src/hg/inc/hapmapPhaseIIISummary.h 1.1

Index: src/hg/inc/hapmapPhaseIIISummary.h
===================================================================
RCS file: src/hg/inc/hapmapPhaseIIISummary.h
diff -N src/hg/inc/hapmapPhaseIIISummary.h
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/hg/inc/hapmapPhaseIIISummary.h	6 Mar 2009 23:34:41 -0000	1.1
@@ -0,0 +1,74 @@
+/* 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. */
+
+#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 */
+