diff --git a/docs/content/installation.rst b/docs/content/installation.rst
index 511008008a2a5630cfcabab73966a80647dfd187..39341ac6b00fe986b78ffdfe20a2e90e57864034 100755
--- a/docs/content/installation.rst
+++ b/docs/content/installation.rst
@@ -3,10 +3,10 @@ Installation
 ############
 
 
-``bedtools`` is intended to run in a "command line" environment on UNIX, LINUX 
-and Apple OS X operating systems. Installing ``bedtools`` involves either 
-downloading the source code and compiling it manually, or installing stable 
-release from package managers such as 
+``bedtools`` is intended to run in a "command line" environment on UNIX, LINUX
+and Apple OS X operating systems. Installing ``bedtools`` involves either
+downloading the source code and compiling it manually, or installing stable
+release from package managers such as
 `homebrew (for OS X) <http://mxcl.github.com/homebrew/>`_.
 
 
@@ -20,14 +20,14 @@ Installing stable releases
 Compiling from source via Google Code
 .....................................
 
-Stable, versioned releases of bedtools are made available The following commands 
-will install ``bedtools`` in a local directory on an UNIX or OS X machine. 
-Note that the **"<version>"** refers to the latest posted version number 
+Stable, versioned releases of bedtools are made available The following commands
+will install ``bedtools`` in a local directory on an UNIX or OS X machine.
+Note that the **"<version>"** refers to the latest posted version number
 on http://bedtools.googlecode.com/.
 
 .. note::
 
-    The bedtools Makefiles utilize the GCC compiler. One should edit the 
+    The bedtools Makefiles utilize the GCC compiler. One should edit the
     Makefiles accordingly if one wants to use a different compiler.
 
 .. code-block:: bash
@@ -36,10 +36,10 @@ on http://bedtools.googlecode.com/.
   $ tar -zxvf BEDTools.tar.gz
   $ cd BEDTools-<version>
   $ make
-  
-At this point, one should copy the binaries in ./bin/ to either 
-``usr/local/bin/`` or some other repository for commonly used UNIX tools in 
-your environment. You will typically require administrator (e.g. "root" or 
+
+At this point, one should copy the binaries in ./bin/ to either
+``usr/local/bin/`` or some other repository for commonly used UNIX tools in
+your environment. You will typically require administrator (e.g. "root" or
 "sudo") privileges to copy to ``usr/local/bin/``. If in doubt, contact you
 system administrator for help.
 
@@ -48,11 +48,11 @@ Installing with package managers
 .....................................
 
 In addition, stable releases of ``bedtools`` are also available through package
-managers such as `homebrew (for OS X) <http://mxcl.github.com/homebrew/>`_, 
+managers such as `homebrew (for OS X) <http://mxcl.github.com/homebrew/>`_,
 ``apt-get`` and ``yum``.
 
-**Fedora/Centos**. Adam Huffman has created a Red Hat package for bedtools so 
-that one can easily install the latest release using "yum", the Fedora 
+**Fedora/Centos**. Adam Huffman has created a Red Hat package for bedtools so
+that one can easily install the latest release using "yum", the Fedora
 package manager. It should work with Fedora 13, 14 and EPEL5/6 (
 for Centos, Scientific Linux, etc.).
 
@@ -60,8 +60,8 @@ for Centos, Scientific Linux, etc.).
 
     yum install BEDTools
 
-**Debian/Ubuntu.** Charles Plessy also maintains a Debian package for bedtools 
-that is likely to be found in its derivatives like Ubuntu. Many thanks to 
+**Debian/Ubuntu.** Charles Plessy also maintains a Debian package for bedtools
+that is likely to be found in its derivatives like Ubuntu. Many thanks to
 Charles for doing this.
 
 .. code-block:: bash
@@ -69,11 +69,11 @@ Charles for doing this.
     apt-get install bedtools
 
 
-**Homebrew**. Carlos Borroto has made BEDTools available on the bedtools 
+**Homebrew**. Carlos Borroto has made BEDTools available on the bedtools
 package manager for OSX.
 
