tests: run separately against HXB2 too

cfe-lab · Sep 22, 2023 · c399add · c399add
1 parent cef7223
commit c399add
Show file tree

Hide file tree

Showing 13 changed files with 13,432 additions and 3 deletions.
diff --git a/tests/expected-results-large-hxb2/blast.csv b/tests/expected-results-large-hxb2/blast.csv
diff --git a/tests/expected-results-large-hxb2/errors.json b/tests/expected-results-large-hxb2/errors.json
diff --git a/tests/expected-results-large-hxb2/holistic.json b/tests/expected-results-large-hxb2/holistic.json
diff --git a/tests/expected-results-large-hxb2/intact.fasta b/tests/expected-results-large-hxb2/intact.fasta
diff --git a/tests/expected-results-large-hxb2/nonintact.fasta b/tests/expected-results-large-hxb2/nonintact.fasta
diff --git a/tests/expected-results-large-hxb2/orfs.json b/tests/expected-results-large-hxb2/orfs.json
diff --git a/tests/expected-results-single-hxb2/blast.csv b/tests/expected-results-single-hxb2/blast.csv
@@ -0,0 +1,4 @@
+qseqid,sseqid,sgi,qlen,slen,length,qstart,qend,sstart,send,evalue,bitscore,pident,nident,sstrand,btop
+MN692145,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,0,9689,9718,9752,1,9689,1,9718,0.0,12000,93.294,9098,plus,23ACAG12TC8AG34GA25GA30TA20-C-A-G-A-G-A-A-G-T-T-A-G-A-A-G-A-A-G3CATCGA1CAAG7TCGAAC3AC3CT1GA7CTAG8GT2GA5AT9GA34GA40AT23TG31G-21GA1AT22GC18-T2CT56GA153TC12AG13AC37AG40T-T-T-T-63AG9AG6GA36CA27AG3AG11TC27AT7AC32TC25AG51TGGA19AT5TC23GA6GA8AC1AG21AC7CT33CA1TC5CG11CT42AG28AG62TC41AG107CT65CT41GA8TC17TC17AG3TC10TC17CT14TC8CT48TG1AG20CT19GCAG38GA17AG8CT67GA6GA32GA5TC1TC81AG23AG12CT7GA8AG5CT11GA37TC5AT16TC14TC3CT2GA12T-C-C-7GA10AG106AG47TC24TCCT30GT56AG8TC11CT8TC8AG84AGCT15AG65TC17CT41AG11TC20GA11AC74GA2TC114TA127AGTC26TC109AC23AG11TG26TCGC7CT7AGAG14TC5GA3GA64GA6TC91GA48GA56GA4TA37GAGATC1AG11AG65CT65TC18TG4TC2AG33GA1CT11GA9TA44CT19AG66AC34AG11CA14CTTC58TC3AG7TC2AG38AT14CT47GA7GA84GA95AG14CT5CT41AT11TC8TCAG2AG4AG4AG21GA11GA5CA80CT17AG26TC147GA28TC26GA8CT34TC3AG119AG32AC27TCGA64TC40GA24CTAG1CA14GA20TC11AC13GATG3AT10TC8TC5TG41GA9TC24GA2GT6CA15GA1AG2GA45CA10TC1TCCA1GT62GT32CA18AG43CT2TC8GA10AG16AG3TC3CA9AG15AG37CT8GA12TACA30TC5CT8GA57TCCA3AGGA18TC34AC1CATC2TA3AC4TGCT13AT17CA19TC6TA40TC15AC3GT36GA2TACAATGAGTAC2AC3A-1CGATAGCG2CAATCGTGTGAG-G48GA3GACA2TA38AG46GA66GAAGGT5AT21TC7GA4CGCAAC29TC35GA2GA14CT1CG6TG12GAGAAGCA1GT2GT1GC-T-A-A8AG2AG2TG1AGCGAGGA3GTTG3-A-T-G11AG2GA21TACG1TA6AT1GA2AG6GT3TG13CT16GA2GA9GA4AG3A-G-A-3A-T-G-G-T-A-A-T-T-A-T-T-1TC7GA5TC9TC29AG5AC22TA15GT1AT12GA6GA4AGCAACAG41GA50TC34CT43CAAC14CA13GAGATC10TG2GA1GA1GAGA1TC1AGCT2GC-C-A-G-A-G-A