[med-svn] [maffilter] 02/08: New upstream version 1.2.1
Andreas Tille
tille at debian.org
Thu Jun 22 07:45:16 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository maffilter.
commit 9a5e284b273b09d8d8bb24aa2698069bb4ee0b14
Author: Andreas Tille <tille at debian.org>
Date: Thu Jun 22 08:51:58 2017 +0200
New upstream version 1.2.1
---
AUTHORS.txt => AUTHORS | 0
CMakeLists.txt | 277 +++-----
COPYING.txt | 506 ---------------
ChangeLog | 44 +-
INSTALL.txt => INSTALL | 2 +-
LICENSE | 674 ++++++++++++++++++++
MafFilter/CMakeLists.txt | 23 +-
MafFilter/MafFilter.cpp | 605 ++++++++++++++++--
MafFilter/SystemCallMafIterator.cpp | 84 +++
MafFilter/SystemCallMafIterator.h | 110 ++++
MafFilter/TreeBuildingSystemCallMafIterator.cpp | 82 +++
MafFilter/TreeBuildingSystemCallMafIterator.h | 115 ++++
buildBin.sh | 7 +
doc/CMakeLists.txt | 80 ++-
doc/maffilter.texi | 695 +++++++++++++++++----
...projected.chr22.subset.nogap.cleaned_aln.maf.gz | Bin 0 -> 13206362 bytes
examples/UCSC46ways/MafFilter.bpp | 2 +-
examples/UCSC46ways/README | 1 +
...Mgraminicolav2.FrozenGeneCatalog20080910.gff.gz | Bin 0 -> 809905 bytes
examples/Ztritici/tba_refIPO323.maf.gz | Bin 0 -> 60513136 bytes
maffilter.spec | 66 +-
man/CMakeLists.txt | 47 +-
man/{maffilter.1.txt => maffilter.1} | 2 +-
23 files changed, 2470 insertions(+), 952 deletions(-)
diff --git a/AUTHORS.txt b/AUTHORS
similarity index 100%
rename from AUTHORS.txt
rename to AUTHORS
diff --git a/CMakeLists.txt b/CMakeLists.txt
index ab07947..b9be832 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -3,8 +3,8 @@
# Created: 27/04/2010
# Global parameters
-CMAKE_MINIMUM_REQUIRED(VERSION 2.6)
-PROJECT(maffilter C CXX)
+CMAKE_MINIMUM_REQUIRED(VERSION 2.8.11)
+PROJECT(maffilter CXX)
IF(NOT CMAKE_BUILD_TYPE)
SET(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING
@@ -12,40 +12,9 @@ IF(NOT CMAKE_BUILD_TYPE)
FORCE)
ENDIF()
-SET(CMAKE_CXX_FLAGS "-Wall -Weffc++ -Wshadow")
-IF(NOT NO_VIRTUAL_COV)
- SET(NO_VIRTUAL_COV FALSE CACHE BOOL
- "Disable covariant return type with virtual inheritance, for compilers that do not support it."
- FORCE)
-ENDIF()
-
-IF(NO_VIRTUAL_COV)
- MESSAGE("-- Covariant return with virtual inheritance disabled.")
- SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DNO_VIRTUAL_COV=1")
-ENDIF()
-
-IF(NOT NO_DEP_CHECK)
- SET(NO_DEP_CHECK FALSE CACHE BOOL
- "Disable dependencies check for building distribution only."
- FORCE)
-ENDIF(NOT NO_DEP_CHECK)
-
-IF(NOT DOC_COMPRESS)
- SET(DOC_COMPRESS gzip CACHE STRING
- "Set program for compressing documentation."
- FORCE)
-ENDIF(NOT DOC_COMPRESS)
-
-IF(NOT DOC_COMPRESS_EXT)
- SET(DOC_COMPRESS_EXT gz CACHE STRING
- "Set extension of compressed documentation."
- FORCE)
-ENDIF(NOT DOC_COMPRESS_EXT)
+SET(CMAKE_CXX_FLAGS "-std=c++11 -Wall -Weffc++ -Wshadow")
-IF(NO_DEP_CHECK)
- MESSAGE("-- Dependencies checking disabled. Only distribution can be built.")
-ELSE(NO_DEP_CHECK)
#static linkage?
IF(NOT BUILD_STATIC)
@@ -55,73 +24,60 @@ IF(NOT BUILD_STATIC)
ENDIF()
IF(BUILD_STATIC)
MESSAGE("-- Static linkage requested.")
- SET(CMAKE_CXX_FLAGS "-static -static-libgcc ${CMAKE_CXX_FLAGS}")
+ SET (CMAKE_CXX_FLAGS "-static -static-libgcc ${CMAKE_CXX_FLAGS}")
ENDIF()
-#build info?
-IF(NOT DEFINED INFO)
- SET(INFO UNIX)
-ENDIF(NOT DEFINED INFO)
+# Check compression program
+# COMPRESS_PROGRAM controls the choice of program
+# COMPRESS_EXT can be used to override the file extension
+if (NOT COMPRESS_PROGRAM)
+ set (COMPRESS_PROGRAM gzip CACHE STRING "Set program for compressing documentation" FORCE)
+endif ()
+find_program (COMPRESS_BIN NAMES ${COMPRESS_PROGRAM} DOC "${COMPRESS_PROGRAM} compression program")
+if (NOT COMPRESS_BIN)
+ message (STATUS "${COMPRESS_PROGRAM} program not found, text doc will not be compressed")
+else ()
+ # Deduce COMPRESS_EXT for known compression programs if not set
+ if (NOT COMPRESS_EXT)
+ if (${COMPRESS_PROGRAM} STREQUAL "gzip")
+ set (COMPRESS_EXT "gz")
+ elseif (${COMPRESS_PROGRAM} STREQUAL "bzip2")
+ set (COMPRESS_EXT "bz2")
+ else ()
+ set (COMPRESS_EXT "${COMPRESS_PROGRAM}") # Default: program name (works for xz/lzma)
+ endif ()
+ endif ()
+ # Generate command line args (always add -c to output compressed file to stdout)
+ if (${COMPRESS_PROGRAM} STREQUAL "gzip")
+ # -n for no timestamp in files (reproducible builds)
+ set (COMPRESS_ARGS -c -n)
+ else ()
+ set (COMPRESS_ARGS -c)
+ endif ()
+ message (STATUS "Found ${COMPRESS_BIN} compression program, using file extension .${COMPRESS_EXT}")
+endif ()
+
+# Find dependencies (add install directory to search)
+if (CMAKE_INSTALL_PREFIX)
+ set (CMAKE_PREFIX_PATH "${CMAKE_INSTALL_PREFIX}" ${CMAKE_PREFIX_PATH})
+endif (CMAKE_INSTALL_PREFIX)
+
+include (GNUInstallDirs)
+find_package (bpp-phyl-omics 2.0.0 REQUIRED)
-#build man pages?
-IF(NOT DEFINED MAN)
- SET(MAN UNIX)
-ENDIF(NOT DEFINED MAN)
-
-#find executables for documentation
-IF(MAN)
- FIND_PROGRAM(NROFF_EXE NAMES nroff)
- IF(NROFF_EXE)
- MESSAGE("-- Found nroff here: ${NROFF_EXE}")
- MESSAGE(" Adding targets: man")
-
- ADD_CUSTOM_TARGET(man
- ALL
- COMMAND cp maffilter.1.txt maffilter.1
- COMMAND ${DOC_COMPRESS} -f maffilter.1
- WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/man
- )
- SET_DIRECTORY_PROPERTIES(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES "man/maffilter.1.${DOC_COMPRESS_EXT}")
- ELSE()
- MESSAGE(FATAL_ERROR "Program nroff required but not found.")
- ENDIF()
-ENDIF(MAN)
-
-IF(INFO)
- FIND_PROGRAM(MAKEINFO_EXE NAMES makeinfo)
- IF(MAKEINFO_EXE)
- MESSAGE("-- Found makeinfo here: ${MAKEINFO_EXE}")
- MESSAGE(" Adding targets: info, html")
-
- SET(ADD_INFO_TO "ALL")
- MESSAGE(" Adding target info to target all")
-
- ADD_CUSTOM_TARGET(info
- ${ADD_INFO_TO}
- COMMAND ${MAKEINFO_EXE} maffilter.texi
- WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/doc
- )
-
- ADD_CUSTOM_TARGET(html
- COMMAND ${MAKEINFO_EXE} --html --css-ref=http://www.w3.org/StyleSheets/Core/Steely maffilter.texi
- WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/doc
- )
- ELSE(MAKEINFO_EXE)
- MESSAGE(FATAL_ERROR p"Program makeinfo required but not found.")
- ENDIF(MAKEINFO_EXE)
-ENDIF(INFO)
+#Find boost libraries
+SET(Boost_USE_STATIC_LIBS ${BUILD_STATIC})
+SET(Boost_USE_MULTITHREADED ON)
+FIND_PACKAGE( Boost 1.34.0 COMPONENTS iostreams )
-FIND_PROGRAM(PDFTEX_EXE NAMES pdftex)
-IF(PDFTEX_EXE)
- MESSAGE("-- Found pdftex here: ${PDFTEX_EXE}")
- MESSAGE(" Adding target: pdf")
+IF(Boost_FOUND)
+ INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS})
+ SET(LIBS ${LIBS} ${Boost_LIBRARIES})
+ MESSAGE("-- Boost libraries found here:")
+ MESSAGE(" includes: ${Boost_INCLUDE_DIRS}")
+ MESSAGE(" dynamic libraries: ${Boost_LIBRARIES}")
+ENDIF()
- ADD_CUSTOM_TARGET(pdf
- COMMAND ${PDFTEX_EXE} maffilter.texi
- WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/doc
- )
- SET_DIRECTORY_PROPERTIES(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES "doc/maffilter.pdf;doc/maffilter.aux;doc/maffilter.cp;doc/maffilter.fn;doc/maffilter.info;doc/maffilter.ky;doc/maffilter.log;doc/maffilter.pg;doc/maffilter.toc;doc/maffilter.tp;doc/maffilter.vr")
-ENDIF(PDFTEX_EXE)
#here is a useful function:
MACRO(IMPROVED_FIND_LIBRARY OUTPUT_LIBS lib_name include_to_find)
@@ -163,121 +119,65 @@ IF(CMAKE_INSTALL_PREFIX)
SET(CMAKE_PREFIX_PATH "${CMAKE_INSTALL_PREFIX}" ${CMAKE_PREFIX_PATH})
ENDIF(CMAKE_INSTALL_PREFIX)
-#Find the libraries. The order is very important for static linkage, it won't
-#link if you change it!
-IMPROVED_FIND_LIBRARY(LIBS bpp-phyl-omics Bpp/Seq/Io/Maf/AbstractDistanceEstimationMafIterator.h)
-IMPROVED_FIND_LIBRARY(LIBS bpp-phyl Bpp/Phyl/Tree.h)
-IMPROVED_FIND_LIBRARY(LIBS bpp-seq-omics Bpp/Seq/Feature/SequenceFeature.h)
-IMPROVED_FIND_LIBRARY(LIBS bpp-seq Bpp/Seq/Alphabet/Alphabet.h)
-IMPROVED_FIND_LIBRARY(LIBS bpp-core Bpp/Clonable.h)
-
-#Find boost libraries
-SET(Boost_USE_STATIC_LIBS ${BUILD_STATIC})
-SET(Boost_USE_MULTITHREADED ON)
-FIND_PACKAGE( Boost 1.34.0 COMPONENTS iostreams )
-
-IF(Boost_FOUND)
- INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS})
- SET(LIBS ${LIBS} ${Boost_LIBRARIES})
- MESSAGE("-- Boost found: ${Boost_INCLUDE_DIRS}")
-ENDIF()
# Find the zlib installation
-FIND_PACKAGE(ZLIB REQUIRED)
-IF(ZLIB_FOUND)
- INCLUDE_DIRECTORIES(${ZLIB_INCLUDE_DIR})
- SET(LIBS ${LIBS} ${ZLIB_LIBRARIES})
- MESSAGE("-- Zlib found: ${ZLIB_INCLUDE_DIR}")
-ENDIF()
+IMPROVED_FIND_LIBRARY(LIBS z zlib.h)
+#This does not work with static linkage!!!
