void hashFileList(char *fileList, struct hash *fileHash, struct hash *seqHash)
/* Read file list into hash */
{
if (endsWith(fileList, ".2bit"))
addTwoBit(fileList, fileHash, seqHash);
else if (endsWith(fileList, ".nib"))
addNib(fileList, fileHash, seqHash);
else if (isFa(fileList))
addFa(fileList, fileHash, seqHash);
else
{
struct lineFile *lf = lineFileOpen(fileList, TRUE);
char *row[1];
while (lineFileRow(lf, row))
{
char *file = row[0];
if (endsWith(file, ".2bit"))
addTwoBit(file, fileHash, seqHash);
else if (endsWith(file, ".nib"))
addNib(file, fileHash, seqHash);
else
addFa(file, fileHash, seqHash);
}
lineFileClose(&lf);
}
}
void ctgToChromFa(char *chromName, char *insertFile, char *chromDir,
char *orderLst, char *outName, struct hash *liftHash)
/* ctgToChromFa - convert contig level fa files to chromosome level. */
{
struct hash *uniq = newHash(0);
struct bigInsert *bi;
struct chromInserts *chromInserts;
struct hash *insertHash = newHash(9);
struct lineFile *lf = lineFileOpen(orderLst, TRUE);
FILE *f = mustOpen(outName, "w");
char ctgFaName[512];
char *words[2];
int liftChromSize = 0;
int actualChromSize = 0;
boolean isFirst = TRUE;
chromInsertsRead(insertFile, insertHash);
chromInserts = hashFindVal(insertHash, chromName);
fprintf(f, ">%s\n", chromName);
while (lineFileNextRow(lf, words, 1))
{
char *contig = words[0];
int nSize;
if (liftHash != NULL)
{
struct lift *lift = hashMustFindVal(liftHash, contig);
nSize = lift->nBefore;
liftChromSize = lift->chromSize;
}
else
nSize = chromInsertsGapSize(chromInserts, rmChromPrefix(contig), isFirst);
hashAddUnique(uniq, contig, NULL);
addN(f, nSize);
actualChromSize += nSize;
isFirst = FALSE;
sprintf(ctgFaName, "%s/%s/%s.fa", chromDir, contig, contig);
if (fileExists(ctgFaName))
{
actualChromSize += addFa(f, ctgFaName);
}
else
{
warn("%s does not exist\n", ctgFaName);
if (!cgiVarExists("missOk"))
noWarnAbort();
}
}
lineFileClose(&lf);
if (chromInserts != NULL)
if ((bi = chromInserts->terminal) != NULL)
{
addN(f, bi->size);
actualChromSize += bi->size;
}
if (liftHash != NULL)
{
if (actualChromSize > liftChromSize)
errAbort("Error: chromosome size from lift file is %d, but actual fa size is %d. Possible inconsistency between lift and inserts?",
liftChromSize, actualChromSize);
else if (actualChromSize < liftChromSize)
addN(f, (liftChromSize - actualChromSize));
}
if (linePos != 0)
fputc('\n', f);
fclose(f);
}
