[med-svn] [Git][med-team/mapsembler2][master] 3 commits: Add reference data for autopkgtests
Pranav Ballaney
gitlab at salsa.debian.org
Sat Jun 13 01:15:12 BST 2020
Pranav Ballaney pushed to branch master at Debian Med / mapsembler2
Commits:
3aac8f7a by Pranav Ballaney at 2020-06-13T05:42:32+05:30
Add reference data for autopkgtests
- - - - -
97bd9a13 by Pranav Ballaney at 2020-06-13T05:43:10+05:30
Add autopkgtests
- - - - -
eddadecf by Pranav Ballaney at 2020-06-13T05:43:42+05:30
Install docs
- - - - -
12 changed files:
- + debian/README.test
- debian/changelog
- debian/docs
- + debian/examples
- + debian/tests/control
- + debian/tests/ref/README.test_data
- + debian/tests/ref/ref-mapsembler2_extremities.out.fa
- + debian/tests/ref/ref-reads1_coherent_k_31_c_5_t_1.fasta
- + debian/tests/ref/ref-reads1_uncoherent_k_31_c_5_t_1.fasta
- + debian/tests/ref/ref-res_k_31_c_5_t_3_modified_and_covered.json
- + debian/tests/ref/ref-res_mapsembler_k_31_c_2_t_1.fasta
- + debian/tests/run-unit-test
Changes:
=====================================
debian/README.test
=====================================
@@ -0,0 +1,8 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by running the provided test:
+
+ sh run-unit-test
+
+in order to confirm its integrity.
=====================================
debian/changelog
=====================================
@@ -1,3 +1,15 @@
+mapsembler2 (2.2.4+dfsg-4) UNRELEASED; urgency=medium
+
+ [ Steffen Möller ]
+ * Added ref to conda
+
+ [ Pranav Ballaney ]
+ * Add reference data for autopkgtests
+ * Add autopkgtests
+ * Install docs
+
+ -- Pranav Ballaney <ballaneypranav at gmail.com> Sat, 13 Jun 2020 05:43:14 +0530
+
mapsembler2 (2.2.4+dfsg-3) unstable; urgency=medium
* Provide mapsembler2_extend as symlink to mapsembler_extend since
=====================================
debian/docs
=====================================
@@ -0,0 +1,5 @@
+EXAMPLE.md
+README.md
+debian/README*
+debian/tests/run-unit-test
+debian/tests/ref/README*
\ No newline at end of file
=====================================
debian/examples
=====================================
@@ -0,0 +1,2 @@
+sample_example/*
+debian/tests/ref/*
\ No newline at end of file
=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
=====================================
debian/tests/ref/README.test_data
=====================================
@@ -0,0 +1,3 @@
+Reference files in this directory were obtained by running mapsembler2
+as done in run-unit-test on files provided in the sample_example folder
+that comes with this package.
=====================================
debian/tests/ref/ref-mapsembler2_extremities.out.fa
=====================================
@@ -0,0 +1,18 @@
+>ligne|C1_38|C2_40|
+GCTTCCATTGACTCAATGTAGTCACGCGGATGATGACGGAACTGGTTATTCGGGGCATCACAAAATTGCC
+>extrem_left|id_0|abundance_57
+GCTTCCATTGACTCAATGTA
+>extrem_right|id_0|abundance_61
+CGGGGCATCACAAAATTGCC
+>left_extension_0|C1_969|C2_950|
+TCCGGCCTACAAAATCGCAGCGTGTAGGCCAGATAAGACGCGTCAGCGTCGCATCAGGCGTTACATACCGGATGCGGCTACTTAGCGACGAAACCCGTAATACACTTCGTTCCAGCGCAGCGCGTCTTTAAACGCTGGCAGGCGTGTGTCGTTATCAATCACCGTGATTTCAATGTCGTGCATCTCGGCGAATTGGCGCATATCGTTGAGGTTCAGTGCATGGCTGAAGACGGTATGGTGCGCGCCACCAGCGAGGATCCACGCTTCGGAAGCAGTTGGCAGATCCGGTTGCGCTTTCCACAGCGCATTCGCCACCGGCAGTTTCGGCAGGGAGTGCGGTGTTTTCACCGTGTCGATGCAGTTAACCAGTAGACGGTAACGATCGCCGAGATCAATCAAGCTGGCGACAATCGCTGGGCCGGTTTGGGTATTGAAGATCAGGCGGGCAGGATCGTCCTTACCACCAATACCGAGATGCTGAACGTCGAGGATCGGTTTCTCTTCTGCGGCGATCGACGGGCAGACTTCCAGCATATGGGAGCCGAGCACCAGGTCATTACCTTTCTCGAAGTGATAGGTGTAGTCCTCCATAAAGGAGGTGCCGCCCTGCAGACCGGTTGACATCACCTTCATGATGCGAAGCAGGGCGGCAGTTTTCCAGTCGCCTTCGCCCGCAAAGCCGTAACCCTGCTGCATCAGACGCTGTACGGCCAGACCAGGAAGCTGTTTCAGACCGTGCAAATCTTCAAAGGTGGTGGTGAACGCGTGGAAGCCACCTTGTTCCAGGAAACGCTTCATCCCCAGCTCAATACGCGCCGCTTCCAGCACGTTCTGTCGTTTTTTGCCGTGGATTTGTGTGGCAGGCGTCATGGTGTAGCAGCTTTCGTACTCATCGACCAGCGCGTTAACATCGCCGTCGCTGATGGAGTTCACCACCTGCACCAGATCGCCAACCGCCCAGGTATTGACGGAGAAACCGAACTTGATCTGTGCGGCAACTTTATCGCCATCGGTGACCGCCACTTCACGCATGTTATCGCCAAATCGGCAGACTTTCAGATGACGGGTATCCTGTTTAGAGACCGCCTGACGCATCCAGGAGCCGATACGCTCATGGGCTTGTTTATCCTGCCAGTGACCGGTAACCACGGCATGTTGCTGACGCATACGCGCGCCAATGAAGCCGAACTCGCGACCGCCATGTGCAGTCTGGTTCAGGTTCATAAAGTCCATATCGATACTGTCCCACGGCAGCGCCGCGTTGAACTGGGTGTGGAATTGCAGCAACGGTTTGTTGAGCATGGTCAGGCCGTTGATCCACATTTTGGCCGGGGAGAAGGTGTGCAGCCACACCACCAGACCAGCGCAACGATCGTCGTAATTCGCGTCGCGGCAAATAGCGGTGATTTCATCCGGCGTGGTGCCCAGCGGTTTCAACACCAGTTTGCAGGGCAGTTTCGCTTCCGTATTCAGCGCATTAACGACGTGCTCGGCATGTTGGGTGACCTGACGCAGGGTTTCCGGGCCATACAGATGCTGGCTGCCAATGACAAACCACACTTCATAATTATCAAAAATCGTCATTATCGTGTCCTTATAGAGTCGCAACGGCCTGGGCAGCCTGTGCCGGGGCGGAAGTTGGAAGATAGTGTTGTTCGGCGCTCATCGCCCATTGCTGATAGCGGCGATAAAGCTGTTCAAAGCGTTGTGCCTGCTCGCTGCACGGTTGCAGGGTTTTCTCTACCGCACTGGCCATTTTTTGCTGAGCTGATGGGATGTCTGCGTGCACTTTCGCGGCGACGGCAGCAAAAATCGCCGCACCGAGCGCACAGCACTGGTCAGAGGCAACAATTTGCAGCGGGCGATTCAGCACGTCGCAGCAGGCCTGCATAATGACCTGGTTTTTCCGCGCGATGCCGCCCAGTGCCATCACGTTATTAACGGCGATCCCCTGATCGGTAAAGCACTCCATGATTGCGCGTGCGCCAAAGGCGGTGGCAGCAATCAAACCGCCGAACAGCAGCGGAGCGTCGGTAGCGAGGTTAAGATCGGTAATCACCCCTTTCAGGCGTTGGTTAGCGTTCGGTGTGCGGCGGCCGTTAAACCAGTCGAGCACCACCGGCAGGTGATCCAGAGACGGATTTTTGGCCCATGCTTCGGTCAGCGCCGGAAGCAGTTGTTTCTGGCTGGCGTTGATTTGCGTTTTCAGTTCCGGATGCTGGGCGGCAAGCTGTTCCAGCGGCCAGCCGAGTACGCGACCAAACCAGGCGTAGATATCACCAAACGCCGATTGGCCTGCTTCCAGACCGATAAATCCAGGCACCACGCTGCCATCAACCTGACCGCAAATACCTTTAACTGCCCGCTCGCCAACGCTCTGTTTGTCGGCAATCAGAATGTCGCAGGTGGAAGTACCGATAACTTTTACCAGTGCGTTAGGCTGTGCGCCTGCGCCAACTGCGCCCATATGGCAGTCAAACGCGCCGCCGGAAATCACCACGCTTTCAGGCAGGCCGAGACGCTGCGCCCATTCCGGGCATAAGGTGCCCACCGGAATATCGGCAGTCCAAGTGTCAGTGAACAGCGGGGAAGGCAAATGGCGATTGAGGATCGGGTCCAGCTCATCAAAGAAACTGGCTGGCGGCAGGCCGCCCCAGCTTTCGTGCCACAGAGATTTATGCCCGGCGCTGCAACGTCCGCGACGAATATCCTGCGGGCGGGTGGTACCGGAAAGCAGAGCTGGCACCCAGTCGCACAGCTCAATCCACGATGCGGCAGATTGCGCCACGGCGCTGTCCTGGCGAGTCACATGCAGGATTTTTGCCCAGAACCATTCGCTGGAATAAATACCACCAATGTAGCGGGAGTAGTCAACGTTGCCCGGCGCGTGGCACAAACGGGTAATCTCTTCCGCTTCTTCAACCGCAGTGTGGTCTTTCCACAATACGAACATCGCGTTCGGGTTTTCGGCAAACTCCGGGCGCAGCGCCAGCACGTTTCCGTCGGCATCAATCGGTGCGGGCGTCGAGCCGGTACTGTCAACGCCAATCCCGACCACAGCTGCGCGCTGTTCGACGCTAAGCTCTGCAAGCACGGTTTTCAGTGCCGCTTCCATTGACTCAATGTAGTCACGCGGA
+>extrem_left|id_0|abundance_150
+TCCGGCCTACAAAATCGCAG
+>extrem_right|id_0|abundance_58
+ACTCAATGTAGTCACGCGGA
+>right_extension_0|C1_104|C2_100|
+ACTGGTTATTCGGGGCATCACAAAATTGCCCTTTCTGCCAACGGGGATACCACTCTACGCTGGTGGCGATCTCTTCACCGGTAGCGCAGTCCACCGCCAAAGCTCGCACAGAATCACTGCCAAAATCGAGGCCAATTGCAATCGCCATCGTTTCACTCCATCCAAAAAAACGGGTATGGAGAAACAGTAGAGAGTTGCGATAAAAAGCGTCAGGTAGGATCCGCTAATCTTATGGATAAA
+>extrem_left|id_0|abundance_63
+ACTGGTTATTCGGGGCATCA
+>extrem_right|id_0|abundance_63
+CCGCTAATCTTATGGATAAA
=====================================
debian/tests/ref/ref-reads1_coherent_k_31_c_5_t_1.fasta
=====================================
@@ -0,0 +1,6 @@
+>ligne|C1_38|C2_40|
+GCTTCCATTGACTCAATGTAGTCACGCGGATGATGACGGAACTGGTTATTCGGGGCATCACAAAATTGCC
+>left_extension_0|C1_969|C2_950|
