Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille · Andreas Tille
--- a/.gitmodules
+++ b/.gitmodules
-[submodule "pbbam"]
-	path = pbbam
-	url = ../pbbam.git
-	branch = master
-[submodule "googletest"]
-	path = googletest
-	url = https://github.com/google/googletest.git
-	branch = master
--- a/.travis.yml
+++ b/.travis.yml
-language: cpp
-script: 
-  - ./travis.sh
-compiler:
-  - gcc
-# - clang
-install:
- if [ "$CXX" = "g++" ]; then export CXX="g++-4.8" CC="gcc-4.8"; fi
-addons:
-  apt:
-    sources:
-    - ubuntu-toolchain-r-test
-    packages:
-    - gcc-4.8
-    - g++-4.8
-#   - clang
-#   - libhdf5-serial-1.8.4
-notifications:
-  email: false
-sudo: false
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
-##############################################
-# CMake build script for the BLASRLIBCPP library
-##############################################
-
-cmake_policy(SET CMP0048 NEW)
-project(BLASRLIBCPP VERSION 5.3.0 LANGUAGES CXX C)
-cmake_minimum_required(VERSION 3.6)
-
-set(ROOT_PROJECT_NAME ${PROJECT_NAME} CACHE STRING "root project name")
-
-# Build type
-IF(NOT CMAKE_BUILD_TYPE)
-    SET(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build, options are: Debug Release Profile RelWithDebInfo ReleaseWithAssert" FORCE)
-ENDIF(NOT CMAKE_BUILD_TYPE)
-
-# Main project paths
-set(BLASRLIBCPP_RootDir ${BLASRLIBCPP_SOURCE_DIR})
-
-# Project configuration
-set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR}/cmake ${CMAKE_MODULE_PATH})
-
-# Fixed order, do not sort or shuffle
-include(blasrlibcpp-ccache)
-include(blasrlibcpp-releasewithassert)
-include(blasrlibcpp-dependencies)
-include(blasrlibcpp-compilerflags)
-include(blasrlibcpp-gitsha1)
-
-file(WRITE pbdata/LibBlasrConfig.h "")
-
-GET_PROPERTY(BLASRLIBCPP_COMPIPLE_FLAGS GLOBAL PROPERTY BLASRLIBCPP_COMPIPLE_FLAGS_GLOBAL)
-GET_PROPERTY(BLASRLIBCPP_LINK_FLAGS GLOBAL PROPERTY BLASRLIBCPP_LINK_FLAGS_GLOBAL)
-GET_PROPERTY(HDF5_LINKER_FLAG_LOCAL GLOBAL PROPERTY HDF5_LINKER_FLAG_GLOBAL)
-
-set(LOCAL_LINKER_FLAGS "${HDF5_LINKER_FLAG_LOCAL} ${BLASRLIBCPP_LINK_FLAGS}")
-
-# libcpp library
-file(GLOB HDF5_CPP "${BLASRLIBCPP_RootDir}/hdf/*.cpp")
-file(GLOB_RECURSE ALIGNMENT_CPP "${BLASRLIBCPP_RootDir}/alignment/*.cpp")
-file(GLOB_RECURSE PBDATA_CPP "${BLASRLIBCPP_RootDir}/pbdata/*.cpp")
-
-add_library(libcpp
-    ${HDF5_CPP}
-    ${ALIGNMENT_CPP}
-    ${PBDATA_CPP}
-)
-
-target_include_directories(libcpp PUBLIC
-    ${BLASRLIBCPP_RootDir}/hdf
-    ${BLASRLIBCPP_RootDir}/alignment
-    ${BLASRLIBCPP_RootDir}/pbdata
-    ${HDF5_INCLUDE_DIRS}
-    ${PacBioBAM_INCLUDE_DIRS}
-)
-
-target_link_libraries(libcpp ${PacBioBAM_LIBRARIES})
-
-set_target_properties(libcpp PROPERTIES COMPILE_FLAGS ${BLASRLIBCPP_COMPIPLE_FLAGS})
-if (LOCAL_LINKER_FLAGS)
-    set_target_properties(libcpp PROPERTIES LINK_FLAGS ${LOCAL_LINKER_FLAGS})
-endif()
-
-# Tests
-enable_testing()
-
-## build gtest
-add_subdirectory(${BLASRLIBCPP_RootDir}/googletest/googletest external/gtest)
-
-## build libcpp tests
-file(GLOB_RECURSE TEST_CPP "${BLASRLIBCPP_RootDir}/unittest/*/*.cpp")
-
-add_executable(libcpptest ${TEST_CPP})
-target_include_directories(libcpptest PUBLIC ${BLASRLIBCPP_RootDir}/unittest)
-target_link_libraries(libcpptest gtest_main libcpp hdf5 hdf5_cpp ${ZLIB_LDFLAGS})
-add_test(libcpptest libcpptest)
-
-set_target_properties(libcpptest PROPERTIES COMPILE_FLAGS "${BLASRLIBCPP_COMPIPLE_FLAGS}")
-
-if (LOCAL_LINKER_FLAGS)
-    set_target_properties(libcpptest PROPERTIES LINK_FLAGS ${LOCAL_LINKER_FLAGS})
-endif()
-
-add_custom_target(check_libcpp
-    COMMAND libcpptest --gtest_output=xml:${CMAKE_BINARY_DIR}/libcpp-unit.xml
-    WORKING_DIRECTORY ${BLASRLIBCPP_RootDir})
--- a/DEVELOPER.md
+++ b/DEVELOPER.md
-# Developer environment
-
-## Clang-format pre commit hook
-
-### What?
-The intention here is to get source code formatting automatically
-checked and guaranteed before checkin.
-
-### Why?
- Automate style-guide compliance to avoid squabbles
- Post-checkin reformatting binges mess up history.  It's best to get
-  it right from the get-go.
-
-
-### How?
-See the tools:
-  - `tools/check-formatting --staged` for fast style-checking of
-    changed files, in a git commit/push hook;
-  - `tools/check-formatting --all` for slower style-checking of everything
-  - `tools/format-all`to format everything
-
-To enable the checking as a pre-commit hook, place the following in
-`.git/hooks/pre-commit` (and make that file executable):
-
-```sh
-#!/bin/bash
-./tools/check-formatting --staged
-```
-
-### Tips
- We should *not* reformat bundled third-party code as it will make it
-  difficult to diff with upstream.  Put such code in a subdirectory
-  with its own .clang-format file containing: "BasedOnStyle: None" to
-  disable formatting.
-
- If clang-format mangles something (for example, a comment block with
-  ASCII art or significant whitespace), you can protect a block using
-  `// clang-format off` and then `// clang-format on`.
-
-* What are these binaries?
-  The `clang-format` binaries that are checked in are static builds of
-  clang-format v3.9 from https://github.com/angular/clang-format.
