312002c4b4015a4e5acedd47dad9e5d6b8d3c1b1
markd
  Mon Nov 22 18:38:59 2021 -0800
move rmskAlign and rmskJoined to lib so it they can be used by programs

diff --git src/hg/cgilib/rmskJoined.c src/hg/cgilib/rmskJoined.c
deleted file mode 100644
index a42a767..0000000
--- src/hg/cgilib/rmskJoined.c
+++ /dev/null
@@ -1,215 +0,0 @@
-/* rmskJoined.c was originally generated by the autoSql program, which also 
- * generated rmskJoined.h and rmskJoined.sql.  This module links the database and
- * the RAM representation of objects. */
-
-/* Copyright (C) 2014 The Regents of the University of California 
- * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
-
-#include "common.h"
-#include "linefile.h"
-#include "dystring.h"
-#include "jksql.h"
-#include "rmskJoined.h"
-
-
-struct rmskJoined *rmskJoinedLoad(char **row)
-/* Load a rmskJoined from row fetched with select * from rmskJoined
- * from database.  Dispose of this with rmskJoinedFree(). */
-{
-struct rmskJoined *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]);
-safecpy(ret->strand, sizeof(ret->strand), row[5]);
-ret->alignStart = sqlUnsigned(row[6]);
-ret->alignEnd = 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->blockRelStarts, &sizeOne);
-assert(sizeOne == ret->blockCount);
-}
-ret->id = cloneString(row[12]);
-return ret;
-}
-
-struct rmskJoined *rmskJoinedLoadAll(char *fileName) 
-/* Load all rmskJoined from a whitespace-separated file.
- * Dispose of this with rmskJoinedFreeList(). */
-{
-struct rmskJoined *list = NULL, *el;
-struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[14];
-
-while (lineFileRow(lf, row))
-    {
-    el = rmskJoinedLoad(row);
-    slAddHead(&list, el);
-    }
-lineFileClose(&lf);
-slReverse(&list);
-return list;
-}
-
-struct rmskJoined *rmskJoinedLoadAllByChar(char *fileName, char chopper) 
-/* Load all rmskJoined from a chopper separated file.
- * Dispose of this with rmskJoinedFreeList(). */
-{
-struct rmskJoined *list = NULL, *el;
-struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[14];
-
-while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
-    {
-    el = rmskJoinedLoad(row);
-    slAddHead(&list, el);
-    }
-lineFileClose(&lf);
-slReverse(&list);
-return list;
-}
-
-struct rmskJoined *rmskJoinedCommaIn(char **pS, struct rmskJoined *ret)
-/* Create a rmskJoined out of a comma separated string. 
- * This will fill in ret if non-null, otherwise will
- * return a new rmskJoined */
-{
-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->alignStart = sqlUnsignedComma(&s);
-ret->alignEnd = 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->blockRelStarts, ret->blockCount);
-for (i=0; i<ret->blockCount; ++i)
-    {
-    ret->blockRelStarts[i] = sqlSignedComma(&s);
-    }
-s = sqlEatChar(s, '}');
-s = sqlEatChar(s, ',');
-}
-ret->id = sqlStringComma(&s);
-*pS = s;
-return ret;
-}
-
-void rmskJoinedFree(struct rmskJoined **pEl)
-/* Free a single dynamically allocated rmskJoined such as created
- * with rmskJoinedLoad(). */
-{
-struct rmskJoined *el;
-
-if ((el = *pEl) == NULL) return;
-freeMem(el->chrom);
-freeMem(el->name);
-freeMem(el->blockSizes);
-freeMem(el->blockRelStarts);
-freeMem(el->id);
-freez(pEl);
-}
-
-void rmskJoinedFreeList(struct rmskJoined **pList)
-/* Free a list of dynamically allocated rmskJoined's */
-{
-struct rmskJoined *el, *next;
-
-for (el = *pList; el != NULL; el = next)
-    {
-    next = el->next;
-    rmskJoinedFree(&el);
-    }
-*pList = NULL;
-}
-
-void rmskJoinedOutput(struct rmskJoined *el, FILE *f, char sep, char lastSep) 
-/* Print out rmskJoined.  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->alignStart);
-fputc(sep,f);
-fprintf(f, "%u", el->alignEnd);
-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->blockRelStarts[i]);
-    fputc(',', f);
-    }
-if (sep == ',') fputc('}',f);
-}
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->id);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fputc(lastSep,f);
-}
-
-/* -------------------------------- End autoSql Generated Code -------------------------------- */