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 doVcfTabixDetails(struct trackDb *tdb, char *item)
/* Show details of an alignment from a VCF file compressed and indexed by tabix. */
{
knetUdcInstall();
if (udcCacheTimeout() < 300)
udcSetCacheTimeout(300);
struct sqlConnection *conn = hAllocConnTrack(database, tdb);
char *fileOrUrl = bbiNameFromSettingOrTableChrom(tdb, conn, tdb->table, seqName);
hFreeConn(&conn);
doVcfDetailsCore(tdb, fileOrUrl, TRUE);
}
void vcfTabixMethods(struct track *track)
/* Methods for VCF + tabix files. */
{
knetUdcInstall();
pgSnpMethods(track);
track->mapItem = indelTweakMapItem;
// Disinherit next/prev flag and methods since we don't support next/prev:
track->nextExonButtonable = FALSE;
track->nextPrevExon = NULL;
track->nextPrevItem = NULL;
track->loadItems = vcfTabixLoadItems;
track->canPack = TRUE;
}
int main(int argc, char *argv[])
/* Process command line. */
{
optionInit(&argc, argv, options);
if (argc != 2 && !optionExists("settings"))
usage();
struct trackHubCheckOptions *checkOptions = NULL;
AllocVar(checkOptions);
checkOptions->specHost = (optionExists("test") ? "genome-test.soe.ucsc.edu" : "genome.ucsc.edu");
checkOptions->specHost = optionVal("specHost", checkOptions->specHost);
checkOptions->printMeta = optionExists("printMeta");
checkOptions->checkFiles = !optionExists("noTracks");
checkOptions->checkSettings = optionExists("checkSettings");
struct trackHubSettingSpec *setting = NULL;
AllocVar(setting);
setting->level = optionVal("level", "all");
if (trackHubSettingLevel(setting) < 0)
{
fprintf(stderr, "ERROR: Unrecognized support level %s\n\n", setting->level);
usage();
}
checkOptions->level = setting->level;
char *version = NULL;
if (optionExists("version"))
version = optionVal("version", NULL);
checkOptions->version = version;
char *extraFile = optionVal("extra", NULL);
if (extraFile != NULL)
addExtras(extraFile, checkOptions);
cacheTime = optionInt("cacheTime", cacheTime);
udcSetCacheTimeout(cacheTime);
// UDC cache dir: first check for hg.conf setting, then override with command line option if given.
setUdcCacheDir();
udcSetDefaultDir(optionVal("udcDir", udcDefaultDir()));
knetUdcInstall(); // make the htslib library use udc
if (optionExists("settings"))
{
showSettings(checkOptions);
return 0;
}
struct dyString *errors = newDyString(1024);
if (trackHubCheck(argv[1], checkOptions, errors))
{
// uniquify and count errors
struct slName *errs = slNameListFromString(errors->string, '\n');
slUniqify(&errs, slNameCmp, slNameFree);
int errCount = slCount(errs);
printf("Found %d problem%s:\n", errCount, errCount == 1 ? "" : "s");
printf("%s\n", slNameListToString(errs, '\n'));
return 1;
}
return 0;
}
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);
}
}
}
int main(int argc, char *argv[])
{
optionInit(&argc, argv, optionSpecs);
if (argc < 2 || argc > 3)
usage();
pushCarefulMemHandler(LIMIT_2or6GB);
char *db = argv[1];
char *test = NULL;
boolean doAllTests = (argc == 2);
if (!doAllTests)
{
if (sameString(argv[2], pgSnpDbToTabOut) ||
sameString(argv[2], pgSnpKgDbToTabOutShort) ||
sameString(argv[2], pgSnpKgDbToTabOutLong) ||
sameString(argv[2], pgSnpKgDbToGpFx) ||
sameString(argv[2], snpConsDbToTabOutShort) ||
sameString(argv[2], snpConsDbToTabOutLong) ||
sameString(argv[2], vcfEx1) ||
sameString(argv[2], vcfEx2) ||
sameString(argv[2], bigBedToTabOut) ||
sameString(argv[2], snpBigWigToTabOut) ||
sameString(argv[2], vepOut) ||
sameString(argv[2], gpFx))
test = cloneString(argv[2]);
else
{
warn("Unrecognized test name '%s'\n", argv[2]);
usage();
}
}
if (udcCacheTimeout() < 300)
udcSetCacheTimeout(300);
udcSetDefaultDir("./udcCache");
