src/hg/hgTables/sumStats.c 1.29

Index: src/hg/hgTables/sumStats.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgTables/sumStats.c,v
retrieving revision 1.28
retrieving revision 1.29
diff -b -B -U 1000000 -r1.28 -r1.29
--- src/hg/hgTables/sumStats.c	20 May 2009 20:59:57 -0000	1.28
+++ src/hg/hgTables/sumStats.c	3 Jun 2010 18:54:00 -0000	1.29
@@ -1,386 +1,386 @@
 /* sumStats - show summary statistics output. */
 
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "obscure.h"
 #include "htmshell.h"
 #include "cheapcgi.h"
 #include "cart.h"
 #include "jksql.h"
 #include "hdb.h"
 #include "web.h"
 #include "hui.h"
 #include "hdb.h"
 #include "bits.h"
 #include "trackDb.h"
 #include "customTrack.h"
 #include "hgSeq.h"
 #include "agpGap.h"
 #include "portable.h"
 #include "botDelay.h"
 #include "hgTables.h"
 #include "wikiTrack.h"
 
 static char const rcsid[] = "$Id$";
 
 long long basesInRegion(struct region *regionList, int limit)
 /* Count up all bases in regions to limit number of regions, 0 == no limit */
 {
 long long total = 0;
 struct region *region;
 int regionCount = 0;
 
 for (region = regionList;
 	(region != NULL) && (!(limit && (regionCount >= limit)));
 	    region = region->next, ++regionCount)
     {
     total += region->end - region->start;
     }
 return total;
 }
 
 long long gapsInRegion(struct sqlConnection *conn, struct region *regionList,
 	int limit)
 /* Return count of gaps in all regions to limit number of regions,
  *	limit=0 == no limit, do them all
  */
 {
 long long gapBases = 0;
 char *splitTable = chromTable(conn, "gap");
 int regionCount = 0;
 
 if (sqlTableExists(conn, splitTable))
     {
     struct region *region;
     for (region = regionList;
 	    (region != NULL) && (!(limit && (regionCount >= limit)));
 		region = region->next, ++regionCount)
 	{
 	int rowOffset;
 	char **row;
 	struct agpGap gap;
 	struct sqlResult *sr = hRangeQuery(conn, "gap",
 		region->chrom, region->start, region->end,
 		NULL, &rowOffset);
 	while ((row = sqlNextRow(sr)) != NULL)
 	    {
 	    agpGapStaticLoad(row + rowOffset, &gap);
 	    if (gap.chromStart < region->start) gap.chromStart = region->start;
 	    if (gap.chromEnd > region->end) gap.chromEnd = region->end;
 	    gapBases += gap.chromEnd - gap.chromStart;
 	    }
 	sqlFreeResult(&sr);
 	}
     }
 freez(&splitTable);
 return gapBases;
 }
 
 struct covStats
 /* Coverage stats on one region. */
     {
     struct covStats *next;
     struct region *region;  /* Region this refers to. */
     Bits *bits;	    	    /* Bitmap for region. */
     long long basesCovered; /* No double counting of bases. */
     long long sumBases;	    /* Sum of bases in items. */
     int itemCount;	    /* Number of items. */
     int minBases, maxBases; /* Min/max size of items. */
     };
 
 struct covStats *covStatsNew(struct region *region)
 /* Get new covStats. */
 {
 struct covStats *cov;
 AllocVar(cov);
 cov->region = region;
 cov->minBases = BIGNUM;
 if (region != NULL)
     {
     cov->bits = bitAlloc(region->end - region->start);
     }
 return cov;
 }
 
 static void covAddRange(struct covStats *cov, int start, int end)
 /* Add range to stats. */
 {
 struct region *r = cov->region;
 if (end > r->start && start < r->end)
     {
     int unclippedSize, size;
     unclippedSize = end - start;
     if (start < r->start) start = r->start;
     if (end > r->end) end = r->end;
     size = end-start;
     bitSetRange(cov->bits, start - r->start, size);
     cov->sumBases += size;
     cov->itemCount += 1;
     if (unclippedSize > cov->maxBases) cov->maxBases = unclippedSize;
     if (unclippedSize < cov->minBases) cov->minBases = unclippedSize;
     }
 }
 
 void covStatsFree(struct covStats **pCov)
 /* Free up memory associated with covStats. */
 {
 struct covStats *cov = *pCov;
 if (cov != NULL)
     {
     bitFree(&cov->bits);
     freez(pCov);
     }
 }
 
