39fb35ef6bc3d14b837e5b6f523acc2f1cedd414 hartera Thu Feb 28 10:43:51 2013 -0800 Removed oldScore column as no longer needed and renamed oldIntronCount to alignGapCount in ucscRetroInfo table so change code and variable names to match. diff --git src/hg/inc/ucscRetroInfo.h src/hg/inc/ucscRetroInfo.h index 59d4ae3..5d2aa67 100644 --- src/hg/inc/ucscRetroInfo.h +++ src/hg/inc/ucscRetroInfo.h @@ -1,138 +1,138 @@ /* ucscRetroInfo.h was originally generated by the autoSql program, which also * generated ucscRetroInfo.c and ucscRetroInfo.sql. This header links the database and * the RAM representation of objects. */ #ifndef UCSCRETROINFO_H #define UCSCRETROINFO_H #include "jksql.h" #define UCSCRETROINFO_NUM_COLS 53 struct ucscRetroInfo /* Retrogenes based on cDNA alignments that are expressed or processed pseudogenes. */ { struct ucscRetroInfo *next; /* Next in singly linked list. */ char *chrom; /* Reference sequence chromosome or scaffold col1 */ unsigned chromStart; /* pseudogene alignment start position col2 */ unsigned chromEnd; /* pseudogene alignment end position col3 */ char *name; /* Name of pseudogene col4 */ unsigned score; /* score of pseudogene with gene col5 */ char strand[3]; /* + or - */ unsigned thickStart; /* Start of where display should be thick (start codon) */ unsigned thickEnd; /* End of where display should be thick (stop codon) */ unsigned reserved; /* Always zero for now */ int blockCount; /* Number of blocks */ int *blockSizes; /* Comma separated list of block sizes */ int *chromStarts; /* Start positions relative to chromStart */ int retroExonCount; /* number of exons in retroGene col13 */ int axtScore; /* blastz score, parent mrna aligned to pseudogene col14 */ char *type; /* type of evidence col15 */ char *gChrom; /* Chromosome name col16 */ int gStart; /* gene alignment start position col17 */ int gEnd; /* gene alignment end position col18 */ char gStrand[3]; /* strand of gene col19 */ unsigned parentSpliceCount; /* # of splice sites in parent gene col20 */ unsigned geneOverlap; /* bases overlapping col21 */ unsigned polyA; /* count of As in polyA col22 */ int polyAstart; /* start of polyA, relative to end of pseudogene col23 */ int exonCover; /* number of exons in Gene covered col24 */ unsigned intronCount; /* number of introns in pseudogene col25 */ unsigned bestAliCount; /* number of good mrnas aligning col26 */ unsigned matches; /* matches + repMatches col27 */ unsigned qSize; /* aligning bases in pseudogene col28 */ unsigned qEnd; /* end of cdna alignment col29 */ unsigned tReps; /* repeats in gene col30 */ unsigned coverage; /* % of bases that align to gene col31 */ int label; /* 1=pseudogene,-1 not pseudogene -2 expressed retroGene col32 */ unsigned milliBad; /* milliBad score, pseudogene aligned to genome col33 */ - unsigned oldScore; /* another heuristic col34 */ - int oldIntronCount; /* old simple intron count col35 */ - int processedIntrons; /* count of introns removed via retrotransposition col36 */ - int conservedSpliceSites; /* conserved splice site count col37 */ - int maxOverlap; /* largest overlap with another mrna col38 */ - char *refSeq; /* Name of closest regSeq to gene col39 */ - int rStart; /* refSeq alignment start position col40 */ - int rEnd; /* refSeq alignment end position col41 */ - char *mgc; /* Name of closest mgc to gene col42 */ - int mStart; /* mgc alignment start position col43 */ - int mEnd; /* mgc alignment end position col44 */ - char *kgName; /* Name of closest knownGene to gene col45 */ - int kStart; /* kg alignment start position col46 */ - int kEnd; /* kg alignment end position col47 */ - char *overName; /* name of overlapping mrna col48 */ - int overStart; /* overlapping mrna start position col49 */ - int overExonCover; /* count of overlapping mrna exons col50 */ - char overStrand[3]; /* strand of overlapping mrna col51 */ - float posConf; /* pvalue for positive col52 */ - unsigned polyAlen; /* length of polyA col53 */ +/* unsigned oldScore; */ /* another heuristic col34 */ + int alignGapCount; /* old simple intron count col34 */ + int processedIntrons; /* count of introns removed via retrotransposition col35 */ + int conservedSpliceSites; /* conserved