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Searched refs:m_cigar (Results 1 – 22 of 22) sorted by relevance

/dports/biology/canu/canu-2.2/src/utility/src/utility/
H A Dalign-ksw2.H29 int m_cigar, n_cigar; member
103 static inline uint32_t *ksw_push_cigar(void *km, int *n_cigar, int *m_cigar, uint32_t *cigar, uint3… in ksw_push_cigar() argument
106 if (*n_cigar == *m_cigar) { in ksw_push_cigar()
107 *m_cigar = *m_cigar? (*m_cigar)<<1 : 4; in ksw_push_cigar()
108 cigar = (uint32_t*)krealloc(km, cigar, (*m_cigar) << 2); in ksw_push_cigar()
122 int n_cigar = 0, m_cigar = *m_cigar_, i = i0, j = j0, r, state = 0; in ksw_backtrack() local
140 if (state == 0) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, 0, 1), --i, --j; // match in ksw_backtrack()
142 …else if (state == 3 && min_intron_len > 0) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, 3… in ksw_backtrack()
143 else cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, 1, 1), --j; // insertion in ksw_backtrack()
146 if (j >= 0) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, 1, j + 1); // first insertion in ksw_backtrack()
[all …]
H A Dalign-ksw2-extz.C130 …ksw_backtrack(km, 0, rev_cigar, 0, z, off, 0, n_col, tlen-1, qlen-1, &ez->m_cigar, &ez->n_cigar, &… in ksw_extz()
132 …ksw_backtrack(km, 0, rev_cigar, 0, z, off, 0, n_col, ez->max_t, ez->max_q, &ez->m_cigar, &ez->n_ci… in ksw_extz()
H A Dalign-ksw2-extz2-sse.C295 …rev_cigar, 0, (uint8_t*)p, off, off_end, n_col_*16, tlen-1, qlen-1, &ez->m_cigar, &ez->n_cigar, &e… in ksw_extz2_sse41()
298 …_cigar, 0, (uint8_t*)p, off, off_end, n_col_*16, ez->mqe_t, qlen-1, &ez->m_cigar, &ez->n_cigar, &e… in ksw_extz2_sse41()
300 …gar, 0, (uint8_t*)p, off, off_end, n_col_*16, ez->max_t, ez->max_q, &ez->m_cigar, &ez->n_cigar, &e… in ksw_extz2_sse41()
/dports/biology/mmseqs2/MMseqs2-13-45111/lib/ksw2/
H A Dksw2.h56 int m_cigar, n_cigar; member
132 if (*n_cigar == *m_cigar) { in ksw_push_cigar()
133 *m_cigar = *m_cigar? (*m_cigar)<<1 : 4; in ksw_push_cigar()
134 cigar = (uint32_t*)krealloc(km, cigar, (*m_cigar) << 2); in ksw_push_cigar()
148 int n_cigar = 0, m_cigar = *m_cigar_, i = i0, j = j0, r, state = 0; in ksw_backtrack() local
166 if (state == 0) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, 0, 1), --i, --j; // match in ksw_backtrack()
168 …else if (state == 3 && with_N) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, 3, 1), --i; /… in ksw_backtrack()
169 else cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, 1, 1), --j; // insertion in ksw_backtrack()
171 if (i >= 0) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, 2, i + 1); // first deletion in ksw_backtrack()
172 if (j >= 0) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, 1, j + 1); // first insertion in ksw_backtrack()
[all …]
H A Dksw2_extz2_sse.cpp280 …rev_cigar, 0, (uint8_t*)p, off, off_end, n_col_*16, tlen-1, qlen-1, &ez->m_cigar, &ez->n_cigar, &e… in ksw_extz2_sse41()
282 …gar, 0, (uint8_t*)p, off, off_end, n_col_*16, ez->max_t, ez->max_q, &ez->m_cigar, &ez->n_cigar, &e… in ksw_extz2_sse41()
/dports/biology/minimap2/minimap2-2.24/
H A Dksw2.h36 int m_cigar, n_cigar; member
110 static inline uint32_t *ksw_push_cigar(void *km, int *n_cigar, int *m_cigar, uint32_t *cigar, uint3… in ksw_push_cigar() argument
113 if (*n_cigar == *m_cigar) { in ksw_push_cigar()
114 *m_cigar = *m_cigar? (*m_cigar)<<1 : 4; in ksw_push_cigar()
115 cigar = (uint32_t*)krealloc(km, cigar, (*m_cigar) << 2); in ksw_push_cigar()