 void covStatsFreeList(struct covStats **pList)
 /* Free a list of dynamically allocated covStats's */
 {
 struct covStats *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     covStatsFree(&el);
     }
 *pList = NULL;
 }
 
 struct covStats *covStatsSum(struct covStats *list)
 /* Add together list of covStats. */
 {
 struct covStats *tot, *cov;
 tot = covStatsNew(NULL);
 for (cov = list; cov != NULL; cov = cov->next)
     {
     if (cov->itemCount > 0)
         {
 	tot->basesCovered += cov->basesCovered;
 	tot->sumBases += cov->sumBases;
 	tot->itemCount += cov->itemCount;
 	if (tot->minBases > cov->minBases) tot->minBases = cov->minBases;
 	if (tot->maxBases < cov->maxBases) tot->maxBases = cov->maxBases;
 	}
     }
 return tot;
 }
 
 static void basesCoveredFromBits(struct covStats *cov)
 /* Calculate basesCovered from bits for each item on list. */
 {
 int regionSize = cov->region->end - cov->region->start;
 cov->basesCovered = bitCountRange(cov->bits, 0, regionSize);
 bitFree(&cov->bits);
 }
 
 static struct covStats *calcSpanOverRegion(struct region *region,
 	struct bed *bedList)
 /* Get stats calculated over regions. */
 {
 struct covStats *cov = covStatsNew(region);
 struct bed *bed;
 
 for (bed = bedList; bed != NULL; bed = bed->next)
     covAddRange(cov, bed->chromStart, bed->chromEnd);
 basesCoveredFromBits(cov);
 return cov;
 }
 
 static struct covStats *calcBlocksOverRegion(struct region *region,
 	struct bed *bedList)
 /* Get stats calculated over blocks in regions. */
 {
 struct covStats *cov = covStatsNew(region);
 struct bed *bed;
 
 for (bed = bedList; bed != NULL; bed = bed->next)
     {
     int i, blockCount = bed->blockCount;
     for (i=0; i<blockCount; ++i)
 	{
 	int start = bed->chromStarts[i] + bed->chromStart;
 	covAddRange(cov, start, start + bed->blockSizes[i]);
 	}
     }
 basesCoveredFromBits(cov);
 return cov;
 }
 
 void percentStatRow(char *label, long long p, long long q)
 /* Print label, p, and p/q */
 {
 hPrintf("<TR><TD>%s</TD><TD ALIGN=RIGHT>", label);
 printLongWithCommas(stdout, p);
 if (q != 0)
     hPrintf(" (%3.2f%%)", 100.0 * p/q);
 hPrintf("</TD></TR>\n");
 }
 
 void numberStatRow(char *label, long long x)
 /* Print label, x in table. */
 {
 hPrintf("<TR><TD>%s</TD><TD ALIGN=RIGHT>", label);
 printLongWithCommas(stdout, x);
 hPrintf("</TD></TR>\n");
 }
 
 void floatStatRow(char *label, double x)
 /* Print label, x in table. */
 {
 hPrintf("<TR><TD>%s</TD><TD ALIGN=RIGHT>", label);
 hPrintf("%3.2f", x);
 hPrintf("</TD></TR>\n");
 }
 
 
 void stringStatRow(char *label, char *val)
 /* Print label, string value. */
 {
 hPrintf("<TR><TD>%s</TD><TD ALIGN=RIGHT>%s</TD></TR>\n", label, val);
 }
 
 void wigFilterStatRow(struct sqlConnection *conn)
 /* Put row in statistics table that says what wig filter is on. */
 {
 hPrintf("<TR><TD>filter</TD><TD ALIGN=RIGHT>");
 if (anyFilter())
     wigShowFilter(conn);
 else
     hPrintf("off");
 hPrintf("</TD></TR>\n");
 }
 
 void doSummaryStatsBed(struct sqlConnection *conn)
 /* Put up page showing summary stats for track that is in database
  * or that is bed-format custom. */
 {
 struct bed *bedList = NULL;
 struct region *regionList = getRegions(), *region;
 char *regionName = getRegionName();
 long long regionSize = 0, gapTotal = 0, realSize = 0;
 long startTime, midTime, endTime;
 long loadTime = 0, calcTime = 0, freeTime = 0;
 struct covStats *itemCovList = NULL, *blockCovList = NULL, *cov;
 int itemCount = 0;
 struct hTableInfo *hti = getHti(database, curTable, conn);
 int minScore = BIGNUM, maxScore = -BIGNUM;
 long long sumScores = 0;
 boolean hasBlocks = hti->hasBlocks;
 boolean hasScore = (hti->scoreField[0] != 0);
 int fieldCount;
 
