Merge branches 'master' and 'iodevice' into iodevice

diff --git a/README b/README
index 1780ede32a7abf818f2a5cf725e0e5a9ade71b1e..498f4be06dc0ecc00162c43cdaa65841cea5dff8 100644 (file)
--- a/README
+++ b/README
@@ -56,6 +56,5 @@ Derek Barnett
 Marth Lab
 Biology Dept., Boston College
 
-Email: barnetde@bc.edu
-Project Websites: http://github.com/pezmaster31/bamtools   (ACTIVE SUPPORT)
-                  http://sourceforge.net/projects/bamtools (major updates only)
+Email: derekwbarnett@gmail.com
+Project Website: http://github.com/pezmaster31/bamtools

diff --git a/src/api/BamAlignment.cpp b/src/api/BamAlignment.cpp
index 0077f64a9eb5306033811a6e49261cebfacb5969..91ca8ad68fafab2d0f84375459d7cc72c1c226b0 100644 (file)
--- a/src/api/BamAlignment.cpp
+++ b/src/api/BamAlignment.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // BamAlignment.cpp (c) 2009 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 22 April 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/BamAlignment.h b/src/api/BamAlignment.h
index 7535d93f8f7a8fcd1062348b7d406a4082fa0abe..aa1d940d14c4ea8b8ddf3c2ee477804228744593 100644 (file)
--- a/src/api/BamAlignment.h
+++ b/src/api/BamAlignment.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // BamAlignment.h (c) 2009 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 22 April 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/BamAux.h b/src/api/BamAux.h
index d171e7069db998da82ac346689cea68fee068611..4c5a99aca66eb76d3e0646f152ff25bf402cbdae 100644 (file)
--- a/src/api/BamAux.h
+++ b/src/api/BamAux.h
@@ -1,7 +1,6 @@
 // ***************************************************************************\r
 // BamAux.h (c) 2009 Derek Barnett, Michael Str�mberg\r
 // Marth Lab, Department of Biology, Boston College\r
-// All rights reserved.\r
 // ---------------------------------------------------------------------------\r
 // Last modified: 4 March 2011 (DB)\r
 // ---------------------------------------------------------------------------\r

diff --git a/src/api/BamIndex.h b/src/api/BamIndex.h
index 00a8f0174458f542268944d30aa39997400d0338..a52922e76b6d3f0bc4272ba142b7215a02b9c765 100644 (file)
--- a/src/api/BamIndex.h
+++ b/src/api/BamIndex.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // BamIndex.h (c) 2009 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 5 April 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/BamMultiReader.cpp b/src/api/BamMultiReader.cpp
index 06055df393daae3cb96233eebb5787b21c0b71d2..854345193b3a3f51bfcd393c3543e7d49565c2ea 100644 (file)
--- a/src/api/BamMultiReader.cpp
+++ b/src/api/BamMultiReader.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // BamMultiReader.cpp (c) 2010 Erik Garrison, Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 15 March 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/BamMultiReader.h b/src/api/BamMultiReader.h
index cc49ec8eb2076469be2585bdf978bd603acec8a3..561ce7a1e4d4407e2c85975b3a2ab2cd455a5ee3 100644 (file)
--- a/src/api/BamMultiReader.h
+++ b/src/api/BamMultiReader.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // BamMultiReader.h (c) 2010 Erik Garrison, Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 15 March 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/BamReader.cpp b/src/api/BamReader.cpp
index eaa68827f95b06d09dea64f21a3d16277b9b9c69..4b25b15960c40d351bf7786de75637289ea0ee18 100644 (file)
--- a/src/api/BamReader.cpp
+++ b/src/api/BamReader.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // BamReader.cpp (c) 2009 Derek Barnett, Michael Str�mberg
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 4 March 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/BamReader.h b/src/api/BamReader.h
index 85b0c0d5713ed15f4a616ec4a6f7e1c2ab9d3c1b..836fbf5e3cbac860f62916c3e717c72618089a7b 100644 (file)
--- a/src/api/BamReader.h
+++ b/src/api/BamReader.h
@@ -1,7 +1,6 @@
 // ***************************************************************************\r
 // BamReader.h (c) 2009 Derek Barnett, Michael Str�mberg\r
 // Marth Lab, Department of Biology, Boston College\r
-// All rights reserved.\r
 // ---------------------------------------------------------------------------\r
 // Last modified: 4 March 2011 (DB)\r
 // ---------------------------------------------------------------------------\r

diff --git a/src/api/BamWriter.cpp b/src/api/BamWriter.cpp
index 8582f34be92b30e5e0d09a0465d729cf880b52c0..8bf6f18c5caf31c404d88cb24ca2020996a128e7 100644 (file)
--- a/src/api/BamWriter.cpp
+++ b/src/api/BamWriter.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************\r
 // BamWriter.cpp (c) 2009 Michael Str�mberg, Derek Barnett\r
 // Marth Lab, Department of Biology, Boston College\r
-// All rights reserved.\r
 // ---------------------------------------------------------------------------\r
 // Last modified: 4 March 2011 (DB)\r
 // ---------------------------------------------------------------------------\r

diff --git a/src/api/BamWriter.h b/src/api/BamWriter.h
index 476dbecf271e35ea8db22883055faa69c62babf0..56ac30142949c034c209b2e872e70aed9bebb3fa 100644 (file)
--- a/src/api/BamWriter.h
+++ b/src/api/BamWriter.h
@@ -1,7 +1,6 @@
 // ***************************************************************************\r
 // BamWriter.h (c) 2009 Michael Str�mberg, Derek Barnett\r
 // Marth Lab, Department of Biology, Boston College\r
-// All rights reserved.\r
 // ---------------------------------------------------------------------------\r
 // Last modified: 4 March 2011 (DB)\r
 // ---------------------------------------------------------------------------\r