129 int n_cigar = 0, m_cigar = *m_cigar_, i = i0, j = j0, r, state = 0; in ksw_backtrack() local
147 …if (state == 0) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, KSW_CIGAR_MATCH, 1), --i, --… in ksw_backtrack()
149 …else if (state == 3 && min_intron_len > 0) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, K… in ksw_backtrack()
150 else cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, KSW_CIGAR_INS, 1), --j; in ksw_backtrack()
153 …if (j >= 0) cigar = ksw_push_cigar(km, &n_cigar, &m_cigar, cigar, KSW_CIGAR_INS, j + 1); // first … in ksw_backtrack()
[all …]
H A Dksw2_extz2_sse.c303 …rev_cigar, 0, (uint8_t*)p, off, off_end, n_col_*16, tlen-1, qlen-1, &ez->m_cigar, &ez->n_cigar, &e… in ksw_extz2_sse41()
306 …_cigar, 0, (uint8_t*)p, off, off_end, n_col_*16, ez->mqe_t, qlen-1, &ez->m_cigar, &ez->n_cigar, &e… in ksw_extz2_sse41()
308 …gar, 0, (uint8_t*)p, off, off_end, n_col_*16, ez->max_t, ez->max_q, &ez->m_cigar, &ez->n_cigar, &e… in ksw_extz2_sse41()
H A Dksw2_extd2_sse.c392 …rev_cigar, 0, (uint8_t*)p, off, off_end, n_col_*16, tlen-1, qlen-1, &ez->m_cigar, &ez->n_cigar, &e… in ksw_extd2_sse41()
395 …_cigar, 0, (uint8_t*)p, off, off_end, n_col_*16, ez->mqe_t, qlen-1, &ez->m_cigar, &ez->n_cigar, &e… in ksw_extd2_sse41()
397 …gar, 0, (uint8_t*)p, off, off_end, n_col_*16, ez->max_t, ez->max_q, &ez->m_cigar, &ez->n_cigar, &e… in ksw_extd2_sse41()
H A Dksw2_exts2_sse.c410 …, long_thres, (uint8_t*)p, off, off_end, n_col_*16, tlen-1, qlen-1, &ez->m_cigar, &ez->n_cigar, &e… in ksw_exts2_sse41()
412 …_thres, (uint8_t*)p, off, off_end, n_col_*16, ez->max_t, ez->max_q, &ez->m_cigar, &ez->n_cigar, &e… in ksw_exts2_sse41()
H A Dalign.c751 ez->cigar = ksw_push_cigar(km, &ez->n_cigar, &ez->m_cigar, ez->cigar, MM_CIGAR_MATCH, qe - qs); in mm_align1()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/oligofar/
H A Dcsamalignments.cpp132 m_cigar.Assign( cigar ); in CMappedAlignment()
371 …int prefix = m_cigar.front().GetEvent() == CTrBase::eEvent_SoftMask ? m_cigar.front().GetCount() :… in ValidateConsistency()
372 …int suffix = m_cigar.back().GetEvent() == CTrBase::eEvent_SoftMask ? m_cigar.back().GetCount() : 0; in ValidateConsistency()
388 << m_cigar.ToString() << "\t" in ValidateConsistency()
567 m_cigar( other.m_cigar ), in CMappedAlignment()
604 m_cigar = other->m_cigar; in Assign()
685 ASSERT( x != m_cigar.end() ); in AdjustAlignment()
696 m_cigar = result; in AdjustAlignment()
732 m_cigar = result; in AdjustAlignment()
830 m_cigar = tmp; in AdjustAlignment()
[all …]
H A Dcsamrecords.cpp101 m_cigar = other.GetImprovedCigar(); in operator =()
114 m_cigar.clear(); in SetNull()
175 m_cigar = samMdParser.GetFullCigar(); in Init()
229 for( TCigar::const_iterator x = m_cigar.begin(); x != m_cigar.end(); ++x ) { in GetBasicCigar()
300 if( int l = m_cigar.ComputeLengths().first ) { in GetQryBounding()
302 TCigar::const_iterator x = m_cigar.begin(); in GetQryBounding()
426 if( m_mdtag.length() == 0 ) return m_cigar; in GetFullCigar()
427 if( m_cigar.size() == 0 ) return m_cigar; in GetFullCigar()
428 m_current = m_cigar.begin(); in GetFullCigar()
436 if( m_current == m_cigar.end() ) return fullcigar; in GetFullCigar()
[all …]
H A Dcsamrecords.hpp26 const TCigar& GetImprovedCigar() const { return m_cigar; } in GetImprovedCigar()
81 { return ComputeScore( m_cigar, id, mm, go, ge ); } in ComputeScore()
101 TCigar m_cigar; member in CSamRecord
110 : m_cigar( cigar ), m_mdtag( mdtag ), m_current( cigar.begin() ) {} in CSamMdParser()
115 if( m_current == m_cigar.end() ) return m_cevent = eEvent_NULL; in NextEvent()
