[med-svn] [Git][med-team/nanolyse][master] 3 commits: Get some rudimentary autopkgtest working

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / nanolyse


Commits:
e715d8ae by Andreas Tille at 2020-06-24T18:17:27+02:00
Get some rudimentary autopkgtest working

- - - - -
25572efd by Andreas Tille at 2020-06-24T18:18:44+02:00
Add FIXME

- - - - -
0c01ca75 by Andreas Tille at 2020-06-24T18:20:34+02:00
cleanup after running

- - - - -


5 changed files:

- + debian/docs
- + debian/examples
- + debian/tests/data/README
- + debian/tests/data/paired_reads.fastq
- debian/tests/run-unit-test


Changes:

=====================================
debian/docs
=====================================
@@ -0,0 +1,2 @@
+debian/README.test
+debian/tests/run-unit-test


=====================================
debian/examples
=====================================
@@ -0,0 +1 @@
+debian/tests/data/*


=====================================
debian/tests/data/README
=====================================
@@ -0,0 +1,6 @@
+This fastq file was taken from package ncbi-blast+
+   c++/src/algo/blast/blastinput/unit_test/data/paired_reads.fastq
+
+FIXME: I have no idea whether this data set makes any sense at all.
+
+ -- Andreas Tille <tille at debian.org>  Fri, 15 May 2020 15:27:17 +0200


=====================================
debian/tests/data/paired_reads.fastq
=====================================
@@ -0,0 +1,24 @@
+ at pair1  (both are read)
+GAATGTCCGTCTGGGTCTCCTTGTGCTGCGGTCCTGGCAACTCGTAGAATTTCTTACCAAAGTATCGATCCGGGAGATAGTACGATGGATACTCCGCCCTCAGCCTCTCG
++pair1
+BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFBFFFF<FFFFFFFFFFFFFFFFBFFFFF<FFFFFFFFFFFFFFFFFFFFFFFF
+ at pair2
+ATGTTTTCCGATCCCGCCCAGGAGTCGGTTGCCACGCAGACGGAGGCACAACCGGTTCCGTCGCCCATCTGCACCCCACTGCTGATGGTGGACGAGGATGGACGAAAGCG
++pair2
+BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFBFFFF<FFFFFFFFFFFFFFFFBFFFFF<FFFFFFFFFFFFFFFFFFFFFFFF
+ at incomplete1.1  (only the first is accepted)
+ATGTTTTCCGATCCCGCCCAGGAGTCGGTTGCCACGCAGACGGAGGCACAACCGGTTCCGTCGCCCATCTGCACCCCACTGCTGATGGTGGACGAGGATGGACGAAAGCG
++incomplete1.1
+BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFBFFFF<FFFFFFFFFFFFFFFFBFFFFF<FFFFFFFFFFFFFFFFFFFFFFFF
+ at incomplete1.2
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
++incomplete1.2
+BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFBFFFF<FFFFFFFFFFFFFFFFBFFFFFF
+ at incomplete2.1   (only the second is accepted)
+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
++incomplete2.1
+BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFBFFFF<FFFFFFFFFFFFFFFFBFFFFFF
+ at incomplete2.2
+ATGTTTTCCGATCCCGCCCAGGAGTCGGTTGCCACGCAGACGGAGGCACAACCGGTTCCGTCGCCCATCTGCACCCCACTGCTGATGGTGGACGAGGATGGACGAAAGCG
++incomplete2.2
+BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFBFFFF<FFFFFFFFFFFFFFFFBFFFFF<FFFFFFFFFFFFFFFFFFFFFFFF


=====================================
debian/tests/run-unit-test
=====================================
@@ -11,5 +11,4 @@ fi
 
 cd "${AUTOPKGTEST_TMP}"
 
-gunzip -c /usr/share/${pkg}/reference/lambda.fasta.gz > lambda.fasta
-cat lambda.fasta | NanoLyse > reads_without_lambda.fastq
+cat paired_reads.fastq | NanoLyse > reads_without_lambda.fastq



View it on GitLab: https://salsa.debian.org/med-team/nanolyse/-/compare/e8eb16bedd156400e79ab24cadaf2176e6451f63...0c01ca756817f05bf1ce45b4f5c813020fbc0c92

-- 
View it on GitLab: https://salsa.debian.org/med-team/nanolyse/-/compare/e8eb16bedd156400e79ab24cadaf2176e6451f63...0c01ca756817f05bf1ce45b4f5c813020fbc0c92
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