/* basicBed.h contains the basic interface to Browser Extensible Data (bed) files and tables. * The idea behind bed is that the first three fields are defined and required. * A total of 15 fields are defined, and the file can contain any number of these. * In addition after any number of defined fields there can be custom fields that * are not defined in the bed spec. * * There's additional bed-related code in src/hg/inc/bed.h. This module contains the * stuff that's independent of the database and other genomic structures. */ #ifndef BASICBED_H #define BASICBED_H #include "psl.h" #include "asParse.h" #include "memgfx.h" struct bed /* Browser extensible data */ { struct bed *next; /* Next in singly linked list. */ char *chrom; /* Human chromosome or FPC contig */ unsigned chromStart; /* Start position in chromosome */ unsigned chromEnd; /* End position in chromosome */ char *name; /* Name of item */ /* The following items are not loaded by the bedLoad routines. */ int score; /* Score - 0-1000 */ /* Should be uint but there are still some ct users with neg values, .as DOES say uint */ char strand[2]; /* + or -. */ unsigned thickStart; /* Start of where display should be thick (start codon for genes) */ unsigned thickEnd; /* End of where display should be thick (stop codon for genes) */ unsigned itemRgb; /* RGB 8 bits each */ unsigned blockCount; /* Number of blocks. */ int *blockSizes; /* Comma separated list of block sizes. */ int *chromStarts; /* Start positions inside chromosome. Relative to chromStart*/ int expCount; /* Experiment count */ int *expIds; /* Comma separated list of Experiment ids */ float *expScores; /* Comma separated list of Experiment scores. */ char *label; /* Label to use on element if bigBed. */ }; #define bedKnownFields 15 /* Maximum known fields in bed */ #define BB_MAX_CHROM_STRING 255 /* Maximum string length for chromosome length */ struct bed3 /* Browser extensible data - first three fields */ { struct bed3 *next; /* Next in singly linked list. */ char *chrom; /* Human chromosome or FPC contig */ unsigned chromStart; /* Start position in chromosome */ unsigned chromEnd; /* End position in chromosome */ }; struct bed3 *bed3New(char *chrom, int start, int end); /* Make new bed3. */ void bed3Free(struct bed3 **pBed); /* Free up bed3 */ void bed3FreeList(struct bed3 **pList); /* Free a list of dynamically allocated bed3's */ struct bed3 *bed3LoadAll(char *fileName); /* Load three columns from file as bed3. */ long long bed3TotalSize(struct bed3 *bedList); /* Return sum of chromEnd-chromStart. */ struct bed4 /* Browser extensible data - first four fields */ { struct bed4 *next; /* Next in singly linked list. */ char *chrom; /* Human chromosome or FPC contig */ unsigned chromStart; /* Start position in chromosome */ unsigned chromEnd; /* End position in chromosome */ char *name; /* Name of item */ }; struct bed4 *bed4New(char *chrom, int start, int end, char *name); /* Make new bed4. */ void bed4Free(struct bed4 **pBed); /* Free up bed4 */ void bed4FreeList(struct bed4 **pList); /* Free a list of dynamically allocated bed4's */ void bedStaticLoad(char **row, struct bed *ret); /* Load a row from bed table into ret. The contents of ret will * be replaced at the next call to this function. */ struct bed *bedLoad(char **row); /* Load a bed from row fetched with select * from bed * from database. Dispose of this with bedFree(). * This loads first four fields. */ struct bed *bedCommaIn(char **pS, struct bed *ret); /* Create a bed out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new bed */ void bedFree(struct bed **pEl); /* Free a single dynamically allocated bed such as created * with bedLoad(). */ void bedFreeList(struct bed **pList); /* Free a list of dynamically allocated bed's */ void bedOutput(struct bed *el, FILE *f, char sep, char lastSep); /* Print out bed. Separate fields with sep. Follow last field with lastSep. */ #define bedTabOut(el,f) bedOutput(el,f,'\t','\n'); /* Print out bed as a line in a tab-separated file. */ #define bedCommaOut(el,f) bedOutput(el,f,',',','); /* Print out bed as a comma separated list including final comma. */ /* --------------- End of AutoSQL generated code. --------------- */ int bedCmp(const void *va, const void *vb); /* Compare to sort based on chrom,chromStart. */ int bedCmpEnd(const void *va, const void *vb); /* Compare to sort based on chrom,chromEnd. */ int bedCmpScore(const void *va, const void *vb); /* Compare to sort based on score - lowest first. */ int bedCmpPlusScore(const void *va, const void *vb); /* Compare