Esempio n. 1
0
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;
}
Esempio n. 2
0
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);
}