 .. code-block:: bash
-    
+
     brew install bedtools
 
 **MacPorts**. Alternatively, the MacPorts ports system can be used to install BEDTools on OSX.
@@ -86,11 +86,11 @@ package manager for OSX.
 Development versions
 -----------------------------
 
-The development version of bedtools is maintained in a Github 
-`repository <https://www.github.com/arq5x/bedtools>`_. Bug fixes are addressed
+The development version of bedtools is maintained in a Github
+`repository <https://www.github.com/arq5x/bedtools2>`_. Bug fixes are addressed
 in this repository prior to release, so there may be situations where you will
-want to use a development version of bedtools prior to its being promoted to 
-a stable release.  One would either clone the repository with ``git``, as 
+want to use a development version of bedtools prior to its being promoted to
+a stable release.  One would either clone the repository with ``git``, as
 follows and then compile the source code as describe above:
 
 .. code-block:: bash
@@ -98,7 +98,7 @@ follows and then compile the source code as describe above:
     git clone https://github.com/arq5x/bedtools2.git
 
 
-or, one can download the source code as a ``.zip`` file using the Github 
+or, one can download the source code as a ``.zip`` file using the Github
 website.  Once the zip file is downloaded and uncompressed with the ``unzip``
 command, one can compile and install using the instructions above.
 
diff --git a/docs/templates/page.html b/docs/templates/page.html
index 4e1e3cb09af86eaa5cd81ee5a0b1e25f2bfdfdd3..023b320193a86711cc19e1598026a65c2af3d0bd 100644
--- a/docs/templates/page.html
+++ b/docs/templates/page.html
@@ -5,7 +5,7 @@
 
 {# note, currently these must be set... #}
 {% set github_base_account = 'arq5x' %}
-{% set github_project = 'bedtools' %}
+{% set github_project = 'bedtools2' %}
 
 {##################################################}
 {# for plone-derived "edit me" & Google analytics #}
@@ -137,4 +137,3 @@
 {% endif %}
 
 {%- endblock %}
-
diff --git a/docs/templates/sidebar-intro.html b/docs/templates/sidebar-intro.html
index ed9f59cf6ac7111d0e35295b6bba9ac2a9643ece..262da46e7bd131b06fe996d73725d45a954ccdf0 100644
--- a/docs/templates/sidebar-intro.html
+++ b/docs/templates/sidebar-intro.html
@@ -3,9 +3,9 @@
 </p>
 <h3>Bedtools links</h3>
 <ul>
-  <li><a target="_blank" href="https://github.com/arq5x/bedtools/issues">Issue Tracker</a></li>
-  <li><a target="_blank" href="https://github.com/arq5x/bedtools">Source @ GitHub</a></li>
-  <li><a target="_blank" href="https://bedtools.googlecode.com">Releases @ Google Code</a></li>
+  <li><a target="_blank" href="https://github.com/arq5x/bedtools2/issues">Issue Tracker</a></li>
+  <li><a target="_blank" href="https://github.com/arq5x/bedtools2">Source @ GitHub</a></li>
+  <li><a target="_blank" href="https://bedtools.googlecode.com">Old Releases @ Google Code</a></li>
   <li><a target="_blank" href="http://groups.google.com/group/bedtools-discuss">Mailing list @ Google Groups</a></li>
   <li><a target="_blank" href="http://www.biostars.org/show/tag/bedtools/">Queries @ Biostar</a></li>
   <li><a target="_blank" href="http://quinlanlab.org">Quinlan lab @ UVa</a></li>
@@ -13,10 +13,9 @@
 </ul>
 
 <h3>Sources</h3>
-<p><a href="https://github.com/arq5x/bedtools">Browse source @ GitHub</a>.</p>
+<p><a href="https://github.com/arq5x/bedtools2">Browse source @ GitHub</a>.</p>
 
 <h3>Releases</h3>
 <ul>
-    <li><a href="https://github.com/arq5x/bedtools2/releases">Stable releasees now @ Github</a></li>
+    <li><a href="https://github.com/arq5x/bedtools2/releases">Stable releases now @ Github</a></li>
 </ul>
-
diff --git a/src/intersectFile/intersectFile.h b/src/intersectFile/intersectFile.h
index c1f8674349e22eabdb16d2aeccae46180835a258..869e7e159160476eb65f4e7c52431f7cca90f174 100644
--- a/src/intersectFile/intersectFile.h
+++ b/src/intersectFile/intersectFile.h
@@ -12,8 +12,6 @@
 #ifndef INTERSECTFILE_H
 #define INTERSECTFILE_H
 
