACAAGGAATTTGGAGTGACTGGCCTCC	VdMOhLchXhhhh^hhhZhhhhhhh_hhhhhhhhh	NM:i:0
+EAS38_8_6_640_930	16	chr1	3254072	255	35M	*	0	0	TCAACTTCACAAGGAATTTGGAGTGACTGGCCTCC	IHhOhJThchhhhWhhh_hhYhhhhhhhhehhhhh	NM:i:0
+EAS38_8_261_856_180	0	chr1	3254263	255	35M	*	0	0	GTTCCGCAACACCTGCCCTCACATTCCACTGAACT	hhhhhhhhhhhhhhhhhhhhMhThh[NCKQD?DJK	NM:i:1
+EAS38_8_97_169_815	0	chr1	3254597	3	35M	*	0	0	ATCAGGCTACTTTCAGCAAGCACTTCTTGTCATCT	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhAh^hUh	NM:i:1
+EAS38_8_250_270_899	0	chr1	3259536	255	35M	*	0	0	CTAGATTAGCAGGTAATTTCTAAATCACACATTTA	hhhhhhhhhhhhhhhhhhhhhhhhhahUJOhhYhb	NM:i:0
+EAS38_8_267_436_563	0	chr1	3273793	255	35M	*	0	0	TTTTTTTGTTTGTTTGTTTGTTTTTATACAACAGA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhchhh	NM:i:1
+EAS38_8_244_916_490	16	chr1	3274218	255	35M	*	0	0	GAGCCTAAACCAACCAACCAATGAATATACATAGG	ThCYE@AhhhOhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_111_703_424	16	chr1	3274366	255	35M	*	0	0	ACAGGGCACATGTTCTTCTAGCTGAGCTGCCTTGT	L[gE[hhhhhghhhhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_224_315_306	16	chr1	3274921	255	35M	*	0	0	GGAACTGTGCAAATTGTGTAACTGGAGAAAATAAT	hhhh^hh_hhhhhhhhhhhhh`hhhhhhhhhhhhh	NM:i:0
+EAS38_8_256_842_769	0	chr1	3277156	255	35M	*	0	0	AATGATATTGGTTTGAAGTTCTTTAGCCCCATATT	hhhhhhhhhhhhhhhhhhhhhhhhhhhh\hhh]hh	NM:i:0
+EAS38_8_292_619_933	0	chr1	3277156	255	35M	*	0	0	AATGATATTGGTTTGAAGTTCTTTAGCCTCATATT	hhhhhhhhhhhhhhhhhhhhhhhhhhbOLhMhhhh	NM:i:1
+EAS38_8_212_928_881	0	chr1	3277700	0	35M	*	0	0	TCCTTTTCCTTTCCTTCCTTCCTTCCATCCTTCCT	hhhhhhhdZghhaehhTVhhZhhhNT?h^MX]OBQ	NM:i:2
+EAS38_8_223_507_484	0	chr1	3277914	255	35M	*	0	0	TTCTGAAACTTGAGTACAGTGTTATTACCAATATT	hhhhhhhhhhhhhhhhhhhLhhhhhhhKhLbheha	NM:i:0
+EAS38_8_264_464_724	0	chr1	3277925	255	35M	*	0	0	GAGTACAGTGTTATTACCAATATTCCCCCATTTTT	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhghhhhh	NM:i:0
+EAS38_8_97_398_795	0	chr1	3277927	255	35M	*	0	0	GTACAGTGTTATTACCAATATTCCCCCATTTTTCC	hhhhhhhhhhhhhhhhhhhhhhhLhhhVhhhhh^h	NM:i:0
+EAS38_8_271_224_790	16	chr1	3277983	255	35M	*	0	0	AGTGATGTCCTAACATGCTTGCTCTCTCATAACCA	FhhQ`hhhhhhhhhhhhhhhhhghhhhhhhhhhhh	NM:i:0
+EAS38_8_249_919_47	16	chr1	3277988	255	35M	*	0	0	TGTCCTAACATGCTTGCTCTCTCATAACCAGACTT	K=DFHUhLXhaJSbfLPfhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_264_398_810	16	chr1	3278029	255	35M	*	0	0	AGTTTTGTTAGGTTTGCTGGTCTTTTAAAAGGTCT	ZghhHhhhhTh[hhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_202_252_118	16	chr1	3278057	255	35M	*	0	0	AAGGTCTAGATTTTTGTTTCATTATTTTTTTTCTG	hhhTDhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_195_472_45	0	chr1	3278134	255	35M	*	0	0	CTTTTATTATATTCTTCCTCTTCGTTATTTTGAAT	hhhhhhhhhhhhhhhhhhhhhhhPhhh]hhhWENh	NM:i:1
+EAS38_8_200_268_981	0	chr1	3278134	255	35M	*	0	0	CTTTTATTATATTCTTCCTCTTCGTTAGTTTGAAT	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheh	NM:i:0
+EAS38_8_87_755_875	16	chr1	3278180	255	35M	*	0	0	TTCTCTTAAGTATATGTTCTTATTAACTATTTTTT	hhhUhhhhhThhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_184_481_627	16	chr1	3278254	255	35M	*	0	0	GAGGCATTTTAGTGTTATGAACTCCCCTTGGCACT	NH?=BNI[BT^YdUZ[hKJhhhPhhhhhhhhhhhh	NM:i:0
+EAS38_8_241_955_483	16	chr1	3278295	255	35M	*	0	0	GACACAGATAGGTTTTTATGTGCTATACTTACATT	DbHYMhVhhhVhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_24_420_629	0	chr1	3278309	255	35M	*	0	0	TTTATGTGCTATACTTACATTCAGTTCAATGTAAT	hhhhhhhhhhhhhhhhhhhhhhhhhhhhfhhhhhh	NM:i:0
+EAS38_8_307_620_12	16	chr1	3278356	255	35M	*	0	0	TTAGACTTCATTTTCTTCTTCTTTTTGGTTGTGAG	IOhKhhJdLhhhJhIeTVZhhhhhhhfWhhhhhhh	NM:i:0
+EAS38_8_55_835_895	0	chr1	3278373	255	35M	*	0	0	CTTCTTTTTGGTTGTGAGCCTAGCCTTCAACGGTT	hhhhhhhhhhhhhhhhhhWWhhhMTIhPTHIhc>D	NM:i:1
+EAS38_8_230_275_815	16	chr1	3278376	0	35M	*	0	0	TTTTTTGTTTGTGAGCCTAGCCTTCAACGGCTGAG	\_NF]RQGZhWPOXPhhhahhhhhhhMhhXhhhhh	NM:i:2
+EAS38_8_24_167_957	16	chr1	3278397	255	35M	*	0	0	CTTCAACGTCTGAGCCATCTCTCCAGCCCTCTTCT	VFA`N?hQ@hhLhehhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_253_546_769	0	chr1	3278576	255	35M	*	0	0	TTCCCACTCTCTGGGGCCTCAAGTCTCTCAAATTA	hhhhhhhhhhhhhhhhhhhhKRZhhhhh`KMhRTM	NM:i:2
+EAS38_8_283_280_992	0	chr1	3278576	255	35M	*	0	0	TTCCCACTCTCTGGGGCCTCAAGTCTCTCAAATGT	hhhhhhhhhhhhhhhhhhhYhhhFHcBQJHUNK?C	NM:i:0
+EAS38_8_4_499_790	0	chr1	3278607	255	35M	*	0	0	ATGTTAGGCACATCTCCCACTGATTCCAGACCAGG	hhhhhhhhhhhhhhhhe[hhhhUhcVOP`I?LTXH	NM:i:0
+EAS38_8_166_353_693	0	chr1	3278725	255	35M	*	0	0	GGTTAGTTGAGATTGCTGGTCTTTCTATGGGTTGC	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhKhhhFS	NM:i:0
+EAS38_8_227_305_410	16	chr1	3278920	255	35M	*	0	0	TCAGACCTCTGCTGATCACCTGCATAGTTGGAGAT	KJhH@NRIA_B`hhhhhhhhThhhhhhhhhhhhhh	NM:i:1
+EAS38_8_151_783_299	16	chr1	3279317	255	35M	*	0	0	CTTTTTTGTTCTATAGATATCAATTATTTACCCAC	BTS^WdIUehQhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_130_64_600	0	chr1	3280118	255	35M	*	0	0	GGTTTCGAGAAAATGTTTTGAAGTGTTTATGCGCT	hhhhhhhhhhhhhhhhhhhhhhhhhhhhchKOhSh	NM:i:0
+EAS38_8_204_14_612	0	chr1	3280118	255	35M	*	0	0	GGTTTCGAGAAAATGTTTTGAAGTGTTTATTCGCT	hhhhhhhhhhhhhhhhhhhhfhhhhhhhhhBQhL\	NM:i:1
+EAS38_8_242_889_996	0	chr1	3280118	255	35M	*	0	0	GGTTTCGAGAAAATGTTTTGAAGTGTTTATGCGCT	hhhhhhhhhhhhhhhhhhhhh^hVhaahgeh@Z?N	NM:i:0
+EAS38_8_82_262_363	0	chr1	3280320	255	35M	*	0	0	AACATATTTTAAATTCCTCTCAGATTAAGAGAATT	hhhhhhhhhhhhehhhhhhhh^hWhKhShWD@hhB	NM:i:2
+EAS38_8_111_150_178	0	chr1	3282505	255	35M	*	0	0	AGATACATAGAAAAGCTACTTGACTTTAGGTCAAC	hhhhhhhhhhhhhhhhhhhhhUfhhhhhQOhh\Sh	NM:i:0
+EAS38_8_260_477_698	0	chr1	3282505	255	35M	*	0	0	AGATACATAGAAAAGCTACTTGACTTTAGGTCAAC	hhhhhhhhhhhhhhhhhhhhhhhhhhhXhhhh`hM	NM:i:0
+EAS38_8_187_894_354	16	chr1	3282753	255	35M	*	0	0	CTGCACTTGTTTAGAGAAGTGCTGTCTACATGAAG	dhNhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_219_350_890	0	chr1	3282806	255	35M	*	0	0	TTTTGGAACTTAGGCAAGAATGTTCTTTGGCTCCT	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhPVh	NM:i:0
+EAS38_8_185_258_316	16	chr1	3282902	255	35M	*	0	0	TGAGAGCTAAATGTAAAGCTCAGTAATGCCAGCTC	IJhhhhh^hhhhMhhhhhhhhhhhhhhhhhhhhhh	NM:i:2
+EAS38_8_5_912_317	16	chr1	3284777	255	35M	*	0	0	CTCTCGCTCTCTCTCTCTCTCCCCTCACTCCTTTC	BPWFbChNSRhFhShehOh_hhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_119_362_614	0	chr1	3284967	255	35M	*	0	0	TGTACCCTGAGATCAAGTACTTATTGCTTTCACTT	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_276_838_443	0	chr1	3284967	255	35M	*	0	0	TGTACCCTGAGATCAAGTACTTATTGCTTTCACTT	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhahhhh	NM:i:0
+EAS38_8_74_720_526	0	chr1	3286259	255	35M	*	0	0	CAAATTGTAGAAAATTTGCATGTGTACTGAACACA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhL	NM:i:0
+EAS38_8_273_582_300	16	chr1	3289456	255	35M	*	0	0	TCTTCAGTTCTTTGTTAAATATATCATCTGGGTCT	HhYchhhQhRhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_232_852_815	0	chr1	3290417	255	35M	*	0	0	TTTTTTTTTTTAACTTTCATATGTAGTAGTTATTT	hhhhhhhhhhhhh^hhhKhhhhhhhGV^hh[MHhh	NM:i:2
+EAS38_8_121_748_181	0	chr1	3290799	255	35M	*	0	0	ACCACACCCTGCTGCTCCATATTTCTTATCTTTTT	hhhhhhhhhhhhhhhhhhhhhhhhhhh\Bhhhhhh	NM:i:1
+EAS38_8_36_138_632	0	chr1	3290826	255	35M	*	0	0	AGCTTTTTTTTTTTAACAGCTACTGGGTGGTTTGC	hhhhhhhhhhhhhhhhhhhhhOhhbhCXHZLI\BF	NM:i:1
+EAS38_8_141_369_534	0	chr1	3290833	255	35M	*	0	0	TTTTTTTAACAGCTACTGGGTGGTCTGCATAGCTT	hhhhhhhhhhhhhhhhhhhhhhhhhhhfPRLdhhS	NM:i:0
+EAS38_8_84_402_647	0	chr1	3290833	255	35M	*	0	0	TTTTTTTAACAGCTACTGGGTGGTCTGCCTAGCTT	hhhhhhhhhhhhhhhhhhhhhhhhhhVhBhThahe	NM:i:1
+EAS38_8_169_576_313	16	chr1	3290912	255	35M	*	0	0	ATGCTTCTTTCCACAGTTGAGTGGAATTGTAGGGG	hPhRWPJhVLhhhhhh[hhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_279_571_717	16	chr1	3290912	255	35M	*	0	0	ATGCTTCTTTCCACAGTTGAGTGGAATTGTAGGGG	he\hhYhaOYhhThhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_234_793_825	16	chr1	3290951	255	35M	*	0	0	AAAAGACATTTCTGAGTTCTAGCACTCTCAGGTCT	hhhhRhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_217_210_636	16	chr1	3290952	255	35M	*	0	0	AANGACATTTCTGAGTTCTAGCACTCTCAGGTCTG	hh;PYhhWXhh^hhhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_168_998_377	0	chr1	3290961	255	35M	*	0	0	TCTGAGTTCTAGCACTCTCAGGTCTGGCTTTGACA	hhhhhhWhhhhhhhhhhhhTe\YThhOIWJaC@A?	NM:i:0
+EAS38_8_179_44_982	16	chr1	3290986	255	35M	*	0	0	GCCTTTGACATTAGCTTCCTGACAGGCTGGCAGGT	?@[_GhH[hhhhhEhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_210_147_536	0	chr1	3291026	255	35M	*	0	0	TCCTGAAGGTCAGGACTGTGCAAAACTGTCAGGCA	hhhhhhhhhhhhhhhhhhhhhhQg`hh^hbGYYPH	NM:i:0
+EAS38_8_228_906_499	0	chr1	3291047	255	35M	*	0	0	AAAACTGTCAGGCAGCTATTTCAGGAGTGCCTTTT	hhhhhhhhhhhhhThhh_hhhhUThYZPVED[@C@	NM:i:2
+EAS38_8_223_934_468	16	chr1	3291092	255	35M	*	0	0	GCCCTGGATGATTTTTGAATGGGAATAATCCCTAT	RXhf\Phh`hhhhhVhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_27_794_86	16	chr1	3291130	255	35M	*	0	0	TCCATATAGGCTCATATATTTAAACACCTAGTCAT	X@FSSZhhhADhShhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_205_713_101	16	chr1	3291163	255	35M	*	0	0	ATTGTTGGTGGCACTGTCTGTAAGGATCACGAACC	CEJLUB`WcgZ]hLhheHahhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_269_175_878	16	chr1	3291192	255	35M	*	0	0	CAAACCCATTAGAAGGTAACAACATGCTAAAAAAA	eChhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_127_466_820	0	chr1	3291247	255	35M	*	0	0	GTGAGGGCTTGTGTTCTCTCTGCTTCCTCTGTGTG	hhhhhhhhhhhhhhhhhhhhhhhhhV_hTeSWhhh	NM:i:0
+EAS38_8_29_659_107	0	chr1	3291649	255	35M	*	0	0	TCCTGAGTTGGGAGGACAGATGAGAAGGGCTTTTT	hhhhhhhhhhhhhhhXhhhShhh`PFVhALNChJd	NM:i:2
+EAS38_8_210_520_140	16	chr1	3299511	255	35M	*	0	0	GAAATAAAGAAAATTCTAATCTACAGGCTGACCAT	VhhLDhhhhhhhhVLHShhPhfhhhhhhhhhhhhh	NM:i:2
+EAS38_8_45_100_198	0	chr1	3299523	255	35M	*	0	0	ATTCTAATCTACAGGCTGACCATACTGTATTTCAC	hhhhhhhhhhhhhhhhhhhhhhhZhhIh^hhhhHh	NM:i:0
+EAS38_8_145_894_137	0	chr1	3299538	255	35M	*	0	0	CTGACCATACTGTATTTCACTAATATAATGGTGTC	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhRChhhU	NM:i:0
+EAS38_8_231_634_172	16	chr1	3299568	255	35M	*	0	0	GTGACAGTGATGCCAGAGAGCTCTAGCTGTGGCTG	MHS?]hVChhPhHVhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_68_279_670	16	chr1	3299606	255	35M	*	0	0	TGAATACTGGGTAGAAAATAAAAAAATTTACGGAC	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_157_544_34	16	chr1	3299684	255	35M	*	0	0	TCATAAGATCGGGTAGTTAGTAAACCCTGCCTAGA	?MhFhhHMRZGSdhhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_317_518_457	0	chr1	3299798	255	35M	*	0	0	GATTTCTGTCTACTAGATCAAAACCTGATAACATA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhMhh	NM:i:0
+EAS38_8_87_383_194	16	chr1	3300173	255	35M	*	0	0	AAACTACAAAATTGTGGATGTTTGGCTGTTCTTTT	hhhSZhhhhhhKhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_220_990_452	16	chr1	3300259	255	35M	*	0	0	TGCACCATCTTAGGAGTGAGGGAGGCAGCTGAGTG	NHPUJ]hhSPa`ChhhYhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_168_713_356	0	chr1	3307749	255	35M	*	0	0	GGTTAACCCGAAGCCAAACTTTTCTTTGTAATTTC	hhhhhhhhhhhhhhhhhRhhhhhhhHhRhhIhhhJ	NM:i:1
+EAS38_8_222_724_349	0	chr1	3307749	255	35M	*	0	0	GGTTAACCCGAAGCCAAACTTTTCTGTGTAATTTC	hhhhhhhhhhahhhh`eGhhhhhhhJhPhNKhhhQ	NM:i:0
+EAS38_8_223_971_288	16	chr1	3310176	255	35M	*	0	0	AATAATCATCACCTGAATGTCATGATCTAAAGGCT	hhChhAhh\Ghhh[hhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_288_770_517	0	chr1	3310786	255	35M	*	0	0	AGGTTTTGAGTTTTTGATCCAGAGGCTATGTTTAT	hhhhhhhhhhhhhhhhgh\h]hQgQH\FS`HRJEW	NM:i:0
+EAS38_8_310_958_947	16	chr1	3311201	255	35M	*	0	0	CAATTTTTGATCATTCATCTTGTTTTCTTAACAAT	hP\hJhh_Hhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_140_291_179	16	chr1	3313701	255	35M	*	0	0	ACCGCTGCCTTCCTTTCTTCTCTCCTTCCTTTCTT	PW`@dP@hYhKhhhhchh]hZhahhhhhhhhhhhh	NM:i:2
+EAS38_8_113_205_724	16	chr1	3318613	255	35M	*	0	0	ACCTGGAAGAATTTCATAAAAATTCCCTTCCCAGC	HhedLQhhbhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_236_727_634	16	chr1	3318613	255	35M	*	0	0	ACCTGGAAGAATTTCATAAAAATTCCCTTCCCAGC	Sd]QXehhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_21_827_590	0	chr1	3319045	255	35M	*	0	0	TACAAACCAAGAGAAAAATCTGAAAATGAAAAATT	hhhhhhhhhhhhhhhhhhhhhh_hhhhhhghhhhh	NM:i:0
+EAS38_8_204_62_686	0	chr1	3321977	255	35M	*	0	0	AAGCTGGCAATGTTTGGGATATAAACAAGCAAACA	hhhhhhhhhhhhhhhhhhhhhhhhhhhahhhh[Yh	NM:i:0
+EAS38_8_86_854_652	16	chr1	3324385	255	35M	*	0	0	GCAGTGGCTGAGTGATATAACACAGGGATGCAGGT	hhhhhhh[hhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_192_343_954	0	chr1	3329232	255	35M	*	0	0	CTGCCCTTTTTCTCCCTGCCTATTCATTATAGTTC	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhU	NM:i:0
+EAS38_8_6_774_928	0	chr1	3330010	255	35M	*	0	0	GCACTGTAGCCAGGAGTGACACACAGCAAGGATGC	hhhhhhhhhhhhhhhhhhhhhhhN`hUhhhhT`h?	NM:i:0
+EAS38_8_256_461_804	16	chr1	3330063	1	23M11637N12M	*	0	0	TTTGTTTGTTTGTTTGTTTGTTTGTTTTGACAGGG	dhh@ZhhRhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:2	XS:A:+	NS:i:2
+EAS38_8_288_334_735	0	chr1	3330212	0	35M	*	0	0	TTATAGCTATAAAAAGTAACATTCTTTGATTGGTC	hhQhhhhhKhhQ`hhNKaXAXUaGQQVLOWKRFC>	NM:i:1
+EAS38_8_11_615_231	0	chr1	3330440	255	35M	*	0	0	ATTGGTTACAAAAAAGTTAGCTTTAACTTTGTAAC	hhhhhhhhhhhhhhhhhhhhhhhhIhhhhTLhehR	NM:i:1
+EAS38_8_284_883_215	0	chr1	3330528	255	35M	*	0	0	ACTAGGCCTCTAGAGTACTTCTAAATTGAGATATT	hhhhhhhhhhhhhhhhhhhhhhYhhhhIWEKh`hh	NM:i:0
+EAS38_8_30_530_423	16	chr1	3330584	255	35M	*	0	0	AGTAGACTTATAGAGATAAGCATTAAAATTTGTAC	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_202_722_286	16	chr1	3330653	255	35M	*	0	0	ACTTTGTAACGTTAAAGTGATGTTTCTGGTATTGA	NB[KZhhcYhhhdhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_214_253_466	16	chr1	3330653	255	35M	*	0	0	ACTTGGTAACGTTAAAGTGATGTTTCTGGTATTGA	hSN[DRShhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_4_564_326	16	chr1	3330653	255	35M	*	0	0	ACTTTGTAACGTTAAAGTGATGTTTCTGGTATTGA	ZXSVTYQhehh\hhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_142_357_440	16	chr1	3330660	255	35M	*	0	0	AACGTTAAAGTGATGTTTCTGGTATTGATCTTTAA	hhhhhdhhhhhhhhhhh_hhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_317_782_44	16	chr1	3330660	255	35M	*	0	0	AACGTTAAAGTGATGTTTCTGGTATTGATCTTTAA	hhFHbhhhhhhbhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_137_536_758	16	chr1	3330697	255	35M	*	0	0	TAATAAATTGTTTAAAATTGGGTTTTGCTAACCAA	`hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_129_924_268	16	chr1	3330838	255	35M	*	0	0	CAATTCACCTATATATTGTAATTAGGATAATTACA	BhhhDhhCZhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_48_834_938	0	chr1	3331062	255	35M	*	0	0	GTTGTTCTAAATAAAGATTAAATTCAGAATTTATA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_154_283_922	0	chr1	3331674	255	35M	*	0	0	TTAACTAGTAAAGAACAAAAGGCTTTGCAGAAAGA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh_hhX	NM:i:0
+EAS38_8_215_43_278	0	chr1	3331674	255	35M	*	0	0	TTAACTAGTAAAGAACAAAAGGCTTTGCAGAAATA	hhhhhhhhhhhhhhhhhhh\hhhhhhKhhVONhB@	NM:i:1
+EAS38_8_227_874_535	16	chr1	3341199	255	35M	*	0	0	AGACCAAGATGATGGGAACATCTTCTCCACCCCAT	=>?NBTPFLEDVHOaEhhhh\hghhYhhhhhhhhh	NM:i:2
+EAS38_8_255_514_861	0	chr1	3341232	255	35M	*	0	0	ATCAGAATTCCCAAGTCCCTGGGTCTTCAAGTCTC	hhhhhhhhhhhhhhhhhhhhhhhhhhhhY^h_RhH	NM:i:0
+EAS38_8_135_67_741	16	chr1	3341341	255	35M	*	0	0	AACTCAGCTGTTGTATGCTGCCTGGTTGGTGACTC	@FHPQGOXhYO[Whhhhhhhhhhhhhhhhhhhhhh	NM:i:2
+EAS38_8_230_743_701	16	chr1	3341490	255	35M	*	0	0	GCTTCTGTCCATTTGTTGGGTATGAGTATCTGCAT	NhLahhUKhhhhhcWhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_212_374_788	0	chr1	3341507	255	35M	*	0	0	GGGTATGAGTATCTGCATCTTACTCTTTCAGCTGC	hhhhhhhhhhhhhhhhghhhhhhhhhhhh\hHhh[	NM:i:0
+EAS38_8_250_863_818	0	chr1	3341507	255	35M	*	0	0	GGGTATGAGTATCTGCATCTTACTCTTTCAGGTGC	hhhhhhhhhhhhfhh[Ph]hh]\^N`XhLQE>LGD	NM:i:1
+EAS38_8_48_225_977	0	chr1	3341551	255	35M	*	0	0	TTCTCAGAAGGTAGTTATGCTAGGCTCCTGTCTGC	hhhhhhhhhhhhhhhhhhhhhhhhOhSYh\MF]hI	NM:i:0
+EAS38_8_83_343_929	16	chr1	3341762	255	35M	*	0	0	TCCCCTATTTCTCTACTGAAGGAGGACTCTACCAC	TRhhhhhhhbhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_96_862_886	16	chr1	3341818	255	35M	*	0	0	CCCCATGATTGTTTTCTTCTCCCTCCCATGTTGAA	hhhh^hJhhhhhhhhhbhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_134_781_817	0	chr1	3342105	255	35M	*	0	0	ACTCTTTAATAGAGTCTCCTGAAGAGGTAAAAATT	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_155_230_356	16	chr1	3342124	255	35M	*	0	0	TGAAGAGGTAAAAATTTTAATTTTGACAGTCCAAT	]hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_179_463_472	16	chr1	3347662	255	35M	*	0	0	TACCCTTGCGTCAAGGTGTGTTTTCTTACTCAAAT	OG?[DIQhbAhdhLhhhhRhhhhhhhhhhhhhhhh	NM:i:2
+EAS38_8_4_219_976	16	chr1	3347662	255	35M	*	0	0	TATCCTTGCCTCAAGGTGTGTTTTCTTACTCAAAT	hhhhhhhchhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_79_243_815	16	chr1	3349048	0	35M	*	0	0	AAAAAGAGAAACCCTGTCTCAGAAAGAAAAAAAAA	]WhAhHh_hhhhhhehhhhhhhhhhhhhhhhhhhh	NM:i:2
+EAS38_8_133_197_589	0	chr1	3349165	255	35M	*	0	0	CACCAGTTCTCCTGTGCATCCTCAGGAGAAATCAT	hhhhhhhhhhhhhhhhhhhhhhhhhhUhKSPhUJh	NM:i:0
+EAS38_8_188_649_421	0	chr1	3351241	255	35M	*	0	0	GTAGATGGACAAACATCTCCCTCACGCATTCTCAG	hhhhhhhhhhhhhhhhhhhhhhhhhhhhahhhbP>	NM:i:0
+EAS38_8_268_213_808	0	chr1	3355908	255	35M	*	0	0	ATCTAACTAAGTAAACTATGTTATAGGAAAGAAAT	hhhhhhhhhhhhhhhhhhhh^hhhhhhhhhhZhhZ	NM:i:0
+EAS38_8_11_161_707	0	chr1	3355956	255	35M	*	0	0	TTTGTCACATGATCAGCATAGTAGATGATGTGTCT	hhhhhhhhhhhhhhhhhhhhhhhhhhhPhhhhhHh	NM:i:0
+EAS38_8_291_670_580	16	chr1	3356011	255	35M	*	0	0	GAAGCAGTTAAAATTGTGTGTGTGTGGTTCTGGAT	hV_OXh[VIhXNhP^hhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_44_851_834	16	chr1	3356011	255	35M	*	0	0	GAAGCAGTTAAAATTGTGTGTGTGTGTTTCTGGAT	ECD@MDGhJXDSAChdhPh]hUhbhhEhhhhhHhh	NM:i:1
+EAS38_8_105_754_762	0	chr1	3356093	255	35M	*	0	0	TATAGATGTAGTTTATCTCCTAATCCCACCCTTCC	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_219_312_881	16	chr1	3356191	255	35M	*	0	0	TTTAATTACTTTCCCATCAAAGGCCCATTGAGCAG	XZNhNLhHhhZhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_299_450_385	0	chr1	3356483	255	35M	*	0	0	ATTCTGGTGGGCTTTCGAGTGTTTCAGTTTCATCT	hhhhhhhhhhhhhhhhhVhhhhhhhhhhhhhhhAh	NM:i:1
+EAS38_8_52_623_649	0	chr1	3356578	255	35M	*	0	0	GGAGCATATGTGAGTAAGCAAATGATGTTCTTGGA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhh]hEUNE	NM:i:1
+EAS38_8_117_306_426	16	chr1	3359531	255	35M	*	0	0	TCAGAGTGTCCACCTCATTCCTCTGGGTCAGTCTT	@EN_DgWhhhh_hhhhhhdhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_120_120_744	16	chr1	3361583	255	35M	*	0	0	CAAAGACAAGTAGGATAATGCTGAAAGCCCAAGCA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_307_422_12	0	chr1	3362018	255	35M	*	0	0	CTGAAAAATTACAGTGTTCTTGTACTGGACACTAC	hhhhhhhhhhhhhhhdhSahhKDYGhECFJF@TI?	NM:i:2
+EAS38_8_101_691_200	0	chr1	3363077	255	35M	*	0	0	CTTTTTTCCATTTTAATGTTTGCATGCAAATCTTA	hhhhhhhhhhhhhhhhhXhNhh`hhhhhMhhChhI	NM:i:2
+EAS38_8_205_648_802	0	chr1	3363077	255	35M	*	0	0	CTTTTTTCCATTTTAATGTGTGCATGCAAATGTTA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhZ	NM:i:0
+EAS38_8_265_441_688	0	chr1	3363150	255	35M	*	0	0	CAGGAATCAATCTCAACCACTTTTCATCTTACTCA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhOhhch	NM:i:0
+EAS38_8_53_996_162	0	chr1	3363150	255	35M	*	0	0	CAGGAATCAATCTCAACCACTTTTCATCTTACTCA	hhhhUhh_hYhUhc^LEHALV^]]MIVE_MMB[MO	NM:i:0
+EAS38_8_28_805_359	0	chr1	3363388	255	35M	*	0	0	CCAACACCTTATTATCACTTATTTTTGTCATTCTA	hhhhhhhhhhhhhhhhhhhhhhhhhhIhhhh@hhZ	NM:i:1
