# HG changeset patch
# User iuc
# Date 1521597534 14400
# Node ID 8c39f704d21ac0703ba5a59515c24e48b50361b9
# Parent  506625098e20fd14bbb8ca3938bd355adee1fe7e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3

diff -r 506625098e20 -r 8c39f704d21a lefse.xml
--- a/lefse.xml	Tue Sep 05 16:56:54 2017 -0400
+++ b/lefse.xml	Tue Mar 20 21:58:54 2018 -0400
@@ -7,38 +7,41 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s '$otu' shared.dat &&
-        ln -s '$design' design.dat &&
+## create symlinks to input datasets
+ln -s '$otu' shared.dat &&
+ln -s '$design' design.dat &&
 
-        echo 'lefse(
-            shared=shared.dat,
-            design=design.dat,
-            #if $class:
-                class=$class,
-            #end if
-            #if $sclass:
-                subclass=$sclass,
-            #end if
-            #if $label:
-                label=${ str($label).replace(",","-") },
-            #end if
-            aalpha=$aalpha,
-            walpha=$walpha,
-            lda=$lda,
-            iters=$iters,
-            fboots=$fboots,
-            strict=$strict,
-            minc=$minc,
-            wilc=$wilc,
-            curv=$curv,
-            norm=$norm
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'lefse(
+    shared=shared.dat,
+    design=design.dat,
+    #if $class:
+        class=$class,
+    #end if
+    #if $sclass:
+        subclass=$sclass,
+    #end if
+    #if $label:
+        label=${ str($label).replace(",","-") },
+    #end if
+    #if $sets:
+        sets=${ str($sets).replace(",","-") },
+    #end if
+    aalpha=$aalpha,
+    walpha=$walpha,
+    lda=$lda,
+    iters=$iters,
+    fboots=$fboots,
+    strict=$strict,
+    minc=$minc,
+    wilc=$wilc,
+    curv=$curv,
+    norm=$norm
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
@@ -46,6 +49,15 @@
         <param name="label" type="select" multiple="true" optional="true" label="label - OTU Label filter">
             <expand macro="labeloptions"/>
         </param>
+        <param name="sets" type="text" label="sets - Which of the sets in your design file you would like to analyze?" help="separate sets by dashes or commas, e.g. set1,set2 or set1-set2-set3"/>
+        <!-- TODO: update galaxy datatypes to set metadata for design files, then can switch to a select box
+        <param argument="sets" type="select" multiple="true" label="sets - Which of the sets in your design file you would like to analyze."
+            help="The set names are separated by dashes. The defualt is all sets in designfile">
+            <options>
+                <filter type="data_meta" ref="design" key="sets"/>
+            </options>
+         </param>
+         -->
         <param name="class" type="text" optional="true" value="" label="class -indicate the which category you would like used for the Kruskal Wallis analysis" help="If none is provided first category is used"/>
         <param name="sclass" type="text" optional="true" value="" label="subclass - indicate the which category you would like used for the Kruskal Wallis analysis" help="If none is provided second category is used"/>
         <param name="aalpha" type="float" value="0.05" label="aalpha - alpha value for the Krukal Wallis Anova test" help=""/>
@@ -58,6 +70,7 @@
         <param name="wilc" type="boolean" truevalue="T" falsevalue="F" checked="true" label="wilc - indicate whether to perform the Wilcoxon test" help=""/>
         <param name="curv" type="boolean" truevalue="T" falsevalue="F" checked="false" label="curv - whether perform the wilcoxon testing the Curtis's approach (beta)" help=""/>
         <param name="norm" type="boolean" truevalue="T" falsevalue="F" checked="true" label="norm - multiply relative abundances by 1000000" help="Recommended when very low values are present"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -68,6 +81,7 @@
             <param name="otu" value="final.tx.1.subsample.1.pick.shared" ftype="mothur.shared"/>
             <param name="design" value="mouse.design"/>
             <output name="summary" md5="d2c3d2e813607aef0844ec2fb53a5955" ftype="tabular"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with label and class select -->
@@ -76,6 +90,17 @@
             <param name="label" value="1"/>
             <param name="class" value="dpw"/>
             <output name="summary" md5="d2c3d2e813607aef0844ec2fb53a5955" ftype="tabular"/>
+            <param name="savelog" value="true"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with sets -->
+            <param name="otu" value="final.tx.1.subsample.1.pick.shared" ftype="mothur.shared"/>
+            <param name="design" value="mouse.design"/>
+            <param name="sets" value="8,142"/>
+            <param name="label" value="1"/>
+            <param name="class" value="dpw"/>
+            <output name="summary" md5="64ebfb48d8c3e0bcd993a7ea8aa60e62" ftype="tabular"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
diff -r 506625098e20 -r 8c39f704d21a macros.xml
--- a/macros.xml	Tue Sep 05 16:56:54 2017 -0400
+++ b/macros.xml	Tue Mar 20 21:58:54 2018 -0400
@@ -1,11 +1,13 @@
 <macros>
+    <token name="@WRAPPER_VERSION@">1.39.5</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="1.36.1">mothur</requirement>
+            <requirement type="package" version="@WRAPPER_VERSION@">mothur</requirement>
+            <yield/>
         </requirements>
     </xml>
     <xml name="version_command">
-        <version_command>mothur "#help()" | sed '7q;d' | cut -d" " -f2 </version_command>
+        <version_command><![CDATA[ mothur "#help()" | sed '7q;d' | cut -d" " -f2 ]]></version_command>
     </xml>
     <xml name="stdio">
         <stdio>
@@ -13,20 +15,10 @@
             <exit_code range="1:" level="fatal"/>
         </stdio>
     </xml>
-    <token name="@WRAPPER_VERSION@">1.36.1</token>
     <token name="@SHELL_OPTIONS@">set -o pipefail;</token>
-    <token name="@MOTHUR_OVERVIEW@">
-<![CDATA[
-
-**Mothur Overview**
 
-Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team
-in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki_.
