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.sql src/hg/lib/samAlignment.sql
index 0899148..21c1a26 100644
--- src/hg/lib/samAlignment.sql
+++ src/hg/lib/samAlignment.sql
@@ -1,21 +1,21 @@
 # samAlignment.sql was originally generated by the autoSql program, which also 
 # generated samAlignment.c and samAlignment.h.  This creates the database representation of
 # an object which can be loaded and saved from RAM in a fairly 
 # automatic way.
 
-#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.
 CREATE TABLE samAlignment (
     qName varchar(255) not null,	# Query template name - name of a read
     flag smallint unsigned not null,	# Flags.  0x10 set for reverse complement.  See SAM docs for others.
     rName varchar(255) not null,	# Reference sequence name (often a chromosome)
     pos int unsigned not null,	# 1 based position
     mapQ tinyint unsigned not null,	# Mapping quality 0-255, 255 is best
     cigar varchar(255) not null,	# CIGAR encoded alignment string.
     rNext varchar(255) not null,	# Ref sequence for next (mate) read. '=' if same as rName, '*' if no mate
     pNext int not null,	# Position (1-based) of next (mate) sequence. May be -1 or 0 if no mate
     tLen int not null,	# Size of DNA template for mated pairs.  -size for one of mate pairs
     seq varchar(255) not null,	# Query template sequence
     qual varchar(255) not null,	# ASCII of Phred-scaled base QUALity+33.  Just '*' if no quality scores
     tagTypeVals varchar(255) not null,	# Tab-delimited list of tag:type:value optional extra fields
               #Indices
     PRIMARY KEY(qName)