src/hg/makeDb/trackDb/README 1.71

Index: src/hg/makeDb/trackDb/README
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/trackDb/README,v
retrieving revision 1.70
retrieving revision 1.71
diff -b -B -U 4 -r1.70 -r1.71
--- src/hg/makeDb/trackDb/README	9 May 2009 00:24:47 -0000	1.70
+++ src/hg/makeDb/trackDb/README	20 May 2009 22:58:26 -0000	1.71
@@ -59,11 +59,12 @@
 trackDb.ra file is the type field.  Here's an explanation
 of that field.  Explanations of several other less-than-obvious
 fields follow.
 
-Currently there are fourteen different track types:
+Currently there are seventeen different track types:
 axt, bed, chain, clonePos, ctgPos, expRatio, genePred,
-maf, netAlign, psl, rmsk, sample, wigMaf and wig
+maf, netAlign, psl, rmsk, sample, wigMaf, wig, bedGraph, 
+chromGraph, bigBed
 
 	(notation: <angle brackets> indicate required field,
 		[square brackets] indicate optional field)
 
@@ -241,8 +242,11 @@
        linesAt <val1,val2,...> # Default is none
                             # If present labeled horizontal lines will be drawn
 			    # at the given values in full mode.
 
+17. type bigBed
+   Need description here
+
 If something lacks a type field it needs to have custom
 display routines.   You can remove a track from the
 browser by removing it from the .ra file and doing
 a make update.
@@ -388,17 +392,21 @@
       (such as genbank mRNA, EST etc) tracks.  Specifies where CDS coordinates
       can be found (if any) so that codons can be drawn when viewing a
       sufficiently small region.  If `table' is specified, an additional
       parameter of a table name, in cdsSpec format, is required.
-    o baseColorUseSequence {genbank,seq,extFile,none} - For genePred or psl
-      tracks.  Specifies where item sequence can be found (if any) so that
+    o baseColorUseSequence {genbank,seq,extFile,nameIsSequence,none}
+      - For genePred or psl tracks, or bed/bigBed tracks where the sequence 
+      is stored in the name column (see kent/src/hg/lib/encode/tagAlign.as).
+      Specifies where item sequence can be found (if any) so that
       item sequence, or differences from genomic sequence, can be drawn when
       viewing a sufficiently small region.  If `extFile' is specified, two
       additional parameters are required, the name of the seq table followed
       by the name of the extFile table to use in looking up the sequence.
-      These tables are loaded by hgLoadSeq.
-    o baseColorDefaults {genomicCodons,itemBases,itemCodons,diffBases,
+      These tables are loaded by hgLoadSeq. If 'nameIsSequence' is specified
+      then the name column can be interpreted as the sequence.
+    o baseColorDefault {genomicCodons,itemBases,itemCodons,diffBases,
       diffCodons,none} - For tracks with CDS and/or sequence information.
+      (See baseColorUseSequence above)
       Specifies the default drawing mode.  itemBases, itemCodons, diffBases
       and diffCodons are applicable only if the track has sequence
       (baseColorUseSequence).  genomicCodons, itemCodons and diffCodons
       are applicable only if the track has CDS info (baseColorUseCds).