src/lib/bigBed.c 1.16

Index: src/lib/bigBed.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/lib/bigBed.c,v
retrieving revision 1.15
retrieving revision 1.16
diff -b -B -U 4 -r1.15 -r1.16
--- src/lib/bigBed.c	20 Apr 2009 23:16:18 -0000	1.15
+++ src/lib/bigBed.c	20 Apr 2009 23:21:04 -0000	1.16
@@ -16,10 +16,8 @@
 #include "udc.h"
 #include "bbiFile.h"
 #include "bigBed.h"
 
-#define TIMING 0
-
 struct bbiFile *bigBedFileOpen(char *fileName)
 /* Open up big bed file. */
 {
 return bbiFileOpen(fileName, bigBedSig, "big bed");
@@ -312,65 +310,47 @@
     /* Parse it and do sanity check. */
     as = asParseFile(asFileName);
     if (as->next != NULL)
         errAbort("Can only handle .as files containing a single object.");
-    if (TIMING)
-	uglyTime("Parsed file %s", asFileName);
     }
 
 /* Load in chromosome sizes. */
 struct hash *chromHash = bbiChromSizesFromFile(chromSizes);
 verbose(1, "Read %d chromosomes and sizes from %s\n",  chromHash->elCount, chromSizes);
-if (TIMING)
-    uglyTime("bbiChromSizesFromFile()");
 
 /* Load and sort input file. */
 bits64 fullSize;
 struct ppBed *pb, *pbList = ppBedLoadAll(inName, chromHash, chromHash->lm, as, 
 	definedFieldCount, &fullSize, &fieldCount);
 if (definedFieldCount == 0)
     definedFieldCount = fieldCount;
-if (TIMING)
-    uglyTime("ppBedLoadAll()");
 bits64 pbCount = slCount(pbList);
-if (TIMING)
-    uglyTime("slCount()");
 verbose(1, "Read %llu items from %s\n", pbCount, inName);
 if (!sorted)
     {
     slSort(&pbList, ppBedCmp);
-    if (TIMING)
-	uglyTime("slSort()");
     }
 
 /* Make chromosomes. */
 int chromCount, maxChromNameSize;
 struct bbiChromInfo *chromInfoArray;
 makeChromInfo(pbList, chromHash, &chromCount, &chromInfoArray, &maxChromNameSize);
 verbose(1, "%d of %d chromosomes used (%4.2f%%)\n", chromCount, chromHash->elCount, 
 	100.0*chromCount/chromHash->elCount);
-if (TIMING)
-    uglyTime("makeChromInfo()");
 
 /* Calculate first meaningful reduction size and make first reduction. */
 bits16 summaryCount = 0;
 bits16 version = 1;
 int initialReduction = ppBedAverageSize(pbList)*10;
-if (TIMING)
-    uglyTime("ppBedAverageSize()");
 verbose(2, "averageBedSize=%d\n", initialReduction/10);
 if (initialReduction > 10000)
     initialReduction = 10000;
 bits64 lastSummarySize = 0, summarySize;
 struct bbiSummary *summaryList, *firstSummaryList;
 for (;;)
     {
     summaryList = summaryOnDepth(pbList, chromInfoArray, initialReduction);
-    if (TIMING)
-	uglyTime("summaryOnDepth(initialReduction=%d)", initialReduction);
     summarySize = bbiTotalSummarySize(summaryList);
-    if (TIMING)
-	uglyTime("bbiTotalSummarySize(summarySize=%d,fullSize=%ld,lastSummarySize=%ld)", summarySize, fullSize, lastSummarySize);
     if (summarySize >= fullSize && summarySize != lastSummarySize)
         {
 	initialReduction *= 2;
 	bbiSummaryFreeList(&summaryList);
@@ -383,10 +363,8 @@
 reduceSummaries[0] = firstSummaryList = summaryList;
 reductionAmounts[0] = initialReduction;
 verbose(1, "Initial zoom reduction x%d data size %4.2f%%\n", 
 	initialReduction, 100.0 * summarySize/fullSize);
-if (TIMING)
-    uglyTime("first summary list");
 