+EAS38_8_229_300_432	16	chr1	3363412	255	35M	*	0	0	TTGTGATGCTATATATGTGTGCATTAACCACTGCC	RObh>QWGShUahhhhBUhNhPhhhhhhhhhhhhh	NM:i:2
+EAS38_8_247_121_676	16	chr1	3363412	255	35M	*	0	0	TTGTCATGCTATATATTTGTGCATTAACCACTGCC	QQMhgLRNfhh[hhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_180_822_42	16	chr1	3363658	255	35M	*	0	0	GAGTAACTGCTGCATGTTAATCTATGTCATCCCTA	MXE@dhhIP__Xhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_83_317_544	0	chr1	3364348	255	35M	*	0	0	GCATTTCTGAGCCTGGGTGATCTTACTTTATATTC	hhhhhhhhhhhhhhhhhhhhhhhhchhhhhhhhhb	NM:i:0
+EAS38_8_194_299_688	16	chr1	3364585	255	35M	*	0	0	AAGGATGTTATAATTGAATCATATGGAAGTTCTTT	^hh_h_hhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_42_578_279	0	chr1	3364694	255	35M	*	0	0	AAGATGTATTTTTATTTGTTTACTGTATAATTTCC	hhhhhhhhhhhhhhhhhhhhhhhhChhhh_hhCP\	NM:i:2
+EAS38_8_309_762_904	16	chr1	3364864	255	35M	*	0	0	AAAAGGACATCTGAATTACCTACTTGTTTTTATCA	hhhhhFhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_236_498_116	16	chr1	3364885	255	35M	*	0	0	ACTTGTTTTTATCAGGTTGGTCTGTAAGCATATCT	LI_hhQhhMahh\hhbhFhhh\hhhhhhhhhhhhh	NM:i:0
+EAS38_8_184_968_83	0	chr1	3365051	255	35M	*	0	0	TAATTGCCAGGAGTTCATTGTTTTCCATATTGTCT	hhhhhhhhhhhhhhhhfhhhhhhhh]EhVhhHhUh	NM:i:0
+EAS38_8_194_34_599	16	chr1	3367203	255	35M	*	0	0	ATTGTGGATATAAGTGGAGAAAGAGCAAGAAAAAA	hhHhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_73_896_111	16	chr1	3367203	255	35M	*	0	0	ATTGTGGATATAAGTGGAGAAAGAGCAAGAAAAAA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_115_579_578	16	chr1	3369573	255	35M	*	0	0	TCAGAGCATTTGGATTTTGGTCTTTAGATTAAGGT	^hhhhhhhhXhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_260_546_322	16	chr1	3369573	255	35M	*	0	0	TCAGAGCATTGGGATTTTGGTCTTTAGATTAAGGT	>>NELH=IJ@@@QIMBDDKOS\KJfhhh[Phhhhh	NM:i:1
+EAS38_8_168_10_541	16	chr1	3375680	255	35M	*	0	0	CCGTGCAGACATTCTGATGTTGGGTAATATCAAAT	LT>IKNhhhWhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_8_316_251_752	0	chr1	3377312	255	35M	*	0	0	TCACAATATTGTCTATACTTCTAAACATCCTCAGA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhchhh	NM:i:0
+EAS38_8_127_130_231	0	chr1	3379889	255	35M	*	0	0	AATAAATTTCTCTTGTTTGCAAGCTATCTACTCTA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhbhhhhe	NM:i:1
+EAS38_8_262_614_438	0	chr1	3379889	255	35M	*	0	0	AATAAATTTCTCTTGTTTGCAAGCTATCTACTCTA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhA	NM:i:1
+EAS38_8_152_675_620	0	chr1	3379983	255	35M	*	0	0	ATCACACTTCAATTTTCATTTTCCAGCAAAAGCTT	hhhhhhhhhhhhhhhhhhhhhhhhhhhghZhhhhh	NM:i:2
+EAS38_8_315_641_621	16	chr1	3380977	255	35M	*	0	0	CATTTATTCTATGTCAATTTATCTTTTGAGTATAA	hhhhhhahhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_223_839_518	16	chr1	3381656	255	35M	*	0	0	GTCCTTTTTCTAGTGTCGTGTTTAAGCTCCCGTGA	PVLMUG`YLSVhaNhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_189_893_589	16	chr1	3382043	255	35M	*	0	0	GCAGAGCCTCTGTGTCATTGCCTGGCAGGTAGGAG	=L`KeShhhhdhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_8_228_882_739	0	chr1	3383793	255	35M	*	0	0	TGGTGAGTATTGGAACGACTAAATCAGTGTATTAA	hhhhhhhhhhhhhhh]hhfhhhh]^]hehbghNHO	NM:i:0
+EAS38_8_290_281_824	16	chr1	3386732	255	35M	*	0	0	GTAGAAAACTGGATTTTTTTTTTTTGGTGATATAG	`GUEhEhhhd\hhhhhhhhhhhhhhhhhhhhhhhh	NM:i:1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffdiff_in2.sam	Fri Nov 08 14:54:01 2013 -0600
@@ -0,0 +1,400 @@
+EAS38_1_126_860_867	16	chr1	3009675	0	35M	*	0	0	ATAGTCCCTTACTGCTTTTAGTATTCTATCTTTAT	WFGAeC\gVShhhLh`hhPbPhhhhhhhhhhhhhh	NM:i:2
+EAS38_1_125_842_97	0	chr1	3023056	0	35M	*	0	0	ATCTTCTTCAATTTGTTTCTTCAGAGACTTTAATT	hhhhhhhhhhhhhhhhhhhhhhhJhhNhhh_KINh	NM:i:2
+EAS38_1_261_52_728	16	chr1	3035247	0	35M	*	0	0	AATCCCCCACCCCACAGGAACAAAGTCCTGATGCA	@???GIH@C?HXINLQJ=VVhhgTFHfhYhhJLhb	NM:i:2
+EAS38_1_71_500_217	16	chr1	3081731	0	35M	*	0	0	AGGAGATAAATAACTAATAAAAAATGAAAAAAAAA	h?DhLhFhfhKhRFhhhShhhhhhThhhhhhhhhh	NM:i:2
+EAS38_1_2_666_566	0	chr1	3111450	255	35M	*	0	0	CCACTCACAAGACAAGACCAGGATCCTGGAGAGAT	hhhhhhhhhhhhhhNh^Yh]d]GRNVYURK^JU>I	NM:i:0
+EAS38_1_220_990_991	0	chr1	3111546	255	35M	*	0	0	AAAAGCTGAGAGTCAGCATGAATCAAGAGATAGAA	hhchhMabNhP_>BKXQSNKDRD?@@TBJJ=GL@G	NM:i:1
+EAS38_1_133_518_728	0	chr1	3111550	255	35M	*	0	0	GCTGAGAGTCAGCATGAATCCAGAGATAGAAAAAG	hhhhhhhhhhhhhhhhhhhOhQhhhNL^ZT[PLNN	NM:i:0
+EAS38_1_219_471_934	0	chr1	3117684	255	35M	*	0	0	TGTCCTTTGGCTTACAGAAGTTTTATAATTTTATG	hhhhhhhhhhhhhhhhhhhhhhhhRhhehhhh]hH	NM:i:0
+EAS38_1_180_265_430	16	chr1	3131249	0	35M	*	0	0	TGATCAGCCCTTTGGCATTCCTCAGTTGAGAATTC	GICHVhhCY`\TYhhhh[fdhhhhhhhhhhhhhhh	NM:i:2
+EAS38_1_155_516_677	0	chr1	3137065	0	35M	*	0	0	CTGGAATTATGTGATTATAATTTTCTTATCATTTT	hhhhhhhhhhhhhhhhhhhhhhhhhhh`Dhhhhhh	NM:i:1
+EAS38_1_156_788_924	0	chr1	3137065	0	35M	*	0	0	CTGGAATTATGTGATTATAATTTTCTTAGCATTTT	hhhhhhhhhhhhhhhhhhhhhhhhbhhhh]Shhhh	NM:i:0
+EAS38_1_219_907_956	0	chr1	3137065	0	35M	*	0	0	CTGGAATTATGTGATTATAATTTTCTTAGCATTTT	hhhhhhhhhhh\hhhhhhhhRhhh^hhg`h\hhhh	NM:i:0
+EAS38_1_224_924_816	0	chr1	3137074	0	35M	*	0	0	TGTGATTATAATTTTNTTAGCATTTTCTTCGTAAA	hhhhhhhhhhhhhhh;hhhhh`hhhhhhhXhhhg]	NM:i:2
+EAS38_1_128_932_926	16	chr1	3137133	0	35M	*	0	0	GTTGGTGTATAGTAAAAAGTAAAGAAATTCTGAGA	XYV[Lhfhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_146_271_903	16	chr1	3137133	0	35M	*	0	0	TTTGGTGTATAGTAAAAAGTAAAGAAATTCTGAGA	HVhT[`hhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_1_127_823_362	0	chr1	3137183	0	35M	*	0	0	GATAATACATATATACATATGCAGTGTGTGTGCCA	hhhhhhhhhhhhhhhhhhhhhhhXhhhhhhhNU[H	NM:i:0
+EAS38_1_282_34_255	16	chr1	3137183	0	35M	*	0	0	GATAATACATATATAAATATGCAGTGTGTGTGCCA	KhNhhLhQh\h`hJhCh`h^hLhhdhhhhhhhheh	NM:i:1
+EAS38_1_215_971_567	0	chr1	3137204	0	35M	*	0	0	CAGTGTGTGTGCCAGTGGTGTTAACAATACTAATA	hhhhh[hhhhhhhhh\hSQeLYcVFKGAKH]XD^H	NM:i:1
+EAS38_1_143_6_639	16	chr1	3137450	0	35M	*	0	0	ATGTTCCCACACGGTCTATCTCCCTGACAAATCCC	RH?>EJUcHhhILIhFhhYShb`hhhhhhhhchhh	NM:i:2
+EAS38_1_132_603_749	0	chr1	3154107	255	35M	*	0	0	TATATTTGGAAAAAAAAAGAAAGGAGTGTAGAGTC	hhhhhhhhhhhhhhhhhhhhhhhhhhehhhhPhSS	NM:i:0
+EAS38_1_238_595_598	0	chr1	3178632	0	35M	*	0	0	GCTTTTTGCTTTTTGCTTTTTGCTTTTTGCTTTTT	hhhhhhhhhhhhhhdhhhhhhOhhhhhhLXhhhhh	NM:i:0
+EAS38_1_238_595_598	0	chr1	3178639	0	35M	*	0	0	GCTTTTTGCTTTTTGCTTTTTGCTTTTTGCTTTTT	hhhhhhhhhhhhhhdhhhhhhOhhhhhhLXhhhhh	NM:i:0
+EAS38_1_238_595_598	0	chr1	3178646	0	35M	*	0	0	GCTTTTTGCTTTTTGCTTTTTGCTTTTTGCTTTTT	hhhhhhhhhhhhhhdhhhhhhOhhhhhhLXhhhhh	NM:i:0
+EAS38_1_238_595_598	0	chr1	3178653	0	35M	*	0	0	GCTTTTTGCTTTTTGCTTTTTGCTTTTTGCTTTTT	hhhhhhhhhhhhhhdhhhhhhOhhhhhhLXhhhhh	NM:i:0
+EAS38_1_118_1000_212	0	chr1	3179061	0	35M	*	0	0	ATGTGATTTTAAATCATAGTCTTGCTTTTCCATTG	hhhhhhhhhhhhghhhEMDPKhhLNh[hhMPNETJ	NM:i:2
+EAS38_1_311_90_296	16	chr1	3179539	255	35M	*	0	0	ACATAGGAAATGGAAGAGTACTTTATTATTATTAT	bEhIhhhhTCNhhhhhhhVhRQhhhhhhhhhhhhh	NM:i:1
+EAS38_1_221_489_194	16	chr1	3183282	3	35M	*	0	0	ACTGACAGAAAAGAGACAGAGGTAGGACTTCTAGG	>>FL[@RL@^WSRYUP@`UZeSLhhRQbOGWThhh	NM:i:2
+EAS38_1_221_489_194	16	chr1	3183945	3	35M	*	0	0	ACTGACAGAAAAGAGACAGAGGTAGGACTTCTAGG	>>FL[@RL@^WSRYUP@`UZeSLhhRQbOGWThhh	NM:i:2
+EAS38_1_205_642_159	16	chr1	3186543	255	35M	*	0	0	CACATGCCTTTTTCATTTTTTCCAAGTGCCATCTG	KhUhSHT]VS]_hFhhMhDbheHhhhhhhhhhhhh	NM:i:0
+EAS38_1_26_282_635	16	chr1	3188051	255	35M	*	0	0	TTCTGATCCTCAGGATCTGGAGTTACAGATGGTTG	ECaSghKhh]ZhhhhdhVhhhh]hhhhhhhhhhhh	NM:i:0
+EAS38_1_221_487_440	16	chr1	3188179	255	35M	*	0	0	TTACTAAATTTTGTAATACTACTTAGTCTGGAAAA	Oge[WhhhTKRShhhhbhhYhhchhh]hhhhhhhh	NM:i:0
+EAS38_1_7_602_714	16	chr1	3188938	255	35M	*	0	0	GACTGTCATTACATTATTTTAGTAGTTGTATTTTC	A\h^SLhhChQhhhhhhhhUhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_239_803_441	16	chr1	3189316	255	35M	*	0	0	AGATGTATCATAGCTCAGAAAGTACATTTGTAAGA	hhhVhWhRJhYhh^Wbhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_318_649_84	16	chr1	3189316	255	35M	*	0	0	AGATGTATCATAGCTCAGAAAGTACATTTGTAAGA	hhh\hhhhKhhhhKMhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_178_556_269	0	chr1	3189808	255	35M	*	0	0	CTTTTTTTAAAATGACCACAGTGTACTTTATTTAA	hhhhhhhhhhhhhhhhhhhhLhhhXhhhhZhhhhX	NM:i:2
+EAS38_1_184_810_767	16	chr1	3189830	255	35M	*	0	0	GTACTTTATTTAATGATTTTTGTACTTTGTGTTGC	dhah]hhhhhhhhhchh_hhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_307_56_994	16	chr1	3189841	255	35M	*	0	0	AATGATTTTTGTACTTTGTGTTGCAATAAAATAAA	hh[Shhhhhh`hhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_1_924_497	16	chr1	3189853	255	35M	*	0	0	ACTTTGTGTTGAAATAAAATAAAAAAAAAATCTAC	SNT[Za]ahh]Lhhhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_1_95_808_182	0	chr1	3189880	255	35M	*	0	0	AAATCTACAAAATTCAAATATATAAAATTTCAAGT	hhhhhhhhhhhhhhhehhhhhhhhhMhhhhh\h^h	NM:i:0
+EAS38_1_43_924_188	0	chr1	3189887	255	35M	*	0	0	CAAAATTCAAATATATAAAATTTCAAGTTTTCTTT	hhhhhhhhh^Xhhhh?hh[RhhhhOMDhhhhhhhh	NM:i:0
+EAS38_1_11_826_352	16	chr1	3189890	255	35M	*	0	0	AATTCAAATATATAAAATTTCACGTTTTCTTTGTT	hhIQAhhhShchchhhhUNU[hChhehhhhbhAhh	NM:i:2
+EAS38_1_131_730_378	16	chr1	3189892	255	35M	*	0	0	TTCAAATATATAAAATTTCAAGTTTTCTTTCTTTT	HIhhhhhhhhhhhhhhhZhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_317_700_555	16	chr1	3189893	255	35M	*	0	0	ACAAATATATAAAAGTTCAAGTTTTCTTTCTTTTA	?hhhhhh[hThhhhHhYhEhhhhhhhhhhhhhhhh	NM:i:2
+EAS38_1_46_519_952	0	chr1	3189903	255	35M	*	0	0	AAAATTTCAAGTTTTNTTTCTTTTAAAGTTTTACA	hhhhhhhhhhhhhhh;hhhhhhhhhhhhhhhhhPf	NM:i:1
+EAS38_1_26_849_836	0	chr1	3189906	255	35M	*	0	0	ATTTCAAGTTTTCTTTCTTTTAAAGTTTTACAAGA	hhhhhhhhhhhhhhhhhhhhhdhhhhhhhhhhNXU	NM:i:0
+EAS38_1_271_964_726	0	chr1	3189906	255	35M	*	0	0	ATTTCAAGTTTTCTTACTTTTAAAGTTTTACAAGA	hhhhhhhhhhhhhhhCXhhhhhhhHhhhhhhVhhh	NM:i:1
+EAS38_1_305_225_753	16	chr1	3189909	255	35M	*	0	0	TCAAGTTTTCTTTCTTTTAAAGTTTTACAAGAAAA	Zhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_210_231_735	16	chr1	3189912	255	35M	*	0	0	AGTTTTCTTTCTTTTAAAGTTTTACAAGAAAAAAA	hhVhhhhhh_hhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_210_55_110	0	chr1	3189915	255	35M	*	0	0	TTTCTTTCTTTTAAATTTTTACAATAAAAAAAATC	hhhhhhhhhhhhUPh\hhhhdhLRcCLTRW@FMhh	NM:i:2
+EAS38_1_230_130_609	16	chr1	3189915	255	35M	*	0	0	TTTCTTTCTTTTAAAGTTTTACAAGAAAAAAAATC	TDMO]K^FLYWWhhhh[S^Rhhhh^hhhhhhhhhh	NM:i:0
+EAS38_1_203_262_383	16	chr1	3189917	255	35M	*	0	0	TCTTTCTTTTAAAGTTTTACAAGAAAAAAAATCAG	]hJh[ahhhPhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_23_872_103	0	chr1	3189918	255	35M	*	0	0	CTTTCTTTTAAATTTTTACAATAAAAAAAATCAGA	hhhhhhhhhb_[Dhhhhhh[XAT[hUfKFhhVTM>	NM:i:2
+EAS38_1_74_546_492	0	chr1	3189937	255	35M	*	0	0	AAGAAAAAAAATCAGATAACCGAGGAAAATTCTTC	hhhhhhhhhhhhhhh`h]hhhhThaRPOOhhBhhX	NM:i:1
+EAS38_1_177_466_463	0	chr1	3189943	255	35M	*	0	0	AAAAATCAGATAACCGAGGAAAATTATTCATTATG	hhhhhhhhhhhhhhhhOhMSIIhhhdhh\hhhfhB	NM:i:0
+EAS38_1_326_846_82	0	chr1	3189943	255	35M	*	0	0	AAAAATCAGATAACCGAGGAAAATTATTCATTATT	hhhhhhhhhhhhhhhh]hJdRdhhhZhhhYhbhhG	NM:i:1
+EAS38_1_235_891_810	0	chr1	3189957	255	35M	*	0	0	CGAGGAAAATTATTCATTATGAAGTACTACTTTCC	hhhhhhhhhhhhhhhhhhhhhhhhh_HhOJhhPWI	NM:i:0
+EAS38_1_73_865_289	16	chr1	3189961	255	35M	*	0	0	GAAAATTATTCATTATGAAGTACTACTTTCCACTT	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_201_984_898	0	chr1	3189963	255	35M	*	0	0	AAATTATTCATTATGAAGTACTACTTTCCACTTCA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_37_723_474	16	chr1	3189968	255	35M	*	0	0	ATTCATTATGAAGTACTACTTTCCACTTCATTTCA	hHEJhFThZhhhhXhUShhhhhhhhhXhhhhhhhh	NM:i:0
+EAS38_1_183_791_724	0	chr1	3189973	255	35M	*	0	0	TTATGAAGTACTACTTTCCACTTCAGTTCATCACA	hhhhhhhhhhhhhhhhhafhhhhdWBhhPYhHPh[	NM:i:1
+EAS38_1_69_87_770	16	chr1	3189978	255	35M	*	0	0	AAGTACTACTTTCCACTTCATTTCATCACAAATTG	hhJhghhhhhhghhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_54_211_781	16	chr1	3189984	255	35M	*	0	0	TACTTTCCACTTCATTTCATCACAAATTGTAACTT	hghhhLhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_203_766_573	16	chr1	3189985	255	35M	*	0	0	ACTTTCCACTTCATTTCATCACAAATTGTAACTTA	SQPbUhhZhhhhhhhWhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_195_866_158	0	chr1	3189991	255	35M	*	0	0	CACTTCATTTCAACACAAATTGTAACTTACTTAAC	hhhhhhRhhhhh@hchHOThhRh[F`hhPShbNSI	NM:i:1
+EAS38_1_122_739_820	16	chr1	3190001	255	35M	*	0	0	CATCACAAATTGTAACATACTTAACTGACCAAAAA	hhXhfYhhhhSORhhhAghhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_1_144_950_152	16	chr1	3190008	255	35M	*	0	0	AATTGTAACTTACTTAACTGAACAAAAAAACTATG	hhIIc_hhI[\hHghhhYhhhHhhhhhhhhhhhhh	NM:i:1
+EAS38_1_168_613_587	0	chr1	3190008	255	35M	*	0	0	AATTGTAACTTACTTAACTGACCAAAAAAACTATG	hhhhhhhhhhhhhhhhhhhhgh`SNhfhhRahZf\	NM:i:0
+EAS38_1_134_699_616	16	chr1	3190013	255	35M	*	0	0	TAACTTACTTAACTGACCAAAAAAACTATGGTACT	hhhQhMhhehhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_210_777_789	0	chr1	3190014	255	35M	*	0	0	AACTTACTTAACTGACCAAAAAAACTATGGTACTG	hhhhhhhhhhhhhhhWfh\`hHhhShgYhXGZIQU	NM:i:0
+EAS38_1_66_446_787	0	chr1	3190014	255	35M	*	0	0	AACTTACTTAACTGACCAAAAAAACTATGGTACTG	hhhhhhhhhhhhhhhhhhhhhhh]dhhhhdghShh	NM:i:0
+EAS38_1_179_978_676	16	chr1	3190032	255	35M	*	0	0	AAAAAACTATGGTACTGCAGTATAGCAAATACTCC	hhhhhghWhZhFhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_308_776_503	16	chr1	3190032	255	35M	*	0	0	AAAAAACTATGGTACTGCAGTATAGCAAATACTCC	hhhhhh^?hRhThhhghbhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_172_693_734	16	chr1	3190040	255	35M	*	0	0	ATGGTACTGCAGTATAGCANATACTCCACACACTG	hLD?UFaLLhaJhhhh[hh;hhhhhhhhhhhhhhh	NM:i:1
+EAS38_1_239_423_396	16	chr1	3190040	255	35M	*	0	0	AGGGTACTGAAGTATAGCAAATACTCCACACACTG	_AH?>LADTCZh^h]hhDhhhZhhehhhhhhhhhh	NM:i:2
+EAS38_1_284_912_582	16	chr1	3190042	255	35M	*	0	0	GGTACTGCAGTATAGCAAATACTCCACACACTGTG	LhhhhhhhhhhhhhhWhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_209_687_576	0	chr1	3190073	255	35M	*	0	0	TGTGCTTTGAGCTAGAGCACTTGGAGTCACTGCCC	hhhhhhhhhhhhhhhdhhZdhhYhPMhRPIeMWGP	NM:i:0
+EAS38_1_185_490_551	16	chr1	3190085	255	35M	*	0	0	TAGAGCACTTGGAGTCACTGCCCAGGGCAGCAGCC	FJDFJGJJODb\`hJQ_hNghhhhhhhh`hhhhhh	NM:i:0
+EAS38_1_65_838_419	0	chr1	3190102	255	35M	*	0	0	CTGCCCAGGGCAGCAGCCTCCAACCAAGAAAGACA	hhhhhhhhhhh]_hKhhchceBdGaOCG@?BGIIP	NM:i:0
+EAS38_1_323_255_975	0	chr1	3190107	255	35M	*	0	0	CAGGGCAGCAGCCTCCAACCAAGAAAGACACACTT	hhhhhhhh\hhUShNYh]@Uh\hMXMaJ?YRRBFH	NM:i:0
+EAS38_1_296_538_461	0	chr1	3190126	255	35M	*	0	0	CAAGAAATACACACTTACAAGTTGAATTCTAAAGG	hhhhhhhhhhhhhhhhhh]hhhhh\hhhhhMhbhh	NM:i:1
+EAS38_1_132_195_514	16	chr1	3190129	255	35M	*	0	0	GAAAGACACACTTACAAGTTGAATTCTAAAGGAAG	chbhhhShFhhYhhghhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_155_895_725	16	chr1	3190140	255	35M	*	0	0	TTTCAAGTTGAATTCTAAAGGAAGGTCTGGTTATG	VhO[ghWSchhh_hZhhhhhhhhhXhhhhhhhhhh	NM:i:1
+EAS38_1_193_609_633	16	chr1	3190140	255	35M	*	0	0	TTACAAGTTGAATTCTAAAGGAAGGTCTGGTTATG	Q`hbhhh[hhhhShhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_135_816_228	16	chr1	3190142	255	35M	*	0	0	AAAAGTTGAATTCTAAAGGAAGGTCTGGTTATGTG	fC_]SH_VhhIABLhhhhfhhhWfZhhhhhhhhhh	NM:i:1
+EAS38_1_145_593_539	0	chr1	3190150	255	35M	*	0	0	AATTCTAAAGGAAGGTCTGGTTATGTGGGGTTGTA	hhhhhhhhhhhhhhhhhhhhhhhhQh`ShhhhhAH	NM:i:1
+EAS38_1_121_577_810	16	chr1	3190177	255	35M	*	0	0	GGGTTGGAGTATGTATATCTATATATCTCTATATA	KJM]OSdhbXhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_1_194_207_828	0	chr1	3190207	255	35M	*	0	0	ATATATATTTACATCAAAGAATTTAATAACTCATT	hhhhhhhhhhhhhhhhhhhhhhhhchhTh_h_`hh	NM:i:0
+EAS38_1_113_803_974	0	chr1	3190221	255	35M	*	0	0	CAAAGAATTTAATAACTCATTTAAATTTTTGTTTC	hhhhhhhhhhhhhhhchQhhhhhgOhh_hhh_hhL	NM:i:0
+EAS38_1_160_812_510	16	chr1	3190244	255	35M	*	0	0	AATTTTTGTTTCAAATAAAATTCCAAATACACTTG	hhWOhG]h^hhQhhhhhhhhh_\hhhhhhhhBhhh	NM:i:1
+EAS38_1_40_88_508	16	chr1	3190249	255	35M	*	0	0	TTGTTTCAAATAAAATTCCAAATACATTTGTACAA	QhhgVhdhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_84_935_631	16	chr1	3190249	255	35M	*	0	0	TTGTTTCAAATAAAATTCCAAATACATTTGTACAA	^]hJhZWhhhhhhhhhUhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_36_762_603	0	chr1	3190263	255	35M	*	0	0	ATTCCAAATACATTTGTACAATGTTTACAAAGTAA	hhhhhhhhhhhhhhhhhhhhhh^hhhhahX\]_hb	NM:i:0
+EAS38_1_16_788_728	16	chr1	3190265	255	35M	*	0	0	TCCAAATACATTTGTACAATGTTTACAAAGTAAGA	@hEhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_172_782_398	16	chr1	3190269	255	35M	*	0	0	AATACATTTGTACAATGTTNACAAAGTAAGAGACA	hhZhhhaZhhWhhhhhheh;hThhhhehhhhhhhh	NM:i:1
+EAS38_1_319_78_862	16	chr1	3190274	255	35M	*	0	0	ATTTGTACAATGTTTACAAAGTAAGAGACAGGACT	dLhZM_ehdhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_27_817_428	16	chr1	3190276	255	35M	*	0	0	TTGTAAAATGTTTACAAAGTAAGAGACAGGACTGG	VPhchChh_ghfhhEhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_1_188_256_713	0	chr1	3190325	255	35M	*	0	0	AGGCCAGGCACCGTGATGTCCGGGTGATATATCTT	hhhhhhhhhhhhhhhKhhaMhUhhNgA_E[GhM[G	NM:i:0
+EAS38_1_315_859_502	16	chr1	3190329	255	35M	*	0	0	CAGGAACCGTGATGTCCGGGTGATATATCTTCACG	BNSIKHNI\SK]VdXZR`Uhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_1_152_381_800	16	chr1	3190355	255	35M	*	0	0	ATCTTCACGTTGCCTGCACACACCTTATTTCTGAA	ZVhQIhhhhhhXhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_282_558_872	0	chr1	3190364	255	35M	*	0	0	TTGTCTGCACACACCTTATTTCTGAAATGGAGAGA	hhh=hhhhhhhhh_hhhhhhhYhh`hhhhhQhhhC	NM:i:1
+EAS38_1_215_759_830	0	chr1	3190407	255	35M	*	0	0	AGAATGTCACCGACTATGCATCAGAATACTATGTA	hhhhhhhhhhhhhhhhhhh_hh[hUWhhbh^hhXc	NM:i:0
+EAS38_1_277_471_798	16	chr1	3190412	255	35M	*	0	0	GTCACCGACTATGCATCAGAATACTATGTACAGTT	KJYK\eYhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_279_405_802	16	chr1	3190418	255	35M	*	0	0	GACTATGCATCAGAATACTATGTACAGTTGAAGTT	Chhhhhhhhhhhhhhhhhhhhhhhhh`hhhhhhhh	NM:i:0
+EAS38_1_75_573_457	16	chr1	3190428	255	35M	*	0	0	CAGAATACTATGTACAGTTGAAGTTAGGGAGCTGA	Zhdhh_dhYhRh\hhhhUKhhhhhUhhhhhhhhhh	NM:i:0
+EAS38_1_238_427_419	16	chr1	3190444	255	35M	*	0	0	GTTGAAGTTAGGGAGCTGAGAACCTAGTGGTCTGT	XKEQdhhNKZhhhhhhdhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_24_788_817	0	chr1	3190444	255	35M	*	0	0	GTTGAAGTTAGGGAGCTGAGAACCTAGTGGGCTGT	hhhhhhhhhhhhhQhHhhUeK_AGXKhNfe>=ITO	NM:i:1
+EAS38_1_307_22_417	16	chr1	3190449	255	35M	*	0	0	AGTTAGGGAGCTGAGAACCTAGTGGTCTGTTCTCT	KU@DX`XWbV@JhghhTETVhh^hTWh_hh[hhhh	NM:i:0
+EAS38_1_104_731_910	0	chr1	3190455	255	35M	*	0	0	GGAGCTGAGAACCTAGTGGTCTGTTCTCTTCTGGT	hhhhhhhhhhhJYhhhhhhZOhhhhBhF\hFhhaO	NM:i:0
+EAS38_1_189_367_978	16	chr1	3190466	255	35M	*	0	0	CCTAGTGTTCTGTTCTCTTCTGGTTTGTCTTCATC	HhCMIbQEShcKTYhhh\hhhYPhhhhhhhhhhhh	NM:i:1
+EAS38_1_288_697_269	0	chr1	3190470	255	35M	*	0	0	GTGGTCTGTTCTCTTCTTGTTTGTCTTCATCTACC	hhhhhhhhhhhhhhhhhBChhhDhhhhhQhhhI?c	NM:i:1
+EAS38_1_239_232_371	16	chr1	3190490	255	35M	*	0	0	GTGTCTTAATCTACCAGCTATTACTCCTCTTTTGC	DKK?ADHAhKCIhVhhhB_hchhhbhhZhhhhhhh	NM:i:2
+EAS38_1_17_329_620	16	chr1	3190509	255	35M	*	0	0	ATTACTCCTCTTTTGCTCAGAGATAAATTTAAAAT	h^E_hMhchhhThVhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_145_66_863	0	chr1	3190520	255	35M	*	0	0	TTTGCTCAGAGATAAATTTAAAATACAAACATTGG	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhc	NM:i:0
+EAS38_1_318_476_736	0	chr1	3190562	255	35M	*	0	0	AAGGAGAAAAGCACAAAATATTTAAGGCAAATTAA	hhhhhhhhhhhhhhhhhhhhhhhhfhh^hF\hhhH	NM:i:0
+EAS38_1_91_887_139	16	chr1	3190577	255	35M	*	0	0	AAATATTTAAGGCAAATTAAGCAAATATGTACAGT	hhhhhK^ThhZhThhh\hhhhZhhhhhhhhhhhhh	NM:i:0
