Galaxy |

Changeset 1:220e2f7ff8bb (2024-05-11)

Previous changeset 0:4e61ec4fd5f5 (2024-04-13) Next changeset 2:6a8df4d75f3a (2024-06-07)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 2564b0ca982636c6c6f221d0c5072f52d39e6751

modified:
macros.xml
test-data/JoinedProfile.tsv
test-data/allelecallevaluator_report.html
test-data/allelecallevaluator_report_annotate.html
test-data/cds_coordinates.tsv
test-data/results_alleles.tsv
test-data/results_statistics.tsv

added:
test-data/GCA_000007265.1_ASM726v1_genomic

diff -r 4e61ec4fd5f5 -r 220e2f7ff8bb macros.xml
--- a/macros.xml Sat Apr 13 16:09:20 2024 +0000
+++ b/macros.xml Sat May 11 22:50:19 2024 +0000

@@ -1,6 +1,6 @@
<macros>
     <token name="@CHEW_VERSION@">3.3.3</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">22.05</token>
     <xml name="requirements">
         <requirements>

diff -r 4e61ec4fd5f5 -r 220e2f7ff8bb test-data/GCA_000007265.1_ASM726v1_genomic
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/GCA_000007265.1_ASM726v1_genomic Sat May 11 22:50:19 2024 +0000

