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

Changeset 0:1f0a3e4497d4 (2017-09-06)
Commit message:
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/fraggenescan/ commit 59ac8955ccb33e3fcd6649c61779bb3ae9ccb6d4
added:
fraggenescan.xml
test-data/NC_000913-454.faa
test-data/NC_000913-454.fasta
test-data/NC_000913-454.ffn
test-data/NC_000913-454.gff
test-data/NC_000913-454.out
test-data/NC_000913.faa
test-data/NC_000913.fasta
test-data/NC_000913.ffn
test-data/NC_000913.gff
test-data/NC_000913.out
test-data/contigs.faa
test-data/contigs.fasta
test-data/contigs.ffn
test-data/contigs.gff
test-data/contigs.out
b
diff -r 000000000000 -r 1f0a3e4497d4 fraggenescan.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/fraggenescan.xml Wed Sep 06 13:23:14 2017 -0400
[
@@ -0,0 +1,86 @@
+<tool id="fraggenescan" name="FragGeneScan" version="@WRAPPER_VERSION@.0">
+    <description>for finding (fragmented) genes in short reads</description>
+    <macros>
+        <token name="@WRAPPER_VERSION@">1.30</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@WRAPPER_VERSION@">fraggenescan</requirement>
+    </requirements>
+    <version_command>@WRAPPER_VERSION@</version_command>
+    <command detect_errors="aggressive"><![CDATA[
+run_FragGeneScan.pl
+    -genome='$genome'
+    -out="output_file_name"
+    -complete='$complete'
+    -train='$train'
+    -thread=\${GALAXY_SLOTS:-4}
+    ]]></command>
+    <inputs>
+        <param argument="-genome" type="data" format="fasta" label="Input equence file"/>
+        <param argument="-complete" type="boolean" truevalue="1" falsevalue="0" label="Does the sequence file have complete genomic sequences?"/>
+        <param argument="-train" type="select" label="Model">
+            <option value="454_5">454 pyrosequencing reads with about 0.5% error rate (454_5)</option>
+            <option value="454_10">454 pyrosequencing reads with about 1% error rate (454_10)</option>
+            <option value="454_30">454 pyrosequencing reads with about 3% error rate (454_30)</option>
+            <option value="complete">complete genomic sequences or short sequence reads without sequencing error (complete)</option>
+            <option value="gene">gene</option>
+            <option value="illumina_1">Illumina sequencing reads with about 0.01% error rate (illumina_1)</option>
+            <option value="illumina_5">Illumina sequencing reads with about 0.5% error rate (illumina_5)</option>
+            <option value="illumina_10">Illumina sequencing reads with about 1% error rate (illumina_10)</option>
+            <option value="noncoding">noncoding</option>
+            <option value="pwm">pwm</option>
+            <option value="rgene">rgene</option>
+            <option value="sanger_5">Sanger sequencing reads with about 0.5% error rate (sanger_5)</option>
+            <option value="sanger_10">Sanger sequencing reads with about 1% error rate (sanger_10)</option>
+            <option value="start">start</option>
+            <option value="start1">start1</option>
+            <option value="stop">stop</option>
+            <option value="stop1">stop1</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="coord" format="tabular" from_work_dir="output_file_name.out" label="${tool.name} on ${on_string}: Coordinates of putative genes"/>
+        <data name="nt_seq" format="fasta" from_work_dir="output_file_name.ffn" label="${tool.name} on ${on_string}: Nucleotide equences of putative genes"/>
+        <data name="prot_seq" format="fasta" from_work_dir="output_file_name.faa" label="${tool.name} on ${on_string}: Protein equences of putative genes"/>
+        <data name="gff" format="gff" from_work_dir="output_file_name.gff" label="${tool.name} on ${on_string}"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="genome" value="contigs.fasta"/>
+            <param name="complete" value="False"/>
+            <param name="train" value="complete"/>
+            <output name="coord" ftype="tabular" value="contigs.out"/>
+            <output name="nt_seq" ftype="fasta" value="contigs.ffn"/>
+            <output name="prot_seq" ftype="fasta" value="contigs.faa"/>
+            <output name="gff" ftype="gff" value="contigs.gff"/>
+        </test>
+        <test>
+            <param name="genome" value="NC_000913.fasta"/>
+            <param name="complete" value="True"/>
+            <param name="train" value="complete"/>
+            <output name="coord" ftype="tabular" value="NC_000913.out"/>
+            <output name="nt_seq" ftype="fasta" value="NC_000913.ffn"/>
+            <output name="prot_seq" ftype="fasta" value="NC_000913.faa"/>
+            <output name="gff" ftype="gff" value="NC_000913.gff"/>
+        </test>
+        <test>
+            <param name="genome" value="NC_000913-454.fasta"/>
+            <param name="complete" value="False"/>
+            <param name="train" value="454_10"/>
+            <output name="coord" ftype="tabular" value="NC_000913-454.out"/>
+            <output name="nt_seq" ftype="fasta" value="NC_000913-454.ffn"/>
+            <output name="prot_seq" ftype="fasta" value="NC_000913-454.faa"/>
+            <output name="gff" ftype="gff" value="NC_000913-454.gff"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+FragGeneScan is an application for finding (fragmented) genes in short reads.
+It can also be applied to predict prokaryotic genes in incomplete assemblies or complete genomes. 
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/nar/gkq747</citation>
+    </citations>
+</tool>
b
diff -r 000000000000 -r 1f0a3e4497d4 test-data/NC_000913-454.faa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/NC_000913-454.faa Wed Sep 06 13:23:14 2017 -0400
b
b'@@ -0,0 +1,6364 @@\n+>r1.1_1_80_-\n+ARQHLLPRDVVQAHERGDIHYHDLDY\n+>r2.1_1_93_-\n+RMVVVTSGEMLQQLWSLIPNGIVSTGYYTVD\n+>r3.1_1_90_-\n+LTLTIRHYWSHLADDEDKYRLWFSDVVAR\n+>r4.1_1_89_-\n+AKLVLQDYASGSRPLIDAALARNGIQANI\n+>r11.1_1_106_+\n+VKGGSEKTAISGYPTFLPDAIHHPTNSINYESIR\n+>r15.1_1_104_-\n+LVPVVSSSMFVTGAAPNVLGLEFVSKIAGIQISW\n+>r16.1_1_108_+\n+YSSVHTRYVVMTDGNVPLVPYYRPGDKRIAQDLAE\n+>r18.1_1_95_-\n+GTREELMAEAKKRLALKPGSEYHYPRQTLKS\n+>r19.1_11_91_+\n+MVRPALLALTVRPFFSERYASGLRWL\n+>r20.1_1_99_+\n+REEAMTWWSRDFPTLAFPDQVIRVFLSLHAEG\n+>r21.1_1_101_-\n+RSAVYWDDFFPTLEEIDFNGKLVALFGCGDQED\n+>r23.1_1_94_+\n+ASSLTISADSLRKIYDNMDYFASRIVLRPQ\n+>r25.1_1_101_-\n+TGHAIGIEVHEDPRFSPRDTTTLQPGMLLTVEP\n+>r26.1_1_119_-\n+NLIPVTIGNITGGGLLVGLTYWVIYLRENDLPINGCRS\n+>r28.1_1_104_+\n+VLENTPASRSLYSAAWAVIYPLIVWWLMYGGFFA\n+>r29.1_1_100_+\n+QHNVPETANAKLDAKCVMVGNIHVATGWCDAF\n+>r30.1_1_108_-\n+LSFELAEPLHIRQVDINPQIVFSYIKSKGNLSLNN\n+>r32.1_1_99_+\n+SLGPVIISAVVALLVSNLINHSDALLYNVQLS\n+>r34.1_1_91_+\n+RLLACALLRPSATRLGEISEQYGDTTANR\n+>r36.1_1_95_-\n+LGKVRNIVNMKPAHPWKLKDFVTRLYISESL\n+>r40.1_1_103_-\n+GTLFAARQGFVSPESFTFAESAFVSGDVVLGGM\n+>r43.1_33_107_-\n+GAGDEEPGVSLLKKSCKFGHDNNS\n+>r45.1_1_102_-\n+IVSLNYAVREKENNEDDATRLARLNERFKREGK\n+>r51.1_1_105_-\n+RPGLSILVPESPDHVLNVAGLLRALADAPFDAWCG\n+>r53.1_1_97_+\n+IETQGETAQALAIRLARPVVVIDKMAGKVVTI\n+>r54.1_1_117_-\n+RWWFDCCSHVNDAGFWLFGKFTGATEAETLKTWTMMETI\n+>r56.1_1_96_-\n+HETQLLLLSIVTATRSAIALATLVNTATKTE\n+>r60.1_1_102_-\n+NEKTLQQGDTWHNLATGETGDTVVQGLGWEML\n+>r61.1_7_100_+\n+MEIRSRAASLLHGLGFSNEQLERPVSDFSG\n+>r63.1_15_110_+\n+VTPTLLSAFWTYTLITAMTPGPNNILALSSA\n+>r66.1_1_103_+\n+LLMAALYTSTAFRMSNKLALRWGDKSCFIQPPN\n+>r70.1_1_102_-\n+SNFSRNLTRFFIKDMIVIGINDNLEGFIAYFFDL\n+>r74.1_1_91_-\n+HPASSEQASKAAKKITMVLMLSPSYLVCQ\n+>r75.1_1_108_+\n+RDALMEALKERGIGTGLHFRAAHTQKYYRERFPTL\n+>r76.1_1_97_+\n+GPMPVERGPEMTALRDGVRGKDKLDVPIKNDL\n+>r79.1_1_92_+\n+LFGDLLAVTPEDLISIALERGHRGGYFVL\n+>r81.1_1_105_+\n+GTMAPLSAYSSTVMDLWFTALERYNGIPSMEILG\n+>r82.1_1_96_+\n+RFRSIVSRQFSQPWYDTVDKQASIAYQGMAM\n+>r83.1_1_102_-\n+RSANSDRQFKPRVIASSLNILIWPQAVRQMHPL\n+>r84.1_1_94_-\n+GSVQWRFVMAADHPLANVEETANRSAVAALS\n+>r87.1_1_97_-\n+IIAIAQLILRYDEKAFYSAEAGRLSKVIVKH\n+>r88.1_1_93_+\n+SAAAHNELTKLGVRVLTQTMVTSADEGGLH\n+>r91.1_1_116_+\n+INLDELYTAPGDYKYYDNGFNLTAFSVTLVAVIFISWT\n+>r96.1_1_92_+\n+LLIRRVKHKTWQIAMVWQPEITATHAGRYS\n+>r97.1_1_107_-\n+FDRKHGTVTAANSTPLTDGAAAVILMTESRAKELR\n+>r99.1_1_99_-\n+STALGLCGATSMDFTLPVLQRTGGLDMVPAAI\n+>r101.1_1_108_+\n+LVISGLIALDKLANSDAVFSDALTWIPALGSTAW\n+>r102.1_1_107_+\n+GVTEKVTKQHKPKSRETYAFTQAELELLETDERL\n+>r104.1_1_101_+\n+TTSRTVGNIPQDTFGIDFRVRLIMHPTGPHLGT\n+>r106.1_1_102_+\n+GSRAHPFLTYLKRAAIMAEIRRFFADRGVLEV\n+>r107.1_1_91_-\n+SHISRFGLLEMSRQRLSPSLGESSHHVCP\n+>r108.1_1_98_-\n+RPGVMAGMIAIFMSFAGQFAFFTYIRPVYMNL\n+>r116.1_1_111_-\n+PSVAGLAPIGGNGAMSNAINEIDNTDLVFVFGYNPA\n+>r117.1_1_102_+\n+VVGVWCYLLDGMFIGATRATEMRNSMAVAVRRF\n+>r123.1_1_101_-\n+GSQDAFVGLMNSYVNALGLKNTHFQTVHGLDAD\n+>r124.1_1_103_+\n+LFPPMWRRLIYHPDINYALRQTLVLCLPVAVGLM\n+>r127.1_1_108_+\n+SVAKPTAVETKAEAPAAQSKAAVPAKASDEEGTRV\n+>r128.1_1_97_+\n+RHWIALPIGFALFWHDTWLPGPESISEPGFA\n+>r130.1_1_126_-\n+ETGPNGPLVPRTESTIPRYTLHSLAREILTPGDNEDFVKAVK\n+>r132.1_1_102_+\n+PDINQGNYLTANDVSKIRVGMTQQQVAYALGTP\n+>r133.1_1_101_+\n+GERLHYGQSAHQRLKDLHPELGVIGTNADDAV\n+>r136.1_1_90_+\n+VKNIAFYILMQIVSEYIALLQDGRSEERY\n+>r137.1_1_109_-\n+PFAEHRSLYAASVLAEYPNGKDAPSERLPVLNATVD\n+>r140.1_1_107_+\n+VRDAKEGSVKGYAGDTATTSEIKAKLLADDIVPSR\n+>r141.1_1_90_-\n+VSTVYIVSIAKDIMNKEESDAFMAQVKAF\n+>r146.1_1_98_-\n+NIDEVGAAPNLVTLRANYFVRHTPKSTGLACP\n+>r147.1_1_115_-\n+WFADDKQEIRQGGFAGWLTDGTPLWVTGSGTSKTVLTR\n+>r148.1_1_89_-\n+ATDLRASASLVLAGCIAEGTTVVDRIYHI\n+>r150.1_1_115_+\n+TDVDGRFLTVVSHHSTVIKNVNSPTAASLRMDKHRSN\n+>r152.1_1_109_+\n+CCGKSQTQRASYYASREKDTPIKYEDETVLAHGPV\n+>r154.1_1_105_-\n+RKVGDRYVLEKMQEKGWRIGAENSGHVILLDKTTT\n+>r156.1_1_105_-\n+LGFCFIRLAKVKGFVAKSRLLAGKIADHSQCVTL\n+>r159.1_1_102_-\n+VYPAHLTRLPVVALDNQGDLFYDLGEEVITTG\n+>r160.1_1_100_+\n+PYLAYETLGRLVDTHAIAKDYRTVMLNYRNGI\n+>r163.1_1_103_-\n+RMWHIRYPLADGAKTDSGKDYLVVATTRPETLLG\n+>r164.1_1_101_-\n+LIAAAKAGMDSHGFGMASVRFICGTQDSHKELE\n+>r166.1_1_116_-\n+TMKVGFIGLGIKGKPMSKNLLKAGYSLVVADRNPEAIA\n+>r168.1_1_97_+\n+LVKANDIDVPAALIDSEIDVLRRQAAQRFGGN\n+>r169.1_1_109_-\n+YNKLFNGAPPEGD'..b'GALIAQRL\n+>r6496.1_1_93_-\n+QDRSRKETVIVITANHQIEMMLVTYFQNMLR\n+>r6498.1_1_96_-\n+PDDAALIRPTMNDVDPINPQLRAFNAAISAG\n+>r6499.1_1_127_-\n+LSSIYRELYSKGVKITLLTNRKGGEFLSNNKNIFEFCIKEST\n+>r6500.1_1_114_+\n+ATICRQKVNGLKTIYNSIPGFEDFFIAVDPQTDLSAV\n+>r6501.1_40_109_+\n+MELAAKKSTDRKTEGGLTEERLM\n+>r6502.1_1_95_+\n+ELNCRSDKTHSVASDNNLDPTNDNNDEDNI\n+>r6503.1_1_117_-\n+PGLAADGDFLRAVGLTLSGWGFIAVMLLLKITLNLLPDY\n+>r6504.1_1_103_+\n+SDSAAMTSMLIGLGVAQSGQIVGKIGETFGVSNL\n+>r6505.1_1_105_+\n+IRQGLGIALQPELTLKSIAGELCSVPLEPTFYRQ\n+>r6511.1_1_75_+\n+VSLGVVFGILVMTFIINAWGELSA\n+>r6512.1_1_96_-\n+DYHNFDALNILVTTRRALTTTLFWFDTTRLL\n+>r6514.1_1_98_+\n+QRLSMVAAVSCFFAFTLTPRLARQAYYIHVYF\n+>r6515.1_1_103_-\n+SFLFNPHNLPGAQRYFITQYINFTNQIPTMQISN\n+>r6517.1_1_97_+\n+GILVRRSREQLEMEIDKFTIIQRDNTTIASR\n+>r6518.1_1_125_+\n+SLFFKAMVFHLLPEVTDVLSRFVPRIIPFYLLLLVAGGTAN\n+>r6520.1_1_111_-\n+DWPAYGRNQEGQRFSPLKQINADNVHNLKEAWVFRT\n+>r6522.1_1_83_+\n+LDVLLVLLLIFMATAPIITQSVEVDLP\n+>r6530.1_1_102_+\n+QAFAHSPHNTHFEDFLLSVFTVAIIHGHAVVQA\n+>r6531.1_1_101_+\n+VVVGCGVNAFPTYPPGMIKRTNNASGLVAQLP\n+>r6537.1_1_97_+\n+ASFDRRVLPEMPGEWICTMKLALVVAWDQVQ\n+>r6538.1_1_90_-\n+YEAQPSGGVSAHYLHYDSDIHTPDPTNAL\n+>r6539.1_1_103_-\n+EQAVNALLLIRSSISAAVPGLIELAVGGKNGGDR\n+>r6540.1_1_87_+\n+WSYSTSSALKAVLAIQQRAKRGDTGQMM\n+>r6541.1_1_92_-\n+RPRVVIASGASRITDEMLMSASETLAQYSP\n+>r6543.1_1_94_-\n+RISLLQVTNFAGLVARELITGLGMDTPTENP\n+>r6544.1_1_99_+\n+ELAKLVGQSSVQKSVLSAYGDQGGFVLAPQDN\n+>r6545.1_1_106_+\n+PHIHLDTTQTAGQPNWKQSGTLFEGIERWARDVK\n+>r6550.1_1_91_-\n+GEGEGEYRVPAAKMLAMVLHGMQGTPYIYQ\n+>r6558.1_1_96_-\n+LPKGTRVAFGTSREQQLQPHTQETWTGSVLAS\n+>r6562.1_1_115_-\n+DSHIIRGIKMETTKPSFQDVLEFVRLFRRKNKLQREI\n+>r6567.1_1_95_-\n+VAVVTSIALDHTDWLGPDRESIGREKAGIFR\n+>r6569.1_1_101_+\n+SSKRYGETGRRMVVLDRWAVGCAKAAQEDILK\n+>r6570.1_1_91_-\n+YADVSQGNVRYNIATKADIAIIATAQNGNK\n+>r6571.1_1_113_-\n+CHVFPYTVDGGFTRYKMVETSQCVPYPAKATKRLWLL\n+>r6572.1_3_109_-\n+DLTHGKYVPDHRGETVYSTKTGESKEIKAPGDYP\n+>r6573.1_1_110_+\n+FGTVNHANISAGEMKSINHVRAEGNQPAPPDKILQK\n+>r6574.1_1_89_+\n+IDLLQRRGQIASLWQYTPLSMRYPHDVVR\n+>r6575.1_1_87_+\n+GPAIAQSWLVKALHIQQFADQTFFVQVN\n+>r6576.1_1_97_+\n+VAIADVTAFGIYMGVWFPTVPHWIWVLSVVL\n+>r6577.1_1_106_-\n+LMVEQLDNETWDAAADTVRKLRFLDKLRSSAELN\n+>r6580.1_1_90_+\n+GVSCAIETAGDAPASKLLPLAKLCDEVLF\n+>r6581.1_1_101_+\n+SYIALQLPTVTYELPALLHDFNISRPCEERYFL\n+>r6583.1_1_95_-\n+HMAKDVEQALLEVIAEFGMDTEAADEFLSEL\n+>r6584.1_1_111_+\n+QSSTPHDALFKLFLRQPDTARDFRCVSFYRHPFTRF\n+>r6585.1_1_103_-\n+LNNNSAMRFFMSVFPYPKYGEVNIMFHNFIVSGS\n+>r6588.1_1_113_-\n+LISAANTPPVPQKPGRHSRQYPDGSGSYGVEVETTVA\n+>r6589.1_57_129_-\n+TYRQFKNITPKIKGPKIKALYNQ\n+>r6592.1_1_92_+\n+DELMKGLNLPVKKKNGLRVTPADQIDIITG\n+>r6594.1_1_107_-\n+GHPLIAKHLPAFTSPNTLYIPIRQPSSAGVFIDGD\n+>r6599.1_1_85_-\n+NTGIALVLIFMPTLLVAAQPDLGTSILV\n+>r6600.1_1_90_+\n+NCLRLLQDWHRSIRNYAAMHESLLALLCD\n+>r6604.1_1_91_-\n+NKLVVHPYTVRSDKRREYTPDVNQLYDAL\n+>r6608.1_1_111_-\n+PSITGRHVQALGLGQLTPTGDIKKYSAVPSVNFRSVK\n+>r6613.1_1_111_+\n+HICDPGGQRLGGQGASGNSGSFSLKILQPFVGSVVI\n+>r6614.1_1_109_+\n+GPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARSH\n+>r6615.1_1_93_+\n+KEGHTVSGARDIADKLLASLSSILLYWYHY\n+>r6616.1_1_77_+\n+YDAFVQVLHPLNIVPVFNIPLNHI\n+>r6617.1_1_105_+\n+IAAPENISPEKGTTYKLVRKVFQNTEHVHVVGLR\n+>r6618.1_1_94_+\n+IIVQTANLINTFKYYFVAYAHKVAAKAQIC\n+>r6621.1_1_103_-\n+LTVTPYQNRRFDSCFLTAKKAIESGKLGEIVEVE\n+>r6623.1_1_112_-\n+LTGILPASERLGRLCFKAGDVSESADNGEFLRQYFAE\n+>r6624.1_1_92_-\n+IKRIFFFACSSLSDSRNHAIFYLALTLRCN\n+>r6625.1_1_101_+\n+LWLKAHYPAEFYGGGMTADMDNTEKVVGLVDE\n+>r6627.1_1_105_-\n+VQGRFAASLRLRLPLIAPVSFFLLVVNLVYAFVR\n+>r6628.1_1_112_+\n+RKDGIEYSQAFYVLAVREDNAIDVNTRLFKYAADLI\n+>r6629.1_1_99_-\n+DTCASYPTDSDSNDAQRVGRIRTLAPHPALLP\n+>r6630.1_1_95_-\n+PTVYVKGDRVVVDGQAYEALFWTQSDNPALV\n+>r6631.1_1_99_+\n+ADLALALLLDVQQGLRDDLKLLIMSATLDNDR\n+>r6632.1_22_107_-\n+SPELQGVDGIKILVPITGDALINTSAL\n+>r6633.1_1_96_+\n+YRLMAEWATDAVCRKLGNTRPCTTADLALPG\n+>r6634.1_1_108_-\n+SAPVPMTPLQEFWHYFKRNKGAVVGLVYVVIVAVH\n+>r6635.1_1_97_-\n+QYAQAYMVSYQQAITPIGKASNGRGIYEGPG\n+>r6645.1_1_113_+\n+HNTNFTPYTLRRCLIERFTRIYIDNLGKEFLVWLAGL\n+>r6647.1_1_94_-\n+QLVAAQTEQNPQVGQVMPGVQGADAPVVAL\n+>r6649.1_1_120_-\n+PNPLVALGLRAGLMLEKKANTYAESHSAGIKLLSYKLI\n+>r6651.1_1_100_-\n+TFKNMYFSGDGARRDEDGYYWITGRVDDVLNV\n+>r6652.1_1_102_-\n+TPNMEQRTVGIGRLDPEIARDFSNVGPMVPCQR\n'
b
diff -r 000000000000 -r 1f0a3e4497d4 test-data/NC_000913-454.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/NC_000913-454.fasta Wed Sep 06 13:23:14 2017 -0400
b
b'@@ -0,0 +1,10000 @@\n+>r1.1 |SOURCES={GI=49175990,fw,4460184-4460264}|ERRORS={}|SOURCE_1="Escherichia coli str. K-12 substr. MG1655" (cf77cbe42208fbf232179e8864f9dcf39151cb85)\n+AGTAATCGAGATCGTGATAGTGAATATCGCCACGCTCATGTGCCTGCACCACGTCACGCGGCAGC\n+AGGTGCTGACGTGCA\n+>r2.1 |SOURCES={GI=49175990,fw,3987220-3987313}|ERRORS={}|SOURCE_1="Escherichia coli str. K-12 substr. MG1655" (cf77cbe42208fbf232179e8864f9dcf39151cb85)\n+GTCGACAGTGTAGTAACCAGTGCTCACGATACCATTGTGGGATCAGCGACCAGAGTTGCTGCAAC\n+ATTTCACCGCTGGTAACAACGACCATCG\n+>r3.1 |SOURCES={GI=49175990,fw,1788591-1788680}|ERRORS={78_1:T}|SOURCE_1="Escherichia coli str. K-12 substr. MG1655" (cf77cbe42208fbf232179e8864f9dcf39151cb85)\n+GTACGTGCGACAACATCGCTAAACCAGAGACGGTATTTGTCCTCATCATCTGCAAGATGTGACCA\n+GTAATGACGAATAGTCAAAGTCAGC\n+>r4.1 |SOURCES={GI=49175990,fw,2524219-2524308}|ERRORS={}|SOURCE_1="Escherichia coli str. K-12 substr. MG1655" (cf77cbe42208fbf232179e8864f9dcf39151cb85)\n+ACAATATTCGCCTGAATACCATTGCGCGCCAGCGCTGCGTCAATCAGCGGTCGGCTGCCTGACGC\n+GTAATCCTGCAACACCAATTTCGC\n+>r10.1 |SOURCES={GI=49175990,fw,3984360-3984462}|ERRORS={22_1:C}|SOURCE_1="Escherichia coli str. K-12 substr. MG1655" (cf77cbe42208fbf232179e8864f9dcf39151cb85)\n+AGTTATTACTCAGGAAGCAAAGACGGATTACAGAATTATCTCATAACAAGTGTTAAGGGATGTTA\n+TTTCCCGATTCTCTGTGGCATAATAAACGAGTAGATGC\n+>r11.1 |SOURCES={GI=49175990,fw,3825309-3825415}|ERRORS={}|SOURCE_1="Escherichia coli str. K-12 substr. MG1655" (cf77cbe42208fbf232179e8864f9dcf39151cb85)\n+CGTAAAAGGCGGCAGTGAGAAGACCGCCATTTCAGGTTACCCTACCTTCCTGCCGGATGCGATTC\n+ATCACCCTACAAATTCAATAAATTATGAATCAATACGCAGG\n+>r15.1 |SOURCES={GI=49175990,fw,645102-645205}|ERRORS={90_1:C}|SOURCE_1="Escherichia coli str. K-12 substr. MG1655" (cf77cbe42208fbf232179e8864f9dcf39151cb85)\n+AACCAGCTAATCTGGATACCGGCAATTTTGCTGACGAACTCCAGACCCAGCACGTTTGGTGCCGC\n+ACCGGTGACAAACATGGACGAACTCACGACTGGTACTAA\n+>r16.1 |SOURCES={GI=49175990,fw,2861966-2862071}|ERRORS={16_1:C,18_1:G,31_1:A}|SOURCE_1="Escherichia coli str. K-12 substr. MG1655" (cf77cbe42208fbf232179e8864f9dcf39151cb85)\n+TTATTCGTCCGTTCACACCCGATACGTGGTGATGACGGATGGGAAATGTCCCGCTGGTGCCTTAT\n+TACCGACCGGGCGATAAACGCATCGCACAGGATCTGGCGGAAC\n+>r18.1 |SOURCES={GI=49175990,fw,3142456-3142551}|ERRORS={}|SOURCE_1="Escherichia coli str. K-12 substr. MG1655" (cf77cbe42208fbf232179e8864f9dcf39151cb85)\n+CAGATTTCAGCGTCTGACGCGGATAGTGGTATTCGCTGCCAGGCTTCAGCGCCAGACGTTTTTTC\n+GCCTCCGCCATCAGCTCTTCACGCGTACCG\n+>r19.1 |SOURCES={GI=49175990,fw,2749965-2750057}|ERRORS={79:-}|SOURCE_1="Escherichia coli str. K-12 substr. MG1655" (cf77cbe42208fbf232179e8864f9dcf39151cb85)\n+TGAAGCCGACATGGTGCGTACCGGCGCTGCTCGCGCTGACCTGTGCGCCCGTTTTTCTCTGAAAG\n+ATACGCCAGCGGCTTGCGCTGGCTGG\n+>r20.1 |SOURCES={GI=49175990,fw,2183340-2183438}|ERRORS={25_1:C}|SOURCE_1="Escherichia coli str. K-12 substr. MG1655" (cf77cbe42208fbf232179e8864f9dcf39151cb85)\n+ACGTGAAGAAGCAATGACCTGGTGGTCCCGTGACTTCCCTACGCTGGCATTATCCAGATCAGGTG\n+ATACGGGTATTTCTCAGCCTTCACGCAGAAGGGC\n+>r21.1 |SOURCES={GI=49175990,fw,710407-710509}|ERRORS={88:-}|SOURCE_1="Escherichia coli str. K-12 substr. MG1655" (cf77cbe42208fbf232179e8864f9dcf39151cb85)\n+TAATCTTCCTGGTCACCACAACCAAACAGCGCAACCAGTTTGCCGTTGAAATCAATCTCTTCGAG\n+AGTCGGGAAGAAGTCATCCCAGTACACTGCGCTTCG\n+>r23.1 |SOURCES={GI=49175990,fw,3063738-3063831}|ERRORS={25_1:C}|SOURCE_1="Escherichia coli str. K-12 substr. MG1655" (cf77cbe42208fbf232179e8864f9dcf39151cb85)\n+GCCTCCAGCCTGACAATCTCGGCCGACTTCCCTGCGCAAGATTTACGACAATATGGATTACTTTG\n+CCAGCCGCATTGTGTTGCGTCCGCAGGAG\n+>r25.1 |SOURCES={GI=49175990,fw,2503687-2503788}|ERRORS={}|SOURCE_1="Escherichia coli str. K-12 substr. MG1655" (cf77cbe42208fbf232179e8864f9dcf39151cb85)\n+CCGGCTCCACGGTCAGTAACATGCCTGGCTGTAGCGTCGTGGTGTCCCGCGGTGAAAAACGCGGA\n+TCTTCATGAACTTCAATGCCGATAGCGTGACCGGTG\n+>r26.1 |SOURCES={GI=49175990,fw,952817-952933}|ERRORS={18_1:C,21_1:A,81_1:G}|SOURCE_1="Escherichia coli str. K-12 substr. MG1655" (cf77cbe42208fbf232179e8864f9dcf39151cb85)\n+TACTTCGACAACCATTAATCGGTAGGTCGTTTTCACGCAGGTAAATGACCCAGTATGTCAACCCA\n+ACCAACAAACCACCACCGAGTAATGTTGCCGATCGTAACCGGAATCAGGTTATC\n+>r28.1 |SOURCES={GI=49175990,fw,34196'..b'GTG\n+>r6627.1 |SOURCES={GI=49175990,fw,3588247-3588350}|ERRORS={5_1:C,65_1:T}|SOURCE_1="Escherichia coli str. K-12 substr. MG1655" (cf77cbe42208fbf232179e8864f9dcf39151cb85)\n+GTCGAACGAAGGCATACACCAGGTTCACTACCAGCAGGAAGAAACTCACCGGGGCGATAAGCGGC\n+AGTCGCAATCTTAAAGAAGCGGCGAATCGGCCCTGCACCG\n+>r6628.1 |SOURCES={GI=49175990,fw,3516248-3516359}|ERRORS={38_1:G}|SOURCE_1="Escherichia coli str. K-12 substr. MG1655" (cf77cbe42208fbf232179e8864f9dcf39151cb85)\n+GCCGTAAAGACGGTATCGAGTACAGCCAGGCTTTTATACGTGCTCGCCGTCAGGGAGGATAACGC\n+TATCGACGTTAACACCCGCCTGTTCAAGTACGCCGCGGACCTTATCG\n+>r6629.1 |SOURCES={GI=49175990,fw,4151423-4151520}|ERRORS={30_1:T,46_1:C}|SOURCE_1="Escherichia coli str. K-12 substr. MG1655" (cf77cbe42208fbf232179e8864f9dcf39151cb85)\n+TTTGGCAACAGTGCCGGATGCGGCGCGAGCGTCCTTATCCGGCCTACACGTTGGGCATCGTTTGA\n+GTCACTGTCGGTCGGATAAGATGCGCAAGTATCG\n+>r6630.1 |SOURCES={GI=49175990,fw,3466388-3466482}|ERRORS={91_1:A}|SOURCE_1="Escherichia coli str. K-12 substr. MG1655" (cf77cbe42208fbf232179e8864f9dcf39151cb85)\n+GCCACCAGAGCAGGGTTGTCACTTTGCGTCCAGAACAGCGCTTCATAAGCCTGCCCATCAACAAC\n+AACGCGATCACCTTTCACGTACACAGTAGG\n+>r6631.1 |SOURCES={GI=49175990,fw,162495-162593}|ERRORS={96_1:T}|SOURCE_1="Escherichia coli str. K-12 substr. MG1655" (cf77cbe42208fbf232179e8864f9dcf39151cb85)\n+AGGCGGATTTGGCGTTGGCGCTGTTACTCGATGTGCAACAAGGTCTGCGTGATGACCTTAAACTG\n+CTGATTATGTCGGCTACCCTGGACAACGACCGTC\n+>r6632.1 |SOURCES={GI=49175990,fw,4116430-4116536}|ERRORS={77_1:C}|SOURCE_1="Escherichia coli str. K-12 substr. MG1655" (cf77cbe42208fbf232179e8864f9dcf39151cb85)\n+GCTTCATACAATCGGAGCTAACTAAAGTGCGCTCGTATTTATTAAGGCGTCACCGGTAATCGGGA\n+CGAGGATTTTTATCCCATCAACGCCTTGCAATTCAGGAGAGG\n+>r6633.1 |SOURCES={GI=49175990,fw,2351739-2351834}|ERRORS={13_1:G}|SOURCE_1="Escherichia coli str. K-12 substr. MG1655" (cf77cbe42208fbf232179e8864f9dcf39151cb85)\n+TATCGGCTGATGGCGTGAATGGGCTACCGACGCGGTATGCCGCAAACTGGGCAACACGCGCCCCT\n+GTACGACTGCCGATCTGGCACTGCCTGGTTC\n+>r6634.1 |SOURCES={GI=49175990,fw,3702649-3702756}|ERRORS={9_1:T}|SOURCE_1="Escherichia coli str. K-12 substr. MG1655" (cf77cbe42208fbf232179e8864f9dcf39151cb85)\n+GATGAACAGCTACGATGACGACGTAAACCAGCCCGACGACCGCGCCTTTGTTGCGTTTAAAATAG\n+TGCCAGAACTCCTGTAACGGGGTCATCGGCACCGGTGCGCTAA\n+>r6635.1 |SOURCES={GI=49175990,fw,1077130-1077225}|ERRORS={44_1:G,88_1:A}|SOURCE_1="Escherichia coli str. K-12 substr. MG1655" (cf77cbe42208fbf232179e8864f9dcf39151cb85)\n+GCCCGGCCCTTCATAGATGCCACGACCGTTAGACGCTTTACCGATGGGCGTGAATCGCCTGCTGA\n+TAGGAAACCATATACGCCTGTGCATACTGCGG\n+>r6645.1 |SOURCES={GI=49175990,fw,1737869-1737978}|ERRORS={54_1:C,66_1:C,67_1:A,82_1:G}|SOURCE_1="Escherichia coli str. K-12 substr. MG1655" (cf77cbe42208fbf232179e8864f9dcf39151cb85)\n+CACAACACTAATTTCACTCCCTACACTTTGCGGCGGTGTTTAATTGAGAGATTTACGAGAATATA\n+CATCGACAACCTGGGAAAAGAGTTTTTAGTCTGGCTGGCGGGTTTGAG\n+>r6647.1 |SOURCES={GI=49175990,fw,3690431-3690523}|ERRORS={2_1:A,84_1:T}|SOURCE_1="Escherichia coli str. K-12 substr. MG1655" (cf77cbe42208fbf232179e8864f9dcf39151cb85)\n+TCTAGCGCCACGACTGGCGCATCAGCGCCCTGCACGCCCGGCATCACTTGCCCCACCTGCGGATT\n+TTGTTCCGTCTGGGCGGCTACTAGCTGGC\n+>r6649.1 |SOURCES={GI=49175990,fw,1823922-1824041}|ERRORS={39_1:C}|SOURCE_1="Escherichia coli str. K-12 substr. MG1655" (cf77cbe42208fbf232179e8864f9dcf39151cb85)\n+TATTAATTTATAAGAAAGCAACTTAATACCCGCAGAATGACTTTCTGCGGGTAAGTATTAGCTTA\n+TTTTTTCGAGCATTAATCCCGCGCGTAATCCCAACGCTACCAACGGATTAGGGAA\n+>r6651.1 |SOURCES={GI=49175990,fw,4283826-4283926}|ERRORS={}|SOURCE_1="Escherichia coli str. K-12 substr. MG1655" (cf77cbe42208fbf232179e8864f9dcf39151cb85)\n+GAGACGTTCAGCACGTCGTCCACACGCCCGGTTATCCAGTAATAGCCATCTTCATCGCGACGCGC\n+GCCGTCGCCGCTGAAATACATATTTTTGAAGGTGG\n+>r6652.1 |SOURCES={GI=49175990,fw,2843298-2843399}|ERRORS={11_1:G}|SOURCE_1="Escherichia coli str. K-12 substr. MG1655" (cf77cbe42208fbf232179e8864f9dcf39151cb85)\n+GACCGCTGGCACGGGACCATCGGGCCGACGTTACTGAAGTCGCGAGCGATTTCCGGGTCCAGACG\n+ACCAATGCCGACAGTGCGCTGTTCCATGTTCGGAGTG\n+>r6653.1 |SOURCES={GI=49175990,fw,3845215-3845312}|ERRORS={}|SOURCE_1="Escherichia coli str. K-12 substr. MG1655" (cf77cbe42208fbf232179e8864f9dcf39151cb85)\n'
b
diff -r 000000000000 -r 1f0a3e4497d4 test-data/NC_000913-454.ffn
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/NC_000913-454.ffn Wed Sep 06 13:23:14 2017 -0400
