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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tracy commit 8a1c82789c6ef97008ecf8f55e060422fd72f217" |
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added:
macros.xml test-data/input1.ab1 test-data/input2.scf 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/output3.fasta test-data/reference1.fasta tracy_decompose.xml |
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| diff -r 000000000000 -r 6ec40b104f9d macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Oct 12 14:21:06 2021 +0000 |
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| @@ -0,0 +1,79 @@ +<macros> + <token name="@TOOL_VERSION@">0.6.1</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">tracy</requirement> + <yield/> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1186/s12864-020-6635-8</citation> + <yield /> + </citations> + </xml> + <xml name="version_command"> + <version_command>tracy --version</version_command> + </xml> + <xml name="common_options"> + <param argument="--pratio" type="float" value="0.33" label="Peak ratio to call base" /> + <param argument="--maxindel" type="integer" value="1000" label="Maximum indel size in Sanger trace" min="1" /> + <param argument="--linelimit" type="integer" value="60" label="Alignment line length" min="1" /> + </xml> + <xml name="kmer_options"> + <section name="kmer" title="Kmer options"> + <param argument="--kmer" type="integer" value="15" label="Kmer size to anchor trace" min="1" /> + <param argument="--support" type="integer" value="3" label="Minimum kmer support" min="1" /> + </section> + </xml> + <xml name="trim_options"> + <section name="trim" title="Trimming options"> + <param argument="--trim" type="integer" value="0" label="Trimming stringency (0: use trimLeft and trimRight)" /> + <param argument="--trimLeft" type="integer" value="50" label="Trim size left" min="0" /> + <param argument="--trimRight" type="integer" value="50" label="Trim size right" min="0" /> + </section> + </xml> + <xml name="alignment_options"> + <section name="alignment" title="Alignment options"> + <param argument="--gapopen" type="integer" value="-10" max="0" label="Gap open penalty" /> + <param argument="--gapext" type="integer" value="-4" max="0" label="Gap extension penalty" /> + <param argument="--match" type="integer" value="3" min="0" label="Match score" /> + <param argument="--mismatch" type="integer" value="-5" max="0" label="Mismatch penalty" /> + </section> + </xml> + <token name="@pratio@"><![CDATA[ +The *pratio* parameter is a floating point value expressing the minimum proportion of the maximum trace value that will still be +called as a base. For example, if the maximum value found in the trace file is 10, and pratio is 0.3, a peak needs to be +higher than 3 to be called as a base. + ]]></token> + <token name="@trim_options@"><![CDATA[ +Prior to alignment the trace file is trimmed. Either a fixed number of bases can be trimmed from the left or right sides of +the trace, or trimming points (on the left or right or the trace) can be automatically found using an algorithm that works +outwards from the best 10% of the trace and uses a sliding window (of size 10 bases) to find the point where the trace +quality falls below a computed threshold. This automated trimming algorithm can be tuned using a *trimming stringency* (higher +values mean stricter trimming). + ]]></token> + <token name="@alignment@"><![CDATA[ +The dynamic programming step of the alignment uses the `Gotoh's algorithm <http://rna.informatik.uni-freiburg.de/Teaching/index.jsp?toolName=Gotoh>`_ +which can be tuned using scores for nucleotide matches, mismatches, gap opening and gap extension. + ]]></token> + <xml name="optional_outputs"> + <param name="optional_outputs" type="select" multiple="true" label="Optional outputs"> + <option value="json">JSON</option> + <option value="tabular">tabular statistics report</option> + </param> + </xml> + <xml name="json_output" token_toolname=""> + <data name="out_json" format="json" from_work_dir="out.json" label="tracy @TOOLNAME@ JSON on ${on_string}"> + <filter>optional_outputs and 'json' in optional_outputs</filter> + </data> + </xml> + <xml name="tabular_output" token_toolname=""> + <data name="out_stats" format="tabular" from_work_dir="out.abif" label="tracy @TOOLNAME@ stats on ${on_string}"> + <actions> + <action name="column_names" type="metadata" default="pos,peakA,peakC,peakG,peakT,basenum,primary,secondary,consensus,qual,trim" /> + </actions> + <filter>optional_outputs and 'tabular' in optional_outputs</filter> + </data> + </xml> +</macros> |
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| diff -r 000000000000 -r 6ec40b104f9d test-data/input1.ab1 |
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| Binary file test-data/input1.ab1 has changed |
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| diff -r 000000000000 -r 6ec40b104f9d test-data/input2.scf |
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| Binary file test-data/input2.scf has changed |
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| diff -r 000000000000 -r 6ec40b104f9d test-data/out1.align1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out1.align1.fasta Tue Oct 12 14:21:06 2021 +0000 |
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| @@ -0,0 +1,106 @@ +>Alt1 (Estimated allelic Fraction: 0.52) +TCNGCNGGNGTNNTCCGTATTTTNNTTGGATCCNCATTCATAGCAAACACCANAAATCCATATTGGGACCACAA +TCCCAACAAAGACCACTGGACAGAAGCCAACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCCCAC +ACGGAGGCCTTTTGGGGTGGAGCCCTCAGGCTCAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCC +TCCACCAATCGACAGTCAGGAAGGCAGCCTACCCCAATCACTCCACCTTTGAGAGACACTCATCCTCAGGCCAT +GCAGTGGAATTCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAATCCTGCTGGTGGCTCCAGTTCCG +GAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATCTCGTCAATCTTCTCGAGGATTGGGGACCCTGCACCG +AACATGGAAAGCATCACATCAGGATTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAA +AATCCTCACAATACCGCAGAGTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGTGTC +TTGGCCAAAATTCGCAGTCCCAAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTCCTGCCTATCGC +TGGATGTGTCTGCGGCGGTTTATCATCTTCCTCTTCATCGTGCTGCTATGCCTCATCATCCTGTTGGGTTCGTC +TGCACTATCAAAGGTATGTTGCCCCGGTTTGTCNTTNNTAATTCCAAGGATCATGAAAGCCACCCACTACGGGA +ACCNTTGCCGCAAGCTGCACGACTCATTTCTCAAAGGAAANTCNANGNTTTTCCCTCATNGTTGCTGTTCAAAA +GCTTCGGACGGAAAATGCACATTGTAGTTNCNNATCCCATCATCATGGGNTTTGGGAAATNCCATATGGTANNG +GGCNNNAGCCCGCNTNNCCT +>Ref X75657.1 Human hepatitis virus genotype E Bas preS1 preS2 S C X antigens core antigen X protein and polymerase:1-718 forward +TTCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAGAGGCCTGTATTTTCCTGCTGGTGGCTCCAGTT +CCGGAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATCTCGTCAATCTTCTCGAGGATTGGGGACCCTGCA +CCGAACATGGAAAGCATCACATCAGGATTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGAC +AAAAATCCTCACAATACCGCAGAGTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGT +GTCTTGGCCAAAATTCGCAGTCCCCAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTCCTGGCTAT +CGCTGGATGTGTCTGCGGCGTTTTATCATCTTCCTCTTCATCCTGCTGCTATGCCTCATCTTCTTGTTGGTTCT +TCTGGACTATCAAGGTATGTTGCCCGTTTGTCCTCTAATTCCAGGATCATCAACCACCAGTACGGGACCCTGCC +GAACCTGCACGACTCTTGCTCAAGGAACCTCTATGTTTCCCTCATGTTGCTGTTCAAAACCTTCGGACGGAAAT +TGCACTTGTATTCCCATCCCATCATCATGGGCTTTCGGAAAATTCCTATGGGAGTGGGCCTCAGCCCGTTTCTC +CTGGCTCAGTTTACTAGTGCCATTTGTTCAGTGGTTCGCCGGGCTTTCCCCC + +Alignment score: 118 +#------------------------------------------------------------------------- + +Alt 1 TCNGCNGGNGTNNTCCGTATTTTNNTTGGATCCNCATTCATAGCAAACACCANAAATCCA + | +Ref 1 T----------------------------------------------------------- + +Alt 61 TATTGGGACCACAATCCCAACAAAGACCACTGGACAGAAGCCAACAAGGTAGGAGTGGGA + +Ref 2 ------------------------------------------------------------ + +Alt 121 GCATTCGGGCCTGGGTTCACTCCCCCACACGGAGGCCTTTTGGGGTGGAGCCCTCAGGCT + +Ref 2 ------------------------------------------------------------ + +Alt 181 CAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCCTCCACCAATCGACAGTCA + +Ref 2 ------------------------------------------------------------ + +Alt 241 GGAAGGCAGCCTACCCCAATCACTCCACCTTTGAGAGACACTCATCCTCAGGCCATGCAG + +Ref 2 ------------------------------------------------------------ + +Alt 301 TGGAATTCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAA------------T + |||||||||||||||||||||||||||||||||||||||| | +Ref 2 ------TCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAGAGGCCTGTATTTT + +Alt 349 CCTGCTGGTGGCTCCAGTTCCGGAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATC + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Ref 56 CCTGCTGGTGGCTCCAGTTCCGGAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATC + +Alt 409 TCGTCAATCTTCTCGAGGATTGGGGACCCTGCACCGAACATGGAAAGCATCACATCAGGA + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Ref 116 TCGTCAATCTTCTCGAGGATTGGGGACCCTGCACCGAACATGGAAAGCATCACATCAGGA + +Alt 469 TTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAAAATCCTCACA + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Ref 176 TTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAAAATCCTCACA + +Alt 529 ATACCGCAGAGTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTG + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Ref 236 ATACCGCAGAGTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTG + +Alt 589 TGTCTTGGCCAAAATTCGCAGTCCCAAACCTCCAGTCACTCACCAACCTCTTGTCCTCCA + ||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||| +Ref 296 TGTCTTGGCCAAAATTCGCAGTCCCCAACCTCCAGTCACTCACCAACCTCTTGTCCTCCA + +Alt 649 ATTTGTCCTGCCTATCGCTGGATGTGTCTGCGGCGGTTTATCATCTTCCTCTTCATCGTG + |||||||||| |||||||||||||||||||||||| ||||||||||||||||||||| || +Ref 356 ATTTGTCCTGGCTATCGCTGGATGTGTCTGCGGCGTTTTATCATCTTCCTCTTCATCCTG + +Alt 709 CTGCTATGCCTCATCATCCTGTTGGGTTCGTCTGCACTATCAAAGGTATGTTGCCCCGGT + ||||||||||||||| || |||||| ||| |||| |||||||| |||||||||||| || +Ref 416 CTGCTATGCCTCATCTTCTTGTTGG-TTCTTCTGGACTATCAA-GGTATGTTGCCC--GT + +Alt 769 TTGTCNTTNNTAATTCCAAGGATCATGAAAGCCACCCACTACGGGAACCNTTGCCGCAAG + ||||| | |||||||| ||||||| || ||||| | ||||||| || ||||| || +Ref 472 TTGTCCTC--TAATTCCA-GGATCATCAA--CCACC-AGTACGGGACCC--TGCCG-AAC + +Alt 829 CTGCACGACTCATTTCTCAAAGGAAANTCNANGNTTTTCCCTCATNGTTGCTGTTCAAAA + ||||||||||| || ||||| |||| || | | |||||||||| |||||||||||||| +Ref 523 CTGCACGACTC-TTGCTCAA-GGAACCTCTATG--TTTCCCTCAT-GTTGCTGTTCAAAA + +Alt 889 GCTTCGGACGGAAAATGCACATTGTAGTTNCNNATCCCATCATCATGGGNTTTGGGAAAT + ||||||||||||| ||||| ||||| | | |||||||||||||||| ||| ||||| +Ref 578 CCTTCGGACGGAAATTGCAC-TTGTATTCCC--ATCCCATCATCATGGGCTTTCGGAAAA + +Alt 949 NCCATATGGTANNGGGCNNNAGCCCGCNTNNCCT-------------------------- + | ||||| | |||| |||||| | ||| +Ref 635 TTCCTATGGGAGTGGGCCTCAGCCCGTTTCTCCTGGCTCAGTTTACTAGTGCCATTTGTT + +Alt 983 ------------------------ + +Ref 695 CAGTGGTTCGCCGGGCTTTCCCCC + +#------------------------------------------------------------------------- +#------------------------------------------------------------------------- + + |
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| diff -r 000000000000 -r 6ec40b104f9d test-data/out1.align2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out1.align2.fasta Tue Oct 12 14:21:06 2021 +0000 |
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| @@ -0,0 +1,106 @@ +>Alt2 (Estimated allelic Fraction: 0.28) +TANTTNTTNGGNNGTCACTCGCCNNGGGGATCANAGTTATGTGGGGACATTANTCATTTTGTTTGGGATTTCCC +TCTCTTCTTAGAACACTGGACATAAGCCAACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCCCAC +ACGGAGGCCTTTTGGGGTGGAGCACTCAGGCTCAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCC +TCCACCAATCGACAGTCAGGAAGGCAGCCTACCCAAATTACACCACCTTTGAGAGACACTCATCCTCAGGCCAT +GCAGTGGAATTCCACAACATGCCACCAACCTCTGCAGGATCCCAAAGTAAGTCCTGCTGGTGGCTCCAGTTCCG +GAACAGTGAACCCTGTTCCGACTACAGCCTCACTCATCTCGTCAACCTTCTCGAGGATTGGGGACCCTGCACCG +AACATGGACAGCATCACATCAGGATTCCGATGACCCCCGCTCATGTTACAAGCGGGGTTTTTCTTGTTGACAAA +AATAAACAGGATACCGCGTAGACAACAGGCGTGGTGGACTTCTCTCTCTTTTGGAAGGGGAGGACCTTTGTGTG +ATGGTGGGAAATCTTAGTCCCTCGCCTCCAATCACTCTCCACCCTCTTGTGGGCCTAATTGAGGTGAGTCCCGC +TGAAAGAAGTGGCAGCGGGGTATCACATACCTCTTCATCTTGCGGGAGAGCCGCCACGTCCTGTGTGGGTGAGC +TCCCCCAGAACAAAAGGGTGTTGCGGGGGGGGGNGGNNACAAACCGCGGGGGGAAGGAGGGAACCCACTAAAAG +AACNGGTGCGGTTTCAAAAAAGGGACTGTTTAGTTGAGAANGGNCNGNCATTTTTCATANTTTCTGTGGGTGAG +TAAAAAACACGGGGGACGCAGATGGGAGGNTNNTCCAAACACCAAAAAANGAGGGAGGGGNAATTTATTCTNNA +AGGNNNGCGCAAGNCNNTTC +>Ref X75657.1 Human hepatitis virus genotype E Bas preS1 preS2 S C X antigens core antigen X protein and polymerase:1-714 forward +TTCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAGAGGCCTGTATTTTCCTGCTGGTGGCTCCAGTT +CCGGAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATCTCGTCAATCTTCTCGAGGATTGGGGACCCTGCA +CCGAACATGGAAAGCATCACATCAGGATTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGAC +AAAAATCCTCACAATACCGCAGAGTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGT +GTCTTGGCCAAAATTCGCAGTCCCCAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTCCTGGCTAT +CGCTGGATGTGTCTGCGGCGTTTTATCATCTTCCTCTTCATCCTGCTGCTATGCCTCATCTTCTTGTTGGTTCT +TCTGGACTATCAAGGTATGTTGCCCGTTTGTCCTCTAATTCCAGGATCATCAACCACCAGTACGGGACCCTGCC +GAACCTGCACGACTCTTGCTCAAGGAACCTCTATGTTTCCCTCATGTTGCTGTTCAAAACCTTCGGACGGAAAT +TGCACTTGTATTCCCATCCCATCATCATGGGCTTTCGGAAAATTCCTATGGGAGTGGGCCTCAGCCCGTTTCTC +CTGGCTCAGTTTACTAGTGCCATTTGTTCAGTGGTTCGCCGGGCTTTC + +Alignment score: -1120 +#------------------------------------------------------------------------- + +Alt 1 TANTTNTTNGGNNGTCACTCGCCNNGGGGATCANAGTTATGTGGGGACATTANTCATTTT + | +Ref 1 T----------------------------------------------------------- + +Alt 61 GTTTGGGATTTCCCTCTCTTCTTAGAACACTGGACATAAGCCAACAAGGTAGGAGTGGGA + ||| +Ref 2 ----------TCC----------------------------------------------- + +Alt 121 GCATTCGGGCCTGGGTTCACTCCCCCACACGGAGGCCTTTTGGGGTGGAGCACTCAGGCT + +Ref 5 ------------------------------------------------------------ + +Alt 181 CAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCCTCCACCAATCGACAGTCA + |||||||| ||||||| | | | || +Ref 5 ------------ACAACATT-----------------------CCACCAAGCT-CTG-CA + +Alt 241 GGAAGGCAGCCTACCCAAATTACACCACCTTTGAGAGACACTCATCCTCAGGCCATGCAG + ||| |||| | || |||| ||| +Ref 28 GGAT---------CCCAGAGTA-----------AGAG--------------GCC------ + +Alt 