src/hg/hgTracks/bamTrack.c 1.24
1.24 2010/01/14 07:39:19 kent
Moving cartOrTdbClosest to library as cartOrTdbString. Making bigBed pay attention to scoreFilter in case where not using linked features.
Index: src/hg/hgTracks/bamTrack.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgTracks/bamTrack.c,v
retrieving revision 1.23
retrieving revision 1.24
diff -b -B -U 1000000 -r1.23 -r1.24
--- src/hg/hgTracks/bamTrack.c 5 Jan 2010 05:36:26 -0000 1.23
+++ src/hg/hgTracks/bamTrack.c 14 Jan 2010 07:39:19 -0000 1.24
@@ -1,572 +1,563 @@
/* 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 "htmshell.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;
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;
}
INLINE int shadeTransform(int min, int max, int score)
/* Linearly transform score's place between min and max into a visible shade. */
{
int minShade = 2;
int ix = minShade + (maxShade - minShade) * ((double)(score - min) / (double)(max-min));
if (ix > maxShade)
ix = maxShade;
if (ix < minShade)
ix = minShade;
return ix;
}
static struct simpleFeature *expandSfQuals(struct simpleFeature *blocksIn, UBYTE *quals,
int orientation, int qLen)
/* Chop up blocksIn into one sf per query base, with sf->grayIx set according to
* base quality score. */
{
struct simpleFeature *sf, *blocksOut = NULL;
for (sf = blocksIn; sf != NULL; sf = sf->next)
{
struct simpleFeature *newSf;
int i;
for (i = sf->qStart; i < sf->qEnd; i++)
{
AllocVar(newSf);
newSf->start = sf->start + (i - sf->qStart);
newSf->end = newSf->start + 1;
newSf->qStart = i;
newSf->qEnd = i + 1;
int offset = (orientation < 0) ? (qLen - i - 1) : i;
// hardcode min & max for now; if user demand, make into tdb/cart vars.
newSf->grayIx = shadeTransform(0, 40, quals[offset]);
slAddHead(&blocksOut, newSf);
}
}
slReverse(&blocksOut);
return blocksOut;
}
// similar but not identical to customFactory.c's parseRgb:
static boolean parseRgb(char *s, unsigned char *retR, unsigned char *retG, unsigned char *retB)
/* Turn comma separated list to RGB vals; return FALSE if input is not as expected. */
{
char *row[4];
int wordCount = chopString(s, ",", row, ArraySize(row));
if ((wordCount != 3) || (!isdigit(row[0][0]) || !isdigit(row[1][0]) || !isdigit(row[2][0])))
return FALSE;
*retR = atoi(row[0]);
*retG = atoi(row[1]);
*retB = atoi(row[2]);
return TRUE;
}
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;
lf->name = cloneString(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, TRUE);
if (sameString(btd->colorMode, BAM_COLOR_MODE_GRAY) &&
sameString(btd->grayMode, BAM_GRAY_MODE_ALI_QUAL))
{
// hardcode min & max for now; if user demand, make into tdb/cart vars.
lf->grayIx = shadeTransform(0, 99, core->qual);
}
else if (sameString(btd->colorMode, BAM_COLOR_MODE_GRAY) &&
sameString(btd->grayMode, BAM_GRAY_MODE_BASE_QUAL))
{
UBYTE *quals = bamGetQueryQuals(bam, TRUE);
lf->components = expandSfQuals(lf->components, quals, lf->orientation, core->l_qseq);
lf->grayIx = maxShade - 3;
}
else if (sameString(btd->colorMode, BAM_COLOR_MODE_TAG) && isNotEmpty(btd->userTag))
{
char buf[16];
char *rgb = bamGetTagString(bam, btd->userTag, buf, sizeof(buf));
if (rgb != NULL)
{
// We don't have access to hvg at loadtime, so can't allocate color here.
// Instead, pack RGB values into lf->filterColor which fortunately is an int.
unsigned char r, g, b;
if (parseRgb(rgb, &r, &g, &b))
lf->filterColor = ((r & 0xff) << 16) | ((g & 0xff) << 8) | (b & 0xff);
else
{
static boolean already = FALSE;
if (! already)
{
warn("%s: At least one BAM tag value for %s (%s) is not in the expected "
"RGB format: N,N,N where each N is from 0 to 255.",
btd->tg->tdb->shortLabel, btd->userTag, htmlEncode(rgb));
already = TRUE;
btd->userTag = NULL;
}
}
}
else
lf->grayIx = maxShade;
}
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);
lf->name = cloneString("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 ? max(lf->next->end, lf->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) || (core->flag & BAM_FMUNMAP))
{
if (lf->start < winEnd && lf->end > winStart)
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;
if (lf->orientation > 0)
offscreen = max(winEnd, lf->end) + 10;
else
offscreen = min(winStart, lf->start) - 10;
if (offscreen < 0) offscreen = 0;
stub = lfStub(offscreen, -lf->orientation);
}
else
{
stub = lfStub(core->mpos, -lf->orientation);
}
lf->next = stub;
}
else if (sameString(btd->colorMode, BAM_COLOR_MODE_GRAY) &&
sameString(btd->grayMode, BAM_GRAY_MODE_UNPAIRED))
// not properly paired: make it a lighter shade.
