void bigBedAddLinkedFeaturesFrom(struct track *track,
char *chrom, int start, int end, int scoreMin, int scoreMax, boolean useItemRgb,
int fieldCount, struct linkedFeatures **pLfList)
/* Read in items in chrom:start-end from bigBed file named in track->bbiFileName, convert
* them to linkedFeatures, and add to head of list. */
{
struct lm *lm = lmInit(0);
struct trackDb *tdb = track->tdb;
struct bigBedInterval *bb, *bbList = bigBedSelectRange(track, chrom, start, end, lm);
char *bedRow[32];
char startBuf[16], endBuf[16];
char *scoreFilter = cartOrTdbString(cart, track->tdb, "scoreFilter", NULL);
char *mouseOverField = cartOrTdbString(cart, track->tdb, "mouseOverField", NULL);
int minScore = 0;
if (scoreFilter)
minScore = atoi(scoreFilter);
int mouseOverIdx = bbExtraFieldIndex(tdb, mouseOverField);
for (bb = bbList; bb != NULL; bb = bb->next)
{
char* mouseOver = restField(bb, mouseOverIdx);
bigBedIntervalToRow(bb, chromName, startBuf, endBuf, bedRow, ArraySize(bedRow));
struct bed *bed = bedLoadN(bedRow, fieldCount);
struct linkedFeatures *lf = bedMungToLinkedFeatures(&bed, tdb, fieldCount,
scoreMin, scoreMax, useItemRgb);
if (scoreFilter == NULL || lf->score >= minScore)
slAddHead(pLfList, lf);
lf->mouseOver = mouseOver; // leaks some memory, cloneString handles NULL ifself
if (sameString(track->tdb->type, "bigGenePred"))
lf->original = genePredFromBigGenePred(chromName, bb);
}
lmCleanup(&lm);
}
void bamMethods(struct track *track)
/* Methods for BAM alignment files. */
{
knetUdcInstall();
boolean isBamWig = cartUsualBooleanClosestToHome(cart, track->tdb, FALSE,
BAMWIG_MODE, (trackDbSettingClosestToHome(track->tdb, BAMWIG_MODE) != NULL));
if (isBamWig)
{
bamWigMethods(track, track->tdb, 0, NULL);
return;
}
track->canPack = TRUE;
boolean isPaired = cartUsualBooleanClosestToHome(cart, track->tdb, FALSE,
BAM_PAIR_ENDS_BY_NAME,
(trackDbSettingClosestToHome(track->tdb, BAM_PAIR_ENDS_BY_NAME) != NULL));
char *tdbShowNames = trackDbSetting(track->tdb, BAM_SHOW_NAMES);
boolean showNames = cartUsualBooleanClosestToHome(cart, track->tdb, FALSE,
BAM_SHOW_NAMES, SETTING_IS_ON(tdbShowNames));
char *colorMode = cartOrTdbString(cart, track->tdb, BAM_COLOR_MODE, BAM_COLOR_MODE_DEFAULT);
char *userTag = cartOrTdbString(cart, track->tdb, BAM_COLOR_TAG, BAM_COLOR_TAG_DEFAULT);
if (sameString(colorMode, BAM_COLOR_MODE_TAG) && userTag != NULL)
{
if (! (isalpha(userTag[0]) && isalnum(userTag[1]) && userTag[2] == '\0'))
{
warn("%s: BAM tag '%s' is not valid -- must be a letter followed by a letter or number.",
track->tdb->shortLabel, htmlEncode(userTag));
cartRemoveVariableClosestToHome(cart, track->tdb, FALSE, BAM_COLOR_TAG);
}
}
addBamBaseAndIndelSettings(track->tdb);
if (isPaired)
{
linkedFeaturesSeriesMethods(track);
track->loadItems = bamPairedLoadItems;
track->drawItems = bamLinkedFeaturesSeriesDraw;
track->drawItemAt = bamPairedDrawAt;
}
else
{
linkedFeaturesMethods(track);
track->loadItems = bamLoadItems;
track->drawItems = bamLinkedFeaturesDraw;
track->drawItemAt = bamDrawAt;
}
if (!showNames)
{
track->drawName = TRUE; // ironic, but this is how to suppress item labels in pack mode.
