inc/nt4.h File Reference

#include "dnautil.h"

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Data Structures
struct	nt4Seq
Functions
nt4Seq *	newNt4 (DNA *dna, int size, char *name)
void	freeNt4 (struct nt4Seq **pSeq)
nt4Seq *	loadNt4 (char *fileName, char *seqName)
void	saveNt4 (char *fileName, DNA *dna, bits32 dnaSize)
int	nt4BaseCount (char *fileName)
DNA *	nt4Unpack (struct nt4Seq *n, int start, int size)
DNA *	nt4LoadPart (char *nt4FileName, int start, int size)

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Function Documentation

void freeNt4

(

struct nt4Seq **

pSeq

)

Definition at line 55 of file nt4.c.

References nt4Seq::bases, freeMem(), freez(), and nt4Seq::name.

Referenced by flyFreeNt4Genome(), wormFreeNt4Genome(), and xenAlignBig().

{
struct nt4Seq *seq = *pSeq;
if (seq == NULL)
    return;
freeMem(seq->bases);
freeMem(seq->name);
freez(pSeq);
}

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struct nt4Seq* loadNt4	(	char *	fileName,
		char *	seqName
	)			[read]

Definition at line 78 of file nt4.c.

References allocNt4(), nt4Seq::bases, bits32, bits32PaddedSize(), carefulClose(), mustRead(), mustReadOne, and nt4OpenVerify().

Referenced by flyLoadNt4Genome(), and wormLoadNt4Genome().

{
bits32 size;
struct nt4Seq *seq;
FILE *f = nt4OpenVerify(fileName);

mustReadOne(f, size);
if (seqName == NULL)
    seqName = fileName;
seq = allocNt4(size, seqName);
mustRead(f, seq->bases, bits32PaddedSize(size));
carefulClose(&f);
return seq;
}

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struct nt4Seq* newNt4	(	DNA *	dna,
		int	size,
		char *	name
	)			[read]

Definition at line 32 of file nt4.c.

References allocNt4(), nt4Seq::bases, bits32, and packDna16().

Referenced by xenAlignBig().

{
bits32 *packed;
DNA *unpacked;
char last[16];
struct nt4Seq *seq = allocNt4(size, name);
packed = seq->bases;
unpacked = dna;
while (size > 16)
    {
    *packed++ = packDna16(dna);
    dna += 16;
    size -= 16;
    }
if (size > 0)
    {
    memcpy(last, dna, size);
    *packed++ = packDna16(dna);
    }
return seq;
}

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int nt4BaseCount

(

char *

fileName

)

Definition at line 121 of file nt4.c.

References bits32, mustReadOne, and nt4OpenVerify().

Referenced by wormChromSize().

{
bits32 size;
FILE *f = nt4OpenVerify(fileName);

mustReadOne(f, size);
fclose(f);
return (int)size;
}

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DNA* nt4LoadPart	(	char *	nt4FileName,
		int	start,
		int	size
	)

Definition at line 226 of file nt4.c.

References bits32, freeMem(), mustRead(), mustReadOne, needLargeMem(), nt4OpenVerify(), SEEK_CUR, and unalignedUnpackDna().

Referenced by wormChromPart().

{
bits32 basesInFile;
int tStart, tEnd, tSize;
int end;
FILE *f;
DNA *unpacked;
bits32 *tiles;

/* Open file, and make sure request is covered by file. */
f = nt4OpenVerify(fileName);
mustReadOne(f, basesInFile);

assert(start >= 0);
end = start + size;
assert(end <= (int)basesInFile);

/* Figure out tiles to load */
tStart = (start>>4);
tEnd = ((end+15)>>4);
tSize = tEnd - tStart;

/* Allocate tile array and read it from disk. */
tiles = needLargeMem(tSize * sizeof(*tiles));
fseek(f, tStart * sizeof(*tiles), SEEK_CUR);
mustRead(f, tiles, tSize * sizeof(*tiles) );

/* Allocate and unpack array. */
unpacked = needLargeMem(size+1);
unalignedUnpackDna(tiles, start - (tStart<<4), size, unpacked);

freeMem(tiles);
fclose(f);
return unpacked;
}

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DNA* nt4Unpack	(	struct nt4Seq *	n,
		int	start,
		int	size
	)

Definition at line 217 of file nt4.c.

References nt4Seq::bases, needLargeMem(), and unalignedUnpackDna().

Referenced by scoreNoninsertingExtensions().

{
DNA *unpacked = needLargeMem(size+1);
unalignedUnpackDna(n->bases, start, size, unpacked);
return unpacked;
}

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void saveNt4	(	char *	fileName,
		DNA *	dna,
		bits32	dnaSize
	)

Definition at line 94 of file nt4.c.

References nt4Seq::bases, bits32, mustOpen(), nt4Signature, packDna16(), writeOne, and zeroBytes().

{
FILE *f = mustOpen(fileName, "wb");
bits32 signature = nt4Signature;
bits32 bases;
char last[16];

writeOne(f, signature);
writeOne(f, dnaSize);
while (dnaSize >= 16)
    {
    bases = packDna16(dna);
    writeOne(f, bases);
    dna += 16;
    dnaSize -= 16;
    }
if (dnaSize > 0)
    {
    zeroBytes(last, sizeof(last));
    memcpy(last, dna, dnaSize);
    bases = packDna16(last);
    writeOne(f, bases);
    }
fclose(f);
}

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