changeset 1:acaa8e8a0b88 draft default tip

Uploaded test-data & added tool help
author chmaramis
date Mon, 30 Apr 2018 04:47:52 -0400
parents 0e37e5b73273
children
files README.rst clonotype_computation.xml data_filtering.xml exclusive_clonotype_computation.xml gene_comparison.xml gene_computation.xml public_clonotype_computation.xml test-data/README.html test-data/clono_compute_def1_BCR_input1.csv test-data/clono_compute_def1_BCR_output1.csv test-data/clono_compute_def1_BCR_output2.csv test-data/clono_compute_def1_BCR_output3.csv test-data/clono_compute_def1_TCR_input1.csv test-data/clono_compute_def1_TCR_output1.csv test-data/clono_compute_def1_TCR_output2.csv test-data/clono_compute_def1_TCR_output3.csv test-data/clono_compute_def2_BCR_input1.csv test-data/clono_compute_def2_BCR_output1.csv test-data/clono_compute_def2_BCR_output2.csv test-data/clono_compute_def2_BCR_output3.csv test-data/clono_compute_def2_TCR_input1.csv test-data/clono_compute_def2_TCR_output1.csv test-data/clono_compute_def2_TCR_output2.csv test-data/clono_compute_def2_TCR_output3.csv test-data/clono_compute_def3_BCR_input1.csv test-data/clono_compute_def3_BCR_output1.csv test-data/clono_compute_def3_BCR_output2.csv test-data/clono_compute_def3_BCR_output3.csv test-data/clono_compute_def3_TCR_input1.csv test-data/clono_compute_def3_TCR_output1.csv test-data/clono_compute_def3_TCR_output2.csv test-data/clono_compute_def3_TCR_output3.csv test-data/clono_compute_def4_BCR_input1.csv test-data/clono_compute_def4_BCR_output1.csv test-data/clono_compute_def4_BCR_output2.csv test-data/clono_compute_def4_BCR_output3.csv test-data/clono_compute_def4_TCR_input1.csv test-data/clono_compute_def4_TCR_output1.csv test-data/clono_compute_def4_TCR_output2.csv test-data/clono_compute_def4_TCR_output3.csv test-data/clono_compute_def5_BCR_input1.csv test-data/clono_compute_def5_BCR_output1.csv test-data/clono_compute_def5_BCR_output2.csv test-data/clono_compute_def5_BCR_output3.csv test-data/clono_compute_def5_TCR_input1.csv test-data/clono_compute_def5_TCR_output1.csv test-data/clono_compute_def5_TCR_output2.csv test-data/clono_compute_def5_TCR_output3.csv test-data/data_filter_BCR_input1.csv test-data/data_filter_BCR_output1.csv test-data/data_filter_BCR_output2.csv test-data/data_filter_BCR_output3.csv test-data/data_filter_BCR_parameters.txt test-data/data_filter_TCR_input1.csv test-data/data_filter_TCR_output1.csv test-data/data_filter_TCR_output2.csv test-data/data_filter_TCR_output3.csv test-data/data_filter_TCR_parameters.txt test-data/exclusive_clonos_def1_BCR_input1.csv test-data/exclusive_clonos_def1_BCR_input2.csv test-data/exclusive_clonos_def1_BCR_output1.csv test-data/exclusive_clonos_def1_BCR_parameters.txt test-data/exclusive_clonos_def1_TCR_input1.csv test-data/exclusive_clonos_def1_TCR_input2.csv test-data/exclusive_clonos_def1_TCR_output1.csv test-data/exclusive_clonos_def1_TCR_parameters.txt test-data/exclusive_clonos_def2_BCR_input1.csv test-data/exclusive_clonos_def2_BCR_input2.csv test-data/exclusive_clonos_def2_BCR_output1.csv test-data/exclusive_clonos_def2_BCR_parameters.txt test-data/exclusive_clonos_def2_TCR_input1.csv test-data/exclusive_clonos_def2_TCR_input2.csv test-data/exclusive_clonos_def2_TCR_output1.csv test-data/exclusive_clonos_def2_TCR_parameters.txt test-data/exclusive_clonos_def3_BCR_input1.csv test-data/exclusive_clonos_def3_BCR_input2.csv test-data/exclusive_clonos_def3_BCR_output1.csv test-data/exclusive_clonos_def3_BCR_parameters.txt test-data/exclusive_clonos_def3_TCR_input1.csv test-data/exclusive_clonos_def3_TCR_input2.csv test-data/exclusive_clonos_def3_TCR_output1.csv test-data/exclusive_clonos_def3_TCR_parameters.txt test-data/gene_compare_geneJ_BCR_input1.csv test-data/gene_compare_geneJ_BCR_input2.csv test-data/gene_compare_geneJ_BCR_output1.csv test-data/gene_compare_geneJ_TCR_input1.csv test-data/gene_compare_geneJ_TCR_input2.csv test-data/gene_compare_geneJ_TCR_output1.csv test-data/gene_compare_geneV_BCR_input1.csv test-data/gene_compare_geneV_BCR_input2.csv test-data/gene_compare_geneV_BCR_output1.csv test-data/gene_compare_geneV_TCR_input1.csv test-data/gene_compare_geneV_TCR_input2.csv test-data/gene_compare_geneV_TCR_output1.csv test-data/gene_usage_geneJ_BCR_input1.csv test-data/gene_usage_geneJ_BCR_output1.csv test-data/gene_usage_geneJ_BCR_output2.csv test-data/gene_usage_geneJ_BCR_output3.csv test-data/gene_usage_geneJ_TCR_input1.csv test-data/gene_usage_geneJ_TCR_output1.csv test-data/gene_usage_geneJ_TCR_output2.csv test-data/gene_usage_geneJ_TCR_output3.csv test-data/gene_usage_geneV_BCR_input1.csv test-data/gene_usage_geneV_BCR_output1.csv test-data/gene_usage_geneV_BCR_output2.csv test-data/gene_usage_geneV_BCR_output3.csv test-data/gene_usage_geneV_TCR_input1.csv test-data/gene_usage_geneV_TCR_output1.csv test-data/gene_usage_geneV_TCR_output2.csv test-data/gene_usage_geneV_TCR_output3.csv test-data/public_clonos_def1_BCR_input1.csv test-data/public_clonos_def1_BCR_input2.csv test-data/public_clonos_def1_BCR_output1.csv test-data/public_clonos_def1_BCR_parameters.txt test-data/public_clonos_def1_TCR_input1.csv test-data/public_clonos_def1_TCR_input2.csv test-data/public_clonos_def1_TCR_output1.csv test-data/public_clonos_def1_TCR_parameters.txt test-data/public_clonos_def2_BCR_input1.csv test-data/public_clonos_def2_BCR_input2.csv test-data/public_clonos_def2_BCR_output1.csv test-data/public_clonos_def2_BCR_parameters.txt test-data/public_clonos_def2_TCR_input1.csv test-data/public_clonos_def2_TCR_input2.csv test-data/public_clonos_def2_TCR_output1.csv test-data/public_clonos_def2_TCR_parameters.txt test-data/public_clonos_def3_BCR_input1.csv test-data/public_clonos_def3_BCR_input2.csv test-data/public_clonos_def3_BCR_output1.csv test-data/public_clonos_def3_BCR_parameters.txt test-data/public_clonos_def3_TCR_input1.csv test-data/public_clonos_def3_TCR_input2.csv test-data/public_clonos_def3_TCR_output1.csv test-data/public_clonos_def3_TCR_parameters.txt
diffstat 134 files changed, 1688 insertions(+), 18 deletions(-) [+]
line wrap: on
line diff
--- a/README.rst	Fri Mar 30 07:22:29 2018 -0400
+++ b/README.rst	Mon Apr 30 04:47:52 2018 -0400
@@ -1,7 +1,7 @@
 About
 -----
 
-IRProfiler is a Galaxy toolbox for immunogenetic repertoire profiling. It is made available as supplementary material for the article *IRProfiler - A Software Toolbox for High Throughput Immune Receptor Profiling*, authored by C. Maramis et al. and submitted for possible publication to `BMC Bioinformatics <https://bmcbioinformatics.biomedcentral.com>`_.
+IRProfiler is a Galaxy toolbox for immunogenetic repertoire profiling. It is made available as supplementary material for the article *IRProfiler - A Software Toolbox for High Throughput Immune Receptor Profiling*, authored by C. Maramis et al. and published in `BMC Bioinformatics <https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2144-z>`_.
 
 Tools
 -----
--- a/clonotype_computation.xml	Fri Mar 30 07:22:29 2018 -0400
+++ b/clonotype_computation.xml	Mon Apr 30 04:47:52 2018 -0400
@@ -1,8 +1,8 @@
-<tool id="clonoComput" name="Clonotype Diversity &amp; Expression" version="0.9">
+<tool id="clonoComput" name="Clonotype Diversity &amp; Expression" version="1.0">
     <description>Compute clonotype diversity and expression from filtered file</description>
     <requirements>
       <requirement type="package" version="0.19">pandas</requirement>
-    </requirements>
+		</requirements>
     <command interpreter="python">clonotype_computation.py $input $clonotype $clonos_file $top10_file $summary_file ${input.name}</command>
     <inputs>
         <param name="clonotype" type="select" label="Clonotype definition">
@@ -20,6 +20,6 @@
         <data name="summary_file" format="tabular" label="${input.name}_clonotypesSummary" />
     </outputs>
     <help>
-Coming soon
+This tool calculates the clonotype diversity and expression of a filtered-in dataset (1st output file of the Data Filtering tool) according to the 5 supported clonotype definitions.
   </help>
 </tool>
--- a/data_filtering.xml	Fri Mar 30 07:22:29 2018 -0400
+++ b/data_filtering.xml	Mon Apr 30 04:47:52 2018 -0400
@@ -1,8 +1,8 @@
-<tool id="dataFilter" name="Data Filtering" version="0.9">
+<tool id="dataFilter" name="Data Filtering" version="1.0">
     <description>Filter IMGT Summary dataset</description>
     <requirements>
       <requirement type="package" version="0.19">pandas</requirement>
-    </requirements>
+		</requirements>
     <command interpreter="python">data_filtering.py $input $TCR_or_BCR $Vfun $spChar $prod $delCF $threshold $Vg.Vgid $clen.cdr3len1 $cdp.cdr3part $filterin_file $filterout_file $summary_file $Jg.Jgid $Dg.Dgid $clen.cdr3len2 $process_id
   </command>
     <inputs>
--- a/exclusive_clonotype_computation.xml	Fri Mar 30 07:22:29 2018 -0400
+++ b/exclusive_clonotype_computation.xml	Mon Apr 30 04:47:52 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="exclClonoComput" name="Exclusive Clonotypes" version="0.9">
+<tool id="exclClonoComput" name="Exclusive Clonotypes" version="1.0">
 <description>Compute exclusive clonotypes between 2 repertoires</description>
 <requirements>
       <requirement type="package" version="0.19">pandas</requirement>
@@ -13,13 +13,13 @@
         </param>
 	<conditional name="Th">
 	
-		<param name="thres_select" type="select" label="Remove CDR3 With Reads Fewer Than Threshold?">
+		<param name="thres_select" type="select" label="Remove Clonotypes With Reads Fewer Than Threshold?">
 			<option value="y">Yes</option>
 			<option value="n" selected="true">No</option>
 		</param>
 	
 		<when value="y">
-			<param name="thres" type="integer" size="4" value="1" min="1"  label="Keep CDR3 with Number of Reads more than"/>
+			<param name="thres" type="integer" size="4" value="1" min="1"  label="Keep Clonotypes with Number of Reads more than"/>
 		</when>
 	
 		<when value="n">
@@ -35,6 +35,6 @@
 <data format="tabular" name="output_file" label="exclusiveClonotypes"/>
 </outputs>
 <help>
-Coming soon
+This tool extracts the exclusive (i.e., found in the 1st dataset but not in the 2nd) clonotypes between 2 clonotype repertoires (1st output of the Clonotype Diversity &amp; Expression tool) according to 3 of the 5 supported clonotype definitions.
 </help>
 </tool>
--- a/gene_comparison.xml	Fri Mar 30 07:22:29 2018 -0400
+++ b/gene_comparison.xml	Mon Apr 30 04:47:52 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="geneCompar" name="Gene Usage Comparison" version="0.9">
+<tool id="geneCompar" name="Gene Usage Comparison" version="1.0">
 <description>Compare gene usages from multiple repertoires</description>
 <requirements>
       <requirement type="package" version="0.19">pandas</requirement>
@@ -18,6 +18,6 @@
 <data format="tabular" name="output_file" label="geneUsageComparison"/>
 </outputs>
 <help>
-Coming soon
+This tool compares the usage of each gene of the V or J family in 2 or more clonotype repertoires; uses the 1st output of the Gene Usage tool.
 </help>
 </tool>
--- a/gene_computation.xml	Fri Mar 30 07:22:29 2018 -0400
+++ b/gene_computation.xml	Mon Apr 30 04:47:52 2018 -0400
@@ -1,8 +1,8 @@
-<tool id="geneComput" name="Gene Usage" version="0.9">
+<tool id="geneComput" name="Gene Usage" version="1.0">
     <description>Compute gene usage from clonotype file</description>
     <requirements>
       <requirement type="package" version="0.19">pandas</requirement>
-    </requirements>
+		</requirements>
     <command interpreter="python">gene_computation.py $input $gene $usage_file $top10_file $summary_file ${input.name}</command>
     <inputs>
         <param name="gene" type="select" label="Gene family">
@@ -17,6 +17,6 @@
         <data name="summary_file" format="tabular" label="${input.name}_geneUsageSummary" />
     </outputs>
     <help>
-Coming soon
+This tool caclulates the usage of each gene of the V or J family in a clonotype repertoire (1st output of the Clonotype Diversity &amp; Expression tool). 
   </help>
 </tool>
--- a/public_clonotype_computation.xml	Fri Mar 30 07:22:29 2018 -0400
+++ b/public_clonotype_computation.xml	Mon Apr 30 04:47:52 2018 -0400
@@ -1,8 +1,8 @@
-<tool id="pubClonoComput" name="Public Clonotypes" version="0.9">
+<tool id="pubClonoComput" name="Public Clonotypes" version="1.0">
     <description>Compute public clonotypes from multiple repertoires</description>
     <requirements>
       <requirement type="package" version="0.19">pandas</requirement>
-    </requirements>
+		</requirements>
     <command interpreter="python">public_clonotype_computation.py "$clonotype" "$output_file" "$Th.thres"
 #for x in $clono_files
   "$x.clfile"
@@ -35,6 +35,6 @@
         <data format="tabular" name="output_file" label="publicClonotypes" />
     </outputs>
     <help>
-Coming soon
+This tool extracts the public (i.e., shared in at least two datasets) clonotypes between 2 or more clonotype repertoires (1st output of the Clonotype Diversity &amp; Expression tool) according to 3 of the 5 supported clonotype definitions.
 </help>
 </tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/README.html	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,93 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="utf-8">
+    <!--<link rel="stylesheet" href="style/base.css" type="text/css" />-->
+</head>
+<body style="margin-left: 1cm">
+<div class="jumbotron">
+<div class="container">
+<h3>Test Data Name Conventions</h3>
+<p>Concerning the naming of the execution parameters, input and output files, the following convention applies: </p>
+<ul>
+<li class="container">The name starts with the tool specifier; see Tool Specifiers Table below.</li>
+<li class="container">The clonotype definition specifier follows, if needed; see Clonotype Definition Specifiers Table below.</li>
+<li class="container">The gene specifier (geneV or geneJ) follows, if needed.</li>
+<li class="container">The cell type specifier (BCR or TCR) follows.</li>
+<li class="container">The name ends with the file content specifier (input, output or parameters).</li>
+</ul>
+
+<p><i>Tool Specifiers Table</i></p>
+<table style="border-spacing: 10px 0px">
+<tr align="left">
+<th>Index</th>
+<th>Tool</th>
+<th>Specifier</th>
+</tr>
+<tr>
+<td>1</td>
+<td>Data Filtering</td>
+<td>data_filter</td>
+</tr>
+<tr>
+<td>2</td>
+<td>Clonotype Diversity &amp; Expression</td>
+<td>clono_compute</td>
+</tr>
+<tr>
+<td>3</td>
+<td>Gene Usage</td>
+<td>gene_usage</td>
+</tr>
+<tr>
+<td>4</td>
+<td>Public Clonotypes</td>
+<td>public_clonos</td>
+</tr>
+<tr>
+<td>5</td>
+<td>Exclusive Clonotypes</td>
+<td>exclusive_clonos</td>
+</tr>
+<tr>
+<td>6</td>
+<td>Gene Usage Comparison</td>
+<td>gene_compare</td>
+</tr>
+</table>
+
+<br>
+
+<p><i>Clonotype Definition Specifiers Table</i></p>
+<table style="border-spacing: 10px 0px">
+<tr align="left">
+<th>Index</th>
+<th>Clonotype Definition</th>
+<th>Specifier</th>
+</tr>
+<tr>
+<td>1</td>
+<td>CDR3</td>
+<td>def1</td>
+</tr>
+<tr>
+<td>2</td>
+<td>V+CDR3</td>
+<td>def2</td>
+</tr>
+<tr>
+<td>3</td>
+<td>J+CDR3</td>
+<td>def3</td>
+</tr>
+<tr>
+<td>4</td>
+<td>V+J+CDR3</td>
+<td>def4</td>
+</tr>
+<tr>
+<td>5</td>
+<td>V+D+J+CDR3</td>
+<td>def5</td>
+</tr>
+</table>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def1_BCR_input1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	Sequence ID	Functionality	V-GENE	V-REGION score	V-REGION identity %	V-REGION identity nt	V-REGION identity % (with ins/del events)	V-REGION identity nt (with ins/del events)	J-GENE	J-REGION score	J-REGION identity %	J-REGION identity nt	D-GENE	D-REGION reading frame	CDR1-IMGT length	CDR2-IMGT length	CDR3-IMGT length	CDR-IMGT lengths	FR-IMGT lengths	AA JUNCTION	JUNCTION frame	Orientation	Functionality comment	V-REGION potential ins/del	J-GENE and allele comment	V-REGION insertions	V-REGION deletions	Sequence
+1	lcl|FLN1FA001B9SVM.1|	productive	IGHV1-69 or IGHV1-69D	790	100	159/159 nt			IGHJ4	186	87.5	42/48 nt	IGHD2-15	2	X	8	16	X.8.16	[X.7.38.11]	CYLGYCSGGSCYPQVGYW	in-frame	+						gggcttgagtggatgggagggatcatccctatctttggtacagcaaactacgcacagaagttccagggcagagtcacgattaccgcggacgaatccacgagcacagcctacatggagctgagcagcctgagatctgaggacacggccgtgtattactgttatttaggatattgtagtggtggtagctgctaccctcaggttggctactggggccagggaaccctggtcaccgtctcctcag
+2	lcl|FLN1FA001CUVDF.1|	productive	IGHV3-30 or IGHV3-30-3	786	99.38	159/160 nt			IGHJ4	231	97.92	47/48 nt	IGHD2-15	2	X	8	13	X.8.13	[X.7.38.11]	CVTYCSGGSCYFDYW	in-frame	+						ggggctggagtgggtggcagttatatcatatgatggaagtaataaatactacgtagactccgtgaagggccgattcaccatctccagagacaattccaagaacacgctgtatctgcaaatgaacagcctgagagctgaggacacggctgtgtattactgtgttacatattgtagtggtggtagctgctactttgactactggggccagggaaccctggtcaccgtctcctcag
+3	lcl|FLN1FA001DLPHD.1|	productive	IGHV1-3	775	100	156/156 nt			IGHJ4	186	87.5	42/48 nt	IGHD3-16	2	X	8	9	X.8.9	[X.6.38.11]	CYISGSYVGYW	in-frame	+						cttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttacatttcggggagttatgtaggctactggggccagggaaccctggtcaccgtctcctcag
+4	lcl|FLN1FA002QTWMQ.1|	productive	IGHV4-39	775	100	156/156 nt			IGHJ4	195	89.58	43/48 nt	IGHD3-10	3	X	7	11	X.7.11	[X.7.38.11]	CYSAVVRGRFDYW	in-frame	+						gggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag
+5	lcl|FLN1FA002Q975Z.1|	productive	IGHV3-53	771	99.36	156/157 nt			IGHJ4	168	83.33	40/48 nt	IGHD2-21	3	X	7	10	X.7.10	[X.7.38.11]	CVVVTATPHGYW	in-frame	+						ggggctggagtgggtctcagttatttatagcggtggtagcacatactacgcagactccgtgaagggccgattcaccatctccagagacaattccaaggacacgctgtatcttcaaatgaacagcctgagagccgaggacacggccgtgtattactgtgtggtggtgactgctactccccatgggtactggggccagggaaccctggtcaccgtctcctcag
+6	lcl|FLN1FA001AX4MF.1|	productive	IGHV4-39	770	100	155/155 nt			IGHJ4	222	95.83	46/48 nt	IGHD3-22	2	X	7	15	X.7.15	[X.6.38.11]	CVVNYYDSSGYYYIDYW	in-frame	+						ggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgtgtggtaaattactatgatagtagtggttattactacatagactactggggccagggaaccctggtcaccgtctcctcag
+7	lcl|FLN1FA0074PUDE.1|	productive	IGHV4-39	770	100	155/155 nt			IGHJ4	222	95.83	46/48 nt	IGHD3-22	2	X	7	15	X.7.15	[X.6.38.11]	CVVNYYDSSGYYYIDYW	in-frame	+						ggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgtgtggtaaattactatgatagtagtggttattactacatagactactggggccagggaaccctggtcaccgtctcctcag
+8	lcl|FLN1FA0013V4SA.1|	productive	IGHV1-3	790	100	159/159 nt			IGHJ4	186	87.5	42/48 nt	IGHD2-15	2	X	8	16	X.8.16	[X.7.38.11]	CYLGYCSGGSCYPQVGYW	in-frame	+						aggcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttatttaggatattgtagtggtggtagctgctaccctcaggttggctactggggccagggaaccctggtcaccgtctcctcag
+9	lcl|FLN1FA00056KW6.1|	productive	IGHV1-3	775	100	156/156 nt			IGHJ4	186	87.5	42/48 nt	IGHD3-16	2	X	8	9	X.8.9	[X.6.38.11]	CYISGSYVGYW	in-frame	+						cttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttacatttcggggagttatgtaggctactggggccagggaaccctggtcaccgtctcctcag
+10	lcl|FLN1FA006WKNJR.1|	productive	IGHV3-53	771	99.36	156/157 nt			IGHJ4	168	83.33	40/48 nt	IGHD2-21	3	X	7	10	X.7.10	[X.7.38.11]	CVVVTATPHGYW	in-frame	+						ggggctggagtgggtctcagttatttatagcggtggtagcacatactacgcagactccgtgaagggccgattcaccatctccagagacaattccaaggacacgctgtatcttcaaatgaacagcctgagagccgaggacacggccgtgtattactgtgtggtggtgactgctactccccatgggtactggggccagggaaccctggtcaccgtctcctcag
+11	lcl|FLN1FA008ANOPH.1|	productive	IGHV4-39	775	100	156/156 nt			IGHJ4	195	89.58	43/48 nt	IGHD3-10	3	X	7	11	X.7.11	[X.7.38.11]	CYSAVVRGRFDYW	in-frame	+						gggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag
+12	lcl|FLN1FA005T7JJ8.1|	productive	IGHV3-33	795	100	160/160 nt			IGHJ4	222	95.83	46/48 nt	IGHD3-22	2	X	8	15	X.8.15	[X.7.38.11]	CVTYYYDSSGYPYFDYW	in-frame	+						ggggctggagtgggtggcagttatatggtatgatggaagtaataaatactatgcagactccgtgaagggccgattcaccatctccagagacaattccaagaacacgctgtatctgcaaatgaacagcctgagagccgaggacacggctgtgtattactgtgtaacgtattactatgatagtagtggttatccttactttgactactggggccagggaaccctggtcaccgtctcctcag
+13	lcl|FLN1FA0018WER7.1|	productive	IGHV4-39	770	100	155/155 nt			IGHJ4	222	95.83	46/48 nt	IGHD3-22	2	X	7	15	X.7.15	[X.6.38.11]	CVVNYYDSSGYYYIDYW	in-frame	+						ggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgtgtggtaaattactatgatagtagtggttattactacatagactactggggccagggaaccctggtcaccgtctcctcag
+14	lcl|FLN1FA004BRKX9.1|	productive	IGHV1-3	775	100	156/156 nt			IGHJ4	186	87.5	42/48 nt	IGHD3-16	2	X	8	9	X.8.9	[X.6.38.11]	CYISGSYVGYW	in-frame	+						cttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttacatttcggggagttatgtaggctactggggccagggaaccctggtcaccgtctcctcag
+15	lcl|FLN1FA00826HO1.1|	productive	IGHV4-39	775	100	156/156 nt			IGHJ4	195	89.58	43/48 nt	IGHD3-10	3	X	7	11	X.7.11	[X.7.38.11]	CYSAVVRGRFDYW	in-frame	+						gggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag
+16	lcl|FLN1FA0041SQ1V.1|	productive	IGHV3-53	771	99.36	156/157 nt			IGHJ4	168	83.33	40/48 nt	IGHD2-21	3	X	7	10	X.7.10	[X.7.38.11]	CVVVTATPHGYW	in-frame	+						ggggctggagtgggtctcagttatttatagcggtggtagcacatactacgcagactccgtgaagggccgattcaccatctccagagacaattccaaggacacgctgtatcttcaaatgaacagcctgagagccgaggacacggccgtgtattactgtgtggtggtgactgctactccccatgggtactggggccagggaaccctggtcaccgtctcctcag
+17	lcl|FLN1FA000BBO91.1|	productive	IGHV3-33	795	100	160/160 nt			IGHJ4	222	95.83	46/48 nt	IGHD3-22	2	X	8	15	X.8.15	[X.7.38.11]	CVTYYYDSSGYPYFDYW	in-frame	+						ggggctggagtgggtggcagttatatggtatgatggaagtaataaatactatgcagactccgtgaagggccgattcaccatctccagagacaattccaagaacacgctgtatctgcaaatgaacagcctgagagccgaggacacggctgtgtattactgtgtaacgtattactatgatagtagtggttatccttactttgactactggggccagggaaccctggtcaccgtctcctcag
+18	lcl|FLN1FA008W37HH.1|	productive	IGHV4-39	775	100	156/156 nt			IGHJ4	195	89.58	43/48 nt	IGHD3-10	3	X	7	11	X.7.11	[X.7.38.11]	CYSAVVRGRFDYW	in-frame	+						gggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag
+19	lcl|FLN1FA0080EWJB.1|	productive	IGHV1-3	775	100	156/156 nt			IGHJ4	186	87.5	42/48 nt	IGHD3-16	2	X	8	9	X.8.9	[X.6.38.11]	CYISGSYVGYW	in-frame	+						cttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttacatttcggggagttatgtaggctactggggccagggaaccctggtcaccgtctcctcag
+20	lcl|FLN1FA003C09AP.1|	productive	IGHV1-3	790	100	159/159 nt			IGHJ4	186	87.5	42/48 nt	IGHD2-15	2	X	8	16	X.8.16	[X.7.38.11]	CYLGYCSGGSCYPQVGYW	in-frame	+						aggcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttatttaggatattgtagtggtggtagctgctaccctcaggttggctactggggccagggaaccctggtcaccgtctcctcag
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def1_BCR_output1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,8 @@
+	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	CYISGSYVGYW	4	4/20	20.0000
+2	CYSAVVRGRFDYW	4	4/20	20.0000
+3	CVVNYYDSSGYYYIDYW	3	3/20	15.0000
+4	CVVVTATPHGYW	3	3/20	15.0000
+5	CYLGYCSGGSCYPQVGYW	3	3/20	15.0000
+6	CVTYYYDSSGYPYFDYW	2	2/20	10.0000
+7	CVTYCSGGSCYFDYW	1	1/20	5.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def1_BCR_output2.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,8 @@
+	AA JUNCTION	Frequency %
+1	CYISGSYVGYW	20.0000
+2	CYSAVVRGRFDYW	20.0000
+3	CVVNYYDSSGYYYIDYW	15.0000
+4	CVVVTATPHGYW	15.0000
+5	CYLGYCSGGSCYPQVGYW	15.0000
+6	CVTYYYDSSGYPYFDYW	10.0000
+7	CVTYCSGGSCYFDYW	5.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def1_BCR_output3.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,6 @@
