# HG changeset patch
# User iuc
# Date 1479747575 18000
# Node ID d4128a4e49ca3255133daeaacdcf45d5653f7dea

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c

diff -r 000000000000 -r d4128a4e49ca README.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,18 @@
+Trinity memory usage
+====================
+
+As described on the official Trinity website
+`FAQ <http://trinityrnaseq.sourceforge.net/trinity_faq.html#ques_comp_resources_required>`_,
+trinity requires a large amount of memory to perform the assembly: "roughly
+~1G of RAM per 1M reads to be assembled"
+
+By default, this tool is configured to limit the memory consumption to 30G.
+You might need to lower this limit if the machine(s) executing the jobs have less memory available.
+If you have a lot of reads to assemble and a machine with enough memory, you can increase it.
+In both cases, you can edit the TRINITY_MEM_OPTIONS in the file:
+
+<tool_dependency_dir>/environment_settings/TRINITY_MEM_OPTIONS/iuc/trinity/<hash_string>/env.sh
+
+to lower the maximum memory usage to 2G for example:
+
+TRINITY_MEM_OPTIONS='--max_memory 2G --bflyHeapSpaceMax 2G'
diff -r 000000000000 -r d4128a4e49ca analyze_diff_expr.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/analyze_diff_expr.xml	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,179 @@
+<tool id="trinity_analyze_diff_expr" name="Extract and cluster differentially expressed transcripts" version="@WRAPPER_VERSION@.0">
+    <description>from a Trinity assembly</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+        <requirement type="package" version="2.30.0">bioconductor-biobase</requirement>
+        <requirement type="package" version="2.2.2">bioconductor-qvalue</requirement>
+        <requirement type="package" version="1.22.0">bioconductor-goseq</requirement>
+        <requirement type="package" version="3.3.0">bioconductor-go.db</requirement>
+    </expand>
+    <expand macro="stdio"/>
+    <command><![CDATA[
+    ## DE results input files must be in the working directory and have suffix .DE_results
+    #import re
+    #for $input in $DE_results
+        ln -s "${input}" "${re.sub('[^\w\-_.]', '_', input.element_identifier)}.DE_results"
+        &&
+    #end for
+
+    analyze_diff_expr.pl
+        --matrix "${matrix}"
+        --samples "${samples}"
+        -P ${p}
+        -C ${c}
+
+        #if str( $additional_params.max_DE_genes_per_comparison ):
+            --max_DE_genes_per_comparison ${additional_params.max_DE_genes_per_comparison}
+        #end if
+
+        $additional_params.order_columns_by_samples_file
+
+        #if $additional_params.max_genes_clust:
+            --max_genes_clust ${additional_params.max_genes_clust}
+        #end if
+
+        #if str( $additional_params.GO_enrichment.examine_GO_enrichment ) == "yes":
+            --examine_GO_enrichment
+            --GO_annots "${$additional_params.GO_enrichment.GO_annots}"
+            --gene_lengths "${$additional_params.GO_enrichment.gene_lengths}"
+        #end if
+
+        --output results
+    ]]></command>
+    <inputs>
+        <param format="tabular" name="matrix" argument="--matrix" type="data" label="Expression matrix" help="Raw counts matrix produced by 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity' tool"/>
+        <param format="tabular" name="samples" argument="--samples" type="data" label="Sample description" help="File describing samples and replicates"/>
+        <param format="tabular" name="DE_results" type="data_collection" collection_type="list" label="Differential expression results"/>
+        <param name="p" type="float" argument="-P" value="0.001" label="p-value cutoff for FDR"/>
+        <param name="c" type="float" argument="-C" value="2" label="min abs(log2(a/b)) fold change" help="Default: 2 (meaning 2^(2) or 4-fold"/>
+        <section name="additional_params" title="Additional Options" expanded="False">
+            <param name="max_DE_genes_per_comparison" argument="--max_DE_genes_per_comparison" type="integer" value="" optional="true" label="Maximum differential expression genes per comparison" help="Extract only up to the top number of DE features within each pairwise comparison. This is useful when you have massive numbers of DE features but still want to make useful heatmaps and other plots with more manageable numbers of data points."/>
+            <param name="order_columns_by_samples_file" argument="--order_columns_by_samples_file" type="boolean" checked="false" truevalue="--order_columns_by_samples_file" falsevalue="" label="Order columns by samples file" help="Instead of clustering samples or replicates hierarchically based on gene expression patterns, order columns according to order in the --samples file."/>
+            <param name="max_genes_clust" argument="--max_genes_clust" type="integer" value="10000" label="Maximum genes in cluster" help="If more than 10000, heatmaps are not generated, since too time consuming"/>
+            <conditional name="GO_enrichment">
+                <param type="select" name="examine_GO_enrichment" argument="--examine_GO_enrichment" label="Run GO enrichment analysis" help="To examine GO enrichment, you must first run Trinotate and then extract all GO assignments for each gene feature, with the Trinotate script extract_GO_assignments_from_Trinotate_xls.pl">
+                    <option value="no">No</option>
+                    <option value="yes">Yes</option>
+                </param>
+                <when value="no">
+                </when>
+                <when value="yes">
+                    <param format="tabular" name="GO_annots" argument="--GO_annots" type="data" label="Extracted GO assignments file" help="Generated by the Trinotate script extract_GO_assignments_from_Trinotate_xls.pl. Must have 2 columns: feature_id GO:000001,GO:00002,..."/>
+                    <param format="tabular" name="gene_lengths" argument="--gene_lengths" type="data" label="Gene length file" help="Must have 2 columns: feature_id length"/>
+                </when>
+        </conditional> 
+        </section>
+    </inputs>
+    <outputs>
+        <collection name="extracted_DE_genes" type="list" label="${tool.name} on ${on_string}: extracted differentially expressed genes">
+            <discover_datasets pattern="(?P&lt;name&gt;.+)\.subset$" ext="tabular" />
+        </collection>
+        <collection name="summary_files" type="list" label="${tool.name} on ${on_string}: summary files">
+            <data format="tabular" name="results_matrix" from_work_dir="results.matrix"/>
+            <data format="tabular" name="results_matrix_log2_centered" from_work_dir="results.matrix.log2.centered.dat"/>
+            <data format="pdf" name="results_matrix_log2_centered_heatmap" from_work_dir="results.matrix.log2.centered.genes_vs_samples_heatmap.pdf"/>
+            <data format="tabular" name="results_matrix_log2" from_work_dir="results.matrix.log2.dat"/>
+            <data format="tabular" name="results_matrix_log2_sample_cor" from_work_dir="results.matrix.log2.sample_cor.dat"/>
+            <data format="pdf" name="results_matrix_log2_sample_cor_matrix" from_work_dir="results.matrix.log2.sample_cor_matrix.pdf"/>
+        </collection>
+        <data format="RData" name="rdata" label="${tool.name} on ${on_string}: RData file" from_work_dir="results.matrix.RData"/>
+        <collection name="GOseq_enrichment" type="list" label="${tool.name} on ${on_string}: GOseq enriched and depleted categories">
+            <discover_datasets pattern="(?P&lt;name&gt;.+\.subset\.GOseq\.(enriched|depleted))$" ext="tabular" />
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
+            <param name="samples" value="count/samples.txt"/>
+            <param name="DE_results">
+                <collection type="list">
+                    <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2" value="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results" ftype="tabular" />
+                    <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2" value="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results" ftype="tabular" />
+                    <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2" value="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results" ftype="tabular" />
+              </collection>
+            </param>
+            <output_collection name="extracted_DE_genes">
+                <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.0.wt_37-UP" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset"/>
+                <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.0.wt_GSNO-UP" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset"/>
+                <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.wt_37-UP" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset"/>
+                <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.wt_ph8-UP" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset"/>
+                <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.wt_GSNO-UP" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset"/>
+                <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.wt_ph8-UP" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset"/>
+            </output_collection>
+            <output_collection name="summary_files">
+                <element name="results_matrix" compare="sim_size" file="count/analyze_diff_expr/results.matrix"/>
+                <element name="results_matrix_log2_centered" compare="sim_size" file="count/analyze_diff_expr/results.matrix.log2.centered.dat"/>
+                <element name="results_matrix_log2_centered_heatmap" delta="100" compare="sim_size" file="count/analyze_diff_expr/results.matrix.log2.centered.genes_vs_samples_heatmap.pdf"/>
+                <element name="results_matrix_log2" compare="sim_size" file="count/analyze_diff_expr/results.matrix.log2.dat"/>
+                <element name="results_matrix_log2_sample_cor" compare="sim_size" file="count/analyze_diff_expr/results.matrix.log2.sample_cor.dat"/>
+                <element name="results_matrix_log2_sample_cor_matrix" delta="100" compare="sim_size" file="count/analyze_diff_expr/results.matrix.log2.sample_cor_matrix.pdf"/>
+            </output_collection>
+            <output name="rdata" compare="sim_size" file="count/analyze_diff_expr/results.matrix.RData"/>
+        </test>
+        <test>
+            <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
+            <param name="samples" value="count/samples.txt"/>
+            <param name="DE_results">
+                <collection type="list">
+                    <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2" value="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results" ftype="tabular" />
+                    <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2" value="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results" ftype="tabular" />
+                    <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2" value="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results" ftype="tabular" />
+                </collection>
+            </param>
+            <section name="additional_params">
+                <conditional name="GO_enrichment">
+                    <param name="examine_GO_enrichment" value="yes"/>
+                    <param name="GO_annots" value="count/trinotate/go_annotations.txt"/>
+                    <param name="gene_lengths" value="count/trinotate/genes.lengths.txt"/>
+                </conditional>
+            </section>
+            <assert_command>
+                <has_text text="--examine_GO_enrichment" />
+                <has_text text="--GO_annots" />
+                <has_text text="--gene_lengths" />
+            </assert_command>
+            <output_collection name="GOseq_enrichment">
+                <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.wt_37-UP.subset.GOseq.enriched" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.enriched"/>
+            </output_collection>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
+This tool extracts the transcripts that are most differentially expressed (most significant FDR and fold-changes), once differential expression analyses have been runned. 
+
+**Inputs**
+
+This tool uses the raw counts matrix produced by 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity' tool.
+
+You must describe your samples and replicates with a tabular file looking like this:
+
+=========== ================
+ConditionA  CondA_replicate1
+----------- ----------------
+ConditionA  CondA_replicate2
+----------- ----------------
+ConditionB  CondB_replicate1
+----------- ----------------
+ConditionB  CondB_replicate2
+----------- ----------------
+ConditionC  CondC_replicate1
+----------- ----------------
+ConditionC  CondC_replicate2
+----------- ----------------
+ConditionC  CondC_replicate3
+=========== ================
+
+This file can be generated with the 'Describe samples and replicates' tool.
+It will probably be the same file as used in the tool 'RNASeq samples quality check for transcript quantification' or in the tool 'Differential expression analysis'.
+The names in column 2 must match the names given in the tool 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity'.
+
+You must also provide as a data collection the files resulting from the differential expression analysis (outputs of tool 'Differential expression analysis').
+
+.. _Trinity: http://trinityrnaseq.github.io
+]]>
+    </help>
+    <expand macro="citation" />
+</tool>
diff -r 000000000000 -r d4128a4e49ca macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,23 @@
+<?xml version="1.0"?>
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="2.2.0">trinity</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+
+    <token name="@WRAPPER_VERSION@">2.2.0</token>
+
+    <xml name="stdio">
+        <stdio>
+            <exit_code range="1:" level="fatal" description="Error in Trinity execution" />
+        </stdio>
+    </xml>
+
+    <xml name="citation">
+        <citations>
+            <citation type="doi">10.1038/nbt.1883</citation>
+        </citations>
+    </xml>
+</macros>
diff -r 000000000000 -r d4128a4e49ca test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,7 @@
+id	baseMeanA	baseMeanB	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj	wt_37_2	wt_37_3	wt_37_1	wt_GSNO_3	wt_GSNO_1	wt_GSNO_2	wt_ph8_3	wt_ph8_1	wt_ph8_2
+TR4277|c0_g1_i1	3852.97388871986	161.116814813422	2007.04535176664	-4.57259674791206	0.121601866332754	-37.6030145409076	0	0	4466.00	4701.00	4284.00	118.00	134.00	164.00	172.00	162.00	170.00
+TR4761|c0_g1_i1	1645.20640957447	193.196157329029	919.201283451752	-3.08847487551254	0.143642016580712	-21.5011940728159	1.51733402752078e-102	1.66906743027286e-101	2089.00	1746.00	1875.00	155.00	174.00	165.00	394.00	389.00	406.00
+TR2107|c1_g1_i1	48.9228907410258	7.40521775805688	28.1640542495414	-2.6949883047084	0.431525668867458	-6.24525607429428	4.23106352657394e-10	1.55138995974378e-09	59.00	65.00	47.00	6.00	6.00	7.00	3.00	1.00	2.00
+TR2672|c0_g1_i1	18.3155337236093	2.26581902751323	10.2906763755613	-2.88818323474529	0.724350842979802	-3.98727117216294	6.68376171815065e-05	0.000157545811927837	14.00	29.00	22.00	0.00	4.00	2.00	14.00	4.00	7.00
+TR127|c1_g1_i1	13.461799216177	1.21881296083961	7.34030608850831	-3.33218181130749	0.914685635912973	-3.64298036448506	0.000269499403689035	0.000576210779000196	9.00	23.00	16.00	2.00	0.00	1.00	3.00	1.00	1.00
+TR5055|c0_g2_i1	23.3590211688541	5.52768338415684	14.4433522765055	-2.04478780320925	0.562727305023446	-3.63370994255211	0.00027937492315161	0.000576210779000196	36.00	17.00	27.00	4.00	7.00	3.00	4.00	4.00	11.00
diff -r 000000000000 -r d4128a4e49ca test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.depleted
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.depleted	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,1 @@
+category	over_represented_pvalue	under_represented_pvalue	numDEInCat	numInCat	term	ontology	over_represented_FDR	under_represented_FDR
diff -r 000000000000 -r d4128a4e49ca test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.enriched
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.enriched	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,1 @@
+category	over_represented_pvalue	under_represented_pvalue	numDEInCat	numInCat	term	ontology	over_represented_FDR
diff -r 000000000000 -r d4128a4e49ca test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,4 @@
+id	baseMeanA	baseMeanB	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj	wt_37_2	wt_37_3	wt_37_1	wt_GSNO_3	wt_GSNO_1	wt_GSNO_2	wt_ph8_3	wt_ph8_1	wt_ph8_2
+TR131|c0_g1_i1	26.1866396538608	1340.30918254958	683.247911101723	5.67372481552909	0.187406695960058	30.274931140872	2.45144211418965e-201	4.04487948841292e-200	32.00	28.00	31.00	1001.00	1233.00	1208.00	1486.00	1492.00	1457.00
+TR3091|c0_g1_i1	16.7444693227929	328.569936894811	172.657203108802	4.29039998257063	0.240421038467916	17.8453599980735	3.14072644239509e-71	2.59109931497595e-70	22.00	17.00	19.00	250.00	308.00	284.00	333.00	343.00	316.00
+TR3788|c0_g1_i1	19.5075441237117	134.95369713876	77.2306206312357	2.77038513264018	0.262760026053246	10.5434040871909	5.44900939296595e-26	2.56881871382681e-25	17.00	30.00	22.00	91.00	132.00	125.00	32.00	22.00	27.00
diff -r 000000000000 -r d4128a4e49ca test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset.GOseq.depleted
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset.GOseq.depleted	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,1 @@
+category	over_represented_pvalue	under_represented_pvalue	numDEInCat	numInCat	term	ontology	over_represented_FDR	under_represented_FDR
diff -r 000000000000 -r d4128a4e49ca test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset.GOseq.enriched
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset.GOseq.enriched	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,1 @@
+category	over_represented_pvalue	under_represented_pvalue	numDEInCat	numInCat	term	ontology	over_represented_FDR
diff -r 000000000000 -r d4128a4e49ca test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,7 @@
+id	baseMeanA	baseMeanB	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj	wt_37_2	wt_37_3	wt_37_1	wt_GSNO_3	wt_GSNO_1	wt_GSNO_2	wt_ph8_3	wt_ph8_1	wt_ph8_2
+TR4277|c0_g1_i1	4705.34614971641	162.902721493704	2434.12443560506	-4.84860951090545	0.124597307945428	-38.9142397284305	0	0	4466.00	4701.00	4284.00	118.00	134.00	164.00	172.00	162.00	170.00
+TR4761|c0_g1_i1	2012.6141923276	384.620292965437	1198.61724264652	-2.38450946693381	0.143863830576436	-16.5747669680385	1.06073316501088e-61	1.34359534234711e-60	2089.00	1746.00	1875.00	155.00	174.00	165.00	394.00	389.00	406.00
+TR2107|c1_g1_i1	59.5986596731862	1.89840873462066	30.7485342039034	-4.81058600791914	0.641850436461167	-7.49487066557473	6.63637683134955e-14	2.29256654173894e-13	59.00	65.00	47.00	6.00	6.00	7.00	3.00	1.00	2.00
+TR127|c1_g1_i1	16.3791628279609	1.58772512712498	8.98344397754296	-3.19771077466237	0.834376974262452	-3.83245328346816	0.00012687169720824	0.000267840249661839	9.00	23.00	16.00	2.00	0.00	1.00	3.00	1.00	1.00
+TR1894|c2_g1_i1	16.2826445742552	1.67571344127509	8.97917900776516	-3.15659686337855	0.834779400611257	-3.7813545244015	0.00015597736029041	0.000307529893573321	21.00	14.00	11.00	1.00	2.00	5.00	1.00	3.00	1.00
+TR5055|c0_g2_i1	28.6665933385886	6.05959103586122	17.3630921872249	-2.17768048931004	0.577307428800381	-3.77213314894485	0.000161857838722801	0.000307529893573321	36.00	17.00	27.00	4.00	7.00	3.00	4.00	4.00	11.00
diff -r 000000000000 -r d4128a4e49ca test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.depleted
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.depleted	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,1 @@
+category	over_represented_pvalue	under_represented_pvalue	numDEInCat	numInCat	term	ontology	over_represented_FDR	under_represented_FDR
diff -r 000000000000 -r d4128a4e49ca test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.enriched
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.enriched	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,2 @@
+category	over_represented_pvalue	under_represented_pvalue	numDEInCat	numInCat	term	ontology	over_represented_FDR	go_term
+GO:0008270	0.0469428206943769	0.996332779511344	3	6	zinc ion binding	MF	0.790651800018629	MF zinc ion binding
diff -r 000000000000 -r d4128a4e49ca test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,5 @@
+id	baseMeanA	baseMeanB	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj	wt_37_2	wt_37_3	wt_37_1	wt_GSNO_3	wt_GSNO_1	wt_GSNO_2	wt_ph8_3	wt_ph8_1	wt_ph8_2
+TR131|c0_g1_i1	32.0461070493257	1436.30905989883	734.177583474076	5.48367743370229	0.196017912869615	27.9753893581648	3.23827538807456e-172	6.15272323734167e-171	32.00	28.00	31.00	1001.00	1233.00	1208.00	1486.00	1492.00	1457.00
+TR3091|c0_g1_i1	20.4914097091341	321.651020117047	171.071214913091	3.96886910507283	0.256323110469072	15.4838519937191	4.45952081812589e-54	4.2365447772196e-53	22.00	17.00	19.00	250.00	308.00	284.00	333.00	343.00	316.00
+TR2779|c0_g1_i1	191.51955185349	1058.15934185376	624.839446853626	2.46616535412611	0.177102083131526	13.9251064161374	4.4587691300744e-44	3.38866453885655e-43	186.00	137.00	217.00	147.00	186.00	197.00	1088.00	1094.00	1086.00
+TR5075|c0_g1_i1	19.3833722195684	136.98672801182	78.1850501156942	2.80049241151413	0.293976352213923	9.52625063350759	1.63066468983638e-21	8.85217974482605e-21	13.00	22.00	21.00	6.00	8.00	10.00	163.00	121.00	142.00
diff -r 000000000000 -r d4128a4e49ca test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset.GOseq.depleted
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset.GOseq.depleted	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,1 @@
+category	over_represented_pvalue	under_represented_pvalue	numDEInCat	numInCat	term	ontology	over_represented_FDR	under_represented_FDR
diff -r 000000000000 -r d4128a4e49ca test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset.GOseq.enriched
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset.GOseq.enriched	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,1 @@
+category	over_represented_pvalue	under_represented_pvalue	numDEInCat	numInCat	term	ontology	over_represented_FDR
diff -r 000000000000 -r d4128a4e49ca test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,1 @@
+id	baseMeanA	baseMeanB	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj	wt_37_2	wt_37_3	wt_37_1	wt_GSNO_3	wt_GSNO_1	wt_GSNO_2	wt_ph8_3	wt_ph8_1	wt_ph8_2
diff -r 000000000000 -r d4128a4e49ca test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,3 @@
+id	baseMeanA	baseMeanB	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj	wt_37_2	wt_37_3	wt_37_1	wt_GSNO_3	wt_GSNO_1	wt_GSNO_2	wt_ph8_3	wt_ph8_1	wt_ph8_2
+TR2779|c0_g1_i1	195.849684476753	966.924129135581	581.386906806167	2.25621220756415	0.156114979193812	14.4522467940961	2.42639762934434e-47	5.82335431042642e-46	186.00	137.00	217.00	147.00	186.00	197.00	1088.00	1094.00	1086.00
+TR24|c0_g1_i1	39.3724575919554	183.288101009647	111.330279300801	2.11680322693425	0.240338854880295	8.80757806717753	1.27878744153922e-18	7.67272464923531e-18	90.00	67.00	85.00	36.00	35.00	34.00	222.00	196.00	201.00
diff -r 000000000000 -r d4128a4e49ca test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset.GOseq.depleted
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset.GOseq.depleted	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,1 @@
+category	over_represented_pvalue	under_represented_pvalue	numDEInCat	numInCat	term	ontology	over_represented_FDR	under_represented_FDR
diff -r 000000000000 -r d4128a4e49ca test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset.GOseq.enriched
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset.GOseq.enriched	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,1 @@
+category	over_represented_pvalue	under_represented_pvalue	numDEInCat	numInCat	term	ontology	over_represented_FDR
diff -r 000000000000 -r d4128a4e49ca test-data/count/analyze_diff_expr/results.matrix
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/results.matrix	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,14 @@
+	wt_37_2	wt_37_3	wt_37_1	wt_GSNO_3	wt_GSNO_1	wt_GSNO_2	wt_ph8_3	wt_ph8_1	wt_ph8_2
+TR24|c0_g1_i1	90.00	67.00	85.00	36.00	35.00	34.00	222.00	196.00	201.00
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+TR2779|c0_g1_i1	186.00	137.00	217.00	147.00	186.00	197.00	1088.00	1094.00	1086.00
+TR2672|c0_g1_i1	14.00	29.00	22.00	0.00	4.00	2.00	14.00	4.00	7.00
+TR127|c1_g1_i1	9.00	23.00	16.00	2.00	0.00	1.00	3.00	1.00	1.00
+TR2107|c1_g1_i1	59.00	65.00	47.00	6.00	6.00	7.00	3.00	1.00	2.00
+TR5055|c0_g2_i1	36.00	17.00	27.00	4.00	7.00	3.00	4.00	4.00	11.00
+TR3091|c0_g1_i1	22.00	17.00	19.00	250.00	308.00	284.00	333.00	343.00	316.00
+TR4761|c0_g1_i1	2089.00	1746.00	1875.00	155.00	174.00	165.00	394.00	389.00	406.00
+TR131|c0_g1_i1	32.00	28.00	31.00	1001.00	1233.00	1208.00	1486.00	1492.00	1457.00
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+TR1894|c2_g1_i1	21.00	14.00	11.00	1.00	2.00	5.00	1.00	3.00	1.00
+TR3788|c0_g1_i1	17.00	30.00	22.00	91.00	132.00	125.00	32.00	22.00	27.00
diff -r 000000000000 -r d4128a4e49ca test-data/count/analyze_diff_expr/results.matrix.RData
Binary file test-data/count/analyze_diff_expr/results.matrix.RData has changed
diff -r 000000000000 -r d4128a4e49ca test-data/count/analyze_diff_expr/results.matrix.log2.centered.dat
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/results.matrix.log2.centered.dat	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,14 @@
+wt_37_2	wt_37_3	wt_37_1	wt_GSNO_3	wt_GSNO_1	wt_GSNO_2	wt_ph8_3	wt_ph8_1	wt_ph8_2
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diff -r 000000000000 -r d4128a4e49ca test-data/count/analyze_diff_expr/results.matrix.log2.centered.genes_vs_samples_heatmap.pdf
Binary file test-data/count/analyze_diff_expr/results.matrix.log2.centered.genes_vs_samples_heatmap.pdf has changed
diff -r 000000000000 -r d4128a4e49ca test-data/count/analyze_diff_expr/results.matrix.log2.dat
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/results.matrix.log2.dat	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,14 @@
+wt_37_2	wt_37_3	wt_37_1	wt_GSNO_3	wt_GSNO_1	wt_GSNO_2	wt_ph8_3	wt_ph8_1	wt_ph8_2
+TR24|c0_g1_i1	6.5077946401987	6.08746284125034	6.4262647547021	5.20945336562895	5.16992500144231	5.12928301694497	7.8008998999203	7.62205181945638	7.65821148275179
+TR4277|c0_g1_i1	12.1250905393033	12.199058823653	12.0650794889999	6.89481776330794	7.07681559705083	7.36632221424582	7.43462822763672	7.34872815423108	7.4178525148859
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diff -r 000000000000 -r d4128a4e49ca test-data/count/analyze_diff_expr/results.matrix.log2.sample_cor.dat
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/results.matrix.log2.sample_cor.dat	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,10 @@
+wt_37_2	wt_37_3	wt_37_1	wt_GSNO_3	wt_GSNO_1	wt_GSNO_2	wt_ph8_3	wt_ph8_1	wt_ph8_2
+wt_37_2	1	0.968650822800566	0.985499030254524	0.457364683078012	0.443497697874748	0.451451348748615	0.41961787977306	0.444203836374748	0.448348619980356
+wt_37_3	0.968650822800566	1	0.98879028662025	0.400031307625771	0.378330685571456	0.396636302989378	0.39057945325073	0.383299487197462	0.388022080096891
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+wt_GSNO_3	0.457364683078012	0.400031307625771	0.452638132682111	1	0.965144031362199	0.979742518682039	0.844139129634192	0.862862111399854	0.857171072391268
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+wt_ph8_3	0.41961787977306	0.39057945325073	0.461437515072935	0.844139129634192	0.858668155107621	0.854388461031158	1	0.984071267766826	0.98764423106737
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diff -r 000000000000 -r d4128a4e49ca test-data/count/analyze_diff_expr/results.matrix.log2.sample_cor_matrix.pdf
Binary file test-data/count/analyze_diff_expr/results.matrix.log2.sample_cor_matrix.pdf has changed
diff -r 000000000000 -r d4128a4e49ca test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,39 @@
+id	baseMeanA	baseMeanB	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj
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diff -r 000000000000 -r d4128a4e49ca test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano.pdf
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano.pdf has changed
diff -r 000000000000 -r d4128a4e49ca test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,39 @@
+logFC	logCPM	PValue	FDR
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diff -r 000000000000 -r d4128a4e49ca test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.MA_n_Volcano.pdf
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.MA_n_Volcano.pdf has changed
diff -r 000000000000 -r d4128a4e49ca test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,39 @@
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+TR1982|c2_g1_i1	0.132112224684827	9.08491674138301	0.763974995328257	0.806418050624271
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diff -r 000000000000 -r d4128a4e49ca test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results.MA_n_Volcano.pdf
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results.MA_n_Volcano.pdf has changed
diff -r 000000000000 -r d4128a4e49ca test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,39 @@
+id	baseMeanA	baseMeanB	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj
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+TR4761|c0_g1_i1	2012.6141923276	384.620292965437	1198.61724264652	-2.38450946693381	0.143863830576436	-16.5747669680385	1.06073316501088e-61	1.34359534234711e-60
+TR3091|c0_g1_i1	20.4914097091341	321.651020117047	171.071214913091	3.96886910507283	0.256323110469072	15.4838519937191	4.45952081812589e-54	4.2365447772196e-53
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+TR1894|c2_g1_i1	16.2826445742552	1.67571344127509	8.97917900776516	-3.15659686337855	0.834779400611257	-3.7813545244015	0.00015597736029041	0.000307529893573321
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+TR1859|c3_g1_i1	0.361569353912422	2.25550826604853	1.30853880998047	2.09887277242766	1.59427549709957	1.31650569568817	0.188004367989136	0.255148785128113
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+TR2011|c5_g1_i1	6.84875389533898	4.81927837273561	5.8340161340373	-0.467994718304978	0.83497566164615	-0.560489053516039	0.575145904101733	0.62444412445331
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+TR3788|c0_g1_i1	23.7579432209456	26.0024682525169	24.8802057367313	0.125242792795277	0.407913046833573	0.307033064442226	0.75881820512208	0.779326805260514
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diff -r 000000000000 -r d4128a4e49ca test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf has changed
diff -r 000000000000 -r d4128a4e49ca test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,39 @@
+logFC	logCPM	PValue	FDR
