Merge pull request #69 from nkindlon/master

added changes to stop CLANG compiler warnings.

src/utils/BamTools/src/api/BamAlignment.h

@@ -29,7 +29,7 @@ namespace Internal {
 //! \endcond
 
 // BamAlignment data structure
-struct API_EXPORT BamAlignment {
+class API_EXPORT BamAlignment {
 
     // constructors & destructor
     public:

src/utils/BamTools/src/api/SamHeader.h

@@ -19,8 +19,8 @@
 
 namespace BamTools {
 
-struct API_EXPORT SamHeader {
-
+class API_EXPORT SamHeader {
+public:
     // ctor & dtor
     SamHeader(const std::string& headerText = "");
     SamHeader(const SamHeader& other);

src/utils/BamTools/src/api/internal/io/TcpSocketEngine_p.h

@@ -30,7 +30,7 @@
 namespace BamTools {
 namespace Internal {
 
-struct TcpSocketEngine {
+class TcpSocketEngine {
 
     // ctors & dtor
     public:

src/utils/BamTools/src/api/internal/sam/SamHeaderValidator_p.h

@@ -27,8 +27,8 @@
 namespace BamTools {
 
 class SamHeader;
-class SamReadGroup;
-class SamSequence;
+struct SamReadGroup;
+struct SamSequence;
 
 namespace Internal {
 

src/utils/FileRecordTools/Records/BamRecord.h

@@ -23,9 +23,25 @@ public:
 
 	BamRecord();
 	virtual const BamRecord &operator=(const BamRecord &);
+
+
+	// This using statement is only being added to supress warning from the CLANG compiler regarding
+	// hidden overriden methods. Though it makes the base class methods available, developers should
+	// not actually call them on a BamRecord object.
+	using Bed6Interval::initFromFile;
+
+
 	bool initFromFile(FileReader *);
 	virtual bool initFromFile(BamFileReader *);
 	virtual void clear();
+
+
+	// As above, this using statement is only being added to supress warning from the CLANG compiler
+	// regarding hidden overriden methods. Though it makes the base class methods available, developers
+	// should not actually call them on a BamRecord object.
+	using Bed6Interval::print;
+
+
 	virtual void print(QuickString &outBuf, int start, int end, RecordKeyList *keyList) const;
 	virtual void print(QuickString &outBuf, RecordKeyList *keyList) const;
 	virtual void print(QuickString &outBuf, const QuickString & start, const QuickString & end, RecordKeyList *keyList) const;

test/merge/precisionTest.bed

+chr2L	1	54	.	0.05
+chr2L	65	128	.	0.33
+chr2L	129	180	.	0.04
+chr2L	193	259	.	-0.18
+chr2L	257	317	.	-0.07
+chr2L	321	375	.	-0.07
+chr2L	385	448	.	-0.11
+chr2L	449	502	.	0.4
+chr2L	513	570	.	0.48
+chr2L	577	635	.	-0.24

test/merge/test-merge.sh

@@ -276,3 +276,20 @@ $BT merge -i a.full.bed > obs
 check exp obs
 rm exp obs
 
+###########################################################
+#  Test that precision is correct
+###########################################################
+echo "    merge.t22...\c"
+echo \
+"chr2L	1	54	0.05
+chr2L	65	128	0.33
+chr2L	129	180	0.04
+chr2L	193	317	-0.125
+chr2L	321	375	-0.07
+chr2L	385	448	-0.11
+chr2L	449	502	0.4
+chr2L	513	570	0.48
+chr2L	577	635	-0.24" > exp
+$BT merge -i precisionTest.bed -c 5 -o mean > obs
+check obs exp
+rm obs exp