splice site count col36 */ + int maxOverlap; /* largest overlap with another mrna col37 */ + char *refSeq; /* Name of closest regSeq to gene col38 */ + int rStart; /* refSeq alignment start position col39 */ + int rEnd; /* refSeq alignment end position col40 */ + char *mgc; /* Name of closest mgc to gene col41 */ + int mStart; /* mgc alignment start position col42 */ + int mEnd; /* mgc alignment end position col43 */ + char *kgName; /* Name of closest knownGene to gene col44 */ + int kStart; /* kg alignment start position col45 */ + int kEnd; /* kg alignment end position col46 */ + char *overName; /* name of overlapping mrna col47 */ + int overStart; /* overlapping mrna start position col48 */ + int overExonCover; /* count of overlapping mrna exons col49 */ + char overStrand[3]; /* strand of overlapping mrna col50 */ + float posConf; /* pvalue for positive col51 */ + unsigned polyAlen; /* length of polyA col52 */ }; struct ucscRetroInfo *ucscRetroInfoLoadByQuery(struct sqlConnection *conn, char *query); /* Load all ucscRetroInfo from table that satisfy the query given. * Where query is of the form 'select * from example where something=something' * or 'select example.* from example, anotherTable where example.something = * anotherTable.something'. * Dispose of this with ucscRetroInfoFreeList(). */ void ucscRetroInfoSaveToDb(struct sqlConnection *conn, struct ucscRetroInfo *el, char *tableName, int updateSize); /* Save ucscRetroInfo as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. Note that strings must be escaped to allow insertion into the database. * For example "autosql's features include" --> "autosql\'s features include" * If worried about this use ucscRetroInfoSaveToDbEscaped() */ void ucscRetroInfoSaveToDbEscaped(struct sqlConnection *conn, struct ucscRetroInfo *el, char *tableName, int updateSize); /* Save ucscRetroInfo as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size. * of a string that would contain the entire query. Automatically * escapes all simple strings (not arrays of string) but may be slower than ucscRetroInfoSaveToDb(). * For example automatically copies and converts: * "autosql's features include" --> "autosql\'s features include" * before inserting into database. */ struct ucscRetroInfo *ucscRetroInfoLoad(char **row); /* Load a ucscRetroInfo from row fetched with select * from ucscRetroInfo * from database. Dispose of this with ucscRetroInfoFree(). */ struct ucscRetroInfo *ucscRetroInfoLoadAll(char *fileName); /* Load all ucscRetroInfo from whitespace-separated file. * Dispose of this with ucscRetroInfoFreeList(). */ struct ucscRetroInfo *ucscRetroInfoLoadAllByChar(char *fileName, char chopper); /* Load all ucscRetroInfo from chopper separated file. * Dispose of this with ucscRetroInfoFreeList(). */ #define ucscRetroInfoLoadAllByTab(a) ucscRetroInfoLoadAllByChar(a, '\t'); /* Load all ucscRetroInfo from tab separated file. * Dispose of this with ucscRetroInfoFreeList(). */ struct ucscRetroInfo *ucscRetroInfoCommaIn(char **pS, struct ucscRetroInfo *ret); /* Create a ucscRetroInfo out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new ucscRetroInfo */ void ucscRetroInfoFree(struct ucscRetroInfo **pEl); /* Free a single dynamically allocated ucscRetroInfo such as created * with ucscRetroInfoLoad(). */ void ucscRetroInfoFreeList(struct ucscRetroInfo **pList); /* Free a list of dynamically allocated ucscRetroInfo's */ void ucscRetroInfoOutput(struct ucscRetroInfo *el, FILE *f, char sep, char lastSep); /* Print out ucscRetroInfo. Separate fields with sep. Follow last field with lastSep. */ #define ucscRetroInfoTabOut(el,f) ucscRetroInfoOutput(el,f,'\t','\n'); /* Print out ucscRetroInfo as a line in a tab-separated file. */ #define ucscRetroInfoCommaOut(el,f) ucscRetroInfoOutput(el,f,',',','); /* Print out ucscRetroInfo as a comma separated list including final comma. */ /* -------------------------------- End autoSql Generated Code -------------------------------- */ struct ucscRetroInfo *ucscRetroInfoQuery(struct sqlConnection *conn, char *table, char *mappedId); /* load a single retro object for an mapped id from a table or error if not found */ #endif /* UCSCRETROINFO_H */