.clang-format

+BasedOnStyle:  Google
+BreakBeforeBraces: Mozilla
+
+AllowShortLoopsOnASingleLine: false
+AccessModifierOffset: -4
+BreakConstructorInitializersBeforeComma: true
+ColumnLimit: 100
+IndentWidth: 4
+PointerAlignment: Left
+DerivePointerAlignment: false
+TabWidth: 4
+
+ReflowComments: false  # protect ASCII art in comments
+KeepEmptyLinesAtTheStartOfBlocks: true

.gitignore

 make/Config.mk
 *.o
 *.d
-build/
+build*/
 .project
 .cproject
 .settings
@@ -9,3 +9,8 @@ ConsensusCore.xcodeproj
 *~
 bin/
 obj/
+/.p4config
+
+# Meson WrapDB stuff
+subprojects/packagecache/
+subprojects/googletest*

Makefile

@@ -15,7 +15,7 @@ include make/Defs.mk
 all: lib
 
 lib:
-	${MAKE} -f make/Cpp.mk
+	${MAKE} -f make/Cpp.mk -j8
 
 #
 # SWIG targets

README.md

@@ -36,3 +36,7 @@ client tools to use the ``libConsensusCore.so``, the library needs to
 be copied to the bin/{Debug,Release} directory for every assembly that
 transitively depends on ConsensusCore and creates an executable.  You
 can do this using a pre-build rule.
+
+DISCLAIMER
+----------
+THIS WEBSITE AND CONTENT AND ALL SITE-RELATED SERVICES, INCLUDING ANY DATA, ARE PROVIDED "AS IS," WITH ALL FAULTS, WITH NO REPRESENTATIONS OR WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTIES OF MERCHANTABILITY, SATISFACTORY QUALITY, NON-INFRINGEMENT OR FITNESS FOR A PARTICULAR PURPOSE. YOU ASSUME TOTAL RESPONSIBILITY AND RISK FOR YOUR USE OF THIS SITE, ALL SITE-RELATED SERVICES, AND ANY THIRD PARTY WEBSITES OR APPLICATIONS. NO ORAL OR WRITTEN INFORMATION OR ADVICE SHALL CREATE A WARRANTY OF ANY KIND. ANY REFERENCES TO SPECIFIC PRODUCTS OR SERVICES ON THE WEBSITES DO NOT CONSTITUTE OR IMPLY A RECOMMENDATION OR ENDORSEMENT BY PACIFIC BIOSCIENCES.

bamboo_build.sh

+#!/usr/bin/env bash
+set -vex
+
+################
+# DEPENDENCIES #
+################
+
+## Load modules
+type module >& /dev/null || . /mnt/software/Modules/current/init/bash
+
+module purge
+
+module load meson
+module load ninja
+
+module load gcc
+module load ccache
+
+module load boost
+
+module load gtest
+module load python/2
+module load swig
+
+
+BOOST_ROOT="${BOOST_ROOT%/include}"
+# unset these variables to have meson discover all
+# boost-dependent variables from BOOST_ROOT alone
+unset BOOST_INCLUDEDIR
+unset BOOST_LIBRARYDIR
+
+export CXX="ccache g++"
+export CCACHE_BASEDIR="${PWD}"
+
+if [[ $USER == bamboo ]]; then
+  export CCACHE_DIR=/mnt/secondary/Share/tmp/bamboo.${bamboo_shortPlanKey}.ccachedir
+  export CCACHE_TEMPDIR=/scratch/bamboo.ccache_tempdir
+fi
+
+export ENABLED_TESTS="true"
+
+source scripts/ci/setup.sh
+source scripts/ci/build.sh
+source scripts/ci/test.sh

