Galaxy |

Changeset 2:5b752525bd6f (2020-03-16)

Previous changeset 1:7f8f0e9fcb37 (2019-12-05) Next changeset 3:b6dddf8c2e6f (2020-07-14)

Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"

modified:
dada2_removeBimeraDenovo.xml
macros.xml
test-data/F3D0_S188_L001_R1_001.fastq.gz
test-data/F3D0_S188_L001_R2_001.fastq.gz
test-data/complexity.pdf
test-data/dada2_species.loc
test-data/dada2_taxonomy.loc
test-data/filterAndTrim_F3D0_R1.fq.gz
test-data/filterAndTrim_F3D0_R2.fq.gz
test-data/filterAndTrim_single_F3D0_R1.fq.gz
test-data/filterAndTrim_single_filters_F3D0_R1.fq.gz
test-data/filterAndTrim_single_trimmers_F3D0_R1.fq.gz
test-data/gentest.R
test-data/qualityProfile.pdf
test-data/removeBimeraDenovo_F3D0_dada_uniques.tab
test-data/removeBimeraDenovo_F3D0_mergepairs.Rdata

added:
test-data.sh
test-data/F3D0_S188_L001_R1_001.tab
test-data/F3D141_S207_L001_R1_001.fastq.gz
test-data/F3D141_S207_L001_R1_001.tab
test-data/F3D141_S207_L001_R2_001.fastq.gz
test-data/assignTaxonomyAddspecies.tab
test-data/assignTaxonomyAddspecies_boot.tab
test-data/complexity_fwd.pdf
test-data/complexity_rev.pdf
test-data/dada_F3D0_S188_L001_R1.Rdata
test-data/dada_F3D0_S188_L001_R2.Rdata
test-data/dada_F3D141_S207_L001_R1.Rdata
test-data/dada_F3D141_S207_L001_R2.Rdata
test-data/filterAndTrim.tab
test-data/filterAndTrim_F3D141_R1.fq.gz
test-data/filterAndTrim_F3D141_R2.fq.gz
test-data/filterAndTrim_single_F3D141_R1.fq.gz
test-data/filterAndTrim_single_filters_F3D141_R1.fq.gz
test-data/filterAndTrim_single_trimmers_F3D141_R1.fq.gz
test-data/learnErrors.pdf
test-data/learnErrors_R1.Rdata
test-data/learnErrors_R1.pdf
test-data/learnErrors_R2.Rdata
test-data/makeSequenceTable.pdf
test-data/makeSequenceTable.tab
test-data/mergePairs_F3D0_S188_L001.Rdata
test-data/mergePairs_F3D0_S188_L001_nondefault.Rdata
test-data/mergePairs_F3D141_S207_L001.Rdata
test-data/mergePairs_F3D141_S207_L001_nondefault.Rdata
test-data/qualityProfile_fwd.pdf
test-data/qualityProfile_rev.pdf
test-data/reference.fa.gz
test-data/reference_species.fa.gz
test-data/removeBimeraDenovo.tab
test-data/seqCounts_dadaF.tab
test-data/seqCounts_filter.tab
test-data/seqCounts_filter_both.tab
test-data/seqCounts_merge.tab
test-data/seqCounts_nochim.tab
test-data/seqCounts_seqtab.tab

removed:
test-data/assignTaxonomyAddspecies_F3D0.tab
test-data/assignTaxonomyAddspecies_F3D0_boot.tab
test-data/dada_F3D0_R1.Rdata
test-data/dada_F3D0_R2.Rdata
test-data/filterAndTrim_F3D0.tab
test-data/gentest.sh
test-data/learnErrors_F3D0_R1.Rdata
test-data/learnErrors_F3D0_R1.pdf
test-data/learnErrors_F3D0_R2.Rdata
test-data/learnErrors_F3D0_R2.pdf
test-data/makeSequenceTable_F3D0.pdf
test-data/makeSequenceTable_F3D0.tab
test-data/mergePairs_F3D0.Rdata
test-data/mergePairs_F3D0_nondefault.Rdata
test-data/reference.fa
test-data/reference_species.fa
test-data/removeBimeraDenovo_F3D0.tab
test-data/removeBimeraDenovo_F3D0_derep_uniques.tab
test-data/seqCounts_F3D0_dadaF.tab
test-data/seqCounts_F3D0_filter.tab
test-data/seqCounts_F3D0_merge.tab
test-data/seqCounts_F3D0_nochim.tab
test-data/seqCounts_F3D0_seqtab.tab

diff -r 7f8f0e9fcb37 -r 5b752525bd6f dada2_removeBimeraDenovo.xml
--- a/dada2_removeBimeraDenovo.xml Thu Dec 05 17:59:57 2019 -0500
+++ b/dada2_removeBimeraDenovo.xml Mon Mar 16 07:37:41 2020 -0400

@@ -65,17 +65,17 @@
     </outputs>
     <tests>
         <test expect_num_outputs="1">
-            <param name="unqs" ftype="dada2_sequencetable" value="makeSequenceTable_F3D0.tab"/>
-            <output name="stable_sequencetable" value="removeBimeraDenovo_F3D0.tab" ftype="dada2_sequencetable" />
+            <param name="unqs" ftype="dada2_sequencetable" value="makeSequenceTable.tab"/>
+            <output name="stable_sequencetable" value="removeBimeraDenovo.tab" ftype="dada2_sequencetable" />
         </test>
         
         <test expect_num_outputs="1">
-            <param name="unqs" ftype="dada2_dada" value="dada_F3D0_R1.Rdata"/>
+            <param name="unqs" ftype="dada2_dada" value="dada_F3D0_S188_L001_R1.Rdata"/>
             <output name="stable_uniques" value="removeBimeraDenovo_F3D0_dada_uniques.tab" ftype="dada2_uniques" />
         </test>
         
         <test expect_num_outputs="1">
-            <param name="unqs" ftype="dada2_mergepairs" value="mergePairs_F3D0.Rdata"/>
+            <param name="unqs" ftype="dada2_mergepairs" value="mergePairs_F3D0_S188_L001.Rdata"/>
             <param name="method" value="pooled"/>
             <output name="stable_mergepairs" value="removeBimeraDenovo_F3D0_mergepairs.Rdata" ftype="dada2_mergepairs" compare="sim_size" delta="400"/>
         </test>

diff -r 7f8f0e9fcb37 -r 5b752525bd6f macros.xml
--- a/macros.xml Thu Dec 05 17:59:57 2019 -0500
+++ b/macros.xml Mon Mar 16 07:37:41 2020 -0400

[

@@ -7,8 +7,8 @@
         </requirements>
     </xml>

-    <token name="@DADA2_VERSION@">1.12</token>
-    <token name="@WRAPPER_VERSION@">1</token>
+    <token name="@DADA2_VERSION@">1.14</token>
+    <token name="@WRAPPER_VERSION@">0</token>

     <xml name="version_command">
         <version_command><![CDATA[

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data.sh Mon Mar 16 07:37:41 2020 -0400

@@ -0,0 +1,58 @@
+#!/usr/bin/env bash
+
+# install conda
+if type conda > /dev/null; then
+ true
+else
+ tmp=$(mktemp -d)
+ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
+ bash Miniconda3-latest-Linux-x86_64.sh -b -p "$tmp/miniconda"
+ source "$tmp/miniconda/bin/activate"
+fi
+
+eval "$(conda shell.bash hook)"
+
+# install conda env
+if grep -Fq __bioconductor-dada2@1.14 <<< $(conda env list); then
+ true
+else
+ conda create -y --quiet --override-channels --channel conda-forge --channel bioconda --channel defaults --name __bioconductor-dada2@1.14 bioconductor-dada2=1.14
+fi
+
+conda activate __bioconductor-dada2@1.14
+
+# create test data
+cd test-data/
+
+# download Mothur SOP data from zenodo (GTN), same as
+# http://www.mothur.org/w/images/d/d6/MiSeqSOPData.zip but stable links
+# but file names need to be fixed
+wget -nc -O F3D0_S188_L001_R1_001.fastq https://zenodo.org/record/800651/files/F3D0_R1.fastq?download=1
+wget -nc -O F3D0_S188_L001_R2_001.fastq https://zenodo.org/record/800651/files/F3D0_R2.fastq?download=1
+wget -nc -O F3D141_S207_L001_R1_001.fastq https://zenodo.org/record/800651/files/F3D141_R1.fastq?download=1
+wget -nc -O F3D141_S207_L001_R2_001.fastq https://zenodo.org/record/800651/files/F3D141_R2.fastq?download=1
+
+# zip and reduce data to ~ 10% (for speed)
+for i in *fastq
+do
+ head -n 3000 "$i" | gzip -c > "$i.gz"
+done
+rm *fastq
+
+# download data bases from https://zenodo.org/record/158955
+# as mentioned in https://benjjneb.github.io/dada2/training.html
+wget -nc -O reference.fa.gz https://zenodo.org/record/158955/files/rdp_train_set_14.fa.gz?download=1
+wget -nc -O reference_species.fa.gz https://zenodo.org/record/158955/files/rdp_species_assignment_14.fa.gz?download=1
+
+# take ~ 5% of the reference (for speed)
+zcat reference.fa.gz | head -n 1000 | gzip -c > t && mv t reference.fa.gz
+zcat reference_species.fa.gz | head -n 1000 | gzip -c > t && mv t reference_species.fa.gz
+
+
+# generate outputs
+Rscript gentest.R
+
+conda deactivate
+
+# # remove files only needed for test generation
+# rm learnErrors_F3D0_R2.pdf dada_F3D0_R2.Rdata

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/F3D0_S188_L001_R1_001.fastq.gz

Binary file test-data/F3D0_S188_L001_R1_001.fastq.gz has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/F3D0_S188_L001_R1_001.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/F3D0_S188_L001_R1_001.tab Mon Mar 16 07:37:41 2020 -0400

@@ -0,0 +1,2 @@
+ reads.in reads.out
+F3D0_S188_L001_R1_001.fastq.gz 750 745

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/F3D0_S188_L001_R2_001.fastq.gz

Binary file test-data/F3D0_S188_L001_R2_001.fastq.gz has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/F3D141_S207_L001_R1_001.fastq.gz

Binary file test-data/F3D141_S207_L001_R1_001.fastq.gz has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/F3D141_S207_L001_R1_001.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/F3D141_S207_L001_R1_001.tab Mon Mar 16 07:37:41 2020 -0400

@@ -0,0 +1,2 @@
+ reads.in reads.out
+F3D141_S207_L001_R1_001.fastq.gz 750 744

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/F3D141_S207_L001_R2_001.fastq.gz

