changeset 0:acff96adcbec draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit b9a2194247d728ef4d5a3c5511aa6ea63e9b2bcb

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Tue Dec 13 14:43:00 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'

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/define_clusters_by_cutting_tree.xml	Tue Dec 13 14:43:00 2016 -0500
@@ -0,0 +1,92 @@
+<tool id="trinity_define_clusters_by_cutting_tree" name="Partition genes into expression clusters" version="@WRAPPER_VERSION@.0">
+    <description>after differential expression analysis using a Trinity assembly</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+        <requirement type="package" version="2.30.0">bioconductor-biobase</requirement>
+    </expand>
+    <expand macro="stdio"/>
+    <command><![CDATA[
+
+        define_clusters_by_cutting_tree.pl
+
+        -R '${rdata}'
+
+        #if str( $method.method_selector ) == "--Ptree":
+            --Ptree ${method.ptree}
+        #else
+            #if str( $method.method_selector ) == "--Ktree":
+                --Ktree ${method.ktree}
+            #else
+                -K ${method.k}
+            #end if
+        #end if
+
+        $additional_params.column_ordering
+
+        &&
+        mv *.clusters_fixed_*/* .
+
+    ]]></command>
+    <inputs>
+        <param format="RData" name="rdata" argument="-R" type="data" label="RData file" help="RData file produced by 'Extract and cluster differentially expressed transcripts from a Trinity assembly' tool"/>
+        <conditional name="method">
+            <param name="method_selector" type="select" label="Method for partitioning genes into clusters">
+                <option value="--Ptree">Cut tree based on x percent of max(height) of tree</option>
+                <option value="--Ktree">Cut tree into K clusters</option>
+                <option value="-K">Define K clusters via k-means algorithm</option>
+            </param>
+            <when value="--Ptree">
+                <param name="ptree" type="float" argument="--Ptree" value="20" label="Cut tree based on this percent of max(height) of tree" help="Give a percent value"/>
+            </when>
+            <when value="--Ktree">
+                <param name="ktree" type="integer" argument="--Ktree" value="2" label="Cut tree into K clusters "/>
+            </when>
+            <when value="-K">
+                <param name="k" type="integer" argument="-K" value="2" label="Define K clusters via k-means algorithm" help="This does not leverage the already hierarchically clustered genes, and instead uses a least-sum-of-squares method to define exactly k gene clusters."/>
+            </when>
+        </conditional> 
+        <section name="additional_params" title="Additional Options" expanded="False">
+            <param name="column_ordering" type="select" label="Column ordering in expression matrices" argument="--no_column_reordering / --lexical_column_ordering">
+                <option value="">Order based on sample clustering</option>
+                <option value="--no_column_reordering">No reordering based on sample clustering</option>
+                <option value="--lexical_column_ordering">Reorder column names according to lexical ordering</option>
+            </param>
+        </section>
+    </inputs>
+    <outputs>
+        <collection name="expression_matrices" type="list" label="${tool.name} on ${on_string}: expression matrices for each cluster">
+            <discover_datasets pattern="(?P&lt;name&gt;.+_log2_medianCentered_fpkm\.matrix)$" ext="tabular" />
+        </collection>
+        <data format="pdf" name="cluster_plots" label="${tool.name} on ${on_string}: cluster plots" from_work_dir="my_cluster_plots.pdf"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="rdata" value="count/analyze_diff_expr/results.matrix.RData"/>
+            <conditional name="method">
+                <param name="method_selector" value="--Ptree"/>
+                <param name="ptree" value="60"/>
+            </conditional>
+            <output_collection name="expression_matrices">
+                <element name="subcluster_1_log2_medianCentered_fpkm.matrix" compare="sim_size" file="count/define_clusters_by_cutting_tree/subcluster_1_log2_medianCentered_fpkm.matrix"/>
+                <element name="subcluster_2_log2_medianCentered_fpkm.matrix" compare="sim_size" file="count/define_clusters_by_cutting_tree/subcluster_2_log2_medianCentered_fpkm.matrix"/>
+            </output_collection>
+            <output name="rdata" delta="100" compare="sim_size" file="count/define_clusters_by_cutting_tree/my_cluster_plots.pdf"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
+This tool partitions the differentially expressed genes into gene clusters with similar expression patterns by one of several available methods, once differential expression analyses have been runned. It is a companion tool for the tool 'Extract and cluster differentially expressed transcripts from a Trinity assembly'.
+
+**Inputs**
+
+This tool uses the RData file produced by 'Extract and cluster differentially expressed transcripts from a Trinity assembly' tool.
+
+.. _Trinity: http://trinityrnaseq.github.io
+]]>
+    </help>
+
+    <expand macro="citation" />
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Dec 13 14:43:00 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>

