70668f5dd4d6bbcf079a1025649e17b9885335c7
angie
  Mon May 13 10:17:53 2013 -0700
Added 2 new args to annoStreamer:nextRow: minChrom and minEnd(which could also be called regionStart depending on point of view).
Streamers may use those hints to skip over data that precedes
minChrom and minEnd, to avoid the overhead of creating annoRows
that annoGrators will then have to skip over.  When primary data
are sparse and grator data are very dense, this saves significant
memory and user-cycles.  Unfortunately mysql can still be the
bottleneck for elapsed time.  Room for improvement in annoStreamDb:
when assembly has a reasonably small number of sequences (<1000),
genome-wide queries could be internally broken down into per-seq
queries; that would let us skip over chroms that precede minChrom.
refs #6152

diff --git src/lib/annoGrator.c src/lib/annoGrator.c
index f2b4055..74bffda 100644
--- src/lib/annoGrator.c
+++ src/lib/annoGrator.c
@@ -1,252 +1,253 @@
 /* annoGrator -- join two inputs on position, keeping all original fields intact. */
 
 #include "annoGrator.h"
 
 INLINE void agCheckPrimarySorting(struct annoGrator *self, struct annoRow *primaryRow)
 /* Die if primaryRow seems to have arrived out of order. */
 {
 if (self->prevPChrom == NULL)
     self->prevPChrom = cloneString(primaryRow->chrom);
 else if (differentString(primaryRow->chrom, self->prevPChrom))
     {
     if (strcmp(primaryRow->chrom, self->prevPChrom) < 0)
 	errAbort("annoGrator %s: Unsorted input from primary source (%s < %s)",
 		 self->streamer.name, primaryRow->chrom, self->prevPChrom);
     self->prevPChrom = cloneString(primaryRow->chrom);
     }
 else if (primaryRow->start < self->prevPStart)
     errAbort("annoGrator %s:Unsorted input from primary source (%s, %u < %u)",
 	     self->streamer.name, primaryRow->chrom, primaryRow->start, self->prevPStart);
 self->prevPStart = primaryRow->start;
 }
 
 INLINE void agTrimToStart(struct annoGrator *self, char *chrom, uint start)
 /* If queue contains items whose end is to the left of start, splice them out. */
 {
 struct annoRow *qRow, *prevQRow = NULL, *nextQRow;
 for (qRow = self->qHead;  qRow != NULL;  qRow = nextQRow)
     {
     nextQRow = qRow->next;
     int cDifRowP = strcmp(qRow->chrom, chrom);
     if (cDifRowP > 0 || (cDifRowP == 0 && qRow->start >= start))
 	break;
     else if (cDifRowP < 0 || qRow->end < start)
 	{
 	if (prevQRow == NULL)
 	    self->qHead = qRow->next;
 	else
 	    prevQRow->next = qRow->next;
 	if (self->qTail == qRow)
 	    self->qTail = prevQRow;
 	}
     else
 	prevQRow = qRow;
     }
 if (self->qHead == NULL)
     {
     // Queue is empty - clean up lm
     lmCleanup(&(self->qLm));
     self->qLm = lmInit(0);
     }
 }
 
 INLINE void agCheckInternalSorting(struct annoGrator *self, struct annoRow *newRow)
 /* Die if newRow precedes qTail. */
 {
 if (self->qTail != NULL)
     {
     int cDifNewTail = strcmp(newRow->chrom, self->qTail->chrom);
     if (cDifNewTail < 0)
 	errAbort("annoGrator %s: Unsorted input from internal source %s (%s < %s)",
 		 self->streamer.name, self->mySource->name, newRow->chrom, self->qTail->chrom);
     else if (cDifNewTail == 0 && newRow->start < self->qTail->start)
 	errAbort("annoGrator %s: Unsorted input from internal source %s (%s, %u < %u)",
 		 self->streamer.name, self->mySource->name,
 		 newRow->chrom, newRow->start, self->qTail->start);
     }
 }
 