-using namespace std;
-
 #include "RecordKeyList.h"
 
 using namespace std;
diff --git a/src/intersectFile/intersectMain.cpp b/src/intersectFile/intersectMain.cpp
index 9f38f3c3f509e3197dc989f50a4ff6c7468dd4e3..98f140fe4e9f2b6c20d77c4f8cb3a481128131e8 100644
--- a/src/intersectFile/intersectMain.cpp
+++ b/src/intersectFile/intersectMain.cpp
@@ -9,11 +9,12 @@
 
   Licenced under the GNU General Public License 2.0 license.
 ******************************************************************************/
-using namespace std;
 
 #include "intersectFile.h"
 #include "ContextIntersect.h"
 
+using namespace std;
+
 // define our program name
 #define PROGRAM_NAME "bedtools intersect"
 
diff --git a/src/mapFile/mapFile.h b/src/mapFile/mapFile.h
index 6009bf88081a2bae4bf8e22efbe0227726b805dc..38cbcda1f1b1e78cb0bde8cb2c0ab00b37c3e0e2 100644
--- a/src/mapFile/mapFile.h
+++ b/src/mapFile/mapFile.h
@@ -12,8 +12,6 @@
 #ifndef MAPFILE_H
 #define MAPFILE_H
 
-using namespace std;
-
 #include <sstream>
 #include <iomanip>
 #include "VectorOps.h"
diff --git a/src/mapFile/mapMain.cpp b/src/mapFile/mapMain.cpp
index 933fe0c1312bb47e6e66af72ea44ecce0e0fb098..99b5e881388d7daa77ea899e2d8836c9747c4f4c 100644
--- a/src/mapFile/mapMain.cpp
+++ b/src/mapFile/mapMain.cpp
@@ -9,11 +9,12 @@
 
   Licenced under the GNU General Public License 2.0 license.
 ******************************************************************************/
-using namespace std;
 
 #include "mapFile.h"
 #include "ContextMap.h"
 
+using namespace std;
+
 // define our program name
 #define PROGRAM_NAME "bedtools map"
 
diff --git a/src/nekSandbox1/nekSandboxMain.cpp b/src/nekSandbox1/nekSandboxMain.cpp
index 6e895b2ec4aad16dd81efba9e7be970c0a636f45..406d315b077d8c6ae1d4924aa882d34c0a5fc47d 100644
--- a/src/nekSandbox1/nekSandboxMain.cpp
+++ b/src/nekSandbox1/nekSandboxMain.cpp
@@ -1,5 +1,3 @@
-using namespace std;
-
 #include "ContextIntersect.h"
 #include "FileRecordMgr.h"
 #include <iostream>
diff --git a/src/regressTest/RegressTest.h b/src/regressTest/RegressTest.h
index 93064dc097598c1166d91722af2b170f3c7848a6..51fd33a31c171aecb4144040c029bd64b76e8ae6 100644
--- a/src/regressTest/RegressTest.h
+++ b/src/regressTest/RegressTest.h
@@ -8,12 +8,13 @@
 #ifndef REGRESSTEST_H_
 #define REGRESSTEST_H_
 
-using namespace std;
-
 #include <string>
 #include <cstdio>
 #include <vector>
 #include <fstream>
+
+using namespace std;
+
 class SingleLineDelimTextFileReader;
 class BufferedStreamMgr;
 
diff --git a/src/sampleFile/SampleFile.h b/src/sampleFile/SampleFile.h
index 11a1b49bd6ad1be67947c3b580229ea5de1e6c64..f4778c187fd1445fdc207d2a8accffd8b8a96099 100644
--- a/src/sampleFile/SampleFile.h
+++ b/src/sampleFile/SampleFile.h
@@ -8,12 +8,12 @@
 #ifndef SAMPLEFILE_H_
 #define SAMPLEFILE_H_
 
-using namespace std;
-
 #include "ContextSample.h"
 #include "Record.h"
 #include <vector>
 
