[med-svn] [Git][med-team/hisat2][master] Fix problematic test cases

[Saira Hussain]

Saira Hussain pushed to branch master at Debian Med / hisat2


Commits:
af749803 by Saira Hussain at 2019-08-02T14:58:51Z
Fix problematic test cases

- - - - -


1 changed file:

- debian/tests/run-unit-tests


Changes:

=====================================
debian/tests/run-unit-tests
=====================================
@@ -11,7 +11,7 @@ if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
 #  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
 fi
 
-cp /usr/share/doc/${pkg}/examples/* -a "${AUTOPKGTEST_TMP}"
+cp /usr/share/doc/${pkg}/example/* -a "${AUTOPKGTEST_TMP}"
 
 cd "${AUTOPKGTEST_TMP}"
 
@@ -26,6 +26,16 @@ hisat2 -f -x index/22_20-21M_snp -U reads/reads_1.fa -S eg1.sam
 
 # Paired-end example
 hisat2 -f -x index/22_20-21M_snp -1 reads/reads_1.fa -2 reads/reads_2.fa -S eg2.sam
+hisat2 -f -x index/22_20-21M_snp -1 reads/reads_1.fa -2 reads/reads_2.fa -S eg2.sam
+
+# Convert to BAM
+samtools view -bS eg2.sam > eg2.bam
+
+# Sort the BAM file
+samtools sort eg2.bam -o eg2.sorted.bam
+
+# Generate the variant
+bcftools mpileup -f reference/22_20-21M.fa eg2.sorted.bam | bcftools view - > eg2.raw.bcf
 
-hisat -f -x index/22_20-21M_snp -1 reads/reads_1.fa -2 reads/reads_2.fa -S eg2.sam
-samtools mpileup -uf reference/22_20-21M.fa eg2.sorted.bam | bcftools view -bvcg - > eg2.raw.bcf
+# View the variant
+bcftools view eg2.raw.bcf



View it on GitLab: https://salsa.debian.org/med-team/hisat2/commit/af749803c7d04d49825d2ed2d85794446964986f

-- 
View it on GitLab: https://salsa.debian.org/med-team/hisat2/commit/af749803c7d04d49825d2ed2d85794446964986f
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20190802/125f42f3/attachment-0001.html>