+	input	%
+Dominant CDR3	CYISGSYVGYW	
+Frequency	20.0000	
+Number of unique CDR3	7	
+Num of unique CDR3 > 1	6	85.7143
+Num of unique CDR3 = 1	1	14.2857
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def1_TCR_input1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	Sequence ID	Functionality	V-GENE	V-REGION score	V-REGION identity %	V-REGION identity nt	V-REGION identity % (with ins/del events)	V-REGION identity nt (with ins/del events)	J-GENE	J-REGION score	J-REGION identity %	J-REGION identity nt	D-GENE	D-REGION reading frame	CDR1-IMGT length	CDR2-IMGT length	CDR3-IMGT length	CDR-IMGT lengths	FR-IMGT lengths	AA JUNCTION	JUNCTION frame	Orientation	Functionality comment	V-REGION potential ins/del	J-GENE and allele comment	V-REGION insertions	V-REGION deletions	Sequence
+1	@SRR060727.12120 SOLEXA7:7:2:351:1247 length=202	productive	TRBV28	145	100	30/30 nt			TRBJ2-7	235	100	47/47 nt	TRBD1	3	X	X	12	X.X.12	[X.X.10.10]	CAAGGQGNSYEQYF	in-frame	+						agcaccaaccagacatctatgtacctctgtgccgctggggggcagggaaactcctacgagcagtacttcgggccgggcaccaggctcacggtcacagaggataacgggtgggaacacgtttttcaggtcctctgtgaccgtgagcctggtgcccggcccgaagtactgctcgtaggagtttccctgccccccagcggcacag
+2	@SRR060727.14069 SOLEXA7:7:2:622:201 length=202	productive	TRBV30	95	100	20/20 nt			TRBJ1-1	195	89.58	43/48 nt	TRBD2	3	X	X	10	X.X.10	[X.X.6.10]	CAAEGILAEAFF	in-frame	+						actctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaacaaggtgttctaacgggtgggnacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag
+3	@SRR060727.45221 SOLEXA7:7:5:1541:638 length=202	productive	TRBV30	145	100	30/30 nt			TRBJ1-1	195	89.58	43/48 nt	TRBD2	3	X	X	10	X.X.10	[X.X.10.10]	CAAEGILAEAFF	in-frame	+						cttctcagtgactctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaataacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag
+4	@SRR060727.49324 SOLEXA7:7:6:384:121 length=202	productive	TRBV10-3	165	100	34/34 nt			TRBJ1-1	240	100	48/48 nt	TRBD1	2	X	X	11	X.X.11	[X.X.11.10]	CAACEGLNTEAFF	in-frame	+						cgctaccagctcccagacatctgtgtacttctgtgccgcatgtgaggggctgaacactgaagctttctttggacaaggcaccagactcacagttgtagaggtaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgttcagcccctcacatgcggcacagaag
+5	@SRR060727.85642 SOLEXA7:7:10:98:1840 length=202	productive	TRBV30	115	100	24/24 nt			TRBJ1-1	195	89.58	43/48 nt	TRBD2	3	X	X	10	X.X.10	[X.X.8.10]	CAAEGILAEAFF	in-frame	+						agtgactctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagcggacctgaacaagggtaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag
+6	@SRR060727.100243 SOLEXA7:7:11:766:821 length=202	productive	TRBV15	105	100	22/22 nt			TRBJ1-1	222	95.83	46/48 nt	TRBD1	1	X	X	11	X.X.11	[X.X.7.10]	CAAGGKRYTEAFF	in-frame	-						ggacgcagccatgtacctgtgtgccgcaggggggaaacggtacactgaagctttctttggacaaggcaccagactcacagttgtagaggacctggacaaggtacaactgtgagtctggtgccttgtccaaagaaagcttcagtgtaccgtttcccccctgcggcacacaggtacatggctgcgtcccccaggcctggtgagc
+7	@SRR060727.114177 SOLEXA7:7:12:1063:980 length=202	productive	TRBV19	150	100	31/31 nt			TRBJ1-5	241	98	49/50 nt	TRBD1	2	X	X	13	X.X.13	[X.X.10.10]	CAAGEGEVRNQPQHF	in-frame	+						ccaaaagaacccgacagctttctatctctgtgctgcgggtgagggggaggttagaaatcagccccagcattttggtgatgggactcgactctccatcctagtaacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatcaccaaaatgctggggctgatttctaacctccccctcacccgcagca
+8	@SRR060727.130541 SOLEXA7:7:14:145:1124 length=202	productive	TRBV3-1	160	100	33/33 nt			TRBJ1-5	232	96	48/50 nt	TRBD1	2	X	X	12	X.X.12	[X.X.11.10]	CAAGQGFGNQPQHF	in-frame	+						ctggagcttggtgactctgctgtgtatttctgtgccgcaggtcagggttttgggaatcagccccagcattttggtgatgggactcgactctccatcctagataacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatcaccaaaatgctggggctgattcccaaaaccctgacctgcggcacag
+9	@SRR060727.175366 SOLEXA7:7:18:291:1226 length=202	productive	TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6	95	100	20/20 nt			TRBJ1-1	231	97.92	47/48 nt	TRBD1	1	X	X	13	X.X.13	[X.X.6.10]	CAAGPRAGTNTEAFF	in-frame	+						agacatctgtgtacttctgtgccgctggaccaagggcagggacgaacactgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaactaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgttcgtccctgcccttggtccagcggca
+10	@SRR060727.184926 SOLEXA7:7:19:439:598 length=202	productive	TRBV6-1 or TRBV6-5 or TRBV6-6	140	100	29/29 nt			TRBJ1-1	231	97.92	47/48 nt	TRBD1	2	X	X	12	X.X.12	[X.X.9.10]	CAADAQGGNTEAFF	in-frame	+						ctccctcccagacatctgtgtacttctgtgccgcggacgcacagggggggaacactgaagctttctttggacaaggcaccagactcacagttgtagaggactaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgttccccccctgtgcgtccgcggcacag
+11	@SRR060727.187683 SOLEXA7:7:19:809:1493 length=202	productive	TRBV19	135	100	28/28 nt			TRBJ1-5	232	96	48/50 nt	TRBD1	2	X	X	13	X.X.13	[X.X.9.10]	CAAGEGEVRNQPQHF	in-frame	+						aaagaacccgacagctttctatctctgtgctgcgggtgagggggaggttagaaatcagccccagcattttggagatgggactcgactctccatcctagaggtaacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatctccaaaatgctggggctgatttctaacctccccctcacccgcagca
+12	@SRR060727.190355 SOLEXA7:7:19:1314:185 length=202	productive	TRBV27	130	100	27/27 nt			TRBJ1-5	223	94	47/50 nt	TRBD1	3	X	X	9	X.X.9	[X.X.9.10]	CAAGPNQPQHF	in-frame	+						cccaaccagacctctctgtacttctgtgccgccgggcccaatcagccccagcattttggtgatgggactcgactctccatcctagaggacctgaacaaggttaacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatcaccaaaatgctggggctgattgggcccggcggcacagaagtacaga
+13	@SRR060727.196094 SOLEXA7:7:20:579:567 length=202	productive	TRBV12-3 or TRBV12-4	120	100	25/25 nt			TRBJ2-5	195	89.58	43/48 nt	TRBD1	1	X	X	9	X.X.9	[X.X.8.10]	CAAGTIETQYF	in-frame	+						cagggactcagctgtgtacttctgtgccgcggggacaattgagacccagtacttcgggccaggcacgcggctcctggtgctcgaggacatgaaaaaagtgttaacgggtgggaacacgtttttcaggtcctcgagcaccaggagccgcgtgcctggcccgaagtactgggtctcaattgtccccgcggcacagaagtacaca
+14	@SRR060727.208531_SOLEXA7:7:21:1082:1793_length=20	productive	TRBV25-1	120	100	25/25 nt			TRBJ1-1	195	89.58	43/48 nt	TRBD2	2	X	X	10	X.X.10	[X.X.8.10]	CAAGGGAPEAFF	in-frame	+						ctcacatacctctcagtacctctgtgcagcgggtggaggggccccagaagctttctttggacaaggcaccagactcacagttgtagaggacctgaacaaggtaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttctggggcccctccacccgctgcacagagggaa
+15	@SRR060727.236848 SOLEXA7:7:24:1329:676 length=202	productive	TRBV10-3 or TRBV6-1 or TRBV6-5 or TRBV6-6	120	100	25/25 nt			TRBJ2-7	235	100	47/47 nt	TRBD1	1	X	X	11	X.X.11	[X.X.8.10]	CAAGTGLSYEQYF	in-frame	+						ctcccagacatctgtgtacttctgtgccgcggggacaggactctcctacgagcagtacttcgggccgggcaccaggctcacggtcacagaggacctgaaaataacgggtgggaacacgtttttcaggtcctctgtgaccgtgagcctggtgcccggcccgaagtactgctcgtaggagagtcctgtccccgcggcacagaag
+16	@SRR060727.258473 SOLEXA7:7:27:271:1727 length=202	productive	TRBV30	100	100	21/21 nt			TRBJ1-4	201	88.24	45/51 nt	TRBD1	2	X	X	10	X.X.10	[X.X.7.10]	CAAGQVGEKLFF	in-frame	+						gactctggcttctatctctgtgccgcgggacaagtgggtgaaaaactgttttttggcagtggaacccagctctctgtcttggaggacctgaacaacgaggttaacgggtgggaacaccttgttcaggtcctccaagacagagagctgggttccactgccaaaaaacagtttttcacccacttgtcccgcggcacagagatag
+17	@SRR060727.274111 SOLEXA7:7:28:1699:290 length=202	productive	TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6	100	100	21/21 nt			TRBJ1-1	222	95.83	46/48 nt	TRBD1	1	X	X	13	X.X.13	[X.X.7.10]	CAAGPRAGTNTEAFF	in-frame	+						cagacatctgtgtacttctgtgccgctggaccaagggcagggacgaacactgaagctttctttgtacaaggcaccagactcacagttgtagaggacctgaataacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtacaaagaaagcttcagtgttcgtccctgcccttggtccagcggca
+18	@SRR060727.275014 SOLEXA7:7:29:152:1739 length=202	productive	TRBV30	130	100	27/27 nt			TRBJ1-1	195	89.58	43/48 nt	TRBD2	3	X	X	10	X.X.10	[X.X.9.10]	CAAEGILAEAFF	in-frame	+						ctcagtgactctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaacaataacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag
+19	@SRR060727.281458_SOLEXA7:7:29:1133:1441_length=20	productive	TRBV15	141	96.77	30/31 nt			TRBJ1-1	222	95.83	46/48 nt	TRBD1	1	X	X	11	X.X.11	[X.X.10.10]	CAAGGKRYTEAFF	in-frame	+						atgcctgggggacgcagccatgtacctgtgtgccgcaggggggaaacggtacactgaagctttctttggacaaggcaccagactcacagttgtagaggacctaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgtaccgtttcccccctgcggcacacagg
+20	@SRR060727.283135_SOLEXA7:7:29:1539:1405_length=20	productive	TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6	100	100	21/21 nt			TRBJ2-3	200	89.8	44/49 nt	TRBD2	1	X	X	8	X.X.8	[X.X.7.10]	CAAGEDTQYF	in-frame	+						cagacatctgtgtacttctgtgccgccggggaggatacgcagtattttggcccaggcacccggctgacagtgctcgaggacctgaaaaacgtgttcccacctaacgggtgggaacacgtttttcaggtcctcgagcactgtcagccgggtgcctgggccaaaatactgcgtatcctccccggcggcacagaagtacacagat
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def1_TCR_output1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,15 @@
+	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	CAAEGILAEAFF	4	4/20	20.0000
+2	CAAGEGEVRNQPQHF	2	2/20	10.0000
+3	CAAGGKRYTEAFF	2	2/20	10.0000
+4	CAAGPRAGTNTEAFF	2	2/20	10.0000
+5	CAACEGLNTEAFF	1	1/20	5.0000
+6	CAADAQGGNTEAFF	1	1/20	5.0000
+7	CAAGEDTQYF	1	1/20	5.0000
+8	CAAGGGAPEAFF	1	1/20	5.0000
+9	CAAGGQGNSYEQYF	1	1/20	5.0000
+10	CAAGPNQPQHF	1	1/20	5.0000
+11	CAAGQGFGNQPQHF	1	1/20	5.0000
+12	CAAGQVGEKLFF	1	1/20	5.0000
+13	CAAGTGLSYEQYF	1	1/20	5.0000
+14	CAAGTIETQYF	1	1/20	5.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def1_TCR_output2.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,11 @@
+	AA JUNCTION	Frequency %
+1	CAAEGILAEAFF	20.0000
+2	CAAGEGEVRNQPQHF	10.0000
+3	CAAGGKRYTEAFF	10.0000
+4	CAAGPRAGTNTEAFF	10.0000
+5	CAACEGLNTEAFF	5.0000
+6	CAADAQGGNTEAFF	5.0000
+7	CAAGEDTQYF	5.0000
+8	CAAGGGAPEAFF	5.0000
+9	CAAGGQGNSYEQYF	5.0000
+10	CAAGPNQPQHF	5.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def1_TCR_output3.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,6 @@
+	input1.csv	%
+Dominant CDR3	CAAEGILAEAFF	
+Frequency	20.0000	
+Number of unique CDR3	14	
+Num of unique CDR3 > 1	4	28.5714
+Num of unique CDR3 = 1	10	71.4286
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def2_BCR_input1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	Sequence ID	Functionality	V-GENE	V-REGION score	V-REGION identity %	V-REGION identity nt	V-REGION identity % (with ins/del events)	V-REGION identity nt (with ins/del events)	J-GENE	J-REGION score	J-REGION identity %	J-REGION identity nt	D-GENE	D-REGION reading frame	CDR1-IMGT length	CDR2-IMGT length	CDR3-IMGT length	CDR-IMGT lengths	FR-IMGT lengths	AA JUNCTION	JUNCTION frame	Orientation	Functionality comment	V-REGION potential ins/del	J-GENE and allele comment	V-REGION insertions	V-REGION deletions	Sequence
+1	lcl|FLN1FA001B9SVM.1|	productive	IGHV1-69 or IGHV1-69D	790	100	159/159 nt			IGHJ4	186	87.5	42/48 nt	IGHD2-15	2	X	8	16	X.8.16	[X.7.38.11]	CYLGYCSGGSCYPQVGYW	in-frame	+						gggcttgagtggatgggagggatcatccctatctttggtacagcaaactacgcacagaagttccagggcagagtcacgattaccgcggacgaatccacgagcacagcctacatggagctgagcagcctgagatctgaggacacggccgtgtattactgttatttaggatattgtagtggtggtagctgctaccctcaggttggctactggggccagggaaccctggtcaccgtctcctcag
+2	lcl|FLN1FA001CUVDF.1|	productive	IGHV3-30 or IGHV3-30-3	786	99.38	159/160 nt			IGHJ4	231	97.92	47/48 nt	IGHD2-15	2	X	8	13	X.8.13	[X.7.38.11]	CVTYCSGGSCYFDYW	in-frame	+						ggggctggagtgggtggcagttatatcatatgatggaagtaataaatactacgtagactccgtgaagggccgattcaccatctccagagacaattccaagaacacgctgtatctgcaaatgaacagcctgagagctgaggacacggctgtgtattactgtgttacatattgtagtggtggtagctgctactttgactactggggccagggaaccctggtcaccgtctcctcag
+3	lcl|FLN1FA001DLPHD.1|	productive	IGHV1-3	775	100	156/156 nt			IGHJ4	186	87.5	42/48 nt	IGHD3-16	2	X	8	9	X.8.9	[X.6.38.11]	CYISGSYVGYW	in-frame	+						cttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttacatttcggggagttatgtaggctactggggccagggaaccctggtcaccgtctcctcag
+4	lcl|FLN1FA002QTWMQ.1|	productive	IGHV4-39	775	100	156/156 nt			IGHJ4	195	89.58	43/48 nt	IGHD3-10	3	X	7	11	X.7.11	[X.7.38.11]	CYSAVVRGRFDYW	in-frame	+						gggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag
+5	lcl|FLN1FA002Q975Z.1|	productive	IGHV3-53	771	99.36	156/157 nt			IGHJ4	168	83.33	40/48 nt	IGHD2-21	3	X	7	10	X.7.10	[X.7.38.11]	CVVVTATPHGYW	in-frame	+						ggggctggagtgggtctcagttatttatagcggtggtagcacatactacgcagactccgtgaagggccgattcaccatctccagagacaattccaaggacacgctgtatcttcaaatgaacagcctgagagccgaggacacggccgtgtattactgtgtggtggtgactgctactccccatgggtactggggccagggaaccctggtcaccgtctcctcag
+6	lcl|FLN1FA001AX4MF.1|	productive	IGHV4-39	770	100	155/155 nt			IGHJ4	222	95.83	46/48 nt	IGHD3-22	2	X	7	15	X.7.15	[X.6.38.11]	CVVNYYDSSGYYYIDYW	in-frame	+						ggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgtgtggtaaattactatgatagtagtggttattactacatagactactggggccagggaaccctggtcaccgtctcctcag
+7	lcl|FLN1FA0074PUDE.1|	productive	IGHV4-39	770	100	155/155 nt			IGHJ4	222	95.83	46/48 nt	IGHD3-22	2	X	7	15	X.7.15	[X.6.38.11]	CVVNYYDSSGYYYIDYW	in-frame	+						ggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgtgtggtaaattactatgatagtagtggttattactacatagactactggggccagggaaccctggtcaccgtctcctcag
+8	lcl|FLN1FA0013V4SA.1|	productive	IGHV1-3	790	100	159/159 nt			IGHJ4	186	87.5	42/48 nt	IGHD2-15	2	X	8	16	X.8.16	[X.7.38.11]	CYLGYCSGGSCYPQVGYW	in-frame	+						aggcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttatttaggatattgtagtggtggtagctgctaccctcaggttggctactggggccagggaaccctggtcaccgtctcctcag
+9	lcl|FLN1FA00056KW6.1|	productive	IGHV1-3	775	100	156/156 nt			IGHJ4	186	87.5	42/48 nt	IGHD3-16	2	X	8	9	X.8.9	[X.6.38.11]	CYISGSYVGYW	in-frame	+						cttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttacatttcggggagttatgtaggctactggggccagggaaccctggtcaccgtctcctcag
+10	lcl|FLN1FA006WKNJR.1|	productive	IGHV3-53	771	99.36	156/157 nt			IGHJ4	168	83.33	40/48 nt	IGHD2-21	3	X	7	10	X.7.10	[X.7.38.11]	CVVVTATPHGYW	in-frame	+						ggggctggagtgggtctcagttatttatagcggtggtagcacatactacgcagactccgtgaagggccgattcaccatctccagagacaattccaaggacacgctgtatcttcaaatgaacagcctgagagccgaggacacggccgtgtattactgtgtggtggtgactgctactccccatgggtactggggccagggaaccctggtcaccgtctcctcag
+11	lcl|FLN1FA008ANOPH.1|	productive	IGHV4-39	775	100	156/156 nt			IGHJ4	195	89.58	43/48 nt	IGHD3-10	3	X	7	11	X.7.11	[X.7.38.11]	CYSAVVRGRFDYW	in-frame	+						gggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag
+12	lcl|FLN1FA005T7JJ8.1|	productive	IGHV3-33	795	100	160/160 nt			IGHJ4	222	95.83	46/48 nt	IGHD3-22	2	X	8	15	X.8.15	[X.7.38.11]	CVTYYYDSSGYPYFDYW	in-frame	+						ggggctggagtgggtggcagttatatggtatgatggaagtaataaatactatgcagactccgtgaagggccgattcaccatctccagagacaattccaagaacacgctgtatctgcaaatgaacagcctgagagccgaggacacggctgtgtattactgtgtaacgtattactatgatagtagtggttatccttactttgactactggggccagggaaccctggtcaccgtctcctcag
+13	lcl|FLN1FA0018WER7.1|	productive	IGHV4-39	770	100	155/155 nt			IGHJ4	222	95.83	46/48 nt	IGHD3-22	2	X	7	15	X.7.15	[X.6.38.11]	CVVNYYDSSGYYYIDYW	in-frame	+						ggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgtgtggtaaattactatgatagtagtggttattactacatagactactggggccagggaaccctggtcaccgtctcctcag
+14	lcl|FLN1FA004BRKX9.1|	productive	IGHV1-3	775	100	156/156 nt			IGHJ4	186	87.5	42/48 nt	IGHD3-16	2	X	8	9	X.8.9	[X.6.38.11]	CYISGSYVGYW	in-frame	+						cttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttacatttcggggagttatgtaggctactggggccagggaaccctggtcaccgtctcctcag
+15	lcl|FLN1FA00826HO1.1|	productive	IGHV4-39	775	100	156/156 nt			IGHJ4	195	89.58	43/48 nt	IGHD3-10	3	X	7	11	X.7.11	[X.7.38.11]	CYSAVVRGRFDYW	in-frame	+						gggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag
+16	lcl|FLN1FA0041SQ1V.1|	productive	IGHV3-53	771	99.36	156/157 nt			IGHJ4	168	83.33	40/48 nt	IGHD2-21	3	X	7	10	X.7.10	[X.7.38.11]	CVVVTATPHGYW	in-frame	+						ggggctggagtgggtctcagttatttatagcggtggtagcacatactacgcagactccgtgaagggccgattcaccatctccagagacaattccaaggacacgctgtatcttcaaatgaacagcctgagagccgaggacacggccgtgtattactgtgtggtggtgactgctactccccatgggtactggggccagggaaccctggtcaccgtctcctcag
+17	lcl|FLN1FA000BBO91.1|	productive	IGHV3-33	795	100	160/160 nt			IGHJ4	222	95.83	46/48 nt	IGHD3-22	2	X	8	15	X.8.15	[X.7.38.11]	CVTYYYDSSGYPYFDYW	in-frame	+						ggggctggagtgggtggcagttatatggtatgatggaagtaataaatactatgcagactccgtgaagggccgattcaccatctccagagacaattccaagaacacgctgtatctgcaaatgaacagcctgagagccgaggacacggctgtgtattactgtgtaacgtattactatgatagtagtggttatccttactttgactactggggccagggaaccctggtcaccgtctcctcag
+18	lcl|FLN1FA008W37HH.1|	productive	IGHV4-39	775	100	156/156 nt			IGHJ4	195	89.58	43/48 nt	IGHD3-10	3	X	7	11	X.7.11	[X.7.38.11]	CYSAVVRGRFDYW	in-frame	+						gggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag
+19	lcl|FLN1FA0080EWJB.1|	productive	IGHV1-3	775	100	156/156 nt			IGHJ4	186	87.5	42/48 nt	IGHD3-16	2	X	8	9	X.8.9	[X.6.38.11]	CYISGSYVGYW	in-frame	+						cttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttacatttcggggagttatgtaggctactggggccagggaaccctggtcaccgtctcctcag
+20	lcl|FLN1FA003C09AP.1|	productive	IGHV1-3	790	100	159/159 nt			IGHJ4	186	87.5	42/48 nt	IGHD2-15	2	X	8	16	X.8.16	[X.7.38.11]	CYLGYCSGGSCYPQVGYW	in-frame	+						aggcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttatttaggatattgtagtggtggtagctgctaccctcaggttggctactggggccagggaaccctggtcaccgtctcctcag
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def2_BCR_output1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,9 @@
+	V-GENE	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	IGHV1-3	CYISGSYVGYW	4	4/20	20.0000
+2	IGHV4-39	CYSAVVRGRFDYW	4	4/20	20.0000
+3	IGHV3-53	CVVVTATPHGYW	3	3/20	15.0000
+4	IGHV4-39	CVVNYYDSSGYYYIDYW	3	3/20	15.0000
+5	IGHV1-3	CYLGYCSGGSCYPQVGYW	2	2/20	10.0000
+6	IGHV3-33	CVTYYYDSSGYPYFDYW	2	2/20	10.0000
+7	IGHV1-69 or IGHV1-69D	CYLGYCSGGSCYPQVGYW	1	1/20	5.0000
+8	IGHV3-30 or IGHV3-30-3	CVTYCSGGSCYFDYW	1	1/20	5.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def2_BCR_output2.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,9 @@
+	V-GENE	AA JUNCTION	Frequency %
+1	IGHV1-3	CYISGSYVGYW	20.0000
+2	IGHV4-39	CYSAVVRGRFDYW	20.0000
+3	IGHV3-53	CVVVTATPHGYW	15.0000
+4	IGHV4-39	CVVNYYDSSGYYYIDYW	15.0000
+5	IGHV1-3	CYLGYCSGGSCYPQVGYW	10.0000
+6	IGHV3-33	CVTYYYDSSGYPYFDYW	10.0000
+7	IGHV1-69 or IGHV1-69D	CYLGYCSGGSCYPQVGYW	5.0000
+8	IGHV3-30 or IGHV3-30-3	CVTYCSGGSCYFDYW	5.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def2_BCR_output3.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,6 @@
+	input	%
+Dominant Clonotype	IGHV1-3,CYISGSYVGYW	
+Frequency	20.0000	
+Number of Clonotypes	8	
+Expanding Clonotypes	6	75.0000
+Singletons	2	25.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def2_TCR_input1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	Sequence ID	Functionality	V-GENE	V-REGION score	V-REGION identity %	V-REGION identity nt	V-REGION identity % (with ins/del events)	V-REGION identity nt (with ins/del events)	J-GENE	J-REGION score	J-REGION identity %	J-REGION identity nt	D-GENE	D-REGION reading frame	CDR1-IMGT length	CDR2-IMGT length	CDR3-IMGT length	CDR-IMGT lengths	FR-IMGT lengths	AA JUNCTION	JUNCTION frame	Orientation	Functionality comment	V-REGION potential ins/del	J-GENE and allele comment	V-REGION insertions	V-REGION deletions	Sequence
+1	@SRR060727.12120 SOLEXA7:7:2:351:1247 length=202	productive	TRBV28	145	100	30/30 nt			TRBJ2-7	235	100	47/47 nt	TRBD1	3	X	X	12	X.X.12	[X.X.10.10]	CAAGGQGNSYEQYF	in-frame	+						agcaccaaccagacatctatgtacctctgtgccgctggggggcagggaaactcctacgagcagtacttcgggccgggcaccaggctcacggtcacagaggataacgggtgggaacacgtttttcaggtcctctgtgaccgtgagcctggtgcccggcccgaagtactgctcgtaggagtttccctgccccccagcggcacag
+2	@SRR060727.14069 SOLEXA7:7:2:622:201 length=202	productive	TRBV30	95	100	20/20 nt			TRBJ1-1	195	89.58	43/48 nt	TRBD2	3	X	X	10	X.X.10	[X.X.6.10]	CAAEGILAEAFF	in-frame	+						actctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaacaaggtgttctaacgggtgggnacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag
+3	@SRR060727.45221 SOLEXA7:7:5:1541:638 length=202	productive	TRBV30	145	100	30/30 nt			TRBJ1-1	195	89.58	43/48 nt	TRBD2	3	X	X	10	X.X.10	[X.X.10.10]	CAAEGILAEAFF	in-frame	+						cttctcagtgactctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaataacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag
+4	@SRR060727.49324 SOLEXA7:7:6:384:121 length=202	productive	TRBV10-3	165	100	34/34 nt			TRBJ1-1	240	100	48/48 nt	TRBD1	2	X	X	11	X.X.11	[X.X.11.10]	CAACEGLNTEAFF	in-frame	+						cgctaccagctcccagacatctgtgtacttctgtgccgcatgtgaggggctgaacactgaagctttctttggacaaggcaccagactcacagttgtagaggtaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgttcagcccctcacatgcggcacagaag
+5	@SRR060727.85642 SOLEXA7:7:10:98:1840 length=202	productive	TRBV30	115	100	24/24 nt			TRBJ1-1	195	89.58	43/48 nt	TRBD2	3	X	X	10	X.X.10	[X.X.8.10]	CAAEGILAEAFF	in-frame	+						agtgactctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagcggacctgaacaagggtaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag
+6	@SRR060727.100243 SOLEXA7:7:11:766:821 length=202	productive	TRBV15	105	100	22/22 nt			TRBJ1-1	222	95.83	46/48 nt	TRBD1	1	X	X	11	X.X.11	[X.X.7.10]	CAAGGKRYTEAFF	in-frame	-						ggacgcagccatgtacctgtgtgccgcaggggggaaacggtacactgaagctttctttggacaaggcaccagactcacagttgtagaggacctggacaaggtacaactgtgagtctggtgccttgtccaaagaaagcttcagtgtaccgtttcccccctgcggcacacaggtacatggctgcgtcccccaggcctggtgagc
+7	@SRR060727.114177 SOLEXA7:7:12:1063:980 length=202	productive	TRBV19	150	100	31/31 nt			TRBJ1-5	241	98	49/50 nt	TRBD1	2	X	X	13	X.X.13	[X.X.10.10]	CAAGEGEVRNQPQHF	in-frame	+						ccaaaagaacccgacagctttctatctctgtgctgcgggtgagggggaggttagaaatcagccccagcattttggtgatgggactcgactctccatcctagtaacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatcaccaaaatgctggggctgatttctaacctccccctcacccgcagca
+8	@SRR060727.130541 SOLEXA7:7:14:145:1124 length=202	productive	TRBV3-1	160	100	33/33 nt			TRBJ1-5	232	96	48/50 nt	TRBD1	2	X	X	12	X.X.12	[X.X.11.10]	CAAGQGFGNQPQHF	in-frame	+						ctggagcttggtgactctgctgtgtatttctgtgccgcaggtcagggttttgggaatcagccccagcattttggtgatgggactcgactctccatcctagataacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatcaccaaaatgctggggctgattcccaaaaccctgacctgcggcacag
+9	@SRR060727.175366 SOLEXA7:7:18:291:1226 length=202	productive	TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6	95	100	20/20 nt			TRBJ1-1	231	97.92	47/48 nt	TRBD1	1	X	X	13	X.X.13	[X.X.6.10]	CAAGPRAGTNTEAFF	in-frame	+						agacatctgtgtacttctgtgccgctggaccaagggcagggacgaacactgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaactaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgttcgtccctgcccttggtccagcggca
+10	@SRR060727.184926 SOLEXA7:7:19:439:598 length=202	productive	TRBV6-1 or TRBV6-5 or TRBV6-6	140	100	29/29 nt			TRBJ1-1	231	97.92	47/48 nt	TRBD1	2	X	X	12	X.X.12	[X.X.9.10]	CAADAQGGNTEAFF	in-frame	+						ctccctcccagacatctgtgtacttctgtgccgcggacgcacagggggggaacactgaagctttctttggacaaggcaccagactcacagttgtagaggactaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgttccccccctgtgcgtccgcggcacag
+11	@SRR060727.187683 SOLEXA7:7:19:809:1493 length=202	productive	TRBV19	135	100	28/28 nt			TRBJ1-5	232	96	48/50 nt	TRBD1	2	X	X	13	X.X.13	[X.X.9.10]	CAAGEGEVRNQPQHF	in-frame	+						aaagaacccgacagctttctatctctgtgctgcgggtgagggggaggttagaaatcagccccagcattttggagatgggactcgactctccatcctagaggtaacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatctccaaaatgctggggctgatttctaacctccccctcacccgcagca
+12	@SRR060727.190355 SOLEXA7:7:19:1314:185 length=202	productive	TRBV27	130	100	27/27 nt			TRBJ1-5	223	94	47/50 nt	TRBD1	3	X	X	9	X.X.9	[X.X.9.10]	CAAGPNQPQHF	in-frame	+						cccaaccagacctctctgtacttctgtgccgccgggcccaatcagccccagcattttggtgatgggactcgactctccatcctagaggacctgaacaaggttaacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatcaccaaaatgctggggctgattgggcccggcggcacagaagtacaga
