| /dports/biology/bowtie2/bowtie2-2.4.4/ |
| H A D | ival_list.cpp | 113 assert(list1.repOk()); in main()
114 assert(list2.repOk()); in main()
116 assert(list1.repOk()); in main()
117 assert(list2.repOk()); in main()
146 assert(list1.repOk()); in main()
147 assert(list2.repOk()); in main()
149 assert(list1.repOk()); in main()
150 assert(list2.repOk()); in main()
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| H A D | aligner_cache.h | 174 bool repOk() const { in repOk() function
259 bool repOk(const AlignmentCache& ac) const;
294 bool repOk(const AlignmentCache& ac) const;
354 bool repOk() const { in repOk() function
355 assert(offs.repOk()); in repOk()
597 assert(qv.repOk(*this)); in queryQvalImpl()
612 assert(sav.repOk(*this)); in queryQvalImpl()
765 assert(repOk());
831 assert(repOk());
877 assert(repOk());
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| H A D | ival_list.h | 93 bool repOk() const { in repOk() function
170 assert(repOk()); in locusPresentSorted()
242 bool repOk() const { in repOk() function
244 assert(bins_[i].repOk()); in repOk()
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| H A D | aligner_sw_common.h | 79 bool repOk() const { in repOk() function
80 assert(alres.repOk()); in repOk()
87 bool repOk(const Read& rd) const { in repOk() function
88 assert(alres.repOk(rd)); in repOk()
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| H A D | ds.h | 82 bool repOk() const { in repOk() function
2931 assert(repOk()); in insert()
2981 assert(repOk()); in pop()
3090 assert(repOk()); in cat_()
3111 assert(repOk()); in alloc()
3121 assert(repOk()); in clear()
3174 assert(repOk()); in add()
3181 assert(repOk()); in add()
3198 assert(repOk()); in add()
3343 assert(repOk()); in ensure()
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| H A D | aligner_cache.cpp | 29 bool QVal::repOk(const AlignmentCache& ac) const { in repOk() function in QVal
44 bool SAVal::repOk(const AlignmentCache& ac) const { in repOk() function in SAVal
85 assert(s->key.repOk()); in addOnTheFlyImpl()
98 assert(s->payload.repOk(*this)); in addOnTheFlyImpl()
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| H A D | group_walk.h | 361 bool repOk(const SARangeWithOffs<T>& sa) const { in repOk() function
705 assert(tloc.valid()); assert(tloc.repOk(ebwt.eh())); in init()
706 assert(bloc.valid()); assert(bloc.repOk(ebwt.eh())); in init()
709 assert(tloc.valid()); assert(tloc.repOk(ebwt.eh())); in init()
719 bool repOk( in repOk() function
725 assert(doneResolving(hit) || (tloc.valid() && tloc.repOk(ebwt.eh()))); in repOk()
881 assert(tloc.valid()); assert(tloc.repOk(ebwt.eh())); in advance()
1140 assert(hit_.repOk(sa)); in init()
1173 assert(hit_.repOk(sa)); in advanceElement()
1227 bool repOk(const SARangeWithOffs<T>& sa) const { in repOk() function
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| H A D | aligner_result.h | 373 bool repOk() const { in repOk() function
728 bool repOk() const { in repOk() function
1077 bool repOk() const { in repOk() function
1078 assert(refcoord_.repOk()); in repOk()
1082 assert(refival_.repOk()); in repOk()
1096 bool repOk(const Read& rd) const { in repOk() function
1097 assert(Edit::repOk(ned_, refcoord_.fw() ? rd.patFw : rd.patRc, in repOk()
1099 return repOk(); in repOk()
1804 assert(repOk()); in init()
1811 assert(repOk()); in empty()
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| H A D | scoring.h | 172 assert(repOk()); in Scoring()
182 assert(repOk()); in setMatchBonus()
208 bool repOk() const { in repOk() function
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| H A D | aln_sink.cpp | 1503 assert(repOk()); in selectByScore()
1647 assert(repOk()); in selectAlnsToReport()
2138 assert(st.repOk()); in testDones()
2167 assert(st.repOk()); in main()
2212 assert(st.repOk()); in main()
2273 assert(st.repOk()); in main()
2334 assert(st.repOk()); in main()
2371 assert(st.repOk()); in main()
2407 assert(st.repOk()); in main()
2520 assert(st.repOk()); in main()
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| H A D | aligner_seed.h | 471 bool repOk() const { in repOk() function
576 bool repOk(const Read& rd) const { in repOk() function
651 assert(qv.repOk(ac)); in add()
652 assert(repOk(&ac)); in add()
681 assert(repOk(&ac)); in add()
952 assert(repOk(NULL)); in hitsAtOffIdx()
961 assert(repOk(NULL)); in instantiatedSeeds()
979 bool repOk(
998 assert(rrs[i].repOk(*ac));
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| H A D | ref_coord.h | 152 bool repOk() const { in repOk() function
406 bool repOk() const { in repOk() function
407 assert(upstream_.repOk()); in repOk()
