jkOwnLib/gfInternal.h File Reference

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Data Structures
struct	gfRange
Functions
void	gfRangeFree (struct gfRange **pEl)
void	gfRangeFreeList (struct gfRange **pList)
int	gfRangeCmpTarget (const void *va, const void *vb)
gfRange *	gfRangesBundle (struct gfRange *exonList, int maxIntron)
ssFfItem *	gfRangesToFfItem (struct gfRange *rangeList, aaSeq *qSeq)
ssBundle *	ffSeedExtInMem (struct genoFind *gf, struct dnaSeq *qSeq, Bits *qMaskBits, int qOffset, struct lm *lm, int minScore, boolean isRc)
void	dumpBuns (struct ssBundle *bunList)
void	dumpFf (struct ffAli *left, DNA *needle, DNA *hay)
void	gfiExpandRange (struct gfRange *range, int qSize, int tSize, boolean respectFrame, boolean isRc, int expansion)
dnaSeq *	gfiExpandAndLoadCached (struct gfRange *range, struct hash *tFileCache, char *tSeqDir, int querySize, int *retTotalSeqSize, boolean respectFrame, boolean isRc, int expansion)
void	gfiGetSeqName (char *spec, char *name, char *file)

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Function Documentation

void dumpBuns

(

struct ssBundle *

bunList

)

Definition at line 93 of file supStitch.c.

References dnaSeq::dna, dumpFf(), ssFfItem::ff, ssBundle::ffList, ssBundle::genoSeq, ssBundle::next, ssFfItem::next, ssBundle::qSeq, and slCount().

{
struct ssBundle *bun;
struct ssFfItem *ffl;
for (bun = bunList; bun != NULL; bun = bun->next)
    {
    struct dnaSeq *qSeq = bun->qSeq;        /* Query sequence (not owned by bundle.) */
    struct dnaSeq *genoSeq = bun->genoSeq;     /* Genomic sequence (not owned by bundle.) */
    printf("Bundle of %d between %s and %s\n", slCount(bun->ffList), qSeq->name, genoSeq->name);
    for (ffl = bun->ffList; ffl != NULL; ffl = ffl->next)
        {
        dumpFf(ffl->ff, bun->qSeq->dna, bun->genoSeq->dna);
        }
    }
}

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void dumpFf	(	struct ffAli *	left,
		DNA *	needle,
		DNA *	hay
	)

Definition at line 81 of file supStitch.c.

References ffAli::hEnd, ffAli::hStart, ffAli::left, ffAli::nEnd, ffAli::nStart, and ffAli::right.

{
struct ffAli *ff;
for (ff = left; ff != NULL; ff = ff->right)
    {
    printf("(%ld - %ld)[%ld-%ld] ", (long)(ff->hStart-hay), (long)(ff->hEnd-hay),
        (long)(ff->nStart - needle), (long)(ff->nEnd - needle));
    }
printf("\n");
}

struct ssBundle* ffSeedExtInMem	(	struct genoFind *	gf,
		struct dnaSeq *	qSeq,
		Bits *	qMaskBits,
		int	qOffset,
		struct lm *	lm,
		int	minScore,
		boolean	isRc
	)			[read]

Definition at line 1251 of file ffSeedExtend.c.

References AllocVar, clumpToExactRange(), FALSE, ffCdna, ffIntronMax, gfClumpFreeList(), gfFindClumpsWithQmask(), gfRangeCmpTarget(), gfRangeFreeList(), gfRangesBundle(), gfRangesToFfItem(), lm, gfClump::next, rangeList, refineBundle(), slAddHead, slSort(), ssStitch(), genoFind::tileSize, and TRUE.

