jkOwnLib/bandExt.c

Go to the documentation of this file.

/* bandExt - banded Smith-Waterman extension of alignments. 
 * An aligner might first find perfectly matching hits of
 * a small size, then extend these hits as far as possible
 * while the sequences perfectly match, then call on routines
 * in this module to do further extensions allowing small
 * gaps and mismatches. 
 *
 * This version of the algorithm uses affine gap scorea and
 * has the neat feature that the band can wander around.  
 * When a score exceeds any previous score, the band will be 
 * recentered around the highest scoring position. */
/* Copyright 2003-5 Jim Kent.  All rights reserved. */

#include "common.h"
#include "dnaseq.h"
#include "axt.h"
#include "fuzzyFind.h"
#include "localmem.h"
#include "bandExt.h"

static char const rcsid[] = "$Id: bandExt.c,v 1.13 2006/03/14 19:02:31 angie Exp $";

/* Definitions for traceback byte.  This is encoded as so:
 *     xxxxLUMM
 * where the x's are not used.  The L bit is set if parent of the left insert
 * is also a left insert (otherwise it is a match). Likewise the U bit is set
 * if the parent of an up insert is also an up insert.  The MM bits contain the
 * parent of the match state. */

#define mpMatch 1
#define mpUp 2
#define mpLeft 3
#define mpMask 3
#define upExt (1<<2)
#define lpExt (1<<3)

struct score
/* Info on score in our three states. */
   {
   int match;
   int up;
   int left;
   };

boolean bandExt(boolean global, struct axtScoreScheme *ss, int maxInsert,
        char *aStart, int aSize, char *bStart, int bSize, int dir,
        int symAlloc, int *retSymCount, char *retSymA, char *retSymB, 
        int *retStartA, int *retStartB)
/* Try to extend an alignment from aStart/bStart onwards.
 * Set maxInsert to the maximum gap size allowed.  3 is often
 * a good choice.  aStart/aSize bStart/bSize describe the
 * sequence to extend through (not including any of the existing
 * alignment. Set dir = 1 for forward extension, dir = -1 for backwards. 
 * retSymA and retSymB should point to arrays of characters of
 * symAlloc size.  symAlloc needs to be aSize*2 or so.  The
 * alignment is returned in the various ret values.  The function
 * overall returns TRUE if an extension occurred, FALSE if not. */
{
int i;                  /* A humble index or two. */
int *bOffsets = NULL;   /* Offset of top of band. */
UBYTE **parents = NULL; /* Array of parent positions. */
struct score *curScores = NULL; /* Scores for current column. */
struct score *prevScores = NULL;        /* Scores for previous column. */
struct score *swapScores;       /* Helps to swap cur & prev column. */
int bandSize = 2*maxInsert + 1;  /* Size of band including middle */
int maxIns1 = maxInsert + 1;     /* Max insert plus one. */
int bandPlus = bandSize + 2*maxIns1;  /* Band plus sentinels on either end. */
int bestScore = 0;               /* Best score so far. */
int aPos, aBestPos = -1;         /* Current and best position in a. */
int bPos, bBestPos = -1;         /* Current and best position in b. */
int bandCenter = 0;     /* b Coordinate of current band center. */
int colShift = 1;       /* Vertical shift between this column and previous. */
int prevScoreOffset;    /* Offset into previous score column. */
int curScoreOffset;     /* Offset into current score column. */
int symCount = 0;       /* Size of alignment and size allocated for it. */
int gapOpen = ss->gapOpen;       /* First base in gap costs this. */
int gapExtend = ss->gapExtend;   /* Extra bases in gap cost this. */
int badScore = -gapOpen*100;     /* A score bad enough no one will want to link with us. */
int maxDrop = gapOpen + gapExtend*maxInsert; /* Max score drop allowed before giving up. */
int midScoreOff;                 /* Offset to middle of scoring array. */
struct lm *lm;                   /* Local memory pool. */
boolean didExt = FALSE;
int initGapScore = -gapOpen;

/* For reverse direction just reverse bytes here and there.  It's
 * a lot easier than the alternative and doesn't cost much time in
 * the global scheme of things. */
if (dir < 0)
    {
    reverseBytes(aStart, aSize);
    reverseBytes(bStart, bSize);
    }
#ifdef DEBUG
uglyf("bandExt: dir %d, aStart %d, aSize %d, symAlloc %d\n", dir,
        aSize, bSize, symAlloc);
mustWrite(uglyOut, aStart, aSize);
uglyf("\n");
mustWrite(uglyOut, bStart, bSize);
uglyf("\n");
#endif /* DEBUG */

