/dports/biology/canu/canu-2.2/src/utility/src/utility/ |
H A D | align-ksw2.H | 29 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 …]
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H A D | align-ksw2-extz.C | 130 …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()
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H A D | align-ksw2-extz2-sse.C | 295 …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()
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/dports/biology/mmseqs2/MMseqs2-13-45111/lib/ksw2/ |
H A D | ksw2.h | 56 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 …]
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H A D | ksw2_extz2_sse.cpp | 280 …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()
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/dports/biology/minimap2/minimap2-2.24/ |
H A D | ksw2.h | 36 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 …]
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H A D | ksw2_extz2_sse.c | 303 …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()
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H A D | ksw2_extd2_sse.c | 392 …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()
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H A D | ksw2_exts2_sse.c | 410 …, 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()
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H A D | align.c | 751 ez->cigar = ksw_push_cigar(km, &ez->n_cigar, &ez->m_cigar, ez->cigar, MM_CIGAR_MATCH, qe - qs); in mm_align1()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/oligofar/ |
H A D | csamalignments.cpp | 132 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 …]
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H A D | csamrecords.cpp | 101 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 …]
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H A D | csamrecords.hpp | 26 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
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H A D | csammdformatter.hpp | 13 m_target( target_ncbi8na ), m_query( queryS_iupacna ), m_cigar( cigar ), m_keepCount(0) {} in CSamMdFormatter() 26 TTrSequence m_cigar; member in CSamMdFormatter
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H A D | csamalignments.hpp | 105 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
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H A D | cguidesam.hpp | 34 TTrVector m_cigar[2]; member in CGuideSamFile
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H A D | csammdformatter.cpp | 13 const TTrSequence& tr = m_cigar; in Format()
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/dports/biology/samtools/samtools-1.14/misc/ |
H A D | ace2sam.c | 73 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()
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/dports/www/h2o-devel/h2o-dcc7134/deps/klib/ |
H A D | ksw.c | 445 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()
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/dports/biology/bwa/bwa-0.7.17/ |
H A D | ksw.c | 494 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/gnomon/ |
H A D | variations.hpp | 46 string m_cigar; member
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/ |
H A D | variations.cpp | 69 string cigar = ad.m_cigar; in CLiteAlign()
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