+using namespace std;
+
 class FileRecordMgr;
 class Context;
 class RecordOutputMgr;
diff --git a/src/subtractBed/subtractBed.cpp b/src/subtractBed/subtractBed.cpp
index d46ce8c0991e24b9c53051517a11055d371736e4..1a9cac9e43cb034dafd39a3adc62b13cb5acbcfb 100644
--- a/src/subtractBed/subtractBed.cpp
+++ b/src/subtractBed/subtractBed.cpp
@@ -123,7 +123,7 @@ void BedSubtract::FindAndSubtractOverlaps(BED &a, vector<BED> &hits) {
 
         vector<bool> aKeep(a.end - a.start, true);
 
-        if ((numConsumedByB == 0)) {
+        if (numConsumedByB == 0) {
             if(_removeAll){ return; }
             
             // if there's any overlap, then we don't report.
diff --git a/src/utils/BinTree/BinTree.h b/src/utils/BinTree/BinTree.h
index ce15c481e9831cc4bd95f544bb4f3585084e956b..161696c1739763530f21a500a161cea0ef06aad1 100644
--- a/src/utils/BinTree/BinTree.h
+++ b/src/utils/BinTree/BinTree.h
@@ -8,8 +8,6 @@
 #ifndef BINTREE_H_
 #define BINTREE_H_
 
-using namespace std;
-
 #include <stdint.h>
 #include <string>
 #include <set>
@@ -19,6 +17,8 @@ using namespace std;
 #include "RecordKeyList.h"
 #include "ContextIntersect.h"
 
+using namespace std;
+
 class FileRecordMgr;
 class Record;
 
diff --git a/src/utils/Fasta/Fasta.cpp b/src/utils/Fasta/Fasta.cpp
index 076f06d2a1b99352e00e5d7d45878ed0760dbbe7..be9e53e80cdadde19d30b9fd870bba498a6cd830 100644
--- a/src/utils/Fasta/Fasta.cpp
+++ b/src/utils/Fasta/Fasta.cpp
@@ -26,11 +26,11 @@ FastaIndexEntry::~FastaIndexEntry(void)
 void FastaIndexEntry::clear(void)
 {
     name = "";
-    length = NULL;
+    length = 0;
     offset = -1;  // no real offset will ever be below 0, so this allows us to
                   // check if we have already recorded a real offset
-    line_blen = NULL;
-    line_len  = NULL;
+    line_blen = 0;
+    line_len  = 0;
     useFullHeader = false;
 }
 
diff --git a/src/utils/FileRecordTools/FileReaders/BamFileReader.h b/src/utils/FileRecordTools/FileReaders/BamFileReader.h
index d299cc918cdbac3a34af584b342768466c6717a4..c158a08a12e0415fd6916a4ee72d7134e72af36b 100644
--- a/src/utils/FileRecordTools/FileReaders/BamFileReader.h
+++ b/src/utils/FileRecordTools/FileReaders/BamFileReader.h
@@ -8,8 +8,6 @@
 #ifndef BAMFILEREADER_H_
 #define BAMFILEREADER_H_
 
-using namespace std;
-
 #include "FileReader.h"
 #include "QuickString.h"
 #include "api/BamReader.h"
diff --git a/src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.h b/src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.h
index 9be5d51df9880e68b04a35443a99f8c6393fca1b..4fd7a5f58f99392e9cdd02f2e5546af6ed0df150 100644
--- a/src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.h
+++ b/src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.h
@@ -8,8 +8,6 @@
 #ifndef BUFFEREDSTREAMMGR_H_
 #define BUFFEREDSTREAMMGR_H_
 
-using namespace std;
-
 #include <iostream>
 #include "QuickString.h"
 #include "FileRecordTypeChecker.h"
diff --git a/src/utils/FileRecordTools/FileReaders/FileReader.h b/src/utils/FileRecordTools/FileReaders/FileReader.h
index 29c25630918e27408fb6e099549781a94d97cf47..73a968bace4b39e9b0b5c6536e959834a1cf88d1 100644
--- a/src/utils/FileRecordTools/FileReaders/FileReader.h
+++ b/src/utils/FileRecordTools/FileReaders/FileReader.h
@@ -1,8 +1,6 @@
 #ifndef FILEREADER_H_
 #define FILEREADER_H_
 