/* Make up a local mem structure big enough for everything. 
 * This is just a minor, perhaps misguided speed tweak to
 * avoid multiple mallocs. */
lm = lmInit(
    sizeof(bOffsets[0])*aSize +
    sizeof(parents[0])*bandSize +
    bandSize*(sizeof(parents[0][0])*aSize) +
    sizeof(curScores[0]) * bandPlus +
    sizeof(prevScores[0]) * bandPlus );

/* Allocate data structures out of local memory pool. */
lmAllocArray(lm, bOffsets, aSize);
lmAllocArray(lm, parents, bandSize);
for (i=0; i<bandSize; ++i)
    lmAllocArray(lm, parents[i], aSize);
lmAllocArray(lm, curScores, bandPlus);
lmAllocArray(lm, prevScores, bandPlus);

/* Set up scoring arrays so that stuff outside of the band boundary 
 * looks bad.  There will be maxIns+1 of these sentinel values at
 * the start and at the beginning. */
for (i=0; i<bandPlus; ++i)
    {
    struct score *cs = &curScores[i];
    cs->match = cs->up = cs->left = badScore;
    cs = &prevScores[i];
    cs->match = cs->up = cs->left = badScore;
    }

/* Set up scoring array so that extending without an initial insert
 * looks relatively good. */
midScoreOff = 1 + 2 * maxInsert;
prevScores[midScoreOff].match = 0;

/* Set up scoring array so that initial inserts of up to maxInsert
 * are allowed but penalized appropriately. */
    {
    int score = -gapOpen;
    for (i=0; i<maxInsert; ++i)
        {
        prevScores[midScoreOff+i].up = score;
        score -= gapExtend;
        }
    }

for (aPos=0; aPos < aSize; ++aPos)
    {
    char aBase = aStart[aPos];
    int *matRow = ss->matrix[(int)aBase];
    int bestColScore = badScore;
    int bestColPos = -1;
    int colTop = bandCenter - maxInsert;
    int colBottom = bandCenter + maxIns1;

    if (colTop < 0) colTop = 0;
    if (colBottom > bSize) colBottom = bSize;
    curScoreOffset =  maxIns1 + colTop - (bandCenter - maxInsert);
    prevScoreOffset = curScoreOffset + colShift;
#ifdef DEBUG
    uglyf("curScoreOffset %d, maxIns %d, prevScoreOffset %d\n", curScoreOffset, maxInsert, prevScoreOffset);
#endif /* DEBUG */

    /* At top we deal with possibility of initial insert that
     * comes in at this point, unless the band has wandered off. */
    if (aPos < maxInsert)
        {
        curScores[curScoreOffset-1].up = initGapScore;
        initGapScore -= gapExtend;
        }
    else
        curScores[curScoreOffset-1].up = badScore;

    for (bPos = colTop; bPos < colBottom; ++bPos)
        {
        UBYTE parent;
        struct score *curScore = &curScores[curScoreOffset];

#ifdef DEBUG
        uglyf("aPos %d, bPos %d, %c vs %c\n", aPos, bPos, aBase, bStart[bPos]);
        uglyf("  diag[%d %d %d], left[%d %d %d], up[%d %d %d]\n", 
                prevScores[prevScoreOffset-1].match, 
                prevScores[prevScoreOffset-1].left, 
                prevScores[prevScoreOffset-1].up, 
                prevScores[prevScoreOffset].match, 
                prevScores[prevScoreOffset].left, 
                prevScores[prevScoreOffset].up, 
                curScores[curScoreOffset-1].match, 
                curScores[curScoreOffset-1].left, 
                curScores[curScoreOffset-1].up);
#endif /* DEBUG */