to sort based on chrom, chromStart and score - lowest first. */ int bedCmpSize(const void *va, const void *vb); /* Compare to sort based on size of element (end-start == size) */ int bedCmpChromStrandStart(const void *va, const void *vb); /* Compare to sort based on chrom,strand,chromStart. */ int bedCmpChromStrandStartName(const void *va, const void *vb); /* Compare to sort based on name, chrom,strand,chromStart. */ struct bedLine /* A line in a bed file with chromosome, start position parsed out. */ { struct bedLine *next; /* Next in list. */ char *chrom; /* Chromosome parsed out. */ int chromStart; /* Start position (still in rest of line). */ char *line; /* Rest of line. */ }; struct bedLine *bedLineNew(char *line); /* Create a new bedLine based on tab-separated string s. */ void bedLineFree(struct bedLine **pBl); /* Free up memory associated with bedLine. */ void bedLineFreeList(struct bedLine **pList); /* Free a list of dynamically allocated bedLine's */ int bedLineCmp(const void *va, const void *vb); /* Compare to sort based on chrom,chromStart. */ void bedSortFile(char *inFile, char *outFile); /* Sort a bed file (in place, overwrites old file. */ struct bed *bedLoad3(char **row); /* Load first three fields of bed. */ struct bed *bedLoad5(char **row); /* Load first five fields of bed. */ struct bed *bedLoad6(char **row); /* Load first six fields of bed. */ struct bed *bedLoad12(char **row); /* Load all 12 fields of bed. */ struct bed *bedLoadN(char *row[], int wordCount); /* Convert a row of strings to a bed. */ struct bed *bedLoadNAllChrom(char *fileName, int numFields, char* chrom); /* Load bed entries from a tab-separated file that have the given chrom. * Dispose of this with bedFreeList(). */ struct bed *bedLoadNAll(char *fileName, int numFields); /* Load all bed from a tab-separated file. * Dispose of this with bedFreeList(). */ struct bed *bedLoadAll(char *fileName); /* Determines how many fields are in a bedFile and load all beds from * a tab-separated file. Dispose of this with bedFreeList(). */ void bedLoadAllReturnFieldCount(char *fileName, struct bed **retList, int *retFieldCount); /* Load bed of unknown size and return number of fields as well as list of bed items. * Ensures that all lines in bed file have same field count. */ void bedLoadAllReturnFieldCountAndRgb(char *fileName, struct bed **retList, int *retFieldCount, boolean *retRgb); /* Load bed of unknown size and return number of fields as well as list of bed items. * Ensures that all lines in bed file have same field count. Also returns whether * column 9 is being used as RGB or not. */ void bedOutputN(struct bed *el, int wordCount, FILE *f, char sep, char lastSep); /* Write a bed of wordCount fields. */ void bedOutputNitemRgb(struct bed *el, int wordCount, FILE *f, char sep, char lastSep); /* Write a bed of wordCount fields, interpret column 9 as RGB. */ void bedOutFlexible(struct bed *el, int wordCount, FILE *f, char sep, char lastSep, boolean useItemRgb); /* Write a bed of wordCount fields, optionally interpreting field nine as R,G,B values. */ #define bedTabOutNitemRgb(el,wordCount, f) bedOutputNitemRgb(el,wordCount,f,'\t','\n') /* Print out bed as a line in a tab-separated file. Interpret column 9 as RGB */ #define bedTabOutN(el,wordCount, f) bedOutputN(el,wordCount,f,'\t','\n') /* Print out bed as a line in a tab-separated file. */ #define bedCommaOutN(el,wordCount, f) bedOutputN(el,wordCount,f,',',',') /* Print out bed as a comma separated list including final comma. */ int bedTotalBlockSize(struct bed *bed); /* Return total size of all blocks. */ int bedTotalThickBlockSize(struct bed *bed); /* Return total size of all thick blocks. */ int bedStartThinSize(struct bed *bed); /* Return total size of all blocks before thick part. */ int bedEndThinSize(struct bed *bed); /* Return total size of all blocks after thick part. */ int bedBlockSizeInRange(struct bed *bed, int rangeStart, int rangeEnd); /* Get size of all parts of all exons between rangeStart and rangeEnd. */ struct bed *bedFromPsl(struct psl *psl); /* Convert a single psl to a bed structure */ void makeItBed12(struct bed *bedList, int numFields); /* If it's less than bed 12, make it bed 12. The numFields */ /* param is for how many fields the bed *currently* has. */ struct bed *cloneBed(struct bed *bed); /* Make an all-newly-allocated copy of a single bed record. */ struct bed *cloneBedList(struct bed *bed); /* Make an all-newly-allocated list copied from bed. */ struct bed *bedListNextDifferentChrom(struct bed *bedList); /* Return