# HG changeset patch
# User iuc
# Date 1571259443 14400
# Node ID 6302d40828d2eaf0b3186b32876ab551c2263aef

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"

diff -r 000000000000 -r 6302d40828d2 est-abundance.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/est-abundance.xml	Wed Oct 16 16:57:23 2019 -0400
@@ -0,0 +1,65 @@
+<tool id="est_abundance" name="Estimate Abundance at Taxonomic Level" version="@VERSION@+galaxy0">
+    <description>Bayesian Reestimation of Abundance with KrakEN</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <edam_topics>
+        <edam_topic>topic_3174</edam_topic>
+        <edam_topic>topic_3697</edam_topic>
+    </edam_topics>
+    <edam_operations>
+        <edam_operation>operation_2238</edam_operation>
+    </edam_operations>
+    <expand macro="requirements" />    
+    <command detect_errors="exit_code"><![CDATA[
+    est_abundance.py 
+    -i '$input' 
+    -k '$kmer_distr.fields.path' 
+    -l $level 
+    -t $threshold 
+    -o '$report'
+    ]]>
+    </command>    
+    <inputs>
+        <param name="input" type="data" format="tabular" label="Kraken report file" />
+        <param label="Select a Kmer distribution" name="kmer_distr" type="select">
+            <options from_data_table="bracken_databases">
+                <validator message="No database is available" type="no_options" />
+            </options>
+        </param>
+        <param name="level" type="select" label="Level" help="Level to push all reads to" >
+            <option value="S" selected="true">Species</option>
+            <option value="G">Genus</option>
+            <option value="F">Family</option>
+            <option value="O">Order</option>
+            <option value="C">Class</option>
+            <option value="P">Phylum</option>
+            <option value="D">Domain</option>
+        </param>
+        <param name="threshold" type="integer" value="10" label="Number of mismatches allowed when matching tag"
+               help="Threshold for the minimum number of reads kraken must assign to a classification for that 
+                     classification to be considered in the final abundance estimation." />
+    </inputs>
+    <outputs>
+        <data name="report" format="tabular" label="${tool.name} on ${on_string}: Report" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="NC_003198.1_simulated_kraken_report.txt" ftype="tabular"/>
+            <param name="level" value="S" />
+            <param name="bracken_database" value="test_entry"/>
+	    <output name="report" file="NC_003198.1_simulated_bracken_report.txt" ftype="tabular"/>
+        </test>
+	<test>
+            <param name="input" value="NC_011750.1_simulated_kraken_report.txt" ftype="tabular"/>
+            <param name="level" value="S" />
+            <param name="bracken_database" value="test_entry"/>
+	    <output name="report" file="NC_011750.1_simulated_bracken_report.txt" ftype="tabular"/>
+        </test>
+    </tests>
+    <help>
+    <![CDATA[
+        Documentation can be found at `site <http://ccb.jhu.edu/software/bracken/index.shtml?t=manual>`_.
+    ]]></help>
+    <expand macro="citations" />
+</tool>
diff -r 000000000000 -r 6302d40828d2 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Oct 16 16:57:23 2019 -0400
@@ -0,0 +1,17 @@
+<macros>
+    <token name="@TOOL_VERSION@">2.5</token>
+    <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy0</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">bracken</requirement>
+        </requirements>
+    </xml>
+    <xml name="version">
+        <version_command>echo @WRAPPER_VERSION@</version_command>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.7717/peerj-cs.104</citation>
+        </citations>
+    </xml>
+</macros>
diff -r 000000000000 -r 6302d40828d2 test-data/NC_003198.1_1kb.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/NC_003198.1_1kb.fasta	Wed Oct 16 16:57:23 2019 -0400
@@ -0,0 +1,14 @@
+>NC_003198.1 Salmonella enterica subsp. enterica serovar Typhi str. CT18, complete genome
+AGAGATTACGTCTGGTTGCAAGAGATCATAACAGGGGAAATTGATTGAAAATAAATATATCGCCAGCAGC
+ACATGAACAAGTTTCGGAATGTGATCAATTTAAAAATTTATTGACTTAGGCGGGCAGATACTTTAACCAA
+TATAGGAATACAAGACAGACAAATAAAAATGACAGAGTACACAACATCCATGAACCGCATCAGCACCACC
+ACCATTACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG
+CCCGCACCTGAACAGTGCGGGCTTTTTTTTCGACCAGAGATCACGAGGTAACAACCATGCGAGTGTTGAA
+GTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATTCC
+AGGCAAGGGCAGGTAGCGACCGTACTTTCCGCCCCCGCGAAAATTACCAACCATCTGGTGGCGATGATTG
+AAAAAACTATCGGCGGCCAGGATGCTTTGCCGAATATCAGCGATGCCGAACGTATTTTTTCTGACCTGCT
+CGCAGGACTTGCCAGCGCGCAGCCGGGATTCCCGCTTGCACGGTTGAAAATGGTTGTCGAACAAGAATTC
+GCTCAGATCAAACATGTTTTGCATGGTATCAGCCTGCTGGGTCAGTGCCCGGATAGCATCAACGCCGCGC
+TGATTTGCCGTGGCGAAAAAATGTCGATCGCGATTATGGCGGGACTCCTGGAGGCGCGTGGACATCGCGT
+CACGGTGATCGATCCGGTAGAAAAACTGCTGGCGGTGGGCCATTACCTTGAATCTACCGTCGATATCGCG
+GAATCGACTCGCCGTATCGCCGCCAGCCAGATCCCGGCCGATCACATGATCCTGATGGCGGGCTTTACTG
diff -r 000000000000 -r 6302d40828d2 test-data/NC_003198.1_simulated_R1.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/NC_003198.1_simulated_R1.fastq	Wed Oct 16 16:57:23 2019 -0400
@@ -0,0 +1,180 @@
+@NC_003198.1-90/1
+AATAAAAATGACAGAGTTCACAACATCCATGAACCGCATCAGCACTACCACCATGACCACCATCACGATTACTACAGGTAACTCTGCGGGCGGACGCGTA
++
+@CCF1FFF2HHHF@29I)IJIHIGIJGJE?CHJJBJGJHGHFJJH#J>2G0IJI#EHD=JFDDACF#GCE=J#;FC>DEA5F##D0B>CD9##CAA>B5D
+@NC_003198.1-88/1
+TCATAACAGGGGAAATTTATTGAAATTAAATATATCGCCAGCAGCACATGAACAGGTTTCGGACTGTGATGAATTTAAAAAGTTATTGACTTCGGCGCTC
++
+CCCFDFFBDHDHHJF#2#<GJGJJA#JJEE#JJII;?IEGIIBAGGBGGDJCIJ#JJJI;=I6#CI=DDD#31;ABDC#>H#CDECCDB>DC##DAD##?
+@NC_003198.1-86/1
+GGCGATACGGCGAGTTGATTCCGCGATATCGACGGTAGATTCAAGGTAATGGCCCACCGCCAGCAGTTTTTCTACCGGATCGATCACCCTGAGGCGAAGT
++
+@CCFFF?DCHCH+IJ#GIJHICHGHHJHGGEIJCIGJJJ?GJIGHHGJ=GDJII?<A;GHFJDE6#J'IG>?F#E>C>=EDCDAADCC#9?C#D#9D#>C
+@NC_003198.1-84/1
+CACAGAAAAAAGCCCGCACCTGAACAGTTCGGGCTTTTTTTTCGATCTGAGATCACGAGTTAACAAGCATGCGAGTGTTGAAGTACTGCAGAACATCAGT
++
+@CCFFFD<HDFHHJIJIJJJJFFJJJIF+JIGGDDJJIJJJFHIE#F#JFJHIBDH#J##HFD=IG#HA#G8C?FE@>F?DEHA(?#->#;#CD:CA>@D
+@NC_003198.1-82/1
+CCGGGCACTGACCCAGCAGGCTGATACCATGCAAAACATGTTTGATGTGAGCGAATTTTTGTTCGACAACCATTTTCAACCGTGCAACCCAGTATCCCGG
++
+CC@+DFDFHHGDHHIIIJGIFJIAJ#I7JIIHDJHIIJAFHIIG:?#I#GFCB4F=:#AJGIDJIJDDHFIBADGADH@EAD#DECD#C##>#A:D@D?,
+@NC_003198.1-80/1
+ATAATCGCGAGCGACATTTGTTCGCCGCGGCAAATCAGCGCGGCGTTGATGCTATCCGGGCACTGATCCAGCAGTCTGATAACATGCAAAAAATGTTTGA
++
+C@CDBFFD:F#HH#BBGJI!JIIIBJ!GHDFCI>IJIFAIIAHDBIGII?HIIBCJ?BAHFGJ>HE(CJ@2ECE!DBCB=D#FB@;@CCC<#<2>#D@AC
+@NC_003198.1-78/1
+CAGAAAAAAGCCCGCACCTGAACAGGGCGGGCTTTTTTTTCGACCAGAGATCACGAGGTAACAACCATGCCAGAGTTGAAGTTCGGCGGTACATCAGTGG
++
+@7@FFFFDFFFHDJJJIBJIJGIIA#IJIJJ*JE#IJJJDBBJGJICHJ<BIGJ?HJIFEHEFGIEBHD@#FD#=ADC#CDA<8>BD5>@C#D:CDD#B>
+@NC_003198.1-76/1
+GCGAAAATTACCAACTCTCTGGTGGCGATTATTTAAAATACTATCGGCGGCCAGGATGCTTTGCCGACTATCAGCGGTGCCGAACATTTTTGCTCTGTCC
++
+?<BFF<E?HHHHHJJ##II#IJ;<JJA<J#IJ:7JJ@D#IJIBJGJJGGGH?EHB4FE@BEI@FI(D#BDG>:##C!H>CBEDDB#F#B2<##BCDC##,
+@NC_003198.1-74/1
+GAGGTTACAACCATGCGAGTGTTGTAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGCTATTATGGAACGCAATTCCAGCC
++
+B1C(F#FBHHHHHJJGJGIEJ@JH#G1AC>BJAJJJJJJJHJIGIIJI<DJ#GIFF>GHDHJ@IH5FFIEDCD@H=#E#=(#?CDD(#?DA#DCDBDB#C
+@NC_003198.1-72/1
+CGCAGAAAACGTTCTGCATTTGCCACGGATGTACCGCCGAACTTCAACACTCGCATGGTTGTTACCTCGTCGCCTCTGGTCACAAAAAAAGCTCGCTCAG
++
+BCCFFFDFHHHH:BIEIIJEJHJECI#GJI+FEI?BFGJE@IJCJDHGJGIJ#F;?)?GIIH;8CABGH?###I?F=F@;A##BC<CCB>B>#CA@#D#D
+@NC_003198.1-70/1
+CCCGGCTGCGCGCTGGCAAGACCTGGGAGCAGGTCAGAAAAAATACGTTCGGCATCGCTGATATTCGGCAAAGCATCCTGGCCGCCGACAGTTTTTTCAA
++
+@CC?FFDFH#DFHJF@JEF1#IHID#IGJJDCG#EEJIJHI<JGJBHHGJIGG9.I:I>JED:JDD@B=;J#@HC93#ED#B;CC?@D#CCC#DBB>DEB
+@NC_003198.1-68/1
+AAGTTCGGCGGTACATCAGTGGTAAATGGAGAACGTTTTCTGCGTGTTCCCGATATCCTGGAAAGCAATTTCAGGCAAGGGCAGAGACCGAATTCACTTT
++
+CB:FFFADDHF;>IJIHJJHJI#JIIJJ#JCJGEIDJJICGJDIGCBJ#AFIIFHD#GC3DFJIIF.HCG#JFBD:DF3D#CCE##;#DC:#####D#D,
+@NC_003198.1-66/1
+TAACCAATATAGGAATACAAGACAGACAAATAAAAATGACAGAGTACACTACATCCATGAACCGAATCAGCATGACCTCCCTTACCTCGATCACCATTAC
++
+@B@DFFFDD@HGBEHI#+JIJIGIJIJ?+CIGJJJIIDJJGEFHIJAIJ#CIGHDEA9GCC=H8#DHHGEF;#(FCI#?F#CDC>##C(CDBDCC##ADD
+@NC_003198.1-64/1
+CCAGCAGGCTGATACCATGCAAAACATGTTTGATCTGAGCGAATTCTTGTTCGACAACCATTTTCAACCGTGCACGCGGGATTTCCGGCAGCGCGCTGGC
++
+@8CFFFF@GHF+HFIJIIBGII@I?IJJIIFJIDGI@DIIC#IJE@IJJJ@EFDJGJJCDEH?=JGH9#DG=DC(HDEECD#E#ADC>D#D9D#@CC3DC
+@NC_003198.1-62/1
+GCCTCCAGGAGTCCCGCCATAATCGCGATCTACATTTTTTGGTCACGGCAAATCAGCGCGGCGTTCAAGCTATCCGGGCACTGAACCAGCAGGCTGATAA
++
+C@=FFDDFHDGHHBHGEJC6JGDHBHEGJJ#I?AIIGJDF#I#JJGA9@F@'IEGJJICIGCDHE#C#HFBHABE;HJA,AC;5#D#FCBD+D5E@9?A,
+@NC_003198.1-60/1
+AGAATATCGGCAACACGGAGAAAACGTCCTGCATTTGCCACTGATGTACCGCCTAACTTCAACACTAGCATGGTTGTCACCTCGTGCTATCTGGTCGACA
++
+??#DFFFFDG@:HJIJ@2JEJJHJ*EI!HJJIAJ0<IJ6JBB#I>GICHGHD?#(AAIAIH.DJJE#FA7EDAD@B;#FECB.DB;#D#?ADAEC@AD#D
+@NC_003198.1-58/1
+GTAATGGCCCACCGCCAGCAGTTTTTCTACCGGATCGATCACCGTGATGCGATGTCCACGAGCCTCCACGAGTCCCTCCATAATAGCGGTCGTCATTATT
++
+B@CFFDDFHHGFHJB<J;JHIG#J>ACAJ?JIGGD#JHJJFC?#BD?#F#HJEGIFIJHH#F@DJEDG#@DCDECE#DGBDBB8#5DD#AA5#DCD:#C<
+@NC_003198.1-56/1
+ACAGAGTACACAACATCCATGAACCGCATCAGCACCACCACCACTACCACCATCACCATTACCACAGGTAACGGTTCGGGCTGACGCGTACGGGATACAC
++
+C@CFDF?FD#HF?4JI;JE3IEHIIJJ9EII9J?JF)JEDJBI#DCIF>JGI?JCIG9JJID#IFH8FECJCEDC#E;C#5HD@E#5B=#?#B>E###DC
+@NC_003198.1-54/1
+CGTGCAATTACTTTAACCAATATAGGAATACAAGACAGACAAATAAAAATTACAGAGTACACAACATCCATGAACCGCATCAGCACCACACCCATTACCA
++
+@C#DFF##HHCHGIH@<JJJCFIIJJHF7JIFHII@EIA9FFJJJFJ)DJ#G@G);BFFCE+HJHC7#)A8CF#?DB>EE9F@ABBCD###A2D@D:C#?
