4851eeb9404c9ce52d4d34f0d360fd06252cd482
galt
  Wed Aug 27 11:12:21 2014 -0700
Fixes #13850. use oneSize instead of seq->size to reflect stripped out Ns and Xs
diff --git src/hg/hgBlat/hgBlat.c src/hg/hgBlat/hgBlat.c
index 5b03dd8..d4e1a4f 100644
--- src/hg/hgBlat/hgBlat.c
+++ src/hg/hgBlat/hgBlat.c
@@ -580,37 +580,37 @@
 for (seq = seqList; seq != NULL; seq = seq->next)
     {
     printf(" "); fflush(stdout);  /* prevent apache cgi timeout by outputting something */
     oneSize = realSeqSize(seq, !isTx);
     if ((seqCount&1) == 0)	// Call bot delay every 2nd time starting with first time
 	hgBotDelay();
     if (++seqCount > maxSeqCount)
         {
 	warn("More than 25 input sequences, stopping at %s.",
 	    seq->name);
 	break;
 	}
     if (oneSize > maxSingleSize)
 	{
 	warn("Sequence %s is %d letters long (max is %d), skipping",
-	    seq->name, seq->size, maxSingleSize);
+	    seq->name, oneSize, maxSingleSize);
 	continue;
 	}
     if (oneSize < minSingleSize)
         {
 	warn("Warning: Sequence %s is only %d letters long (%d is the recommended minimum)", 
-		seq->name, seq->size, minSingleSize);
+		seq->name, oneSize, minSingleSize);
 	// we could use "continue;" here to actually enforce skipping, 
 	// but let's give the short sequence a chance, it might work.
 	// minimum possible length = tileSize+stepSize, so mpl=16 for dna stepSize=5, mpl=10 for protein.
 	if (qIsProt && oneSize < 1) // protein does not tolerate oneSize==0
 	    continue;
 	}
     totalSize += oneSize;
     if (totalSize > maxTotalSize)
         {
 	warn("Sequence %s would take us over the %d letter limit, stopping here.",
 	     seq->name, maxTotalSize);
 	break;
 	}
     conn = gfConnect(serve->host, serve->port);
     if (isTx)