/dports/biology/gmap/gmap-2020-09-12/src/ |
H A D | dynprog_single.c | 181 Pairpool_T pairpool, int dynprogindex) { in augment_pairs() 356 int roffset, int goffset, Pairpool_T pairpool, in single_gap_simple() 435 bool watsonp, int genestrand, bool jump_late_p, Pairpool_T pairpool, in Dynprog_single_gap() 677 Pairpool_T pairpool, char gapchar, int dynprogindex) { in make_microexon_pairs_double() 896 bool watsonp, int genestrand, Pairpool_T pairpool) { in Dynprog_microexon_int()
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H A D | dynprog_end.c | 659 int queryoffset, int genomeoffset, Pairpool_T pairpool, in traceback_nogaps() 737 int queryoffset, int genomeoffset, Pairpool_T pairpool, bool revp, in traceback_local_8_upper() 837 int queryoffset, int genomeoffset, Pairpool_T pairpool, in traceback_local_8_lower() 932 int queryoffset, int genomeoffset, Pairpool_T pairpool, bool revp, in traceback_local_16_upper() 1031 int queryoffset, int genomeoffset, Pairpool_T pairpool, in traceback_local_16_lower() 1126 int queryoffset, int genomeoffset, Pairpool_T pairpool, bool revp, in traceback_local_std() 1276 bool watsonp, int genestrand, bool jump_late_p, Pairpool_T pairpool, in Dynprog_end5_gap() 1628 bool watsonp, int genestrand, bool jump_late_p, Pairpool_T pairpool, in Dynprog_end5_splicejunction() 1890 bool watsonp, int genestrand, bool jump_late_p, Pairpool_T pairpool, in Dynprog_end3_gap() 2699 Pairpool_T pairpool, int extraband_end, double defect_rate) { in Dynprog_end5_known() [all …]
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H A D | smooth.c | 746 delete_and_mark_exons (List_T pairs, Pairpool_T pairpool, in delete_and_mark_exons() 935 Smooth_pairs_by_netgap (bool *deletep, List_T pairs, Pairpool_T pairpool) { in Smooth_pairs_by_netgap() 994 Smooth_pairs_by_size (bool *shortp, bool *deletep, List_T pairs, Pairpool_T pairpool, int stage2_in… in Smooth_pairs_by_size() 1162 Smooth_pairs_by_intronprobs (bool *badp, List_T pairs, Pairpool_T pairpool) { in Smooth_pairs_by_intronprobs()
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H A D | stage3.c | 1744 Pairpool_T pairpool) { in assign_gap_types() 2028 Pairpool_T pairpool) { in assign_intron_probs() 2294 , Pairpool_T pairpool in remove_indel_gaps() 2562 bool watsonp, Pairpool_T pairpool) { in add_intron() 4028 Pairpool_T pairpool, double defect_rate) { in trim_end5_indels() 4191 Pairpool_T pairpool, double defect_rate) { in trim_end5_exons() 4513 Pairpool_T pairpool, double defect_rate) { in trim_end3_indels() 4677 Pairpool_T pairpool, double defect_rate) { in trim_end3_exons() 5175 , Pairpool_T pairpool in add_queryseq_offset() 5237 Pairpool_T pairpool, char *queryseq_ptr, in make_pairarray() [all …]
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H A D | gmap.c | 1150 Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool, in update_stage3middle_list() 1442 Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool, in stage3_from_usersegment() 1764 Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool, in stage3_from_gregions() 2373 Pairpool_T pairpool, Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR, in merge_left_and_right_readthrough() 2486 Univ_IIT_T chromosome_iit, Pairpool_T pairpool) { in find_breakpoint() 2662 Matchpool_T matchpool, Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool, in check_for_local() 3526 Pairpool_T pairpool, Dynprog_T dynprogL, Dynprog_T dynprogM, Dynprog_T dynprogR, in merge_middlepieces() 3622 Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool, in check_middle_piece_local() 4664 Pairpool_T pairpool; in worker_mpi_process() local 4880 Pairpool_T pairpool; in single_thread() local [all …]
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H A D | pairpool.c | 801 Pairpool_join_end3 (List_T path_orig, List_T end3_pairs_orig, Pairpool_T pairpool, in Pairpool_join_end3() 891 Pairpool_join_end5 (List_T pairs_orig, List_T end5_path_orig, Pairpool_T pairpool, in Pairpool_join_end5() 982 int queryoffset, int genomeoffset, Pairpool_T pairpool, bool revp, int dynprogindex) { in Pairpool_add_queryskip() 1085 char *genomesequence, int queryoffset, int genomeoffset, Pairpool_T pairpool, bool revp, in Pairpool_add_genomeskip()
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H A D | splicetrie.c | 179 Pairpool_T pairpool, int extraband_end, double defect_rate) { in solve_end5_aux() 459 Pairpool_T pairpool, int extraband_end, double defect_rate) { in solve_end3_aux() 732 Pairpool_T pairpool, int extraband_end, double defect_rate) { in Splicetrie_solve_end5() 799 Pairpool_T pairpool, int extraband_end, double defect_rate) { in Splicetrie_solve_end3()
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H A D | stage2.c | 4129 Pairpool_T pairpool, bool fwdp) { in traceback_one() 4233 Pairpool_T pairpool, bool fwdp) { in traceback_one_snps() 4320 int indexsize, Pairpool_T pairpool, in align_compute_lookback() 5000 int indexsize, Pairpool_T pairpool, in align_compute_lookforward() 5288 int query_offset, Pairpool_T pairpool, int indexsize_nt, in convert_to_nucleotides() 5563 int query_offset, Pairpool_T pairpool, int indexsize_nt, in convert_to_nucleotides_snps() 6554 Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool, in Stage2_compute() 7073 Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool, in Stage2_compute_one() 7244 Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool, in Stage2_compute_starts() 7437 Pairpool_T pairpool, Diagpool_T diagpool, Cellpool_T cellpool, in Stage2_compute_ends()
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H A D | dynprog_cdna.c | 815 bool watsonp, int genestrand, bool jump_late_p, Pairpool_T pairpool, in Dynprog_cdna_gap()
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H A D | dynprog_simd.c | 8932 int queryoffset, int genomeoffset, Pairpool_T pairpool, bool revp, in Dynprog_traceback_8() 9089 int queryoffset, int genomeoffset, Pairpool_T pairpool, bool revp, in Dynprog_traceback_8_upper() 9203 int queryoffset, int genomeoffset, Pairpool_T pairpool, in Dynprog_traceback_8_lower() 9312 int queryoffset, int genomeoffset, Pairpool_T pairpool, bool revp, in Dynprog_traceback_16() 9467 int queryoffset, int genomeoffset, Pairpool_T pairpool, bool revp, in Dynprog_traceback_16_upper() 9581 int queryoffset, int genomeoffset, Pairpool_T pairpool, in Dynprog_traceback_16_lower()
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H A D | dynprog.c | 1726 int queryoffset, int genomeoffset, Pairpool_T pairpool, bool revp, in Dynprog_traceback_std()
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H A D | dynprog_genome.c | 3003 Chrnum_T chrnum, Univcoord_T chroffset, Univcoord_T chrhigh, Pairpool_T pairpool, in genome_gap_simple() 3278 bool jump_late_p, Pairpool_T pairpool, int extraband_paired, in Dynprog_genome_gap()
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H A D | pair.c | 10487 Chrpos_T chrlength, Pairpool_T pairpool, bool plusp) { in Pair_split_circular()
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