 
-.. _Mothur-Wiki: https://www.mothur.org/wiki/Main_Page
-
-]]>
-    </token>
+    <!-- Input parameters -->
     <xml name="labeloptions">
         <options>
             <filter type="data_meta" ref="otu" key="labels"/>
@@ -78,9 +70,70 @@
         <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option>
         <yield/>
     </xml>
+
+    <!-- CLUSTERING -->
+    <xml name="param-clustermethods">
+        <param argument="method" type="select" label="Clustering Method">
+            <option value="opti" selected="true">Opticlust method</option>
+            <option value="furthest">Furthest neighbor</option>
+            <option value="nearest">Nearest neighbor</option>
+            <option value="average">Average neighbor</option>
+            <yield/>
+        </param>
+    </xml>
+    <xml name="option-vsearch-clustermethods">
+        <option value="agc">Abundance-based greedy clustering (agc)(VSEARCH)</option>
+        <option value="dgc">Distance-based greedy clustering (dgc)(VSEARCH)</option>
+    </xml>
+    <xml name="params-opticlust">
+        <param argument="metric" type="select" label="metric - select the metric in the opticluster method"
+            help="Options are Matthews correlation coefficient (mcc), sensitivity (sens), specificity (spec), true positives + true negatives (tptn),
+            false positives + false negatives (fpfn), true positives (tp), true negative (tn), false positive (fp), false negative (fn), f1score (f1score),
+            accuracy (accuracy), positive predictive value (ppv), negative predictive value (npv), false discovery rate (fdr). Default=mcc.">
+            <option value="mcc" selected="true">Matthews correlation coefficient (mcc)</option>
+            <option value="sens">Sensitivity</option>
+            <option value="spec">specificity</option>
+            <option value="tptn">true positives + true negatives</option>
+            <option value="fpfn">false positives + false negatives</option>
+            <option value="tp">true positives</option>
+            <option value="tn">true negative</option>
+            <option value="fp">false positive</option>
+            <option value="fn">false negative</option>
+            <option value="f1score">f1score</option>
+            <option value="accuracy">accuracy</option>
+            <option value="ppv">positive predictive value</option>
+            <option value="npv">negative predictive value</option>
+            <option value="fdr">false discovery rate</option>
+        </param>
+        <param argument="initialize" type="select" label="Initial randomization"
+            help="singleton: each sequence is randomly assigned to its own OTU; oneotu: all sequences are assigned to one otu">
+            <option value="singleton" selected="true">Singleton</option>
+            <option value="oneotu">Oneotu</option>
+        </param>
+        <param argument="delta" type="float" value="0.0001" label="set the stable value for the metric in the opticluster method"
+            help="The delta parameter allows to set the stable value for the metric in the opticluster method. To reach a full convergence, set delta=0."/>
+        <param argument="iters" type="integer" value="100" label="Maximum number of iterations"/>
+    </xml>
+    <xml name="param-output">
+        <param argument="output" type="select" label="Tax summary output type"
+            help="The detail format outputs the totals at each level, where as the simple format outputs the highest level">
+            <option value="simple" selected="true">simple</option>
+            <option value="detail">detail</option>
+        </param>
+    </xml>
+    <xml name="param-printlevel">
+        <param argument="printlevel" type="integer" value="-1" min="-1" label="Print level" help="specify taxlevel of your *tax.summary file to print to. Options are 1 to the maz level in the file. The default is -1, meaning max level" />
+    </xml>
+    <xml name="param-savelog">
+        <param name="savelog" type="boolean" checked="false" label="Output logfile?"/>
+    </xml>
     <xml name="logfile-output">
-        <data name="logfile" format="txt" from_work_dir="mothur.out.log" label="${tool.name} on ${on_string}: logfile"/>
+        <data name="logfile" format="txt" from_work_dir="mothur.out.log" label="${tool.name} on ${on_string}: logfile">
+            <filter>savelog</filter>
+        </data>
     </xml>
+
+    <!-- Output file tests -->
     <xml name="logfile-test">
         <output name="logfile" ftype="txt">
             <assert_contents>
@@ -89,6 +142,101 @@
             </assert_contents>
         </output>
     </xml>
+
+    <xml name="test-accnos-format">
+        <!-- one or two columns -->
+        <has_line_matching expression="^[\w\d\-]+(\t[^\t]+)?$"/>
+    </xml>
+    <xml name="test-align-format">
+        <has_line_matching expression="^>.+$"/>
+        <has_line_matching expression="^[ACTG\-\.]+$"/>
+    </xml>
+    <xml name="test-aligncheck-format">
+        <has_n_columns n="9"/>
+        <has_line_matching expression="^name\tpound\tdash\tplus\tequal\tloop\ttilde\ttotal\tnumseqs$"/>
+    </xml>
+    <xml name="test-alignreport-format">
+        <has_line_matching expression="^QueryName\tQueryLength\tTemplateName\tTemplateLength\tSearchMethod\tSearchScore\tAlignmentMethod\tQueryStart\tQueryEnd\tTemplateStart\tTemplateEnd\tPairwiseAlignmentLength\tGapsInQuery\tGapsInTemplate\tLongestInsert\tSimBtwnQuery&amp;Template$"/>
+    </xml>
+    <xml name="test-axes-format">
+        <has_line_matching expression="^group(\taxis\d+)+$"/>
+    </xml>
+    <xml name="test-chimera-format">
+        <has_line_matching expression="Score\tQuery\tParentA\tParentB\tIdQM\tIdQA\tIdQB\tIdAB\tIdQT\tLY\tLN\tLA\tRY\tRN\tRA\tDiv\tYN"/>
+    </xml>
+    <xml name="test-column-format">
+        <has_n_columns n="3"/>
+        <has_line_matching expression="^[\w\d\-]+\t[\w\d\-]+\t[\d\.]+$"/>
+    </xml>
+    <xml name="test-contigsreport-format">
+        <has_n_columns n="7"/>
+        <has_line_matching expression="^Name\tLength\tOverlap_Length\tOverlap_Start\tOverlap_End\tMisMatches\tNum_Ns$"/>
+    </xml>
+    <xml name="test-count-format">
+        <has_line_matching expression="^Representative_Sequence\ttotal(\t\w+)*$"/>
+        <has_line_matching expression="^\w+(\t\d+)+(\s)*$"/>
+    </xml>
+    <xml name="test-dist-format">
+        <has_line_matching expression="^[ \t]*\d+$"/>
+        <has_line_matching expression="^[\w\d\-]+(\t[\d\.]+)+\s?$"/>
+    </xml>
+    <xml name="test-fasta-format">
+        <has_line_matching expression="^>.+$"/>
+        <has_line_matching expression="^[ACTGN-]+$"/>
+    </xml>
+    <xml name="test-fastq-format">
+        <has_line_matching expression="^@.+$"/>
+        <has_line_matching expression="^[ACTGN]+$"/>
+        <has_line_matching expression="^\+$"/>
+    </xml>
+    <xml name="test-group-format">
+        <has_line_matching expression="^Representative_Sequence\ttotal(\t[\w\d\-]+)+$"/>
+        <has_line_matching expression="^[\w\d\-]+(\t\d+)+$"/>
+    </xml>
+    <xml name="test-list-format">
+        <has_line_matching expression="^label\tnumOtus(\tOtu\d+)+$"/>
+        <has_line_matching expression="^(unique|0\.\d+)\t\d+(\t[\w\d\-,]+)+$"/>
+    </xml>
+    <xml name="test-names-format">
+        <has_line_matching expression="^[a-zA-Z0-9]+\t[a-zA-Z0-9]+$"/>
+    </xml>
+    <xml name="test-qfile-format">
+        <has_line_matching expression="^(\d+ )+$"/>
+        <has_line_matching expression="^>.+$"/>
+    </xml>
+    <xml name="test-rabund-format">
+        <has_line_matching expression="^(unique|0\.\d+)(\t\d+\.?\d*)+$"/>
+    </xml>
+    <xml name="test-sabund-format">
+        <has_line_matching expression="^(unique|0\.\d+)(\t\d+)+$"/>
+    </xml>
+    <xml name="test-sensspec-format">
+        <has_n_columns n="14"/>
+        <has_line_matching expression="^label\tcutoff\ttp\ttn\tfp\tfn\tsensitivity\tspecificity\tppv\tnpv\tfdr\taccuracy\t\w+\tf1score$"/>
+    </xml>
+    <xml name="test-shared-format">
+        <has_line_matching expression="^label\tGroup\tnumOtus(\t(Otu|rareOTUs|.*OTU.*)\d+)+$"/>
+    </xml>
+    <xml name="test-taxonomy-format">
+        <has_n_columns n="3"/>
+        <has_line_matching expression="^OTU\tSize\tTaxonomy$"/>
+    </xml>
+    <xml name="test-taxsummary-format">
+        <has_line_matching expression="^((taxlevel\trankID\ttaxon\tdaughterlevels\ttotal(\t[\w\d\-]+)*)|(taxonomy\ttotal(\t[\w\d]+)*))$"/>
+    </xml>
+    <!-- backmatter -->
+    <token name="@MOTHUR_OVERVIEW@">
+<![CDATA[
+
+**Mothur Overview**
+
+Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team
+in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki_.
