void bamMethods(struct track *track) /* Methods for BAM alignment files. */ { knetUdcInstall(); boolean isBamWig = cartUsualBooleanClosestToHome(cart, track->tdb, FALSE, BAMWIG_MODE, (trackDbSettingClosestToHome(track->tdb, BAMWIG_MODE) != NULL)); if (isBamWig) { bamWigMethods(track, track->tdb, 0, NULL); return; } track->canPack = TRUE; boolean isPaired = cartUsualBooleanClosestToHome(cart, track->tdb, FALSE, BAM_PAIR_ENDS_BY_NAME, (trackDbSettingClosestToHome(track->tdb, BAM_PAIR_ENDS_BY_NAME) != NULL)); char *tdbShowNames = trackDbSetting(track->tdb, BAM_SHOW_NAMES); boolean showNames = cartUsualBooleanClosestToHome(cart, track->tdb, FALSE, BAM_SHOW_NAMES, SETTING_IS_ON(tdbShowNames)); char *colorMode = cartOrTdbString(cart, track->tdb, BAM_COLOR_MODE, BAM_COLOR_MODE_DEFAULT); char *userTag = cartOrTdbString(cart, track->tdb, BAM_COLOR_TAG, BAM_COLOR_TAG_DEFAULT); if (sameString(colorMode, BAM_COLOR_MODE_TAG) && userTag != NULL) { if (! (isalpha(userTag[0]) && isalnum(userTag[1]) && userTag[2] == '\0')) { warn("%s: BAM tag '%s' is not valid -- must be a letter followed by a letter or number.", track->tdb->shortLabel, htmlEncode(userTag)); cartRemoveVariableClosestToHome(cart, track->tdb, FALSE, BAM_COLOR_TAG); } } addBamBaseAndIndelSettings(track->tdb); if (isPaired) { linkedFeaturesSeriesMethods(track); track->loadItems = bamPairedLoadItems; track->drawItems = bamLinkedFeaturesSeriesDraw; track->drawItemAt = bamPairedDrawAt; } else { linkedFeaturesMethods(track); track->loadItems = bamLoadItems; track->drawItems = bamLinkedFeaturesDraw; track->drawItemAt = bamDrawAt; } if (!showNames) { track->drawName = TRUE; // ironic, but this is how to suppress item labels in pack mode. track->drawLeftLabels = maybeDrawLeftLabels; } track->nextItemButtonable = track->nextExonButtonable = FALSE; track->nextPrevItem = NULL; track->nextPrevExon = NULL; if (sameString(colorMode, BAM_COLOR_MODE_GRAY)) track->colorShades = shadesOfGray; }
void loadSimpleBed(struct track *tg) /* Load the items in one track - just move beds in * window... */ { struct bed *(*loader)(char **row); struct bed *bed, *list = NULL; char **row; int rowOffset; char *words[3]; int wordCt; char query[128]; char *setting = NULL; bool doScoreCtFilter = FALSE; int scoreFilterCt = 0; char *topTable = NULL; if (tg->bedSize <= 3) loader = bedLoad3; else if (tg->bedSize == 4) loader = bedLoad; else if (tg->bedSize == 5) loader = bedLoad5; else loader = bedLoad6; // pairedTagAlign loader is required for base coloring using sequence from seq1 & seq2 // after removing optional bin column, this loader assumes seq1 and seq2 are in // row[6] and row[7] respectively of the sql result. if ((setting = trackDbSetting(tg->tdb, BASE_COLOR_USE_SEQUENCE)) && sameString(setting, "seq1Seq2")) loader = bedLoadPairedTagAlign; /* limit to a specified count of top scoring items. * If this is selected, it overrides selecting item by specified score */ if ((setting = trackDbSettingClosestToHome(tg->tdb, "filterTopScorers")) != NULL) { wordCt = chopLine(cloneString(setting), words); if (wordCt >= 3) { doScoreCtFilter = cartUsualBooleanClosestToHome(cart, tg->tdb, FALSE, "filterTopScorersOn",sameString(words[0], "on")); scoreFilterCt = cartUsualIntClosestToHome(cart, tg->tdb, FALSE, "filterTopScorersCt", atoi(words[1])); topTable = words[2]; /* if there are not too many rows in the table then can define */ /* top table as the track or subtrack table */ if (sameWord(topTable, "self")) topTable = cloneString(tg->table); } } /* Get list of items */ if (tg->isBigBed) { // avoid opening an unneeded db connection for bigBed; required not to use mysql for parallel fetch tracks char *scoreFilter = cartOrTdbString(cart, tg->tdb, "scoreFilter", NULL); struct lm *lm = lmInit(0); struct bigBedInterval *bb, *bbList = bigBedSelectRange(tg, chromName, winStart, winEnd, lm); char *bedRow[32]; char startBuf[16], endBuf[16]; int minScore = 0; if (scoreFilter) minScore = atoi(scoreFilter); for (bb = bbList; bb != NULL; bb = bb->next) { bigBedIntervalToRow(bb, chromName, startBuf, endBuf, bedRow, ArraySize(bedRow)); bed = loader(bedRow); if (scoreFilter == NULL || bed->score >= minScore) slAddHead(&list, bed); } lmCleanup(&lm); } else { struct sqlConnection *conn = hAllocConnTrack(database, tg->tdb); struct sqlResult *sr = NULL; /* limit to items above a specified score */ char *scoreFilterClause = getScoreFilterClause(cart, tg->tdb,NULL); if (doScoreCtFilter && (topTable != NULL) && hTableExists(database, topTable)) { sqlSafef(query, sizeof(query),"select * from %s order by score desc limit %d", topTable, scoreFilterCt); sr = sqlGetResult(conn, query); rowOffset = hOffsetPastBin(database, hDefaultChrom(database), topTable); } else if(scoreFilterClause != NULL && tg->bedSize >= 5) { sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd, scoreFilterClause, &rowOffset); } else { sr = hRangeQuery(conn, tg->table, chromName, winStart, winEnd, NULL, &rowOffset); } freeMem(scoreFilterClause); while ((row = sqlNextRow(sr)) != NULL) { bed = loader(row+rowOffset); slAddHead(&list, bed); } sqlFreeResult(&sr); hFreeConn(&conn); } if (doScoreCtFilter) { /* filter out items not in this window */ struct bed *newList = bedFilterListInRange(list, NULL, chromName, winStart, winEnd); list = newList; } slReverse(&list); tg->items = list; }
static void mafOrAxtClick2(struct sqlConnection *conn, struct sqlConnection *conn2, struct trackDb *tdb, char *axtOtherDb, char *fileName) /* Display details for MAF or AXT tracks. */ { hgBotDelay(); if (winEnd - winStart > 30000) { printf("Zoom so that window is 30,000 bases or less to see alignments and conservation statistics\n"); } else { struct mafAli *mafList = NULL, *maf, *subList = NULL; int aliIx = 0, realCount = 0; char dbChrom[64]; char option[128]; char *capTrack; struct consWiggle *consWig, *consWiggles; struct hash *speciesOffHash = NULL; char *speciesOrder = NULL; char *speciesTarget = trackDbSetting(tdb, SPECIES_TARGET_VAR); char buffer[1024]; int useTarg = FALSE; int useIrowChains = FALSE; safef(option, sizeof(option), "%s.