0b52ad3ec2c6113bfdd692a58fee812b7dd0a7b2
kent
  Fri Feb 4 20:47:27 2011 -0800
Getting Table Browser to handle BAM files.  This is ready for testing by folks other than me now. Should work for both built-in BAM files and BAM files from track data hubs. I've tested it more though via the hubs. Works mostly by converting bam->sam->array-of-strings and then slotting into the same code bigBed processing uses.
diff --git src/hg/lib/samAlignment.as src/hg/lib/samAlignment.as
index 6af6bd4..3e1067b 100644
--- src/hg/lib/samAlignment.as
+++ src/hg/lib/samAlignment.as
@@ -1,16 +1,16 @@
 table samAlignment
-"The fields of a SAM short read alignment.  Follows conventions in SAM docs out of Sanger"
+"The fields of a SAM short read alignment, the text version of BAM."
     (
     string qName;	"Query template name - name of a read"
     ushort flag;	"Flags.  0x10 set for reverse complement.  See SAM docs for others."
     string rName;	"Reference sequence name (often a chromosome)"
     uint pos;		"1 based position"
     ubyte mapQ;		"Mapping quality 0-255, 255 is best"
     string cigar;	"CIGAR encoded alignment string."
     string rNext;	"Ref sequence for next (mate) read. '=' if same as rName, '*' if no mate"
     int pNext;		"Position (1-based) of next (mate) sequence. May be -1 or 0 if no mate"
     int tLen;	        "Size of DNA template for mated pairs.  -size for one of mate pairs"
     string seq;		"Query template sequence"
     string qual;	"ASCII of Phred-scaled base QUALity+33.  Just '*' if no quality scores"
     string tagTypeVals; "Tab-delimited list of tag:type:value optional extra fields"
     )