diff --git a/src/api/SamConstants.h b/src/api/SamConstants.h
index d34592027891a8233e6e27b6b4f2cb8a84a8f9a6..913c21391cda75030a4b1bb9f190857730666faf 100644 (file)
--- a/src/api/SamConstants.h
+++ b/src/api/SamConstants.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // SamConstants.h (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 19 April 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/SamHeader.cpp b/src/api/SamHeader.cpp
index 9104978ba7492c77db439b3c037984c5874051d1..77e1c6d4b5fee014aadb6e6e702f4cc60f9f8867 100644 (file)
--- a/src/api/SamHeader.cpp
+++ b/src/api/SamHeader.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // SamHeader.cpp (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 19 April 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/SamHeader.h b/src/api/SamHeader.h
index 5c7a1019120f74981ad8ee3e73559d8247b569a9..3b67621ac4dca6bd94aba4293b7d944bf7eba5e8 100644 (file)
--- a/src/api/SamHeader.h
+++ b/src/api/SamHeader.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // SamHeader.h (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 18 April 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/SamProgram.cpp b/src/api/SamProgram.cpp
index b89a10bf0e1a1cf31ae2d88c0424e79446523262..fed9b8b70dd833d102059c94c7b94211f48e0dbf 100644 (file)
--- a/src/api/SamProgram.cpp
+++ b/src/api/SamProgram.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // SamProgram.cpp (c) 2011 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 19 April 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/SamProgram.h b/src/api/SamProgram.h
index 3c89059bdaedeeaf0b287b9c4fd3a2aae794002e..97a9ae5069e13d335adb1db2f56955eb035630a7 100644 (file)
--- a/src/api/SamProgram.h
+++ b/src/api/SamProgram.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // SamProgram.h (c) 2011 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 19 April 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/SamProgramChain.cpp b/src/api/SamProgramChain.cpp
index 66b7f071abdacd8a99d4e8863666d8e346c9c2d2..287dcdf4529cdec578c10c266582182432abb2ce 100644 (file)
--- a/src/api/SamProgramChain.cpp
+++ b/src/api/SamProgramChain.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // SamProgramChain.cpp (c) 2011 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 19 April 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/SamProgramChain.h b/src/api/SamProgramChain.h
index 4cb16fc337fc2b834dded709804f8879f15968f2..02f023758580e3568b2ab94f1dbdb58cd8f02dff 100644 (file)
--- a/src/api/SamProgramChain.h
+++ b/src/api/SamProgramChain.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // SamProgramChain.h (c) 2011 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 19 April 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/SamReadGroup.cpp b/src/api/SamReadGroup.cpp
index 2ba75f16b46b7e7a548581a3aa04144895675097..a9170d7bee13854dc1116c0491c6fa2e5ac04e37 100644 (file)
--- a/src/api/SamReadGroup.cpp
+++ b/src/api/SamReadGroup.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // SamReadGroup.cpp (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 18 April 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/SamReadGroup.h b/src/api/SamReadGroup.h
index b203d3cdb16927c5363272c9810b74b84bd2ecba..b1fbfb8ac04d72bb6c4cb9ebd4f3a5ea0d99a565 100644 (file)
--- a/src/api/SamReadGroup.h
+++ b/src/api/SamReadGroup.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // SamReadGroup.h (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 18 April 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/SamReadGroupDictionary.cpp b/src/api/SamReadGroupDictionary.cpp
index 69903ff8051f2f83da5c3a23d4e8725f2694939b..f243f929a49223495181913a8e079c7ceb2fcfda 100644 (file)
--- a/src/api/SamReadGroupDictionary.cpp
+++ b/src/api/SamReadGroupDictionary.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // SamReadGroupDictionary.cpp (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 18 April 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/SamReadGroupDictionary.h b/src/api/SamReadGroupDictionary.h
index 8ec40e227ba5f020699cd1a0021a2785587e447c..328763a61f72dddb6d674381ed801ae1e2e392a5 100644 (file)
--- a/src/api/SamReadGroupDictionary.h
+++ b/src/api/SamReadGroupDictionary.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // SamReadGroupDictionary.h (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 18 April 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/SamSequence.cpp b/src/api/SamSequence.cpp
index 0231988dd901300c1937f7abb20775f19607b599..c8e375f8c87d00610436dbeb5bf3223fa9acdbf6 100644 (file)
--- a/src/api/SamSequence.cpp
+++ b/src/api/SamSequence.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // SamSequence.cpp (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 18 April 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/SamSequence.h b/src/api/SamSequence.h
index 054e58f985ec40c74820f37a8318157202dfd2ed..6f1a2ab0808e726bf27c41103dfd2ff571895dd8 100644 (file)
--- a/src/api/SamSequence.h
+++ b/src/api/SamSequence.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // SamSequence.h (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 18 April 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/SamSequenceDictionary.cpp b/src/api/SamSequenceDictionary.cpp
index 3e5240df386099cc5199fe0d3d173d5374b22303..10d0437a1fdb3073d75ef23c0929c2e796c365a8 100644 (file)
--- a/src/api/SamSequenceDictionary.cpp
+++ b/src/api/SamSequenceDictionary.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // SamSequenceDictionary.cpp (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 18 April 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/SamSequenceDictionary.h b/src/api/SamSequenceDictionary.h
index 1ac73261fef989f3f38adf9d6a9d1db1c16701b7..76bd45a89fa73b66bde5a2cbef960f9aa14cdf47 100644 (file)
--- a/src/api/SamSequenceDictionary.h
+++ b/src/api/SamSequenceDictionary.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // SamSequenceDictionary.h (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 18 April 2011
 // ---------------------------------------------------------------------------

diff --git a/src/api/api_global.h b/src/api/api_global.h
index 84fcad214c1e141d8f227dba3961e6570f03aec8..f1c2353485eeda8f10ac146b3b295098e711050c 100644 (file)
--- a/src/api/api_global.h
+++ b/src/api/api_global.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // api_global.h (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 19 November 2010 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/internal/BamHeader_p.cpp b/src/api/internal/BamHeader_p.cpp
index 2f4ef3480e20c5b93fc9e1c650a6dd0e21977af2..45dc379f52327c6cc9a77d232e1b53a9b83bd56e 100644 (file)
--- a/src/api/internal/BamHeader_p.cpp
+++ b/src/api/internal/BamHeader_p.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // BamHeader_p.cpp (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 21 March 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/internal/BamHeader_p.h b/src/api/internal/BamHeader_p.h
index 1f1a31c355dc41ac2f400e51f1421aeb0f907f0c..3738c6066177cec90924394052084aeb5886c27e 100644 (file)
--- a/src/api/internal/BamHeader_p.h
+++ b/src/api/internal/BamHeader_p.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // BamHeader_p.h (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 26 January 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/internal/BamIndexFactory_p.cpp b/src/api/internal/BamIndexFactory_p.cpp
index 69b372bb02a770cbaa3d6c1449c1a73d23ffc1e8..c91f43374f1fc0318c43c46e869fe0619afa4b1d 100644 (file)
--- a/src/api/internal/BamIndexFactory_p.cpp
+++ b/src/api/internal/BamIndexFactory_p.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // BamIndexFactory_p.cpp (c) 2011 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 5 April 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/internal/BamIndexFactory_p.h b/src/api/internal/BamIndexFactory_p.h
index f060d2cd4e766179cf81162897727ec06a0236a5..7b1ff96a6425f42e717c800f55f839ea08ec5b09 100644 (file)
--- a/src/api/internal/BamIndexFactory_p.h
+++ b/src/api/internal/BamIndexFactory_p.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // BamIndexFactory_p.h (c) 2011 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 5 April 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/internal/BamMultiMerger_p.h b/src/api/internal/BamMultiMerger_p.h
index ae67eea238df983b4e8968b41414ef1c5abd5fcc..15ae437dc44ba1f55d5dd54b37ee3c39e6f9f23e 100644 (file)
--- a/src/api/internal/BamMultiMerger_p.h
+++ b/src/api/internal/BamMultiMerger_p.h
@@ -1,9 +1,8 @@
 // ***************************************************************************
 // BamMultiMerger_p.h (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 18 March 2011 (DB)
+// Last modified: 9 September 2011 (DB)
 // ---------------------------------------------------------------------------
 // Provides merging functionality for BamMultiReader.  At this point, supports
 // sorting results by (refId, position) or by read name.
@@ -42,7 +41,7 @@ class IBamMultiMerger {
         virtual ~IBamMultiMerger(void) { }
 
