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);
}
struct edwQaContamTarget *getContamTargets(struct sqlConnection *conn,
struct edwFile *ef, struct edwValidFile *vf)
/* Get list of contamination targets for file - basically all targets that aren't in same
* taxon as self. */
{
assert(vf->ucscDb != NULL);
struct edwAssembly *origAsm = edwAssemblyForUcscDb(conn, vf->ucscDb);
assert(origAsm != NULL);
char query[256];
sqlSafef(query, sizeof(query),
"select edwQaContamTarget.* from edwQaContamTarget,edwAssembly "
"where edwQaContamTarget.assemblyId = edwAssembly.id "
" and edwAssembly.taxon != %d", origAsm->taxon);
struct edwQaContamTarget *targetList = edwQaContamTargetLoadByQuery(conn, query);
edwAssemblyFree(&origAsm);
return targetList;
}
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);
}
void screenFastqForContaminants(struct sqlConnection *conn,
struct edwFile *ef, struct edwValidFile *vf)
/* The ef/vf point to same file, which is fastq format. Set alignments up for a sample against all
* contamination targets. */
{
/* Get target list and see if we have any work to do. */
struct edwQaContamTarget *target, *targetList;
targetList = getContamTargets(conn, ef, vf);
boolean needScreen = FALSE;
for (target = targetList; target != NULL; target = target->next)
{
if (edwQaContamMade(conn, ef->id, target->id) <= 0)
{
needScreen = TRUE;
break;
}
}
if (needScreen)
{
verbose(1, "screenFastqForContaminants(%u(%s))\n", ef->id, ef->submitFileName);
/* Get fastq record. */
struct edwFastqFile *fqf = edwFastqFileFromFileId(conn, ef->id);
if (fqf == NULL)
errAbort("No edwFastqFile record for file id %lld", (long long)ef->id);
/* Create downsampled fastq in temp directory - downsampled more than default even. */
char sampleFastqName[PATH_LEN];
edwMakeTempFastqSample(fqf->sampleFileName, FASTQ_SAMPLE_SIZE, sampleFastqName);
verbose(1, "downsampled %s into %s\n", vf->licensePlate, sampleFastqName);
for (target = targetList; target != NULL; target = target->next)
{
/* Get assembly associated with target */
int assemblyId = target->assemblyId;
char query[512];
sqlSafef(query, sizeof(query), "select * from edwAssembly where id=%d", assemblyId);
struct edwAssembly *newAsm = edwAssemblyLoadByQuery(conn, query);
if (newAsm == NULL)
errAbort("warehouse edwQaContamTarget %d not found", assemblyId);
/* If we don't already have a match, do work to create contam record. */
int matchCount = edwQaContamMade(conn, ef->id, target->id);
if (matchCount <= 0)
{
/* We run the bed-file maker, just for side effect calcs. */
double mapRatio = 0, depth = 0, sampleCoverage = 0, uniqueMapRatio;
edwAlignFastqMakeBed(ef, newAsm, sampleFastqName, vf, NULL,
&mapRatio, &depth, &sampleCoverage, &uniqueMapRatio);
verbose(1, "%s mapRatio %g, depth %g, sampleCoverage %g\n",
newAsm->name, mapRatio, depth, sampleCoverage);
struct edwQaContam contam =
{.fileId=ef->id, .qaContamTargetId=target->id, .mapRatio = mapRatio};
edwQaContamSaveToDb(conn, &contam, "edwQaContam", 256);
}
edwAssemblyFree(&newAsm);
}
edwQaContamTargetFreeList(&targetList);
if (keepTemp)
verbose(1, "%s\n", sampleFastqName);
else
remove(sampleFastqName);
edwFastqFileFree(&fqf);
}
}
