int pscmFindColorIx(struct pscmGfx *pscm, int r, int g, int b)
/* Returns closest color in color map to rgb values. If it doesn't
* already exist in color map and there's room, it will create
* exact color in map. */
{
return MAKECOLOR_32(r,g,b);
}
void floatPicIntoHvg(struct floatPic *pic, int xOff, int yOff, struct hvGfx *hvg)
/* Copy float pic into hvg image at given offset. */
{
int width = pic->width, height = pic->height;
Color *lineBuf;
AllocArray(lineBuf, width);
int y;
for (y=0; y<height; ++y)
{
float *fp = pic->lines[y];
Color *cp = lineBuf;
int i = width;
while (--i >= 0)
{
int red = fp[0]*FLOAT_FOR_BIGGEST_BYTE;
int green = fp[1]*FLOAT_FOR_BIGGEST_BYTE;
int blue = fp[2]*FLOAT_FOR_BIGGEST_BYTE;
*cp++ = MAKECOLOR_32(red, green, blue);
fp += 3;
}
if (hvg->rc)
reverseLineOfColors(lineBuf, width);
hvGfxVerticalSmear(hvg, xOff, y + yOff, width, 1, lineBuf, TRUE);
}
freez(&lineBuf);
}
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;
struct psl *original = pslFromBam(bam);
if (original == NULL)
return NULL;
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, FALSE); // cds.c reverses if psl != NULL
lf->original = original;
int clippedQLen;
bamGetSoftClipping(bam, NULL, NULL, &clippedQLen);
if (sameString(btd->colorMode, BAM_COLOR_MODE_GRAY) &&
sameString(btd->grayMode, BAM_GRAY_MODE_ALI_QUAL))
{
lf->grayIx = shadeTransform(btd->aliQualShadeMin, btd->aliQualShadeMax, 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, clippedQLen,
btd->baseQualShadeMin, btd->baseQualShadeMax);
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 = MAKECOLOR_32(r,g,b);
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;
}
