static void showOverlap(const bam1_t *leftBam, const bam1_t *rightBam)
/* If the two reads overlap, show how. */
{
const bam1_core_t *leftCore = &(leftBam->core), *rightCore = &(rightBam->core);
int leftStart = leftCore->pos, rightStart = rightCore->pos;
int leftLen = bamGetTargetLength(leftBam), rightLen = bamGetTargetLength(rightBam);
char *leftSeq = bamGetQuerySequence(leftBam, useStrand);
char *rightSeq = bamGetQuerySequence(rightBam, useStrand);
if (useStrand && bamIsRc(leftBam))
reverseComplement(leftSeq, strlen(leftSeq));
if (useStrand && bamIsRc(rightBam))
reverseComplement(rightSeq, strlen(rightSeq));
if ((rightStart > leftStart && leftStart + leftLen > rightStart) ||
(leftStart > rightStart && rightStart+rightLen > leftStart))
{
int leftClipLow, rightClipLow;
bamGetSoftClipping(leftBam, &leftClipLow, NULL, NULL);
bamGetSoftClipping(rightBam, &rightClipLow, NULL, NULL);
leftStart -= leftClipLow;
rightStart -= rightClipLow;
printf("<B>Note: End read alignments overlap:</B><BR>\n<PRE><TT>");
int i = leftStart - rightStart;
while (i-- > 0)
putc(' ', stdout);
puts(leftSeq);
i = rightStart - leftStart;
while (i-- > 0)
putc(' ', stdout);
puts(rightSeq);
puts("</TT></PRE>");
}
}
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;
}
