bc21bd3d27fe3d29971231955b3fc544fa1c3d1e
angie
  Wed Oct 16 11:51:39 2013 -0700
Two new tracks for Locus Reference Genomic (LRG) (#11863) with customhandlers: LRG Regions and LRG Transcripts.
LRGs are frozen reference sequences for a particular gene plus some
upstream and downstream sequence.  They are intended to provide a
stable coordinate system for gene annotations that won't change
with every new genome assembly, but can be mapped to each genome
assembly.  Since there is a lot of metadata associated with each
region, I made LRG Regions a bigBed 12 + with fields describing
mismatches and indels, so that PSL can be derived from the bigBed
and the original LRG sequence can be reconstructed using genome
assembly sequence and the mismatch/indel info.  hgTracks shows
differences and LRG insertions into the reference assembly using
the cds.c baseColor code.  (LRG deletions from the reference appear
as gaps, which we get for free with bed12 info).
For LRG Transcripts, I found the genePred codon-coloring code
inadequate for showing an insertion into hg19 (or even mismatches),
so instead of genePred I ended up using PSL + sequence, more like
the mRNA track representation and display.

diff --git src/hg/hgTracks/hgTracks.h src/hg/hgTracks/hgTracks.h
index 95ff496..6302aae 100644
--- src/hg/hgTracks/hgTracks.h
+++ src/hg/hgTracks/hgTracks.h
@@ -1343,30 +1343,33 @@
 
 void pgSnpMapItem(struct track *tg, struct hvGfx *hvg, void *item, char *itemName,
 		  char *mapItemName, int start, int end, int x, int y, int width, int height);
 /* create a special map box item with different pop-up statusLine with allele counts */
 
 void gvfMethods(struct track *tg);
 /* Load GVF variant data. */
 
 void messageLineMethods(struct track *track);
 /* Methods for drawing a single-height message line instead of track items,
  * e.g. if source was compiled without a necessary library. */
 
 void jRepeatMethods(struct track *track);
 /* construct track for detailed repeat visualization */
 
+void lrgMethods(struct track *tg);
+/* Locus Reference Genomic (bigBed 12 +) handlers. */
+
 void parentChildCartCleanup(struct track *trackList,struct cart *newCart,struct hash *oldVars);
 /* When composite/view settings changes, remove subtrack specific vis
    When superTrackChild is found and selected, shape superTrack to match. */
 
 void dontLoadItems(struct track *tg);
 /* No-op loadItems when we aren't going to try. */
 
 //#define REMOTE_TRACK_AJAX_CALLBACK
 #ifdef REMOTE_TRACK_AJAX_CALLBACK
 #define REMOTE_TRACK_HEIGHT (tl.fontHeight*2)
 
 boolean trackShouldUseAjaxRetrieval(struct track *track);
 /* Tracks with remote data sources should berendered via an ajax callback */
 
 #else//ifndef