7f7a9a5579d7acec698c51dbf93f5030ce1a0439
braney
  Tue Apr 8 15:43:17 2025 -0700
support genePred in quickLift

diff --git src/hg/lib/quickLift.c src/hg/lib/quickLift.c
index e1710061e89..448909ae095 100644
--- src/hg/lib/quickLift.c
+++ src/hg/lib/quickLift.c
@@ -1,251 +1,251 @@
 
 /* Copyright (C) 2023 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #include "common.h"
 #include "obscure.h"
 #include "limits.h"
 #include "float.h"
 #include "asParse.h"
 #include "chain.h"
 #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"
 
 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;
     cb = chain->blockList; 
 
     if (cb == NULL)
         continue;
 
     int qStart = cb->qStart;
     int qEnd = cb->qEnd;
 
     // get the range for the links on the "other" species
     for(; cb; cb = cb->next)
         {
         if (cb->qStart < qStart)
             qStart = cb->qStart;
         if (cb->qEnd > qEnd)
             qEnd = cb->qEnd;
         }
 
     // now grab the items , probably we should parameterize the max number of items, but to what?
     struct bigBedInterval *thisInterval = NULL;
     if (chain->qStrand == '-')
         thisInterval = bigBedIntervalQuery(bbi, chain->qName, chain->qSize - qEnd, chain->qSize - qStart,  1000000, lm);
     else
         thisInterval = bigBedIntervalQuery(bbi, chain->qName, qStart, qEnd, 1000000, lm);
 
     // find how much of the items are beyond the viewport
     for(bb=thisInterval; bb; bb = bb->next)
         {
         if (bb->start < qStart)
             {
             int gap = qStart - bb->start;
             if (gap > maxGapBefore)
                 maxGapBefore = gap;
             }
         if (bb->end > qEnd)
             {
             int gap = bb->end - qEnd;
             if (gap > maxGapAfter)
                 maxGapAfter = gap;
             }
         }
     bbList = slCat(thisInterval, bbList);
     }
 
 // now we need to grab the links outside of our viewport so we can map long items
 // probably we could reuse the chains from above but for the moment this is easier
 int newStart = start - maxGapBefore * 2;
 if (newStart < 0)
     newStart = 0;
 int newEnd = end + maxGapAfter * 2;
 chainList = chainLoadIdRangeHub(NULL, quickLiftFile, linkFileName, chrom, newStart, newEnd, -1);
 for(chain = chainList; chain; chain = chain->next)
     {
     chainSwap(chain);
 
     if (*pChainHash == NULL)
         *pChainHash = newHash(0);
     liftOverAddChainHash(*pChainHash, chain);
     }
 
 return bbList;
 }
 
 static void make12(struct bed *bed)
 /* Make a bed12 out of something less than that. */
 {
 bed->blockCount = 1;
 bed->blockSizes = needMem(sizeof(int));
 bed->blockSizes[0] = bed->chromEnd - bed->chromStart;
 bed->chromStarts = needMem(sizeof(int));
 bed->chromStarts[0] = 0;
 }
 
 struct bed *quickLiftIntervalsToBed(struct bbiFile *bbi, struct hash *chainHash, struct bigBedInterval *bb)
 /* Using chains stored in chainHash, port a bigBedInterval from another assembly to a bed
  * on the reference.
  */
 {
 char startBuf[16], endBuf[16];
 char *bedRow[bbi->fieldCount];
 char chromName[256];
 static int lastChromId = -1;
 
 bbiCachedChromLookup(bbi, bb->chromId, lastChromId, chromName, sizeof(chromName));
 
 bigBedIntervalToRow(bb, chromName, startBuf, endBuf, bedRow, ArraySize(bedRow));
 
 struct bed *bed = bedLoadN(bedRow, bbi->definedFieldCount);
 char *error;
 if (bbi->definedFieldCount < 12)
     make12(bed);
 
 if ((error = remapBlockedBed(chainHash, bed, 0.0, 0.1, TRUE, TRUE, NULL, NULL)) == NULL)
     return bed;
 //else
     //printf("bed %s error:%s<BR>", bed->name, error);
 