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| H A D | aligner_sw_driver.cpp | 208 assert(hit.repOk(rd)); in eeSaTups()
1027 assert(resEe_.repOk(rd)); in extendSeeds()
1086 assert(rect.repOk()); in extendSeeds()
1231 assert(res->repOk()); in extendSeeds()
1733 assert(resEe_.repOk(rd)); in extendSeedsPaired()
1781 assert(rect.repOk()); in extendSeedsPaired()
1861 assert(res->repOk(rd)); in extendSeedsPaired()
1867 assert(res->repOk(rd)); in extendSeedsPaired()
1880 assert(res->repOk(rd)); in extendSeedsPaired()
2176 assert(res->repOk()); in extendSeedsPaired()
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| H A D | edit.h | 290 bool repOk() const;
297 static bool repOk(
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| /dports/biology/hisat2/hisat2-2.2.1/ |
| H A D | ival_list.cpp | 113 assert(list1.repOk()); in main()
114 assert(list2.repOk()); in main()
116 assert(list1.repOk()); in main()
117 assert(list2.repOk()); in main()
146 assert(list1.repOk()); in main()
147 assert(list2.repOk()); in main()
149 assert(list1.repOk()); in main()
150 assert(list2.repOk()); in main()
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| H A D | aligner_cache.h | 174 bool repOk() const { in repOk() function
358 bool repOk() const { in repOk() function
359 assert(offs.repOk()); in repOk()
471 assert(qv.repOk(*this));
486 assert(sav.repOk(*this));
732 assert(repOk());
798 assert(repOk());
844 assert(repOk());
884 bool repOk() const { in repOk() function
992 assert(s->key.repOk()); in addOnTheFly()
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| H A D | aln_sink.cpp | 366 assert(st.repOk()); in testDones()
395 assert(st.repOk()); in main()
440 assert(st.repOk()); in main()
501 assert(st.repOk()); in main()
562 assert(st.repOk()); in main()
599 assert(st.repOk()); in main()
635 assert(st.repOk()); in main()
748 assert(st.repOk()); in main()
750 assert(st.repOk()); in main()
752 assert(st.repOk()); in main()
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| H A D | ival_list.h | 93 bool repOk() const { in repOk() function
170 assert(repOk()); in locusPresentSorted()
242 bool repOk() const { in repOk() function
244 assert(bins_[i].repOk()); in repOk()
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| H A D | aligner_sw_common.h | 81 bool repOk() const { in repOk() function
82 assert(alres.repOk()); in repOk()
89 bool repOk(const Read& rd) const { in repOk() function
90 assert(alres.repOk(rd)); in repOk()
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| H A D | ds.h | 84 bool repOk() const { in repOk() function
2971 assert(repOk()); in insert()
3021 assert(repOk()); in pop()
3124 assert(repOk()); in cat_()
3142 assert(repOk()); in alloc()
3154 assert(repOk()); in clear()
3208 assert(repOk()); in add()
3215 assert(repOk()); in add()
3232 assert(repOk()); in add()
3377 assert(repOk()); in ensure()
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| H A D | scoring.h | 190 assert(repOk());
200 assert(repOk()); in setMatchBonus()
226 bool repOk() const { in repOk() function
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| H A D | group_walk.h | 376 bool repOk(const SARangeWithOffs<T, index_t>& sa) const { in repOk() function
877 assert(tloc.valid()); assert(tloc.repOk(gfm.gh())); in init()
878 assert(bloc.valid()); assert(bloc.repOk(gfm.gh())); in init()
881 assert(tloc.valid()); assert(tloc.repOk(gfm.gh())); in init()
891 bool repOk( in repOk() function
897 assert(doneResolving(hit) || (tloc.valid() && tloc.repOk(gfm.gh()))); in repOk()
1053 assert(tloc.valid()); assert(tloc.repOk(gfm.gh())); in advance()
1470 assert(hit_.repOk(sa)); in init()
1503 assert(hit_.repOk(sa)); in advanceElement()
1559 bool repOk(const SARangeWithOffs<T, index_t>& sa) const { in repOk() function
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| H A D | ref_coord.h | 155 bool repOk() const { in repOk() function
412 bool repOk() const { in repOk() function
413 assert(upstream_.repOk()); in repOk()
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| /dports/biology/bowtie/bowtie-1.3.1/ |
| H A D | ds.h | 82 bool repOk() const { in repOk() function
2930 assert(repOk()); in insert()
2980 assert(repOk()); in pop()
3089 assert(repOk()); in cat_()
3110 assert(repOk()); in alloc()
3120 assert(repOk()); in clear()
3173 assert(repOk()); in add()
3180 assert(repOk()); in add()
3197 assert(repOk()); in add()
3342 assert(repOk()); in ensure()
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| H A D | range_cache.h | 390 bool repOk() { in repOk() function
473 if(sanity_) assert(repOk()); in tunnel()
511 if(sanity_) assert(repOk()); in tunnel()
525 if(sanity_) assert(repOk()); in tunnel()
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