     public:
-        virtual void Add(const ReaderAlignment& value) =0;
+        virtual void Add(ReaderAlignment value) =0;
         virtual void Clear(void) =0;
         virtual const ReaderAlignment& First(void) const =0;
         virtual bool IsEmpty(void) const =0;
@@ -59,7 +58,7 @@ class PositionMultiMerger : public IBamMultiMerger {
         ~PositionMultiMerger(void) { }
 
     public:
-        void Add(const ReaderAlignment& value);
+        void Add(ReaderAlignment value);
         void Clear(void);
         const ReaderAlignment& First(void) const;
         bool IsEmpty(void) const;
@@ -87,7 +86,7 @@ class ReadNameMultiMerger : public IBamMultiMerger {
         ~ReadNameMultiMerger(void) { }
 
     public:
-        void Add(const ReaderAlignment& value);
+        void Add(ReaderAlignment value);
         void Clear(void);
         const ReaderAlignment& First(void) const;
         bool IsEmpty(void) const;
@@ -115,7 +114,7 @@ class UnsortedMultiMerger : public IBamMultiMerger {
         ~UnsortedMultiMerger(void) { }
 
     public:
-        void Add(const ReaderAlignment& value);
+        void Add(ReaderAlignment value);
         void Clear(void);
         const ReaderAlignment& First(void) const;
         bool IsEmpty(void) const;
@@ -135,7 +134,7 @@ class UnsortedMultiMerger : public IBamMultiMerger {
 // ------------------------------------------
 // PositionMultiMerger implementation
 
-inline void PositionMultiMerger::Add(const ReaderAlignment& value) {
+inline void PositionMultiMerger::Add(ReaderAlignment value) {
     const KeyType key( value.second->RefID, value.second->Position );
     m_data.insert( ElementType(key, value) );
 }
@@ -188,9 +187,12 @@ inline ReaderAlignment PositionMultiMerger::TakeFirst(void) {
 // ------------------------------------------
 // ReadNameMultiMerger implementation
 
-inline void ReadNameMultiMerger::Add(const ReaderAlignment& value) {
-    const KeyType key(value.second->Name);
-    m_data.insert( ElementType(key, value) );
+inline void ReadNameMultiMerger::Add(ReaderAlignment value) {
+    BamAlignment* al = value.second;
+    if ( al->BuildCharData() ) {
+        const KeyType key(al->Name);
+        m_data.insert( ElementType(key, value) );
+    }
 }
 
 inline void ReadNameMultiMerger::Clear(void) {
@@ -242,7 +244,7 @@ inline ReaderAlignment ReadNameMultiMerger::TakeFirst(void) {
 // ------------------------------------------
 // UnsortedMultiMerger implementation
 
-inline void UnsortedMultiMerger::Add(const ReaderAlignment& value) {
+inline void UnsortedMultiMerger::Add(ReaderAlignment value) {
     m_data.push_back(value);
 }
 

diff --git a/src/api/internal/BamMultiReader_p.cpp b/src/api/internal/BamMultiReader_p.cpp
index e789d06ee35c93d3945427ec99a4fe544af49930..189f0ec2710048d446991992e8e8e996e9c1178a 100644 (file)
--- a/src/api/internal/BamMultiReader_p.cpp
+++ b/src/api/internal/BamMultiReader_p.cpp
@@ -1,9 +1,8 @@
 // ***************************************************************************
 // BamMultiReader_p.cpp (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 5 April 2011 (DB)
+// Last modified: 9 September 2011 (DB)
 // ---------------------------------------------------------------------------
 // Functionality for simultaneously reading multiple BAM files
 // *************************************************************************
@@ -25,7 +24,6 @@ using namespace std;
 // ctor
 BamMultiReaderPrivate::BamMultiReaderPrivate(void)
     : m_alignments(0)
-    , m_isCoreMode(false)
     , m_sortOrder(BamMultiReader::SortedByPosition)
 { }
 
@@ -261,14 +259,12 @@ string BamMultiReaderPrivate::GetHeaderText(void) const {
 
 // get next alignment among all files
 bool BamMultiReaderPrivate::GetNextAlignment(BamAlignment& al) {
-    m_isCoreMode = false;
-    return LoadNextAlignment(al);
+    return PopNextCachedAlignment(al, true);
 }
 
 // get next alignment among all files without parsing character data from alignments
 bool BamMultiReaderPrivate::GetNextAlignmentCore(BamAlignment& al) {
-    m_isCoreMode = true;
-    return LoadNextAlignment(al);
+    return PopNextCachedAlignment(al, false);
 }
 
 // ---------------------------------------------------------------------------------------
@@ -406,25 +402,10 @@ bool BamMultiReaderPrivate::Jump(int refID, int position) {
     return true;
 }
 
-bool BamMultiReaderPrivate::LoadNextAlignment(BamAlignment& al) {
-
-    // bail out if no more data to process
-    if ( !HasAlignmentData() )
-        return false;
-
-    // "pop" next alignment and reader
-    ReaderAlignment nextReaderAlignment = m_alignments->TakeFirst();
-    BamReader* reader = nextReaderAlignment.first;
-    BamAlignment* alignment = nextReaderAlignment.second;
-
-    // store cached alignment into destination parameter (by copy)
-    al = *alignment;
-
-    // peek to next alignment & store in cache
-    SaveNextAlignment(reader, alignment);
-
-    // return success
-    return true;
+bool BamMultiReaderPrivate::LoadNextAlignment(BamReader* reader, BamAlignment* alignment) {
+    // lazy building of alignment's char data,
+    // only populated on demand by sorting merger or client call to GetNextAlignment()
+    return reader->GetNextAlignmentCore(*alignment);
 }
 
 // locate (& load) index files for BAM readers that don't already have one loaded
@@ -456,6 +437,9 @@ bool BamMultiReaderPrivate::Open(const vector<string>& filenames) {
         if ( m_alignments == 0 ) return false;
     }
 
+    // put all current readers back at beginning (refreshes alignment cache)
+    Rewind();
+
     // iterate over filenames
     vector<string>::const_iterator filenameIter = filenames.begin();
     vector<string>::const_iterator filenameEnd  = filenames.end();
@@ -464,18 +448,17 @@ bool BamMultiReaderPrivate::Open(const vector<string>& filenames) {
         if ( filename.empty() ) continue;
 
