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);
}
void doReplicatePair(struct sqlConnection *conn, struct cdwAssembly *assembly,
struct cdwFile *elderEf, struct cdwValidFile *elderVf,
struct cdwFile *youngerEf, struct cdwValidFile *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 (cdwIsSupportedBigBedFormat(format))
{
doBigBedReplicate(conn, format, assembly, elderEf, elderVf, youngerEf, youngerVf);
}
else if (startsWith("bed_", format) && cdwIsSupportedBigBedFormat(format+4))
{
doBedReplicate(conn, format+4, assembly, elderEf, elderVf, youngerEf, youngerVf);
}
else if (sameString(format, "bigWig"))
{
doBigWigReplicate(conn, assembly, elderEf, elderVf, youngerEf, youngerVf);
}
else if (sameString(format, "rcc") || sameString(format, "idat")
|| sameString(format, "customTrack"))
{
warn("Don't know how to compare %s files", format);
}
else if (sameString(format, "unknown"))
{
// Nothing we can do
}
else
errAbort("Unrecognized format %s in doReplicatePair", format);
}
