Repository 'mothur_filter_shared'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/mothur_filter_shared

Changeset 0:bccb5efbc4ee (2017-05-19)
Next changeset 1:6cca4d09073c (2017-09-05)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
added:
README
filter.shared.xml
macros.xml
test-data/98_sq_phylip_amazon.dist
test-data/Fasting_Example1.fasta
test-data/Fasting_Example1.qual
test-data/Fasting_Example1.sff
test-data/Fasting_Example2.sff
test-data/GQY1XT001.oligos
test-data/HMP_MOCK.v35.align
test-data/HMP_MOCK.v35.align.names
test-data/HMP_MOCK.v35.fasta
test-data/HMP_MOCK.v35.pintail.quan
test-data/HMP_MOCK.v35.slayer.chimeras
test-data/HMPv5-v3_1368-1369.oligos
test-data/LookUp_Titanium.pat
test-data/M00967_43_000000000-A3JHG_1_1101_14010_4122.chimeracheck.svg
test-data/Mock_S280_L001_R1_001_small.contigs.report
test-data/Mock_S280_L001_R1_001_small.fastq
test-data/Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos
test-data/Mock_S280_L001_R1_001_small.trim.contigs.fasta
test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.Mock_S280_L001_R1_001_small.trim.contigs.good.groups
test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.align.report
test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.align_head
test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.align_head.names
test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.align_head_withchimera
test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.bellerophon.accnos
test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.ccode.accnos
test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.chimeracheck.chimeras
test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.chop.fasta
test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.denovo.uchime.chimeras
test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.error.summary
test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.fasta
test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.names
test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.names_tiny
test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.ng.fasta
test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.pintail.accnos
test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.rc.align_head
test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.accnos
test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.alns
test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.chimeras
test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.slayer.chimeras
test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.unique.align_head
test-data/Mock_S280_L001_R1_001_small.trim.contigs.qual
test-data/Mock_S280_L001_R1_001_small.trim.contigs.summary
test-data/Mock_S280_L001_R2_001_small.fastq
test-data/abrecovery.fasta
test-data/abrecovery.groups
test-data/abrecovery.names
test-data/abrecovery.pds.wang.taxonomy
test-data/abrecovery.pds.wang.tree.sum
test-data/abrecovery.tre
test-data/amazon.accnos.otulabels
test-data/amazon.align_head
test-data/amazon.align_head.count_table
test-data/amazon.align_head.list
test-data/amazon.align_head.names
test-data/amazon.align_head.wang.taxonomy
test-data/amazon.align_head_short
test-data/amazon.an.0.03.-.0.05.otu.hierarchy
test-data/amazon.an.jclass.unique.tre
test-data/amazon.an.list
test-data/amazon.an.rabund
test-data/amazon.an.rabund2
test-data/amazon.an.relabund
test-data/amazon.an.sabund
test-data/amazon.an.sabund2
test-data/amazon.an.sabund3
test-data/amazon.an.shared
test-data/amazon.bad.accnos
test-data/amazon.count_table
test-data/amazon.design
test-data/amazon.dist
test-data/amazon.fasta
test-data/amazon.fasta_head
test-data/amazon.fragclust.fasta
test-data/amazon.fragclust.names
test-data/amazon.groupaccnos
test-data/amazon.groups
test-data/amazon.head.names
test-data/amazon.metadata
test-data/amazon.mothur.shared
test-data/amazon.names
test-data/amazon.pair.dist
test-data/amazon.pcoa.axes
test-data/amazon.pcoa.loadings
test-data/amazon.silva.wang.tax.summary
test-data/amazon.square.pcoa.axes
test-data/amazon.unique.fasta
test-data/amazon.unique.names
test-data/amazon.wang.knn.tax.summary
test-data/amazon.wang.wang.taxonomy
test-data/amazon1.count_table
test-data/amazon1.names
test-data/amazon_withgroups.count_table
test-data/amazon_withgroups.redundant.groups
test-data/amazon_withgroups_pasture.count_table
test-data/biosample.source
test-data/biosample.tsv
test-data/biosample.xml
test-data/cd-test.constaxonomy
test-data/cd-test.count_table
test-data/cd-test.database
test-data/cd-test.list
test-data/cd-test.repfasta
test-data/cd-test.repname
test-data/env.dist
test-data/example.biom
test-data/example.constaxonomy
test-data/final.tx.1.cons.taxonomy
test-data/final.tx.1.subsample.1.pick.shared
test-data/makesra.project
test-data/metadata
test-data/mock.flow
test-data/mouse.design
test-data/output.fa
test-data/sample1.fa
test-data/sample2.fa
test-data/sample3.fa
test-data/silva.ss.map.head
test-data/testflow.flow
test-data/toymothur.design
test-data/toymothur.design2
test-data/treetest.deunique.tre
test-data/treetest.groups
test-data/treetest.names
test-data/treetest.tre
test-data/veg.dist
tool-data/mothur_aligndb.loc.sample
tool-data/mothur_lookup.loc.sample
tool-data/mothur_map.loc.sample
tool-data/mothur_taxonomy.loc.sample
tool_data_table_conf.xml.sample
tools.yaml
b
diff -r 000000000000 -r bccb5efbc4ee README
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,57 @@
+Galaxy wrappers for the Mothur metagenomics tools (http://www.mothur.org/wiki/Main_Page)
+
+The Mothur Tool Suite repository:
+ - Provides Mothur wrappers for the Mothur tools
+ - Downloads and builds Mothur and all its dependencies on the Linux or Mac operating system
+
+Installing Tools via the API:
+This is a rather large tool suite, if you are having problems installing via the toolshed, try using the API instead
+    - Install ephemeris: pip install ephemeris -U
+    - Use ephemeris to install tools: shed_install -a <your admin API key> -t tools.yaml
+    - (You can find a tools.yaml you can use in this repo as well)
+
+Installing reference data from silva and greengenes:
+    - There is a Galaxy datamanager for available for Mothur
+
+ RDP reference file (modified for mothur):
+  http://www.mothur.org/wiki/RDP_reference_files
+   - 16S rRNA reference (RDP): A collection of 9,662 bacterial and 384 archaeal 16S rRNA gene sequences with an improved taxonomy compared to version 6.
+     http://www.mothur.org/w/images/2/29/Trainset7_112011.rdp.zip
+   - 16S rRNA reference (PDS): The RDP reference with three sequences reversed and 119 mitochondrial 16S rRNA gene sequences added as members of the Rickettsiales
+     http://www.mothur.org/w/images/4/4a/Trainset7_112011.pds.zip
+   - 28S rRNA reference (RDP): A collection of 8506 reference 28S rRNA gene sequences from the Fungi that were curated by the Kuske lab
+     http://www.mothur.org/w/images/3/36/FungiLSU_train_v7.zip
+ Silva reference:
+  http://www.mothur.org/wiki/Silva_reference_files
+  - Bacterial references (14,956 sequences)
+    http://www.mothur.org/w/images/9/98/Silva.bacteria.zip
+  - Archaeal references (2,297 sequences)
+    http://www.mothur.org/w/images/3/3c/Silva.archaea.zip
+  - Eukaryotic references (1,238 sequences)
+    http://www.mothur.org/w/images/1/1a/Silva.eukarya.zip
+  - Silva-based alignment of template file for chimera.slayer (5,181 sequences)
+    http://www.mothur.org/w/images/f/f1/Silva.gold.bacteria.zip
+ Alignment database rRNA gene sequences:
+  http://www.mothur.org/wiki/Alignment_database
+  - greengenes reference alignment
+    http://www.mothur.org/w/images/7/72/Greengenes.alignment.zip
+  - SILVA (Silva reference)
+    http://www.mothur.org/w/images/f/f1/Silva.gold.bacteria.zip
+ Secondary structure mapping files:
+  http://www.mothur.org/wiki/Secondary_structure_map
+    http://www.mothur.org/w/images/6/6d/Silva_ss_map.zip
+    http://www.mothur.org/w/images/4/4b/Gg_ss_map.zip
+ Lane masks:
+  http://www.mothur.org/wiki/Lane_mask
+  greengenes-compatible mask:
+     - lane1241.gg.filter - A Lane Masks that comes with the greengenes arb database
+       http://www.mothur.org/w/images/2/2a/Lane1241.gg.filter
+     - lane1287.gg.filter - A Lane Masks that comes with the greengenes arb database
+       http://www.mothur.org/w/images/a/a0/Lane1287.gg.filter
+     - lane1349.gg.filter - Pat Schloss's transcription of the mask from the Lane paper
+       http://www.mothur.org/w/images/3/3d/Lane1349.gg.filter
+  SILVA-compatible mask:
+     - lane1349.silva.filter - Pat Schloss's transcription of the mask from the Lane paper
+       http://www.mothur.org/w/images/6/6d/Lane1349.silva.filter
+ Lookup Files for sff flow analysis using shhh.flows:
+  http://www.mothur.org/wiki/Alignment_database
b
diff -r 000000000000 -r bccb5efbc4ee filter.shared.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/filter.shared.xml Fri May 19 05:47:34 2017 -0400
[
@@ -0,0 +1,97 @@
+<tool profile="16.07" id="mothur_filter_shared" name="Filter.shared" version="@WRAPPER_VERSION@.0">
+    <description>remove OTUs based on various critieria</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+    <command><![CDATA[
+        @SHELL_OPTIONS@
+
+        ## create symlinks to input datasets
+        ln -s "$otu" otu.dat &&
+
+        echo 'filter.shared(
+            shared=otu.dat,
+            #if $label:
+                label=${ str($label).replace(",","-") },
+            #end if
+            #if $label:
+                groups=${ str($groups).replace(",","-") },
+            #end if
+            minabund=$minabund,
+            minpercent=$minpercent,
+            rarepercent=$rarepercent,
+            keepties=$keepties,
+            minnumsamples=$minnumsamples,
+            minpercentsamples=$minpercentsamples,
+            mintotal=$mintotal,
+            makerare=$makerare
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="otu" type="data" format="mothur.shared" label="shared - specify your shared file"/>
+        <param name="label" type="select" optional="true" multiple="true" label="label - OTU Labels" help="If none selected, all labels will be output">
+            <expand macro="labeloptions"/>
+        </param>
+        <param name="groups" type="select" optional="true" multiple="true" label="Select groups for to include in this grouping">
+            <options>
+                <filter type="data_meta" ref="otu" key="groups"/>
+            </options>
+        </param>
+        <param name="minabund" type="integer" value="0" min="0" label="minabund - indicate the minimum abundance required for each sample in a given OTU" help="If any samples abundance falls below the minimum, the OTU is removed. Default=0"/>
+        <param name="minpercent" type="integer" value="0" min="0" max="100" label="minpercent - indicate the minimum relative abundance of an OTU" help="For example, if the OTUs total abundance across all samples is 8, and the total abundance across all OTUs is 1000, and minpercent=1. The OTU's relative abundance is 0.008, the minimum is 0.01, so the OTU will be removed (Default=0)"/>
+        <param name="rarepercent" type="integer" value="0" min="0" max="100" label="rarepercent - indicate the percentage of otus to remove" help="The OTUs chosen to be removed are the rarest.  For example if you have 1000 OTUs, rarepercent=20 would remove the 200 OTUs with the lowest abundance (Default=0)"/>
+        <param name="keepties" type="boolean" truevalue="true" falsevalue="false" checked="true" label="keepties - indicate you want to keep the OTUs with the same abundance as the first 'not rare' OTU" help="For example if you have 10 OTUs, rarepercent=20 abundances of 20, 18, 15, 15, 10, 5, 3, 3, 3, 1. keepties=t, would remove the 10th OTU, but keep the 9th because its abundance ties the 8th OTU. keepties=f would remove OTUs 9 and 10 (Default=T)"/>
+        <param name="minnumsamples" type="integer" value="0" min="0" label="minnumsamples - indicate the minimum number of samples present in an OTU" help="If the number of samples present falls below the minimum, the OTU is removed (Default=0)"/>
+        <param name="minpercentsamples" type="integer" value="0" min="0" max="100" label="minpercentsamples - indicate the minimum percent of sample present in an OTU" help="For example, if the total number of samples is 10, the number present is 3, and the minpercentsamples=50. The OTU's precent of samples is 0.333, the minimum is 0.50, so the OTU will be removed (Default=0)"/>
+        <param name="mintotal" type="integer" value="0" min="0" max="100" label="mintotal - indicate the minimum abundance required for a given OTU" help="If abundance across all samples falls below the minimum, the OTU is removed (Default=0)"/>
+        <param name="makerare" type="boolean" truevalue="true" falsevalue="false" checked="true" label="makerare - indicate you want the abundances of any removed OTUs to be saved and a new rare OTU created with its abundances equal to the sum of the OTUs removed" help="This will preserve the number of reads in your dataset (Default=T)"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <collection name="filter_shared" type="list" label="${tool.name} on ${on_string}: filter.shared">
+            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.filter\.dat" format="mothur.shared"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test><!-- test with defaults -->
+            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
+            <param name="minabund" value="1"/>
+            <output_collection name="filter_shared" count="36">
+                <element name="0.29" md5="db8387475c126110f2ac21066344c933" ftype="mothur.shared"/>
+            </output_collection>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with label and group select -->
+            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
+            <param name="label" value="0.05,0.29,0.33"/>
+            <param name="groups" value="forest,pasture"/>
+            <param name="minabund" value="1"/>
+            <output_collection name="filter_shared" count="3">
+                <element name="0.29" md5="db8387475c126110f2ac21066344c933" ftype="mothur.shared"/>
+            </output_collection>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The filter.shared_ is used to remove OTUs based on various critieria.
+
+.. _filter.shared: https://www.mothur.org/wiki/Filter.shared
+
+]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1128/AEM.01541-09</citation>
+    </citations>
+</tool>
b
diff -r 000000000000 -r bccb5efbc4ee macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Fri May 19 05:47:34 2017 -0400
[
@@ -0,0 +1,98 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="1.36.1">mothur</requirement>
+        </requirements>
+    </xml>
+    <xml name="version_command">
+        <version_command>mothur "#help()" | sed '7q;d' | cut -d" " -f2 </version_command>
+    </xml>
+    <xml name="stdio">
+        <stdio>
+            <regex match="\[ERROR\]" source="stdout" level="fatal"/>
+            <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>
+    <xml name="labeloptions">
+        <options>
+            <filter type="data_meta" ref="otu" key="labels"/>
+        </options>
+    </xml>
+    <xml name="calc-common">
+        <!-- you can set defaults in tool xml by repeating those options again after macro expand, overriding first -->
+        <option value="anderberg">anderberg - Community Membership Similarity the Anderberg similarity coefficient</option>
+        <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option>
+        <option value="canberra">canberra - Community Structure Similarity</option>
+        <option value="gower">gower - Community Structure Similarity</option>
+        <option value="hamming">hamming - Community Membership Similarity</option>
+        <option value="hellinger">hellinger - Community Structure Similarity</option>
+        <option value="jabund">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option>
+        <option value="jclass">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option>
+        <option value="jest">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option>
+        <option value="jsd">jsd</option>
+        <option value="kulczynski">kulczynski - Community Membership Similarity the Kulczynski similarity coefficient</option>
+        <option value="kulczynskicody">kulczynskicody - Community Membership Similarity the Kulczynski-Cody similarity coefficient</option>
+        <option value="kstest">kstest - Community Membership Similarity Kolmogorov-Smirnov test</option>
+        <option value="lennon">lennon - Community Membership Similarity the Lennon similarity coefficient</option>
+        <option value="manhattan">manhattan - Community Structure Similarity</option>
+        <option value="memchi2">memchi2 - Community Membership Similarity</option>
+        <option value="memchord">memchord - Community Membership Similarity</option>
+        <option value="memeuclidean">memeuclidean - Community Membership Similarity</option>
+        <option value="mempearson">mempearson - Community Membership Similarity</option>
+        <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option>
+        <option value="ochiai">ochiai - Community Membership Similarity the Ochiai similarity coefficient</option>
+        <option value="odum">odum - Community Structure Similarity</option>
+        <option value="rjsd">rjsd</option>
+        <option value="sharedace">sharedace - Shared community richness the two sample shared ACE richness estimator</option>
+        <option value="sharednseqs">sharednseqs - Utility the number of sequences in two samples</option>
+        <option value="sharedobserved">sharedobserved - Utility the number of sequences in two samples</option>
+        <option value="sharedsobs">sharedsobs - Shared community richness the observed richness shared between two or more samples</option>
+        <option value="sharedchao">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option>
+        <option value="soergel">soergel - Community Structure Similarity</option>
+        <option value="sorabund">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option>
+        <option value="sorclass">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option>
+        <option value="sorest">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option>
+        <option value="spearman">spearman - Community Structure Similarity</option>
+        <option value="speciesprofile">speciesprofile - Community Structure Similarity</option>
+        <option value="structchi2">structchi2 - Community Structure Similarity</option>
+        <option value="structchord">structchord - Community Structure Similarity</option>
+        <option value="structeuclidean">structeuclidean - Community Structure Similarity</option>
+        <option value="structkulczynski">structkulczynski - Community Structure Similarity</option>
+        <option value="structpearson">structpearson - Community Structure Similarity</option>
+        <option value="thetan">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
+        <option value="thetayc">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
+        <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option>
+        <yield/>
+    </xml>
+    <xml name="logfile-output">
+        <data name="logfile" format="txt" from_work_dir="mothur.out.log" label="${tool.name} on ${on_string}: logfile"/>
+    </xml>
+    <xml name="logfile-test">
+        <output name="logfile" ftype="txt">
+            <assert_contents>
+                <has_text text="mothur"/>
+                <has_text text="@WRAPPER_VERSION@"/>
+            </assert_contents>
+        </output>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1128/AEM.01541-09</citation>
+            <yield/>
+        </citations>
+    </xml>
+</macros>
b
diff -r 000000000000 -r bccb5efbc4ee test-data/98_sq_phylip_amazon.dist
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/98_sq_phylip_amazon.dist Fri May 19 05:47:34 2017 -0400
b
b'@@ -0,0 +1,99 @@\n+\t98\n+U68589\t0.000000\t0.337144\t0.360977\t0.415506\t0.287299\t0.297057\t0.392240\t0.309315\t0.320066\t0.328638\t0.257245\t0.337227\t0.301773\t0.307105\t0.477681\t0.364754\t0.320363\t0.340712\t0.643389\t0.433138\t0.376207\t0.351515\t0.373270\t0.325136\t0.289019\t0.310340\t0.307018\t0.308559\t0.324956\t0.368119\t0.324956\t0.259707\t0.409194\t0.273253\t0.348793\t0.338829\t0.289890\t0.460196\t0.287313\t0.304876\t0.293627\t0.398745\t0.323458\t0.343931\t0.270320\t0.328638\t0.360667\t0.317641\t0.307311\t0.318242\t0.315163\t0.334519\t0.259354\t0.513252\t0.321245\t0.382122\t0.338989\t0.311488\t0.341095\t0.306169\t0.343707\t0.348475\t0.243919\t0.301619\t0.371532\t0.377102\t0.428155\t0.343582\t0.363540\t0.320583\t0.377095\t0.334577\t0.328665\t0.438795\t0.309493\t0.394408\t0.334519\t0.338675\t0.228291\t0.376110\t0.348863\t0.282832\t0.281554\t0.289504\t0.460089\t0.290337\t0.225920\t0.353872\t0.301641\t0.318305\t0.236932\t0.387405\t0.329749\t0.306586\t0.365423\t0.322928\t0.412271\t0.323601\n+U68590\t0.337144\t0.000000\t0.378254\t0.319757\t0.169021\t0.329311\t0.273158\t0.312653\t0.266838\t0.206259\t0.328665\t0.341084\t0.323764\t0.220396\t0.362613\t0.274376\t0.201198\t0.317527\t0.530014\t0.373379\t0.294704\t0.286594\t0.293104\t0.214397\t0.304876\t0.294032\t0.296294\t0.318935\t0.228159\t0.215592\t0.228159\t0.285269\t0.383119\t0.287768\t0.248463\t0.330389\t0.331258\t0.359192\t0.314346\t0.282537\t0.308195\t0.273482\t0.265198\t0.272626\t0.323924\t0.216451\t0.281824\t0.241593\t0.230389\t0.228159\t0.255453\t0.219740\t0.357218\t0.507737\t0.178105\t0.215419\t0.133686\t0.292498\t0.280214\t0.206522\t0.225386\t0.300901\t0.269939\t0.216102\t0.274415\t0.312052\t0.365054\t0.244067\t0.239423\t0.322718\t0.331029\t0.347334\t0.307230\t0.410098\t0.300178\t0.278594\t0.219740\t0.304895\t0.274172\t0.304876\t0.304882\t0.278803\t0.190897\t0.278803\t0.379815\t0.310886\t0.281221\t0.215933\t0.310375\t0.297172\t0.287175\t0.386427\t0.307257\t0.199943\t0.313533\t0.223156\t0.313533\t0.316704\n+U68591\t0.360977\t0.378254\t0.000000\t0.414843\t0.336162\t0.356376\t0.427517\t0.322673\t0.352060\t0.344952\t0.369658\t0.122794\t0.372984\t0.369623\t0.467881\t0.377089\t0.324100\t0.365825\t0.548815\t0.490123\t0.450700\t0.363708\t0.396633\t0.363488\t0.311317\t0.329411\t0.347363\t0.328716\t0.384142\t0.397333\t0.384142\t0.315472\t0.415027\t0.310736\t0.388493\t0.359680\t0.334111\t0.500022\t0.350766\t0.333145\t0.333379\t0.442063\t0.319388\t0.395174\t0.355606\t0.372774\t0.425988\t0.367269\t0.363032\t0.342135\t0.362984\t0.392626\t0.425088\t0.518779\t0.344833\t0.433896\t0.360705\t0.369193\t0.320658\t0.325439\t0.383119\t0.379501\t0.347418\t0.316998\t0.421263\t0.378254\t0.445836\t0.413887\t0.422482\t0.380263\t0.378280\t0.369961\t0.382431\t0.394891\t0.336453\t0.450824\t0.392626\t0.320439\t0.369357\t0.371101\t0.412218\t0.322132\t0.307547\t0.325439\t0.458067\t0.338335\t0.353510\t0.389953\t0.330669\t0.333647\t0.365609\t0.420026\t0.425707\t0.321169\t0.405119\t0.371826\t0.408262\t0.372984\n+U68592\t0.415506\t0.319757\t0.414843\t0.000000\t0.284235\t0.332574\t0.229894\t0.363330\t0.325227\t0.265168\t0.338989\t0.364319\t0.350376\t0.266663\t0.418468\t0.331206\t0.301152\t0.384448\t0.587163\t0.416497\t0.215923\t0.319670\t0.359680\t0.254598\t0.332803\t0.338989\t0.326397\t0.347490\t0.281664\t0.312183\t0.281664\t0.373185\t0.359680\t0.365184\t0.301866\t0.362488\t0.382122\t0.420349\t0.356390\t0.342170\t0.340183\t0.179474\t0.326851\t0.298352\t0.302463\t0.260630\t0.164494\t0.275794\t0.268092\t0.355578\t0.303351\t0.295152\t0.347147\t0.556294\t0.353384\t0.281513\t0.354194\t0.355266\t0.345025\t0.328101\t0.297497\t0.213459\t0.326145\t0.323619\t0.311791\t0.336626\t0.424992\t0.299483\t0.277780\t0.373994\t0.399403\t0.362410\t0.369636\t0.442027\t0.380785\t0.211525\t0.295152\t0.326489\t0.370307\t0.363330\t0.176486\t0.365609\t0.237569\t0.309315\t0.378434\t0.346768\t0.331129\t0.288419\t0.385769\t0.336467\t0.363330\t0.401870\t0.181103\t0.296007\t0.116013\t0.276453\t0.065911\t0.382445\n+U68593\t0.287299\t0.169021\t0.336162\t0.284235\t0.000000\t0.276866\t0.283055\t0.291774\t0.217362\t0.189372\t0.294160\t0.302449\t0.284617\t0.219618\t0.385130\t0.257535\t0.122862\t0.324013\t0.518760\t0.391165\t0.284617\t0.253894\t0.273158\t0.213889\t0.267779\t0.274252\t0.271113\t0.291080\t0.214579\t0.240602\t0.214579\t0.223590\t0.344108\t0.247344\t0.236421\t0.222528\t0.254171\t0.396586\t0.289841\t0.278520\t0.259933\t0.283223\t0.225527\t0.244836\t0.268053\t0.20'..b'132969\t0.213271\t0.207032\t0.305619\t0.469464\t0.181735\t0.212120\t0.197861\t0.263926\t0.216845\t0.121627\t0.180162\t0.310285\t0.230563\t0.122862\t0.253369\t0.255453\t0.363488\t0.203088\t0.229150\t0.296162\t0.316581\t0.252567\t0.287448\t0.405905\t0.271528\t0.321801\t0.207032\t0.220011\t0.282358\t0.281859\t0.269811\t0.213727\t0.176543\t0.219470\t0.330887\t0.238770\t0.255229\t0.187204\t0.264391\t0.266901\t0.278185\t0.372901\t0.293195\t0.000000\t0.309357\t0.186800\t0.358431\t0.286170\n+U68685\t0.365423\t0.313533\t0.405119\t0.116013\t0.300336\t0.309315\t0.227713\t0.349614\t0.319374\t0.292542\t0.344149\t0.348044\t0.329101\t0.282017\t0.478115\t0.334008\t0.309357\t0.360611\t0.586500\t0.410286\t0.212203\t0.358766\t0.375352\t0.276933\t0.336148\t0.367583\t0.334619\t0.329937\t0.295744\t0.326668\t0.295744\t0.348044\t0.346279\t0.355521\t0.335561\t0.350766\t0.379082\t0.415352\t0.334876\t0.322618\t0.333010\t0.185184\t0.338989\t0.315857\t0.299159\t0.280409\t0.170628\t0.277833\t0.276712\t0.365261\t0.307129\t0.323281\t0.333145\t0.569768\t0.325227\t0.318457\t0.340427\t0.353588\t0.340729\t0.336995\t0.301129\t0.209657\t0.313678\t0.320049\t0.324434\t0.329525\t0.412742\t0.311920\t0.311667\t0.364131\t0.373185\t0.377826\t0.371187\t0.407906\t0.370049\t0.202565\t0.323281\t0.304895\t0.340427\t0.396572\t0.169638\t0.337847\t0.255321\t0.287010\t0.406129\t0.331880\t0.320138\t0.317889\t0.365261\t0.368000\t0.346439\t0.391855\t0.166464\t0.309357\t0.000000\t0.296666\t0.118751\t0.372984\n+U68686\t0.322928\t0.223156\t0.371826\t0.276453\t0.191909\t0.281513\t0.300211\t0.286451\t0.225078\t0.085685\t0.333874\t0.349992\t0.257463\t0.093482\t0.386847\t0.236499\t0.218231\t0.317777\t0.522903\t0.364001\t0.286170\t0.288785\t0.211388\t0.073795\t0.275573\t0.310075\t0.288419\t0.279986\t0.079795\t0.092710\t0.079795\t0.275120\t0.355097\t0.285469\t0.134401\t0.241633\t0.301830\t0.371596\t0.268092\t0.253764\t0.282537\t0.280475\t0.182924\t0.159261\t0.253005\t0.043762\t0.259354\t0.070985\t0.061001\t0.229921\t0.147447\t0.106638\t0.294934\t0.485847\t0.262301\t0.096299\t0.287010\t0.277657\t0.198885\t0.210837\t0.112948\t0.297172\t0.217019\t0.217085\t0.103167\t0.263548\t0.355401\t0.087958\t0.114629\t0.276029\t0.355097\t0.315321\t0.304099\t0.414843\t0.298075\t0.300336\t0.106638\t0.268562\t0.277573\t0.330550\t0.290224\t0.266373\t0.087708\t0.246819\t0.348130\t0.257541\t0.255902\t0.083710\t0.291481\t0.310785\t0.297392\t0.347187\t0.271852\t0.186800\t0.296666\t0.000000\t0.296666\t0.297339\n+U68687\t0.412271\t0.313533\t0.408262\t0.065911\t0.357920\t0.386580\t0.228897\t0.367366\t0.367276\t0.271435\t0.389291\t0.375794\t0.360148\t0.262636\t0.442034\t0.344247\t0.334817\t0.437586\t0.597979\t0.406702\t0.213348\t0.359238\t0.388467\t0.262900\t0.349656\t0.403898\t0.375748\t0.349886\t0.281484\t0.318118\t0.281484\t0.387518\t0.381696\t0.405765\t0.309357\t0.402710\t0.416988\t0.403588\t0.361088\t0.350376\t0.406654\t0.180258\t0.335656\t0.301609\t0.319116\t0.277406\t0.160611\t0.257463\t0.270760\t0.374644\t0.316294\t0.292099\t0.371022\t0.561599\t0.405293\t0.325351\t0.374436\t0.357459\t0.354291\t0.368248\t0.321376\t0.230269\t0.336101\t0.363452\t0.311061\t0.326299\t0.408028\t0.311920\t0.380934\t0.378150\t0.391254\t0.395909\t0.376972\t0.489142\t0.411804\t0.212488\t0.292099\t0.324272\t0.377214\t0.374703\t0.169254\t0.380582\t0.233238\t0.356923\t0.383851\t0.351372\t0.346968\t0.290558\t0.419507\t0.405876\t0.385406\t0.383533\t0.169021\t0.358431\t0.118751\t0.296666\t0.000000\t0.385499\n+U68688\t0.323601\t0.316704\t0.372984\t0.382445\t0.336085\t0.273784\t0.390245\t0.221892\t0.294195\t0.286451\t0.291580\t0.349854\t0.233168\t0.302582\t0.386206\t0.295536\t0.274451\t0.257572\t0.561908\t0.435867\t0.373578\t0.278247\t0.350106\t0.295676\t0.207032\t0.304857\t0.207984\t0.198309\t0.307927\t0.330148\t0.307927\t0.270760\t0.395785\t0.157775\t0.310948\t0.350243\t0.163469\t0.426170\t0.219999\t0.222823\t0.236621\t0.359680\t0.294195\t0.329525\t0.216845\t0.274415\t0.339877\t0.313301\t0.285014\t0.308667\t0.264831\t0.333145\t0.301811\t0.475087\t0.312513\t0.319500\t0.354966\t0.106779\t0.320446\t0.280287\t0.271549\t0.376843\t0.068529\t0.288293\t0.341922\t0.318118\t0.417649\t0.334876\t0.324266\t0.083849\t0.375352\t0.355032\t0.020272\t0.438400\t0.008059\t0.391000\t0.333145\t0.296162\t0.241891\t0.328691\t0.355843\t0.253369\t0.268975\t0.230455\t0.406129\t0.072600\t0.207438\t0.332052\t0.009987\t0.313227\t0.238036\t0.418616\t0.363081\t0.286170\t0.372984\t0.297339\t0.385499\t0.000000\n'
b
diff -r 000000000000 -r bccb5efbc4ee test-data/Fasting_Example1.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Fasting_Example1.fasta Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,20 @@
+>FLP3FBN01ELBSX xy=1766_111
+ACAGAGTCGGCTCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTTACCCTCTCAGGCCGGCTACGCATCATCGCCTTGGTGGGCCGTTACCTCACCAACTAGCTAATGCGCCGCAGGTCCATCCATGTTCACGCCTTGATGGGCGCTTTAATATACTGAGCATGCGCTCTGTATACCTATCCGGTTTTAGCTACCGTTTCCAGCAGTTATCCCGGACACATGGGCTAGg
+>FLP3FBN01EG8AX xy=1719_1463
+ACAGAGTCGGCTCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGCCTTCCTCTCAGAACCCCTATCCATCGAAGGCTTGGTGGGCCGTTACCCCGCCAACAACCTAATGGAACGCATCCCCATCGATGACCGAAGTTCTTTAATAGTTCTACCATGCGGAAGAACTATGCCATCGGGTATTAATCTTTCTTTCGAAAGGCTATCCCCGAGTCATCGGCAGGTTGGATACGTGTTACTCACCCGTGCGCCGGTCGCCa
+>FLP3FBN01EEWKD xy=1692_3531
+AGCACGAGCCTACATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGATCAGTCTCTTAACTCGGCTATGCATCATTGCCTTGGTAAGCCGTTACCTTACCAACTAGCTAATGCACCGCAGGTCCATCCAAGAGTGATAGCAGAACCATCTTTCAAACTCTAGACATGCGTCTAGTGTTGTTATCCGGTATTAGCATCTGTTTCCAGGTGTTATCCCAGTCTCTTGGg
+>FLP3FBN01DEHK3 xy=1278_245
+ACCAGCGACTAGCATGCTGCCTCCCGTAGGAGTCTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCAACCTCTCAGTCCGGCTACTGATCGTCGACTTGGTGAGCCGTTACCTCACCAACTATCTAATCAGACGCGAGCCCATCTTTCAGCGGATTGCTCCTTTGGTATTCCGGCGATGCCGCCAAAATCATTATGCGGTATTAGCAGTCGTTTCCAACTGTTGTCCCCCTCTGAAAGGCAGGTTGCTCACg
+>FLP3FBN01DGFYQ xy=1300_1344
+ACAGAGTCGGCTCATGCTGCCTCCCGTAGGAGTTTGGGCCGTGTCTCAGTCCCAATGTGGCCGTTCACCCTCTCAGGCCGGCTACTGATCGTCGCTTTGGTAGGCCGTTACCCTGCCAACTGGCTAATCAGACGCGGGTCCATCTCACACCGATTAATCTTTTTCCAACCAGAGCATGCGCCCCTGTTGGCTTATGCGGTATTAGCGGTCGTTTCCAACTGTTATCCCCCTGTGTGAGGCAGGTTACCCACGCGTTACTCACCCGTCCg
+>FLP3FBN01A55WZ xy=363_481
+ACGGTGAGTGTCCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCCCGCCTACTATCTAATGGAACGCATCCCCATCTTATACCGGTAAACCTTTAATCATGAGAAAATGCTCACTCATGATACCATCTTGTATTAATCTCCCTTTCAGAAGGCTATCCAAGAGTATAAGGCAGGTTGGATACGCGTTACTCACCCGTGCGCCGg
+>FLP3FBN01D7O1S xy=1610_3070
+ACAGAGTCGGCTCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCCCGCCTACTATCTAATGGAACGCATCCCCATCGATAACCGAAATTCTTTAATAGTGAAACCATGCGGAAATACTATACTATCGGGTATTAATCTTTCTTTCGAAAGGCTATCCCCGAGTTATCGGCAGGTTGGATACGTGTTACTCACCCGTGCGCCGGTCGCCATc
+>FLP3FBN01CV5ZU xy=1069_1480
+ACAGAGTCGGCTCATGCTGCCTCCCGTAGGAGTTTGGTCCGTGTCTCAGTACCAATGTGGGGGGTTAACCTCTCAGTCCCCCTATGTATCGTCGCCTTGGTAAGCCGTTACCTTACCAACCAGCTAATACAACGCATGCCCATCTGTAACCGCCGAAACTTTCAACCACAAGAGATGCCTCTCATAGTGTTATGCGGTATTAGTACCGATTTCTCAGTGTTATCCCCCTGTTACAGGTAGGTTGCATACGCGTTACGCACCCGTGCGCCGGTCg
+>FLP3FBN01DQ783 xy=1423_757
+ACAGAGTCGGCTCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCCCGCCTACTATCTAATGGAACGCATCCCCATCGTCTACCGGAATACCTTTAATCATGTGAACATGCGGACTCATGATGCCATCTTGTATTAATCTTCCTTTCAGAAGGCTGTCCAAGAGTAGACGGCAGGTTGGATACGTGTTACTCACCCg
+>FLP3FBN01DDPFF xy=1269_617
+ACAGAGTCGGCTCATGCTGCCTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGAAGACTAGGTGGGCCGTTACCCCGCCTACTATCTAATGGAACGCATCCCCATCGTCTACCGGAATACCTTTAATCATGTGAACATGCGGACTCATGATGCCATCTTGTATTAATCTCCCTTTCAGAAGGCTATCCAAGAGTATAAGGCAGGTTGGGTACGCGTTACTc
b
diff -r 000000000000 -r bccb5efbc4ee test-data/Fasting_Example1.qual
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Fasting_Example1.qual Fri May 19 05:47:34 2017 -0400
b
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t35\t35\t35\t32\t33\t33\t32\t35\t35\t32\t25\t25\t15\t20\t20\t20\t28\t35\t33\t33\t33\t33\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t29\t24\t24\t24\t29\t35\t35\t35\t35\t33\t33\t31\t31\t34\t34\t34\t34\t34\t34\t31\t20\t20\t20\t20\t20\t31\t34\t31\t31\t31'..b'35\t35\t35\t35\t35\t35\t32\t32\t32\t32\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t34\t34\t26\t26\t26\t26\t32\t35\t35\t35\t35\t35\t35\t34\t34\t34\t34\t34\t34\t34\t35\t35\t35\t35\t35\t35\t35\t35\t35\t26\t26\t26\t26\t35\t35\t35\t35\t35\t35\t35\t35\t34\t34\t34\t34\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t30\t22\t24\t21\t21\t21\t30\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t29\t29\t26\t34\t35\t27\t27\t27\t27\t35\t35\t35\t35\t35\t35\t35\t32\t32\t32\t32\t32\t35\t35\t35\t35\t35\t35\t35\t35\t35\t35\t31\t32\t32\t25\t28\t25\t25\t25\t25\t30\t30\t30\t30\t30\t30\t30\t30\t28\t22\t22\t22\t28\t28\t30\t25\t22\t22\t22\t30\t30\t\n+>FLP3FBN01D7O1S xy=1610_3070 length=279\n+36\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t38\t37\t36\t40\t28\t28\t28\t33\t40\t38\t37\t37\t39\t37\t40\t37\t38\t38\t38\t40\t40\t40\t40\t40\t40\t40\t40\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t36\t36\t33\t33\t33\t36\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t36\t35\t35\t37\t31\t24\t21\t21\t21\t21\t23\t32\t36\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t36\t28\t28\t28\t28\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t36\t28\t28\t28\t33\t33\t37\t37\t37\t37\t37\t28\t28\t28\t33\t33\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t36\t33\t33\t33\t33\t37\t36\t28\t28\t26\t36\t37\t37\t37\t37\t36\t31\t31\t26\t31\t31\t36\t36\t30\t17\t16\t16\t19\t19\t19\t26\t30\t30\t32\t33\t36\t36\t36\t36\t36\t33\t33\t33\t36\t36\t33\t33\t28\t31\t31\t31\t31\t31\t28\t28\t28\t31\t31\t31\t31\t25\t22\t22\t22\t25\t28\t28\t28\t31\t28\t28\t28\t28\t31\t29\t28\t28\t28\t29\t25\t16\t\n+>FLP3FBN01CV5ZU xy=1069_1480 length=274\n+37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t31\t31\t31\t31\t31\t31\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t38\t38\t33\t33\t33\t33\t33\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t38\t38\t38\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t38\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t38\t38\t38\t38\t40\t38\t38\t38\t38\t38\t38\t38\t38\t38\t38\t38\t38\t38\t30\t30\t31\t32\t32\t32\t32\t32\t32\t32\t32\t32\t32\t32\t32\t32\t32\t32\t32\t32\t32\t32\t32\t32\t32\t32\t32\t28\t28\t\n+>FLP3FBN01DQ783 xy=1423_757 length=264\n+37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t38\t38\t38\t38\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t38\t38\t38\t37\t37\t38\t38\t38\t38\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t40\t40\t40\t40\t40\t40\t40\t40\t38\t38\t38\t38\t40\t38\t38\t38\t38\t38\t38\t38\t38\t38\t36\t38\t37\t37\t36\t36\t36\t30\t31\t31\t31\t31\t31\t31\t31\t31\t31\t32\t31\t31\t31\t31\t31\t25\t25\t25\t\n+>FLP3FBN01DDPFF xy=1269_617 length=259\n+37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t40\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t34\t33\t33\t33\t33\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t38\t38\t38\t38\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t37\t38\t38\t31\t31\t31\t38\t37\t37\t36\t36\t33\t33\t33\t36\t37\t36\t38\t38\t38\t37\t38\t38\t38\t38\t38\t38\t36\t36\t36\t36\t38\t36\t36\t36\t28\t28\t29\t21\t21\t22\t28\t32\t31\t31\t31\t31\t31\t32\t31\t31\t28\t\n'