configure

 #!/usr/bin/env bash
 
-CPP_ABI=c++98
+CPP_STD=c++14
 
 usage ()
 {
@@ -10,7 +10,7 @@ usage ()
     echo "            [--swig=SWIG]                      # location of swig executable"
     echo "            [--swig-lib=SWIG_LIB]              # location of swig library"
     echo "            [--debug]                          # build debug library (1)"
-    echo "            [--c++11]                          # build using C++11 ABI"
+    echo "            [--c++98]                          # build using old C++98 standard"
     echo
     echo "    (Python only:)"
     echo "            [--python-include=PYTHON_INCLUDE]  # location of Python.h"
@@ -71,8 +71,8 @@ while test x$1 != x; do
         --debug)
             DEBUG=1
             ;;
-        --c++11)
-            CPP_ABI=c++11
+        --c++98)
+            CPP_STD=c++98
             ;;
         --python-include=*)
             PYTHON_INCLUDE=`echo $1 | sed 's/--python-include=//'`
@@ -115,7 +115,7 @@ echo "    SWIG_LIB       = $SWIG_LIB"
 echo "    PYTHON_INCLUDE = $PYTHON_INCLUDE"
 echo "    NUMPY_INCLUDE  = $NUMPY_INCLUDE"
 echo "    DEBUG          = $DEBUG"
-echo "    CPP_ABI        = $CPP_ABI"
+echo "    CPP_STD        = $CPP_STD"
 echo
 
 echo > make/Config.mk
@@ -125,4 +125,4 @@ echo "SWIG_LIB:=$SWIG_LIB"             >> make/Config.mk
 echo "PYTHON_INCLUDE:=$PYTHON_INCLUDE" >> make/Config.mk
 echo "NUMPY_INCLUDE:=$NUMPY_INCLUDE"   >> make/Config.mk
 echo "DEBUG?=$DEBUG"                   >> make/Config.mk
-echo "CPP_ABI:=$CPP_ABI"               >> make/Config.mk
+echo "CPP_STD:=$CPP_STD"               >> make/Config.mk

debian/changelog

+consensuscore (1.1.1+dfsg-1) unstable; urgency=medium
+
+  * Team upload
+  * New upstream release
+  * Exclude precompiled binaries
+  * Standards-Version: 4.2.1
+
+ -- Andreas Tille <tille@debian.org>  Tue, 09 Oct 2018 17:43:54 +0200
+
 consensuscore (1.0.2-3) unstable; urgency=medium
 
   * Team upload.

debian/control

@@ -17,7 +17,7 @@ Build-Depends: debhelper (>= 11~),
                python3-setuptools,
                python3-all-dev,
                python3-numpy
-Standards-Version: 4.1.5
+Standards-Version: 4.2.1
 Vcs-Browser: https://salsa.debian.org/med-team/consensuscore
 Vcs-Git: https://salsa.debian.org/med-team/consensuscore.git
 Homepage: https://github.com/PacificBiosciences/ConsensusCore

debian/copyright

-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: ConsensusCore
 Upstream-Contact: Pacific Biosciences <devnet@pacificbiosciences.com>
 Source: https://github.com/PacificBiosciences/ConsensusCore
+Files-Excluded: */clang-format*
 
 Files: *
 Copyright: 2011-2015 Pacific Biosciences <devnet@pacificbiosciences.com>

debian/patches/compiler-flags.patch

@@ -3,10 +3,10 @@ Description: Honor CPPFLAGS, CXXFLAGS, and LDFLAGS
 Author: Afif Elghraoui <afif@ghraoui.name>
 Forwarded: https://github.com/PacificBiosciences/ConsensusCore/pull/5
 Last-Update: 2015-09-02
---- consensuscore.orig/make/Defs.mk
-+++ consensuscore/make/Defs.mk
-@@ -53,8 +53,8 @@
-     CXX_STRICT_FLAGS    = $(CXX_FLAGS) -pedantic -std=$(CPP_ABI) -Wall
+--- a/make/Defs.mk
++++ b/make/Defs.mk
+@@ -53,8 +53,8 @@ else
+     CXX_STRICT_FLAGS    = $(CXX_FLAGS) -pedantic -std=$(CPP_STD) -Wall
  endif
  
