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/lib/bgiSnp.c src/hg/lib/bgiSnp.c
index 9efd0430f..8800b63 100644
--- src/hg/lib/bgiSnp.c
+++ src/hg/lib/bgiSnp.c
@@ -1,233 +1,236 @@
 /* bgiSnp.c was originally generated by the autoSql program, which also 
  * generated bgiSnp.h and bgiSnp.sql.  This module links the database and
  * the RAM representation of objects. */
 
+/* Copyright (C) 2014 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
+
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "bgiSnp.h"
 
 
 void bgiSnpStaticLoad(char **row, struct bgiSnp *ret)
 /* Load a row from bgiSnp 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];
 strcpy(ret->snpType, row[4]);
 ret->readStart = sqlUnsigned(row[5]);
 ret->readEnd = sqlUnsigned(row[6]);
 ret->qualChr = sqlUnsigned(row[7]);
 ret->qualReads = sqlUnsigned(row[8]);
 ret->snpSeq = row[9];
 ret->readName = row[10];
 strcpy(ret->readDir, row[11]);
 strcpy(ret->inBroiler, row[12]);
 strcpy(ret->inLayer, row[13]);
 strcpy(ret->inSilkie, row[14]);
 ret->primerL = row[15];
 ret->primerR = row[16];
 strcpy(ret->questionM, row[17]);
 ret->extra = row[18];
 }
 
 struct bgiSnp *bgiSnpLoad(char **row)
 /* Load a bgiSnp from row fetched with select * from bgiSnp
  * from database.  Dispose of this with bgiSnpFree(). */
 {
 struct bgiSnp *ret;
 AllocVar(ret);
 ret->chrom = cloneString(row[0]);
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = cloneString(row[3]);
 strcpy(ret->snpType, row[4]);
 ret->readStart = sqlUnsigned(row[5]);
 ret->readEnd = sqlUnsigned(row[6]);
 ret->qualChr = sqlUnsigned(row[7]);
 ret->qualReads = sqlUnsigned(row[8]);
 ret->snpSeq = cloneString(row[9]);
 ret->readName = cloneString(row[10]);
 strcpy(ret->readDir, row[11]);
 strcpy(ret->inBroiler, row[12]);
 strcpy(ret->inLayer, row[13]);
 strcpy(ret->inSilkie, row[14]);
 ret->primerL = cloneString(row[15]);
 ret->primerR = cloneString(row[16]);
 strcpy(ret->questionM, row[17]);
 ret->extra = cloneString(row[18]);
 return ret;
 }
 
 struct bgiSnp *bgiSnpLoadAll(char *fileName) 
 /* Load all bgiSnp from a whitespace-separated file.
  * Dispose of this with bgiSnpFreeList(). */
 {
 struct bgiSnp *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[19];
 
 while (lineFileRow(lf, row))
     {
     el = bgiSnpLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct bgiSnp *bgiSnpLoadAllByChar(char *fileName, char chopper) 
 /* Load all bgiSnp from a chopper separated file.
  * Dispose of this with bgiSnpFreeList(). */
 {
 struct bgiSnp *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[19];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = bgiSnpLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct bgiSnp *bgiSnpCommaIn(char **pS, struct bgiSnp *ret)
 /* Create a bgiSnp out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new bgiSnp */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->chrom = sqlStringComma(&s);
 ret->chromStart = sqlUnsignedComma(&s);
 ret->chromEnd = sqlUnsignedComma(&s);
 ret->name = sqlStringComma(&s);
 sqlFixedStringComma(&s, ret->snpType, sizeof(ret->snpType));
 ret->readStart = sqlUnsignedComma(&s);
 ret->readEnd = sqlUnsignedComma(&s);
 ret->qualChr = sqlUnsignedComma(&s);
 ret->qualReads = sqlUnsignedComma(&s);
 ret->snpSeq = sqlStringComma(&s);
 ret->readName = sqlStringComma(&s);
 sqlFixedStringComma(&s, ret->readDir, sizeof(ret->readDir));
 sqlFixedStringComma(&s, ret->inBroiler, sizeof(ret->inBroiler));
 sqlFixedStringComma(&s, ret->inLayer, sizeof(ret->inLayer));
 sqlFixedStringComma(&s, ret->inSilkie, sizeof(ret->inSilkie));
 ret->primerL = sqlStringComma(&s);
 ret->primerR = sqlStringComma(&s);
 sqlFixedStringComma(&s, ret->questionM, sizeof(ret->questionM));
 ret->extra = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void bgiSnpFree(struct bgiSnp **pEl)
 /* Free a single dynamically allocated bgiSnp such as created
  * with bgiSnpLoad(). */
 {
 struct bgiSnp *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->snpSeq);
 freeMem(el->readName);
 freeMem(el->primerL);
 freeMem(el->primerR);
 freeMem(el->extra);
 freez(pEl);
 }
 
 void bgiSnpFreeList(struct bgiSnp **pList)
 /* Free a list of dynamically allocated bgiSnp's */
 {
 struct bgiSnp *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     bgiSnpFree(&el);
     }
 *pList = NULL;
 }
 
 void bgiSnpOutput(struct bgiSnp *el, FILE *f, char sep, char lastSep) 
 /* Print out bgiSnp.  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);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->snpType);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->readStart);
 fputc(sep,f);
 fprintf(f, "%u", el->readEnd);
 fputc(sep,f);
 fprintf(f, "%u", el->qualChr);
 fputc(sep,f);
 fprintf(f, "%u", el->qualReads);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->snpSeq);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->readName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->readDir);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->inBroiler);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->inLayer);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->inSilkie);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->primerL);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->primerR);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->questionM);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->extra);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */