void doReplicateQa(struct sqlConnection *conn, struct edwFile *ef)
/* Try and do replicate level QA - find matching file and do correlation-like
* things. */
{
/* Get validated file info. If not validated we don't bother. */
struct edwValidFile *vf = edwValidFileFromFileId(conn, ef->id);
if (vf == NULL)
return;
char *replicate = vf->replicate;
if (!isEmpty(replicate) && !sameString(replicate, "n/a")
&& !sameString(replicate, "pooled")) // If expanding this, to expand bits in edwWebBrowse as well
{
/* Try to find other replicates of same experiment, format, and output type. */
struct edwValidFile *elder, *elderList = edwFindElderReplicates(conn, vf);
if (elderList != NULL)
{
struct edwAssembly *assembly = edwAssemblyForUcscDb(conn, vf->ucscDb);
for (elder = elderList; elder != NULL; elder = elder->next)
{
doReplicatePair(conn, assembly, edwFileFromIdOrDie(conn, elder->fileId), elder, ef, vf);
}
edwAssemblyFree(&assembly);
}
}
edwValidFileFree(&vf);
}
void doContaminationQa(struct sqlConnection *conn, struct edwFile *ef)
/* Try and do contamination level QA - mostly mapping fastq files to other
* genomes. */
{
/* Get validated file info. If not validated we don't bother. */
struct edwValidFile *vf = edwValidFileFromFileId(conn, ef->id);
if (vf == NULL)
return;
/* We only work on fastq. */
if (!sameString(vf->format, "fastq"))
return;
screenFastqForContaminants(conn, ef, vf);
}
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);
}
long long totalReadsForExp(struct sqlConnection *conn, struct fullExperiment *exp,
struct edwExperiment *ee, struct eapGraph *eg)
/* Return total number of reads in both good replicates of this experiment */
{
boolean uglyOne = TRUE;
if (uglyOne) uglyf("Got you %s %s\n", exp->name, exp->exp->biosample);
// We start with broad peaks because they are relatively rare, only generated by hotspot
long long total = 0;
long long pooledPeakId = pooledBroadPeaksForExp(exp);
if (uglyOne) uglyf("Broad is %lld\n", pooledPeakId);
struct slRef *ref, *refList = NULL;
eapGraphAncestorsOfFormat(eg, pooledPeakId, "fastq", -1, &refList);
for (ref = refList; ref != NULL; ref = ref->next)
{
struct eapInput *in = ref->val;
struct edwValidFile *vf = edwValidFileFromFileId(conn, in->fileId);
if (uglyOne) uglyf("Fastq is %u, reads %lld\n", vf->fileId, (long long)vf->itemCount);
total += vf->itemCount;
}
return total;
}
void edwChangeFormat(char *format, int idCount, char *idStrings[])
/* edwChangeFormat - Change format and force a revalidation for a file.. */
{
struct sqlConnection *conn = edwConnectReadWrite();
/* Convert ascii id's to valid file ids so we catch errors early. */
long long ids[idCount];
struct edwValidFile *vfs[idCount];
int i;
for (i=0; i<idCount; ++i)
{
long long id = ids[i] = sqlLongLong(idStrings[i]);
struct edwValidFile *vf = vfs[i] = edwValidFileFromFileId(conn, id);
if (vf == NULL)
errAbort("%lld is not a fileId in the edwValidFile table", id);
}
/* Loop through each file and change format. */
for (i=0; i<idCount; ++i)
{
changeFormat(conn, vfs[i], format);
}
sqlDisconnect(&conn);
}
void doEnrichments(struct sqlConnection *conn, struct edwFile *ef, char *path,
struct hash *assemblyToTarget)
/* Calculate enrichments on for all targets file. The targetList and the
* grtList are in the same order. */
{
/* Get validFile from database. */
struct edwValidFile *vf = edwValidFileFromFileId(conn, ef->id);
if (vf == NULL)
return; /* We can only work if have validFile table entry */
if (!isEmpty(vf->enrichedIn))
{
/* Get our assembly */
char *format = vf->format;
char *ucscDb = vf->ucscDb;
struct edwAssembly *assembly = edwAssemblyForUcscDb(conn, ucscDb);
struct target *targetList = hashFindVal(assemblyToTarget, assembly->name);
if (targetList == NULL)
{
targetList = targetsForAssembly(conn, assembly);
if (targetList == NULL)
errAbort("No targets for assembly %s", assembly->name);
hashAdd(assemblyToTarget, assembly->name, targetList);
}
/* Loop through targetList zeroing out existing ovelaps. */
struct target *target;
boolean allSkip = TRUE;
for (target = targetList; target != NULL; target = target->next)
{
target->overlapBases = target->uniqOverlapBases = 0;
target->skip = enrichmentExists(conn, ef, target->target);
if (!target->skip)
allSkip = FALSE;
}
/* Do a big dispatch based on format. */
if (!allSkip)
{
if (sameString(format, "fastq"))
doEnrichmentsFromSampleBed(conn, ef, vf, assembly, targetList);
else if (sameString(format, "bigWig"))
doEnrichmentsFromBigWig(conn, ef, vf, assembly, targetList);
else if (edwIsSupportedBigBedFormat(format))
doEnrichmentsFromBigBed(conn, ef, vf, assembly, targetList);
else if (sameString(format, "gtf"))
doEnrichmentsFromSampleBed(conn, ef, vf, assembly, targetList);
else if (sameString(format, "gff"))
doEnrichmentsFromSampleBed(conn, ef, vf, assembly, targetList);
else if (sameString(format, "bam"))
doEnrichmentsFromSampleBed(conn, ef, vf, assembly, targetList);
else if (sameString(format, "unknown"))
verbose(2, "Unknown format in doEnrichments(%s), that's chill.", ef->edwFileName);
else
errAbort("Unrecognized format %s in doEnrichments(%s)", format, path);
}
/* Clean up and go home. */
edwAssemblyFree(&assembly);
}
edwValidFileFree(&vf);
}
