src/hg/hgTracks/bamTrack.c 1.11

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 1000000 -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
@@ -1,294 +1,461 @@
 /* bamTrack -- handlers for alignments in BAM format (produced by MAQ,
  * BWA and some other short-read alignment tools). */
 
 #ifdef USE_BAM
 
 #include "common.h"
 #include "hCommon.h"
 #include "hash.h"
 #include "linefile.h"
 #include "jksql.h"
 #include "hdb.h"
 #include "hgTracks.h"
+#include "cds.h"
 #include "bamFile.h"
 
 static char const rcsid[] = "$Id$";
 
 struct bamTrackData
     {
     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, 
  * and tally up length on reference sequence while we're at it. */
 {
 const bam1_core_t *core = &bam->core;
 struct simpleFeature *sf, *sfList = NULL;
 int tLength=0, tPos = core->pos, qPos = 0;
 unsigned int *cigar = bam1_cigar(bam);
 int i;
 for (i = 0;  i < core->n_cigar;  i++)
     {
     char op;
     int n = bamUnpackCigarElement(cigar[i], &op);
     switch (op)
 	{
 	case 'M': // match or mismatch (gapless aligned block)
 	    AllocVar(sf);
 	    sf->start = tPos;
 	    sf->qStart = qPos;
 	    tPos = sf->end = tPos + n;
 	    qPos = sf->qEnd = qPos + n;
 	    slAddHead(&sfList, sf);
 	    tLength += n;
 	    break;
 	case 'I': // inserted in query
 	case 'S': // skipped query bases at beginning or end ("soft clipping")
 	    qPos += n;
 	    break;
 	case 'D': // deleted from query
 	case 'N': // long deletion from query (intron as opposed to small del)
 	    tPos += n;
 	    tLength += n;
 	    break;
 	case 'H': // skipped query bases not stored in record's query sequence ("hard clipping")
 	case 'P': // P="silent deletion from padded reference sequence" -- ignore these.
 	    break;
 	default:
 	    errAbort("sfFromNumericCigar: unrecognized CIGAR op %c -- update me", op);
 	}
     }
 if (retLength != NULL)
     *retLength = tLength;
 return sfList;
 }
 
 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;
 safef(lf->name, sizeof(lf->name), bam1_qname(bam));
 lf->orientation = (core->flag & BAM_FREVERSE) ? -1 : 1;
 int length;
 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)
 /* Return TRUE if bam passes hgTrackUi-set filters. */
 {
 if (bam == NULL)
     return FALSE;
 const bam1_core_t *core = &bam->core;
 // Always reject unmapped items -- nowhere to draw them.
 if (core->flag & BAM_FUNMAP)
     return FALSE;
 if (core->qual < btd->minAliQual)
     return FALSE;
 return TRUE;
 }
 
 int addBam(const bam1_t *bam, void *data)
 /* bam_fetch() calls this on each bam alignment retrieved.  Translate each bam 
  * into a linkedFeatures item, and add it to tg->items. */
 {
 struct bamTrackData *btd = (struct bamTrackData *)data;
 if (!passesFilters(bam, btd))
     return 0;
 struct linkedFeatures *lf = bamToLf(bam, data);
 struct track *tg = btd->tg;
 slAddHead(&(tg->items), lf);
 return 0;
 }
 
 static struct linkedFeatures *lfStub(int startEnd, int orientation)
 /* Make a linkedFeatures for a zero-length item (so that an arrow will be drawn
  * toward the given coord. */
 {
 struct linkedFeatures *lf;
 AllocVar(lf);
 safef(lf->name, sizeof(lf->name), "stub");
 lf->orientation = orientation;
 struct simpleFeature *sf;
 AllocVar(sf);
 sf->start = sf->end = lf->start = lf->end = lf->tallStart = lf->tallEnd = startEnd;
 lf->components = sf;
 lf->extra = cloneString("");
 lf->grayIx = maxShade;
 return lf;
 }
 