         // attempt to open BamReader on filename
-        BamReader* reader = OpenReader(filename);
-        if ( reader == 0 ) continue;
-
-        // store reader with new alignment
-        m_readers.push_back( make_pair(reader, new BamAlignment) );
+        bool openedOk = false;
+        ReaderAlignment ra = OpenReader(filename, &openedOk);
+        if ( openedOk ) {
+            m_readers.push_back(ra); // store reader/alignment in local list
+            m_alignments->Add(ra);   // add reader/alignment to sorting cache
+        }
     }
 
-    // validate & rewind any opened readers, also refreshes alignment cache
-    if ( !m_readers.empty() ) {
+    // if more than one reader open, check for reference consistency
+    if ( m_readers.size() > 1 )
         ValidateReaders();
-        Rewind();
-    }
 
     // return success
     return true;
@@ -524,19 +507,23 @@ bool BamMultiReaderPrivate::OpenIndexes(const vector<string>& indexFilenames) {
     return result;
 }
 
-BamReader* BamMultiReaderPrivate::OpenReader(const std::string& filename) {
+ReaderAlignment BamMultiReaderPrivate::OpenReader(const string& filename, bool* ok) {
+
+    // clear status flag
+    *ok = false;
 
-    // create new BamReader
+    // create new BamReader & BamAlignment
     BamReader* reader = new BamReader;
+    BamAlignment* alignment = new BamAlignment;
 
     // if reader opens OK
     if ( reader->Open(filename) ) {
 
-        // attempt to read first alignment (sanity check)
-        // if ok, then return BamReader pointer
-        BamAlignment al;
-        if ( reader->GetNextAlignmentCore(al) )
-            return reader;
+        // if first alignment reads OK
+        if ( LoadNextAlignment(reader, alignment) ) {
+            *ok = true;
+            return make_pair(reader, alignment);
+        }
 
         // could not read alignment
         else {
@@ -554,7 +541,8 @@ BamReader* BamMultiReaderPrivate::OpenReader(const std::string& filename) {
     // if we get here, there was a problem with this BAM file (opening or reading)
     // clean up memory allocation & return null pointer
     delete reader;
-    return 0;
+    delete alignment;
+    return ReaderAlignment();
 }
 
 // print associated filenames to stdout
@@ -566,6 +554,33 @@ void BamMultiReaderPrivate::PrintFilenames(void) const {
         cout << (*filenameIter) << endl;
 }
 
+bool BamMultiReaderPrivate::PopNextCachedAlignment(BamAlignment& al, const bool needCharData) {
+
+    // bail out if no more data to process
+    if ( !HasAlignmentData() )
+        return false;
+
+    // pop next reader/alignment pair
+    ReaderAlignment nextReaderAlignment = m_alignments->TakeFirst();
+    BamReader*    reader    = nextReaderAlignment.first;
+    BamAlignment* alignment = nextReaderAlignment.second;
+
+    // store cached alignment into destination parameter (by copy)
+    al = *alignment;
+
+    // set char data if requested
+    if ( needCharData ) {
+        al.BuildCharData();
+        al.Filename = reader->GetFilename();
+    }
+
+    // load next alignment from reader & store in cache
+    SaveNextAlignment(reader, alignment);
+
+    // return success
+    return true;
+}
+
 // returns BAM file pointers to beginning of alignment data & resets alignment cache
 bool BamMultiReaderPrivate::Rewind(void) {
 
@@ -604,17 +619,9 @@ bool BamMultiReaderPrivate::RewindReaders(void) {
 
 void BamMultiReaderPrivate::SaveNextAlignment(BamReader* reader, BamAlignment* alignment) {
 
-    // must be in core mode && NOT sorting by read name to call GNACore()
-    if ( m_isCoreMode && m_sortOrder != BamMultiReader::SortedByReadName ) {
-        if ( reader->GetNextAlignmentCore(*alignment) )
-            m_alignments->Add( make_pair(reader, alignment) );
-    }
-
-    // not in core mode and/or sorting by readname, must call GNA()
-    else {
-        if ( reader->GetNextAlignment(*alignment) )
-            m_alignments->Add( make_pair(reader, alignment) );
-    }
+    // if can read alignment from reader, store in cache
+    if ( LoadNextAlignment(reader, alignment) )
+        m_alignments->Add( make_pair(reader, alignment) );
 }
 
 // sets the index caching mode on the readers
@@ -703,10 +710,6 @@ void BamMultiReaderPrivate::UpdateAlignmentCache(void) {
     // clear the cache
     m_alignments->Clear();
 
-    // seed cache with fully-populated alignments
-    // further updates will fill with full/core-only as requested
-    m_isCoreMode = false;
-
     // iterate over readers
     vector<ReaderAlignment>::iterator readerIter = m_readers.begin();
     vector<ReaderAlignment>::iterator readerEnd  = m_readers.end();

diff --git a/src/api/internal/BamMultiReader_p.h b/src/api/internal/BamMultiReader_p.h
index b34fb0c583eb016167846d2cf937e14cab669c01..33048eb61f11638b8686e607e83efbafe5c96dab 100644 (file)
--- a/src/api/internal/BamMultiReader_p.h
+++ b/src/api/internal/BamMultiReader_p.h
@@ -1,9 +1,8 @@
 // ***************************************************************************
 // BamMultiReader_p.h (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 13 March 2011 (DB)
+// Last modified: 9 September 2011 (DB)
 // ---------------------------------------------------------------------------
 // Functionality for simultaneously reading multiple BAM files
 // *************************************************************************
@@ -33,6 +32,10 @@ class IBamMultiMerger;
 
 class BamMultiReaderPrivate {
 
+    // typedefs
+    public:
+        typedef std::pair<BamReader*, BamAlignment*> ReaderAlignment;
+
     // constructor / destructor
     public:
         BamMultiReaderPrivate(void);
@@ -78,21 +81,19 @@ class BamMultiReaderPrivate {
         IBamMultiMerger* CreateMergerForCurrentSortOrder(void) const;
         const std::string ExtractReadGroup(const std::string& headerLine) const;
         bool HasAlignmentData(void) const;
-        bool LoadNextAlignment(BamAlignment& al);
-        BamTools::BamReader* OpenReader(const std::string& filename);
+        bool LoadNextAlignment(BamReader* reader, BamAlignment* alignment);
+        ReaderAlignment OpenReader(const std::string& filename, bool* ok);
+        bool PopNextCachedAlignment(BamAlignment& al, const bool needCharData);
         bool RewindReaders(void);
-        void SaveNextAlignment(BamTools::BamReader* reader, BamTools::BamAlignment* alignment);
+        void SaveNextAlignment(BamReader* reader, BamAlignment* alignment);
         const std::vector<std::string> SplitHeaderText(const std::string& headerText) const;
         void UpdateAlignmentCache(void);
         void ValidateReaders(void) const;
 