+#FIND_PACKAGE(ZLIB REQUIRED)
+#IF(ZLIB_FOUND)
+# INCLUDE_DIRECTORIES(${ZLIB_INCLUDE_DIR})
+# SET(LIBS ${LIBS} ${ZLIB_LIBRARIES})
+# MESSAGE("-- Zlib found here:")
+# MESSAGE(" includes: ${ZLIB_INCLUDE_DIR}")
+# MESSAGE(" libraries: ${ZLIB_LIBRARIES}")
+#ENDIF()
# Find the bz2 installation
-FIND_PACKAGE(BZip2 REQUIRED)
-IF(BZIP2_FOUND)
- INCLUDE_DIRECTORIES(${BZIP2_INCLUDE_DIR})
- SET(LIBS ${LIBS} ${BZIP2_LIBRARIES})
- MESSAGE("-- BZip2 found: ${BZIP2_INCLUDE_DIR}")
-ENDIF()
+IMPROVED_FIND_LIBRARY(LIBS bz2 bzlib.h)
+#This does not work with static linkage!!!
+#FIND_PACKAGE(BZip2 REQUIRED)
+#IF(BZIP2_FOUND)
+# INCLUDE_DIRECTORIES(${BZIP2_INCLUDE_DIR})
+# SET(LIBS ${LIBS} ${BZIP2_LIBRARIES})
+# MESSAGE("-- BZip2 found here:")
+# MESSAGE(" includes: ${BZIP2_INCLUDE_DIR}")
+# MESSAGE(" libraries: ${BZIP2_LIBRARIES}")
+#ENDIF()
# Subdirectories
ADD_SUBDIRECTORY(MafFilter)
ADD_SUBDIRECTORY(doc)
ADD_SUBDIRECTORY(man)
-ENDIF(NO_DEP_CHECK)
-
# Packager
SET(CPACK_PACKAGE_NAME "maffilter")
-SET(CPACK_PACKAGE_VENDOR "Julien Dutheil")
-SET(CPACK_PACKAGE_VERSION "1.1.0")
+SET(CPACK_PACKAGE_VENDOR "Julien Y. Dutheil")
+SET(CPACK_PACKAGE_VERSION "1.2.1")
SET(CPACK_PACKAGE_VERSION_MAJOR "1")
-SET(CPACK_PACKAGE_VERSION_MINOR "1")
-SET(CPACK_PACKAGE_VERSION_PATCH "0-1")
+SET(CPACK_PACKAGE_VERSION_MINOR "2")
+SET(CPACK_PACKAGE_VERSION_PATCH "1")
SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Filtering of genome alignment in the Multiple Alignment Format (MAF)")
-SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
-SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")
-SET(CPACK_RESOURCE_FILE_INSTALL "${CMAKE_SOURCE_DIR}/INSTALL.txt")
+SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/LICENSE")
+SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS")
+SET(CPACK_RESOURCE_FILE_INSTALL "${CMAKE_SOURCE_DIR}/INSTALL")
SET(CPACK_SOURCE_GENERATOR "TGZ")
-SET(CPACK_SOURCE_IGNORE_FILES
- "CMakeFiles"
- "Makefile"
- "_CPack_Packages"
- "CMakeCache.txt"
- ".*\\\\.cmake"
- ".*\\\\.git"
- ".*\\\\.gz"
- ".*\\\\.zip"
- ".*\\\\.deb"
- ".*\\\\.rpm"
- ".*\\\\.dmg"
- ".*\\\\.sh"
- ".*\\\\..*\\\\.swp"
- ".*stamp"
- "\\\\.sh"
- "\\\\..*\\\\.swp"
- "MafFilter/\\\\..*"
- "man/.*\\\\.1.${DOC_COMPRESS_EXT}"
- "debian/tmp"
- "debian/maffilter/"
- "debian/maffilter\\\\.substvars"
- "debian/maffilter\\\\.debhelper"
- "debian/debhelper\\\\.log"
- "install_manifest.txt"
- "DartConfiguration.tcl"
- ${CPACK_SOURCE_IGNORE_FILES}
-)
-IF (MACOS)
- SET(CPACK_GENERATOR "Bundle")
-ENDIF()
+# /!\ This assumes that an external build is used
+SET(CPACK_SOURCE_IGNORE_FILES
+ "/build/"
+ "/examples/"
+ "/\\\\.git/"
+ "/\\\\.gitignore"
+ ${CPACK_SOURCE_IGNORE_FILES}
+ )
SET(CPACK_SOURCE_PACKAGE_FILE_NAME "${CMAKE_PROJECT_NAME}-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}")
SET(CPACK_DEBSOURCE_PACKAGE_FILE_NAME "${CMAKE_PROJECT_NAME}_${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}.orig")
INCLUDE(CPack)
#This adds the 'dist' target
-add_custom_target(dist COMMAND ${CMAKE_MAKE_PROGRAM} package_source)
-# 'clean' is not (yet) a first class target. However, we need to clean the directories before building the sources:
-IF("${CMAKE_GENERATOR}" MATCHES "Make")
- ADD_CUSTOM_TARGET(make_clean
- COMMAND ${CMAKE_MAKE_PROGRAM} clean
- WORKING_DIRECTORY ${CMAKE_CURRENT_DIR}
- )
- ADD_DEPENDENCIES(dist make_clean)
-
- ADD_CUSTOM_TARGET(make_clean_man
- COMMAND rm -f *.${DOC_COMPRESS_EXT}
- WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/man
- )
- ADD_DEPENDENCIES(dist make_clean_man)
-ENDIF()
+ADD_CUSTOM_TARGET(dist COMMAND ${CMAKE_MAKE_PROGRAM} package_source)
-IF(NOT NO_DEP_CHECK)
IF (UNIX)
-#This creates deb packages:
-ADD_CUSTOM_TARGET(origdist COMMAND cp ${CPACK_SOURCE_PACKAGE_FILE_NAME}.tar.gz ../${CPACK_DEBSOURCE_PACKAGE_FILE_NAME}.tar.gz)
-ADD_DEPENDENCIES(origdist dist)
-ADD_CUSTOM_TARGET(deb dpkg-buildpackage -uc -us -i${CPACK_SOURCE_PACKAGE_FILE_NAME}.tar.gz)
-ADD_DEPENDENCIES(deb origdist)
-ADD_DEPENDENCIES(deb info man)
#This creates rpm packages:
ADD_CUSTOM_TARGET(rpm rpmbuild -ta ${CPACK_SOURCE_PACKAGE_FILE_NAME}.tar.gz)
@@ -285,4 +185,3 @@ ADD_DEPENDENCIES(rpm dist info man)
ENDIF(UNIX)
-ENDIF(NOT NO_DEP_CHECK)
diff --git a/COPYING.txt b/COPYING.txt
deleted file mode 100644
index d424827..0000000
--- a/COPYING.txt
+++ /dev/null
@@ -1,506 +0,0 @@
-CeCILL FREE SOFTWARE LICENSE AGREEMENT
-
-
- Notice
-
-This Agreement is a Free Software license agreement that is the result
-of discussions between its authors in order to ensure compliance with
-the two main principles guiding its drafting:
-
- * firstly, compliance with the principles governing the distribution
- of Free Software: access to source code, broad rights granted to
- users,
- * secondly, the election of a governing law, French law, with which
- it is conformant, both as regards the law of torts and
- intellectual property law, and the protection that it offers to
- both authors and holders of the economic rights over software.
-
-The authors of the CeCILL (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre])
-license are:
-
-Commissariat à l'Energie Atomique - CEA, a public scientific, technical
-and industrial research establishment, having its principal place of
-business at 25 rue Leblanc, immeuble Le Ponant D, 75015 Paris, France.
-
-Centre National de la Recherche Scientifique - CNRS, a public scientific
-and technological establishment, having its principal place of business
-at 3 rue Michel-Ange, 75794 Paris cedex 16, France.
-
-Institut National de Recherche en Informatique et en Automatique -
-INRIA, a public scientific and technological establishment, having its
-principal place of business at Domaine de Voluceau, Rocquencourt, BP
-105, 78153 Le Chesnay cedex, France.
-
-
- Preamble
-
-The purpose of this Free Software license agreement is to grant users
-the right to modify and redistribute the software governed by this
-license within the framework of an open source distribution model.
-
-The exercising of these rights is conditional upon certain obligations
-for users so as to preserve this status for all subsequent redistributions.
-
-In consideration of access to the source code and the rights to copy,
-modify and redistribute granted by the license, users are provided only
-with a limited warranty and the software's author, the holder of the
-economic rights, and the successive licensors only have limited liability.
-
-In this respect, the risks associated with loading, using, modifying
-and/or developing or reproducing the software by the user are brought to
-the user's attention, given its Free Software status, which may make it
-complicated to use, with the result that its use is reserved for
-developers and experienced professionals having in-depth computer
-knowledge. Users are therefore encouraged to load and test the
-suitability of the software as regards their requirements in conditions
-enabling the security of their systems and/or data to be ensured and,
-more generally, to use and operate it in the same conditions of
-security. This Agreement may be freely reproduced and published,
-provided it is not altered, and that no provisions are either added or
-removed herefrom.
-
-This Agreement may apply to any or all software for which the holder of
-the economic rights decides to submit the use thereof to its provisions.
-
-
- Article 1 - DEFINITIONS
-
-For the purpose of this Agreement, when the following expressions
-commence with a capital letter, they shall have the following meaning:
-
-Agreement: means this license agreement, and its possible subsequent
-versions and annexes.
-
-Software: means the software in its Object Code and/or Source Code form
-and, where applicable, its documentation, "as is" when the Licensee
-accepts the Agreement.
-
-Initial Software: means the Software in its Source Code and possibly its
-Object Code form and, where applicable, its documentation, "as is" when
-it is first distributed under the terms and conditions of the Agreement.
-
-Modified Software: means the Software modified by at least one
-Contribution.
-
-Source Code: means all the Software's instructions and program lines to
-which access is required so as to modify the Software.
-
-Object Code: means the binary files originating from the compilation of
-the Source Code.
-
-Holder: means the holder(s) of the economic rights over the Initial
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-Licensee: means the Software user(s) having accepted the Agreement.
-
-Contributor: means a Licensee having made at least one Contribution.
-
-Licensor: means the Holder, or any other individual or legal entity, who
-distributes the Software under the Agreement.
-
-Contribution: means any or all modifications, corrections, translations,
-adaptations and/or new functions integrated into the Software by any or
-all Contributors, as well as any or all Internal Modules.
-
-Module: means a set of sources files including their documentation that
-enables supplementary functions or services in addition to those offered
-by the Software.
-
-External Module: means any or all Modules, not derived from the
-Software, so that this Module and the Software run in separate address
-spaces, with one calling the other when they are run.
-
-Internal Module: means any or all Module, connected to the Software so
-that they both execute in the same address space.
-
-GNU GPL: means the GNU General Public License version 2 or any
-subsequent version, as published by the Free Software Foundation Inc.
-
-Parties: mean both the Licensee and the Licensor.
-
-These expressions may be used both in singular and plural form.
-
-
- Article 2 - PURPOSE
-
-The purpose of the Agreement is the grant by the Licensor to the
-Licensee of a non-exclusive, transferable and worldwide license for the
-Software as set forth in Article 5 hereinafter for the whole term of the
-protection granted by the rights over said Software.
-
-
- Article 3 - ACCEPTANCE
-
-3.1 The Licensee shall be deemed as having accepted the terms and
-conditions of this Agreement upon the occurrence of the first of the
-following events:
-
- * (i) loading the Software by any or all means, notably, by
- downloading from a remote server, or by loading from a physical
- medium;
- * (ii) the first time the Licensee exercises any of the rights
- granted hereunder.
-
-3.2 One copy of the Agreement, containing a notice relating to the
-characteristics of the Software, to the limited warranty, and to the
-fact that its use is restricted to experienced users has been provided
-to the Licensee prior to its acceptance as set forth in Article 3.1
-hereinabove, and the Licensee hereby acknowledges that it has read and
-understood it.
