inc/nib.h File Reference

#include "dnautil.h"
#include "hash.h"

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Data Structures
struct	nibInfo
Defines
#define	NIB_MASK_MIXED   0x01
#define	NIB_MASK_MAP   0x02
#define	NIB_BASE_NAME   0x04
Functions
void	nibOpenVerify (char *fileName, FILE **retFile, int *retSize)
dnaSeq *	nibLoadPart (char *fileName, int start, int size)
dnaSeq *	nibLoadPartMasked (int options, char *fileName, int start, int size)
dnaSeq *	nibLdPart (char *fileName, FILE *f, int seqSize, int start, int size)
dnaSeq *	nibLdPartMasked (int options, char *fileName, FILE *f, int seqSize, int start, int size)
dnaSeq *	nibLoadAll (char *fileName)
dnaSeq *	nibLoadAllMasked (int options, char *fileName)
void	nibWrite (struct dnaSeq *seq, char *fileName)
void	nibWriteMasked (int options, struct dnaSeq *seq, char *fileName)
boolean	nibIsFile (char *fileName)
boolean	nibIsRange (char *fileName)
void	nibParseName (unsigned options, char *fileSpec, char *filePath, char *name, unsigned *start, unsigned *end)
nibStream *	nibStreamOpen (char *fileName)
void	nibStreamClose (struct nibStream **pNs)
void	nibStreamOne (struct nibStream *ns, DNA base)
void	nibStreamMany (struct nibStream *ns, DNA *dna, int size)
nibInfo *	nibInfoNew (char *path)
void	nibInfoFree (struct nibInfo **pNib)
nibInfo *	nibInfoFromCache (struct hash *hash, char *nibDir, char *nibName)
int	nibGetSize (char *nibFile)

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Define Documentation

#define NIB_BASE_NAME   0x04

Definition at line 26 of file nib.h.

Referenced by gfClientSeqList(), and nibParseName().

#define NIB_MASK_MAP   0x02

Definition at line 22 of file nib.h.

Referenced by nibOutput().

#define NIB_MASK_MIXED   0x01

Options for controlling masking

Definition at line 20 of file nib.h.

Referenced by dnaLoadSingle(), gfClientSeqList(), nibInput(), nibOutput(), nibTwoCacheSeqPartExt(), nibTwoLoadOne(), readMaskedNib(), and searchOneIndex().

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Function Documentation

int nibGetSize

(

char *

nibFile

)

Definition at line 507 of file nib.c.

References carefulClose(), nibOpenVerify(), and nibInfo::size.

{
FILE* fh;
int size;

nibOpenVerify(nibFile, &fh, &size);
carefulClose(&fh);
return size;
}

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void nibInfoFree

(

struct nibInfo **

pNib

)

Definition at line 480 of file nib.c.

References carefulClose(), nibInfo::f, nibInfo::fileName, freeMem(), and freez().

Referenced by gfFileCacheFreeEl(), and nibTwoCacheFree().

{
struct nibInfo *nib = *pNib;
if (nib != NULL)
    {
    carefulClose(&nib->f);
    freeMem(nib->fileName);
    freez(pNib);
    }
}

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struct nibInfo* nibInfoFromCache	(	struct hash *	hash,
		char *	nibDir,
		char *	nibName
	)			[read]

Definition at line 492 of file nib.c.

References hashAdd(), hashFindVal(), nibInfoNew(), PATH_LEN, and safef().

Referenced by nibTwoCacheSeq(), and nibTwoCacheSeqPartExt().

{
struct nibInfo *nib;
char path[PATH_LEN];
safef(path, sizeof(path), "%s/%s.nib", nibDir, nibName);
nib = hashFindVal(hash, path);
if (nib == NULL)
    {
    nib = nibInfoNew(path);
    hashAdd(hash, path, nib);
    }
return nib;
}

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struct nibInfo* nibInfoNew

(

char *

path

)

[read]

Definition at line 470 of file nib.c.

References AllocVar, cloneString(), nibInfo::f, nibInfo::fileName, nibOpenVerify(), and nibInfo::size.

Referenced by gfiExpandAndLoadCached(), and nibInfoFromCache().

{
struct nibInfo *nib;
AllocVar(nib);
nib->fileName = cloneString(path);
nibOpenVerify(path, &nib->f, &nib->size);
return nib;
}

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boolean nibIsFile

(

char *

fileName

)

Definition at line 444 of file nib.c.

References endsWith(), and findNibSubrange().

Referenced by dnaLoadSingle(), gfClientFileArray(), gfClientSeqList(), gfFileCacheFreeEl(), gfiExpandAndLoadCached(), gfiGetSeqName(), gfIndexNibsAndTwoBits(), gfIndexTransNibsAndTwoBits(), gfMakeOoc(), readSeqFrag(), and searchOneIndex().

{
boolean isANib;
char *subrange = findNibSubrange(fileName);
if (subrange != NULL)
    *subrange = '\0';
isANib = endsWith(fileName, ".nib") || endsWith(fileName, ".NIB");
if (subrange != NULL)
    *subrange = ':';
return isANib;
}

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boolean nibIsRange

(

char *

fileName

)

Definition at line 457 of file nib.c.

