コード例 #1
0
ファイル: NewChromsweep.cpp プロジェクト: Yixf-Self/bedtools2
bool NewChromSweep::chromChange(int dbIdx, RecordKeyVector &retList, bool wantScan)
{
	const Record *dbRec = _currDbRecs[dbIdx];

	if (_currQueryRec != NULL && _currQueryChromName != _prevQueryChromName) {
		_context->testNameConventions(_currQueryRec);
		testChromOrder(_currQueryRec);
	}

	if (dbRec != NULL) {
		_context->testNameConventions(dbRec);
		testChromOrder(dbRec);
	}

	// If the query rec and db rec are on the same chrom, stop.
	if (dbRec != NULL && _currQueryRec != NULL && _currQueryRec->sameChrom(dbRec)) return false;


	if (dbRec == NULL || _currQueryRec == NULL) return false;

	if (queryChromAfterDbRec(dbRec)) {
		// the query is ahead of the database. fast-forward the database to catch-up.
		QuickString oldDbChrom(dbRec->getChrName());
		while (dbRec != NULL &&
				queryChromAfterDbRec(dbRec)) {
				_dbFRMs[dbIdx]->deleteRecord(dbRec);
			if (!nextRecord(false, dbIdx)) break;
			dbRec =  _currDbRecs[dbIdx];
			const QuickString &newDbChrom = dbRec->getChrName();
			if (newDbChrom != oldDbChrom) {
				testChromOrder(dbRec);
				oldDbChrom = newDbChrom;
			}
		}
		clearCache(dbIdx);
        return false;
    } else {
        // the database is ahead of the query.
        // scan the cache for remaining hits on the query's current chrom.
    	if (wantScan) scanCache(dbIdx, retList);
        return true;
    }
}
コード例 #2
0
ファイル: CloseSweep.cpp プロジェクト: nkindlon/bedtools2
bool CloseSweep::chromChange(int dbIdx, RecordKeyVector &retList, bool wantScan)
{
    Record *dbRec = _currDbRecs[dbIdx];

    bool haveQuery = _currQueryRec != NULL;
    bool haveDB = dbRec != NULL;

    if (haveQuery && _currQueryChromName != _prevQueryChromName) {
        _context->testNameConventions(_currQueryRec);
        testChromOrder(_currQueryRec);
    }

    if (haveDB) {
        _context->testNameConventions(dbRec);
        testChromOrder(dbRec);
    }

    // the files are on the same chrom
    if (haveQuery && (!haveDB || _currQueryRec->sameChrom(dbRec))) {

        //if this is the first time the query's chrom is ahead of the chrom that was in this cache,
        //then we have to clear the cache.
        if (!_caches[dbIdx].empty() && queryChromAfterDbRec(_caches[dbIdx].begin()->value())) {
            clearCache(dbIdx);
            clearClosestEndPos(dbIdx);
        }
        return false;
    }

    if (!haveQuery || !haveDB) return false;

    if (!_caches[dbIdx].empty() && (_caches[dbIdx].begin()->value()->sameChrom(_currQueryRec))) {
        //the newest DB record's chrom is ahead of the query, but the cache still
        //has old records on that query's chrom
        scanCache(dbIdx, retList);
        finalizeSelections(dbIdx, retList);
        return true;
    }


    // the query is ahead of the database. fast-forward the database to catch-up.
    if (queryChromAfterDbRec(dbRec)) {
        string oldDbChrom(dbRec->getChrName());

        while (dbRec != NULL &&
                queryChromAfterDbRec(dbRec)) {
            _dbFRMs[dbIdx]->deleteRecord(dbRec);
            if (!nextRecord(false, dbIdx)) break;
            dbRec =  _currDbRecs[dbIdx];
            const string &newDbChrom = dbRec->getChrName();
            if (newDbChrom != oldDbChrom) {
                testChromOrder(dbRec);
                oldDbChrom = newDbChrom;
            }
        }
        clearCache(dbIdx);
        clearClosestEndPos(dbIdx);
        return false;
    }
    // the database is ahead of the query.
    else {
        // 1. scan the cache for remaining hits on the query's current chrom.
        if (wantScan) scanCache(dbIdx, retList);

        return true;
    }

    //control can't reach here, but compiler still wants a return statement.
    return true;
}