void chainPair(struct seqPair *sp, FILE *f)
/* Make chains for all alignments in sp. */
{
long startTime, dt;
struct axt *axt;
struct cBlock *blockList, *block;
struct chain *chainList = NULL, *chain;
uglyf("%s %d nodes\n", sp->name, slCount(sp->blockList));
/* Make up tree and time it for debugging. */
startTime = clock1000();
chainList = chainBlocks(&sp->blockList, gapCost);
dt = clock1000() - startTime;
uglyf("Made %d chains in %5.3f seconds\n", slCount(chainList), dt*0.001);
/* Dump chains to file. */
for (chain = chainList; chain != NULL; chain = chain->next)
{
struct cBlock *first = chain->blockList;
struct cBlock *last = slLastEl(first);
struct cBlock *block;
fprintf(f, "%s Chain %d, score %d, %d %d, %d %d:\n",
sp->name, slCount(chain->blockList), chain->score,
first->qStart, last->qEnd, first->tStart, last->qEnd);
for (block = chain->blockList; block != NULL; block = block->next)
{
fprintf(f, " %s q %d, t %d, score %d\n", sp->name,
block->qStart, block->tStart, block->score);
}
fprintf(f, "\n");
}
chainFreeList(&chainList);
uglyf("\n");
}
static void setExonBounds(struct cdsExon *exon)
/* set isExonStart/isExonEnd flags on frames associated with an exon */
{
if (exon->frames != NULL)
{
exon->frames->mf.isExonStart = TRUE;
struct exonFrames *ef = slLastEl(exon->frames);
ef->mf.isExonEnd = TRUE;
}
}
void jsValidateKeysOnDb(struct joiner *joiner, struct joinerSet *js,
char *db, struct hash *keyHash, struct keyHitInfo *khiList)
/* Validate keys pertaining to this database. */
{
struct joinerField *jf;
struct hash *localKeyHash = NULL;
struct keyHitInfo *localKhiList = NULL;
struct joinerField *keyField;
if ((keyField = js->fieldList) == NULL)
return;
if (keyHash == NULL)
{
char *keyDb;
if (slNameInList(keyField->dbList, db))
{
keyDb = db;
}
else if (!dbInAnyField(js->fieldList->next, db))
{
return;
}
else
{
if (slCount(keyField->dbList) == 1)
keyDb = keyField->dbList->name;
else
{
struct slName *lastDb = slLastEl(keyField->dbList);
keyDb = lastDb->name;
verbose(1, " note - using %s database as reference for identifier %s\n",
keyDb, js->name);
}
}
keyHash = localKeyHash = readKeyHash(keyDb, joiner, keyField,
&localKhiList);
khiList = localKhiList;
}
if (keyHash != NULL)
{
for (jf = js->fieldList; jf != NULL; jf = jf->next)
{
if (jf != keyField && slNameInList(jf->dbList, db))
{
doKeyChecks(db, joiner, js, keyHash, khiList, keyField, jf);
}
}
}
hashFree(&localKeyHash);
slFreeList(&localKhiList);
}
struct ntContig *readNtFile(char *fileName,
struct hash *ntContigHash, struct hash *ntCloneHash)
/* Read in NT contig info. (NT contigs are contigs of finished clones.) */
{
struct lineFile *lf;
int lineSize, wordCount;
char *line, *words[8];
struct ntContig *contigList = NULL, *contig = NULL;
struct ntClonePos *pos;
char *contigName;
struct hashEl *hel;
/* Parse file into ntContig/ntClonePos data structures. */
lf = lineFileOpen(fileName, TRUE);
while (lineFileNext(lf, &line, &lineSize))
{
wordCount = chopLine(line, words);
if (wordCount == 0)
continue;
if (wordCount != 5)
errAbort("Expecting 5 words line %d of %s", lf->lineIx, lf->fileName);
contigName = words[0];