--- /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	Tue Dec 13 14:43:00 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

--- /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	Tue Dec 13 14:43:00 2016 -0500
@@ -0,0 +1,1 @@
+category	over_represented_pvalue	under_represented_pvalue	numDEInCat	numInCat	term	ontology	over_represented_FDR	under_represented_FDR

--- /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	Tue Dec 13 14:43:00 2016 -0500
@@ -0,0 +1,1 @@
+category	over_represented_pvalue	under_represented_pvalue	numDEInCat	numInCat	term	ontology	over_represented_FDR

--- /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	Tue Dec 13 14:43:00 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

--- /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	Tue Dec 13 14:43:00 2016 -0500
@@ -0,0 +1,1 @@
+category	over_represented_pvalue	under_represented_pvalue	numDEInCat	numInCat	term	ontology	over_represented_FDR	under_represented_FDR

--- /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	Tue Dec 13 14:43:00 2016 -0500
@@ -0,0 +1,1 @@
+category	over_represented_pvalue	under_represented_pvalue	numDEInCat	numInCat	term	ontology	over_represented_FDR

--- /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	Tue Dec 13 14:43:00 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

--- /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	Tue Dec 13 14:43:00 2016 -0500
@@ -0,0 +1,1 @@
+category	over_represented_pvalue	under_represented_pvalue	numDEInCat	numInCat	term	ontology	over_represented_FDR	under_represented_FDR

--- /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	Tue Dec 13 14:43:00 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

--- /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	Tue Dec 13 14:43:00 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

--- /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	Tue Dec 13 14:43:00 2016 -0500
@@ -0,0 +1,1 @@
+category	over_represented_pvalue	under_represented_pvalue	numDEInCat	numInCat	term	ontology	over_represented_FDR	under_represented_FDR

--- /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	Tue Dec 13 14:43:00 2016 -0500
@@ -0,0 +1,1 @@
+category	over_represented_pvalue	under_represented_pvalue	numDEInCat	numInCat	term	ontology	over_represented_FDR

--- /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	Tue Dec 13 14:43:00 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

--- /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	Tue Dec 13 14:43:00 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

--- /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	Tue Dec 13 14:43:00 2016 -0500
@@ -0,0 +1,1 @@
+category	over_represented_pvalue	under_represented_pvalue	numDEInCat	numInCat	term	ontology	over_represented_FDR	under_represented_FDR

--- /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	Tue Dec 13 14:43:00 2016 -0500
@@ -0,0 +1,1 @@
+category	over_represented_pvalue	under_represented_pvalue	numDEInCat	numInCat	term	ontology	over_represented_FDR

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/results.matrix	Tue Dec 13 14:43:00 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
+TR4277|c0_g1_i1	4466.00	4701.00	4284.00	118.00	134.00	164.00	172.00	162.00	170.00
+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
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Binary file test-data/count/analyze_diff_expr/results.matrix.RData has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/results.matrix.log2.centered.dat	Tue Dec 13 14:43:00 2016 -0500
@@ -0,0 +1,14 @@
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Binary file test-data/count/analyze_diff_expr/results.matrix.log2.centered.genes_vs_samples_heatmap.pdf has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/results.matrix.log2.dat	Tue Dec 13 14:43:00 2016 -0500
@@ -0,0 +1,14 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/analyze_diff_expr/results.matrix.log2.sample_cor.dat	Tue Dec 13 14:43:00 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
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Binary file test-data/count/analyze_diff_expr/results.matrix.log2.sample_cor_matrix.pdf has changed

