13b584581e6d7b1860e0cab97adc3594b1899308
braney
  Mon Aug 7 12:05:10 2023 -0700
add instaPort to bigBed support

diff --git src/hg/lib/instaPort.c src/hg/lib/instaPort.c
new file mode 100644
index 0000000..9af0ac1
--- /dev/null
+++ src/hg/lib/instaPort.c
@@ -0,0 +1,111 @@
+
+/* 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 "instaPort.h"
+
+static char *getLinkFile(char *instaPortFile)
+/* Construct the file name of the chain link file from the name of a chain file. 
+ * That is, change file.bb to file.link.bb */
+{
+char linkBuffer[4096];
+
+if (!endsWith(instaPortFile, ".bb"))
+    errAbort("instaPort file (%s) must end in .bb", instaPortFile);
+
+safef(linkBuffer, sizeof linkBuffer, "%s", instaPortFile);
+
+// truncate string at ending ".bb"
+int insertOffset = strlen(linkBuffer) - sizeof ".bb" + 1;
+char *insert = &linkBuffer[insertOffset];
+*insert = 0;
+
+// add .link.bb
+strcpy(insert, ".link.bb");
+
+return cloneString(linkBuffer);
+}
+
+struct bigBedInterval *instaIntervals(char *instaPortFile, 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 = getLinkFile(instaPortFile);
+// need to add some padding to these coordinates
+struct chain *chain, *chainList = chainLoadIdRangeHub(NULL, instaPortFile, linkFileName, chrom, start-100000, end+100000, -1);
+struct lm *lm = lmInit(0);
+struct bigBedInterval *bbList = 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;
+        }
+
+    // now grab the items 
+    struct bigBedInterval *thisInterval = bigBedIntervalQuery(bbi, chain->qName, qStart, qEnd, 10000, lm);
+    bbList = slCat(thisInterval, bbList);
+    
+    // for the mapping we're going to use the same chain we queried on to map the items, but we need to swap it
+    chainSwap(chain);
+
+    if (*pChainHash == NULL)
+        *pChainHash = newHash(0);
+    liftOverAddChainHash(*pChainHash, chain);
+    }
+
+return bbList;
+}
+
+struct bed *instaBed(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));
+//lastChromId=bb->chromId;
+
+bigBedIntervalToRow(bb, chromName, startBuf, endBuf, bedRow, ArraySize(bedRow));
+
+struct bed *bed = bedLoadN(bedRow, bbi->definedFieldCount);
+char *error;
+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;
+}