C++ (Cpp) gt_string_clear Examples

Example #1

File: gt_dna_read.c Project: MarcosFernandez/gemtools-cnv

GT_INLINE void gt_dna_read_clear(gt_dna_read* read) {
  GT_DNA_READ_CHECK(read);
  gt_string_clear(read->tag);
  gt_string_clear(read->read);
  gt_string_clear(read->qualities);
  gt_attributes_clear(read->attributes);
}

Example #2

File: gt_suite_template_utils.c Project: maikroeder/gemtools

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));
  }

Example #3

File: gt_suite_template_utils.c Project: maikroeder/gemtools

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);

}

Example #4

File: gt_segmented_sequence.c Project: fransua/gemtools

GT_INLINE void gt_segmented_sequence_clear(gt_segmented_sequence* const sequence) {
  GT_SEGMENTED_SEQ_CHECK(sequence);
  GT_VECTOR_ITERATE(sequence->blocks,block,block_num,uint64_t*) {
    if (*block) gt_free(*block);
  }
  gt_vector_clear(sequence->blocks);
  gt_string_clear(sequence->seq_name);
}

Example #5

File: gt_sam_attributes.c Project: fransua/gemtools

GT_INLINE void gt_sam_attribute_func_params_clear(gt_sam_attribute_func_params* const func_params) {
  GT_NULL_CHECK(func_params);
  /* Return Values */
  if (func_params->return_s!=NULL) gt_string_clear(func_params->return_s);
  /* Sequence Archive */
  func_params->sequence_archive = NULL;
  /* Template/Alignment source */
  func_params->alignment_info=NULL;
  /* Placeholder Vector */
  func_params->mmap_placeholder = NULL;
}

Example #6

File: gt_sam_attributes.c Project: fransua/gemtools

GT_INLINE void gt_sam_header_clear(gt_sam_headers* const sam_headers) {
  GT_SAM_HEADERS_CHECK(sam_headers);
  // Header
  gt_string_clear(sam_headers->header);
  // Read group
  GT_VECTOR_ITERATE(sam_headers->read_group,record_h,nh,gt_string*) { gt_string_delete(*record_h); }
  gt_vector_clear(sam_headers->read_group);
  // Program
  GT_VECTOR_ITERATE(sam_headers->program,record_p,np,gt_string*) { gt_string_delete(*record_p); }
  gt_vector_clear(sam_headers->program);
  // Comments
  GT_VECTOR_ITERATE(sam_headers->comments,comment,nc,gt_string*) { gt_string_delete(*comment); }
  gt_vector_clear(sam_headers->comments);
  // Seq Archive
  sam_headers->sequence_archive=NULL;
}