track->drawLeftLabels = maybeDrawLeftLabels;
}
track->nextItemButtonable = track->nextExonButtonable = FALSE;
track->nextPrevItem = NULL;
track->nextPrevExon = NULL;
if (sameString(colorMode, BAM_COLOR_MODE_GRAY))
track->colorShades = shadesOfGray;
}
static int multiWigTotalHeight(struct track *tg, enum trackVisibility vis)
/* Return total height of multiWigcontainer. */
{
char *aggregate = cartOrTdbString(cart, tg->tdb, "aggregate", NULL);
boolean overlay = isOverlayTypeAggregate(aggregate);
int totalHeight = 0;
if (overlay)
totalHeight = wigTotalHeight(tg, vis);
struct track *subtrack;
for (subtrack = tg->subtracks; subtrack != NULL; subtrack = subtrack->next)
{
if (isSubtrackVisible(subtrack))
{
// Logic is slightly complicated by fact we want to call the totalHeight
// method for each subtrack even if in overlay mode.
int oneHeight = subtrack->totalHeight(subtrack, vis);
if (!overlay)
{
if (totalHeight != 0)
totalHeight += 1;
totalHeight += oneHeight;
}
}
}
tg->height = totalHeight;
return totalHeight;
}
static void multiWigDraw(struct track *tg, int seqStart, int seqEnd,
struct hvGfx *hvg, int xOff, int yOff, int width,
MgFont *font, Color color, enum trackVisibility vis)
/* Draw items in multiWig container. */
{
struct track *subtrack;
char *aggregate = cartOrTdbString(cart, tg->tdb, "aggregate", NULL);
boolean overlay = isOverlayTypeAggregate(aggregate);
int y = yOff;
for (subtrack = tg->subtracks; subtrack != NULL; subtrack = subtrack->next)
{
if (isSubtrackVisible(subtrack))
{
int height = subtrack->totalHeight(subtrack, vis);
hvGfxSetClip(hvg, xOff, y, width, height);
if (sameString(WIG_AGGREGATE_TRANSPARENT, aggregate))
hvGfxSetWriteMode(hvg, MG_WRITE_MODE_MULTIPLY);
if (overlay)
subtrack->lineHeight = tg->lineHeight;
subtrack->drawItems(subtrack, seqStart, seqEnd, hvg, xOff, y, width, font, color, vis);
if (!overlay)
y += height + 1;
hvGfxSetWriteMode(hvg, MG_WRITE_MODE_NORMAL);
hvGfxUnclip(hvg);
}
}
char *url = trackUrl(tg->track, chromName);
//fprintf(stderr, "mapBoxHgcOrHgGene(id: %s;) in multiWigDraw\n",
// tg->track);
mapBoxHgcOrHgGene(hvg, seqStart, seqEnd, xOff, y, width, tg->height, tg->track, tg->track, NULL,
url, TRUE, NULL);
}
static enum hapColorMode getColorMode(struct trackDb *tdb)
/* Get the hap-cluster coloring mode from cart & tdb. */
{
enum hapColorMode colorMode = altOnlyMode;
char *colorBy = cartOrTdbString(cart, tdb, VCF_HAP_COLORBY_VAR, VCF_DEFAULT_HAP_COLORBY);
if (sameString(colorBy, VCF_HAP_COLORBY_ALTONLY))
colorMode = altOnlyMode;
else if (sameString(colorBy, VCF_HAP_COLORBY_REFALT))
colorMode = refAltMode;
else if (sameString(colorBy, VCF_HAP_COLORBY_BASE))
colorMode = baseMode;
return colorMode;
}
static void colorByCfg(struct cart *cart, struct trackDb *tdb,
char *name, boolean parentLevel)
{
char *colorBy = cartOrTdbString(cart, tdb,
SNAKE_COLOR_BY, SNAKE_DEFAULT_COLOR_BY);
printf("<B>Block coloring method:</B>\n");
