11e45667d4e291b3038ccda729a1cdf5bcaf004a
braney
  Mon Jul 11 15:46:54 2016 -0700
incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
defines, modify a bunch of makefiles to include kentSrc variable
pointing to top of the tree.

diff --git src/hg/lib/hui.c src/hg/lib/hui.c
index 9a3a489..640cccc 100644
--- src/hg/lib/hui.c
+++ src/hg/lib/hui.c
@@ -3972,34 +3972,32 @@
     case cfgPeak:
                         encodePeakCfgUi(cart,tdb,prefix,title,boxed);
                         break;
     case cfgWig:        wigCfgUi(cart,tdb,prefix,title,boxed);
                         break;
     case cfgWigMaf:     wigMafCfgUi(cart,tdb,prefix,title,boxed, db);
                         break;
     case cfgGenePred:   genePredCfgUi(cart,tdb,prefix,title,boxed);
                         break;
     case cfgChain:      chainCfgUi(db,cart,tdb,prefix,title,boxed, NULL);
                         break;
     case cfgNetAlign:   netAlignCfgUi(db,cart,tdb,prefix,title,boxed);
                         break;
     case cfgBedFilt:    bedFiltCfgUi(cart,tdb,prefix,title, boxed);
                         break;
-#ifdef USE_BAM
     case cfgBam:        bamCfgUi(cart, tdb, prefix, title, boxed);
                         break;
-#endif
     case cfgVcf:        vcfCfgUi(cart, tdb, prefix, title, boxed);
                         break;
     case cfgLong:       longRangeCfgUi(cart, tdb, prefix, title, boxed);
                         break;
     case cfgSnake:      snakeCfgUi(cart, tdb, prefix, title, boxed);
                         break;
     case cfgPsl:        pslCfgUi(db,cart,tdb,prefix,title,boxed);
                         break;
     default:            warn("Track type is not known to multi-view composites. type is: %d ",
                              cType);
                         break;
     }
 }
 
 char *encodeRestrictionDate(char *db,struct trackDb *trackDb,boolean excludePast)
@@ -6569,31 +6567,30 @@
     }
 
 treeImage = trackDbSetting(tdb, "treeImage");
 if (treeImage)
     printf("</TD><TD VALIGN=\"TOP\"><IMG SRC=\"../images/%s\"></TD></TR></TABLE>", treeImage);
 else
     puts("</TD></TR></TABLE>");
 
 if (trackDbSetting(tdb, CONS_WIGGLE) != NULL)
     {
     wigCfgUi(cart,tdb,name,"Conservation graph:",FALSE);
     }
 cfgEndBox(boxed);
 }
 
-#ifdef USE_BAM
 static char *grayLabels[] =
     { "alignment quality",
       "base qualities",
       "unpaired ends",
     };
 static char *grayValues[] =
     { BAM_GRAY_MODE_ALI_QUAL,
       BAM_GRAY_MODE_BASE_QUAL,
       BAM_GRAY_MODE_UNPAIRED,
     };
 
 // When a child input of a radio set is changed, click its radio button:
 #define UPDATE_RADIO_FORMAT "%s=\"\
     var inputs = document.getElementsByName('%s'); \
     if (inputs) { \
@@ -6685,31 +6682,30 @@
     }
 cgiMakeRadioButton(cartVarName, BAM_COLOR_MODE_OFF, sameString(selected, BAM_COLOR_MODE_OFF));
 printf("No additional coloring");
 
 // let the user choose to see the track in wiggle mode
 wigOption(cart, name, title, tdb);
 
 //TODO: include / exclude flags
 
 if (!boxed && fileExists(hHelpFile("hgBamTrackHelp")))
     printf("<P><A HREF=\"../goldenPath/help/hgBamTrackHelp.html\" TARGET=_BLANK>BAM "
            "configuration help</A></P>");
 
 cfgEndBox(boxed);
 }
-#endif//def USE_BAM
 
 void lrgCfgUi(struct cart *cart, struct trackDb *tdb, char *name, char *title, boolean boxed)
 /* LRG: Locus Reference Genomic sequences mapped to assembly. */
 {
 boxed = cfgBeginBoxAndTitle(tdb, boxed, title);
 printf("<TABLE%s><TR><TD>",boxed?" width='100%'":"");
 baseColorDrawOptDropDown(cart, tdb);
 indelShowOptionsWithNameExt(cart, tdb, name, "LRG sequence", FALSE, FALSE);
 cfgEndBox(boxed);
 }
 
 void lrgTranscriptAliCfgUi(struct cart *cart, struct trackDb *tdb, char *name, char *title,
 			   boolean boxed)
 /* LRG Transcripts: Locus Reference Genomic transcript sequences mapped to assembly. */
 {