12d0f12bd304787c52cab0780e367d36b020f84e
kent
  Tue Feb 26 12:11:18 2013 -0800
Adding name index to bigBed files.  The write side I _think_ is working.  Still developing read side.
diff --git src/lib/bbiWrite.c src/lib/bbiWrite.c
index fce4c04..811d116 100644
--- src/lib/bbiWrite.c
+++ src/lib/bbiWrite.c
@@ -120,53 +120,62 @@
 }
 
 void bbiChromUsageFreeList(struct bbiChromUsage **pList)
 /* free a list of bbiChromUsage structures */
 {
 struct bbiChromUsage *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     bbiChromUsageFree(&el);
     }
 *pList = NULL;
 }
 
-struct bbiChromUsage *bbiChromUsageFromBedFile(struct lineFile *lf, 
-	struct hash *chromSizesHash, int *retMinDiff, double *retAveSize, bits64 *retBedCount)
+struct bbiChromUsage *bbiChromUsageFromBedFile(struct lineFile *lf, struct hash *chromSizesHash, 
+	int *retMinDiff, double *retAveSize, bits64 *retBedCount, int *retMaxNameSize)
 /* Go through bed file and collect chromosomes and statistics. */
 {
-char *row[3];
+char *row[4];
+int maxRowSize = (retMaxNameSize != NULL ? 4 : 3);
 struct hash *uniqHash = hashNew(0);
 struct bbiChromUsage *usage = NULL, *usageList = NULL;
 int lastStart = -1;
 bits32 id = 0;
 bits64 totalBases = 0, bedCount = 0;
 int minDiff = BIGNUM;
+int maxNameSize = 0;
 
 lineFileRemoveInitialCustomTrackLines(lf);
 
 for (;;)
     {
-    int rowSize = lineFileChopNext(lf, row, ArraySize(row));
+    int rowSize = lineFileChopNext(lf, row, maxRowSize);
     if (rowSize == 0)
         break;
-    lineFileExpectWords(lf, 3, rowSize);
+    lineFileExpectAtLeast(lf, maxRowSize, rowSize);
     char *chrom = row[0];
     int start = lineFileNeedNum(lf, row, 1);
     int end = lineFileNeedNum(lf, row, 2);
+    if (rowSize > 3)
+        {
+	char *name = row[3];
+	int nameSize = strlen(name);
+	if (nameSize > maxNameSize)
+	    maxNameSize = nameSize;
+	}
     if (start > end)
         {
 	    errAbort("end (%d) before start (%d) line %d of %s",
 	    	end, start, lf->lineIx, lf->fileName);
 	}
     ++bedCount;
     totalBases += (end - start);
     if (usage == NULL || differentString(usage->name, chrom))
         {
 	if (hashLookup(uniqHash, chrom))
 	    {
 	    errAbort("%s is not sorted at line %d.  Please use \"sort -k1,1 -k2,2n\" or bedSort and try again.",
 	    	lf->fileName, lf->lineIx);
 	    }
 	hashAdd(uniqHash, chrom, NULL);
@@ -189,30 +198,32 @@
 	int diff = start - lastStart;
 	if (diff < minDiff)
 	    {
 	    if (diff < 0)
 		errAbort("%s is not sorted at line %d.  Please use \"sort -k1,1 -k2,2n\" or bedSort and try again.",
 		    lf->fileName, lf->lineIx);
 	    minDiff = diff;
 	    }
 	}
     lastStart = start;
     }
 slReverse(&usageList);
 *retMinDiff = minDiff;
 *retAveSize = (double)totalBases/bedCount;
 *retBedCount = bedCount;
+if (retMaxNameSize != NULL)
+    *retMaxNameSize = maxNameSize;
 freeHash(&uniqHash);
 return usageList;
 }
 
 int bbiCountSectionsNeeded(struct bbiChromUsage *usageList, int itemsPerSlot)
 /* Count up number of sections needed for data. */
 {
 struct bbiChromUsage *usage;
 int count = 0;
 for (usage = usageList; usage != NULL; usage = usage->next)
     {
     int countOne = (usage->itemCount + itemsPerSlot - 1)/itemsPerSlot;
     count += countOne;
     verbose(2, "%s %d, %d blocks of %d\n", usage->name, usage->itemCount, countOne, itemsPerSlot);
     }