char varName[1024];
safef(varName, sizeof(varName), "%s." SNAKE_COLOR_BY, name);
cgiMakeDropListFull(varName, colorByOptionLabels,
colorByOptionValues,
ArraySize(colorByOptionLabels),
colorBy, NULL);
puts("<BR>");
}
static void multiWigLeftLabels(struct track *tg, int seqStart, int seqEnd,
struct hvGfx *hvg, int xOff, int yOff, int width, int height,
boolean withCenterLabels, MgFont *font, Color color,
enum trackVisibility vis)
/* Draw left labels - by deferring to first subtrack. */
{
char *aggregate = cartOrTdbString(cart, tg->tdb, "aggregate", NULL);
boolean overlay = isOverlayTypeAggregate(aggregate);
if (overlay)
{
struct track *firstVisibleSubtrack = NULL;
boolean showNumbers = graphLimitsAllSame(tg->subtracks, &firstVisibleSubtrack);
struct track *subtrack = (showNumbers ? firstVisibleSubtrack : tg->subtracks);
wigLeftAxisLabels(tg, seqStart, seqEnd, hvg, xOff, yOff, width, height, withCenterLabels,
font, color, vis, tg->shortLabel, subtrack->graphUpperLimit,
subtrack->graphLowerLimit, showNumbers);
}
else
{
struct track *subtrack;
int y = yOff;
if (withCenterLabels)
y += tl.fontHeight+1;
for (subtrack = tg->subtracks; subtrack != NULL; subtrack = subtrack->next)
{
if (isSubtrackVisible(subtrack))
{
int height = subtrack->totalHeight(subtrack, vis);
wigLeftAxisLabels(subtrack, seqStart, seqEnd, hvg, xOff, y, width, height, withCenterLabels,
font, subtrack->ixColor, vis, subtrack->shortLabel, subtrack->graphUpperLimit,
subtrack->graphLowerLimit, TRUE);
y += height+1;
}
}
}
}
static void bigBedClick(char *fileName, struct trackDb *tdb,
char *item, int start, int end, int bedSize)
/* Handle click in generic bigBed track. */
{
boolean showUrl = FALSE;
char *chrom = cartString(cart, "c");
/* Open BigWig file and get interval list. */
struct bbiFile *bbi = bigBedFileOpen(fileName);
struct lm *lm = lmInit(0);
int ivStart = start, ivEnd = end;
if (start == end)
{
// item is an insertion; expand the search range from 0 bases to 2 so we catch it:
ivStart = max(0, start-1);
ivEnd++;
}
struct bigBedInterval *bbList = bigBedIntervalQuery(bbi, chrom, ivStart, ivEnd, 0, lm);
/* Get bedSize if it's not already defined. */
if (bedSize == 0)
{
bedSize = bbi->definedFieldCount;
showUrl = TRUE;
}
char *scoreFilter = cartOrTdbString(cart, tdb, "scoreFilter", NULL);
int minScore = 0;
if (scoreFilter)
minScore = atoi(scoreFilter);
/* Find particular item in list - matching start, and item if possible. */
boolean found = FALSE;
boolean firstTime = TRUE;
struct bigBedInterval *bb;
for (bb = bbList; bb != NULL; bb = bb->next)
{
if (!(bb->start == start && bb->end == end))
continue;
if (bedSize > 3)
{
char *name = cloneFirstWordByTab(bb->rest);
boolean match = sameString(name, item);
freez(&name);
if (!match)
continue;
}
found = TRUE;
if (firstTime)
printf("<BR>\n");
int seq1Seq2Fields = 0;
// check for seq1 and seq2 in columns 7+8 (eg, pairedTagAlign)