b'@@ -0,0 +1,1500 @@\n+>AE009948.1 Streptococcus agalactiae 2603V/R, complete genome\n+AATTAACATTGTTGATTTTATTCTTCAACATCTGTGGAAAACTTTATTTTTTTATGGTACAATATAACAATAATTATCCA\n+CAAGACAATAAGGAAGAAGCTATGACGGAAAACGAACAACTATTTTGGAATAGAGTACTAGAGCTATCTCGTTCTCAAAT\n+AGCACCAGCAGCTTATGAATTTTTTGTTCTAGAGGCTAGACTCCTCAAAATTGAACATCAAACTGCAGTTATTACTTTAG\n+ATAACATTGAAATGAAAAAGCTATTCTGGGAACAAAATTTGGGGCCTGTTATCCTAACAGCTGGTTTTGAAATTTTCAAT\n+GCTGAAATTACAGCTAACTATGTCTCAAACGATTTACATTTACAAGAAACTAGTTTTTCTAACTACCAGCAATCTAGCAA\n+TGAAGTAAATACTTTACCAATTAGAAAAATCGACTCTAACCTTAAAGAGAAATATACTTTTGCTAATTTTGTTCAAGGAG\n+ATGAAAATAGATGGGCTGTTTCAGCATCAATTGCTGTAGCTGATAGTCCTGGCACGACTTATAATCCTCTATTTATCTGG\n+GGGGGACCTGGTCTAGGAAAGACGCATCTACTAAATGCTATTGGAAATCAAGTCTTAAGAGATAATCCAAACGCGAGGGT\n+TTTATACATCACTGCTGAGAATTTTATTAATGAATTTGTCAGTCATATTCGTTTAGATTCGATGGAAGAATTAAAAGAAA\n+AGTTTCGCAACTTAGACTTACTCCTGATTGATGATATTCAGTCGCTTGCTAAGAAAACCTTAGGGGGGACCCAAGAGGAG\n+TTCTTCAATACTTTCAATGCTTTACATACAAACGATAAACAAATCGTATTGACCAGTGACCGAAATCCAAATCAATTAAA\n+TGATCTAGAAGAACGTCTAGTCACGCGCTTTAGTTGGGGACTCCCAGTAAATATCACACCACCTGATTTTGAAACACGAG\n+TTGCTATTTTAACCAATAAAATTCAAGAATATCCTTATGATTTTCCTCAAGATACCATTGAATACTTAGCAGGAGAATTT\n+GATTCCAACGTACGTGAATTAGAAGGAGCCTTGAAAAATATTAGTCTAGTTGCTGACTTTAAGCATGCTAAAACTATTAC\n+AGTAGATATAGCTGCAGAAGCTATCAGAGCACGTAAAAATGATGGTCCTATTGTTACTGTCATTCCTATAGAAGAAATTC\n+AAATACAAGTTGGTAAATTCTATGGCGTAACTGTAAAAGAGATAAAAGCAACTAAAAGAACACAAGATATTGTCCTTGCA\n+AGACAGGTAGCCATGTACTTAGCTCGTGAGATGACAGATAACAGTCTCCCAAAAATAGGTAAAGAATTTGGGGGACGAGA\n+TCACTCAACTGTTCTCCACGCTTATAATAAAATAAAAAATATGGTTGCTCAAGATGACAACTTACGAATTGAGATAGAAA\n+CTATCAAAAATAAAATCAGATAGGCTTTGTGGATAAGTATCAGAAAAATACGAGACTTTTCCACAGGTTGTGAACAAGTT\n+ATTTTCCTTATGAATATTAAAGTTATAATACTTATTCACAACTTTAACAGGACCTACTATTACTACTAAATTTATACTAA\n+TATATAAAGGATATACTATGATTCATTTTTCAATAAATAAAAATTTCTTCTTGCATGCTCTAACGGTAACCAAACGAGCT\n+ATTAGTCATAAAAATGCGATTCCAATCCTTTCAACTGTTAAAATAGAAGTGACTAGGGATGCTATCATTTTAACGGGGTC\n+AAATGGACAAATTTCAATTGAAAATACTATTCCTGCTTCAAATGAAAATGCAGGTTTACTAGTAACGAATCCAGGCTCTA\n+TTTTGTTAGAAGCTGGTTTCTTTATTAATATTATTTCAAGTTTACCAGATGTAACTTTAGAATTTACAGAGATTGAACAA\n+CATCAAATTGTTCTTACTAGTGGAAAATCAGAGATTACTTTGAAAGGTAAGGATGTCGATCAATACCCTCGTCTGCAGGA\n+AATGACAACAGATACTCCATTAACATTAGAAACTAAACTGTTAAAATCAATTATTAATGAAACTGCTTTTGCTGCTAGCC\n+AACAAGAAAGCCGTCCAATCTTAACAGGTGTTCATTTGGTTATCAGTCAAAATAAATACTTTAAGGCTGTTGCGACAGAT\n+TCACACCGTATGAGTCAACGCACTTTCCAATTAGAGAAATCGGCTAATAATTTTGATTTGGTTGTTCCAAGTAAATCCCT\n+TCGAGAATTTTCGGCTGTTTTTACAGATGATATTGAAACTGTAGAGGTTTTCTTCTCAGATAGTCAAATGTTATTTAGAA\n+GTGAAAATATCAGCTTCTATACACGTTTGCTTGAAGGAAACTACCCTGATACTGATCGCCTCCTAACTAATCAGTTTGAA\n+ACCGAAATTATCTTTAATACAAATGCTTTACGCCATGCTATGGAACGTGCTTATTTAATTTCGAATGCAACTCAGAACGG\n+TACTGTTCGTTTAGAAATTCAAAATGAGACAGTCTCAGCTCATGTAAACTCTCCAGAAGTTGGTAAAGTTAATGAGGAAT\n+TGGATACTGTTAGTCTTAAAGGTGATAGTTTAAATATTAGCTTTAATCCAACTTACCTAATTGAATCTTTAAAAGCAGTA\n+AAAAGCGAAACAGTTACGATTCGATTTATTTCTCCAGTACGTCCATTTACTTTGACACCTGGTGAAGATACTGAAGATTT\n+CATCCAATTAATAACTCCTGTTCGTACTAACTAAATAAGAAAACTACCCAAGTTATTCTTGGGTAGTTTTCTTATTCTAA\n+GATATGCTATAATGATGAGTAATATGACTCTATATATAATAGCTAACCCCCATGCTGGTAATAAAAATGCCTCCACTATT\n+GTTGGTAAAATTCAGGAGCTTTATCATACTGAAGATATTTCTGTGTTCTATACAGAACAGAAAGATGATGAAAAAAAACA\n+AGTCATTAATATACTAAGGTCTTTTAAAGAAAGTGATCATCTAATGATTATAGGAGGAGATGGTACCTTATCAAAAGTAA\n+TGACTTATCTCCCCCAACATATTCCGTGCACTTATTATCCTGTTGGTTCGGGAAATGATTTTGCCAGAGCTTTGAAAATT\n+CCTAACCTCAAAGAAACCCTTACCGCTATTCAGACAGAAAGATTAAAGGAAATTAATTGCTTTATTTATGATAAAGGGCT\n+GATTTTGAATAGTTTAGATTTAGGTTTTGCAGCCTATGTCGTTTGGAAAGCATCTAACTCTAAAATAAAAAATATTTTGA\n+ATAGATATCGTCTAGGAAAAATAACTTACATTGTTATAGCTATCAAATCATTATTACATTCTTCTAAAGTACAAGTATTA\n+GTGGAAGGAGAGACAGGACAGCAGATAAAACTAAATGACCTTTATTTTTTCGCATTAGCAAATAACACTTATTTTGGAGG\n+TGGCATTACTATTTGGCCTAAAGCAAGTGCTTTAACTGCAGAGTTAGATATGGTTTACGCTAAAGGGCATACTTTTCTAA\n+AACGATTAAGTATTTTATTATCTTTGGTTTTTAAAAGGCATACTACCTCTAAAAGTATAAAACACCAGACTTTCAAAGCT\n+ATGACCGTATATTTTCCTAAAAATAGTTTGATTGAAATAGATGGCGAAATAGTTGAGTTAGATCAGATTAGTTTAAAATG\n+TCAAAAAAGGTATTTATATATGTAAGGAGAAAAGATGTATCAAGTTGGATCACTTGTTGAAATGAAAAAACCTCATGCTT\n+GTGTAATTAAAGAAACTGGTAAAAAGGCTAATCAATGGAAGGTACTGAGAGTAGGAGCTGAT'..