struct samAlignment *bamFetchSamAlignmentPlus(char *fileOrUrl, char *chrom, int start, int end,
struct lm *lm, char *refUrl, char *cacheDir)
/* Fetch region as a list of samAlignments - which is more or less an unpacked
* bam record. Results is allocated out of lm, since it tends to be large... */
{
struct bamToSamHelper helper;
helper.lm = lm;
helper.chrom = chrom;
helper.dy = dyStringNew(0);
helper.samList = NULL;
char posForBam[256];
safef(posForBam, sizeof(posForBam), "%s:%d-%d", chrom, start+1, end);
bamFetchPlus(fileOrUrl, posForBam, bamAddOneSamAlignment, &helper, &helper.samFile,
refUrl, cacheDir);
dyStringFree(&helper.dy);
slReverse(&helper.samList);
return helper.samList;
}
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. */
{
/* protect against temporary network error */
struct errCatch *errCatch = errCatchNew();
if (errCatchStart(errCatch))
{
struct hash *pairHash = isPaired ? hashNew(18) : NULL;
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);
int aliQualShadeMin = 0, aliQualShadeMax = 99, baseQualShadeMin = 0, baseQualShadeMax = 40;
parseIntRangeSetting(tg->tdb, "aliQualRange", &aliQualShadeMin, &aliQualShadeMax);
parseIntRangeSetting(tg->tdb, "baseQualRange", &baseQualShadeMin, &baseQualShadeMax);
struct bamTrackData btd = {tg, pairHash, minAliQual, colorMode, grayMode, userTag,
aliQualShadeMin, aliQualShadeMax, baseQualShadeMin, baseQualShadeMax};
char *fileName = trackDbSetting(tg->tdb, "bigDataUrl");
if (fileName == NULL)
{
if (tg->customPt)
{
errAbort("bamLoadItemsCore: can't find bigDataUrl for custom track %s", tg->track);
}
else
{
struct sqlConnection *conn = hAllocConnTrack(database, tg->tdb);
fileName = bamFileNameFromTable(conn, tg->table, chromName);
hFreeConn(&conn);
}
}
char *fileName2 = hReplaceGbdb(fileName);
char posForBam[512];
safef(posForBam, sizeof(posForBam), "%s:%d-%d", chromName, winStart, winEnd);
char *cacheDir = cfgOption("cramRef");
char *refUrl = trackDbSetting(tg->tdb, "refUrl");
if (!isPaired)
bamFetchPlus(fileName2, posForBam, addBam, &btd, NULL, refUrl, cacheDir);
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);
bamFetchPlus(fileName2, posForBam, addBamPaired, &btd, NULL, refUrl, cacheDir);
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));
}
}
freez(&fileName2);
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 if (sameString(colorMode, BAM_COLOR_MODE_GRAY) &&
sameString(grayMode, BAM_GRAY_MODE_ALI_QUAL))
slSort(&(tg->items), linkedFeaturesCmpScore);
else
slSort(&(tg->items), linkedFeaturesCmpStart);
if (slCount(tg->items) > MAX_ITEMS_FOR_MAPBOX)
{
// flag drawItems to make a mapBox for the whole track
tg->customInt = 1;
tg->mapItem = dontMapItem;
}
}
}
errCatchEnd(errCatch);
if (errCatch->gotError)
{
tg->networkErrMsg = cloneString(errCatch->message->string);
tg->drawItems = bigDrawWarning;
tg->totalHeight = bigWarnTotalHeight;
}
errCatchFree(&errCatch);
}
