| Previous changeset 0:99d31ec6629b (2021-10-12) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8eb3532d394f6a44d1edbcbe5ef05fd0474cdab3 |
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modified:
macros.xml test-data/out1.align1.fasta test-data/out1.align2.fasta test-data/out1.align3.fasta test-data/out1.alignment.fasta test-data/out1.bcf test-data/out1.consensus.fasta test-data/out1.fasta test-data/out1.txt test-data/out2.alignment.fasta test-data/out2.fasta test-data/out2.txt test-data/output1.fasta test-data/output1.json test-data/output2.fasta test-data/reference1.fasta tracy_assemble.xml |
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added:
test-data/input1_f.ab1 test-data/input1_r.ab1 test-data/out2.consensus.fasta |
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removed:
test-data/input1.ab1 |
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| diff -r 99d31ec6629b -r 897b1ff9e906 macros.xml --- a/macros.xml Tue Oct 12 14:20:41 2021 +0000 +++ b/macros.xml Thu Mar 20 07:18:34 2025 +0000 |
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| @@ -1,5 +1,6 @@ <macros> - <token name="@TOOL_VERSION@">0.6.1</token> + <token name="@TOOL_VERSION@">0.7.8</token> + <token name="@PROFILE@">23.1</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">tracy</requirement> |
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| diff -r 99d31ec6629b -r 897b1ff9e906 test-data/input1.ab1 |
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| Binary file test-data/input1.ab1 has changed |
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| diff -r 99d31ec6629b -r 897b1ff9e906 test-data/input1_f.ab1 |
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| Binary file test-data/input1_f.ab1 has changed |
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| diff -r 99d31ec6629b -r 897b1ff9e906 test-data/input1_r.ab1 |
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| Binary file test-data/input1_r.ab1 has changed |
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| diff -r 99d31ec6629b -r 897b1ff9e906 test-data/out1.align1.fasta --- a/test-data/out1.align1.fasta Tue Oct 12 14:20:41 2021 +0000 +++ b/test-data/out1.align1.fasta Thu Mar 20 07:18:34 2025 +0000 |
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| b'@@ -1,104 +1,114 @@\n->Alt1 (Estimated allelic Fraction: 0.52)\n-TCNGCNGGNGTNNTCCGTATTTTNNTTGGATCCNCATTCATAGCAAACACCANAAATCCATATTGGGACCACAA\n-TCCCAACAAAGACCACTGGACAGAAGCCAACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCCCAC\n-ACGGAGGCCTTTTGGGGTGGAGCCCTCAGGCTCAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCC\n-TCCACCAATCGACAGTCAGGAAGGCAGCCTACCCCAATCACTCCACCTTTGAGAGACACTCATCCTCAGGCCAT\n-GCAGTGGAATTCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAATCCTGCTGGTGGCTCCAGTTCCG\n-GAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATCTCGTCAATCTTCTCGAGGATTGGGGACCCTGCACCG\n-AACATGGAAAGCATCACATCAGGATTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAA\n-AATCCTCACAATACCGCAGAGTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGTGTC\n-TTGGCCAAAATTCGCAGTCCCAAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTCCTGCCTATCGC\n-TGGATGTGTCTGCGGCGGTTTATCATCTTCCTCTTCATCGTGCTGCTATGCCTCATCATCCTGTTGGGTTCGTC\n-TGCACTATCAAAGGTATGTTGCCCCGGTTTGTCNTTNNTAATTCCAAGGATCATGAAAGCCACCCACTACGGGA\n-ACCNTTGCCGCAAGCTGCACGACTCATTTCTCAAAGGAAANTCNANGNTTTTCCCTCATNGTTGCTGTTCAAAA\n-GCTTCGGACGGAAAATGCACATTGTAGTTNCNNATCCCATCATCATGGGNTTTGGGAAATNCCATATGGTANNG\n-GGCNNNAGCCCGCNTNNCCT\n->Ref X75657.1 Human hepatitis virus genotype E Bas preS1 preS2 S C X antigens core antigen X protein and polymerase:1-718 forward\n-TTCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAGAGGCCTGTATTTTCCTGCTGGTGGCTCCAGTT\n-CCGGAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATCTCGTCAATCTTCTCGAGGATTGGGGACCCTGCA\n-CCGAACATGGAAAGCATCACATCAGGATTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGAC\n-AAAAATCCTCACAATACCGCAGAGTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGT\n-GTCTTGGCCAAAATTCGCAGTCCCCAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTCCTGGCTAT\n-CGCTGGATGTGTCTGCGGCGTTTTATCATCTTCCTCTTCATCCTGCTGCTATGCCTCATCTTCTTGTTGGTTCT\n-TCTGGACTATCAAGGTATGTTGCCCGTTTGTCCTCTAATTCCAGGATCATCAACCACCAGTACGGGACCCTGCC\n-GAACCTGCACGACTCTTGCTCAAGGAACCTCTATGTTTCCCTCATGTTGCTGTTCAAAACCTTCGGACGGAAAT\n-TGCACTTGTATTCCCATCCCATCATCATGGGCTTTCGGAAAATTCCTATGGGAGTGGGCCTCAGCCCGTTTCTC\n-CTGGCTCAGTTTACTAGTGCCATTTGTTCAGTGGTTCGCCGGGCTTTCCCCC\n+>Alt1 (Estimated allelic Fraction: 0.63)\n+ACAGGCATTAATTTACGTGTTTCCTCAGCATGTGCAAGCATTTCTCGCAAATTCCAAGAAACAGTTCCAAGAAT\n+TTCTTCTTTCTCATTAGAGACAATGGATGGTAGTATGTAAAAAGCGCTCTTGCACTTTTTAAGCACTGTCTTTG\n+CCTCTTCTAATGTATAACCATTATTACCCTGTCCAGGGTAGGTGGTTATATAATTGTCTACTGGTAACTTCTTT\n+AATGCTTTTGTAAGCATTTCGGTAGTACCACCAGCTTTTTTAGTAGGTATAACTACAGCAGTTAAAACACCTTC\n+CTTAATGACATCACCTACTATGTAAGGAGCATCTTTCTTTAGAAAGGTGGTGTCAGTGTCTTTAACAAGCATGG\n+CAGAATCTGGATGAAGGTTGCCATTAATGTCTATATAAAGTAACAAATTCTCTGTGAGAAACTTAGTTTCTTCC\n+AAAGTGGTTGTAACTTCTTCAACACAAGCCTTGACTTTCTTTTCTTCAGCCTGTTGCTTTTGTTCAACTGAAGG\n+TTTATTTTCAGTTGTTGGTGGCTCAACTTCCATTTTAGGAACTTCAGCAATCTGTTGTTCTACTTGTGCCTCAC\n+TCTTCATTTCTAAAAAGCTAGAAACAAGTTTTTCATAGAGATCTTTGTCAAAGACAGTCAAGTAAACATTTGTG\n+CGAACAGTGTCTACACAAACTCTTAAGGATTGGACAGGGTCAGCACCAAAGATGCCTGCTGACAATAAAGGTGC\n+TAGTAAAGTATCATACTGATTGAAATTTTCATATGCAGTTTTAAGAAGTTGAATGCTTTCACCCTTGTTGATAT\n+TAGGACCAACAACATGAAGACAATTTTTAGCAAGATTATGTCCACTCAGAACACAACTACCACCAACATTCAGA\n+GGTCCGTTTGTGGCTATGTAATTGTCTGATTCTACTTGCATAGCGTTGTTTGTAGCTTTGTTTAAAGCTCCAGC\n+AACACCTCCTCCATGTTTAAGTAAACATTAGCTGCATTAACAACTACTGTTGTTTCCCCTGTT\n+>Ref MT121216.12501-5000 Pangolin coronavirus isolate MP789 complete genome:720-1846 reversecomplement\n+CCTTGTATTTACGTTGTATGGTTGAAACTATAGCTTTAGTTTCCATACAAACAGGCATTAATTTACGTGTTTCC\n+TCAGCATGTGCAAGCATTTCTCGCAAATTCCAAGAAACAGTTCCAAGAATTTCTTCTTTCTCATTAGAGACAAT\n+GGATGGTAGTATGTAAAAAGCGCTCTTGCACTTTTTAAGCACTGTCTTTGCCTCTTCTAATGTATAACCATTAT\n+TACCCTGTCCAGGGTAGGTGGTTATATAATTGTCTACTGGTAACTTCTTTAATGCTTTTGTAAGCATTTCGGTA\n+GTACCACCAGCTTTTTTAGTAGGTATAACTACAGCAGTTAAAACACCTTCCTTAATGACATCACCTACTATGTA\n+AGGAGCATCTTTCTTTAGAAAGGTGGTGTCAGTGTCTTTAACAAGCATGGCAGAATCTGGATGAAGGTTGCCAT\n+TAATGTCTATATAAAGTAACAAATTCTCTGTGAGAAACTTAGTTTCTTCCAAAGTGGTTGTAACTTCTTCAACA\n+CAAGCCTTGACTTTCTTTTCTTCAGCCTGTTGCTTTTGTTCAACTGAAGGTTTATTTTCAGTTGTTGGTGGCTC\n+AACTTCCATTTTAGGAACTTCAGCAATCTGTTGTTCTACTTGTGCCTCACTCTTCATTTCTAAAAAGCTAGAAA\n+CAAGTTTTTCATAGAGATCTTTGTCAAAGACAGTCAAGTAAACATTTGTGCGAACAGTGTCTACACAAACTCTT\n+AAGGATTGGACAGGGTCAGCACCAAAGATGCCTGCTGACAATAAAGGTGCTAGTAAAGTATCATACTGATTGAA\n+ATTTTCATATGCAGTTTTAAGA'..b'TTTCTAGGGGGAGCTCCCGTG\n+Ref 1306 CAGCCTGTTGCTTTTGTTCAACTGAAGGTTTATTTTCAGTTGTTGGTGGCTCAACTTCCA\n \n-Alt 589 TGTCTTGGCCAAAATTCGCAGTCCCAAACCTCCAGTCACTCACCAACCTCTTGTCCTCCA\n- ||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||\n-Ref 296 TGTCTTGGCCAAAATTCGCAGTCCCCAACCTCCAGTCACTCACCAACCTCTTGTCCTCCA\n+Alt 551 TTTTAGGAACTTCAGCAATCTGTTGTTCTACTTGTGCCTCACTCTTCATTTCTAAAAAGC\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Ref 1246 TTTTAGGAACTTCAGCAATCTGTTGTTCTACTTGTGCCTCACTCTTCATTTCTAAAAAGC\n \n-Alt 649 ATTTGTCCTGCCTATCGCTGGATGTGTCTGCGGCGGTTTATCATCTTCCTCTTCATCGTG\n- |||||||||| |||||||||||||||||||||||| ||||||||||||||||||||| ||\n-Ref 356 ATTTGTCCTGGCTATCGCTGGATGTGTCTGCGGCGTTTTATCATCTTCCTCTTCATCCTG\n+Alt 611 TAGAAACAAGTTTTTCATAGAGATCTTTGTCAAAGACAGTCAAGTAAACATTTGTGCGAA\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Ref 1186 TAGAAACAAGTTTTTCATAGAGATCTTTGTCAAAGACAGTCAAGTAAACATTTGTGCGAA\n \n-Alt 709 CTGCTATGCCTCATCATCCTGTTGGGTTCGTCTGCACTATCAAAGGTATGTTGCCCCGGT\n- ||||||||||||||| || |||||| ||| |||| |||||||| |||||||||||| ||\n-Ref 416 CTGCTATGCCTCATCTTCTTGTTGG-TTCTTCTGGACTATCAA-GGTATGTTGCCC--GT\n+Alt 671 CAGTGTCTACACAAACTCTTAAGGATTGGACAGGGTCAGCACCAAAGATGCCTGCTGACA\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Ref 1126 CAGTGTCTACACAAACTCTTAAGGATTGGACAGGGTCAGCACCAAAGATGCCTGCTGACA\n+\n+Alt 731 ATAAAGGTGCTAGTAAAGTATCATACTGATTGAAATTTTCATATGCAGTTTTAAGAAGTT\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Ref 1066 ATAAAGGTGCTAGTAAAGTATCATACTGATTGAAATTTTCATATGCAGTTTTAAGAAGTT\n \n-Alt 769 TTGTCNTTNNTAATTCCAAGGATCATGAAAGCCACCCACTACGGGAACCNTTGCCGCAAG\n- ||||| | |||||||| ||||||| || ||||| | ||||||| || ||||| || \n-Ref 472 TTGTCCTC--TAATTCCA-GGATCATCAA--CCACC-AGTACGGGACCC--TGCCG-AAC\n+Alt 791 GAATGCTTTCACCCTTGTTGATATTAGGACCAACAACATGAAGACAATTTTTAGCAAGAT\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Ref 1006 GAATGCTTTCACCCTTGTTGATATTAGGACCAACAACATGAAGACAATTTTTAGCAAGAT\n \n-Alt 829 CTGCACGACTCATTTCTCAAAGGAAANTCNANGNTTTTCCCTCATNGTTGCTGTTCAAAA\n- ||||||||||| || ||||| |||| || | | |||||||||| ||||||||||||||\n-Ref 523 CTGCACGACTC-TTGCTCAA-GGAACCTCTATG--TTTCCCTCAT-GTTGCTGTTCAAAA\n+Alt 851 TATGTCCACTCAGAACACAACTACCACCAACATTCAGAGGTCCGTTTGTGGCTATGTAAT\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Ref 946 TATGTCCACTCAGAACACAACTACCACCAACATTCAGAGGTCCGTTTGTGGCTATGTAAT\n \n-Alt 889 GCTTCGGACGGAAAATGCACATTGTAGTTNCNNATCCCATCATCATGGGNTTTGGGAAAT\n- ||||||||||||| ||||| ||||| | | |||||||||||||||| ||| ||||| \n-Ref 578 CCTTCGGACGGAAATTGCAC-TTGTATTCCC--ATCCCATCATCATGGGCTTTCGGAAAA\n+Alt 911 TGTCTGATTCTACTTGCATAGCGTTGTTTGTAGCTTTGTTTAAAGCTCCAGCAACACCTC\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Ref 886 TGTCTGATTCTACTTGCATAGCGTTGTTTGTAGCTTTGTTTAAAGCTCCAGCAACACCTC\n \n-Alt 949 NCCATATGGTANNGGGCNNNAGCCCGCNTNNCCT--------------------------\n- | ||||| | |||| |||||| | ||| \n-Ref 635 TTCCTATGGGAGTGGGCCTCAGCCCGTTTCTCCTGGCTCAGTTTACTAGTGCCATTTGTT\n+Alt 971 CTCCATGTTTAAG-TAAACATTAGCTGCATTAACAACTACTGTTG-TTTCCCCTGTT---\n+ ||||||||||||| ||||||||||||||||||||||||||||||| |||| |||||| \n+Ref 826 CTCCATGTTTAAGGTAAACATTAGCTGCATTAACAACTACTGTTGGTTTCACCTGTTTAG\n \n-Alt 983 ------------------------\n- \n-Ref 695 CAGTGGTTCGCCGGGCTTTCCCCC\n+Alt 1026 -----------------------------------------------\n+ \n+Ref 766 CTTCTTCCACAATGTCTGCATTTTTAATGAAAACATTGTTAGTGAGT\n \n #-------------------------------------------------------------------------\n #-------------------------------------------------------------------------\n' |
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| diff -r 99d31ec6629b -r 897b1ff9e906 test-data/out1.align2.fasta --- a/test-data/out1.align2.fasta Tue Oct 12 14:20:41 2021 +0000 +++ b/test-data/out1.align2.fasta Thu Mar 20 07:18:34 2025 +0000 |