+EAS38_1_42_628_869	16	chr1	3190582	255	35M	*	0	0	TTTAAGGCAAATTAAGCAAATATGTACAGTCTCTT	EYEhhBDYhhh^hhhLhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_266_296_122	16	chr1	3190587	255	35M	*	0	0	GGAAAATTAAGAAAATATGTACAGTCTCTTTGTGC	hUJhhh@ehhhFhhhShIhehhhh`h\hhbhhhhh	NM:i:2
+EAS38_1_296_47_651	0	chr1	3190588	255	35M	*	0	0	GCAAATTAAGCAAATATGTACAGTCTCTTTTTTCC	hhhhhhhhhhhhhhhhhhhhh[hhhhhhhhDhIRE	NM:i:2
+EAS38_1_298_622_554	16	chr1	3190612	255	35M	*	0	0	CTCTGTGTGCCAGGAGGATGTGACTTTCTTTTTAA	QXfIBXhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_1_55_346_335	16	chr1	3190613	255	35M	*	0	0	TCGGTGTGCCAGGAGGATGTGACTTTCTTTTTAAA	KABCGhGh@hhhhhhhhhh^hhhhhhhhhhhhhhh	NM:i:2
+EAS38_1_144_104_681	16	chr1	3190646	255	35M	*	0	0	AATCCCAAACCATGCTTTAAAAAATTCAAATAAAG	hhVhJThhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_307_505_905	0	chr1	3190650	255	35M	*	0	0	CCAAACCATGCTTTAAAAAATTCAAATAAAGCAAG	hhhhhhhhhhhhhhhhhhhhhhhhShhhh_h\`hh	NM:i:0
+EAS38_1_4_468_915	0	chr1	3190667	255	35M	*	0	0	AAATTCAAATAAAGCAAGTCTGGTGTGAGTTGGGT	hhhhhhhhhhhhhhhhhhhhhhhahfhJhhhhhha	NM:i:0
+EAS38_1_177_100_872	0	chr1	3190682	255	35M	*	0	0	AAGTCTGGTGTGAGTTGGGTTGCTTGTGTTGTTTT	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhThhhhh	NM:i:0
+EAS38_1_201_448_983	0	chr1	3190733	255	35M	*	0	0	TGTTTTGCACAAAATAACCATTTGGAATTTGCAGT	hhhhhhhahhhhhhhhhZMhhhhhhNhhhhXGXhH	NM:i:0
+EAS38_1_205_905_511	16	chr1	3190740	255	35M	*	0	0	AACAAAATAACCATTTGGAATTTGCAGTGGAATAA	hhFhhhhahhhhhhahhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_1_22_834_621	0	chr1	3190741	255	35M	*	0	0	ACAAAATAACCATTTGGAATTTGCAGTGGAATAAT	hhhhhhhhhhhhhhhhhYhhhhhh]h]h[NVhI`h	NM:i:0
+EAS38_1_297_847_594	16	chr1	3190753	255	35M	*	0	0	TTTGGAATTTGCAGTGGAATAATTTGTTAATTGTG	`KYZ\hX^dhYhhhhbhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_105_929_305	16	chr1	3190768	255	35M	*	0	0	GGAATAATTTGTTAATTGAGAAGTGTATGGTTTTG	hhhhhhhQ]hhhhhh_hhEhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_1_323_29_609	0	chr1	3190771	255	35M	*	0	0	ATAATTTGTTAATTGTGAAGTGTATGGTTTTGTAT	hhhhhhhhhhhhhhhhhhhOhhhhhhhhhhh@hGh	NM:i:0
+EAS38_1_174_674_495	0	chr1	3190781	255	35M	*	0	0	AATTGTGAAGTGTATGGTTTTGTATTTTTAAACCA	hhhhhhhhhhhhhhhhhhhhhFhhhhhhLUPaeSG	NM:i:1
+EAS38_1_156_965_73	16	chr1	3190814	255	35M	*	0	0	CAAAAAACAGTAGCTGAGGTAGTTAAATGTGAAAC	DhhhCghNhhhhhRhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_1_264_136_776	0	chr1	3190842	255	35M	*	0	0	GTGAAACTTACACAACTTAAAATAATGAGAGAATG	hhhhhhhhhh`hbhhYhhbh_eh_hhbM\O]IVYR	NM:i:0
+EAS38_1_269_103_855	16	chr1	3190853	255	35M	*	0	0	ACAACTTAAAATAATGAGAGAATGGAGAACCAATG	ShhhhhXhhhhchhLhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_133_823_893	0	chr1	3190856	255	35M	*	0	0	GCTTAAAATAATGAGAGAATGGAGAAACAATGTAA	hhhhhhhhhhhhhhhbhhVhhhahQZ@KZhSUKgH	NM:i:2
+EAS38_1_316_626_26	0	chr1	3190872	255	35M	*	0	0	GAATGGAGAACCAATGTAAGGAGCCCAGACTCTTG	hhhhhhhhhh]hhhhh^hXNhhXLcGGFEMVIL\A	NM:i:0
+EAS38_1_14_936_623	0	chr1	3190882	255	35M	*	0	0	CCAATGTAAGGAGCCCAGACTCTTGCCATCTGGGA	hhhhhhhhdhhhhYTbFhTWehhNJdKDJVREM?E	NM:i:1
+EAS38_1_112_85_814	16	chr1	3190885	255	35M	*	0	0	ATGTAAGGAACCCAGACTCTTGCCATCTGGAAGCA	dBCDhhRNh?RhWhWhhWhZh[hhhhhhhhhhhhh	NM:i:1
+EAS38_1_153_136_402	16	chr1	3190885	255	35M	*	0	0	ATGTAAGGAGCCCAGACTCTTGCCATCTGGAAGCA	QUhWhhh[hTahhhhQhhUhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_267_293_629	16	chr1	3190891	255	35M	*	0	0	GGAGCCCAGACTCTTGCCATCTGGAAGCAGGCTCA	Zg]YhEhhhhfd`hZhJhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_60_948_719	16	chr1	3190944	255	35M	*	0	0	TACCCAGAAAAACATTTGTTCTTTTGGATGCCATT	BAHQQhFehhhRhUPKJVf\hh^bWh_hhhhhhhh	NM:i:0
+EAS38_1_279_273_497	0	chr1	3190975	255	35M	*	0	0	CATTAGTTCAGCCAGTGTCAACATGACTAGTGGTT	hhhhhhhhhhhhhhhZYhhhhahhh`Uh`ELGVVg	NM:i:0
+EAS38_1_35_405_941	16	chr1	3190979	255	35M	*	0	0	AGTTCAGCCAGTGTCAACATGACTAGTGGTTTCCC	E??>bfB^hhOIT_hhhhhhUWhhhhh^hhhhhhh	NM:i:0
+EAS38_1_307_828_462	16	chr1	3190995	255	35M	*	0	0	ACATGACTAGTGGTTTCCCAAGCACTTGCTTGGAA	hRhhhhh^hhhhhhhhGfhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_118_418_323	16	chr1	3191023	255	35M	*	0	0	CGTGGAAGCAAAGATAAAGAAAGTCTGCTTTCCAG	IS@dWhh]NhhhHhbhhhhhhhhZhchhhhghhhh	NM:i:2
+EAS38_1_144_10_603	0	chr1	3191023	255	35M	*	0	0	CTTGGAAGCAAATATAAAGAAAGTCTGCTTTCCAG	hhhhhhhhhhZhhhhhhdhWhhhhhhh^hhhDhKU	NM:i:0
+EAS38_1_219_965_773	16	chr1	3191038	255	35M	*	0	0	AAAGAAAGTCTGCTTTCCACGCTTCTCATCTATAG	hhhIhhh[ehXQhhhahhhJhhhhhhhhhhhhhhh	NM:i:1
+EAS38_1_56_375_762	16	chr1	3191134	255	35M	*	0	0	CATTATTAGAAATTCCAACCCTAGTTATGAAAGAT	hh_VhKZhMhhhSXbhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_148_601_688	16	chr1	3191142	255	35M	*	0	0	GAAATTCCAACCCTAGTTATGAAAGATTGAGGGGA	hhhhhTdhhhhhhhhhhhhhhhhhhhhhhhhhh>h	NM:i:1
+EAS38_1_236_489_757	0	chr1	3191149	255	35M	*	0	0	CAACCCTAGTTATGAAAGATTGAGGGAAAGTGATA	hhhhhhhhhhhhhhhhhhThhhbhhhSKhhXhTh_	NM:i:0
+EAS38_1_144_552_470	0	chr1	3191153	255	35M	*	0	0	CCTAGTTATGAAAGATTGAGGGAAAGTGATAAAGA	hhhhhhhhhhhhhhehhhh`h\IPThhhThGKUML	NM:i:0
+EAS38_1_288_225_365	16	chr1	3191173	255	35M	*	0	0	GGAAAGTGATAAAGAACAAAAGGGAGGGATATTAT	hhhhhh\hh`hhhhhhMhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_33_904_669	0	chr1	3191192	255	35M	*	0	0	AAGGGAGGGATATTATTCTCTCATTTTTAACAGCA	hhhhhhhhhhhhhhhhhhhhhhghhhhhhhhYKJH	NM:i:0
+EAS38_1_123_430_125	16	chr1	3191220	255	35M	*	0	0	AACAGCATATTTGTCTTAGCTTTAAATCCAGAGTA	hhDh`Ch`h[UTh[RhehhcThhhhhhhhhhhhhh	NM:i:0
+EAS38_1_179_676_404	16	chr1	3191241	255	35M	*	0	0	TTAAATCCAGAGTACTGTTTGGCTTCAAAGAAGAT	QhhhhLZUhhhhfhhbhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_120_22_725	0	chr1	3191250	255	35M	*	0	0	GAGTACTGTTTGGCTTCAAAGAAGATAGTCATCTC	hhhhhhhhhhhhhhhhfhhhhahhhhdhhhZhNhX	NM:i:0
+EAS38_1_223_373_449	0	chr1	3191268	255	35M	*	0	0	AAGAAGATAGTCATCACTGGTTCTCTTACTGAGAA	hhhhhhhhhhhhhhhDhhhhZhhhhhh^hh[NFCQ	NM:i:1
+EAS38_1_112_183_986	0	chr1	3191269	255	35M	*	0	0	AGAAGATAGTCATCTCTGGTTCTCTTACTGAGAAT	hhhhhhhhhhhhhhhfhhhehhhfhhX\hhVhbKg	NM:i:0
+EAS38_1_172_99_819	16	chr1	3191287	255	35M	*	0	0	GTTCTCTTACTGAGAATAGNAAGTCTCTCCTTACT	U\VhOhhhhhhhhhhhhhh;hhhhhhhhhhhhhhh	NM:i:1
+EAS38_1_210_930_591	16	chr1	3191287	255	35M	*	0	0	GTTCTCTTACTGAGAATAGAAAGTCTCTCCTTACT	LWK^Khh^ShNhhhhhhhhhhhhXhhhhhhhhhhh	NM:i:0
+EAS38_1_100_778_539	16	chr1	3191290	255	35M	*	0	0	CTCTTACTGAGAATAGAAAGTCTCTCCTTACTGAG	hhfhhhThhhhhhhhhhhhh^hhhhhhhhhhhhhh	NM:i:0
+EAS38_1_25_830_623	16	chr1	3191298	255	35M	*	0	0	GAGAATAGAAAGTCTCTCCTTACTGAGAATAGGAA	YhRhhLhhhhhh`h\hhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_304_473_442	0	chr1	3191304	255	35M	*	0	0	AGAAAGTCTCTCCTTACTGAGAATAGGAAGCCATC	`hhhThehhhhh\hhXYhgJ`ILQLDNBIAAM=HD	NM:i:0
+EAS38_1_205_508_718	16	chr1	3191307	255	35M	*	0	0	AAGTCTCTCCTTACTGAGAATAGGAAGCCATCTTC	hhRBOThbhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_293_376_615	16	chr1	3191307	255	35M	*	0	0	AAGTCTCTCCTTACTGAGAATAGGAAGCCATCTTC	hhh@hFhOhhghhh[hh`hhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_182_907_727	16	chr1	3191326	255	35M	*	0	0	ATAGGAAGCNATCTTCATACCTGTCCCTCTGCATT	hM^FJg`Mh;hhhhfhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_1_222_741_776	0	chr1	3191358	255	35M	*	0	0	ATTTATTCTTGAGGTTACTGAGCCATCTGGCTACA	hhhhhhhhhhhhhhChhYhTehDVghIhh][ZF?K	NM:i:0
+EAS38_1_88_323_543	16	chr1	3191374	255	35M	*	0	0	ACTGAGCCATCTGGCTACAGAGAAGAAAAGCAAGA	X\Ghhe^JhNaXhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_66_197_743	16	chr1	3191383	255	35M	*	0	0	TCTGGCTACAGAGAAGAAAAGCAAGAGTTGTTTTT	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_173_864_740	16	chr1	3191391	255	35M	*	0	0	CAGAGAAGAAAAGCAAGAGTTGTTTTTTTATTTTT	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_124_858_171	16	chr1	3191398	255	35M	*	0	0	GAAAAGCAAGAGTTGTTTTTTTATTTTTATTTTAT	chhhhU\hhhhcOchhObh]hhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_126_138_418	16	chr1	3191410	255	35M	*	0	0	TTGTGTTTTTATTTTTATTTTATTTTTATTTTTTT	U`hhBfhZZhhh`Yhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_1_221_397_462	0	chr1	3191429	255	35M	*	0	0	TTTTTTTTATTTTTTTAAGTAGAAGCAAGATTCTC	hhhhhhhhZhhhhhhhhVFhbKMSWhRG]?hhQh[	NM:i:1
+EAS38_1_216_901_971	0	chr1	3191444	255	35M	*	0	0	TAAGTAGAAGCAAGATTCTCATTAAGGCTAACTAT	hhhhhhhhhhhhhhhhhahZZhbhabfQ[MKFWGU	NM:i:0
+EAS38_1_282_128_662	0	chr1	3191445	255	35M	*	0	0	AAGTAGAAGCAAGATTCTCATTAAGGCTAACTATG	hhhhhhhchhhhh]hhhhhVhhZhhhZhZ@MbMaL	NM:i:0
+EAS38_1_77_686_871	0	chr1	3191446	255	35M	*	0	0	AGTAGAAGCAAGATTCTCATTAAGGCTAATTATGT	hhhhhhhhhhhhhhhdhhhhhhhhh^hh]@hhh`B	NM:i:2
+EAS38_1_95_356_853	0	chr1	3191446	255	35M	*	0	0	AGTAGAAGCAAGATTCTCATTAAGGCTAACTATGC	hhhhhhhhhhhhhhhhhhhhhhPhhfh\HJGUhLN	NM:i:0
+EAS38_1_315_80_525	0	chr1	3191449	255	35M	*	0	0	AGATGCAAGATTCTCATTAAGGCTAACTATGCTAT	hhhhhhhhhhhhhhhehhhR\Khh]]gh[hZ_hJh	NM:i:1
+EAS38_1_211_797_532	0	chr1	3191471	255	35M	*	0	0	CTAACTATGCTATTCTCCACTGCGCCCCATTGATC	hhhhhhhhhhhhhhhhhhhhhfcIhLh[HhgUUhK	NM:i:0
+EAS38_1_326_311_799	0	chr1	3191471	255	35M	*	0	0	CTAACTATGCTATTCTCCACTGCGCCCCATTGATC	hhhhhhhhhhhhhhhhhhhhhhhhghhhhhhhVhG	NM:i:0
+EAS38_1_107_806_891	16	chr1	3191478	255	35M	*	0	0	TCCTATTCTCCACTGCGCCCCATTGATCAGACAAT	LBfP^MWhAhh_hh^hZhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_1_121_349_512	0	chr1	3191489	255	35M	*	0	0	ACTGCGCCCCATTGATCAGACAATGGCTTTAAGTG	hhhhhhhhhhhhhhhhhhhhhBhhhhhhhhOOJeT	NM:i:0
+EAS38_1_219_430_836	16	chr1	3191498	255	35M	*	0	0	CATTGATCAGACAATGGCTTTAAGTGGGGCCTAAA	c_WRRdUhhN[hhhdaWhOhhhghhhhhhhhhhhh	NM:i:0
+EAS38_1_98_807_431	16	chr1	3191517	255	35M	*	0	0	TTAAGTGGGGCCTAAATGAACTGTTGGACATCAGG	PQg^SGhO[eOKhhhh`hhhYahhXhhhhhhhhhh	NM:i:0
+EAS38_1_155_241_829	16	chr1	3191535	255	35M	*	0	0	AACTGTTGGACATCAGGTTCATGAAAACGGTTTTG	]QbLHKRRThhhWhhh[hdghhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_223_732_501	0	chr1	3191535	255	35M	*	0	0	AACTGTTGGACATCAGGTTCATGAAAACGGTTTTG	hhhhhhhhhYhahh\EQghh\hPMJd_hSX[XhgE	NM:i:0
+EAS38_1_320_444_109	16	chr1	3191535	255	35M	*	0	0	AACTGTTGGACATCAGGTTCATGAAAACGGTTTTG	hbHUhhGhhhRhhhhhWZhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_103_761_542	0	chr1	3191537	255	35M	*	0	0	CTGTTGGACATCAGGTTCATGAAAACGGTTTTGTG	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_245_218_950	0	chr1	3191539	255	35M	*	0	0	GTTGGACATCAGGTTCATGAAAACGGTTTTGTGCA	hhhhhhhhhchhhhhhhhhhhhhKhhhhhh_\R>f	NM:i:1
+EAS38_1_54_654_789	0	chr1	3191548	255	35M	*	0	0	CAGGTTCATGAAAACGGTTTTGTGAAGGTAATATA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhLhChhh^	NM:i:0
+EAS38_1_242_532_556	0	chr1	3191553	255	35M	*	0	0	TCATGAAAACGGTTTTGTGAAGGTAATATATCAGT	hhhhhh]hhhhhhhhhZhTfchhO[LhUhXTCJJP	NM:i:0
+EAS38_1_37_578_493	16	chr1	3191563	255	35M	*	0	0	GGTTTGGTGAAGGTAATATATCAGTAATATGGTTG	THOCeDUEhhZQgchhhhhhJhhhhhhhhhhhhhh	NM:i:1
+EAS38_1_151_713_632	0	chr1	3191572	255	35M	*	0	0	AAGGTAATATATCAGTAATATGGTTGACATAAATA	hhhhhhhhhhhhhhhhhhhhhhhhhhh`hhhSThh	NM:i:0
+EAS38_1_152_680_718	0	chr1	3191572	255	35M	*	0	0	AAGGTAATATATCAGTAATATGGTTGACATAAATA	hhhhhhhhhhhhhhhhhhhhhhhhh^g\hhbhhh^	NM:i:0
+EAS38_1_152_24_706	0	chr1	3191573	255	35M	*	0	0	AGGTAATATATCAGTAATATGGTTGACATAAATAA	hhhhhhhhhhhhhhhhhhhhhhhhhOehhhWhhhW	NM:i:0
+EAS38_1_330_686_422	16	chr1	3191575	255	35M	*	0	0	GTAATATATCAGTAATATGGTTGACATAAATAAGC	GLhhdhbhGJhh_hhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_275_44_659	0	chr1	3191579	255	35M	*	0	0	TATATCAGTAATATGGTTGACATAAATAAGCTGGG	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhTcg	NM:i:0
+EAS38_1_324_589_894	0	chr1	3191579	255	35M	*	0	0	TATATCAGTAATATGGTTGACATAAATAAGATGGG	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhXhhhh	NM:i:1
+EAS38_1_121_763_313	0	chr1	3191589	255	35M	*	0	0	ATATGGTTGACATAAATAAGCTGGGAAATAGTTCT	hhhhhhhhhhhhhhhhhhhhhhchhWFhhTChhfh	NM:i:0
+EAS38_1_130_668_987	16	chr1	3191610	255	35M	*	0	0	TGGGAAATAGTTCTTTTAGGAAGTAGAAGATTTTT	UT>Khbhbhhh[hhhhZhhfhhhhhhhhhhhhhBh	NM:i:0
+EAS38_1_80_262_758	16	chr1	3191611	255	35M	*	0	0	GGGAAATAGTTCTTTTAGGAAGTAGAAGATTTTTC	PYdhhhMhh\HhhVhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_272_104_967	0	chr1	3191614	255	35M	*	0	0	AAATAGTTCTTTTAGAAAGTAGAAGATTTTTCTCT	hhhhhhhhhhhhhhhGhhhhhhhehXhhhhhZhZh	NM:i:1
+EAS38_1_142_144_587	16	chr1	3191617	255	35M	*	0	0	TAGTTCTTTTAGGAAGTAGAAGATTTTTCTCTTTG	bhhhHPhNhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_282_509_344	16	chr1	3191618	255	35M	*	0	0	AGTTCTTTTAGGAAGTAGAAGATTTTTCTCTTTGT	hh^YdVSKWhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_3_797_743	0	chr1	3191619	255	35M	*	0	0	GTTCTTTTAGGAAGCAGAAGATTTTTCTCTTTTTG	hhhhhhhhhhhhhhAhhhhhXhhhhhhhfhhhHhb	NM:i:2
+EAS38_1_311_266_241	16	chr1	3191633	255	35M	*	0	0	TAGAAGATTTTTCTCTTTGTGTCTGTGTCTTTCAT	LhhhhhhXGFHH_HhhhThhhdhhhhhhhhhhhhh	NM:i:0
+EAS38_1_282_320_153	16	chr1	3191635	255	35M	*	0	0	GAAGATTTTTCTCTTTGTGTCTGTGTCTTTCATTT	OQ\\PEA[JHNGRQJhhhhXNhhWhVhhUfhhhhh	NM:i:0
+EAS38_1_74_839_687	16	chr1	3191635	255	35M	*	0	0	GAAGATTTTTCTCTTTGTGTCTGTGTCTTTCATTT	MhhWhS[hhGhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_119_931_54	16	chr1	3191636	255	35M	*	0	0	AAGATTTTTCTCTTTGTGTCTGTGTCTTTCATTTG	QJ?JRKXIZaOhYYdbhhhhbhhhfhhhhhhhhhh	NM:i:0
+EAS38_1_171_559_793	16	chr1	3191638	255	35M	*	0	0	GATTTTTCTCTTTGTGTCTGTGTCTTTCATTTGCC	U_NhR[ZhhhRhWhhhhhh>hhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_9_831_797	0	chr1	3191643	255	35M	*	0	0	TTCTCTTTGTGTCTGTGTCTTTCATTTGCCTTTGT	hhhhhhhhhhhhhhhhhhGhhhGChhhH>Kd?hEA	NM:i:2
+EAS38_1_112_463_853	0	chr1	3191663	255	35M	*	0	0	TTCATTTGCCTATGAAAAGAATGTTAGTTGGCTGT	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhah^h	NM:i:0
+EAS38_1_200_507_523	16	chr1	3191673	255	35M	*	0	0	TATGAAAAGAATGTTAGTTGGCTGTAACCATAAAA	@hW^hhhhehhKgXh\hh^hhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_307_105_716	0	chr1	3191676	255	35M	*	0	0	GAAAAGAATGTTAGTTGGCTGTAACCATAAAATTG	hhhhhhhhhhhhhhhhhhhhhhUh[_Hh]aQdhhZ	NM:i:0
+EAS38_1_81_670_875	16	chr1	3191698	255	35M	*	0	0	AACCATAAAATTGGCAGTTGTATTTACAAATAATC	hehhhhhhhhhhhZhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_285_30_406	0	chr1	3191712	255	35M	*	0	0	CAGTTGTATTTACAAATAATCACATATATTATGCT	h_hhhhh_hhh]hQQShILhhYhQhIhHhCIh@U_	NM:i:1
+EAS38_1_45_791_522	16	chr1	3191716	255	35M	*	0	0	TGTATTTACAAATAATCACATATATGATGCTTACA	hh`hhXhhhhhhhhhfhhhHhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_43_819_567	16	chr1	3191719	255	35M	*	0	0	ATTTACAAATAATCACATATATGATGCTTACAGAA	hhQhhChhhhhhhhhhhhh@hhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_26_772_717	0	chr1	3191761	255	35M	*	0	0	CTCATTTCTAAATAATCACATATGCTAAAAGCTAG	hhhhhhhhhhhhhhhhhhhhhZhhYhWfahSIhHS	NM:i:0
+EAS38_1_130_865_419	0	chr1	3191766	255	35M	*	0	0	TTCTAAATAATCACATATGCTAAAAGCTAGGTTTT	hhhhhhhhhhhhhhhhhhhhh\`hhOhhELh_hhh	NM:i:0
+EAS38_1_327_933_866	0	chr1	3191766	255	35M	*	0	0	TTCTAAATAATCACATATGCTAAAAGCTAGGTTTT	hhhhhhhhhhhhhhhhhhhhhhh]chYhPhLYhhh	NM:i:0
+EAS38_1_126_547_811	16	chr1	3191773	255	35M	*	0	0	TAATCACATATGCTAAAAGCTAGGTTTTTCTAATA	hhhThhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_277_668_994	16	chr1	3191773	255	35M	*	0	0	TAATCACATATGCTAAAAGCTAGGTTTTTCTAATA	_hhJhhhhhhh]hhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_181_734_387	16	chr1	3191780	255	35M	*	0	0	ATATGCTAAAAGCTAGGTTTTTCTAATACACTTTT	hNhNTARh`hhhIOhhhXeRMhLahhhhhhhhhhh	NM:i:0
+EAS38_1_174_224_835	16	chr1	3191785	255	35M	*	0	0	CTAAAAGCTAGGTTTTTCTAATACACTTTTACTTT	hhhhhhhhhhdghhhhhhhhhhhhhhhhhhh>hhh	NM:i:1
+EAS38_1_192_253_159	16	chr1	3191794	255	35M	*	0	0	AGGTTTTTATAATACACTTTTATTTTCATGGAGGG	hhc\PLNGAfhhhhhh[hZ[_hh[ahhhYhhhhhh	NM:i:1
+EAS38_1_184_325_530	16	chr1	3191800	255	35M	*	0	0	TTCTAATACACTTTTATTTTCATGGAGGGCTCTAG	hGV[hhWhhhhhXh^hghhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_250_311_830	16	chr1	3191810	255	35M	*	0	0	CTTTTATTTTCATGGAGGGCTCTAGAGGATTCCAC	YLGJTUPJNNXgKQR_VKThhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_275_852_575	16	chr1	3191813	255	35M	*	0	0	TTATTTTCATGGAGGGCTCTAGAGGATTCCACGTG	JVeYM[E`hJSLV]SQVRChhhhhhhhhhhShhhh	NM:i:0
+EAS38_1_77_390_526	0	chr1	3191818	255	35M	*	0	0	TTCATGGAGGGCTCTAGAGGATTCCCCGTGGCATA	hhhhhhhhhhhhhhhThNhhOhhOQA_^TEV=^EG	NM:i:2
+EAS38_1_299_893_564	16	chr1	3191846	255	35M	*	0	0	TGGAATAGAAACCACTGAAAAGAGACTCAACTCTT	@aVhhKhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_294_440_933	16	chr1	3191865	255	35M	*	0	0	TAGAGACTCAACTCTTTTTCCCCCCAGCAATATTA	O^EV?MhDhhUh\hYKVTKhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_1_278_780_674	16	chr1	3191873	255	35M	*	0	0	CAACTCTTTTTCCCCCCAGCAATATTATGTTGCTC	hhVWchcZHXMhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_86_970_279	0	chr1	3191876	255	35M	*	0	0	CTCTTTTTCCCCCCAGCAATATTATGTTGCTCTGT	hhhhhhhhhhhhhhPhheHhfhhehOhhEOhUhAF	NM:i:0
+EAS38_1_148_146_536	0	chr1	3191881	255	35M	*	0	0	TCTCCCCCCAGCAATATTATGTTGCTCTGTGCTGC	hDhhhhhhh]hhhdhhhhhhhhhEhhhh\hEhhHG	NM:i:1
+EAS38_1_224_888_484	16	chr1	3191884	255	35M	*	0	0	CACCCCAGCAATATTATGTTGCTCTGTGCTGCTCT	P?KJEARLNW`TdVWhF^OThhMgQ\hhhhfhhhh	NM:i:1
+EAS38_1_223_648_752	0	chr1	3191887	255	35M	*	0	0	CCCAGCAATATTATGCTGCTCTGTGCTGCTCTATG	h_hhhhhhhhhhhhh=hhhhYhhOVghhB\AhWhM	NM:i:1
+EAS38_1_300_220_617	0	chr1	3191891	255	35M	*	0	0	GCAATATTATGTTGCTCTGTGCTGCTCTATGCATA	hhdhhhhhhhhhhhhhhhhhh\hhhhZhhhhPKhL	NM:i:0
+EAS38_1_63_467_696	16	chr1	3191897	255	35M	*	0	0	TTATGTTGCTCTGTGCTGCTCTATGCATATGGCAT	FHh^h]Fhe?hfhhchhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_24_141_869	0	chr1	3191905	255	35M	*	0	0	CTCTGTGCTGCTCTATGCATATGGCATGTTGTTGG	hhhhhhh^hhUhUhhhhYhhfhh_BPcfh`RXOLS	NM:i:0
+EAS38_1_184_494_683	16	chr1	3191911	255	35M	*	0	0	GCTGCTCTATGCATATGGCATGTTGTTGGTACCTG	=Qab\ahVhchahhh]hhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_263_460_363	16	chr1	3191919	255	35M	*	0	0	ATGCATATGGCATGTTGTTGGTACCTGTACCATTC	h?UIhJhWhhOhghhKhDhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_80_670_426	16	chr1	3191919	255	35M	*	0	0	ATGCATATGGCATGTTGTTGGTACCTGTACCATTC	cPgPhNh\hhhh[hhhhUahhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_118_725_870	0	chr1	3191927	255	35M	*	0	0	GGCATGTTGTTGGTACCTGTACCATTCTCTTCCAT	hhhhhhhhhhhhhhhcghhhhRSQhhUhHhhGKLh	NM:i:0
+EAS38_1_88_806_693	16	chr1	3191952	255	35M	*	0	0	TCTCTTCCATTGAGAATTCTAAGCCATTATGTGGA	fhhhhahhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_160_191_877	16	chr1	3191955	255	35M	*	0	0	CTTCCATTGAGAATTCTAAGCCATTATGTGGAGGA	hhXhhh\hhhhhhehhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_300_179_943	16	chr1	3191975	255	35M	*	0	0	CCATTATGTGGAGGAGCTGTTCAGCTCTCTCTAAC	h^IRPXZNMBIMZL[Ehh[hdhhQhchhhhhhhhh	NM:i:0
+EAS38_1_208_195_556	0	chr1	3191986	255	35M	*	0	0	AGGAGCTGTTCAGCTCTCTCTAACCTATTTAGATT	hhhhhhhhhhhdhhhhhhhhhPhehhMhhhTH?bh	NM:i:0
+EAS38_1_16_568_852	0	chr1	3191993	255	35M	*	0	0	GTTCAGCTCTCTCTAACCTATTTAGATTTTATCTT	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhLhMhh	NM:i:0
+EAS38_1_290_6_992	16	chr1	3192030	255	35M	*	0	0	ACTTTGTGATAGAATCTCTCTATAGAATGTTCTCT	F_UhhHhLhbeKhhhh^hhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_300_29_772	16	chr1	3192030	255	35M	*	0	0	TCTTTGTGATAGAATCTCTCTATAGAATGTTCTCT	Ahh`Vhh[hhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_1_109_466_314	0	chr1	3192031	255	35M	*	0	0	CTTTGTGATAGAATCTCTCTATAGAATGTTCTCTC	hhhhhhhhhhhfhhhhhhhhKhhGLXhRhhPhLhS	NM:i:0