 static struct linkedFeaturesSeries *lfsFromLf(struct linkedFeatures *lf)
 /* Make a linkedFeaturesSeries from one or two linkedFeatures elements. */
 {
 struct linkedFeaturesSeries *lfs;
 AllocVar(lfs);
 lfs->name = cloneString(lf->name);
 lfs->grayIx = lf->grayIx;
 if (lf->next != NULL)
     slSort(&lf, linkedFeaturesCmpStart);
 lfs->orientation = 0;
 lfs->start = lf->start;
 lfs->end = lf->next ? lf->next->end : lf->end;
 lfs->features = lf;
 return lfs;
 }
 
 int addBamPaired(const bam1_t *bam, void *data)
 /* bam_fetch() calls this on each bam alignment retrieved.  Translate each bam 
  * into a linkedFeaturesSeries item, and either store it until we find its mate
  * or add it to tg->items. */
 {
 const bam1_core_t *core = &bam->core;
 struct bamTrackData *btd = (struct bamTrackData *)data;
 if (! passesFilters(bam, btd))
     return 0;
 struct linkedFeatures *lf = bamToLf(bam, data);
 struct track *tg = btd->tg;
 if (! (core->flag & BAM_FPAIRED))
     {
     slAddHead(&(tg->items), lfsFromLf(lf));
     }
 else
     {
     struct linkedFeatures *lfMate = (struct linkedFeatures *)hashFindVal(btd->pairHash, lf->name);
     if (lfMate == NULL)
 	{
 	if (core->flag & BAM_FPROPER_PAIR)
 	    {
 	    // If we know that this is properly paired, but don't have the mate,
 	    // make a bogus item off the edge of the window so that if we don't
 	    // encounter its mate later, we can at least draw an arrow off the
 	    // edge of the window.
 	    struct linkedFeatures *stub;
 	    if (core->mpos < 0)
 		{
 		int offscreen = (lf->orientation > 0) ? winEnd + 10 : winStart - 10;
 		if (offscreen < 0) offscreen = 0;
 		stub = lfStub(offscreen, -lf->orientation);
 		}
 	    else
 		{
 		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
 	{
 	lfMate->next = lf;
 	slAddHead(&(tg->items), lfsFromLf(lfMate));
 	hashRemove(btd->pairHash, lf->name);
 	}
     }
 return 0;
 }
 
 #define MAX_ITEMS_FOR_MAPBOX 1500
 static void dontMapItem(struct track *tg, struct hvGfx *hvg, void *item,
 			char *itemName, char *mapItemName, int start, int end,
 			int x, int y, int width, int height)
 /* 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. */
 {
 char *seqNameForBam = chromName;
 char *stripPrefix = trackDbSetting(tg->tdb, "stripPrefix");
 if (stripPrefix && startsWith(stripPrefix, chromName))
     seqNameForBam = chromName + strlen(stripPrefix);
 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");
     if (fileName == NULL)
 	errAbort("bamLoadItemsCore: can't find bigDataUrl for custom track %s", tg->mapName);
     }
 else
     fileName = bamFileNameFromTable(database, tg->mapName, seqNameForBam);
 bamFetch(fileName, posForBam, (isPaired ? addBamPaired : addBam), &btd);
 if (isPaired)
     {
     struct hashEl *hel;
     struct hashCookie cookie = hashFirst(pairHash);
     int count = 0;
     while ((hel = hashNext(&cookie)) != NULL)
 	{
 	struct linkedFeatures *lf = hel->val;
 	slAddHead(&(tg->items), lfsFromLf(lf));
 	count++;
 	}
     }
 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;
     }
 }
 
 void bamLoadItems(struct track *tg)
 /* Load single-ended-only 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. */
 {
 bamLoadItemsCore(tg, FALSE);
 }
 
 void bamPairedLoadItems(struct track *tg)
 /* Load possibly paired 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. */
 {
 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;
 track->colorShades = shadesOfGray;
 }
 
 #endif /* USE_BAM */