b'AAGGTGACAATTCAAAAATTTGATCCATATATTAATATTGATCCAGGGACAATGAGCCCTTA\n+TCAACATGGAGAAGTTTATGTTACAGATGATGGTGCAGAAACTGACCTTGACCTTGGACACTACGAGCGTTTTATTGATA\n+TTAACTTAAACAAATATTCAAATGTTACAACGGGTAAGATTTATAGTGAAGTTCTTAAAAAAGAACGCCGTGGAGAATAC\n+CTTGGTGCAACTGTTCAAGTTATCCCACACGTTACAGATGCTTTGAAAGAAAAAATCAAACGTGCTGCGACAACTACAGA\n+TTCAGATGTTATTATTACTGAAGTTGGCGGTACTGTTGGAGATATTGAGAGCCTTCCGTTTTTAGAAGCACTTCGTCAAA\n+TGAAGGCAGATGTTGGTTCTGATAATGTTATGTACATTCATACAACGTTATTACCATACCTAAAGGCTGCCGGCGAAATG\n+AAAACAAAACCGACTCAACATTCTGTTAAAGAGTTACGTGGCCTAGGTATCCAACCTAATATGCTTGTTATCCGTACAGA\n+GCAACCAGCAGGTCAAAGTATTAAGAATAAATTGGCACAATTTTGTGATGTTGCACCAGAGGCTGTTATAGAGTCCCTTG\n+ACGTTGACCATATTTATCAAATTCCACTTAACATGCAAGCTCAAAATATGGATCAAATTGTTTGTGATCACTTGAAGCTT\n+GAGACACCTGCTGCTGATATGACAGAATGGTCAGCAATGGTTGATAAAGTAATGAACCTTGAGAAAAAAGTTAAAATTGC\n+ATTGGTTGGTAAATATGTTGAATTACCTGATGCCTACCTTTCAGTTGTGGAAGCCCTTAAGCACTCAGGGTACGTCAACG\n+ATGTTGCTATTGATCTAAAATGGGTAAATGCTGCTGAAGTGACAGAAGATAATATTAAAGAACTTGTCGGAGATGCAGAT\n+GGTATCATCGTTCCTGGTGGATTTGGCCAAAGAGGTAGTGAGGGTAAAATTGAAGCAATTCGCTATGCACGTGAAAATGA\n+TGTTCCAATGCTTGGTGTTTGTCTCGGAATGCAGCTAACTTGTGTCGAATTTGCGCGTAATGTTTTAAACCTTCATGGAG\n+CTAATTCAGCAGAGCTTGACCCTAAAACACCGTTCCCAATCATTGATATCATGCGTGATCAAATCGATATTGAAGATATG\n+GGTGGTACACTTCGCCTTGGTCTATATCCATGTAAATTGAAATCAGGTTCAAGAGCTGCGGCAGCTTATAATAATCAAGA\n+AGTTGTCCAACGTCGTCACCGTCACCGTTATGAATTTAATACAAAATTCCGTGAGCAATTTGAGGCTGCTGGATTTGTCT\n+TCTCAGGGGTATCACCGGATAATCGTTTGATGGAAGTTGTTGAGTTACCAGAGAAAAAATTCTTTGTTGCAGCACAATAC\n+CATCCAGAATTACAATCACGTCCTAACCATGCTGAAGAGCTTTACACAGCTTTTGTAACCGCAGCAGTTGAAAATATGAA\n+ATAACTTTATCGCCTCCCAGTATTAGGAGGCGATTTTATTTTTTTAGATAGTTTCACTATCAAAGTATCATTAGCTCTTT\n+TCTTTTTCTAAAAATAAGGTATAATAGGTTGCATGAAAAAGATTCGATTATCAAAGTTTATTAAAATGATTGTTGTTATT\n+TTGTTTTTAATTAGTGTAGCAGCTAGTTTTTATTTTTTCCACGTTGCCCAAGTTCGAGATGATAAATCCTTTATTTCAAA\n+TGGTCAACGTAAGCCTGGAAACTCTTTATATGCTTATGATAAATCCTTTGATAAGCTATTAAAGCAAAAAATAGAAATGA\n+CAAACCAAAATATAAAGCAAGTTGCTTGGTATGTTCCTGCTGTTAAGAAAACTCATAAGACAGCTGTTGTCGTTCATGGT\n+TTTGCGAATAGCAAAGAGAATATGAAGGCATATGGTTGGCTGTTTCATAAGTTAGGATACAATGTTCTTATGCCTGACAA\n+TATTGCACATGGTGAAAGTCATGGGCAGTTGATAGGCTATGGCTGGAACGACCGCGAGAACATTATCAAATGGACAGAAA\n+TGATAGTTGATAAGAATCCATCAAGCCAAATTACTTTATTTGGTGTTTCAATGGGTGGAGCAACAGTCATGATGGCTAGT\n+GGTGAAAAATTACCTAGTCAGGTTGTTAATATCATTGAAGATTGCGGTTATTCTAGTGTTTGGGATGAATTAAAATTTCA\n+GGCTAAAGAGATGTATGGTTTACCAGCCTTCCCACTCTTATATGAAGTTTCAACAATTTCTAAAATCAGAGCAGGTTTTT\n+CGTATGGACAAGCAAGTAGTGTCGAACAATTGAAAAAGAATAATTTACCAGCCCTCTTTATTCATGGTGATAAGGATAAT\n+TTTGTTCCAACAAGTATGGTTTATGACAACTATAAAGCTACAGCAGGTAAGAAAGAGCTTTATATTGTAAAAGGGGCAAA\n+ACATGCGAAATCTTTTGAAACAGAGCCAGAAAAATATGAGAAACGTATCTCTAGTTTTTTGAAAAAATATGAAAAATAAT\n+ATTGACAACAATATGATAAGTTGATATAATTTATTATGTTGTTAAGCGGGGATGGCGGAATTGGCAGACGCGCAAGACTA\n+AGGATCTTGTGACCGCTTTTGGTCGTGAGGGTTCAAGTCCCTCTCTCCGCAGACTAGTCGAGTTCATTTGGAACTCGACT\n+TTTTGCATATTTAAGATAAAGATGGAGTATCACATGTCAAAAGTACGTGGCTTTGAATTAGTTAGCCAATTTAGCAATAA\n+AGAGTTATTACCAAAACGAGAAACAGCTCACGCAGCTGGCTATGATTTAAAAGTAGCTAAAAAAACGGTTATTGAACCTG\n+GTGAAATTACATTGGTCCCGACCGGTATTAAAGCATACATGCAACCAGGGGAGGTCCTGTACCTTTATGATCGTTCATCG\n+AATCCACGTAAAAAAGGGATTGTCCTAATAAATTCAGTTGGTGTTATTGATGGTGACTACTATAATAACCAAGTCAATGA\n+AGGACATATTTTTGCACAGATGCAAAATATTACTGATCAGGCTGTTATTTTAGAAGAAGGGGAACGGATTGTTCAGGCTG\n+TTTTTGCCCCATTCTTATTGGCAGATGACGATCAGGCTACAGGAATGCGTACAGGTGGTTTTGGTAGTACTGGAAAATAA\n+AATTATTTTACGAATAATGTTAGAAAAGGCTAGACTTACTTCTTAGCCTTTTTTGATGAGAGTAAACTTATATTTTCTCT\n+AACTTGGTGTGATATAATGAGTGTACTAGTTATTTGGTACCAAGCTATCATATTAATTTAGAAGTTATAAAGGAGGCCTG\n+AGTGGCTAAGAAAAAATCAGTCTTCACCTGTCAAGAGTGTGGTTACCAATCACCTAAGTATTTGGGACGTTGTCCAAATT\n+GCTCAGCCTGGTCTTCATTTGTAGAAGAGGTTGAAGTTCAAGAAGTTAAAAATGCACGAGTTAGTTTGAACGGTGAAAAG\n+TCCCGACCGACGAAGTTAAAAGATGTTTCCTCAATTAACTATTCTAGAACTAAGACTGATATGGATGAATTTAACCGTGT\n+TCTAGGAGGCGGTGTTGTACCAGGAAGTTTGGTTCTGATTGGAGGAGACCCTGGGATAGGTAAATCTACTTTATTACTAC\n+AAGTATCAACTCAGCTAGCTAATAAAGGTACAGTATTATATGTCTCAGGTGAGGAATCTGCAGAACAGATTAAGTTACGA\n+AGTGAGCGTCTAGGCGATATCGATAATGAATTTTACCTTTATGCCGAGACTAATATGCAAAGTATTCGGTCGGAGATTGA\n+GAAGATTAAACCAGATTTTCTTATTATTGATTCTATACAAACTATTATGAGTCCCGAAGTATCAAGTGTCCAAGGCTCTG\n'