Binary file test-data/F3D141_S207_L001_R2_001.fastq.gz has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/assignTaxonomyAddspecies.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/assignTaxonomyAddspecies.tab Mon Mar 16 07:37:41 2020 -0400

b'@@ -0,0 +1,32 @@\n+\tLevel1\tLevel2\tLevel3\tLevel4\tLevel5\tNA\tSpecies\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAGG\tBacteria\tBacteroidetes\tCytophagia\tCytophagales\tNA\tNA\tNA\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGCTTTTAAGTCAGCGGTAAAAATTCGGGGCTCAACCCCGTCCGGCCGTTGAAACTGGGGGCCTTGAGTGGGCGAGAAGAAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCCTTCCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCGAACAGG\tBacteria\tBacteroidetes\tCytophagia\tCytophagales\tCytophagaceae\tNA\tNA\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGACTCTCAAGTCAGCGGTCAAATCGCGGGGCTCAACCCCGTTCCGCCGTTGAAACTGGGAGCCTTGAGTGCGCGAGAAGTAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCCTACCGGCGCGCAACTGACGCTCATGCACGAAAGCGTGGGTATCGAACAGG\tBacteria\tBacteroidetes\tNA\tNA\tNA\tNA\tNA\n+TACGGAGGATTCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTCGATAAGTTAGAGGTGAAATCCCGGGGCTCAACTCCGGCACTGCCTCTGATACTGTCGGGCTAGAGTTTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCATAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTACGACTGACGTTGAGGCACGAAAGCGTGGGGAGCAAACAGG\tBacteria\tBacteroidetes\tCytophagia\tCytophagales\tNA\tNA\tNA\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGTCAAGTCAGCGGTAAAATTGTGGAGCTCAACTCCATCGAGCCGTTGAAACTGACGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAAGCACGAAAGCGTGGGTATCGAACAGG\tBacteria\tBacteroidetes\tCytophagia\tCytophagales\tNA\tNA\tNA\n+TACGTAGGGGGCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGTAGACGGTAATGCAAGTCTGGAGTGAAAGGCGGGGGCCCAACCCCCGGACTGCTCTGGAAACTGTGTAACTGGAGTGCAGGAGAGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tNA\tNA\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGACTGCAACTGACACTGATGCTCGAAAGTGTGGGTATCAAACAGG\tBacteria\tNA\tNA\tNA\tNA\tNA\tNA\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGCCAAGTCAGCGGTAAAAAAGCGGTGCTCAACGCCGTCGAGCCGTTGAAACTGGCGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAGG\tBacteria\tBacteroidetes\tCytophagia\tCytophagales\tNA\tNA\tNA\n+TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGAGCGCGCAGGTGGTTAATTAAGTCTGATGTGAAAGCCCACGGCTTAACCGTGGAGGGTCATTGGAAACTGGTTGACTTGAGTGCAGAAGAGGGAAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGAGATATGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGTCTGCAACTGACACTGAGGCGCGAAAGCGTGGGGAGCAAACAGG\tBacteria\tFirmicutes\tBacilli\tBacillales\tPlanococcaceae\tSolibacillus\tNA\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGAGACAAGTCTGAAGTGAAAGCCCGGGGCTCAACCCCGGGACTGCTTTGGAAACTGCCTGACTGGAGTGCTGGAGAGGCAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTGCTGGACAGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tNA\tNA\n+TACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGTGCAGGCGGTTCAATAAGTCTGATGTGAAAGCCTTCGGCTCAACCGGAGAATTGCATCAGAAACTGTTGAACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGG\tBacteria\tFirmicutes\tBacilli\tBacillales\tBacillaceae_2\tNA\tNA\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCAGCGCAAGTCTGGAGTGAAATGCCGGGGCCCAACCCCGGAACTGCTTTGGAAACTGTGCAGCTCGAGTGCAGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tNA\tNA\n+TACGTATGGAGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGCATGGCAAGTCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGAAACTGCCAGGCTAGAGTGTCGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGG'..b'CAACCCCGGTACTGCATTGGAAACTGCCGGACTGGAGTGTCGGAGGGGTAAGCGGAATTCCTGGTGTAGCGGTGAAATGCGTAGATATCAGGAGGAACACCGGTGGCGAAGGCGGCTTACTGGACGATGACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tNA\tNA\n+TACGTAGGGAGCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGAAGTGAAATCCATGGGCTTAACCCATGAACTGCTTTTGAAACTGCAGAGCTTGAGTGGAGTAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGAAATGCGTAGAGATCGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTCTAACTGACGCTGAGGCACGAAAGCGTGGGTAGCAAACAGG\tBacteria\tNA\tNA\tNA\tNA\tNA\tNA\n+TACGTAGGGAGCGAGCGTTATCCGGAATTATTGGGCGTAAAGGGTGCGTAGATGGCATAGTAAGTCTTTTGTAAAAATGCTGGGCTCAACCCAGTAGGGCAAAAGATACTGCAAAGCTAGAGTATGACAGAGGCAAGTGGAACTACATGTGTAGCGGTAAAATGCGTAAATATATGTAAGAACACCAGTGGCGAAGGCGGCTTGCTGGGTCGATACTGACATTGAGGCACGAAAGCGTGGGGAGCAAACAGG\tBacteria\tNA\tNA\tNA\tNA\tNA\tNA\n+TACGTAGGTGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGTGTAGGCGGGGACGCAAGTCAGATGTGAAAACCACGGGCTCAACCTGTGGCCTGCATTTGAAACTGTGTTTCTTGAGTACTGGAGAGGCAGACGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGTCTGCTGGACAGCAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAGG\tBacteria\tFirmicutes\tClostridia\tClostridiales\tRuminococcaceae\tOscillibacter\tNA\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGCGCCAAGTCTGGAGTGAAATGCCGCAGCTTAACTGCGGAACTGCTTTGGAAACTGGCGGACTAGAGTGCGGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCGGTGGCGAAGGCGGCTTACTGGACCGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tLachnoanaerobaculum\tNA\n+TACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTGCTTAGGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGAAGTGCATCGGAAACCGGGCGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGG\tBacteria\tFirmicutes\tBacilli\tBacillales\tNA\tNA\tNA\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCAATGCAAGCCAGATGTGAAAACCCGCAGCTCAACTGGGGGAGTGCATTTGGAACTGTGTAGCTGGAGTGCAGGAGAGGTAAGCGGAATTCCTGGTGTAGCGGTGAAATGCGTAGATATCAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tNA\tNA\n+TACGTAGGGGGCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGAGTAGGCGGCAAGGTAAGCGATATGTGAAAGCCTTAGGCTTAACCAAAGGATTGCATAACGAACTATCTAGCTAGAGTACAGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGAAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCGAACAGG\tBacteria\tFirmicutes\tNA\tNA\tNA\tNA\tNA\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGACGGCAGTGCAAGTCTGGAGTGAAAGCCCGGGGCCCAACCCCGGAACTGCTCTGGAAACTGTGCGGCTAGAGTACTGGAGGGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACAGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tNA\tNA\n+TACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGGAGTAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGTAGCAAACAGG\tBacteria\tFirmicutes\tBacilli\tBacillales\tBacillaceae_2\tPullulanibacillus\tNA\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCCAGACAAGTCTGAAGTGAAAATCCAGCGCTTAACGTTGGAAGTGCTTTGGAAACTGCCGGGCTAGAGTGCAGGAGGGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACTGCAACTGACGTTGAGGCTCGAAGGCGTGGGGAGCAAACAGG\tBacteria\tFirmicutes\tClostridia\tClostridiales\tLachnospiraceae\tLachnoanaerobaculum\tNA\n+TACGTAGGTGGCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGCGTGTAGCCGGGTTGACAAGTCAGATGTGAAATCCTGCGGCTTAACCGCAGAACTGCATTTGAAACTGTTGATCTTGAGTACTGGAGAGGCAGACGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGTCTGCTGGACAGCAACTGACGGTGAGGCGCGAAAGCGTGGGGAGCAAACAGG\tBacteria\tFirmicutes\tClostridia\tClostridiales\tRuminococcaceae\tOscillibacter\tNA\n+TACGTAGGGAGCAAGCGTTGTTCGGAATGACTGGGCGTAAAGGGTGCGTAGGCGGTTGTACAAGTTAGAAGTGAAATACCCAGGGCTTAACTCGGGTGCTGCTTCTAAAACTGTATGACTTGAGTGCAGTAGAGGTTAGTGGAATTCCTAGTGTAGCGGTGGAATGCGTAGATATTAGGAGGAACACCAGAGGCGAAGGCGGCTAACTGGACTGCAACTGACGCTGAGGCACGAAAGTGTGGGGAGCAAACAGG\tBacteria\tFirmicutes\tNA\tNA\tNA\tNA\tNA\n'

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/assignTaxonomyAddspecies_F3D0.tab
--- a/test-data/assignTaxonomyAddspecies_F3D0.tab Thu Dec 05 17:59:57 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,8 +0,0 @@
- Level1 Level2 Level3 Level4 Level5 Species
-TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAGG A B C D E NA
-TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGCCAAGTCAGCGGTAAAAAAGCGGTGCTCAACGCCGTCGAGCCGTTGAAACTGGCGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAGG A B C D E NA
-TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTACGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGCCGGACTGGAGTGTCGGAGGGGTAAGCGGAATTCCTGGTGTAGCGGTGAAATGCGTAGATATCAGGAGGAACACCGGTGGCGAAGGCGGCTTACTGGACGATGACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG A B C D E NA
-TACGGAGGATTCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTCGATAAGTTAGAGGTGAAATCCCGGGGCTCAACTCCGGCACTGCCTCTGATACTGTCGGGCTAGAGTTTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCATAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTACGACTGACGTTGAGGCACGAAAGCGTGGGGAGCAAACAGG A B C D E NA
-TACGTAGGTGGCGAGCGTTGTCCGGATTTACTGGGCGTAAAGGGAGCGTAGGCGGACTTTTAAGTGAGATGTGAAATACTCGGGCTCAACTTGAGTGCTGCATTTCAAACTGGAAGTCTAGAGTGCAGGAGAGGAGAATGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCAGTGGCGAAGGCGATTCTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG A B C D E NA
-TACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGGAGTAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGTAGCAAACAGG A B C D E NA
-TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCCAGACAAGTCTGAAGTGAAAATCCAGCGCTTAACGTTGGAAGTGCTTTGGAAACTGCCGGGCTAGAGTGCAGGAGGGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACTGCAACTGACGTTGAGGCTCGAAGGCGTGGGGAGCAAACAGG A B C D E NA