%s", tdb->track, MAF_CHAIN_VAR); if (cartCgiUsualBoolean(cart, option, FALSE) && trackDbSetting(tdb, "irows") != NULL) useIrowChains = TRUE; safef(buffer, sizeof(buffer), "%s.vis",tdb->track); if (useIrowChains) { if (!cartVarExists(cart, buffer) && (speciesTarget != NULL)) useTarg = TRUE; else { char *val; val = cartUsualString(cart, buffer, "useCheck"); useTarg = sameString("useTarg",val); } } if (sameString(tdb->type, "bigMaf")) { char *fileName = trackDbSetting(tdb, "bigDataUrl"); struct bbiFile *bbi = bigBedFileOpen(fileName); mafList = bigMafLoadInRegion(bbi, seqName, winStart, winEnd); } else mafList = mafOrAxtLoadInRegion2(conn,conn2, tdb, seqName, winStart, winEnd, axtOtherDb, fileName); safef(dbChrom, sizeof(dbChrom), "%s.%s", hubConnectSkipHubPrefix(database), seqName); safef(option, sizeof(option), "%s.speciesOrder", tdb->track); speciesOrder = cartUsualString(cart, option, NULL); if (speciesOrder == NULL) speciesOrder = trackDbSetting(tdb, "speciesOrder"); for (maf = mafList; maf != NULL; maf = maf->next) { int mcCount = 0; struct mafComp *mc; struct mafAli *subset; struct mafComp *nextMc; /* remove empty components and configured off components * from MAF, and ignore * the entire MAF if all components are empty * (solely for gap annotation) */ if (!useTarg) { for (mc = maf->components->next; mc != NULL; mc = nextMc) { char buf[64]; char *organism; mafSrcDb(mc->src, buf, sizeof buf); organism = hOrganism(buf); if (!organism) organism = buf; nextMc = mc->next; safef(option, sizeof(option), "%s.%s", tdb->track, buf); if (!cartUsualBoolean(cart, option, TRUE)) { if (speciesOffHash == NULL) speciesOffHash = newHash(4); hashStoreName(speciesOffHash, organism); } if (!cartUsualBoolean(cart, option, TRUE)) slRemoveEl(&maf->components, mc); else mcCount++; } } if (mcCount == 0) continue; if (speciesOrder) { int speciesCt; char *species[2048]; struct mafComp **newOrder, *mcThis; int i; mcCount = 0; speciesCt = chopLine(cloneString(speciesOrder), species); newOrder = needMem((speciesCt + 1) * sizeof (struct mafComp *)); newOrder[mcCount++] = maf->components; for (i = 0; i < speciesCt; i++) { if ((mcThis = mafMayFindCompSpecies(maf, species[i], '.')) == NULL) continue; newOrder[mcCount++] = mcThis; } maf->components = NULL; for (i = 0; i < mcCount; i++) { newOrder[i]->next = 0; slAddHead(&maf->components, newOrder[i]); } slReverse(&maf->components); } subset = mafSubsetE(maf, dbChrom, winStart, winEnd, TRUE); if (subset != NULL) { /* Reformat MAF if needed so that sequence from current * database is the first component and on the * plus strand. */ mafMoveComponentToTop(subset, dbChrom); if (subset->components->strand == '-') mafFlipStrand(subset); subset->score = mafScoreMultiz(subset); slAddHead(&subList, subset); ++realCount; } } slReverse(&subList); mafAliFreeList(&mafList); if (subList != NULL) { char *showVarName = "hgc.showMultiBase"; char *showVarVal = cartUsualString(cart, showVarName, "all"); boolean onlyDiff = sameWord(showVarVal, "diff"); #ifdef ADDEXONCAPITAL char *codeVarName = "hgc.multiCapCoding"; char *codeVarVal = cartUsualString(cart, codeVarName, "coding"); boolean onlyCds = sameWord(codeVarVal, "coding"); #endif /* add links for conservation score statistics */ consWiggles = wigMafWiggles(database, tdb); int wigCount = slCount(consWiggles); if (wigCount == 1) { conservationStatsLink(tdb, "Conservation score statistics", consWiggles->table); } else if (wigCount > 1) { /* multiple wiggles. List all that have been turned on with * checkboxes */ /* Scan for cart