+@NC_003198.1-52/1
+GTGCGGGCTTTTTTTTCGACCGGAGCTCAGGAGGTAACAACCATGCGAGTGTTCAACTTCGGCGGTACATCAGTTGCAAATGCCGAACGTTTTCTGCGAG
++
+@?@DFDFF<HHHHJJ=IJGJJ#IJJ#JIF##JCDCJHJGIHJGBJCEGBIG?I#JH*IBDIBA#FDI.@AFH@9#<BBED:?F!@DCBCFDB;(CDCA#,
+@NC_003198.1-50/1
+GTCAGAAAAAATACGTTCGGCATCGCTGATATTCGGCAAAGCTCCCTAGCCGCCGATAGTTTTATCAATCATCGCCACCAGATGGTTGCGAGTTTCCGAG
++
+@C@FFDFDGFHHHJ#AI@GEHJEIGJHCJGJDJF0IJIJB/I##E*>#AGCIBG?HEHJA#IF#?FF#AD=C7>BA@CCD+E>BBB#E##4#DD2#@D#D
+@NC_003198.1-48/1
+TTACCAACCATCTGGTGGCGATGATTGAAAAAACTATCGGCGGCCAGGATCCTTTGCCGAATATCAGCGATGCCGGACGAATTTTTTCAGACCAGCTAGC
++
+CBCFFFF3HG7G=IJBJJJFIAJIIIGJH9JGIJJ?IIBD8DIAJGFICE#JGJD<HIJ&JHEEFDG;3JC==9B#DFE#<EEDD<FA#DBEC#A8A#@C
+@NC_003198.1-46/1
+AAAAAAAGCCCGCACTGTTCAGGTGCGGGCTTTTTTCTGTGTTTCCTGTAAGCGTCTGCCGGCACCGTTACCTGTGGTAATGGTGATGGTGGTAATGGTG
++
+@CCDB:F#1FHHFJ<IIJJHJ9IJ8I>I=IAGEJIHJDHJI4GJJHGHG@#DCGBD#DJ=#3FAI?HGDAE;B5;?DDH?FHC:CECC?CD?C?CBCA<,
+@NC_003198.1-44/1
+ACAAGACAGACAAATAAAAATGACAGAGTACACAACATCCAAGAACCGCATAAGCACCACCACCATTACGGCCATCACCATTACCACAGGCAACGGTGCG
++
+C@CAFFDFGB+FH2G9GJ<JJJ>JEGJC)=IJIH9IGF#JH*@#<H9GCAC#5EIDIHGII?HCHIJ=>#&G#?F:FHD::#<?B#D>C>#ABDD<DDB,
+@NC_003198.1-42/1
+GAAAAAAGCCCGCACCTGAACAGTGCGGGCATTTTGTTCGACCAGAGATCACGAGGTAACAACCATGAGAGTGTTGAAGTTCGGCGGTACATCAGTGGCA
++
+B8CFAFF3DHGDDFJ@I+HIJ@JIGDGJHJ#3JJJ#IH9J@H?GJ)HG:##J=JGG#JCFHBGG@DG##HJ?A,E;;>D@?D:BCD#DC>;?CD#E@DEA
+@NC_003198.1-40/1
+TGAGCGAATTCTTGTTCGACAACCATTTTAAACCGTGCAAGCGGGAATCCCGGCTGCGCGCTGGCAAGCCTTGCGATCAGGTCAGAAAAAATACGTTCTG
++
+B@?+?DFFHHHHBIII#IAIJ+B<EIJJG#HJDIJGJGFICEIGJD:JJCGIDHIGBICHIIG6DFDA#I#A<EF3#H#F<CCC<B4C<B9#>D:DAD#B
+@NC_003198.1-38/1
+CAGAAAACGTTCTGCATTTGCAACTGATGTGCAGCCGAACCTCAACACTCGCATGGTTCTTGCCTCGCGATCTCTGGTCGCAAAAAAAGCCCGCAATATT
++
+B;?FFF=FHFFHDJFJIHHIJ#JJGI9?GJ#J#BIJIIIG#JFCJI*G9G=JGJJJGJ#JJ#JJAEI#>CC>BHC>CDED)#DDHCCCACC>CB;####:
+@NC_003198.1-36/1
+TGAAAATAAATATATCGCCAGCAGCACATGAACAAGTTTCGGAATGTGATCAATTCAAAAATTTATTGACTTACGCTGGCAGATACTTTTACCAATATAG
++
+C=CF=FDAGHDHHJGB?JIIFJIJJIEHFJI<JHJ0C?CI(HHJEJJGIG94CII#C#EHJ5IIFFJIH;DHE#D##DCE;DFCADCDD#AC#9BDDACC
+@NC_003198.1-34/1
+TTCAACACTCGCATGGTTGTCACCTCGTGATCTCTGGTCGGAAAAAAAGCCCGCACTGTCCAGGTGCTGGCTTTTTTCTGTGGTTCCTGTACGCGTCAGC
++
+;C@?BFFFHHHH?JIJ@JJG!EIDIHIJFIIGI;HJIDGG!GF9:J4BHJHH;>JIHFF!=@CHCIE#:#C8CG?CDAFA?C#BDE9@@D?C#D>>CD@D
+@NC_003198.1-32/1
+GCTATCCGGGGACTGACCCAGCAGGCTGATACCATGTAAAACATGTTTGATCTGAGCGAATTCTTGTTCGACAACCATTTTCAACCGTGCAAGCGGGAAT
++
+@@CFFBFFHH#HHJIJIGJGHJJIJG#HIIDJJJIG#IBH@B9IJIGH<EJHCJ?=B@HIIJHHHC?H#C@8ECHC;@;AD3H##6:@AE8:DE#C>;?;
+@NC_003198.1-30/1
+GGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATTCCAGACAAGTGCAGGTTGCGAACGAACTTTCCGCCCCCGCGAGAATTACC
++
+?C<D;FDFHG@DGABFHHJJ@IJJJGI3EIBGGFJHD:4CHBG#FIDJ9=IBIE#EIFF#.HDE(A#CC)E#@3#DE@CIC==>D<DAD<AD#D@#3ABC
+@NC_003198.1-28/1
+TTATCAACCATGTGGTGGCGATGATTGAAAAAACTATCGACGTCCAGGATGCTTTGACGAATATCAGCGATGCCGGACGTAGTTTATATGACCTCCTAGC
++
+?CC#FDFFHHC#HGEIJHIDCHGIJ>>GG>IIJ?IFHHJ#DJ'?FDJDIEHJJJGI#H8EIH#FIGJC>FCDECE#ECBCF#CDF#B#CCBA>B#43#C@
+@NC_003198.1-26/1
+TGTGCAAGCGGGAATCCCGGCTGCGCGCTGGCAAGTCCTGCGAGCACGTCAGAAAAAATACGATCGGCATCGCCGATATTCGGCAAAGCATCCAGGGCGC
++
+#CCF?FD>F-FHACBJJFHHI:#IHI?JGJGFIJJIJ#J(9@#BFA#BGGI2HII*BIIGG>#@8H#IHH#J##;@>>DEEBFB;CCCB@-#C#?C#?CD
+@NC_003198.1-24/1
+CGGCATCGCTGATATTCGGCAAAGCATCCTGGCCGCCGATAGGTTTTTCAATCATCGCCACTAGATGGTAGGTAATTCTCGCGTGGGTGGATATGACGGA
++
+@C=FFFFFFHFHH+JGGIJ8IIEFIJHJIJF?GGIAJFJBJ<#G@JJGGIH7CJEJIIICG#E#E@=DE#ED3E5>C#F#DC<#ADH#CDB#D##?>?D,
+@NC_003198.1-22/1
+CAGCAGTTTTTCTACCGGATCGATCACCGTGACGCGATGTCCACGCTCCTCCAGGAGTCCCCCTATAATTGCGATCGACATTTTTTCGTCACGGCAAATC
++
+@CCFFFBFDBHH2JJGEIJIJIJ#J<JIHFBJBJEIDGDGIDGI#D#CJIIGBIG:IFIBI#7#ICH9I#ED@6?>BAD@.BFB5BC##A?DAAE>DCBD
+@NC_003198.1-20/1
+CGACCGTACTTTCCGCCCCCGCGAAAATTACCAGCCATCTAGTGGAGATGATTGAAAAGACTATCGGCGGCCAGGATGCTTGGGCGAATAACATCGATGC
++
+?CCDDFDDHHCHHGFJA<JG>IAGJJJHICHJ9#9GHEI8#JJI??IDCDIEJJIGIF#CHF9IE?>2DI=DF#>H>G>C;#H#FDDC:D##>(DD@##,
+@NC_003198.1-18/1
+TTAACCAATATAGGAATACAAGACAGACATATAAAAATCACAGATTACGCAACAACCATGAACCGCATCAGCACCACCACGTTTACCACGATCACCAATA
++
+@BCDFFFFGHDH?JII:#IFHJ<IGF5JJ#;GIJIGFC#JBCHE##J9#IFGFG#II0HG7IJHFF.JI:F(C@CA@BDB##FCCHA@###9D#EAC#AB
+@NC_003198.1-16/1
+GCGGGCTTTTTTTTCGACCAGAGATCACGAGGTAAAAACCATGCTAGTGTTGAGGTTCGGCGGTACATAAGTGGCAAATGCAAAACGTCCTCTGCGTTTT
++
+?@1FDFFDHGFB2EIJ)CJHEIHJIJJHGGJIJJ?#IJFIFIIG#DB#G@GII#HB#DIDIEJE@-EJ#JDBE?FDC#E9>@##@C?@##DDCD@DD#DD
+@NC_003198.1-14/1
+AACGTTTTCTGCGTGTTGCCGATATACTCGAAGGCAATTCCAGGCAAGGGCAGGTAGCGACCGTACTTTCCGCCCCCGCGAAAGTTAGCAACCTCCTGGT
++
+?@CFFDDFDHDDHIDIGJIC+FG:3#HJ#I=B##@ICGIGDJI9EJIII@JJGDJGCDBC(DF.DHHG<B;C?HDCE>BDCAB#DAC#DDAE>##DDDB,
+@NC_003198.1-12/1
+ACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTCGCCGATATTCTGGAAAGCAATTCCAGGCAAGGGC
++
+BCCFFFFDH3HFGADGGEJJBJJIJHEGFIJJHIG#GECDFIIJJJBB?BJD6JJJC>CHJ=GDI-DACGEGC?D@;HDA7DD>CD>FECCDD=:C@D#D
+@NC_003198.1-10/1
+ACAGTGGAAATTGATTGAAAATAAAGATATCGCCAGCAGCACATGAACAAGTTTCGGAATTTGATCAATTTAAAAATTTATTGAGTTATGCCGCCAGATA
++
+@<CF#FFFDDGFDEIBIJJJGIJE##?EFEIJGIGG)FDDIIIJJA#GJJFEHFHHEIJI#EHD)5I9C,C#F#JD>#<?#DDC#>;C#(@#C#CD8@#C
+@NC_003198.1-8/1
+GGCCGGGTTCTGGCTGGCGGCGATACGGCGAGTCGATTCCGCGATACCGACGGTAGATTCGAGGTAATGGCCAACCGCCTGCAGTTTTTCTACCGGAGCG
++
+CC@7FAD#HHHHHII+AHIEJIGJEGJ:IIJGF?GCDIC<GAJ#JF4JJHBJBHHG#EGF#CJCECEH:HJD#FDG;EG#A5FDDC5D#D@#5?ADD#C,
+@NC_003198.1-6/1
+CTTCAACACTTGCATGGTTGTTACCTCGTGATCTCTGGTCGAAAAAAAAGCCCGCACTGTTCAGGTGCGGGCTTTTTTCTGTGTTTCCTGTGCACATCAG
++
+CCB=FFFFHD#AH<JJIJJJJ?IDIHI#ICIH46IJ0CIJGI9BJJJGJJFI)#JHFFH7H?FIB<ECCAAJ#C;HA:A>/EF<EDE@@CC#D#E#>BAD
+@NC_003198.1-4/1
+ATCGCCACCAGATGGTTGGTAATTTTCGCGGGGGCGGAAAGTACGGTCGCTACCTACGCTTGGCTGGAATTGCATTCTAGAATATCGACAGCATGCAGAA
++
+C@@FFFFF?HAHHE7BIICHJJJJDHEJEGHJJJJIIF@J?EFIHGJ@:;HJJDI#I#I#EB#B8IJH<6EAC#)#B#>D<FC#>?(#@##D>(2A##<,
+@NC_003198.1-2/1
+ACAACATCCATGAACCGCATCAGCACCACCACCATTACCACCATCACCATTACCACAGGTAACTGTGCGGGCCGACGCGTACAGGAAACACCGAACAGAG
++
+@@@+FFFFHFFF)JJAJIJJI@+IJGJJIJJ?GDAJ#<JJGA?GJ8IIIFGDHHJGJHBGG8I#CJJC)H@D#C##CDD@7>DDED>D@CA#D9##5#C>
diff -r 000000000000 -r 6302d40828d2 test-data/NC_003198.1_simulated_R2.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/NC_003198.1_simulated_R2.fastq	Wed Oct 16 16:57:23 2019 -0400
@@ -0,0 +1,180 @@
+@NC_003198.1-90/2
+TTTCGCGGGGGCGGAAAGTACGGTCTCGACCTGCCCTTGCTTGGAATAGCTTTCCAGAATATCGGTAACAAGCGAAAACCATTCTGCATTTGACCCTGAT
++
+=@CAFDF+CHFFHHHEI,IEJJGJH#G#HIJJDI?9B??H#I3IBI*(JIDHI#HD&9DI#@HC#!E@;I!>D###H:#E#DCFD9>HADDB#A##@CAC
+@NC_003198.1-88/2
+GTGATTTCTGGTCGAAAAGAAAGCTCGCACTGGCCATGTGCGGGCTTTTTTCTGTGTGTCCTGGTCGCGCCACCATGCACAGGTAGCTCTGGTAATGGTG
++
+@:BFA!C0HFDHFJCBHJ#+<JJC#HJJHJE;##JF#?GIIJB0JHEGFFFHEE#F#!EHJJJ##ID#+#FI####ECC>#:#CD##D#CC#CC3CADCC
+@NC_003198.1-86/2
+TTTTTCGGACCTGCTCGCAGGACTTGCCAGCGCGGAGTCTGGATTCCCGCTTGCAAGGTTAGAATTGGTTGCCCAACAACTATGCTCGTGGATCACACTT
++
+CB1DFF!D?A8HHJFBI#JIAD@E9CI#F*JCIJ#GJ#J#@##8JFFFFE*HID;#IJ#=#!GI!FCIF?##@#).DDD##EH#:#####>(####CB#?