-
-
- Article 4 - EFFECTIVE DATE AND TERM
-
-
- 4.1 EFFECTIVE DATE
-
-The Agreement shall become effective on the date when it is accepted by
-the Licensee as set forth in Article 3.1.
-
-
- 4.2 TERM
-
-The Agreement shall remain in force for the entire legal term of
-protection of the economic rights over the Software.
-
-
- Article 5 - SCOPE OF RIGHTS GRANTED
-
-The Licensor hereby grants to the Licensee, who accepts, the following
-rights over the Software for any or all use, and for the term of the
-Agreement, on the basis of the terms and conditions set forth hereinafter.
-
-Besides, if the Licensor owns or comes to own one or more patents
-protecting all or part of the functions of the Software or of its
-components, the Licensor undertakes not to enforce the rights granted by
-these patents against successive Licensees using, exploiting or
-modifying the Software. If these patents are transferred, the Licensor
-undertakes to have the transferees subscribe to the obligations set
-forth in this paragraph.
-
-
- 5.1 RIGHT OF USE
-
-The Licensee is authorized to use the Software, without any limitation
-as to its fields of application, with it being hereinafter specified
-that this comprises:
-
- 1. permanent or temporary reproduction of all or part of the Software
- by any or all means and in any or all form.
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- 2. loading, displaying, running, or storing the Software on any or
- all medium.
-
- 3. entitlement to observe, study or test its operation so as to
- determine the ideas and principles behind any or all constituent
- elements of said Software. This shall apply when the Licensee
- carries out any or all loading, displaying, running, transmission
- or storage operation as regards the Software, that it is entitled
- to carry out hereunder.
-
-
- 5.2 ENTITLEMENT TO MAKE CONTRIBUTIONS
-
-The right to make Contributions includes the right to translate, adapt,
-arrange, or make any or all modifications to the Software, and the right
-to reproduce the resulting software.
-
-The Licensee is authorized to make any or all Contributions to the
-Software provided that it includes an explicit notice that it is the
-author of said Contribution and indicates the date of the creation thereof.
-
-
- 5.3 RIGHT OF DISTRIBUTION
-
-In particular, the right of distribution includes the right to publish,
-transmit and communicate the Software to the general public on any or
-all medium, and by any or all means, and the right to market, either in
-consideration of a fee, or free of charge, one or more copies of the
-Software by any means.
-
-The Licensee is further authorized to distribute copies of the modified
-or unmodified Software to third parties according to the terms and
-conditions set forth hereinafter.
-
-
- 5.3.1 DISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION
-
-The Licensee is authorized to distribute true copies of the Software in
-Source Code or Object Code form, provided that said distribution
-complies with all the provisions of the Agreement and is accompanied by:
-
- 1. a copy of the Agreement,
-
- 2. a notice relating to the limitation of both the Licensor's
- warranty and liability as set forth in Articles 8 and 9,
-
-and that, in the event that only the Object Code of the Software is
-redistributed, the Licensee allows future Licensees unhindered access to
-the full Source Code of the Software by indicating how to access it, it
-being understood that the additional cost of acquiring the Source Code
-shall not exceed the cost of transferring the data.
-
-
- 5.3.2 DISTRIBUTION OF MODIFIED SOFTWARE
-
-When the Licensee makes a Contribution to the Software, the terms and
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- 5.3.4 COMPATIBILITY WITH THE GNU GPL
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- Article 6 - INTELLECTUAL PROPERTY
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-The Holder undertakes that the Initial Software will remain ruled at
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- 6.3 OVER THE EXTERNAL MODULES
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-intellectual property rights over this External Module as defined by
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- 6.4 JOINT PROVISIONS
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- 1. not to remove, or modify, in any manner, the intellectual property
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- 2. to reproduce said notices, in an identical manner, in the copies
- of the Software modified or not.
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-The Licensee undertakes not to directly or indirectly infringe the
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- Article 7 - RELATED SERVICES
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-7.1 Under no circumstances shall the Agreement oblige the Licensor to
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- Article 8 - LIABILITY
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-8.2 The Licensor's liability is limited to the commitments made under
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- Article 9 - WARRANTY
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- Article 11 - MISCELLANEOUS
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- 11.5 LANGUAGE
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-The Agreement is drafted in both French and English and both versions
-are deemed authentic.
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- Article 12 - NEW VERSIONS OF THE AGREEMENT
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-12.1 Any person is authorized to duplicate and distribute copies of this
-Agreement.
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-12.2 So as to ensure coherence, the wording of this Agreement is
-protected and may only be modified by the authors of the License, who
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-Agreement, each with a separate number. These subsequent versions may
-address new issues encountered by Free Software.
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-only be subsequently distributed under the same version of the Agreement
-or a subsequent version, subject to the provisions of Article 5.3.4.
-
-
- Article 13 - GOVERNING LAW AND JURISDICTION
-
-13.1 The Agreement is governed by French law. The Parties agree to
-endeavor to seek an amicable solution to any disagreements or disputes
-that may arise during the performance of the Agreement.
-
-13.2 Failing an amicable solution within two (2) months as from their
-occurrence, and unless emergency proceedings are necessary, the
-disagreements or disputes shall be referred to the Paris Courts having
-jurisdiction, by the more diligent Party.
-
-
-Version 2.0 dated 2006-09-05.
-
diff --git a/ChangeLog b/ChangeLog
index 6d350f2..246a761 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,5 +1,45 @@
-31/03/15 -*- Version 1.1.0-1 -*-
-* Removed .all includes to enable compilation by homebrew.
+18/05/17 -*- Version 1.2.0 -*-
+
+13/04/17 Julien Dutheil
+* Possibility to allow for dots in maf alignments (treated as gaps)
+* VCF output can included non-variable sites (experimental)
+* Added support for tree-based filtering
+
+04/06/16 Julien Dutheil
+* Alignment filters now accept frequencies as maximum amount of gaps.
+
+23/06/16 Julien Dutheil
+* Possibility to count characters for a selection of species only.
+
+18/06/16 Julien Dutheil
+* Added call to external tree reconstruction program.
+
+26/04/16 Julien Dutheil
+* Added distance matrix output.
+* Added RemoveEmptySequences filter.
+
+09/02/16 Julien Dutheil
+* Features in BedGraph format are now supported.
+* New LiftOver filter.
+
+18/12/15 Julien Dutheil
+* SequenceStatistics can now write in compressed file.
+
+10/12/15 Julien Dutheil
+* Added PLINK export filter.
+
+22/11/15 Julien Dutheil
+* Fixed bug in FeatureFilter in case two features are exactly consecutive.
+
+20/10/15 Julien Dutheil
+* Added Tajima's pi to diversity statistics.
+
+13/01/15 Julien Dutheil
+* More options for OutputAlignments (output file names).
+
+09/01/15 Julien Dutheil
+* Add formatting options (sequence names) for trees and distance matrices.
+* ML parameter estimation outputs parameter names in terminal.
26/09/14 -*- Version 1.1.0 -*-
diff --git a/INSTALL.txt b/INSTALL
similarity index 88%
rename from INSTALL.txt
rename to INSTALL
index 7f0d53a..8eccbf1 100644
--- a/INSTALL.txt
+++ b/INSTALL
@@ -1,7 +1,7 @@
This software needs cmake >= 2.6 to build.
The dependencies include:
-- Bio++ libraries: bpp-core, seq, phyls, seq-omics and phyl-omics
+- Bio++ libraries: bpp-core, seq, phyl, seq-omics and phyl-omics
- The boost-iostreams library.
After installing cmake, run it with the following command:
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..9cecc1d
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,674 @@
+ GNU GENERAL PUBLIC LICENSE
+ Version 3, 29 June 2007
+
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diff --git a/MafFilter/CMakeLists.txt b/MafFilter/CMakeLists.txt
index 905e112..830805a 100644
--- a/MafFilter/CMakeLists.txt
+++ b/MafFilter/CMakeLists.txt
@@ -2,12 +2,21 @@
# Author: Julien Dutheil
# Created: 27/04/2010
-ADD_EXECUTABLE(maffilter MafFilter.cpp OutputAsFeaturesMafIterator.cpp)
-TARGET_LINK_LIBRARIES(maffilter ${LIBS} ${Boost_LIBRARIES})
-SET_TARGET_PROPERTIES(maffilter PROPERTIES LINK_SEARCH_END_STATIC ${BUILD_STATIC})
-
-# Install progs
-INSTALL(TARGETS
+ADD_EXECUTABLE(maffilter MafFilter.cpp OutputAsFeaturesMafIterator.cpp SystemCallMafIterator.cpp TreeBuildingSystemCallMafIterator.cpp)
+set (maffilter-targets
maffilter
- DESTINATION bin)
+ )
+
+foreach (target ${maffilter-targets})
+ # Link (static or shared)
+ if (BUILD_STATIC)
+ target_link_libraries (${target} ${BPP_LIBS_STATIC})
+ target_link_libraries (${target} ${LIBS})
+ set_target_properties (${target} LINK_SEARCH_END_STATIC TRUE)
+ else (BUILD_STATIC)
+ target_link_libraries (${target} ${BPP_LIBS_SHARED})
+ target_link_libraries (${target} ${LIBS})
+ endif (BUILD_STATIC)
+endforeach (target)
+install (TARGETS ${maffilter-targets} DESTINATION ${CMAKE_INSTALL_BINDIR})
diff --git a/MafFilter/MafFilter.cpp b/MafFilter/MafFilter.cpp
index ac05d28..0d95720 100644
--- a/MafFilter/MafFilter.cpp
+++ b/MafFilter/MafFilter.cpp
@@ -45,6 +45,8 @@ knowledge of the CeCILL license and that you accept its terms.
