54406b80d5d435970989acff7b22dd6146c6b411
braney
  Sat Jan 22 15:24:59 2022 -0800
adding chrom alias support to big files

diff --git src/inc/bigBed.h src/inc/bigBed.h
index 5f151b3..e45945f 100644
--- src/inc/bigBed.h
+++ src/inc/bigBed.h
@@ -47,30 +47,33 @@
 struct bigBedInterval
 /* A partially parsed out bed record plus some extra fields.  Use this directly
  * or convert it to an array of characters with bigBedIntervalToRow. */
     {
     struct bigBedInterval *next;	/* Next in list. */
     bits32 start, end;		/* Range inside chromosome - half open zero based. */
     char *rest;			/* Rest of line. May be NULL*/
     bits32 chromId;             /* ID of chromosome.  */
     };
 
 /*** Routines to open & close bigBed files, and to do chromosome range queries on them. ***/
 
 struct bbiFile *bigBedFileOpen(char *fileName);
 /* Open up big bed file.   Free this up with bbiFileClose. */
 
+struct bbiFile *bigBedFileOpenAlias(char *fileName, struct hash *aliasHash);
+/* Open up big bed file with chrom alias hash. */
+
 #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,