cf293df150f4b256d195e90b5a20817d8479ece0 galt Sat Jul 2 13:17:59 2016 -0700 fixes #17624. -maxIntron= was broken in blat whenever a non-default value was used causing it to run cutAtBigIntrons() which did not support protein. The fix was using trans3GenoPos() to get correct coordinates handling 3 frames, and also calling ffScoreProtein() instead of ffScore() when it is a protein query. diff --git src/jkOwnLib/supStitch.c src/jkOwnLib/supStitch.c index 90317dc..c8525cf 100644 --- src/jkOwnLib/supStitch.c +++ src/jkOwnLib/supStitch.c @@ -1,912 +1,924 @@ /* supStitch stitches together a bundle of ffAli alignments that share * a common query and target sequence into larger alignments if possible. * This is commonly used when the query sequence was broken up into * overlapping blocks in the initial alignment, and also to look for * introns larger than fuzzyFinder can handle. */ /* Copyright 2000-2005 Jim Kent. All rights reserved. */ #include "common.h" #include "dnautil.h" #include "dlist.h" #include "fuzzyFind.h" #include "localmem.h" #include "patSpace.h" #include "trans3.h" #include "supStitch.h" #include "chainBlock.h" static void ssFindBestBig(struct ffAli *ffList, bioSeq *qSeq, bioSeq *tSeq, enum ffStringency stringency, boolean isProt, struct trans3 *t3List, struct ffAli **retBestAli, int *retScore, struct ffAli **retLeftovers); void ssFfItemFree(struct ssFfItem **pEl) /* Free a single ssFfItem. */ { struct ssFfItem *el; if ((el = *pEl) != NULL) { ffFreeAli(&el->ff); freez(pEl); } } void ssFfItemFreeList(struct ssFfItem **pList) /* Free a list of ssFfItems. */ { struct ssFfItem *el, *next; for (el = *pList; el != NULL; el = next) { next = el->next; ssFfItemFree(&el); } *pList = NULL; } void ssBundleFree(struct ssBundle **pEl) /* Free up one ssBundle */ { struct ssBundle *el; if ((el = *pEl) != NULL) { ssFfItemFreeList(&el->ffList); freez(pEl); } } void ssBundleFreeList(struct ssBundle **pList) /* Free up list of ssBundles */ { struct ssBundle *el, *next; for (el = *pList; el != NULL; el = next) { next = el->next; ssBundleFree(&el); } *pList = NULL; } void dumpNearCrossover(char *what, DNA *n, DNA *h, int size) /* Print sequence near crossover */ { printf("%s: ", what); mustWrite(stdout, n, size); printf("\n"); printf("%s: ", what); mustWrite(stdout, h, size); printf("\n"); } -void dumpFf(struct ffAli *left, DNA *needle, DNA *hay) +void dumpFf(struct ffAli *left, bioSeq *qSeq, bioSeq *tSeq, struct trans3 *t3List) /* Print info on ffAli. */ { struct ffAli *ff; for (ff = left; ff != NULL; ff = ff->right) { - printf("(%ld - %ld)[%ld-%ld] ", (long)(ff->hStart-hay), (long)(ff->hEnd-hay), - (long)(ff->nStart - needle), (long)(ff->nEnd - needle)); + int hStart = trans3GenoPos(ff->hStart, tSeq, t3List, FALSE); + int hEnd = trans3GenoPos(ff->hEnd , tSeq, t3List, TRUE); + + printf("(%d - %d)[%ld-%ld] ", hStart, hEnd, + (long)(ff->nStart - qSeq->dna), (long)(ff->nEnd - qSeq->dna)); } printf("\n"); } void dumpBuns(struct ssBundle *bunList) /* Print diagnostic info on bundles. */ { struct ssBundle *bun; struct ssFfItem *ffl; for (bun = bunList; bun != NULL; bun = bun->next) { struct dnaSeq *qSeq = bun->qSeq; /* Query sequence (not owned by bundle.) */ struct dnaSeq *genoSeq = bun->genoSeq; /* Genomic sequence (not owned by bundle.) */ printf("Bundle of %d between %s and %s\n", slCount(bun->ffList), qSeq->name, genoSeq->name); for (ffl = bun->ffList; ffl != NULL; ffl = ffl->next) { - dumpFf(ffl->ff, bun->qSeq->dna, bun->genoSeq->dna); + dumpFf(ffl->ff, bun->qSeq, bun->genoSeq, bun->t3List); } } } static int bioScoreMatch(boolean isProt, char *a, char *b, int size) /* Return score of match (no inserts) between two bio-polymers. */ { if (isProt) { return dnaOrAaScoreMatch(a, b, size, 2, -1, 'X'); } else { return dnaOrAaScoreMatch(a, b, size, 1, -1, 'n'); } } static int findCrossover(struct ffAli *left, struct ffAli *right, int overlap, boolean isProt) /* Find ideal crossover point of overlapping blocks. That is * the point where we should start using the right block rather * than the left block. This point is an offset from the start * of the overlapping region (which is the same as the start of the * right block). */ { int bestPos = 0; char *nStart = right->nStart; char *lhStart = left->hEnd - overlap; char *rhStart = right->hStart; int i; int (*scoreMatch)(char a, char b); int score, bestScore; if (isProt) { scoreMatch = aaScore2; score = bestScore = aaScoreMatch(nStart, rhStart, overlap); } else { scoreMatch = dnaScore2; score = bestScore = dnaScoreMatch(nStart, rhStart, overlap); } for (i=0; i<overlap; ++i) { char n = nStart[i]; score += scoreMatch(lhStart[i], n); score -= scoreMatch(rhStart[i], n); if (score > bestScore) { bestScore = score; bestPos = i+1; } } return bestPos; } static void trans3Offsets(struct trans3 *t3List, AA *startP, AA *endP, int *retStart, int *retEnd) /* Figure out offset of peptide in context of larger sequences. */ { struct trans3 *t3; int frame; aaSeq *seq; for (t3 = t3List; t3 != NULL; t3 = t3->next) { for (frame = 0; frame < 3; ++frame) { seq = t3->trans[frame]; if (seq->dna <= startP && startP < seq->dna + seq->size) { *retStart = 3*(startP - seq->dna)+frame + t3->start; *retEnd = 3*(endP - seq->dna)+frame + t3->start; return; } } } internalErr(); } static boolean isMonotonic(struct ffAli *left) /* Return TRUE if this is monotonic on both query and target */ { struct ffAli *right; while ((right = left->right) != NULL) { if (left->nEnd <= right->nStart && left->hEnd <= right->hStart) left = right; else { verbose(2, "not monotonic dn %d, dh %d\n", (int)(right->nStart - left->nEnd), (int)(right->hStart - right->hEnd)); return FALSE; } } return TRUE; } static struct ffAli *forceMonotonic(struct ffAli *aliList, struct dnaSeq *qSeq, struct dnaSeq *tSeq, enum ffStringency stringency, boolean isProt, struct trans3 *t3List) /* Remove any blocks that violate strictly increasing order in both coordinates. * This is not optimal, but it turns out to be very rarely used. */ { if (!isProt) { if (!isMonotonic(aliList)) { struct ffAli *leftovers = NULL; int score; ssFindBestBig(aliList, qSeq, tSeq, stringency, isProt, t3List, &aliList, &score, &leftovers); ffFreeAli(&leftovers); } } return aliList; } struct ffAli *smallMiddleExons(struct ffAli *aliList, struct ssBundle *bundle, enum ffStringency stringency) /* Look for small exons in the middle. */ { if (bundle->t3List != NULL) return aliList; /* Can't handle intense translated stuff. */ else { struct dnaSeq *qSeq = bundle->qSeq; struct dnaSeq *genoSeq = bundle->genoSeq; struct ffAli *right, *left = NULL, *newLeft, *newRight; left = aliList; for (right = aliList->right; right != NULL; right = right->right) { if (right->hStart - left->hEnd >= 3 && right->nStart - left->nEnd >= 3) { newLeft = ffFind(left->nEnd, right->nStart, left->hEnd, right->hStart, stringency); if (newLeft != NULL) { newLeft = forceMonotonic(newLeft, qSeq, genoSeq, stringency, bundle->isProt, bundle->t3List ); newRight = ffRightmost(newLeft); if (left != NULL) { left->right = newLeft; newLeft->left = left; } else { aliList = newLeft; } if (right != NULL) { right->left = newRight; newRight->right = right; } } } left = right; } } return aliList; } struct ssNode /* Node of superStitch graph. */ { struct ssEdge *waysIn; /* Edges leading into this node. */ struct ffAli *ff; /* Alignment block associated with node. */ struct ssEdge *bestWayIn; /* Dynamic programming best edge in. */ int cumScore; /* Dynamic programming score of edge. */ int nodeScore; /* Score of this node. */ }; struct ssEdge /* Edge of superStitch graph. */ { struct ssEdge *next; /* Next edge in waysIn list. */ struct ssNode *nodeIn; /* The node that leads to this edge. */ int score; /* Score you get taking this edge. */ int overlap; /* Overlap between two nodes. */ int crossover; /* Offset from overlap where crossover occurs. */ }; struct ssGraph /* Super stitcher graph for dynamic programming to find best * way through. */ { int nodeCount; /* Number of nodes. */ struct ssNode *nodes; /* Array of nodes. */ int edgeCount; /* Number of edges. */ struct ssEdge *edges; /* Array of edges. */ }; static void ssGraphFree(struct ssGraph **pGraph) /* Free graph. */ { struct ssGraph *graph; if ((graph = *pGraph) != NULL) { freeMem(graph->nodes); freeMem(graph->edges); freez(pGraph); } } boolean tripleCanFollow(struct ffAli *a, struct ffAli *b, aaSeq *qSeq, struct trans3 *t3List) /* Figure out if a can follow b in any one of three reading frames of haystack. */ { int ahStart, ahEnd, bhStart, bhEnd; trans3Offsets(t3List, a->hStart, a->hEnd, &ahStart, &ahEnd); trans3Offsets(t3List, b->hStart, b->hEnd, &bhStart, &bhEnd); return (a->nStart < b->nStart && a->nEnd < b->nEnd && ahStart < bhStart && ahEnd < bhEnd); } static struct ssGraph *ssGraphMake(struct ffAli *ffList, bioSeq *qSeq, enum ffStringency stringency, boolean isProt, struct trans3 *t3List) /* Make a graph corresponding to ffList */ { int nodeCount = ffAliCount(ffList); int maxEdgeCount = (nodeCount+1)*(nodeCount)/2; int edgeCount = 0; struct ssEdge *edges, *e; struct ssNode *nodes; struct ssGraph *graph; struct ffAli *ff, *mid; int i, midIx; int overlap; boolean canFollow; if (nodeCount == 1) maxEdgeCount = 1; AllocVar(graph); graph->nodeCount = nodeCount; graph->nodes = AllocArray(nodes, nodeCount+1); for (i=1, ff = ffList; i<=nodeCount; ++i, ff = ff->right) { nodes[i].ff = ff; nodes[i].nodeScore = bioScoreMatch(isProt, ff->nStart, ff->hStart, ff->hEnd - ff->hStart); } graph->edges = AllocArray(edges, maxEdgeCount); for (mid = ffList, midIx=1; mid != NULL; mid = mid->right, ++midIx) { int midScore; struct ssNode *midNode = &nodes[midIx]; e = &edges[edgeCount++]; assert(edgeCount <= maxEdgeCount); e->nodeIn = &nodes[0]; e->score = midScore = midNode->nodeScore; midNode->waysIn = e; for (ff = ffList,i=1; ff != mid; ff = ff->right,++i) { int mhStart = 0, mhEnd = 0; if (t3List) { canFollow = tripleCanFollow(ff, mid, qSeq, t3List); trans3Offsets(t3List, mid->hStart, mid->hEnd, &mhStart, &mhEnd); } else { canFollow = (ff->nStart < mid->nStart && ff->nEnd < mid->nEnd && ff->hStart < mid->hStart && ff->hEnd < mid->hEnd); } if (canFollow) { struct ssNode *ffNode = &nodes[i]; int score; int hGap; int nGap; int crossover; nGap = mid->nStart - ff->nEnd; if (t3List) { int fhStart, fhEnd; trans3Offsets(t3List, ff->hStart, ff->hEnd, &fhStart, &fhEnd); hGap = mhStart - fhEnd; } else { hGap = mid->hStart - ff->hEnd; } e = &edges[edgeCount++]; assert(edgeCount <= maxEdgeCount); e->nodeIn = ffNode; e->overlap = overlap = -nGap; if (overlap > 0) { int midSize = mid->hEnd - mid->hStart; int ffSize = ff->hEnd - ff->hStart; int newMidScore, newFfScore; e->crossover = crossover = findCrossover(ff, mid, overlap, isProt); newMidScore = bioScoreMatch(isProt, mid->nStart, mid->hStart, midSize-overlap+crossover); newFfScore = bioScoreMatch(isProt, ff->nStart+crossover, ff->hStart+crossover, ffSize-crossover); score = newMidScore - ffNode->nodeScore + newFfScore; nGap = 0; hGap -= overlap; } else { score = midScore; } score -= ffCalcGapPenalty(hGap, nGap, stringency); e->score = score; slAddHead(&midNode->waysIn, e); } } slReverse(&midNode->waysIn); } return graph; } static struct ssNode *ssDynamicProgram(struct ssGraph *graph) /* Do dynamic programming to find optimal path though * graph. Return best ending node (with back-trace * pointers and score set). */ { int veryBestScore = -0x3fffffff; struct ssNode *veryBestNode = NULL; int nodeIx; for (nodeIx = 1; nodeIx <= graph->nodeCount; ++nodeIx) { int bestScore = -0x3fffffff; int score; struct ssEdge *bestEdge = NULL; struct ssNode *curNode = &graph->nodes[nodeIx]; struct ssEdge *edge; for (edge = curNode->waysIn; edge != NULL; edge = edge->next) { score = edge->score + edge->nodeIn->cumScore; if (score > bestScore) { bestScore = score; bestEdge = edge; } } curNode->bestWayIn = bestEdge; curNode->cumScore = bestScore; if (bestScore >= veryBestScore) { veryBestScore = bestScore; veryBestNode = curNode; } } return veryBestNode; } static void ssGraphFindBest(struct ssGraph *graph, struct ffAli **retBestAli, int *retScore, struct ffAli **retLeftovers) /* Traverse graph and put best alignment in retBestAli. Return score. * Put blocks not part of best alignment in retLeftovers. */ { struct ssEdge *edge; struct ssNode *node; struct ssNode *startNode = &graph->nodes[0]; struct ffAli *bestAli = NULL, *leftovers = NULL; struct ffAli *ff, *left = NULL; int i; int overlap, crossover, crossDif; /* Find best path and save score. */ node = ssDynamicProgram(graph); *retScore = node->cumScore; /* Trace back and trim overlaps. */ while (node != startNode) { ff = node->ff; ff->right = bestAli; bestAli = ff; node->ff = NULL; edge = node->bestWayIn; if ((overlap = edge->overlap) > 0) { left = edge->nodeIn->ff; crossover = edge->crossover; crossDif = overlap-crossover; left->hEnd -= crossDif; left->nEnd -= crossDif; ff->hStart += crossover; ff->nStart += crossover; } node = node->bestWayIn->nodeIn; } /* Make left links. */ left = NULL; for (ff = bestAli; ff != NULL; ff = ff->right) { ff->left = left; left = ff; } /* Make leftover list. */ for (i=1, node=graph->nodes+1; i<=graph->nodeCount; ++i,++node) { if ((ff = node->ff) != NULL) { ff->left = leftovers; leftovers = ff; } } leftovers = ffMakeRightLinks(leftovers); *retBestAli = bestAli; *retLeftovers = leftovers; } static void ssFindBestSmall(struct ffAli *ffList, bioSeq *qSeq, bioSeq *tSeq, enum ffStringency stringency, boolean isProt, struct trans3 *t3List, struct ffAli **retBestAli, int *retScore, struct ffAli **retLeftovers) /* Build a graph and do a dynamic program on it to find best chains. * For small ffLists this is faster than the stuff in chainBlock. */ { struct ssGraph *graph = ssGraphMake(ffList, qSeq, stringency, isProt, t3List); ssGraphFindBest(graph, retBestAli, retScore, retLeftovers); *retBestAli = forceMonotonic(*retBestAli, qSeq, tSeq, stringency, isProt, t3List); ssGraphFree(&graph); } static enum ffStringency ssStringency; static boolean ssIsProt; static int ssGapCost(int dq, int dt, void *data) /* Return gap penalty. This just need be a lower bound on * the penalty actually. */ { int cost; if (dt < 0) dt = 0; if (dq < 0) dq = 0; cost = ffCalcGapPenalty(dt, dq, ssStringency); return cost; } static int findOverlap(struct cBlock *a, struct cBlock *b) /* Figure out how much a and b overlap on either sequence. */ { int dq = b->qStart - a->qEnd; int dt = b->tStart - a->tEnd; return -min(dq, dt); } static int ssConnectCost(struct cBlock *a, struct cBlock *b, void *data) /* Calculate connection cost - including gap score * and overlap adjustments if any. */ { struct ffAli *aFf = a->data, *bFf = b->data; int overlapAdjustment = 0; int overlap = findOverlap(a, b); int dq = b->qStart - a->qEnd; int dt = b->tStart - a->tEnd; if (overlap > 0) { int aSize = aFf->hEnd - aFf->hStart; int bSize = bFf->hEnd - bFf->hStart; if (overlap >= bSize || overlap >= aSize) { /* Give stiff overlap adjustment for case where * one block completely enclosed in the other on * either sequence. This will make it never happen. */ overlapAdjustment = a->score + b->score; } else { /* More normal case - partial overlap on one or both strands. */ int crossover = findCrossover(aFf, bFf, overlap, ssIsProt); int remain = overlap - crossover; overlapAdjustment = bioScoreMatch(ssIsProt, aFf->nEnd - remain, aFf->hEnd - remain, remain) + bioScoreMatch(ssIsProt, bFf->nStart, bFf->hStart, crossover); dq -= overlap; dt -= overlap; } } return overlapAdjustment + ssGapCost(dq, dt, data); } static void ssFindBestBig(struct ffAli *ffList, bioSeq *qSeq, bioSeq *tSeq, enum ffStringency stringency, boolean isProt, struct trans3 *t3List, struct ffAli **retBestAli, int *retScore, struct ffAli **retLeftovers) /* Go set up things to call chainBlocks to find best way to string together * blocks in alignment. */ { struct cBlock *boxList = NULL, *box, *prevBox; struct ffAli *ff, *farRight = NULL; struct lm *lm = lmInit(0); int boxSize; DNA *firstH = tSeq->dna; struct chain *chainList, *chain, *bestChain; int tMin = BIGNUM, tMax = -BIGNUM; /* Make up box list for chainer. */ for (ff = ffList; ff != NULL; ff = ff->right) { lmAllocVar(lm, box); boxSize = ff->nEnd - ff->nStart; box->qStart = ff->nStart - qSeq->dna; box->qEnd = box->qStart + boxSize; if (t3List) { trans3Offsets(t3List, ff->hStart, ff->hEnd, &box->tStart, &box->tEnd); } else { box->tStart = ff->hStart - firstH; box->tEnd = box->tStart + boxSize; } box->data = ff; box->score = bioScoreMatch(isProt, ff->nStart, ff->hStart, boxSize); if (tMin > box->tStart) tMin = box->tStart; if (tMax < box->tEnd) tMax = box->tEnd; slAddHead(&boxList, box); } /* Adjust boxes so that tMin is always 0. */ for (box = boxList; box != NULL; box = box->next) { box->tStart -= tMin; box->tEnd -= tMin; } tMax -= tMin; ssStringency = stringency; ssIsProt = isProt; chainList = chainBlocks(qSeq->name, qSeq->size, '+', "tSeq", tMax, &boxList, ssConnectCost, ssGapCost, NULL, NULL); /* Fixup crossovers on best (first) chain. */ bestChain = chainList; prevBox = bestChain->blockList; for (box = prevBox->next; box != NULL; box = box->next) { int overlap = findOverlap(prevBox, box); if (overlap > 0) { struct ffAli *left = prevBox->data; struct ffAli *right = box->data; int crossover = findCrossover(left, right, overlap, isProt); int remain = overlap - crossover; left->nEnd -= remain; left->hEnd -= remain; right->nStart += crossover; right->hStart += crossover; } prevBox = box; } /* Copy stuff from first chain to bestAli. */ farRight = NULL; for (box = chainList->blockList; box != NULL; box = box->next) { ff = box->data; ff->left = farRight; farRight = ff; } *retBestAli = ffMakeRightLinks(farRight); /* Copy stuff from other chains to leftovers. */ farRight = NULL; for (chain = chainList->next; chain != NULL; chain = chain->next) { for (box = chain->blockList; box != NULL; box = box->next) { ff = box->data; ff->left = farRight; farRight = ff; } } *retLeftovers = ffMakeRightLinks(farRight); *retScore = bestChain->score; for (chain = chainList; chain != NULL; chain = chain->next) chain->blockList = NULL; /* Don't want to free this, it's local. */ chainFreeList(&chainList); lmCleanup(&lm); } static void ssFindBest(struct ffAli *ffList, bioSeq *qSeq, bioSeq *tSeq, enum ffStringency stringency, boolean isProt, struct trans3 *t3List, struct ffAli **retBestAli, int *retScore, struct ffAli **retLeftovers) /* String together blocks in alignment into chains. */ { int count = ffAliCount(ffList); if (count >= 10) { ssFindBestBig(ffList, qSeq, tSeq, stringency, isProt, t3List, retBestAli, retScore, retLeftovers); } else { ssFindBestSmall(ffList, qSeq, tSeq, stringency, isProt, t3List, retBestAli, retScore, retLeftovers); } } struct ffAli *cutAtBigIntrons(struct ffAli *ffList, int maxIntron, int *pScore, enum ffStringency stringency, + boolean isProt, bioSeq *tSeq, struct trans3 *t3List, struct ffAli **returnLeftovers) /* Return ffList up to the first intron that's too big. * Put the rest of the blocks back onto the leftovers list. */ { struct ffAli *prevFf, *ff, *cutFf = NULL; prevFf = ffList; for (ff = prevFf->right; ff != NULL; ff = ff->right) { - int dt = ff->hStart - prevFf->hEnd; + int nhStart = trans3GenoPos( ff->hStart, tSeq, t3List, FALSE); + int ohEnd = trans3GenoPos(prevFf->hEnd , tSeq, t3List, TRUE); + int dt = nhStart - ohEnd; if (dt > maxIntron) { cutFf = prevFf; break; } prevFf = ff; } if (cutFf != NULL) { ff = cutFf->right; cutFf->right = NULL; ff->left = NULL; ffCat(returnLeftovers, &ff); + if (isProt) + *pScore = ffScoreProtein(ffList, stringency); + else *pScore = ffScore(ffList, stringency); } return ffList; } void ssStitch(struct ssBundle *bundle, enum ffStringency stringency, int minScore, int maxToReturn) /* Glue together mrnas in bundle as much as possible. Returns number of * alignments after stitching. Updates bundle->ffList with stitched * together version. */ { struct dnaSeq *qSeq = bundle->qSeq; struct dnaSeq *genoSeq = bundle->genoSeq; struct ffAli *ffList = NULL; struct ssFfItem *ffl; struct ffAli *bestPath; int score; boolean firstTime = TRUE; if (bundle->ffList == NULL) return; /* The score may improve when we stitch together more alignments, * so don't let minScore be too harsh at this stage. */ if (minScore > 20) minScore = 20; /* Create