+@NC_003198.1-84/2
+CTGCCAAGTCCTGCGAGCAGGTAAGAAAAAATACGTTCGGCATCGCTGATATTCCGCAAAGCATGCTGGCGGGCGATAGTTTTTTCTATAATCGCCATCA
++
+@?+!DFFF<HCHHBCJHFJJHA#B#CJGIDE?HF@<D3<GJGEGJICF3BCHGF#HJ#;GCGJ##+=D@C#;#CGH;7@BCF59@<!9>#EDDDD###B<
+@NC_003198.1-82/2
+ATGCAGAACGTTTTCTGCGCGTTGCCGATATTCTGGAAGGCAATTCCAGGCAAGGGCAGGTAGCAACCGTAGTGTCCGCCCCCGCGAGAATTCCGAACCA
++
+@@BFFDDFFHGHHIHHDGI#HIEI>IGIGJ#0DI*DCI0JGIJ=FEJIJGHF?@<F#I;FI=H)#ID@DF:#B#>IC(DBDD##H<C##DCF#:###C@C
+@NC_003198.1-80/2
+GCCCCCGCGAAAATTACCAACCATCTGGCGGCGATGATTGAAAAAACTATCGGCGGCCAGGATGCTTTGCCGAATCTCAGCGATCCCGATAGTAATTTTT
++
+BB@ADD<FHH@HH<:#FGI#?J3G<GI#!?IIJ?9DIDDIJHDIIGI='D<BCDJGJGGJJDHIHJ=C@E5?;D##3F>?;CDD#D=#>#!:AD#(C@D'
+@NC_003198.1-78/2
+AATACGTTTGTCCTCGCTGTTATTCGGCAAAGCCTCCTGGCCGCCGATAGTTTTTTCAATAATCGCCACAAGAGTGTTAGTAAGTGTAGAGGGGGCGGCA
++
+@B<FFDDD!H!H#AJDIJH#?A*:GJJFJGJCC#B)GJGGFG?GJ9JG#DF;HID@GCIE#GIAH6C=##HCE##C>J#>@DC#C#@#@,C@EBDCD:#D
+@NC_003198.1-76/2
+AGGAGTCCCGCCATAATCGCGATCGACATTTTTTAGCCACGGCAACTCAGCGCAGCGTTGATGCTATCCGGGCACTGACCCAGCAGGCTTATACCGTGCA
++
+BC@FFDEFFHDHH)I@1IAIJHHJ3@JJEJJ)HC!FJH@CGH??I!GIHICFB#FECBBI8AJIGJ@EDDJ#95AI5IEHD9C#?#CD@#CC>CB#BDC'
+@NC_003198.1-74/2
+TGTTCGACAACCATTCTGGTCCGTGAAAGCGGGAATCCCGGCTACGCGCAGGCACGTCCCGCGACCAGCTCGGAAAAACTACATTTGGCATTGATGATCT
++
+=C@F=?2D#:H<:JJ!I!##JG+H<#;)GFJID:HHFIJFJGI#GF#<F#>BGC#ID8J#HII##CGD.E##<E#F26#D>>#HD#D#<D0#C##CAD#C
+@NC_003198.1-72/2
+CGGAATGTGATCAATGTAAAAACTTATTGACTTAGGCGGTCAGATACTTTAACCGATATAGGAATACAAGACGAACAAATGATACTGGCAGAATACACGA
++
+;@C4=?+D,FHFFJJ#<HIIJ@#JJGEJDHJGJII@JJJ#?HGIGGJI9GB.ID#IJFIB;GJ9CGDBD@CG##DCDA;G#D#F#3D#DBB##A9C#D#D
+@NC_003198.1-70/2
+TGAACAGTGCGGGCTTTTTTTTCGACCAGACATCCCGAGTTAACAACCATGCGAGTGTTGAAGTTCGGCGGTCCACCAGTGGGAAATGCAGATCGTTGTC
++
+1CBDF8F#AFHAHJJHCAEEJ+JJJGGDFG#GFI#DJIE#?9D>5?JFF;IBAJBAEJHJDHDJCD@>;GBC!FE##DDCEC#(B?C#::HD#@CB##D'
+@NC_003198.1-68/2
+TTAGCGAATTCTTGTTCGACAACCATTTTCAACCGTGCAAGCGGGAATCCCGGCTGCTCGCTGGCAAGACCTGCCAGCAGGACAGAAAAAATACGTTCGG
++
+C#?FDFF>H:HHHGIJHJJCH>GIEGJ@IIGIIJE?IEFEGD>BJJ0FJ#HEBB@IJ##FJG>GDGJ7#AEFGH#DF;5D@#<D@CB<DCFC9+>D#9#'
+@NC_003198.1-66/2
+TTGCCTGGAATTGCTTTCCAGAATATCGGCAACACGCAGAAAACGATCTGCATTTACTACTGGTGTACGGCCGAACTCCAACACTCGCATTGTATTTACC
++
+<@84FFFFH>G#H@I+AIIFGHJE:IEA<<:EIBHF?G1?IIAGJ!H;IAF=IHH#B#CF@F!#JFE.#FBHCEBBE#DCA?D>#BA@CD#FA##?CCCD
+@NC_003198.1-64/2
+GCAAATGCAGAACGTTTTATGCGTGTTGCCGATATTCTGGAAAGCAATTACAGGCAAGGGCAGGTAGCGACCGTACCTTTCGCCCCCGCGAAACTTAACA
++
+BBCB=2DFHAFGCDII?C#JDJ<+JIJGJI?IG??IDIIBJ9J?GG#IJ#G=JJCIG=@G#FCGIGC;@6D>ACCJ#CD!DA5C@C>#ECC#:#C#D#@'
+@NC_003198.1-62/2
+TCCGCCCCCGCGAAAATTACCAACCATCTGGTTGCGATGATTGAGCAAACTATCGGCGGCCAGGATCCTTTGCCGAATATCAGCGATGCCGAACATAGAC
++
+:C1DBFFDHAFAHJGJGHJ33ID#JCG?I#EJ#GFFD@J?GCGD*#BIG?HHJ;IJFC7@DG8D)F!DJHHC.@I?@=##CGDC#CBD#D#C?8#C###'
+@NC_003198.1-60/2
+ACTTAGGCGGGCAGATCCTTTGACCAATAGAGGAATACAAGACAGACAAATAAAAATGACACAGTACACAAGATGGGTGACCCGCATCAGCACCACCGCC
++
+CC@BDFFF#HGHBIFI#GG#J!JDJHJGE#EDJJICII)JHIFJEJIED=D@=CH<JFICF.IC#EHIBIF#D.###ECC##F>BCCA#>DDBC#C:#BD
+@NC_003198.1-58/2
+ATATCAGAGATGCCGAACGTATTTTTTCTAAGCTTCTCGCAGGACTTGCTATCGCGCAGCCGGAATTCCCTCTTGTAGGGTTGCGAATGATTGTCGAACC
++
+@?C+FDF#:HFHDJ:F:JACCIGCG@AJF#@#@41?G)?I#IIDIJJJI#9#IICD#H@FHFF#HH=AID#I>F>#D##A<3B)#FC#C#C>C7??#CD!
+@NC_003198.1-56/2
+GTTGGTAATTTTCGCGGGGGGGGAAAGTACAGTCGCTACCTGCCCTTGCCTGGAGTTGCTTTCCAGGATACCGGGAACATGCACAAAACGTTCTGCATCT
++
+@C@BBFDB:HDCH2IJAJCH#IIH+II@IH#FGEJJCC?GCGJAIG*JFEEF8>(@JJFIFG;####CC>#HHH#DB=C!D#B#@D<>CE#2C>>CA@#'
+@NC_003198.1-54/2
+GTTTCCAGAATATCGGCAACACGCAGAAAACGTTCTGCATTTGCCATTGATGTACCGCCGAACTTCAACACTCGCAAGGTTATTACCACGTGATCTCGTG
++
+#?CFAADFGEHHB+?JHJHHJI+6HG0J<9E=ED#IIGH@JC#>F@###GF#AI;JBBJFEBIJHIGCBAF@FFD9#D<57!;CDBC#EBC@EB@C>##D
+@NC_003198.1-52/2
+CGGCTGCGCGCTGGCATGTCCTGCGAGCAGGTCAGAAAGGATACGTTCAGCATCGCTGAGATTAGCCAAAGCGTCCTTGCCGCGGATAGGTGATTACAAC
++
+CCC4#)DDFEAHH@I#+FGIEFCIIJHEFIGCGFGGG*##FBI*GG6H!HBC0I(IHI>+DID#<#DH;EHF!DHC8#58EDD#ADD#C#>#!E###D#9
+@NC_003198.1-50/2
+GGCTGACGCGTACCGGAACCACATTCAATAGCCCGCACCTTAACAGTGCGTGATTATTTGTCGACCAGAGACCACGTGGTAACAACCATGCCAGTGATGA
++
+@@?DFF<;DHHFH#J+G.#I4?J##+AG#GBFJH)IC@JI#I?HI?IACI!F#JG##JF#CJECDF#IJ#D#FHDC#BFC6E#:DD>DCED#D>B<#C#'
+@NC_003198.1-48/2
+ACGCGCCTCCAGGAGTCCCGCGATAATCGCGCTCGACATTTTTTCTCCACGGCAAATCAGCGCGGAGTTGATGCTATCCGGGCATTGACCCATCAGGCTT
++
+=CCD4DDFBEHG?JE#+CG9?#1J2H:IJHC#HBGJI#I#FIHIG!IGA>GFAJDEFG,DAEE#I#IE;EFF?@BG?3BDB89D#D<D?A(D#DD##CC'
+@NC_003198.1-46/2
+TTGTTGCAAGAGATCATAACAGGGTATATTGATTGATAATAAAGATATCACCAGCAGCACATGAACAAGTTTCGGAATGTGACCAATTTAAAAATTTATT
++
+C#@=:FFFDHBDHJH<J:J>IHHE#A#IIDJHECJH#IHFDJI#JC<IF#J>GGHHIIBG(=@EF?8F#H#BFJBD>DAFD@#@#E#DCAADDD??#C#'
+@NC_003198.1-44/2
+TCGCGACCTGCCATTGCATGGAATTGCTTTCCAGTATATCGGCAGCACGCAGAGAACTTTCTGCACTTGCGAGTGTTGTACAGCCGAACGTCAACACTCG
++
+CBCF#F?FHH8H#EBGE#J#CJGJJE<I@IJ2GI*GGCFB@HAA#GIDGHDIG#IGE#BII>JB##JFBA#E#?##IFBCC#B##>DC@#>:@<CB?C#D
+@NC_003198.1-42/2
+CCTCCGAGCAGGTCAGAAAACATACGTTCGGCATCGATGATATTCGGCAAAGCATGCTTACCGCCGATTGTTTATTCACTCACCGCTCCGACATGGTTGG
++
+@CC#4DADH#H?HJIGII<C)GIIFJIJHIG>ID?J!G9JGJ*EJJJGG'IGGHE#D=###E@HJEDI#GHFE!)CF##B:##FDC##F#8!CCCB#5@:
+@NC_003198.1-40/2
+CATTCGAATGTCGAAGGTCGGAGGTACATCAGTGGCAAATGCAGAATGGTTTCTGCATATTGCCTATATCCAGGAAAGCAATACCAGGGTAGGGCACATA
++
+B?C!FF=#HCH#HHH<#JICD!GIJIGEHI#DJ#EJJGJHJJHID?#D#IGDI=3H#H#GC##@#D9J##D##3FABFFCCD#@F3#H!#C>:CC@##>:
+@NC_003198.1-38/2
+GTGATCAATTTAAAAATTTAGTGACTTAGGCGGGCAGATACTTTATCCAATATAGGAGTACAAGACAGACAAATAAAAATAACAGAGTAAACAACGGTCA
++
+BBB4D=D:HEH#DHID,CJH!HJI+AJ>GJH:G?C*FJAB99CGI#JJDJCCDD4GI#I<JCCDGHF#EJCH(HAJI>F?0?DDD#5C##D#A9A###>D
+@NC_003198.1-36/2
+TGGTTGTTACCTCGTGATCTCTGGTCGAAAAAAAAGCCCGCACTGCTCATGAGCGGTCTTTTTTCTGTGTTTCCTGTACGCGTCCGCAAGCATCTTTCCC
++
+B?BDACED2?;DH)JDJG0HGHAIJJGIE@H;GAIJID@JGF8GG#JBG#I#G9ID#C?EHJH=5D2IICFCII#B#HECHDDB#B##!:CC#>#?E#;D
+@NC_003198.1-34/2
+AAATATATCGCCAACAGCACATGAACAAGTTTCGGAAGGTGATCAACTTAAAAATTTAAAGACTTAGGCGGGCAGATACTTTAACCAATATAGGGATACA
++
++C+DFC;FH+#1G#HAJJIDH#JHJCJGBFDCFFJBJ#JH*JII#B!J'H@GH@?GH>##HDB8J=DH@CBCC57CC8CDGF@C(D5E#>EDD:#DCAC'
+@NC_003198.1-32/2
+ATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAATCAATTCCAAGCAGGGGCAGGTAGCGAGCGTACTTTCCACTCCCGCGAAAGACACCAACCA
++
+BC@D=D=DHEHGGJHI+J+GJDJICJCI?I*#GIHJ9JD!??GJ08G>#HHI#GFCFJ#IG;I>JD##?D#DGEA#H!9!D#EDD@#3;###@D:>>@AC
+@NC_003198.1-30/2