-INLINE void agFetchToEnd(struct annoGrator *self, char *chrom, uint end)
+INLINE void agFetchToEnd(struct annoGrator *self, char *chrom, uint start, uint end)
 /* Fetch rows until we are sure we have all items that start to the left of end,
  * i.e. we have an item that starts at/after end or we hit eof. */
 {
 while (!self->eof &&
        (self->qTail == NULL || strcmp(self->qTail->chrom, chrom) < 0 || self->qTail->start < end))
     {
-    struct annoRow *newRow = self->mySource->nextRow(self->mySource, self->qLm);
+    struct annoRow *newRow = self->mySource->nextRow(self->mySource, chrom, start, self->qLm);
     if (newRow == NULL)
 	self->eof = TRUE;
     else
 	{
 	agCheckInternalSorting(self, newRow);
 	int cDifNewP = strcmp(newRow->chrom, chrom);
 	if (cDifNewP >= 0)
 	    {
 	    // Add newRow to qTail
 	    if (self->qTail == NULL)
 		{
 		if (self->qHead != NULL)
 		    errAbort("annoGrator %s: qTail is NULL but qHead is non-NULL",
 			     self->streamer.name);
 		self->qHead = self->qTail = newRow;
 		}
 	    else
 		{
 		self->qTail->next = newRow;
 		self->qTail = newRow;
 		}
 	    if (cDifNewP > 0)
 		// newRow->chrom comes after chrom; we're done for now
 		break;
 	    }
 	}
     }
 }
 
 struct annoRow *annoGratorIntegrate(struct annoGrator *self, struct annoStreamRows *primaryData,
 				    boolean *retRJFilterFailed, struct lm *callerLm)
 /* Given a single row from the primary source, get all overlapping rows from internal
  * source, and produce joined output rows.
  * If retRJFilterFailed is non-NULL:
  * - any overlapping row has a rightJoin filter failure (see annoFilter.h), or
  * - overlap rule is agoMustOverlap and no rows overlap, or
  * - overlap rule is agoMustNotOverlap and any overlapping row is found,
  * then set retRJFilterFailed and stop. */
 {
 struct annoRow *primaryRow = primaryData->rowList;
 struct annoRow *rowList = NULL;
 agCheckPrimarySorting(self, primaryRow);
 agTrimToStart(self, primaryRow->chrom, primaryRow->start);
-agFetchToEnd(self, primaryRow->chrom, primaryRow->end);
+agFetchToEnd(self, primaryRow->chrom, primaryRow->start, primaryRow->end);
 boolean rjFailHard = (retRJFilterFailed != NULL);
 if (rjFailHard)
     *retRJFilterFailed = FALSE;
 struct annoRow *qRow;
 for (qRow = self->qHead;  qRow != NULL;  qRow = qRow->next)
     {
     if (qRow->start < primaryRow->end && qRow->end > primaryRow->start &&
 	sameString(qRow->chrom, primaryRow->chrom))
 	{
 	int numCols = self->mySource->numCols;
 	enum annoRowType rowType = self->mySource->rowType;
 	slAddHead(&rowList, annoRowClone(qRow, rowType, numCols, callerLm));
 	if (rjFailHard && qRow->rightJoinFail)
 	    {
 	    *retRJFilterFailed = TRUE;
 	    break;
 	    }
 	}
     }
 slReverse(&rowList);
 // If no rows overlapped primary, and there is a right-join, !isExclude (i.e. isInclude) filter,
 // then we need to set retRJFilterFailed because the condition was not met to include
 // the primary item.
 if (retRJFilterFailed &&
     ((rowList == NULL && (self->haveRJIncludeFilter || self->overlapRule == agoMustOverlap)) ||
      (rowList != NULL && self->overlapRule == agoMustNotOverlap)))
     *retRJFilterFailed = TRUE;
 return rowList;
 }
 
 void annoGratorClose(struct annoStreamer **pSelf)
 /* Free self (including mySource). */
 {
 if (pSelf == NULL)
     return;
 struct annoGrator *self = *(struct annoGrator **)pSelf;
 lmCleanup(&(self->qLm));
 self->mySource->close(&(self->mySource));
 freeMem(self->prevPChrom);
 freez(pSelf);
 }
 
