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/lib/hdb.c src/hg/lib/hdb.c
index 4c5817c..67b4cb3 100644
--- src/hg/lib/hdb.c
+++ src/hg/lib/hdb.c
@@ -4703,30 +4703,42 @@
 struct hash *hChromSizeHash(char *db)
 /* Get hash of chromosome sizes for database.  Just hashFree it when done. */
 {
 struct sqlConnection *conn = sqlConnect(db);
 struct sqlResult *sr;
 char **row;
 struct hash *hash = newHash(0);
 sr = sqlGetResult(conn, "NOSQLINJ select chrom,size from chromInfo");
 while ((row = sqlNextRow(sr)) != NULL)
     hashAddInt(hash, row[0], sqlUnsigned(row[1]));
 sqlFreeResult(&sr);
 sqlDisconnect(&conn);
 return hash;
 }
 
+struct hash *hChromSizeHashFromFile(char *fileName)
+/* Get hash of chromosome sizes from 2- or 3-column chrom.sizes file. hashFree when done. */
+{
+struct hash *chromHash = hashNew(0);
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[2];
+while (lineFileRow(lf, row))
+    hashAddInt(chromHash, row[0], sqlUnsigned(row[1]));
+lineFileClose(&lf);
+return chromHash;
+}
+
 struct slName *hChromList(char *db)
 /* Get the list of chrom names from the database's chromInfo table. */
 {
 struct sqlConnection *conn = hAllocConn(db);
 struct slName *list = sqlQuickList(conn, "NOSQLINJ select chrom from chromInfo");
 hFreeConn(&conn);
 return list;
 }
 
 char *hgDirForOrg(char *org)
 /* Make directory name from organism name - getting
  * rid of dots and spaces. */
 {
 org = cloneString(org);
 stripChar(org, '.');