     // data members
-    public:
-        typedef std::pair<BamReader*, BamAlignment*> ReaderAlignment;
+    public:        
         std::vector<ReaderAlignment> m_readers;
-
         IBamMultiMerger* m_alignments;
-        bool m_isCoreMode;
         BamMultiReader::SortOrder m_sortOrder;
 };
 

diff --git a/src/api/internal/BamRandomAccessController_p.cpp b/src/api/internal/BamRandomAccessController_p.cpp
index 9187b3a0025a919ab8932b7c28d723f7ae5da3e9..a44563f5489952fb13a1f0e7d8fc0cac35db1b8c 100644 (file)
--- a/src/api/internal/BamRandomAccessController_p.cpp
+++ b/src/api/internal/BamRandomAccessController_p.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // BamRandomAccessController_p.cpp (c) 2011 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 5 April 2011(DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/internal/BamRandomAccessController_p.h b/src/api/internal/BamRandomAccessController_p.h
index 372ea4a5e9a300dfc24ff2e2f4ea7ccdac92f21a..86af28c26cbd36efda32f1fde8ec58580927086d 100644 (file)
--- a/src/api/internal/BamRandomAccessController_p.h
+++ b/src/api/internal/BamRandomAccessController_p.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // BamRandomAccessController_p.h (c) 2011 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 24 February 2011(DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/internal/BamReader_p.cpp b/src/api/internal/BamReader_p.cpp
index e4e2310bb451b0490f6086cb5f88ced80060f7aa..384e2fe59d50b5912b6bb2091a413813dd6339ae 100644 (file)
--- a/src/api/internal/BamReader_p.cpp
+++ b/src/api/internal/BamReader_p.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // BamReader_p.cpp (c) 2009 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 10 May 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/internal/BamReader_p.h b/src/api/internal/BamReader_p.h
index c0d07d88a863d84efa81c96328e70778de892cf9..2901e54d2edca656d77810322672c0c0ae08aa76 100644 (file)
--- a/src/api/internal/BamReader_p.h
+++ b/src/api/internal/BamReader_p.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // BamReader_p.h (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 5 April 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/internal/BamStandardIndex_p.cpp b/src/api/internal/BamStandardIndex_p.cpp
index 6d8273e9c1477a965aebb0bea553026014c90d4a..b92c47b287c0b10a13ed1309131188bba2f5b5ef 100644 (file)
--- a/src/api/internal/BamStandardIndex_p.cpp
+++ b/src/api/internal/BamStandardIndex_p.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // BamStandardIndex.cpp (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 24 June 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/internal/BamStandardIndex_p.h b/src/api/internal/BamStandardIndex_p.h
index 7123ae72a0dda76234541a4e7f8671ef6fae812c..3fbc7772404c26cfa3a440c204c293c9a7ae69d8 100644 (file)
--- a/src/api/internal/BamStandardIndex_p.h
+++ b/src/api/internal/BamStandardIndex_p.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // BamStandardIndex.h (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 24 June 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/internal/BamToolsIndex_p.cpp b/src/api/internal/BamToolsIndex_p.cpp
index 05d43275e1c307372481eb559004a741ff81fa88..f6e05ceab0cc96e84e8a96ab924d89743825820c 100644 (file)
--- a/src/api/internal/BamToolsIndex_p.cpp
+++ b/src/api/internal/BamToolsIndex_p.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // BamToolsIndex.cpp (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 27 April 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/internal/BamToolsIndex_p.h b/src/api/internal/BamToolsIndex_p.h
index 16aef8c9afd85e23ea1b946d0009b9274034e5e0..269792ed979152e09131a232d512b83dd35aa523 100644 (file)
--- a/src/api/internal/BamToolsIndex_p.h
+++ b/src/api/internal/BamToolsIndex_p.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // BamToolsIndex.h (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 5 April 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/internal/BamWriter_p.cpp b/src/api/internal/BamWriter_p.cpp
index 8f1b167d26e42a021c934071cd1b5899d175b261..c9199b9a7b7859dfbfd4b0ef48f0de8aa58dc0f3 100644 (file)
--- a/src/api/internal/BamWriter_p.cpp
+++ b/src/api/internal/BamWriter_p.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // BamWriter_p.cpp (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 16 June 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/internal/BamWriter_p.h b/src/api/internal/BamWriter_p.h
index dd2b0fe1178ce8c2c52a9b2b4b0406ba9a81c122..caa440eaee91e777f760c35ae7505e5ab6729644 100644 (file)
--- a/src/api/internal/BamWriter_p.h
+++ b/src/api/internal/BamWriter_p.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // BamWriter_p.h (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 24 February 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/internal/BgzfStream_p.cpp b/src/api/internal/BgzfStream_p.cpp
index 4db9b15e25bbda89cec73ce2a0b4f17d8eabba5c..3b7074950031b7e0a92fd1c653348a69b2e63174 100644 (file)
--- a/src/api/internal/BgzfStream_p.cpp
+++ b/src/api/internal/BgzfStream_p.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // BgzfStream_p.cpp (c) 2011 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 9 September 2011(DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/internal/BgzfStream_p.h b/src/api/internal/BgzfStream_p.h
index 04b6c34b88c0d122e3bc43f966b1cbafc4d39108..f7ea268b8de25cbda9ab88ad3728ac6957bac874 100644 (file)
--- a/src/api/internal/BgzfStream_p.h
+++ b/src/api/internal/BgzfStream_p.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // BgzfStream_p.h (c) 2011 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 5 April 2011(DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/internal/SamFormatParser_p.cpp b/src/api/internal/SamFormatParser_p.cpp
index 316f75f73b5d49522297937588264ea5b4c8156e..1431b7a2753a49095b6974db528963cf41f29a5c 100644 (file)
--- a/src/api/internal/SamFormatParser_p.cpp
+++ b/src/api/internal/SamFormatParser_p.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // SamFormatParser.cpp (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 19 April 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/internal/SamFormatParser_p.h b/src/api/internal/SamFormatParser_p.h
index daabe394f3b440b43cc98ffa2b5ba41427f6a2c1..cf6d54c08069a53e8bcf0c391a3045a71cec64bd 100644 (file)
--- a/src/api/internal/SamFormatParser_p.h
+++ b/src/api/internal/SamFormatParser_p.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // SamFormatParser.h (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 23 December 2010 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/internal/SamFormatPrinter_p.cpp b/src/api/internal/SamFormatPrinter_p.cpp
index 1e670b0155be479d88d9ed6d21b1c406600313af..df13fe55b9419cfc1eb19aee3ec9c68b8c4eb274 100644 (file)
--- a/src/api/internal/SamFormatPrinter_p.cpp
+++ b/src/api/internal/SamFormatPrinter_p.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // SamFormatPrinter.cpp (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 19 April 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/internal/SamFormatPrinter_p.h b/src/api/internal/SamFormatPrinter_p.h
index 5e28e9717c7d6a030b1f82e1968c742a433a5643..8250db660cab02e545f4fbbc505a4083a1b6064b 100644 (file)
--- a/src/api/internal/SamFormatPrinter_p.h
+++ b/src/api/internal/SamFormatPrinter_p.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // SamFormatPrinter.h (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 23 December 2010 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/internal/SamHeaderValidator_p.cpp b/src/api/internal/SamHeaderValidator_p.cpp
index 7ecec2ca90c5fc3f201cdd7e95943d8950a02c0c..936da49c04bf13ae431ee01f875f1eab450cdeb6 100644 (file)
--- a/src/api/internal/SamHeaderValidator_p.cpp
+++ b/src/api/internal/SamHeaderValidator_p.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // SamHeaderValidator.cpp (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 18 April 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/internal/SamHeaderValidator_p.h b/src/api/internal/SamHeaderValidator_p.h
index 06a82abeaa04d9ee1043ba89f47c41703ed12160..1fc1644dd5e1033019724bff5826e2218e246c24 100644 (file)
--- a/src/api/internal/SamHeaderValidator_p.h
+++ b/src/api/internal/SamHeaderValidator_p.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // SamHeaderValidator.h (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 13 January 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/api/internal/SamHeaderVersion_p.h b/src/api/internal/SamHeaderVersion_p.h
index 256401739ece8c3db2713f5b60a1eb212902ac23..d166ca2e5fcc2b869226477ef9a252cecf71ee7d 100644 (file)
--- a/src/api/internal/SamHeaderVersion_p.h
+++ b/src/api/internal/SamHeaderVersion_p.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // SamHeaderVersion.h (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 24 February 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/shared/bamtools_global.h b/src/shared/bamtools_global.h
index 6380bb07afe145decd3c13602685c724f9bf1d66..1b2a8af7834f7445d193f2bff5d14fb75ac22fe6 100644 (file)
--- a/src/shared/bamtools_global.h
+++ b/src/shared/bamtools_global.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_global.h (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 3 March 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/toolkit/bamtools.cpp b/src/toolkit/bamtools.cpp
index 1230e04986c4ccb66c29b58cc879b312b60dcd6f..97c032f6f70586382e10955de24f4bbf8d270e5d 100644 (file)
--- a/src/toolkit/bamtools.cpp
+++ b/src/toolkit/bamtools.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools.cpp (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 18 May 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/toolkit/bamtools_convert.cpp b/src/toolkit/bamtools_convert.cpp
index f3bc486d85df74f7abb956e7d65ce8b03c801a85..991cebce7512c625896cfc0f7ee62a44ce36222b 100644 (file)
--- a/src/toolkit/bamtools_convert.cpp
+++ b/src/toolkit/bamtools_convert.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_convert.cpp (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 11 June 2011
 // ---------------------------------------------------------------------------

