2c0f74b4fbfefc533d27bf3ccdc18e4ecfdecae7
angie
  Fri Oct 5 17:07:18 2012 -0700
Follow-up to ce70491d:1. Move hgTracks left-base-of-indel trimming code up to vcf.[ch] for
sharing w/hgc.
2. Correct chromStart in hgTracks mapBox links to hgc when we have
trimmed a left base.
3. In hgc, abbreviate long sequences (e.g. 40kb deletion) and show
trimmed left base in parentheses for consistency with VCF file (and
sometimes INFO fields that use left-inclusive coords/seqs).
4. In pgSnpFromVcfRecord, don't truncate long alleles because hgTracks
and hgc do their own abbreviating.

diff --git src/hg/hgTracks/hgTracks.h src/hg/hgTracks/hgTracks.h
index 13325bb..1cad17b 100644
--- src/hg/hgTracks/hgTracks.h
+++ src/hg/hgTracks/hgTracks.h
@@ -1316,30 +1316,34 @@
 #define SMALLDYBUF 64
 
 char *trackUrl(char *mapName, char *chromName);
 /* Return hgTrackUi url; chromName is optional. */
 
 void bedDetailCtMethods (struct track *tg, struct customTrack *ct);
 /* Load bedDetail track from custom tracks as bed or linked features */
 
 void pgSnpMethods (struct track *tg);
 /* Personal Genome SNPs: show two alleles with stacked color bars for base alleles and
  * (if available) allele counts in mouseover. */
 
 void pgSnpCtMethods (struct track *tg);
 /* Load pgSnp track from custom tracks */
 
+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 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