diff -r 4e61ec4fd5f5 -r 220e2f7ff8bb test-data/JoinedProfile.tsv
--- a/test-data/JoinedProfile.tsv Sat Apr 13 16:09:20 2024 +0000
+++ b/test-data/JoinedProfile.tsv Sat May 11 22:50:19 2024 +0000

@@ -1,3 +1,3 @@
FILE GCA-000007265-protein1 GCA-000007265-protein10 GCA-000007265-protein100 GCA-000007265-protein101 GCA-000007265-protein102 GCA-000007265-protein103 GCA-000007265-protein104 GCA-000007265-protein105 GCA-000007265-protein106 GCA-000007265-protein107 GCA-000007265-protein108 GCA-000007265-protein109 GCA-000007265-protein11 GCA-000007265-protein110 GCA-000007265-protein111 GCA-000007265-protein112 GCA-000007265-protein113 GCA-000007265-protein114 GCA-000007265-protein12 GCA-000007265-protein13 GCA-000007265-protein14 GCA-000007265-protein16 GCA-000007265-protein19 GCA-000007265-protein2 GCA-000007265-protein20 GCA-000007265-protein21 GCA-000007265-protein22 GCA-000007265-protein23 GCA-000007265-protein24 GCA-000007265-protein25 GCA-000007265-protein26 GCA-000007265-protein27 GCA-000007265-protein28 GCA-000007265-protein29 GCA-000007265-protein3 GCA-000007265-protein30 GCA-000007265-protein31 GCA-000007265-protein32 GCA-000007265-protein33 GCA-000007265-protein34 GCA-000007265-protein35 GCA-000007265-protein36 GCA-000007265-protein37 GCA-000007265-protein38 GCA-000007265-protein39 GCA-000007265-protein40 GCA-000007265-protein41 GCA-000007265-protein42 GCA-000007265-protein43 GCA-000007265-protein44 GCA-000007265-protein45 GCA-000007265-protein46 GCA-000007265-protein47 GCA-000007265-protein48 GCA-000007265-protein49 GCA-000007265-protein5 GCA-000007265-protein50 GCA-000007265-protein51 GCA-000007265-protein52 GCA-000007265-protein53 GCA-000007265-protein54 GCA-000007265-protein55 GCA-000007265-protein56 GCA-000007265-protein57 GCA-000007265-protein58 GCA-000007265-protein59 GCA-000007265-protein6 GCA-000007265-protein60 GCA-000007265-protein61 GCA-000007265-protein62 GCA-000007265-protein63 GCA-000007265-protein64 GCA-000007265-protein65 GCA-000007265-protein66 GCA-000007265-protein67 GCA-000007265-protein68 GCA-000007265-protein69 GCA-000007265-protein7 GCA-000007265-protein70 GCA-000007265-protein71 GCA-000007265-protein72 GCA-000007265-protein74 GCA-000007265-protein75 GCA-000007265-protein76 GCA-000007265-protein77 GCA-000007265-protein79 GCA-000007265-protein8 GCA-000007265-protein80 GCA-000007265-protein81 GCA-000007265-protein82 GCA-000007265-protein84 GCA-000007265-protein85 GCA-000007265-protein86 GCA-000007265-protein87 GCA-000007265-protein9 GCA-000007265-protein93 GCA-000007265-protein94 GCA-000007265-protein95 GCA-000007265-protein96 GCA-000007265-protein97 GCA-000007265-protein98 GCA-000007265-protein99
+GCA_000007265_1_ASM726v1_genomic 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 NIPHEM 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
GCA_000007265 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 NIPHEM 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
-GCA_000007265 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 NIPHEM 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

diff -r 4e61ec4fd5f5 -r 220e2f7ff8bb test-data/allelecallevaluator_report.html
--- a/test-data/allelecallevaluator_report.html Sat Apr 13 16:09:20 2024 +0000
+++ b/test-data/allelecallevaluator_report.html Sat May 11 22:50:19 2024 +0000

[

b'@@ -9,7 +9,7 @@\n <body style="background-color: #f6f6f6">\n <noscript> You need to enable JavaScript to run this app. </noscript>\n <div id="root"></div>\n- <script> preComputedData = {"summaryData": [{"columns": ["Total Samples", "Total Loci", "Total CDSs", "Total CDSs Classified", "EXC", "INF", "PLOT3", "PLOT5", "LOTSC", "NIPH", "NIPHEM", "ALM", "ASM", "PAMA", "LNF"]}, {"rows": [[1, 102, 114, 104, 101, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0]]}], "sample_ids": ["GCA_000007265"], "sample_data": [[101], [0], [0], [0], [0], [0], [1], [0], [0], [0], [0]], "loci_ids": ["GCA-000007265-protein1", "GCA-000007265-protein58", "GCA-000007265-protein67", "GCA-000007265-protein66", "GCA-000007265-protein65", "GCA-000007265-protein64", "GCA-000007265-protein63", "GCA-000007265-protein62", "GCA-000007265-protein61", "GCA-000007265-protein60", "GCA-000007265-protein6", "GCA-000007265-protein59", "GCA-000007265-protein57", "GCA-000007265-protein69", "GCA-000007265-protein56", "GCA-000007265-protein55", "GCA-000007265-protein54", "GCA-000007265-protein53", "GCA-000007265-protein52", "GCA-000007265-protein51", "GCA-000007265-protein50", "GCA-000007265-protein5", "GCA-000007265-protein49", "GCA-000007265-protein48", "GCA-000007265-protein68", "GCA-000007265-protein7", "GCA-000007265-protein10", "GCA-000007265-protein84", "GCA-000007265-protein98", "GCA-000007265-protein97", "GCA-000007265-protein96", "GCA-000007265-protein95", "GCA-000007265-protein94", "GCA-000007265-protein93", "GCA-000007265-protein9", "GCA-000007265-protein87", "GCA-000007265-protein86", "GCA-000007265-protein85", "GCA-000007265-protein82", "GCA-000007265-protein70", "GCA-000007265-protein81", "GCA-000007265-protein80", "GCA-000007265-protein8", "GCA-000007265-protein79", "GCA-000007265-protein77", "GCA-000007265-protein76", "GCA-000007265-protein75", "GCA-000007265-protein74", "GCA-000007265-protein72", "GCA-000007265