| /dports/biology/gmap/gmap-2020-09-12/src/ |
| H A D | genome128_hr.h | 17 int pos5, int pos3, bool plusp, int genestrand);
20 Univcoord_T left, int pos5, int pos3, bool plusp, int genestrand);
25 Univcoord_T left, int pos5, int pos3, bool plusp, int genestrand);
29 Univcoord_T left, int pos5, int pos3, bool plusp, int genestrand);
33 Univcoord_T left, int pos5, int pos3, bool plusp, int genestrand);
37 Univcoord_T left, int pos5, int pos3, bool plusp, int genestrand);
41 Univcoord_T left, int pos5, int pos3, bool plusp, int genestrand,
45 Univcoord_T left, int pos5, int pos3, bool plusp, int genestrand,
51 bool plusp, int genestrand);
55 bool plusp, int genestrand);
|
| H A D | genome128_hr.c | 2197 if (plusp) { in block_diff_cmet_32()
2203 if (plusp) { in block_diff_cmet_32()
2216 if (plusp) { in block_diff_cmet_128()
2222 if (plusp) { in block_diff_cmet_128()
2237 if (plusp) { in block_diff_cmet_128_wrap_lo()
2245 if (plusp) { in block_diff_cmet_128_wrap_lo()
2260 if (plusp) { in block_diff_cmet_128_wrap_hi()
2268 if (plusp) { in block_diff_cmet_128_wrap_hi()
2284 if (plusp) { in block_diff_cmet_256()
2290 if (plusp) { in block_diff_cmet_256()
[all …]
|
| H A D | terminal.c | 65 bool plusp, int genestrand) { in find_terminals() argument
143 pos5,pos3,querylength,plusp,genestrand); in find_terminals()
146 pos5,pos3,querylength,plusp,genestrand); in find_terminals()
147 if (plusp == true) { in find_terminals()
157 plusp,genestrand,query_compress,chrnum,chroffset,chrhigh,chrlength, in find_terminals()
162 plusp == true ? "plus" : "minus",Substring_nmismatches_bothdiff(substring), in find_terminals()
171 plusp,genestrand,query_compress,chrnum,chroffset,chrhigh,chrlength, in find_terminals()
212 pos5,pos3,querylength,plusp,genestrand); in find_terminals()
215 pos5,pos3,querylength,plusp,genestrand); in find_terminals()
216 if (plusp == true) { in find_terminals()
[all …]
|
| H A D | genome128_consec.c | 1538 if (plusp) { in block_diff_cmet_sarray_32()
1544 if (plusp) { in block_diff_cmet_sarray_32()
1557 if (plusp) { in block_diff_cmet_sarray_128()
1563 if (plusp) { in block_diff_cmet_sarray_128()
1577 if (plusp) { in block_diff_cmet_sarray_128_shift_lo()
1585 if (plusp) { in block_diff_cmet_sarray_128_shift_lo()
1600 if (plusp) { in block_diff_cmet_sarray_128_shift_hi()
1608 if (plusp) { in block_diff_cmet_sarray_128_shift_hi()
1626 if (plusp) { in block_diff_cmet_sarray_128_wrap_lo()
1634 if (plusp) { in block_diff_cmet_sarray_128_wrap_lo()
[all …]
|
| H A D | indel.h | 25 int max_mismatches_allowed, bool plusp, int genestrand,
36 int max_mismatches_allowed, bool plusp, int genestrand,
45 int max_mismatches_allowed, bool plusp, int genestrand,
54 int nmismatches_allowed, bool plusp, int genestrand,
62 int nmismatches_allowed, bool plusp, int genestrand,
|
| H A D | substring.h | 64 int pos5, int pos3, int querylength, bool plusp, int genestrand);
68 int pos5, int pos3, int querylength, bool plusp, int genestrand);
73 bool plusp, int genestrand, int *mismatch_positions_alloc, Compress_T query_compress,
77 Univcoord_T univdiagonal, int pos3, int querylength, bool plusp, int genestrand,
84 bool plusp, int genestrand, int *mismatch_positions_alloc, Compress_T query_compress,
89 Univcoord_T univdiagonal, int pos5, int querylength, bool plusp, int genestrand,
96 bool plusp, int genestrand, Compress_T query_compress,
117 bool plusp, int genestrand, Compress_T query_compress,
125 bool plusp, int genestrand, Compress_T query_compress,
