# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1383938924 21600
# Node ID 2d7eee38ab5b77e56a628b5ef02a01540a7b0e2d
# Parent  d10befb0867aa94a81dafce4a45792883f5ec697
Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output

diff -r d10befb0867a -r 2d7eee38ab5b README
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Fri Nov 08 13:28:44 2013 -0600
@@ -0,0 +1,20 @@
+CummeRbund is an R package that is designed to aid and simplify the task of analyzing Cufflinks RNA-Seq output.
+( http://compbio.mit.edu/cummeRbund/ )  
+
+
+Prerequisites for installing cumme=Rbund:
+The linux package: libxml2-dev
+In ubuntu:   sudo apt-get install libxml2-dev
+
+R package: ggplot2
+   install.packages("ggplot2",dependencies = TRUE)
+
+To install cummeRbund on your R server, follow the directions in:
+( http://www.bioconductor.org/packages/release/bioc/html/cummeRbund.html )
+   source("http://bioconductor.org/biocLite.R")
+   biocLite("cummeRbund")
+
+This galaxy tool package includes a replacement variation of the cuffdiff wrapper that will generate an output that can be used directly in cummeRbund.
+
+
+
diff -r d10befb0867a -r 2d7eee38ab5b cuffdiff_wrapper.xml
--- a/cuffdiff_wrapper.xml	Wed Jul 17 08:25:52 2013 -0500
+++ b/cuffdiff_wrapper.xml	Fri Nov 08 13:28:44 2013 -0600
@@ -1,80 +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=$min_alignment_count
             --library-norm-method=$library_norm_method
             --dispersion-method=$dispersion_method
 
-            #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
-
-            #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?
@@ -84,57 +34,60 @@
 
             ## 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>
@@ -152,11 +105,6 @@
 
         <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>
@@ -182,142 +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"/>
@@ -329,6 +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>
 
diff -r d10befb0867a -r 2d7eee38ab5b cummerbund_wrapper.py
--- a/cummerbund_wrapper.py	Wed Jul 17 08:25:52 2013 -0500
+++ b/cummerbund_wrapper.py	Fri Nov 08 13:28:44 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__():
diff -r d10befb0867a -r 2d7eee38ab5b cummerbund_wrapper.xml
--- a/cummerbund_wrapper.xml	Wed Jul 17 08:25:52 2013 -0500
+++ b/cummerbund_wrapper.xml	Fri Nov 08 13:28:44 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})
diff -r d10befb0867a -r 2d7eee38ab5b test-data/cuffcompare_out5.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffcompare_out5.gtf	Fri Nov 08 13:28:44 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";
diff -r d10befb0867a -r 2d7eee38ab5b test-data/cuffdiff_in1.sam
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffdiff_in1.sam	Fri Nov 08 13:28:44 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
diff -r d10befb0867a -r 2d7eee38ab5b test-data/cuffdiff_in2.sam
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffdiff_in2.sam	Fri Nov 08 13:28:44 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
diff -r d10befb0867a -r 2d7eee38ab5b test-data/cuffdiff_out1.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffdiff_out1.txt	Fri Nov 08 13:28:44 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
diff -r d10befb0867a -r 2d7eee38ab5b test-data/cuffdiff_out10.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffdiff_out10.txt	Fri Nov 08 13:28:44 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
diff -r d10befb0867a -r 2d7eee38ab5b test-data/cuffdiff_out11.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffdiff_out11.txt	Fri Nov 08 13:28:44 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
diff -r d10befb0867a -r 2d7eee38ab5b test-data/cuffdiff_out2.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffdiff_out2.txt	Fri Nov 08 13:28:44 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
diff -r d10befb0867a -r 2d7eee38ab5b test-data/cuffdiff_out3.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffdiff_out3.txt	Fri Nov 08 13:28:44 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
diff -r d10befb0867a -r 2d7eee38ab5b test-data/cuffdiff_out4.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffdiff_out4.txt	Fri Nov 08 13:28:44 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
diff -r d10befb0867a -r 2d7eee38ab5b test-data/cuffdiff_out5.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffdiff_out5.txt	Fri Nov 08 13:28:44 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
diff -r d10befb0867a -r 2d7eee38ab5b test-data/cuffdiff_out6.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffdiff_out6.txt	Fri Nov 08 13:28:44 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
diff -r d10befb0867a -r 2d7eee38ab5b test-data/cuffdiff_out7.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffdiff_out7.txt	Fri Nov 08 13:28:44 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
diff -r d10befb0867a -r 2d7eee38ab5b test-data/cuffdiff_out8.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffdiff_out8.txt	Fri Nov 08 13:28:44 2013 -0600
@@ -0,0 +1,1 @@
+tracking_id	class_code	nearest_ref_id	gene_id	gene_short_name	tss_id	locus	length	coverage
diff -r d10befb0867a -r 2d7eee38ab5b test-data/cuffdiff_out9.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cuffdiff_out9.txt	Fri Nov 08 13:28:44 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
diff -r d10befb0867a -r 2d7eee38ab5b tool-data/sam_fa_indices.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/sam_fa_indices.loc.sample	Fri Nov 08 13:28:44 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
diff -r d10befb0867a -r 2d7eee38ab5b tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Nov 08 13:28:44 2013 -0600
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="cufflinks" version="2.1.1">
+        <repository changeset_revision="1b08f4e80509" name="package_cufflinks_2_1_1" owner="devteam" toolshed="http://http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>