+EAS38_1_112_657_773	0	chr1	3192037	255	35M	*	0	0	GATAGAATCTCTCTATAGAATGTTCTCTCCACCCA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh]BG	NM:i:2
+EAS38_1_137_971_213	16	chr1	3192048	255	35M	*	0	0	TATATAGAATGTTCTCTCAACCACCTCCTGCTAGT	C@BHTcZhaFFRSB\hVT@Oehhhhhhhhhhhhhh	NM:i:2
+EAS38_1_185_636_515	16	chr1	3192048	255	35M	*	0	0	TCTATAGAATGATCTCTCAACCACCTCCTGCTAGT	F@J\Jd]Q\ABBAcA[Mhhhhhhhhhhhhhhhhhh	NM:i:2
+EAS38_1_44_970_650	0	chr1	3192058	255	35M	*	0	0	GTTCTCTCCACCACCCCCTGCTAGTCATACCAAAC	hhhhhhhhhhhhhhThMhhhac\h[e_WRGfUIMH	NM:i:1
+EAS38_1_92_965_745	0	chr1	3192064	255	35M	*	0	0	TCCACCACCTCCTGCTAGTCATACCAAACCCACCC	hhhhhhhhhhhhhhhhhhhhhhhJh_hhPIV_X?G	NM:i:0
+EAS38_1_261_922_44	0	chr1	3192119	255	35M	*	0	0	ACTTCAGTTTTTCTTTATAAAACTTAATCAAAACC	hhhh_hhfhhhhhhEh_hTTY]hh@aJhOFMTOLM	NM:i:2
+EAS38_1_123_430_987	16	chr1	3192133	255	35M	*	0	0	GTATAAAACTGAATCAAAACCGATGTTTATTTTTA	GZhdhhh]hhdhhdhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_234_381_448	0	chr1	3192142	255	35M	*	0	0	TGAATCAAAACCGATGTTTATTTTTATGATAAAAA	hhBhhh]hhhhhhhhhhhhFhhhhhThB_hQ]O@Y	NM:i:0
+EAS38_1_46_449_600	0	chr1	3192148	255	35M	*	0	0	AAAACCGATGTTTATNTTTATGATAAAAAGGATAT	hhhhhhhahhhhhhh;hhhhhhfhThNh^OGWh]h	NM:i:1
+EAS38_1_239_737_373	0	chr1	3192153	255	35M	*	0	0	CGATGTTTATTTTTATTATAAAAAGGATATACTTT	hhhhhhhhhhhhhhdhK[hhhRW\JMPhbhNhhhh	NM:i:1
+EAS38_1_24_496_314	0	chr1	3192169	255	35M	*	0	0	GATAAAAAGGATATACTTTTGTATTTTGTTGTAGA	hhhhhhhhhhhhhhhhhhhhDhLhhhhHM[O]EA?	NM:i:2
+EAS38_1_150_229_75	16	chr1	3192202	255	35M	*	0	0	GAAAAAATATTGGTTTAAGAAGGAGATAAAAAGTC	hhhhhhhJhA]hhSPARhhhhhhhhhbhhhhhhhh	NM:i:1
+EAS38_1_170_110_874	16	chr1	3192248	255	35M	*	0	0	AATTACCTTTTACCCACTTACTGTTCTTACATGAC	hhhhXhh]hQhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_142_857_213	0	chr1	3192280	255	35M	*	0	0	GACCTGACTATCCTAACAAACTCTATTCTAGCACT	hhhhhhhhhhhhhhh\hQh_hhhhYhhhhRB]Wbh	NM:i:0
+EAS38_1_7_223_584	0	chr1	3192314	255	35M	*	0	0	TGTAGATATTTTTGAGGAGTCACATACTTTTCTAT	hhhhhhhhhhhhhghhK^YhhhhJhhDhhhhhhMh	NM:i:1
+EAS38_1_95_195_644	16	chr1	3192330	255	35M	*	0	0	GAGTCACATAATTTTCTATGCTACAGTCATGCTTC	hhhbPhZhhhhOhh`hhhYhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_219_903_777	0	chr1	3192346	255	35M	*	0	0	TATGCTACAGTCATGATTCAGAAAGTCTAATGTCG	hhhhhhhhhhhhhhhBhhhhhhhhhghh\hhhhJ[	NM:i:1
+EAS38_1_108_439_554	16	chr1	3192349	255	35M	*	0	0	GCTACAGTCATGCTTCAGAAAGTCTAATGTCGTGA	aThhhhhehhdhhXhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_239_516_540	0	chr1	3192442	255	35M	*	0	0	TAATTTTAGAGAATCAGAGGAGATTATATTGTGTG	hhhhhhhhhhhhhhhhhhhhNhLhhThhhheOfhW	NM:i:1
+EAS38_1_196_124_875	16	chr1	3192460	255	35M	*	0	0	GGAGATTATATTGGGTGTCAATACTGTAAGTATTC	?N[Mhh_hWhXh[LVhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_222_834_314	16	chr1	3192460	255	35M	*	0	0	GGAGATTAGATTGGGTGTCGATACTGTAAGTATTC	WDXGRJOR?hCMfKhR]OAIhPXZRh^hhhhhhSh	NM:i:2
+EAS38_1_230_638_588	0	chr1	3192551	255	35M	*	0	0	TATTTGAAGAGTATGGAATTTATTTTGTAAATGAA	hhhhhhhhhhhhhhhhhhhhhWhhhhhh\`hhhG`	NM:i:0
+EAS38_1_264_255_706	0	chr1	3192603	255	35M	*	0	0	AGTACTGAATGGAGCCACATCATTCACATATTTCC	hhhhhhhhhhhhhhhhhhhhhghhbhhdhfhhhdP	NM:i:0
+EAS38_1_105_766_448	16	chr1	3192724	255	35M	*	0	0	TTAGTTTAGTCATTTAGGCAAGGAAATAGACATTG	Ghhhhhhhhhhhghhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_281_8_752	0	chr1	3192785	255	35M	*	0	0	GCTCAGGTTGTTTTTCCTACCATCTCTCCACATTT	hhhEhhhhhhhhhhhN\hh@MOhHU>WDGHW?WTd	NM:i:1
+EAS38_1_273_517_672	16	chr1	3192933	255	35M	*	0	0	ATAATATGGAGATGAATCAGCTCAAGAGTTCTGAG	hhhhghCfdhhhhhhhhhhhhahhhhhhhhhhhhh	NM:i:0
+EAS38_1_194_915_453	16	chr1	3192959	255	35M	*	0	0	AGTCCTGAGCAGAAACACCATTCCACATTCTTCTG	hbIGI_hhhOhhhhhfV\hhhdhhhhhhQhhhhhh	NM:i:1
+EAS38_1_270_767_516	16	chr1	3193008	255	35M	*	0	0	TGTTAGAAATGGTATAAAATCCCAGTTAAACCATT	ThUchhhhhfhJhhhhhhhDOhchhhhhhhhhhhh	NM:i:1
+EAS38_1_311_398_506	16	chr1	3193008	255	35M	*	0	0	TGTTAGAAATGGTATAAAAACCCAGTTAAACCATT	OWRbhhhhhUhZhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_77_151_681	16	chr1	3193008	255	35M	*	0	0	TGTTAGAAATGGTATAAAAACCCAGTTAAACCATT	WCP`hhhhhRhO\hhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_210_41_603	16	chr1	3193471	255	35M	*	0	0	CACATTCCTTATAACACACTGTGAGGTAGGTGAAG	^bZV`R]hh_hOhhh`hhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_124_634_862	16	chr1	3193821	255	35M	*	0	0	TTTCTGGGTATGATTGCTGTTAGCCTTTCTGTTTT	h^HhhhDBhhhhhhhdhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_101_162_624	0	chr1	3194186	255	35M	*	0	0	TTGCACTGTGTTTAGAAATCCCTCAAAAGGTTTGC	hhhhhhhhhhhhhhhhhhhhhhhhW[hPfeUhhVY	NM:i:0
+EAS38_1_235_609_726	0	chr1	3194200	255	35M	*	0	0	GACATCCCTCAAAAGGTTTGCATAGCCAAATGCCT	QJH]I]TaV[_X^\QIERLJHEG?H>JFFD@BCC?	NM:i:1
+EAS38_1_162_13_894	16	chr1	3194295	255	35M	*	0	0	GGGAATTGTTCACACAATTTGTGTGTTTTTCTGTC	?HCMeVTN?Sh[hRhhhhZhbhhhhhhhhhhhhhh	NM:i:2
+EAS38_1_201_123_722	0	chr1	3194814	255	35M	*	0	0	AACCATTATGTAAAGTATACTTTATAAATGTTTAA	hhhhhhhhhhhhhhhhhhhhhhhhh]hhhhhhh\M	NM:i:0
+EAS38_1_251_938_580	16	chr1	3195076	255	35M	*	0	0	TATTTATCTTTGTACAACAAAGAGACTCTTAGCAG	dYGWNFSQhWVPhhGhh`hhhehhhhhhhhhhhhh	NM:i:1
+EAS38_1_8_777_292	16	chr1	3195076	255	35M	*	0	0	TATTTATCTTTGTACAAAAAAGAGACTCTTAGCAG	JQFAH@BLJGRNEhQhhDhhhfhhhh]]hhhhhhh	NM:i:2
+EAS38_1_212_466_584	0	chr1	3195258	255	35M	*	0	0	GCTATCCCAAAACCATATGTGCTGCTTGTATGAAC	hhhhhhhhhghhhhfhhhh]hZhhhhhbhfhOD>M	NM:i:1
+EAS38_1_137_805_954	0	chr1	3195451	255	35M	*	0	0	GGAAAAGTCAGAACTTTGGGGTGATCAAACGTCTA	hhhhhhhhhhhhhhhhhhhhhghhhCPhPIhMJYD	NM:i:1
+EAS38_1_63_741_75	0	chr1	3195451	255	35M	*	0	0	GGAAAAGTCAGAACTTTTGTGTGATCAACCGTCTA	hhhhhhhhhhhVhhhhhFEJFhOHhSVRG@N_D_Q	NM:i:2
+EAS38_1_146_999_561	16	chr1	3197082	255	35M	*	0	0	GGAATCCATTGGCTGATCTTTTAAGAAGTAGTTCT	SahhhRhhhXh\hhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_295_1_556	16	chr1	3197082	255	35M	*	0	0	GGAATCCATTGGCTGATCTTTTAAGAAGTAGTTCT	bdhhMFhhgehhhhhhbIhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_133_696_323	16	chr1	3197239	255	35M	*	0	0	CCTGCAATGAACCAACTGCTCCTTTCCCATTAATT	??FCJ??@DSCECKJ]JbhLXbXh\hUhhh^hhhf	NM:i:2
+EAS38_1_184_992_275	0	chr1	3197347	255	35M	*	0	0	GATTAATTAACTGCAATTCATCTCCAGTAAAATTT	hhhhhhhhhhhhhhhShhhhhhhhh^`WILU_hhh	NM:i:0
+EAS38_1_261_311_801	16	chr1	3197969	255	35M	*	0	0	ATAAAAATTGAACAAAAAAAAGAAATGGGTTTCTT	hchhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_199_494_378	16	chr1	3198110	255	35M	*	0	0	GCCATGCCAGAATGCTAGGACAATAGTTAAATTAA	?Dhh\hKPhhhhUhZhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_1_186_296_431	16	chr1	3199201	255	35M	*	0	0	GTTAGCACTTTGTCACATATTCCACTGCTTTTAAA	S>MhSKKDFJVhGHhPh]hdWhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_32_939_527	0	chr1	3199927	255	35M	*	0	0	TTTCCCTAGTTTAGCTGTGATGCCTTTGACAAGCT	hhhhhhhhhhhhhhhhhhhhhhghhhhVFYNVGYh	NM:i:0
+EAS38_1_174_562_297	0	chr1	3200023	255	35M	*	0	0	AAGGGAGATAGATCCCAGAGGTAAGGATCTTCAAG	hbhRL^hCXHWNdNTMIH?IJG?DDE?C>KFH@B?	NM:i:2
+EAS38_1_80_292_639	0	chr1	3200090	255	35M	*	0	0	GATACTCTTAACTGATATGGGAATCAAGCCACACG	hhhhhhhhhhhhhhhhhhhYcEhhh^d^TOhh]K?	NM:i:1
+EAS38_1_146_971_305	16	chr1	3200157	255	35M	*	0	0	ACGTTCAGCTTAGATTGTTTCTGAGTTTGTGTCCT	RMOUAJ[YRHYh\hZhhhW[hhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_103_633_813	16	chr1	3200318	255	35M	*	0	0	TATAATATAATAAGGATCTAACATGTTGCTTTCTC	YghhhNhUhh^hhThh]hhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_268_250_819	16	chr1	3200318	255	35M	*	0	0	TATAATATAATAAGGATCTAACATGTTGCTTTCTC	hhhhhVhhhhhhhgVhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_195_376_807	16	chr1	3200796	255	35M	*	0	0	TCAGGGAGGGGGACTAAAGTGAGGTCACCTATTCC	Ihe[Ihh]XahhhhhhhhhhhhFhhhhhhhhhhhh	NM:i:1
+EAS38_1_92_137_414	0	chr1	3200902	0	35M	*	0	0	TTTTTTTTTTTTTTTTTTTTTTTTCTCTATTTTCC	hhhhhhhhhhhhhhhhhhhhhhdhCA@hJ@IK@AE	NM:i:2
+EAS38_1_142_636_259	0	chr1	3200903	0	35M	*	0	0	TTTTTTTTTTTTTTTTTTTTTTTTCCTATTTTCTA	hhhhhhhhhhhhhhhhhhhhhhM?EM@>FLICF@@	NM:i:2
+EAS38_1_72_206_749	0	chr1	3200905	0	35M	*	0	0	TTTTTTTTTTTTTTTTTTTTTTGATACTTTCCAAA	hhhhhhhhhhhhhhhhhhhhhhBAN@UOE@YEE=@	NM:i:2
+EAS38_1_111_883_143	16	chr1	3201070	255	35M	*	0	0	AAAGACAGTTGGAACTATTTTTAAAAGGCGCTTTA	hhhhhQhhH`hchhfhhh\ghhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_255_841_137	0	chr1	3201133	255	35M	*	0	0	CAGGCATCTCATCCAAGCTTTATATATAAATAGTC	hhhhh\hhhhdhahDPDhhhhKhSh`LFPEePCYI	NM:i:1
+EAS38_1_25_534_590	0	chr1	3201133	255	35M	*	0	0	CAGGCATCTCATCCAAGCTTTATATAGAAATAGTC	hhhhhUhhhhhh`hVYhYhchMgO^LWKGJHFDNE	NM:i:0
+EAS38_1_11_826_739	0	chr1	3201151	255	35M	*	0	0	CTAATATAGAAATAGTCGTGGCTAATGGCAAAGAT	hhBhhhhhhhhhhhhhhhLhhR]`]TY^@DNPQ@D	NM:i:2
+EAS38_1_200_667_750	0	chr1	3201166	255	35M	*	0	0	TCGTGGCTAATGGCAAAGATATGTGATGAATGCAA	hhhhhhhhhhhhhLRhIhbQ]fZYULURBNRG?EP	NM:i:0
+EAS38_1_148_510_997	0	chr1	3201180	255	35M	*	0	0	AAAGATATGTGATGAATGCAAGGGAGCATATATTT	hhhhhhhhhhhehhhhhhZhMhhZD`FOXSV_SPZ	NM:i:0
+EAS38_1_221_65_299	16	chr1	3201185	255	35M	*	0	0	TATGTGATGAATGAAAGGGAGAATATATTTAGTCT	BhG[Egh]hhhLhAhhhhhhhPhbhUhTWMhhSVh	NM:i:2
+EAS38_1_149_164_972	0	chr1	3201186	255	35M	*	0	0	ATGTGATGAATGCAAGGGAGGATATATTTAGTGTA	hhhhhhhhhhhhNhhhhhdhCWh_MhhWOVhVBhU	NM:i:2
+EAS38_1_269_935_919	16	chr1	3201203	255	35M	*	0	0	AAACATATATTTAGTCTAGAAAGTAGTTCATTAGA	FWQhh[hbhhbhhQXhhhhhhhhhhhhhhhhhhhh	NM:i:2
+EAS38_1_289_238_636	0	chr1	3201226	255	35M	*	0	0	TAGTTCATTAGAAAAAATTCACAGGATTCTTGTCT	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_125_517_695	16	chr1	3201271	255	35M	*	0	0	TCAGAATTTGTTTCCACTCAGTAGCATCCAATGCA	hJhHhhhWPehh\hhhhhchhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_22_489_754	16	chr1	3201281	255	35M	*	0	0	TTTCCACTCGGTAGCATCCAATGCATTTGAAAGTG	VNChUNhM\fDhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_1_122_450_662	16	chr1	3201346	255	35M	*	0	0	TACACGTTTTCCTTGACTTAAGCCACGTGTTCAAT	\PhJh`h[hKhhhhh`hhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_157_676_368	16	chr1	3201388	255	35M	*	0	0	GAAGTAACATAAACTATTCAATTAGGCCACTTACA	ghhYehhhhThhhhhh[Yhhh]hhhhhhhhhhhhh	NM:i:0
+EAS38_1_4_358_468	16	chr1	3201390	255	35M	*	0	0	AGTAAAAGAAACTATTCAATTAGGCCACTTACAAG	hNDhhAhBhhhhWhMKdhhKbhhhhhhhhhhhhhh	NM:i:2
+EAS38_1_15_825_658	16	chr1	3201447	255	35M	*	0	0	AGTTCAGTCAAATCATGGAGCAAGGAATTCCATGT	]BZOJhZ`hhhhhhhhhhhhhhh]hhhhhhhhhhh	NM:i:0
+EAS38_1_222_809_300	0	chr1	3201569	255	35M	*	0	0	CAAAAAGTCATGGAAGTTTAAATTATCCCATGCAT	hhhhh]hhhhhhS\c>hhhYhPhhhhhhhUhPhWh	NM:i:1
+EAS38_1_116_429_381	16	chr1	3201665	255	35M	*	0	0	TGTGTGTTTATTGAGAGTATGTGAGAAGATACCTG	PhhhLhhchhh`hhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_156_372_572	16	chr1	3201665	255	35M	*	0	0	TGTGTGTTTATTGAGAGTATGTGAGAAGATACCTG	hhhhhhhEhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_79_182_652	16	chr1	3201849	255	35M	*	0	0	TACAAAAAGCTATCATATAACAATCCATCTATCAT	IAYhhhhhbhXhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_1_186_626_713	16	chr1	3202147	255	35M	*	0	0	CATTTATCAATCAATCTAATCTAACTTATCTATCT	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_16_258_505	16	chr1	3203603	255	35M	*	0	0	TTCCAGCTGGGAGGGTGAGTCTTCAGAGTTCATCA	?AIDSAPEhhhhhhhhhhhhhhfhhhhhhhhhhhh	NM:i:1
+EAS38_1_197_118_218	16	chr1	3204368	255	35M	*	0	0	GGTGAGGTAGGCTGATGGATTTGTAGACTGGATTC	VPGgUMhAXhh@GchGdhhOXLhfhhfhhhhhhhh	NM:i:1
+EAS38_1_141_404_857	0	chr1	3204755	255	35M	*	0	0	TTTTTAATGGCATACACATTGCATCTGTATGCTCT	hhhhhhhhhhhhhhhhhhhhhhhh_hdhhhhIhEh	NM:i:0
+EAS38_1_125_490_276	16	chr1	3204799	255	35M	*	0	0	AATTGTGACCCAAAGTCTCTAGTAGACACATCATT	h\]@VFQ@QPAhhhhGhhI_hhhhhhhhhhhhhhh	NM:i:1
+EAS38_1_171_771_691	16	chr1	3205563	255	35M	*	0	0	TATGGGTATTTTGCCTGCATATATGTCTATGCACC	]hOhKfhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_284_911_331	0	chr1	3210849	255	35M	*	0	0	CTCTGTATTCTCTTCTTCTATTCACATCTCTACAA	hhhhhhhhhhhhhhhhhhhbhhhhhbhhhhhFhhG	NM:i:0
+EAS38_1_101_808_273	0	chr1	3212214	255	35M	*	0	0	AGATGGTTGGTTGTAGTTTGACCCTTGAAGTTTAT	hhhhhhhhhhhhhh^XhhhhJ]hhhhHLHR\hhKh	NM:i:0
+EAS38_1_161_452_506	16	chr1	3212258	255	35M	*	0	0	CCGGAGTTCCCGGTGTGTTGCTACTGGCATGGTGG	HJ>@_ZEEc]R[hWhfhhThhhhh]hhhhhhhhhh	NM:i:2
+EAS38_1_246_740_824	0	chr1	3212368	255	35M	*	0	0	TGTGTTGTTCTCTTCCACCAGAATGAACTATTGTG	hhhhhhhhhhhhhh]hh[OhhhhhhOZZhMh_`Lh	NM:i:0
+EAS38_1_328_863_236	0	chr1	3212368	255	35M	*	0	0	TGTGTTGTTCTCTTCCACCAGAATGAACTATTGTG	hhhhhhhhhhhfhhhh[hhRIhahh`ghh[hhhhW	NM:i:0
+EAS38_1_71_507_507	0	chr1	3212368	255	35M	*	0	0	TGTGTTGTTCTCTTCCACCAGAATGAACTATTGTT	hhhhhhhhhhhhhhhhhhhg]LQhhhOhhShhHc?	NM:i:1
+EAS38_1_156_360_657	0	chr1	3212393	255	35M	*	0	0	AACTATTGTGAGTCTAGAGCTTCTCCAAATGCCTC	hhhhhhhhhhhhhhhhhhhhhhXhVhChhhhhdbh	NM:i:0
+EAS38_1_327_554_773	0	chr1	3212413	255	35M	*	0	0	TTCTCCAAATGCCTCTTGTTACAAACATGCATATA	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_316_581_646	0	chr1	3213096	255	35M	*	0	0	TTTTAATCTTATCTCCTCACTGCCTCCCTCTTAGG	hhhhhhhhhhhhhhhhhgdhh_dRhhG^hfhYKJF	NM:i:0
+EAS38_1_90_952_487	16	chr1	3214147	255	35M	*	0	0	TCCCTGGATGAAGGAGGTTCAATTGGATTGAATTA	DCQNQXOaeUhhUThcNhh`hhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_191_680_14	0	chr1	3225128	255	35M	*	0	0	ATATTTTCCAACAGGTAAGAAGTATGCAAGCTCCA	hhMhhhhhhchhhJJUIhEOPPDHhE[T@@IDD?A	NM:i:1
+EAS38_1_138_982_940	0	chr1	3233636	0	35M	*	0	0	TACCTCTCGCCATCTGTCAATCTCTGGAGTCAGTT	hJhhhhh^hahYhhhhJBhhhLhJhhVaXJAB_BL	NM:i:2
+EAS38_1_158_9_677	16	chr1	3242626	255	35M	*	0	0	AAAATAAATAAGAGAGAGGAGCCTTACTGTGCTTG	hhhhPhhh^hhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_253_923_934	16	chr1	3242672	255	35M	*	0	0	AACATTGTCTTTCTGCCAGGTTTCTGTGGAGCATA	CIOHFhHOhO@LhTLhhhhKhh[hhhhhchXhhhh	NM:i:1
+EAS38_1_5_178_743	16	chr1	3242672	255	35M	*	0	0	AACATTTTCTGTCTGCCAGGTTTCTGTGGAGCATA	QEDJM@C?]OOKhKRh^fUOR^Nhchehhhhhhhh	NM:i:1
+EAS38_1_198_267_632	0	chr1	3242722	255	35M	*	0	0	CGACACACCCCTTCTGCATACTGGCCTGTCACTGA	hhhhhhhhhhhhhhhhhhhhhhhhhQhJT?ISHLA	NM:i:2
+EAS38_1_19_755_678	0	chr1	3242782	255	35M	*	0	0	GAGAACAGCAACTCCTCCTATAGCTTCTAGAGACA	hhhhhhhhhhVRhUZghFgEhYhLQROfI?OCIGE	NM:i:0
+EAS38_1_243_907_786	0	chr1	3242782	255	35M	*	0	0	GAGAACAGCAACTCCTCCTATAGCTTCTAGAGACC	hhhhhVhhNhhhhUahhWhJWhZOKhO\MPTGN?>	NM:i:1
+EAS38_1_278_440_897	0	chr1	3242782	255	35M	*	0	0	GAGAACAGCAACTCCTCCTATAGCTTCTAGAGACA	hhhhhhhhhhhhhehh_YhhhhhDhhDhNMEXANO	NM:i:0
+EAS38_1_173_938_288	0	chr1	3242827	255	35M	*	0	0	GCACTGGGCCTTTCTTCTGTGTCTGAGCTATTTCA	hhhhhhhhhhhhhhhhhhhhhINhg?e\hVhhHhC	NM:i:1
+EAS38_1_157_930_237	16	chr1	3242836	255	35M	*	0	0	CTTTCTTCTGTGTCTGAGCTATTGCATTATATCTT	PMUNNFZYHhFaVhUhhh^Shhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_266_172_602	16	chr1	3242889	255	35M	*	0	0	TTCTAATCACTGATGCATTAATTAAAAGAATCATA	XJLLBhchhNehhhhYhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_1_149_88_885	0	chr1	3243019	255	35M	*	0	0	TTCTCTATATTCCTAGAGTTGTGTGGAAACTAATA	hhhhhhhhhhhhhhhhhhhhhhhhhadLhObALgf	NM:i:1
+EAS38_1_62_896_441	16	chr1	3243045	255	35M	*	0	0	AAAATCATATGATACCATTTATGCTTGCCAGAACG	hh_CZJh[hhhhhhhhhhXhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_1_12_294_576	16	chr1	3243367	255	35M	*	0	0	AGAATAATAAATTATCCTATAAGCTGGGCTTGATG	_hhhQhhahhhNNhDh[\hNhhhhWhhhhdhh>hh	NM:i:1
+EAS38_1_2_533_514	16	chr1	3243367	255	35M	*	0	0	AGAATAATAAATGATCCTATAAGCGGGGCTTGGTG	hahhPh\ChZhhXhPhBNRZKhhh\hhhhhhhhhh	NM:i:2
+EAS38_1_305_285_786	16	chr1	3243648	255	35M	*	0	0	CAAAATATTGTTAGATTTGTTTGAGAGATTTGTTG	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_67_916_874	0	chr1	3243986	255	35M	*	0	0	GATTATAATACCCTCGTTGAGATTTGTTTGTTATT	hhhhhhhhhhhhhhhhhhh\hZhhhhhhhh^hfhh	NM:i:0
+EAS38_1_123_564_954	16	chr1	3254091	255	35M	*	0	0	GGAGTGACTGGCCTCCCCTCTTCTTTATAAAGCGT	CDM?P<Mh@=FhhThhhhhhhdhhhhhhhhhhhhh	NM:i:0
+EAS38_1_55_599_652	16	chr1	3254559	3	35M	*	0	0	GTGTCAAGCTCTTGCAGAGCCTCTCAGGAGACAGC	@AC=EhKFhAZMGW^Zhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_1_143_932_612	16	chr1	3256967	255	35M	*	0	0	CCTAGAGACAAGGGCTGAAGCAGGCCAGTTATTTT	JEEKSVIQNMSdN_h[dhhhhhehhhhhhhhhhhh	NM:i:0
+EAS38_1_212_69_386	16	chr1	3256977	255	35M	*	0	0	AGGGCTGAAGCAGGCCAGTTATTTTAGGAGAGCAG	ROJUGJhhhhCUh]RJhhhhhh[hhhhhhhhhhhh	NM:i:0
+EAS38_1_256_785_413	16	chr1	3256977	255	35M	*	0	0	AGGGATGAAGCAGGCCAGTTATTTTAGGAGAGCAG	U`MUAAebhaM[WbHHhhNhhfhh`hhhhhhhhhh	NM:i:1
+EAS38_1_105_481_788	16	chr1	3268974	255	35M	*	0	0	GCCCGAAAAAATCTGCTTTATATTGGCCACATACG	DhGaahhhhhhhhhchhhhhhhhhhhhhhhhhhhh	NM:i:1
+EAS38_1_16_282_422	16	chr1	3273908	255	35M	*	0	0	CAAATGGGACACCATTGTCTACATTTATGGTAAGT	AOBNCFVEVCWFM_PCdOFGhRhXLahhhhehhhh	NM:i:2
+EAS38_1_283_187_798	0	chr1	3274213	255	35M	*	0	0	TTAGTGAGCCTGAACCAACCAACCAATGAATATAC	hhhhhhhhhhhhhhVhhhPhhhLhhXhhZOhhhhY	NM:i:0
+EAS38_1_329_178_196	0	chr1	3274786	255	35M	*	0	0	GGAAGGCAGATCAGTATAGGTTACCAATAAAATTG	hhhhhhhdhhhhhhhchh_@ERhhhEhhCgUWhha	NM:i:1
+EAS38_1_300_318_77	16	chr1	3276576	255	35M	*	0	0	GAAGAAGAAATATAAGCAGTCCAAGCAGGTTTCAG	hhhhMhhhhhhhZKhhghhhARhhhhhhhhhhhhh	NM:i:2
+EAS38_1_118_479_935	0	chr1	3276843	255	35M	*	0	0	TTTTATCCTCTAGCATGTCAGTCAGGTACAGGGAT	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh?O	NM:i:0
+EAS38_1_41_971_61	0	chr1	3277038	255	35M	*	0	0	TGATAAAACAAAAATGTAGACCTTTTAACAGACCC	hhhhh\`Z^NhV[]hO[ODJJHW`TbIE?GDBDE>	NM:i:2
+EAS38_1_183_306_813	16	chr1	3277183	255	35M	*	0	0	CCCATATTATCTTGGAGGTAGGATGATAGTGGTTT	ehhhhhdhVNhZhhhhh[hhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_288_251_841	16	chr1	3277184	255	35M	*	0	0	CCATATTATCTTGGAGGTAGGATGATAGTGGTTTC	U[h^hNhh]hehhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_40_672_870	16	chr1	3277184	255	35M	*	0	0	CCATATTATCTTGGAGGTAGGATGATAGTGGTTTC	Uhh]hMhhNhhgQ[h_Nhh_fhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_325_652_299	0	chr1	3278086	255	35M	*	0	0	TTTCTGTTTTAAATTAATTACCTTTATTCCATGTC	hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhPhh	NM:i:0
+EAS38_1_188_971_708	16	chr1	3278146	255	35M	*	0	0	TCTTCCTCTTCGTTAGTTTGAATTTATTTCGTTCT	P_QOhhWhhhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_295_186_302	16	chr1	3278229	255	35M	*	0	0	CTTGTTGAGTGTTCTGCATGGAATAGAGGCATTTT	CDG@ENd`[KQF@J?TEOBXYXaR\`V`hRhLhPh	NM:i:1
+EAS38_1_314_975_553	16	chr1	3279235	255	35M	*	0	0	ATTTGATAGGGACAGAATAAAAAGTGATAATTCTG	hNJaVhahQDLhhhhhhRhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_220_655_831	16	chr1	3279355	255	35M	*	0	0	AGAAAATACTTGCTTATTGCTGGAACACGTGACAT	hShchXMRhK]Rhahhhhhhh^QhhhShhhhhhhh	NM:i:0
+EAS38_1_267_333_743	16	chr1	3280494	255	35M	*	0	0	CGTGATGCATCACCAGGGTATCCATGTATAGACTA	FQNFhGVHhPfehVehKhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_165_158_507	16	chr1	3280679	255	35M	*	0	0	GGGAACGTTATTTGGTGTCTATTGTGATTATTTCC	hhbU`ZhhhhdX`hhYhhNhhhghhhhhhhhhchh	NM:i:0
+EAS38_1_218_851_888	16	chr1	3280707	255	35M	*	0	0	TATTTCCTAAATGCCCCTCNGTTTTTGTATGTTCT	MPDILT_PI[`OLhc]hCh;hhh\VhKhhhdhhhh	NM:i:1
+EAS38_1_144_853_896	16	chr1	3282690	255	35M	*	0	0	GTATCACAAAGGCTCTTTTAACTCAAGAGTTTCTG	MhhhhhhhhhXhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_232_504_623	0	chr1	3290489	255	35M	*	0	0	TCCCTACATCTCTCCATGTTACTGTAAATGATAGT	hhhhhhhhhhhhhhhhhhhhhhhh\Oee_PK`OV@	NM:i:1
+EAS38_1_238_304_582	0	chr1	3290527	255	35M	*	0	0	TCATTCTTATTTAGCACTGAAATAATAACCGCCTA	hhhhhhhhhhhhhMhhhhhhK]hRehha\DCGWhK	NM:i:0
+EAS38_1_125_161_809	0	chr1	3290844	255	35M	*	0	0	GCTACTGGGTGGTCTGCATAGCTTAGTGATACACT	hh`bhhhhSYhhTE[QH@RFT>RJEVDCFLMCCBI	NM:i:0