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| b'@@ -1,104 +1,114 @@\n->Alt2 (Estimated allelic Fraction: 0.28)\n-TANTTNTTNGGNNGTCACTCGCCNNGGGGATCANAGTTATGTGGGGACATTANTCATTTTGTTTGGGATTTCCC\n-TCTCTTCTTAGAACACTGGACATAAGCCAACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCCCAC\n-ACGGAGGCCTTTTGGGGTGGAGCACTCAGGCTCAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCC\n-TCCACCAATCGACAGTCAGGAAGGCAGCCTACCCAAATTACACCACCTTTGAGAGACACTCATCCTCAGGCCAT\n-GCAGTGGAATTCCACAACATGCCACCAACCTCTGCAGGATCCCAAAGTAAGTCCTGCTGGTGGCTCCAGTTCCG\n-GAACAGTGAACCCTGTTCCGACTACAGCCTCACTCATCTCGTCAACCTTCTCGAGGATTGGGGACCCTGCACCG\n-AACATGGACAGCATCACATCAGGATTCCGATGACCCCCGCTCATGTTACAAGCGGGGTTTTTCTTGTTGACAAA\n-AATAAACAGGATACCGCGTAGACAACAGGCGTGGTGGACTTCTCTCTCTTTTGGAAGGGGAGGACCTTTGTGTG\n-ATGGTGGGAAATCTTAGTCCCTCGCCTCCAATCACTCTCCACCCTCTTGTGGGCCTAATTGAGGTGAGTCCCGC\n-TGAAAGAAGTGGCAGCGGGGTATCACATACCTCTTCATCTTGCGGGAGAGCCGCCACGTCCTGTGTGGGTGAGC\n-TCCCCCAGAACAAAAGGGTGTTGCGGGGGGGGGNGGNNACAAACCGCGGGGGGAAGGAGGGAACCCACTAAAAG\n-AACNGGTGCGGTTTCAAAAAAGGGACTGTTTAGTTGAGAANGGNCNGNCATTTTTCATANTTTCTGTGGGTGAG\n-TAAAAAACACGGGGGACGCAGATGGGAGGNTNNTCCAAACACCAAAAAANGAGGGAGGGGNAATTTATTCTNNA\n-AGGNNNGCGCAAGNCNNTTC\n->Ref X75657.1 Human hepatitis virus genotype E Bas preS1 preS2 S C X antigens core antigen X protein and polymerase:1-714 forward\n-TTCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAGAGGCCTGTATTTTCCTGCTGGTGGCTCCAGTT\n-CCGGAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATCTCGTCAATCTTCTCGAGGATTGGGGACCCTGCA\n-CCGAACATGGAAAGCATCACATCAGGATTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGAC\n-AAAAATCCTCACAATACCGCAGAGTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGT\n-GTCTTGGCCAAAATTCGCAGTCCCCAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTCCTGGCTAT\n-CGCTGGATGTGTCTGCGGCGTTTTATCATCTTCCTCTTCATCCTGCTGCTATGCCTCATCTTCTTGTTGGTTCT\n-TCTGGACTATCAAGGTATGTTGCCCGTTTGTCCTCTAATTCCAGGATCATCAACCACCAGTACGGGACCCTGCC\n-GAACCTGCACGACTCTTGCTCAAGGAACCTCTATGTTTCCCTCATGTTGCTGTTCAAAACCTTCGGACGGAAAT\n-TGCACTTGTATTCCCATCCCATCATCATGGGCTTTCGGAAAATTCCTATGGGAGTGGGCCTCAGCCCGTTTCTC\n-CTGGCTCAGTTTACTAGTGCCATTTGTTCAGTGGTTCGCCGGGCTTTC\n+>Alt2 (Estimated allelic Fraction: 0.34)\n+ACAGGCATTAATTTACGTGTTTCCTCAGCATGTGCAAGCATTTCTCGCAAATTCCAAGAAACAGTTCCAAGAAT\n+TTCTTCTTTCTCATTAGAGACAATGGATGGTAGTATGTAAAAAGCGCTCTTGCACTTTTTAAGCACTGTCTTTG\n+CCTCTTCTAATGTATAACCATTATTACCCTGTCCAGGGTAGGTGGTTATATAATTGTCTACTGGTAACTTCTTT\n+AATGCTTTTGTAAGCATTTCGGTAGTACCACCAGCTTTTTTAGTAGGTATAACTACAGCAGTTAAAACACCTTC\n+CTTAATGACATCACCTACTATGTAAGGAGCATCTTTCTTTAGAAAGGTGGTGTCAGTGTCTTTAACAAGCATGG\n+CAGAATCTGGATGAAGGTTGCCATTAATGTCTATATAAAGTAACAAATTCTCTGTGAGAAACTTAGTTTCTTCC\n+AAAGTGGTTGTAACTTCTTCAACACAAGCCTTGACTTTCTTTTCTTCAGCCTGTTGCTTTTGTTCAACTGAAGG\n+TTTATTTTCAGTTGTTGGTGGCTCAACTTCCATTTTAGGAACTTCAGCAATCTGTTGTTCTACTTGTGCCTCAC\n+TCTTCATTTCTAAAAAGCTAGAAACAAGTTTTTCATAGAGATCTTTGTCAAAGACAGTCAAGTAAACATTTGTG\n+CGAACAGTGTCTACACAAACTCTTAAGGATTGGACAGGGTCAGCACCAAAGATGCCTGCTGACAATAAAGGTGC\n+TAGTAAAGTATCATACTGATTGAAATTTTCATATGCAGTTTTAAGAAGTTGAATGCTTTCACCCTTGTTGATAT\n+TAGGACCAACAACATGAAGACAATTTTTAGCAAGATTATGTCCACTCAGAACACAACTACCACCAACATTCAGA\n+GGTCCGTTTGTGGCTATGTAAATGTCTGAATCTACTTGCATAGCGTTGTTTGTAGCTTTGTTTAAAGCTCCAGC\n+CACACCTTCTTCATGTTTAAGTAAACATTAGCTGCATTTACAACTACTGTGGTTTCACCTGTT\n+>Ref MT121216.12501-5000 Pangolin coronavirus isolate MP789 complete genome:720-1846 reversecomplement\n+CCTTGTATTTACGTTGTATGGTTGAAACTATAGCTTTAGTTTCCATACAAACAGGCATTAATTTACGTGTTTCC\n+TCAGCATGTGCAAGCATTTCTCGCAAATTCCAAGAAACAGTTCCAAGAATTTCTTCTTTCTCATTAGAGACAAT\n+GGATGGTAGTATGTAAAAAGCGCTCTTGCACTTTTTAAGCACTGTCTTTGCCTCTTCTAATGTATAACCATTAT\n+TACCCTGTCCAGGGTAGGTGGTTATATAATTGTCTACTGGTAACTTCTTTAATGCTTTTGTAAGCATTTCGGTA\n+GTACCACCAGCTTTTTTAGTAGGTATAACTACAGCAGTTAAAACACCTTCCTTAATGACATCACCTACTATGTA\n+AGGAGCATCTTTCTTTAGAAAGGTGGTGTCAGTGTCTTTAACAAGCATGGCAGAATCTGGATGAAGGTTGCCAT\n+TAATGTCTATATAAAGTAACAAATTCTCTGTGAGAAACTTAGTTTCTTCCAAAGTGGTTGTAACTTCTTCAACA\n+CAAGCCTTGACTTTCTTTTCTTCAGCCTGTTGCTTTTGTTCAACTGAAGGTTTATTTTCAGTTGTTGGTGGCTC\n+AACTTCCATTTTAGGAACTTCAGCAATCTGTTGTTCTACTTGTGCCTCACTCTTCATTTCTAAAAAGCTAGAAA\n+CAAGTTTTTCATAGAGATCTTTGTCAAAGACAGTCAAGTAAACATTTGTGCGAACAGTGTCTACACAAACTCTT\n+AAGGATTGGACAGGGTCAGCACCAAAGATGCCTGCTGACAATAAAGGTGCTAGTAAAGTATCATACTGATTGAA\n+ATTTTCATATGCAGTTTTAAGAAGTT'..b'|||||||||||||||||||||||||||||||||||||||||||||\n+Ref 1306 CAGCCTGTTGCTTTTGTTCAACTGAAGGTTTATTTTCAGTTGTTGGTGGCTCAACTTCCA\n \n-Alt 601 AAATCTTAGTCCCTCGCCTCCAATCACTCTCCACCCTCTTGTGGGCCTAATTGAGGTGAG\n- || || |||||| |||||| |||||| ||| |||||||| || | ||| || \n-Ref 308 AATTCGCAGTCCCCAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTCCTGGC\n+Alt 551 TTTTAGGAACTTCAGCAATCTGTTGTTCTACTTGTGCCTCACTCTTCATTTCTAAAAAGC\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Ref 1246 TTTTAGGAACTTCAGCAATCTGTTGTTCTACTTGTGCCTCACTCTTCATTTCTAAAAAGC\n \n-Alt 661 TCCCGCTGAAAGAAGTGGCAGCGGGGT---ATCACATACCTCTTCATCTTGCGGGAGAGC\n- | ||||| || ||| | |||| || |||| | |||||||||| ||| | ||\n-Ref 368 TATCGCTG---GATGTGTCTGCGGCGTTTTATCATCTTCCTCTTCATCCTGCTGCTATGC\n+Alt 611 TAGAAACAAGTTTTTCATAGAGATCTTTGTCAAAGACAGTCAAGTAAACATTTGTGCGAA\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Ref 1186 TAGAAACAAGTTTTTCATAGAGATCTTTGTCAAAGACAGTCAAGTAAACATTTGTGCGAA\n \n-Alt 718 CGCCACGTCCTGTGTGGGTGAGCTCCCCCAGAACAAAAGGGTGTTGCGGGGGGGGGNGGN\n- | | | || ||| ||| | || | | | || | |||||| | | \n-Ref 425 CTCATCTTCTTGT-TGGTT---CTTCTGGACTATCAAGGTATGTTGCCCGTTTGT-----\n+Alt 671 CAGTGTCTACACAAACTCTTAAGGATTGGACAGGGTCAGCACCAAAGATGCCTGCTGACA\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Ref 1126 CAGTGTCTACACAAACTCTTAAGGATTGGACAGGGTCAGCACCAAAGATGCCTGCTGACA\n+\n+Alt 731 ATAAAGGTGCTAGTAAAGTATCATACTGATTGAAATTTTCATATGCAGTTTTAAGAAGTT\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Ref 1066 ATAAAGGTGCTAGTAAAGTATCATACTGATTGAAATTTTCATATGCAGTTTTAAGAAGTT\n \n-Alt 778 NACAAACCGCGGGGGGAAGGAGGGAACCCACTAAAAGAACNGGTGCGGTTTCAAAAAAGG\n- || | |||| | | || | || || || | | | || |\n-Ref 476 ------CCTCTAATTCCAGGATC--ATCAACCACCAGTACGGGACCC--TGCCGAACCTG\n+Alt 791 GAATGCTTTCACCCTTGTTGATATTAGGACCAACAACATGAAGACAATTTTTAGCAAGAT\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Ref 1006 GAATGCTTTCACCCTTGTTGATATTAGGACCAACAACATGAAGACAATTTTTAGCAAGAT\n \n-Alt 838 GACTGTTTAGTTGAGAANGGNCNGNCATTTTTCATANTTTCTGTGGGTGAGTAAAAAACA\n- || | | | || | | || |||| | ||| | || | ||||| \n-Ref 526 CAC-GACTCTTGCTCAAGGAACCTCTATGTTTCCC---TCATGTTGCTG--TTCAAAAC-\n+Alt 851 TATGTCCACTCAGAACACAACTACCACCAACATTCAGAGGTCCGTTTGTGGCTATGTAAA\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| \n+Ref 946 TATGTCCACTCAGAACACAACTACCACCAACATTCAGAGGTCCGTTTGTGGCTATGTAAT\n \n-Alt 898 CGGGGGACGCAGATGGGAGGN-TNNTCCAAACACCAAAAAANGAGGGAGGGGNAATTTAT\n- | ||||| | || | | | ||| | | | | | | | || || || \n-Ref 579 CTTCGGACGGAAATTGCACTTGTATTCCCATCCCATCATCATGGGCTTTCGGAAAATTCC\n+Alt 911 TGTCTGAATCTACTTGCATAGCGTTGTTTGTAGCTTTGTTTAAAGCTCCAGCCACACCTT\n+ ||||||| |||||||||||||||||||||||||||||||||||||||||||| |||||| \n+Ref 886 TGTCTGATTCTACTTGCATAGCGTTGTTTGTAGCTTTGTTTAAAGCTCCAGCAACACCTC\n \n-Alt 957 TCTNNAAGGNNNGCGCAAGNCNNTTC----------------------------------\n- | | || | || | ||| \n-Ref 639 TATGGGAGTGGGCCTCAGCCCGTTTCTCCTGGCTCAGTTTACTAGTGCCATTTGTTCAGT\n+Alt 971 CTTCATGTTTAAG-TAAACATTAGCTGCATTTACAACTACTGT-GGTTTCACCTGTT---\n+ || |||||||||| ||||||||||||||||| ||||||||||| ||||||||||||| \n+Ref 826 CTCCATGTTTAAGGTAAACATTAGCTGCATTAACAACTACTGTTGGTTTCACCTGTTTAG\n \n-Alt 983 ----------------\n- \n-Ref 699 GGTTCGCCGGGCTTTC\n+Alt 1026 -----------------------------------------------\n+ \n+Ref 766 CTTCTTCCACAATGTCTGCATTTTTAATGAAAACATTGTTAGTGAGT\n \n #-------------------------------------------------------------------------\n #-------------------------------------------------------------------------\n' |
| b |
| diff -r 99d31ec6629b -r 897b1ff9e906 test-data/out1.align3.fasta --- a/test-data/out1.align3.fasta Tue Oct 12 14:20:41 2021 +0000 +++ b/test-data/out1.align3.fasta Thu Mar 20 07:18:34 2025 +0000 |
| b |
| b'@@ -1,104 +1,108 @@\n->Alt1 (Estimated allelic Fraction: 0.52)\n-TCNGCNGGNGTNNTCCGTATTTTNNTTGGATCCNCATTCATAGCAAACACCANAAATCCATATTGGGACCACAA\n-TCCCAACAAAGACCACTGGACAGAAGCCAACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCCCAC\n-ACGGAGGCCTTTTGGGGTGGAGCCCTCAGGCTCAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCC\n-TCCACCAATCGACAGTCAGGAAGGCAGCCTACCCCAATCACTCCACCTTTGAGAGACACTCATCCTCAGGCCAT\n-GCAGTGGAATTCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAATCCTGCTGGTGGCTCCAGTTCCG\n-GAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATCTCGTCAATCTTCTCGAGGATTGGGGACCCTGCACCG\n-AACATGGAAAGCATCACATCAGGATTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAA\n-AATCCTCACAATACCGCAGAGTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGTGTC\n-TTGGCCAAAATTCGCAGTCCCAAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTCCTGCCTATCGC\n-TGGATGTGTCTGCGGCGGTTTATCATCTTCCTCTTCATCGTGCTGCTATGCCTCATCATCCTGTTGGGTTCGTC\n-TGCACTATCAAAGGTATGTTGCCCCGGTTTGTCNTTNNTAATTCCAAGGATCATGAAAGCCACCCACTACGGGA\n-ACCNTTGCCGCAAGCTGCACGACTCATTTCTCAAAGGAAANTCNANGNTTTTCCCTCATNGTTGCTGTTCAAAA\n-GCTTCGGACGGAAAATGCACATTGTAGTTNCNNATCCCATCATCATGGGNTTTGGGAAATNCCATATGGTANNG\n-GGCNNNAGCCCGCNTNNCCT\n->Alt2 (Estimated allelic Fraction: 0.28)\n-TANTTNTTNGGNNGTCACTCGCCNNGGGGATCANAGTTATGTGGGGACATTANTCATTTTGTTTGGGATTTCCC\n-TCTCTTCTTAGAACACTGGACATAAGCCAACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCCCAC\n-ACGGAGGCCTTTTGGGGTGGAGCACTCAGGCTCAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCC\n-TCCACCAATCGACAGTCAGGAAGGCAGCCTACCCAAATTACACCACCTTTGAGAGACACTCATCCTCAGGCCAT\n-GCAGTGGAATTCCACAACATGCCACCAACCTCTGCAGGATCCCAAAGTAAGTCCTGCTGGTGGCTCCAGTTCCG\n-GAACAGTGAACCCTGTTCCGACTACAGCCTCACTCATCTCGTCAACCTTCTCGAGGATTGGGGACCCTGCACCG\n-AACATGGACAGCATCACATCAGGATTCCGATGACCCCCGCTCATGTTACAAGCGGGGTTTTTCTTGTTGACAAA\n-AATAAACAGGATACCGCGTAGACAACAGGCGTGGTGGACTTCTCTCTCTTTTGGAAGGGGAGGACCTTTGTGTG\n-ATGGTGGGAAATCTTAGTCCCTCGCCTCCAATCACTCTCCACCCTCTTGTGGGCCTAATTGAGGTGAGTCCCGC\n-TGAAAGAAGTGGCAGCGGGGTATCACATACCTCTTCATCTTGCGGGAGAGCCGCCACGTCCTGTGTGGGTGAGC\n-TCCCCCAGAACAAAAGGGTGTTGCGGGGGGGGGNGGNNACAAACCGCGGGGGGAAGGAGGGAACCCACTAAAAG\n-AACNGGTGCGGTTTCAAAAAAGGGACTGTTTAGTTGAGAANGGNCNGNCATTTTTCATANTTTCTGTGGGTGAG\n-TAAAAAACACGGGGGACGCAGATGGGAGGNTNNTCCAAACACCAAAAAANGAGGGAGGGGNAATTTATTCTNNA\n-AGGNNNGCGCAAGNCNNTTC\n+>Alt1 (Estimated allelic Fraction: 0.63)\n+ACAGGCATTAATTTACGTGTTTCCTCAGCATGTGCAAGCATTTCTCGCAAATTCCAAGAAACAGTTCCAAGAAT\n+TTCTTCTTTCTCATTAGAGACAATGGATGGTAGTATGTAAAAAGCGCTCTTGCACTTTTTAAGCACTGTCTTTG\n+CCTCTTCTAATGTATAACCATTATTACCCTGTCCAGGGTAGGTGGTTATATAATTGTCTACTGGTAACTTCTTT\n+AATGCTTTTGTAAGCATTTCGGTAGTACCACCAGCTTTTTTAGTAGGTATAACTACAGCAGTTAAAACACCTTC\n+CTTAATGACATCACCTACTATGTAAGGAGCATCTTTCTTTAGAAAGGTGGTGTCAGTGTCTTTAACAAGCATGG\n+CAGAATCTGGATGAAGGTTGCCATTAATGTCTATATAAAGTAACAAATTCTCTGTGAGAAACTTAGTTTCTTCC\n+AAAGTGGTTGTAACTTCTTCAACACAAGCCTTGACTTTCTTTTCTTCAGCCTGTTGCTTTTGTTCAACTGAAGG\n+TTTATTTTCAGTTGTTGGTGGCTCAACTTCCATTTTAGGAACTTCAGCAATCTGTTGTTCTACTTGTGCCTCAC\n+TCTTCATTTCTAAAAAGCTAGAAACAAGTTTTTCATAGAGATCTTTGTCAAAGACAGTCAAGTAAACATTTGTG\n+CGAACAGTGTCTACACAAACTCTTAAGGATTGGACAGGGTCAGCACCAAAGATGCCTGCTGACAATAAAGGTGC\n+TAGTAAAGTATCATACTGATTGAAATTTTCATATGCAGTTTTAAGAAGTTGAATGCTTTCACCCTTGTTGATAT\n+TAGGACCAACAACATGAAGACAATTTTTAGCAAGATTATGTCCACTCAGAACACAACTACCACCAACATTCAGA\n+GGTCCGTTTGTGGCTATGTAATTGTCTGATTCTACTTGCATAGCGTTGTTTGTAGCTTTGTTTAAAGCTCCAGC\n+AACACCTCCTCCATGTTTAAGTAAACATTAGCTGCATTAACAACTACTGTTGTTTCCCCTGTT\n+>Alt2 (Estimated allelic Fraction: 0.34)\n+ACAGGCATTAATTTACGTGTTTCCTCAGCATGTGCAAGCATTTCTCGCAAATTCCAAGAAACAGTTCCAAGAAT\n+TTCTTCTTTCTCATTAGAGACAATGGATGGTAGTATGTAAAAAGCGCTCTTGCACTTTTTAAGCACTGTCTTTG\n+CCTCTTCTAATGTATAACCATTATTACCCTGTCCAGGGTAGGTGGTTATATAATTGTCTACTGGTAACTTCTTT\n+AATGCTTTTGTAAGCATTTCGGTAGTACCACCAGCTTTTTTAGTAGGTATAACTACAGCAGTTAAAACACCTTC\n+CTTAATGACATCACCTACTATGTAAGGAGCATCTTTCTTTAGAAAGGTGGTGTCAGTGTCTTTAACAAGCATGG\n+CAGAATCTGGATGAAGGTTGCCATTAATGTCTATATAAAGTAACAAATTCTCTGTGAGAAACTTAGTTTCTTCC\n+AAAGTGGTTGTAACTTCTTCAACACAAGCCTTGACTTTCTTTTCTTCAGCCTGTTGCTTTTGTTCAACTGAAGG\n+TTTATTTTCAGTTGTTGGTGGCTCAACTTCCATTTTAGGAACTTCAGCAATCTGTTGTTCTACTTGTGCCTCAC\n+TCTTCATTTCTAAAAAGCTAGAAACAAGTTTTTCATAGAGATCTTTGTCAAAGACAGTCAAGTAAACATTTGTG\n+CGAACAGTGTCTACACAAACTCTTAAGGATTGGACAGGGTCAGCACCAAAGAT'..b'CCTCACAATACCGCAGAGT\n- | |||| ||||||| |||||||||||||||||||||||||| || ||||||| || \n-Alt2 481 CCGCTCATGTTACAAGCGGGGTTTTTCTTGTTGACAAAAATAAACAGGATACCGCGTAGA\n+Alt1 541 TCAACTTCCATTTTAGGAACTTCAGCAATCTGTTGTTCTACTTGTGCCTCACTCTTCATT\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Alt2 541 TCAACTTCCATTTTAGGAACTTCAGCAATCTGTTGTTCTACTTGTGCCTCACTCTTCATT\n \n-Alt1 541 CTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGTGTCTTGGCCAA\n- | | | ||||||||||||||||| |||| | |||||| || ||||| ||| \n-Alt2 541 CAACAGGCGTGGTGGACTTCTCTCTCTTTTGGAAGGGGAGGACCTTTGTGTGATGGTGGG\n+Alt1 601 TCTAAAAAGCTAGAAACAAGTTTTTCATAGAGATCTTTGTCAAAGACAGTCAAGTAAACA\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Alt2 601 TCTAAAAAGCTAGAAACAAGTTTTTCATAGAGATCTTTGTCAAAGACAGTCAAGTAAACA\n \n-Alt1 601 AATTCGCAGTCCCAAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTCCTGCC\n- || || |||||| |||||| |||||| ||| |||||||| || | ||| || \n-Alt2 601 AAATCTTAGTCCCTCGCCTCCAATCACTCTCCACCCTCTTGTGGGCCTAATTGAGGTGAG\n+Alt1 661 TTTGTGCGAACAGTGTCTACACAAACTCTTAAGGATTGGACAGGGTCAGCACCAAAGATG\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Alt2 661 TTTGTGCGAACAGTGTCTACACAAACTCTTAAGGATTGGACAGGGTCAGCACCAAAGATG\n \n-Alt1 661 TATCGCTGGATGTGTCTGCGGCGGTTTATCATCTTCCTCTTCATCGTGCTGCTATGCCTC\n- | ||||| | | || |||| ||||| | |||||||||| ||| | ||| |\n-Alt2 661 TCCCGCTGAAAGAAGTGGCAGCGGGGTATCACATACCTCTTCATCTTGCGGGAGAGCCGC\n+Alt1 721 CCTGCTGACAATAAAGGTGCTAGTAAAGTATCATACTGATTGAAATTTTCATATGCAGTT\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Alt2 721 CCTGCTGACAATAAAGGTGCTAGTAAAGTATCATACTGATTGAAATTTTCATATGCAGTT\n \n-Alt1 721 ATCATCCTGT-TGGGTTCG-TCTGCACTATCAAAGGTATGTTGCCCCGGTTTGTCNTTNN\n- | |||||| ||||| | || | | |||| | |||||| || | | ||\n-Alt2 721 CACGTCCTGTGTGGGTGAGCTCCCCCAGAACAAAAGGGTGTTGCGGGGGGGGG--NGGNN\n+Alt1 781 TTAAGAAGTTGAATGCTTTCACCCTTGTTGATATTAGGACCAACAACATGAAGACAATTT\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Alt2 781 TTAAGAAGTTGAATGCTTTCACCCTTGTTGATATTAGGACCAACAACATGAAGACAATTT\n \n-Alt1 779 TAATTCCAAGGATC-ATGAAAGCCACCCACTACGGGAACCNTTGCCGC-----AAGCTGC\n- | || || | | | | |||||||| |||| ||| | || | \n-Alt2 779 ACAAACCGCGGGGGGAAGGAGGGAACCCACTAAAAGAACNGGTGCGGTTTCAAAAAAGGG\n+Alt1 841 TTAGCAAGATTATGTCCACTCAGAACACAACTACCACCAACATTCAGAGGTCCGTTTGTG\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Alt2 841 TTAGCAAGATTATGTCCACTCAGAACACAACTACCACCAACATTCAGAGGTCCGTTTGTG\n \n-Alt1 833 ACGACTCATTTCTCAAAGGAAANTCNANGNTTTTCCCTCATNGTTGCTGT-------TCA\n- || | | || || || || | |||| |||| || |||| | |\n-Alt2 839 ACTGTTTAGTTGAGAANGGN----CNGNCATTTT---TCATANTTTCTGTGGGTGAGTAA\n+Alt1 901 GCTATGTAATTGTCTGATTCTACTTGCATAGCGTTGTTTGTAGCTTTGTTTAAAGCTCCA\n+ ||||||||| ||||||| ||||||||||||||||||||||||||||||||||||||||||\n+Alt2 901 GCTATGTAAATGTCTGAATCTACTTGCATAGCGTTGTTTGTAGCTTTGTTTAAAGCTCCA\n \n-Alt1 886 AAAGCTTCGGACGGAAAATGCACATTGTAGTTNCNNATCCCATCATCAT-----GGGNTT\n- ||| | |||| | ||| || | || | || ||| | || || | | \n-Alt2 892 AAAAC-----ACGGGGGACGCAGATGGGAGG-NTNN-TCCAAACACCAAAAAANGAGGGA\n+Alt1 961 GCAACACCTCCTCCATGTTTAAGTAAACATTAGCTGCATTAACAACTACTGTTGTTTCCC\n+ || |||||| || ||||||||||||||||||||||||||| ||||||||||| ||||| |\n+Alt2 961 GCCACACCTTCTTCATGTTTAAGTAAACATTAGCTGCATTTACAACTACTGTGGTTTCAC\n \n-Alt1 941 TGGGAAATNCCATATGGTANNGGGCNNNAGCCCGCNTNNCCT\n- ||| ||| ||| | | || || || | | || \n-Alt2 945 GGGGNAATT---TATTCTNNAAGGNNNGCGCAAG-NCNNTTC\n+Alt1 1021 CTGTT\n+ |||||\n+Alt2 1021 CTGTT\n \n #-------------------------------------------------------------------------\n #-------------------------------------------------------------------------\n' |
| b |
| diff -r 99d31ec6629b -r 897b1ff9e906 test-data/out1.alignment.fasta --- a/test-data/out1.alignment.fasta Tue Oct 12 14:20:41 2021 +0000 +++ b/test-data/out1.alignment.fasta Thu Mar 20 07:18:34 2025 +0000 |
| b |
| @@ -1,4 +1,4 @@ ->input1 (forward) -TATTGGGACCACAATCCCAACAAAGACCACTGGACAGAAGCCAACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCCCACACGGAGGCCTTTTGGGGTGGAGCCCTCAGGCTCAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCCTCCACCAATCGACAGTCAGGAAGGCAGCCTACCCCAATCACTCCACCTTTGAGAGACACTCATCCTCAGGCCATGCAGTGGAATTCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAATCCTGCTGGTGGCTCCAGTTCCGGAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATCTCGTCAATCTTCTCGAGGATTGGGGACCCTGCACCGAACATGGAAAGCATCACATCAGGATTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAAAATCCTCACAATACCGCAGAGTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGTGTCTTGGCCAAAATTCTCAGTCCCAAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTC ->input1 (forward) -TATTGGGACCACAATCCCAACAAAGACCACTGGACAGAAGCCAACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCCCACACGGAGGCCTTTTGGGGTGGAGCCCTCAGGCTCAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCCTCCACCAATCGACAGTCAGGAAGGCAGCCTACCCCAATCACTCCACCTTTGAGAGACACTCATCCTCAGGCCATGCAGTGGAATTCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAATCCTGCTGGTGGCTCCAGTTCCGGAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATCTCGTCAATCTTCTCGAGGATTGGGGACCCTGCACCGAACATGGAAAGCATCACATCAGGATTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAAAATCCTCACAATACCGCAGAGTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGTGTCTTGGCCAAAATTCTCAGTCCCAAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTC +>dataset_7d5c1ca2-834e-418b-b20b-df3f1b6c4f5d (reverse) +-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGACAGTCAAGTAAACATTTGTGCGAACAGTGTCTACACAAACTCTTAAGGATTGGACAGGGTCAGCACCAAAGATGCCTGCTGACAATAAAGGTGCTAGTAAAGTATCATACTGATTGAAATTTTCATATGCAGTTTTAAGAAGTTGAATGCTTTCACCCTTGTTGATATTAGGACCAACAACATGAAGACAATTTTTAGCAAGATTATGTCCACTCAGAACACAACTACCACCAACATTCAGAGGTCCGTTTGTGGCTATGTAATTGTCTGATTCTACTTGCATAGCGTTGTTTGTAGCTTTGTTTAAAGCTCCAGCAACACCTCCTCCATGTTTAAGGTAAACATTAGCTGCATTAACAACTACTGTTGGTTTCACCTGTTTAGCTTCTTCCACAATGTCTGCATTTTTAATGAAAACATTGTTAGTGAGTTTTAAATAACCAGTAAAATTGTTCACTGATTCATTTATCTCAGAGACAACTGGTGTAGAGTCAATCTCCTGAGATTGCACTTCAACAGTTGTTGTCTGCTCTTCTTGCATAGCAATTTCCTCATTGCCATCTTCTAACCAATCTTCCTCTGGTTCTTCTTCTATTTGAGAAGCAGAAGAGGTTGAACCAAATTCCAAAGATTTACCTTGGTAATCATCCTCTGTACCATACTCATACTGAGTTGATGGTTCATACTGTTCCTCTTCACACTCATCTTCTTCATAATCCTCATCTGGAGGATAGAAAGAACAGTACATATGAGAGGCTAAATTAAACTC +>dataset_41387b57-448c-4975-a12c-7f4c35e7ad3f (forward) +GCTTTAGTTTCCATACAAACAGGCATTAATTTACGTGTTTCCTCAGCATGTGCAAGCATTTCTCGCAAATTCCAAGAAACAGTTCCAAGAATTTCTTCTTTCTCATTAGAGACAATGGATGGTAGTATGTAAAAAGCGCTCTTGCACTTTTTAAGCACTGTCTTTGCCTCTTCTAATGTATAACCATTATTACCCTGTCCAGGGTAGGTGGTTATATAATTGTCTACTGGTAACTTCTTTAATGCTTTTGTAAGCATTTCGGTAGTACCACCAGCTTTTTTAGTAGGTATAACTACAGCAGTTAAAACACCTTCCTTAATGACATCACCTACTATGTAAGGAGCATCTTTCTTTAGAAAGGTGGTGTCAGTGTCTTTAACAAGCATGGCAGAATCTGGATGAAGGTTGCCATTAATGTCTATATAAAGTAACAAATTCTCTGTGAGAAACTTAGTTTCTTCCAAAGTGGTTGTAACTTCTTCAACACAAGCCTTGACTTTCTTTTCTTCAGCCTGTTGCTTTTGTTCAACTGAAGGTTTATTTTCAGTTGTTGGTGGCTCAACTTCCATTTTAGGAACTTCAGCAATCTGTTGTTCTACTTGTGCCTCACTCTTCATTTCTAAAAAGCTAGAAACAAGTTTTTCATAGAGATCTTTGTCAAAGACAGTCAAGTAAACATTTGTGCGAACAGTGTCTACACAAACTCTTAAGGATTGGACAGGGTCAGCACCAAAGATGCCTGCTGACAATAAAGGTGCTAGTAAAGTATCATACTGATTGAAATTTTCATATGCAGT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| b |
| diff -r 99d31ec6629b -r 897b1ff9e906 test-data/out1.bcf |
| b |
| Binary file test-data/out1.bcf has changed |
| b |
| diff -r 99d31ec6629b -r 897b1ff9e906 test-data/out1.consensus.fasta --- a/test-data/out1.consensus.fasta Tue Oct 12 14:20:41 2021 +0000 +++ b/test-data/out1.consensus.fasta Thu Mar 20 07:18:34 2025 +0000 |
| b |
| @@ -1,2 +1,2 @@ >Consensus -TATTGGGACCACAATCCCAACAAAGACCACTGGACAGAAGCCAACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCCCACACGGAGGCCTTTTGGGGTGGAGCCCTCAGGCTCAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCCTCCACCAATCGACAGTCAGGAAGGCAGCCTACCCCAATCACTCCACCTTTGAGAGACACTCATCCTCAGGCCATGCAGTGGAATTCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAATCCTGCTGGTGGCTCCAGTTCCGGAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATCTCGTCAATCTTCTCGAGGATTGGGGACCCTGCACCGAACATGGAAAGCATCACATCAGGATTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAAAATCCTCACAATACCGCAGAGTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGTGTCTTGGCCAAAATTCTCAGTCCCAAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTC +GCTTTAGTTTCCATACAAACAGGCATTAATTTACGTGTTTCCTCAGCATGTGCAAGCATTTCTCGCAAATTCCAAGAAACAGTTCCAAGAATTTCTTCTTTCTCATTAGAGACAATGGATGGTAGTATGTAAAAAGCGCTCTTGCACTTTTTAAGCACTGTCTTTGCCTCTTCTAATGTATAACCATTATTACCCTGTCCAGGGTAGGTGGTTATATAATTGTCTACTGGTAACTTCTTTAATGCTTTTGTAAGCATTTCGGTAGTACCACCAGCTTTTTTAGTAGGTATAACTACAGCAGTTAAAACACCTTCCTTAATGACATCACCTACTATGTAAGGAGCATCTTTCTTTAGAAAGGTGGTGTCAGTGTCTTTAACAAGCATGGCAGAATCTGGATGAAGGTTGCCATTAATGTCTATATAAAGTAACAAATTCTCTGTGAGAAACTTAGTTTCTTCCAAAGTGGTTGTAACTTCTTCAACACAAGCCTTGACTTTCTTTTCTTCAGCCTGTTGCTTTTGTTCAACTGAAGGTTTATTTTCAGTTGTTGGTGGCTCAACTTCCATTTTAGGAACTTCAGCAATCTGTTGTTCTACTTGTGCCTCACTCTTCATTTCTAAAAAGCTAGAAACAAGTTTTTCATAGAGATCTTTGTCAAAGACAGTCAAGTAAACATTTGTGCGAACAGTGTCTACACAAACTCTTAAGGATTGGACAGGGTCAGCACCAAAGATGCCTGCTGACAATAAAGGTGCTAGTAAAGTATCATACTGATTGAAATTTTCATATGCAGTTTTAAGAAGTTGAATGCTTTCACCCTTGTTGATATTAGGACCAACAACATGAAGACAATTTTTAGCAAGATTATGTCCACTCAGAACACAACTACCACCAACATTCAGAGGTCCGTTTGTGGCTATGTAATTGTCTGATTCTACTTGCATAGCGTTGTTTGTAGCTTTGTTTAAAGCTCCAGCAACACCTCCTCCATGTTTAAGGTAAACATTAGCTGCATTAACAACTACTGTTGGTTTCACCTGTTTAGCTTCTTCCACAATGTCTGCATTTTTAATGAAAACATTGTTAGTGAGTTTTAAATAACCAGTAAAATTGTTCACTGATTCATTTATCTCAGAGACAACTGGTGTAGAGTCAATCTCCTGAGATTGCACTTCAACAGTTGTTGTCTGCTCTTCTTGCATAGCAATTTCCTCATTGCCATCTTCTAACCAATCTTCCTCTGGTTCTTCTTCTATTTGAGAAGCAGAAGAGGTTGAACCAAATTCCAAAGATTTACCTTGGTAATCATCCTCTGTACCATACTCATACTGAGTTGATGGTTCATACTGTTCCTCTTCACACTCATCTTCTTCATAATCCTCATCTGGAGGATAGAAAGAACAGTACATATGAGAGGCTAAATTAAACTC |
