Merge branch 'master' of https://github.com/arq5x/bedtools2

src/utils/Contexts/ContextBase.cpp

@@ -56,7 +56,8 @@ ContextBase::ContextBase()
   _keyListOps(NULL),
   _desiredStrand(FileRecordMergeMgr::ANY_STRAND),
   _maxDistance(0),
-  _useMergedIntervals(false)
+  _useMergedIntervals(false),
+  _reportPrecision(-1)
 
 {
 	_programNames["intersect"] = INTERSECT;
@@ -127,10 +128,6 @@ bool ContextBase::parseCmdArgs(int argc, char **argv, int skipFirstArgs) {
 	_argc = argc;
 	_argv = argv;
 	_skipFirstArgs = skipFirstArgs;
-	if (_argc < 2) {
-		setShowHelp(true);
-		return false;
-	}
 
 	setProgram(_programNames[argv[0]]);
 
@@ -171,6 +168,9 @@ bool ContextBase::parseCmdArgs(int argc, char **argv, int skipFirstArgs) {
         else if (strcmp(_argv[_i], "-iobuf") == 0) {
 			if (!handle_iobuf()) return false;
         }
+        else if (strcmp(_argv[_i], "-prec") == 0) {
+			if (!handle_prec()) return false;
+        }
         else if (strcmp(_argv[_i], "-header") == 0) {
 			if (!handle_header()) return false;
         }
@@ -213,14 +213,18 @@ bool ContextBase::isValidState()
 	}
 	if (hasColumnOpsMethods()) {
 
-		//TBD: Adjust column ops for multiple databases.
-		//For now, use last file.
-//		FileRecordMgr *dbFile = getFile(hasIntersectMethods() ? _databaseFileIdx : 0);
+		// 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;
 		}
+		//if user specified a precision, pass it to
+		//keyList ops
+		if (_reportPrecision != -1) {
+			_keyListOps->setPrecision(_reportPrecision);
+		}
 	}
 	return true;
 }
@@ -460,10 +464,33 @@ bool ContextBase::handle_o()
         markUsed(_i - _skipFirstArgs);
         _i++;
         markUsed(_i - _skipFirstArgs);
+        return true;
     }
-    return true;
+    return false;
 }
 
+bool ContextBase::handle_prec()
+{
+	if (!hasColumnOpsMethods()) {
+		return false;
+	}
+    if ((_i+1) < _argc) {
+    	int prec = atoi(_argv[_i + 1]);
+    	if (prec < 1) {
+    		_errorMsg += "\n***** ERROR: -prec must be followed by a positive integer. Exiting. *****";
+    		return false;
+    	}
+    	 _reportPrecision = prec;
+        markUsed(_i - _skipFirstArgs);
+        _i++;
+        markUsed(_i - _skipFirstArgs);
+        return true;
+    }
+	_errorMsg += "\n***** ERROR: -prec must be followed by a positive integer. Exiting. *****";
+    return false;
+}
+
+
 
 // for col ops, -null is a NULL value assigned
 // when no overlaps are detected.

src/utils/Contexts/ContextBase.h

@@ -143,6 +143,7 @@ public:
     virtual bool hasColumnOpsMethods() const { return _hasColumnOpsMethods; }
     const QuickString &getColumnOpsVal(RecordKeyVector &keyList) const;
     //methods applicable only to column operations.
+    int getReportPrecision() const { return _reportPrecision; }
 
 protected:
 	PROGRAM_TYPE _program;
@@ -214,6 +215,8 @@ protected:
 	int _maxDistance;
 	bool _useMergedIntervals;
 
+	int _reportPrecision; //used in fields reported from numeric ops from map and merge.
+
 
 	void markUsed(int i) { _argsProcessed[i] = true; }
 	bool isUsed(int i) const { return _argsProcessed[i]; }
@@ -249,7 +252,7 @@ protected:
 	virtual bool handle_null();
 	virtual bool handle_delim();
 	virtual bool handle_sortout();
-
+	bool handle_prec();
 	bool parseIoBufSize(QuickString bufStr);
 
