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 gt_string* gt_qualities_dup__adapt_offset64_to_offset33(gt_string* const qualities) {
gt_string* qualities_dst = gt_string_new(gt_string_get_length(qualities)+1);
gt_string_set_length(qualities_dst,gt_string_get_length(qualities)+1);
char* const qualities_dst_buf = gt_string_get_string(qualities_dst);
GT_STRING_ITERATE(qualities,qualities_buf,pos) {
qualities_dst_buf[pos] = qualities_buf[pos]-64+33;
}
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"));
}
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_INLINE void gt_sam_header_add_sequence_record(gt_sam_headers* const sam_headers,gt_sam_header_record* const header_record) {
GT_SAM_HEADERS_CHECK(sam_headers);
gt_string *sn_tag=gt_sam_header_record_get_tag(header_record,"SN");
gt_cond_error(!sn_tag,PARSE_SAM_HEADER_MISSING_TAG,"SQ","SN");
gt_cond_error(!gt_sam_header_record_get_tag(header_record,"LN"),PARSE_SAM_HEADER_MISSING_TAG,"SQ","LN");
if(sn_tag) {
if(!sam_headers->sequence_dictionary_sn_hash) sam_headers->sequence_dictionary_sn_hash=gt_shash_new();
char *sn_str=gt_string_get_string(sn_tag);
size_t* ix=gt_shash_get_element(sam_headers->sequence_dictionary_sn_hash,sn_str);
// If SN Tag already exists, overwrite.
if(ix) {
gt_sam_header_record_delete(*(gt_sam_header_record **)gt_vector_get_elm(sam_headers->sequence_dictionary,*ix,gt_sam_header_record*));
gt_vector_set_elm(sam_headers->sequence_dictionary,*ix,gt_sam_header_record*,header_record);
gt_error(PARSE_SAM_HEADER_DUPLICATE_TAG,"SQ","SN",sn_str);
} else {
ix=gt_alloc(size_t);
*ix=gt_vector_get_used(sam_headers->sequence_dictionary);
gt_shash_insert(sam_headers->sequence_dictionary_sn_hash,sn_str,ix,size_t*);
gt_vector_insert(sam_headers->sequence_dictionary,header_record,gt_sam_header_record*);
}
}
GT_INLINE char* gt_dna_read_get_qualities(gt_dna_read* const read) {
GT_DNA_READ_CHECK(read);
return gt_string_get_string(read->qualities);
}
GT_INLINE char* gt_dna_read_get_read(gt_dna_read* const read) {
GT_DNA_READ_CHECK(read);
return gt_string_get_string(read->read);
}
GT_INLINE char* gt_segmented_sequence_get_name(gt_segmented_sequence* const sequence) {
GT_SEGMENTED_SEQ_CHECK(sequence);
return gt_string_get_string(sequence->seq_name);
}
gt_status parse_arguments(int argc,char** argv) {
gt_status err=GT_STATUS_OK;
struct option* gt_coverage_getopt = gt_options_adaptor_getopt(gt_coverage_options);
gt_string* const gt_coverage_short_getopt = gt_options_adaptor_getopt_short(gt_coverage_options);
int option, option_index;
while (true) {
if ((option=getopt_long(argc,argv,
gt_string_get_string(gt_coverage_short_getopt),gt_coverage_getopt,&option_index))==-1) break;
switch (option) {
case 'c':
parameters.combine=true;
break;
case 'd':
parameters.detailed_output=true;
break;
case 'b':
parameters.block_size = atol(optarg);
break;
case 'o':
parameters.output_file = optarg;
break;
case 'p':
parameters.prefix = optarg;
break;
case 'r':
parameters.ranges_file = optarg;
break;
case 't':
parameters.target_file = optarg;
break;
case 'x':
parameters.extend = atol(optarg);
break;
case 'P':
parameters.paired = true;
break;
case 'U':
if(!strcasecmp("first",optarg)) parameters.unique=GT_UNIQUE_FIRST;
else if(!strcasecmp("gem",optarg)) parameters.unique=GT_UNIQUE_GEM;
else if(!strcasecmp("xt",optarg)) parameters.unique=GT_UNIQUE_XT;
else if(!strncasecmp("mq:",optarg,3)) {
parameters.unique=GT_UNIQUE_MQ;
parameters.MQ_limit=atol(optarg+3);
} else {
gt_fatal_error_msg("Unique mode not recognized: '%s'",optarg);
}
break;
case 'D':
if(!strcasecmp("ignore",optarg)) parameters.duplicate=GT_DUPLICATE_IGNORE;
else if(!strcasecmp("remove",optarg)) parameters.duplicate=GT_DUPLICATE_REMOVE;
else {
gt_fatal_error_msg("Duplicate mode not recognized: '%s'",optarg);
}
break;
case 'q':
parameters.min_quality = atol(optarg);
break;
case 'v':
parameters.verbose=true;
break;
case 'T':
#ifdef HAVE_OPENMP
parameters.num_threads = atol(optarg);
#endif
break;
case 'h':
usage(gt_coverage_options,gt_coverage_groups,false);
exit(1);
break;
case 'H':
usage(gt_coverage_options,gt_coverage_groups,true);
exit(1);
case 'J':
gt_options_fprint_json_menu(stderr,gt_coverage_options,gt_coverage_groups,true,false);
exit(1);
break;
case '?':
default:
usage(gt_coverage_options,gt_coverage_groups,false);
gt_fatal_error_msg("Option '%c' %d not recognized",option,option);
break;
}
}
if(!parameters.ranges_file) {
fputs("No ranges file specified. Use -r or --ranges_file option\n",stderr);
}
return err;
}
"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));
}
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");
