5c2dea36479f0669a316e693c21a375d192b9e38
kent
  Wed Mar 13 12:13:20 2019 -0700
Making cdwPairedEnd basically ignore 10x files by allowing new paired_end values cell_barcode and sample_barcode instead of 1 2.

diff --git src/hg/cirm/cdw/lib/cdwLib.c src/hg/cirm/cdw/lib/cdwLib.c
index 392ca6f..cedcb59 100644
--- src/hg/cirm/cdw/lib/cdwLib.c
+++ src/hg/cirm/cdw/lib/cdwLib.c
@@ -2102,41 +2102,45 @@
 cdwVcfFileSaveToDb(conn, vcf, "cdwVcfFile", 1024);
 remove(statsFile);
 
 /* Clean up and go home. */
 freez(&path);
 return vcf;
 }
 
 char *cdwOppositePairedEndString(char *end)
 /* Return "1" for "2" and vice versa */
 {
 if (sameString(end, "1"))
     return "2";
 else if (sameString(end, "2"))
     return "1";
+else if (sameString(end, "cell_barcode") || sameString(end, "sample_barcode"))
+    return NULL;
 else
     {
     errAbort("Expecting 1 or 2, got %s in oppositeEnd", end);
     return NULL;
     }
 }
 
 struct cdwValidFile *cdwOppositePairedEnd(struct sqlConnection *conn, struct cdwFile *ef, struct cdwValidFile *vf)
 /* Given one file of a paired end set of fastqs, find the file with opposite ends. */
 {
 char *otherEnd = cdwOppositePairedEndString(vf->pairedEnd);
+if (otherEnd == NULL)
+    return NULL;
 char query[1024];
 sqlSafef(query, sizeof(query), 
     "select cdwValidFile.* from cdwValidFile join cdwFile on cdwValidFile.fileId=cdwFile.id"
     " where experiment='%s' and submitDirId=%d and outputType='%s' and replicate='%s' "
     " and part='%s' and pairedEnd='%s' and itemCount=%lld and deprecated=''"
     , vf->experiment, ef->submitDirId, vf->outputType, vf->replicate, vf->part, otherEnd
     , vf->itemCount);
 struct cdwValidFile *otherVf = cdwValidFileLoadByQuery(conn, query);
 if (otherVf == NULL)
     return NULL;
 if (otherVf->next != NULL)
     errAbort("Multiple results from pairedEnd query %s", query);
 return otherVf;
 }