 };

src/utils/Contexts/ContextMerge.cpp

@@ -32,10 +32,6 @@ bool ContextMerge::parseCmdArgs(int argc, char **argv, int skipFirstArgs)
 	_argc = argc;
 	_argv = argv;
 	_skipFirstArgs = skipFirstArgs;
-	if (_argc < 2) {
-		setShowHelp(true);
-		return false;
-	}
 
 	setProgram(_programNames[argv[0]]);
 
@@ -79,12 +75,12 @@ bool ContextMerge::isValidState()
 		delete _keyListOps;
 		_keyListOps = NULL;
 	}
-	if (!ContextBase::isValidState()) {
-		return false;
+
+	//default to stdin
+	if (getNumInputFiles() == 0) {
+		addInputFile("-");
 	}
-	if (_files.size() != 1) {
-		_errorMsg = "\n***** ERROR: input file not specified. *****";
-		// Allow only one input file for now
+	if (!ContextBase::isValidState()) {
 		return false;
 	}
 

src/utils/KeyListOps/KeyListOps.cpp

@@ -7,6 +7,8 @@
 #include "KeyListOps.h"
 #include "FileRecordMgr.h"
 #include <cmath> //for isnan
+#include <sstream>
+#include <iomanip>
 
 KeyListOps::KeyListOps():
 _dbFileType(FileRecordTypeChecker::UNKNOWN_FILE_TYPE)
@@ -60,6 +62,7 @@ _dbFileType(FileRecordTypeChecker::UNKNOWN_FILE_TYPE)
 	_columns = "5";
 	// default to "sum"
 	_operations = "sum";
+	_precision = DEFAULT_PRECISION;
 
 }
 
@@ -172,7 +175,7 @@ const QuickString & KeyListOps::getOpVals(RecordKeyVector &hits)
 			if (isnan(val)) {
 				_outVals.append(_methods.getNullValue());
 			} else {
-				_outVals.append(val);
+				_outVals.append(format(val));
 			}
 			break;
 
@@ -181,7 +184,7 @@ const QuickString & KeyListOps::getOpVals(RecordKeyVector &hits)
 			if (isnan(val)) {
 				_outVals.append(_methods.getNullValue());
 			} else {
-				_outVals.append(val);
+				_outVals.append(format(val));
 			}
 			break;
 
@@ -190,7 +193,7 @@ const QuickString & KeyListOps::getOpVals(RecordKeyVector &hits)
 			if (isnan(val)) {
 				_outVals.append(_methods.getNullValue());
 			} else {
-				_outVals.append(val);
+				_outVals.append(format(val));
 			}
 			break;
 
@@ -199,7 +202,7 @@ const QuickString & KeyListOps::getOpVals(RecordKeyVector &hits)
 			if (isnan(val)) {
 				_outVals.append(_methods.getNullValue());
 			} else {
-				_outVals.append(val);
+				_outVals.append(format(val));
 			}
 			break;
 
@@ -208,7 +211,7 @@ const QuickString & KeyListOps::getOpVals(RecordKeyVector &hits)
 			if (isnan(val)) {
 				_outVals.append(_methods.getNullValue());
 			} else {
-				_outVals.append(val);
+				_outVals.append(format(val));
 			}
 			break;
 
@@ -225,7 +228,7 @@ const QuickString & KeyListOps::getOpVals(RecordKeyVector &hits)
 			if (isnan(val)) {
 				_outVals.append(_methods.getNullValue());
 			} else {
-				_outVals.append(val);
+				_outVals.append(format(val));
 			}
 			break;
 
@@ -234,7 +237,7 @@ const QuickString & KeyListOps::getOpVals(RecordKeyVector &hits)
 			if (isnan(val)) {
 				_outVals.append(_methods.getNullValue());
 			} else {
-				_outVals.append(val);
+				_outVals.append(format(val));
 			}
 			break;
 
