static struct dnaSeq *faReadAllMixableInLf(struct lineFile *lf,
boolean isDna, boolean mixed)
/* Return list of all sequences from open fa file.
* Mixed case parameter overrides isDna. If mixed is false then
* will return DNA in lower case and non-DNA in upper case. */
{
struct dnaSeq *seqList = NULL, *seq;
DNA *dna;
char *name;
int size;
boolean ok;
for (;;)
{
if (mixed)
ok = faMixedSpeedReadNext(lf, &dna, &size, &name);
else
ok = faSomeSpeedReadNext(lf, &dna, &size, &name, isDna);
if (!ok)
break;
AllocVar(seq);
seq->name = cloneString(name);
seq->size = size;
seq->dna = cloneMem(dna, size+1);
slAddHead(&seqList, seq);
}
slReverse(&seqList);
faFreeFastBuf();
return seqList;
}
int main(int argc, char *argv[])
/*
Process command line then delegate main work to splitFaIntoContigs().
*/
{
char *arg = NULL;
/* Turn off I/O buffering for more sequential output */
setbuf(stdout, NULL);
optionHash(&argc, argv);
if (argc < 4 || argc > 6)
{
usage();
}
arg = optionVal("nSize", NULL);
if (NULL != arg && atoi(arg) > 0)
{
_nSize = atoi(arg);
}
else if (NULL != arg)
{
usage();
}
arg = optionVal("bSize", NULL);
if (NULL != arg && atoi(arg) > 0)
{
_bSize = atoi(arg);
}
else if (NULL != arg)
{
usage();
}
arg = optionVal("aSize", NULL);
if (NULL != arg && atoi(arg) > 0)
{
_aSize = atoi(arg);
}
else if (NULL != arg)
{
usage();
}
if ((_aSize != 0 && _aSize <= _bSize)
|| (_bSize != 0 && _bSize <= _nSize)
|| (_aSize != 0 && _aSize <= _nSize))
{
usage();
}
strcpy(outputDir, argv[3]);
makeDir(outputDir);
splitFaIntoContigs(argv[1], argv[2]);
faFreeFastBuf();
return 0;
}
