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/hgTables/bam.c src/hg/hgTables/bam.c
index 478e23c..79ce7dd 100644
--- src/hg/hgTables/bam.c
+++ src/hg/hgTables/bam.c
@@ -12,35 +12,30 @@
 #include "bed.h"
 #include "hdb.h"
 #include "trackDb.h"
 #include "obscure.h"
 #include "hmmstats.h"
 #include "correlate.h"
 #include "asParse.h"
 #include "bbiFile.h"
 #include "bigBed.h"
 #include "hubConnect.h"
 #include "trackHub.h"
 #include "hgTables.h"
 #include "asFilter.h"
 #include "xmlEscape.h"
 #include "hgBam.h"
-#if (defined USE_BAM && defined KNETFILE_HOOKS)
-#include "knetUdc.h"
-#include "udc.h"
-#endif//def USE_BAM && KNETFILE_HOOKS
-
 
 boolean isBamTable(char *table)
 /* Return TRUE if table corresponds to a BAM file. */
 {
 if (isHubTrack(table))
     {
     struct trackDb *tdb = hashFindVal(fullTableToTdbHash, table);
     return startsWithWord("bam", tdb->type);
     }
 else
     return trackIsType(database, table, curTrack, "bam", ctLookupName);
 }
 
 char *bamFileName(char *table, struct sqlConnection *conn, char *seqName)
 /* Return file name associated with BAM.  This handles differences whether it's