-  They are bundled because the LLVM toolchain has a reputation for
-  rapid change and incompatibility.  We want to guarantee that devs
-  are using the same version as CI is.
--- a/LICENSE
+++ b/LICENSE
-```
-// Copyright (c) 2014-2015, 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.
+Copyright (c) 2014-2018, 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.

 See pbdata/MD5Utils.* for the following:
 /*
@@ -96,5 +95,3 @@ See alignment/algorithms/sorting/qsufsort.cpp for the following:
   distributed, the copyright notice must be retained and any alterations in
   the code must be clearly marked. No warranty is given regarding the quality
   of this software.*/
-
-```
--- a/README.md
+++ b/README.md
-[![Build Status](https://travis-ci.org/PacificBiosciences/blasr_libcpp.svg?branch=master)](https://travis-ci.org/PacificBiosciences/blasr_libcpp)
+<h1 align="center"><img src="http://www.pacb.com/wp-content/themes/pacific-biosciences/img/pacific-biosciences-logo-mobile.svg"/></h1>
+<h1 align="center">blasr_libcpp</h1>
+<p align="center">A C++ library for blasr</p>

-#What is blasr_libcpp#
+***
+
+## Availability
+This library is part of blasr and latest version can be installed via bioconda package `blasr`.
+
+Please refer to our [official pbbioconda page](https://github.com/PacificBiosciences/pbbioconda)
+for information on Installation, Support, License, Copyright, and Disclaimer.
+
+# What is blasr_libcpp

 **Blasr_libcpp** is a *library* used by **blasr** and other executables such as samtoh5, loadPulses for analyzing PacBio sequences. This library contains three sub-libraries, including pbdata, hdf and alignment:
 + pbdata
@@ -10,41 +20,6 @@
 + alignment
   - contains source code for aligning Pacbio reads to target sequences used in blasr and builds ```libblasr```.

-For more information, see
-* https://github.com/PacificBiosciences/blasr_libcpp/wiki
-
-## Building using make
-The simplest way is:
-```
-NOPBBAM=1 ./configure.py
-make -j all
-```
-That will skip pbbam, and it will download HDF5 headers.
-
-## Building using cmake
-
-Make sure that you are using cmake >=3.7 and
-always start from an empty build subdirectory!
-
-    git clone git://github.com/PacificBiosciences/blasr_libcpp.git && cd blasr_libcpp
-    git submodule update --init --remote
-    mkdir build && cd build
-    cmake -GNinja .. && ninja check_libcpp
-
-Is your HDF5 in a custom location?
-
-    cmake -GNinja -DHDF5_ROOT=/your/location/hdf-1.8.16 ..
-
-Are HDF$ libraries and include folders in different locations?
-
-    cmake -GNinja -DHDF5_LIBRARIES=/your/location/hdf-1.8.16/lib
-                  -DHDF5_INCLUDE_DIRS=/other/location/hdf-1.8.16/include ..
-
-Prefer a custom libz implementation?
-
-    cmake -GNinja -DZLIB_INCLUDE_DIRS=/your/location/zlib/include \
-                  -DZLIB_LIBRARIES=/your/location/zlib/libz.so ..
-
 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.
--- a/alignment/build.mk
+++ b/alignment/build.mk
-makefile
\ No newline at end of file
--- a/alignment/format/BAMPrinterImpl.hpp
+++ b/alignment/format/BAMPrinterImpl.hpp
@@ -72,7 +72,6 @@ void AlignmentToBamRecord(T_AlignmentCandidate &alignment, T_Sequence &read, T_S
            exit(-1);
        }
        bamRecord.Impl().SetSequenceAndQualities(seqString, alignedSequence.qual.ToString());
-        bamRecord.Impl().CigarData(cigar);
        bamRecord.Impl().Bin(0);
        bamRecord.Impl().InsertSize(0);
        bamRecord.Impl().MapQuality(static_cast<uint8_t>(alignment.mapQV));
@@ -134,6 +133,7 @@ void AlignmentToBamRecord(T_AlignmentCandidate &alignment, T_Sequence &read, T_S
            tags["dt"] = deletionTags;
        }
        bamRecord.Impl().Tags(tags);
+        bamRecord.Impl().CigarData(cigar);
    } else {
        // The following code can be used to hard-clip reads, if needed.
        // PacBio::BAM::Position clipStart = read.bamRecord.QueryStart() + alignment.QAlignStart();

--- a/alignment/makefile
+++ b/alignment/makefile
-all:
-
-THISDIR:=$(dir $(realpath $(lastword $(MAKEFILE_LIST))))
-include ${CURDIR}/defines.mk
-include ${THISDIR}/../rules.mk
-
-CXXOPTS  := -std=c++14 -pedantic -Wno-long-long -Wall -Wextra -Wno-overloaded-virtual
-SYSINCLUDES = ${HDF5_INC} ${PBBAM_INC} ${BOOST_INC}
-LIBS     += ${LIBPBDATA_LIB} ${LIBPBIHDF_LIB} ${HDF5_LIB} ${PBBAM_LIB} ${ZLIB_LIB}
-LDFLAGS  += $(patsubst %,-L%,${LIBS})
-LDLIBS += -lpbdata $(HTSLIB_LIBS)
-
-ifeq (${nohdf},)
-  LDLIBS+= -lpbihdf
-  #LDFLAGS+= -flat_namespace # so we do not need LDLIBS+= -lhdf5 -lhdf5_cpp
-endif
-# We might also need some -l* for pbbam, etc.
