src/hg/ratStuff/mafFrags/mafFrags.c 1.11

Index: src/hg/ratStuff/mafFrags/mafFrags.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/ratStuff/mafFrags/mafFrags.c,v
retrieving revision 1.10
retrieving revision 1.11
diff -b -B -U 4 -r1.10 -r1.11
--- src/hg/ratStuff/mafFrags/mafFrags.c	23 Jun 2009 16:40:19 -0000	1.10
+++ src/hg/ratStuff/mafFrags/mafFrags.c	11 Jul 2009 17:30:44 -0000	1.11
@@ -26,8 +26,9 @@
   "   -thickOnly - Only extract subset between thickStart/thickEnd\n"
   "   -meFirst - Put native sequence first in maf\n"
   "   -txStarts - Add MAF txstart region definitions ('r' lines) using BED name\n"
   "    and output actual reference genome coordinates in MAF.\n"
+  "   -refCoords - output actual reference genome coordinates in MAF.\n"
   );
 }
 
 static struct optionSpec options[] = {
@@ -35,15 +36,17 @@
    {"bed12", OPTION_BOOLEAN},
    {"thickOnly", OPTION_BOOLEAN},
    {"meFirst", OPTION_BOOLEAN},
    {"txStarts", OPTION_BOOLEAN},
+   {"refCoords", OPTION_BOOLEAN},
    {NULL, 0},
 };
 
 static boolean bed12 = FALSE;
 static boolean thickOnly = FALSE;
 static boolean meFirst = FALSE;
 static boolean txStarts = FALSE;
+static boolean refCoords = FALSE;
 
 static struct mafAli *mafFromBed12(char *database, char *track,
     struct bed *bed, struct slName *orgList)
 /* Construct a maf out of exons in bed. */
@@ -159,13 +162,14 @@
                         struct slName *orgList)
 /* generate MAF alignment for a bed6 */
 {
 struct mafAli *maf; 
+char *useName = refCoords ? NULL : bed->name;
 if (txStarts)
     {
     maf = hgMafFrag(database, track, 
                     bed->chrom, bed->chromStart, bed->chromEnd, bed->strand[0],
-                    NULL, orgList);
+                    useName, orgList);
     maf->regDef = mafRegDefNew(mafRegDefTxUpstream,
                                bed->chromEnd-bed->chromStart,
                                bed->name);
     if (meFirst)
@@ -174,9 +178,9 @@
 else
     {
     maf = hgMafFrag(database, track, 
                     bed->chrom, bed->chromStart, bed->chromEnd, bed->strand[0],
-                    bed->name, orgList);
+                    useName, orgList);
     if (meFirst)
         moveMeToFirst(maf, bed->name);
     }
 mafWrite(f, maf);
@@ -246,7 +250,10 @@
 bed12 = optionExists("bed12");
 thickOnly = optionExists("thickOnly");
 meFirst = optionExists("meFirst");
 txStarts = optionExists("txStarts");
+refCoords = optionExists("refCoords") || txStarts;
+if (refCoords && bed12)
+    errAbort("can't specify -txStart or -refCoords with -bed12");
 mafFrags(argv[1], argv[2], argv[3], argv[4]);
 return 0;
 }