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/inc/samAlignment.h src/hg/inc/samAlignment.h
index 8ef70d8..9375926 100644
--- src/hg/inc/samAlignment.h
+++ src/hg/inc/samAlignment.h
@@ -1,26 +1,26 @@
 /* samAlignment.h was originally generated by the autoSql program, which also 
  * generated samAlignment.c and samAlignment.sql.  This header links the database and
  * the RAM representation of objects. */
 
 #ifndef SAMALIGNMENT_H
 #define SAMALIGNMENT_H
 
 #define SAMALIGNMENT_NUM_COLS 12
 
 struct 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. */
     {
     struct samAlignment *next;  /* Next in singly linked list. */
     char *qName;	/* Query template name - name of a read */
     unsigned short flag;	/* Flags.  0x10 set for reverse complement.  See SAM docs for others. */
     char *rName;	/* Reference sequence name (often a chromosome) */
     unsigned pos;	/* 1 based position */
     unsigned char mapQ;	/* Mapping quality 0-255, 255 is best */
     char *cigar;	/* CIGAR encoded alignment string. */
     char *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 */
     char *seq;	/* Query template sequence */
     char *qual;	/* ASCII of Phred-scaled base QUALity+33.  Just '*' if no quality scores */
     char *tagTypeVals;	/* Tab-delimited list of tag:type:value optional extra fields */
     };