dc4322ce21733176ef6b04f060f15c6a3c7c773a
hiram
  Thu Sep 29 12:09:25 2022 -0700
moving the reading of rmsk .out files into library function refs #29819

diff --git src/inc/repMask.h src/inc/repMask.h
index 6e25563..19ee71a 100644
--- src/inc/repMask.h
+++ src/inc/repMask.h
@@ -1,56 +1,59 @@
 /* repMask.h was originally generated by the autoSql program, which also 
  * generated repMask.c and repMask.sql.  This header links the database and the RAM 
  * representation of objects. */
 
 #ifndef REPMASK_H
 #define REPMASK_H
 
 struct repeatMaskOut
 /* Repeat Masker out format */
     {
     struct repeatMaskOut *next;  /* Next in singly linked list. */
     unsigned score;	/* Smith-Waterman score. */
     float percDiv;	/* Percentage base divergence. */
     float percDel;	/* Percentage deletions. */
     float percInc;	/* Percentage inserts. */
     char *qName;	/* Name of query. */
     int qStart;	/* Start query position. */
     int qEnd;	/* End query position. */
     char *qLeft;	/* Bases left in query. */
     char strand[2];	/* Query strand (+ or C) */
     char *rName;	/* Repeat name */
     char *rFamily;	/* Repeat name */
     char *rStart;	/* Start position in repeat. */
     unsigned rEnd;	/* End position in repeat. */
     char *rLeft;	/* Bases left in repeat. */
     };
 
 void repeatMaskOutStaticLoad(char **row, struct repeatMaskOut *ret);
 /* Load a row from repeatMaskOut table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 
 struct repeatMaskOut *repeatMaskOutLoad(char **row);
 /* Load a repeatMaskOut from row fetched with select * from repeatMaskOut
  * from database.  Dispose of this with repeatMaskOutFree(). */
 
 struct repeatMaskOut *repeatMaskOutCommaIn(char **pS);
 /* Create a repeatMaskOut out of a comma separated string. */
 
 void repeatMaskOutFree(struct repeatMaskOut **pEl);
 /* Free a single dynamically allocated repeatMaskOut such as created
  * with repeatMaskOutLoad(). */
 
 void repeatMaskOutFreeList(struct repeatMaskOut **pList);
 /* Free a list of dynamically allocated repeatMaskOut's */
 
 void repeatMaskOutOutput(struct repeatMaskOut *el, FILE *f, char sep, char lastSep);
 /* Print out repeatMaskOut.  Separate fields with sep. Follow last field with lastSep. */
 
 #define repeatMaskOutTabOut(el,f) repeatMaskOutOutput(el,f,'\t','\n');
 /* Print out repeatMaskOut as a line in a tab-separated file. */
 
 #define repeatMaskOutCommaOut(el,f) repeatMaskOutOutput(el,f,',',',');
 /* Print out repeatMaskOut as a comma separated list including final comma. */
 
+struct lineFile *rmskLineFileOpen(char *fileName);
+/* open a repeat masker .out file or die trying */
+
 #endif /* REPMASK_H */