-static struct annoRow *noNextRow(struct annoStreamer *self, struct lm *callerLm)
+static struct annoRow *noNextRow(struct annoStreamer *self, char *minChrom, uint minEnd,
+				 struct lm *callerLm)
 /* nextRow() is N/A for annoGrator, which needs caller to use integrate() instead. */
 {
 errAbort("annoGrator %s: nextRow() called, but integrate() should be called instead",
 	 self->name);
 return NULL;
 }
 
 static void agReset(struct annoGrator *self)
 /* Reset all state associated with position */
 {
 freez(&(self->prevPChrom));
 self->prevPStart = 0;
 self->eof = FALSE;
 lmCleanup(&(self->qLm));
 self->qLm = lmInit(0);
 self->qHead = self->qTail = NULL;
 }
 
 static boolean filtersHaveRJInclude(struct annoFilter *filters)
 /* Return TRUE if filters have at least one active filter with !isExclude && rightJoin. */
 {
 struct annoFilter *filter;
 for (filter = filters;  filter != NULL;  filter = filter->next)
     if (filter->op != afNoFilter && !filter->isExclude && filter->rightJoin)
 	return TRUE;
 return FALSE;
 }
 
 static void agSetFilters(struct annoStreamer *vSelf, struct annoFilter *newFilters)
 /* Update filters and re-evaluate self->haveRJIncludeFilter */
 {
 annoStreamerSetFilters(vSelf, newFilters);
 struct annoGrator *self = (struct annoGrator *)vSelf;
 self->haveRJIncludeFilter = filtersHaveRJInclude(vSelf->filters);
 }
 
 void annoGratorSetRegion(struct annoStreamer *vSelf, char *chrom, uint rStart, uint rEnd)
 /* Set genomic region for query, and reset internal state. */
 {
 struct annoGrator *self = (struct annoGrator *)vSelf;
 self->mySource->setRegion((struct annoStreamer *)(self->mySource), chrom, rStart, rEnd);
 agReset(self);
 }
 
 static void agSetAutoSqlObject(struct annoStreamer *sSelf, struct asObject *asObj)
 /* Use new asObj and update internal state derived from asObj. */
 {
 struct annoGrator *gSelf = (struct annoGrator *)sSelf;
 annoStreamerSetAutoSqlObject(sSelf, asObj);
 gSelf->haveRJIncludeFilter = filtersHaveRJInclude(sSelf->filters);
 }
 
 void agSetOverlapRule(struct annoGrator *self, enum annoGratorOverlap rule)
 /* Tell annoGrator how to handle overlap of its rows with primary row. */
 {
 self->overlapRule = rule;
 }
 
 void annoGratorInit(struct annoGrator *self, struct annoStreamer *mySource)
 /* Initialize an integrator of columns from mySource with (positions of)
  * rows passed to integrate().
  * mySource becomes property of the annoGrator. */
 {
 struct annoStreamer *streamer = &(self->streamer);
 annoStreamerInit(streamer, mySource->assembly, mySource->getAutoSqlObject(mySource),
 		 mySource->name);
 streamer->rowType = mySource->rowType;
 streamer->setAutoSqlObject = agSetAutoSqlObject;
 streamer->setFilters = agSetFilters;
 streamer->setRegion = annoGratorSetRegion;
 streamer->nextRow = noNextRow;
 streamer->close = annoGratorClose;
 self->qLm = lmInit(0);
 self->integrate = annoGratorIntegrate;
 self->setOverlapRule = agSetOverlapRule;
 self->overlapRule = agoNoConstraint;
 self->mySource = mySource;
 self->haveRJIncludeFilter = filtersHaveRJInclude(streamer->filters);
 }
 
 struct annoGrator *annoGratorNew(struct annoStreamer *mySource)
 /* Make a new integrator of columns from mySource with (positions of) rows passed to integrate().
  * mySource becomes property of the new annoGrator. */
 {
 struct annoGrator *self;
 AllocVar(self);
 annoGratorInit(self, mySource);
 return self;
 }