e3828b90be3c817778a057af993f236bb5f9753b
markd
  Sun Mar 13 11:07:35 2022 -0700
fixed repeat counts

diff --git src/hg/utils/rmskAlignToPsl/rmskAlignToPsl.c src/hg/utils/rmskAlignToPsl/rmskAlignToPsl.c
index 2c72ad4..fecc67b 100644
--- src/hg/utils/rmskAlignToPsl/rmskAlignToPsl.c
+++ src/hg/utils/rmskAlignToPsl/rmskAlignToPsl.c
@@ -543,32 +543,31 @@
 for (struct blkCoord *blk = blkCoords; blk != NULL; blk = blk->next)
     {
     if (blk->qSize == 0)
         {
         psl->tNumInsert++;
         psl->tBaseInsert += blk->tSize;
         }
     else if (blk->tSize == 0)
         {
         psl->qNumInsert++;
         psl->qBaseInsert += blk->qSize;
         }
     else
         {
         assert(blk->qSize == blk->tSize);
-        psl->match += blk->matches;
-        psl->repMatch += blk->matches;
+        psl->repMatch += blk->matches;  // all matches are repeat matches
         psl->misMatch += blk->mismatches;
         if (psl->blockCount >= *blockSpacePtr)
             pslGrow(psl, blockSpacePtr);
         psl->tStarts[psl->blockCount] = blk->tStart;
         psl->qStarts[psl->blockCount] = blk->qStart;
         psl->blockSizes[psl->blockCount] = blk->tSize;
         psl->blockCount += 1;
         }
     }
 }
 
 static struct psl *convertBlocksToPsl(struct rmskAlign *alignParts,
                                       struct blkCoord *blkCoords,
                                       struct hash* repSizes)
 /* create a PSL from a repeat masker alignment */