| /dports/biology/subread/subread-2.0.2-source/src/ |
| H A D | gene-algorithms.h | 59 …r, gene_value_index_t * array_index, char * read_txt, int read_len, int max_indel, int total_subre…
94 void show_cigar(char * info, int len, int is_reversed_map, char * buf, int max_indel, int total_sub…
96 … read_len, gene_value_index_t * index, unsigned int begin_position, int max_indel, char * movement…
98 … read_len, gene_value_index_t * index, unsigned int begin_position, int max_indel, char * movement…
100 …r, gene_value_index_t * array_index, char * read_txt, int read_len, int max_indel, int total_subre…
102 …r, gene_value_index_t * array_index, char * read_txt, int read_len, int max_indel, int total_subre…
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| H A D | gene-algorithms.c | 966 …vote, qid , pos, max_indel_recorder, array_index, read_txt, read_len, max_indel, total_subreads,… in find_and_explain_indel()
1001 if (i >= max_indel*3) break; in explain_indel_in_middle()
1009 if (max_indel_recorder[i+3]- black_subread_end>2 || i >= max_indel*3-3) break; in explain_indel_in_middle()
1033 …ack_base_end-black_base_start , array_index, pos + blackref_base_start, max_indel, indel_operation… in explain_indel_in_middle()
1109 … max_indel_recorder + qid * allvote -> indel_recorder_length+1, max_indel_recorder, 3 * max_indel); in explain_indel_in_middle()
1766 …ad_len, index, begin_position, path_i , path_j -1, table , table_mask, max_indel, movement_buffer… in search_DP_branch()
1781 …_len, index, begin_position, path_i -1 , path_j -1, table , table_mask, max_indel, movement_buffer… in search_DP_branch()
1790 … read_len, gene_value_index_t * index, unsigned int begin_position, int max_indel, char * movement… in window_indel_align() argument
1900 … read_len, gene_value_index_t * index, unsigned int begin_position, int max_indel, char * movement… in dynamic_align() argument
1922 if (j < i - max_indel || j > max_indel + i) in dynamic_align()
[all …]
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| H A D | core-indel.c | 4584 int max_indel = min(16 , global_context->config.max_indel_length); in core_dynamic_align() local
4592 if(read_len < 3 || abs(expected_offset) > max_indel) in core_dynamic_align()
4640 if (j < i - max_indel || j > max_indel + i) in core_dynamic_align()
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| /dports/biology/cd-hit/cdhit-4.8.1/ |
| H A D | cdhit-common.h | 281 int max_indel; // -D member
343 max_indel = 1; in Options()
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| H A D | cdhit-common.c++ | 277 else if( strcmp(flag, "-D") == 0 ){ max_indel = atoi(value); return true; } in SetOption()
1097 if( options.is454 and max_indels > options.max_indel ) return FAILED_FUNC; in local_band_align()
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| /dports/biology/bcftools/bcftools-1.14/ |
| H A D | mpileup.c | 410 int min_indel = INT_MAX, max_indel = INT_MIN; in mplp_realn() local
424 if (max_indel < p->indel) in mplp_realn()
425 max_indel = p->indel; in mplp_realn()
433 (has_clip < 0.2*nt && max_indel == min_indel && in mplp_realn()
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| /dports/biology/bio-mocha/bcftools-1.14/ |
| H A D | mpileup.c | 410 int min_indel = INT_MAX, max_indel = INT_MIN; in mplp_realn() local
424 if (max_indel < p->indel) in mplp_realn()
425 max_indel = p->indel; in mplp_realn()
433 (has_clip < 0.2*nt && max_indel == min_indel && in mplp_realn()
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| /dports/biology/py-pysam/pysam-0.18.0/bcftools/ |
| H A D | mpileup.c | 410 int min_indel = INT_MAX, max_indel = INT_MIN; in mplp_realn() local
424 if (max_indel < p->indel) in mplp_realn()
425 max_indel = p->indel; in mplp_realn()
433 (has_clip < 0.2*nt && max_indel == min_indel && in mplp_realn()
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| H A D | mpileup.c.pysam.c | 412 int min_indel = INT_MAX, max_indel = INT_MIN; in mplp_realn() local
426 if (max_indel < p->indel) in mplp_realn()
427 max_indel = p->indel; in mplp_realn()
435 (has_clip < 0.2*nt && max_indel == min_indel && in mplp_realn()
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