-protein71", "GCA-000007265-protein47", "GCA-000007265-protein46", "GCA-000007265-protein45", "GCA-000007265-protein44", "GCA-000007265-protein2", "GCA-000007265-protein19", "GCA-000007265-protein14", "GCA-000007265-protein13", "GCA-000007265-protein12", "GCA-000007265-protein114", "GCA-000007265-protein113", "GCA-000007265-protein112", "GCA-000007265-protein111", "GCA-000007265-protein110", "GCA-000007265-protein11", "GCA-000007265-protein109", "GCA-000007265-protein108", "GCA-000007265-protein107", "GCA-000007265-protein106", "GCA-000007265-protein105", "GCA-000007265-protein104", "GCA-000007265-protein103", "GCA-000007265-protein102", "GCA-000007265-protein101", "GCA-000007265-protein100", "GCA-000007265-protein20", "GCA-000007265-protein21", "GCA-000007265-protein22", "GCA-000007265-protein33", "GCA-000007265-protein43", "GCA-000007265-protein42", "GCA-000007265-protein41", "GCA-000007265-protein40", "GCA-000007265-protein39", "GCA-000007265-protein38", "GCA-000007265-protein37", "GCA-000007265-protein36", "GCA-000007265-protein35", "GCA-000007265-protein34", "GCA-000007265-protein32", "GCA-000007265-protein23", "GCA-000007265-protein31", "GCA-000007265-protein30", "GCA-000007265-protein3", "GCA-000007265-protein29", "GCA-000007265-protein28", "GCA-000007265-protein27", "GCA-000007265-protein26", "GCA-000007265-protein25", "GCA-000007265-protein24", "GCA-000007265-protein99", "GCA-000007265-protein16"], "loci_data": [[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, '..b', 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein27", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein26", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein25", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein24", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein99", 1, 1, 0, 1.0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], ["GCA-000007265-protein16", 3, 0, 1, 0.0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0]]}], "annotations": [{"columns": []}, {"rows": []}], "presence_absence": [{"rows": [[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0]]}, {"loci_ids": ["GCA-000007265-protein1", "GCA-000007265-protein58", "GCA-000007265-protein67", "GCA-000007265-protein66", "GCA-000007265-protein65", "GCA-000007265-protein64", "GCA-000007265-protein63", "GCA-000007265-protein62", "GCA-000007265-protein61", "GCA-000007265-protein60", "GCA-000007265-protein6", "GCA-000007265-protein59", "GCA-000007265-protein57", "GCA-000007265-protein69", "GCA-000007265-protein56", "GCA-000007265-protein55", "GCA-000007265-protein54", "GCA-000007265-protein53", "GCA-000007265-protein52", "GCA-000007265-protein51", "GCA-000007265-protein50", "GCA-000007265-protein5", "GCA-000007265-protein49", "GCA-000007265-protein48", "GCA-000007265-protein68", "GCA-000007265-protein7", "GCA-000007265-protein10", "GCA-000007265-protein84", "GCA-000007265-protein98", "GCA-000007265-protein97", "GCA-000007265-protein96", "GCA-000007265-protein95", "GCA-000007265-protein94", "GCA-000007265-protein93", "GCA-000007265-protein9", "GCA-000007265-protein87", "GCA-000007265-protein86", "GCA-000007265-protein85", "GCA-000007265-protein82", "GCA-000007265-protein70", "GCA-000007265-protein81", "GCA-000007265-protein80", "GCA-000007265-protein8", "GCA-000007265-protein79", "GCA-000007265-protein77", "GCA-000007265-protein76", "GCA-000007265-protein75", "GCA-000007265-protein74", "GCA-000007265-protein72", "GCA-000007265-protein71", "GCA-000007265-protein47", "GCA-000007265-protein46", "GCA-000007265-protein45", "GCA-000007265-protein44", "GCA-000007265-protein2", "GCA-000007265-protein19", "GCA-000007265-protein14", "GCA-000007265-protein13", "GCA-000007265-protein12", "GCA-000007265-protein114", "GCA-000007265-protein113", "GCA-000007265-protein112", "GCA-000007265-protein111", "GCA-000007265-protein110", "GCA-000007265-protein11", "GCA-000007265-protein109", "GCA-000007265-protein108", "GCA-000007265-protein107", "GCA-000007265-protein106", "GCA-000007265-protein105", "GCA-000007265-protein104", "GCA-000007265-protein103", "GCA-000007265-protein102", "GCA-000007265-protein101", "GCA-000007265-protein100", "GCA-000007265-protein20", "GCA-000007265-protein21", "GCA-000007265-protein22", "GCA-000007265-protein33", "GCA-000007265-protein43", "GCA-000007265-protein42", "GCA-000007265-protein41", "GCA-000007265-protein40", "GCA-000007265-protein39", "GCA-000007265-protein38", "GCA-000007265-protein37", "GCA-000007265-protein36", "GCA-000007265-protein35", "GCA-000007265-protein34", "GCA-000007265-protein32", "GCA-000007265-protein23", "GCA-000007265-protein31", "GCA-000007265-protein30", "GCA-000007265-protein3", "GCA-000007265-protein29", "GCA-000007265-protein28", "GCA-000007265-protein27", "GCA-000007265-protein26", "GCA-000007265-protein25", "GCA-000007265-protein24", "GCA-000007265-protein99", "GCA-000007265-protein16"]}, {"sample_ids": ["GCA_000007265_1_ASM726v1_genomic"]}], "distance_matrix": [{"rows": [[0]]}, {"sample_ids": ["GCA_000007265_1_ASM726v1_genomic"]}], "cgMLST_tree": {"phylo_data": "(GCA_000007265_1_ASM726v1_genomic:0.000000000);\\n"}, "cgMLST_size": [{"cgMLST100": 101}]} </script>\n <script src="./report_bundle.js"></script>\n </body>\n </html>\n'