{
struct ssBundle *bunList = NULL, *bun;
int hitCount;
struct gfClump *clumpList, *clump;
struct gfRange *rangeList = NULL, *range;
struct dnaSeq *tSeq;

clumpList = gfFindClumpsWithQmask(gf, qSeq, qMaskBits, qOffset, lm, &hitCount);
for (clump = clumpList; clump != NULL; clump = clump->next)
    clumpToExactRange(clump, qSeq, gf->tileSize, 0, NULL, &rangeList);
slSort(&rangeList, gfRangeCmpTarget);
rangeList = gfRangesBundle(rangeList, ffIntronMax);
for (range = rangeList; range != NULL; range = range->next)
    {
    range->qStart += qOffset;
    range->qEnd += qOffset;
    tSeq = range->tSeq;
    AllocVar(bun);
    bun->qSeq = qSeq;
    bun->genoSeq = tSeq;
    bun->ffList = gfRangesToFfItem(range->components, qSeq);
    bun->isProt = FALSE;
    bun->avoidFuzzyFindKludge = TRUE;
    ssStitch(bun, ffCdna, 16, 10);
    refineBundle(gf, qSeq, qMaskBits, qOffset, tSeq, lm, bun, isRc);
    slAddHead(&bunList, bun);
    }
gfRangeFreeList(&rangeList);
gfClumpFreeList(&clumpList);
return bunList;
}

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struct dnaSeq* gfiExpandAndLoadCached	(	struct gfRange *	range,
		struct hash *	tFileCache,
		char *	tSeqDir,
		int	querySize,
		int *	retTotalSeqSize,
		boolean	respectFrame,
		boolean	isRc,
		int	expansion
	)			[read]

Definition at line 57 of file gfInternal.c.

References dnaSeq::dna, errAbort(), nibInfo::f, gfiExpandRange(), hashAdd(), hashFindVal(), nibInfoNew(), nibIsFile(), nibLdPart(), PATH_LEN, reverseComplement(), reverseIntRange(), safef(), dnaSeq::size, nibInfo::size, gfRange::tEnd, gfRange::tName, gfRange::tStart, twoBitOpen(), twoBitReadSeqFragLower(), and twoBitSeqSize().

Referenced by gfAlignStrand(), gfPcrOneViaNet(), and loadHashT3Ranges().

{
struct dnaSeq *target = NULL;
char fileName[PATH_LEN+256];

safef(fileName, sizeof(fileName), "%s/%s", tSeqDir, range->tName);
if (nibIsFile(fileName))
    {
    struct nibInfo *nib = hashFindVal(tFileCache, fileName);
    if (nib == NULL)
        {
        nib = nibInfoNew(fileName);
        hashAdd(tFileCache, fileName, nib);
        }
    if (isRc)
        reverseIntRange(&range->tStart, &range->tEnd, nib->size);
    gfiExpandRange(range, querySize, nib->size, respectFrame, isRc, expansion);
    target = nibLdPart(fileName, nib->f, nib->size, 
        range->tStart, range->tEnd - range->tStart);
    if (isRc)
        {
        reverseComplement(target->dna, target->size);
        reverseIntRange(&range->tStart, &range->tEnd, nib->size);
        }
    *retTotalSeqSize = nib->size;
    }
else
    {
    struct twoBitFile *tbf = NULL;
    char *tSeqName = strchr(fileName, ':');
    int tSeqSize = 0;
    if (tSeqName == NULL)
        errAbort("No colon in .2bit response from gfServer");
    *tSeqName++ = 0;
    tbf = hashFindVal(tFileCache, fileName);
    if (tbf == NULL)
        {
        tbf = twoBitOpen(fileName);
        hashAdd(tFileCache, fileName, tbf);
        }
    tSeqSize = twoBitSeqSize(tbf, tSeqName);
    if (isRc)
        reverseIntRange(&range->tStart, &range->tEnd, tSeqSize);
    gfiExpandRange(range, querySize, tSeqSize, respectFrame, isRc, expansion);
    target = twoBitReadSeqFragLower(tbf, tSeqName, range->tStart, range->tEnd);
    if (isRc)
        {
        reverseComplement(target->dna, target->size);
        reverseIntRange(&range->tStart, &range->tEnd, tSeqSize);
        }
    *retTotalSeqSize = tSeqSize;
    }
return target;
}

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void gfiExpandRange	(	struct gfRange *	range,
		int	qSize,
		int	tSize,
		boolean	respectFrame,
		boolean	isRc,
		int	expansion
	)

Definition at line 24 of file gfInternal.c.

