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;
}
int addBamPaired(const bam1_t *bam, void *data)
#endif
/* 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));
if ((core->flag & BAM_FMUNMAP) && 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;
}
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;
// don't link to pair that's not on the same chrom
if ((core->mpos < 0) || (core->tid != core->mtid))
{
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;
}