+13	@SRR060727.196094 SOLEXA7:7:20:579:567 length=202	productive	TRBV12-3 or TRBV12-4	120	100	25/25 nt			TRBJ2-5	195	89.58	43/48 nt	TRBD1	1	X	X	9	X.X.9	[X.X.8.10]	CAAGTIETQYF	in-frame	+						cagggactcagctgtgtacttctgtgccgcggggacaattgagacccagtacttcgggccaggcacgcggctcctggtgctcgaggacatgaaaaaagtgttaacgggtgggaacacgtttttcaggtcctcgagcaccaggagccgcgtgcctggcccgaagtactgggtctcaattgtccccgcggcacagaagtacaca
+14	@SRR060727.208531_SOLEXA7:7:21:1082:1793_length=20	productive	TRBV25-1	120	100	25/25 nt			TRBJ1-1	195	89.58	43/48 nt	TRBD2	2	X	X	10	X.X.10	[X.X.8.10]	CAAGGGAPEAFF	in-frame	+						ctcacatacctctcagtacctctgtgcagcgggtggaggggccccagaagctttctttggacaaggcaccagactcacagttgtagaggacctgaacaaggtaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttctggggcccctccacccgctgcacagagggaa
+15	@SRR060727.236848 SOLEXA7:7:24:1329:676 length=202	productive	TRBV10-3 or TRBV6-1 or TRBV6-5 or TRBV6-6	120	100	25/25 nt			TRBJ2-7	235	100	47/47 nt	TRBD1	1	X	X	11	X.X.11	[X.X.8.10]	CAAGTGLSYEQYF	in-frame	+						ctcccagacatctgtgtacttctgtgccgcggggacaggactctcctacgagcagtacttcgggccgggcaccaggctcacggtcacagaggacctgaaaataacgggtgggaacacgtttttcaggtcctctgtgaccgtgagcctggtgcccggcccgaagtactgctcgtaggagagtcctgtccccgcggcacagaag
+16	@SRR060727.258473 SOLEXA7:7:27:271:1727 length=202	productive	TRBV30	100	100	21/21 nt			TRBJ1-4	201	88.24	45/51 nt	TRBD1	2	X	X	10	X.X.10	[X.X.7.10]	CAAGQVGEKLFF	in-frame	+						gactctggcttctatctctgtgccgcgggacaagtgggtgaaaaactgttttttggcagtggaacccagctctctgtcttggaggacctgaacaacgaggttaacgggtgggaacaccttgttcaggtcctccaagacagagagctgggttccactgccaaaaaacagtttttcacccacttgtcccgcggcacagagatag
+17	@SRR060727.274111 SOLEXA7:7:28:1699:290 length=202	productive	TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6	100	100	21/21 nt			TRBJ1-1	222	95.83	46/48 nt	TRBD1	1	X	X	13	X.X.13	[X.X.7.10]	CAAGPRAGTNTEAFF	in-frame	+						cagacatctgtgtacttctgtgccgctggaccaagggcagggacgaacactgaagctttctttgtacaaggcaccagactcacagttgtagaggacctgaataacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtacaaagaaagcttcagtgttcgtccctgcccttggtccagcggca
+18	@SRR060727.275014 SOLEXA7:7:29:152:1739 length=202	productive	TRBV30	130	100	27/27 nt			TRBJ1-1	195	89.58	43/48 nt	TRBD2	3	X	X	10	X.X.10	[X.X.9.10]	CAAEGILAEAFF	in-frame	+						ctcagtgactctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaacaataacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag
+19	@SRR060727.281458_SOLEXA7:7:29:1133:1441_length=20	productive	TRBV15	141	96.77	30/31 nt			TRBJ1-1	222	95.83	46/48 nt	TRBD1	1	X	X	11	X.X.11	[X.X.10.10]	CAAGGKRYTEAFF	in-frame	+						atgcctgggggacgcagccatgtacctgtgtgccgcaggggggaaacggtacactgaagctttctttggacaaggcaccagactcacagttgtagaggacctaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgtaccgtttcccccctgcggcacacagg
+20	@SRR060727.283135_SOLEXA7:7:29:1539:1405_length=20	productive	TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6	100	100	21/21 nt			TRBJ2-3	200	89.8	44/49 nt	TRBD2	1	X	X	8	X.X.8	[X.X.7.10]	CAAGEDTQYF	in-frame	+						cagacatctgtgtacttctgtgccgccggggaggatacgcagtattttggcccaggcacccggctgacagtgctcgaggacctgaaaaacgtgttcccacctaacgggtgggaacacgtttttcaggtcctcgagcactgtcagccgggtgcctgggccaaaatactgcgtatcctccccggcggcacagaagtacacagat
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def2_TCR_output1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,15 @@
+	V-GENE	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	TRBV30	CAAEGILAEAFF	4	4/20	20.0000
+2	TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6	CAAGPRAGTNTEAFF	2	2/20	10.0000
+3	TRBV15	CAAGGKRYTEAFF	2	2/20	10.0000
+4	TRBV19	CAAGEGEVRNQPQHF	2	2/20	10.0000
+5	TRBV10-3	CAACEGLNTEAFF	1	1/20	5.0000
+6	TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6	CAAGEDTQYF	1	1/20	5.0000
+7	TRBV10-3 or TRBV6-1 or TRBV6-5 or TRBV6-6	CAAGTGLSYEQYF	1	1/20	5.0000
+8	TRBV12-3 or TRBV12-4	CAAGTIETQYF	1	1/20	5.0000
+9	TRBV25-1	CAAGGGAPEAFF	1	1/20	5.0000
+10	TRBV27	CAAGPNQPQHF	1	1/20	5.0000
+11	TRBV28	CAAGGQGNSYEQYF	1	1/20	5.0000
+12	TRBV3-1	CAAGQGFGNQPQHF	1	1/20	5.0000
+13	TRBV30	CAAGQVGEKLFF	1	1/20	5.0000
+14	TRBV6-1 or TRBV6-5 or TRBV6-6	CAADAQGGNTEAFF	1	1/20	5.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def2_TCR_output2.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,11 @@
+	V-GENE	AA JUNCTION	Frequency %
+1	TRBV30	CAAEGILAEAFF	20.0000
+2	TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6	CAAGPRAGTNTEAFF	10.0000
+3	TRBV15	CAAGGKRYTEAFF	10.0000
+4	TRBV19	CAAGEGEVRNQPQHF	10.0000
+5	TRBV10-3	CAACEGLNTEAFF	5.0000
+6	TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6	CAAGEDTQYF	5.0000
+7	TRBV10-3 or TRBV6-1 or TRBV6-5 or TRBV6-6	CAAGTGLSYEQYF	5.0000
+8	TRBV12-3 or TRBV12-4	CAAGTIETQYF	5.0000
+9	TRBV25-1	CAAGGGAPEAFF	5.0000
+10	TRBV27	CAAGPNQPQHF	5.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def2_TCR_output3.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,6 @@
+	input1.csv	%
+Dominant Clonotype	TRBV30,CAAEGILAEAFF	
+Frequency	20.0000	
+Number of Clonotypes	14	
+Expanding Clonotypes	4	28.5714
+Singletons	10	71.4286
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def3_BCR_input1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	Sequence ID	Functionality	V-GENE	V-REGION score	V-REGION identity %	V-REGION identity nt	V-REGION identity % (with ins/del events)	V-REGION identity nt (with ins/del events)	J-GENE	J-REGION score	J-REGION identity %	J-REGION identity nt	D-GENE	D-REGION reading frame	CDR1-IMGT length	CDR2-IMGT length	CDR3-IMGT length	CDR-IMGT lengths	FR-IMGT lengths	AA JUNCTION	JUNCTION frame	Orientation	Functionality comment	V-REGION potential ins/del	J-GENE and allele comment	V-REGION insertions	V-REGION deletions	Sequence
+1	lcl|FLN1FA001B9SVM.1|	productive	IGHV1-69 or IGHV1-69D	790	100	159/159 nt			IGHJ4	186	87.5	42/48 nt	IGHD2-15	2	X	8	16	X.8.16	[X.7.38.11]	CYLGYCSGGSCYPQVGYW	in-frame	+						gggcttgagtggatgggagggatcatccctatctttggtacagcaaactacgcacagaagttccagggcagagtcacgattaccgcggacgaatccacgagcacagcctacatggagctgagcagcctgagatctgaggacacggccgtgtattactgttatttaggatattgtagtggtggtagctgctaccctcaggttggctactggggccagggaaccctggtcaccgtctcctcag
+2	lcl|FLN1FA001CUVDF.1|	productive	IGHV3-30 or IGHV3-30-3	786	99.38	159/160 nt			IGHJ4	231	97.92	47/48 nt	IGHD2-15	2	X	8	13	X.8.13	[X.7.38.11]	CVTYCSGGSCYFDYW	in-frame	+						ggggctggagtgggtggcagttatatcatatgatggaagtaataaatactacgtagactccgtgaagggccgattcaccatctccagagacaattccaagaacacgctgtatctgcaaatgaacagcctgagagctgaggacacggctgtgtattactgtgttacatattgtagtggtggtagctgctactttgactactggggccagggaaccctggtcaccgtctcctcag
+3	lcl|FLN1FA001DLPHD.1|	productive	IGHV1-3	775	100	156/156 nt			IGHJ4	186	87.5	42/48 nt	IGHD3-16	2	X	8	9	X.8.9	[X.6.38.11]	CYISGSYVGYW	in-frame	+						cttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttacatttcggggagttatgtaggctactggggccagggaaccctggtcaccgtctcctcag
+4	lcl|FLN1FA002QTWMQ.1|	productive	IGHV4-39	775	100	156/156 nt			IGHJ4	195	89.58	43/48 nt	IGHD3-10	3	X	7	11	X.7.11	[X.7.38.11]	CYSAVVRGRFDYW	in-frame	+						gggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag
+5	lcl|FLN1FA002Q975Z.1|	productive	IGHV3-53	771	99.36	156/157 nt			IGHJ4	168	83.33	40/48 nt	IGHD2-21	3	X	7	10	X.7.10	[X.7.38.11]	CVVVTATPHGYW	in-frame	+						ggggctggagtgggtctcagttatttatagcggtggtagcacatactacgcagactccgtgaagggccgattcaccatctccagagacaattccaaggacacgctgtatcttcaaatgaacagcctgagagccgaggacacggccgtgtattactgtgtggtggtgactgctactccccatgggtactggggccagggaaccctggtcaccgtctcctcag
+6	lcl|FLN1FA001AX4MF.1|	productive	IGHV4-39	770	100	155/155 nt			IGHJ4	222	95.83	46/48 nt	IGHD3-22	2	X	7	15	X.7.15	[X.6.38.11]	CVVNYYDSSGYYYIDYW	in-frame	+						ggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgtgtggtaaattactatgatagtagtggttattactacatagactactggggccagggaaccctggtcaccgtctcctcag
+7	lcl|FLN1FA0074PUDE.1|	productive	IGHV4-39	770	100	155/155 nt			IGHJ4	222	95.83	46/48 nt	IGHD3-22	2	X	7	15	X.7.15	[X.6.38.11]	CVVNYYDSSGYYYIDYW	in-frame	+						ggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgtgtggtaaattactatgatagtagtggttattactacatagactactggggccagggaaccctggtcaccgtctcctcag
+8	lcl|FLN1FA0013V4SA.1|	productive	IGHV1-3	790	100	159/159 nt			IGHJ4	186	87.5	42/48 nt	IGHD2-15	2	X	8	16	X.8.16	[X.7.38.11]	CYLGYCSGGSCYPQVGYW	in-frame	+						aggcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttatttaggatattgtagtggtggtagctgctaccctcaggttggctactggggccagggaaccctggtcaccgtctcctcag
+9	lcl|FLN1FA00056KW6.1|	productive	IGHV1-3	775	100	156/156 nt			IGHJ4	186	87.5	42/48 nt	IGHD3-16	2	X	8	9	X.8.9	[X.6.38.11]	CYISGSYVGYW	in-frame	+						cttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttacatttcggggagttatgtaggctactggggccagggaaccctggtcaccgtctcctcag
+10	lcl|FLN1FA006WKNJR.1|	productive	IGHV3-53	771	99.36	156/157 nt			IGHJ4	168	83.33	40/48 nt	IGHD2-21	3	X	7	10	X.7.10	[X.7.38.11]	CVVVTATPHGYW	in-frame	+						ggggctggagtgggtctcagttatttatagcggtggtagcacatactacgcagactccgtgaagggccgattcaccatctccagagacaattccaaggacacgctgtatcttcaaatgaacagcctgagagccgaggacacggccgtgtattactgtgtggtggtgactgctactccccatgggtactggggccagggaaccctggtcaccgtctcctcag
+11	lcl|FLN1FA008ANOPH.1|	productive	IGHV4-39	775	100	156/156 nt			IGHJ4	195	89.58	43/48 nt	IGHD3-10	3	X	7	11	X.7.11	[X.7.38.11]	CYSAVVRGRFDYW	in-frame	+						gggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag
+12	lcl|FLN1FA005T7JJ8.1|	productive	IGHV3-33	795	100	160/160 nt			IGHJ4	222	95.83	46/48 nt	IGHD3-22	2	X	8	15	X.8.15	[X.7.38.11]	CVTYYYDSSGYPYFDYW	in-frame	+						ggggctggagtgggtggcagttatatggtatgatggaagtaataaatactatgcagactccgtgaagggccgattcaccatctccagagacaattccaagaacacgctgtatctgcaaatgaacagcctgagagccgaggacacggctgtgtattactgtgtaacgtattactatgatagtagtggttatccttactttgactactggggccagggaaccctggtcaccgtctcctcag
+13	lcl|FLN1FA0018WER7.1|	productive	IGHV4-39	770	100	155/155 nt			IGHJ4	222	95.83	46/48 nt	IGHD3-22	2	X	7	15	X.7.15	[X.6.38.11]	CVVNYYDSSGYYYIDYW	in-frame	+						ggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgtgtggtaaattactatgatagtagtggttattactacatagactactggggccagggaaccctggtcaccgtctcctcag
+14	lcl|FLN1FA004BRKX9.1|	productive	IGHV1-3	775	100	156/156 nt			IGHJ4	186	87.5	42/48 nt	IGHD3-16	2	X	8	9	X.8.9	[X.6.38.11]	CYISGSYVGYW	in-frame	+						cttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttacatttcggggagttatgtaggctactggggccagggaaccctggtcaccgtctcctcag
+15	lcl|FLN1FA00826HO1.1|	productive	IGHV4-39	775	100	156/156 nt			IGHJ4	195	89.58	43/48 nt	IGHD3-10	3	X	7	11	X.7.11	[X.7.38.11]	CYSAVVRGRFDYW	in-frame	+						gggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag
+16	lcl|FLN1FA0041SQ1V.1|	productive	IGHV3-53	771	99.36	156/157 nt			IGHJ4	168	83.33	40/48 nt	IGHD2-21	3	X	7	10	X.7.10	[X.7.38.11]	CVVVTATPHGYW	in-frame	+						ggggctggagtgggtctcagttatttatagcggtggtagcacatactacgcagactccgtgaagggccgattcaccatctccagagacaattccaaggacacgctgtatcttcaaatgaacagcctgagagccgaggacacggccgtgtattactgtgtggtggtgactgctactccccatgggtactggggccagggaaccctggtcaccgtctcctcag
+17	lcl|FLN1FA000BBO91.1|	productive	IGHV3-33	795	100	160/160 nt			IGHJ4	222	95.83	46/48 nt	IGHD3-22	2	X	8	15	X.8.15	[X.7.38.11]	CVTYYYDSSGYPYFDYW	in-frame	+						ggggctggagtgggtggcagttatatggtatgatggaagtaataaatactatgcagactccgtgaagggccgattcaccatctccagagacaattccaagaacacgctgtatctgcaaatgaacagcctgagagccgaggacacggctgtgtattactgtgtaacgtattactatgatagtagtggttatccttactttgactactggggccagggaaccctggtcaccgtctcctcag
+18	lcl|FLN1FA008W37HH.1|	productive	IGHV4-39	775	100	156/156 nt			IGHJ4	195	89.58	43/48 nt	IGHD3-10	3	X	7	11	X.7.11	[X.7.38.11]	CYSAVVRGRFDYW	in-frame	+						gggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag
+19	lcl|FLN1FA0080EWJB.1|	productive	IGHV1-3	775	100	156/156 nt			IGHJ4	186	87.5	42/48 nt	IGHD3-16	2	X	8	9	X.8.9	[X.6.38.11]	CYISGSYVGYW	in-frame	+						cttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttacatttcggggagttatgtaggctactggggccagggaaccctggtcaccgtctcctcag
+20	lcl|FLN1FA003C09AP.1|	productive	IGHV1-3	790	100	159/159 nt			IGHJ4	186	87.5	42/48 nt	IGHD2-15	2	X	8	16	X.8.16	[X.7.38.11]	CYLGYCSGGSCYPQVGYW	in-frame	+						aggcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttatttaggatattgtagtggtggtagctgctaccctcaggttggctactggggccagggaaccctggtcaccgtctcctcag
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def3_BCR_output1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,8 @@
+	J-GENE	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	IGHJ4	CYISGSYVGYW	4	4/20	20.0000
+2	IGHJ4	CYSAVVRGRFDYW	4	4/20	20.0000
+3	IGHJ4	CVVNYYDSSGYYYIDYW	3	3/20	15.0000
+4	IGHJ4	CVVVTATPHGYW	3	3/20	15.0000
+5	IGHJ4	CYLGYCSGGSCYPQVGYW	3	3/20	15.0000
+6	IGHJ4	CVTYYYDSSGYPYFDYW	2	2/20	10.0000
+7	IGHJ4	CVTYCSGGSCYFDYW	1	1/20	5.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def3_BCR_output2.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,8 @@
+	J-GENE	AA JUNCTION	Frequency %
+1	IGHJ4	CYISGSYVGYW	20.0000
+2	IGHJ4	CYSAVVRGRFDYW	20.0000
+3	IGHJ4	CVVNYYDSSGYYYIDYW	15.0000
+4	IGHJ4	CVVVTATPHGYW	15.0000
+5	IGHJ4	CYLGYCSGGSCYPQVGYW	15.0000
+6	IGHJ4	CVTYYYDSSGYPYFDYW	10.0000
+7	IGHJ4	CVTYCSGGSCYFDYW	5.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def3_BCR_output3.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,6 @@
+	input	%
+Dominant Clonotype(J-CDR3)	IGHJ4,CYISGSYVGYW	
+Frequency	20.0000	
+Number of Clonotypes(J-CDR3)	7	
+Expanding Clonotypes(J-CDR3)	6	85.7143
+Singletons	1	14.2857
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def3_TCR_input1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	Sequence ID	Functionality	V-GENE	V-REGION score	V-REGION identity %	V-REGION identity nt	V-REGION identity % (with ins/del events)	V-REGION identity nt (with ins/del events)	J-GENE	J-REGION score	J-REGION identity %	J-REGION identity nt	D-GENE	D-REGION reading frame	CDR1-IMGT length	CDR2-IMGT length	CDR3-IMGT length	CDR-IMGT lengths	FR-IMGT lengths	AA JUNCTION	JUNCTION frame	Orientation	Functionality comment	V-REGION potential ins/del	J-GENE and allele comment	V-REGION insertions	V-REGION deletions	Sequence
+1	@SRR060727.12120 SOLEXA7:7:2:351:1247 length=202	productive	TRBV28	145	100	30/30 nt			TRBJ2-7	235	100	47/47 nt	TRBD1	3	X	X	12	X.X.12	[X.X.10.10]	CAAGGQGNSYEQYF	in-frame	+						agcaccaaccagacatctatgtacctctgtgccgctggggggcagggaaactcctacgagcagtacttcgggccgggcaccaggctcacggtcacagaggataacgggtgggaacacgtttttcaggtcctctgtgaccgtgagcctggtgcccggcccgaagtactgctcgtaggagtttccctgccccccagcggcacag
+2	@SRR060727.14069 SOLEXA7:7:2:622:201 length=202	productive	TRBV30	95	100	20/20 nt			TRBJ1-1	195	89.58	43/48 nt	TRBD2	3	X	X	10	X.X.10	[X.X.6.10]	CAAEGILAEAFF	in-frame	+						actctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaacaaggtgttctaacgggtgggnacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag
+3	@SRR060727.45221 SOLEXA7:7:5:1541:638 length=202	productive	TRBV30	145	100	30/30 nt			TRBJ1-1	195	89.58	43/48 nt	TRBD2	3	X	X	10	X.X.10	[X.X.10.10]	CAAEGILAEAFF	in-frame	+						cttctcagtgactctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaataacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag
+4	@SRR060727.49324 SOLEXA7:7:6:384:121 length=202	productive	TRBV10-3	165	100	34/34 nt			TRBJ1-1	240	100	48/48 nt	TRBD1	2	X	X	11	X.X.11	[X.X.11.10]	CAACEGLNTEAFF	in-frame	+						cgctaccagctcccagacatctgtgtacttctgtgccgcatgtgaggggctgaacactgaagctttctttggacaaggcaccagactcacagttgtagaggtaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgttcagcccctcacatgcggcacagaag
+5	@SRR060727.85642 SOLEXA7:7:10:98:1840 length=202	productive	TRBV30	115	100	24/24 nt			TRBJ1-1	195	89.58	43/48 nt	TRBD2	3	X	X	10	X.X.10	[X.X.8.10]	CAAEGILAEAFF	in-frame	+						agtgactctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagcggacctgaacaagggtaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag
+6	@SRR060727.100243 SOLEXA7:7:11:766:821 length=202	productive	TRBV15	105	100	22/22 nt			TRBJ1-1	222	95.83	46/48 nt	TRBD1	1	X	X	11	X.X.11	[X.X.7.10]	CAAGGKRYTEAFF	in-frame	-						ggacgcagccatgtacctgtgtgccgcaggggggaaacggtacactgaagctttctttggacaaggcaccagactcacagttgtagaggacctggacaaggtacaactgtgagtctggtgccttgtccaaagaaagcttcagtgtaccgtttcccccctgcggcacacaggtacatggctgcgtcccccaggcctggtgagc
+7	@SRR060727.114177 SOLEXA7:7:12:1063:980 length=202	productive	TRBV19	150	100	31/31 nt			TRBJ1-5	241	98	49/50 nt	TRBD1	2	X	X	13	X.X.13	[X.X.10.10]	CAAGEGEVRNQPQHF	in-frame	+						ccaaaagaacccgacagctttctatctctgtgctgcgggtgagggggaggttagaaatcagccccagcattttggtgatgggactcgactctccatcctagtaacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatcaccaaaatgctggggctgatttctaacctccccctcacccgcagca
+8	@SRR060727.130541 SOLEXA7:7:14:145:1124 length=202	productive	TRBV3-1	160	100	33/33 nt			TRBJ1-5	232	96	48/50 nt	TRBD1	2	X	X	12	X.X.12	[X.X.11.10]	CAAGQGFGNQPQHF	in-frame	+						ctggagcttggtgactctgctgtgtatttctgtgccgcaggtcagggttttgggaatcagccccagcattttggtgatgggactcgactctccatcctagataacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatcaccaaaatgctggggctgattcccaaaaccctgacctgcggcacag
+9	@SRR060727.175366 SOLEXA7:7:18:291:1226 length=202	productive	TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6	95	100	20/20 nt			TRBJ1-1	231	97.92	47/48 nt	TRBD1	1	X	X	13	X.X.13	[X.X.6.10]	CAAGPRAGTNTEAFF	in-frame	+						agacatctgtgtacttctgtgccgctggaccaagggcagggacgaacactgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaactaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgttcgtccctgcccttggtccagcggca
+10	@SRR060727.184926 SOLEXA7:7:19:439:598 length=202	productive	TRBV6-1 or TRBV6-5 or TRBV6-6	140	100	29/29 nt			TRBJ1-1	231	97.92	47/48 nt	TRBD1	2	X	X	12	X.X.12	[X.X.9.10]	CAADAQGGNTEAFF	in-frame	+						ctccctcccagacatctgtgtacttctgtgccgcggacgcacagggggggaacactgaagctttctttggacaaggcaccagactcacagttgtagaggactaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgttccccccctgtgcgtccgcggcacag
+11	@SRR060727.187683 SOLEXA7:7:19:809:1493 length=202	productive	TRBV19	135	100	28/28 nt			TRBJ1-5	232	96	48/50 nt	TRBD1	2	X	X	13	X.X.13	[X.X.9.10]	CAAGEGEVRNQPQHF	in-frame	+						aaagaacccgacagctttctatctctgtgctgcgggtgagggggaggttagaaatcagccccagcattttggagatgggactcgactctccatcctagaggtaacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatctccaaaatgctggggctgatttctaacctccccctcacccgcagca
+12	@SRR060727.190355 SOLEXA7:7:19:1314:185 length=202	productive	TRBV27	130	100	27/27 nt			TRBJ1-5	223	94	47/50 nt	TRBD1	3	X	X	9	X.X.9	[X.X.9.10]	CAAGPNQPQHF	in-frame	+						cccaaccagacctctctgtacttctgtgccgccgggcccaatcagccccagcattttggtgatgggactcgactctccatcctagaggacctgaacaaggttaacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatcaccaaaatgctggggctgattgggcccggcggcacagaagtacaga
+13	@SRR060727.196094 SOLEXA7:7:20:579:567 length=202	productive	TRBV12-3 or TRBV12-4	120	100	25/25 nt			TRBJ2-5	195	89.58	43/48 nt	TRBD1	1	X	X	9	X.X.9	[X.X.8.10]	CAAGTIETQYF	in-frame	+						cagggactcagctgtgtacttctgtgccgcggggacaattgagacccagtacttcgggccaggcacgcggctcctggtgctcgaggacatgaaaaaagtgttaacgggtgggaacacgtttttcaggtcctcgagcaccaggagccgcgtgcctggcccgaagtactgggtctcaattgtccccgcggcacagaagtacaca
+14	@SRR060727.208531_SOLEXA7:7:21:1082:1793_length=20	productive	TRBV25-1	120	100	25/25 nt			TRBJ1-1	195	89.58	43/48 nt	TRBD2	2	X	X	10	X.X.10	[X.X.8.10]	CAAGGGAPEAFF	in-frame	+						ctcacatacctctcagtacctctgtgcagcgggtggaggggccccagaagctttctttggacaaggcaccagactcacagttgtagaggacctgaacaaggtaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttctggggcccctccacccgctgcacagagggaa
+15	@SRR060727.236848 SOLEXA7:7:24:1329:676 length=202	productive	TRBV10-3 or TRBV6-1 or TRBV6-5 or TRBV6-6	120	100	25/25 nt			TRBJ2-7	235	100	47/47 nt	TRBD1	1	X	X	11	X.X.11	[X.X.8.10]	CAAGTGLSYEQYF	in-frame	+						ctcccagacatctgtgtacttctgtgccgcggggacaggactctcctacgagcagtacttcgggccgggcaccaggctcacggtcacagaggacctgaaaataacgggtgggaacacgtttttcaggtcctctgtgaccgtgagcctggtgcccggcccgaagtactgctcgtaggagagtcctgtccccgcggcacagaag
+16	@SRR060727.258473 SOLEXA7:7:27:271:1727 length=202	productive	TRBV30	100	100	21/21 nt			TRBJ1-4	201	88.24	45/51 nt	TRBD1	2	X	X	10	X.X.10	[X.X.7.10]	CAAGQVGEKLFF	in-frame	+						gactctggcttctatctctgtgccgcgggacaagtgggtgaaaaactgttttttggcagtggaacccagctctctgtcttggaggacctgaacaacgaggttaacgggtgggaacaccttgttcaggtcctccaagacagagagctgggttccactgccaaaaaacagtttttcacccacttgtcccgcggcacagagatag
+17	@SRR060727.274111 SOLEXA7:7:28:1699:290 length=202	productive	TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6	100	100	21/21 nt			TRBJ1-1	222	95.83	46/48 nt	TRBD1	1	X	X	13	X.X.13	[X.X.7.10]	CAAGPRAGTNTEAFF	in-frame	+						cagacatctgtgtacttctgtgccgctggaccaagggcagggacgaacactgaagctttctttgtacaaggcaccagactcacagttgtagaggacctgaataacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtacaaagaaagcttcagtgttcgtccctgcccttggtccagcggca
+18	@SRR060727.275014 SOLEXA7:7:29:152:1739 length=202	productive	TRBV30	130	100	27/27 nt			TRBJ1-1	195	89.58	43/48 nt	TRBD2	3	X	X	10	X.X.10	[X.X.9.10]	CAAEGILAEAFF	in-frame	+						ctcagtgactctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaacaataacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag
+19	@SRR060727.281458_SOLEXA7:7:29:1133:1441_length=20	productive	TRBV15	141	96.77	30/31 nt			TRBJ1-1	222	95.83	46/48 nt	TRBD1	1	X	X	11	X.X.11	[X.X.10.10]	CAAGGKRYTEAFF	in-frame	+						atgcctgggggacgcagccatgtacctgtgtgccgcaggggggaaacggtacactgaagctttctttggacaaggcaccagactcacagttgtagaggacctaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgtaccgtttcccccctgcggcacacagg
+20	@SRR060727.283135_SOLEXA7:7:29:1539:1405_length=20	productive	TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6	100	100	21/21 nt			TRBJ2-3	200	89.8	44/49 nt	TRBD2	1	X	X	8	X.X.8	[X.X.7.10]	CAAGEDTQYF	in-frame	+						cagacatctgtgtacttctgtgccgccggggaggatacgcagtattttggcccaggcacccggctgacagtgctcgaggacctgaaaaacgtgttcccacctaacgggtgggaacacgtttttcaggtcctcgagcactgtcagccgggtgcctgggccaaaatactgcgtatcctccccggcggcacagaagtacacagat
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def3_TCR_output1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,15 @@
+	J-GENE	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	TRBJ1-1	CAAEGILAEAFF	4	4/20	20.0000
+2	TRBJ1-1	CAAGGKRYTEAFF	2	2/20	10.0000
+3	TRBJ1-1	CAAGPRAGTNTEAFF	2	2/20	10.0000
+4	TRBJ1-5	CAAGEGEVRNQPQHF	2	2/20	10.0000
+5	TRBJ1-1	CAACEGLNTEAFF	1	1/20	5.0000
+6	TRBJ1-1	CAADAQGGNTEAFF	1	1/20	5.0000
+7	TRBJ1-1	CAAGGGAPEAFF	1	1/20	5.0000
+8	TRBJ1-4	CAAGQVGEKLFF	1	1/20	5.0000
+9	TRBJ1-5	CAAGPNQPQHF	1	1/20	5.0000
+10	TRBJ1-5	CAAGQGFGNQPQHF	1	1/20	5.0000
+11	TRBJ2-3	CAAGEDTQYF	1	1/20	5.0000
+12	TRBJ2-5	CAAGTIETQYF	1	1/20	5.0000
+13	TRBJ2-7	CAAGGQGNSYEQYF	1	1/20	5.0000
+14	TRBJ2-7	CAAGTGLSYEQYF	1	1/20	5.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def3_TCR_output2.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,11 @@
+	J-GENE	AA JUNCTION	Frequency %
+1	TRBJ1-1	CAAEGILAEAFF	20.0000
+2	TRBJ1-1	CAAGGKRYTEAFF	10.0000
+3	TRBJ1-1	CAAGPRAGTNTEAFF	10.0000
+4	TRBJ1-5	CAAGEGEVRNQPQHF	10.0000
+5	TRBJ1-1	CAACEGLNTEAFF	5.0000
+6	TRBJ1-1	CAADAQGGNTEAFF	5.0000
+7	TRBJ1-1	CAAGGGAPEAFF	5.0000
+8	TRBJ1-4	CAAGQVGEKLFF	5.0000
+9	TRBJ1-5	CAAGPNQPQHF	5.0000
+10	TRBJ1-5	CAAGQGFGNQPQHF	5.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def3_TCR_output3.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,6 @@
+	input1.csv	%
+Dominant Clonotype(J-CDR3)	TRBJ1-1,CAAEGILAEAFF	
+Frequency	20.0000	
+Number of Clonotypes(J-CDR3)	14	
+Expanding Clonotypes(J-CDR3)	4	28.5714
+Singletons	10	71.4286