ffAlis for all in bundle and move to one big list. */ for (ffl = bundle->ffList; ffl != NULL; ffl = ffl->next) { ffCat(&ffList, &ffl->ff); } slFreeList(&bundle->ffList); ffAliSort(&ffList, ffCmpHitsNeedleFirst); ffList = ffMergeClose(ffList, qSeq->dna, genoSeq->dna); while (ffList != NULL) { + ssFindBest(ffList, qSeq, genoSeq, stringency, bundle->isProt, bundle->t3List, &bestPath, &score, &ffList); + bestPath = ffMergeNeedleAlis(bestPath, TRUE); bestPath = ffRemoveEmptyAlis(bestPath, TRUE); if (!bestPath) { ffFreeAli(&ffList); break; } bestPath = ffMergeHayOverlaps(bestPath); bestPath = ffRemoveEmptyAlis(bestPath, TRUE); bestPath = forceMonotonic(bestPath, qSeq, genoSeq, stringency, bundle->isProt, bundle->t3List); if (firstTime && stringency == ffCdna && bundle->avoidFuzzyFindKludge == FALSE) { /* Only look for middle exons the first time. Next times * this might regenerate most of the first alignment... */ bestPath = smallMiddleExons(bestPath, bundle, stringency); } bestPath = ffMergeNeedleAlis(bestPath, TRUE); if (ffIntronMax != ffIntronMaxDefault) { bestPath = cutAtBigIntrons(bestPath, ffIntronMax, &score, stringency, + bundle->isProt, genoSeq, bundle->t3List, &ffList); } if (!bundle->isProt) ffSlideIntrons(bestPath); bestPath = ffRemoveEmptyAlis(bestPath, TRUE); if (score >= minScore) { AllocVar(ffl); ffl->ff = bestPath; slAddHead(&bundle->ffList, ffl); } else { ffFreeAli(&bestPath); ffFreeAli(&ffList); break; } firstTime = FALSE; if (--maxToReturn <= 0) { ffFreeAli(&ffList); break; } } slReverse(&bundle->ffList); return; } static struct ssBundle *findBundle(struct ssBundle *list, struct dnaSeq *genoSeq) /* Find bundle in list that has matching genoSeq pointer, or NULL * if none such. This routine is used by psLayout but not blat. */ { struct ssBundle *el; for (el = list; el != NULL; el = el->next) if (el->genoSeq == genoSeq) return el; return NULL; } struct ssBundle *ssFindBundles(struct patSpace *ps, struct dnaSeq *cSeq, char *cName, enum ffStringency stringency, boolean avoidSelfSelf) /* Find patSpace alignments. This routine is used by psLayout but not blat. */ { struct patClump *clumpList, *clump; struct ssBundle *bundleList = NULL, *bun = NULL; DNA *cdna = cSeq->dna; int totalCdnaSize = cSeq->size; DNA *endCdna = cdna+totalCdnaSize; struct ssFfItem *ffl; struct dnaSeq *lastSeq = NULL; int maxSize = 700; int preferredSize = 500; int overlapSize = 250; for (;;) { int cSize = endCdna - cdna; if (cSize > maxSize) cSize = preferredSize; clumpList = patSpaceFindOne(ps, cdna, cSize); for (clump = clumpList; clump != NULL; clump = clump->next) { struct ffAli *ff; struct dnaSeq *seq = clump->seq; DNA *tStart = seq->dna + clump->start; if (!avoidSelfSelf || !sameString(seq->name, cSeq->name)) { ff = ffFind(cdna, cdna+cSize, tStart, tStart + clump->size, stringency); if (ff != NULL) { if (lastSeq != seq) { lastSeq = seq; if ((bun = findBundle(bundleList, seq)) == NULL) { AllocVar(bun); bun->qSeq = cSeq; bun->genoSeq = seq; bun->genoIx = clump->bacIx; bun->genoContigIx = clump->seqIx; slAddHead(&bundleList, bun); } } AllocVar(ffl); ffl->ff = ff; slAddHead(&bun->ffList, ffl); } } } cdna += cSize; if (cdna >= endCdna) break; cdna -= overlapSize; slFreeList(&clumpList); } slReverse(&bundleList); cdna = cSeq->dna; for (bun = bundleList; bun != NULL; bun = bun->next) { ssStitch(bun, stringency, 20, 16); } return bundleList; }