331 Univcoord_T left, Compress_T query_compress, int querylength, bool plusp, int genestrand,
[all …]
|
| H A D | gregion.c | 55 bool plusp; member
160 return this->plusp; in Gregion_plusp()
165 return !(this->plusp); in Gregion_revcompp()
272 new->plusp = plusp; in Gregion_new()
275 if (plusp == true) { in Gregion_new()
442 bool plusp; in gregion_overlap_p() local
444 if (x->plusp != y->plusp) { in gregion_overlap_p()
449 plusp = x->plusp; in gregion_overlap_p()
891 if (this->plusp == true) { in Gregion_extend()
906 if (this->plusp == true) { in Gregion_extend()
[all …]
|
| H A D | cigar.c | 85 if (plusp == true) { in length_cigar_M()
190 if (plusp == true) { in print_cigar()
662 bool plusp; in Cigar_length_substrings() local
1092 bool plusp; in print_substrings() local
1656 bool plusp; in print_halfdonor() local
1841 bool plusp; in print_halfacceptor() local
2036 *plusp = true; in Cigar_compute_main()
2139 *plusp = true; in Cigar_compute_main()
2164 *plusp = true; in Cigar_compute_main()
2307 *plusp = true; in Cigar_compute_supplemental()
[all …]
|
| H A D | substring.c | 275 bool plusp; member
641 } else if (substring5->plusp == true && substring3->plusp == true) { in Substring_insert_length()
643 } else if (substring5->plusp == false && substring3->plusp == false) { in Substring_insert_length()
1650 if (plusp) { in Substring_compute_nmatches()
1683 if (plusp) { in Substring_compute_nmatches()
1854 new->plusp = plusp; in Substring_new()
1943 if (plusp) { in Substring_new()
2402 new->plusp = plusp;
2619 new->plusp = plusp; in Substring_new_alts_D()
2738 new->plusp = plusp; in Substring_new_alts_A()
[all …]
|
| H A D | stage2.h | 53 Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp,
60 Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp, int genestrand,
73 Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp, int genestrand,
82 Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp, int genestrand,
91 Univcoord_T chroffset, Univcoord_T chrhigh, bool plusp, int genestrand,
|
| H A D | indel.c | 108 plusp,genestrand); in Indel_resolve_middle_insertion()
136 plusp,genestrand); in Indel_resolve_middle_insertion()
358 } else if (plusp == true) { in Indel_resolve_middle_insertion()
426 plusp,genestrand); in Indel_resolve_middle_deletion()
453 plusp,genestrand); in Indel_resolve_middle_deletion()
652 } else if (plusp == true) { in Indel_resolve_middle_deletion()
749 plusp,genestrand); in Indel_resolve_middle_deletion_or_splice()
766 plusp,genestrand); in Indel_resolve_middle_deletion_or_splice()
1066 } else if (plusp == true) { in Indel_resolve_middle_deletion_or_splice()
1140 tr_left,pos5,pos3,plusp,genestrand); in Indel_solve_end_low()
[all …]
|
| H A D | path-solve.c | 785 if (plusp == true) { in attach_qstart_diagonal()
820 if (plusp == true) { in attach_qstart_diagonal()
863 if (plusp == true) { in attach_qstart_diagonal()
923 if (plusp == true) { in attach_qstart_diagonal()
958 if (plusp == true) { in attach_qstart_diagonal()
1001 if (plusp == true) { in attach_qstart_diagonal()
1778 if (plusp == true) { in attach_qend_diagonal()
1813 if (plusp == true) { in attach_qend_diagonal()
2665 if (plusp == true) { in solve_via_segments_genome()
2769 if (plusp == true) { in solve_via_segments_genome()
[all …]
|
| H A D | splice.h | 66 bool plusp, int genestrand, int max_deletionlen, int max_insertionlen,
80 bool plusp, int genestrand, int max_deletionlen, int max_insertionlen,
101 int max_nconsecutive, bool plusp, int sensedir);