10AGGA6TGAT1GA2GAGT2CG2TA2CT4GA4AG3AC12TA5AG2AG12CT1GATC7GA2TA1GA3TC1GACGAC8TA2GA6AG1GA-A-A-T13AT5CATG3CT28AG39AT5AC20ATAT1G-C-2CT1CG-T2AT1-G2TG2AC2GATAAGCGTG1GCGA3GA1TC5GA4AG1-G-A-C-A-C-A45GA34AT20CA12TC25GT1CGTC3GA1-T3CTA-A-C-A-C-C-A-10TC23AG40GA15GA66CT44AG1GC2GA3GA2TC40AG20AG17AG3TC23GA20GA8CG35TA36AC38GA3AG6GA1GTAC3TC18AC9GA1TC18TC2AT1TC6AGCA9GA1TA3AG6CA8AC7GA8GA13AG16GAGA9CT11CT6AT4TC20AG59CT22GA1TC5GA30TC37GACT2CG9AC4TC3AG13TA6AG50ATAG42TC9CT1TG5GA17CGAT72AG11TG5AG3TC2TG9CT1TG3TC2CA4CG18TG6GACT16GT21TG2GA12AC40GA12TC10TC6GA21TC9AG3AC8AC22AG129AG12TC8AG91TA20-C-A-G-A-T-A-A-G-A-T-A-G-A-A-G-A-G-G3CA1GA1CAAG7TCGAAC3AC3CT1GA7CTAG8GT8AT9GA34GA12AG27AT23TG31G-21GA1AT22GC20CT-T56GA134
+MN692145,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,0,9689,9718,635,1,616,9085,9718,0.0,763,92.441,587,plus,24AG12TC8AG91TA20-C-A-G-A-T-A-A-G-A-T-A-G-A-A-G-A-G-G3CA1GA1CAAG7TCGAAC3AC3CT1GA7CTAG8GT8AT9GA34GA12AG27AT23TG31G-21GA1AT22GC18-T2CT56GA134
+MN692145,Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455,0,9689,9718,635,9074,9689,1,634,0.0,752,91.811,583,plus,23ACAG12TC8AG34GA25GA30TA20-C-A-G-A-G-A-A-G-T-T-A-G-A-A-G-A-A-G3CATCGA1CAAG7TCGAAC3AC3CT1GA7CTAG8GT2GA5AT9GA34GA40AT23TG31G-21GA1AT22GC18-T2CT56GA134
diff --git a/tests/expected-results-single-hxb2/errors.json b/tests/expected-results-single-hxb2/errors.json
@@ -0,0 +1,3 @@
+{
+    "MN692145": []
+}
diff --git a/tests/expected-results-single-hxb2/holistic.json b/tests/expected-results-single-hxb2/holistic.json
@@ -0,0 +1,14 @@
+{
+    "MN692145": {
+        "qlen": 9689,
+        "hypermutation_probablility": 0.1672411051048176,
+        "inferred_subtype": "Ref.B.FR.83.HXB2_LAI_IIIB_BRU.K03455",
+        "blast_matched_qlen": 9689,
+        "blast_sseq_coverage": 1.130479522535501,
+        "blast_qseq_coverage": 1.1271545051088863,
+        "blast_sseq_orfs_coverage": 1.0,
+        "orfs_start": 789,
+        "orfs_end": 8794,
+        "blast_n_conseqs": 3
+    }
+}
diff --git a/tests/expected-results-single-hxb2/intact.fasta b/tests/expected-results-single-hxb2/intact.fasta
@@ -0,0 +1,163 @@
+>MN692145
+TGGAAGGGCTAATTCACTCCCAAAAAAGACAAGATATTCTTGATCTATGGATCTACCACA
+CACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGGTCAGATATCCAC
+TGACCTTTGGATGGTGCTTCAAGCTAGTACCAGTTGAGCCCACTGACAGAGAGAATGACA
+GATTGCTGCACCCTGCAAGCCTGCAGGGGATGGAAGACCCGGAGGGAGAAGTGTTAGAGT
+GGAGGTTTGACAGCCGCCTGGCATTTCATCACATGGCCCGAGAGCTGCATCCGGAGTACT
+ACAAGAACTGCTGACATCGAGCTTTCTACAAGGGACTTTCCGCTGGGGACTTTCCAGGGG
+AGGCGTGGCCTGGGCGGGGCAGGGGAGTGGCGAGCCCTCAGATGCTGCATATAAGCAGCT
+GCTTCTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGC
+TGACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTG
+TGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTG
+TGGAAAATCTCTAGCAGTGGCGCCCGAACAGGGACTTGAAAGCGAAAGAGAAACCAGAGG
+AGATCTCTCGACGCAGGACTCGGCTTGCTGAAGCGCGCACAGCAAGAGGCGAGGGGCGGC
+GACTGGTGAGTACGCCAAAAATTTTTTTTGACTAGCGGAGGCTAGAAGGAGAGAGATGGG
+TGCGAGAGCGTCAGTATTAAGCGGGGGAAAATTAGATCAATGGGAGAAAATTCGGTTAAG
+GCCAGGGGGAAAGAAAAAATATCAATTAAAACATATAGTATGGGCAAGCAAGGAACTAGA
+ACGATTTGCAGTTAATCCTGGCCTGTTAGAAACAACAGAAGGATGTAGACAAATACTGGG
+ACAGCTACAACCATCTCTTCAGACAGGATCAGAAGAACTTAAATCATTATATAATACAGT
+AGCAACCCTCTATTGTGTGCATCAAAGGATAGATGTAAAAGACACCAAGGAAGCATTAGA
+TAAGATAGAGGAAGAGCAAAACAAGAGTAAGGAAAAAGCAAAACAAGCAGCAGCTGACAC
+AGGAAACAGCAACCAGGTCAGCCAAAATTACCCTATAGTGCAGAACCTTCAGGGCCAAAT
+GGTACACCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAAGTAATAGAAGAGAA
+GGCTTTCAGCCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCCCACA
+AGATTTAAACACCATGCTAAATACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAA
+AGAAACCATCAATGAGGAAGCTGCAGAATGGGATAGAGTGCATCCAGTGCATGCAGGGCC
+TATTGCACCAGGCCAGATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACCACTAGTAC
+CCTTCAGGAACAAATAGGATGGATGACAAATAATCCACCTATCCCAGTAGGAGAAATCTA
+TAAAAGATGGATAATCCTGGGATTAAATAAAATAGTAAGGATGTATAGTCCTACCAGCAT
+TCTGGATATAAGACAAGGACCAAAAGAATCCTTTAGAGATTATGTAGACCGGTTCTACAA
+AACTCTAAGAGCTGAGCAAGCCTCACAGGAGGTAAAAAATTGGATGACAGAAACCTTGTT
+GGTCCAAAATTCAAACCCAGATTGTAAGACTATCTTAAAAGCATTGGGACCAGGAGCTAC
+ACTAGAAGAAATGATGACAGCATGTCAGGGAGTGGGAGGACCCGGCCATAAAGCAAGAGT
+CTTGGCTGAAGCAATGAGCCAAGTAACAAATTCAGCTACCATAATGATGCAGAGAGGCAA
+TTTTAGGAGCCAAAGGAAGATTGTTAAGTGTTTCAATTGTGGCAAAGAGGGGCATATAGC
+CAGAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTGGAAATGTGGAAAGGAAGGACACCA
+AATGAAAGATTGTACTGAAAGACAGGCTAATTTTTTAGGGAAAATCTGGCCTTCCCACAA
+GGGGAGGCCAGGAAATTTCCTTCAGAGCAGGCCAGAGCCAACAGCCCCACCAGAAGAGAG
+CTTCAGGTTTGGGGAAGAGACAACAACTCCCTCTCAGAAGCAGGAGTCGACAGGCAAGGA
+ACTGTATCCTCCTTTAGCTTCCCTCAGATCACTCTTTGGCAACGACCCCTCGTCACAATA
+AAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTA
+GAAGAAATGAGTTTACCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTT
+ATTAAAGTAAGACAGTATGATCAGATATCCATAGAAATCTGTGGACATAAAGCTATAGGG
+ACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAAATT
+GGTTGTACTTTAAATTTCCCCATTAGTCCTATTGAAACTGTACCAGTAAAATTAAAGCCA
+GGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTA
+ACAGAAATTTGTACAGAAATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAAT
+CCATACAATACTCCAGTATTTGCTATAAAGAAAAAAGACAGCACTAAATGGAGAAAATTA
+GTAGATTTCAGAGAACTTAATAAAAGAACTCAAGATTTCTGGGAAGTTCAATTAGGGATA
+CCACATCCAGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCA
+TATTTTTCAGTTCCCTTAGATGAGGATTTCAGGAAGTATACTGCATTTACCATACCTAGT
+ATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAA
+GGATCACCAGCAATATTCCAATGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAA
+AATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAA
+ATAGGGCAGCATAGAACAAAAATAGAGGAATTGAGACAACATCTGTTGAGGTGGGGATTT
+ACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTC
+CATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGAAAGCTGGACTGTC
+AATGACATACAAAAGTTAGTGGGTAAATTGAATTGGGCAAGTCAGATTTATGCAGGGATC
+AAAGTAAAACAATTATGTAAACTTCTTAGGGGAGCCAAAGCACTAACAGAAGTAATACCA
+CTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGGGAGATTTTAAAAGAACCAGTA
+CATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAA
+GGCCAATGGACATATCAGATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATAT
+GCAAGAGTGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAA
+ATAGCCACTGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAGGTTACCCATACAA
+AAAGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGG
+GAGTTTGTCAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATA
+GTAGGAGCAGAAACTTTCTATGTAGATGGGGCATCTAATAGAGAGACTAAATTAGGAAAA
+GCAGGATATGTTACTGACAGAGGAAGACAGAAAGTTGTCTCCCTAACTGACACAACAAAT
+CAGAAGACTGAGTTACAAGCAATTCATCTAGCTTTGCAGGATTCAGGATTAGAAGTAAAC
+ATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATAAAAGTGAA
+TCAGAGTTAGTCAATCAAATAATAGAACAGTTAATAAACAAGGAAAAGGTCTACTTGGCA
+TGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTTAGTACT
+GGAATTAGAAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGAAGAACATGAGAAA
+TACCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTGGTAGCAAGA
+GAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTA
+GACTGTAGTCCAGGAATATGGCAGCTAGATTGTACACATTTAGAAGGAAAAGTTATCCTG
+GTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGA
+CAGGAAACAGCATACTTTCTCTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACAT
+ACAGACAATGGCAGTAATTTCACTAGTACTACAGTTAAGGCCGCCTGTTGGTGGGCGGGG
+ATCAAGCAGGAGTTTGGCATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATG
+AATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGACCAGGCTGAACATCTTAAAACA
+GCAGTACAAATGGCAGTATTCATTCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTAC
+AGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAA
+AAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAGATCCACTT
+TGGAAAGGACCAGCAAAGCTTCTCTGGAAAGGTGAAGGGGCAGTAGTGATACAAGACAAT
+AGTGACATAAAAGTAGTGCCAAGAAGAAAAGTAAAAATCATTAGGGATTATGGAAAACAG
+ATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAGAACATGGAAAAGTTT
+AGTAAAACACCATATGTATGTTTCAGGGAAAGCTAAGGGATGGTTTTATAGACATCACTA
+TGAAAGCCATCATCCAAGAATAAGTTCAGAAGTACATGTCCCACTAGGGGATGCTAGATT
+GGTAATAACAACATATTGGGGTCTGCATACAGGAGAAAGAGATTGGCATTTGGGTCAGGG
+AGTCTCCATAGAATGGAGGAAAAGGAGATATAGCACACAAGTAGACCCCAACCTAGCAGA
+CCAACTGATTCATCTGTATTACTTTGATTGTTTTTCAGAATCTGCTATAAGAAGTGCCAT
+ATTAGGACATATAGTTAGTCCTAGTTGTGAATATCAAGCAGGACATAACAAGGTAGGATC
+TCTACAGTACTTGGCATTAGCAGCATTAATAACACCAAAAAGGAGAAAGCCCCCTTTGCC
+TAGTGTTGCAAAGCTGACAGAGGATAGATGGAACAAGCCCCAGAAGACCAAGGGCCACCG
+AGGGAGCCATATCAGGAATGGACACTAGAGCTTTTAGAGGAGCTTAAGAATGAAGCTGTT
+AGACATTTTCCTAGGATGTGGCTCCATGGCTTAGGGCAACATATCTATGACACTTATGGG
+GATACTTGGACAGGAGTGGAAGCCATAATAAGAATTCTGCAACAACTGCTGTTCATTCAT
+TTCAGGATTGGGTGTCAACATAGCAGAATAGGCATTATTCGCCAGAGGAGAACAAGAAAT
+GGAGCCAATAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGCCAGCCTAAGACTGC
+TTGTACCTCTTGCTATTGTAAAAAGTGTTGCTTTCATTGTCAAGTCTGTTTCATGACAAA
+AGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTTCTCAAGA
+CAGTCAGACTCATCAAGTTTCTCTATCAAAGCAGTAAGTAGTACATGTAATGAACTCTTT
+ACAAATATCAGCAATAGTAGCAATAGTAGTAGCAATAATACTAGCAATAGTTGTGTGGTC
+TATAGTATTCATAGAATATAGGAAAATATTAAGACAAAGAAAAATAGATAGGTTAATTGA
+TAGAATAAGAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGAAGGGGATCAGGAAGAACT
+ATCAACAGCACTTATGGAGATGGGGCACCATGCTCCTTGGGATGTTGATGATCTGTAGTG
+CTGCAGGCAATTTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAAGAAGCAACCA
+CCACTCTATTTTGTGCATCAGATGCTAAAGCATATGGTACAGAGGTACATAATGTTTGGG
+CCACACATGCCTGTGTACCCACAGACCCCAACCCACAAGAAGTGAGATTGGAAAATGTGA
+CAGAAAATTTTAATATGTGGAGAAATCCAATGGTAGAACAGATGCATGAGGATATAATTA
+GTTTATGGGATCAAAGCCTAAAGCCATGTGTAAAGTTGACCCCACTCTGTGTCACTTTAA
+ATTGCACTGATTTGGGACAGGAGAGTACCAATAATAATATCACAGGAAGTATAGAGAAAG
+GAGAAATGAAAAACTGCTCTTTCAATATCTCCTCAAGCAAAGGAAGTAAGGGGCATAAAG
+AATATGCATCTTTTTATAAACTTGATGTAGTACCAATAGGTAATAATAAGACTAATGGTA
+ATTATTCTAGCTATAGGTTGATAAGTTGTAATACCTCAGTCATTACACAGGCCTGTCCAA
+AAGTATCATTTGAGCCAATTCCCATACATTTTTGTGCCCCGGCTGGGTATGCGATTCTAA
+AGTGTAATGATAAACAATTCAATGGAACAGGACCATGTACAAATGTCAGCACAGTACAGT
+GTACACATGGAATTAGGCCAGTAGTATCAACTCAACTGCTGTTAAATGGTAGTCTAGCAG
+AAGAAGAGGTAGTAATTAGATCTGCCAATTTCACGGACAATGCTAAAACCATAATAGTAC
+AGCTGAACCAATCTGTAGAAATTACTTGTACAAGACCCGGTAACAATACAATAAGAGGGG
+TTCACATGGGACCAGGGAAGGCATTTTATGCAGGAGCAATAACAGGAGATATAAGAAAAG
+CACATTGTATCATTAATAAAGCAAAATGGAACAGTACTTTAAGACTGGTAGTTGCAAAAT
+TAAGTGAGCAATTTAGGAATAAAACAATAAACTTTACTCAACCCTCAGGAGGGGACCCAG
+AAATTGTAACACACAGTTTTAATTGTGGAGGGGAATTTTTCTACTGTAATACAACAAAAC
+TGTTTAATAGTACTTGGAATGCAACACACATGATTAATGGTACTTGGAATGATACTGAGG
+GAAATATCACCCTCCCATGCAGAATAAAACAAATTATAAACATGTGGCAGGAAGTAGGAA