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def4_BCR_input1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	Sequence ID	Functionality	V-GENE	V-REGION score	V-REGION identity %	V-REGION identity nt	V-REGION identity % (with ins/del events)	V-REGION identity nt (with ins/del events)	J-GENE	J-REGION score	J-REGION identity %	J-REGION identity nt	D-GENE	D-REGION reading frame	CDR1-IMGT length	CDR2-IMGT length	CDR3-IMGT length	CDR-IMGT lengths	FR-IMGT lengths	AA JUNCTION	JUNCTION frame	Orientation	Functionality comment	V-REGION potential ins/del	J-GENE and allele comment	V-REGION insertions	V-REGION deletions	Sequence
+1	lcl|FLN1FA001B9SVM.1|	productive	IGHV1-69 or IGHV1-69D	790	100	159/159 nt			IGHJ4	186	87.5	42/48 nt	IGHD2-15	2	X	8	16	X.8.16	[X.7.38.11]	CYLGYCSGGSCYPQVGYW	in-frame	+						gggcttgagtggatgggagggatcatccctatctttggtacagcaaactacgcacagaagttccagggcagagtcacgattaccgcggacgaatccacgagcacagcctacatggagctgagcagcctgagatctgaggacacggccgtgtattactgttatttaggatattgtagtggtggtagctgctaccctcaggttggctactggggccagggaaccctggtcaccgtctcctcag
+2	lcl|FLN1FA001CUVDF.1|	productive	IGHV3-30 or IGHV3-30-3	786	99.38	159/160 nt			IGHJ4	231	97.92	47/48 nt	IGHD2-15	2	X	8	13	X.8.13	[X.7.38.11]	CVTYCSGGSCYFDYW	in-frame	+						ggggctggagtgggtggcagttatatcatatgatggaagtaataaatactacgtagactccgtgaagggccgattcaccatctccagagacaattccaagaacacgctgtatctgcaaatgaacagcctgagagctgaggacacggctgtgtattactgtgttacatattgtagtggtggtagctgctactttgactactggggccagggaaccctggtcaccgtctcctcag
+3	lcl|FLN1FA001DLPHD.1|	productive	IGHV1-3	775	100	156/156 nt			IGHJ4	186	87.5	42/48 nt	IGHD3-16	2	X	8	9	X.8.9	[X.6.38.11]	CYISGSYVGYW	in-frame	+						cttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttacatttcggggagttatgtaggctactggggccagggaaccctggtcaccgtctcctcag
+4	lcl|FLN1FA002QTWMQ.1|	productive	IGHV4-39	775	100	156/156 nt			IGHJ4	195	89.58	43/48 nt	IGHD3-10	3	X	7	11	X.7.11	[X.7.38.11]	CYSAVVRGRFDYW	in-frame	+						gggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag
+5	lcl|FLN1FA002Q975Z.1|	productive	IGHV3-53	771	99.36	156/157 nt			IGHJ4	168	83.33	40/48 nt	IGHD2-21	3	X	7	10	X.7.10	[X.7.38.11]	CVVVTATPHGYW	in-frame	+						ggggctggagtgggtctcagttatttatagcggtggtagcacatactacgcagactccgtgaagggccgattcaccatctccagagacaattccaaggacacgctgtatcttcaaatgaacagcctgagagccgaggacacggccgtgtattactgtgtggtggtgactgctactccccatgggtactggggccagggaaccctggtcaccgtctcctcag
+6	lcl|FLN1FA001AX4MF.1|	productive	IGHV4-39	770	100	155/155 nt			IGHJ4	222	95.83	46/48 nt	IGHD3-22	2	X	7	15	X.7.15	[X.6.38.11]	CVVNYYDSSGYYYIDYW	in-frame	+						ggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgtgtggtaaattactatgatagtagtggttattactacatagactactggggccagggaaccctggtcaccgtctcctcag
+7	lcl|FLN1FA0074PUDE.1|	productive	IGHV4-39	770	100	155/155 nt			IGHJ4	222	95.83	46/48 nt	IGHD3-22	2	X	7	15	X.7.15	[X.6.38.11]	CVVNYYDSSGYYYIDYW	in-frame	+						ggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgtgtggtaaattactatgatagtagtggttattactacatagactactggggccagggaaccctggtcaccgtctcctcag
+8	lcl|FLN1FA0013V4SA.1|	productive	IGHV1-3	790	100	159/159 nt			IGHJ4	186	87.5	42/48 nt	IGHD2-15	2	X	8	16	X.8.16	[X.7.38.11]	CYLGYCSGGSCYPQVGYW	in-frame	+						aggcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttatttaggatattgtagtggtggtagctgctaccctcaggttggctactggggccagggaaccctggtcaccgtctcctcag
+9	lcl|FLN1FA00056KW6.1|	productive	IGHV1-3	775	100	156/156 nt			IGHJ4	186	87.5	42/48 nt	IGHD3-16	2	X	8	9	X.8.9	[X.6.38.11]	CYISGSYVGYW	in-frame	+						cttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttacatttcggggagttatgtaggctactggggccagggaaccctggtcaccgtctcctcag
+10	lcl|FLN1FA006WKNJR.1|	productive	IGHV3-53	771	99.36	156/157 nt			IGHJ4	168	83.33	40/48 nt	IGHD2-21	3	X	7	10	X.7.10	[X.7.38.11]	CVVVTATPHGYW	in-frame	+						ggggctggagtgggtctcagttatttatagcggtggtagcacatactacgcagactccgtgaagggccgattcaccatctccagagacaattccaaggacacgctgtatcttcaaatgaacagcctgagagccgaggacacggccgtgtattactgtgtggtggtgactgctactccccatgggtactggggccagggaaccctggtcaccgtctcctcag
+11	lcl|FLN1FA008ANOPH.1|	productive	IGHV4-39	775	100	156/156 nt			IGHJ4	195	89.58	43/48 nt	IGHD3-10	3	X	7	11	X.7.11	[X.7.38.11]	CYSAVVRGRFDYW	in-frame	+						gggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag
+12	lcl|FLN1FA005T7JJ8.1|	productive	IGHV3-33	795	100	160/160 nt			IGHJ4	222	95.83	46/48 nt	IGHD3-22	2	X	8	15	X.8.15	[X.7.38.11]	CVTYYYDSSGYPYFDYW	in-frame	+						ggggctggagtgggtggcagttatatggtatgatggaagtaataaatactatgcagactccgtgaagggccgattcaccatctccagagacaattccaagaacacgctgtatctgcaaatgaacagcctgagagccgaggacacggctgtgtattactgtgtaacgtattactatgatagtagtggttatccttactttgactactggggccagggaaccctggtcaccgtctcctcag
+13	lcl|FLN1FA0018WER7.1|	productive	IGHV4-39	770	100	155/155 nt			IGHJ4	222	95.83	46/48 nt	IGHD3-22	2	X	7	15	X.7.15	[X.6.38.11]	CVVNYYDSSGYYYIDYW	in-frame	+						ggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgtgtggtaaattactatgatagtagtggttattactacatagactactggggccagggaaccctggtcaccgtctcctcag
+14	lcl|FLN1FA004BRKX9.1|	productive	IGHV1-3	775	100	156/156 nt			IGHJ4	186	87.5	42/48 nt	IGHD3-16	2	X	8	9	X.8.9	[X.6.38.11]	CYISGSYVGYW	in-frame	+						cttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttacatttcggggagttatgtaggctactggggccagggaaccctggtcaccgtctcctcag
+15	lcl|FLN1FA00826HO1.1|	productive	IGHV4-39	775	100	156/156 nt			IGHJ4	195	89.58	43/48 nt	IGHD3-10	3	X	7	11	X.7.11	[X.7.38.11]	CYSAVVRGRFDYW	in-frame	+						gggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag
+16	lcl|FLN1FA0041SQ1V.1|	productive	IGHV3-53	771	99.36	156/157 nt			IGHJ4	168	83.33	40/48 nt	IGHD2-21	3	X	7	10	X.7.10	[X.7.38.11]	CVVVTATPHGYW	in-frame	+						ggggctggagtgggtctcagttatttatagcggtggtagcacatactacgcagactccgtgaagggccgattcaccatctccagagacaattccaaggacacgctgtatcttcaaatgaacagcctgagagccgaggacacggccgtgtattactgtgtggtggtgactgctactccccatgggtactggggccagggaaccctggtcaccgtctcctcag
+17	lcl|FLN1FA000BBO91.1|	productive	IGHV3-33	795	100	160/160 nt			IGHJ4	222	95.83	46/48 nt	IGHD3-22	2	X	8	15	X.8.15	[X.7.38.11]	CVTYYYDSSGYPYFDYW	in-frame	+						ggggctggagtgggtggcagttatatggtatgatggaagtaataaatactatgcagactccgtgaagggccgattcaccatctccagagacaattccaagaacacgctgtatctgcaaatgaacagcctgagagccgaggacacggctgtgtattactgtgtaacgtattactatgatagtagtggttatccttactttgactactggggccagggaaccctggtcaccgtctcctcag
+18	lcl|FLN1FA008W37HH.1|	productive	IGHV4-39	775	100	156/156 nt			IGHJ4	195	89.58	43/48 nt	IGHD3-10	3	X	7	11	X.7.11	[X.7.38.11]	CYSAVVRGRFDYW	in-frame	+						gggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag
+19	lcl|FLN1FA0080EWJB.1|	productive	IGHV1-3	775	100	156/156 nt			IGHJ4	186	87.5	42/48 nt	IGHD3-16	2	X	8	9	X.8.9	[X.6.38.11]	CYISGSYVGYW	in-frame	+						cttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttacatttcggggagttatgtaggctactggggccagggaaccctggtcaccgtctcctcag
+20	lcl|FLN1FA003C09AP.1|	productive	IGHV1-3	790	100	159/159 nt			IGHJ4	186	87.5	42/48 nt	IGHD2-15	2	X	8	16	X.8.16	[X.7.38.11]	CYLGYCSGGSCYPQVGYW	in-frame	+						aggcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttatttaggatattgtagtggtggtagctgctaccctcaggttggctactggggccagggaaccctggtcaccgtctcctcag
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def4_BCR_output1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,9 @@
+	V-GENE	J-GENE	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	IGHV1-3	IGHJ4	CYISGSYVGYW	4	4/20	20.0000
+2	IGHV4-39	IGHJ4	CYSAVVRGRFDYW	4	4/20	20.0000
+3	IGHV3-53	IGHJ4	CVVVTATPHGYW	3	3/20	15.0000
+4	IGHV4-39	IGHJ4	CVVNYYDSSGYYYIDYW	3	3/20	15.0000
+5	IGHV1-3	IGHJ4	CYLGYCSGGSCYPQVGYW	2	2/20	10.0000
+6	IGHV3-33	IGHJ4	CVTYYYDSSGYPYFDYW	2	2/20	10.0000
+7	IGHV1-69 or IGHV1-69D	IGHJ4	CYLGYCSGGSCYPQVGYW	1	1/20	5.0000
+8	IGHV3-30 or IGHV3-30-3	IGHJ4	CVTYCSGGSCYFDYW	1	1/20	5.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def4_BCR_output2.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,9 @@
+	V-GENE	J-GENE	AA JUNCTION	Frequency %
+1	IGHV1-3	IGHJ4	CYISGSYVGYW	20.0000
+2	IGHV4-39	IGHJ4	CYSAVVRGRFDYW	20.0000
+3	IGHV3-53	IGHJ4	CVVVTATPHGYW	15.0000
+4	IGHV4-39	IGHJ4	CVVNYYDSSGYYYIDYW	15.0000
+5	IGHV1-3	IGHJ4	CYLGYCSGGSCYPQVGYW	10.0000
+6	IGHV3-33	IGHJ4	CVTYYYDSSGYPYFDYW	10.0000
+7	IGHV1-69 or IGHV1-69D	IGHJ4	CYLGYCSGGSCYPQVGYW	5.0000
+8	IGHV3-30 or IGHV3-30-3	IGHJ4	CVTYCSGGSCYFDYW	5.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def4_BCR_output3.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,6 @@
+	input	%
+Dominant Clonotype(V-J-CDR3)	IGHV1-3,IGHJ4,CYISGSYVGYW	
+Frequency	20.0000	
+Number of Clonotypes(V-J-CDR3)	8	
+Expanding Clonotypes(V-J-CDR3)	6	75.0000
+Singletons	2	25.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def4_TCR_input1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	Sequence ID	Functionality	V-GENE	V-REGION score	V-REGION identity %	V-REGION identity nt	V-REGION identity % (with ins/del events)	V-REGION identity nt (with ins/del events)	J-GENE	J-REGION score	J-REGION identity %	J-REGION identity nt	D-GENE	D-REGION reading frame	CDR1-IMGT length	CDR2-IMGT length	CDR3-IMGT length	CDR-IMGT lengths	FR-IMGT lengths	AA JUNCTION	JUNCTION frame	Orientation	Functionality comment	V-REGION potential ins/del	J-GENE and allele comment	V-REGION insertions	V-REGION deletions	Sequence
+1	@SRR060727.12120 SOLEXA7:7:2:351:1247 length=202	productive	TRBV28	145	100	30/30 nt			TRBJ2-7	235	100	47/47 nt	TRBD1	3	X	X	12	X.X.12	[X.X.10.10]	CAAGGQGNSYEQYF	in-frame	+						agcaccaaccagacatctatgtacctctgtgccgctggggggcagggaaactcctacgagcagtacttcgggccgggcaccaggctcacggtcacagaggataacgggtgggaacacgtttttcaggtcctctgtgaccgtgagcctggtgcccggcccgaagtactgctcgtaggagtttccctgccccccagcggcacag
+2	@SRR060727.14069 SOLEXA7:7:2:622:201 length=202	productive	TRBV30	95	100	20/20 nt			TRBJ1-1	195	89.58	43/48 nt	TRBD2	3	X	X	10	X.X.10	[X.X.6.10]	CAAEGILAEAFF	in-frame	+						actctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaacaaggtgttctaacgggtgggnacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag
+3	@SRR060727.45221 SOLEXA7:7:5:1541:638 length=202	productive	TRBV30	145	100	30/30 nt			TRBJ1-1	195	89.58	43/48 nt	TRBD2	3	X	X	10	X.X.10	[X.X.10.10]	CAAEGILAEAFF	in-frame	+						cttctcagtgactctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaataacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag
+4	@SRR060727.49324 SOLEXA7:7:6:384:121 length=202	productive	TRBV10-3	165	100	34/34 nt			TRBJ1-1	240	100	48/48 nt	TRBD1	2	X	X	11	X.X.11	[X.X.11.10]	CAACEGLNTEAFF	in-frame	+						cgctaccagctcccagacatctgtgtacttctgtgccgcatgtgaggggctgaacactgaagctttctttggacaaggcaccagactcacagttgtagaggtaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgttcagcccctcacatgcggcacagaag
+5	@SRR060727.85642 SOLEXA7:7:10:98:1840 length=202	productive	TRBV30	115	100	24/24 nt			TRBJ1-1	195	89.58	43/48 nt	TRBD2	3	X	X	10	X.X.10	[X.X.8.10]	CAAEGILAEAFF	in-frame	+						agtgactctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagcggacctgaacaagggtaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag
+6	@SRR060727.100243 SOLEXA7:7:11:766:821 length=202	productive	TRBV15	105	100	22/22 nt			TRBJ1-1	222	95.83	46/48 nt	TRBD1	1	X	X	11	X.X.11	[X.X.7.10]	CAAGGKRYTEAFF	in-frame	-						ggacgcagccatgtacctgtgtgccgcaggggggaaacggtacactgaagctttctttggacaaggcaccagactcacagttgtagaggacctggacaaggtacaactgtgagtctggtgccttgtccaaagaaagcttcagtgtaccgtttcccccctgcggcacacaggtacatggctgcgtcccccaggcctggtgagc
+7	@SRR060727.114177 SOLEXA7:7:12:1063:980 length=202	productive	TRBV19	150	100	31/31 nt			TRBJ1-5	241	98	49/50 nt	TRBD1	2	X	X	13	X.X.13	[X.X.10.10]	CAAGEGEVRNQPQHF	in-frame	+						ccaaaagaacccgacagctttctatctctgtgctgcgggtgagggggaggttagaaatcagccccagcattttggtgatgggactcgactctccatcctagtaacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatcaccaaaatgctggggctgatttctaacctccccctcacccgcagca
+8	@SRR060727.130541 SOLEXA7:7:14:145:1124 length=202	productive	TRBV3-1	160	100	33/33 nt			TRBJ1-5	232	96	48/50 nt	TRBD1	2	X	X	12	X.X.12	[X.X.11.10]	CAAGQGFGNQPQHF	in-frame	+						ctggagcttggtgactctgctgtgtatttctgtgccgcaggtcagggttttgggaatcagccccagcattttggtgatgggactcgactctccatcctagataacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatcaccaaaatgctggggctgattcccaaaaccctgacctgcggcacag
+9	@SRR060727.175366 SOLEXA7:7:18:291:1226 length=202	productive	TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6	95	100	20/20 nt			TRBJ1-1	231	97.92	47/48 nt	TRBD1	1	X	X	13	X.X.13	[X.X.6.10]	CAAGPRAGTNTEAFF	in-frame	+						agacatctgtgtacttctgtgccgctggaccaagggcagggacgaacactgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaactaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgttcgtccctgcccttggtccagcggca
+10	@SRR060727.184926 SOLEXA7:7:19:439:598 length=202	productive	TRBV6-1 or TRBV6-5 or TRBV6-6	140	100	29/29 nt			TRBJ1-1	231	97.92	47/48 nt	TRBD1	2	X	X	12	X.X.12	[X.X.9.10]	CAADAQGGNTEAFF	in-frame	+						ctccctcccagacatctgtgtacttctgtgccgcggacgcacagggggggaacactgaagctttctttggacaaggcaccagactcacagttgtagaggactaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgttccccccctgtgcgtccgcggcacag
+11	@SRR060727.187683 SOLEXA7:7:19:809:1493 length=202	productive	TRBV19	135	100	28/28 nt			TRBJ1-5	232	96	48/50 nt	TRBD1	2	X	X	13	X.X.13	[X.X.9.10]	CAAGEGEVRNQPQHF	in-frame	+						aaagaacccgacagctttctatctctgtgctgcgggtgagggggaggttagaaatcagccccagcattttggagatgggactcgactctccatcctagaggtaacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatctccaaaatgctggggctgatttctaacctccccctcacccgcagca
+12	@SRR060727.190355 SOLEXA7:7:19:1314:185 length=202	productive	TRBV27	130	100	27/27 nt			TRBJ1-5	223	94	47/50 nt	TRBD1	3	X	X	9	X.X.9	[X.X.9.10]	CAAGPNQPQHF	in-frame	+						cccaaccagacctctctgtacttctgtgccgccgggcccaatcagccccagcattttggtgatgggactcgactctccatcctagaggacctgaacaaggttaacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatcaccaaaatgctggggctgattgggcccggcggcacagaagtacaga
+13	@SRR060727.196094 SOLEXA7:7:20:579:567 length=202	productive	TRBV12-3 or TRBV12-4	120	100	25/25 nt			TRBJ2-5	195	89.58	43/48 nt	TRBD1	1	X	X	9	X.X.9	[X.X.8.10]	CAAGTIETQYF	in-frame	+						cagggactcagctgtgtacttctgtgccgcggggacaattgagacccagtacttcgggccaggcacgcggctcctggtgctcgaggacatgaaaaaagtgttaacgggtgggaacacgtttttcaggtcctcgagcaccaggagccgcgtgcctggcccgaagtactgggtctcaattgtccccgcggcacagaagtacaca
+14	@SRR060727.208531_SOLEXA7:7:21:1082:1793_length=20	productive	TRBV25-1	120	100	25/25 nt			TRBJ1-1	195	89.58	43/48 nt	TRBD2	2	X	X	10	X.X.10	[X.X.8.10]	CAAGGGAPEAFF	in-frame	+						ctcacatacctctcagtacctctgtgcagcgggtggaggggccccagaagctttctttggacaaggcaccagactcacagttgtagaggacctgaacaaggtaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttctggggcccctccacccgctgcacagagggaa
+15	@SRR060727.236848 SOLEXA7:7:24:1329:676 length=202	productive	TRBV10-3 or TRBV6-1 or TRBV6-5 or TRBV6-6	120	100	25/25 nt			TRBJ2-7	235	100	47/47 nt	TRBD1	1	X	X	11	X.X.11	[X.X.8.10]	CAAGTGLSYEQYF	in-frame	+						ctcccagacatctgtgtacttctgtgccgcggggacaggactctcctacgagcagtacttcgggccgggcaccaggctcacggtcacagaggacctgaaaataacgggtgggaacacgtttttcaggtcctctgtgaccgtgagcctggtgcccggcccgaagtactgctcgtaggagagtcctgtccccgcggcacagaag
+16	@SRR060727.258473 SOLEXA7:7:27:271:1727 length=202	productive	TRBV30	100	100	21/21 nt			TRBJ1-4	201	88.24	45/51 nt	TRBD1	2	X	X	10	X.X.10	[X.X.7.10]	CAAGQVGEKLFF	in-frame	+						gactctggcttctatctctgtgccgcgggacaagtgggtgaaaaactgttttttggcagtggaacccagctctctgtcttggaggacctgaacaacgaggttaacgggtgggaacaccttgttcaggtcctccaagacagagagctgggttccactgccaaaaaacagtttttcacccacttgtcccgcggcacagagatag
+17	@SRR060727.274111 SOLEXA7:7:28:1699:290 length=202	productive	TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6	100	100	21/21 nt			TRBJ1-1	222	95.83	46/48 nt	TRBD1	1	X	X	13	X.X.13	[X.X.7.10]	CAAGPRAGTNTEAFF	in-frame	+						cagacatctgtgtacttctgtgccgctggaccaagggcagggacgaacactgaagctttctttgtacaaggcaccagactcacagttgtagaggacctgaataacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtacaaagaaagcttcagtgttcgtccctgcccttggtccagcggca
+18	@SRR060727.275014 SOLEXA7:7:29:152:1739 length=202	productive	TRBV30	130	100	27/27 nt			TRBJ1-1	195	89.58	43/48 nt	TRBD2	3	X	X	10	X.X.10	[X.X.9.10]	CAAEGILAEAFF	in-frame	+						ctcagtgactctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaacaataacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag
+19	@SRR060727.281458_SOLEXA7:7:29:1133:1441_length=20	productive	TRBV15	141	96.77	30/31 nt			TRBJ1-1	222	95.83	46/48 nt	TRBD1	1	X	X	11	X.X.11	[X.X.10.10]	CAAGGKRYTEAFF	in-frame	+						atgcctgggggacgcagccatgtacctgtgtgccgcaggggggaaacggtacactgaagctttctttggacaaggcaccagactcacagttgtagaggacctaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgtaccgtttcccccctgcggcacacagg
+20	@SRR060727.283135_SOLEXA7:7:29:1539:1405_length=20	productive	TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6	100	100	21/21 nt			TRBJ2-3	200	89.8	44/49 nt	TRBD2	1	X	X	8	X.X.8	[X.X.7.10]	CAAGEDTQYF	in-frame	+						cagacatctgtgtacttctgtgccgccggggaggatacgcagtattttggcccaggcacccggctgacagtgctcgaggacctgaaaaacgtgttcccacctaacgggtgggaacacgtttttcaggtcctcgagcactgtcagccgggtgcctgggccaaaatactgcgtatcctccccggcggcacagaagtacacagat
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def4_TCR_output1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,15 @@
+	V-GENE	J-GENE	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	TRBV30	TRBJ1-1	CAAEGILAEAFF	4	4/20	20.0000
+2	TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6	TRBJ1-1	CAAGPRAGTNTEAFF	2	2/20	10.0000
+3	TRBV15	TRBJ1-1	CAAGGKRYTEAFF	2	2/20	10.0000
+4	TRBV19	TRBJ1-5	CAAGEGEVRNQPQHF	2	2/20	10.0000
+5	TRBV10-3	TRBJ1-1	CAACEGLNTEAFF	1	1/20	5.0000
+6	TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6	TRBJ2-3	CAAGEDTQYF	1	1/20	5.0000
+7	TRBV10-3 or TRBV6-1 or TRBV6-5 or TRBV6-6	TRBJ2-7	CAAGTGLSYEQYF	1	1/20	5.0000
+8	TRBV12-3 or TRBV12-4	TRBJ2-5	CAAGTIETQYF	1	1/20	5.0000
+9	TRBV25-1	TRBJ1-1	CAAGGGAPEAFF	1	1/20	5.0000
+10	TRBV27	TRBJ1-5	CAAGPNQPQHF	1	1/20	5.0000
+11	TRBV28	TRBJ2-7	CAAGGQGNSYEQYF	1	1/20	5.0000
+12	TRBV3-1	TRBJ1-5	CAAGQGFGNQPQHF	1	1/20	5.0000
+13	TRBV30	TRBJ1-4	CAAGQVGEKLFF	1	1/20	5.0000
+14	TRBV6-1 or TRBV6-5 or TRBV6-6	TRBJ1-1	CAADAQGGNTEAFF	1	1/20	5.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def4_TCR_output2.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,11 @@
+	V-GENE	J-GENE	AA JUNCTION	Frequency %
+1	TRBV30	TRBJ1-1	CAAEGILAEAFF	20.0000
+2	TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6	TRBJ1-1	CAAGPRAGTNTEAFF	10.0000
+3	TRBV15	TRBJ1-1	CAAGGKRYTEAFF	10.0000
+4	TRBV19	TRBJ1-5	CAAGEGEVRNQPQHF	10.0000
+5	TRBV10-3	TRBJ1-1	CAACEGLNTEAFF	5.0000
+6	TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6	TRBJ2-3	CAAGEDTQYF	5.0000
+7	TRBV10-3 or TRBV6-1 or TRBV6-5 or TRBV6-6	TRBJ2-7	CAAGTGLSYEQYF	5.0000
+8	TRBV12-3 or TRBV12-4	TRBJ2-5	CAAGTIETQYF	5.0000
+9	TRBV25-1	TRBJ1-1	CAAGGGAPEAFF	5.0000
+10	TRBV27	TRBJ1-5	CAAGPNQPQHF	5.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def4_TCR_output3.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,6 @@
+	input1.csv	%
+Dominant Clonotype(V-J-CDR3)	TRBV30,TRBJ1-1,CAAEGILAEAFF	
+Frequency	20.0000	
+Number of Clonotypes(V-J-CDR3)	14	
+Expanding Clonotypes(V-J-CDR3)	4	28.5714
+Singletons	10	71.4286
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def5_BCR_input1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	Sequence ID	Functionality	V-GENE	V-REGION score	V-REGION identity %	V-REGION identity nt	V-REGION identity % (with ins/del events)	V-REGION identity nt (with ins/del events)	J-GENE	J-REGION score	J-REGION identity %	J-REGION identity nt	D-GENE	D-REGION reading frame	CDR1-IMGT length	CDR2-IMGT length	CDR3-IMGT length	CDR-IMGT lengths	FR-IMGT lengths	AA JUNCTION	JUNCTION frame	Orientation	Functionality comment	V-REGION potential ins/del	J-GENE and allele comment	V-REGION insertions	V-REGION deletions	Sequence
+1	lcl|FLN1FA001B9SVM.1|	productive	IGHV1-69 or IGHV1-69D	790	100	159/159 nt			IGHJ4	186	87.5	42/48 nt	IGHD2-15	2	X	8	16	X.8.16	[X.7.38.11]	CYLGYCSGGSCYPQVGYW	in-frame	+						gggcttgagtggatgggagggatcatccctatctttggtacagcaaactacgcacagaagttccagggcagagtcacgattaccgcggacgaatccacgagcacagcctacatggagctgagcagcctgagatctgaggacacggccgtgtattactgttatttaggatattgtagtggtggtagctgctaccctcaggttggctactggggccagggaaccctggtcaccgtctcctcag
+2	lcl|FLN1FA001CUVDF.1|	productive	IGHV3-30 or IGHV3-30-3	786	99.38	159/160 nt			IGHJ4	231	97.92	47/48 nt	IGHD2-15	2	X	8	13	X.8.13	[X.7.38.11]	CVTYCSGGSCYFDYW	in-frame	+						ggggctggagtgggtggcagttatatcatatgatggaagtaataaatactacgtagactccgtgaagggccgattcaccatctccagagacaattccaagaacacgctgtatctgcaaatgaacagcctgagagctgaggacacggctgtgtattactgtgttacatattgtagtggtggtagctgctactttgactactggggccagggaaccctggtcaccgtctcctcag
+3	lcl|FLN1FA001DLPHD.1|	productive	IGHV1-3	775	100	156/156 nt			IGHJ4	186	87.5	42/48 nt	IGHD3-16	2	X	8	9	X.8.9	[X.6.38.11]	CYISGSYVGYW	in-frame	+						cttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttacatttcggggagttatgtaggctactggggccagggaaccctggtcaccgtctcctcag
+4	lcl|FLN1FA002QTWMQ.1|	productive	IGHV4-39	775	100	156/156 nt			IGHJ4	195	89.58	43/48 nt	IGHD3-10	3	X	7	11	X.7.11	[X.7.38.11]	CYSAVVRGRFDYW	in-frame	+						gggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag
+5	lcl|FLN1FA002Q975Z.1|	productive	IGHV3-53	771	99.36	156/157 nt			IGHJ4	168	83.33	40/48 nt	IGHD2-21	3	X	7	10	X.7.10	[X.7.38.11]	CVVVTATPHGYW	in-frame	+						ggggctggagtgggtctcagttatttatagcggtggtagcacatactacgcagactccgtgaagggccgattcaccatctccagagacaattccaaggacacgctgtatcttcaaatgaacagcctgagagccgaggacacggccgtgtattactgtgtggtggtgactgctactccccatgggtactggggccagggaaccctggtcaccgtctcctcag
+6	lcl|FLN1FA001AX4MF.1|	productive	IGHV4-39	770	100	155/155 nt			IGHJ4	222	95.83	46/48 nt	IGHD3-22	2	X	7	15	X.7.15	[X.6.38.11]	CVVNYYDSSGYYYIDYW	in-frame	+						ggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgtgtggtaaattactatgatagtagtggttattactacatagactactggggccagggaaccctggtcaccgtctcctcag
+7	lcl|FLN1FA0074PUDE.1|	productive	IGHV4-39	770	100	155/155 nt			IGHJ4	222	95.83	46/48 nt	IGHD3-22	2	X	7	15	X.7.15	[X.6.38.11]	CVVNYYDSSGYYYIDYW	in-frame	+						ggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgtgtggtaaattactatgatagtagtggttattactacatagactactggggccagggaaccctggtcaccgtctcctcag
+8	lcl|FLN1FA0013V4SA.1|	productive	IGHV1-3	790	100	159/159 nt			IGHJ4	186	87.5	42/48 nt	IGHD2-15	2	X	8	16	X.8.16	[X.7.38.11]	CYLGYCSGGSCYPQVGYW	in-frame	+						aggcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttatttaggatattgtagtggtggtagctgctaccctcaggttggctactggggccagggaaccctggtcaccgtctcctcag
+9	lcl|FLN1FA00056KW6.1|	productive	IGHV1-3	775	100	156/156 nt			IGHJ4	186	87.5	42/48 nt	IGHD3-16	2	X	8	9	X.8.9	[X.6.38.11]	CYISGSYVGYW	in-frame	+						cttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttacatttcggggagttatgtaggctactggggccagggaaccctggtcaccgtctcctcag
+10	lcl|FLN1FA006WKNJR.1|	productive	IGHV3-53	771	99.36	156/157 nt			IGHJ4	168	83.33	40/48 nt	IGHD2-21	3	X	7	10	X.7.10	[X.7.38.11]	CVVVTATPHGYW	in-frame	+						ggggctggagtgggtctcagttatttatagcggtggtagcacatactacgcagactccgtgaagggccgattcaccatctccagagacaattccaaggacacgctgtatcttcaaatgaacagcctgagagccgaggacacggccgtgtattactgtgtggtggtgactgctactccccatgggtactggggccagggaaccctggtcaccgtctcctcag
+11	lcl|FLN1FA008ANOPH.1|	productive	IGHV4-39	775	100	156/156 nt			IGHJ4	195	89.58	43/48 nt	IGHD3-10	3	X	7	11	X.7.11	[X.7.38.11]	CYSAVVRGRFDYW	in-frame	+						gggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag
+12	lcl|FLN1FA005T7JJ8.1|	productive	IGHV3-33	795	100	160/160 nt			IGHJ4	222	95.83	46/48 nt	IGHD3-22	2	X	8	15	X.8.15	[X.7.38.11]	CVTYYYDSSGYPYFDYW	in-frame	+						ggggctggagtgggtggcagttatatggtatgatggaagtaataaatactatgcagactccgtgaagggccgattcaccatctccagagacaattccaagaacacgctgtatctgcaaatgaacagcctgagagccgaggacacggctgtgtattactgtgtaacgtattactatgatagtagtggttatccttactttgactactggggccagggaaccctggtcaccgtctcctcag
