diff --git a/src/utils/Contexts/ContextBase.cpp b/src/utils/Contexts/ContextBase.cpp
index 051050f78d8611019c9da6f174547c0490d7e977..19f855e31cc20291e99f54da38783f42876add84 100644
--- a/src/utils/Contexts/ContextBase.cpp
+++ b/src/utils/Contexts/ContextBase.cpp
@@ -65,7 +65,6 @@ ContextBase::ContextBase()
{
_programNames["intersect"] = INTERSECT;
_programNames["sample"] = SAMPLE;
- _programNames["spacing"] = SPACING;
_programNames["map"] = MAP;
_programNames["merge"] = MERGE;
@@ -220,12 +219,12 @@ bool ContextBase::isValidState()
}
if (hasColumnOpsMethods()) {
- // TBD: Adjust column ops for multiple databases.
- // For now, use last file.
- FileRecordMgr *dbFile = getFile(getNumInputFiles()-1);
- _keyListOps->setDBfileType(dbFile->getFileType());
- if (!_keyListOps->isValidColumnOps(dbFile)) {
- return false;
+ for (int i=0; i < (int)_dbFileIdxs.size(); i++) {
+ FileRecordMgr *dbFile = getFile(_dbFileIdxs[i]);
+ _keyListOps->setDBfileType(dbFile->getFileType());
+ if (!_keyListOps->isValidColumnOps(dbFile)) {
+ return false;
+ }
}
//if user specified a precision, pass it to
//keyList ops
@@ -521,6 +520,7 @@ bool ContextBase::handle_null()
bool ContextBase::handle_delim()
{
if (!hasColumnOpsMethods()) {
+ _errorMsg = "\n***** ERROR: Can't set delimiter for tools without column operations. Exiting. *****";
return false;
}
if ((_i+1) < _argc) {
diff --git a/src/utils/NewChromsweep/CloseSweep.h b/src/utils/NewChromsweep/CloseSweep.h
index f4708684c29929690c0c76c5b9b32656645ae6eb..10ece3eb17fb5836e9e5647131a713dff5ccaa45 100644
--- a/src/utils/NewChromsweep/CloseSweep.h
+++ b/src/utils/NewChromsweep/CloseSweep.h
@@ -27,7 +27,18 @@ public:
class DistanceTupleSortAscFunctor {
public:
bool operator()(const distanceTuple & d1, const distanceTuple & d2) const {
- return ((d1._dist < d2._dist) ? true : (d1._dist == d2._dist ? (d1._isNeg && !d2._isNeg) : false)) ; }
+// return ((d1._dist < d2._dist) ? true : (d1._dist == d2._dist ? (d1._rec->lessThan(d2._rec)) : false)); }
+
+ return (d1._dist < d2._dist ? true : (d1._dist == d2._dist ? d1._rec->lessThan(d2._rec) : false));
+// if (d1._dist < d2._dist) {
+// return true;
+// } else if (d1._dist == d2._dist) {
+// if () {
+// return true;
+// }
+// }
+// return false;
+ }
};
diff --git a/src/utils/RecordOutputMgr/RecordOutputMgr.cpp b/src/utils/RecordOutputMgr/RecordOutputMgr.cpp
index a557b42c9d24e7bade27b5dda9501b14882d375b..1d58ef59702a8a2fc6dbd2ef23bf4a59f0c4d589 100644
--- a/src/utils/RecordOutputMgr/RecordOutputMgr.cpp
+++ b/src/utils/RecordOutputMgr/RecordOutputMgr.cpp
@@ -218,6 +218,8 @@ void RecordOutputMgr::printRecord(RecordKeyVector &keyList, RecordKeyVector *blo
if (printKeyAndTerminate(keyList)) {
_currBamBlockList = NULL;
+ const_cast<Record *>(keyList.getKey())->adjustZeroLength();
+
return;
}
tab();
@@ -231,6 +233,7 @@ void RecordOutputMgr::printRecord(RecordKeyVector &keyList, RecordKeyVector *blo
if (printKeyAndTerminate(keyList)) {
_currBamBlockList = NULL;
+ const_cast<Record *>(keyList.getKey())->adjustZeroLength();
return;
}
tab();
@@ -245,6 +248,7 @@ void RecordOutputMgr::printRecord(RecordKeyVector &keyList, RecordKeyVector *blo
