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.h src/hg/hgTracks/cds.h
index bbd2392..ea6403d 100644
--- src/hg/hgTracks/cds.h
+++ src/hg/hgTracks/cds.h
@@ -106,37 +106,33 @@
         enum baseColorDrawOpt drawOpt, struct track *tg);
 /* Given an lf and the psl from which the lf was constructed, 
  * return a list of simpleFeature elements, one per codon (or partial 
  * codon if the codon falls on a gap boundary.  sizeMul, isXeno and maxShade
  * are for defaulting to one-simpleFeature-per-exon if cds is not found. */
 
 
 INLINE boolean baseColorCanDraw(struct track *tg)
 /* baseColor uses tg->drawItems as a proxy for type of tg->items, which must be 
  * linkedFeatures or linkedFeaturesSeries.  Return TRUE if tg->drawItems
  * implies that tg->items is linkedFeatures or linkedFeaturesSeries, and from
  * a subtype supported by the baseColor code. */
 {
 return (tg->drawItems == linkedFeaturesDraw || tg->drawItems == linkedFeaturesAverageDense ||
 	tg->drawItems == linkedFeaturesAverageDenseOrientEst ||
-#ifdef USE_BAM
 	tg->drawItems == linkedFeaturesSeriesDraw ||
 	tg->drawItems == bamLinkedFeaturesDraw ||
 	tg->drawItems == bamLinkedFeaturesSeriesDraw);
-#else
-	tg->drawItems == linkedFeaturesSeriesDraw);
-#endif // USE_BAM
 
 }
 
 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, but note that this should be called only if
  * baseColorCanDraw(tg) (above). */
 
 enum baseColorDrawOpt baseColorDrawSetup(struct hvGfx *hvg, struct track *tg,
 			struct linkedFeatures *lf,
 			struct dnaSeq **retMrnaSeq, struct psl **retPsl);
 /* Returns the CDS coloring option, allocates colors if necessary, and 
  * returns the sequence and psl record for the given item if applicable. 
  * Note: even if base coloring is not enabled, this will return psl and