Binary file test-data/count/define_clusters_by_cutting_tree/my_cluster_plots.pdf has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/define_clusters_by_cutting_tree/subcluster_1_log2_medianCentered_fpkm.matrix	Tue Dec 13 14:43:00 2016 -0500
@@ -0,0 +1,7 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/define_clusters_by_cutting_tree/subcluster_2_log2_medianCentered_fpkm.matrix	Tue Dec 13 14:43:00 2016 -0500
@@ -0,0 +1,8 @@
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--- /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	Tue Dec 13 14:43:00 2016 -0500
@@ -0,0 +1,39 @@
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+TR4859|c0_g1_i1	7.32690480813971	3.17910584569163	5.25300532691567	-1.18284590433612	0.789581441931072	-1.49806700299749	0.134115843085064	0.158065100778825
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+TR2090|c0_g1_i1	0	9.55638889228537	4.77819444614269	3.06235120305875	2.04796345977052	1.49531535264887	NA	1

Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano.pdf has changed

--- /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	Tue Dec 13 14:43:00 2016 -0500
@@ -0,0 +1,39 @@
+logFC	logCPM	PValue	FDR
+TR131|c0_g1_i1	5.8364197685119	16.0402624962907	0	0
+TR4277|c0_g1_i1	-4.41329137350676	17.4523259866001	0	0
+TR3091|c0_g1_i1	4.45193883524837	14.0450613692144	2.75977672027703e-191	3.0023764016608e-190
+TR4761|c0_g1_i1	-2.92753980838104	16.3343761538543	3.16039621227453e-191	3.0023764016608e-190
+TR2487|c0_g1_i1	1.58705373680526	15.8895982491351	1.69098562804069e-123	1.28514907731092e-122
+TR1479|c0_g1_i1	1.67068054401246	14.5625418524933	4.82942248775202e-81	3.05863424224295e-80
+TR3638|c0_g1_i1	-1.49936398500381	15.1049693447894	1.31792237756209e-64	7.15443576390849e-64
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+TR1122|c0_g1_i1	-0.015204817268041	8.26206767263358	1	1

Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.MA_n_Volcano.pdf has changed

--- /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	Tue Dec 13 14:43:00 2016 -0500
@@ -0,0 +1,39 @@
+logFC	logCPM	PValue	FDR
+TR131|c0_g1_i1	5.8235943392439	16.1127963113785	7.14846919291531e-10	2.71641829330782e-08
+TR4277|c0_g1_i1	-4.41182125975734	17.3835558041266	1.56187740933885e-09	2.96756707774382e-08
+TR3091|c0_g1_i1	4.43711915085412	14.1189484156579	4.80332538807657e-08	5.96619459206176e-07
+TR2487|c0_g1_i1	1.58597331690052	15.926957585609	6.28020483374923e-08	5.96619459206176e-07
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+TR1479|c0_g1_i1	1.67737907773679	14.6004783880878	9.51214752241748e-07	5.52604916020242e-06
+TR3638|c0_g1_i1	-1.50273266496817	15.0596817330556	1.02518921423282e-06	5.52604916020242e-06
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+TR1492|c0_g1_i2	-0.0324123498367541	17.1356104672946	0.389074079094509	0.462025468924729

Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results.MA_n_Volcano.pdf has changed