b
b'@@ -0,0 +1,6364 @@\n+>r1.1_1_80_-\n+GCACGTCAGCACCTGCTGCCGCGTGACGTGGTGCAGGCACATGAGCGTGGCGATATTCACTATCACGATCTCGATTAC\n+>r2.1_1_93_-\n+CGAATGGTCGTTGTTACCAGCGGTGAAATGTTGCAGCAACTCTGGTCGCTGATCCCCAATGGTATCGTGAGCACTGGTTACTACACTGTCGAC\n+>r3.1_1_90_-\n+CTGACTTTGACTATTCGTCATTACTGGTCACATCTTGCAGATGATGAGGACAAATACCGTCTCTGGTTTAGCGATGTTGTCGCACGT\n+>r4.1_1_89_-\n+GCGAAATTGGTGTTGCAGGATTACGCGTCAGGCAGCCGACCGCTGATTGACGCAGCGCTGGCGCGCAATGGTATTCAGGCGAATATT\n+>r11.1_1_106_+\n+GTAAAAGGCGGCAGTGAGAAGACCGCCATTTCAGGTTACCCTACCTTCCTGCCGGATGCGATTCATCACCCTACAAATTCAATAAATTATGAATCAATACGC\n+>r15.1_1_104_-\n+TTAGTACCAGTCGTGAGTTCGTCCATGTTTGTCACCGGTGCGGCACCAAACGTGCTGGGTCTGGAGTTCGTCAGCAAAATTGCCGGTATCCAGATTAGCTGG\n+>r16.1_1_108_+\n+TATTCGTCCGTTCACACCCGATACGTGGTGATGACGGATGGGAATGTCCCGCTGGTGCCTTATTACCGACCGGGCGATAAACGCATCGCACAGGATCTGGCGGAA\n+>r18.1_1_95_-\n+GGTACGCGTGAAGAGCTGATGGCGGAGGCGAAAAAACGTCTGGCGCTGAAGCCTGGCAGCGAATACCACTATCCGCGTCAGACGCTGAAATCT\n+>r19.1_11_91_+\n+ATGGTGCGACCGGCGCTGCTCGCGCTGACCGTGCGCCCGTTTTTCTCTGAAAGATACGCCAGCGGCTTGCGCTGGCTG\n+>r20.1_1_99_+\n+CGTGAAGAAGCAATGACCTGGTGGTCCCGTGACTTCCCTACGCTGGCATTTCCAGATCAGGTGATACGGGTATTTCTCAGCCTTCACGCAGAAGGG\n+>r21.1_1_101_-\n+CGAAGCGCAGTGTACTGGGATGACTTCTTCCCGACTCTCGAAGAGATTGATTTCAACGGCAAACTGGTTGCGCTGTTTGGTTGTGGTGACCAGGAAGAT\n+>r23.1_1_94_+\n+GCCTCCAGCCTGACAATCTCGGCCGACTCCCTGCGCAAGATTTACGACAATATGGATTACTTTGCCAGCCGCATTGTGTTGCGTCCGCAG\n+>r25.1_1_101_-\n+ACCGGTCACGCTATCGGCATTGAAGTTCATGAAGATCCGCGTTTTTCACCGCGGGACACCACGACGCTACAGCCAGGCATGTTACTGACCGTGGAGCCG\n+>r26.1_1_119_-\n+AACCTGATTCCGGTTACGATCGGCAACATTACCGGTGGTGGTTTGTTGGTTGGGTTGACATACTGGGTCATTTACCTGCGTGAAAACGACCTACCGATTAATGGTTGTCGAAGT\n+>r28.1_1_104_+\n+GTTCTGGAAAATACTCCCGCATCGCGGTCGCTATATTCCGCGGCCTGGGCGGTGATTTACCCACTGATTGTCTGGTGGCTGATGTATGGCGGTTTTTTTGCT\n+>r29.1_1_100_+\n+CAGCACAACGTGCCGGAGACCGCTAACGCCAAGCTGGACGCCAAGTGCGTAATGGTCGGCAATATCCACGTCGCAACTGGCTGGTGCGACGCTTTT\n+>r30.1_1_108_-\n+CTCAGTTTTGAACTGGCCGAACCCCTGCATATCCGCCAGGTAGATATTAACCCACAAATTGTCTTTAGCTATATCAAGAGCAAGGGCAACTTGTCGTTAAACAAT\n+>r32.1_1_99_+\n+TCTCTCGGCCCGGTGATTATTTCCGCCGTCGTGGCATTGCTGGTTAGCAATCTGATTAATCATAGCGACGCGTTACTCTACAACGTACAACTCTCA\n+>r34.1_1_91_+\n+AGACTGTTGGCCTGCGCTTTACTGCGGCCTTCTGCCACGCGCCTCGGCGAAATTAGCGAACAGTACGGTGATACCACAGCCAACCGC\n+>r36.1_1_95_-\n+CTGGGGAAAGTGAGAAATATTGTCAACATGAAGCCGGCGCACCCATGGAAGCTGAAAGATTTTGTGACTCGCCTGTACATCAGTGAAAGCCTG\n+>r40.1_1_103_-\n+GGAACGCTGTTTGCGGCGCGTCAGGGCTTTGTCAGCCCGGAATCCTTCACCTTTGCCGAATCGGCGTTTGTGTCTGGCGATGTGGTGCTCGGCGGTATG\n+>r43.1_33_107_-\n+GGCGCTGGGGATGAAGAACCAGGCGTTTCCTTGCTGAAGAAGAGTTGTAAATTCGGTCATGATAATAATTCT\n+>r45.1_1_102_-\n+ATCGTTTCTCTGAATTACGCTGTGCGTGAGAAAGAGAATAATGAAGATGATGCGACGCGTCTGGCGCGTTTGAACGAACGCTTTAAACGCGAAGGTAAA\n+>r51.1_1_105_-\n+CGCCCGGGCTTAAGTATTCTGGTACCTGAATCACCAGACCACGTGCTCAATGTCGCCGGTTTGTTACGGGCGCTGGCAGATGCCCCCTTTGATGCCTGGTGCGGT\n+>r53.1_1_97_+\n+ATTGAGACACAAGGCGAGACGGCACAGGCGCTGGCAATACGACTGGCACGCCCGGTGGTAGTGATCGATAAAATGGCGGGCAAGGTGGTGACCATT\n+>r54.1_1_117_-\n+CGCTGGTGGTTCGATTGTTGTAGCCACGTTAACGACGCCGGTTTCTGGTTGTTCGGTAAATTTACCGGCGCGACCGAAGCCGAAACGCTGAAAACCTGGACCATGATGGAAACCATC\n+>r56.1_1_96_-\n+CATGAGACGCAACTTCTACTGTTGTCCATTGTTACAGCAACTCGGTCAGCAATCGCGCTGGCAACTCTGGTTAACACCGCAACAAAAACTGAG\n+>r60.1_1_102_-\n+AATGAGAAAACGCTTCAACAAGGGGATACCTGGCACAATCTCGCTACTGGCGAAACCGGCGATACTGTAGTACAGGGCCTGGGCTGGGAAATGCTG\n+>r61.1_7_100_+\n+ATGGAGATTCGCTCCCGTGCTGCCAGCCTGCTGCACGGCCTCGGTTTCAGCAATGAACAACTGGAGCGCCCGGTAAGTGATTTTTCCGGG\n+>r63.1_15_110_+\n+GTGACACCGACCCTTTTAAGTGCTTTTTGGACTTACACCCTGATTACCGCTATGACGCCAGGACCGAACAATATTCTCGCCCTTAGCTCTGCT\n+>r66.1_1_103_+\n+TTGCTGATGGCGGCTTTGTATACCTCAACGGCATTCAGGATGAGTAACAAACTTGCTTTACGCTGGGGTGACAAATCTTGTTTTATTCAACCACCCAAT\n+>r70.1_1_102_-\n+TCTAATTTCTCCAGAAATTTAACTCGCTTCTTCATCAAGGATATGATTGTGATAGGTATCAATGATAACCTTGAAGGGTTTATTGCCTACTTTTTTGATCTC\n+>r74.1_1_91_-\n+CATCCCGCAAGTAGTGAGCAGGCCAGCAAAGCAGCTAAAAAAATCACAATGGTGCTCATGCTTTCCCCATCTTACTTAGTCTGTCAG\n+>r75.1_1_108_+\n+CGCGATGCGTTGATGGAAGCGTTAAAAGAAAGAGGCATTGGTACCGGGTTACATTTCCGCGCCGCTCACACACAAAAATATTATCGCGAGCGTTTTCCCACGCTG\n+>r76.1_1_97_+\n+GGACCGATGCCAGTTGAACGTGGCCCGGAAATGACGGCGCTGCGTGATGGTGTACGCGGGAAAGATAAGCTGGATGTGCCGATCAAAAATGATCTG\n+>r79.1_1_92_+\n'..b'ACCGAAGCGGCGGATGAATTTTTAAGTGAGCTG\n+>r6584.1_1_111_+\n+CAGAGTTCCACCCCACACGATGCGCTGTTCAAACTCTTTTTACGCCAACCGGACACGGCTCGTGATTTTCGTTGCGTTTCATTTTACCGGCACCCATTCACGCGCTTT\n+>r6585.1_1_103_-\n+TTAAATAACAACTCAGCAATGAGATTTTTCATGTCTGTATTTCCTTATCCAAAGTATGGAGAAGTTAACATTATGTTTCACAACTTCATAGTGTCTGGAAGT\n+>r6588.1_1_113_-\n+CTAATCAGCGCCGCAAACACGCCGCCAGTTCCGCAGAAGCCAGGAAGACATTCGCGCCAGTACCCAGACGGTTCGGGAAGTTACGGGGTAGAGGTGGAAACCACCGTTGCA\n+>r6589.1_57_129_-\n+ACTTATAGACAATTTAAAAACATAACACCAAAAATAAAAGGGCCAAAAATTAAAGCCCTTTATAATCAA\n+>r6592.1_1_92_+\n+GATGAGCTGATGAAAGGGCTGAATCTGCCGGTGAAAAAGAAAAACGGCCTGCGGGTGACGCCTGCTGATCAGATAGACATTATCACCGGA\n+>r6594.1_1_107_-\n+GGCCACCCGCTGATCGCGAAGCATTTACCCGCATTCACCTCCCCGAACACACTTTATATCCCCATACGCCAGCCATCGTCCGCTGGCGTTTTTATTGACGGAGAC\n+>r6599.1_1_85_-\n+AACACTGGCATCGCGCTGGTGCTGATATTTATGCCCACGCTGCTGGTGGCTGCACAGCCTGACCTGGGAACATCAATCCTCGTT\n+>r6600.1_1_90_+\n+AATTGCCTACGTTTGTTGCAGGACTGGCACCGCAGCATCCGCAACTATGCGGCGATGCATGAATCGTTACTGGCCTTACTCTGTGAC\n+>r6604.1_1_91_-\n+AATAAACTGGTAGTGCATCCTTATACCGTGCGGTCAGATAAACGCCGTGAATACACTCCTGATGTGAATCAGTTATATGATGCTCTG\n+>r6608.1_1_111_-\n+CCAAGTATTACTGGCCGCCACGTTCAGGCGCTGGGACTCGGGCAGTTAACGCCGACCGGCGATATCAAAAAATATTCAGCAGTGCCATCCGTTAATTTCCGCTCTGTAAAA\n+>r6613.1_1_111_+\n+CATATTTGCGACCCTGGCGGTCAACGTTTAGGTGGGCAGGGGGCAAGCGGTAATAGCGGTAGCTTTTCCCTGAAAATATTGCAGCCGTTCGTTGGCTCGGTCGTCATT\n+>r6614.1_1_109_+\n+GGCCCCTGCCTGGTGCTGGCGGGCGCGGGTTCCGGTAAAACTCGTGTTATCACCAATAAAATCGCCCATCTGATCCGCGGTTGCGGTTATCAGGCGCGGTCACAT\n+>r6615.1_1_93_+\n+AAAGAGGGGCATACCGTCTCTGGCGCGCGGGATATTGCCGACAAACTGCTGGCGTCGCTTAGCTCGATTCTCCTTTATTGGTATCACTAC\n+>r6616.1_1_77_+\n+TATGACGCTTTTGTGCAAGTTTTACATCCTTTGAATATTGTCCCAGTATTCAATATCCCTTTGAATCATATT\n+>r6617.1_1_105_+\n+ATCGCAGCGCCGGAAAATATCAGCCCGGAGAAAGGCACCACCTATAAACTGGTGCGTAAAGTCTTCCAGAATACCGAACACGTTCATGTCGTCGGCCTGCGA\n+>r6618.1_1_94_+\n+ATCATTGTGCAAACTGCTAATTTAATTAATACTTTTAAATATTATTTTGTAGCATATGCACATAAGGTTGCCGCTAAAGCACAGATTTGC\n+>r6621.1_1_103_-\n+CTGACCGTCACGCCGTATCAGAATCGTCGCTTTGACTCCTGCTTCCTGACAGCGAAAAAAGCGATTGAAAGTGGCAAGTTGGGAGAGATTGTTGAAGTGGAA\n+>r6623.1_1_112_-\n+CTAACCGGAATATTACCAGCCAGCGAACGTCTGGGCCGTTTATGTTTCAAGGCTGGCGACGTCAGCGAAAGTGCGGATAACGGAGAATTTTTACGCCAGTATTTTGCCGAG\n+>r6624.1_1_92_-\n+ATAAAACGCATCTTCTTCTTTGCCTGCTCATCCCTTTCTGACAGCAGAAATCATGCCATCTTTTATCTAGCGCTTACCCTGCGCTGTAAC\n+>r6625.1_1_101_+\n+TTATGGCTGAAAGCGCACTATCCTGCGGAGTTTTATGGCGGCGGTATGACCGCCGATATGGACAACACCGAGAAGGTGGTGGGTCTGGTGGATGAG\n+>r6627.1_1_105_-\n+GTGCAGGGCCGATTCGCCGCTTCTTTAAGATTGCGACTGCCGCTTATCGCCCCGGTGAGTTTCTTCCTGCTGGTAGTGAACCTGGTGTATGCCTTCGTTCGA\n+>r6628.1_1_112_+\n+CGTAAAGACGGTATCGAGTACAGCCAGGCTTTTTACGTGCTCGCCGTCAGGGAGGATAACGCTATCGACGTTAACACCCGCCTGTTCAAGTACGCCGCGGACCTTATC\n+>r6629.1_1_99_-\n+GATACTTGCGCATCTTATCCGACCGACAGTGACTCAAACGATGCCCAACGTGTAGGCCGGATAAGGACGCTCGCGCCGCATCCGGCACTGTTGCCA\n+>r6630.1_1_95_-\n+CCTACTGTGTACGTGAAAGGTGATCGCGTTGTTGTTGATGGGCAGGCTTATGAAGCGCTGTTCTGGACGCAAAGTGACAACCCTGCTCTGGTG\n+>r6631.1_1_99_+\n+GCGGATTTGGCGTTGGCGCTGTTACTCGATGTGCAACAAGGTCTGCGTGATGACCTTAAACTGCTGATTATGTCGGCTACCCTGGACAACGACCGT\n+>r6632.1_22_107_-\n+TCTCCTGAATTGCAAGGCGTTGATGGGATAAAAATCCTCGTCCCGATTACCGGTGACGCCTTAATAAATACGAGCGCACTT\n+>r6633.1_1_96_+\n+TATCGGCTGATGGCGGAATGGGCTACCGACGCGGTATGCCGCAAACTGGGCAACACGCGCCCCTGTACGACTGCCGATCTGGCACTGCCTGGT\n+>r6634.1_1_108_-\n+AGCGCACCGGTGCCGATGACCCCGTTACAGGAGTTCTGGCACTATTTTAAACGCAACAAAGGCGCGGTCGTCGGGCTGGTTTACGTCGTCATCGTAGCTGTTCAT\n+>r6635.1_1_97_-\n+CAGTATGCACAGGCGTATATGGTTTCCTATCAGCAGGCGATCACGCCCATCGGTAAAGCGTCTAACGGTCGTGGCATCTATGAAGGGCCGGGC\n+>r6645.1_1_113_+\n+CACAACACTAATTTCACTCCCTACACTTTGCGGCGGTGTTTAATTGAGAGATTTACGAGAATATACATCGACAACCTGGGAAAAGAGTTTTTAGTCTGGCTGGCGGGTTTG\n+>r6647.1_1_94_-\n+CAGCTAGTAGCCGCCCAGACGGAACAAAATCCGCAGGTGGGGCAAGTGATGCCGGGCGTGCAGGGCGCTGATGCGCCAGTCGTGGCGCTA\n+>r6649.1_1_120_-\n+CCTAATCCGTTGGTAGCGTTGGGATTACGCGCGGGATTAATGCTCGAAAAAAAAGCTAATACTTACGCAGAAAGTCATTCTGCGGGTATTAAGTTGCTTTCTTATAAATTAATA\n+>r6651.1_1_100_-\n+ACCTTCAAAAATATGTATTTCAGCGGCGACGGCGCGCGTCGCGATGAAGATGGCTATTACTGGATAACCGGGCGTGTGGACGACGTGCTGAACGTC\n+>r6652.1_1_102_-\n+ACTCCGAACATGGAACAGCGCACTGTCGGCATTGGTCGTCTGGACCCGGAAATCGCTCGCGACTTCAGTAACGTCGGCCCGATGGTCCCGTGCCAGCGG\n'
b
diff -r 000000000000 -r 1f0a3e4497d4 test-data/NC_000913-454.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/NC_000913-454.gff Wed Sep 06 13:23:14 2017 -0400
b
b'@@ -0,0 +1,3183 @@\n+##gff-version 3\n+r1.1\tFGS\tCDS\t1\t80\t.\t-\t1\tID=r1.1_1_80_-;product=predicted protein\n+r2.1\tFGS\tCDS\t1\t93\t.\t-\t0\tID=r2.1_1_93_-;product=predicted protein\n+r3.1\tFGS\tCDS\t1\t90\t.\t-\t2\tID=r3.1_1_90_-;product=predicted protein\n+r4.1\tFGS\tCDS\t1\t89\t.\t-\t2\tID=r4.1_1_89_-;product=predicted protein\n+r11.1\tFGS\tCDS\t1\t106\t.\t+\t1\tID=r11.1_1_106_+;product=predicted protein\n+r15.1\tFGS\tCDS\t1\t104\t.\t-\t2\tID=r15.1_1_104_-;product=predicted protein\n+r16.1\tFGS\tCDS\t1\t108\t.\t+\t1\tID=r16.1_1_108_+;product=predicted protein\n+r18.1\tFGS\tCDS\t1\t95\t.\t-\t1\tID=r18.1_1_95_-;product=predicted protein\n+r19.1\tFGS\tCDS\t11\t91\t.\t+\t1\tID=r19.1_11_91_+;product=predicted protein\n+r20.1\tFGS\tCDS\t1\t99\t.\t+\t1\tID=r20.1_1_99_+;product=predicted protein\n+r21.1\tFGS\tCDS\t1\t101\t.\t-\t2\tID=r21.1_1_101_-;product=predicted protein\n+r23.1\tFGS\tCDS\t1\t94\t.\t+\t0\tID=r23.1_1_94_+;product=predicted protein\n+r25.1\tFGS\tCDS\t1\t101\t.\t-\t1\tID=r25.1_1_101_-;product=predicted protein\n+r26.1\tFGS\tCDS\t1\t119\t.\t-\t1\tID=r26.1_1_119_-;product=predicted protein\n+r28.1\tFGS\tCDS\t1\t104\t.\t+\t1\tID=r28.1_1_104_+;product=predicted protein\n+r29.1\tFGS\tCDS\t1\t100\t.\t+\t0\tID=r29.1_1_100_+;product=predicted protein\n+r30.1\tFGS\tCDS\t1\t108\t.\t-\t2\tID=r30.1_1_108_-;product=predicted protein\n+r32.1\tFGS\tCDS\t1\t99\t.\t+\t0\tID=r32.1_1_99_+;product=predicted protein\n+r34.1\tFGS\tCDS\t1\t91\t.\t+\t1\tID=r34.1_1_91_+;product=predicted protein\n+r36.1\tFGS\tCDS\t1\t95\t.\t-\t2\tID=r36.1_1_95_-;product=predicted protein\n+r40.1\tFGS\tCDS\t1\t103\t.\t-\t0\tID=r40.1_1_103_-;product=predicted protein\n+r43.1\tFGS\tCDS\t33\t107\t.\t-\t2\tID=r43.1_33_107_-;product=predicted protein\n+r45.1\tFGS\tCDS\t1\t102\t.\t-\t2\tID=r45.1_1_102_-;product=predicted protein\n+r51.1\tFGS\tCDS\t1\t105\t.\t-\t0\tID=r51.1_1_105_-;product=predicted protein\n+r53.1\tFGS\tCDS\t1\t97\t.\t+\t0\tID=r53.1_1_97_+;product=predicted protein\n+r54.1\tFGS\tCDS\t1\t117\t.\t-\t0\tID=r54.1_1_117_-;product=predicted protein\n+r56.1\tFGS\tCDS\t1\t96\t.\t-\t1\tID=r56.1_1_96_-;product=predicted protein\n+r60.1\tFGS\tCDS\t1\t102\t.\t-\t1\tID=r60.1_1_102_-;product=predicted protein\n+r61.1\tFGS\tCDS\t7\t100\t.\t+\t0\tID=r61.1_7_100_+;product=predicted protein\n+r63.1\tFGS\tCDS\t15\t110\t.\t+\t2\tID=r63.1_15_110_+;product=predicted protein\n+r66.1\tFGS\tCDS\t1\t103\t.\t+\t1\tID=r66.1_1_103_+;product=predicted protein\n+r70.1\tFGS\tCDS\t1\t102\t.\t-\t0\tID=r70.1_1_102_-;product=predicted protein\n+r74.1\tFGS\tCDS\t1\t91\t.\t-\t2\tID=r74.1_1_91_-;product=predicted protein\n+r75.1\tFGS\tCDS\t1\t108\t.\t+\t0\tID=r75.1_1_108_+;product=predicted protein\n+r76.1\tFGS\tCDS\t1\t97\t.\t+\t0\tID=r76.1_1_97_+;product=predicted protein\n+r79.1\tFGS\tCDS\t1\t92\t.\t+\t2\tID=r79.1_1_92_+;product=predicted protein\n+r81.1\tFGS\tCDS\t1\t105\t.