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/assignTaxonomyAddspecies_F3D0_boot.tab
--- a/test-data/assignTaxonomyAddspecies_F3D0_boot.tab Thu Dec 05 17:59:57 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,8 +0,0 @@
- Level1 Level2 Level3 Level4 Level5
-TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAGG 100 100 100 100 100
-TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGCCAAGTCAGCGGTAAAAAAGCGGTGCTCAACGCCGTCGAGCCGTTGAAACTGGCGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAGG 100 100 100 100 100
-TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTACGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGCCGGACTGGAGTGTCGGAGGGGTAAGCGGAATTCCTGGTGTAGCGGTGAAATGCGTAGATATCAGGAGGAACACCGGTGGCGAAGGCGGCTTACTGGACGATGACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 100 100 100 100 100
-TACGGAGGATTCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTCGATAAGTTAGAGGTGAAATCCCGGGGCTCAACTCCGGCACTGCCTCTGATACTGTCGGGCTAGAGTTTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCATAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTACGACTGACGTTGAGGCACGAAAGCGTGGGGAGCAAACAGG 100 100 100 100 100
-TACGTAGGTGGCGAGCGTTGTCCGGATTTACTGGGCGTAAAGGGAGCGTAGGCGGACTTTTAAGTGAGATGTGAAATACTCGGGCTCAACTTGAGTGCTGCATTTCAAACTGGAAGTCTAGAGTGCAGGAGAGGAGAATGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCAGTGGCGAAGGCGATTCTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 100 100 100 100 100
-TACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGGAGTAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGTAGCAAACAGG 100 100 100 100 100
-TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCCAGACAAGTCTGAAGTGAAAATCCAGCGCTTAACGTTGGAAGTGCTTTGGAAACTGCCGGGCTAGAGTGCAGGAGGGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACTGCAACTGACGTTGAGGCTCGAAGGCGTGGGGAGCAAACAGG 100 100 100 100 100

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/assignTaxonomyAddspecies_boot.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/assignTaxonomyAddspecies_boot.tab Mon Mar 16 07:37:41 2020 -0400

b'@@ -0,0 +1,32 @@\n+\tLevel1\tLevel2\tLevel3\tLevel4\tLevel5\tNA\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAGG\t98\t80\t70\t70\t48\t48\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGCTTTTAAGTCAGCGGTAAAAATTCGGGGCTCAACCCCGTCCGGCCGTTGAAACTGGGGGCCTTGAGTGGGCGAGAAGAAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCCTTCCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCGAACAGG\t97\t88\t76\t76\t50\t48\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGACTCTCAAGTCAGCGGTCAAATCGCGGGGCTCAACCCCGTTCCGCCGTTGAAACTGGGAGCCTTGAGTGCGCGAGAAGTAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCCTACCGGCGCGCAACTGACGCTCATGCACGAAAGCGTGGGTATCGAACAGG\t100\t82\t49\t49\t42\t42\n+TACGGAGGATTCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTCGATAAGTTAGAGGTGAAATCCCGGGGCTCAACTCCGGCACTGCCTCTGATACTGTCGGGCTAGAGTTTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCATAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTACGACTGACGTTGAGGCACGAAAGCGTGGGGAGCAAACAGG\t100\t76\t73\t73\t46\t46\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGTCAAGTCAGCGGTAAAATTGTGGAGCTCAACTCCATCGAGCCGTTGAAACTGACGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAAGCACGAAAGCGTGGGTATCGAACAGG\t97\t82\t68\t68\t33\t33\n+TACGTAGGGGGCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGTAGACGGTAATGCAAGTCTGGAGTGAAAGGCGGGGGCCCAACCCCCGGACTGCTCTGGAAACTGTGTAACTGGAGTGCAGGAGAGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\t100\t100\t99\t99\t99\t91\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGACTGCAACTGACACTGATGCTCGAAAGTGTGGGTATCAAACAGG\t96\t45\t31\t31\t13\t13\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGCCAAGTCAGCGGTAAAAAAGCGGTGCTCAACGCCGTCGAGCCGTTGAAACTGGCGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAGG\t99\t92\t80\t80\t49\t49\n+TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGAGCGCGCAGGTGGTTAATTAAGTCTGATGTGAAAGCCCACGGCTTAACCGTGGAGGGTCATTGGAAACTGGTTGACTTGAGTGCAGAAGAGGGAAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGAGATATGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGTCTGCAACTGACACTGAGGCGCGAAAGCGTGGGGAGCAAACAGG\t100\t100\t100\t100\t72\t72\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGAGACAAGTCTGAAGTGAAAGCCCGGGGCTCAACCCCGGGACTGCTTTGGAAACTGCCTGACTGGAGTGCTGGAGAGGCAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTGCTGGACAGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\t100\t100\t100\t100\t100\t43\n+TACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGTGCAGGCGGTTCAATAAGTCTGATGTGAAAGCCTTCGGCTCAACCGGAGAATTGCATCAGAAACTGTTGAACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGG\t100\t94\t87\t87\t68\t41\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCAGCGCAAGTCTGGAGTGAAATGCCGGGGCCCAACCCCGGAACTGCTTTGGAAACTGTGCAGCTCGAGTGCAGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\t100\t100\t100\t100\t100\t57\n+TACGTATGGAGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGCATGGCAAGTCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGAAACTGCCAGGCTAGAGTGTCGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACGATCACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\t100\t100\t100\t100\t100\t96\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCAGTGCAAGTCTGAAGTGAAAGGCGGGGGCCCAACCCCCGGACTGCTTTGGAAACTGTGCTGCTGGAGTGCAGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\t100\t100\t100\t100\t100\t64\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGGCGGCCATGCAAGTCAGAAGTGAAAACCCGGGGCTCAACCCTGG'..b'CAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACGGTGACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\t100\t100\t100\t100\t100\t97\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTTTTGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTGGAAACTGTATGACTGGAGTGCAGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\t100\t100\t100\t100\t100\t70\n+TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTACGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGCCGGACTGGAGTGTCGGAGGGGTAAGCGGAATTCCTGGTGTAGCGGTGAAATGCGTAGATATCAGGAGGAACACCGGTGGCGAAGGCGGCTTACTGGACGATGACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\t100\t100\t99\t99\t99\t81\n+TACGTAGGGAGCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGAAGTGAAATCCATGGGCTTAACCCATGAACTGCTTTTGAAACTGCAGAGCTTGAGTGGAGTAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGAAATGCGTAGAGATCGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTCTAACTGACGCTGAGGCACGAAAGCGTGGGTAGCAAACAGG\t100\t49\t46\t46\t43\t30\n+TACGTAGGGAGCGAGCGTTATCCGGAATTATTGGGCGTAAAGGGTGCGTAGATGGCATAGTAAGTCTTTTGTAAAAATGCTGGGCTCAACCCAGTAGGGCAAAAGATACTGCAAAGCTAGAGTATGACAGAGGCAAGTGGAACTACATGTGTAGCGGTAAAATGCGTAAATATATGTAAGAACACCAGTGGCGAAGGCGGCTTGCTGGGTCGATACTGACATTGAGGCACGAAAGCGTGGGGAGCAAACAGG\t97\t33\t27\t17\t15\t15\n+TACGTAGGTGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGTGTAGGCGGGGACGCAAGTCAGATGTGAAAACCACGGGCTCAACCTGTGGCCTGCATTTGAAACTGTGTTTCTTGAGTACTGGAGAGGCAGACGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGTCTGCTGGACAGCAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAGG\t100\t99\t98\t98\t70\t70\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGCGCCAAGTCTGGAGTGAAATGCCGCAGCTTAACTGCGGAACTGCTTTGGAAACTGGCGGACTAGAGTGCGGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCGGTGGCGAAGGCGGCTTACTGGACCGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\t100\t100\t100\t100\t100\t50\n+TACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTGCTTAGGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGAAGTGCATCGGAAACCGGGCGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGG\t100\t66\t57\t57\t35\t35\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCAATGCAAGCCAGATGTGAAAACCCGCAGCTCAACTGGGGGAGTGCATTTGGAACTGTGTAGCTGGAGTGCAGGAGAGGTAAGCGGAATTCCTGGTGTAGCGGTGAAATGCGTAGATATCAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\t100\t100\t100\t100\t99\t75\n+TACGTAGGGGGCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGAGTAGGCGGCAAGGTAAGCGATATGTGAAAGCCTTAGGCTTAACCAAAGGATTGCATAACGAACTATCTAGCTAGAGTACAGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGAAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCGAACAGG\t100\t96\t42\t42\t42\t42\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGACGGCAGTGCAAGTCTGGAGTGAAAGCCCGGGGCCCAACCCCGGAACTGCTCTGGAAACTGTGCGGCTAGAGTACTGGAGGGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACAGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\t100\t100\t100\t100\t100\t41\n+TACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGGAGTAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGTAGCAAACAGG\t100\t100\t98\t98\t87\t52\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCCAGACAAGTCTGAAGTGAAAATCCAGCGCTTAACGTTGGAAGTGCTTTGGAAACTGCCGGGCTAGAGTGCAGGAGGGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACTGCAACTGACGTTGAGGCTCGAAGGCGTGGGGAGCAAACAGG\t100\t100\t100\t100\t100\t62\n+TACGTAGGTGGCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGCGTGTAGCCGGGTTGACAAGTCAGATGTGAAATCCTGCGGCTTAACCGCAGAACTGCATTTGAAACTGTTGATCTTGAGTACTGGAGAGGCAGACGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGTCTGCTGGACAGCAACTGACGGTGAGGCGCGAAAGCGTGGGGAGCAAACAGG\t100\t98\t98\t98\t89\t89\n+TACGTAGGGAGCAAGCGTTGTTCGGAATGACTGGGCGTAAAGGGTGCGTAGGCGGTTGTACAAGTTAGAAGTGAAATACCCAGGGCTTAACTCGGGTGCTGCTTCTAAAACTGTATGACTTGAGTGCAGTAGAGGTTAGTGGAATTCCTAGTGTAGCGGTGGAATGCGTAGATATTAGGAGGAACACCAGAGGCGAAGGCGGCTAACTGGACTGCAACTGACGCTGAGGCACGAAAGTGTGGGGAGCAAACAGG\t100\t53\t38\t38\t38\t26\n'

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/complexity.pdf

Binary file test-data/complexity.pdf has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/complexity_fwd.pdf

Binary file test-data/complexity_fwd.pdf has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/complexity_rev.pdf

Binary file test-data/complexity_rev.pdf has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/dada2_species.loc
--- a/test-data/dada2_species.loc Thu Dec 05 17:59:57 2019 -0500
+++ b/test-data/dada2_species.loc Mon Mar 16 07:37:41 2020 -0400

