Lines Matching refs:indels
64 Univcoord_T left, int indels, in Indel_resolve_middle_insertion() argument
83 assert(indels > 0); in Indel_resolve_middle_insertion()
135 ome,ome_alt,query_compress,left-indels,pos5,pos3, in Indel_resolve_middle_insertion()
151 gbuffer = (char *) CALLOC(querylength-indels+1,sizeof(char)); in Indel_resolve_middle_insertion()
152 Genome_fill_buffer_blocks(left+indels,querylength-indels,gbuffer); in Indel_resolve_middle_insertion()
154 plusp,want_lowest_coordinate_p,(unsigned long long) left,indels,(unsigned long long) left+indels); in Indel_resolve_middle_insertion()
156 printf("g2: %s\n",&(gbuffer[indels])); in Indel_resolve_middle_insertion()
170 … while (lefti >= 0 && mismatch_positions_left[lefti] > mismatch_positions_right[righti] - indels) { in Indel_resolve_middle_insertion()
175 sum,righti,lefti+1,mismatch_positions_right[righti]-indels+1)); in Indel_resolve_middle_insertion()
177 indel_pos = mismatch_positions_right[righti] - indels + 1; in Indel_resolve_middle_insertion()
178 …if (indel_pos >= min_indel_end_matches && indel_pos + indels <= querylength - min_indel_end_matche… in Indel_resolve_middle_insertion()
180 indel_pos > pos5 && indel_pos + indels < pos3) { in Indel_resolve_middle_insertion()
198 …while (righti >= 0 && mismatch_positions_right[righti] < mismatch_positions_left[lefti] + indels) { in Indel_resolve_middle_insertion()
206 …if (indel_pos >= min_indel_end_matches && indel_pos + indels <= querylength - min_indel_end_matche… in Indel_resolve_middle_insertion()
208 indel_pos > pos5 && indel_pos + indels < pos3) { in Indel_resolve_middle_insertion()
218 …if (indel_pos >= min_indel_end_matches && indel_pos + indels <= querylength - min_indel_end_matche… in Indel_resolve_middle_insertion()
220 indel_pos > pos5 && indel_pos + indels < pos3) { in Indel_resolve_middle_insertion()
241 …while (righti >= 0 && mismatch_positions_right[righti] < mismatch_positions_left[lefti] + indels) { in Indel_resolve_middle_insertion()
249 …if (indel_pos >= min_indel_end_matches && indel_pos + indels <= querylength - min_indel_end_matche… in Indel_resolve_middle_insertion()
251 indel_pos > pos5 && indel_pos + indels < pos3) { in Indel_resolve_middle_insertion()
269 … while (lefti >= 0 && mismatch_positions_left[lefti] > mismatch_positions_right[righti] - indels) { in Indel_resolve_middle_insertion()
274 sum,righti,lefti+1,mismatch_positions_right[righti]-indels+1)); in Indel_resolve_middle_insertion()
276 indel_pos = mismatch_positions_right[righti] - indels + 1; in Indel_resolve_middle_insertion()
277 …if (indel_pos >= min_indel_end_matches && indel_pos + indels <= querylength - min_indel_end_matche… in Indel_resolve_middle_insertion()
279 indel_pos > pos5 && indel_pos + indels < pos3) { in Indel_resolve_middle_insertion()
287 indel_pos = mismatch_positions_right[righti] - indels + 1; in Indel_resolve_middle_insertion()
289 …if (indel_pos >= min_indel_end_matches && indel_pos + indels <= querylength - min_indel_end_matche… in Indel_resolve_middle_insertion()
291 indel_pos > pos5 && indel_pos + indels < pos3) { in Indel_resolve_middle_insertion()
346 …_substring(&(*best_ref_nmismatches_j),genomebits,genomebits_alt,query_compress,/*left*/left-indels, in Indel_resolve_middle_insertion()
