[med-svn] [Git][med-team/nanosv][master] 3 commits: Remove test data
Shruti Sridhar (@shruti_sridhar)
gitlab at salsa.debian.org
Sat May 29 16:09:55 BST 2021
Shruti Sridhar pushed to branch master at Debian Med / nanosv
Commits:
2ac7efaf by Shruti Sridhar at 2021-05-29T20:29:22+05:30
Remove test data
- - - - -
b60bca24 by Shruti Sridhar at 2021-05-29T20:29:35+05:30
Add test data
- - - - -
a0c6fe0a by Shruti Sridhar at 2021-05-29T20:29:55+05:30
Fix Autopkgtests
- - - - -
8 changed files:
- debian/README.test
- debian/copyright
- debian/tests/control
- + debian/tests/data/read.sam
- − debian/tests/data/read.sorted.bam
- − debian/tests/data/read.sorted.bam.bai
- − debian/tests/data/target.bed
- debian/tests/run-unit-test
Changes:
=====================================
debian/README.test
=====================================
@@ -9,6 +9,7 @@ in order to confirm its integrity.
Notes on the files used for testing
────────────────────────────────────────
-
+Files: debian/tests/data/*
+Source: https://github.com/samtools/samtools/blob/develop/examples/toy.sam
=====================================
debian/copyright
=====================================
@@ -10,6 +10,10 @@ Files: debian/*
Copyright: 2020 Steffen Moeller <moeller at debian.org>
License: MIT
+Files: debian/tests/data/*
+Copyright: 2008-2020 Genome Research Ltd.
+License : MIT
+
License: MIT
Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the "Software"),
@@ -28,3 +32,5 @@ License: MIT
CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+
=====================================
debian/tests/control
=====================================
@@ -1,3 +1,3 @@
Tests: run-unit-test
-Depends: @, sambamba
+Depends: @, sambamba, samtools, bedtools
Restrictions: allow-stderr
=====================================
debian/tests/data/read.sam
=====================================
@@ -0,0 +1,14 @@
+ at SQ SN:ref LN:45
+ at SQ SN:ref2 LN:40
+r001 163 ref 7 30 8M4I4M1D3M = 37 39 TTAGATAAAGAGGATACTG * XX:B:S,12561,2,20,112
+r002 0 ref 9 30 1S2I6M1P1I1P1I4M2I * 0 0 AAAAGATAAGGGATAAA *
+r003 0 ref 9 30 5H6M * 0 0 AGCTAA *
+r004 0 ref 16 30 6M14N1I5M * 0 0 ATAGCTCTCAGC *
+r003 16 ref 29 30 6H5M * 0 0 TAGGC *
+r001 83 ref 37 30 9M = 7 -39 CAGCGCCAT *
+x1 0 ref2 1 30 20M * 0 0 aggttttataaaacaaataa ????????????????????
+x2 0 ref2 2 30 21M * 0 0 ggttttataaaacaaataatt ?????????????????????
+x3 0 ref2 6 30 9M4I13M * 0 0 ttataaaacAAATaattaagtctaca ??????????????????????????
+x4 0 ref2 10 30 25M * 0 0 CaaaTaattaagtctacagagcaac ?????????????????????????
+x5 0 ref2 12 30 24M * 0 0 aaTaattaagtctacagagcaact ????????????????????????
+x6 0 ref2 14 30 23M * 0 0 Taattaagtctacagagcaacta ???????????????????????
\ No newline at end of file
=====================================
debian/tests/data/read.sorted.bam deleted
=====================================
Binary files a/debian/tests/data/read.sorted.bam and /dev/null differ
=====================================
debian/tests/data/read.sorted.bam.bai deleted
=====================================
Binary files a/debian/tests/data/read.sorted.bam.bai and /dev/null differ
=====================================
debian/tests/data/target.bed deleted
=====================================
@@ -1,372 +0,0 @@
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=====================================
debian/tests/run-unit-test
=====================================
@@ -13,7 +13,12 @@ cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
cd "${AUTOPKGTEST_TMP}"
- NanoSV read.sorted.bam -b target.bed -s sambamba -o output.vcf
+cat read.sam| samtools view -Sb > reads.bam
+samtools sort reads.bam > reads_sort.bam
+samtools index reads_sort.bam reads_sort.bai
+bedtools bamtobed -i reads_sort.bam > target.bed
+
+NanoSV reads_sort.bam -b target.bed -s sambamba -o output.vcf
[ -s "output.vcf" ] || exit 1 && echo "PASS Test"
#Output generated is not consistent and cannot be compared with a reference.
View it on GitLab: https://salsa.debian.org/med-team/nanosv/-/compare/fb47da4e14a666ac7b62d42ae9bd62b3347edc4b...a0c6fe0a2d2402755e55659a12e88a885771b908
--
View it on GitLab: https://salsa.debian.org/med-team/nanosv/-/compare/fb47da4e14a666ac7b62d42ae9bd62b3347edc4b...a0c6fe0a2d2402755e55659a12e88a885771b908
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