New upstream version 1.4.0+dfsg

if (WIN32)

    cmake_minimum_required(VERSION 3.1.0)

else ()

    cmake_minimum_required(VERSION 2.8.0)

    cmake_minimum_required(VERSION 2.8.12)

endif ()

message (STATUS "==== Initializing project cmake configuration ====")

#

set(CMAKE_CONFIGURATION_TYPES_TMP Debug Release RelWithDebInfo)

if (NOT WIN32)

    set(CMAKE_CONFIGURATION_TYPES_TMP ${CMAKE_CONFIGURATION_TYPES_TMP} ASan)

    set(CMAKE_CONFIGURATION_TYPES_TMP ${CMAKE_CONFIGURATION_TYPES_TMP} ASan GCov)

endif ()

set(CMAKE_CONFIGURATION_TYPES ${CMAKE_CONFIGURATION_TYPES_TMP} CACHE STRING "" FORCE)

project (${THIS_PROJECT_NAME})

# find interpreters

find_package(PythonInterp)

# Find python2 interpreter

find_package(PythonInterp 2 QUIET)

if (NOT PYTHONINTERP_FOUND)

    message (WARNING "No python interpreter found, disabling optional python build and installation components. Installed workflow requires python interpreter to run")

    message (WARNING "No python2 interpreter found, disabling optional python build and installation components. Installed workflow requires python2 interpreter to run.")

else()

    set (MINIMUM_PYTHON_VERSION "2.6")

    if (${PYTHON_VERSION_STRING} VERSION_LESS ${MINIMUM_PYTHON_VERSION})

        message (WARNING

            "Python2 interpretor must be at least version (${MINIMUM_PYTHON_VERSION}). Found version ${PYTHON_VERSION_STRING} at '${PYTHON_EXECUTABLE}'."

		    " Disabling optional python build and installation components. Installed workflow requires python ${MINIMUM_PYTHON_VERSION} or higher to run.")

        set(PYTHONINTERP_FOUND false)

    endif ()

endif()

set (THIS_ARCH ${CMAKE_SYSTEM_PROCESSOR})

if (NOT WIN32)

set (TARGET_ARCHITECTURE ${CMAKE_SYSTEM_PROCESSOR})

if (APPLE)

    # On OS X, CMAKE_SYSTEM_PROCESSOR is set to 'i386' regardless of the actual processor, so

    # architecture is inferred from pointer size instead:

    if (CMAKE_SIZEOF_VOID_P MATCHES 8)

        set (THIS_ARCH "x86_64")

        set (TARGET_ARCHITECTURE "x86_64")

    else ()

        set (THIS_ARCH "x86")

        set (TARGET_ARCHITECTURE "x86")

    endif ()

endif ()

message (STATUS "TARGET_ARCHITECTURE: " ${THIS_ARCH} )

message (STATUS "TARGET_ARCHITECTURE: " ${TARGET_ARCHITECTURE} )

# Create package versioning target - version derived from git describe except for

Manta - Stuctural Variant and Indel Caller

Copyright (c) 2013-2017 Illumina, Inc.

Copyright (c) 2013-2018 Illumina, Inc.

This program is free software: you can redistribute it and/or modify

it under the terms of the GNU General Public License as published by

******************************************************************

htslib 1.2.1-204-g8197cfd

htslib 1.7-6-g6d2bfb7

[Files in this distribution outwith the cram/ subdirectory are distributed

according to the terms of the following MIT/Expat license.]

******************************************************************

Boost 1.56.0

samtools 1.6

The MIT/Expat License

Copyright (C) 2008-2014 Genome Research Ltd.

Permission is hereby granted, free of charge, to any person obtaining a copy

of this software and associated documentation files (the "Software"), to deal

in the Software without restriction, including without limitation the rights

to use, copy, modify, merge, publish, distribute, sublicense, and/or sell

copies of the Software, and to permit persons to whom the Software is

furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in

all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR

IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,

FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL

THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER

LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING

FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER

DEALINGS IN THE SOFTWARE.

[The use of a range of years within a copyright notice in this distribution

should be interpreted as being equivalent to a list of years including the

first and last year specified and all consecutive years between them.

For example, a copyright notice that reads "Copyright (C) 2005, 2007-2009,

2011-2012" should be interpreted as being identical to a notice that reads

"Copyright (C) 2005, 2007, 2008, 2009, 2011, 2012" and a copyright notice

that reads "Copyright (C) 2005-2012" should be interpreted as being identical

to a notice that reads "Copyright (C) 2005, 2006, 2007, 2008, 2009, 2010,

2011, 2012".]

******************************************************************

Boost 1.58.0

Boost Software License - Version 1.0 - August 17th, 2003

******************************************************************

pyFlow 1.1.14

pyFlow 1.1.20

pyFlow - a lightweight parallel task engine

Copyright (c) 2012-2015 Illumina, Inc.

Copyright (c) 2012-2017 Illumina, Inc.

All rights reserved.

Redistribution and use in source and binary forms, with or without

(See accompanying file `LICENSE_1_0.txt` or copy at

<http://www.boost.org/LICENSE_1_0.txt>)

******************************************************************

zlib 1.2.8

 (C) 1995-2013 Jean-loup Gailly and Mark Adler

  This software is provided 'as-is', without any express or implied

  warranty.  In no event will the authors be held liable for any damages

  arising from the use of this software.

  Permission is granted to anyone to use this software for any purpose,

  including commercial applications, and to alter it and redistribute it

  freely, subject to the following restrictions:

  1. The origin of this software must not be misrepresented; you must not

     claim that you wrote the original software. If you use this software

     in a product, an acknowledgment in the product documentation would be

     appreciated but is not required.

  2. Altered source versions must be plainly marked as such, and must not be

     misrepresented as being the original software.

  3. This notice may not be removed or altered from any source distribution.

                          allow version control within eclipse

  --build-type=TYPE       specify the build type for CMake (affects compiler

                          options). Allowed values are "Debug", "Release",

                          "RelWithDebInfo", "ASan" [$build_type]

                          "RelWithDebInfo", "ASan", "GCov" [$build_type]

                            Debug: No optimization and all debug symbols

                            Release: All portable optimization

                            RelWithDebInfo: Most optimizations, try to keep stack trace info

                            ASan: Light optimization with google addresss sanitizer on

                            ASan: Light optimization with google address sanitizer on

                            GCov: Debug mode with code coverage options to enable gcov

Directory and file names:

  --prefix=PREFIX         install files in tree rooted at PREFIX

This directory aggregates all project documentation. The documentation is divided into the following sections:

  * [User Guide](userGuide/README.md) - This is the primary documentation resource for all Manta users.

  * [Developer Guide](developerGuide/README.md) - This provides guidelines for anyone contributing to the Manta source.

  * [User Guide](userGuide/README.md) - This is the primary documentation resource for all users.

  * [Developer Guide](developerGuide/README.md) - This provides guidelines for anyone contributing to methods development.

  * [Methods](methods/README.md) - This directory aggregates detailed method and model descriptions.