7f5b0b5cf3ed7efc0f9e84aa5bdcc097473c7584
kent
  Thu Feb 3 21:18:16 2011 -0800
Some preliminary work putting proper bam support in table browser.  Still quite a ways to go, but have implemented a way to get a list of alignments in 'sam' format out of a BAM.  This I think contains all the info.
diff --git src/hg/lib/samAlignment.as src/hg/lib/samAlignment.as
new file mode 100644
index 0000000..6af6bd4
--- /dev/null
+++ src/hg/lib/samAlignment.as
@@ -0,0 +1,16 @@
+table samAlignment
+"The fields of a SAM short read alignment.  Follows conventions in SAM docs out of Sanger"
+    (
+    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"
+    )