433ed3d13a7fd8e09901031c223c54d5abc77178
braney
  Fri Apr 24 13:11:54 2020 -0700
add a flag to bedToBigBed to allow exons to have 1bp overlapping

diff --git src/inc/basicBed.h src/inc/basicBed.h
index 4aaf0ae..20389fc 100644
--- src/inc/basicBed.h
+++ src/inc/basicBed.h
@@ -309,18 +309,21 @@
 /* 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. */
 #endif /* BASICBED_H */