+TR131|c0_g1_i1	5.83867709149149	16.0447742820606	3.67956255674e-64	1.3982337715612e-62
+TR3091|c0_g1_i1	4.35104356420213	13.9337836495047	7.47918124727105e-59	1.4210444369815e-57
+TR4277|c0_g1_i1	-4.51249642920563	17.4585638169146	1.30305812944242e-53	1.65054029729373e-52
+TR5075|c0_g1_i1	3.18286810352713	12.8084040893566	8.25600206225396e-24	7.84320195914126e-23
+TR2107|c1_g1_i1	-4.48477961203985	11.2510359028096	1.80754966502889e-22	1.37373774542196e-21
+TR2779|c0_g1_i1	2.75442228103487	15.7797198210508	8.23352696880425e-15	5.21456708024269e-14
+TR1891|c0_g1_i1	1.85607282303223	14.4424161372431	4.82341414399837e-12	2.61842482102769e-11
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+TR1492|c0_g1_i2	-0.847097868783511	16.8160271449712	0.00265383515294934	0.00504228679060374
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+TR1859|c3_g1_i1	2.64648031785777	8.0811923384908	0.0677782555815868	0.0858524570700099
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+TR1837|c2_g1_i1	2.21076601464763	7.9226544260522	0.248563909756302	0.269869387735413
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+TR2011|c5_g1_i1	-0.075980865610854	9.27931055760989	0.901508002533997	0.925873083683564
+TR2182|c3_g2_i6	-0.147124070779728	8.45393312498213	1	1
diff -r 000000000000 -r d4128a4e49ca test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf has changed
diff -r 000000000000 -r d4128a4e49ca test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,39 @@
+logFC	logCPM	PValue	FDR
+TR131|c0_g1_i1	5.89108692370307	16.0946870940125	4.52958285205525e-36	1.721241483781e-34
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diff -r 000000000000 -r d4128a4e49ca test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf has changed
diff -r 000000000000 -r d4128a4e49ca test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,40 @@
+id	baseMeanA	baseMeanB	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj
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diff -r 000000000000 -r d4128a4e49ca test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf
Binary file test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf has changed
diff -r 000000000000 -r d4128a4e49ca test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,40 @@
+logFC	logCPM	PValue	FDR
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diff -r 000000000000 -r d4128a4e49ca test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf
Binary file test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf has changed
diff -r 000000000000 -r d4128a4e49ca test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,40 @@
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+TR1894|c2_g1_i1	-0.899367664455804	7.86698528437277	0.236693956821629	0.369242572641742
+TR5212|c0_g1_i1	-0.317453614519532	13.3093804544918	0.0408068910563242	0.0982500353944082
+TR2182|c3_g2_i6	0.988859576038597	7.34392475064937	0.332144974966109	0.462630500845651
+TR3249|c0_g1_i1	1.18548803762213	8.36747688877935	0.296376188714782	0.444564283072173
+TR1837|c2_g1_i1	-0.83411458992077	7.6102620160458	0.393260306376011	0.528867308574635
+TR3807|c0_g1_i1	-0.40219136988549	5.09566487188118	0.681998347783062	0.765740423023185
+TR4669|c0_g2_i1	-6.05037553674292	13.1239272719772	0.480074268471172	0.603964402270185
+TR1122|c0_g1_i1	-0.184244267394782	6.64199260311611	0.869699168726351	0.892585988955992
+TR127|c1_g1_i1	0.354388761220407	7.15556768591471	0.687202943738756	0.765740423023185
+TR2844|c0_g1_i1	-0.251980888130202	14.4425124782726	0.0594765231313145	0.128865800117848
+TR2090|c0_g1_i1	0.862128177746631	9.64998833298881	0.646749723219784	0.764340581987017
+TR3091|c0_g1_i1	-0.148831558112849	14.9878570236746	0.0841354210369957	0.160877282494822
+TR5055|c0_g2_i1	-0.0583511298028353	9.18288041060754	0.918331019801174	0.918331019801174
+TR4163|c0_g1_i1	-0.161834057105857	14.4879250602579	0.126768900432688	0.214955961603254
+TR4277|c0_g1_i1	-0.103273026252208	13.9874746529507	0.30829078508145	0.445308911784317
+TR939|c0_g1_i1	-0.0333503331526365	13.2856573711711	0.715260879184748	0.774865952450143
+TR1449|c0_g1_i1	0.049884213852527	13.4293306544833	0.75234222467997	0.793009371959969
+TR2487|c0_g1_i1	-0.0480185034754555	16.5239765307922	0.407818984620182	0.530164680006236
+TR131|c0_g1_i1	-0.0203187870937255	17.0810493411762	0.539920494505425	0.658028102678487
diff -r 000000000000 -r d4128a4e49ca test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf
Binary file test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf has changed
diff -r 000000000000 -r d4128a4e49ca test-data/count/express_bowtie/results.xprs
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/express_bowtie/results.xprs	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,8 @@
+bundle_id	target_id	length	eff_length	tot_counts	uniq_counts	est_counts	eff_counts	ambig_distr_alpha	ambig_distr_beta	fpkm	fpkm_conf_low	fpkm_conf_high	solvable	tpm
+1	TRINITY_DN2_c3_g1_i1	202	0.000000	0	0	0.000000	0.000000	0.000000e00	0.000000e00	0.000000e00	0.000000e00	0.000000e00	F	0.000000e+00
+2	TRINITY_DN1_c0_g1_i1	380	109.247050	5	5	5.000000	17.391774	0.000000e00	0.000000e00	4.160711e06	4.160711e06	4.160711e06	T	6.610131e+05
+3	TRINITY_DN2_c0_g1_i1	279	0.000000	0	0	0.000000	0.000000	0.000000e00	0.000000e00	0.000000e00	0.000000e00	0.000000e00	F	0.000000e+00
+4	TRINITY_DN0_c0_g1_i1	229	0.000000	0	0	0.000000	0.000000	0.000000e00	0.000000e00	0.000000e00	0.000000e00	0.000000e00	F	0.000000e+00
+5	TRINITY_DN2_c1_g1_i1	541	259.008053	5	5	5.000000	10.443691	0.000000e00	0.000000e00	1.754947e06	1.754947e06	1.754947e06	T	2.788088e+05
+6	TRINITY_DN2_c2_g1_i1	240	240.000000	1	1	1.000000	1.000000	0.000000e00	0.000000e00	3.787879e05	3.787879e05	3.787879e05	T	6.017811e+04
+7	TRINITY_DN3_c0_g1_i1	216	0.000000	0	0	0.000000	0.000000	0.000000e00	0.000000e00	0.000000e00	0.000000e00	0.000000e00	F	0.000000e+00
diff -r 000000000000 -r d4128a4e49ca test-data/count/express_bowtie/results_B.xprs
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/express_bowtie/results_B.xprs	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,8 @@
+bundle_id	target_id	length	eff_length	tot_counts	uniq_counts	est_counts	eff_counts	ambig_distr_alpha	ambig_distr_beta	fpkm	fpkm_conf_low	fpkm_conf_high	solvable	tpm
+1	TRINITY_DN0_c0_g1_i1	380	109.247050	5	5	5.000000	17.391774	0.000000e+00	0.000000e+00	4.160711e+06	4.160711e+06	4.160711e+06	T	6.610131e+05
+2	TRINITY_DN2_c0_g1_i1	279	0.000000	0	0	0.000000	0.000000	0.000000e+00	0.000000e+00	0.000000e+00	0.000000e+00	0.000000e+00	F	0.000000e+00
+3	TRINITY_DN2_c1_g1_i1	240	240.000000	1	1	1.000000	1.000000	0.000000e+00	0.000000e+00	3.787879e+05	3.787879e+05	3.787879e+05	T	6.017811e+04
+4	TRINITY_DN1_c0_g1_i1	229	0.000000	0	0	0.000000	0.000000	0.000000e+00	0.000000e+00	0.000000e+00	0.000000e+00	0.000000e+00	F	0.000000e+00
+5	TRINITY_DN3_c0_g1_i1	216	0.000000	0	0	0.000000	0.000000	0.000000e+00	0.000000e+00	0.000000e+00	0.000000e+00	0.000000e+00	F	0.000000e+00
+6	TRINITY_DN2_c3_g1_i1	202	0.000000	0	0	0.000000	0.000000	0.000000e+00	0.000000e+00	0.000000e+00	0.000000e+00	0.000000e+00	F	0.000000e+00
+7	TRINITY_DN2_c2_g1_i1	541	259.008053	5	5	5.000000	10.443691	0.000000e+00	0.000000e+00	1.754947e+06	1.754947e+06	1.754947e+06	T	2.788088e+05
diff -r 000000000000 -r d4128a4e49ca test-data/count/express_bowtie/sample_A
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/express_bowtie/sample_A	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,8 @@
+bundle_id	target_id	length	eff_length	tot_counts	uniq_counts	est_counts	eff_counts	ambig_distr_alpha	ambig_distr_beta	fpkm	fpkm_conf_low	fpkm_conf_high	solvable	tpm
+NA	TRINITY_DN3_c0_g1	216.00	1.00	NA	NA	NA	0.00	NA	NA	0.00	NA	NA	NA	0
+NA	TRINITY_DN2_c2_g1	240.00	240.00	NA	NA	NA	1.00	NA	NA	378787.90	NA	NA	NA	60178.11
+NA	TRINITY_DN2_c3_g1	202.00	1.00	NA	NA	NA	0.00	NA	NA	0.00	NA	NA	NA	0
+NA	TRINITY_DN0_c0_g1	229.00	1.00	NA	NA	NA	0.00	NA	NA	0.00	NA	NA	NA	0
+NA	TRINITY_DN2_c0_g1	279.00	1.00	NA	NA	NA	0.00	NA	NA	0.00	NA	NA	NA	0
+NA	TRINITY_DN1_c0_g1	380.00	109.25	NA	NA	NA	17.39	NA	NA	4160711.00	NA	NA	NA	661013.1
+NA	TRINITY_DN2_c1_g1	541.00	259.01	NA	NA	NA	10.44	NA	NA	1754947.00	NA	NA	NA	278808.8
diff -r 000000000000 -r d4128a4e49ca test-data/count/express_bowtie/sample_B
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/express_bowtie/sample_B	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,8 @@
+bundle_id	target_id	length	eff_length	tot_counts	uniq_counts	est_counts	eff_counts	ambig_distr_alpha	ambig_distr_beta	fpkm	fpkm_conf_low	fpkm_conf_high	solvable	tpm
+NA	TRINITY_DN3_c0_g1	216.00	1.00	NA	NA	NA	0.00	NA	NA	0.00	NA	NA	NA	0
+NA	TRINITY_DN2_c1_g1	240.00	240.00	NA	NA	NA	1.00	NA	NA	378787.90	NA	NA	NA	60178.11
+NA	TRINITY_DN2_c3_g1	202.00	1.00	NA	NA	NA	0.00	NA	NA	0.00	NA	NA	NA	0
+NA	TRINITY_DN0_c0_g1	380.00	109.25	NA	NA	NA	17.39	NA	NA	4160711.00	NA	NA	NA	661013.1
+NA	TRINITY_DN1_c0_g1	229.00	1.00	NA	NA	NA	0.00	NA	NA	0.00	NA	NA	NA	0
+NA	TRINITY_DN2_c0_g1	279.00	1.00	NA	NA	NA	0.00	NA	NA	0.00	NA	NA	NA	0
+NA	TRINITY_DN2_c2_g1	541.00	259.01	NA	NA	NA	10.44	NA	NA	1754947.00	NA	NA	NA	278808.8
diff -r 000000000000 -r d4128a4e49ca test-data/count/matrix_express_bowtie/matrix.TMM.EXPR.matrix
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_express_bowtie/matrix.TMM.EXPR.matrix	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,8 @@
+	sample_A.tsv	sample_B.tsv
+TRINITY_DN2_c1_g1_i1	278808.8	60178.11
+TRINITY_DN1_c0_g1_i1	0	0
+TRINITY_DN2_c2_g1_i1	60178.11	278808.8
+TRINITY_DN2_c0_g1_i1	0	0
+TRINITY_DN3_c0_g1_i1	0	0
+TRINITY_DN2_c3_g1_i1	0	0
+TRINITY_DN0_c0_g1_i1	661013.1	661013.1
diff -r 000000000000 -r d4128a4e49ca test-data/count/matrix_express_bowtie/matrix.TPM.not_cross_norm
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_express_bowtie/matrix.TPM.not_cross_norm	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,8 @@
+	sample_A.tsv	sample_B.tsv
+TRINITY_DN2_c1_g1_i1	278808.8	60178.11
+TRINITY_DN1_c0_g1_i1	0	0
+TRINITY_DN2_c2_g1_i1	60178.11	278808.8
+TRINITY_DN2_c0_g1_i1	0	0
+TRINITY_DN3_c0_g1_i1	0	0
+TRINITY_DN2_c3_g1_i1	0	0
+TRINITY_DN0_c0_g1_i1	661013.1	661013.1
diff -r 000000000000 -r d4128a4e49ca test-data/count/matrix_express_bowtie/matrix.counts.matrix
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_express_bowtie/matrix.counts.matrix	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,8 @@
+	sample_A.tsv	sample_B.tsv
+TRINITY_DN2_c1_g1_i1	10.443691	1.000000
+TRINITY_DN1_c0_g1_i1	0.000000	0.000000
+TRINITY_DN2_c2_g1_i1	1.000000	10.443691
+TRINITY_DN2_c0_g1_i1	0.000000	0.000000
+TRINITY_DN3_c0_g1_i1	0.000000	0.000000
+TRINITY_DN2_c3_g1_i1	0.000000	0.000000
+TRINITY_DN0_c0_g1_i1	17.391774	17.391774
diff -r 000000000000 -r d4128a4e49ca test-data/count/matrix_rsem_bowtie/matrix.TMM.EXPR.matrix
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie/matrix.TMM.EXPR.matrix	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,8 @@
+	sample_A.tsv	sample_B.tsv
+TRINITY_DN3_c0_g1	0	0
+TRINITY_DN4_c0_g1	0	0
+TRINITY_DN0_c0_g1	331152.79	331152.79
+TRINITY_DN2_c0_g1	0	0
+TRINITY_DN3_c2_g1	524034.76	144812.45
+TRINITY_DN3_c1_g1	144812.45	524034.76
+TRINITY_DN3_c3_g1	0	0
diff -r 000000000000 -r d4128a4e49ca test-data/count/matrix_rsem_bowtie/matrix.TPM.not_cross_norm
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie/matrix.TPM.not_cross_norm	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,8 @@
+	sample_A.tsv	sample_B.tsv
+TRINITY_DN3_c0_g1	0	0
+TRINITY_DN4_c0_g1	0	0
+TRINITY_DN0_c0_g1	331152.79	331152.79
+TRINITY_DN2_c0_g1	0	0
+TRINITY_DN3_c2_g1	524034.76	144812.45
+TRINITY_DN3_c1_g1	144812.45	524034.76
+TRINITY_DN3_c3_g1	0	0
diff -r 000000000000 -r d4128a4e49ca test-data/count/matrix_rsem_bowtie/matrix.counts.matrix
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie/matrix.counts.matrix	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,8 @@
+	sample_A.tsv	sample_B.tsv
+TRINITY_DN3_c0_g1	0.00	0.00
+TRINITY_DN4_c0_g1	0.00	0.00
+TRINITY_DN0_c0_g1	5.00	5.00
+TRINITY_DN2_c0_g1	0.00	0.00
+TRINITY_DN3_c2_g1	1.00	5.00
+TRINITY_DN3_c1_g1	5.00	1.00
+TRINITY_DN3_c3_g1	0.00	0.00
diff -r 000000000000 -r d4128a4e49ca test-data/count/matrix_rsem_bowtie2/matrix.TMM.EXPR.matrix
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie2/matrix.TMM.EXPR.matrix	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,8 @@
+	sample_A.tsv	sample_B.tsv
+TRINITY_DN3_c0_g1	0	0
+TRINITY_DN2_c2_g1	529174.03	161779.66
+TRINITY_DN2_c3_g1	0	0
+TRINITY_DN0_c0_g1	309046.31	309046.31
+TRINITY_DN2_c0_g1	0	0
+TRINITY_DN1_c0_g1	0	0
+TRINITY_DN2_c1_g1	161779.66	529174.03
diff -r 000000000000 -r d4128a4e49ca test-data/count/matrix_rsem_bowtie2/matrix.TPM.not_cross_norm
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie2/matrix.TPM.not_cross_norm	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,8 @@
+	sample_A.tsv	sample_B.tsv
+TRINITY_DN3_c0_g1	0	0
+TRINITY_DN2_c2_g1	529174.03	161779.66
+TRINITY_DN2_c3_g1	0	0
+TRINITY_DN0_c0_g1	309046.31	309046.31
+TRINITY_DN2_c0_g1	0	0
+TRINITY_DN1_c0_g1	0	0
+TRINITY_DN2_c1_g1	161779.66	529174.03
diff -r 000000000000 -r d4128a4e49ca test-data/count/matrix_rsem_bowtie2/matrix.counts.matrix
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie2/matrix.counts.matrix	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,8 @@
+	sample_A.tsv	sample_B.tsv
+TRINITY_DN3_c0_g1	0.00	0.00
+TRINITY_DN2_c2_g1	1.00	6.00
+TRINITY_DN2_c3_g1	0.00	0.00
+TRINITY_DN0_c0_g1	5.00	5.00
+TRINITY_DN2_c0_g1	0.00	0.00
+TRINITY_DN1_c0_g1	0.00	0.00
+TRINITY_DN2_c1_g1	6.00	1.00
diff -r 000000000000 -r d4128a4e49ca test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.TPM.not_cross_norm
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.TPM.not_cross_norm	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,8 @@
+	sample_A.tsv	sample_B.tsv
+TRINITY_DN3_c0_g1	0	0
+TRINITY_DN4_c0_g1	0	0
+TRINITY_DN0_c0_g1	331152.79	331152.79
+TRINITY_DN2_c0_g1	0	0
+TRINITY_DN3_c2_g1	524034.76	144812.45
+TRINITY_DN3_c1_g1	144812.45	524034.76
+TRINITY_DN3_c3_g1	0	0
diff -r 000000000000 -r d4128a4e49ca test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.TPM.not_cross_norm.upper_quartile_norm.matrix
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.TPM.not_cross_norm.upper_quartile_norm.matrix	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,8 @@
+RSEM	RSEM.isoforms_B.results
+TRINITY_DN3_c2_g1_i1	524034.76	144812.45
+TRINITY_DN4_c0_g1_i1	0	0
+TRINITY_DN3_c3_g1_i1	0	0
+TRINITY_DN3_c1_g1_i1	144812.45	524034.76
+TRINITY_DN2_c0_g1_i1	0	0
+TRINITY_DN3_c0_g1_i1	0	0
+TRINITY_DN0_c0_g1_i1	331152.79	331152.79
diff -r 000000000000 -r d4128a4e49ca test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.UpperQuartile.EXPR.matrix
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.UpperQuartile.EXPR.matrix	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,8 @@
+sample_A	sample_B
+TRINITY_DN2_c0_g1	0	0
+TRINITY_DN1_c0_g1	329523.81	329523.81
+TRINITY_DN0_c0_g1	0	0
+TRINITY_DN2_c1_g1	145165.14	525311.05
+TRINITY_DN3_c0_g1	0	0
+TRINITY_DN2_c2_g1	525311.05	145165.14
+TRINITY_DN2_c3_g1	0	0
diff -r 000000000000 -r d4128a4e49ca test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.counts.matrix
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.counts.matrix	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,8 @@
+	sample_A.tsv	sample_B.tsv
+TRINITY_DN3_c0_g1	0.00	0.00
+TRINITY_DN4_c0_g1	0.00	0.00
+TRINITY_DN0_c0_g1	5.00	5.00
+TRINITY_DN2_c0_g1	0.00	0.00
+TRINITY_DN3_c2_g1	1.00	5.00
+TRINITY_DN3_c1_g1	5.00	1.00
+TRINITY_DN3_c3_g1	0.00	0.00
diff -r 000000000000 -r d4128a4e49ca test-data/count/matrix_rsem_bowtie_none/matrix.TPM.not_cross_norm