-
-all: static shared
-static: libblasr.a
-shared: libblasr${SH_LIB_EXT}
-
-paths := . simulator format files utils tuples statistics qvs suffixarray \
-	datastructures/alignment datastructures/alignmentset datastructures/anchoring datastructures/tuplelists \
-	algorithms/alignment algorithms/alignment/sdp algorithms/anchoring algorithms/compare algorithms/sorting \
-	query
-paths := ${paths} $(patsubst %,${THISDIR}%,${paths})
-sources := $(shell find ${THISDIR} -name '*.cpp')
-
-ifdef nohdf
-sources := $(filter-out ${THISDIR}files/% ${THISDIR}utils/FileOfFileNames.cpp ${THISDIR}format/SAMHeaderPrinter.cpp, $(sources))
-endif
-
-sources := $(notdir ${sources})
-objects := $(sources:.cpp=.o)
-shared_objects := $(sources:.cpp=.shared.o)
-dependencies := $(objects:.o=.d) $(shared_objects:.o=.d)
-
-vpath %.cpp ${paths}
-
-libblasr.a: $(objects)
-	$(AR) $(ARFLAGS) $@ $^
-
-libblasr${SH_LIB_EXT}: $(shared_objects)
-
-clean: 
-	rm -f libblasr.a libblasr.so *.o *.d
-
-include $(dependencies)
-depend: $(dependencies:.d=.depend)
--- a/cmake/blasrlibcpp-ccache.cmake
+++ b/cmake/blasrlibcpp-ccache.cmake
-
-find_program(CCACHE_FOUND ccache)
-if(CCACHE_FOUND)
-    set_property(GLOBAL PROPERTY RULE_LAUNCH_COMPILE ccache)
-    set_property(GLOBAL PROPERTY RULE_LAUNCH_LINK    ccache)
-endif()
--- a/cmake/blasrlibcpp-compilerflags.cmake
+++ b/cmake/blasrlibcpp-compilerflags.cmake
-
-include(CheckCXXCompilerFlag)
-
-# shared CXX flags for all source code & tests
-SET_PROPERTY(GLOBAL PROPERTY BLASRLIBCPP_COMPIPLE_FLAGS_GLOBAL "-pedantic -g -Wno-long-long -Wall -Wextra -Wno-return-type -Wno-overloaded-virtual -Wno-unused-parameter -Wno-div-by-zero -Wno-unused-variable -Wno-unused-local-typedefs -DUSE_PBBAM")
-set(CMAKE_CXX_STANDARD          14)
-set(CMAKE_CXX_STANDARD_REQUIRED ON)
-set(CMAKE_CXX_EXTENSIONS OFF)
-
-# static linking
-IF(${CMAKE_SYSTEM_NAME} MATCHES "Linux")
-    set(BLASRLIBCPP_LINKER_FLAGS "${BLASRLIBCPP_LINKER_FLAGS} -static-libstdc++")
-ENDIF()
-
-if (HDF5_INCLUDE_DIR)
-    message(FATAL_ERROR "Please specify HDF5_INCLUDE_DIRS not HDF5_INCLUDE_DIR!")
-endif()
-if (HDF5_LIBRARY)
-    message(FATAL_ERROR "Please specify HDF5_LIBRARIES not HDF5_LIBRARY!")
-endif()
-
-if (NOT HDF5_INCLUDE_DIRS OR NOT HDF5_LIBRARIES)
-    find_package(HDF5 REQUIRED)
-    if (HDF5_ROOT)
-        SET_PROPERTY(GLOBAL PROPERTY HDF5_LINKER_FLAG_GLOBAL "-L${HDF5_ROOT}/lib")
-    endif()
-else()
-    SET_PROPERTY(GLOBAL PROPERTY HDF5_LINKER_FLAG_GLOBAL "-L${HDF5_LIBRARIES}")
-    find_library(HDF5_LIBRARIES_     hdf5    ${HDF5_LIBRARIES} NO_CMAKE_SYSTEM_PATH)
-    find_library(HDF5_CPP_LIBRARIES hdf5_cpp ${HDF5_LIBRARIES} NO_CMAKE_SYSTEM_PATH)
-endif()
-
-if (NOT "${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
-    set(BLASRLIBCPP_LINKER_FLAGS "${BLASRLIBCPP_LINKER_FLAGS} -lrt")
-endif()
-
-SET_PROPERTY(GLOBAL PROPERTY BLASRLIBCPP_LINK_FLAGS_GLOBAL ${BLASRLIBCPP_LINKER_FLAGS})
--- a/cmake/blasrlibcpp-dependencies.cmake
+++ b/cmake/blasrlibcpp-dependencies.cmake
-
-# External libraries
-
-# Boost
-if(NOT Boost_INCLUDE_DIRS)
-    find_package(Boost REQUIRED)
-endif()
-
-# Threads
-if (NOT Threads)
-    find_package(Threads REQUIRED)
-endif()
-
-# ZLIB
-if (NOT ZLIB_INCLUDE_DIRS OR NOT ZLIB_LIBRARIES)
-    find_package(PkgConfig REQUIRED)
-    pkg_check_modules(ZLIB zlib)
-else()
-    set(ZLIB_LDFLAGS ${ZLIB_LIBRARIES})
-endif()
-
-
-# pbbam
-if (NOT PacBioBAM_INCLUDE_DIRS OR
-    NOT PacBioBAM_LIBRARIES)
-    set(PacBioBAM_build_docs    OFF CACHE INTERNAL "" FORCE)
-    set(PacBioBAM_build_tests   OFF CACHE INTERNAL "" FORCE)
-    set(PacBioBAM_build_tools   OFF CACHE INTERNAL "" FORCE)
-    add_subdirectory(${BLASRLIBCPP_RootDir}/pbbam external/pbbam/build)
-endif()
--- a/cmake/blasrlibcpp-gitsha1.cmake
+++ b/cmake/blasrlibcpp-gitsha1.cmake
-
-if(__find_git_sha1)
-    return()
-endif()
-set(__find_git_sha1 YES)
-
-function(find_git_sha1 _GIT_SHA1)
-    find_package(Git QUIET REQUIRED)
-    execute_process(COMMAND
-        "${GIT_EXECUTABLE}" "describe" "--always" "--dirty=-dirty"
-        WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
-        RESULT_VARIABLE res
-        OUTPUT_VARIABLE out
-        ERROR_QUIET
-        OUTPUT_STRIP_TRAILING_WHITESPACE)
-    if (NOT res EQUAL 0)
-        message(FATAL_ERROR "Could not determine git sha1 via `git describe --always --dirty=*`")
-    endif()
-    set(${_GIT_SHA1} "${out}" PARENT_SCOPE)
-endfunction()
--- a/cmake/blasrlibcpp-releasewithassert.cmake
+++ b/cmake/blasrlibcpp-releasewithassert.cmake
-string(REGEX REPLACE "[/-][dD][^/-]*NDEBUG" "" CMAKE_C_FLAGS_RELEASEWITHASSERT_INIT "${CMAKE_C_FLAGS_RELEASE_INIT}")
-string(REGEX REPLACE "[/-][dD][^/-]*NDEBUG" "" CMAKE_CXX_FLAGS_RELEASEWITHASSERT_INIT "${CMAKE_CXX_FLAGS_RELEASE_INIT}")
-set(CMAKE_C_FLAGS_RELEASEWITHASSERT "${CMAKE_C_FLAGS_RELEASEWITHASSERT_INIT}" CACHE STRING "C flags for release with assert builds.")
-set(CMAKE_CXX_FLAGS_RELEASEWITHASSERT "${CMAKE_CXX_FLAGS_RELEASEWITHASSERT_INIT}" CACHE STRING "C++ flags for release with assert builds.")
-set(CMAKE_EXE_LINKER_FLAGS_RELEASEWITHASSERT "" CACHE STRING "Linker flags for release with assert builds.")
-mark_as_advanced(CMAKE_CXX_FLAGS_RELEASEWITHASSERT CMAKE_C_FLAGS_RELEASEWITHASSERT)
\ No newline at end of file
--- a/configure.py
+++ b/configure.py
-#!/usr/bin/env python
-"""Configure the build.