\t+\t1\tID=r81.1_1_105_+;product=predicted protein\n+r82.1\tFGS\tCDS\t1\t96\t.\t+\t2\tID=r82.1_1_96_+;product=predicted protein\n+r83.1\tFGS\tCDS\t1\t102\t.\t-\t2\tID=r83.1_1_102_-;product=predicted protein\n+r84.1\tFGS\tCDS\t1\t94\t.\t-\t1\tID=r84.1_1_94_-;product=predicted protein\n+r87.1\tFGS\tCDS\t1\t97\t.\t-\t2\tID=r87.1_1_97_-;product=predicted protein\n+r88.1\tFGS\tCDS\t1\t93\t.\t+\t0\tID=r88.1_1_93_+;product=predicted protein\n+r91.1\tFGS\tCDS\t1\t116\t.\t+\t1\tID=r91.1_1_116_+;product=predicted protein\n+r96.1\tFGS\tCDS\t1\t92\t.\t+\t0\tID=r96.1_1_92_+;product=predicted protein\n+r97.1\tFGS\tCDS\t1\t107\t.\t-\t0\tID=r97.1_1_107_-;product=predicted protein\n+r99.1\tFGS\tCDS\t1\t99\t.\t-\t2\tID=r99.1_1_99_-;product=predicted protein\n+r101.1\tFGS\tCDS\t1\t108\t.\t+\t2\tID=r101.1_1_108_+;product=predicted protein\n+r102.1\tFGS\tCDS\t1\t107\t.\t+\t2\tID=r102.1_1_107_+;product=predicted protein\n+r104.1\tFGS\tCDS\t1\t101\t.\t+\t0\tID=r104.1_1_101_+;product=predicted protein\n+r106.1\tFGS\tCDS\t1\t102\t.\t+\t2\tID=r106.1_1_102_+;product=predicted protein\n+r107.1\tFGS\tCDS\t1\t91\t.\t-\t2\tID=r107.1_1_91_-;product=predicted protein\n+r108.1\tFGS\tCDS\t1\t98\t.\t-\t2\tID=r108.1_1_98_-;product=predicted protein\n+r116.1\tFGS\tCDS\t1\t111\t.\t-\t1\tID=r116.1_1_111_-;product=predicted protein\n+r117.1\tFGS\tCDS\t1\t102\t.\t+\t1\tID=r117.1_1_102_+;product=predicted protein\n+r123.1\tFGS\tCDS\t1\t101\t.\t-\t0\tID=r123.1_1_101_-;product=predicted protein\n+r124.1\tFGS\tCDS\t1\t103\t.\t+\t0\tID=r124.1_1_103_+;product=predicted protein\n+r127.1\tFGS\tCDS\t1\t108\t.\t+\t0\tID=r127.1_1_108_+;product=predicted protein\n+'..b'\t.\t+\t2\tID=r6540.1_1_87_+;product=predicted protein\n+r6541.1\tFGS\tCDS\t1\t92\t.\t-\t1\tID=r6541.1_1_92_-;product=predicted protein\n+r6543.1\tFGS\tCDS\t1\t94\t.\t-\t1\tID=r6543.1_1_94_-;product=predicted protein\n+r6544.1\tFGS\tCDS\t1\t99\t.\t+\t0\tID=r6544.1_1_99_+;product=predicted protein\n+r6545.1\tFGS\tCDS\t1\t106\t.\t+\t0\tID=r6545.1_1_106_+;product=predicted protein\n+r6550.1\tFGS\tCDS\t1\t91\t.\t-\t1\tID=r6550.1_1_91_-;product=predicted protein\n+r6558.1\tFGS\tC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b
diff -r 000000000000 -r 1f0a3e4497d4 test-data/NC_000913-454.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/NC_000913-454.out Wed Sep 06 13:23:14 2017 -0400
b
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b
diff -r 000000000000 -r 1f0a3e4497d4 test-data/NC_000913.faa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/NC_000913.faa Wed Sep 06 13:23:14 2017 -0400
b
b'@@ -0,0 +1,1374 @@\n+>gi|49175990|ref|NC_000913.2|_337_2799_+\n+MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV\n+>gi|49175990|ref|NC_000913.2|_2801_3733_+\n+MVKVYAPASSANMSVGFDVLGAAVTPVDGALLGDVVTVEAAETFSLNNLGRFADKLPSEPRENIVYQCWERFCQELGKQIPVAMTLEKNMPIGSGLGSSACSVVAALMAMNEHCGKPLNDTRLLALMGELEGRISGSIHYDNVAPCFLGGMQLMIEENDIISQQVPGFDEWLWVLAYPGIKVSTAEARAILPAQYRRQDCIAHGRHLAGFIHACYSRQPELAAKLMKDVIAEPYRERLLPGFRQARQAVAEIGAVASGISGSGPTLFALCDKPETAQRVADWLGKNYLQNQEGFVHICRLDTAGARVLEN\n+>gi|49175990|ref|NC_000913.2|_3734_5020_+\n+MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDEMLKLDFVTRSAKILSAFIGDEIPQEILEERVRAAFAFPAPVANVESDVGCLELFHGPTLAFKDFGGRFMAQMLTHIAGDKPVTILTATSGDTGAAVAHAFYGLPNVKVVILYPRGKISPLQEKLFCTLGGNIETVAIDGDFDACQALVKQAFDDEELKVALGLNSANSINISRLLAQICYYFEAVAQLPQETRNQLVVSVPSGNFGDLTAGLLAKSLGLPVKRFIAATNVNDTVPRFLHDGQWSPKATQATLSNAMDVSQPNNWPRVEELFRRKIWQLKELGYAAVDDETTQQTMRELKELGYTSEPHAAVAYRALRDQLNPGEYGLFLGTAHPAKFKESVEAILGETLDLPKELAERADLPLLSHNLPADFAALRKLMMNHQ\n+>gi|49175990|ref|NC_000913.2|_5234_5530_+\n+MKKMQSIVLALSLVLVAPMAAQAAEITLVPSVKLQIGDRDNRGYYWDGGHWRDHGWWKQHYEWRGNRWHLHGPPPPPRHHKKAPHDHHGGHGPGKHHR\n+>gi|49175990|ref|NC_000913.2|_5683_6459_-\n+MLILISPAKTLDYQSPLTTTRYTLPELLDNSQQLIHEARKLTPPQISTLMRISDKLAGINAARFHDWQPDFTPANARQAILAFKGDVYTGLQAETFSEDDFDFAQQHLRMLSGLYGVLRPLDLMQPYRLEMGIRLENARGKDLYQFWGDIITNKLNEALAAQGDNVVINLASDEYFKSVKPKKLNAEIIKPVFLDEKNGKFKIISFYAKKARGLMSRFIIENRLTKPEQLTGFNSEGYFFDEDSSSNGELVFKRYEQR\n+>gi|49175990|ref|NC_000913.2|_6529_7959_-\n+MPDFFSFINSVLWGSVMIYLLFGAGCWFTFRTGFVQFRYIRQFGKSLKNSIHPQPGGLTSFQSLCTSLAARVGSGNLAGVALAITAGGPGAVFWMWVAAFIGMATSFAECSLAQLYKERDVNGQFRGGPAWYMARGLGMRWMGVLFAVFLLIAYGIIFSGVQANAVARALSFSFDFPPLVTGIILAVFTLLAITRGLHGVARLMQGFVPLMAIIWVLTSLVICVMNIGQLPHVIWSIFESAFGWQEAAGGAAGYTLSQAITNGFQRSMFSNEAGMGSTPNAAAAAASWPPHPAAQGIVQMIGIFIDTLVICTASAMLILLAGNGTTYMPLEGIQLIQKAMRVLMGSWGAEFVTLVVILFAFSSIVANYIYAENNLFFLRLNNPKAIWCLRICTFATVIGGTLLSLPLMWQLADIIMACMAITNLTAILLLSPVVHTIASDYLRQRKLGVRPVFDPLRYPDIGRQLSPDAWDDVSQE\n+>gi|49175990|ref|NC_000913.2|_8238_9191_+\n+MTDKLTSLRQYTTVVADTGDIAAMKLYQPQDATTNPSLILNAAQIPEYRKLIDDAVAWAKQQSNDRAQQIVDATDKLAVNIGLEILKLVPGRISTEVDARLSYDTEASIAKAKRLIKLYNDAGISNDRILIKLASTWQGIRAAEQLEKEGINCNLTLLFSFAQARACAEAGVFLISPFVGRILDWYKANTDKKEYAPAEDPGVVSVSEIYQYYKEHGYETVVMGASFRNIGEILELAGCDRLTIAPALLKELAESEGAIERKLSYTGEVKARPARITESEFLWQHNQDPMAVDKLAEGIRKFAIDQEKLEKMIGDLL\n+>gi|49175990|ref|NC_000913.2|_9306_9893_+\n+MNTLRIGLVSISDRASSGVYQDKGIPALEEWLTSALTTPFELETRLIPDEQAIIEQTLCELVDEMSCHLVLTTGGTGPARRDVTPDATLAVADREMPGFGEQMRQISLHFVPTAILSRQVGVIRKQALILNLPGQPKSIKETLEGVKDAEGNVVVHGIFASVPYCIQLLEGPYVETAPEVVAAFRPKSARRDVSE\n+>gi|49175990|ref|NC_000913.2|_9928_10494_-\n+MGNTKLANPAPLGLMGFGMTTILLNLHNVGYFALDGIILAMGIFYGGIAQIFAGLLEYKKGNTFGLTAFTSYGSFWLTLVAILLMPKLGLTDAPNAQFLGVYLGLWGVFTLFMFFGTLKGARVLQFVFFSLTVLFALLAIGNIAGNAAIIHFAGWIGLICGASAIYLAMGEVLNEQFGRTVLPIGESH\n+>gi|49175990|ref|NC_000913.2|_10643_11356_-\n+MNVNYLNDSDLDFLQHCSEEQLANFARLLTHNEKGKTRLSSVLMRNELFKSMEGHPEQHRRNWQLIAGELQHFGGDSIANKLRGHGKLYRAILLDVSKRLKLKADKEMSTFEIEQQLLEQFLRNTWKKMDEEHKQEFLHAVDARVNELEELLPLLMKDKLLAKGVSHLLSSQLTRILRTHAAMSVLGHGLLRGAGLGGPVGAALNGVKAVSGSAYRVTIPAVLQIACLRRMVSATQV\n+>gi|49175990|ref|NC_000913.2|_11382_11786_-\n+MKSVFTISASLAISLMLCCTAQANDHKLLGAIAMPRNETNDLALKLPVCRIVKRIQLSADHGDLQLSGASVYFKAARSASQSLNIPSEIKEGQTTDWININSDNDNKRCVSKITFSGHTVNSSDMATLKIIGDD\n+>gi|49175990|ref|NC'..b'SIRARVEHPFRIIKRQFGFVKARYKGLLKNDNQLAMLFTLANLFRADQMIRQWERSH\n+>gi|49175990|ref|NC_000913.2|_688566_690104_-\n+MAFASLIERQRIRLLLALLFGACGTLAFSPYDVWPAAIISLMGLQALTFNRRPLQSAAIGFCWGFGLFGSGINWVYVSIATFGGMPGPVNIFLVVLLAAYLSLYTGLFAGVLSRLWPKTTWLRVAIAAPALWQVTEFLRGWVLTGFPWLQFGYSQIDGPLKGLAPIMGVEAINFLLMMVSGLLALALVKRNWRPLVVAVVLFALPFPLRYIQWFTPQPEKTIQVSMVQGDIPQSLKWDEGQLLNTLKIYYNATAPLMGKSSLIIWPESAITDLEINQQPFLKALDGELRDKGSSLVTGIVDARLNKQNRYDTYNTIITLGKGAPYSYESADRYNKNHLVPFGEFVPLESILRPLAPFFDLPMSSFSRGPYIQPPLSANGIELTAAICYEIILGEQVRDNFRPDTDYLLTISNDAWFGKSIGPWQHFQMARMRALELARPLLRSTNNGITAVIGPQGEIQAMIPQFTREVLTTNVTPTTGLTPYARTGNWPLWVLTALFGFAAVLMSLRQRRK\n+>gi|49175990|ref|NC_000913.2|_690129_691007_-\n+MSDDNSHSSDTISNKKGFFSLLLSQLFHGEPKNRDELLALIRDSGQNDLIDEDTRDMLEGVMDIADQRVRDIMIPRSQMITLKRNQTLDECLDVIIESAHSRFPVISEDKDHIEGILMAKDLLPFMRSDAEAFSMDKVLRQAVVVPESKRVDRMLKEFRSQRYHMAIVIDEFGGVSGLVTIEDILELIVGEIEDEYDEEDDIDFRQLSRHTWTVRALASIEDFNEAFGTHFSDEEVDTIGGLVMQAFGHLPARGETIDIDGYQFKVAMADSRRIIQVHVKIPDDSPQPKLDE\n+>gi|49175990|ref|NC_000913.2|_691097_691564_-\n+MSQVILDLQLACEDNSGLPEESQFQTWLNAVIPQFQEESEVTIRVVDTAESHSLNLTYRGKDKPTNVLSFPFEVPPGMEMSLLGDLVICRQVVEKEAQEQGKPLEAHWAHMVVHGSLHLLGYDHIEDDEAEEMEALETEIMLALGYEDPYIAEKE\n+>gi|49175990|ref|NC_000913.2|_691561_692640_-\n+MFSFRRHTDKRNGLNIDTREITLEPADNARLLSLCGPFDDNIKQLERRLGIEINRRDNHFKLTGRPICVTAAADILRSLYVDTAPMRGQIQDIEPEQIHLAIKEARVLEQSAESVPEYGKAVNIKTKRGVIKPRTPNQAQYIANILDHDITFGVGPAGTGKTYLAVAAAVDALERQEIRRILLTRPAVEAGEKLGFLPGDLSQKVDPYLRPLYDALFEMLGFEKVEKLIERNVIEVAPLAYMRGRTLNDAFIILDESQNTTIEQMKMFLTRIGFNSKAVITGDVTQIDLPRNTKSGLRHAIEVLADVEEISFNFFHSEDVVRHPVVARIVNAYEAWEEAEQKRKAALAAERKREEQEQK\n+>gi|49175990|ref|NC_000913.2|_692754_694178_-\n+MTKKLHIKTWGCQMNEYDSSKMADLLDATHGYQLTDVAEEADVLLLNTCSIREKAQEKVFHQLGRWKLLKEKNPDLIIGVGGCVASQEGEHIRQRAHYVDIIFGPQTLHRLPEMINSVRGDRSPVVDISFPEIEKFDRLPEPRAEGPTAFVSIMEGCNKYCTYCVVPYTRGEEVSRPSDDILFEIAQLAAQGVREVNLLGQNVNAWRGENYDGTTGSFADLLRLVAAIDGIDRIRFTTSHPIEFTDDIIEVYRDTPELVSFLHLPVQSGSDRILNLMGRTHTALEYKAIIRKLRAARPDIQISSDFIVGFPGETTEDFEKTMKLIADVNFDMSYSFIFSARPGTPAADMVDDVPEEEKKQRLYILQERINQQAMAWSRRMLGTTQRILVEGTSRKSIMELSGRTENNRVVNFEGTPDMIGKFVDVEITDVYPNSLRGKVVRTEDEMGLRVAETPESVIARTRKENDLGVGYYQP\n+>gi|49175990|ref|NC_000913.2|_694324_695499_+\n+MTNQPTEIAIVGGGMVGGALALGLAQHGFAVTVIEHAEPAPFVADSQPDVRISAISAASVSLLKGLGVWDAVQAMRCHPYRRLETWEWETAHVVFDAAELKLPLLGYMVENTVLQQALWQALEAHPKVTLRVPGSLIALHRHDDLQELELKGGEVIRAKLVIGADGANSQVRQMAGIGVHAWQYAQSCMLISVQCENDPGDSTWQQFTPDGPRAFLPLFDNWASLVWYDSPARIRQLQNMNMAQLQAEIAKHFPSRLGYVTPLAAGAFPLTRRHALQYVQPGLALVGDAAHTIHPLAGQGVNLGYRDVDALIDVLVNARSYGEAWASYPVLKRYQMRRMADNFIMQSGMDLFYAGFSNNLPPLRFMRNLGLMAAERAGVLKRQALKYALGL\n+>gi|49175990|ref|NC_000913.2|_695581_695916_+\n+MSTSHSTLNERRKAKSSPKRAFLMWLGYEDSNLGMPESESGALPLGDTPTGCTYKVSVLNKLAGVRGFEPRNAGIRIRCLTAWRYPNKLVLNLPNIFDTFRIWWLRRDSNL\n+>gi|49175990|ref|NC_000913.2|_695978_696184_+\n+MAGVPGFEPGNAGIKNRCLTAWRYPNNRAVNRLLEEDGWGTWIRTRECRYQKPVPYRLAIPHPYNAFW\n+>gi|49175990|ref|NC_000913.2|_696185_696337_+\n+MVREARLELAHLAAPEPKSGASTNFATPAKKDGGYDGIRTCDPIIMSDVL\n+>gi|49175990|ref|NC_000913.2|_696736_698481_-\n+MRTVLLCGIFLNKQTQQATNTRLTEKVMCSIFGVFDIKTDAVELRKKALELSRLMRHRGPDWSGIYASDNAILAHERLSIVDVNAGAQPLYNQQKTHVLAVNGEIYNHQALRAEYGDRYQFQTGSDCEVILALYQEKGPEFLDDLQGMFAFALYDSEKDAYLIGRDHLGIIPLYMGYDEHGQLYVASEMKALVPVCRTIKEFPAGSYLWSQDGEIRSYYHRDWFDYDAVKDNVTDKNELRQALEDSVKSHLMSDVPYGVLLSGGLDSSIISAITKKYAARRVEDQERSEAWWPQLHSFAVGLPGSPDLKAAQEVANHLGTVHHEIHFTVQEGLDAIRDVIYHIETYDVTTIRASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGGYLYFHKAPNAKELHEETVRKLLALHMYDCARANKAMSAWGVEARVPFLDKKFLDVAMRINPQDKMCGNGKMEKHILRECFEAYLPASVAWRQKEQFSDGVGYSWIDTLKEVAAQQVSDQQLETARFRFPYNTPTSKEAYLYREIFEELFPLPSAAECVPGGPSVACSSAKAIEWDEAFKKMDDPSGRAVGVHQSAYK\n+>gi|49175990|ref|NC_000913.2|_698797_699549_-\n+MTIKNVICDIDGVLMHDNVAVPGAAEFLHGIMDKGLPLVLLTNYPSQTGQDLANRFATAGVDVPDSVFYTSAMATADFLRRQEGKKAYVVGEGALIHELYKAGFTITDVNPDFVIVGETRSYNWDMMHKAAYFVANGARFIATNPDTHGRGFYPACGALCAGIEKISGRKPFYVGKPSPWIIRAALNKMQAHSEETVIVGDNLRTDILAGFQAGLETILVLSGVSSLDDIDSMPFRPSWIYPSVAEIDVI\n+>gi|49175990|ref|NC_000913.2|_699597_699930_-\n+IKTICKAANKGDSLASEVIEYVGRHLGKTIAIAINLFNPQKIVIAGEITEADKVLLPAIESCINTQALKAFRTNLPVVRSELDHRSAIGAFALVKRAMLNGILLQHLLEN\n'
b
diff -r 000000000000 -r 1f0a3e4497d4 test-data/NC_000913.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/NC_000913.fasta Wed Sep 06 13:23:14 2017 -0400
b