+13	lcl|FLN1FA0018WER7.1|	productive	IGHV4-39	770	100	155/155 nt			IGHJ4	222	95.83	46/48 nt	IGHD3-22	2	X	7	15	X.7.15	[X.6.38.11]	CVVNYYDSSGYYYIDYW	in-frame	+						ggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgtgtggtaaattactatgatagtagtggttattactacatagactactggggccagggaaccctggtcaccgtctcctcag
+14	lcl|FLN1FA004BRKX9.1|	productive	IGHV1-3	775	100	156/156 nt			IGHJ4	186	87.5	42/48 nt	IGHD3-16	2	X	8	9	X.8.9	[X.6.38.11]	CYISGSYVGYW	in-frame	+						cttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttacatttcggggagttatgtaggctactggggccagggaaccctggtcaccgtctcctcag
+15	lcl|FLN1FA00826HO1.1|	productive	IGHV4-39	775	100	156/156 nt			IGHJ4	195	89.58	43/48 nt	IGHD3-10	3	X	7	11	X.7.11	[X.7.38.11]	CYSAVVRGRFDYW	in-frame	+						gggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag
+16	lcl|FLN1FA0041SQ1V.1|	productive	IGHV3-53	771	99.36	156/157 nt			IGHJ4	168	83.33	40/48 nt	IGHD2-21	3	X	7	10	X.7.10	[X.7.38.11]	CVVVTATPHGYW	in-frame	+						ggggctggagtgggtctcagttatttatagcggtggtagcacatactacgcagactccgtgaagggccgattcaccatctccagagacaattccaaggacacgctgtatcttcaaatgaacagcctgagagccgaggacacggccgtgtattactgtgtggtggtgactgctactccccatgggtactggggccagggaaccctggtcaccgtctcctcag
+17	lcl|FLN1FA000BBO91.1|	productive	IGHV3-33	795	100	160/160 nt			IGHJ4	222	95.83	46/48 nt	IGHD3-22	2	X	8	15	X.8.15	[X.7.38.11]	CVTYYYDSSGYPYFDYW	in-frame	+						ggggctggagtgggtggcagttatatggtatgatggaagtaataaatactatgcagactccgtgaagggccgattcaccatctccagagacaattccaagaacacgctgtatctgcaaatgaacagcctgagagccgaggacacggctgtgtattactgtgtaacgtattactatgatagtagtggttatccttactttgactactggggccagggaaccctggtcaccgtctcctcag
+18	lcl|FLN1FA008W37HH.1|	productive	IGHV4-39	775	100	156/156 nt			IGHJ4	195	89.58	43/48 nt	IGHD3-10	3	X	7	11	X.7.11	[X.7.38.11]	CYSAVVRGRFDYW	in-frame	+						gggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgttatagcgcggtggtacggggaagatttgactactggggccagggaaccctggtcaccgtctcctcag
+19	lcl|FLN1FA0080EWJB.1|	productive	IGHV1-3	775	100	156/156 nt			IGHJ4	186	87.5	42/48 nt	IGHD3-16	2	X	8	9	X.8.9	[X.6.38.11]	CYISGSYVGYW	in-frame	+						cttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttacatttcggggagttatgtaggctactggggccagggaaccctggtcaccgtctcctcag
+20	lcl|FLN1FA003C09AP.1|	productive	IGHV1-3	790	100	159/159 nt			IGHJ4	186	87.5	42/48 nt	IGHD2-15	2	X	8	16	X.8.16	[X.7.38.11]	CYLGYCSGGSCYPQVGYW	in-frame	+						aggcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgttatttaggatattgtagtggtggtagctgctaccctcaggttggctactggggccagggaaccctggtcaccgtctcctcag
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def5_BCR_output1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,9 @@
+	V-GENE	D-GENE	J-GENE	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	IGHV1-3	IGHD3-16	IGHJ4	CYISGSYVGYW	4	4/20	20.0000
+2	IGHV4-39	IGHD3-10	IGHJ4	CYSAVVRGRFDYW	4	4/20	20.0000
+3	IGHV3-53	IGHD2-21	IGHJ4	CVVVTATPHGYW	3	3/20	15.0000
+4	IGHV4-39	IGHD3-22	IGHJ4	CVVNYYDSSGYYYIDYW	3	3/20	15.0000
+5	IGHV1-3	IGHD2-15	IGHJ4	CYLGYCSGGSCYPQVGYW	2	2/20	10.0000
+6	IGHV3-33	IGHD3-22	IGHJ4	CVTYYYDSSGYPYFDYW	2	2/20	10.0000
+7	IGHV1-69 or IGHV1-69D	IGHD2-15	IGHJ4	CYLGYCSGGSCYPQVGYW	1	1/20	5.0000
+8	IGHV3-30 or IGHV3-30-3	IGHD2-15	IGHJ4	CVTYCSGGSCYFDYW	1	1/20	5.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def5_BCR_output2.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,9 @@
+	V-GENE	D-GENE	J-GENE	AA JUNCTION	Frequency %
+1	IGHV1-3	IGHD3-16	IGHJ4	CYISGSYVGYW	20.0000
+2	IGHV4-39	IGHD3-10	IGHJ4	CYSAVVRGRFDYW	20.0000
+3	IGHV3-53	IGHD2-21	IGHJ4	CVVVTATPHGYW	15.0000
+4	IGHV4-39	IGHD3-22	IGHJ4	CVVNYYDSSGYYYIDYW	15.0000
+5	IGHV1-3	IGHD2-15	IGHJ4	CYLGYCSGGSCYPQVGYW	10.0000
+6	IGHV3-33	IGHD3-22	IGHJ4	CVTYYYDSSGYPYFDYW	10.0000
+7	IGHV1-69 or IGHV1-69D	IGHD2-15	IGHJ4	CYLGYCSGGSCYPQVGYW	5.0000
+8	IGHV3-30 or IGHV3-30-3	IGHD2-15	IGHJ4	CVTYCSGGSCYFDYW	5.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def5_BCR_output3.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,6 @@
+	input	%
+Dominant Clonotype(V-D-J-CDR3)	IGHV1-3,IGHD3-16,IGHJ4,CYISGSYVGYW	
+Frequency	20.0000	
+Number of Clonotypes(V-D-J-CDR3)	8	
+Expanding Clonotypes(V-D-J-CDR3)	6	75.0000
+Singletons	2	25.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def5_TCR_input1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	Sequence ID	Functionality	V-GENE	V-REGION score	V-REGION identity %	V-REGION identity nt	V-REGION identity % (with ins/del events)	V-REGION identity nt (with ins/del events)	J-GENE	J-REGION score	J-REGION identity %	J-REGION identity nt	D-GENE	D-REGION reading frame	CDR1-IMGT length	CDR2-IMGT length	CDR3-IMGT length	CDR-IMGT lengths	FR-IMGT lengths	AA JUNCTION	JUNCTION frame	Orientation	Functionality comment	V-REGION potential ins/del	J-GENE and allele comment	V-REGION insertions	V-REGION deletions	Sequence
+1	@SRR060727.12120 SOLEXA7:7:2:351:1247 length=202	productive	TRBV28	145	100	30/30 nt			TRBJ2-7	235	100	47/47 nt	TRBD1	3	X	X	12	X.X.12	[X.X.10.10]	CAAGGQGNSYEQYF	in-frame	+						agcaccaaccagacatctatgtacctctgtgccgctggggggcagggaaactcctacgagcagtacttcgggccgggcaccaggctcacggtcacagaggataacgggtgggaacacgtttttcaggtcctctgtgaccgtgagcctggtgcccggcccgaagtactgctcgtaggagtttccctgccccccagcggcacag
+2	@SRR060727.14069 SOLEXA7:7:2:622:201 length=202	productive	TRBV30	95	100	20/20 nt			TRBJ1-1	195	89.58	43/48 nt	TRBD2	3	X	X	10	X.X.10	[X.X.6.10]	CAAEGILAEAFF	in-frame	+						actctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaacaaggtgttctaacgggtgggnacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag
+3	@SRR060727.45221 SOLEXA7:7:5:1541:638 length=202	productive	TRBV30	145	100	30/30 nt			TRBJ1-1	195	89.58	43/48 nt	TRBD2	3	X	X	10	X.X.10	[X.X.10.10]	CAAEGILAEAFF	in-frame	+						cttctcagtgactctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaataacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag
+4	@SRR060727.49324 SOLEXA7:7:6:384:121 length=202	productive	TRBV10-3	165	100	34/34 nt			TRBJ1-1	240	100	48/48 nt	TRBD1	2	X	X	11	X.X.11	[X.X.11.10]	CAACEGLNTEAFF	in-frame	+						cgctaccagctcccagacatctgtgtacttctgtgccgcatgtgaggggctgaacactgaagctttctttggacaaggcaccagactcacagttgtagaggtaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgttcagcccctcacatgcggcacagaag
+5	@SRR060727.85642 SOLEXA7:7:10:98:1840 length=202	productive	TRBV30	115	100	24/24 nt			TRBJ1-1	195	89.58	43/48 nt	TRBD2	3	X	X	10	X.X.10	[X.X.8.10]	CAAEGILAEAFF	in-frame	+						agtgactctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagcggacctgaacaagggtaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag
+6	@SRR060727.100243 SOLEXA7:7:11:766:821 length=202	productive	TRBV15	105	100	22/22 nt			TRBJ1-1	222	95.83	46/48 nt	TRBD1	1	X	X	11	X.X.11	[X.X.7.10]	CAAGGKRYTEAFF	in-frame	-						ggacgcagccatgtacctgtgtgccgcaggggggaaacggtacactgaagctttctttggacaaggcaccagactcacagttgtagaggacctggacaaggtacaactgtgagtctggtgccttgtccaaagaaagcttcagtgtaccgtttcccccctgcggcacacaggtacatggctgcgtcccccaggcctggtgagc
+7	@SRR060727.114177 SOLEXA7:7:12:1063:980 length=202	productive	TRBV19	150	100	31/31 nt			TRBJ1-5	241	98	49/50 nt	TRBD1	2	X	X	13	X.X.13	[X.X.10.10]	CAAGEGEVRNQPQHF	in-frame	+						ccaaaagaacccgacagctttctatctctgtgctgcgggtgagggggaggttagaaatcagccccagcattttggtgatgggactcgactctccatcctagtaacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatcaccaaaatgctggggctgatttctaacctccccctcacccgcagca
+8	@SRR060727.130541 SOLEXA7:7:14:145:1124 length=202	productive	TRBV3-1	160	100	33/33 nt			TRBJ1-5	232	96	48/50 nt	TRBD1	2	X	X	12	X.X.12	[X.X.11.10]	CAAGQGFGNQPQHF	in-frame	+						ctggagcttggtgactctgctgtgtatttctgtgccgcaggtcagggttttgggaatcagccccagcattttggtgatgggactcgactctccatcctagataacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatcaccaaaatgctggggctgattcccaaaaccctgacctgcggcacag
+9	@SRR060727.175366 SOLEXA7:7:18:291:1226 length=202	productive	TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6	95	100	20/20 nt			TRBJ1-1	231	97.92	47/48 nt	TRBD1	1	X	X	13	X.X.13	[X.X.6.10]	CAAGPRAGTNTEAFF	in-frame	+						agacatctgtgtacttctgtgccgctggaccaagggcagggacgaacactgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaactaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgttcgtccctgcccttggtccagcggca
+10	@SRR060727.184926 SOLEXA7:7:19:439:598 length=202	productive	TRBV6-1 or TRBV6-5 or TRBV6-6	140	100	29/29 nt			TRBJ1-1	231	97.92	47/48 nt	TRBD1	2	X	X	12	X.X.12	[X.X.9.10]	CAADAQGGNTEAFF	in-frame	+						ctccctcccagacatctgtgtacttctgtgccgcggacgcacagggggggaacactgaagctttctttggacaaggcaccagactcacagttgtagaggactaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgttccccccctgtgcgtccgcggcacag
+11	@SRR060727.187683 SOLEXA7:7:19:809:1493 length=202	productive	TRBV19	135	100	28/28 nt			TRBJ1-5	232	96	48/50 nt	TRBD1	2	X	X	13	X.X.13	[X.X.9.10]	CAAGEGEVRNQPQHF	in-frame	+						aaagaacccgacagctttctatctctgtgctgcgggtgagggggaggttagaaatcagccccagcattttggagatgggactcgactctccatcctagaggtaacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatctccaaaatgctggggctgatttctaacctccccctcacccgcagca
+12	@SRR060727.190355 SOLEXA7:7:19:1314:185 length=202	productive	TRBV27	130	100	27/27 nt			TRBJ1-5	223	94	47/50 nt	TRBD1	3	X	X	9	X.X.9	[X.X.9.10]	CAAGPNQPQHF	in-frame	+						cccaaccagacctctctgtacttctgtgccgccgggcccaatcagccccagcattttggtgatgggactcgactctccatcctagaggacctgaacaaggttaacgggtgggaacaccttgttcaggtcctctaggatggagagtcgagtcccatcaccaaaatgctggggctgattgggcccggcggcacagaagtacaga
+13	@SRR060727.196094 SOLEXA7:7:20:579:567 length=202	productive	TRBV12-3 or TRBV12-4	120	100	25/25 nt			TRBJ2-5	195	89.58	43/48 nt	TRBD1	1	X	X	9	X.X.9	[X.X.8.10]	CAAGTIETQYF	in-frame	+						cagggactcagctgtgtacttctgtgccgcggggacaattgagacccagtacttcgggccaggcacgcggctcctggtgctcgaggacatgaaaaaagtgttaacgggtgggaacacgtttttcaggtcctcgagcaccaggagccgcgtgcctggcccgaagtactgggtctcaattgtccccgcggcacagaagtacaca
+14	@SRR060727.208531_SOLEXA7:7:21:1082:1793_length=20	productive	TRBV25-1	120	100	25/25 nt			TRBJ1-1	195	89.58	43/48 nt	TRBD2	2	X	X	10	X.X.10	[X.X.8.10]	CAAGGGAPEAFF	in-frame	+						ctcacatacctctcagtacctctgtgcagcgggtggaggggccccagaagctttctttggacaaggcaccagactcacagttgtagaggacctgaacaaggtaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttctggggcccctccacccgctgcacagagggaa
+15	@SRR060727.236848 SOLEXA7:7:24:1329:676 length=202	productive	TRBV10-3 or TRBV6-1 or TRBV6-5 or TRBV6-6	120	100	25/25 nt			TRBJ2-7	235	100	47/47 nt	TRBD1	1	X	X	11	X.X.11	[X.X.8.10]	CAAGTGLSYEQYF	in-frame	+						ctcccagacatctgtgtacttctgtgccgcggggacaggactctcctacgagcagtacttcgggccgggcaccaggctcacggtcacagaggacctgaaaataacgggtgggaacacgtttttcaggtcctctgtgaccgtgagcctggtgcccggcccgaagtactgctcgtaggagagtcctgtccccgcggcacagaag
+16	@SRR060727.258473 SOLEXA7:7:27:271:1727 length=202	productive	TRBV30	100	100	21/21 nt			TRBJ1-4	201	88.24	45/51 nt	TRBD1	2	X	X	10	X.X.10	[X.X.7.10]	CAAGQVGEKLFF	in-frame	+						gactctggcttctatctctgtgccgcgggacaagtgggtgaaaaactgttttttggcagtggaacccagctctctgtcttggaggacctgaacaacgaggttaacgggtgggaacaccttgttcaggtcctccaagacagagagctgggttccactgccaaaaaacagtttttcacccacttgtcccgcggcacagagatag
+17	@SRR060727.274111 SOLEXA7:7:28:1699:290 length=202	productive	TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6	100	100	21/21 nt			TRBJ1-1	222	95.83	46/48 nt	TRBD1	1	X	X	13	X.X.13	[X.X.7.10]	CAAGPRAGTNTEAFF	in-frame	+						cagacatctgtgtacttctgtgccgctggaccaagggcagggacgaacactgaagctttctttgtacaaggcaccagactcacagttgtagaggacctgaataacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtacaaagaaagcttcagtgttcgtccctgcccttggtccagcggca
+18	@SRR060727.275014 SOLEXA7:7:29:152:1739 length=202	productive	TRBV30	130	100	27/27 nt			TRBJ1-1	195	89.58	43/48 nt	TRBD2	3	X	X	10	X.X.10	[X.X.9.10]	CAAEGILAEAFF	in-frame	+						ctcagtgactctggcttctatctctgtgccgccgagggtattttggctgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaacaataacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagccaaaataccctcggcggcacagagatag
+19	@SRR060727.281458_SOLEXA7:7:29:1133:1441_length=20	productive	TRBV15	141	96.77	30/31 nt			TRBJ1-1	222	95.83	46/48 nt	TRBD1	1	X	X	11	X.X.11	[X.X.10.10]	CAAGGKRYTEAFF	in-frame	+						atgcctgggggacgcagccatgtacctgtgtgccgcaggggggaaacggtacactgaagctttctttggacaaggcaccagactcacagttgtagaggacctaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgtaccgtttcccccctgcggcacacagg
+20	@SRR060727.283135_SOLEXA7:7:29:1539:1405_length=20	productive	TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6	100	100	21/21 nt			TRBJ2-3	200	89.8	44/49 nt	TRBD2	1	X	X	8	X.X.8	[X.X.7.10]	CAAGEDTQYF	in-frame	+						cagacatctgtgtacttctgtgccgccggggaggatacgcagtattttggcccaggcacccggctgacagtgctcgaggacctgaaaaacgtgttcccacctaacgggtgggaacacgtttttcaggtcctcgagcactgtcagccgggtgcctgggccaaaatactgcgtatcctccccggcggcacagaagtacacagat
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def5_TCR_output1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,15 @@
+	V-GENE	D-GENE	J-GENE	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	TRBV30	TRBD2	TRBJ1-1	CAAEGILAEAFF	4	4/20	20.0000
+2	TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6	TRBD1	TRBJ1-1	CAAGPRAGTNTEAFF	2	2/20	10.0000
+3	TRBV15	TRBD1	TRBJ1-1	CAAGGKRYTEAFF	2	2/20	10.0000
+4	TRBV19	TRBD1	TRBJ1-5	CAAGEGEVRNQPQHF	2	2/20	10.0000
+5	TRBV10-3	TRBD1	TRBJ1-1	CAACEGLNTEAFF	1	1/20	5.0000
+6	TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6	TRBD2	TRBJ2-3	CAAGEDTQYF	1	1/20	5.0000
+7	TRBV10-3 or TRBV6-1 or TRBV6-5 or TRBV6-6	TRBD1	TRBJ2-7	CAAGTGLSYEQYF	1	1/20	5.0000
+8	TRBV12-3 or TRBV12-4	TRBD1	TRBJ2-5	CAAGTIETQYF	1	1/20	5.0000
+9	TRBV25-1	TRBD2	TRBJ1-1	CAAGGGAPEAFF	1	1/20	5.0000
+10	TRBV27	TRBD1	TRBJ1-5	CAAGPNQPQHF	1	1/20	5.0000
+11	TRBV28	TRBD1	TRBJ2-7	CAAGGQGNSYEQYF	1	1/20	5.0000
+12	TRBV3-1	TRBD1	TRBJ1-5	CAAGQGFGNQPQHF	1	1/20	5.0000
+13	TRBV30	TRBD1	TRBJ1-4	CAAGQVGEKLFF	1	1/20	5.0000
+14	TRBV6-1 or TRBV6-5 or TRBV6-6	TRBD1	TRBJ1-1	CAADAQGGNTEAFF	1	1/20	5.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def5_TCR_output2.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,11 @@
+	V-GENE	D-GENE	J-GENE	AA JUNCTION	Frequency %
+1	TRBV30	TRBD2	TRBJ1-1	CAAEGILAEAFF	20.0000
+2	TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6	TRBD1	TRBJ1-1	CAAGPRAGTNTEAFF	10.0000
+3	TRBV15	TRBD1	TRBJ1-1	CAAGGKRYTEAFF	10.0000
+4	TRBV19	TRBD1	TRBJ1-5	CAAGEGEVRNQPQHF	10.0000
+5	TRBV10-3	TRBD1	TRBJ1-1	CAACEGLNTEAFF	5.0000
+6	TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6	TRBD2	TRBJ2-3	CAAGEDTQYF	5.0000
+7	TRBV10-3 or TRBV6-1 or TRBV6-5 or TRBV6-6	TRBD1	TRBJ2-7	CAAGTGLSYEQYF	5.0000
+8	TRBV12-3 or TRBV12-4	TRBD1	TRBJ2-5	CAAGTIETQYF	5.0000
+9	TRBV25-1	TRBD2	TRBJ1-1	CAAGGGAPEAFF	5.0000
+10	TRBV27	TRBD1	TRBJ1-5	CAAGPNQPQHF	5.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/clono_compute_def5_TCR_output3.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,6 @@
+	input1.csv	%
+Dominant Clonotype(V-D-J-CDR3)	TRBV30,TRBD2,TRBJ1-1,CAAEGILAEAFF	
+Frequency	20.0000	
+Number of Clonotypes(V-D-J-CDR3)	14	
+Expanding Clonotypes(V-D-J-CDR3)	4	28.5714
+Singletons	10	71.4286
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/data_filter_BCR_input1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,11 @@
+Sequence number	Sequence ID	Functionality	V-GENE and allele	V-REGION score	V-REGION identity %	V-REGION identity nt	V-REGION identity % (with ins/del events)	V-REGION identity nt (with ins/del events)	J-GENE and allele	J-REGION score	J-REGION identity %	J-REGION identity nt	D-GENE and allele	D-REGION reading frame	CDR1-IMGT length	CDR2-IMGT length	CDR3-IMGT length	CDR-IMGT lengths	FR-IMGT lengths	AA JUNCTION	JUNCTION frame	Orientation	Functionality comment	V-REGION potential ins/del	J-GENE and allele comment	V-REGION insertions	V-REGION deletions	Sequence	Unnamed: 29
+1	lcl|FLN1FA002RWEZA.1|	productive	Homsap IGHV3-48*01 F	740	96.84	153/158 nt			Homsap IGHJ4*02 F	177	85.42	41/48 nt	Homsap IGHD3-22*01 F	2	X	8	17	X.8.17	[X.6.38.11]	CARAIPRYYYDTSGPNDYW	in-frame	+						ggctggagtgggtttcatacattagtagtaatagtggtgccatatactacgcagactctgtgaagggccgattcaccatctccagaaacaatgccaaggactcactgtatctgcaaatgaacagcctgagagccgaggacacggctgtgtattactgtgcgagagcgatcccccggtattactatgatactagtggcccaaacgactactggggccagggaaccctggtcaccgtctcctcag	
+2	lcl|FLN1FA001BLION.1|	unproductive	Homsap IGHV1-3*01 F	790	100	159/159 nt			Homsap IGHJ3*02 F	160	80	40/50 nt	Homsap IGHD6-13*01 F	2	X	8	X	X.8.X	[X.7.38.11]	CARVGSSWSDAFD#IW	out-of-frame	+						aggcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgtgcgagagtgggcagcagctggtctgatgcttttgattatctggggccaagggacaatggtcaccgtctcctcag	
+3	lcl|FLN1FA002SGU3N.1|	unproductive	Homsap IGHV3-9*01 F, or Homsap IGHV3-9*02 F	777	98.75	158/160 nt			Homsap IGHJ4*02 F	177	85.42	41/48 nt	Homsap IGHD3-16*02 F	3	X	8	X	X.8.X	[X.7.38.11]	CAKDKIGYYDYVWGSYRLG#YW	out-of-frame	+						gggcctggagtgggtctcaggtattagttggaatagtggtagaataggctatgcggactctgtgaacggccgattcaccatctccagagacaacgccaagaactccctgtatctgcaaatgaacagtctgagagctgaggacacggccttgtattactgtgcaaaagataaaattgggtattatgattacgtttgggggagttatcgtttgggtctactggggccagggaaccctggtcaccgtctcctcag	
+4	lcl|FLN1FA001D9GHY.1|	productive	Homsap IGHV3-33*01 F, or Homsap IGHV3-33*06 F	785	100	158/158 nt			Homsap IGHJ4*02 F	213	93.75	45/48 nt	Homsap IGHD3-22*01 F	2	X	8	18	X.8.18	[X.6.38.11]	CAREMYYYDSSGYYYAFDYW	in-frame	+						ggctggagtgggtggcagttatatggtatgatggaagtaataaatactatgcagactccgtgaagggccgattcaccatctccagagacaattccaagaacacgctgtatctgcaaatgaacagcctgagagccgaggacacggctgtgtattactgtgcgagagagatgtattactatgatagtagtggttattactacgcatttgactactggggccagggaaccctggtcaccgtctcctcag	
+5	lcl|FLN1FA001A1B0O.1|	productive	Homsap IGHV3-23*01 F, or Homsap IGHV3-23*04 F or Homsap IGHV3-23D*01 F or Homsap IGHV3-23D*02 F	776	99.37	157/158 nt			Homsap IGHJ4*02 F	168	83.33	40/48 nt	Homsap IGHD5-12*01 F	3	X	8	13	X.8.13	[X.6.38.11]	CARDMKGYDWSWVYW	in-frame	+						ggctggagtgggtctcagctattagtggtagtggtggtagcacatactacgcagactccgtgaagggccggttcaccatctccagagacaattccaagaacacgctgtatctgcaaatgaacagcctgagagccgaggacacggccgtgtattactgtgcgagagatatgaagggctacgattggagttgggtctactggggccagggaaccctggtcaccgtctcctcag	
+6	lcl|FLN1FA001DNXA5.1|	productive	Homsap IGHV4-39*03 F, or Homsap IGHV4-39*07 F	752	98.7	152/154 nt			Homsap IGHJ5*02 F	237	96.08	49/51 nt	Homsap IGHD3-10*01 F	2	X	7	25	X.7.25	[X.6.38.11]	CARDRPAAMKGYYGSGSYLMGNWFDPW	in-frame	+						ggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgctgcggacacggccgtgtattactgtgcgagagataggccagctgctatgaagggctactatggttcggggagttacctaatggggaactggttcgacccctggggccagggaaccctggtcaccgtctcctcag	
+7	lcl|FLN1FA002TLD0B.1|	productive	Homsap IGHV7-4-1*02 F	790	100	159/159 nt			Homsap IGHJ4*02 F	204	91.67	44/48 nt	Homsap IGHD3-10*01 F	2	X	8	26	X.8.26	[X.7.38.11]	CARGSRWLEVNYYGSGSYSSEKGPFDYW	in-frame	+						gggcttgagtggatgggatggatcaacaccaacactgggaacccaacgtatgcccagggcttcacaggacggtttgtcttctccttggacacctctgtcagcacggcatatctgcagatcagcagcctaaaggctgaggacactgccgtgtattactgtgcgagagggagtaggtggttggaggtaaattactatggttcggggagttatagctcagaaaaaggtccctttgactactggggccagggaaccctggtcaccgtctcctcag	
+8	lcl|FLN1FA001DMRRX.1|	productive	Homsap IGHV4-59*08 F	761	99.35	154/155 nt			Homsap IGHJ4*02 F	168	83.33	40/48 nt	Homsap IGHD5-18*01 F	2	X	7	9	X.7.9	[X.6.38.11]	CARALWFGEFW	in-frame	+						gactggagtggattgggtatatctattacagtgggagcaccaactacaacccctccctcaagagtcgagtcaccatatcagtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgtgcgagagcgctatggttcggggagttctggggccagggaaccctggtcaccgtctcctcag	
+9	lcl|FLN1FA001DN3RX.1|	unproductive (see comment)	Homsap IGHV3-72*01 F	825	100	166/166 nt			Homsap IGHJ4*02 F	213	93.75	45/48 nt	Homsap IGHD3-9*01 F	3	X	10	X	X.10.X	[X.7.38.11]	CARDRLGRSRVYDILTFYL##DYW	out-of-frame	+	 stop codons					ggggctggagtgggttggccgtactagaaacaaagctaacagttacaccacagaatacgccgcgtctgtgaaaggcagattcaccatctcaagagatgattcaaagaactcactgtatctgcaaatgaacagcctgaaaaccgaggacacggccgtgtattactgtgctagagatcgtttgggtcgttcccgtgtttacgatattttgaccttctacctaaattgactactggggccagggaaccctggtcaccgtctcctcag	
+10	lcl|FLN1FA001AOHI5.1|	productive	Homsap IGHV4-31*02 F, or Homsap IGHV4-31*03 F or Homsap IGHV4-31*04 F or Homsap IGHV4-31*06 F or Homsap IGHV4-31*07 F or Homsap IGHV4-59*06 F	667	92.31	144/156 nt			Homsap IGHJ4*02 F	195	89.58	43/48 nt	Homsap IGHD3-3*01 F	2	X	7	14	X.7.14	[X.7.38.11]	CARTSGYRLAPHSDYW	in-frame	+						ggcctggagtggattggatacatccattacagggggaacacctactccaatccgtccctcaagagtcgtgttaccatttcagtagacacgtctaagaaccaggtctccctgaagctgagctctgtgacggccgcggacacggccgtctatttctgtgcgagaacgagtggttatagattagcgccccattcggactactggggccagggaaccctggtcaccgtctcctcag	
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/data_filter_BCR_output1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,8 @@
+	Sequence ID	Functionality	V-GENE	V-REGION score	V-REGION identity %	V-REGION identity nt	V-REGION identity % (with ins/del events)	V-REGION identity nt (with ins/del events)	J-GENE	J-REGION score	J-REGION identity %	J-REGION identity nt	D-GENE	D-REGION reading frame	CDR1-IMGT length	CDR2-IMGT length	CDR3-IMGT length	CDR-IMGT lengths	FR-IMGT lengths	AA JUNCTION	JUNCTION frame	Orientation	Functionality comment	V-REGION potential ins/del	J-GENE and allele comment	V-REGION insertions	V-REGION deletions	Sequence
+1	lcl|FLN1FA002RWEZA.1|	productive	IGHV3-48	740	96.84	153/158 nt			IGHJ4	177	85.42	41/48 nt	IGHD3-22	2	X	8	17	X.8.17	[X.6.38.11]	CARAIPRYYYDTSGPNDYW	in-frame	+						ggctggagtgggtttcatacattagtagtaatagtggtgccatatactacgcagactctgtgaagggccgattcaccatctccagaaacaatgccaaggactcactgtatctgcaaatgaacagcctgagagccgaggacacggctgtgtattactgtgcgagagcgatcccccggtattactatgatactagtggcccaaacgactactggggccagggaaccctggtcaccgtctcctcag
+2	lcl|FLN1FA001D9GHY.1|	productive	IGHV3-33	785	100.0	158/158 nt			IGHJ4	213	93.75	45/48 nt	IGHD3-22	2	X	8	18	X.8.18	[X.6.38.11]	CAREMYYYDSSGYYYAFDYW	in-frame	+						ggctggagtgggtggcagttatatggtatgatggaagtaataaatactatgcagactccgtgaagggccgattcaccatctccagagacaattccaagaacacgctgtatctgcaaatgaacagcctgagagccgaggacacggctgtgtattactgtgcgagagagatgtattactatgatagtagtggttattactacgcatttgactactggggccagggaaccctggtcaccgtctcctcag
+3	lcl|FLN1FA001A1B0O.1|	productive	IGHV3-23 or IGHV3-23D	776	99.37	157/158 nt			IGHJ4	168	83.33	40/48 nt	IGHD5-12	3	X	8	13	X.8.13	[X.6.38.11]	CARDMKGYDWSWVYW	in-frame	+						ggctggagtgggtctcagctattagtggtagtggtggtagcacatactacgcagactccgtgaagggccggttcaccatctccagagacaattccaagaacacgctgtatctgcaaatgaacagcctgagagccgaggacacggccgtgtattactgtgcgagagatatgaagggctacgattggagttgggtctactggggccagggaaccctggtcaccgtctcctcag
+4	lcl|FLN1FA001DNXA5.1|	productive	IGHV4-39	752	98.7	152/154 nt			IGHJ5	237	96.08	49/51 nt	IGHD3-10	2	X	7	25	X.7.25	[X.6.38.11]	CARDRPAAMKGYYGSGSYLMGNWFDPW	in-frame	+						ggctggagtggattgggagtatctattatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatccgtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgctgcggacacggccgtgtattactgtgcgagagataggccagctgctatgaagggctactatggttcggggagttacctaatggggaactggttcgacccctggggccagggaaccctggtcaccgtctcctcag
+5	lcl|FLN1FA002TLD0B.1|	productive	IGHV7-4-1	790	100.0	159/159 nt			IGHJ4	204	91.67	44/48 nt	IGHD3-10	2	X	8	26	X.8.26	[X.7.38.11]	CARGSRWLEVNYYGSGSYSSEKGPFDYW	in-frame	+						gggcttgagtggatgggatggatcaacaccaacactgggaacccaacgtatgcccagggcttcacaggacggtttgtcttctccttggacacctctgtcagcacggcatatctgcagatcagcagcctaaaggctgaggacactgccgtgtattactgtgcgagagggagtaggtggttggaggtaaattactatggttcggggagttatagctcagaaaaaggtccctttgactactggggccagggaaccctggtcaccgtctcctcag
+6	lcl|FLN1FA001DMRRX.1|	productive	IGHV4-59	761	99.35	154/155 nt			IGHJ4	168	83.33	40/48 nt	IGHD5-18	2	X	7	9	X.7.9	[X.6.38.11]	CARALWFGEFW	in-frame	+						gactggagtggattgggtatatctattacagtgggagcaccaactacaacccctccctcaagagtcgagtcaccatatcagtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggctgtgtattactgtgcgagagcgctatggttcggggagttctggggccagggaaccctggtcaccgtctcctcag