b
diff -r 000000000000 -r bccb5efbc4ee test-data/Fasting_Example1.sff
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Binary file test-data/Fasting_Example1.sff has changed
b
diff -r 000000000000 -r bccb5efbc4ee test-data/Fasting_Example2.sff
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Binary file test-data/Fasting_Example2.sff has changed
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diff -r 000000000000 -r bccb5efbc4ee test-data/GQY1XT001.oligos
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/GQY1XT001.oligos Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,12 @@
+forward CCGTCAATTCMTTTRAGT
+barcode AATGGTAC F003D000
+barcode AACCTGGC F003D002
+barcode TTCGTGGC F003D004
+barcode TTCTTGAC F003D006
+barcode TTCGCGAC F003D008
+barcode TCCAGAAC F003D142
+barcode AAGGCCTC F003D144
+barcode TGACCGTC F003D146
+barcode AGGTTGTC F003D148
+barcode TGGTGAAC F003D150
+barcode AACCGTGTC MOCK.GQY1XT001
b
diff -r 000000000000 -r bccb5efbc4ee test-data/HMP_MOCK.v35.align
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/HMP_MOCK.v35.align Fri May 19 05:47:34 2017 -0400
b
b'@@ -0,0 +1,64 @@\n+>A.baumannii.1\n+.............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................'..b'..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................\n'
b
diff -r 000000000000 -r bccb5efbc4ee test-data/HMP_MOCK.v35.align.names
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/HMP_MOCK.v35.align.names Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,32 @@
+A.baumannii.1 A.baumannii.1
+A.odontolyticus.1 A.odontolyticus.1
+B.cereus.1 B.cereus.1
+B.vulgatus.1 B.vulgatus.1
+B.vulgatus.2 B.vulgatus.2
+B.vulgatus.4 B.vulgatus.4
+B.vulgatus.5 B.vulgatus.5
+B.vulgatus.7 B.vulgatus.7
+C.beijerinckii.1 C.beijerinckii.1
+C.beijerinckii.3 C.beijerinckii.3
+C.beijerinckii.4 C.beijerinckii.4
+D.radiodurans.1 D.radiodurans.1
+E.faecalis.1 E.faecalis.1
+E.faecalis.2 E.faecalis.2
+E.coli.1 E.coli.1
+H.pylori.1 H.pylori.1
+L.gasseri.1 L.gasseri.1
+L.monocytogenes.1 L.monocytogenes.1
+N.meningitidis.1 N.meningitidis.1
+P.acnes.1 P.acnes.1
+P.aeruginosa.1 P.aeruginosa.1
+P.aeruginosa.2 P.aeruginosa.2
+P.gingivalis.1 P.gingivalis.1
+R.sphaeroides.1 R.sphaeroides.1
+S.aureus.1 S.aureus.1
+S.aureus.5 S.aureus.5
+S.epidermidis.1 S.epidermidis.1
+S.epidermidis.2 S.epidermidis.2
+S.epidermidis.5 S.epidermidis.5
+S.agalactiae.1 S.agalactiae.1
+S.mutans.1 S.mutans.1
+S.pneumoniae.1 S.pneumoniae.1
b
diff -r 000000000000 -r bccb5efbc4ee test-data/HMP_MOCK.v35.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/HMP_MOCK.v35.fasta Fri May 19 05:47:34 2017 -0400
b
b'@@ -0,0 +1,64 @@\n+>A.baumannii.1\n+TGGGGAATATTGGACAATGGGGGGAACCCTGATCCAGCCATGCCGCGTGTGTGAAGAAGGCCTTATGGTTGTAAAGCACTTTAAGCGAGGAGGAGGCTACTTTAGTTAATACCTAGAGATAGTGGACGTTACTCGCAGAATAAGCACCGGCTAACTCTGTGCCAGCAGCCGCGGTAATACAGAGGGTGCGAGCGTTAATCGGATTTACTGGGCGTAAAGCGTGCGTAGGCGGCTTATTAAGTCGGATGTGAAATCCCCGAGCTTAACTTGGGAATTGCATTCGATACTGGTGAGCTAGAGTATGGGAGAGGATGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGATGGCGAAGGCAGCCATCTGGCCTAATACTGACGCTGAGGTACGAAAGCATGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCATGCCGTAAACGATGTCTACTAGCCGTTGGGGCCTTTGAGGCTTTAGTGGCGCAGCTAACGCGATAAGTAGACCGCCTGGGGAGTACGGTC\n+>A.odontolyticus.1\n+TGGGGAATATTGCACAATGGGCGAAAGCCTGATGCAGCGACGCCGCGTGAGGGATGGAGGCCTTCGGGTTGTAAACCTCTTTCGCTCATGGTCAAGCCGCAACTCAAGGTTGTGGTGAGGGTAGTGGGTAAAGAAGCGCCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGCGCGAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTTGTAGGCGGTTGGTCGCGTCTGCCGTGAAATCCTCTGGCTTAACTGGGGGCGTGCGGTGGGTACGGGCTGACTTGAGTGCGGTAGGGGAGACTGGAACTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAAGAACACCGGTGGCGAAGGCGGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCTGTAAACGTTGGGCACTAGGTGTGGGGGCCACCCGTGGTTTCTGCGCCGTAGCTAACGCTTTAAGTGCCCCGCCTGGGGAGTACGGCC\n+>B.cereus.1\n+TAGGGAATCTTCCGCAATGGACGAAAGTCTGACGGAGCAACGCCGCGTGAGTGATGAAGGCTTTCGGGTCGTAAAACTCTGTTGTTAGGGAAGAACAAGTGCTAGTTGAATAAGCTGGCACCTTGACGGTACCTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGCAGGTGGTTTCTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACACTGAGGCGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTAGAGGGTTTCCGCCCTTTAGTGCTGAAGTTAACGCATTAAGCACTCCGCCTGGGGAGTACGGCC\n+>B.vulgatus.1\n+TGAGGAATATTGGTCAATGGGCGCAGGCCTGAACCAGCCAAGTAGCGTGAAGGATGACTGCCCTATGGGTTGTAAACTTCTTTTATAAAGGAATAAAGTCGGGTATGGATACCCGTTTGCATGTACTTTATGAATAAGGATCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAACAGGATTAGATACCCTGGTAGTCCACACGGTAAACGATGAATACTCGCTGTTTGCGATATACGGCAAGCGGCCAAGCGAAAGCGTTAAGTATTCCACCTGGGGAGTACGCCG\n+>B.vulgatus.2\n+TGAGGAATATTGGTCAATGGGCGAGAGCCTGAACCAGCCAAGTAGCGTGAAGGATGACTGCCCTATGGGTTGTAAACTTCTTTTATAAAGGAATAAAGTCGGGTATGGATACCCGTTTGCATGTACTTTATGAATAAGGATCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAACAGGATTAGATACCCTGGTAGTCCACACGGTAAACGATGAATACTCGCTGTTTGCGATATACGGCAAGCGGCCAAGCGAAAGCGTTAAGTATTCCACCTGGGGAGTACGCCG\n+>B.vulgatus.4\n+TGAGGAATATTGGTCAATGGGCGAGAGCCTGAACCAGCCAAGTAGCGTGAAGGATGACTGCCCTATGGGTTGTAAACTTCTTTTATAAAGGAATAAAGTCGGGTATGGATACCCGTTTGCATGTACTTTATGAATAAGGATCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATATTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAACAGGATTAGATACCCTGGTAGTCCACACGGTAAACGATGAATACTCGCTGTTTGCGATATACTGCAAGCGGCCAAGCGAAAGCGTTAAGTATTCCACCTGGGGAGTACGCCG\n+>B.vulgatus.5\n+TGAGGAATATTGGTCAATGGGCGAGAGCCTGAACCAGCCAAGTAGCGTGAAGGATGACTGCCCTATGGGTTGTAAACTTCTTTTATAAAGGAATAAAGTCGGGTATGGATACCCGTTTGCATGTACTTTATGAATAAGGATCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAACAGGATTAGATACCCTGGTAGTCCACACGGTAAACGATGAATACTCGCTGTTTGCGATATACTGCAAGCGGCCAAGCGAAAGCGTTAAGTATTCCACCTGGGGAGTACGCCG\n+>B.vulgatus.7\n+TGAGGAATATTGGTCAATGGGCGAGAGCCTGAACCAGCCAAGTAGCGTGAAGGATGACTGCCCTATGGGTTGTAAACTTCTTTTATAAAGGAATAAAG'..b'ACGATGAGTGCTAAGTGTTAGGGGGTTTCCGCCCCTTAGTGCTGCAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGACC\n+>S.aureus.5\n+TAGGGAATCTTCCGCAATGGGCGAAAGCCTGACGGAGCAACGCCGCGTGAGTGATGAAGGTCTTCGGATCGTAAAACTCTGTTATTAGGGAAGAACATATGTGTAAGTAACTGTGCACATCTTGACGGTACCTAATCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTTATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGGGATCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTAGGGGGTTTCCGCCCCTTAGTGCTGCAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGACC\n+>S.epidermidis.1\n+TAGGGAATCTTCCGCAATGGGCGAAAGCCTGACGGAGCAACGCCGCGTGAGTGATGAAGGTCTTCGGATCGTAAAACTCTGTTATTAGGGAAGAACAAATGTGTAAGTAACTATGCACGTCTTGACGGTACCTAATCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGGGATCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTAGGGGGTTTCCGCCCCTTAGTGCTGCAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGACC\n+>S.epidermidis.2\n+TAGGGAATCTTCCGCAATGGGCGAAAGCTTGACGGAGCAACGCCGCGTGAGTGATGAAGGTCTTCGGATCGTAAAACTCTGTTATTAGGGAAGAACAAATGTGTAAGTAACTATGCACGTCTTGACGGTACCTAATCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGGGATCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTAGGGGGTTTCCGCCCCTTAGTGCTGCAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGACC\n+>S.epidermidis.5\n+TAGGGAATCTTCCGCAATGGGCGAAAGCTTGACGGAGCAACGCCGCGTGAGTGATGAAGGTCTTCGGATCGTAAAACTCTGTTATTAGGGAAGAACAAATGTCTAAGTAACTATGCACGTCTTGACGGTACCTAATCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATCATTGGGCGTAAAGCGCGCGTAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAGGACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGGGATCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTAGGGGGTTTCCGCCCCTTAGTGCTGCAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGACC\n+>S.agalactiae.1\n+TAGGGAATCTTCGGCAATGGACGGAAGTCTGACCGAGCAACGCCGCGTGAGTGAAGAAGGTTTTCGGATCGTAAAGCTCTGTTGTTAGAGAAGAACGTTGGTAGGAGTGGAAAATCTACCAAGTGACGGTAACTAACCAGAAAGGGACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTCCCGAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTCTTTAAGTCTGAAGTTAAAGGCAGTGGCTTAACCATTGTACGCTTTGGAAACTGGAGGACTTGAGTGCAGAAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCGGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAGGTGTTAGGCCCTTTCCGGGGCTTAGTGCCGCAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGACC\n+>S.mutans.1\n+TAGGGAATCTTCGGCAATGGACGAAAGTCTGACCGAGCAACGCCGCGTGAGTGAAGAAGGTTTTCGGATCGTAAAGCTCTGTTGTAAGTCAAGAACGTGTGTGAGAGTGGAAAGTTCACACAGTGACGGTAGCTTACCAGAAAGGGACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTCCCGAGCGTTGTCCGGATTTATTGGGCGTAAAGGGAGCGCAGGCGGTCAGGAAAGTCTGGAGTAAAAGGCTATGGCTCAACCATAGTGTGCTCTGGAAACTGTCTGACTTGAGTGCAGAAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTCACTGACGCTGAGGCTCGAAAGCGTGGGTAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAGGTGTTAGGCCCTTTCCGGGGCTTAGTGCCGGAGCTAACGCAATAAGCACTCCGCCTGGGGAGTACGACC\n+>S.pneumoniae.1\n+TAGGGAATCTTCGGCAATGGACGGAAGTCTGACCGAGCAACGCCGCGTGAGTGAAGAAGGTTTTCGGATCGTAAAGCTCTGTTGTAAGAGAAGAACGAGTGTGAGAGTGGAAAGTTCACACTGTGACGGTATCTTACCAGAAAGGGACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTCCCGAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTAGATAAGTCTGAAGTTAAAGGCTGTGGCTTAACCATAGTAGGCTTTGGAAACTGTTTAACTTGAGTGCAAGAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCGGTGGCGAAAGCGGCTCTCTGGCTTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCTGTAAACGATGAGTGCTAGGTGTTAGACCCTTTCCGGGGTTTAGTGCCGTAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGACC\n'
b
diff -r 000000000000 -r bccb5efbc4ee test-data/HMP_MOCK.v35.pintail.quan
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/HMP_MOCK.v35.pintail.quan Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,101 @@
+#1.36.1
+1 0 0 0 0 0 0
+2 0.0401289 0.0401329 0.0686107 0.0957638 0.131891 0.131891
+3 0.129874 0.129874 0.129874 0.129874 0.129874 0.129874
+4 0 0 0 0 0 0
+5 0 0 0 0 0 0
+6 0 0 0 0 0 0
+7 0 0 0 0 0 0
+8 0 0 0 0 0 0
+9 0.570673 0.574425 0.597189 0.598318 0.598318 0.598318
+10 0.58334 0.58334 0.616837 0.617589 0.621807 0.621807
+11 0.624381 0.624381 0.629133 0.629753 0.629753 0.629753
+12 0 0 0 0 0 0
+13 0 0 0 0 0 0
+14 0.85247 0.85247 0.857164 0.857164 0.857164 0.857164
+15 0.848826 0.848826 0.848826 0.848826 0.848826 0.848826
+16 0.825389 0.831909 0.850142 0.872023 0.901994 0.901994
+17 0.844032 0.867226 0.874392 0.915192 0.960654 0.960654
+18 0.916939 0.916939 0.932322 0.938464 0.938464 0.938464
+19 0 0 0 0 0 0
+20 0 0 0 0 0 0
+21 0 0 0 0 0 0
+22 1.14494 1.14965 1.15471 1.16133 1.16828 1.16828
+23 0.997234 1.01547 1.21699 1.22643 1.24343 1.24343
+24 0.965161 1.03942 1.05406 1.21764 1.23287 1.23287
+25 1.29418 1.29515 1.29922 1.30707 1.31744 1.31744
+26 1.25809 1.26771 1.30164 1.34484 1.35981 1.35981
+27 1.22549 1.28661 1.32407 1.35436 1.39091 1.3986
+28 1.2438 1.31499 1.39699 1.42888 1.45945 1.46939
+29 1.37043 1.39346 1.45174 1.49716 1.55458 1.55551
+30 1.40454 1.42884 1.46383 1.51374 1.54414 1.56418
+31 1.44839 1.46554 1.46665 1.47655 1.49737 1.49737
+32 1.47282 1.49415 1.50836 1.52294 1.54801 1.5841
+33 1.5124 1.5231 1.53378 1.56165 1.59736 1.60412
+34 1.54717 1.563 1.59252 1.60734 1.63868 1.63868
+35 0 0 0 0 0 0
+36 0 0 0 0 0 0
+37 0 0 0 0 0 0
+38 0 0 0 0 0 0
+39 0 0 0 0 0 0
+40 0 0 0 0 0 0
+41 0 0 0 0 0 0
+42 0 0 0 0 0 0
+43 0 0 0 0 0 0
+44 0 0 0 0 0 0
+45 0 0 0 0 0 0
+46 0 0 0 0 0 0
+47 0 0 0 0 0 0
+48 0 0 0 0 0 0
+49 0 0 0 0 0 0
+50 0 0 0 0 0 0
+51 0 0 0 0 0 0
+52 0 0 0 0 0 0
+53 0 0 0 0 0 0
+54 0 0 0 0 0 0
+55 0 0 0 0 0 0
+56 0 0 0 0 0 0
+57 0 0 0 0 0 0
+58 0 0 0 0 0 0
+59 0 0 0 0 0 0
+60 0 0 0 0 0 0
+61 0 0 0 0 0 0
+62 0 0 0 0 0 0
+63 0 0 0 0 0 0
+64 0 0 0 0 0 0
+65 0 0 0 0 0 0
+66 0 0 0 0 0 0
+67 0 0 0 0 0 0
+68 0 0 0 0 0 0
+69 0 0 0 0 0 0
+70 0 0 0 0 0 0
+71 0 0 0 0 0 0
+72 0 0 0 0 0 0
+73 0 0 0 0 0 0
+74 0 0 0 0 0 0
+75 0 0 0 0 0 0
+76 0 0 0 0 0 0
+77 0 0 0 0 0 0
+78 0 0 0 0 0 0
+79 0 0 0 0 0 0
+80 0 0 0 0 0 0
+81 0 0 0 0 0 0
+82 0 0 0 0 0 0
+83 0 0 0 0 0 0
+84 0 0 0 0 0 0
+85 0 0 0 0 0 0
+86 0 0 0 0 0 0
+87 0 0 0 0 0 0
+88 0 0 0 0 0 0
+89 0 0 0 0 0 0
+90 0 0 0 0 0 0
+91 0 0 0 0 0 0
+92 0 0 0 0 0 0
+93 0 0 0 0 0 0
+94 0 0 0 0 0 0
+95 0 0 0 0 0 0
+96 0 0 0 0 0 0
+97 0 0 0 0 0 0
+98 0 0 0 0 0 0
+99 0 0 0 0 0 0
+100 0 0 0 0 0 0
b
diff -r 000000000000 -r bccb5efbc4ee test-data/HMP_MOCK.v35.slayer.chimeras
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/HMP_MOCK.v35.slayer.chimeras Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,33 @@
+Name LeftParent RightParent DivQLAQRB PerIDQLAQRB BootStrapA DivQLBQRA PerIDQLBQRA BootStrapB Flag LeftWindow RightWindow
+D.radiodurans.1 no
+N.meningitidis.1 no
+R.sphaeroides.1 no
+A.baumannii.1 no
+P.aeruginosa.1 no
+P.aeruginosa.2 no
+C.beijerinckii.4 no
+C.beijerinckii.3 no
+C.beijerinckii.1 no
+P.acnes.1 no
+E.coli.1 no
+A.odontolyticus.1 no
+B.vulgatus.1 no
+P.gingivalis.1 no
+B.vulgatus.5 no
+B.vulgatus.2 no
+B.vulgatus.4 no
+B.vulgatus.7 no
+S.agalactiae.1 no
+S.pneumoniae.1 no
+S.mutans.1 no
+E.faecalis.2 no
+E.faecalis.1 no
+S.epidermidis.2 no
+S.epidermidis.5 no
+S.aureus.5 no
+S.aureus.1 no
+S.epidermidis.1 no
+L.monocytogenes.1 no
+B.cereus.1 no
+L.gasseri.1 no
+H.pylori.1 no
b
diff -r 000000000000 -r bccb5efbc4ee test-data/HMPv5-v3_1368-1369.oligos
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/HMPv5-v3_1368-1369.oligos Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,2 @@
+forward GACACTATAGCCGTCAATTCMTTTRAGT
+#reverse    CACTATAGGGCCTACGGGAGGCAGCAG
b
diff -r 000000000000 -r bccb5efbc4ee test-data/LookUp_Titanium.pat
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/LookUp_Titanium.pat Fri May 19 05:47:34 2017 -0400
b
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diff -r 000000000000 -r bccb5efbc4ee test-data/M00967_43_000000000-A3JHG_1_1101_14010_4122.chimeracheck.svg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/M00967_43_000000000-A3JHG_1_1101_14010_4122.chimeracheck.svg Fri May 19 05:47:34 2017 -0400
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@@ -0,0 +1,13 @@
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diff -r 000000000000 -r bccb5efbc4ee test-data/Mock_S280_L001_R1_001_small.contigs.report
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mock_S280_L001_R1_001_small.contigs.report Fri May 19 05:47:34 2017 -0400
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diff -r 000000000000 -r bccb5efbc4ee test-data/Mock_S280_L001_R1_001_small.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mock_S280_L001_R1_001_small.fastq Fri May 19 05:47:34 2017 -0400
b
b'@@ -0,0 +1,100 @@\n+@M00967:43:000000000-A3JHG:1:1101:19936:3208 1:N:0:280\n+TACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACA\n++\n+BCCCCFFCFFCFGGGGGGGGGGHGGGGGHHHHHHHHGGGGHHHGGGGGGGGGGGGGGGGHHGHHHHHHHGHHHHHHHHHHGGGGGGGHHHHGGGGCGGGDHHHHHHHHHHHHHGAFFGHHHHHHHGHHGHHHHHHGHGFHGHHGHHHHGHHHCHHHGGGAGGGGGGGDDGGGGBFFGGFGGGGFFFFFFFFFFFFFFFFFFF-AFFFFF0BFBBFFFFEFFFFFFD?FFAF-9FDA/A.DCFFECDFFFF.\n+@M00967:43:000000000-A3JHG:1:1101:15923:3823 1:N:0:280\n+TACGGAGGGTGCAAGCGTTACCCGGAATCACTGGGCGTAAAGGGCGTGTAGGCGGAAATTTAAGTCTGGTTTTAAAGACCGGGGCTCAACCTCGGGGATGGACTGGATACTGGATTTCTTGACCTCTGGAGAGGTAACTGGAATTCCTGGTGTAGCGGTGGAATGCGTAGATACCAGGAGGAACACCAATGGCGAAGGCAAGTTACTGGACAGAAGGTGACGCTGAGGCGCGAAAGTGTGGGGAGCAAAC\n++\n+3ABBCCCCCBABGGGGGGGGGGHGGGGGHHHHHHGHGEEGHHGGEG?FEHHFHGGGGGHHHGHHHHHHHGHHGHHHHHHHGGGGGGGHHHHHHGGGGGGGGHHHGHHHHHHHHHHHHHHHHHGHHHHHHHHHGGGCGHHHHHHHHHHHHHHHHFHHGGGGGGGGGGGGGGGGGGFGGGGEDDGFFFFFFFFFFFFFFFFFFFFFFFBFFBAFFFFFEFFFFFFFDFFFFFFF-CFF/B9F?FFECFFFFF\n+@M00967:43:000000000-A3JHG:1:1101:14010:4122 1:N:0:280\n+TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGCAGGTGGTTTCTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGGGTAGCGGGGAAAGGCGTAGAGATATGGAGGAACACCAGTGGCAAAGGCGACTTTCGGGGCTGAAACTGCCCCTGAGGCCCGAAAGGGGGGGGAGGAACCG\n++\n+AAAA1FFA@DAFFGGGGGGGGGHGGGCGHHHHHHHG?EEGHHFGEGGGGGGG0BFEFGHHFHHHHHBHDBGHFHHH1GFHEFEGGGGHHHG@<F?/??C<FCGHHBHHG01FHA0/C<GDF1F11<1FHFCHHAG0<C1F1>1<1>=000/</0./<--9;E..999.--.900;0;09C.AFE-B-9-9B/--;9B--9-;@B/B-@;-@---;9/////--;--;-9---9;----9@==----9;---\n+@M00967:43:000000000-A3JHG:1:1101:10776:4204 1:N:0:280\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAGGAAATCCGATTGCGAAGGCAGCCGGCTAAGCTGCAACTGACATTGCGGCTTCAAAGAGAGGGGATCAAACA\n++\n+11AAAA?DAC1C1E10EFGEEGHCCAA/11A2DEFAFGHHF1AE/AAEEECEBGHHDCGHHGHFFGHB2DFGGEGHHHDFBE//>EEHHF0EEGEHFGHFDGFBF1BBFEG2G<FGG1GD2DF1<FGFFF1FHBFGA/?C/CCA<G.0>A..<000-@.-CF0G00CH000:0CGFG..:A-C/00/.C.A?0.-9A.C.;;A-----9BB/B/FBF://9:BFF/-;-9--//;:/---9--9---9//-\n+@M00967:43:000000000-A3JHG:1:1101:22487:4260 1:N:0:280\n+TACGTAGGGCGCGAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTTGTAGGCGGTTGGTCGCGTCTGCCGTGAAATCCTCTGGCTTAACTGGGGGCGTGCGGTGGGTACGGGCTGACTTGAGTGCGGTAGGGGAGACTGGAACTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAAGAACACCGGTGGCGAAGGCGGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACG\n++\n+BCCCCFFBAFCCGGGGGGGGGGHGGGGGHHHHGGHGGGGGHHHGGHHGHHHHHGGGGGGEH@EFEGFFHHCEEGGHGHHFHFFHHHHFFFHHHHGGGGGGDCGEGGG?GGGDGFCDCHGHGGFGEFGG;DFGGG.-.EFFGGFFFFFFFFFFAFFFFF.@DEFFFBDDCFFBF0FFFFFF?FFFFFFFF=AFFFFCFFEFFF=B/9BFFFFEA>DDFFEFF.AF.;AA0A.B@@-.:AADFFF?B.;->9-\n+@M00967:43:000000000-A3JHG:1:1101:13293:4703 1:N:0:280\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGTTGTTCGGTAAGTCAGCGGTGAAACCTGAGCGCTCAACGTTCAGCCTGCCGTTGAAACTGCCGGGCTTGAGTTCAGCGGCGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCATAGATATCACGAGGAACTCCGATTGCGAAGGCAGCTTGCCATACTGCGACTGACACTGAAGCACGAAGGCGTGGGTATCAAACA\n++\n+BBBBBBBDBFFFGGGGGGGGGGHGGGGGHHHHHHHEFGHHHHHGHGGGGGGGHHHGHHGGFHGHHHHHHGCEEGGHHHHHHHHGGGGGGHGHGGHHHHGHHHGGGFHHHHBGHHCGGGGHGGHHHHHGHGGGGGG-CGGBCGGGGGGBEGAEFGFFADFFFFFFFFFFFFFBFFFFFFAFFFFEFFFFCDFAFFFFFFEFFDFFFFFFFFBFFFFDCFFB/BFFFFEFFFFA.;9?EFAFAC:9FFFFFF.\n+@M00967:43:000000000-A3JHG:1:1101:24357:4866 1:N:0:280\n+TACGTAGGGCGCGAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTTGTAGGCGGTTGGTCGCGTCTGCCGTGAAATCCTCTGGCTTAACTGGGGGCGTGCGGTGGGTACGGGCTGACTTGAGTGCGGTAGGGGAGACTGGAACTCCTGGTGTAGCGGTGGGATGCGCAGATATCAGGAAGAACACCGGTGGCGAAGGCGGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACA\n++\n+?3AAAFFBBFBBGGGCFGGGGGHGGGFFHHHHH3FCGAFFHHHGGHHGGFHHGCF>/EGEGEEEFGGGEFCDFFFHEGHHEH2FHHHCG2DGFHGGCC@DGGGEGGGFBCDGG?GGEHFHFFF9BFBC.DFGGBDFDGFGGFFFFFFBFB;BEFFFFFDFA-99.BFDFAFFFFFFFFEFFFFFFFFFA9@DFFFFADAAFF@CFFFFBFFEB=?:EFBBFAADFBFF/.A@AACABDAA=A-.-9--@@-\n+@M00967:43:000000000-A3JHG:'..b'FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFECFFFF\n+@M00967:43:000000000-A3JHG:1:1101:10073:7632 1:N:0:280\n+TACGTAGGTCCCGAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTCTTTAAGTCTGAAGTTAAAGGCAGTGGCTTAACCATTGTACGCTTTGGAAACTGGAGGACTTGAGTGCAGAAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCGGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGGGGGGAGCAAACCG\n++\n+CCCBCFFCFFFFCGGGGGGGGGHGGGGGHHHHHHHHGGGGHGCGDGGGGGGGGGGEEF3GHFFHFFGFHHHHFFHH4FGF?3?FFHHFFGHFFF4BFFHGAFF2F2FD2BDGB@D<F=FBGFDFH1=GHHGFG.@DDBGE1GGHBHBFB<<0==0-A<:.GHC0;..::.;00000F0CA.C.//;9A-:C?9-9B./.;--;:B90B0;0/00;0:9:09A....;..:9-BD./:--;CF-CD.BB.:;\n+@M00967:43:000000000-A3JHG:1:1101:5170:7771 1:N:0:280\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGTTGTTCGGTAAGTCAGCGGTGAAACCTGAGCGCTCAACGTTCAGCCTGCCGTTGAAACTGCCGGGCTTGAGTTCAGCGGCGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCATAGATATCACGAGGAACTCCGATTGCGAAGGCAGCTTGCCATACTGCGACTGACACTGAAGCACGAAGGCGTGGGTATCAAACA\n++\n+CCCCCCCCCFFFGGGGGGGGGGHGGGGGHHHHHHHGFGHHHHHGHGGGFGGGGHHGHHGG?GGHHHHHHFGGGGHHHHHHHHHGGGGGHGGHHHHHHGHHHHGDGGHHGGHHHHGGGGGHGHHHHHHHGGGGGCGGGGGGG?FGGFGFFGCECFFFFFDFEBFFF0BFFFFFFFFFFFFFFFFFFFFDDFFFFFF;@FE.ADFFFFFFFFF0FFFF=BFFFFFFFFBFFFFFFFDFFFFFDF.9BBBFFF9\n+@M00967:43:000000000-A3JHG:1:1101:18966:7778 1:N:0:280\n+TACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGGGCGCAGACGGTTACTTAAGCAGGATGTGAAATCCCCGGGCTCAACCCGGGAACTGCGTTCTGAACTGGGTGACTCGAGTGTGTCAGAGGGAGGTAGAATTCCACGTGTAGCAGTGAAATGCGTAGAGATGTGGAGGAATACCGATGGCGAAGGCAGCCTCCTGGGACAACACTGACGTTCATGCCCGAAAGCGTGGGTAGCAAACA\n++\n+ABBBAFFB?FBBGGGGGGGGGGHGGGGGHHHHHHHHGGGGHHGGGGGGGGGGHGGGGGHHHHHHHGFHGHHHHHHHHHHHGGGGGGHHHHHG?GGFGGHHHGGGGGHHHHHHHHFFEHHHGHGHHHHHHHHHHGGGGG;CHHHHHHHHGGHHGGGGGGGGGGGGGGGGGGGGGGGGFFFGGGGFFFFFFFFFFFFFFFFFFFFFFFEFBAFFFEFFFFFFFFFFFFFFFFFFFFFFFF;DFFAFFFFFFF.\n+@M00967:43:000000000-A3JHG:1:1101:5494:7973 1:N:0:280\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAACA\n++\n+BBCCCCCCCFFFGGGGGGGGGGHGGGGGHHHHHHHGFGFHHHHGHGGGFGGGHHHHFHHFHHHHHHHHFHHHGHHHHFHHHHGGGGGHHHHGEHGHHHHHHHHHHHHFFHHHHHHHHGHBHHHGHHHHHHHHHGGGDGDCGDGGHHFBFGHGHGHHGGGGFHHHFHHGFCFHFFHHHGGG?EFFFGG?ADDEFGGGADEFADFFFFBFBBFBFFFFFEFFFFFFFFFFFFFF=FFF/;:FFF./;B/BFB.\n+@M00967:43:000000000-A3JHG:1:1101:10246:8076 1:N:0:280\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTTTAGCGGTGAAATGCTTAGATATCACGAGGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAACA\n++\n+BBBBBAADBFFFGGCGGGGFEGFGGGGEHHFHHHGGFGHHHFB1GFGGGGGGFHHHHFHHDFGHGHHHHHHFEFGHGHFHHF?/EEEHHHHGEHGHHHFHHHE3FBDEGHGGHG3BGHHHBGB3FGFFHB2@FGAFG@/D?DGGCB.<<<..</=D-@ECGHFH0CFGCBGFFFHFH:.A9?FG0C9;;..;09-AGGEGDDEB?FFFFFF//BFFFFFF/////9BBAEF99.DD///999.9//99BF.\n+@M00967:43:000000000-A3JHG:1:1101:23931:8157 1:N:0:280\n+TACGTAGGTGGCAAGCGTTGTCCGGATTTACTGGGCGTAAAGGGAGCGTAGGTGGATATTTAAGTGGGATGTGAAATACTCGGGCTTAACCTGGGTGCTGCATTCCAAACTGGATATCTAGAGTGCAGGAGAGGAAAGTAGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAATACCAGTGGCGAAGGCGACTTTCTGGACTGTAACTGACACTGAGGATCGAAAGCGTGGGGAGCAAACA\n++\n+BBBBAFFB54AFFGGGGGGEGGHGGGGGHHFHHHHCEEEEHHHGCEGGGGGG5FF1E5DGHHHHHHGHC@FHBFHH4F@4@FFGGGHHHHHBGHG?E/B?GGHHB4BGHGDGH33B?FG44?F1FDGH0C?GG/GFBG1@>F2FGFFBDDGFFFHHGGDCFHFGHBD.<<.0DGBDGGHD.GB<=G0GFHHC.-C@BE.A?-;.;FFFGFEFAFFF0009BBB9/9B?/9/;AFDD/A9AB?B?B.AFFA.\n+@M00967:43:000000000-A3JHG:1:1101:18269:8162 1:N:0:280\n+TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGCAGGTGGTTTCTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGAGATATGGAGGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTCACTGACGCTGAGGCTCGAAAGCGTGGGTAGCGAACA\n++\n+CDCCCFFCFFCFGGGGGGGGGGHGGGGFHHHHHHGHGGGGHHGGGGGGGGGG?GFGGHHHHHHHFGHHHHHHHHGHHHHHHGGGGEGHHHHGGHGGHGGGHHHHHHHHHHHHHHHGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHGHHHHHGGFGGHHHHHGGGGGHHHHGGGGGGGGGGGGGGGGGGGGGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFBFDFFFFFFFFFFF-\n'
b
diff -r 000000000000 -r bccb5efbc4ee test-data/Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,3 @@
+M00967_43_000000000-A3JHG_1_1101_10776_4204 ambig
+M00967_43_000000000-A3JHG_1_1101_22487_4260 ambig
+M00967_43_000000000-A3JHG_1_1101_23931_8157 ambig
b
diff -r 000000000000 -r bccb5efbc4ee test-data/Mock_S280_L001_R1_001_small.trim.contigs.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.fasta Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,50 @@
+>M00967_43_000000000-A3JHG_1_1101_19936_3208
+TACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG
+>M00967_43_000000000-A3JHG_1_1101_15923_3823
+TACGGAGGGTGCAAGCGTTACCCGGAATCACTGGGCGTAAAGGGCGTGTAGGCGGAAATTTAAGTCTGGTTTTAAAGACCGGGGCTCAACCTCGGGGATGGACTGGATACTGGATTTCTTGACCTCTGGAGAGGTAACTGGAATTCCTGGTGTAGCGGTGGAATGCGTAGATACCAGGAGGAACACCAATGGCGAAGGCAAGTTACTGGACAGAAGGTGACGCTGAGGCGCGAAAGTGTGGGGAGCAAACCGG
+>M00967_43_000000000-A3JHG_1_1101_14010_4122
+TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGCAGGTGGTTTCTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGAGATATGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGTCTGTAACTGACACTGAGGCGCGAAAGCGTGGGGAGCAAACAGG
+>M00967_43_000000000-A3JHG_1_1101_10776_4204
+TACGGAGGATNCGAGGTTATCCGGATTTATTGGGTTTAAAGGGNGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGNGGTGTAGCGGTGAAATGCTTAGATATCACGGGGAANTCCGATTGCGAAGGCAGCCNGCTAAGCNGCAACTGACATTGAGGCTNGAAAGTGTGGGTATCAANCAGG
+>M00967_43_000000000-A3JHG_1_1101_22487_4260
+TACGTAGGGCGCGAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTTGTAGGCGGTTGGTCGCGTCTGCCGTGAAATCCTCTGGCTTAACTGGGGGCGTGCGGTGGGTACGGGCTGACTTGAGTGCGGTAGGGGAGACTGGAACTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAAGAACACCGGTGGCGAAGGCGGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAANGCGTGGGGAGCGAACAGG
+>M00967_43_000000000-A3JHG_1_1101_13293_4703
+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGTTGTTCGGTAAGTCAGCGGTGAAACCTGAGCGCTCAACGTTCAGCCTGCCGTTGAAACTGCCGGGCTTGAGTTCAGCGGCGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCATAGATATCACGAGGAACTCCGATTGCGAAGGCAGCTTGCCATACTGCGACTGACACTGAAGCACGAAGGCGTGGGTATCAAACAGG
+>M00967_43_000000000-A3JHG_1_1101_24357_4866
+TACGTAGGGCGCGAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTTGTAGGCGGTTGGTCGCGTCTGCCGTGAAATCCTCTGGCTTAACTGGGGGCGTGCGGTGGGTACGGGCTGACTTGAGTGCGGTAGGGGAGACTGGAACTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAAGAACACCGGTGGCGAAGGCGGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGG
+>M00967_43_000000000-A3JHG_1_1101_23552_5194
+TACAGAGGGTGCGAGCGTTAATCGGATTTACTGGGCGTAAAGCGTGCGTAGGCGGCTTATTAAGTCGGATGTGAAATCCCCGAGCTTAACTTGGGAATTGCATTCGATACTGGTGAGCTAGAGTATGGGAGAGGATGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGATGGCGAAGGCAGCCATCTGGCCTAATACTGACGCTGAGGTACGAAAGCATGGGGAGCAAACAGG
+>M00967_43_000000000-A3JHG_1_1101_7326_5417
+TACGGAGGGTGCAAGCGTTACCCGGAATCACTGGGCGTAAAGGGCGTGTAGGCGGAAATTTAAGTCTGGTTTTAAAGACCGGGGCTCAACCTCGGGGATGGACTGGATACTGGATTTCTTGACCTCTGGAGAGGTAACTGGAATTCCTGGTGTAGCGGTGGAATGCGTAGATACCAGGAGGAACACCAATGGCGAAGGCAAGTTACTGGACAGAAGGTGACGCTGAGGCGCGAAAGTGTGGGGAGCAAACCTG
+>M00967_43_000000000-A3JHG_1_1101_11148_6457
+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGTTGTTCGGTAAGTCAGCGGTGAAACCTGAGCGCTCAACGTTCAGCCTGCCGTTGAAACTGCCGGGCTTGAGTTCAGCGGCGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCATAGATATCACGAGGAACTCCGATTGCGAAGGCAGCTTGCCATACTGCGACTGACACTGAAGCACGAAGGCGTGGGTATCAAACAGG
+>M00967_43_000000000-A3JHG_1_1101_7079_6722
+TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGG
+>M00967_43_000000000-A3JHG_1_1101_8607_6805
+TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGGGATCAAACAGG
+>M00967_43_000000000-A3JHG_1_1101_15208_7185
+TACGGAGGGTGCAAGCGTTACCCGGAATCACTGGGCGTAAAGGGCGTGTAGGCGGAAATTTAAGTCTGGTTTTAAAGACCGGGGCTCAACCTCGGGGATGGACTGGATACTGGATTTCTTGACCTCTGGAGAGGTAACTGGAATTCCTGGTGTAGCGGTGGAATGCGTAGATACCAGGAGGAACACCAATGGCGAAGGCAAGTTACTGGACAGAAGGTGACGCTGAGGCGCGAAAGTGTGGGGAGCAAACCGG
+>M00967_43_000000000-A3JHG_1_1101_4525_7317
+TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGGGATCAAACAGG
+>M00967_43_000000000-A3JHG_1_1101_9121_7358
+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAACAGG
+>M00967_43_000000000-A3JHG_1_1101_8480_7498
+TACGTAGGTCCCGAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTCTTTAAGTCTGAAGTTAAAGGCAGTGGCTTAACCATTGTACGCTTTGGAAACTGGAGGACTTGAGTGCAGAAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCGGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG
+>M00967_43_000000000-A3JHG_1_1101_11790_7581
+TACGTAGGGCGCGAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTTGTAGGCGGTTGGTCGCGTCTGCCGTGAAATCCTCTGGCTTAACTGGGGGCGTGCGGTGGGTACGGGCTGACTTGAGTGCGGTAGGGGAGACTGGAACTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAAGAACACCGGTGGCGAAGGCGGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGG
+>M00967_43_000000000-A3JHG_1_1101_20566_7622
+TACGGAGGGTGCAAGCGTTACTCGGAATCACTGGGCGTAAAGAGCGCGTAGGCGGGATAGTCAGTCAGGTGTGAAATCCTATGGCTTAACCATAGAACTGCATTTGAAACTACTATTCTAGAGTGTGGGAGAGGTAGGTGGAATTCTTGGTGTAGGGGTAAAATCCGTAGAGATCAAGAGGAATACTCATTGCGAAGGCGACCTGCTGGAACATTACTGACGCTGATTGCGCGAAAGCGTGGGGAGCAAACAGG
+>M00967_43_000000000-A3JHG_1_1101_10073_7632
+TACGTAGGTCCCGAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTCTTTAAGTCTGAAGTTAAAGGCAGTGGCTTAACCATTGTACGCTTTGGAAACTGGAGGACTTGAGTGCAGAAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCGGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACCGG
+>M00967_43_000000000-A3JHG_1_1101_5170_7771
+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGTTGTTCGGTAAGTCAGCGGTGAAACCTGAGCGCTCAACGTTCAGCCTGCCGTTGAAACTGCCGGGCTTGAGTTCAGCGGCGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCATAGATATCACGAGGAACTCCGATTGCGAAGGCAGCTTGCCATACTGCGACTGACACTGAAGCACGAAGGCGTGGGTATCAAACAGG
+>M00967_43_000000000-A3JHG_1_1101_18966_7778
+TACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGGGCGCAGACGGTTACTTAAGCAGGATGTGAAATCCCCGGGCTCAACCCGGGAACTGCGTTCTGAACTGGGTGACTCGAGTGTGTCAGAGGGAGGTAGAATTCCACGTGTAGCAGTGAAATGCGTAGAGATGTGGAGGAATACCGATGGCGAAGGCAGCCTCCTGGGACAACACTGACGTTCATGCCCGAAAGCGTGGGTAGCAAACAGG
+>M00967_43_000000000-A3JHG_1_1101_5494_7973
+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAACAGG
+>M00967_43_000000000-A3JHG_1_1101_10246_8076
+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAGGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAACAGG
+>M00967_43_000000000-A3JHG_1_1101_23931_8157
+TACGTAGGTGGCAAGCGTTGTCCGGATTTACTGGGCGTAAAGGGAGCGTAGGTGGATATTTAAGTGGGATGTGAAATACTCGGGCTTAACCTGGGTGCTGCATTCCAAACTGGANATCTAGAGTGCAGGAGAGGAAAGTAGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAATACCAGTGGCGAAGGCGACTTTCTGGACTGTAACTGACACTGAGGCTCGAAAGCGTGGGGAGCAAACAGG
+>M00967_43_000000000-A3JHG_1_1101_18269_8162
+TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGCAGGTGGTTTCTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGAGATATGGAGGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTCACTGACGCTGAGGCTCGAAAGCGTGGGTAGCGAACAGG
b
diff -r 000000000000 -r bccb5efbc4ee test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.Mock_S280_L001_R1_001_small.trim.contigs.good.groups
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.Mock_S280_L001_R1_001_small.trim.contigs.good.groups Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,20 @@
+M00967_43_000000000-A3JHG_1_1101_19936_3208 testgroup
+M00967_43_000000000-A3JHG_1_1101_15923_3823 testgroup
+M00967_43_000000000-A3JHG_1_1101_14010_4122 testgroup
+M00967_43_000000000-A3JHG_1_1101_13293_4703 testgroup
+M00967_43_000000000-A3JHG_1_1101_24357_4866 testgroup
+M00967_43_000000000-A3JHG_1_1101_23552_5194 testgroup
+M00967_43_000000000-A3JHG_1_1101_7326_5417 testgroup
+M00967_43_000000000-A3JHG_1_1101_11148_6457 testgroup
+M00967_43_000000000-A3JHG_1_1101_7079_6722 testgroup
+M00967_43_000000000-A3JHG_1_1101_8607_6805 testgroup
+M00967_43_000000000-A3JHG_1_1101_19936_3208 testgroup2
+M00967_43_000000000-A3JHG_1_1101_15923_3823 testgroup2
+M00967_43_000000000-A3JHG_1_1101_14010_4122 testgroup2
+M00967_43_000000000-A3JHG_1_1101_13293_4703 testgroup2
+M00967_43_000000000-A3JHG_1_1101_24357_4866 testgroup2
+M00967_43_000000000-A3JHG_1_1101_23552_5194 testgroup2
+M00967_43_000000000-A3JHG_1_1101_7326_5417 testgroup2
+M00967_43_000000000-A3JHG_1_1101_11148_6457 testgroup2
+M00967_43_000000000-A3JHG_1_1101_7079_6722 testgroup2
+M00967_43_000000000-A3JHG_1_1101_8607_6805 testgroup2
b
diff -r 000000000000 -r bccb5efbc4ee test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.align.report
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.align.report Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,23 @@
+QueryName QueryLength TemplateName TemplateLength SearchMethod SearchScore AlignmentMethod QueryStart QueryEnd TemplateStart TemplateEnd PairwiseAlignmentLength GapsInQuery GapsInTemplate LongestInsert SimBtwnQuery&Template
+M00967_43_000000000-A3JHG_1_1101_19936_3208 253 E.faecalis.1 541 kmer 100.00 needleman 1 253 177 429 253 0 0 0 100.00
+M00967_43_000000000-A3JHG_1_1101_15923_3823 253 D.radiodurans.1 524 kmer 100.00 needleman 1 253 164 416 253 0 0 0 100.00
+M00967_43_000000000-A3JHG_1_1101_14010_4122 253 B.cereus.1 542 kmer 96.75 needleman 1 253 178 430 253 0 0 0 99.60
+M00967_43_000000000-A3JHG_1_1101_13293_4703 253 P.gingivalis.1 534 kmer 98.78 needleman 1 253 172 424 253 0 0 0 100.00
+M00967_43_000000000-A3JHG_1_1101_24357_4866 253 A.odontolyticus.1 534 kmer 99.59 needleman 1 253 170 422 253 0 0 0 100.00
+M00967_43_000000000-A3JHG_1_1101_23552_5194 253 A.baumannii.1 541 kmer 100.00 needleman 1 253 178 430 253 0 0 0 100.00
+M00967_43_000000000-A3JHG_1_1101_7326_5417 253 D.radiodurans.1 524 kmer 99.19 needleman 1 253 164 416 253 0 0 0 99.60
+M00967_43_000000000-A3JHG_1_1101_11148_6457 253 P.gingivalis.1 534 kmer 98.78 needleman 1 253 172 424 253 0 0 0 100.00
+M00967_43_000000000-A3JHG_1_1101_7079_6722 253 E.coli.1 540 kmer 100.00 needleman 1 253 177 429 253 0 0 0 100.00
+M00967_43_000000000-A3JHG_1_1101_8607_6805 253 S.aureus.1 541 kmer 99.59 needleman 1 253 177 429 253 0 0 0 100.00
+M00967_43_000000000-A3JHG_1_1101_15208_7185 253 D.radiodurans.1 524 kmer 100.00 needleman 1 253 164 416 253 0 0 0 100.00
+M00967_43_000000000-A3JHG_1_1101_4525_7317 253 S.aureus.1 541 kmer 99.59 needleman 1 253 177 429 253 0 0 0 100.00
+M00967_43_000000000-A3JHG_1_1101_9121_7358 253 B.vulgatus.1 532 kmer 99.19 needleman 1 253 172 424 253 0 0 0 100.00
+M00967_43_000000000-A3JHG_1_1101_8480_7498 252 S.agalactiae.1 541 kmer 99.59 needleman 1 252 178 429 252 0 0 0 100.00
+M00967_43_000000000-A3JHG_1_1101_11790_7581 253 A.odontolyticus.1 534 kmer 99.59 needleman 1 253 170 422 253 0 0 0 100.00
+M00967_43_000000000-A3JHG_1_1101_20566_7622 254 H.pylori.1 517 kmer 100.00 needleman 1 254 152 405 254 0 0 0 100.00
+M00967_43_000000000-A3JHG_1_1101_10073_7632 252 S.agalactiae.1 541 kmer 98.37 needleman 1 252 178 429 252 0 0 0 99.60
+M00967_43_000000000-A3JHG_1_1101_5170_7771 253 P.gingivalis.1 534 kmer 98.78 needleman 1 253 172 424 253 0 0 0 100.00
+M00967_43_000000000-A3JHG_1_1101_18966_7778 253 N.meningitidis.1 540 kmer 100.00 needleman 1 253 177 429 253 0 0 0 100.00
+M00967_43_000000000-A3JHG_1_1101_5494_7973 253 B.vulgatus.1 532 kmer 99.19 needleman 1 253 172 424 253 0 0 0 100.00
+M00967_43_000000000-A3JHG_1_1101_10246_8076 253 B.vulgatus.7 532 kmer 99.19 needleman 1 253 172 424 253 0 0 0 100.00
+M00967_43_000000000-A3JHG_1_1101_18269_8162 253 B.cereus.1 542 kmer 80.49 needleman 1 253 178 430 253 0 0 0 96.84
b
diff -r 000000000000 -r bccb5efbc4ee test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.align_head
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.align_head Fri May 19 05:47:34 2017 -0400
b
b'@@ -0,0 +1,20 @@\n+>M00967_43_000000000-A3JHG_1_1101_19936_3208\n+...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................'..b'..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................\n'
b
diff -r 000000000000 -r bccb5efbc4ee test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.align_head.names
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.align_head.names Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,10 @@
+M00967_43_000000000-A3JHG_1_1101_19936_3208 M00967_43_000000000-A3JHG_1_1101_19936_3208
+M00967_43_000000000-A3JHG_1_1101_15923_3823 M00967_43_000000000-A3JHG_1_1101_15923_3823
+M00967_43_000000000-A3JHG_1_1101_14010_4122 M00967_43_000000000-A3JHG_1_1101_14010_4122
+M00967_43_000000000-A3JHG_1_1101_13293_4703 M00967_43_000000000-A3JHG_1_1101_13293_4703