boolean seq1Seq2 = sameOk(trackDbSetting(tdb, BASE_COLOR_USE_SEQUENCE), "seq1Seq2");
if (seq1Seq2 && bedSize == 6)
seq1Seq2Fields = 2;
char *fields[bedSize+seq1Seq2Fields];
char startBuf[16], endBuf[16];
char *rest = cloneString(bb->rest);
int bbFieldCount = bigBedIntervalToRow(bb, chrom, startBuf, endBuf, fields,
bedSize+seq1Seq2Fields);
if (bbFieldCount != bedSize+seq1Seq2Fields)
{
errAbort("Disagreement between trackDb field count (%d) and %s fieldCount (%d)",
bedSize, fileName, bbFieldCount);
}
struct bed *bed = bedLoadN(fields, bedSize);
if (bedSize >= 6 && scoreFilter && bed->score < minScore)
continue;
if (showUrl && (bedSize >= 4))
printCustomUrl(tdb, item, TRUE);
bedPrintPos(bed, bedSize, tdb);
// display seq1 and seq2
if (seq1Seq2 && bedSize+seq1Seq2Fields == 8)
printf("<table><tr><th>Sequence 1</th><th>Sequence 2</th></tr>"
"<tr><td> %s </td><td> %s </td></tr></table>", fields[6], fields[7]);
else if (isNotEmpty(rest))
{
char *restFields[256];
int restCount = chopTabs(rest, restFields);
int restBedFields = bedSize - 3;
if (restCount > restBedFields)
{
if (0 == extraFieldsPrint(tdb,NULL,restFields + restBedFields,restCount - restBedFields))
{
int i;
char label[20];
safef(label, sizeof(label), "nonBedFieldsLabel");
printf("<B>%s </B>",
trackDbSettingOrDefault(tdb, label, "Non-BED fields:"));
for (i = restBedFields; i < restCount; i++)
printf("%s%s", (i > 0 ? "\t" : ""), restFields[i]);
printf("<BR>\n");
}
}
}
if (isCustomTrack(tdb->track))
{
time_t timep = bbiUpdateTime(bbi);
printBbiUpdateTime(&timep);
}
}
if (!found)
{
printf("No item %s starting at %d\n", emptyForNull(item), start);
}
lmCleanup(&lm);
bbiFileClose(&bbi);
}
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;
}
void bamDrawAt(struct track *tg, void *item,
struct hvGfx *hvg, int xOff, int y, double scale,
MgFont *font, Color color, enum trackVisibility vis)
/* Draw a single bam linkedFeatures item. Borrows a lot from linkedFeaturesDrawAt,
* but cuts a lot of unneeded features (like coding region) and adds a couple
* additional sources of color. */
{
struct linkedFeatures *lf = item;
struct simpleFeature *sf;
int heightPer = tg->heightPer;
int x1 = round((double)((int)lf->start-winStart)*scale) + xOff;
int x2 = round((double)((int)lf->end-winStart)*scale) + xOff;
int w = x2-x1;
int midY = y + (heightPer>>1);
char *exonArrowsDense = trackDbSettingClosestToHome(tg->tdb, "exonArrowsDense");
boolean exonArrowsEvenWhenDense = (exonArrowsDense != NULL && SETTING_IS_ON(exonArrowsDense));
boolean exonArrows = (tg->exonArrows &&
(vis != tvDense || exonArrowsEvenWhenDense));
struct dnaSeq *mrnaSeq = NULL;
enum baseColorDrawOpt drawOpt = baseColorDrawOff;
boolean indelShowDoubleInsert, indelShowQueryInsert, indelShowPolyA;
struct psl *psl = (struct psl *)(lf->original);
char *colorMode = cartOrTdbString(cart, tg->tdb, BAM_COLOR_MODE, BAM_COLOR_MODE_DEFAULT);
