183696cf2ea83033b4bf4a34ab1b0db38f1c4567
kent
  Mon Nov 15 15:47:14 2021 -0800
Moving bed12Source.c from cgilib to lib since it is not propriatary, and a HCA thing wanted to use it.

diff --git src/hg/cgilib/bed12Source.c src/hg/cgilib/bed12Source.c
deleted file mode 100644
index 352a7ec..0000000
--- src/hg/cgilib/bed12Source.c
+++ /dev/null
@@ -1,214 +0,0 @@
-/* bed12Source.c was originally generated by the autoSql program, which also 
- * generated bed12Source.h and bed12Source.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 "bed12Source.h"
-
-
-struct bed12Source *bed12SourceLoad(char **row)
-/* Load a bed12Source from row fetched with select * from bed12Source
- * from database.  Dispose of this with bed12SourceFree(). */
-{
-struct bed12Source *ret;
-
-AllocVar(ret);
-ret->blockCount = sqlSigned(row[9]);
-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]);
-strcpy(ret->strand, row[5]);
-ret->thickStart = sqlUnsigned(row[6]);
-ret->thickEnd = sqlUnsigned(row[7]);
-ret->reserved = sqlUnsigned(row[8]);
-{
-int sizeOne;
-sqlSignedDynamicArray(row[10], &ret->blockSizes, &sizeOne);
-assert(sizeOne == ret->blockCount);
-}
-{
-int sizeOne;
-sqlSignedDynamicArray(row[11], &ret->chromStarts, &sizeOne);
-assert(sizeOne == ret->blockCount);
-}
-ret->source = cloneString(row[12]);
-return ret;
-}
-
-struct bed12Source *bed12SourceLoadAll(char *fileName) 
-/* Load all bed12Source from a whitespace-separated file.
- * Dispose of this with bed12SourceFreeList(). */
-{
-struct bed12Source *list = NULL, *el;
-struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[13];
-
-while (lineFileRow(lf, row))
-    {
-    el = bed12SourceLoad(row);
-    slAddHead(&list, el);
-    }
-lineFileClose(&lf);
-slReverse(&list);
-return list;
-}
-
-struct bed12Source *bed12SourceLoadAllByChar(char *fileName, char chopper) 
-/* Load all bed12Source from a chopper separated file.
- * Dispose of this with bed12SourceFreeList(). */
-{
-struct bed12Source *list = NULL, *el;
-struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[13];
-
-while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
-    {
-    el = bed12SourceLoad(row);
-    slAddHead(&list, el);
-    }
-lineFileClose(&lf);
-slReverse(&list);
-return list;
-}
-
-struct bed12Source *bed12SourceCommaIn(char **pS, struct bed12Source *ret)
-/* Create a bed12Source out of a comma separated string. 
- * This will fill in ret if non-null, otherwise will
- * return a new bed12Source */
-{
-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->thickStart = sqlUnsignedComma(&s);
-ret->thickEnd = sqlUnsignedComma(&s);
-ret->reserved = sqlUnsignedComma(&s);
-ret->blockCount = sqlSignedComma(&s);
-{
-int i;
-s = sqlEatChar(s, '{');
-AllocArray(ret->blockSizes, ret->blockCount);
-for (i=0; i<ret->blockCount; ++i)
-    {
-    ret->blockSizes[i] = sqlSignedComma(&s);
-    }
-s = sqlEatChar(s, '}');
-s = sqlEatChar(s, ',');
-}
-{
-int i;
-s = sqlEatChar(s, '{');
-AllocArray(ret->chromStarts, ret->blockCount);
-for (i=0; i<ret->blockCount; ++i)
-    {
-    ret->chromStarts[i] = sqlSignedComma(&s);
-    }
-s = sqlEatChar(s, '}');
-s = sqlEatChar(s, ',');
-}
-ret->source = sqlStringComma(&s);
-*pS = s;
-return ret;
-}
-
-void bed12SourceFree(struct bed12Source **pEl)
-/* Free a single dynamically allocated bed12Source such as created
- * with bed12SourceLoad(). */
-{
-struct bed12Source *el;
-
-if ((el = *pEl) == NULL) return;
-freeMem(el->chrom);
-freeMem(el->name);
-freeMem(el->blockSizes);
-freeMem(el->chromStarts);
-freeMem(el->source);
-freez(pEl);
-}
-
-void bed12SourceFreeList(struct bed12Source **pList)
-/* Free a list of dynamically allocated bed12Source's */
-{
-struct bed12Source *el, *next;
-
-for (el = *pList; el != NULL; el = next)
-    {
-    next = el->next;
-    bed12SourceFree(&el);
-    }
-*pList = NULL;
-}
-
-void bed12SourceOutput(struct bed12Source *el, FILE *f, char sep, char lastSep) 
-/* Print out bed12Source.  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);
-fprintf(f, "%u", el->thickStart);
-fputc(sep,f);
-fprintf(f, "%u", el->thickEnd);
-fputc(sep,f);
-fprintf(f, "%u", el->reserved);
-fputc(sep,f);
-fprintf(f, "%d", el->blockCount);
-fputc(sep,f);
-{
-int i;
-if (sep == ',') fputc('{',f);
-for (i=0; i<el->blockCount; ++i)
-    {
-    fprintf(f, "%d", el->blockSizes[i]);
-    fputc(',', f);
-    }
-if (sep == ',') fputc('}',f);
-}
-fputc(sep,f);
-{
-int i;
-if (sep == ',') fputc('{',f);
-for (i=0; i<el->blockCount; ++i)
-    {
-    fprintf(f, "%d", el->chromStarts[i]);
-    fputc(',', f);
-    }
-if (sep == ',') fputc('}',f);
-}
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->source);
-if (sep == ',') fputc('"',f);
-fputc(lastSep,f);
-}
-
-/* -------------------------------- End autoSql Generated Code -------------------------------- */
-