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie_none/matrix.TPM.not_cross_norm	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,8 @@
+	sample_A.tsv	sample_B.tsv
+TRINITY_DN3_c0_g1	0	0
+TRINITY_DN4_c0_g1	0	0
+TRINITY_DN0_c0_g1	331152.79	331152.79
+TRINITY_DN2_c0_g1	0	0
+TRINITY_DN3_c2_g1	524034.76	144812.45
+TRINITY_DN3_c1_g1	144812.45	524034.76
+TRINITY_DN3_c3_g1	0	0
diff -r 000000000000 -r d4128a4e49ca test-data/count/matrix_rsem_bowtie_none/matrix.counts.matrix
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie_none/matrix.counts.matrix	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,8 @@
+	sample_A.tsv	sample_B.tsv
+TRINITY_DN3_c0_g1	0.00	0.00
+TRINITY_DN4_c0_g1	0.00	0.00
+TRINITY_DN0_c0_g1	5.00	5.00
+TRINITY_DN2_c0_g1	0.00	0.00
+TRINITY_DN3_c2_g1	1.00	5.00
+TRINITY_DN3_c1_g1	5.00	1.00
+TRINITY_DN3_c3_g1	0.00	0.00
diff -r 000000000000 -r d4128a4e49ca test-data/count/qcheck/input.matrix.CPM.log2.principal_components.pdf
Binary file test-data/count/qcheck/input.matrix.CPM.log2.principal_components.pdf has changed
diff -r 000000000000 -r d4128a4e49ca test-data/count/qcheck/input.matrix.CPM.log2.sample_cor_matrix.pdf
Binary file test-data/count/qcheck/input.matrix.CPM.log2.sample_cor_matrix.pdf has changed
diff -r 000000000000 -r d4128a4e49ca test-data/count/qcheck/matrix.counts.matrix
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/qcheck/matrix.counts.matrix	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,41 @@
+	wt_37_2	wt_37_3	wt_37_1	wt_GSNO_3	wt_GSNO_1	wt_GSNO_2	wt_ph8_3	wt_ph8_1	wt_ph8_2
+TR24|c0_g1_i1	90.00	67.00	85.00	36.00	35.00	34.00	222.00	196.00	201.00
+TR2779|c0_g1_i1	186.00	137.00	217.00	147.00	186.00	197.00	1088.00	1094.00	1086.00
+TR127|c1_g1_i1	9.00	23.00	16.00	2.00	0.00	1.00	3.00	1.00	1.00
+TR2107|c1_g1_i1	59.00	65.00	47.00	6.00	6.00	7.00	3.00	1.00	2.00
+TR2011|c5_g1_i1	11.00	4.00	4.00	8.00	5.00	7.00	3.00	4.00	8.00
+TR4163|c0_g1_i1	368.00	422.00	425.00	172.00	216.00	210.00	234.00	254.00	212.00
+TR5055|c0_g2_i1	36.00	17.00	27.00	4.00	7.00	3.00	4.00	4.00	11.00
+TR1449|c0_g1_i1	196.00	230.00	207.00	66.00	113.00	91.00	124.00	130.00	107.00
+TR1982|c2_g1_i1	7.00	7.00	6.00	4.00	3.00	8.00	16.00	9.00	11.00
+TR1859|c3_g1_i1	0.00	0.00	1.00	0.00	0.00	0.00	1.00	2.00	4.00
+TR1492|c0_g1_i2	1895.00	1906.00	1921.00	1104.00	1263.00	1319.00	899.00	929.00	922.00
+TR1122|c0_g1_i1	2.00	3.00	0.00	3.00	0.00	0.00	1.00	1.00	0.00
+TR2278|c0_g1_i1	497.00	610.00	598.00	333.00	406.00	413.00	323.00	409.00	337.00
+TR4084|c0_g1_i1	95.00	148.00	86.00	77.00	111.00	127.00	175.00	201.00	158.00
+TR4761|c0_g1_i1	2089.00	1746.00	1875.00	155.00	174.00	165.00	394.00	389.00	406.00
+TR3638|c0_g1_i1	647.00	676.00	712.00	117.00	184.00	174.00	324.00	344.00	338.00
+TR2090|c0_g1_i1	0.00	0.00	0.00	22.00	0.00	0.02	10.33	0.00	9.09
+TR3854|c0_g1_i1	1878.00	1734.00	1864.00	1775.00	2173.00	2151.00	2216.00	2142.00	2155.00
+TR131|c0_g1_i1	32.00	28.00	31.00	1001.00	1233.00	1208.00	1486.00	1492.00	1457.00
+TR5075|c0_g1_i1	13.00	22.00	21.00	6.00	8.00	10.00	163.00	121.00	142.00
+TR2182|c3_g2_i6	1.44	2.70	3.84	3.35	0.00	0.00	1.22	2.18	2.63
+TR3788|c0_g1_i1	17.00	30.00	22.00	91.00	132.00	125.00	32.00	22.00	27.00
+TR4859|c0_g1_i1	6.00	12.00	8.00	4.00	1.00	3.00	1.00	1.00	2.00
+TR2487|c0_g1_i1	386.00	383.00	424.00	689.00	866.00	806.00	963.00	989.00	1032.00
+TR2122|c0_g2_i2	145.00	135.00	136.00	155.00	157.00	201.00	369.00	398.00	344.00
+TR4277|c0_g1_i1	4466.00	4701.00	4284.00	118.00	134.00	164.00	172.00	162.00	170.00
+TR4669|c0_g2_i1	0.00	0.00	0.00	209.00	0.00	217.50	0.14	0.06	0.18
+TR3091|c0_g1_i1	22.00	17.00	19.00	250.00	308.00	284.00	333.00	343.00	316.00
+TR2130|c1_g3_i1	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
+TR3807|c0_g1_i1	6.00	4.00	2.00	0.00	0.00	1.00	0.00	1.00	0.00
+TR1894|c2_g1_i1	21.00	14.00	11.00	1.00	2.00	5.00	1.00	3.00	1.00
+TR5212|c0_g1_i1	64.00	89.00	78.00	73.00	98.00	108.00	103.00	105.00	84.00
+TR939|c0_g1_i1	96.00	99.00	99.00	72.00	89.00	88.00	107.00	103.00	108.00
+TR1891|c0_g1_i1	115.00	137.96	124.00	96.53	139.00	110.94	364.77	411.00	384.00
+TR2672|c0_g1_i1	14.00	29.00	22.00	0.00	4.00	2.00	14.00	4.00	7.00
+TR2844|c0_g1_i1	166.00	211.00	178.00	161.00	214.00	223.00	199.00	245.00	213.00
+TR1837|c2_g1_i1	1.00	0.00	0.00	1.00	1.00	4.00	0.00	3.00	2.00
+TR1678|c0_g1_i1	1.00	0.00	1.00	0.00	0.00	2.00	8.00	10.00	6.00
+TR3249|c0_g1_i1	1.00	2.00	1.00	4.00	1.00	0.00	6.00	1.00	7.00
+TR1479|c0_g1_i1	136.00	178.00	141.00	277.00	324.00	354.00	367.00	363.00	302.00
diff -r 000000000000 -r d4128a4e49ca test-data/count/qcheck/wt_37.rep_compare.pdf
Binary file test-data/count/qcheck/wt_37.rep_compare.pdf has changed
diff -r 000000000000 -r d4128a4e49ca test-data/count/qcheck/wt_GSNO.rep_compare.pdf
Binary file test-data/count/qcheck/wt_GSNO.rep_compare.pdf has changed
diff -r 000000000000 -r d4128a4e49ca test-data/count/qcheck/wt_ph8.rep_compare.pdf
Binary file test-data/count/qcheck/wt_ph8.rep_compare.pdf has changed
diff -r 000000000000 -r d4128a4e49ca test-data/count/rsem_bowtie/RSEM.isoforms.results
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie/RSEM.isoforms.results	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,8 @@
+transcript_id	gene_id	length	effective_length	expected_count	TPM	FPKM	IsoPct
+TRINITY_DN0_c0_g1_i1	TRINITY_DN0_c0_g1	229	11.55	0.00	0.00	0.00	0.00
+TRINITY_DN1_c0_g1_i1	TRINITY_DN1_c0_g1	380	123.91	5.00	329523.81	3668378.58	100.00
+TRINITY_DN2_c0_g1_i1	TRINITY_DN2_c0_g1	279	35.45	0.00	0.00	0.00	0.00
+TRINITY_DN2_c1_g1_i1	TRINITY_DN2_c1_g1	541	281.27	5.00	145165.14	1616031.03	100.00
+TRINITY_DN2_c2_g1_i1	TRINITY_DN2_c2_g1	240	15.55	1.00	525311.05	5847953.22	100.00
+TRINITY_DN2_c3_g1_i1	TRINITY_DN2_c3_g1	202	3.45	0.00	0.00	0.00	0.00
+TRINITY_DN3_c0_g1_i1	TRINITY_DN3_c0_g1	216	6.82	0.00	0.00	0.00	0.00
diff -r 000000000000 -r d4128a4e49ca test-data/count/rsem_bowtie/RSEM.isoforms_B.results
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie/RSEM.isoforms_B.results	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,8 @@
+transcript_id	gene_id	length	effective_length	expected_count	TPM	FPKM	IsoPct
+TRINITY_DN0_c0_g1_i1	TRINITY_DN0_c0_g1	229	11.55	0.00	0.00	0.00	0.00
+TRINITY_DN1_c0_g1_i1	TRINITY_DN1_c0_g1	380	123.91	5.00	329523.81	3668378.58	100.00
+TRINITY_DN2_c0_g1_i1	TRINITY_DN2_c0_g1	279	35.45	0.00	0.00	0.00	0.00
+TRINITY_DN2_c2_g1_i1	TRINITY_DN2_c2_g1	541	281.27	5.00	145165.14	1616031.03	100.00
+TRINITY_DN2_c1_g1_i1	TRINITY_DN2_c1_g1	240	15.55	1.00	525311.05	5847953.22	100.00
+TRINITY_DN2_c3_g1_i1	TRINITY_DN2_c3_g1	202	3.45	0.00	0.00	0.00	0.00
+TRINITY_DN3_c0_g1_i1	TRINITY_DN3_c0_g1	216	6.82	0.00	0.00	0.00	0.00
diff -r 000000000000 -r d4128a4e49ca test-data/count/rsem_bowtie/sample_A
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie/sample_A	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,8 @@
+gene_id	transcript_id(s)	length	effective_length	expected_count	TPM	FPKM
+TRINITY_DN0_c0_g1	TRINITY_DN0_c0_g1_i1	229.00	11.55	0.00	0.00	0.00
+TRINITY_DN1_c0_g1	TRINITY_DN1_c0_g1_i1	380.00	123.91	5.00	329523.81	3668378.58
+TRINITY_DN2_c0_g1	TRINITY_DN2_c0_g1_i1	279.00	35.45	0.00	0.00	0.00
+TRINITY_DN2_c1_g1	TRINITY_DN2_c1_g1_i1	541.00	281.27	5.00	145165.14	1616031.03
+TRINITY_DN2_c2_g1	TRINITY_DN2_c2_g1_i1	240.00	15.55	1.00	525311.05	5847953.22
+TRINITY_DN2_c3_g1	TRINITY_DN2_c3_g1_i1	202.00	3.45	0.00	0.00	0.00
+TRINITY_DN3_c0_g1	TRINITY_DN3_c0_g1_i1	216.00	6.82	0.00	0.00	0.00
diff -r 000000000000 -r d4128a4e49ca test-data/count/rsem_bowtie/sample_B
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie/sample_B	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,8 @@
+gene_id	transcript_id(s)	length	effective_length	expected_count	TPM	FPKM
+TRINITY_DN0_c0_g1	TRINITY_DN0_c0_g1_i1	229.00	11.55	0.00	0.00	0.00
+TRINITY_DN1_c0_g1	TRINITY_DN1_c0_g1_i1	380.00	123.91	5.00	329523.81	3668378.58
+TRINITY_DN2_c0_g1	TRINITY_DN2_c0_g1_i1	279.00	35.45	0.00	0.00	0.00
+TRINITY_DN2_c2_g1	TRINITY_DN2_c2_g1_i1	541.00	281.27	5.00	145165.14	1616031.03
+TRINITY_DN2_c1_g1	TRINITY_DN2_c1_g1_i1	240.00	15.55	1.00	525311.05	5847953.22
+TRINITY_DN2_c3_g1	TRINITY_DN2_c3_g1_i1	202.00	3.45	0.00	0.00	0.00
+TRINITY_DN3_c0_g1	TRINITY_DN3_c0_g1_i1	216.00	6.82	0.00	0.00	0.00
diff -r 000000000000 -r d4128a4e49ca test-data/count/rsem_bowtie2/RSEM.isoforms.results
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie2/RSEM.isoforms.results	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,8 @@
+transcript_id	gene_id	length	effective_length	expected_count	TPM	FPKM	IsoPct
+TRINITY_DN0_c0_g1_i1	TRINITY_DN0_c0_g1	229	10.58	0.00	0.00	0.00	0.00
+TRINITY_DN1_c0_g1_i1	TRINITY_DN1_c0_g1	380	122.00	5.00	309046.31	3415300.55	100.00
+TRINITY_DN2_c0_g1_i1	TRINITY_DN2_c0_g1	279	32.50	0.00	0.00	0.00	0.00
+TRINITY_DN2_c1_g1_i1	TRINITY_DN2_c1_g1	541	279.67	6.00	161779.66	1787842.67	100.00
+TRINITY_DN2_c2_g1_i1	TRINITY_DN2_c2_g1	240	14.25	1.00	529174.03	5847953.22	100.00
+TRINITY_DN2_c3_g1_i1	TRINITY_DN2_c3_g1	202	3.17	0.00	0.00	0.00	0.00
+TRINITY_DN3_c0_g1_i1	TRINITY_DN3_c0_g1	216	6.25	0.00	0.00	0.00	0.00
diff -r 000000000000 -r d4128a4e49ca test-data/count/rsem_bowtie2/RSEM.isoforms_B.results
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie2/RSEM.isoforms_B.results	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,8 @@
+transcript_id	gene_id	length	effective_length	expected_count	TPM	FPKM	IsoPct
+TRINITY_DN0_c0_g1_i1	TRINITY_DN0_c0_g1	380	122.00	5.00	309046.31	3415300.55	100.00
+TRINITY_DN1_c0_g1_i1	TRINITY_DN1_c0_g1	229	10.58	0.00	0.00	0.00	0.00
+TRINITY_DN2_c0_g1_i1	TRINITY_DN2_c0_g1	279	32.50	0.00	0.00	0.00	0.00
+TRINITY_DN2_c2_g1_i1	TRINITY_DN2_c2_g1	541	279.67	6.00	161779.66	1787842.67	100.00
+TRINITY_DN2_c1_g1_i1	TRINITY_DN2_c1_g1	240	14.25	1.00	529174.03	5847953.22	100.00
+TRINITY_DN2_c3_g1_i1	TRINITY_DN2_c3_g1	202	3.17	0.00	0.00	0.00	0.00
+TRINITY_DN3_c0_g1_i1	TRINITY_DN3_c0_g1	216	6.25	0.00	0.00	0.00	0.00
diff -r 000000000000 -r d4128a4e49ca test-data/count/rsem_bowtie2/sample_A
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie2/sample_A	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,8 @@
+gene_id	transcript_id(s)	length	effective_length	expected_count	TPM	FPKM
+TRINITY_DN0_c0_g1	TRINITY_DN0_c0_g1_i1	229.00	10.58	0.00	0.00	0.00
+TRINITY_DN1_c0_g1	TRINITY_DN1_c0_g1_i1	380.00	122.00	5.00	309046.31	3415300.55
+TRINITY_DN2_c0_g1	TRINITY_DN2_c0_g1_i1	279.00	32.50	0.00	0.00	0.00
+TRINITY_DN2_c1_g1	TRINITY_DN2_c1_g1_i1	541.00	279.67	6.00	161779.66	1787842.67
+TRINITY_DN2_c2_g1	TRINITY_DN2_c2_g1_i1	240.00	14.25	1.00	529174.03	5847953.22
+TRINITY_DN2_c3_g1	TRINITY_DN2_c3_g1_i1	202.00	3.17	0.00	0.00	0.00
+TRINITY_DN3_c0_g1	TRINITY_DN3_c0_g1_i1	216.00	6.25	0.00	0.00	0.00
diff -r 000000000000 -r d4128a4e49ca test-data/count/rsem_bowtie2/sample_B
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie2/sample_B	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,8 @@
+gene_id	transcript_id(s)	length	effective_length	expected_count	TPM	FPKM
+TRINITY_DN0_c0_g1	TRINITY_DN0_c0_g1_i1	380.00	122.00	5.00	309046.31	3415300.55
+TRINITY_DN1_c0_g1	TRINITY_DN1_c0_g1_i1	229.00	10.58	0.00	0.00	0.00
+TRINITY_DN2_c0_g1	TRINITY_DN2_c0_g1_i1	279.00	32.50	0.00	0.00	0.00
+TRINITY_DN2_c2_g1	TRINITY_DN2_c2_g1_i1	541.00	279.67	6.00	161779.66	1787842.67
+TRINITY_DN2_c1_g1	TRINITY_DN2_c1_g1_i1	240.00	14.25	1.00	529174.03	5847953.22
+TRINITY_DN2_c3_g1	TRINITY_DN2_c3_g1_i1	202.00	3.17	0.00	0.00	0.00
+TRINITY_DN3_c0_g1	TRINITY_DN3_c0_g1_i1	216.00	6.25	0.00	0.00	0.00
diff -r 000000000000 -r d4128a4e49ca test-data/count/salmon/sample_A
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/salmon/sample_A	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,8 @@
+Name	Length	EffectiveLength	TPM	NumReads
+TRINITY_DN1_c0_g1_i1	380	120.403	179183	13
+TRINITY_DN0_c0_g1_i1	229	229	55271.5	7.62686
+TRINITY_DN2_c0_g1_i1	279	31.1522	565494	10.6151
+TRINITY_DN2_c1_g1_i1	541	278.129	113370	19
+TRINITY_DN2_c2_g1_i1	240	240	32900.7	4.75801
+TRINITY_DN2_c3_g1_i1	202	202	0	0
+TRINITY_DN3_c0_g1_i1	216	216	53781.8	7
diff -r 000000000000 -r d4128a4e49ca test-data/count/salmon/sample_B
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/salmon/sample_B	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,8 @@
+Name	Length	EffectiveLength	TPM	NumReads
+TRINITY_DN2_c2_g1	240.00	240.00	32900.70	4.76
+TRINITY_DN0_c0_g1	229.00	229.00	55271.50	7.63
+TRINITY_DN1_c0_g1	380.00	120.40	179183.00	13.00
+TRINITY_DN2_c0_g1	279.00	31.15	565494.00	10.62
+TRINITY_DN2_c3_g1	202.00	202.00	0.00	0.00
+TRINITY_DN3_c0_g1	216.00	216.00	53781.80	7.00
+TRINITY_DN2_c1_g1	541.00	278.13	113370.00	19.00
diff -r 000000000000 -r d4128a4e49ca test-data/count/samples.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/samples.txt	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,9 @@
+wt_37	wt_37_1	/broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_37_1-SRX707647-SRR1582649_1.fastq	/broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_37_1-SRX707647-SRR1582649_2.fastq
+wt_37	wt_37_2	/broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_37_2-SRX707648-SRR1582650_1.fastq	/broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_37_2-SRX707648-SRR1582650_2.fastq
+wt_37	wt_37_3	/broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_37_3-SRX707649-SRR1582651_1.fastq	/broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_37_3-SRX707649-SRR1582651_2.fastq
+wt_GSNO	wt_GSNO_1	/broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_GSNO_1-SRX707644-SRR1582646_1.fastq	/broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_GSNO_1-SRX707644-SRR1582646_2.fastq
+wt_GSNO	wt_GSNO_2	/broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_GSNO_2-SRX707645-SRR1582647_1.fastq	/broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_GSNO_2-SRX707645-SRR1582647_2.fastq
+wt_GSNO	wt_GSNO_3	/broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_GSNO_3-SRX707646-SRR1582648_1.fastq	/broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_GSNO_3-SRX707646-SRR1582648_2.fastq
+wt_ph8	wt_ph8_1	/broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_ph8_1-SRX707641-SRR1582643_1.fastq	/broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_ph8_1-SRX707641-SRR1582643_2.fastq
+wt_ph8	wt_ph8_2	/broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_ph8_2-SRX707642-SRR1582644_1.fastq	/broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_ph8_2-SRX707642-SRR1582644_2.fastq
+wt_ph8	wt_ph8_3	/broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_ph8_3-SRX707643-SRR1582645_1.fastq	/broad/hptmp/bhaas/candida/FASTQ/2M/2M.wt_ph8_3-SRX707643-SRR1582645_2.fastq
diff -r 000000000000 -r d4128a4e49ca test-data/count/trinotate/genes.lengths.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/trinotate/genes.lengths.txt	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,40 @@
+gene_id	length
+TR24|c0_g1_i1	290.00
+TR2779|c0_g1_i1	186.00
+TR127|c1_g1_i1	229.00
+TR2107|c1_g1_i1	259.00
+TR2011|c5_g1_i1	211.00
+TR4163|c0_g1_i1	368.00
+TR5055|c0_g2_i1	236.00
+TR1449|c0_g1_i1	196.00
+TR1982|c2_g1_i1	227.00
+TR1859|c3_g1_i1	220.00
+TR1492|c0_g1_i2	195.00
+TR1122|c0_g1_i1	222.00
+TR2278|c0_g1_i1	497.00
+TR4084|c0_g1_i1	295.00
+TR4761|c0_g1_i1	289.00
+TR3638|c0_g1_i1	247.00
+TR2090|c0_g1_i1	220.00
+TR3854|c0_g1_i1	178.00
+TR131|c0_g1_i1	232.00
+TR5075|c0_g1_i1	213.00
+TR2182|c3_g2_i6	221.44
+TR3788|c0_g1_i1	217.00
+TR4859|c0_g1_i1	226.00
+TR2487|c0_g1_i1	386.00
+TR2122|c0_g2_i2	145.00
+TR4277|c0_g1_i1	466.00
+TR3091|c0_g1_i1	222.00
+TR2130|c1_g3_i1	220.00
+TR3807|c0_g1_i1	226.00
+TR1894|c2_g1_i1	221.00
+TR5212|c0_g1_i1	264.00
+TR939|c0_g1_i1	296.00
+TR1891|c0_g1_i1	115.00
+TR2672|c0_g1_i1	214.00