+7	lcl|FLN1FA001AOHI5.1|	productive	IGHV4-31 or IGHV4-59	667	92.31	144/156 nt			IGHJ4	195	89.58	43/48 nt	IGHD3-3	2	X	7	14	X.7.14	[X.7.38.11]	CARTSGYRLAPHSDYW	in-frame	+						ggcctggagtggattggatacatccattacagggggaacacctactccaatccgtccctcaagagtcgtgttaccatttcagtagacacgtctaagaaccaggtctccctgaagctgagctctgtgacggccgcggacacggccgtctatttctgtgcgagaacgagtggttatagattagcgccccattcggactactggggccagggaaccctggtcaccgtctcctcag
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/data_filter_BCR_output2.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,4 @@
+	Sequence ID	Functionality	V-GENE and allele	V-REGION score	V-REGION identity %	V-REGION identity nt	V-REGION identity % (with ins/del events)	V-REGION identity nt (with ins/del events)	J-GENE and allele	J-REGION score	J-REGION identity %	J-REGION identity nt	D-GENE and allele	D-REGION reading frame	CDR1-IMGT length	CDR2-IMGT length	CDR3-IMGT length	CDR-IMGT lengths	FR-IMGT lengths	AA JUNCTION	JUNCTION frame	Orientation	Functionality comment	V-REGION potential ins/del	J-GENE and allele comment	V-REGION insertions	V-REGION deletions	Sequence	Reason
+2	lcl|FLN1FA001BLION.1|	unproductive	IGHV1-3	790	100.0	159/159 nt			Homsap IGHJ3*02 F	160	80.0	40/50 nt	Homsap IGHD6-13*01 F	2	X	8	X	X.8.X	[X.7.38.11]	CARVGSSWSDAFD#IW	out-of-frame	+						aggcttgagtggatgggatggatcaacgctggcaatggtaacacaaaatattcacagaagttccagggcagagtcaccattaccagggacacatccgcgagcacagcctacatggagctgagcagcctgagatctgaagacacggctgtgtattactgtgcgagagtgggcagcagctggtctgatgcttttgattatctggggccaagggacaatggtcaccgtctcctcag	X,#,*
+3	lcl|FLN1FA002SGU3N.1|	unproductive	IGHV3-9	777	98.75	158/160 nt			Homsap IGHJ4*02 F	177	85.42	41/48 nt	Homsap IGHD3-16*02 F	3	X	8	X	X.8.X	[X.7.38.11]	CAKDKIGYYDYVWGSYRLG#YW	out-of-frame	+						gggcctggagtgggtctcaggtattagttggaatagtggtagaataggctatgcggactctgtgaacggccgattcaccatctccagagacaacgccaagaactccctgtatctgcaaatgaacagtctgagagctgaggacacggccttgtattactgtgcaaaagataaaattgggtattatgattacgtttgggggagttatcgtttgggtctactggggccagggaaccctggtcaccgtctcctcag	X,#,*
+9	lcl|FLN1FA001DN3RX.1|	unproductive (see comment)	IGHV3-72	825	100.0	166/166 nt			Homsap IGHJ4*02 F	213	93.75	45/48 nt	Homsap IGHD3-9*01 F	3	X	10	X	X.10.X	[X.7.38.11]	CARDRLGRSRVYDILTFYL##DYW	out-of-frame	+	 stop codons					ggggctggagtgggttggccgtactagaaacaaagctaacagttacaccacagaatacgccgcgtctgtgaaaggcagattcaccatctcaagagatgattcaaagaactcactgtatctgcaaatgaacagcctgaaaaccgaggacacggccgtgtattactgtgctagagatcgtttgggtcgttcccgtgtttacgatattttgaccttctacctaaattgactactggggccagggaaccctggtcaccgtctcctcag	X,#,*
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/data_filter_BCR_output3.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,18 @@
+	sample	%
+Total reads of raw data	10	100.0000
+Not Null CDR3/V	10	100.0000
+filter out	0	0.0000
+Functional TRBV	10	100.0000
+filter out	0	0.0000
+Not Containing X,#,*	7	70.0000
+filter out	3	30.0000
+Productive	7	70.0000
+filter out	0	0.0000
+CDR3 landmarks C-W	7	70.0000
+filter out	0	0.0000
+Identity >= 70.0%	7	70.0000
+filter out	0	0.0000
+Total filter out A	3	30.0000
+Total filter in A	7	70.0000
+Total filter out	3	30.0000
+Total filter in	7	70.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/data_filter_BCR_parameters.txt	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,14 @@
+Process ID: sample,
+T-cell or B-cell option: B-cell,
+Only Take Into Account Fuctional V-GENE?: Yes,
+Only Take Into Account CDR3 with no Special Characters (X,*,#)?: Yes,
+Only Take Into Account Productive Sequences?: Yes,
+Only Take Into Account CDR3 with valid start/end landmarks?: Yes,
+V-REGION identity %: 70,
+Select Specific V gene?: No,
+Select Specific J gene?: No,
+Select Specific D gene?: No,
+Select CDR3 length range?: No,
+Only select CDR3 containing specific amino-acid sequence?: No
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/data_filter_TCR_input1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+Sequence number	Sequence ID	Functionality	V-GENE and allele	V-REGION score	V-REGION identity %	V-REGION identity nt	V-REGION identity % (with ins/del events)	V-REGION identity nt (with ins/del events)	J-GENE and allele	J-REGION score	J-REGION identity %	J-REGION identity nt	D-GENE and allele	D-REGION reading frame	CDR1-IMGT length	CDR2-IMGT length	CDR3-IMGT length	CDR-IMGT lengths	FR-IMGT lengths	AA JUNCTION	JUNCTION frame	Orientation	Functionality comment	V-REGION potential ins/del	J-GENE and allele comment	V-REGION insertions	V-REGION deletions	Sequence
+1	@SRR060727.1 SOLEXA7:7:1:6:706 length=202	productive	Homsap TRBV20-1*01 F, or Homsap TRBV20-1*02 F or Homsap TRBV20-1*03 (F) or Homsap TRBV20-1*04 (F) or Homsap TRBV20-1*05 (F) or Homsap TRBV20-1*06 (F) or Homsap TRBV20-1*07 (F)	175	100	36/36 nt			Homsap TRBJ1-3*01 F	169	82	41/50 nt	Homsap TRBD1*01 F	3	X	X	9	X.X.9	[X.X.12.10]	CSARRLGTIYF	in-frame	+						agtgcccatcctgaagacagcagcttctacatctgcagtgcccgaaggcttggcaccatatattttggagagggaagttggctcactgttgtagaggaccttaacgggtgggaacaccttgttcaggtcctctacaacagtgagccaacttccctctccaaaatatatggtgccaagccttcgggcactgcagatgtagaag
+2	@SRR060727.2 SOLEXA7:7:1:6:556 length=202	productive	Homsap TRBV10-3*01 F, or Homsap TRBV10-3*02 F or Homsap TRBV10-3*03 [F] or Homsap TRBV10-3*04 [F] or Homsap TRBV6-1*01 F or Homsap TRBV6-4*01 F or Homsap TRBV6-4*02 F or Homsap TRBV6-5*01 F or Homsap TRBV6-6*01 F or Homsap TRBV6-6*02 F or Homsap TRBV6-6*03 (F) or Homsap TRBV6-6*04 (F) or Homsap TRBV6-6*05 (F)	95	100	20/20 nt			Homsap TRBJ1-1*01 F	222	95.83	46/48 nt	Homsap TRBD2*01 F	2	X	X	11	X.X.11	[X.X.6.10]	CASSSGGYTEAFF	in-frame	+						agacatctgtgtacttctgtgccagcagttcgggggggtacactgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaacaaggtgtaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgtacccccccgaactgctggcaccgaag
+3	@SRR060727.3 SOLEXA7:7:1:9:1224 length=202	No results																										
+4	@SRR060727.4 SOLEXA7:7:1:9:193 length=202	productive	Homsap TRBV2*01 F, or Homsap TRBV2*02 (F) or Homsap TRBV2*03 (F)	100	100	21/21 nt			Homsap TRBJ2-3*01 F	245	100	49/49 nt			X	X	9	X.X.9	[X.X.7.10]	CASSSTDTQYF	in-frame	+						gactcagccatgtacttctgtgccagctcaagcacagatacgcagtattttggcccaggcacccggctgacagtgctcgaggacctgaaaatcgtgttccctaacgggtgggaacacgattttcaggtcctcgagcactgtcagccgggtgcctgggccaaaatactgcgtatctgtgcttgagctggcacagaagtacatg
+5	@SRR060727.5 SOLEXA7:7:1:9:1328 length=202	No results																										
+6	@SRR060727.6 SOLEXA7:7:1:11:979 length=202	No results																										
+7	@SRR060727.7 SOLEXA7:7:1:11:499 length=202	No results																										
+8	@SRR060727.8 SOLEXA7:7:1:15:1714 length=202	productive	Homsap TRBV20-1*01 F, or Homsap TRBV20-1*02 F or Homsap TRBV20-1*03 (F) or Homsap TRBV20-1*04 (F) or Homsap TRBV20-1*05 (F) or Homsap TRBV20-1*06 (F) or Homsap TRBV20-1*07 (F)	180	100	37/37 nt			Homsap TRBJ2-3*01 F	227	95.92	47/49 nt	Homsap TRBD2*01 F	3	X	X	11	X.X.11	[X.X.12.10]	CSVKLRPTDTQYF	in-frame	+						cagtgcccatcctgaagacagcagcttctacatctgcagtgttaagctccgccccacagatacgcagtattttggcccaggcacccggctgacagtgctcgtaacgggtgggaacacgtttttcaggtcctcgagcactgtcagccgggtgcctgggccaaaatactgcgtatctgtggggcggagcttaacactgcagatg
+9	@SRR060727.9 SOLEXA7:7:1:16:1132 length=202	No results																										
+10	@SRR060727.10 SOLEXA7:7:1:16:803 length=202	No results																										
+11	@SRR060727.11 SOLEXA7:7:1:17:1854 length=202	No results																										
+12	@SRR060727.12 SOLEXA7:7:1:17:955 length=202	No results																										
+13	@SRR060727.13 SOLEXA7:7:1:19:1481 length=202	No results																										
+14	@SRR060727.14 SOLEXA7:7:1:19:1339 length=202	productive	Homsap TRBV2*01 F, or Homsap TRBV2*02 (F) or Homsap TRBV2*03 (F)	120	100	25/25 nt			Homsap TRBJ2-3*01 F	245	100	49/49 nt			X	X	9	X.X.9	[X.X.8.10]	CASSSTDTQYF	in-frame	+						ggaggactcagccatgtacttctgtgccagctcaagcacagatacgcagtattttggcccaggcacccggctgacagtgctcgaggccctgacaaacgtgttaacgggtgggaacacgtttttcaggtcctcgagcactgtcagccgggtgcctgggccaaaatactgcgtatctgtgcttgagctggcacagaagtacatg
+15	@SRR060727.15 SOLEXA7:7:1:19:820 length=202	No results																										
+16	@SRR060727.16 SOLEXA7:7:1:20:1001 length=202	No results																										
+17	@SRR060727.17 SOLEXA7:7:1:20:734 length=202	No results																										
+18	@SRR060727.18 SOLEXA7:7:1:20:560 length=202	No results																										
+19	@SRR060727.19 SOLEXA7:7:1:20:1343 length=202	productive	Homsap TRBV29-1*01 F, or Homsap TRBV29-1*02 (F) or Homsap TRBV29-1*03 (F)	110	100	23/23 nt			Homsap TRBJ2-1*01 F	223	94	47/50 nt	Homsap TRBD1*01 F	3	X	X	10	X.X.10	[X.X.7.10]	CSVADRYNEQFF	in-frame	+						aagacagcagcatatatctctgcagcgtagcggacaggtacaatgagcagttcttcgggccagggacacggctcaccgtgctagaggacctgaaaaacgtgtaacgggtgggaacacgtttttcaggtcctctagcacggtgagccgtgtccctggcccgaagaactgctcattgtacctgtccgctacgctgcagagatat
+20	@SRR060727.20 SOLEXA7:7:1:20:838 length=202	productive	Homsap TRBV20-1*01 F, or Homsap TRBV20-1*02 F or Homsap TRBV20-1*03 (F) or Homsap TRBV20-1*04 (F) or Homsap TRBV20-1*05 (F) or Homsap TRBV20-1*06 (F) or Homsap TRBV20-1*07 (F)	125	100	26/26 nt			Homsap TRBJ1-1*01 F	213	93.75	45/48 nt	Homsap TRBD1*01 F	2	X	X	10	X.X.10	[X.X.8.10]	CSAKGVSPEAFF	in-frame	+						ctgaagacagcagcttctacatctgcagtgccaagggggtcagccctgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaacaagtaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagggctgacccccttggcactgcagatgtag
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/data_filter_TCR_output1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,8 @@
+	Sequence ID	Functionality	V-GENE	V-REGION score	V-REGION identity %	V-REGION identity nt	V-REGION identity % (with ins/del events)	V-REGION identity nt (with ins/del events)	J-GENE	J-REGION score	J-REGION identity %	J-REGION identity nt	D-GENE	D-REGION reading frame	CDR1-IMGT length	CDR2-IMGT length	CDR3-IMGT length	CDR-IMGT lengths	FR-IMGT lengths	AA JUNCTION	JUNCTION frame	Orientation	Functionality comment	V-REGION potential ins/del	J-GENE and allele comment	V-REGION insertions	V-REGION deletions	Sequence
+1	@SRR060727.1 SOLEXA7:7:1:6:706 length=202	productive	TRBV20-1	175.0	100.0	36/36 nt			TRBJ1-3	169.0	82.0	41/50 nt	TRBD1	3.0	X	X	9.0	X.X.9	[X.X.12.10]	CSARRLGTIYF	in-frame	+						agtgcccatcctgaagacagcagcttctacatctgcagtgcccgaaggcttggcaccatatattttggagagggaagttggctcactgttgtagaggaccttaacgggtgggaacaccttgttcaggtcctctacaacagtgagccaacttccctctccaaaatatatggtgccaagccttcgggcactgcagatgtagaag
+2	@SRR060727.2 SOLEXA7:7:1:6:556 length=202	productive	TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6	95.0	100.0	20/20 nt			TRBJ1-1	222.0	95.83	46/48 nt	TRBD2	2.0	X	X	11.0	X.X.11	[X.X.6.10]	CASSSGGYTEAFF	in-frame	+						agacatctgtgtacttctgtgccagcagttcgggggggtacactgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaacaaggtgtaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagtgtacccccccgaactgctggcaccgaag
+3	@SRR060727.4 SOLEXA7:7:1:9:193 length=202	productive	TRBV2	100.0	100.0	21/21 nt			TRBJ2-3	245.0	100.0	49/49 nt	none		X	X	9.0	X.X.9	[X.X.7.10]	CASSSTDTQYF	in-frame	+						gactcagccatgtacttctgtgccagctcaagcacagatacgcagtattttggcccaggcacccggctgacagtgctcgaggacctgaaaatcgtgttccctaacgggtgggaacacgattttcaggtcctcgagcactgtcagccgggtgcctgggccaaaatactgcgtatctgtgcttgagctggcacagaagtacatg
+4	@SRR060727.8 SOLEXA7:7:1:15:1714 length=202	productive	TRBV20-1	180.0	100.0	37/37 nt			TRBJ2-3	227.0	95.92	47/49 nt	TRBD2	3.0	X	X	11.0	X.X.11	[X.X.12.10]	CSVKLRPTDTQYF	in-frame	+						cagtgcccatcctgaagacagcagcttctacatctgcagtgttaagctccgccccacagatacgcagtattttggcccaggcacccggctgacagtgctcgtaacgggtgggaacacgtttttcaggtcctcgagcactgtcagccgggtgcctgggccaaaatactgcgtatctgtggggcggagcttaacactgcagatg
+5	@SRR060727.14 SOLEXA7:7:1:19:1339 length=202	productive	TRBV2	120.0	100.0	25/25 nt			TRBJ2-3	245.0	100.0	49/49 nt	none		X	X	9.0	X.X.9	[X.X.8.10]	CASSSTDTQYF	in-frame	+						ggaggactcagccatgtacttctgtgccagctcaagcacagatacgcagtattttggcccaggcacccggctgacagtgctcgaggccctgacaaacgtgttaacgggtgggaacacgtttttcaggtcctcgagcactgtcagccgggtgcctgggccaaaatactgcgtatctgtgcttgagctggcacagaagtacatg
+6	@SRR060727.19 SOLEXA7:7:1:20:1343 length=202	productive	TRBV29-1	110.0	100.0	23/23 nt			TRBJ2-1	223.0	94.0	47/50 nt	TRBD1	3.0	X	X	10.0	X.X.10	[X.X.7.10]	CSVADRYNEQFF	in-frame	+						aagacagcagcatatatctctgcagcgtagcggacaggtacaatgagcagttcttcgggccagggacacggctcaccgtgctagaggacctgaaaaacgtgtaacgggtgggaacacgtttttcaggtcctctagcacggtgagccgtgtccctggcccgaagaactgctcattgtacctgtccgctacgctgcagagatat
+7	@SRR060727.20 SOLEXA7:7:1:20:838 length=202	productive	TRBV20-1	125.0	100.0	26/26 nt			TRBJ1-1	213.0	93.75	45/48 nt	TRBD1	2.0	X	X	10.0	X.X.10	[X.X.8.10]	CSAKGVSPEAFF	in-frame	+						ctgaagacagcagcttctacatctgcagtgccaagggggtcagccctgaagctttctttggacaaggcaccagactcacagttgtagaggacctgaacaagtaacgggtgggaacaccttgttcaggtcctctacaactgtgagtctggtgccttgtccaaagaaagcttcagggctgacccccttggcactgcagatgtag
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/data_filter_TCR_output2.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,14 @@
+	Sequence ID	Functionality	V-GENE and allele	V-REGION score	V-REGION identity %	V-REGION identity nt	V-REGION identity % (with ins/del events)	V-REGION identity nt (with ins/del events)	J-GENE and allele	J-REGION score	J-REGION identity %	J-REGION identity nt	D-GENE and allele	D-REGION reading frame	CDR1-IMGT length	CDR2-IMGT length	CDR3-IMGT length	CDR-IMGT lengths	FR-IMGT lengths	AA JUNCTION	JUNCTION frame	Orientation	Functionality comment	V-REGION potential ins/del	J-GENE and allele comment	V-REGION insertions	V-REGION deletions	Sequence	Reason
+3	@SRR060727.3 SOLEXA7:7:1:9:1224 length=202	No results																											NoResults
+5	@SRR060727.5 SOLEXA7:7:1:9:1328 length=202	No results																											NoResults
+6	@SRR060727.6 SOLEXA7:7:1:11:979 length=202	No results																											NoResults
+7	@SRR060727.7 SOLEXA7:7:1:11:499 length=202	No results																											NoResults
+9	@SRR060727.9 SOLEXA7:7:1:16:1132 length=202	No results																											NoResults
+10	@SRR060727.10 SOLEXA7:7:1:16:803 length=202	No results																											NoResults
+11	@SRR060727.11 SOLEXA7:7:1:17:1854 length=202	No results																											NoResults
+12	@SRR060727.12 SOLEXA7:7:1:17:955 length=202	No results																											NoResults
+13	@SRR060727.13 SOLEXA7:7:1:19:1481 length=202	No results																											NoResults
+15	@SRR060727.15 SOLEXA7:7:1:19:820 length=202	No results																											NoResults
+16	@SRR060727.16 SOLEXA7:7:1:20:1001 length=202	No results																											NoResults
+17	@SRR060727.17 SOLEXA7:7:1:20:734 length=202	No results																											NoResults
+18	@SRR060727.18 SOLEXA7:7:1:20:560 length=202	No results																											NoResults
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/data_filter_TCR_output3.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,18 @@
+	sample	%
+Total reads of raw data	20	100.0000
+Not Null CDR3/V	7	35.0000
+filter out	13	65.0000
+Functional TRBV	7	35.0000
+filter out	0	0.0000
+Not Containing X,#,*	7	35.0000
+filter out	0	0.0000
+Productive	7	35.0000
+filter out	0	0.0000
+CDR3 landmarks C-F	7	35.0000
+filter out	0	0.0000
+Identity >= 70.0%	7	35.0000
+filter out	0	0.0000
+Total filter out A	13	65.0000
+Total filter in A	7	35.0000
+Total filter out	13	65.0000
+Total filter in	7	35.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/data_filter_TCR_parameters.txt	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,14 @@
+Process ID: sample,
+T-cell or B-cell option: T-cell,
+Only Take Into Account Fuctional V-GENE?: Yes,
+Only Take Into Account CDR3 with no Special Characters (X,*,#)?: Yes,
+Only Take Into Account Productive Sequences?: Yes,
+Only Take Into Account CDR3 with valid start/end landmarks?: Yes,
+V-REGION identity %: 70,
+Select Specific V gene?: No,
+Select Specific J gene?: No,
+Select Specific D gene?: No,
+Select CDR3 length range?: No,
+Only select CDR3 containing specific amino-acid sequence?: No
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/exclusive_clonos_def1_BCR_input1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	CTREEQYSSWYFDFW	191	191/240554	0.0794
+2	CARGMVRGVNYYYYYGMDVW	119	119/240554	0.0495
+3	CARGTWYNDGWPHFDYW	107	107/240554	0.0445
+4	CARDLGVLGYCSGGSCYSHVW	102	102/240554	0.0424
+5	CARVLGDSFDYW	97	97/240554	0.0403
+6	CATITMAYYFDYW	95	95/240554	0.0395
+7	CARGGGSYPYYYYGMDVW	93	93/240554	0.0387
+8	CARDGGQLGIYFDYW	89	89/240554	0.037
+9	CARGLPRPYSGSYSGFDYW	88	88/240554	0.0366
+10	CARVRELDAFDIW	88	88/240554	0.0366
+11	CARVQYVWDSPGAFDIW	86	86/240554	0.0358
+12	CARGQGTVTTEIDYW	86	86/240554	0.0358
+13	CARDRANYGSGSPIDYW	85	85/240554	0.0353
+14	CARLGRLERSPYYYMDVW	85	85/240554	0.0353
+15	CARGPFYCSGGSCNLHYYYGMDVW	84	84/240554	0.0349
+16	CARDDSTGGNWDAFDIW	84	84/240554	0.0349
+17	CARYKRGGIAVAGTLSSSFDYW	84	84/240554	0.0349
+18	CARINYYDSSGYYHKGMYYFDYW	83	83/240554	0.0345
+19	CARVGSYSGIRAFDIW	83	83/240554	0.0345
+20	CARGPRHYDSSGYCVKLDYW	82	82/240554	0.0341
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/exclusive_clonos_def1_BCR_input2.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	CARGYYDSSGYYGVGQYYYYYMDVW	133	133/198331	0.0671
+2	CARGMVRGVNYYYYYGMDVW	122	122/198331	0.0615
+3	CARDRDLKDHHIAAAGSGYYYGMDVW	115	115/198331	0.058
+4	CARSYYYGSGSYLAYAFDIW	104	104/198331	0.0524
+5	CARDLGVLGYCSGGSCYSHVW	101	101/198331	0.0509
+6	CASFPEQQLKWYGMDVW	101	101/198331	0.0509
+7	CASTESGGYYFDAFDIW	97	97/198331	0.0489
+8	CARDPRSGYDFDYW	95	95/198331	0.0479
+9	CARDHSTAEDAFDIW	92	92/198331	0.0464
+10	CARDGYDSSGYYVGGALRLGVLQSYYGMDVW	88	88/198331	0.0444
+11	CATDPARITDTDYW	88	88/198331	0.0444
+12	CARAGRVTMIVVVIKPLDYW	87	87/198331	0.0439
+13	CARGEGYGDCW	86	86/198331	0.0434
+14	CARAGDYGSGTNAFDIW	85	85/198331	0.0429
+15	CARLGRLERSPYYYMDVW	84	84/198331	0.0424
+16	CARDGIAAATSGLDVW	84	84/198331	0.0424
+17	CARDVEYYYDSSGQYFDYW	84	84/198331	0.0424
+18	CARDRHCSGGSCRGLW	83	83/198331	0.0418
+19	CARVGSYSGIRAFDIW	82	82/198331	0.0413
+20	CARGDLVVVRGVINQGKLDYW	81	81/198331	0.0408
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/exclusive_clonos_def1_BCR_output1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,17 @@
+	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	CTREEQYSSWYFDFW	191	191/240554	0.0794
+2	CARGTWYNDGWPHFDYW	107	107/240554	0.0445
+3	CARVLGDSFDYW	97	97/240554	0.0403
+4	CATITMAYYFDYW	95	95/240554	0.0395
+5	CARGGGSYPYYYYGMDVW	93	93/240554	0.0387
+6	CARDGGQLGIYFDYW	89	89/240554	0.037
+7	CARGLPRPYSGSYSGFDYW	88	88/240554	0.0366
+8	CARVRELDAFDIW	88	88/240554	0.0366
+9	CARVQYVWDSPGAFDIW	86	86/240554	0.0358
+10	CARGQGTVTTEIDYW	86	86/240554	0.0358
+11	CARDRANYGSGSPIDYW	85	85/240554	0.0353
+12	CARGPFYCSGGSCNLHYYYGMDVW	84	84/240554	0.0349
+13	CARDDSTGGNWDAFDIW	84	84/240554	0.0349
+14	CARYKRGGIAVAGTLSSSFDYW	84	84/240554	0.0349
+15	CARINYYDSSGYYHKGMYYFDYW	83	83/240554	0.0345
+16	CARGPRHYDSSGYCVKLDYW	82	82/240554	0.0341
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/exclusive_clonos_def1_BCR_parameters.txt	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,2 @@
+Remove Clonotypes With Reads Fewer Than Threshold?: Yes,
+Keep Clonotypes with Number of Reads more than: 3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/exclusive_clonos_def1_TCR_input1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	CASSSTDTQYF	3569	3569/56731	6.2911
+2	CASSLSGNTEAFF	673	673/56731	1.1863
+3	CASSEGGWTEAFF	399	399/56731	0.7033
+4	CASSEIGQGANEQFF	203	203/56731	0.3578
+5	CASSYMSSGSEQYF	105	105/56731	0.1851
+6	CASSRTETQYF	95	95/56731	0.1675
+7	CASSSRDPLNTEAFF	85	85/56731	0.1498
+8	CASMGGLNIYNSPLHF	78	78/56731	0.1375
+9	CSASRGEEAFF	69	69/56731	0.1216
+10	CASSKSGGAFNEQFF	63	63/56731	0.1111
+11	CASSLIPGQYQYF	59	59/56731	0.104
+12	CASSEMGNEQFF	52	52/56731	0.0917
+13	CASSPEVEGQPQHF	48	48/56731	0.0846
+14	CAITGTAGNTEAFF	47	47/56731	0.0828
+15	CSANRGEEAFF	45	45/56731	0.0793
+16	CAWSVGAEAFF	44	44/56731	0.0776
+17	CASSPGTAEAFF	42	42/56731	0.074
+18	CASSASGYEQYF	40	40/56731	0.0705
+19	CASSRGLNGADTQYF	40	40/56731	0.0705
+20	CASSRQIEAEAFF	39	39/56731	0.0687
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/exclusive_clonos_def1_TCR_input2.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	CASRLVPDTQYF	2898	2898/54828	5.2856
+2	CASSSFDEQFF	544	544/54828	0.9922
+3	CASSPGSTDTQYF	332	332/54828	0.6055
+4	CASSVLGVMNTEAFF	182	182/54828	0.3319
+5	CSAFLGGTQFF	104	104/54828	0.1897
+6	CASSSRDPLNTEAFF	81	81/54828	0.1477
+7	CASSEHGRAAEAFF	73	73/54828	0.1331
+8	CASSVRRYSNQPQHF	69	69/54828	0.1258
+9	CASSKSGGAFNEQFF	62	62/54828	0.1131
+10	CASSSPYANNEQFF	61	61/54828	0.1113
+11	CASSFRTGFTDTQYF	55	55/54828	0.1003
+12	CASSVTGYEQFF	49	49/54828	0.0894
+13	CATATSGSTDTQYF	47	47/54828	0.0857
+14	CAITGTAGNTEAFF	47	47/54828	0.0857
+15	CASSFRAPNTDTQYF	46	46/54828	0.0839
+16	CSVGSGEGYEQYF	44	44/54828	0.0803
+17	CSGIAGSTDTQYF	43	43/54828	0.0784
+18	CSARRLGTIYF	41	41/54828	0.0748
+19	CASGGNTQYF	40	40/54828	0.073
+20	CASLSSNEQYF	39	39/54828	0.0711
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/exclusive_clonos_def1_TCR_output1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,18 @@
+	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	CASSSTDTQYF	3569	3569/56731	6.2911
+2	CASSLSGNTEAFF	673	673/56731	1.1863
+3	CASSEGGWTEAFF	399	399/56731	0.7033
+4	CASSEIGQGANEQFF	203	203/56731	0.3578
+5	CASSYMSSGSEQYF	105	105/56731	0.1851
+6	CASSRTETQYF	95	95/56731	0.1675
+7	CASMGGLNIYNSPLHF	78	78/56731	0.1375
+8	CSASRGEEAFF	69	69/56731	0.1216
+9	CASSLIPGQYQYF	59	59/56731	0.104
+10	CASSEMGNEQFF	52	52/56731	0.0917
+11	CASSPEVEGQPQHF	48	48/56731	0.0846
+12	CSANRGEEAFF	45	45/56731	0.0793
+13	CAWSVGAEAFF	44	44/56731	0.0776
+14	CASSPGTAEAFF	42	42/56731	0.074
+15	CASSASGYEQYF	40	40/56731	0.0705
+16	CASSRGLNGADTQYF	40	40/56731	0.0705
+17	CASSRQIEAEAFF	39	39/56731	0.0687
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/exclusive_clonos_def1_TCR_parameters.txt	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,2 @@
+Remove Clonotypes With Reads Fewer Than Threshold?: Yes,
+Keep Clonotypes with Number of Reads more than: 2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/exclusive_clonos_def2_BCR_input1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	V-GENE	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	IGHV3-23 or IGHV3-23D	CTREEQYSSWYFDFW	84	84/240554	0.0349
+2	IGHV1-69	CASRMVRGVILPPYYYYYMDVW	74	74/240554	0.0308
+3	IGHV7-4-1	CARASSHHYCSGGSCYSYYYYYYYMDVW	72	72/240554	0.0299
+4	IGHV1-18	CARELYVWGSRHEVFDIW	71	71/240554	0.0295
+5	IGHV3-33	CAKGGGSYYGVYYFDYW	69	69/240554	0.0287
+6	IGHV4-59 or IGHV4-61	CARDLGYSGSYLGRAFDIW	66	66/240554	0.0274
+7	IGHV3-33	CARDLHPRARGVIVIPGYW	65	65/240554	0.027
+8	IGHV1-69	CARLGRLERSPYYYMDVW	64	64/240554	0.0266
+9	IGHV1-69	CARDSSGGTDYYYYYMDVW	62	62/240554	0.0258
+10	IGHV3-49	CTRPRGIVISAGIYFDYW	61	61/240554	0.0254
+11	IGHV1-69	CARDPVLYCGGDCSSSDAFDIW	60	60/240554	0.0249
+12	IGHV7-4-1	CARDTLYPPNYYGSGSYEGMDVW	60	60/240554	0.0249
+13	IGHV4-39	CAGRASPFGPSYYFNSW	60	60/240554	0.0249
+14	IGHV3-9	CAKDISLRDEGDSSVGYDYW	59	59/240554	0.0245
+15	IGHV4-39	CARLMLGTMVKTPDAFDIW	59	59/240554	0.0245
+16	IGHV1-3	CARALPPRYCSGGSCYYPSNWGQGTLVGYYPSNW	59	59/240554	0.0245