| b |
| diff -r 99d31ec6629b -r 897b1ff9e906 test-data/out1.fasta --- a/test-data/out1.fasta Tue Oct 12 14:20:41 2021 +0000 +++ b/test-data/out1.fasta Thu Mar 20 07:18:34 2025 +0000 |
| b |
| @@ -1,4 +1,4 @@ ->input1 -TTTTTTTTTGAGCGGGTCGAACCGTCACGAAAAGAAAAGGGGAAGAACCATCAGCAGGAGTAATCCGTATTTTAATTGGATCCACATTCATAGCAAACACCAAAAATCCATATTGGGACCACAATCCCAACAAAGACCACTGGACAGAAGCCAACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCCCACACGGAGGCCTTTTGGGGTGGAGCCCTCAGGCTCAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCCTCCACCAATCGACAGTCAGGAAGGCAGCCTACCCCAATCACTCCACCTTTGAGAGACACTCATCCTCAGGCCATGCAGTGGAATTCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAA------------TCCTGCTGGTGGCTCCAGTTCCGGAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATCTCGTCAATCTTCTCGAGGATTGGGGACCCTGCACCGAACATGGAAAGCATCACATCAGGATTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAAAATCCTCACAATACCGCAGAGTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGTGTCTTGGCCAAAATTCTCAGTCCCAAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTCCTGCCTATCGCTGGATGTGTCTGCGGCGGTTTATCATATTCCTCTTCATCGTGCTGCTATGCCTCATCATCCTGTTGGGTTCGTCTGCACCATCAAAAGAATGTTGCCCCGGGTTGTGATTAAAAATTCCAAGGAGCAAGAAAGCCACCCACTACGGGAACCAGGGCCGGAAGCTGAACAAGTCATTTTTCAAAGGAAAATGAAAGATTTTCTTTCTTATTTGTGGGGGAAAAGCAAAAAAAGGAAAAAGGAAATTGGGGTTACAAACCCCACCCCCAAGGGATTTGGGAAATACCATATTTTAAAGGGGAAAGGGCCGCATAACCCATTAAAAATTGCATATTTTA-AATTTTTTTTTTTTGAGAAAGAGGGGGGAC-------- ->X75657.1 Human hepatitis virus genotype E Bas preS1 preS2 S C X antigens core antigen X protein and polymerase (forward) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAGAGGCCTGTATTTTCCTGCTGGTGGCTCCAGTTCCGGAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATCTCGTCAATCTTCTCGAGGATTGGGGACCCTGCACCGAACATGGAAAGCATCACATCAGGATTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAAAATCCTCACAATACCGCAGAGTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGTGTCTTGGCCAAAATTCGCAGTCCCCAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTCCTGGCTATCGCTGGATGTGTCTGCGGCGTTTTATCATCTTCCTCTTCATCCTGCTGCTATGCCTCATCTTCTTGTT-GGTTCTTCTGGACTATCA-AGGTATGTTGCCC--GTTTGTCCT--CTAATTCCA-GGATCATCAA--CCA-CCAGTACGGGACCC--TGCCG-AACCTGCACGACTC-TTGCTCAA-GGAACCTCTATG--TTTCCCTCAT-GTTGCTGTTCAAAACCTTCGGACGGAAATTGCAC-TTGTA--TTCCCATCCCATCATCATGGGCTTTCGGAAAATTCCTATGGGAGTGGGCCTCAGCCCGTTTCTCC---------TGGCTCAGTTTACTAGTGCCATTTGTTCAGTGGTTCGCCGGGCTTTCCCCC +>dataset_41387b57-448c-4975-a12c-7f4c35e7ad3f +TTCCTTGT-TTTACGTTGTATGGTTGAA-CTATAGCTTTAGTTTCCATACAAACAGGCATTAATTTACGTGTTTCCTCAGCATGTGCAAGCATTTCTCGCAAATTCCAAGAAACAGTTCCAAGAATTTCTTCTTTCTCATTAGAGACAATGGATGGTAGTATGTAAAAAGCGCTCTTGCACTTTTTAAGCACTGTCTTTGCCTCTTCTAATGTATAACCATTATTACCCTGTCCAGGGTAGGTGGTTATATAATTGTCTACTGGTAACTTCTTTAATGCTTTTGTAAGCATTTCGGTAGTACCACCAGCTTTTTTAGTAGGTATAACTACAGCAGTTAAAACACCTTCCTTAATGACATCACCTACTATGTAAGGAGCATCTTTCTTTAGAAAGGTGGTGTCAGTGTCTTTAACAAGCATGGCAGAATCTGGATGAAGGTTGCCATTAATGTCTATATAAAGTAACAAATTCTCTGTGAGAAACTTAGTTTCTTCCAAAGTGGTTGTAACTTCTTCAACACAAGCCTTGACTTTCTTTTCTTCAGCCTGTTGCTTTTGTTCAACTGAAGGTTTATTTTCAGTTGTTGGTGGCTCAACTTCCATTTTAGGAACTTCAGCAATCTGTTGTTCTACTTGTGCCTCACTCTTCATTTCTAAAAAGCTAGAAACAAGTTTTTCATAGAGATCTTTGTCAAAGACAGTCAAGTAAACATTTGTGCGAACAGTGTCTACACAAACTCTTAAGGATTGGACAGGGTCAGCACCAAAGATGCCTGCTGACAATAAAGGTGCTAGTAAAGTATCATACTGATTGAAATTTTCATATGCAGTTTTAAGAAGTTGAATGCTTTCACCCTTGTTGATATTAGGACCAACAACATGAAGACAATTTTTAGCAAGATTATGTCCACTCAGAACACAACTACCACCAACATTCAGAGGTCCGTTTGTGGCTATGTAATTGTCTGATTCTACTTGCATAGCGTTGTTTGTAGCTTTGTTTAAAGCTCCAGCAACACCTCCTCCATGTTTAAG-TAAACATTAGCTGCATTAACAACTACTGT-GGTTTCCCCTGTT-AGCTTCTTCCACAATGTCTGCATTTTTAATGAAAACATTTGTTAGGGGAG +>MT121216.12501-5000 Pangolin coronavirus isolate MP789 complete genome (reverse) +--CCTTGTATTTACGTTGTATGGTTGAAACTATAGCTTTAGTTTCCATACAAACAGGCATTAATTTACGTGTTTCCTCAGCATGTGCAAGCATTTCTCGCAAATTCCAAGAAACAGTTCCAAGAATTTCTTCTTTCTCATTAGAGACAATGGATGGTAGTATGTAAAAAGCGCTCTTGCACTTTTTAAGCACTGTCTTTGCCTCTTCTAATGTATAACCATTATTACCCTGTCCAGGGTAGGTGGTTATATAATTGTCTACTGGTAACTTCTTTAATGCTTTTGTAAGCATTTCGGTAGTACCACCAGCTTTTTTAGTAGGTATAACTACAGCAGTTAAAACACCTTCCTTAATGACATCACCTACTATGTAAGGAGCATCTTTCTTTAGAAAGGTGGTGTCAGTGTCTTTAACAAGCATGGCAGAATCTGGATGAAGGTTGCCATTAATGTCTATATAAAGTAACAAATTCTCTGTGAGAAACTTAGTTTCTTCCAAAGTGGTTGTAACTTCTTCAACACAAGCCTTGACTTTCTTTTCTTCAGCCTGTTGCTTTTGTTCAACTGAAGGTTTATTTTCAGTTGTTGGTGGCTCAACTTCCATTTTAGGAACTTCAGCAATCTGTTGTTCTACTTGTGCCTCACTCTTCATTTCTAAAAAGCTAGAAACAAGTTTTTCATAGAGATCTTTGTCAAAGACAGTCAAGTAAACATTTGTGCGAACAGTGTCTACACAAACTCTTAAGGATTGGACAGGGTCAGCACCAAAGATGCCTGCTGACAATAAAGGTGCTAGTAAAGTATCATACTGATTGAAATTTTCATATGCAGTTTTAAGAAGTTGAATGCTTTCACCCTTGTTGATATTAGGACCAACAACATGAAGACAATTTTTAGCAAGATTATGTCCACTCAGAACACAACTACCACCAACATTCAGAGGTCCGTTTGTGGCTATGTAATTGTCTGATTCTACTTGCATAGCGTTGTTTGTAGCTTTGTTTAAAGCTCCAGCAACACCTCCTCCATGTTTAAGGTAAACATTAGCTGCATTAACAACTACTGTTGGTTTCACCTGTTTAGCTTCTTCCACAATGTCTGCATTTTTAATGAAAACA-TTGTTAGTGAGT |
| b |
| diff -r 99d31ec6629b -r 897b1ff9e906 test-data/out1.txt --- a/test-data/out1.txt Tue Oct 12 14:20:41 2021 +0000 +++ b/test-data/out1.txt Thu Mar 20 07:18:34 2025 +0000 |
| b |
| b'@@ -1,109 +1,116 @@\n >Alt\n-TTTTTTTTTGAGCGGGTCGAACCGTCACGAAAAGAAAAGGGGAAGAACCATCAGCAGGAGTAATCCGTATTTTA\n-ATTGGATCCACATTCATAGCAAACACCAAAAATCCATATTGGGACCACAATCCCAACAAAGACCACTGGACAGA\n-AGCCAACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCCCACACGGAGGCCTTTTGGGGTGGAGCC\n-CTCAGGCTCAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCCTCCACCAATCGACAGTCAGGAAGG\n-CAGCCTACCCCAATCACTCCACCTTTGAGAGACACTCATCCTCAGGCCATGCAGTGGAATTCCACAACATTCCA\n-CCAAGCTCTGCAGGATCCCAGAGTAAATCCTGCTGGTGGCTCCAGTTCCGGAACAGTGAACCCTGTTCCGACTA\n-CTGCCTCACTCATCTCGTCAATCTTCTCGAGGATTGGGGACCCTGCACCGAACATGGAAAGCATCACATCAGGA\n-TTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAAAATCCTCACAATACCGCAGAGTCT\n-AGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGTGTCTTGGCCAAAATTCTCAGTCCCAAA\n-CCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTCCTGCCTATCGCTGGATGTGTCTGCGGCGGTTTATC\n-ATATTCCTCTTCATCGTGCTGCTATGCCTCATCATCCTGTTGGGTTCGTCTGCACCATCAAAAGAATGTTGCCC\n-CGGGTTGTGATTAAAAATTCCAAGGAGCAAGAAAGCCACCCACTACGGGAACCAGGGCCGGAAGCTGAACAAGT\n-CATTTTTCAAAGGAAAATGAAAGATTTTCTTTCTTATTTGTGGGGGAAAAGCAAAAAAAGGAAAAAGGAAATTG\n-GGGTTACAAACCCCACCCCCAAGGGATTTGGGAAATACCATATTTTAAAGGGGAAAGGGCCGCATAACCCATTA\n-AAAATTGCATATTTTAAATTTTTTTTTTTTGAGAAAGAGGGGGGAC\n->Ref X75657.1 Human hepatitis virus genotype E Bas preS1 preS2 S C X antigens core antigen X protein and polymerase:1-718 forward\n-TTCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAGAGGCCTGTATTTTCCTGCTGGTGGCTCCAGTT\n-CCGGAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATCTCGTCAATCTTCTCGAGGATTGGGGACCCTGCA\n-CCGAACATGGAAAGCATCACATCAGGATTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGAC\n-AAAAATCCTCACAATACCGCAGAGTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGT\n-GTCTTGGCCAAAATTCGCAGTCCCCAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTCCTGGCTAT\n-CGCTGGATGTGTCTGCGGCGTTTTATCATCTTCCTCTTCATCCTGCTGCTATGCCTCATCTTCTTGTTGGTTCT\n-TCTGGACTATCAAGGTATGTTGCCCGTTTGTCCTCTAATTCCAGGATCATCAACCACCAGTACGGGACCCTGCC\n-GAACCTGCACGACTCTTGCTCAAGGAACCTCTATGTTTCCCTCATGTTGCTGTTCAAAACCTTCGGACGGAAAT\n-TGCACTTGTATTCCCATCCCATCATCATGGGCTTTCGGAAAATTCCTATGGGAGTGGGCCTCAGCCCGTTTCTC\n-CTGGCTCAGTTTACTAGTGCCATTTGTTCAGTGGTTCGCCGGGCTTTCCCCC\n+TTCCTTGTTTTACGTTGTATGGTTGAACTATAGCTTTAGTTTCCATACAAACAGGCATTAATTTACGTGTTTCC\n+TCAGCATGTGCAAGCATTTCTCGCAAATTCCAAGAAACAGTTCCAAGAATTTCTTCTTTCTCATTAGAGACAAT\n+GGATGGTAGTATGTAAAAAGCGCTCTTGCACTTTTTAAGCACTGTCTTTGCCTCTTCTAATGTATAACCATTAT\n+TACCCTGTCCAGGGTAGGTGGTTATATAATTGTCTACTGGTAACTTCTTTAATGCTTTTGTAAGCATTTCGGTA\n+GTACCACCAGCTTTTTTAGTAGGTATAACTACAGCAGTTAAAACACCTTCCTTAATGACATCACCTACTATGTA\n+AGGAGCATCTTTCTTTAGAAAGGTGGTGTCAGTGTCTTTAACAAGCATGGCAGAATCTGGATGAAGGTTGCCAT\n+TAATGTCTATATAAAGTAACAAATTCTCTGTGAGAAACTTAGTTTCTTCCAAAGTGGTTGTAACTTCTTCAACA\n+CAAGCCTTGACTTTCTTTTCTTCAGCCTGTTGCTTTTGTTCAACTGAAGGTTTATTTTCAGTTGTTGGTGGCTC\n+AACTTCCATTTTAGGAACTTCAGCAATCTGTTGTTCTACTTGTGCCTCACTCTTCATTTCTAAAAAGCTAGAAA\n+CAAGTTTTTCATAGAGATCTTTGTCAAAGACAGTCAAGTAAACATTTGTGCGAACAGTGTCTACACAAACTCTT\n+AAGGATTGGACAGGGTCAGCACCAAAGATGCCTGCTGACAATAAAGGTGCTAGTAAAGTATCATACTGATTGAA\n+ATTTTCATATGCAGTTTTAAGAAGTTGAATGCTTTCACCCTTGTTGATATTAGGACCAACAACATGAAGACAAT\n+TTTTAGCAAGATTATGTCCACTCAGAACACAACTACCACCAACATTCAGAGGTCCGTTTGTGGCTATGTAATTG\n+TCTGATTCTACTTGCATAGCGTTGTTTGTAGCTTTGTTTAAAGCTCCAGCAACACCTCCTCCATGTTTAAGTAA\n+ACATTAGCTGCATTAACAACTACTGTGGTTTCCCCTGTTAGCTTCTTCCACAATGTCTGCATTTTTAATGAAAA\n+CATTTGTTAGGGGAG\n+>Ref MT121216.12501-5000 Pangolin coronavirus isolate MP789 complete genome:720-1846 reversecomplement\n+CCTTGTATTTACGTTGTATGGTTGAAACTATAGCTTTAGTTTCCATACAAACAGGCATTAATTTACGTGTTTCC\n+TCAGCATGTGCAAGCATTTCTCGCAAATTCCAAGAAACAGTTCCAAGAATTTCTTCTTTCTCATTAGAGACAAT\n+GGATGGTAGTATGTAAAAAGCGCTCTTGCACTTTTTAAGCACTGTCTTTGCCTCTTCTAATGTATAACCATTAT\n+TACCCTGTCCAGGGTAGGTGGTTATATAATTGTCTACTGGTAACTTCTTTAATGCTTTTGTAAGCATTTCGGTA\n+GTACCACCAGCTTTTTTAGTAGGTATAACTACAGCAGTTAAAACACCTTCCTTAATGACATCACCTACTATGTA\n+AGGAGCATCTTTCTTTAGAAAGGTGGTGTCAGTGTCTTTAACAAGCATGGCAGAATCTGGATGAAGGTTGCCAT\n+TAATGTCTATATAAAGTAACAAATTCTCTGTGAGAAACTTAGTTTCTTCCAAAGTGGTTGTAACTTCTTCAACA\n+CAAGCCTTGACTTTCTTTTCTTCAGCCTGTTGCTTTTGTTCAACTGAAGGTTTATTTTCAGTTGTTGGTGGCTC\n+AACTTCCATTTTAGGAACTTCAGCAATCTGTTGTTCTACTTGTGCCTCACTCTTCATTTCTAAAAAGCTAGAAA\n+CAAGTTTTTCATAGAGATCTTTGTCAAAGACAGTCAAGTAAACATT'..b'TCCCGTGTGTCTTGGCC\n+Alt 599 CATTTTAGGAACTTCAGCAATCTGTTGTTCTACTTGTGCCTCACTCTTCATTTCTAAAAA\n ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n-Ref 246 GTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGTGTCTTGGCC\n+Ref 1248 CATTTTAGGAACTTCAGCAATCTGTTGTTCTACTTGTGCCTCACTCTTCATTTCTAAAAA\n \n-Alt 649 AAAATTCTCAGTCCCAAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTCCTG\n- ||||||| ||||||| ||||||||||||||||||||||||||||||||||||||||||||\n-Ref 306 AAAATTCGCAGTCCCCAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTCCTG\n+Alt 659 GCTAGAAACAAGTTTTTCATAGAGATCTTTGTCAAAGACAGTCAAGTAAACATTTGTGCG\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Ref 1188 GCTAGAAACAAGTTTTTCATAGAGATCTTTGTCAAAGACAGTCAAGTAAACATTTGTGCG\n \n-Alt 709 CCTATCGCTGGATGTGTCTGCGGCGGTTTATCATATTCCTCTTCATCGTGCTGCTATGCC\n- |||||||||||||||||||||||| |||||||| |||||||||||| ||||||||||||\n-Ref 366 GCTATCGCTGGATGTGTCTGCGGCGTTTTATCATCTTCCTCTTCATCCTGCTGCTATGCC\n+Alt 719 AACAGTGTCTACACAAACTCTTAAGGATTGGACAGGGTCAGCACCAAAGATGCCTGCTGA\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Ref 1128 AACAGTGTCTACACAAACTCTTAAGGATTGGACAGGGTCAGCACCAAAGATGCCTGCTGA\n \n-Alt 769 