+M00967_43_000000000-A3JHG_1_1101_24357_4866 M00967_43_000000000-A3JHG_1_1101_24357_4866
+M00967_43_000000000-A3JHG_1_1101_23552_5194 M00967_43_000000000-A3JHG_1_1101_23552_5194
+M00967_43_000000000-A3JHG_1_1101_7326_5417  M00967_43_000000000-A3JHG_1_1101_7326_5417
+M00967_43_000000000-A3JHG_1_1101_11148_6457 M00967_43_000000000-A3JHG_1_1101_11148_6457
+M00967_43_000000000-A3JHG_1_1101_7079_6722  M00967_43_000000000-A3JHG_1_1101_7079_6722
+M00967_43_000000000-A3JHG_1_1101_8607_6805  M00967_43_000000000-A3JHG_1_1101_8607_6805
b
diff -r 000000000000 -r bccb5efbc4ee test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.align_head_withchimera
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.align_head_withchimera Fri May 19 05:47:34 2017 -0400
b
b'@@ -0,0 +1,6 @@\n+>M00967_43_000000000-A3JHG_1_1101_11148_6457\n+................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................'..b'..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................\n'
b
diff -r 000000000000 -r bccb5efbc4ee test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.bellerophon.accnos
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.bellerophon.accnos Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,12 @@
+M00967_43_000000000-A3JHG_1_1101_10073_7632
+M00967_43_000000000-A3JHG_1_1101_8480_7498
+M00967_43_000000000-A3JHG_1_1101_23552_5194
+M00967_43_000000000-A3JHG_1_1101_5170_7771
+M00967_43_000000000-A3JHG_1_1101_13293_4703
+M00967_43_000000000-A3JHG_1_1101_11148_6457
+M00967_43_000000000-A3JHG_1_1101_24357_4866
+M00967_43_000000000-A3JHG_1_1101_11790_7581
+M00967_43_000000000-A3JHG_1_1101_15923_3823
+M00967_43_000000000-A3JHG_1_1101_7326_5417
+M00967_43_000000000-A3JHG_1_1101_15208_7185
+M00967_43_000000000-A3JHG_1_1101_7079_6722
b
diff -r 000000000000 -r bccb5efbc4ee test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.ccode.accnos
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.ccode.accnos Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,1 @@
+M00967_43_000000000-A3JHG_1_1101_7326_5417
b
diff -r 000000000000 -r bccb5efbc4ee test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.chimeracheck.chimeras
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.chimeracheck.chimeras Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,20 @@
+M00967_43_000000000-A3JHG_1_1101_19936_3208
+IS scores:  -19 -29 -39 -49 -59 -67 -77 -87 -97 -107 -117 -127 -136 -146 -156 -166 -173 -173 -173 -173 -174
+M00967_43_000000000-A3JHG_1_1101_15923_3823
+IS scores:  -19 -29 -39 -49 -59 -69 -79 -89 -99 -107 -117 -126 -136 -146 -156 -160 -160 -160 -160 -160 -160
+M00967_43_000000000-A3JHG_1_1101_14010_4122
+IS scores:  -19 -29 -39 -49 -60 -68 -78 -88 -98 -108 -118 -128 -138 -145 -155 -165 -173 -173 -168 -165 -165
+M00967_43_000000000-A3JHG_1_1101_13293_4703
+IS scores:  -19 -29 -39 -49 -59 -65 -74 -84 -93 -103 -113 -123 -133 -143 -153 -163 -165 -164 -163 -163 -163
+M00967_43_000000000-A3JHG_1_1101_24357_4866
+IS scores:  -19 -29 -39 -49 -59 -69 -79 -89 -98 -107 -117 -126 -136 -146 -156 -166 -166 -166 -166 -166 -166
+M00967_43_000000000-A3JHG_1_1101_23552_5194
+IS scores:  -19 -29 -39 -48 -58 -68 -76 -86 -96 -106 -116 -126 -136 -146 -156 -165 -173 -173 -172 -172 -173
+M00967_43_000000000-A3JHG_1_1101_7326_5417
+IS scores:  -19 -29 -39 -49 -59 -69 -79 -89 -99 -107 -117 -126 -136 -146 -156 -160 -160 -160 -160 -160 -160
+M00967_43_000000000-A3JHG_1_1101_11148_6457
+IS scores:  -19 -29 -39 -49 -59 -65 -74 -84 -93 -103 -113 -123 -133 -143 -153 -163 -165 -164 -163 -163 -163
+M00967_43_000000000-A3JHG_1_1101_7079_6722
+IS scores:  -19 -29 -39 -49 -59 -69 -78 -88 -98 -108 -118 -127 -137 -147 -157 -167 -173 -173 -173 -173 -173
+M00967_43_000000000-A3JHG_1_1101_8607_6805
+IS scores:  -19 -29 -39 -49 -59 -67 -76 -86 -96 -106 -116 -126 -136 -143 -153 -163 -170 -170 -170 -170 -169
b
diff -r 000000000000 -r bccb5efbc4ee test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.chop.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.chop.fasta Fri May 19 05:47:34 2017 -0400
b
b'@@ -0,0 +1,4 @@\n+>M00967_43_000000000-A3JHG_1_1101_19936_3208\n+................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................'..b'........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................T-------AC---GG-AG-GGT\n'
b
diff -r 000000000000 -r bccb5efbc4ee test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.denovo.uchime.chimeras
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.denovo.uchime.chimeras Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,10 @@
+Score Query ParentA ParentB IdQM IdQA IdQB IdAB IdQT LY LN LA RY RN RA Div YN
+0.0000 M00967_43_000000000-A3JHG_1_1101_13293_4703/ab=2/ * * * * * * * * * * * * * * N
+0.0000 M00967_43_000000000-A3JHG_1_1101_19936_3208/ab=1/ * * * * * * * * * * * * * * N
+0.0000 M00967_43_000000000-A3JHG_1_1101_8607_6805/ab=1/ * * * * * * * * * * * * * * N
+0.0000 M00967_43_000000000-A3JHG_1_1101_14010_4122/ab=1/ * * * * * * * * * * * * * * N
+0.0000 M00967_43_000000000-A3JHG_1_1101_24357_4866/ab=1/ * * * * * * * * * * * * * * N
+0.0000 M00967_43_000000000-A3JHG_1_1101_7326_5417/ab=1/ * * * * * * * * * * * * * * N
+0.0000 M00967_43_000000000-A3JHG_1_1101_15923_3823/ab=1/ * * * * * * * * * * * * * * N
+0.0000 M00967_43_000000000-A3JHG_1_1101_7079_6722/ab=1/ * * * * * * * * * * * * * * N
+0.0000 M00967_43_000000000-A3JHG_1_1101_23552_5194/ab=1/ * * * * * * * * * * * * * * N
b
diff -r 000000000000 -r bccb5efbc4ee test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.error.summary
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.error.summary Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,4 @@
+query reference weight AA AT AG AC TA TT TG TC GA GT GG GC CA CT CG CC NA NT NG NC Ai Ti Gi Ci Ni dA dT dG dC insertions deletions substitutions ambig matches mismatches total error numparents
+M00967_43_000000000-A3JHG_1_1101_11148_6457 P.gingivalis.1 1 60 0 0 0 0 56 0 0 0 0 85 0 0 0 0 52 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 253 0 253 0.000000 1
+M00967_43_000000000-A3JHG_1_1101_7079_6722 E.coli.1 1 64 0 0 0 0 47 0 0 0 0 91 0 0 0 0 51 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 253 0 253 0.000000 1
+M00967_43_000000000-A3JHG_1_1101_18269_8162 B.cereus.1 1 65 0 0 0 0 53 0 0 0 0 89 0 0 0 0 46 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 253 0 253 0.000000 2
b
diff -r 000000000000 -r bccb5efbc4ee test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.fasta Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,44 @@
+>M00967_43_000000000-A3JHG_1_1101_19936_3208
+TACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG
+>M00967_43_000000000-A3JHG_1_1101_15923_3823
+TACGGAGGGTGCAAGCGTTACCCGGAATCACTGGGCGTAAAGGGCGTGTAGGCGGAAATTTAAGTCTGGTTTTAAAGACCGGGGCTCAACCTCGGGGATGGACTGGATACTGGATTTCTTGACCTCTGGAGAGGTAACTGGAATTCCTGGTGTAGCGGTGGAATGCGTAGATACCAGGAGGAACACCAATGGCGAAGGCAAGTTACTGGACAGAAGGTGACGCTGAGGCGCGAAAGTGTGGGGAGCAAACCGG
+>M00967_43_000000000-A3JHG_1_1101_14010_4122
+TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGCAGGTGGTTTCTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGAGATATGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGTCTGTAACTGACACTGAGGCGCGAAAGCGTGGGGAGCAAACAGG
+>M00967_43_000000000-A3JHG_1_1101_13293_4703
+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGTTGTTCGGTAAGTCAGCGGTGAAACCTGAGCGCTCAACGTTCAGCCTGCCGTTGAAACTGCCGGGCTTGAGTTCAGCGGCGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCATAGATATCACGAGGAACTCCGATTGCGAAGGCAGCTTGCCATACTGCGACTGACACTGAAGCACGAAGGCGTGGGTATCAAACAGG
+>M00967_43_000000000-A3JHG_1_1101_24357_4866
+TACGTAGGGCGCGAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTTGTAGGCGGTTGGTCGCGTCTGCCGTGAAATCCTCTGGCTTAACTGGGGGCGTGCGGTGGGTACGGGCTGACTTGAGTGCGGTAGGGGAGACTGGAACTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAAGAACACCGGTGGCGAAGGCGGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGG
+>M00967_43_000000000-A3JHG_1_1101_23552_5194
+TACAGAGGGTGCGAGCGTTAATCGGATTTACTGGGCGTAAAGCGTGCGTAGGCGGCTTATTAAGTCGGATGTGAAATCCCCGAGCTTAACTTGGGAATTGCATTCGATACTGGTGAGCTAGAGTATGGGAGAGGATGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGATGGCGAAGGCAGCCATCTGGCCTAATACTGACGCTGAGGTACGAAAGCATGGGGAGCAAACAGG
+>M00967_43_000000000-A3JHG_1_1101_7326_5417
+TACGGAGGGTGCAAGCGTTACCCGGAATCACTGGGCGTAAAGGGCGTGTAGGCGGAAATTTAAGTCTGGTTTTAAAGACCGGGGCTCAACCTCGGGGATGGACTGGATACTGGATTTCTTGACCTCTGGAGAGGTAACTGGAATTCCTGGTGTAGCGGTGGAATGCGTAGATACCAGGAGGAACACCAATGGCGAAGGCAAGTTACTGGACAGAAGGTGACGCTGAGGCGCGAAAGTGTGGGGAGCAAACCTG
+>M00967_43_000000000-A3JHG_1_1101_11148_6457
+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGTTGTTCGGTAAGTCAGCGGTGAAACCTGAGCGCTCAACGTTCAGCCTGCCGTTGAAACTGCCGGGCTTGAGTTCAGCGGCGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCATAGATATCACGAGGAACTCCGATTGCGAAGGCAGCTTGCCATACTGCGACTGACACTGAAGCACGAAGGCGTGGGTATCAAACAGG
+>M00967_43_000000000-A3JHG_1_1101_7079_6722
+TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGG
+>M00967_43_000000000-A3JHG_1_1101_8607_6805
+TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGGGATCAAACAGG
+>M00967_43_000000000-A3JHG_1_1101_15208_7185
+TACGGAGGGTGCAAGCGTTACCCGGAATCACTGGGCGTAAAGGGCGTGTAGGCGGAAATTTAAGTCTGGTTTTAAAGACCGGGGCTCAACCTCGGGGATGGACTGGATACTGGATTTCTTGACCTCTGGAGAGGTAACTGGAATTCCTGGTGTAGCGGTGGAATGCGTAGATACCAGGAGGAACACCAATGGCGAAGGCAAGTTACTGGACAGAAGGTGACGCTGAGGCGCGAAAGTGTGGGGAGCAAACCGG
+>M00967_43_000000000-A3JHG_1_1101_4525_7317
+TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGGGATCAAACAGG
+>M00967_43_000000000-A3JHG_1_1101_9121_7358
+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAACAGG
+>M00967_43_000000000-A3JHG_1_1101_8480_7498
+TACGTAGGTCCCGAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTCTTTAAGTCTGAAGTTAAAGGCAGTGGCTTAACCATTGTACGCTTTGGAAACTGGAGGACTTGAGTGCAGAAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCGGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG
+>M00967_43_000000000-A3JHG_1_1101_11790_7581
+TACGTAGGGCGCGAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTTGTAGGCGGTTGGTCGCGTCTGCCGTGAAATCCTCTGGCTTAACTGGGGGCGTGCGGTGGGTACGGGCTGACTTGAGTGCGGTAGGGGAGACTGGAACTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAAGAACACCGGTGGCGAAGGCGGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGG
+>M00967_43_000000000-A3JHG_1_1101_20566_7622
+TACGGAGGGTGCAAGCGTTACTCGGAATCACTGGGCGTAAAGAGCGCGTAGGCGGGATAGTCAGTCAGGTGTGAAATCCTATGGCTTAACCATAGAACTGCATTTGAAACTACTATTCTAGAGTGTGGGAGAGGTAGGTGGAATTCTTGGTGTAGGGGTAAAATCCGTAGAGATCAAGAGGAATACTCATTGCGAAGGCGACCTGCTGGAACATTACTGACGCTGATTGCGCGAAAGCGTGGGGAGCAAACAGG
+>M00967_43_000000000-A3JHG_1_1101_10073_7632
+TACGTAGGTCCCGAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTCTTTAAGTCTGAAGTTAAAGGCAGTGGCTTAACCATTGTACGCTTTGGAAACTGGAGGACTTGAGTGCAGAAGGGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCGGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACCGG
+>M00967_43_000000000-A3JHG_1_1101_5170_7771
+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGTTGTTCGGTAAGTCAGCGGTGAAACCTGAGCGCTCAACGTTCAGCCTGCCGTTGAAACTGCCGGGCTTGAGTTCAGCGGCGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCATAGATATCACGAGGAACTCCGATTGCGAAGGCAGCTTGCCATACTGCGACTGACACTGAAGCACGAAGGCGTGGGTATCAAACAGG
+>M00967_43_000000000-A3JHG_1_1101_18966_7778
+TACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGGGCGCAGACGGTTACTTAAGCAGGATGTGAAATCCCCGGGCTCAACCCGGGAACTGCGTTCTGAACTGGGTGACTCGAGTGTGTCAGAGGGAGGTAGAATTCCACGTGTAGCAGTGAAATGCGTAGAGATGTGGAGGAATACCGATGGCGAAGGCAGCCTCCTGGGACAACACTGACGTTCATGCCCGAAAGCGTGGGTAGCAAACAGG
+>M00967_43_000000000-A3JHG_1_1101_5494_7973
+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAACAGG
+>M00967_43_000000000-A3JHG_1_1101_10246_8076
+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGATGGATGTTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGATACTGGATATCTTGAGTGCAGTTGAGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAGGAACTCCGATTGCGAAGGCAGCCTGCTAAGCTGCAACTGACATTGAGGCTCGAAAGTGTGGGTATCAAACAGG
+>M00967_43_000000000-A3JHG_1_1101_18269_8162
+TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGCAGGTGGTTTCTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGAGATATGGAGGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTCACTGACGCTGAGGCTCGAAAGCGTGGGTAGCGAACAGG
b
diff -r 000000000000 -r bccb5efbc4ee test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.names
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.names Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,9 @@
+M00967_43_000000000-A3JHG_1_1101_19936_3208 M00967_43_000000000-A3JHG_1_1101_19936_3208
+M00967_43_000000000-A3JHG_1_1101_15923_3823 M00967_43_000000000-A3JHG_1_1101_15923_3823
+M00967_43_000000000-A3JHG_1_1101_14010_4122 M00967_43_000000000-A3JHG_1_1101_14010_4122
+M00967_43_000000000-A3JHG_1_1101_13293_4703 M00967_43_000000000-A3JHG_1_1101_13293_4703,M00967_43_000000000-A3JHG_1_1101_11148_6457
+M00967_43_000000000-A3JHG_1_1101_24357_4866 M00967_43_000000000-A3JHG_1_1101_24357_4866
+M00967_43_000000000-A3JHG_1_1101_23552_5194 M00967_43_000000000-A3JHG_1_1101_23552_5194
+M00967_43_000000000-A3JHG_1_1101_7326_5417 M00967_43_000000000-A3JHG_1_1101_7326_5417
+M00967_43_000000000-A3JHG_1_1101_7079_6722 M00967_43_000000000-A3JHG_1_1101_7079_6722
+M00967_43_000000000-A3JHG_1_1101_8607_6805 M00967_43_000000000-A3JHG_1_1101_8607_6805
b
diff -r 000000000000 -r bccb5efbc4ee test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.names_tiny
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.names_tiny Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,3 @@
+M00967_43_000000000-A3JHG_1_1101_14010_4122 M00967_43_000000000-A3JHG_1_1101_14010_4122
+M00967_43_000000000-A3JHG_1_1101_13293_4703 M00967_43_000000000-A3JHG_1_1101_13293_4703,M00967_43_000000000-A3JHG_1_1101_11148_6457
+
b
diff -r 000000000000 -r bccb5efbc4ee test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.ng.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.ng.fasta Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,20 @@
+>M00967_43_000000000-A3JHG_1_1101_19936_3208
+TACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGGGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAGGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG
+>M00967_43_000000000-A3JHG_1_1101_15923_3823
+TACGGAGGGTGCAAGCGTTACCCGGAATCACTGGGCGTAAAGGGCGTGTAGGCGGAAATTTAAGTCTGGTTTTAAAGACCGGGGCTCAACCTCGGGGATGGACTGGATACTGGATTTCTTGACCTCTGGAGAGGTAACTGGAATTCCTGGTGTAGCGGTGGAATGCGTAGATACCAGGAGGAACACCAATGGCGAAGGCAAGTTACTGGACAGAAGGTGACGCTGAGGCGCGAAAGTGTGGGGAGCAAACCGG
+>M00967_43_000000000-A3JHG_1_1101_14010_4122
+TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGCAGGTGGTTTCTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGAGATATGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGTCTGTAACTGACACTGAGGCGCGAAAGCGTGGGGAGCAAACAGG
+>M00967_43_000000000-A3JHG_1_1101_13293_4703
+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGTTGTTCGGTAAGTCAGCGGTGAAACCTGAGCGCTCAACGTTCAGCCTGCCGTTGAAACTGCCGGGCTTGAGTTCAGCGGCGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCATAGATATCACGAGGAACTCCGATTGCGAAGGCAGCTTGCCATACTGCGACTGACACTGAAGCACGAAGGCGTGGGTATCAAACAGG
+>M00967_43_000000000-A3JHG_1_1101_24357_4866
+TACGTAGGGCGCGAGCGTTGTCCGGAATTATTGGGCGTAAAGGGCTTGTAGGCGGTTGGTCGCGTCTGCCGTGAAATCCTCTGGCTTAACTGGGGGCGTGCGGTGGGTACGGGCTGACTTGAGTGCGGTAGGGGAGACTGGAACTCCTGGTGTAGCGGTGGAATGCGCAGATATCAGGAAGAACACCGGTGGCGAAGGCGGGTCTCTGGGCCGTTACTGACGCTGAGGAGCGAAAGCGTGGGGAGCGAACAGG
+>M00967_43_000000000-A3JHG_1_1101_23552_5194
+TACAGAGGGTGCGAGCGTTAATCGGATTTACTGGGCGTAAAGCGTGCGTAGGCGGCTTATTAAGTCGGATGTGAAATCCCCGAGCTTAACTTGGGAATTGCATTCGATACTGGTGAGCTAGAGTATGGGAGAGGATGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGATGGCGAAGGCAGCCATCTGGCCTAATACTGACGCTGAGGTACGAAAGCATGGGGAGCAAACAGG
+>M00967_43_000000000-A3JHG_1_1101_7326_5417
+TACGGAGGGTGCAAGCGTTACCCGGAATCACTGGGCGTAAAGGGCGTGTAGGCGGAAATTTAAGTCTGGTTTTAAAGACCGGGGCTCAACCTCGGGGATGGACTGGATACTGGATTTCTTGACCTCTGGAGAGGTAACTGGAATTCCTGGTGTAGCGGTGGAATGCGTAGATACCAGGAGGAACACCAATGGCGAAGGCAAGTTACTGGACAGAAGGTGACGCTGAGGCGCGAAAGTGTGGGGAGCAAACCTG
+>M00967_43_000000000-A3JHG_1_1101_11148_6457
+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGTTGTTCGGTAAGTCAGCGGTGAAACCTGAGCGCTCAACGTTCAGCCTGCCGTTGAAACTGCCGGGCTTGAGTTCAGCGGCGGCAGGCGGAATTCGTGGTGTAGCGGTGAAATGCATAGATATCACGAGGAACTCCGATTGCGAAGGCAGCTTGCCATACTGCGACTGACACTGAAGCACGAAGGCGTGGGTATCAAACAGG
+>M00967_43_000000000-A3JHG_1_1101_7079_6722
+TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGG
+>M00967_43_000000000-A3JHG_1_1101_8607_6805
+TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTTTTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGAAAACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTGAAATGCGCAGAGATATGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTAACTGACGCTGATGTGCGAAAGCGTGGGGATCAAACAGG
b
diff -r 000000000000 -r bccb5efbc4ee test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.pintail.accnos
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.pintail.accnos Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,4 @@
+M00967_43_000000000-A3JHG_1_1101_15923_3823
+M00967_43_000000000-A3JHG_1_1101_13293_4703
+M00967_43_000000000-A3JHG_1_1101_24357_4866
+M00967_43_000000000-A3JHG_1_1101_11148_6457
b
diff -r 000000000000 -r bccb5efbc4ee test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.rc.align_head
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.rc.align_head Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,20 @@
+>M00967_43_000000000-A3JHG_1_1101_19936_3208
+CCTGTTTGCTCCCCACGCTTTCGAGCCTCAGCGTCAGTTACAGACCAGAGAGCCGCCTTCGCCACTGGTGTTCCTCCATATATCTACGCATTTCACCGCTACACATGGAATTCCACTCTCCTCTTCTGCACTCAAGTCTCCCAGTTTCCAATGACCCTCCCCGGTTGAGCCGGGGGCTTTCACATCAGACTTAAGAAACCGCCTGCGCTCGCTTTACGCCCAATAAATCCGGACAACGCTTGCCACCTACGTA
+>M00967_43_000000000-A3JHG_1_1101_15923_3823
+CCGGTTTGCTCCCCACACTTTCGCGCCTCAGCGTCACCTTCTGTCCAGTAACTTGCCTTCGCCATTGGTGTTCCTCCTGGTATCTACGCATTCCACCGCTACACCAGGAATTCCAGTTACCTCTCCAGAGGTCAAGAAATCCAGTATCCAGTCCATCCCCGAGGTTGAGCCCCGGTCTTTAAAACCAGACTTAAATTTCCGCCTACACGCCCTTTACGCCCAGTGATTCCGGGTAACGCTTGCACCCTCCGTA
+>M00967_43_000000000-A3JHG_1_1101_14010_4122
+CCTGTTTGCTCCCCACGCTTTCGCGCCTCAGTGTCAGTTACAGACCAGAAAGCCGCCTTCGCCACTGGTGTTCCTCCATATCTCTACGCATTTCACCGCTACACATGGAATTCCACTTTCCTCTTCTGCACTCAAGTCTCCCAGTTTCCAATGACCCTCCACGGTTGAGCCGTGGGCTTTCACATCAGACTTAAGAAACCACCTGCGCGCGCTTTACGCCCAATAATTCCGGATAACGCTTGCCACCTACGTA
+>M00967_43_000000000-A3JHG_1_1101_13293_4703
+CCTGTTTGATACCCACGCCTTCGTGCTTCAGTGTCAGTCGCAGTATGGCAAGCTGCCTTCGCAATCGGAGTTCCTCGTGATATCTATGCATTTCACCGCTACACCACGAATTCCGCCTGCCGCCGCTGAACTCAAGCCCGGCAGTTTCAACGGCAGGCTGAACGTTGAGCGCTCAGGTTTCACCGCTGACTTACCGAACAACCTACGCACCCTTTAAACCCAATAAATCCGGATAACGCTCGCATCCTCCGTA
+>M00967_43_000000000-A3JHG_1_1101_24357_4866
+CCTGTTCGCTCCCCACGCTTTCGCTCCTCAGCGTCAGTAACGGCCCAGAGACCCGCCTTCGCCACCGGTGTTCTTCCTGATATCTGCGCATTCCACCGCTACACCAGGAGTTCCAGTCTCCCCTACCGCACTCAAGTCAGCCCGTACCCACCGCACGCCCCCAGTTAAGCCAGAGGATTTCACGGCAGACGCGACCAACCGCCTACAAGCCCTTTACGCCCAATAATTCCGGACAACGCTCGCGCCCTACGTA
+>M00967_43_000000000-A3JHG_1_1101_23552_5194
+CCTGTTTGCTCCCCATGCTTTCGTACCTCAGCGTCAGTATTAGGCCAGATGGCTGCCTTCGCCATCGGTATTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGAATTCTACCATCCTCTCCCATACTCTAGCTCACCAGTATCGAATGCAATTCCCAAGTTAAGCTCGGGGATTTCACATCCGACTTAATAAGCCGCCTACGCACGCTTTACGCCCAGTAAATCCGATTAACGCTCGCACCCTCTGTA
+>M00967_43_000000000-A3JHG_1_1101_7326_5417
+CAGGTTTGCTCCCCACACTTTCGCGCCTCAGCGTCACCTTCTGTCCAGTAACTTGCCTTCGCCATTGGTGTTCCTCCTGGTATCTACGCATTCCACCGCTACACCAGGAATTCCAGTTACCTCTCCAGAGGTCAAGAAATCCAGTATCCAGTCCATCCCCGAGGTTGAGCCCCGGTCTTTAAAACCAGACTTAAATTTCCGCCTACACGCCCTTTACGCCCAGTGATTCCGGGTAACGCTTGCACCCTCCGTA
+>M00967_43_000000000-A3JHG_1_1101_11148_6457
+CCTGTTTGATACCCACGCCTTCGTGCTTCAGTGTCAGTCGCAGTATGGCAAGCTGCCTTCGCAATCGGAGTTCCTCGTGATATCTATGCATTTCACCGCTACACCACGAATTCCGCCTGCCGCCGCTGAACTCAAGCCCGGCAGTTTCAACGGCAGGCTGAACGTTGAGCGCTCAGGTTTCACCGCTGACTTACCGAACAACCTACGCACCCTTTAAACCCAATAAATCCGGATAACGCTCGCATCCTCCGTA
+>M00967_43_000000000-A3JHG_1_1101_7079_6722
+CCTGTTTGCTCCCCACGCTTTCGCACCTGAGCGTCAGTCTTCGTCCAGGGGGCCGCCTTCGCCACCGGTATTCCTCCAGATCTCTACGCATTTCACCGCTACACCTGGAATTCTACCCCCCTCTACGAGACTCAAGCTTGCCAGTATCAGATGCAGTTCCCAGGTTGAGCCCGGGGATTTCACATCTGACTTAACAAACCGCCTGCGTGCGCTTTACGCCCAGTAATTCCGATTAACGCTTGCACCCTCCGTA
+>M00967_43_000000000-A3JHG_1_1101_8607_6805
+CCTGTTTGATCCCCACGCTTTCGCACATCAGCGTCAGTTACAGACCAGAAAGTCGCCTTCGCCACTGGTGTTCCTCCATATCTCTGCGCATTTCACCGCTACACATGGAATTCCACTTTCCTCTTCTGCACTCAAGTTTTCCAGTTTCCAATGACCCTCCACGGTTGAGCCGTGGGCTTTCACATCAGACTTAAAAAACCGCCTACGCGCGCTTTACGCCCAATAATTCCGGATAACGCTTGCCACCTACGTA
b
diff -r 000000000000 -r bccb5efbc4ee test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.accnos
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.accnos Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,1 @@
+M00967_43_000000000-A3JHG_1_1101_18269_8162
b
diff -r 000000000000 -r bccb5efbc4ee test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.alns
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.alns Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,36 @@
+
+------------------------------------------------------------------------
+Query   (  253 nt) M00967_43_000000000-A3JHG_1_1101_18269_8162
+ParentA (  542 nt) B.cereus.1
+ParentB (  541 nt) S.mutans.1
+
+A   178 TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGCAGGTGGTTTCTTAAGTCTGATGTGAAAGCCC 257
+Q     1 TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGCGCGCGCAGGTGGTTTCTTAAGTCTGATGTGAAAGCCC 80
+B   178 TACGTAGGTccCgAGCGTTgTCCGGAtTTATTGGGCGTAAAGgGaGCGCAGGcGGTcaggaAAGTCTGgaGTaAAAGgCt 257
+Diffs            AA A      A      A               A A       A   AAAAA       AA  A    A A
+Votes            ++ +      +      +               + +       +   +++++       ++  +    + +
+Model   AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+
+A   258 ACGGCTCAACCGTGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTG 337
+Q    81 ACGGCTCAACCGTGGAGGGTCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAAAGTGGAATTCCATGTGTAGCGGTG 160
+B   258 AtGGCTCAACCaTaGtGtG-CtcTGGAAACTGtctGACTTGAGTGCAGAAGgGGAgAGTGGAATTCCATGTGTAGCGGTG 336
+Diffs    A         A A A A   AA         AAA                A   A                        
+Votes    +         + + + +   ++         +++                +   +                        
+Model   AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+
+A   338 AAATGCGTAGAGATATGGAGGAACACCAGTGGCGAAgGCGaCTtTCTGGTCTGTaACTGACaCTGAGGCgCGAAAGCGTG 417
+Q   161 AAATGCGTAGAGATATGGAGGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTCACTGACGCTGAGGCTCGAAAGCGTG 240
+B   337 AAATGCGTAGAtATATGGAGGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTCACTGACGCTGAGGCTCGAAAGCGTG 416
+Diffs              A                        B   B  B          B      B       B          
+Votes              +                        +   +  +          +      +       +          
+Model   AAAAAAAAAAAAxxxxxxxxxxxxxxxxxxxxxxxBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+
+A   418 GGgAGCaAACAGG 430
+Q   241 GGTAGCGAACAGG 253
+B   417 GGTAGCGAACAGG 429
+Diffs     B   B      
+Votes     +   +      
+Model   BBBBBBBBBBBBB
+
+Ids.  QA 96.8%, QB 87.7%, AB 84.5%, QModel 100.0%, Div. +3.3%
+Diffs Left 32: N 0, A 0, Y 32 (100.0%); Right 8: N 0, A 0, Y 8 (100.0%), Score 2.0408
b
diff -r 000000000000 -r bccb5efbc4ee test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.chimeras
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.ref.uchime.chimeras Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,4 @@
+Score Query ParentA ParentB IdQM IdQA IdQB IdAB IdQT LY LN LA RY RN RA Div YN
+0.0000 M00967_43_000000000-A3JHG_1_1101_11148_6457 * * * * * * * * * * * * * * N
+0.0000 M00967_43_000000000-A3JHG_1_1101_7079_6722 * * * * * * * * * * * * * * N
+2.0408 M00967_43_000000000-A3JHG_1_1101_18269_8162 B.cereus.1 S.mutans.1 100.0 96.8 87.7 84.5 96.8 32 0 0 8 0 0 3.28 Y
b
diff -r 000000000000 -r bccb5efbc4ee test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.slayer.chimeras
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.slayer.chimeras Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,11 @@
+Name LeftParent RightParent DivQLAQRB PerIDQLAQRB BootStrapA DivQLBQRA PerIDQLBQRA BootStrapB Flag LeftWindow RightWindow
+M00967_43_000000000-A3JHG_1_1101_19936_3208 no
+M00967_43_000000000-A3JHG_1_1101_15923_3823 no
+M00967_43_000000000-A3JHG_1_1101_14010_4122 no
+M00967_43_000000000-A3JHG_1_1101_13293_4703 no
+M00967_43_000000000-A3JHG_1_1101_24357_4866 no
+M00967_43_000000000-A3JHG_1_1101_23552_5194 no
+M00967_43_000000000-A3JHG_1_1101_7326_5417 no
+M00967_43_000000000-A3JHG_1_1101_11148_6457 no
+M00967_43_000000000-A3JHG_1_1101_7079_6722 no
+M00967_43_000000000-A3JHG_1_1101_8607_6805 no
b
diff -r 000000000000 -r bccb5efbc4ee test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.unique.align_head
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.good.unique.align_head Fri May 19 05:47:34 2017 -0400
b
b'@@ -0,0 +1,18 @@\n+>M00967_43_000000000-A3JHG_1_1101_19936_3208\n+...............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................'..b'..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................\n'
b
diff -r 000000000000 -r bccb5efbc4ee test-data/Mock_S280_L001_R1_001_small.trim.contigs.qual
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.qual Fri May 19 05:47:34 2017 -0400
b
b'@@ -0,0 +1,50 @@\n+>M00967_43_000000000-A3JHG_1_1101_19936_3208\t\n+33 34 32 33 33 33 33 33 33 33 29 33 32 12 33 12 32 35 35 35 35 33 33 32 35 35 35 35 35 35 35 35 29 26 30 35 35 35 12 33 35 35 35 35 35 35 32 35 32 35 35 33 32 35 35 35 35 35 32 36 36 35 36 36 36 36 36 35 36 35 36 36 36 36 35 32 32 36 36 36 35 33 36 36 36 36 35 36 36 36 36 35 35 33 33 33 36 35 15 33 35 36 36 36 36 36 36 36 36 36 36 36 36 36 30 35 35 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 35 36 36 33 36 36 36 36 36 36 36 36 36 18 36 36 36 33 36 36 36 36 36 36 32 36 35 35 35 35 35 36 33 33 36 36 36 36 33 35 35 35 36 33 36 36 35 36 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 12 32 35 35 35 35 35 15 33 33 33 32 35 35 35 35 33 35 35 35 35 35 35 33 30 35 35 32 35 12 24 35 33 32 14 32 12 33 33 33 33 33 33 33 33 33 32 33 12 34 34 \n+>M00967_43_000000000-A3JHG_1_1101_15923_3823\t\n+18 32 12 30 30 12 30 24 14 1 12 30 33 32 29 26 14 32 24 12 12 35 35 35 35 32 35 32 35 35 35 35 35 32 32 32 32 32 15 35 32 30 32 30 33 35 30 35 33 30 36 35 36 35 35 35 35 35 35 33 35 35 33 35 35 35 36 36 35 36 36 36 36 36 36 36 36 30 33 36 35 33 35 36 36 36 35 36 36 36 36 33 33 35 35 35 36 33 35 36 35 36 36 36 35 36 36 36 36 33 35 36 36 36 36 36 36 36 36 36 36 36 33 36 36 36 36 36 36 35 36 36 36 35 36 33 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 36 35 36 36 36 36 36 36 36 35 35 35 35 35 36 36 36 35 35 30 1 35 35 36 36 36 36 35 33 33 36 33 20 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 32 35 35 33 32 35 35 35 35 35 33 35 35 35 35 35 35 35 33 35 35 33 35 33 35 35 12 33 35 35 14 32 24 35 30 33 33 33 33 32 32 30 30 32 33 33 33 \n+>M00967_43_000000000-A3JHG_1_1101_14010_4122\t\n+32 32 24 30 15 12 30 30 29 26 12 12 14 1 14 14 1 32 26 12 24 12 35 14 32 14 24 24 26 1 35 35 35 32 33 32 14 32 30 35 33 26 12 24 24 12 12 24 14 35 35 33 15 12 35 32 26 26 15 15 35 36 33 14 15 36 30 33 15 30 33 15 33 35 36 36 15 32 27 27 12 12 27 29 15 15 29 12 35 12 33 15 27 33 30 14 26 30 15 15 15 15 36 36 33 33 36 35 35 15 15 35 36 30 12 14 27 17 17 33 35 15 33 15 15 18 15 18 18 33 33 33 35 32 35 15 18 33 15 35 15 29 15 27 14 27 26 15 15 15 1 27 14 12 12 14 27 12 1 24 26 33 12 1 24 24 24 12 12 12 12 18 15 15 26 15 26 15 18 33 12 32 35 33 12 33 12 24 12 24 30 14 12 1 26 24 32 12 12 24 1 26 30 33 14 32 1 30 26 1 18 12 12 1 26 24 14 14 14 1 14 1 12 26 12 12 26 12 24 1 12 12 24 26 12 12 1 12 1 30 27 27 12 12 12 37 1 24 26 12 1 12 33 \n+>M00967_43_000000000-A3JHG_1_1101_10776_4204\t\n+16 16 12 24 14 14 14 26 26 12 2 12 15 14 15 14 14 24 12 24 12 24 14 14 30 30 14 12 15 15 12 14 14 1 15 26 26 1 15 12 15 24 1 2 30 12 15 15 26 1 15 30 1 24 24 15 15 15 33 33 35 36 32 33 14 24 12 12 15 15 15 33 32 35 33 12 33 30 12 27 12 14 14 14 14 27 12 15 12 15 15 15 15 33 15 32 36 35 29 15 15 15 15 30 14 15 15 15 15 27 14 15 15 15 15 35 14 35 29 12 33 33 14 26 15 29 15 30 1 15 15 27 15 14 14 27 14 15 30 14 27 29 26 27 14 11 2 29 30 12 12 14 12 12 12 11 17 12 11 17 33 15 15 15 15 15 33 12 15 12 17 15 33 29 30 14 11 1 24 15 12 30 2 12 15 12 12 1 12 14 27 15 12 12 24 30 12 15 12 26 14 15 2 12 12 11 12 24 14 30 2 15 12 33 30 33 24 14 12 24 15 32 35 32 1 12 15 11 15 2 1 12 12 15 24 1 12 1 12 15 12 1 24 11 11 12 24 2 14 12 29 16 \n+>M00967_43_000000000-A3JHG_1_1101_22487_4260\t\n+33 34 34 12 12 1 24 12 12 1 12 1 12 1 24 1 12 12 1 24 12 24 1 32 26 14 1 12 12 1 24 12 38 24 24 12 14 12 12 12 1 14 33 24 14 1 14 26 14 14 24 1 1 1 24 12 24 12 26 12 12 24 1 26 1 12 1 24 1 12 26 14 24 14 14 1 12 26 12 12 1 12 24 12 1 14 12 1 24 1 1 30 30 30 26 26 12 12 30 32 12 33 35 33 33 30 32 12 1 12 24 12 26 12 14 26 1 15 14 14 33 27 27 12 27 12 27 15 12 33 33 27 15 29 12 11 12 15 1 33 27 27 15 14 14 27 15 14 15 30 15 30 1 14 30 30 33 35 12 30 30 14 14 14 32 27 29 17 17 35 33 32 15 15 15 33 32 33 15 35 29 14 14 14 14 29 14 33 29 1 30 30 14 32 32 14 14 29 1 33 33 32 1 14 12 24 14 30 33 14 14 14 30 29 33 30 30 33 30 33 33 12 30 35 12 26 29 15 15 15 11 32 15 15 2 12 24 32 30 33 33 30 29 15 15 12 18 12 27 24 32 11 32 \n+>M00967_43_000000'..b'3JHG_1_1101_18966_7778\t\n+32 33 12 30 30 33 33 32 27 29 30 30 26 24 30 12 15 35 32 26 26 1 14 35 35 32 32 33 35 33 12 33 35 33 32 32 35 15 33 32 12 33 24 32 33 32 32 35 33 30 35 32 35 35 35 35 35 35 26 33 36 36 35 35 15 35 35 35 33 15 26 15 36 36 36 35 33 36 35 12 12 35 36 33 35 35 33 35 33 36 33 33 30 36 36 33 35 35 36 36 36 36 35 36 36 36 36 36 36 36 36 36 36 35 17 33 33 30 36 32 36 35 35 36 36 33 36 35 17 35 36 17 36 36 35 36 35 35 26 33 36 36 36 36 32 35 32 33 33 35 18 36 32 36 36 36 35 36 36 36 36 35 35 33 35 35 36 35 35 36 36 35 36 35 36 35 35 35 35 36 36 36 35 35 33 35 35 35 35 35 35 35 35 35 33 35 35 33 35 15 33 33 35 35 33 35 35 35 33 32 35 33 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 26 33 35 33 30 33 33 33 33 33 33 33 12 34 34 \n+>M00967_43_000000000-A3JHG_1_1101_5494_7973\t\n+33 33 12 33 30 33 33 27 24 30 24 12 26 12 32 30 35 35 35 33 33 35 36 35 35 35 35 32 36 35 36 36 36 36 35 35 35 35 35 33 14 35 35 32 35 33 35 35 35 36 36 36 36 35 35 36 35 36 36 35 35 36 36 36 36 36 36 36 35 36 36 36 35 36 35 36 33 35 36 36 36 36 36 36 36 35 30 36 36 36 36 35 35 36 36 36 36 35 36 36 35 35 36 36 36 36 35 35 35 36 36 36 35 36 36 36 36 36 35 17 35 36 36 36 36 35 36 35 36 36 36 18 35 35 33 33 33 35 33 33 36 33 36 35 36 36 35 15 35 35 36 35 36 35 36 36 36 36 35 35 35 36 36 36 33 36 36 36 35 33 35 36 35 35 35 36 36 36 36 36 30 35 35 35 35 35 35 30 32 33 33 33 35 36 36 36 32 33 35 35 30 33 32 35 35 32 32 35 33 33 35 33 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 35 27 35 35 35 14 26 24 35 35 33 12 14 26 32 14 32 32 30 12 33 32 \n+>M00967_43_000000000-A3JHG_1_1101_10246_8076\t\n+33 33 12 26 12 1 12 24 12 26 24 26 12 1 26 24 14 15 24 12 12 12 30 32 33 32 24 24 15 14 30 32 26 14 15 15 33 32 15 24 26 26 30 15 12 12 32 35 33 15 15 15 26 14 15 15 15 32 36 33 33 35 36 35 36 36 27 27 15 36 27 33 33 35 33 36 36 36 33 30 33 30 30 14 15 30 30 27 30 14 1 15 15 15 33 36 36 33 35 35 33 36 33 18 32 32 33 33 29 27 36 36 36 33 18 32 35 36 35 15 33 36 32 18 33 35 33 33 15 15 17 26 33 33 14 30 35 30 14 33 30 33 36 35 33 32 12 27 27 27 12 1 27 14 27 33 12 30 33 32 17 36 35 36 15 33 33 35 33 33 35 33 15 15 33 29 14 24 12 30 24 30 30 32 12 30 24 26 14 12 11 26 15 24 12 32 35 35 33 15 33 32 15 32 30 35 15 33 35 33 15 14 14 15 17 32 35 35 33 33 14 14 14 14 14 24 32 30 15 33 35 24 24 12 33 33 14 14 14 24 24 24 12 18 12 12 24 24 30 30 12 32 32 \n+>M00967_43_000000000-A3JHG_1_1101_23931_8157\t\n+33 33 26 12 1 12 12 26 1 18 1 14 24 14 24 12 14 26 12 36 24 12 32 14 14 15 32 35 24 1 33 30 1 32 26 12 15 32 15 32 33 12 12 26 24 12 12 14 26 12 33 33 18 26 26 12 15 14 33 35 26 15 33 27 27 1 14 27 27 27 27 15 30 35 36 36 18 33 27 18 30 33 35 33 35 35 36 36 35 12 35 30 33 14 35 29 27 14 1 30 35 27 33 36 30 18 33 36 36 36 33 35 35 18 2 17 30 35 35 15 18 30 35 15 32 15 33 35 15 33 30 35 33 14 35 33 17 35 15 29 29 35 17 33 15 35 15 32 15 33 36 35 35 35 36 36 36 36 33 33 35 36 35 35 36 32 15 12 27 27 12 12 33 35 17 33 32 36 35 33 12 35 30 15 1 35 15 15 14 35 14 33 12 12 33 30 32 33 12 30 15 12 15 12 15 33 15 33 32 17 15 33 17 17 17 35 15 15 15 24 32 30 33 24 14 24 32 30 1 24 14 26 32 35 33 33 14 32 24 32 32 30 32 29 15 12 30 33 30 29 12 32 32 \n+>M00967_43_000000000-A3JHG_1_1101_18269_8162\t\n+34 35 30 30 24 30 33 33 33 33 12 24 24 12 30 12 14 32 32 24 33 35 35 35 35 35 24 14 35 35 32 12 35 32 35 35 35 32 30 33 33 27 30 30 32 30 30 32 14 35 33 24 12 35 33 32 15 24 15 36 36 35 35 35 24 24 15 35 36 35 36 36 36 36 33 36 36 33 33 30 27 30 35 35 33 32 30 33 30 30 27 12 1 36 36 36 36 36 36 36 36 36 35 36 36 36 35 36 33 36 35 36 36 36 33 35 33 35 36 36 36 36 36 36 36 36 35 35 35 35 36 36 36 36 35 36 30 35 18 36 36 36 36 35 35 36 33 35 1 36 35 35 33 36 36 36 36 36 35 36 36 36 35 36 35 35 35 35 35 36 35 36 36 36 36 36 36 36 36 36 36 35 36 35 35 36 35 32 35 35 35 35 33 33 32 33 15 33 30 35 35 33 17 33 33 33 33 35 35 35 33 33 35 35 20 35 35 35 35 35 33 32 35 35 33 35 35 33 33 33 35 35 32 35 35 35 32 35 33 35 35 32 32 32 32 32 33 33 30 30 12 33 32 \n'
b
diff -r 000000000000 -r bccb5efbc4ee test-data/Mock_S280_L001_R1_001_small.trim.contigs.summary
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mock_S280_L001_R1_001_small.trim.contigs.summary Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,26 @@
+seqname start end nbases ambigs polymer numSeqs
+M00967_43_000000000-A3JHG_1_1101_19936_3208 1 253 253 0 5 1
+M00967_43_000000000-A3JHG_1_1101_15923_3823 1 253 253 0 4 1
+M00967_43_000000000-A3JHG_1_1101_14010_4122 1 253 253 0 4 1
+M00967_43_000000000-A3JHG_1_1101_10776_4204 1 252 252 8 4 1
+M00967_43_000000000-A3JHG_1_1101_22487_4260 1 253 253 1 5 1
+M00967_43_000000000-A3JHG_1_1101_13293_4703 1 253 253 0 3 1
+M00967_43_000000000-A3JHG_1_1101_24357_4866 1 253 253 0 5 1
+M00967_43_000000000-A3JHG_1_1101_23552_5194 1 253 253 0 4 1
+M00967_43_000000000-A3JHG_1_1101_7326_5417 1 253 253 0 4 1
+M00967_43_000000000-A3JHG_1_1101_11148_6457 1 253 253 0 3 1
+M00967_43_000000000-A3JHG_1_1101_7079_6722 1 253 253 0 6 1
+M00967_43_000000000-A3JHG_1_1101_8607_6805 1 253 253 0 6 1
+M00967_43_000000000-A3JHG_1_1101_15208_7185 1 253 253 0 4 1
+M00967_43_000000000-A3JHG_1_1101_4525_7317 1 253 253 0 6 1
+M00967_43_000000000-A3JHG_1_1101_9121_7358 1 253 253 0 4 1
+M00967_43_000000000-A3JHG_1_1101_8480_7498 1 252 252 0 4 1
+M00967_43_000000000-A3JHG_1_1101_11790_7581 1 253 253 0 5 1
+M00967_43_000000000-A3JHG_1_1101_20566_7622 1 254 254 0 4 1
+M00967_43_000000000-A3JHG_1_1101_10073_7632 1 252 252 0 4 1
+M00967_43_000000000-A3JHG_1_1101_5170_7771 1 253 253 0 3 1
+M00967_43_000000000-A3JHG_1_1101_18966_7778 1 253 253 0 4 1
+M00967_43_000000000-A3JHG_1_1101_5494_7973 1 253 253 0 4 1
+M00967_43_000000000-A3JHG_1_1101_10246_8076 1 253 253 0 4 1
+M00967_43_000000000-A3JHG_1_1101_23931_8157 1 253 253 1 4 1