using namespace std;
#include "OutputAsFeaturesMafIterator.h"
+#include "SystemCallMafIterator.h"
+#include "TreeBuildingSystemCallMafIterator.h"
//From boost:
#include <boost/iostreams/device/file.hpp>
@@ -63,49 +65,61 @@ using namespace boost::iostreams;
#include <Bpp/Seq/SequenceWithQuality.h>
#include <Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h>
#include <Bpp/Seq/Io/BppOAlignmentWriterFormat.h>
+#include <Bpp/Seq/Io/BppOAlignmentReaderFormat.h>
#include <Bpp/Seq/Container/SiteContainerTools.h>
// From bpp-seq-omics and bpp-phyl-omics:
#include <Bpp/Seq/Io/Maf/MafParser.h>
-#include <Bpp/Seq/Io/Maf/OutputMafIterator.h>
#include <Bpp/Seq/Io/Maf/SequenceStreamToMafIterator.h>
#include <Bpp/Seq/Io/Maf/SequenceFilterMafIterator.h>
#include <Bpp/Seq/Io/Maf/OrphanSequenceFilterMafIterator.h>
#include <Bpp/Seq/Io/Maf/BlockMergerMafIterator.h>
-#include <Bpp/Seq/Io/Maf/ConcatenateMafIterator.h>
-#include <Bpp/Seq/Io/Maf/FullGapFilterMafIterator.h>
-#include <Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.h>
-#include <Bpp/Seq/Io/Maf/EntropyFilterMafIterator.h>
-#include <Bpp/Seq/Io/Maf/MaskFilterMafIterator.h>
-#include <Bpp/Seq/Io/Maf/QualityFilterMafIterator.h>
-#include <Bpp/Seq/Io/Maf/FeatureFilterMafIterator.h>
#include <Bpp/Seq/Io/Maf/BlockLengthMafIterator.h>
#include <Bpp/Seq/Io/Maf/BlockSizeMafIterator.h>
#include <Bpp/Seq/Io/Maf/ChromosomeMafIterator.h>
+#include <Bpp/Seq/Io/Maf/ConcatenateMafIterator.h>
+#include <Bpp/Seq/Io/Maf/RemoveEmptySequencesMafIterator.h>
#include <Bpp/Seq/Io/Maf/DuplicateFilterMafIterator.h>
+#include <Bpp/Seq/Io/Maf/FeatureFilterMafIterator.h>
+#include <Bpp/Seq/Io/Maf/QualityFilterMafIterator.h>
+#include <Bpp/Seq/Io/Maf/MaskFilterMafIterator.h>
+#include <Bpp/Seq/Io/Maf/EntropyFilterMafIterator.h>
+#include <Bpp/Seq/Io/Maf/OutputMafIterator.h>
+#include <Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.h>
+#include <Bpp/Seq/Io/Maf/PlinkOutputMafIterator.h>
+#include <Bpp/Seq/Io/Maf/SequenceLDhotOutputMafIterator.h>
+#include <Bpp/Seq/Io/Maf/CoordinateTranslatorMafIterator.h>
+#include <Bpp/Seq/Io/Maf/CoordinatesOutputMafIterator.h>
+#include <Bpp/Seq/Io/Maf/FullGapFilterMafIterator.h>
+#include <Bpp/Seq/Io/Maf/FilterTreeMafIterator.h>
+#include <Bpp/Seq/Io/Maf/OutputTreeMafIterator.h>
+#include <Bpp/Seq/Io/Maf/OutputAlignmentMafIterator.h>
+#include <Bpp/Seq/Io/Maf/OutputDistanceMatrixMafIterator.h>
+#include <Bpp/Seq/Io/Maf/VcfOutputMafIterator.h>
+#include <Bpp/Seq/Io/Maf/MsmcOutputMafIterator.h>
#include <Bpp/Seq/Io/Maf/SequenceStatisticsMafIterator.h>
#include <Bpp/Seq/Io/Maf/FeatureExtractorMafIterator.h>
#include <Bpp/Seq/Io/Maf/WindowSplitMafIterator.h>
-#include <Bpp/Seq/Io/Maf/OutputAlignmentMafIterator.h>
-#include <Bpp/Seq/Io/Maf/CoordinatesOutputMafIterator.h>
-#include <Bpp/Seq/Io/Maf/VcfOutputMafIterator.h>
#include <Bpp/Seq/Io/Maf/CountDistanceEstimationMafIterator.h>
#include <Bpp/Seq/Io/Maf/MaximumLikelihoodDistanceEstimationMafIterator.h>
-#include <Bpp/Seq/Io/Maf/IterationListener.h>
-#include <Bpp/Seq/Io/Maf/CountClustersMafStatistics.h>
-#include <Bpp/Seq/Io/Maf/MaximumLikelihoodModelFitMafStatistics.h>
#include <Bpp/Seq/Io/Maf/DistanceBasedPhylogenyReconstructionMafIterator.h>
#include <Bpp/Seq/Io/Maf/TreeManipulationMafIterators.h>
-#include <Bpp/Seq/Io/Maf/OutputTreeMafIterator.h>
+#include <Bpp/Seq/Io/Maf/MafStatistics.h>
+#include <Bpp/Seq/Io/Maf/CountClustersMafStatistics.h>
+#include <Bpp/Seq/Io/Maf/MaximumLikelihoodModelFitMafStatistics.h>
+#include <Bpp/Seq/Io/Maf/IterationListener.h>
#include <Bpp/Seq/Feature/Gff/GffFeatureReader.h>
#include <Bpp/Seq/Feature/Gtf/GtfFeatureReader.h>
+#include <Bpp/Seq/Feature/Bed/BedGraphFeatureReader.h>
// From bpp-phyl:
-#include <Bpp/Phyl/OptimizationTools.h>
+#include <Bpp/Phyl/Distance/DistanceEstimation.h>
#include <Bpp/Phyl/Distance/NeighborJoining.h>
#include <Bpp/Phyl/Distance/BioNJ.h>
#include <Bpp/Phyl/Io/BppOSubstitutionModelFormat.h>
#include <Bpp/Phyl/Io/BppORateDistributionFormat.h>
+#include <Bpp/Phyl/Io/BppOTreeReaderFormat.h>
+#include <Bpp/Phyl/OptimizationTools.h>
#include <Bpp/Phyl/App/PhylogeneticsApplicationTools.h>
using namespace bpp;
@@ -125,9 +139,9 @@ void help()
int main(int args, char** argv)
{
cout << "******************************************************************" << endl;
- cout << "* MAF Filter, version 1.1.0 *" << endl;
+ cout << "* MAF Filter, version 1.2.1 *" << endl;
cout << "* Author: J. Dutheil Created on 10/09/10 *" << endl;
- cout << "* Last Modif. 26/09/14 *" << endl;
+ cout << "* Last Modif. 09/06/17 *" << endl;
cout << "******************************************************************" << endl;
cout << endl;
@@ -145,6 +159,7 @@ int main(int args, char** argv)
string inputFile = ApplicationTools::getAFilePath("input.file", maffilter.getParams(), true, true);
string inputFormat = ApplicationTools::getStringParameter("input.format", maffilter.getParams(), "Maf", "", true, false);
string compress = ApplicationTools::getStringParameter("input.file.compression", maffilter.getParams(), "none");
+ string inputDot = ApplicationTools::getStringParameter("input.dots", maffilter.getParams(), "error", "", true, false);
filtering_istream stream;
if (compress == "none") {
@@ -163,9 +178,23 @@ int main(int args, char** argv)
StlOutputStream log(new ofstream(logFile.c_str(), ios::out));
MafIterator* currentIterator;
+
if (inputFormat == "Maf") {
- currentIterator = new MafParser(&stream, true);
+ short dotOption = MafParser::DOT_ERROR;
+ if (inputDot == "as_gaps") {
+ ApplicationTools::displayResult("Maf 'dotted' alignment input", string("converted to gaps"));
+ dotOption = MafParser::DOT_ASGAP;
+ } else if (inputDot == "as_unresolved") {
+ ApplicationTools::displayResult("Maf 'dotted' alignment input", string("converted to unresolved"));
+ dotOption = MafParser::DOT_ASUNRES;
+ }
+
+ bool checkSize = ApplicationTools::getBooleanParameter("input.check_sequence_size", maffilter.getParams(), true, "", true, false);
+ if (!checkSize)
+ ApplicationTools::displayBooleanResult("Check size of sequences", false);
+ currentIterator = new MafParser(&stream, true, checkSize, dotOption);
} else {
+ if (inputDot == "as_gaps") throw Exception("'dot_as_gaps' option only available with Maf input.");
BppOSequenceStreamReaderFormat reader;
ISequenceStream* seqStream = reader.read(inputFormat);
map<string, string> cmdArgs(reader.getUnparsedArguments());
@@ -181,7 +210,7 @@ int main(int args, char** argv)
vector<MafIterator*> its;
its.push_back(currentIterator);
vector<filtering_ostream*> ostreams;
- for (unsigned int a = 0; a < actions.size(); a++) {
+ for (size_t a = 0; a < actions.size(); a++) {
string cmdName;
map<string, string> cmdArgs;
KeyvalTools::parseProcedure(actions[a], cmdName, cmdArgs);
@@ -273,8 +302,11 @@ int main(int args, char** argv)
// +---------------------+
else if (cmdName == "Concatenate") {
unsigned int minimumSize = ApplicationTools::getParameter<unsigned int>("minimum_size", cmdArgs, 0);
+ string ref = ApplicationTools::getStringParameter("ref_species", cmdArgs, "", "", true, 2);
ApplicationTools::displayResult("-- Minimum final block size", minimumSize);
- ConcatenateMafIterator* iterator = new ConcatenateMafIterator(currentIterator, minimumSize);
+ if (ref != "")
+ ApplicationTools::displayResult("-- Reference species", ref);
+ ConcatenateMafIterator* iterator = new ConcatenateMafIterator(currentIterator, minimumSize, ref);
iterator->setLogStream(&log);
iterator->setVerbose(verbose);
currentIterator = iterator;
@@ -306,18 +338,31 @@ int main(int args, char** argv)
throw Exception("At least one species should be provided for command 'AlnFilter'.");
unsigned int ws = ApplicationTools::getParameter<unsigned int>("window.size", cmdArgs, 10);
unsigned int st = ApplicationTools::getParameter<unsigned int>("window.step", cmdArgs, 5);
- unsigned int gm = ApplicationTools::getParameter<unsigned int>("max.gap", cmdArgs, 0);
+ bool relative = ApplicationTools::getBooleanParameter("relative", cmdArgs, false);
+ unsigned int gm = 0;
+ double rm = 0;
+ if (relative)
+ rm = ApplicationTools::getDoubleParameter("max.gap", cmdArgs, 0);
+ else
+ gm = ApplicationTools::getParameter<unsigned int>("max.gap", cmdArgs, 0);
double em = ApplicationTools::getParameter<double>("max.ent", cmdArgs, 0); //Default means no entropy threshold
bool missingAsGap = ApplicationTools::getParameter<bool>("missing_as_gap", cmdArgs, false);
string outputFile = ApplicationTools::getAFilePath("file", cmdArgs, false, false);
bool trash = outputFile == "none";
ApplicationTools::displayResult("-- Window size", ws);
ApplicationTools::displayResult("-- Window step", st);
- ApplicationTools::displayResult("-- Max. gaps allowed in Window", gm);
+ if (relative)
+ ApplicationTools::displayResult("-- Max. gaps allowed in Window", TextTools::toString(rm * 100) + "%");
+ else
+ ApplicationTools::displayResult("-- Max. gaps allowed in Window", gm);
ApplicationTools::displayResult("-- Max. total entropy in Window", em);
ApplicationTools::displayBooleanResult("-- Missing sequence replaced by gaps", missingAsGap);
ApplicationTools::displayBooleanResult("-- Output removed blocks", !trash);
- AlignmentFilterMafIterator* iterator = new AlignmentFilterMafIterator(currentIterator, species, ws, st, gm, em, !trash, missingAsGap);
+ AlignmentFilterMafIterator* iterator;
+ if (relative)
+ iterator = new AlignmentFilterMafIterator(currentIterator, species, ws, st, rm, em, !trash, missingAsGap);
+ else
+ iterator = new AlignmentFilterMafIterator(currentIterator, species, ws, st, gm, em, !trash, missingAsGap);
iterator->setLogStream(&log);
iterator->setVerbose(verbose);
its.push_back(iterator);
@@ -365,18 +410,31 @@ int main(int args, char** argv)
throw Exception("At least one species should be provided for command 'AlnFilter2'.");
unsigned int ws = ApplicationTools::getParameter<unsigned int>("window.size", cmdArgs, 10);
unsigned int st = ApplicationTools::getParameter<unsigned int>("window.step", cmdArgs, 5);
- unsigned int gm = ApplicationTools::getParameter<unsigned int>("max.gap", cmdArgs, 0);
+ bool relative = ApplicationTools::getBooleanParameter("relative", cmdArgs, false);
+ unsigned int gm = 0;
+ double rm = 0;
+ if (relative)
+ rm = ApplicationTools::getDoubleParameter("max.gap", cmdArgs, 0);
+ else
+ gm = ApplicationTools::getParameter<unsigned int>("max.gap", cmdArgs, 0);
unsigned int pm = ApplicationTools::getParameter<unsigned int>("max.pos", cmdArgs, 0);
bool missingAsGap = ApplicationTools::getParameter<bool>("missing_as_gap", cmdArgs, false);
string outputFile = ApplicationTools::getAFilePath("file", cmdArgs, false, false);
bool trash = outputFile == "none";
ApplicationTools::displayResult("-- Window size", ws);
ApplicationTools::displayResult("-- Window step", st);
- ApplicationTools::displayResult("-- Max. gaps allowed per position", gm);
+ if (relative)
+ ApplicationTools::displayResult("-- Max. gaps allowed per position", TextTools::toString(rm * 100) + "%");
+ else
+ ApplicationTools::displayResult("-- Max. gaps allowed per position", gm);