diff --git a/src/toolkit/bamtools_convert.h b/src/toolkit/bamtools_convert.h
index 8dd685728b38e6b8f02f5bf86faec75983721f8d..9cc3b897269a3d8861a470f01c3b308a3a1ad51a 100644 (file)
--- a/src/toolkit/bamtools_convert.h
+++ b/src/toolkit/bamtools_convert.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_convert.h (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 9 July 2010
 // ---------------------------------------------------------------------------
@@ -35,4 +34,4 @@ class ConvertTool : public AbstractTool {
   
 } // namespace BamTools
 
-#endif // BAMTOOLS_CONVERT_H
\ No newline at end of file
+#endif // BAMTOOLS_CONVERT_H

diff --git a/src/toolkit/bamtools_count.cpp b/src/toolkit/bamtools_count.cpp
index c17b25776df476a1317cef2218b8693202a27b47..3c46f679d93c2e2860af15b3439cbb5d7ec936c3 100644 (file)
--- a/src/toolkit/bamtools_count.cpp
+++ b/src/toolkit/bamtools_count.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_count.cpp (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 7 April 2011
 // ---------------------------------------------------------------------------

diff --git a/src/toolkit/bamtools_count.h b/src/toolkit/bamtools_count.h
index d9c3c3d486fbc6834471ac6a4c36a611d2fec803..553f9b0d174959013eba38fac35c91cce0bc3577 100644 (file)
--- a/src/toolkit/bamtools_count.h
+++ b/src/toolkit/bamtools_count.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_count.h (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 7 April 2011
 // ---------------------------------------------------------------------------

diff --git a/src/toolkit/bamtools_coverage.cpp b/src/toolkit/bamtools_coverage.cpp
index c3eaa20451e1d382faad52bb4b2497f6cba9dd8b..c0ecd8f455034c0b3918b5f83be33b637e1f6326 100644 (file)
--- a/src/toolkit/bamtools_coverage.cpp
+++ b/src/toolkit/bamtools_coverage.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_coverage.cpp (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 7 April 2011
 // ---------------------------------------------------------------------------

diff --git a/src/toolkit/bamtools_coverage.h b/src/toolkit/bamtools_coverage.h
index e9e8a712d3277ed28b8c067bcdc94948cd4db540..a542ec2cb29b6436864ecf015c4633a7a6685577 100644 (file)
--- a/src/toolkit/bamtools_coverage.h
+++ b/src/toolkit/bamtools_coverage.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_coverage.h (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 1 August 2010
 // ---------------------------------------------------------------------------

diff --git a/src/toolkit/bamtools_filter.cpp b/src/toolkit/bamtools_filter.cpp
index 9ea3660d9874a09bbac6d5d151f5c0af974654d9..baf28167b1ecd8a2b1246002be92fe388bcaa585 100644 (file)
--- a/src/toolkit/bamtools_filter.cpp
+++ b/src/toolkit/bamtools_filter.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_filter.cpp (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 7 April 2011
 // ---------------------------------------------------------------------------

diff --git a/src/toolkit/bamtools_filter.h b/src/toolkit/bamtools_filter.h
index 4d125c971df9d7de6de60651dfd81dba074ccc82..7fa5f73d99add8916b7ca08384a49a58bd222723 100644 (file)
--- a/src/toolkit/bamtools_filter.h
+++ b/src/toolkit/bamtools_filter.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_filter.h (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 28 August 2010
 // ---------------------------------------------------------------------------

diff --git a/src/toolkit/bamtools_header.cpp b/src/toolkit/bamtools_header.cpp
index 984ddd47d5d5f23acd4061c86159b1c98725c8b7..a08c632defa5bbbce75609f040e03d7a536c28da 100644 (file)
--- a/src/toolkit/bamtools_header.cpp
+++ b/src/toolkit/bamtools_header.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_header.cpp (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 7 April 2011
 // ---------------------------------------------------------------------------

diff --git a/src/toolkit/bamtools_header.h b/src/toolkit/bamtools_header.h
index 7b5f100c96368693477771903d7c317cdb8e8d6f..7e59d6836f21ef14b898f742f7ceb2feee295ae9 100644 (file)
--- a/src/toolkit/bamtools_header.h
+++ b/src/toolkit/bamtools_header.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_header.h (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 7 April 2011
 // ---------------------------------------------------------------------------