@@ -7,4 +7,4 @@
# Datasets can be retrieved from http://busco.ezlab.org/frame_wget.html
#
# Datasets can be retrieved from https://benjjneb.github.io/dada2/training.html
-test_buildid test_displayname ${__HERE__}/reference_species.fa
+test_buildid test_displayname ${__HERE__}/reference_species.fa.gz

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/dada2_taxonomy.loc
--- a/test-data/dada2_taxonomy.loc Thu Dec 05 17:59:57 2019 -0500
+++ b/test-data/dada2_taxonomy.loc Mon Mar 16 07:37:41 2020 -0400

@@ -7,4 +7,4 @@
# Datasets can be retrieved from https://benjjneb.github.io/dada2/training.html
#
# taxlevels is a comma separated list of taxonomy levels
-test_buildid test_displayname ${__HERE__}/reference.fa Level1,Level2,Level3,Level4,Level5
+test_buildid test_displayname ${__HERE__}/reference.fa.gz Level1,Level2,Level3,Level4,Level5

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/dada_F3D0_R1.Rdata

Binary file test-data/dada_F3D0_R1.Rdata has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/dada_F3D0_R2.Rdata

Binary file test-data/dada_F3D0_R2.Rdata has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/dada_F3D0_S188_L001_R1.Rdata

Binary file test-data/dada_F3D0_S188_L001_R1.Rdata has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/dada_F3D0_S188_L001_R2.Rdata

Binary file test-data/dada_F3D0_S188_L001_R2.Rdata has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/dada_F3D141_S207_L001_R1.Rdata

Binary file test-data/dada_F3D141_S207_L001_R1.Rdata has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/dada_F3D141_S207_L001_R2.Rdata

Binary file test-data/dada_F3D141_S207_L001_R2.Rdata has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/filterAndTrim.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filterAndTrim.tab Mon Mar 16 07:37:41 2020 -0400

@@ -0,0 +1,2 @@
+ reads.in reads.out
+F3D141_S207_L001_R1_001.fastq.gz 750 744

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/filterAndTrim_F3D0.tab
--- a/test-data/filterAndTrim_F3D0.tab Thu Dec 05 17:59:57 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,2 +0,0 @@
- reads.in reads.out
-Unnamed Collection 250 249

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/filterAndTrim_F3D0_R1.fq.gz

Binary file test-data/filterAndTrim_F3D0_R1.fq.gz has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/filterAndTrim_F3D0_R2.fq.gz

Binary file test-data/filterAndTrim_F3D0_R2.fq.gz has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/filterAndTrim_F3D141_R1.fq.gz

Binary file test-data/filterAndTrim_F3D141_R1.fq.gz has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/filterAndTrim_F3D141_R2.fq.gz

Binary file test-data/filterAndTrim_F3D141_R2.fq.gz has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/filterAndTrim_single_F3D0_R1.fq.gz

Binary file test-data/filterAndTrim_single_F3D0_R1.fq.gz has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/filterAndTrim_single_F3D141_R1.fq.gz

Binary file test-data/filterAndTrim_single_F3D141_R1.fq.gz has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/filterAndTrim_single_filters_F3D0_R1.fq.gz

Binary file test-data/filterAndTrim_single_filters_F3D0_R1.fq.gz has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/filterAndTrim_single_filters_F3D141_R1.fq.gz

Binary file test-data/filterAndTrim_single_filters_F3D141_R1.fq.gz has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/filterAndTrim_single_trimmers_F3D0_R1.fq.gz

Binary file test-data/filterAndTrim_single_trimmers_F3D0_R1.fq.gz has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/filterAndTrim_single_trimmers_F3D141_R1.fq.gz

Binary file test-data/filterAndTrim_single_trimmers_F3D141_R1.fq.gz has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/gentest.R
--- a/test-data/gentest.R Thu Dec 05 17:59:57 2019 -0500
+++ b/test-data/gentest.R Mon Mar 16 07:37:41 2020 -0400

[

b'@@ -1,99 +1,192 @@\n library(dada2, quietly=T)\n library(ggplot2, quietly=T)\n \n-fwd <- c(\'F3D0_S188_L001_R1_001.fastq.gz\')\n-rev <- c(\'F3D0_S188_L001_R2_001.fastq.gz\')\n+sample.names <- c(\'F3D0_S188_L001\', \'F3D141_S207_L001\')\n+fwd <- c(\'F3D0_S188_L001_R1_001.fastq.gz\', \'F3D141_S207_L001_R1_001.fastq.gz\')\n+rev <- c(\'F3D0_S188_L001_R2_001.fastq.gz\', \'F3D141_S207_L001_R2_001.fastq.gz\')\n+\n+filt.fwd <- c(\'filterAndTrim_F3D0_R1.fq.gz\', \'filterAndTrim_F3D141_R1.fq.gz\')\n+filt.rev <- c(\'filterAndTrim_F3D0_R2.fq.gz\', \'filterAndTrim_F3D141_R2.fq.gz\')\n+\n+print("filterAndTrim")\n \n-sample.names <- c(\'F3D0_S188_L001\')\n+for(i in 1:length(fwd)){\n+\tftout <- filterAndTrim(fwd[i], filt.fwd[i], rev[i], filt.rev[i])\n+ b <- paste(strsplit(fwd[i], ".", fixed=T)[[1]][1], "tab", sep=".")\n+ write.table(ftout, b, quote=F, sep="\\t", col.names=NA)\n+}\n+\n+# In the test only the 1st data set is used\n+t <- data.frame()\n+t <- rbind(t, ftout[1,])\n+colnames(t) <- colnames(ftout)\n+rownames(t) <- rownames(ftout)[1]\n+write.table(t, "filterAndTrim.tab", quote=F, sep="\\t", col.names=NA)\n \n names(fwd) <- sample.names\n names(rev) <- sample.names\n-\n-\n-filt.fwd <- c(\'filterAndTrim_F3D0_R1.fq.gz\')\n-filt.rev <- c(\'filterAndTrim_F3D0_R2.fq.gz\')\n-\n-ftout <- filterAndTrim(fwd, filt.fwd, rev, filt.rev)\n-\n-# In the test no name can be given to the collection\n-rownames(ftout) <- c( \'Unnamed Collection\' )\n-write.table(ftout, "filterAndTrim_F3D0.tab", quote=F, sep="\\t", col.names=NA)\n+names(filt.fwd) <- sample.names\n+names(filt.rev) <- sample.names\n \n # Plot quality profile (just for one file, Galaxy compares with sim_size)\n-\n+print("plots")\n qp <- plotQualityProfile(fwd)\n+ggsave(\'qualityProfile_fwd.pdf\', qp, width = 20,height = 15,units = c("cm"))\n+qp <- plotQualityProfile(rev)\n+ggsave(\'qualityProfile_rev.pdf\', qp, width = 20,height = 15,units = c("cm"))\n+qp <- plotQualityProfile(fwd[1])\n ggsave(\'qualityProfile.pdf\', qp, width = 20,height = 15,units = c("cm"))\n \n # Plot complexity (just for one file, Galaxy compares with sim_size)\n \n cp <- plotComplexity(fwd)\n+ggsave(\'complexity_fwd.pdf\', cp, width = 20,height = 15,units = c("cm"))\n+cp <- plotComplexity(rev)\n+ggsave(\'complexity_rev.pdf\', cp, width = 20,height = 15,units = c("cm"))\n+cp <- plotComplexity(fwd[1])\n ggsave(\'complexity.pdf\', cp, width = 20,height = 15,units = c("cm"))\n \n \n # learn Errors\n+print("learnErrors")\n err.fwd <- learnErrors(filt.fwd) \n-saveRDS(err.fwd, file=\'learnErrors_F3D0_R1.Rdata\')\n+saveRDS(err.fwd, file=\'learnErrors_R1.Rdata\')\n plot <- plotErrors(err.fwd)\n-ggsave(\'learnErrors_F3D0_R1.pdf\', plot, width = 20,height = 15,units = c("cm"))\n+ggsave(\'learnErrors_R1.pdf\', plot, width = 20,height = 15,units = c("cm"))\n \n-err.rev <- learnErrors(filt.fwd) \n-saveRDS(err.rev, file=\'learnErrors_F3D0_R2.Rdata\')\n+err.rev <- learnErrors(filt.rev) \n+saveRDS(err.rev, file=\'learnErrors_R2.Rdata\')\n plot <- plotErrors(err.rev)\n-ggsave(\'learnErrors_F3D0_R2.pdf\', plot, width = 20,height = 15,units = c("cm"))\n+ggsave(\'learnErrors.pdf\', plot, width = 20,height = 15,units = c("cm"))\n \n-# dada \n+# dada\n+print("dada")\n dada.fwd <- dada(filt.fwd, err.fwd)\n-saveRDS(dada.fwd, file="dada_F3D0_R1.Rdata")\n dada.rev <- dada(filt.rev, err.rev)\n-saveRDS(dada.rev, file="dada_F3D0_R2.Rdata")\n+for( id in sample.names ){\n+\tsaveRDS(dada.fwd[[id]], file=paste("dada_", id,"_R1.Rdata", sep=""))\n+\tsaveRDS(dada.rev[[id]], file=paste("dada_", id,"_R2.Rdata", sep=""))\n+}\n \n # merge pairs\n+print("mergePairs")\n merged <- mergePairs(dada.fwd, filt.fwd, dada.rev, filt.rev)\n-saveRDS(merged, file=\'mergePairs_F3D0.Rdata\')\n+for( id in sample.names ){\n+\tsaveRDS(merged[[id]], file=paste("mergePairs_", id,".Rdata", sep=""))\n+}\n+\n \n # make sequence table\n+print("makeSequenceTable")\n seqtab <- makeSequenceTable(merged)\n-write.table(t(seqtab), file="makeSequenceTable_F3D0.tab", quote=F, sep="\\t", row.names = T, col.names = NA)\n+write.table(t(seqtab), file="makeSequenceTable.tab", quote=F, sep="\\t", row.names = T, col.names = NA)\n \n reads.per.seqlen <- tapply(colSums'..b'rAndTrim_single_trimmers_F3D0_R1.fq.gz\'), truncQ = 30, truncLen = 2, trimLeft = 150, trimRight = 2)\n+filterAndTrim(fwd, c(\'filterAndTrim_single_trimmers_F3D0_R1.fq.gz\', \'filterAndTrim_single_trimmers_F3D141_R1.fq.gz\'), truncQ = 30, truncLen = 2, trimLeft = 150, trimRight = 2)\n \n-filterAndTrim(fwd, c(\'filterAndTrim_single_filters_F3D0_R1.fq.gz\'), maxLen = 255, minLen = 60, maxN = 100, minQ = 13, maxEE = 1)\n+filterAndTrim(fwd, c(\'filterAndTrim_single_filters_F3D0_R1.fq.gz\', \'filterAndTrim_single_filters_F3D141_R1.fq.gz\'), maxLen = 255, minLen = 60, maxN = 100, minQ = 13, maxEE = 1)\n \n \n merged_nondef <- mergePairs(dada.fwd, filt.fwd, dada.rev, filt.rev, minOverlap = 8, maxMismatch = 1, justConcatenate = TRUE, trimOverhang = TRUE)\n-saveRDS(merged_nondef, file=\'mergePairs_F3D0_nondefault.Rdata\')\n-\n-rb.dada.fwd <- removeBimeraDenovo(dada.fwd)\n+for( id in sample.names ){\n+\tsaveRDS(merged_nondef[[id]], file=paste("mergePairs_", id,"_nondefault.Rdata", sep=""))\n+}\n+rb.dada.fwd <- removeBimeraDenovo(dada.fwd[["F3D0_S188_L001"]])\n write.table(rb.dada.fwd, file = \'removeBimeraDenovo_F3D0_dada_uniques.tab\', quote = F, sep = "\\t", row.names = T, col.names = F)\n \n rb.merged <- removeBimeraDenovo(merged, method="pooled")\n saveRDS(rb.merged, file=\'removeBimeraDenovo_F3D0_mergepairs.Rdata\')\n+ \n+# SeqCounts\n+getN <- function(x){ sum(getUniques(x)) }\n+\n+read.uniques <- function ( fname ) {\n+ p <- read.table(fname, header=F, sep="\\t")\n+ n <-x[,2]\n+ names(n)<-x[,1]\n+}\n+\n+\n+print("seqCounts ft")\n+samples = list()\n+samples[["F3D0_S188_L001_R1_001.tab"]] <- read.table("F3D0_S188_L001_R1_001.tab", header=T, sep="\\t", row.names=1)\n+dname <- "filter"\n+tdf <- samples[["F3D0_S188_L001_R1_001.tab"]]\n+names(tdf) <- paste( dname, names(tdf) )\n+tdf <- cbind( data.frame(samples=names( samples )), tdf)\n+write.table(tdf, "seqCounts_filter.tab", quote=F, sep="\\t", row.names = F, col.names = T)\n+\n+samples = list()\n+samples[["F3D0_S188_L001_R1_001.tab"]] <- read.table("F3D0_S188_L001_R1_001.tab", header=T, sep="\\t", row.names=1)\n+samples[["F3D141_S207_L001_R1_001.tab"]] <- read.table("F3D141_S207_L001_R1_001.tab", header=T, sep="\\t", row.names=1)\n+dname <- "filter"\n+tdf <- samples[["F3D0_S188_L001_R1_001.tab"]]\n+tdf <- rbind(tdf, samples[["F3D141_S207_L001_R1_001.tab"]])\n+names(tdf) <- paste( dname, names(tdf) )\n+tdf <- cbind( data.frame(samples=names( samples )), tdf)\n+write.table(tdf, "seqCounts_filter_both.tab", quote=F, sep="\\t", row.names = F, col.names = T)\n+\n+print("seqCounts dada")\n+samples = list()\n+samples[["dada_F3D0_S188_L001_R1.Rdata"]] <- readRDS(\'dada_F3D0_S188_L001_R1.Rdata\')\n+samples[["dada_F3D141_S207_L001_R1.Rdata"]] <- readRDS(\'dada_F3D141_S207_L001_R1.Rdata\')\n+dname <- "dadaF"\n+tdf <- data.frame( samples = names(samples) )\n+tdf[[ dname ]] <- sapply(samples, getN)\n+write.table(tdf, "seqCounts_dadaF.tab", quote=F, sep="\\t", row.names = F, col.names = T)\n+\n+print("seqCounts mp")\n+samples = list()\n+samples[["mergePairs_F3D0_S188_L001.Rdata"]] <- readRDS(\'mergePairs_F3D0_S188_L001.Rdata\')\n+samples[["mergePairs_F3D141_S207_L001.Rdata"]] <- readRDS(\'mergePairs_F3D141_S207_L001.Rdata\')\n+dname <- "merge"\n+tdf <- data.frame( samples = names(samples) )\n+tdf[[ dname ]] <- sapply(samples, getN)\n+write.table(tdf, "seqCounts_merge.tab", quote=F, sep="\\t", row.names = F, col.names = T)\n+\n+print("seqCounts st")\n+samples = list()\n+samples <- t(as.matrix( read.table("makeSequenceTable.tab", header=T, sep="\\t", row.names=1) ))\n+dname <- "seqtab"\n+tdf <- data.frame( samples = row.names(samples) )\n+tdf[[ dname ]] <- rowSums(samples)\n+write.table(tdf, "seqCounts_seqtab.tab", quote=F, sep="\\t", row.names = F, col.names = T)\n+\n+print("seqCounts rb")\n+samples = list()\n+samples <- t(as.matrix( read.table("removeBimeraDenovo.tab", header=T, sep="\\t", row.names=1) ))\n+dname <- "nochim"\n+tdf <- data.frame( samples = row.names(samples) )\n+tdf[[ dname ]] <- rowSums(samples)\n+write.table(tdf, "seqCounts_nochim.tab", quote=F, sep="\\t", row.names = F, col.names = T)\n+\n'