diff -r 4e61ec4fd5f5 -r 220e2f7ff8bb test-data/allelecallevaluator_report_annotate.html
--- a/test-data/allelecallevaluator_report_annotate.html Sat Apr 13 16:09:20 2024 +0000
+++ b/test-data/allelecallevaluator_report_annotate.html Sat May 11 22:50:19 2024 +0000

[

b'@@ -9,7 +9,7 @@\n <body style="background-color: #f6f6f6">\n <noscript> You need to enable JavaScript to run this app. </noscript>\n <div id="root"></div>\n- <script> preComputedData = {"summaryData": [{"columns": ["Total Samples", "Total Loci", "Total CDSs", "Total CDSs Classified", "EXC", "INF", "PLOT3", "PLOT5", "LOTSC", "NIPH", "NIPHEM", "ALM", "ASM", "PAMA", "LNF"]}, {"rows": [[1, 102, 114, 104, 101, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0]]}], "sample_ids": ["GCA_000007265"], "sample_data": [[101], [0], [0], [0], [0], [0], [1], [0], [0], [0], [0]], "loci_ids": ["GCA-000007265-protein1", "GCA-000007265-protein58", "GCA-000007265-protein67", "GCA-000007265-protein66", "GCA-000007265-protein65", "GCA-000007265-protein64", "GCA-000007265-protein63", "GCA-000007265-protein62", "GCA-000007265-protein61", "GCA-000007265-protein60", "GCA-000007265-protein6", "GCA-000007265-protein59", "GCA-000007265-protein57", "GCA-000007265-protein69", "GCA-000007265-protein56", "GCA-000007265-protein55", "GCA-000007265-protein54", "GCA-000007265-protein53", "GCA-000007265-protein52", "GCA-000007265-protein51", "GCA-000007265-protein50", "GCA-000007265-protein5", "GCA-000007265-protein49", "GCA-000007265-protein48", "GCA-000007265-protein68", "GCA-000007265-protein7", "GCA-000007265-protein10", "GCA-000007265-protein84", "GCA-000007265-protein98", "GCA-000007265-protein97", "GCA-000007265-protein96", "GCA-000007265-protein95", "GCA-000007265-protein94", "GCA-000007265-protein93", "GCA-000007265-protein9", "GCA-000007265-protein87", "GCA-000007265-protein86", "GCA-000007265-protein85", "GCA-000007265-protein82", "GCA-000007265-protein70", "GCA-000007265-protein81", "GCA-000007265-protein80", "GCA-000007265-protein8", "GCA-000007265-protein79", "GCA-000007265-protein77", "GCA-000007265-protein76", "GCA-000007265-protein75", "GCA-000007265-protein74", "GCA-000007265-protein72", "GCA-000007265-protein71", "GCA-000007265-protein47", "GCA-000007265-protein46", "GCA-000007265-protein45", "GCA-000007265-protein44", "GCA-000007265-protein2", "GCA-000007265-protein19", "GCA-000007265-protein14", "GCA-000007265-protein13", "GCA-000007265-protein12", "GCA-000007265-protein114", "GCA-000007265-protein113", "GCA-000007265-protein112", "GCA-000007265-protein111", "GCA-000007265-protein110", "GCA-000007265-protein11", "GCA-000007265-protein109", "GCA-000007265-protein108", "GCA-000007265-protein107", "GCA-000007265-protein106", "GCA-000007265-protein105", "GCA-000007265-protein104", "GCA-000007265-protein103", "GCA-000007265-protein102", "GCA-000007265-protein101", "GCA-000007265-protein100", "GCA-000007265-protein20", "GCA-000007265-protein21", "GCA-000007265-protein22", "GCA-000007265-protein33", "GCA-000007265-protein43", "GCA-000007265-protein42", "GCA-000007265-protein41", "GCA-000007265-protein40", "GCA-000007265-protein39", "GCA-000007265-protein38", "GCA-000007265-protein37", "GCA-000007265-protein36", "GCA-000007265-protein35", "GCA-000007265-protein34", "GCA-000007265-protein32", "GCA-000007265-protein23", "GCA-000007265-protein31", "GCA-000007265-protein30", "GCA-000007265-protein3", "GCA-000007265-protein29", "GCA-000007265-protein28", "GCA-000007265-protein27", "GCA-000007265-protein26", "GCA-000007265-protein25", "GCA-000007265-protein24", "GCA-000007265-protein99", "GCA-000007265-protein16"], "loci_data": [[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, '..b', "GCA_000007265", "AE009948.1", "79220", "79498", "64", "1", "Small ribosomal subunit protein uS19", "http://purl.uniprot.org/uniprot/Q1JE54", "", "", "", "", ""], ["GCA-000007265-protein52", "GCA_000007265", "AE009948.1", "66381", "66818", "52", "1", "protein-tyrosine-phosphatase", "http://purl.uniprot.org/uniprot/A0A0E1EJB3", "", "", "", "", ""], ["GCA-000007265-protein10", "GCA_000007265", "AE009948.1", "10295", "10666", "10", "1", "Cell division protein DivIC", "http://purl.uniprot.org/uniprot/Q8E7Y5", "", "", "", "", ""]]}], "presence_absence": [{"rows": [[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0]]}, {"loci_ids": ["GCA-000007265-protein1", "GCA-000007265-protein58", "GCA-000007265-protein67", "GCA-000007265-protein66", "GCA-000007265-protein65", "GCA-000007265-protein64", "GCA-000007265-protein63", "GCA-000007265-protein62", "GCA-000007265-protein61", "GCA-000007265-protein60", "GCA-000007265-protein6", "GCA-000007265-protein59", "GCA-000007265-protein57", "GCA-000007265-protein69", "GCA-000007265-protein56", "GCA-000007265-protein55", "GCA-000007265-protein54", "GCA-000007265-protein53", "GCA-000007265-protein52", "GCA-000007265-protein51", "GCA-000007265-protein50", "GCA-000007265-protein5", "GCA-000007265-protein49", "GCA-000007265-protein48", "GCA-000007265-protein68", "GCA-000007265-protein7", "GCA-000007265-protein10", "GCA-000007265-protein84", "GCA-000007265-protein98", "GCA-000007265-protein97", "GCA-000007265-protein96", "GCA-000007265-protein95", "GCA-000007265-protein94", "GCA-000007265-protein93", "GCA-000007265-protein9", "GCA-000007265-protein87", "GCA-000007265-protein86", "GCA-000007265-protein85", "GCA-000007265-protein82", "GCA-000007265-protein70", "GCA-000007265-protein81", "GCA-000007265-protein80", "GCA-000007265-protein8", "GCA-000007265-protein79", "GCA-000007265-protein77", "GCA-000007265-protein76", "GCA-000007265-protein75", "GCA-000007265-protein74", "GCA-000007265-protein72", "GCA-000007265-protein71", "GCA-000007265-protein47", "GCA-000007265-protein46", "GCA-000007265-protein45", "GCA-000007265-protein44", "GCA-000007265-protein2", "GCA-000007265-protein19", "GCA-000007265-protein14", "GCA-000007265-protein13", "GCA-000007265-protein12", "GCA-000007265-protein114", "GCA-000007265-protein113", "GCA-000007265-protein112", "GCA-000007265-protein111", "GCA-000007265-protein110", "GCA-000007265-protein11", "GCA-000007265-protein109", "GCA-000007265-protein108", "GCA-000007265-protein107", "GCA-000007265-protein106", "GCA-000007265-protein105", "GCA-000007265-protein104", "GCA-000007265-protein103", "GCA-000007265-protein102", "GCA-000007265-protein101", "GCA-000007265-protein100", "GCA-000007265-protein20", "GCA-000007265-protein21", "GCA-000007265-protein22", "GCA-000007265-protein33", "GCA-000007265-protein43", "GCA-000007265-protein42", "GCA-000007265-protein41", "GCA-000007265-protein40", "GCA-000007265-protein39", "GCA-000007265-protein38", "GCA-000007265-protein37", "GCA-000007265-protein36", "GCA-000007265-protein35", "GCA-000007265-protein34", "GCA-000007265-protein32", "GCA-000007265-protein23", "GCA-000007265-protein31", "GCA-000007265-protein30", "GCA-000007265-protein3", "GCA-000007265-protein29", "GCA-000007265-protein28", "GCA-000007265-protein27", "GCA-000007265-protein26", "GCA-000007265-protein25", "GCA-000007265-protein24", "GCA-000007265-protein99", "GCA-000007265-protein16"]}, {"sample_ids": ["GCA_000007265_1_ASM726v1_genomic"]}], "distance_matrix": [{"rows": [[0]]}, {"sample_ids": ["GCA_000007265_1_ASM726v1_genomic"]}], "cgMLST_tree": {"phylo_data": "(GCA_000007265_1_ASM726v1_genomic:0.000000000);\\n"}, "cgMLST_size": [{"cgMLST100": 101}]} </script>\n <script src="./report_bundle.js"></script>\n </body>\n </html>\n'

diff -r 4e61ec4fd5f5 -r 220e2f7ff8bb test-data/cds_coordinates.tsv
--- a/test-data/cds_coordinates.tsv Sat Apr 13 16:09:20 2024 +0000
+++ b/test-data/cds_coordinates.tsv Sat May 11 22:50:19 2024 +0000