--- /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	Tue Dec 13 14:43:00 2016 -0500
@@ -0,0 +1,39 @@
+id	baseMeanA	baseMeanB	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj
+TR4277|c0_g1_i1	4705.34614971641	162.902721493704	2434.12443560506	-4.84860951090545	0.124597307945428	-38.9142397284305	0	0
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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
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+TR2779|c0_g1_i1	191.51955185349	1058.15934185376	624.839446853626	2.46616535412611	0.177102083131526	13.9251064161374	4.4587691300744e-44	3.38866453885655e-43
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+TR1982|c2_g1_i1	7.00144976454503	11.520013112092	9.26073143831853	0.70490953188932	0.647715898283926	1.0883004937148	0.276462472665158	0.362261171078483
+TR3854|c0_g1_i1	1925.26464813324	2107.16376011081	2016.21420412203	0.130534071096341	0.124633726123269	1.04734147936199	0.29494211171073	0.373593341500258
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Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf has changed

--- /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	Tue Dec 13 14:43:00 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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+TR2011|c5_g1_i1	-0.075980865610854	9.27931055760989	0.901508002533997	0.925873083683564
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Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf has changed

--- /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	Tue Dec 13 14:43:00 2016 -0500
@@ -0,0 +1,39 @@
+logFC	logCPM	PValue	FDR
+TR131|c0_g1_i1	5.89108692370307	16.0946870940125	4.52958285205525e-36	1.721241483781e-34
+TR4277|c0_g1_i1	-4.47812345668175	17.3786096664403	1.7008141018303e-32	3.23154679347758e-31
+TR3091|c0_g1_i1	4.37454375877296	13.9751350003907	7.58044859691792e-23	9.60190155609603e-22
+TR2779|c0_g1_i1	2.89398117484377	15.8061264352363	3.97828335136821e-18	3.7793691837998e-17
+TR5075|c0_g1_i1	3.21512246000432	12.8334153580766	2.0588784190888e-14	1.56474759850749e-13
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+TR4761|c0_g1_i1	-2.00464775189483	16.4172477083723	2.27235196662378e-10	1.23356249616719e-09
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+TR2122|c0_g2_i2	1.68823123696301	14.4430864744705	3.40183177422869e-08	1.436328971341e-07
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+TR2182|c3_g2_i6	0.0429471548350905	7.57134083040984	0.956400717774849	0.956400717774849
+TR939|c0_g1_i1	0.398499350568058	13.0523653134109	0.192129988432482	0.214733516483362
+TR2011|c5_g1_i1	0.0410416962762211	8.85697121679121	0.9477445647389	0.956400717774849

Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf has changed

--- /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	Tue Dec 13 14:43:00 2016 -0500
@@ -0,0 +1,40 @@
+id	baseMeanA	baseMeanB	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj
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+TR4277|c0_g1_i1	153.969096204861	149.159426886469	151.564261545665	-0.0459267760105497	0.128823197370029	-0.356510139075578	0.721458560376159	0.9108498942696
+TR1982|c2_g1_i1	5.5352448786851	10.687042573374	8.11114372602957	0.110416157924497	0.359967068804195	0.306739608962835	0.759041578558	0.9108498942696
+TR127|c1_g1_i1	1.20754470361908	1.49113571265046	1.34934020813477	0.142968860758062	0.541343527667515	0.26410006484066	0.791702813929264	1
+TR3854|c0_g1_i1	2260.55060252051	1927.46472630351	2094.00766441201	-0.135348942475858	0.546438760787258	-0.247692792291784	0.804372109047297	0.919282410339768
+TR2090|c0_g1_i1	9.46045896251181	5.6546754787973	7.55756722065455	-0.0586395744056909	0.302337767579782	-0.193953851267414	0.846212017000596	1
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+TR131|c0_g1_i1	1275.67603302799	1312.2934796972	1293.9847563626	0.0343724958045096	0.405262489992082	0.0848153891695754	0.932408158838271	0.963782835492881
+TR5055|c0_g2_i1	5.17791343714095	5.60171771495863	5.38981557604979	0.043552763660028	0.53975688204026	0.0806895939805349	0.935688812631814	1
+TR939|c0_g1_i1	92.2508462008296	94.0990807885678	93.1749634946987	0.0253693962827489	0.353966153466169	0.0716718139130601	0.942863087697354	0.963782835492881
+TR2487|c0_g1_i1	875.181494043204	882.631049341941	878.906271692572	0.0115839334384507	0.255112918612705	0.0454070828770402	0.963782835492881	0.963782835492881