-using namespace std;
-
 #include <string>
 #include <fstream>
 #include <map>
@@ -11,6 +9,8 @@ using namespace std;
 
 #include "BufferedStreamMgr.h"
 
+using namespace std;
+
 class FileReader {
 public:
 	FileReader();
diff --git a/src/utils/FileRecordTools/FileReaders/InputStreamMgr.h b/src/utils/FileRecordTools/FileReaders/InputStreamMgr.h
index 400f80a3686df553ff7dfef6eab6a29cad0feb98..da7dcde94c4225dc22daf1a14940b9b2195cfdfa 100644
--- a/src/utils/FileRecordTools/FileReaders/InputStreamMgr.h
+++ b/src/utils/FileRecordTools/FileReaders/InputStreamMgr.h
@@ -8,8 +8,6 @@
 #ifndef INPUTSTREAMMGR_H_
 #define INPUTSTREAMMGR_H_
 
-using namespace std;
-
 #include "PushBackStreamBuf.h"
 #include "InflateStreamBuf.h"
 #include "QuickString.h"
@@ -18,6 +16,8 @@ using namespace std;
 
 #include <iostream>
 
+using namespace std;
+
 class InputStreamMgr {
 public:
 	 //Contsructor: 1st arg can be "-" for stdin. set 2nd arg false if fileType already known.
diff --git a/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h b/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h
index 954ca2a17dcac76110220ac95f754b902762b3d4..cfb6241247ac7feddd2a856c36a52454cd7c0186 100644
--- a/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h
+++ b/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h
@@ -8,8 +8,6 @@
 #ifndef SINGLELINETEXTFILEREADER_H_
 #define SINGLELINETEXTFILEREADER_H_
 
-using namespace std;
-
 #include "FileReader.h"
 #include "QuickString.h"
 
diff --git a/src/utils/FileRecordTools/FileReaders/SingleLineDelimTransferBuffer.cpp b/src/utils/FileRecordTools/FileReaders/SingleLineDelimTransferBuffer.cpp
index dec5e317d92ddc11d4c21fd7d107bbc6c0322b0a..5500cae6122e41e53596bbdbe33dfcb606b86f37 100644
--- a/src/utils/FileRecordTools/FileReaders/SingleLineDelimTransferBuffer.cpp
+++ b/src/utils/FileRecordTools/FileReaders/SingleLineDelimTransferBuffer.cpp
@@ -4,6 +4,8 @@
 #include <cstdio>
 #include <cstdlib>
 
+using namespace std;
+
 SingleLineDelimTransferBuffer::SingleLineDelimTransferBuffer(int numFields, char delimChar)
 : _numFields(numFields),
   _delimChar(delimChar)
diff --git a/src/utils/FileRecordTools/FileReaders/SingleLineDelimTransferBuffer.h b/src/utils/FileRecordTools/FileReaders/SingleLineDelimTransferBuffer.h
index 9398ff773b7a26a8e645a3e7cf3d94331860d63c..457e4fe5f5d408669cc20968e746b34b9c8ee970 100644
--- a/src/utils/FileRecordTools/FileReaders/SingleLineDelimTransferBuffer.h
+++ b/src/utils/FileRecordTools/FileReaders/SingleLineDelimTransferBuffer.h
@@ -8,8 +8,6 @@
 #ifndef SINGLELINEDELIMTRANSFERBUFFER_H_
 #define SINGLELINEDELIMTRANSFERBUFFER_H_
 
-using namespace std;
-
 class SingleLineDelimTransferBuffer {
 public:
 	SingleLineDelimTransferBuffer(int numFields, char delim='\t');
diff --git a/src/utils/FileRecordTools/FileRecordMgr.h b/src/utils/FileRecordTools/FileRecordMgr.h
index 42f346816fcc9a7e39576e9bde94e68db5173d3f..95e459e7add14b299fc45e6043d71f89aeb1d2db 100644
--- a/src/utils/FileRecordTools/FileRecordMgr.h
+++ b/src/utils/FileRecordTools/FileRecordMgr.h
@@ -8,8 +8,6 @@
 #ifndef FILERECORDMGR_H_
 #define FILERECORDMGR_H_
 
