dbb7cbfd254794919a8e491cc3d3eb7c6009ba15 angie Tue Jan 25 14:58:05 2011 -0800 Track #1684 (SNPs 132 (dbSNP)): Added new coloring and filtering optionsfor new columns exceptions and bitfields. Fixed remaining hardcoded cart var names to use track name, keeping backwards compat with old sessions. Lots of refactoring -- got rid of snp125Extended business (mostly so I wouldn't have to make a snp132Extended); color is stored in snp->weight now, and extraName stuff overwrites name. Added new color-sorting in squish mode so the most interesting SNPs appear at the top. Also added new trackDb var defaultMaxWeight for the NonUnique subset (so its items aren't invisible by default). diff --git src/hg/inc/snp125.h src/hg/inc/snp125.h index bb3451d..dc9487a 100644 --- src/hg/inc/snp125.h +++ src/hg/inc/snp125.h @@ -1,126 +1,121 @@ /* snp125.h was originally generated by the autoSql program, which also * generated snp125.c and snp125.sql. This header links the database and * the RAM representation of objects. */ #ifndef SNP125_H #define SNP125_H #include "memgfx.h" #define SNP125_NUM_COLS 17 struct snp125 /* Polymorphism data from dbSnp database or genotyping arrays */ { struct snp125 *next; /* Next in singly linked list. */ char *chrom; /* Reference sequence chromosome or scaffold */ unsigned chromStart; /* Start position in chrom */ unsigned chromEnd; /* End position in chrom */ char *name; /* Reference SNP identifier or Affy SNP name */ unsigned score; /* Not used */ char *strand; /* Which DNA strand contains the observed alleles */ char *refNCBI; /* Reference genomic from dbSNP */ char *refUCSC; /* Reference genomic from nib lookup */ char *observed; /* The sequences of the observed alleles from rs-fasta files */ char *molType; /* Sample type from exemplar ss */ char *class; /* The class of variant (simple, insertion, deletion, range, etc.) */ char *valid; /* The validation status of the SNP */ float avHet; /* The average heterozygosity from all observations */ float avHetSE; /* The Standard Error for the average heterozygosity */ char *func; /* The functional category of the SNP (coding-synon, coding-nonsynon, intron, etc.) */ char *locType; /* How the variant affects the reference sequence */ unsigned weight; /* The quality of the alignment */ }; void snp125StaticLoad(char **row, struct snp125 *ret); /* Load a row from snp125 table into ret. The contents of ret will * be replaced at the next call to this function. */ struct snp125 *snp125Load(char **row); /* Load a snp125 from row fetched with select * from snp125 * from database. Dispose of this with snp125Free(). */ struct snp125 *snp125LoadAll(char *fileName); /* Load all snp125 from whitespace-separated file. * Dispose of this with snp125FreeList(). */ struct snp125 *snp125LoadAllByChar(char *fileName, char chopper); /* Load all snp125 from chopper separated file. * Dispose of this with snp125FreeList(). */ #define snp125LoadAllByTab(a) snp125LoadAllByChar(a, '\t'); /* Load all snp125 from tab separated file. * Dispose of this with snp125FreeList(). */ struct snp125 *snp125CommaIn(char **pS, struct snp125 *ret); /* Create a snp125 out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new snp125 */ void snp125Free(struct snp125 **pEl); /* Free a single dynamically allocated snp125 such as created * with snp125Load(). */ void snp125FreeList(struct snp125 **pList); /* Free a list of dynamically allocated snp125's */ void snp125Output(struct snp125 *el, FILE *f, char sep, char lastSep); /* Print out snp125. Separate fields with sep. Follow last field with lastSep. */ #define snp125TabOut(el,f) snp125Output(el,f,'\t','\n'); /* Print out snp125 as a line in a tab-separated file. */ #define snp125CommaOut(el,f) snp125Output(el,f,',',','); /* Print out snp125 as a comma separated list including final comma. */ /* -------------------------------- End autoSql Generated Code -------------------------------- */ void snp125TableCreate(struct sqlConnection *conn, char *tableName); /* create a snp125 table */ int snp125Cmp(const void *va, const void *vb); struct snp125Extended /* Polymorphism data from dbSnp database or genotyping arrays */ { struct snp125Extended *next; /* Next in singly linked list. */ char *chrom; /* Reference sequence chromosome or scaffold */ unsigned chromStart; /* Start position in chrom */ unsigned chromEnd; /* End position in chrom */ char *name; /* Reference SNP identifier or Affy SNP name */ unsigned score; /* Not used */ char *strand; /* Which DNA strand contains the observed alleles */ char *refNCBI; /* Reference genomic from dbSNP */ char *refUCSC; /* Reference genomic from nib lookup */ char *observed; /* The sequences of the observed alleles from rs-fasta files */ char *molType; /* Sample type from exemplar ss */ char *class; /* The class of variant (simple, insertion, deletion, range, etc.) */ char *valid; /* The validation status of the SNP */ float avHet; /* The average heterozygosity from all observations */ float avHetSE; /* The Standard Error for the average heterozygosity */ char *func; /* The functional category of the SNP (coding-synon, coding-nonsynon, intron, etc.) */ char *locType; /* How the variant affects the reference sequence */ unsigned weight; /* The quality of the alignment */ /* extra fields */ char *nameExtra; /* additional text to be drawn with name in image */ Color color; /* color for drawing in hgTracks */ }; struct snp125Extended *snpExtendedLoad(char **row); /* Load a snp125 from row fetched with select * from snp125 from * database. Additional fields are for run-time drawing and * calculations */ -struct snp125Extended *snp125ExtendedLoad(char **row); -/* Load a snp125 from row fetched with select * from snp125 from - * database. Additional fields are for run-time drawing and - * calculations */ - int snpVersion(char *track); /* If track starts with snpNNN where NNN is 125 or later, return the number; * otherwise return 0. */ #endif /* SNP125_H */