b'@@ -0,0 +1,10000 @@\n+>gi|49175990|ref|NC_000913.2| Escherichia coli str. K-12 substr. MG1655, complete genome\n+AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC\n+TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA\n+TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC\n+ATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG\n+CCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAA\n+GTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC\n+AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTG\n+AAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTT\n+GACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTT\n+GCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGC\n+TGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGT\n+TACTGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCT\n+GAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCAGGTTTCACCG\n+CCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGC\n+TGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGT\n+CAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCG\n+CTAAAGTTCTTCACCCCCGCACCATTACCCCCATCGCCCAGTTCCAGATCCCTTGCCTGATTAAAAATAC\n+CGGAAATCCTCAAGCACCAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGGC\n+ATTTCCAATCTGAATAACATGGCAATGTTCAGCGTTTCTGGTCCGGGGATGAAAGGGATGGTCGGCATGG\n+CGGCGCGCGTCTTTGCAGCGATGTCACGCGCCCGTATTTCCGTGGTGCTGATTACGCAATCATCTTCCGA\n+ATACAGCATCAGTTTCTGCGTTCCACAAAGCGACTGTGTGCGAGCTGAACGGGCAATGCAGGAAGAGTTC\n+TACCTGGAACTGAAAGAAGGCTTACTGGAGCCGCTGGCAGTGACGGAACGGCTGGCCATTATCTCGGTGG\n+TAGGTGATGGTATGCGCACCTTGCGTGGGATCTCGGCGAAATTCTTTGCCGCACTGGCCCGCGCCAATAT\n+CAACATTGTCGCCATTGCTCAGGGATCTTCTGAACGCTCAATCTCTGTCGTGGTAAATAACGATGATGCG\n+ACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTGTTTGTGATTG\n+GCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAAAGCTGGCTGAAGAATAAACA\n+TATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCTCTGCTCACCAATGTACATGGCCTTAATCTG\n+GAAAACTGGCAGGAAGAACTGGCGCAAGCCAAAGAGCCGTTTAATCTCGGGCGCTTAATTCGCCTCGTGA\n+AAGAATATCATCTGCTGAACCCGGTCATTGTTGACTGCACTTCCAGCCAGGCAGTGGCGGATCAATATGC\n+CGACTTCCTGCGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCAACACCTCGTCGATGGATTAC\n+TACCATCAGTTGCGTTATGCGGCGGAAAAATCGCGGCGTAAATTCCTCTATGACACCAACGTTGGGGCTG\n+GATTACCGGTTATTGAGAACCTGCAAAATCTGCTCAATGCAGGTGATGAATTGATGAAGTTCTCCGGCAT\n+TCTTTCTGGTTCGCTTTCTTATATCTTCGGCAAGTTAGACGAAGGCATGAGTTTCTCCGAGGCGACCACG\n+CTGGCGCGGGAAATGGGTTATACCGAACCGGACCCGCGAGATGATCTTTCTGGTATGGATGTGGCGCGTA\n+AACTATTGATTCTCGCTCGTGAAACGGGACGTGAACTGGAGCTGGCGGATATTGAAATTGAACCTGTGCT\n+GCCCGCAGAGTTTAACGCCGAGGGTGATGTTGCCGCTTTTATGGCGAATCTGTCACAACTCGACGATCTC\n+TTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAATATTGATGAAG\n+ATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTGTTCAAAGTGAAAAATGGCGA\n+AAACGCCCTGGCCTTCTATAGCCACTATTATCAGCCGCTGCCGTTGGTACTGCGCGGATATGGTGCGGGC\n+AATGACGTTACAGCTGCCGGTGTCTTTGCTGATCTGCTACGTACCCTCTCATGGAAGTTAGGAGTCTGAC\n+ATGGTTAAAGTTTATGCCCCGGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGG\n+TGACACCTGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAA\n+CAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTGGGAG\n+CGTTTTTGCCAGGAACTGGGTAAGCAAATTCCAGTGGCGATGACCCTGGAAAAGAATATGCCGATCGGTT\n+CGGGCTTAGGCTCCAGTGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGCGGCAAGCC\n+GCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGCCGTATCTCCGGCAGCATTCATTAC\n+GACAACGTGGCACCGTGTTTTCTCGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGC\n+AAGTGCCAGGGTTTGATGAGTGGCTGTGGGTGCTGGCGTATCCGGGGATTAAAGTCTCGACGGCAGAAGC\n+CAGGGCTATTTTACCGGCGCAGTATCGCCGCCAGGATTGCATTGCGCACGGGCGACATCTGGCAGGCTTC\n+ATTCACGCCTGCTATTCCCGTCAGCCTGAGCTTGCCGCGAAGCTGATGAAAGATGTTATCGCTGAACCCT\n+ACCGTGAACGGTTACTGCCAGGCTTCCGGCAGGCGCGGCAGGCGGTCGCGGAAATCGGCGCGGTAGCGAG\n+CGGTATCTCCGGCTCCGGCCCGACCTTGTTCGCTCTGTGTGACAAGCCGGAAACCGCCCAGCGCGTTGCC\n+GACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGG\n+GCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCAGGTCAGCTTTGC\n+'..b'GCGATACCCCAATAACCGGGCGGTGAACCGCTTACTCG\n+AAGAAGATGGCTGGGGTACCTGGATTCGAACCAGGGAATGCCGGTATCAAAAACCGGTGCCTTACCGCTT\n+GGCGATACCCCATCCGTACAACGCTTTCTGGTGAATGGTGCGGGAGGCGAGACTTGAACTCGCACACCTT\n+GCGGCGCCAGAACCTAAATCTGGTGCGTCTACCAATTTCGCCACTCCCGCAAAAAAAGATGGTGGCTACG\n+ACGGGATTCGAACCTGTGACCCCATCATTATGAGTGATGTGCTCTAACCAACTGAGCTACGTAGCCATCT\n+TTTTTTTCGCGATACCTTATCGGCGTTGCGGGGCGCATTATGCGTATAGAGCCTTGCAGCGTCAACCTCT\n+TTTTCAAGGAAAATTGCTCGAAAGTGACTGTTTGGTTAGGTTGCGAACAGCGTGGCGCTATATTCGTCAA\n+TTATTGTTTACTTTGTGTTTTTTCCCACCCTACAGCCATTCTTTTGTCATACAGGATGAAATTCGGAATT\n+TAACAATAGTGGTGGGAAATTAATCTATGAAATACTGGCCTACAGTGATGAGTTGTCAAACAGTGATGTG\n+GCAAACCCGGAACATTTCCTTACTGCATATCAGAATCAACAAGCACCTCAATAACTGAAACAGCCCCGGA\n+TTTCACCGGGGCTGTTTCGCATTTCTTACTTATACGCCGACTGGTGAACACCAACCGCGCGACCAGACGG\n+ATCGTCCATTTTCTTGAACGCTTCATCCCATTCGATCGCTTTAGCGGAAGAACAAGCGACGGAAGGACCG\n+CCCGGCACGCACTCAGCGGCGCTCGGAAGCGGGAATAGTTCTTCAAAGATCTCCCGATACAAGTACGCTT\n+CTTTAGAGGTTGGCGTGTTGTACGGGAAGCGGAAGCGGGCAGTTTCCAGTTGCTGATCAGAAACCTGCTG\n+CGCAGCCACTTCTTTCAGGGTGTCGATCCAACTGTAACCGACGCCATCGGAGAACTGCTCTTTCTGCCGC\n+CAGGCCACGCTTGCAGGCAGATACGCTTCAAAACATTCACGCAGGATGTGTTTTTCCATTTTGCCGTTAC\n+CGCACATTTTATCCTGTGGGTTAATACGCATCGCCACATCAAGGAATTTTTTGTCGAGGAACGGAACGCG\n+TGCTTCCACGCCCCAGGCTGACATCGCTTTGTTGGCACGCGCGCAGTCATACATATGCAGGGCCAGCAGT\n+TTACGCACCGTCTCTTCATGCAGTTCTTTGGCATTCGGTGCTTTGTGGAAGTAAAGATAACCGCCGAACA\n+CTTCATCAGAACCTTCACCGGACAGCACCATTTTAATGCCCATCGCCTTGATCTTACGCGACATTAAATA\n+CATCGGTGTTGAAGCGCGAATAGTGGTCACATCATAAGTTTCGATGTGGTAAATCACGTCGCGGATGGCA\n+TCCAGACCTTCCTGTACAGTGAAGTGAATTTCGTGATGCACCGTGCCCAGATGGTTTGCCACTTCCTGGG\n+CTGCTTTCAGATCCGGTGAACCCGGCAGACCTACAGCAAAGGAGTGTAACTGCGGCCACCAGGCTTCAGA\n+GCGTTCCTGATCTTCCACGCGACGGGCTGCGTATTTCTTGGTGATAGCGGAAATAATTGAGGAATCCAGA\n+CCACCAGAAAGCAGCACACCGTAAGGCACATCAGACATCAGATGGCTTTTAACTGAATCTTCCAGTGCCT\n+GACGCAGCTCGTTTTTGTCGGTCACGTTATCTTTCACCGCATCGTAGTCGAACCAGTCGCGATGATAGTA\n+AGAACGGATTTCGCCGTCCTGGCTCCACAAATAGCTCCCCGCCGGGAACTCTTTAATCGTGCGGCAAACT\n+GGCACCAGCGCTTTCATTTCTGAGGCCACATACAGCTGACCGTGTTCGTCATACCCCATATACAGTGGGA\n+TGATCCCCAGATGGTCGCGACCAATCAGGTAGGCATCTTTTTCGCTGTCGTACAGTGCAAAGGCAAACAT\n+GCCCTGCAAGTCGTCGAGAAATTCCGGCCCTTTTTCCTGATACAGCGCGAGGATCACTTCACAGTCAGAC\n+CCGGTCTGGAACTGGTAACGATCGCCATATTCGGCGCGCAATGCCTGGTGGTTGTAGATTTCACCGTTTA\n+CCGCCAGTACGTGGGTTTTTTGTTGGTTGTAGAGAGGTTGCGCCCCCGCGTTAACGTCAACAATTGACAG\n+ACGTTCGTGGGCGAGAATGGCGTTATCGCTGGCATAAATACCGGACCAGTCCGGGCCACGATGACGCATC\n+AGGCGTGACAGCTCGAGGGCTTTCTTACGCAGCTCAACTGCGTCTGTTTTGATATCGAATACGCCAAAAA\n+TTGAACACATAACCTTCTCCGTTAACCTGGTATTTGTTGCTTGTTGTGTTTGCTTGTTTAAAAAAATGCC\n+GCAAAGCAGCACTGTGCGCAAGCGATTTGGCGGTGAAAAAATAAAAAACGTAATGGTGATTGTCGATTGG\n+TGAAAAAAGGTCTGGTGTGAGGATATATTTATTGATGAATCGATAATTTTTAGCGGGTTTTATTGAATGT\n+TTATATTTTACGGGGGCCAAATTGCTGACAAAGTGCGATTTGTTCATGCCGGATGCGGCGTGAACGCCTT\n+ATCCGGCCTACAAAAGCATGAAAATTCAATATATTGCAGGAGCTGCGTAGGCCTGATAAGCGTAGCGCAT\n+CAGGCAGTTTGGCGTTTGTCATCAGAGCCAACCACGTCCGCAGACGTGGTTGCTATTCAGATAACGTCGA\n+TTTCAGCGACTGACGGGTAAATCCAGCTGGGGCGGAAAGGCATACTGTCGATATCGTCGAGCGACGAAAC\n+ACCAGAAAGCACCAGAATCGTCTCCAGACCTGCCTGGAAGCCGGCCAGAATATCGGTACGCAGGTTATCG\n+CCGACAATCACCGTTTCTTCCGAATGCGCCTGCATTTTGTTTAATGCTGCGCGGATGATCCACGGGCTGG\n+GCTTACCAACATAGAACGGTTTGCGCCCGGAGATTTTCTCAATCCCTGCACACAACGCGCCACAAGCGGG\n+ATAAAAACCGCGCCCGTGGGTGTCCGGATTGGTGGCGATAAAACGTGCACCGTTAGCGACGAAATAGGCT\n+GCTTTATGCATCATGTCCCAGTTGTAGGAACGCGTTTCGCCAACAATCACGAAATCAGGGTTCACATCGG\n+TAATAGTGAAACCGGCTTTGTACAGTTCATGAATCAGTGCGCCTTCGCCCACCACATACGCTTTCTTGCC\n+TTCCTGGCGACGCAGGAAATCGGCAGTCGCCATCGCAGAGGTATAAAACACGCTGTCAGGTACATCGACA\n+CCTGCGGTGGCAAAGCGGTTCGCCAGATCTTGCCCAGTCTGCGAAGGATAGTTGGTCAGCAACACCAGCG\n+GCAGGCCTTTATCCATAATCCCGTGCAAAAATTCCGCTGCACCCGGTACGGCGACGTTATCGTGCATCAG\n+CACGCCGTCGATATCGCAAATTACATTTTTAATGGTCATGGACTACCCAGAATATTGACAACAATAAGCG\n+CCACTATAAAAGCACATTAATTTTCCAGCAAATGCTGGAGCAAAATACCGTTGAGCATGGCGCGTTTTAC\n+CAGCGCAAAAGCGCCGATTGCCGAGCGGTGATCCAGCTCAGAACGTACCACCGGCAGATTAGTGCGAAAC\n+GCCTTCAGCGCCTGGGTATTAATGCAGCTTTCAATAGCAGGGAGCAGCACTTTATCGGCTTCGGTGATTT\n+CACCGGCAATAACAATTTTTTGCGGATTAAATAAGTTGATAGCAATGGCGATGGTTTTACCCAGATGACG\n+ACCGACATACTCAATTACTTCCGACGCCAGACTATCGCCTTTGTTCGCGGCTTTGCAGATAGTTTTGATG\n'
b
diff -r 000000000000 -r 1f0a3e4497d4 test-data/NC_000913.ffn
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/NC_000913.ffn Wed Sep 06 13:23:14 2017 -0400
b
b'@@ -0,0 +1,1374 @@\n+>gi|49175990|ref|NC_000913.2|_337_2799_+\n+ATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTTGACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGCTGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGTTACTGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCTGAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCAGGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGCACCATTACCCCCATCGCCCAGTTCCAGATCCCTTGCCTGATTAAAAATACCGGAAATCCTCAAGCACCAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGGCATTTCCAATCTGAATAACATGGCAATGTTCAGCGTTTCTGGTCCGGGGATGAAAGGGATGGTCGGCATGGCGGCGCGCGTCTTTGCAGCGATGTCACGCGCCCGTATTTCCGTGGTGCTGATTACGCAATCATCTTCCGAATACAGCATCAGTTTCTGCGTTCCACAAAGCGACTGTGTGCGAGCTGAACGGGCAATGCAGGAAGAGTTCTACCTGGAACTGAAAGAAGGCTTACTGGAGCCGCTGGCAGTGACGGAACGGCTGGCCATTATCTCGGTGGTAGGTGATGGTATGCGCACCTTGCGTGGGATCTCGGCGAAATTCTTTGCCGCACTGGCCCGCGCCAATATCAACATTGTCGCCATTGCTCAGGGATCTTCTGAACGCTCAATCTCTGTCGTGGTAAATAACGATGATGCGACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTGTTTGTGATTGGCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAAAGCTGGCTGAAGAATAAACATATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCTCTGCTCACCAATGTACATGGCCTTAATCTGGAAAACTGGCAGGAAGAACTGGCGCAAGCCAAAGAGCCGTTTAATCTCGGGCGCTTAATTCGCCTCGTGAAAGAATATCATCTGCTGAACCCGGTCATTGTTGACTGCACTTCCAGCCAGGCAGTGGCGGATCAATATGCCGACTTCCTGCGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCAACACCTCGTCGATGGATTACTACCATCAGTTGCGTTATGCGGCGGAAAAATCGCGGCGTAAATTCCTCTATGACACCAACGTTGGGGCTGGATTACCGGTTATTGAGAACCTGCAAAATCTGCTCAATGCAGGTGATGAATTGATGAAGTTCTCCGGCATTCTTTCTGGTTCGCTTTCTTATATCTTCGGCAAGTTAGACGAAGGCATGAGTTTCTCCGAGGCGACCACGCTGGCGCGGGAAATGGGTTATACCGAACCGGACCCGCGAGATGATCTTTCTGGTATGGATGTGGCGCGTAAACTATTGATTCTCGCTCGTGAAACGGGACGTGAACTGGAGCTGGCGGATATTGAAATTGAACCTGTGCTGCCCGCAGAGTTTAACGCCGAGGGTGATGTTGCCGCTTTTATGGCGAATCTGTCACAACTCGACGATCTCTTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAATATTGATGAAGATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTGTTCAAAGTGAAAAATGGCGAAAACGCCCTGGCCTTCTATAGCCACTATTATCAGCCGCTGCCGTTGGTACTGCGCGGATATGGTGCGGGCAATGACGTTACAGCTGCCGGTGTCTTTGCTGATCTGCTACGTACCCTCTCATGGAAGTTAGGAGTC\n+>gi|49175990|ref|NC_000913.2|_2801_3733_+\n+ATGGTTAAAGTTTATGCCCCGGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGGTGACACCTGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTGGGAGCGTTTTTGCCAGGAACTGGGTAAGCAAATTCCAGTGGCGATGACCCTGGAAAAGAATATGCCGATCGGTTCGGGCTTAGGCTCCAGTGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGCGGCAAGCCGCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGCCGTATCTCCGGCAGCATTCATTACGACAACGTGGCACCGTGTTTTCTCGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGCAAGTGCCAGGGTTTGATGAGTGGCTGTGGGTGCTGGCGTATCCGGGGATTAAAGTCTCGACGGCAGAAGCCAGGGCTATTTTACCGGCGCAGTATCGCCGCCAGGATTGCATTGCGCACGGGCGACATCTGGCAGGCTTCATTCACGCCTGCTATTCCCGTCAGCCTGAGCTTGCCGCGAAGCTGATGAAAGATGTTATCGCTGAACCCTACCGTGAACGGTTACTGCCAGGCTTCCGGCAGGCGCGGCAGGCGGTCGCGGAAATCGGCGCGGTAGCGAGCGGTATCTCCGGCTCCGGCCCGACCTTGTTCGCTCTGTGTGACAAGCCGGAAACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAAC\n+>gi|49175990|ref|NC_000913.2|_3734_5020_+\n+ATGAAACTCTACAATCTGAAAGATCACAACGAGCAGGTCAGCTTTGCGCAAGCCGTAACCCAGGGGTTGGGCAAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCCGGAATTCAGCCTGACTGAAATTGATGAGATGCTGAAGCTGGATTTTGTCACCCGCAGTGCGAAGATCCTCTCGGCGTTTATTGGTGATGAAATCCCACAGGAAATCCTGGAAGAGCGCGTGCGCGCGGCGTTTGCCTTCCCGGCTCCGGTCGCCAATGTTGAAAGCGATGTCGGTTGTCTGGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTTCGGCGGTCGCTTTATGGCACAAATGCTGACCCATATTGCGGGTGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGATACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTACCGAATGTGAAAG'..b'ATCCTGTCCTCAAGCGTTACCAGATGCGGCGCATGGCGGATAACTTCATTATGCAAAGCGGTATGGATCTGTTTTATGCCGGATTCAGCAATAATCTGCCACCACTGCGTTTTATGCGTAATCTCGGGTTAATGGCGGCGGAGCGTGCTGGCGTGTTGAAACGTCAGGCGCTGAAATATGCGTTAGGGTTG\n+>gi|49175990|ref|NC_000913.2|_695581_695916_+\n+GTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACAAATTGGTTTTGAATTTGCCGAACATATTCGATACATTCAGAATTTGGTGGCTACGACGGGATTCGAACCTGTGA\n+>gi|49175990|ref|NC_000913.2|_695978_696184_+\n+ATGGCTGGGGTACCTGGATTCGAACCAGGGAATGCCGGTATCAAAAACCGGTGCCTTACCGCTTGGCGATACCCCAATAACCGGGCGGTGAACCGCTTACTCGAAGAAGATGGCTGGGGTACCTGGATTCGAACCAGGGAATGCCGGTATCAAAAACCGGTGCCTTACCGCTTGGCGATACCCCATCCGTACAACGCTTTCTGG\n+>gi|49175990|ref|NC_000913.2|_696185_696337_+\n+ATGGTGCGGGAGGCGAGACTTGAACTCGCACACCTTGCGGCGCCAGAACCTAAATCTGGTGCGTCTACCAATTTCGCCACTCCCGCAAAAAAAGATGGTGGCTACGACGGGATTCGAACCTGTGACCCCATCATTATGAGTGATGTGCTC\n+>gi|49175990|ref|NC_000913.2|_696736_698481_-\n+TTGCGCACAGTGCTGCTTTGCGGCATTTTTTTAAACAAGCAAACACAACAAGCAACAAATACCAGGTTAACGGAGAAGGTTATGTGTTCAATTTTTGGCGTATTCGATATCAAAACAGACGCAGTTGAGCTGCGTAAGAAAGCCCTCGAGCTGTCACGCCTGATGCGTCATCGTGGCCCGGACTGGTCCGGTATTTATGCCAGCGATAACGCCATTCTCGCCCACGAACGTCTGTCAATTGTTGACGTTAACGCGGGGGCGCAACCTCTCTACAACCAACAAAAAACCCACGTACTGGCGGTAAACGGTGAAATCTACAACCACCAGGCATTGCGCGCCGAATATGGCGATCGTTACCAGTTCCAGACCGGGTCTGACTGTGAAGTGATCCTCGCGCTGTATCAGGAAAAAGGGCCGGAATTTCTCGACGACTTGCAGGGCATGTTTGCCTTTGCACTGTACGACAGCGAAAAAGATGCCTACCTGATTGGTCGCGACCATCTGGGGATCATCCCACTGTATATGGGGTATGACGAACACGGTCAGCTGTATGTGGCCTCAGAAATGAAAGCGCTGGTGCCAGTTTGCCGCACGATTAAAGAGTTCCCGGCGGGGAGCTATTTGTGGAGCCAGGACGGCGAAATCCGTTCTTACTATCATCGCGACTGGTTCGACTACGATGCGGTGAAAGATAACGTGACCGACAAAAACGAGCTGCGTCAGGCACTGGAAGATTCAGTTAAAAGCCATCTGATGTCTGATGTGCCTTACGGTGTGCTGCTTTCTGGTGGTCTGGATTCCTCAATTATTTCCGCTATCACCAAGAAATACGCAGCCCGTCGCGTGGAAGATCAGGAACGCTCTGAAGCCTGGTGGCCGCAGTTACACTCCTTTGCTGTAGGTCTGCCGGGTTCACCGGATCTGAAAGCAGCCCAGGAAGTGGCAAACCATCTGGGCACGGTGCATCACGAAATTCACTTCACTGTACAGGAAGGTCTGGATGCCATCCGCGACGTGATTTACCACATCGAAACTTATGATGTGACCACTATTCGCGCTTCAACACCGATGTATTTAATGTCGCGTAAGATCAAGGCGATGGGCATTAAAATGGTGCTGTCCGGTGAAGGTTCTGATGAAGTGTTCGGCGGTTATCTTTACTTCCACAAAGCACCGAATGCCAAAGAACTGCATGAAGAGACGGTGCGTAAACTGCTGGCCCTGCATATGTATGACTGCGCGCGTGCCAACAAAGCGATGTCAGCCTGGGGCGTGGAAGCACGCGTTCCGTTCCTCGACAAAAAATTCCTTGATGTGGCGATGCGTATTAACCCACAGGATAAAATGTGCGGTAACGGCAAAATGGAAAAACACATCCTGCGTGAATGTTTTGAAGCGTATCTGCCTGCAAGCGTGGCCTGGCGGCAGAAAGAGCAGTTCTCCGATGGCGTCGGTTACAGTTGGATCGACACCCTGAAAGAAGTGGCTGCGCAGCAGGTTTCTGATCAGCAACTGGAAACTGCCCGCTTCCGCTTCCCGTACAACACGCCAACCTCTAAAGAAGCGTACTTGTATCGGGAGATCTTTGAAGAACTATTCCCGCTTCCGAGCGCCGCTGAGTGCGTGCCGGGCGGTCCTTCCGTCGCTTGTTCTTCCGCTAAAGCGATCGAATGGGATGAAGCGTTCAAGAAAATGGACGATCCGTCTGGTCGCGCGGTTGGTGTTCACCAGTCGGCGTATAAG\n+>gi|49175990|ref|NC_000913.2|_698797_699549_-\n+ATGACCATTAAAAATGTAATTTGCGATATCGACGGCGTGCTGATGCACGATAACGTCGCCGTACCGGGTGCAGCGGAATTTTTGCACGGGATTATGGATAAAGGCCTGCCGCTGGTGTTGCTGACCAACTATCCTTCGCAGACTGGGCAAGATCTGGCGAACCGCTTTGCCACCGCAGGTGTCGATGTACCTGACAGCGTGTTTTATACCTCTGCGATGGCGACTGCCGATTTCCTGCGTCGCCAGGAAGGCAAGAAAGCGTATGTGGTGGGCGAAGGCGCACTGATTCATGAACTGTACAAAGCCGGTTTCACTATTACCGATGTGAACCCTGATTTCGTGATTGTTGGCGAAACGCGTTCCTACAACTGGGACATGATGCATAAAGCAGCCTATTTCGTCGCTAACGGTGCACGTTTTATCGCCACCAATCCGGACACCCACGGGCGCGGTTTTTATCCCGCTTGTGGCGCGTTGTGTGCAGGGATTGAGAAAATCTCCGGGCGCAAACCGTTCTATGTTGGTAAGCCCAGCCCGTGGATCATCCGCGCAGCATTAAACAAAATGCAGGCGCATTCGGAAGAAACGGTGATTGTCGGCGATAACCTGCGTACCGATATTCTGGCCGGCTTCCAGGCAGGTCTGGAGACGATTCTGGTGCTTTCTGGTGTTTCGTCGCTCGACGATATCGACAGTATGCCTTTCCGCCCCAGCTGGATTTACCCGTCAGTCGCTGAAATCGACGTTATC\n+>gi|49175990|ref|NC_000913.2|_699597_699930_-\n+ATCAAAACTATCTGCAAAGCCGCGAACAAAGGCGATAGTCTGGCGTCGGAAGTAATTGAGTATGTCGGTCGTCATCTGGGTAAAACCATCGCCATTGCTATCAACTTATTTAATCCGCAAAAAATTGTTATTGCCGGTGAAATCACCGAAGCCGATAAAGTGCTGCTCCCTGCTATTGAAAGCTGCATTAATACCCAGGCGCTGAAGGCGTTTCGCACTAATCTGCCGGTGGTACGTTCTGAGCTGGATCACCGCTCGGCAATCGGCGCTTTTGCGCTGGTAAAACGCGCCATGCTCAACGGTATTTTGCTCCAGCATTTGCTGGAAAAT\n'
b
diff -r 000000000000 -r 1f0a3e4497d4 test-data/NC_000913.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/NC_000913.gff Wed Sep 06 13:23:14 2017 -0400
b
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b
diff -r 000000000000 -r 1f0a3e4497d4 test-data/NC_000913.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/NC_000913.out Wed Sep 06 13:23:14 2017 -0400
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b
diff -r 000000000000 -r 1f0a3e4497d4 test-data/contigs.faa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/contigs.faa Wed Sep 06 13:23:14 2017 -0400
b
b'@@ -0,0 +1,2590 @@\n+>1506879_1_1328_+\n+HNIPLFFSFRFELICILLKKLGKINTERTIQTYLVNKKGYRTMNILYCGDKPMQKGILLSSMSLVENVDEPLNIYIITVDYREKGVNYKPVDKVFAEYLKKELNKSDIDVNVSLIDITRYFVEELPEANMQTRFTACCMLRLFADKTDINERLLYLDTDVLCRKNFSDFYYQDMEGIEIAGVSDYYGRWIFGDGYINSGVMLMNMNMIRENGLLEKCREQCIRKEMFMPDQTAINTFATRVNLCGHRFNDQRRLHGNTVFQHFTTTFRVFPVIRTVAVKPWEIDKMHNVLGLHEYDALLESYNREYEEYKAVSRIPVVFSINEKYAPYLAVCLKSLAVHVAVDERYRIIVMCDNVKNITMIQLRNVIKDYENIDIEFVDIRKKMHEFSESFGQTVTDRQENRLYSGEFTLTIYFRLFIAELFPELDKAVYIDSDTVINDDIA\n+>1506881_43_216_-\n+MRDVFVEEVEIKDPEEYIRKKFQGKDVSYDKTVLADGTIVFDITTSQIKQRCSFTEI\n+>1506881_267_449_-\n+MAVEKYCKQNGIAGRLLPVPREISASCGLAWAVPLEQKGELAAVEAEFADEIEGKWSLEL\n+>1506881_500_1117_-\n+MEQKYTVDARGEQCPIPVVRTKKVLDGILGDAELTVLVDNETAVQNLTRMGKHAGAEVLSEKKSDNEFQVVIRVKDRKPTEGGEETAECIPDVKGDFVIAVDTAIMGRGNDELGKVLMKGFIFAVTQLEKLPKTILFYNGGATLTTEGSDSLDDIKSLEAQGVEIKTCGTCLNYYGLTDKLKVGEVTNMYDIVENLAKASKVVKP\n+>1506883_1_1328_+\n+KQIAIAADVPIIPGVDHAMKSYEEAAKIADMVGYPIMLKASNGGGGRGMRIVNDPADLEKEFNEARNESKKAFGDDMIFVEKYLKGPKHIEVQVIGDNYGNVVHLFDRDCSVQRRHQKVVEYAPAFTIPDETREKIFDAAIRLCKNVGYVNAGTLEFLVDRDNNPYFIEMNPRIQVEHTVSEMVTGIDIVQAQILVAEGYALDSEEIHIKSQEDVTCNGYSIQTRVTSEDPANNFLPDTGEMTVYRSGSGNGIRLDGGCAYVGAVVSPHYDSLLVKIISHDRTFAGAVRKSERALQEMRIRGVKTNIPFLINVLNHPTFQSGQCYTTFIEETPELFRLTHSLNRATKIIEFIGDRIINSDMGKKKQFDNRILPTFDHDKPVYGARDEFLKLGAEGYMQKILKEEKLYVTDTSMRDAQQSLVATRMRSKDLCGAAYATNAFM\n+>1506885_1_235_+\n+PSSLKNYFQGVYGKNISTWLREARMSVASSALREGNQPVAEIAASVGYENASKFSAAFKNFLGETPLEYRRQSRCGI\n+>1506885_261_857_+\n+MNEKANTKKSKRLVSAGVFIALYFVVFLIIGMCCMPAPPLYLCMSSLIALVAAPVYLMLLAKAPMHGPIFIAAILPCLFLLLQGNIWVVAVTGAVAGILAEIIAGIGKFRNNKLNILSYVFFSQNLLGGFLPIWIMRDYYFADTLERGMSADFCNTLEAMTPIWVLFLMIAGTVIFALIGCLIGKKMFRKHFEKAGMI\n+>1506885_899_1328_+\n+MLILVVNLFLLLSHSLAFELVLVFGCLILIAIDGQPKSAFHFLIAFFIMLGIDQIITPYMSGFIFTLVSFITVALRKFLPCFILGKWILTKTEVSEFVAVMWKLRLPQTAIIPLSVVFRYFPTIKEEWDSIRAAMKMRGIHIS\n+>1506887_1_1328_-\n+EQAGRTLLLDKTLEYVRTPHVQHTANEWQTTEHNRHIRSNRVYQMNYYIYENTRYDKEAQKSIPYSWTLTWSVRTNSPSRTQAKIAGQDRKVFTDKAAMEKYLNGRIKAYDRLFTEISPPIPQEYADYFKVNGMLMPDYTIEGEEPPQQQQAAAIPENTGQEKEREHMSEQFSIMIGNRSRFDAGDPGGYWLDMPATKEQLHEAMRNVGITADNPQDFSIRGYSDDPEKHIALPYEMVCAADVDELNFLAARLEQLDPAEVGKLNAALQQKNGLANIGQVIDFTYNVDFYVHIPEVHNYHDLGDYYLNQSGMVQMPEEWKGGIDLSTFGRNAAAQEKGAFTEYGYIVESGDEWERQFEGREVPEEYRIMSYPQPERGEQDKAYMDAAETQQADAQAAEPQQPRPVVPIILTSEKPAEKVKEITARLEQGVQAIFDSDRYKEF\n+>1506889_1_304_-\n+MAFWKKSEDPWDIAPDQRRTAPEPAEKAPGLLDTLRGDWDAMRAEWQETRESLKLPPEKCPWCGKDMEQGFLMGGRGVAWHRGIPTGKVRWLSPGGENIMR\n+>1506889_307_495_-\n+MLKVFNVIGVIVLLLLLRKLIWCLRWLWCWKHDRETPPPIGWLPSRDGGRFDAHVQKFDGED\n+>1506889_531_758_-\n+MGFLLGLPLKLLALVFGLLRVLIPVLLLILVVRWLWRKYGGHKRSESAKKDEPHFKGPVYTVDYKEVKDDDRHKE\n+>1506889_760_1328_-\n+AALAEVMPEEPADIRIFNQAMMELGATVCGPNTAPRCDDCPVSGLCLGRQRGTAETLPVKKAKKERRVEEKTVFLLMRDRKIALRKRPKTGLLAGLWEFPNVEGTLDETAAGAAVEAVGLSVIDWQSRLTAKHIFTHVEWRMTGYALTVRGDGPAELEWVDAAGLAARSVPSAFARYYEEAKRELEMK\n+>1506891_61_957_-\n+MMLVTILFGALAALFAALFFLQRANLRRACRELRQINQEGGTRRLHLSSPDGEMEALFEEINRALDRRQSEEIQHMLAEKELRRQIANISHDLRTPLTSIIGYLQLAQADGTSTEERTHALEVIGARTRSLQMLISGFYDLSRLDANEYSLNLQQVDLGRSLCAQLASFYDDFTRKNLVMHVDVPQRLPLVLADEDAAQRIFVNLLQNVLRYAESEVWVAVRAGTTITTVFTNDTSLVSQEDVPHVFDRFYTGDQTRSGHNTGIGLAIVKRLAEQMGCEVSASLAGNRFSISVSWKTI\n+>1506891_981_1328_-\n+LPLWLGMLGMLNLLAFAFRSNTLFGFGAMLLFSFPGPVLGLMRGVVPELSTFYKLTITRQFEQLTGGAGFMLGGPGPAARPVEPELIPWCLLVGLAWFIGSSIAGYLLFRRRELK\n+>1506893_1_875_-\n+MSTENESRQEGAANEENQNVSRDGGYKSYNRDSNYNRYNNDGEQRPYRPRTNSYNREGGDRPYRSSYNNGDRPSYNRYNNNGDRPQRPRFNPNSEDGGEQRSYRPRTNYNREGGEQRPYTPRPRFNNGEEGGERQYRPRTNYNREGGEQRPYTPRPRTGGYNREGGEQRPYTPRPRFNSGEGGEQRSYTPRPRTGGYNQGGDRPYRPRTGGYQGGGYNRPYRPRTADYNPNAKYSLKKQIEYKDILTDPNEPIRLNKFLANAGICSRREADEFITAGVVSVNGEVVTELGT\n+>1506893_951_1328_-\n+LSSKLPVSRLQRDLTDSTVLRNVGVPFGHIVIAIQSSLKGLRKLLLNEKAIYADLDNCWSVVAEAIQTILRREAYPHPYEALKALTRTNQAITEGAIKEFIETLNVSEDIKKELRVITPHNYTGI\n+>1506895_93_1241_-\n+MTYILLQHYWWFLVSLLGALLVFLLFVQGGQSLLFTIGKTELQQKMLLNSTGRKWEFTFTTLVTFGGAFFASFPLFYSTSFGGAYWVWMLILACFVLQAVSYEYQSKKGNLLGKKTYQAFLLLNGILGPILLGTAVGTFFSGAEFVVNKGQLTDVAMPVISTWANPWHGLEAAFVFWNICLGLAVFFLARIQALLYFINNIDDAEIVKHSRKHLVIETALFLVFFLVFLIHLLLADGFAVDPVTQEVYMQPHKYFINLIEMPAVLVVLLAG'..b'EGVFLGGNISPGLEMRFNGLHRFTARLPLVTPTETYGGIGQSTEEAIRNGVMSGMLFEVQQYIECFLGQYPEGHVLITGGNAHFLERHLTPDILFCKYLSFVGLNEILKYVKKSNY\n+>1508195_250_1353_-\n+LLLIPIAFGVLLANFPGGEMGVVQADENGMVMVNGALKNIWEMPLHEIAHDLGLMNFIYYMLIKTGFLPPIIFMGVGALTDFGPMLRNLRLSIFGAAAQLGIFTVLLVAILMGFTPKEAASLGIIGGADGPTAIFTTIKLAPHLLGPIAIAAYSYMALVPVIIPLVVKIWCTKKELSINMKEQEKKYPSSVEIKNLRVLKIVFPIVVTTVVALFVPSAVPLIGMLMFGNLIKEIGSDTSRLFDAASNSIMNAATIFLGLSVGATMTTEAFLNWTTIGIVIGGFLAFALSISGGILFVKLVNLFTKKKINPLIGATGLSAVPMASRVANEIALKYDPKNHVLQYCMASNISGVIGSAVAAGVLISFLQ\n+>1508197_1_128_+\n+MAFFDHVSFEWKEDRVYMKRWVNMNSQALERPVVTAKICES\n+>1508197_174_530_+\n+MINTTKQILMQMDVKEEARMEIKKPAIAGTLESSDCQVTVEAGEGKVDFSLESAVINQYGNQIKKVAYETLENLGIDNVKLTIVDKGALDCTIKARIEAAVYRSVGQIEDLPWGGAIR\n+>1508197_563_1353_+\n+MMFLNAQKPGLIKDPYIYKPDSIMLDLEDAVAENQKDAARFSLYHALKTINYRGCERVVRINGLDTPYWKEDIRCAVAGGCDAIRIPKTESAQDVKVVEAEVIQAEKDFGREEGSVLIMAAIESARGVMRALDICESSERLFGIALSGGDYTKDLQTHITGTGIELMGARQNMVIAARAAGVQCFDTVYTDLDDMDGFRQDVENIHLMGFDGKSIINPRQINIVHEIFTPKQKDIIFAEKVVREIDTKKAQGIGVFTVDGKMI\n+>1508199_1_231_-\n+MAKVLISPSKYLQGAGEMKNIGTYAANCGKKALVLISKGGYKRIGKMIEDSFAASDCDVVFDYFNGECCNSEINRLV\n+>1508199_422_721_+\n+VEGIILFYGSGIVIGIAVSAHMDTGIIRSNVISHKAGARLSKRLFLRDRKCGMKCFLVGSLCHASAAVGAISSQFLSFPAWVNRHSMGSRDLDHIFPKI\n+>1508199_732_1007_-\n+MAGGVLKLHPKIVVGNGAMNASKKYRGKIASVIMSYVKDMENDLKNARPERVFITHSGCDRETVEAVWFPAIAVWGRLAFCILRYDFSNTL\n+>1508199_1171_1296_+\n+MSVKCLPDGELPEDEKRNLAVRGLLLAATEDKYESIDYLLL\n+>1508201_1_553_-\n+MAECEDCDVILLPEMFTSGCMMIKKSAEVAFAAKESVANAYPVVEEKMLAWAKRQHALVMGSTVYRENGKYYNRLIAAFPEGNCRYYDKRHCFRMGGENEHFTPGDRQLTFEFRGVKIAAFICYDLRFPVWCRNTQNYDLAVFVANWPESRREVWKTLLKARAIENQAFVAGVNCVGEDDNGLT\n+>1508201_625_1263_-\n+MNTTIIGVAGGTASGKSTLVKKLQEAFEGESVITLCHDYYYKAHDDLSFEERTKLNYDHPGAFDTDMMIEDIIKLKKGRSVFRPVYSFVNHNRTDKTVKVEPAQVIIIDGILILENRTLRELMDVKVYVDTDPDVRLGRRLLRDVQERGRSIESVLTQYFCTVKPMHDEFVEPSKRYADIIIPEGGFNSVAVSMLIHNINSLIHHESERDRR\n+>1508203_1_1353_-\n+TSLTATNSGIVTAVRTAEHTADDGTIYTRVVFDLTGKKNYTITQSADKSKLTIAFKSVTVSDIAIRHNSSTDRDIIEVGGDSALGVSVYTLSNPSRIVVDIPNAVSELDSTFDVSALEYVTAGRAAMFNDTTLRLVFEVDGMAKYSYTTDNHAMTLQIFSSSMKNMSYDTSANKLYLQKKDTIQTGSVKINDHYLDGYTDVVLPGDYSETFGSGTYDIDNGVIKSIQVSTSGGKTTIRFNQSRISCYSITEEQERYVISVKNPQDVYSKVLLLDAGHGGSDPGASGNGLTEKNLTLTIMQKVANYLDGSGIKVYVTRNSDTYPTNSSRAQSANAIADAMVSIHMNSGSAVANGTEVLYKNHSNDTGSNLTSLKLAQLIQNSIVSATGNTNRGTKLRTDLLILNTTTVPAVIVETVFISNPGDALKISQEDYQNKVAKAIADAIEEAFTYP\n+>1508205_1_1353_+\n+IYPKLKDFNSNMNVSKSDKWEKLRSYSSEKKWNSVFAVAVDTTYTIQDQFYQNKVAYDNNIPYFKGTTWLLVLSIILFLGATIWLTLEAGRTAEDEELHLNGFDHWKTEIAAVLIVLIWIVGSYIGIHFWNGNIYTMINDIPTYLKDGGTYFEYYYARGMDVSSAYMSASLYLPSLSIAELAEIYFYGVFTLGCFFMGYVSLIKRIKGRNLWKNSLLRVIVRFIYKIYDNRKKTTKTVLLLCGFFLVQGIAVLFRNGVTMLLVLLADVGVFYVVLNGLLLKEKLKKGIEEIALGNMEYQIPLQGLRGENLKLAEMINGIANGFHMAVEEAMKNERLKTDLITNVSHDIKTPLTSIINYVAILKQSDIADPKIQGYLDILEAKAQRLKTLTEDVVEASKVSSGNISLEYMDVDLVEMIQQTEGEMAEKFEARNLKMIVNLPAEPAVVHVDG\n+>1508207_1_777_+\n+QFNKEIVDATYDLIPAVKPQVAMYEQFGIEGVKAFKKTVDYCHEKGLVVIGDVKRGDIGSTSEAYAVGHLGKVKVGSQQFAGFDEDFATVNPYLGSDGIKPFIKVCKEENKGLFILVKTSNPSSGEFQDRLIDGRPLYEWVGEQVDAWGKEHMGDSYSYIGAVVGATYPEQGKVLRKLMPKTFILVPGYGAQGGRGKDLVHFFNEDGLGAIINSSRGIIAAYKQEAYAQFGAQNFAEASRQAVKDMIADIDGALQAAK\n+>1508207_803_1353_+\n+MKKKEICTVIRQKEIGDGIFSMWIQTENIGKEAKPGQFVSLYSKDGSKLLPRPISLCEIDRENSRLRLVYRVTGAKTGTEEFSRLKAGDTIPVIGPLGNGFPVEKAEGKRAFLMGGGIGVPPILELAKQMQCEKKQIVVGYRNAQTFLKEEFEAAGELYISTEDGSVGTKGNVMDAIREQKLE\n+>1508209_13_1221_-\n+VLGMLEKNIYIRIIFTLNTCDMKQLTVVFALLCIFACSSEDIVSTVEESVKPANEVAIQTVNLLDSLEIMDYIYSIIGPMAKTRSNLPGGGYILPDNWDSQLTDEQRELIRNSFPRPLFSAERNALRKSFPLVEYSNTVVMNYPSSGYNCFAYSLGFNNKWIEFSTWDQVRYGYENASSVYHAAYDYMKGATSISRYYPVVWGWGNTPLHASLGGSPHCEAPYSKMGRMWLLWHLVSVFSNGMYGVPVETYGAVSPTRSLSEIDANAMKEISEDIHENIIFSPDELMMIARKVKTCRDSSRFESLFNEWKEAWHYSLSNNTATTRNLPQYADLKAMGKEIIPLLIEKMVTEEDNFFAIRLYEDLQDNPNLIIRYANDDPHQLEGLQQTTKKTIKKWLEYNSN\n+>1508211_1_900_+\n+PVLSGKAVDMILGPGQVDFAGLGKIAIAMAATIACTALAQWLMNVVNNRITFQVVRDMRVRAFGQLEILPLKYMDAHRPGDAISRITTDVEQFSDGLLMGFTQLFTGVLTILGTLGVMLFIDWRIALVVVALTPLSIFVARFIATHTYSMFKVQSETRAEMTSLVEELVGNEHLVRAFGYERRAEERFDKINLDLQKCGVKATFFSSTTNPCTRFVNALVYAAVGVLGAFVAIAGGITVGQLSVFLNYANQYTKPFNDISDVMTELQNALACAQRVFDLIDETPIVPDGPDAVALPHGA\n'