if (printBamRecord(keyList, true) == BAM_AS_BAM) {
_currBamBlockList = NULL;
+ const_cast<Record *>(keyList.getKey())->adjustZeroLength();
return;
}
int hitIdx = 0;
@@ -261,24 +265,12 @@ void RecordOutputMgr::printRecord(RecordKeyVector &keyList, RecordKeyVector *blo
if (!printKeyAndTerminate(keyList)) {
newline();
}
- _currBamBlockList = NULL;
-
- return;
- } else if (_context->getProgram() == ContextBase::MAP) {
- printKeyAndTerminate(keyList);
- _currBamBlockList = NULL;
-
- return;
- } else if (_context->getProgram() == ContextBase::MERGE) {
+ } else if (_context->getProgram() == ContextBase::MAP || _context->getProgram() == ContextBase::MERGE) {
printKeyAndTerminate(keyList);
- _currBamBlockList = NULL;
-
- return;
- } else if (_context->getProgram() == ContextBase::SPACING) {
- keyList.getKey()->print(_outBuf);
- _currBamBlockList = NULL;
- return;
}
+ _currBamBlockList = NULL;
+ const_cast<Record *>(keyList.getKey())->adjustZeroLength();
+
}
void RecordOutputMgr::checkForHeader() {
@@ -397,7 +389,7 @@ void RecordOutputMgr::reportOverlapDetail(const Record *keyRecord, const Record
newline();
if (needsFlush()) flush();
}
- const_cast<Record *>(keyRecord)->adjustZeroLength();
+ const_cast<Record *>(hitRecord)->adjustZeroLength();
}
void RecordOutputMgr::reportOverlapSummary(RecordKeyVector &keyList)
diff --git a/test/closest/kclosest/test-kclosest.sh b/test/closest/kclosest/test-kclosest.sh
index 10cf7f525443a332a790c94b97c2cc3fa3153daa..7a99886e7a4982a2a482314c8f3d2be4f1decc05 100644
--- a/test/closest/kclosest/test-kclosest.sh
+++ b/test/closest/kclosest/test-kclosest.sh
@@ -471,21 +471,22 @@ rm obs exp
# Test multiple databases and mdb = all mode
###########################################################
+
echo " kclosest.t30...\c"
echo \
-"chr1 100 110 q2.1 20 + 1 chr1 98 108 2.2 20 + 0
-chr1 100 110 q2.1 20 + 1 chr1 105 115 2.3 20 + 0
+"chr1 100 110 q2.1 20 + 2 chr1 90 105 3.7 20 + 0
chr1 100 110 q2.1 20 + 1 chr1 95 105 2.1 20 + 0
chr1 100 110 q2.1 20 + 2 chr1 95 110 3.8 20 - 0
-chr1 100 110 q2.1 20 + 2 chr1 90 105 3.7 20 + 0
+chr1 100 110 q2.1 20 + 1 chr1 98 108 2.2 20 + 0
+chr1 100 110 q2.1 20 + 1 chr1 105 115 2.3 20 + 0
chr1 100 110 q2.1 20 + 2 chr1 110 115 3.9 20 + 1
chr1 100 110 q2.1 20 + 1 chr1 120 130 2.4 20 + 11
chr1 100 110 q2.1 20 + 2 chr1 120 130 3.10 20 - 11
chr1 100 110 q2.1 20 + 2 chr1 70 80 3.6 20 + -21
chr1 100 110 q2.1 20 + 2 chr1 75 80 3.65 20 + -21
-chr1 105 110 q2.2 20 - 1 chr1 105 115 2.3 20 + 0
-chr1 105 110 q2.2 20 - 1 chr1 98 108 2.2 20 + 0
chr1 105 110 q2.2 20 - 2 chr1 95 110 3.8 20 - 0
+chr1 105 110 q2.2 20 - 1 chr1 98 108 2.2 20 + 0
+chr1 105 110 q2.2 20 - 1 chr1 105 115 2.3 20 + 0
chr1 105 110 q2.2 20 - 2 chr1 90 105 3.7 20 + -1
chr1 105 110 q2.2 20 - 1 chr1 95 105 2.1 20 + -1
chr1 105 110 q2.2 20 - 2 chr1 110 115 3.9 20 + 1
@@ -500,7 +501,7 @@ rm obs exp
echo " kclosest.t31...\c"
echo \
-"chr1 100 110 q2.1 20 + 1 chr1 95 105 2.1 20 + 0
+"chr1 100 110 q2.1 20 + 2 chr1 90 105 3.7 20 + 0
chr1 100 110 q2.1 20 + 2 chr1 110 115 3.9 20 + 1
chr1 100 110 q2.1 20 + 1 chr1 120 130 2.4 20 + 11
chr1 100 110 q2.1 20 + 2 chr1 70 80 3.6 20 + -21
@@ -509,8 +510,8 @@ chr1 100 110 q2.1 20 + 1 chr1 140 160 2.5 20 + 31