Binary file test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf has changed

--- /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	Tue Dec 13 14:43:00 2016 -0500
@@ -0,0 +1,40 @@
+logFC	logCPM	PValue	FDR
+TR2779|c0_g1_i1	2.23948335958727	15.9163308249372	1.20766376889896e-237	4.70988869870595e-236
+TR1492|c0_g1_i2	-0.807859120941235	16.8439348559211	2.37986391219743e-61	4.64073462878498e-60
+TR1891|c0_g1_i1	1.35697452203657	14.6311197032228	1.60645028176433e-35	2.08838536629363e-34
+TR4761|c0_g1_i1	0.880921757190946	14.8138260614735	1.59143301924913e-24	1.5516471937679e-23
+TR2122|c0_g2_i2	0.729785350305026	14.7699678361852	6.52776857951534e-13	5.09165949202196e-12
+TR3854|c0_g1_i1	-0.289859344737128	17.7786469452325	6.1302236270955e-12	3.98464535761207e-11
+TR3638|c0_g1_i1	0.702510801497461	14.6355179638282	5.62335492840333e-11	3.133012031539e-10
+TR2278|c0_g1_i1	-0.490901034745758	15.2921454021456	1.53296499052609e-09	7.47320432881468e-09
+TR24|c0_g1_i1	2.16007337608378	13.5636496776551	8.67157466173412e-09	3.75768235341812e-08
+TR5075|c0_g1_i1	3.7524485458028	12.8683202800317	5.50095216588421e-08	2.14537134469484e-07
+TR4669|c0_g2_i1	-10.4044948993067	13.1110475123695	1.35189372056785e-06	4.79307773655872e-06
+TR3788|c0_g1_i1	-2.47698512550917	13.0240883091698	1.80487840553907e-05	5.86585481800198e-05
+TR1479|c0_g1_i1	-0.272661827455658	15.1172528121102	0.000483095512098729	0.00144928653629619
+TR1678|c0_g1_i1	3.02812287247775	9.36059212330112	0.0074853976481696	0.0208521791627582
+TR2107|c1_g1_i1	-1.98032359155541	9.36544178725855	0.0305238827180189	0.0756824353198294
+TR2844|c0_g1_i1	-0.244755727600329	14.4560017424587	0.0310492042337762	0.0756824353198294
+TR1859|c3_g1_i1	4.12978123132011	8.37588761488442	0.0428877609330621	0.0983895691993777
+TR3091|c0_g1_i1	-0.148576217250104	14.9963238698071	0.0547318692708507	0.11858571675351
+TR2672|c0_g1_i1	1.64029381826409	9.53984158811941	0.100507062957769	0.206303971334369
+TR4163|c0_g1_i1	-0.156926020788278	14.5006265631178	0.113620071038851	0.22155913852576
+TR4859|c0_g1_i1	-1.3062724221166	8.73091245897321	0.181160758857669	0.3364414093071
+TR4084|c0_g1_i1	0.390578563212142	13.8603174460746	0.270419882900116	0.479380701504752
+TR1982|c2_g1_i1	0.866592651710305	10.0958159836705	0.312186869456376	0.515984430920105
+TR1894|c2_g1_i1	-0.989932992780787	8.78384403630691	0.317528880566218	0.515984430920105
+TR4277|c0_g1_i1	-0.107189584823599	14.0046148411409	0.347278576725125	0.541754579691195
+TR2487|c0_g1_i1	-0.0467513454249246	16.526653433485	0.376403968202147	0.560230359736405
+TR3249|c0_g1_i1	1.00369455926223	9.08504250192555	0.387851787509819	0.560230359736405
+TR5212|c0_g1_i1	-0.310409394484433	13.3365591825697	0.416163942507532	0.572783249883747
+TR2011|c5_g1_i1	-0.799376994792807	9.70509536731836	0.425915749913555	0.572783249883747
+TR1837|c2_g1_i1	-0.59484087321072	8.66193471010726	0.588495494688377	0.76504414309489
+TR2090|c0_g1_i1	-0.766971023107968	9.89421471118339	0.638322407555079	0.8030507707951
+TR131|c0_g1_i1	-0.0187996511046741	17.0827735361623	0.697507705031756	0.850087515507453
+TR1122|c0_g1_i1	-0.908051089281089	8.22928258978683	0.753364106379395	0.890339398448377
+TR1449|c0_g1_i1	0.0452741219590205	13.4583026590017	0.919111339143084	1
+TR939|c0_g1_i1	-0.0309689709592036	13.3146949564453	0.956245904999637	1
+TR5055|c0_g2_i1	0.0548476287872344	9.62768102188797	0.999999999999985	1
+TR2182|c3_g2_i6	0.517423422896207	8.5297276065799	1	1
+TR127|c1_g1_i1	0.299043611515333	8.4576897025083	1	1
+TR3807|c0_g1_i1	-0.266132577378544	7.94319410024963	1	1