 -CXX             = $(CCACHE) $(GXX) $(MACHINE) $(CXX_FLAGS) $(INCLUDES) -isystem $(BOOST)

debian/patches/gcc-6.patch

@@ -2,10 +2,10 @@ Description: Remove -isystem flag to fix build on GCC-6
 Author: Afif Elghraoui <afif@debian.org>
 Forwarded: no
 Last-Update: 2016-07-16
---- consensuscore.orig/make/Defs.mk
-+++ consensuscore/make/Defs.mk
-@@ -53,8 +53,8 @@
-     CXX_STRICT_FLAGS    = $(CXX_FLAGS) -pedantic -std=$(CPP_ABI) -Wall
+--- a/make/Defs.mk
++++ b/make/Defs.mk
+@@ -53,8 +53,8 @@ else
+     CXX_STRICT_FLAGS    = $(CXX_FLAGS) -pedantic -std=$(CPP_STD) -Wall
  endif
  
 -CXX             = $(CCACHE) $(GXX) $(MACHINE) $(CPPFLAGS) $(CXXFLAGS) $(CXX_FLAGS) $(INCLUDES) -isystem $(BOOST) $(LDFLAGS)
@@ -15,9 +15,9 @@ Last-Update: 2016-07-16
  
  ifeq ($(UNAME), Darwin)
      SHLIB_FLAGS = -shared -undefined dynamic_lookup
---- consensuscore.orig/make/Tests.mk
-+++ consensuscore/make/Tests.mk
-@@ -27,7 +27,7 @@
+--- a/make/Tests.mk
++++ b/make/Tests.mk
+@@ -27,7 +27,7 @@ $(TEST_OBJS): CXX_OPT_FLAGS := $(CXX_OPT
  
  $(TEST_OBJS): $(TEST_BUILD_ROOT)/%.o : %.cpp $(CXX_LIB)
  	-mkdir -p $(TEST_BUILD_ROOT)

debian/watch

-version=3
+version=4
 
-opts="filenamemangle=s/(?:.*)?v?(\d[\d\.]*)\.tar\.gz/python-pbconsensuscore-$1.tar.gz/" \
-         https://github.com/PacificBiosciences/ConsensusCore/releases (?:.*/)?v?(\d[\d\.]*)\.tar\.gz
+opts="repacksuffix=+dfsg,dversionmangle=auto,repack,compression=xz" \
+         https://github.com/PacificBiosciences/ConsensusCore/releases .*/archive/v?@ANY_VERSION@@ARCHIVE_EXT@

external/meson.build

+####################
+# external headers #
+####################
+
+quiver_include_directories += include_directories('.')

include/ConsensusCore/Align/AffineAlignment.hpp

-// Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
-//
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted (subject to the limitations in the
-// disclaimer below) provided that the following conditions are met:
-//
-//  * Redistributions of source code must retain the above copyright
-//    notice, this list of conditions and the following disclaimer.
-//
-//  * Redistributions in binary form must reproduce the above
-//    copyright notice, this list of conditions and the following
-//    disclaimer in the documentation and/or other materials provided
-//    with the distribution.
-//
-//  * Neither the name of Pacific Biosciences nor the names of its
-//    contributors may be used to endorse or promote products derived
-//    from this software without specific prior written permission.
-//
-// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
-// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
-// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
-// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
-// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
-// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
-// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
-// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
-// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
-// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
-// SUCH DAMAGE.
-
 // Author: David Alexander
 
 //
@@ -48,39 +13,37 @@ namespace ConsensusCore {
 
 class PairwiseAlignment;
 
-    struct AffineAlignmentParams {
+struct AffineAlignmentParams
+{
     float MatchScore;
     float MismatchScore;
     float GapOpen;
     float GapExtend;
     float PartialMatchScore;
 
-        AffineAlignmentParams(float matchScore,
-                              float mismatchScore,
-                              float gapOpen,
-                              float gapExtend,
+    AffineAlignmentParams(float matchScore, float mismatchScore, float gapOpen, float gapExtend,
                           float partialMatchScore = 0);
 };
 