chr1 100 110 q2.1 20 + 2 chr1 45 60 3.3 20 - -41
chr1 100 110 q2.1 20 + 2 chr1 30 40 3.2 20 + -61
chr1 100 110 q2.1 20 + 2 chr1 10 20 3.1 20 - -81
-chr1 105 110 q2.2 20 - 1 chr1 98 108 2.2 20 + 0
-chr1 105 110 q2.2 20 - 1 chr1 95 105 2.1 20 + -1
+chr1 105 110 q2.2 20 - 2 chr1 95 110 3.8 20 - 0
+chr1 105 110 q2.2 20 - 2 chr1 90 105 3.7 20 + -1
chr1 105 110 q2.2 20 - 1 chr1 120 130 2.4 20 + 11
chr1 105 110 q2.2 20 - 2 chr1 130 140 3.11 20 + 21
chr1 105 110 q2.2 20 - 2 chr1 70 80 3.6 20 + -26
@@ -526,7 +527,7 @@ rm obs exp
echo " kclosest.t32...\c"
echo \
-"chr1 100 110 q2.1 20 + 2 chr1 95 110 3.8 20 - 0
+"chr1 100 110 q2.1 20 + 1 chr1 105 115 2.3 20 + 0
chr1 100 110 q2.1 20 + 2 chr1 110 115 3.9 20 + 1
chr1 100 110 q2.1 20 + 2 chr1 120 130 3.10 20 - 11
chr1 100 110 q2.1 20 + 2 chr1 130 140 3.11 20 + 21
@@ -535,7 +536,7 @@ chr1 100 110 q2.1 20 + 1 chr1 140 150 2.7 20 + 31
chr1 100 110 q2.1 20 + 2 chr1 150 155 3.14 20 - 41
chr1 100 110 q2.1 20 + 2 chr1 170 180 3.15 20 + 61
chr1 100 110 q2.1 20 + 2 chr1 190 200 3.16 20 - 81
-chr1 105 110 q2.2 20 - 2 chr1 95 110 3.8 20 - 0
+chr1 105 110 q2.2 20 - 1 chr1 105 115 2.3 20 + 0
chr1 105 110 q2.2 20 - 2 chr1 110 115 3.9 20 + 1
chr1 105 110 q2.2 20 - 2 chr1 120 130 3.10 20 - 11
chr1 105 110 q2.2 20 - 2 chr1 130 140 3.11 20 + 21
@@ -648,3 +649,6 @@ chr1 105 110 q2.2 20 - chr1 30 40 3.2 20 + 66" > exp
$BT closest -a q2.bed -b d3.bed -k 5 -D b -t first -fd > obs
check obs exp
rm obs exp
+
+
+
diff --git a/test/intersect/test-intersect.sh b/test/intersect/test-intersect.sh
index 7af4d715f934e95c66c0c6e2c9d5e3d7ead987d8..42aa93a8e31615e0d69a7fd05a2629c123d2e0f3 100644
--- a/test/intersect/test-intersect.sh
+++ b/test/intersect/test-intersect.sh
@@ -502,8 +502,8 @@ $BT intersect -a a.bed -b b.bed -f 1.00001 2>&1 > /dev/null | cat - | head -2 |
check exp obs
rm exp obs
-##################################################################bug167_strandSweep.bed
-# Test that -s works with chromsweep
+##################################################################
+# bug167_strandSweep.bed
##################################################################
echo " intersect.t41...\c"
echo \
@@ -512,8 +512,8 @@ $BT intersect -a bug167_strandSweep.bed -b bug167_strandSweep.bed -sorted -s -wa
check exp obs
rm exp obs
-##################################################################bug167_strandSweep.bed
-# Test that -S works with chromsweep
+##################################################################
+# bug167_strandSweep.bed
##################################################################
echo " intersect.t42...\c"
echo \
@@ -525,6 +525,19 @@ rm exp obs
rm one_block.bam two_blocks.bam three_blocks.bam
+##################################################################
+# Bug 187 0 length records
+##################################################################
+echo " intersect.t43...\c"
+echo \
+"chr7 33059403 33059403 chr7 33059336 33060883 NT5C3A intron 0
+chr7 33059403 33059403 chr7 32599076 33069221 NAq intron 0" > exp
+$BT intersect -a bug187_a.bed -b bug187_b.bed -wao > obs
+check exp obs
+rm exp obs
+
+
+
cd multi_intersect
bash test-multi_intersect.sh
cd ..