variables -- do any exist, are any turned on ? */ boolean wigSet = FALSE; boolean wigOn = FALSE; for (consWig = consWiggles; consWig != NULL; consWig = consWig->next) { char *wigVarSuffix = NULL; (void)wigMafWiggleVar(tdb->track, consWig, &wigVarSuffix); if (cartVarExistsAnyLevel(cart, tdb, FALSE, wigVarSuffix)) { wigSet = TRUE; if (cartBooleanClosestToHome(cart, tdb, FALSE, wigVarSuffix)) wigOn = TRUE; } } /* If there are no cart vars, turn on the first (default) wig */ if (!wigSet) { char *prefix = tdb->track; // use when setting things to the cart if (tdbIsContainerChild(tdb)) prefix = tdbGetContainer(tdb)->track; cartSetBoolean(cart, wigMafWiggleVar(prefix, consWiggles, NULL), TRUE); wigOn = TRUE; } if (wigOn) { boolean first = TRUE; for (consWig = consWiggles; consWig != NULL; consWig = consWig->next) { if (first) { printf("Conservation score statistics:"); first = FALSE; } char *wigVarSuffix = NULL; (void)wigMafWiggleVar(tdb->track, consWig, &wigVarSuffix); if (cartUsualBooleanClosestToHome(cart, tdb, FALSE, wigVarSuffix,FALSE)) { printf(" "); subChar(consWig->uiLabel, '_', ' '); conservationStatsLink(tdb, consWig->uiLabel, consWig->table); } } } } puts("</P>\n"); /* no alignment to display when in visibilities where only wiggle is shown */ char *vis = cartOptionalString(cart, tdb->track); if (vis) { enum trackVisibility tv = hTvFromStringNoAbort(vis); if (tv == tvSquish || tv == tvDense) return; } #ifdef ADDEXONCAPITAL puts("<FORM ACTION=\"../cgi-bin/hgc\" NAME=\"gpForm\" METHOD=\"GET\">"); cartSaveSession(cart); cgiContinueHiddenVar("g"); cgiContinueHiddenVar("c"); cgiContinueHiddenVar("i"); printf("Capitalize "); cgiMakeDropListFull(codeVarName, codeAll, codeAll, ArraySize(codeAll), codeVarVal, autoSubmit); printf("exons based on "); capTrack = genePredDropDown(cart, trackHash, "gpForm", "hgc.multiCapTrack"); #endif printf("show "); cgiMakeDropListFull(showVarName, showAll, showAll, ArraySize(showAll), showVarVal, autoSubmit); printf("bases"); printf("<BR>\n"); printf("</FORM>\n"); #ifdef REVERSESTRAND /* notify if bases are complemented (hgTracks is on reverse strand) */ if (cartCgiUsualBoolean(cart, COMPLEMENT_BASES_VAR, FALSE)) puts("<EM>Alignment displayed on reverse strand</EM><BR>"); #endif puts("Place cursor over species for alignment detail. Click on 'B' to link to browser "); puts("for aligned species, click on 'D' to get DNA for aligned species.<BR>"); printf("<TT><PRE>"); /* notify if species removed from alignment */ if (speciesOffHash) { char *species; struct hashCookie hc = hashFirst(speciesOffHash); puts("<B>Components not displayed:</B> "); while ((species = hashNextName(&hc)) != NULL) printf("%s ", species); puts("<BR>"); } for (maf = subList; maf != NULL; maf = maf->next) { mafLowerCase(maf); #ifdef ADDEXONCAPITAL if (capTrack != NULL) capMafOnTrack(maf, capTrack, onlyCds); #endif printf("<B>Alignment block %d of %d in window, %d - %d, %d bps </B>\n", ++aliIx,realCount,maf->components->start + 1, maf->components->start + maf->components->size, maf->components->size); mafPrettyOut(stdout, maf, 70,onlyDiff, aliIx); } mafAliFreeList(&subList); } else { printf("No multiple alignment in browser window"); } printf("</PRE></TT>"); } }