-
- Fetch HDF5 headers.
- Create pbdata/LibBlasrConfig.h
- Create defines.mk
-
-Putting LibBlasrConfig.h into a src-dir is not ideal, but simplifies a lot.
-
-This is not used by './unittest/'.
-"""
-import commands
-import contextlib
-import os
-import sys
-
-thisdir = os.path.dirname(os.path.abspath(__file__))
-
-def log(msg):
-    sys.stderr.write(msg)
-    sys.stderr.write('\n')
-
-def shell(cmd):
-    log(cmd)
-    status, output = commands.getstatusoutput(cmd)
-    if status:
-        raise Exception('%d <- %r' %(status, cmd))
-    return output
-
-def update_content(fn, content):
-    direc = os.path.abspath(os.path.dirname(fn))
-    if not os.path.isdir(direc):
-        shell('mkdir -p %s' %direc)
-    current_content = open(fn).read() if os.path.exists(fn) else None
-    if content != current_content:
-        log('writing to %r' %fn)
-        log('"""\n' + content + '"""')
-        open(fn, 'w').write(content)
-
-def compose_libconfig(pbbam=False):
-    if pbbam:
-        content = """
-#define USE_PBBAM
-"""
-    else:
-        content = """
-"""
-    return content
-
-def compose_defines_with_hdf(HDF5_INC, HDF5_LIB):
-    """We have to use := for HDF5_LIB b/c blasr
-    is using it to mean the directory, not the file,
-    and it's in the environment.
-    """
-    return """
-HDF5_INC:=%(HDF5_INC)s
-HDF5_LIB:=%(HDF5_LIB)s
-LIBPBDATA_INC     ?=../pbdata
-LIBPBIHDF_INC     ?=../hdf
-LIBBLASR_INC      ?=../alignment
-LIBPBDATA_LIB     ?=../pbdata
-LIBPBIHDF_LIB     ?=../hdf
-LIBBLASR_LIB      ?=../alignment
-"""%(dict(
-    thisdir=thisdir,
-    HDF5_INC=HDF5_INC,
-    HDF5_LIB=HDF5_LIB))
-
-
-def compose_defines_with_hdf_headers(HDF_HEADERS):
-    return """
-HDF_HEADERS:=%(HDF_HEADERS)s
-#HDF5_INC  ?=${HDF_HEADERS}/src
-CPPFLAGS+= -I${HDF_HEADERS}/src -I${HDF_HEADERS}/c++/src
-LIBPBDATA_LIB     ?=../pbdata/
-LIBPBIHDF_LIB     ?=../hdf/
-LIBBLASR_LIB      ?=../alignment/
-"""%(dict(thisdir=thisdir, HDF_HEADERS=HDF_HEADERS))
-
-def compose_defines():
-    """
-    Note that our local 'hdf' subdir will not even build
-    in this case.
-    """
-    return """
-LIBPBDATA_INC ?=../pbdata
-LIBPBIHDF_INC ?=../hdf
-LIBBLASR_INC  ?=../alignment
-LIBPBDATA_LIB ?=%(thisdir)s/pbdata/
-LIBPBIHDF_LIB ?=%(thisdir)s/hdf/
-LIBBLASR_LIB  ?=%(thisdir)s/alignment/
-nohdf         ?=1
-"""%(dict(thisdir=thisdir))
-
-def get_OS_STRING():
-    G_BUILDOS_CMD = """bash -c 'set -e; set -o pipefail; id=$(lsb_release -si | tr "[:upper:]" "[:lower:]"); rel=$(lsb_release -sr); case $id in ubuntu) printf "$id-%04d\n" ${rel/./};; centos) echo "$id-${rel%%.*}";; *) echo "$id-$rel";; esac' 2>/dev/null"""
-    return shell(G_BUILDOS_CMD)
-
-def get_PBBAM(env, prefix):
-    """
-    key = 'PBBAM'
-    if key in env:
-        return env[key]
-    cmd = 'cd $(THIRD_PARTY_PREFIX)/../lib/cpp/pbbam 2>/dev/null && pwd || echo -n notfound' %(
-            THIRD_PARTY_PREFIX=prefix)
-    return shell(cmd)
-    """
-def get_HTSLIB(env, prefix):
-    """
-    key = 'HTSLIB'
-    if key in env:
-        return env[key]
-    cmd = 'cd $(THIRD_PARTY_PREFIX)/../lib/cpp/htslib 2>/dev/null && pwd || echo -n notfound' %(
-            THIRD_PARTY_PREFIX=prefix)
-    return shell(cmd)
-    """
-def ifenvf(env, key, func):
-    if key in env:
-        return env[key]
-    else:
-        return func()
-def setifenvf(envout, envin, key, func):
-    envout[key] = ifenvf(envin, key, func)
-def setifenv(envout, envin, key, val):
-    envout[key] = envin.get(key, val)
-def setenv(envout, key, val):
-    envout[key] = val
-def update_env_if(envout, envin, keys):
-    for key in keys:
-        if key in envin:
-            envout[key] = envin[key]
-def compose_defs_env(env):
-    # We disallow env overrides for anything with a default from GNU make.
-    nons = ['CXX', 'CC', 'AR'] # 'SHELL'?
-    ovr    = ['%-20s ?= %s' %(k, v) for k,v in sorted(env.items()) if k not in nons]
-    nonovr = ['%-20s := %s' %(k, v) for k,v in sorted(env.items()) if k in nons]
-    return '\n'.join(ovr + nonovr + [''])
-def append_common(envin, content):
-    """Dumb way to do this, but this whole thing is evolving.
-    """
-    content += """
-# Use PREFIX dir, if available.
-INCLUDES      += ${PREFIX_INC} ../pbdata
-LIBS          += ${PREFIX_LIB}
-"""
-    env = dict(envin)
-    # Some extra defs.
-    if 'PREFIX' in envin:
-        PREFIX = envin['PREFIX']
-        setenv(env, 'PREFIX_INC', os.path.join(PREFIX, 'include'))
-        setenv(env, 'PREFIX_LIB', os.path.join(PREFIX, 'lib'))
-    poss = [
-        'CXXFLAGS',
-        'SH_LIB_EXT',
-        'EXTRA_LDFLAGS',
-        'PREFIX_LIB', 'PREFIX_INC',
-    ]
-    vals = ['%-20s := %s' %(k, v) for k,v in sorted(env.items()) if k in poss]
-    return '\n'.join([''] + vals + ['']) + content
-def compose_defines_pacbio(envin):
-    """
-    This is used by mobs via buildcntl.sh.