ApplicationTools::displayResult("-- Max. gap positions allowed", pm);
ApplicationTools::displayBooleanResult("-- Missing sequence replaced by gaps", missingAsGap);
ApplicationTools::displayBooleanResult("-- Output removed blocks", !trash);
- AlignmentFilter2MafIterator* iterator = new AlignmentFilter2MafIterator(currentIterator, species, ws, st, gm, pm, !trash, missingAsGap);
+ AlignmentFilter2MafIterator* iterator;
+ if (relative)
+ iterator = new AlignmentFilter2MafIterator(currentIterator, species, ws, st, rm, pm, !trash, missingAsGap);
+ else
+ iterator = new AlignmentFilter2MafIterator(currentIterator, species, ws, st, gm, pm, !trash, missingAsGap);
iterator->setLogStream(&log);
iterator->setVerbose(verbose);
its.push_back(iterator);
@@ -618,19 +676,21 @@ int main(int args, char** argv)
} else
throw Exception("Bad input incompression format: " + compress);
featureStream.push(file_source(featureFile));
- auto_ptr<FeatureReader> ftReader;
+ unique_ptr<FeatureReader> ftReader;
SequenceFeatureSet featuresSet;
if (featureFormat == "GFF") {
ftReader.reset(new GffFeatureReader(featureStream));
} else if (featureFormat == "GTF") {
ftReader.reset(new GtfFeatureReader(featureStream));
- } else
+ } else if (featureFormat == "BedGraph") {
+ ftReader.reset(new BedGraphFeatureReader(featureStream));
+ } else
throw Exception("Unsupported feature format: " + featureFormat);
if (featureType.size() == 1 && featureType[0] == "all")
ftReader->getAllFeatures(featuresSet);
else {
for (size_t i = 0; i < featureType.size(); ++i) {
- ApplicationTools::displayResult("-- Extract features of type", featureType[i]);
+ ApplicationTools::displayResult("-- Filter features of type", featureType[i]);
ftReader->getFeaturesOfType(featureType[i], featuresSet);
}
}
@@ -744,6 +804,72 @@ int main(int args, char** argv)
}
+ // +---------------------------+
+ // | Empty sequences filtering |
+ // +---------------------------+
+ else if (cmdName == "RemoveEmptySequences") {
+ bool unresolvedAsGaps = ApplicationTools::getBooleanParameter("unresolved_as_gaps", cmdArgs, "");
+ ApplicationTools::displayBooleanResult("-- Unresolved as gaps", unresolvedAsGaps);
+ RemoveEmptySequencesMafIterator* iterator = new RemoveEmptySequencesMafIterator(currentIterator, unresolvedAsGaps);
+ iterator->setLogStream(&log);
+ iterator->setVerbose(verbose);
+ currentIterator = iterator;
+ its.push_back(iterator);
+ }
+
+
+ // +----------------+
+ // | Tree filtering |
+ // +----------------+
+ else if (cmdName == "TreeFilter") {
+ string treeProperty = ApplicationTools::getStringParameter("tree", cmdArgs, "none");
+ double maxBrLen = ApplicationTools::getDoubleParameter("max_brlen", cmdArgs, 0.1);
+
+ ApplicationTools::displayResult("-- Max. branch length", maxBrLen);
+ string outputFile = ApplicationTools::getAFilePath("file", cmdArgs, false, false);
+ bool trash = outputFile == "none";
+ FilterTreeMafIterator* iterator = new FilterTreeMafIterator(currentIterator, treeProperty, maxBrLen, !trash);
+ iterator->setLogStream(&log);
+ iterator->setVerbose(verbose);
+ its.push_back(iterator);
+
+ if (!trash) {
+ compress = ApplicationTools::getStringParameter("compression", cmdArgs, "none");
+ filtering_ostream* out = new filtering_ostream;
+ if (compress == "none") {
+ } else if (compress == "gzip") {
+ out->push(gzip_compressor());
+ } else if (compress == "zip") {
+ out->push(zlib_compressor());
+ } else if (compress == "bzip2") {
+ out->push(bzip2_compressor());
+ } else
+ throw Exception("Bad output compression format: " + compress);
+ out->push(file_sink(outputFile));
+ ostreams.push_back(out);
+ ApplicationTools::displayResult("-- File compression for removed blocks", compress);
+
+ //Now build an adaptor for retrieving the trashed blocks:
+ TrashIteratorAdapter* trashIt = new TrashIteratorAdapter(iterator);
+ //Add an output iterator:
+ OutputMafIterator* outIt = new OutputMafIterator(trashIt, out);
+ //And then synchronize the two iterators:
+ MafIteratorSynchronizer* syncIt = new MafIteratorSynchronizer(iterator, outIt);
+ //Returns last iterator:
+ currentIterator = syncIt;
+ //Keep track of all those iterators:
+ its.push_back(trashIt);
+ its.push_back(syncIt);
+ } else {
+ //We only get the remaining blocks here:
+ currentIterator = iterator;
+ }
+ }
+
+
+
+
+
// +---------------------+
// | Sequence statistics |
// +---------------------+
@@ -768,7 +894,9 @@ int main(int args, char** argv)
} else if (statName == "AlnScore") {
mafStat = new AlignmentScoreMafStatistics();
} else if (statName == "BlockCounts") {
- mafStat = new CharacterCountsMafStatistics(&AlphabetTools::DNA_ALPHABET);
+ vector<string> species = ApplicationTools::getVectorParameter<string>("species", statArgs, ',', "", "", false, true);
+ string suffix = ApplicationTools::getStringParameter("suffix", statArgs, "");
+ mafStat = new CharacterCountsMafStatistics(&AlphabetTools::DNA_ALPHABET, species, suffix);
} else if (statName == "PairwiseDivergence") {
string sp1 = ApplicationTools::getStringParameter("species1", statArgs, "");
string sp2 = ApplicationTools::getStringParameter("species2", statArgs, "");
@@ -808,23 +936,38 @@ int main(int args, char** argv)
mafStat = new CountClustersMafStatistics(treeProperty, threshold);
statDesc = " / " + treeProperty;
} else if (statName == "ModelFit") {
- SubstitutionModel* model = PhylogeneticsApplicationTools::getSubstitutionModel(&AlphabetTools::DNA_ALPHABET, 0, 0, statArgs, "", true, false);
- ApplicationTools::displayResult("-- Substitution model", model->getName());
- string freqDescription = ApplicationTools::getStringParameter("root_freq", statArgs, "None");
- FrequenciesSet* rootFreqs = 0;
- if (freqDescription != "None") {
- rootFreqs = PhylogeneticsApplicationTools::getFrequenciesSet(
- &AlphabetTools::DNA_ALPHABET, 0, freqDescription, 0, vector<double>(), 0);
- ApplicationTools::displayResult("-- Root frequencies", rootFreqs->getName());
+ unique_ptr<SubstitutionModel> model;
+ unique_ptr<SubstitutionModelSet> modelSet;
+ unique_ptr<FrequenciesSet> rootFreqs;
+
+ string modelType = ApplicationTools::getStringParameter("model_type", statArgs, "Homogeneous");
+ if (modelType == "Homogeneous") {
+ model.reset(PhylogeneticsApplicationTools::getSubstitutionModel(&AlphabetTools::DNA_ALPHABET, 0, 0, statArgs, "", true, true));
+ ApplicationTools::displayResult("-- Substitution model", model->getName());
+ string freqDescription = ApplicationTools::getStringParameter("root_freq", statArgs, "None");
+ if (freqDescription != "None") {
+ rootFreqs.reset(PhylogeneticsApplicationTools::getFrequenciesSet(
+ &AlphabetTools::DNA_ALPHABET, 0, freqDescription, 0, vector<double>(), 0));
+ ApplicationTools::displayResult("-- Root frequencies", rootFreqs->getName());
+ }
+ } else if (modelType == "Nonhomogeneous") {
+ modelSet.reset(PhylogeneticsApplicationTools::getSubstitutionModelSet(&AlphabetTools::DNA_ALPHABET, 0, 0, statArgs, "", true, true));
+ } else {
+ throw Exception("Unknown model type: " + modelType + ". Must be either Homogeneous or Nonhomogeneous.");
}
- DiscreteDistribution* rDist = PhylogeneticsApplicationTools::getRateDistribution(statArgs, "", true, false);
+
+ unique_ptr<DiscreteDistribution> rDist(PhylogeneticsApplicationTools::getRateDistribution(statArgs, "", true, false));
ApplicationTools::displayResult("-- Rate distribution", rDist->getName());
string treeProperty = ApplicationTools::getStringParameter("tree", statArgs, "none");
vector<string> parametersOutput = ApplicationTools::getVectorParameter<string>("parameters_output", statArgs, ',', "");
vector<string> fixedParametersNames = ApplicationTools::getVectorParameter<string>("fixed_parameters", statArgs, ',', "");
ParameterList fixedParameters;
if (fixedParametersNames.size() > 0) {
- ParameterList parameters = model->getParameters();
+ ParameterList parameters;
+ if (modelSet.get())
+ parameters = modelSet->getParameters();
+ else
+ parameters = model->getParameters();
parameters.addParameters(rDist->getParameters());
fixedParameters = parameters.subList(fixedParametersNames);
}
@@ -834,8 +977,23 @@ int main(int args, char** argv)
ApplicationTools::displayResult("-- Max. frequency of gaps", propGapsToKeep);
bool gapsAsUnresolved = ApplicationTools::getBooleanParameter("gaps_as_unresolved", statArgs, true);
ApplicationTools::displayBooleanResult("-- Gaps as unresolved", gapsAsUnresolved);
- mafStat = new MaximumLikelihoodModelFitMafStatistics(model, rDist, dynamic_cast<NucleotideFrequenciesSet*>(rootFreqs), treeProperty, parametersOutput,
- fixedParameters, reestimateBrLen, propGapsToKeep, gapsAsUnresolved);
+ bool useClock = ApplicationTools::getBooleanParameter("global_clock", statArgs, false);
+ ApplicationTools::displayBooleanResult("-- Use a global molecular clock", useClock);
+ bool reparametrize = ApplicationTools::getBooleanParameter("reparametrize", statArgs, false);
+ ApplicationTools::displayBooleanResult("-- Reparametrization", reparametrize);
+ if (treeProperty == "none") {
+ unique_ptr<Tree> tree(PhylogeneticsApplicationTools::getTree(statArgs, "", "", true, false));
+ if (modelSet.get()) {
+ mafStat = new MaximumLikelihoodModelFitMafStatistics(modelSet.release(), rDist.release(), tree.release(), parametersOutput,
+ fixedParameters, reestimateBrLen, propGapsToKeep, gapsAsUnresolved, useClock, reparametrize);
+ } else {
+ mafStat = new MaximumLikelihoodModelFitMafStatistics(model.release(), rDist.release(), dynamic_cast<NucleotideFrequenciesSet*>(rootFreqs.release()), tree.release(), parametersOutput,
+ fixedParameters, reestimateBrLen, propGapsToKeep, gapsAsUnresolved, useClock, reparametrize);
+ }
+ } else {
+ mafStat = new MaximumLikelihoodModelFitMafStatistics(model.release(), rDist.release(), dynamic_cast<NucleotideFrequenciesSet*>(rootFreqs.release()), treeProperty, parametersOutput,
+ fixedParameters, reestimateBrLen, propGapsToKeep, gapsAsUnresolved, useClock, reparametrize);
+ }
} else {
throw Exception("Unknown statistic: " + statName);
}
@@ -845,8 +1003,25 @@ int main(int args, char** argv)
//Get output file:
string outputFile = ApplicationTools::getAFilePath("file", cmdArgs, true, false);
+ compress = ApplicationTools::getStringParameter("compression", cmdArgs, "none");
ApplicationTools::displayResult("-- Output file", outputFile);
- StlOutputStream* output = new StlOutputStream(new ofstream(outputFile.c_str(), ios::out));
+ filtering_ostream* out = new filtering_ostream;
+ if (compress == "none") {
+ } else if (compress == "gzip") {
+ out->push(gzip_compressor());
+ } else if (compress == "zip") {
+ out->push(zlib_compressor());
+ } else if (compress == "bzip2") {
+ out->push(bzip2_compressor());
+ } else
+ throw Exception("Bad output compression format: " + compress);
+ out->push(file_sink(outputFile));
+ ostreams.push_back(out);
+ //ostreams.push_back(out);
+ ApplicationTools::displayResult("-- File compression", compress);
+ //StlOutputStream* output = new StlOutputStream(new ofstream(outputFile.c_str(), ios::out));
+ StlOutputStream* output = new StlOutputStream(out);
+
SequenceStatisticsMafIterator* iterator = new SequenceStatisticsMafIterator(currentIterator, statistics);