301 TGGAATTCCACAACATGCCACCAACCTCTGCAGGATCCCAAAGTAAGTCCTGCTGGTGGC + || | || ||||||||||||| +Ref 48 TGTATTT----------------------------------------TCCTGCTGGTGGC + +Alt 361 TCCAGTTCCGGAACAGTGAACCCTGTTCCGACTACAGCCTCACTCATCTCGTCAACCTTC + ||||||||||||||||||||||||||||||||||| ||||||||||||||||||| |||| +Ref 68 TCCAGTTCCGGAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATCTCGTCAATCTTC + +Alt 421 TCGAGGATTGGGGACCCTGCACCGAACATGGACAGCATCACATCAGGATTCCGATGACCC + |||||||||||||||||||||||||||||||| ||||||||||||||||||| | ||||| +Ref 128 TCGAGGATTGGGGACCCTGCACCGAACATGGAAAGCATCACATCAGGATTCCTAGGACCC + +Alt 481 CCGCTCATGTTACAAGCGGGGTTTTTCTTGTTGACAAAAATAAACAGGATACCGCGTAGA + | |||| ||||||| |||||||||||||||||||||||||| || ||||||| || +Ref 188 CTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAAAATCCTCACAATACCGCAGAGT + +Alt 541 CAACAGGCGTGGTGGACTTCTCTCTCTTTTGGAAGGGGAGGACCTTTGTGTGATGGTGGG + | | | ||||||||||||||||| |||| | |||||| || ||||| ||| +Ref 248 CTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGTGTCTTGGCCAA + +Alt 601 AAATCTTAGTCCCTCGCCTCCAATCACTCTCCACCCTCTTGTGGGCCTAATTGAGGTGAG + || || |||||| |||||| |||||| ||| |||||||| || | ||| || +Ref 308 AATTCGCAGTCCCCAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTCCTGGC + +Alt 661 TCCCGCTGAAAGAAGTGGCAGCGGGGT---ATCACATACCTCTTCATCTTGCGGGAGAGC + | ||||| || ||| | |||| || |||| | |||||||||| ||| | || +Ref 368 TATCGCTG---GATGTGTCTGCGGCGTTTTATCATCTTCCTCTTCATCCTGCTGCTATGC + +Alt 718 CGCCACGTCCTGTGTGGGTGAGCTCCCCCAGAACAAAAGGGTGTTGCGGGGGGGGGNGGN + | | | || ||| ||| | || | | | || | |||||| | | +Ref 425 CTCATCTTCTTGT-TGGTT---CTTCTGGACTATCAAGGTATGTTGCCCGTTTGT----- + +Alt 778 NACAAACCGCGGGGGGAAGGAGGGAACCCACTAAAAGAACNGGTGCGGTTTCAAAAAAGG + || | |||| | | || | || || || | | | || | +Ref 476 ------CCTCTAATTCCAGGATC--ATCAACCACCAGTACGGGACCC--TGCCGAACCTG + +Alt 838 GACTGTTTAGTTGAGAANGGNCNGNCATTTTTCATANTTTCTGTGGGTGAGTAAAAAACA + || | | | || | | || |||| | ||| | || | ||||| +Ref 526 CAC-GACTCTTGCTCAAGGAACCTCTATGTTTCCC---TCATGTTGCTG--TTCAAAAC- + +Alt 898 CGGGGGACGCAGATGGGAGGN-TNNTCCAAACACCAAAAAANGAGGGAGGGGNAATTTAT + | ||||| | || | | | ||| | | | | | | | || || || +Ref 579 CTTCGGACGGAAATTGCACTTGTATTCCCATCCCATCATCATGGGCTTTCGGAAAATTCC + +Alt 957 TCTNNAAGGNNNGCGCAAGNCNNTTC---------------------------------- + | | || | || | ||| +Ref 639 TATGGGAGTGGGCCTCAGCCCGTTTCTCCTGGCTCAGTTTACTAGTGCCATTTGTTCAGT + +Alt 983 ---------------- + +Ref 699 GGTTCGCCGGGCTTTC + +#------------------------------------------------------------------------- +#------------------------------------------------------------------------- + + |
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| diff -r 000000000000 -r 6ec40b104f9d test-data/out1.align3.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out1.align3.fasta Tue Oct 12 14:21:06 2021 +0000 |
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| @@ -0,0 +1,106 @@ +>Alt1 (Estimated allelic Fraction: 0.52) +TCNGCNGGNGTNNTCCGTATTTTNNTTGGATCCNCATTCATAGCAAACACCANAAATCCATATTGGGACCACAA +TCCCAACAAAGACCACTGGACAGAAGCCAACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCCCAC +ACGGAGGCCTTTTGGGGTGGAGCCCTCAGGCTCAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCC +TCCACCAATCGACAGTCAGGAAGGCAGCCTACCCCAATCACTCCACCTTTGAGAGACACTCATCCTCAGGCCAT +GCAGTGGAATTCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAATCCTGCTGGTGGCTCCAGTTCCG +GAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATCTCGTCAATCTTCTCGAGGATTGGGGACCCTGCACCG +AACATGGAAAGCATCACATCAGGATTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAA +AATCCTCACAATACCGCAGAGTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGTGTC +TTGGCCAAAATTCGCAGTCCCAAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTCCTGCCTATCGC +TGGATGTGTCTGCGGCGGTTTATCATCTTCCTCTTCATCGTGCTGCTATGCCTCATCATCCTGTTGGGTTCGTC +TGCACTATCAAAGGTATGTTGCCCCGGTTTGTCNTTNNTAATTCCAAGGATCATGAAAGCCACCCACTACGGGA +ACCNTTGCCGCAAGCTGCACGACTCATTTCTCAAAGGAAANTCNANGNTTTTCCCTCATNGTTGCTGTTCAAAA +GCTTCGGACGGAAAATGCACATTGTAGTTNCNNATCCCATCATCATGGGNTTTGGGAAATNCCATATGGTANNG +GGCNNNAGCCCGCNTNNCCT +>Alt2 (Estimated allelic Fraction: 0.28) +TANTTNTTNGGNNGTCACTCGCCNNGGGGATCANAGTTATGTGGGGACATTANTCATTTTGTTTGGGATTTCCC +TCTCTTCTTAGAACACTGGACATAAGCCAACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCCCAC +ACGGAGGCCTTTTGGGGTGGAGCACTCAGGCTCAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCC +TCCACCAATCGACAGTCAGGAAGGCAGCCTACCCAAATTACACCACCTTTGAGAGACACTCATCCTCAGGCCAT +GCAGTGGAATTCCACAACATGCCACCAACCTCTGCAGGATCCCAAAGTAAGTCCTGCTGGTGGCTCCAGTTCCG +GAACAGTGAACCCTGTTCCGACTACAGCCTCACTCATCTCGTCAACCTTCTCGAGGATTGGGGACCCTGCACCG +AACATGGACAGCATCACATCAGGATTCCGATGACCCCCGCTCATGTTACAAGCGGGGTTTTTCTTGTTGACAAA +AATAAACAGGATACCGCGTAGACAACAGGCGTGGTGGACTTCTCTCTCTTTTGGAAGGGGAGGACCTTTGTGTG +ATGGTGGGAAATCTTAGTCCCTCGCCTCCAATCACTCTCCACCCTCTTGTGGGCCTAATTGAGGTGAGTCCCGC +TGAAAGAAGTGGCAGCGGGGTATCACATACCTCTTCATCTTGCGGGAGAGCCGCCACGTCCTGTGTGGGTGAGC +TCCCCCAGAACAAAAGGGTGTTGCGGGGGGGGGNGGNNACAAACCGCGGGGGGAAGGAGGGAACCCACTAAAAG +AACNGGTGCGGTTTCAAAAAAGGGACTGTTTAGTTGAGAANGGNCNGNCATTTTTCATANTTTCTGTGGGTGAG +TAAAAAACACGGGGGACGCAGATGGGAGGNTNNTCCAAACACCAAAAAANGAGGGAGGGGNAATTTATTCTNNA +AGGNNNGCGCAAGNCNNTTC + +Alignment score: 730 +#------------------------------------------------------------------------- + +Alt1 1 TCNGCNGGNGTNNTCCGTATTTTNNTTGGATCCNCATTCATAGCAAACACCANAAATCCA + | | | || || | || ||||| | || | ||| || || +Alt2 1 TANTTNTTNGGNNGTCACTCGCCNNGGGGATCANAGTTATGTGGGGACATTANTCATTTT + +Alt1 61 TATTGGGACCACAATCCCAACAAAGACCACTGGACAGAAGCCAACAAGGTAGGAGTGGGA + |||||| | || | | ||| ||||||||| ||||||||||||||||||||||| +Alt2 61 GTTTGGGATTTCCCTCTCTTCTTAGAACACTGGACATAAGCCAACAAGGTAGGAGTGGGA + +Alt1 121 GCATTCGGGCCTGGGTTCACTCCCCCACACGGAGGCCTTTTGGGGTGGAGCCCTCAGGCT + ||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||| +Alt2 121 GCATTCGGGCCTGGGTTCACTCCCCCACACGGAGGCCTTTTGGGGTGGAGCACTCAGGCT + +Alt1 181 CAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCCTCCACCAATCGACAGTCA + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Alt2 181 CAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCCTCCACCAATCGACAGTCA + +Alt1 241 GGAAGGCAGCCTACCCCAATCACTCCACCTTTGAGAGACACTCATCCTCAGGCCATGCAG + |||||||||||||||| ||| || |||||||||||||||||||||||||||||||||||| +Alt2 241 GGAAGGCAGCCTACCCAAATTACACCACCTTTGAGAGACACTCATCCTCAGGCCATGCAG + +Alt1 301 TGGAATTCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAATCCTGCTGGTGGC + |||||||||||||||| ||||||| ||||||||||||||| ||||| ||||||||||||| +Alt2 301 TGGAATTCCACAACATGCCACCAACCTCTGCAGGATCCCAAAGTAAGTCCTGCTGGTGGC + +Alt1 361 TCCAGTTCCGGAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATCTCGTCAATCTTC + ||||||||||||||||||||||||||||||||||| ||||||||||||||||||| |||| +Alt2 361 TCCAGTTCCGGAACAGTGAACCCTGTTCCGACTACAGCCTCACTCATCTCGTCAACCTTC + +Alt1 421 TCGAGGATTGGGGACCCTGCACCGAACATGGAAAGCATCACATCAGGATTCCTAGGACCC + |||||||||||||||||||||||||||||||| ||||||||||||||||||| | ||||| +Alt2 421 TCGAGGATTGGGGACCCTGCACCGAACATGGACAGCATCACATCAGGATTCCGATGACCC + +Alt1 481 CTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAAAATCCTCACAATACCGCAGAGT + | |||| ||||||| |||||||||||||||||||||||||| || ||||||| || +Alt2 481 CCGCTCATGTTACAAGCGGGGTTTTTCTTGTTGACAAAAATAAACAGGATACCGCGTAGA + +Alt1 541 CTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGTGTCTTGGCCAA + | | | ||||||||||||||||| |||| | |||||| || ||||| ||| +Alt2 541 CAACAGGCGTGGTGGACTTCTCTCTCTTTTGGAAGGGGAGGACCTTTGTGTGATGGTGGG + +Alt1 601 AATTCGCAGTCCCAAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTCCTGCC + || || |||||| |||||| |||||| ||| |||||||| || | ||| || +Alt2 601 AAATCTTAGTCCCTCGCCTCCAATCACTCTCCACCCTCTTGTGGGCCTAATTGAGGTGAG + +Alt1 661 TATCGCTGGATGTGTCTGCGGCGGTTTATCATCTTCCTCTTCATCGTGCTGCTATGCCTC + | ||||| | | || |||| ||||| | |||||||||| ||| | ||| | +Alt2 661 TCCCGCTGAAAGAAGTGGCAGCGGGGTATCACATACCTCTTCATCTTGCGGGAGAGCCGC + +Alt1 721 ATCATCCTGT-TGGGTTCG-TCTGCACTATCAAAGGTATGTTGCCCCGGTTTGTCNTTNN + | |||||| ||||| | || | | |||| | |||||| || | | || +Alt2 721 CACGTCCTGTGTGGGTGAGCTCCCCCAGAACAAAAGGGTGTTGCGGGGGGGGG--NGGNN + +Alt1 779 TAATTCCAAGGATC-ATGAAAGCCACCCACTACGGGAACCNTTGCCGC-----AAGCTGC + | || || | | | | |||||||| |||| ||| | || | +Alt2 779 ACAAACCGCGGGGGGAAGGAGGGAACCCACTAAAAGAACNGGTGCGGTTTCAAAAAAGGG + +Alt1 833 ACGACTCATTTCTCAAAGGAAANTCNANGNTTTTCCCTCATNGTTGCTGT-------TCA + || | | || || || || | |||| |||| || |||| | | +Alt2 839 ACTGTTTAGTTGAGAANGGN----CNGNCATTTT---TCATANTTTCTGTGGGTGAGTAA + +Alt1 886 AAAGCTTCGGACGGAAAATGCACATTGTAGTTNCNNATCCCATCATCAT-----GGGNTT + ||| | |||| | ||| || | || | || ||| | || || | | +Alt2 892 AAAAC-----ACGGGGGACGCAGATGGGAGG-NTNN-TCCAAACACCAAAAAANGAGGGA + +Alt1 941 TGGGAAATNCCATATGGTANNGGGCNNNAGCCCGCNTNNCCT + ||| ||| ||| | | || || || | | || +Alt2 945 GGGGNAATT---TATTCTNNAAGGNNNGCGCAAG-NCNNTTC + +#------------------------------------------------------------------------- +#------------------------------------------------------------------------- + + |
| b |
| diff -r 000000000000 -r 6ec40b104f9d test-data/out1.alignment.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out1.alignment.fasta Tue Oct 12 14:21:06 2021 +0000 |
| b |
| @@ -0,0 +1,4 @@ +>input1 (forward) +TATTGGGACCACAATCCCAACAAAGACCACTGGACAGAAGCCAACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCCCACACGGAGGCCTTTTGGGGTGGAGCCCTCAGGCTCAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCCTCCACCAATCGACAGTCAGGAAGGCAGCCTACCCCAATCACTCCACCTTTGAGAGACACTCATCCTCAGGCCATGCAGTGGAATTCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAATCCTGCTGGTGGCTCCAGTTCCGGAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATCTCGTCAATCTTCTCGAGGATTGGGGACCCTGCACCGAACATGGAAAGCATCACATCAGGATTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAAAATCCTCACAATACCGCAGAGTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGTGTCTTGGCCAAAATTCTCAGTCCCAAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTC +>input1 (forward) +TATTGGGACCACAATCCCAACAAAGACCACTGGACAGAAGCCAACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCCCACACGGAGGCCTTTTGGGGTGGAGCCCTCAGGCTCAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCCTCCACCAATCGACAGTCAGGAAGGCAGCCTACCCCAATCACTCCACCTTTGAGAGACACTCATCCTCAGGCCATGCAGTGGAATTCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAATCCTGCTGGTGGCTCCAGTTCCGGAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATCTCGTCAATCTTCTCGAGGATTGGGGACCCTGCACCGAACATGGAAAGCATCACATCAGGATTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAAAATCCTCACAATACCGCAGAGTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGTGTCTTGGCCAAAATTCTCAGTCCCAAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTC |
| b |
| diff -r 000000000000 -r 6ec40b104f9d test-data/out1.bcf |
| b |
| Binary file test-data/out1.bcf has changed |
| b |
| diff -r 000000000000 -r 6ec40b104f9d test-data/out1.consensus.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out1.consensus.fasta Tue Oct 12 14:21:06 2021 +0000 |
| b |
| @@ -0,0 +1,2 @@ +>Consensus +TATTGGGACCACAATCCCAACAAAGACCACTGGACAGAAGCCAACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCCCACACGGAGGCCTTTTGGGGTGGAGCCCTCAGGCTCAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCCTCCACCAATCGACAGTCAGGAAGGCAGCCTACCCCAATCACTCCACCTTTGAGAGACACTCATCCTCAGGCCATGCAGTGGAATTCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAATCCTGCTGGTGGCTCCAGTTCCGGAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATCTCGTCAATCTTCTCGAGGATTGGGGACCCTGCACCGAACATGGAAAGCATCACATCAGGATTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAAAATCCTCACAATACCGCAGAGTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGTGTCTTGGCCAAAATTCTCAGTCCCAAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTC |
| b |
| diff -r 000000000000 -r 6ec40b104f9d test-data/out1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out1.fasta Tue Oct 12 14:21:06 2021 +0000 |
| b |
| @@ -0,0 +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 |
| b |
| diff -r 000000000000 -r 6ec40b104f9d test-data/out1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out1.txt Tue Oct 12 14:21:06 2021 +0000 |
| b |
| @@ -0,0 +1,111 @@ +>Alt +TTTTTTTTTGAGCGGGTCGAACCGTCACGAAAAGAAAAGGGGAAGAACCATCAGCAGGAGTAATCCGTATTTTA +ATTGGATCCACATTCATAGCAAACACCAAAAATCCATATTGGGACCACAATCCCAACAAAGACCACTGGACAGA +AGCCAACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCCCACACGGAGGCCTTTTGGGGTGGAGCC +CTCAGGCTCAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCCTCCACCAATCGACAGTCAGGAAGG +CAGCCTACCCCAATCACTCCACCTTTGAGAGACACTCATCCTCAGGCCATGCAGTGGAATTCCACAACATTCCA +CCAAGCTCTGCAGGATCCCAGAGTAAATCCTGCTGGTGGCTCCAGTTCCGGAACAGTGAACCCTGTTCCGACTA +CTGCCTCACTCATCTCGTCAATCTTCTCGAGGATTGGGGACCCTGCACCGAACATGGAAAGCATCACATCAGGA +TTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAAAATCCTCACAATACCGCAGAGTCT +AGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGTGTCTTGGCCAAAATTCTCAGTCCCAAA +CCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTCCTGCCTATCGCTGGATGTGTCTGCGGCGGTTTATC +ATATTCCTCTTCATCGTGCTGCTATGCCTCATCATCCTGTTGGGTTCGTCTGCACCATCAAAAGAATGTTGCCC +CGGGTTGTGATTAAAAATTCCAAGGAGCAAGAAAGCCACCCACTACGGGAACCAGGGCCGGAAGCTGAACAAGT +CATTTTTCAAAGGAAAATGAAAGATTTTCTTTCTTATTTGTGGGGGAAAAGCAAAAAAAGGAAAAAGGAAATTG +GGGTTACAAACCCCACCCCCAAGGGATTTGGGAAATACCATATTTTAAAGGGGAAAGGGCCGCATAACCCATTA +AAAATTGCATATTTTAAATTTTTTTTTTTTGAGAAAGAGGGGGGAC +>Ref X75657.1 Human hepatitis virus genotype E Bas preS1 preS2 S C X antigens core antigen X protein and polymerase:1-718 forward +TTCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAGAGGCCTGTATTTTCCTGCTGGTGGCTCCAGTT +CCGGAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATCTCGTCAATCTTCTCGAGGATTGGGGACCCTGCA +CCGAACATGGAAAGCATCACATCAGGATTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGAC +AAAAATCCTCACAATACCGCAGAGTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGT +GTCTTGGCCAAAATTCGCAGTCCCCAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTCCTGGCTAT +CGCTGGATGTGTCTGCGGCGTTTTATCATCTTCCTCTTCATCCTGCTGCTATGCCTCATCTTCTTGTTGGTTCT +TCTGGACTATCAAGGTATGTTGCCCGTTTGTCCTCTAATTCCAGGATCATCAACCACCAGTACGGGACCCTGCC +GAACCTGCACGACTCTTGCTCAAGGAACCTCTATGTTTCCCTCATGTTGCTGTTCAAAACCTTCGGACGGAAAT +TGCACTTGTATTCCCATCCCATCATCATGGGCTTTCGGAAAATTCCTATGGGAGTGGGCCTCAGCCCGTTTCTC +CTGGCTCAGTTTACTAGTGCCATTTGTTCAGTGGTTCGCCGGGCTTTCCCCC + +Alignment score: -906 +#------------------------------------------------------------------------- + +Alt 1 TTTTTTTTTGAGCGGGTCGAACCGTCACGAAAAGAAAAGGGGAAGAACCATCAGCAGGAG + +Ref 1 ------------------------------------------------------------ + +Alt 61 TAATCCGTATTTTAATTGGATCCACATTCATAGCAAACACCAAAAATCCATATTGGGACC + +Ref 1 ------------------------------------------------------------ + +Alt 121 ACAATCCCAACAAAGACCACTGGACAGAAGCCAACAAGGTAGGAGTGGGAGCATTCGGGC + +Ref 1 ------------------------------------------------------------ + +Alt 181 CTGGGTTCACTCCCCCACACGGAGGCCTTTTGGGGTGGAGCCCTCAGGCTCAAGGCATGC + +Ref 1 ------------------------------------------------------------ + +Alt 241 TGACAACATTACCAGCAAATCCGCCTCCTGCCTCCACCAATCGACAGTCAGGAAGGCAGC + +Ref 1 ------------------------------------------------------------ + +Alt 301 CTACCCCAATCACTCCACCTTTGAGAGACACTCATCCTCAGGCCATGCAGTGGAATTCCA + ||||| +Ref 1 -------------------------------------------------------TTCCA + +Alt 361 CAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAA------------TCCTGCTGGTG + |||||||||||||||||||||||||||||||||||| ||||||||||| +Ref 6 CAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAGAGGCCTGTATTTTCCTGCTGGTG + +Alt 409 GCTCCAGTTCCGGAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATCTCGTCAATCT + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Ref 66 GCTCCAGTTCCGGAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATCTCGTCAATCT + +Alt 469 TCTCGAGGATTGGGGACCCTGCACCGAACATGGAAAGCATCACATCAGGATTCCTAGGAC + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Ref 126 TCTCGAGGATTGGGGACCCTGCACCGAACATGGAAAGCATCACATCAGGATTCCTAGGAC + +Alt 529 CCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAAAATCCTCACAATACCGCAGA + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Ref 186 CCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAAAATCCTCACAATACCGCAGA + +Alt 589 GTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGTGTCTTGGCC + |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| +Ref 246 GTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGTGTCTTGGCC + +Alt 649 AAAATTCTCAGTCCCAAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTCCTG + ||||||| ||||||| |||||||||||||||||||||||||||||||||||||||||||| +Ref 306 AAAATTCGCAGTCCCCAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTCCTG + +Alt 709 CCTATCGCTGGATGTGTCTGCGGCGGTTTATCATATTCCTCTTCATCGTGCTGCTATGCC + |||||||||||||||||||||||| |||||||| |||||||||||| |||||||||||| +Ref 366 GCTATCGCTGGATGTGTCTGCGGCGTTTTATCATCTTCCTCTTCATCCTGCTGCTATGCC + +Alt 769 TCATCATCCTGTTGGGTTCGTCTGCACCATCAAAAGAATGTTGCCCCGGGTTGTGATTAA + ||||| || |||| ||||| |||| || |||| | | ||||||||| | |||| | +Ref 426 TCATCTTCTTGTT-GGTTCTTCTGGACTATCA-AGGTATGTTGCCC--GTTTGTCCT--C + +Alt 829 AAATTCCAAGGAGCAAGAAAGCCACCCACTACGGGAACCAGGGCCGGAAGCTGAACAAGT + ||||||| ||| || || ||| ||| ||||||| || |||| || ||| || | | +Ref 480 TAATTCCA-GGATCATCAA--CCA-CCAGTACGGGACCC--TGCCG-AACCTGCACGACT + +Alt 889 CATTTTTCAAAGGAAAATGAAAGATTTTCTTTCTTATTTGTGGGGGAAAAGCAAAAAAAG + | || |||| |||| | | | |||| || | ||| | |||| | | | +Ref 533 C-TTGCTCAA-GGAACCTCTATG--TTTCCCTCAT-GTTGCTGTTCAAAACCTTCGGACG + +Alt 949 GAAAAAGGAAATTGGGGTTACAAACCCCACCCCCAAGGGATTTGGGAAATACCATATTTT + |||| | | ||| | | | |||| | || ||| ||| ||||| | ||| +Ref 588 GAAATTGCAC-TTGTA--TTCCCATCCCATCATCATGGGCTTTCGGAAAATTCCTATGGG + +Alt 1009 AAAGGGGAAAGGGCCGCATAACCCATTAAAAATTGCATATTTTA-AATTTTTTTTTTTTG + | ||| | ||| | || | || | |||| | | ||| || +Ref 645 AGTGGGCCTCAGCCCGTTTCTCC---------TGGCTCAGTTTACTAGTGCCATTTGTTC + +Alt 1068 AGAAAGAGGGGGGAC-------- + || | || | +Ref 696 AGTGGTTCGCCGGGCTTTCCCCC + +#------------------------------------------------------------------------- +#------------------------------------------------------------------------- + + |
| b |
| diff -r 000000000000 -r 6ec40b104f9d test-data/out2.alignment.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out2.alignment.fasta Tue Oct 12 14:21:06 2021 +0000 |
| b |
| b'@@ -0,0 +1,6 @@\n+>input1 (forward)\n+TATTGGGACCACAATCCCAACAAAGACCACTGGACAGAAGCCAACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCCCACACGGAGGCCTTTTGGGGTGGAGCCCTCAGGCTCAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCCTCCACCAATCGACAGTCAGGAAGGCAGCCTACCCCAATCACTCCACCTTTGAGAGACACTCATCCTCAGGCCATGCAGTGGAATTCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAA------------TCCTGCTGGTGGCTCCAGTTCCGGAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATCTCGTCAATCTTCTCGAGGATTGGGGACCCTGCACCGAACATGGAAAGCATCACATCAGGATTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAAAATCCTCACAATACCGCAGAGTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGTGTCTTGGCCAAAATTCTCAGTCCCAAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n+>input1 (forward)\n+TATTGGGACCACAATCCCAACAAAGACCACTGGACAGAAGCCAACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCCCACACGGAGGCCTTTTGGGGTGGAGCCCTCAGGCTCAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCCTCCACCAATCGACAGTCAGGAAGGCAGCCTACCCCAATCACTCCACCTTTGAGAGACACTCATCCTCAGGCCATGCAGTGGAATTCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAA------------TCCTGCTGGTGGCTCCAGTTCCGGAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATCTCGTCAATCTTCTCGAGGATTGGGGACCCTGCACCGAACATGGAAAGCATCACATCAGGATTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAAAATCCTCACAATACC'..b'-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\n+>Reference\n+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAGAGGCCTGTATTTTCCTGCTGGTGGCTCCAGTTCCGGAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATCTCGTCAATCTTCTCGAGGATTGGGGACCCTGCACCGAACATGGAAAGCATCACATCAGGATTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAAAATCCTCACAATACCGCAGAGTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGTGTCTTGGCCAAAATTCGCAGTCCCCAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTCCTGGCTATCGCTGGATGTGTCTGCGGCGTTTTATCATCTTCCTCTTCATCCTGCTGCTATGCCTCATCTTCTTGTTGGTTCTTCTGGACTATCAAGGTATGTTGCCCGTTTGTCCTCTAATTCCAGGATCATCAACCACCAGTACGGGACCCTGCCGAACCTGCACGACTCTTGCTCAAGGAACCTCTATGTTTCCCTCATGTTGCTGTTCAAAACCTTCGGACGGAAATTGCACTTGTATTCCCATCCCATCATCATGGGCTTTCGGAAAATTCCTATGGGAGTGGGCCTCAGCCCGTTTCTCCTGGCTCAGTTTACTAGTGCCATTTGTTCAGTGGTTCGCCGGGCTTTCCCCCACTGTCTGGCTTTCAGTTATATGGATGATGTGGTATTGGGGGCCAAGTCTGTACAACATCTTGAGTCCCTTTATACCGCTGTTACCAATTTTCTTTTGTCTTTGGGTATACATTTAAATCCCAACAAAACAAAAAGATGGGGCTATTCCCTTAATTTCATGGGTTATGTAATTGGAAGTTGGGGCTCATTACCACAGGAACACATCATACAAAAAATCAAAGACTGTTTTAGAAAACTCCCTGTTAACCGGCCTATTGATTGGAAAGTATGTCAAAGAATTGTGGGTCTTTTGGGCTTTGCTGCCCCCTTTACACAATGTGGATATCCTGCTTTAATGCCTCTGTATGCATGTACTCAATCTAAGCAGGCTTTCACTTTCTCGCCAACTTACAAGGCCTTTCTGTGTAAACAATACCTGAACCTTTACCCCGTTGCCCGGCAACGGCCAGGTCTGTGCCAAGTGTTTGCTGATGCAACCCCCACTGGCTGGGGCTTGGCCATAGGCATTCAGCGCATGCGCGGAACCTTTGTGGCTCCTCTGCCGATCCATACTGCGGAACTCCTAGCCGCTTGTTTTGCTCGCAGCAGGTCTGGAGCAAAACTTATCGGGACCGATAATTCTGTCGTTCTCTCCCGGAAGTATACATCCTTTCCATGGCTGCTAGGCTGTGCTGCCAACTGGATCCTGCGAGGGACGTCCTTTGTCTACGTCCCGTCAGCGCTGAATCCTGCGGACGACCCGTCTCGGGGTCGCTTGGGGATCTATCGTCCCCTTCTCCGTCTGCCGTTCCAGCCGACCACGGGGCGCACCTCTCTTTACGCGGTCTCCCCGTCTGTTCCTTCTCATCTGCCGGACCGTGTGCACTTCGCTTCACCTCTGCACGTCGCATGGAGACCACCGTGAACGCCCACCAAATATTGCCCAAGGTCTTACATAAGAGGACTCTTGGACTCTCTGCAATGTCAACGACCGACCTTGAGGCATACTTCAAAGACTGTTTGTTTAAAGACTGGGAGGAGTCGGGGGAGGAGATTAGATTAAAGGTCTTTGTACTAGGAGGCTGTAGGCATAAATTGGTCTGCGCACCAGCACCATGCAACTTTTTCACCTCTGCCTAATCATCTCTTGTTCATGTCCTACTGTTCAAGCCTCCAAGCTGTGCCTTGGGTGGCTTTGGGGCATGGACATTGACCCTTATAAAGAATTTGGAGCTACTGTGGAGTTACTCTCGTTTTTGCCTTCTGACTTCTTTCCTTCAGTAAGAGATCTTCTAGATACCGCCTCAGCTCTGTATCGGGATGCCTTAGAGTCTCCTGAGCATTGTTCACCTCACCACACTGCACTCAGGCAAGCCATTCTTTGCTGGGGAGAACTAATGACTCTAGCTACCTGGGTGGGTGTAAATTTGGAAGATCCAGCATCCAGGGACCTAGTAGTCAGTTATGTCAATACTAATATGGGCCTAAAGTTCAGGCAATTATTGTGGTTTCACATTTCTTGTCTCACTTTTGGAAGAGAAACCGTCATAGAGTATTTGGTGTCTTTTGGAGTGTGGATTCGCACTCCTCCAGCTTATAGACCACCAAATGCCCCTATCTTATCAACACTTCCGGAGAATACTGTTGTTAGACGAAGAGGCAGGTCCCCTAGAAGAAGAACTCCCTCGCCTCGCAGACGAAGATCTCAATCGCCGCGTCGCAGAAGATCTCAATCTCCAGCTTCCCAATGTTAGTATTCCTTGGACTCATAAGGTGGGAAATTTTACGGGGCTTTACTCTTCTACTATACCTGTCTTTAATCCTAACTGGAAAACTCCATCTTTTCCTGATATTCATTTGCACCAGGACATTATTAACAAATGTGAACAATTTGTAGGTCCTCTAACTGTAAATGAAAAACGAAGATTAAACTTAGTCATGCCTGCTAGATTTTTTCCCATCTCTACGAAATATTTGCCCCTAGAGAAAGGTATAAAACCTTATTATCCAGATAATGTAGTTAATCATTACTTCCAAACCAGACACTATTTACATACCCTATGGAAGGCGGGCATCTTATATAAAAGAGAAACTACACGTAGCGCCTCATTTTGTGGGTCACCTTATTCTTGGGAACAAGAGCTACATCATGGGGCTTTCTTGGACGGTCCCTCTCGAATGGGGGAAGAATATTTCCACCACCAATCCTCTGGGATTTTTTCCCGACCACCAGTTGGATCCAGCATTCAGAGCAAACACCAGAAATCCAGATTGGGACCACAATCCCAACAAAGACCACTGGACAGAAGCCAACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCCCACACGGAGGCCTTTTGGGGTGGAGCCCTCAGGCTCAAGGCATGCTAAAAACATTGCCAGCAGATCCGCCTCCTGCCTCCACCAATCGGCAGTCAGGAAGGCAGCCTACCCCAATCACTCCACCTTTGAGAGACACTCATCCTCAGGCCATGCAGTGGAA\n' |
| b |
| diff -r 000000000000 -r 6ec40b104f9d test-data/out2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out2.fasta Tue Oct 12 14:21:06 2021 +0000 |
| b |
| @@ -0,0 +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 |
| b |
| diff -r 000000000000 -r 6ec40b104f9d test-data/out2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out2.txt Tue Oct 12 14:21:06 2021 +0000 |
| b |
| @@ -0,0 +1,115 @@ +>Alt +TTTTTTTTTGAGCGGGTCGAACCGTCACGAAAAGAAAAGGGGAAGAACCATCAGCAGGAGTAATCCGTATTTTA +ATTGGATCCACATTCATAGCAAACACCAAAAATCCATATTGGGACCACAATCCCAACAAAGACCACTGGACAGA +AGCCAACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCCCACACGGAGGCCTTTTGGGGTGGAGCC +CTCAGGCTCAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCCTCCACCAATCGACAGTCAGGAAGG +CAGCCTACCCCAATCACTCCACCTTTGAGAGACACTCATCCTCAGGCCATGCAGTGGAATTCCACAACATTCCA +CCAAGCTCTGCAGGATCCCAGAGTAAATCCTGCTGGTGGCTCCAGTTCCGGAACAGTGAACCCTGTTCCGACTA +CTGCCTCACTCATCTCGTCAATCTTCTCGAGGATTGGGGACCCTGCACCGAACATGGAAAGCATCACATCAGGA +TTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAAAATCCTCACAATACCGCAGAGTCT +AGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGTGTCTTGGCCAAAATTCTCAGTCCCAAA +CCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTCCTGCCTATCGCTGGATGTGTCTGCGGCGGTTTATC +ATATTCCTCTTCATCGTGCTGCTATGCCTCATCATCCTGTTGGGTTCGTCTGCACCATCAAAAGAATGTTGCCC +CGGGTTGTGATTAAAAATTCCAAGGAGCAAGAAAGCCACCCACTACGGGAACCAGGGCCGGAAGCTGAACAAGT +CATTTTTCAAAGGAAAATGAAAGATTTTCTTTCTTATTTGTGGGGGAAAAGCAAAAAAAGGAAAAAGGAAATTG +GGGTTACAAACCCCACCCCCAAGGGATTTGGGAAATACCATATTTTAAAGGGGAAAGGGCCGCATAACCCATTA +AAAATTGCATATTTTAAATTTTTTTTTTTTGAGAAAGAGGGGGGAC +>Ref X75657.1:2091-3110 forward +AACTAATGACTCTAGCTACCTGGGTGGGTGTAAATTTGGAAGATCCAGCATCCAGGGACCTAGTAGTCAGTTAT +GTCAATACTAATATGGGCCTAAAGTTCAGGCAATTATTGTGGTTTCACATTTCTTGTCTCACTTTTGGAAGAGA +AACCGTCATAGAGTATTTGGTGTCTTTTGGAGTGTGGATTCGCACTCCTCCAGCTTATAGACCACCAAATGCCC +CTATCTTATCAACACTTCCGGAGAATACTGTTGTTAGACGAAGAGGCAGGTCCCCTAGAAGAAGAACTCCCTCG +CCTCGCAGACGAAGATCTCAATCGCCGCGTCGCAGAAGATCTCAATCTCCAGCTTCCCAATGTTAGTATTCCTT +GGACTCATAAGGTGGGAAATTTTACGGGGCTTTACTCTTCTACTATACCTGTCTTTAATCCTAACTGGAAAACT +CCATCTTTTCCTGATATTCATTTGCACCAGGACATTATTAACAAATGTGAACAATTTGTAGGTCCTCTAACTGT +AAATGAAAAACGAAGATTAAACTTAGTCATGCCTGCTAGATTTTTTCCCATCTCTACGAAATATTTGCCCCTAG +AGAAAGGTATAAAACCTTATTATCCAGATAATGTAGTTAATCATTACTTCCAAACCAGACACTATTTACATACC +CTATGGAAGGCGGGCATCTTATATAAAAGAGAAACTACACGTAGCGCCTCATTTTGTGGGTCACCTTATTCTTG +GGAACAAGAGCTACATCATGGGGCTTTCTTGGACGGTCCCTCTCGAATGGGGGAAGAATATTTCCACCACCAAT +CCTCTGGGATTTTTTCCCGACCACCAGTTGGATCCAGCATTCAGAGCAAACACCAGAAATCCAGATTGGGACCA +CAATCCCAACAAAGACCACTGGACAGAAGCCAACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCC +CACACGGAGGCCTTTTGGGGTGGAGCCCTCAGGCTCAAGGCATGCTAAAAACATTGCC + +Alignment score: -2113 +#------------------------------------------------------------------------- + +Alt 1 --------TTTTTTTTTGAGCGGGTCGAACCGTCACGAAAAGAAAAGGGGAAGAACCATC + | | | |||| | || | | | || || | | +Ref 2091 AACTAATGACTCTAGCTACCTGGGTGG----GTGTAAATTTGGA-AGATCCAGCATCCAG + +Alt 53 AGCAGGAGTAATCCGTATTTTAATTGGATCCACAT-TCATAGCAAACACCAAAAATCCAT + | |||| || || || | || | || | ||| || | || +Ref 2146 GGACCTAGTAGTCAGT----TATGTCAATACTAATATGGGCCTAAAGTTCAGGCAATTAT + +Alt 112 ATTGGGACCACAATCCCAACAAAGACCACTGGAC-AGAAGCCAACAAGGTAGGAGTGGGA + ||| ||| || | || |||| |||| || || | || | | || +Ref 2202 TGTGGTTTCAC-ATTTCTTGTCTCACTTTTGGAAGAGAAACCGTCATAG-AGTATTTGGT + +Alt 171 G-CATTCGG-GCCTGGGTTC--ACTCCCCCACACGGAGGCCTTTTGGGGTGGAGCCCTCA + | | || || | ||| ||| ||||| ||| || | | || || | +Ref 2260 GTCTTTTGGAGTGTGGATTCGCACTCCTCCA-------GCTTAT--------AGACCAC- + +Alt 227 GGCTCAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCCTCCACCAATCGACA + ||| |||| | | ||| || || |||| | | | ||| | +Ref 2304 ----CAA---ATGCCCCTATC-TTATCAACACTTCCGGAGAATACTGTTGTTAGACGA-A + +Alt 287 GTCAGGAAGGCAGCCTACCCCAATCACTCCACCTTTGAG-AGACACTCATCCTCAGGCCA + | ||| ||| |||| || ||||| | | |||| ||| ||| | +Ref 2355 G--AGGCAGGTCCCCTAGAAGAAGAACTCCCTCGCCTCGCAGACGAAGATC-TCAATCGC + +Alt 346 TGCAGTGGAATTCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAATCCTGCTG + || || | || || || || ||| ||| ||||| || | | | || +Ref 2412 CGC-GTCG-----CAGAAGATCTCAA-----TCTCCAGCTTCCCAATGTTAGTATTCCTT + +Alt 406 GTGGCTCCAGTTCCGGAACAGTGAACCCTG-TTCCGACTACTGCCTCACTCATCTCGTCA + | | ||| || | | | || | || || || | || ||| | | +Ref 2461 G-GACTCATAAGGTGGGAAATTTTACGGGGCTTTACTCTTCTACTATACCTGTCT--TTA + +Alt 465 ATCTTCTCGAGGATTGGGGACCCTGCACCGAACATGGAAAGCATCACATCAGGATTCCTA + ||| | | | | | | | | || | ||| || || ||| | +Ref 2518 ATCCTAACTGGAAAACTCCATCTTTTCCTGATATTCATTTGCACCAGGACATTATT---A + +Alt 525 GGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAAAATCCTCACAATACCG + | || | || | || | | ||| | |||| | | || +Ref 2575 ACAAATGTGAACAATTTGTA---GGTCCTCTAACTGTAAATGAAAAACG--AAGATTAAA + +Alt 585 CAGAGTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCT--CCCGTGTGTC + | |||| | | || | || || | || | |||| | | ||| | +Ref 2630 CTTAGTC---ATGCCTGCTAGATTTTT-TCCCATCTCTACGAAATATTTGCCCCTAGAGA + +Alt 643 TTGGCCAAAATTCTCAGT--CCCAAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAAT + || ||| || | | || | | ||| | ||| | | | || | +Ref 2686 AAGGTATAAAACCTTATTATCCAGATAATGTAGTTAATCATTACTTCCAAACCAGACACT + +Alt 701 TTGTCCTGCCTATCGCTGGATGTGTCTGCGGCGGTTTATCATATTCCT-CTTCATCGTGC + | | | | | |||| | | || | | ||| | | || || || +Ref 2746 ATTTACATAC--CCTATGGAAG-GCGGGCATCT-TATATAAAAGAGAAACTACACGTAGC + +Alt 760 TGCT------ATGCCTCATCATCCTGTTGGGTTCGTCTGCACCATCAAAAGAATGTTGCC + || || ||| | | | ||||| | || ||||| | | | | +Ref 2802 GCCTCATTTTGTGGGTCACCTTATTCTTGGGAACAAGAGCTACATCATGGG---GCTTTC + +Alt 814 CCGGGTTGTGATTAAAAATTCCAAGGAGCAAGAAAGCCACCCACTACGGGAACCAGGGCC + || || | || || | | | || |||| || || | +Ref 2859 TTGGACGGTCCCTC-----TCGAATGGGGGAAGAATATTTCCACCACC--AATCCTCTGG + +Alt 874 GGAAGCTGAACAAGTCATTTTTCAAAGGAAAATGAAAGATTTTCTTTCTTATTTGTGGGG + | |||||| | | || || | | || | +Ref 2912 G---------------ATTTTTTCCCG---ACCACCAG--TTGGATCCAGCATTCAG--- + +Alt 934 GAAAAGCAAAAAAAGGAAAAAGGAAATTGGGGTTACAAACCCCACCCCCAAGGGATTTGG + |||||| | |||| | |||||| |||| ||| || ||| ||| +Ref 2949 ----AGCAAACACCAGAAA-TCCAGATTGGGACCACAATCCCAACA---AAGACCACTGG + +Alt 994 G--AAATACCATATTTTAAAGGGGAAAGGGCCGCATAACCCATTAAAAATTGCATATTTT + || | | | || | | || || | || | +Ref 3001 ACAGAAGCCAACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCCCACACGGA + +Alt 1052 AAATTTTTTTTTTTTGAGAAAGAGGGGGGAC------------------- + |||| | ||| | +Ref 3061 GGCCTTTTGGGGTGGAGCCCTCAGGCTCAAGGCATGCTAAAAACATTGCC + +#------------------------------------------------------------------------- +#------------------------------------------------------------------------- + + |