b
diff -r 000000000000 -r 1f0a3e4497d4 test-data/contigs.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/contigs.fasta Wed Sep 06 13:23:14 2017 -0400
b
b'@@ -0,0 +1,10000 @@\n+>1506879 length 1328 cvg_4.0_tip_1\n+CATAACATTCCTCTATTCTTTAGTTTTCGTTTTGAACTTATATGTATTTTACTTAAGAAATTGGGGAAAATCAATACAGAGAGGACAATTCAGACATATT\n+TAGTAAATAAGAAAGGATACAGAACTATGAACATATTGTATTGCGGGGATAAACCTATGCAGAAGGGAATTCTATTATCTTCAATGTCTCTTGTTGAAAA\n+TGTGGACGAACCGTTAAATATATATATTATTACGGTTGATTACAGGGAAAAAGGTGTTAATTACAAACCGGTTGATAAAGTATTTGCAGAGTATCTTAAA\n+AAAGAATTGAATAAATCGGACATTGATGTAAATGTTTCACTTATTGATATTACAAGATATTTTGTTGAGGAACTGCCAGAGGCAAATATGCAGACAAGGT\n+TTACTGCATGCTGTATGCTGCGCCTGTTTGCTGATAAGACAGATATTAATGAAAGACTTCTTTACCTTGATACAGATGTGCTTTGCAGGAAGAATTTCAG\n+CGACTTCTATTATCAGGATATGGAGGGGATAGAGATTGCGGGAGTTTCTGACTATTATGGCAGATGGATTTTTGGTGATGGTTACATTAATTCCGGTGTA\n+ATGCTTATGAATATGAATATGATACGGGAGAATGGACTTTTGGAAAAATGTCGTGAACAATGCATAAGAAAGGAAATGTTTATGCCTGACCAGACGGCTA\n+TTAATACATTTGCAACAAGAGTCAATCTGTGTGGACACAGGTTTAATGACCAGAGGAGACTGCATGGCAACACTGTTTTTCAGCATTTTACAACTACGTT\n+CCGTGTATTTCCGGTAATAAGAACTGTTGCGGTCAAACCGTGGGAGATTGACAAAATGCATAATGTACTTGGGCTTCATGAATATGATGCACTTCTTGAA\n+TCTTATAACAGAGAATATGAGGAATACAAGGCCGTTTCGCGTATTCCGGTGGTTTTCTCTATTAATGAAAAGTATGCACCGTATCTGGCTGTGTGTCTTA\n+AATCTCTGGCTGTACATGTGGCTGTGGATGAGCGTTACCGCATTATTGTTATGTGCGATAATGTGAAGAATATTACTATGATTCAGCTTCGCAATGTAAT\n+AAAGGACTACGAAAACATAGATATTGAATTCGTTGATATAAGAAAGAAAATGCATGAATTTTCAGAAAGCTTTGGACAGACCGTTACAGACAGGCAGGAA\n+AACAGGCTTTATTCAGGCGAGTTTACGTTGACAATATATTTCAGGTTATTTATTGCAGAGCTTTTTCCTGAATTAGATAAGGCTGTATATATTGATTCGG\n+ACACGGTAATAAATGATGACATTGCAAA\n+>1506881 length 1328 cvg_4.0_tip_1\n+CAGGTGTAAATATAATCCCAAAATCATATTATAACACAGCCGCTAAATCTCTGTAAAGGAACATCTCTGTTTTATCTGTGATGTTGTGATATCAAAGACT\n+ATGGTCCCATCGGCGAGAACCGTCTTGTCATAGGAGACATCCTTTCCCTGAAACTTCTTTCTGATATATTCCTCCGGGTCTTTGATTTCTACTTCCTCTA\n+CAAATACGTCACGCATCTGATTTCTGGGACATTTATTAAAAATCTCCCAGATCACCTCGTATTCTTTCATAATTCCAGACTCCATTTTCCCTCAATCTCA\n+TCTGCAAATTCTGCTTCTACTGCCGCCAGTTCTCCTTTCTGTTCCAGCGGCACAGCCCATGCAAGGCCGCAGCTTGCAGAAATTTCTCTTGGTACGGGAA\n+GCAGTCTTCCTGCAATCCCATTCTGTTTACAGTATTTCTCTACTGCCATAGCACCGCTGGTGCTGAAAAAGGTCAGAAGATATCTCGGAATCTTTCTGAT\n+CATGGTTTCACTACTTTGGAAGCTTTTGCAAGATTTTCTACGATATCATACATATTTGTAACTTCTCCGACCTTAAGCTTATCTGTCAGTCCATAATAGT\n+TCAGACAGGTTCCACAGGTTTTGATCTCCACGCCCTGTGCTTCCAGACTCTTTATATCGTCAAGAGAATCTGAACCCTCTGTCGTCAGAGTTGCACCGCC\n+ATTATAAAAAAGGATGGTCTTTGGAAGCTTTTCAAGCTGAGTCACTGCAAAAATAAATCCCTTCATCAGGACTTTTCCCAGTTCATCATTTCCTCTTCCC\n+ATGATTGCGGTATCTACCGCGATCACAAAGTCACCCTTGACATCCGGGATACATTCTGCGGTTTCTTCTCCTCCTTCAGTTGGTTTCCGATCTTTTACAC\n+GAATGACAACCTGAAATTCATTGTCGGATTTTTTCTCTGAAAGTACTTCTGCACCTGCATGTTTCCCCATTCTGGTGAGATTCTGCACTGCGGTCTCATT\n+ATCCACCAAAACTGTGAGCTCAGCATCTCCCAGAATGCCATCCAGAACCTTCTTGGTCCTGACAACCGGAATCGGACACTGTTCGCCTCTTGCATCTACT\n+GTATATTTCTGTTCCATAAGAGCAACCTCCCTGTATTCATTTTGCGATATTTTCCTGCATTTACATTGTTTTTATTGTACCAGACCTTCTGTTTTTTTGC\n+AAATCTGCCTTCCACACAATCTCCGGCTTTTCTTTCATAAGAGAATACCGCCTTCCACATTCATAGCGAAACATCTTGCGGAATATTATCTGTAAACATT\n+AAACAAACTTTTTATTTCTTTATAAAAA\n+>1506883 length 1328 cvg_3.0_tip_1\n+CCAAACAGATTGCCATTGCAGCAGATGTACCGATCATCCCTGGAGTAGATCACGCGATGAAATCTTATGAAGAGGCAGCGAAGATCGCAGACATGGTCGG\n+ATATCCGATTATGCTGAAAGCTTCCAACGGTGGTGGCGGACGCGGTATGCGTATTGTCAATGATCCGGCTGATCTGGAAAAAGAATTCAACGAGGCGAGA\n+AATGAATCTAAAAAAGCTTTCGGTGATGATATGATCTTCGTTGAGAAGTATCTGAAAGGACCAAAGCATATTGAGGTTCAGGTGATCGGAGATAATTACG\n+GCAATGTTGTGCATCTGTTCGACCGTGACTGCTCTGTGCAGAGACGTCACCAGAAGGTCGTAGAGTATGCGCCGGCATTTACCATTCCAGACGAGACAAG\n+AGAGAAGATTTTTGATGCAGCAATCCGTCTTTGTAAAAATGTTGGATATGTCAATGCAGGAACACTGGAGTTTCTGGTAGACAGAGATAACAATCCATAC\n+TTTATTGAAATGAACCCTCGTATTCAGGTAGAGCATACAGTCAGTGAGATGGTGACAGGAATTGATATCGTGCAGGCTCAGATCCTGGTTGCAGAAGGAT\n+ATGCTCTTGATTCAGAAGAGATACATATTAAATCACAGGAAGATGTTACATGTAACGGATATTCTATTCAGACTCGTGTTACTTCTGAAGATCCGGCAAA\n+TAACTTCCTGCCGGATACAGGTGAGATGACAGTATATCGTTCCGGTTCCGGTAATGGTATCCGTCTGGACGGTGGCTGTGCATATGTCGGAGCCGTTGTA\n+TCACCACACTATGACAGTTTGCTTGTAAAGATTATTTCTCATGACCGTACCTTTGCAGGTGCAGTGAGAAAATCCGAGCGTGCCCTTCAGGAGATGCGTA\n+TCCGTGGAGTTAAGACAAATATTCCGTTCCTGATCAATGTGCTGAACCACCCGACATTTCAGTCCGGTCAGTGTTACACAACATTTATCGAGGAGACACC\n+GGAGTTATTCCGCCTGACACACAGCCTGAACCGTGCGACTAAGATCATTGAGTTTATCGGTGATCGTATCATCAATTCTGACATGGGTAAGAAGAAACAG\n+TTCGATAACCGTATTCTGCCGACATTTGACCATGAT'..b'CACAGAGGCTGAAGACACTGACGGAAGACGTTGTTGAGGCATCCAAGGTAAG\n+CAGTGGGAATATTTCTCTGGAGTATATGGATGTAGATCTTGTGGAGATGATCCAGCAGACGGAAGGTGAGATGGCTGAGAAGTTTGAGGCAAGGAATCTG\n+AAAATGATCGTCAATCTGCCGGCAGAACCTGCGGTTGTTCATGTAGACGGGCG\n+>1508207 length 1353 cvg_5.0_tip_1\n+CAGTTCAACAAAGAGATCGTGGATGCTACCTATGATCTGATCCCGGCGGTAAAACCACAGGTTGCCATGTATGAGCAGTTTGGTATCGAAGGTGTGAAAG\n+CGTTTAAAAAGACCGTGGATTACTGCCATGAAAAAGGACTGGTAGTTATCGGTGATGTAAAACGTGGAGATATCGGTTCTACTTCCGAGGCCTACGCGGT\n+AGGTCATCTGGGAAAAGTAAAAGTAGGTTCCCAGCAGTTCGCAGGATTTGATGAGGATTTCGCTACGGTCAATCCGTATCTCGGTTCTGACGGCATCAAA\n+CCGTTCATCAAGGTCTGCAAAGAAGAAAACAAAGGTCTGTTTATCTTGGTAAAAACATCCAATCCATCCAGTGGAGAATTCCAGGATCGTCTGATCGACG\n+GCCGTCCACTGTATGAGTGGGTAGGAGAACAGGTAGACGCATGGGGCAAAGAACATATGGGAGATTCTTATAGTTATATCGGCGCGGTCGTAGGAGCAAC\n+TTATCCAGAACAGGGAAAAGTATTAAGAAAACTGATGCCGAAGACCTTTATTCTGGTACCTGGCTACGGGGCACAGGGCGGAAGAGGAAAGGATCTGGTG\n+CATTTCTTTAATGAAGACGGACTGGGTGCGATCATCAACTCTTCCAGAGGTATCATCGCAGCATACAAACAGGAAGCATATGCACAGTTCGGTGCACAGA\n+ATTTTGCAGAAGCATCCCGACAGGCAGTGAAAGATATGATCGCAGATATCGACGGTGCACTGCAGGCGGCAAAATAAACTGGAATAGACAGGAGTATCGA\n+ACATGAAAAAGAAAGAAATCTGTACTGTGATCCGTCAGAAAGAAATTGGTGACGGAATCTTCAGCATGTGGATCCAGACGGAAAACATTGGGAAAGAAGC\n+AAAACCGGGACAGTTCGTATCGTTGTATAGTAAGGATGGAAGTAAACTACTTCCGCGTCCGATCAGTCTTTGTGAGATCGACCGGGAAAACAGCCGACTT\n+CGTCTGGTGTATCGTGTCACGGGAGCGAAGACCGGAACCGAAGAGTTTTCCAGACTGAAAGCCGGAGATACGATCCCGGTGATCGGACCGCTGGGAAATG\n+GCTTCCCTGTAGAAAAAGCAGAAGGAAAACGAGCTTTTCTGATGGGCGGAGGTATCGGAGTACCGCCGATCCTGGAACTGGCAAAACAGATGCAGTGTGA\n+GAAAAAACAGATCGTTGTGGGATACCGTAACGCGCAGACGTTCTTAAAAGAAGAATTCGAAGCAGCCGGAGAACTGTATATTTCCACAGAAGATGGCAGT\n+GTGGGAACAAAAGGAAATGTAATGGATGCGATCCGGGAACAGAAATTGGAAGC\n+>1508209 length 1353 cvg_16.7_tip_0\n+CCCAAGATAACTTTAATTGGAATTATATTCTAACCACTTCTTTATAGTTTTTTTGGTTGTTTGTTGTAATCCTTCAAGTTGGTGTGGATCATCGTTCGCA\n+TATCGTATTATCAGATTAGGATTATCTTGTAGATCTTCATACAATCTTATTGCAAAGAAATTATCCTCTTCTGTTACCATCTTCTCAATCAATAATGGAA\n+TGATTTCTTTTCCCATAGCCTTTAAATCGGCATATTGAGGTAAATTTCTTGTAGTAGCAGTGTTATTACTAAGCGAGTAATGCCATGCTTCCTTCCATTC\n+ATTAAACAGAGATTCAAACCTTGAACTATCTCTACATGTTTTTACTTTTCTAGCAATCATCATCAACTCATCCGGTGAGAAGATTATATTTTCGTGAATA\n+TCCTCACTTATTTCTTTCATTGCATTAGCATCTATTTCACTTAGACTACGGGTAGGAGAAACTGCCCCATAGGTTTCCACAGGAACTCCATACATTCCAT\n+TAGAAAACACACTTACAAGGTGCCACAATAGCCACATACGCCCCATCTTAGAATAAGGTGCCTCGCAATGGGGACTACCTCCAAGAGATGCATGCAGAGG\n+GGTATTTCCCCAACCCCAAACTACAGGATAGTATCTTGATATTGAGGTTGCCCCTTTCATGTAATCATAAGCGGCATGATACACGGAACTCGCATTTTCA\n+TATCCATATCTTACTTGATCCCAAGTACTAAACTCTATCCACTTATTATTAAACCCCAACGAATAGGCAAAACAATTATATCCAGATGACGGATAATTCA\n+TAACAACTGTATTGGAATATTCAACTAAAGGAAACGATTTCCTTAAAGCATTCCTTTCAGCAGAAAAGAGAGGTCGTGGGAAAGAGTTCCTGATCAATTC\n+GCGCTGTTCATCTGTTAATTGAGAATCCCAATTATCAGGAAGAATATACCCTCCCCCTGGTAGATTTGATCGTGTCTTAGCCATCGGTCCAATAATGCTA\n+TAAATATAATCCATAATTTCAAGGCTATCAAGCAAATTAACAGTTTGTATAGCCACTTCATTAGCCGGCTTTACAGATTCCTCAACGGTACTTACAATAT\n+CTTCGCTACTACAAGCAAAAATACACAACAGAGCGAATACTACAGTTAATTGCTTCATATCACAAGTATTTAAGGTGAATATTATACGAATGTATATATT\n+TTTTTCGAGCATTCCTAACACTTTTCTGTTTTTTTACTCAATAATATTCCATTCTTTTGTTATTAAATGATATAGATGCTAGTGACTTTAAAAACCTTTT\n+GAATATTTTAAAATAGCAGCAGCCAGAGGAGATGCAATCGCATGGTTAAATCT\n+>1508211 length 1353 cvg_5.0_tip_1\n+CCCCGGTACTGTCCGGTAAGGCCGTGGATATGATCCTGGGACCCGGTCAGGTTGATTTTGCAGGCCTTGGCAAAATTGCGATAGCGATGGCTGCCACGAT\n+TGCCTGCACAGCGCTGGCCCAGTGGCTGATGAATGTCGTCAATAACCGCATTACCTTTCAGGTCGTGCGTGATATGCGTGTCCGTGCGTTTGGCCAGTTG\n+GAGATTCTGCCGCTCAAATATATGGACGCCCACCGCCCCGGCGATGCTATCAGCCGCATTACCACCGACGTGGAGCAGTTCAGCGACGGTCTGCTGATGG\n+GCTTTACCCAGCTGTTCACCGGCGTGCTGACGATTTTGGGCACGCTGGGAGTCATGCTGTTCATCGACTGGCGCATTGCGCTGGTCGTTGTGGCGTTGAC\n+GCCGCTGTCAATTTTCGTCGCGCGGTTCATTGCCACCCACACCTATTCTATGTTCAAGGTGCAGAGCGAGACCCGCGCCGAAATGACGAGTCTGGTCGAA\n+GAACTGGTCGGCAACGAGCATCTTGTCCGCGCGTTCGGCTATGAGCGCCGCGCCGAGGAACGCTTCGATAAGATCAACCTCGATTTGCAGAAGTGCGGCG\n+TCAAGGCGACGTTCTTCTCCTCTACCACGAACCCCTGCACCCGCTTTGTGAATGCGCTGGTCTACGCCGCCGTCGGCGTGCTGGGTGCGTTCGTCGCCAT\n+TGCTGGCGGCATCACGGTGGGCCAGCTGTCTGTCTTTCTGAACTACGCCAACCAGTACACGAAGCCGTTCAATGACATTTCGGACGTTATGACCGAACTG\n+CAGAACGCGCTGGCTTGTGCGCAGCGCGTGTTTGACCTGATTGACGAGACGCCCATTGTGCCCGATGGCCCGGATGCTGTTGCCCTGCCCCACGGCGCGG\n'
b
diff -r 000000000000 -r 1f0a3e4497d4 test-data/contigs.ffn
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/contigs.ffn Wed Sep 06 13:23:14 2017 -0400
b
b'@@ -0,0 +1,2590 @@\n+>1506879_1_1328_+\n+CATAACATTCCTCTATTCTTTAGTTTTCGTTTTGAACTTATATGTATTTTACTTAAGAAATTGGGGAAAATCAATACAGAGAGGACAATTCAGACATATTTAGTAAATAAGAAAGGATACAGAACTATGAACATATTGTATTGCGGGGATAAACCTATGCAGAAGGGAATTCTATTATCTTCAATGTCTCTTGTTGAAAATGTGGACGAACCGTTAAATATATATATTATTACGGTTGATTACAGGGAAAAAGGTGTTAATTACAAACCGGTTGATAAAGTATTTGCAGAGTATCTTAAAAAAGAATTGAATAAATCGGACATTGATGTAAATGTTTCACTTATTGATATTACAAGATATTTTGTTGAGGAACTGCCAGAGGCAAATATGCAGACAAGGTTTACTGCATGCTGTATGCTGCGCCTGTTTGCTGATAAGACAGATATTAATGAAAGACTTCTTTACCTTGATACAGATGTGCTTTGCAGGAAGAATTTCAGCGACTTCTATTATCAGGATATGGAGGGGATAGAGATTGCGGGAGTTTCTGACTATTATGGCAGATGGATTTTTGGTGATGGTTACATTAATTCCGGTGTAATGCTTATGAATATGAATATGATACGGGAGAATGGACTTTTGGAAAAATGTCGTGAACAATGCATAAGAAAGGAAATGTTTATGCCTGACCAGACGGCTATTAATACATTTGCAACAAGAGTCAATCTGTGTGGACACAGGTTTAATGACCAGAGGAGACTGCATGGCAACACTGTTTTTCAGCATTTTACAACTACGTTCCGTGTATTTCCGGTAATAAGAACTGTTGCGGTCAAACCGTGGGAGATTGACAAAATGCATAATGTACTTGGGCTTCATGAATATGATGCACTTCTTGAATCTTATAACAGAGAATATGAGGAATACAAGGCCGTTTCGCGTATTCCGGTGGTTTTCTCTATTAATGAAAAGTATGCACCGTATCTGGCTGTGTGTCTTAAATCTCTGGCTGTACATGTGGCTGTGGATGAGCGTTACCGCATTATTGTTATGTGCGATAATGTGAAGAATATTACTATGATTCAGCTTCGCAATGTAATAAAGGACTACGAAAACATAGATATTGAATTCGTTGATATAAGAAAGAAAATGCATGAATTTTCAGAAAGCTTTGGACAGACCGTTACAGACAGGCAGGAAAACAGGCTTTATTCAGGCGAGTTTACGTTGACAATATATTTCAGGTTATTTATTGCAGAGCTTTTTCCTGAATTAGATAAGGCTGTATATATTGATTCGGACACGGTAATAAATGATGACATTGCA\n+>1506881_43_216_-\n+ATGCGTGACGTATTTGTAGAGGAAGTAGAAATCAAAGACCCGGAGGAATATATCAGAAAGAAGTTTCAGGGAAAGGATGTCTCCTATGACAAGACGGTTCTCGCCGATGGGACCATAGTCTTTGATATCACAACATCACAGATAAAACAGAGATGTTCCTTTACAGAGATT\n+>1506881_267_449_-\n+ATGGCAGTAGAGAAATACTGTAAACAGAATGGGATTGCAGGAAGACTGCTTCCCGTACCAAGAGAAATTTCTGCAAGCTGCGGCCTTGCATGGGCTGTGCCGCTGGAACAGAAAGGAGAACTGGCGGCAGTAGAAGCAGAATTTGCAGATGAGATTGAGGGAAAATGGAGTCTGGAATTA\n+>1506881_500_1117_-\n+ATGGAACAGAAATATACAGTAGATGCAAGAGGCGAACAGTGTCCGATTCCGGTTGTCAGGACCAAGAAGGTTCTGGATGGCATTCTGGGAGATGCTGAGCTCACAGTTTTGGTGGATAATGAGACCGCAGTGCAGAATCTCACCAGAATGGGGAAACATGCAGGTGCAGAAGTACTTTCAGAGAAAAAATCCGACAATGAATTTCAGGTTGTCATTCGTGTAAAAGATCGGAAACCAACTGAAGGAGGAGAAGAAACCGCAGAATGTATCCCGGATGTCAAGGGTGACTTTGTGATCGCGGTAGATACCGCAATCATGGGAAGAGGAAATGATGAACTGGGAAAAGTCCTGATGAAGGGATTTATTTTTGCAGTGACTCAGCTTGAAAAGCTTCCAAAGACCATCCTTTTTTATAATGGCGGTGCAACTCTGACGACAGAGGGTTCAGATTCTCTTGACGATATAAAGAGTCTGGAAGCACAGGGCGTGGAGATCAAAACCTGTGGAACCTGTCTGAACTATTATGGACTGACAGATAAGCTTAAGGTCGGAGAAGTTACAAATATGTATGATATCGTAGAAAATCTTGCAAAAGCTTCCAAAGTAGTGAAACCA\n+>1506883_1_1328_+\n+AAACAGATTGCCATTGCAGCAGATGTACCGATCATCCCTGGAGTAGATCACGCGATGAAATCTTATGAAGAGGCAGCGAAGATCGCAGACATGGTCGGATATCCGATTATGCTGAAAGCTTCCAACGGTGGTGGCGGACGCGGTATGCGTATTGTCAATGATCCGGCTGATCTGGAAAAAGAATTCAACGAGGCGAGAAATGAATCTAAAAAAGCTTTCGGTGATGATATGATCTTCGTTGAGAAGTATCTGAAAGGACCAAAGCATATTGAGGTTCAGGTGATCGGAGATAATTACGGCAATGTTGTGCATCTGTTCGACCGTGACTGCTCTGTGCAGAGACGTCACCAGAAGGTCGTAGAGTATGCGCCGGCATTTACCATTCCAGACGAGACAAGAGAGAAGATTTTTGATGCAGCAATCCGTCTTTGTAAAAATGTTGGATATGTCAATGCAGGAACACTGGAGTTTCTGGTAGACAGAGATAACAATCCATACTTTATTGAAATGAACCCTCGTATTCAGGTAGAGCATACAGTCAGTGAGATGGTGACAGGAATTGATATCGTGCAGGCTCAGATCCTGGTTGCAGAAGGATATGCTCTTGATTCAGAAGAGATACATATTAAATCACAGGAAGATGTTACATGTAACGGATATTCTATTCAGACTCGTGTTACTTCTGAAGATCCGGCAAATAACTTCCTGCCGGATACAGGTGAGATGACAGTATATCGTTCCGGTTCCGGTAATGGTATCCGTCTGGACGGTGGCTGTGCATATGTCGGAGCCGTTGTATCACCACACTATGACAGTTTGCTTGTAAAGATTATTTCTCATGACCGTACCTTTGCAGGTGCAGTGAGAAAATCCGAGCGTGCCCTTCAGGAGATGCGTATCCGTGGAGTTAAGACAAATATTCCGTTCCTGATCAATGTGCTGAACCACCCGACATTTCAGTCCGGTCAGTGTTACACAACATTTATCGAGGAGACACCGGAGTTATTCCGCCTGACACACAGCCTGAACCGTGCGACTAAGATCATTGAGTTTATCGGTGATCGTATCATCAATTCTGACATGGGTAAGAAGAAACAGTTCGATAACCGTATTCTGCCGACATTTGACCATGATAAACCGGTCTATGGTGCAAGAGATGAATTTTTAAAACTTGGTGCAGAAGGCTACATGCAGAAGATTTTAAAAGAAGAAAAGCTTTATGTTACAGATACAAGTATGCGTGATGCGCAGCAGTCACTGGTGGCAACACGTATGCGTAGCAAAGATCTGTGCGGTGCCGCTTATGCGACAAATGCATTTATG\n+>1506885_1_235_+\n+CCATCCTCGTTGAAAAATTATTTTCAAGGCGTATATGGGAAAAACATTTCCACTTGGCTTAGGGAAGCAAGAATGTCTGTGGCTTCATCTGCATTGCGGGAAGGAAATCAGCCTGTGGCAGAAATTGCAGCAAGTGTCGGATACGAAAACGCAAGTAAATTCTCCGCAGCATTTAAAAACTTTTTGGGAGAAACCCCGTTAGAGTACCGGCGTCAGAGTCGGTGCGGAATC\n+>1506'..b'TGAAGAAATTGCATTGGGAAATATGGAATATCAGATCCCGCTGCAAGGCTTAAGAGGTGAGAACTTAAAGCTGGCAGAGATGATCAATGGAATTGCCAACGGATTCCATATGGCCGTAGAAGAGGCAATGAAAAATGAGCGTCTTAAGACGGATCTGATCACGAATGTATCACATGATATCAAGACACCGTTGACTTCGATCATTAATTATGTAGCGATCCTGAAGCAGTCGGATATTGCAGATCCAAAGATCCAGGGCTATCTGGATATACTGGAGGCGAAAGCACAGAGGCTGAAGACACTGACGGAAGACGTTGTTGAGGCATCCAAGGTAAGCAGTGGGAATATTTCTCTGGAGTATATGGATGTAGATCTTGTGGAGATGATCCAGCAGACGGAAGGTGAGATGGCTGAGAAGTTTGAGGCAAGGAATCTGAAAATGATCGTCAATCTGCCGGCAGAACCTGCGGTTGTTCATGTAGACGGG\n+>1508207_1_777_+\n+CAGTTCAACAAAGAGATCGTGGATGCTACCTATGATCTGATCCCGGCGGTAAAACCACAGGTTGCCATGTATGAGCAGTTTGGTATCGAAGGTGTGAAAGCGTTTAAAAAGACCGTGGATTACTGCCATGAAAAAGGACTGGTAGTTATCGGTGATGTAAAACGTGGAGATATCGGTTCTACTTCCGAGGCCTACGCGGTAGGTCATCTGGGAAAAGTAAAAGTAGGTTCCCAGCAGTTCGCAGGATTTGATGAGGATTTCGCTACGGTCAATCCGTATCTCGGTTCTGACGGCATCAAACCGTTCATCAAGGTCTGCAAAGAAGAAAACAAAGGTCTGTTTATCTTGGTAAAAACATCCAATCCATCCAGTGGAGAATTCCAGGATCGTCTGATCGACGGCCGTCCACTGTATGAGTGGGTAGGAGAACAGGTAGACGCATGGGGCAAAGAACATATGGGAGATTCTTATAGTTATATCGGCGCGGTCGTAGGAGCAACTTATCCAGAACAGGGAAAAGTATTAAGAAAACTGATGCCGAAGACCTTTATTCTGGTACCTGGCTACGGGGCACAGGGCGGAAGAGGAAAGGATCTGGTGCATTTCTTTAATGAAGACGGACTGGGTGCGATCATCAACTCTTCCAGAGGTATCATCGCAGCATACAAACAGGAAGCATATGCACAGTTCGGTGCACAGAATTTTGCAGAAGCATCCCGACAGGCAGTGAAAGATATGATCGCAGATATCGACGGTGCACTGCAGGCGGCAAAA\n+>1508207_803_1353_+\n+ATGAAAAAGAAAGAAATCTGTACTGTGATCCGTCAGAAAGAAATTGGTGACGGAATCTTCAGCATGTGGATCCAGACGGAAAACATTGGGAAAGAAGCAAAACCGGGACAGTTCGTATCGTTGTATAGTAAGGATGGAAGTAAACTACTTCCGCGTCCGATCAGTCTTTGTGAGATCGACCGGGAAAACAGCCGACTTCGTCTGGTGTATCGTGTCACGGGAGCGAAGACCGGAACCGAAGAGTTTTCCAGACTGAAAGCCGGAGATACGATCCCGGTGATCGGACCGCTGGGAAATGGCTTCCCTGTAGAAAAAGCAGAAGGAAAACGAGCTTTTCTGATGGGCGGAGGTATCGGAGTACCGCCGATCCTGGAACTGGCAAAACAGATGCAGTGTGAGAAAAAACAGATCGTTGTGGGATACCGTAACGCGCAGACGTTCTTAAAAGAAGAATTCGAAGCAGCCGGAGAACTGTATATTTCCACAGAAGATGGCAGTGTGGGAACAAAAGGAAATGTAATGGATGCGATCCGGGAACAGAAATTGGAA\n+>1508209_13_1221_-\n+GTGTTAGGAATGCTCGAAAAAAATATATACATTCGTATAATATTCACCTTAAATACTTGTGATATGAAGCAATTAACTGTAGTATTCGCTCTGTTGTGTATTTTTGCTTGTAGTAGCGAAGATATTGTAAGTACCGTTGAGGAATCTGTAAAGCCGGCTAATGAAGTGGCTATACAAACTGTTAATTTGCTTGATAGCCTTGAAATTATGGATTATATTTATAGCATTATTGGACCGATGGCTAAGACACGATCAAATCTACCAGGGGGAGGGTATATTCTTCCTGATAATTGGGATTCTCAATTAACAGATGAACAGCGCGAATTGATCAGGAACTCTTTCCCACGACCTCTCTTTTCTGCTGAAAGGAATGCTTTAAGGAAATCGTTTCCTTTAGTTGAATATTCCAATACAGTTGTTATGAATTATCCGTCATCTGGATATAATTGTTTTGCCTATTCGTTGGGGTTTAATAATAAGTGGATAGAGTTTAGTACTTGGGATCAAGTAAGATATGGATATGAAAATGCGAGTTCCGTGTATCATGCCGCTTATGATTACATGAAAGGGGCAACCTCAATATCAAGATACTATCCTGTAGTTTGGGGTTGGGGAAATACCCCTCTGCATGCATCTCTTGGAGGTAGTCCCCATTGCGAGGCACCTTATTCTAAGATGGGGCGTATGTGGCTATTGTGGCACCTTGTAAGTGTGTTTTCTAATGGAATGTATGGAGTTCCTGTGGAAACCTATGGGGCAGTTTCTCCTACCCGTAGTCTAAGTGAAATAGATGCTAATGCAATGAAAGAAATAAGTGAGGATATTCACGAAAATATAATCTTCTCACCGGATGAGTTGATGATGATTGCTAGAAAAGTAAAAACATGTAGAGATAGTTCAAGGTTTGAATCTCTGTTTAATGAATGGAAGGAAGCATGGCATTACTCGCTTAGTAATAACACTGCTACTACAAGAAATTTACCTCAATATGCCGATTTAAAGGCTATGGGAAAAGAAATCATTCCATTATTGATTGAGAAGATGGTAACAGAAGAGGATAATTTCTTTGCAATAAGATTGTATGAAGATCTACAAGATAATCCTAATCTGATAATACGATATGCGAACGATGATCCACACCAACTTGAAGGATTACAACAAACAACCAAAAAAACTATAAAGAAGTGGTTAGAATATAATTCCAAT\n+>1508211_1_900_+\n+CCGGTACTGTCCGGTAAGGCCGTGGATATGATCCTGGGACCCGGTCAGGTTGATTTTGCAGGCCTTGGCAAAATTGCGATAGCGATGGCTGCCACGATTGCCTGCACAGCGCTGGCCCAGTGGCTGATGAATGTCGTCAATAACCGCATTACCTTTCAGGTCGTGCGTGATATGCGTGTCCGTGCGTTTGGCCAGTTGGAGATTCTGCCGCTCAAATATATGGACGCCCACCGCCCCGGCGATGCTATCAGCCGCATTACCACCGACGTGGAGCAGTTCAGCGACGGTCTGCTGATGGGCTTTACCCAGCTGTTCACCGGCGTGCTGACGATTTTGGGCACGCTGGGAGTCATGCTGTTCATCGACTGGCGCATTGCGCTGGTCGTTGTGGCGTTGACGCCGCTGTCAATTTTCGTCGCGCGGTTCATTGCCACCCACACCTATTCTATGTTCAAGGTGCAGAGCGAGACCCGCGCCGAAATGACGAGTCTGGTCGAAGAACTGGTCGGCAACGAGCATCTTGTCCGCGCGTTCGGCTATGAGCGCCGCGCCGAGGAACGCTTCGATAAGATCAACCTCGATTTGCAGAAGTGCGGCGTCAAGGCGACGTTCTTCTCCTCTACCACGAACCCCTGCACCCGCTTTGTGAATGCGCTGGTCTACGCCGCCGTCGGCGTGCTGGGTGCGTTCGTCGCCATTGCTGGCGGCATCACGGTGGGCCAGCTGTCTGTCTTTCTGAACTACGCCAACCAGTACACGAAGCCGTTCAATGACATTTCGGACGTTATGACCGAACTGCAGAACGCGCTGGCTTGTGCGCAGCGCGTGTTTGACCTGATTGACGAGACGCCCATTGTGCCCGATGGCCCGGATGCTGTTGCCCTGCCCCACGGCGCG\n'
b
diff -r 000000000000 -r 1f0a3e4497d4 test-data/contigs.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/contigs.gff Wed Sep 06 13:23:14 2017 -0400
b
b'@@ -0,0 +1,1296 @@\n+##gff-version 3\n+1506879\tFGS\tCDS\t1\t1328\t.\t+\t0\tID=1506879_1_1328_+;product=predicted protein\n+1506881\tFGS\tCDS\t43\t216\t.\t-\t0\tID=1506881_43_216_-;product=predicted protein\n+1506881\tFGS\tCDS\t267\t449\t.\t-\t2\tID=1506881_267_449_-;product=predicted protein\n+1506881\tFGS\tCDS\t500\t1117\t.\t-\t1\tID=1506881_500_1117_-;product=predicted protein\n+1506883\tFGS\tCDS\t1\t1328\t.\t+\t2\tID=1506883_1_1328_+;product=predicted protein\n+1506885\tFGS\tCDS\t1\t235\t.\t+\t1\tID=1506885_1_235_+;product=predicted protein\n+1506885\tFGS\tCDS\t261\t857\t.\t+\t2\tID=1506885_261_857_+;product=predicted protein\n+1506885\tFGS\tCDS\t899\t1328\t.\t+\t1\tID=1506885_899_1328_+;product=predicted protein\n+1506887\tFGS\tCDS\t1\t1328\t.\t-\t2\tID=1506887_1_1328_-;product=predicted protein\n+1506889\tFGS\tCDS\t1\t304\t.\t-\t1\tID=1506889_1_304_-;product=predicted protein\n+1506889\tFGS\tCDS\t307\t495\t.\t-\t0\tID=1506889_307_495_-;product=predicted protein\n+1506889\tFGS\tCDS\t531\t758\t.\t-\t2\tID=1506889_531_758_-;product=predicted protein\n+1506889\tFGS\tCDS\t760\t1328\t.\t-\t0\tID=1506889_760_1328_-;product=predicted protein\n+1506891\tFGS\tCDS\t61\t957\t.\t-\t0\tID=1506891_61_957_-;product=predicted protein\n+1506891\tFGS\tCDS\t981\t1328\t.\t-\t2\tID=1506891_981_1328_-;product=predicted protein\n+1506893\tFGS\tCDS\t1\t875\t.\t-\t2\tID=1506893_1_875_-;product=predicted protein\n+1506893\tFGS\tCDS\t951\t1328\t.\t-\t2\tID=1506893_951_1328_-;product=predicted protein\n+1506895\tFGS\tCDS\t93\t1241\t.\t-\t2\tID=1506895_93_1241_-;product=predicted protein\n+1506897\tFGS\tCDS\t1\t112\t.\t+\t1\tID=1506897_1_112_+;product=predicted protein\n+1506897\tFGS\tCDS\t206\t1285\t.\t+\t1\tID=1506897_206_1285_+;product=predicted protein\n+1506899\tFGS\tCDS\t1\t1328\t.\t-\t2\tID=1506899_1_1328_-;product=predicted protein\n+1506901\tFGS\tCDS\t1\t1328\t.\t+\t1\tID=1506901_1_1328_+;product=predicted protein\n+1506903\tFGS\tCDS\t167\t1328\t.\t-\t1\tID=1506903_167_1328_-;product=predicted protein\n+1506905\tFGS\tCDS\t1\t821\t.\t-\t2\tID=1506905_1_821_-;product=predicted protein\n+1506905\tFGS\tCDS\t894\t1328\t.\t-\t2\tID=1506905_894_1328_-;product=predicted protein\n+1506907\tFGS\tCDS\t1\t146\t.\t-\t2\tID=1506907_1_146_-;product=predicted protein\n+1506907\tFGS\tCDS\t177\t680\t.\t+\t2\tID=1506907_177_680_+;product=predicted protein\n+1506907\tFGS\tCDS\t790\t1328\t.\t+\t0\tID=1506907_790_1328_+;product=predicted protein\n+1506909\tFGS\tCDS\t1\t261\t.\t-\t0\tID=1506909_1_261_-;product=predicted protein\n+1506909\tFGS\tCDS\t618\t1328\t.\t-\t2\tID=1506909_618_1328_-;product=predicted protein\n+1506911\tFGS\tCDS\t1\t380\t.\t+\t2\tID=1506911_1_380_+;product=predicted protein\n+1506911\tFGS\tCDS\t448\t690\t.\t+\t0\tID=1506911_448_690_+;product=predicted protein\n+1506911\tFGS\tCDS\t720\t1025\t.\t+\t2\tID=1506911_720_1025_+;product=predicted protein\n+1506911\tFGS\tCDS\t1061\t1329\t.\t+\t1\tID=1506911_1061_1329_+;product=predicted protein\n+1506913\tFGS\tCDS\t104\t1030\t.\t-\t1\tID=1506913_104_1030_-;product=predicted protein\n+1506913\tFGS\tCDS\t1039\t1149\t.\t-\t0\tID=1506913_1039_1149_-;product=predicted protein\n+1506913\tFGS\tCDS\t1165\t1329\t.\t+\t0\tID=1506913_1165_1329_+;product=predicted protein\n+1506915\tFGS\tCDS\t1\t634\t.\t+\t1\tID=1506915_1_634_+;product=predicted protein\n+1506915\tFGS\tCDS\t654\t1329\t.\t+\t2\tID=1506915_654_1329_+;product=predicted protein\n+1506917\tFGS\tCDS\t1\t1329\t.\t+\t1\tID=1506917_1_1329_+;product=predicted protein\n+1506919\tFGS\tCDS\t1\t1329\t.\t+\t2\tID=1506919_1_1329_+;product=predicted protein\n+1506921\tFGS\tCDS\t1\t1329\t.\t-\t1\tID=1506921_1_1329_-;product=predicted protein\n+1506923\tFGS\tCDS\t1\t855\t.\t+\t0\tID=1506923_1_855_+;product=predicted protein\n+1506923\tFGS\tCDS\t891\t1329\t.\t+\t2\tID=1506923_891_1329_+;product=predicted protein\n+1506925\tFGS\tCDS\t328\t1329\t.\t-\t0\tID=1506925_328_1329_-;product=predicted protein\n+1506927\tFGS\tCDS\t1\t1066\t.\t-\t1\tID=1506927_1_1066_-;product=predicted protein\n+1506927\tFGS\tCDS\t1148\t1329\t.\t-\t1\tID=1506927_1148_1329_-;product=predicted protein\n+1506929\tFGS\tCDS\t1\t797\t.\t-\t2\tID=1506929_1_797_-;product=predicted protein\n+1506929\tFGS\tCDS\t985\t1329\t.\t-\t0\tID=1506929_985_1329_-;product=predicted protein\n+1506931\tFGS\tCDS\t60\t1329\t.\t+\t2\tID=1506931_60_1329_+;product=predicted protein\n+1506933\tFGS\tCDS\t307\t1329\t.\t+\t0\tID=1506933_307_1329_+;product=predicted protein\n+'..b'duct=predicted protein\n+1508161\tFGS\tCDS\t1\t124\t.\t-\t1\tID=1508161_1_124_-;product=predicted protein\n+1508161\tFGS\tCDS\t192\t1016\t.\t-\t2\tID=1508161_192_1016_-;product=predicted protein\n+1508161\tFGS\tCDS\t1018\t1352\t.\t-\t0\tID=1508161_1018_1352_-;product=predicted protein\n+1508163\tFGS\tCDS\t1\t1060\t.\t-\t1\tID=1508163_1_1060_-;product=predicted protein\n+1508163\tFGS\tCDS\t1120\t1352\t.\t-\t0\tID=1508163_1120_1352_-;product=predicted protein\n+1508165\tFGS\tCDS\t1\t624\t.\t+\t0\tID=1508165_1_624_+;product=predic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b
diff -r 000000000000 -r 1f0a3e4497d4 test-data/contigs.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/contigs.out Wed Sep 06 13:23:14 2017 -0400
b
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