de438b6041d00b72be32bcdec70436a9d201baf2
braney
  Sat May 21 12:17:40 2016 -0700
libify the guts of ave so I can use it in hgc

diff --git src/utils/ave/ave.c src/utils/ave/ave.c
index 418a4b0..c989841 100644
--- src/utils/ave/ave.c
+++ src/utils/ave/ave.c
@@ -1,125 +1,68 @@
 /* ave - Compute average and basic stats. */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "sqlNum.h"
 #include "hmmstats.h"
+#include "aveStats.h"
 #include <float.h>
 
 
 static int col = 1;
 static bool tableOut = FALSE;
 static bool noQuartiles = FALSE;
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "ave - Compute average and basic stats\n"
   "usage:\n"
   "   ave file\n"
   "options:\n"
   "   -col=N Which column to use.  Default 1\n"
   "   -tableOut - output by columns (default output in rows)\n"
   "   -noQuartiles - only calculate min,max,mean,standard deviation\n"
   "                - for large data sets that will not fit in memory."
   );
 }
 
-int cmpDouble(const void *va, const void *vb)
-/* Compare two slNames. */
-{
-const double *a = va;
-const double *b = vb;
-double diff = *a - *b;
-if (diff < 0)
-   return -1;
-else if (diff > 0)
-   return 1;
-else
-   return 0;
-}
-
 void showStats(double *array, int count)
 /* Compute stats on sorted array */
 {
-double val, minVal = DBL_MAX, maxVal = -DBL_MAX;
-double total = 0, average;
-int i;
-int q1Index, q3Index;		/*	quartile positions	*/
-double q1, q3;			/*	quartile values	*/
-double oneVar, totalVar = 0;
-
-for (i=0; i<count; ++i)
-    {
-    val = array[i];
-    if (minVal > val) minVal = val;
-    if (maxVal < val) maxVal = val;
-    total += val;
-    }
-average = total/count;
-
-q1Index = (count+1)/4;		/*	one fourth, rounded down	*/
-q3Index = (3*(count+1))/4;	/*	three fourths, rounded down	*/
-if (q1Index < (count-1))
-    {
-    double range = array[q1Index+1] - array[q1Index];
-    q1 = array[q1Index] +
-	((((double)count+1.0)/4.0)-(double)q1Index)*range;
-    }
-else
-    q1 = array[q1Index];
-if (q3Index < (count-1))
-    {
-    double range = array[q3Index+1] - array[q3Index];
-    q3 = array[q3Index] +
-	((3.0*((double)count+1.0)/4.0)-(double)q3Index)*range;
-    }
-else
-    q3 = array[q3Index];
-
-for (i=0; i<count; ++i)
-    {
-    val = array[i];
-    oneVar = (average-val);
-    totalVar += oneVar*oneVar;
-    }
+struct aveStats *as = aveStatsCalc(array, count);
 
-    double var = totalVar;
-    if (count > 1)
-	var /= count-1;
-    double stdDev = sqrt(var);
 if (tableOut)
     {
     printf("# min Q1 median Q3 max mean N sum stddev\n");
-    printf("%g %g %g %g %g %g %d %g %g\n", minVal, q1, array[count/2],
-	q3, maxVal, average, count, total, stdDev);
+    printf("%g %g %g %g %g %g %d %g %g\n", as->minVal, as->q1, as->median,
+	as->q3, as->maxVal, as->average, as->count, as->total, as->stdDev);
     }
 else
     {
-    printf("Q1 %f\n", q1);
-    printf("median %f\n", array[count/2]);
-    printf("Q3 %f\n", q3);
-    printf("average %f\n", average);
-    printf("min %f\n", minVal);
-    printf("max %f\n", maxVal);
-    printf("count %d\n", count);
-    printf("total %f\n", total);
-    printf("standard deviation %f\n", stdDev);
+    printf("Q1 %f\n", as->q1);
+    printf("median %f\n", as->median);
+    printf("Q3 %f\n", as->q3);
+    printf("average %f\n", as->average);
+    printf("min %f\n", as->minVal);
+    printf("max %f\n", as->maxVal);
+    printf("count %d\n", as->count);
+    printf("total %f\n", as->total);
+    printf("standard deviation %f\n", as->stdDev);
     }
 }
 
 void aveNoQuartiles(char *fileName)
 /* aveNoQuartiles - Compute only min,max,mean,stdDev no quartiles */
 {
 bits64 count = 0;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *words[128], *word;
 int wordCount;
 int wordIx = col-1;
 double sumData = 0.0, sumSquares = 0.0;
 double minVal = DBL_MAX, maxVal = -DBL_MAX;
 
 while ((wordCount = lineFileChop(lf, words)) > 0)
@@ -171,31 +114,30 @@
 while ((wordCount = lineFileChop(lf, words)) > 0)
     {
     if (count >= alloc)
         {
 	alloc <<= 1;
 	ExpandArray(array, count, alloc);
 	}
     word = words[wordIx];
     if (word[0] == '-' || isdigit(word[0]))
         {
 	array[count++] = atof(word);
 	}
     }
 if (count == 0)
     errAbort("No numerical data column %d of %s", col, fileName);
-qsort(array, count, sizeof(array[0]), cmpDouble);
 showStats(array, count);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionHash(&argc, argv);
 if (argc != 2)
     usage();
 col = optionInt("col", col);
 tableOut = optionExists("tableOut");
 noQuartiles = optionExists("noQuartiles");
 if (noQuartiles)
     aveNoQuartiles(argv[1]);
 else