+
+.. _Mothur-Wiki: https://www.mothur.org/wiki/Main_Page
+
+]]>
+    </token>
     <xml name="citations">
         <citations>
             <citation type="doi">10.1128/AEM.01541-09</citation>
diff -r 506625098e20 -r 8c39f704d21a test-data/Fasting_Example1.scrap.sff
Binary file test-data/Fasting_Example1.scrap.sff has changed
diff -r 506625098e20 -r 8c39f704d21a test-data/amazon.an.0.03.pearson.otu.corr
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.an.0.03.pearson.otu.corr	Tue Mar 20 21:58:54 2018 -0400
@@ -0,0 +1,3829 @@
+OTUA	OTUB	pearsonCoef	Significance
+Otu02	Otu01	-1.000000	0.000000
+Otu03	Otu01	1.000000	0.000000
+Otu03	Otu02	-1.000000	0.000000
+Otu04	Otu01	-1.000000	0.000000
+Otu04	Otu02	1.000000	0.000000
+Otu04	Otu03	-1.000000	0.000000
+Otu05	Otu01	-nan	0.000000
+Otu05	Otu02	-nan	0.000000
+Otu05	Otu03	-nan	0.000000
+Otu05	Otu04	-nan	0.000000
+Otu06	Otu01	1.000000	0.000000
+Otu06	Otu02	-1.000000	0.000000
+Otu06	Otu03	1.000000	0.000000
+Otu06	Otu04	-1.000000	0.000000
+Otu06	Otu05	-nan	0.000000
+Otu07	Otu01	1.000000	0.000000
+Otu07	Otu02	-1.000000	0.000000
+Otu07	Otu03	1.000000	0.000000
+Otu07	Otu04	-1.000000	0.000000
+Otu07	Otu05	-nan	0.000000
+Otu07	Otu06	1.000000	0.000000
+Otu08	Otu01	1.000000	0.000000
+Otu08	Otu02	-1.000000	0.000000
+Otu08	Otu03	1.000000	0.000000
+Otu08	Otu04	-1.000000	0.000000
+Otu08	Otu05	-nan	0.000000
+Otu08	Otu06	1.000000	0.000000
+Otu08	Otu07	1.000000	0.000000
+Otu09	Otu01	1.000000	0.000000
+Otu09	Otu02	-1.000000	0.000000
+Otu09	Otu03	1.000000	0.000000
+Otu09	Otu04	-1.000000	0.000000
+Otu09	Otu05	-nan	0.000000
+Otu09	Otu06	1.000000	0.000000
+Otu09	Otu07	1.000000	0.000000
+Otu09	Otu08	1.000000	0.000000
+Otu10	Otu01	1.000000	0.000000
+Otu10	Otu02	-1.000000	0.000000
+Otu10	Otu03	1.000000	0.000000
+Otu10	Otu04	-1.000000	0.000000
+Otu10	Otu05	-nan	0.000000
+Otu10	Otu06	1.000000	0.000000
+Otu10	Otu07	1.000000	0.000000
+Otu10	Otu08	1.000000	0.000000
+Otu10	Otu09	1.000000	0.000000
+Otu11	Otu01	1.000000	0.000000
+Otu11	Otu02	-1.000000	0.000000
+Otu11	Otu03	1.000000	0.000000
+Otu11	Otu04	-1.000000	0.000000
+Otu11	Otu05	-nan	0.000000
+Otu11	Otu06	1.000000	0.000000
+Otu11	Otu07	1.000000	0.000000
+Otu11	Otu08	1.000000	0.000000
+Otu11	Otu09	1.000000	0.000000
+Otu11	Otu10	1.000000	0.000000
+Otu12	Otu01	1.000000	0.000000
+Otu12	Otu02	-1.000000	0.000000
+Otu12	Otu03	1.000000	0.000000
+Otu12	Otu04	-1.000000	0.000000
+Otu12	Otu05	-nan	0.000000
+Otu12	Otu06	1.000000	0.000000
+Otu12	Otu07	1.000000	0.000000
+Otu12	Otu08	1.000000	0.000000
+Otu12	Otu09	1.000000	0.000000
+Otu12	Otu10	1.000000	0.000000
+Otu12	Otu11	1.000000	0.000000
+Otu13	Otu01	1.000000	0.000000
+Otu13	Otu02	-1.000000	0.000000
+Otu13	Otu03	1.000000	0.000000
+Otu13	Otu04	-1.000000	0.000000
+Otu13	Otu05	-nan	0.000000
+Otu13	Otu06	1.000000	0.000000
+Otu13	Otu07	1.000000	0.000000
+Otu13	Otu08	1.000000	0.000000
+Otu13	Otu09	1.000000	0.000000
+Otu13	Otu10	1.000000	0.000000
+Otu13	Otu11	1.000000	0.000000
+Otu13	Otu12	1.000000	0.000000
+Otu14	Otu01	1.000000	0.000000
+Otu14	Otu02	-1.000000	0.000000
+Otu14	Otu03	1.000000	0.000000
+Otu14	Otu04	-1.000000	0.000000
+Otu14	Otu05	-nan	0.000000
+Otu14	Otu06	1.000000	0.000000
+Otu14	Otu07	1.000000	0.000000
+Otu14	Otu08	1.000000	0.000000
+Otu14	Otu09	1.000000	0.000000
+Otu14	Otu10	1.000000	0.000000
+Otu14	Otu11	1.000000	0.000000
+Otu14	Otu12	1.000000	0.000000
+Otu14	Otu13	1.000000	0.000000
+Otu15	Otu01	1.000000	0.000000
+Otu15	Otu02	-1.000000	0.000000
+Otu15	Otu03	1.000000	0.000000
+Otu15	Otu04	-1.000000	0.000000
+Otu15	Otu05	-nan	0.000000
+Otu15	Otu06	1.000000	0.000000
+Otu15	Otu07	1.000000	0.000000
+Otu15	Otu08	1.000000	0.000000
+Otu15	Otu09	1.000000	0.000000
+Otu15	Otu10	1.000000	0.000000
+Otu15	Otu11	1.000000	0.000000
+Otu15	Otu12	1.000000	0.000000
+Otu15	Otu13	1.000000	0.000000
+Otu15	Otu14	1.000000	0.000000
+Otu16	Otu01	1.000000	0.000000
+Otu16	Otu02	-1.000000	0.000000
+Otu16	Otu03	1.000000	0.000000
+Otu16	Otu04	-1.000000	0.000000
+Otu16	Otu05	-nan	0.000000
+Otu16	Otu06	1.000000	0.000000
+Otu16	Otu07	1.000000	0.000000
+Otu16	Otu08	1.000000	0.000000
+Otu16	Otu09	1.000000	0.000000
+Otu16	Otu10	1.000000	0.000000
+Otu16	Otu11	1.000000	0.000000
+Otu16	Otu12	1.000000	0.000000
+Otu16	Otu13	1.000000	0.000000
+Otu16	Otu14	1.000000	0.000000
+Otu16	Otu15	1.000000	0.000000
+Otu17	Otu01	1.000000	0.000000
+Otu17	Otu02	-1.000000	0.000000
+Otu17	Otu03	1.000000	0.000000
+Otu17	Otu04	-1.000000	0.000000
+Otu17	Otu05	-nan	0.000000
+Otu17	Otu06	1.000000	0.000000
+Otu17	Otu07	1.000000	0.000000
+Otu17	Otu08	1.000000	0.000000
+Otu17	Otu09	1.000000	0.000000
+Otu17	Otu10	1.000000	0.000000
+Otu17	Otu11	1.000000	0.000000
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+Otu17	Otu13	1.000000	0.000000
+Otu17	Otu14	1.000000	0.000000
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+Otu18	Otu04	-1.000000	0.000000