 AffineAlignmentParams DefaultAffineAlignmentParams();
 AffineAlignmentParams IupacAwareAffineAlignmentParams();
 
-
 //
 // Affine gap-penalty alignment.
 //
-    PairwiseAlignment* AlignAffine(const std::string& target,
-                                   const std::string& query,
+PairwiseAlignment* AlignAffine(
+    const std::string& target, const std::string& query,
     AffineAlignmentParams params = DefaultAffineAlignmentParams());  // NOLINT
 
 //
-    // Affine gap-penalty alignment with partial awareness of IUPAC ambiguous bases---
+// Affine gap-penalty alignment with partial awareness of IUPAC ambiguous
+// bases---
 // half-penalizes partial mismatches.  For example:  (M = IUPAC A/C)
 //   T->A = -1,
 //   T->M = -1,
 //   A->M = -0.5
 //
-    PairwiseAlignment* AlignAffineIupac(const std::string& target,
-                                        const std::string& query,
+PairwiseAlignment* AlignAffineIupac(
+    const std::string& target, const std::string& query,
     AffineAlignmentParams params = IupacAwareAffineAlignmentParams());  // NOLINT
 }

include/ConsensusCore/Align/AlignConfig.hpp

-// Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
-//
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted (subject to the limitations in the
-// disclaimer below) provided that the following conditions are met:
-//
-//  * Redistributions of source code must retain the above copyright
-//    notice, this list of conditions and the following disclaimer.
-//
-//  * Redistributions in binary form must reproduce the above
-//    copyright notice, this list of conditions and the following
-//    disclaimer in the documentation and/or other materials provided
-//    with the distribution.
-//
-//  * Neither the name of Pacific Biosciences nor the names of its
-//    contributors may be used to endorse or promote products derived
-//    from this software without specific prior written permission.
-//
-// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
-// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
-// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
-// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
-// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
-// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
-// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
-// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
-// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
-// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
-// SUCH DAMAGE.
-
 // Author: David Alexander
 
 #pragma once
@@ -41,30 +6,28 @@ namespace ConsensusCore {
 //
 // Scoring params for Needleman-Wunsch or Smith-Waterman style aligners
 //
-    struct AlignParams {
+struct AlignParams
+{
     int Match;
     int Mismatch;
     int Insert;
     int Delete;
 
-        AlignParams(int match,
-                    int mismatch,
-                    int insert,
-                    int delete_);
+    AlignParams(int match, int mismatch, int insert, int delete_);
 
     // Edit distance params
     static AlignParams Default();
 };
 
-
-    enum AlignMode {
+enum AlignMode
+{
     GLOBAL = 0,      // Global in both sequences
     SEMIGLOBAL = 1,  // Global in query, local in target
     LOCAL = 2        // Local in both sequences
 };
 
-
-    struct AlignConfig {
+struct AlignConfig
+{
     AlignParams Params;
     AlignMode Mode;
 

include/ConsensusCore/Align/LinearAlignment.hpp

-// Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
-//
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted (subject to the limitations in the
-// disclaimer below) provided that the following conditions are met:
-//
-//  * Redistributions of source code must retain the above copyright
-//    notice, this list of conditions and the following disclaimer.
-//
-//  * Redistributions in binary form must reproduce the above
-//    copyright notice, this list of conditions and the following
-//    disclaimer in the documentation and/or other materials provided
-//    with the distribution.
-//
-//  * Neither the name of Pacific Biosciences nor the names of its
-//    contributors may be used to endorse or promote products derived
-//    from this software without specific prior written permission.
-//
-// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
-// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
-// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
-// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
-// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
-// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
-// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
-// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
-// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
-// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
-// SUCH DAMAGE.
-
 // Author: David Alexander
 
 //
@@ -49,13 +14,9 @@ namespace ConsensusCore {
 
 class PairwiseAlignment;
 