diff --git a/src/toolkit/bamtools_index.cpp b/src/toolkit/bamtools_index.cpp
index c1bd2e55fb2cd07b753e17aef15a9439fdb21300..ef0e76519e70e7de36926a774a450e549463e85b 100644 (file)
--- a/src/toolkit/bamtools_index.cpp
+++ b/src/toolkit/bamtools_index.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_index.cpp (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 7 April 2011
 // ---------------------------------------------------------------------------

diff --git a/src/toolkit/bamtools_index.h b/src/toolkit/bamtools_index.h
index 11cc057c2f0cdfedea1626b142e597a319f8800e..a6707410ad052062126c245f70de6635546f3f44 100644 (file)
--- a/src/toolkit/bamtools_index.h
+++ b/src/toolkit/bamtools_index.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_index.h (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 7 April 2011
 // ---------------------------------------------------------------------------

diff --git a/src/toolkit/bamtools_merge.cpp b/src/toolkit/bamtools_merge.cpp
index 7cfc0990a83f4da8910d972c16ee95b9edd5495e..1e8312f063b2444de61bc6ef6810c07d49508cbf 100644 (file)
--- a/src/toolkit/bamtools_merge.cpp
+++ b/src/toolkit/bamtools_merge.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_merge.cpp (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 7 April 2011
 // ---------------------------------------------------------------------------

diff --git a/src/toolkit/bamtools_merge.h b/src/toolkit/bamtools_merge.h
index b1c2e1fcb718094872a0884e70240054f70f4684..cab851c5d2f308274b792cd52ea774b03bcc4c09 100644 (file)
--- a/src/toolkit/bamtools_merge.h
+++ b/src/toolkit/bamtools_merge.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_merge.h (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 7 April 2011
 // ---------------------------------------------------------------------------

diff --git a/src/toolkit/bamtools_random.cpp b/src/toolkit/bamtools_random.cpp
index 927349e062730f0082659ef4fd6555df64d25c7f..e28ea70962088578ddb27989c25f996925185f11 100644 (file)
--- a/src/toolkit/bamtools_random.cpp
+++ b/src/toolkit/bamtools_random.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_random.cpp (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 7 April 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/toolkit/bamtools_random.h b/src/toolkit/bamtools_random.h
index 688ab5c23150f6b879c1174587e2afd5352a5778..ce70b86ec677bd90c21dd33c9f37652097cfb156 100644 (file)
--- a/src/toolkit/bamtools_random.h
+++ b/src/toolkit/bamtools_random.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_random.h (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 7 April 2010 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/toolkit/bamtools_resolve.cpp b/src/toolkit/bamtools_resolve.cpp
index 8be405fa8b2a49a12bb77eb91b5e46d0f6fbf8f5..9a1a3b023680f04e80c246fe3461a0027bfda2e0 100644 (file)
--- a/src/toolkit/bamtools_resolve.cpp
+++ b/src/toolkit/bamtools_resolve.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_resolve.cpp (c) 2011
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 6 July 2011
 // ---------------------------------------------------------------------------

diff --git a/src/toolkit/bamtools_resolve.h b/src/toolkit/bamtools_resolve.h
index 681a557de4a801dd07d7f91dea4d1af9e68a55c0..f90dec049bbec6ab7195dbaea91a98a0bbcc4993 100644 (file)
--- a/src/toolkit/bamtools_resolve.h
+++ b/src/toolkit/bamtools_resolve.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_resolve.h (c) 2011 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 23 June 2011
 // ---------------------------------------------------------------------------

diff --git a/src/toolkit/bamtools_revert.cpp b/src/toolkit/bamtools_revert.cpp
index c751ce4f6be05363568fb8813fbf76c5888ae554..ba0debef68d953f09b86328c76d20cf306fc939f 100644 (file)
--- a/src/toolkit/bamtools_revert.cpp
+++ b/src/toolkit/bamtools_revert.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_revert.cpp (c) 2010 Derek Barnett, Alistair Ward
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 7 April 2011
 // ---------------------------------------------------------------------------

diff --git a/src/toolkit/bamtools_revert.h b/src/toolkit/bamtools_revert.h
index 4b2a24cdb0f1e2a9ca5c06737eb07bc0aa9941f5..7aa270d21434354f50be82c61a02bcec52a4f5cd 100644 (file)
--- a/src/toolkit/bamtools_revert.h
+++ b/src/toolkit/bamtools_revert.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_revert.h (c) 2010 Derek Barnett, Alistair Ward
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 7 April 2011
 // ---------------------------------------------------------------------------

diff --git a/src/toolkit/bamtools_sort.cpp b/src/toolkit/bamtools_sort.cpp
index dd6d9519061cacb7058883356a088a88ab256541..fb181a8b7566abd8b47b0574c78a0b332a84319c 100644 (file)
--- a/src/toolkit/bamtools_sort.cpp
+++ b/src/toolkit/bamtools_sort.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_sort.cpp (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 14 June 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/toolkit/bamtools_sort.h b/src/toolkit/bamtools_sort.h
index fe0ed5d30708009108afb2eb628e4415d7c531ec..d746f5e3d1797d939f7c7e2f954669d1fff06a1b 100644 (file)
--- a/src/toolkit/bamtools_sort.h
+++ b/src/toolkit/bamtools_sort.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_sort.h (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 7 April 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/toolkit/bamtools_split.cpp b/src/toolkit/bamtools_split.cpp
index bfbf303e4d2259275dbc800d475311034c3e1ceb..4575d8596cc9c1dc8b808e8690f3ca2bfbb2d08d 100644 (file)
--- a/src/toolkit/bamtools_split.cpp
+++ b/src/toolkit/bamtools_split.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_split.cpp (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 7 April 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/toolkit/bamtools_split.h b/src/toolkit/bamtools_split.h
index 776037cfc677c4ef05e9da2f1b16202624d1902a..a294f4f6615e5e4921aea7607a2661168bc4ab9a 100644 (file)
--- a/src/toolkit/bamtools_split.h
+++ b/src/toolkit/bamtools_split.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_split.h (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 7 April 2011 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/toolkit/bamtools_stats.cpp b/src/toolkit/bamtools_stats.cpp
index f66c462d34e2a43cbadf1c8b2cdf012778055f52..eb57a95c4a1abb1981ca86bb182020a290afe1db 100644 (file)
--- a/src/toolkit/bamtools_stats.cpp
+++ b/src/toolkit/bamtools_stats.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_cpp (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 7 April 2011
 // ---------------------------------------------------------------------------

diff --git a/src/toolkit/bamtools_stats.h b/src/toolkit/bamtools_stats.h
index 799befe70b328d73eab0cb83999e31ce27a70040..29cc99800945409b6c382bd5ec63463761a1380e 100644 (file)
--- a/src/toolkit/bamtools_stats.h
+++ b/src/toolkit/bamtools_stats.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_stats.h (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 7 April 2011
 // ---------------------------------------------------------------------------

