boolean chromSeqFileExists(char *db, char *chrom)
/* Check whether chromInfo exists for a database, find the path of the */
/* sequence file for this chromosome and check if the file exists. */
{
char seqFile[512];
struct sqlConnection *conn = sqlConnect(db);
char query[256];
char *res = NULL;
boolean exists = FALSE;
/* if the database exists, check for the chromInfo file */
if (sqlDatabaseExists(db))
{
sqlSafef(query, sizeof(query), "select fileName from chromInfo where chrom = '%s'", chrom);
res = sqlQuickQuery(conn, query, seqFile, 512);
sqlDisconnect(&conn);
}
/* if there is not table or no information in the table or if the table */
/* exists but the file can not be opened return false, otherwise sequence */
/* file exists and return true */
if (res != NULL)
{
char *seqFile2 = hReplaceGbdb(seqFile);
exists = udcExists(seqFile2);
freeMem(seqFile2);
}
return exists;
}
boolean isSearchTracksSupported(char *database, struct cart *cart)
// Return TRUE if searchTracks is supported for this database and javascript is supported too
{
char trixFile[HDB_MAX_PATH_STRING];
getSearchTrixFile(database, trixFile, sizeof(trixFile));
char *trixPath = hReplaceGbdb(trixFile);
bool ret = udcExists(trixPath);
freez(&trixPath);
return ret;
}
void getSearchTrixFile(char *database, char *buf, int len)
// Fill-in the name of the track search trix file
{
char *trixPath = cfgOptionDefault("browser.trixPath", "/gbdb/$db/trackDb.ix");
struct subText *subList = subTextNew("$db", database);
subTextStatic(subList, trixPath, buf, len);
char *subBuf = hReplaceGbdb(buf);
safecpy(buf, len, subBuf);
freez(&subBuf);
}
static void checkWibFile(struct annoStreamWig *self, char *wibFile)
/* If self doesn't have a .wib file name and handle open, or if the new wibFile is
* not the same as the old one, update self to use new wibFile. */
{
char *realWibFile = hReplaceGbdb(wibFile);
if (self->wibFile == NULL || !sameString(self->wibFile, realWibFile))
{
udcFileClose(&self->wibFH);
freeMem(self->wibFile);
self->wibFile = cloneString(realWibFile);
self->wibFH = udcFileMayOpen(self->wibFile, NULL);
if (self->wibFH == NULL)
errAbort("annoStreamWig: udc can't open wibFile '%s'", self->wibFile);
}
freeMem(realWibFile);
}
//#*** duplicated from hgVarAnnoGrator... libify me!
struct annoAssembly *getAnnoAssembly(char *db)
/* Make annoAssembly for db. */
{
static struct annoAssembly *aa = NULL;
if (aa == NULL)
{
char *nibOrTwoBitDir = hDbDbNibPath(db);
if (nibOrTwoBitDir == NULL)
errAbort("Can't find .2bit for db '%s'", db);
char twoBitPath[HDB_MAX_PATH_STRING];
safef(twoBitPath, sizeof(twoBitPath), "%s/%s.2bit", nibOrTwoBitDir, db);
char *path = hReplaceGbdb(twoBitPath);
aa = annoAssemblyNew(db, path);
freeMem(path);
}
return aa;
}
static struct aHubMatch *searchPublicHubs(struct dbDb *dbDbList, char *term)
/* Search for term in public hub trix files -- return a list of matches to assembly hubs
* (i.e. hubs that host an assembly with 2bit etc as opposed to only providing tracks.) */
{
struct aHubMatch *aHubMatchList = NULL;
char *trixFile = cfgOptionEnvDefault("HUBSEARCHTRIXFILE", "hubSearchTrixFile",
hReplaceGbdb("/gbdb/hubs/public.ix"));
if (fileExists(trixFile))
{
struct trix *trix = trixOpen(trixFile);
char termCopy[strlen(term)+1];
safecpy(termCopy, sizeof(termCopy), term);
tolowers(termCopy);
char *words[512];
int wordCount = chopByWhite(termCopy, words, ArraySize(words));
struct trixSearchResult *tsrList = trixSearch(trix, wordCount, words, tsmFirstFive);
aHubMatchList = filterTrixSearchMatches(dbDbList, tsrList);
trixClose(&trix);
}
return aHubMatchList;
}
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);
}
