e70152e44cc66cc599ff6b699eb8adc07f3e656a
kent
  Sat May 24 21:09:34 2014 -0700
Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
diff --git src/hg/inc/rmskOut2.h src/hg/inc/rmskOut2.h
index d41dc4d..1accf8b 100644
--- src/hg/inc/rmskOut2.h
+++ src/hg/inc/rmskOut2.h
@@ -1,105 +1,108 @@
 /* rmskOut2.h was originally generated by the autoSql program, which also 
  * generated rmskOut2.c and rmskOut2.sql.  This header links the database and
  * the RAM representation of objects. */
 
+/* Copyright (C) 2013 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
+
 #ifndef RMSKOUT2_H
 #define RMSKOUT2_H
 
 #ifndef LINEFILE_H
 #include "linefile.h"
 #endif
 
 #define RMSKOUT2_NUM_COLS 16
 
 struct rmskOut2
 /* RepeatMasker .out record */
     {
     struct rmskOut2 *next;  /* Next in singly linked list. */
     unsigned swScore;	/* Smith Waterman alignment score */
     unsigned milliDiv;	/* Base mismatches in parts per thousand */
     unsigned milliDel;	/* Bases deleted in parts per thousand */
     unsigned milliIns;	/* Bases inserted in parts per thousand */
     char *genoName;	/* Genomic sequence name */
     unsigned genoStart;	/* Start in genomic sequence */
     unsigned genoEnd;	/* End in genomic sequence */
     int genoLeft;	/* -#bases after match in genomic sequence */
     char strand[2];	/* Relative orientation + or - */
     char *repName;	/* Name of repeat */
     char *repClass;	/* Class of repeat */
     char *repFamily;	/* Family of repeat */
     int repStart;	/* Start in repeat sequence - regardless of orient. */
     unsigned repEnd;	/* End in repeat sequence - reglardless of orient. */
     int repLeft;	/* -#bases after match in repeat sequence - regardless of orient */
     unsigned id;	/* The ID of the hit. Used to link related fragments */
     };
 
 void rmskOut2StaticLoad(char **row, struct rmskOut2 *ret);
 /* Load a row from rmskOut2 table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 
 struct rmskOut2 *rmskOut2Load(char **row);
 /* Load a rmskOut2 from row fetched with select * from rmskOut2
  * from database.  Dispose of this with rmskOut2Free(). */
 
 struct rmskOut2 *rmskOut2LoadAll(char *fileName);
 /* Load all rmskOut2 from whitespace-separated file.
  * Dispose of this with rmskOut2FreeList(). */
 
 struct rmskOut2 *rmskOut2LoadAllByChar(char *fileName, char chopper);
 /* Load all rmskOut2 from chopper separated file.
  * Dispose of this with rmskOut2FreeList(). */
 
 #define rmskOut2LoadAllByTab(a) rmskOut2LoadAllByChar(a, '\t');
 /* Load all rmskOut2 from tab separated file.
  * Dispose of this with rmskOut2FreeList(). */
 
 struct rmskOut2 *rmskOut2CommaIn(char **pS, struct rmskOut2 *ret);
 /* Create a rmskOut2 out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new rmskOut2 */
 
 void rmskOut2Free(struct rmskOut2 **pEl);
 /* Free a single dynamically allocated rmskOut2 such as created
  * with rmskOut2Load(). */
 
 void rmskOut2FreeList(struct rmskOut2 **pList);
 /* Free a list of dynamically allocated rmskOut2's */
 
 void rmskOut2Output(struct rmskOut2 *el, FILE *f, char sep, char lastSep);
 /* Print out rmskOut2.  Separate fields with sep. Follow last field with lastSep. */
 
 #define rmskOut2TabOut(el,f) rmskOut2Output(el,f,'\t','\n');
 /* Print out rmskOut2 as a line in a tab-separated file. */
 
 #define rmskOut2CommaOut(el,f) rmskOut2Output(el,f,',',',');
 /* Print out rmskOut2 as a comma separated list including final comma. */
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 struct rmskOut2 *rmskOut2Read(char *fileName);
 /* Read all records in .out file and return as list. */
 
 void rmskOut2OpenVerify(char *fileName, struct lineFile **retFile, boolean *retEmpty);
 /* Open repeat masker .out file and verify that it is good.
  * Set retEmpty if it has header characteristic of an empty file. */
 
 struct rmskOut2 *rmskOut2ReadNext(struct lineFile *lf);
 /* Read next record from repeat masker file.  Return NULL at EOF. */
 
 void rmskOut2WriteHead(FILE *f);
 /* Write out rmsk header lines. */
 
 void rmskOut2WriteOneOut(struct rmskOut2 *rmsk, FILE *f);
 /* Write one rmsk in .out format to file. */
 
 void rmskOut2WriteAllOut(char *fileName, struct rmskOut2 *rmskList);
 /* Write .out format file containing all in rmskList. */
 
 struct binKeeper *readRepeats2(char *chrom, char *rmskFileName, struct hash *tSizeHash);
 /* read all repeats for a chromosome of size size, returns results in binKeeper structure for fast query*/
 
 struct hash *readRepeatsAll2(char *sizeFileName, char *rmskDir);
 /* read all repeats for a all chromosomes getting sizes from sizeFileNmae , returns results in hash of binKeeper structure for fast query*/
 
 #endif /* RMSKOUT2_H */