inc/chainToPsl.h File Reference

#include "psl.h"
#include "chainBlock.h"

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Functions
psl *	chainToPsl (struct chain *chain)
psl *	chainToFullPsl (struct chain *chain, struct dnaSeq *query, struct dnaSeq *rQuery, struct dnaSeq *target)

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Function Documentation

struct psl* chainToFullPsl	(	struct chain *	chain,
		struct dnaSeq *	query,
		struct dnaSeq *	rQuery,
		struct dnaSeq *	target
	)			[read]

Definition at line 110 of file chainToPsl.c.

References chainToPsl(), fillInMatchEtc(), and chain::qStrand.

{
struct psl *psl = chainToPsl(chain);
struct dnaSeq *qSeq = (chain->qStrand == '-' ? rQuery : query);
fillInMatchEtc(chain, qSeq, target, psl);
return psl;
}

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struct psl* chainToPsl

(

struct chain *

chain

)

[read]

Definition at line 14 of file chainToPsl.c.

References AllocArray, AllocVar, psl::blockCount, chain::blockList, psl::blockSizes, cloneString(), cBlock::next, psl::qBaseInsert, chain::qEnd, psl::qEnd, cBlock::qEnd, psl::qName, chain::qName, psl::qNumInsert, psl::qSize, chain::qSize, psl::qStart, chain::qStart, cBlock::qStart, psl::qStarts, chain::qStrand, slCount(), psl::strand, psl::tBaseInsert, psl::tEnd, chain::tEnd, cBlock::tEnd, psl::tName, chain::tName, psl::tNumInsert, psl::tSize, chain::tSize, psl::tStart, chain::tStart, cBlock::tStart, and psl::tStarts.

Referenced by chainToFullPsl().

{
struct psl *psl;
int blockCount, i;
struct cBlock *b, *nextB;

blockCount = slCount(chain->blockList);
AllocVar(psl);
AllocArray(psl->blockSizes, blockCount);
AllocArray(psl->qStarts, blockCount);
AllocArray(psl->tStarts, blockCount);
psl->strand[0] = chain->qStrand;
psl->qName = cloneString(chain->qName);
psl->qSize = chain->qSize;
if (chain->qStrand == '-')
    {
    psl->qStart = chain->qSize - chain->qEnd;
    psl->qEnd = chain->qSize - chain->qStart;
    }
else
    {
    psl->qStart = chain->qStart;
    psl->qEnd = chain->qEnd;
    }
psl->tName = cloneString(chain->tName);
psl->tSize = chain->tSize;
psl->tStart = chain->tStart;
psl->tEnd = chain->tEnd;
psl->blockCount = blockCount;
for (i=0, b=chain->blockList; i < blockCount; ++i, b = nextB)
    {
    nextB = b->next;
    psl->tStarts[i] = b->tStart;
    psl->qStarts[i] = b->qStart;
    psl->blockSizes[i] = b->qEnd - b->qStart;
    if (nextB != NULL)
        {
        int qGap = nextB->qStart - b->qEnd;
        int tGap = nextB->tStart - b->tEnd;
        if (qGap != 0)
            {
            psl->qBaseInsert += qGap;
            psl->qNumInsert += 1;
            }
        if (tGap != 0)
            {
            psl->tBaseInsert += tGap;
            psl->tNumInsert += 1;
            }
        }
    }
return psl;
}

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