Binary file test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf has changed

--- /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	Tue Dec 13 14:43:00 2016 -0500
@@ -0,0 +1,40 @@
+logFC	logCPM	PValue	FDR
+TR2779|c0_g1_i1	2.23795519272237	15.9076254017254	2.92187316761645e-09	1.13953053537042e-07
+TR1492|c0_g1_i2	-0.807554446371668	16.8426446227048	5.58321346448906e-08	1.08872662557537e-06
+TR24|c0_g1_i1	2.16839334936064	13.5222768601527	3.73856822091501e-07	4.86013868718952e-06
+TR3788|c0_g1_i1	-2.47096654484901	13.0144557887788	1.245732049043e-06	9.71670998253539e-06
+TR5075|c0_g1_i1	3.68481140303272	12.7944067233298	3.44359702134355e-06	2.23833806387331e-05
+TR3854|c0_g1_i1	-0.290746293924475	17.7782076349597	5.25322144866517e-07	5.12189091244854e-06
+TR1891|c0_g1_i1	1.35768165107067	14.6117632515968	5.28666359293828e-06	2.79053243123467e-05
+TR4761|c0_g1_i1	0.878920056028248	14.8002262876656	5.72416908971214e-06	2.79053243123467e-05
+TR2122|c0_g2_i2	0.730166040402744	14.7551588447381	0.000213340170514583	0.000924474072229861
+TR3638|c0_g1_i1	0.708321413581678	14.6195575978943	0.000258928735946659	0.00100982207019197
+TR2107|c1_g1_i1	-1.90861736829884	8.90712643491077	0.00457979737107378	0.0148843414559898
+TR1678|c0_g1_i1	2.86408187112217	8.67828416118206	0.00614682516189	0.01844047548567
+TR2278|c0_g1_i1	-0.503051556783977	15.2850549214884	0.00155857674629228	0.00552586300958173
+TR1859|c3_g1_i1	1.96144637998691	6.77065030795652	0.0428269385052548	0.0982500353944082
+TR2672|c0_g1_i1	1.69730734417424	8.97832173338033	0.0866262290356731	0.160877282494822
+TR1479|c0_g1_i1	-0.277933522953326	15.1098597149167	0.0157877120065803	0.0439800548754737
+TR1982|c2_g1_i1	0.859948395691952	9.74982883974683	0.0845253825418736	0.160877282494822
+TR4859|c0_g1_i1	-1.04376243585308	7.84838377560073	0.178339170085147	0.289801151388364
+TR2011|c5_g1_i1	-0.835627288758852	9.33803398810951	0.117576176969539	0.20843049553691
+TR4084|c0_g1_i1	0.383433512314591	13.8345091917852	0.0320674039619619	0.083375250301101
+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