        /* Handle ways into the matching state and record if it's
         * best score so far. */
            {
            int match = matRow[(int)bStart[bPos]];
            struct score *a = &prevScores[prevScoreOffset-1];
            int diagScore = a->match;
            int leftScore = a->left;
            int upScore = a->up;
            int score;
            if (diagScore >= leftScore && diagScore >= upScore)
                {
                score = diagScore + match;
                parent = mpMatch;
                }
            else if (leftScore > upScore)
                {
                score = leftScore + match;
                parent = mpLeft;
                }
            else
                {
                score = upScore + match;
                parent = mpUp;
                }
            curScore->match = score;
            if (score > bestColScore)
                {
                bestColScore = score;
                bestColPos = bPos;
                }
            }

        /* Handle ways into left gap state. */
            {
            struct score *a = &prevScores[prevScoreOffset];
            int extScore = a->left - gapExtend;
            int openScore = a->match - gapOpen;
            if (extScore >= openScore)
                {
                parent |= lpExt;
                curScore->left = extScore;
                }
            else
                {
                curScore->left = openScore;
                }
            }

        /* Handle ways into up gap state. */
            {
            struct score *a = &curScore[-1];
            int extScore = a->up - gapExtend;
            int openScore = a->match - gapOpen;
            if (extScore >= openScore)
                {
                parent |= upExt;
                curScore->up = extScore;
                }
            else
                {
                curScore->up = openScore;
                }
            }

        parents[curScoreOffset - maxIns1][aPos] = parent;

#ifdef DEBUG
        uglyf(" cur [%d %d %d]\n", 
                curScore->match, 
                curScore->left, 
                curScore->up);
#endif /* DEBUG */
        /* Advance to next row in column. */
        curScoreOffset += 1;
        prevScoreOffset += 1;
        }


    /* If this column's score is best so far make note of
     * it and shift things so that the matching bases at the
     * best score are centered in the band.  This allows the
     * band to wander where appropriate.  Having the band shift
     * to the best column position if it is not the best score
     * so far doesn't work so well though.  */
    if (bestScore < bestColScore)
        {
        bestScore = bestColScore;
        aBestPos = aPos;
        bBestPos = bestColPos;
        colShift = (bestColPos + 1) - bandCenter;
        }
    else if (bestColScore < bestScore - maxDrop)
        {
        if (!global)
            break;
        }
    else
        {
        colShift = 1;
        }

    /* Keep track of vertical offset of this column, and
     * set up offset of next column. */
    bOffsets[aPos] = bandCenter;
    bandCenter += colShift;

    /* Swap scoring arrays so current becomes next iteration's previous. */
    swapScores = curScores;
    curScores = prevScores;
    prevScores = swapScores;
    }


/* Trace back. */
#ifdef DEBUG
uglyf("traceback: bestScore %d, aBestPos %d, bBestPos %d\n", bestScore, aBestPos, bBestPos);
#endif /* DEBUG */
if (global || bestScore > 0)
    {
    boolean upState = FALSE;
    boolean leftState = FALSE;
    didExt = TRUE;
    if (global)
        {
        aPos = aSize-1;
        bPos = bSize-1;
        }
    else
        {
        aPos = aBestPos;
        bPos = bBestPos;
        }
    for (;;)
        {
        int pOffset;
        UBYTE parent;
        pOffset = bPos - bOffsets[aPos] + maxInsert;
        if (pOffset < 0) pOffset = 0;
        // FIXME: there may be some cases near beginning where
        // pOffset is not right.  Clamping it at 0 prevents a crash
        // and produces correct behavior in many cases.  However
        // I'm thinking a better fix would be to have bOffsets follow
        // colTop rather than bandCenter somehow. Exactly how is
        // beyond me at the moment.
        if (pOffset >= bandSize)
            {
#ifdef DEBUG
            uglyf("bPos %d, aPos %d, bOffsets[aPos] %d, maxInsert %d\n", bPos, aPos, bOffsets[aPos], maxInsert);
            uglyf("pOffset = %d, bandSize = %d\n", pOffset, bandSize);
            uglyf("aSize %d, bSize %d\n", aSize, bSize);
            faWriteNext(uglyOut, "uglyA", aStart, aSize);
            faWriteNext(uglyOut, "uglyB", bStart, bSize);
#endif /* DEBUG */
            assert(global);
            return FALSE;
            }
        parent = parents[pOffset][aPos];
#ifdef DEBUG
        uglyf("aPos %d, bPos %d, parent %d, pMask %d upState %d, leftState %d\n", aPos, bPos, parent, parent & mpMask, upState, leftState);
#endif /* DEBUG */
        if (upState)
            {
            retSymA[symCount] = '-';
            retSymB[symCount] = bStart[bPos];
            bPos -= 1;
            upState = (parent&upExt);
            }
        else if (leftState)
            {
            retSymA[symCount] = aStart[aPos];
            retSymB[symCount] = '-';
            aPos -= 1;
            leftState = (parent&lpExt);
            }
        else
            {
            retSymA[symCount] = aStart[aPos];
            retSymB[symCount] = bStart[bPos];
            aPos -= 1;
            bPos -= 1;
            parent &= mpMask;
            if (parent == mpUp)
                upState = TRUE;
            else if (parent == mpLeft)
                leftState = TRUE;
            }
        if (++symCount >= symAlloc)
            errAbort("unsufficient symAlloc in bandExt");
        if (aPos < 0 || bPos < 0)
            {
            while (aPos >= 0)
                {
                retSymA[symCount] = aStart[aPos];
                retSymB[symCount] = '-';
                if (++symCount >= symAlloc)
                    errAbort("unsufficient symAlloc in bandExt");
                --aPos;
                }
            while (bPos >= 0)
                {
                retSymA[symCount] = '-';
                retSymB[symCount] = bStart[bPos];
                if (++symCount >= symAlloc)
                    errAbort("unsufficient symAlloc in bandExt");
                --bPos;
                }
            break;
            }
        }
    if (dir > 0)
        {
        reverseBytes(retSymA, symCount);
        reverseBytes(retSymB, symCount);
        }
    retSymA[symCount] = 0;
    retSymB[symCount] = 0;
    }
else
    {
    retSymA[0] = retSymB[0] = 0;
    }

