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/hapmapPhaseIIISummary.h src/hg/inc/hapmapPhaseIIISummary.h
index 7b32b7e..58bc947 100644
--- src/hg/inc/hapmapPhaseIIISummary.h
+++ src/hg/inc/hapmapPhaseIIISummary.h
@@ -1,74 +1,77 @@
 /* hapmapPhaseIIISummary.h was originally generated by the autoSql program, which also 
  * generated hapmapPhaseIIISummary.c and hapmapPhaseIIISummary.sql.  This header links the database and
  * the RAM representation of objects. */
 
+/* Copyright (C) 2009 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
+
 #ifndef HAPMAPPHASEIIISUMMARY_H
 #define HAPMAPPHASEIIISUMMARY_H
 
 #define HAPMAPPHASEIIISUMMARY_NUM_COLS 18
 
 struct hapmapPhaseIIISummary
 /* HapMap Phase III allele summaries for filtering (BED 5+) */
     {
     struct hapmapPhaseIIISummary *next;  /* Next in singly linked list. */
     char *chrom;	/* Chromosome */
     unsigned chromStart;	/* Start position in chrom (0 based) */
     unsigned chromEnd;	/* End position in chrom (1 based) */
     char *name;	/* Reference SNP identifier from dbSnp */
     unsigned score;	/* Average of population heterozygosities in parts per thousand (0-500) */
     char *observed;	/* Observed string from genotype file */
     char overallMajorAllele;	/* This allele has been observed in at least half of the populations that have data for this SNP */
     char overallMinorAllele;	/* This allele may not have been observed in any HapMap sample */
     unsigned char popCount;	/* How many Phase III populations have data (1-11) */
     unsigned char phaseIIPopCount;	/* How many Phase II populations have data (0-4) */
     unsigned char isMixed;	/* 0 if all populations have the same major allele, 1 otherwise. */
     unsigned char foundInPop[11];	/* Got data for each of the 11 Phase III populations? */
     unsigned char monomorphicInPop[11];	/* Monomorphic in each of the 11 Phase III populations? */
     float minFreq;	/* Minimum minor allele frequency across all populations */
     float maxFreq;	/* Maximum minor allele frequency across all populations */
     unsigned orthoCount;	/* Species for which orthologous alleles have been determined */
     char *orthoAlleles;	/* Orthologous allele for each species (or N if not found) */
     unsigned short *orthoQuals;	/* Base quality score (0-100) for each species */
     };
 
 struct hapmapPhaseIIISummary *hapmapPhaseIIISummaryLoad(char **row);
 /* Load a hapmapPhaseIIISummary from row fetched with select * from hapmapPhaseIIISummary
  * from database.  Dispose of this with hapmapPhaseIIISummaryFree(). */
 
 struct hapmapPhaseIIISummary *hapmapPhaseIIISummaryLoadAll(char *fileName);
 /* Load all hapmapPhaseIIISummary from whitespace-separated file.
  * Dispose of this with hapmapPhaseIIISummaryFreeList(). */
 
 struct hapmapPhaseIIISummary *hapmapPhaseIIISummaryLoadAllByChar(char *fileName, char chopper);
 /* Load all hapmapPhaseIIISummary from chopper separated file.
  * Dispose of this with hapmapPhaseIIISummaryFreeList(). */
 
 #define hapmapPhaseIIISummaryLoadAllByTab(a) hapmapPhaseIIISummaryLoadAllByChar(a, '\t');
 /* Load all hapmapPhaseIIISummary from tab separated file.
  * Dispose of this with hapmapPhaseIIISummaryFreeList(). */
 
 struct hapmapPhaseIIISummary *hapmapPhaseIIISummaryCommaIn(char **pS, struct hapmapPhaseIIISummary *ret);
 /* Create a hapmapPhaseIIISummary out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new hapmapPhaseIIISummary */
 
 void hapmapPhaseIIISummaryFree(struct hapmapPhaseIIISummary **pEl);
 /* Free a single dynamically allocated hapmapPhaseIIISummary such as created
  * with hapmapPhaseIIISummaryLoad(). */
 
 void hapmapPhaseIIISummaryFreeList(struct hapmapPhaseIIISummary **pList);
 /* Free a list of dynamically allocated hapmapPhaseIIISummary's */
 
 void hapmapPhaseIIISummaryOutput(struct hapmapPhaseIIISummary *el, FILE *f, char sep, char lastSep);
 /* Print out hapmapPhaseIIISummary.  Separate fields with sep. Follow last field with lastSep. */
 
 #define hapmapPhaseIIISummaryTabOut(el,f) hapmapPhaseIIISummaryOutput(el,f,'\t','\n');
 /* Print out hapmapPhaseIIISummary as a line in a tab-separated file. */
 
 #define hapmapPhaseIIISummaryCommaOut(el,f) hapmapPhaseIIISummaryOutput(el,f,',',',');
 /* Print out hapmapPhaseIIISummary as a comma separated list including final comma. */
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 #endif /* HAPMAPPHASEIIISUMMARY_H */