lf->grayIx -= 4;
hashAdd(btd->pairHash, lf->name, lf);
}
else
{
lfMate->next = lf;
if (min(lfMate->start, lf->start) < winEnd && max(lfMate->end, lf->end) > winStart)
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;
}
-static char *cartOrTdbClosest(struct trackDb *tdb, char *var, char *defaultVal)
-/* Combine cart and tdb closest-to-home search */
-// (shouldn't there already be a lib routine to do this?)
-{
-char *tdbDefault = trackDbSettingClosestToHomeOrDefault(tdb, var, defaultVal);
-boolean compositeLevel = isNameAtCompositeLevel(tdb, var);
-return cartUsualStringClosestToHome(cart, tdb, compositeLevel, var, tdbDefault);
-}
-
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. */
{
struct hash *pairHash = isPaired ? hashNew(18) : NULL;
-int minAliQual = atoi(cartOrTdbClosest(tg->tdb, BAM_MIN_ALI_QUAL, BAM_MIN_ALI_QUAL_DEFAULT));
-char *colorMode = cartOrTdbClosest(tg->tdb, BAM_COLOR_MODE, BAM_COLOR_MODE_DEFAULT);
-char *grayMode = cartOrTdbClosest(tg->tdb, BAM_GRAY_MODE, BAM_GRAY_MODE_DEFAULT);
-char *userTag = cartOrTdbClosest(tg->tdb, BAM_COLOR_TAG, BAM_COLOR_TAG_DEFAULT);
+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);
struct bamTrackData btd = {tg, pairHash, minAliQual, colorMode, grayMode, userTag};
char *fileName;
if (tg->customPt)
{
- fileName = trackDbSettingClosestToHome(tg->tdb, "bigDataUrl");
+ 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, chromName);
char posForBam[512];
safef(posForBam, sizeof(posForBam), "%s:%d-%d", chromName, winStart, winEnd);
if (!isPaired)
bamFetch(fileName, posForBam, addBam, &btd);
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);
bamFetch(fileName, posForBam, addBamPaired, &btd);
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));
}
}
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
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 = trackDbSettingClosestToHome(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;
-char *colorMode = cartOrTdbClosest(tg->tdb, BAM_COLOR_MODE, BAM_COLOR_MODE_DEFAULT);
-char *grayMode = cartOrTdbClosest(tg->tdb, BAM_GRAY_MODE, BAM_GRAY_MODE_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);
bool baseQualMode = (sameString(colorMode, BAM_COLOR_MODE_GRAY) &&
sameString(grayMode, BAM_GRAY_MODE_BASE_QUAL));
if (vis != tvDense)
{
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 a packed int. Unpack:
int r, g, b;
r = (lf->filterColor >> 16) & 0xff;
g = (lf->filterColor >> 8) & 0xff;
b = lf->filterColor & 0xff;
color = hvGfxFindColorIx(hvg, r, g, b);
}
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;
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)
{
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)
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;
boolean compositeLevel = isNameAtCompositeLevel(track->tdb, BAM_PAIR_ENDS_BY_NAME);
boolean isPaired = cartUsualBooleanClosestToHome(cart, track->tdb, compositeLevel,
BAM_PAIR_ENDS_BY_NAME,
(trackDbSettingClosestToHome(track->tdb, BAM_PAIR_ENDS_BY_NAME) != NULL));
-char *colorMode = cartOrTdbClosest(track->tdb, BAM_COLOR_MODE, BAM_COLOR_MODE_DEFAULT);
-char *userTag = cartOrTdbClosest(track->tdb, BAM_COLOR_TAG, BAM_COLOR_TAG_DEFAULT);
+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));
compositeLevel = isNameAtCompositeLevel(track->tdb, BAM_COLOR_TAG);
cartRemoveVariableClosestToHome(cart, track->tdb, compositeLevel, BAM_COLOR_TAG);
}
}
if (isPaired)
{
linkedFeaturesSeriesMethods(track);
track->loadItems = bamPairedLoadItems;
track->drawItemAt = bamPairedDrawAt;
}
else
{
linkedFeaturesMethods(track);
track->loadItems = bamLoadItems;
track->drawItemAt = bamDrawAt;
}
track->nextItemButtonable = track->nextExonButtonable = FALSE;
track->nextPrevItem = NULL;
track->nextPrevExon = NULL;
track->colorShades = shadesOfGray;
}
#endif /* USE_BAM */