END_TEST
START_TEST(gt_test_loosing_alignments)
{
// test no maps no mmaps
fail_unless(gt_input_map_parse_template(
"67999,0\t"
"CAAAAATGAAGTAAAACTCTCACTCTTCACAGATGACATGATATTTTTATGTGGGAAACCCAAAAGAGTTCAACAGAAAACTGCTAGAACTGATACGTGAATTCAGCAAAGTTGCAAGATATAAAATCAATGTACAGATCGGTTGCATTTCTAGACACCAATAATGAAGCAGCAGAAAGAGATACCAAGAAATCGATCCTATTTACAATTGCACCCAAAACTGTCAGATACCAAGGAATAAACCTCACCAAAGAGGTATGCTGAAAACTATCGAAAGCTTAATGAAAGAAATTGAAGAAGATACAAAGAAATAGAAAAGCATGCCATGTTCATGGATTGGAAGAACAAATATTGTTAAAATGTCGATAGTACCCAAAGCAGTCTACACATTCAGTGCAATCCCTATCAAAATAACACCAGCATTCTTCATAGAGCTAGAACAAACAATTCTAAAATTTGTATGGAACCACGAAAGACCCCGAATAGCCGAGGTAATGTTTAAAAGGAAATCCAAAGATGGAGGCATCACAATTCCAGACTTCAAGCTGTATTACAAAGCTGTAATCATCAAACAAAAGGGTACTGGCACAAAACTAGAGACAGAGATCAATGGAACAGAATAGAGAACCCACAAATGGACTCACAAATGTATGGCCAACTAATCTTCAACAAAGCAGGAAAGAATATCCAATGGGAAAGAGTCTTCACAAATGGTATTGGCAAAACGGGACAACAACATGCAGAAGAATGAGCCTGGACCACTTTCTTACACCGTACACAAAAATGTATTCAAAATGGATGGAAGACCTAAATGTAAGACAGAAAACCATCAAAAATCCTAGAAGAGAACAGAAGCAGTAACTTCTTTGATTTTGGCCTTAGCAACTTCTTTCTAGACATGTATCCTGAGGCAAGCAAAAAAAACACAAAAATAAACTATTGGGACTACATCAAAACAAAAAGCTTCTGCACAGTGAAAGAAATAATCAACAAAACTAAA\t"
"2:0:0:0:0:1:0:0:0:1:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:1:0:1:0:0:1\t"
"267999:+:1:1000,302802:+:1:1000,283693:-:311:184T116C50C45C11G589,308701:+:1:37G9>1-6A14C114T116C50C45C11G589,302802:-:7693:773A52T2A1>1-11G2>1+1>1+5>2-3CC3C7C5>2-2>2+11A9CC1>1-2>1+7>1+1G3C4>1-8G11>1+2>1-6G1T17>1-C3>1+4C16,267998:+:1:773A52T2A5>1-7G3>1+2>1+3>2-3CC3C7C5TTGC11A9CC2>1-2>1+7>1+G3C4>1-8G12>1+1>1-6G1T17C>1-4>1+3C16,283521:-:317:184T116C50C45C11G362A52T2A1>1-11G2>1+1>1+5>2-3CC3C7C5>2-2>2+11A9CC1>1-2>1+7>1+1G3C4>1-8G11>1+2>1-6G1T17>1-C3>1+4C16",source)==0);
gt_string* string = gt_string_new(1024);
gt_output_map_sprint_template(string, source, output_attributes);
// convert to string
char * line = gt_string_get_string(string);
fail_unless(gt_streq(line,
"67999,0\t"
"CAAAAATGAAGTAAAACTCTCACTCTTCACAGATGACATGATATTTTTATGTGGGAAACCCAAAAGAGTTCAACAGAAAACTGCTAGAACTGATACGTGAATTCAGCAAAGTTGCAAGATATAAAATCAATGTACAGATCGGTTGCATTTCTAGACACCAATAATGAAGCAGCAGAAAGAGATACCAAGAAATCGATCCTATTTACAATTGCACCCAAAACTGTCAGATACCAAGGAATAAACCTCACCAAAGAGGTATGCTGAAAACTATCGAAAGCTTAATGAAAGAAATTGAAGAAGATACAAAGAAATAGAAAAGCATGCCATGTTCATGGATTGGAAGAACAAATATTGTTAAAATGTCGATAGTACCCAAAGCAGTCTACACATTCAGTGCAATCCCTATCAAAATAACACCAGCATTCTTCATAGAGCTAGAACAAACAATTCTAAAATTTGTATGGAACCACGAAAGACCCCGAATAGCCGAGGTAATGTTTAAAAGGAAATCCAAAGATGGAGGCATCACAATTCCAGACTTCAAGCTGTATTACAAAGCTGTAATCATCAAACAAAAGGGTACTGGCACAAAACTAGAGACAGAGATCAATGGAACAGAATAGAGAACCCACAAATGGACTCACAAATGTATGGCCAACTAATCTTCAACAAAGCAGGAAAGAATATCCAATGGGAAAGAGTCTTCACAAATGGTATTGGCAAAACGGGACAACAACATGCAGAAGAATGAGCCTGGACCACTTTCTTACACCGTACACAAAAATGTATTCAAAATGGATGGAAGACCTAAATGTAAGACAGAAAACCATCAAAAATCCTAGAAGAGAACAGAAGCAGTAACTTCTTTGATTTTGGCCTTAGCAACTTCTTTCTAGACATGTATCCTGAGGCAAGCAAAAAAAACACAAAAATAAACTATTGGGACTACATCAAAACAAAAAGCTTCTGCACAGTGAAAGAAATAATCAACAAAACTAAA\t"
"\t"
"2:0:0:0:0:1:0:0:0:1:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:1:0:1:0:0:1\t"
"267999:+:1:1000,302802:+:1:1000,283693:-:311:184T116C50C45C11G589,308701:+:1:37G9>1-6A14C114T116C50C45C11G589,302802:-:7693:773A52T2A1>1-11G2>1+1>1+5>2-3CC3C7C5>2-2>2+11A9CC1>1-2>1+7>1+1G3C4>1-8G11>1+2>1-6G1T17>1-C3>1+4C16,267998:+:1:773A52T2A5>1-7G3>1+2>1+3>2-3CC3C7C5TTGC11A9CC2>1-2>1+7>1+G3C4>1-8G12>1+1>1-6G1T17C>1-4>1+3C16,283521:-:317:184T116C50C45C11G362A52T2A1>1-11G2>1+1>1+5>2-3CC3C7C5>2-2>2+11A9CC1>1-2>1+7>1+1G3C4>1-8G11>1+2>1-6G1T17>1-C3>1+4C16\n"
));
gt_string_clear(string);
// try parsing the alignment
fail_unless(gt_input_map_parse_alignment(
"67999,0\t"
"CAAAAATGAAGTAAAACTCTCACTCTTCACAGATGACATGATATTTTTATGTGGGAAACCCAAAAGAGTTCAACAGAAAACTGCTAGAACTGATACGTGAATTCAGCAAAGTTGCAAGATATAAAATCAATGTACAGATCGGTTGCATTTCTAGACACCAATAATGAAGCAGCAGAAAGAGATACCAAGAAATCGATCCTATTTACAATTGCACCCAAAACTGTCAGATACCAAGGAATAAACCTCACCAAAGAGGTATGCTGAAAACTATCGAAAGCTTAATGAAAGAAATTGAAGAAGATACAAAGAAATAGAAAAGCATGCCATGTTCATGGATTGGAAGAACAAATATTGTTAAAATGTCGATAGTACCCAAAGCAGTCTACACATTCAGTGCAATCCCTATCAAAATAACACCAGCATTCTTCATAGAGCTAGAACAAACAATTCTAAAATTTGTATGGAACCACGAAAGACCCCGAATAGCCGAGGTAATGTTTAAAAGGAAATCCAAAGATGGAGGCATCACAATTCCAGACTTCAAGCTGTATTACAAAGCTGTAATCATCAAACAAAAGGGTACTGGCACAAAACTAGAGACAGAGATCAATGGAACAGAATAGAGAACCCACAAATGGACTCACAAATGTATGGCCAACTAATCTTCAACAAAGCAGGAAAGAATATCCAATGGGAAAGAGTCTTCACAAATGGTATTGGCAAAACGGGACAACAACATGCAGAAGAATGAGCCTGGACCACTTTCTTACACCGTACACAAAAATGTATTCAAAATGGATGGAAGACCTAAATGTAAGACAGAAAACCATCAAAAATCCTAGAAGAGAACAGAAGCAGTAACTTCTTTGATTTTGGCCTTAGCAACTTCTTTCTAGACATGTATCCTGAGGCAAGCAAAAAAAACACAAAAATAAACTATTGGGACTACATCAAAACAAAAAGCTTCTGCACAGTGAAAGAAATAATCAACAAAACTAAA\t"
"2:0:0:0:0:1:0:0:0:1:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:1:0:1:0:0:1\t"
