void copySelectedFasta(struct gbSelect* select)
/* copy FASTA records that were selected for alignment, segregating by
* native/xeno, and partitioning large files. */
{
char inFasta[PATH_LEN];
struct gbFa* inFa;
struct outFa* nativeFa = NULL;
struct outFa* xenoFa = NULL;
if (select->orgCats & GB_NATIVE)
nativeFa = outFaNew(select, GB_NATIVE);
if (select->orgCats & GB_XENO)
xenoFa = outFaNew(select, GB_XENO);
gbProcessedGetPath(select, "fa", inFasta);
gbVerbEnter(2, "copying from %s", inFasta);
inFa = gbFaOpen(inFasta, "r");
while (copyFastaRec(select, inFa, nativeFa, xenoFa))
continue;
outFaFree(&nativeFa);
outFaFree(&xenoFa);
gbFaClose(&inFa);
gbVerbLeave(2, "copying from %s", inFasta);
}
void gbMetaDataProcess(struct sqlConnection *conn,
struct gbStatusTbl* statusTbl,
struct gbSelect* select)
/* process metadata for an update */
{
HGID faFileId, pepFaId = 0;
char raPath[PATH_LEN], faPath[PATH_LEN];
/* need fasta file id */
gbProcessedGetPath(select, "fa", faPath);
faFileId = getExtFileId(conn, faPath);
if (select->release->srcDb == GB_REFSEQ)
pepFaId = getPeptideFaId(conn, select);
/* parse and save for loading metadata from this update */
gbProcessedGetPath(select, "ra.gz", raPath);
metaDataProcess(conn, statusTbl, raPath, faFileId, pepFaId);
}
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);
}