struct annoAssembly *assembly = getAnnoAssembly(db);
// First test: some rows of a pgSnp table
struct streamerInfo pgSnpInfo = { NULL, assembly, db, "pgNA12878", arWords, pgSnpAsObj() };
if (doAllTests || sameString(test, pgSnpDbToTabOut))
dbToTabOut(&pgSnpInfo, "stdout", "chr1", 705881, 752721, FALSE);
// Second test: some rows of a pgSnp table integrated with knownGene
struct streamerInfo kgInfo = { NULL, assembly, db, "knownGene", arWords,
asParseFile("../knownGene.as") };
pgSnpInfo.next = &kgInfo;
if (doAllTests || sameString(test, pgSnpKgDbToTabOutShort))
dbToTabOut(&pgSnpInfo, "stdout", "chr1", 705881, 752721, FALSE);
// Third test: all rows of a pgSnp table integrated with knownGene
if (doAllTests || sameString(test, pgSnpKgDbToTabOutLong))
dbToTabOut(&pgSnpInfo, "stdout", NULL, 0, 0, FALSE);
// Fourth test: some rows of snp135 integrated with phyloP scores
if (doAllTests || sameString(test, snpConsDbToTabOutShort) ||
sameString(test, snpConsDbToTabOutLong))
{
struct streamerInfo snp135Info = { NULL, assembly, db, "snp135", arWords,
asParseFile("../snp132Ext.as") };
struct streamerInfo phyloPInfo = { NULL, assembly, db, "phyloP46wayPlacental", arWig, NULL };
snp135Info.next = &phyloPInfo;
if (sameString(test, snpConsDbToTabOutShort))
dbToTabOut(&snp135Info, "stdout", "chr1", 737224, 738475, FALSE);
else
dbToTabOut(&snp135Info, "stdout", NULL, 0, 0, FALSE);
}
// Fifth test: VCF with genotypes
if (doAllTests || sameString(test, vcfEx1))
{
#if (defined USE_TABIX && defined KNETFILE_HOOKS)
knetUdcInstall();
#endif//def USE_TABIX && KNETFILE_HOOKS
struct streamerInfo vcfEx1 = { NULL, assembly, NULL,
"http://genome.ucsc.edu/goldenPath/help/examples/vcfExample.vcf.gz",
arWords, vcfAsObj() };
dbToTabOut(&vcfEx1, "stdout", NULL, 0, 0, FALSE);
}
if (doAllTests || sameString(test, vcfEx2))
{
struct streamerInfo vcfEx2 = { NULL, assembly, NULL,
"http://genome.ucsc.edu/goldenPath/help/examples/vcfExampleTwo.vcf",
arWords, vcfAsObj() };
dbToTabOut(&vcfEx2, "stdout", NULL, 0, 0, FALSE);
}
if (doAllTests || sameString(test, pgSnpKgDbToGpFx))
{
struct streamerInfo pg2SnpInfo = { NULL, assembly, NULL,
"input/annoGrator/pgForTestingGpFx.pgSnp.tab",
arWords, pgSnpAsObj() };
pg2SnpInfo.next = &kgInfo;
dbToTabOut(&pg2SnpInfo, "stdout", NULL, 0, 0, TRUE);
/*
FIXME
// 3base insertion CDS - chr3:124,646,699-124,646,718
dbToTabOut(&pg2SnpInfo, "stdout", "chr3",124646699,124646718, TRUE);
*/
}
if (doAllTests || sameString(test, bigBedToTabOut))
{
struct streamerInfo bigBedInfo = { NULL, assembly, NULL,
"http://genome.ucsc.edu/goldenPath/help/examples/bigBedExample.bb",
arWords, NULL };
dbToTabOut(&bigBedInfo, "stdout", "chr21", 34716800, 34733700, FALSE);
}
if (doAllTests || sameString(test, snpBigWigToTabOut))
{
struct streamerInfo snp135Info = { NULL, assembly, db, "snp135", arWords,
asParseFile("../snp132Ext.as") };
struct streamerInfo bigWigInfo = { NULL, assembly, NULL,
"http://genome.ucsc.edu/goldenPath/help/examples/bigWigExample.bw",
arWig, NULL };
snp135Info.next = &bigWigInfo;
dbToTabOut(&snp135Info, "stdout", "chr21", 34716800, 34733700, FALSE);
}
if (doAllTests || sameString(test, vepOut))
{
struct streamerInfo vepSamplePgSnp = { NULL, assembly, NULL,
"input/annoGrator/vepSample.pgSnp.tab",
arWords, asParseFile("../pgSnp.as") };
struct streamerInfo kgInfo = { NULL, assembly, db, "ensGene", arWords,
asParseFile("../genePredExt.as") };
struct streamerInfo snpInfo = { NULL, assembly, db, "snp135", arWords,
asParseFile("../snp132Ext.as") };
vepSamplePgSnp.next = &kgInfo;
kgInfo.next = &snpInfo;
// Instead of dbToTabOut, we need to make a VEP config data structure and
// use it to create an annoFormatVep.