"267999:+:1:1000,302802:+:1:1000,283693:-:311:184T116C50C45C11G589,308701:+:1:37G9>1-6A14C114T116C50C45C11G589,302802:-:7693:773A52T2A1>1-11G2>1+1>1+5>2-3CC3C7C5>2-2>2+11A9CC1>1-2>1+7>1+1G3C4>1-8G11>1+2>1-6G1T17>1-C3>1+4C16,267998:+:1:773A52T2A5>1-7G3>1+2>1+3>2-3CC3C7C5TTGC11A9CC2>1-2>1+7>1+G3C4>1-8G12>1+1>1-6G1T17C>1-4>1+3C16,283521:-:317:184T116C50C45C11G362A52T2A1>1-11G2>1+1>1+5>2-3CC3C7C5>2-2>2+11A9CC1>1-2>1+7>1+1G3C4>1-8G11>1+2>1-6G1T17>1-C3>1+4C16",alignment)==0);
gt_output_map_sprint_alignment(string, alignment, output_attributes);
// convert to string
line = gt_string_get_string(string);
fail_unless(gt_streq(line,
"67999,0\t"
"CAAAAATGAAGTAAAACTCTCACTCTTCACAGATGACATGATATTTTTATGTGGGAAACCCAAAAGAGTTCAACAGAAAACTGCTAGAACTGATACGTGAATTCAGCAAAGTTGCAAGATATAAAATCAATGTACAGATCGGTTGCATTTCTAGACACCAATAATGAAGCAGCAGAAAGAGATACCAAGAAATCGATCCTATTTACAATTGCACCCAAAACTGTCAGATACCAAGGAATAAACCTCACCAAAGAGGTATGCTGAAAACTATCGAAAGCTTAATGAAAGAAATTGAAGAAGATACAAAGAAATAGAAAAGCATGCCATGTTCATGGATTGGAAGAACAAATATTGTTAAAATGTCGATAGTACCCAAAGCAGTCTACACATTCAGTGCAATCCCTATCAAAATAACACCAGCATTCTTCATAGAGCTAGAACAAACAATTCTAAAATTTGTATGGAACCACGAAAGACCCCGAATAGCCGAGGTAATGTTTAAAAGGAAATCCAAAGATGGAGGCATCACAATTCCAGACTTCAAGCTGTATTACAAAGCTGTAATCATCAAACAAAAGGGTACTGGCACAAAACTAGAGACAGAGATCAATGGAACAGAATAGAGAACCCACAAATGGACTCACAAATGTATGGCCAACTAATCTTCAACAAAGCAGGAAAGAATATCCAATGGGAAAGAGTCTTCACAAATGGTATTGGCAAAACGGGACAACAACATGCAGAAGAATGAGCCTGGACCACTTTCTTACACCGTACACAAAAATGTATTCAAAATGGATGGAAGACCTAAATGTAAGACAGAAAACCATCAAAAATCCTAGAAGAGAACAGAAGCAGTAACTTCTTTGATTTTGGCCTTAGCAACTTCTTTCTAGACATGTATCCTGAGGCAAGCAAAAAAAACACAAAAATAAACTATTGGGACTACATCAAAACAAAAAGCTTCTGCACAGTGAAAGAAATAATCAACAAAACTAAA\t"
"\t"
"2:0:0:0:0:1:0:0:0:1:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:1:0:1:0:0:1\t"
"267999:+:1:1000,302802:+:1:1000,283693:-:311:184T116C50C45C11G589,308701:+:1:37G9>1-6A14C114T116C50C45C11G589,302802:-:7693:773A52T2A1>1-11G2>1+1>1+5>2-3CC3C7C5>2-2>2+11A9CC1>1-2>1+7>1+1G3C4>1-8G11>1+2>1-6G1T17>1-C3>1+4C16,267998:+:1:773A52T2A5>1-7G3>1+2>1+3>2-3CC3C7C5TTGC11A9CC2>1-2>1+7>1+G3C4>1-8G12>1+1>1-6G1T17C>1-4>1+3C16,283521:-:317:184T116C50C45C11G362A52T2A1>1-11G2>1+1>1+5>2-3CC3C7C5>2-2>2+11A9CC1>1-2>1+7>1+1G3C4>1-8G11>1+2>1-6G1T17>1-C3>1+4C16\n"
));
gt_string_clear(string);
gt_alignment *alignment_dst;
alignment_dst = gt_alignment_copy(alignment,false);
GT_ALIGNMENT_ITERATE(alignment,map) {
gt_alignment_insert_map(alignment_dst,gt_map_copy(map));
}
END_TEST
START_TEST(gt_test_template_copy)
{
// test no maps no mmaps
fail_unless(gt_input_map_parse_template(
