Fix tests

sanger-pathogens · Oct 21, 2019 · 0dbdfc0 · 0dbdfc0
1 parent 11e2f3c
commit 0dbdfc0
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Showing 2 changed files with 11 additions and 9 deletions.
diff --git a/README.md b/README.md
@@ -91,6 +91,8 @@ make
 make check
 ```
 
+This requires libcheck (the `check` package in Ubuntu) to be installed.
+
 ## Usage
 
 ```

diff --git a/tests/check-snp-sites.c b/tests/check-snp-sites.c
@@ -183,64 +183,64 @@ END_TEST
 
 START_TEST (valid_genome_length)
 {
-  detect_snps("../tests/data/alignment_file_one_line_per_sequence.aln",0,0);
+  detect_snps("../tests/data/alignment_file_one_line_per_sequence.aln",0,0,0);
   fail_unless( get_length_of_genome() == 2000 );
 }
 END_TEST
 
 START_TEST (valid_genome_length_with_multiple_lines_per_sequence)
 {
-  detect_snps("../tests/data/alignment_file_multiple_lines_per_sequence.aln",0,0);
+  detect_snps("../tests/data/alignment_file_multiple_lines_per_sequence.aln",0,0,0);
   fail_unless( get_length_of_genome() == 2000 );
 }
 END_TEST
 
 START_TEST (valid_number_of_sequences_in_file)
 {
-  detect_snps("../tests/data/alignment_file_one_line_per_sequence.aln",0,0);
+  detect_snps("../tests/data/alignment_file_one_line_per_sequence.aln",0,0,0);
   fail_unless( get_number_of_samples() == 109 );
 }
 END_TEST
 
 START_TEST (valid_number_of_sequences_in_file_with_multiple_lines_per_sequence)
 {
-  detect_snps("../tests/data/alignment_file_multiple_lines_per_sequence.aln",0,0);
+  detect_snps("../tests/data/alignment_file_multiple_lines_per_sequence.aln",0,0,0);
   fail_unless( get_number_of_samples() == 109 );
 }
 END_TEST 
 
 START_TEST (number_of_snps_detected)
 {
-  detect_snps("../tests/data/alignment_file_multiple_lines_per_sequence.aln",0,0);
+  detect_snps("../tests/data/alignment_file_multiple_lines_per_sequence.aln",0,0,0);
   fail_unless( get_number_of_snps()  == 5);
 }
 END_TEST
 
 START_TEST (number_of_snps_detected_small)
 {
-  detect_snps("../tests/data/small_alignment.aln",0,0);
+  detect_snps("../tests/data/small_alignment.aln",0,0,0);
   fail_unless(  get_number_of_snps()  == 1);
 }
 END_TEST
 
 START_TEST (detect_snps_pure_mode)
 {
-  detect_snps("../tests/data/pure_mode_alignment.aln",1,0);
+  detect_snps("../tests/data/pure_mode_alignment.aln",1,0,0);
   fail_unless(  get_number_of_snps()  == 2);
 }
 END_TEST
 
 
 START_TEST (detect_snps_pure_mode_monomorphic)
 {
-  detect_snps("../tests/data/pure_mode_monomorphic_alignment.aln",1,1);
+  detect_snps("../tests/data/pure_mode_monomorphic_alignment.aln",1,1,0);
   fail_unless(  get_number_of_snps()  == 3);
 }
 END_TEST
 
 START_TEST (sample_names_from_alignment_file)
 {
-  detect_snps("../tests/data/small_alignment.aln",0,0);
+  detect_snps("../tests/data/small_alignment.aln",0,0,0);
   char ** current_sequence_names = get_sequence_names();
 
   fail_unless(strcmp(current_sequence_names[0],"reference_sequence") == 0);