@@ -243,7 +246,7 @@ const QuickString & KeyListOps::getOpVals(RecordKeyVector &hits)
 			if (isnan(val)) {
 				_outVals.append(_methods.getNullValue());
 			} else {
-				_outVals.append(val);
+				_outVals.append(format(val));
 			}
 			break;
 
@@ -252,7 +255,7 @@ const QuickString & KeyListOps::getOpVals(RecordKeyVector &hits)
 			if (isnan(val)) {
 				_outVals.append(_methods.getNullValue());
 			} else {
-				_outVals.append(val);
+				_outVals.append(format(val));
 			}
 			break;
 
@@ -317,6 +320,14 @@ const QuickString & KeyListOps::getOpVals(RecordKeyVector &hits)
 	return _outVals;
 }
 
+const QuickString &KeyListOps::format(double val)
+{
+   std::stringstream strmBuf;
+   strmBuf << std::setprecision (_precision) << val;
+   _formatStr = strmBuf.str();
+   return _formatStr;
+}
+
 void KeyListOpsHelp() {
 
     cerr << "\t-o\t"             << "Specify the operation that should be applied to -c." << endl;

src/utils/KeyListOps/KeyListOps.h

@@ -49,6 +49,7 @@ public:
 	bool isValidColumnOps(FileRecordMgr *dbFile);
 
 	const QuickString &getOpVals(RecordKeyVector &hits);
+	void setPrecision(int val) { _precision = val; }
 
 private:
     void init();
@@ -65,9 +66,14 @@ private:
     colOpsType _colOps;
     QuickString _outVals;
 
+    QuickString _formatStr;
+    int _precision;
+
+    static const int DEFAULT_PRECISION = 10;
     OP_TYPES getOpCode(const QuickString &operation) const;
     bool isNumericOp(OP_TYPES op) const;
     bool isNumericOp(const QuickString &op) const;
+    const QuickString &format(double val);
 
 };
 

test/jaccard/test-jaccard.sh

@@ -119,7 +119,7 @@ rm obs exp
 echo "    jaccard.t11...\c"
 echo \
 "intersection	union-intersection	jaccard	n_intersections
-120	290	0.413793	4" >exp
+70	340	0.205882	3" >exp
 $BT jaccard -a aMixedStrands.bed -b bMixedStrands.bed -s > obs
 check obs exp
 rm obs exp

test/map/test-map.sh

@@ -773,11 +773,11 @@ rm obs exp
 ############################################################
 echo "    map.t51...\c"
 echo \
-"chr1	0	100	12.9167
+"chr1	0	100	12.91666667
 chr1	100	200	0
 chr2	0	100	.
 chr2	100	200	.
-chr3	0	100	76.2222
+chr3	0	100	76.22222222
 chr3	100	200	0.25" > exp
 $BT map -a ivls.bed -b values4.bed -c 7 -o stddev > obs
 check obs exp
@@ -792,7 +792,7 @@ echo \
 chr1	100	200	.
 chr2	0	100	.
 chr2	100	200	.
-chr3	0	100	114.333
+chr3	0	100	114.3333333
 chr3	100	200	0.5" > exp
 $BT map -a ivls.bed -b values4.bed -c 7 -o sample_stddev > obs
 check obs exp
@@ -804,7 +804,7 @@ rm obs exp
 echo "    map.t53...\c"
 echo \
 "chr1	10000	12000	2.5
-chr1	15000	20000	11.4444" > exp
+chr1	15000	20000	11.44444444" > exp
 $BT map -a d.bed -b fullFields.bam -c 5 -o mean > obs
 check exp obs
 rm exp obs