"ID\tACGT\t####\t1\tchr1:-:20:4",source)==0);
gt_template* copy = gt_template_copy(source, false, false);
gt_string* string = gt_string_new(1024);
gt_output_map_sprint_template(string, copy, output_attributes);
// convert to string for simple check
char * line = gt_string_get_string(string);
fail_unless(gt_streq(line,"ID\tACGT\t####\t0\t-\n"));
gt_template_delete(copy);
// test maps no mmaps
gt_string_clear(string);
copy = gt_template_copy(source, true, false);
string = gt_string_new(1024);
gt_output_map_sprint_template(string, copy, output_attributes);
// convert to string for simple check
line = gt_string_get_string(string);
fail_unless(gt_streq(line,"ID\tACGT\t####\t1\tchr1:-:20:4\n"));
gt_template_delete(copy);
// test maps no mmaps with multi map string
fail_unless(gt_input_map_parse_template(
"ID\tACGT\t####\t2\tchr1:-:20:4,chr2:-:40:4",source)==0);
gt_string_clear(string);
copy = gt_template_copy(source, true, false);
string = gt_string_new(1024);
gt_output_map_sprint_template(string, copy, output_attributes);
// convert to string for simple check
line = gt_string_get_string(string);
fail_unless(gt_streq(line,"ID\tACGT\t####\t2\tchr1:-:20:4,chr2:-:40:4\n"));
gt_template_delete(copy);
// test maps and mmaps
gt_string_clear(string);
copy = gt_template_copy(source, true, true);
string = gt_string_new(1024);
gt_output_map_sprint_template(string, copy, output_attributes);
// convert to string for simple check
line = gt_string_get_string(string);
fail_unless(gt_streq(line,"ID\tACGT\t####\t2\tchr1:-:20:4,chr2:-:40:4\n"));
gt_template_delete(copy);
}
GT_INLINE void gt_options_fprint_menu(
FILE* const stream,const gt_option* const options,char* groups[],
const bool print_description,const bool print_inactive) {
const uint64_t num_options = gt_options_get_num_options(options);
int64_t i, last_group = -1;
for (i=0;i<num_options;++i) {
if (!print_inactive && !options[i].active) continue;
// Print group (if not printed yet)
if (last_group!=options[i].group_id) {
fprintf(stream," [%s]\n",groups[options[i].group_id]);
last_group=options[i].group_id;
}
// Print Long Option
fprintf(stream," --%s",options[i].long_option);
// Print Short Option (if it has)
const char short_option = options[i].option_id;
if (options[i].option_id<128 && gt_is_alphanumeric(short_option)) {
fprintf(stream,"|-%c",short_option);
}
// Print extra command line syntax info
fprintf(stream," %s\n",options[i].command_info);