+M00967_43_000000000-A3JHG_1_1101_18269_8162 1 253 253 0 3 1
b
diff -r 000000000000 -r bccb5efbc4ee test-data/Mock_S280_L001_R2_001_small.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Mock_S280_L001_R2_001_small.fastq Fri May 19 05:47:34 2017 -0400
b
b'@@ -0,0 +1,100 @@\n+@M00967:43:000000000-A3JHG:1:1101:19936:3208 2:N:0:280\n+CCTGTTTGCTCCCCACGCTTTCGAGCCTCAGCGTCAGTTACAGACCAGAGAGCCGCCTTCGCCACTGGTGTTCCTCCATATATCTACGCATTTCACCGCTACACATGGAATTCCACTCTCCTCTTCTGCACTCAAGTCTCCCAGTTTCCAATGACCCTCCCCGGTTGAGCCGGGGGCTTTCACATCAGACTTAAGAAACCGCCTGCGCTCGCTTTACGCCCAATAAATCCGGACAACGCTTGCCACCTACG\n++\n+CCCCBFFFFFFFGGGGGGGGGGGGHGGHHHHGGGGGGHHGHFHGHHHHHHHGHHGGGGGHGGGGGHHHHHHGHHFHGHGHHHHHGHHGGGGGHHHHHGGGGGHH3GGHHHHHHHFHGFHHHHGHHHHHHHHHHHHHHHFHHHHHHHHHHHHHEH1FHFEDGGGGGGGHHHHCFGGGAAEGGGGGGFGGGGGGGGBFFGFGADFFAFAFFFFFFE.FFF?;>FEFFFFFFBDDFFFFA-C.AE?FFFFFFFD\n+@M00967:43:000000000-A3JHG:1:1101:15923:3823 2:N:0:280\n+CCGGTTTGCTCCCCACACTTTCGCGCCTCAGCGTCACCTTCTGTCCAGTAACTTGCCTTCGCCATTGGTGTTCCTCCTGGCATCTACGCATTCCACCGCTACACCAGGAATTCCAGTTACCTCTCCAGAGGTCAAGAAATCCAGTATCCAGTCCATCCCCGAGGTTGAGCCCCGGTCTTTAAAACCAGACTTAAATTTCCGCCTACACGCCCTTTACGCCCAGTGATTCCGGGTAACGCTTGCCCCCTCCG\n++\n+BBBB?ABBFFFFGGGGGGGGGGGCGCGGGHHHGGGGGGHHHHHHHHGHHHHHHHHHGHHHGGGGGHHH5FHGHHHHHHHG1?FFHHHGGGGGHHHHHGGGGGHHHHHGHGHHHHHGHHHFHHHFGHHGGHEHGHHGHGHHHHFBGGGHGGHHGHGDHFGFCCGGGHGHHHFEFGC@GGHHHHHHFGHEEEBFFBFFGFGGGGG?DGGGD?A?AF0CBAAAFFFFFBFBFFFF-.9B/;>AEA.//:B-AD.\n+@M00967:43:000000000-A3JHG:1:1101:14010:4122 2:N:0:280\n+CCTGTTTGCTCCCCACGCTTTCGCGCCTCAGTGTCAGTTACAGACCAGAAAGCCGCCTTCGCCACTGGTGTTCCTCCATATCTCTACGCATTTCACCGCTACACATGGAATTCCACTTTCCTCTTCTGCACTCAAGTCTCCCAGTTTCCAATGACCCTCCACGGTTGAGCCGTGGGCTTTCACATCAGACTTAAGAAACCACCTGCGCGCGCTTTACGCCCAAAAATTCCGGATAAAGCCTGCCACCTACG\n++\n+BBBBBFFFBFDFGGGGGGGGGGGFGGGGFGHGGHHHHHHCHC3EGHHGFHEH3BFGGGGHHGDGGBGHBFGGHF4GGBEGF4FGHHHGGGGGGHHHHGG/EGHHFB??3BBGHH?G4FGGFDGF33B3DDFBHH22>@2FGGFHGFHHDGH1111G<<FDB0C-F.>01><-.<<AEHGFF0CC0CBG0/CGH00;;CH.CEGF/9--:9-;BF?B/ADAFFF.;99/B/F-9.;B///./..;BF?.;B9\n+@M00967:43:000000000-A3JHG:1:1101:10776:4204 2:N:0:280\n+CCTGATTGATACCCACACTTTCGAGCCTCAATGTCAGTTGCCGCTTAGCAGGCTGCCTTCGCAACCGGAGTTCCCCGTGATATCTAAGCATTTCACCGCTACACCCCGAATTCCGCCTGCCTCCACTGCACTCAAGATATCCAGTATCAACTGCAATTTTACGGTTGAGCCGCAAACTTTCACAACTGACTTAAACATCTATATACGCCACCTTAAAATCCAATAAATCCGGATACACCTCGTATCCTCCG\n++\n+1>AA1B311@FD1BBEEE111B0000AFBGG1A2FEFBF111A/AE/FF11/AG0CCFF1AA/B/B/>//BG1B@0/?>F>22@2B1BE1GD22B21////>FFG///E<?<>B0<?//0<1@/@0>1@1FH0?F1F11111<11111@1010>FHB1F111>.0.<//CG-<-AC.CGCC0000.:/CBGFBB0009:;C00;00.C-.9A.00;;00//00;/BFF//:-9-9///9/:---;;///9-\n+@M00967:43:000000000-A3JHG:1:1101:22487:4260 2:N:0:280\n+CCTGTTCGCTCCCCACGCCTTCGCTCCTCAGCGTCAGTAACGGCCCAGAGCCCCCCCTTCGCCCCCGGTGTTCTTCCTGATATCTGCGCATTCCACCGCTCCACCAGGAGTTCCTGTCTCCCCTACCGCACTCAAGCCAGCCCGCACCCACCGCACGCCCCCCCTCAACCCACAGGACTTCACGCCCGCCCCGACCAACACACTACATGCCCGTTAACGCCAACAAATCCCGACCACACCCCCCCCCCAC\n++\n+A1AAAB3>11>AFEFGCC000F00E0AGGGFFCEAE?BFFF///E?/A//0BFE/>//BB/?E/>E/>////BG1EBF1F1GEG22>>B///@DDGF?@//?1?0/0<//0<<F11111>1<EF.0<-<-<<C//00;/.;.:---A?CGGG.A?--;;@@@--9--/--9----;--//9/;--9---;;9--;-9-9---9//;///:B/-----/-99-9----/;B/:-9----9-------9---\n+@M00967:43:000000000-A3JHG:1:1101:13293:4703 2:N:0:280\n+CCTGTTTGATACCCACGCCTTCGTGCTTCAGTGTCAGTCGCAGTATGGCAAGCTGCCTTCGCAATCGGAGTTCCTCGTGATATCTATGCATTTCACCGCTACACCACGAATTCCGCCTGCCGCCGCTGAACTCAAGCCCGGCAGTTTCAACGGCAGGCTGAACGTTGAGCGCTCAGGTTTCACCGCTGACTTACCGAACAACCTACGCAACCCTTAAACCCAATAAAACCGGATAACGCTCGCAACCTCC\n++\n+AAB@BFBFFFFFGGGGEGGGGGHGFGFFGBGGBAFGGHHGGEGGHHFGGHHGGAGHHHHHHGGGGHED?EGHHHFHDGHF3FGGFFHHGHHGHFHHHEEEFEHHGHHGGGAGHHGGFEHHFFGCDCGGCHHHHEHFFGHC<A-AF1FFHGH.@C-<-:GC.0GA::.;:0-;.C./;00;;00:9?@CF/0;BFGB.9@BF.D:/9.-.-9..;BBF//:AE../B///A=BD.;//99..@9=.-;//;\n+@M00967:43:000000000-A3JHG:1:1101:24357:4866 2:N:0:280\n+CCTGTTCGCTCCCCACGCTTTCGCTCCTCAGCGTCAGTAACGGCCCAGAGACCCGCCTTCGCCACCGGTGTTCTTCCTGATATCTGCGCATTCCACCGCTACACCAGGAGTTCCAGTCTCCCCTACCGCACTCAAGTCAGCCCGTACCCACCGCACGCCCCCAGTTAAGCCAGAGGATTTCACGGCAGACGCGACCAACCGCCTACAAGCCCTTTACGCCCACTAATTCCGGACAACGCTCGCGCCCTACG\n++\n+BBB@BFFBBBBBGGGF2EGFGGGGFHGHGFFHGFEGGHHGFGGGGGEHEEFFFH?GGGGHHGGGGHGG/EGGHHFHHBFGFG4FGBGGGGGEHHHHHE?CGGHHH/<FCFGHHHHHF2@GHGGEG?CG?ADGHHHGHHHFFHGGGGFE<0:C.@DGGGEGGG-9FF09FGGF..;..FGGGBB9.;-9.FA;BFFFF?D9--@ADFF/BF?EFFFBFED@BA.9B//;BFF-DBBFFBF9D---@BC-.A.\n+@M00967:43:000000000-A3JHG:1:'..b'GHABCGBDGGGGGEGGGGGGG0FFFFFFAAF09.CDFEEFFFFEF\n+@M00967:43:000000000-A3JHG:1:1101:10073:7632 2:N:0:280\n+CCGGTTTGCTCCCCACGCTTTCGAGCCTCAGCGTCAGTTACAGACCAGAGAGCCGCTTTCGCCACCGGTGTTCCTCCATATATCTACGCATTTCACCGCTACACATGGAATTCCACTCTCCCCTTCTGCACTCAAGTCCTCCAGTTTCCAAAGCGTACAATGGTTAAGCCACTGCCTTTAACTTCAGACTTAAAGAACCGCCTGCGCTCGCTTTACGCCCAATAAATCCGGACAACGCTCGGGACCTACGT\n++\n+ABA?ABBBFFFFGGGGGGGGGGFGHGGHHGHHGGGGGHHHHHHHHHHHEHGFGHEGAEGHGGGGGHGG>EFEHHHHHHHGHHHHGHHGGGGGHHEHHGGGGGEH3E3GHHHHHHHHFHHHHHGGHFGHHHHHHHHFGHHHHHGFHFGHHHHEGHDDDDDDDDHFHFHHHHBGCGGHHHGFHHHFFCHGHHHHFCCGCBGD?BCEG-D?EFAAEG0/9DDFFFFFFFFFFAF?CFFF-@.D-@;-9A9FFB;\n+@M00967:43:000000000-A3JHG:1:1101:5170:7771 2:N:0:280\n+CCTGTTTGATACCCACGCCTTCGTGCTTCAGTGTCAGTCGCAGTATGGCAAGCTGCCTTCGCAATCGGAGTTCCTCGTGATATCTATGCATTTCACCGCTACACCACGAATTCCGCCTGCCGCCGCTGAACTCAAGCCCGGCAGTTTCAACGGCAGGCTGAACGTTGAGCGCTCAGGGTTCACCGCTGCCTTACCGAACAACCTCCGGACCCTTTAAACCCAATAAATCCGGATAACGCTCGCCTCCCACG\n++\n+>ABBBFFFFFFFGFGGGGCGGGHFGAFHGGG5DGHBGG52EGGGHEHHFGHGHFHHHGFHEGGGFHGGEGGG5GH5EGFGHFFDGFFF3FGHHFFHGGEFGGGHCH/?EFHHHHHG?GEFHGGGC/B@DF2FHHGHHGHGCGGGHHFHGHD.@?-CFGCGCGHAGB../;;@.9./C.99;0CFBDFG..9FB/BDA-9-9.AB/.;-.;;AFFF/9;/9DE..//;BB/9>D.A//.-..---.....9-\n+@M00967:43:000000000-A3JHG:1:1101:18966:7778 2:N:0:280\n+CCTGTTTGCTACCCACGCTTTCGGGCATGAACGTCAGTGTTGTCCCAGGAGGCTGCCTTCGCCATCGGTATTCCTCCACATCTCTACGCATTTCACTGCTACACGTGGAATTCTACCTCCCTCTGACACACTCGAGTCACCCAGTTCAGAACGCAGTTCCCGGGTTGAGCCCGGGGATTTCACATCCTGCTTAAGTAACCGTCTGCGCCCGCTTTACGCCCAGTAATTCCGCTTAACGCTCGCACCCTACG\n++\n+CCCCCFFFFFFFGGGGGGGGGGGGGGGHHHGHHHHGGHHHHDHHHHHHFHGDE1GFHHFHGGGGGHGGEHGHHHHHHFHGHGHHFFHFFEGGHHHHGHHHBG3GEBAFAGHHHHFFGHGHG2GF2FGDGHGFHAH?GF2FHHGHHHHHHHFHGGGGGFHHHECGDFCFGCHG--EGCEHHH0;0CFGF0FFGGB;FFGFFFAF?EGABDB:D-AE0FAABFB.BFEBBFF/.;;AF0.@:;BA>>FDFFA.\n+@M00967:43:000000000-A3JHG:1:1101:5494:7973 2:N:0:280\n+CCTGTTTGATACCCACACTTTCGAGCCTCAATGTCAGTTGCAGCTTAGCAGGCTGCCTTCGCAATCGGAGTTCTTCGTGATATCTAAGCATTTCACCGCTACACCACGAATTCCGCCTGCCTCAACTGCACTCAAGATATCCAGTATCAACTGCAATTTTACGGTTGAGCCGCAAACTTTCACAACTGACTTAAACATCCATCTACGCTCCCTTTAAACCCAATAAATCCGGATAACGCTCGGATCCTCCG\n++\n+ABAABFFFFFFFGGGGFGGGGGGGHGGHHGHGHHHHGHHHHHHHHHGBGHBEEHHGHHHHGGGGGHGGGGGHHHHHGHFHHHGHHHHHFHHHHGGHHGGGGGHGH1GGGGHHHHFGGEEGF3GGHFHFHHHHF2FHHHHHEHHHGGFGHHGFFHHEHHHHHGGGHG?GHHHGGGGGCGFHGHGHHGHGHHHHFHHHGHFFHHHHGGGCEAEE/BGGGGFGGGGFGBFFFGGGDDFGF?A.;-9A9>FFBF.\n+@M00967:43:000000000-A3JHG:1:1101:10246:8076 2:N:0:280\n+CCTGTTTGATACCCACACTTTCGAGCCTCAATGTCAGTTGCAGCTTAGCAGGCTGCCTTCGCAATCGGAGTTCCTCGTGATATCTAAGCATTTCACCGCTACACCACGAATTCCGCCTGCCTCAACTGCACTCAAGATATCCAGTATCAACTGCAATTTTACCGTTGAGCCGCAAACTTTCACAACTGACTTAAACATCCATCTACGCTCCCTTTAAACCCAATAAATCCGGATAACGCCCGGATCCCCCG\n++\n+AAAAAFF113DFGGGGGGGGGGGF0AEFHHHHFFFGHB21FB1FGD1GHF1CE0FFFGHHHG/E/FBA/AAFFD2F/>B00DGHHFFHHGGH2EFGHEC@EE1GECGGGGHEHHBEGA/CC<F11FFFFGGHH0FHFGGDGHH<>FFGBGFGCFHBGHE1111/?<?A1FG@C?CGHHDHFD<G0<=GHFHHHCGB000/;000CGA-.CC;;90BF00/;AA/0:9BCBA-..90/9;--;9;-9---;-\n+@M00967:43:000000000-A3JHG:1:1101:23931:8157 2:N:0:280\n+CCTGTTTGCTCCCCACGCTTTCGAGCCTCAGTGTCAGTTACAGTCCAGAAAGTCGCCTTCGCCACTGGGATTCTTCCTAATCTCTACGCATTTCACCGCTACACTAGGAATTCTACTTTCCTCTCCTGCACTCTAGATCTCCAGTTTGGAATGCCGCACCCAGGTTAAGCCCGAGTATTTCACATCCAACTTAAATATCCACCTACGCTCCCTTTACGCCAAGAAAATCCGGAAACAGCTTGACCCCTCCG\n++\n+AAAAAFDF1BFFGGGGGGGGGGGGHGEHHHHAFHHHHH222F12BF1F1F1G1BEFGGGHHG/E/1BG/0BGHHFHBG2FF1FHHH1FGGGGHHHHHGGGGGHH1F1G1FGHHBBF2FGHDGGFHFD1BGHFH1FGH21>FGHHHHHGCGD<GH1><CG/CCF.FGHGFEGECG@EGHHHB0==<</0<<C0;FH000;;:CC.;/.-:;..CC0C0.;AA@E.:FB0//A-9-;//-9/:/;9/;----;\n+@M00967:43:000000000-A3JHG:1:1101:18269:8162 2:N:0:280\n+CCTGTTCGCTACCCACGCTTTCGAGCCTCAGCGTCAGTGACAGACCAGAGAGCCGCTTTCGCCACTGGTGTTCCTCCATATCTCTACGCATTTCACCGCTACACCTGGAATTCCACTTTCCTCTTCTGCACTCAAGTCTCCCAGTTTCCAATGACCCTCCCCGGTTGAGCCGTGGGCTTTCACATCAGACTTAAGAAACCACCTGCGCGCGCTTTACGCCCAATAATTCCGGATAACGCTTGCCACCTACG\n++\n+ABB@AFFBBBBBGGGGGGGGGGGCFFGHCHHBFGGGGH5GHFFGHHCFFC2EGH?E0EADEGGGGBFHFGHGHHHHHHHHHGGHGFFEEGFGHHHHHGGGCFFH3FCGFFGHHH3F?GFHHHHFFFFHHHHHHHGFDGDGGHEGBGFHHHEHHHHHHHHG..<@@D?CCGG@<@CCGHEHHGHFHF0::FFFGG090BFG.9CF/A??B?@=BD?BFEFAF.AFF/9FFFFFD9AB/.@.::.FFFF?9BA\n'
b
diff -r 000000000000 -r bccb5efbc4ee test-data/abrecovery.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/abrecovery.fasta Fri May 19 05:47:34 2017 -0400
b
b'@@ -0,0 +1,2301 @@\n+>AY457915\n+CCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGAAGC\n+ATTTAAGACAGATTACTTCGGTTTGAAGTCTTTTATGACTGAGTGGCGGACGGGTGAGTAACGCGTGGGT\n+AACCTGCCTCATACAGGGGGATAGCAGCTGGAAACGGCTGGTAATACCGCATAAGCGCACAGTACCACAT\n+GGTACAGTGTGAAAAACTCCGGTGGTATGAGATGGACCCGCGTCTGATTAGCTTGTTGGCGGGGTAACGG\n+CCCACCAAGGCGACGATCAGTAGCCGACCTGAGAGGGTGACCGGCCACATTGGGACTGAGACACGGCCCA\n+GACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGAGGAAACTCTGATGCAGCGACGCCGCGTG\n+AGTGAAGAAGTAGTTCGCTATGTAAAGCTCTATCAGCAGGGAAGATAGAGACGGTACCTGACTAAGAAGC\n+TCCGGCAAATC\n+\n+>AY457914\n+CCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGAAGC\n+ATTTAGAACAGATTACTTCGGTTTGAAGTTCTTTATGACTGAGTGGCGGACGGGTGAGTAACGCGTGGGT\n+AACCTGCCTTGTACTGGGGGATAGCAGCTGGAAACGGCTGGTAATACCGCATAAGCGCACAATGTTGCAT\n+GACATGGTGTGAAAAACTCCGGTGGTATAAGATGGACCCGCGTCTGATTAGCTAGTTGGTGAGATAACAG\n+CCCACCAAGGCGACGATCAGTAGCCGACCTGAGAGGGTGACCGGCCACATTGGGACTGAGACACGGCCCA\n+GACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGAGGAAACTCTGATGCAGCGACGCCGCGTG\n+AGTGAAGAAGTAATTCGTTATGTAAAGCTCTATCAGCAGGGAAGATAGAGACGGTACCTAACTAAGAAGC\n+TCCGGCTAA\n+\n+>AY457913\n+CCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGAAGC\n+ACTTTTACAGATTTCTTCGGAATGAAGTTTTAGTGACTGAGTGGCGGACGGGTGAGTAACGCGTGGGTAA\n+CCTGCCTCACACAGGGGGATAACAGTTGGAAACGGCTGCTAATACCGCATAAGCGCACAGTACCGCATGG\n+TACAGTGTGAAAAACTCCGGTGGTGTGAGATGGACCCGCGTCTGATTAGCTAGTTGGCAGGGTAACGGCC\n+TACCAAGGCGACGATCAGTAGCCGACCTGAGAGGGTGACCGGCCACATTGGGACTGAGACACGGCCCAAA\n+CTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCGACGCCGCGTGAG\n+CGAAGAAGTATTTCGGTATGTAAAGCTCTATCAGCAGGGAAGAAGAAATGACGGTACCTGACTAAGAAGC\n+ACCGGCAAATCTG\n+\n+>AY457912\n+CCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGAAGC\n+ATTTGCGACAGATTTCTTCGGATTGAAGTTGCTTATGACTGAGTGGCGGACGGGTGAGTAACGCGTGGGT\n+AACCTGCCTCACACAGGGGGATAGCAGTTGGAAACGGCTGATAATACCGCATAAGCGCACAGTACCGCAT\n+GGTACAGTGTGAAAAACTCCGGTGGTGTGAGATGGACCCGCGTCTGATTAGCTTGTTGGCAGGGTAACGG\n+CCTACCAAGGCAACGATCAGTAGCCGACCTGAGAGGGTGACCGGCCACATTGGGACTGAGACACGGCCCA\n+GACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGAGGAAACTCTGATGCAGCGACGCCGCGTG\n+AGTGAAGAAGTAATTCGTTATGTAAAGCTCTATCAGCAGGGAAGATAGTGACGGTACCTGACTAAGAAGC\n+TCCGGCTAATCGT\n+\n+>AY457911\n+CCCTTAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGCGCCTAACACATGCAAGTCGAACGAGCG\n+AGAGAGAGTTTACTTTTTCGAGCGAGTGGCGAACGGGTGAGTAACGCGTGAGGAACCTGCCTCAAAGAGG\n+GGGACAACAGTTGGAAACGACTGCTAATACCGCATAAGCCCACGACCCGGCATCGGGTAGAGGGAAAAGG\n+AGCAATCCGCTTTGAGATGGCCTCGCGTCCGATTAGCTAGTTGGTGAGGTAACGGCCCACCAAGGCGACG\n+ATCGGTAGCCGGACTGAGAGGTTGAACGGCCACATTGGGACTGAGACACGGCCCGGACTCCTACGGGAGG\n+CAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCGACGCCGCGTGGAGGAAGAAGGTCTT\n+CGGATTGTAAACTCCTGTTGTTGGGGGAGATAATGACGGTACTCAACAGGGAAGGACGGCTACTCTG\n+\n+>AY457910\n+CCCTTAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGCGCCTAACACATGCAAGTCGAACGAGAG\n+AGAGGGAGCTTGCTTCCTTGATCGAGTGGCGAACGGGTGAGTAACGCGTGAGGAACCTGCCTCAAAGAGG\n+GGGACAACAGTTGGAAACGACTGCTAATACCGCATAAGCCCACGACCCGGCATCGGGTAGAGGGAAAAGG\n+AGCAATCCGCTTTGAGATGGCCTCGCGTCCGATTAGCTAGTTGGTGAGGTAATGGCCCACCAAGGCGACG\n+ATCGGTAGCCGGACTGAGAGGTTGAACGGCCACATTGGGACTGAGACACGGCCCAGACTCCTACGGGAGG\n+CAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCGACGCCGCGTGGAGGAAGAAGGTCTT\n+CGGATTGTAAACTCCTGTTGTGAGGAAGATAAAGACGGTCTCAACAAGGAAGGACGGCTACTC\n+\n+>AY457909\n+CCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTAGCTACAGGCTTAACACATGCAAGTCGAGGGGCAG\n+CATGGTCTTAGCTTGCTAAGGCCGATGGCGACCGGCGCACGGGTGAGTAACGCGTATCCAACCTGCCTTA\n+CACTCTTGGACAGCCTTCTGAAAGGGAGATTAATACAAGATGTTATCATGAGTAAGCATTTTCGCATGAT\n+TAAAGGTTTACCGGTGTAAGATGGGGATGCGTTCCATTAGATAGTAGGCGGGGTAACGGCCCACCTAGTC\n+TTCGATGGATAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGAACTGAGACACGGTCCAAGCTCCTACGG\n+GAGGCAGCAGTGAGGAATATTGGTCAATGGACGAGAGTCTGAACCAGCCAAGTAGCGTGAAGGATGAAGG\n+TTCTATGGATTGTAAACTTCTTTTATACGGGAATAAACGAATCCACGTGTGGATTTAGCAGTACCGATGA\n+ATA\n+\n+>AY457908\n+CCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGAAGC\n+ACTTTGATCGATTTCTTCGGATTGGAATTTTAGTGACTGAGTGGCGGACGGGTGAGTAACGCGTGGGTAA\n+CCTGCCTCACACAGGGGGATAACAGTTGGAAACGGCTGCTAATACCGCATAAGCGCACAGTACCGCATGG\n+TACAGTGTGAAAAACTCCGGTGGTGTGAGATGGACCCGCGTCTGATTAGCTAGTTGGCAGGGTAACGGCC\n+TACCAAGGCGAC'..b'TCGCAAGACCAAAGTGGGGGACCTTCGGGC\n+CTCATGCCATCAGATGTGCCCAGATGGGATTAGCTAGTAGGTGAGGTAACGGCTCACCTAGGCGACGATC\n+CCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAG\n+CAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTGTGAAGAAGGCCTTCGG\n+GTTGTAAAGCACTTTCAGCGGGGAGGAAGGCGTTAAGGTTAATAACCTTGGCGATTGACGTACCCGCAGA\n+AGAAGCCACCGGCAACTCC\n+\n+>AY457680\n+CCCTTAGAGTTTGATCCTGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAA\n+CAGGAAGCAGCTTGCTGCTTCGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGG\n+AGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGG\n+GCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGA\n+TCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGGCACGGTCCAGACTCCTACGGGAGGC\n+AGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTC\n+GGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGTGCTGAGGTTAATAACCTCAGCAATTGGCGTACCCGCA\n+GAAGAAGCCCGCACTCG\n+\n+>AY457679\n+GCCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTAGCGACAGGCTTAACACATGCAAGTCGAGGGGCA\n+GCACAGGTAGTAATACCGGGTGGCGACCGGCGCACGGGTGAGTAACGCGTATGCAACTTGCCTATCAGAG\n+GGGGATAACCCGGCGAAAGTCGGACTAATACCGCATGAAGCAGGGGCCCCGCATGGGGATATTTGCTAAA\n+GATTCATCGCTGATAGATAGGCATGCGTTCCATTAGGCAGTTGGCGGGGTAACGGCCCACCAAACCGACG\n+ATGGATAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGTACTGAGACACGGACCAAACTCCTACGGGAGG\n+CAGCAGTGAGGAATATTGGTCAATGGCCGAGAGGCTGAACCAGCCAAGTCGCGTGAGGGATGAAGGTTCT\n+ATGGATCGTAAACCTCTTTTATAAGGGAATAAAGTGTGGGACGTGTCCTATTTTGTATGTACCTTAGAAT\n+AAGGATCGGCAA\n+\n+>AY457678\n+CCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTAGCGACAGGCTTAACACATGCAAGTCGAGGGGCAG\n+CGGGGGTAGCAATACCCGCCGGCGACCGGCGCACGGGTGAGTAACGCGTATGCAACTTACCTATCAGAGG\n+GGGATAACCCGGCGAAAGTCGGACTAATACCGCATGGAGCAGGGATCCCGCATGGGAATATTTGCTAAAG\n+ATTCATCGCTGATAGATAGGCATGCGTTCCATTAGGCAGTTGGCGGGGTAACGGCCCACCAAACCGACGA\n+TGGATAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGTACTGAGACACGGACCAAACTCCTACGGGAGGC\n+AGCAGTGAGGAATATTGGTCAATGGCCGAGAGGCTGAACCAGCCCAGTCGCGTGAGGGATGAAGGTTCTA\n+TGGATCGTAAACCTCTTTTATAAGGGAATAAAGTGCGGGACGTGTCCCGTTTGTATGTACCTATGATAGA\n+TGGTA\n+\n+>AY457677\n+GCCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTAGCGACAGGCTTAACACATGCAAGTCGAGGGGCA\n+GCGGGGGTAGCAATACCCGCCGGCGACCGGCGCACGGGTGAGTAACGCGTATGCAACTTACCTATCAGAG\n+GGGGATAACCCGGCGAAAGTCGGACTAATACCGCATGAAGCAGGGATCCCGCATGGGAATATTTGCTAAA\n+GAATTATCGCTGATAGATGGGCATGCGTTCCATTAGATAGTTGGTGAGGTAACGGCTCACCAAGTCCACG\n+ATGGATAGGGGTTCTGAGAGGAAGGTCCCCCACACTGGTACTGAGACACGGACCAGACTCCTACGGGAGG\n+CAGCAGTGAGGAATATTGGTCAATGGGCGAGAGCCTGAACCAGCCAAGTCGCGTGAAGGATGAAGGATCT\n+ATGGTTTGTAAACTTCTTTTATATGGGAATAAAGTGAGGAACGTGTTCCTTTAGTATGTACCATAGAATA\n+AGCATGGCAACTCT\n+\n+>AY457676\n+GCCCTTAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCGGCGCGCCTAACACATGCAAGTCGAACGAGA\n+GATGAGGAGCTTGCTCTTCAAATCGAGTGGCGAACGGGTGAGTAACGCGTGAGGAACCTGCCTCAAAGAG\n+GGGGACAACAGTTGGAAACGACTGCTAATACCGCATAAGCCCACGGCTCGGCATCGAGCAGAGGGAAAAG\n+GAGCAATCCGCTTTGAGATGGCCTCGCGTCCGATTAGCTAGTTGGTGAGGTAACGGCCCACCAAGGCGAC\n+GATCGGTAGCCGGACTGAGAGGTTGAACGGCCACATTGGGACTGAGACACGGCCCAGACTCCTACGGGAG\n+GCAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCGACGCCGCGTGGAGGAAGAAGGTCT\n+TCGGATTGTAAACTCCTGTTGTGAGGAAGATAAAGACGGTACTCAACAAGGAAGCA\n+\n+>AY457675\n+GCTCAGGATGAACGCTAGCGACAGGCTTAACACATGCAAGTCGAGGGGCAGCACGATGTAGCAATACATT\n+GGTGGCGACCGGCGCACGGGTGAGTAACGCGTATGCAACCTACCTATCAGAGGGGAATAACCCGGCGAAA\n+GTCGGACTAATACCGCATAAAACAGGGGTTCCACATGGAAATATTTGTTAAAGAATTATCGCTGATAGAT\n+GGGCATGCGTTCCATTAGATAGTTGGTGAGGTAACGGCTCACCAAGTCCACGATGGATAGGGGTTCTGAG\n+AGGAAGGTCCCCCACACTGGTACTGAGACACGGACCAGACTCCTACGGGAGGCAGCAGTGAGGAATATTG\n+GTCAATGGGCGAGAGCCTGAACCAGCCAAGTCGCGTGAAGGATGAAGGATCTATGGTTTGTAAACTTCTT\n+TTATATGGGAATAAAGTGAGGAACGTGTTCCTTTAGTATGTACCATAGAATAGCATGG\n+\n+>AY457674\n+CCCTTAGAGTTCGATCCTGGCTCAGGATGAACGCTAGCGACAGGCTTAACACATGCAAGTCGAGGGGCAG\n+CACAGGTAGCAATTCCGGGTGGCGACCGGCGCACGGGTGAGTAACGCGTATGCAACTTACCTATCAGAGG\n+GGGATAACCCGGCGAAAGTCGGACTAATACCGCATGAAGCAGGGGCCCCGCATGGGGATATTTGCTAAAG\n+ATTCATCGCTGATAGATAGGCATGCGTTCCATTAGGCAGTTGGCGGGGTAACGGCCCACCAAACCGACGA\n+TGGATAGGGGTTCTGAGAGGAAGGTCCCCCACATTGGTACTGAGACACGGACCAAACTCCTACGGGAGGC\n+AGCAGTGAGGAATATTGGTCAATGGCCGAGAGGCTGAACCAGCCAAGTCGCGTGAGGGATGAAGGTTCTA\n+TGGATCGTAAACCTCTTTTATAAGGGAATAAAGTGCGGGACGTGTCCCGTTAGTATGTACCTATAATAGC\n+ATCGGC\n+\n'
b
diff -r 000000000000 -r bccb5efbc4ee test-data/abrecovery.groups
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/abrecovery.groups Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,242 @@
+AY457915 A
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b
diff -r 000000000000 -r bccb5efbc4ee test-data/abrecovery.names
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/abrecovery.names Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,242 @@
+AY457915 AY457915
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b
diff -r 000000000000 -r bccb5efbc4ee test-data/abrecovery.pds.wang.taxonomy
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/abrecovery.pds.wang.taxonomy Fri May 19 05:47:34 2017 -0400
b
b'@@ -0,0 +1,242 @@\n+AY457915\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Lachnospiracea_incertae_sedis(88);\n+AY457914\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Lachnospiracea_incertae_sedis(100);\n+AY457913\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Roseburia(100);\n+AY457912\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Lachnospiracea_incertae_sedis(96);\n+AY457911\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Faecalibacterium(100);\n+AY457910\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Faecalibacterium(100);\n+AY457909\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);Bacteroidaceae(100);Bacteroides(100);\n+AY457908\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Roseburia(100);\n+AY457907\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);Bacteroidaceae(100);Bacteroides(100);\n+AY457906\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);Bacteroidaceae(100);Bacteroides(100);\n+AY457905\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);Bacteroidaceae(100);Bacteroides(100);\n+AY457904\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);Bacteroidaceae(100);Bacteroides(100);\n+AY457903\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);Bacteroidaceae(100);Bacteroides(100);\n+AY457902\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);Bacteroidaceae(100);Bacteroides(100);\n+AY457901\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Roseburia(100);\n+AY457900\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);Bacteroidaceae(100);Bacteroides(100);\n+AY457899\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);Bacteroidaceae(100);Bacteroides(100);\n+AY457898\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Lachnospiracea_incertae_sedis(67);\n+AY457897\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);Bacteroidaceae(100);Bacteroides(100);\n+AY457896\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);Bacteroidaceae(100);Bacteroides(100);\n+AY457895\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Lachnospiracea_incertae_sedis(98);\n+AY457894\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Lachnospiracea_incertae_sedis(90);\n+AY457893\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Faecalibacterium(100);\n+AY457892\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);Bacteroidaceae(100);Bacteroides(100);\n+AY457891\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Lachnospiracea_incertae_sedis(88);\n+AY457890\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);Bacteroidaceae(100);Bacteroides(100);\n+AY457889\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);Bacteroidaceae(100);Bacteroides(100);\n+AY457888\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Lachnospiracea_incertae_sedis(89);\n+AY457887\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Faecalibacterium(100);\n+AY457886\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);Bacteroidaceae(100);Bacteroides(100);\n+AY457885\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);Bacteroidaceae(100);Bacteroides(100);\n+AY457884\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);Bacteroidaceae(100);Bacteroides(100);\n+AY457883\tBacteria(100);"Bact'..b'0);"Bacteroidales"(100);"Porphyromonadaceae"(100);Parabacteroides(100);\n+AY457703\tBacteria(100);"Proteobacteria"(100);Betaproteobacteria(100);Burkholderiales(100);Sutterellaceae(100);Sutterella(100);\n+AY457702\tBacteria(100);"Proteobacteria"(100);Gammaproteobacteria(100);"Enterobacteriales"(100);Enterobacteriaceae(100);Citrobacter(67);\n+AY457701\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Faecalibacterium(100);\n+AY457700\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);Parabacteroides(100);\n+AY457699\tBacteria(100);"Proteobacteria"(100);Gammaproteobacteria(100);"Enterobacteriales"(100);Enterobacteriaceae(100);Enterobacter(45);\n+AY457698\tBacteria(100);"Proteobacteria"(100);Betaproteobacteria(100);Burkholderiales(100);Sutterellaceae(100);Sutterella(100);\n+AY457697\tBacteria(100);"Proteobacteria"(100);Gammaproteobacteria(100);"Enterobacteriales"(100);Enterobacteriaceae(100);Citrobacter(54);\n+AY457696\tBacteria(100);"Proteobacteria"(100);Gammaproteobacteria(100);"Enterobacteriales"(100);Enterobacteriaceae(100);Enterobacter(36);\n+AY457695\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Faecalibacterium(100);\n+AY457694\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Faecalibacterium(100);\n+AY457693\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);Bacteroidaceae(100);Bacteroides(100);\n+AY457692\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Faecalibacterium(100);\n+AY457691\tBacteria(100);"Proteobacteria"(100);Gammaproteobacteria(100);"Enterobacteriales"(100);Enterobacteriaceae(100);Escherichia_Shigella(95);\n+AY457690\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Faecalibacterium(100);\n+AY457689\tBacteria(100);"Proteobacteria"(100);Gammaproteobacteria(100);"Enterobacteriales"(100);Enterobacteriaceae(100);Citrobacter(54);\n+AY457688\tBacteria(100);"Proteobacteria"(100);Gammaproteobacteria(100);"Enterobacteriales"(100);Enterobacteriaceae(100);Enterobacter(39);\n+AY457687\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);Parabacteroides(100);\n+AY457686\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);Parabacteroides(100);\n+AY457685\tBacteria(100);"Proteobacteria"(100);Gammaproteobacteria(100);"Enterobacteriales"(100);Enterobacteriaceae(100);Enterobacter(69);\n+AY457684\tBacteria(100);"Proteobacteria"(100);Gammaproteobacteria(100);"Enterobacteriales"(100);Enterobacteriaceae(100);Citrobacter(64);\n+AY457683\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);Parabacteroides(100);\n+AY457682\tBacteria(100);Firmicutes(88);Clostridia(76);Clostridiales(76);Ruminococcaceae(46);Pseudoflavonifractor(16);\n+AY457681\tBacteria(100);"Proteobacteria"(100);Gammaproteobacteria(100);"Enterobacteriales"(100);Enterobacteriaceae(100);Klebsiella(99);\n+AY457680\tBacteria(100);"Proteobacteria"(100);Gammaproteobacteria(100);"Enterobacteriales"(100);Enterobacteriaceae(100);Citrobacter(78);\n+AY457679\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);Parabacteroides(100);\n+AY457678\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);Parabacteroides(100);\n+AY457677\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);Parabacteroides(100);\n+AY457676\tBacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Faecalibacterium(100);\n+AY457675\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);Parabacteroides(100);\n+AY457674\tBacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);Parabacteroides(100);\n'
b
diff -r 000000000000 -r bccb5efbc4ee test-data/abrecovery.pds.wang.tree.sum
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/abrecovery.pds.wang.tree.sum Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,174 @@
+#1.36.1
+171
+6
+0 Root 3 Bacteria 2 unclassified 59 unknown 1
+1 unknown 1 unclassified 117
+1 Bacteria 6 "Actinobacteria" 32 "Bacteroidetes" 3 "Proteobacteria" 13 Firmicutes 8 TM7 40 unclassified 60
+2 "Bacteroidetes" 2 "Bacteroidia" 4 unclassified 66
+3 "Bacteroidia" 2 "Bacteroidales" 5 unclassified 67
+4 "Bacteroidales" 3 "Porphyromonadaceae" 6 Bacteroidaceae 22 unclassified 68
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+6 Parabacteroides 1 unclassified 70
+2 Firmicutes 4 Clostridia 9 Erysipelotrichia 55 Negativicutes 47 unclassified 88
+3 Clostridia 2 Clostridiales 10 unclassified 89
+4 Clostridiales 4 Lachnospiraceae 28 Peptostreptococcaceae 30 Ruminococcaceae 11 unclassified 90
+5 Ruminococcaceae 4 Faecalibacterium 12 Pseudoflavonifractor 19 Subdoligranulum 53 unclassified 100
+6 Faecalibacterium 1 unclassified 101
+2 "Proteobacteria" 3 Betaproteobacteria 24 Gammaproteobacteria 14 unclassified 73
+3 Gammaproteobacteria 3 "Enterobacteriales" 15 Pasteurellales 37 unclassified 78
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+5 Enterobacteriaceae 5 Citrobacter 17 Enterobacter 20 Escherichia_Shigella 21 Klebsiella 18 unclassified 80
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+6 Lachnospiracea_incertae_sedis 1 unclassified 96
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+4 Selenomonadales 2 Acidaminococcaceae 49 unclassified 109
+5 Acidaminococcaceae 2 Phascolarctobacterium 50 unclassified 110
+6 Phascolarctobacterium 1 unclassified 111
+6 Clostridium_XlVa 1 unclassified 93
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+4 Erysipelotrichales 2 Erysipelotrichaceae 57 unclassified 105
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b
diff -r 000000000000 -r bccb5efbc4ee test-data/abrecovery.tre
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/abrecovery.tre Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,1 @@
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b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.accnos.otulabels
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.accnos.otulabels Fri May 19 05:47:34 2017 -0400
b
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b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.align_head
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.align_head Fri May 19 05:47:34 2017 -0400
b
b'@@ -0,0 +1,6 @@\n+>U68589\n+.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................'..b'................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................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b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.align_head.count_table
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.align_head.count_table Fri May 19 05:47:34 2017 -0400
b
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b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.align_head.list
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.align_head.list Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,4 @@
+label numOtus Otu1 Otu2 Otu3
+unique 3 U68589 U68590 U68591
+0.30 2 U68589,U68590 U68591
+0.33 1 U68589,U68590,U68591
b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.align_head.names
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.align_head.names Fri May 19 05:47:34 2017 -0400
b
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b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.align_head.wang.taxonomy
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.align_head.wang.taxonomy Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,3 @@
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b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.align_head_short
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.align_head_short Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,6 @@
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b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.an.0.03.-.0.05.otu.hierarchy
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.an.0.03.-.0.05.otu.hierarchy Fri May 19 05:47:34 2017 -0400
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diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.an.jclass.unique.tre
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.an.jclass.unique.tre Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,1 @@
+(pasture:0.5,forest:0.5):0;
b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.an.list
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.an.list Fri May 19 05:47:34 2017 -0400
b
b'@@ -0,0 +1,37 @@\n+label\tnumOtus\tOtu01\tOtu02\tOtu03\tOtu04\tOtu05\tOtu06\tOtu07\tOtu08\tOtu09\tOtu10\tOtu11\tOtu12\tOtu13\tOtu14\tOtu15\tOtu16\tOtu17\tOtu18\tOtu19\tOtu20\tOtu21\tOtu22\tOtu23\tOtu24\tOtu25\tOtu26\tOtu27\tOtu28\tOtu29\tOtu30\tOtu31\tOtu32\tOtu33\tOtu34\tOtu35\tOtu36\tOtu37\tOtu38\tOtu39\tOtu40\tOtu41\tOtu42\tOtu43\tOtu44\tOtu45\tOtu46\tOtu47\tOtu48\tOtu49\tOtu50\tOtu51\tOtu52\tOtu53\tOtu54\tOtu55\tOtu56\tOtu57\tOtu58\tOtu59\tOtu60\tOtu61\tOtu62\tOtu63\tOtu64\tOtu65\tOtu66\tOtu67\tOtu68\tOtu69\tOtu70\tOtu71\tOtu72\tOtu73\tOtu74\tOtu75\tOtu76\tOtu77\tOtu78\tOtu79\tOtu80\tOtu81\tOtu82\tOtu83\tOtu84\tOtu85\tOtu86\tOtu87\tOtu88\tOtu89\tOtu90\tOtu91\tOtu92\tOtu93\tOtu94\tOtu95\tOtu96\tOtu97\tOtu98\n+unique\t96\tU68667,U68641\tU68620,U68618\tU68663\tU68662\tU68661\tU68660\tU68659\tU68658\tU68657\tU68656\tU68655\tU68654\tU68653\tU68652\tU68651\tU68649\tU68648\tU68647\tU68646\tU68645\tU68644\tU68643\tU68642\tU68640\tU68639\tU68688\tU68687\tU68686\tU68685\tU68684\tU68683\tU68682\tU68681\tU68680\tU68679\tU68678\tU68677\tU68676\tU68675\tU68674\tU68673\tU68672\tU68671\tU68670\tU68669\tU68668\tU68666\tU68665\tU68664\tU68613\tU68612\tU68611\tU68610\tU68609\tU68608\tU68607\tU68606\tU68605\tU68603\tU68602\tU68601\tU68600\tU68599\tU68598\tU68597\tU68596\tU68595\tU68594\tU68593\tU68592\tU68591\tU68590\tU68589\tU68638\tU68637\tU68636\tU68635\tU68634\tU68633\tU68632\tU68631\tU68630\tU68629\tU68628\tU68627\tU68626\tU68625\tU68624\tU68623\tU68622\tU68621\tU68619\tU68617\tU68616\tU68615\tU68614\n+0.01\t93\tU68688,U68665\tU68636,U68631\tU68667,U68641\tU68620,U68618\tU68680,U68615\tU68661\tU68660\tU68659\tU68658\tU68657\tU68656\tU68655\tU68654\tU68653\tU68652\tU68651\tU68649\tU68648\tU68647\tU68646\tU68645\tU68644\tU68643\tU68642\tU68640\tU68639\tU68687\tU68686\tU68685\tU68684\tU68683\tU68682\tU68681\tU68679\tU68678\tU68677\tU68676\tU68675\tU68674\tU68673\tU68672\tU68671\tU68670\tU68669\tU68668\tU68666\tU68664\tU68663\tU68662\tU68613\tU68612\tU68611\tU68610\tU68609\tU68608\tU68607\tU68606\tU68605\tU68603\tU68602\tU68601\tU68600\tU68599\tU68598\tU68597\tU68596\tU68595\tU68594\tU68593\tU68592\tU68591\tU68590\tU68589\tU68638\tU68637\tU68635\tU68634\tU68633\tU68632\tU68630\tU68629\tU68628\tU68627\tU68626\tU68625\tU68624\tU68623\tU68622\tU68621\tU68619\tU68617\tU68616\tU68614\n+0.02\t90\tU68688,U68665,U68679,U68663\tU68673,U68667,U68641\tU68636,U68631\tU68620,U68618\tU68680,U68615\tU68658\tU68657\tU68656\tU68655\tU68686\tU68654\tU68653\tU68652\tU68651\tU68649\tU68648\tU68647\tU68646\tU68645\tU68644\tU68643\tU68642\tU68640\tU68639\tU68638\tU68687\tU68683\tU68682\tU68681\tU68684\tU68678\tU68677\tU68676\tU68675\tU68674\tU68685\tU68672\tU68671\tU68670\tU68669\tU68668\tU68666\tU68664\tU68662\tU68661\tU68660\tU68659\tU68612\tU68611\tU68610\tU68609\tU68608\tU68607\tU68606\tU68605\tU68603\tU68602\tU68601\tU68600\tU68599\tU68598\tU68597\tU68596\tU68595\tU68594\tU68593\tU68592\tU68591\tU68590\tU68589\tU68637\tU68635\tU68634\tU68633\tU68632\tU68630\tU68629\tU68628\tU68627\tU68626\tU68625\tU68624\tU68623\tU68622\tU68621\tU68619\tU68617\tU68616\tU68614\tU68613\n+0.03\t88\tU68688,U68665,U68679,U68663\tU68658,U68638,U68620,U68618\tU68673,U68667,U68641\tU68636,U68631\tU68680,U68615\tU68686\tU68657\tU68656\tU68655\tU68654\tU68653\tU68652\tU68651\tU68649\tU68648\tU68647\tU68646\tU68645\tU68644\tU68643\tU68642\tU68640\tU68639\tU68637\tU68687\tU68683\tU68682\tU68681\tU68684\tU68678\tU68677\tU68676\tU68675\tU68674\tU68685\tU68672\tU68671\tU68670\tU68669\tU68668\tU68666\tU68664\tU68662\tU68661\tU68660\tU68659\tU68613\tU68612\tU68611\tU68610\tU68609\tU68608\tU68607\tU68606\tU68605\tU68603\tU68602\tU68601\tU68600\tU68599\tU68598\tU68597\tU68596\tU68595\tU68594\tU68593\tU68592\tU68591\tU68590\tU68589\tU68635\tU68634\tU68633\tU68632\tU68630\tU68629\tU68628\tU68627\tU68626\tU68625\tU68624\tU68623\tU68622\tU68621\tU68619\tU68617\tU68616\tU68614\n+0.04\t83\tU68688,U68665,U68679,U68663\tU68658,U68638,U68620,U68618\tU68673,U68667,U68641\tU68636,U68631\tU68637,U68602\tU68652,U68610\tU68614,U68596\tU68678,U68619\tU68680,U68615\tU68681,U68677\tU68656\tU68655\tU68654\tU68653\tU68685\tU68651\tU68649\tU68648\tU68647\tU68646\tU68645\tU68644\tU68643\tU68642\tU68640\tU68639\tU68686\tU68687\tU68676\tU68675\tU68674\tU68682\tU68672\tU68671\tU68670\tU68669\tU68668\tU68666\tU68664\tU68662\tU68661\tU68660\tU68683\tU68659\tU68684\tU68657\tU68613\tU68612\tU68611\tU68609\tU68608\tU68607\tU68606\tU68605\tU68603\tU68601\tU68600\tU68599\tU68598\tU68597\tU68595\tU68594\tU68593\tU68592\tU68591\tU68590\tU68589\tU68635\tU68634\t'..b'677,U68669,U68589,U68642,U68599,U68686,U68635,U68613,U68637,U68602,U68678,U68619,U68645,U68673,U68667,U68641,U68598,U68658,U68638,U68620,U68618,U68659,U68624,U68655,U68651,U68640,U68633,U68612,U68648,U68632,U68605,U68597,U68684,U68654,U68593,U68649,U68639,U68606,U68646,U68590,U68644,U68680,U68615,U68670,U68611,U68625,U68672,U68621,U68656,U68668,U68662,U68661,U68594,U68687,U68592,U68685,U68683,U68652,U68610,U68671,U68666,U68595,U68636,U68631\tU68682,U68657,U68675,U68627,U68609,U68603,U68643\tU68600,U68591\tU68664\tU68622\tU68608\n+0.36\t5\tU68688,U68665,U68679,U68663,U68653,U68676,U68660,U68647,U68626,U68623,U68674,U68630,U68634,U68628,U68601,U68607,U68629,U68617,U68614,U68596,U68616,U68681,U68677,U68669,U68589,U68642,U68599,U68686,U68635,U68613,U68637,U68602,U68678,U68619,U68645,U68673,U68667,U68641,U68598,U68658,U68638,U68620,U68618,U68659,U68624,U68655,U68651,U68640,U68633,U68612,U68648,U68632,U68605,U68597,U68684,U68654,U68593,U68649,U68639,U68606,U68646,U68590,U68644,U68680,U68615,U68670,U68611,U68625,U68672,U68621,U68656,U68668,U68662,U68661,U68594,U68687,U68592,U68685,U68683,U68652,U68610,U68671,U68666,U68595,U68636,U68631,U68600,U68591\tU68682,U68657,U68675,U68627,U68609,U68603,U68643\tU68622\tU68664\tU68608\n+0.38\t4\tU68688,U68665,U68679,U68663,U68653,U68676,U68660,U68647,U68626,U68623,U68674,U68630,U68634,U68628,U68601,U68607,U68629,U68617,U68614,U68596,U68616,U68681,U68677,U68669,U68589,U68642,U68599,U68686,U68635,U68613,U68637,U68602,U68678,U68619,U68645,U68673,U68667,U68641,U68598,U68658,U68638,U68620,U68618,U68659,U68624,U68655,U68651,U68640,U68633,U68612,U68648,U68632,U68605,U68597,U68684,U68654,U68593,U68649,U68639,U68606,U68646,U68590,U68644,U68680,U68615,U68670,U68611,U68625,U68672,U68621,U68656,U68668,U68662,U68661,U68594,U68687,U68592,U68685,U68683,U68652,U68610,U68671,U68666,U68595,U68636,U68631,U68600,U68591,U68622\tU68682,U68657,U68675,U68627,U68609,U68603,U68643\tU68664\tU68608\n+0.41\t3\tU68688,U68665,U68679,U68663,U68653,U68676,U68660,U68647,U68626,U68623,U68674,U68630,U68634,U68628,U68601,U68607,U68629,U68617,U68614,U68596,U68616,U68681,U68677,U68669,U68589,U68642,U68599,U68686,U68635,U68613,U68637,U68602,U68678,U68619,U68645,U68673,U68667,U68641,U68598,U68658,U68638,U68620,U68618,U68659,U68624,U68655,U68651,U68640,U68633,U68612,U68648,U68632,U68605,U68597,U68684,U68654,U68593,U68649,U68639,U68606,U68646,U68590,U68644,U68680,U68615,U68670,U68611,U68625,U68672,U68621,U68656,U68668,U68662,U68661,U68594,U68687,U68592,U68685,U68683,U68652,U68610,U68671,U68666,U68595,U68636,U68631,U68600,U68591,U68622,U68682,U68657,U68675,U68627,U68609,U68603,U68643\tU68664\tU68608\n+0.45\t2\tU68688,U68665,U68679,U68663,U68653,U68676,U68660,U68647,U68626,U68623,U68674,U68630,U68634,U68628,U68601,U68607,U68629,U68617,U68614,U68596,U68616,U68681,U68677,U68669,U68589,U68642,U68599,U68686,U68635,U68613,U68637,U68602,U68678,U68619,U68645,U68673,U68667,U68641,U68598,U68658,U68638,U68620,U68618,U68659,U68624,U68655,U68651,U68640,U68633,U68612,U68648,U68632,U68605,U68597,U68684,U68654,U68593,U68649,U68639,U68606,U68646,U68590,U68644,U68680,U68615,U68670,U68611,U68625,U68672,U68621,U68656,U68668,U68662,U68661,U68594,U68687,U68592,U68685,U68683,U68652,U68610,U68671,U68666,U68595,U68636,U68631,U68600,U68591,U68622,U68682,U68657,U68675,U68627,U68609,U68603,U68643,U68664\tU68608\n+0.55\t1\tU68688,U68665,U68679,U68663,U68653,U68676,U68660,U68647,U68626,U68623,U68674,U68630,U68634,U68628,U68601,U68607,U68629,U68617,U68614,U68596,U68616,U68681,U68677,U68669,U68589,U68642,U68599,U68686,U68635,U68613,U68637,U68602,U68678,U68619,U68645,U68673,U68667,U68641,U68598,U68658,U68638,U68620,U68618,U68659,U68624,U68655,U68651,U68640,U68633,U68612,U68648,U68632,U68605,U68597,U68684,U68654,U68593,U68649,U68639,U68606,U68646,U68590,U68644,U68680,U68615,U68670,U68611,U68625,U68672,U68621,U68656,U68668,U68662,U68661,U68594,U68687,U68592,U68685,U68683,U68652,U68610,U68671,U68666,U68595,U68636,U68631,U68600,U68591,U68622,U68682,U68657,U68675,U68627,U68609,U68603,U68643,U68664,U68608\n'