diff --git a/src/toolkit/bamtools_tool.h b/src/toolkit/bamtools_tool.h
index 816c8c5cb5338b82205e8753101b3772b13b9477..f14d460c05c8a5f80121e06345a20eefb2391153 100644 (file)
--- a/src/toolkit/bamtools_tool.h
+++ b/src/toolkit/bamtools_tool.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_tool.h (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 2 June 2010
 // ---------------------------------------------------------------------------

diff --git a/src/toolkit/bamtools_version.h.in b/src/toolkit/bamtools_version.h.in
index aa7c06ad50d0d2bd12e1c9ead8b315b2a6032488..325314cfe5a703286a29a56fdcc970d6d0bd670c 100644 (file)
--- a/src/toolkit/bamtools_version.h.in
+++ b/src/toolkit/bamtools_version.h.in
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_version.h.in (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 19 November 2010 (DB)
 // ---------------------------------------------------------------------------

diff --git a/src/utils/bamtools_fasta.cpp b/src/utils/bamtools_fasta.cpp
index f6434d344041b154c9f182499bbdb62d2e6350a8..2e7a784d9f606684d7854ba2eb1b7cef7cb60032 100644 (file)
--- a/src/utils/bamtools_fasta.cpp
+++ b/src/utils/bamtools_fasta.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_fasta.cpp (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 13 July 2010
 // ---------------------------------------------------------------------------

diff --git a/src/utils/bamtools_fasta.h b/src/utils/bamtools_fasta.h
index d0ae8e4a38a5173a65fa08475865c06a7b899485..5cf85b356761f0bc6b0830bfa83f13bee05846f9 100644 (file)
--- a/src/utils/bamtools_fasta.h
+++ b/src/utils/bamtools_fasta.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_fasta.h (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 19 November 2010
 // ---------------------------------------------------------------------------

diff --git a/src/utils/bamtools_filter_engine.h b/src/utils/bamtools_filter_engine.h
index 9ea1e8d2138823cf22363a54f7ff6f0206d04721..ae1415d8e90e9b37907277e21ee2e821e4f33a2d 100644 (file)
--- a/src/utils/bamtools_filter_engine.h
+++ b/src/utils/bamtools_filter_engine.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_filter_engine.h (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 19 November 2010
 // ---------------------------------------------------------------------------

diff --git a/src/utils/bamtools_filter_properties.h b/src/utils/bamtools_filter_properties.h
index 9de3e275fe9055d42a6508167c996783fd5ac235..c810ba24c5a20b47570a73f13890ca79801ccd68 100644 (file)
--- a/src/utils/bamtools_filter_properties.h
+++ b/src/utils/bamtools_filter_properties.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_filter_properties.h (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 19 November 2010
 // ---------------------------------------------------------------------------

diff --git a/src/utils/bamtools_filter_ruleparser.h b/src/utils/bamtools_filter_ruleparser.h
index 3ad2bfa5332c9a34149a5262137ec1a92c5e5bb1..07328cb4b89e5852e395516358f9fb0f2328c798 100644 (file)
--- a/src/utils/bamtools_filter_ruleparser.h
+++ b/src/utils/bamtools_filter_ruleparser.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_filter_ruleparser.h (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 19 November 2010
 // ---------------------------------------------------------------------------

diff --git a/src/utils/bamtools_options.cpp b/src/utils/bamtools_options.cpp
index 157357f66d778201371ddbc748b484f3578ee007..359018b3b788f14d5ef277644061999a6907051a 100644 (file)
--- a/src/utils/bamtools_options.cpp
+++ b/src/utils/bamtools_options.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_options.cpp (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 11 June 2011
 // ---------------------------------------------------------------------------

diff --git a/src/utils/bamtools_options.h b/src/utils/bamtools_options.h
index 98ddc3d36c29e9f784509e4d88c2af194757d2bc..b49fd535a432f47eb64a82b053a681e794fdfcfb 100644 (file)
--- a/src/utils/bamtools_options.h
+++ b/src/utils/bamtools_options.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_options.h (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 11 June 2011
 // ---------------------------------------------------------------------------

diff --git a/src/utils/bamtools_pileup_engine.cpp b/src/utils/bamtools_pileup_engine.cpp
index bc0e7c85e832b0bfa49c703fe6e09e45df74ca12..e0a0ea98c5cbddbda7582b4675382eebba93cdbf 100644 (file)
--- a/src/utils/bamtools_pileup_engine.cpp
+++ b/src/utils/bamtools_pileup_engine.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_pileup_engine.cpp (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 19 November 2010
 // ---------------------------------------------------------------------------

diff --git a/src/utils/bamtools_pileup_engine.h b/src/utils/bamtools_pileup_engine.h
index 6900dc94cb6f86d071dc9f0b76655e93e9a38184..24d70849e16fd1ab8eccb137dd15573f853d80b0 100644 (file)
--- a/src/utils/bamtools_pileup_engine.h
+++ b/src/utils/bamtools_pileup_engine.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_pileup_engine.h (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 18 September 2010
 // ---------------------------------------------------------------------------

diff --git a/src/utils/bamtools_utilities.cpp b/src/utils/bamtools_utilities.cpp
index 1d5e00d3a5f62ef419667e38df90971295987fb5..f79faacfaec80917b6e6cc726794563d7ea76c7a 100644 (file)
--- a/src/utils/bamtools_utilities.cpp
+++ b/src/utils/bamtools_utilities.cpp
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_utilities.cpp (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 9 June 2011
 // ---------------------------------------------------------------------------

diff --git a/src/utils/bamtools_utilities.h b/src/utils/bamtools_utilities.h
index 71d46830df6667895a3ad8a1fcc02fa2652b7784..d9a319271c1da6e856325cacc7371e20cc0a978a 100644 (file)
--- a/src/utils/bamtools_utilities.h
+++ b/src/utils/bamtools_utilities.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_utilities.h (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 8 September 2011
 // ---------------------------------------------------------------------------

diff --git a/src/utils/bamtools_variant.h b/src/utils/bamtools_variant.h
index 116a2c0addf6c06ff48cddfc62ef795e69e3d8ca..020b3363baa1a316d4bea7a6fa75e1901c7a953f 100644 (file)
--- a/src/utils/bamtools_variant.h
+++ b/src/utils/bamtools_variant.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // bamtools_variant.h (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 19 November 2010
 // ---------------------------------------------------------------------------

diff --git a/src/utils/utils_global.h b/src/utils/utils_global.h
index 8aa2826ba3c1139797e365937e2ca96a91c791d3..c793e8c832800463e9fa7fe0ad4199ee15523522 100644 (file)
--- a/src/utils/utils_global.h
+++ b/src/utils/utils_global.h
@@ -1,7 +1,6 @@
 // ***************************************************************************
 // utils_global.h (c) 2010 Derek Barnett
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
 // Last modified: 19 November 2010 (DB)
 // ---------------------------------------------------------------------------