Commit 2a865446 authored by Saira Hussain's avatar Saira Hussain 💬
Browse files

Add the suite tests

parent 58054b96

debian/tests/run-unit-tests

+9 −0
Original line number Diff line number Diff line
@@ -19,4 +19,13 @@ cd "${AUTOPKGTEST_TMP}" 
set -x



# Run the reproducible suite

hisat2-build reference/22_20-21M.fa --snp reference/22_20-21M.snp 22_20-21M_snp



# Aligning example reads

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



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