b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.an.rabund
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.an.rabund Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,36 @@
+unique 96 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+0.01 93 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+0.02 90 4 3 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+0.03 88 4 4 3 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+0.04 83 4 4 3 2 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+0.05 78 4 4 3 3 2 2 2 2 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+0.06 69 4 4 4 4 3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+0.07 65 7 4 4 4 3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+0.08 56 11 7 4 4 3 3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+0.09 55 11 7 5 4 4 3 3 2 2 2 2 2 2 2 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+0.10 49 16 7 5 4 4 4 4 4 2 2 2 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+0.11 45 16 8 8 5 4 4 4 3 3 2 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+0.12 43 17 8 8 5 4 4 4 3 3 3 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+0.13 40 17 8 8 8 5 5 4 3 3 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+0.14 36 19 8 8 8 6 5 4 3 3 2 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+0.15 35 21 8 8 8 6 5 4 3 3 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+0.16 34 21 8 8 8 6 5 4 3 3 3 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+0.17 33 21 10 8 8 6 5 4 3 3 3 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+0.18 31 21 10 8 8 6 5 4 4 3 3 3 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+0.19 30 21 10 8 8 6 5 4 4 3 3 3 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+0.20 27 23 11 10 8 6 5 4 4 3 3 3 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+0.21 25 23 11 10 9 9 5 4 4 3 3 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1
+0.22 23 23 11 11 10 9 5 4 4 4 3 2 1 1 1 1 1 1 1 1 1 1 1 1
+0.23 21 23 21 11 9 5 5 4 4 3 2 1 1 1 1 1 1 1 1 1 1 1
+0.24 17 36 21 11 5 5 5 4 2 1 1 1 1 1 1 1 1 1
+0.25 15 36 21 11 6 5 5 5 2 1 1 1 1 1 1 1
+0.26 13 36 26 11 6 5 5 2 2 1 1 1 1 1
+0.27 12 36 26 11 10 6 2 2 1 1 1 1 1
+0.29 9 73 11 6 2 2 1 1 1 1
+0.32 7 75 11 7 2 1 1 1
+0.33 6 86 7 2 1 1 1
+0.36 5 88 7 1 1 1
+0.38 4 89 7 1 1
+0.41 3 96 1 1
+0.45 2 97 1
+0.55 1 98
b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.an.rabund2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.an.rabund2 Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,2 @@
+0.03 88 4 4 3 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+0.05 78 4 4 3 3 2 2 2 2 2 2 2 2 2 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.an.relabund
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.an.relabund Fri May 19 05:47:34 2017 -0400
b
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b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.an.sabund
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.an.sabund Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,36 @@
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b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.an.sabund2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.an.sabund2 Fri May 19 05:47:34 2017 -0400
b
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b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.an.sabund3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.an.sabund3 Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,2 @@
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b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.an.shared
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.an.shared Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,73 @@
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b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.bad.accnos
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.bad.accnos Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,8 @@
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\ No newline at end of file
b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.count_table
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.count_table Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,97 @@
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b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.design
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.design Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,98 @@
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b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.dist
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.dist Fri May 19 05:47:34 2017 -0400
b
b'@@ -0,0 +1,1079 @@\n+   98\n+U68589      0.0000  0.3371  0.3610  0.4155  0.2873  0.2971  0.3922  0.3093\n+  0.3201  0.3286  0.2572  0.3372  0.3018  0.3071  0.4777  0.3648  0.3204\n+  0.3407  0.6434  0.4331  0.3762  0.3515  0.3733  0.3251  0.2890  0.3103\n+  0.3070  0.3086  0.3250  0.3681  0.3250  0.2597  0.4092  0.2733  0.3488\n+  0.3388  0.2899  0.4602  0.2873  0.3049  0.2936  0.3987  0.3235  0.3439\n+  0.2703  0.3286  0.3607  0.3176  0.3073  0.3182  0.3152  0.3345  0.2594\n+  0.5133  0.3212  0.3821  0.3390  0.3115  0.3411  0.3062  0.3437  0.3485\n+  0.2439  0.3016  0.3715  0.3771  0.4282  0.3436  0.3635  0.3206  0.3771\n+  0.3346  0.3287  0.4388  0.3095  0.3944  0.3345  0.3387  0.2283  0.3761\n+  0.3489  0.2828  0.2816  0.2895  0.4601  0.2903  0.2259  0.3539  0.3016\n+  0.3183  0.2369  0.3874  0.3297  0.3066  0.3654  0.3229  0.4123  0.3236\n+U68590      0.3371  0.0000  0.3783  0.3198  0.1690  0.3293  0.2732  0.3127\n+  0.2668  0.2063  0.3287  0.3411  0.3238  0.2204  0.3626  0.2744  0.2012\n+  0.3175  0.5300  0.3734  0.2947  0.2866  0.2931  0.2144  0.3049  0.2940\n+  0.2963  0.3189  0.2282  0.2156  0.2282  0.2853  0.3831  0.2878  0.2485\n+  0.3304  0.3313  0.3592  0.3143  0.2825  0.3082  0.2735  0.2652  0.2726\n+  0.3239  0.2165  0.2818  0.2416  0.2304  0.2282  0.2555  0.2197  0.3572\n+  0.5077  0.1781  0.2154  0.1337  0.2925  0.2802  0.2065  0.2254  0.3009\n+  0.2699  0.2161  0.2744  0.3121  0.3651  0.2441  0.2394  0.3227  0.3310\n+  0.3473  0.3072  0.4101  0.3002  0.2786  0.2197  0.3049  0.2742  0.3049\n+  0.3049  0.2788  0.1909  0.2788  0.3798  0.3109  0.2812  0.2159  0.3104\n+  0.2972  0.2872  0.3864  0.3073  0.1999  0.3135  0.2232  0.3135  0.3167\n+U68591      0.3610  0.3783  0.0000  0.4148  0.3362  0.3564  0.4275  0.3227\n+  0.3521  0.3450  0.3697  0.1228  0.3730  0.3696  0.4679  0.3771  0.3241\n+  0.3658  0.5488  0.4901  0.4507  0.3637  0.3966  0.3635  0.3113  0.3294\n+  0.3474  0.3287  0.3841  0.3973  0.3841  0.3155  0.4150  0.3107  0.3885\n+  0.3597  0.3341  0.5000  0.3508  0.3331  0.3334  0.4421  0.3194  0.3952\n+  0.3556  0.3728  0.4260  0.3673  0.3630  0.3421  0.3630  0.3926  0.4251\n+  0.5188  0.3448  0.4339  0.3607  0.3692  0.3207  0.3254  0.3831  0.3795\n+  0.3474  0.3170  0.4213  0.3783  0.4458  0.4139  0.4225  0.3803  0.3783\n+  0.3700  0.3824  0.3949  0.3365  0.4508  0.3926  0.3204  0.3694  0.3711\n+  0.4122  0.3221  0.3075  0.3254  0.4581  0.3383  0.3535  0.3900  0.3307\n+  0.3336  0.3656  0.4200  0.4257  0.3212  0.4051  0.3718  0.4083  0.3730\n+U68592      0.4155  0.3198  0.4148  0.0000  0.2842  0.3326  0.2299  0.3633\n+  0.3252  0.2652  0.3390  0.3643  0.3504  0.2667  0.4185  0.3312  0.3012\n+  0.3844  0.5872  0.4165  0.2159  0.3197  0.3597  0.2546  0.3328  0.3390\n+  0.3264  0.3475  0.2817  0.3122  0.2817  0.3732  0.3597  0.3652  0.3019\n+  0.3625  0.3821  0.4203  0.3564  0.3422  0.3402  0.1795  0.3269  0.2984\n+  0.3025  0.2606  0.1645  0.2758  0.2681  0.3556  0.3034  0.2952  0.3471\n+  0.5563  0.3534  0.2815  0.3542  0.3553  0.3450  0.3281  0.2975  0.2135\n+  0.3261  0.3236  0.3118  0.3366  0.4250  0.2995  0.2778  0.3740  0.3994\n+  0.3624  0.3696  0.4420  0.3808  0.2115  0.2952  0.3265  0.3703  0.3633\n+  0.1765  0.3656  0.2376  0.3093  0.3784  0.3468  0.3311  0.2884  0.3858\n+  0.3365  0.3633  0.4019  0.1811  0.2960  0.1160  0.2765  0.0659  0.3824\n+U68593      0.2873  0.1690  0.3362  0.2842  0.0000  0.2769  0.2831  0.2918\n+  0.2174  0.1894  0.2942  0.3024  0.2846  0.2196  0.3851  0.2575  0.1229\n+  0.3240  0.5188  0.3912  0.2846  0.2539  0.2732  0.2139  0.2678  0.2743\n+  0.2711  0.2911  0.2146  0.2406  0.2146  0.2236  0.3441  0.2473  0.2364\n+  0.2225  0.2542  0.3966  0.2898  0.2785  0.2599  0.2832  0.2255  0.2448\n+  0.2681  0.2028  0.2698  0.2141  0.1969  0.1134  0.2321  0.2310  0.3243\n+  0.4861  0.2113  0.2501  0.1830  0.2924  0.2326  0.1121  0.2294  0.3037\n+  0.2600  0.0787  0.2485  0.3127  0.3650  0.2276  0.2835  0.3146  0.3340\n+  0.2882  0.3299  0.3826  0.2870  0.2957  0.2310  0.2758  0.2858  0.2845\n+  0.2702  0.2408  0.1779  0.2396  0.3425'..b'1979  0.1639  0.2876  0.2931  0.2594  0.1844  0.4162  0.2239  0.1163\n+  0.3280  0.5025  0.3974  0.3049  0.2436  0.2382  0.1881  0.2514  0.2661\n+  0.2654  0.2599  0.1838  0.2098  0.1838  0.1956  0.3388  0.2580  0.2094\n+  0.2042  0.2614  0.4086  0.2715  0.2550  0.2416  0.3071  0.2028  0.2178\n+  0.2470  0.1876  0.2873  0.1937  0.1635  0.1330  0.2133  0.2070  0.3056\n+  0.4695  0.1817  0.2121  0.1979  0.2639  0.2168  0.1216  0.1802  0.3103\n+  0.2306  0.1229  0.2534  0.2555  0.3635  0.2031  0.2291  0.2962  0.3166\n+  0.2526  0.2874  0.4059  0.2715  0.3218  0.2070  0.2200  0.2824  0.2819\n+  0.2698  0.2137  0.1765  0.2195  0.3309  0.2388  0.2552  0.1872  0.2644\n+  0.2669  0.2782  0.3729  0.2932  0.0000  0.3094  0.1868  0.3584  0.2862\n+U68685      0.3654  0.3135  0.4051  0.1160  0.3003  0.3093  0.2277  0.3496\n+  0.3194  0.2925  0.3441  0.3480  0.3291  0.2820  0.4781  0.3340  0.3094\n+  0.3606  0.5865  0.4103  0.2122  0.3588 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b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.fasta Fri May 19 05:47:34 2017 -0400
b
b'@@ -0,0 +1,196 @@\n+>U68589\n+TAATACGTAGGGTGCAAGCGTTGCCCGGGTTTATTGGGCGTAAAGGGCGCGTAGGCGGCTCGACACGTCCGTTGTGAAATCGCCCGGCTCAACTGGCGGGGTCAGCGGATACGGTCGAGCTTGAGCAAGCTAGGGGGCAATGGAATTCCCGGTGTAGTGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGTTGCCTGGGGCTTTGCTGACGCTGATGCGCGAAAGCGTGGGGAGCGATCCGGATTAGATACCCGGGTAGTCCACGCCGTAAACGATGTCGACTAAGCGTCGGGGGTATCGACCCCTCGGCCCGCAGCTAACGCATTAAGTCAACCGCCTGGGGACTACGGCCGCCAGGCTAAAACTCAAAGAATTGACGGGGGCCGCACAGCAGCGACGTGTGTTTAATTCGATGNACGCGCAGAACCNTACNTCNGCNTTGACATGCACGTNGTACTGACCNGAAANGGAAGGGACCCGCGAGGGAGCGTGCACAGATGNTGCATGGCTGTCGTCAGTTCGTGCCGTGAGGTGTTGGGTTAAGTCCCGCAACGAGGCGCAACCCTTGTCCCTTAGTTGCCTTTTCTAAGGAGACCGCCGGTCTAAACCGGAGGAAGGTGGGGATGACGTCAAGTCAGCACGGCTCTTACGTCGAGGGCTACACACACGCTACAATGGCCGGTACAACGGGCTGCCAAGGGGTGACCTGGAGCTAACCCCACCAAAGCCGGTCTCAGTTCGGATTGCAGACTGCAACTCGCCTGCATGAAGTCGGAGTTGCTAGTAANTGCCAGTCAGCACATGGCAGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTTGGATACGCCTGAAGCCGGTGGCCTAACCCGCAAGGGAGGGAGCCGTCGAGGGCGGAGCCAGCGATTGGGACG\n+>U68590\n+TAATACGGGGGGAGCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTATGCGGCCAGCGCAAGTCAGTTGTGAAATCTCCGGGCTTAACTCGGAACGGTCAACTGATACTGCGCGGCTAGAGTGCGGAAGGGGCAACTGGAATTCTCGGTGTAGCGGTGAAATGCGTAGATATCGAGAGGAACACCTGCGGCGAAAGCGGGTTGCTGGGCCGACACTGACGCTGATGCGCGAAAGCCAGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCTGGCCTTAAACGATGGATGCTTGGTGTCTGGAGTTTTATAATCTCCGGGTGCCGCAGCTAACGCGTTAAGCATCCCCCCTGGGGAGTACGGTCGCAAGACTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTCAATTCGACGCAACCCGAAAGAACTTACCTGGGCTAGAATGCCTCTGACACCCTAGAAATACGGTTTC\n+>U68591\n+CGTAGGGTCCAAGCGTTATCCGGAATTACTGGGCGTAAAGAGTTGCGTAGGTGGCATAGTAAGCAGATAGTGAAATGATACGGCTCAACCGTATGTCCATTATCTGAACTGCTAAGCTTGAGCATGGTAGAGGTAGCTGGAATTGCTAGTGTAGGAGTGGAATCCGTAGATATTAGCAGGAACACCGATGGCGTAGGCAGGCTACTGGGCTATTGCTGACACTAAGGCACGAAAGCGTGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCACGCCGTAAACTATGGATGCTAGCTGTAATCAGTATCGACCCTGGTTGTAGCGAAGCTAACGCGTTAAGCATCCCGCCTGTGGAGTACCGCCGCAAGGCTAAAACATAAAGGAATTGACGGGGTCTCGCACAAGCGGTGGAGCGTGTTGTTTAATTCGACGNTAAGCGCAGAACCTTACCAAGGTTTGACATCCTGATAAGGTCTCCGAAAGGAGACTGTACCTTCGGGCTCCAGTGACAGGTGATGCATGGCCGTCGTCAGCTCGTGTCGTGAGATGTTTGGTTAAGTCCATCAACGAGCGCAACCCTTATAGTTAGTTGAATTTCTCTAGCTAGACTGCCCCGGTAACGGGGAGGAAGGAGGGGATGATGTCAGGTCATTATTTCCCTTACACCTTGGGCGACAAACACGCTACAATGGCCGGTACAAAGGGCTGCCAAGCAGTAATGTGGAGCAAATCCCATCAAAGCCGGTCCCAGTTCGGATTGAGGGCTGAAACTCGCCCTCATGAAGCCGGAATCGCTAGTAATGGCAGGTCAGCACACTGCCGTGAATACGTTCCCGAGACTTGTACACACCGCCCGTCAAACCATGAAAGTCGCAAATACCCGAAGTCCAACCTCAGGTTGGCCTAAGGTAGGGGAGATGATTGGGGTT\n+>U68592\n+TAATACAGAGGTCCCGAGCGTTGTTCGGATTCACTGGGCGTAAAGGGTGCGTAGGTGGTGGGATAAGTCGGATGTGAAATCTCGGAGCTCAACTCCGAAAATGCATTGGAAACTGTCCTGCTAGAGGGTTGGAGGGGGGACTGGAATACTTGGTGTAGCAGTGAAATGCGTAGATATCAAGTGGAACACCGGTGGCGAAGGCGAGTCCCTGGACAACACCTGACACTGAGGCACGAAAGCTAGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCTAGCCGTAAACGGTGCACGTTTGCTGTAAGAGGAATCGACCCCTTTTGTGGCGAAGCCAACGCGATAAACGTGCCGCCTGGGGAAGTACGGTCGCAAGATTAAAACTCAAAGAAATTGACGGGGGCCTGCACAAGCCGGTGGAGTATGTGGCTCAATTCGATGCCACGCCAAAGAACCTTACCTGGCCTTGACATGCACGTAGTTAGGAAGATGAAAATCCGACGAGGTAGCAATTCCAGCGTGCACAGGTGCT\n+>U68593\n+TAATACGTAAGGACCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTANGCGGCATGACAAGTCACTTGTGAAATCTCCGGGCTTAACTCGGAACGGCCAAGTGATACTGTCGCGCTAGAGTGCGGAAGGGGCAATCAGAATTCTTGGTGTAGCGGTGAAATGCGTAGATATCTGGAGGAACACCGGTGGCGAAGGCGGCATCCTGGACCAATTCTGACGCTGAGTGAGCGAAAGCCAGGGGAGCAAACGGGATTAGATACCCCGGTAGTCCTGGCCCTAGACGATGAATGCTTGGTGTGGCGGGTATCGATCCCTGCCGTGCCGAAGCTAACGCATTAAGCATTCCGCCTGGGGAGTACGGTCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGANCATGTGGTTCAATTCGACGCNACGCGAAGAACTTACCCAGGCTTGAACAGCGAGTGACTGCTTACGAAAGTAAGTTTCCGCAAGGACACTCGTAGAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTTTGCTGTTGNCCATCAGGTTATGCTGGGCACTCTGCAAAGACTGCCGGNTGATAAACCGGAGGAAGGTGGGGATGACGTCAAGTCAGCATGGCNTTTATGTCTGGGGCTACACACGTGCTACAATGGCCGACACAAACCGTCGCGAGCCCGCGAGGGGGAGCTAATCGGAGAAAGTCGGTCTCAGTTCGGATAGCAGGCTGCAACTCGCCTGCTTGAAGTTGGAATCGCTAGTAATCGCGGATCAGCACGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACATCACGAAAGCCGGTTGTACTAGAAGTCGTCATACCAACCCGCAAGGGAGGGAGGCGCCTAAGGTATGGTCGGTGATTGGGGTG\n+>U68594\n+TAATCCCAAGGGTGCAANCGTTACTCGGAATTACTGGGCGTAAAGCGTGCG'..b'GGGCGTAAAGGGTGCGTANGCGGCGCGGTAAGTCGGGTGTGAAATCTCGGAGCTTAACTCCGAAACTGCATTCGATACTGCCGTGCTTGAGGACTGGAGANGAGACTGGAATTTACGGTGTAGCGGTGAAATGCGTATATATCGTAAGGAAGACCAGTGGCGAAGGCGGGTCTCTGGACAGTTCCTGACGCTGANGCACGAAGGCCAGGGGAGCAAACGGGATTAGATACCCCGGTAGTCCTGGCAGTAAACGGTGCACCTTTGGTGTGGGAGGATTCGACCCCTTCCGTGCCGGAGCTAACGCGTTAAACCTTGCCGCCTGGTGGAGTACGGTCCGCAAGATTAAAACTCACACAAATTGACGGGGGCCCGCACAAGCGGTGGAGTATGTGGCTTAATTCCATGCAACGCGAAGAACCTTTATCCATGGCCCTGACATGCATCTCTTAGTTGGTGAAAGCCACG\n+>U68684\n+TAATACGGGGGGGGCAAGCGTTGTTCGGAATTACTGGGCGTAAAGGGCTCGTAGGTGGCCAACTAAGTCATACGTGAAATCCCTCGGCTTAACCGGGGAACTGCGTCTGATACTGGATGGCTTGAGTTTGGGAGAGGGACGCGGAATTCCAGGTGTAGCGGTGAAATGCGTAGATATCTGGAGGAACACCGGTGGCGAAGGCGGCGTCCTGGACCAACACTGACACTGATGGGCGAAAGCCAGGGGAGCAAACGGGATTAGATACCCCGGTAGTCCTGGCCCTAAACGATGAATGCTTGGTGTGGCGGGTATCGATCCCTGCCGTGCCGAAGCTAACGCATTAAGCATTCCGCCTGGGGAGTACGGTCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAACATGTGGTTCAATTCGACGCAACGCGAAGAACCTTACCTGGGCTCGAAATGGANTGGAATCCGGTGGAAACATCNGCGCCCGCAAGGGCCGCTCTATAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCGTTAGTTGCCATCGGGTCAAGCCGGGCACTCTAGCGAAACCGCCTCGGATAACGGGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCTTTATGTCCAGGGCTACACACGTGCTACAATGCACGGTACAAACCGTCGCAAACCCGCGAGGGGGAGCTAATCGGAAAAAGCCGTGCTCAGTTCGGATTGGAGTCTGCAACCCGACTCCATGAAGCTGGAATCGCTAGTAATCGCAGATCAGAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACATCACGAAAGTGGACCATACTAGAAGCAGGTGGGCCAACCGCAAGGGGGCAGCCTTCCAAGGTATAGTTCATGATTGGGGTG\n+>U68685\n+TAATACAGANGTCCCAAGCGTTGTTCGGATTCACTGGGCGTAAAGGGCGCGTANGTGGCTGGGTAAGTTTGATGTGAAATCTCCGAGCCTAACTCGGAAAATGCATTGAATACTATCCAGCTTGAGGATTGGAGGGGAGACTGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACCAGTGGCGAAGGCGAGTCTCTGGACAATTCCTGACACTGAGGCGCGAAAGCTAGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCTAGCCTTAAACGGTGCACATTTGCTGTAAGAAGAATCGACCCCTCTTGTGGCGAAGCTAACGCGTTAAATGTGCCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGAAATTGACGGGGGCCTGCACAAGCGGTGGAGTATGTGGCTTAATTCGATGCAACGCGAAGAACCTTACCTGGCCTTGACATGTAGGTAGTAGAACCTGAAAGGGTGACGAGAGTAACAATACTCACTTACACAGGTGN\n+>U68686\n+TAATACAGAAGGTGCAAGCGTTGTTCGGAATTATTGGGCGTAAAGGGCGCGTAGGCGGTGCGGTAAGTCTCTAGTGAAATCTCCGGGCTCAACTCGGAGCCTGCTAGGGAAACTGCCGTGCTTGAGTGTGGGAGAGGTGAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCTGTGGCGAAAGCGGCTCACTGGACCACAACTGACGCTGAGGCGCGAAAGCTAGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCTAGCCCTAAACGATGATTGCTTGGTGTAGCAGGTACCCAATCCTGCCGTGCCGAAGCTAACGCGATAAGCAATCCGCCTGGGGAGTACGGTCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAACATGTGGTTCAATTCGACCCACGCGAAGAACCTTACCTGGGCTCGAAGCGCAGTGGACTGCGGTAGAAATATCGCTTTCCCGCAAGGGACTGCTGCGTT\n+>U68687\n+TAATACAGAGGTCCCAAGCGTTGTTCGGATTCACTGGGCGTAAAGGGTGCGTAGGTGGTGAGGTAAGTCGGATGTGAAATCTCCGAGCTCAACTCGGAAACTGCATTGGAAACTACCTTGCTCGAGGGTTGGAGGGGGGACTGGAATGCTTGGTGTAGCAGTGAAATGCGTAGGTATCAAGCGGAACACCAGTGGCGAAGGCGAGTCCCTGGACAACTCCTGACACTGATGCACGAAAGCTAGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCTAGCCGTAAACGGTGCACGTTTGCTGTAAAAGGAATCGACCCCTTTTGTGGCGTACCAACGCGTTAAACGTGCCGCCTGGGAAGTACGGTCGCAAGATTAAAACTCAAAGAAATTGACGGGGGCCTGCACAAGCGGTGGAGTATGTGGCTCAATTCGATGCAACGCGAAGAACCTTACCTGGCCTTGACATGCNACNTAGTAGAAGGGTGAAAGCCTGAAGAAGTTAGCAATACCAGTGTGCAACGGGTGTTGAAGGGCTGTTGTCAAGNTCGTTTGNGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCNTGNNTCCTGTCGCCACTCGTTCGCAAGACCGAAGCACTCGGGACAGACTGCTTCGCTTAAACGAGGAGGAAGGTGGGGATGACGTCAAGTCAGTATGGCCCTTACGGCCAGGGCTGCACANGTACCACAATGCCCGGCACAAAGGGAAGCGAGACCGTAAGGTGGAGCAAATCCCCAAAAACCGGGCCCAGTTCAGATTGTCGTCTGCAACTCGACGGCATGAAGCTGGAATCGCTAGTAATGGCGCATCAGCTACGGCGCCGTGAATACGTTCCCAGGCCTTGNACACACCGCCCGTCACATCATGAAAGCNGTTTGTACCNGAAGTCACCCCTTAAAAGGTGCCGAAGGTATGGATGGTGATTGGGATG\n+>U68688\n+TAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGTCCTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGGGGACTTGAGTGCAGGAGANAAAAGTGGAATTCCACGTGTAGCGGTGAAATGCGTAGAGATGTGGAGGAACACCAGTGGCGAAGGCGACTTTTTGGCCTGTAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTAGANGGTTTCCGCCCTTTAGTGCTGAAGTAAACGCATTAAGCACTCCGCCTGGGGAGTACGGCCGCAAGGCTGAAACTCAAAGGAATCGACGGGGACCGCACAAGCGGTGGGGCATGTGGTTTAATTCGAAACAACGCGAAGAACCTTACCAGGTCTTGACATCCTCTGACAATCCTAGAGATAGGACTTCCCCTTCCGGGGGACAGA\n'
b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.fasta_head
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.fasta_head Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,10 @@
+>U68589
+TAATACGTAGGGTGCAAGCGTTGCCCGGGTTTATTGGGCGTAAAGGGCGCGTAGGCGGCTCGACACGTCCGTTGTGAAATCGCCCGGCTCAACTGGCGGGGTCAGCGGATACGGTCGAGCTTGAGCAAGCTAGGGGGCAATGGAATTCCCGGTGTAGTGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGTTGCCTGGGGCTTTGCTGACGCTGATGCGCGAAAGCGTGGGGAGCGATCCGGATTAGATACCCGGGTAGTCCACGCCGTAAACGATGTCGACTAAGCGTCGGGGGTATCGACCCCTCGGCCCGCAGCTAACGCATTAAGTCAACCGCCTGGGGACTACGGCCGCCAGGCTAAAACTCAAAGAATTGACGGGGGCCGCACAGCAGCGACGTGTGTTTAATTCGATGNACGCGCAGAACCNTACNTCNGCNTTGACATGCACGTNGTACTGACCNGAAANGGAAGGGACCCGCGAGGGAGCGTGCACAGATGNTGCATGGCTGTCGTCAGTTCGTGCCGTGAGGTGTTGGGTTAAGTCCCGCAACGAGGCGCAACCCTTGTCCCTTAGTTGCCTTTTCTAAGGAGACCGCCGGTCTAAACCGGAGGAAGGTGGGGATGACGTCAAGTCAGCACGGCTCTTACGTCGAGGGCTACACACACGCTACAATGGCCGGTACAACGGGCTGCCAAGGGGTGACCTGGAGCTAACCCCACCAAAGCCGGTCTCAGTTCGGATTGCAGACTGCAACTCGCCTGCATGAAGTCGGAGTTGCTAGTAANTGCCAGTCAGCACATGGCAGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTTGGATACGCCTGAAGCCGGTGGCCTAACCCGCAAGGGAGGGAGCCGTCGAGGGCGGAGCCAGCGATTGGGACG
+>U68590
+TAATACGGGGGGAGCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTATGCGGCCAGCGCAAGTCAGTTGTGAAATCTCCGGGCTTAACTCGGAACGGTCAACTGATACTGCGCGGCTAGAGTGCGGAAGGGGCAACTGGAATTCTCGGTGTAGCGGTGAAATGCGTAGATATCGAGAGGAACACCTGCGGCGAAAGCGGGTTGCTGGGCCGACACTGACGCTGATGCGCGAAAGCCAGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCTGGCCTTAAACGATGGATGCTTGGTGTCTGGAGTTTTATAATCTCCGGGTGCCGCAGCTAACGCGTTAAGCATCCCCCCTGGGGAGTACGGTCGCAAGACTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTCAATTCGACGCAACCCGAAAGAACTTACCTGGGCTAGAATGCCTCTGACACCCTAGAAATACGGTTTC
+>U68591
+CGTAGGGTCCAAGCGTTATCCGGAATTACTGGGCGTAAAGAGTTGCGTAGGTGGCATAGTAAGCAGATAGTGAAATGATACGGCTCAACCGTATGTCCATTATCTGAACTGCTAAGCTTGAGCATGGTAGAGGTAGCTGGAATTGCTAGTGTAGGAGTGGAATCCGTAGATATTAGCAGGAACACCGATGGCGTAGGCAGGCTACTGGGCTATTGCTGACACTAAGGCACGAAAGCGTGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCACGCCGTAAACTATGGATGCTAGCTGTAATCAGTATCGACCCTGGTTGTAGCGAAGCTAACGCGTTAAGCATCCCGCCTGTGGAGTACCGCCGCAAGGCTAAAACATAAAGGAATTGACGGGGTCTCGCACAAGCGGTGGAGCGTGTTGTTTAATTCGACGNTAAGCGCAGAACCTTACCAAGGTTTGACATCCTGATAAGGTCTCCGAAAGGAGACTGTACCTTCGGGCTCCAGTGACAGGTGATGCATGGCCGTCGTCAGCTCGTGTCGTGAGATGTTTGGTTAAGTCCATCAACGAGCGCAACCCTTATAGTTAGTTGAATTTCTCTAGCTAGACTGCCCCGGTAACGGGGAGGAAGGAGGGGATGATGTCAGGTCATTATTTCCCTTACACCTTGGGCGACAAACACGCTACAATGGCCGGTACAAAGGGCTGCCAAGCAGTAATGTGGAGCAAATCCCATCAAAGCCGGTCCCAGTTCGGATTGAGGGCTGAAACTCGCCCTCATGAAGCCGGAATCGCTAGTAATGGCAGGTCAGCACACTGCCGTGAATACGTTCCCGAGACTTGTACACACCGCCCGTCAAACCATGAAAGTCGCAAATACCCGAAGTCCAACCTCAGGTTGGCCTAAGGTAGGGGAGATGATTGGGGTT
+>U68592
+TAATACAGAGGTCCCGAGCGTTGTTCGGATTCACTGGGCGTAAAGGGTGCGTAGGTGGTGGGATAAGTCGGATGTGAAATCTCGGAGCTCAACTCCGAAAATGCATTGGAAACTGTCCTGCTAGAGGGTTGGAGGGGGGACTGGAATACTTGGTGTAGCAGTGAAATGCGTAGATATCAAGTGGAACACCGGTGGCGAAGGCGAGTCCCTGGACAACACCTGACACTGAGGCACGAAAGCTAGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCTAGCCGTAAACGGTGCACGTTTGCTGTAAGAGGAATCGACCCCTTTTGTGGCGAAGCCAACGCGATAAACGTGCCGCCTGGGGAAGTACGGTCGCAAGATTAAAACTCAAAGAAATTGACGGGGGCCTGCACAAGCCGGTGGAGTATGTGGCTCAATTCGATGCCACGCCAAAGAACCTTACCTGGCCTTGACATGCACGTAGTTAGGAAGATGAAAATCCGACGAGGTAGCAATTCCAGCGTGCACAGGTGCT
+>U68593
+TAATACGTAAGGACCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTANGCGGCATGACAAGTCACTTGTGAAATCTCCGGGCTTAACTCGGAACGGCCAAGTGATACTGTCGCGCTAGAGTGCGGAAGGGGCAATCAGAATTCTTGGTGTAGCGGTGAAATGCGTAGATATCTGGAGGAACACCGGTGGCGAAGGCGGCATCCTGGACCAATTCTGACGCTGAGTGAGCGAAAGCCAGGGGAGCAAACGGGATTAGATACCCCGGTAGTCCTGGCCCTAGACGATGAATGCTTGGTGTGGCGGGTATCGATCCCTGCCGTGCCGAAGCTAACGCATTAAGCATTCCGCCTGGGGAGTACGGTCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGANCATGTGGTTCAATTCGACGCNACGCGAAGAACTTACCCAGGCTTGAACAGCGAGTGACTGCTTACGAAAGTAAGTTTCCGCAAGGACACTCGTAGAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTTTGCTGTTGNCCATCAGGTTATGCTGGGCACTCTGCAAAGACTGCCGGNTGATAAACCGGAGGAAGGTGGGGATGACGTCAAGTCAGCATGGCNTTTATGTCTGGGGCTACACACGTGCTACAATGGCCGACACAAACCGTCGCGAGCCCGCGAGGGGGAGCTAATCGGAGAAAGTCGGTCTCAGTTCGGATAGCAGGCTGCAACTCGCCTGCTTGAAGTTGGAATCGCTAGTAATCGCGGATCAGCACGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACATCACGAAAGCCGGTTGTACTAGAAGTCGTCATACCAACCCGCAAGGGAGGGAGGCGCCTAAGGTATGGTCGGTGATTGGGGTG
b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.fragclust.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.fragclust.fasta Fri May 19 05:47:34 2017 -0400
b
b'@@ -0,0 +1,192 @@\n+>U68622\n+TAAGACGAACCGTGCGAACGTTGTTCGGAATCACTGGGCTTAAAGGGCGCGTAGGCGGGCCATCAAGTCCGGGGTGAAATCCTCCAGCTCAACTGGAGAAGTGCCTTGGATACTGATGGCCTCGAGGAAGGTAGGGGAGCGCGGAACGGATGGTGGAGCGGTGAAATGTGTTGATATCATCCGGAACTCCGGTGGCGAAGGCGGCGCTCTGGACCTTTTCTGACGCTGAGGCGCGAAAGCCAGGGGAGAGAACGGGATTAGATACCCCGGTATTCCTGGCCCTAAACGATGAGTACTAGGTTGTAGACTAGACATGGGTTTACAGCCGAAGCAAAAGTGCTAAGTACTCCGCCTGGGGAGTATGGTCGCAAGGCTGAAACTCCAAGGAATTGACGGGGGCTCACACAAGCGGTGGAGCATGTGGCTTAATTCGANGCTACGCCGAAGAACCTTATCCTGGTCTTGANATGTTCGAAAAGANGTNNGNAAGTAGCGTGCGGGAAACGTTAACGGCGATCAGTAANGTCTGGAACCTATCACAGGTGCTGCATGGCTGTTGTCAGCTCGTGTCGTGAGATGTCGGGTTAAGTCCCTTAAACGAGCGAAACCCCTTGCTTTTCAGTTGCTACGGGGTAATGCCGAAGGACTCTGGGAGGACTGCCGGTGTTAAACCGGAGGAAGGTGGGGGACGTCAAGTCCTCATGGCCTTTATGACCAGGGCTGCACACGTGCTACAATGGCGTGAACAAAGGGACGCGAACGCGCGAGCGGGAGCAAATCCCAAAAAACACGCCCCAGTTCAGATCGAAGGCTGCAACTCGCCTTCGTGAAGTTGGAATCGCTAGTAATCGCAGGTCAGCAACACTGCGGTGAATGTGTTCCTGAGCCTTGTACACACCGCCCGTCAAGCCACGAAAGGGAGGGGCACCTGAAGTCGCTTTTACCAGTGCCGAAGGTGAACTTCCTGATTGGGATTAA\n+>U68608\n+TAAGACGTATAGAGCCAGTGTTATTTTTCGTGATTTGGCGTAAAGGGTGCGTAGGCGGTATGTTAAACAGAGAAGAGTGAGACATGGGTCGAACTGTGGCAGCTTTTTCTGAAATGGCAAACTAGAATTTTTTGGAAGTAAGCGGTATTTATAGGGTACAGGTGAAAAGGGTAGATCCTATAGGAACCATCAATTGCGAAGGCGGCTTACTATAAAGAATCGACGCTGAGGCACGAAGGCATGGGTATCGAATGGGATTAGACACCCCAGTAGTCCATGCGGACAACTATGGGAATTGGATTTCAAGGATCCGAGCTAGCGTGTGAAATTCCCCGCCTGGGGATGTACGATCGCAAGGTTTAAACCCAAGGGAATTGACGGGGGCTTAATCAAGCGGTGGAACATGTGGTTTAATTCGATACAACACGCAAAATCTTACCAACGTTCCGAGAAGAAAATATAAGGGGGTGNGAAAACACAGCAATAGGAAAATAGTTTGAGAAAAGAATTACTTCCTAAACCTTCGGCTTCATAGGCGCTGCATGGTNGTGGTTAGTCCGTGTCTTGAGATGTACGGTTCGATCCTATAACGGACAATACCCGTGTTTCTAATTAATAAAATAGAAAAATCACCACCTAAAGTTTGGATGAAGGGCGATTACCTCAAATCTTCATGGCCCGATCAAACGTTGGGCTACACACGTGTTACAATGGCCGTCACAAAGCGTGGCAAGAGTGCAAACTGGAGCAAATCGTGAATCGTGGTCGTAGTTCGAATTATTTTCTGGAACTCGAAAATATGAAGTTGAAATCGCAAGTAATCGGAGATCATGGAGCTTCGGTGAATGCAACCTTAGGTCTTATACACACCGCCCGTCACATTNTGAAAGTCGATCACATGTTAAGCTCTAATAATTATACGGTTTTAAATTCCGTTATAGTATCAGGAGTGCGAGTGTGGTTGGTAATTAGAGTG\n+>U68599\n+TAATACGGAGGGTGCGAGCATTAATCGGATTTATTGGGCGTAAAGGGCGCGTAGGCGGGAGCATAAGTCAGATGTGAAAGCCCGGGGCTCAACCCCGGAATAGCATATGATACTGTGAATCTAGAGGATAGGCGGAGGAAATGGAATTCCACAAGTAGCGGTGAAATGCGTAGATATGTGGAAGAACACCGGTGGCGAAAGCGATTTTCTAGCTTATACCTGACGCTGAGGCGCGAAAGCAAGGGGATCAAACAGGATTAGATACCCTGGTAGTCCTTGCTGTAAACGATGTATACTTGGTGTAACCGGACTCAACCCTGGTTGTGCCGAAGCTAACGCGATATAGTATACCGCCTGGGGAGTACAGTCGCAAGGCTGAAACTCCAAAGAATTGACGGGGACCGCACAAGCAGTGGAGCATGTGGTTTAATTCGATGCACGCGAAAAACCTTACCAGGCTTGAACATGCACTTGGAAGATTAGCAGAGATGTTATTGCCCTTTAGGGGCTGGTGCACAGGTGCTGCATGGCTGTCGTCAGCTCGTGCCGTGAGGTGTTGGGTTAAGTCCCGNNAAACGGAGCGGCAACCCTTCATCATTAGTTGCCAACAACGTGAAAGGTGGGGAACTCTAATGAGACTGCCTGGGTTAACCAGGAGGAAGGTGAGGTGACGTCAAGTCCGCATGGCCCTTATGTCTGGGGCTACACACGTGCTACAATGGACGGTGCAGAAGGCAGCAAAACCGCGAGGTGAAGCAAATCCTAAGAAAGCCGTCCTCAGTTCAGATTGTAGTCTGCAACTCGACTACATGAAGACGGAGTTGCTAGTAATGGCGAGTCAGCAACATCGCCGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGTCACATCATGGGAGTTGGTTTTACCCGAAGCCGCTGGCCTAACCGCAAGGGGGGAGGCGTCTAAGGTGAGGCCGATGTCGCGGATG\n+>U68646\n+TAATACGTAGGGAGCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTAGGCGGCAATTCAAGTCAGCTGTGAAATCTCCGAGCTTAACTCGGAACGGTCAGCTGATACTGTCTTGCTTGAGTGCGGAAGGGGCAATCGGAATTCTTGGTGTAGCGGTGAAATGCGTAGATATCAAGAGGAACACCTGAGGTGAAGACGGGTTGCTGGGCCGACACTGACGCTGACAGCGCGAAAGCCAGGGGAGCAAACGGGATTAGATACCCCGGTAGTCCTGGCCTTAAACGATGAATACTTGGTGTCTGGAGTCTCTATAGCTCCGGGTGCCGTCGCTAACGTTTTTAGTATTCCGCCTGGGGAGTACGCACGCAAGTGTGAAACTCAAAGGAATTGACCGGGACCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGACGCAACGCGAAGAACCTTACNTGGANTAGAATGTGNAGGGGATCTTGGGTAANCGCCAAGAGTNTGGGAAACCANACCCAAAACAAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTATTGATAGTCGCTAACATTAAGTTGAGAACTCTATCAAGACTGCTGTTGATAAAACGGAGGAAGGTGGGGATGATGTCAAGTCATCATGGCCTTTATGTTCAGGGCTACACACGTGCTACAATGGCCGGTACAAAACGTCGCAATCTCGCAAGAGGGAGCTAATCGCAAAAACCGGTCTCAGTTCGGATTGAAGTCTGCAACTCGACTTCATGAAGTTGGAATCGCTAGTAATCGCAAATCAGCATGTTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACATCACGAAAGTAGGTTGTACTAGAAGTGGCCGGACCAACTCGCAAGAGAGGTAGGTTACCACGGTATGATTTATGATTGGGGTG\n+>U68623\n+TAATACGTAGGGGGCAAGCGTTGTCCGGAATT'..b'AGTGGCGAAGGCGACTTTCTGGACGATAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCTGTAAACGATGGATACTANGTGTNNGAGGTNTCGACCCCTTCTGTGCCGGAGTTAACACAATAAGTTTCCCNCCTGGGGAGTNCCGCCGCNAGGTTGAAACTCAAANGAATTGACCGGGGCCCGCACCACCCACTTGGAATTATGTGGTTTAATTCCAAGCCACGCGAAGAACCTTNCCAAGGGCTTGACATAATGGTGGATA\n+>U68675\n+TAGCGTTGTTCGGATTCACTGGGTTTAAAGGGTGCGTAGGAGGGCAGGTAAGTCAGTGTGAAATCCTGGGGCTTAACCCCAGAACTGCCATTGATACTCTCTGTCTTGAATACAGTGGAGGTGAGCGGAATATGTCATGTAGCGGTGAAATGCTTAGATATGACATAGAACACCAATTGCGAAGGCAGCTCGCTACACTACTATTGACTCTGAGGCACGAAAGCGTGGGGATCAAACAGGATTAGATACCCTGGTAGTCCACGCCCTAAACGATGGATACTCGACATACGCGATACACTGTGTGTGTCTGAGCGAAAGCATTAAGTATCCCACCTGGGAAGTACGACCGCAAGGTTGAAACTCAAAGGAATTGGCGGGGGTCCGCACAAGCGGTGGAACATGTGGTTTAATTCGATGATACGCGAGGAACCTTACCTGGGCTANAATGCTGGTGGAACGTGGGTGAAAACTCACTTTG\n+>U68633\n+TAATACGAGGGGGGCAAGCGTTGTTCGGAATTATTGGGTGTAAAGGGTTCGTACGCGGTGTGGCAAGTCGGGAGTGAAATCTCTGGGCTTAACTCAGAGGCTGCTTCCGAAACTGCTGTGCTTGAGTGTGGGAGAAGCGCGTGGAATTGCAGGTGTANCGGTGAAATGCGTANATATCTGCGGGAACACCCGTGGCGAAAGCGGCGCGCTGGACCACAACTGACGCTGAGGAACNAAANCTAGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCTAGCCCTAAACGATCAGGACTTGGGGTGGCGCCCGTTCGGGCGTCGTCCCNGAGCTAACCGCGTTAAATCCTGCACCCTGGGGGAGTACGGTCGCAAGACTGACACTCCAAAGGAATTGACGGGGGGCCCGCACCAACCGGTGGAAACATGTTGGTTCAAATTCGAACGCTACGCCGAGGAACCTTTACCTGGGCTCC\n+>U68677\n+TAATACGTAGGGGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGAGCGCGTAGGCGGTCCGATAAGTCGGCTGTGAAAGTCAGGGGCTCAACCCTTGAAAGCCGGCCGACACTGTCGGACTAGAGTCCGGAAGANGCAAGTGGAATTCCCGGTGTAGCGGTGAAATGCGCAGATATCGGGAGGAACACCAATGGCGAAGGCAGCTTGCTGGGACGGTACTGACGCTGANGCGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTATTCCNCGCCGTAAACGATGGGCACTACGTGTGGGAGGTGTCGACTCCTCCCGTGCCGCAGCTAACGCATTAAGTGCCCCGCCTGGGGAGTACGCCGCTANGCTAAAACTCAAAGGAATCNGCCGGGGCCCGCACAAACAGCGGAACATGTGGTTTAATTCCACGCACCGCAAATAACCTACCTGGGCTTGACATGTT\n+>U68676\n+TAATACGTNGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGTCCTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCNTTGGAAACTGGGGGACTTGAGTACAGAAGAAGAAAGCGGAATTCCACGTGTAGCGGTGAAATGCGTATAGATGTGGAGGAACACCAGTGGCGAAGGCGGCTTTCTGGTCTGTAACTGACGCTGANGCGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGAGGAATGCTAAGTGTTAGAAGGTTTCCGCCCTTTAATGCTGCACTAACCCATTTAGCACTCCGCCTGGGGAGTACGGCCGCCAGGCTGAAACTCAAATGAATTGACCGGGGCCGCCCAANCGGTGGAACATGTTTGTTTATATTCTAATCCACCGCCAAGAACTTTACANG\n+>U68673\n+TAATACAGAGGGTGCGAGCGTTGTTCGGAATTATTGGGCGTAAAGGGCGCGTANGCGGTGCGGTAAGTCACCTGTGAAATCTCCTGGCTCAACTGGGAGCTTGCAGGCGAAACTGCCGTGCTGGAGTGTGGGAGAGGTGCGTGGAATTCCCGGTGTAGCGGTGAAATGCGTATATATCGGGAGGAACACCTGTGGCGAAAGCGGCGCACTGGACCACAACTGACGCTGAGGCGCGAAAGCTAGGGGAGCAAACGGGATTAGATACCCTGGTAGTCCTAGCCCTAAACTATGGATGCTTGGTGTGATGGGTACCCAATCCCATCGTGCCGCAGCTAACGCGTTAAGCATCCCGCCTGGGGAGTACCGTCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCCCAAGCGTGGACATGTTGTCAATTCGACGCACGCGAAGATACTT\n+>U68647\n+CGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGTCCTTTAAGTCTGANGTGAAAGCCCTCGGCTCAACCGAGGAGGGTCATTGGAAACTGGAGGACTTGAGTGCNNAATACGAAAGTGGAATTCCAAGTGTACCGGTGAAATGCGTNCAGATTTGGAGGAACACCAGTGGCGAAGGCGACTTTCTGGTCTGTATCTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTTTTCCCCGCCGTAAACAATTAAGTGCTAAGTGTTNTGGGGTTTCCGCCCCTTANTGCTGCAGCTAACGCATTATNCTCTCCGCCTGGGGAGTACTGTCGCCAGACTGACACTCCCATGAATTGACTGGGGCCCGCACAANCGGTGGAGCATGTGGTTTAATTCCAACCAACNCGAAAAAACTT\n+>U68682\n+TAATACCGAAGGTGCAAGCGTTATCCGGATTCACTGGGTTTAAAGGGTGCNTANGTGGACTANTAANTCAGTGGTGAAATCTCCGGGCTTAACTCGGAGACTGCCATTGATACTATCTGTCTTGAATATCCTGGAGGTGAGCGGAATATGTCATGTANCGGTGAAATGCCTAGATATGACATACGAACACCAATTGCGAAGGCNGCTCACTACGGGGTTATTGACACTGAGGCACGAAAGCGTGGGGATCAAACNGGATTAGATACCCTGCGTAGTCCACCGCCCTAAACGAAGGGATACTCGACATCANCGATACACTGTTGGTGTCTGAACGAAAAGCATTAAGTTTCCCCACCCTGGGGAAGTTCGAACCGCCAAGGTTGAAAACCTCCAAACGAATTGACCGGGGGTCCGCCCACAAGCGCGTGGG\n+>U68653\n+TAATACGTACGTGGCAAGCGTTGTCCGGAATTATTGGGTGTAAAGNGCNCGCAGGNGGTCCNTTANATCTGATGTGAAANCCCACGGCTCAACCCTGGNCGGTCATTGGATACTGGGGGACTTGAGTGCAGNAGAGAAGAATGGAATTCCACGTGTNGCGGTGAAATGCGTAGATATNTGGAGGAACACCNGTGGCGAAGGCGACTCTCTGGNCTGTAACTGACGCTGAAGCAGCGAAAGCGTGGGGAGCAAACAGGATTAGATATCCTGGNATCCACCCGTAAACGATTGAGTGCTAAGTGTTGGGAGTNGTTTCCGCCCATTCCGTGCTGCAGCTAACGCATTAAGCACTCCGCCTGGGGGAGTACCGGCGCCAAGCTGAAAACTCAAAAGAATTGACGGGGNNCCGCACAAGCGGTGGG\n'
b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.fragclust.names
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.fragclust.names Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,96 @@
+U68622 U68622
+U68608 U68608
+U68599 U68599
+U68646 U68646
+U68623 U68623
+U68644 U68644
+U68680 U68680
+U68621 U68621
+U68597 U68597
+U68594 U68594
+U68649 U68649
+U68593 U68593
+U68662 U68662
+U68607 U68607
+U68639 U68639
+U68674 U68674
+U68654 U68654
+U68615 U68615
+U68606 U68606
+U68612 U68612
+U68684 U68684
+U68659 U68659
+U68679 U68679
+U68687 U68687
+U68626 U68626
+U68672 U68672
+U68665 U68665
+U68632 U68632
+U68625 U68625
+U68652 U68652
+U68648 U68648
+U68630 U68630
+U68616 U68616
+U68664 U68664
+U68589 U68589
+U68600 U68600
+U68591 U68591
+U68605 U68605
+U68614 U68614
+U68611 U68611
+U68645 U68645
+U68602 U68602
+U68596 U68596
+U68681 U68681
+U68619 U68619
+U68670 U68670
+U68661 U68661
+U68617 U68617
+U68592 U68592
+U68669 U68669
+U68603 U68603
+U68610 U68610
+U68642 U68642
+U68631 U68631
+U68685 U68685
+U68595 U68595
+U68666 U68666
+U68651 U68651
+U68624 U68624
+U68686 U68686
+U68640 U68640
+U68628 U68628
+U68601 U68601
+U68641 U68641,U68667
+U68609 U68609
+U68678 U68678
+U68688 U68688
+U68627 U68627
+U68629 U68629
+U68643 U68643
+U68637 U68637
+U68618 U68618,U68620
+U68655 U68655
+U68656 U68656
+U68663 U68663
+U68636 U68636
+U68657 U68657
+U68658 U68658
+U68613 U68613
+U68635 U68635
+U68671 U68671
+U68683 U68683
+U68638 U68638
+U68598 U68598
+U68590 U68590
+U68660 U68660
+U68668 U68668