-    """
-    env = dict()
-    setenv(env, 'SHELL', 'bash')
-    #setifenvf(env, envin, 'OS_STRING', get_OS_STRING)
-    setifenv(env, envin, 'LIBPBDATA_INC', '../pbdata')
-    setifenv(env, envin, 'LIBPBIHDF_INC', '../hdf')
-    setifenv(env, envin, 'LIBBLASR_INC', '../alignment')
-    setifenv(env, envin, 'LIBPBDATA_LIB', '../pbdata/')
-    setifenv(env, envin, 'LIBPBIHDF_LIB', '../hdf/')
-    setifenv(env, envin, 'LIBBLASR_LIB', '../alignment/')
-    if 'nohdf' in envin:
-        env['nohdf'] = envin['nohdf']
-        # Otherwise, do not define it at all. TODO(CD): Remove nohdf, as it is not used.
-    nondefaults = set([
-            'CXX', 'AR',
-            'HDF5_INC', 'HDF5_LIB',
-            'PBBAM_INC', 'PBBAM_LIB',
-            'HTSLIB_CFLAGS', 'HTSLIB_LIBS',
-            'BOOST_INC',
-            'ZLIB_LIB',
-            'GCC_LIB',
-            'GTEST_INC', 'GTEST_SRCDIR',
-    ])
-    update_env_if(env, envin, nondefaults)
-    return compose_defs_env(env)
-
-@contextlib.contextmanager
-def cd(nwd):
-    cwd = os.getcwd()
-    log('cd %r -> %r' %(cwd, nwd))
-    os.chdir(nwd)
-    yield
-    os.chdir(cwd)
-    log('cd %r <- %r' %(cwd, nwd))
-
-def fetch_hdf5_headers():
-    """Fetch into ./hdf/HEADERS directory.
-    This should not be used when an external build-dir is needed.
-    Return actual directory path, relative to subdirs.
-    """
-    version = 'hdf5-1.8.12-headers'
-    version_dn = os.path.join(thisdir, 'hdf', version)
-    if not os.path.isdir(version_dn):
-        with cd(os.path.dirname(version_dn)):
-            cmd = 'curl -k -L https://www.dropbox.com/s/8971bcyy5o42rxb/hdf5-1.8.12-headers.tar.bz2\?dl\=0 | tar xjf -'
-            shell(cmd)
-    return version_dn # Relative path might help caching.
-
-def update(content_defines_mk, content_libconfig_h):
-    """ Write these relative to the same directory as *this* file.
-    """
-    fn_libconfig_h = os.path.join(thisdir, 'pbdata', 'LibBlasrConfig.h')
-    update_content(fn_libconfig_h, content_libconfig_h)
-    fn_defines_mk = 'defines.mk'
-    update_content(fn_defines_mk, content_defines_mk)
-    if thisdir == os.path.abspath('.'):
-        # This was run in the root directory, so symlink defines.mk
-        # in sub-dirs, which now include defines.mk from CURDIR
-        # in order to facilitate building in external output directories.
-        for sub in ('pbdata', 'hdf', 'alignment', 'unittest'):
-            lname = os.path.join(sub, 'defines.mk')
-            if not os.path.lexists(lname):
-                os.symlink(os.path.join('..', 'defines.mk'), lname)
-
-def configure_nopbbam(envin):
-    """Use HDF5 from env-vars.
-    This is the path used by blasr in a GitHub build, for now.
-    """
-    HDF5_INC = envin.get('HDF5_INC')
-    if not HDF5_INC:
-        HDF5_INC = envin['HDF5_INCLUDE']
-    HDF5_LIB = envin['HDF5_LIB']
-    content1 = compose_defines_with_hdf(HDF5_INC, HDF5_LIB)
-    content1 = append_common(envin, content1)
-    content2 = compose_libconfig(pbbam=False)
-    update(content1, content2)
-
-def configure_nopbbam_skip_hdf(envin):
-    """Fetch HDF5 headers.
-    We lack HDF5 libs, so we cannot build our hdf/ subdir.
-    But the others are fine.
-    """
-    HDF_HEADERS = fetch_hdf5_headers()
-    content1 = compose_defines_with_hdf_headers(HDF_HEADERS)
-    content1 = append_common(envin, content1)
-    content2 = compose_libconfig(pbbam=False)
-    update(content1, content2)
-
-def configure_nopbbam_nohdf5(envin):
-    content1 = compose_defines()
-    content1 = append_common(envin, content1)
-    content2 = compose_libconfig(pbbam=False)
-    update(content1, content2)
-
-def configure_pacbio(envin):
-    content1 = compose_defines_pacbio(envin)
-    content1 = append_common(envin, content1)
-    content2 = compose_libconfig(pbbam=True)
-    update(content1, content2)
-
-def get_make_style_env(envin, args):
-    envout = dict()
-    for arg in args:
-        if '=' in arg:
-            k, v = arg.split('=')
-            envout[k] = v
-    envout.update(envin)
-    return envout
-
-class OsType:
-    Unknown, Linux, Darwin = range(3)
-
-def getOsType():
-    uname = shell('uname -s')
-    log('uname=%r' %uname)
-    if 'Darwin' in uname:
-        return OsType.Darwin
-    elif 'Linux' in uname:
-        return OsType.Linux
-    else:
-        return OsType.Unknown
-
-def update_env_for_linux(env):
-    env['SET_LIB_NAME'] = '-soname'
-    env['SH_LIB_EXT'] = '.so'
-def update_env_for_darwin(env):
-    env['SET_LIB_NAME'] = '-install_name'
-    env['SH_LIB_EXT'] = '.dylib'
-    env['EXTRA_LDFLAGS'] = '-flat_namespace'
-    # -flat_namespace makes BSD ld act like Linux ld, finding
-    # shared libs recursively.
-def update_env_for_unknown(env):
-    env['SET_LIB_NAME'] = '-soname'
-    env['SH_LIB_EXT'] = '.so'
-update_env_for_os = {
-    OsType.Linux: update_env_for_linux,
-    OsType.Darwin: update_env_for_darwin,
-    OsType.Unknown: update_env_for_unknown,
-}
-
-def main(prog, *args):
-    """Include shell environ plus KEY=VAL pairs in args.
-    """
-    ost = getOsType()
-    envin = get_make_style_env(os.environ, args)
-    update_env_for_os[ost](envin)
-    if 'NOPBBAM' in envin:
-        if 'NOHDF' in envin:
-            configure_nopbbam_nohdf5(envin)
-        else:
-            if 'HDF5_LIB' in envin:
-                if 'HDF5_INCLUDE' in envin:
-                    if 'HDF5_INC' not in envin:
-                        envin['HDF5_INC'] = envin['HDF5_INCLUDE']
-                    else:
-                        print("WARNING: Found both HDF5_INC and HDF5_INCLUDE in environ!")
-                assert 'HDF5_INC' in envin, 'Hey! You have HDF5_LIB but not HDF5_INC!'