if (contig == NULL || !sameString(contigName, contig->name))
{
AllocVar(contig);
hel = hashAddUnique(ntContigHash, contigName, contig);
contig->name = hel->name;
slAddHead(&contigList, contig);
}
AllocVar(pos);
hel = hashAddUnique(ntCloneHash, words[1], pos);
pos->name = hel->name;
pos->ntContig = contig;
pos->pos = atoi(words[2]);
pos->orientation = ((words[3][0] == '-') ? -1 : 1);
pos->size = atoi(words[4]);
slAddHead(&contig->cloneList, pos);
}
lineFileClose(&lf);
/* Make sure everything is nicely sorted and sized. */
for (contig = contigList; contig != NULL; contig = contig->next)
{
slSort(&contig->cloneList, cmpNtClonePos);
pos = slLastEl(contig->cloneList);
contig->size = pos->pos + pos->size;
}
slReverse(&contigList);
return contigList;
}
struct splatAlign *splatExtendTag(struct splatTag *tag,
struct dnaSeq *qSeqF, struct dnaSeq *qSeqR, struct splix *splix,
struct axtScoreScheme *scoreScheme)
/* Convert a single tag to an alignment. */
{
int maxSingleGap = 9;
int maxTotalGap = maxSingleGap * 3;
struct splatAlign *ali = tagToAlign(tag, qSeqF, qSeqR, splix, scoreScheme);
struct chain *chain = ali->chain;
chainAddAxtScore(chain, ali->qDna, ali->tDna, scoreScheme);
int qxSize = chain->qSize - chain->qEnd; /* extra q size. */
int txSize = chain->tSize - chain->tEnd; /* extra t size. */
if (qxSize > 0 && txSize > 0)
{
int qxStart = chain->qEnd;
int qxEnd = chain->qSize;
int txStart = chain->tEnd;
int txEnd = chain->tSize;
int txMaxSize = qxSize + maxTotalGap;
if (txSize > txMaxSize)
txSize = txMaxSize;
int symAlloc = qxSize + txSize;
char *qSym, *tSym;
AllocArray(qSym, symAlloc);
AllocArray(tSym, symAlloc);
int symCount, revStartQ, revStartT;
if (bandExt(FALSE, scoreScheme, 9,
ali->qDna + qxStart, qxSize,
ali->tDna + txStart, txSize, 1,
symAlloc, &symCount, qSym, tSym, &revStartQ, &revStartT))
{
struct cBlock *newBlocks = cBlocksFromAliSym(symCount,
qSym, tSym, qxStart, txStart);
struct cBlock *lastOldBlock = slLastEl(chain->blockList);
lastOldBlock->next = newBlocks;
chainMergeAbutting(chain);
chainCalcBounds(chain);
chainAddAxtScore(chain, ali->qDna, ali->tDna, scoreScheme);
}
freeMem(qSym);
freeMem(tSym);
}
return ali;
}
void printCloneEndInfo(struct clone *clone, FILE *f)
/* Print out end information on one clone. */
{
struct frag *frag, *endFrag;
if (clone->fragCount == 1)
{
frag = clone->fragList;
printCloneStart(clone, f);
fprintf(f, "%s\tL\t%s\tR\n", frag->name, frag->name);
}
else if (clone->isFin || clone->phase >= 2)
{
frag = clone->fragList;
endFrag = slLastEl(clone->fragList);
printCloneStart(clone, f);
fprintf(f, "%s\tL\t%s\tR\n", frag->name, endFrag->name);
}
else
{
int gsCount = slCount(clone->gsList);
int spCount = slCount(clone->spList);
if (gsCount == 1 && spCount <= 1 || spCount == 1 && gsCount <= 1)
{
if (gsCount == 1)
oneSideOut(clone->gsList, clone, f);
else
oneSideOut(clone->spList, clone, f);
}
else if (gsCount == 2 || spCount == 2)
{
if (gsCount == 2)
twoSidesOut(clone->gsList, clone, f);
else
twoSidesOut(clone->spList, clone, f);
}
else if (gsCount >= 3 || spCount >= 3)
{
warn("Three or more ends (%d %d) in %s, skipping for now",
gsCount, spCount, clone->name);
}
}
}
