060ada2535fca719656219c1214a3e1c16490693
tdreszer
  Wed Nov 9 16:06:41 2011 -0800
Moved as code in hgTables down to lib and access it from hgc and hgTrackUi.  This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
diff --git src/inc/bigBed.h src/inc/bigBed.h
index 8ef3ece..8aee277 100644
--- src/inc/bigBed.h
+++ src/inc/bigBed.h
@@ -1,75 +1,83 @@
 /* bigBed - interface to binary file with bed-style values (that is a bunch of
  * possibly overlapping regions.
  *
  * This shares a lot with the bigWig module. */
 
 #ifndef BIGBED_H
 #define BIGBED_H
 
+#include "asParse.h"
+
 #ifndef BBIFILE
 #include "bbiFile.h"
 #endif
 
 struct bigBedInterval
 /* A partially parsed out bed record plus some extra fields. */
     {
     struct bigBedInterval *next;	/* Next in list. */
     bits32 start, end;		/* Range inside chromosome - half open zero based. */
     char *rest;			/* Rest of line. May be NULL*/
     };
 
 struct ppBed
 /* A partially parsed out bed record plus some extra fields. */
     {
     struct ppBed *next;	/* Next in list. */
     char *chrom;		/* Chromosome name (not allocated here) */
     bits32 start, end;		/* Range inside chromosome - half open zero based. */
     char *rest;			/* The rest of the bed. */
     bits64 fileOffset;		/* File offset. */
     bits32 chromId;		/* Chromosome ID. */
     };
 
 struct bbiFile *bigBedFileOpen(char *fileName);
 /* Open up big bed file.   Free this up with bbiFileClose. */
 
 #define bigBedFileClose(a) bbiFileClose(a)
 
 struct bigBedInterval *bigBedIntervalQuery(struct bbiFile *bbi, char *chrom, 
 	bits32 start, bits32 end, int maxItems, struct lm *lm);
 /* Get data for interval.  Return list allocated out of lm.  Set maxItems to maximum
  * number of items to return, or to 0 for all items. */
 
 int bigBedIntervalToRow(struct bigBedInterval *interval, char *chrom, char *startBuf, char *endBuf,
 	char **row, int rowSize);
 /* Convert bigBedInterval into an array of chars equivalent to what you'd get by
  * parsing the bed file. The startBuf and endBuf are used to hold the ascii representation of
  * start and end.  Note that the interval->rest string will have zeroes inserted as a side effect. 
  * Returns number of fields in row.  */
 
 boolean bigBedSummaryArray(struct bbiFile *bbi, char *chrom, bits32 start, bits32 end,
 	enum bbiSummaryType summaryType, int summarySize, double *summaryValues);
 /* Fill in summaryValues with  data from indicated chromosome range in bigBed file.
  * Be sure to initialize summaryValues to a default value, which will not be touched
  * for regions without data in file.  (Generally you want the default value to either
  * be 0.0 or nan("") depending on the application.)  Returns FALSE if no data
  * at that position. */
 
 boolean bigBedSummaryArrayExtended(struct bbiFile *bbi, char *chrom, bits32 start, bits32 end,
 	int summarySize, struct bbiSummaryElement *summary);
 /* Get extended summary information for summarySize evenely spaced elements into
  * the summary array. */
 
 bits64 bigBedItemCount(struct bbiFile *bbi);
 /* Return total items in file. */
 
 char *bigBedAutoSqlText(struct bbiFile *bbi);
 /* Get autoSql text if any associated with file.  Do a freeMem of this when done. */
 
 struct asObject *bigBedAs(struct bbiFile *bbi);
 /* Get autoSql object definition if any associated with file. */
 
+struct asObject *bigBedAsOrDefault(struct bbiFile *bbi);
+// Get asObject associated with bigBed - if none exists in file make it up from field counts.
+
+struct asObject *bigBedFileAsObjOrDefault(char *fileName);
+// Get asObject associated with bigBed file, or the default.
+
 boolean bigBedFileCheckSigs(char *fileName);
 /* check file signatures at beginning and end of file */
 
 #endif /* BIGBED_H */