-                configure_nopbbam(envin)
-            else:
-                configure_nopbbam_skip_hdf(envin)
-    else:
-        configure_pacbio(envin)
-
-
-if __name__=="__main__":
-    main(*sys.argv)
--- a/debian/changelog
+++ b/debian/changelog
-pbseqlib (5.3.1+dfsg-3) UNRELEASED; urgency=medium
+pbseqlib (5.3.3+dfsg-1) UNRELEASED; urgency=medium

+  [ Andreas Tille ]
  * Add myself to Uploaders to have at least one human uploader after
    Afif removed himself.
+  * New upstream version
+  * debhelper-compat 12
+  * Standards-Version: 4.4.0
+  * Add new Build-Depends needed for testing
+
+  [ Helmut Grohne ]
+  * Covnert libpbseq-dev to Architecture: any. (Closes: #940327)

- -- Andreas Tille <tille@debian.org>  Thu, 07 Feb 2019 08:30:09 +0100
+ -- Andreas Tille <tille@debian.org>  Mon, 05 Aug 2019 16:53:23 +0200

 pbseqlib (5.3.1+dfsg-2.1) unstable; urgency=medium


--- a/debian/compat
+++ b/debian/compat
-12
--- a/debian/control
+++ b/debian/control
@@ -3,16 +3,20 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Andreas Tille <tille@debian.org>
 Section: libs
 Priority: optional
-Build-Depends: debhelper (>= 12~),
+Build-Depends: debhelper-compat (= 12),
               dh-exec,
-               python,
+               meson,
+               pkg-config,
+               cmake,
+               googletest,
+               libgtest-dev,
               zlib1g-dev,
               libhdf5-dev,
               libboost-dev,
               libpbbam-dev (>= 0.18.0+dfsg-1~),
               libhts-dev,
               libgtest-dev <!nocheck>
-Standards-Version: 4.3.0
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/pbseqlib
 Vcs-Git: https://salsa.debian.org/med-team/pbseqlib.git
 Homepage: https://github.com/PacificBiosciences/blasr_libcpp
@@ -31,12 +35,12 @@ Description: library for analyzing PacBio sequencing data
 This is a metapackage that depends on the pbseqlib component shared libraries.

 Package: libpbseq-dev
-Architecture: all
+Architecture: any
 Section: libdevel
 Depends: ${misc:Depends},
-         libpbdata-dev (>= ${source:Version}),
-         libpbihdf-dev (>= ${source:Version}),
-         libblasr-dev  (>= ${source:Version})
+         libpbdata-dev (= ${binary:Version}),
+         libpbihdf-dev (= ${binary:Version}),
+         libblasr-dev  (= ${binary:Version})
 Description: library for analyzing PacBio sequencing data (development files)
 Blasr_libcpp is a library used by blasr and other executables such as
 samtoh5, loadPulses for analyzing PacBio sequences. This library contains

--- a/debian/rules
+++ b/debian/rules
@@ -24,9 +24,6 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 %:
 	dh $@

-override_dh_auto_configure:
-	./configure.py PREFIX=/usr/
-
 override_dh_auto_build:
 	dh_auto_build -- PREFIX_INC=..


--- a/exports
+++ b/exports
-./alignment/MappingMetrics.hpp
-./alignment/algorithms/alignment/AffineGuidedAlign.hpp
-./alignment/algorithms/alignment/AffineKBandAlign.hpp
-./alignment/algorithms/alignment/AlignmentFormats.hpp
-./alignment/algorithms/alignment/AlignmentUtils.hpp
-./alignment/algorithms/alignment/AlignmentUtilsImpl.hpp
-./alignment/algorithms/alignment/BaseScoreFunction.hpp
-./alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp
-./alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp
-./alignment/algorithms/alignment/ExtendAlign.hpp
-./alignment/algorithms/alignment/FullQVAlign.hpp
-./alignment/algorithms/alignment/GraphPaper.hpp
-./alignment/algorithms/alignment/GraphPaperImpl.hpp
-./alignment/algorithms/alignment/GuidedAlign.hpp
-./alignment/algorithms/alignment/IDSScoreFunction.hpp
-./alignment/algorithms/alignment/KBandAlign.hpp
-./alignment/algorithms/alignment/OneGapAlignment.hpp
-./alignment/algorithms/alignment/QualityValueScoreFunction.hpp
-./alignment/algorithms/alignment/SDPAlign.hpp
-./alignment/algorithms/alignment/SDPAlignImpl.hpp
-./alignment/algorithms/alignment/SWAlign.hpp
-./alignment/algorithms/alignment/SWAlignImpl.hpp
-./alignment/algorithms/alignment/ScoreMatrices.hpp
-./alignment/algorithms/alignment/StringToScoreMatrix.hpp
-./alignment/algorithms/alignment/sdp/FragmentSort.hpp
-./alignment/algorithms/alignment/sdp/FragmentSortImpl.hpp
-./alignment/algorithms/alignment/sdp/SDPColumn.hpp
-./alignment/algorithms/alignment/sdp/SDPFragment.hpp
-./alignment/algorithms/alignment/sdp/SDPSet.hpp
-./alignment/algorithms/alignment/sdp/SDPSetImpl.hpp
-./alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp
-./alignment/algorithms/alignment/sdp/SparseDynamicProgrammingImpl.hpp
-./alignment/algorithms/anchoring/BWTSearch.hpp
-./alignment/algorithms/anchoring/BWTSearchImpl.hpp
-./alignment/algorithms/anchoring/BasicEndpoint.hpp
-./alignment/algorithms/anchoring/BasicEndpointImpl.hpp
-./alignment/algorithms/anchoring/ClusterProbability.hpp
-./alignment/algorithms/anchoring/Coordinate.hpp
-./alignment/algorithms/anchoring/FindMaxInterval.hpp