b'@@ -1,115 +1,115 @@\n Genome\tContig\tStart\tStop\tProtein_ID\tCoding_Strand\n-GCA_000007265\tAE009948.1\t54\t1463\t1\t1\n-GCA_000007265\tAE009948.1\t1618\t2754\t2\t1\n-GCA_000007265\tAE009948.1\t2812\t3705\t3\t1\n-GCA_000007265\tAE009948.1\t3715\t3912\t4\t1\n-GCA_000007265\tAE009948.1\t4114\t4317\t5\t1\n-GCA_000007265\tAE009948.1\t4477\t5592\t6\t1\n-GCA_000007265\tAE009948.1\t5676\t6251\t7\t1\n-GCA_000007265\tAE009948.1\t6248\t9745\t8\t1\n-GCA_000007265\tAE009948.1\t10036\t10308\t9\t1\n-GCA_000007265\tAE009948.1\t10295\t10666\t10\t1\n-GCA_000007265\tAE009948.1\t10803\t12089\t11\t1\n-GCA_000007265\tAE009948.1\t12091\t13365\t12\t1\n-GCA_000007265\tAE009948.1\t13370\t13912\t13\t1\n-GCA_000007265\tAE009948.1\t13935\t15911\t14\t1\n-GCA_000007265\tAE009948.1\t17272\t17466\t15\t-1\n-GCA_000007265\tAE009948.1\t23103\t23297\t17\t-1\n-GCA_000007265\tAE009948.1\t92080\t92274\t88\t-1\n-GCA_000007265\tAE009948.1\t20579\t20866\t16\t1\n-GCA_000007265\tAE009948.1\t26410\t26697\t18\t1\n-GCA_000007265\tAE009948.1\t95387\t95674\t89\t1\n-GCA_000007265\tAE009948.1\t28902\t30245\t19\t1\n-GCA_000007265\tAE009948.1\t30369\t31337\t20\t1\n-GCA_000007265\tAE009948.1\t31334\t32620\t21\t1\n-GCA_000007265\tAE009948.1\t32610\t33371\t22\t1\n-GCA_000007265\tAE009948.1\t33434\t34312\t23\t1\n-GCA_000007265\tAE009948.1\t34390\t35382\t24\t1\n-GCA_000007265\tAE009948.1\t35393\t35632\t25\t1\n-GCA_000007265\tAE009948.1\t35756\t36460\t26\t1\n-GCA_000007265\tAE009948.1\t36583\t40308\t27\t1\n-GCA_000007265\tAE009948.1\t40720\t42174\t28\t1\n-GCA_000007265\tAE009948.1\t42202\t43224\t29\t1\n-GCA_000007265\tAE009948.1\t43392\t43940\t30\t1\n-GCA_000007265\tAE009948.1\t43963\t44715\t31\t1\n-GCA_000007265\tAE009948.1\t44735\t46282\t32\t1\n-GCA_000007265\tAE009948.1\t46475\t47374\t33\t1\n-GCA_000007265\tAE009948.1\t47521\t48825\t34\t1\n-GCA_000007265\tAE009948.1\t49072\t49770\t35\t1\n-GCA_000007265\tAE009948.1\t49817\t51133\t36\t1\n-GCA_000007265\tAE009948.1\t51221\t52108\t37\t1\n-GCA_000007265\tAE009948.1\t52118\t52948\t38\t1\n-GCA_000007265\tAE009948.1\t52961\t53404\t39\t1\n-GCA_000007265\tAE009948.1\t53424\t54086\t40\t1\n-GCA_000007265\tAE009948.1\t54083\t55000\t41\t1\n-GCA_000007265\tAE009948.1\t55017\t55898\t42\t1\n-GCA_000007265\tAE009948.1\t55906\t56883\t43\t1\n-GCA_000007265\tAE009948.1\t56906\t57709\t44\t-1\n-GCA_000007265\tAE009948.1\t57991\t59256\t45\t1\n-GCA_000007265\tAE009948.1\t59588\t60025\t46\t1\n-GCA_000007265\tAE009948.1\t60012\t61103\t47\t1\n-GCA_000007265\tAE009948.1\t61157\t62548\t48\t1\n-GCA_000007265\tAE009948.1\t62573\t63871\t49\t1\n-GCA_000007265\tAE009948.1\t64023\t64934\t50\t1\n-GCA_000007265\tAE009948.1\t65231\t66229\t51\t1\n-GCA_000007265\tAE009948.1\t66381\t66818\t52\t1\n-GCA_000007265\tAE009948.1\t66825\t67205\t53\t1\n-GCA_000007265\tAE009948.1\t67202\t68980\t54\t1\n-GCA_000007265\tAE009948.1\t69250\t71892\t55\t1\n-GCA_000007265\tAE009948.1\t72071\t73087\t56\t1\n-GCA_000007265\tAE009948.1\t73207\t74697\t57\t1\n-GCA_000007265\tAE009948.1\t74802\t76082\t58\t1\n-GCA_000007265\tAE009948.1\t76288\t76596\t59\t1\n-GCA_000007265\tAE009948.1\t76701\t77327\t60\t1\n-GCA_000007265\tAE009948.1\t77351\t77974\t61\t1\n-GCA_000007265\tAE009948.1\t77974\t78270\t62\t1\n-GCA_000007265\tAE009948.1\t78288\t79121\t63\t1\n-GCA_000007265\tAE009948.1\t79220\t79498\t64\t1\n-GCA_000007265\tAE009948.1\t79514\t79858\t65\t1\n-GCA_000007265\tAE009948.1\t79871\t80524\t66\t1\n-GCA_000007265\tAE009948.1\t80528\t80941\t67\t1\n-GCA_000007265\tAE009948.1\t80951\t81157\t68\t1\n-GCA_000007265\tAE009948.1\t81183\t81443\t69\t1\n-GCA_000007265\tAE009948.1\t81468\t81836\t70\t1\n-GCA_000007265\tAE009948.1\t81916\t82221\t71\t1\n-GCA_000007265\tAE009948.1\t82245\t82787\t72\t1\n-GCA_000007265\tAE009948.1\t82805\t82990\t73\t1\n-GCA_000007265\tAE009948.1\t83145\t83543\t74\t1\n-GCA_000007265\tAE009948.1\t83653\t84189\t75\t1\n-GCA_000007265\tAE009948.1\t84290\t84646\t76\t1\n-GCA_000007265\tAE009948.1\t84665\t85159\t77\t1\n-GCA_000007265\tAE009948.1\t85174\t85353\t78\t1\n-GCA_000007265\tAE009948.1\t85478\t85918\t79\t1\n-GCA_000007265\tAE009948.1\t85939\t87243\t80\t1\n-GCA_000007265\tAE009948.1\t87338\t87976\t81\t1\n-GCA_000007265\tAE009948.1\t88092\t88310\t82\t1\n-GCA_000007265\tAE009948.1\t88336\t88452\t83\t1\n-GCA_000007265\tAE009948.1\t88470\t88835\t84\t1\n-GCA_000007265\tAE009948.1\t88853\t89236\t85\t1\n-GCA_000007265\tAE009948.1\t89286\t90224\t86\t1\n-GCA_000007265\tAE009948.1\t90239\t90625\t87\t1\n-GCA_000007265\tAE009948.1\t97888\t98076\t90\t1\n-GCA_000007265\tAE009948.1\t98076\t98246\t91\t1\n-GCA_000007265\tAE009948.1\t98316\t98486\t'..b'genomic\tAE009948.1\t62573\t63871\t49\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t64023\t64934\t50\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t65231\t66229\t51\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t66381\t66818\t52\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t66825\t67205\t53\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t67202\t68980\t54\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t69250\t71892\t55\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t72071\t73087\t56\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t73207\t74697\t57\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t74802\t76082\t58\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t76288\t76596\t59\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t76701\t77327\t60\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t77351\t77974\t61\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t77974\t78270\t62\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t78288\t79121\t63\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t79220\t79498\t64\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t79514\t79858\t65\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t79871\t80524\t66\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t80528\t80941\t67\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t80951\t81157\t68\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t81183\t81443\t69\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t81468\t81836\t70\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t81916\t82221\t71\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t82245\t82787\t72\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t82805\t82990\t73\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t83145\t83543\t74\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t83653\t84189\t75\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t84290\t84646\t76\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t84665\t85159\t77\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t85174\t85353\t78\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t85478\t85918\t79\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t85939\t87243\t80\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t87338\t87976\t81\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t88092\t88310\t82\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t88336\t88452\t83\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t88470\t88835\t84\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t88853\t89236\t85\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t89286\t90224\t86\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t90239\t90625\t87\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t97888\t98076\t90\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t98076\t98246\t91\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t98316\t98486\t92\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t98822\t99082\t93\t-1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t99401\t99952\t94\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t100172\t100591\t95\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t100791\t101270\t96\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t101392\t102084\t97\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t102081\t102833\t98\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t102830\t103405\t99\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t103548\t104582\t100\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t104624\t105157\t101\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t105338\t107167\t102\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t107456\t108595\t103\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t108709\t109956\t104\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t110027\t110803\t105\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t110766\t111524\t106\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t111534\t111998\t107\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t111995\t112564\t108\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t112601\t113443\t109\t-1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t113600\t114883\t110\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t115072\t115647\t111\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t115920\t117524\t112\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t117633\t118559\t113\t1\n+GCA_000007265_1_ASM726v1_genomic\tAE009948.1\t118754\t119200\t114\t1\n'

