void chainMethods(struct track *tg, struct trackDb *tdb,
int wordCount, char *words[])
/* Fill in custom parts of alignment chains. */
{
struct cartOptions *chainCart;
AllocVar(chainCart);
boolean normScoreAvailable = chainDbNormScoreAvailable(tdb);
/* what does the cart say about coloring option */
chainCart->chainColor = chainFetchColorOption(cart, tdb, FALSE);
chainCart->scoreFilter = cartUsualIntClosestToHome(cart, tdb,
FALSE, SCORE_FILTER, 0);
linkedFeaturesMethods(tg);
tg->itemColor = lfChromColor; /* default coloring option */
/* if normScore column is available, then allow coloring */
if (normScoreAvailable)
{
switch (chainCart->chainColor)
{
case (chainColorScoreColors):
tg->itemColor = chainScoreColor;
tg->colorShades = shadesOfGray;
break;
case (chainColorNoColors):
setNoColor(tg);
break;
default:
case (chainColorChromColors):
break;
}
}
else
{
char *optionStr; /* this old option was broken before */
optionStr = cartUsualStringClosestToHome(cart, tdb, FALSE, "color", "on");
if (differentWord("on",optionStr))
{
setNoColor(tg);
chainCart->chainColor = chainColorNoColors;
}
else
chainCart->chainColor = chainColorChromColors;
}
tg->loadItems = chainLoadItems;
tg->drawItems = chainDraw;
tg->mapItemName = lfMapNameFromExtra;
tg->subType = lfSubChain;
tg->extraUiData = (void *) chainCart;
}
static int getCenterVariantIx(struct track *tg, int seqStart, int seqEnd,
struct vcfRecord *records)
// If the user hasn't specified a local variant/position to use as center,
// just use the median variant in window.
{
int defaultIx = (slCount(records)-1) / 2;
char *centerChrom = cartOptionalStringClosestToHome(cart, tg->tdb, FALSE, "centerVariantChrom");
if (centerChrom != NULL && sameString(chromName, centerChrom))
{
int centerPos = cartUsualIntClosestToHome(cart, tg->tdb, FALSE, "centerVariantPos", -1);
int winSize = seqEnd - seqStart;
if (centerPos > (seqStart - winSize) && centerPos < (seqEnd + winSize))
{
int i;
struct vcfRecord *rec;
for (rec = records, i = 0; rec != NULL; rec = rec->next, i++)
if (rec->chromStart >= centerPos)
return i;
return i-1;
}
}
return defaultIx;
}
void loadSimpleBed(struct track *tg)
/* Load the items in one track - just move beds in
* window... */
{
struct bed *(*loader)(char **row);
struct bed *bed, *list = NULL;
char **row;
int rowOffset;
char *words[3];
int wordCt;
char query[128];
char *setting = NULL;
bool doScoreCtFilter = FALSE;
int scoreFilterCt = 0;
char *topTable = NULL;
if (tg->bedSize <= 3)
loader = bedLoad3;
else if (tg->bedSize == 4)
loader = bedLoad;
else if (tg->bedSize == 5)
loader = bedLoad5;
else
loader = bedLoad6;
// pairedTagAlign loader is required for base coloring using sequence from seq1 & seq2
// after removing optional bin column, this loader assumes seq1 and seq2 are in
// row[6] and row[7] respectively of the sql result.
if ((setting = trackDbSetting(tg->tdb, BASE_COLOR_USE_SEQUENCE))
&& sameString(setting, "seq1Seq2"))
loader = bedLoadPairedTagAlign;
/* limit to a specified count of top scoring items.
* If this is selected, it overrides selecting item by specified score */
if ((setting = trackDbSettingClosestToHome(tg->tdb, "filterTopScorers")) != NULL)
{
wordCt = chopLine(cloneString(setting), words);
if (wordCt >= 3)
{
doScoreCtFilter = cartUsualBooleanClosestToHome(cart, tg->tdb, FALSE,
"filterTopScorersOn",sameString(words[0], "on"));
scoreFilterCt = cartUsualIntClosestToHome(cart, tg->tdb, FALSE,
"filterTopScorersCt", atoi(words[1]));
topTable = words[2];
/* if there are not too many rows in the table then can define */
/* top table as the track or subtrack table */
if (sameWord(topTable, "self"))
topTable = cloneString(tg->table);
}
}
/* Get list of items */
if (tg->isBigBed)
{ // avoid opening an unneeded db connection for bigBed; required not to use mysql for parallel fetch tracks
char *scoreFilter = cartOrTdbString(cart, tg->tdb, "scoreFilter", NULL);
struct lm *lm = lmInit(0);
struct bigBedInterval *bb, *bbList = bigBedSelectRange(tg, chromName, winStart, winEnd, lm);
char *bedRow[32];
char startBuf[16], endBuf[16];
int minScore = 0;
if (scoreFilter)
minScore = atoi(scoreFilter);
for (bb = bbList; bb != NULL; bb = bb->next)
{
bigBedIntervalToRow(bb, chromName, startBuf, endBuf, bedRow, ArraySize(bedRow));
bed = loader(bedRow);
if (scoreFilter == NULL || bed->score >= minScore)
slAddHead(&list, bed);
}
lmCleanup(&lm);
}
else
{
struct sqlConnection *conn = hAllocConnTrack(database, tg->tdb);
struct sqlResult *sr = NULL;
/* limit to items above a specified score */
char *scoreFilterClause = getScoreFilterClause(cart, tg->tdb,NULL);
if (doScoreCtFilter && (topTable != NULL) && hTableExists(database, topTable))
{
sqlSafef(query, sizeof(query),"select * from %s order by score desc limit %d",
topTable, scoreFilterCt);
sr = sqlGetResult(conn, query);
rowOffset = hOffsetPastBin(database, hDefaultChrom(database), topTable);
}
else if(scoreFilterClause != NULL && tg->bedSize >= 5)
{
sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd, scoreFilterClause, &rowOffset);
}
else
{
sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd, NULL, &rowOffset);
}
freeMem(scoreFilterClause);
while ((row = sqlNextRow(sr)) != NULL)
{
bed = loader(row+rowOffset);
slAddHead(&list, bed);
}
sqlFreeResult(&sr);
hFreeConn(&conn);
}
if (doScoreCtFilter)
{
/* filter out items not in this window */
struct bed *newList = bedFilterListInRange(list, NULL, chromName, winStart, winEnd);
list = newList;
}
slReverse(&list);
tg->items = list;
}