char *grayMode = cartOrTdbString(cart, tg->tdb, BAM_GRAY_MODE, BAM_GRAY_MODE_DEFAULT);
bool baseQualMode = (sameString(colorMode, BAM_COLOR_MODE_GRAY) &&
sameString(grayMode, BAM_GRAY_MODE_BASE_QUAL));
char *qSeq = lf->extra;
if (vis != tvDense && isNotEmpty(qSeq) && !sameString(qSeq, "*"))
{
drawOpt = baseColorDrawSetup(hvg, tg, lf, &mrnaSeq, &psl);
if (drawOpt > baseColorDrawOff)
exonArrows = FALSE;
}
static Color darkBlueColor = 0;
static Color darkRedColor = 0;
if (darkRedColor == 0)
{
darkRedColor = hvGfxFindColorIx(hvg, 100,0,0);
darkBlueColor = hvGfxFindColorIx(hvg, 0,0,100);
}
if (sameString(colorMode, BAM_COLOR_MODE_STRAND))
color = (lf->orientation < 0) ? darkRedColor : darkBlueColor;
else if (lf->filterColor != 0)
{
// In bamTrack, lf->filterColor is an RGBA value
color = lf->filterColor;
}
else if (tg->colorShades)
color = tg->colorShades[lf->grayIx];
else
color = tg->ixColor;
indelEnabled(cart, tg->tdb, basesPerPixel, &indelShowDoubleInsert, &indelShowQueryInsert,
&indelShowPolyA);
if (!indelShowDoubleInsert)
innerLine(hvg, x1, midY, w, color);
for (sf = lf->components; sf != NULL; sf = sf->next)
{
int s = sf->start, e = sf->end;
if (e <= s || e < winStart || s > winEnd)
continue;
if (baseQualMode)
color = tg->colorShades[sf->grayIx];
baseColorDrawItem(tg, lf, sf->grayIx, hvg, xOff, y, scale, font, s, e, heightPer,
zoomedToCodonLevel, mrnaSeq, sf, psl, drawOpt, MAXPIXELS, winStart, color);
if (tg->exonArrowsAlways ||
(exonArrows &&
(sf->start <= winStart || sf->start == lf->start) &&
(sf->end >= winEnd || sf->end == lf->end)))
{
Color barbColor = hvGfxContrastingColor(hvg, color);
x1 = round((double)((int)s-winStart)*scale) + xOff;
x2 = round((double)((int)e-winStart)*scale) + xOff;
w = x2-x1;
clippedBarbs(hvg, x1+1, midY, x2-x1-2, tl.barbHeight, tl.barbSpacing, lf->orientation,
barbColor, TRUE);
}
}
if (indelShowDoubleInsert && psl)
{
int intronGap = 0;
if (vis != tvDense)
intronGap = atoi(trackDbSettingClosestToHomeOrDefault(tg->tdb, "intronGap", "0"));
lfDrawSpecialGaps(lf, intronGap, TRUE, 0, tg, hvg, xOff, y, scale, color, color, vis);
}
if (vis != tvDense)
{
/* If highlighting differences between aligned sequence and genome when
* zoomed way out, this must be done in a separate pass after exons are
* drawn so that exons sharing the pixel don't overdraw differences. */
if ((indelShowQueryInsert || indelShowPolyA) && psl)
baseColorOverdrawQInsert(tg, lf, hvg, xOff, y, scale, heightPer, mrnaSeq, psl, winStart,
drawOpt, indelShowQueryInsert, indelShowPolyA);
baseColorOverdrawDiff(tg, lf, hvg, xOff, y, scale, heightPer, mrnaSeq, psl, winStart, drawOpt);
baseColorDrawCleanup(lf, &mrnaSeq, &psl);
}
}
void bamLoadItemsCore(struct track *tg, boolean isPaired)
/* Load BAM data into tg->items item list, unless zoomed out so far
* that the data would just end up in dense mode and be super-slow. */
{
/* protect against temporary network error */
struct errCatch *errCatch = errCatchNew();