| b |
| diff -r 000000000000 -r 6ec40b104f9d test-data/output1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output1.fasta Tue Oct 12 14:21:06 2021 +0000 |
| b |
| @@ -0,0 +1,2 @@ +>primary +TTTTTTTTTGAGCGGGTCGNACCGTCACGAANAGNAAAGGGGAAGAACCATCNGCNGGNGTNNTCCGTATTTTNNTTGGATCCNCATTCATAGCAAACACCANAAATCCATATTGGGACCACAATCCCAACAAAGACCACTGGACAGAAGCCAACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCCCACACGGAGGCCTTTTGGGGTGGAGCCCTCAGGCTCAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCCTCCACCAATCGACAGTCAGGAAGGCAGCCTACCCCAATCACTCCACCTTTGAGAGACACTCATCCTCAGGCCATGCAGTGGAATTCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAATCCTGCTGGTGGCTCCAGTTCCGGAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATCTCGTCAATCTTCTCGAGGATTGGGGACCCTGCACCGAACATGGAAAGCATCACATCAGGATTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAAAATCCTCACAATACCGCAGAGTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGTGTCTTGGCCAAAATTCTCAGTCCCAAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTCCTGCCTATCGCTGGATGTGTCTGCGGCGGTTTATCATATTCCTCTTCATCGTGCTGCTATGCCTCATCATCCTGTTGGGTTCGTCTGCACCATCAAAAGAATGTTGCCCCGGGTTGTGNTTNNAAATTCCAAGGAGCAAGAAAGCCACCCACTACGGGAACCNTGGCCGCAAGCTGCACAAGTCATTTTTCAAAGGAAANTGNANGNTTTTCTTTCTTNTTTGTGGGGGAAAAGCAAAAAAAGGAAAAAGGAAATTGGGGTTNCNNACCCCACCCCCAAGGGNTTTGGGAAATNCCATATTTTANNGGGGNNNGGGCCGCNTNNCCCNTTNNNNNTTGCNTATTTTAAATTTTTTTTTTTTGNGAAAGAGGGGGGAC |
| b |
| diff -r 000000000000 -r 6ec40b104f9d test-data/output1.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output1.json Tue Oct 12 14:21:06 2021 +0000 |
| [ |
| b'@@ -0,0 +1,12 @@\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, 816'..b'12420":"995:A|G|T", "12436":"996:A|G|T", "12451":"997:A|G|T", "12464":"998:T|G", "12490":"999:N", "12498":"1000:C|A", "12507":"1001:C|A|G", "12531":"1002:A|T", "12534":"1003:T", "12547":"1004:A|T", "12565":"1005:T|A|G", "12582":"1006:T|A|G", "12595":"1007:T|G", "12604":"1008:T|A|C", "12622":"1009:A|C|T", "12636":"1010:N", "12645":"1011:N", "12663":"1012:G|A|T", "12678":"1013:G|A|C", "12707":"1014:G", "12722":"1015:G|A|C", "12740":"1016:N", "12756":"1017:N", "12768":"1018:N", "12786":"1019:G|A|C", "12803":"1020:G|C", "12817":"1021:G|A|C", "12823":"1022:C", "12844":"1023:C|A|G", "12848":"1024:G|A", "12856":"1025:C|A|G", "12873":"1026:N", "12890":"1027:T|A|C", "12914":"1028:N", "12924":"1029:N", "12944":"1030:C|T", "12962":"1031:C|T", "12972":"1032:C|G|T", "12992":"1033:N", "13009":"1034:T|C|G", "13024":"1035:T|A|G", "13042":"1036:N", "13053":"1037:N", "13084":"1038:N", "13096":"1039:N", "13109":"1040:N", "13140":"1041:T|C|G", "13152":"1042:T|C|G", "13167":"1043:G|A|T", "13176":"1044:C|A", "13197":"1045:N", "13218":"1046:T|A|C", "13237":"1047:A|T", "13249":"1048:T|G", "13267":"1049:T|A|G", "13277":"1050:T|A|G", "13301":"1051:T|A", "13311":"1052:A|T", "13323":"1053:A|C|T", "13345":"1054:A|G", "13362":"1055:T|A", "13372":"1056:T|A|G", "13389":"1057:T|G", "13417":"1058:T|G", "13428":"1059:T|G", "13438":"1060:T|C|G", "13468":"1061:T|C|G", "13478":"1062:T|G", "13512":"1063:T|G", "13525":"1064:T|C|G", "13535":"1065:T|C|G", "13552":"1066:T|C|G", "13566":"1067:G|A|C", "13581":"1068:N", "13594":"1069:G|A|T", "13624":"1070:A|G", "13641":"1071:A|G", "13657":"1072:A|G|T", "13670":"1073:G|A|T", "13694":"1074:A|T", "13701":"1075:G", "13711":"1076:G|T", "13732":"1077:G|C|T", "13765":"1078:G|C", "13778":"1079:G|C", "13790":"1080:G|A|C", "13820":"1081:A|C|G", "13826":"1082:C|A"},\n+"primarySeq": "TTTTTTTTTGAGCGGGTCGNACCGTCACGAANAGNAAAGGGGAAGAACCATCNGCNGGNGTNNTCCGTATTTTNNTTGGATCCNCATTCATAGCAAACACCANAAATCCATATTGGGACCACAATCCCAACAAAGACCACTGGACAGAAGCCAACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCCCACACGGAGGCCTTTTGGGGTGGAGCCCTCAGGCTCAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCCTCCACCAATCGACAGTCAGGAAGGCAGCCTACCCCAATCACTCCACCTTTGAGAGACACTCATCCTCAGGCCATGCAGTGGAATTCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAATCCTGCTGGTGGCTCCAGTTCCGGAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATCTCGTCAATCTTCTCGAGGATTGGGGACCCTGCACCGAACATGGAAAGCATCACATCAGGATTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAAAATCCTCACAATACCGCAGAGTCTAGACTCGTGGTGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGTGTCTTGGCCAAAATTCTCAGTCCCAAACCTCCAGTCACTCACCAACCTCTTGTCCTCCAATTTGTCCTGCCTATCGCTGGATGTGTCTGCGGCGGTTTATCATATTCCTCTTCATCGTGCTGCTATGCCTCATCATCCTGTTGGGTTCGTCTGCACCATCAAAAGAATGTTGCCCCGGGTTGTGNTTNNAAATTCCAAGGAGCAAGAAAGCCACCCACTACGGGAACCNTGGCCGCAAGCTGCACAAGTCATTTTTCAAAGGAAANTGNANGNTTTTCTTTCTTNTTTGTGGGGGAAAAGCAAAAAAAGGAAAAAGGAAATTGGGGTTNCNNACCCCACCCCCAAGGGNTTTGGGAAATNCCATATTTTANNGGGGNNNGGGCCGCNTNNCCCNTTNNNNNTTGCNTATTTTAAATTTTTTTTTTTTGNGAAAGAGGGGGGAC",\n+"secondarySeq": "MGTTTTTTTCATAWGGTTGNTWAGAGTAGTSNSMNACAMMTASCYSGKTCTANYWNTTNGGNNRTCWCYSRCCNNGSGGATCANAGTTATGTGRGGACATTANTYATTTKGTTTGGGATTTCYCTCTCTTCTTAGAACACTGGACATAAGCCAACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCCCACACGGAGGCCTTTTGGGGTGGAGCACTCAGGCTCAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCCTCCACCAATCGACAGTCAGGAAGGCAGCCTACCCAAATTACACCACCTTTGAGAGACACTCATCCTCAGGCCATGCAGTGGAATTCCACAACATGCCACCAACCTCTGCAGGATCCCAAAGTAAGTCCTGCTGGTGGCTCCAGTTCCGGAACAGTGAACCCTGTTCCGACTACAGCCTCACTCATCTCGTCAACCTTCTCGAGGATTGGGGACCCTGCACCGAACATGGACAGCATCACATCAGGATTCCGATGACCCCCGCTCATGTTACAAGCGGGGTTTTTCTTGTTGACAAAAATAAACAGGATACCGCGYAGACRACAGGCGTGGTGGACTTCTCTCTCTTTTGGAAGGGGAGRACCTTTGTGTGRTGGTGGGAAATCGTAGTCCCTCGCCTCCAMTCACTCKCCACCCTCTTGTGGGCCTAATTGAGGTGAGTSCCGCTGAAAGAAGKGGCWGCGGGGTATCACCTACCTCTTCATCWTGCGGGRGAGCCGCCACGTCCTGTGTGGGTRAGCTCCCCKAGAACAGATGGGTGTTGCGGGTGGGGYNRRNNYCAAACCGCGGGTRGKASGAGGGAACCCWMTAAAAGARCNRTTKCGKTYWCRAWAAGGYRRCTGTCTAGKTGAGAANRMNCNGNMMTTWMCCAAMNSTTCCTTTTYKKAGTAYYYSSCCCGSGGGKMMSCSRTGTWAGSNKNNKWCAAAWWWWAAYAAANRAGGGAKKKGNARTTTRRGMYNNWMGMNNNMCMCRARNMNNTTKNSRNNNNNSSWANMTGRRATYGARGGGSSGGSSSMNWGGKWTGTYCCMSA"\n+\n+}\n' |
| b |
| diff -r 000000000000 -r 6ec40b104f9d test-data/output2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output2.fasta Tue Oct 12 14:21:06 2021 +0000 |
| b |
