void doMiddle(struct cart *cart)
/* Write body of web page. */
{
struct trackDb *tdbList = NULL;
char *organism = NULL;
char *db = NULL;
getDbAndGenome(cart, &db, &organism, NULL);
char *chrom = cartUsualString(cart, "c", hDefaultChrom(db));
measureTiming = isNotEmpty(cartOptionalString(cart, "measureTiming"));
// QUESTION: Do We need track list ??? trackHash ??? Can't we just get one track and no children
trackHash = trackHashMakeWithComposites(db,chrom,&tdbList,FALSE);
cartWebStart(cart, db, "Search for " FILE_SEARCH_WHAT " in the %s %s Assembly",
organism, hFreezeFromDb(db));
webIncludeResourceFile("HGStyle.css");
webIncludeResourceFile("jquery-ui.css");
webIncludeResourceFile("ui.dropdownchecklist.css");
jsIncludeFile("jquery.js", NULL);
jsIncludeFile("jquery-ui.js", NULL);
jsIncludeFile("ui.dropdownchecklist.js",NULL);
jsIncludeFile("utils.js",NULL);
// This line is needed to get the multi-selects initialized
jsIncludeFile("ddcl.js",NULL);
printf("<script type='text/javascript'>$(document).ready(function() "
"{ findTracks.updateMdbHelp(0); });</script>\n");
doFileSearch(db,organism,cart,tdbList);
printf("<BR>\n");
webEnd();
}
struct slName *randomVcfIds(char *table, struct sqlConnection *conn, int count, boolean isTabix)
/* Return some semi-random IDs from a VCF file. */
{
/* Read 10000 items from vcf file, or if they ask for a big list, then 4x what they ask for. */
struct trackDb *tdb = hashFindVal(fullTableToTdbHash, table);
char *fileName = vcfFileName(tdb, conn, table, hDefaultChrom(database));
struct lineFile *lf = isTabix ? lineFileTabixMayOpen(fileName, TRUE) :
lineFileMayOpen(fileName, TRUE);
if (lf == NULL)
noWarnAbort();
int orderedCount = count * 4;
if (orderedCount < 100)
orderedCount = 100;
struct slName *idList = NULL;
char *words[4];
int i;
for (i = 0; i < orderedCount && lineFileChop(lf, words); i++)
{
// compress runs of identical ID, in case most are placeholder
if (i == 0 || !sameString(words[2], idList->name))
slAddHead(&idList, slNameNew(words[2]));
}
lineFileClose(&lf);
/* Shuffle list and trim it to count if necessary. */
shuffleList(&idList);
struct slName *sl;
for (sl = idList, i = 0; sl != NULL; sl = sl->next, i++)
{
if (i+1 >= count)
{
slNameFreeList(&(sl->next));
break;
}
}
freez(&fileName);
return idList;
}
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;
}
void showSchemaVcf(char *table, struct trackDb *tdb, boolean isTabix)
/* Show schema on vcf. */
{
struct sqlConnection *conn = hAllocConn(database);
char *fileName = vcfFileName(tdb, conn, table, hDefaultChrom(database));
struct asObject *as = vcfAsObj();
hPrintf("<B>Database:</B> %s", database);
hPrintf(" <B>Primary Table:</B> %s<br>", table);
hPrintf("<B>VCF File:</B> %s", fileName);
hPrintf("<BR>\n");
hPrintf("<B>Format description:</B> %s<BR>", as->comment);
hPrintf("See the <A HREF=\"%s\" target=_blank>Variant Call Format specification</A> for more details<BR>\n",
"http://www.1000genomes.org/wiki/analysis/vcf4.0");
/* Put up table that describes fields. */
hTableStart();
hPrintf("<TR><TH>field</TH>");
hPrintf("<TH>description</TH> ");
puts("</TR>\n");
struct asColumn *col;
int colCount = 0;
for (col = as->columnList; col != NULL; col = col->next)
{
hPrintf("<TR><TD><TT>%s</TT></TD>", col->name);
hPrintf("<TD>%s</TD></TR>", col->comment);
++colCount;
}
hTableEnd();
/* Put up another section with sample rows. */
webNewSection("Sample Rows");
hTableStart();
/* Fetch sample rows. */
struct lineFile *lf = isTabix ? lineFileTabixMayOpen(fileName, TRUE) :
lineFileMayOpen(fileName, TRUE);
if (lf == NULL)
noWarnAbort();
char *row[VCF_MAX_SCHEMA_COLS];
int i;
for (i = 0; i < 10; i++)
{
int colCount = lineFileChop(lf, row);
int colIx;
if (i == 0)
{
// Print field names as column headers, using colCount to compute genotype span
hPrintf("<TR>");
for (colIx = 0, col = as->columnList; col != NULL && colIx < colCount;
colIx++, col = col->next)
{
if (sameString("genotypes", col->name) && colCount > colIx+1)
hPrintf("<TH colspan=%d>%s</TH>", colCount - colIx, col->name);
else
hPrintf("<TH>%s</TH>", col->name);
}
hPrintf("</TR>\n");
}
hPrintf("<TR>");
for (colIx=0; colIx < colCount; ++colIx)
{
if (colCount > VCFDATALINE_NUM_COLS && colIx == colCount - 1)
hPrintf("<TD>...</TD>");
else
writeHtmlCell(row[colIx]);
}
hPrintf("</TR>\n");
}
hTableEnd();
printTrackHtml(tdb);
/* Clean up and go home. */
lineFileClose(&lf);
freeMem(fileName);
hFreeConn(&conn);
}
