b622d147b7dbac52dbf3ba26928cd18e02d42bd8 braney Sat Feb 26 12:34:37 2022 -0800 add support for using a bigBed as the chromAlias file diff --git src/hg/hgTracks/hgTracks.c src/hg/hgTracks/hgTracks.c index f2f15d3..c4ea42a 100644 --- src/hg/hgTracks/hgTracks.c +++ src/hg/hgTracks/hgTracks.c @@ -4658,31 +4658,31 @@ /* Support setting to suppress display of empty subtracks. * If multiBed is available, return hash with subtrack names as keys */ char *multiBedFile = NULL; char *subtrackIdFile = NULL; if (!compositeHideEmptySubtracks(cart, track->tdb, &multiBedFile, &subtrackIdFile)) return NULL; if (!multiBedFile) return NULL; // load multiBed items in window // TODO: filters here ? // TODO: protect against temporary network error ? */ struct lm *lm = lmInit(0); -struct bbiFile *bbi = bigBedFileOpenAlias(multiBedFile, chromAliasChromToAliasHash(database)); +struct bbiFile *bbi = bigBedFileOpenAlias(multiBedFile, chromAliasFindAliases); struct bigBedInterval *bb, *bbList = bigBedIntervalQuery(bbi, chromName, winStart, winEnd, 0, lm); char *row[bbi->fieldCount]; char startBuf[16], endBuf[16]; struct hash *nonEmptySubtracksHash = hashNew(0); for (bb = bbList; bb != NULL; bb = bb->next) { bigBedIntervalToRow(bb, chromName, startBuf, endBuf, row, ArraySize(row)); // TODO: do this in bed3Sources.c char *idList = row[4]; struct slName *ids = slNameListFromComma(idList); struct slName *id = NULL; for (id = ids; id != NULL; id = id->next) hashStore(nonEmptySubtracksHash, id->name); // TODO: free some stuff ? } @@ -10104,75 +10104,66 @@ printf("Total: %d", count); cgiTableFieldEnd(); cgiTableFieldStartAlignRight(); printLongWithCommas(stdout, total); puts(" "); cgiTableFieldEnd(); if (hasAlias) { cgiSimpleTableFieldStart(); puts(" "); cgiTableFieldEnd(); } cgiTableRowEnd(); } -static char *chrAliases(struct hash *aliasHash, char *sequenceName) +static char *chrAliases(struct slName *names, char *sequenceName) /* lookup the sequenceName in the aliasHash and return csv string * of alias names */ { -if (NULL == aliasHash) +if (NULL == names) return NULL; struct dyString *returned = dyStringNew(512); -struct hashEl *hel = hashLookup(aliasHash, sequenceName); -if (hel) - { - dyStringPrintf(returned, "%s", ((struct chromAlias *)hel->val)->alias); - hel = hashLookupNext(hel); - while (hel != NULL) - { - dyStringPrintf(returned, ", %s",((struct chromAlias *)hel->val)->alias); - hel = hashLookupNext(hel); - } - } +dyStringPrintf(returned, "%s", names->name); +for(names = names->next; names; names = names->next) + dyStringPrintf(returned, ", %s",names->name); return dyStringCannibalize(&returned); } void chromInfoRowsChromExt(char *sortType) /* Make table rows of chromosomal chromInfo name & size, sorted by name. */ { struct slName *chromList = hAllChromNames(database); struct slName *chromPtr = NULL; long long total = 0; boolean hasAlias = hTableExists(database, "chromAlias"); -struct hash *aliasHash = chromAliasMakeReverseLookupTable(database); /* key is database sequence name, value is an alias name, can be multiple * entries for the same sequence name. NULL if no chromAlias available */ if (sameString(sortType,"default")) slSort(&chromList, chrSlNameCmp); else if (sameString(sortType,"withAltRandom")) slSort(&chromList, chrSlNameCmpWithAltRandom); else errAbort("unknown sort type in chromInfoRowsChromExt: %s", sortType); for (chromPtr = chromList; chromPtr != NULL; chromPtr = chromPtr->next) { unsigned size = hChromSize(database, chromPtr->name); - char *aliasNames = chrAliases(aliasHash, chromPtr->name); + char *aliasNames = chrAliases(chromAliasFindAliases(chromPtr->name), chromPtr->name); cgiSimpleTableRowStart(); cgiSimpleTableFieldStart(); htmlPrintf("<A HREF=\"%s|none|?