7f98bf75bd712a44b8ed9ededdd10e0f387cd35a
angie
  Thu Aug 13 10:31:58 2015 -0700
Moved averaging of wiggle values back from annoFormatTab to annoGrateWig,
so that it can be done properly across multiple regions with data.
A user was trying to get average GC over 1MB regions, but averages of
smaller subregions were returned instead.
refs #15834

diff --git src/lib/annoFormatTab.c src/lib/annoFormatTab.c
index 8971be0..06259e7 100644
--- src/lib/annoFormatTab.c
+++ src/lib/annoFormatTab.c
@@ -5,33 +5,30 @@
 
 #include "annoFormatTab.h"
 #include "annoGratorQuery.h"
 #include "dystring.h"
 
 struct annoFormatTab
     {
     struct annoFormatter formatter;     // External interface
     char *fileName;                     // Output file name, can be "stdout"
     FILE *f;                            // Output file handle
     struct hash *columnVis;             // Hash of columns that have been explicitly selected
                                         // or deselected by user.
     boolean needHeader;			// TRUE if we should print out the header
     };
 
-//#*** config options: avg? more stats? list of values?
-static boolean doAvg = TRUE;
-
 static void makeFullColumnName(char *fullName, size_t size, char *sourceName, char *colName)
 /* If sourceName is non-empty, make fullName sourceName.colName, otherwise just colName. */
 {
 if (isNotEmpty(sourceName))
     safef(fullName, size, "%s.%s", sourceName, colName);
 else
     safecpy(fullName, size, colName);
 }
 
 void annoFormatTabSetColumnVis(struct annoFormatter *vSelf, char *sourceName, char *colName,
                                boolean enabled)
 /* Explicitly include or exclude column in output.  sourceName must be the same
  * as the corresponding annoStreamer source's name. */
 {
 struct annoFormatTab *self = (struct annoFormatTab *)vSelf;
@@ -44,166 +41,132 @@
 
 static boolean columnIsIncluded(struct annoFormatTab *self, char *sourceName, char *colName)
 // Return TRUE if column has not been explicitly deselected.
 {
 if (self->columnVis)
     {
     char fullName[PATH_LEN];
     makeFullColumnName(fullName, sizeof(fullName), sourceName, colName);
     int vis = hashIntValDefault(self->columnVis, fullName, 1);
     if (vis == 0)
         return FALSE;
     }
 return TRUE;
 }
 
-static boolean isWiggle(struct asColumn *colList)
-/* Recognize wiggle/bigWig data by its column signature. */
-{
-return (slCount(colList) == 4 &&
-        sameString(colList->name, "chrom") &&
-        sameString(colList->next->name, "chromStart") &&
-        sameString(colList->next->next->name, "chromEnd") &&
-        sameString(colList->next->next->next->name, "value"));
-}
-
 static void printHeaderColumns(struct annoFormatTab *self, struct annoStreamer *source,
                                boolean isFirst)
 /* Print names of included columns from this source. */
 {
 FILE *f = self->f;
 char *sourceName = source->name;
-boolean isAvg = isWiggle(source->asObj->columnList) && doAvg;
 struct asColumn *col;
-int i;
-for (col = source->asObj->columnList, i = 0;  col != NULL;  col = col->next, i++)
+for (col = source->asObj->columnList;  col != NULL;  col = col->next)
     {
     if (columnIsIncluded(self, sourceName, col->name))
         {
         if (isFirst)
             {
             fputc('#', f);
             isFirst = FALSE;
             }
         else
             fputc('\t', f);
         char fullName[PATH_LEN];
         makeFullColumnName(fullName, sizeof(fullName), sourceName, col->name);
-        if (isAvg && sameString(col->name, "value"))
-            safecat(fullName, sizeof(fullName), "Average");
         fputs(fullName, f);
         }
     }
 }
 
 static void aftInitialize(struct annoFormatter *vSelf, struct annoStreamer *primary,
 			  struct annoStreamer *integrators)
 /* Print header, regardless of whether we get any data after this. */
 {
 struct annoFormatTab *self = (struct annoFormatTab *)vSelf;
 if (self->needHeader)
     {
     char *primaryHeader = primary->getHeader(primary);
     if (isNotEmpty(primaryHeader))
 	fprintf(self->f, "# Header from primary input:\n%s", primaryHeader);
     printHeaderColumns(self, primary, TRUE);
     struct annoStreamer *grator;
     for (grator = integrators;  grator != NULL;  grator = grator->next)
 	printHeaderColumns(self, grator, FALSE);
     fputc('\n', self->f);
     self->needHeader = FALSE;
     }
 }
 
