7f65d3da8f2138d847f15a8398f8dcee1a079027
braney
  Fri Aug 7 12:07:59 2026 -0700
quickLift: clip an oversized item to the chains we loaded instead of dropping it, refs #38042

quickLift loads chains for the window plus padding, capped at 1 Mb.  An item that
reaches further than that has ends where no chain reaches, remapRangeList can
place neither of them, and the whole item is dropped even though the part on
screen maps fine.  ClinVar copy number variants run to 159 Mb, so 44 of the 46 in
one window disappeared.

Pull the ends in to what the chains cover before mapping.  The browser never
draws the ends of an item that spans the window, so their exact position does not
matter, and the existing spanned-item merge still reports it.  A clipped end is
snapped to a base inside an aligned block, since remapRangeList will only place a
coordinate that lands on real alignment.

The clip is in the quickLift code, not the shared liftOver remap path.  Only
hgTracks asks for it, so the details page keeps the item's true extent.  Gated by
quickLiftClipToChains, on by default.

diff --git src/hg/inc/liftOver.h src/hg/inc/liftOver.h
index d849fff3fe2..f293a83045e 100644
--- src/hg/inc/liftOver.h
+++ src/hg/inc/liftOver.h
@@ -128,20 +128,24 @@
 
 char *liftOverErrHelp();
 /* Help message explaining liftOver failures */
 
 char *remapBlockedBed(struct hash *chainHash, struct bed *bed,  
                              double minMatch, double minBlocks, bool fudgeThick,
                              bool multiple, char *db, char *chainTable);
 /* Remap blocks in bed, and also chromStart/chromEnd.  If multiple, then bed->next may be
  * changed to point to additional newly allocated mapped beds, and bed's pointer members may
  * be free'd so be sure to pass in a properly allocated bed.
  * Return NULL on success, an error string on failure. */
 
 void liftOverAddChainHash(struct hash *chainHash, struct chain *chain);
 /* Add this chain to the hash of chains used by remapBlockedBed */
 
+struct chain *liftOverChainForRange(struct hash *chainHash, char *chrom, int start, int end);
+/* Return the chain in chainHash covering the most aligned bases in the given range,
+ * or NULL if none overlap it.  This is the chain remapBlockedBed would also pick. */
+
 char *liftOverChainTable();
 /* Return the name of the liftOverChain table. */
 #endif