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/genomicSuperDups.h src/hg/inc/genomicSuperDups.h
index e5e76a0..b1fe588 100644
--- src/hg/inc/genomicSuperDups.h
+++ src/hg/inc/genomicSuperDups.h
@@ -1,82 +1,85 @@
 /* genomicSuperDups.h was originally generated by the autoSql program, which also 
  * generated genomicSuperDups.c and genomicSuperDups.sql.  This header links the database and
  * the RAM representation of objects. */
 
+/* Copyright (C) 2002 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
+
 #ifndef GENOMICSUPERDUPS_H
 #define GENOMICSUPERDUPS_H
 
 struct genomicSuperDups
 /* Summary of large genomic Duplications (>1KB >90% similar) */
     {
     struct genomicSuperDups *next;  /* Next in singly linked list. */
     char *chrom;	/* Human chromosome or FPC contig */
     unsigned chromStart;	/* Start position in chromosome */
     unsigned chromEnd;	/* End position in chromosome */
     char *name;	/* Other chromosome involved */
     unsigned score;	/* Score from 900-1000.  1000 is best */
     char strand[2];	/* Value should be + or - */
     char *otherChrom;	/* Other Human chromosome or FPC contig */
     unsigned otherStart;	/* Start in other  sequence */
     unsigned otherEnd;	/* End in other  sequence */
     unsigned otherSize;	/* Total size of other sequence */
     unsigned uid;	/* unique id */
     unsigned posBasesHit;	/* HitPositive UnCovered */
     char *testResult;	/* HitPositive (yes or no) UnCovered (covered=0) */
     char *verdict;	/* Real or Allele */
     char *chits;	/* dup positive coverage */
     char *ccov;	/* clone coverage celera screened */
     char *alignfile;	/* alignment file path */
     unsigned alignL;	/* spaces/positions in alignment */
     unsigned indelN;	/* number of indels */
     unsigned indelS;	/* indel spaces */
     unsigned alignB;	/* bases Aligned */
     unsigned matchB;	/* aligned bases that match */
     unsigned mismatchB;	/* aligned bases that do not match */
     unsigned transitionsB;	/* number of transitions */
     unsigned transversionsB;	/* number of transversions */
     float fracMatch;	/* fraction of matching bases */
     float fracMatchIndel;	/* fraction of matching bases with indels */
     float jcK;	/* K-value calculated with Jukes-Cantor */
     float k2K;	/* Kimura K */
     };
 
 void genomicSuperDupsStaticLoad(char **row, struct genomicSuperDups *ret);
 /* Load a row from genomicSuperDups table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 
 struct genomicSuperDups *genomicSuperDupsLoad(char **row);
 /* Load a genomicSuperDups from row fetched with select * from genomicSuperDups
  * from database.  Dispose of this with genomicSuperDupsFree(). */
 
 struct genomicSuperDups *genomicSuperDupsLoadAll(char *fileName);
 /* Load all genomicSuperDups from a tab-separated file.
  * Dispose of this with genomicSuperDupsFreeList(). */
 
 struct genomicSuperDups *genomicSuperDupsLoadWhere(struct sqlConnection *conn, char *table, char *where);
 /* Load all genomicSuperDups from table that satisfy where clause. The
  * where clause may be NULL in which case whole table is loaded
  * Dispose of this with genomicSuperDupsFreeList(). */
 
 struct genomicSuperDups *genomicSuperDupsCommaIn(char **pS, struct genomicSuperDups *ret);
 /* Create a genomicSuperDups out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new genomicSuperDups */
 
 void genomicSuperDupsFree(struct genomicSuperDups **pEl);
 /* Free a single dynamically allocated genomicSuperDups such as created
  * with genomicSuperDupsLoad(). */
 
 void genomicSuperDupsFreeList(struct genomicSuperDups **pList);
 /* Free a list of dynamically allocated genomicSuperDups's */
 
 void genomicSuperDupsOutput(struct genomicSuperDups *el, FILE *f, char sep, char lastSep);
 /* Print out genomicSuperDups.  Separate fields with sep. Follow last field with lastSep. */
 
 #define genomicSuperDupsTabOut(el,f) genomicSuperDupsOutput(el,f,'\t','\n');
 /* Print out genomicSuperDups as a line in a tab-separated file. */
 
 #define genomicSuperDupsCommaOut(el,f) genomicSuperDupsOutput(el,f,',',',');
 /* Print out genomicSuperDups as a comma separated list including final comma. */
 
 #endif /* GENOMICSUPERDUPS_H */