18f572b767889300089237bcada2073f46cd06f5 markd Wed Feb 8 11:59:16 2017 -0800 added more label options and made more readable diff --git src/hg/inc/bigTransMap.h src/hg/inc/bigTransMap.h index 3a49a96..b4d0d3f 100644 --- src/hg/inc/bigTransMap.h +++ src/hg/inc/bigTransMap.h @@ -1,68 +1,69 @@ /* bigTransMap.h was originally generated by the autoSql program, which also * generated bigTransMap.c and bigTransMap.sql. This header links the database and * the RAM representation of objects. */ #ifndef BIGTRANSMAP_H #define BIGTRANSMAP_H -#define BIGTRANSMAP_NUM_COLS 39 +#define BIGTRANSMAP_NUM_COLS 40 extern char *bigTransMapCommaSepFieldNames; struct bigTransMap /* bigPsl derived pairwise alignment with additional information */ { struct bigTransMap *next; /* Next in singly linked list. */ char *chrom; /* Reference sequence chromosome or scaffold */ unsigned chromStart; /* Start position in chromosome */ unsigned chromEnd; /* End position in chromosome */ - char *name; /* Name or ID of item, ideally both human readable and unique */ + char *name; /* alignment Id */ unsigned score; /* Score (0-1000), faction identity * 1000 */ char strand[2]; /* + or - indicates whether the query aligns to the + or - strand on the reference */ unsigned thickStart; /* Start of where display should be thick (start codon) */ unsigned thickEnd; /* End of where display should be thick (stop codon) */ unsigned reserved; /* RGB value (use R,G,B string in input file) */ int blockCount; /* Number of blocks */ int *blockSizes; /* Comma separated list of block sizes */ int *chromStarts; /* Start positions relative to chromStart */ unsigned oChromStart; /* Start position in other chromosome */ unsigned oChromEnd; /* End position in other chromosome */ char oStrand[2]; /* + or -, - means that psl was reversed into BED-compatible coordinates */ unsigned oChromSize; /* Size of other chromosome. */ int *oChromStarts; /* Start positions relative to oChromStart or from oChromStart+oChromSize depending on strand */ char *oSequence; /* Sequence on other chrom (or edit list, or empty) */ char *oCDS; /* CDS in NCBI format */ unsigned chromSize; /* Size of target chromosome */ unsigned match; /* Number of bases matched. */ unsigned misMatch; /* Number of bases that don't match */ unsigned repMatch; /* Number of bases that match but are part of repeats */ unsigned nCount; /* Number of 'N' bases */ unsigned seqType; /* 0=empty, 1=nucleotide, 2=amino_acid */ - char *srcDb; /* source organism database names */ - char *srcChrom; /* source organism chromosome name */ + char *srcDb; /* source database */ + char *srcTransId; /* source transcript id */ + char *srcChrom; /* source chromosome */ unsigned srcChromStart; /* start position in source chromosome */ unsigned srcChromEnd; /* end position in source chromosome */ unsigned srcScore; /* source source (faction identity * 1000) */ unsigned srcAligned; /* fraction of source aligned (faction identity * 1000) */ char *geneName; /* gene name */ - char *geneId; /* gene identifier */ - char *geneType; /* type of gene */ - char *transcriptType; /* type of transcript */ + char *geneId; /* gene id */ + char *geneType; /* gene type */ + char *transcriptType; /* transcript type */ char *chainType; /* type of chains used for mapping */ - char *commonName; /* common organism name */ - char *scientificName; /* scientific organism name */ + char *commonName; /* common name */ + char *scientificName; /* scientific name */ char *orgAbbrev; /* organism abbreviation */ }; struct bigTransMap *bigTransMapLoad(char **row); /* Load a bigTransMap from row fetched with select * from bigTransMap * from database. Dispose of this with bigTransMapFree(). */ struct bigTransMap *bigTransMapLoadAll(char *fileName); /* Load all bigTransMap from whitespace-separated file. * Dispose of this with bigTransMapFreeList(). */ struct bigTransMap *bigTransMapLoadAllByChar(char *fileName, char chopper); /* Load all bigTransMap from chopper separated file. * Dispose of this with bigTransMapFreeList(). */