347 /*pos5*/best_indel_pos+indels,pos3,plusp,genestrand); in Indel_resolve_middle_insertion()
361 return querylength - best_indel_pos - indels; in Indel_resolve_middle_insertion()
382 Univcoord_T left, int indels, in Indel_resolve_middle_deletion() argument
401 assert(indels < 0); in Indel_resolve_middle_deletion()
452 ome,ome_alt,query_compress,left-indels,pos5,pos3, in Indel_resolve_middle_deletion()
468 gbuffer = (char *) CALLOC(querylength-indels+1,sizeof(char)); in Indel_resolve_middle_deletion()
469 Genome_fill_buffer_blocks(left,querylength-indels,gbuffer); in Indel_resolve_middle_deletion()
471 plusp,want_lowest_coordinate_p,indels,nmismatches_allowed,(unsigned long long) left); in Indel_resolve_middle_deletion()
473 printf("g2: %s\n",&(gbuffer[-indels])); in Indel_resolve_middle_deletion()
641 …_substring(&(*best_ref_nmismatches_j),genomebits,genomebits_alt,query_compress,/*left*/left-indels, in Indel_resolve_middle_deletion()
669 Univcoord_T left, int indels, in Indel_resolve_middle_deletion_or_splice() argument
719 assert(indels < 0); in Indel_resolve_middle_deletion_or_splice()
722 queryend = querylength - indels; /* Extends past querylength */ in Indel_resolve_middle_deletion_or_splice()
729 if (-indels >= min_intronlength) { in Indel_resolve_middle_deletion_or_splice()
730 queryend = pos3 - indels; /* Extends past pos3 */ in Indel_resolve_middle_deletion_or_splice()
739 plusp,want_lowest_coordinate_p,indels,nmismatches_allowed,querylength,(unsigned long long) left)); in Indel_resolve_middle_deletion_or_splice()
741 debug2(printf("g2: %s\n",&(gbuffer[-indels]))); in Indel_resolve_middle_deletion_or_splice()
765 ome,ome_alt,query_compress,left-indels,pos5,pos3, in Indel_resolve_middle_deletion_or_splice()
792 if (-indels >= min_intronlength) { in Indel_resolve_middle_deletion_or_splice()
797 right2 = gbuffer[indel_pos-indels-2]; in Indel_resolve_middle_deletion_or_splice()
798 right1 = gbuffer[indel_pos-indels-1]; in Indel_resolve_middle_deletion_or_splice()
849 if (-indels >= min_intronlength) { in Indel_resolve_middle_deletion_or_splice()
854 right2 = gbuffer[indel_pos-indels-2]; in Indel_resolve_middle_deletion_or_splice()
855 right1 = gbuffer[indel_pos-indels-1]; in Indel_resolve_middle_deletion_or_splice()
860 … gbuffer[indel_pos],gbuffer[indel_pos+1],gbuffer[indel_pos-indels-2],gbuffer[indel_pos-indels-1])); in Indel_resolve_middle_deletion_or_splice()
911 if (-indels >= min_intronlength) { in Indel_resolve_middle_deletion_or_splice()
916 right2 = gbuffer[indel_pos-indels-2]; in Indel_resolve_middle_deletion_or_splice()
917 right1 = gbuffer[indel_pos-indels-1]; in Indel_resolve_middle_deletion_or_splice()
922 … gbuffer[indel_pos],gbuffer[indel_pos+1],gbuffer[indel_pos-indels-2],gbuffer[indel_pos-indels-1])); in Indel_resolve_middle_deletion_or_splice()
968 if (-indels >= min_intronlength) { in Indel_resolve_middle_deletion_or_splice()
973 right2 = gbuffer[indel_pos-indels-2]; in Indel_resolve_middle_deletion_or_splice()
974 right1 = gbuffer[indel_pos-indels-1]; in Indel_resolve_middle_deletion_or_splice()
1022 if (-indels >= min_intronlength) { in Indel_resolve_middle_deletion_or_splice()
1054 …_substring(&(*best_ref_nmismatches_j),genomebits,genomebits_alt,query_compress,/*left*/left-indels, in Indel_resolve_middle_deletion_or_splice()