src/hg/hgTracks/bamTrack.c 1.11
1.11 2009/10/16 00:34:31 angie
Added enhanced coloring options (user-requested) to hgTrackUi and implemented 3 out of 5 in hgTracks.
Index: src/hg/hgTracks/bamTrack.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgTracks/bamTrack.c,v
retrieving revision 1.10
retrieving revision 1.11
diff -b -B -U 4 -r1.10 -r1.11
--- src/hg/hgTracks/bamTrack.c 8 Oct 2009 06:38:23 -0000 1.10
+++ src/hg/hgTracks/bamTrack.c 16 Oct 2009 00:34:31 -0000 1.11
@@ -9,8 +9,9 @@
#include "linefile.h"
#include "jksql.h"
#include "hdb.h"
#include "hgTracks.h"
+#include "cds.h"
#include "bamFile.h"
static char const rcsid[] = "$Id$";
@@ -18,8 +19,12 @@
{
struct track *tg;
struct hash *pairHash;
int minAliQual;
+ char *colorMode;
+ char *grayMode;
+ boolean grayUnpaired;
+ char *userTag;
};
struct simpleFeature *sfFromNumericCigar(const bam1_t *bam, int *retLength)
/* Translate BAM's numeric CIGAR encoding into a list of simpleFeatures,
@@ -68,8 +73,9 @@
struct linkedFeatures *bamToLf(const bam1_t *bam, void *data)
/* Translate a BAM record into a linkedFeatures item. */
{
+struct bamTrackData *btd = (struct bamTrackData *)data;
const bam1_core_t *core = &bam->core;
struct linkedFeatures *lf;
AllocVar(lf);
lf->score = core->qual;
@@ -79,9 +85,23 @@
lf->components = sfFromNumericCigar(bam, &length);
lf->start = lf->tallStart = core->pos;
lf->end = lf->tallEnd = core->pos + length;
lf->extra = bamGetQuerySequence(bam);
-lf->grayIx = maxShade;
+if (sameString(btd->colorMode, BAM_COLOR_MODE_GRAY) &&
+ sameString(btd->grayMode, BAM_GRAY_MODE_ALI_QUAL))
+ {
+ // hardcode transform coefficients for now; if user demand, make into tdb/cart vars.
+ int min = 0, max = 99;
+ int minShade = 2;
+ int ix = minShade + (maxShade - minShade) * ((double)(core->qual - min) / (double)(max-min));
+ if (ix > maxShade)
+ ix = maxShade;
+ if (ix < minShade)
+ ix = minShade;
+ lf->grayIx = ix;
+ }
+else
+ lf->grayIx = maxShade;
return lf;
}
boolean passesFilters(const bam1_t *bam, struct bamTrackData *btd)
@@ -182,11 +202,11 @@
stub = lfStub(core->mpos, -lf->orientation);
}
lf->next = stub;
}
- else
+ else if (btd->grayUnpaired)
// not properly paired: make it a lighter shade.
- lf->grayIx -= 2;
+ lf->grayIx -= 3;
hashAdd(btd->pairHash, lf->name, lf);
}
else
{
@@ -205,8 +225,19 @@
/* When there are many many items, drawing hgc links can really slow us down. */
{
}
+static int linkedFeaturesCmpOri(const void *va, const void *vb)
+/* Help sort linkedFeatures by strand, then by starting pos. */
+{
+const struct linkedFeatures *a = *((struct linkedFeatures **)va);
+const struct linkedFeatures *b = *((struct linkedFeatures **)vb);
+int ret = a->orientation - b->orientation;
+if (ret == 0)
+ ret = a->start - b->start;
+return ret;
+}
+
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. */
{
@@ -217,12 +248,24 @@
char posForBam[512];
safef(posForBam, sizeof(posForBam), "%s:%d-%d", seqNameForBam, winStart, winEnd);
struct hash *pairHash = isPaired ? hashNew(18) : NULL;
-char cartVarName[512];
-safef(cartVarName, sizeof(cartVarName), "%s_minAliQual", tg->tdb->tableName);
-int minAliQual = cartUsualInt(cart, cartVarName, 0);
-struct bamTrackData btd = {tg, pairHash, minAliQual};
+char cartVarName[1024];
+safef(cartVarName, sizeof(cartVarName), "%s_" BAM_MIN_ALI_QUAL, tg->tdb->tableName);
+int minAliQual = cartUsualInt(cart, cartVarName,
+ atoi(trackDbSettingOrDefault(tg->tdb, BAM_MIN_ALI_QUAL, BAM_MIN_ALI_QUAL_DEFAULT)));
+safef(cartVarName, sizeof(cartVarName), "%s_" BAM_COLOR_MODE, tg->tdb->tableName);
+char *colorMode = cartUsualString(cart, cartVarName,
+ trackDbSettingOrDefault(tg->tdb, BAM_COLOR_MODE, BAM_COLOR_MODE_DEFAULT));
+safef(cartVarName, sizeof(cartVarName), "%s_" BAM_GRAY_MODE, tg->tdb->tableName);
+char *grayMode = cartUsualString(cart, cartVarName,
+ trackDbSettingOrDefault(tg->tdb, BAM_GRAY_MODE, BAM_GRAY_MODE_DEFAULT));
+boolean grayUnpaired = (sameString(colorMode, BAM_COLOR_MODE_GRAY) &&
