e9ed25747e3d8ab10963306b826f7cedc5e71897
Merge parents b18f2f9facb 992aeef92fe
braney
  Mon Sep 7 11:35:30 2026 -0700
Merge branch 'quickLiftAlign38249' -- alignment tracks in quickLift, refs #38249

# Conflicts:
#       src/hg/lib/trackHub.c

diff --cc src/hg/inc/chainNetDbLoad.h
index d3a3b980553,4f5bca16631..a00f2c0d9c7
--- src/hg/inc/chainNetDbLoad.h
+++ src/hg/inc/chainNetDbLoad.h
@@@ -8,72 -8,53 +8,77 @@@
  #ifndef CHAINNETDBLOAD_H
  #define CHAINNETDBLOAD_H
  
  #ifndef JKSQL_H
  #include "jksql.h"
  #endif
  
  #ifndef NETALIGN_H
  #include "netAlign.h"
  #endif
  
  #ifndef CHAINNET_H
  #include "chainNet.h"
  #endif
  
 +#ifndef BIGNET_H
 +#include "bigNet.h"
 +#endif
 +
 +#ifndef BIGBED_H
 +#include "bigBed.h"
 +#endif
 +
  
  struct cnFill *cnFillFromNetAlign(struct netAlign *na, struct hash *nameHash);
  /* Convert netAlign to cnFill. Name hash is a place to store
   * the strings. */
  
  struct chainNet *chainNetLoadResult(struct sqlResult *sr, int rowOffset);
  /* Given a query result that returns a bunch netAligns, make up
   * a list of chainNets that has the equivalent information. 
   * Note the net->size field is not filled in. */
  
  struct chainNet *chainNetLoadRange(char *database, char *track,
  	char *chrom, int start, int end, char *extraWhere);
  /* Load parts of a net track that intersect range. */
  
 +struct chainNet *chainNetLoadRangeHub(char *fileName, char *chrom, int start, int end);
 +/* Load the parts of a bigNet file that intersect range into a chainNet.
 + * Note the net->size field is not filled in. */
 +
 +struct chainNet *chainNetLoadRangeQuickLift(char *quickLiftFile, char *fileName,
 +                                            char *chrom, int start, int end);
 +/* Load the part of a bigNet file that quickLifts into chrom:start-end, and build a
 + * chainNet in the destination assembly's coordinates.  Only the target side of the net
 + * moves; the query side describes a third assembly and is carried across untouched.
 + * Note the net->size field is not filled in. */
 +
 +struct bigNet *bigNetFromInterval(struct bbiFile *bbi, struct bigBedInterval *bb,
 +                                  char *fileName, struct bigNet *bn);
 +/* Fill in bn from one interval of a bigNet file.  The chrom name is the one the file
 + * carries, which for a quickLifted net is in the source assembly. */
 +
  struct chainNet *chainNetLoadChrom(char *database, char *track,
  	char *chrom, char *extraWhere);
  /* Load net on whole chromosome. */
  
+ struct chain *chainLoadRange(char *database, char *track, char *chrom, int start, int end);
+ /* Load every chain in a range from the database, each carrying the blocks that overlap the
+  * range.  As with chainLoadIdRange the chain header still describes the whole chain, not
+  * just the part in range. */
+ 
  struct chain *chainLoadIdRangeHub(char *database, char *fileName, char *track, char *chrom, 
  	int start, int end, int id);
  /* Load parts of chain of given ID from bigChain file.  Note the chain header
   * including score, tStart, tEnd, will still reflect the whole chain,
   * not just the part in range.  However only the blocks of the chain
   * overlapping the range will be loaded. */
  
  struct chain *chainLoadIdRange(char *database, char *track, char *chrom, 
  	int start, int end, int id);
  /* Load parts of chain of given ID from database.  Note the chain header
   * including score, tStart, tEnd, will still reflect the whole chain,
   * not just the part in range.  However only the blocks of the chain
   * overlapping the range will be loaded. */
  
  struct chain *chainLoadId(char *database, char *track, char *chrom, int id);