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 @@ -1,72 +1,72 @@ /* 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 */ }; void samAlignmentStaticLoad(char **row, struct samAlignment *ret); /* Load a row from samAlignment table into ret. The contents of ret will * be replaced at the next call to this function. */ struct samAlignment *samAlignmentLoad(char **row); /* Load a samAlignment from row fetched with select * from samAlignment * from database. Dispose of this with samAlignmentFree(). */ struct samAlignment *samAlignmentLoadAll(char *fileName); /* Load all samAlignment from whitespace-separated file. * Dispose of this with samAlignmentFreeList(). */ struct samAlignment *samAlignmentLoadAllByChar(char *fileName, char chopper); /* Load all samAlignment from chopper separated file. * Dispose of this with samAlignmentFreeList(). */ #define samAlignmentLoadAllByTab(a) samAlignmentLoadAllByChar(a, '\t'); /* Load all samAlignment from tab separated file. * Dispose of this with samAlignmentFreeList(). */ struct samAlignment *samAlignmentCommaIn(char **pS, struct samAlignment *ret); /* Create a samAlignment out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new samAlignment */ void samAlignmentFree(struct samAlignment **pEl); /* Free a single dynamically allocated samAlignment such as created * with samAlignmentLoad(). */ void samAlignmentFreeList(struct samAlignment **pList); /* Free a list of dynamically allocated samAlignment's */ void samAlignmentOutput(struct samAlignment *el, FILE *f, char sep, char lastSep); /* Print out samAlignment. Separate fields with sep. Follow last field with lastSep. */ #define samAlignmentTabOut(el,f) samAlignmentOutput(el,f,'\t','\n'); /* Print out samAlignment as a line in a tab-separated file. */ #define samAlignmentCommaOut(el,f) samAlignmentOutput(el,f,',',','); /* Print out samAlignment as a comma separated list including final comma. */ /* -------------------------------- End autoSql Generated Code -------------------------------- */ #endif /* SAMALIGNMENT_H */