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/gentest.sh
--- a/test-data/gentest.sh Thu Dec 05 17:59:57 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,8 +0,0 @@
-
-conda create -y --quiet --override-channels --channel conda-forge --channel bioconda --channel defaults --name __bioconductor-dada2@1.12 bioconductor-dada2=1.12
-conda activate bioconductor-dada2@1.12
-
-Rscript gentest.R
-
-# remove files only needed for test generation
-rm learnErrors_F3D0_R2.pdf dada_F3D0_R2.Rdata

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/learnErrors.pdf

Binary file test-data/learnErrors.pdf has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/learnErrors_F3D0_R1.Rdata

Binary file test-data/learnErrors_F3D0_R1.Rdata has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/learnErrors_F3D0_R1.pdf

Binary file test-data/learnErrors_F3D0_R1.pdf has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/learnErrors_F3D0_R2.Rdata

Binary file test-data/learnErrors_F3D0_R2.Rdata has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/learnErrors_F3D0_R2.pdf

Binary file test-data/learnErrors_F3D0_R2.pdf has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/learnErrors_R1.Rdata

Binary file test-data/learnErrors_R1.Rdata has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/learnErrors_R1.pdf

Binary file test-data/learnErrors_R1.pdf has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/learnErrors_R2.Rdata

Binary file test-data/learnErrors_R2.Rdata has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/makeSequenceTable.pdf

Binary file test-data/makeSequenceTable.pdf has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/makeSequenceTable.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/makeSequenceTable.tab Mon Mar 16 07:37:41 2020 -0400