if (errCatchStart(errCatch))
{
struct hash *pairHash = isPaired ? hashNew(18) : NULL;
int minAliQual = atoi(cartOrTdbString(cart, tg->tdb, BAM_MIN_ALI_QUAL, BAM_MIN_ALI_QUAL_DEFAULT));
char *colorMode = cartOrTdbString(cart, tg->tdb, BAM_COLOR_MODE, BAM_COLOR_MODE_DEFAULT);
char *grayMode = cartOrTdbString(cart, tg->tdb, BAM_GRAY_MODE, BAM_GRAY_MODE_DEFAULT);
char *userTag = cartOrTdbString(cart, tg->tdb, BAM_COLOR_TAG, BAM_COLOR_TAG_DEFAULT);
int aliQualShadeMin = 0, aliQualShadeMax = 99, baseQualShadeMin = 0, baseQualShadeMax = 40;
parseIntRangeSetting(tg->tdb, "aliQualRange", &aliQualShadeMin, &aliQualShadeMax);
parseIntRangeSetting(tg->tdb, "baseQualRange", &baseQualShadeMin, &baseQualShadeMax);
struct bamTrackData btd = {tg, pairHash, minAliQual, colorMode, grayMode, userTag,
aliQualShadeMin, aliQualShadeMax, baseQualShadeMin, baseQualShadeMax};
char *fileName = trackDbSetting(tg->tdb, "bigDataUrl");
if (fileName == NULL)
{
if (tg->customPt)
{
errAbort("bamLoadItemsCore: can't find bigDataUrl for custom track %s", tg->track);
}
else
{
struct sqlConnection *conn = hAllocConnTrack(database, tg->tdb);
fileName = bamFileNameFromTable(conn, tg->table, chromName);
hFreeConn(&conn);
}
}
char *fileName2 = hReplaceGbdb(fileName);
char posForBam[512];
safef(posForBam, sizeof(posForBam), "%s:%d-%d", chromName, winStart, winEnd);
char *cacheDir = cfgOption("cramRef");
char *refUrl = trackDbSetting(tg->tdb, "refUrl");
if (!isPaired)
bamFetchPlus(fileName2, posForBam, addBam, &btd, NULL, refUrl, cacheDir);
else
{
char *setting = trackDbSettingClosestToHomeOrDefault(tg->tdb, "pairSearchRange", "20000");
int pairSearchRange = atoi(setting);
if (pairSearchRange > 0)
safef(posForBam, sizeof(posForBam), "%s:%d-%d", chromName,
max(0, winStart-pairSearchRange), winEnd+pairSearchRange);
bamFetchPlus(fileName2, posForBam, addBamPaired, &btd, NULL, refUrl, cacheDir);
struct hashEl *hel;
struct hashCookie cookie = hashFirst(btd.pairHash);
while ((hel = hashNext(&cookie)) != NULL)
{
struct linkedFeatures *lf = hel->val;
if (lf->start < winEnd && lf->end > winStart)
slAddHead(&(tg->items), lfsFromLf(lf));
}
}
freez(&fileName2);
if (tg->visibility != tvDense)
{
slReverse(&(tg->items));
if (isPaired)
slSort(&(tg->items), linkedFeaturesSeriesCmp);
else if (sameString(colorMode, BAM_COLOR_MODE_STRAND))
slSort(&(tg->items), linkedFeaturesCmpOri);
else if (sameString(colorMode, BAM_COLOR_MODE_GRAY) &&
sameString(grayMode, BAM_GRAY_MODE_ALI_QUAL))
slSort(&(tg->items), linkedFeaturesCmpScore);
else
slSort(&(tg->items), linkedFeaturesCmpStart);
if (slCount(tg->items) > MAX_ITEMS_FOR_MAPBOX)
{
// flag drawItems to make a mapBox for the whole track
tg->customInt = 1;
tg->mapItem = dontMapItem;
}
}
}
errCatchEnd(errCatch);
if (errCatch->gotError)
{
tg->networkErrMsg = cloneString(errCatch->message->string);
tg->drawItems = bigDrawWarning;
tg->totalHeight = bigWarnTotalHeight;
}
