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/inc/hgMaf.h src/hg/inc/hgMaf.h
index ada43160c5e..7b35382b5b8 100644
--- src/hg/inc/hgMaf.h
+++ src/hg/inc/hgMaf.h
@@ -91,84 +91,30 @@
 	char *track, 	    /* Name of MAF track */
 	char *chrom, 	    /* Chromosome (in database genome) */
 	int start, int end, /* start/end in chromosome */
 	char strand, 	    /* Chromosome strand. */
 	char *outName, 	    /* Optional name to use in first component */
 	struct slName *orderList /* Optional order of organisms. */
 	);
 /* mafFrag- Extract maf sequences for a region from database.
  * This creates a somewhat unusual MAF that extends from start
  * to end whether or not there are actually alignments.  Where
  * there are no alignments (or alignments missing a species)
  * a . character fills in.   The score is always zero, and
  * the sources just indicate the species.  You can mafFree this
  * as normal. */
 
-struct mafAli *hgMafFragFromMafList(
-	char *database,     /* Database, must already have hSetDb to this */
-	char *chrom, 	    /* Chromosome (in database genome) */
-	int start, int end, /* start/end in chromosome */
-	char strand, 	    /* Chromosome strand. */
-	struct mafAli *mafList, /* Pre-loaded list of maf alignments */
-	char *outName, 	    /* Optional name to use in first component */
-	struct slName *orderList /* Optional order of organisms. */
-	);
-/* Extract maf sequences for a region from a pre-loaded mafList.
- * Same behavior as hgMafFrag but takes mafList directly instead
- * of loading from database.  Caller should not free mafList
- * afterwards (it is consumed). */
-
-struct mafAli *hgBigMafFragNoDots(
-	char *database,     /* Database, must already have hSetDb to this */
-        struct bbiFile *bbi,
-	char *chrom, 	    /* Chromosome (in database genome) */
-	int start, int end, /* start/end in chromosome */
-	char strand, 	    /* Chromosome strand. */
-	char *outName, 	    /* Optional name to use in first component */
-	struct slName *orderList /* Optional order of organisms. */
-	);
-/* hgBigMafFragNoDots - Extract maf sequences for a region from a bigMaf.
- * Returns a list of maf blocks with no dots - each block only contains
- * assemblies that have actual sequence. */
-
-struct mafAli *hgMafFragNoDots(
-	char *database,     /* Database, must already have hSetDb to this */
-	char *track, 	    /* Name of MAF track */
-	char *chrom, 	    /* Chromosome (in database genome) */
-	int start, int end, /* start/end in chromosome */
-	char strand, 	    /* Chromosome strand. */
-	char *outName, 	    /* Optional name to use in first component */
-	struct slName *orderList /* Optional order of organisms. */
-	);
-/* hgMafFragNoDots - Extract maf sequences for a region from database.
- * Returns a list of maf blocks with no dots - each block only contains
- * assemblies that have actual sequence. */
-
-struct mafAli *hgMafFragFromMafListNoDots(
-	char *database,     /* Database, must already have hSetDb to this */
-	char *chrom, 	    /* Chromosome (in database genome) */
-	int start, int end, /* start/end in chromosome */
-	char strand, 	    /* Chromosome strand. */
-	struct mafAli *mafList, /* Pre-loaded list of maf alignments */
-	char *outName, 	    /* Optional name to use in first component */
-	struct slName *orderList /* Optional order of organisms. */
-	);
-/* Extract maf sequences for a region from a pre-loaded mafList.
- * Returns a list of maf blocks with no dots - each block only contains
- * assemblies that have actual sequence.  Caller should not free mafList
- * afterwards (it is consumed). */
-
 int mafCmp(const void *va, const void *vb);
 /* Compare to sort based on start of first component. */
 
 struct consWiggle {
     struct consWiggle *next;    /* Next in list */
     char *table;                /* phastCons table */
     char *leftLabel;            /* Left label for hgTracks */
     char *uiLabel;              /* Label to print on trackUi */
 };
 
 struct consWiggle *wigMafWiggles(char *db, struct trackDb *tdb);
 /* get conservation wiggle table names and labels from trackDb setting,
    ignoring those where table doesn't exist */
 
 char *wigMafWiggleVar(char *prefix, struct consWiggle *wig,char **suffix);