-./alignment/algorithms/anchoring/FindMaxIntervalImpl.hpp
-./alignment/algorithms/anchoring/GlobalChain.hpp
-./alignment/algorithms/anchoring/GlobalChainImpl.hpp
-./alignment/algorithms/anchoring/LISPValue.hpp
-./alignment/algorithms/anchoring/LISPValueImpl.hpp
-./alignment/algorithms/anchoring/LISPValueWeightor.hpp
-./alignment/algorithms/anchoring/LISPValueWeightorImpl.hpp
-./alignment/algorithms/anchoring/LISQValueWeightor.hpp
-./alignment/algorithms/anchoring/LISSizeWeightor.hpp
-./alignment/algorithms/anchoring/LISSizeWeightorImpl.hpp
-./alignment/algorithms/anchoring/LongestIncreasingSubsequence.hpp
-./alignment/algorithms/anchoring/LongestIncreasingSubsequenceImpl.hpp
-./alignment/algorithms/anchoring/MapBySuffixArray.hpp
-./alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp
-./alignment/algorithms/anchoring/PrioritySearchTree.hpp
-./alignment/algorithms/anchoring/PrioritySearchTreeImpl.hpp
-./alignment/algorithms/anchoring/ScoreAnchors.hpp
-./alignment/algorithms/anchoring/ScoreAnchorsImpl.hpp
-./alignment/algorithms/compare/CompareStrings.hpp
-./alignment/algorithms/sorting/DifferenceCovers.hpp
-./alignment/algorithms/sorting/Karkkainen.hpp
-./alignment/algorithms/sorting/LightweightSuffixArray.hpp
-./alignment/algorithms/sorting/MultikeyQuicksort.hpp
-./alignment/algorithms/sorting/qsufsort.hpp
-./alignment/anchoring/AnchorParameters.hpp
-./alignment/bwt/BWT.hpp
-./alignment/bwt/Occ.hpp
-./alignment/bwt/PackedHash.hpp
-./alignment/bwt/Pos.hpp
-./alignment/datastructures/alignment/Alignment.hpp
-./alignment/datastructures/alignment/AlignmentCandidate.hpp
-./alignment/datastructures/alignment/AlignmentContext.hpp
-./alignment/datastructures/alignment/AlignmentMap.hpp
-./alignment/datastructures/alignment/AlignmentStats.hpp
-./alignment/datastructures/alignment/CmpFile.hpp
-./alignment/datastructures/alignment/FilterCriteria.hpp
-./alignment/datastructures/alignment/SAMToAlignmentCandidateAdapter.hpp
-./alignment/datastructures/alignmentset/AlignmentSetToCmpH5Adapter.hpp
-./alignment/datastructures/alignmentset/AlignmentSetToCmpH5AdapterImpl.hpp
-./alignment/datastructures/alignmentset/SAMQVConversion.hpp
-./alignment/datastructures/alignmentset/SAMSupplementalQVList.hpp
-./alignment/datastructures/anchoring/AnchorParameters.hpp
-./alignment/datastructures/anchoring/ClusterList.hpp
-./alignment/datastructures/anchoring/MatchPos.hpp
-./alignment/datastructures/anchoring/WeightedInterval.hpp
-./alignment/files/BaseSequenceIO.hpp
-./alignment/files/CCSIterator.hpp
-./alignment/files/FragmentCCSIterator.hpp
-./alignment/files/ReaderAgglomerate.hpp
-./alignment/files/ReaderAgglomerateImpl.hpp
-./alignment/format/BAMPrinter.hpp
-./alignment/format/BAMPrinterImpl.hpp
-./alignment/format/CompareSequencesPrinter.hpp
-./alignment/format/CompareSequencesPrinterImpl.hpp
-./alignment/format/IntervalPrinter.hpp
-./alignment/format/SAMHeaderPrinter.hpp
-./alignment/format/SAMPrinter.hpp
-./alignment/format/SAMPrinterImpl.hpp
-./alignment/format/StickAlignmentPrinter.hpp
-./alignment/format/SummaryPrinter.hpp
-./alignment/format/VulgarPrinter.hpp
-./alignment/format/XMLPrinter.hpp
-./alignment/ipc/SharedMemoryAllocator.hpp
-./alignment/qvs/QualityValueProfile.hpp
-./alignment/simulator/CDFMap.hpp
-./alignment/simulator/ContextOutputList.hpp
-./alignment/simulator/ContextSample.hpp
-./alignment/simulator/ContextSet.hpp
-./alignment/simulator/LengthHistogram.hpp
-./alignment/simulator/OutputList.hpp
-./alignment/simulator/OutputSample.hpp
-./alignment/simulator/OutputSampleList.hpp
-./alignment/simulator/OutputSampleListSet.hpp
-./alignment/simulator/QualitySample.hpp
-./alignment/statistics/AnchorDistributionTable.hpp
-./alignment/statistics/LookupAnchorDistribution.hpp
-./alignment/statistics/StatUtils.hpp
-./alignment/statistics/StatUtilsImpl.hpp
-./alignment/statistics/VarianceAccumulator.hpp
-./alignment/statistics/VarianceAccumulatorImpl.hpp
-./alignment/statistics/cdfs.hpp
-./alignment/statistics/pdfs.hpp
-./alignment/suffixarray/LCPTable.hpp
-./alignment/suffixarray/SharedSuffixArray.hpp
-./alignment/suffixarray/SuffixArray.hpp
-./alignment/suffixarray/SuffixArrayTypes.hpp
-./alignment/suffixarray/ssort.hpp
-./alignment/tuples/BaseTuple.hpp
-./alignment/tuples/CompressedDNATuple.hpp
-./alignment/tuples/DNATuple.hpp
-./alignment/tuples/DNATupleImpl.hpp
-./alignment/tuples/HashedTupleList.hpp
-./alignment/tuples/HashedTupleListImpl.hpp
-./alignment/tuples/TupleCountTable.hpp
-./alignment/tuples/TupleCountTableImpl.hpp
-./alignment/tuples/TupleList.hpp
-./alignment/tuples/TupleListImpl.hpp
-./alignment/tuples/TupleMatching.hpp
-./alignment/tuples/TupleMatchingImpl.hpp
-./alignment/tuples/TupleMetrics.hpp
-./alignment/utils/FileOfFileNames.hpp
-./alignment/utils/FileUtils.hpp
-./alignment/utils/LogUtils.hpp
-./alignment/utils/PhredUtils.hpp
-./alignment/utils/RangeUtils.hpp
-./alignment/utils/RegionUtils.hpp