-using namespace std;
-
 #include <string>
 #include "QuickString.h"
 #include <set>
@@ -27,6 +25,8 @@ using namespace std;
 #include "RecordKeyList.h"
 #include "BlockMgr.h"
 
+using namespace std;
+
 class Record;
 class NewGenomeFile;
 
diff --git a/src/utils/FileRecordTools/Records/BlockMgr.h b/src/utils/FileRecordTools/Records/BlockMgr.h
index bf6f116f5a0f060a912aec16d4fb6910102f9ea8..13b76fa87b299a4325d9143df012365d11ae4d64 100644
--- a/src/utils/FileRecordTools/Records/BlockMgr.h
+++ b/src/utils/FileRecordTools/Records/BlockMgr.h
@@ -8,14 +8,15 @@
 #ifndef BLOCKMGR_H_
 #define BLOCKMGR_H_
 
+#include <vector>
+
 //This class handles blocks inside of a larger record, such as BED12 and BAM records.
 //Produce and manage seperate records for the sub-intervals inside the
 
-using namespace std;
-
 #include "FileRecordTypeChecker.h"
 #include "RecordKeyList.h"
 
+using namespace std;
 
 class RecordMgr;
 
diff --git a/src/utils/FileRecordTools/Records/Record.h b/src/utils/FileRecordTools/Records/Record.h
index 8e4376c1a9f6d2eb112c69d9c87a6b3b742d0a59..5adbc787035c551c9d8910cb1687453469b830ab 100644
--- a/src/utils/FileRecordTools/Records/Record.h
+++ b/src/utils/FileRecordTools/Records/Record.h
@@ -5,15 +5,16 @@
  *      Author: nek3d
  */
 
-using namespace std;
-
 #ifndef RECORD_H_
 #define RECORD_H_
 
+#include <string>
 #include "FreeList.h"
 #include "QuickString.h"
 #include "FileRecordTypeChecker.h"
 
+using namespace std;
+
 class FileRecordMgr;
 class FileReader;
 class ChromIdLookup;
diff --git a/src/utils/FileRecordTools/Records/RecordKeyList.h b/src/utils/FileRecordTools/Records/RecordKeyList.h
index f5d1251427d16143d57c8744dc5263782e1af646..948f677b0f6e427c3559ca60ae9e7732d7ed85a3 100644
--- a/src/utils/FileRecordTools/Records/RecordKeyList.h
+++ b/src/utils/FileRecordTools/Records/RecordKeyList.h
@@ -8,11 +8,6 @@
 #ifndef KEYLIST_H_
 #define KEYLIST_H_
 
-
-
-
-using namespace std;
-
 #include "Record.h"
 #include "BTlist.h"
 
diff --git a/src/utils/FileRecordTools/Records/StrandQueue.h b/src/utils/FileRecordTools/Records/StrandQueue.h
index e6f0bb49d7eab3160850ba03f13958b867054f37..bd02b4090fc4577bc85425f27bcba8019b0f8cf5 100644
--- a/src/utils/FileRecordTools/Records/StrandQueue.h
+++ b/src/utils/FileRecordTools/Records/StrandQueue.h
@@ -7,14 +7,14 @@
 #ifndef STRANDQUEUE_H_
 #define STRANDQUEUE_H_
 
-using namespace std;
-
 #include <vector>
 #include <queue>
 #include <cstdio>
 #include <cstdlib>
 #include "Record.h"
 
+using namespace std;
+
 class StrandQueue {
 public:
 	StrandQueue();
diff --git a/src/utils/KeyListOps/KeyListOpsMethods.h b/src/utils/KeyListOps/KeyListOpsMethods.h
index 10af9c2620e17906d34e0f26da1d1f3b0dfff921..16796858841eea0524015dd9c0073e641c5ecab6 100644
--- a/src/utils/KeyListOps/KeyListOpsMethods.h
+++ b/src/utils/KeyListOps/KeyListOpsMethods.h
@@ -8,14 +8,14 @@
 #ifndef KEYLISTOPSMETHODS_H_
 #define KEYLISTOPSMETHODS_H_
 