if (cmdArgs.find("reference") != cmdArgs.end()) {
@@ -874,8 +1049,8 @@ int main(int args, char** argv)
string featureFormat = ApplicationTools::getStringParameter("feature.format", cmdArgs, "GFF");
vector<string> featureType = ApplicationTools::getVectorParameter<string>("feature.type", cmdArgs, ',', "all");
if (featureType.size() == 0)
- throw Exception("At least one feature should be provided for command 'FeatureFilter'.");
- ApplicationTools::displayResult("-- Features to remove", featureFile + " (" + featureFormat + ")");
+ throw Exception("At least one feature should be provided for command 'ExtractFeature'.");
+ ApplicationTools::displayResult("-- Features to extract", featureFile + " (" + featureFormat + ")");
ApplicationTools::displayResult("-- Features are for species", refSpecies);
ApplicationTools::displayBooleanResult("-- Features are strand-aware", !ignoreStrand);
ApplicationTools::displayBooleanResult("-- Extract incomplete features", !completeOnly);
@@ -891,13 +1066,15 @@ int main(int args, char** argv)
} else
throw Exception("Bad input incompression format: " + compress);
featureStream.push(file_source(featureFile));
- auto_ptr<FeatureReader> ftReader;
+ unique_ptr<FeatureReader> ftReader;
SequenceFeatureSet featuresSet;
if (featureFormat == "GFF") {
ftReader.reset(new GffFeatureReader(featureStream));
} else if (featureFormat == "GTF") {
ftReader.reset(new GtfFeatureReader(featureStream));
- } else
+ } else if (featureFormat == "BedGraph") {
+ ftReader.reset(new BedGraphFeatureReader(featureStream));
+ } else
throw Exception("Unsupported feature format: " + featureFormat);
if (featureType.size() == 1 && featureType[0] == "all")
ftReader->getAllFeatures(featuresSet);
@@ -908,7 +1085,7 @@ int main(int args, char** argv)
}
}
ApplicationTools::displayResult("-- Total number of features", featuresSet.getNumberOfFeatures());
- FeatureExtractor* iterator = new FeatureExtractor(currentIterator, refSpecies, featuresSet, completeOnly, ignoreStrand);
+ FeatureExtractorMafIterator* iterator = new FeatureExtractorMafIterator(currentIterator, refSpecies, featuresSet, completeOnly, ignoreStrand);
iterator->setLogStream(&log);
iterator->setVerbose(verbose);
its.push_back(iterator);
@@ -939,8 +1116,11 @@ int main(int args, char** argv)
splitOption = WindowSplitMafIterator::ADJUST;
else throw Exception("Unvalid alignment option for WindowSplit: " + splitOptionStr);
ApplicationTools::displayResult("-- Alignment option", splitOptionStr);
+ bool keepSmallBlocks = ApplicationTools::getBooleanParameter("keep_small_blocks", cmdArgs, false);
+ if (splitOptionStr == "adjust")
+ ApplicationTools::displayBooleanResult("-- Keep small blocks", keepSmallBlocks);
- WindowSplitMafIterator* iterator = new WindowSplitMafIterator(currentIterator, preferredSize, splitOption);
+ WindowSplitMafIterator* iterator = new WindowSplitMafIterator(currentIterator, preferredSize, splitOption, keepSmallBlocks);
iterator->setLogStream(&log);
currentIterator = iterator;
its.push_back(iterator);
@@ -970,8 +1150,10 @@ int main(int args, char** argv)
ApplicationTools::displayResult("-- Gap option", gapOption);
bool unresolvedAsGap = ApplicationTools::getBooleanParameter("unresolved_as_gap", cmdArgs, "no");
ApplicationTools::displayBooleanResult("-- Unresolved as gaps", unresolvedAsGap);
+ bool extendedSeqNames = ApplicationTools::getBooleanParameter("extended_names", cmdArgs, true);
+ ApplicationTools::displayBooleanResult("-- Use extended names in matrix", extendedSeqNames);
- CountDistanceEstimationMafIterator* iterator = new CountDistanceEstimationMafIterator(currentIterator, gapOption, unresolvedAsGap);
+ CountDistanceEstimationMafIterator* iterator = new CountDistanceEstimationMafIterator(currentIterator, gapOption, unresolvedAsGap, extendedSeqNames);
ApplicationTools::displayResult("-- Block-wise matrices are registered as", iterator->getPropertyName());
iterator->setLogStream(&log);
currentIterator = iterator;
@@ -995,11 +1177,14 @@ int main(int args, char** argv)
ApplicationTools::displayResult("-- Max. frequency of gaps", propGapsToKeep);
ApplicationTools::displayBooleanResult("-- Gaps as unresolved", gapsAsUnresolved);
+ bool extendedSeqNames = ApplicationTools::getBooleanParameter("extended_names", cmdArgs, true);
+ ApplicationTools::displayBooleanResult("-- Use extended names in matrix", extendedSeqNames);
+
BppOSubstitutionModelFormat modelReader(BppOSubstitutionModelFormat::DNA, false, false, true, true, 1);
- auto_ptr<SubstitutionModel> model(modelReader.read(&AlphabetTools::DNA_ALPHABET, modelDesc, 0, true));
+ unique_ptr<SubstitutionModel> model(modelReader.read(&AlphabetTools::DNA_ALPHABET, modelDesc, 0, true));
BppORateDistributionFormat rdistReader(true);
- auto_ptr<DiscreteDistribution> rdist(rdistReader.read(rdistDesc, true));
- auto_ptr<DistanceEstimation> distEst(new DistanceEstimation(model.release(), rdist.release()));
+ unique_ptr<DiscreteDistribution> rdist(rdistReader.read(rdistDesc, true));
+ unique_ptr<DistanceEstimation> distEst(new DistanceEstimation(model.release(), rdist.release()));
OutputStream* profiler =
(prPath == "none") ? 0 :
@@ -1021,7 +1206,8 @@ int main(int args, char** argv)
ApplicationTools::displayResult("-- Optimization messages in", mhPath);
distEst->getOptimizer()->setMessageHandler(messenger);
- MaximumLikelihoodDistanceEstimationMafIterator* iterator = new MaximumLikelihoodDistanceEstimationMafIterator(currentIterator, distEst.release(), propGapsToKeep, gapsAsUnresolved, paramOpt);
+ MaximumLikelihoodDistanceEstimationMafIterator* iterator = new MaximumLikelihoodDistanceEstimationMafIterator(currentIterator,
+ distEst.release(), propGapsToKeep, gapsAsUnresolved, paramOpt, extendedSeqNames);
ApplicationTools::displayResult("-- Block-wise matrices are registered as", iterator->getPropertyName());
iterator->setLogStream(&log);
iterator->setVerbose(verbose);
@@ -1065,6 +1251,40 @@ int main(int args, char** argv)
+ // +-----------------------------------+
+ // | External phylogeny reconstruction |
+ // +-----------------------------------+
+ else if (cmdName == "ExternalTreeBuilding") {
+ string name = ApplicationTools::getStringParameter("name", cmdArgs, "external");
+
+ string programInputFile = ApplicationTools::getAFilePath("input.file", cmdArgs, true, false);
+ string programInputFormat = ApplicationTools::getStringParameter("input.format", cmdArgs, "Fasta");
+ BppOAlignmentWriterFormat bppoWriter(1);
+ OAlignment* alnWriter(bppoWriter.read(programInputFormat));
+
+ string programOutputFile = ApplicationTools::getAFilePath("output.file", cmdArgs, true, false);
+ string programOutputFormat = ApplicationTools::getStringParameter("output.format", cmdArgs, "Newick");
+ BppOTreeReaderFormat bppoReader(1);
+ ITree* treeReader(bppoReader.read(programOutputFormat));
+
+ string propertyName = ApplicationTools::getStringParameter("property_name", cmdArgs, "ExternalTree");
+ ApplicationTools::displayResult("-- Registering block-wise trees to", propertyName);
+
+ string command = ApplicationTools::getStringParameter("call", cmdArgs, "echo \"TODO: implement wrapper!\"");
+
+ ApplicationTools::displayResult("-- External call (tree building)", name);
+ ApplicationTools::displayResult(" Command", command);
+
+ TreeBuildingSystemCallMafIterator* iterator = new TreeBuildingSystemCallMafIterator(currentIterator, alnWriter, programInputFile, treeReader, programOutputFile, command, propertyName);
+
+ iterator->setLogStream(&log);
+ currentIterator = iterator;
+ its.push_back(iterator);
+ }
+
+
+
+
// +-------------------+
// | Phylogeny rooting |
// +-------------------+
@@ -1139,13 +1359,20 @@ int main(int args, char** argv)
ApplicationTools::displayResult("-- Output alignment file" + string(multipleFiles ? "s" : ""), outputFile);
bool mask = ApplicationTools::getBooleanParameter("mask", cmdArgs, true);
ApplicationTools::displayBooleanResult("-- Output mask", mask);
+ bool coords = ApplicationTools::getBooleanParameter("coordinates", cmdArgs, true);
+ ApplicationTools::displayBooleanResult("-- Output coordinates", coords);
+ bool header = ApplicationTools::getBooleanParameter("ldhat_header", cmdArgs, false);
+ ApplicationTools::displayBooleanResult("-- Output header line", header);
+ string reference = ApplicationTools::getStringParameter("reference", cmdArgs, "", "", true, 1);
+ if (reference != "")
+ ApplicationTools::displayResult("-- Reference species", reference);
OutputAlignmentMafIterator* iterator;
BppOAlignmentWriterFormat bppoWriter(1);
string description = ApplicationTools::getStringParameter("format", cmdArgs, "Clustal");
OAlignment* oAln = bppoWriter.read(description);
if (multipleFiles) {
- iterator = new OutputAlignmentMafIterator(currentIterator, outputFile, oAln, mask);
+ iterator = new OutputAlignmentMafIterator(currentIterator, outputFile, oAln, mask, coords, header, reference);
} else {
compress = ApplicationTools::getStringParameter("compression", cmdArgs, "none");
filtering_ostream* out = new filtering_ostream;
@@ -1161,7 +1388,7 @@ int main(int args, char** argv)
out->push(file_sink(outputFile));
ostreams.push_back(out);
ApplicationTools::displayResult("-- File compression", compress);
- iterator = new OutputAlignmentMafIterator(currentIterator, out, oAln, mask);
+ iterator = new OutputAlignmentMafIterator(currentIterator, out, oAln, mask, coords, header, reference);
}
currentIterator = iterator;
its.push_back(iterator);
@@ -1231,7 +1458,126 @@ int main(int args, char** argv)
for (size_t i = 0; i < genotypes.size(); ++i) {
ApplicationTools::displayResult("-- Adding genotype info for", genotypes[i]);
}
- VcfOutputMafIterator* iterator = new VcfOutputMafIterator(currentIterator, out, reference, genotypes);
+
+ bool outputAll = ApplicationTools::getBooleanParameter("all", cmdArgs, false);
+ ApplicationTools::displayBooleanResult("-- Output non-variable positions", outputAll);
+
+ VcfOutputMafIterator* iterator = new VcfOutputMafIterator(currentIterator, out, reference, genotypes, outputAll);
+
+ iterator->setLogStream(&log);
+ iterator->setVerbose(verbose);
+ currentIterator = iterator;
+ its.push_back(iterator);
+ }
+
+
+
+ // +-------------+
+ // | MSMC output |
+ // +-------------+
+ else if (cmdName == "MsmcOutput") {
+ string outputFile = ApplicationTools::getAFilePath("file", cmdArgs, true, false);
+ compress = ApplicationTools::getStringParameter("compression", cmdArgs, "none");
+ ApplicationTools::displayResult("-- Output file", outputFile);
+ filtering_ostream* out = new filtering_ostream;
+ if (compress == "none") {
+ } else if (compress == "gzip") {
+ out->push(gzip_compressor());
+ } else if (compress == "zip") {
+ out->push(zlib_compressor());
+ } else if (compress == "bzip2") {
+ out->push(bzip2_compressor());
+ } else
+ throw Exception("Bad output compression format: " + compress);
+ out->push(file_sink(outputFile));
+ ostreams.push_back(out);
+ ApplicationTools::displayResult("-- File compression", compress);
+
+ string reference = ApplicationTools::getStringParameter("reference", cmdArgs, "");
+ if (reference == "")