TCATCATCCTGTTGGGTTCGTCTGCACCATCAAAAGAATGTTGCCCCGGGTTGTGATTAA\n- ||||| || |||| ||||| |||| || |||| | | ||||||||| | |||| | \n-Ref 426 TCATCTTCTTGTT-GGTTCTTCTGGACTATCA-AGGTATGTTGCCC--GTTTGTCCT--C\n+Alt 779 CAATAAAGGTGCTAGTAAAGTATCATACTGATTGAAATTTTCATATGCAGTTTTAAGAAG\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Ref 1068 CAATAAAGGTGCTAGTAAAGTATCATACTGATTGAAATTTTCATATGCAGTTTTAAGAAG\n \n-Alt 829 AAATTCCAAGGAGCAAGAAAGCCACCCACTACGGGAACCAGGGCCGGAAGCTGAACAAGT\n- ||||||| ||| || || ||| ||| ||||||| || |||| || ||| || | |\n-Ref 480 TAATTCCA-GGATCATCAA--CCA-CCAGTACGGGACCC--TGCCG-AACCTGCACGACT\n+Alt 839 TTGAATGCTTTCACCCTTGTTGATATTAGGACCAACAACATGAAGACAATTTTTAGCAAG\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Ref 1008 TTGAATGCTTTCACCCTTGTTGATATTAGGACCAACAACATGAAGACAATTTTTAGCAAG\n \n-Alt 889 CATTTTTCAAAGGAAAATGAAAGATTTTCTTTCTTATTTGTGGGGGAAAAGCAAAAAAAG\n- | || |||| |||| | | | |||| || | ||| | |||| | | |\n-Ref 533 C-TTGCTCAA-GGAACCTCTATG--TTTCCCTCAT-GTTGCTGTTCAAAACCTTCGGACG\n+Alt 899 ATTATGTCCACTCAGAACACAACTACCACCAACATTCAGAGGTCCGTTTGTGGCTATGTA\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Ref 948 ATTATGTCCACTCAGAACACAACTACCACCAACATTCAGAGGTCCGTTTGTGGCTATGTA\n \n-Alt 949 GAAAAAGGAAATTGGGGTTACAAACCCCACCCCCAAGGGATTTGGGAAATACCATATTTT\n- |||| | | ||| | | | |||| | || ||| ||| ||||| | ||| \n-Ref 588 GAAATTGCAC-TTGTA--TTCCCATCCCATCATCATGGGCTTTCGGAAAATTCCTATGGG\n+Alt 959 ATTGTCTGATTCTACTTGCATAGCGTTGTTTGTAGCTTTGTTTAAAGCTCCAGCAACACC\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Ref 888 ATTGTCTGATTCTACTTGCATAGCGTTGTTTGTAGCTTTGTTTAAAGCTCCAGCAACACC\n \n-Alt 1009 AAAGGGGAAAGGGCCGCATAACCCATTAAAAATTGCATATTTTA-AATTTTTTTTTTTTG\n- | ||| | ||| | || | || | |||| | | ||| || \n-Ref 645 AGTGGGCCTCAGCCCGTTTCTCC---------TGGCTCAGTTTACTAGTGCCATTTGTTC\n+Alt 1019 TCCTCCATGTTTAAG-TAAACATTAGCTGCATTAACAACTACTGT-GGTTTCCCCTGTT-\n+ ||||||||||||||| ||||||||||||||||||||||||||||| |||||| |||||| \n+Ref 828 TCCTCCATGTTTAAGGTAAACATTAGCTGCATTAACAACTACTGTTGGTTTCACCTGTTT\n \n-Alt 1068 AGAAAGAGGGGGGAC--------\n- || | || | \n-Ref 696 AGTGGTTCGCCGGGCTTTCCCCC\n+Alt 1076 AGCTTCTTCCACAATGTCTGCATTTTTAATGAAAACATTTGTTAGGGGAG\n+ ||||||||||||||||||||||||||||||||||||| ||||||| | \n+Ref 768 AGCTTCTTCCACAATGTCTGCATTTTTAATGAAAACA-TTGTTAGTGAGT\n \n #-------------------------------------------------------------------------\n #-------------------------------------------------------------------------\n' |
| b |
| diff -r 99d31ec6629b -r 897b1ff9e906 test-data/out2.alignment.fasta --- a/test-data/out2.alignment.fasta Tue Oct 12 14:20:41 2021 +0000 +++ b/test-data/out2.alignment.fasta Thu Mar 20 07:18:34 2025 +0000 |
| b |
| b'@@ -1,6 +1,6 @@\n->input1 (forward)\n-TATTGGGACCACAATCCCAACAAAGACCACTGGACAGAAGCCAACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCCCACACGGAGGCCTTTTGGGGTGGAGCCCTCAGGCTCAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCCTCCACCAATCGACAGTCAGGAAGGCAGCCTACCCCAATCACTCCACCTTTGAGAGACACTCATCCTCAGGCCATGCAGTGGAATTCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAA------------TCCTGCTGGTGGCTCCAGTTCCGGAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATCTCGTCAATCTTCTCGAGGATTGGGGACCCTGCACCGAACATGGAAAGCATCACATCAGGATTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAAAATCCTCACAATACCGCAGAGTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGTGTCTTGGCCAAAATTCTCAGTCCCAAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n->input1 (forward)\n-TATTGGGACCACAATCCCAACAAAGACCACTGGACAGAAGCCAACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCCCACACGGAGGCCTTTTGGGGTGGAGCCCTCAGGCTCAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCCTCCACCAATCGACAGTCAGGAAGGCAGCCTACCCCAATCACTCCACCTTTGAGAGACACTCATCCTCAGGCCATGCAGTGGAATTCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAA------------TCCTGCTGGTGGCTCCAGTTCCGGAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATCTCGTCAATCTTCTCGAGGATTGGGGACCCTGCACCGAACATGGAAAGCATCACATCAGGATTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAAAATCCTCACAATACC'..b'GTTTGTTTAAAGACTGGGAGGAGTCGGGGGAGGAGATTAGATTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGCGCACCAGCACCATGCAACTTTTTCACCTCTGCCTAATCATCTCTTGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATTGACCCTTATAAAGAATTTGGAGCTACTGTGGAGTTACTCTCGTTTTTGCCTTCTGACTTCTTTCCTTCAGTAAGAGATCTTCTAGATACCGCCTCAGCTCTGTATCGGGATGCCTTAGAGTCTCCTGAGCATTGTTCACCTCACCACACTGCACTCAGGCAAGCCATTCTTTGCTGGGGAGAACTAATGACTCTAGCTACCTGGGTGGGTGTAAATTTGGAAGATCCAGCATCCAGGGACCTAGTAGTCAGTTATGTCAATACTAATATGGGCCTAAAGTTCAGGCAATTATTGTGGTTTCACATTTCTTGTCTCACTTTTGGAAGAGAAACCGTCATAGAGTATTTGGTGTCTTTTGGAGTGTGGATTCGCACTCCTCCAGCTTATAGACCACCAAATGCCCCTATCTTATCAACACTTCCGGAGAATACTGTTGTTAGACGAAGAGGCAGGTCCCCTAGAAGAAGAACTCCCTCGCCTCGCAGACGAAGATCTCAATCGCCGCGTCGCAGAAGATCTCAATCTCCAGCTTCCCAATGTTAGTATTCCTTGGACTCATAAGGTGGGAAATTTTACGGGGCTTTACTCTTCTACTATACCTGTCTTTAATCCTAACTGGAAAACTCCATCTTTTCCTGATATTCATTTGCACCAGGACATTATTAACAAATGTGAACAATTTGTAGGTCCTCTAACTGTAAATGAAAAACGAAGATTAAACTTAGTCATGCCTGCTAGATTTTTTCCCATCTCTACGAAATATTTGCCCCTAGAGAAAGGTATAAAACCTTATTATCCAGATAATGTAGTTAATCATTACTTCCAAACCAGACACTATTTACATACCCTATGGAAGGCGGGCATCTTATATAAAAGAGAAACTACACGTAGCGCCTCATTTTGTGGGTCACCTTATTCTTGGGAACAAGAGCTACATCATGGGGCTTTCTTGGACGGTCCCTCTCGAATGGGGGAAGAATATTTCCACCACCAATCCTCTGGGATTTTTTCCCGACCACCAGTTGGATCCAGCATTCAGAGCAAACACCAGAAATCCAGATTGGGACCACAATCCCAACAAAGACCACTGGACAGAAGCCAACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCCCACACGGAGGCCTTTTGGGGTGGAGCCCTCAGGCTCAAGGCATGCTAAAAACATTGCCAGCAGATCCGCCTCCTGCCTCCACCAATCGGCAGTCAGGAAGGCAGCCTACCCCAATCACTCCACCTTTGAGAGACACTCATCCTCAGGCCATGCAGTGGAA\n+AACGGGCTTATGTTGCTCGAAATTAAAGATACAGAGAAGTATTGTGCTCTTGCACCTAACATGATGGTTACAAATAACACCTTCACACTTAAAGGTGGTGCACCAACAAGAGTTACTTTTGGTGATGACACCGTAATTGAAGTACAGGGTTACAAAAGTGTAAGTATCACTTTTGAACTCGATGAGAGAGTAGATAAAGTACTTAATGAAAAGTGCTCTAACTACACAGTTGAACTTGGAACAGAAGTAAATGAGTTTGCTTGTGTTGTCGCTGATGCTGTTATAAAGACTTTACAGCCAGTATCTGAATTACTTACACCACTAGGCATAGATTTAGACGAGTGGGGTATGGCAACATACTACTTGTTTGATGAATCTGGTGAGTTTAATTTAGCCTCTCATATGTACTGTTCTTTCTATCCTCCAGATGAGGATTATGAAGAAGATGAGTGTGAAGAGGAACAGTATGAACCATCAACTCAGTATGAGTATGGTACAGAGGATGATTACCAAGGTAAATCTTTGGAATTTGGTTCAACCTCTTCTGCTTCTCAAATAGAAGAAGAACCAGAGGAAGATTGGTTAGAAGATGGCAATGAGGAAATTGCTATGCAAGAAGAGCAGACAACAACTGTTGAAGTGCAATCTCAGGAGATTGACTCTACACCAGTTGTCTCTGAGATAAATGAATCAGTGAACAATTTTACTGGTTATTTAAAACTCACTAACAATGTTTTCATTAAAAATGCAGACATTGTGGAAGAAGCTAAACAGGTGAAACCAACAGTAGTTGTTAATGCAGCTAATGTTTACCTTAAACATGGAGGAGGTGTTGCTGGAGCTTTAAACAAAGCTACAAACAACGCTATGCAAGTAGAATCAGACAATTACATAGCCACAAACGGACCTCTGAATGTTGGTGGTAGTTGTGTTCTGAGTGGACATAATCTTGCTAAAAATTGTCTTCATGTTGTTGGTCCTAATATCAACAAGGGTGAAAGCATTCAACTTCTTAAAACTGCATATGAAAATTTCAATCAGTATGATACTTTACTAGCACCTTTATTGTCAGCAGGCATCTTTGGTGCTGACCCTGTCCAATCCTTAAGAGTTTGTGTAGACACTGTTCGCACAAATGTTTACTTGACTGTCTTTGACAAAGATCTCTATGAAAAACTTGTTTCTAGCTTTTTAGAAATGAAGAGTGAGGCACAAGTAGAACAACAGATTGCTGAAGTTCCTAAAATGGAAGTTGAGCCACCAACAACTGAAAATAAACCTTCAGTTGAACAAAAGCAACAGGCTGAAGAAAAGAAAGTCAAGGCTTGTGTTGAAGAAGTTACAACCACTTTGGAAGAAACTAAGTTTCTCACAGAGAATTTGTTACTTTATATAGACATTAATGGCAACCTTCATCCAGATTCTGCCATGCTTGTTAAAGACACTGACACCACCTTTCTAAAGAAAGATGCTCCTTACATAGTAGGTGATGTCATTAAGGAAGGTGTTTTAACTGCTGTAGTTATACCTACTAAAAAAGCTGGTGGTACTACCGAAATGCTTACAAAAGCATTAAAGAAGTTACCAGTAGACAATTATATAACCACCTACCCTGGACAGGGTAATAATGGTTATACATTAGAAGAGGCAAAGACAGTGCTTAAAAAGTGCAAGAGCGCTTTTTACATACTACCATCCATTGTCTCTAATGAGAAAGAAGAAATTCTTGGAACTGTTTCTTGGAATTTGCGAGAAATGCTTGCACATGCTGAGGAAACACGTAAATTAATGCCTGTTTGTATGGAAACTAAAGCTATAGTTTCAACCATACAACGTAAATACAAGGGTATTAAAATACAGGAAGGTGTGGTTGATTATGGTGCTAGGTTTTACTTCTATACTAGTAAAACAACAGTAGCATCACTCATCAACACACTTAACAATCTAAATGAGACTCTCGTTACAATGCCTTTGGGTTATGTAACACATGGCCTTAACCTAGAAGAAGCTGCGCGGTACATGAGATCTCTTAAGGTACCAGCGACAGTTTCTGTTTCTTCACCAGATGCTGTAACAGCATATAATGGTTATCTTACTTCTTCTTCAAAAACACCTGAAGAACATTTCATAGAAACCATCTCTCTAGCTGGTTCTTACAAAGATTGGTCCTATTCTGGACAATCAACACAACTTGGTATAGAATTTCTTAAAAGAGGTGATAAAACTGTTTATTACACCATTAACCCTATTGCTTTTCATACAGAGGGTCAAATTATCACCTTTGATGATTTAAAAACACTTCTCTCATTGAGAGAGGTTAGAACAATCAAAGTGTTTACAACTGTAGACAATGTTAATCTCCATACACAAGTTGTGGACATGTCTATGACTTATGGACAACAGTTTGGTCCCACTTATTTGGATGGAGCTGATGTCACTAAAATAAAACCTCATAATTCACATGAAGGTAAGACATTTTATGTCTTGCCTAATGATGACA\n' |
| b |
| diff -r 99d31ec6629b -r 897b1ff9e906 test-data/out2.consensus.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out2.consensus.fasta Thu Mar 20 07:18:34 2025 +0000 |
| b |
| @@ -0,0 +1,2 @@ +>Consensus +GAGTTTAATTTAGCCTCTCATATGTACTGTTCTTTCTATCCTCCAGATGAGGATTATGAAGAAGATGAGTGTGAAGAGGAACAGTATGAACCATCAACTCAGTATGAGTATGGTACAGAGGATGATTACCAAGGTAAATCTTTGGAATTTGGTTCAACCTCTTCTGCTTCTCAAATAGAAGAAGAACCAGAGGAAGATTGGTTAGAAGATGGCAATGAGGAAATTGCTATGCAAGAAGAGCAGACAACAACTGTTGAAGTGCAATCTCAGGAGATTGACTCTACACCAGTTGTCTCTGAGATAAATGAATCAGTGAACAATTTTACTGGTTATTTAAAACTCACTAACAATGTTTTCATTAAAAATGCAGACATTGTGGAAGAAGCTAAACAGGTGAAACCAACAGTAGTTGTTAATGCAGCTAATGTTTACCTTAAACATGGAGGAGGTGTTGCTGGAGCTTTAAACAAAGCTACAAACAACGCTATGCAAGTAGAATCAGACAATTACATAGCCACAAACGGACCTCTGAATGTTGGTGGTAGTTGTGTTCTGAGTGGACATAATCTTGCTAAAAATTGTCTTCATGTTGTTGGTCCTAATATCAACAAGGGTGAAAGCATTCAACTTCTTAAAACTGCATATGAAAATTTCAATCAGTATGATACTTTACTAGCACCTTTATTGTCAGCAGGCATCTTTGGTGCTGACCCTGTCCAATCCTTAAGAGTTTGTGTAGACACTGTTCGCACAAATGTTTACTTGACTGTCTTTGACAAAGATCTCTATGAAAAACTTGTTTCTAGCTTTTTAGAAATGAAGAGTGAGGCACAAGTAGAACAACAGATTGCTGAAGTTCCTAAAATGGAAGTTGAGCCACCAACAACTGAAAATAAACCTTCAGTTGAACAAAAGCAACAGGCTGAAGAAAAGAAAGTCAAGGCTTGTGTTGAAGAAGTTACAACCACTTTGGAAGAAACTAAGTTTCTCACAGAGAATTTGTTACTTTATATAGACATTAATGGCAACCTTCATCCAGATTCTGCCATGCTTGTTAAAGACACTGACACCACCTTTCTAAAGAAAGATGCTCCTTACATAGTAGGTGATGTCATTAAGGAAGGTGTTTTAACTGCTGTAGTTATACCTACTAAAAAAGCTGGTGGTACTACCGAAATGCTTACAAAAGCATTAAAGAAGTTACCAGTAGACAATTATATAACCACCTACCCTGGACAGGGTAATAATGGTTATACATTAGAAGAGGCAAAGACAGTGCTTAAAAAGTGCAAGAGCGCTTTTTACATACTACCATCCATTGTCTCTAATGAGAAAGAAGAAATTCTTGGAACTGTTTCTTGGAATTTGCGAGAAATGCTTGCACATGCTGAGGAAACACGTAAATTAATGCCTGTTTGTATGGAAACTAAAGC |
| b |
| diff -r 99d31ec6629b -r 897b1ff9e906 test-data/out2.fasta --- a/test-data/out2.fasta Tue Oct 12 14:20:41 2021 +0000 +++ b/test-data/out2.fasta Thu Mar 20 07:18:34 2025 +0000 |
| b |