-using namespace std;
-
 #include <map>
 #include <utility> //for pair
 #include "QuickString.h"
 #include <stdint.h>
 #include "RecordKeyList.h"
 
+using namespace std;
+
 class KeyListOpsMethods {
 public:
 	KeyListOpsMethods();
diff --git a/src/utils/NewChromsweep/NewChromsweep.h b/src/utils/NewChromsweep/NewChromsweep.h
index 9552b91552fb74e83d68c9fe7bb5bb6785350087..480b399ce0af0fecbf4c7cbe00662ac8d425aafe 100644
--- a/src/utils/NewChromsweep/NewChromsweep.h
+++ b/src/utils/NewChromsweep/NewChromsweep.h
@@ -12,8 +12,6 @@
 #ifndef NEW_CHROMSWEEP_H
 #define NEW_CHROMSWEEP_H
 
-using namespace std;
-
 #include <string>
 #include "BTlist.h"
 #include "RecordKeyList.h"
diff --git a/src/utils/RecordOutputMgr/RecordOutputMgr.h b/src/utils/RecordOutputMgr/RecordOutputMgr.h
index 07891cc2cfdcc3bf3d5de19349939953ae31c523..1a7fe609835e2e87fcbbf0e13e662362430e68d7 100644
--- a/src/utils/RecordOutputMgr/RecordOutputMgr.h
+++ b/src/utils/RecordOutputMgr/RecordOutputMgr.h
@@ -8,8 +8,6 @@
 #ifndef RECORDOUTPUTMGR_H_
 #define RECORDOUTPUTMGR_H_
 
-using namespace std;
-
 #include "ContextBase.h"
 #include "RecordKeyList.h"
 #include "api/BamWriter.h"
diff --git a/src/utils/fileType/FileRecordTypeChecker.cpp b/src/utils/fileType/FileRecordTypeChecker.cpp
index 8ac393b2c2979f385b386bfd73096071b421746c..f2450891e1a33a869fa9a707c120b7c43f4a4f2f 100644
--- a/src/utils/fileType/FileRecordTypeChecker.cpp
+++ b/src/utils/fileType/FileRecordTypeChecker.cpp
@@ -110,6 +110,7 @@ bool FileRecordTypeChecker::isBinaryBuffer(const char *buffer, size_t len)
 
 	//Let's say that in a text file, at least 90% of the characters
 	//should be alphanumeric, whitespace, or punctuation.
+	static const float PERCENTAGE_PRINTABLE = .9;
 
 	int alphaNumCount = 0;
 	int whiteSpaceCount = 0;
diff --git a/src/utils/fileType/FileRecordTypeChecker.h b/src/utils/fileType/FileRecordTypeChecker.h
index 35bcc4bc9d41112e8fb997c96d025433ff242a37..45dcac7a03e943a90f2c728b998d92112d65b6fb 100644
--- a/src/utils/fileType/FileRecordTypeChecker.h
+++ b/src/utils/fileType/FileRecordTypeChecker.h
@@ -8,8 +8,6 @@
 #ifndef FILERECORDTYPECHECKER_H_
 #define FILERECORDTYPECHECKER_H_
 
-using namespace std;
-
 #include <string>
 #include <cstring>
 #include <cstdio>
@@ -20,6 +18,8 @@ using namespace std;
 #include "PushBackStreamBuf.h"
 #include "Tokenizer.h"
 
+using namespace std;
+
 class FileRecordTypeChecker {
 public:
 
@@ -116,8 +116,6 @@ private:
 
 	bool _eofHit;
 
-	//this will be used in determining whether we are looking at a binary or text file.
-	static const float PERCENTAGE_PRINTABLE = .9;
 	bool isBinaryBuffer(const char *buffer, size_t len);
 	bool isBAM(const char *buffer);
 	bool handleTextFormat(const char *buffer, size_t len);
diff --git a/src/utils/general/CompressionTools.h b/src/utils/general/CompressionTools.h
index 8b41336a7c3607a678fb694b9a4b5c48f4fb7115..dff6630bcd2e5eb5b18d3d4e6af1eb78a30575e4 100644
--- a/src/utils/general/CompressionTools.h
+++ b/src/utils/general/CompressionTools.h
@@ -8,8 +8,6 @@
 #ifndef COMPRESSIONTOOLS_H_
 #define COMPRESSIONTOOLS_H_
 