+EAS38_1_155_358_888	16	chr1	3290932	255	35M	*	0	0	GTGGAATTGTAGGGGTGAAAAAAGACATTTCTGAG	ghhRhhhhfhhhhhhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_157_904_203	0	chr1	3291089	255	35M	*	0	0	ACAGCCCTGGATGATTTTTGAATGGGAATAATCCC	hhhhhhhhhhLhh]hhhhhM^hhNI_@hhQ^hUMW	NM:i:0
+EAS38_1_180_814_759	16	chr1	3291152	255	35M	*	0	0	AACACCTAGTCATTGTTGGTGGCACTGTCTGTAAG	NNWAgXVhhVh_RYhhSeYJh_hhhhhhhhhhhhh	NM:i:0
+EAS38_1_170_391_724	16	chr1	3291373	255	35M	*	0	0	AAGTAAACCCTTTCTCCTGTAAGTTTCCTTTGGTC	_hhWhgQhhhUbchhhhhhhhhhhhhhhhhhhXhh	NM:i:0
+EAS38_1_315_950_278	16	chr1	3291611	255	35M	*	0	0	TCCATGCCCAGTTTCAGGTGGGAAAACAACTAAGT	QAchLb^ChhhhhYhhhhhhhhhhhhhhhhhhhhh	NM:i:0
+EAS38_1_330_167_763	16	chr1	3299360	255	35M	*	0	0	AAAAATCTTTTTTCTTCTTCTTTCTTTCTTTCTAT	hhhhhhhhLh__hhhhhhhhhhhhhhhhhhhhh=h	NM:i:1
+EAS38_1_7_984_851	16	chr1	3299360	255	35M	*	0	0	AAAAATCTTTTTTCTTCTTNTTTCTTTCTTTCTTT	NLPMNN`LEdULNhVhhhh;Phhhhhhhhhhhhhh	NM:i:1
+EAS38_1_133_814_850	0	chr1	3299443	1	35M	*	0	0	TTTGAGACAGGGTTTCTTTATATAGCCATGGTTGG	hhhhhhhhhhhhEhhChhhhhhhhhOTUhhf?SSG	NM:i:2
+EAS38_1_303_411_338	16	chr1	3299602	255	35M	*	0	0	GAGATGAATACTGGGTAGAAAATAAAAAAATTTAC	ThYhFHhhI_JXh_XhhhhhhhYhhhhhhhhhhhh	NM:i:0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffdiff_out1.txt	Fri Nov 08 14:54:01 2013 -0600
@@ -0,0 +1,91 @@
+test_id	gene_id	gene	locus	sample_1	sample_2	status	value_1	value_2	log2(fold_change)	test_stat	p_value	q_value	significant
+TCONS_00000001	XLOC_000001	Xkr4	chr1:3204754-3204833	q1	q2	OK	0	8.3103e+06	1.79769e+308	1.79769e+308	0.0786496	0.150149	no
+TCONS_00000002	XLOC_000002	-	chr1:3111449-3111490	q1	q2	OK	0	2.1403e+08	1.79769e+308	1.79769e+308	0.158655	0.158655	no
+TCONS_00000003	XLOC_000003	-	chr1:3111545-3111576	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000009	XLOC_000011	-	chr1:3192441-3192494	q1	q2	OK	0	5.68095e+07	1.79769e+308	1.79769e+308	0.0786496	0.150149	no
+TCONS_00000010	XLOC_000012	-	chr1:3192550-3192629	q1	q2	OK	0	4.15515e+06	1.79769e+308	1.79769e+308	0.158655	0.158655	no
+TCONS_00000011	XLOC_000014	-	chr1:3192731-3192811	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000012	XLOC_000015	-	chr1:3192940-3193042	q1	q2	OK	0	6.02976e+06	1.79769e+308	1.79769e+308	0.0512352	0.150149	no
+TCONS_00000013	XLOC_000016	-	chr1:3194185-3194226	q1	q2	OK	0	2.1403e+08	1.79769e+308	1.79769e+308	0.158655	0.158655	no
+TCONS_00000014	XLOC_000017	-	chr1:3194302-3194329	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000015	XLOC_000019	-	chr1:3195083-3195110	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000016	XLOC_000020	-	chr1:3195450-3195477	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000017	XLOC_000021	-	chr1:3197089-3197116	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000018	XLOC_000022	-	chr1:3197246-3197273	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000019	XLOC_000023	-	chr1:3197346-3197373	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000020	XLOC_000025	-	chr1:3200022-3200191	q1	q2	NOTEST	959058	705514	-0.442943	0.376027	0.706897	1	no
+TCONS_00000021	XLOC_000026	-	chr1:3200325-3200352	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000022	XLOC_000029	-	chr1:3201077-3201481	q1	q2	NOTEST	77513.9	285108	1.87898	-1.76152	0.0781506	1	no
+TCONS_00000023	XLOC_000031	-	chr1:3201672-3201699	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000024	XLOC_000034	Xkr4	chr1:3212213-3212292	q1	q2	OK	0	8.3103e+06	1.79769e+308	1.79769e+308	0.0786496	0.150149	no
+TCONS_00000025	XLOC_000035	Xkr4	chr1:3212367-3212439	q1	q2	OK	0	2.4671e+07	1.79769e+308	1.79769e+308	0.0512352	0.150149	no
+TCONS_00000026	XLOC_000037	Xkr4	chr1:3213095-3213242	q1	q2	NOTEST	3.99739e+06	1.82908e+06	-1.12794	0.781831	0.434314	1	no
+TCONS_00000027	XLOC_000040	Xkr4	chr1:3242633-3242923	q1	q2	NOTEST	56312.4	372827	2.72698	-1.67622	0.0936947	1	no
+TCONS_00000028	XLOC_000042	Xkr4	chr1:3243018-3243079	q1	q2	OK	0	2.66226e+07	1.79769e+308	1.79769e+308	0.0786496	0.150149	no
+TCONS_00000029	XLOC_000044	Xkr4	chr1:3243347-3243401	q1	q2	OK	0	5.0951e+07	1.79769e+308	1.79769e+308	0.0786496	0.150149	no
+TCONS_00000030	XLOC_000046	Xkr4	chr1:3256974-3257011	q1	q2	OK	0	2.06814e+09	1.79769e+308	1.79769e+308	0.0786496	0.150149	no
+TCONS_00000031	XLOC_000048	Xkr4	chr1:3277190-3277218	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000033	XLOC_000052	Xkr4	chr1:3280686-3280741	q1	q2	OK	0	2.29576e+07	1.79769e+308	1.79769e+308	0.158655	0.158655	no
+TCONS_00000034	XLOC_000057	Xkr4	chr1:3290488-3290553	q1	q2	OK	0	9.79535e+06	1.79769e+308	1.79769e+308	0.158655	0.158655	no
+TCONS_00000037	XLOC_000060	Xkr4	chr1:3299443-3299664	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000038	XLOC_000062	Xkr4	chr1:3300051-3300078	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000039	XLOC_000065	Xkr4	chr1:3318999-3319051	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000040	XLOC_000068	Xkr4	chr1:3355887-3356119	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000041	XLOC_000071	Xkr4	chr1:3363214-3363278	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000042	XLOC_000073	Xkr4	chr1:3363753-3363849	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000043	XLOC_000075	Xkr4	chr1:3367135-3367162	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000044	XLOC_000077	Xkr4	chr1:3367333-3367382	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000045	XLOC_000080	Xkr4	chr1:3377211-3377262	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000046	XLOC_000083	Xkr4	chr1:3391325-3391352	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000047	XLOC_000084	Xkr4	chr1:3435841-3435880	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000048	XLOC_000085	Xkr4	chr1:3447761-3447788	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000049	XLOC_000086	Xkr4	chr1:3450906-3450965	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000050	XLOC_000087	Xkr4	chr1:3451051-3451109	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000051	XLOC_000004	-	chr1:3174765-3174792	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000052	XLOC_000005	-	chr1:3187401-3187428	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000053	XLOC_000006	-	chr1:3188521-3188548	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000054	XLOC_000007	-	chr1:3189810-3190789	q1	q2	NOTEST	368900	429265	0.21864	-0.483034	0.629072	1	no
+TCONS_00000055	XLOC_000008	-	chr1:3190858-3191434	q1	q2	NOTEST	404373	338500	-0.25653	0.342922	0.731657	1	no
+TCONS_00000056	XLOC_000009	-	chr1:3191512-3192077	q1	q2	NOTEST	402276	686974	0.772069	-1.24554	0.212932	1	no
+TCONS_00000057	XLOC_000010	-	chr1:3192250-3192336	q1	q2	NOTEST	3.994e+06	2.93812e+06	-0.442943	0.217099	0.828131	1	no
+TCONS_00000058	XLOC_000013	-	chr1:3192649-3192676	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000059	XLOC_000018	-	chr1:3194706-3194733	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000060	XLOC_000024	-	chr1:3197425-3197452	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000062	XLOC_000027	-	chr1:3200430-3200457	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000063	XLOC_000028	-	chr1:3201007-3201039	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000065	XLOC_000030	-	chr1:3201596-3201666	q1	q2	OK	1.89853e+07	0	-1.79769e+308	-1.79769e+308	0.0786496	0.150149	no
+TCONS_00000066	XLOC_000032	-	chr1:3201725-3201809	q1	q2	OK	1.31744e+07	0	-1.79769e+308	-1.79769e+308	0.0416323	0.150149	no
+TCONS_00000067	XLOC_000033	Xkr4	chr1:3211521-3211561	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000068	XLOC_000036	Xkr4	chr1:3212717-3212801	q1	q2	NOTEST	4.39147e+06	0	-1.79769e+308	-1.79769e+308	0.158655	1	no
+TCONS_00000069	XLOC_000037	Xkr4	chr1:3213095-3213242	q1	q2	NOTEST	1.36901e+06	0	0	0	1	1	no
+TCONS_00000070	XLOC_000038	Xkr4	chr1:3240606-3240633	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000071	XLOC_000039	Xkr4	chr1:3242479-3242512	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000072	XLOC_000041	Xkr4	chr1:3242924-3243005	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000073	XLOC_000043	Xkr4	chr1:3243108-3243154	q1	q2	OK	9.99919e+07	0	-1.79769e+308	-1.79769e+308	0.158655	0.158655	no
+TCONS_00000074	XLOC_000045	Xkr4	chr1:3254079-3254106	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000075	XLOC_000047	Xkr4	chr1:3277155-3277182	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000076	XLOC_000049	Xkr4	chr1:3277913-3278390	q1	q2	NOTEST	265614	41870.3	-2.66534	2.48499	0.0129556	1	no
+TCONS_00000077	XLOC_000050	Xkr4	chr1:3280117-3280144	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000078	XLOC_000051	Xkr4	chr1:3280498-3280525	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000079	XLOC_000053	Xkr4	chr1:3282504-3282531	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000080	XLOC_000054	Xkr4	chr1:3282650-3282677	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000081	XLOC_000055	Xkr4	chr1:3282760-3282832	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000082	XLOC_000056	Xkr4	chr1:3284966-3284993	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000083	XLOC_000058	Xkr4	chr1:3290798-3290859	q1	q2	OK	1.8095e+07	0	-1.79769e+308	-1.79769e+308	0.158655	0.158655	no
+TCONS_00000084	XLOC_000059	Xkr4	chr1:3290919-3291273	q1	q2	NOTEST	342218	75524	-2.17991	1.96162	0.049807	1	no
+TCONS_00000085	XLOC_000060	Xkr4	chr1:3299443-3299664	q1	q2	NOTEST	937403	137917	-2.76487	1.66807	0.0953024	1	no
+TCONS_00000086	XLOC_000061	Xkr4	chr1:3299691-3299733	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000087	XLOC_000063	Xkr4	chr1:3307748-3307775	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000088	XLOC_000064	Xkr4	chr1:3318620-3318647	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000089	XLOC_000066	Xkr4	chr1:3330527-3330554	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000090	XLOC_000067	Xkr4	chr1:3351240-3351311	q1	q2	OK	8.91489e+06	0	-1.79769e+308	-1.79769e+308	0.158655	0.158655	no
+TCONS_00000091	XLOC_000068	Xkr4	chr1:3355887-3356119	q1	q2	NOTEST	585828	0	-1.79769e+308	-1.79769e+308	0.0512352	1	no
+TCONS_00000092	XLOC_000069	Xkr4	chr1:3356180-3356225	q1	q2	OK	1.19208e+08	0	-1.79769e+308	-1.79769e+308	0.158655	0.158655	no
+TCONS_00000093	XLOC_000070	Xkr4	chr1:3363076-3363176	q1	q2	NOTEST	4.42166e+06	0	-1.79769e+308	-1.79769e+308	0.0786496	1	no
+TCONS_00000094	XLOC_000072	Xkr4	chr1:3363387-3363446	q1	q2	OK	4.28358e+07	0	-1.79769e+308	-1.79769e+308	0.0786496	0.150149	no
+TCONS_00000095	XLOC_000074	Xkr4	chr1:3364871-3364919	q1	q2	OK	7.29939e+07	0	-1.79769e+308	-1.79769e+308	0.158655	0.158655	no
+TCONS_00000096	XLOC_000076	Xkr4	chr1:3367210-3367237	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000097	XLOC_000078	Xkr4	chr1:3369580-3369607	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000098	XLOC_000079	Xkr4	chr1:3375001-3375028	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000099	XLOC_000081	Xkr4	chr1:3379888-3379915	q1	q2	NOTEST	0	0	0	0	1	1	no
+TCONS_00000100	XLOC_000082	Xkr4	chr1:3386739-3386836	q1	q2	NOTEST	0	0	0	0	1	1	no
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffdiff_out10.txt	Fri Nov 08 14:54:01 2013 -0600
@@ -0,0 +1,88 @@
+test_id	gene_id	gene	locus	sample_1	sample_2	status	value_1	value_2	sqrt(JS)	test_stat	p_value	q_value	significant
+XLOC_000001	XLOC_000001	Xkr4	chr1:3204754-3204833	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000002	XLOC_000002	-	chr1:3111449-3111490	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000003	XLOC_000003	-	chr1:3111545-3111576	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000004	XLOC_000004	-	chr1:3174765-3174792	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000005	XLOC_000005	-	chr1:3187401-3187428	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000006	XLOC_000006	-	chr1:3188521-3188548	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000007	XLOC_000007	-	chr1:3189810-3190789	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000008	XLOC_000008	-	chr1:3190858-3191434	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000009	XLOC_000009	-	chr1:3191512-3192077	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000010	XLOC_000010	-	chr1:3192250-3192336	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000011	XLOC_000011	-	chr1:3192441-3192494	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000012	XLOC_000012	-	chr1:3192550-3192629	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000013	XLOC_000013	-	chr1:3192649-3192676	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000014	XLOC_000014	-	chr1:3192731-3192811	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000015	XLOC_000015	-	chr1:3192940-3193042	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000016	XLOC_000016	-	chr1:3194185-3194226	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000017	XLOC_000017	-	chr1:3194302-3194329	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000018	XLOC_000018	-	chr1:3194706-3194733	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000019	XLOC_000019	-	chr1:3195083-3195110	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000020	XLOC_000020	-	chr1:3195450-3195477	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000021	XLOC_000021	-	chr1:3197089-3197116	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000022	XLOC_000022	-	chr1:3197246-3197273	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000023	XLOC_000023	-	chr1:3197346-3197373	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000024	XLOC_000024	-	chr1:3197425-3197452	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000025	XLOC_000025	-	chr1:3200022-3200191	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000026	XLOC_000026	-	chr1:3200325-3200352	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000027	XLOC_000027	-	chr1:3200430-3200457	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000028	XLOC_000028	-	chr1:3201007-3201039	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000029	XLOC_000029	-	chr1:3201077-3201481	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000030	XLOC_000030	-	chr1:3201596-3201666	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000031	XLOC_000031	-	chr1:3201672-3201699	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000032	XLOC_000032	-	chr1:3201725-3201809	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000033	XLOC_000033	Xkr4	chr1:3211521-3211561	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000034	XLOC_000034	Xkr4	chr1:3212213-3212292	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000035	XLOC_000035	Xkr4	chr1:3212367-3212439	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000036	XLOC_000036	Xkr4	chr1:3212717-3212801	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000037	XLOC_000037	Xkr4	chr1:3213095-3213242	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000038	XLOC_000038	Xkr4	chr1:3240606-3240633	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000039	XLOC_000039	Xkr4	chr1:3242479-3242512	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000040	XLOC_000040	Xkr4	chr1:3242633-3242923	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000041	XLOC_000041	Xkr4	chr1:3242924-3243005	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000042	XLOC_000042	Xkr4	chr1:3243018-3243079	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000043	XLOC_000043	Xkr4	chr1:3243108-3243154	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000044	XLOC_000044	Xkr4	chr1:3243347-3243401	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000045	XLOC_000045	Xkr4	chr1:3254079-3254106	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000046	XLOC_000046	Xkr4	chr1:3256974-3257011	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000047	XLOC_000047	Xkr4	chr1:3277155-3277182	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000048	XLOC_000048	Xkr4	chr1:3277190-3277218	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000049	XLOC_000049	Xkr4	chr1:3277913-3278390	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000050	XLOC_000050	Xkr4	chr1:3280117-3280144	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000051	XLOC_000051	Xkr4	chr1:3280498-3280525	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000052	XLOC_000052	Xkr4	chr1:3280686-3280741	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000053	XLOC_000053	Xkr4	chr1:3282504-3282531	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000054	XLOC_000054	Xkr4	chr1:3282650-3282677	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000055	XLOC_000055	Xkr4	chr1:3282760-3282832	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000056	XLOC_000056	Xkr4	chr1:3284966-3284993	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000057	XLOC_000057	Xkr4	chr1:3290488-3290553	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000058	XLOC_000058	Xkr4	chr1:3290798-3290859	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000059	XLOC_000059	Xkr4	chr1:3290919-3291273	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000060	XLOC_000060	Xkr4	chr1:3299443-3299664	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000061	XLOC_000061	Xkr4	chr1:3299691-3299733	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000062	XLOC_000062	Xkr4	chr1:3300051-3300078	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000063	XLOC_000063	Xkr4	chr1:3307748-3307775	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000064	XLOC_000064	Xkr4	chr1:3318620-3318647	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000065	XLOC_000065	Xkr4	chr1:3318999-3319051	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000066	XLOC_000066	Xkr4	chr1:3330527-3330554	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000067	XLOC_000067	Xkr4	chr1:3351240-3351311	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000068	XLOC_000068	Xkr4	chr1:3355887-3356119	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000069	XLOC_000069	Xkr4	chr1:3356180-3356225	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000070	XLOC_000070	Xkr4	chr1:3363076-3363176	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000071	XLOC_000071	Xkr4	chr1:3363214-3363278	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000072	XLOC_000072	Xkr4	chr1:3363387-3363446	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000073	XLOC_000073	Xkr4	chr1:3363753-3363849	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000074	XLOC_000074	Xkr4	chr1:3364871-3364919	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000075	XLOC_000075	Xkr4	chr1:3367135-3367162	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000076	XLOC_000076	Xkr4	chr1:3367210-3367237	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000077	XLOC_000077	Xkr4	chr1:3367333-3367382	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000078	XLOC_000078	Xkr4	chr1:3369580-3369607	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000079	XLOC_000079	Xkr4	chr1:3375001-3375028	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000080	XLOC_000080	Xkr4	chr1:3377211-3377262	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000081	XLOC_000081	Xkr4	chr1:3379888-3379915	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000082	XLOC_000082	Xkr4	chr1:3386739-3386836	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000083	XLOC_000083	Xkr4	chr1:3391325-3391352	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000084	XLOC_000084	Xkr4	chr1:3435841-3435880	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000085	XLOC_000085	Xkr4	chr1:3447761-3447788	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000086	XLOC_000086	Xkr4	chr1:3450906-3450965	q1	q2	LOWDATA	0	0	0	0	0	1	no
+XLOC_000087	XLOC_000087	Xkr4	chr1:3451051-3451109	q1	q2	LOWDATA	0	0	0	0	0	1	no
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffdiff_out11.txt	Fri Nov 08 14:54:01 2013 -0600
@@ -0,0 +1,1 @@
+test_id	gene_id	gene	locus	sample_1	sample_2	status	value_1	value_2	sqrt(JS)	test_stat	p_value	q_value	significant
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffdiff_out2.txt	Fri Nov 08 14:54:01 2013 -0600
@@ -0,0 +1,88 @@
+test_id	gene_id	gene	locus	sample_1	sample_2	status	value_1	value_2	log2(fold_change)	test_stat	p_value	q_value	significant
+XLOC_000001	XLOC_000001	Xkr4	chr1:3204754-3204833	q1	q2	OK	0	8.3103e+06	1.79769e+308	1.79769e+308	0.0786496	0.157299	no
+XLOC_000002	XLOC_000002	-	chr1:3111449-3111490	q1	q2	OK	0	2.1403e+08	1.79769e+308	1.79769e+308	0.158655	0.16621	no
+XLOC_000003	XLOC_000003	-	chr1:3111545-3111576	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000004	XLOC_000004	-	chr1:3174765-3174792	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000005	XLOC_000005	-	chr1:3187401-3187428	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000006	XLOC_000006	-	chr1:3188521-3188548	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000007	XLOC_000007	-	chr1:3189810-3190789	q1	q2	NOTEST	368900	429265	0.21864	-0.483034	0.629072	1	no
+XLOC_000008	XLOC_000008	-	chr1:3190858-3191434	q1	q2	NOTEST	404373	338500	-0.25653	0.342922	0.731657	1	no
+XLOC_000009	XLOC_000009	-	chr1:3191512-3192077	q1	q2	NOTEST	402276	686974	0.772069	-1.24554	0.212932	1	no
+XLOC_000010	XLOC_000010	-	chr1:3192250-3192336	q1	q2	NOTEST	3.994e+06	2.93812e+06	-0.442943	0.217099	0.828131	1	no
+XLOC_000011	XLOC_000011	-	chr1:3192441-3192494	q1	q2	OK	0	5.68095e+07	1.79769e+308	1.79769e+308	0.0786496	0.157299	no
+XLOC_000012	XLOC_000012	-	chr1:3192550-3192629	q1	q2	OK	0	4.15515e+06	1.79769e+308	1.79769e+308	0.158655	0.16621	no
+XLOC_000013	XLOC_000013	-	chr1:3192649-3192676	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000014	XLOC_000014	-	chr1:3192731-3192811	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000015	XLOC_000015	-	chr1:3192940-3193042	q1	q2	OK	0	6.02976e+06	1.79769e+308	1.79769e+308	0.0512352	0.157299	no
+XLOC_000016	XLOC_000016	-	chr1:3194185-3194226	q1	q2	OK	0	2.1403e+08	1.79769e+308	1.79769e+308	0.158655	0.16621	no
+XLOC_000017	XLOC_000017	-	chr1:3194302-3194329	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000018	XLOC_000018	-	chr1:3194706-3194733	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000019	XLOC_000019	-	chr1:3195083-3195110	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000020	XLOC_000020	-	chr1:3195450-3195477	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000021	XLOC_000021	-	chr1:3197089-3197116	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000022	XLOC_000022	-	chr1:3197246-3197273	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000023	XLOC_000023	-	chr1:3197346-3197373	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000024	XLOC_000024	-	chr1:3197425-3197452	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000025	XLOC_000025	-	chr1:3200022-3200191	q1	q2	NOTEST	959058	705514	-0.442943	0.376027	0.706897	1	no
+XLOC_000026	XLOC_000026	-	chr1:3200325-3200352	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000027	XLOC_000027	-	chr1:3200430-3200457	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000028	XLOC_000028	-	chr1:3201007-3201039	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000029	XLOC_000029	-	chr1:3201077-3201481	q1	q2	NOTEST	77513.9	285108	1.87898	-1.76152	0.0781506	1	no
+XLOC_000030	XLOC_000030	-	chr1:3201596-3201666	q1	q2	OK	1.89853e+07	0	-1.79769e+308	-1.79769e+308	0.0786496	0.157299	no
+XLOC_000031	XLOC_000031	-	chr1:3201672-3201699	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000032	XLOC_000032	-	chr1:3201725-3201809	q1	q2	OK	1.31744e+07	0	-1.79769e+308	-1.79769e+308	0.0416323	0.157299	no
+XLOC_000033	XLOC_000033	Xkr4	chr1:3211521-3211561	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000034	XLOC_000034	Xkr4	chr1:3212213-3212292	q1	q2	OK	0	8.3103e+06	1.79769e+308	1.79769e+308	0.0786496	0.157299	no
+XLOC_000035	XLOC_000035	Xkr4	chr1:3212367-3212439	q1	q2	OK	0	2.4671e+07	1.79769e+308	1.79769e+308	0.0512352	0.157299	no
+XLOC_000036	XLOC_000036	Xkr4	chr1:3212717-3212801	q1	q2	NOTEST	4.39147e+06	0	-1.79769e+308	-1.79769e+308	0.158655	1	no
+XLOC_000037	XLOC_000037	Xkr4	chr1:3213095-3213242	q1	q2	OK	5.3664e+06	1.82908e+06	-1.55284	0.839459	0.401212	0.401212	no
+XLOC_000038	XLOC_000038	Xkr4	chr1:3240606-3240633	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000039	XLOC_000039	Xkr4	chr1:3242479-3242512	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000040	XLOC_000040	Xkr4	chr1:3242633-3242923	q1	q2	NOTEST	56312.4	372827	2.72698	-1.67622	0.0936947	1	no
+XLOC_000041	XLOC_000041	Xkr4	chr1:3242924-3243005	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000042	XLOC_000042	Xkr4	chr1:3243018-3243079	q1	q2	OK	0	2.66226e+07	1.79769e+308	1.79769e+308	0.0786496	0.157299	no
+XLOC_000043	XLOC_000043	Xkr4	chr1:3243108-3243154	q1	q2	OK	9.99919e+07	0	-1.79769e+308	-1.79769e+308	0.158655	0.16621	no
+XLOC_000044	XLOC_000044	Xkr4	chr1:3243347-3243401	q1	q2	OK	0	5.0951e+07	1.79769e+308	1.79769e+308	0.0786496	0.157299	no
+XLOC_000045	XLOC_000045	Xkr4	chr1:3254079-3254106	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000046	XLOC_000046	Xkr4	chr1:3256974-3257011	q1	q2	OK	0	2.06814e+09	1.79769e+308	1.79769e+308	0.0786496	0.157299	no
+XLOC_000047	XLOC_000047	Xkr4	chr1:3277155-3277182	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000048	XLOC_000048	Xkr4	chr1:3277190-3277218	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000049	XLOC_000049	Xkr4	chr1:3277913-3278390	q1	q2	NOTEST	265614	41870.3	-2.66534	2.48499	0.0129556	1	no
+XLOC_000050	XLOC_000050	Xkr4	chr1:3280117-3280144	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000051	XLOC_000051	Xkr4	chr1:3280498-3280525	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000052	XLOC_000052	Xkr4	chr1:3280686-3280741	q1	q2	OK	0	2.29576e+07	1.79769e+308	1.79769e+308	0.158655	0.16621	no
+XLOC_000053	XLOC_000053	Xkr4	chr1:3282504-3282531	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000054	XLOC_000054	Xkr4	chr1:3282650-3282677	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000055	XLOC_000055	Xkr4	chr1:3282760-3282832	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000056	XLOC_000056	Xkr4	chr1:3284966-3284993	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000057	XLOC_000057	Xkr4	chr1:3290488-3290553	q1	q2	OK	0	9.79535e+06	1.79769e+308	1.79769e+308	0.158655	0.16621	no
+XLOC_000058	XLOC_000058	Xkr4	chr1:3290798-3290859	q1	q2	OK	1.8095e+07	0	-1.79769e+308	-1.79769e+308	0.158655	0.16621	no
+XLOC_000059	XLOC_000059	Xkr4	chr1:3290919-3291273	q1	q2	NOTEST	342218	75524	-2.17991	1.96162	0.049807	1	no
+XLOC_000060	XLOC_000060	Xkr4	chr1:3299443-3299664	q1	q2	NOTEST	937403	137917	-2.76487	1.66807	0.0953024	1	no
+XLOC_000061	XLOC_000061	Xkr4	chr1:3299691-3299733	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000062	XLOC_000062	Xkr4	chr1:3300051-3300078	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000063	XLOC_000063	Xkr4	chr1:3307748-3307775	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000064	XLOC_000064	Xkr4	chr1:3318620-3318647	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000065	XLOC_000065	Xkr4	chr1:3318999-3319051	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000066	XLOC_000066	Xkr4	chr1:3330527-3330554	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000067	XLOC_000067	Xkr4	chr1:3351240-3351311	q1	q2	OK	8.91489e+06	0	-1.79769e+308	-1.79769e+308	0.158655	0.16621	no
+XLOC_000068	XLOC_000068	Xkr4	chr1:3355887-3356119	q1	q2	NOTEST	585828	0	-1.79769e+308	-1.79769e+308	0.0512352	1	no
+XLOC_000069	XLOC_000069	Xkr4	chr1:3356180-3356225	q1	q2	OK	1.19208e+08	0	-1.79769e+308	-1.79769e+308	0.158655	0.16621	no
+XLOC_000070	XLOC_000070	Xkr4	chr1:3363076-3363176	q1	q2	NOTEST	4.42166e+06	0	-1.79769e+308	-1.79769e+308	0.0786496	1	no
+XLOC_000071	XLOC_000071	Xkr4	chr1:3363214-3363278	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000072	XLOC_000072	Xkr4	chr1:3363387-3363446	q1	q2	OK	4.28358e+07	0	-1.79769e+308	-1.79769e+308	0.0786496	0.157299	no
+XLOC_000073	XLOC_000073	Xkr4	chr1:3363753-3363849	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000074	XLOC_000074	Xkr4	chr1:3364871-3364919	q1	q2	OK	7.29939e+07	0	-1.79769e+308	-1.79769e+308	0.158655	0.16621	no
+XLOC_000075	XLOC_000075	Xkr4	chr1:3367135-3367162	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000076	XLOC_000076	Xkr4	chr1:3367210-3367237	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000077	XLOC_000077	Xkr4	chr1:3367333-3367382	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000078	XLOC_000078	Xkr4	chr1:3369580-3369607	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000079	XLOC_000079	Xkr4	chr1:3375001-3375028	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000080	XLOC_000080	Xkr4	chr1:3377211-3377262	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000081	XLOC_000081	Xkr4	chr1:3379888-3379915	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000082	XLOC_000082	Xkr4	chr1:3386739-3386836	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000083	XLOC_000083	Xkr4	chr1:3391325-3391352	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000084	XLOC_000084	Xkr4	chr1:3435841-3435880	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000085	XLOC_000085	Xkr4	chr1:3447761-3447788	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000086	XLOC_000086	Xkr4	chr1:3450906-3450965	q1	q2	NOTEST	0	0	0	0	1	1	no
+XLOC_000087	XLOC_000087	Xkr4	chr1:3451051-3451109	q1	q2	NOTEST	0	0	0	0	1	1	no
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffdiff_out3.txt	Fri Nov 08 14:54:01 2013 -0600
@@ -0,0 +1,91 @@
+test_id	gene_id	gene	locus	sample_1	sample_2	status	value_1	value_2	log2(fold_change)	test_stat	p_value	q_value	significant
+TSS1	XLOC_000001	Xkr4	chr1:3204754-3204833	q1	q2	OK	0	8.3103e+06	1.79769e+308	1.79769e+308	0.0786496	0.150149	no
+TSS11	XLOC_000008	-	chr1:3190858-3191434	q1	q2	NOTEST	404373	338500	-0.25653	0.342922	0.731657	1	no
+TSS12	XLOC_000009	-	chr1:3191512-3192077	q1	q2	NOTEST	402276	686974	0.772069	-1.24554	0.212932	1	no
+TSS15	XLOC_000010	-	chr1:3192250-3192336	q1	q2	NOTEST	3.994e+06	2.93812e+06	-0.442943	0.217099	0.828131	1	no
+TSS16	XLOC_000011	-	chr1:3192441-3192494	q1	q2	OK	0	5.68095e+07	1.79769e+308	1.79769e+308	0.0786496	0.150149	no
+TSS17	XLOC_000012	-	chr1:3192550-3192629	q1	q2	OK	0	4.15515e+06	1.79769e+308	1.79769e+308	0.158655	0.158655	no
+TSS18	XLOC_000013	-	chr1:3192649-3192676	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS19	XLOC_000014	-	chr1:3192731-3192811	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS2	XLOC_000002	-	chr1:3111449-3111490	q1	q2	OK	0	2.1403e+08	1.79769e+308	1.79769e+308	0.158655	0.158655	no
+TSS20	XLOC_000015	-	chr1:3192940-3193042	q1	q2	OK	0	6.02976e+06	1.79769e+308	1.79769e+308	0.0512352	0.150149	no
+TSS21	XLOC_000016	-	chr1:3194185-3194226	q1	q2	OK	0	2.1403e+08	1.79769e+308	1.79769e+308	0.158655	0.158655	no
+TSS22	XLOC_000017	-	chr1:3194302-3194329	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS23	XLOC_000018	-	chr1:3194706-3194733	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS24	XLOC_000019	-	chr1:3195083-3195110	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS25	XLOC_000020	-	chr1:3195450-3195477	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS26	XLOC_000021	-	chr1:3197089-3197116	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS27	XLOC_000022	-	chr1:3197246-3197273	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS28	XLOC_000023	-	chr1:3197346-3197373	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS29	XLOC_000024	-	chr1:3197425-3197452	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS3	XLOC_000003	-	chr1:3111545-3111576	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS30	XLOC_000025	-	chr1:3200022-3200191	q1	q2	NOTEST	959058	705514	-0.442943	0.376027	0.706897	1	no
+TSS32	XLOC_000026	-	chr1:3200325-3200352	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS33	XLOC_000027	-	chr1:3200430-3200457	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS34	XLOC_000028	-	chr1:3201007-3201039	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS35	XLOC_000029	-	chr1:3201077-3201481	q1	q2	NOTEST	77513.9	285108	1.87898	-1.76152	0.0781506	1	no
+TSS37	XLOC_000030	-	chr1:3201596-3201666	q1	q2	OK	1.89853e+07	0	-1.79769e+308	-1.79769e+308	0.0786496	0.150149	no
+TSS38	XLOC_000031	-	chr1:3201672-3201699	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS39	XLOC_000032	-	chr1:3201725-3201809	q1	q2	OK	1.31744e+07	0	-1.79769e+308	-1.79769e+308	0.0416323	0.150149	no
+TSS4	XLOC_000004	-	chr1:3174765-3174792	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS40	XLOC_000033	Xkr4	chr1:3211521-3211561	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS41	XLOC_000034	Xkr4	chr1:3212213-3212292	q1	q2	OK	0	8.3103e+06	1.79769e+308	1.79769e+308	0.0786496	0.150149	no
+TSS42	XLOC_000035	Xkr4	chr1:3212367-3212439	q1	q2	OK	0	2.4671e+07	1.79769e+308	1.79769e+308	0.0512352	0.150149	no
+TSS43	XLOC_000036	Xkr4	chr1:3212717-3212801	q1	q2	NOTEST	4.39147e+06	0	-1.79769e+308	-1.79769e+308	0.158655	1	no
+TSS44	XLOC_000037	Xkr4	chr1:3213095-3213242	q1	q2	NOTEST	3.99739e+06	1.82908e+06	-1.12794	0.489836	0.62425	1	no
+TSS45	XLOC_000037	Xkr4	chr1:3213095-3213242	q1	q2	NOTEST	1.36901e+06	0	0	0	1	1	no
+TSS46	XLOC_000038	Xkr4	chr1:3240606-3240633	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS47	XLOC_000039	Xkr4	chr1:3242479-3242512	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS48	XLOC_000040	Xkr4	chr1:3242633-3242923	q1	q2	NOTEST	56312.4	372827	2.72698	-1.67622	0.0936947	1	no
+TSS49	XLOC_000041	Xkr4	chr1:3242924-3243005	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS5	XLOC_000005	-	chr1:3187401-3187428	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS50	XLOC_000042	Xkr4	chr1:3243018-3243079	q1	q2	OK	0	2.66226e+07	1.79769e+308	1.79769e+308	0.0786496	0.150149	no
+TSS51	XLOC_000043	Xkr4	chr1:3243108-3243154	q1	q2	OK	9.99919e+07	0	-1.79769e+308	-1.79769e+308	0.158655	0.158655	no
+TSS52	XLOC_000044	Xkr4	chr1:3243347-3243401	q1	q2	OK	0	5.0951e+07	1.79769e+308	1.79769e+308	0.0786496	0.150149	no
+TSS53	XLOC_000045	Xkr4	chr1:3254079-3254106	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS54	XLOC_000046	Xkr4	chr1:3256974-3257011	q1	q2	OK	0	2.06814e+09	1.79769e+308	1.79769e+308	0.0786496	0.150149	no
+TSS55	XLOC_000047	Xkr4	chr1:3277155-3277182	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS56	XLOC_000048	Xkr4	chr1:3277190-3277218	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS57	XLOC_000049	Xkr4	chr1:3277913-3278390	q1	q2	NOTEST	265614	41870.3	-2.66534	2.48499	0.0129556	1	no
+TSS59	XLOC_000050	Xkr4	chr1:3280117-3280144	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS6	XLOC_000006	-	chr1:3188521-3188548	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS60	XLOC_000051	Xkr4	chr1:3280498-3280525	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS61	XLOC_000052	Xkr4	chr1:3280686-3280741	q1	q2	OK	0	2.29576e+07	1.79769e+308	1.79769e+308	0.158655	0.158655	no
+TSS62	XLOC_000053	Xkr4	chr1:3282504-3282531	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS63	XLOC_000054	Xkr4	chr1:3282650-3282677	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS64	XLOC_000055	Xkr4	chr1:3282760-3282832	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS65	XLOC_000056	Xkr4	chr1:3284966-3284993	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS66	XLOC_000057	Xkr4	chr1:3290488-3290553	q1	q2	OK	0	9.79535e+06	1.79769e+308	1.79769e+308	0.158655	0.158655	no
+TSS67	XLOC_000058	Xkr4	chr1:3290798-3290859	q1	q2	OK	1.8095e+07	0	-1.79769e+308	-1.79769e+308	0.158655	0.158655	no
+TSS68	XLOC_000059	Xkr4	chr1:3290919-3291273	q1	q2	NOTEST	342218	75524	-2.17991	1.96162	0.049807	1	no
+TSS7	XLOC_000007	-	chr1:3189810-3190789	q1	q2	NOTEST	368900	429265	0.21864	-0.483034	0.629072	1	no
+TSS70	XLOC_000060	Xkr4	chr1:3299443-3299664	q1	q2	NOTEST	937403	137917	-2.76487	1.66807	0.0953024	1	no
+TSS71	XLOC_000060	Xkr4	chr1:3299443-3299664	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS72	XLOC_000061	Xkr4	chr1:3299691-3299733	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS73	XLOC_000062	Xkr4	chr1:3300051-3300078	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS74	XLOC_000063	Xkr4	chr1:3307748-3307775	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS75	XLOC_000064	Xkr4	chr1:3318620-3318647	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS76	XLOC_000065	Xkr4	chr1:3318999-3319051	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS77	XLOC_000066	Xkr4	chr1:3330527-3330554	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS78	XLOC_000067	Xkr4	chr1:3351240-3351311	q1	q2	OK	8.91489e+06	0	-1.79769e+308	-1.79769e+308	0.158655	0.158655	no
+TSS79	XLOC_000068	Xkr4	chr1:3355887-3356119	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS80	XLOC_000068	Xkr4	chr1:3355887-3356119	q1	q2	NOTEST	585828	0	-1.79769e+308	-1.79769e+308	0.0512352	1	no
+TSS81	XLOC_000069	Xkr4	chr1:3356180-3356225	q1	q2	OK	1.19208e+08	0	-1.79769e+308	-1.79769e+308	0.158655	0.158655	no
+TSS82	XLOC_000070	Xkr4	chr1:3363076-3363176	q1	q2	NOTEST	4.42166e+06	0	-1.79769e+308	-1.79769e+308	0.0786496	1	no
+TSS83	XLOC_000071	Xkr4	chr1:3363214-3363278	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS84	XLOC_000072	Xkr4	chr1:3363387-3363446	q1	q2	OK	4.28358e+07	0	-1.79769e+308	-1.79769e+308	0.0786496	0.150149	no
+TSS85	XLOC_000073	Xkr4	chr1:3363753-3363849	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS86	XLOC_000074	Xkr4	chr1:3364871-3364919	q1	q2	OK	7.29939e+07	0	-1.79769e+308	-1.79769e+308	0.158655	0.158655	no