 /* Now calculate up to 10 levels of further summary. */
 bits64 reduction = initialReduction;
 for (i=0; i<ArraySize(reduceSummaries)-1; i++)
@@ -395,13 +373,9 @@
     if (reduction > 1000000000)
         break;
     summaryList = bbiReduceSummaryList(reduceSummaries[summaryCount-1], chromInfoArray, 
     	reduction);
-    if (TIMING)
-	uglyTime("bbiReduceSummaryList(reduction=%ld)", reduction);
     summarySize = bbiTotalSummarySize(summaryList);
-    if (TIMING)
-	uglyTime("bbiTotalSummarySize(summarySize=%ld,summaryCount=%ld,lastSummarySize=%ld)", summarySize, summaryCount, lastSummarySize);
     if (summarySize != lastSummarySize)
         {
  	reduceSummaries[summaryCount] = summaryList;
 	reductionAmounts[summaryCount] = reduction;
@@ -411,10 +385,8 @@
     if (summaryItemCount <= chromCount)
         break;
     }
 
-if (TIMING)
-    uglyTime("reduce summaries");
 
 /* Open output file and write out fixed size header, including some dummy values for
  * offsets we'll fill in later. */
 FILE *f = mustOpen(outName, "wb");
@@ -442,10 +414,8 @@
     reductionDataOffsetPos[i] = ftell(f);
     writeOne(f, reserved64);	// Fill in with data offset later
     writeOne(f, reserved64);	// Fill in with index offset later
     }
-if (TIMING)
-    uglyTime("write summary headers");
 
 /* Optionally write out .as file. */
 if (asFileName != NULL)
     {
@@ -466,10 +436,8 @@
 bptFileBulkIndexToOpenFile(chromInfoArray, sizeof(chromInfoArray[0]), chromCount, chromBlockSize,
     bbiChromInfoKey, maxChromNameSize, bbiChromInfoVal, 
     sizeof(chromInfoArray[0].id) + sizeof(chromInfoArray[0].size), 
     f);
-if (TIMING)
-    uglyTime("write chromosome tree");
 
 /* Write the main data. */
 dataOffset = ftell(f);
 writeOne(f, pbCount);
@@ -487,10 +455,8 @@
 	}
     putc(0, f);
     }
 
-if (TIMING)
-    uglyTime("write the main data");
 /* Write the main index. */
 indexOffset = ftell(f);
 struct ppBed **pbArray;
 AllocArray(pbArray, pbCount);
@@ -499,20 +465,16 @@
 cirTreeFileBulkIndexToOpenFile(pbArray, sizeof(pbArray[0]), pbCount,
     blockSize, itemsPerSlot, NULL, ppBedFetchKey, ppBedFetchOffset, 
     indexOffset, f);
 freez(&pbArray);
-if (TIMING)
-    uglyTime("write the main index");
 
 /* Write out summary sections. */
 verbose(2, "bigBedFileCreate writing %d summaries\n", summaryCount);
 for (i=0; i<summaryCount; ++i)
     {
     reductionDataOffsets[i] = ftell(f);
     reductionIndexOffsets[i] = bbiWriteSummaryAndIndex(reduceSummaries[i], blockSize, itemsPerSlot, f);
     }
-if (TIMING)
-    uglyTime("write summary sections");
 
 /* Go back and fill in offsets properly in header. */
 fseek(f, dataOffsetPos, SEEK_SET);
 writeOne(f, dataOffset);
@@ -533,10 +495,8 @@
     writeOne(f, reductionDataOffsets[i]);
     writeOne(f, reductionIndexOffsets[i]);
     }
 
-if (TIMING)
-    uglyTime("filled in header and done.");
 carefulClose(&f);
 freez(&chromInfoArray);
 }