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+Otu18	Otu08	1.000000	0.000000
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+Otu19	Otu04	-1.000000	0.000000
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diff -r 506625098e20 -r 8c39f704d21a test-data/amazon.otus.accnos
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.otus.accnos	Tue Mar 20 21:58:54 2018 -0400
@@ -0,0 +1,3 @@
+Otu01
+Otu17
+Otu42
diff -r 506625098e20 -r 8c39f704d21a test-data/esophagus.fn.shared
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/esophagus.fn.shared	Tue Mar 20 21:58:54 2018 -0400
@@ -0,0 +1,12 @@
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+0.10	B	58	50	37	14	52	2	1	8	6	1	1	3	5	1	2	3	2	1	1	2	1	1	1	2	1	2	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	
+0.10	C	58	19	41	42	41	2	10	7	1	0	0	2	0	5	13	4	0	0	1	0	6	0	2	14	0	0	7	0	0	4	2	2	2	4	3	1	8	4	1	1	1	1	1	1	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	
+0.10	D	58	5	18	10	124	2	0	1	3	0	1	9	2	1	0	0	0	0	6	1	2	0	1	4	0	1	1	0	0	0	1	1	0	1	0	1	0	0	0	0	1	0	0	0	2	1	2	2	3	1	1	1	1	1	1	1	1	3	1	
diff -r 506625098e20 -r 8c39f704d21a test-data/samplebiom.biom1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samplebiom.biom1	Tue Mar 20 21:58:54 2018 -0400
@@ -0,0 +1,8668 @@
+{
+      "id":"otu.dat-0.03",
+      "format": "Biological Observation Matrix 0.9.1",
+      "format_url": "http://biom-format.org",
+      "type": "OTU table",
+      "generated_by": "mothur1.36.1",
+      "date": "Mon Jun 26 15:11:52 2017",
+      "rows":[
+            {"id":"Otu00001", "metadata":null},
+            {"id":"Otu00002", "metadata":null},
+            {"id":"Otu00003", "metadata":null},
+            {"id":"Otu00004", "metadata":null},
+            {"id":"Otu00005", "metadata":null},
+            {"id":"Otu00006", "metadata":null},
+            {"id":"Otu00007", "metadata":null},
+            {"id":"Otu00008", "metadata":null},
+            {"id":"Otu00009", "metadata":null},
+            {"id":"Otu00010", "metadata":null},
+            {"id":"Otu00011", "metadata":null},
+            {"id":"Otu00012", "metadata":null},
+            {"id":"Otu00013", "metadata":null},
+            {"id":"Otu00014", "metadata":null},
+            {"id":"Otu00015", "metadata":null},
+            {"id":"Otu00016", "metadata":null},
+            {"id":"Otu00017", "metadata":null},
+            {"id":"Otu00018", "metadata":null},
+            {"id":"Otu00019", "metadata":null},
+            {"id":"Otu00020", "metadata":null},
+            {"id":"Otu00021", "metadata":null},
+            {"id":"Otu00022", "metadata":null},
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+            [3923,0,1],
+            [3924,0,1],
+            [3925,1,1],
+            [3926,0,1],
+            [3927,0,1],
+            [3928,0,1],
+            [3929,1,1],
+            [3930,0,1],
+            [3931,1,1],
+            [3932,0,1],
+            [3933,0,1],
+            [3934,0,1],
+            [3935,0,1],
+            [3936,0,1],
+            [3937,0,1],
+            [3938,0,1],
+            [3939,0,1],
+            [3940,0,1],
+            [3941,1,1],
+            [3942,0,1],
+            [3943,0,1],
+            [3944,0,1],
+            [3945,0,1],
+            [3946,0,1],
+            [3947,0,1],
+            [3948,1,1],
+            [3949,0,1],
+            [3950,1,1],
+            [3951,0,1],
+            [3952,1,1],
+            [3953,0,1],
+            [3954,0,1],
+            [3955,0,1],
+            [3956,0,1],
+            [3957,1,1],
+            [3958,0,1],
+            [3959,0,1],
+            [3960,0,1],
+            [3961,1,1],
+            [3962,1,1],
+            [3963,0,1],
+            [3964,0,1],
+            [3965,0,1],
+            [3966,0,1],
+            [3967,0,1],
+            [3968,1,1],
+            [3969,0,1],
+            [3970,0,1],
+            [3971,0,1],
+            [3972,0,1],
+            [3973,0,1],
+            [3974,0,1],
+            [3975,0,1],
+            [3976,1,1],
+            [3977,1,1],
+            [3978,0,1],
+            [3979,0,1],
+            [3980,0,1],
+            [3981,1,1],
+            [3982,0,1],
+            [3983,1,1],
+            [3984,0,1],
+            [3985,0,1],
+            [3986,0,1]]
+}
diff -r 506625098e20 -r 8c39f704d21a test-data/stool_small.count_table
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/stool_small.count_table	Tue Mar 20 21:58:54 2018 -0400
@@ -0,0 +1,47 @@
+Representative_Sequence	total
+F11Fcsw_12747	1
+F11Fcsw_13125	1
+F11Fcsw_13572	2
+F11Fcsw_13584	1
+F11Fcsw_13612	2
+F11Fcsw_13784	2
+F11Fcsw_14513	1
+F11Fcsw_14920	1
+F11Fcsw_14954	1
+F11Fcsw_14980	1
+F11Fcsw_15042	1
+F11Fcsw_15664	1
+F11Fcsw_17394	1
+F11Fcsw_17898	1
+F11Fcsw_18564	1
+F11Fcsw_19115	1
+F11Fcsw_19402	1
+F11Fcsw_19500	1
+F11Fcsw_20028	1
+F11Fcsw_20361	1
+F11Fcsw_20429	1
+F11Fcsw_20462	1
+F11Fcsw_20686	1