+TSS87	XLOC_000075	Xkr4	chr1:3367135-3367162	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS88	XLOC_000076	Xkr4	chr1:3367210-3367237	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS89	XLOC_000077	Xkr4	chr1:3367333-3367382	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS90	XLOC_000078	Xkr4	chr1:3369580-3369607	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS91	XLOC_000079	Xkr4	chr1:3375001-3375028	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS92	XLOC_000080	Xkr4	chr1:3377211-3377262	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS93	XLOC_000081	Xkr4	chr1:3379888-3379915	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS94	XLOC_000082	Xkr4	chr1:3386739-3386836	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS95	XLOC_000083	Xkr4	chr1:3391325-3391352	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS96	XLOC_000084	Xkr4	chr1:3435841-3435880	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS97	XLOC_000085	Xkr4	chr1:3447761-3447788	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS98	XLOC_000086	Xkr4	chr1:3450906-3450965	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS99	XLOC_000087	Xkr4	chr1:3451051-3451109	q1	q2	NOTEST	0	0	0	0	1	1	no
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffdiff_out4.txt	Fri Nov 08 14:54:01 2013 -0600
@@ -0,0 +1,1 @@
+test_id	gene_id	gene	locus	sample_1	sample_2	status	value_1	value_2	log2(fold_change)	test_stat	p_value	q_value	significant
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffdiff_out5.txt	Fri Nov 08 14:54:01 2013 -0600
@@ -0,0 +1,91 @@
+tracking_id	class_code	nearest_ref_id	gene_id	gene_short_name	tss_id	locus	length	coverage	q1_FPKM	q1_conf_lo	q1_conf_hi	q1_status	q2_FPKM	q2_conf_lo	q2_conf_hi	q2_status
+TCONS_00000001	c	Xkr4	XLOC_000001	Xkr4	TSS1	chr1:3204754-3204833	79	-	0	0	0	OK	8.3103e+06	0	2.00628e+07	OK
+TCONS_00000002	-	-	XLOC_000002	-	TSS2	chr1:3111449-3111490	41	-	0	0	0	OK	2.1403e+08	0	6.42089e+08	OK
+TCONS_00000003	-	-	XLOC_000003	-	TSS3	chr1:3111545-3111576	31	-	0	0	0	OK	0	0	0	OK
+TCONS_00000009	-	-	XLOC_000011	-	TSS16	chr1:3192441-3192494	53	-	0	0	0	OK	5.68095e+07	0	1.3715e+08	OK
+TCONS_00000010	-	-	XLOC_000012	-	TSS17	chr1:3192550-3192629	79	-	0	0	0	OK	4.15515e+06	0	1.24654e+07	OK
+TCONS_00000011	-	-	XLOC_000014	-	TSS19	chr1:3192731-3192811	80	-	0	0	0	OK	0	0	0	OK
+TCONS_00000012	-	-	XLOC_000015	-	TSS20	chr1:3192940-3193042	102	-	0	0	0	OK	6.02976e+06	0	1.34147e+07	OK
+TCONS_00000013	-	-	XLOC_000016	-	TSS21	chr1:3194185-3194226	41	-	0	0	0	OK	2.1403e+08	0	6.42089e+08	OK
+TCONS_00000014	-	-	XLOC_000017	-	TSS22	chr1:3194302-3194329	27	-	0	0	0	OK	0	0	0	OK
+TCONS_00000015	-	-	XLOC_000019	-	TSS24	chr1:3195083-3195110	27	-	0	0	0	OK	0	0	0	OK
+TCONS_00000016	-	-	XLOC_000020	-	TSS25	chr1:3195450-3195477	27	-	0	0	0	OK	0	0	0	OK
+TCONS_00000017	-	-	XLOC_000021	-	TSS26	chr1:3197089-3197116	27	-	0	0	0	OK	0	0	0	OK
+TCONS_00000018	-	-	XLOC_000022	-	TSS27	chr1:3197246-3197273	27	-	0	0	0	OK	0	0	0	OK
+TCONS_00000019	-	-	XLOC_000023	-	TSS28	chr1:3197346-3197373	27	-	0	0	0	OK	0	0	0	OK
+TCONS_00000020	-	-	XLOC_000025	-	TSS30	chr1:3200022-3200191	169	-	959058	0	2.06648e+06	OK	705514	0	1.52017e+06	OK
+TCONS_00000021	-	-	XLOC_000026	-	TSS32	chr1:3200325-3200352	27	-	0	0	0	OK	0	0	0	OK
+TCONS_00000022	-	-	XLOC_000029	-	TSS35	chr1:3201077-3201481	404	-	77513.9	0	167019	OK	285108	21736.5	548480	OK
+TCONS_00000023	-	-	XLOC_000031	-	TSS38	chr1:3201672-3201699	27	-	0	0	0	OK	0	0	0	OK
+TCONS_00000024	i	Xkr4	XLOC_000034	Xkr4	TSS41	chr1:3212213-3212292	79	-	0	0	0	OK	8.3103e+06	0	2.00628e+07	OK
+TCONS_00000025	i	Xkr4	XLOC_000035	Xkr4	TSS42	chr1:3212367-3212439	72	-	0	0	0	OK	2.4671e+07	0	5.48867e+07	OK
+TCONS_00000026	i	Xkr4	XLOC_000037	Xkr4	TSS44	chr1:3213095-3213242	97	-	3.99739e+06	3.99339e+06	4.00139e+06	LOWDATA	1.82908e+06	0	5.48723e+06	OK
+TCONS_00000027	i	Xkr4	XLOC_000040	Xkr4	TSS48	chr1:3242633-3242923	290	-	56312.4	0	168937	OK	372827	0	761430	OK
+TCONS_00000028	i	Xkr4	XLOC_000042	Xkr4	TSS50	chr1:3243018-3243079	61	-	0	0	0	OK	2.66226e+07	0	6.42725e+07	OK
+TCONS_00000029	i	Xkr4	XLOC_000044	Xkr4	TSS52	chr1:3243347-3243401	54	-	0	0	0	OK	5.0951e+07	0	1.23007e+08	OK
+TCONS_00000030	i	Xkr4	XLOC_000046	Xkr4	TSS54	chr1:3256974-3257011	37	-	0	0	0	OK	2.06814e+09	0	4.99293e+09	OK
+TCONS_00000031	i	Xkr4	XLOC_000048	Xkr4	TSS56	chr1:3277190-3277218	28	-	0	0	0	OK	0	0	0	OK
+TCONS_00000033	i	Xkr4	XLOC_000052	Xkr4	TSS61	chr1:3280686-3280741	55	-	0	0	0	OK	2.29576e+07	0	6.88728e+07	OK
+TCONS_00000034	i	Xkr4	XLOC_000057	Xkr4	TSS66	chr1:3290488-3290553	65	-	0	0	0	OK	9.79535e+06	0	2.9386e+07	OK
+TCONS_00000037	i	Xkr4	XLOC_000060	Xkr4	TSS71	chr1:3299443-3299664	55	-	0	0	0	OK	0	0	0	OK
+TCONS_00000038	i	Xkr4	XLOC_000062	Xkr4	TSS73	chr1:3300051-3300078	27	-	0	0	0	OK	0	0	0	OK
+TCONS_00000039	i	Xkr4	XLOC_000065	Xkr4	TSS76	chr1:3318999-3319051	52	-	0	0	0	OK	0	0	0	OK
+TCONS_00000040	i	Xkr4	XLOC_000068	Xkr4	TSS79	chr1:3355887-3356119	27	-	0	0	0	OK	0	0	0	OK
+TCONS_00000041	i	Xkr4	XLOC_000071	Xkr4	TSS83	chr1:3363214-3363278	64	-	0	0	0	OK	0	0	0	OK
+TCONS_00000042	i	Xkr4	XLOC_000073	Xkr4	TSS85	chr1:3363753-3363849	96	-	0	0	0	OK	0	0	0	OK
+TCONS_00000043	i	Xkr4	XLOC_000075	Xkr4	TSS87	chr1:3367135-3367162	27	-	0	0	0	OK	0	0	0	OK
+TCONS_00000044	i	Xkr4	XLOC_000077	Xkr4	TSS89	chr1:3367333-3367382	49	-	0	0	0	OK	0	0	0	OK
+TCONS_00000045	i	Xkr4	XLOC_000080	Xkr4	TSS92	chr1:3377211-3377262	51	-	0	0	0	OK	0	0	0	OK
+TCONS_00000046	i	Xkr4	XLOC_000083	Xkr4	TSS95	chr1:3391325-3391352	27	-	0	0	0	OK	0	0	0	OK
+TCONS_00000047	i	Xkr4	XLOC_000084	Xkr4	TSS96	chr1:3435841-3435880	39	-	0	0	0	OK	0	0	0	OK
+TCONS_00000048	i	Xkr4	XLOC_000085	Xkr4	TSS97	chr1:3447761-3447788	27	-	0	0	0	OK	0	0	0	OK
+TCONS_00000049	i	Xkr4	XLOC_000086	Xkr4	TSS98	chr1:3450906-3450965	59	-	0	0	0	OK	0	0	0	OK
+TCONS_00000050	i	Xkr4	XLOC_000087	Xkr4	TSS99	chr1:3451051-3451109	58	-	0	0	0	OK	0	0	0	OK
+TCONS_00000051	-	-	XLOC_000004	-	TSS4	chr1:3174765-3174792	27	-	0	0	0	OK	0	0	0	OK
+TCONS_00000052	-	-	XLOC_000005	-	TSS5	chr1:3187401-3187428	27	-	0	0	0	OK	0	0	0	OK
+TCONS_00000053	-	-	XLOC_000006	-	TSS6	chr1:3188521-3188548	27	-	0	0	0	OK	0	0	0	OK
+TCONS_00000054	-	-	XLOC_000007	-	TSS7	chr1:3189810-3190789	979	-	368900	151353	586447	OK	429265	337221	521309	OK
+TCONS_00000055	-	-	XLOC_000008	-	TSS11	chr1:3190858-3191434	576	-	404373	101434	707312	OK	338500	95761.5	581239	OK
+TCONS_00000056	-	-	XLOC_000009	-	TSS12	chr1:3191512-3192077	565	-	402276	96829.4	707722	OK	686974	410563	963384	OK
+TCONS_00000057	-	-	XLOC_000010	-	TSS15	chr1:3192250-3192336	86	-	3.994e+06	0	1.1982e+07	OK	2.93812e+06	0	8.81435e+06	OK
+TCONS_00000058	-	-	XLOC_000013	-	TSS18	chr1:3192649-3192676	27	-	0	0	0	OK	0	0	0	OK
+TCONS_00000059	-	-	XLOC_000018	-	TSS23	chr1:3194706-3194733	27	-	0	0	0	OK	0	0	0	OK
+TCONS_00000060	-	-	XLOC_000024	-	TSS29	chr1:3197425-3197452	27	-	0	0	0	OK	0	0	0	OK
+TCONS_00000062	-	-	XLOC_000027	-	TSS33	chr1:3200430-3200457	27	-	0	0	0	OK	0	0	0	OK
+TCONS_00000063	-	-	XLOC_000028	-	TSS34	chr1:3201007-3201039	32	-	0	0	0	OK	0	0	0	OK
+TCONS_00000065	-	-	XLOC_000030	-	TSS37	chr1:3201596-3201666	70	-	1.89853e+07	0	4.58345e+07	OK	0	0	0	OK
+TCONS_00000066	-	-	XLOC_000032	-	TSS39	chr1:3201725-3201809	84	-	1.31744e+07	0	2.83869e+07	OK	0	0	0	OK
+TCONS_00000067	i	Xkr4	XLOC_000033	Xkr4	TSS40	chr1:3211521-3211561	40	-	0	0	0	OK	0	0	0	OK
+TCONS_00000068	i	Xkr4	XLOC_000036	Xkr4	TSS43	chr1:3212717-3212801	84	-	4.39147e+06	0	1.31744e+07	OK	0	0	0	OK
+TCONS_00000069	i	Xkr4	XLOC_000037	Xkr4	TSS45	chr1:3213095-3213242	124	-	1.36901e+06	1.36667e+06	1.37135e+06	LOWDATA	0	0	0	OK
+TCONS_00000070	i	Xkr4	XLOC_000038	Xkr4	TSS46	chr1:3240606-3240633	27	-	0	0	0	OK	0	0	0	OK
+TCONS_00000071	i	Xkr4	XLOC_000039	Xkr4	TSS47	chr1:3242479-3242512	33	-	0	0	0	OK	0	0	0	OK
+TCONS_00000072	i	Xkr4	XLOC_000041	Xkr4	TSS49	chr1:3242924-3243005	81	-	0	0	0	OK	0	0	0	OK
+TCONS_00000073	i	Xkr4	XLOC_000043	Xkr4	TSS51	chr1:3243108-3243154	46	-	9.99919e+07	0	2.99976e+08	OK	0	0	0	OK
+TCONS_00000074	i	Xkr4	XLOC_000045	Xkr4	TSS53	chr1:3254079-3254106	27	-	0	0	0	OK	0	0	0	OK
+TCONS_00000075	i	Xkr4	XLOC_000047	Xkr4	TSS55	chr1:3277155-3277182	27	-	0	0	0	OK	0	0	0	OK
+TCONS_00000076	i	Xkr4	XLOC_000049	Xkr4	TSS57	chr1:3277913-3278390	477	-	265614	16793	514436	OK	41870.3	0	90217.9	OK
+TCONS_00000077	i	Xkr4	XLOC_000050	Xkr4	TSS59	chr1:3280117-3280144	27	-	0	0	0	OK	0	0	0	OK
+TCONS_00000078	i	Xkr4	XLOC_000051	Xkr4	TSS60	chr1:3280498-3280525	27	-	0	0	0	OK	0	0	0	OK
+TCONS_00000079	i	Xkr4	XLOC_000053	Xkr4	TSS62	chr1:3282504-3282531	27	-	0	0	0	OK	0	0	0	OK
+TCONS_00000080	i	Xkr4	XLOC_000054	Xkr4	TSS63	chr1:3282650-3282677	27	-	0	0	0	OK	0	0	0	OK
+TCONS_00000081	i	Xkr4	XLOC_000055	Xkr4	TSS64	chr1:3282760-3282832	72	-	0	0	0	OK	0	0	0	OK
+TCONS_00000082	i	Xkr4	XLOC_000056	Xkr4	TSS65	chr1:3284966-3284993	27	-	0	0	0	OK	0	0	0	OK
+TCONS_00000083	i	Xkr4	XLOC_000058	Xkr4	TSS67	chr1:3290798-3290859	61	-	1.8095e+07	0	5.4285e+07	OK	0	0	0	OK
+TCONS_00000084	i	Xkr4	XLOC_000059	Xkr4	TSS68	chr1:3290919-3291273	354	-	342218	0	691214	OK	75524	0	162732	OK
+TCONS_00000085	i	Xkr4	XLOC_000060	Xkr4	TSS70	chr1:3299443-3299664	197	-	937403	0	1.99795e+06	OK	137917	0	413751	OK
+TCONS_00000086	i	Xkr4	XLOC_000061	Xkr4	TSS72	chr1:3299691-3299733	42	-	0	0	0	OK	0	0	0	OK
+TCONS_00000087	i	Xkr4	XLOC_000063	Xkr4	TSS74	chr1:3307748-3307775	27	-	0	0	0	OK	0	0	0	OK
+TCONS_00000088	i	Xkr4	XLOC_000064	Xkr4	TSS75	chr1:3318620-3318647	27	-	0	0	0	OK	0	0	0	OK
+TCONS_00000089	i	Xkr4	XLOC_000066	Xkr4	TSS77	chr1:3330527-3330554	27	-	0	0	0	OK	0	0	0	OK
+TCONS_00000090	i	Xkr4	XLOC_000067	Xkr4	TSS78	chr1:3351240-3351311	71	-	8.91489e+06	0	2.67447e+07	OK	0	0	0	OK
+TCONS_00000091	i	Xkr4	XLOC_000068	Xkr4	TSS80	chr1:3355887-3356119	212	-	585828	0	1.30332e+06	OK	0	0	0	OK
+TCONS_00000092	i	Xkr4	XLOC_000069	Xkr4	TSS81	chr1:3356180-3356225	45	-	1.19208e+08	0	3.57623e+08	OK	0	0	0	OK
+TCONS_00000093	i	Xkr4	XLOC_000070	Xkr4	TSS82	chr1:3363076-3363176	100	-	4.42166e+06	0	1.06748e+07	OK	0	0	0	OK
+TCONS_00000094	i	Xkr4	XLOC_000072	Xkr4	TSS84	chr1:3363387-3363446	59	-	4.28358e+07	0	1.03415e+08	OK	0	0	0	OK
+TCONS_00000095	i	Xkr4	XLOC_000074	Xkr4	TSS86	chr1:3364871-3364919	48	-	7.29939e+07	0	2.18982e+08	OK	0	0	0	OK
+TCONS_00000096	i	Xkr4	XLOC_000076	Xkr4	TSS88	chr1:3367210-3367237	27	-	0	0	0	OK	0	0	0	OK
+TCONS_00000097	i	Xkr4	XLOC_000078	Xkr4	TSS90	chr1:3369580-3369607	27	-	0	0	0	OK	0	0	0	OK
+TCONS_00000098	i	Xkr4	XLOC_000079	Xkr4	TSS91	chr1:3375001-3375028	27	-	0	0	0	OK	0	0	0	OK
+TCONS_00000099	i	Xkr4	XLOC_000081	Xkr4	TSS93	chr1:3379888-3379915	27	-	0	0	0	OK	0	0	0	OK
+TCONS_00000100	i	Xkr4	XLOC_000082	Xkr4	TSS94	chr1:3386739-3386836	97	-	0	0	0	OK	0	0	0	OK
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffdiff_out6.txt	Fri Nov 08 14:54:01 2013 -0600
@@ -0,0 +1,88 @@
+tracking_id	class_code	nearest_ref_id	gene_id	gene_short_name	tss_id	locus	length	coverage	q1_FPKM	q1_conf_lo	q1_conf_hi	q1_status	q2_FPKM	q2_conf_lo	q2_conf_hi	q2_status
+XLOC_000001	-	-	XLOC_000001	Xkr4	TSS1	chr1:3204754-3204833	-	-	0	0	0	OK	8.3103e+06	0	2.00628e+07	OK
+XLOC_000002	-	-	XLOC_000002	-	TSS2	chr1:3111449-3111490	-	-	0	0	0	OK	2.1403e+08	0	6.42089e+08	OK
+XLOC_000003	-	-	XLOC_000003	-	TSS3	chr1:3111545-3111576	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000004	-	-	XLOC_000004	-	TSS4	chr1:3174765-3174792	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000005	-	-	XLOC_000005	-	TSS5	chr1:3187401-3187428	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000006	-	-	XLOC_000006	-	TSS6	chr1:3188521-3188548	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000007	-	-	XLOC_000007	-	TSS7	chr1:3189810-3190789	-	-	368900	151353	586447	OK	429265	337221	521309	OK
+XLOC_000008	-	-	XLOC_000008	-	TSS11	chr1:3190858-3191434	-	-	404373	101434	707312	OK	338500	95761.5	581239	OK
+XLOC_000009	-	-	XLOC_000009	-	TSS12	chr1:3191512-3192077	-	-	402276	96829.4	707722	OK	686974	410563	963384	OK
+XLOC_000010	-	-	XLOC_000010	-	TSS15	chr1:3192250-3192336	-	-	3.994e+06	0	1.1982e+07	OK	2.93812e+06	0	8.81435e+06	OK
+XLOC_000011	-	-	XLOC_000011	-	TSS16	chr1:3192441-3192494	-	-	0	0	0	OK	5.68095e+07	0	1.3715e+08	OK
+XLOC_000012	-	-	XLOC_000012	-	TSS17	chr1:3192550-3192629	-	-	0	0	0	OK	4.15515e+06	0	1.24654e+07	OK
+XLOC_000013	-	-	XLOC_000013	-	TSS18	chr1:3192649-3192676	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000014	-	-	XLOC_000014	-	TSS19	chr1:3192731-3192811	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000015	-	-	XLOC_000015	-	TSS20	chr1:3192940-3193042	-	-	0	0	0	OK	6.02976e+06	0	1.34147e+07	OK
+XLOC_000016	-	-	XLOC_000016	-	TSS21	chr1:3194185-3194226	-	-	0	0	0	OK	2.1403e+08	0	6.42089e+08	OK
+XLOC_000017	-	-	XLOC_000017	-	TSS22	chr1:3194302-3194329	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000018	-	-	XLOC_000018	-	TSS23	chr1:3194706-3194733	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000019	-	-	XLOC_000019	-	TSS24	chr1:3195083-3195110	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000020	-	-	XLOC_000020	-	TSS25	chr1:3195450-3195477	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000021	-	-	XLOC_000021	-	TSS26	chr1:3197089-3197116	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000022	-	-	XLOC_000022	-	TSS27	chr1:3197246-3197273	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000023	-	-	XLOC_000023	-	TSS28	chr1:3197346-3197373	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000024	-	-	XLOC_000024	-	TSS29	chr1:3197425-3197452	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000025	-	-	XLOC_000025	-	TSS30	chr1:3200022-3200191	-	-	959058	0	2.06648e+06	OK	705514	0	1.52017e+06	OK
+XLOC_000026	-	-	XLOC_000026	-	TSS32	chr1:3200325-3200352	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000027	-	-	XLOC_000027	-	TSS33	chr1:3200430-3200457	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000028	-	-	XLOC_000028	-	TSS34	chr1:3201007-3201039	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000029	-	-	XLOC_000029	-	TSS35	chr1:3201077-3201481	-	-	77513.9	0	167019	OK	285108	21736.5	548480	OK
+XLOC_000030	-	-	XLOC_000030	-	TSS37	chr1:3201596-3201666	-	-	1.89853e+07	0	4.58345e+07	OK	0	0	0	OK
+XLOC_000031	-	-	XLOC_000031	-	TSS38	chr1:3201672-3201699	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000032	-	-	XLOC_000032	-	TSS39	chr1:3201725-3201809	-	-	1.31744e+07	0	2.83869e+07	OK	0	0	0	OK
+XLOC_000033	-	-	XLOC_000033	Xkr4	TSS40	chr1:3211521-3211561	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000034	-	-	XLOC_000034	Xkr4	TSS41	chr1:3212213-3212292	-	-	0	0	0	OK	8.3103e+06	0	2.00628e+07	OK
+XLOC_000035	-	-	XLOC_000035	Xkr4	TSS42	chr1:3212367-3212439	-	-	0	0	0	OK	2.4671e+07	0	5.48867e+07	OK
+XLOC_000036	-	-	XLOC_000036	Xkr4	TSS43	chr1:3212717-3212801	-	-	4.39147e+06	0	1.31744e+07	OK	0	0	0	OK
+XLOC_000037	-	-	XLOC_000037	Xkr4	TSS44,TSS45	chr1:3213095-3213242	-	-	5.3664e+06	0	1.39795e+07	LOWDATA	1.82908e+06	0	5.48723e+06	OK
+XLOC_000038	-	-	XLOC_000038	Xkr4	TSS46	chr1:3240606-3240633	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000039	-	-	XLOC_000039	Xkr4	TSS47	chr1:3242479-3242512	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000040	-	-	XLOC_000040	Xkr4	TSS48	chr1:3242633-3242923	-	-	56312.4	0	168937	OK	372827	0	761430	OK
+XLOC_000041	-	-	XLOC_000041	Xkr4	TSS49	chr1:3242924-3243005	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000042	-	-	XLOC_000042	Xkr4	TSS50	chr1:3243018-3243079	-	-	0	0	0	OK	2.66226e+07	0	6.42725e+07	OK
+XLOC_000043	-	-	XLOC_000043	Xkr4	TSS51	chr1:3243108-3243154	-	-	9.99919e+07	0	2.99976e+08	OK	0	0	0	OK
+XLOC_000044	-	-	XLOC_000044	Xkr4	TSS52	chr1:3243347-3243401	-	-	0	0	0	OK	5.0951e+07	0	1.23007e+08	OK
+XLOC_000045	-	-	XLOC_000045	Xkr4	TSS53	chr1:3254079-3254106	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000046	-	-	XLOC_000046	Xkr4	TSS54	chr1:3256974-3257011	-	-	0	0	0	OK	2.06814e+09	0	4.99293e+09	OK
+XLOC_000047	-	-	XLOC_000047	Xkr4	TSS55	chr1:3277155-3277182	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000048	-	-	XLOC_000048	Xkr4	TSS56	chr1:3277190-3277218	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000049	-	-	XLOC_000049	Xkr4	TSS57	chr1:3277913-3278390	-	-	265614	16793	514436	OK	41870.3	0	90217.9	OK
+XLOC_000050	-	-	XLOC_000050	Xkr4	TSS59	chr1:3280117-3280144	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000051	-	-	XLOC_000051	Xkr4	TSS60	chr1:3280498-3280525	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000052	-	-	XLOC_000052	Xkr4	TSS61	chr1:3280686-3280741	-	-	0	0	0	OK	2.29576e+07	0	6.88728e+07	OK
+XLOC_000053	-	-	XLOC_000053	Xkr4	TSS62	chr1:3282504-3282531	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000054	-	-	XLOC_000054	Xkr4	TSS63	chr1:3282650-3282677	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000055	-	-	XLOC_000055	Xkr4	TSS64	chr1:3282760-3282832	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000056	-	-	XLOC_000056	Xkr4	TSS65	chr1:3284966-3284993	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000057	-	-	XLOC_000057	Xkr4	TSS66	chr1:3290488-3290553	-	-	0	0	0	OK	9.79535e+06	0	2.9386e+07	OK
+XLOC_000058	-	-	XLOC_000058	Xkr4	TSS67	chr1:3290798-3290859	-	-	1.8095e+07	0	5.4285e+07	OK	0	0	0	OK
+XLOC_000059	-	-	XLOC_000059	Xkr4	TSS68	chr1:3290919-3291273	-	-	342218	0	691214	OK	75524	0	162732	OK
+XLOC_000060	-	-	XLOC_000060	Xkr4	TSS70,TSS71	chr1:3299443-3299664	-	-	937403	0	1.99795e+06	OK	137917	0	413751	OK
+XLOC_000061	-	-	XLOC_000061	Xkr4	TSS72	chr1:3299691-3299733	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000062	-	-	XLOC_000062	Xkr4	TSS73	chr1:3300051-3300078	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000063	-	-	XLOC_000063	Xkr4	TSS74	chr1:3307748-3307775	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000064	-	-	XLOC_000064	Xkr4	TSS75	chr1:3318620-3318647	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000065	-	-	XLOC_000065	Xkr4	TSS76	chr1:3318999-3319051	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000066	-	-	XLOC_000066	Xkr4	TSS77	chr1:3330527-3330554	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000067	-	-	XLOC_000067	Xkr4	TSS78	chr1:3351240-3351311	-	-	8.91489e+06	0	2.67447e+07	OK	0	0	0	OK
+XLOC_000068	-	-	XLOC_000068	Xkr4	TSS79,TSS80	chr1:3355887-3356119	-	-	585828	0	1.30332e+06	OK	0	0	0	OK
+XLOC_000069	-	-	XLOC_000069	Xkr4	TSS81	chr1:3356180-3356225	-	-	1.19208e+08	0	3.57623e+08	OK	0	0	0	OK
+XLOC_000070	-	-	XLOC_000070	Xkr4	TSS82	chr1:3363076-3363176	-	-	4.42166e+06	0	1.06748e+07	OK	0	0	0	OK
+XLOC_000071	-	-	XLOC_000071	Xkr4	TSS83	chr1:3363214-3363278	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000072	-	-	XLOC_000072	Xkr4	TSS84	chr1:3363387-3363446	-	-	4.28358e+07	0	1.03415e+08	OK	0	0	0	OK
+XLOC_000073	-	-	XLOC_000073	Xkr4	TSS85	chr1:3363753-3363849	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000074	-	-	XLOC_000074	Xkr4	TSS86	chr1:3364871-3364919	-	-	7.29939e+07	0	2.18982e+08	OK	0	0	0	OK