-static double wigRowAvg(struct annoRow *row)
-/* Return the average value of floats in row->data. */
-{
-float *vector = row->data;
-int len = row->end - row->start;
-int count = 0;
-double sum = 0.0;
-int i;
-for (i = 0;  i < len;  i++)
-    {
-    // skip NAN values so they don't convert sum to a NAN:
-    if (! isnan(vector[i]))
-        {
-        sum += vector[i];
-        count++;
-        }
-    }
-// I expected "double avg = sum / (double)count" to yield NAN if count is 0 --
-// but avg was negative NAN!  Avoid the fp exception and weird value by testing count:
-return (count > 0) ? sum / (double)count : NAN;
-}
-
 static char **bed4WordsFromAnnoRow(struct annoRow *row, char *fourth)
 /* Return an array of 4 words with row's chrom, chromStart, and chromEnd, and cloned fourth. */
 {
 char **words;
 AllocArray(words, 4);
 words[0] = cloneString(row->chrom);
 char buf[PATH_LEN];
 safef(buf, sizeof(buf), "%u", row->start);
 words[1] = cloneString(buf);
 safef(buf, sizeof(buf), "%u", row->end);
 words[2] = cloneString(buf);
 words[3] = cloneString(fourth);
 return words;
 }
 
-static char **wordsFromWigRowAvg(struct annoRow *row)
-/* Return chrom, chromStart, chromEnd and a string containing the average of values in row. */
+static char **wordsFromWigRow(struct annoRow *row, enum annoRowType rowType)
+/* Return chrom, chromStart, chromEnd and a string containing comma-sep per-base wiggle values
+ * if rowType is arWigVec, or one value if rowType is arWigSingle. */
 {
-double avg = wigRowAvg(row);
-if (isnan(avg))
-    return NULL;
-char avgStr[32];
-safef(avgStr, sizeof(avgStr), "%lf", avg);
-return bed4WordsFromAnnoRow(row, avgStr);
-}
-
-static char **wordsFromWigRowVals(struct annoRow *row)
-/* Return chrom, chromStart, chromEnd and a string containing comma-sep per-base wiggle values. */
+struct dyString *dy = NULL;
+if (rowType == arWigVec)
     {
     float *vector = row->data;
     int len = row->end - row->start;
-struct dyString *dy = dyStringNew(10*len);
+    dy = dyStringNew(10*len);
     int i;
     for (i = 0;  i < len;  i++)
-    dyStringPrintf(dy, "%g,", vector[i]);
+        {
+        if (i > 0)
+            dyStringAppendC(dy, ',');
+        dyStringPrintf(dy, "%g", vector[i]);
+        }
+    }
+else if (rowType == arWigSingle)
+    {
+    double *pValue = row->data;
+    dy = dyStringCreate("%lf", *pValue);
+    }
+else
+    errAbort("wordsFromWigRow: invalid rowType %d", rowType);
 char **words = bed4WordsFromAnnoRow(row, dy->string);
 dyStringFree(&dy);
 return words;
 }
 
 static char **wordsFromRow(struct annoRow *row, struct annoStreamer *source,
 			   boolean *retFreeWhenDone)
 /* If source->rowType is arWords, return its words.  Otherwise translate row->data into words. */
 {
 if (row == NULL)
     return NULL;
 boolean freeWhenDone = FALSE;
 char **words = NULL;
 if (source->rowType == arWords)
     words = row->data;
-else if (source->rowType == arWig)
+else if (source->rowType == arWigVec || source->rowType == arWigSingle)
     {
-    if (doAvg)
-	words = wordsFromWigRowAvg(row);
-    else
-	words = wordsFromWigRowVals(row);
+    words = wordsFromWigRow(row, source->rowType);
     if (words != NULL)
         freeWhenDone = TRUE;
     }
 else
     errAbort("annoFormatTab: unrecognized row type %d from source %s",
 	     source->rowType, source->name);
 if (retFreeWhenDone != NULL)
     *retFreeWhenDone = freeWhenDone;
 return words;
 }
 
 static void printColumns(struct annoFormatTab *self, struct annoStreamer *streamer,
 			 struct annoRow *row, boolean isFirst)
 /* Print columns in streamer's row (if NULL, print the right number of empty fields). */
 {