+TR2844|c0_g1_i1	166.00
+TR1837|c2_g1_i1	221.00
+TR1678|c0_g1_i1	221.00
+TR3249|c0_g1_i1	221.00
+TR1479|c0_g1_i1	136.00
diff -r 000000000000 -r d4128a4e49ca test-data/count/trinotate/go_annotations.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/trinotate/go_annotations.txt	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,39 @@
+TR24|c0_g1_i1	GO:0003674,GO:0003824,GO:0003865,GO:0005575,GO:0005783,GO:0005789,GO:0006629,GO:0008150,GO:0008152,GO:0008202,GO:0016020,GO:0016021,GO:0016229,GO:0016491,GO:0016627,GO:0031090,GO:0033765,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044238,GO:0044422,GO:0044424,GO:0044425,GO:0044432,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0071704,GO:0098588,GO:0098589,GO:1901360
+TR2779|c0_g1_i1	GO:0003674,GO:0003824,GO:0004596,GO:0005575,GO:0005634,GO:0005737,GO:0008080,GO:0016407,GO:0016410,GO:0016740,GO:0016746,GO:0016747,GO:0034212,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044424,GO:0044464
+TR127|c1_g1_i1	GO:0003674,GO:0003824,GO:0004310,GO:0004311,GO:0004659,GO:0005575,GO:0005789,GO:0006066,GO:0006629,GO:0006694,GO:0006720,GO:0008150,GO:0008152,GO:0008202,GO:0008299,GO:0008610,GO:0009058,GO:0009987,GO:0016020,GO:0016021,GO:0016125,GO:0016126,GO:0016491,GO:0016740,GO:0016765,GO:0031090,GO:0044237,GO:0044238,GO:0044249,GO:0044255,GO:0044281,GO:0044283,GO:0044422,GO:0044424,GO:0044425,GO:0044432,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0044711,GO:0044763,GO:0046165,GO:0051996,GO:0071704,GO:0098588,GO:0098589,GO:1901360,GO:1901362,GO:1901576,GO:1901615,GO:1901617
+TR2107|c1_g1_i1	GO:0003674,GO:0003676,GO:0003677,GO:0003723,GO:0003824,GO:0003887,GO:0003964,GO:0004175,GO:0004190,GO:0004518,GO:0004519,GO:0005488,GO:0006139,GO:0006259,GO:0006310,GO:0006725,GO:0006807,GO:0008150,GO:0008152,GO:0008233,GO:0009987,GO:0015074,GO:0016740,GO:0016772,GO:0016779,GO:0016787,GO:0016788,GO:0034061,GO:0034641,GO:0043167,GO:0043169,GO:0043170,GO:0044237,GO:0044238,GO:0044260,GO:0046483,GO:0046872,GO:0070001,GO:0070011,GO:0071704,GO:0090304,GO:0097159,GO:1901360,GO:1901363
+TR2011|c5_g1_i1	GO:0003674,GO:0005488,GO:0005507,GO:0005575,GO:0005737,GO:0006801,GO:0006810,GO:0006811,GO:0006812,GO:0008047,GO:0008150,GO:0008152,GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234,GO:0043167,GO:0043169,GO:0044237,GO:0044424,GO:0044464,GO:0044699,GO:0044710,GO:0044765,GO:0046872,GO:0046914,GO:0051234,GO:0055114,GO:0072593
+TR4163|c0_g1_i1	GO:0003674,GO:0005488,GO:0005507,GO:0005575,GO:0005634,GO:0005743,GO:0005829,GO:0006801,GO:0006873,GO:0006875,GO:0006878,GO:0008047,GO:0008150,GO:0008152,GO:0009987,GO:0010035,GO:0010038,GO:0016020,GO:0016530,GO:0016531,GO:0016532,GO:0019725,GO:0019866,GO:0030003,GO:0030234,GO:0031090,GO:0031966,GO:0042221,GO:0042592,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044237,GO:0044422,GO:0044424,GO:0044429,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0044763,GO:0046872,GO:0046914,GO:0046916,GO:0048878,GO:0050801,GO:0050896,GO:0051716,GO:0055065,GO:0055070,GO:0055076,GO:0055080,GO:0055082,GO:0055114,GO:0065007,GO:0065008,GO:0070887,GO:0071241,GO:0071248,GO:0072593
+TR5055|c0_g2_i1	GO:0003674,GO:0005488,GO:0005575,GO:0005634,GO:0008270,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044424,GO:0044464,GO:0046872,GO:0046914
+TR1449|c0_g1_i1	GO:0003674,GO:0005488,GO:0005575,GO:0005634,GO:0008270,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044424,GO:0044464,GO:0046872,GO:0046914
+TR1982|c2_g1_i1	GO:0003674,GO:0003824,GO:0003865,GO:0005575,GO:0005783,GO:0005789,GO:0006629,GO:0008150,GO:0008152,GO:0008202,GO:0016020,GO:0016021,GO:0016229,GO:0016491,GO:0016627,GO:0031090,GO:0033765,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044238,GO:0044422,GO:0044424,GO:0044425,GO:0044432,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0071704,GO:0098588,GO:0098589,GO:1901360
+TR1859|c3_g1_i1	GO:0003676
+TR1492|c0_g1_i2	GO:0005783,GO:0005789,GO:0006629,GO:0008150,GO:0008152,GO:0008202,GO:0016020,GO:0016021,GO:0016229
+TR1122|c0_g1_i1	GO:0008152,GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234
+TR2278|c0_g1_i1	GO:0031090,GO:0033765
+TR4084|c0_g1_i1	GO:0003674,GO:0005488,GO:0005575,GO:0005634,GO:0008270,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044424,GO:0044464,GO:0046872,GO:0046914
+TR4761|c0_g1_i1	GO:0008152,GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234
+TR3638|c0_g1_i1	GO:0003865,GO:0005575,GO:0005783
+TR2090|c0_g1_i1	GO:0003674,GO:0005488,GO:0005507,GO:0005575,GO:0005634,GO:0005743,GO:0005829,GO:0006801,GO:0006873,GO:0006875,GO:0006878,GO:0008047,GO:0008150,GO:0008152,GO:0009987,GO:0010035,GO:0010038,GO:0016020,GO:0016530,GO:0016531,GO:0016532,GO:0019725,GO:0019866,GO:0030003,GO:0030234,GO:0031090,GO:0031966,GO:0042221,GO:0042592,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044237,GO:0044422,GO:0044424,GO:0044429,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0044763,GO:0046872,GO:0046914,GO:0046916,GO:0048878,GO:0050801,GO:0050896,GO:0051716,GO:0055065,GO:0055070,GO:0055076,GO:0055080,GO:0055082,GO:0055114,GO:0065007,GO:0065008,GO:0070887,GO:0071241,GO:0071248,GO:0072593
+TR3854|c0_g1_i1	GO:0003674,GO:0003824,GO:0003865,GO:0005575,GO:0005783,GO:0005789,GO:0006629,GO:0008150,GO:0008152,GO:0008202,GO:0016020,GO:0016021,GO:0016229,GO:0016491,GO:0016627,GO:0031090,GO:0033765,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044238,GO:0044422,GO:0044424,GO:0044425,GO:0044432,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0071704,GO:0098588,GO:0098589,GO:1901360
+TR131|c0_g1_i1	GO:0031090,GO:0033765
+TR5075|c0_g1_i1	GO:0031090,GO:0033765
+TR2182|c3_g2_i6	GO:0003674,GO:0003676,GO:0003677,GO:0003723,GO:0003824,GO:0003887,GO:0003964,GO:0004175,GO:0004190,GO:0004518,GO:0004519,GO:0005488,GO:0006139
+TR3788|c0_g1_i1	GO:0005783,GO:0005789,GO:0006629,GO:0008150,GO:0008152,GO:0008202,GO:0016020,GO:0016021,GO:0016229
+TR4859|c0_g1_i1	GO:0003674,GO:0003676,GO:0003677,GO:0003723,GO:0003824,GO:0003887,GO:0003964,GO:0004175,GO:0004190,GO:0004518,GO:0004519,GO:0005488,GO:0006139
+TR2487|c0_g1_i1	GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234,GO:0043167,GO:0043169
+TR2122|c0_g2_i2	GO:0005575,GO:0005634,GO:0008270,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044424,GO:0044464,GO:0046872
+TR4277|c0_g1_i1	GO:0005575,GO:0005634,GO:0008270,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044424,GO:0044464,GO:0046872
+TR3091|c0_g1_i1	GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234,GO:0043167,GO:0043169
+TR2130|c1_g3_i1	GO:0003674,GO:0003824,GO:0003865,GO:0005575,GO:0005783,GO:0005789,GO:0006629,GO:0008150,GO:0008152,GO:0008202,GO:0016020,GO:0016021,GO:0016229,GO:0016491,GO:0016627,GO:0031090,GO:0033765,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044238,GO:0044422,GO:0044424,GO:0044425,GO:0044432,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0071704,GO:0098588,GO:0098589,GO:1901360
+TR3807|c0_g1_i1	GO:0003674,GO:0005488,GO:0005507,GO:0005575,GO:0005634,GO:0005743,GO:0005829,GO:0006801,GO:0006873,GO:0006875,GO:0006878,GO:0008047,GO:0008150,GO:0008152,GO:0009987,GO:0010035,GO:0010038,GO:0016020,GO:0016530,GO:0016531,GO:0016532,GO:0019725,GO:0019866,GO:0030003,GO:0030234,GO:0031090,GO:0031966,GO:0042221,GO:0042592,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044237,GO:0044422,GO:0044424,GO:0044429,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0044763,GO:0046872,GO:0046914,GO:0046916,GO:0048878,GO:0050801,GO:0050896,GO:0051716,GO:0055065,GO:0055070,GO:0055076,GO:0055080,GO:0055082,GO:0055114,GO:0065007,GO:0065008,GO:0070887,GO:0071241,GO:0071248,GO:0072593
+TR1894|c2_g1_i1	GO:0005575,GO:0005634,GO:0008270,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044424,GO:0044464,GO:0046872
+TR5212|c0_g1_i1	GO:0003865,GO:0005575,GO:0005783
+TR939|c0_g1_i1	GO:0003674,GO:0003676,GO:0003677,GO:0003723,GO:0003824,GO:0003887,GO:0003964,GO:0004175,GO:0004190,GO:0004518,GO:0004519,GO:0005488,GO:0006139
+TR1891|c0_g1_i1	GO:0003674,GO:0003676,GO:0003677,GO:0003723,GO:0003824,GO:0003887,GO:0003964,GO:0004175
+TR2672|c0_g1_i1	GO:0003865,GO:0005575,GO:0005783
+TR2844|c0_g1_i1	GO:0008152,GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234
+TR1837|c2_g1_i1	GO:0003674,GO:0005488,GO:0005507,GO:0005575,GO:0005737,GO:0006801,GO:0006810,GO:0006811,GO:0006812,GO:0008047,GO:0008150,GO:0008152,GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234,GO:0043167,GO:0043169,GO:0044237,GO:0044424,GO:0044464,GO:0044699,GO:0044710,GO:0044765,GO:0046872,GO:0046914,GO:0051234,GO:0055114,GO:0072593
+TR1678|c0_g1_i1	GO:0003674,GO:0003676,GO:0003677,GO:0003723,GO:0003824,GO:0003887,GO:0003964,GO:0004175
+TR3249|c0_g1_i1	GO:0003674,GO:0003676,GO:0003677,GO:0003723,GO:0003824,GO:0003887,GO:0003964,GO:0004175
+TR1479|c0_g1_i1	GO:0003674,GO:0005488,GO:0005507,GO:0005575,GO:0005737,GO:0006801,GO:0006810,GO:0006811,GO:0006812,GO:0008047,GO:0008150,GO:0008152,GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234,GO:0043167,GO:0043169,GO:0044237,GO:0044424,GO:0044464,GO:0044699,GO:0044710,GO:0044765,GO:0046872,GO:0046914,GO:0051234,GO:0055114,GO:0072593
diff -r 000000000000 -r d4128a4e49ca test-data/filtered/Trinity_filtered_exp.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filtered/Trinity_filtered_exp.fasta	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,34 @@
+>TRINITY_DN1_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG
+CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC
+AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT
+ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG
+GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG
+AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG
+TATATGGTACAGATGTAAAG
+>TRINITY_DN0_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT
+TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT
+ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA
+TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC
+>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT
+TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA
+TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT
+TGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGT
+AATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT
+ATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAA
+AGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCAC
+CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG
+GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT
+G
+>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC
+AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC
+CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC
+ATACATGATTCTATTCAACCAA
+>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG
+CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT
+ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA
+TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
diff -r 000000000000 -r d4128a4e49ca test-data/filtered/Trinity_filtered_pct_iso.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filtered/Trinity_filtered_pct_iso.fasta	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,45 @@
+>TRINITY_DN1_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG
+CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC
+AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT
+ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG
+GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG
+AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG
+TATATGGTACAGATGTAAAG
+>TRINITY_DN0_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT
+TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT
+ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA
+TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC
+>TRINITY_DN2_c0_g1_i1 len=279 path=[257:0-278] [-1, 257, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGA
+ACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACC
+AAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAG
+AGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGA
+AAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA
+>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT
+TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA
+TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT
+TGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGT
+AATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT
+ATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAA
+AGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCAC
+CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG
+GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT
+G
+>TRINITY_DN2_c2_g1_i1 len=240 path=[218:0-239] [-1, 218, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGA
+GTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGC
+TACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTG
+TTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC
+>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC
+AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC
+CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC
+ATACATGATTCTATTCAACCAA
+>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100
+ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG
+CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT
+ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA
+TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
diff -r 000000000000 -r d4128a4e49ca test-data/filtered/counts.matrix
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filtered/counts.matrix	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,8 @@
+	wt_37_2	wt_37_3	wt_37_1	wt_GSNO_3	wt_GSNO_1	wt_GSNO_2	wt_ph8_3	wt_ph8_1	wt_ph8_2
+TRINITY_DN1_c0_g1_i1	90.00	67.00	85.00	36.00	35.00	34.00	222.00	196.00	201.00
+TRINITY_DN0_c0_g1_i1	186.00	137.00	217.00	147.00	186.00	197.00	1088.00	1094.00	1086.00
+TRINITY_DN2_c0_g1_i1	9.00	23.00	16.00	2.00	0.00	1.00	3.00	1.00	1.00
+TRINITY_DN2_c1_g1_i1	59.00	65.00	47.00	6.00	6.00	7.00	3.00	1.00	2.00
+TRINITY_DN2_c2_g1_i1	11.00	4.00	4.00	8.00	5.00	7.00	3.00	4.00	8.00
+TRINITY_DN2_c3_g1_i1	368.00	422.00	425.00	172.00	216.00	210.00	234.00	254.00	212.00
+TRINITY_DN3_c0_g1_i1	36.00	17.00	27.00	4.00	7.00	3.00	4.00	4.00	11.00
diff -r 000000000000 -r d4128a4e49ca test-data/norm/Trinity.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/norm/Trinity.fasta	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,46 @@
+>TRINITY_DN1_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2]
+AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT
+TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT
+ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA
+TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC
+>TRINITY_DN0_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2]
+CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG
+CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC
+AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT
+ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG
+GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG
+AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG
+TATATGGTACAGATGTAAAG
+>TRINITY_DN2_c0_g1_i1 len=279 path=[257:0-278] [-1, 257, -2]
+TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGA
+ACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACC
+AAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAG
+AGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGA
+AAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA
+>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2]
+GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT
+TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA
+TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT
+TGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGT
+AATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT
+ATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAA
+AGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCAC
+CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG
+GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT
+G
+>TRINITY_DN2_c2_g1_i1 len=240 path=[218:0-239] [-1, 218, -2]
+ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGA
+GTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGC
+TACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTG
+TTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC
+>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2]
+GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC
+AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC
+CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC
+ATACATGATTCTATTCAACCAA
+>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2]
+ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG
+CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT
+ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA
+TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
+
diff -r 000000000000 -r d4128a4e49ca test-data/raw/Trinity.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/raw/Trinity.fasta	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,46 @@
+>TRINITY_DN1_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2]
+CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG
+CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC
+AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT
+ATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTG
+GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG
+AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG
+TATATGGTACAGATGTAAAG
+>TRINITY_DN0_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2]
+AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT
+TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT
+ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA
+TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC
+>TRINITY_DN2_c0_g1_i1 len=279 path=[257:0-278] [-1, 257, -2]
+TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGA
+ACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACC
+AAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAG
+AGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGA
+AAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA
+>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2]
+GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT
+TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA
+TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT
+TGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGT
+AATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT
+ATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAA
+AGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCAC
+CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG
+GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT
+G
+>TRINITY_DN2_c2_g1_i1 len=240 path=[218:0-239] [-1, 218, -2]
+ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGA
+GTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGC
+TACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTG
+TTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC
+>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2]
+GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC
+AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC
+CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC
+ATACATGATTCTATTCAACCAA
+>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2]
+ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG
+CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT
+ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA
+TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
+
diff -r 000000000000 -r d4128a4e49ca test-data/raw/map.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/raw/map.tsv	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,7 @@
+TRINITY_DN1_c0_g1	TRINITY_DN1_c0_g1_i1
+TRINITY_DN0_c0_g1	TRINITY_DN0_c0_g1_i1
+TRINITY_DN2_c0_g1	TRINITY_DN2_c0_g1_i1
+TRINITY_DN2_c1_g1	TRINITY_DN2_c1_g1_i1
+TRINITY_DN2_c2_g1	TRINITY_DN2_c2_g1_i1
+TRINITY_DN2_c3_g1	TRINITY_DN2_c3_g1_i1
+TRINITY_DN3_c0_g1	TRINITY_DN3_c0_g1_i1
diff -r 000000000000 -r d4128a4e49ca test-data/reads.left.fq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reads.left.fq	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,400 @@
+@61DFRAAXX100204:1:100:10494:3070/1
+ACTGCATCCTGGAAAGAATCAATGGTGGCCGGAAAGTGTTTTTCAAATACAAGAGTGACAATGTGCCCTGTTGTTT
++
+ACCCCCCCCCCCCCCCCCCCCCCCCCCCCCBC?CCCCCCCCC@@CACCCCCACCCCCCCCCCCCCCCCCCCCCCCC
+@61DFRAAXX100204:1:100:10497:13422/1
+GTAATTTCCGTACCTGCCACAGTGTGGGCTCACCCTGCTTAGAGGACAGGGAAGGACCCTAAAGGTAGGCTGATGC
++
+CCCCCCCCCCCCCCCCCCCCCCDCDCCCCCCCCCCCCCCCCCCCDDCCDDCDCBDCCDDDDBADDADDB@DBBBA@
+@61DFRAAXX100204:1:100:10546:4478/1
+CTGGGCTGCAGCTAAGTTCTCTGCATCCTCCTTCTTGCTTGTGGCTGGGAAGAAGACAATGTTGTCGATGGTCTGG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC7CB@CA:>AB?C=C@@@@?A@?5:88:
+@61DFRAAXX100204:1:100:10609:6818/1
+CACGTTTTCTAAGCAGTTTGTACCAGATCGTGCTAACTGCTCATTGTCTTGTTGTACACACCAGTAAAGCTGGGCA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+@61DFRAAXX100204:1:100:10648:5988/1
+TGCTCATTGTCTTGTTGTACACACCAGTAAAGCTGGGCAAAAATATCATCCAAAAGTACATCGCTGAGAACTCCTA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCDCCCCCCCCCCCCCCCCCCC
+@61DFRAAXX100204:1:100:11486:13583/1
+CCCACCTGAAAACATTTTCTACATCCACTGTTATATGGAATGCTTGATAAGCTTTTCATTCTAACCATCAGAGCAC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBC
+@61DFRAAXX100204:1:100:1176:14271/1
+TCTGAATAAGTCCTGCCACCAATGTTTTTCATAAGTGTGGCCATATGTTTTCATTATTTCAAACATTACTGTTAAG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCCDCDCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCDBBABDB
+@61DFRAAXX100204:1:100:12152:16425/1
+CTCCGTTTTTTGAGAGTGCAACACATAGATACTGCTTGATAGCATTAATAAACATCTCATTTGTCCTGAAAACAGG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+@61DFRAAXX100204:1:100:14680:13081/1
+GCCTGAGTGTGCAAAAATCTTCAGAGTAAGAATACCATAGTTGCTAAATATCTTTTACCATGAGCAATAATTTTTT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC;CCCCCC
+@61DFRAAXX100204:1:100:16086:14019/1
+TCTGGTGCAGCTAGATGGAATACTGAGAAAATGTTCTTCCATCCTGAACGAATATTTGCAGCCTGAGAATTAACCA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCBCCDDCDCC
+@61DFRAAXX100204:1:100:17458:1622/1
+GTGAAAGGTCATCTATTTTAATGGCTTGTCTTTAAAAACCCTAAGAGAGGGAGGATGTCACAGGGAGGGCTTGTCA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCC5A###############################################
+@61DFRAAXX100204:1:100:17716:21197/1
+CCAGGCTTCCCGGTGACTTTCGGATGTTAGAGTGAGGAAGTAGCTCAGCGCTTCCCTGCAGACGTTTAAAAGCCTC
++
+CCCCCCCCCCCCCBCCCCCCCCC@CCCCCC@BBCCCCCCCBDB>CCCCAC@BCBBCDDBD@?BCBA@6BBB>;A;:
+@61DFRAAXX100204:1:100:19734:13092/1
+ATCATCTTGGAGACTTTTATCCACATCATGTGTTTGGGGCTCAAGATCCCCTTCATGCTCTTGGTTTATATGATCA
++
+;CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCDC
+@61DFRAAXX100204:1:100:2082:1789/1
+ACGGGTGTGGTGCCAAGCATCCCTTGTTCTTGGAGGTATTGTATTCCTCTCTTTGGTTTCTTATTAAATAAATCAA
++
+CCCCCDCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCADCCCDBCCCCCCCCCCDABBCCDCC@CBBBDDDD;@B?=
+@61DFRAAXX100204:1:100:2172:8797/1
+GCCAAAACATAAGCAGTATCTGCACTAGCAAAAAGGGTTTGTCCTTGGTTGCACTCTAGGGATCTTGCAGCAAATT
++
+############################################################################
+@61DFRAAXX100204:1:100:2238:12815/1
+ACCATAGTTGCTAAATATCTTTTACCATGAGCAATAATTTTTTTCTCCCTTCCCCCACCCCCAATTATAAACATTT
++
+############################################################################
+@61DFRAAXX100204:1:100:2327:5980/1
+CTCCTAAATAATTTCCATCAGTGTGGGCCACCGTGATGAGTGTTTTTATTGTGTCGATATTCTTCTGTTTCATTTC
++
+CCCCCCCCCCCCCCCCCCCCCCCCC0BBBACCCBCCCCCC=CCCCCB@B@=DC@CCDDBCC-CC@CABBBB<CCCA
+@61DFRAAXX100204:1:100:3665:17139/1
+ATACTTCTTTGGGTAATTTCCGTACCTGCCACAGTGTGGGCTCACCCTGCTTAGAGGACAGGGAAGGACCCTAAAG
++
+CCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCDCBCCCCCCCCCCCCCCCCCCCCCCCCBCBCDCCCBDBA>DC
+@61DFRAAXX100204:1:100:6480:5393/1
+TGGAGACTTTTATCCACATCATGTGTTTGGGGCTCAAGATCCCCTTCATGCTCTTGGTTTATATGATCAACAGTCT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCBCCCCBDCBDDADBDC
+@61DFRAAXX100204:1:100:8693:14085/1
+AGCTATTTCGTTATAAATGGCTGATAGATACTCTTCAGGGAGATCTTTACTGTCATTGATACCACGATTCATTTTA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+@61DFRAAXX100204:1:100:9306:14527/1
+GTAGAATGATGCGTGAGCTTTAAACCTGCTGTCACTGATCTTCAGAACTTTAGTGAGGAACAGTAACAGTAAGTTA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCCCBACDCCBCDCBCC
+@61DFRAAXX100204:1:100:9656:2687/1
+CTTCTAGGCAAAGAGAGGCTACTTCAGTATCATCACAGTCTTGGAGACCCACACTGAATGCAGCCAGAAAAGGTGT
++
+BBBBBBBBBBBBBBBBBBBBB>>B>;=;=7>>?>>B>>;>BB>B################################
+@61DFRAAXX100204:1:101:11219:19264/1
+TTTGCTAACTTCTTCACTCACAGTAGAAACAGAAACCAGTGGTGCTTGCTGTCTGTTATCTGAAGATCTNGGTTGA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCABCCCCCCCCCCCCCC@CBCC;DB<>>A&>99>;@
+@61DFRAAXX100204:1:101:11349:8542/1
+GGGTAATTTCCGTACCTGCCACAGTGTGGGCTCACCCTGCTTAGAGGACAGGGAAGGACCCTAAAGGTANGCTGAT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCAA;A'??@=@>
+@61DFRAAXX100204:1:101:11674:10443/1
+CACCCACACCCTGTCTTCAGGTGCCACGCTCATGTCATCACTTGTGTACTCCTTGAAAGCCTGCGGTCTNTCAGAC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCACCCCCCCCCCACC&AAA?AC
+@61DFRAAXX100204:1:101:1179:19106/1
+TTGGTTGAATAGAATCATGTATGTCTACAGATTTTTGTGATATTGCATCCAACGGCTTTTCACTCACAGNTGATGG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@BCCCCCCCCCCCCCCCCCACCCCADCCBCA@'AA=@??
+@61DFRAAXX100204:1:101:12110:12654/1
+CTTCCCAGGCACTGACTCTGCTCTCGTCCATGTACATCCGGAAGAGAATGCGCAGCCCACACGCCAGGCNGCTTGT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCDCDCCCBCCDCCBCCDCCDCBCDAD@ABBDDDAD@BABB.625'?A=:@0
+@61DFRAAXX100204:1:101:13165:4417/1
+CTGGATTATCAGTGCCAGACATCTGTGTACTGTAGCTGCCAATTCCTGATGATGATGTGGATTCTAAGGNGTTTAA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCA?&75:;8C
+@61DFRAAXX100204:1:101:13420:13159/1
+GGTGGATCCCCTCCTGTTGTCATCTTGACAGGCATCAGCCACAACAGATTCAGGGCACAGCAAGCCCTCNAAATGA
++
+CCCCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACAC&89848C
+@61DFRAAXX100204:1:101:14810:10441/1
+CAGGAAAGAATCAATGGTGGCCGGAAAGTGTTTTTCAAATACAAGAGTGACAATGTGCCCTGTTGTCTGNAATGCA
++
+CCCCCCCCCCCCCCCCCDCCCCCCCCCCBCBCCCBBCCCCCCCBCCCDCCCCCCCDCCDCCCDCC:A?A'AAAAAC
+@61DFRAAXX100204:1:101:15025:8342/1
+GTGGGTAGGAAGCCTCTGCTGCAGGATCCTTTCACAGAGCAGAGCAATGTAAACACCAACAGAAAAACANCGGCTC
++
+CCCCCDCCCCC@CCCCCCCCCCCCCCCCCCCCCCCCCDCCCCBDBCCBCDCCCDCCDCBDACBBD=999%8====B
+@61DFRAAXX100204:1:101:15551:15592/1
+CTCCCAAAACCATGCCAGGTTTGTTATTTTTAATATATTCAACATTAAATTCTGTACATAGAATAAAATNTACATC
++
+CCCCCCCCCCCCCCCCCCCDCCCCCCCCCBBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCA=7A'AAB?AC
+@61DFRAAXX100204:1:101:16061:6897/1
+ATGGAATGCTTGATAAGCTTTTCATTCTAACCATCAGAGCACAGTTCACAGTATGAATACATTTCCAGTNAATCTA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCDCCCCCCCDCCCCDC=C@'ABAAAC
+@61DFRAAXX100204:1:101:16516:11581/1
+GGCCCTAAAGGTAGGCTGATGCTGTGGGAACAGCCTTTCTGCTCAATATGAGCCCAACACGCGACAGAGNCCACTG
++
+74/8588857;-84;<<<<<-88;8488+8A<286A9AA#####################################
+@61DFRAAXX100204:1:101:17825:1193/1
+ACGCTCATGTCATCACTTGTGTACTCCTTGAAAGCCTGCGGTCTATCAGACACATATTTTGCACAATGGNGAATAA
++
+BCCCCCCCCCCCCCCCDCCCCCCCCCCCC@CBCCCCCCC@CCCCCBCDCCCCCCCCCCCCCCCCCAABA&A>>??A
+@61DFRAAXX100204:1:101:2920:3823/1
+TCCATCAGAGCACAGTTCACAGTATGAATACATTTCCAGTAAATCTAACCTCCCAAAACCATGCCAGGTNTGTTAT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCB'CCBC@C
+@61DFRAAXX100204:1:101:4549:18278/1
+AGGTGGATCCCCTCCTGTTGTCATCTTGACAGGCATCAGCCACAACAGATTCAGGGCACAGCAAGCCCTNAAAATG
++
+AB?BA:?B<?>:>:7;=BB=??>A>>>:+>//000BBBB@B@BBBBABBBB>B@?ABBBBBB>@############
+@61DFRAAXX100204:1:101:5059:19347/1
+TTTGGACTTGCCTTTGAAGCCTGCTTTCCACAGAGCAGTCCTCTGTTCATTGTTGGAATTAAATGCTTTNGCAAAT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCC&89:79C
+@61DFRAAXX100204:1:101:5741:4886/1
+CCCACCCCCAATTATAAACATTTTATCCTTCAAAATACAGCTCTCCTGAGTTGTACTTCTCGCAGAAGCNCAGTCT
++
+CCCCCCBBBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'B?BAAC
+@61DFRAAXX100204:1:101:6207:10801/1
+GCCAAAACATAAGCAGTATCTGCACTAGCAAAAAGGGTTTGTCCTTGGTTGCACTCTAGGTATCTTGCANCAAATT
++
+DCCCCCCCDBCCCCCCCCCCCCCCCCCCCCCAC@CAA9AACCCCCCCC@CCCCCCCCCCB@CCCC###########
+@61DFRAAXX100204:1:101:6228:11229/1
+CAGTGATTCAAGTTTCAGTCTGTGAAAGGTCATCTATTTTAATGGCTTTTCTTTAAAAGCCCTAAGAGANTGAGTA
++
+CBCCCCCCCCCCCCC@CCBBCC@CC@<BB@C@CC@CC?CBC?C<CCC?CCC?>>:<5?/:>A?:A###########
+@61DFRAAXX100204:1:101:7284:17741/1
+CAGGTTTGTTATTTTTAATATATTCAACATTAAATTCTGTACATAGAATAAAATCTACATCAAGCCCCGNCACCCA
++
+CCCCCCCCCCCCCCBBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCCCCC@'CCCCCC
+@61DFRAAXX100204:1:101:7317:19738/1
+ATGAGAATCAATATTGTACAGAAAGTTGTACAGAATTTTTTTACATAGAAAACTTTACATCTGTACCATNTACATA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCACC'AAAAA@
+@61DFRAAXX100204:1:101:7386:20759/1
+CCCGGAAAGTGTTTTTCAAATACAAGAGTGACAATGTGCCCTGTTGTCTGAAATGCAAGTTCTACTATGNTTTCAT
++
+CCCCCCCCCCCCCCCBBCCCCCCCCCCCBCCCCCCCDCCCCCCDCCBCCCCCCDCCBBCBCCCCCCBBC)ACBA@D
+@61DFRAAXX100204:1:101:7661:3279/1
+TTGGGGCTCAAGATCCCCTTCATGCTCTTGGTTTATATGATCAACAGTCTGAGGTGGCAAATATCTAAGNTGAGGT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCC'@????=
+@61DFRAAXX100204:1:101:7989:14539/1
+CGTGCTCCAAGTGTGTTGCACTTGTAAAAGGTGCCTGAACATGGCTCACAGCTTCCATGAGTGCTTTAGNCGTCTT
++
+CCCDCCCCCCCCCCCCCCCCCCCCCCCCCCCBDCCCCCCCCCABCCCCCBCCCCCCBCC=CBCCCCCCC'AA<A@C
+@61DFRAAXX100204:1:101:8630:9416/1
+GAGGGAGACAGGCGAGTAGGTGGCGGTGGGGGCGAGGAGGCGTGGATGCTAGCCGCCGTCTCCGTTAGCNTCCGTC
++
+############################################################################
+@61DFRAAXX100204:1:101:9622:17436/1
+GCCAAAACATAAGCAGTATCTGCACTAGCAAAAAGGGTTTGTCCTTGGTTGCACTCTAGGTATCTTGCANCAAATT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCCCBBCCCBBBB'AAA=AC
+@61DFRAAXX100204:1:102:10071:12692/1
+TGCGTGAGCTTTAAATTTAAAAGCCTCTGCTGGANTTCTTCCCAGGCACTGACTCTGCTCTCGTCCATGTACATCC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'CCCCCCCCCCCCCCCCCCCCCCCCCCCCDCDBCCDCCDDAC
+@61DFRAAXX100204:1:102:10556:11503/1
+TCCTGGGATTCCATTTGCTTGGATGTTTTCACTGNCACTACCATCTTCTACAGTTCCAGTGTTGCCTTCTGTACTT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'BBBBBCCCCCCCCCCCCCCCCCBCBCDCDCCCDBDBCAABB
+@61DFRAAXX100204:1:102:10558:14342/1
+ATGTTTTCTACCTTGGTGGATCCCCTCCTGTTGTNATCTTGACAGGCATCAGCCACAACAGATTCAGGGCACAGCA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCC'CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBC
+@61DFRAAXX100204:1:102:12109:19420/1
+TCTGTTATCTGAAGATCTTGGTTGAATAGAATCANGTATGTCTACAGATTTTTGTGATATTGCATCTTACCAACGG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'>????DCCCCCCCCCCCCC@BACCCCCCBCDCCCDCDBDDB
+@61DFRAAXX100204:1:102:12757:13134/1
+GGGATGTATTGAACCACTGCTCTCAGGACAGGAANAAACAATGCACAAGCAATTTTCTTCCTAAATAACAATTCAG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC)BBBBBCCCCCCCCCCCCCCCCCC@BCCCCCCCCCCACCCCC
+@61DFRAAXX100204:1:102:13549:15464/1
+GTCCATGTACATCCGGAAGAGAATGCGCAGCCCANACGCCAGGCTGCTTGTCTCCTGTTTTAGAAGATTGGGCTTG
++
+CCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCC'CCCCCCCCCCC?CCCDCCBCCCBDCDBDDBBCADA<AC@BB
+@61DFRAAXX100204:1:102:13777:6235/1
+CGCAGGACTCACAAGGGTAAAGCAAATTAAGAACNCGTCTGTCTGCGGGTAGGAGAGGGGACGCAATCTGTCATAC
++
+############################################################################
+@61DFRAAXX100204:1:102:14960:18241/1
+GCCACGAATTTCCTAAATAATTTCCATCAGTGTGNGCCACCGTGATGAGTGTTTTTATTGTGTCGATATTCTTCTG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC&CCCCCCCCCCCCCCDCCCCCB@BB@DCCCCDCBCCCCCCCC