References endsWith(), FALSE, and findNibSubrange().

{
boolean isANib;
char *subrange = findNibSubrange(fileName);;
if (subrange == NULL)
    return FALSE;
*subrange = '\0';
isANib = endsWith(fileName, ".nib") || endsWith(fileName, ".NIB");
*subrange = ':';
return isANib;
}

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struct dnaSeq* nibLdPart	(	char *	fileName,
		FILE *	f,
		int	seqSize,
		int	start,
		int	size
	)			[read]

Definition at line 301 of file nib.c.

References nibLdPartMasked().

Referenced by gfAddTilesInNib(), gfCountTilesInNib(), gfiExpandAndLoadCached(), and nibTwoCacheSeq().

{
return nibLdPartMasked(0, fileName, f, seqSize, start, size);
}

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struct dnaSeq* nibLdPartMasked	(	int	options,
		char *	fileName,
		FILE *	f,
		int	seqSize,
		int	start,
		int	size
	)			[read]

Definition at line 292 of file nib.c.

References nibInput(), and safef().

Referenced by nibLdPart(), nibLoadPartMasked(), and nibTwoCacheSeqPartExt().

{
char nameBuf[512];
safef(nameBuf, sizeof(nameBuf), "%s:%d-%d", fileName, start, start+size);
return nibInput(options, fileName, nameBuf, f, seqSize, start, size);
}

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struct dnaSeq* nibLoadAll

(

char *

fileName

)

[read]

Definition at line 352 of file nib.c.

References nibLoadAllMasked().

Referenced by gfMakeOoc(), and readMaskedNib().

{
return nibLoadAllMasked(0, fileName);
}

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struct dnaSeq* nibLoadAllMasked	(	int	options,
		char *	fileName
	)			[read]

Definition at line 325 of file nib.c.

References name, nibInput(), nibOpenVerify(), nibParseName(), and PATH_LEN.

Referenced by dnaLoadSingle(), gfClientSeqList(), nibLoadAll(), nibTwoLoadOne(), readMaskedNib(), and searchOneIndex().

                   :
 *    /path/file.nib:seqid:start-end
 * or\n"
 *    /path/file.nib:start-end
 * With the first form, seqid becomes the id of the subrange, with the second
 * form, a sequence id of file:start-end will be used.
 */
{
struct dnaSeq *seq;
FILE *f;
int seqSize;
char filePath[PATH_LEN];
char name[PATH_LEN];
unsigned start, end;

nibParseName(options, fileName, filePath, name, &start, &end);
nibOpenVerify(filePath, &f, &seqSize);
if (end == 0)
    end = seqSize;
seq = nibInput(options, fileName, name, f, seqSize, start, end-start);
fclose(f);
return seq;
}

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struct dnaSeq* nibLoadPart	(	char *	fileName,
		int	start,
		int	size
	)			[read]

Definition at line 319 of file nib.c.

References nibLoadPartMasked().

Referenced by readSeqFrag().

{
return nibLoadPartMasked(0, fileName, start, size);
}

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struct dnaSeq* nibLoadPartMasked	(	int	options,
		char *	fileName,
		int	start,
		int	size
	)			[read]

Definition at line 307 of file nib.c.

References nibLdPartMasked(), and nibOpenVerify().

Referenced by nibLoadPart().

{
struct dnaSeq *seq;
FILE *f;
int seqSize;
nibOpenVerify(fileName, &f, &seqSize);
seq = nibLdPartMasked(options, fileName, f, seqSize, start, size);
fclose(f);
return seq;
}

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void nibOpenVerify	(	char *	fileName,
		FILE **	retFile,
		int *	retSize
	)

Definition at line 84 of file nib.c.

References bits32, byteSwap32(), dnaUtilOpen(), errAbort(), errno, mustReadOne, nibSig, and safef().

Referenced by dnaLoadSingle(), gfAddTilesInNib(), gfCountTilesInNib(), nibGetSize(), nibInfoNew(), nibLoadAllMasked(), and nibLoadPartMasked().

{
bits32 size;
bits32 sig;
FILE *f = fopen(fileName, "rb");
char buffer[512];
char buffer2[512];
char buffer3[512];

if (f == NULL)
    {
    /* see if nib is down a few directories ala faSplit -outDirDepth */
    char *ptr = NULL;
    char *dir, *file;
    struct stat statBuf;

    /* divide fileName into file and directory components */
    safef(buffer, sizeof(buffer), "%s", fileName);
    if ((ptr = strrchr(buffer, '/')) != NULL)
        {
        *ptr++ = 0;
        dir = buffer;
        file = ptr;
        }
    else
        {
        dir = "";
        file = buffer;
        }
    
    buffer3[0] = 0;
    /* start at the end of the fileName (minus .nib) */
    for(ptr = &file[strlen(file) - 5]; ; )
        {
        strcpy(buffer2, buffer3);
        if (isdigit(*ptr))
            {
            /* if we have a digit in the fileName, see if there is a directory with this name */
            safef(buffer3, sizeof(buffer3), "%c/%s",*ptr,buffer2);
            ptr--;
            }
        else
            /* we've run out of digits in the fileName, just add 0's */
            safef(buffer3, sizeof(buffer3), "0/%s",buffer2);