+AGGCTGATACCATGCAAAACCTGTTAGATCTGAGCGAATTCTTGTTCGACAACCATTTTCACGCGTGCAAGCGGGAATCCCGGCTGCTCGATGACAAGCC
++
+@?B#BFFA4EAHHGJCJIIH#>G#3!>EGI04#J9FHJIIBJFJFE@?4#I8?D?DDEJJA##BI@HD>D>DCFD#8H=A#/C;CGD#AC#DC##BB##D
+@NC_003198.1-28/2
+CACGCGCCTCCAGGTGTCCCGCCATGATAGGGATCGAACTATTTTCGCCACGGCCAATCAGCCCGGCGTTGATGCTATACGGGTACTGACCCAGGAGGCC
++
+B=1DFFFED2<B6I#,IG3F?IJH?#JG#G#JI)CGJ!#B(@G?#HCI8F9C20#D8JJ=EJ#=#DH#CI@D.JH2D;!EE05#?;@C->DD<##@AD@'
+@NC_003198.1-26/2
+TTTTTGCGACCATAGATCACGAGGTAACAACCATGCGAGTGTTGAAGTTCGCCGGTACATCAGTGGCAAATACAGAACGTTTCCTGCGTGTTGCCAATAT
++
+?BCAF)F2DGH<#JICG@JJH#0?AG#@JI/AFJI@#GDD0BG;:?GIFCG#EICICD#B/4GG(BJ3J@D#E(?IAGDH;@#D6ACCFC##DDD##D#'
+@NC_003198.1-24/2
+GAAACACAGAAAAAAGCCCGCACCTGAGCAATGCGGGCTTTTTTTTCGACCAAAGATCACGAGGTAAGAACCATCCGAGTATTGTAGTTCGGCGGTACCT
++
+@BBDBFF+HH?HDGIJ<IJIEGJAH#I!FH#J?IGIHGIGCJ9IFJGHFGBI#@8HCJHJEHIID@D#H;E5;H!EECA8#E#,#?EB;C@D>0CDC##@
+@NC_003198.1-22/2
+CTATCGGCGGCCAGGATGCTTTGCCGAATATCAGCGGCGCCGAACGTAATTAATCTGACCTGATCGCAGGACCTGCTAGTCCGTAGTCGGGATTCCCGCA
++
+B?@4DFDFA?CDH@JJIGJIJAHEIHJIDEH<I9E1#!*B;FIJIGID#H3!!IDIE=FJG<#BCDDDDEGF#CDG#A<0#B1#>C!DFBDCDD#3>BD'
+@NC_003198.1-20/2
+AATCGCGATAGACATGCTTTCGCCACGGCAAATCAGCGCCAGGTTGATGCTATGCGGAGACTGACCCAGCAGGTTGATACCATGCAAAACATCTTTGTTC
++
++@BFDFFFH#C++C>##JIBIIC#J<#FC)GDF9:J*JI!#!##B@#C;IGJG##G:##F3FJFH'DJ#9I#9#9C>?IC(CCDCC?EC@AD#@BDC#DD
+@NC_003198.1-18/2
+CCCTTGCATGGAATTGCTTTCGAGGATATCGGCAACACGGAGAAAACGTTTTGCATTTGCCTCTGATGTACCGCCGAACGTCAACACTCTCATGGTTGGT
++
+?@CFD>C#HHFHHGFHFJJH##JJ#JFIJJD?@*#JCCJ#@FJ?JBJD:I!;II1JGGHFG#IJ=JIE;IED@DF?HDE#CD@@CC?:4#DD:DDCCD#'
+@NC_003198.1-16/2
+TCGTGCAAGCGGGAATCTCGGCTGCGCGCTGGCAAGTCCTGCGTGCCGTTCAGTAAAAATCCGTTCGGCATCGCTGATATGCGCCAAAGCATCCTGGGAG
++
+#@@FF=DDBCGGHHI#A#GC3A?I#IHJIGJIJ?GHF##ICGB#:J#F#GH-I#JJIGJE#H@##IFCIE5;=C>CCB#C#ED#FCFD9D6?CC@C@##>
+@NC_003198.1-14/2
+CGTTGATGCTAACCGGCCGCTGACCGAGCAGGCGGATACCATGCGAAGCTAGTTTGATCTGAGCGCATTCTTGTTAGATAACCATTTTCCCCCGTGTACG
++
+?B@DF?CDFH2#:H#J#I!JHGJJG!IEJCG?**JIC?BJ#EJ2####H##=GJ8)JJGI@##D=#=E>DC>#BC#BC##D)@3#C?#C#!###@?#D#@
+@NC_003198.1-12/2
+TCTTGTTCGACACCCATTTTCACCCGTGCAAGCGGGAATCCCGGCGGCGCGCTGGCAAGTCCTGCGAGCAGGCCATAAAAAATATGTTCTGCATCGGTGA
++
+@BC++DDBDEHG#GJI<<I3JC!IIBG1*H#ICJIF?EIHIF;JJ#G4@6?/FAJ5GDAH#CDC;>IDFE(C#A@#CH>E#D#C#FDC?#>ACDFD#D>D
+@NC_003198.1-10/2
+CGCATGGTTGTTACCTCGTGTTCTCTGGTCGACAAAAAAGCCCGCACTGTTCAGGTGAGGGCTTTTTTGGGTGTATCCTGTATACGTCAGCCCGCAACGT
++
+@@CBDF?FHF>H<JHC?JJC#EGIG)GJGGH:#GHHDJGBCI@GHJJJII5H;HFII#GBH<EHH8C)#!CCEF#@DG;@DB###DDFD?;ACD8@#CC'
+@NC_003198.1-8/2
+CAGGACATTCCAGCGCGCAGCCGGGATTCCCGCTTGCACGGTTGAAAATGGTTGTCTGACCAGAATTCGCTCAGACTAAGCATGTTTTACAGGATATGAG
++
+#BB+BC#F2HHF3I=JEEJGAAIGI;BGCJHCG@F#HGIIFG@G?FGHJC63HIHC##JC!FHEI<EDG>=7GDF##@D#EH-BDFEE!D>!A#B>?#D'
+@NC_003198.1-6/2
+TCGCCGGCAGCACATGAACAAGTTTCCGCATCTGTTCCATTAAAAAATTTATAGACTTAGGCGGGCAGATACTTCAACGCTTAGACGAATACAAGCCTCG
++
+CCC+D##FAF<DC,IAJGIC,?GJEF#I#HH#GF##G#JIG#0J7I#(CICE#JDDDE=D#JDGBEGIEDE5EF#HD6###BC#A#CEBD?CDE>#A##'
+@NC_003198.1-4/2
+AACCGCATCAGCACCACCACCATTACCAACATCTCCATTACCCCAGGTAACGGTGCAGGCTGACGCGTACAGGAAACACAGACACAACGCCGCACCTCTA
++
+@+BF4FFFHAD<<JBG?GHIGJGJ#ID)#IEEI(BJJBHJGJ#IJD?#JJGBHA>I#GI)C=F<BJ7@;H;HH@DEEHFDEC#C!>:###9A@DDDD##'
+@NC_003198.1-2/2
+ATTGTTTTTTCAATCATCGCCACCAGATGGTTGGTCATTTTCGCGGGGGCGCAAACTACGGTAGCTACCTTCCCTTGCCTGGAACCGATTTCCAGTAAAT
++
+C#!+D+*<HHF##@JJJ4JBIADHGFIJGF?GF?G#CH:9EI>FJ#EJ9=8#FGG##CJFI.#ACFBH=D!E?55>;D3BHABA##C#BAC?CDD#?#EC
diff -r 000000000000 -r 6302d40828d2 test-data/NC_003198.1_simulated_bracken_report.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/NC_003198.1_simulated_bracken_report.txt	Wed Oct 16 16:57:23 2019 -0400
@@ -0,0 +1,2 @@
+name	taxonomy_id	taxonomy_lvl	kraken_assigned_reads	added_reads	new_est_reads	fraction_total_reads
+Salmonella enterica	28901	S	40	2	42	1.00000
diff -r 000000000000 -r 6302d40828d2 test-data/NC_003198.1_simulated_kraken_report.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/NC_003198.1_simulated_kraken_report.txt	Wed Oct 16 16:57:23 2019 -0400
@@ -0,0 +1,13 @@
+  6.67	3	3	U	0	unclassified
+ 93.33	42	0	R	1	root
+ 93.33	42	0	R1	131567	  cellular organisms
+ 93.33	42	0	D	2	    Bacteria
+ 93.33	42	0	P	1224	      Proteobacteria
+ 93.33	42	0	C	1236	        Gammaproteobacteria
+ 93.33	42	0	O	91347	          Enterobacterales
+ 93.33	42	2	F	543	            Enterobacteriaceae
+ 88.89	40	0	G	590	              Salmonella
+ 88.89	40	0	S	28901	                Salmonella enterica
+ 88.89	40	0	S1	59201	                  Salmonella enterica subsp. enterica
+ 88.89	40	0	S2	90370	                    Salmonella enterica subsp. enterica serovar Typhi
+ 88.89	40	40	S3	220341	                      Salmonella enterica subsp. enterica serovar Typhi str. CT18
diff -r 000000000000 -r 6302d40828d2 test-data/NC_011750.1_1kb.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/NC_011750.1_1kb.fasta	Wed Oct 16 16:57:23 2019 -0400
@@ -0,0 +1,14 @@
+>NC_011750.1 Escherichia coli IAI39 chromosome, complete genome
+GCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCT
+TCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAAT
+ATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACCA
+TTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGC
+CCGCACCTGACAGTGCGGGCTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGT
+TCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAG
+GCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAA
+AAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTCTGA
+CGGGACTCGCCGCTGCCCAACCGGGATTCCCGCTGGCGCAACTGAAAACTTTCGTCGATCAGGAATTTGC
+CCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTG
+ATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTA
+CCGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCTGA
+GTCCACCCGCCGTATTGCGGCAAGTCGTATTCCGGCTGATCACATGGTGCTGATGGCAGGTTTCACCGCC
diff -r 000000000000 -r 6302d40828d2 test-data/NC_011750.1_simulated_R1.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/NC_011750.1_simulated_R1.fastq	Wed Oct 16 16:57:23 2019 -0400
@@ -0,0 +1,180 @@
+@NC_011750.1-90/1
+TAAAATTTTATTGACTTAGGTCACTAAATACTTTAAGCAATATAGGCATAGCGCATAGACAGATAAAAATTATAGAGTGCACCACATCCATGTAACCCAT
++
+CB@D#FFDFBHFDJHJJIEHJJIFIJGJFIJ#?EG?#DGFGCII0?FJJIDIGJ*#GEIJ#IJ?)BC5EHD##>F8A;#@FA#A>;BDD>DD#C#8#@?C
+@NC_011750.1-88/1