+17	IGHV3-30 or IGHV3-30-3	CARDQFGVVTVKGGYFQHW	58	58/240554	0.0241
+18	IGHV1-3	CARERYYNRGAFDIW	57	57/240554	0.0237
+19	IGHV3-9	CAIGRGVISTFFDYW	57	57/240554	0.0237
+20	IGHV3-23 or IGHV3-23D	CAKERALGFGEPHYW	56	56/240554	0.0233
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/exclusive_clonos_def2_BCR_input2.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	V-GENE	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	IGHV3-11	CARGMVRGVNYYYYYGMDVW	78	78/251182	0.0311
+2	IGHV1-46	CARDRDLKDHHIAAAGSGYYYGMDVW	74	74/251182	0.0295
+3	IGHV4-59 or IGHV4-61	CARGTWYNDGWPHFDYW	71	71/251182	0.0283
+4	IGHV1-46	CASAGGVYTSGWHGTFYW	70	70/251182	0.0279
+5	IGHV3-33	CAKGGGSYYGVYYFDYW	68	68/251182	0.0271
+6	IGHV1-24	CATGDYDVLTGNYRAFW	67	67/251182	0.0267
+7	IGHV3-33	CARDLHPRARGVIVIPGYW	65	65/251182	0.0259
+8	IGHV4-34	CARVYPYDSSSWQAPYYYGMDVW	64	64/251182	0.0255
+9	IGHV3-49	CTRDRGERQYDAFDIW	61	61/251182	0.0243
+10	IGHV1-69	CARDPVLYCGGDCSSSDAFDIW	60	60/251182	0.0239
+11	IGHV1-69	CARPRIAAAVYWYFDLW	60	60/251182	0.0239
+12	IGHV3-21	CARDHFVWGSPSPMDIW	60	60/251182	0.0239
+13	IGHV3-23 or IGHV3-23D	CARVGSYSGIRAFDIW	59	59/251182	0.0235
+14	IGHV4-39	CARLMLGTMVKTPDAFDIW	59	59/251182	0.0235
+15	IGHV4-59 or IGHV4-61	CARHDGIAAAGHFDYW	59	59/251182	0.0235
+16	IGHV1-69	CAREEKFGELLERSYYYYYYMDVW	59	59/251182	0.0235
+17	IGHV1-69	CARGYYDSSGYYGVGQYYYYYMDVW	58	58/251182	0.0231
+18	IGHV3-33	CAKGPRMVRGVLDYW	57	57/251182	0.0227
+19	IGHV3-9	CAIGRGVISTFFDYW	57	57/251182	0.0227
+20	IGHV3-64	CATEHIAAAGEASAFDIW	57	57/251182	0.0227
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/exclusive_clonos_def2_BCR_output1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,16 @@
+	V-GENE	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	IGHV3-23 or IGHV3-23D	CTREEQYSSWYFDFW	84	84/240554	0.0349
+2	IGHV1-69	CASRMVRGVILPPYYYYYMDVW	74	74/240554	0.0308
+3	IGHV7-4-1	CARASSHHYCSGGSCYSYYYYYYYMDVW	72	72/240554	0.0299
+4	IGHV1-18	CARELYVWGSRHEVFDIW	71	71/240554	0.0295
+5	IGHV4-59 or IGHV4-61	CARDLGYSGSYLGRAFDIW	66	66/240554	0.0274
+6	IGHV1-69	CARLGRLERSPYYYMDVW	64	64/240554	0.0266
+7	IGHV1-69	CARDSSGGTDYYYYYMDVW	62	62/240554	0.0258
+8	IGHV3-49	CTRPRGIVISAGIYFDYW	61	61/240554	0.0254
+9	IGHV7-4-1	CARDTLYPPNYYGSGSYEGMDVW	60	60/240554	0.0249
+10	IGHV4-39	CAGRASPFGPSYYFNSW	60	60/240554	0.0249
+11	IGHV3-9	CAKDISLRDEGDSSVGYDYW	59	59/240554	0.0245
+12	IGHV1-3	CARALPPRYCSGGSCYYPSNWGQGTLVGYYPSNW	59	59/240554	0.0245
+13	IGHV3-30 or IGHV3-30-3	CARDQFGVVTVKGGYFQHW	58	58/240554	0.0241
+14	IGHV1-3	CARERYYNRGAFDIW	57	57/240554	0.0237
+15	IGHV3-23 or IGHV3-23D	CAKERALGFGEPHYW	56	56/240554	0.0233
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/exclusive_clonos_def2_BCR_parameters.txt	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,2 @@
+Remove Clonotypes With Reads Fewer Than Threshold?: Yes,
+Keep Clonotypes with Number of Reads more than: 3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/exclusive_clonos_def2_TCR_input1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	V-GENE	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	TRBV2	CASSSTDTQYF	3545	3545/56731	6.2488
+2	TRBV2	CASRLVPDTQYF	2893	2893/56731	5.0995
+3	TRBV13	CASSLSGNTEAFF	670	670/56731	1.181
+4	TRBV2	CASSEGGWTEAFF	398	398/56731	0.7016
+5	TRBV5-1	CASSPGSTDTQYF	329	329/56731	0.5799
+6	TRBV2	CASSEIGQGANEQFF	201	201/56731	0.3543
+7	TRBV20-1	CSAFLGGTQFF	104	104/56731	0.1833
+8	TRBV12-3 or TRBV12-4	CASSSRDPLNTEAFF	84	84/56731	0.1481
+9	TRBV25-1	CASSEHGRAAEAFF	72	72/56731	0.1269
+10	TRBV20-1	CSASRGEEAFF	69	69/56731	0.1216
+11	TRBV27	CASSLIPGQYQYF	59	59/56731	0.104
+12	TRBV10-2	CASSEMGNEQFF	52	52/56731	0.0917
+13	TRBV3-1	CASSPEVEGQPQHF	48	48/56731	0.0846
+14	TRBV7-8	CASSFRAPNTDTQYF	46	46/56731	0.0811
+15	TRBV30	CAWSVGAEAFF	44	44/56731	0.0776
+16	TRBV29-1	CSGIAGSTDTQYF	43	43/56731	0.0758
+17	TRBV20-1	CSARRLGTIYF	41	41/56731	0.0723
+18	TRBV2	CASGGNTQYF	40	40/56731	0.0705
+19	TRBV2	CASLSSNEQYF	39	39/56731	0.0687
+20	TRBV25-1	CASTSGTGSDTQYF	37	37/56731	0.0652
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/exclusive_clonos_def2_TCR_input2.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	V-GENE	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	TRBV2	CASRLVPDTQYF	2931	2931/57218	5.1225
+2	TRBV13	CASSLSGNTEAFF	753	753/57218	1.316
+3	TRBV27	CASSSFDEQFF	544	544/57218	0.9507
+4	TRBV5-1	CASSPGSTDTQYF	322	322/57218	0.5628
+5	TRBV10-2	CASSVLGVMNTEAFF	181	181/57218	0.3163
+6	TRBV20-1	CSAFLGGTQFF	107	107/57218	0.187
+7	TRBV12-3 or TRBV12-4	CASSRTETQYF	94	94/57218	0.1643
+8	TRBV2	CASMGGLNIYNSPLHF	77	77/57218	0.1346
+9	TRBV25-1	CASSEHGRAAEAFF	74	74/57218	0.1293
+10	TRBV9	CASSVRRYSNQPQHF	69	69/57218	0.1206
+11	TRBV2	CASSKSGGAFNEQFF	62	62/57218	0.1084
+12	TRBV7-8	CASSFRTGFTDTQYF	55	55/57218	0.0961
+13	TRBV25-1	CASSVTGYEQFF	49	49/57218	0.0856
+14	TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6	CASSYMSSGSEQYF	47	47/57218	0.0821
+15	TRBV20-1	CSANRGEEAFF	45	45/57218	0.0786
+16	TRBV29-1	CSVGSGEGYEQYF	44	44/57218	0.0769
+17	TRBV12-3 or TRBV12-4	CASSPGTAEAFF	42	42/57218	0.0734
+18	TRBV7-9	CASSSPYANNEQFF	41	41/57218	0.0717
+19	TRBV25-1	CASSASGYEQYF	40	40/57218	0.0699
+20	TRBV12-3 or TRBV12-4	CASSRQIEAEAFF	38	38/57218	0.0664
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/exclusive_clonos_def2_TCR_output1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,16 @@
+	V-GENE	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	TRBV2	CASSSTDTQYF	3545	3545/56731	6.2488
+2	TRBV2	CASSEGGWTEAFF	398	398/56731	0.7016
+3	TRBV2	CASSEIGQGANEQFF	201	201/56731	0.3543
+4	TRBV12-3 or TRBV12-4	CASSSRDPLNTEAFF	84	84/56731	0.1481
+5	TRBV20-1	CSASRGEEAFF	69	69/56731	0.1216
+6	TRBV27	CASSLIPGQYQYF	59	59/56731	0.104
+7	TRBV10-2	CASSEMGNEQFF	52	52/56731	0.0917
+8	TRBV3-1	CASSPEVEGQPQHF	48	48/56731	0.0846
+9	TRBV7-8	CASSFRAPNTDTQYF	46	46/56731	0.0811
+10	TRBV30	CAWSVGAEAFF	44	44/56731	0.0776
+11	TRBV29-1	CSGIAGSTDTQYF	43	43/56731	0.0758
+12	TRBV20-1	CSARRLGTIYF	41	41/56731	0.0723
+13	TRBV2	CASGGNTQYF	40	40/56731	0.0705
+14	TRBV2	CASLSSNEQYF	39	39/56731	0.0687
+15	TRBV25-1	CASTSGTGSDTQYF	37	37/56731	0.0652
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/exclusive_clonos_def2_TCR_parameters.txt	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,2 @@
+Remove Clonotypes With Reads Fewer Than Threshold?: Yes,
+Keep Clonotypes with Number of Reads more than: 2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/exclusive_clonos_def3_BCR_input1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	J-GENE	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	IGHJ4	CTREEQYSSWYFDFW	191	191/240554	0.0794
+2	IGHJ6	CARGMVRGVNYYYYYGMDVW	119	119/240554	0.0495
+3	IGHJ4	CARGTWYNDGWPHFDYW	107	107/240554	0.0445
+4	IGHJ4	CARDLGVLGYCSGGSCYSHVW	102	102/240554	0.0424
+5	IGHJ3	CASTESGGYYFDAFDIW	97	97/240554	0.0403
+6	IGHJ4	CATITMAYYFDYW	95	95/240554	0.0395
+7	IGHJ6	CARGGGSYPYYYYGMDVW	93	93/240554	0.0387
+8	IGHJ4	CARDGGQLGIYFDYW	89	89/240554	0.037
+9	IGHJ6	CARDGYDSSGYYVGGALRLGVLQSYYGMDVW	88	88/240554	0.0366
+10	IGHJ4	CATDPARITDTDYW	88	88/240554	0.0366
+11	IGHJ4	CARGLPRPYSGSYSGFDYW	88	88/240554	0.0366
+12	IGHJ4	CARGEGYGDCW	86	86/240554	0.0358
+13	IGHJ4	CARGQGTVTTEIDYW	86	86/240554	0.0358
+14	IGHJ3	CARAGDYGSGTNAFDIW	85	85/240554	0.0353
+15	IGHJ4	CARYKRGGIAVAGTLSSSFDYW	84	84/240554	0.0349
+16	IGHJ4	CARDVEYYYDSSGQYFDYW	84	84/240554	0.0349
+17	IGHJ6	CARDGIAAATSGLDVW	84	84/240554	0.0349
+18	IGHJ4	CARINYYDSSGYYHKGMYYFDYW	83	83/240554	0.0345
+19	IGHJ4	CARGPRHYDSSGYCVKLDYW	82	82/240554	0.0341
+20	IGHJ6	CARGVSGYYNFFYMDVW	81	81/240554	0.0337
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/exclusive_clonos_def3_BCR_input2.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	J-GENE	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	IGHJ6	CARGYYDSSGYYGVGQYYYYYMDVW	133	133/229003	0.0581
+2	IGHJ6	CARGMVRGVNYYYYYGMDVW	124	124/229003	0.0541
+3	IGHJ6	CARDRDLKDHHIAAAGSGYYYGMDVW	115	115/229003	0.0502
+4	IGHJ3	CARSYYYGSGSYLAYAFDIW	104	104/229003	0.0454
+5	IGHJ6	CASFPEQQLKWYGMDVW	101	101/229003	0.0441
+6	IGHJ4	CARVLGDSFDYW	97	97/229003	0.0424
+7	IGHJ4	CARDPRSGYDFDYW	95	95/229003	0.0415
+8	IGHJ3	CARDHSTAEDAFDIW	92	92/229003	0.0402
+9	IGHJ6	CARDGYDSSGYYVGGALRLGVLQSYYGMDVW	88	88/229003	0.0384
+10	IGHJ3	CARVRELDAFDIW	88	88/229003	0.0384
+11	IGHJ4	CARAGRVTMIVVVIKPLDYW	87	87/229003	0.038
+12	IGHJ3	CARVQYVWDSPGAFDIW	86	86/229003	0.0376
+13	IGHJ6	CARLGRLERSPYYYMDVW	85	85/229003	0.0371
+14	IGHJ4	CARDRANYGSGSPIDYW	85	85/229003	0.0371
+15	IGHJ6	CARGPFYCSGGSCNLHYYYGMDVW	84	84/229003	0.0367
+16	IGHJ3	CARDDSTGGNWDAFDIW	84	84/229003	0.0367
+17	IGHJ6	CARDGIAAATSGLDVW	83	83/229003	0.0362
+18	IGHJ5	CARDRHCSGGSCRGLW	83	83/229003	0.0362
+19	IGHJ3	CARVGSYSGIRAFDIW	83	83/229003	0.0362
+20	IGHJ4	CARGDLVVVRGVINQGKLDYW	81	81/229003	0.0354
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/exclusive_clonos_def3_BCR_output1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,18 @@
+	J-GENE	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	IGHJ4	CTREEQYSSWYFDFW	191	191/240554	0.0794
+2	IGHJ4	CARGTWYNDGWPHFDYW	107	107/240554	0.0445
+3	IGHJ4	CARDLGVLGYCSGGSCYSHVW	102	102/240554	0.0424
+4	IGHJ3	CASTESGGYYFDAFDIW	97	97/240554	0.0403
+5	IGHJ4	CATITMAYYFDYW	95	95/240554	0.0395
+6	IGHJ6	CARGGGSYPYYYYGMDVW	93	93/240554	0.0387
+7	IGHJ4	CARDGGQLGIYFDYW	89	89/240554	0.037
+8	IGHJ4	CATDPARITDTDYW	88	88/240554	0.0366
+9	IGHJ4	CARGLPRPYSGSYSGFDYW	88	88/240554	0.0366
+10	IGHJ4	CARGEGYGDCW	86	86/240554	0.0358
+11	IGHJ4	CARGQGTVTTEIDYW	86	86/240554	0.0358
+12	IGHJ3	CARAGDYGSGTNAFDIW	85	85/240554	0.0353
+13	IGHJ4	CARYKRGGIAVAGTLSSSFDYW	84	84/240554	0.0349
+14	IGHJ4	CARDVEYYYDSSGQYFDYW	84	84/240554	0.0349
+15	IGHJ4	CARINYYDSSGYYHKGMYYFDYW	83	83/240554	0.0345
+16	IGHJ4	CARGPRHYDSSGYCVKLDYW	82	82/240554	0.0341
+17	IGHJ6	CARGVSGYYNFFYMDVW	81	81/240554	0.0337
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/exclusive_clonos_def3_BCR_parameters.txt	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,2 @@
+Remove Clonotypes With Reads Fewer Than Threshold?: Yes,
+Keep Clonotypes with Number of Reads more than: 3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/exclusive_clonos_def3_TCR_input1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	J-GENE	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	TRBJ2-3	CASSSTDTQYF	3569	3569/56731	6.2911
+2	TRBJ1-1	CASSLSGNTEAFF	673	673/56731	1.1863
+3	TRBJ2-1	CASSSFDEQFF	544	544/56731	0.9589
+4	TRBJ1-1	CASSEGGWTEAFF	399	399/56731	0.7033
+5	TRBJ2-1	CASSEIGQGANEQFF	203	203/56731	0.3578
+6	TRBJ2-7	CASSYMSSGSEQYF	105	105/56731	0.1851
+7	TRBJ2-3	CASSRTETQYF	95	95/56731	0.1675
+8	TRBJ1-1	CASSSRDPLNTEAFF	85	85/56731	0.1498
+9	TRBJ1-6	CASMGGLNIYNSPLHF	78	78/56731	0.1375
+10	TRBJ1-5	CASSVRRYSNQPQHF	69	69/56731	0.1216
+11	TRBJ2-1	CASSKSGGAFNEQFF	63	63/56731	0.1111
+12	TRBJ2-3	CASSLIPGQYQYF	59	59/56731	0.104
+13	TRBJ2-1	CASSEMGNEQFF	52	52/56731	0.0917
+14	TRBJ1-5	CASSPEVEGQPQHF	48	48/56731	0.0846
+15	TRBJ1-1	CAITGTAGNTEAFF	47	47/56731	0.0828
+16	TRBJ1-1	CSANRGEEAFF	45	45/56731	0.0793
+17	TRBJ1-1	CAWSVGAEAFF	44	44/56731	0.0776
+18	TRBJ1-1	CASSPGTAEAFF	42	42/56731	0.074
+19	TRBJ2-3	CASSRGLNGADTQYF	40	40/56731	0.0705
+20	TRBJ2-7	CASSASGYEQYF	40	40/56731	0.0705
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/exclusive_clonos_def3_TCR_input2.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	J-GENE	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	TRBJ2-3	CASRLVPDTQYF	2898	2898/57339	5.0542
+2	TRBJ2-1	CASSSFDEQFF	618	618/57339	1.0778
+3	TRBJ2-3	CASSPGSTDTQYF	332	332/57339	0.579
+4	TRBJ1-1	CASSVLGVMNTEAFF	182	182/57339	0.3174
+5	TRBJ2-7	CASSYMSSGSEQYF	112	112/57339	0.1953
+6	TRBJ2-1	CSAFLGGTQFF	104	104/57339	0.1814
+7	TRBJ1-1	CASSSRDPLNTEAFF	86	86/57339	0.15
+8	TRBJ1-1	CASSEHGRAAEAFF	73	73/57339	0.1273
+9	TRBJ1-1	CSASRGEEAFF	69	69/57339	0.1203
+10	TRBJ2-1	CASSSPYANNEQFF	61	61/57339	0.1064
+11	TRBJ2-3	CASSFRTGFTDTQYF	55	55/57339	0.0959
+12	TRBJ2-1	CASSEMGNEQFF	50	50/57339	0.0872
+13	TRBJ2-1	CASSVTGYEQFF	49	49/57339	0.0855
+14	TRBJ2-3	CATATSGSTDTQYF	47	47/57339	0.082
+15	TRBJ2-3	CASSFRAPNTDTQYF	46	46/57339	0.0802
+16	TRBJ2-7	CSVGSGEGYEQYF	44	44/57339	0.0767
+17	TRBJ2-3	CSGIAGSTDTQYF	43	43/57339	0.075
+18	TRBJ1-3	CSARRLGTIYF	41	41/57339	0.0715
+19	TRBJ2-3	CASGGNTQYF	40	40/57339	0.0698
+20	TRBJ1-1	CASSRQIEAEAFF	39	39/57339	0.068
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/exclusive_clonos_def3_TCR_output1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,17 @@
+	J-GENE	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	TRBJ2-3	CASSSTDTQYF	3569	3569/56731	6.2911
+2	TRBJ1-1	CASSLSGNTEAFF	673	673/56731	1.1863
+3	TRBJ1-1	CASSEGGWTEAFF	399	399/56731	0.7033
+4	TRBJ2-1	CASSEIGQGANEQFF	203	203/56731	0.3578
+5	TRBJ2-3	CASSRTETQYF	95	95/56731	0.1675
+6	TRBJ1-6	CASMGGLNIYNSPLHF	78	78/56731	0.1375
+7	TRBJ1-5	CASSVRRYSNQPQHF	69	69/56731	0.1216
+8	TRBJ2-1	CASSKSGGAFNEQFF	63	63/56731	0.1111
+9	TRBJ2-3	CASSLIPGQYQYF	59	59/56731	0.104
+10	TRBJ1-5	CASSPEVEGQPQHF	48	48/56731	0.0846
+11	TRBJ1-1	CAITGTAGNTEAFF	47	47/56731	0.0828
+12	TRBJ1-1	CSANRGEEAFF	45	45/56731	0.0793
+13	TRBJ1-1	CAWSVGAEAFF	44	44/56731	0.0776
+14	TRBJ1-1	CASSPGTAEAFF	42	42/56731	0.074
+15	TRBJ2-3	CASSRGLNGADTQYF	40	40/56731	0.0705
+16	TRBJ2-7	CASSASGYEQYF	40	40/56731	0.0705
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/exclusive_clonos_def3_TCR_parameters.txt	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,2 @@
+Remove Clonotypes With Reads Fewer Than Threshold?: Yes,
+Keep Clonotypes with Number of Reads more than: 2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_compare_geneJ_BCR_input1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,7 @@
+	J-GENE	Reads	Reads/Total	Frequency %
+1	IGHJ4	3946	3946/8445	46.7259
+2	IGHJ3	1781	1781/8445	21.0894
+3	IGHJ6	1410	1410/8445	16.6963
+4	IGHJ5	798	798/8445	9.4494
+5	IGHJ2	292	292/8445	3.4577
+6	IGHJ1	218	218/8445	2.5814
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_compare_geneJ_BCR_input2.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,7 @@
+	J-GENE	Reads	Reads/Total	Frequency %
+1	IGHJ4	4114	4114/11970	34.3693
+2	IGHJ1	2276	2276/11970	19.0142
+3	IGHJ6	2008	2008/11970	16.7753
+4	IGHJ5	1743	1743/11970	14.5614
+5	IGHJ3	1691	1691/11970	14.127
+6	IGHJ2	138	138/11970	1.1529
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_compare_geneJ_BCR_output1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,7 @@
+	J-GENE	input1.csv	input2.csv	mean
+1	IGHJ4	46.7259	34.3693	40.5476
+2	IGHJ3	21.0894	14.127	17.6082
+3	IGHJ6	16.6963	16.7753	16.7358
+4	IGHJ5	9.4494	14.5614	12.0054
+5	IGHJ1	2.5814	19.0142	10.7978
+6	IGHJ2	3.4577	1.1529	2.3053
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_compare_geneJ_TCR_input1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,8 @@
+	J-GENE	Reads	Reads/Total	Frequency %
+1	TRBJ1-1	5562	5562/26646	20.8737
+2	TRBJ2-3	3665	3665/26646	13.7544
+3	TRBJ1-5	2692	2692/26646	10.1028
+4	TRBJ2-2	1575	1575/26646	5.9108
+5	TRBJ1-3	1009	1009/26646	3.7867
+6	TRBJ2-4	289	289/26646	1.0846
+7	TRBJ2-6	105	105/26646	0.3941
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_compare_geneJ_TCR_input2.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,8 @@
+	J-GENE	Reads	Reads/Total	Frequency %
+1	TRBJ2-1	4400	4400/25009	17.5937
+2	TRBJ2-7	3569	3569/25009	14.2709
+3	TRBJ2-5	1736	1736/25009	6.9415
+4	TRBJ1-6	1253	1253/25009	5.0102
+5	TRBJ1-4	650	650/25009	2.5991
+6	TRBJ1-2	140	140/25009	0.5598
+7	TRAJ27	1	1/25009	0.004
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_compare_geneJ_TCR_output1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,15 @@
+	J-GENE	input1.csv	input2.csv	mean
+1	TRBJ1-1	20.8737	0.0	10.4368
+2	TRBJ2-1	0.0	17.5937	8.7968
+3	TRBJ2-7	0.0	14.2709	7.1354
+4	TRBJ2-3	13.7544	0.0	6.8772
+5	TRBJ1-5	10.1028	0.0	5.0514
+6	TRBJ2-5	0.0	6.9415	3.4707
+7	TRBJ2-2	5.9108	0.0	2.9554
+8	TRBJ1-6	0.0	5.0102	2.5051
+9	TRBJ1-3	3.7867	0.0	1.8934
+10	TRBJ1-4	0.0	2.5991	1.2995
+11	TRBJ2-4	1.0846	0.0	0.5423
+12	TRBJ1-2	0.0	0.5598	0.2799
+13	TRBJ2-6	0.3941	0.0	0.1971
+14	TRAJ27	0.0	0.004	0.0020
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_compare_geneV_BCR_input1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,11 @@
+	V-GENE	Reads	Reads/Total	Frequency %
+1	IGHV4-39	859	859/10166	8.4497
+2	IGHV3-23 or IGHV3-23D	604	604/10166	5.9414
+3	IGHV3-33	582	582/10166	5.725
+4	IGHV4-34	444	444/10166	4.3675
+5	IGHV1-3	398	398/10166	3.915
+6	IGHV3-9	376	376/10166	3.6986
+7	IGHV1-8	342	342/10166	3.3642
+8	IGHV1-69	306	306/10166	3.01
+9	IGHV1-46	302	302/10166	2.9707
+10	IGHV3-11	272	272/10166	2.6756
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_compare_geneV_BCR_input2.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,11 @@
+	V-GENE	Reads	Reads/Total	Frequency %
+1	IGHV4-59 or IGHV4-61	726	726/12004	6.048
+2	IGHV3-21	582	582/12004	4.8484
+3	IGHV1-18	514	514/12004	4.2819
+4	IGHV1-69 or IGHV1-69D	415	415/12004	3.4572
+5	IGHV3-30 or IGHV3-30-3	398	398/12004	3.3156
+6	IGHV3-7	343	343/12004	2.8574
+7	IGHV7-4-1	308	308/12004	2.5658
+8	IGHV3-48	304	304/12004	2.5325
+9	IGHV2-5	291	291/12004	2.4242
+10	IGHV4-31 or IGHV4-59	212	212/12004	1.7661
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_compare_geneV_BCR_output1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	V-GENE	input1.csv	input2.csv	mean
+1	IGHV4-39	8.4497	0.0	4.2248
+2	IGHV4-59 or IGHV4-61	0.0	6.048	3.0240
+3	IGHV3-23 or IGHV3-23D	5.9414	0.0	2.9707
+4	IGHV3-33	5.725	0.0	2.8625
+5	IGHV3-21	0.0	4.8484	2.4242
+6	IGHV4-34	4.3675	0.0	2.1837
+7	IGHV1-18	0.0	4.2819	2.1410
+8	IGHV1-3	3.915	0.0	1.9575
+9	IGHV3-9	3.6986	0.0	1.8493
+10	IGHV1-69 or IGHV1-69D	0.0	3.4572	1.7286
+11	IGHV1-8	3.3642	0.0	1.6821
+12	IGHV3-30 or IGHV3-30-3	0.0	3.3156	1.6578
+13	IGHV1-69	3.01	0.0	1.5050
+14	IGHV1-46	2.9707	0.0	1.4853
+15	IGHV3-7	0.0	2.8574	1.4287
+16	IGHV3-11	2.6756	0.0	1.3378
+17	IGHV7-4-1	0.0	2.5658	1.2829
+18	IGHV3-48	0.0	2.5325	1.2663
+19	IGHV2-5	0.0	2.4242	1.2121
+20	IGHV4-31 or IGHV4-59	0.0	1.7661	0.8831
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_compare_geneV_TCR_input1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,11 @@
+	V-GENE	Reads	Reads/Total	Frequency %
+1	TRBV20-1	5516	5516/28836	19.1289
+2	TRBV29-1	2162	2162/28836	7.4976
+3	TRBV10-3 or TRBV6-1 or TRBV6-5 or TRBV6-6	1679	1679/28836	5.8226
+4	TRBV2	1368	1368/28836	4.7441
+5	TRBV10-3	1011	1011/28836	3.506
+6	TRBV5-1	609	609/28836	2.1119
+7	TRBV9	575	575/28836	1.994
+8	TRBV28	568	568/28836	1.9698
+9	TRBV3-1	467	467/28836	1.6195
+10	TRBV25-1	321	321/28836	1.1132
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_compare_geneV_TCR_input2.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,11 @@
+	V-GENE	Reads	Reads/Total	Frequency %
+1	TRBV12-3 or TRBV12-4	3388	3388/27418	12.3568
+2	TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6	2044	2044/27418	7.455
+3	TRBV6-1 or TRBV6-5 or TRBV6-6	1587	1587/27418	5.7882
+4	TRBV19	1331	1331/27418	4.8545
+5	TRBV27	787	787/27418	2.8704
+6	TRBV4-1	605	605/27418	2.2066
+7	TRBV7-9	572	572/27418	2.0862
+8	TRBV18	471	471/27418	1.7178
+9	TRBV11-1 or TRBV11-3 or TRBV7-9	411	411/27418	1.499
+10	TRBV6-2 or TRBV6-3	270	270/27418	0.9848
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_compare_geneV_TCR_output1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	V-GENE	input1.csv	input2.csv	mean
+1	TRBV20-1	19.1289	0.0	9.5645
+2	TRBV12-3 or TRBV12-4	0.0	12.3568	6.1784
+3	TRBV29-1	7.4976	0.0	3.7488
+4	TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6	0.0	7.455	3.7275
+5	TRBV10-3 or TRBV6-1 or TRBV6-5 or TRBV6-6	5.8226	0.0	2.9113
+6	TRBV6-1 or TRBV6-5 or TRBV6-6	0.0	5.7882	2.8941
+7	TRBV19	0.0	4.8545	2.4272
+8	TRBV2	4.7441	0.0	2.3721
+9	TRBV10-3	3.506	0.0	1.7530
+10	TRBV27	0.0	2.8704	1.4352
+11	TRBV4-1	0.0	2.2066	1.1033
+12	TRBV5-1	2.1119	0.0	1.0559
+13	TRBV7-9	0.0	2.0862	1.0431
+14	TRBV9	1.994	0.0	0.9970
+15	TRBV28	1.9698	0.0	0.9849
+16	TRBV18	0.0	1.7178	0.8589
+17	TRBV3-1	1.6195	0.0	0.8097
+18	TRBV11-1 or TRBV11-3 or TRBV7-9	0.0	1.499	0.7495
+19	TRBV25-1	1.1132	0.0	0.5566
+20	TRBV6-2 or TRBV6-3	0.0	0.9848	0.4924
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_usage_geneJ_BCR_input1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	J-GENE	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	IGHJ4	CTREEQYSSWYFDFW	191	191/240554	0.0794
+2	IGHJ6	CARGYYDSSGYYGVGQYYYYYMDVW	133	133/240554	0.0553
+3	IGHJ6	CARGMVRGVNYYYYYGMDVW	119	119/240554	0.0495
+4	IGHJ6	CARDRDLKDHHIAAAGSGYYYGMDVW	115	115/240554	0.0478
+5	IGHJ4	CARGTWYNDGWPHFDYW	107	107/240554	0.0445
+6	IGHJ3	CARSYYYGSGSYLAYAFDIW	104	104/240554	0.0432
+7	IGHJ4	CARDLGVLGYCSGGSCYSHVW	102	102/240554	0.0424
+8	IGHJ6	CASFPEQQLKWYGMDVW	101	101/240554	0.042
+9	IGHJ3	CASTESGGYYFDAFDIW	97	97/240554	0.0403
+10	IGHJ4	CARVLGDSFDYW	97	97/240554	0.0403
+11	IGHJ4	CATITMAYYFDYW	95	95/240554	0.0395
+12	IGHJ4	CARDPRSGYDFDYW	95	95/240554	0.0395
+13	IGHJ6	CARGGGSYPYYYYGMDVW	93	93/240554	0.0387
+14	IGHJ3	CARDHSTAEDAFDIW	92	92/240554	0.0382
+15	IGHJ4	CARDGGQLGIYFDYW	89	89/240554	0.037
+16	IGHJ6	CARDGYDSSGYYVGGALRLGVLQSYYGMDVW	88	88/240554	0.0366
+17	IGHJ4	CATDPARITDTDYW	88	88/240554	0.0366
+18	IGHJ3	CARVRELDAFDIW	88	88/240554	0.0366
+19	IGHJ4	CARGLPRPYSGSYSGFDYW	88	88/240554	0.0366
+20	IGHJ4	CARAGRVTMIVVVIKPLDYW	87	87/240554	0.0362
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_usage_geneJ_BCR_output1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,4 @@
+	J-GENE	Reads	Reads/Total	Frequency %
+1	IGHJ4	10	10/20	50.0000
+2	IGHJ6	6	6/20	30.0000
+3	IGHJ3	4	4/20	20.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_usage_geneJ_BCR_output2.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,4 @@
+	J-GENE	Frequency %
+1	IGHJ4	50
+2	IGHJ6	30
+3	IGHJ3	20
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_usage_geneJ_BCR_output3.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,3 @@
+	input	%
+Dominant J-GENE	IGHJ4	
+Frequency	50.0000	
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_usage_geneJ_TCR_input1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	J-GENE	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	TRBJ2-3	CASSSTDTQYF	3569	3569/56731	6.2911
+2	TRBJ2-3	CASRLVPDTQYF	2898	2898/56731	5.1083
+3	TRBJ1-1	CASSLSGNTEAFF	673	673/56731	1.1863
+4	TRBJ2-1	CASSSFDEQFF	544	544/56731	0.9589
+5	TRBJ1-1	CASSEGGWTEAFF	399	399/56731	0.7033
+6	TRBJ2-3	CASSPGSTDTQYF	332	332/56731	0.5852
+7	TRBJ2-1	CASSEIGQGANEQFF	203	203/56731	0.3578
+8	TRBJ1-1	CASSVLGVMNTEAFF	182	182/56731	0.3208
+9	TRBJ2-7	CASSYMSSGSEQYF	105	105/56731	0.1851
+10	TRBJ2-1	CSAFLGGTQFF	104	104/56731	0.1833
+11	TRBJ2-3	CASSRTETQYF	95	95/56731	0.1675
+12	TRBJ1-1	CASSSRDPLNTEAFF	85	85/56731	0.1498
+13	TRBJ1-6	CASMGGLNIYNSPLHF	78	78/56731	0.1375
+14	TRBJ1-1	CASSEHGRAAEAFF	73	73/56731	0.1287
+15	TRBJ1-5	CASSVRRYSNQPQHF	69	69/56731	0.1216
+16	TRBJ1-1	CSASRGEEAFF	69	69/56731	0.1216
+17	TRBJ2-1	CASSKSGGAFNEQFF	63	63/56731	0.1111
+18	TRBJ2-1	CASSSPYANNEQFF	61	61/56731	0.1075
+19	TRBJ2-3	CASSLIPGQYQYF	59	59/56731	0.104
+20	TRBJ2-3	CASSFRTGFTDTQYF	55	55/56731	0.0969
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_usage_geneJ_TCR_output1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,7 @@
+	J-GENE	Reads	Reads/Total	Frequency %
+1	TRBJ1-1	6	6/20	30.0000
+2	TRBJ2-3	6	6/20	30.0000
