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>");
}
}