+ sameString(grayMode, BAM_GRAY_MODE_UNPAIRED));
+safef(cartVarName, sizeof(cartVarName), "%s_" BAM_COLOR_TAG, tg->tdb->tableName);
+char *userTag = cartUsualString(cart, cartVarName,
+ trackDbSettingOrDefault(tg->tdb, BAM_COLOR_TAG, BAM_COLOR_TAG_DEFAULT));
+struct bamTrackData btd = {tg, pairHash, minAliQual, colorMode, grayMode, grayUnpaired, userTag};
char *fileName;
if (tg->customPt)
{
fileName = trackDbSetting(tg->tdb, "bigDataUrl");
@@ -246,9 +289,14 @@
}
if (tg->visibility != tvDense)
{
slReverse(&(tg->items));
- slSort(&(tg->items), isPaired ? linkedFeaturesSeriesCmp : linkedFeaturesCmpStart);
+ if (isPaired)
+ slSort(&(tg->items), linkedFeaturesSeriesCmp);
+ else if (sameString(colorMode, BAM_COLOR_MODE_STRAND))
+ slSort(&(tg->items), linkedFeaturesCmpOri);
+ else
+ slSort(&(tg->items), linkedFeaturesCmpStart);
if (slCount(tg->items) > MAX_ITEMS_FOR_MAPBOX)
tg->mapItem = dontMapItem;
}
}
@@ -266,25 +314,144 @@
{
bamLoadItemsCore(tg, TRUE);
}
+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 = trackDbSetting(tg->tdb, "exonArrowsDense");
+boolean exonArrowsEvenWhenDense = (exonArrowsDense != NULL &&
+ !sameWord(exonArrowsDense, "off"));
+boolean exonArrows = (tg->exonArrows &&
+ (vis != tvDense || exonArrowsEvenWhenDense));
+struct dnaSeq *mrnaSeq = NULL;
+enum baseColorDrawOpt drawOpt = baseColorDrawOff;
+boolean indelShowDoubleInsert, indelShowQueryInsert, indelShowPolyA;
+struct psl *psl = NULL;
+if (vis != tvDense)
+ {
+ drawOpt = baseColorDrawSetup(hvg, tg, lf, &mrnaSeq, &psl);
+ if (drawOpt > baseColorDrawOff)
+ exonArrows = FALSE;
+ }
+
+char cartVarName[1024];
+safef(cartVarName, sizeof(cartVarName), "%s_" BAM_COLOR_MODE, tg->tdb->tableName);
+char *colorMode = cartUsualString(cart, cartVarName,
+ trackDbSettingOrDefault(tg->tdb, BAM_COLOR_MODE, BAM_COLOR_MODE_DEFAULT));
+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)
+ color = lf->filterColor;
+else if (tg->colorShades)
+ color = tg->colorShades[lf->grayIx];
+
+
+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;
+ 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)
+ {
+ int intronGap = 0;
+ if (vis != tvDense)
+ intronGap = atoi(trackDbSettingOrDefault(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)
+ 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 bamPairedDrawAt(struct track *tg, void *item, struct hvGfx *hvg, int xOff, int y,
+ double scale, MgFont *font, Color color, enum trackVisibility vis)
+/* Draw a bam linked features series item at position. (like linkedFeaturesSeriesDrawAt,
+ * but calls bamDrawAt instead of linkedFeaturesDrawAt) */
+{
+struct linkedFeaturesSeries *lfs = item;
+struct linkedFeatures *lf;
+int midY = y + (tg->heightPer>>1);
+int prevEnd = lfs->start;
+
+if ((lf = lfs->features) == NULL)
+ return;
+for (lf = lfs->features; lf != NULL; lf = lf->next)
+ {
+
+ int x1 = round((double)((int)prevEnd-winStart)*scale) + xOff;
+ int x2 = round((double)((int)lf->start-winStart)*scale) + xOff;
+ int w = x2-x1;
+ if (w > 0)
+ hvGfxLine(hvg, x1, midY, x2, midY, color);
+ bamDrawAt(tg, lf, hvg, xOff, y, scale, font, color, vis);
+ prevEnd = lf->end;
+ }
+}
+
+
void bamMethods(struct track *track)
/* Methods for BAM alignment files. */
{
track->canPack = TRUE;
char varName[1024];
-safef(varName, sizeof(varName), "%s_pairEndsByName", track->mapName);
+safef(varName, sizeof(varName), "%s_" BAM_PAIR_ENDS_BY_NAME, track->mapName);
boolean isPaired = cartUsualBoolean(cart, varName,
- (trackDbSetting(track->tdb, "pairEndsByName") != NULL));
+ (trackDbSetting(track->tdb, BAM_PAIR_ENDS_BY_NAME) != NULL));
if (isPaired)
{
linkedFeaturesSeriesMethods(track);
track->loadItems = bamPairedLoadItems;
+ track->drawItemAt = bamPairedDrawAt;
}
else
{
linkedFeaturesMethods(track);
track->loadItems = bamLoadItems;
+ track->drawItemAt = bamDrawAt;
}
track->labelNextItemButtonable = track->nextItemButtonable = FALSE;
track->labelNextPrevItem = NULL;
track->nextPrevItem = NULL;