+F11Fcsw_21035	1
+F11Fcsw_21196	1
+F11Fcsw_21505	1
+F11Fcsw_21636	1
+F11Fcsw_21645	1
+F11Fcsw_21954	1
+F11Fcsw_22687	1
+F11Fcsw_22831	1
+F11Fcsw_22880	1
+F11Fcsw_22900	1
+F11Fcsw_23043	1
+F11Fcsw_23322	1
+F11Fcsw_23608	1
+F11Fcsw_23684	1
+F11Fcsw_24087	1
+F11Fcsw_24273	1
+F11Fcsw_24701	2
+F11Fcsw_24967	1
+F11Fcsw_25501	1
+F11Fcsw_25574	1
+F11Fcsw_26078	1
+F11Fcsw_26175	1
+F11Fcsw_26418	1
diff -r 506625098e20 -r 8c39f704d21a test-data/stool_small.denovo.vsearch.accnos
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/stool_small.denovo.vsearch.accnos	Tue Mar 20 21:58:54 2018 -0400
@@ -0,0 +1,2 @@
+F11Fcsw_21505
+F11Fcsw_23322
diff -r 506625098e20 -r 8c39f704d21a test-data/stool_small.names
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/stool_small.names	Tue Mar 20 21:58:54 2018 -0400
@@ -0,0 +1,46 @@
+F11Fcsw_12747	F11Fcsw_12747
+F11Fcsw_13125	F11Fcsw_13125
+F11Fcsw_13572	F11Fcsw_13572,F11Fcsw_14202
+F11Fcsw_13584	F11Fcsw_13584
+F11Fcsw_13612	F11Fcsw_13612,F11Fcsw_23132
+F11Fcsw_13784	F11Fcsw_13784,F11Fcsw_21715
+F11Fcsw_14513	F11Fcsw_14513
+F11Fcsw_14920	F11Fcsw_14920
+F11Fcsw_14954	F11Fcsw_14954
+F11Fcsw_14980	F11Fcsw_14980
+F11Fcsw_15042	F11Fcsw_15042
+F11Fcsw_15664	F11Fcsw_15664
+F11Fcsw_17394	F11Fcsw_17394
+F11Fcsw_17898	F11Fcsw_17898
+F11Fcsw_18564	F11Fcsw_18564
+F11Fcsw_19115	F11Fcsw_19115
+F11Fcsw_19402	F11Fcsw_19402
+F11Fcsw_19500	F11Fcsw_19500
+F11Fcsw_20028	F11Fcsw_20028
+F11Fcsw_20361	F11Fcsw_20361
+F11Fcsw_20429	F11Fcsw_20429
+F11Fcsw_20462	F11Fcsw_20462
+F11Fcsw_20686	F11Fcsw_20686
+F11Fcsw_21035	F11Fcsw_21035
+F11Fcsw_21196	F11Fcsw_21196
+F11Fcsw_21505	F11Fcsw_21505
+F11Fcsw_21636	F11Fcsw_21636
+F11Fcsw_21645	F11Fcsw_21645
+F11Fcsw_21954	F11Fcsw_21954
+F11Fcsw_22687	F11Fcsw_22687
+F11Fcsw_22831	F11Fcsw_22831
+F11Fcsw_22880	F11Fcsw_22880
+F11Fcsw_22900	F11Fcsw_22900
+F11Fcsw_23043	F11Fcsw_23043
+F11Fcsw_23322	F11Fcsw_23322
+F11Fcsw_23608	F11Fcsw_23608
+F11Fcsw_23684	F11Fcsw_23684
+F11Fcsw_24087	F11Fcsw_24087
+F11Fcsw_24273	F11Fcsw_24273
+F11Fcsw_24701	F11Fcsw_24701,F11Fcsw_24794
+F11Fcsw_24967	F11Fcsw_24967
+F11Fcsw_25501	F11Fcsw_25501
+F11Fcsw_25574	F11Fcsw_25574
+F11Fcsw_26078	F11Fcsw_26078
+F11Fcsw_26175	F11Fcsw_26175
+F11Fcsw_26418	F11Fcsw_26418
diff -r 506625098e20 -r 8c39f704d21a test-data/stool_small.unique.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/stool_small.unique.fasta	Tue Mar 20 21:58:54 2018 -0400
@@ -0,0 +1,92 @@
+>F11Fcsw_12747
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACTGATCGCAGCCTTGGTGAGCCGTTACCTCACCAACTAGCTAATCAGATATGAGCCCATCTTTCAGCGGATTGCTCCTTTGGTATCCCAGAGATGCCTCCAAAATACATTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTCTGAAAGGCAGG
+>F11Fcsw_13125
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAATGTGGCCGTTCATCCTCTCAGACCGGCTACTGATCGTCGCCTTGGTAGGCCGTTACCCCACCAACTAGCTAATCAGACGCAGACCCATCGTAAAGCGATAGCTTACAAGTAGAGGCCATCTTTAGTCGAGCTTCCATGCGGAAGTTCGACAACATTCGGTATTAGCAGTCCTTTCGAACTGTTGTCCCCATCTTTACGG
+>F11Fcsw_13572
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTACCCATCGTCGCCTTGGTGGGCCGTTACCCCGCCAACAAGCTAATGGGACGCATCCCCATCCTTTACCAATTAATCTTTATTTGTCGCTCCCATGCGGAAAGACAAACACATCCGGTATTAAACTCCCTTTCAGGAGACTATCCCGGAGTAAAGGGCAGGTTGGATACGCGTTACTCACCCGTGCGCCGGTCGCCATCAAAA
+>F11Fcsw_13584
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGATGTCTTGGTGGGCCGTTACCCCGCCAACAAACTAATGGAACGCATCCCCATCGGTTATCGAAATTCTTTAATAACAAGAAGATGCCTTCTCGTTATACTATCCGGTATTAATCTTTCTTTCGAAAGGCTATCCCGGAATAACCGGTAGGTTGGATACGTGTTACTCACCCGTGCGCCGGTCGCCATCAACCTA
+>F11Fcsw_13612
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGTCCGTGTCTCAGTACCAATGTGGGGGACCTTCCTCTCAGAACCCCTACGCATCGTCGCCTTGGTGGGCCGTTACCCCCCAACTAGCTAATGCGCCGCATGCCCATCCCTGTCCGGATTACTCCTTTGGCGCTCGCAGGATGCCCCGCAAACGCTTTATGCGATATTAGACCGGATTTCTCCGGATTATCCCTCTGACAGGGGCAGGTTGCATACGTGTTACTCACCCG
+>F11Fcsw_13784
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACCGATCGTCGACTTGGTGAGCCGTTACCTCACCAACTATCTAATCGGACGCGAGCCCATCTTTCAGCGGATTGCTCCTTTGATCACTGTATCATGCGGTACTGTAATCTTATGCGGTATTAGCATCTGTTTCCAAATGTTATCCCCCTCTGAAAGGCAGGTTG
+>F11Fcsw_14513
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGACCGTATCTCAGTTCCAATGTGGCCGATCACCCTCTCAGGTCGGCTAACCATCGTCGACTTGGTAGTCCGTTACACTACCAACTATCTAATGGTACGCGAGCCCATCCACATCCGATAAATCTTTTACCCCTGAGAGATGCCTCTCTGTGGTCTTATGCGGTATTAGCACACATTTCTATGTGTTATTCCCCAGATGTGGGCAGGTTG
+>F11Fcsw_14920
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGTCCATCCTCTCAGACCGGCTACTGATCGTCGCCTTGGTGAGCCATTACCTCTCCAACTAGCTAATCAGACGCGGGCCCATCCTATACCACCTGAGTTTTTCCTACCGTATCATGCGGTACTGTAGGCTTATGCGGTTTTAGCACAGATTTCTCTGTGTTATCCCCTGTATAGGGCAGGTTACCCACGCGTTT
+>F11Fcsw_14954
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAATGTGGCCGGCCAACCTCTCAGTCCGGCTACCGATCGTCGACTTGGTGGGCCGTTACCCCGCCAACTATCTAATCGGACGCGAGGCCATCTTTCAGCGATAAATCTTTGGCATGTCCGGGATGCCCCGGTCATGCGTCATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTCTGAAAGGCAGGTTCCTCACGCGTTACT