%s|url|=%s|url|&position=%s|url|\">%s</A>", hgTracksName(), cartSessionVarName(), cartSessionId(cart), chromPtr->name, chromPtr->name); cgiTableFieldEnd(); cgiTableFieldStartAlignRight(); printLongWithCommas(stdout, size); puts(" "); cgiTableFieldEnd(); if (hasAlias) { cgiSimpleTableFieldStart(); if (aliasNames) htmlPrintf("%s", aliasNames); @@ -10190,54 +10181,50 @@ void chromInfoRowsChrom() /* Make table rows of chromosomal chromInfo name & size, sorted by name. */ { chromInfoRowsChromExt("default"); } static int chromInfoCmpSize(const void *va, const void *vb) /* Compare to sort based on chrom size */ { const struct chromInfo *a = *((struct chromInfo **)va); const struct chromInfo *b = *((struct chromInfo **)vb); return b->size - a->size; } -void chromInfoRowsNonChromTrackHub(int limit) +void chromInfoRowsNonChromTrackHub(boolean hasAlias, int limit) /* Make table rows of non-chromosomal chromInfo name & size */ /* leaks chromInfo list */ { struct chromInfo *chromInfo = trackHubAllChromInfo(database); slSort(&chromInfo, chromInfoCmpSize); int seqCount = slCount(chromInfo); -struct hash *aliasHash = chromAliasMakeReverseLookupTable(database); -boolean hasAlias = FALSE; -if (aliasHash) - hasAlias = TRUE; long long total = 0; char msg1[512], msg2[512]; boolean truncating; int lineCount = 0; truncating = (limit > 0) && (seqCount > limit); for( ;lineCount < seqCount && (chromInfo != NULL); ++lineCount, chromInfo = chromInfo->next) { unsigned size = chromInfo->size; if (lineCount < limit) { - char *aliasNames = chrAliases(aliasHash, chromInfo->chrom); + char *aliasNames = chrAliases(chromAliasFindAliases(chromInfo->chrom), chromInfo->chrom); cgiSimpleTableRowStart(); cgiSimpleTableFieldStart(); htmlPrintf("<A HREF=\"%s|none|?%s|url|=%s|url|&position=%s|url|\">%s</A>", hgTracksName(), cartSessionVarName(), cartSessionId(cart), chromInfo->chrom,chromInfo->chrom); cgiTableFieldEnd(); cgiTableFieldStartAlignRight(); printLongWithCommas(stdout, size); puts(" "); cgiTableFieldEnd(); if (hasAlias) { cgiSimpleTableFieldStart(); if (aliasNames) htmlPrintf("%s", aliasNames); @@ -10276,42 +10263,40 @@ cgiSimpleTableFieldStart(); puts(msg2); cgiTableFieldEnd(); cgiTableRowEnd(); cgiSimpleTableRowStart(); cgiSimpleTableFieldStart(); printLongWithCommas(stdout, scafCount); cgiTableFieldEnd(); cgiSimpleTableFieldStart(); printLongWithCommas(stdout, total); cgiTableFieldEnd(); cgiTableRowEnd(); } } -void chromInfoRowsNonChrom(int limit) +void chromInfoRowsNonChrom(boolean hasAlias, int limit) /* Make table rows of non-chromosomal chromInfo name & size, sorted by size. */ { if (trackHubDatabase(database)) { - chromInfoRowsNonChromTrackHub(limit); + chromInfoRowsNonChromTrackHub(hasAlias, limit); return; } struct sqlConnection *conn = hAllocConn(database); -boolean hasAlias = hTableExists(database, "chromAlias"); -struct hash *aliasHash = chromAliasMakeReverseLookupTable(database); /* key