src/hg/lib/hapmapSnps.c 1.4

Index: src/hg/lib/hapmapSnps.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/lib/hapmapSnps.c,v
retrieving revision 1.3
retrieving revision 1.4
diff -b -B -U 1000000 -r1.3 -r1.4
--- src/hg/lib/hapmapSnps.c	12 Mar 2007 17:11:43 -0000	1.3
+++ src/hg/lib/hapmapSnps.c	3 Mar 2009 01:03:40 -0000	1.4
@@ -1,184 +1,189 @@
 /* hapmapSnps.c was originally generated by the autoSql program, which also 
  * generated hapmapSnps.h and hapmapSnps.sql.  This module links the database and
  * the RAM representation of objects. */
 
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "hapmapSnps.h"
 
 static char const rcsid[] = "$Id$";
 
 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. */
 {
 
 ret->chrom = row[0];
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = row[3];
 ret->score = sqlUnsigned(row[4]);
 safecpy(ret->strand, sizeof(ret->strand), row[5]);
 ret->observed = row[6];
 safecpy(ret->allele1, sizeof(ret->allele1), row[7]);
 ret->homoCount1 = sqlUnsigned(row[8]);
 ret->allele2 = row[9];
 ret->homoCount2 = sqlUnsigned(row[10]);
 ret->heteroCount = sqlUnsigned(row[11]);
 }
 
 struct hapmapSnps *hapmapSnpsLoad(char **row)
 /* Load a hapmapSnps from row fetched with select * from hapmapSnps
  * from database.  Dispose of this with hapmapSnpsFree(). */
 {
 struct hapmapSnps *ret;
 
 AllocVar(ret);
 ret->chrom = cloneString(row[0]);
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = cloneString(row[3]);
 ret->score = sqlUnsigned(row[4]);
 safecpy(ret->strand, sizeof(ret->strand), row[5]);
 ret->observed = cloneString(row[6]);
 safecpy(ret->allele1, sizeof(ret->allele1), row[7]);
 ret->homoCount1 = sqlUnsigned(row[8]);
 ret->allele2 = cloneString(row[9]);
 ret->homoCount2 = sqlUnsigned(row[10]);
 ret->heteroCount = sqlUnsigned(row[11]);
 return ret;
 }
 
 struct hapmapSnps *hapmapSnpsLoadAll(char *fileName) 
 /* Load all hapmapSnps from a whitespace-separated file.
  * Dispose of this with hapmapSnpsFreeList(). */
 {
 struct hapmapSnps *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[12];
 
 while (lineFileRow(lf, row))
     {
     el = hapmapSnpsLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct hapmapSnps *hapmapSnpsLoadAllByChar(char *fileName, char chopper) 
 /* Load all hapmapSnps from a chopper separated file.
  * Dispose of this with hapmapSnpsFreeList(). */
 {
 struct hapmapSnps *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[12];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = hapmapSnpsLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 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 */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->chrom = sqlStringComma(&s);
 ret->chromStart = sqlUnsignedComma(&s);
 ret->chromEnd = sqlUnsignedComma(&s);
 ret->name = sqlStringComma(&s);
 ret->score = sqlUnsignedComma(&s);
 sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
 ret->observed = sqlStringComma(&s);
 sqlFixedStringComma(&s, ret->allele1, sizeof(ret->allele1));
 ret->homoCount1 = sqlUnsignedComma(&s);
 ret->allele2 = sqlStringComma(&s);
 ret->homoCount2 = sqlUnsignedComma(&s);
 ret->heteroCount = sqlUnsignedComma(&s);
 *pS = s;
 return ret;
 }
 
 void hapmapSnpsFree(struct hapmapSnps **pEl)
 /* Free a single dynamically allocated hapmapSnps such as created
  * with hapmapSnpsLoad(). */
 {
 struct hapmapSnps *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->observed);
 freeMem(el->allele2);
 freez(pEl);
 }
 
 void hapmapSnpsFreeList(struct hapmapSnps **pList)
 /* Free a list of dynamically allocated hapmapSnps's */
 {
 struct hapmapSnps *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     hapmapSnpsFree(&el);
     }
 *pList = NULL;
 }
 
 void hapmapSnpsOutput(struct hapmapSnps *el, FILE *f, char sep, char lastSep) 
 /* Print out hapmapSnps.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->chrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->chromStart);
 fputc(sep,f);
 fprintf(f, "%u", el->chromEnd);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->name);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->score);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->strand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->observed);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->allele1);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->homoCount1);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->allele2);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->homoCount2);
 fputc(sep,f);
 fprintf(f, "%u", el->heteroCount);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
+char *hapmapPhaseIIPops[] = { "CEU", "CHB", "JPT", "YRI" };
+char *hapmapPhaseIIIPops[] =
+    { "ASW", "CEU", "CHB", "CHD", "GIH", "JPT", "LWK", "MEX", "MKK", "TSI", "YRI" };
+
+char *hapmapOrthoSpecies[] = {"Chimp", "Macaque", NULL};