Merge pull request #6 from rki-mf1/CI-case-test

add CI case test using public SC2 data

Author: Krannich479

.github/workflows/build.yml

@@ -44,3 +44,17 @@ jobs:
           make -C lib/htslib
           make
 
+      - name: Run amplisim on public Sars-Cov-2 data
+        run: |
+          mkdir testdata && cd testdata
+          wget https://raw.githubusercontent.com/artic-network/primer-schemes/master/nCoV-2019/V5.3.2/SARS-CoV-2.primer.bed
+          wget https://www.ebi.ac.uk/ena/browser/api/fasta/MN908947.3
+          sed 's/>ENA|MN908947|MN908947.3 Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome./>MN908947.3/g' MN908947.3 > MN908947.3.fasta
+          cd ..
+          ./amplisim -s 479 -o testdata/amplicons.fasta testdata/MN908947.3.fasta testdata/SARS-CoV-2.primer.bed
+
+      - name: Verify md5sum (macOS)
+        if: runner.os == 'macOS'
+        run: |
+          brew install coreutils
+          md5sum testdata/amplicons.fasta | md5sum -c test/sarscov2_s479.macos.md5

src/argparser.h

@@ -12,8 +12,8 @@
 
 
 const char *argp_program_version = VERSION; // defined in Makefile
-const char *argp_program_bug_address = "";
-static char doc[] = "amplisim -- a program to simulate amplicon sequencing data";
+const char *argp_program_bug_address = "https://github.com/rki-mf1/amplisim/issues";
+static char doc[] = "amplisim -- a program to simulate amplicon sequences from a reference genome";
 static char args_doc[] = "REFERENCE PRIMERS";
 
 static struct argp_option options[] = {

test/sarscov2_s479.macos.md5

@@ -0,0 +1 @@
+3ce2bb236e611f5d5e569d68b631bd81  testdata/amplicons.fasta