+>F11Fcsw_14980
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTTTCTCAGTTCCAATGTGGCCGTTCATCCTCTCAGATCGGCTACCCATCGTCGCCTTGGTGAGCCGTTACCTCTCCAACTAGCTAATGGGCCGCGAGCCCCTCCTATACCGCCTCAGCTTTTACCCCTCTCCGATGCCGGAGTGTGGTCTTATACCGTATTAGCACAAATTTCTCTGTGTTATCCCGTTGTATAGGATAGGTTGCTCACGTGTTACTCACCCG
+>F11Fcsw_15042
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTCGCCCTCTCAGGCCGGCTACTGATCGTCGGTTTGGTGGGCCGTTACCCCGCCAACTGCCTAATCAGACGCGGGCCCATCCCATACCACCGGAGTTTTTCACACTGAGCCATGCAGCTCTGTGCGCTTATGCGGTATTAGCAGCCGTTTCCAGCTGTTATCCCCCGGTATGGGGCAGGTCACCCACGCGTTACT
+>F11Fcsw_15664
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCTCACCAACCAGCTAATCAGACGCGGGTCCATCTTGTACCACCGGAGTTTTTCACACTGCTTCATGCGAAGCTGTGCGCTTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCAGTACAAGGCAGGTTACCCACGCGTTACT
+>F11Fcsw_17394
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTCACCCTCTCAGGTCGGCTACTGATCGTTGCCTTGGTAGGCCGTTACCCCGCCAACAAGCTAATCAGACGCGGGTCCATCTCACACCACCGGAGTTTTTCACACTGTACCATGCGGTACTGTGCGCTTATGCGGTATTATCAGCCGTTTCCAACTGCTATCCCCCTGTGTGAGGCAGGTTACCCACGCGTTA
+>F11Fcsw_17898
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCTCACCAACCAGCTAATCAGACGCGGGTCCATCTTATACCACCGGAGTTTTTCACACTGTATCATGCGATACCGTGCGCTTATGCGGTATTAGCAGTCGTTTCCAACTGTTATCCCCCTGTATAAGGCAGGTTACCCACGCGTTACTCACCCG
+>F11Fcsw_18564
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCAACCTCTCAGTCCGGCTACTGATCGTCGACTTGGTGAGCCGTTACCTCACCAACTATCTAATCGGACGCGAGCCCATCTTTCAGCGGATTGCTCCTTTGATCACTGTATCATGCGGTACTGTAATCTTATGCGGTATTAGCATCTGTTTCCAAATGTTATCCCCCTCTGAAAGG
+>F11Fcsw_19115
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTACTGATCGTTGCCTTGGTGGGCCGTTACCCCGCCAACAAGCTAATCAGACGCATCCCCATCCATCACCGATAAATCTTTAATCTCTTTCAGATGCCTTCTAGAGATATCATTGGGTATTAGTCTTACTTTGCAGGTTATCCCCAACGTGGTGGGCGAGGTTGGATACGCGTTACTCACCCGTCCCG
+>F11Fcsw_19402
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCTGTGTCTCAGTCCCAATGTGGCCGATCAACCTCTCAGTCCGGCTACTGATCGTCGACTTGGTGAGCCGTTACCTCACCAACTATCTAATCAGACGCGAGCCCATCTTTCAGCGGATTGCTCCTTTGATTGCCAAACGATGCCGTTCGGCAATGTTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCACTGAAAGGTAGGTTG
+>F11Fcsw_19500
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCTCACCAACCAGCTAATCAGACGCGAGGCCATCTTTCAGCGGATTGCTCCTTTGATCACTGTATCATGCGGTACTGTAATCTTATGCGGTATTAGCATCTGTTTCCAAATGTTATCCCCCTCTGAAAGGCAGGTTG
+>F11Fcsw_20028
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTATGGGCCGTGTCTCAGTCCCATTGTGGCTGATCATCCTCTCAAACCAGCTACTGATCGTCGCCTTGGTAGTCCATTACACCACCAACAAGCTAATCAGGTGCAGGCTCATCCTAGAGCACCGGAGTTTTCAAGATTGGTATTTCAACCAAGCTCATATGGGGTATTAGCAGAAGTTTCCTTCTGTTGTCCCCCTCTCTAGGGCAGATTT
+>F11Fcsw_20361
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGTCCGTGTCTCAGTACCAGTGTGGGGGGTTAACCTCTCAGTCCCCCTATGTATCGTTGCCTTGGTGAGCCGTTACCTCACCAACTAGCTAATACAACGCATGTCCATCTATAACCACCGGAGTTTTCAACCCGGAGAGATGCCTCTCCGAATATTATGGGGAATTAGTACCAATTTCTCAGTGTTATGCCCCTGTTATAGGTAGGTTACATACGCGTTACGCACCCGTGCGCCGG
+>F11Fcsw_20429
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGTTGTCTTGGTGGGCCGTTACCCCGCCAACAAACTAATGGAACGCATCCCCATCGATAACCGAAATTCTTTAATAAAAATATCATGCGATATTCGTATGCTATCCGGTATTAATCTTTCTTTCGAAAGGCTATCCCCGAGTTATCGGCAGGTTGGATACGTGTTACTCACCCGTGCGCCGGTCGCCA
+>F11Fcsw_20462
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTATGGGCCGTGTCTCAGTCCCATTGTGGCTGATCATCCTCTCAAACCAGCTACTGATCGTCGCCTTGGTAGTCCATTACACCACCAACAAGCTAATCAGGTGCAGGCTCATCCTAGAGCACCGGAGTTTTCAAGATTGGTATTTCAACCAAGCTCATATGGGGTATTAGCAGAAGTTTCCTTCTGTTGTCCCCCTCTCTAGGGCAGATTTT
+>F11Fcsw_20686
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCTCACCAACCAGCTAATCAGACGCGGGTCCATCTTATACCACCGGAGTTTTTCACACGGAACCATGCGGTTCTGTGCGCTTATGCGGTATTAGCAGCCATTTCTGGCTGTTATCCCCCTCTGAAAGGCAGGTTGCTCACGCG
+>F11Fcsw_21035
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGACCGTATCTCAGTTCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACTGATCGTCGGCTTGGTGAGCCGTTACCTCACCAACTACCTAATCAGACGCGAGTCCATCTGCAAGCGGTTTCCCTTTGGCATCATCTCCATGCGGAATCGATGCGTTATGCGGTATTAGCAACAGTTTCCCGTTGTTATCCCCCTCTCGCAGGCAGGTTACT
+>F11Fcsw_21196
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACCGATCGTCGGCTTGGTGGGCTGTTATCTCACCAACTACCTAATCGGCCGCGAGCCCATCTCTCAGCGATAAAATCTTTGATAGTCTCCGGATGCCCGGAAACTATGTTATGCGGTATTAGCGTTCGTTTCCAAACGTTATTCCACTCTGAAAGGCAGGTTACTCACGTGTTACT
+>F11Fcsw_21505
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTACCCATCGTTGGCTTGGTGGGCCGTTACCCCTCCAACTACCTAATGGGACGCGAACCCCTCTCAAAGCGATAAATCTTTGACCCCTTCATCATGCGGTGTTGTGGTCTCATGCGGTATTAGCAACAGTTTCCCGTTGTTATCCCCCTCTTTGAGTCAGGTTATCCACGCGTTACTCACCCGTCCGCCACTCAGT
+>F11Fcsw_21636
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCATCCTCTCAGACCGGCTACTGATCATCGCCTTGGTAGGCCGTTACCCCACCAACTAGCTAATCAGACGCAGGCCCATCCTCTAGCGATAGCTTATAAATAGAGGCCATCTTTCACAGCATCCTCATGCGAGATTGCTGTCACATTCGGTATTAGCACCCTTCGGA
+>F11Fcsw_21645
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGGCTTGGTGGGCCGTTACCCCGCCAACAACCTAATGGAACGCATCCCCATCGATGACCGAAATTCTTTAATAGTTCTACCATGCGGAAGAACTATGCCATCGGGTATTAATCTTTCTTTCGAAAGGCTATCCCCGAGTCATCGGCAGGTTGGATACGTGTTACTCACCCGTGCGCCGGTCG
