void faToTwoBit(char *inFiles[], int inFileCount, char *outFile)
/* Convert inFiles in fasta format to outfile in 2 bit
* format. */
{
struct twoBit *twoBitList = NULL, *twoBit;
int i;
struct hash *uniqHash = newHash(18);
FILE *f;
for (i=0; i<inFileCount; ++i)
{
char *fileName = inFiles[i];
struct lineFile *lf = lineFileOpen(fileName, TRUE);
struct dnaSeq seq;
ZeroVar(&seq);
while (faMixedSpeedReadNext(lf, &seq.dna, &seq.size, &seq.name))
{
if (seq.size == 0)
{
warn("Skipping item %s which has no sequence.\n",seq.name);
continue;
}
/* strip off version number */
if (stripVersion)
{
char *sp = NULL;
sp = strchr(seq.name,'.');
if (sp != NULL)
*sp = '\0';
}
if (hashLookup(uniqHash, seq.name))
{
if (!ignoreDups)
errAbort("Duplicate sequence name %s", seq.name);
else
continue;
}
hashAdd(uniqHash, seq.name, NULL);
if (noMask)
faToDna(seq.dna, seq.size);
else
unknownToN(seq.dna, seq.size);
twoBit = twoBitFromDnaSeq(&seq, !noMask);
slAddHead(&twoBitList, twoBit);
}
lineFileClose(&lf);
}
slReverse(&twoBitList);
f = mustOpen(outFile, "wb");
twoBitWriteHeader(twoBitList, f);
for (twoBit = twoBitList; twoBit != NULL; twoBit = twoBit->next)
{
twoBitWriteOne(twoBit, f);
}
carefulClose(&f);
}
FastaRecord(const std::string & name, T && seq) :
name_(name), seq_(std::forward<T>(seq)) {
static_assert(std::is_constructible<std::string, T>::value,
"Parameter seq can't be used to construct a std::string in constructing seqInfo");
unknownToN(seq_);
//determine masks and ns
storeBlocksOfLower();
storeBlocksOfN();
}