+U68634 U68634
+U68675 U68675
+U68633 U68633
+U68677 U68677
+U68676 U68676
+U68673 U68673
+U68647 U68647
+U68682 U68682
+U68653 U68653
b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.groupaccnos
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.groupaccnos Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,2 @@
+forest
+pasture
b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.groups
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.groups Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,1 @@
+U68589 forest U68590 forest U68591 forest U68592 forest U68593 forest U68594 forest U68595 forest U68596 forest U68597 forest U68598 forest U68599 forest U68600 forest U68601 forest U68602 forest U68603 forest U68605 forest U68606 forest U68607 forest U68608 forest U68609 forest U68610 forest U68611 forest U68612 forest U68613 forest U68614 forest U68615 forest U68616 forest U68617 forest U68618 forest U68619 forest U68620 forest U68621 forest U68622 forest U68623 forest U68624 forest U68625 forest U68626 forest U68627 forest U68628 forest U68629 forest U68630 forest U68631 forest U68632 forest U68633 forest U68634 forest U68635 forest U68636 forest U68637 forest U68638 forest U68639 pasture U68640 pasture U68641 pasture U68642 pasture U68643 pasture U68644 pasture U68645 pasture U68646 pasture U68647 pasture U68648 pasture U68649 pasture U68651 pasture U68652 pasture U68653 pasture U68654 pasture U68655 pasture U68656 pasture U68657 pasture U68658 pasture U68659 pasture U68660 pasture U68661 pasture U68662 pasture U68663 pasture U68664 pasture U68665 pasture U68666 pasture U68667 pasture U68668 pasture U68669 pasture U68670 pasture U68671 pasture U68672 pasture U68673 pasture U68674 pasture U68675 pasture U68676 pasture U68677 pasture U68678 pasture U68679 pasture U68680 pasture U68681 pasture U68682 pasture U68683 pasture U68684 pasture U68685 pasture U68686 pasture U68687 pasture U68688 pasture
\ No newline at end of file
b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.head.names
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.head.names Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,5 @@
+U68593 U68593
+U68592 U68592
+U68591 U68591
+U68590 U68590
+U68589 U68589
b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.metadata
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.metadata Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,3 @@
+group feature
+forest 98
+pasture 98
b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.mothur.shared
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.mothur.shared Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,3 @@
+label Group numOtus Otu01 Otu02 Otu03 Otu04 Otu05 Otu06 Otu07 Otu08 Otu09 Otu10
+0.10 forest 10 0 5 2 3 1 1 3 3 1 0
+0.10 pasture 10 7 2 5 1 3 2 0 0 1 2
b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.names
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.names Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,96 @@
+U68630 U68630
+U68595 U68595
+U68600 U68600
+U68591 U68591
+U68647 U68647
+U68661 U68661
+U68605 U68605
+U68622 U68622
+U68612 U68612
+U68608 U68608
+U68610 U68610
+U68656 U68656
+U68655 U68655
+U68668 U68668
+U68686 U68686
+U68683 U68683
+U68635 U68635
+U68627 U68627
+U68672 U68672
+U68621 U68621
+U68638 U68638
+U68613 U68613
+U68618 U68618,U68620
+U68602 U68602
+U68637 U68637
+U68641 U68641,U68667
+U68673 U68673
+U68658 U68658
+U68664 U68664
+U68687 U68687
+U68592 U68592
+U68671 U68671
+U68636 U68636
+U68631 U68631
+U68652 U68652
+U68666 U68666
+U68674 U68674
+U68685 U68685
+U68625 U68625
+U68682 U68682
+U68609 U68609
+U68603 U68603
+U68640 U68640
+U68680 U68680
+U68615 U68615
+U68670 U68670
+U68662 U68662
+U68678 U68678
+U68598 U68598
+U68619 U68619
+U68633 U68633
+U68651 U68651
+U68645 U68645
+U68643 U68643
+U68611 U68611
+U68657 U68657
+U68599 U68599
+U68642 U68642
+U68590 U68590
+U68644 U68644
+U68684 U68684
+U68606 U68606
+U68639 U68639
+U68654 U68654
+U68593 U68593
+U68679 U68679
+U68607 U68607
+U68597 U68597
+U68653 U68653
+U68646 U68646
+U68616 U68616
+U68677 U68677
+U68681 U68681
+U68623 U68623
+U68669 U68669
+U68589 U68589
+U68665 U68665
+U68663 U68663
+U68688 U68688
+U68617 U68617
+U68628 U68628
+U68629 U68629
+U68660 U68660
+U68614 U68614
+U68632 U68632
+U68634 U68634
+U68676 U68676
+U68649 U68649
+U68648 U68648
+U68626 U68626
+U68596 U68596
+U68624 U68624
+U68594 U68594
+U68659 U68659
+U68601 U68601
+U68675 U68675
b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.pair.dist
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.pair.dist Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,3 @@
+U68590 U68589 0.2937
+U68591 U68589 0.3192
+U68591 U68590 0.3347
b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.pcoa.axes
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.pcoa.axes Fri May 19 05:47:34 2017 -0400
b
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b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.pcoa.loadings
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.pcoa.loadings Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,99 @@
+axis loading
+1 5.209297
+2 4.419977
+3 3.507522
+4 2.856806
+5 2.267862
+6 2.073816
+7 1.852071
+8 1.742582
+9 1.675175
+10 1.559590
+11 1.476943
+12 1.423754
+13 1.400448
+14 1.373608
+15 1.288984
+16 1.278740
+17 1.220963
+18 1.192054
+19 1.168860
+20 1.144852
+21 1.085866
+22 1.054236
+23 1.036880
+24 1.020942
+25 0.992328
+26 0.987332
+27 0.971493
+28 0.968304
+29 0.951738
+30 0.937392
+31 0.915684
+32 0.911642
+33 0.894907
+34 0.886563
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+96 0.361096
+97 0.000000
+98 0.000000
b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.silva.wang.tax.summary
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.silva.wang.tax.summary Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,23 @@
+taxlevel rankID taxon daughterlevels total
+0 0 Root 1 3
+1 0.1 Bacteria 2 3
+2 0.1.2 Actinobacteria 1 2
+3 0.1.2.1 Actinobacteria 1 2
+4 0.1.2.1.2 Actinobacteridae 1 2
+5 0.1.2.1.2.1 Actinomycetales 2 2
+6 0.1.2.1.2.1.8 Micrococcineae 1 1
+7 0.1.2.1.2.1.8.11 Microbacteriaceae 1 1
+8 0.1.2.1.2.1.8.11.24 Zimmermannella 1 1
+9 0.1.2.1.2.1.8.11.24.1 unclassified 0 1
+6 0.1.2.1.2.1.12 Pseudonocardineae 1 1
+7 0.1.2.1.2.1.12.2 Pseudonocardiaceae 1 1
+8 0.1.2.1.2.1.12.2.9 Saccharomonospora 1 1
+9 0.1.2.1.2.1.12.2.9.1 unclassified 0 1
+2 0.1.34 Firmicutes 1 1
+3 0.1.34.2 Clostridia 1 1
+4 0.1.34.2.1 Clostridiales 1 1
+5 0.1.34.2.1.9 Gracilibacteraceae 1 1
+6 0.1.34.2.1.9.1 Gracilibacter 1 1
+7 0.1.34.2.1.9.1.1 unclassified 1 1
+8 0.1.34.2.1.9.1.1.1 unclassified 1 1
+9 0.1.34.2.1.9.1.1.1.1 unclassified 0 1
b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.square.pcoa.axes
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.square.pcoa.axes Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,3 @@
+group axis1 axis2 axis3
+forest 0.045166 0.143659 -0.000000
+pasture 0.129005 -0.103932 -0.000000
b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.unique.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.unique.fasta Fri May 19 05:47:34 2017 -0400
b
b'@@ -0,0 +1,192 @@\n+>U68589\n+TAATACGTAGGGTGCAAGCGTTGCCCGGGTTTATTGGGCGTAAAGGGCGCGTAGGCGGCTCGACACGTCCGTTGTGAAATCGCCCGGCTCAACTGGCGGGGTCAGCGGATACGGTCGAGCTTGAGCAAGCTAGGGGGCAATGGAATTCCCGGTGTAGTGGTGGAATGCGTAGATATCGGGAGGAACACCAGTGGCGAAGGCGGTTGCCTGGGGCTTTGCTGACGCTGATGCGCGAAAGCGTGGGGAGCGATCCGGATTAGATACCCGGGTAGTCCACGCCGTAAACGATGTCGACTAAGCGTCGGGGGTATCGACCCCTCGGCCCGCAGCTAACGCATTAAGTCAACCGCCTGGGGACTACGGCCGCCAGGCTAAAACTCAAAGAATTGACGGGGGCCGCACAGCAGCGACGTGTGTTTAATTCGATGNACGCGCAGAACCNTACNTCNGCNTTGACATGCACGTNGTACTGACCNGAAANGGAAGGGACCCGCGAGGGAGCGTGCACAGATGNTGCATGGCTGTCGTCAGTTCGTGCCGTGAGGTGTTGGGTTAAGTCCCGCAACGAGGCGCAACCCTTGTCCCTTAGTTGCCTTTTCTAAGGAGACCGCCGGTCTAAACCGGAGGAAGGTGGGGATGACGTCAAGTCAGCACGGCTCTTACGTCGAGGGCTACACACACGCTACAATGGCCGGTACAACGGGCTGCCAAGGGGTGACCTGGAGCTAACCCCACCAAAGCCGGTCTCAGTTCGGATTGCAGACTGCAACTCGCCTGCATGAAGTCGGAGTTGCTAGTAANTGCCAGTCAGCACATGGCAGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACGTCATGAAAGTTGGATACGCCTGAAGCCGGTGGCCTAACCCGCAAGGGAGGGAGCCGTCGAGGGCGGAGCCAGCGATTGGGACG\n+>U68590\n+TAATACGGGGGGAGCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTATGCGGCCAGCGCAAGTCAGTTGTGAAATCTCCGGGCTTAACTCGGAACGGTCAACTGATACTGCGCGGCTAGAGTGCGGAAGGGGCAACTGGAATTCTCGGTGTAGCGGTGAAATGCGTAGATATCGAGAGGAACACCTGCGGCGAAAGCGGGTTGCTGGGCCGACACTGACGCTGATGCGCGAAAGCCAGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCTGGCCTTAAACGATGGATGCTTGGTGTCTGGAGTTTTATAATCTCCGGGTGCCGCAGCTAACGCGTTAAGCATCCCCCCTGGGGAGTACGGTCGCAAGACTGAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTCAATTCGACGCAACCCGAAAGAACTTACCTGGGCTAGAATGCCTCTGACACCCTAGAAATACGGTTTC\n+>U68591\n+CGTAGGGTCCAAGCGTTATCCGGAATTACTGGGCGTAAAGAGTTGCGTAGGTGGCATAGTAAGCAGATAGTGAAATGATACGGCTCAACCGTATGTCCATTATCTGAACTGCTAAGCTTGAGCATGGTAGAGGTAGCTGGAATTGCTAGTGTAGGAGTGGAATCCGTAGATATTAGCAGGAACACCGATGGCGTAGGCAGGCTACTGGGCTATTGCTGACACTAAGGCACGAAAGCGTGGGGAGCGAACGGGATTAGATACCCCGGTAGTCCACGCCGTAAACTATGGATGCTAGCTGTAATCAGTATCGACCCTGGTTGTAGCGAAGCTAACGCGTTAAGCATCCCGCCTGTGGAGTACCGCCGCAAGGCTAAAACATAAAGGAATTGACGGGGTCTCGCACAAGCGGTGGAGCGTGTTGTTTAATTCGACGNTAAGCGCAGAACCTTACCAAGGTTTGACATCCTGATAAGGTCTCCGAAAGGAGACTGTACCTTCGGGCTCCAGTGACAGGTGATGCATGGCCGTCGTCAGCTCGTGTCGTGAGATGTTTGGTTAAGTCCATCAACGAGCGCAACCCTTATAGTTAGTTGAATTTCTCTAGCTAGACTGCCCCGGTAACGGGGAGGAAGGAGGGGATGATGTCAGGTCATTATTTCCCTTACACCTTGGGCGACAAACACGCTACAATGGCCGGTACAAAGGGCTGCCAAGCAGTAATGTGGAGCAAATCCCATCAAAGCCGGTCCCAGTTCGGATTGAGGGCTGAAACTCGCCCTCATGAAGCCGGAATCGCTAGTAATGGCAGGTCAGCACACTGCCGTGAATACGTTCCCGAGACTTGTACACACCGCCCGTCAAACCATGAAAGTCGCAAATACCCGAAGTCCAACCTCAGGTTGGCCTAAGGTAGGGGAGATGATTGGGGTT\n+>U68592\n+TAATACAGAGGTCCCGAGCGTTGTTCGGATTCACTGGGCGTAAAGGGTGCGTAGGTGGTGGGATAAGTCGGATGTGAAATCTCGGAGCTCAACTCCGAAAATGCATTGGAAACTGTCCTGCTAGAGGGTTGGAGGGGGGACTGGAATACTTGGTGTAGCAGTGAAATGCGTAGATATCAAGTGGAACACCGGTGGCGAAGGCGAGTCCCTGGACAACACCTGACACTGAGGCACGAAAGCTAGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCTAGCCGTAAACGGTGCACGTTTGCTGTAAGAGGAATCGACCCCTTTTGTGGCGAAGCCAACGCGATAAACGTGCCGCCTGGGGAAGTACGGTCGCAAGATTAAAACTCAAAGAAATTGACGGGGGCCTGCACAAGCCGGTGGAGTATGTGGCTCAATTCGATGCCACGCCAAAGAACCTTACCTGGCCTTGACATGCACGTAGTTAGGAAGATGAAAATCCGACGAGGTAGCAATTCCAGCGTGCACAGGTGCT\n+>U68593\n+TAATACGTAAGGACCAAGCGTTGTTCGGATTTACTGGGCGTAAAGGGCGCGTANGCGGCATGACAAGTCACTTGTGAAATCTCCGGGCTTAACTCGGAACGGCCAAGTGATACTGTCGCGCTAGAGTGCGGAAGGGGCAATCAGAATTCTTGGTGTAGCGGTGAAATGCGTAGATATCTGGAGGAACACCGGTGGCGAAGGCGGCATCCTGGACCAATTCTGACGCTGAGTGAGCGAAAGCCAGGGGAGCAAACGGGATTAGATACCCCGGTAGTCCTGGCCCTAGACGATGAATGCTTGGTGTGGCGGGTATCGATCCCTGCCGTGCCGAAGCTAACGCATTAAGCATTCCGCCTGGGGAGTACGGTCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGANCATGTGGTTCAATTCGACGCNACGCGAAGAACTTACCCAGGCTTGAACAGCGAGTGACTGCTTACGAAAGTAAGTTTCCGCAAGGACACTCGTAGAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTTTGCTGTTGNCCATCAGGTTATGCTGGGCACTCTGCAAAGACTGCCGGNTGATAAACCGGAGGAAGGTGGGGATGACGTCAAGTCAGCATGGCNTTTATGTCTGGGGCTACACACGTGCTACAATGGCCGACACAAACCGTCGCGAGCCCGCGAGGGGGAGCTAATCGGAGAAAGTCGGTCTCAGTTCGGATAGCAGGCTGCAACTCGCCTGCTTGAAGTTGGAATCGCTAGTAATCGCGGATCAGCACGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACATCACGAAAGCCGGTTGTACTAGAAGTCGTCATACCAACCCGCAAGGGAGGGAGGCGCCTAAGGTATGGTCGGTGATTGGGGTG\n+>U68594\n+TAATCCCAAGGGTGCAANCGTTACTCGGAATTACTGGGCGTAAAGCGTGCG'..b'GGGCGTAAAGGGTGCGTANGCGGCGCGGTAAGTCGGGTGTGAAATCTCGGAGCTTAACTCCGAAACTGCATTCGATACTGCCGTGCTTGAGGACTGGAGANGAGACTGGAATTTACGGTGTAGCGGTGAAATGCGTATATATCGTAAGGAAGACCAGTGGCGAAGGCGGGTCTCTGGACAGTTCCTGACGCTGANGCACGAAGGCCAGGGGAGCAAACGGGATTAGATACCCCGGTAGTCCTGGCAGTAAACGGTGCACCTTTGGTGTGGGAGGATTCGACCCCTTCCGTGCCGGAGCTAACGCGTTAAACCTTGCCGCCTGGTGGAGTACGGTCCGCAAGATTAAAACTCACACAAATTGACGGGGGCCCGCACAAGCGGTGGAGTATGTGGCTTAATTCCATGCAACGCGAAGAACCTTTATCCATGGCCCTGACATGCATCTCTTAGTTGGTGAAAGCCACG\n+>U68684\n+TAATACGGGGGGGGCAAGCGTTGTTCGGAATTACTGGGCGTAAAGGGCTCGTAGGTGGCCAACTAAGTCATACGTGAAATCCCTCGGCTTAACCGGGGAACTGCGTCTGATACTGGATGGCTTGAGTTTGGGAGAGGGACGCGGAATTCCAGGTGTAGCGGTGAAATGCGTAGATATCTGGAGGAACACCGGTGGCGAAGGCGGCGTCCTGGACCAACACTGACACTGATGGGCGAAAGCCAGGGGAGCAAACGGGATTAGATACCCCGGTAGTCCTGGCCCTAAACGATGAATGCTTGGTGTGGCGGGTATCGATCCCTGCCGTGCCGAAGCTAACGCATTAAGCATTCCGCCTGGGGAGTACGGTCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAACATGTGGTTCAATTCGACGCAACGCGAAGAACCTTACCTGGGCTCGAAATGGANTGGAATCCGGTGGAAACATCNGCGCCCGCAAGGGCCGCTCTATAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCGTTAGTTGCCATCGGGTCAAGCCGGGCACTCTAGCGAAACCGCCTCGGATAACGGGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCTTTATGTCCAGGGCTACACACGTGCTACAATGCACGGTACAAACCGTCGCAAACCCGCGAGGGGGAGCTAATCGGAAAAAGCCGTGCTCAGTTCGGATTGGAGTCTGCAACCCGACTCCATGAAGCTGGAATCGCTAGTAATCGCAGATCAGAACGCTGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACATCACGAAAGTGGACCATACTAGAAGCAGGTGGGCCAACCGCAAGGGGGCAGCCTTCCAAGGTATAGTTCATGATTGGGGTG\n+>U68685\n+TAATACAGANGTCCCAAGCGTTGTTCGGATTCACTGGGCGTAAAGGGCGCGTANGTGGCTGGGTAAGTTTGATGTGAAATCTCCGAGCCTAACTCGGAAAATGCATTGAATACTATCCAGCTTGAGGATTGGAGGGGAGACTGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACCAGTGGCGAAGGCGAGTCTCTGGACAATTCCTGACACTGAGGCGCGAAAGCTAGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCTAGCCTTAAACGGTGCACATTTGCTGTAAGAAGAATCGACCCCTCTTGTGGCGAAGCTAACGCGTTAAATGTGCCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGAAATTGACGGGGGCCTGCACAAGCGGTGGAGTATGTGGCTTAATTCGATGCAACGCGAAGAACCTTACCTGGCCTTGACATGTAGGTAGTAGAACCTGAAAGGGTGACGAGAGTAACAATACTCACTTACACAGGTGN\n+>U68686\n+TAATACAGAAGGTGCAAGCGTTGTTCGGAATTATTGGGCGTAAAGGGCGCGTAGGCGGTGCGGTAAGTCTCTAGTGAAATCTCCGGGCTCAACTCGGAGCCTGCTAGGGAAACTGCCGTGCTTGAGTGTGGGAGAGGTGAGTGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAGGAACACCTGTGGCGAAAGCGGCTCACTGGACCACAACTGACGCTGAGGCGCGAAAGCTAGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCTAGCCCTAAACGATGATTGCTTGGTGTAGCAGGTACCCAATCCTGCCGTGCCGAAGCTAACGCGATAAGCAATCCGCCTGGGGAGTACGGTCGCAAGGCTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGCGGAACATGTGGTTCAATTCGACCCACGCGAAGAACCTTACCTGGGCTCGAAGCGCAGTGGACTGCGGTAGAAATATCGCTTTCCCGCAAGGGACTGCTGCGTT\n+>U68687\n+TAATACAGAGGTCCCAAGCGTTGTTCGGATTCACTGGGCGTAAAGGGTGCGTAGGTGGTGAGGTAAGTCGGATGTGAAATCTCCGAGCTCAACTCGGAAACTGCATTGGAAACTACCTTGCTCGAGGGTTGGAGGGGGGACTGGAATGCTTGGTGTAGCAGTGAAATGCGTAGGTATCAAGCGGAACACCAGTGGCGAAGGCGAGTCCCTGGACAACTCCTGACACTGATGCACGAAAGCTAGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCTAGCCGTAAACGGTGCACGTTTGCTGTAAAAGGAATCGACCCCTTTTGTGGCGTACCAACGCGTTAAACGTGCCGCCTGGGAAGTACGGTCGCAAGATTAAAACTCAAAGAAATTGACGGGGGCCTGCACAAGCGGTGGAGTATGTGGCTCAATTCGATGCAACGCGAAGAACCTTACCTGGCCTTGACATGCNACNTAGTAGAAGGGTGAAAGCCTGAAGAAGTTAGCAATACCAGTGTGCAACGGGTGTTGAAGGGCTGTTGTCAAGNTCGTTTGNGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCNTGNNTCCTGTCGCCACTCGTTCGCAAGACCGAAGCACTCGGGACAGACTGCTTCGCTTAAACGAGGAGGAAGGTGGGGATGACGTCAAGTCAGTATGGCCCTTACGGCCAGGGCTGCACANGTACCACAATGCCCGGCACAAAGGGAAGCGAGACCGTAAGGTGGAGCAAATCCCCAAAAACCGGGCCCAGTTCAGATTGTCGTCTGCAACTCGACGGCATGAAGCTGGAATCGCTAGTAATGGCGCATCAGCTACGGCGCCGTGAATACGTTCCCAGGCCTTGNACACACCGCCCGTCACATCATGAAAGCNGTTTGTACCNGAAGTCACCCCTTAAAAGGTGCCGAAGGTATGGATGGTGATTGGGATG\n+>U68688\n+TAATACGTAGGTGGCAAGCGTTGTCCGGAATTATTGGGCGTAAAGCGCGCGCAGGCGGTCCTTTAAGTCTGATGTGAAAGCCCACGGCTCAACCGTGGAGGGTCATTGGAAACTGGGGGACTTGAGTGCAGGAGANAAAAGTGGAATTCCACGTGTAGCGGTGAAATGCGTAGAGATGTGGAGGAACACCAGTGGCGAAGGCGACTTTTTGGCCTGTAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTAGANGGTTTCCGCCCTTTAGTGCTGAAGTAAACGCATTAAGCACTCCGCCTGGGGAGTACGGCCGCAAGGCTGAAACTCAAAGGAATCGACGGGGACCGCACAAGCGGTGGGGCATGTGGTTTAATTCGAAACAACGCGAAGAACCTTACCAGGTCTTGACATCCTCTGACAATCCTAGAGATAGGACTTCCCCTTCCGGGGGACAGA\n'
b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.unique.names
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.unique.names Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,96 @@
+U68589 U68589
+U68590 U68590
+U68591 U68591
+U68592 U68592
+U68593 U68593
+U68594 U68594
+U68595 U68595
+U68596 U68596
+U68597 U68597
+U68598 U68598
+U68599 U68599
+U68600 U68600
+U68601 U68601
+U68602 U68602
+U68603 U68603
+U68605 U68605
+U68606 U68606
+U68607 U68607
+U68608 U68608
+U68609 U68609
+U68610 U68610
+U68611 U68611
+U68612 U68612
+U68613 U68613
+U68614 U68614
+U68615 U68615
+U68616 U68616
+U68617 U68617
+U68618 U68618,U68620
+U68619 U68619
+U68621 U68621
+U68622 U68622
+U68623 U68623
+U68624 U68624
+U68625 U68625
+U68626 U68626
+U68627 U68627
+U68628 U68628
+U68629 U68629
+U68630 U68630
+U68631 U68631
+U68632 U68632
+U68633 U68633
+U68634 U68634
+U68635 U68635
+U68636 U68636
+U68637 U68637
+U68638 U68638
+U68639 U68639
+U68640 U68640
+U68641 U68641,U68667
+U68642 U68642
+U68643 U68643
+U68644 U68644
+U68645 U68645
+U68646 U68646
+U68647 U68647
+U68648 U68648
+U68649 U68649
+U68651 U68651
+U68652 U68652
+U68653 U68653
+U68654 U68654
+U68655 U68655
+U68656 U68656
+U68657 U68657
+U68658 U68658
+U68659 U68659
+U68660 U68660
+U68661 U68661
+U68662 U68662
+U68663 U68663
+U68664 U68664
+U68665 U68665
+U68666 U68666
+U68668 U68668
+U68669 U68669
+U68670 U68670
+U68671 U68671
+U68672 U68672
+U68673 U68673
+U68674 U68674
+U68675 U68675
+U68676 U68676
+U68677 U68677
+U68678 U68678
+U68679 U68679
+U68680 U68680
+U68681 U68681
+U68682 U68682
+U68683 U68683
+U68684 U68684
+U68685 U68685
+U68686 U68686
+U68687 U68687
+U68688 U68688
b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.wang.knn.tax.summary
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.wang.knn.tax.summary Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,8 @@
+taxlevel rankID taxon daughterlevels total
+0 0 Root 1 98
+1 0.3 unknown 1 98
+2 0.3.1 unclassified 1 98
+3 0.3.1.1 unclassified 1 98
+4 0.3.1.1.1 unclassified 1 98
+5 0.3.1.1.1.1 unclassified 1 98
+6 0.3.1.1.1.1.1 unclassified 0 98
b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon.wang.wang.taxonomy
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon.wang.wang.taxonomy Fri May 19 05:47:34 2017 -0400
b
b'@@ -0,0 +1,98 @@\n+U68589\tBacteria(92);"Proteobacteria"(40);Gammaproteobacteria(40);"Enterobacteriales"(40);Enterobacteriaceae(40);Escherichia_Shigella(40);\n+U68590\tBacteria(94);Firmicutes(69);Erysipelotrichia(68);Erysipelotrichales(68);Erysipelotrichaceae(68);Turicibacter(68);\n+U68591\tBacteria(97);"Proteobacteria"(55);Gammaproteobacteria(55);"Enterobacteriales"(55);Enterobacteriaceae(55);Escherichia_Shigella(55);\n+U68592\tBacteria(93);"Proteobacteria"(31);Gammaproteobacteria(31);"Enterobacteriales"(31);Enterobacteriaceae(31);Escherichia_Shigella(31);\n+U68593\tBacteria(98);Firmicutes(55);Erysipelotrichia(31);Erysipelotrichales(31);Erysipelotrichaceae(31);Turicibacter(31);\n+U68594\tBacteria(93);Firmicutes(72);Clostridia(46);Clostridiales(46);Lachnospiraceae(46);Dorea(22);\n+U68595\tBacteria(88);TM7(37);TM7_class_incertae_sedis(37);TM7_order_incertae_sedis(37);TM7_family_incertae_sedis(37);TM7_genus_incertae_sedis(37);\n+U68596\tBacteria(74);TM7(29);TM7_class_incertae_sedis(29);TM7_order_incertae_sedis(29);TM7_family_incertae_sedis(29);TM7_genus_incertae_sedis(29);\n+U68597\tBacteria(100);Firmicutes(87);Clostridia(54);Clostridiales(54);Lachnospiraceae(54);Clostridium_XlVa(28);\n+U68598\tBacteria(80);TM7(39);TM7_class_incertae_sedis(39);TM7_order_incertae_sedis(39);TM7_family_incertae_sedis(39);TM7_genus_incertae_sedis(39);\n+U68599\tBacteria(98);Firmicutes(57);Erysipelotrichia(30);Erysipelotrichales(30);Erysipelotrichaceae(30);Turicibacter(30);\n+U68600\tBacteria(98);"Proteobacteria"(60);Gammaproteobacteria(60);"Enterobacteriales"(60);Enterobacteriaceae(60);Escherichia_Shigella(60);\n+U68601\tBacteria(82);Firmicutes(31);Erysipelotrichia(14);Erysipelotrichales(14);Erysipelotrichaceae(14);Turicibacter(14);\n+U68602\tBacteria(89);"Proteobacteria"(30);Gammaproteobacteria(30);"Enterobacteriales"(30);Enterobacteriaceae(30);Escherichia_Shigella(30);\n+U68603\tBacteria(91);Firmicutes(76);Erysipelotrichia(51);Erysipelotrichales(51);Erysipelotrichaceae(51);Turicibacter(51);\n+U68605\tBacteria(86);Firmicutes(79);Clostridia(70);Clostridiales(70);Lachnospiraceae(70);Clostridium_XlVa(39);\n+U68606\tBacteria(98);TM7(41);TM7_class_incertae_sedis(41);TM7_order_incertae_sedis(41);TM7_family_incertae_sedis(41);TM7_genus_incertae_sedis(41);\n+U68607\tBacteria(87);TM7(24);TM7_class_incertae_sedis(24);TM7_order_incertae_sedis(24);TM7_family_incertae_sedis(24);TM7_genus_incertae_sedis(24);\n+U68608\tBacteria(98);TM7(45);TM7_class_incertae_sedis(45);TM7_order_incertae_sedis(45);TM7_family_incertae_sedis(45);TM7_genus_incertae_sedis(45);\n+U68609\tBacteria(74);Firmicutes(46);Erysipelotrichia(46);Erysipelotrichales(46);Erysipelotrichaceae(46);Turicibacter(46);\n+U68610\tBacteria(83);Firmicutes(48);Clostridia(40);Clostridiales(40);Lachnospiraceae(40);Clostridium_XlVa(30);\n+U68611\tBacteria(80);TM7(32);TM7_class_incertae_sedis(32);TM7_order_incertae_sedis(32);TM7_family_incertae_sedis(32);TM7_genus_incertae_sedis(32);\n+U68612\tBacteria(97);TM7(47);TM7_class_incertae_sedis(47);TM7_order_incertae_sedis(47);TM7_family_incertae_sedis(47);TM7_genus_incertae_sedis(47);\n+U68613\tBacteria(81);Firmicutes(36);Erysipelotrichia(14);Erysipelotrichales(14);Erysipelotrichaceae(14);Turicibacter(14);\n+U68614\tBacteria(79);Firmicutes(53);Erysipelotrichia(15);Erysipelotrichales(15);Erysipelotrichaceae(15);Turicibacter(15);\n+U68615\tBacteria(97);Firmicutes(69);Clostridia(50);Clostridiales(50);Lachnospiraceae(50);Dorea(32);\n+U68616\tBacteria(94);Firmicutes(69);Erysipelotrichia(33);Erysipelotrichales(33);Erysipelotrichaceae(33);Turicibacter(33);\n+U68617\tBacteria(79);Firmicutes(36);Erysipelotrichia(14);Erysipelotrichales(14);Erysipelotrichaceae(14);Turicibacter(14);\n+U68618\tBacteria(73);Firmicutes(31);Erysipelotrichia(25);Erysipelotrichales(25);Erysipelotrichaceae(25);Turicibacter(25);\n+U68619\tBacteria(86);TM7(41);TM7_class_incertae_sedis(41);TM7_order_incertae_sedis(41);TM7_family_incertae_sedis(41);TM7_genus_incertae_sedis(41);\n+U68620\tBacteria(67);Firmicutes(24);Erysipelotrichia(18);Erysipelotrichales(18);Erysipel'..b'657\tBacteria(70);Firmicutes(44);Erysipelotrichia(32);Erysipelotrichales(32);Erysipelotrichaceae(32);Turicibacter(32);\n+U68658\tBacteria(61);Firmicutes(23);Erysipelotrichia(17);Erysipelotrichales(17);Erysipelotrichaceae(17);Turicibacter(17);\n+U68659\tBacteria(97);Firmicutes(36);Erysipelotrichia(28);Erysipelotrichales(28);Erysipelotrichaceae(28);Turicibacter(28);\n+U68660\tBacteria(95);Firmicutes(85);Clostridia(72);Clostridiales(72);Lachnospiraceae(72);Dorea(40);\n+U68661\tBacteria(94);Firmicutes(52);Erysipelotrichia(24);Erysipelotrichales(24);Erysipelotrichaceae(24);Turicibacter(24);\n+U68662\tBacteria(98);TM7(42);TM7_class_incertae_sedis(42);TM7_order_incertae_sedis(42);TM7_family_incertae_sedis(42);TM7_genus_incertae_sedis(42);\n+U68663\tBacteria(95);Firmicutes(89);Erysipelotrichia(49);Erysipelotrichales(49);Erysipelotrichaceae(49);Turicibacter(49);\n+U68664\tBacteria(100);Firmicutes(61);Clostridia(44);Clostridiales(44);Lachnospiraceae(44);Coprococcus(17);\n+U68665\tBacteria(100);Firmicutes(83);Erysipelotrichia(20);Erysipelotrichales(20);Erysipelotrichaceae(20);Turicibacter(20);\n+U68666\tBacteria(91);TM7(27);TM7_class_incertae_sedis(27);TM7_order_incertae_sedis(27);TM7_family_incertae_sedis(27);TM7_genus_incertae_sedis(27);\n+U68667\tBacteria(78);Firmicutes(33);Erysipelotrichia(26);Erysipelotrichales(26);Erysipelotrichaceae(26);Turicibacter(26);\n+U68668\tBacteria(56);Firmicutes(28);Erysipelotrichia(14);Erysipelotrichales(14);Erysipelotrichaceae(14);Turicibacter(14);\n+U68669\tBacteria(67);Firmicutes(50);Erysipelotrichia(34);Erysipelotrichales(34);Erysipelotrichaceae(34);Turicibacter(34);\n+U68670\tBacteria(69);Firmicutes(30);Clostridia(30);Clostridiales(30);Lachnospiraceae(30);Coprococcus(21);\n+U68671\tBacteria(98);Firmicutes(59);Clostridia(41);Clostridiales(41);Lachnospiraceae(41);Clostridium_XlVa(24);\n+U68672\tBacteria(89);Firmicutes(57);Erysipelotrichia(21);Erysipelotrichales(21);Erysipelotrichaceae(21);Turicibacter(21);\n+U68673\tBacteria(89);"Proteobacteria"(41);Gammaproteobacteria(41);"Enterobacteriales"(41);Enterobacteriaceae(41);Escherichia_Shigella(41);\n+U68674\tBacteria(99);"Proteobacteria"(57);Gammaproteobacteria(57);"Enterobacteriales"(57);Enterobacteriaceae(57);Escherichia_Shigella(57);\n+U68675\tBacteria(79);Firmicutes(55);Erysipelotrichia(37);Erysipelotrichales(37);Erysipelotrichaceae(37);Turicibacter(37);\n+U68676\tBacteria(85);Firmicutes(65);Clostridia(54);Clostridiales(54);Lachnospiraceae(54);Dorea(38);\n+U68677\tBacteria(49);TM7(22);TM7_class_incertae_sedis(22);TM7_order_incertae_sedis(22);TM7_family_incertae_sedis(22);TM7_genus_incertae_sedis(22);\n+U68678\tBacteria(85);Firmicutes(49);Erysipelotrichia(41);Erysipelotrichales(41);Erysipelotrichaceae(41);Turicibacter(41);\n+U68679\tBacteria(98);Firmicutes(94);Clostridia(62);Clostridiales(62);Lachnospiraceae(62);Dorea(40);\n+U68680\tBacteria(99);Firmicutes(43);Clostridia(33);Clostridiales(33);Lachnospiraceae(33);Dorea(25);\n+U68681\tBacteria(59);TM7(16);TM7_class_incertae_sedis(16);TM7_order_incertae_sedis(16);TM7_family_incertae_sedis(16);TM7_genus_incertae_sedis(16);\n+U68682\tBacteria(82);TM7(26);TM7_class_incertae_sedis(26);TM7_order_incertae_sedis(26);TM7_family_incertae_sedis(26);TM7_genus_incertae_sedis(26);\n+U68683\tBacteria(86);Firmicutes(49);Erysipelotrichia(24);Erysipelotrichales(24);Erysipelotrichaceae(24);Turicibacter(24);\n+U68684\tBacteria(100);TM7(39);TM7_class_incertae_sedis(39);TM7_order_incertae_sedis(39);TM7_family_incertae_sedis(39);TM7_genus_incertae_sedis(39);\n+U68685\tBacteria(88);TM7(59);TM7_class_incertae_sedis(59);TM7_order_incertae_sedis(59);TM7_family_incertae_sedis(59);TM7_genus_incertae_sedis(59);\n+U68686\tBacteria(85);"Proteobacteria"(37);Gammaproteobacteria(37);"Enterobacteriales"(37);Enterobacteriaceae(37);Escherichia_Shigella(37);\n+U68687\tBacteria(100);Firmicutes(46);Erysipelotrichia(34);Erysipelotrichales(34);Erysipelotrichaceae(34);Turicibacter(34);\n+U68688\tBacteria(95);Firmicutes(88);Erysipelotrichia(34);Erysipelotrichales(34);Erysipelotrichaceae(34);Turicibacter(34);\n'
b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon1.count_table
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon1.count_table Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,99 @@
+Representative_Sequence total
+U68630 1
+U68595 1
+U68600 1
+U68591 1
+U68647 1
+U68661 1
+U68605 1
+U68622 1
+U68612 1
+U68608 1
+U68610 1
+U68656 1
+U68655 1
+U68668 1
+U68686 1
+U68683 1
+U68635 1
+U68627 1
+U68672 1
+U68621 1
+U68638 1
+U68613 1
+U68618 1
+U68620 1
+U68602 1
+U68637 1
+U68641 1
+U68667 1
+U68673 1
+U68658 1
+U68664 1
+U68687 1
+U68592 1
+U68671 1
+U68636 1
+U68631 1
+U68652 1
+U68666 1
+U68674 1
+U68685 1
+U68625 1
+U68682 1
+U68609 1
+U68603 1
+U68640 1
+U68680 1
+U68615 1
+U68670 1
+U68662 1
+U68678 1
+U68598 1
+U68619 1
+U68633 1
+U68651 1
+U68645 1
+U68643 1
+U68611 1
+U68657 1
+U68599 1
+U68642 1
+U68590 1
+U68644 1
+U68684 1
+U68606 1
+U68639 1
+U68654 1
+U68593 1
+U68679 1
+U68607 1
+U68597 1
+U68653 1
+U68646 1
+U68616 1
+U68677 1
+U68681 1
+U68623 1
+U68669 1
+U68589 1
+U68665 1
+U68663 1
+U68688 1
+U68617 1
+U68628 1
+U68629 1
+U68660 1
+U68614 1
+U68632 1
+U68634 1
+U68676 1
+U68649 1
+U68648 1
+U68626 1
+U68596 1
+U68624 1
+U68594 1
+U68659 1
+U68601 1
+U68675 1
b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon1.names
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon1.names Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,98 @@
+U68630 U68630
+U68595 U68595
+U68600 U68600
+U68591 U68591
+U68647 U68647
+U68661 U68661
+U68605 U68605
+U68622 U68622
+U68612 U68612
+U68608 U68608
+U68610 U68610
+U68656 U68656
+U68655 U68655
+U68668 U68668
+U68686 U68686
+U68683 U68683
+U68635 U68635
+U68627 U68627
+U68672 U68672
+U68621 U68621
+U68638 U68638
+U68613 U68613
+U68618 U68618
+U68620 U68620
+U68602 U68602
+U68637 U68637
+U68641 U68641
+U68667 U68667
+U68673 U68673
+U68658 U68658
+U68664 U68664
+U68687 U68687
+U68592 U68592
+U68671 U68671
+U68636 U68636
+U68631 U68631
+U68652 U68652
+U68666 U68666
+U68674 U68674
+U68685 U68685
+U68625 U68625
+U68682 U68682
+U68609 U68609
+U68603 U68603
+U68640 U68640
+U68680 U68680
+U68615 U68615
+U68670 U68670
+U68662 U68662
+U68678 U68678
+U68598 U68598
+U68619 U68619
+U68633 U68633
+U68651 U68651
+U68645 U68645
+U68643 U68643
+U68611 U68611
+U68657 U68657
+U68599 U68599
+U68642 U68642
+U68590 U68590
+U68644 U68644
+U68684 U68684
+U68606 U68606
+U68639 U68639
+U68654 U68654
+U68593 U68593
+U68679 U68679
+U68607 U68607
+U68597 U68597
+U68653 U68653
+U68646 U68646
+U68616 U68616
+U68677 U68677
+U68681 U68681
+U68623 U68623
+U68669 U68669
+U68589 U68589
+U68665 U68665
+U68663 U68663
+U68688 U68688
+U68617 U68617
+U68628 U68628
+U68629 U68629
+U68660 U68660
+U68614 U68614
+U68632 U68632
+U68634 U68634
+U68676 U68676
+U68649 U68649
+U68648 U68648
+U68626 U68626
+U68596 U68596
+U68624 U68624
+U68594 U68594
+U68659 U68659
+U68601 U68601
+U68675 U68675
b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon_withgroups.count_table
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon_withgroups.count_table Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,97 @@
+Representative_Sequence total forest pasture
+U68630 1 1 0
+U68595 1 1 0
+U68600 1 1 0
+U68591 1 1 0
+U68647 1 0 1
+U68661 1 0 1
+U68605 1 1 0
+U68622 1 1 0
+U68612 1 1 0
+U68608 1 1 0
+U68610 1 1 0
+U68656 1 0 1
+U68655 1 0 1
+U68668 1 0 1
+U68686 1 0 1
+U68683 1 0 1
+U68635 1 1 0
+U68627 1 1 0
+U68672 1 0 1
+U68621 1 1 0
+U68638 1 1 0
+U68613 1 1 0
+U68618 2 2 0
+U68602 1 1 0
+U68637 1 1 0
+U68641 2 0 2
+U68673 1 0 1
+U68658 1 0 1
+U68664 1 0 1
+U68687 1 0 1
+U68592 1 1 0
+U68671 1 0 1
+U68636 1 1 0
+U68631 1 1 0
+U68652 1 0 1
+U68666 1 0 1
+U68674 1 0 1
+U68685 1 0 1
+U68625 1 1 0
+U68682 1 0 1
+U68609 1 1 0
+U68603 1 1 0
+U68640 1 0 1
+U68680 1 0 1
+U68615 1 1 0
+U68670 1 0 1
+U68662 1 0 1
+U68678 1 0 1
+U68598 1 1 0
+U68619 1 1 0
+U68633 1 1 0
+U68651 1 0 1
+U68645 1 0 1
+U68643 1 0 1
+U68611 1 1 0
+U68657 1 0 1
+U68599 1 1 0
+U68642 1 0 1
+U68590 1 1 0
+U68644 1 0 1
+U68684 1 0 1
+U68606 1 1 0
+U68639 1 0 1
+U68654 1 0 1
+U68593 1 1 0
+U68679 1 0 1
+U68607 1 1 0
+U68597 1 1 0
+U68653 1 0 1
+U68646 1 0 1
+U68616 1 1 0
+U68677 1 0 1
+U68681 1 0 1
+U68623 1 1 0
+U68669 1 0 1
+U68589 1 1 0
+U68665 1 0 1
+U68663 1 0 1
+U68688 1 0 1
+U68617 1 1 0
+U68628 1 1 0
+U68629 1 1 0
+U68660 1 0 1
+U68614 1 1 0
+U68632 1 1 0
+U68634 1 1 0
+U68676 1 0 1
+U68649 1 0 1
+U68648 1 0 1
+U68626 1 1 0
+U68596 1 1 0
+U68624 1 1 0
+U68594 1 1 0
+U68659 1 0 1
+U68601 1 1 0
+U68675 1 0 1
b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon_withgroups.redundant.groups
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon_withgroups.redundant.groups Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,98 @@
+U68589_1 forest
+U68590_1 forest
+U68591_1 forest
+U68592_1 forest
+U68593_1 forest
+U68594_1 forest
+U68595_1 forest
+U68596_1 forest
+U68597_1 forest
+U68598_1 forest
+U68599_1 forest
+U68600_1 forest
+U68601_1 forest
+U68602_1 forest
+U68603_1 forest
+U68605_1 forest
+U68606_1 forest
+U68607_1 forest
+U68608_1 forest
+U68609_1 forest
+U68610_1 forest
+U68611_1 forest
+U68612_1 forest
+U68613_1 forest
+U68614_1 forest
+U68615_1 forest
+U68616_1 forest
+U68617_1 forest
+U68618_1 forest
+U68618_2 forest
+U68619_1 forest
+U68621_1 forest
+U68622_1 forest
+U68623_1 forest
+U68624_1 forest
+U68625_1 forest
+U68626_1 forest
+U68627_1 forest
+U68628_1 forest
+U68629_1 forest
+U68630_1 forest
+U68631_1 forest
+U68632_1 forest
+U68633_1 forest
+U68634_1 forest
+U68635_1 forest
+U68636_1 forest
+U68637_1 forest
+U68638_1 forest
+U68639_1 pasture
+U68640_1 pasture
+U68641_1 pasture
+U68641_2 pasture
+U68642_1 pasture
+U68643_1 pasture
+U68644_1 pasture
+U68645_1 pasture
+U68646_1 pasture
+U68647_1 pasture
+U68648_1 pasture
+U68649_1 pasture
+U68651_1 pasture
+U68652_1 pasture
+U68653_1 pasture
+U68654_1 pasture
+U68655_1 pasture
+U68656_1 pasture
+U68657_1 pasture
+U68658_1 pasture
+U68659_1 pasture
+U68660_1 pasture
+U68661_1 pasture
+U68662_1 pasture
+U68663_1 pasture
+U68664_1 pasture
+U68665_1 pasture
+U68666_1 pasture
+U68668_1 pasture
+U68669_1 pasture
+U68670_1 pasture
+U68671_1 pasture
+U68672_1 pasture
+U68673_1 pasture
+U68674_1 pasture
+U68675_1 pasture
+U68676_1 pasture
+U68677_1 pasture
+U68678_1 pasture
+U68679_1 pasture
+U68680_1 pasture
+U68681_1 pasture
+U68682_1 pasture
+U68683_1 pasture
+U68684_1 pasture
+U68685_1 pasture
+U68686_1 pasture
+U68687_1 pasture
+U68688_1 pasture
b
diff -r 000000000000 -r bccb5efbc4ee test-data/amazon_withgroups_pasture.count_table
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/amazon_withgroups_pasture.count_table Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,49 @@
+Representative_Sequence total pasture
+U68647 1 1
+U68661 1 1
+U68656 1 1
+U68655 1 1
+U68668 1 1
+U68686 1 1
+U68683 1 1
+U68672 1 1
+U68641 2 2
+U68673 1 1
+U68658 1 1
+U68664 1 1
+U68687 1 1
+U68671 1 1
+U68652 1 1
+U68666 1 1
+U68674 1 1
+U68685 1 1
+U68682 1 1
+U68640 1 1
+U68680 1 1
+U68670 1 1
+U68662 1 1
+U68678 1 1
+U68651 1 1
+U68645 1 1
+U68643 1 1
+U68657 1 1
+U68642 1 1
+U68644 1 1
+U68684 1 1
+U68639 1 1
+U68654 1 1
+U68679 1 1
+U68653 1 1
+U68646 1 1
+U68677 1 1
+U68681 1 1
+U68669 1 1
+U68665 1 1
+U68663 1 1
+U68688 1 1
+U68660 1 1
+U68676 1 1
+U68649 1 1
+U68648 1 1
+U68659 1 1
+U68675 1 1
b
diff -r 000000000000 -r bccb5efbc4ee test-data/biosample.source
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/biosample.source Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,24 @@
+if (package == "soil") {
+ out << "#MIMARKS.survey.soil.4.0" << endl;
+  if (requiredonly) {
+ out << "#{sample name} {description of sample} {sample title} {description of library_construction_protocol} {http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=408169&lvl=3&keep=1&srchmode=1&unlock}" << endl;
+ out << "#{text} {text} {text} {text} {controlled vacabulary}" << endl;
+ out << "*sample_name *description *sample_title *seq_methods *organism" << endl;
+ }else {
+ out << "#{sample name} {description of sample} {sample title} {description of library_construction_protocol} {http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=408169&lvl=3&keep=1&srchmode=1&unlock} {soil classification from the FAO World Reference Database for Soil Resources}" << endl;
+ out << "#{text} {text} {text} {text} {controlled vacabulary} {{term}}" << endl;
+ out << "*sample_name *description *sample_title *seq_methods *organism fao_class" << endl;
+ }
+}
+
+if ((package == "soil") ) {}
+
+vector<string> requiredFieldsForPackage;
+requiredFieldsForPackage.push_back("sample_name");
+requiredFieldsForPackage.push_back("description");
+requiredFieldsForPackage.push_back("sample_title");
+requiredFieldsForPackage.push_back("seq_methods");
+requiredFieldsForPackage.push_back("organism");
+
+
+if (packageType == "MIMARKS.survey.soil.4.0") {}
b
diff -r 000000000000 -r bccb5efbc4ee test-data/biosample.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/biosample.tsv Fri May 19 05:47:34 2017 -0400
[
@@ -0,0 +1,10 @@
+#This is a tab-delimited file. Additional Documentation can be found at http://www.mothur.org/wiki/MIMarks_Data_Packages.