+>F11Fcsw_21954
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTACCCATCGTCGCCTTGGTGGGCCGTTACCCCGCCAACAAGCTAATGGGACGCATCCCCATCCTTTACCAATTAATCTTTATTTGTCGCTCCCATGCGGAAAGACAAACACATCCGGTATTAAACTCCCTTTCAGGAGACTATCCCGGAGTAAAGGGCAGGTTGGATACGCGTTACTCACCCGTGCGCCGGTCGCCATCAAA
+>F11Fcsw_22687
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTACTGATCGTTGCCTTGGTGGGCCATTACCCCGCCAACAAGCTAATCAGACGCATCCCCATCCATCACCGATAAATCTTTAATCTCTTTCAGATGTCTTCTAGAGATATCATTGGGTATTAGTCTTACTTTGCAGGTTATCCCAACGTGGTGGGCGAGGTTGGATACGCGTTACTCACCCG
+>F11Fcsw_22831
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGGCCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCCCGCCTACTATCTAATGGAACGCATCCCCATCGTCTACCGGAATACCTTTAATCATGTGAACATGCGGACTCATGATGCCATCTTGTATTAATCTTCCTTTCAGAAGGCTGTCCAAGAGTAGACGGCAGGTTGGATACGTGTTACT
+>F11Fcsw_22880
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTATGGATCGTCGCCTTGGTGGGCCGTTACCCCACCAACTAGCTAATCCAACGCGGGTCCATCTTATACCACCGGAGTTTTTCACACTGAGCCATGCAGCTCTGTGCGCTTATGCGGTATTAGCAGTCATTTCTGACTGTTATCCCCCTGTATAAGGCAGGTTACCCACGCG
+>F11Fcsw_22900
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCCGATCAGCCTCTCAGCTCGGCTACCCATCGTTGGCTTGGTGGGCCGTTACCCCTCCAACTACCTAATGGGACGCGAACCCCTCTCAAAGCGATAAATCTTTGACCCCTTCATCATGCGGTGTTGTGGTCTCATGCGGTATTAGCAACAGTTTCCCGTTGTTATCCCCCTCTTTGAGTCAGGTTATTCACGCGTTACTCACCCG
+>F11Fcsw_23043
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAATGTGGCCGGTCAACCTCTCAGTCCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCTCACCAACCAGCTAATCAGACGCGGGTCCATCTTGTACCACCGGAGTTTTTCACACTGCTTCATGCGAAGCTGTGCGCTTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCAGTACAAGGCAGGTTACCCACGCGTTA
+>F11Fcsw_23322
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCAGCCTCTCAGCTCGGCTACCCATCGTCGGCTAGGTGGGCCGTTACCCCGCCTACTACCTAATGGGACGCGAACCCCTCCCAAAGCGATTTTCTTTGACCCCTTCGTCATGCGACATTGTGGTCTTATGCGGTATTAGCACCTGTTTCCAGGTGTTATCCCCCTCTTTGGGTCAGGTTATTCACGTGTTACTCACCCGTGCGCCAA
+>F11Fcsw_23608
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTACTGATCGTAGCCTTGGTGGGCCGTTACCCCGCCAACAAGCTAATCAGACGCATCCCCATCCATCACCGATAAATCTTTAATCTCTTTCAGATGTCTTCTAGAGATATCATTGGGTATTAGTCTTACTTTGCAAGGTTATCCCAAGTGATGGGCAGGTTGGATACGCGTTACTCACCCG
+>F11Fcsw_23684
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTACTGATCGTCGCCTTGGTGGGCCGTTACCCCGCCAACAAGCTAATCAGACGCATCCCCATCCATCACCGATAAATCTTTAATCCCTTTCAGATGTCTTCTAGAGACGTCATTGGGTATTAGTCTTACTTTCGCAAGGTTATCCCAAGTGATGGGCAGGTTGGATACGCGTTACTCACCCGTGCG
+>F11Fcsw_24087
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTATGGATCGTCGCCTTGGTGGGCCGTTACCTCACCAACAAGCTAATCCAACGCGGGTCCATCTTATACCACCGGAGTTTTTCACACTGAGCCATGCAGCTCTGTGCGCTTATGCGGTATTAGCAGCCATTTCTGACTGTTATCCCCCTGTATAAGGCAGGTTACCCACG
+>F11Fcsw_24273
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTATCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACTGATCGTCGACTTGGTAGGCCGTTACCCCACCAACTATCTAATCAGACGCGAGCCCATCTATCAGCGGATTACTCCTTTCCCACTTTCATCATGTGATATTTATTGGCATATGCGGTATTAGCAATGATTTCTCACTGTTATTCCCCTCCTGATAGGCG
+>F11Fcsw_24701
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCCGATCAGCCTCTCAGCTCGGCTACCCATCGTCGGCTAGGTGGGCTGTTACCCCGCCTACTACCTAATGGGACGCGAACCCCTCCCAAAGCGATTTTCTTTGACCCCTTCGTCATGCGACATTGTGGTCTTATGCGGTATTAGCACCTGTTTCCAGGTGTTATCCCCCTCTTTGGGTCAGGTTATTCACGTGTTACTCACCCGTGCG
+>F11Fcsw_24967
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCCCGCCTACTATCTAATGGAACGCATCCCCATCGTCTACCGGAATACCTTTAATCATGTGAACATGCGGACTCATGATGCCATCTTGTATTAATCTTCCTTTCAGAAGGCTGTCCAAGAGTAGACGGCAGGTTGGATACGTGTTACT
+>F11Fcsw_25501
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTCAACCTCTCAGTCCGGCTACTGATCGTCGACTTGGTGGGCCGTTACCCCGCCAACTATCTAATCAGACGCGAGGCCATCTTTCAGCGATAAATCTTTGGCATTTCGACCATGCGATCAAAATGCGTCATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTCTGAAAGGCAGGTTCCTCACG
+>F11Fcsw_25574
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCACCCTCTCAGGTCGGCTACCGATCGTCGGCTTGGTGGGCCGTTACCTCACCAACTACCTAATCGGACGCGAGCCCACCCCAAACCGATAAATCTTTTACCTCAGAACCATGTGATCCCGTGGTCTTATGCGGTATTAGTACACCTTTCGGTGTGTTATTCCCCTGTCTGGAAAAGGTTGCTCACGCGTTACTCACCCGTCCGCCGCTAAAACAG
+>F11Fcsw_26078
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCCGATCAGCCTCTCAGCTCGGCTACCCATCGTCGGCTAGGTGGGCTGTTATCCCGCCTACTACCTAATGGGACGCGAACCCCTCCCAAAGCGATTTTCTTTGACCCCTTCGTCATGCGACATTGTGGTCTTATGCGGTATTAGCACCTGTTTCCAGGTGTTATCCCCCCTCTTTGGGTCAGGTTATTCACGTGTTACTCA
+>F11Fcsw_26175
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCACCCTCTCAGGTCGGCTACCGATCGTCGGCTTGGTGGGCCGTTACCTCACCAACTACCTAATCGGACGCGAGCCCACCCCAAACCGATAAATCTTTTACCCCAGAACCATGTGATCCCGTGGTCTTATGCGGTATTAGTACACCTTTCGGTGTGTTATTCCCCTGTCTGGGAAAGGTTGCTCACGCGTTACTCACCCGTCCGCCGCTAAAACAG
+>F11Fcsw_26418
+AGAGAGCAAGTGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGGTCACCCTCTCAGGTCGGCTACTGATCGTCGCCTTGGTGGGCCGTTACCCCGCCAACCAGCTAATCAGACGCGGGTCCATCCTGTACCACCGGAGTTTTTCACACTGCTTCATGCGAAGCTGTGCGCTTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTGTACAGGGCAGGTTACCCACGCGTTACT
