f05629f294dcd4cf31ce55d835218d30f7a82516
cline
  Fri Sep 23 15:27:52 2011 -0700
Revert "Updated the process of building the kegg pathway tables, modeling after what Fan did for hg19"
This reverts commit 946ad6602b09a56d6ccc661a0bfc84de9c345eac.

diff --git src/hg/inc/hdb.h src/hg/inc/hdb.h
index 6e27196..e7bf03d 100644
--- src/hg/inc/hdb.h
+++ src/hg/inc/hdb.h
@@ -216,75 +216,62 @@
 
 struct chromInfo *hGetChromInfo(char *db, char *chrom);
 /* Get chromInfo for named chromosome (case-insens.) from db.
  * Return NULL if no such chrom. */
 
 struct dnaSeq *hFetchSeq(char *fileName, char *seqName, int start, int end);
 /* Fetch sequence from file.  If it is a .2bit file then fetch the named sequence.
 If it is .nib then just ignore seqName. */
 
 struct dnaSeq *hFetchSeqMixed(char *fileName, char *seqName, int start, int end);
 /* Fetch mixed case sequence. */
 
 struct dnaSeq *hChromSeq(char *db, char *chrom, int start, int end);
 /* Return lower case DNA from chromosome. */
 
-struct dnaSeq *hChromSeqFromPath(char *nibPath, char *db, char *chrom, 
-				 int start, int end);
-/* Return lower case DNA from chromosome. */
-
 struct dnaSeq *hChromSeqMixed(char *db, char *chrom, int start, int end);
 /* Return mixed case (repeats in lower case) DNA from chromosome. */
 
-struct dnaSeq *hChromSeqMixedFromPath(char *nibPath, char *db, char *chrom, 
-				      int start, int end);
-/* Return mixed case (repeats in lower case) DNA from chromosome, given an
- * input nib path. */
-
 struct dnaSeq *hSeqForBed(char *db, struct bed *bed);
 /* Get the sequence associated with a particular bed concatenated together. */
 
 boolean hChromBand(char *db, char *chrom, int pos, char retBand[HDB_MAX_BAND_STRING]);
 /* Fill in text string that says what band pos is on.
  * Return FALSE if not on any band, or table missing. */
 
 boolean hChromBandConn(struct sqlConnection *conn,
 	char *chrom, int pos, char retBand[HDB_MAX_BAND_STRING]);
 /* Fill in text string that says what band pos is on.
  * Return FALSE if not on any band, or table missing. */
 
 boolean hScaffoldPos(char *db, char *chrom, int start, int end,
                      char **retScaffold, int *retStart, int *retEnd);
 /* Return the scaffold, and start end coordinates on a scaffold, for
  * a chromosome range.  If the range extends past end of a scaffold,
  * it is truncated to the scaffold end.
  * Return FALSE if unable to convert */
 
 struct dnaSeq *hDnaFromSeq(char *db, char *seqName,
 	int start, int end, enum dnaCase dnaCase);
 /* Fetch DNA in a variety of cases.  */
 
 struct dnaSeq *hLoadChrom(char *db, char *chromName);
 /* Fetch entire chromosome into memory. */
 
 void hNibForChrom(char *db, char *chromName, char retNibName[HDB_MAX_PATH_STRING]);
 /* Get .nib file associated with chromosome. */
 
-void hNibForChromFromPath(char *nibPath, char *db, char *chromName, 
-			  char retNibName[HDB_MAX_PATH_STRING]);
-/* Get .nib file associated with chromosome, given a nib file path. */
-
 struct slName *hAllChromNames(char *db);
 /* Get list of all chromosomes in database. */
 
 char *hExtFileNameC(struct sqlConnection *conn, char *extFileTable, unsigned extFileId);
 /* Get external file name from table and ID.  Typically
  * extFile table will be 'extFile' or 'gbExtFile'
  * Abort if the id is not in the table or if the file
  * fails size check.  Please freeMem the result when you
  * are done with it. (requires conn passed in) */
 
 char *hExtFileName(char *db, char *extFileTable, unsigned extFileId);
 /* Get external file name from table and ID.  Typically
  * extFile table will be 'extFile' or 'gbExtFile'
  * Abort if the id is not in the table or if the file
  * fails size check.  Please freeMem the result when you