118 if( ++m_current == m_cigar.end() ) return m_cevent = eEvent_NULL; in NextEvent()
126 const TCigar& m_cigar; member in CSamMdParser
H A Dcsammdformatter.hpp13 m_target( target_ncbi8na ), m_query( queryS_iupacna ), m_cigar( cigar ), m_keepCount(0) {} in CSamMdFormatter()
26 TTrSequence m_cigar; member in CSamMdFormatter
H A Dcsamalignments.hpp105 virtual const TTrSequence GetCigar() const { return m_cigar; } in GetCigar()
138 …out << m_cigar.ToString() << DISPLAY( m_sstart ) << DISPLAY( m_slength ) << DISPLAY( m_qstart ) <<… in PrintDebug()
147 m_cigar == other.m_cigar; in operator ==()
172 TTrSequence m_cigar; member in CMappedAlignment
H A Dcguidesam.hpp34 TTrVector m_cigar[2]; member in CGuideSamFile
H A Dcsammdformatter.cpp13 const TTrSequence& tr = m_cigar; in Format()
/dports/biology/samtools/samtools-1.14/misc/
H A Dace2sam.c73 long m_cigar = 0, n_cigar = 0; in main() local
129 if (l_M) write_cigar(cigar, n_cigar, m_cigar, l_M<<4); \ in main()
132 if (l_D) write_cigar(cigar, n_cigar, m_cigar, l_D<<4 | 2); \ in main()
136 if (l_M) write_cigar(cigar, n_cigar, m_cigar, l_M<<4); \ in main()
137 else write_cigar(cigar, n_cigar, m_cigar, l_D<<4 | 2); \ in main()
143 else write_cigar(cigar, n_cigar, m_cigar, t[2].l<<4); in main()
204 if (beg) write_cigar(cigar, n_cigar, m_cigar, beg<<4|4); in main()
216 write_cigar(cigar, n_cigar, m_cigar, k<<4|op); in main()
220 write_cigar(cigar, n_cigar, m_cigar, k<<4|op); in main()
233 if (end < t[2].l) write_cigar(cigar, n_cigar, m_cigar, (t[2].l - end)<<4|4); in main()
/dports/www/h2o-devel/h2o-dcc7134/deps/klib/
H A Dksw.c445 static inline uint32_t *push_cigar(int *n_cigar, int *m_cigar, uint32_t *cigar, int op, int len) in push_cigar() argument
448 if (*n_cigar == *m_cigar) { in push_cigar()
449 *m_cigar = *m_cigar? (*m_cigar)<<1 : 4; in push_cigar()
450 cigar = realloc(cigar, (*m_cigar) << 2); in push_cigar()
514 int n_cigar = 0, m_cigar = 0, which = 0; in ksw_global() local
519 if (which == 0) cigar = push_cigar(&n_cigar, &m_cigar, cigar, 0, 1), --i, --k; in ksw_global()
520 else if (which == 1) cigar = push_cigar(&n_cigar, &m_cigar, cigar, 2, 1), --i; in ksw_global()
521 else cigar = push_cigar(&n_cigar, &m_cigar, cigar, 1, 1), --k; in ksw_global()
523 if (i >= 0) cigar = push_cigar(&n_cigar, &m_cigar, cigar, 2, i + 1); in ksw_global()
524 if (k >= 0) cigar = push_cigar(&n_cigar, &m_cigar, cigar, 1, k + 1); in ksw_global()
/dports/biology/bwa/bwa-0.7.17/
H A Dksw.c494 static inline uint32_t *push_cigar(int *n_cigar, int *m_cigar, uint32_t *cigar, int op, int len) in push_cigar() argument
497 if (*n_cigar == *m_cigar) { in push_cigar()
498 *m_cigar = *m_cigar? (*m_cigar)<<1 : 4; in push_cigar()
499 cigar = realloc(cigar, (*m_cigar) << 2); in push_cigar()
591 int n_cigar = 0, m_cigar = 0, which = 0; in ksw_global2() local
596 if (which == 0) cigar = push_cigar(&n_cigar, &m_cigar, cigar, 0, 1), --i, --k; in ksw_global2()
597 else if (which == 1) cigar = push_cigar(&n_cigar, &m_cigar, cigar, 2, 1), --i; in ksw_global2()
598 else cigar = push_cigar(&n_cigar, &m_cigar, cigar, 1, 1), --k; in ksw_global2()
600 if (i >= 0) cigar = push_cigar(&n_cigar, &m_cigar, cigar, 2, i + 1); in ksw_global2()
601 if (k >= 0) cigar = push_cigar(&n_cigar, &m_cigar, cigar, 1, k + 1); in ksw_global2()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/gnomon/
H A Dvariations.hpp46 string m_cigar; member
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/
H A Dvariations.cpp69 string cigar = ad.m_cigar; in CLiteAlign()