lib/chainToPsl.c File Reference

#include "common.h"
#include "linefile.h"
#include "hash.h"
#include "psl.h"
#include "chain.h"

Include dependency graph for chainToPsl.c:

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Functions
psl *	chainToPsl (struct chain *chain)
static void	fillInMatchEtc (struct chain *chain, struct dnaSeq *query, struct dnaSeq *target, struct psl *psl)
psl *	chainToFullPsl (struct chain *chain, struct dnaSeq *query, struct dnaSeq *rQuery, struct dnaSeq *target)
Variables
static char const	rcsid [] = "$Id: chainToPsl.c,v 1.5 2005/04/10 14:41:21 markd Exp $"

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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, cBlock::qEnd, psl::qEnd, chain::qEnd, chain::qName, psl::qName, psl::qNumInsert, chain::qSize, psl::qSize, cBlock::qStart, chain::qStart, psl::qStart, psl::qStarts, chain::qStrand, slCount(), psl::strand, psl::tBaseInsert, cBlock::tEnd, chain::tEnd, psl::tEnd, chain::tName, psl::tName, psl::tNumInsert, chain::tSize, psl::tSize, cBlock::tStart, chain::tStart, psl::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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static void fillInMatchEtc	(	struct chain *	chain,
		struct dnaSeq *	query,
		struct dnaSeq *	target,
		struct psl *	psl
	)			[static]

Definition at line 71 of file chainToPsl.c.

References chain::blockList, dnaSeq::dna, psl::match, psl::misMatch, psl::nCount, cBlock::next, ntVal, cBlock::qEnd, cBlock::qStart, psl::repMatch, repMatch, and cBlock::tStart.

Referenced by chainToFullPsl().

{
struct cBlock *block;
unsigned match = 0, misMatch=0, repMatch=0, nCount=0;
for (block = chain->blockList; block != NULL; block = block->next)
    {
    DNA *qDna = query->dna + block->qStart;
    DNA *tDna = target->dna + block->tStart;
    int i, size = block->qEnd - block->qStart;
    for (i=0; i<size; ++i)
        {
        DNA q,t;
        int qv, tv;
        q = qDna[i];
        t = tDna[i];
        qv = ntVal[(int)q];
        tv = ntVal[(int)t];
        if (qv < 0 || tv < 0)
            ++nCount;
        else if (qv == tv)
            {
            if (isupper(q) && isupper(t))
                ++match;
            else
                ++repMatch;
            }
        else 
            ++misMatch;
        }
    }
psl->match = match;
psl->misMatch = misMatch;
psl->repMatch = repMatch;
psl->nCount = nCount;
}

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Variable Documentation

char const rcsid[] = "$Id: chainToPsl.c,v 1.5 2005/04/10 14:41:21 markd Exp $" [static]

Definition at line 11 of file chainToPsl.c.

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