void cdwMakeRepeatQa(int startFileId, int endFileId)
/* cdwMakeRepeatQa - Figure out what proportion of things align to repeats.. */
{
struct sqlConnection *conn = cdwConnectReadWrite();
struct cdwFile *ef, *efList = cdwFileAllIntactBetween(conn, startFileId, endFileId);
for (ef = efList; ef != NULL; ef = ef->next)
{
struct cdwValidFile *vf = cdwValidFileFromFileId(conn, ef->id);
if (vf != NULL)
{
if (sameString(vf->format, "fastq"))
fastqRepeatQa(conn, ef, vf);
}
}
sqlDisconnect(&conn);
}
void cdwMakePairedEndQa(unsigned startId, unsigned endId)
/* cdwMakePairedEndQa - Do alignments of paired-end fastq files and calculate distrubution of
* insert size. */
{
struct sqlConnection *conn = cdwConnectReadWrite();
struct cdwFile *ef, *efList = cdwFileAllIntactBetween(conn, startId, endId);
for (ef = efList; ef != NULL; ef = ef->next)
{
struct cdwValidFile *vf = cdwValidFileFromFileId(conn, ef->id);
if (vf != NULL)
{
if (sameString(vf->format, "fastq") && !isEmpty(vf->pairedEnd))
pairedEndQa(conn, ef, vf);
}
}
sqlDisconnect(&conn);
}
void cdwMakeEnrichments(int startFileId, int endFileId)
/* cdwMakeEnrichments - 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(cdwDatabase);
struct cdwFile *ef, *efList = cdwFileAllIntactBetween(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", cdwRootDir, ef->cdwFileName);
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);
}