-    PairwiseAlignment* AlignLinear(const std::string& target,
-                                   const std::string& query,
+PairwiseAlignment* AlignLinear(const std::string& target, const std::string& query,
                                AlignConfig config = AlignConfig::Default());
 
-    PairwiseAlignment* AlignLinear(const std::string& target,
-                                   const std::string& query,
-                                   int* score,
+PairwiseAlignment* AlignLinear(const std::string& target, const std::string& query, int* score,
                                AlignConfig config = AlignConfig::Default());
-
 }

include/ConsensusCore/Align/PairwiseAlignment.hpp

-// Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
-//
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted (subject to the limitations in the
-// disclaimer below) provided that the following conditions are met:
-//
-//  * Redistributions of source code must retain the above copyright
-//    notice, this list of conditions and the following disclaimer.
-//
-//  * Redistributions in binary form must reproduce the above
-//    copyright notice, this list of conditions and the following
-//    disclaimer in the documentation and/or other materials provided
-//    with the distribution.
-//
-//  * Neither the name of Pacific Biosciences nor the names of its
-//    contributors may be used to endorse or promote products derived
-//    from this software without specific prior written permission.
-//
-// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
-// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
-// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
-// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
-// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
-// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
-// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
-// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
-// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
-// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
-// SUCH DAMAGE.
-
 // Author: David Alexander
 
 #pragma once
@@ -46,23 +11,23 @@ namespace {
 
 // Utility functions common to implementations of aligners
 
-    inline int Max3(int a, int b, int c)
-    {
-        return std::max((a), std::max((b), (c)));
-    }
+inline int Max3(int a, int b, int c) { return std::max((a), std::max((b), (c))); }
 
 inline int ArgMax3(int a, int b, int c)
 {
-        if      (a >= b && a >= c) return 0;
-        else if (b >= c)           return 1;
-        else                       return 2;
+    if (a >= b && a >= c)
+        return 0;
+    else if (b >= c)
+        return 1;
+    else
+        return 2;
 }
 }
 
-
 namespace ConsensusCore {
 /// \brief A pairwise alignment
-    class PairwiseAlignment {
+class PairwiseAlignment
+{
 private:
     std::string target_;
     std::string query_;
@@ -88,27 +53,21 @@ namespace ConsensusCore {
     int Length() const;
 
 public:
-        PairwiseAlignment(const std::string& target,
-                          const std::string& query);
+    PairwiseAlignment(const std::string& target, const std::string& query);
 
     static PairwiseAlignment* FromTranscript(const std::string& transcript,
                                              const std::string& unalnTarget,
                                              const std::string& unalnQuery);
 };
 
-
-    PairwiseAlignment* Align(const std::string& target,
-                             const std::string& query,
-                             int* score,
+PairwiseAlignment* Align(const std::string& target, const std::string& query, int* score,
                          AlignConfig config = AlignConfig::Default());
 
-    PairwiseAlignment* Align(const std::string& target,
-                             const std::string& query,
+PairwiseAlignment* Align(const std::string& target, const std::string& query,
                          AlignConfig config = AlignConfig::Default());
 
-
-
-    // These calls return an array, same len as target, containing indices into the query string.
+// These calls return an array, same len as target, containing indices into the
+// query string.
 std::vector<int> TargetToQueryPositions(const std::string& transcript);
 std::vector<int> TargetToQueryPositions(const PairwiseAlignment& aln);
 }

include/ConsensusCore/Checksum.hpp

-// Copyright (c) 2011-2014, Pacific Biosciences of California, Inc.
-//
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted (subject to the limitations in the
-// disclaimer below) provided that the following conditions are met:
-//
-//  * Redistributions of source code must retain the above copyright
-//    notice, this list of conditions and the following disclaimer.
-//
-//  * Redistributions in binary form must reproduce the above
-//    copyright notice, this list of conditions and the following
-//    disclaimer in the documentation and/or other materials provided
-//    with the distribution.
-//
-//  * Neither the name of Pacific Biosciences nor the names of its
-//    contributors may be used to endorse or promote products derived
-//    from this software without specific prior written permission.
-//
-// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
-// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
-// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
-// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
-// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
-// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
-// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
-// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
-// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
-// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
-// SUCH DAMAGE.
-
 // Author: David Alexander
 