b'@@ -0,0 +1,32 @@\n+\tF3D0_S188_L001\tF3D141_S207_L001\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAGG\t49\t56\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGCTTTTAAGTCAGCGGTAAAAATTCGGGGCTCAACCCCGTCCGGCCGTTGAAACTGGGGGCCTTGAGTGGGCGAGAAGAAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCCTTCCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCGAACAGG\t38\t65\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGACTCTCAAGTCAGCGGTCAAATCGCGGGGCTCAACCCCGTTCCGCCGTTGAAACTGGGAGCCTTGAGTGCGCGAGAAGTAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCCTACCGGCGCGCAACTGACGCTCATGCACGAAAGCGTGGGTATCGAACAGG\t31\t45\n+TACGGAGGATTCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTCGATAAGTTAGAGGTGAAATCCCGGGGCTCAACTCCGGCACTGCCTCTGATACTGTCGGGCTAGAGTTTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCATAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTACGACTGACGTTGAGGCACGAAAGCGTGGGGAGCAAACAGG\t17\t47\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGTCAAGTCAGCGGTAAAATTGTGGAGCTCAACTCCATCGAGCCGTTGAAACTGACGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAAGCACGAAAGCGTGGGTATCGAACAGG\t19\t24\n+TACGTAGGGGGCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGTAGACGGTAATGCAAGTCTGGAGTGAAAGGCGGGGGCCCAACCCCCGGACTGCTCTGGAAACTGTGTAACTGGAGTGCAGGAGAGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\t39\t0\n+TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGACTGCAACTGACACTGATGCTCGAAAGTGTGGGTATCAAACAGG\t13\t25\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGCCAAGTCAGCGGTAAAAAAGCGGTGCTCAACGCCGTCGAGCCGTTGAAACTGGCGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAGG\t37\t0\n+TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGAGCGCGCAGGTGGTTAATTAAGTCTGATGTGAAAGCCCACGGCTTAACCGTGGAGGGTCATTGGAAACTGGTTGACTTGAGTGCAGAAGAGGGAAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGAGATATGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGTCTGCAACTGACACTGAGGCGCGAAAGCGTGGGGAGCAAACAGG\t11\t22\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGAGACAAGTCTGAAGTGAAAGCCCGGGGCTCAACCCCGGGACTGCTTTGGAAACTGCCTGACTGGAGTGCTGGAGAGGCAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTGCTGGACAGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\t13\t18\n+TACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGCGTAAAGCGAGTGCAGGCGGTTCAATAAGTCTGATGTGAAAGCCTTCGGCTCAACCGGAGAATTGCATCAGAAACTGTTGAACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTCTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGG\t0\t29\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCAGCGCAAGTCTGGAGTGAAATGCCGGGGCCCAACCCCGGAACTGCTTTGGAAACTGTGCAGCTCGAGTGCAGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\t10\t16\n+TACGTATGGAGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGCATGGCAAGTCAGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTTGAAACTGCCAGGCTAGAGTGTCGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACGATCACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\t16\t0\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCAGTGCAAGTCTGAAGTGAAAGGCGGGGGCCCAACCCCCGGACTGCTTTGGAAACTGTGCTGCTGGAGTGCAGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\t12\t0\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGGCGGCCATGCAAGTCAGAAGTGAAAACCCGGGGCTCAACCCTGGGAGTGCTTTTGAAACTGTGCGGCTAGAGTGTCGGAGGGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGATGACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\t11\t0\n+TACGTAGGTGGCGAGCGTTGTCCGGATTTACTGGGCGTAAAGG'..b'AGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCAGTGGCGAAGGCGATTCTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\t11\t0\n+TACGTATGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGGCGGCCTGGCAAGCCTGATGTGAAATACCGGGGCCCAACCCCGGGGCTGCATTGGGAACTGCCAGGCTGGAGTGCCGGAGAGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACGGTGACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\t0\t11\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTTTTGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTGGAAACTGTATGACTGGAGTGCAGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\t10\t0\n+TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTACGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGCCGGACTGGAGTGTCGGAGGGGTAAGCGGAATTCCTGGTGTAGCGGTGAAATGCGTAGATATCAGGAGGAACACCGGTGGCGAAGGCGGCTTACTGGACGATGACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\t10\t0\n+TACGTAGGGAGCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCTTTGCAAGTCAGAAGTGAAATCCATGGGCTTAACCCATGAACTGCTTTTGAAACTGCAGAGCTTGAGTGGAGTAGAGGTAGGCGGAATTCCCGGTGTAGCGGTGAAATGCGTAGAGATCGGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGGCTCTAACTGACGCTGAGGCACGAAAGCGTGGGTAGCAAACAGG\t8\t0\n+TACGTAGGGAGCGAGCGTTATCCGGAATTATTGGGCGTAAAGGGTGCGTAGATGGCATAGTAAGTCTTTTGTAAAAATGCTGGGCTCAACCCAGTAGGGCAAAAGATACTGCAAAGCTAGAGTATGACAGAGGCAAGTGGAACTACATGTGTAGCGGTAAAATGCGTAAATATATGTAAGAACACCAGTGGCGAAGGCGGCTTGCTGGGTCGATACTGACATTGAGGCACGAAAGCGTGGGGAGCAAACAGG\t8\t0\n+TACGTAGGTGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGTGTAGGCGGGGACGCAAGTCAGATGTGAAAACCACGGGCTCAACCTGTGGCCTGCATTTGAAACTGTGTTTCTTGAGTACTGGAGAGGCAGACGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGTCTGCTGGACAGCAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAGG\t7\t0\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGCGCCAAGTCTGGAGTGAAATGCCGCAGCTTAACTGCGGAACTGCTTTGGAAACTGGCGGACTAGAGTGCGGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCGGTGGCGAAGGCGGCTTACTGGACCGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\t7\t0\n+TACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGAGCGCAGGCGGTTGCTTAGGTCTGATGTGAAAGCCTTCGGCTTAACCGAAGAAGTGCATCGGAAACCGGGCGACTTGAGTGCAGAAGAGGACAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTGTCTGGTCTGCAACTGACGCTGAGGCTCGAAAGCATGGGTAGCGAACAGG\t7\t0\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCAATGCAAGCCAGATGTGAAAACCCGCAGCTCAACTGGGGGAGTGCATTTGGAACTGTGTAGCTGGAGTGCAGGAGAGGTAAGCGGAATTCCTGGTGTAGCGGTGAAATGCGTAGATATCAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\t7\t0\n+TACGTAGGGGGCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGAGTAGGCGGCAAGGTAAGCGATATGTGAAAGCCTTAGGCTTAACCAAAGGATTGCATAACGAACTATCTAGCTAGAGTACAGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGAAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCGAACAGG\t5\t0\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGACGGCAGTGCAAGTCTGGAGTGAAAGCCCGGGGCCCAACCCCGGAACTGCTCTGGAAACTGTGCGGCTAGAGTACTGGAGGGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACAGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACAGG\t5\t0\n+TACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGGAGTAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGTAGCAAACAGG\t4\t0\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCCAGACAAGTCTGAAGTGAAAATCCAGCGCTTAACGTTGGAAGTGCTTTGGAAACTGCCGGGCTAGAGTGCAGGAGGGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACTGCAACTGACGTTGAGGCTCGAAGGCGTGGGGAGCAAACAGG\t4\t0\n+TACGTAGGTGGCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGCGTGTAGCCGGGTTGACAAGTCAGATGTGAAATCCTGCGGCTTAACCGCAGAACTGCATTTGAAACTGTTGATCTTGAGTACTGGAGAGGCAGACGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGTCTGCTGGACAGCAACTGACGGTGAGGCGCGAAAGCGTGGGGAGCAAACAGG\t0\t4\n+TACGTAGGGAGCAAGCGTTGTTCGGAATGACTGGGCGTAAAGGGTGCGTAGGCGGTTGTACAAGTTAGAAGTGAAATACCCAGGGCTTAACTCGGGTGCTGCTTCTAAAACTGTATGACTTGAGTGCAGTAGAGGTTAGTGGAATTCCTAGTGTAGCGGTGGAATGCGTAGATATTAGGAGGAACACCAGAGGCGAAGGCGGCTAACTGGACTGCAACTGACGCTGAGGCACGAAAGTGTGGGGAGCAAACAGG\t0\t3\n'

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/makeSequenceTable_F3D0.pdf

Binary file test-data/makeSequenceTable_F3D0.pdf has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/makeSequenceTable_F3D0.tab
--- a/test-data/makeSequenceTable_F3D0.tab Thu Dec 05 17:59:57 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,8 +0,0 @@
- V1
-TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAGG 22
-TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGCCAAGTCAGCGGTAAAAAAGCGGTGCTCAACGCCGTCGAGCCGTTGAAACTGGCGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAGG 18
-TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTACGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGCCGGACTGGAGTGTCGGAGGGGTAAGCGGAATTCCTGGTGTAGCGGTGAAATGCGTAGATATCAGGAGGAACACCGGTGGCGAAGGCGGCTTACTGGACGATGACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 11
-TACGGAGGATTCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTCGATAAGTTAGAGGTGAAATCCCGGGGCTCAACTCCGGCACTGCCTCTGATACTGTCGGGCTAGAGTTTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCATAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTACGACTGACGTTGAGGCACGAAAGCGTGGGGAGCAAACAGG 5
-TACGTAGGTGGCGAGCGTTGTCCGGATTTACTGGGCGTAAAGGGAGCGTAGGCGGACTTTTAAGTGAGATGTGAAATACTCGGGCTCAACTTGAGTGCTGCATTTCAAACTGGAAGTCTAGAGTGCAGGAGAGGAGAATGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCAGTGGCGAAGGCGATTCTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACAGG 5
-TACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGGAGTAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGTAGCAAACAGG 3
-TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCCAGACAAGTCTGAAGTGAAAATCCAGCGCTTAACGTTGGAAGTGCTTTGGAAACTGCCGGGCTAGAGTGCAGGAGGGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACTGCAACTGACGTTGAGGCTCGAAGGCGTGGGGAGCAAACAGG 2

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/mergePairs_F3D0.Rdata

Binary file test-data/mergePairs_F3D0.Rdata has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/mergePairs_F3D0_S188_L001.Rdata

Binary file test-data/mergePairs_F3D0_S188_L001.Rdata has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/mergePairs_F3D0_S188_L001_nondefault.Rdata

Binary file test-data/mergePairs_F3D0_S188_L001_nondefault.Rdata has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/mergePairs_F3D0_nondefault.Rdata

Binary file test-data/mergePairs_F3D0_nondefault.Rdata has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/mergePairs_F3D141_S207_L001.Rdata

Binary file test-data/mergePairs_F3D141_S207_L001.Rdata has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/mergePairs_F3D141_S207_L001_nondefault.Rdata

Binary file test-data/mergePairs_F3D141_S207_L001_nondefault.Rdata has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/qualityProfile.pdf

Binary file test-data/qualityProfile.pdf has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/qualityProfile_fwd.pdf

Binary file test-data/qualityProfile_fwd.pdf has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/qualityProfile_rev.pdf

Binary file test-data/qualityProfile_rev.pdf has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/reference.fa
--- a/test-data/reference.fa Thu Dec 05 17:59:57 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,4 +0,0 @@
->A;B;C;D;E;
-ACCTAGAAAGTCGTAGATCGAAGTTGAAGCATCGCCCGATGATCGTCTGAAGCTGTAGCATGAGTCGATTTTCACATTCAGGGATACCATAGGATAC
->A;B;C;F;G;
-CGCTAGAAAGTCGTAGAAGGCTCGGAGGTTTGAAGCATCGCCCGATGGGATCTCGTTGCTGTAGCATGAGTACGGACATTCAGGGATCATAGGATAC

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/reference.fa.gz

Binary file test-data/reference.fa.gz has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/reference_species.fa
--- a/test-data/reference_species.fa Thu Dec 05 17:59:57 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,4 +0,0 @@
->IDA GenusA speciesA
-ACCTAGAAAGTCGTAGATCGAAGTTGAAGCATCGCCCGATGATCGTCTGAAGCTGTAGCATGAGTCGATTTTCACATTCAGGGATACCATAGGATAC
->IDB GenusB speciesB
-CGCTAGAAAGTCGTAGAAGGCTCGGAGGTTTGAAGCATCGCCCGATGGGATCTCGTTGCTGTAGCATGAGTACGGACATTCAGGGATCATAGGATAC

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/reference_species.fa.gz

Binary file test-data/reference_species.fa.gz has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/removeBimeraDenovo.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/removeBimeraDenovo.tab Mon Mar 16 07:37:41 2020 -0400

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/removeBimeraDenovo_F3D0.tab
--- a/test-data/removeBimeraDenovo_F3D0.tab Thu Dec 05 17:59:57 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/removeBimeraDenovo_F3D0_dada_uniques.tab
--- a/test-data/removeBimeraDenovo_F3D0_dada_uniques.tab Thu Dec 05 17:59:57 2019 -0500
+++ b/test-data/removeBimeraDenovo_F3D0_dada_uniques.tab Mon Mar 16 07:37:41 2020 -0400

