src/hg/inc/hapmapSnps.h 1.6

Index: src/hg/inc/hapmapSnps.h
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/inc/hapmapSnps.h,v
retrieving revision 1.5
retrieving revision 1.6
diff -b -B -U 1000000 -r1.5 -r1.6
--- src/hg/inc/hapmapSnps.h	8 May 2007 21:54:33 -0000	1.5
+++ src/hg/inc/hapmapSnps.h	3 Mar 2009 01:07:24 -0000	1.6
@@ -1,106 +1,123 @@
 /* hapmapSnps.h was originally generated by the autoSql program, which also 
  * generated hapmapSnps.c and hapmapSnps.sql.  This header links the database and
  * the RAM representation of objects. */
 
 #ifndef HAPMAPSNPS_H
 #define HAPMAPSNPS_H
 
 #define HAPMAPSNPS_NUM_COLS 12
 
 struct hapmapSnps
 /* HapMap genotype summary */
     {
     struct hapmapSnps *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;	/* Not used */
     char strand[2];	/* Which genomic strand contains the observed alleles */
     char *observed;	/* Observed string from genotype file */
     char allele1[2];	/* This allele has been observed */
     unsigned homoCount1;	/* Count of individuals who are homozygous for allele1 */
     char *allele2;	/* This allele may not have been observed */
     unsigned homoCount2;	/* Count of individuals who are homozygous for allele2 */
     unsigned heteroCount;	/* Count of individuals who are heterozygous */
     };
 
 void hapmapSnpsStaticLoad(char **row, struct hapmapSnps *ret);
 /* Load a row from hapmapSnps table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 
 struct hapmapSnps *hapmapSnpsLoad(char **row);
 /* Load a hapmapSnps from row fetched with select * from hapmapSnps
  * from database.  Dispose of this with hapmapSnpsFree(). */
 
 struct hapmapSnps *hapmapSnpsLoadAll(char *fileName);
 /* Load all hapmapSnps from whitespace-separated file.
  * Dispose of this with hapmapSnpsFreeList(). */
 
 struct hapmapSnps *hapmapSnpsLoadAllByChar(char *fileName, char chopper);
 /* Load all hapmapSnps from chopper separated file.
  * Dispose of this with hapmapSnpsFreeList(). */
 
 #define hapmapSnpsLoadAllByTab(a) hapmapSnpsLoadAllByChar(a, '\t');
 /* Load all hapmapSnps from tab separated file.
  * Dispose of this with hapmapSnpsFreeList(). */
 
 struct hapmapSnps *hapmapSnpsCommaIn(char **pS, struct hapmapSnps *ret);
 /* Create a hapmapSnps out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new hapmapSnps */
 
 void hapmapSnpsFree(struct hapmapSnps **pEl);
 /* Free a single dynamically allocated hapmapSnps such as created
  * with hapmapSnpsLoad(). */
 
 void hapmapSnpsFreeList(struct hapmapSnps **pList);
 /* Free a list of dynamically allocated hapmapSnps's */
 
 void hapmapSnpsOutput(struct hapmapSnps *el, FILE *f, char sep, char lastSep);
 /* Print out hapmapSnps.  Separate fields with sep. Follow last field with lastSep. */
 
 #define hapmapSnpsTabOut(el,f) hapmapSnpsOutput(el,f,'\t','\n');
 /* Print out hapmapSnps as a line in a tab-separated file. */
 
 #define hapmapSnpsCommaOut(el,f) hapmapSnpsOutput(el,f,',',',');
 /* Print out hapmapSnps as a comma separated list including final comma. */
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 /* items for trackUi options and filters */
 
-#define HAP_POP_MIXED "hapmapSnps.isMixed"
-#define HAP_POP_COUNT "hapmapSnps.popCount"
-#define HAP_TYPE "hapmapSnps.polyType"
-#define HAP_MIN_FREQ "hapmapSnps.minorAlleleFreqMinimum"
-#define HAP_MAX_FREQ "hapmapSnps.minorAlleleFreqMaximum"
-#define HAP_MIN_HET "hapmapSnps.hetMinimum"
-#define HAP_MAX_HET "hapmapSnps.hetMaximum"
+#define HAP_POP_MIXED "hapmapSnps_isMixed"
+#define HAP_POP_COUNT "hapmapSnps_popCount"
+#define HAP_TYPE "hapmapSnps_polyType"
+#define HAP_MIN_FREQ "hapmapSnps_minorAlleleFreqMinimum"
+#define HAP_MAX_FREQ "hapmapSnps_minorAlleleFreqMaximum"
+#define HAP_MIN_HET "hapmapSnps_hetMinimum"
+#define HAP_MAX_HET "hapmapSnps_hetMaximum"
+#define HAP_MONO_PREFIX "hapmapSnps_monomorphic"
+#define HAP_ORTHO_PREFIX "hapmapSnps_ortho"
+#define HAP_ORTHO_QUAL_PREFIX "hapmapSnps_orthoQual"
+
+/* OLD -- Keeping these until I can check in the changes to hgTracks/hapmapTrack.c. */
 #define HAP_MONO_CEU "hapmapSnps.monomorphic.ceu"
 #define HAP_MONO_CHB "hapmapSnps.monomorphic.chb"
 #define HAP_MONO_JPT "hapmapSnps.monomorphic.jpt"
 #define HAP_MONO_YRI "hapmapSnps.monomorphic.yri"
 #define HAP_CHIMP "hapmapSnps.chimp"
 #define HAP_CHIMP_QUAL "hapmapSnps.chimpQualScore"
 #define HAP_MACAQUE "hapmapSnps.macaque"
 #define HAP_MACAQUE_QUAL "hapmapSnps.macaqueQualScore"
-
 #define HAP_POP_MIXED_DEFAULT "no filter"
 #define HAP_POP_COUNT_DEFAULT "no filter"
 #define HAP_TYPE_DEFAULT      "no filter"
+#define HAP_MONO_DEFAULT      "no filter"
+#define HAP_CHIMP_DEFAULT     "no filter"
+#define HAP_CHIMP_QUAL_DEFAULT "0"
+#define HAP_MACAQUE_DEFAULT   "no filter"
+#define HAP_MACAQUE_QUAL_DEFAULT "0"
+/* End of old stuff. */
+
+#define HAP_FILTER_DEFAULT "no filter"
 
 #define HAP_MIN_FREQ_DEFAULT  "0.0"
 #define HAP_MAX_FREQ_DEFAULT  "0.5"
 #define HAP_MIN_HET_DEFAULT   "0.0"
 #define HAP_MAX_HET_DEFAULT   "0.5"
 
-#define HAP_MONO_DEFAULT      "no filter"
+#define HAP_ORTHO_QUAL_DEFAULT "0"
 
-#define HAP_CHIMP_DEFAULT     "no filter"
-#define HAP_CHIMP_QUAL_DEFAULT "0"
-#define HAP_MACAQUE_DEFAULT   "no filter"
-#define HAP_MACAQUE_QUAL_DEFAULT "0"
+#define HAP_PHASEII_POPCOUNT 4
+#define HAP_PHASEIII_POPCOUNT 11
+#define HAP_ORTHO_COUNT 2
+
+char *hapmapPhaseIIPops[HAP_PHASEII_POPCOUNT];
+char *hapmapPhaseIIIPops[HAP_PHASEIII_POPCOUNT];
+
+/* Someday this should come from a trackDb setting: */
+extern char *hapmapOrthoSpecies[HAP_ORTHO_COUNT+1];
 
 #endif /* HAPMAPSNPS_H */