+TGGCGCAACTGAAAACTATCGTCGATCAGGAATTCGCCCAAATAAAACATATCCTGCATGGCACTAGTTTGTTGGGGCAGTGCCCGGATAGCAGCAACGC
++
+CC1FFFF=D2D+HGIHJ#3JFIIAIIAIGJJFEJ#JGJJIJ?IIGC@BDB#HIHIB<JJGHGJ#DJHIHFCEH8A@BCDEFDBD>;FA5D#DA#D#FCDC
+@NC_011750.1-86/1
+CTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCAAGCGAGTGTTGACGTTCGGCGGTACATCGGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGA
++
+5C>FAFAFHD<FHGJFIJJIJHH,JJIJJJJJI6IJ#JIJ#IFI#/JI#JDJDI#=HH#DFJ?7#II#FD#E>CA=C@#D<@DC#DDD>D:DDA#D?ED,
+@NC_011750.1-84/1
+GAAAACGTTCTGCATTTGCCACTGATGTACCACCGAACTTCAACACTCGCCTGGTAGTTACCTCGTTACCGTTGGTCGAAAAAAAAGGCCGCACTGTCAG
++
+@C=DFDFFFHGDCGEIIIJD?#JAIIDBHJ?#JEGGIBFJIJ=J>FGIJD##DI?!EE=JBBJ#FBD=DI#?E;<FCDDC#DDACD@#>CECDDCB53DD
+@NC_011750.1-82/1
+TGCTTTACCCAATATCAGCGATGCCGCACGTATTTTTGCCGAACTTCCGACGTGACTCGCCGCTGCCCAACCGGGCTTCCGGCTGGCGCAACTGAATACT
++
+@@?A#FDDHGHF<>JJ4GAIIICCD0###EEIIHIIJ#JHGJJHJIB#'FHH#IJCJJCJ8GEG7??-?>EF(C?#;C7?#DH#CDABDDAD?DBA#DC@
+@NC_011750.1-80/1
+TGGCGCAACTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATTTGTTTGGTGGGCCAGTACCTGGATAGCATCTACGC
++
+@C=DFEFFDHHHH#CHEEIICIJHJJJJ#JGGGHJFJIJBED=?DEIHH>BJI#CGIBEI#I>DC#HBGED)HE?:##ED5#CE#EAE2EC5DDC##BAC
+@NC_011750.1-78/1
+GTCCCGTCAGAAGTTCGGCAAAAATACGTTCGGCATTGCTGACATTGGGTAAAGCATCCTGGCTGCTTGTGGTTTGTTCAATCATCTCCACCATGTGAAT
++
+@@CFFFFFFHHH#JJJIJJHJHFAJJI#J#I:HIJG#JBGH@#H3JEII@?IIFIHBFH9EC@#J=D##FCEIC;#@CD4EFECAD#D3DDC8#C+>##@
+@NC_011750.1-76/1
+GCAGAACTTCAACACTCGCATGGTTGTTAACTCGTTACCTTTGGTCGAAATAAGAGCCCGCACTGTAGGGTGCGGGCTTTTTTCTGTGTTTCCTGTACGC
++
+C?!DD#;FC7FHAHI2JJEI=HJ?IIJJI#HICHJGHJ8IJGI;JD@H*FB@J#CGI@EBA#JEEG##E#GDCCE?DHJFA<#>>AD#C>?E>8AD#ADB
+@NC_011750.1-74/1
+AGAACGTTTTCTGCGTGTTGCCGATATTCTGCAAAGTAATGCCGGGCAGGGGGAGGTGGGCATCGTGCTCCCTGCCCCCGCGATAATCACCATCCACCTG
++
+??CFFDF1HFH<FBJ?IIGDEIJHGI;IJ)J#DIHJ)AJHIHI!ID:DJGHB#GIC=I##JH#<CE#CGI#@CD@7HBCHH)9#DF?ED?ED##DABD#3
+@NC_011750.1-72/1
+TGCCAGGCAGGGGCAAGTGGCCACCGTCGTCTCTGCCCCCGCCAAAACCACCAACCAGCTGGGGGCGATCATTTAGAAAAACATTAGCGGCCAGGGTGCT
++
+@+@DD?FFHHHHGIA#E?IGHBJIJG9I#GJHGBJIEJH#E@IIIJJ#JFFEH3JEF#JFDI#I(IDCE#CJ>#E#FC(E#C;CD:#,>#CDDCC#B#?,
+@NC_011750.1-70/1
+ATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGAAGCTTCTGCACTGGTTCCCTTACGCGAGTAAAGTAAAATGTTATTGGCGTAGTTCTCAAA
++
+CCCFFBFFHA@HCJIHJGGGBJJJJJIJFA1>J#IHBAD#FG#HAH#@#FH@BC1##IJD!#FH#7@?AD@E!A>:I@B#D#;#??#A##D##@D#B#?D
+@NC_011750.1-68/1
+CCGCTAATGGTTTTTTCAATCACCGCCACCAGGTGGTTGGTGATTTTGGTGGGGGCAGAGAGGACGGCGGCCACCCGCCCCTACCTGGCATGGCTTTCCA
++
+@CCDFFEDHDHH=#EIIJIJHH#JJIB:EGJIFI096HGJIEFJFIGJE#JIGJIBHJDJCBFGJGH#;?HID;E#F>I=@F#EDD5BDC@#D#DDCCDD
+@NC_011750.1-66/1
+CTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTTTTCGACCAAAGGTGACGAGGTAACAACCATGAGAGTGTTGAAGT
++
+@@@FF+FFHFHHHIJ<JFIIJI@CGIJ*JJGEGIJCIGJGJI>I?/IJECGEJHHB;FC(EHCJD?5;F#EDEF=EH#D?@<D>E>C#DF#>CB5#D??A
+@NC_011750.1-64/1
+AAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACGATTACCACCACCATCACCAGTACCACAGGTAACGGTGTGTGGTGACGCGTTTTG
++
+?@CDDDFADH?HHJG#JBGJ@BJJAJHEGJIIFGJIIIJJBJIJI##IAEHDGCAIBH#HGFAJJ#GFHDD#D;#;=#GCBCE#D#D#DDDA>#@<###,
+@NC_011750.1-62/1
+TCAACACTCGCATGGTTGTTGCCTCGTTACCTTTGGTCGAAAAAAAAGCCCGGACTGTCAGGTGCGGGCTTCTTTCTGTGTTTCCTGTACGTGTCACTCC
++
+C@+FFFFD<?HFGIHFCFFI#GGIJFH#CJIBAIIJ?HFCIJH.G)EIEIAF#H#JJFJ)CFBE=JDBCIE#F;9=>C#D=>#?E,;DC5D#D,BE##<C
+@NC_011750.1-60/1
+GTGTGGATTAAAGAATGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGCAAATTAACATTTTACTTACTTAGATCACTAAATAGTGTACC
++
+B@?=DFFFHHHD#JJ#IEJGJJHHJI1IBI?JJGJ?CJ:JJIAJEJJJ?HCJHICDAD#EJ>AIF>!I7#GJE#F#HD#.>@#E#A;@D>DDB#C#@C#B
+@NC_011750.1-58/1
+CTCAGTAATATCGACGGTAGATTCGAGGTAATGCCCCACTGCGACCAGTTTTTCGACAGTATCGATAACGGTAACGTTGTGACCGCGCGCTTTTAATACG
++
+@@@F8#FFHDHDH#GGJJIHHECIJFIJ?@JGICJICJFJ:##J#F?JEIFIJHCIJ#H#;DEHGDCI@GFCHF>G8BFC2>A#EDEDDCED#@CCD#C,
+@NC_011750.1-56/1
+GTTTTTCGACCGGATCGATAACGGTAACGTTGTGACCGGGCGCTTCTAATACGCCGGCCATAATGGCGGTCGACATTTGCTCGCCACGGCAAATCAGGGC
++
+@@CAFDFBCHFHDEFH?EIJIJJJI#JJ>JIHBGIJIG!JAFIGI#JIBGGJGDH3DEIF<C#CHG;D#:C@D3E;4D#A:C?DE#D;ACDC#D#DA#?B
+@NC_011750.1-54/1
+CACCACCATTACCAACACCATCGCCATTACCACAGGAAACGGTTCGGGCTGATGCGTACAGGAAACACAGAAAAAAGCCCGCTCCGGGCAGTGCGGGCTT
++
+CC@=FFFF7FHHHI#IJIAHJB#HJGDFEJIDH#FC#JJ)?JJ#HJIFHJJH#J#JBB;G5IIGI=IH#II<GG=@EHFBDD#DD#C#ADCCCA6AC#<C
+@NC_011750.1-52/1
+GTTGTGACCGCGCGCTTTTAATACGCCGGCCATAATGGCGATCAACATTTTCTCGCCACGGTAAATCAGTGCAGCGTTGATGCTATCCGGGTACTACCCC
++
+@C?@FFDDHHHG?HGJJ#IIAJI?JJIJFFJJ?6JJIFGFJ0J#HAJBBGJFBGG?B>7GE#DG-CFHH#5F.JFC:DHB=FFCABDDCD?#DDD#:AD,
+@NC_011750.1-50/1
+TTTCATTCTGACTGCAACGGGCAATATGTCTCTGTTTGGATTAAACAAAGAGTGTCTGATAACAGCTTCGGAACTGGTTACCTGCCGTGGGTCAGTTAAA
++
+CCCF;2FFGHHHHJGJHJH?GFEGIDFJI9JIJGH#GGJJBGI>D#9I#HJEJ:IED/>J>#D;CJ>IB#FDCBFEAHDCCCEBDCD#D##E#B#AA>>D
+@NC_011750.1-48/1
+CACGGCAAATCAGCACAGCGTTGATGCTATCCGGGCACTGCCCCAACAAACTAATGCCATGCAGGACCTGTGTTATTTGGGCATACTCCTGATCGACTAA
++
++1@DFDFF+?HHG<#IHJBJJIJJB>JBGHJGH<IEGBJGFIAJJAFCJHJIBIDEJCGBIDHBFDF#FDC#?EH(H>AGFAD#5#C#@3@0C#B8C#68
+@NC_011750.1-46/1
+CCACGGCAAATCAGCGCAGCGTTGATGCTATCCGGGCACTGCCCCATCAAACTAATGCCATGCAGGACATGTTTAATTTGGGCGAGTTCCTGAGAGACGA
++
+@@@FDF?DH?FHCJJ:EGH:GJJJJ<GEE#JJF<HIIIJ?IBJJJI#=9GBGC#E>:IEDIA<=CGH#BE>5G=(D#:H6D8D#;#;@FDDD###@CDB,
+@NC_011750.1-44/1
+TTGCCGAACTTCTGACGGGACTCGCCGCTGCCCAACCGGGATTCCCGCTGGCGCAGCTGAAAACTCTCGTCGCTCAGTAATTTGCCCGAATAAAACATGT
++
+BC@DFF<FFHHDHJJJJBJGIGJJJIJG<HHICJ##I8J36JFJI9JGCIJJ5HG#@DECJJ#=I#=E:4E>##>C9#>CF7@#DF##@CA>AAB>BCEC
+@NC_011750.1-42/1
+CCACGGCAAAACAGCGCAGCGTTGATGCTATCCGCGCACTGCCCCAGCGAACTAATGCCATGTAGAACATGTTTTATTTGGGCAAATTCCTGATCGACGA
++
+@C@FFFBFHH#BHIIDIE9CIIIIIJ?FEC1IJI#IGC@J8A8JJI#E#=HII@C?<EFEHF#F9#?EACDBDD>AA@GCCC5:DBAEFE?CB@:CAB9D
+@NC_011750.1-40/1
+TGGCCACCGTCCTCTCTGCCCCCGCCATAATCACCAACCACCTGGTGGCGAAGATTGAAAAAACCATTAGCCGGCAGGATGCTTAAGGCAATAACAGCGA
++
+C?CDFADFADH:GCJH;IHJ>JICHGJ#J9DIDBJJFBJHGJHJ#FF<JJJ#HHB8##;H5DCCFCBJE@C#9##;ABAB?@CF#D##D;DFC#>;AC8,
+@NC_011750.1-38/1
+GGTTACCTGCCGTGATTAAATTAAAATATTATTGACTTAGGTCACTAAAGACTTTTACCAATATAGGCATAGCGTACCGCAAGACAAAAATTACAGCATA
++
+;@CFFFF23HFFCJG#DG?IGHJJI:H#JJAJ?7EI#JJ3I>GJJJJ9B#IHFHD#IJ#EH@AIBEFBDCC=DJ#AE#D##@CC##CDDC:CDBB5##CC
+@NC_011750.1-36/1
+GAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGGACGTATTTTTGCCGAACTGCTCATGGGGCTAGCTGCTGCCCAACCTGGAT
++
+@C?FFF?FFHFHHGGGGHJIBJIJJH)?J:GHIIDFIGDJJIGJJJ?ED#JGJGFIJGJJGBCBJFFD#JD#D#GBG#H<#ED#A=D@DD=B#CD#>AC>
