void alignNt(char *nt)
/* Do alignments of draft bacs against one NT. */
{
char indexFileName[512];
char ntFaName[512];
struct lineFile *indexLf;
int lineSize;
char *line;
char *words[3];
int wordCount;
struct patSpace *ps;
struct dnaSeq *ntSeq;
printf("<H1>Check Layout of %s</H1>\n", nt);
printf("<PRE>");
sprintf(ntFaName, "%s/p%s.fa", faDir, nt);
ntSeq = faReadAllDna(ntFaName);
ps = makePatSpace(&ntSeq, 1, oocFile, 10, 500);
sprintf(indexFileName, "%s/%s.index", indexDir, nt);
uglyf("Checking out %s and %s\n", indexFileName, ntFaName);
indexLf = lineFileOpen(indexFileName, TRUE);
while (lineFileNext(indexLf, &line, &lineSize))
{
wordCount = chopLine(line, words);
if (wordCount > 0)
{
char bacFaName[512];
struct dnaSeq *contigList, *contig;
char *bacAcc = words[0];
char *s = strrchr(bacAcc, '.');
if (s != NULL)
*s = 0;
uglyf("%s\n", bacAcc);
sprintf(bacFaName, "%s/%s.fa", faDir, bacAcc);
contigList = faReadAllDna(bacFaName);
for (contig = contigList; contig != NULL; contig = contig->next)
{
boolean isRc;
uglyf(" %s\n", contig->name);
for (isRc = FALSE; isRc <= TRUE; isRc += 1)
{
struct ssBundle *bunList, *bun;
bunList = ssFindBundles(ps, contig, contig->name, ffTight);
for (bun = bunList; bun != NULL; bun = bun->next)
{
showBundle(bun, isRc);
}
ssBundleFreeList(&bunList);
reverseComplement(contig->dna, contig->size);
}
}
freeDnaSeqList(&contigList);
}
}
lineFileClose(&indexLf);
freeDnaSeqList(&ntSeq);
}
void oneStrand(struct patSpace *ps, struct hash *repeatHash, struct dnaSeq *otherSeq,
boolean isRc, enum ffStringency stringency, FILE *out)
/* Search one strand of other sequence. */
{
struct ssBundle *bundleList, *bun;
bundleList = ssFindBundles(ps, otherSeq, otherSeq->name, stringency, avoidSelfSelf);
for (bun = bundleList; bun != NULL; bun = bun->next)
{
struct ssFfItem *ffi;
struct dnaSeq *genoSeq = bun->genoSeq;
struct repeatTracker *rt = hashLookup(repeatHash, genoSeq->name)->val;
for (ffi = bun->ffList; ffi != NULL; ffi = ffi->next)
{
struct ffAli *ff = ffi->ff;
oneAli(ff, otherSeq, rt, isRc, stringency, out);
}
}
ssBundleFreeList(&bundleList);
}
