Bug fixes and more unit tests for closest

src/utils/NewChromsweep/CloseSweep.cpp

@@ -121,6 +121,19 @@ CloseSweep::rateOvlpType CloseSweep::considerRecord(const Record *cacheRec, int
 		return IGNORE;
 	}
 
+	// If strand is specified, and either record has an unknown strand, ignore
+	if ((_context->getSameStrand() || _context->getDiffStrand()) && ((_currQueryRec->getStrandVal() == Record::UNKNOWN) || cacheRec->getStrandVal() == Record::UNKNOWN)) {
+		return IGNORE;
+	}
+	// If want same strand, and aren't sure they're the same, ignore
+	if (_context->getSameStrand() &&  (_currQueryRec->getStrandVal() != cacheRec->getStrandVal())) {
+		return IGNORE;
+	}
+	// If we want diff strand, and aren't sure they're different, ignore.
+	if (_context->getDiffStrand() && (_currQueryRec->getStrandVal() == cacheRec->getStrandVal())) {
+		return IGNORE;
+	}
+
 	// Now determine whether the hit and query intersect, and if so, what to do about it.
 	int currDist = 0;
 

src/utils/RecordOutputMgr/RecordOutputMgr.cpp

@@ -137,6 +137,7 @@ void RecordOutputMgr::printRecord(const Record *record, const QuickString & valu
 }
 
 void RecordOutputMgr::printClosest(RecordKeyVector &keyList, const vector<int> *dists) {
+	const ContextClosest *context = static_cast<const ContextClosest *>(_context);
 	bool deleteBlocks = false;
 	RecordKeyVector blockList(keyList.getKey());
 	if (keyList.getKey()->getType() == FileRecordTypeChecker::BAM_RECORD_TYPE) {
@@ -148,6 +149,7 @@ void RecordOutputMgr::printClosest(RecordKeyVector &keyList, const vector<int> *
 		for (RecordKeyVector::const_iterator_type iter = keyList.begin(); iter != keyList.end(); iter = keyList.next()) {
 			printKey(keyList.getKey());
 			tab();
+			addDbFileId((*iter)->getFileIdx());
 			(*iter)->print(_outBuf);
 			if (dists != NULL) {
 				tab();
@@ -161,7 +163,7 @@ void RecordOutputMgr::printClosest(RecordKeyVector &keyList, const vector<int> *
 		printKey(keyList.getKey());
 		tab();
 		null(true, false);
-		if ((static_cast<ContextClosest *>(_context))->reportDistance()) {
+		if (context->reportDistance()) {
 			tab();
 			_outBuf.append(-1);
 		}
@@ -172,7 +174,6 @@ void RecordOutputMgr::printClosest(RecordKeyVector &keyList, const vector<int> *
 		_currBamBlockList = NULL;
 	}
 	return;
-
 }
 
 

test/closest/mdb1.bed

-chr1	5	15
-chr1	20	60
-chr1	200	220
+chr1	5	15	d1.1	1	+
+chr1	20	60	d1.2	2	-
+chr1	200	220	d1.3	3	-
 

test/closest/mdb2.bed

-chr1	15	35
-chr1	120	170
-chr1	210	230
+chr1	15	35	db2.1	1	-
+chr1	120	170	db2.2	2	-
+chr1	210	230	db3	3	+

test/closest/mdb3.bed

-chr1	70	90
+chr1	70	90	d3.1	3	-
+

test/closest/mq1.bed

-chr1	80	100
+chr1	80	100	q1	1	+

test/closest/test-closest.sh

@@ -166,19 +166,45 @@ rm obs exp
 ###########################################################
 echo "    closest.t13...\c"
 echo \
-"chr1	80	100	chr1	20	60
-chr1	80	100	chr1	120	170
-chr1	80	100	chr1	70	90" > exp
+"chr1	80	100	q1	1	+	1	chr1	20	60	d1.2	2	-
+chr1	80	100	q1	1	+	2	chr1	120	170	db2.2	2	-
+chr1	80	100	q1	1	+	3	chr1	70	90	d3.1	3	-" > exp
 $BT closest -a mq1.bed -b mdb1.bed mdb2.bed mdb3.bed > obs
 check obs exp
 rm obs exp
 
