ea980437e9a5c43edab7e228fac5cb33c2494370
aamp
  Wed Dec 29 22:48:49 2010 -0800
Changes associated with the lift of the clonePos (coverage) track to hg19
diff --git src/hg/inc/clonePos.h src/hg/inc/clonePos.h
index 34311da..ddad7d4 100644
--- src/hg/inc/clonePos.h
+++ src/hg/inc/clonePos.h
@@ -1,52 +1,68 @@
 /* clonePos.h was originally generated by the autoSql program, which also 
- * generated clonePos.c and clonePos.sql.  This header links the database and the RAM 
- * representation of objects. */
+ * generated clonePos.c and clonePos.sql.  This header links the database and
+ * the RAM representation of objects. */
 
 #ifndef CLONEPOS_H
 #define CLONEPOS_H
 
+#define CLONEPOS_NUM_COLS 8
+
 struct clonePos
 /* A clone's position and other info. */
     {
     struct clonePos *next;  /* Next in singly linked list. */
-    char *name;	/* Name of clone including version. */
+    char *name;	/* Name of clone including version */
     unsigned seqSize;	/* base count not including gaps */
     unsigned char phase;	/* htg phase */
-    char *chrom;	/* Chromosome name */
+    char *chrom;	/* Reference sequence chromosome or scaffold */
     unsigned chromStart;	/* Start in chromosome */
     unsigned chromEnd;	/* End in chromosome */
     char stage[2];	/* F/D/P for finished/draft/predraft */
     char *faFile;	/* File with sequence. */
     };
 
 void clonePosStaticLoad(char **row, struct clonePos *ret);
 /* Load a row from clonePos table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 
 struct clonePos *clonePosLoad(char **row);
 /* Load a clonePos from row fetched with select * from clonePos
  * from database.  Dispose of this with clonePosFree(). */
 
+struct clonePos *clonePosLoadAll(char *fileName);
+/* Load all clonePos from whitespace-separated file.
+ * Dispose of this with clonePosFreeList(). */
+
+struct clonePos *clonePosLoadAllByChar(char *fileName, char chopper);
+/* Load all clonePos from chopper separated file.
+ * Dispose of this with clonePosFreeList(). */
+
+#define clonePosLoadAllByTab(a) clonePosLoadAllByChar(a, '\t');
+/* Load all clonePos from tab separated file.
+ * Dispose of this with clonePosFreeList(). */
+
 struct clonePos *clonePosCommaIn(char **pS, struct clonePos *ret);
 /* Create a clonePos out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new clonePos */
 
 void clonePosFree(struct clonePos **pEl);
 /* Free a single dynamically allocated clonePos such as created
  * with clonePosLoad(). */
 
 void clonePosFreeList(struct clonePos **pList);
 /* Free a list of dynamically allocated clonePos's */
 
 void clonePosOutput(struct clonePos *el, FILE *f, char sep, char lastSep);
 /* Print out clonePos.  Separate fields with sep. Follow last field with lastSep. */
 
 #define clonePosTabOut(el,f) clonePosOutput(el,f,'\t','\n');
 /* Print out clonePos as a line in a tab-separated file. */
 
 #define clonePosCommaOut(el,f) clonePosOutput(el,f,',',',');
 /* Print out clonePos as a comma separated list including final comma. */
 
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+
 #endif /* CLONEPOS_H */