test/merge/bamCol4Mean.txt

@@ -2,7 +2,7 @@ chr1	10003	10143	10024.5
 chr1	10358	10428	10358
 chr1	11780	11921	11800.5
 chr1	11996	12101	11998.5
-chr1	12136	12347	12213.2
+chr1	12136	12347	12213.25
 chr1	12400	12503	12401.5
 chr1	12635	12779	12661
 chr1	12819	12919	12819
@@ -11,8 +11,8 @@ chr1	13165	13287	13176
 chr1	13561	13731	13595
 chr1	14025	14125	14025
 chr1	14221	14340	14230.5
-chr1	14440	14715	14553.7
-chr1	14805	15172	14944.7
+chr1	14440	14715	14553.66667
+chr1	14805	15172	14944.71429
 chr1	15250	15350	15250
 chr1	15470	15603	15486.5
 chr1	15924	16065	15944.5
@@ -30,7 +30,7 @@ chr1	18264	18364	18264
 chr1	18577	18742	18610
 chr1	19658	19758	19658
 chr1	19819	19966	19842.5
-chr1	20059	20320	20143.3
+chr1	20059	20320	20143.33333
 chr1	20457	20627	20494
 chr1	20641	20741	20641
 chr1	20754	20854	20754
@@ -47,7 +47,7 @@ chr1	23130	23228	23130
 chr1	23250	23350	23250
 chr1	23557	23615	23557
 chr1	24000	24120	24010
-chr1	24248	24612	24351.7
+chr1	24248	24612	24351.66667
 chr1	24683	24850	24711
 chr1	24921	25011	24921
 chr1	25055	25291	25128.5
@@ -74,7 +74,7 @@ chr1	32519	32619	32519
 chr1	32732	32832	32732
 chr1	32926	33120	32973
 chr1	33143	33289	33189.5
-chr1	33449	33669	33502.3
+chr1	33449	33669	33502.33333
 chr1	33842	33931	33842
 chr1	33933	34044	33938.5
 chr1	34070	34162	34070
@@ -99,7 +99,7 @@ chr1	44085	44185	44085
 chr1	44304	44504	44354
 chr1	44688	44788	44688
 chr1	45372	45472	45372
-chr1	45738	45867	45750.3
+chr1	45738	45867	45750.33333
 chr1	46111	46212	46111.5
 chr1	47250	47346	47250
 chr1	47593	47693	47593

test/merge/bamCol5Mean.txt

@@ -12,7 +12,7 @@ chr1	13561	13731	2
 chr1	14025	14125	3
 chr1	14221	14340	14.5
 chr1	14440	14715	14.5
-chr1	14805	15172	12.1429
+chr1	14805	15172	12.14285714
 chr1	15250	15350	21
 chr1	15470	15603	3
 chr1	15924	16065	12
@@ -30,7 +30,7 @@ chr1	18264	18364	0
 chr1	18577	18742	1.5
 chr1	19658	19758	25
 chr1	19819	19966	26
-chr1	20059	20320	31.3333
+chr1	20059	20320	31.33333333
 chr1	20457	20627	37
 chr1	20641	20741	1
 chr1	20754	20854	1
@@ -47,8 +47,8 @@ chr1	23130	23228	3
 chr1	23250	23350	0
 chr1	23557	23615	0
 chr1	24000	24120	0.5
-chr1	24248	24612	0.833333
-chr1	24683	24850	0.666667
+chr1	24248	24612	0.8333333333
+chr1	24683	24850	0.6666666667
 chr1	24921	25011	1
 chr1	25055	25291	1
 chr1	25403	25740	1.4
@@ -56,7 +56,7 @@ chr1	25767	25867	3
 chr1	26053	26153	1
 chr1	26406	26506	1
 chr1	26680	26883	0.75
-chr1	27102	27252	0.666667
+chr1	27102	27252	0.6666666667
 chr1	27582	27785	1
 chr1	27995	28187	1
 chr1	28198	28298	13
@@ -74,7 +74,7 @@ chr1	32519	32619	1
 chr1	32732	32832	3
 chr1	32926	33120	1
 chr1	33143	33289	2
-chr1	33449	33669	1.33333
+chr1	33449	33669	1.333333333
 chr1	33842	33931	1
 chr1	33933	34044	1
 chr1	34070	34162	1
@@ -91,7 +91,7 @@ chr1	38283	38380	1
 chr1	38609	38709	1
 chr1	38980	39088	1
 chr1	39099	39199	3
-chr1	39418	39585	1.66667
+chr1	39418	39585	1.666666667
 chr1	39920	40020	1
 chr1	43646	43746	3
 chr1	43974	44074	3