+XLOC_000075	-	-	XLOC_000075	Xkr4	TSS87	chr1:3367135-3367162	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000076	-	-	XLOC_000076	Xkr4	TSS88	chr1:3367210-3367237	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000077	-	-	XLOC_000077	Xkr4	TSS89	chr1:3367333-3367382	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000078	-	-	XLOC_000078	Xkr4	TSS90	chr1:3369580-3369607	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000079	-	-	XLOC_000079	Xkr4	TSS91	chr1:3375001-3375028	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000080	-	-	XLOC_000080	Xkr4	TSS92	chr1:3377211-3377262	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000081	-	-	XLOC_000081	Xkr4	TSS93	chr1:3379888-3379915	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000082	-	-	XLOC_000082	Xkr4	TSS94	chr1:3386739-3386836	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000083	-	-	XLOC_000083	Xkr4	TSS95	chr1:3391325-3391352	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000084	-	-	XLOC_000084	Xkr4	TSS96	chr1:3435841-3435880	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000085	-	-	XLOC_000085	Xkr4	TSS97	chr1:3447761-3447788	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000086	-	-	XLOC_000086	Xkr4	TSS98	chr1:3450906-3450965	-	-	0	0	0	OK	0	0	0	OK
+XLOC_000087	-	-	XLOC_000087	Xkr4	TSS99	chr1:3451051-3451109	-	-	0	0	0	OK	0	0	0	OK
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffdiff_out7.txt	Fri Nov 08 14:54:01 2013 -0600
@@ -0,0 +1,89 @@
+tracking_id	class_code	nearest_ref_id	gene_id	gene_short_name	tss_id	locus	length	coverage	q1_FPKM	q1_conf_lo	q1_conf_hi	q1_status	q2_FPKM	q2_conf_lo	q2_conf_hi	q2_status
+TSS1	-	-	XLOC_000001	Xkr4	TSS1	chr1:3204754-3204833	-	-	0	0	0	OK	5.42247e+06	0	1.83844e+07	OK
+TSS10	-	-	XLOC_000008	-	TSS10	chr1:3190858-3191434	-	-	227564	0	483427	OK	240951	0	505030	OK
+TSS11	-	-	XLOC_000009	-	TSS11	chr1:3191512-3192077	-	-	241366	0	509259	OK	482731	109420	856042	OK
+TSS13	-	-	XLOC_000010	-	TSS13	chr1:3192250-3192336	-	-	1.91712e+06	0	7.66198e+06	OK	1.91712e+06	0	7.66198e+06	OK
+TSS14	-	-	XLOC_000011	-	TSS14	chr1:3192441-3192494	-	-	0	0	0	OK	5.56023e+07	0	1.86077e+08	OK
+TSS15	-	-	XLOC_000012	-	TSS15	chr1:3192550-3192629	-	-	0	0	0	OK	2.71123e+06	0	1.08357e+07	OK
+TSS16	-	-	XLOC_000013	-	TSS16	chr1:3192649-3192676	-	-	0	0	0	OK	0	0	0	OK
+TSS17	-	-	XLOC_000014	-	TSS17	chr1:3192731-3192811	-	-	0	0	0	OK	0	0	0	OK
+TSS18	-	-	XLOC_000015	-	TSS18	chr1:3192940-3193042	-	-	0	0	0	OK	3.93442e+06	0	1.25021e+07	OK
+TSS19	-	-	XLOC_000016	-	TSS19	chr1:3194185-3194226	-	-	0	0	0	OK	1.39654e+08	0	5.58144e+08	OK
+TSS2	-	-	XLOC_000002	-	TSS2	chr1:3111449-3111490	-	-	0	0	0	OK	1.39654e+08	0	5.58144e+08	OK
+TSS20	-	-	XLOC_000017	-	TSS20	chr1:3194302-3194329	-	-	0	0	0	OK	0	0	0	OK
+TSS21	-	-	XLOC_000018	-	TSS21	chr1:3194706-3194733	-	-	0	0	0	OK	0	0	0	OK
+TSS22	-	-	XLOC_000019	-	TSS22	chr1:3195083-3195110	-	-	0	0	0	OK	0	0	0	OK
+TSS23	-	-	XLOC_000020	-	TSS23	chr1:3195450-3195477	-	-	0	0	0	OK	0	0	0	OK
+TSS24	-	-	XLOC_000021	-	TSS24	chr1:3197089-3197116	-	-	0	0	0	OK	0	0	0	OK
+TSS25	-	-	XLOC_000022	-	TSS25	chr1:3197246-3197273	-	-	0	0	0	OK	0	0	0	OK
+TSS26	-	-	XLOC_000023	-	TSS26	chr1:3197346-3197373	-	-	0	0	0	OK	0	0	0	OK
+TSS27	-	-	XLOC_000024	-	TSS27	chr1:3197425-3197452	-	-	0	0	0	OK	0	0	0	OK
+TSS28	-	-	XLOC_000025	-	TSS28	chr1:3200022-3200191	-	-	460348	0	1.54058e+06	OK	460348	0	1.54058e+06	OK
+TSS29	-	-	XLOC_000026	-	TSS29	chr1:3200325-3200352	-	-	0	0	0	OK	0	0	0	OK
+TSS3	-	-	XLOC_000003	-	TSS3	chr1:3111545-3111576	-	-	0	0	0	OK	0	0	0	OK
+TSS30	-	-	XLOC_000027	-	TSS30	chr1:3200430-3200457	-	-	0	0	0	OK	0	0	0	OK
+TSS31	-	-	XLOC_000028	-	TSS31	chr1:3201007-3201039	-	-	0	0	0	OK	0	0	0	OK
+TSS32	-	-	XLOC_000029	-	TSS32	chr1:3201077-3201481	-	-	37206.6	0	124514	OK	186033	0	476912	OK
+TSS33	-	-	XLOC_000030	-	TSS33	chr1:3201596-3201666	-	-	9.11292e+06	0	3.08965e+07	OK	0	0	0	OK
+TSS34	-	-	XLOC_000031	-	TSS34	chr1:3201672-3201699	-	-	0	0	0	OK	0	0	0	OK
+TSS35	-	-	XLOC_000032	-	TSS35	chr1:3201725-3201809	-	-	8.43162e+06	0	2.67925e+07	OK	0	0	0	OK
+TSS36	-	-	XLOC_000033	Xkr4	TSS36	chr1:3211521-3211561	-	-	0	0	0	OK	0	0	0	OK
+TSS37	-	-	XLOC_000034	Xkr4	TSS37	chr1:3212213-3212292	-	-	0	0	0	OK	5.42247e+06	0	1.83844e+07	OK
+TSS38	-	-	XLOC_000035	Xkr4	TSS38	chr1:3212367-3212439	-	-	0	0	0	OK	1.60978e+07	0	5.11527e+07	OK
+TSS39	-	-	XLOC_000036	Xkr4	TSS39	chr1:3212717-3212801	-	-	2.10791e+06	0	8.42447e+06	OK	0	0	0	OK
+TSS4	-	-	XLOC_000004	-	TSS4	chr1:3174765-3174792	-	-	0	0	0	OK	0	0	0	OK
+TSS40	-	-	XLOC_000037	Xkr4	TSS40	chr1:3213095-3213242	-	-	2.84535e+06	0	1.07397e+07	OK	1.19347e+06	0	5.96736e+06	OK
+TSS41	-	-	XLOC_000038	Xkr4	TSS41	chr1:3240606-3240633	-	-	0	0	0	OK	0	0	0	OK
+TSS42	-	-	XLOC_000039	Xkr4	TSS42	chr1:3242479-3242512	-	-	0	0	0	OK	0	0	0	OK
+TSS43	-	-	XLOC_000040	Xkr4	TSS43	chr1:3242633-3242923	-	-	27029.9	0	108028	OK	243269	0	681799	OK
+TSS44	-	-	XLOC_000041	Xkr4	TSS44	chr1:3242924-3243005	-	-	0	0	0	OK	0	0	0	OK
+TSS45	-	-	XLOC_000042	Xkr4	TSS45	chr1:3243018-3243079	-	-	0	0	0	OK	1.73712e+07	0	5.88955e+07	OK
+TSS46	-	-	XLOC_000043	Xkr4	TSS46	chr1:3243108-3243154	-	-	4.79961e+07	0	1.91822e+08	OK	0	0	0	OK
+TSS47	-	-	XLOC_000044	Xkr4	TSS47	chr1:3243347-3243401	-	-	0	0	0	OK	3.32455e+07	0	1.12716e+08	OK
+TSS48	-	-	XLOC_000045	Xkr4	TSS48	chr1:3254079-3254106	-	-	0	0	0	OK	0	0	0	OK
+TSS49	-	-	XLOC_000046	Xkr4	TSS49	chr1:3256974-3257011	-	-	0	0	0	OK	1.34946e+09	0	4.57522e+09	OK
+TSS5	-	-	XLOC_000005	-	TSS5	chr1:3187401-3187428	-	-	0	0	0	OK	0	0	0	OK
+TSS50	-	-	XLOC_000047	Xkr4	TSS50	chr1:3277155-3277182	-	-	0	0	0	OK	0	0	0	OK
+TSS51	-	-	XLOC_000048	Xkr4	TSS51	chr1:3277190-3277218	-	-	0	0	0	OK	0	0	0	OK
+TSS52	-	-	XLOC_000049	Xkr4	TSS52	chr1:3277913-3278390	-	-	127495	0	331348	OK	27320.3	0	91429.2	OK
+TSS54	-	-	XLOC_000050	Xkr4	TSS54	chr1:3280117-3280144	-	-	0	0	0	OK	0	0	0	OK
+TSS55	-	-	XLOC_000051	Xkr4	TSS55	chr1:3280498-3280525	-	-	0	0	0	OK	0	0	0	OK
+TSS56	-	-	XLOC_000052	Xkr4	TSS56	chr1:3280686-3280741	-	-	0	0	0	OK	1.49798e+07	0	5.98686e+07	OK
+TSS57	-	-	XLOC_000053	Xkr4	TSS57	chr1:3282504-3282531	-	-	0	0	0	OK	0	0	0	OK
+TSS58	-	-	XLOC_000054	Xkr4	TSS58	chr1:3282650-3282677	-	-	0	0	0	OK	0	0	0	OK
+TSS59	-	-	XLOC_000055	Xkr4	TSS59	chr1:3282760-3282832	-	-	0	0	0	OK	0	0	0	OK
+TSS6	-	-	XLOC_000006	-	TSS6	chr1:3188521-3188548	-	-	0	0	0	OK	0	0	0	OK
+TSS60	-	-	XLOC_000056	Xkr4	TSS60	chr1:3284966-3284993	-	-	0	0	0	OK	0	0	0	OK
+TSS61	-	-	XLOC_000057	Xkr4	TSS61	chr1:3290488-3290553	-	-	0	0	0	OK	6.39146e+06	0	2.55442e+07	OK
+TSS62	-	-	XLOC_000058	Xkr4	TSS62	chr1:3290798-3290859	-	-	8.68561e+06	0	3.4713e+07	OK	0	0	0	OK
+TSS63	-	-	XLOC_000059	Xkr4	TSS63	chr1:3290919-3291273	-	-	164265	0	453103	OK	49279.4	0	164917	OK
+TSS65	-	-	XLOC_000060	Xkr4	TSS65	chr1:3299443-3299664	-	-	449954	0	1.56567e+06	OK	89990.7	0	449954	OK
+TSS66	-	-	XLOC_000060	Xkr4	TSS66	chr1:3299443-3299664	-	-	0	0	0	OK	0	0	0	OK
+TSS67	-	-	XLOC_000061	Xkr4	TSS67	chr1:3299691-3299733	-	-	0	0	0	OK	0	0	0	OK
+TSS68	-	-	XLOC_000062	Xkr4	TSS68	chr1:3300051-3300078	-	-	0	0	0	OK	0	0	0	OK
+TSS69	-	-	XLOC_000063	Xkr4	TSS69	chr1:3307748-3307775	-	-	0	0	0	OK	0	0	0	OK
+TSS7	-	-	XLOC_000007	-	TSS7	chr1:3189810-3190789	-	-	199608	33901.5	365315	OK	299412	183619	415206	OK
+TSS70	-	-	XLOC_000064	Xkr4	TSS70	chr1:3318620-3318647	-	-	0	0	0	OK	0	0	0	OK
+TSS71	-	-	XLOC_000065	Xkr4	TSS71	chr1:3318999-3319051	-	-	0	0	0	OK	0	0	0	OK
+TSS72	-	-	XLOC_000066	Xkr4	TSS72	chr1:3330527-3330554	-	-	0	0	0	OK	0	0	0	OK
+TSS73	-	-	XLOC_000067	Xkr4	TSS73	chr1:3351240-3351311	-	-	4.27915e+06	0	1.71021e+07	OK	0	0	0	OK
+TSS74	-	-	XLOC_000068	Xkr4	TSS74	chr1:3355887-3356119	-	-	281197	0	1.06014e+06	OK	0	0	0	OK
+TSS75	-	-	XLOC_000069	Xkr4	TSS75	chr1:3356180-3356225	-	-	5.72196e+07	0	2.28684e+08	OK	0	0	0	OK
+TSS76	-	-	XLOC_000070	Xkr4	TSS76	chr1:3363076-3363176	-	-	2.1224e+06	0	7.19579e+06	OK	0	0	0	OK
+TSS77	-	-	XLOC_000071	Xkr4	TSS77	chr1:3363214-3363278	-	-	0	0	0	OK	0	0	0	OK
+TSS78	-	-	XLOC_000072	Xkr4	TSS78	chr1:3363387-3363446	-	-	3.08417e+07	0	1.03214e+08	OK	0	0	0	OK
+TSS79	-	-	XLOC_000073	Xkr4	TSS79	chr1:3363753-3363849	-	-	0	0	0	OK	0	0	0	OK
+TSS80	-	-	XLOC_000074	Xkr4	TSS80	chr1:3364871-3364919	-	-	3.50371e+07	0	1.40029e+08	OK	0	0	0	OK
+TSS81	-	-	XLOC_000075	Xkr4	TSS81	chr1:3367135-3367162	-	-	0	0	0	OK	0	0	0	OK
+TSS82	-	-	XLOC_000076	Xkr4	TSS82	chr1:3367210-3367237	-	-	0	0	0	OK	0	0	0	OK
+TSS83	-	-	XLOC_000077	Xkr4	TSS83	chr1:3367333-3367382	-	-	0	0	0	OK	0	0	0	OK
+TSS84	-	-	XLOC_000078	Xkr4	TSS84	chr1:3369580-3369607	-	-	0	0	0	OK	0	0	0	OK
+TSS85	-	-	XLOC_000079	Xkr4	TSS85	chr1:3375001-3375028	-	-	0	0	0	OK	0	0	0	OK
+TSS86	-	-	XLOC_000080	Xkr4	TSS86	chr1:3377211-3377262	-	-	0	0	0	OK	0	0	0	OK
+TSS87	-	-	XLOC_000081	Xkr4	TSS87	chr1:3379888-3379915	-	-	0	0	0	OK	0	0	0	OK
+TSS88	-	-	XLOC_000082	Xkr4	TSS88	chr1:3386739-3386836	-	-	0	0	0	OK	0	0	0	OK
+TSS89	-	-	XLOC_000083	Xkr4	TSS89	chr1:3391325-3391352	-	-	0	0	0	OK	0	0	0	OK
+TSS90	-	-	XLOC_000084	Xkr4	TSS90	chr1:3435841-3435880	-	-	0	0	0	OK	0	0	0	OK
+TSS91	-	-	XLOC_000085	Xkr4	TSS91	chr1:3447761-3447788	-	-	0	0	0	OK	0	0	0	OK
+TSS92	-	-	XLOC_000086	Xkr4	TSS92	chr1:3450906-3450965	-	-	0	0	0	OK	0	0	0	OK
+TSS93	-	-	XLOC_000087	Xkr4	TSS93	chr1:3451051-3451109	-	-	0	0	0	OK	0	0	0	OK
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffdiff_out8.txt	Fri Nov 08 14:54:01 2013 -0600
@@ -0,0 +1,1 @@
+tracking_id	class_code	nearest_ref_id	gene_id	gene_short_name	tss_id	locus	length	coverage
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffdiff_out9.txt	Fri Nov 08 14:54:01 2013 -0600
@@ -0,0 +1,89 @@
+test_id	gene_id	gene	locus	sample_1	sample_2	status	value_1	value_2	sqrt(JS)	test_stat	p_value	q_value	significant
+TSS1	XLOC_000001	Xkr4	chr1:3204754-3204833	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS10	XLOC_000008	-	chr1:3190858-3191434	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS11	XLOC_000009	-	chr1:3191512-3192077	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS13	XLOC_000010	-	chr1:3192250-3192336	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS14	XLOC_000011	-	chr1:3192441-3192494	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS15	XLOC_000012	-	chr1:3192550-3192629	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS16	XLOC_000013	-	chr1:3192649-3192676	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS17	XLOC_000014	-	chr1:3192731-3192811	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS18	XLOC_000015	-	chr1:3192940-3193042	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS19	XLOC_000016	-	chr1:3194185-3194226	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS2	XLOC_000002	-	chr1:3111449-3111490	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS20	XLOC_000017	-	chr1:3194302-3194329	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS21	XLOC_000018	-	chr1:3194706-3194733	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS22	XLOC_000019	-	chr1:3195083-3195110	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS23	XLOC_000020	-	chr1:3195450-3195477	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS24	XLOC_000021	-	chr1:3197089-3197116	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS25	XLOC_000022	-	chr1:3197246-3197273	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS26	XLOC_000023	-	chr1:3197346-3197373	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS27	XLOC_000024	-	chr1:3197425-3197452	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS28	XLOC_000025	-	chr1:3200022-3200191	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS29	XLOC_000026	-	chr1:3200325-3200352	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS3	XLOC_000003	-	chr1:3111545-3111576	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS30	XLOC_000027	-	chr1:3200430-3200457	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS31	XLOC_000028	-	chr1:3201007-3201039	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS32	XLOC_000029	-	chr1:3201077-3201481	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS33	XLOC_000030	-	chr1:3201596-3201666	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS34	XLOC_000031	-	chr1:3201672-3201699	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS35	XLOC_000032	-	chr1:3201725-3201809	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS36	XLOC_000033	Xkr4	chr1:3211521-3211561	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS37	XLOC_000034	Xkr4	chr1:3212213-3212292	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS38	XLOC_000035	Xkr4	chr1:3212367-3212439	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS39	XLOC_000036	Xkr4	chr1:3212717-3212801	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS4	XLOC_000004	-	chr1:3174765-3174792	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS40	XLOC_000037	Xkr4	chr1:3213095-3213242	q1	q2	NOTEST	0	0	0.249947	0	0.557805	1	no
+TSS41	XLOC_000038	Xkr4	chr1:3240606-3240633	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS42	XLOC_000039	Xkr4	chr1:3242479-3242512	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS43	XLOC_000040	Xkr4	chr1:3242633-3242923	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS44	XLOC_000041	Xkr4	chr1:3242924-3243005	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS45	XLOC_000042	Xkr4	chr1:3243018-3243079	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS46	XLOC_000043	Xkr4	chr1:3243108-3243154	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS47	XLOC_000044	Xkr4	chr1:3243347-3243401	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS48	XLOC_000045	Xkr4	chr1:3254079-3254106	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS49	XLOC_000046	Xkr4	chr1:3256974-3257011	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS5	XLOC_000005	-	chr1:3187401-3187428	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS50	XLOC_000047	Xkr4	chr1:3277155-3277182	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS51	XLOC_000048	Xkr4	chr1:3277190-3277218	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS52	XLOC_000049	Xkr4	chr1:3277913-3278390	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS54	XLOC_000050	Xkr4	chr1:3280117-3280144	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS55	XLOC_000051	Xkr4	chr1:3280498-3280525	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS56	XLOC_000052	Xkr4	chr1:3280686-3280741	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS57	XLOC_000053	Xkr4	chr1:3282504-3282531	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS58	XLOC_000054	Xkr4	chr1:3282650-3282677	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS59	XLOC_000055	Xkr4	chr1:3282760-3282832	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS6	XLOC_000006	-	chr1:3188521-3188548	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS60	XLOC_000056	Xkr4	chr1:3284966-3284993	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS61	XLOC_000057	Xkr4	chr1:3290488-3290553	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS62	XLOC_000058	Xkr4	chr1:3290798-3290859	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS63	XLOC_000059	Xkr4	chr1:3290919-3291273	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS65	XLOC_000060	Xkr4	chr1:3299443-3299664	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS66	XLOC_000060	Xkr4	chr1:3299443-3299664	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS67	XLOC_000061	Xkr4	chr1:3299691-3299733	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS68	XLOC_000062	Xkr4	chr1:3300051-3300078	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS69	XLOC_000063	Xkr4	chr1:3307748-3307775	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS7	XLOC_000007	-	chr1:3189810-3190789	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS70	XLOC_000064	Xkr4	chr1:3318620-3318647	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS71	XLOC_000065	Xkr4	chr1:3318999-3319051	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS72	XLOC_000066	Xkr4	chr1:3330527-3330554	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS73	XLOC_000067	Xkr4	chr1:3351240-3351311	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS74	XLOC_000068	Xkr4	chr1:3355887-3356119	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS75	XLOC_000069	Xkr4	chr1:3356180-3356225	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS76	XLOC_000070	Xkr4	chr1:3363076-3363176	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS77	XLOC_000071	Xkr4	chr1:3363214-3363278	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS78	XLOC_000072	Xkr4	chr1:3363387-3363446	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS79	XLOC_000073	Xkr4	chr1:3363753-3363849	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS80	XLOC_000074	Xkr4	chr1:3364871-3364919	q1	q2	NOTEST	0	0	0	0	1	1	no
+TSS81	XLOC_000075	Xkr4	chr1:3367135-3367162	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS82	XLOC_000076	Xkr4	chr1:3367210-3367237	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS83	XLOC_000077	Xkr4	chr1:3367333-3367382	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS84	XLOC_000078	Xkr4	chr1:3369580-3369607	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS85	XLOC_000079	Xkr4	chr1:3375001-3375028	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS86	XLOC_000080	Xkr4	chr1:3377211-3377262	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS87	XLOC_000081	Xkr4	chr1:3379888-3379915	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS88	XLOC_000082	Xkr4	chr1:3386739-3386836	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS89	XLOC_000083	Xkr4	chr1:3391325-3391352	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS90	XLOC_000084	Xkr4	chr1:3435841-3435880	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS91	XLOC_000085	Xkr4	chr1:3447761-3447788	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS92	XLOC_000086	Xkr4	chr1:3450906-3450965	q1	q2	LOWDATA	0	0	0	0	0	1	no
+TSS93	XLOC_000087	Xkr4	chr1:3451051-3451109	q1	q2	LOWDATA	0	0	0	0	0	1	no
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/sam_fa_indices.loc.sample	Fri Nov 08 14:54:01 2013 -0600
@@ -0,0 +1,28 @@
+#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 sam_fa_indices.loc file 
+#similar to this one (store it in this directory) that points to 
+#the directories in which those files are stored. The sam_fa_indices.loc 
+#file has this format (white space characters are TAB characters):
+#
+#index	<seq>	<location>
+#
+#So, for example, if you had hg18 indexed stored in 
+#/depot/data2/galaxy/sam/, 
+#then the sam_fa_indices.loc entry would look like this:
+#
+#index	hg18	/depot/data2/galaxy/sam/hg18.fa
+#
+#and your /depot/data2/galaxy/sam/ directory
+#would contain hg18.fa and hg18.fa.fai files:
+#
+#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.fa
+#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg18.fa.fai
+#
+#Your sam_fa_indices.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:
+#
+#index	hg18	/depot/data2/galaxy/sam/hg18.fa
+#index	hg19	/depot/data2/galaxy/sam/hg19.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Nov 08 14:54:01 2013 -0600
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="cufflinks" version="2.1.1">
+        <repository changeset_revision="394b13717223" name="package_cufflinks_2_1_1" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>