inc/chainToAxt.h File Reference

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Functions
axt *	chainToAxt (struct chain *chain, struct dnaSeq *qSeq, int qOffset, struct dnaSeq *tSeq, int tOffset, int maxGap, int maxChain)

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Function Documentation

struct axt* chainToAxt	(	struct chain *	chain,
		struct dnaSeq *	qSeq,
		int	qOffset,
		struct dnaSeq *	tSeq,
		int	tOffset,
		int	maxGap,
		int	maxChain
	)			[read]

Definition at line 91 of file chainToAxt.c.

References axtFromBlocks(), chain::blockList, cBlock::next, cBlock::qStart, slAddHead, slReverse(), and cBlock::tStart.

{
struct cBlock *startB = chain->blockList, *a = NULL, *b;
struct axt *axtList = NULL, *axt;

for (b = chain->blockList; b != NULL; b = b->next)
    {
    if (a != NULL)
        {
        int dq = b->qStart - a->qEnd;
        int dt = b->tStart - a->tEnd;
        if ((dq > 0 && dt > 0) || dt > maxGap || dq > maxGap || (b->tEnd - startB->tStart) > maxChain)
            {
            axt = axtFromBlocks(chain, startB, b, qSeq, qOffset, tSeq, tOffset);
            slAddHead(&axtList, axt);
            startB = b;
            }
        }
    a = b;
    }
axt = axtFromBlocks(chain, startB, NULL, qSeq, qOffset, tSeq, tOffset);
slAddHead(&axtList, axt);
slReverse(&axtList);
return axtList;
}

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