4898794edd81be5285ea6e544acbedeaeb31bf78
max
  Tue Nov 23 08:10:57 2021 -0800
Fixing pointers to README file for license in all source code files. refs #27614

diff --git src/hg/hgTables/hal.c src/hg/hgTables/hal.c
index 62bca50..cfb0582 100644
--- src/hg/hgTables/hal.c
+++ src/hg/hgTables/hal.c
@@ -1,95 +1,95 @@
 /* Copyright (C) 2013 The Regents of the University of California 
- * See README in this or parent directory for licensing information. */
+ * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #include "common.h"
 #include "cart.h"
 #include "jksql.h"
 #include "grp.h"
 #include "hubConnect.h"
 #include "hdb.h"
 #include "maf.h"
 #include "hgTables.h"
 #include "trackHub.h"
 #ifdef USE_HAL
 #include "halBlockViz.h"
 #endif // USE_HAL
 
 extern struct trackDb *curTrack;	/* Currently selected track. */
 extern char *database;
 extern struct hash *fullTableToTdbHash;        /* All tracks and subtracks keyed by tdb->table field. */
 
 boolean isHalTable(char *table)
 /* Return TRUE if table corresponds to a HAL file. */
 {
 if (isHubTrack(table))
     {
     struct trackDb *tdb = hashFindVal(fullTableToTdbHash, table);
     return startsWithWord("halSnake", tdb->type);
     }
 else
     return trackIsType(database, table, curTrack, "halSnake", ctLookupName);
 }
 
 struct trackDb *findTrackDb(struct trackDb *trackDb, char *table)
 // find a child of a composite that corresponds to this table
 {
 if (sameString(trackDb->table, table))
     return trackDb;
 
 struct trackDb *subTrack = trackDb->subtracks;
 struct trackDb *childTrackDb;
 for(; subTrack; subTrack = subTrack->next)
     {
     if ((childTrackDb = findTrackDb(subTrack, table)) != NULL)
 	return childTrackDb;
     }
 return NULL;
 }
 
 void doHalMaf(struct trackDb *parentTrack, char *table, struct sqlConnection *conn)
 /* Output regions as MAF.  maf tables look bed-like enough for
  * cookedBedsOnRegions to handle intersections. */
 {
 #ifdef USE_HAL
 struct region *region = NULL, *regionList = getRegions();
 struct trackDb *tdb;
 
 if ((tdb = findTrackDb(parentTrack, table)) == NULL)
     errAbort("cannot find track named %s under %s\n", table, parentTrack->table);
 char *fileName = trackDbSetting(tdb, "bigDataUrl");
 char *otherSpecies = trackDbSetting(tdb, "otherSpecies");
 char *errString;
 int handle = halOpenLOD(fileName, &errString);
 if (handle < 0)
     errAbort("HAL open error: %s\n", errString);
 
 struct hal_species_t *speciesList = halGetSpecies(handle, &errString);
 
 if (speciesList == NULL)
     errAbort("HAL get species error: %s\n", errString);
 
 for(; speciesList; speciesList = speciesList->next)
     {
     if  (sameString(speciesList->name, otherSpecies))
 	break;
     }
 if (speciesList == NULL)
     errAbort("cannot find species %s in hal file %s\n",
 	otherSpecies, fileName);
 
 speciesList->next = NULL;
 
 textOpen();
 
 for (region = regionList; region != NULL; region = region->next)
     {
     if (halGetMAF(stdout, handle, speciesList,
 		trackHubSkipHubName(database), region->chrom,
 		region->start, region->end, FALSE, &errString) < 0 )
 	errAbort("HAL get MAF error: %s\n", errString);
 
     }
 #else // USE_HAL
 errAbort("hgTables not compiled with HAL support.");
 #endif // USE_HAL
 }