+
+###########################################################
+# test 3 dbs with -names option
+###########################################################
+echo "    closest.t14...\c"
+echo \
+"chr1	80	100	q1	1	+	a	chr1	20	60	d1.2	2	-
+chr1	80	100	q1	1	+	b	chr1	120	170	db2.2	2	-
+chr1	80	100	q1	1	+	c	chr1	70	90	d3.1	3	-" > exp
+$BT closest -a mq1.bed -b mdb1.bed mdb2.bed mdb3.bed -names a b c > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# test 3 dbs with -filenames option
+###########################################################
+echo "    closest.t15...\c"
+echo \
+"chr1	80	100	q1	1	+	mdb1.bed	chr1	20	60	d1.2	2	-
+chr1	80	100	q1	1	+	mdb2.bed	chr1	120	170	db2.2	2	-
+chr1	80	100	q1	1	+	mdb3.bed	chr1	70	90	d3.1	3	-" > exp
+$BT closest -a mq1.bed -b mdb1.bed mdb2.bed mdb3.bed -filenames > obs
+check obs exp
+rm obs exp
+
 ###########################################################
 # test 3 dbs, -all mode
 ###########################################################
-echo "    closest.t13...\c"
+echo "    closest.t16...\c"
 echo \
-"chr1	80	100	chr1	70	90" > exp
+"chr1	80	100	q1	1	+	3	chr1	70	90	d3.1	3	-" > exp
 $BT closest -a mq1.bed -b mdb1.bed mdb2.bed mdb3.bed -mdb all > obs
 check obs exp
 rm obs exp
@@ -187,10 +213,10 @@ rm obs exp
 ###########################################################
 # test 2 dbs, tie mode = all
 ###########################################################
-echo "    closest.t14...\c"
+echo "    closest.t17...\c"
 echo \
-"chr1	80	100	chr1	20	60
-chr1	80	100	chr1	120	170" > exp
+"chr1	80	100	q1	1	+	1	chr1	20	60	d1.2	2	-
+chr1	80	100	q1	1	+	2	chr1	120	170	db2.2	2	-" > exp
 $BT closest -a mq1.bed -b mdb1.bed mdb2.bed -t all > obs
 check obs exp
 rm obs exp
@@ -198,9 +224,9 @@ rm obs exp
 ###########################################################
 # test 2 dbs, tie mode = first
 ###########################################################
-echo "    closest.t15...\c"
+echo "    closest.t18...\c"
 echo \
-"chr1	80	100	chr1	20	60" > exp
+"chr1	80	100	q1	1	+	1	chr1	20	60	d1.2	2	-" > exp
 $BT closest -a mq1.bed -b mdb1.bed mdb2.bed -mdb all -t first > obs
 check obs exp
 rm obs exp
@@ -208,10 +234,53 @@ rm obs exp
 ###########################################################
 # test 2 dbs, tie mode = last
 ###########################################################
-echo "    closest.t16...\c"
+echo "    closest.t19...\c"
 echo \
-"chr1	80	100	chr1	120	170" > exp
+"chr1	80	100	q1	1	+	2	chr1	120	170	db2.2	2	-" > exp
 $BT closest -a mq1.bed -b mdb1.bed mdb2.bed -mdb all -t last > obs
 check obs exp
 rm obs exp
 
+###########################################################
+# test same strand 
+###########################################################
+echo "    closest.t20...\c"
+echo \
+"chr1	80	100	q1	1	+	chr1	5	15	d1.1	1	+" > exp
+$BT closest -a mq1.bed -b mdb1.bed -s> obs
+check obs exp
+rm obs exp
+
+###########################################################
+# test diff strand 
+###########################################################
+echo "    closest.t21...\c"
+echo \
+"chr1	80	100	q1	1	+	chr1	20	60	d1.2	2	-" > exp
+$BT closest -a mq1.bed -b mdb1.bed -S> obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# test 2 dbs, tie mode = all, same strand
+###########################################################
+echo "    closest.t22...\c"
+echo \
+"chr1	80	100	q1	1	+	1	chr1	5	15	d1.1	1	+" > exp
+$BT closest -a mq1.bed -b mdb1.bed mdb2.bed -t all -mdb all -s > obs
+check obs exp
+rm obs exp
+
+
+###########################################################
+# test 2 dbs, tie mode = all, diff strand
+###########################################################
+echo "    closest.t23...\c"
+echo \
+"chr1	80	100	q1	1	+	1	chr1	20	60	d1.2	2	-
+chr1	80	100	q1	1	+	2	chr1	120	170	db2.2	2	-" > exp
+$BT closest -a mq1.bed -b mdb1.bed mdb2.bed -t all -mdb all -S > obs
+check obs exp
+rm obs exp
+