| @@ -0,0 +1,2 @@ +>primary +TTTTTTTTTGAGCGGGTCGNACCGTCACGAANAGNANANGGCAAGAACCATCNGCNGGNGTNNTCCGTANTTTNNNTGGATCCNNATTCATAGCAAACACCANAAATCCATATTGGGACCACAATCCCAACAAAGACCACTGGACAGAAGCCAACAAGGTAGGAGTGGGAGCATTCGGGCCTGGGTTCACTCCCCCACACGGAGGCCTTTTGGGGTGGAGCCCTCAGGCTCAAGGCATGCTGACAACATTACCAGCAAATCCGCCTCCTGCCTCCACCAATCGACAGTCAGGAAGGCAGCCTACCCCAATCACTCCACCTTTGAGAGACACTCATCCTCAGGCCATGCAGTGGAATTCCACAACATTCCACCAAGCTCTGCAGGATCCCAGAGTAAATCCTGCTGGTGGCTCCAGTTCCGGAACAGTGAACCCTGTTCCGACTACTGCCTCACTCATCTCGTCAATCTTCTCGAGGATTGGGGACCCTGCACCGAACATGGAAAGCATCACATCAGGATTCCTAGGACCCCTGCTCGTGTTACAGGCGGGGTTTTTCTTGTTGACAAAAATCCTCACAATACCGCAGAGTCTAGACTCGTGATGGACTTCTCTCAATTTTCTAGGGGGAGCTCCCGTGTGTCTTGGCCAAAATTCTCAGTCGCAAACCTCCAGTCACTCACCAACCTCTTGTCCTCCNATTTGTCCTGCCTATCGCTGGATGTGTNTGCGGCGGTTTATCATATTCATCTTCATCGTGCTGCTATGCCTCATCATCCTGTTGGGTTCGTNTGCACCATCAAAAGAATGTTGCCCCGGGTTGTGNTTNNNAATTCCAAAGAGCAAGAAAGCCACCCANTACGNGAANCNTGGCCGCANGCTGCACAAGTCATNTTTCAAAGGAAANTGNANGNTTATNNTTCTNNTTTGTGGGGGNNAAGCAAAAAAAGGAAAANGGANANTGGNGTNNCNNACCCCACNCCCAANGGNTTTGGGAAATNCNATATTNNNNNGGGGNNNNGGCCGCNTNNCCCNNTNNNNNNNGCNTNTTTNANATNNTTTTTTNTTGNNAAAGAGGGGNGAC |
| b |
| diff -r 000000000000 -r 6ec40b104f9d test-data/output3.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output3.fasta Tue Oct 12 14:21:06 2021 +0000 |
| b |
| @@ -0,0 +1,2 @@ +>primary +GAAATTCTCTTGTTCTACTTCAGCAGTAGTTGTAAGGCTTGCATGAAAGTTATTTGTTCGAAACTATTCTCTGTTACTTTCAATCTGTGCCGTACTTCTTCAATCAACCACCTTATTTCCTCAAATTTCTGTCCCAATTGCTCTCGCCACTTTTCATTCCTGTTCTGGAGGTAGTGAAGATCACCCATCCTCATTACGGTTTCTCCAAGCGAATCTCTGTAGATTTTCAGAGCCTCGAACCGTGTTACCATTCCATTCAAGTCCTCCGATGAGGACCCCAATTGCATTTTTGACATCCTCATTAGTATGTCCTGGAAGAGAAGGTAATGGTGAAATTTCTCCAACGATTGCTCCCTCTTCAGTGAAAGCCCTTAGTAGTATCAAAGTCTCCAATCGACTAAAGACCACACTGAAGGG |
| b |
| diff -r 000000000000 -r 6ec40b104f9d test-data/reference1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reference1.fasta Tue Oct 12 14:21:06 2021 +0000 |
| b |
| @@ -0,0 +1,48 @@ +>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 + |
| b |
| diff -r 000000000000 -r 6ec40b104f9d tracy_decompose.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tracy_decompose.xml Tue Oct 12 14:21:06 2021 +0000 |
| [ |
| @@ -0,0 +1,124 @@ +<tool id="tracy_decompose" name="tracy Decompose" version="@TOOL_VERSION@+galaxy0" profile="20.09"> + <description>heterozygous mutations (and call variants)</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="version_command" /> + <command detect_errors="exit_code"><![CDATA[ + #if $index_genome == True + bgzip -c '$genome' > genome.fasta.gz ; + tracy index -o genome.fasta.fm9 genome.fasta.gz && + #set refgenome = "genome.fasta.gz" + #else + #set refgenome = $genome + #end if + tracy decompose + --genome '$refgenome' + $callVariants + --pratio $pratio + --kmer $kmer.kmer + --support $kmer.support + --maxindel $maxindel + --trim $trim.trim + --trimLeft $trim.trimLeft + --trimRight $trim.trimRight + --linelimit $linelimit + --gapopen $alignment.gapopen + --gapext $alignment.gapext + --match $alignment.match + --mismatch $alignment.mismatch + '$tracefile' + ]]></command> + <inputs> + <param argument="--genome" type="data" format="fasta,ab1,scf" label="FASTA, ABI or SCF format genome" /> + <param name="tracefile" type="data" format="ab1,scf" label="Sanger chromatogram tracefile to align" /> + <param name="index_genome" type="boolean" label="Pre-index the reference" help="Pre-indexing builds a FM index of the reference. This is required for sequences larger than 50 kilobases" /> + <param argument="--callVariants" type="boolean" truevalue="--callVariants" falsevalue="" label="Call variants in chromatogram" /> + <!-- annotate option is not yet supported --> + <expand macro="common_options" /> + <expand macro="kmer_options" /> + <expand macro="alignment_options" /> + <expand macro="trim_options" /> + <expand macro="optional_outputs" /> + </inputs> + <outputs> + <expand macro="json_output" toolname="decompose" /> + <data name="out_fasta1" format="fasta" from_work_dir="out.align1" label="tracy decompose allele1 on ${on_string}" /> + <data name="out_fasta2" format="fasta" from_work_dir="out.align2" label="tracy decompose allele2 on ${on_string}" /> + <data name="out_fasta3" format="fasta" from_work_dir="out.align3" label="tracy decompose both alleles on ${on_string}" /> + <expand macro="tabular_output" toolname="decompose" /> + <data name="out_bcf" format="bcf" from_work_dir="out.bcf" label="tracy decompose variants on ${on_string}"> + <filter>callVariants</filter> + </data> + </outputs> + <tests> + <test expect_num_outputs="3"> + <param name="genome" value="reference1.fasta" ftype="fasta" /> + <param name="tracefile" value="input1.ab1" ftype="ab1" /> + <output name="out_fasta1" value="out1.align1.fasta" ftype="fasta" /> + <output name="out_fasta2" value="out1.align2.fasta" ftype="fasta" /> + <output name="out_fasta3" value="out1.align3.fasta" ftype="fasta" /> + </test> + <test expect_num_outputs="4"> + <param name="genome" value="reference1.fasta" ftype="fasta" /> + <param name="tracefile" value="input1.ab1" ftype="ab1" /> + <param name="callVariants" value="true" /> + <output name="out_fasta1" value="out1.align1.fasta" ftype="fasta" /> + <output name="out_fasta2" value="out1.align2.fasta" ftype="fasta" /> + <output name="out_fasta3" value="out1.align3.fasta" ftype="fasta" /> + <output name="out_bcf" compare="sim_size" value="out1.bcf" ftype="bcf" /> + </test> + <test expect_num_outputs="5"> + <param name="genome" value="reference1.fasta" ftype="fasta" /> + <param name="tracefile" value="input1.ab1" ftype="ab1" /> + <param name="callVariants" value="true" /> + <param name="optional_outputs" value="json" /> + <output name="out_json" ftype="json"> + <assert_contents> + <has_text text='"peakA": [5, 5, 5, 5, 5, 4' /> + </assert_contents> + </output> + <output name="out_fasta1" value="out1.align1.fasta" ftype="fasta" /> + <output name="out_fasta2" value="out1.align2.fasta" ftype="fasta" /> + <output name="out_fasta3" value="out1.align3.fasta" ftype="fasta" /> + <output name="out_bcf" compare="sim_size" value="out1.bcf" ftype="bcf" /> + </test> + <test expect_num_outputs="5"> + <param name="genome" value="reference1.fasta" ftype="fasta" /> + <param name="tracefile" value="input1.ab1" ftype="ab1" /> + <param name="callVariants" value="true" /> + <param name="optional_outputs" value="tabular" /> + <output name="out_stats" ftype="tabular"> + <assert_contents> + <has_text_matching expression="13\s1\s2\s2\s11\s2\sT\sG\sN\s5\sY" /> + </assert_contents> + </output> + <output name="out_fasta1" value="out1.align1.fasta" ftype="fasta" /> + <output name="out_fasta2" value="out1.align2.fasta" ftype="fasta" /> + <output name="out_fasta3" value="out1.align3.fasta" ftype="fasta" /> + <output name="out_bcf" compare="sim_size" value="out1.bcf" ftype="bcf" /> + </test> + </tests> + <help><![CDATA[ +**What this does** + +Double-peaks in a trace file can cause alignment issues. This tool uses tracy_ to decompose +heterozygous variants in a trace file into two separate alleles. Each allele is then aligned +separately to the reference sequence. + +Optionally, variants between the trace file and the reference are also output in BCF format. + +@pratio@ + +@trim_options@ + +@alignment@ + +Read more here_. + +.. _tracy: https://github.com/gear-genomics/tracy +.. _here: https://www.gear-genomics.com/docs/tracy/cli/#deconvolution-of-heterozygous-mutations + ]]></help> + <expand macro="citations" /> +</tool> \ No newline at end of file |