+ throw Exception("A reference sequence should be provided for filter 'MsmcOutput'.");
+ ApplicationTools::displayResult("-- Reference sequence", reference);
+
+ vector<string> species = ApplicationTools::getVectorParameter<string>("genotypes", cmdArgs, ',', "");
+ if (species.size() < 2)
+ throw Exception("MsmcOutput: at least two genomes are necessary to call SNPs.");
+ MsmcOutputMafIterator* iterator = new MsmcOutputMafIterator(currentIterator, out, species, reference);
+
+ iterator->setLogStream(&log);
+ iterator->setVerbose(verbose);
+ currentIterator = iterator;
+ its.push_back(iterator);
+ }
+
+
+
+ // +--------------+
+ // | PLINK output |
+ // +--------------+
+ else if (cmdName == "PlinkOutput") {
+ string outputPedFile = ApplicationTools::getAFilePath("ped_file", cmdArgs, true, false);
+ string outputMapFile = ApplicationTools::getAFilePath("map_file", cmdArgs, true, false);
+ compress = ApplicationTools::getStringParameter("compression", cmdArgs, "none");
+ ApplicationTools::displayResult("-- Output Ped file", outputPedFile);
+ ApplicationTools::displayResult("-- Output Map file", outputMapFile);
+ filtering_ostream* outPed = new filtering_ostream;
+ filtering_ostream* outMap = new filtering_ostream;
+ if (compress == "none") {
+ } else if (compress == "gzip") {
+ outPed->push(gzip_compressor());
+ outMap->push(gzip_compressor());
+ } else if (compress == "zip") {
+ outPed->push(zlib_compressor());
+ outMap->push(zlib_compressor());
+ } else if (compress == "bzip2") {
+ outPed->push(bzip2_compressor());
+ outMap->push(bzip2_compressor());
+ } else
+ throw Exception("Bad output compression format: " + compress);
+ outPed->push(file_sink(outputPedFile));
+ outMap->push(file_sink(outputMapFile));
+ ostreams.push_back(outPed);
+ ostreams.push_back(outMap);
+ ApplicationTools::displayResult("-- File compression", compress);
+
+ string reference = ApplicationTools::getStringParameter("reference", cmdArgs, "");
+ if (reference == "")
+ throw Exception("A reference sequence should be provided for filter 'PlinkOutput'.");
+ ApplicationTools::displayResult("-- Reference sequence", reference);
+
+ bool map3 = ApplicationTools::getBooleanParameter("map3", cmdArgs, false);
+ ApplicationTools::displayBooleanResult("-- Ouput map3 file", map3);
+
+ vector<string> species = ApplicationTools::getVectorParameter<string>("genotypes", cmdArgs, ',', "");
+ if (species.size() < 2)
+ throw Exception("PlinkOutput: at least two genomes are necessary to call SNPs.");
+ PlinkOutputMafIterator* iterator = new PlinkOutputMafIterator(currentIterator, outPed, outMap, species, reference, map3);
+
+ iterator->setLogStream(&log);
+ iterator->setVerbose(verbose);
+ currentIterator = iterator;
+ its.push_back(iterator);
+ }
+
+
+
+ // +----------------------+
+ // | SequenceLDhot output |
+ // +----------------------+
+ else if (cmdName == "SequenceLDhotOutput") {
+ string outputFile = ApplicationTools::getAFilePath("file", cmdArgs, true, false);
+ ApplicationTools::displayResult("-- Output file", outputFile);
+
+ string reference = ApplicationTools::getStringParameter("reference", cmdArgs, "");
+ if (!TextTools::isEmpty(reference))
+ ApplicationTools::displayResult("-- Reference sequence", reference);
+ else
+ reference = "";
+
+ bool completeOnly = ApplicationTools::getBooleanParameter("complete_only", cmdArgs, true);
+ ApplicationTools::displayBooleanResult("-- Use only complete sites", completeOnly);
+
+ SequenceLDhotOutputMafIterator* iterator = new SequenceLDhotOutputMafIterator(currentIterator, outputFile, completeOnly, reference);
iterator->setLogStream(&log);
iterator->setVerbose(verbose);
@@ -1267,10 +1613,13 @@ int main(int args, char** argv)
throw Exception("At least one species should be provided for filter 'OutputCoordinates'.");
ApplicationTools::displayResult("-- Output coordinates for", TextTools::toString(species.size()) + " species");
+ bool includeSrcSize = ApplicationTools::getBooleanParameter("output_src_size", cmdArgs, true);
+ ApplicationTools::displayBooleanResult("-- Output src size", includeSrcSize);
+
for (size_t i = 0; i < species.size(); ++i) {
ApplicationTools::displayResult("-- Output coordinates for species", species[i]);
}
- CoordinatesOutputMafIterator* iterator = new CoordinatesOutputMafIterator(currentIterator, out, species);
+ CoordinatesOutputMafIterator* iterator = new CoordinatesOutputMafIterator(currentIterator, out, species, includeSrcSize);
iterator->setLogStream(&log);
iterator->setVerbose(verbose);
@@ -1281,6 +1630,72 @@ int main(int args, char** argv)
+ // +------------------------+
+ // | Coordinates conversion |
+ // +------------------------+
+ else if (cmdName == "LiftOver") {
+ //Input
+ string refSpecies = ApplicationTools::getStringParameter("ref_species", cmdArgs, "none");
+ string targetSpecies = ApplicationTools::getStringParameter("target_species", cmdArgs, "none");
+ string featureFile = ApplicationTools::getAFilePath("feature.file", cmdArgs, false, false);
+ string featureFormat = ApplicationTools::getStringParameter("feature.format", cmdArgs, "GFF");
+ ApplicationTools::displayResult("-- Features to lift over", featureFile + " (" + featureFormat + ")");
+ ApplicationTools::displayResult("-- from species", refSpecies);
+ ApplicationTools::displayResult("-- to species", targetSpecies);
+ compress = ApplicationTools::getStringParameter("feature.file.compression", cmdArgs, "none");
+ filtering_istream featureStream;
+ if (compress == "none") {
+ } else if (compress == "gzip") {
+ featureStream.push(gzip_decompressor());
+ } else if (compress == "zip") {
+ featureStream.push(zlib_decompressor());
+ } else if (compress == "bzip2") {
+ featureStream.push(bzip2_decompressor());
+ } else
+ throw Exception("Bad input incompression format: " + compress);
+ featureStream.push(file_source(featureFile));
+ unique_ptr<FeatureReader> ftReader;
+ SequenceFeatureSet featuresSet;
+ if (featureFormat == "GFF") {
+ ftReader.reset(new GffFeatureReader(featureStream));
+ } else if (featureFormat == "GTF") {
+ ftReader.reset(new GtfFeatureReader(featureStream));
+ } else if (featureFormat == "BedGraph") {
+ ftReader.reset(new BedGraphFeatureReader(featureStream));
+ } else
+ throw Exception("Unsupported feature format: " + featureFormat);
+ ftReader->getAllFeatures(featuresSet);
+ ApplicationTools::displayResult("-- Total number of features", featuresSet.getNumberOfFeatures());
+
+ //Output
+ string outputFile = ApplicationTools::getAFilePath("file", cmdArgs, true, false);
+ compress = ApplicationTools::getStringParameter("compression", cmdArgs, "none");
+ ApplicationTools::displayResult("-- Output file", outputFile);
+ filtering_ostream* out = new filtering_ostream;
+ if (compress == "none") {
+ } else if (compress == "gzip") {
+ out->push(gzip_compressor());
+ } else if (compress == "zip") {
+ out->push(zlib_compressor());
+ } else if (compress == "bzip2") {
+ out->push(bzip2_compressor());
+ } else
+ throw Exception("Bad output compression format: " + compress);
+ out->push(file_sink(outputFile));
+ ostreams.push_back(out);
+ ApplicationTools::displayResult("-- File compression", compress);
+
+ //Iterator initialization:
+ CoordinateTranslatorMafIterator* iterator = new CoordinateTranslatorMafIterator(currentIterator, refSpecies, targetSpecies, featuresSet, *out);
+ iterator->setLogStream(&log);
+ iterator->setVerbose(verbose);
+ its.push_back(iterator);
+
+ currentIterator = iterator;
+ }
+
+
+
// +--------------+
// | Output trees |
// +--------------+
@@ -1303,14 +1718,82 @@ int main(int args, char** argv)
ApplicationTools::displayResult("-- File compression", compress);
string treeProperty = ApplicationTools::getStringParameter("tree", cmdArgs, "none");
ApplicationTools::displayResult("-- Tree to write", treeProperty);
- OutputTreeMafIterator* iterator = new OutputTreeMafIterator(currentIterator, out, treeProperty);
+ bool stripNames = ApplicationTools::getBooleanParameter("strip_names", cmdArgs, false);
+ ApplicationTools::displayBooleanResult("-- Strip names", stripNames);
+
+ OutputTreeMafIterator* iterator = new OutputTreeMafIterator(currentIterator, out, treeProperty, !stripNames);
currentIterator = iterator;
its.push_back(iterator);
}
+
+
+
+ // +--------------------------+
+ // | Output Distance matrices |
+ // +--------------------------+
+ else if (cmdName == "OutputDistanceMatrices") {
+ string outputFile = ApplicationTools::getAFilePath("file", cmdArgs, true, false);
+ compress = ApplicationTools::getStringParameter("compression", cmdArgs, "none");
+ ApplicationTools::displayResult("-- Output matrix file", outputFile);
+ filtering_ostream* out = new filtering_ostream;
+ if (compress == "none") {
+ } else if (compress == "gzip") {
+ out->push(gzip_compressor());
+ } else if (compress == "zip") {
+ out->push(zlib_compressor());
+ } else if (compress == "bzip2") {
+ out->push(bzip2_compressor());
+ } else
+ throw Exception("Bad output compression format: " + compress);
+ out->push(file_sink(outputFile));
+ ostreams.push_back(out);
+ ApplicationTools::displayResult("-- File compression", compress);
+ string distProperty = ApplicationTools::getStringParameter("distance", cmdArgs, "none");
+ ApplicationTools::displayResult("-- Matrix to write", distProperty);
+ bool stripNames = ApplicationTools::getBooleanParameter("strip_names", cmdArgs, false);
+ ApplicationTools::displayBooleanResult("-- Strip names", stripNames);
+
+ OutputDistanceMatrixMafIterator* iterator = new OutputDistanceMatrixMafIterator(currentIterator, out, distProperty, !stripNames);
+ currentIterator = iterator;
+ its.push_back(iterator);
+ }
+
+
+
+
+ // +--------------------------+
+ // | External program wrapper |
+ // +--------------------------+
+ else if (cmdName == "SystemCall") {
+ string name = ApplicationTools::getStringParameter("name", cmdArgs, "external");
+
+ string programInputFile = ApplicationTools::getAFilePath("input.file", cmdArgs, true, false);
+ string programInputFormat = ApplicationTools::getStringParameter("input.format", cmdArgs, "Fasta");
+ BppOAlignmentWriterFormat bppoWriter(1);
+ OAlignment* alnWriter(bppoWriter.read(programInputFormat));
+
+ string programOutputFile = ApplicationTools::getAFilePath("output.file", cmdArgs, true, false);
+ string programOutputFormat = ApplicationTools::getStringParameter("output.format", cmdArgs, "Fasta");
+ BppOAlignmentReaderFormat bppoReader(1);
+ IAlignment* alnReader(bppoReader.read(programOutputFormat));
+
+ string command = ApplicationTools::getStringParameter("call", cmdArgs, "echo \"TODO: implement wrapper!\"");
+
+ ApplicationTools::displayResult("-- External call", name);
+ ApplicationTools::displayResult(" Command", command);
+
+ SystemCallMafIterator* iterator = new SystemCallMafIterator(currentIterator, alnWriter, programInputFile, alnReader, programOutputFile, command);
+
+ iterator->setLogStream(&log);
+ iterator->setVerbose(verbose);
+ currentIterator = iterator;
+ its.push_back(iterator);
+ }
+
+
else
throw Exception("Unknown filter: " + cmdName);
-
}
//Now loop over the last iterator and that's it!