// Print description (@print_description)
if (print_description && !gt_streq(options[i].description,"")) {
fprintf(stream,"%s",options[i].description);
}
}
}
END_TEST
START_TEST(gt_test_template_merge_inconsistent)
{
fail_unless(gt_input_map_parse_template(
"ID/1\t"
"GAGAGAACAGGCCTCTGAGCCCAAGCCAAGCCATCGCATCCCCTGTGACTTGCCCGTATATATGCCCAGATGGCCTGAAGTAACTGAAGAATCACAAAAGA\t"
"BPYcceeegegggiiiiiiiiiiiiiiighhhfgghhiiihhhifhfhhhfhhdghhiiihfbggedddeabbcdcccb`ZaW[^^abbcGW[`^`R]`BB\t"
"0:0:0:0:1:4+27:46:45:34:12:16:3:0:1\t"
"chr7:+:24435865:1T>5-46A8C38,chr2:+:64479547:>1-1T>1-1T>1-94,chr4:+:16999371:1T>5-35>2-9A8C38,chr9:+:90025610:1T>5-28A17A8C38,chr11:-:130623749:2>1-1T1T46A2>2-43",source)==0);
fail_unless(gt_input_map_parse_template(
"ID/1\t"
"GAGAGAACAGGCCTCTGAGCCCAAGCCAAGCCATCGCATCCCCTGTGACTTGCCCGTATATATGCCCAGATGGCCTGAAGTAACTGAAGAATCACAAAAGA\t"
"BPYcceeegegggiiiiiiiiiiiiiiighhhfgghhiiihhhifhfhhhfhhdghhiiihfbggedddeabbcdcccb`ZaW[^^abbcGW[`^`R]`BB\t"
"0:1:0:0:0:0:1:3\t"
"chr2:+:64479108:10>436*91,chr2:+:64479544:TTC1TGT94,chr13:+:91496959:1GA1TGT27T18A47,chr2:+:216792393:1GA1TGT46A8C38,chr2:+:64478959:AG1T1G1TT1>585*91",target)==0);
// merge into source
gt_template_recalculate_counters(source);
gt_template_merge_template_mmaps(source,target);
gt_string* string = gt_string_new(1024);
gt_output_map_sprint_template(string, source, output_attributes);
// convert to string
char* line = gt_string_get_string(string);
fail_unless(gt_streq(line,
"ID/1\t"
"GAGAGAACAGGCCTCTGAGCCCAAGCCAAGCCATCGCATCCCCTGTGACTTGCCCGTATATATGCCCAGATGGCCTGAAGTAACTGAAGAATCACAAAAGA\t"
"BPYcceeegegggiiiiiiiiiiiiiiighhhfgghhiiihhhifhfhhhfhhdghhiiihfbggedddeabbcdcccb`ZaW[^^abbcGW[`^`R]`BB\t"
"0:1:0:0:1:4+1:3\t"
"chr2:+:64479108:10>436*91,chr7:+:24435865:1T>5-46A8C38,chr2:+:64479547:(1)1T>1-1T>1-94,"
"chr4:+:16999371:1T>5-35>2-9A8C38,chr9:+:90025610:1T>5-28A17A8C38,chr11:-:130623749:2>1-1T1T46A2>2-43,"
"chr2:+:64479544:TTC1TGT94,chr13:+:91496959:1GA1TGT27T18A47,chr2:+:216792393:1GA1TGT46A8C38,"
"chr2:+:64478959:AG1T1G1TT1>585*91\n"));
}
END_TEST
START_TEST(gt_test_template_merge_error)
{
fail_unless(gt_input_map_parse_template(
"HISEQ8_0071:3:1101:19107:2010#TGACCA/1\t"
"NGTCATGAGTGCAAAATGCAAATGCAAGTTTGGCCAGAAGTCCGGTCACCATCCAGGGGAGACTCCACCTCTCATCACCCCAGGCTCAGCCCAAAGCTGAT\t"
"BPYcceeegegggiiiiiiiiiiiiiiighhhfgghhiiihhhifhfhhhfhhdghhiiihfbggedddeabbcdcccb`ZaW[^^abbcGW[`^`R]`BB\t"
"0:0:0:0:1\t"
