e2ec5ef77645a662ba31c7cfbd7499794975275a
angie
  Fri Mar 23 16:44:07 2012 -0700
Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch.  Superclasses annoColumn, annoFilter,
annoRow, annoStreamer, annoGrator, and annoFormatter define the core
interfaces for passing data and configuration to and from components.
The annoGrator superclass can join annoRows on position and pass
forward all rows of secondary source.  The annoGratorQuery module
orchestrates the passing of annoRows between the primary source,
annoGrator(s) and annoFormatter(s).  The subclasses annoStreamDb and
annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join
columns of two database tables such as hg19's pgNA12878 and knownGene
into tab-separated output.

diff --git src/lib/options.c src/lib/options.c
index ed6889a..9cc4981 100644
--- src/lib/options.c
+++ src/lib/options.c
@@ -6,33 +6,30 @@
  *
  * This file is copyright 2002 Jim Kent, but license is hereby
  * granted for all use - public, private or commercial. */
 
 #include "common.h"
 #include "hash.h"
 #include "verbose.h"
 #include "options.h"
 #include <limits.h>
 
 
 #ifdef MACHTYPE_alpha
     #define strtoll strtol
 #endif
 
-/* mask for type in optionSpec.flags */
-#define OPTION_TYPE_MASK (OPTION_BOOLEAN|OPTION_STRING|OPTION_INT|OPTION_FLOAT|OPTION_LONG_LONG|OPTION_DOUBLE)
-
 static struct optionSpec commonOptions[] = {
    {"verbose", OPTION_INT},
    {NULL, 0},
 };
 
 static struct optionSpec *matchingOption(char *name, struct optionSpec *optionSpecs)
 /* Go through spec table and return spec that matches name, or NULL
  * if none. */
 {
 while (optionSpecs->name != NULL)
     {
     if (sameString(optionSpecs->name, name))
         return optionSpecs;
     optionSpecs += 1;
     }