+@61DFRAAXX100204:1:102:15063:6971/1
+CAGAAAAGGTGTCCAAGCCAACTTAAACATCGGCNTCACGTGCTCCAAGTGTGTTGCACTTGTAAAAGGTGCCTGA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'8;9;9CCCCCCC@CBCCCCCCCCCCCCCCCCDCAACBBBBC
+@61DFRAAXX100204:1:102:16420:15231/1
+GTTGTACTTCTCGCAGAAGCTCAGTCTTTACATCNATACTTCTTTGGGTAATTTCCGTACCTGCCACAGTGTGGGC
++
+CCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCC'CCCBCCCCACCCCCCDCCCDCDDDCAB@BDBBDDCBCACCB
+@61DFRAAXX100204:1:102:16908:12433/1
+CACTGATGAAATAATTCAAAAACTTTATTGACCTNTAACCTGATTAGATATGCCAGATGAGAATCAATATTGTACA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCC
+@61DFRAAXX100204:1:102:17677:10400/1
+CGCACATCTTATCCCTTCTAGGCAAAGAGAGGCTNCTTCAGTATCATCACAGTCTTGGAGACCCACACTGAATGCA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC',00.-;7;<4?@>:A##########################
+@61DFRAAXX100204:1:102:17711:7491/1
+ACTCTGGACAATATCAAGTGGCTTTTCTTCATAGNCTCCATCATACAAGATATCATTTTTAGATAATGTTTCAGCT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCC'CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCDCCCCBCA
+@61DFRAAXX100204:1:102:17798:2084/1
+CCTTGTTCTTGGAGGTTTTGTATTCCTCTCTTTGNTTTCTTATTAAATAAATCAATCCCTTGTTCTATTATTTCTT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBBB'BBBBBCCCCCCCCCCBBCCACCCCCCCCCCCCCCDCCCCCC
+@61DFRAAXX100204:1:102:18807:10059/1
+CTGCACTGGAAATATCAGATCCGTTTTCAGGCTCNGTATCATCTTGGAGACTTTTATCCACATCATGTGTTTGGGG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC&CBCCCCCCCCCC@CDCCCCCCCDCDCDC@ACDBADDBB;BA
+@61DFRAAXX100204:1:102:19518:11565/1
+CCTGGGAAGAAGACAATGTTGTCGATGGTCTGGANGAGTTCCAGCTGCACAACACATTTAATCAACAGGGCAGCAA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCC'BAB>BCCCBCCCCCCCDDACABCCBACCACDAD@DDBD<>C
+@61DFRAAXX100204:1:102:2639:2051/1
+CTGCCTCAGAGAGTCTACTGCAAATATGGCTACANCTTCATTAGGATTACAACCAACCTTATTAAAATGATCTCCA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCAA3A##########################################
+@61DFRAAXX100204:1:102:3101:2926/1
+CTTCCCAGGCACTGACTCTGCTCTCGTCCATGTANATCCGGAAGAGAATGCGCAGCCCACACGCCAGGCTGCTTGT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'BBBBBCCBCCCCCCCCCCCCCCCCCCC<CCCDDCAAB@B<B
+@61DFRAAXX100204:1:102:5977:14503/1
+GGGGGTTCGGCCTCGCCAGAGGTGGGACGCCAAGNCAGAAGCGCGTGAGGAATTGTGGTTTTGAAGATATCCAGGG
++
+CCCCCCCCCCCCCCCCCCCCCCACCCCCCCCCCC'CCCCCCCCCCDCACCBCBCC?CCBCCCCAACDCCCBCDCCA
+@61DFRAAXX100204:1:102:6251:21399/1
+CCCAGCTATTTCGTTATAAATGGCTGATAGATACNCTTCAGGGAGATCTTTACTGTCATTGATACCACGATTCATT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'BBBBACCCCCCCCCCC@CCCDCCCCCDCDCCBCCBCDD@CC
+@61DFRAAXX100204:1:102:7093:4246/1
+CGGGTCTTGTCAGCAGGGATGTTTTCTACCTTGGNGGATCCCCTCCTGTTGTCATCTTGACAGGCATCAGCCACAA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC(CCCCCCCCCCB@CDCCDCCCCCCCDDDCBDDBDDBDCDABB
+@61DFRAAXX100204:1:102:7907:21314/1
+AGACACATATTTTGCACAATGGCGAATAAGTCGGNTTGCTTCCATACTTGTGTCTGGGAAAGCTGCATTACATGCG
++
+>BBB>BB>BBB<B?>?>??<99:<9:A<??0000%*000089:;<74;?8BABBBBA>B#################
+@61DFRAAXX100204:1:102:8037:6949/1
+TCTAGGTATCTTGCAGCAAATTTTTCCATTAATCNATCAATTTTCTGAGCTTCTCCTGGAAGCCGGAATCCTTCCA
++
+CCCCCCDCCCCCCCCCCCCCCCCCCCCCCCCCCC(BBBBBCCCCCCCCCCCCCCCCCCCBCCCCCCDDDCCCCCCC
+@61DFRAAXX100204:1:102:8724:1888/1
+CGGGTGTGGTGCCAAGCATCCCTTGTTCTTGGAGNTATTGTATTCCTCTCTTTGGTTTCTTATTAAATAAATCAAT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBB@B&28;88DCCCCCCCCCCCCCCDCCCCCBCCDC@BCA>@BD@B
+@61DFRAAXX100204:1:102:8903:16361/1
+CCTATAAGTTGTGCCAGCTCTAACTGACTGATGCNCTTCAGGATCTCATGCCACGAATTTCCTAAATAATTTCCAT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC(CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+@61DFRAAXX100204:1:102:9691:18717/1
+ATAAGTTGTGCCAGCTCTAACTGACTGATGCACTNCAGGATCTCATGCCACGAATTTCCTAAATAATTTCCATCAG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC'BABBACCCCCCC;CCCCCBCCCCCCCCCCCCCCCCDCCCAC
+@61DFRAAXX100204:1:103:10201:1449/1
+CTGAACACTAGAAAGGCATCCTTTTGTAAAATGTGGGAAAACTTAGCACCAGGTGAAGGTCCTGAAGAATTTCCAG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCCCCCCDCCCCCCCC?CCBCCCCCACC;CCCCCCC
+@61DFRAAXX100204:1:103:11572:6697/1
+CAAAATTGAAACTAAACATTCTAACCCCTTTTTTCGCAGGCTCAATTCCTGAACATTACTCATACCGAGTTCTTGG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC8CDCCCCDD
+@61DFRAAXX100204:1:103:12517:20251/1
+GCCGGAAAGTGTTTTTCAAATACAAGAGTGACAATGTGCCCTGTTGTCTGAAATGCAAGTTCTACTATGCTTTCAT
++
+CCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+@61DFRAAXX100204:1:103:13105:12342/1
+CTGGACTTCTTCCCAGGCACTGACTCTGCTCTCGTCCATGTACATCCGGAAGAGAATGCGCAGCCCACACGCCAGG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCBCCCB@CCCCCB?BCCCCCCB@C@B;
+@61DFRAAXX100204:1:103:13548:1359/1
+GGTGACTTTCGGATGTTAGAGTGAGGAAGAAGCTCAGCGCTTCCCTGCAGACGTTTAAAAGCCTCTGCTGGACTTC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCC+??AA?CCCCCCCCCCDCCDCBDCBCC@BBDDBDDDDBBABBACAAB
+@61DFRAAXX100204:1:103:13762:1440/1
+CTCCCTTCCCCCACCCCCAATTATAAACATTTTATCCTCCAAAATACAGCTCTCCTGAGTTGTACTTCTCGCTGAA
++
+CCCCCCCCCCCCCBBBBBBCCCCCCCCCC?CCCCCCCCCCCCACCCCCCCCCCCCCCCCDCCDCCCCCCCACCBB@
+@61DFRAAXX100204:1:103:13776:4298/1
+TGATATTTGAAATACTATTCCAATTCGCAGGAAAAATCTTCTAAGAACAGCACGCAGTTCCGGAATCAAGTCAAAT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDC@BCC
+@61DFRAAXX100204:1:103:13798:6365/1
+GGTCACAGTCATAATTTACATAAATGTCCACCACACTCTGAGCATCTGCACAGATCCTTGTCAGTGTCTGAATAAC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCC
+@61DFRAAXX100204:1:103:14748:1375/1
+CCAGGTTTGTTATTTTTAATATATTCAACATTAAATTCTGTACATAGAATAAAATCTACATCAAGCCCCGCCACCC
++
+CCCCCCCCCCCCCCCBBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@BCCCCCCCCCACCCDBD@@DDB
+@61DFRAAXX100204:1:103:16156:9928/1
+CATGAGCAATAATTTTTTTCTCCCTTCCCCCACCCCCAATTATAAACATTTTATCCTTCAAAATACAGCTCTCCTG
++
+CCCCCCCCCCCCCCCCCCBBBBCCCCCCCCCC@B@BB@CCCCCCCCCACCCCCCCCCCCCAACCCCCCCCCCCCCC
+@61DFRAAXX100204:1:103:16292:7311/1
+CTGGTTCTTACATCTAATTTGCATCTATTGATGATACAAGACAACTCAAAGAGGATCGGGAACCACCCTCTCACCC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDBCDCDCCCCCCCCCCBDC
+@61DFRAAXX100204:1:103:1757:15756/1
+GGCAAAAATATCATCCAAAAGTACATCGCTGAGAACTTCTAAATACTGGGTGAATACATCACATATTGCATAAAGG
++
+CCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCCCCCC
+@61DFRAAXX100204:1:103:19512:1223/1
+CTGTTAAGCCCCTGGTTCTTACATCTAATTTGCATCTATTGATGATACAAGACAACTCAAAGAGGATCGGGAACCA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCDCCDADBB@C@BB@
+@61DFRAAXX100204:1:103:2005:9846/1
+TGCTTCCCTGCAGACGTTTAAAAGCCTCTGCTGGACTTCTTCCCAGGCACTGACTCTGCTCTCGTCCATGTACATC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCCCCCCBCCCCABDBBCBBDDDC
+@61DFRAAXX100204:1:103:2755:14644/1
+CTTACATCTAATTTGCATCTATTGATGATACAAGACAACTCAAAGAGGATCGGGAACCACCCTCTCACCCACACCC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC=C
+@61DFRAAXX100204:1:103:3597:13520/1
+GTTGTTGTGATGTTAAAAAGCGGTACATTCCTTGGTCTTGAGTATCAACTCGAACATCGAAGTCTACTACATCTCT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCDCCCCCCCCCCCCCCCCCDCBCCCCDADDCDCDC
+@61DFRAAXX100204:1:103:4062:11566/1
+GATGATACAAGACAACTCAAAGAGGATCGGGAACCACCCTCTCACCCACACCCTGTCTTCAGGTGCCACGCTCATG
++
+CCCCCCCCCCCCCBCCCCCCCCCCCCBCCCCC@CACCBCCCCCCCCCACCBCC=@BCBAC3;;-6AC@C@C?@:AB
+@61DFRAAXX100204:1:103:5147:16732/1
+CATGGTTACAAGTTGTTGTCATCCATTCAGCTTTCTCTGTCTGCTGTTCTGGCAATTTCATGTTGTCAAAGATTCT
++
+CCCCCCCCCC;????CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+@61DFRAAXX100204:1:103:6646:12936/1
+GTGCAACACATAGATACTGCTTGATAGCATTAATAAACATCTCATTTGTCCTGAAAACAGGTCCTGCATTCTGCAG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCDC
+@61DFRAAXX100204:1:103:7220:15954/1
+GAGGAATTGTGGTTTTGAAGATATCCAGGGTGCAGTTACACGTTTTATCCCAGATTTCAAGAGTAAACTTTTCACC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCABCCCCCCCA
+@61DFRAAXX100204:1:103:7253:3680/1
+CTTTACATCTGTACCATATACATATCCACCTGAAAACATTTTCTACATCCACTGTTATATGGAATGCTTGATAAGC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+@61DFRAAXX100204:1:103:8055:11636/1
+TTCCTGATGATGATGTGGATTCTAAGGAGTTTAAACTTCCATATCTGTTTATAGTCTCTGGGTGTTTAACTTCACT
++
+CCCCCCCCCCCCCCCCCC<CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCBCDCCCABCCCDCC
+@61DFRAAXX100204:1:103:8348:14452/1
+GTCAGAGCACAGTTCACAGTATGAATACATTTCCAGTAAATCTAACCTCCCAAAACCATGCCAGGTTTGTTATTTT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDBCCDCCCDCCCBCB
+@61DFRAAXX100204:1:104:12460:3347/1
+CTGATGCTGTGGGAACAGCCTTTCTGCTCAACATGAGCCCAACACGAGACAGAGGCCACTGGGTTACTAAAGGGAC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCCCC@CCDCDDCCCCBCCDCBB@BBAAB
+@61DFRAAXX100204:1:104:12993:12947/1
+GGTGAATACATCACATATTGCATAAAGGACATGGTTACAAGTTGTTGTCATCCATTCAGCTTTCTCTGTCTGCTGT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+@61DFRAAXX100204:1:104:13501:6860/1
+GTGATATTTGAAATACTATTCCAATTCGCAGGAAAAATCTTCTAAGAACAGCACGCAGTTCCGGAATCAAGTCAAA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCBCCCCCCACCCDCBCC>A
diff -r 000000000000 -r d4128a4e49ca test-data/reads.right.fq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reads.right.fq	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,400 @@
+@61DFRAAXX100204:1:100:10494:3070/2
+CTCAAATGGTTAATTCTCAGGCTGCAAATATTCGTTCAGGATGGAAGAACATTTTCTCAGTATTCCATCTAGCTGC
++
+C<CCCCCCCACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCACCCCCACCC=
+@61DFRAAXX100204:1:100:10497:13422/2
+GAGTTACTGGTAAGACGCTTACACCTATAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCACCC
+@61DFRAAXX100204:1:100:10546:4478/2
+CTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGACATACATGATTCTATTCAACC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@BCDCBCCCCCCCCCCCACCCCCCCCCBDC
+@61DFRAAXX100204:1:100:10609:6818/2
+AGCAGACAGAGAAAGCTGAATGGATGACAACAACTTGTAACCATGCCCTTTATGCAATATGTGATGTATTCACCCA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC?CBCC
+@61DFRAAXX100204:1:100:10648:5988/2
+AGATGGGCTTAACAGTAATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCACCCBCCBACC
+@61DFRAAXX100204:1:100:11486:13583/2
+CTTGAATCACTGCAAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTTATT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCCCCBBBB@CCDCCCCDB@BDCCABCDDCBBCCCBC@
+@61DFRAAXX100204:1:100:1176:14271/2
+TGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTATTCGCCATTGTGCAAAATATGTGTCTGATAGACCG
++
+CCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCDCCCCCCCCCC:BBBACCABC@CDDAB@DDCABDDABDBB
+@61DFRAAXX100204:1:100:12152:16425/2
+CCTTTCTAGTGTTCAGGTCATTGTGTAAGCTGTCAATGAAACCACTGTCAGATGGACCACCAGATCCAAAGTCTCA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCC=
+@61DFRAAXX100204:1:100:14680:13081/2
+CACAGCATCAGCCTACCTTTAGGGTCCTTCCCTGTCCTCTAAGCAGGGTGAGCCCACACTGTGGCAGGGACGGGAA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCDCCCCCCCCCBCCDCCB'299@'9@
+@61DFRAAXX100204:1:100:16086:14019/2
+AGAAAGGAGAGCTTGCAAACTTCAGATTCCAAAAGGATTTCTTACGACCTTTTGAACATATAATGAAACGAAACAG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCBCCCBCCCCCC
+@61DFRAAXX100204:1:100:17458:1622/2
+AAAACATTTGGGTTGAACTTTTAGTCTTTGGGGGAGTGGTGGTCATTTTGAGGGCTTGCTGTGCCCTGAATCTGTT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCB@CCCCCBCCCCCCCDCCCDDCBDCBB@BABA=BBDB@AB<
+@61DFRAAXX100204:1:100:17716:21197/2
+GCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGAAAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCAC?CCDBBCCBD@BCBBBB@B??BBA=@A?@
+@61DFRAAXX100204:1:100:19734:13092/2
+GGCTTTACTTACCGCAGTGACATCACAACACATAGAAATCCATGAAGGAACTGTGCTGCAAGCTGTGAGGACATGC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCCCCC?CC@CBCCCBCAACCC
+@61DFRAAXX100204:1:100:2082:1789/2
+GGAGCAAGGATCAGTATGTGAACCCCAACTCTCAAACTACCCTTGGTCAGGAAAAACCCTCAGAGCAAGAGATACG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCBCBCCCBCDBBDACCDBCDCA@B##
+@61DFRAAXX100204:1:100:2172:8797/2
+TATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCTACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAA
++
+############################################################################
+@61DFRAAXX100204:1:100:2238:12815/2
+CCCCTCCAGACCCTTTAGAAACCCAGAGGCCTCGGGCTCGCGTGTGGCTCATTTTCGCCAGAAAGGCGGTTCCCAC
++
+############################################################################
+@61DFRAAXX100204:1:100:2327:5980/2
+CAAGACTGTGATGATACTGAAGTAGCCTCTCTTTGCCTAGAAGGGATAAGATGTGCTATCAGGATTGCATGCATTT
++
+CCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCACCCC?BCCCCACBCCBCCCCCCCDDDAA@CCDBBC
+@61DFRAAXX100204:1:100:3665:17139/2
+AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGTTTTTCTGTTGGTGTTT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC?CCCCCC@CC@@CB@@@@DABBBCBBB
+@61DFRAAXX100204:1:100:6480:5393/2
+TGCTACAATATCTATTTAGCCAGCAAAAATCTCATCAATCAGACAACAGCCAAAGCTACTCTTACTGAAATGCTGA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCB
+@61DFRAAXX100204:1:100:8693:14085/2
+TGCAACCAAGGACAAACCCTTTTTGCTAGTGCAGATACTGCTTATGTTTTGGCCTACTCAATTATCATGTTGACTA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+@61DFRAAXX100204:1:100:9306:14527/2
+GCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGCTACTTCCTCACTCTAACATCCG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCC
+@61DFRAAXX100204:1:100:9656:2687/2
+TAGAAATGGAACAGATGGCCAAGACGGCTAAAGCACTCATGGAAGCTGTGAGCCATGTTCAGGCACCTTTTACAAG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCD3DBBCCCDCBBCCDCBDC
+@61DFRAAXX100204:1:101:11219:19264/2
+GTGATGTATTCACCCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@B@CBBCCCADDCCA@BC
+@61DFRAAXX100204:1:101:11349:8542/2
+GTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCTACCTGAAAAATGTTTCTCTCAATTGTAG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC?DDD@CDDDDDBCBBCDDDBDABB)BBBB
+@61DFRAAXX100204:1:101:11674:10443/2
+CTCTGAGGCAGCTATCAATGAAGTTTTTAGAGAAAGGAGAGCTTGCAAACTTCAGATTCCAAAAGGATTTCTTACG
++
+CCCCCCCCCCC@CCCCBC?CC@CBBCCC=C@CCCCAC:B@BBCC>@=@@@B>@BC@ACBB@>CBB=0;C@BBCC/?
+@61DFRAAXX100204:1:101:1179:19106/2
+AAAACATTGGTGGCAGGACTTATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCBCCBBCCCCACCCCACCCCCCCCCCCCCCCCBABDB>D@BDDD@
+@61DFRAAXX100204:1:101:12110:12654/2
+GCAAGCACCACTGGTTTCTGTTTCTACTGTGAGTGAAGAAGTTAGCAAAGTGAAATCCACAGCAAAATTCCCAGAA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCBCDCCCCCBCCCCCDCCBCDCCBCAACCDCCAA>BBC=B<B?B
+@61DFRAAXX100204:1:101:13165:4417/2
+GGACATTTATGTAAATTATGACTGTGACCTAAATGCAGCAAATATATTTGAAAGACTAGTAAATGACCTGTCGAAA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCAC
+@61DFRAAXX100204:1:101:13420:13159/2
+CCGGAAATCATCATCTTTCTGTGAAAATGTACAGAGATGCAGGTCTGTAATATAAAAATCTTAAACATATTGTTCC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCDCCCCCCCCC@@CCCCBCCCCCCDCDBC@
+@61DFRAAXX100204:1:101:14810:10441/2
+GGTGTATAGCACAAATGGTTAATTCTCAGGCTGCAAATATTCGTTCAGGATGGAAGAACATTTTCTCAGTATTCCA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCBCCCCCC
+@61DFRAAXX100204:1:101:15025:8342/2
+GCCTGGACTAACTTACTGTTACTGTTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCAT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCDCCDCDCACCB
+@61DFRAAXX100204:1:101:15551:15592/2
+GACCTACCTGTGACATACTCACTCTCTTAGGGCTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCCCCCCCCCCCCDCC@
+@61DFRAAXX100204:1:101:16061:6897/2
+GGCTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGCAAAATGAATCTAGG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCC
+@61DFRAAXX100204:1:101:16516:11581/2
+GATCCTGCAGCAGAGGCTTCCTACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTA
++
+C@CCCCCC@CCCCBBCBBCCC=@8@CC:CCCBC?C@@CC@C@>@@CCC>C>@>A<A8@8=<??<<=:C5>BCCBCC
+@61DFRAAXX100204:1:101:17825:1193/2
+AACGAAGCAGGTCTCCAACAATTCGAGATATGGTTGTACGGTGTATAGCACAAATGGTTAATTCTCAGGCTGCAAA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCDCCCCCCCCCCCCCBCCCCCCACCCDC<ABBBA
+@61DFRAAXX100204:1:101:2920:3823/2
+CAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGGCTTTTAAAGACAAGCCA
++
+CCCCCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCBCCCCCCCCCCCDCCCCCCCACCCCCCC=C?
+@61DFRAAXX100204:1:101:4549:18278/2
+GTCTGTAATATAAAAATCTTAAACATATTGTTCCTCCTGCACTGTTTTATTTCTTTATTTTCTTATCTACTTGCTA
++
+CCCCCCCCCACCCCC@@CCCBB?CCCCCCCCCCCCCCCCCCCCCCCCCCC@@@CC@=CC@@@C@@CCCCCCCCACC
+@61DFRAAXX100204:1:101:5059:19347/2
+AAGAAGACAATGTTGTCGATGGTCTGGATGAGTTCCAGCTGCACAACACATTTAATCAACAGGGCAGCAAACAATT
++
+CCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCDCCCCCCCCCCCCCCCCACCCCCCCCCCCCCCCBCDADCA?ACC
+@61DFRAAXX100204:1:101:5741:4886/2
+GGATCCTGCAGCAGAGGCTTCCTACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTT
++
+CCCCCCCCCCCCCCCCCCCCACCCCCCCCCCCCCCACCCCBCC:CCCCCDCDCDCBCBCBC@BCCC@?BBCBCCBD
+@61DFRAAXX100204:1:101:6207:10801/2
+GGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCATATGTAGACCAACATGACTTTTCAGGAAAAGACTTT
++
+CCCCCACCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCBCCCCACCCCCCCCD@BCBB@BBCABC
+@61DFRAAXX100204:1:101:6228:11229/2
+CTGTAATATAAAAATCTTAAACATATTGTTCCTCCTGCACTGTTTTATTTCTTTATTTTCTTATCTACTTGCTAAA
++
+CCBBCCCCCCCCC@@CCC>CCCBBC??>@BCCCCCBBCCCCC@CCCBC@@@CC@@CC@@@C@>CCCCCCCCCCC@C
+@61DFRAAXX100204:1:101:7284:17741/2
+AAAAATCTTAAACATATTGTTCCTCCTGCACTGTTTTATTTCTTTATTTTCTTATCTACTTGCTAAATACCCATAA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBBCCB@CCBBBCBBCCCCCCCCCBCCCCCCCCCCBA
+@61DFRAAXX100204:1:101:7317:19738/2
+CATGGTTTTGGGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATGAAAAGC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCBCCCCCCAAC?BCCCCDCCCCCDC@
+@61DFRAAXX100204:1:101:7386:20759/2
+GATGTAGCCATATTTGCAGTAGACTCTCTGAGGCAGCTATCAATGAAGTTTTTAGAGAAAGGAGAGCTTGCAAACT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCD@CACBDDB@CABCCCB@BBABBAABB>>BAB>?AA>AB
+@61DFRAAXX100204:1:101:7661:3279/2
+GCTGCAAGCTGTGAGGACATGCTACAATATCTATTTAGCCAGCAAAAATCTCATCAATCAGACAACAGCCAAAGCT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCD@CCC
+@61DFRAAXX100204:1:101:7989:14539/2
+TGACTACAGACCTTCACAGTCCACAGGTTAAAAACAAAATGACAAAAGAACAGTACATTAAAATGAATCGTGGTAT
++
+CDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBBBBCCCCCCCC?BBCCCCCCCCCC@CCCCCCC?BCCBC=
+@61DFRAAXX100204:1:101:8630:9416/2
+GGCGCAGGCACCTCCACCGGCCCCGCCTTCTCTCCGCAAACGCTCCACGCACACAAAGGAGGCCCTTGAGCCTCAA
++
+############################################################################
+@61DFRAAXX100204:1:101:9622:17436/2
+ACCTCCAAGAACAAGGGATGCTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCACCBCCCBCCCCCCCC
+@61DFRAAXX100204:1:102:10071:12692/2
+GCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACCAAGGAATGTACCGCTTTTTAACATCAC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCDCCCCCDCCCCDCCCCCBC
+@61DFRAAXX100204:1:102:10556:11503/2
+CGGATCTGATATTTCCAGTGCAGAAAATGAACAGACAGAAGCTGATCAGGCAACTGCAGCTGAAACATTATCTAAA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCDCCC
+@61DFRAAXX100204:1:102:10558:14342/2
+AGAGATGCAGGTCTGTAATATAAAAATCTTAAACATATTGTTCCTCCTGCACTGTTTTATTTCTTTATTTTCTTAT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBBCCBBCCBBBCBBC
+@61DFRAAXX100204:1:102:12109:19420/2
+AAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTGTACAACAAGACAATGAGCAGTT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCBCCC@CCCCCCCC?CCBCCADCDCAB
+@61DFRAAXX100204:1:102:12757:13134/2
+CAACGGAGCAGATTGCGTCTCACACAGAGGAACGAGAGGAAGTCTGTAACGCTCAGAGACTTGATGACAGTTCTTG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCBCCCDCCCCCBCDCDCDDDDDBDCBBBDCBDBDD
+@61DFRAAXX100204:1:102:13549:15464/2
+GCAAGAAGGAGGATGCAGAGAACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCA
++
+CCCCCCCCCCCCCCCCCCBCDCCCCCCCCCBCCCCCCCCCCCCCBCCCACC@CCCCCCCBDCCC=CC?CC?CCACA
+@61DFRAAXX100204:1:102:13777:6235/2
+GAAGGCCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTGTACAACACGACCATGAGCCGC
++
+############################################################################
+@61DFRAAXX100204:1:102:14960:18241/2
+GCTGCATTCAGTGTGGGTCTCCAAGACTGTGATGATACTGAAGTAGCCTCTCTTTGCCTAGAAGGGATAAGATGTG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCACCCCCCCCCDC
+@61DFRAAXX100204:1:102:15063:6971/2
+GTATCTATCAGCCATTTATAACGAAATAGCTGGGAAAAAAATATCAATGAAAGAAACAAAAGAACTAACAATCCCT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBBBCCCCCCCCCCCBBCC@BBCBBCCCCC?CCCAC
+@61DFRAAXX100204:1:102:16420:15231/2
+CTACTACCCTCTCTTATGTGAAATTATGCAATTTGACTTGATTCCGGAACTGCGTGCTGTTCTTAGAAGATTTTTC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCC@CCCCCCCC>@CCCCCCCCCBC@DCBCCC
+@61DFRAAXX100204:1:102:16908:12433/2
+TGGGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATGAAAAGCTTATCAAG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCDCCCCCBCCACCCCBCC
+@61DFRAAXX100204:1:102:17677:10400/2
+CAATCCCTACAAAGTCAACTAAACAGAATGTAGCCAGTGAAAAGCAAAGACGACTTCTGTATAACTTAGAAATGGA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCCCCCCCCBCCCCACDCC;@BBB@C
+@61DFRAAXX100204:1:102:17711:7491/2
+TATAAACCAAGAGCATGAAGGGGATCTTGAGCCCCAAACACATGATGTGGATAAAAGTCTCCAAGATGATACAGAG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCDCCCCCCCADC=DCCBCDA
+@61DFRAAXX100204:1:102:17798:2084/2
+AGTGAAGTTAAACACCCAGAGACTATAAACAGATATGGAAGTTTAAACTCCTTAGAATCCACATCATCATCAGGAA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCDC
+@61DFRAAXX100204:1:102:18807:10059/2
+CTACAATATCTATTTAGCCAGCAAAAATCTCATCAATCAGACAACAGCCAAAGCTACTCTTACTCAAATGCTGAAC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCACC
+@61DFRAAXX100204:1:102:19518:11565/2
+CTTCAAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCCCCATCTCCATCA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCBCC@BCCCDBCCDABDDDDCDBCBDCBDDA
+@61DFRAAXX100204:1:102:2639:2051/2
+CAGGAGTCTATTGGAGAAACCAGCTCTCAAAGTGTGGTAGTTGCTGTGGATAGAATATTCACCGGATCCACAAGGC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCDCCACCDCCCCCACCBCB@<A88>>5?>@>@17>A1;5;:=;
+@61DFRAAXX100204:1:102:3101:2926/2
+GAGAACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACCAAGGAATGTACC
++
+CCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCACCCCCCCCCCCDBCC
+@61DFRAAXX100204:1:102:5977:14503/2
+GAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTGTACAACAAGACAATGAGCAGT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCDCDCDCCCCCCDCDCCCCCDBCDCB
+@61DFRAAXX100204:1:102:6251:21399/2
+GTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCATATGTAGACCAACATGACTTTTCAGG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCDCCCCDCCCCDCACCBCBCCBDDCC@D<BCBDDBDAB
+@61DFRAAXX100204:1:102:7093:4246/2
+GAAGATTTTTGCACACTCAGGCTATCTGAGACACCGGAAATCATCATCTTTCTGTGAAAATGTACAGAGATGCAGG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCBCCBCB@ABBBADB@C=
+@61DFRAAXX100204:1:102:7907:21314/2
+GACTCTCTGAGGCAGCTATCAATGAAGTTTTTAGAGAAAGGAGAGCTTGCAAACTTCAGATTCCAAAAGGACTTCT
++
+@@@9@#######################################################################
+@61DFRAAXX100204:1:102:8037:6949/2
+CTCTACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCATATGTAGACCAA
++
+CCCCCCCCCCCDCCCBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCDCCCCCCCCADCBCCABCAD@C@
+@61DFRAAXX100204:1:102:8724:1888/2
+TGAACTCCTTAGAATCCACATCATCATCAGGAATTGGCAGCTACAGTACACAGATGTCTGGCACTGATAATCCAGA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@=B?@99;>?BB==<@=@A?B=<<BBB>DB2(?=;@
+@61DFRAAXX100204:1:102:8903:16361/2
+GCATTTTCAGCATTCAGCTGGAAAGAGATGCATATGTCCAAGCACTAGCCAGATTTACCTTACTTACAGTGAGTTC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCBCBCC
+@61DFRAAXX100204:1:102:9691:18717/2
+CTAGAAGGGATAAGATGTGCTATCAGGATTGCATGCATTTTCAGCATTCAGCTGGAAAGAGATGCATATGTCCAAG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+@61DFRAAXX100204:1:103:10201:1449/2
+GAGACTATGAAGAAAAGCCACTTGATATTGTCCAGAGCATTGTAGAAGAAATGTTGAACATCATTGTTGGAGACAT
++
+CCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCBCCCCCCCDCBCCCCDCCCCCCCDCCCCDCA@BCBBB?
+@61DFRAAXX100204:1:103:11572:6697/2
+AGCTCATTTGACCATAAGTGGATGGTTATTCAGACACTGACAAGGATCTGTGCAGATGCTCAGAGTGTGGTGGACA
++
+CCCCCCCCCCCCCCCCCCAC???AAACCCCCCCCCCCCCCCCCCCBCCCCCCCC@CABCCCCAACBC>CB<A?:BB
+@61DFRAAXX100204:1:103:12517:20251/2
+CAGCTATCAATGAAGTTTTTAGAGAAAGGAGAGCTTGCAAACTTCAGATTCCAAAAGGATTTCTTACGACCTTTTG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCCCCCCCCCCCDDCDCCCCCCCDCDDDBCD
+@61DFRAAXX100204:1:103:13105:12342/2
+TCAAGCTACTGGACTGCTTATTAGAGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGC
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCBCDD@BAAA
+@61DFRAAXX100204:1:103:13548:1359/2
+GGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAGAGTCGCATAGATTTGCAA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCBDCDCCCBDCCCBDDBCCDDCDCADDBDC@B
+@61DFRAAXX100204:1:103:13762:1440/2
+GAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTATAACTCAAGGTCGGAATAGT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCBCCCCCCCCDCCCDDCBCCCCB@BCC>
+@61DFRAAXX100204:1:103:13776:4298/2
+CCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTGTTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCBCCCCCCCC
+@61DFRAAXX100204:1:103:13798:6365/2
+GTTTATTAATGCTATCAAGCAGTATCTATGTGTTGCACTCTCAAAAAACGGAGTCTCATCTGTTCCAGAGGTTTTT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCDCCCCCCCCDCCDDCDCCBDDC@
+@61DFRAAXX100204:1:103:14748:1375/2
+TAAAAATCTTAAACATATTGTTCCTCCTGCACTGTTTTATTTCTTTATTTTCTTATCTACTTGCTAAATACCCATA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCB@BCCB=CCBBBC@@CCCACCCACCCCBCCCDD>DC
+@61DFRAAXX100204:1:103:16156:9928/2
+CTCATGTTGAGCAGAAAGGCTGTTCCCACAGCATCAGCCTACCTTTAGGGTCCTTCCCTGTCCTCTAAGCAGGGTG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCDCCCDCCDCCA@ACBABB?B
+@61DFRAAXX100204:1:103:16292:7311/2
+CACCATTGATTCTTTCCAGGATGCAGTGAAGTGTTTGTCTGAATTCACATGTAATGCAGCTTTCCCAGACACAAGT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCC5CCCCDCCCCCBCCBCCCBDDDBDBBBBCD
+@61DFRAAXX100204:1:103:1757:15756/2
+TGCAAATTAGATGTAAGAACCAGGGGCTTAACAGTAATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
+@61DFRAAXX100204:1:103:19512:1223/2
+TGTCACTCTTGTATTTGAAAAACACTTTCCGGCCACCATTGATTCTTTCCAGGATGCAGTGAAGTGTTTGTCTGAA
++
+CCCCCCCCCCCCCCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCC@CBA8=A=CCACCCBCCA#
+@61DFRAAXX100204:1:103:2005:9846/2
+TTTAATTCCAACAATGAACAGAGGGCTGCTCTGTGGAAAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA
++
+CCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBDDBCDCCDBDCBCCDDDCDADBBDDC
+@61DFRAAXX100204:1:103:2755:14644/2
+GCTGCATCAGACCAAGATGAAAGCATAGTAGAACTTGCATTTCAGACAACAGGGCACATTGTCACTCTTGTATTTG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCACCCCC>CCC@CBACDCCDCC
+@61DFRAAXX100204:1:103:3597:13520/2
+CACCTCTGGCGAGGCCGAACCCCCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCACACDDCCDDCCB@A?B@BB@ABBBBADABD<?>AA
+@61DFRAAXX100204:1:103:4062:11566/2
+CAACAATTCGAGATATGGTTGTACGGTGTATAGCACAAATGGTTAATTCTCAGGCTGCAAATATTCGTTCAGGATG
++
+CCCCCCCBCCCCCCCCCCCCC?CCCC=CCCCCA=@A@CCACBCC?ABAABCCCCACC>BC<CCCACCCCB@C@B@?
+@61DFRAAXX100204:1:103:5147:16732/2
+GGCTTTCAAGGAGTACACAAGTGATGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCBCCCBCCCCCCCBCCBBCCBC
+@61DFRAAXX100204:1:103:6646:12936/2
+CTCCAATGATACTCAGGAATCTGGAAATTCTTCAGGACCTTCACCTGGTGCTAAGTTTTCCCACATTTTACAAAAG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCC@CDCCDCCCCCDCCCDBDBADDC
+@61DFRAAXX100204:1:103:7220:15954/2
+GATGTATTCACCCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBBBCCCCCCCCCCCCCBCDC
+@61DFRAAXX100204:1:103:7253:3680/2
+GTAGATTTTATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTGGGAGGTT
++
+CCCCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCB@BCCCCCCCBCDCCCBCCCCCCB=CDA
+@61DFRAAXX100204:1:103:8055:11636/2
+AAATGACCTGTCGAAAATTGCACAAGGAAGGGGCAGCCAAGAACTTGGTATGAGTAATGTTCAGGAATTGAGCCTG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCDCCCCDACCCCCCCCCACCCCC
+@61DFRAAXX100204:1:103:8348:14452/2
+AACATTTGGGTTGAACTTTTAGTCTTTGGGGGAGTGGTGGTCATTTTGAGGGCTTGCTGTGCCCTGAATCTGTTGT
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCB@CCCCCDCCCCCCCCCCCCCACBCCDCCCCCAB@CBCCDCBB
+@61DFRAAXX100204:1:104:12460:3347/2
+CACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGTTTTTCTGTTGGTGTTTACATTG
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACCCCCCCBCCC@@@BBCCCACBCCC@ACBC
+@61DFRAAXX100204:1:104:12993:12947/2
+GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTATTTGCCATTGTGCAAAA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCC@CCACBCDDCBCC,BBC?BBBBB@BBBD
+@61DFRAAXX100204:1:104:13501:6860/2
+CTGAGCTACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTGTTCCTCACTA
++
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCC
diff -r 000000000000 -r d4128a4e49ca test-data/samples.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samples.tsv	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,4 @@
+ConditionA	CondA_replicate1
+ConditionA	CondA_replicate2
+ConditionB	CondB_replicate1
+ConditionB	CondB_replicate2
diff -r 000000000000 -r d4128a4e49ca tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Nov 21 11:59:35 2016 -0500
@@ -0,0 +1,30 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="trinity" version="2.2.0">
+        <repository changeset_revision="76d63b5c571a" name="package_trinity_2_2_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="bowtie" version="1.1.2">
+        <repository changeset_revision="a1c1a92e13a6" name="package_bowtie_1_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="bowtie2" version="2.2.6">
+        <repository changeset_revision="0d9cd7487cc9" name="package_bowtie_2_2_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="bioconductor-edger" version="3.14.0">
+        <repository changeset_revision="5f4abad5b2c1" name="package_bioconductor_edger_3_14_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="rsem" version="1.2.28">
+        <repository changeset_revision="4567331d510a" name="package_rsem_1_2_28" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="eXpress" version="1.5.1">
+        <repository changeset_revision="93017e8743e5" name="package_express_1_5_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="bioconductor-limma" version="3.28.10">
+        <repository changeset_revision="b313488c66bd" name="package_bioconductor_limma_3_28_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="deseq2" version="1.10.0">
+       <repository changeset_revision="e4a11a7d33d6" name="package_deseq2_1_10_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <set_environment version="1.0">
+        <environment_variable action="set_to" name="TRINITY_MEM_OPTIONS">'--max_memory 30G --bflyHeapSpaceMax 30G'</environment_variable>
+    </set_environment>
+</tool_dependency>