b'@@ -1,18 +1,43 @@\n-TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAG\t22\n-TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGAAGATCAAGTCAGCGGTAAAATTGAGAGGCTCAACCTCTTCGAGCCGTTGAAACTGGTTTTCTTGAGTGAGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCTCAACTGACGCTCATGCACGAAAGTGTGGGTATCGAACAG\t20\n-TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGACTCTCAAGTCAGCGGTCAAATCGCGGGGCTCAACCCCGTTCCGCCGTTGAAACTGGGAGCCTTGAGTGCGCGAGAAGTAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCCTACCGGCGCGCAACTGACGCTCATGCACGAAAGCGTGGGTATCGAACAG\t16\n-TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGCCAAGTCAGCGGTAAAAAAGCGGTGCTCAACGCCGTCGAGCCGTTGAAACTGGCGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAG\t19\n-TACGGAGGATTCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTCGATAAGTTAGAGGTGAAATCCCGGGGCTCAACTCCGGCACTGCCTCTGATACTGTCGGGCTAGAGTTTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCATAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTACGACTGACGTTGAGGCACGAAAGCGTGGGGAGCAAACA\t5\n-TACGTAGGTGGCGAGCGTTGTCCGGATTTACTGGGCGTAAAGGGAGCGTAGGCGGACTTTTAAGTGAGATGTGAAATACTCGGGCTCAACTTGAGTGCTGCATTTCAAACTGGAAGTCTAGAGTGCAGGAGAGGAGAATGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCAGTGGCGAAGGCGATTCTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACA\t5\n-TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGCTGTTAAGTCAGCGGTCAAATGTCGGGGCTCAACCCCGGCCTGCCGTTGAAACTGGCGGCCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCGACTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAG\t17\n-TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCAGTGCAAGTCTGAAGTGAAAGGCGGGGGCCCAACCCCCGGACTGCTTTGGAAACTGTGCTGCTGGAGTGCAGGAGAGGCAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACA\t25\n-TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGCTTTTAAGTCAGCGGTAAAAATTCGGGGCTCAACCCCGTCCGGCCGTTGAAACTGGGGGCCTTGAGTGGGCGAGAAGAAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCCTTCCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCGAACAG\t9\n-TACGTAGGTGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGAGCGCGCAGGTGGTTAATTAAGTCTGATGTGAAAGCCCACGGCTTAACCGTGGAGGGTCATTGGAAACTGGTTGACTTGAGTGCAGAAGAGGGAAGTGGAATTCCATGTGTAGCGGTGAAATGCGTAGAGATATGGAGGAACACCAGTGGCGAAGGCGGCTTCCTGGTCTGCAACTGACACTGAGGCGCGAAAGCGTGGGGAGCAAACA\t4\n-TACGTAGGTGGCAAGCGTTGTCCGGATTTACTGGGTGTAAAGGGCGTGCAGCCGGGAAGACAAGTCAGATGTGAAATCCCGCGGCTCAACCGCGGAACTGCATTTGAAACTGTTTTTCTTGAGTACCGGAGAGGTCATCGGAATTCCTTGTGTAGCGGTGAAATGCGTAGATATAAGGAAGAACACCAGTGGCGAAGGCGGATGACTGGACGGCAACTGACGGTGAGGCGCGAAAGCGTGGGGAGCAAACA\t10\n-TACGTAGGTGGCAAGCGTTGTCCGGAATTACTGGGTGTAAAGGGAGCGTAGGCGGGAAGCCAAGTCAGCTGTGAAAACTACGGGCTTAACCTGTAGACTGCAGTTGAAACTGGCTTTCTTGAGTGAAGTAGAGGTTGGCGGAATTCCGAGTGTAGCGGTGAAATGCGTAGATATTCGGAGGAACACCGGTGGCGAAGGCGGCCAACTGGGCTTTAACTGACGCTGAGGCTCGAAAGTGTGGGGAGCAAACA\t2\n-TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGTCAAGTCAGCGGTAAAATTGTGGAGCTCAACTCCATCGAGCCGTTGAAACTGACGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAAGCACGAAAGCGTGGGTATCGAACAG\t9\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGAAGATCAAGTCAGCGGTAAAATTGAGAGGCTCAACCTCTTCGAGCCGTTGAAACTGGTTTTCTTGAGTGAGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCTCAACTGACGCTCATGCACGAAAGTGTGGGTATCGAACAG\t70\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGCTGTTAAGTCAGCGGTCAAATGTCGGGGCTCAACCCCGGCCTGCCGTTGAAACTGGCGGCCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCGACTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAG\t53\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCG'..b'GCTTAACCGGAGTAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGTAGCAAACA\t4\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGGATGCCAAGTCAGCGGTCAAATTTCGGGGCTCAACCCCGACCTGCCGTTGAAACTGGTGTCCTAGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCAACTGACGCTCATGCACGAAAGCGTGGGTATCGAACAG\t10\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGCGCCAAGTCTGGAGTGAAATGCCGCAGCTTAACTGCGGAACTGCTTTGGAAACTGGCGGACTAGAGTGCGGGAGGGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCGGTGGCGAAGGCGGCTTACTGGACCGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACA\t7\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTCCGTTAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTCGAGCCGTTGAAACTGGCAGACTTGAGTTGGCGAGAAGTACGCGGAATGCGCGGTGTAGCGGTGAAATGCATAGATATCGCGCAGAACTCCGATTGCGAAGGCAGCGTACCGGCGCCAGACTGACGCTGAGGCACGAAAGCGTGGGGATCGAACAG\t6\n+TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTACGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGCCGGACTGGAGTGTCGGAGGGGTAAGCGGAATTCCTGGTGTAGCGGTGAAATGCGTAGATATCAGGAGGAACACCGGTGGCGAAGGCGGCTTACTGGACGATGACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACA\t10\n+TACGTAGGGGGCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGAGTAGGCGGCAAGGTAAGCGATATGTGAAAGCCTTAGGCTTAACCAAAGGATTGCATAACGAACTATCTAGCTAGAGTACAGGAGAGGAAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAAGAACACCAGTGGCGAAGGCGGCTTTCTGGACTGAAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCGAACA\t5\n+TACGTAGGGGGCAAGCGTTATCCGGAATCACTGGGTGTAAAGGGAGCGTAGACGGCTGTGCAAGCCTGAAGTGAAAGGCGGGGGCCCAACCCCTGGACTGCTTTGGGAACTGTACGGCTGGAGTGCAGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACA\t6\n+TACGTAGGTGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGCGTGTAGGCGGGGACGCAAGTCAGATGTGAAAACCACGGGCTCAACCTGTGGCCTGCATTTGAAACTGTGTTTCTTGAGTACTGGAGAGGCAGACGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGTCTGCTGGACAGCAACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACA\t9\n TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGGGCGCAGACGGCCATGGCAAGCCCGGTGTGAAAGGCAGGGGCATAACCCCTGGACTGCACTGGGAACTGTCAGGCTGGAGTGCCGGAGGGGTAAGCGGAATTCCTGGTGTAGCGGTGAAATGCGTAGATATCAGGAGGAACACCGGCGGCGAAGGCGGCTTACTGGACGGCAACTGACGTTGAGGCCCGAAAGCGTGGGGAGCGAA\t2\n-TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGCAGGCGGTACGGCAAGTCTGATGTGAAAGCCCGGGGCTCAACCCCGGTACTGCATTGGAAACTGCCGGACTGGAGTGTCGGAGGGGTAAGCGGAATTCCTGGTGTAGCGGTGAAATGCGTAGATATCAGGAGGAACACCGGTGGCGAAGGCGGCTTACTGGACGATGACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACA\t15\n-TACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGGGAACGCAGGCGGTCTTTTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGGAGTAGTGCATTGGAAACTGGGAGACTTGAGTGCAGAAGAGGAGAGTGGAACTCCATGTGTAGCGGTGAAATGCGTAGATATATGGAAGAACACCAGTGGCGAAAGCGGCTCTCTGGTCTGTAACTGACGCTGAGGTTCGAAAGCGTGGGTAGCAAACA\t3\n-TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGCCAGACAAGTCTGAAGTGAAAATCCAGCGCTTAACGTTGGAAGTGCTTTGGAAACTGCCGGGCTAGAGTGCAGGAGGGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACTGCAACTGACGTTGAGGCTCGAAGGCGTGGGGAGCAAACA\t2\n-TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTTGTCAAGTCAGCGGTAAAAATTCCGGGCTCAACCCGGTCCCGCCGTTGAAACTGGCGAACTCGAGAGGGAGAGAAGTAGGCGGAATGCGCAGTGTAGCGGTGAAATGCATAGATATTGCGCAGAACTCCGATTGCGAAGGCAGCCTACCGGCTCCTGTCTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAG\t4\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGACAGTTAAGTCAGCGGTAAAATTGAGAGGCTCAACCTCTTCCCGCCGTTGAAACTGATTGTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCAACTGACGCTGAAGCACGAAAGCGTGGGTATCGAACAG\t5\n+TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCGACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAG\t23\n+TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGATAAGCAAGTCTGATGTGAAAATCCGGGGCCCAACCCCGGAATTGCATTGGAAACTGCATATCTAGAGTGTCGGAGAGGCAAGTGGAATTCCTGGTGTAGCGGTGAAATGCGTAGATATCAGGAGGAACACCAGTGGCGAAGGCGGCTTGCTGGACGATGACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACA\t2\n'

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/removeBimeraDenovo_F3D0_derep_uniques.tab
--- a/test-data/removeBimeraDenovo_F3D0_derep_uniques.tab Thu Dec 05 17:59:57 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

