a75cfac22803c312074299aa0dcf286ca336ce89
braney
  Wed Aug 27 13:28:08 2025 -0700
ongoing work on quickLift hgc page plus a fix for genepreds that don't
successfully quickLift

diff --git src/hg/lib/quickLift.c src/hg/lib/quickLift.c
index 813bfb27624..1cb075c0af7 100644
--- src/hg/lib/quickLift.c
+++ src/hg/lib/quickLift.c
@@ -11,44 +11,30 @@
 #include "binRange.h"
 #include "basicBed.h"
 #include "liftOver.h"
 #include "hash.h"
 #include "bigBed.h"
 #include "bbiFile.h"
 #include "chainNetDbLoad.h"
 #include "hdb.h"
 #include "jksql.h"
 #include "hgConfig.h"
 #include "quickLift.h"
 #include "bigChain.h"
 #include "bigLink.h"
 #include "chromAlias.h"
 
-#define QUICKTYPE_INSERT     0
-#define QUICKTYPE_DEL      1
-#define QUICKTYPE_DOUBLE     2
-#define QUICKTYPE_MISMATCH     3
-#define QUICKTYPE_NOTHING     4
-
-char *quickTypeStrings[] = 
-{
-    "insert",
-    "deletion",
-    "double",
-    "mismatch"
-};
-
 struct bigBedInterval *quickLiftGetIntervals(char *quickLiftFile, struct bbiFile *bbi,   char *chrom, int start, int end, struct hash **pChainHash)
 /* Return intervals from "other" species that will map to the current window.
  * These intervals are NOT YET MAPPED to the current assembly.
  */
 {
 char *linkFileName = bigChainGetLinkFile(quickLiftFile);
 int maxGapBefore = 0;
 int maxGapAfter = 0;
 struct chain *chain, *chainList = chainLoadIdRangeHub(NULL, quickLiftFile, linkFileName, chrom, start, end, -1);
 struct lm *lm = lmInit(0);
 struct bigBedInterval *bbList = NULL, *bb;
 
 for(chain = chainList; chain; chain = chain->next)
     {
     struct cBlock *cb;
@@ -402,40 +388,30 @@
     int previousQEnd = -1;
     for (bbLink = bbLinkList; bbLink != NULL; bbLink = bbLink->next)
         {
         bigBedIntervalToRow(bbLink, chrom, startBuf, endBuf, linkRow, ArraySize(linkRow));
         struct bigLink *bl = bigLinkLoad(linkRow);
 
         if (!sameString(bl->name, bc->name))
             continue;
 
         int tStart = bl->chromStart;
         int tEnd = bl->chromEnd;
         int qStart = bl->qStart;
         int qEnd = qStart + (tEnd - tStart);
 
         struct quickLiftRegions *hr;
-        AllocVar(hr);
-        //slAddHead(&hrList, hr);
-        hr->chrom = cloneString(bc->chrom);
-        hr->oChrom = cloneString(bc->qName);
-        hr->chromStart = tStart;
-        hr->chromEnd = tEnd;
-        hr->oChromStart = qStart;
-        hr->oChromEnd = qEnd;
-        hr->type = QUICKTYPE_NOTHING;
-        hr->id = bc->name;
 
         if ((previousTEnd != -1) && (previousTEnd == tStart))
             {
             hr = fillWithGap(bc, previousTEnd, tStart, previousQEnd, qStart);
             slAddHead(&hrList, hr);
             hr->type = QUICKTYPE_DEL;
             struct dnaSeq *qSeq = NULL;
             if (bc->strand[0] == '-')
                 {
                 qSeq = hDnaFromSeq(liftDb, bc->qName, bc->qSize - hr->oChromEnd, bc->qSize - hr->oChromStart, dnaUpper);
                 reverseComplement(qSeq->dna, qSeq->size);
                 }
             else
                 qSeq = hDnaFromSeq(liftDb, bc->qName, hr->oChromStart, hr->oChromEnd, dnaUpper);
             hr->otherBases = qSeq->dna;