test/merge/bamCol8Mean.txt

 chr1	10003	10143	10024.5
-chr1	10358	10428	1.35524e+08
+chr1	10358	10428	135524043
 chr1	11780	11921	12189
 chr1	11996	12101	12401.5
-chr1	12136	12347	12225.8
+chr1	12136	12347	12225.75
 chr1	12400	12503	11998.5
-chr1	12635	12779	12504.7
+chr1	12635	12779	12504.66667
 chr1	12819	12919	13187
 chr1	13039	13139	12681
 chr1	13165	13287	13190
 chr1	13561	13731	13595
 chr1	14025	14125	13629
 chr1	14221	14340	14607.5
-chr1	14440	14715	14683.3
-chr1	14805	15172	14904.3
+chr1	14440	14715	14683.33333
+chr1	14805	15172	14904.28571
 chr1	15250	15350	14837
 chr1	15470	15603	15068.5
 chr1	15924	16065	16326
@@ -31,13 +31,13 @@ chr1	18577	18742	18208
 chr1	19658	19758	20059
 chr1	19819	19966	20224
 chr1	20059	20320	20137.5
-chr1	20457	20627	20117.7
+chr1	20457	20627	20117.66667
 chr1	20641	20741	21047
 chr1	20754	20854	21177
 chr1	21047	21139	20641
 chr1	21177	21277	20754
 chr1	21449	21549	21834
-chr1	21834	22029	22086.2
+chr1	21834	22029	22086.25
 chr1	22061	22149	22512
 chr1	22242	22448	22052.6
 chr1	22512	22566	22061
@@ -47,18 +47,18 @@ chr1	23130	23228	22748
 chr1	23250	23350	22870
 chr1	23557	23615	24000
 chr1	24000	24120	23989
-chr1	24248	24612	24499.3
-chr1	24683	24850	24540.7
+chr1	24248	24612	24499.33333
+chr1	24683	24850	24540.66667
 chr1	24921	25011	24512
-chr1	25055	25291	25339.8
+chr1	25055	25291	25339.75
 chr1	25403	25740	25455.8
 chr1	25767	25867	25403
 chr1	26053	26153	25640
 chr1	26406	26506	26791
-chr1	26680	26883	26945.2
-chr1	27102	27252	26710.3
+chr1	26680	26883	26945.25
+chr1	27102	27252	26710.33333
 chr1	27582	27785	28041.5
-chr1	27995	28187	27905.3
+chr1	27995	28187	27905.33333
 chr1	28198	28298	28577
 chr1	28439	28545	28031
 chr1	28577	28674	28198
@@ -74,7 +74,7 @@ chr1	32519	32619	32926
 chr1	32732	32832	33143
 chr1	32926	33120	32984
 chr1	33143	33289	33150.5
-chr1	33449	33669	33396.3
+chr1	33449	33669	33396.33333
 chr1	33842	33931	34268
 chr1	33933	34044	33920
 chr1	34070	34162	34511
@@ -91,7 +91,7 @@ chr1	38283	38380	37904
 chr1	38609	38709	38980
 chr1	38980	39088	39013.5
 chr1	39099	39199	39488
-chr1	39418	39585	39335.7
+chr1	39418	39585	39335.66667
 chr1	39920	40020	39528
 chr1	43646	43746	44085
 chr1	43974	44074	44404
@@ -105,7 +105,7 @@ chr1	47250	47346	47593
 chr1	47593	47693	47250
 chr1	47820	47920	48088
 chr1	48088	48193	48149
-chr1	48445	48677	48630.7
+chr1	48445	48677	48630.66667
 chr1	48681	48781	49092
 chr1	48832	48932	48445
 chr1	48967	49067	48577

