From 80ea76da53644875f7dd0087689085d0bb812304 Mon Sep 17 00:00:00 2001 From: andrewjpage Date: Wed, 13 Mar 2013 09:41:27 +0000 Subject: [PATCH] move inwards one at a time, remove gap extending, Bonferroni correction --- src/branch_sequences.c | 24 +++++++++++++++--------- tests/check_branch_sequences.c | 2 +- 2 files changed, 16 insertions(+), 10 deletions(-) diff --git a/src/branch_sequences.c b/src/branch_sequences.c index 028d01df..a4c775ee 100644 --- 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 index 5e2bcf8d..51027063 100644 --- 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);