char *bamFileName(char *table, struct sqlConnection *conn, char *seqName) /* Return file name associated with BAM. This handles differences whether it's * a custom or built-in track. Do a freeMem on returned string when done. */ { char *fileName = bigFileNameFromCtOrHub(table, conn); if (fileName == NULL) fileName = bamFileNameFromTable(conn, table, seqName); return fileName; }
void doBamDetails(struct trackDb *tdb, char *item) /* Show details of an alignment from a BAM file. */ { if (item == NULL) errAbort("doBamDetails: NULL item name"); int start = cartInt(cart, "o"); if (!tdb || !trackDbSetting(tdb, "bamSkipPrintQualScore")) skipQualityScore = FALSE; else skipQualityScore = TRUE; // TODO: libify tdb settings table_pairEndsByName, stripPrefix and pairSearchRange knetUdcInstall(); if (udcCacheTimeout() < 300) udcSetCacheTimeout(300); if (sameString(item, "zoom in")) printf("Zoom in to a region with fewer items to enable 'detail page' links for individual items.<BR>"); char varName[1024]; safef(varName, sizeof(varName), "%s_pairEndsByName", tdb->track); boolean isPaired = cartUsualBoolean(cart, varName, (trackDbSetting(tdb, "pairEndsByName") != NULL)); char position[512]; safef(position, sizeof(position), "%s:%d-%d", seqName, winStart, winEnd); struct hash *pairHash = isPaired ? hashNew(0) : NULL; struct bamTrackData btd = {start, item, pairHash}; char *fileName = hReplaceGbdb(trackDbSetting(tdb, "bigDataUrl")); if (fileName == NULL) { if (isCustomTrack(tdb->table)) { errAbort("bamLoadItemsCore: can't find bigDataUrl for custom track %s", tdb->track); } else { struct sqlConnection *conn = hAllocConnTrack(database, tdb); fileName = hReplaceGbdb(bamFileNameFromTable(conn, tdb->table, seqName)); hFreeConn(&conn); } } char *indexName = hReplaceGbdb(trackDbSetting(tdb, "bigDataIndex")); char *cacheDir = cfgOption("cramRef"); char *refUrl = trackDbSetting(tdb, "refUrl"); bamAndIndexFetchPlus(fileName, indexName, position, oneBam, &btd, NULL, refUrl, cacheDir); if (isPaired) { char *setting = trackDbSettingOrDefault(tdb, "pairSearchRange", "20000"); int pairSearchRange = atoi(setting); if (pairSearchRange > 0 && hashNumEntries(pairHash) > 0) { // Repeat the search for item in a larger window: struct hash *newPairHash = hashNew(0); btd.pairHash = newPairHash; safef(position, sizeof(position), "%s:%d-%d", seqName, max(0, winStart-pairSearchRange), winEnd+pairSearchRange); bamFetch(fileName, position, oneBam, &btd, NULL); } struct hashEl *hel; struct hashCookie cookie = hashFirst(btd.pairHash); while ((hel = hashNext(&cookie)) != NULL) { bam1_t *bam = hel->val; const bam1_core_t *core = &bam->core; if (! (core->flag & BAM_FMUNMAP)) printf("<B>Note: </B>unable to find paired end for %s " "within +-%d bases of viewing window %s<BR>\n", item, pairSearchRange, addCommasToPos(database, cartString(cart, "position"))); else printf("<B>Paired read name:</B> %s<BR>\n", item); singleBamDetails(bam); } } }
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); }