-using namespace std;
-
 #include <zlib.h>
 #include "BTlist.h"
 
diff --git a/src/utils/general/FreeList.h b/src/utils/general/FreeList.h
index 4aaa6f551ed96964a8034ea74954e4296de05c20..ebe253cb53358fae0532add873a30239e7256692 100644
--- a/src/utils/general/FreeList.h
+++ b/src/utils/general/FreeList.h
@@ -8,12 +8,12 @@
 #ifndef FREELIST_H_
 #define FREELIST_H_
 
-using namespace std;
-
 #include <cstddef> //defines NULL
 #include <deque>
 #include <vector>
 
+using namespace std;
+
 template <class T>
 class FreeList {
 public:
diff --git a/src/utils/general/ParseTools.h b/src/utils/general/ParseTools.h
index 871f53bfea150ad615c2416c53701d4e94600fdc..2ba28df37578a7fc5f31148ca2c84a8e28787abe 100644
--- a/src/utils/general/ParseTools.h
+++ b/src/utils/general/ParseTools.h
@@ -8,13 +8,13 @@
 #ifndef PARSETOOLS_H_
 #define PARSETOOLS_H_
 
-using namespace std;
-
 #include <cstring> //for memset
 #include <string>
 #include <vector>
 #include "QuickString.h"
 
+using namespace std;
+
 bool isNumeric(const QuickString &str);
 
 //This method is a faster version of atoi, but is limited to a maximum of
diff --git a/src/utils/general/PushBackStreamBuf.h b/src/utils/general/PushBackStreamBuf.h
index 0c41cd5a1937d4b441424fe3747d1e21ed5f83cb..d2538eaa3209ef77477bbdd8ffd8f63606806401 100644
--- a/src/utils/general/PushBackStreamBuf.h
+++ b/src/utils/general/PushBackStreamBuf.h
@@ -8,11 +8,11 @@
 #ifndef PUSHBACKSTREAM_H_
 #define PUSHBACKSTREAM_H_
 
-using namespace std;
-
 #include <iostream>
 #include "BTlist.h"
 
+using namespace std;
+
 class PushBackStreamBuf: public std::streambuf {
 public:
 	friend class InputStreamMgr;
diff --git a/src/utils/general/QuickString.h b/src/utils/general/QuickString.h
index ebdfb714324382ea1dfa5529c37abed096681c6e..1024a25f4449149bf19a68c23112228ec8e72a89 100644
--- a/src/utils/general/QuickString.h
+++ b/src/utils/general/QuickString.h
@@ -8,12 +8,13 @@
 #ifndef QUICKSTRING_H_
 #define QUICKSTRING_H_
 
-using namespace std;
 #include <string>
 #include <stdint.h>
 #include <climits>
 #include <ostream>
 
+using namespace std;
+
 class QuickString {
 public:
 	QuickString(size_t capacity = DEFAULT_CAPACITY);
diff --git a/src/utils/general/Tokenizer.h b/src/utils/general/Tokenizer.h
index 7e9e8005db26a89d5323d0a3a3e694546f4c303e..f0f7dc17759de37b4ae28253e1176d0bc3005638 100644
--- a/src/utils/general/Tokenizer.h
+++ b/src/utils/general/Tokenizer.h
@@ -8,11 +8,11 @@
 #ifndef TOKENIZER_H_
 #define TOKENIZER_H_
 
-using namespace std;
-
 #include "QuickString.h"
 #include <vector>
 
+using namespace std;
+
 class Tokenizer {
 public:
 	Tokenizer();
diff --git a/test/general/test-general.sh b/test/general/test-general.sh
index e2da83d01a698d19bd1348d61e0165c3d1a0c2b0..4965a51c94c23fbef9378b982557f195701839ad 100644
--- a/test/general/test-general.sh
+++ b/test/general/test-general.sh
@@ -84,7 +84,7 @@ rm obs exp
 #  Don't fail on existent, yet empty files.
 ###########################################################
 echo "    general.t07...\c"
-$BT merge -i empty.bed > obs
+$BT merge -i empty.bed 2> obs
 touch exp
 check obs exp
 rm obs exp