void doReplicatePair(struct sqlConnection *conn, struct edwAssembly *assembly,
struct edwFile *elderEf, struct edwValidFile *elderVf,
struct edwFile *youngerEf, struct edwValidFile *youngerVf)
/* Do processing on a pair of replicates. */
{
verbose(1, "processing pair %lld %s %lld %s\n", (long long)elderEf->id,
elderEf->submitFileName, (long long)youngerEf->id, youngerEf->submitFileName);
char *format = elderVf->format;
if (sameString(format, "fastq") || sameString(format, "bam") || sameString(format, "gff")
|| sameString(format, "gtf"))
{
doSampleReplicate(conn, format, assembly, elderEf, elderVf, youngerEf, youngerVf);
}
else if (edwIsSupportedBigBedFormat(format))
{
doBigBedReplicate(conn, format, assembly, elderEf, elderVf, youngerEf, youngerVf);
}
else if (sameString(format, "bigWig"))
{
doBigWigReplicate(conn, assembly, elderEf, elderVf, youngerEf, youngerVf);
}
else if (sameString(format, "unknown"))
{
// Nothing we can do
}
else
errAbort("Unrecognized format %s in doReplicatePair", format);
}
boolean isSupportedFormat(char *format)
/* Return TRUE if this is one of our supported formats */
{
/* First deal with non bigBed */
static char *otherSupportedFormats[] = {"unknown", "fastq", "bam", "bed", "gtf",
"bigWig", "bigBed",
"bedLogR", "bedRrbs", "bedMethyl", "broadPeak", "narrowPeak",
"bed_bedLogR", "bed_bedRrbs", "bed_bedMethyl", "bed_broadPeak", "bed_narrowPeak",
"bedRnaElements", "openChromCombinedPeaks", "peptideMapping", "shortFrags",
"rcc", "idat", "fasta", "customTrack",
};
static int otherSupportedFormatsCount = ArraySize(otherSupportedFormats);
if (stringArrayIx(format, otherSupportedFormats, otherSupportedFormatsCount) >= 0)
return TRUE;
/* If starts with bed_ then skip over prefix. It will be caught by bigBed */
if (startsWith("bed_", format))
format += 4;
return edwIsSupportedBigBedFormat(format);
}
char *printFormatSpecificViewInfo(FILE *f, char *indent, struct view *view,
struct composite *comp, struct taggedFile *tfList)
/* Print out part of a view trackDb stanza that are format specific. */
{
char *format = view->format;
if (sameString(format, "bigWig"))
{
return printBigWigViewInfo(f, indent, view, comp, tfList);
}
else if (sameString(format, "bam"))
{
return printBamViewInfo(f, indent, view, comp, tfList);
}
else if (edwIsSupportedBigBedFormat(format))
{
return printBigBedViewInfo(f, indent, view, comp, tfList);
}
else
{
errAbort("Unrecognized format in printFormatSpecificViewInfo");
return NULL;
}
}
boolean viewableFormat(char *format)
/* Return TRUE if it's a format we can visualize. */
{
return sameString(format, "bigWig") || sameString(format, "bam")
|| edwIsSupportedBigBedFormat(format);
}
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);
}