+#Please fill all the required fields indicated with '*'
+#Unknown or inapplicable fields can be assigned 'missing' value.
+#You may add extra custom fields to this template. Make sure all the fields are separated by tabs.
+#You may remove any fields not required (marked with '*'). Make sure all the fields are separated by tabs.
+#You can edit this template using Microsoft Excel or any other editor. But while saving the file please make sure to save them as 'TAB-DELIMITED' TEXT FILE.
+#MIMARKS.survey.miscellaneous.4.0
+#{sample name} {description of sample} {sample title} {description of library_construction_protocol} {http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=408169&lvl=3&keep=1&srchmode=1&unlock} {Date of sampling, in "DD-Mmm-YYYY", "Mmm-YYYY" or "YYYY" format (eg., 30-Oct-1990, Oct-1990 or 1990) or ISO 8601 standard "YYYY-mm-dd", "YYYY-mm" or "YYYY-mm-ddThh:mm:ss" (eg., 1990-10-30, 1990-10 or 1990-10-30T14:41:36)} {descriptor of the broad ecological context of a sample. Examples include: desert, taiga, deciduous woodland, or coral reef. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO} {descriptor of the local environment. Examples include: harbor, cliff, or lake. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO} {material that was displaced by the sample, or material in which a sample was embedded, prior to the sampling event. Examples include: air, soil, or water. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO} {Geographical origin of the sample; use the appropriate name from this list http://www.insdc.org/documents/country-qualifier-vocabulary. Use a colon to separate the country or ocean from more detailed information about the location, eg "Canada: Vancouver" or "Germany: halfway down Zugspitze, Alps"} {The geographical coordinates of the location where the sample was collected. Specify as degrees latitude and longitude in format "d[d.dddd] N|S d[dd.dddd] W|E", eg, 38.98 N 77.11 W} {alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate} {The altitude of the sample is the vertical distance between Earth's surface above Sea Level and the sampled position in the air.} {concentration of ammonium} {amount of biomass; should include the name for the part of biomass measured, e.g. microbial, total. can include multiple measurements} {concentration of bromide} {concentration of calcium} {list of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, N fertilizer, air filter); can include multiple compounds. For Chemical Entities of Biological Interest ontology (CHEBI) (v1.72), please see http://bioportal.bioontology.org/visualize/44603} {concentration of chloride} {concentration of chlorophyll} {density of sample} {Depth is defined as the vertical distance below surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectivly. Depth can be reported as an interval for subsurface samples.} {concentration of diether lipids; can include multiple types of diether lipids} {concentration of dissolved carbon dioxide} {concentration of dissolved hydrogen} {dissolved inorganic carbon concentration} {dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2} {concentration of dissolved oxygen} {The elevation of the sampling site as measured by the vertical distance from mean sea level.} {any other measurement performed or parameter collected, that is not listed here} {concentration of nitrate} {concentration of nitrite} {concentration of nitrogen (total)} {concentration of organic carbon} {concentration of organic matter} {concentration of organic nitrogen} {total count of any organism per gram or volume of sample,should include name of organism followed by count; can include multiple organism counts} {oxygenation status of sample} {type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types} {pH measurement} {concentration of phosphate} {concentration of phospholipid fatty acids; can include multiple values} {concentration of potassium} {pressure to which the sample is subject, in atmospheres} {Aerobic or anaerobic} {salinity measurement} {Method or device employed for collecting sample} {Processing applied to the sample during or after isolation} {Amount or size of sample (volume, mass or area) that was collected} {none} {none} {none} {volume (mL) or weight (g) of sample processed for DNA extraction} {concentration of silicate} {sodium concentration} {unique identifier assigned to a material sample used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples.} {concentration of sulfate} {concentration of sulfide} {temperature of the sample at time of sampling} {measurement of magnitude and direction of flow within a fluid}
+#{text} {text} {text} {text} {controlled vacabulary} {{timestamp}} {{term}} {{term}} {{term}} {{term}:{term}:{text}} {{float} {float}} {{float} {unit}} {{float} m} {{float} {unit}} {{text};{float} {unit}} {{float} {unit}} {{float} {unit}} {{term}; {timestamp}} {{float} {unit}} {{float} {unit}} {{float} {unit}} {{float} m} {{text};{float} {unit}} {{float} {unit}} {{float} {unit}} {{float} {unit}} {{float} {unit}} {{float} {unit}} {{float} {unit}} {{text};{float} {unit}} {{float} {unit}} {{float} {unit}} {{float} {unit}} {{float} {unit}} {{float} {unit}} {{float} {unit}} {{text};{float} {unit}} {['', 'aerobic', 'anaerobic']} {{text};{interval}} {{float} {unit}} {{float} {unit}} {{text};{float} {unit}} {{float} {unit}} {{float} {unit}} {['', 'aerobe', 'anaerobe', 'facultative', 'microaerophilic', 'microanaerobe', 'obligate aerobe', 'obligate anaerobe']} {{float} {unit}} {{text}} {{text|term}} {{float} {unit}} {{none}} {{none}} {{none}} {{float} {unit}} {{float} {unit}} {{float} {unit}} {{text}} {{float} {unit}} {{float} {unit}} {{float} {unit}} {{float} {unit}}
+*sample_name *description *sample_title *seq_methods *organism *collection_date *env_biome *env_feature *env_material *geo_loc_name *lat_lon alkalinity altitude ammonium biomass bromide calcium chem_administration chloride chlorophyll density depth diether_lipids diss_carb_dioxide diss_hydrogen diss_inorg_carb diss_org_nitro diss_oxygen elev misc_param nitrate nitrite nitro org_carb org_matter org_nitro organism_count oxy_stat_samp perturbation ph phosphate phosplipid_fatt_acid potassium pressure rel_to_oxygen salinity samp_collect_device samp_mat_process samp_size samp_store_dur samp_store_loc samp_store_temp samp_vol_we_dna_ext silicate sodium source_material_id sulfate sulfide temp water_current
b
diff -r 000000000000 -r bccb5efbc4ee test-data/biosample.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/biosample.xml Fri May 19 05:47:34 2017 -0400
[
@@ -0,0 +1,33 @@
+<BioSampleAttributes>
+  <Attribute>
+    <Name>EDTA inhibitor tested</Name>
+    <HarmonizedName>edta_inhibitor_tested</HarmonizedName>
+    <Description>Was carbapenemase activity tested in the presence of EDTA? If carbapenemase activity was tested in the presence of EDTA, the response should be "yes", otherwise "no”.</Description>
+    <Format>['', 'yes', 'no', 'missing', 'not applicable', 'not collected']</Format>
+    <Synonym>edta inhibitor tested</Synonym>
+    <Package use="mandatory">Beta-lactamase.1.0</Package>
+  </Attribute>
+  <Attribute>
+    <Name>FAO classification</Name>
+    <HarmonizedName>fao_class</HarmonizedName>
+    <Description>soil classification from the FAO World Reference Database for Soil Resources</Description>
+    <Format>{term}</Format>
+    <Synonym>fao class</Synonym>
+    <Synonym>fao classification</Synonym>
+    <Synonym>soil taxonomic/fao classification</Synonym>
+    <Package use="optional" group_name="Soil">MIGS.ba.soil.4.0</Package>
+    <Package use="optional" group_name="Soil">MIGS.eu.soil.4.0</Package>
+    <Package use="optional" group_name="Soil">MIGS.vi.soil.4.0</Package>
+    <Package use="optional" group_name="Soil">MIMARKS.specimen.soil.4.0</Package>
+    <Package use="optional" group_name="Soil">MIMARKS.survey.soil.4.0</Package>
+    <Package use="optional" group_name="Soil">MIMS.me.soil.4.0</Package>
+  </Attribute>
+  <Attribute>
+    <Name>HIV status</Name>
+    <HarmonizedName>hiv_stat</HarmonizedName>
+    <Description>HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO]</Description>
+    <Format>{boolean};{boolean}</Format>
+    <Synonym>hiv stat</Synonym>
+    <Synonym>hiv status</Synonym>
+  </Attribute>
+</BioSampleAttributes>
b
diff -r 000000000000 -r bccb5efbc4ee test-data/cd-test.constaxonomy
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cd-test.constaxonomy Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,6 @@
+OTU Size Taxonomy
+Otu0001 4 Bacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);unclassified(100);
+Otu1000 1 Bacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);unclassified(100);
+Otu1676 1 Bacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);unclassified(100);
+Otu2360 1 Bacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);unclassified(100);
+Otu2439 1 Bacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);unclassified(100);
b
diff -r 000000000000 -r bccb5efbc4ee test-data/cd-test.count_table
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cd-test.count_table Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,6 @@
+Representative_Sequence total
+GQY1XT001C296C 4
+GQY1XT001AUA36 1
+GQY1XT001DLSKT 1
+GQY1XT001B3W8S 1
+GQY1XT001A4UXI 1
b
diff -r 000000000000 -r bccb5efbc4ee test-data/cd-test.database
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cd-test.database Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,6 @@
+OTUNumber Abundance repSeqName repSeq OTUConTaxonomy
+Otu0001 4 GQY1XT001C296C A-GC--GA-G-A-A-G-T-A--TG-C--GG-A-ATG-C-G-T-G-GT-GT-A-G-CGGT-G-AAA--TG-C-AT-AG--AT-A-TCA-C-GCA-G-A-AC-T-CC--GAT-T-GC-GAA-GG-C-A-G-C-A-T-A--CCG-G--CG-C-T-C-A-A-CT--GACG-CTC--A-TGC-A-CG-AAA-G-T-G-TGGGT--ATC-G-AA-----CA-GGATTAG-ATA-CCCT-GGTA-GT-C-CAC-A-CAGT-AAAC-G-A-TG-A-A----TA-C-T-A-A-TT-G-T-T--C-G-G-G-G--A--------GAA-TGA--------T-C-C-C-T--G---A-G-T-G--A-T-----AC--A--G-C-G-AA-A-G-C-G-T-TAA-G-T-ATT---CC-ACC-T-GGGG-AGTA--CG-CC-G-G-C-A-A-CGGT-GAA Bacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);unclassified(100);
+Otu1000 1 GQY1XT001AUA36 G-GC--GA-G-A-A-G-T-A--TG-C--GG-A-ATG-C-G-T-G-GT-GT-A-G-CGGT-G-AAA--TG-C-AT-AG--AT-A-TCA-C-GCA-G-A-AC-T-CC--GAT-T-GC-GAA-GG-C-A-G-C-A-T-A--CCG-G--CT-T-C-C-T-A-CT--GACG-CTC--A-TGC-A-CG-AAA-G-T-G-TGGGT--ATC-G-AA-----CA-GGATTAG-ATA-CCCT-GGTA-GT-C-CAC-A-CAGT-AAAC-G-A-TG-A-A----TA-C-T-A-A-TT-G-T-T--C-G-G-G-G--A--------GAA-TGA--------T-C-C-C-T--G---A-G-T-G--A-T-----AC--A--G-C-G-AA-A-G-C-G-T-TAA-G-T-ATT---CC-ACC-T-GGGG-AGTA--CG-CC-G-G-C-A-A-CGGT-GAA Bacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);unclassified(100);
+Otu1676 1 GQY1XT001DLSKT ..GC--GA-G-A-A-G-T-A--TG-C--GG-A-ATG-C-G-T-G-GT-GT-A-G-CGGT-G-AAA--TG-C-AT-AG--AT-A-TCA-C-GCA-G-A-AC-T-CC--GAT-T-GC-GAA-GG-C-A-G-C-C-T-A--CCG-G--CG-C-T-C-A-A-CT--GACG-CTC--A-TGC-A-CG-AAA-G-T-G-TGGGT--ATC-G-AA-----CA-GGATTAG-ATA-CCCT-GGTA-GT-C-CAC-A-CAGT-AAAC-G-A-TG-A-A----TA-C-T-A-A-TT-G-T-T--C-G-G-G-G--A--------GAA-TGA--------T-C-C-C-T--G---A-G-T-G--A-T-----AC--A--G-C-G-AA-A-G-C-G-T-TAA-G-T-ATT---CC-ACC-T-GGGG-AGTA--CG-CC-G-G-C-A-A-CGGT-GAA Bacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);unclassified(100);
+Otu2360 1 GQY1XT001B3W8S A-GC--GA-G-A-A-G-T-A--TG-C--GG-A-ATG-C-G-T-G-GT-GT-A-G-CGGT-G-AAA--TG-C-AT-AG--AT-A-TCA-C-GCA-G-A-AC-T-CC--GAT-T-GC-GAA-GG-C-A-G-C-A-T-A--CCG-G--CG-C-T-C-A-A-CT--GACG-CTC--A-TGC-A-CG-AAA-G-T-G-TGGGT--ATC-G-AA-----CA-GGATTAG-ATA-CCCT-GGTA-GT-C-CAC-A-CAGT-AAAC-G-A-TG-A-A----TA-C-T-A-A-TT-G-T-T--C-G-G-G-G--A--------GAA-TGA--------T-C-C-C-T--G---A-G-T-G--A-T-----AC--A--G-C-G-AA-A-G-C-G-T-TAA-G-T-ATT---CC-ACC-T-GGGG-AGTA--CG-AC-C-G-C-A-A-GGTT-GAA Bacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);unclassified(100);
+Otu2439 1 GQY1XT001A4UXI C-GC--GA-G-A-A-G-T-A--TG-C--GG-A-ATG-C-G-T-G-GC-GT-A-G-CGGT-G-AAA--TG-C-AT-AG--AT-A-TCA-C-GCA-G-A-AC-T-CC--GAT-T-GC-GAA-GG-C-A-G-C-A-T-A--CCG-G--CG-C-C-C-G-A-CT--GACG-CTG--A-GGC-A-CG-AAA-G-T-G-TGGGT--ATC-G-AA-----CA-GGATTAG-ATA-CCCT-GGTA-GT-C-CAC-A-CAGT-AAAC-G-A-TG-A-A----TA-C-T-A-A-TT-G-T-T--C-G-G-G-G--A--------GAA-TGA--------T-C-C-C-T--G---A-G-T-G--A-T-----AC--A--G-C-G-AA-A-G-C-G-T-TAA-G-T-ATT---CC-ACC-T-GGGG-AGTA--CG-CC-G-G-C-A-A-CGGT-GAA Bacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);unclassified(100);
b
diff -r 000000000000 -r bccb5efbc4ee test-data/cd-test.list
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cd-test.list Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,2 @@
+label numOtus Otu0001 Otu1000 Otu1676 Otu2360 Otu2439
+unique 5 GQY1XT001C296C,GQY1XT001BOB1X,GQY1XT001AT26X,GQY1XT001DWCTO GQY1XT001AUA36 GQY1XT001DLSKT GQY1XT001B3W8S GQY1XT001A4UXI
b
diff -r 000000000000 -r bccb5efbc4ee test-data/cd-test.repfasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cd-test.repfasta Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,10 @@
+>GQY1XT001C296C Otu0001|4
+A-GC--GA-G-A-A-G-T-A--TG-C--GG-A-ATG-C-G-T-G-GT-GT-A-G-CGGT-G-AAA--TG-C-AT-AG--AT-A-TCA-C-GCA-G-A-AC-T-CC--GAT-T-GC-GAA-GG-C-A-G-C-A-T-A--CCG-G--CG-C-T-C-A-A-CT--GACG-CTC--A-TGC-A-CG-AAA-G-T-G-TGGGT--ATC-G-AA-----CA-GGATTAG-ATA-CCCT-GGTA-GT-C-CAC-A-CAGT-AAAC-G-A-TG-A-A----TA-C-T-A-A-TT-G-T-T--C-G-G-G-G--A--------GAA-TGA--------T-C-C-C-T--G---A-G-T-G--A-T-----AC--A--G-C-G-AA-A-G-C-G-T-TAA-G-T-ATT---CC-ACC-T-GGGG-AGTA--CG-CC-G-G-C-A-A-CGGT-GAA
+>GQY1XT001AUA36 Otu1000|1
+G-GC--GA-G-A-A-G-T-A--TG-C--GG-A-ATG-C-G-T-G-GT-GT-A-G-CGGT-G-AAA--TG-C-AT-AG--AT-A-TCA-C-GCA-G-A-AC-T-CC--GAT-T-GC-GAA-GG-C-A-G-C-A-T-A--CCG-G--CT-T-C-C-T-A-CT--GACG-CTC--A-TGC-A-CG-AAA-G-T-G-TGGGT--ATC-G-AA-----CA-GGATTAG-ATA-CCCT-GGTA-GT-C-CAC-A-CAGT-AAAC-G-A-TG-A-A----TA-C-T-A-A-TT-G-T-T--C-G-G-G-G--A--------GAA-TGA--------T-C-C-C-T--G---A-G-T-G--A-T-----AC--A--G-C-G-AA-A-G-C-G-T-TAA-G-T-ATT---CC-ACC-T-GGGG-AGTA--CG-CC-G-G-C-A-A-CGGT-GAA
+>GQY1XT001DLSKT Otu1676|1
+..GC--GA-G-A-A-G-T-A--TG-C--GG-A-ATG-C-G-T-G-GT-GT-A-G-CGGT-G-AAA--TG-C-AT-AG--AT-A-TCA-C-GCA-G-A-AC-T-CC--GAT-T-GC-GAA-GG-C-A-G-C-C-T-A--CCG-G--CG-C-T-C-A-A-CT--GACG-CTC--A-TGC-A-CG-AAA-G-T-G-TGGGT--ATC-G-AA-----CA-GGATTAG-ATA-CCCT-GGTA-GT-C-CAC-A-CAGT-AAAC-G-A-TG-A-A----TA-C-T-A-A-TT-G-T-T--C-G-G-G-G--A--------GAA-TGA--------T-C-C-C-T--G---A-G-T-G--A-T-----AC--A--G-C-G-AA-A-G-C-G-T-TAA-G-T-ATT---CC-ACC-T-GGGG-AGTA--CG-CC-G-G-C-A-A-CGGT-GAA
+>GQY1XT001B3W8S Otu2360|1
+A-GC--GA-G-A-A-G-T-A--TG-C--GG-A-ATG-C-G-T-G-GT-GT-A-G-CGGT-G-AAA--TG-C-AT-AG--AT-A-TCA-C-GCA-G-A-AC-T-CC--GAT-T-GC-GAA-GG-C-A-G-C-A-T-A--CCG-G--CG-C-T-C-A-A-CT--GACG-CTC--A-TGC-A-CG-AAA-G-T-G-TGGGT--ATC-G-AA-----CA-GGATTAG-ATA-CCCT-GGTA-GT-C-CAC-A-CAGT-AAAC-G-A-TG-A-A----TA-C-T-A-A-TT-G-T-T--C-G-G-G-G--A--------GAA-TGA--------T-C-C-C-T--G---A-G-T-G--A-T-----AC--A--G-C-G-AA-A-G-C-G-T-TAA-G-T-ATT---CC-ACC-T-GGGG-AGTA--CG-AC-C-G-C-A-A-GGTT-GAA
+>GQY1XT001A4UXI Otu2439|1
+C-GC--GA-G-A-A-G-T-A--TG-C--GG-A-ATG-C-G-T-G-GC-GT-A-G-CGGT-G-AAA--TG-C-AT-AG--AT-A-TCA-C-GCA-G-A-AC-T-CC--GAT-T-GC-GAA-GG-C-A-G-C-A-T-A--CCG-G--CG-C-C-C-G-A-CT--GACG-CTG--A-GGC-A-CG-AAA-G-T-G-TGGGT--ATC-G-AA-----CA-GGATTAG-ATA-CCCT-GGTA-GT-C-CAC-A-CAGT-AAAC-G-A-TG-A-A----TA-C-T-A-A-TT-G-T-T--C-G-G-G-G--A--------GAA-TGA--------T-C-C-C-T--G---A-G-T-G--A-T-----AC--A--G-C-G-AA-A-G-C-G-T-TAA-G-T-ATT---CC-ACC-T-GGGG-AGTA--CG-CC-G-G-C-A-A-CGGT-GAA
b
diff -r 000000000000 -r bccb5efbc4ee test-data/cd-test.repname
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cd-test.repname Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,5 @@
+GQY1XT001C296C GQY1XT001C296C,GQY1XT001BOB1X,GQY1XT001AT26X,GQY1XT001DWCTO
+GQY1XT001AUA36 GQY1XT001AUA36
+GQY1XT001DLSKT GQY1XT001DLSKT
+GQY1XT001B3W8S GQY1XT001B3W8S
+GQY1XT001A4UXI GQY1XT001A4UXI
b
diff -r 000000000000 -r bccb5efbc4ee test-data/env.dist
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/env.dist Fri May 19 05:47:34 2017 -0400
b
b'@@ -0,0 +1,25 @@\n+24\n+group18 0 2.07679533239178 6.88145502389971 4.47292990349355 2.50815747366843 3.58036212296744 2.6591292750976 2.29553760953804 4.71171667874897 5.16305059040855 2.21426134242764 3.92961213866286 3.13399015473536 4.90270725079791 5.49476199174931 4.24083600731234 6.11441501785041 6.05615282291975 4.95222984315722 4.21090492925648 2.85939902504818 4.97193013540636 6.55517500441812 2.54101803759533\n+group15 2.07679533239178 0 6.90291144667953 4.64003084174476 3.72544116897342 4.23057909059422 3.32236571813861 2.52327233791657 5.13562550988481 5.1437583829781 2.50862666200143 4.72257599677909 3.43881324942989 4.85150831682718 5.50342943536056 3.52222099128756 5.87491943777315 5.49066317297654 4.27208092800677 3.15270231033824 1.74819033890028 4.12374288054719 6.15931692104792 3.35050234347791\n+group24 6.88145502389971 6.90291144667953 0 5.48014130249836 5.71422767011491 5.44458516207639 6.21128694887343 7.57897769844682 5.72787031540342 5.50347777475312 6.05215034685817 5.13756253132332 6.81750519634229 8.76568212120474 9.04444618731187 8.33992506606364 9.11412838063313 5.67503738892289 6.94693258686523 5.30131540387761 6.85740763239976 5.5325902108287 6.30781548936649 7.84284307315349\n+group27 4.47292990349355 4.64003084174476 5.48014130249836 0 3.48549610587919 3.96397362332123 3.14459815680532 5.59791469171996 2.25198909783448 5.18311849821211 4.54741248463763 3.71058624754798 2.69797588499755 7.8250450422056 7.61406607135237 7.13381545095109 8.44384430044265 6.71088081591996 6.35910146136893 5.18001442223706 5.2381960545819 4.7094220651569 6.46329094926891 5.88708881996361\n+group23 2.50815747366843 3.72544116897342 5.71422767011491 3.48549610587919 0 2.09064557523382 2.35007842477788 3.84437623072582 3.37982049066074 4.82948860655148 2.61344414995761 3.08212085298007 3.39826001248126 6.34083256759322 6.7804402439463 5.9882682085243 7.368182657586 6.29229240618139 5.93365009305124 4.74001147278235 4.16875045563175 5.19193126631916 6.60549692940372 3.75170839493609\n+group19 3.58036212296744 4.23057909059422 5.44458516207639 3.96397362332123 2.09064557523382 0 2.91550590841545 4.53693024483879 4.16796766816088 4.70318440048524 2.79541837375649 3.79457424274492 4.23335312544269 6.52562476479155 7.28216604836819 6.15919058556992 7.48332275942444 6.29601002300864 6.13547796850531 4.6792323698443 4.45343001677936 5.90808732531762 7.12563061433389 4.29741620103145\n+group22 2.6591292750976 3.32236571813861 6.21128694887343 3.14459815680532 2.35007842477788 2.91550590841545 0 3.03537232143609 3.19717141237262 4.78031309163852 2.41753325811849 3.59607995374352 2.12854912039549 5.46704031619679 5.33701156479808 4.96043060818422 6.44826304723108 6.36381765874823 5.33050747387333 4.28625407689455 3.30334570818273 4.94667231796753 6.31277712868333 3.58610710419189\n+group16 2.29553760953804 2.52327233791657 7.57897769844682 5.59791469171996 3.84437623072582 4.53693024483879 3.03537232143609 0 5.42581905199784 5.5382425777602 2.21628461900339 4.91569734557852 3.76898373844346 3.66958270784948 3.7596809535214 3.09087676998529 5.16423793264611 6.19348191138961 4.67007617153741 4.11204634372634 2.12921147954829 5.20716627366845 6.64769970583513 2.40407490833653\n+group28 4.71171667874897 5.13562550988481 5.72787031540342 2.25198909783448 3.37982049066074 4.16796766816088 3.19717141237262 5.42581905199784 0 4.78731905692567 4.50479586376459 3.38670838656427 3.20693742829686 7.42683056394166 7.34570046678601 7.1701579995315 7.98002716787638 6.41561622183692 6.2124182195955 5.39657010741707 5.54110800674231 5.1577675165935 6.8516874226519 6.10574081766257\n+group13 5.16305059040855 5.1437583829781 5.50347777475312 5.18311849821211 4.82948860655148 4.70318440048524 4.78031309163852 5.5382425777602 4.78731905692567 0 4.67746569480341 4.08051856974203 5.63341628143736 6.13993687315028 7.7127998868603 6.72017341542958 6.71492819699427 4.33113554849634 4.44684649984502 4.82408553908334 5.61768442520245 5.26230208160398 6.54992709860'..b' 4.64487610678987\n+group5 5.49476199174931 5.50342943536056 9.04444618731187 7.61406607135237 6.7804402439463 7.28216604836819 5.33701156479808 3.7596809535214 7.34570046678601 7.7127998868603 5.29902826407876 7.18535849292866 5.5528259214464 3.95581421039689 0 4.04435991796256 5.01228422881506 8.11947221764963 5.86295047339197 5.99126094814824 4.58960572590818 6.61131730349409 7.40381675001318 4.84021195384958\n+group6 4.24083600731234 3.52222099128756 8.33992506606364 7.13381545095109 5.9882682085243 6.15919058556992 4.96043060818422 3.09087676998529 7.1701579995315 6.72017341542958 4.05541661524461 6.60015854488732 5.28753056505203 2.89070054815662 4.04435991796256 0 3.64256798987379 6.01870458325898 4.26211882754801 3.82653767294834 2.5630508080946 5.89444500689165 6.82255468001791 4.23311465341886\n+group3 6.11441501785041 5.87491943777315 9.11412838063313 8.44384430044265 7.368182657586 7.48332275942444 6.44826304723108 5.16423793264611 7.98002716787638 6.71492819699427 6.11473384050956 7.50539564845393 6.86459352948227 2.00584491640009 5.01228422881506 3.64256798987379 0 6.60501226761683 3.94055918447939 5.63216883653706 5.30106624617202 6.83112869949915 6.80321310613232 6.05396442753773\n+group4 6.05615282291975 5.49066317297654 5.67503738892289 6.71088081591996 6.29229240618139 6.29601002300864 6.36381765874823 6.19348191138961 6.41561622183692 4.33113554849634 5.23487714375643 4.98323825896227 6.60873730627615 6.4169416509523 8.11947221764963 6.01870458325898 6.60501226761683 0 4.58594627180039 3.55328319122345 5.54504004833869 5.61499654775589 6.828621895957 7.2430575511398\n+group2 4.95222984315722 4.27208092800677 6.94693258686523 6.35910146136893 5.93365009305124 6.13547796850531 5.33050747387333 4.67007617153741 6.2124182195955 4.44684649984502 4.87089053925741 5.96071394777962 5.6314567316324 3.98054063154574 5.86295047339197 4.26211882754801 3.94055918447939 4.58594627180039 0 3.90515299381786 4.28027849695426 4.38635292373633 5.39036567068314 6.01887662312089\n+group9 4.21090492925648 3.15270231033824 5.30131540387761 5.18001442223706 4.74001147278235 4.6792323698443 4.28625407689455 4.11204634372634 5.39657010741707 4.82408553908334 3.21806378630338 4.63371782472599 4.5625504604801 5.12176871169235 5.99126094814824 3.82653767294834 5.63216883653706 3.55328319122345 3.90515299381786 0 2.65742337348713 3.85104238688071 5.57317463010724 5.08393769559955\n+group12 2.85939902504818 1.74819033890028 6.85740763239976 5.2381960545819 4.16875045563175 4.45343001677936 3.30334570818273 2.12921147954829 5.54110800674231 5.61768442520245 2.37451207574614 5.21021128432828 3.80862359775727 4.25495681827209 4.58960572590818 2.5630508080946 5.30106624617202 5.54504004833869 4.28027849695426 2.65742337348713 0 4.28103353313767 5.86614162833534 3.27887996130286\n+group10 4.97193013540636 4.12374288054719 5.5325902108287 4.7094220651569 5.19193126631916 5.90808732531762 4.94667231796753 5.20716627366845 5.1577675165935 5.26230208160398 5.0909474774308 5.3351470840398 4.74234966729958 6.42605641292207 6.61131730349409 5.89444500689165 6.83112869949915 5.61499654775589 4.38635292373633 3.85104238688071 4.28103353313767 0 3.33721452854301 5.88678552682047\n+group11 6.55517500441812 6.15931692104792 6.30781548936649 6.46329094926891 6.60549692940372 7.12563061433389 6.31277712868333 6.64769970583513 6.8516874226519 6.54992709860496 6.73970215554685 6.70375146848393 6.39367296383052 6.84353264931 7.40381675001318 6.82255468001791 6.80321310613232 6.828621895957 5.39036567068314 5.57317463010724 5.86614162833534 3.33721452854301 0 6.7434003020233\n+group21 2.54101803759533 3.35050234347791 7.84284307315349 5.88708881996361 3.75170839493609 4.29741620103145 3.58610710419189 2.40407490833653 6.10574081766257 6.42845550946653 3.03452592937357 5.02891238126826 4.14114063107224 4.64487610678987 4.84021195384958 4.23311465341886 6.05396442753773 7.2430575511398 6.01887662312089 5.08393769559955 3.27887996130286 5.88678552682047 6.7434003020233 0\n'
b
diff -r 000000000000 -r bccb5efbc4ee test-data/example.biom
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.biom Fri May 19 05:47:34 2017 -0400
[
@@ -0,0 +1,55 @@
+{
+ "id":null,
+ "format": "Biological Observation Matrix 0.9.1-dev",
+ "format_url": "http://biom-format.org/documentation/format_versions/biom-1.0.html",
+ "type": "OTU table",
+ "generated_by": "QIIME revision 1.4.0-dev",
+ "date": "2011-12-19T19:00:00",
+ "rows":[
+    {"id":"GG_OTU_1", "metadata":{"taxonomy":["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Escherichia", "s__"]}},
+    {"id":"GG_OTU_2", "metadata":{"taxonomy":["k__Bacteria", "p__Cyanobacteria", "c__Nostocophycideae", "o__Nostocales", "f__Nostocaceae", "g__Dolichospermum", "s__"]}},
+    {"id":"GG_OTU_3", "metadata":{"taxonomy":["k__Archaea", "p__Euryarchaeota", "c__Methanomicrobia", "o__Methanosarcinales", "f__Methanosarcinaceae", "g__Methanosarcina", "s__"]}},
+    {"id":"GG_OTU_4", "metadata":{"taxonomy":["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Halanaerobiales", "f__Halanaerobiaceae", "g__Halanaerobium", "s__Halanaerobiumsaccharolyticum"]}},
+    {"id":"GG_OTU_5", "metadata":{"taxonomy":["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Escherichia", "s__"]}}
+    ],
+ "columns":[
+    {"id":"Sample1", "metadata":{
+                             "BarcodeSequence":"CGCTTATCGAGA",
+                             "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
+                             "BODY_SITE":"gut",
+                             "Description":"human gut"}},
+    {"id":"Sample2", "metadata":{
+                             "BarcodeSequence":"CATACCAGTAGC",
+                             "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
+                             "BODY_SITE":"gut",
+                             "Description":"human gut"}},
+    {"id":"Sample3", "metadata":{
+                             "BarcodeSequence":"CTCTCTACCTGT",
+                             "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
+                             "BODY_SITE":"gut",
+                             "Description":"human gut"}},
+    {"id":"Sample4", "metadata":{
+                             "BarcodeSequence":"CTCTCGGCCTGT",
+                             "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
+                             "BODY_SITE":"skin",
+                             "Description":"human skin"}},
+    {"id":"Sample5", "metadata":{
+                             "BarcodeSequence":"CTCTCTACCAAT",
+                             "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
+                             "BODY_SITE":"skin",
+                             "Description":"human skin"}},
+    {"id":"Sample6", "metadata":{
+                             "BarcodeSequence":"CTAACTACCAAT",
+                             "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT",
+                             "BODY_SITE":"skin",
+                             "Description":"human skin"}}
+            ],
+ "matrix_type": "dense",
+ "matrix_element_type": "int",
+ "shape": [5,6],
+ "data":  [[0,0,1,0,0,0],
+           [5,1,0,2,3,1],
+           [0,0,1,4,2,0],
+           [2,1,1,0,0,1],
+           [0,1,1,0,0,0]]
+}
b
diff -r 000000000000 -r bccb5efbc4ee test-data/example.constaxonomy
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.constaxonomy Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,9 @@
+OTU Size Taxonomy
+Otu1 34003 Bacteria(100);Bacteroidetes(100);Bacteroidia(99);Bacteroidales(99);Porphyromonadaceae(90);unclassified(87);
+Otu2 11218 Bacteria(100);Firmicutes(100);Clostridia(70);Clostridiales(70);Lachnospiraceae(51);unclassified;
+Otu3 3343 Bacteria(100);Bacteroidetes(100);Bacteroidia"(100);Bacteroidales(100);Bacteroidaceae(100);Bacteroides(100);
+Otu4 2223 Bacteria(100);Bacteroidetes(100);Bacteroidia"(100);Bacteroidales(100);Rikenellaceae"(100);Alistipes(100);
+Otu5 623 Bacteria(100);Firmicutes(72);unclassified(53);unclassified(53);unclassified(53);unclassified(53);
+Otu6 48 Bacteria(100);Actinobacteria(94);Actinobacteria(94);Coriobacteriales(71);Coriobacteriaceae(71);unclassified;
+Otu7 4 Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);unclassified;unclassified;unclassified;
+Otu8 2 Bacteria(100);TM7(100);TM7_class_incertae_sedis(100);TM7_order_incertae_sedis(100);TM7_family_incertae_sedis(100);TM7_genus_incertae_sedis(100);
b
diff -r 000000000000 -r bccb5efbc4ee test-data/final.tx.1.cons.taxonomy
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/final.tx.1.cons.taxonomy Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,63 @@
+OTU Size Taxonomy
+1 29357 Bacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);unclassified(100);
+2 2223 Bacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Rikenellaceae"(100);Alistipes(100);
+3 3211 Bacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);unclassified(100);unclassified(100);
+4 4646 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);unclassified(100);unclassified(100);
+5 4462 Bacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);Bacteroidaceae(100);Bacteroides(100);
+6 445 Bacteria(100);"Bacteroidetes"(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);
+7 1194 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Lachnospiraceae"(100);unclassified(100);
+8 467 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Ruminococcaceae"(100);Oscillibacter(100);
+9 417 Bacteria(100);"Firmicutes"(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);
+10 1571 Bacteria(100);"Bacteroidetes"(100);"Bacteroidia"(100);"Bacteroidales"(100);"Porphyromonadaceae"(100);Barnesiella(100);
+11 365 Bacteria(100);"Firmicutes"(100);"Erysipelotrichi"(100);"Erysipelotrichales"(100);Erysipelotrichaceae(100);Turicibacter(100);
+12 3851 Bacteria(100);"Firmicutes"(100);"Bacilli"(100);"Lactobacillales"(100);Lactobacillaceae(100);Lactobacillus(100);
+13 46 Bacteria(100);"Tenericutes"(100);Mollicutes(100);Anaeroplasmatales(100);Anaeroplasmataceae(100);Anaeroplasma(100);
+14 832 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Ruminococcaceae"(100);unclassified(100);
+15 74 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);Clostridiaceae(100);unclassified(100);
+16 80 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Ruminococcaceae"(100);Papillibacter(100);
+17 24 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Ruminococcaceae"(100);Anaerotruncus(100);
+18 26 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Ruminococcaceae"(100);Butyricicoccus(100);
+19 150 Bacteria(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);
+20 6 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);unclassified(100);unclassified(100);unclassified(100);
+21 10 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Lachnospiraceae"(100);Dorea(100);
+22 10 Bacteria(100);"Actinobacteria"(100);Actinobacteria(100);Bifidobacteriales(100);Bifidobacteriaceae(100);Bifidobacterium(100);
+23 13 Bacteria(100);"Actinobacteria"(100);Actinobacteria(100);Coriobacteriales(100);Coriobacteriaceae(100);unclassified(100);
+24 99 Bacteria(100);"Proteobacteria"(100);Gammaproteobacteria(100);Pseudomonadales(100);Pseudomonadaceae(100);Pseudomonas(100);
+25 2 Bacteria(100);"Firmicutes"(100);"Bacilli"(100);"Lactobacillales"(100);"Carnobacteriaceae"(100);Atopostipes(100);
+26 17 Bacteria(100);"Actinobacteria"(100);Actinobacteria(100);Coriobacteriales(100);Coriobacteriaceae(100);Enterorhabdus(100);
+27 641 Bacteria(100);"Firmicutes"(100);"Bacilli"(100);"Lactobacillales"(100);Streptococcaceae(100);Streptococcus(100);
+28 1 Bacteria(100);"Actinobacteria"(100);Actinobacteria(100);Actinomycetales(100);Corynebacteriaceae(100);Corynebacterium(100);
+29 2 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);Clostridiaceae(100);Sarcina(100);
+30 32 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);Incertae_Sedis_XIV(100);Blautia(100);
+31 10 Bacteria(100);"Firmicutes"(100);"Erysipelotrichi"(100);"Erysipelotrichales"(100);Erysipelotrichaceae(100);Coprobacillus(100);
+32 2 Bacteria(100);TM7(100);unclassified(100);unclassified(100);unclassified(100);unclassified(100);
+33 13 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Ruminococcaceae"(100);Ruminococcus(100);
+34 14 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Lachnospiraceae"(100);Johnsonella(100);
+35 19 Bacteria(100);"Firmicutes"(100);"Bacilli"(100);"Lactobacillales"(100);unclassified(100);unclassified(100);
+36 12 Bacteria(100);"Firmicutes"(100);"Bacilli"(100);"Lactobacillales"(100);Lactobacillaceae(100);unclassified(100);
+37 52 Bacteria(100);"Proteobacteria"(100);Gammaproteobacteria(100);"Enterobacteriales"(100);Enterobacteriaceae(100);Cronobacter(100);
+38 10 Bacteria(100);"Firmicutes"(100);"Erysipelotrichi"(100);"Erysipelotrichales"(100);Erysipelotrichaceae(100);Holdemania(100);
+39 5 Bacteria(100);"Actinobacteria"(100);Actinobacteria(100);Coriobacteriales(100);Coriobacteriaceae(100);Olsenella(100);
+40 3 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Eubacteriaceae"(100);Eubacterium(100);
+41 2 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);Incertae_Sedis_XIII(100);unclassified(100);
+42 324 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);Clostridiaceae(100);Clostridium(100);
+43 7 Bacteria(100);"Firmicutes"(100);"Bacilli"(100);unclassified(100);unclassified(100);unclassified(100);
+44 1 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Ruminococcaceae"(100);Acetivibrio(100);
+45 6 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);Incertae_Sedis_XIII(100);Anaerovorax(100);
+46 1912 Bacteria(100);"Firmicutes"(100);"Bacilli"(100);Bacillales(100);"Staphylococcaceae"(100);Staphylococcus(100);
+47 469 Bacteria(100);"Deinococcus-Thermus"(100);Deinococci(100);Deinococcales(100);Deinococcaceae(100);Deinococcus(100);
+48 448 Bacteria(100);"Proteobacteria"(100);Gammaproteobacteria(100);Pseudomonadales(100);Moraxellaceae(100);Acinetobacter(100);
+49 286 Bacteria(100);"Actinobacteria"(100);Actinobacteria(100);Actinomycetales(100);Propionibacteriaceae(100);Propionibacterium(100);
+50 295 Bacteria(100);"Proteobacteria"(100);Betaproteobacteria(100);Neisseriales(100);Neisseriaceae(100);Neisseria(100);
+51 108 Bacteria(100);"Firmicutes"(100);"Bacilli"(100);Bacillales(100);"Listeriaceae"(100);Listeria(100);
+52 67 Bacteria(100);"Firmicutes"(100);"Bacilli"(100);"Lactobacillales"(100);"Enterococcaceae"(100);Enterococcus(100);
+53 58 Bacteria(100);"Firmicutes"(100);"Bacilli"(100);Bacillales(100);Bacillaceae(100);Bacillus(100);
+54 51 Bacteria(100);"Proteobacteria"(100);Epsilonproteobacteria(100);Campylobacterales(100);Helicobacteraceae(100);Helicobacter(100);
+55 54 Bacteria(100);"Actinobacteria"(100);Actinobacteria(100);Actinomycetales(100);Actinomycetaceae(100);Actinomyces(100);
+56 22 Bacteria(100);"Proteobacteria"(100);Alphaproteobacteria(100);Rhodobacterales(100);Rhodobacteraceae(100);unclassified(100);
+57 29 Bacteria(100);"Firmicutes"(100);"Bacilli"(100);Bacillales(100);unclassified(100);unclassified(100);
+58 3 Bacteria(100);"Proteobacteria"(100);Gammaproteobacteria(100);"Enterobacteriales"(100);Enterobacteriaceae(100);unclassified(100);
+59 1 Bacteria(100);"Actinobacteria"(100);Actinobacteria(100);Actinomycetales(100);unclassified(100);unclassified(100);
+60 3 Bacteria(100);"Firmicutes"(100);"Bacilli"(100);Bacillales(100);"Staphylococcaceae"(100);unclassified(100);
+61 1 Bacteria(100);"Proteobacteria"(100);Alphaproteobacteria(100);Rhodobacterales(100);Rhodobacteraceae(100);Rhodobacter(100);
+62 1 Bacteria(100);"Proteobacteria"(100);Gammaproteobacteria(100);Pseudomonadales(100);Pseudomonadaceae(100);unclassified(100);
b
diff -r 000000000000 -r bccb5efbc4ee test-data/final.tx.1.subsample.1.pick.shared
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/final.tx.1.subsample.1.pick.shared Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,10 @@
+label Group numOtus Otu01 Otu02 Otu03 Otu04 Otu05 Otu06 Otu07 Otu08 Otu09 Otu10 Otu11 Otu12 Otu13 Otu14 Otu15 Otu16 Otu17 Otu18 Otu19 Otu20 Otu21 Otu22 Otu23 Otu24 Otu25 Otu26 Otu27 Otu28 Otu29 Otu30 Otu31 Otu32 Otu33 Otu34 Otu35 Otu36 Otu37 Otu38 Otu39 Otu40 Otu41 Otu42 Otu43 Otu45
+1 F003D000 44 1934 191 396 970 156 59 294 74 61 149 40 68 33 143 56 24 9 5 5 4 2 2 2 1 2 2 2 1 2 3 1 1 1 0 0 0 0 0 0 0 0 0 0 0
+1 F003D002 44 2599 394 68 717 85 48 216 85 189 53 1 83 5 121 0 18 0 2 1 0 0 0 0 0 0 2 2 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+1 F003D006 44 3090 123 87 390 295 14 139 56 27 69 1 313 1 76 0 0 0 1 2 0 2 0 0 0 0 0 1 0 0 2 0 0 0 2 0 2 0 0 0 0 0 0 0 0
+1 F003D008 44 2203 288 64 621 713 22 226 59 22 21 1 318 1 88 0 7 6 4 1 2 3 0 1 0 0 2 1 0 0 2 2 1 2 8 2 1 1 0 0 0 0 0 0 0
+1 F003D142 44 3054 101 381 158 366 32 21 7 6 208 34 258 0 34 2 3 0 0 13 0 0 1 1 0 0 1 0 0 0 1 3 0 0 0 1 1 0 2 2 2 0 0 0 0
+1 F003D144 44 2649 32 503 119 162 44 14 8 10 215 86 786 0 24 3 5 0 1 12 0 0 3 2 0 0 2 0 0 0 5 0 0 1 0 3 1 0 0 1 0 2 0 0 0
+1 F003D146 44 2197 160 444 270 374 38 43 80 10 189 30 691 2 116 1 1 5 4 17 0 0 0 1 0 0 2 0 0 0 4 0 0 5 1 1 3 0 0 0 0 0 3 1 0
+1 F003D148 44 2284 285 460 317 232 33 31 3 25 235 101 574 0 37 5 8 2 2 44 0 0 0 1 0 0 1 1 0 0 2 2 0 2 1 0 0 0 0 1 1 0 0 0 3
+1 F003D150 44 2709 236 391 390 326 60 43 23 9 171 21 178 0 64 1 8 1 3 31 0 1 4 5 0 0 2 0 0 0 2 1 0 2 0 2 0 1 4 0 0 0 2 0 2
b
diff -r 000000000000 -r bccb5efbc4ee test-data/makesra.project
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/makesra.project Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,12 @@
+USERNAME userName
+Last yourLastName
+First yourFirstName
+EMAIL yourEmail@mail.com
+CENTER your University or Center Name