+TCCGGCCTACAAAATCGCAGCGTGTAGGCCAGATAAGACGCGTCAGCGTCGCATCAGGCGTTACATACCGGATGCGGCTACTTAGCGACGAAACCCGTAATACACTTCGTTCCAGCGCAGCGCGTCTTTAAACGCTGGCAGGCGTGTGTCGTTATCAATCACCGTGATTTCAATGTCGTGCATCTCGGCGAATTGGCGCATATCGTTGAGGTTCAGTGCATGGCTGAAGACGGTATGGTGCGCGCCACCAGCGAGGATCCACGCTTCGGAAGCAGTTGGCAGATCCGGTTGCGCTTTCCACAGCGCATTCGCCACCGGCAGTTTCGGCAGGGAGTGCGGTGTTTTCACCGTGTCGATGCAGTTAACCAGTAGACGGTAACGATCGCCGAGATCAATCAAGCTGGCGACAATCGCTGGGCCGGTTTGGGTATTGAAGATCAGGCGGGCAGGATCGTCCTTACCACCAATACCGAGATGCTGAACGTCGAGGATCGGTTTCTCTTCTGCGGCGATCGACGGGCAGACTTCCAGCATATGGGAGCCGAGCACCAGGTCATTACCTTTCTCGAAGTGATAGGTGTAGTCCTCCATAAAGGAGGTGCCGCCCTGCAGACCGGTTGACATCACCTTCATGATGCGAAGCAGGGCGGCAGTTTTCCAGTCGCCTTCGCCCGCAAAGCCGTAACCCTGCTGCATCAGACGCTGTACGGCCAGACCAGGAAGCTGTTTCAGACCGTGCAAATCTTCAAAGGTGGTGGTGAACGCGTGGAAGCCACCTTGTTCCAGGAAACGCTTCATCCCCAGCTCAATACGCGCCGCTTCCAGCACGTTCTGTCGTTTTTTGCCGTGGATTTGTGTGGCAGGCGTCATGGTGTAGCAGCTTTCGTACTCATCGACCAGCGCGTTAACATCGCCGTCGCTGATGGAGTTCACCACCTGCACCAGATCGCCAACCGCCCAGGTATTGACGGAGAAACCGAACTTGATCTGTGCGGCAACTTTATCGCCATCGGTGACCGCCACTTCACGCATGTTATCGCCAAATCGGCAGACTTTCAGATGACGGGTATCCTGTTTAGAGACCGCCTGACGCATCCAGGAGCCGATACGCTCATGGGCTTGTTTATCCTGCCAGTGACCGGTAACCACGGCATGTTGCTGACGCATACGCGCGCCAATGAAGCCGAACTCGCGACCGCCATGTGCAGTCTGGTTCAGGTTCATAAAGTCCATATCGATACTGTCCCACGGCAGCGCCGCGTTGAACTGGGTGTGGAATTGCAGCAACGGTTTGTTGAGCATGGTCAGGCCGTTGATCCACATTTTGGCCGGGGAGAAGGTGTGCAGCCACACCACCAGACCAGCGCAACGATCGTCGTAATTCGCGTCGCGGCAAATAGCGGTGATTTCATCCGGCGTGGTGCCCAGCGGTTTCAACACCAGTTTGCAGGGCAGTTTCGCTTCCGTATTCAGCGCATTAACGACGTGCTCGGCATGTTGGGTGACCTGACGCAGGGTTTCCGGGCCATACAGATGCTGGCTGCCAATGACAAACCACACTTCATAATTATCAAAAATCGTCATTATCGTGTCCTTATAGAGTCGCAACGGCCTGGGCAGCCTGTGCCGGGGCGGAAGTTGGAAGATAGTGTTGTTCGGCGCTCATCGCCCATTGCTGATAGCGGCGATAAAGCTGTTCAAAGCGTTGTGCCTGCTCGCTGCACGGTTGCAGGGTTTTCTCTACCGCACTGGCCATTTTTTGCTGAGCTGATGGGATGTCTGCGTGCACTTTCGCGGCGACGGCAGCAAAAATCGCCGCACCGAGCGCACAGCACTGGTCAGAGGCAACAATTTGCAGCGGGCGATTCAGCACGTCGCAGCAGGCCTGCATAATGACCTGGTTTTTCCGCGCGATGCCGCCCAGTGCCATCACGTTATTAACGGCGATCCCCTGATCGGTAAAGCACTCCATGATTGCGCGTGCGCCAAAGGCGGTGGCAGCAATCAAACCGCCGAACAGCAGCGGAGCGTCGGTAGCGAGGTTAAGATCGGTAATCACCCCTTTCAGGCGTTGGTTAGCGTTCGGTGTGCGGCGGCCGTTAAACCAGTCGAGCACCACCGGCAGGTGATCCAGAGACGGATTTTTGGCCCATGCTTCGGTCAGCGCCGGAAGCAGTTGTTTCTGGCTGGCGTTGATTTGCGTTTTCAGTTCCGGATGCTGGGCGGCAAGCTGTTCCAGCGGCCAGCCGAGTACGCGACCAAACCAGGCGTAGATATCACCAAACGCCGATTGGCCTGCTTCCAGACCGATAAATCCAGGCACCACGCTGCCATCAACCTGACCGCAAATACCTTTAACTGCCCGCTCGCCAACGCTCTGTTTGTCGGCAATCAGAATGTCGCAGGTGGAAGTACCGATAACTTTTACCAGTGCGTTAGGCTGTGCGCCTGCGCCAACTGCGCCCATATGGCAGTCAAACGCGCCGCCGGAAATCACCACGCTTTCAGGCAGGCCGAGACGCTGCGCCCATTCCGGGCATAAGGTGCCCACCGGAATATCGGCAGTCCAAGTGTCAGTGAACAGCGGGGAAGGCAAATGGCGATTGAGGATCGGGTCCAGCTCATCAAAGAAACTGGCTGGCGGCAGGCCGCCCCAGCTTTCGTGCCACAGAGATTTATGCCCGGCGCTGCAACGTCCGCGACGAATATCCTGCGGGCGGGTGGTACCGGAAAGCAGAGCTGGCACCCAGTCGCACAGCTCAATCCACGATGCGGCAGATTGCGCCACGGCGCTGTCCTGGCGAGTCACATGCAGGATTTTTGCCCAGAACCATTCGCTGGAATAAATACCACCAATGTAGCGGGAGTAGTCAACGTTGCCCGGCGCGTGGCACAAACGGGTAATCTCTTCCGCTTCTTCAACCGCAGTGTGGTCTTTCCACAATACGAACATCGCGTTCGGGTTTTCGGCAAACTCCGGGCGCAGCGCCAGCACGTTTCCGTCGGCATCAATCGGTGCGGGCGTCGAGCCGGTACTGTCAACGCCAATCCCGACCACAGCTGCGCGCTGTTCGACGCTAAGCTCTGCAAGCACGGTTTTCAGTGCCGCTTCCATTGACTCAATGTAGTCACGCGGA
+>right_extension_0|C1_104|C2_100|
+ACTGGTTATTCGGGGCATCACAAAATTGCCCTTTCTGCCAACGGGGATACCACTCTACGCTGGTGGCGATCTCTTCACCGGTAGCGCAGTCCACCGCCAAAGCTCGCACAGAATCACTGCCAAAATCGAGGCCAATTGCAATCGCCATCGTTTCACTCCATCCAAAAAAACGGGTATGGAGAAACAGTAGAGAGTTGCGATAAAAAGCGTCAGGTAGGATCCGCTAATCTTATGGATAAA
=====================================
debian/tests/ref/ref-reads1_uncoherent_k_31_c_5_t_1.fasta
=====================================
=====================================