108 int max_nconsecutive, bool plusp, int sensedir);
|
| H A D | splice.c | 263 if (plusp == true) { in Splice_resolve_sense()
367 if (plusp == true) { in Splice_resolve_sense()
557 if (plusp == true) { in Splice_resolve_sense()
2428 if (plusp) { in Splice_trim_novel_spliceends_5()
2509 if (plusp) { in Splice_trim_novel_spliceends_5()
2599 if (plusp) { in Splice_trim_novel_spliceends_5()
2628 if (plusp) { in Splice_trim_novel_spliceends_5()
2701 if (plusp) { in Splice_trim_novel_spliceends_3()
2782 if (plusp) { in Splice_trim_novel_spliceends_3()
2872 if (plusp) { in Splice_trim_novel_spliceends_3()
[all …]
|
| H A D | genome128_consec.h | 16 bool plusp, int genestrand);
19 bool plusp, int genestrand);
|
| H A D | junction.c | 205 Univcoord_T chroffset, bool plusp, int sensedir) { in Junction_new_generic() argument
211 left1,querypos1,left2,querypos2,plusp,sensedir)); in Junction_new_generic()
229 if (plusp == true) { in Junction_new_generic()
242 if (plusp == true) { in Junction_new_generic()
405 Junction_deletion_string (T this, Genome_T genome, bool plusp) { in Junction_deletion_string() argument
413 if (plusp == false) { in Junction_deletion_string()
|
| H A D | mapq.c | 157 int querylength, char *quality_string, bool plusp, int genestrand) { in MAPQ_loglik() argument
190 if (plusp == true) { in MAPQ_loglik()
195 plusp,genestrand); in MAPQ_loglik()
231 /*pos3*/querylength - querystart,plusp,genestrand); in MAPQ_loglik()
|
| /dports/lang/sbcl/sbcl-1.3.13/contrib/sb-cover/ |
| H A D | tests.lisp | 56 (assert (plusp (sb-cover::all-of (getf sb-cover::*counts* :expression))))
65 (assert (plusp (sb-cover::ok-of (getf sb-cover::*counts* :expression))))
78 (assert (plusp (sb-cover::all-of (getf sb-cover::*counts* :expression))))
91 (assert (plusp (sb-cover::ok-of (getf sb-cover::*counts* :expression))))
95 (assert (plusp (sb-cover::ok-of (getf sb-cover::*counts* :branch))))
96 (assert (plusp (sb-cover::all-of (getf sb-cover::*counts* :branch))))
|
| /dports/databases/pgloader3/cl-base64-20201016-git/ |
| H A D | encode.lisp | 70 '((num-lines (if (plusp columns)
73 (num-breaks (if (plusp num-lines)
79 (col (if (plusp columns)
229 (last-line-len (if (plusp columns)
234 (num-lines (if (plusp columns)
237 (num-breaks (if (plusp num-lines)
248 (unless (plusp columns)
303 (when (plusp columns)
311 (when (plusp columns)
|
| /dports/lang/sbcl/sbcl-1.3.13/src/code/ |
| H A D | cross-float.lisp | 30 (assert (plusp n))
61 (assert (plusp lisp-significand))
77 (if (plusp exponent) ; if not obviously denormalized
124 (assert (plusp lisp-significand))
128 (if (plusp exponent) ; if not obviously denormalized
|
| /dports/databases/pgloader3/lparallel-20160825-git/src/ |
| H A D | vector-queue.lisp | 81 (if (plusp count)
91 (if (plusp count)
161 (when (or (not (plusp time-remaining))
190 (cond ((plusp timeout)
202 (if (plusp timeout)
|
| H A D | cons-queue.lisp | 91 (when (or (not (plusp time-remaining))
107 (cond ((plusp timeout)
118 (if (plusp timeout)
|
| /dports/math/maxima/maxima-5.43.2/src/ |
| H A D | intpol.lisp | 80 (when (plusp (* (float-sign fa) (float-sign fb)))
86 (when (plusp fa)
102 (if (plusp fc)
107 (setq c (if (plusp (+ fb fa))
115 (if (plusp fc)
|
| /dports/databases/pgloader3/trivial-backtrace-20200610-git/test/ |
| H A D | tests.lisp | 17 (ensure (plusp (length output)))))
31 (ensure (plusp (length output)))))
|
| /dports/lang/sbcl/sbcl-1.3.13/contrib/sb-aclrepl/ |
| H A D | toplevel.lisp | 48 (plusp *break-level*))
51 (plusp *break-level*))
|