-./alignment/utils/RegionUtilsImpl.hpp
-./alignment/utils/SimpleXMLUtils.hpp
-./hdf/BufferedHDF2DArray.hpp
-./hdf/BufferedHDF2DArrayImpl.hpp
-./hdf/BufferedHDFArray.hpp
-./hdf/BufferedHDFArrayImpl.hpp
-./hdf/DatasetCollection.hpp
-./hdf/DatasetCollectionImpl.hpp
-./hdf/HDF2DArray.hpp
-./hdf/HDFAlnGroup.hpp
-./hdf/HDFAlnGroupGroup.hpp
-./hdf/HDFAlnInfoGroup.hpp
-./hdf/HDFArray.hpp
-./hdf/HDFAtom.hpp
-./hdf/HDFAttributable.hpp
-./hdf/HDFBasReader.hpp
-./hdf/HDFBasWriter.hpp
-./hdf/HDFBaseCallsWriter.hpp
-./hdf/HDFBaxWriter.hpp
-./hdf/HDFCCSReader.hpp
-./hdf/HDFCmpExperimentGroup.hpp
-./hdf/HDFCmpData.hpp
-./hdf/HDFCmpFile.hpp
-./hdf/HDFCmpReader.hpp
-./hdf/HDFCmpRootGroup.hpp
-./hdf/HDFCmpRefAlignmentGroup.hpp
-./hdf/HDFCmpSupportedFields.hpp
-./hdf/HDFCommonFG.hpp
-./hdf/HDFConfig.hpp
-./hdf/HDFData.hpp
-./hdf/HDFFile.hpp
-./hdf/HDFGroup.hpp
-./hdf/HDFFileLogGroup.hpp
-./hdf/HDFMovieInfoGroup.hpp
-./hdf/HDFPlsReader.hpp
-./hdf/HDFNewBasReader.hpp
-./hdf/HDFPlsWriter.hpp
-./hdf/HDFPulseCallsWriter.hpp
-./hdf/HDFPulseDataFile.hpp
-./hdf/HDFPulseWriter.hpp
-./hdf/HDFRefGroupGroup.hpp
-./hdf/HDFRefInfoGroup.hpp
-./hdf/HDFRegionTableReader.hpp
-./hdf/HDFRegionTableWriter.hpp
-./hdf/HDFRegionsWriter.hpp
-./hdf/HDFSMRTSequenceReader.hpp
-./hdf/HDFScanDataReader.hpp
-./hdf/HDFScanDataWriter.hpp
-./hdf/HDFUtils.hpp
-./hdf/HDFWriteBuffer.hpp
-./hdf/HDFSentinalFile.hpp
-./hdf/HDFWriterBase.hpp
-./hdf/HDFZMWMetricsWriter.hpp
-./hdf/HDFZMWReader.hpp
-./hdf/HDFZMWWriter.hpp
-./pbdata/CCSSequence.hpp
-./pbdata/ChangeListID.hpp
-./pbdata/CommandLineParser.hpp
-./pbdata/Compare4BitCompressed.hpp
-./pbdata/CompressedDNASequence.hpp
-./pbdata/CompressedSequence.hpp
-./pbdata/CompressedSequenceImpl.hpp
-./pbdata/DNASequence.hpp
-./pbdata/FASTAReader.hpp
-./pbdata/FASTASequence.hpp
-./pbdata/FASTQReader.hpp
-./pbdata/FASTQSequence.hpp
-./pbdata/GFFFile.hpp
-./pbdata/MD5Utils.hpp
-./pbdata/MD5UtilsImpl.hpp
-./pbdata/NucConversion.hpp
-./pbdata/PackedDNASequence.hpp
-./pbdata/ReverseCompressIndex.hpp
-./pbdata/SMRTSequence.hpp
-./pbdata/SeqUtils.hpp
-./pbdata/SeqUtilsImpl.hpp
-./pbdata/StringUtils.hpp
-./pbdata/VectorUtils.hpp
-./pbdata/alignment/CmpAlignment.hpp
-./pbdata/alignment/CmpAlignmentImpl.hpp
-./pbdata/amos/AfgBasWriter.hpp
-./pbdata/loadpulses/MetricField.hpp
-./pbdata/loadpulses/MovieAlnIndexLookupTable.hpp
-./pbdata/matrix/FlatMatrix.hpp
-./pbdata/matrix/FlatMatrixImpl.hpp
-./pbdata/matrix/Matrix.hpp
-./pbdata/matrix/MatrixImpl.hpp
-./pbdata/metagenome/FindRandomSequence.hpp
-./pbdata/metagenome/SequenceIndexDatabase.hpp
-./pbdata/metagenome/SequenceIndexDatabaseImpl.hpp
-./pbdata/metagenome/TitleTable.hpp
-./pbdata/qvs/QualityTransform.hpp
-./pbdata/qvs/QualityValue.hpp
-./pbdata/qvs/QualityValueVector.hpp
-./pbdata/qvs/QualityValueVectorImpl.hpp
-./pbdata/reads/BaseFile.hpp
-./pbdata/reads/BaseFileImpl.hpp
-./pbdata/reads/HoleXY.hpp
-./pbdata/reads/PulseBaseCommon.hpp
-./pbdata/reads/PulseFile.hpp
-./pbdata/reads/PulseFileImpl.hpp
-./pbdata/reads/ReadInterval.hpp
-./pbdata/reads/ReadType.hpp
-./pbdata/reads/RegionAnnotation.hpp
-./pbdata/reads/RegionAnnotations.hpp
-./pbdata/reads/RegionTable.hpp
-./pbdata/reads/RegionTypeMap.hpp
-./pbdata/reads/ScanData.hpp
-./pbdata/reads/ZMWGroupEntry.hpp
-./pbdata/reads/AcqParams.hpp
-./pbdata/saf/AlnGroup.hpp
-./pbdata/saf/AlnInfo.hpp
-./pbdata/saf/MovieInfo.hpp
-./pbdata/saf/RefGroup.hpp
-./pbdata/saf/RefInfo.hpp
-./pbdata/sam/AlignmentSet.hpp
-./pbdata/sam/AlignmentSetImpl.hpp
-./pbdata/sam/ReadGroup.hpp
-./pbdata/sam/ReferenceSequence.hpp
-./pbdata/sam/SAMAlignment.hpp
-./pbdata/sam/SAMHeader.hpp
-./pbdata/sam/SAMKeywordValuePair.hpp
-./pbdata/sam/SAMKeywordValuePairImpl.hpp
-./pbdata/sam/SAMReader.hpp
-./pbdata/sam/SAMReaderImpl.hpp
-./pbdata/utils.hpp
-./pbdata/utils/BitUtils.hpp
-./pbdata/utils/SMRTReadUtils.hpp
-./pbdata/utils/SMRTTitle.hpp
-./pbdata/utils/TimeUtils.hpp
-./pbdata/utilsImpl.hpp
-./alignment/algorithms/alignment/sdp/NonoverlappingSparseDynamicProgramming.h
-./alignment/algorithms/alignment/sdp/VariableLengthSDPFragment.h
-./alignment/datastructures/alignment/AlignedPair.h
-./alignment/datastructures/alignment/AlignmentGapList.h
-./alignment/datastructures/alignment/ByteAlignment.h
-./alignment/datastructures/alignment/CmpIndexedStringTable.h
-./alignment/datastructures/alignment/CmpReadGroupTable.h
-./alignment/datastructures/alignment/CmpRefSeqTable.h
-./alignment/datastructures/alignment/Path.h
-./alignment/query/PbiFilterZmwGroupQuery.h
-./alignment/query/SequentialZmwGroupQuery.h
-./alignment/tuples/CountedTuple.h
-./alignment/tuples/DNATupleList.h
-./alignment/tuples/TupleMask.h
-./alignment/tuples/TupleOperations.h
-./alignment/tuples/TupleTranslations.h
-./alignment/tuples/tuple.h
-./pbdata/Enumerations.h
-./pbdata/PacBioDefs.h
-./pbdata/Types.h
-./pbdata/defs.h
-./pbdata/sam/CigarString.h
-./pbdata/sam/SAMFlag.h
-pbdata/LibBlasrConfig.h