+@NC_011750.1-34/1
+TTCTCGCCACGGCAAATCAGCGCAGCGTTGATGGTATCCGGGCACTGCCCCAACAAACTAATGCCATGCAGGATATGTTTTATTTGGGCAAACGCCTGAT
++
+@@@?F+DFHHA8+JJJIJJJGJI2EJJJI#I#H#?F#GDIFGIG?G=JCJIIGBII:IIHIEH?DJEDCI<G@#=ABA@E>#CEA<DC#B=D###A#C#@
+@NC_011750.1-32/1
+GTATTTTTGCCGAACTTCTGACGGGACTCGCCGCTGCCCAACCGGGATTCCCGCTGGCGCAACTGAATACTTTCGTCGATCAGGACTTTGCCCAAATTAA
++
+?C?FFF,FCHFHH@G?IBEDI>JJJJJIIGIJCJG?HHJIFAH?EJCJ?G0JIJGGGF+7JHI=EBB#H;G;B@AD@DDC=DAFD#B<CC@B>:CDC#D@
+@NC_011750.1-30/1
+TGCCCCACTGCCAGCAGTTTTTCGACCGGATCGATAACGGTAACGTTGTGACCGCGCGCTTCTAATACGCCGGCCATAATGGCGCTCGACATTTTATCGC
++
+@C=FFFFFFGHBDIIJJGI?IG,JFCHJJ#JFIJ;IHIHJ@E*FJHEIJJJGBJ>G4GE#G@D@<EIF?BDCEDHB=>?;<(DC#E#(CC:#DC@#19CA
+@NC_011750.1-28/1
+AAAAAAGAGTGTCCGATAGCAGCTTCTGAACTGGTTACCTGCCGCGAGTAAATTAAAATTTAATTGACTTAGGTCACTTAATACTTTAACCCATATAGGC
++
+@@CAFDFFHHFH<#FIAJAGFEJ=IJJIJJJFEIHI7#IHJJ3J#EG=AIGGJDHEAE74A'DFHJAIJJCGIDEHH>#;HCDEFA?:DA?#CDC?D#:C
+@NC_011750.1-26/1
+AATGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGACGAAGGCGGCCACCGTCCTCTCTGCCACCTCCAAAATATCCAACCACCCCGT
++
+=B#FDFAFDHGGBJF@JGIJIJJIHHIIGI0H<0#GIAJJIFFJCI###I!GEJ#JDGGI=GAAGAGCDFB;#F#?B#ACEA#:>##CDDAE>C9###AB
+@NC_011750.1-24/1
+CGGTGGCCACCTGCCCCTGCCTGGCATTGCTTTCCAGAATTTCGGTAACACGCAGAAAACGTACTGCATTTGCCACTGATGTACCGCCTAACTTCACCCC
++
+CC?FFFFFH3HHHJJJJJH<IJ@IJJHGJJBIJG1GBJJI#IDII!GGJJHDIIJDHDIECJ#7C9EE.D?58DGECA@BAHD#DDB@#:D?4EBC###,
+@NC_011750.1-22/1
+TGATATTGGGTAAAGCATCCTGGCCGCTAATGGTTTTTTCAATCATCGCCACCAGGGGGTTCGTGATTTTGGCTGGGGCCGAGAGGACGGGGGCCACCTG
++
+#CBFFFDFH1HHF@GJJJE9GJEBBJIJJJGJJJCIGHDFHJ@J9HHJEJJIG;JI#FGID#FA#HICA=HI;#F>CA2#;#DD:DC<5(#C3CD0ADCD
+@NC_011750.1-20/1
+TAATGGCGATCGACATTTTCTCGCCACGGCAAATCCGAGCAGCGTTGATGCTATCGGGGTACTGCCCCAACAAACTAATGCCATGCAGCTCATGATTAAT
++
+?@CAFFFFFHHDHJJJ@EJDG@JIHAF@#J?CFJG#I#J#JIBIH'HIDFJIHJ=##F=#DC@H=FHJFEJD><@F?GDD@C@FBCFB##B@AD#C@#C,
+@NC_011750.1-18/1
+CGATGCCGAACGTATTTTTGACGAACTTCTGACGGGACTCCCCGCTGCCCCACCGGGATTCCCGCTGCCGCAACTAAAAACTATCGACGATCAGGAAGTT
++
+@@CDFFFF?G<HHJIIEJJ;#ACGJ2:F?JJI?HJ)BHJE#JJHIG:J@*#@BBG=CHFED@>FH:F#GC@F@;@#CBIFC##D>D#C@B#DD>ABA#B,
+@NC_011750.1-16/1
+GCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCCACAACCACCTGGTGGCGAGGATTGAAAAAACCATTAACGGCCAGGACGCAT
++
+BCCFFFDFFDAH>GIIICHGHIIDJEJJDJFJJJEIEHGIJICJJJHH##JGHGIFIFE#BIJ7G=G#G7EDFICCE#?F#>@DD#1CCCCDAC##DD#B
+@NC_011750.1-14/1
+GAAACACAGAAAAAAGCCCGCACCTGACAGTTCGGGCTTTTTTTTCGACCGAACGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGTCGGTACCAC
++
+@@@DDDAFHB+HF@JFIJH:IIJ?HH#JIHA#JHDCJG#II7)JBJ@JII#EA#GIEFG8JH<J?D78I<FC@GBBDDCC@CECCA>FED#DC:DDD##C
+@NC_011750.1-12/1
+CTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGAACTGGTTACCTTCCATGAGTATATTAAAATTTTATTGACATTTGTCCCTAACTACTTCA
++
+;C>F-FFFDHHHHGJG?JJJJEJJJJJDAIGDGIJGGJ4IIJAID0#FJJ;G#ID#G8@IIH#@A#GGIHBDED:#D;CC#D##BB##C@D@#DC?D?#D
+@NC_011750.1-10/1
+TTCGAGGTAATGCCCCACTGCCAGCAGTTTTTCGACCGGATCGATAACGGTAACGTTGTTACCGCGCGCTTCTAATACGCCGGCCATCATAGCGATCGAC
++
+C<?F44FFHHHGHEHGIJHGIJJHJJGJJHIHIJDIJ1HJ#7@IEH9JCHDJD>B5=HI#)DFGAH@:IHJIJ3E>DF?#BDFDE9E#DD#E7CCBAEC>
+@NC_011750.1-8/1
+TTGACTTAGGTCACTAAATACTTTAACCAATATAGGCATAGTGCACAGACAGATCAAAATTACAGAGTACACAACACCCATGAAACGCATTATCACCACC
++
+@CCFDFDEGHHHFFJI77CJ:HIJJJGIJI?GH3JJ)DBGJ#A=D8JF?#DBGJ.BIFJG(.#F=#C?AEF7DJ?H#5@>:DCDDDIB+E#;#3D:93BC
+@NC_011750.1-6/1
+ACTTGCCGCAATACGGCGGGTGGACTCAGCAATATCGACGGTAGATTCGAGGTAATGCCCCACTGCCAGAAGTTTTTCGATCGGATCGATAACGGTAACG
++
+BC@FF=FFHHDHHGDAJ>GIIIGGJGAJI?I@J)II?GFJ?IIIJJJJJCDHIHJG#0FG@<I#?DGCI#>#EHFCDDBD#E=DB8AC>E4C##C>B>D@
+@NC_011750.1-4/1
+TGCCACTGATGTACCACCGCACTTCAACACTCGCATGGTTGTTACCTCGTTACCTTTGGTCGGAAAACAAGCCAGCTCTGTCAGGTGCGGGCTTGTTTCT
++
+CC?FFDFFDF=HDI+#EJ>#IJH?JFDFJGDIDGE?JJI9@JJGGJGIJHIGE9H/EJDCCH#F8AG#7C4A@#GD#@BGH2B@>#BD#E#?C##D@CDC
+@NC_011750.1-2/1
+CCTGCCTGCCATTGCTTTCCAGAATATCGGTAACACGCAGAAAACGTTCTGCATTTGCCAGTGATGTACCGCCGAACTTCAACGCTCACATGGTTGTTAC
++
+@@CFF8FF#HHAHH7@JIBG@JIHJF2BFJ#IDIB@IIIIB@J;IJCGHGIIEB>/GABJ#BFBJHDED6@F@8H#(:BDD<B#CC)-EB##DC>CAD>,
diff -r 000000000000 -r 6302d40828d2 test-data/NC_011750.1_simulated_R2.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/NC_011750.1_simulated_R2.fastq	Wed Oct 16 16:57:23 2019 -0400
@@ -0,0 +1,180 @@
+@NC_011750.1-90/2
+ATCGGCAACACGCAGAAAACGTGCTGCGTTTGCCACTGTTGTACCGCCAAACTTCAACACTCGCTTGGTTGTTACCTCGTTACCGTTGGTCCAAAAAAAA
++
+?CCB=FFFHH2H<AAGGIC?#,#?J#G!GJIJJHA?CJ#?I0#JDCCJ#I04I7DH=JHIJDGJ#J5CI:FDAHCF7HE>D#CB##5@##5!AFDCE##D
+@NC_011750.1-88/2
+CAGCACCATGTGATCAGCCGGGATACGGCTTGCCGCAATACGGCGGGTGGACTAAGCTAGATACACGGTAGATTTGAGGTAAAGCCCCAATGCCATCAGT
++
+@@@ADFF,FFHD<E#GH#JJJ#IE#IE#EAJJICBB@0EJHC>JIABCB@9=A!HCH#D#C?##G@CJDIG);###?A?DDC##CCA:D!?(5@>#DDF:
+@NC_011750.1-86/2
+ACGAAAGTTTTCAGTTGCGCCAGCGGGAATCCCGGTTGGGCAGCGGCGAGTCCCCTCAGAAGTTCGGCAAAAATACGTTAGGGATCGAGGATATCGGAAA
++
+@1CFD?3<G8HHFGFI<AGG1IEJ?FIHEIIJJHIEJJHE#E?GJI;#JHF#C##HEIBJF#JCHFIEDC#EI<9F#BH!#C#CC#:##C#CD##BC##'
+@NC_011750.1-84/2
+GTTACCTGCCGTGAGTAAATTAAAATTGTATTGATTTAGGTCACTAAATACTTTAACCAGTAGAGGCACAGCGCACAGACAGATAAAAACTACAGAGTAC
++
+=C;F4CFF2GF:C#HJJJJAHJJGIH+#JJJ)J###FJJHG@IJCBI@AGEIEED@#FC#E@#BC5CI#=DED>CID;8#GEF@;=D@E#@@ABDFD(D'
+@NC_011750.1-82/2
+TCGAGGTAATGCCCCCCTGCCAGCAGTTTTTCGACCGGATCAATAAGGGTAACGTTGTGACCGCGCGCTTCTATTACGCCGGCCATAGTCGCGATCGACA
++
+:@?:FDD:<GF<DGB!BIG#GJJJJFE,C)HFFJIDF)GHI#J#F0#IJGHBGH?F)HGEI>J>)GFEH5>C7#DD>DB6>9CHHFA#C#CA@CDC:@3'
+@NC_011750.1-80/2
+ATCAGCCTGAATACGACTTGCGGCGATTCGGCGGGTTGACTCAGCGATATCGTCGTTGCATTCGATTTAATGCCCCACTGCCAGGAGTTTTACGTCCGGA
++
+=<C+FAD#A<HFAEEFAJCGI#IG!FI!#@I:EIBD#IFBJ?I3H#GJJJBH!#?#G##F?IIHE##EHDJFHEHCFCBEAFCA#DACDB5#>#!###C'
+@NC_011750.1-78/2
+CAGTGCGGGCTTTTTATTCGACCAACGGTAACGAGGTAACAACCATGCGAGAGTTGAAGTTCGGCGGTACATCAGTGGCACATTAAGAACGTTTTCAGCG
++
+CB;F=CFFHHHHHIC#EGIHCHAHI#J4A1H@JI<19:I3JHJGA?GHIB;##FHIGFJJHG)FCBHEDDGC5F#C#D4E#BH##CFC5EA#BCC##>CC
+@NC_011750.1-76/2
+TAGCAGCGTCTGAACTGGTTACATGCCGTGAGTAAATTAAATAGCTTTTGAGTTAGGTCACTGAACACTTTAAGCAAGATAGGGATAGAGCAGATAGAGT
++
+BB?4=FD#HGHDHJI2FG:)JG#?JH+I+#FIJIJ#IG*H1##!#I#D;?D#IGBG7EDAFJ#CF#D@FE#HE#HED#)I<D##>ADC!7EB###D#A#!
+@NC_011750.1-74/2
+ATTGCCCCAACAAACTAATGCCATGCAGGACATGTTTGATTTGGGCAAATACCTGATCGCCGGAAGTGTTTAGTTGAGCCAGCGTGAATCCCGTATGGGC
++
+C#BAF#DFF3GFBJG#IJJH@JCEJAJG?JJ0JGGHH#@1:JIFI9GF#F#ADDICHHJ!GI#EBF:#FD#IAGB###C#BDBH#5>EE:EB###AC>A?
