[med-svn] [Git][med-team/lamassemble][master] Update testdata

[Nilesh Patra (@nilesh)]

Nilesh Patra pushed to branch master at Debian Med / lamassemble


Commits:
c27aad26 by Nilesh Patra at 2023-05-09T00:57:24+05:30
Update testdata

- - - - -


4 changed files:

- debian/changelog
- + debian/tests/data/group25-aln.fa
- debian/tests/data/lama-tests.out
- debian/tests/data/lama-tests.sh


Changes:

=====================================
debian/changelog
=====================================
@@ -2,8 +2,9 @@ lamassemble (1.6.0-1) UNRELEASED; urgency=medium
 
   * New upstream version 1.6.0
   * Bump Standards-Version to 4.6.2 (no changes needed)
+  * Update testdata
 
- -- Nilesh Patra <nilesh at debian.org>  Tue, 09 May 2023 00:35:55 +0530
+ -- Nilesh Patra <nilesh at debian.org>  Tue, 09 May 2023 00:56:59 +0530
 
 lamassemble (1.4.2-5) unstable; urgency=medium
 


=====================================
debian/tests/data/group25-aln.fa
=====================================
The diff for this file was not included because it is too large.

=====================================
debian/tests/data/lama-tests.out
=====================================
@@ -6,6 +6,7 @@ Options:
   -h, --help            show this help message and exit
   -a, --alignment       print an alignment, not a consensus
   -c, --consensus       just make a consensus, of already-aligned sequences
+  -f FMT, --format=FMT  output format: fasta/fa or fastq/fq (default=fasta)
   -g G, --gap-max=G     use alignment columns with <= G% gaps (default=50)
   --end                 ... including gaps past the ends of the sequences
   -s S, --seq-min=S     omit consensus flanks with < S sequences (default=1)
@@ -7116,3 +7117,11 @@ ctcatgtttttagatctgtccatagccgtaatctccagaatttagatgtcaagagactcagattaaggccaaacctttta
 tccctcagtgaatggtggataggcattgatataaataatgaatattattcagttcaggagattattttactagaataaatttaggacattgtaatgaataaccaaaggacagacctgtttgaccagttaataaaatatctaatagttaaactctagaacagaaagaatagatcagtggtagtgaaataaaagttgttgtttcataggttgaatttagtttatataaaatcatttagcgatgttatagcaataatatatttaatattatttaactatgttaatatatttagatggtacatttagtttagtattaaaatgattctaaagaatacatttataaccttttcaaatactcaatcataaaatgtcaaaacataagggccagtgcagtggtcatccgtaataaatacagaggctgaggatggagataggaaaagttgaccagcctggcaacataatagaccatctacaaatcacaagcaagaaactggcaaattaaaatatgtgagacttaacagcagactcttggctcaaaatttaatattattaaggtcaatactacagcacaattagtattttcatcaaaacccaatgttacgtttttagaaatatttgtcctaattctagaatatcaggacaatgagtagccaaagactttagagaacgaagttgaggtgtcacattctgatttcaacaattacaaatataaatacaaccagaaagacaaatagatgatggaacgaatagagccagatatagaccatcatgaatatcatcagataatcttcaaacaagttgccattacaaacaacagaataacagaccctttaacaaatagtgttctaaagtgaacatcaaaatggaaatgaaattgacttctgacttgaaccatatacaaaatatcttaaataaattaaacaaatgtaagtagatagctataaactcttaaatatgaggtaaaatcatgacatttgtcttggtaattttaaatatgacattaaaagcaagtaacaagaaaaagcagaaaatggactactcaaatagtagctgacataaaacatttaatgtcacgtaaatgaaaaattacaaatgatatatttgatagaagttaataaccagatgtataacaacttaaactcaaaaactgaacaaccctatttaaaatgggcaaatctcaacagatgtttcacaaagagatatacaatggcaagaggaatttgaaaggatggtcaaattcacgaacttagaaatgagcaaaatcccaatgatattactacaccattagatggccactatcaaacgagaaaataataaatattttcaaggatgtagataaattgatatacttgtcactgagtggtggaaaatataatgcagccattatgaaaatagtacagagttcctagatattaaaatggaattattgtactatcttgttgagtcaaagaatgagtgttgtgaccaactcattataccactgaggctatatgagcaaacagcaaactgttctcatgaatgaggatgttgcgctgacaactgcatctgcaaccagaaggaatgctgagggcagtcatgccccggcacagtgtttcttgtggttatctatagaacatctggacctgttgtacaaagaaaccaattatgtgagcctgtgataaatcaggcgctgactaacattatcttctcctgttgattctacctaatgaatacaaggctgtataagctcaggcccttgttcctaaaaagagccctgacccttctttaaaacagatctttgtcttgtcttcatttctgcgttgtctcttcttcagtcctgaacgacagccaagtggcacctgaacaggacttgaacaagaaaggtctgtgagcagtgaaactgaccagatgaatagaaaccctgatgagtctgcctgcaggatataaggtcagtgtctaagaggtactggagtggaagtttgaatcaggtaacgtggggcgagtttgtctgttgagagcagcattaatgcagttgcttaaagttttacgaaacaatctgatgctcaggttagttctcaacgctgatgctgctgcaggggttatcatgcataaccctcgtttcgtagacaggcgcttgatgtggaaaattgaactggtaggaaggattaaatgggctcatcaaaaggtcttaagtttatccttcctttttctgtttgagtttagtcatactgtctcctgccattatctcattcttattctgccaaccgcaggagccatgttctgaatctcaaatttgaaagaatcttttgtcccaccacaacacccaagaaaataataaacaggaggaggatgaaaattgcatctcacctcagtagcagaaacacctgtccatctccttcagtaacagaaatagagaccccactgcaaaattatgtctgctaccatagctggagagcccttagacattgcactttcactatttctgtaggcctgatcaaataatccacagcagtttatttatgaacatgcctcactagagttttgttgaaggaattaaaagctagtgtagtgaataatggagtacagagcccatttactttaggattgttagaatctgtattttgaactatgtcttccatccttgatgtaaagcatttggctcacacttgtttgtctgctagtgcatatctgaaatggaatttaaattggcaagaactgtgtgcacaccaggctagacaaattgtgccggacacagggacattacagaggatatgctgttggcatggccttattcagacctgaatatcaaatgacactcccagacgctgctataagcagcgcactggctgctaaatgcactagacacaattcagaggaaggtccaatacaacttttacatgcatgcaagggtcaaaggagcactatgcacatttctgcatgattacaagaggcagtgaggcatcagattcccataccactgctgcagaaatgctaaccttaactttagctttgagaatgcaacacggattataaatgtcactggctcctgtgagatgtactaaaacttagacattttctcaaacttgtcaagatgtgagaactgagctcattgctctacaatgttagctcaagcaatggctaatttagtagttaacaaatctaaaagggctaagggtcaaacctaaatgggaaaatcttataattgtggaaaatcgacatttcaaaggaatgccatcagaccttgggcaaagggatcttataatgcaatacccctcagcagaaaattcagaaatttgcccttgttgcaataaagaaatcattgactaatcaatgcagttcaaaatttcatcagaatggcactctgtcgggaaccagaaggagcctgacggtcccctcaaacaatgggcatttcctgtcaggccacaaccccatttcaggaggagtctatggaggaacattgattccctttcccaggaacaccagaagcacaggaatagatctctgtcagaatgggttacattagttggagaaacaaacccactaaaattccactggtatttggagaccttgccaacaggatatatgggattaatttggtaaatccatctcaactacaggacattactgtagtcccagagttgttgactgtgattatgaaggagaaattcaagtagtggtaatatcacaagatttgttagttttgaacctggagaatatgtaactcaactactgcttattcctggagttgtttcttctccacataaggagaaatgagagaatcaaggtttgggagtacagctaggaggaaaatttatttatcacaaccatagcatctaatagacccacctgtacagtgcaaattaaaggaaaaatttcatgggcttatggatatggagtgatgtcagtaatatctaaaaacaattggccccatcctggccctgcaattaactcctacatcgctagtggaatagaacagctcaaagtgttcaacagagtgctgaaattttacctgtctcaaaccagatggacagtcatgtactttaaatttattttgcaaatgtaactgttaacctatggggccaagatttacttacagcatgggatataagacttgcaatgaaactattgacaatcaggttcaaaatgttaaagaaaatgggatgtcaggcgaaaaggcttagaaaagtccctacaggaaacactgatcctatatcaatagctgggcaaacagatagaaagggctaggtcatcaaatttctgatgggagtcactgatattctcccatctactgttttaccgctggagtggttgacaaaaacctgtatgggtggatcagtggctatcacaggagaaataacacatccatcagctagtaaagacaaatggatgcaggacatattgaagagtcagttagcacctggaattcatcagtatttgtaattcctaaaagtcaggaaaatgatgactgctacatgatttgagagctattaatgcacattaaaccaatgggtgcattacagcaagtctgccatccccggcagcctttcaggaggctggcctctcaagtaatatatcttaaagattttatttatttttattttactgttacatgagcaggataagcatcgatttgcctttagtgctctgttaatcaaagagcctgtctcattatcaatggaaagtctaccccaaggcatgttaacagcattatatcagcatgttgtaggataggcattaaggtgctctgaatatgtttccacagcctacatccgtcattatatggatgatattcttctgccctcctacagatcaaatttatatcagttattcagataaataaaatgagctttgacttaaatggaatctcaaaatagctccagaaaaggtgcaaacaacctctgataccagtactaggcactattgttactgaaagaagtgtttggcctcagagtagtcctccataggacagattacaaacttgaatgatttcaaaattattagggacattaactggctgtgccca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tggatttggtgattggtggaaggaaggaggtctggaaagtccttgagcatgcagttatctcttcattctacatcatgggttgtatgtcaaattcgggaagttagtacaaaacatttgattgaaatttgggctacaatcttagcaagcttgttctgtgcagactcagccaccttggtcccaaccgttttcagttagttttcttgatatcacaaatggaggagttcagcatttcagaaagttgttcctttcttatctgctatgctgcaaactcaagaatacctgttagtcatttggtttcttactcttagggcacaatttcagtttcagcccattttctctgctatccgctatcctgtaagcccaagaatttagtttatatttaactctttggggtatggtttatctgcagcctccctgcctagtacaaaatctgcccaggattttggaccccaatggggcagagcctgtcactggaagagccatgggatggagcctttatgggtagtggtggaacactggcctcagtaaaatctgtccctaacatgggtctgggcaagaagggtctcatcaactcagtcttcagctgtggtcactgtgggacccaccagacatgtgaggtccccagtctgggagtggggacagtctgagtagtccctgaaggaatagtctctgggtgttctcaaggaccacatactagagctcatttgctctttctgtaacctgagcaaatgaagcccttcctgtactgacagcccaaaattgggaatctgttgtcccttaactaagacatgatctccatgagcacagaagctgctttggaatcaacagatcatttccctgaaccattttctcactcaactggttttatttcttagctgattcaccagccacagtgagctttagtagaccaaagctgtcatgagatttgtttttaagaaactgggcattttgtgtccttgaattatcccaggaggctgatctgaagggtggcctgcctccacacctgtgggtatttctagttgggtgggacaagagactgagaaaaataagacacagagacaaagtatagagaaacaatagtgggcccagggaccggcgatcagcataccaaggacctgcaccagcaccggtctctgagttccctcagttttattgattattattttcattatttcagcaaaaagtaatgtagtaggagagcagggtaataataaggaaagtcagcaaaacatgtgagcaaagaatctatgtcataattaagttcaaggaaggtactatgcctggatgtgcacgtaggccagattatgtttctctcacccaaatatctcagtggagtaaagaataacaaggcagcattgctgcaaacatgtctcgcctcccaccatagggcggttttctcctatctcagaattgaacaaatgtacagtcgggtttatactgagacattcagttcccaggggcaggcaggagacagtggccttcctctatctcaactgcaagaggctttcctttactaatccaccttagcacagacctttacaggtgtcgggctggggacggttaggtctttctatcccacgaggccatatttcagactatcacatgggagaaaccttggacaataccccactttcaagggcagaggtccctgtggcttcacagtgccctggtttattgagactagagaatggtgatgacttttaccaagtatactgcttgtaagcattttgttaacaaggcaagtcctgcacagccctagatcccttaaaccttgatttcatacaacacatgttttgtgagctcagtttgggtcaaagtggctggggcaaagtggctagggcaaagctacaaattaacatctcagcaaagcaattatttaaagtacaggtctttttcaaaatggagtcttatgtctcctttctacatagacacagtaacagtctgattcttcttttcctacatgatcatatagaggtctctggcccttgaccccactgtgcttccaggtgcccagaacagcccatcataggccctttcccttggcaggtggacattgttcatcctcctgaagcaagcatgtgcccatcttggcgcatttgaagacagacctgctgtccaagcccctgttctcatatcctcaggcaggaactcacccttggacagggcagagactcagagaccctggtcggggtgaggactggtctgggcttttgttcctggtgacagaatggtcaccttgctggctttgagacccaggcaggaccctggtttagggtgttctctgaagttttcaaatgcagtgtaatatcttttcttgcaggatggacatggagcaggatgtggacaccctcttacccagaatcaagggacattattgccaagtatggggacacagggcaggctgctcgttcgaagggcagggatcacactcttctgtgctgtagtcagggtcctaggccacgggacacagggcaggagtggctgcacacaaccccatgcctctgcattcacagtggcccctcacatgacctctgcattgcagggatgccaggccagggtgccagtggacataaggcaggaagattttaatctgaaaatcaccatattccagattctgtagtgtgtcttcgtctcctgagccccaccccagcaatctcgtctcagcaataggtttattttgaaaaggcctctctgaggaaggacatgtctcaagtccacctccttccaggattgaactcctcccaggtgccgcaaccagtcgtcagtgttagccaggctgagtatcccaatgtggacccagaagcaagtggagacgaaatatggtcagccctaggtctcaaggggacagcgcagtcagtctcaagtcaacaagaggggccagcctggggccagcctgctccttggagcctgcctggagatctgcagggtctagccatgggacaaagggtgctggaatggtctgtgggtagtgtccagcaggtctctgagagctaggagcccagccctgccatcccacaggaggtacagggcagccaagctggccctggaggaggatggtcagcctgcgggcatctcatgggaggcaaggaggcaggagcttgcgccaggtgatctaaccaagggtttcaggtaggggatctgaggtctggtggaggcccagtataaagtctgtcctgtagggtcattggaggagctggtagtggtgacaatggaactgatgactttgggatgcatctgatggagccagcctgtgaatggatggagctggaagggcaggagatttggtgaagccaaggcagggactcacctgggaccctcagcagagctttagtcagtcccaaagctctggaacctctgagaccagctcctgctggctggtcagcaccatggccagaggaagactggggactgatcagaaagaacagtggaggaggacagccaggtgcccgtgtcgggctgctgcaacaggaggagaagctgttgctgaagacctaataccatctgggctggggactgggttcgggccattccggttgcctgtgaaccctcagtcaccctattgccctggtgtccaccagcagtgctggcagcccagtaagtgacagaaggtgtggatgatctaagtttgctcagacgtctgacaaacaggataaagaggtctaaagacggaacagaccatggtttccaggcagacaggtaagtagtaacaggaagggtggtagccgtgtacgggaggcggttagatagtcagaccgcgatggcgggccatcagacaggctcaggccaacacactgggcagttctcaggccagttcctgcacctgaggatgtggtcacttctggggtcttctccagacacaaacctgggcagcacggcccaccaagacaagttcttgttcccgaggacgctacaattcgggcaacccatggtacaccatgaatccagcacctgcagcctattctctgttattcagctcttatcagccagcaggctgagacctgggtggatggatgcagtcctcctgggcctgctcaggggatggcccctggcag
 >lamassembled
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+>lamassembled
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+ at lamassembled
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++
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+>lamassembled
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=====================================
debian/tests/data/lama-tests.sh
=====================================
@@ -18,5 +18,7 @@ fa=group25.fa
     lamassemble -z10 -d100 $mat $fa
     lamassemble --end -z20 $mat $fa
     lamassemble -s2 -z20 $mat $fa
-} 2>&1 |
-    diff -u lama-tests.out -
+    lamassemble -c $mat group25-aln.fa
+    lamassemble -c -fFASTQ $mat group25-aln.fa
+    lamassemble PromethION-2019 $fa
+} 2>&1 | diff -u lama-tests.out -



View it on GitLab: https://salsa.debian.org/med-team/lamassemble/-/commit/c27aad26a1c46bcff6eb1fd5193fa0538b01e587

-- 
View it on GitLab: https://salsa.debian.org/med-team/lamassemble/-/commit/c27aad26a1c46bcff6eb1fd5193fa0538b01e587
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