 return NULL;
 }
 
 unsigned quickLiftGetChain(char *fromDb, char *toDb)
 /* Return the id from the quickLiftChain table for given assemblies. */
 {
 unsigned ret = 0;
 struct sqlConnection *conn = hConnectCentral();
 char query[2048];
 sqlSafef(query, sizeof(query), "select q.id from quickLiftChain q  where q.fromDb='%s' and q.toDb='%s'", fromDb, toDb);
 char *geneId = sqlQuickString(conn, query);
 
 hDisconnectCentral(&conn);
 
 if (geneId)
     ret = atoi(geneId);
 
 return ret;
 }
 
 struct slList *quickLiftSql(struct sqlConnection *conn, char *quickLiftFile, char *table, char *chrom, int start, int end,  char *query, char *extraWhere, ItemLoader2 loader, int numFields,struct hash *chainHash)
 // retrieve items for which we have a loader from a SQL database for which we have a set quickLift chains.  
 // Save the chains we used to map the item back to the current reference.
 {
 // need to add some padding to these coordinates
 int padStart = start - 100000;
 if (padStart < 0)
     padStart = 0;
 
 char *linkFileName = bigChainGetLinkFile(quickLiftFile);
 struct chain *chain, *chainList = chainLoadIdRangeHub(NULL, quickLiftFile, linkFileName, chrom, padStart, end+100000, -1);
 
 struct slList *item, *itemList = NULL;
 int rowOffset = 0;
 struct sqlResult *sr = NULL;
 char **row = NULL;
 
 for(chain = chainList; chain; chain = chain->next)
     {
     struct cBlock *cb;
     cb = chain->blockList; 
 
     if (cb == NULL)
         continue;
 
     int qStart = cb->qStart;
     int qEnd = cb->qEnd;
 
     // get the range for the links on the "other" species
     for(; cb; cb = cb->next)
         {
         if (cb->qStart < qStart)
             qStart = cb->qStart;
         if (cb->qEnd > qEnd)
             qEnd = cb->qEnd;
         }
 
     if (chain->qStrand == '-')
         qStart = chain->qSize - qStart;
 
     // now grab the items 
     if (query == NULL)
         sr = hRangeQuery(conn, table, chain->qName,
                          qStart, qEnd, extraWhere, &rowOffset);
     else
         sr = sqlGetResult(conn, query);
 
     while ((row = sqlNextRow(sr)) != NULL)
         {
         item = loader(row + rowOffset, numFields);
         slAddHead(&itemList, item);
         }
 
     // now squirrel the swapped chains we used to use to make the retrieved items back to us
     chainSwap(chain);
     liftOverAddChainHash(chainHash, chain);
     }
 
 return itemList;
 }
 
 struct bed *quickLiftBeds(struct bed *bedList, struct hash *chainHash, boolean blocked)
 // Map a list of bedd in query coordinates to our current reference
 {
 struct bed *liftedBedList = NULL;
 struct bed *nextBed;
 struct bed *bed;
 for(bed = bedList; bed; bed = nextBed)
     {
     // remapBlockedBed may want to add new beds after this bed if the region maps to more than one location
     nextBed = bed->next;
     bed->next = NULL;
 
     char *error;
     if (!blocked)
         {
         error = liftOverRemapRange(chainHash, 0.0, bed->chrom, bed->chromStart, bed->chromEnd, bed->strand[0],
                              
-                            0.1, &bed->chrom, (int *)&bed->chromStart, (int *)&bed->chromEnd, &bed->strand[0]);
+                            0.001, &bed->chrom, (int *)&bed->chromStart, (int *)&bed->chromEnd, &bed->strand[0]);
         }
     else
         error = remapBlockedBed(chainHash, bed, 0.0, 0.1, TRUE, TRUE, NULL, NULL);
 
     if (error == NULL)
         {
         slAddHead(&liftedBedList, bed);
         }
     }
 return liftedBedList;
 }
 
 boolean quickLiftEnabled()
 /* Return TRUE if feature is available */
 {
 char *cfgEnabled = cfgOption("browser.quickLift");
 return cfgEnabled && (sameString(cfgEnabled, "on") || sameString(cfgEnabled, "true")) ;
 }