63120154609787691150cc8a67a1aad40455481c
markd
  Wed Oct 14 13:09:06 2020 -0700
separate -genomeDir into -genome and -genomeDataDir

diff --git src/gfClient/gfClient.c src/gfClient/gfClient.c
index 280b031..6cf683e 100644
--- src/gfClient/gfClient.c
+++ src/gfClient/gfClient.c
@@ -8,31 +8,32 @@
 #include "psl.h"
 #include "options.h"
 #include "fuzzyFind.h"
 
 
 static struct optionSpec optionSpecs[] = {
     {"prot", OPTION_BOOLEAN},
     {"q", OPTION_STRING},
     {"t", OPTION_STRING},
     {"minIdentity", OPTION_FLOAT},
     {"minScore", OPTION_INT},
     {"dots", OPTION_INT},
     {"out", OPTION_STRING},
     {"maxIntron", OPTION_INT},
     {"nohead", OPTION_BOOLEAN},
-    {"genomeDir", OPTION_STRING},
+    {"genome", OPTION_STRING},
+    {"genomeDataDir", OPTION_STRING},
     {NULL, 0}
 };
 
 /* Variables that can be overridden by command line. */
 int dots = 0;
 int minScore = 30;
 double minIdentity = 90;
 char *outputFormat = "psl";
 char *qType = "dna";
 char *tType = "dna";
 char *genome = NULL;
 char *genomeDataDir = NULL;
 
 void usage()
 /* Explain usage and exit. */
@@ -169,24 +170,24 @@
     usage();
 if (optionExists("prot"))
     qType = tType = "prot";
 qType = optionVal("q", qType);
 tType = optionVal("t", tType);
 if (sameWord(tType, "prot") || sameWord(tType, "dnax") || sameWord(tType, "rnax"))
     minIdentity = 25;
 minIdentity = optionFloat("minIdentity", minIdentity);
 minScore = optionInt("minScore", minScore);
 dots = optionInt("dots", 0);
 outputFormat = optionVal("out", outputFormat);
 genome = optionVal("genome", NULL);
 genomeDataDir = optionVal("genomeDataDir", NULL);
 if ((genomeDataDir != NULL) && (genome == NULL))
     errAbort("-genomeDataDir requires the -genome option");
-if ((genome == NULL) && (genomeDataDir != NULL))
+if ((genome != NULL) && (genomeDataDir == NULL))
     genomeDataDir = ".";
 
 
 /* set global for fuzzy find functions */
 setFfIntronMax(optionInt("maxIntron", ffIntronMaxDefault));
 gfClient(argv[1], argv[2], argv[3], argv[4], argv[5], tType, qType);
 return 0;
 }