void edwMakeRepeatQa(int startFileId, int endFileId)
/* edwMakeRepeatQa - Figure out what proportion of things align to repeats.. */
{
struct sqlConnection *conn = edwConnectReadWrite();
struct edwFile *ef, *efList = edwFileAllIntactBetween(conn, startFileId, endFileId);
for (ef = efList; ef != NULL; ef = ef->next)
{
struct edwValidFile *vf = edwValidFileFromFileId(conn, ef->id);
if (vf != NULL)
{
if (sameString(vf->format, "fastq"))
fastqRepeatQa(conn, ef, vf);
}
}
sqlDisconnect(&conn);
}
void edwMakeEnrichments(int startFileId, int endFileId)
/* edwMakeEnrichments - Scan through database and make a makefile to calc. enrichments and store
* in database. */
{
/* Make list with all files in ID range */
struct sqlConnection *conn = sqlConnect(edwDatabase);
struct edwFile *ef, *efList = edwFileAllIntactBetween(conn, startFileId, endFileId);
/* Make up a hash for targets keyed by assembly name. */
struct hash *assemblyToTarget = hashNew(0);
for (ef = efList; ef != NULL; ef = ef->next)
{
char path[PATH_LEN];
safef(path, sizeof(path), "%s%s", edwRootDir, ef->edwFileName);
verbose(1, "%lld processing %s aka %s\n", (long long)ef->id, ef->submitFileName, path);
if (ef->tags) // All ones we care about have tags
doEnrichments(conn, ef, path, assemblyToTarget);
}
sqlDisconnect(&conn);
}
