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Searched defs:pairpool (Results 1 – 13 of 13) sorted by relevance

/dports/biology/gmap/gmap-2020-09-12/src/
H A Ddynprog_single.c181 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()
H A Ddynprog_end.c659 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()
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H A Dsmooth.c746 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()
H A Dstage3.c1744 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()
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H A Dgmap.c1150 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
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H A Dpairpool.c801 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()
H A Dsplicetrie.c179 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()
H A Dstage2.c4129 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()
H A Ddynprog_cdna.c815 bool watsonp, int genestrand, bool jump_late_p, Pairpool_T pairpool, in Dynprog_cdna_gap()
H A Ddynprog_simd.c8932 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()
H A Ddynprog.c1726 int queryoffset, int genomeoffset, Pairpool_T pairpool, bool revp, in Dynprog_traceback_std()
H A Ddynprog_genome.c3003 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()
H A Dpair.c10487 Chrpos_T chrlength, Pairpool_T pairpool, bool plusp) { in Pair_split_circular()