| @@ -1,4 +1,4 @@ ->input1 ---------TTTTTTTTTGAGCGGGTCGAACCGTCACGAAAAGAAAAGGGGAAGAACCATCAGCAGGAGTAATCCGTATTTTAATTGGATCCACAT-TCATAGCAAACACCAAAAATCCATATTGGGACCACAATCCCAACAAAGACCACTGGAC-AGAAGCCAACAAGGTAGGAGTGGGAG-CATTCGG-GCCTGGGTTC--ACTCCCCCACACGGAGGCCTTTTGGGGTGGAGCCCTCAGGCTCAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCCTCCACCAATCGACAGTCAGGAAGGCAGCCTACCCCAATCACTCCACCTTTGAG-AGACACTCATCCTCAGGCCATGCAGTGGAATTCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAATCCTGCTGGTGGCTCCAGTTCCGGAACAGTGAACCCTG-TTCCGACTACTGCCTCACTCATCTCGTCAATCTTCTCGAGGATTGGGGACCCTGCACCGAACATGGAAAGCATCACATCAGGATTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAAAATCCTCACAATACCGCAGAGTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCT--CCCGTGTGTCTTGGCCAAAATTCTCAGT--CCCAAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTCCTGCCTATCGCTGGATGTGTCTGCGGCGGTTTATCATATTCCT-CTTCATCGTGCTGCT------ATGCCTCATCATCCTGTTGGGTTCGTCTGCACCATCAAAAGAATGTTGCCCCGGGTTGTGATTAAAAATTCCAAGGAGCAAGAAAGCCACCCACTACGGGAACCAGGGCCGGAAGCTGAACAAGTCATTTTTCAAAGGAAAATGAAAGATTTTCTTTCTTATTTGTGGGGGAAAAGCAAAAAAAGGAAAAAGGAAATTGGGGTTACAAACCCCACCCCCAAGGGATTTGGG--AAATACCATATTTTAAAGGGGAAAGGGCCGCATAACCCATTAAAAATTGCATATTTTAAATTTTTTTTTTTTGAGAAAGAGGGGGGAC------------------- ->X75657.1 (forward) -AACTAATGACTCTAGCTACCTGGGTGG----GTGTAAATTTGGA-AGATCCAGCATCCAGGGACCTAGTAGTCAGT----TATGTCAATACTAATATGGGCCTAAAGTTCAGGCAATTATTGTGGTTTCAC-ATTTCTTGTCTCACTTTTGGAAGAGAAACCGTCATAG-AGTATTTGGTGTCTTTTGGAGTGTGGATTCGCACTCCTCCA-------GCTTAT--------AGACCAC-----CAA---ATGCCCCTATC-TTATCAACACTTCCGGAGAATACTGTTGTTAGACGA-AG--AGGCAGGTCCCCTAGAAGAAGAACTCCCTCGCCTCGCAGACGAAGATC-TCAATCGCCGC-GTCG-----CAGAAGATCTCAA-----TCTCCAGCTTCCCAATGTTAGTATTCCTTG-GACTCATAAGGTGGGAAATTTTACGGGGCTTTACTCTTCTACTATACCTGTCT--TTAATCCTAACTGGAAAACTCCATCTTTTCCTGATATTCATTTGCACCAGGACATTATT---AACAAATGTGAACAATTTGTA---GGTCCTCTAACTGTAAATGAAAAACG--AAGATTAAACTTAGTC---ATGCCTGCTAGATTTTT-TCCCATCTCTACGAAATATTTGCCCCTAGAGAAAGGTATAAAACCTTATTATCCAGATAATGTAGTTAATCATTACTTCCAAACCAGACACTATTTACATAC--CCTATGGAAG-GCGGGCATCT-TATATAAAAGAGAAACTACACGTAGCGCCTCATTTTGTGGGTCACCTTATTCTTGGGAACAAGAGCTACATCATGGG---GCTTTCTTGGACGGTCCCTC-----TCGAATGGGGGAAGAATATTTCCACCACC--AATCCTCTGGG---------------ATTTTTTCCCG---ACCACCAG--TTGGATCCAGCATTCAG-------AGCAAACACCAGAAA-TCCAGATTGGGACCACAATCCCAACA---AAGACCACTGGACAGAAGCCAACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCCCACACGGAGGCCTTTTGGGGTGGAGCCCTCAGGCTCAAGGCATGCTAAAAACATTGCC +>dataset_41387b57-448c-4975-a12c-7f4c35e7ad3f +TTCCTTGT-TTTACGTTGTATGGTTGAA-CTATAGCTTTAGTTTCCATACAAACAGGCATTAATTTACGTGTTTCCTCAGCATGTGCAAGCATTTCTCGCAAATTCCAAGAAACAGTTCCAAGAATTTCTTCTTTCTCATTAGAGACAATGGATGGTAGTATGTAAAAAGCGCTCTTGCACTTTTTAAGCACTGTCTTTGCCTCTTCTAATGTATAACCATTATTACCCTGTCCAGGGTAGGTGGTTATATAATTGTCTACTGGTAACTTCTTTAATGCTTTTGTAAGCATTTCGGTAGTACCACCAGCTTTTTTAGTAGGTATAACTACAGCAGTTAAAACACCTTCCTTAATGACATCACCTACTATGTAAGGAGCATCTTTCTTTAGAAAGGTGGTGTCAGTGTCTTTAACAAGCATGGCAGAATCTGGATGAAGGTTGCCATTAATGTCTATATAAAGTAACAAATTCTCTGTGAGAAACTTAGTTTCTTCCAAAGTGGTTGTAACTTCTTCAACACAAGCCTTGACTTTCTTTTCTTCAGCCTGTTGCTTTTGTTCAACTGAAGGTTTATTTTCAGTTGTTGGTGGCTCAACTTCCATTTTAGGAACTTCAGCAATCTGTTGTTCTACTTGTGCCTCACTCTTCATTTCTAAAAAGCTAGAAACAAGTTTTTCATAGAGATCTTTGTCAAAGACAGTCAAGTAAACATTTGTGCGAACAGTGTCTACACAAACTCTTAAGGATTGGACAGGGTCAGCACCAAAGATGCCTGCTGACAATAAAGGTGCTAGTAAAGTATCATACTGATTGAAATTTTCATATGCAGTTTTAAGAAGTTGAATGCTTTCACCCTTGTTGATATTAGGACCAACAACATGAAGACAATTTTTAGCAAGATTATGTCCACTCAGAACACAACTACCACCAACATTCAGAGGTCCGTTTGTGGCTATGTAATTGTCTGATTCTACTTGCATAGCGTTGTTTGTAGCTTTGTTTAAAGCTCCAGCAACACCTCCTCCATGTTTAAG-TAAACATTAGCTGCATTAACAACTACTGT-GGTTTCCCCTGTT-AGCTTCTTCCACAATGTCTGCATTTTTAATGAAAACATTTGTTAGGGGAG +>MT121216.1:2501-5000 (reverse) +--CCTTGTATTTACGTTGTATGGTTGAAACTATAGCTTTAGTTTCCATACAAACAGGCATTAATTTACGTGTTTCCTCAGCATGTGCAAGCATTTCTCGCAAATTCCAAGAAACAGTTCCAAGAATTTCTTCTTTCTCATTAGAGACAATGGATGGTAGTATGTAAAAAGCGCTCTTGCACTTTTTAAGCACTGTCTTTGCCTCTTCTAATGTATAACCATTATTACCCTGTCCAGGGTAGGTGGTTATATAATTGTCTACTGGTAACTTCTTTAATGCTTTTGTAAGCATTTCGGTAGTACCACCAGCTTTTTTAGTAGGTATAACTACAGCAGTTAAAACACCTTCCTTAATGACATCACCTACTATGTAAGGAGCATCTTTCTTTAGAAAGGTGGTGTCAGTGTCTTTAACAAGCATGGCAGAATCTGGATGAAGGTTGCCATTAATGTCTATATAAAGTAACAAATTCTCTGTGAGAAACTTAGTTTCTTCCAAAGTGGTTGTAACTTCTTCAACACAAGCCTTGACTTTCTTTTCTTCAGCCTGTTGCTTTTGTTCAACTGAAGGTTTATTTTCAGTTGTTGGTGGCTCAACTTCCATTTTAGGAACTTCAGCAATCTGTTGTTCTACTTGTGCCTCACTCTTCATTTCTAAAAAGCTAGAAACAAGTTTTTCATAGAGATCTTTGTCAAAGACAGTCAAGTAAACATTTGTGCGAACAGTGTCTACACAAACTCTTAAGGATTGGACAGGGTCAGCACCAAAGATGCCTGCTGACAATAAAGGTGCTAGTAAAGTATCATACTGATTGAAATTTTCATATGCAGTTTTAAGAAGTTGAATGCTTTCACCCTTGTTGATATTAGGACCAACAACATGAAGACAATTTTTAGCAAGATTATGTCCACTCAGAACACAACTACCACCAACATTCAGAGGTCCGTTTGTGGCTATGTAATTGTCTGATTCTACTTGCATAGCGTTGTTTGTAGCTTTGTTTAAAGCTCCAGCAACACCTCCTCCATGTTTAAGGTAAACATTAGCTGCATTAACAACTACTGTTGGTTTCACCTGTTTAGCTTCTTCCACAATGTCTGCATTTTTAATGAAAACA-TTGTTAGTGAGT |
| b |
| diff -r 99d31ec6629b -r 897b1ff9e906 test-data/out2.txt --- a/test-data/out2.txt Tue Oct 12 14:20:41 2021 +0000 +++ b/test-data/out2.txt Thu Mar 20 07:18:34 2025 +0000 |
| b |
| b'@@ -1,113 +1,116 @@\n >Alt\n-TTTTTTTTTGAGCGGGTCGAACCGTCACGAAAAGAAAAGGGGAAGAACCATCAGCAGGAGTAATCCGTATTTTA\n-ATTGGATCCACATTCATAGCAAACACCAAAAATCCATATTGGGACCACAATCCCAACAAAGACCACTGGACAGA\n-AGCCAACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCCCACACGGAGGCCTTTTGGGGTGGAGCC\n-CTCAGGCTCAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCCTCCACCAATCGACAGTCAGGAAGG\n-CAGCCTACCCCAATCACTCCACCTTTGAGAGACACTCATCCTCAGGCCATGCAGTGGAATTCCACAACATTCCA\n-CCAAGCTCTGCAGGATCCCAGAGTAAATCCTGCTGGTGGCTCCAGTTCCGGAACAGTGAACCCTGTTCCGACTA\n-CTGCCTCACTCATCTCGTCAATCTTCTCGAGGATTGGGGACCCTGCACCGAACATGGAAAGCATCACATCAGGA\n-TTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAAAATCCTCACAATACCGCAGAGTCT\n-AGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGTGTCTTGGCCAAAATTCTCAGTCCCAAA\n-CCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTCCTGCCTATCGCTGGATGTGTCTGCGGCGGTTTATC\n-ATATTCCTCTTCATCGTGCTGCTATGCCTCATCATCCTGTTGGGTTCGTCTGCACCATCAAAAGAATGTTGCCC\n-CGGGTTGTGATTAAAAATTCCAAGGAGCAAGAAAGCCACCCACTACGGGAACCAGGGCCGGAAGCTGAACAAGT\n-CATTTTTCAAAGGAAAATGAAAGATTTTCTTTCTTATTTGTGGGGGAAAAGCAAAAAAAGGAAAAAGGAAATTG\n-GGGTTACAAACCCCACCCCCAAGGGATTTGGGAAATACCATATTTTAAAGGGGAAAGGGCCGCATAACCCATTA\n-AAAATTGCATATTTTAAATTTTTTTTTTTTGAGAAAGAGGGGGGAC\n->Ref X75657.1:2091-3110 forward\n-AACTAATGACTCTAGCTACCTGGGTGGGTGTAAATTTGGAAGATCCAGCATCCAGGGACCTAGTAGTCAGTTAT\n-GTCAATACTAATATGGGCCTAAAGTTCAGGCAATTATTGTGGTTTCACATTTCTTGTCTCACTTTTGGAAGAGA\n-AACCGTCATAGAGTATTTGGTGTCTTTTGGAGTGTGGATTCGCACTCCTCCAGCTTATAGACCACCAAATGCCC\n-CTATCTTATCAACACTTCCGGAGAATACTGTTGTTAGACGAAGAGGCAGGTCCCCTAGAAGAAGAACTCCCTCG\n-CCTCGCAGACGAAGATCTCAATCGCCGCGTCGCAGAAGATCTCAATCTCCAGCTTCCCAATGTTAGTATTCCTT\n-GGACTCATAAGGTGGGAAATTTTACGGGGCTTTACTCTTCTACTATACCTGTCTTTAATCCTAACTGGAAAACT\n-CCATCTTTTCCTGATATTCATTTGCACCAGGACATTATTAACAAATGTGAACAATTTGTAGGTCCTCTAACTGT\n-AAATGAAAAACGAAGATTAAACTTAGTCATGCCTGCTAGATTTTTTCCCATCTCTACGAAATATTTGCCCCTAG\n-AGAAAGGTATAAAACCTTATTATCCAGATAATGTAGTTAATCATTACTTCCAAACCAGACACTATTTACATACC\n-CTATGGAAGGCGGGCATCTTATATAAAAGAGAAACTACACGTAGCGCCTCATTTTGTGGGTCACCTTATTCTTG\n-GGAACAAGAGCTACATCATGGGGCTTTCTTGGACGGTCCCTCTCGAATGGGGGAAGAATATTTCCACCACCAAT\n-CCTCTGGGATTTTTTCCCGACCACCAGTTGGATCCAGCATTCAGAGCAAACACCAGAAATCCAGATTGGGACCA\n-CAATCCCAACAAAGACCACTGGACAGAAGCCAACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCC\n-CACACGGAGGCCTTTTGGGGTGGAGCCCTCAGGCTCAAGGCATGCTAAAAACATTGCC\n+TTCCTTGTTTTACGTTGTATGGTTGAACTATAGCTTTAGTTTCCATACAAACAGGCATTAATTTACGTGTTTCC\n+TCAGCATGTGCAAGCATTTCTCGCAAATTCCAAGAAACAGTTCCAAGAATTTCTTCTTTCTCATTAGAGACAAT\n+GGATGGTAGTATGTAAAAAGCGCTCTTGCACTTTTTAAGCACTGTCTTTGCCTCTTCTAATGTATAACCATTAT\n+TACCCTGTCCAGGGTAGGTGGTTATATAATTGTCTACTGGTAACTTCTTTAATGCTTTTGTAAGCATTTCGGTA\n+GTACCACCAGCTTTTTTAGTAGGTATAACTACAGCAGTTAAAACACCTTCCTTAATGACATCACCTACTATGTA\n+AGGAGCATCTTTCTTTAGAAAGGTGGTGTCAGTGTCTTTAACAAGCATGGCAGAATCTGGATGAAGGTTGCCAT\n+TAATGTCTATATAAAGTAACAAATTCTCTGTGAGAAACTTAGTTTCTTCCAAAGTGGTTGTAACTTCTTCAACA\n+CAAGCCTTGACTTTCTTTTCTTCAGCCTGTTGCTTTTGTTCAACTGAAGGTTTATTTTCAGTTGTTGGTGGCTC\n+AACTTCCATTTTAGGAACTTCAGCAATCTGTTGTTCTACTTGTGCCTCACTCTTCATTTCTAAAAAGCTAGAAA\n+CAAGTTTTTCATAGAGATCTTTGTCAAAGACAGTCAAGTAAACATTTGTGCGAACAGTGTCTACACAAACTCTT\n+AAGGATTGGACAGGGTCAGCACCAAAGATGCCTGCTGACAATAAAGGTGCTAGTAAAGTATCATACTGATTGAA\n+ATTTTCATATGCAGTTTTAAGAAGTTGAATGCTTTCACCCTTGTTGATATTAGGACCAACAACATGAAGACAAT\n+TTTTAGCAAGATTATGTCCACTCAGAACACAACTACCACCAACATTCAGAGGTCCGTTTGTGGCTATGTAATTG\n+TCTGATTCTACTTGCATAGCGTTGTTTGTAGCTTTGTTTAAAGCTCCAGCAACACCTCCTCCATGTTTAAGTAA\n+ACATTAGCTGCATTAACAACTACTGTGGTTTCCCCTGTTAGCTTCTTCCACAATGTCTGCATTTTTAATGAAAA\n+CATTTGTTAGGGGAG\n+>Ref MT121216.1:2501-5000:720-1846 reversecomplement\n+CCTTGTATTTACGTTGTATGGTTGAAACTATAGCTTTAGTTTCCATACAAACAGGCATTAATTTACGTGTTTCC\n+TCAGCATGTGCAAGCATTTCTCGCAAATTCCAAGAAACAGTTCCAAGAATTTCTTCTTTCTCATTAGAGACAAT\n+GGATGGTAGTATGTAAAAAGCGCTCTTGCACTTTTTAAGCACTGTCTTTGCCTCTTCTAATGTATAACCATTAT\n+TACCCTGTCCAGGGTAGGTGGTTATATAATTGTCTACTGGTAACTTCTTTAATGCTTTTGTAAGCATTTCGGTA\n+GTACCACCAGCTTTTTTAGTAGGTATAACTACAGCAGTTAAAACACCTTCCTTAATGACATCACCTACTATGTA\n+AGGAGCATCTTTCTTTAGAAAGGTGGTGTCAGTGTCTTTAACAAGCATGGCAGAATCTGGATGAAGGTTGCCAT\n+TAATGTCTATATAAAGTAACAAATTCTCTGTGAGAAACTTAGTTTCTTCCAAAGTGGTTGTAACTTCTTCAACA\n+CAAGCCTTGACTTTCTTTTCTTCAGCCTGTTGCTTT'..b'TGCCCCTAGAGA\n+Alt 599 CATTTTAGGAACTTCAGCAATCTGTTGTTCTACTTGTGCCTCACTCTTCATTTCTAAAAA\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Ref 1248 CATTTTAGGAACTTCAGCAATCTGTTGTTCTACTTGTGCCTCACTCTTCATTTCTAAAAA\n \n-Alt 643 TTGGCCAAAATTCTCAGT--CCCAAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAAT\n- || ||| || | | || | | ||| | ||| | | | || |\n-Ref 2686 AAGGTATAAAACCTTATTATCCAGATAATGTAGTTAATCATTACTTCCAAACCAGACACT\n+Alt 659 GCTAGAAACAAGTTTTTCATAGAGATCTTTGTCAAAGACAGTCAAGTAAACATTTGTGCG\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Ref 1188 GCTAGAAACAAGTTTTTCATAGAGATCTTTGTCAAAGACAGTCAAGTAAACATTTGTGCG\n \n-Alt 701 TTGTCCTGCCTATCGCTGGATGTGTCTGCGGCGGTTTATCATATTCCT-CTTCATCGTGC\n- | | | | | |||| | | || | | ||| | | || || ||\n-Ref 2746 ATTTACATAC--CCTATGGAAG-GCGGGCATCT-TATATAAAAGAGAAACTACACGTAGC\n+Alt 719 AACAGTGTCTACACAAACTCTTAAGGATTGGACAGGGTCAGCACCAAAGATGCCTGCTGA\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Ref 1128 AACAGTGTCTACACAAACTCTTAAGGATTGGACAGGGTCAGCACCAAAGATGCCTGCTGA\n \n-Alt 760 TGCT------ATGCCTCATCATCCTGTTGGGTTCGTCTGCACCATCAAAAGAATGTTGCC\n- || || ||| | | | ||||| | || ||||| | | | |\n-Ref 2802 GCCTCATTTTGTGGGTCACCTTATTCTTGGGAACAAGAGCTACATCATGGG---GCTTTC\n+Alt 779 CAATAAAGGTGCTAGTAAAGTATCATACTGATTGAAATTTTCATATGCAGTTTTAAGAAG\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Ref 1068 CAATAAAGGTGCTAGTAAAGTATCATACTGATTGAAATTTTCATATGCAGTTTTAAGAAG\n \n-Alt 814 CCGGGTTGTGATTAAAAATTCCAAGGAGCAAGAAAGCCACCCACTACGGGAACCAGGGCC\n- || || | || || | | | || |||| || || | \n-Ref 2859 TTGGACGGTCCCTC-----TCGAATGGGGGAAGAATATTTCCACCACC--AATCCTCTGG\n+Alt 839 TTGAATGCTTTCACCCTTGTTGATATTAGGACCAACAACATGAAGACAATTTTTAGCAAG\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Ref 1008 TTGAATGCTTTCACCCTTGTTGATATTAGGACCAACAACATGAAGACAATTTTTAGCAAG\n \n-Alt 874 GGAAGCTGAACAAGTCATTTTTCAAAGGAAAATGAAAGATTTTCTTTCTTATTTGTGGGG\n- | |||||| | | || || | | || | \n-Ref 2912 G---------------ATTTTTTCCCG---ACCACCAG--TTGGATCCAGCATTCAG---\n+Alt 899 ATTATGTCCACTCAGAACACAACTACCACCAACATTCAGAGGTCCGTTTGTGGCTATGTA\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Ref 948 ATTATGTCCACTCAGAACACAACTACCACCAACATTCAGAGGTCCGTTTGTGGCTATGTA\n \n-Alt 934 GAAAAGCAAAAAAAGGAAAAAGGAAATTGGGGTTACAAACCCCACCCCCAAGGGATTTGG\n- |||||| | |||| | |||||| |||| ||| || ||| |||\n-Ref 2949 ----AGCAAACACCAGAAA-TCCAGATTGGGACCACAATCCCAACA---AAGACCACTGG\n+Alt 959 ATTGTCTGATTCTACTTGCATAGCGTTGTTTGTAGCTTTGTTTAAAGCTCCAGCAACACC\n+ ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n+Ref 888 ATTGTCTGATTCTACTTGCATAGCGTTGTTTGTAGCTTTGTTTAAAGCTCCAGCAACACC\n \n-Alt 994 G--AAATACCATATTTTAAAGGGGAAAGGGCCGCATAACCCATTAAAAATTGCATATTTT\n- || | | | || | | || || | || | \n-Ref 3001 ACAGAAGCCAACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCCCACACGGA\n+Alt 1019 TCCTCCATGTTTAAG-TAAACATTAGCTGCATTAACAACTACTGT-GGTTTCCCCTGTT-\n+ ||||||||||||||| ||||||||||||||||||||||||||||| |||||| |||||| \n+Ref 828 TCCTCCATGTTTAAGGTAAACATTAGCTGCATTAACAACTACTGTTGGTTTCACCTGTTT\n \n-Alt 1052 AAATTTTTTTTTTTTGAGAAAGAGGGGGGAC-------------------\n- |||| | ||| | \n-Ref 3061 GGCCTTTTGGGGTGGAGCCCTCAGGCTCAAGGCATGCTAAAAACATTGCC\n+Alt 1076 AGCTTCTTCCACAATGTCTGCATTTTTAATGAAAACATTTGTTAGGGGAG\n+ ||||||||||||||||||||||||||||||||||||| ||||||| | \n+Ref 768 AGCTTCTTCCACAATGTCTGCATTTTTAATGAAAACA-TTGTTAGTGAGT\n \n #-------------------------------------------------------------------------\n #-------------------------------------------------------------------------\n' |