        /* check to see if this directory exists */
        safef(buffer2, sizeof(buffer2), "%s/%s", dir, buffer3);
        if (stat(buffer2, &statBuf) < 0)
            break;

        /* directory exists, see if our file is down there */
        safef(buffer2, sizeof(buffer2), "%s/%s/%s", dir, buffer3, file);
        if  ((f = fopen(buffer2, "rb")) != NULL)
            break;
        }
    if (f == NULL)
        errAbort("Can't open %s to read: %s", fileName,  strerror(errno));
    }
dnaUtilOpen();
mustReadOne(f, sig);
mustReadOne(f, size);
if (sig != nibSig)
    {
    sig = byteSwap32(sig);
    size = byteSwap32(size);
    if (sig != nibSig)
        errAbort("%s is not a good .nib file.",  fileName);
    }
*retSize = size;
*retFile = f;
}

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void nibParseName	(	unsigned	options,
		char *	fileSpec,
		char *	filePath,
		char *	name,
		unsigned *	start,
		unsigned *	end
	)

Definition at line 48 of file nib.c.

References findNibSubrange(), NIB_BASE_NAME, parseSubrange(), and splitPath().

Referenced by dnaLoadSingle(), and nibLoadAllMasked().

{
char *subrange = findNibSubrange(fileSpec);
if (subrange != NULL)
    {
    *subrange = '\0';
    parseSubrange(subrange, name, start, end);
    strcpy(filePath, fileSpec);
    *subrange = ':';
    if (strlen(name) == 0)
        {
        /* no name in spec, generate one */
        if (options & NIB_BASE_NAME)
            splitPath(filePath, NULL, name, NULL);
        else
            strcpy(name, filePath);
        sprintf(name+strlen(name), ":%u-%u", *start, *end);
        }
    }
else
    {
    *start = 0;
    *end = 0;
    strcpy(filePath, fileSpec);
    if (options & NIB_BASE_NAME)
        splitPath(fileSpec, NULL, name, NULL);
    else
        strcpy(name, fileSpec);
    }
}

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void nibStreamClose

(

struct nibStream **

pNs

)

Definition at line 401 of file nib.c.

References bits32, nibStream::byte, nibStream::f, nibStream::fileName, freeMem(), freez(), nibSig, SEEK_SET, nibStream::size, and writeOne.

{
struct nibStream *ns = *pNs;
FILE *f;
bits32 sig = nibSig;
if (ns == NULL)
    return;
f = ns->f;
if (ns->size&1)
    writeOne(f, ns->byte);
fseek(f,  0L, SEEK_SET);
writeOne(f, sig);
writeOne(f, ns->size);
fclose(f);
freeMem(ns->fileName);
freez(pNs);
}

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void nibStreamMany	(	struct nibStream *	ns,
		DNA *	dna,
		int	size
	)

Definition at line 436 of file nib.c.

References nibStreamOne().

{
int i;
for (i=0; i<size; ++i)
    nibStreamOne(ns, *dna++);
}

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void nibStreamOne	(	struct nibStream *	ns,
		DNA	base
	)

Definition at line 420 of file nib.c.

References nibStream::byte, nibStream::f, ntVal5, nibStream::size, UBYTE, and writeOne.

Referenced by nibStreamMany().

{
UBYTE ub = ntVal5[(int)base];

if ((++ns->size&1) == 0)
    {
    ub += ns->byte;
    writeOne(ns->f, ub);
    }
else
    {
    ns->byte = (ub<<4);
    }
}

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struct nibStream* nibStreamOpen

(

char *

fileName

)

[read]

Definition at line 383 of file nib.c.

References AllocVar, cloneString(), dnaUtilOpen(), nibStream::f, nibStream::fileName, mustOpen(), nibStream::size, and writeOne.

{
struct nibStream *ns;
FILE *f;

dnaUtilOpen();
AllocVar(ns);
ns->f = f = mustOpen(fileName, "wb");
ns->fileName = cloneString(fileName);

/* Write header - initially zero.  Will fix it up when we close. */
writeOne(f, ns->size);
writeOne(f, ns->size);

return ns;
}

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void nibWrite	(	struct dnaSeq *	seq,
		char *	fileName
	)

Definition at line 365 of file nib.c.

References nibWriteMasked().

{
    nibWriteMasked(0, seq, fileName);
}

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void nibWriteMasked	(	int	options,
		struct dnaSeq *	seq,
		char *	fileName
	)

Definition at line 358 of file nib.c.

References nibOutput().

Referenced by nibWrite().

{
    nibOutput(options, seq, fileName);
}

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