| /dports/biology/gmap/gmap-2020-09-12/src/ |
| H A D | intron.c | 24 int donor_typeint, int acceptor_typeint, Chrnum_T chrnum,
53 donor_typeint,/*sign*/+1) == true) {
63 donor_typeint,/*sign*/-1) == true) {
134 donor_typeint,/*sign*/-1) == true) {
142 donor_typeint,/*sign*/-1) == true) {
|
| H A D | knownsplicing.h | 23 int donor_typeint, int acceptor_typeint, Univ_IIT_T chromosome_iit,
|
| H A D | intron.h | 44 int donor_typeint, int acceptor_typeint, Chrnum_T chrnum,
|
| H A D | knownsplicing.c | 248 int donor_typeint, int acceptor_typeint, Univ_IIT_T chromosome_iit, in Knownsplicing_retrieve_via_splicesites() argument
316 } else if (Interval_type(interval) == donor_typeint) { in Knownsplicing_retrieve_via_splicesites()
426 } else if (Interval_type(interval) == donor_typeint) { in Knownsplicing_retrieve_via_splicesites()
|
| H A D | splicetrie_build.h | 42 int donor_typeint, int acceptor_typeint, Univ_IIT_T chromosome_iit,
|
| H A D | dynprog_genome.c | 126 static int donor_typeint; variable
193 donor_typeint = donor_typeint_in; in Dynprog_genome_setup()
411 if (splicing_iit != NULL && donor_typeint >= 0 && acceptor_typeint >= 0) { in get_known_splicesites()
417 leftoffset+1,leftoffset+glengthL-2,donor_typeint,/*sign*/+1,/*sortp*/false); in get_known_splicesites()
448 rightoffset-glengthR+4,rightoffset+1,donor_typeint,/*sign*/-1,/*sortp*/false); in get_known_splicesites()
464 donor_typeint,/*sign*/-1,/*sortp*/false); in get_known_splicesites()
501 donor_typeint,/*sign*/+1,/*sortp*/false); in get_known_splicesites()
1452 } else if (donor_typeint >= 0 && acceptor_typeint >= 0) { in bridge_intron_gap_8_ud()
2326 } else if (donor_typeint >= 0 && acceptor_typeint >= 0) { in bridge_intron_gap_16_ud()
2964 } else if (donor_typeint >= 0 && acceptor_typeint >= 0) { in bridge_intron_gap()
[all …]
|
| H A D | gsnap.c | 414 static int donor_typeint = -1; /* for splicing_iit */ variable
3306 if ((donor_typeint = IIT_typeint(splicing_iit,"donor")) >= 0 && in worker_setup()
3311 donor_typeint,acceptor_typeint,chromosome_iit, in worker_setup()
3526 splicingp,donor_typeint,acceptor_typeint,chromosome_iit,transcript_iit); in worker_setup()
|
| H A D | splicetrie_build.c | 385 int donor_typeint, int acceptor_typeint, Univ_IIT_T chromosome_iit, in Splicetrie_retrieve_via_splicesites() argument
458 } else if (Interval_type(interval) == donor_typeint) { in Splicetrie_retrieve_via_splicesites()
582 } else if (Interval_type(interval) == donor_typeint) { in Splicetrie_retrieve_via_splicesites()
|
| H A D | stage3.c | 323 static int donor_typeint; variable
384 donor_typeint = donor_typeint_in; in Stage3_setup()
1874 splicesitepos,splicesitepos+1U,donor_typeint,/*sign*/+1)) { in assign_gap_types()
1895 splicesitepos,splicesitepos+1U,donor_typeint,/*sign*/-1)) { in assign_gap_types()
1949 splicesitepos,splicesitepos+1U,donor_typeint,/*sign*/-1)) { in assign_gap_types()
1970 splicesitepos,splicesitepos+1U,donor_typeint,/*sign*/+1)) { in assign_gap_types()
2140 splicesitepos,splicesitepos+1U,donor_typeint,/*sign*/+1)) { in assign_intron_probs()
12386 splicesitepos,splicesitepos+1U,donor_typeint,/*sign*/+1)) { in score_introns()
12409 splicesitepos,splicesitepos+1U,donor_typeint,/*sign*/-1)) { in score_introns()
12474 splicesitepos,splicesitepos+1U,donor_typeint,/*sign*/-1)) { in score_introns()
[all …]
|
| H A D | samprint.c | 69 static int donor_typeint; variable
112 donor_typeint = donor_typeint_in; in SAM_setup()
|
| H A D | gmap.c | 479 static int donor_typeint = -1; /* for splicing_iit */ variable
6902 if ((donor_typeint = IIT_typeint(splicing_iit,"donor")) >= 0 && in main()
6909 donor_typeint,acceptor_typeint,chromosome_iit, in main()
7017 donor_typeint,acceptor_typeint); in main()
7027 donor_typeint,acceptor_typeint,splicesites,circularp,altlocp,alias_starts,alias_ends, in main()
|