Binary file test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/express_bowtie/results.xprs	Tue Dec 13 14:43:00 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/express_bowtie/results_B.xprs	Tue Dec 13 14:43:00 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/express_bowtie/sample_A	Tue Dec 13 14:43:00 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/express_bowtie/sample_B	Tue Dec 13 14:43:00 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_express_bowtie/matrix.TMM.EXPR.matrix	Tue Dec 13 14:43:00 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_express_bowtie/matrix.TPM.not_cross_norm	Tue Dec 13 14:43:00 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_express_bowtie/matrix.counts.matrix	Tue Dec 13 14:43:00 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie/matrix.TMM.EXPR.matrix	Tue Dec 13 14:43:00 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie/matrix.TPM.not_cross_norm	Tue Dec 13 14:43:00 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie/matrix.counts.matrix	Tue Dec 13 14:43:00 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie2/matrix.TMM.EXPR.matrix	Tue Dec 13 14:43:00 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie2/matrix.TPM.not_cross_norm	Tue Dec 13 14:43:00 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie2/matrix.counts.matrix	Tue Dec 13 14:43:00 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.TPM.not_cross_norm	Tue Dec 13 14:43:00 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

--- /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	Tue Dec 13 14:43:00 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.UpperQuartile.EXPR.matrix	Tue Dec 13 14:43:00 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie_UpperQuartile/matrix.counts.matrix	Tue Dec 13 14:43:00 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie_none/matrix.TPM.not_cross_norm	Tue Dec 13 14:43:00 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/matrix_rsem_bowtie_none/matrix.counts.matrix	Tue Dec 13 14:43:00 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

Binary file test-data/count/qcheck/input.matrix.CPM.log2.principal_components.pdf has changed

Binary file test-data/count/qcheck/input.matrix.CPM.log2.sample_cor_matrix.pdf has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/qcheck/matrix.counts.matrix	Tue Dec 13 14:43:00 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

Binary file test-data/count/qcheck/wt_37.rep_compare.pdf has changed

Binary file test-data/count/qcheck/wt_GSNO.rep_compare.pdf has changed

Binary file test-data/count/qcheck/wt_ph8.rep_compare.pdf has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie/RSEM.isoforms.results	Tue Dec 13 14:43:00 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie/RSEM.isoforms_B.results	Tue Dec 13 14:43:00 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie/sample_A	Tue Dec 13 14:43:00 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie/sample_B	Tue Dec 13 14:43:00 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie2/RSEM.isoforms.results	Tue Dec 13 14:43:00 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie2/RSEM.isoforms_B.results	Tue Dec 13 14:43:00 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie2/sample_A	Tue Dec 13 14:43:00 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/rsem_bowtie2/sample_B	Tue Dec 13 14:43:00 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/salmon/sample_A	Tue Dec 13 14:43:00 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/salmon/sample_B	Tue Dec 13 14:43:00 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/samples.txt	Tue Dec 13 14:43:00 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/trinotate/genes.lengths.txt	Tue Dec 13 14:43:00 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/count/trinotate/go_annotations.txt	Tue Dec 13 14:43:00 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filtered/Trinity_filtered_exp.fasta	Tue Dec 13 14:43:00 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filtered/Trinity_filtered_pct_iso.fasta	Tue Dec 13 14:43:00 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/filtered/counts.matrix	Tue Dec 13 14:43:00 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/norm/Trinity.fasta	Tue Dec 13 14:43:00 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
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/raw/Trinity.fasta	Tue Dec 13 14:43:00 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
+

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/raw/map.tsv	Tue Dec 13 14:43:00 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reads.left.fq	Tue Dec 13 14:43:00 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reads.right.fq	Tue Dec 13 14:43:00 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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samples.tsv	Tue Dec 13 14:43:00 2016 -0500
@@ -0,0 +1,4 @@
+ConditionA	CondA_replicate1
+ConditionA	CondA_replicate2
+ConditionB	CondB_replicate1
+ConditionB	CondB_replicate2

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Dec 13 14:43:00 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>