void ooSplitFins(char *finTrans, char *ooDir)
/* ooSplitFins - Create splitFin files (list of split finished clones). */
{
struct hash *splitCloneHash = newHash(8);
struct clone *cloneList, *clone;
char fileName[512];
int i;
struct fileInfo *chromDir = NULL, *ctgDir = NULL, *chrom, *ctg;
int splitCount = 0;
/* Read in finished clones and put ones with more than
* one fragment in hash. */
cloneList = readTrans(finTrans);
for (clone = cloneList; clone != NULL; clone = clone->next)
if (slCount(clone->fragList) > 1)
{
hashAdd(splitCloneHash, clone->name, clone);
++splitCount;
}
printf("Found %d split clones in %s\n", splitCount, finTrans);
/* Scan over all contigs in ooDir. */
chromDir = listDirX(ooDir, "*", FALSE);
for (chrom = chromDir; chrom != NULL; chrom = chrom->next)
{
char *chromName = chrom->name;
if (chrom->isDir && strlen(chromName) <= 2 && chromName[0] != '.')
{
printf("Processing %s\n", chromName);
sprintf(fileName, "%s/%s", ooDir, chromName);
ctgDir = listDirX(fileName, "ctg*", TRUE);
for (ctg = ctgDir; ctg != NULL; ctg = ctg->next)
{
fflush(stdout);
if (ctg->isDir)
writeRelevantSplits(ctg->name, splitCloneHash);
}
slFreeList(&ctgDir);
}
}
}
static void gsFillInSequence(char *gsDir, struct agpFrag *agpList, DNA *dna, int dnaSize)
/* Fill in DNA array with sequences from 'freeze' */
{
struct agpFrag *agp;
int subCount;
char *sub[64];
char transFile[512], faDir[512];
struct hash *cloneHash = newHash(15), *fragHash = newHash(17);
int i;
struct clone *clone;
/* Read in trans-files to hash */
subCount = chopString(subDirs, ",", sub, ArraySize(sub));
if (subCount >= ArraySize(sub))
errAbort("Too many subDirs, limit 64.");
for (i=0; i<subCount; ++i)
{
sprintf(faDir, "%s/%s/fa", gsDir, sub[i]);
sprintf(transFile, "%s/%s/trans", gsDir, sub[i]);
readTrans(transFile, faDir, cloneHash, fragHash);
}
/* Read sequences and copy them to output DNA array. */
printf("Reading source sequences from %s\n", gsDir);
for (agp = agpList; agp != NULL; agp = agp->next)
{
DNA *dest;
int size;
if ((clone = hashFindVal(cloneHash, agp->frag)) == NULL)
errAbort("Couldn't find %s in %s", agp->frag, gsDir);
if (clone->dna == NULL)
getCloneDna(clone, fragHash);
dest = dna + agp->chromStart;
size = agp->chromEnd - agp->chromStart;
memcpy(dest, clone->dna + agp->fragStart, size);
if (agp->strand[0] == '-')
reverseComplement(dest, size);
}
}