 htmlOpen("%s (%s) Summary Statistics", curTableLabel(), curTable);
 
 for (region = regionList; region != NULL; region = region->next)
     {
     struct lm *lm = lmInit(64*1024);
     startTime = clock1000();
     bedList = cookedBedList(conn, curTable, region, lm, &fieldCount);
     if (fieldCount < 12)
          hasBlocks = FALSE;
     if (fieldCount < 5)
          hasScore = FALSE;
     midTime = clock1000();
     loadTime += midTime - startTime;
 
     if (bedList != NULL)
 	{
 	itemCount += slCount(bedList);
 	regionSize += region->end - region->start;
 	cov = calcSpanOverRegion(region, bedList);
 	slAddHead(&itemCovList, cov);
 	if (hasBlocks)
 	    {
 	    cov = calcBlocksOverRegion(region, bedList);
 	    slAddHead(&blockCovList, cov);
 	    }
 	if (hti->scoreField[0] != 0)
 	    {
 	    struct bed *bed;
 	    for (bed = bedList; bed != NULL; bed = bed->next)
 		{
 		int score = bed->score;
 		if (score < minScore) minScore = score;
 		if (score > maxScore) maxScore = score;
 		sumScores += score;
 		}
 	    }
 	}
     endTime = clock1000();
     calcTime += endTime - midTime;
     lmCleanup(&lm);
     bedList = NULL;
     freeTime  += clock1000() - endTime;
     }
 
 regionSize = basesInRegion(regionList, 0);
 gapTotal = gapsInRegion(conn, regionList, 0);
 realSize = regionSize - gapTotal;
 
 
 hTableStart();
 startTime = clock1000();
 numberStatRow("item count", itemCount);
 if (itemCount > 0)
     {
     cov = covStatsSum(itemCovList);
     percentStatRow("item bases", cov->basesCovered, realSize);
     percentStatRow("item total", cov->sumBases, realSize);
     numberStatRow("smallest item", cov->minBases);
     numberStatRow("average item", round((double)cov->sumBases/cov->itemCount));
     numberStatRow("biggest item", cov->maxBases);
     }
 
 if (hasBlocks && itemCount > 0)
     {
     cov = covStatsSum(blockCovList);
     hPrintf("<TR><TD>block count</TD><TD ALIGN=RIGHT>");
     printLongWithCommas(stdout, cov->itemCount);
     hPrintf("</TD></TR>\n");
     percentStatRow("block bases", cov->basesCovered, realSize);
     percentStatRow("block total", cov->sumBases, realSize);
     numberStatRow("smallest block", cov->minBases);
     numberStatRow("average block", round((double)cov->sumBases/cov->itemCount));
     numberStatRow("biggest block", cov->maxBases);
     }
 
 if (hasScore != 0 && itemCount > 0 && sumScores != 0)
     {
     numberStatRow("smallest score", minScore);
     numberStatRow("average score", round((double)sumScores/itemCount));
     numberStatRow("biggest score", maxScore);
     }
 hTableEnd();
 
 /* Show region and time stats part of stats page. */
 webNewSection("Region and Timing Statistics");
 hTableStart();
 stringStatRow("region", regionName);
 numberStatRow("bases in region", regionSize);
 numberStatRow("bases in gaps", gapTotal);
 floatStatRow("load time", 0.001*loadTime);
 floatStatRow("calculation time", 0.001*calcTime);
 floatStatRow("free memory time", 0.001*freeTime);
 stringStatRow("filter", (anyFilter() ? "on" : "off"));
 stringStatRow("intersection", (anyIntersection() ? "on" : "off"));
 hTableEnd();
 covStatsFreeList(&itemCovList);
 covStatsFreeList(&blockCovList);
 htmlClose();
 }
 
 void doSummaryStats(struct sqlConnection *conn)
 /* Put up page showing summary stats for track. */
 {
 hgBotDelay();
 if (isWiggle(database, curTable))
     doSummaryStatsWiggle(conn);
-else if (isBigWig(curTable))
+else if (isBigWigTable(curTable))
     doSummaryStatsBigWig(conn);
 else if (isChromGraph(findTdbForTable(database, curTrack, curTable, ctLookupName)))
     doSummaryStatsChromGraph(conn);
 else if (sameWord(curTable,WIKI_TRACK_TABLE))
     doSummaryStatsWikiTrack(conn);
 else
     doSummaryStatsBed(conn);
 }