References extendRespect(), gfRange::qEnd, gfRange::qStart, gfRange::tEnd, and gfRange::tStart.

Referenced by gfClumpsToBundles(), and gfiExpandAndLoadCached().

{
int x;

x = range->qStart - expansion;
if (x < 0) x = 0;
range->qStart = x;

x = range->qEnd + expansion;
if (x > qSize) x = qSize;
range->qEnd = x;

x = range->tStart - expansion;
if (x < 0) x = 0;
if (respectFrame && !isRc) 
    {
    x = extendRespect(range->tStart, x);
    }
range->tStart = x;

x = range->tEnd + expansion;
if (x > tSize) x = tSize;
if (respectFrame && isRc)
    {
    x = extendRespect(range->tEnd, x);
    if (x > tSize)
        x -= 3;
    }
range->tEnd = x;
}

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void gfiGetSeqName	(	char *	spec,
		char *	name,
		char *	file
	)

Definition at line 117 of file gfInternal.c.

References errAbort(), nibIsFile(), and splitPath().

Referenced by getTargetName(), and gfPcrOneViaNet().

{
if (nibIsFile(spec))
    {
    splitPath(spec, NULL, name, NULL);
    if (file != NULL)
        strcpy(file, spec);
    }
else
    {
    char *s = strchr(spec, ':');
    if (s == NULL)
        errAbort("Expecting colon in %s", spec);
    strcpy(name, s+1);
    if (file != NULL)
        {
        int fileNameSize = s - spec;
        memcpy(file, spec, fileNameSize);
        file[fileNameSize] = 0;
        }
    }
}

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int gfRangeCmpTarget	(	const void *	va,
		const void *	vb
	)

Definition at line 83 of file gfBlatLib.c.

References gfRange::t3, gfRange::tName, and gfRange::tStart.

Referenced by fastMapClumpsToBundles(), ffSeedExtInMem(), gfAlignSomeClumps(), gfAlignStrand(), gfAlignTrans(), gfAlignTransTrans(), gfClumpsToBundles(), gfFindAlignAaTrans(), and gfTransTransFindBundles().

{
const struct gfRange *a = *((struct gfRange **)va);
const struct gfRange *b = *((struct gfRange **)vb);
int diff;

diff = strcmp(a->tName, b->tName);
if (diff == 0)
    {
    long lDiff = a->t3 - b->t3;
    if (lDiff < 0)
       diff = -1;
    else if (lDiff > 0)
       diff = 1;
    else
       diff = 0;
#ifdef SOLARIS_WORKAROUND_COMPILER_BUG_BUT_FAILS_IN_64_BIT
    diff = (unsigned long)(a->t3) - (unsigned long)(b->t3);     /* Casts needed for Solaris.  Thanks Darren Platt! */
#endif /* SOLARIS_WORKAROUND_COMPILER_BUG_BUT_FAILS_IN_64_BIT */
    }
if (diff == 0)
    diff = a->tStart - b->tStart;
return diff;
}

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void gfRangeFree

(

struct gfRange **

pEl

)

Definition at line 41 of file gfBlatLib.c.

References gfRange::components, freeMem(), freez(), gfRangeFreeList(), and gfRange::tName.

Referenced by gfRangeFreeList().

{
struct gfRange *el;

if ((el = *pEl) == NULL) return;
freeMem(el->tName);
if (el->components != NULL)
    gfRangeFreeList(&el->components);
freez(pEl);
}

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void gfRangeFreeList

(

struct gfRange **

pList

)

Definition at line 54 of file gfBlatLib.c.

