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/hgTables/bam.c src/hg/hgTables/bam.c
index 8605887..b45ee7b 100644
--- src/hg/hgTables/bam.c
+++ src/hg/hgTables/bam.c
@@ -10,93 +10,84 @@
 #include "cart.h"
 #include "web.h"
 #include "bed.h"
 #include "hdb.h"
 #include "trackDb.h"
 #include "obscure.h"
 #include "hmmstats.h"
 #include "correlate.h"
 #include "asParse.h"
 #include "bbiFile.h"
 #include "bigBed.h"
 #include "hubConnect.h"
 #include "hgTables.h"
 #include "asFilter.h"
 #include "hgBam.h"
-#include "samAlignment.h"
 #if (defined USE_BAM && defined KNETFILE_HOOKS)
 #include "knetUdc.h"
 #include "udc.h"
 #endif//def USE_BAM && KNETFILE_HOOKS
 
 
 boolean isBamTable(char *table)
 /* Return TRUE if table corresponds to a BAM file. */
 {
 if (isHubTrack(table))
     {
     struct trackDb *tdb = hashFindVal(fullTrackAndSubtrackHash, table);
     return startsWithWord("bam", tdb->type);
     }
 else
     return trackIsType(database, table, curTrack, "bam", ctLookupName);
 }
 
 char *bamFileName(char *table, struct sqlConnection *conn, char *seqName)
 /* Return file name associated with BAM.  This handles differences whether it's
  * a custom or built-in track.  Do a freeMem on returned string when done. */
 {
 char *fileName = bigFileNameFromCtOrHub(table, conn);
 if (fileName == NULL)
     fileName = bamFileNameFromTable(conn, table, seqName);
 return fileName;
 }
 
-struct asObject *bamAsObj()
-/* Return asObject describing fields of BAM */
-{
-return asParseText(samAlignmentAutoSqlString);
-}
-
 struct hTableInfo *bamToHti(char *table)
 /* Get standard fields of BAM into hti structure. */
 {
 struct hTableInfo *hti;
 AllocVar(hti);
 hti->rootName = cloneString(table);
 hti->isPos= TRUE;
 strcpy(hti->chromField, "rName");
 strcpy(hti->startField, "pos");
 strcpy(hti->nameField, "qName");
 hti->type = cloneString("bam");
 return hti;
 }
 
 struct slName *bamGetFields(char *table)
 /* Get fields of bam as simple name list. */
 {
 struct asObject *as = bamAsObj();
-struct slName *names = asColNames(as);
-return names;
+return asColNames(as);
 }
 
 struct sqlFieldType *bamListFieldsAndTypes()
 /* Get fields of bigBed as list of sqlFieldType. */
 {
 struct asObject *as = bamAsObj();
-struct sqlFieldType *list = sqlFieldTypesFromAs(as);
-return list;
+return sqlFieldTypesFromAs(as);
 }
 
 #define BAM_NUM_BUF_SIZE 256
 
 void samAlignmentToRow(struct samAlignment *sam, char *numBuf, char *row[SAMALIGNMENT_NUM_COLS])
 /* Convert samAlignment data structure to an array of strings, using numBuf to store
  * ascii versions of numbers temporarily */
 {
 char *numPt = numBuf;
 char *numBufEnd = numBuf + BAM_NUM_BUF_SIZE;
 row[0] = sam->qName;
 row[1] = numPt; numPt += sprintf(numPt, "%u", sam->flag); numPt += 1;
 row[2] = sam->rName;
 row[3] = numPt; numPt += sprintf(numPt, "%u", sam->pos); numPt += 1;
 row[4] = numPt; numPt += sprintf(numPt, "%u", sam->mapQ); numPt += 1;