[med-svn] [Git][med-team/tiddit][master] 2 commits: Simplify autopkgtest (Closes: #964101)

[Nilesh Patra]

Nilesh Patra pushed to branch master at Debian Med / tiddit


Commits:
eafa7abb by Nilesh Patra at 2020-10-06T22:41:10+05:30
Simplify autopkgtest (Closes: #964101)

- - - - -
a14b7944 by Nilesh Patra at 2020-10-06T22:44:59+05:30
Update changelog

- - - - -


4 changed files:

- debian/changelog
- debian/tests/README.md
- − debian/tests/data/ref.fa
- debian/tests/run-unit-test


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+tiddit (2.12.0+dfsg-3) UNRELEASED; urgency=medium
+
+  * Team Upload.
+  * Simplify autopkgtest (Closes: #964101)
+
+ -- Nilesh Patra <npatra974 at gmail.com>  Tue, 06 Oct 2020 22:41:27 +0530
+
 tiddit (2.12.0+dfsg-2) unstable; urgency=medium
 
   * Team Upload.


=====================================
debian/tests/README.md
=====================================
@@ -1,18 +1,6 @@
 Data for tiddit
 =====================
 
-The data is from NA12878 (tumor) and NA12892 (normal) and represents a tiny chunk of chromsome 21. It was created from 1000 Genomes Project (http://www.1000genomes.org) data available in the following locations:
-* NA12892 - ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/NA12892/high_coverage_alignment/NA12892.mapped.ILLUMINA.bwa.CEU.high_coverage_pcr_free.20130906.bam
-* NA12878 - ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/NA12878/high_coverage_alignment/NA12878.mapped.ILLUMINA.bwa.CEU.high_coverage_pcr_free.20130906.bam
-* Build 37 reference - ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz
+	The test data for tiddit has been referenced from here: https://github.com/genome/somatic-snv-test-data which has further steps for creating the data
+	All work is from public datasets and have been made with tools in the open domain.
 
-Should you wish to recreate the files in this repository, they were processed as follows below.
-
-    samtools view -hb NA12892.mapped.ILLUMINA.bwa.CEU.high_coverage_pcr_free.20130520.bam 21:10400000-10500000 > normal.bam
-    samtools view -hb NA12878.mapped.ILLUMINA.bwa.CEU.high_coverage_pcr_free.20130520.bam 21:10400000-10500000 > tumor.bam
-    gunzip human_g1k_v37.fasta.gz
-    samtools faidx human_g1k_v37.fasta 21:1-10505000 > ref.fa
-    samtools view -h -o normal.sam normal.bam
-    samtools view -h -o tumor.sam tumor.bam
-
-Note that ref.fa was then further edited to change the chromosome name back to 21 as faidx includes the requested region in the name.


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

=====================================
debian/tests/run-unit-test
=====================================
@@ -17,10 +17,24 @@ cat normal.sam | samtools view -Sb - > normal.bam
 cat tumor.sam | samtools view -Sb - > tumor.bam
 
 echo 'Test 1'
-TIDDIT.py --sv --p_ratio 0.10 --bam tumor.bam -o test1 --ref ref.fa
+TIDDIT --cov -b normal.bam -o test1
+TIDDIT --cov -w -b normal.bam -o test1
+for f in test1.*
+do
+	[ -s $f ] || exit 1
+	cat $f | tail -20
+done
+rm -f ./test1*
 echo 'PASS'
 
 echo 'Test 2'
-TIDDIT.py --sv --bam normal.bam -o test2 --ref ref.fa
+TIDDIT --cov -b normal.bam -o test2
+TIDDIT --cov -w -b tumor.bam -o test2
+for f in test2.*
+do
+	[ -s $f ] || exit 1
+	cat $f | tail -20
+done
+rm -f ./test2*
 echo 'PASS'
 



View it on GitLab: https://salsa.debian.org/med-team/tiddit/-/compare/547239cb87136eccdd1966c2b4e7e409bea6f9c4...a14b79445d0e403f5eddbfc9f1983c177996929b

-- 
View it on GitLab: https://salsa.debian.org/med-team/tiddit/-/compare/547239cb87136eccdd1966c2b4e7e409bea6f9c4...a14b79445d0e403f5eddbfc9f1983c177996929b
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