debian/tests/ref/ref-res_k_31_c_5_t_3_modified_and_covered.json
=====================================
@@ -0,0 +1,531 @@
+{
+"Starter_0":{"data":{"id":"S0", "sequence":"GCTTCCATTGACTCAATGTAGTCACGCGGATGATGACGGAACTGGTTATTCGGGGCATCACAAAATTGCC", "length":70,
+"extremGraphs":[
+
+
+{"data":{"id":"k0", "sequence":"ATCCGCGTGACTACATTGAGTCAATGGAAGC", "direction":"LEFT", "type":"original",
+"nodes": [
+{ "data": { "id": "n0", "sequence": "TCCGCGTGACTACATTGAGTCAATGGAAGCGGCACTGAAAACCGTGCTTGCAGAGCTTAGCGTCGAACAGCGCGCAGCTGTGGTCGGGATTGGCGTTGACAGTACCGGCTCGACGCCCGCACCGATTGATGCCGACGGAAACGTGCTGGCGCTGCGCCCGGAGTTTGCCGAAAACCCGAACGCGATGTTCGTATTGTGGAAAGACCACACTGCGGTTGAAGAAGCGGAAGAGATTACCCGTTTGTGCCACGCGCCGGGCAACGTTGACTACTCCCGCTACATTGGTGGTATTTATTCCAGCGAATGGTTCTGGGCAAAAATCCTGCATGTGACTCGCCAGGACAGCGCCGTGGCGCAATCTGCCGCATCGTGGATTGAGCTGTGCGACTGGGTGCCAGCTCTGCTTTCCGGTACCACCCGCCCGCAGGATATTCGTCGCGGACGTTGCAGCGCCGGGCATAAATCTCTGTGGCACGAAAGCTGGGGCGGCCTGCCGCCAGCCAGTTTCTTTGATGAGCTGGACCCGATCCTCAATCGCCATTTGCCTTCCCCGCTGTTCACTGACACTTGGACTGCCGATATTCCGGTGGGCACCTTATGCCCGGAATGGGCGCAGCGTCTCGGCCTGCCTGAAAGCGTGGTGATTTCCGGCGGCGCGTTTGACTGCCATATGGGCGCAGTTGGCGCAGGCGCACAGCCTAACGCACTGGTAAAAGTTATCGGTACTTCCACCTGCGACATTCTGATTGCCGACAAACAGAGCGTTGGCGAGCGGGCAGTTAAAGGTATTTGCGGTCAGGTTGATGGCAGCGTGGTGCCTGGATTTATCGGTCTGGAAGCAGGCCAATCGGCGTTTGGTGATATCTACGCCTGGTTTGGTCGCGTACTCGGCTGGCCGCTGGAACAGCTTGCCGCCCAGCATCCGGAACTGAAAACGCAAATCAACGCCAGCCAGAAACAACTGCTTCCGGCGCTGACCGAAGCATGGGCCAAAAATCCGTCTCTGGATCACCTGCCGGTGGTGCTCGACTGGTTTAACGGCCGCCGCACACCGAACGCTAACCAACGCCTGAAAGGGGTGATTACCGATCTTAACCTCGCTACCGACGCTCCGCTGCTGTTCGGCGGTTTGATTGCTGCCACCGCCTTTGGCGCACGCGCAATCATGGAGTGCTTTACCGATCAGGGGATCGCCGTTAATAACGTGATGGCACTGGGCGGCATCGCGCGGAAAAACCAGGTCATTATGCAGGCCTGCTGCGACGTGCTGAATCGCCCGCTGCAAATTGTTGCCTCTGACCAGTGCTGTGCGCTCGGTGCGGCGATTTTTGCTGCCGTCGCCGCGAAAGTGCACGCAGACATCCCATCAGCTCAGCAAAAAATGGCCAGTGCGGTAGAGAAAACCCTGCAACCGTGCAGCGAGCAGGCACAACGCTTTGAACAGCTTTATCGCCGCTATCAGCAATGGGCGATGAGCGCCGAACAACACTATCTTCCAACTTCCGCCCCGGCACAGGCTGCCCAGGCCGTTGCGACTCTATAAGGACACGATAATGACGATTTTTGATAATTATGAAGTGTGGTTTGTCATTGGCAGCCAGCATCTGTATGGCCCGGAAACCCTGCGTCAGGTCACCCAACATGCCGAGCACGTCGTTAATGCGCTGAATACGGAAGCGAAACTGCCCTGCAAACTGGTGTTGAAACCGCTGGGCACCACGCCGGATGAAATCACCGCTATTTGCCGCGACGCGAATTACGACGATCGTTGCGCTGGTCTGGTGGTGTGGCTGCACACCTTCTCCCCGGCCAAAATGTGGATCAACGGCCTGACCATGCTCAACAAACCGTTGCTGCAATTCCACACCCAGTTCAACGCGGCGCTGCCGTGGGACAGTATCGATATGGACTTTATGAACCTGAACCAGACTGCACATGGCGGTCGCGAGTTCGGCTTCATTGGCGCGCGTATGCGTCAGCAACATGCCGTGGTTACCGGTCACTGGCAGGATAAACAAGCCCATGAGCGTATCGGCTCCTGGATGCGTCAGGCGGTCTCTAAACAGGATACCCGTCATCTGAAAGTCTGCCGATTTGGCGATAACATGCGTGAAGTGGCGGTCACCGATGGCGATAAAGTTGCCGCACAGATCAAGTTCGGTTTCTCCGTCAATACCTGGGCGGTTGGCGATCTGGTGCAGGTGGTGAACTCCATCAGCGACGGCGATGTTAACGCGCTGGTCGATGAGTACGAAAGCTGCTACACCATGACGCCTGCCACACAAATCCACGGCAAAAAACGACAGAACGTGCTGGAAGCGGCGCGTATTGAGCTGGGGATGAAGCGTTTCCTGGAACAAGGTGGCTTCCACGCGTTCACCACCACCTTTGAAGATTTGCACGGTCTGAAACAGCTTCCTGGTCTGGCCGTACAGCGTCTGATGCAGCAGGGTTACGGCTTTGCGGGCGAAGGCGACTGGAAAACTGCCGCCCTGCTTCGCATCATGAAGGTGATGTCAACCGGTCTGCAGGGCGGCACCTCCTTTATGGAGGACTACACCTATCACTTCGAGAAAGGTAATGACCTGGTGCTCGGCTCCCATATGCTGGAAGTCTGCCCGTCGATCGCCGCAGAAGAGAAACCGATCCTCGACGTTCAGCATCTCGGTATTGGTGGTAAGGACGATCCTGCCCGCCTGATCTTCAATACCCAAACCGGCCCAGCGATTGTCGCCAGCTTGATTGATCTCGGCGATCGTTACCGTCTACTGGTTAACTGCATCGACACGGTGAAAACACCGCACTCCCTGCCGAAACTGCCGGTGGCGAATGCGCTGTGGAAAGCGCAACCGGATCTGCCAACTGCTTCCGAAGCGTGGATCCTCGCTGGTGGCGCGCACCATACCGTCTTCAGCCATGCACTGAACCTCAACGATATGCGCCAATTCGCCGAGATGCACGACATTGAAATCACGGTGATTGATAACGACACACGCCTGCCAGCGTTTAAAGACGCGCTGCGCTGGAACGAAGTGTATTACGGGTTTCGTCGCTAAGTAGCCGCATCCGGTATGTAACGCCTGATGCGACGCTGACGCGTCTTATCTGGCCTACACGCTGCGATTTTGTAGGCCGGA", "coverage":[