if (dir < 0)
    {
    reverseBytes(aStart, aSize);
    reverseBytes(bStart, bSize);
    }

/* Clean up, set return values and go home */
lmCleanup(&lm);
if (retStartA != NULL) *retStartA = aBestPos;
if (retStartB != NULL) *retStartB = bBestPos;
*retSymCount = symCount;
return didExt;
}

struct ffAli *bandExtFf(
        struct lm *lm,  /* Local memory pool, NULL to use global allocation for ff */
        struct axtScoreScheme *ss,      /* Scoring scheme to use. */
        int maxInsert,                  /* Maximum number of inserts to allow. */
        struct ffAli *origFf,           /* Alignment block to extend. */
        char *nStart, char *nEnd,       /* Bounds of region to extend through */
        char *hStart, char *hEnd,       /* Bounds of region to extend through */
        int dir,                        /* +1 to extend end, -1 to extend start */
        int maxExt)                     /* Maximum length of extension. */
/* Extend a gapless alignment in one direction.  Returns extending
 * ffAlis, not linked into origFf, or NULL if no extension possible. */
{
int symAlloc = 2*maxExt;
char *symBuf = needMem(4*maxExt);
char *nBuf = symBuf;
char *hBuf = symBuf + symAlloc;
char *ns, *hs;
int symCount, nExt, hExt;
int nSize, hSize;
struct ffAli *ffList = NULL;
boolean gotExt;

if (dir > 0)
    {
    nSize = nEnd - origFf->nEnd;
    hSize = hEnd - origFf->hEnd;
    if (nSize > maxExt) nSize = maxExt;
    if (hSize > maxExt) hSize = maxExt;
    ns = origFf->nEnd;
    hs = origFf->hEnd;
    }
else
    {
    nSize = origFf->nStart - nStart;
    hSize = origFf->hStart - hStart;
    if (nSize > maxExt) nSize = maxExt;
    if (hSize > maxExt) hSize = maxExt;
    ns = origFf->nStart - nSize;
    hs = origFf->hStart - hSize;
    }

gotExt = bandExt(FALSE, ss, maxInsert, ns, nSize, hs, hSize, dir,
        symAlloc, &symCount, nBuf, hBuf, &nExt, &hExt);
if (gotExt)
    {
    char *nExtStart, *hExtStart;
    if (dir > 0)
        {
        nExtStart = ns;
        hExtStart = hs;
        }
    else
        {
        nExtStart = origFf->nStart - nExt - 1;
        hExtStart = origFf->hStart - hExt - 1;
        }
    ffList = ffAliFromSym(symCount, nBuf, hBuf, lm,  nExtStart, hExtStart);
    }
freeMem(symBuf);
return ffList;
}

---