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/hgTables/joining.c src/hg/hgTables/joining.c
index d06396e..0c288cc 100644
--- src/hg/hgTables/joining.c
+++ src/hg/hgTables/joining.c
@@ -334,30 +334,41 @@
 slFreeList(&fieldList);
 }
 
 static void makeBigBedOrderedCommaFieldList(struct joinerDtf *dtfList,
 	struct dyString *dy)
 /* Make comma-separated field list in same order as fields are in
  * big bed. */
 {
 struct sqlConnection *conn = hAllocConn(dtfList->database);
 struct slName *fieldList = bigBedGetFields(dtfList->table, conn);
 makeOrderedCommaFieldList(fieldList, dtfList, dy);
 slFreeList(&fieldList);
 hFreeConn(&conn);
 }
 
+static void makeBamOrderedCommaFieldList(struct joinerDtf *dtfList,
+	struct dyString *dy)
+/* Make comma-separated field list in same order as fields are in
+ * big bed. */
+{
+struct slName *fieldList = bamGetFields(dtfList->table);
+makeOrderedCommaFieldList(fieldList, dtfList, dy);
+slFreeList(&fieldList);
+}
+
+
 struct tableJoiner
 /* List of fields in a single table. */
     {
     struct tableJoiner *next;	/* Next in list. */
     char *database;		/* Database we're in.  Not alloced here. */
     char *table;		/* Table we're in.  Not alloced here. */
     struct joinerDtf *fieldList;	/* Fields. */
     struct slRef *keysOut;	/* Keys that connect to output.
                                  * Value is joinerPair. */
     boolean loaded;	/* If true is loaded. */
     };
 
 void tableJoinerFree(struct tableJoiner **pTf)
 /* Free up memory associated with tableJoiner. */
 {
@@ -976,30 +987,32 @@
 /* Do tab-separated output on selected fields, which may
  * or may not include multiple tables. */
 {
 struct joinerDtf *dtfList = NULL;
 struct joinerDtf *filterTables = NULL;
 boolean doJoin = joinRequired(primaryDb, primaryTable,
 			      fieldList, &dtfList, &filterTables);
 
 if (! doJoin)
     {
     struct sqlConnection *conn = hAllocConn(dtfList->database);
     struct dyString *dy = dyStringNew(0);
     
     if (isBigBed(database, dtfList->table, NULL, ctLookupName))
 	makeBigBedOrderedCommaFieldList(dtfList, dy);
+    else if (isBamTable(dtfList->table))
+        makeBamOrderedCommaFieldList(dtfList, dy);
     else if (isCustomTrack(dtfList->table))
         makeCtOrderedCommaFieldList(dtfList, dy);
     else
 	makeDbOrderedCommaFieldList(conn, dtfList->table, dtfList, dy);
     doTabOutTable(dtfList->database, dtfList->table, f, conn, dy->string);
     hFreeConn(&conn);
     }
 else
     {
     struct joiner *joiner = allJoiner;
     struct joinedTables *joined = joinedTablesCreate(joiner, 
     	primaryDb, primaryTable, dtfList, filterTables, 1000000, getRegions());
     if (f == NULL)
         joinedTablesTabOut(joined);
     else