diff --git a/src/utils/Contexts/ContextBase.cpp b/src/utils/Contexts/ContextBase.cpp
index 1e426ad0367093be5d6c4798f58f53bf60bc3216..2a2afecec8e62ceecaec010ed607993e67fce060 100644
--- a/src/utils/Contexts/ContextBase.cpp
+++ b/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.
diff --git a/src/utils/Contexts/ContextBase.h b/src/utils/Contexts/ContextBase.h
index 1c6cecbdbe66ab8dafcb11875bf0a9835b2ba331..4c81e6f6ff53deba5b8368082e69fd195c52c0e6 100644
--- a/src/utils/Contexts/ContextBase.h
+++ b/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);
};
diff --git a/src/utils/Contexts/ContextMerge.cpp b/src/utils/Contexts/ContextMerge.cpp
index b6391a3ca91635cb16e247b23584f00163ddc99a..3da0d5d573bdebbf8485355f76984b57f4c596fe 100644
--- a/src/utils/Contexts/ContextMerge.cpp
+++ b/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;
}
diff --git a/src/utils/KeyListOps/KeyListOps.cpp b/src/utils/KeyListOps/KeyListOps.cpp
index 531654896363d82a5909f62edf0d5928f03e8b5b..f468d9f0207c119714b965c3961476ad8747f593 100644
--- a/src/utils/KeyListOps/KeyListOps.cpp
+++ b/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;
diff --git a/src/utils/KeyListOps/KeyListOps.h b/src/utils/KeyListOps/KeyListOps.h
index 8262677cd133fe4122be1481c7bb1916e4034e85..ea7ea50877fe836f0fc6c7cf7c84ab1fbbf2cd5d 100644
--- a/src/utils/KeyListOps/KeyListOps.h
+++ b/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);
};
diff --git a/test/jaccard/test-jaccard.sh b/test/jaccard/test-jaccard.sh
index b8d626bd4b50e262dd541ddfc5c90060d5d96296..6aea03c6d2c8f276789cfd43d342200f254e65da 100644
--- a/test/jaccard/test-jaccard.sh
+++ b/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
diff --git a/test/map/test-map.sh b/test/map/test-map.sh
index 5db340f9a47ae05e6bc5edf2b1bba0a99b47aa5d..1d94bd49b992e9036716ff56cc10a796c3fcb2f4 100644
--- a/test/map/test-map.sh
+++ b/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
diff --git a/test/merge/bamCol4Mean.txt b/test/merge/bamCol4Mean.txt
index c630f665cff622648b24de63618e3481f0e8620f..779cb508e0c6405ffe930259f39e8687219988af 100644
--- a/test/merge/bamCol4Mean.txt
+++ b/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
diff --git a/test/merge/bamCol5Mean.txt b/test/merge/bamCol5Mean.txt
index 056a79f175ba30529598f5c752aad0af20b71198..4a82c3073b7ebb076cd42fb09e91f31ad1962079 100644
--- a/test/merge/bamCol5Mean.txt
+++ b/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
diff --git a/test/merge/bamCol8Mean.txt b/test/merge/bamCol8Mean.txt
index 12c62f257a99f92324c501e03c1a3b0e12f85f24..74e39819b7cee9cc70afe9e59848b780d3687430 100644
--- a/test/merge/bamCol8Mean.txt
+++ b/test/merge/bamCol8Mean.txt
@@ -1,18 +1,18 @@
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
diff --git a/test/merge/bamCol9Mean.txt b/test/merge/bamCol9Mean.txt
index 214bbe0aa61fd0aefad93a7df3202e7ac541621c..90cbb567e6d74c622c55272368616c5a1dad3833 100644
--- a/test/merge/bamCol9Mean.txt
+++ b/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
diff --git a/test/merge/precisionTest2.bed b/test/merge/precisionTest2.bed
new file mode 100644
index 0000000000000000000000000000000000000000..75bd7d70698cb307f2a4ed30a4d28649f61dba28
--- /dev/null
+++ b/test/merge/precisionTest2.bed
@@ -0,0 +1,5 @@
+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
diff --git a/test/merge/test-merge.sh b/test/merge/test-merge.sh
index 6488991a0448ca4a6ae9f7520ed097540ec3f119..86dff76062ee72a5cf27cd4ee64655ecaaf6aea9 100644
--- a/test/merge/test-merge.sh
+++ b/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
+