Searched refs:overlap_s (Results 1 – 6 of 6) sorted by relevance
| /dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/loader/ |
| H A D | reference-writer.c | 60 struct overlap_s { struct
86 self->pri_overlap.elem_bits = self->sec_overlap.elem_bits = sizeof(struct overlap_s) * 8; in ReferenceInit()
144 struct overlap_s *const pri_overlap = (struct overlap_s *)self->pri_overlap.base; in FlushBuffers()
145 struct overlap_s *const sec_overlap = (struct overlap_s *)self->sec_overlap.base; in FlushBuffers()
314 …memset(&((struct overlap_s *)self->pri_overlap.base)[end], 0, (chunks - end) * sizeof(struct overl… in ReferenceAddCoverage()
315 …memset(&((struct overlap_s *)self->sec_overlap.base)[end], 0, (chunks - end) * sizeof(struct overl… in ReferenceAddCoverage()
328 if (((struct overlap_s *)overlapBuffer->base)[endChunk].min == 0 || in ReferenceAddCoverage()
329 ((struct overlap_s *)overlapBuffer->base)[endChunk].min > refStart) in ReferenceAddCoverage()
331 ((struct overlap_s *)overlapBuffer->base)[endChunk].min = refStart; in ReferenceAddCoverage()
334 ((struct overlap_s *)overlapBuffer->base)[endChunk].max < refStart + refLength) in ReferenceAddCoverage()
[all …]
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| /dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/loader/ |
| H A D | reference-writer.c | 60 struct overlap_s { struct
86 self->pri_overlap.elem_bits = self->sec_overlap.elem_bits = sizeof(struct overlap_s) * 8; in ReferenceInit()
144 struct overlap_s *const pri_overlap = (struct overlap_s *)self->pri_overlap.base; in FlushBuffers()
145 struct overlap_s *const sec_overlap = (struct overlap_s *)self->sec_overlap.base; in FlushBuffers()
314 …memset(&((struct overlap_s *)self->pri_overlap.base)[end], 0, (chunks - end) * sizeof(struct overl… in ReferenceAddCoverage()
315 …memset(&((struct overlap_s *)self->sec_overlap.base)[end], 0, (chunks - end) * sizeof(struct overl… in ReferenceAddCoverage()
328 if (((struct overlap_s *)overlapBuffer->base)[endChunk].min == 0 || in ReferenceAddCoverage()
329 ((struct overlap_s *)overlapBuffer->base)[endChunk].min > refStart) in ReferenceAddCoverage()
331 ((struct overlap_s *)overlapBuffer->base)[endChunk].min = refStart; in ReferenceAddCoverage()
334 ((struct overlap_s *)overlapBuffer->base)[endChunk].max < refStart + refLength) in ReferenceAddCoverage()
[all …]
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| /dports/biology/sra-tools/sra-tools-2.11.0/tools/bam-loader/ |
| H A D | reference-writer.c | 64 struct overlap_s { struct
87 self->pri_overlap.elem_bits = self->sec_overlap.elem_bits = sizeof(struct overlap_s) * 8; in ReferenceInit() argument
147 struct overlap_s *const pri_overlap = (struct overlap_s *)self->pri_overlap.base; in FlushBuffers()
148 struct overlap_s *const sec_overlap = (struct overlap_s *)self->sec_overlap.base; in FlushBuffers()
434 …memset(&((struct overlap_s *)self->pri_overlap.base)[end], 0, (chunks - end) * sizeof(struct overl… in ReferenceAddCoverage()
435 …memset(&((struct overlap_s *)self->sec_overlap.base)[end], 0, (chunks - end) * sizeof(struct overl… in ReferenceAddCoverage()
448 if (((struct overlap_s *)overlapBuffer->base)[endChunk].min == 0 || in ReferenceAddCoverage()
449 ((struct overlap_s *)overlapBuffer->base)[endChunk].min > refStart) in ReferenceAddCoverage()
451 ((struct overlap_s *)overlapBuffer->base)[endChunk].min = refStart; in ReferenceAddCoverage()
454 ((struct overlap_s *)overlapBuffer->base)[endChunk].max < refStart + refLength) in ReferenceAddCoverage()
[all …]
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| /dports/biology/ncbi-toolkit/ncbi/algo/blast/core/ |
| H A D | hspfilter_mapper.c | 527 Int4 overlap_f, overlap_s; in s_GetOverlapCost() local
560 overlap_f = overlap_s = f->query.end - s->query.offset; in s_GetOverlapCost()
561 ASSERT(overlap_f >= 0 && overlap_s >= 0); in s_GetOverlapCost()
570 overlap_s -= edit_penalty; in s_GetOverlapCost()
574 return MIN(overlap_f, overlap_s); in s_GetOverlapCost()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/core/ |
| H A D | hspfilter_mapper.c | 446 Int4 overlap_f, overlap_s; in s_GetOverlapCost() local
479 overlap_f = overlap_s = f->query.end - s->query.offset; in s_GetOverlapCost()
480 ASSERT(overlap_f >= 0 && overlap_s >= 0); in s_GetOverlapCost()
489 overlap_s -= edit_penalty; in s_GetOverlapCost()
493 return MIN(overlap_f, overlap_s); in s_GetOverlapCost()
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/core/ |
| H A D | hspfilter_mapper.c | 446 Int4 overlap_f, overlap_s; in s_GetOverlapCost() local
479 overlap_f = overlap_s = f->query.end - s->query.offset; in s_GetOverlapCost()
480 ASSERT(overlap_f >= 0 && overlap_s >= 0); in s_GetOverlapCost()
489 overlap_s -= edit_penalty; in s_GetOverlapCost()
493 return MIN(overlap_f, overlap_s); in s_GetOverlapCost()
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