"chr19:+:35613736:C7>78*37>316*38>132*18",source)==0);
fail_unless(gt_input_map_parse_template(
"HISEQ8_0071:3:1101:19107:2010#TGACCA/1\t"
"NGTCATGAGTGCAAAATGCAAATGCAAGTTTGGCCAGAAGTCCGGTCACCATCCAGGGGAGACTCCACCTCTCATCACCCCAGGCTCAGCCCAAAGCTGAT\t"
"BPYcceeegegggiiiiiiiiiiiiiiighhhfgghhiiihhhifhfhhhfhhdghhiiihfbggedddeabbcdcccb`ZaW[^^abbcGW[`^`R]`BB\t"
"0:0:0:0:1+0:1\t"
"chr19:+:35613741:(5)3>78*37>316*36(20),chr19:+:35613819:(5)CAG37>316*36(20)", target)==0);
// merge into source
gt_template_merge_template_mmaps(source,target);
gt_string* string = gt_string_new(1024);
gt_output_map_sprint_template(string, source, output_attributes);
// convert to string
char * line = gt_string_get_string(string);
fail_unless(gt_streq(line,
"HISEQ8_0071:3:1101:19107:2010#TGACCA/1\t"
"NGTCATGAGTGCAAAATGCAAATGCAAGTTTGGCCAGAAGTCCGGTCACCATCCAGGGGAGACTCCACCTCTCATCACCCCAGGCTCAGCCCAAAGCTGAT\t"
"BPYcceeegegggiiiiiiiiiiiiiiighhhfgghhiiihhhifhfhhhfhhdghhiiihfbggedddeabbcdcccb`ZaW[^^abbcGW[`^`R]`BB\t"
"0:0:0:0:2+0:1\t"
"chr19:+:35613736:C7>78*37>316*38>132*18,chr19:+:35613741:(5)3>78*37>316*36(20),chr19:+:35613819:(5)CAG37>316*36(20)\n"));
}
GT_INLINE void gt_options_fprint_json_menu(
FILE* const stream,const gt_option* const options,char* groups[],
const bool print_description,const bool print_inactive) {
const uint64_t num_options = gt_options_get_num_options(options);
int64_t i;
bool at_least_one_printed = false;
fprintf(stream,"{ \n"); // Begin JSON record
fprintf(stream,"\"numOptions\": %"PRIu64",\n",num_options);
fprintf(stream,"\"options\": [ \n");
for (i=0;i<num_options;++i) {
if (!print_inactive && !options[i].active) continue;
if(at_least_one_printed){
fprintf(stream,",\n");
}
at_least_one_printed = true;
fprintf(stream,"\t{ \n");
// Print ID/Short Option
fprintf(stream,"\t \"ID\": %d,\n",options[i].option_id);
// Print Long Option
fprintf(stream,"\t \"longOption\": \"%s\",\n",options[i].long_option);
// Print Short Option
const char short_option = options[i].option_id;
if (options[i].option_id<128 && gt_is_alphanumeric(short_option)) {
fprintf(stream,"\t \"shortOption\": \"%c\",\n",short_option);
} else {
fprintf(stream,"\t \"shortOption\": null,\n");
}
// Group
fprintf(stream,"\t \"group\": \"%s\",\n",groups[options[i].group_id]);
// Option Type
switch (options[i].option_type) {
case GT_OPT_NO_ARGUMENT: fprintf(stream,"\t \"optionType\": \"noArgument\",\n"); break;