is database sequence name, value is an alias name, can be multiple * entries for the same sequence name. NULL if no chromAlias available */ struct sqlResult *sr = NULL; char **row = NULL; long long total = 0; char query[512]; char msg1[512], msg2[512]; int seqCount = 0; boolean truncating; seqCount = sqlQuickNum(conn, NOSQLINJ "select count(*) from chromInfo"); truncating = (limit > 0) && (seqCount > limit); if (!truncating) @@ -10321,31 +10306,31 @@ else { sqlSafef(query, sizeof(query), "select chrom,size from chromInfo order by size desc limit %d", limit); sr = sqlGetResult(conn, query); } while ((row = sqlNextRow(sr)) != NULL) { unsigned size = sqlUnsigned(row[1]); cgiSimpleTableRowStart(); cgiSimpleTableFieldStart(); htmlPrintf("<A HREF=\"%s|none|?%s|url|=%s|url|&position=%s|url|\">%s</A>", hgTracksName(), cartSessionVarName(), cartSessionId(cart), row[0], row[0]); - char *aliasNames = chrAliases(aliasHash, row[0]); + char *aliasNames = chrAliases(chromAliasFindAliases(row[0]), row[0]); cgiTableFieldEnd(); cgiTableFieldStartAlignRight(); printLongWithCommas(stdout, size); puts(" "); cgiTableFieldEnd(); if (hasAlias) { cgiSimpleTableFieldStart(); if (aliasNames) htmlPrintf("%s", aliasNames); else htmlPrintf(" "); cgiTableFieldEnd(); } cgiTableRowEnd(); @@ -10504,36 +10489,36 @@ cgiSimpleTableFieldStart(); puts("alias sequence names "); cgiTableFieldEnd(); } else if (hasAlias) { cgiSimpleTableFieldStart(); puts("alias sequence names "); cgiTableFieldEnd(); } cgiTableRowEnd(); if (sameString(database,"hg38")) chromInfoRowsChromExt("withAltRandom"); else if (trackHubDatabase(database)) - chromInfoRowsNonChrom(1000); + chromInfoRowsNonChrom(hasAlias, 1000); else if ((startsWith("chr", defaultChrom) || startsWith("Group", defaultChrom)) && hChromCount(database) < 100) chromInfoRowsChrom(); else - chromInfoRowsNonChrom(1000); + chromInfoRowsNonChrom(hasAlias, 1000); chromSizesDownloadRow(hasAlias, aliasFile, chromSizesFile); hTableEnd(); cgiDown(0.9); hgPositionsHelpHtml(organism, database); puts("</FORM>"); dyStringFree(&title); webEndSectionTables(); } /* void chromInfoPage() */ void resetVars() /* Reset vars except for position and database. */ { static char *except[] = {"db", "position", NULL}; @@ -10745,31 +10730,35 @@ char *debugTmp = NULL; /* Uncomment this to see parameters for debugging. */ /* struct dyString *state = NULL; */ /* Initialize layout and database. */ if (measureTiming) measureTime("Get cart of %d for user:%s session:%s", theCart->hash->elCount, theCart->userId, theCart->sessionId); /* #if 1 this to see parameters for debugging. */ /* Be careful though, it breaks if custom track * is more than 4k */ #if 0 printf("State: %s\n", cgiUrlString()->string); #endif getDbAndGenome(cart, &database, &organism, oldVars); +if (measureTiming) + measureTime("before chromAliasSetup"); chromAliasSetup(database); +if (measureTiming) + measureTime("after chromAliasSetup"); genomeIsRna = !isHubTrack(database) && hgPdbOk(database); initGenbankTableNames(database); protDbName = hPdbFromGdb(database); debugTmp = cartUsualString(cart, "hgDebug", "off"); if(sameString(debugTmp, "on")) hgDebug = TRUE; else hgDebug = FALSE; int timeout = cartUsualInt(cart, "udcTimeout", 300); if (udcCacheTimeout() < timeout) udcSetCacheTimeout(timeout);