+@NC_011750.1-72/2
+ACATTATCTCGCCACAGCAAATCAGCGCAGCGTTGATGCTATGGGGGCACTGCCCGAACAAACTACTGCCATACAGGACATGTTTTAATTGGGCAAATGC
++
+?C=DF!FFGHHHDJA#<CAGCJB?IJ?B;IGGHI)HIIGCH;!#4?#CGBIJB98#8DCC)JJHG#BCHIHC#GC<#DDD#CD?DFA#?D@CD>>B@D#5
+@NC_011750.1-70/2
+CTCGTTCCCTTGGGTCGAAAAAAAAACCCGCACTGTCAGGTGCGGGCTTTTTTCTGTATTTCCTATACGCTTGAGCCCGCACCATTACCTGTGCTAATGA
++
+BBBF4F#;CF<#FF)JI,BJ,9+:H#C<?I9#GJJIJJJ3D#<JFAI?D#7F<@IJA##GI=GC#E##C##I#AFDDDF#D#D!@ADDBF>?(#D>C#>'
+@NC_011750.1-68/2
+CACCTTCACCATTACCACAGCTAACGGTGCGGGCTGACGCGTACTTGAAAAACGGAAAAAAGCCCGTACCGGACAGTGCGGGCTTTTTTTTCGACTAGAG
++
+CCCD+FFFHH?BFA<E+EJJ!BJJCII)EI#CGJJHHHGG?IJI##4.D##DB!CHI4I9JJFDID#C(F#BCH5DH@D?BDEED1CC@@D>;?D###C'
+@NC_011750.1-66/2
+ATACGTTCGGCATCGCTGATATTGGGTATATCATCATGGACGCTGATGGTTGTTTCAATCACCGCGACCATGTGGATTGTGATTTTGGAGGGGGTAGAGA
++
+@::4FD#FFH>H+J+J@IJ+I1FEIIHG+##G3:I(HJJ#I9JI#JIBHHCAIJIFGC#HD#AF=#GIJF!DJHA#F#ACEFEDDC5@#9#B>B#CC#BC
+@NC_011750.1-64/2
+TGATTTTGGCGGTGGCAGAGAGGACGATGACCACCTGCCCCTGCCTGGCATTGGTTTCCCGAATTGCGGCAAGAGGCAGAAAATGTTGTAATTTTGCTAC
++
+BB:?F=D;AFHH#GIJIGJGAIJHJE!)G#1CH@IGF@IIIDEJJ-IGHI#IF#FDDFE#FGC<!#HCAD75#D#IFFCBCC?#CFB#A###DB<DC#3'
+@NC_011750.1-62/2
+TGGATTAAAAAAAGAGTGTCTGATAGCAGCTGCAGGATTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTAACTTAGGTCACTAAATGATTTAACCGA
++
+##CF=F;DG?BHFF;FHF?AI2BFCJEGJI<#I#J###IG>JEICG8J#D9HFF2JCGECDHC=H=AG=#?C#F=A@C?BHC+B#?AC#!#AC>D@C##'
+@NC_011750.1-60/2
+GTTACCTCGTTAGCTTTGGTCGAAAAAAAAGCCCGCACTGACAAGTGCGGGCTGTTTTCTGTGTTTCATGGACGCGAGAGCCCCCCCCGTGACCTGTGGT
++
+BC@DFDDF2H+F#<C:HHHFJG?FIJH1GII?HDIHIBGJ!HC#IH9D=IH.?#HJJ@#D#JHH=D@#HI#GC@G>##D>FCB#D##CA5#C#D<?;CA'
+@NC_011750.1-58/2
+CCGAAGTTCTGACGGGACTCGCCGATGACCAACTGGGATTCCCGCTGGGGTAACTTAAGACTTTCCGCGATTAGAAATTTGCCTAAGAGAGACATGTCAT
++
+C@CF:#FDFHHHHEJJ+IIJDHID+G##HICH*#FB2=IIJIDI#=H5!B#AJII#@I#JFDFGE##G?GC/CH#C#DD##DB#C9#!#4!CDC>>C@#'
+@NC_011750.1-56/2
+CCATTAGCGGCCAAGAAGCTTTAACCAATATCAGCGATGCCGAACGTATTTTAGCCCTACTTCTGAAGGGACTCGTCGCTGACACACCTGGATGGCCGCT
++
+@CC#+FCAFCHHH!EI#?#GJJ0#H9J2ECIJ?IJCF=GJG>GE>J9?9=G##J.I##JDDGBHC?#IDEG#HAC#@E@C##D##FE##DCAA##E<9DE
+@NC_011750.1-54/2
+GTTTTTTAAATCCTCGCCACCAGGTGGTTGGTGATTTTGGCGGGGGCAGAGAGGGCGGTGGCCACCTGCCCCTGCCTGGAACGGCTTTCCAGAATATCGG
++
+1@+F4AD#AAF##HJJIGJ<EGI#J#GI?JGB?G@EJHF9JJ?#G'I?HHC##?##BHIGG@JJJ;@HIH#HF:H>@DD#?##C@<CD#A@CD?CDC#BC
+@NC_011750.1-52/2
+GTGGCGATGATTGAAAGAACCATTAGCGGCCAGTATGCTTTACCCAAAAGCAGCGATGCCGAACGAATATTTGGCGAACTTCTTCCGGGAATCGCCGCAA
++
+@CCFFFD=DEHHCH<I#JGIIJJIIII)@G<JG#GGI#I9FCJIJ#G!J#GH#GEIB7JGH#D=8#H##C.DH#@F#JE##CF##@EBCD#>FCC#D@#'
+@NC_011750.1-50/2
+GAAAAAAAAGCCCGCACTGTCTGGTTATGGTTTTTTTCTGTGTTTCCTCGACGCGTCAGCCCGCACGGTTACCTGAGGTAATGGTGTTGGTCGTGGTTAC
++
+@=@FDDF2DFHH+GEJ2AJJD!JFG#!)FE#JGHJ>#ICG?JDBFI*G##DC#CJGDJIJ@IIJDG#DCD#FCC#!>9C@>#D@BD##CDE#CDD#A#D'
+@NC_011750.1-48/2
+TGCCAGGCAGGGGCAGGTGGCCACGGTCCTGTCTGCCCCCGCCAAACTCACCAACCGCCTGATGGCGATGAGTGAATAAACCATTATTGACTAGCACGCT
++
+BC@4DACDHHFF2+IC:?FHFJI,!CEHGI!DGEG)IJHDG#JI2G#BIEI=AHCB#I#FE#J#CD86BHD#ICE##EAI:=3C#C##@#C##B#@#<CA
+@NC_011750.1-46/2
+TGCCAGGCAGGGGCAGGTGGCCCCCGTCCTCTCAGCCCCCATCACAATCACCAACCACCTGGTGGCGAAGACTGATAAAACGATTAGCTGCCAGGATGAT
++
+@C@A1D4;H+DFB+GG?IJ=GI#GI+JGJGIFD#JGGJI>##HC#'JBJIE@GGICIIJIAG;HH#;>#ID#J3C#?@@-9#CEC?;@#:#B#@8DBB#C
+@NC_011750.1-44/2
+AATATCGACGGTAGAGTCGATGTACTGCCCCACTGCCAGCAGTTTTTCGACCGGATCGATAAATGTATCGTTGTGACCGCGCGCTTCTAGTACGCCGGAC
++
+CB1FFCFFFHFD<JE#JG+<#GGH#'JIJJFIHGIEJGEFGJJHI=HGIIHHBBCDDB#@AF'#)JC#CHD#FADCD@#@(#5C=C#D###>D8>E3D#D
+@NC_011750.1-42/2
+CAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGACAATATCACCAACTACCTGGTGGCGAAGATTGAAAAAACCATTAACGACCCGGATGCTTTG
++
+#C@FDD?FH:FFHIIF2;E+3III<#EIHIHHHJD/GH#GIG#E4IJAJ<B##9I9@>JJ#FFGD#H#EIE@BEFDCDJCH@D!CB#FD#EDDBB8B>>'
+@NC_011750.1-40/2
+TGGCGATCGACATTGTCTCACCCGGGCAAAGCAGCGCAGCCTTGTTGCTATCCGGGCACTGCTCTAACACCCTAATACGATGCCGGAACTGTTTAATTCG
++
+8C?=FADDHHH#DD#E:,E#E:#)CEEJ8I#@GBGFH0JD*HDF!EJ0G?4JD8#IGEHI;H#I#F=GH##JFCBF!>#CC#B#?CE##CD;?D#AB@#>
+@NC_011750.1-38/2
+TCTGCATTTGCCACTAATGTATCGCCGAACTTCATAACCCGCATGGTTGTTACCTTGATACCTTTGGTCGGAAGAAAAGCCCGCACTGTCAGGGGCGTTC
++
+B;CA40FF4GH>HHI!HCJGJ#:JHI7IJIFIJF##GJ!IGJJGGHG4JAGJCJJ#G#IGI?AIHCJ@AJ#JH#CBD#DD@?CD:ADFBCC?E!5C>##D
+@NC_011750.1-36/2
+CGATAACGGTAACGTTGTGACCGCGCGCTTCTAATATGCCGGACATAATGGCGGTGGACTTTTTCTCGCGCCGGCAATTGAGCGCAGCGTTGATGCTGTC
++
+@=@+=CF:FHDGF<HJGFCC?HJDCIFI?+1IBHJG#HIG?*#IBIII/#.BG#I!H=H!CIHHDG?D?##D1)@CH#@##CBDC;D;CA;#>#CDD#@'
+@NC_011750.1-34/2
+GGCAGGGGCAGGTGGCCATCGTCCTCTCTGCCCCCGCCAACATGACCAACCACCTGGTGGCGATGATTGAAAAAACCAATAGCACCCAGGATGCATTACT
++
+@@@FADDFHHHAH92FFJ!GECAEECJG##JHDAHIJ*GJ!<*!C?DI#D=EHGJ2JJHJJGGAJ=#HBEFBIHA<#F#:<@D#!D5ECFDCCB#CD#@'
+@NC_011750.1-32/2
+ACGGCGGGTGCACTTAGCAATATCGACGGTAGATTCGAGGTAAGGCCCCACTGCCAGCAGATTTTCGACCGGGTCGAGAACCGTAACGTTGTGGTAGCGC
++
+?BCF4;DDH<#3HG#HGHJ#>AGGHAE?DDII+GF?IJIG*JI#BIHICFHGIC6DHGH##DI(#>CG;7>A##C@F#(:D#EBA#I#DC8D##!#?>DC
+@NC_011750.1-30/2
+TTGACCCAATATCACCGATGCGCAACGGATTTTTTGCGAACATCTGACGGGACTCGCCGCGGCCCAACCGTGATCACCGCTCGCGCAACTGCAAGAATTC
++
+B@+D1F0DAEHFGD#HA3JJI##HIFI#IGGGJH!#G#EJG#A#DBIHEFC;GEJBJGCH'J<#E;#.@D#HD>##DDD#7#@EC;,CFC?#CC##!;?5
+@NC_011750.1-28/2
+TACTCGCATTGTTGTTACCTCGTTGCCTTTGGTCGTAAAAAAAGCCCGCATTGTAAGGTGCGGGCTTTGTGCTGTGTTTCCGGTACGCTTCATCGCGCAG
++
++CBFBDFDH#HHHEHHJJJIE<JJ#HDJHIHIGAI!IHEFH#1@FIJ@HI!#JI#JDDI#)DIHHDGD#(#F:4#EIH#CD#CCFCC>#@A9!<#DDD<'
+@NC_011750.1-26/2
+CACTGCCCGAACAATCAACTGCCATACAGAACATGTTCGATTTGGGCACATACCTGATCGACGAAAGCTTTCAGTTGCGCCAGCGGGAATCCCAGGTGAT
++
+BCCFFFAA#HHH+J+E#A#JJGICA#FC1#JJJIIII##IIJHJII>I#AF#IDC#FIEHIDFI;CF!DFF>DB&@+A)3DE4C;CDDA5B>D###CD#'
+@NC_011750.1-24/2
+AATTACAGAGTATACAACATCCATGAAACTCATTAGCACCACCAATACCACCACCATCACCATTACCACATGTAACGGAGCGGGCTGACGCTCCCAGAAA
++
+B@@F4CFFH+B2#+?JII?JJ,?<+IJ@J#GHH#GID>H*BJ?D!F9I9DF1FICHG;JF@D8JEGHJJB#=?@D?HG##=D;ECDC,FAD8##1CD#BD
+@NC_011750.1-22/2
+TCACCATTTCCACAGGTAAAGGTTCGGGCTGACGAGTACAGGAAACACAGTAAACGGCCCGCACCTGACAGTACGGGCCTTTTTTTCGACCATAAATAAC
++
+:@CAFEFB#HDAH2*;JIF#JGI#?IBIG#HIHG#B0IH:HJFG#GIJ9<!#IH##CDIJEEG##GC3D#A)#HF)BC#DE#DCEED8>C2D#E##CA>'
+@NC_011750.1-20/2
+CACCGTCCGCTCTGCCCCCGCCACAATCACCAACCACTTGGTGGCGATGATTGAAAAAATGATTAGCGGCCCAGATGCTTTACCCAACACAAGCGCTGCT
++
+@BCFF;FA+FHF,CEHJC+JGHD#FGIJGF1?1J9#)#D;GBHHH#<FBABIJIJDCHC!#E;>DCBECGH##CDFCH>H:DD6CDD#@##BC#D#C(D'
+@NC_011750.1-18/2
+GTAGATGCGAGGTAATGCCTCACTGCCAGCAGTTTTTCGACCGGATCGATAACGGTAACGTTAGGACCGCGCGCTTCTAGTTCGCTGGCCTCAATGGCGA
++
+@C+F4C!FHHHF#JCCHCJ!J0JHGC<#GIC:IE9JI:II9G9;EFG#IF#GHJB.?F:IBF###9#HBHDDBEGH:@I#J#DCH#D4D###C#9C><@D
+@NC_011750.1-16/2
+ACATTTTCTCGCCACGCCAAATCAGCGCAGCGTTGTTGCAATCCGGGCTCGGCCCCAACAAACTAAGGCCATGCAGGACATGTAATATTTGGGCAACTCC
++
+CC=FFFDFHHGH2JGJ#IHIE@HJJI#IFABF;G?#?II!HBJI@BHB#<#CEG@B>C#HHC;JJD#8<G9H##D@A>DBCDH#?9@CCB@>HC:E#:#@
+@NC_011750.1-14/2
+GGGCAGCGGCGAGTCCCGTCAGAAGTACAGCAAAAATATATCCAGGAGCGCTGATATTGGGTAAAGCACACTGGAAGCAAATGGGTTTTTAAAGCACCGC
++
+=C?DFF>DDHHH?JCIAII<GJ32+##J##HCJJJHH8##J#I#J#J#IG?;BECEECCFE#JC#J#E##E##A##CI#3BBAE#E>B:D#DD#3D#:A'
+@NC_011750.1-12/2
+GTTTCCTTGTTACCTTTGGTCGAAAAAAAAGCCCGCACTGTCAGGTGCGGGCCTTTTTCTGTGTTTCCTATTCGCGTCAGCTCGCACGGTGACCTGTGGT
++
+=@@#=F,!HHGHBI+J2?JIHI<IHJ2GCBEHJJH:GI:GCIFHEGDGIA?C#F0ID@@IGHCEG#H;H#F#F6F5E8ECC##CD3?#CD#+A?D#AC@4
+@NC_011750.1-10/2
+ATGCTTTACCCAATATCAGCGATGCCGAACGTATTCTTGCCGAACGTCTGATGGGACTGGCAGCTGCCCATCCGGGATTCGCGCTGGCGCCACCGATGAC
++
+BB@FF0=FHFHF?I@+J4:JJAI:JEIFEFJ@<@*#DCIDJGI#<#9*5CI#HH@H*##FF#IHA#IG@E#:4J?B#CC#!C<C;C<ADA#9B##E##C<
+@NC_011750.1-8/2
+CCCTGCCTGGCATTGCTTTCCGGAATATCGGCAGCACGCAGAAAACGTTCTGCCTTTGCTACTGATGCACCGACGAACTCCAACACTCGAATGGTTATTA
++
+C@CDA;DDDHHGHBADJAJ;?#GCACHHH<?GG#.J@IBHG#9=BEGBIDDJE#@ICJC#)GFHHHE#CJE##H=@?GD#>:#E;?CD>#DBD?5A#EBC
+@NC_011750.1-6/2
+TGCCCAACCGGGATTCCCGCTGGCGCATCTGAAAACTTTCGTAGATCAGGAGGTTGCCCAAAGTAAACATCTCGTGCATGGCATAAGGCTGTTGGGGCAG
++
+@1B4FDFF=CD?2I#IJF<<EFIGFFJ#JIGBJ<GIICGJHJ#IF*DBGGE##BGFIEGH>8##CDJ#HB#C=#>F=D#G@DHA#B#!#CC<DC@<#?A'
+@NC_011750.1-4/2
+TGGTTACCTGCCGTGAGCAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCACTATGGGCATAGCACACAGACAGATAAAAATCACAGACT
++
+?##D+FD;@H+<#HHEI#4IJA8HE9EJJ?G??HJCGCGI?HJB8FIJGJFF(I7G#GEJJ#;)G#D3C#JFEH#H@EEJDBCD;D@<>E;9#B@CC#!'