| b |
| diff -r 99d31ec6629b -r 897b1ff9e906 test-data/output1.fasta --- a/test-data/output1.fasta Tue Oct 12 14:20:41 2021 +0000 +++ b/test-data/output1.fasta Thu Mar 20 07:18:34 2025 +0000 |
| b |
| @@ -1,2 +1,2 @@ >primary -TTTTTTTTTGAGCGGGTCGNACCGTCACGAANAGNAAAGGGGAAGAACCATCNGCNGGNGTNNTCCGTATTTTNNTTGGATCCNCATTCATAGCAAACACCANAAATCCATATTGGGACCACAATCCCAACAAAGACCACTGGACAGAAGCCAACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCCCACACGGAGGCCTTTTGGGGTGGAGCCCTCAGGCTCAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCCTCCACCAATCGACAGTCAGGAAGGCAGCCTACCCCAATCACTCCACCTTTGAGAGACACTCATCCTCAGGCCATGCAGTGGAATTCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAATCCTGCTGGTGGCTCCAGTTCCGGAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATCTCGTCAATCTTCTCGAGGATTGGGGACCCTGCACCGAACATGGAAAGCATCACATCAGGATTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAAAATCCTCACAATACCGCAGAGTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGTGTCTTGGCCAAAATTCTCAGTCCCAAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTCCTGCCTATCGCTGGATGTGTCTGCGGCGGTTTATCATATTCCTCTTCATCGTGCTGCTATGCCTCATCATCCTGTTGGGTTCGTCTGCACCATCAAAAGAATGTTGCCCCGGGTTGTGNTTNNAAATTCCAAGGAGCAAGAAAGCCACCCACTACGGGAACCNTGGCCGCAAGCTGCACAAGTCATTTTTCAAAGGAAANTGNANGNTTTTCTTTCTTNTTTGTGGGGGAAAAGCAAAAAAAGGAAAAAGGAAATTGGGGTTNCNNACCCCACCCCCAAGGGNTTTGGGAAATNCCATATTTTANNGGGGNNNGGGCCGCNTNNCCCNTTNNNNNTTGCNTATTTTAAATTTTTTTTTTTTGNGAAAGAGGGGGGAC +TTCCTTGTTTTACGTTGTATGGTTGAACTATAGCTTTAGTTTCCATACAAACAGGCATTAATTTACGTGTTTCCTCAGCATGTGCAAGCATTTCTCGCAAATTCCAAGAAACAGTTCCAAGAATTTCTTCTTTCTCATTAGAGACAATGGATGGTAGTATGTAAAAAGCGCTCTTGCACTTTTTAAGCACTGTCTTTGCCTCTTCTAATGTATAACCATTATTACCCTGTCCAGGGTAGGTGGTTATATAATTGTCTACTGGTAACTTCTTTAATGCTTTTGTAAGCATTTCGGTAGTACCACCAGCTTTTTTAGTAGGTATAACTACAGCAGTTAAAACACCTTCCTTAATGACATCACCTACTATGTAAGGAGCATCTTTCTTTAGAAAGGTGGTGTCAGTGTCTTTAACAAGCATGGCAGAATCTGGATGAAGGTTGCCATTAATGTCTATATAAAGTAACAAATTCTCTGTGAGAAACTTAGTTTCTTCCAAAGTGGTTGTAACTTCTTCAACACAAGCCTTGACTTTCTTTTCTTCAGCCTGTTGCTTTTGTTCAACTGAAGGTTTATTTTCAGTTGTTGGTGGCTCAACTTCCATTTTAGGAACTTCAGCAATCTGTTGTTCTACTTGTGCCTCACTCTTCATTTCTAAAAAGCTAGAAACAAGTTTTTCATAGAGATCTTTGTCAAAGACAGTCAAGTAAACATTTGTGCGAACAGTGTCTACACAAACTCTTAAGGATTGGACAGGGTCAGCACCAAAGATGCCTGCTGACAATAAAGGTGCTAGTAAAGTATCATACTGATTGAAATTTTCATATGCAGTTTTAAGAAGTTGAATGCTTTCACCCTTGTTGATATTAGGACCAACAACATGAAGACAATTTTTAGCAAGATTATGTCCACTCAGAACACAACTACCACCAACATTCAGAGGTCCGTTTGTGGCTATGTAATTGTCTGATTCTACTTGCATAGCGTTGTTTGTAGCTTTGTTTAAAGCTCCAGCAACACCTCCTCCATGTTTAAGTAAACATTAGCTGCATTAACAACTACTGTGGTTTCCCCTGTTAGCTTCTTCCACAATGTCTGCATTTTTAATGAAAACAATTGTTAGGGGAG |
| b |
| diff -r 99d31ec6629b -r 897b1ff9e906 test-data/output1.json --- a/test-data/output1.json Tue Oct 12 14:20:41 2021 +0000 +++ b/test-data/output1.json Thu Mar 20 07:18:34 2025 +0000 |
| [ |
| b'@@ -1,12 +1,13 @@\n {\n-"pos": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461, 462, 463, 464, 465, 466, 467, 468, 469, 470, 471, 472, 473, 474, 475, 476, 477, 478, 479, 480, 481, 482, 483, 484, 485, 486, 487, 488, 489, 490, 491, 492, 493, 494, 495, 496, 497, 498, 499, 500, 501, 502, 503, 504, 505, 506, 507, 508, 509, 510, 511, 512, 513, 514, 515, 516, 517, 518, 519, 520, 521, 522, 523, 524, 525, 526, 527, 528, 529, 530, 531, 532, 533, 534, 535, 536, 537, 538, 539, 540, 541, 542, 543, 544, 545, 546, 547, 548, 549, 550, 551, 552, 553, 554, 555, 556, 557, 558, 559, 560, 561, 562, 563, 564, 565, 566, 567, 568, 569, 570, 571, 572, 573, 574, 575, 576, 577, 578, 579, 580, 581, 582, 583, 584, 585, 586, 587, 588, 589, 590, 591, 592, 593, 594, 595, 596, 597, 598, 599, 600, 601, 602, 603, 604, 605, 606, 607, 608, 609, 610, 611, 612, 613, 614, 615, 616, 617, 618, 619, 620, 621, 622, 623, 624, 625, 626, 627, 628, 629, 630, 631, 632, 633, 634, 635, 636, 637, 638, 639, 640, 641, 642, 643, 644, 645, 646, 647, 648, 649, 650, 651, 652, 653, 654, 655, 656, 657, 658, 659, 660, 661, 662, 663, 664, 665, 666, 667, 668, 669, 670, 671, 672, 673, 674, 675, 676, 677, 678, 679, 680, 681, 682, 683, 684, 685, 686, 687, 688, 689, 690, 691, 692, 693, 694, 695, 696, 697, 698, 699, 700, 701, 702, 703, 704, 705, 706, 707, 708, 709, 710, 711, 712, 713, 714, 715, 716, 717, 718, 719, 720, 721, 722, 723, 724, 725, 726, 727, 728, 729, 730, 731, 732, 733, 734, 735, 736, 737, 738, 739, 740, 741, 742, 743, 744, 745, 746, 747, 748, 749, 750, 751, 752, 753, 754, 755, 756, 757, 758, 759, 760, 761, 762, 763, 764, 765, 766, 767, 768, 769, 770, 771, 772, 773, 774, 775, 776, 777, 778, 779, 780, 781, 782, 783, 784, 785, 786, 787, 788, 789, 790, 791, 792, 793, 794, 795, 796, 797, 798, 799, 800, 801, 802, 803, 804, 805, 806, 807, 808, 809, 810, 811, 812, 813, 814, 815, 81'..b'2:A", "12608":"1033:G", "12624":"1034:T", "12637":"1035:A", "12646":"1036:A", "12656":"1037:A", "12674":"1038:C", "12682":"1039:A", "12704":"1040:T", "12713":"1041:T", "12727":"1042:A", "12741":"1043:G", "12755":"1044:C", "12770":"1045:T", "12783":"1046:G", "12795":"1047:C", "12811":"1048:A", "12826":"1049:T", "12833":"1050:T", "12848":"1051:A|T", "12858":"1052:A", "12876":"1053:C", "12893":"1054:A", "12898":"1055:A", "12916":"1056:C", "12932":"1057:T", "12942":"1058:A", "12956":"1059:C", "12972":"1060:T", "12985":"1061:G", "13007":"1062:T", "13025":"1063:G|T", "13035":"1064:G", "13057":"1065:T", "13074":"1066:T", "13075":"1067:T", "13100":"1068:C", "13104":"1069:C|A", "13120":"1070:C", "13129":"1071:C", "13150":"1072:T", "13163":"1073:G", "13193":"1074:T", "13200":"1075:T", "13225":"1076:A", "13234":"1077:G", "13250":"1078:C", "13266":"1079:T", "13274":"1080:T", "13293":"1081:C", "13306":"1082:T|C", "13317":"1083:T", "13336":"1084:C|T", "13344":"1085:C", "13358":"1086:A", "13370":"1087:C|A", "13382":"1088:A", "13396":"1089:A", "13420":"1090:T", "13428":"1091:G", "13449":"1092:T", "13464":"1093:C", "13478":"1094:T", "13492":"1095:G", "13508":"1096:C", "13521":"1097:A", "13537":"1098:T", "13549":"1099:T", "13558":"1100:T", "13573":"1101:T", "13592":"1102:T", "13615":"1103:A", "13622":"1104:A", "13633":"1105:T", "13652":"1106:G", "13678":"1107:A", "13689":"1108:A", "13705":"1109:A", "13713":"1110:A|C", "13724":"1111:C", "13727":"1112:A", "13745":"1113:A|T", "13758":"1114:T", "13766":"1115:T", "13782":"1116:G", "13797":"1117:T|G", "13810":"1118:T", "13833":"1119:A", "13845":"1120:G", "13854":"1121:G|T", "13873":"1122:G", "13888":"1123:G|A", "13898":"1124:A|G", "13906":"1125:G"},\n+"primarySeq": "TTCCTTGTTTTACGTTGTATGGTTGAACTATAGCTTTAGTTTCCATACAAACAGGCATTAATTTACGTGTTTCCTCAGCATGTGCAAGCATTTCTCGCAAATTCCAAGAAACAGTTCCAAGAATTTCTTCTTTCTCATTAGAGACAATGGATGGTAGTATGTAAAAAGCGCTCTTGCACTTTTTAAGCACTGTCTTTGCCTCTTCTAATGTATAACCATTATTACCCTGTCCAGGGTAGGTGGTTATATAATTGTCTACTGGTAACTTCTTTAATGCTTTTGTAAGCATTTCGGTAGTACCACCAGCTTTTTTAGTAGGTATAACTACAGCAGTTAAAACACCTTCCTTAATGACATCACCTACTATGTAAGGAGCATCTTTCTTTAGAAAGGTGGTGTCAGTGTCTTTAACAAGCATGGCAGAATCTGGATGAAGGTTGCCATTAATGTCTATATAAAGTAACAAATTCTCTGTGAGAAACTTAGTTTCTTCCAAAGTGGTTGTAACTTCTTCAACACAAGCCTTGACTTTCTTTTCTTCAGCCTGTTGCTTTTGTTCAACTGAAGGTTTATTTTCAGTTGTTGGTGGCTCAACTTCCATTTTAGGAACTTCAGCAATCTGTTGTTCTACTTGTGCCTCACTCTTCATTTCTAAAAAGCTAGAAACAAGTTTTTCATAGAGATCTTTGTCAAAGACAGTCAAGTAAACATTTGTGCGAACAGTGTCTACACAAACTCTTAAGGATTGGACAGGGTCAGCACCAAAGATGCCTGCTGACAATAAAGGTGCTAGTAAAGTATCATACTGATTGAAATTTTCATATGCAGTTTTAAGAAGTTGAATGCTTTCACCCTTGTTGATATTAGGACCAACAACATGAAGACAATTTTTAGCAAGATTATGTCCACTCAGAACACAACTACCACCAACATTCAGAGGTCCGTTTGTGGCTATGTAATTGTCTGATTCTACTTGCATAGCGTTGTTTGTAGCTTTGTTTAAAGCTCCAGCAACACCTCCTCCATGTTTAAGTAAACATTAGCTGCATTAACAACTACTGTGGTTTCCCCTGTTAGCTTCTTCCACAATGTCTGCATTTTTAATGAAAACAATTGTTAGGGGAG",\n+"secondarySeq": "RMTCCTGTATTACGTTGTATGGTTGAACTATAGCTTTAGTTTCCATACAAACAGGCATTAATTTACGTGTTTCCTCAGCATGTGCAAGCATTTCTCGCAAATTCCAAGAAACAGTTCCAAGAATTTCTTCTTTCTCATTAGAGACAATGGATGGTAGTATGTAAAAAGCGCTCTTGCACTTTTTAAGCACTGTCTTTGCCTCTTCTAATGTATAACCATTATTACCCTGTCCAGGGTAGGTGGTTATATAATTGTCTACTGGTAACTTCTTTAATGCTTTTGTAAGCATTTCGGTAGTACCACCAGCTTTTTTAGTAGGTATAACTACAGCAGTTAAAACACCTTCCTTAATGACATCACCTACTATGTAAGGAGCATCTTTCTTTAGAAAGGTGGTGTCAGTGTCTTTAACAAGCATGGCAGAATCTGGATGAAGGTTGCCATTAATGTCTATATAAAGTAACAAATTCTCTGTGAGAAACTTAGTTTCTTCCAAAGTGGTTGTAACTTCTTCAACACAAGCCTTGACTTTCTTTTCTTCAGCCTGTTGCTTTTGTTCAACTGAAGGTTTATTTTCAGTTGTTGGTGGCTCAACTTCCATTTTAGGAACTTCAGCAATCTGTTGTTCTACTTGTGCCTCACTCTTCATTTCTAAAAAGCTAGAAACAAGTTTTTCATAGAGATCTTTGTCAAAGACAGTCAAGTAAACATTTGTGCGAACAGTGTCTACACAAACTCTTAAGGATTGGACAGGGTCAGCACCAAAGATGCCTGCTGACAATAAAGGTGCTAGTAAAGTATCATACTGATTGAAATTTTCATATGCAGTTTTAAGAAGTTGAATGCTTTCACCCTTGTTGATATTAGGACCAACAACATGAAGACAATTTTTAGCAAGATTATGTCCACTCAGAACACAACTACCACCAACATTCAGAGGTCCGTTTGTGGCTATGTAAATGTCTGAATCTACTTGCATAGCGTTGTTTGTAGCTTTGTTTAAAGCTCCAGCCACACCTTCTTCATGTTTAAGTAAACATTAGCTGCATTTACAACTACTGTTGTTTCACCTGTTAGCTTCCTTCAAAATGTCTGCATTTTTAATGAAACCATTTGGTAGTGAGG"\n \n }\n' |
| b |
| diff -r 99d31ec6629b -r 897b1ff9e906 test-data/output2.fasta --- a/test-data/output2.fasta Tue Oct 12 14:20:41 2021 +0000 +++ b/test-data/output2.fasta Thu Mar 20 07:18:34 2025 +0000 |
| b |
