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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/compart__matching_8cpp.html below:

NCBI C++ ToolKit: src/algo/align/splign/compart_matching.cpp File Reference

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◆ CHECK_MEMMAP #define CHECK_MEMMAP ( mm, ofs, len ) Value:

{{ \

const size_t ofs1 (mm.GetOffset()); \

if(ofs1 != ofs) { \

cerr << "Real offset " << ofs1 << " different from " << ofs << endl; \

} \

const size_t len1 (mm.GetSize()); \

cerr <<

"Real length "

<< len1 <<

" different from "

len

<< endl; \

} \

}}

Definition at line 1223 of file compart_matching.cpp.

◆ EXTEND_USING_SEQUENCE_CHARS #define EXTEND_USING_SEQUENCE_CHARS ◆ QCOMP_COUNT_NrMERS #define QCOMP_COUNT_NrMERS Value:

{{ \

if(gccur + 16 >= current_offset + bases) { \

break; \

} \

const

Uint4

mer4 (ui8 & kUI8_LoWord); \

++NrCounts[mer4 >> 4]; \

gccur += 4; \

ui8 >>= 8; \

}}

uint32_t Uint4

4-byte (32-bit) unsigned integer

◆ QCOMP_CREATE_GENOMIC_IDX [1/2] #define QCOMP_CREATE_GENOMIC_IDX ( w8, gccur ) Value:

{ \

if(gccur + 16 >= current_offset + bases) { \

break; \

} \

const

Uint8

mer (w8 & kUI8_LoWord); \

if(strand) { \

if(m_Mers.get_at(mer)) { \

MersAndCoords[mcidx++] = (mer << 32) | gccur; \

} \

else { \

if(m_Mers.get_at(rc)) { \

MersAndCoords[mcidx++] = (

Uint8

(rc) << 32) | \

((current_offset + bases - gccur - 16) \

+ current_offset); \

} \

gccur += 4; \

w8 >>= 8; \

}

uint64_t Uint8

8-byte (64-bit) unsigned integer

◆ QCOMP_CREATE_GENOMIC_IDX [2/2] #define QCOMP_CREATE_GENOMIC_IDX ( w8, gccur ) Value:

{ \

if(gccur + 16 >= current_offset + bases) { \

break; \

} \

const

Uint8

mer (w8 & kUI8_LoWord); \

if(strand) { \

if(m_Mers.get_at(mer)) { \

MersAndCoords[mcidx++] = (mer << 32) | gccur; \

} \

else { \

if(m_Mers.get_at(rc)) { \

MersAndCoords[mcidx++] = (

Uint8

(rc) << 32) | \

((current_offset + bases - gccur - 16) \

+ current_offset); \

} \

gccur += 4; \

w8 >>= 8; \

}

◆ QCOMP_PREPARE_SHIFTED_GENOMIC_IDX [1/2] #define QCOMP_PREPARE_SHIFTED_GENOMIC_IDX Value:

size_t gccur2 (gccur + 2); \

const

Uint8

ui8_2930 (w8 >> 60); \

Uint8 ui8_ls4 (w8 << 4); \

const

Uint8

ui8_mask (ui8_ls4 & kUI8_LoHalfWordEachByte); \

ui8_ls4 &= kUI8_LoHalfWordEachByte << 4; \

ui8_ls4 |= (ui8_mask >> 16) | (ui8_2930 << 48);

◆ QCOMP_PREPARE_SHIFTED_GENOMIC_IDX [2/2] #define QCOMP_PREPARE_SHIFTED_GENOMIC_IDX Value:

size_t gccur2 (gccur + 2); \

const

Uint8

ui8_2930 (w8 >> 60); \

Uint8 ui8_ls4 (w8 << 4); \

const

Uint8

ui8_mask (ui8_ls4 & kUI8_LoHalfWordEachByte); \

ui8_ls4 &= kUI8_LoHalfWordEachByte << 4; \

ui8_ls4 |= (ui8_mask >> 16) | (ui8_2930 << 48);

◆ CheckWrittenFile() ◆ DecodeSeqDbChar() ◆ g_RestoreFromTemp()

template<typename VectorT >

void g_RestoreFromTemp ( const string & filename, VectorT * pvd ) ◆ g_SaveToTemp()

template<typename VectorT >

◆ GenerateSeed() ◆ GetLocalBaseName() ◆ PDiag() ◆ PLoWord() ◆ ReplaceExt() ◆ ReverseAndComplement()

template<typename T >

T ReverseAndComplement ( T v )

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