| /dports/biology/bowtie/bowtie-1.3.1/ |
| H A D | row_chaser.h | 44 static TIndexOffU toFlatRefOff(const Ebwt* ebwt, TIndexOffU qlen, TIndexOffU row) { in toFlatRefOff()
56 static UPair toRefOff(const Ebwt* ebwt, TIndexOffU qlen, TIndexOffU row) { in toRefOff()
69 void setRow(TIndexOffU row, TIndexOffU qlen, const Ebwt* ebwt) { in setRow()
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| H A D | range_cache.h | 149 void init(RangeCacheMemPool& pool, TIndexOffU top, TIndexOffU ent, Ebwt* ebwt) { in init()
191 TIndexOffU ent, Ebwt* ebwt) in init()
237 Ebwt *ebwt() { in ebwt() function
300 static bool sanityCheckEnts(TIndexOffU len, TIndexOffU *ents, Ebwt* ebwt) { in sanityCheckEnts()
350 RangeCache(TIndexOffU lim, Ebwt* ebwt) : in RangeCache()
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| H A D | bowtie_inspect.cpp | 274 Ebwt& ebwt, in print_index_sequences()
360 Ebwt ebwt( in print_index_summary() local
432 Ebwt ebwt( in driver() local
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| H A D | ebwt_search_backtrack.h | 203 void setEbwt(const Ebwt* ebwt) { in setEbwt()
241 const Ebwt& ebwt = *_ebwt; variable
392 const Ebwt& ebwt = *_ebwt; variable
1309 const Ebwt& ebwt = *_ebwt; in tallyNs() local
1349 const Ebwt& ebwt = *_ebwt; in calcFtabOff() local
1926 const Ebwt& ebwt = *ebwt_; in initBranch() local
2104 const Ebwt& ebwt = *ebwt_; in advanceBranch() local
2491 const Ebwt& ebwt = *ebwt_; in tallyNs() local
2531 const Ebwt& ebwt = *ebwt_; in calcFtabOff() local
2618 ebwt_(ebwt), in ebwt_() argument
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| H A D | range.h | 44 const Ebwt *ebwt; member
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| H A D | range_chaser.h | 130 const Ebwt* ebwt) in setTopBot()
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| H A D | range_source.h | 651 const uint8_t* ebwt, bool ebwtFw, in splitBranch()
946 void prep(const EbwtParams& ep, const uint8_t* ebwt) { in prep()
1463 const EbwtParams& ep, const uint8_t* ebwt, in splitAndPrep()
1534 const EbwtParams& ep, const uint8_t* ebwt, in splitBranch()
1548 void prep(const EbwtParams& ep, const uint8_t* ebwt) { in prep()
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| H A D | ebwt_build.cpp | 420 Ebwt ebwt(TStr(), in driver() local
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| H A D | ebwt_search.cpp | 1142 Ebwt& ebwt = *exactSearch_ebwt; local
1235 Ebwt& ebwt = *exactSearch_ebwt; local
1335 Ebwt& ebwt,
3120 Ebwt ebwt(adjustedEbwtFileBase, local
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| H A D | ebwt.h | 879 uint8_t* ebwt() const { return _ebwt; } in ebwt() function
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| /dports/biology/bowtie2/bowtie2-2.4.4/ |
| H A D | bt2_inspect.cpp | 251 static void print_index_sequences(ostream& fout, Ebwt& ebwt) in print_index_sequences()
334 Ebwt ebwt( in print_index_summary() local
382 Ebwt ebwt( in driver() local
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| H A D | group_walk.h | 450 const Ebwt& ebwt, // index to walk left in in init()
487 const Ebwt& ebwt, // forward Bowtie index in init()
720 const Ebwt& ebwt, in repOk()
864 const Ebwt& ebwt, // the forward Bowtie index, for stepping left in advance()
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| H A D | aligner_seed.cpp | 616 const Ebwt& ebwt, // BWT index in exactSweep()
802 const Ebwt* ebwt = (ebwtfw ? ebwtFw : ebwtBw); in oneMmSearch() local
1202 const Ebwt *ebwt = ebwtFw_; in extendAndReportHit() local
1258 const Ebwt *ebwt = ebwtBw_; in extendAndReportHit() local
1501 const Ebwt* ebwt = ltr ? ebwtBw_ : ebwtFw_; in searchSeedBi() local
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| H A D | bt2_build.cpp | 469 Ebwt ebwt( in driver() local
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| H A D | aligner_sw_driver.cpp | 69 const Ebwt& ebwt, // BWT in eeSaTups()
338 const Ebwt *ebwt = &ebwtFw; in extend() local
404 const Ebwt *ebwt = ebwtBw; in extend() local
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| H A D | bt2_idx.h | 1176 inline uint8_t* ebwt() { return _ebwt.get(); } in ebwt() function
1183 inline const uint8_t* ebwt() const { return _ebwt.get(); } in ebwt() function
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| H A D | aligner_seed2.cpp | 1617 const Ebwt& ebwt = ltr ? ebwtBw : ebwtFw; in followMatches() local
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| H A D | bt2_search.cpp | 4842 Ebwt ebwt( in driver() local
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| /dports/biology/hisat2/hisat2-2.2.1/ |
| H A D | aligner_seed.h | 1880 const Ebwt<index_t>& ebwt, // BWT index in exactSweep()
2067 const Ebwt<index_t>* ebwt = (ebwtfw ? ebwtFw : ebwtBw); in oneMmSearch() local
2467 const Ebwt<index_t> *ebwt = ebwtFw_; in extendAndReportHit() local
2523 const Ebwt<index_t> *ebwt = ebwtBw_; in extendAndReportHit() local
2766 const Ebwt<index_t>* ebwt = ltr ? ebwtBw_ : ebwtFw_; in searchSeedBi() local
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| H A D | hisat_bp.cpp | 3458 HierEbwt<index_t, local_index_t> ebwt( in driver() local
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