4727e0251c76f69905d0748adab43484166d6870
angie
  Fri Mar 14 16:42:14 2014 -0700
In code review, Max pointed out that it's non-standard to conditionallyinclude header files in the middle of a .c file.  While looking at it,
I realized that there were a lot of unnecessary #ifdef's for KNETFILE_HOOKS
in general, all because there was not yet an #else implementation of
knetUdcInstall, which can be a no-op if KNETFILE_HOOKS is not used.
So I yanked out a lot of unnecessary old stuff, and tested basic bam and
vcf track operations with a few settings:

USE_SAMTABIX   USE_BAM   USE_TABIX   KNETFILE_HOOKS
1     (these tree are all implied by USE_SAMTABIX)
0        1          0       0
0        1          0       1
0        0          1       1
USE_TABIX without KNETFILE_HOOKS doesn't work because the tabix lib
wants to download .tbi files into the current working directory,
cgi-bin, and we don't allow that (and shouldn't!).  If we were going
to support that, we could add a change-dir solution as in bamFile.c,
but I don't think we need to support it now that there's samtabix.

refs #6235, refs #12850

diff --git src/hg/lib/vcfUi.c src/hg/lib/vcfUi.c
index d5f7e88..9caed6d 100644
--- src/hg/lib/vcfUi.c
+++ src/hg/lib/vcfUi.c
@@ -1,30 +1,28 @@
 /* vcfUi - Variant Call Format user interface controls that are shared
  * between more than one CGI. */
 
 #include "common.h"
 #include "cheapcgi.h"
 #include "errCatch.h"
 #include "hCommon.h"
 #include "hui.h"
 #include "jsHelper.h"
 #include "vcf.h"
 #include "vcfUi.h"
-#if (defined USE_TABIX && defined KNETFILE_HOOKS)
 #include "knetUdc.h"
 #include "udc.h"
-#endif//def USE_TABIX && KNETFILE_HOOKS
 
 INLINE char *nameOrDefault(char *thisName, char *defaultVal)
 /* If thisName is not a placeholder value, return it; otherwise return default. */
 {
 if (isNotEmpty(thisName) && !sameString(thisName, "."))
     return thisName;
 return defaultVal;
 }
 
 #define VCF_HAPLOSORT_DEFAULT_DESC "middle variant in viewing window"
 
 static void vcfCfgHaplotypeCenterHiddens(char *track, char *ctrName, char *ctrChrom, int ctrPos)
 /* Make hidden form inputs and button for setting the center variant for haplotype
  * clustering/sorting in hgTracks. */
 {
@@ -112,35 +110,33 @@
 		       formName, track);
 	dyStringPrintf(onClick, "updateOrMakeNamedVariable(%s, '%s.centerVariantPos', 0);",
 		       formName, track);
 	dyStringPrintf(onClick, "document.%s.submit(); return false;", formName);
 	cgiMakeButtonWithOnClick("submit", "Clear selection", NULL, onClick->string);
 	printf(" (use " VCF_HAPLOSORT_DEFAULT_DESC ")</TD></TR>\n");
 	}
     puts("</TABLE>");
     }
 }
 
 //TODO: share this code w/hgTracks, hgc in hg/lib/vcfFile.c
 static struct vcfFile *vcfHopefullyOpenHeader(struct cart *cart, struct trackDb *tdb)
 /* Defend against network errors and return the vcfFile object with header data, or NULL. */
 {
-#if (defined USE_TABIX && defined KNETFILE_HOOKS)
 knetUdcInstall();
 if (udcCacheTimeout() < 300)
     udcSetCacheTimeout(300);
-#endif//def USE_TABIX && KNETFILE_HOOKS
 char *db = cartString(cart, "db");
 char *table = tdb->table;
 char *dbTableName = trackDbSetting(tdb, "dbTableName");
 struct sqlConnection *conn;
 if (isCustomTrack(tdb->track) && isNotEmpty(dbTableName))
     {
     conn =  hAllocConn(CUSTOM_TRASH);
     table = dbTableName;
     }
 else
     conn = hAllocConnTrack(db, tdb);
 char *fileOrUrl = NULL;
 char *chrom = cartOptionalString(cart, "c");
 if (chrom != NULL)
     fileOrUrl = bbiNameFromSettingOrTableChrom(tdb, conn, table, chrom);