move inwards one at a time, remove gap extending, Bonferroni correction

nickjcroucher · Mar 13, 2013 · 80ea76d · 80ea76d
1 parent d6f5f43
commit 80ea76d
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Showing 2 changed files with 16 additions and 10 deletions.
diff --git a/src/branch_sequences.c b/src/branch_sequences.c
@@ -473,9 +473,15 @@ void get_likelihood_for_windows(char * child_sequence, int length_of_sequence, i
  number_of_candidate_blocks++;
  break;
  }
- // TODO need a more intelligent way to move inwards.
- current_start++;
- current_end--;
+
+ if(loop_counter %2 == 0)
+ {
+ current_start++;
+ }
+ else
+ {
+ current_end--;
+ }
 
  if(loop_counter > 0)
  {
@@ -590,11 +596,11 @@ int merge_adjacent_blocks(int ** block_coordinates, int number_of_blocks, char *
  return number_of_blocks; 
  }
 
- for(i=0; i < number_of_blocks; i++)
- {
- block_coordinates[0][i] = extend_end_of_block_left_over_gap( block_coordinates[0][i], branch_snp_sequence, number_of_bases, snp_site_coords);
- block_coordinates[1][i] = extend_end_of_block_right_over_gap(block_coordinates[1][i], branch_snp_sequence, number_of_bases, snp_site_coords);
- }
+ //for(i=0; i < number_of_blocks; i++)
+ //{
+ // block_coordinates[0][i] = extend_end_of_block_left_over_gap( block_coordinates[0][i], branch_snp_sequence, number_of_bases, snp_site_coords);
+ // block_coordinates[1][i] = extend_end_of_block_right_over_gap(block_coordinates[1][i], branch_snp_sequence, number_of_bases, snp_site_coords);
+ //}
 
  merged_block_coordinates[0][current_merged_block] = block_coordinates[0][current_merged_block];
  merged_block_coordinates[1][current_merged_block] = block_coordinates[1][current_merged_block]; 
@@ -760,7 +766,7 @@ int p_value_test(int branch_genome_size, int window_size, int num_branch_snps, i
  return 0; 
  }
 
- threshold = 0.05/branch_genome_size;
+ threshold = 0.05/num_branch_snps;
 
  while( cutoff < block_snp_count)
  {

diff --git a/tests/check_branch_sequences.c b/tests/check_branch_sequences.c
@@ -368,7 +368,7 @@ Suite * check_branch_sequences_suite (void)
  tcase_add_test (tc_branch_sequences, check_merge_adjacent_blocks_near_each_other);
  tcase_add_test (tc_branch_sequences, check_merge_adjacent_blocks_overlapping);
  tcase_add_test (tc_branch_sequences, check_exclude_snp_sites_in_block);
- tcase_add_test (tc_branch_sequences, check_merge_block_straddling_gap);
+ //tcase_add_test (tc_branch_sequences, check_merge_block_straddling_gap);
  tcase_add_test (tc_branch_sequences, check_extend_end_of_block_right_over_gap);
  tcase_add_test (tc_branch_sequences, check_dont_extend_right_if_gap_non_contiguous);
  tcase_add_test (tc_branch_sequences, check_extend_right_over_multiple_gaps);