6d0dc8601b91fa9cbc3266992a8e26da73704dc5
braney
  Thu Jul 27 18:06:38 2023 -0700
remove instaPort track type

diff --git src/hg/hgTracks/instaPortTrack.c src/hg/hgTracks/instaPortTrack.c
deleted file mode 100644
index 5da82b2..0000000
--- src/hg/hgTracks/instaPortTrack.c
+++ /dev/null
@@ -1,104 +0,0 @@
-
-/* 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 "hgTracks.h"
-#include "bedCart.h"
-#include "bigWarn.h"
-#include "lolly.h"
-#include "limits.h"
-#include "float.h"
-#include "bigBedFilter.h"
-#include "asParse.h"
-#include "chromAlias.h"
-#include "chain.h"
-#include "binRange.h"
-
-struct chromMap
-/* Remapping information for one (old) chromosome */
-    {
-    char *name;                 /* Chromosome name. */
-    struct binKeeper *bk;       /* Keyed by old position, values are chains. */
-    };
-
-struct hash *makeChainHash(struct chain *chain)
-{
-struct chromMap *map;
-
-struct hash *chainHash = newHash(0);
-
-if ((map = hashFindVal(chainHash, chain->tName)) == NULL)
-    {
-    AllocVar(map);
-    map->bk = binKeeperNew(0, chain->tSize);
-    hashAddSaveName(chainHash, chain->tName, map, &map->name);
-    }
-binKeeperAdd(map->bk, chain->tStart, chain->tEnd, chain);
-
-return chainHash;
-}
-
-static void instaPortLoadItems(struct track *track)
-{
-struct linkedFeatures *lfList = NULL;
-char *fileName = cloneString(trackDbSetting(track->tdb, "bigChainUrl"));
-char *linkFileName = cloneString(trackDbSetting(track->tdb, "linkDataUrl"));
-extern struct chain *chainLoadIdRangeHub(char *db, char *fileName, char *linkFileName,   char *chrom, int start, int end, int id);
-// maybe add some slop here for items that cross the window boundaries ?
-struct chain *chainList = chainLoadIdRangeHub(database, fileName, linkFileName, chromName, winStart, winEnd, -1);
-
-struct chain *chain;
-for(chain = chainList; chain; chain = chain->next)
-    {
-    struct cBlock *cb;
-    cb = chain->blockList; 
-    int qStart = cb->qStart;
-    int qEnd = cb->qEnd;
-    for(; cb; cb = cb->next)
-        {
-        if (cb->qStart < qStart)
-            qStart = cb->qStart;
-        if (cb->qEnd > qEnd)
-            qEnd = cb->qEnd;
-        }
-
-    // now grab the items 
-    struct lm *lm = lmInit(0);
-    struct bbiFile *bbi = fetchBbiForTrack(track);
-    struct bigBedInterval *bb, *bbList = bigBedIntervalQuery(bbi, chain->qName, qStart, qEnd, 10000, lm);
-
-    for (bb = bbList; bb != NULL; bb = bb->next)
-        {
-        char startBuf[16], endBuf[16];
-        char *bedRow[bbi->fieldCount];
-        bigBedIntervalToRow(bb, chain->qName, startBuf, endBuf, bedRow, ArraySize(bedRow));
-
-        // now we're going to use the same chain we queried on to map the items, but we need to swap it
-        chainSwap(chain);
-
-        struct hash *chainHash = makeChainHash(chain);
-        struct bed *bed = bedLoadN(bedRow, 12);//bbi->fieldCount);
-        extern char *remapBlockedBed(struct hash *chainHash, struct bed *bed,
-                                     double minMatch, double minBlocks, bool fudgeThick,
-                                                                  bool multiple, char *db, char *chainTable)
-                                                                  ;
-        if (remapBlockedBed(chainHash, bed, 0.0, 0.1, TRUE, TRUE, NULL, NULL) == NULL)
-            {
-            struct linkedFeatures *lf = lfFromBedExtra(bed, 0, 1000);
-            slAddHead(&lfList, lf);
-            }
-        }
-    }
-track->items = lfList;
-}
-
-void instaPortMethods(struct track *track, struct trackDb *tdb, 
-                                int wordCount, char *words[])
-{
-char *mywords[2];
-mywords[1] = "12";
-bigBedMethods(track, tdb, 2, mywords);
-track->loadItems = instaPortLoadItems;
-}