inc/crudeali.h File Reference

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Data Structures
struct	crudeAli
Functions
crudeAli *	crudeAliFind (DNA *probe, int probeSize, struct nt4Seq **chrome, int chromeCount, int tileSize, int minScore)

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Function Documentation

struct crudeAli* crudeAliFind	(	DNA *	probe,
		int	probeSize,
		struct nt4Seq **	chrome,
		int	chromeCount,
		int	tileSize,
		int	minScore
	)			[read]

Definition at line 794 of file crudeali.c.

References AllocVar, caIsCdna, caTileSize, chromIx(), cmpGenesByScore(), countGenesBetter(), countPrettyGood(), filterPoorGenes(), findCrudeGenes(), freeFastProber(), freeMem(), initWormDnaMatchScores(), makeFastProber(), maxHitsAtOnce, needMem(), reverseComplement(), scoreNoninsertingExtensions(), slAddHead, and slReverse().

Referenced by xenAlignBig(), and xenAlignWorm().

{
int oneGeneCount;
int i;
int chromeIx;
int geneCount = 0;
int maxGeneCount = 2*maxHitsAtOnce;
int isRc;
struct nt4Seq *target;
struct crudeGene *crudeGenes = needMem(maxGeneCount*sizeof(*crudeGenes));
struct fastProber *fps[2];
struct crudeAli *aliList = NULL, *ali;
int goodGeneCount;

initWormDnaMatchScores();
caTileSize = tileSize;
caIsCdna = (tileSize >= 14);
fps[0] = makeFastProber(probe, probeSize);
reverseComplement(probe, probeSize);
fps[1] = makeFastProber(probe, probeSize);
reverseComplement(probe, probeSize);
for (chromeIx = 0; chromeIx < chromeCount; ++chromeIx)
    {
    target = chrome[chromeIx];
    for (isRc = 0; isRc <= 1; ++isRc)
        {
        /* Get crude idea of genes on one strand. */
        oneGeneCount = findCrudeGenes(fps[isRc], target, 
            crudeGenes+geneCount, maxGeneCount-geneCount, isRc);
            
        /* Increment gene count and if necessary compact list. */
        geneCount += oneGeneCount;
        if (maxGeneCount - geneCount < maxHitsAtOnce)
            geneCount = filterPoorGenes(crudeGenes, geneCount);
        }
    if (maxGeneCount - geneCount < maxHitsAtOnce)
        break;
    }

/* Sort genes by initial promise and get rid of some trash. */
    {
    int bestScore, worstScore;
    qsort(crudeGenes, geneCount, sizeof(crudeGenes[0]), cmpGenesByScore);
    bestScore = crudeGenes[0].score;
    worstScore = crudeGenes[geneCount-1].score;
    if (bestScore > worstScore)
        {
        int cutOff = bestScore/10;
        goodGeneCount = geneCount = countGenesBetter(crudeGenes, geneCount, cutOff);
        }
    else if (bestScore >= minScore)
        goodGeneCount = geneCount;
    else
        goodGeneCount = 0;
    }

if (tileSize == 8)
    {
    goodGeneCount = countPrettyGood(crudeGenes, geneCount, 4, 4);
    geneCount = goodGeneCount;
    for (i=0; i<geneCount; ++i)
        scoreNoninsertingExtensions(crudeGenes+i, probe, probeSize);
    qsort(crudeGenes, geneCount, sizeof(crudeGenes[0]), cmpGenesByScore);
    goodGeneCount = countPrettyGood(crudeGenes, geneCount, 4, minScore);
    }
for (i=0; i<goodGeneCount; ++i)
    {
    AllocVar(ali);
    ali->chromIx = chromIx(crudeGenes[i].target, chrome, chromeCount);
    ali->start = crudeGenes[i].targetStart;
    ali->end = crudeGenes[i].targetEnd;
    ali->score = crudeGenes[i].score;
    ali->strand = (crudeGenes[i].isRc ? '-' : '+');
    slAddHead(&aliList, ali);
    }
slReverse(&aliList);
freeFastProber(&fps[0]);
freeFastProber(&fps[1]);
freeMem(crudeGenes);

return aliList;
}

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