Run tests

Run unit tests

From the STRling directory run:

nimble test

End-to-end tests

Download data for end to end tests:

mkdir -p run_tests
      cd run_tests
      wget -O data.zip https://ndownloader.figshare.com/articles/11367851?private_link=207b2a78ddcbdb28781b
      unzip data.zip
      rm data.zip
# Download reference
      wget -O chr4.fa.gz https://hgdownload.soe.ucsc.edu/goldenPath/hg38/chromosomes/chr4.fa.gz
      gzip -d chr4.fa.gz
# End-to-end test single
      mkdir -p single
      ../strling extract -f chr4.fa -g chr4.fa.str -v CANVAS.chr4-39348425_AAGGG_0_400.bam single/CANVAS.chr4-39348425_AAGGG_0_400.str.bin
      ../strling call -v -o single/CANVAS.chr4-39348425_AAGGG_0_400 CANVAS.chr4-39348425_AAGGG_0_400.bam single/CANVAS.chr4-39348425_AAGGG_0_400.str.bin
# End-to-end test joint
      mkdir -p joint
      for i in *.bam; do ../strling extract -f chr4.fa -g chr4.fa.str -v $i joint/$i.str.bin; done
      ../strling merge -f chr4.fa -v -o joint/strling joint/*.bin
      for i in *.bam; do ../strling call -v -b joint/strling-bounds.txt -o joint/$i $i joint/$i.str.bin; done