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/hgTracks/cds.c src/hg/hgTracks/cds.c
index 5761ea8..5005102 100644
--- src/hg/hgTracks/cds.c
+++ src/hg/hgTracks/cds.c
@@ -1819,36 +1819,32 @@
     }
 }
 
 void baseColorInitTrack(struct hvGfx *hvg, struct track *tg)
 /* Set up base coloring state (e.g. cache genomic sequence) for tg.
  * This must be called by tg->drawItems if baseColorDrawSetup is used 
  * in tg->drawItemAt.  Peeks at tg->drawItems method to determine whether
  * tg is linkedFeatures or linkedFeaturesSeries (currently the only
  * two supported track types -- bed, psl etc. are subclasses of these). */
 {
 setGc();
 if (initedTrack == NULL || differentString(tg->track, initedTrack))
     {
     int overallStart, overallEnd;
     boolean isSeries = FALSE;
-#ifdef USE_BAM
     if (tg->drawItems == linkedFeaturesSeriesDraw
         || tg->drawItems == bamLinkedFeaturesSeriesDraw)
-#else
-    if (tg->drawItems == linkedFeaturesSeriesDraw)
-#endif
 	isSeries = TRUE;
     else if (!baseColorCanDraw(tg))
 	errAbort("baseColorInitTrack: track %s has a type not recognized by baseColorCanDraw.",
 		 tg->track);
     getLinkedFeaturesSpan((struct linkedFeatures *)tg->items, &overallStart, &overallEnd,
 			  isSeries);
     if (overallStart < cachedGenoStart || overallEnd > cachedGenoEnd)
 	{
 	// leak mem to save time (don't bother freeing old cached dna)
 	cachedGenoStart = overallStart;
 	cachedGenoEnd = overallEnd;
 	cachedGenoDna = hDnaFromSeq(database, chromName, cachedGenoStart, cachedGenoEnd, dnaUpper);
 	}
     initedTrack = cloneString(tg->track);
     }