test/merge/bamCol9Mean.txt

@@ -4,7 +4,7 @@ chr1	11780	11921	488.5
 chr1	11996	12101	503
 chr1	12136	12347	1
 chr1	12400	12503	-503
-chr1	12635	12779	-174.333
+chr1	12635	12779	-174.3333333
 chr1	12819	12919	468
 chr1	13039	13139	-458
 chr1	13165	13287	14
@@ -12,7 +12,7 @@ chr1	13561	13731	0
 chr1	14025	14125	-496
 chr1	14221	14340	474
 chr1	14440	14715	164
-chr1	14805	15172	-54.7143
+chr1	14805	15172	-54.71428571
 chr1	15250	15350	-513
 chr1	15470	15603	-518
 chr1	15924	16065	481.5
@@ -30,8 +30,8 @@ chr1	18264	18364	478
 chr1	18577	18742	-501.5
 chr1	19658	19758	501
 chr1	19819	19966	477.5
-chr1	20059	20320	-6.83333
-chr1	20457	20627	-471.667
+chr1	20059	20320	-6.833333333
+chr1	20457	20627	-471.6666667
 chr1	20641	20741	498
 chr1	20754	20854	523
 chr1	21047	21139	-498
@@ -47,8 +47,8 @@ chr1	23130	23228	-480
 chr1	23250	23350	-480
 chr1	23557	23615	503
 chr1	24000	24120	-1
-chr1	24248	24612	173.167
-chr1	24683	24850	-191.333
+chr1	24248	24612	173.1666667
+chr1	24683	24850	-191.3333333
 chr1	24921	25011	-499
 chr1	25055	25291	261.25
 chr1	25403	25740	-107
@@ -56,9 +56,9 @@ chr1	25767	25867	-464
 chr1	26053	26153	-513
 chr1	26406	26506	477
 chr1	26680	26883	266.75
-chr1	27102	27252	-514.667
+chr1	27102	27252	-514.6666667
 chr1	27582	27785	503.75
-chr1	27995	28187	-166.333
+chr1	27995	28187	-166.3333333
 chr1	28198	28298	476
 chr1	28439	28545	-508.5
 chr1	28577	28674	-476
@@ -74,7 +74,7 @@ chr1	32519	32619	507
 chr1	32732	32832	511
 chr1	32926	33120	3
 chr1	33143	33289	-39
-chr1	33449	33669	-135.333
+chr1	33449	33669	-135.3333333
 chr1	33842	33931	526
 chr1	33933	34044	-16.5
 chr1	34070	34162	536

test/merge/precisionTest2.bed

+chr1	5333587	5344172	line1	0	-	5334680	5344172
+chr1	5481008	5484749	line2	0	-	5481796	5484749
+chr1	5481008	5484749	line3	0	-	5481796	5484749
+chr1	5481008	5484749	line4	0	-	5481796	5484749
+chr1	6763278	6766882	line5	0	-	7766544	6766882

test/merge/test-merge.sh

@@ -542,3 +542,43 @@ echo \
 $BT merge -i vcfSVtest.vcf > obs
 check exp obs
 rm obs exp
+
+
+###########################################################
+#  Test that stdin is used by default
+###########################################################
+echo "    merge.t45...\c"
+echo \
+"chr1	10	20
+chr1	30	100" >exp
+cat a.bed | $BT merge > obs
+check exp obs
+rm obs exp
+
+
+###########################################################
+#  Test that precision default is high enough for 
+#  formatting not to give scientific notation
+###########################################################
+echo "    merge.t46...\c"
+echo \
+"chr1	5333587	5344172	5344172
+chr1	5481008	5484749	16454247
+chr1	6763278	6766882	6766882" > exp
+$BT merge -i precisionTest2.bed -c 8 -o sum> obs
+check exp obs
+rm obs exp
+
+
+###########################################################
+#  Test that user can specify a lower precision
+###########################################################
+echo "    merge.t47...\c"
+echo \
+"chr1	5333587	5344172	5.3442e+06
+chr1	5481008	5484749	1.6454e+07
+chr1	6763278	6766882	6.7669e+06" > exp
+$BT merge -i precisionTest2.bed -c 8 -o sum -prec 5 > obs
+check exp obs
+rm obs exp
+