 #include <string>
@@ -41,7 +6,8 @@
 
 namespace ConsensusCore {
 
-    class Checksum {
+class Checksum
+{
 public:
     static std::string Of(const QvSequenceFeatures& f);
 };

include/ConsensusCore/Coverage.hpp

-
-// Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
-//
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted (subject to the limitations in the
-// disclaimer below) provided that the following conditions are met:
-//
-//  * Redistributions of source code must retain the above copyright
-//    notice, this list of conditions and the following disclaimer.
-//
-//  * Redistributions in binary form must reproduce the above
-//    copyright notice, this list of conditions and the following
-//    disclaimer in the documentation and/or other materials provided
-//    with the distribution.
-//
-//  * Neither the name of Pacific Biosciences nor the names of its
-//    contributors may be used to endorse or promote products derived
-//    from this software without specific prior written permission.
-//
-// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
-// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
-// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
-// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
-// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
-// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
-// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
-// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
-// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
-// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
-// SUCH DAMAGE.
-
 // Author: David Alexander
 
 #pragma once
 
-#include <vector>
 #include <utility>
+#include <vector>
 
 #include <ConsensusCore/Interval.hpp>
 #include <ConsensusCore/Types.hpp>
 
-namespace ConsensusCore
-{
+namespace ConsensusCore {
 // These APIs are a little more awkward than I'd have liked---see
 // "winLen" instead of winEnd.  Had to contort a bit to get SWIG
 // bindings working well.
 
-    void CoverageInWindow(int  tStartDim,
-                          int* tStart,
-                          int  tEndDim,
-                          int* tEnd,
-                          int  winStart,
-                          int  winLen,
+void CoverageInWindow(int tStartDim, int* tStart, int tEndDim, int* tEnd, int winStart, int winLen,
                       int* coverage);
 
-    std::vector<Interval> CoveredIntervals(int  minCoverage,
-                                           int  tStartDim,
-                                           int* tStart,
-                                           int  tEndDim,
-                                           int* tEnd,
-                                           int  winStart,
-                                           int  winLen);
+std::vector<Interval> CoveredIntervals(int minCoverage, int tStartDim, int* tStart, int tEndDim,
+                                       int* tEnd, int winStart, int winLen);
 }

include/ConsensusCore/Edna/EdnaConfig.hpp

-// Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
-//
-// All rights reserved.
-//
-// Redistribution and use in source and binary forms, with or without
-// modification, are permitted (subject to the limitations in the
-// disclaimer below) provided that the following conditions are met:
-//
-//  * Redistributions of source code must retain the above copyright
-//    notice, this list of conditions and the following disclaimer.
-//
-//  * Redistributions in binary form must reproduce the above
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-//    with the distribution.
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-//    from this software without specific prior written permission.
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-
 // Author: David Alexander
 
 #pragma once
 
 #include <vector>
 
-namespace ConsensusCore
-{
+namespace ConsensusCore {
 /// \brief A parameter vector for analysis using the QV model
 struct EdnaModelParams
 {
@@ -54,15 +18,10 @@ namespace ConsensusCore
     // named parameters. However if the user forgets to set one of
     // the parameters, trouble!
 
-        EdnaModelParams(std::vector<float> pStay,
-                        std::vector<float> pMerge,
-                        std::vector<float> moveDists,
-                        std::vector<float> stayDists)
-            : pStay_(pStay)
-            , pMerge_(pMerge)
-            , moveDists_(moveDists)
-            , stayDists_(stayDists)
-        {}
+    EdnaModelParams(std::vector<float> pStay, std::vector<float> pMerge,
+                    std::vector<float> moveDists, std::vector<float> stayDists)
+        : pStay_(pStay), pMerge_(pMerge), moveDists_(moveDists), stayDists_(stayDists)
+    {
+    }
 };
 }
-