+3	TRBJ2-1	5	5/20	25.0000
+4	TRBJ1-5	1	1/20	5.0000
+5	TRBJ1-6	1	1/20	5.0000
+6	TRBJ2-7	1	1/20	5.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_usage_geneJ_TCR_output2.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,7 @@
+	J-GENE	Frequency %
+1	TRBJ1-1	30
+2	TRBJ2-3	30
+3	TRBJ2-1	25
+4	TRBJ1-5	5
+5	TRBJ1-6	5
+6	TRBJ2-7	5
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_usage_geneJ_TCR_output3.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,3 @@
+	input1.csv	%
+Dominant J-GENE	TRBJ1-1	
+Frequency	30.0000	
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_usage_geneV_BCR_input1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	V-GENE	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	IGHV3-23 or IGHV3-23D	CTREEQYSSWYFDFW	84	84/240554	0.0349
+2	IGHV3-11	CARGMVRGVNYYYYYGMDVW	78	78/240554	0.0324
+3	IGHV1-69	CASRMVRGVILPPYYYYYMDVW	74	74/240554	0.0308
+4	IGHV1-46	CARDRDLKDHHIAAAGSGYYYGMDVW	74	74/240554	0.0308
+5	IGHV7-4-1	CARASSHHYCSGGSCYSYYYYYYYMDVW	72	72/240554	0.0299
+6	IGHV4-59 or IGHV4-61	CARGTWYNDGWPHFDYW	71	71/240554	0.0295
+7	IGHV1-18	CARELYVWGSRHEVFDIW	71	71/240554	0.0295
+8	IGHV1-46	CASAGGVYTSGWHGTFYW	70	70/240554	0.0291
+9	IGHV3-33	CAKGGGSYYGVYYFDYW	69	69/240554	0.0287
+10	IGHV1-24	CATGDYDVLTGNYRAFW	67	67/240554	0.0279
+11	IGHV4-59 or IGHV4-61	CARDLGYSGSYLGRAFDIW	66	66/240554	0.0274
+12	IGHV3-33	CARDLHPRARGVIVIPGYW	65	65/240554	0.027
+13	IGHV1-69	CARLGRLERSPYYYMDVW	64	64/240554	0.0266
+14	IGHV4-34	CARVYPYDSSSWQAPYYYGMDVW	64	64/240554	0.0266
+15	IGHV1-69	CARDSSGGTDYYYYYMDVW	62	62/240554	0.0258
+16	IGHV3-49	CTRDRGERQYDAFDIW	61	61/240554	0.0254
+17	IGHV3-49	CTRPRGIVISAGIYFDYW	61	61/240554	0.0254
+18	IGHV1-69	CARDPVLYCGGDCSSSDAFDIW	60	60/240554	0.0249
+19	IGHV7-4-1	CARDTLYPPNYYGSGSYEGMDVW	60	60/240554	0.0249
+20	IGHV1-69	CARPRIAAAVYWYFDLW	60	60/240554	0.0249
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_usage_geneV_BCR_output1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,12 @@
+	V-GENE	Reads	Reads/Total	Frequency %
+1	IGHV1-69	5	5/20	25.0000
+2	IGHV1-46	2	2/20	10.0000
+3	IGHV3-33	2	2/20	10.0000
+4	IGHV3-49	2	2/20	10.0000
+5	IGHV4-59 or IGHV4-61	2	2/20	10.0000
+6	IGHV7-4-1	2	2/20	10.0000
+7	IGHV1-18	1	1/20	5.0000
+8	IGHV1-24	1	1/20	5.0000
+9	IGHV3-11	1	1/20	5.0000
+10	IGHV3-23 or IGHV3-23D	1	1/20	5.0000
+11	IGHV4-34	1	1/20	5.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_usage_geneV_BCR_output2.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,11 @@
+	V-GENE	Frequency %
+1	IGHV1-69	25.0000
+2	IGHV1-46	10.0000
+3	IGHV3-33	10.0000
+4	IGHV3-49	10.0000
+5	IGHV4-59 or IGHV4-61	10.0000
+6	IGHV7-4-1	10.0000
+7	IGHV1-18	5.0000
+8	IGHV1-24	5.0000
+9	IGHV3-11	5.0000
+10	IGHV3-23 or IGHV3-23D	5.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_usage_geneV_BCR_output3.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,3 @@
+	input	%
+Dominant V-GENE	IGHV1-69	
+Frequency	25.0000	
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_usage_geneV_TCR_input1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	V-GENE	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	TRBV2	CASSSTDTQYF	3545	3545/56731	6.2488
+2	TRBV2	CASRLVPDTQYF	2893	2893/56731	5.0995
+3	TRBV13	CASSLSGNTEAFF	670	670/56731	1.181
+4	TRBV27	CASSSFDEQFF	544	544/56731	0.9589
+5	TRBV2	CASSEGGWTEAFF	398	398/56731	0.7016
+6	TRBV5-1	CASSPGSTDTQYF	329	329/56731	0.5799
+7	TRBV2	CASSEIGQGANEQFF	201	201/56731	0.3543
+8	TRBV10-2	CASSVLGVMNTEAFF	181	181/56731	0.319
+9	TRBV20-1	CSAFLGGTQFF	104	104/56731	0.1833
+10	TRBV12-3 or TRBV12-4	CASSRTETQYF	94	94/56731	0.1657
+11	TRBV12-3 or TRBV12-4	CASSSRDPLNTEAFF	84	84/56731	0.1481
+12	TRBV2	CASMGGLNIYNSPLHF	77	77/56731	0.1357
+13	TRBV25-1	CASSEHGRAAEAFF	72	72/56731	0.1269
+14	TRBV9	CASSVRRYSNQPQHF	69	69/56731	0.1216
+15	TRBV20-1	CSASRGEEAFF	69	69/56731	0.1216
+16	TRBV2	CASSKSGGAFNEQFF	62	62/56731	0.1093
+17	TRBV27	CASSLIPGQYQYF	59	59/56731	0.104
+18	TRBV7-8	CASSFRTGFTDTQYF	55	55/56731	0.0969
+19	TRBV10-2	CASSEMGNEQFF	52	52/56731	0.0917
+20	TRBV25-1	CASSVTGYEQFF	49	49/56731	0.0864
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_usage_geneV_TCR_output1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,11 @@
+	V-GENE	Reads	Reads/Total	Frequency %
+1	TRBV2	6	6/20	30.0000
+2	TRBV10-2	2	2/20	10.0000
+3	TRBV12-3 or TRBV12-4	2	2/20	10.0000
+4	TRBV20-1	2	2/20	10.0000
+5	TRBV25-1	2	2/20	10.0000
+6	TRBV27	2	2/20	10.0000
+7	TRBV13	1	1/20	5.0000
+8	TRBV5-1	1	1/20	5.0000
+9	TRBV7-8	1	1/20	5.0000
+10	TRBV9	1	1/20	5.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_usage_geneV_TCR_output2.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,11 @@
+	V-GENE	Frequency %
+1	TRBV2	30.0000
+2	TRBV10-2	10.0000
+3	TRBV12-3 or TRBV12-4	10.0000
+4	TRBV20-1	10.0000
+5	TRBV25-1	10.0000
+6	TRBV27	10.0000
+7	TRBV13	5.0000
+8	TRBV5-1	5.0000
+9	TRBV7-8	5.0000
+10	TRBV9	5.0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_usage_geneV_TCR_output3.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,3 @@
+	input1.csv	%
+Dominant V-GENE	TRBV2	
+Frequency	30.0000	
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/public_clonos_def1_BCR_input1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	CTREEQYSSWYFDFW	191	191/240554	0.0794
+2	CARGMVRGVNYYYYYGMDVW	119	119/240554	0.0495
+3	CARGTWYNDGWPHFDYW	107	107/240554	0.0445
+4	CARDLGVLGYCSGGSCYSHVW	102	102/240554	0.0424
+5	CARVLGDSFDYW	97	97/240554	0.0403
+6	CATITMAYYFDYW	95	95/240554	0.0395
+7	CARGGGSYPYYYYGMDVW	93	93/240554	0.0387
+8	CARDGGQLGIYFDYW	89	89/240554	0.037
+9	CARGLPRPYSGSYSGFDYW	88	88/240554	0.0366
+10	CARVRELDAFDIW	88	88/240554	0.0366
+11	CARVQYVWDSPGAFDIW	86	86/240554	0.0358
+12	CARGQGTVTTEIDYW	86	86/240554	0.0358
+13	CARDRANYGSGSPIDYW	85	85/240554	0.0353
+14	CARLGRLERSPYYYMDVW	85	85/240554	0.0353
+15	CARGPFYCSGGSCNLHYYYGMDVW	84	84/240554	0.0349
+16	CARDDSTGGNWDAFDIW	84	84/240554	0.0349
+17	CARYKRGGIAVAGTLSSSFDYW	84	84/240554	0.0349
+18	CARINYYDSSGYYHKGMYYFDYW	83	83/240554	0.0345
+19	CARVGSYSGIRAFDIW	83	83/240554	0.0345
+20	CARGPRHYDSSGYCVKLDYW	82	82/240554	0.0341
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/public_clonos_def1_BCR_input2.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	CARGYYDSSGYYGVGQYYYYYMDVW	133	133/198331	0.0671
+2	CARGMVRGVNYYYYYGMDVW	122	122/198331	0.0615
+3	CARDRDLKDHHIAAAGSGYYYGMDVW	115	115/198331	0.058
+4	CARSYYYGSGSYLAYAFDIW	104	104/198331	0.0524
+5	CARDLGVLGYCSGGSCYSHVW	101	101/198331	0.0509
+6	CASFPEQQLKWYGMDVW	101	101/198331	0.0509
+7	CASTESGGYYFDAFDIW	97	97/198331	0.0489
+8	CARDPRSGYDFDYW	95	95/198331	0.0479
+9	CARDHSTAEDAFDIW	92	92/198331	0.0464
+10	CARDGYDSSGYYVGGALRLGVLQSYYGMDVW	88	88/198331	0.0444
+11	CATDPARITDTDYW	88	88/198331	0.0444
+12	CARAGRVTMIVVVIKPLDYW	87	87/198331	0.0439
+13	CARGEGYGDCW	86	86/198331	0.0434
+14	CARAGDYGSGTNAFDIW	85	85/198331	0.0429
+15	CARLGRLERSPYYYMDVW	84	84/198331	0.0424
+16	CARDGIAAATSGLDVW	84	84/198331	0.0424
+17	CARDVEYYYDSSGQYFDYW	84	84/198331	0.0424
+18	CARDRHCSGGSCRGLW	83	83/198331	0.0418
+19	CARVGSYSGIRAFDIW	82	82/198331	0.0413
+20	CARGDLVVVRGVINQGKLDYW	81	81/198331	0.0408
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/public_clonos_def1_BCR_output1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,5 @@
+	AA JUNCTION	input1.csv Reads/Total	input1.csv Relative Frequency %	input2.csv Reads/Total	input2.csv Relative Frequency %	Num of Patients
+1	CARGMVRGVNYYYYYGMDVW	119/240554	0.0495	122/198331	0.0615	2
+3	CARDLGVLGYCSGGSCYSHVW	102/240554	0.0424	101/198331	0.0509	2
+13	CARLGRLERSPYYYMDVW	85/240554	0.0353	84/198331	0.0424	2
+18	CARVGSYSGIRAFDIW	83/240554	0.0345	82/198331	0.0413	2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/public_clonos_def1_BCR_parameters.txt	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,2 @@
+Remove Clonotypes With Reads Fewer Than Threshold?: Yes,
+Keep Clonotypes with Number of Reads more than: 3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/public_clonos_def1_TCR_input1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	CASSSTDTQYF	3569	3569/56731	6.2911
+2	CASSLSGNTEAFF	673	673/56731	1.1863
+3	CASSEGGWTEAFF	399	399/56731	0.7033
+4	CASSEIGQGANEQFF	203	203/56731	0.3578
+5	CASSYMSSGSEQYF	105	105/56731	0.1851
+6	CASSRTETQYF	95	95/56731	0.1675
+7	CASSSRDPLNTEAFF	85	85/56731	0.1498
+8	CASMGGLNIYNSPLHF	78	78/56731	0.1375
+9	CSASRGEEAFF	69	69/56731	0.1216
+10	CASSKSGGAFNEQFF	63	63/56731	0.1111
+11	CASSLIPGQYQYF	59	59/56731	0.104
+12	CASSEMGNEQFF	52	52/56731	0.0917
+13	CASSPEVEGQPQHF	48	48/56731	0.0846
+14	CAITGTAGNTEAFF	47	47/56731	0.0828
+15	CSANRGEEAFF	45	45/56731	0.0793
+16	CAWSVGAEAFF	44	44/56731	0.0776
+17	CASSPGTAEAFF	42	42/56731	0.074
+18	CASSASGYEQYF	40	40/56731	0.0705
+19	CASSRGLNGADTQYF	40	40/56731	0.0705
+20	CASSRQIEAEAFF	39	39/56731	0.0687
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/public_clonos_def1_TCR_input2.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	CASRLVPDTQYF	2898	2898/54828	5.2856
+2	CASSSFDEQFF	544	544/54828	0.9922
+3	CASSPGSTDTQYF	332	332/54828	0.6055
+4	CASSVLGVMNTEAFF	182	182/54828	0.3319
+5	CSAFLGGTQFF	104	104/54828	0.1897
+6	CASSSRDPLNTEAFF	81	81/54828	0.1477
+7	CASSEHGRAAEAFF	73	73/54828	0.1331
+8	CASSVRRYSNQPQHF	69	69/54828	0.1258
+9	CASSKSGGAFNEQFF	62	62/54828	0.1131
+10	CASSSPYANNEQFF	61	61/54828	0.1113
+11	CASSFRTGFTDTQYF	55	55/54828	0.1003
+12	CASSVTGYEQFF	49	49/54828	0.0894
+13	CATATSGSTDTQYF	47	47/54828	0.0857
+14	CAITGTAGNTEAFF	47	47/54828	0.0857
+15	CASSFRAPNTDTQYF	46	46/54828	0.0839
+16	CSVGSGEGYEQYF	44	44/54828	0.0803
+17	CSGIAGSTDTQYF	43	43/54828	0.0784
+18	CSARRLGTIYF	41	41/54828	0.0748
+19	CASGGNTQYF	40	40/54828	0.073
+20	CASLSSNEQYF	39	39/54828	0.0711
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/public_clonos_def1_TCR_output1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,4 @@
+	AA JUNCTION	input1.csv Reads/Total	input1.csv Relative Frequency %	input2.csv Reads/Total	input2.csv Relative Frequency %	Num of Patients
+1	CASSSRDPLNTEAFF	85/56731	0.1498	81/54828	0.1477	2
+2	CASSKSGGAFNEQFF	63/56731	0.1111	62/54828	0.1131	2
+3	CAITGTAGNTEAFF	47/56731	0.0828	47/54828	0.0857	2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/public_clonos_def1_TCR_parameters.txt	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,2 @@
+Remove Clonotypes With Reads Fewer Than Threshold?: Yes,
+Keep Clonotypes with Number of Reads more than: 2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/public_clonos_def2_BCR_input1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	V-GENE	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	IGHV3-23 or IGHV3-23D	CTREEQYSSWYFDFW	84	84/240554	0.0349
+2	IGHV1-69	CASRMVRGVILPPYYYYYMDVW	74	74/240554	0.0308
+3	IGHV7-4-1	CARASSHHYCSGGSCYSYYYYYYYMDVW	72	72/240554	0.0299
+4	IGHV1-18	CARELYVWGSRHEVFDIW	71	71/240554	0.0295
+5	IGHV3-33	CAKGGGSYYGVYYFDYW	69	69/240554	0.0287
+6	IGHV4-59 or IGHV4-61	CARDLGYSGSYLGRAFDIW	66	66/240554	0.0274
+7	IGHV3-33	CARDLHPRARGVIVIPGYW	65	65/240554	0.027
+8	IGHV1-69	CARLGRLERSPYYYMDVW	64	64/240554	0.0266
+9	IGHV1-69	CARDSSGGTDYYYYYMDVW	62	62/240554	0.0258
+10	IGHV3-49	CTRPRGIVISAGIYFDYW	61	61/240554	0.0254
+11	IGHV1-69	CARDPVLYCGGDCSSSDAFDIW	60	60/240554	0.0249
+12	IGHV7-4-1	CARDTLYPPNYYGSGSYEGMDVW	60	60/240554	0.0249
+13	IGHV4-39	CAGRASPFGPSYYFNSW	60	60/240554	0.0249
+14	IGHV3-9	CAKDISLRDEGDSSVGYDYW	59	59/240554	0.0245
+15	IGHV4-39	CARLMLGTMVKTPDAFDIW	59	59/240554	0.0245
+16	IGHV1-3	CARALPPRYCSGGSCYYPSNWGQGTLVGYYPSNW	59	59/240554	0.0245
+17	IGHV3-30 or IGHV3-30-3	CARDQFGVVTVKGGYFQHW	58	58/240554	0.0241
+18	IGHV1-3	CARERYYNRGAFDIW	57	57/240554	0.0237
+19	IGHV3-9	CAIGRGVISTFFDYW	57	57/240554	0.0237
+20	IGHV3-23 or IGHV3-23D	CAKERALGFGEPHYW	56	56/240554	0.0233
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/public_clonos_def2_BCR_input2.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	V-GENE	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	IGHV3-11	CARGMVRGVNYYYYYGMDVW	78	78/251182	0.0311
+2	IGHV1-46	CARDRDLKDHHIAAAGSGYYYGMDVW	74	74/251182	0.0295
+3	IGHV4-59 or IGHV4-61	CARGTWYNDGWPHFDYW	71	71/251182	0.0283
+4	IGHV1-46	CASAGGVYTSGWHGTFYW	70	70/251182	0.0279
+5	IGHV3-33	CAKGGGSYYGVYYFDYW	68	68/251182	0.0271
+6	IGHV1-24	CATGDYDVLTGNYRAFW	67	67/251182	0.0267
+7	IGHV3-33	CARDLHPRARGVIVIPGYW	65	65/251182	0.0259
+8	IGHV4-34	CARVYPYDSSSWQAPYYYGMDVW	64	64/251182	0.0255
+9	IGHV3-49	CTRDRGERQYDAFDIW	61	61/251182	0.0243
+10	IGHV1-69	CARDPVLYCGGDCSSSDAFDIW	60	60/251182	0.0239
+11	IGHV1-69	CARPRIAAAVYWYFDLW	60	60/251182	0.0239
+12	IGHV3-21	CARDHFVWGSPSPMDIW	60	60/251182	0.0239
+13	IGHV3-23 or IGHV3-23D	CARVGSYSGIRAFDIW	59	59/251182	0.0235
+14	IGHV4-39	CARLMLGTMVKTPDAFDIW	59	59/251182	0.0235
+15	IGHV4-59 or IGHV4-61	CARHDGIAAAGHFDYW	59	59/251182	0.0235
+16	IGHV1-69	CAREEKFGELLERSYYYYYYMDVW	59	59/251182	0.0235
+17	IGHV1-69	CARGYYDSSGYYGVGQYYYYYMDVW	58	58/251182	0.0231
+18	IGHV3-33	CAKGPRMVRGVLDYW	57	57/251182	0.0227
+19	IGHV3-9	CAIGRGVISTFFDYW	57	57/251182	0.0227
+20	IGHV3-64	CATEHIAAAGEASAFDIW	57	57/251182	0.0227
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/public_clonos_def2_BCR_output1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,6 @@
+	V-GENE	AA JUNCTION	input1.csv Reads/Total	input1.csv Relative Frequency %	input2.csv Reads/Total	input2.csv Relative Frequency %	Num of Patients
+4	IGHV3-33	CAKGGGSYYGVYYFDYW	69/240554	0.0287	68/251182	0.0271	2
+6	IGHV3-33	CARDLHPRARGVIVIPGYW	65/240554	0.027	65/251182	0.0259	2
+10	IGHV1-69	CARDPVLYCGGDCSSSDAFDIW	60/240554	0.0249	60/251182	0.0239	2
+14	IGHV4-39	CARLMLGTMVKTPDAFDIW	59/240554	0.0245	59/251182	0.0235	2
+18	IGHV3-9	CAIGRGVISTFFDYW	57/240554	0.0237	57/251182	0.0227	2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/public_clonos_def2_BCR_parameters.txt	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,2 @@
+Remove Clonotypes With Reads Fewer Than Threshold?: Yes,
+Keep Clonotypes with Number of Reads more than: 3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/public_clonos_def2_TCR_input1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	V-GENE	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	TRBV2	CASSSTDTQYF	3545	3545/56731	6.2488
+2	TRBV2	CASRLVPDTQYF	2893	2893/56731	5.0995
+3	TRBV13	CASSLSGNTEAFF	670	670/56731	1.181
+4	TRBV2	CASSEGGWTEAFF	398	398/56731	0.7016
+5	TRBV5-1	CASSPGSTDTQYF	329	329/56731	0.5799
+6	TRBV2	CASSEIGQGANEQFF	201	201/56731	0.3543
+7	TRBV20-1	CSAFLGGTQFF	104	104/56731	0.1833
+8	TRBV12-3 or TRBV12-4	CASSSRDPLNTEAFF	84	84/56731	0.1481
+9	TRBV25-1	CASSEHGRAAEAFF	72	72/56731	0.1269
+10	TRBV20-1	CSASRGEEAFF	69	69/56731	0.1216
+11	TRBV27	CASSLIPGQYQYF	59	59/56731	0.104
+12	TRBV10-2	CASSEMGNEQFF	52	52/56731	0.0917
+13	TRBV3-1	CASSPEVEGQPQHF	48	48/56731	0.0846
+14	TRBV7-8	CASSFRAPNTDTQYF	46	46/56731	0.0811
+15	TRBV30	CAWSVGAEAFF	44	44/56731	0.0776
+16	TRBV29-1	CSGIAGSTDTQYF	43	43/56731	0.0758
+17	TRBV20-1	CSARRLGTIYF	41	41/56731	0.0723
+18	TRBV2	CASGGNTQYF	40	40/56731	0.0705
+19	TRBV2	CASLSSNEQYF	39	39/56731	0.0687
+20	TRBV25-1	CASTSGTGSDTQYF	37	37/56731	0.0652
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/public_clonos_def2_TCR_input2.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	V-GENE	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	TRBV2	CASRLVPDTQYF	2931	2931/57218	5.1225
+2	TRBV13	CASSLSGNTEAFF	753	753/57218	1.316
+3	TRBV27	CASSSFDEQFF	544	544/57218	0.9507
+4	TRBV5-1	CASSPGSTDTQYF	322	322/57218	0.5628
+5	TRBV10-2	CASSVLGVMNTEAFF	181	181/57218	0.3163
+6	TRBV20-1	CSAFLGGTQFF	107	107/57218	0.187
+7	TRBV12-3 or TRBV12-4	CASSRTETQYF	94	94/57218	0.1643
+8	TRBV2	CASMGGLNIYNSPLHF	77	77/57218	0.1346
+9	TRBV25-1	CASSEHGRAAEAFF	74	74/57218	0.1293
+10	TRBV9	CASSVRRYSNQPQHF	69	69/57218	0.1206
+11	TRBV2	CASSKSGGAFNEQFF	62	62/57218	0.1084
+12	TRBV7-8	CASSFRTGFTDTQYF	55	55/57218	0.0961
+13	TRBV25-1	CASSVTGYEQFF	49	49/57218	0.0856
+14	TRBV10-3 or TRBV6-1 or TRBV6-4 or TRBV6-5 or TRBV6-6	CASSYMSSGSEQYF	47	47/57218	0.0821
+15	TRBV20-1	CSANRGEEAFF	45	45/57218	0.0786
+16	TRBV29-1	CSVGSGEGYEQYF	44	44/57218	0.0769
+17	TRBV12-3 or TRBV12-4	CASSPGTAEAFF	42	42/57218	0.0734
+18	TRBV7-9	CASSSPYANNEQFF	41	41/57218	0.0717
+19	TRBV25-1	CASSASGYEQYF	40	40/57218	0.0699
+20	TRBV12-3 or TRBV12-4	CASSRQIEAEAFF	38	38/57218	0.0664
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/public_clonos_def2_TCR_output1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,6 @@
+	V-GENE	AA JUNCTION	input1.csv Reads/Total	input1.csv Relative Frequency %	input2.csv Reads/Total	input2.csv Relative Frequency %	Num of Patients
+1	TRBV2	CASRLVPDTQYF	2893/56731	5.0995	2931/57218	5.1225	2
+2	TRBV13	CASSLSGNTEAFF	670/56731	1.181	753/57218	1.316	2
+3	TRBV5-1	CASSPGSTDTQYF	329/56731	0.5799	322/57218	0.5628	2
+4	TRBV20-1	CSAFLGGTQFF	104/56731	0.1833	107/57218	0.187	2
+5	TRBV25-1	CASSEHGRAAEAFF	72/56731	0.1269	74/57218	0.1293	2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/public_clonos_def2_TCR_parameters.txt	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,2 @@
+Remove Clonotypes With Reads Fewer Than Threshold?: Yes,
+Keep Clonotypes with Number of Reads more than: 2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/public_clonos_def3_BCR_input1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	J-GENE	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	IGHJ4	CTREEQYSSWYFDFW	191	191/240554	0.0794
+2	IGHJ6	CARGMVRGVNYYYYYGMDVW	119	119/240554	0.0495
+3	IGHJ4	CARGTWYNDGWPHFDYW	107	107/240554	0.0445
+4	IGHJ4	CARDLGVLGYCSGGSCYSHVW	102	102/240554	0.0424
+5	IGHJ3	CASTESGGYYFDAFDIW	97	97/240554	0.0403
+6	IGHJ4	CATITMAYYFDYW	95	95/240554	0.0395
+7	IGHJ6	CARGGGSYPYYYYGMDVW	93	93/240554	0.0387
+8	IGHJ4	CARDGGQLGIYFDYW	89	89/240554	0.037
+9	IGHJ6	CARDGYDSSGYYVGGALRLGVLQSYYGMDVW	88	88/240554	0.0366
+10	IGHJ4	CATDPARITDTDYW	88	88/240554	0.0366
+11	IGHJ4	CARGLPRPYSGSYSGFDYW	88	88/240554	0.0366
+12	IGHJ4	CARGEGYGDCW	86	86/240554	0.0358
+13	IGHJ4	CARGQGTVTTEIDYW	86	86/240554	0.0358
+14	IGHJ3	CARAGDYGSGTNAFDIW	85	85/240554	0.0353
+15	IGHJ4	CARYKRGGIAVAGTLSSSFDYW	84	84/240554	0.0349
+16	IGHJ4	CARDVEYYYDSSGQYFDYW	84	84/240554	0.0349
+17	IGHJ6	CARDGIAAATSGLDVW	84	84/240554	0.0349
+18	IGHJ4	CARINYYDSSGYYHKGMYYFDYW	83	83/240554	0.0345
+19	IGHJ4	CARGPRHYDSSGYCVKLDYW	82	82/240554	0.0341
+20	IGHJ6	CARGVSGYYNFFYMDVW	81	81/240554	0.0337
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/public_clonos_def3_BCR_input2.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	J-GENE	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	IGHJ6	CARGYYDSSGYYGVGQYYYYYMDVW	133	133/229003	0.0581
+2	IGHJ6	CARGMVRGVNYYYYYGMDVW	124	124/229003	0.0541
+3	IGHJ6	CARDRDLKDHHIAAAGSGYYYGMDVW	115	115/229003	0.0502
+4	IGHJ3	CARSYYYGSGSYLAYAFDIW	104	104/229003	0.0454
+5	IGHJ6	CASFPEQQLKWYGMDVW	101	101/229003	0.0441
+6	IGHJ4	CARVLGDSFDYW	97	97/229003	0.0424
+7	IGHJ4	CARDPRSGYDFDYW	95	95/229003	0.0415
+8	IGHJ3	CARDHSTAEDAFDIW	92	92/229003	0.0402
+9	IGHJ6	CARDGYDSSGYYVGGALRLGVLQSYYGMDVW	88	88/229003	0.0384
+10	IGHJ3	CARVRELDAFDIW	88	88/229003	0.0384
+11	IGHJ4	CARAGRVTMIVVVIKPLDYW	87	87/229003	0.038
+12	IGHJ3	CARVQYVWDSPGAFDIW	86	86/229003	0.0376
+13	IGHJ6	CARLGRLERSPYYYMDVW	85	85/229003	0.0371
+14	IGHJ4	CARDRANYGSGSPIDYW	85	85/229003	0.0371
+15	IGHJ6	CARGPFYCSGGSCNLHYYYGMDVW	84	84/229003	0.0367
+16	IGHJ3	CARDDSTGGNWDAFDIW	84	84/229003	0.0367
+17	IGHJ6	CARDGIAAATSGLDVW	83	83/229003	0.0362
+18	IGHJ5	CARDRHCSGGSCRGLW	83	83/229003	0.0362
+19	IGHJ3	CARVGSYSGIRAFDIW	83	83/229003	0.0362
+20	IGHJ4	CARGDLVVVRGVINQGKLDYW	81	81/229003	0.0354
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/public_clonos_def3_BCR_output1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,4 @@
+	J-GENE	AA JUNCTION	input1.csv Reads/Total	input1.csv Relative Frequency %	input2.csv Reads/Total	input2.csv Relative Frequency %	Num of Patients
+1	IGHJ6	CARGMVRGVNYYYYYGMDVW	119/240554	0.0495	124/229003	0.0541	2
+8	IGHJ6	CARDGYDSSGYYVGGALRLGVLQSYYGMDVW	88/240554	0.0366	88/229003	0.0384	2
+16	IGHJ6	CARDGIAAATSGLDVW	84/240554	0.0349	83/229003	0.0362	2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/public_clonos_def3_BCR_parameters.txt	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,2 @@
+Remove Clonotypes With Reads Fewer Than Threshold?: Yes,
+Keep Clonotypes with Number of Reads more than: 3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/public_clonos_def3_TCR_input1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	J-GENE	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	TRBJ2-3	CASSSTDTQYF	3569	3569/56731	6.2911
+2	TRBJ1-1	CASSLSGNTEAFF	673	673/56731	1.1863
+3	TRBJ2-1	CASSSFDEQFF	544	544/56731	0.9589
+4	TRBJ1-1	CASSEGGWTEAFF	399	399/56731	0.7033
+5	TRBJ2-1	CASSEIGQGANEQFF	203	203/56731	0.3578
+6	TRBJ2-7	CASSYMSSGSEQYF	105	105/56731	0.1851
+7	TRBJ2-3	CASSRTETQYF	95	95/56731	0.1675
+8	TRBJ1-1	CASSSRDPLNTEAFF	85	85/56731	0.1498
+9	TRBJ1-6	CASMGGLNIYNSPLHF	78	78/56731	0.1375
+10	TRBJ1-5	CASSVRRYSNQPQHF	69	69/56731	0.1216
+11	TRBJ2-1	CASSKSGGAFNEQFF	63	63/56731	0.1111
+12	TRBJ2-3	CASSLIPGQYQYF	59	59/56731	0.104
+13	TRBJ2-1	CASSEMGNEQFF	52	52/56731	0.0917
+14	TRBJ1-5	CASSPEVEGQPQHF	48	48/56731	0.0846
+15	TRBJ1-1	CAITGTAGNTEAFF	47	47/56731	0.0828
+16	TRBJ1-1	CSANRGEEAFF	45	45/56731	0.0793
+17	TRBJ1-1	CAWSVGAEAFF	44	44/56731	0.0776
+18	TRBJ1-1	CASSPGTAEAFF	42	42/56731	0.074
+19	TRBJ2-3	CASSRGLNGADTQYF	40	40/56731	0.0705
+20	TRBJ2-7	CASSASGYEQYF	40	40/56731	0.0705
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/public_clonos_def3_TCR_input2.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,21 @@
+	J-GENE	AA JUNCTION	Reads	Reads/Total	Frequency %
+1	TRBJ2-3	CASRLVPDTQYF	2898	2898/57339	5.0542
+2	TRBJ2-1	CASSSFDEQFF	618	618/57339	1.0778
+3	TRBJ2-3	CASSPGSTDTQYF	332	332/57339	0.579
+4	TRBJ1-1	CASSVLGVMNTEAFF	182	182/57339	0.3174
+5	TRBJ2-7	CASSYMSSGSEQYF	112	112/57339	0.1953
+6	TRBJ2-1	CSAFLGGTQFF	104	104/57339	0.1814
+7	TRBJ1-1	CASSSRDPLNTEAFF	86	86/57339	0.15
+8	TRBJ1-1	CASSEHGRAAEAFF	73	73/57339	0.1273
+9	TRBJ1-1	CSASRGEEAFF	69	69/57339	0.1203
+10	TRBJ2-1	CASSSPYANNEQFF	61	61/57339	0.1064
+11	TRBJ2-3	CASSFRTGFTDTQYF	55	55/57339	0.0959
+12	TRBJ2-1	CASSEMGNEQFF	50	50/57339	0.0872
+13	TRBJ2-1	CASSVTGYEQFF	49	49/57339	0.0855
+14	TRBJ2-3	CATATSGSTDTQYF	47	47/57339	0.082
+15	TRBJ2-3	CASSFRAPNTDTQYF	46	46/57339	0.0802
+16	TRBJ2-7	CSVGSGEGYEQYF	44	44/57339	0.0767
+17	TRBJ2-3	CSGIAGSTDTQYF	43	43/57339	0.075
+18	TRBJ1-3	CSARRLGTIYF	41	41/57339	0.0715
+19	TRBJ2-3	CASGGNTQYF	40	40/57339	0.0698
+20	TRBJ1-1	CASSRQIEAEAFF	39	39/57339	0.068
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/public_clonos_def3_TCR_output1.csv	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,5 @@
+	J-GENE	AA JUNCTION	input1.csv Reads/Total	input1.csv Relative Frequency %	input2.csv Reads/Total	input2.csv Relative Frequency %	Num of Patients
+1	TRBJ2-1	CASSSFDEQFF	544/56731	0.9589	618/57339	1.0778	2
+2	TRBJ2-7	CASSYMSSGSEQYF	105/56731	0.1851	112/57339	0.1953	2
+3	TRBJ1-1	CASSSRDPLNTEAFF	85/56731	0.1498	86/57339	0.15	2
+4	TRBJ2-1	CASSEMGNEQFF	52/56731	0.0917	50/57339	0.0872	2
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/public_clonos_def3_TCR_parameters.txt	Mon Apr 30 04:47:52 2018 -0400
@@ -0,0 +1,2 @@
+Remove Clonotypes With Reads Fewer Than Threshold?: Yes,
+Keep Clonotypes with Number of Reads more than: 2