e70152e44cc66cc599ff6b699eb8adc07f3e656a kent Sat May 24 21:09:34 2014 -0700 Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment. diff --git src/hg/inc/snp125.h src/hg/inc/snp125.h index dc9487a..eb09b2c 100644 --- src/hg/inc/snp125.h +++ src/hg/inc/snp125.h @@ -1,121 +1,124 @@ /* 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. */ +/* Copyright (C) 2011 The Regents of the University of California + * See README in this or parent directory for licensing information. */ + #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 */ int snpVersion(char *track); /* If track starts with snpNNN where NNN is 125 or later, return the number; * otherwise return 0. */ #endif /* SNP125_H */