fc13db4566f67eda0bb8d608c8cd691b559a1930
angie
  Fri May 22 16:32:00 2015 -0700
Add chrom, chromStart, chromEnd back into the autoSql for wig and bigWig annoStreamers.
Now the columns can be selected/deselected the usual way instead of being fudged into
the output with no choice.
refs #14579

diff --git src/hg/lib/annoStreamWig.c src/hg/lib/annoStreamWig.c
index 5ee1316..c9c3ad9 100644
--- src/hg/lib/annoStreamWig.c
+++ src/hg/lib/annoStreamWig.c
@@ -1,148 +1,151 @@
 /* annoStreamWig -- subclass of annoStreamer for wiggle database tables */
 
 /* Copyright (C) 2014 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #include "annoStreamWig.h"
 #include "annoStreamDb.h"
 #include "jksql.h"
 #include "wiggle.h"
 
 char *annoRowWigAsText = 
 "table annoRowWig\n"
 "\"autoSql description of a single annoRowWig value, for filtering\"\n"
 "    (\n"
+"    string chrom;     \"Reference sequence chromosome or scaffold\"\n"
+"    uint chromStart;  \"Start position in chromosome\"\n"
+"    uint chromEnd;    \"End position in chromosome\"\n"
 "    float value;      \"data value for this range\"\n"
 "    )\n"
     ;
 
 struct annoStreamWig
     {
     struct annoStreamer streamer;	// Parent class members & methods / external interface
     // Private members
     struct annoStreamer *wigStr;	// Internal streamer for .wig as in wiggle db tables
     FILE *wibF;				// wib file handle
     char *wibFile;			// name of wib file on which wibF was opened
     };
 
 static void aswSetRegion(struct annoStreamer *vSelf, char *chrom, uint regionStart, uint regionEnd)
 /* Set region -- and free current sqlResult if there is one. */
 {
 annoStreamerSetRegion(vSelf, chrom, regionStart, regionEnd);
 struct annoStreamWig *self = (struct annoStreamWig *)vSelf;
 self->wigStr->setRegion(self->wigStr, chrom, regionStart, regionEnd);
 }
 
 static void checkWibFile(struct annoStreamWig *self, char *wibFile)
 /* If self doesn't have a .wib file name and handle open, or if the new wibFile is
  * not the same as the old one, update self to use new wibFile. */
 {
 if (self->wibFile == NULL || !sameString(self->wibFile, wibFile))
     {
     carefulClose(&(self->wibF));
     freeMem(self->wibFile);
     self->wibFile = cloneString(wibFile);
     self->wibF = mustOpen(self->wibFile, "r");
     }
 }
 
 static void paranoidCheckSize(struct annoStreamWig *self, struct wiggle *wiggle)
 /* paranoid, consider taking this out when code is stable: */
 {
 int bpLen = wiggle->chromEnd - wiggle->chromStart;
 if (bpLen != (wiggle->span * wiggle->count))
     errAbort("annoStreamWig %s: length in bases (%u - %u = %d) != span*count (%u * %u = %u)",
 	     self->streamer.name, wiggle->chromEnd, wiggle->chromStart, bpLen,
 	     wiggle->span, wiggle->count, (wiggle->span * wiggle->count));
 }
 
 static void getFloatArray(struct annoStreamWig *self, struct wiggle *wiggle,
 			  boolean *retRightFail, int *retValidCount, float *vector)
 /* expand wiggle bytes & spans to per-bp floats; filter values here! */
 {
 fseek(self->wibF, wiggle->offset, SEEK_SET);
 UBYTE wigBuf[wiggle->count];
 size_t bytesRead = fread(wigBuf, 1, wiggle->count, self->wibF);
 if (bytesRead != wiggle->count)
     errnoAbort("annoStreamWig: failed to read %u bytes from %s (got %llu)\n",
 	       wiggle->count, wiggle->file, (unsigned long long)bytesRead);
 paranoidCheckSize(self, wiggle);
 int i, j, validCount = 0;
 for (i = 0;  i < wiggle->count;  i++)
     {
     float value;
     if (wigBuf[i] == WIG_NO_DATA)
 	value = NAN;
     else
 	{
 	value = BIN_TO_VALUE(wigBuf[i], wiggle->lowerLimit, wiggle->dataRange);
 	if (annoFilterWigValueFails(self->streamer.filters, value, retRightFail))
 	    value = NAN;
 	else
 	    validCount++;
 	}
     int bpOffset = i * wiggle->span;
     for (j = 0;  j < wiggle->span;  j++)
 	vector[bpOffset + j] = value;
     }
 if (retValidCount != NULL)
     *retValidCount = validCount;
 }
 
 static struct annoRow *aswNextRow(struct annoStreamer *vSelf, char *minChrom, uint minEnd,
 				  struct lm *callerLm)
 /* Return an annoRow encoding the next chunk of wiggle data, or NULL if there are no more items. */
 {
 struct annoStreamWig *self = (struct annoStreamWig *)vSelf;
 struct annoRow *rowOut = NULL;
 boolean done = FALSE;
 while (!done)
     {
     struct annoRow *wigRow = self->wigStr->nextRow(self->wigStr, minChrom, minEnd, callerLm);
     if (wigRow == NULL)
 	return NULL;
     struct wiggle wiggle;
     wiggleStaticLoad((char **)wigRow->data, &wiggle);
     checkWibFile(self, wiggle.file);
     // translate wigRow + bytes to float vector
     boolean rightFail = FALSE;
     int validCount = 0;
     int bpLen = wiggle.chromEnd - wiggle.chromStart;
     float vector[bpLen];
     getFloatArray(self, &wiggle, &rightFail, &validCount, vector);
     if (rightFail || validCount > 0)
 	{
 	rowOut = annoRowWigNew(wigRow->chrom, wigRow->start, wigRow->end, rightFail, vector,
 			       callerLm);
 	done = TRUE;
 	}
     }
 return rowOut;
 }
 
 static void aswClose(struct annoStreamer **pVSelf)
 /* Free wiggleDataStream and self. */
 {
 if (pVSelf == NULL)
     return;
 struct annoStreamWig *self = *(struct annoStreamWig **)pVSelf;
 carefulClose(&(self->wibF));
 freeMem(self->wibFile);
 annoStreamerFree(pVSelf);
 }
 
 struct annoStreamer *annoStreamWigDbNew(char *db, char *table, struct annoAssembly *aa,
 					int maxOutput)
 /* Create an annoStreamer (subclass) object from a wiggle database table. */
 {
 struct annoStreamWig *self = NULL;
 AllocVar(self);
 self->wigStr = annoStreamDbNew(db, table, aa, asParseText(wiggleAsText), maxOutput);
 struct annoStreamer *streamer = &(self->streamer);
 annoStreamerInit(streamer, aa, asParseText(annoRowWigAsText), self->wigStr->name);
 streamer->rowType = arWig;
 streamer->setRegion = aswSetRegion;
 streamer->nextRow = aswNextRow;
 streamer->close = aswClose;
 return (struct annoStreamer *)self;
 }