case GT_OPT_REQUIRED: fprintf(stream,"\t \"optionType\": \"required\",\n"); break;
case GT_OPT_OPTIONAL: fprintf(stream,"\t \"optionType\": \"optional\",\n"); break;
}
// Argument Type
switch (options[i].argument_type) {
case GT_OPT_NONE: fprintf(stream,"\t \"argumentType\": null,\n"); break;
case GT_OPT_INT: fprintf(stream,"\t \"argumentType\": \"int\",\n"); break;
case GT_OPT_FLOAT: fprintf(stream,"\t \"argumentType\": \"float\",\n"); break;
case GT_OPT_CHAR: fprintf(stream,"\t \"argumentType\": \"char\",\n"); break;
case GT_OPT_STRING: fprintf(stream,"\t \"argumentType\": \"string\",\n"); break;
case GT_OPT_BOOL: fprintf(stream,"\t \"argumentType\": \"bool\",\n"); break;
}
// Print extra command line syntax info
fprintf(stream,"\t \"commandInfo\": \"%s\"",options[i].command_info);
// Print description (@print_description)
if (print_description && !gt_streq(options[i].description,"")) {
fprintf(stream,",\n\t \"description\": \"%s\"",options[i].description);
}
fprintf(stream,"\n\t}");
}
fprintf(stream,"\n ]\n");
fprintf(stream,"}\n");
}
END_TEST
START_TEST(gt_test_template_to_string)
{
fail_unless(gt_input_map_parse_template(
"ID\tACGT\t####\t1\tchr1:-:20:4",source)==0);
gt_string* string = gt_string_new(1024);
gt_output_map_sprint_template(string, source, output_attributes);
// convert to string
char * line = gt_string_get_string(string);
fail_unless(gt_streq(line,"ID\tACGT\t####\t1\tchr1:-:20:4\n"));
}
END_TEST
START_TEST(gt_test_template_merge_hang)
{
fail_unless(gt_input_map_parse_template(
"HWI-962:71:D0PEYACXX:4:1101:18640:2354/2\tCGCGCGGGAGCCAGCAGGAGCACCAGCTGCGCAGGCAGGTTGAACTGCTGGCTTATAAAGTAGAGCAGGAGAAGT\t"
"@CCFFFFFHHHHHIJIJJIJJJJJJJIIJGIDGIHHHFF6>CCCDEDDDDCBDD>CCDCC>CCCCCDDDDDBDC>\t0:0:0:0:0:0\t-",source)==0);
fail_unless(gt_input_map_parse_template(
"HWI-962:71:D0PEYACXX:4:1101:18640:2354/2\tCGCGCGGGAGCCAGCAGGAGCACCAGCTGCGCAGGCAGGTTGAACTGCTGGCTTATAAAGTAGAGCAGGAGAAGT\t"
"@CCFFFFFHHHHHIJIJJIJJJJJJJIIJGIDGIHHHFF6>CCCDEDDDDCBDD>CCDCC>CCCCCDDDDDBDC>\t0:1\tchr21:+:47848466:39>1419*36",target)==0);
// merge into source
gt_template_merge_template_mmaps(source,target);
gt_string* string = gt_string_new(1024);
gt_output_map_sprint_template(string, source, output_attributes);
// convert to string
char * line = gt_string_get_string(string);
fail_unless(gt_streq(line,"HWI-962:71:D0PEYACXX:4:1101:18640:2354/2\tCGCGCGGGAGCCAGCAGGAGCACCAGCTGCGCAGGCAGGTTGAACTGCTGGCTTATAAAGTAGAGCAGGAGAAGT\t"