next bed in list that is from a different chrom than the start of the list. */ struct bed *lmCloneBed(struct bed *bed, struct lm *lm); /* Make a copy of bed in local memory. */ struct bed *bedCommaInN(char **pS, struct bed *ret, int fieldCount); /* Create a bed out of a comma separated string looking for fieldCount * fields. This will fill in ret if non-null, otherwise will return a * new bed */ struct hash *readBedToBinKeeper(char *sizeFileName, char *bedFileName, int wordCount); /* Read a list of beds and return results in hash of binKeeper structure for fast query * See also bedsIntoKeeperHash, which takes the beds read into a list already, but * dispenses with the need for the sizeFile. */ unsigned int bedParseRgb(char *itemRgb); /* parse a string: "r,g,b" with optional ",a" into three or four unsigned * char values returned as 32 bit number, or -1 for failure. Byte order * has alpha in the highest-order byte, then r, then g, then b in the * lowest-order byte. This is a "bed" concept of an unsigned color, * which may not match the way the graphics libraries handle color bytes. */ unsigned int bedParseColor(char *colorSpec); /* Parse an HTML color string, a string of 3 or 4 comma-sep unsigned color values 0-255, * or a 6-digit hex string preceded by #. * O/w return unsigned integer value. Return -1 on error */ struct rgbColor bedColorToRgb(unsigned int color); /* Convert from the bed concept of a color uint, where the rgb bits * are always in the same order, to a memgfx color structure. */ Color bedColorToGfxColor(unsigned int color); /* Convert from the bed concept of a color uint, where the rgb bits * are always in the same order, to a memgfx concept of color where * the bit order depends on architecture. Assumes that a bed color * will never have 0 alpha. */ void bedOutputRgb(FILE *f, unsigned int color); /* Output a string: "r,g,b" for 24 bit number */ long long bedTotalSize(struct bed *bedList); /* Add together sizes of all beds in list. */ int bedSameStrandOverlap(struct bed *a, struct bed *b); /* Return amount of block-level overlap on same strand between a and b */ boolean bedExactMatch(struct bed *oldBed, struct bed *newBed); /* Return TRUE if it's an exact match. */ boolean bedCompatibleExtension(struct bed *oldBed, struct bed *newBed); /* Return TRUE if newBed is a compatible extension of oldBed, meaning * all internal exons and all introns of old bed are contained, in the * same order in the new bed. */ struct rbTree *bedToRangeTree(struct bed *bed); /* Convert bed into a range tree. */ void bedIntoRangeTree(struct bed *bed, struct rbTree *rangeTree); /* Add all blocks in bed to range tree. For beds without blocks, * add entire bed. */ int bedRangeTreeOverlap(struct bed *bed, struct rbTree *rangeTree); /* Return number of bases bed overlaps with rangeTree. */ struct bed *bedThickOnly(struct bed *in); /* Return a bed that only has the thick part. (Which is usually the CDS). */ struct bed *bedThickOnlyList(struct bed *inList); /* Return a list of beds that only are the thick part of input. */ char *bedAsDef(int bedFieldCount, int totalFieldCount); /* Return an autoSql definition for a bed of given number of fields. * Normally totalFieldCount is equal to bedFieldCount. If there are extra * fields they are just given the names field16, field17, etc and type string. */ boolean asCompareObjAgainstStandardBed(struct asObject *asYours, int numColumnsToCheck, boolean abortOnDifference); /* Compare user's .as object asYours to the standard BED. * abortOnDifference specifies whether to warn or abort if they differ within the first numColumnsToCheck columns. * Returns TRUE if they match. */ void loadAndValidateBed(char *row[], int wordCount, int fieldCount, struct lineFile *lf, struct bed * bed, struct asObject *as, boolean isCt); /* Convert a row of strings to a bed and validate the contents. Abort with message if invalid data. Optionally validate bedPlus via asObject. */ void loadAndValidateBedExt(char *row[], int bedFieldCount, int fieldCount, struct lineFile *lf, struct bed * bed, struct asObject *as, boolean isCt, boolean allow1bpOverlap); /* Convert a row of strings to a bed and validate the contents. Abort with message if invalid data. Optionally validate bedPlus via asObject. Possibly allow one base overlap in exons */ int itemRgbColumn(char *column9); /* Convert color specification to internal format. */ #define BAD_BLOCKS "BED blocks must span chromStart to chromEnd. (chromStart + blockStarts[last] + blockSizes[last]) must equal chromEnd." #endif /* BASICBED_H */