147740e133aa59c5aa7938ef68f1b66f3696c701
braney
  Fri Mar 13 15:29:49 2026 -0700
Revert noDots mafClick/mafFrag work from master, refs #21477

Remove the mafClickMafFrag/noDots code path from mafClick.c, hgMaf.c,
hgMaf.h, and mafFrag.c. Also remove mafFrag unit tests added as part
of this work. The code is preserved on the mafFragNoDots and
mafClickMafFrag branches.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

diff --git src/hg/ratStuff/mafFrag/mafFrag.c src/hg/ratStuff/mafFrag/mafFrag.c
index 8919c34764a..8984b625c77 100644
--- src/hg/ratStuff/mafFrag/mafFrag.c
+++ src/hg/ratStuff/mafFrag/mafFrag.c
@@ -1,99 +1,76 @@
 /* mafFrag - Extract maf sequences for a region from database. */
 
 /* Copyright (C) 2011 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "jksql.h"
 #include "maf.h"
 #include "hdb.h"
 #include "hgMaf.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "mafFrag - Extract maf sequences for a region from database\n"
   "usage:\n"
   "   mafFrag database mafTrack chrom start end strand out.maf\n"
   "options:\n"
   "   -outName=XXX  Use XXX instead of database.chrom for the name\n"
-  "   -noDots       Output only species with sequence (no dot-filled rows)\n"
   );
 }
 
 char *outName = NULL;
-boolean noDots = FALSE;
 
 static struct optionSpec options[] = {
    {"outName", OPTION_STRING},
-   {"noDots", OPTION_BOOLEAN},
    {NULL, 0},
 };
 
 void mafFragCheck(char *database, char *track, 
 	char *chrom, char *startString, char *endString,
 	char *strand, char *outMaf)
 /* mafFragCheck - Check parameters and convert to binary.
- * Call mafFrag or mafFragNoDots. */
+ * Call mafFrag. */
 {
 int start, end, chromSize;
+struct mafAli *maf;
 if (!isdigit(startString[0]) || !isdigit(endString[0]))
     errAbort("%s %s not numbers", startString, endString);
 start = atoi(startString);
 end = atoi(endString);
 if (end <= start)
     errAbort("end before start!");
 chromSize = hChromSize(database, chrom);
 if (end > chromSize)
    errAbort("End past chromSize (%d > %d)", end, chromSize);
-if (noDots)
-    {
-    struct mafAli *mafList = hgMafFragNoDots(database, track,
-	chrom, start, end, *strand,
-	outName, NULL);
-    if (mafList != NULL)
-	{
-	FILE *f = mustOpen(outMaf, "w");
-	mafWriteStart(f, "zero");
-	struct mafAli *maf;
-	for (maf = mafList; maf != NULL; maf = maf->next)
-	    mafWrite(f, maf);
-	mafWriteEnd(f);
-	carefulClose(&f);
-	mafAliFreeList(&mafList);
-	}
-    }
-else
-    {
-    struct mafAli *maf = hgMafFrag(database, track,
+maf = hgMafFrag(database, track, 
 	chrom, start, end, *strand, 
 	outName, NULL);
 if (maf != NULL)
     {
     FILE *f = mustOpen(outMaf, "w");
     mafWriteStart(f, "zero");
     mafWrite(f, maf);
     mafWriteEnd(f);
     carefulClose(&f);
     mafAliFree(&maf);
     }
 }
-}
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 dnaUtilOpen();
 optionInit(&argc, argv, options);
 outName = optionVal("outName", NULL);
-noDots = optionExists("noDots");
 if (argc != 8)
     usage();
 mafFragCheck(argv[1], argv[2], argv[3], argv[4], argv[5], argv[6], argv[7]);
 return 0;
 }