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); }