d99fd7645ac2b1b33ef65111c23660c4076fecf7
kent
  Fri Apr 15 18:30:11 2011 -0700
Adding clipping options.
diff --git src/utils/bigWigMerge/bigWigMerge.c src/utils/bigWigMerge/bigWigMerge.c
index cf6e5f8..58ce49f 100644
--- src/utils/bigWigMerge/bigWigMerge.c
+++ src/utils/bigWigMerge/bigWigMerge.c
@@ -1,170 +1,180 @@
 /* bigWigMerge - Merge together multiple bigWigs into a single one.. */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "localmem.h"
 #include "bbiFile.h"
 #include "bigWig.h"
 
 static char const rcsid[] = "$Id: newProg.c,v 1.30 2010/03/24 21:18:33 hiram Exp $";
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "bigWigMerge - Merge together multiple bigWigs into a single output bedGraph.\n"
   "You'll have to run bedGraphToBigWig to make the output bigWig.\n"
   "The signal values are just added together to merge them\n"
   "usage:\n"
   "   bigWigMerge in1.bw in2.bw .. inN.bw out.bedGraph\n"
   "options:\n"
   "   -threshold=0.N - don't output values at or below this threshold. Default is 0.0\n"
   "   -adjust=0.N - add adjustment to each value\n"
+  "   -clip=NNN.N - values higher than this are clipped to this value\n"
   );
 }
 
 double clThreshold = 0.0;
 double clAdjust = 0.0;
+double clClip = BIGDOUBLE;
 
 static struct optionSpec options[] = {
    {"threshold", OPTION_DOUBLE},
    {"adjust", OPTION_DOUBLE},
+   {"clip", OPTION_DOUBLE},
    {NULL, 0},
 };
 
 struct slName *getAllChroms(struct bbiFile *fileList)
 /* Read chromosomes from all files and make sure they agree, and return merged list. */
 {
 struct bbiFile *file;
 struct hash *hash = hashNew(0);
 struct slName *nameList = NULL;
 for (file = fileList; file != NULL; file = file->next)
     {
     struct bbiChromInfo *info, *infoList = bbiChromList(file);
     for (info = infoList; info != NULL; info = info->next)
         {
 	struct bbiChromInfo *oldInfo = hashFindVal(hash, info->name);
 	if (oldInfo != NULL)
 	    {
 	    if (info->size != oldInfo->size)
 		errAbort("ERROR: Merging from different assemblies? "
 		         "Chromosome %s is %d in %s but %d in another file",
 			 info->name, (int)(info->size), file->fileName, (int)oldInfo->size);
 	    }
 	else
 	    {
 	    hashAdd(hash, info->name, info);
 	    slNameAddHead(&nameList, info->name);
 	    }
 	}
     }
 slSort(&nameList, slNameCmpStringsWithEmbeddedNumbers);
 return nameList;
 }
 
 boolean allStartEndSame(struct bbiInterval *ivList)
 /* Return true if all items in list start and end the same place. */
 {
 int start = ivList->start, end = ivList->end;
 struct bbiInterval *iv;
 for (iv = ivList->next; iv != NULL; iv = iv->next)
     {
     if (iv->start != start || iv->end != end)
         return FALSE;
     }
 return TRUE;
 }
 
 int doublesTheSame(double *pt, int size)
 /* Return count of numbers at start that are the same as first number.  */
 {
 int sameCount = 1;
 int i;
 double x = pt[0];
 for (i=1; i<size; ++i)
     {
     if (pt[i] != x)
         break;
     ++sameCount;
     }
 return sameCount;
 }
 
 void bigWigMerge(int inCount, char *inFiles[], char *outFile)
 /* bigWigMerge - Merge together multiple bigWigs into a single one.. */
 {
 /* Make a list of open bigWig files. */
 struct bbiFile *inFile, *inFileList = NULL;
 int i;
 for (i=0; i<inCount; ++i)
     {
     inFile = bigWigFileOpen(inFiles[i]);
     slAddTail(&inFileList, inFile);
     }
 
 FILE *f = mustOpen(outFile, "w");
 
 struct slName *chrom, *chromList = getAllChroms(inFileList);
-verbose(1, "Got %d chromosomes from %d bigWigs\n", slCount(chromList), slCount(inFileList));
+verbose(1, "Got %d chromosomes from %d bigWigs\nProcessing", 
+	slCount(chromList), slCount(inFileList));
 double *mergeBuf = NULL;
 int mergeBufSize = 0;
 for (chrom = chromList; chrom != NULL; chrom = chrom->next)
     {
     struct lm *lm = lmInit(0);
 
     /* Make sure merge buffer is big enough. */
     int chromSize = bbiChromSize(inFileList, chrom->name);
+    verboseDot();
     verbose(2, "Processing %s (%d bases)\n", chrom->name, chromSize);
     if (chromSize > mergeBufSize)
         {
 	mergeBufSize = chromSize;
 	freeMem(mergeBuf);
 	mergeBuf = needHugeMem(mergeBufSize * sizeof(double));
 	}
     int i;
     for (i=0; i<chromSize; ++i)
         mergeBuf[i] = 0.0;
 
     /* Loop through each input file grabbing data and merging it in. */
     for (inFile = inFileList; inFile != NULL; inFile = inFile->next)
         {
 	struct bbiInterval *ivList = bigWigIntervalQuery(inFile, chrom->name, 0, chromSize, lm);
 	verbose(3, "Got %d intervals in %s\n", slCount(ivList), inFile->fileName);
 	struct bbiInterval *iv;
 	for (iv = ivList; iv != NULL; iv = iv->next)
 	    {
 	    double val = iv->val;
+	    if (val > clClip)
+	        val = clClip;
 	    int end = iv->end;
 	    for (i=iv->start; i < end; ++i)
 	         mergeBuf[i] += val;
 	    }
 	}
 
+
     /* Output each range of same values as a bedGraph item */
     int sameCount;
     for (i=0; i<chromSize; i += sameCount)
         {
 	sameCount = doublesTheSame(mergeBuf+i, chromSize-i);
 	double val = mergeBuf[i] + clAdjust;
 	if (val > clThreshold)
 	    fprintf(f, "%s\t%d\t%d\t%g\n", chrom->name, i, i + sameCount, val);
 	}
 
     lmCleanup(&lm);
     }
+verbose(1, "\n");
 
 carefulClose(&f);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 clThreshold = optionDouble("threshold", clThreshold);
 clAdjust = optionDouble("adjust", clAdjust);
+clClip = optionDouble("clip", clClip);
 if (argc < 4)
     usage();
 bigWigMerge(argc-2, argv+1, argv[argc-1]);
 return 0;
 }