+AAGCAATGTATGCCCCTCCCATCAGAGGACAAATTAGATGTTCATCCAATATTACAGGGT
+TGCTATTAACAAGAGATGGTGGTAAGACTAACGAGAGCAACACCACCGAGATCTTTAGAC
+CTGGAGGAGGAGATATGAGAGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAA
+GAATTGAACCATTAGGGGTAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAA
+AAAGAGCAGTGGGAATAGGAGCTCTGTTCCTTGGGTTCTTGGGAGCAGCAGGAAGCACTA
+TGGGCGCAACGTCGATGGCGTTGACGGTACAGGCCAGACAATTATTGTCTGGTATAGTGC
+AACAGCAGAACAATTTGCTGAGAGCTATTGAGGCGCAACAACATTTGTTGCAACTCACAG
+TCTGGGGCGTCAAGCAGCTCCAGGCAAGAGTCCTGGCTCTGGAAAGATACCTAAAGGATC
+AACAGCTCCTGGGGTTTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGATGTGCCTT
+GGAATGCTAGTTGGAGTAATAAATCTCTGGGACAAATTTGGGAGAACATGACCTGGATGG
+AGTGGGAAAGAGAAATTGATAATTACACAAGCTTAATATACACTTTAATTACAGAATCGC
+AGATCCAACAAGAACAGAATGAAAAAGAATTGTTGGAATTGGATAAATGGGCAAATTTGT
+GGAATTGGTTTGGCATAACAAACTGGCTGTGGTACATAAAAATATTTATAATGATAGTAG
+GAGGCTTAGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGAATAGAGTTAGGC
+AGGGATACTCACCATTATCGTTTCAGACCCGCTTCCCAGCCCCGAGGGGACCCGACAGGC
+CCGAAGGAATCGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCGCTCCATTAGTGA
+AAGGATTCTTAGCACTTATCTGGGTCGATCTACGGAGCCTGTGCCTCTTCAGCTACCACC
+GCTTGAGAGACTTACTCTTGATAATAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGT
+GGGAAGTCCTCAAATACTTGTGGAGTCTCCTACAGTATTGGACACAGGAACTAAAGAATA
+GTGCTGTTAGCTTGCTCAATGCCACAGCCATAGCAGTAGCTGAGGGGACAGATAGGATTA
+TAGAAGTATTACAAAGAGTTTTTAGAGCTATCCTCCATATCCCTACAAGAATAAGACAGG
+GCTTTGAAAGGGCTTTGCTATAAGATGGGGGGCAAGTGGTCAAAAAGTAGTTTGGTTGGA
+TGGCCTAATGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATGGGGTGGGAGCA
+GTATCTCGAGACTTGGAAAGACATGGAGCAATCACAAGTAGTAATACAGCAACTAACAAT
+GCTGATTGTGCCTGGCTAGAAGCACAAAAGGAGGAGGAGGTGGGTTTTCCAGTCACACCT
+CAGGTACCTTTAAGACCAATGACTTACAAGGCAGCTGTAGATCTTAGCCACTTTTTAAAA
+GAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAAAAGACAAGATATTCTTGATCTA
+TGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGG
+GTCAGATATCCACTGACCTTTGGATGGTGCTTCAAGCTAGTACCAGTTGAGCCCACTGAC
+AGAGAGAATGACAGATTGCTGCACCCTGCAAGCCTGCAGGGGATGGAAGACCCGGAGGGA
+GAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTGGCATTTCATCACATGGCCCGAGAGCTG
+CATCCGGAGTACTACAAGAACTGCTGACATCGAGCTTTCTACAAGGGACTTTCCGCTGGG
+GACTTTCCAGGGGAGGCGTGGCCTGGGCGGGGCAGGGGAGTGGCGAGCCCTCAGATGCTG
+CATATAAGCAGCTGCTTCTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTG
+GGAGCTCTCTGGCTGACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGT
+GCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACC
+CTTTTAGTCAGTGTGGAAAATCTCTAGCA
diff --git a/tests/expected-results-single-hxb2/nonintact.fasta b/tests/expected-results-single-hxb2/nonintact.fasta