errCatchFree(&errCatch);
}
static void vcfHapClusterDraw(struct track *tg, int seqStart, int seqEnd,
struct hvGfx *hvg, int xOff, int yOff, int width,
MgFont *font, Color color, enum trackVisibility vis)
/* Split samples' chromosomes (haplotypes), cluster them by center-weighted
* alpha similarity, and draw in the order determined by clustering. */
{
struct vcfFile *vcff = tg->extraUiData;
if (vcff->records == NULL)
return;
purple = hvGfxFindColorIx(hvg, 0x99, 0x00, 0xcc);
undefYellow = hvGfxFindRgb(hvg, &undefinedYellowColor);
enum hapColorMode colorMode = getColorMode(tg->tdb);
pushWarnHandler(ignoreEm);
struct vcfRecord *rec;
for (rec = vcff->records; rec != NULL; rec = rec->next)
vcfParseGenotypes(rec);
popWarnHandler();
unsigned short gtHapCount = 0;
int nRecords = slCount(vcff->records);
int centerIx = getCenterVariantIx(tg, seqStart, seqEnd, vcff->records);
// Limit the number of variants that we compare, to keep from timing out:
// (really what we should limit is the number of distinct haplo's passed to hacTree!)
// In the meantime, this should at least be a cart var...
int maxVariantsPerSide = 50;
int startIx = max(0, centerIx - maxVariantsPerSide);
int endIx = min(nRecords, centerIx+1 + maxVariantsPerSide);
struct hacTree *ht = NULL;
unsigned short *gtHapOrder = clusterHaps(vcff, centerIx, startIx, endIx, >HapCount, &ht);
struct vcfRecord *centerRec = NULL;
int ix;
// Unlike drawing order (last drawn is on top), the first mapBox gets priority,
// so map center variant before drawing & mapping other variants!
for (rec = vcff->records, ix=0; rec != NULL; rec = rec->next, ix++)
{
if (ix == centerIx)
{
centerRec = rec;
mapBoxForCenterVariant(rec, hvg, tg, xOff, yOff, width);
break;
}
}
for (rec = vcff->records, ix=0; rec != NULL; rec = rec->next, ix++)
{
boolean isClustered = (ix >= startIx && ix < endIx);
if (ix != centerIx)
drawOneRec(rec, gtHapOrder, gtHapCount, tg, hvg, xOff, yOff, width, isClustered, FALSE,
colorMode);
}
// Draw the center rec on top, outlined with black lines, to make sure it is very visible:
drawOneRec(centerRec, gtHapOrder, gtHapCount, tg, hvg, xOff, yOff, width, TRUE, TRUE,
colorMode);
// Draw as much of the tree as can fit in the left label area:
int extraPixel = (colorMode == altOnlyMode) ? 1 : 0;
int hapHeight = tg->height- CLIP_PAD - 2*extraPixel;
struct yFromNodeHelper yHelper = {0, NULL, NULL};
initYFromNodeHelper(&yHelper, yOff+extraPixel, hapHeight, gtHapCount, gtHapOrder,
vcff->genotypeCount);
struct titleHelper titleHelper = { NULL, 0, 0, 0, 0, NULL, NULL };
initTitleHelper(&titleHelper, tg->track, startIx, centerIx, endIx, nRecords, vcff);
char *treeAngle = cartOrTdbString(cart, tg->tdb, VCF_HAP_TREEANGLE_VAR, VCF_DEFAULT_HAP_TREEANGLE);
boolean drawRectangle = sameString(treeAngle, VCF_HAP_TREEANGLE_RECTANGLE);
drawTreeInLabelArea(ht, hvg, yOff+extraPixel, hapHeight+CLIP_PAD, &yHelper, &titleHelper,
drawRectangle);
}