+ {
+ "id":"file_1",
+ "avg_coverage": 29.73
+ },
+ {
+ "id":"file_2",
+ "avg_coverage": 29.34
+ }
+]
+, "length": 3137 }},
+{ "data": { "id": "n1", "sequence": "GGCCTACACGCTGCGATTTTGTAGGCCGGATAAGCAAA", "coverage":[
+ {
+ "id":"file_1",
+ "avg_coverage": 42.66
+ },
+ {
+ "id":"file_2",
+ "avg_coverage": 33.71
+ }
+]
+, "length": 38 }},
+{ "data": { "id": "n2", "sequence": "CGCTGCGATTTTGTAGGCCGGATAAGCAAAGCGCATCCGGCA", "coverage":[
+ {
+ "id":"file_1",
+ "avg_coverage": 71.48
+ },
+ {
+ "id":"file_2",
+ "avg_coverage": 59.07
+ }
+]
+, "length": 42 }},
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+{ "data": { "id": "n13", "sequence": "ATTTCAGCGACCTGTTTGGGCAAATCATTAACGCCGGGCAAGGGGAAGGGCGCTATTCGGAGCTGCTGGCGATAAATCTGCTTGAGCAATTGTTACTGCGGCGCATGGAAGCGATTAACGAGTCGCTCCATCCACCGATGGATAATCGGGTACGCGAGGCTTGTCAGTACATCAGCGATCACCTGGCAGACAGCAATTTTGATATCGCCAGCGTCGCACAGCATGTTTGCTTGTCGCCGTCGCGTCTGTCACATCTTTTCCGCCAGCAGTTAGGGATTAGCGTCTTAAGCTGGCGCGAGGACCAACGCATTAGTCAGGCGAAGCTGCTTTTGAGCACTACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGACGATCAACTCTATTTCTCGCGAGTATTTAAAAAATGCACCGGGGCCAGCCCGAGCGAGTTTCGTGCCGGTTGTGAAGAAAAAGTGAATGATGTAGCCGTCAAGTTGTCATAATTGGTAACGAATCAGACAATTGACGGCTTGACGGAGTAGCATAGGGTTTGCAGAATCCCTGCTTCGTCCATTTGACAGGCACATTATGCAAGCATTGCTGGAACACTTTATTACCCAATCCACCGTGTATTCATTGATGGCGGTGGTGTTGGTGGCCTTTCTGGAGTCGCTGGCGCTGGTCGGTTTGATTCTACCCGGTACGGTGCTGATGGCGGGGCTGGGAGCGCTGATTGGCAGCGGCGAGTTAAGTTTCTGGCACGCCTGGCTGGCAGGGATTATTGGCTGCTTGATGGGCGACTGGATTTCTTTCTGGCTGGGTTGGCGTTTTAAAAAGCCGTTGCATCGCTGGTCATTTCTGAAGAAAAACAAAGCACTACTTGATAAAACTGAACATGCGTTGCATCAACACAGCATGTTCACCATTCTGGTCGGTCGTTTTGTTGGCCCGACGCGTCCGCTGGTGCCAATGGTGGCGGGAATGCTGGATCTGCCGGTGGCTAAATTTATTACGCCGAATATTATCGGCTGCCTGCTGTGGCCGCCGTTTTACTTCCTGCCAGGGATTCTGGCGGGCGCGGCGATCGATATTCCTGCCGGAATGCAGAGCGGTGAGTTTAAATGGTTGCTGCTGGCAACAGCGGTGTTTTTGTGGGTTGGTGGCTGGCTGTGCTGGCGGTTATGGCGCAGCGGTAAAGCGACTGACCGTTTGAGTCATTATTTGTCCCGCGGTCGTTTGTTGTGGCTGACGCCGTTGATTTCTGCCATCGGCGTGGTGGCGCTGGTGGTGTTAATTCGCCACCCGTTGATGCCGGTGTATATCGATATTTTGCGTAAAGTGGTTGGGGTTTAGGAGATAGTCTTGTGCGGGTTGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAACGCACTACCCGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACAGTGCATACTAACCCGTAATCCCCAATAGTGCCGAAGCACTCGCCTTACCGCTCAACAACTCATTGGTCATACCCTGCCAGGCGATGCGCCCGTCGGCGACTACTACCGAGCGCGTGGCGATCCGCGCCGCATCTTCCACGCTGTGCGACACCATCAATAGCGTCATTTTTTGCTGCTGGCAGCTCGTGCTCACCAGCGTCAACATCTCCTGACGTAACGCCGGATCGAGCGCAGAGAACGGTTCATCGAGCAATAAAATCGGCTGTTCGCGTACCAGACAACGCGCTAACGCCACTCGCTGTCGCTGACCGCCGGAAAGCTCGCCCGGTAACCGCGCCATTAAATTATCAATCCCCATCTGGCGGGCGATAGCGTGCATTTTCCCCTGCTGTACCGCGTTCAGTTTCAATCCCGGATTTAGCCCCAGCCCGATGTTCTGTGCGACCGTCAGGTGGCTGAACAGGTTGTTCTCCTGAAACAGCATCGACACCGGACGGCGTGACGGCGGCATAGTTGTGTGATCTACGCCATCGATAGTCAGCGAACCGCTGGCTGGCGTCAGAAAACCGGCGATCAAATTCAGCAGGGTACTTTTACCCGCGCCGCTTGGCCCGAGGATCGCCACCTGCTCGCCGCGTTCCACCGTTAAGCTAAAACGCATCGGCAAATGGTGGTAAAGCCAGGTGATATCAGTCAGTTTTAACATTTCGCCCCGGTAGTTTTTCAATCACGGTAAACAGCAGAAAACAGAGCAGCAGCAGAATTAACGCGGTGACCGCACCGTCCTGGCTGCGATAGGAGCCAATTTGCTGGTAGAGATAAAACGGCAGGGTGCGGAAATCATCGTTACCGAACAACGCCACCACGCCAAAATCACCAATCGACAGCACGCATGCAAAGGCCAGCGCCTGCGCCAGTGGACGTTTCAGGGCGCGCAGCTCCACCACTTTTAAGCGTGACCAGCCTTCAATCCCCAGCGACTGACATAACATGCTGTAGCGGGCGGTGATATCGCGCATCGGGTTTTCCAGCACTTTCAGCGCATAAGGGATCGCCATTAACGCATTGGTGAAAATCACAATGCCGTCAGCAGATTGTGGCAGGCCGATAGTGTTGTTGAGCAGTAAAAAGAAGCCGGTAGCCAGCACAATCCCCGGCATGGCGAGGATCAACATGCCGCTCATCTCCAGCACCTGACCCGCCAGCATTTTCTGCCGCGCCCGCAGTTCGCGACTGCTCCATAGCAGCATCATGGTCAGCACTACGCACAATACACCTGCCGCCAGCGCAATACGCAACGAGGTCCACAGCGCCTGCCACAGCACCGGTTGTGCCAGCACTTCCGGCAACTGGCGATTTACCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGTCCGGGTCGCGCCAGCCTTGCAGCAGCGTGGTGCCGGGCGCAATGGCCTTACTCAATCGCTGACTCAACAGCACCAGCCCGAGGCAGCACACCATCTGGAGCAGCGCCAGCATTGCCGCGCGGGCAGGATCGTAGTCGTAACTCAGCGCCTGATAGATTGCCAGCTCGATAGTGGTCGCCTGCGGACCGCCCCCCAGCGATAGCACGGTGGCGAAGCTGGCGAAACAGAGCATAAAGATAAGCGCAGCAACCGGCGGGATTTGTCGCCGTAACCACGGCCATTCGACGAAGCGGAAAAAATGCCAGCTACGCATCCCAAGCTGGGCGGCAAGTTGACGCTGTTCGCCGGGGATGTTTTCCAGTGCCTGGAGTAATAAGCGGCTCGCCATCGGCAGATTAAAAAACACATGGGCCAGCAAAATACCTTGCAGGCCGTAGGGCGAAAAGGTCCACTCCAGACCGAGCGATTGGCAGAGTGTTGCCAGCCAGCCCTGGCGACCATAGACGCTAAGAATGCCGAAAACAGCGACCAACACCGGGAGGATCAAGGTCATTGCACACAGACGCAACAGCGCCAGCCGACCCGGAAAGCGCCTGCGATAGAGCGCGCGGGCGAGGAATATCGCGGGTATGACAGAGAGCAGTGCCGAGAGAAACGCCTGCCAGAAGGAGAAGCGCACCACATGCCACAGATAGCTGTCCTGCCAGACTGCCACCCAGTCATCCTGCGGCGCGTTCCACCACAGGGCGAGAAACGCCGCCAGCGCAACCGCTACCACCAGCGTGGTGGCGCTTACACCTGGAATTAACCAGCCGGGAATTAACGGCTGACGGCGCGTTGCCATTCGCTAATCCATGCCTGACGTTGTGCCGCCACTTCGGCTGGCGTGAACTCCAACGTGGTTGCGGGTTTGGTCAATTTTTCAAAACCGGCAGGCAGCGTGACGTTTGCCACCGGATACATCCAGTTGCCGGTTGGGATCGCATTCTGGAAAGCCGGAGAAACCATAAACTGGAGGAATTTTTGCGCCAGCTCCGGCTGCTTGCTGGCAGCGGTGCGGGCGGCGACTTCCACTTGCAGATAGTGACCTTCGCTGAAGTTCGCGGCGGCGTAGTTATCTTTCTTCTCTTCGAGAATGTGATAAGCCGGAGAGGTGGTGTAACTCAGTACCAGATCGCTTTCACCTTTTAAAAACAGGCCGTAGGCTTCGCTCCAGCCTTTGGTGACCGTGACCGTTTTCTTCGCCAGTTTCTGCCAGGCTTGTGGGGCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTTCTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAGCCGCCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTGGCGGCGTCTAACAGGTTGTTATCCAGCCCCAGCACCACATCGGCTTTACTGTTTTTGCCTTCCATCCGTAGACGGTTGAGAAGCGAAACGCCATCTTCCAGCGCCACCAGTTTCAGTTCGCAATTACAGTCGGCTTCAAAGGCTTTTTTAACCACCGGACCAGGCCCCCAGTCGGCGGCGAAGGAATCGTAGGTATAAACAGTCAGAACGGGTTTAGCGAAAACGGGCGCTGTGCACAGCAACAGCAGGGGCAGACATTTTTTTAACACTTTGCACCTCAAAAAAGAGTGGCAAAGGACTTGAGAAGGAGCCTCAAATCCCTTCGCCGGCGTTATCCGGATCAGGTTCGACGGGTATTTTCTCAGCGCACGCGTACGCGTGGCACCCCGTTGAGAACGGCGTTAGTGTAGTGATTTTGTTATCAACCAGCAATCATGGATCCGGTGGCGCAAACCACGCTGATTTAAAATCGAACCAGCCGAGGGTATTCATGCGCAGGCCGCGCATACTGCGTTGCCCCTGAATGATCAGCCAGTGGTGCAATAATGGCACCATCGCTTTGCTGGCGACCAGTTGCTGGCACCAGTTCGCCAGATTCATCTCGCCATTGCGCCAGCGAGCAGCGTCGGCTTGCCAGTCAATGGGAATGCAATGTTGTAGCAGTGGCACTTCGCATAAATGTGCGAAAACAGAGAAGTCCAGCGGCAGGGTAAAGTTGGCGCTGTTTAGCCAGATATCACTTTCGATCTCTCCTGTATGCCACTGATCGTAGTCGATCTCTTTGATTTTCAGCGTGACCTGGTGACTTGCCAGAATCTGCTGCATGATCCCGGCAATCACCCGATGCTCACTGTGATCCTGATAAAAGGTTAGGGTGAGGCTTTCCAGGCCAGCCGGTTTTTCGCTCTTTATGGTGCGGGCATGGTGCCAACGGGGGAGCAGTCCATAAGCCGGGAACCACAGTTGCTGGTACTGTTCCTCAGCGAAATAGACCAGATTAGTTGGAGAAAGCACATAGCTTACCCAGTCCCTGACTTGCTGATTCGCCCCGCGATGGGTGCGGCTGTCGAACAGTAAATAGTAGCAACCTTCCTCCAGGCGGCTTTCAATCTCTTTTTCCTCGCCCTGTGGACCTTTTAGCATCAGCCCTCCGGCTGGCTCGTCGGCAATTTCCGGCAGAACCCAGACGTTAACTTCGTCGATTAATGCCCGGTAACCGAAGAAGTCATCGAATGCCTGAATTTTCAGTTGATTGGTGCTGTTGCGAATCACCGCATACGGACCGGTGCCGATGGGATGGCTGGCAAAGTTACTGAGGGTTTCCCATTCGCGCGGCAGGATCATCGCCGGAACTTGCCCCAGCAGTAACGGTAACCAGCGGTCCGGTTGCGTGAGATGGATATCCAGCGTCCAGGGCGTCGGCGACACAATGTCAGCAATATGCGAATAGAGCGGCAGCGTATTGATTCGTTTTAAAGAGGCGATCACATCGTCCATTTCCAGTTCACGACCATGGTGAAAATGGACTCCTGGACGCAAAAAGAAACGCCAGTGAAGCGGTGAAATTTGCTGCCAGTGGTGGGCGATGTCTGCTTCCAGTTCCCCATTTTCCTCATTTATGCGCGTTAGCGAACTGAAGATTTGCCGGGCGATATGGGTTTCGGAACGGCGCAATGCGCTGCCAGGTAGCAGATTACGCAACGGACGATAGTAGAGCACGCGCAGGATGTGCCGCCCCTGGCGGAAGCTGCGGCCCAGATGAGAAACCAGCATTTGCCGCACAGTCGCTTTGTCGCCAACCAACTGCACCAGTTGATCGATACGATCCTGCTCCAGCAGGTCTTCCGCCCGCTGTTGCTGAAGCGCCAGCCCGGTATAGAGGAATGTCAGACGCGAGCGTTTACCGCGCCCGACTTCCGCTTCCCACGTCAGCCAGCCGCGATCCTGCATGGTGTTGAGCAGGGTGCGCATATGACGACGCGAGCAGCTCAATAACGCTGCCAGTTCGTTGAGCGTTGTGTCCTGCGATTTACCCTCGCAGCATTGCCACAGGCGGATGAACTGTTGTTGCAGACGAGCAGATGGCATAAAAGGGGAACTCCTGTGCAAAAGACAGCAATTTTATTTTCCCTATATTAAGTCAATAATTCCTAACGATGAAGCAAGGGGGTGCCCCATGCGTCAGTTTTATCAGCACTATTTTACCGCGACAGCGAAGTTGTGCTGGTTGCGTTGGTTAAGCGTCCCACAACGATTAACCATGCTTGAAGGACTGATGCAGTGGGATGACCGCAATTCTGAAAGTTGACTTGCCTGCATCATGTGTGACTGAGTATTGGTGTAAAATCACCCGCCAGCAGATTATACCTGCTGGTTTTTTTTATTCTCGCCGCGCTAAAAAGGGAACGTATGATCTGGATAATGACGATGGCTCGCCGTATGAACGGTGTTTACGCGGCATTTATGCTGGTCGCTTTTATGATGGGGGTGGCCGGGGCGCTACAGGCTCCTACATTGAGCTTATTTCTGAGTCGTGAGGTTGGCGCGCAACCTTTCTGGATCGGCCTCTTTTATACGGTGAATGCTATTGCTGGGATCGGCGTAAGCCTCTGGTT", "coverage":[
+ {
+ "id":"file_1",
+ "avg_coverage": 29.75
+ },
+ {
+ "id":"file_2",
+ "avg_coverage": 29.45
+ }
+]
+, "length": 7055 }}
+],
+"edges": [
+
+{ "data":{ "id": "e16", "source": "n7","target": "n8","direction": "FF", "coverage":[
+ {
+ "id":"file_1",
+ "avg_coverage": 15
+ },
+ {
+ "id":"file_2",
+ "avg_coverage": 12
+ }
+]
+}},
+{ "data":{ "id": "e17", "source": "n7","target": "n9","direction": "FF", "coverage":[
+ {
+ "id":"file_1",
+ "avg_coverage": 12
+ },
+ {
+ "id":"file_2",
+ "avg_coverage": 14
+ }
+]
+}},
+{ "data":{ "id": "e18", "source": "n8","target": "n7","direction": "RR", "coverage":[
+ {
+ "id":"file_1",
+ "avg_coverage": 15
+ },
+ {
+ "id":"file_2",
+ "avg_coverage": 12
+ }
+]
+}},
+{ "data":{ "id": "e19", "source": "n8","target": "n10","direction": "FF", "coverage":[
+ {
+ "id":"file_1",
+ "avg_coverage": 12
+ },
+ {
+ "id":"file_2",
+ "avg_coverage": 12
+ }
+]
+}},
+{ "data":{ "id": "e20", "source": "n9","target": "n7","direction": "RR", "coverage":[
+ {
+ "id":"file_1",
+ "avg_coverage": 12
+ },
+ {
+ "id":"file_2",
+ "avg_coverage": 14
+ }
+]
+}},
+{ "data":{ "id": "e21", "source": "n9","target": "n10","direction": "FF", "coverage":[
+ {
+ "id":"file_1",
+ "avg_coverage": 9
+ },
+ {
+ "id":"file_2",
+ "avg_coverage": 7
+ }
+]
+}},
+{ "data":{ "id": "e22", "source": "n10","target": "n8","direction": "RR", "coverage":[
+ {
+ "id":"file_1",
+ "avg_coverage": 12
+ },
+ {
+ "id":"file_2",
+ "avg_coverage": 12
+ }
+]
+}},
+{ "data":{ "id": "e23", "source": "n10","target": "n9","direction": "RR", "coverage":[
+ {
+ "id":"file_1",
+ "avg_coverage": 9
+ },
+ {
+ "id":"file_2",
+ "avg_coverage": 7
+ }
+]
+}},
+{ "data":{ "id": "e24", "source": "n10","target": "n11","direction": "FF", "coverage":[
+ {
+ "id":"file_1",
+ "avg_coverage": 21
+ },
+ {
+ "id":"file_2",
+ "avg_coverage": 0
+ }
+]
+}},
+{ "data":{ "id": "e25", "source": "n10","target": "n12","direction": "FF", "coverage":[
+ {
+ "id":"file_1",
+ "avg_coverage": 0
+ },
+ {
+ "id":"file_2",
+ "avg_coverage": 27
+ }
+]
+}},
+{ "data":{ "id": "e26", "source": "n11","target": "n10","direction": "RR", "coverage":[
+ {
+ "id":"file_1",
+ "avg_coverage": 21
+ },
+ {
+ "id":"file_2",
+ "avg_coverage": 0
+ }
+]
+}},
+{ "data":{ "id": "e27", "source": "n11","target": "n13","direction": "FF", "coverage":[
+ {
+ "id":"file_1",
+ "avg_coverage": 25
+ },
+ {
+ "id":"file_2",
+ "avg_coverage": 0
+ }
+]
+}},
+{ "data":{ "id": "e28", "source": "n12","target": "n10","direction": "RR", "coverage":[
+ {
+ "id":"file_1",
+ "avg_coverage": 0
+ },
+ {
+ "id":"file_2",
+ "avg_coverage": 27
+ }
+]
+}},
+{ "data":{ "id": "e29", "source": "n12","target": "n13","direction": "FF", "coverage":[
+ {
+ "id":"file_1",
+ "avg_coverage": 0