diff -r 4e61ec4fd5f5 -r 220e2f7ff8bb test-data/results_alleles.tsv
--- a/test-data/results_alleles.tsv Sat Apr 13 16:09:20 2024 +0000
+++ b/test-data/results_alleles.tsv Sat May 11 22:50:19 2024 +0000

@@ -1,2 +1,2 @@
FILE GCA-000007265-protein1 GCA-000007265-protein10 GCA-000007265-protein100 GCA-000007265-protein101 GCA-000007265-protein102 GCA-000007265-protein103 GCA-000007265-protein104 GCA-000007265-protein105 GCA-000007265-protein106 GCA-000007265-protein107 GCA-000007265-protein108 GCA-000007265-protein109 GCA-000007265-protein11 GCA-000007265-protein110 GCA-000007265-protein111 GCA-000007265-protein112 GCA-000007265-protein113 GCA-000007265-protein114 GCA-000007265-protein12 GCA-000007265-protein13 GCA-000007265-protein14 GCA-000007265-protein16 GCA-000007265-protein19 GCA-000007265-protein2 GCA-000007265-protein20 GCA-000007265-protein21 GCA-000007265-protein22 GCA-000007265-protein23 GCA-000007265-protein24 GCA-000007265-protein25 GCA-000007265-protein26 GCA-000007265-protein27 GCA-000007265-protein28 GCA-000007265-protein29 GCA-000007265-protein3 GCA-000007265-protein30 GCA-000007265-protein31 GCA-000007265-protein32 GCA-000007265-protein33 GCA-000007265-protein34 GCA-000007265-protein35 GCA-000007265-protein36 GCA-000007265-protein37 GCA-000007265-protein38 GCA-000007265-protein39 GCA-000007265-protein40 GCA-000007265-protein41 GCA-000007265-protein42 GCA-000007265-protein43 GCA-000007265-protein44 GCA-000007265-protein45 GCA-000007265-protein46 GCA-000007265-protein47 GCA-000007265-protein48 GCA-000007265-protein49 GCA-000007265-protein5 GCA-000007265-protein50 GCA-000007265-protein51 GCA-000007265-protein52 GCA-000007265-protein53 GCA-000007265-protein54 GCA-000007265-protein55 GCA-000007265-protein56 GCA-000007265-protein57 GCA-000007265-protein58 GCA-000007265-protein59 GCA-000007265-protein6 GCA-000007265-protein60 GCA-000007265-protein61 GCA-000007265-protein62 GCA-000007265-protein63 GCA-000007265-protein64 GCA-000007265-protein65 GCA-000007265-protein66 GCA-000007265-protein67 GCA-000007265-protein68 GCA-000007265-protein69 GCA-000007265-protein7 GCA-000007265-protein70 GCA-000007265-protein71 GCA-000007265-protein72 GCA-000007265-protein74 GCA-000007265-protein75 GCA-000007265-protein76 GCA-000007265-protein77 GCA-000007265-protein79 GCA-000007265-protein8 GCA-000007265-protein80 GCA-000007265-protein81 GCA-000007265-protein82 GCA-000007265-protein84 GCA-000007265-protein85 GCA-000007265-protein86 GCA-000007265-protein87 GCA-000007265-protein9 GCA-000007265-protein93 GCA-000007265-protein94 GCA-000007265-protein95 GCA-000007265-protein96 GCA-000007265-protein97 GCA-000007265-protein98 GCA-000007265-protein99
-GCA_000007265 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 NIPHEM 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
+GCA_000007265_1_ASM726v1_genomic 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 NIPHEM 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

diff -r 4e61ec4fd5f5 -r 220e2f7ff8bb test-data/results_statistics.tsv
--- a/test-data/results_statistics.tsv Sat Apr 13 16:09:20 2024 +0000
+++ b/test-data/results_statistics.tsv Sat May 11 22:50:19 2024 +0000

@@ -1,2 +1,2 @@
FILE EXC INF PLOT3 PLOT5 LOTSC NIPH NIPHEM ALM ASM PAMA LNF Invalid CDSs Classified_CDSs Total_CDSs
-GCA_000007265 101 0 0 0 0 0 1 0 0 0 0 0 104 114
+GCA_000007265_1_ASM726v1_genomic 101 0 0 0 0 0 1 0 0 0 0 0 104 114