+TYPE institute
+WEBSITE www.yourWebsite.org
+ProjectName yourProjectName
+ProjectTitle Your Project Title
+Description Your project description
+Grant id=yourGrantID, agency=yourGrantAgency, title=yourGrantTitle
+
b
diff -r 000000000000 -r bccb5efbc4ee test-data/metadata
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/metadata Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,12 @@
+group dpw description
+F003D000 0 "F003D000 description"
+F003D002 2 "F003D002 description"
+F003D004 4  "F003D004 description"
+F003D006 6       "F003D006 description"
+F003D008 8       "F003D008 galaxy rocks"
+F003D142 142     "F003D142 description"
+F003D144 144     "F003D144 description"
+F003D146 146     "F003D146 description"
+F003D148 148     "F003D148 description"
+F003D150 150     "F003D150 description"
+MOCK.GQY1XT001 12 "MOCK.GQY1XT001 description"
b
diff -r 000000000000 -r bccb5efbc4ee test-data/mock.flow
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mock.flow Fri May 19 05:47:34 2017 -0400
b
b'@@ -0,0 +1,108 @@\n+450\n+GQY1XT001ASWK1 450 0.99 0.00 1.01 0.00 0.00 1.06 0.00 1.00 1.07 0.02 0.00 2.06 1.04 0.02 0.00 1.04 0.00 2.18 2.93 0.98 0.98 0.01 0.97 0.00 0.01 2.08 0.00 0.00 1.91 0.02 1.98 0.00 2.88 0.00 0.01 1.00 0.08 1.03 0.00 1.01 2.86 0.01 0.98 0.02 0.08 1.10 1.98 1.05 1.94 0.01 0.05 1.01 0.05 0.00 2.04 1.97 0.01 0.00 1.01 1.00 1.02 1.09 1.01 0.02 0.95 0.00 3.73 0.03 0.04 1.05 0.08 1.98 1.01 0.05 0.00 1.97 0.04 1.88 0.00 0.08 1.02 0.05 0.01 1.02 0.07 0.02 1.01 0.06 2.05 2.20 0.97 1.03 0.14 0.08 1.02 0.07 2.91 0.00 0.97 1.02 0.03 0.00 0.97 0.07 1.00 0.00 0.04 1.02 0.98 0.00 0.02 1.05 0.05 0.01 2.02 0.07 0.02 1.12 3.02 0.05 0.01 1.08 0.04 4.00 1.11 0.11 1.10 0.00 0.10 2.12 0.00 0.12 1.07 0.06 5.69 2.01 0.05 0.86 1.16 0.19 0.00 1.04 0.07 0.96 0.03 0.15 0.87 0.10 1.04 0.90 0.13 0.98 0.09 0.15 1.01 0.13 0.06 1.02 0.12 0.01 2.09 0.10 1.03 0.02 0.13 1.04 0.11 0.05 0.96 0.11 1.03 1.04 3.02 1.04 1.09 0.11 1.18 0.15 0.12 0.97 1.01 0.01 0.08 1.03 0.08 0.08 1.06 2.07 0.07 0.97 1.05 0.12 1.05 1.07 1.98 0.02 0.12 0.99 0.08 3.00 0.94 1.01 0.08 0.13 0.95 0.15 1.03 0.06 0.99 1.93 0.03 0.05 1.02 0.13 2.00 0.08 0.97 0.05 0.08 1.04 2.88 0.11 0.06 1.05 0.14 1.04 0.05 0.11 1.00 0.06 3.80 1.06 0.12 0.08 1.14 0.07 0.04 1.00 0.96 0.08 2.96 0.04 0.99 1.00 1.03 0.03 0.02 1.03 0.06 0.03 1.93 0.04 1.05 0.06 1.05 0.10 0.11 0.91 0.09 1.07 0.11 0.07 1.01 1.02 1.09 0.07 1.04 0.06 0.10 1.02 0.05 1.00 1.00 0.90 0.10 3.04 0.07 0.02 1.07 0.94 0.12 0.08 2.06 2.03 1.02 1.03 0.06 0.06 1.01 0.02 0.08 1.02 0.09 0.01 1.07 0.13 1.03 0.03 0.03 1.13 0.02 0.03 2.06 0.08 2.06 0.07 0.95 1.06 0.04 0.03 0.91 0.13 0.13 2.18 0.10 0.00 0.96 0.00 0.99 4.03 1.92 0.06 1.03 0.12 1.02 0.02 0.10 0.97 0.11 0.02 1.01 0.96 1.01 0.09 0.05 1.04 0.06 1.02 0.05 0.06 0.97 0.98 0.10 0.07 1.01 0.10 1.08 0.06 0.93 1.01 0.07 0.11 1.09 0.05 0.11 1.34 0.10 0.10 1.07 0.03 0.00 1.10 0.02 0.08 3.11 0.09 1.06 0.09 0.04 1.05 1.95 1.05 0.13 0.12 0.89 0.06 1.04 0.97 1.03 0.10 0.02 0.81 1.88 0.10 0.09 1.03 0.93 1.13 0.10 0.11 1.11 0.04 0.09 0.97 0.00 0.11 2.02 0.10 2.01 0.86 0.15 0.14 1.15 0.10 0.09 0.94 0.09 0.07 0.81 1.14 1.16 0.06 1.95 0.10 0.99 0.10 1.10 0.11 1.13 1.15 0.12 0.12 2.77 0.10 0.05 1.09 0.96 0.02 0.96 0.14 1.22 1.01 0.13 0.83 0.05 0.83 0.10 0.09 2.94 2.18 0.19 0.14 1.13 0.12 0.01 1.01 0.12 1.16 3.10 0.00 \n+GQY1XT001EJF0G 450 1.02 0.00 1.06 0.00 0.00 0.97 0.00 0.99 1.07 0.00 0.00 2.11 1.00 0.00 0.02 1.02 0.00 2.13 3.07 1.01 0.94 0.00 1.02 0.00 0.01 2.13 0.00 0.00 2.01 0.08 1.97 0.00 2.98 2.06 0.02 0.91 3.01 0.15 0.95 0.04 0.23 1.00 0.05 0.00 1.87 0.08 1.04 0.01 2.15 0.00 0.02 0.94 0.10 0.00 1.08 1.10 0.00 2.02 1.08 1.04 1.07 1.18 1.08 0.03 1.03 0.04 3.99 0.01 0.05 0.91 0.22 1.82 0.90 0.14 0.00 2.17 0.13 1.06 0.00 0.21 0.92 0.15 0.83 0.03 0.15 0.97 1.09 0.00 2.04 1.29 0.13 0.02 2.15 0.13 0.01 0.89 0.39 0.00 0.97 1.08 2.76 0.00 0.12 1.04 0.46 0.00 0.87 0.15 0.98 0.00 0.12 1.03 0.11 0.00 0.95 2.00 0.01 0.06 1.24 0.21 0.00 1.01 1.96 1.10 0.06 1.04 0.33 0.12 0.92 0.15 0.05 2.81 1.12 0.09 2.07 0.39 0.11 1.06 0.24 0.01 0.98 1.09 2.69 0.01 0.10 1.05 3.08 0.03 0.02 1.08 1.26 0.03 0.01 1.04 2.09 0.01 0.96 1.08 0.19 0.85 1.05 0.13 0.03 1.04 0.12 0.83 0.04 0.08 1.04 0.15 1.03 0.05 0.16 1.01 0.12 0.04 0.99 0.10 0.83 1.08 2.81 1.03 1.12 0.10 1.30 0.11 0.12 1.00 0.10 0.05 0.91 1.11 1.01 0.10 0.11 1.90 0.10 0.84 0.89 0.29 0.93 1.10 1.86 0.11 0.12 1.00 0.20 2.70 0.98 1.08 0.08 0.25 1.13 0.09 1.05 0.08 1.01 1.83 0.03 0.04 1.08 0.17 2.12 0.06 1.03 0.11 0.17 1.02 2.00 0.10 0.93 1.00 0.24 1.00 0.11 0.11 0.95 0.99 2.75 0.11 0.15 0.98 1.21 1.00 0.12 0.05 0.97 0.08 2.93 0.05 1.00 0.91 1.18 0.03 0.10 1.04 0.12 0.04 1.89 0.07 0.91 0.07 1.12 0.11 0.13 0.99 0.07 0.94 0.10 0.10 0.91 1.02 1.11 0.09 1.07 0.20 0.08 0.92 0.08 1.01 0.92 0.93 0.11 3.00 0.17 0.07 0.89 1.10 0.11 0.08 1.95 1.93 1.01 1.01 0.10 0.09 1.04 0.05 0.08 0.96 0.09 0.02 1.08 0.10 1.08 0.00 0.07 0.99 0.04 0.04 1.84 0.07 2.05 0.05 1.05 1.11 0.12 0.12 0.90 0.08 0.08 2.08 0.09 0.05 1.11 0.06 1.01 2.06 0.08 0.76 0.07 1.06 1.93 0.05 0.95 0.12 1.09 '..b'5 1.10 0.03 0.02 1.06 0.04 0.97 0.00 0.09 1.04 0.96 0.03 1.02 0.05 0.99 0.01 0.09 0.97 0.09 1.16 0.03 1.02 0.04 0.01 1.01 0.05 1.05 0.03 1.00 0.05 1.02 0.00 0.11 0.93 1.00 0.03 1.12 0.02 1.07 1.00 0.09 1.05 3.10 1.04 0.04 1.91 0.96 0.04 0.08 2.00 0.06 0.05 2.03 1.02 0.04 1.01 1.03 0.98 0.10 0.10 2.01 0.09 1.05 0.05 0.06 1.05 0.10 0.08 1.07 0.06 1.03 1.06 2.93 1.12 1.01 0.05 0.90 0.10 0.10 0.96 0.13 0.00 1.02 1.04 0.98 0.07 0.07 2.02 0.12 0.89 1.13 0.01 0.95 1.03 1.93 0.09 0.08 0.96 0.02 2.97 1.00 1.08 0.09 0.00 1.02 0.11 1.08 0.03 0.94 1.97 0.03 0.03 0.98 0.01 2.09 0.08 1.09 0.08 0.11 1.03 2.01 0.07 1.07 0.96 0.12 0.98 0.10 0.07 1.08 1.11 3.09 0.09 0.04 0.94 1.02 1.07 0.16 0.08 1.07 0.05 2.94 0.05 0.90 1.02 0.85 0.01 0.11 1.02 0.10 0.04 0.96 0.00 2.16 0.06 1.03 0.08 0.04 1.00 0.09 1.03 0.07 0.03 1.09 1.06 1.19 0.06 1.03 0.06 0.11 0.96 0.06 0.99 2.08 0.08 0.12 2.96 0.01 0.05 0.99 0.76 0.08 0.05 2.03 2.02 1.01 0.97 0.02 0.03 1.02 0.00 0.04 1.09 0.05 0.02 1.11 0.10 1.07 0.03 0.00 1.07 0.02 0.00 2.07 0.10 2.08 0.03 0.83 1.07 0.06 0.01 1.06 0.08 0.04 1.97 0.04 0.02 1.15 0.01 1.07 2.00 0.01 0.91 0.07 0.81 2.06 0.00 1.10 0.10 0.88 0.03 0.10 1.09 0.07 0.04 1.07 0.93 1.13 0.09 0.02 1.02 0.10 1.03 0.11 0.02 1.07 0.96 0.06 0.07 1.05 0.06 0.97 0.14 0.84 1.05 0.06 0.03 0.90 0.02 0.04 1.11 0.11 0.03 1.07 0.00 0.11 1.04 0.11 0.07 3.16 0.04 0.99 0.06 0.01 1.05 2.02 1.17 0.08 0.06 0.82 0.00 1.28 1.16 1.05 0.08 0.05 0.74 2.10 0.11 0.13 1.08 0.76 0.98 0.12 0.10 1.14 0.06 0.10 1.06 0.10 0.05 1.99 0.07 2.06 1.04 0.11 0.00 1.02 0.02 0.11 1.04 0.11 0.06 0.99 0.99 1.13 0.13 1.95 0.11 1.06 0.01 1.01 0.13 0.86 0.91 0.19 0.00 2.96 0.06 0.07 1.00 1.01 0.07 1.15 0.00 1.16 0.09 0.06 2.03 0.11 1.02 0.16 0.78 1.10 0.02 0.09 1.87 \n+GQY1XT001AWPWA 450 1.01 0.00 1.03 0.00 0.00 1.01 0.00 1.02 1.03 0.06 0.00 2.13 1.04 0.00 0.00 1.06 0.04 2.10 3.04 1.04 1.01 0.00 1.00 0.00 0.00 2.21 0.00 0.00 2.07 0.00 1.97 0.00 2.78 2.24 0.00 0.89 2.91 0.04 0.98 0.00 0.02 1.10 1.91 1.08 2.11 0.00 0.05 0.93 0.03 0.07 2.05 1.95 0.13 0.00 0.97 0.99 1.05 1.11 0.96 0.05 1.00 0.03 3.80 0.01 0.06 1.03 0.11 2.03 1.06 0.03 0.13 1.92 0.03 1.00 0.10 0.98 0.00 0.00 1.04 1.11 0.03 0.00 0.96 0.11 2.03 2.12 0.94 1.06 0.13 0.06 1.05 0.00 3.15 0.12 0.86 0.89 0.10 0.00 0.93 0.07 0.95 0.00 0.04 1.13 1.13 0.04 0.00 2.00 0.06 0.00 1.06 0.11 0.07 1.00 2.89 0.10 0.00 1.01 0.05 4.05 0.01 0.06 1.95 0.05 0.04 1.15 0.08 0.03 1.95 0.11 5.45 1.82 0.13 1.04 1.06 0.43 0.06 1.01 1.97 0.05 0.91 1.19 0.30 0.88 0.12 0.14 1.02 1.02 0.03 0.00 1.06 0.08 1.01 0.03 1.11 0.00 0.13 1.02 0.12 0.00 1.02 0.13 0.99 1.02 2.89 1.06 1.96 1.05 0.30 0.09 1.15 1.06 0.98 0.06 0.10 1.98 0.16 0.94 0.89 0.17 0.99 1.10 1.90 0.03 0.12 1.02 0.19 2.83 0.92 1.07 0.06 0.24 1.06 0.07 1.05 0.05 1.04 1.90 0.09 0.08 0.97 0.15 1.93 0.05 1.02 0.04 0.18 1.07 1.99 0.13 0.91 1.00 0.13 0.95 0.18 0.06 1.03 0.11 3.39 0.10 0.14 0.85 1.28 1.01 0.02 0.05 0.95 0.07 2.97 0.02 1.07 0.93 1.18 0.00 0.11 1.09 0.10 0.00 1.10 0.03 2.02 0.05 1.01 0.08 0.17 0.86 0.08 0.90 0.13 0.06 1.01 1.09 1.03 0.08 1.03 0.10 0.09 0.93 0.09 0.91 0.95 1.00 0.09 1.90 0.08 1.89 0.11 1.06 0.08 0.05 1.90 1.88 0.05 0.12 1.01 0.11 0.18 0.99 0.10 0.07 0.90 0.01 0.10 1.08 0.09 0.04 1.14 0.07 0.96 0.07 0.00 1.01 0.08 0.07 1.76 0.03 1.89 0.04 0.96 1.06 0.11 0.11 1.08 0.10 0.10 1.93 0.09 0.04 1.02 0.03 1.00 3.69 1.80 0.06 0.98 0.11 1.02 0.05 0.07 0.98 0.10 0.00 0.93 1.12 1.11 0.03 0.11 0.96 0.07 0.93 0.10 0.00 1.08 0.97 0.06 0.04 1.02 0.05 0.92 0.03 1.04 1.08 0.09 0.06 1.06 0.01 0.02 0.99 0.16 0.10 1.09 0.07 0.13 1.08 0.09 0.09 2.85 0.10 1.01 0.05 0.13 0.97 1.89 0.98 0.15 0.06 0.99 0.01 1.04 1.13 1.12 0.02 0.05 0.87 1.79 0.06 0.09 1.10 1.00 1.04 0.18 0.10 0.95 0.06 0.09 1.04 0.06 0.08 2.31 0.03 2.00 1.21 0.04 0.09 0.92 0.00 0.12 0.93 0.10 0.00 0.99 1.13 1.05 0.03 2.09 0.01 1.09 0.02 0.84 0.08 1.06 0.03 2.04 0.09 1.87 0.01 0.17 1.01 1.13 0.03 1.02 0.00 0.94 0.09 0.07 2.12 0.06 1.06 0.08 0.90 0.10 0.09 1.12 0.11 1.07 1.01 0.18 0.08 1.97 0.00 0.27 1.04 0.03 1.08 3.12 0.15 1.06 0.00 0.10 1.85 \n'
b
diff -r 000000000000 -r bccb5efbc4ee test-data/mouse.design
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mouse.design Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,10 @@
+group dpw
+F003D000        0
+F003D142 142
+F003D144 144
+F003D146 146
+F003D148 148
+F003D150 150
+F003D002 2
+F003D006 6
+F003D008 8
b
diff -r 000000000000 -r bccb5efbc4ee test-data/output.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.fa Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,12 @@
+> seq1 This is the description of my first sequence in sample 1.
+AGTACGTAGTAGCTGCTGCTACGTGCGCTAGCTAGTACGTCACGACGTAGATGCTAGCTGACTCGATGC
+> seq2 This is a description of my second sequence in sample 1.
+CGATCGATCGTACGTCGACTGATCGTAGCTACGTCGTACGTAGCATCGTCAGTTACTGCATGCTCG
+> seq1 This is the description of my first and only sequence in sample 2.
+AGTACGTAGTAGCTGCTGCTACGTGCGCTAGCTAGTACGTCACGACGTAGATGCTAGCTGACTCGATGC
+> seq1 This is the description of my first sequence in sample 3.
+AGTACGTAGTAGCTGCTGCTACGTGCGCTAGCTAGTACGTCACGACGTAGATGCTAGCTGACTCGATGC
+> seq2 This is a description of my second sequence in sample 3.
+CGATCGATCGTACGTCGACTGATCGTAGCTACGTCGTACGTAGCATCGTCAGTTACTGCATGCTCG
+> seq3 This is a description of my third sequence in sample 3.
+CGATCGATCGTACGTCGACTAGTACGTAGTAGCTGCTGCTACGTGCGCTAGCTAGTACGTCACGACGTAGATGCTAGCTGACTCGATGCGATCGTAGCTACGTCGTACGTAGCATCGTCAGTTACTGCATGCTCG
b
diff -r 000000000000 -r bccb5efbc4ee test-data/sample1.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample1.fa Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,4 @@
+> seq1 This is the description of my first sequence in sample 1.
+AGTACGTAGTAGCTGCTGCTACGTGCGCTAGCTAGTACGTCACGACGTAGATGCTAGCTGACTCGATGC
+> seq2 This is a description of my second sequence in sample 1.
+CGATCGATCGTACGTCGACTGATCGTAGCTACGTCGTACGTAGCATCGTCAGTTACTGCATGCTCG
b
diff -r 000000000000 -r bccb5efbc4ee test-data/sample2.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample2.fa Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,2 @@
+> seq1 This is the description of my first and only sequence in sample 2.
+AGTACGTAGTAGCTGCTGCTACGTGCGCTAGCTAGTACGTCACGACGTAGATGCTAGCTGACTCGATGC
b
diff -r 000000000000 -r bccb5efbc4ee test-data/sample3.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample3.fa Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,6 @@
+> seq1 This is the description of my first sequence in sample 3.
+AGTACGTAGTAGCTGCTGCTACGTGCGCTAGCTAGTACGTCACGACGTAGATGCTAGCTGACTCGATGC
+> seq2 This is a description of my second sequence in sample 3.
+CGATCGATCGTACGTCGACTGATCGTAGCTACGTCGTACGTAGCATCGTCAGTTACTGCATGCTCG
+> seq3 This is a description of my third sequence in sample 3.
+CGATCGATCGTACGTCGACTAGTACGTAGTAGCTGCTGCTACGTGCGCTAGCTAGTACGTCACGACGTAGATGCTAGCTGACTCGATGCGATCGTAGCTACGTCGTACGTAGCATCGTCAGTTACTGCATGCTCG
b
diff -r 000000000000 -r bccb5efbc4ee test-data/silva.ss.map.head
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/silva.ss.map.head Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,10 @@
+0
+0
+0
+0
+0
+0
+0
+0
+0
+0
b
diff -r 000000000000 -r bccb5efbc4ee test-data/testflow.flow
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/testflow.flow Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,3 @@
+450
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+GQY1XT001BPRBN 450 1.04 0.00 1.03 0.00 0.00 0.98 0.00 1.00 0.00 2.33 1.06 1.02 1.10 0.00 0.00 1.01 1.11 0.00 2.92 1.03 1.02 0.00 0.93 0.00 0.02 2.05 0.01 0.00 1.94 0.01 1.99 0.00 2.90 0.00 0.00 0.93 0.13 0.88 0.00 0.98 3.72 1.08 0.00 1.04 0.16 0.00 1.94 0.00 1.99 0.01 0.06 0.95 0.13 0.00 0.97 2.04 0.04 0.00 2.06 1.11 1.09 1.04 1.03 0.03 1.02 0.05 4.03 0.01 0.06 1.02 0.13 1.93 0.02 0.05 1.08 4.05 1.09 0.91 1.03 0.11 1.98 3.07 0.01 1.00 0.14 0.11 0.85 1.03 1.96 0.99 0.03 0.90 0.13 0.15 0.95 0.11 1.00 1.17 0.97 2.07 0.07 0.06 1.03 0.09 0.00 1.09 1.00 2.02 0.06 1.97 2.98 1.06 1.03 0.11 0.10 2.03 0.07 1.90 0.00 0.08 1.02 0.10 0.05 2.00 0.04 0.96 3.83 0.12 0.02 0.94 1.15 0.00 0.04 1.05 1.97 0.04 1.03 1.03 0.06 1.06 1.01 1.08 3.05 0.07 0.11 1.09 2.02 1.05 2.95 1.00 1.11 0.10 0.07 0.91 0.13 1.02 0.04 0.06 1.03 1.00 0.90 0.02 0.12 2.05 0.11 0.94 0.99 0.03 0.94 1.12 2.00 0.11 0.07 1.03 0.05 3.10 1.05 1.12 0.07 0.00 1.02 0.10 1.01 0.07 1.00 2.05 0.12 1.01 0.11 0.12 2.01 0.07 0.94 0.00 0.07 0.98 1.98 0.00 1.03 1.01 0.05 0.00 0.93 0.09 1.01 0.04 3.95 0.10 0.10 0.97 1.05 1.05 0.03 0.12 1.00 0.12 3.00 0.05 1.11 1.03 0.10 0.00 1.05 0.09 1.07 0.00 2.08 0.03 1.02 0.06 0.96 0.06 0.14 1.00 0.15 0.98 0.08 0.09 0.98 1.10 1.00 0.07 1.06 0.12 0.14 0.92 0.08 2.12 0.06 3.08 0.02 2.12 0.04 0.11 3.18 0.12 0.02 1.04 0.04 1.06 0.04 0.96 0.05 1.04 0.03 2.17 2.05 0.96 0.13 0.01 1.99 0.08 2.15 0.09 0.92 1.02 0.02 0.11 2.03 0.06 0.12 1.04 1.07 0.03 1.00 0.13 0.11 2.08 0.99 0.05 0.07 0.95 1.92 0.04 2.01 0.07 0.98 0.03 1.98 0.12 1.01 0.09 0.04 1.11 0.14 0.93 0.14 0.12 1.08 1.02 0.07 0.08 0.97 0.11 1.04 0.09 0.99 0.10 0.09 1.08 0.05 0.02 1.01 0.97 0.07 0.11 1.06 0.01 0.10 1.04 0.05 0.03 2.00 0.05 2.01 0.07 0.01 1.00 2.01 1.01 0.07 0.12 1.03 0.04 1.00 0.07 2.01 0.08 0.08 1.06 2.12 0.00 0.13 0.95 0.12 2.38 0.12 1.96 0.08 0.00 1.85 0.10 2.13 0.06 0.00 1.19 0.06 0.02 2.03 0.07 0.96 0.02 0.88 0.06 3.89 0.07 0.97 1.06 1.89 0.06 1.95 0.02 1.82 0.02 1.13 0.03 1.10 0.09 0.06 2.14 0.18 1.06 1.06 0.00 1.03 0.04 0.06 2.11 2.90 0.79 0.92 1.12 0.12 0.04 0.93 0.02 1.21 0.95 0.05 2.94 0.07 0.84 0.10 0.14 1.05 0.13 0.11 1.15 1.05 1.05 0.14 0.11 1.02 0.11 0.93 0.10 1.09 0.04 0.00 0.99 0.16 2.99 2.08 2.06 0.15 1.02 0.07 0.06 4.11 0.03 0.16 2.23 0.14 1.06 0.00 0.95 0.17 0.10 2.04 1.00 
b
diff -r 000000000000 -r bccb5efbc4ee test-data/toymothur.design
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/toymothur.design Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,3 @@
+forest tardis
+pasture tardis
+pasture dalek
b
diff -r 000000000000 -r bccb5efbc4ee test-data/toymothur.design2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/toymothur.design2 Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,2 @@
+forest tardis
+pasture dalek
b
diff -r 000000000000 -r bccb5efbc4ee test-data/treetest.deunique.tre
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/treetest.deunique.tre Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,1 @@
+(((a:0,b:0,c:0):0.5,(d:0,e:0):0.3):0.25,f:0.25):0.5;
b
diff -r 000000000000 -r bccb5efbc4ee test-data/treetest.groups
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/treetest.groups Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,6 @@
+a green
+b green
+c green
+d orange
+e orange
+f orange
b
diff -r 000000000000 -r bccb5efbc4ee test-data/treetest.names
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/treetest.names Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,3 @@
+a a,b,c
+d d,e
+f f
b
diff -r 000000000000 -r bccb5efbc4ee test-data/treetest.tre
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/treetest.tre Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,1 @@
+((a:0.5,d:0.3):0.25,f:0.25):0.5;
\ No newline at end of file
b
diff -r 000000000000 -r bccb5efbc4ee test-data/veg.dist
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/veg.dist Fri May 19 05:47:34 2017 -0400
b
b'@@ -0,0 +1,25 @@\n+24\n+group18 0 0.531002122667858 0.668066081456845 0.562124668311531 0.3747077813648 0.509473807708101 0.623441897868918 0.533760972316003 0.841820910455228 0.345334659061175 0.544980977465613 0.387906855391038 0.631889119284077 0.360369716481462 0.495569929879871 0.338230884557721 0.527747996119875 0.46940182727116 0.572409158546537 0.658356940509915 0.468803827751196 0.624899560429172 0.445852306473965 0.556086425651643\n+group15 0.531002122667858 0 0.359778297016791 0.405560971081094 0.365209673840692 0.456075749605471 0.357951698566990 0.397667376920489 0.522541392379812 0.60638464347191 0.48037557590249 0.378418761774833 0.337611485751577 0.671739130434783 0.717861205915813 0.635512156237545 0.757850272278487 0.684397366160893 0.820626944245034 0.776103945014594 0.679419902681042 0.764456383429945 0.471627356163032 0.760728080850839\n+group24 0.668066081456845 0.359778297016791 0 0.493494677463379 0.502030649266258 0.509231821290175 0.50100504976222 0.590762326930444 0.573666487726319 0.757674655787863 0.653360627772091 0.434689236988378 0.336909757263505 0.793106938610254 0.856175256640914 0.744137292184681 0.83821186778176 0.830987488829312 0.83725508577857 0.759051704257184 0.689453763842811 0.78428294394681 0.567737261531031 0.727272727272727\n+group27 0.562124668311531 0.405560971081094 0.493494677463379 0 0.428611098255195 0.487819025522041 0.465522369035986 0.568393032270116 0.302780246286657 0.754373626373627 0.746791469651645 0.495783259540375 0.500159329903947 0.77929167212542 0.873218985388874 0.749693459050357 0.80902359221629 0.841379965785972 0.758192367410313 0.741589782845171 0.625361639704983 0.70965400435519 0.632291885091214 0.54560014236142\n+group23 0.3747077813648 0.365209673840692 0.502030649266258 0.428611098255195 0 0.360624235718861 0.481270602337428 0.409431221365516 0.697951879101213 0.622147127631921 0.564580791354366 0.287701365077311 0.425861695209191 0.639083780437474 0.729525454839929 0.625248311481923 0.712879825495866 0.711791887728906 0.724986879144997 0.669388904533934 0.538476172358033 0.662547573180473 0.471028037383178 0.495122079839688\n+group19 0.509473807708101 0.456075749605471 0.509231821290175 0.487819025522041 0.360624235718861 0 0.47264827514003 0.449673125625773 0.643173412512372 0.573924437650142 0.63319420574515 0.395377631035906 0.431129869389152 0.695857026807473 0.789820495341968 0.568402976531196 0.530275619878684 0.517760385310054 0.538922155688623 0.539314268896846 0.428855622420053 0.505990964447063 0.329349338004224 0.531589448015961\n+group22 0.623441897868918 0.357951698566990 0.50100504976222 0.465522369035986 0.481270602337428 0.47264827514003 0 0.267803106717773 0.598566633402885 0.69487361209544 0.535760932030719 0.462702018749640 0.382298106172113 0.745988552125364 0.861145064293746 0.724916160609081 0.802615164256341 0.801531425047536 0.83214644589104 0.772508176966776 0.70517511761631 0.787532847973119 0.581221922731357 0.677116737663332\n+group16 0.533760972316003 0.397667376920489 0.590762326930444 0.568393032270116 0.409431221365516 0.449673125625773 0.267803106717773 0 0.701535990362414 0.551494144215115 0.482635012046777 0.373779728755815 0.430605761857816 0.659614382490881 0.718478913197665 0.650987864807943 0.683795276397356 0.646264782232478 0.735420178184445 0.818586585827965 0.634216589861751 0.765659822656361 0.517282479141836 0.747455911343173\n+group28 0.841820910455228 0.522541392379812 0.573666487726319 0.302780246286657 0.697951879101213 0.643173412512372 0.598566633402885 0.701535990362414 0 0.860012230114305 0.82396672731999 0.696356043704593 0.608614963860129 0.896020179372198 0.953959215457244 0.9014440433213 0.9234484979528 0.938116913005677 0.905321324457207 0.868666952421774 0.854316702819956 0.901660445359763 0.754406370224568 0.724877304998332\n+group13 0.345334659061175 0.60638464347191 0.757674655787863 0.754373626373627 0.622147127631921 0.573924437650142 0.69487361209544 0.551494144215115 0.860012230114305 0 0.5547564'..b'9 0.86008579145263 0.323744637900580 0 0.398453833811446 0.563443208895949 0.537750556792873 0.725759700794764 0.901458342917606 0.780864053688773 0.850419084461638 0.556379750493714 0.888831597401258\n+group6 0.338230884557721 0.635512156237545 0.744137292184681 0.749693459050357 0.625248311481923 0.568402976531196 0.724916160609081 0.650987864807943 0.9014440433213 0.351567272898162 0.622747338353674 0.543911776469916 0.734387197501951 0.175471345902557 0.398453833811446 0 0.451762651100795 0.466509988249118 0.555275398861018 0.722312633832977 0.576246207195492 0.656792557980023 0.407794761777063 0.672014090541248\n+group3 0.527747996119875 0.757850272278487 0.83821186778176 0.80902359221629 0.712879825495866 0.530275619878684 0.802615164256341 0.683795276397356 0.9234484979528 0.496547756041427 0.783666100254885 0.669047897880314 0.816868430229662 0.515448702689836 0.563443208895949 0.451762651100795 0 0.359268929503916 0.209920283436670 0.388581148863785 0.264185101779485 0.341337757596926 0.300259669263359 0.750777302759425\n+group4 0.46940182727116 0.684397366160893 0.830987488829312 0.841379965785972 0.711791887728906 0.517760385310054 0.801531425047536 0.646264782232478 0.938116913005677 0.388174807197943 0.67347429120615 0.677185443802873 0.840013416065739 0.560172148132405 0.537750556792873 0.466509988249118 0.359268929503916 0 0.484114532261228 0.622234006652847 0.487074231539852 0.577606177606177 0.321596600394597 0.764130434782609\n+group2 0.572409158546537 0.820626944245034 0.83725508577857 0.758192367410313 0.724986879144997 0.538922155688623 0.83214644589104 0.735420178184445 0.905321324457207 0.596869061623382 0.859248929176213 0.695153896529142 0.817908907547258 0.646577681901937 0.725759700794764 0.555275398861018 0.209920283436670 0.484114532261228 0 0.233028585612046 0.184614740719039 0.145672877846791 0.420959606845713 0.677966101694915\n+group9 0.658356940509915 0.776103945014594 0.759051704257184 0.741589782845171 0.669388904533934 0.539314268896846 0.772508176966776 0.818586585827965 0.868666952421774 0.729252973406388 0.828249694002448 0.698248620855873 0.788424259207976 0.83184352597575 0.901458342917606 0.722312633832977 0.388581148863785 0.622234006652847 0.233028585612046 0 0.227722772277228 0.111727966689799 0.514525993883792 0.595256346665464\n+group12 0.468803827751196 0.679419902681042 0.689453763842811 0.625361639704983 0.538476172358033 0.428855622420053 0.70517511761631 0.634216589861751 0.854316702819956 0.590238621498489 0.750707371556218 0.518242618672176 0.70625642943982 0.699166591988529 0.780864053688773 0.576246207195492 0.264185101779485 0.487074231539852 0.184614740719039 0.227722772277228 0 0.179336829499938 0.368810178817056 0.560213727907933\n+group10 0.624899560429172 0.764456383429945 0.78428294394681 0.70965400435519 0.662547573180473 0.505990964447063 0.787532847973119 0.765659822656361 0.901660445359763 0.716043877642022 0.830408783452603 0.67063492063492 0.784595481217946 0.769745293466224 0.850419084461638 0.656792557980023 0.341337757596926 0.577606177606177 0.145672877846791 0.111727966689799 0.179336829499938 0 0.50435780791633 0.614787397309741\n+group11 0.445852306473965 0.471627356163032 0.567737261531031 0.632291885091214 0.471028037383178 0.329349338004224 0.581221922731357 0.517282479141836 0.754406370224568 0.427280771201043 0.674327728932078 0.446171234812094 0.617593040115998 0.526223291092406 0.556379750493714 0.407794761777063 0.300259669263359 0.321596600394597 0.420959606845713 0.514525993883792 0.368810178817056 0.50435780791633 0 0.671336257723692\n+group21 0.556086425651643 0.760728080850839 0.727272727272727 0.54560014236142 0.495122079839688 0.531589448015961 0.677116737663332 0.747455911343173 0.724877304998332 0.72127723067741 0.80964495077978 0.63204311611955 0.746623195156032 0.793334979017526 0.888831597401258 0.672014090541248 0.750777302759425 0.764130434782609 0.677966101694915 0.595256346665464 0.560213727907933 0.614787397309741 0.671336257723692 0\n'
b
diff -r 000000000000 -r bccb5efbc4ee tool-data/mothur_aligndb.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/mothur_aligndb.loc.sample Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,19 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of metagenomics files.  
+#file has this format (white space characters are TAB characters):
+#
+# Reference Alignments:  http://www.mothur.org/wiki/Alignment_database
+#
+#<dbname> <file_base>
+#
+#greengenes /project/db/galaxy/mothur/core_set_aligned.imputed.fasta
+#silva archaea /project/db/galaxy/mothur/Silva.archaea/silva.archaea.fasta
+#silva bacteria /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.fasta
+#silva eukarya /project/db/galaxy/mothur/silva.eukarya.fasta
+#silva archaea nogap /project/db/galaxy/mothur/Silva.archaea/nogap.archaea.fasta
+#silva bacteria nogap /project/db/galaxy/mothur/silva.bacteria/nogap.bacteria.fasta
+#silva eukarya nogap /project/db/galaxy/mothur/nogap.eukarya.fasta
+#FungiLSU_train_1400bp_8506_mod.fasta /project/db/galaxy/mothur/RDP/FungiLSU_train_1400bp_8506_mod.fasta
+#trainset6_032010.rdp.fasta /project/db/galaxy/mothur/RDP/trainset6_032010.rdp.fasta
+#trainset7_112011.pds.fasta /project/db/galaxy/mothur/RDP/trainset7_112011.pds.fasta
+#trainset7_112011.rdp.fasta /project/db/galaxy/mothur/RDP/trainset7_112011.rdp.fasta
b
diff -r 000000000000 -r bccb5efbc4ee tool-data/mothur_lookup.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/mothur_lookup.loc.sample Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,11 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of metagenomics files.  
+#file has this format (white space characters are TAB characters):
+#
+# lookup files from:   http://www.mothur.org/wiki/Lookup_files
+#
+#<name> <file_base>
+#
+#GS20 /project/db/galaxy/mothur/lookup/LookUp_GS20.pat
+#GSFLX /project/db/galaxy/mothur/lookup/LookUp_GSFLX.pat
+#Titanium /project/db/galaxy/mothur/lookup/LookUp_Titanium.pat
b
diff -r 000000000000 -r bccb5efbc4ee tool-data/mothur_map.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/mothur_map.loc.sample Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,10 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of metagenomics files.  
+#file has this format (white space characters are TAB characters):
+#
+# Secondary structure maps:    http://www.mothur.org/wiki/Secondary_structure_map
+#
+#<name> <file_base>
+#
+#greengenes /project/db/galaxy/mothur/gg.ss.map
+#silva /project/db/galaxy/mothur/silva.ss.map
b
diff -r 000000000000 -r bccb5efbc4ee tool-data/mothur_taxonomy.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/mothur_taxonomy.loc.sample Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,24 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of metagenomics files.  
+#file has this format (white space characters are TAB characters):
+#
+# Silva reference files:    http://www.mothur.org/wiki/Silva_reference_files
+#
+#<taxonomyname> <file_base>
+#
+#archaea.gg /project/db/galaxy/mothur/Silva.archaea/silva.archaea.gg.tax
+#archaea.silva /project/db/galaxy/mothur/Silva.archaea/silva.archaea.silva.tax
+#archaea.rdp /project/db/galaxy/mothur/Silva.archaea/silva.archaea.rdp.tax
+#archaea.ncbi /project/db/galaxy/mothur/Silva.archaea/silva.archaea.ncbi.tax
+#bacteria.gg /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.gg.tax
+#bacteria.silva /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.silva.tax
+#bacteria.ncbi /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.ncbi.tax
+#bacteria.rdp /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.rdp.tax
+#bacteria.rdp6 /project/db/galaxy/mothur/silva.bacteria/silva.bacteria.rdp6.tax
+#eukarya.silva /project/db/galaxy/mothur/silva.eukarya.silva.tax
+#eukarya.ncbi /project/db/galaxy/mothur/silva.eukarya.ncbi.tax
+#trainset6_032010.rdp.tax /project/db/galaxy/mothur/RDP/trainset6_032010.rdp.tax
+#trainset7_112011.pds.tax /project/db/galaxy/mothur/RDP/trainset7_112011.pds.tax
+#trainset7_112011.rdp.tax /project/db/galaxy/mothur/RDP/trainset7_112011.rdp.tax
+#FungiLSU_train_1400bp_8506_mod.tax /project/db/galaxy/mothur/RDP/FungiLSU_train_1400bp_8506_mod.tax
+#
b
diff -r 000000000000 -r bccb5efbc4ee tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Fri May 19 05:47:34 2017 -0400
b
@@ -0,0 +1,18 @@
+<tables>
+  <table name="mothur_aligndb" comment_char="#" allow_duplicate_entries="False">
+    <columns>name, value</columns>
+    <file path="tool-data/mothur_aligndb.loc" />
+  </table>
+  <table name="mothur_lookup" comment_char="#" allow_duplicate_entries="False">
+    <columns>name, value</columns>
+    <file path="tool-data/mothur_lookup.loc" />
+  </table>
+  <table name="mothur_map" comment_char="#" allow_duplicate_entries="False">
+    <columns>name, value</columns>
+    <file path="tool-data/mothur_map.loc" />
+  </table>
+  <table name="mothur_taxonomy" comment_char="#" allow_duplicate_entries="False">
+    <columns>name, value</columns>
+    <file path="tool-data/mothur_taxonomy.loc" />
+  </table>
+</tables>
\ No newline at end of file
b
diff -r 000000000000 -r bccb5efbc4ee tools.yaml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools.yaml Fri May 19 05:47:34 2017 -0400
b
b'@@ -0,0 +1,802 @@\n+---\n+# This is a sample file to be used as a reference for populating a list of\n+# tools that you wish to install into Galaxy from a Tool Shed via the\n+# `install_tool_shed_tools.py` script.\n+#\n+# For each tool you want to install, you must provide the following keys:\n+#  * name: this is is the name of the tool to install\n+#  * owner: owner of the Tool Shed repository from where the tools is being\n+#           installed\n+# Further, you need to provide **one** of the following two keys:\n+#  * tool_panel_section_id: ID of the tool panel section where you want the\n+#                           tool to be installed. The section ID can be found\n+#                           in Galaxy\'s `shed_tool_conf.xml` config file. Note\n+#                           that the specified section must exist in this file.\n+#                           Otherwise, the tool will be installed outside any\n+#                           section.\n+#  * tool_panel_section_label: Display label of a tool panel section where\n+#                              you want the tool to be installed. If it does not\n+#                              exist, this section will be created on the target\n+#                              Galaxy instance (note that this is different than\n+#                              when using the ID).\n+#                              Multi-word labels need to be placed in quotes.\n+#                              Each label will have a corresponding ID created;\n+#                              the ID will be an all lowercase version of the\n+#                              label, with multiple words joined with\n+#                              underscores (e.g., \'BED tools\' -> \'bed_tools\').\n+#\n+# Tou can also specify the following optional keys to further define the\n+# installation properties:\n+#  * tool_shed_url: the URL of the Tool Shed from where the tool should be\n+#                   installed. (default: https://toolshed.g2.bx.psu.edu)\n+#  * revisions: a list of revisions of the tool, all of which will attempt to\n+#               be installed. (default: latest)\n+#  * install_tool_dependencies: True or False - whether to install tool\n+#                               dependencies or not. (default: True)\n+#  * install_repository_dependencies: True or False - whether to install repo\n+#                               dependencies or not. (default: True)\n+\n+\n+# pip install ephemeris -U\n+# shed_install -t tools.yaml -a <galaxy admin API key> -g <galaxy instance>\n+# (the latter two can also be configure inside the yaml with following two lines)\n+#api_key: admin\n+#galaxy_instance: http://localhost:8080/\n+\n+tools:\n+- name: mothur_align_check\n+  install_resolver_dependencies: true\n+  install_tool_dependencies: true\n+  owner: iuc\n+  tool_panel_section_label: "Mothur"\n+  tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_align_seqs\n+  install_resolver_dependencies: true\n+  install_tool_dependencies: true\n+  owner: iuc\n+  tool_panel_section_label: "Mothur"\n+  tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_amova\n+  install_resolver_dependencies: true\n+  install_tool_dependencies: true\n+  owner: iuc\n+  tool_panel_section_label: "Mothur"\n+  tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_anosim\n+  install_resolver_dependencies: true\n+  install_tool_dependencies: true\n+  owner: iuc\n+  tool_panel_section_label: "Mothur"\n+  tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_bin_seqs\n+  install_resolver_dependencies: true\n+  install_tool_dependencies: true\n+  owner: iuc\n+  tool_panel_section_label: "Mothur"\n+  tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_chimera_bellerophon\n+  install_resolver_dependencies: true\n+  install_tool_dependencies: true\n+  owner: iuc\n+  tool_panel_section_label: "Mothur"\n+  tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_chimera_ccode\n+  install_resolver_dependencies: true\n+  install_tool_dependencies: true\n+  owner: iuc\n+  tool_panel_section_labe'..b'true\n+  install_tool_dependencies: true\n+  owner: iuc\n+  tool_panel_section_label: "Mothur"\n+  tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_sffinfo\n+  install_resolver_dependencies: true\n+  install_tool_dependencies: true\n+  owner: iuc\n+  tool_panel_section_label: "Mothur"\n+  tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_shhh_flows\n+  install_resolver_dependencies: true\n+  install_tool_dependencies: true\n+  owner: iuc\n+  tool_panel_section_label: "Mothur"\n+  tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_shhh_seqs\n+  install_resolver_dependencies: true\n+  install_tool_dependencies: true\n+  owner: iuc\n+  tool_panel_section_label: "Mothur"\n+  tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_sort_seqs\n+  install_resolver_dependencies: true\n+  install_tool_dependencies: true\n+  owner: iuc\n+  tool_panel_section_label: "Mothur"\n+  tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_split_abund\n+  install_resolver_dependencies: true\n+  install_tool_dependencies: true\n+  owner: iuc\n+  tool_panel_section_label: "Mothur"\n+  tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_split_groups\n+  install_resolver_dependencies: true\n+  install_tool_dependencies: true\n+  owner: iuc\n+  tool_panel_section_label: "Mothur"\n+  tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_sub_sample\n+  install_resolver_dependencies: true\n+  install_tool_dependencies: true\n+  owner: iuc\n+  tool_panel_section_label: "Mothur"\n+  tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_summary_qual\n+  install_resolver_dependencies: true\n+  install_tool_dependencies: true\n+  owner: iuc\n+  tool_panel_section_label: "Mothur"\n+  tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_summary_seqs\n+  install_resolver_dependencies: true\n+  install_tool_dependencies: true\n+  owner: iuc\n+  tool_panel_section_label: "Mothur"\n+  tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_summary_shared\n+  install_resolver_dependencies: true\n+  install_tool_dependencies: true\n+  owner: iuc\n+  tool_panel_section_label: "Mothur"\n+  tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_summary_single\n+  install_resolver_dependencies: true\n+  install_tool_dependencies: true\n+  owner: iuc\n+  tool_panel_section_label: "Mothur"\n+  tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_summary_tax\n+  install_resolver_dependencies: true\n+  install_tool_dependencies: true\n+  owner: iuc\n+  tool_panel_section_label: "Mothur"\n+  tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_tree_shared\n+  install_resolver_dependencies: true\n+  install_tool_dependencies: true\n+  owner: iuc\n+  tool_panel_section_label: "Mothur"\n+  tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_trim_flows\n+  install_resolver_dependencies: true\n+  install_tool_dependencies: true\n+  owner: iuc\n+  tool_panel_section_label: "Mothur"\n+  tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_trim_seqs\n+  install_resolver_dependencies: true\n+  install_tool_dependencies: true\n+  owner: iuc\n+  tool_panel_section_label: "Mothur"\n+  tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_unifrac_unweighted\n+  install_resolver_dependencies: true\n+  install_tool_dependencies: true\n+  owner: iuc\n+  tool_panel_section_label: "Mothur"\n+  tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_unifrac_weighted\n+  install_resolver_dependencies: true\n+  install_tool_dependencies: true\n+  owner: iuc\n+  tool_panel_section_label: "Mothur"\n+  tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_unique_seqs\n+  install_resolver_dependencies: true\n+  install_tool_dependencies: true\n+  owner: iuc\n+  tool_panel_section_label: "Mothur"\n+  tool_shed_url: https://toolshed.g2.bx.psu.edu\n+- name: mothur_venn\n+  install_resolver_dependencies: true\n+  install_tool_dependencies: true\n+  owner: iuc\n+  tool_panel_section_label: "Mothur"\n+  tool_shed_url: https://toolshed.g2.bx.psu.edu\n'