+ },
+ {
+ "id":"file_2",
+ "avg_coverage": 17
+ }
+]
+}},
+{ "data":{ "id": "e30", "source": "n13","target": "n11","direction": "RR", "coverage":[
+ {
+ "id":"file_1",
+ "avg_coverage": 25
+ },
+ {
+ "id":"file_2",
+ "avg_coverage": 0
+ }
+]
+}},
+{ "data":{ "id": "e31", "source": "n13","target": "n12","direction": "RR", "coverage":[
+ {
+ "id":"file_1",
+ "avg_coverage": 0
+ },
+ {
+ "id":"file_2",
+ "avg_coverage": 17
+ }
+]
+}}
+]
+}}]
+ }}
+
+
+}
\ No newline at end of file
=====================================
debian/tests/ref/ref-res_mapsembler_k_31_c_2_t_1.fasta
=====================================
@@ -0,0 +1,2 @@
+>ligne
+GCTTCCATTGACTCAATGTAGTCACGCGGATGATGACGGAACTGGTTATTCGGGGCATCACAAAATTGCC
=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,72 @@
+#!/bin/bash
+set -e
+
+pkg=mapsembler2
+
+export LC_ALL=C.UTF-8
+if [ "${AUTOPKGTEST_TMP}" = "" ]; then
+ AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+ # Double quote below to expand the temporary directory variable now versus
+ # later is on purpose.
+ # shellcheck disable=SC2064
+ trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+
+gunzip -r *
+#do_stuff_to_test_package#
+echo -e "\e[93m\e[1mTest 1\e[0m"
+run_mapsembler2_pipeline -s starter.fa -r "reads1.fa reads2.fa" -t 3 -p res
+if [ "$?" -ne "0" ]; then
+ echo -e "\e[31m\e[1mTest could not be run.\e[0m"
+ exit 1
+fi
+diff res_k_31_c_5_t_3_modified_and_covered.json ref-res_k_31_c_5_t_3_modified_and_covered.json --suppress-common-lines
+if [ "$?" -ne "0" ]; then
+ echo -e "\e[31m\e[1mOutput did not match the reference.\e[0m"
+ exit 1
+fi
+echo -e "\e[92m\e[1mPassed\e[0m"
+
+echo -e "\e[93m\e[1mTest 2\e[0m"
+run_mapsembler2_pipeline -s starter.fa -r "reads1.fa reads2.fa" -t 1 -p reads1
+if [ "$?" -ne "0" ]; then
+ echo -e "\e[31m\e[1mTest could not be run.\e[0m"
+ exit 1
+fi
+diff reads1_coherent_k_31_c_5_t_1.fasta ref-reads1_coherent_k_31_c_5_t_1.fasta --suppress-common-lines
+diff reads1_uncoherent_k_31_c_5_t_1.fasta ref-reads1_uncoherent_k_31_c_5_t_1.fasta --suppress-common-lines
+if [ "$?" -ne "0" ]; then
+ echo -e "\e[31m\e[1mOutput did not match the reference.\e[0m"
+ exit 1
+fi
+echo -e "\e[92m\e[1mPassed\e[0m"
+
+echo -e "\e[93m\e[1mTest 3\e[0m"
+mapsembler_extend starter.fa reads1.fa reads2.fa
+if [ "$?" -ne "0" ]; then
+ echo -e "\e[31m\e[1mTest could not be run.\e[0m"
+ exit 1
+fi
+diff res_mapsembler_k_31_c_2_t_1.fasta ref-res_mapsembler_k_31_c_2_t_1.fasta --suppress-common-lines
+if [ "$?" -ne "0" ]; then
+ echo -e "\e[31m\e[1mOutput did not match the reference.\e[0m"
+ exit 1
+fi
+echo -e "\e[92m\e[1mPassed\e[0m"
+
+echo -e "\e[93m\e[1mTest 4\e[0m"
+mapsembler2_extremities --k 20 --starters reads1_coherent_k_31_c_5_t_1.fasta --reads "reads1.fa reads2.fa" --output mapsembler2_extremities.out.fa
+if [ "$?" -ne "0" ]; then
+ echo -e "\e[31m\e[1mTest could not be run.\e[0m"
+ exit 1
+fi
+diff mapsembler2_extremities.out.fa ref-mapsembler2_extremities.out.fa --suppress-common-lines
+if [ "$?" -ne "0" ]; then
+ echo -e "\e[31m\e[1mOutput did not match the reference.\e[0m"
+ exit 1
+fi
+echo -e "\e[92m\e[1mPassed\e[0m"
View it on GitLab: https://salsa.debian.org/med-team/mapsembler2/-/compare/1edcf83102d9d53bb7f234a0d1eeaada112cde16...eddadecf0ba0c2853e93da06ba7c74acfb87b675
--
View it on GitLab: https://salsa.debian.org/med-team/mapsembler2/-/compare/1edcf83102d9d53bb7f234a0d1eeaada112cde16...eddadecf0ba0c2853e93da06ba7c74acfb87b675
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