b'@@ -1,2304 +0,0 @@\n-TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGAAGATCAAGTCAGCGGTAAAATTGAGAGGCTCAACCTCTTCGAGCCGTTGAAACTGGTTTTCTTGAGTGAGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCTCAACTGACGCTCATGCACGAAAGTGTGGGTATCGAACAG\t451\n-TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAG\t373\n-TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGCTGTTAAGTCAGCGGTCAAATGTCGGGGCTCAACCCCGGCCTGCCGTTGAAACTGGCGGCCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCGACTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAG\t347\n-TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGCTTTTAAGTCAGCGGTAAAAATTCGGGGCTCAACCCCGTCCGGCCGTTGAAACTGGGGGCCTTGAGTGGGCGAGAAGAAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCCTTCCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCGAACAG\t327\n-TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGACTCTCAAGTCAGCGGTCAAATCGCGGGGCTCAACCCCGTTCCGCCGTTGAAACTGGGAGCCTTGAGTGCGCGAGAAGTAGGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCCTACCGGCGCGCAACTGACGCTCATGCACGAAAGCGTGGGTATCGAACAG\t273\n-TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGCCAAGTCAGCGGTAAAAAAGCGGTGCTCAACGCCGTCGAGCCGTTGAAACTGGCGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAG\t215\n-TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCGACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAG\t169\n-TACGGAGGATTCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTCGATAAGTTAGAGGTGAAATCCCGGGGCTCAACTCCGGCACTGCCTCTGATACTGTCGGGCTAGAGTTTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCATAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTACGACTGACGTTGAGGCACGAAAGCGTGGGGAGCAAACA\t127\n-TACGGAGGATCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGAGCGTAGGTGGATTGTTAAGTCAGTTGTGAAAGTTTGCGGCTCAACCGTAAAATTGCAGTTGAAACTGGCAGTCTTGAGTACAGTAGAGGTGGGCGGAATTCGTGGTGTAGCGGTGAAATGCTTAGATATCACGAAGAACTCCGATTGCGAAGGCAGCTCACTGGACTGCAACTGACACTGATGCTCGAAAGTGTGGGTATCAAACA\t115\n-TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGTCAAGTCAGCGGTAAAATTGTGGAGCTCAACTCCATCGAGCCGTTGAAACTGACGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAAGCACGAAAGCGTGGGTATCGAACAG\t113\n-TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGCCAAGTCAGCGGTAAAAATGCGGTGCTCAACGCCGTCGAGCCGTTGAAACTGGCGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAG\t80\n-TACGTAGGTGGCGAGCGTTGTCCGGATTTACTGGGCGTAAAGGGAGCGTAGGCGGACTTTTAAGTGAGATGTGAAATACTCGGGCTCAACTTGAGTGCTGCATTTCAAACTGGAAGTCTAGAGTGCAGGAGAGGAGAATGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCAGTGGCGAAGGCGATTCTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAACA\t78\n-TACGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGGATGCCAAGTCAGCGGTCAAATTTCGGGGCTCAACCCCGACCTGCCGTTGAAACTGGTGTCCTAGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCAACTGACGCTCATGCACGAAAGCGTGGGTATCGAACAG\t71\n-TACGTAGGGGGCAAGCGTTATCCGGAATTACTGGGTGTAAAGGGAGCGTAGACGGTAATGCAAGTCTGGAGTGAAAGGCGGGGGCCCAACCCCCGGACTGCTCTGGAAACTGTGTAACTGGAGTGCAGGAGAGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACTGTAACTGACGTTGAGGCTCGAAAGCGTGGGGAGCAAACA\t68\n-TACGTAGGGAGCGAGCGTTATCCGGAATTATTGGGCGTAAAGGGTGCGTAGATGGCATAGTAAGTCTTTTGTAAAAATGCTGGGCTCAACCCAGTAGGGCAAAAGATACTGCAAAGCTAGAGTATGACAGAGGCAAGTGGAACTACATGTGTAGCGGTAAAATGCGTAAATATATGTAAGAACACCAGTGGCGAAGGCGGCTTGCTGGGTCGATACTGACATTGAGGCACGAAAGCGTGGGGAGCAAACAG\t59\n-TACGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTGATGCAAGTCTGAAGTGAAAGGCGGGGGCTCAACCCCCGGACTGCTTTGGAAACTGTATGACTGGAGTGCAGG'..b'CGAGGCTCAACCACGGGAGTGCATTGGAAACTGGCGAGCTGGAGTGCCGGAGAGGTAAGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCTTACTGGACGGCAACTGACGCTGAGGCTCGCAAGCGTGGGGAGCCACCA\t1\n-TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGGTGGCAGGGCAAGTCAGATGTGAAAACCCGGGGCTCAACTCCGGGATTGCATTTGAAACTGTCCGGCTGGAGTGCAGGAGAGGTAAGTGGAATTCCTAGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCCTACCGGCGCGCAACTGACGCTCATGCACGAAAGCGTGGGTATCGAACA\t1\n-TACGTATGGTGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGTGCGTAGGCGGCCTTGCAAGTCAGAAGTGAAATCCATGGGCTTAACCCGGGTACTGCTTTTGAAACTGTAGGGCTTGAGGGAAGTAGAGGCAGCCGGAATTCCCGGGGTAGCGGGGAAATGCGAGGGGTTCGGGAGGACCACCAGTGGCGAAGGGGGCCTGCGGGGCGTTAACTGAGGCTGAGGAACGAAAGCGTGGGGAGCAAAAG\t1\n-TACGTATGGTGCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGAAGATCAAGTCAGCGGTAAAATTGAGAGGCTCAACCTCTTCGAGCCGTTGAAACTGGTTTTCTTGAGTGAGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCTCAACTGACGCTCATGCACGAAAGTGTGGGTATCGAACAG\t1\n-TAGGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGCTGTTAAGTCAGCGGTCAAATGTCGGGGCTCAACCCCGGCCTGCCGTTGAAACTGGCGGCCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCAACTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAG\t1\n-TAGGGAGGATTCAAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGTTCGATAAGTTAGAGGTGAAATCCCGGGGCTCAACTCCGGCACTGCCTCTGATACTGTCGGGCTAGAGTTTAGTTGCGGTAGGCGGAATGTATGGTGTAGCGGTGAAATGCATAGAGATCATACAGAACACCGATTGCGAAGGCAGCTTACCAAACTACGACTGACGTTGAGGCACGAAAGCGTGGGGAGCAAACA\t1\n-TATGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGAAGATCAAGTCAGCGGTAAAATTGAGAGGCTCAACCTCTTCGAGCCGTTGAAACTGGTTTTCTTGAGTGAGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCTCAACTGACGCTCATGCACGAAAGTGTGGGTATCGAACAG\t1\n-TATGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGGATGCCAAGTCAGCGGTAAAAATGCGGTGCTCAACGCCGTCGAGCCGTTGAAACTGGCGTTCTTGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGCGTGGGTATCGAACAG\t1\n-TATGTAGGGAGCGAGCGTTATCCGGAATTATTGGGCGTAAAGGGTGCGTAGATGGCATAGTAAGTCTTTTGTAAAAATGCTGGGCTCAACCCAGTAGGGCAAAAGATACTGCAAAGCTAGAGTATGACAGAGGCAAGTGGAACTACATGTGTAGCGGTAAAATGCGTAAATATATGTAAGAACACCAGTGGCGAAGGCGGCTTGCTGGGTCGATACTGACATTGAGGCACGAAAGCGTGGGGAGCAAACAG\t1\n-TATGTATGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGGCGGCAGGGCAAGCCTGATGTGAAAGCCCGGGGCTCAACCCCGGGACTGCATTGGGAACTGCCCCGCTCGAGTGCCGGAGGGGCAGGCGGAATTCCTAGTGTAGCGGTGAAATGCGTAGATATTAGGAGGAACACCAGTGGCGAAGGCGGCCTGCTGGACGGTGTACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAA\t1\n-TCCCGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCGACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAG\t1\n-TCCGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGAAGATCAAGTCAGCGGTAAAATTGAGAGGCTCAACCTCTTCGAGCCGTTGAAACTGGTTTTCTTGAGTGAGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCTCAACTGACGCTCATGCACGAAAGGGTGGGTATCGAACAG\t1\n-TCCTTCGCCCGCACGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGAAGATCAAGTCAGCGGTAAAATTGAGAGGCTCAACCTCTTCGAGCCGTTGAAACTGGTTTTCTTGAGTGAGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCTCAACTGACGCTCATGCACGAAAGTGTGGGTATCGAACAG\t1\n-TGCGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGGATGCCAAGTCAGCGGTCAAATTTCGGGGCTCAACCCCGACCTGCCGTTGAAACTGGGGTCCTAGAGTGGGCGAGAAGGATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACTCCGATTGCGAAGGCAGCATACCGGCGCCCAACTGACGCTCATGCACGAAAGCGGGGGTATCGAACAG\t1\n-TGCGGAGGATGCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGTAGGCGGCCTGCCAAGTCAGCGGTAAAATTGCGGGGCTCAACCCCGTACAGCCGTTGAAACTGCCGGGCTCGAGTGGGCGAGAAGTATGCGGAATGCGTGGTGTAGCGGTGAAATGCATAGATATCACGCAGAACCCCGATTGCGAAGGCAGCATACCGGCGCCCTACTGACGCTGAGGCACGAAAGTGCGGGGATCAAACAG\t1\n-TTCGTAGGGGGCAAGCGTTATCCGGATTTACTGGGTGTAAAGGGAGCGTAGACGGTTATGTAAGTCTGGAGTGAAAGCCCGGGGCCCAACCCCGGGACTGCTTTGGAAACTGTGTAACTGGAGTACAGGAGGGGCAGGCGGAATTCCTGGTGTAGCGGTGAAATGCGTAGATATCAGGAGGAACACCGGCGGCGAAGGCGGCCTGCTGGACTGAAACTGACGTTGAGGCTCGAAAGCGTGGGGGGCAACCG\t1\n'

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/removeBimeraDenovo_F3D0_mergepairs.Rdata

Binary file test-data/removeBimeraDenovo_F3D0_mergepairs.Rdata has changed

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/seqCounts_F3D0_dadaF.tab
--- a/test-data/seqCounts_F3D0_dadaF.tab Thu Dec 05 17:59:57 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,2 +0,0 @@
-samples dadaF
-dada_F3D0_R1.Rdata 189

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/seqCounts_F3D0_filter.tab
--- a/test-data/seqCounts_F3D0_filter.tab Thu Dec 05 17:59:57 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,2 +0,0 @@
-samples filter reads.in filter reads.out
-filterAndTrim_F3D0.tab 250 249

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/seqCounts_F3D0_merge.tab
--- a/test-data/seqCounts_F3D0_merge.tab Thu Dec 05 17:59:57 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,2 +0,0 @@
-samples merge
-mergePairs_F3D0.Rdata 66

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/seqCounts_F3D0_nochim.tab
--- a/test-data/seqCounts_F3D0_nochim.tab Thu Dec 05 17:59:57 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,2 +0,0 @@
-samples nochim
-V1 66

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/seqCounts_F3D0_seqtab.tab
--- a/test-data/seqCounts_F3D0_seqtab.tab Thu Dec 05 17:59:57 2019 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

@@ -1,2 +0,0 @@
-samples seqtab
-V1 66

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/seqCounts_dadaF.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/seqCounts_dadaF.tab Mon Mar 16 07:37:41 2020 -0400

@@ -0,0 +1,3 @@
+samples dadaF
+dada_F3D0_S188_L001_R1.Rdata 671
+dada_F3D141_S207_L001_R1.Rdata 670

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/seqCounts_filter.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/seqCounts_filter.tab Mon Mar 16 07:37:41 2020 -0400

@@ -0,0 +1,2 @@
+samples filter reads.in filter reads.out
+F3D0_S188_L001_R1_001.tab 750 745

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/seqCounts_filter_both.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/seqCounts_filter_both.tab Mon Mar 16 07:37:41 2020 -0400

@@ -0,0 +1,3 @@
+samples filter reads.in filter reads.out
+F3D0_S188_L001_R1_001.tab 750 745
+F3D141_S207_L001_R1_001.tab 750 744

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/seqCounts_merge.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/seqCounts_merge.tab Mon Mar 16 07:37:41 2020 -0400

@@ -0,0 +1,3 @@
+samples merge
+mergePairs_F3D0_S188_L001.Rdata 409
+mergePairs_F3D141_S207_L001.Rdata 365

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/seqCounts_nochim.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/seqCounts_nochim.tab Mon Mar 16 07:37:41 2020 -0400

@@ -0,0 +1,3 @@
+samples nochim
+F3D0_S188_L001 409
+F3D141_S207_L001 365

diff -r 7f8f0e9fcb37 -r 5b752525bd6f test-data/seqCounts_seqtab.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/seqCounts_seqtab.tab Mon Mar 16 07:37:41 2020 -0400

@@ -0,0 +1,3 @@
+samples seqtab
+F3D0_S188_L001 409
+F3D141_S207_L001 365