struct streamerInfo *primaryInfo = &vepSamplePgSnp;
struct annoStreamer *primary = NULL;
struct annoGrator *gratorList = NULL;
sourcesFromInfoList(primaryInfo, TRUE, &primary, &gratorList);
struct annoStreamer *gpVarSource = (struct annoStreamer *)gratorList;
struct annoStreamer *snpSource = gpVarSource->next;
struct annoFormatter *vepOut = annoFormatVepNew("stdout", FALSE, primary, "vepSamplePgSnp",
gpVarSource, "UCSC Genes ...",
snpSource, "just dbSNP 135");
struct annoGratorQuery *query = annoGratorQueryNew(assembly, primary, gratorList, vepOut);
annoGratorQuerySetRegion(query, "chr1", 876900, 886920);
annoGratorQueryExecute(query);
annoGratorQuerySetRegion(query, "chr5", 135530, 145535);
annoGratorQueryExecute(query);
annoGratorQueryFree(&query);
}
if (doAllTests || sameString(test, gpFx))
{
struct streamerInfo variants = { NULL, assembly, NULL,
"input/annoGrator/moreVariants.pgSnp.tab",
arWords, asParseFile("../pgSnp.as") };
struct streamerInfo kgInfo = { NULL, assembly, db, "knownGene", arWords,
asParseFile("../knownGene.as") };
struct streamerInfo snpInfo = { NULL, assembly, db, "snp137", arWords,
asParseFile("../snp132Ext.as") };
struct asObject *dbNsfpSeqChangeAs =
bigBedAsFromFileName("/gbdb/hg19/dbNsfp/dbNsfpSeqChange.bb");
struct streamerInfo dbNsfpSeqChange =
{ NULL, assembly, NULL, "/gbdb/hg19/dbNsfp/dbNsfpSeqChange.bb",
arWords, dbNsfpSeqChangeAs };
struct asObject *dbNsfpSiftAs = bigBedAsFromFileName("/gbdb/hg19/dbNsfp/dbNsfpSift.bb");
struct streamerInfo dbNsfpSift = { NULL, assembly, NULL, "/gbdb/hg19/dbNsfp/dbNsfpSift.bb",
arWords, dbNsfpSiftAs };
variants.next = &kgInfo;
kgInfo.next = &snpInfo;
snpInfo.next = &dbNsfpSeqChange;
dbNsfpSeqChange.next = &dbNsfpSift;
// Instead of dbToTabOut, we need to make a VEP config data structure and
// use it to create an annoFormatVep.
struct streamerInfo *primaryInfo = &variants;
struct annoStreamer *primary = NULL;
struct annoGrator *gratorList = NULL;
sourcesFromInfoList(primaryInfo, TRUE, &primary, &gratorList);
struct annoStreamer *gpVarSource = (struct annoStreamer *)gratorList;
struct annoStreamer *snpSource = gpVarSource->next;
struct annoStreamer *dbNsfpSource = snpSource->next->next;
struct annoFormatter *vepOut = annoFormatVepNew("stdout", FALSE, primary, "some more variants",
gpVarSource, "UCSC Genes of course",
snpSource, "now snp137.");
annoFormatVepAddExtraItem(vepOut, dbNsfpSource, "SIFT", "SIFT score from dbNSFP", "");
struct annoGratorQuery *query = annoGratorQueryNew(assembly, primary, gratorList, vepOut);
annoGratorQuerySetRegion(query, "chr19", 45405960, 45419476);
annoGratorQueryExecute(query);
annoGratorQueryFree(&query);
}
return 0;
}