END_TEST
START_TEST (valid_with_only_aln_file_output)
{
generate_snp_sites("../tests/data/alignment_file_one_line_per_sequence.aln",1,0,0,"");
fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.snp_sites.aln","alignment_file_one_line_per_sequence.aln.snp_sites.aln" ) == 1 ,"Invalid ALN file for multiple lines per seq");
remove("alignment_file_one_line_per_sequence.aln.snp_sites.aln");
}
END_TEST
START_TEST (valid_with_phylip_outputted_with_custom_name)
{
generate_snp_sites("../tests/data/alignment_file_one_line_per_sequence.aln",0,0,1,"some_custom_name");
fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.phylip", "some_custom_name" ) == 1, "Custom name needs extra extension for phylip" );
remove("some_custom_name");
}
END_TEST
START_TEST (valid_with_only_aln_file_output_with_custom_name)
{
char output_filename[100] = {"some_custom_name"};
generate_snp_sites("../tests/data/alignment_file_multiple_lines_per_sequence.aln",1,0,0,output_filename);
fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.snp_sites.aln","some_custom_name" ) == 1 ,"Only aln with custom name should be outputted");
remove("some_custom_name");
}
END_TEST
START_TEST (valid_alignment_with_multiple_lines_per_sequence)
{
generate_snp_sites("../tests/data/alignment_file_multiple_lines_per_sequence.aln",1,1,1,"");
fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.vcf", "alignment_file_multiple_lines_per_sequence.aln.vcf" ) == 1, "Invalid VCF file for multiple lines per seq" );
fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.phylip", "alignment_file_multiple_lines_per_sequence.aln.phylip" ) == 1, "Invalid Phylip file for multiple lines per seq" );
fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.snp_sites.aln","alignment_file_multiple_lines_per_sequence.aln.snp_sites.aln" ) == 1 ,"Invalid ALN file for multiple lines per seq");
remove("alignment_file_multiple_lines_per_sequence.aln.vcf");
remove("alignment_file_multiple_lines_per_sequence.aln.phylip");
remove("alignment_file_multiple_lines_per_sequence.aln.snp_sites.aln");
}
END_TEST
START_TEST (valid_alignment_with_n_as_gap)
{
generate_snp_sites("../tests/data/alignment_file_with_n.aln",1,1,1, "");
fail_unless( compare_files("../tests/data/alignment_file_with_n.aln.vcf", "alignment_file_with_n.aln.vcf" ) == 1, "Invalid VCF file for 1 line per seq" );
fail_unless( compare_files("../tests/data/alignment_file_with_n.aln.phylip", "alignment_file_with_n.aln.phylip" ) == 1, "Invalid Phylip file for 1 line per seq" );
fail_unless( compare_files("../tests/data/alignment_file_with_n.aln.snp_sites.aln","alignment_file_with_n.aln.snp_sites.aln" ) == 1 , "Invalid ALN file for 1 line per seq");
remove("alignment_file_with_n.aln.vcf");
remove("alignment_file_with_n.aln.phylip");
remove("alignment_file_with_n.aln.snp_sites.aln");
}
END_TEST
START_TEST (valid_alignment_with_one_line_per_sequence_gzipped)
{
generate_snp_sites("../tests/data/alignment_file_one_line_per_sequence.aln.gz",1,1,1, NULL);
fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.vcf", "alignment_file_one_line_per_sequence.aln.gz.vcf" ) == 1, "Invalid VCF file for 1 line per seq" );
fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.phylip", "alignment_file_one_line_per_sequence.aln.gz.phylip" ) == 1, "Invalid Phylip file for 1 line per seq" );
fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.snp_sites.aln","alignment_file_one_line_per_sequence.aln.gz.snp_sites.aln" ) == 1 , "Invalid ALN file for 1 line per seq");
remove("alignment_file_one_line_per_sequence.aln.gz.vcf");
remove("alignment_file_one_line_per_sequence.aln.gz.phylip");
remove("alignment_file_one_line_per_sequence.aln.gz.snp_sites.aln");
}
int main (int argc, char **argv) {
char multi_fasta_filename[FILENAME_MAX] = {""};
char output_filename[FILENAME_MAX] = {""};
int c;
int index;
int output_multi_fasta_file = 0;
int output_vcf_file = 0;
int output_phylip_file = 0;
while ((c = getopt (argc, argv, "mvpo:V")) != -1)
switch (c)
{
case 'm':
output_multi_fasta_file = 1;
break;
case 'v':
output_vcf_file = 1;
break;
case 'V':
print_version();
return 0;
case 'p':
output_phylip_file = 1;
break;
case 'o':
strncpy(output_filename, optarg, FILENAME_MAX);
break;
case 'h':
print_usage();
return 0;
default:
output_multi_fasta_file = 1;
}
if(optind < argc)
{
strncpy(multi_fasta_filename, argv[optind], FILENAME_MAX);
generate_snp_sites(multi_fasta_filename, output_multi_fasta_file, output_vcf_file, output_phylip_file, output_filename);
}
else
{
print_usage();
}
return 0;
}
int main (int argc, char **argv) {
char multi_fasta_filename[FILENAME_MAX] = {""};
char output_filename[FILENAME_MAX] = {""};
int c;
int index;
int output_multi_fasta_file = 0;
int output_vcf_file = 0;
int output_phylip_file = 0;
int output_reference = 0;
int pure_mode = 0;
int output_monomorphic =0;
while ((c = getopt (argc, argv, "mvrbpco:V")) != -1)
switch (c)
{
case 'm':
output_multi_fasta_file = 1;
break;
case 'v':
output_vcf_file = 1;
break;
case 'V':
print_version();
return 0;
case 'p':
output_phylip_file = 1;
break;
case 'r':
output_reference = 1;
break;
case 'c':
pure_mode = 1;
break;
case 'b':
output_monomorphic = 1;
break;
case 'o':
strncpy(output_filename, optarg, FILENAME_MAX);
break;
case 'h':
print_usage();
exit(EXIT_SUCCESS);
default:
output_multi_fasta_file = 1;
}
if(optind < argc)
{
// check to see if the input alignment file exists
if( access( argv[optind], F_OK ) == -1 ) {
fprintf(stderr,"ERROR: cannot access input alignment file '%s'\n", argv[optind]);
fflush(stderr);
exit(EXIT_FAILURE);
}
strncpy(multi_fasta_filename, argv[optind], FILENAME_MAX);
if( pure_mode || output_monomorphic)
{
generate_snp_sites_with_ref_pure_mono(multi_fasta_filename,
output_multi_fasta_file,
output_vcf_file, output_phylip_file,
output_filename,output_reference,pure_mode,output_monomorphic);
}
else if(output_reference ) {
generate_snp_sites_with_ref(multi_fasta_filename,
output_multi_fasta_file,
output_vcf_file, output_phylip_file,
output_filename);
} else {
generate_snp_sites(multi_fasta_filename, output_multi_fasta_file,
output_vcf_file, output_phylip_file,
output_filename);
}
}
else
{
print_usage();
}
exit(EXIT_SUCCESS);
}
END_TEST
START_TEST (invalid_with_uneven_file_lengths)
{
generate_snp_sites("../tests/data/uneven_alignment.aln",1,0,0,"");
}