"@CCFFFFFHHHHHIJIJJIJJJJJJJIIJGIDGIHHHFF6>CCCDEDDDDCBDD>CCDCC>CCCCCDDDDDBDC>\t0:1+0:0:0:0\tchr21:+:47848466:39>1419*36\n"));
}
));
gt_string_clear(string);
gt_alignment *alignment_dst;
alignment_dst = gt_alignment_copy(alignment,false);
GT_ALIGNMENT_ITERATE(alignment,map) {
gt_alignment_insert_map(alignment_dst,gt_map_copy(map));
}
gt_output_map_sprint_alignment(string, alignment_dst, output_attributes);
// convert to string
line = gt_string_get_string(string);
fail_unless(gt_streq(line,
"67999,0\t"
"CAAAAATGAAGTAAAACTCTCACTCTTCACAGATGACATGATATTTTTATGTGGGAAACCCAAAAGAGTTCAACAGAAAACTGCTAGAACTGATACGTGAATTCAGCAAAGTTGCAAGATATAAAATCAATGTACAGATCGGTTGCATTTCTAGACACCAATAATGAAGCAGCAGAAAGAGATACCAAGAAATCGATCCTATTTACAATTGCACCCAAAACTGTCAGATACCAAGGAATAAACCTCACCAAAGAGGTATGCTGAAAACTATCGAAAGCTTAATGAAAGAAATTGAAGAAGATACAAAGAAATAGAAAAGCATGCCATGTTCATGGATTGGAAGAACAAATATTGTTAAAATGTCGATAGTACCCAAAGCAGTCTACACATTCAGTGCAATCCCTATCAAAATAACACCAGCATTCTTCATAGAGCTAGAACAAACAATTCTAAAATTTGTATGGAACCACGAAAGACCCCGAATAGCCGAGGTAATGTTTAAAAGGAAATCCAAAGATGGAGGCATCACAATTCCAGACTTCAAGCTGTATTACAAAGCTGTAATCATCAAACAAAAGGGTACTGGCACAAAACTAGAGACAGAGATCAATGGAACAGAATAGAGAACCCACAAATGGACTCACAAATGTATGGCCAACTAATCTTCAACAAAGCAGGAAAGAATATCCAATGGGAAAGAGTCTTCACAAATGGTATTGGCAAAACGGGACAACAACATGCAGAAGAATGAGCCTGGACCACTTTCTTACACCGTACACAAAAATGTATTCAAAATGGATGGAAGACCTAAATGTAAGACAGAAAACCATCAAAAATCCTAGAAGAGAACAGAAGCAGTAACTTCTTTGATTTTGGCCTTAGCAACTTCTTTCTAGACATGTATCCTGAGGCAAGCAAAAAAAACACAAAAATAAACTATTGGGACTACATCAAAACAAAAAGCTTCTGCACAGTGAAAGAAATAATCAACAAAACTAAA\t"
"\t"
"2:0:0:0:0:1:0:0:0:1:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:0:1:0:1:0:0:1\t"
"267999:+:1:1000,302802:+:1:1000,283693:-:311:184T116C50C45C11G589,308701:+:1:37G9>1-6A14C114T116C50C45C11G589,302802:-:7693:773A52T2A1>1-11G2>1+1>1+5>2-3CC3C7C5>2-2>2+11A9CC1>1-2>1+7>1+1G3C4>1-8G11>1+2>1-6G1T17>1-C3>1+4C16,267998:+:1:773A52T2A5>1-7G3>1+2>1+3>2-3CC3C7C5TTGC11A9CC2>1-2>1+7>1+G3C4>1-8G12>1+1>1-6G1T17C>1-4>1+3C16,283521:-:317:184T116C50C45C11G362A52T2A1>1-11G2>1+1>1+5>2-3CC3C7C5>2-2>2+11A9CC1>1-2>1+7>1+1G3C4>1-8G11>1+2>1-6G1T17>1-C3>1+4C16\n"
));
gt_string_clear(string);
}
END_TEST
Suite *gt_template_utils_suite(void) {
Suite *s = suite_create("gt_template_utils");
/* String parsers test case */
TCase *test_case = tcase_create("Template Utils");
tcase_add_checked_fixture(test_case,gt_template_utils_setup,gt_template_utils_teardown);
tcase_add_test(test_case,gt_test_template_merge);