| @@ -1,2 +1,2 @@ >primary -TTTTTTTTTGAGCGGGTCGNACCGTCACGAANAGNANANGGCAAGAACCATCNGCNGGNGTNNTCCGTANTTTNNNTGGATCCNNATTCATAGCAAACACCANAAATCCATATTGGGACCACAATCCCAACAAAGACCACTGGACAGAAGCCAACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCCCACACGGAGGCCTTTTGGGGTGGAGCCCTCAGGCTCAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCCTCCACCAATCGACAGTCAGGAAGGCAGCCTACCCCAATCACTCCACCTTTGAGAGACACTCATCCTCAGGCCATGCAGTGGAATTCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAATCCTGCTGGTGGCTCCAGTTCCGGAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATCTCGTCAATCTTCTCGAGGATTGGGGACCCTGCACCGAACATGGAAAGCATCACATCAGGATTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAAAATCCTCACAATACCGCAGAGTCTAGACTCGTGATGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGTGTCTTGGCCAAAATTCTCAGTCGCAAACCTCCAGTCACTCACCAACCTCTTGTCCTCCNATTTGTCCTGCCTATCGCTGGATGTGTNTGCGGCGGTTTATCATATTCATCTTCATCGTGCTGCTATGCCTCATCATCCTGTTGGGTTCGTNTGCACCATCAAAAGAATGTTGCCCCGGGTTGTGNTTNNNAATTCCAAAGAGCAAGAAAGCCACCCANTACGNGAANCNTGGCCGCANGCTGCACAAGTCATNTTTCAAAGGAAANTGNANGNTTATNNTTCTNNTTTGTGGGGGNNAAGCAAAAAAAGGAAAANGGANANTGGNGTNNCNNACCCCACNCCCAANGGNTTTGGGAAATNCNATATTNNNNNGGGGNNNNGGCCGCNTNNCCCNNTNNNNNNNGCNTNTTTNANATNNTTTTTTNTTGNNAAAGAGGGGNGAC +TNCCTTGTTTTACGTTGTATGGTTGAACTATAGCTTTAGTTTCCATACAAACAGGCATTAATTTACGTGTTTCCTCAGCATGTGCAAGCATTTCTCGCAAATTCCAAGAAACAGTTCCAAGAATTTCTTCTTTCTCATTAGAGACAATGGATGGTAGTATGTAAAAAGCGCTCTTGCACTTTTTAAGCACTGTCTTTGCCTCTTCTAATGTATAACCATTATTACCCTGTCCAGGGTAGGTGGTTATATAATTGTCTACTGGTAACTTCTTTAATGCTTTTGTAAGCATTTCGGTAGTACCACCAGCTTTTTTAGTAGGTATAACTACAGCAGTTAAAACACCTTCCTTAATGACATCACCTACTATGTAAGGAGCATCTTTCTTTAGAAAGGTGGTGTCAGTGTCTTTAACAAGCATGGCAGAATCTGGATGAAGGTTGCCATTAATGTCTATATAAAGTAACAAATTCTCTGTGAGAAACTTAGTTTCTTCCAAAGTGGTTGTAACTTCTTCAACACAAGCCTTGACTTTCTTTTCTTCAGCCTGTTGCTTTTGTTCAACTGAAGGTTTATTTTCAGTTGTTGGTGGCTCAACTTCCATTTTAGGAACTTCAGCAATCTGTTGTTCTACTTGTGCCTCACTCTTCATTTCTAAAAAGCTAGAAACAAGTTTTTCATAGAGATCTTTGTCAAAGACAGTCAAGTAAACATTTGTGCGAACAGTGTCTACACAAACTCTTAAGGATTGGACAGGGTCAGCACCAAAGATGCCTGCTGACAATAAAGGTGCTAGTAAAGTATCATACTGATTGAAATTTTCATATGCAGTTTTAAGAAGTTGAATGCTTTCACCCTTGTTGATATTAGGACCAACAACATGAAGACAATTTTTAGCAAGATTATGTCCACTCAGAACACAACTACCACCAACATTCAGAGGTCCGTTTGTGGCTATGTAATTGTCTGATTCTACTTGCATAGCGTTGTTTGTAGCTTTGTTTAAAGCTCCAGCAACACCTCCTCCATGTTTAAGTAAACATTAGCTGCATTAACAACTACTGTGGTTTCCCCTGTTAGCTTCTTCCACAATGTCTGCATTTTTAATGAAAACAATTGTTAGGGGAG |
| b |
| diff -r 99d31ec6629b -r 897b1ff9e906 test-data/reference1.fasta --- a/test-data/reference1.fasta Tue Oct 12 14:20:41 2021 +0000 +++ b/test-data/reference1.fasta Thu Mar 20 07:18:34 2025 +0000 |
| b |
| @@ -1,48 +1,2 @@ ->X75657.1 Human hepatitis virus (genotype E, Bas) preS1, preS2, S, C, X, antigens, core antigen, X protein and polymerase -TTCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAGAGGCCTGTATTTTCCTGCTGGTGGCTCC -AGTTCCGGAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATCTCGTCAATCTTCTCGAGGATTGGGG -ACCCTGCACCGAACATGGAAAGCATCACATCAGGATTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTT -TTTCTTGTTGACAAAAATCCTCACAATACCGCAGAGTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTA -GGGGGAGCTCCCGTGTGTCTTGGCCAAAATTCGCAGTCCCCAACCTCCAGTCACTCACCAACCTCTTGTC -CTCCAATTTGTCCTGGCTATCGCTGGATGTGTCTGCGGCGTTTTATCATCTTCCTCTTCATCCTGCTGCT -ATGCCTCATCTTCTTGTTGGTTCTTCTGGACTATCAAGGTATGTTGCCCGTTTGTCCTCTAATTCCAGGA -TCATCAACCACCAGTACGGGACCCTGCCGAACCTGCACGACTCTTGCTCAAGGAACCTCTATGTTTCCCT -CATGTTGCTGTTCAAAACCTTCGGACGGAAATTGCACTTGTATTCCCATCCCATCATCATGGGCTTTCGG -AAAATTCCTATGGGAGTGGGCCTCAGCCCGTTTCTCCTGGCTCAGTTTACTAGTGCCATTTGTTCAGTGG -TTCGCCGGGCTTTCCCCCACTGTCTGGCTTTCAGTTATATGGATGATGTGGTATTGGGGGCCAAGTCTGT -ACAACATCTTGAGTCCCTTTATACCGCTGTTACCAATTTTCTTTTGTCTTTGGGTATACATTTAAATCCC -AACAAAACAAAAAGATGGGGCTATTCCCTTAATTTCATGGGTTATGTAATTGGAAGTTGGGGCTCATTAC -CACAGGAACACATCATACAAAAAATCAAAGACTGTTTTAGAAAACTCCCTGTTAACCGGCCTATTGATTG -GAAAGTATGTCAAAGAATTGTGGGTCTTTTGGGCTTTGCTGCCCCCTTTACACAATGTGGATATCCTGCT -TTAATGCCTCTGTATGCATGTACTCAATCTAAGCAGGCTTTCACTTTCTCGCCAACTTACAAGGCCTTTC -TGTGTAAACAATACCTGAACCTTTACCCCGTTGCCCGGCAACGGCCAGGTCTGTGCCAAGTGTTTGCTGA -TGCAACCCCCACTGGCTGGGGCTTGGCCATAGGCATTCAGCGCATGCGCGGAACCTTTGTGGCTCCTCTG -CCGATCCATACTGCGGAACTCCTAGCCGCTTGTTTTGCTCGCAGCAGGTCTGGAGCAAAACTTATCGGGA -CCGATAATTCTGTCGTTCTCTCCCGGAAGTATACATCCTTTCCATGGCTGCTAGGCTGTGCTGCCAACTG -GATCCTGCGAGGGACGTCCTTTGTCTACGTCCCGTCAGCGCTGAATCCTGCGGACGACCCGTCTCGGGGT -CGCTTGGGGATCTATCGTCCCCTTCTCCGTCTGCCGTTCCAGCCGACCACGGGGCGCACCTCTCTTTACG -CGGTCTCCCCGTCTGTTCCTTCTCATCTGCCGGACCGTGTGCACTTCGCTTCACCTCTGCACGTCGCATG -GAGACCACCGTGAACGCCCACCAAATATTGCCCAAGGTCTTACATAAGAGGACTCTTGGACTCTCTGCAA -TGTCAACGACCGACCTTGAGGCATACTTCAAAGACTGTTTGTTTAAAGACTGGGAGGAGTCGGGGGAGGA -GATTAGATTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGCGCACCAGCACCATGCAAC -TTTTTCACCTCTGCCTAATCATCTCTTGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTG -GCTTTGGGGCATGGACATTGACCCTTATAAAGAATTTGGAGCTACTGTGGAGTTACTCTCGTTTTTGCCT -TCTGACTTCTTTCCTTCAGTAAGAGATCTTCTAGATACCGCCTCAGCTCTGTATCGGGATGCCTTAGAGT -CTCCTGAGCATTGTTCACCTCACCACACTGCACTCAGGCAAGCCATTCTTTGCTGGGGAGAACTAATGAC -TCTAGCTACCTGGGTGGGTGTAAATTTGGAAGATCCAGCATCCAGGGACCTAGTAGTCAGTTATGTCAAT -ACTAATATGGGCCTAAAGTTCAGGCAATTATTGTGGTTTCACATTTCTTGTCTCACTTTTGGAAGAGAAA -CCGTCATAGAGTATTTGGTGTCTTTTGGAGTGTGGATTCGCACTCCTCCAGCTTATAGACCACCAAATGC -CCCTATCTTATCAACACTTCCGGAGAATACTGTTGTTAGACGAAGAGGCAGGTCCCCTAGAAGAAGAACT -CCCTCGCCTCGCAGACGAAGATCTCAATCGCCGCGTCGCAGAAGATCTCAATCTCCAGCTTCCCAATGTT -AGTATTCCTTGGACTCATAAGGTGGGAAATTTTACGGGGCTTTACTCTTCTACTATACCTGTCTTTAATC -CTAACTGGAAAACTCCATCTTTTCCTGATATTCATTTGCACCAGGACATTATTAACAAATGTGAACAATT -TGTAGGTCCTCTAACTGTAAATGAAAAACGAAGATTAAACTTAGTCATGCCTGCTAGATTTTTTCCCATC -TCTACGAAATATTTGCCCCTAGAGAAAGGTATAAAACCTTATTATCCAGATAATGTAGTTAATCATTACT -TCCAAACCAGACACTATTTACATACCCTATGGAAGGCGGGCATCTTATATAAAAGAGAAACTACACGTAG -CGCCTCATTTTGTGGGTCACCTTATTCTTGGGAACAAGAGCTACATCATGGGGCTTTCTTGGACGGTCCC -TCTCGAATGGGGGAAGAATATTTCCACCACCAATCCTCTGGGATTTTTTCCCGACCACCAGTTGGATCCA -GCATTCAGAGCAAACACCAGAAATCCAGATTGGGACCACAATCCCAACAAAGACCACTGGACAGAAGCCA -ACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCCCACACGGAGGCCTTTTGGGGTGGAGCCC -TCAGGCTCAAGGCATGCTAAAAACATTGCCAGCAGATCCGCCTCCTGCCTCCACCAATCGGCAGTCAGGA -AGGCAGCCTACCCCAATCACTCCACCTTTGAGAGACACTCATCCTCAGGCCATGCAGTGGAA - +>MT121216.1:2501-5000 Pangolin coronavirus isolate MP789, complete genome +AACGGGCTTATGTTGCTCGAAATTAAAGATACAGAGAAGTATTGTGCTCTTGCACCTAACATGATGGTTACAAATAACACCTTCACACTTAAAGGTGGTGCACCAACAAGAGTTACTTTTGGTGATGACACCGTAATTGAAGTACAGGGTTACAAAAGTGTAAGTATCACTTTTGAACTCGATGAGAGAGTAGATAAAGTACTTAATGAAAAGTGCTCTAACTACACAGTTGAACTTGGAACAGAAGTAAATGAGTTTGCTTGTGTTGTCGCTGATGCTGTTATAAAGACTTTACAGCCAGTATCTGAATTACTTACACCACTAGGCATAGATTTAGACGAGTGGGGTATGGCAACATACTACTTGTTTGATGAATCTGGTGAGTTTAATTTAGCCTCTCATATGTACTGTTCTTTCTATCCTCCAGATGAGGATTATGAAGAAGATGAGTGTGAAGAGGAACAGTATGAACCATCAACTCAGTATGAGTATGGTACAGAGGATGATTACCAAGGTAAATCTTTGGAATTTGGTTCAACCTCTTCTGCTTCTCAAATAGAAGAAGAACCAGAGGAAGATTGGTTAGAAGATGGCAATGAGGAAATTGCTATGCAAGAAGAGCAGACAACAACTGTTGAAGTGCAATCTCAGGAGATTGACTCTACACCAGTTGTCTCTGAGATAAATGAATCAGTGAACAATTTTACTGGTTATTTAAAACTCACTAACAATGTTTTCATTAAAAATGCAGACATTGTGGAAGAAGCTAAACAGGTGAAACCAACAGTAGTTGTTAATGCAGCTAATGTTTACCTTAAACATGGAGGAGGTGTTGCTGGAGCTTTAAACAAAGCTACAAACAACGCTATGCAAGTAGAATCAGACAATTACATAGCCACAAACGGACCTCTGAATGTTGGTGGTAGTTGTGTTCTGAGTGGACATAATCTTGCTAAAAATTGTCTTCATGTTGTTGGTCCTAATATCAACAAGGGTGAAAGCATTCAACTTCTTAAAACTGCATATGAAAATTTCAATCAGTATGATACTTTACTAGCACCTTTATTGTCAGCAGGCATCTTTGGTGCTGACCCTGTCCAATCCTTAAGAGTTTGTGTAGACACTGTTCGCACAAATGTTTACTTGACTGTCTTTGACAAAGATCTCTATGAAAAACTTGTTTCTAGCTTTTTAGAAATGAAGAGTGAGGCACAAGTAGAACAACAGATTGCTGAAGTTCCTAAAATGGAAGTTGAGCCACCAACAACTGAAAATAAACCTTCAGTTGAACAAAAGCAACAGGCTGAAGAAAAGAAAGTCAAGGCTTGTGTTGAAGAAGTTACAACCACTTTGGAAGAAACTAAGTTTCTCACAGAGAATTTGTTACTTTATATAGACATTAATGGCAACCTTCATCCAGATTCTGCCATGCTTGTTAAAGACACTGACACCACCTTTCTAAAGAAAGATGCTCCTTACATAGTAGGTGATGTCATTAAGGAAGGTGTTTTAACTGCTGTAGTTATACCTACTAAAAAAGCTGGTGGTACTACCGAAATGCTTACAAAAGCATTAAAGAAGTTACCAGTAGACAATTATATAACCACCTACCCTGGACAGGGTAATAATGGTTATACATTAGAAGAGGCAAAGACAGTGCTTAAAAAGTGCAAGAGCGCTTTTTACATACTACCATCCATTGTCTCTAATGAGAAAGAAGAAATTCTTGGAACTGTTTCTTGGAATTTGCGAGAAATGCTTGCACATGCTGAGGAAACACGTAAATTAATGCCTGTTTGTATGGAAACTAAAGCTATAGTTTCAACCATACAACGTAAATACAAGGGTATTAAAATACAGGAAGGTGTGGTTGATTATGGTGCTAGGTTTTACTTCTATACTAGTAAAACAACAGTAGCATCACTCATCAACACACTTAACAATCTAAATGAGACTCTCGTTACAATGCCTTTGGGTTATGTAACACATGGCCTTAACCTAGAAGAAGCTGCGCGGTACATGAGATCTCTTAAGGTACCAGCGACAGTTTCTGTTTCTTCACCAGATGCTGTAACAGCATATAATGGTTATCTTACTTCTTCTTCAAAAACACCTGAAGAACATTTCATAGAAACCATCTCTCTAGCTGGTTCTTACAAAGATTGGTCCTATTCTGGACAATCAACACAACTTGGTATAGAATTTCTTAAAAGAGGTGATAAAACTGTTTATTACACCATTAACCCTATTGCTTTTCATACAGAGGGTCAAATTATCACCTTTGATGATTTAAAAACACTTCTCTCATTGAGAGAGGTTAGAACAATCAAAGTGTTTACAACTGTAGACAATGTTAATCTCCATACACAAGTTGTGGACATGTCTATGACTTATGGACAACAGTTTGGTCCCACTTATTTGGATGGAGCTGATGTCACTAAAATAAAACCTCATAATTCACATGAAGGTAAGACATTTTATGTCTTGCCTAATGATGACA |
| b |
| diff -r 99d31ec6629b -r 897b1ff9e906 tracy_assemble.xml --- a/tracy_assemble.xml Tue Oct 12 14:20:41 2021 +0000 +++ b/tracy_assemble.xml Thu Mar 20 07:18:34 2025 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="tracy_assemble" name="tracy Assemble" version="@TOOL_VERSION@+galaxy0" profile="20.09"> +<tool id="tracy_assemble" name="tracy Assemble" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>genomic region from tiled, overlapping Sanger Chromatogram trace files</description> <macros> <import>macros.xml</import> @@ -70,26 +70,26 @@ <data name="out_alignment" format="fasta" from_work_dir="out.align.fa" label="tracy assemble alignment on ${on_string}" /> </outputs> <tests> - <test expect_num_outputs="2"> - <param name="tracefiles" value="input1.ab1,input1.ab1" ftype="ab1" /> + <test expect_num_outputs="2"> <!-- test1 --> + <param name="tracefiles" value="input1_f.ab1,input1_r.ab1" ftype="ab1" /> <output name="out_consensus" value="out1.consensus.fasta" ftype="fasta" /> <output name="out_alignment" value="out1.alignment.fasta" ftype="fasta" lines_diff="4" /> </test> - <test expect_num_outputs="2"> - <param name="tracefiles" value="input1.ab1,input1.ab1" ftype="ab1" /> + <test expect_num_outputs="2"> <!-- test2 --> + <param name="tracefiles" value="input1_f.ab1,input1_r.ab1" ftype="ab1" /> <conditional name="ref"> <param name="useref" value="yes" /> <param name="reference" value="reference1.fasta" /> </conditional> - <output name="out_consensus" value="out1.consensus.fasta" ftype="fasta" /> + <output name="out_consensus" value="out2.consensus.fasta" ftype="fasta" /> <output name="out_alignment" value="out2.alignment.fasta" ftype="fasta" lines_diff="4" /> </test> - <test expect_num_outputs="3"> - <param name="tracefiles" value="input1.ab1,input1.ab1" ftype="ab1" /> + <test expect_num_outputs="3"> <!-- test3 --> + <param name="tracefiles" value="input1_f.ab1,input1_r.ab1" ftype="ab1" /> <param name="json_output" value="true" /> <output name="out_json" ftype="json"> <assert_contents> - <has_text text='"peakA": [5, 5, 5, 5, 5, 4' /> + <has_text text='"peakA": [283, 278, 264, 236, 194, 143' /> </assert_contents> </output> <output name="out_consensus" value="out1.consensus.fasta" ftype="fasta" /> |