diff -r 506625098e20 -r 8c39f704d21a test-data/stool_small.vsearch.chimeras
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/stool_small.vsearch.chimeras	Tue Mar 20 21:58:54 2018 -0400
@@ -0,0 +1,47 @@
+Score	Query	ParentA	ParentB	IdQM	IdQA	IdQB	IdAB	IdQT	LY	LN	LA	RY	RN	RA	Div	YN
+0.0000	F11Fcsw_13572;size=2;	*	*	*	*	*	*	*	*	0	0	0	0	0	0	*	N
+0.0000	F11Fcsw_13612;size=2;	*	*	*	*	*	*	*	*	0	0	0	0	0	0	*	N
+0.0000	F11Fcsw_13784;size=2;	*	*	*	*	*	*	*	*	0	0	0	0	0	0	*	N
+0.0000	F11Fcsw_24701;size=2;	*	*	*	*	*	*	*	*	0	0	0	0	0	0	*	N
+0.0000	F11Fcsw_12747;size=1;	*	*	*	*	*	*	*	*	0	0	0	0	0	0	*	N
+0.0514	F11Fcsw_13125;size=1;	F11Fcsw_13572;size=2;	F11Fcsw_13784;size=2;	F11Fcsw_13784;size=2;	80.5	77.1	80.1	72.7	80.1	21	20	19	8	0	6	0.4	N
+0.1560	F11Fcsw_13584;size=1;	F11Fcsw_13572;size=2;	F11Fcsw_13784;size=2;	F11Fcsw_13572;size=2;	82.5	80.4	72.9	73.3	80.4	23	0	8	15	10	24	2.1	N
+0.0259	F11Fcsw_14513;size=1;	F11Fcsw_13784;size=2;	F11Fcsw_24701;size=2;	F11Fcsw_24701;size=2;	82.7	79.3	81.4	81.9	81.4	11	8	11	11	3	19	1.3	N
+0.0550	F11Fcsw_14920;size=1;	F11Fcsw_13784;size=2;	F11Fcsw_24701;size=2;	F11Fcsw_13784;size=2;	84.7	83.5	76.3	80.9	83.5	23	3	21	5	2	10	1.3	N
+0.0000	F11Fcsw_14954;size=1;	*	*	*	*	*	*	*	*	0	0	0	0	0	0	*	N
+0.0216	F11Fcsw_14980;size=1;	F11Fcsw_13784;size=2;	F11Fcsw_24701;size=2;	F11Fcsw_24701;size=2;	82.0	79.1	80.8	82.4	80.8	7	4	6	12	5	28	1.3	N
+0.0400	F11Fcsw_15042;size=1;	F11Fcsw_13784;size=2;	F11Fcsw_24701;size=2;	F11Fcsw_13784;size=2;	84.6	82.9	79.1	79.9	82.9	21	8	18	5	1	9	1.7	N
+0.0524	F11Fcsw_15664;size=1;	F11Fcsw_13784;size=2;	F11Fcsw_13572;size=2;	F11Fcsw_13784;size=2;	84.6	83.8	71.7	72.9	83.8	41	10	25	3	1	1	0.8	N
+0.0000	F11Fcsw_17394;size=1;	*	*	*	*	*	*	*	*	0	0	0	0	0	0	*	N
+0.0428	F11Fcsw_17898;size=1;	F11Fcsw_13784;size=2;	F11Fcsw_13572;size=2;	F11Fcsw_13784;size=2;	86.7	86.2	71.7	72.5	86.2	45	9	21	2	1	1	0.4	N
+0.0000	F11Fcsw_18564;size=1;	*	*	*	*	*	*	*	*	0	0	0	0	0	0	*	N
+0.0000	F11Fcsw_19115;size=1;	*	*	*	*	*	*	*	*	0	0	0	0	0	0	*	N
+0.0000	F11Fcsw_19402;size=1;	*	*	*	*	*	*	*	*	0	0	0	0	0	0	*	N
+0.0000	F11Fcsw_19500;size=1;	*	*	*	*	*	*	*	*	0	0	0	0	0	0	*	N
+0.0158	F11Fcsw_20028;size=1;	F11Fcsw_13784;size=2;	F11Fcsw_13572;size=2;	F11Fcsw_13784;size=2;	77.8	77.4	70.4	73.0	77.4	32	15	35	1	0	1	0.4	N
+0.0161	F11Fcsw_20361;size=1;	F11Fcsw_13572;size=2;	F11Fcsw_13784;size=2;	F11Fcsw_13784;size=2;	77.5	71.4	77.1	73.1	77.1	2	1	3	28	14	33	0.4	N
+0.1919	F11Fcsw_20429;size=1;	F11Fcsw_13572;size=2;	F11Fcsw_13784;size=2;	F11Fcsw_13572;size=2;	84.6	82.1	75.4	73.3	82.1	22	0	5	16	10	22	2.5	N
+0.0158	F11Fcsw_20462;size=1;	F11Fcsw_13784;size=2;	F11Fcsw_13572;size=2;	F11Fcsw_13784;size=2;	77.8	77.4	70.4	73.0	77.4	32	15	35	1	0	1	0.4	N
+0.0000	F11Fcsw_20686;size=1;	*	*	*	*	*	*	*	*	0	0	0	0	0	0	*	N
+0.0422	F11Fcsw_21035;size=1;	F11Fcsw_13784;size=2;	F11Fcsw_24701;size=2;	F11Fcsw_13784;size=2;	86.3	84.6	81.3	82.2	84.6	16	4	4	8	4	21	1.7	N
+0.0000	F11Fcsw_21196;size=1;	*	*	*	*	*	*	*	*	0	0	0	0	0	0	*	N
+0.5878	F11Fcsw_21505;size=1;	F11Fcsw_13572;size=2;	F11Fcsw_24701;size=2;	F11Fcsw_24701;size=2;	92.4	76.7	88.2	72.1	88.2	11	0	0	48	7	13	4.2	Y
+0.0000	F11Fcsw_21636;size=1;	*	*	*	*	*	*	*	*	0	0	0	0	0	0	*	N
+0.0000	F11Fcsw_21645;size=1;	*	*	*	*	*	*	*	*	0	0	0	0	0	0	*	N
+0.0000	F11Fcsw_21954;size=1;	*	*	*	*	*	*	*	*	0	0	0	0	0	0	*	N
+0.0000	F11Fcsw_22687;size=1;	*	*	*	*	*	*	*	*	0	0	0	0	0	0	*	N
+0.0000	F11Fcsw_22831;size=1;	*	*	*	*	*	*	*	*	0	0	0	0	0	0	*	N
+0.0322	F11Fcsw_22880;size=1;	F11Fcsw_13784;size=2;	F11Fcsw_13572;size=2;	F11Fcsw_13784;size=2;	83.3	82.9	70.8	72.5	82.9	41	11	27	2	1	1	0.4	N
+0.0000	F11Fcsw_22900;size=1;	*	*	*	*	*	*	*	*	0	0	0	0	0	0	*	N
+0.0000	F11Fcsw_23043;size=1;	*	*	*	*	*	*	*	*	0	0	0	0	0	0	*	N
+0.5123	F11Fcsw_23322;size=1;	F11Fcsw_13784;size=2;	F11Fcsw_24701;size=2;	F11Fcsw_24701;size=2;	99.2	83.0	97.9	81.7	97.9	3	0	1	40	1	0	1.2	Y
+0.0000	F11Fcsw_23608;size=1;	*	*	*	*	*	*	*	*	0	0	0	0	0	0	*	N
+0.0000	F11Fcsw_23684;size=1;	*	*	*	*	*	*	*	*	0	0	0	0	0	0	*	N
+0.0324	F11Fcsw_24087;size=1;	F11Fcsw_13784;size=2;	F11Fcsw_13572;size=2;	F11Fcsw_13784;size=2;	83.8	83.3	71.2	72.5	83.3	41	11	26	2	1	1	0.4	N
+0.0000	F11Fcsw_24273;size=1;	*	*	*	*	*	*	*	*	0	0	0	0	0	0	*	N
+0.0000	F11Fcsw_24967;size=1;	*	*	*	*	*	*	*	*	0	0	0	0	0	0	*	N
+0.0000	F11Fcsw_25501;size=1;	*	*	*	*	*	*	*	*	0	0	0	0	0	0	*	N
+0.0461	F11Fcsw_25574;size=1;	F11Fcsw_13784;size=2;	F11Fcsw_24701;size=2;	F11Fcsw_24701;size=2;	84.9	80.8	82.0	82.4	82.0	12	5	3	14	4	24	2.9	N
+0.0000	F11Fcsw_26078;size=1;	*	*	*	*	*	*	*	*	0	0	0	0	0	0	*	N
+0.0509	F11Fcsw_26175;size=1;	F11Fcsw_13784;size=2;	F11Fcsw_24701;size=2;	F11Fcsw_24701;size=2;	85.8	81.2	82.8	82.4	82.8	12	5	3	15	4	22	2.9	N
+0.0696	F11Fcsw_26418;size=1;	F11Fcsw_13784;size=2;	F11Fcsw_13572;size=2;	F11Fcsw_13784;size=2;	83.3	82.1	72.5	72.9	82.1	38	12	27	3	0	1	1.2	N