References gfRangeFree(), and gfRange::next.

Referenced by fastMapClumpsToBundles(), ffSeedExtInMem(), gfAlignSomeClumps(), gfAlignStrand(), gfAlignTrans(), gfAlignTransTrans(), gfFindAlignAaTrans(), gfPcrOneViaNet(), gfRangeFree(), and gfTransTransFindBundles().

{
struct gfRange *el, *next;

for (el = *pList; el != NULL; el = next)
    {
    next = el->next;
    gfRangeFree(&el);
    }
*pList = NULL;
}

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struct gfRange* gfRangesBundle	(	struct gfRange *	exonList,
		int	maxIntron
	)			[read]

Definition at line 355 of file gfBlatLib.c.

References AllocVar, cloneString(), gfRange::next, sameString, slAddHead, and slAddTail().

Referenced by fastMapClumpsToBundles(), ffSeedExtInMem(), gfAlignSomeClumps(), gfAlignStrand(), gfAlignTrans(), gfAlignTransTrans(), gfClumpsToBundles(), gfFindAlignAaTrans(), and gfTransTransFindBundles().

{
struct gfRange *geneList = NULL, *gene = NULL, *lastExon = NULL, *exon, *nextExon;

for (exon = exonList; exon != NULL; exon = nextExon)
    {
    nextExon = exon->next;
    if (lastExon == NULL || !sameString(lastExon->tName, exon->tName) 
        || exon->t3  != lastExon->t3
        || exon->tStart - lastExon->tEnd > maxIntron)
        {
        AllocVar(gene);
        gene->tStart = exon->tStart;
        gene->tEnd = exon->tEnd;
        gene->tName = cloneString(exon->tName);
        gene->tSeq = exon->tSeq;
        gene->qStart = exon->qStart;
        gene->qEnd = exon->qEnd;
        gene->hitCount = exon->hitCount;
        gene->t3 = exon->t3;
        slAddHead(&gene->components, exon);
        slAddHead(&geneList, gene);
        }
    else
        {
        if (exon->qStart < gene->qStart) gene->qStart = exon->qStart;
        if (exon->qEnd > gene->qEnd) gene->qEnd = exon->qEnd;
        if (exon->tStart < gene->tStart) gene->tStart = exon->tStart;
        if (exon->tEnd > gene->tEnd) gene->tEnd = exon->tEnd;
        gene->hitCount += exon->hitCount;
        slAddTail(&gene->components, exon);
        }
    lastExon = exon;
    }
slReverse(&geneList);
return geneList;
}

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struct ssFfItem* gfRangesToFfItem	(	struct gfRange *	rangeList,
		aaSeq *	qSeq
	)			[read]

Definition at line 824 of file gfBlatLib.c.

References AllocVar, dnaSeq::dna, ssFfItem::ff, ffMakeRightLinks(), gfRange::next, gfRange::qEnd, gfRange::qStart, rangeList, gfRange::tEnd, gfRange::tSeq, and gfRange::tStart.

Referenced by fastMapClumpsToBundles(), ffSeedExtInMem(), gfAlignSomeClumps(), gfAlignTrans(), gfAlignTransTrans(), gfFindAlignAaTrans(), and gfTransTransFindBundles().

{
AA *q = qSeq->dna;
struct ffAli *ffList = NULL, *ff;
struct gfRange *range;
struct ssFfItem *ffi;

for (range = rangeList; range != NULL; range = range->next)
    {
    aaSeq *tSeq = range->tSeq;
    AA *t = tSeq->dna;
    AllocVar(ff);
    ff->nStart = q + range->qStart;
    ff->nEnd = q + range->qEnd;
    ff->hStart = t + range->tStart;
    ff->hEnd = t + range->tEnd;
    ff->left = ffList;
    ffList = ff;
    }
AllocVar(ffi);
ffi->ff = ffMakeRightLinks(ffList);
return ffi;
}

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