| /dports/biology/canu/canu-2.2/src/utility/src/utility/ |
| H A D | align-ssw.H | 69 int32_t ref_begin1; member
167 int32_t mark_mismatch (int32_t ref_begin1,
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| H A D | align-ssw.C | 796 r->ref_begin1 = -1; in ssw_align()
849 r->ref_begin1 = bests_reverse[0].ref; in ssw_align()
852 …g) != 0 && r->score1 < filters) || ((4&flag) != 0 && (r->ref_end1 - r->ref_begin1 > filterd || r->… in ssw_align()
855 refLen = r->ref_end1 - r->ref_begin1 + 1; in ssw_align()
858 …path = banded_sw(ref + r->ref_begin1, prof->read + r->read_begin1, refLen, readLen, r->score1, wei… in ssw_align()
913 int32_t mark_mismatch (int32_t ref_begin1, in mark_mismatch() argument
926 ref += ref_begin1; in mark_mismatch()
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| H A D | align-ssw-driver.C | 173 uint32 nMismatch = mark_mismatch(result->ref_begin1, in align()
189 _bgnB = _offB + result->ref_begin1; in align()
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| /dports/biology/py-scikit-bio/scikit-bio-0.5.6/skbio/alignment/_lib/ |
| H A D | ssw.h | 40 int32_t ref_begin1; member
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| H A D | ssw.c | 787 r->ref_begin1 = -1; in ssw_align()
837 r->ref_begin1 = bests_reverse[0].ref; in ssw_align()
840 …g) != 0 && r->score1 < filters) || ((4&flag) != 0 && (r->ref_end1 - r->ref_begin1 > filterd || r->… in ssw_align()
843 refLen = r->ref_end1 - r->ref_begin1 + 1; in ssw_align()
846 …path = banded_sw(ref + r->ref_begin1, prof->read + r->read_begin1, refLen, readLen, r->score1, wei… in ssw_align()
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| /dports/biology/vcflib/vcflib-1.0.2/src/ |
| H A D | ssw.hpp | 59 int32_t ref_begin1; member
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| H A D | ssw.cpp | 806 r->ref_begin1 = -1; in ssw_align()
859 r->ref_begin1 = bests_reverse[0].ref; in ssw_align()
862 …g) != 0 && r->score1 < filters) || ((4&flag) != 0 && (r->ref_end1 - r->ref_begin1 > filterd || r->… in ssw_align()
865 refLen = r->ref_end1 - r->ref_begin1 + 1; in ssw_align()
868 …path = banded_sw(ref + r->ref_begin1, prof->read + r->read_begin1, refLen, readLen, r->score1, wei… in ssw_align()
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| H A D | ssw_cpp.cpp | 64 al->ref_begin = s_al.ref_begin1; in ConvertAlignment()
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| /dports/biology/freebayes/freebayes-1.3.5/contrib/SeqLib/SeqLib/ |
| H A D | ssw.h | 49 int32_t ref_begin1; member
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| /dports/biology/freebayes/freebayes-1.3.5/vcflib/src/ |
| H A D | ssw.hpp | 50 int32_t ref_begin1; member
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| H A D | ssw.cpp | 797 r->ref_begin1 = -1; in ssw_align()
850 r->ref_begin1 = bests_reverse[0].ref; in ssw_align()
853 …g) != 0 && r->score1 < filters) || ((4&flag) != 0 && (r->ref_end1 - r->ref_begin1 > filterd || r->… in ssw_align()
856 refLen = r->ref_end1 - r->ref_begin1 + 1; in ssw_align()
859 …path = banded_sw(ref + r->ref_begin1, prof->read + r->read_begin1, refLen, readLen, r->score1, wei… in ssw_align()
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| H A D | ssw_cpp.cpp | 55 al->ref_begin = s_al.ref_begin1; in ConvertAlignment()
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| /dports/biology/freebayes/freebayes-1.3.5/vcflib-temp/src/ |
| H A D | ssw.hpp | 50 int32_t ref_begin1; member
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| H A D | ssw.cpp | 797 r->ref_begin1 = -1; in ssw_align()
850 r->ref_begin1 = bests_reverse[0].ref; in ssw_align()
853 …g) != 0 && r->score1 < filters) || ((4&flag) != 0 && (r->ref_end1 - r->ref_begin1 > filterd || r->… in ssw_align()
856 refLen = r->ref_end1 - r->ref_begin1 + 1; in ssw_align()
859 …path = banded_sw(ref + r->ref_begin1, prof->read + r->read_begin1, refLen, readLen, r->score1, wei… in ssw_align()
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| H A D | ssw_cpp.cpp | 55 al->ref_begin = s_al.ref_begin1; in ConvertAlignment()
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| /dports/biology/freebayes/freebayes-1.3.5/contrib/SeqLib/src/ |
| H A D | ssw.c | 795 r->ref_begin1 = -1; in ssw_align()
848 r->ref_begin1 = bests_reverse[0].ref; in ssw_align()
851 …g) != 0 && r->score1 < filters) || ((4&flag) != 0 && (r->ref_end1 - r->ref_begin1 > filterd || r->… in ssw_align()
854 refLen = r->ref_end1 - r->ref_begin1 + 1; in ssw_align()
857 …path = banded_sw(ref + r->ref_begin1, prof->read + r->read_begin1, refLen, readLen, r->score1, wei… in ssw_align()
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| H A D | ssw_cpp.cpp | 55 al->ref_begin = s_al.ref_begin1; in ConvertAlignment()
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| /dports/biology/canu/canu-2.2/src/utility/src/tests/ |
| H A D | alignTest-ssw.C | 102 …fprintf(stdout, "B: 0 - %5d - %5d - %5d best score %5d\n", result->ref_begin1, result->ref_end1,… in native_interface()
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| /dports/biology/py-scikit-bio/scikit-bio-0.5.6/skbio/alignment/ |
| H A D | _ssw_wrapper.pyx | 19 cnp.int32_t ref_begin1
169 return self.p.ref_begin1 + self.index_starts_at if (self.p.ref_begin1
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| H A D | _ssw_wrapper.c | 3234 if (((__pyx_v_self->p->ref_begin1 >= 0) != 0)) { in __pyx_pf_5skbio_9alignment_12_ssw_wrapper_18AlignmentStructure_12target_begin___get__()
3243 …__pyx_t_2 = __Pyx_PyInt_From_npy_int32((__pyx_v_self->p->ref_begin1 + __pyx_v_self->index_starts_a… in __pyx_pf_5skbio_9alignment_12_ssw_wrapper_18AlignmentStructure_12target_begin___get__()
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| /dports/biology/canu/canu-2.2/src/utility/src/parasail/ |
| H A D | parasail.h | 435 int32_t ref_begin1; member
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