060ada2535fca719656219c1214a3e1c16490693
tdreszer
  Wed Nov 9 16:06:41 2011 -0800
Moved as code in hgTables down to lib and access it from hgc and hgTrackUi.  This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
diff --git src/hg/lib/samAlignment.c src/hg/lib/samAlignment.c
index 1dd2eb2..6213a58 100644
--- src/hg/lib/samAlignment.c
+++ src/hg/lib/samAlignment.c
@@ -1,205 +1,212 @@
 /* samAlignment.c was originally generated by the autoSql program, which also 
  * generated samAlignment.h and samAlignment.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 "samAlignment.h"
 
 static char const rcsid[] = "$Id:$";
 
 void samAlignmentStaticLoad(char **row, struct samAlignment *ret)
 /* Load a row from samAlignment table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->qName = row[0];
 ret->flag = sqlUnsigned(row[1]);
 ret->rName = row[2];
 ret->pos = sqlUnsigned(row[3]);
 ret->mapQ = sqlUnsigned(row[4]);
 ret->cigar = row[5];
 ret->rNext = row[6];
 ret->pNext = sqlSigned(row[7]);
 ret->tLen = sqlSigned(row[8]);
 ret->seq = row[9];
 ret->qual = row[10];
 ret->tagTypeVals = row[11];
 }
 
 struct samAlignment *samAlignmentLoad(char **row)
 /* Load a samAlignment from row fetched with select * from samAlignment
  * from database.  Dispose of this with samAlignmentFree(). */
 {
 struct samAlignment *ret;
 
 AllocVar(ret);
 ret->qName = cloneString(row[0]);
 ret->flag = sqlUnsigned(row[1]);
 ret->rName = cloneString(row[2]);
 ret->pos = sqlUnsigned(row[3]);
 ret->mapQ = sqlUnsigned(row[4]);
 ret->cigar = cloneString(row[5]);
 ret->rNext = cloneString(row[6]);
 ret->pNext = sqlSigned(row[7]);
 ret->tLen = sqlSigned(row[8]);
 ret->seq = cloneString(row[9]);
 ret->qual = cloneString(row[10]);
 ret->tagTypeVals = cloneString(row[11]);
 return ret;
 }
 
 struct samAlignment *samAlignmentLoadAll(char *fileName) 
 /* Load all samAlignment from a whitespace-separated file.
  * Dispose of this with samAlignmentFreeList(). */
 {
 struct samAlignment *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[12];
 
 while (lineFileRow(lf, row))
     {
     el = samAlignmentLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct samAlignment *samAlignmentLoadAllByChar(char *fileName, char chopper) 
 /* Load all samAlignment from a chopper separated file.
  * Dispose of this with samAlignmentFreeList(). */
 {
 struct samAlignment *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[12];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = samAlignmentLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct samAlignment *samAlignmentCommaIn(char **pS, struct samAlignment *ret)
 /* Create a samAlignment out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new samAlignment */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->qName = sqlStringComma(&s);
 ret->flag = sqlUnsignedComma(&s);
 ret->rName = sqlStringComma(&s);
 ret->pos = sqlUnsignedComma(&s);
 ret->mapQ = sqlUnsignedComma(&s);
 ret->cigar = sqlStringComma(&s);
 ret->rNext = sqlStringComma(&s);
 ret->pNext = sqlSignedComma(&s);
 ret->tLen = sqlSignedComma(&s);
 ret->seq = sqlStringComma(&s);
 ret->qual = sqlStringComma(&s);
 ret->tagTypeVals = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void samAlignmentFree(struct samAlignment **pEl)
 /* Free a single dynamically allocated samAlignment such as created
  * with samAlignmentLoad(). */
 {
 struct samAlignment *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->qName);
 freeMem(el->rName);
 freeMem(el->cigar);
 freeMem(el->rNext);
 freeMem(el->seq);
 freeMem(el->qual);
 freeMem(el->tagTypeVals);
 freez(pEl);
 }
 
 void samAlignmentFreeList(struct samAlignment **pList)
 /* Free a list of dynamically allocated samAlignment's */
 {
 struct samAlignment *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     samAlignmentFree(&el);
     }
 *pList = NULL;
 }
 
 void samAlignmentOutput(struct samAlignment *el, FILE *f, char sep, char lastSep) 
 /* Print out samAlignment.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->qName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->flag);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->rName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->pos);
 fputc(sep,f);
 fprintf(f, "%u", el->mapQ);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->cigar);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->rNext);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->pNext);
 fputc(sep,f);
 fprintf(f, "%d", el->tLen);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->seq);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->qual);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->tagTypeVals);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
-char *samAlignmentAutoSqlString = 
+static char *samAlignmentAutoSqlString =
 "table samAlignment\n"
 "\"The fields of a SAM short read alignment, the text version of BAM.\"\n"
     "(\n"
     "string qName;	\"Query template name - name of a read\"\n"
     "ushort flag;	\"Flags.  0x10 set for reverse complement.  See SAM docs for others.\"\n"
     "string rName;	\"Reference sequence name (often a chromosome)\"\n"
     "uint pos;		\"1 based position\"\n"
     "ubyte mapQ;		\"Mapping quality 0-255, 255 is best\"\n"
     "string cigar;	\"CIGAR encoded alignment string.\"\n"
     "string rNext;	\"Ref sequence for next (mate) read. '=' if same as rName, '*' if no mate\"\n"
     "int pNext;		\"Position (1-based) of next (mate) sequence. May be -1 or 0 if no mate\"\n"
     "int tLen;	        \"Size of DNA template for mated pairs.  -size for one of mate pairs\"\n"
     "string seq;		\"Query template sequence\"\n"
     "string qual;	\"ASCII of Phred-scaled base QUALity+33.  Just '*' if no quality scores\"\n"
     "string tagTypeVals; \"Tab-delimited list of tag:type:value optional extra fields\"\n"
     ")\n";
+
+struct asObject *samAsObj()
+// Return asObject describing fields of SAM/BAM
+{
+return asParseText(samAlignmentAutoSqlString);
+}
+