ae63ce55185746c5fabb2ead8cc20215faada36d
max
  Mon Nov 3 08:03:14 2025 -0800
adding ancient dna track, refs #36592

diff --git src/hg/makeDb/hgLoadMaf/hgLoadMafSummary.c src/hg/makeDb/hgLoadMaf/hgLoadMafSummary.c
index 8f31bd9e10c..9e0355fa181 100644
--- src/hg/makeDb/hgLoadMaf/hgLoadMafSummary.c
+++ src/hg/makeDb/hgLoadMaf/hgLoadMafSummary.c
@@ -105,87 +105,107 @@
 }
 
 struct mafComp *mafMaster(struct mafAli *maf, struct mafFile *mf, 
                                         char *fileName)
 /* Get master component from maf. Error abort if no master component */
 {
 struct mafComp *mcMaster = mafMayFindCompPrefix(maf, database, ".");
 if (mcMaster == NULL) 
     {
     errAbort("Couldn't find %s. sequence line %d of %s\n",
                     database, mf->lf->lineIx, fileName);
     }
 return mcMaster;
 }
 
-char *mafSplitSrcGetChrom(char *src) 
+char *mafSplitSrcGetChrom(char *src, char* database) 
 /* src can be in format chrom, db|chrom or db.chrom: split string on separator and return pointer to chrom.
- * Can even handle a db with a single dot in it and the db.chrom format, but only if db has a single dot (=NCBI format)
- * The side effect of this function is that src contains only the db, not the chrom anymore.
+ * the db part of src can also have a dot in it, but only if the 'database' argument is not null.
+ * Changes 'src': The side effect of this function is that src contains only the db, not the chrom anymore.
  * */
 {
 char *pipe = strchr(src, '|');
 // pipe found? It's the new format, db|chrom
 if (pipe) {
     *pipe = '\0';
     return pipe+1;
     }
 
 char *dot1 = strchr(src, '.');
 if (!dot1)
     return src;  // if there are no dots, assume the name is the chrom
-else
+
+if (database)
+    {
+    // if 'database' is not NULL we can resolve a situation like GCF_1234.3.CJS12323.4 because we know that
+    // GCF_1234.3 is the db part
+    if (differentString(src, database))
         {
-    // the most common format: db.chrom
+        // the database name isn't matching the first part of the component source,
+        // look to see if maybe the database has a dot in it
+        *dot1 = '.';   // replace the dot
+        char *dot2 = strchr(dot1 + 1, '.'); // look for the next dot
+        if (dot2 != NULL)
+            {
+            *dot2 = 0;
+            char *chrom = dot2 + 1;
+            return chrom;
+            }
+
+        if ((dot2 == NULL) || differentString(src, database))
+            errAbort("expecting first component to have assembly name with no more than one dot");
+        }
+    }
+
+// if database is NULL and there is no pipe character, just split on the first dot and that's it
 char* chrom = dot1 + 1;
 *dot1 = '\0';
 return chrom;
 }
-}
 
 long processMaf(struct mafAli *maf, struct hash *componentHash, 
                 FILE *f, struct mafFile *mf, char *fileName)
 /* Compute scores for each pairwise component in the maf and output to .tab file */
 {
 struct mafComp *mc = NULL, *nextMc = NULL;
 struct mafSummary *ms, *msPending;
 struct mafAli pairMaf;
 long componentCount = 0;
 struct mafComp *mcMaster = mafMaster(maf, mf, fileName);
 struct mafComp *oldMasterNext = mcMaster->next; 
 char *chrom;
 char src[256];
 
 strcpy(src, mcMaster->src);
 
-chrom = mafSplitSrcGetChrom(src);
+chrom = mafSplitSrcGetChrom(src, database);
 
 for (mc = maf->components; mc != NULL; mc = nextMc)
     {
     nextMc = mc->next;
     if (sameString(mcMaster->src, mc->src) || mc->size == 0)
         continue;
 
     /* create maf summary for this alignment component */
     AllocVar(ms);
     ms->chrom = cloneString(chrom);
     /* both MAF and BED format define chromStart as 0-based */
     ms->chromStart = mcMaster->start;
     /* BED chromEnd is start+size */
     ms->chromEnd = mcMaster->start + mcMaster->size;
     ms->src = cloneString(mc->src);
-    mafSplitSrcGetChrom(ms->src);
+    mafSplitSrcGetChrom(ms->src, database);
 
     /* construct pairwise maf for scoring */
     ZeroVar(&pairMaf);
     pairMaf.textSize = maf->textSize;
     pairMaf.components = mcMaster;
     mcMaster->next = mc;
     mc->next = NULL;
     ms->score = scorePairwise(&pairMaf);
     ms->leftStatus[0] = mc->leftStatus;
     ms->rightStatus[0] = mc->rightStatus;
 
     /* restore component links to allow memory recovery */
     mcMaster->next = oldMasterNext; 
     mc->next = nextMc;