+@NC_011750.1-2/2
+TTTATTGCCTTAGGTCACTAAATACTTTAACCAATACATCCATAGCGCACAGACACATAAAAATTACAGAGTACACAACATCCATGAAATGCGATAGCAC
++
+8BCDFFD)HHHH>AIIJJJJE*J<JBJC?CEC#?J##B##@JIF0D>#A9JH@JJ#9JDD=JIA)FA:#C==?#FCA#DD9CBCBADD?#(C###9D?BD
diff -r 000000000000 -r 6302d40828d2 test-data/NC_011750.1_simulated_bracken_report.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/NC_011750.1_simulated_bracken_report.txt	Wed Oct 16 16:57:23 2019 -0400
@@ -0,0 +1,2 @@
+name	taxonomy_id	taxonomy_lvl	kraken_assigned_reads	added_reads	new_est_reads	fraction_total_reads
+Escherichia coli	562	S	42	1	43	1.00000
diff -r 000000000000 -r 6302d40828d2 test-data/NC_011750.1_simulated_kraken_report.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/NC_011750.1_simulated_kraken_report.txt	Wed Oct 16 16:57:23 2019 -0400
@@ -0,0 +1,11 @@
+  4.44	2	2	U	0	unclassified
+ 95.56	43	0	R	1	root
+ 95.56	43	0	R1	131567	  cellular organisms
+ 95.56	43	0	D	2	    Bacteria
+ 95.56	43	0	P	1224	      Proteobacteria
+ 95.56	43	0	C	1236	        Gammaproteobacteria
+ 95.56	43	0	O	91347	          Enterobacterales
+ 95.56	43	1	F	543	            Enterobacteriaceae
+ 93.33	42	0	G	561	              Escherichia
+ 93.33	42	0	S	562	                Escherichia coli
+ 93.33	42	42	S1	585057	                  Escherichia coli IAI39
diff -r 000000000000 -r 6302d40828d2 test-data/bracken_databases.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bracken_databases.loc	Wed Oct 16 16:57:23 2019 -0400
@@ -0,0 +1,6 @@
+# Tab separated with three columns:
+# - value (Galaxy records this in the Galaxy DB)
+# - name (Galaxy shows this in the UI)
+# - path (folder name containing the Kraken DB)
+#
+test_entry	"Test Database"	${__HERE__}/test_db/database100mers.kmer_distrib
diff -r 000000000000 -r 6302d40828d2 test-data/reproduce_test_data.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reproduce_test_data.sh	Wed Oct 16 16:57:23 2019 -0400
@@ -0,0 +1,29 @@
+#!/bin/bash
+
+# This script produces a small kraken2 database containing only a ~1kb portion each of a salmonella and ecoli genome
+# It requires kraken2, art and entrez-direct (all available on bioconda)
+kraken2-build --db test_db --download_taxonomy
+mv test_db/taxonomy/nucl_gb.accession2taxid test_db/taxonomy/nucl_gb.accession2taxid_full
+grep -e 'NC_003198.1' -e 'NC_011750.1' test_db/taxonomy/nucl_gb.accession2taxid_full > test_db/taxonomy/nucl_gb.accession2taxid
+esearch -db nucleotide -query "NC_003198.1" | efetch -format fasta > NC_003198.1.fasta
+esearch -db nucleotide -query "NC_011750.1" | efetch -format fasta > NC_011750.1.fasta
+head -n 14 NC_003198.1.fasta > NC_003198.1_1kb.fasta
+head -n 14 NC_011750.1.fasta > NC_011750.1_1kb.fasta
+kraken2-build --db test_db --add-to-library NC_003198.1_1kb.fasta
+kraken2-build --db test_db --add-to-library NC_011750.1_1kb.fasta
+kraken2-build --db test_db --build
+
+# Simulate 100bp reads from ~1kb portions of genomes
+art_illumina -sam -i NC_011750.1_1kb.fasta -p -m 300 -f 10 -s 10 -l 100 -o NC_011750.1_simulated_R
+art_illumina -sam -i NC_003198.1_1kb.fasta -p -m 300 -f 10 -s 10 -l 100 -o NC_003198.1_simulated_R
+
+# Generate kraken reports
+kraken2 --db test_db --report NC_011750.1_simulated_kraken_report.txt --paired NC_011750.1_simulated_R1.fastq NC_011750.1_simulated_R2.fastq
+kraken2 --db test_db --report NC_003198.1_simulated_kraken_report.txt --paired NC_003198.1_simulated_R1.fastq NC_003198.1_simulated_R2.fastq
+
+# Build bracken kmer distribution files using default kmer-len=35 and read-len=100
+bracken-build -d test_db
+
+# 
+# est_abundance.py --kmer_distr test_db/database100mers.kmer_distrib --level S -i NC_003198.1_simulated_kraken_report.txt -o NC_003198.1_simulated_bracken_report.txt
+# est_abundance.py --kmer_distr test_db/database100mers.kmer_distrib --level S -i NC_011750.1_simulated_kraken_report.txt -o NC_011750.1_simulated_bracken_report.txt
diff -r 000000000000 -r 6302d40828d2 test-data/test_db/database.kraken
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_db/database.kraken	Wed Oct 16 16:57:23 2019 -0400
@@ -0,0 +1,2 @@
+C	NC_003198.1	220341	910	220341:169 A:67 543:23 220341:9 A:42 220341:9 543:65 220341:134 543:2 220341:356
+C	NC_011750.1	585057	910	585057:11 A:41 585057:116 A:67 543:24 585057:7 A:42 585057:10 543:64 585057:134 543:2 585057:358
diff -r 000000000000 -r 6302d40828d2 test-data/test_db/database100mers.kmer_distrib
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_db/database100mers.kmer_distrib	Wed Oct 16 16:57:23 2019 -0400
@@ -0,0 +1,5 @@
+mapped_taxid	genome_taxids:kmers_mapped:total_genome_kmers
+0	220341:2:811 585057:2:811 
+543	220341:23:811 585057:24:811 
+220341	220341:786:811 
+585057	585057:785:811 
diff -r 000000000000 -r 6302d40828d2 test-data/test_db/database100mers.kraken
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_db/database100mers.kraken	Wed Oct 16 16:57:23 2019 -0400
@@ -0,0 +1,2 @@
+NC_003198.1	220341	220341	910	0:2 543:23 220341:786 
+NC_011750.1	585057	585057	910	0:2 543:24 585057:785 
diff -r 000000000000 -r 6302d40828d2 test-data/test_db/hash.k2d
Binary file test-data/test_db/hash.k2d has changed
diff -r 000000000000 -r 6302d40828d2 test-data/test_db/library/added/9C7DdW7GAD.fna
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_db/library/added/9C7DdW7GAD.fna	Wed Oct 16 16:57:23 2019 -0400
@@ -0,0 +1,17 @@
+>NC_003198.1 Salmonella enterica subsp. enterica serovar Typhi str. CT18, complete genome
+AGAGATTACGTCTGGTTGCAAGAGATCATAACAGGGGAAATTGATTGAAAATAAATATAT
+CGCCAGCAGCACATGAACAAGTTTCGGAATGTGATCAATTTAAAAATTTATTGACTTAGG
+CGGGCAGATACTTTAACCAATATAGGAATACAAGACAGACAAATAAAAATGACAGAGTAC
+ACAACATCCATGAACCGCATCAGxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxAGGT
+AACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGAACAGTGCGG
+GCxxxxxxxxCGACCAGAGATCACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGT
+ACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATTCC
+AGGCAAGGGCAGGTAGCGACCGTACTTTCCGCCCCCGCGAAAATTACCAACCATCTGGTG
+GCGATGATTGAAAAAACTATCGGCGGCCAGGATGCTTTGCCGAATATCAGCGATGCCGAA
+CGTATTTTTTCTGACCTGCTCGCAGGACTTGCCAGCGCGCAGCCGGGATTCCCGCTTGCA
+CGGTTGAAAATGGTTGTCGAACAAGAATTCGCTCAGATCAAACATGTTTTGCATGGTATC
+AGCCTGCTGGGTCAGTGCCCGGATAGCATCAACGCCGCGCTGATTTGCCGTGGCGAAAAA
+ATGTCGATCGCGATTATGGCGGGACTCCTGGAGGCGCGTGGACATCGCGTCACGGTGATC
+GATCCGGTAGAAAAACTGCTGGCGGTGGGCCATTACCTTGAATCTACCGTCGATATCGCG
+GAATCGACTCGCCGTATCGCCGCCAGCCAGATCCCGGCCGATCACATGATCCTGATGGCG
+GGCTTTACTG
diff -r 000000000000 -r 6302d40828d2 test-data/test_db/library/added/9C7DdW7GAD.fna.masked
diff -r 000000000000 -r 6302d40828d2 test-data/test_db/library/added/cWk1IBlK73.fna
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_db/library/added/cWk1IBlK73.fna	Wed Oct 16 16:57:23 2019 -0400
@@ -0,0 +1,17 @@
+>NC_011750.1 Escherichia coli IAI39 chromosome, complete genome
+GCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTxxxxxxxGAGTGTCT
+GATAGCAGCTTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGT
+CACTAAATACTTTAACCAATATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACA
+CAACATCCATGAAACGCATTAGxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxAGGTA
+ACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGC
+xxxxxxxxCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTAC
+ATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAG
+GCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGC
+GATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACG
+TATTTTTGCCGAACTTCTGACGGGACTCGCCGCTGCCCAACCGGGATTCCCGCTGGCGCA
+ACTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATTAG
+TTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAAAT
+GTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACCGTTATCGA
+TCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCTGA
+GTCCACCCGCCGTATTGCGGCAAGTCGTATTCCGGCTGATCACATGGTGCTGATGGCAGG
+TTTCACCGCC
diff -r 000000000000 -r 6302d40828d2 test-data/test_db/library/added/cWk1IBlK73.fna.masked
diff -r 000000000000 -r 6302d40828d2 test-data/test_db/library/added/prelim_map.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_db/library/added/prelim_map.txt	Wed Oct 16 16:57:23 2019 -0400
@@ -0,0 +1,2 @@
+ACCNUM	NC_011750.1	NC_011750
+ACCNUM	NC_003198.1	NC_003198
diff -r 000000000000 -r 6302d40828d2 test-data/test_db/library/added/prelim_map_QXr8C5PiOX.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_db/library/added/prelim_map_QXr8C5PiOX.txt	Wed Oct 16 16:57:23 2019 -0400
@@ -0,0 +1,1 @@
+ACCNUM	NC_003198.1	NC_003198
diff -r 000000000000 -r 6302d40828d2 test-data/test_db/library/added/prelim_map_l8ftMYsZv0.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_db/library/added/prelim_map_l8ftMYsZv0.txt	Wed Oct 16 16:57:23 2019 -0400
@@ -0,0 +1,1 @@
+ACCNUM	NC_011750.1	NC_011750
diff -r 000000000000 -r 6302d40828d2 test-data/test_db/opts.k2d
Binary file test-data/test_db/opts.k2d has changed
diff -r 000000000000 -r 6302d40828d2 test-data/test_db/seqid2taxid.map
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_db/seqid2taxid.map	Wed Oct 16 16:57:23 2019 -0400
@@ -0,0 +1,2 @@
+NC_003198.1	220341
+NC_011750.1	585057
diff -r 000000000000 -r 6302d40828d2 test-data/test_db/taxo.k2d
Binary file test-data/test_db/taxo.k2d has changed
diff -r 000000000000 -r 6302d40828d2 tool-data/bracken_databases.loc.sample
diff -r 000000000000 -r 6302d40828d2 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Wed Oct 16 16:57:23 2019 -0400
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of bracken database in the required format -->
+    <table name="bracken_databases" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, name, path</columns>
+        <file path="tool-data/bracken_databases.loc" />
+    </table>
+</tables>
diff -r 000000000000 -r 6302d40828d2 tool_data_table_conf.xml.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Wed Oct 16 16:57:23 2019 -0400
@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<tables>
+    <!-- Locations of bracken database in the required format -->
+    <table name="bracken_databases" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="${__HERE__}/test-data/bracken_databases.loc" />
+    </table>
+</tables>