void seqDataProcessUpdate(struct gbSelect* select)
/* Get sequences for a partition and update. Partition processed index should
* be loaded and selected versions flaged. */
{
char inFasta[PATH_LEN];
struct gbFa* inFa;
gbProcessedGetPath(select, "fa", inFasta);
inFa = gbFaOpen(inFasta, "r");
while (gbFaReadNext(inFa))
processSeq(select, inFa);
gbFaClose(&inFa);
}
static
uint64
readSeq(FILE *F,
char *N,
ilFragment *fr,
char end,
uint32 fastqType,
uint32 fastqOrient,
bool forcePacked,
uint32 packedLength) {
fr->fr.gkFragment_setType(GKFRAGMENT_PACKED);
fr->fr.gkFragment_setIsDeleted(1);
fr->fr.gkFragment_setMateIID(0);
fr->fr.gkFragment_setLibraryIID(0);
fr->snam[0] = 0;
fr->sstr[0] = 0;
fr->qnam[0] = 0;
fr->qstr[0] = 0;
fgets(fr->snam, NAME_MAX_LEN, F);
fgets(fr->sstr, BASE_MAX_LEN, F);
fgets(fr->qnam, NAME_MAX_LEN, F);
fgets(fr->qstr, BASE_MAX_LEN, F);
chomp(fr->snam);
chomp(fr->sstr);
chomp(fr->qnam);
chomp(fr->qstr);
if (feof(F))
return(0);
return(processSeq(N, fr, end, fastqType, fastqOrient, forcePacked, packedLength));
}