diff --git a/MafFilter/SystemCallMafIterator.cpp b/MafFilter/SystemCallMafIterator.cpp
new file mode 100644
index 0000000..749afbb
--- /dev/null
+++ b/MafFilter/SystemCallMafIterator.cpp
@@ -0,0 +1,84 @@
+//
+// File: SystemCallMafIterator.cpp
+// Authors: Julien Dutheil
+// Created: Tue Sep 29 2015
+//
+
+/*
+Copyright or © or Copr. Julien Y. Dutheil, (2015)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "SystemCallMafIterator.h"
+
+using namespace bpp;
+using namespace std;
+
+MafBlock* SystemCallMafIterator::analyseCurrentBlock_() throw (Exception) {
+ currentBlock_ = iterator_->nextBlock();
+ if (! currentBlock_)
+ return 0;
+ unique_ptr<AlignedSequenceContainer> aln(currentBlock_->getAlignment().clone());
+
+ //We translate sequence names to avoid compatibility issues
+ vector<string> names(aln->getNumberOfSequences());
+ for (size_t i = 0; i < names.size(); ++i) {
+ names[i] = "seq" + TextTools::toString(i);
+ }
+ aln->setSequencesNames(names);
+
+ //Write sequences to file:
+ alnWriter_->writeAlignment(inputFile_, *aln, true);
+
+ //Call the external program:
+ int rc = system(call_.c_str());
+ if (rc) throw Exception("SystemCallMafIterator::analyseCurrentBlock_(). System call exited with non-zero status.");
+
+ //Then read and assign the realigned sequences:
+ unique_ptr<SiteContainer> result(alnReader_->readAlignment(outputFile_, &AlphabetTools::DNA_ALPHABET));
+ vector<MafSequence*> tmp;
+ for (size_t i = 0; i < currentBlock_->getNumberOfSequences(); ++i) {
+ MafSequence* mseq = currentBlock_->getSequence(i).cloneMeta();
+ //NB: we discard any putative score associated to this sequence.
+ string name = "seq" + TextTools::toString(i);
+ mseq->setContent(dynamic_cast<const BasicSequence&>(result->getSequence(name)).toString()); //NB shall we use getContent here?
+ tmp.push_back(mseq);
+ }
+ currentBlock_->getAlignment().clear();
+ for (size_t i = 0; i < tmp.size(); ++i) {
+ currentBlock_->getAlignment().addSequence(*tmp[i], false);
+ delete tmp[i];
+ }
+
+ //Done:
+ return currentBlock_;
+}
+
diff --git a/MafFilter/SystemCallMafIterator.h b/MafFilter/SystemCallMafIterator.h
new file mode 100644
index 0000000..472f5fb
--- /dev/null
+++ b/MafFilter/SystemCallMafIterator.h
@@ -0,0 +1,110 @@
+//
+// File: SystemCallMafIterator.h
+// Authors: Julien Dutheil
+// Created: Tue Sep 29 2015
+//
+
+/*
+Copyright or © or Copr. Julien Y. Dutheil, (2015)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _SYSTEMCALLMAFITERATOR_H_
+#define _SYSTEMCALLMAFITERATOR_H_
+
+#include <Bpp/Seq/Io/Maf/MafIterator.h>
+#include <Bpp/Seq/Io/ISequence.h>
+#include <Bpp/Seq/Io/OSequence.h>
+
+//From the STL:
+#include <iostream>
+#include <string>
+#include <memory>
+
+namespace bpp {
+
+/**
+ * @brief This iterator calls an external program on each block.
+ */
+class SystemCallMafIterator:
+ public AbstractFilterMafIterator
+{
+ private:
+ std::unique_ptr<OAlignment> alnWriter_;
+ std::string inputFile_;
+ std::unique_ptr<IAlignment> alnReader_;
+ std::string outputFile_;
+ std::string call_;
+
+ public:
+ SystemCallMafIterator(
+ MafIterator* iterator,
+ OAlignment* alnWriter,
+ const std::string& inputFile,
+ IAlignment* alnReader,
+ const std::string& outputFile,
+ const std::string& callCmd) :
+ AbstractFilterMafIterator(iterator),
+ alnWriter_(alnWriter),
+ inputFile_(inputFile),
+ alnReader_(alnReader),
+ outputFile_(outputFile),
+ call_(callCmd)
+ {}
+
+ private:
+ SystemCallMafIterator(const SystemCallMafIterator& iterator) :
+ AbstractFilterMafIterator(0),
+ alnWriter_(),
+ inputFile_(iterator.inputFile_),
+ alnReader_(),
+ outputFile_(iterator.outputFile_),
+ call_(iterator.call_)
+ {}
+
+ SystemCallMafIterator& operator=(const SystemCallMafIterator& iterator)
+ {
+ inputFile_ = iterator.inputFile_;
+ outputFile_ = iterator.outputFile_;
+ call_ = iterator.call_;
+ return *this;
+ }
+
+
+ public:
+ MafBlock* analyseCurrentBlock_() throw (Exception);
+
+};
+
+} // namespace bpp.
+
+#endif //_SYSTEMCALLMAFITERATOR_H_
+
diff --git a/MafFilter/TreeBuildingSystemCallMafIterator.cpp b/MafFilter/TreeBuildingSystemCallMafIterator.cpp
new file mode 100644
index 0000000..952554b
--- /dev/null
+++ b/MafFilter/TreeBuildingSystemCallMafIterator.cpp
@@ -0,0 +1,82 @@
+//
+// File: TreeBuildingSystemCallMafIterator.cpp
+// Authors: Julien Dutheil
+// Created: Sat Jun 18 2016
+//
+
+/*
+Copyright or © or Copr. Julien Y. Dutheil, (2016)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#include "TreeBuildingSystemCallMafIterator.h"
+
+// From bpp-phyl
+#include "Bpp/Phyl/TreeTemplate.h"
+
+using namespace bpp;
+using namespace std;
+
+MafBlock* TreeBuildingSystemCallMafIterator::analyseCurrentBlock_() throw (Exception) {
+ currentBlock_ = iterator_->nextBlock();
+ if (! currentBlock_)
+ return 0;
+ unique_ptr<AlignedSequenceContainer> aln(currentBlock_->getAlignment().clone());
+
+ //We translate sequence names to avoid compatibility issues
+ vector<string> names(aln->getNumberOfSequences());
+ map<string, string> nameIndex;
+ for (size_t i = 0; i < names.size(); ++i) {
+ names[i] = "seq" + TextTools::toString(i);
+ nameIndex[names[i]] = currentBlock_->getSequence(i).getName();
+ }
+ aln->setSequencesNames(names);
+
+ //Write sequences to file:
+ alnWriter_->writeAlignment(inputFile_, *aln, true);
+
+ //Call the external program:
+ int rc = system(call_.c_str());
+ if (rc) throw Exception("TreeBuildingSystemCallMafIterator::analyseCurrentBlock_(). System call exited with non-zero status.");
+
+ //Then read the generated tree and assign sequence names:
+ unique_ptr< Tree > result(treeReader_->read(outputFile_));
+ unique_ptr< TreeTemplate<Node> > tree(new TreeTemplate<Node>(*result));
+ vector<Node*> leaves = tree->getLeaves();
+ for (size_t i = 0; i < leaves.size(); ++i) {
+ leaves[i]->setName(nameIndex[leaves[i]->getName()]);
+ }
+ currentBlock_->setProperty(propertyName_, tree.release());
+
+ //Done:
+ return currentBlock_;
+}
+
diff --git a/MafFilter/TreeBuildingSystemCallMafIterator.h b/MafFilter/TreeBuildingSystemCallMafIterator.h
new file mode 100644
index 0000000..e93a94a
--- /dev/null
+++ b/MafFilter/TreeBuildingSystemCallMafIterator.h
@@ -0,0 +1,115 @@
+//
+// File: TreeBuildingSystemCallMafIterator.h
+// Authors: Julien Dutheil
+// Created: Sat Jun 18 2016
+//
+
+/*
+Copyright or © or Copr. Julien Y. Dutheil, (2016)
+
+This software is a computer program whose purpose is to provide classes
+for sequences analysis.
+
+This software is governed by the CeCILL license under French law and
+abiding by the rules of distribution of free software. You can use,
+modify and/ or redistribute the software under the terms of the CeCILL
+license as circulated by CEA, CNRS and INRIA at the following URL
+"http://www.cecill.info".
+
+As a counterpart to the access to the source code and rights to copy,
+modify and redistribute granted by the license, users are provided only
+with a limited warranty and the software's author, the holder of the
+economic rights, and the successive licensors have only limited
+liability.
+
+In this respect, the user's attention is drawn to the risks associated
+with loading, using, modifying and/or developing or reproducing the
+software by the user in light of its specific status of free software,
+that may mean that it is complicated to manipulate, and that also
+therefore means that it is reserved for developers and experienced
+professionals having in-depth computer knowledge. Users are therefore
+encouraged to load and test the software's suitability as regards their
+requirements in conditions enabling the security of their systems and/or
+data to be ensured and, more generally, to use and operate it in the
+same conditions as regards security.
+
+The fact that you are presently reading this means that you have had
+knowledge of the CeCILL license and that you accept its terms.
+*/
+
+#ifndef _TREEBUILDINGSYSTEMCALLMAFITERATOR_H_
+#define _TREEBUILDINGSYSTEMCALLMAFITERATOR_H_
+
+#include <Bpp/Seq/Io/Maf/MafIterator.h>
+#include <Bpp/Phyl/Io/IoTree.h>
+#include <Bpp/Seq/Io/OSequence.h>
+
+//From the STL:
+#include <iostream>
+#include <string>
+#include <memory>
+
+namespace bpp {
+
+/**
+ * @brief This iterator calls an external program on each block.
+ */
+class TreeBuildingSystemCallMafIterator:
+ public AbstractFilterMafIterator
+{
+ private:
+ std::unique_ptr<OAlignment> alnWriter_;
+ std::string inputFile_;
+ std::unique_ptr<ITree> treeReader_;
+ std::string outputFile_;
+ std::string call_;
+ std::string propertyName_;
+
+ public:
+ TreeBuildingSystemCallMafIterator(
+ MafIterator* iterator,
+ OAlignment* alnWriter,
+ const std::string& inputFile,
+ ITree* treeReader,
+ const std::string& outputFile,
+ const std::string& callCmd,
+ const std::string& propertyName) :
+ AbstractFilterMafIterator(iterator),
+ alnWriter_(alnWriter),
+ inputFile_(inputFile),
+ treeReader_(treeReader),
+ outputFile_(outputFile),
+ call_(callCmd),
+ propertyName_(propertyName)
+ {}
+
+ private:
+ TreeBuildingSystemCallMafIterator(const TreeBuildingSystemCallMafIterator& iterator) :
+ AbstractFilterMafIterator(0),
+ alnWriter_(),
+ inputFile_(iterator.inputFile_),
+ treeReader_(),
+ outputFile_(iterator.outputFile_),
+ call_(iterator.call_),
+ propertyName_(iterator.propertyName_)
+ {}
+
+ TreeBuildingSystemCallMafIterator& operator=(const TreeBuildingSystemCallMafIterator& iterator)
+ {
+ inputFile_ = iterator.inputFile_;
+ outputFile_ = iterator.outputFile_;
+ call_ = iterator.call_;
+ propertyName_ = iterator.propertyName_;
+ return *this;
+ }
+
+
+ public:
+ MafBlock* analyseCurrentBlock_() throw (Exception);
+
+};
+
+} // namespace bpp.
+
+#endif //_TREEBUILDINGSYSTEMCALLMAFITERATOR_H_
+
diff --git a/buildBin.sh b/buildBin.sh
new file mode 100755
index 0000000..6fa30da
--- /dev/null
+++ b/buildBin.sh
@@ -0,0 +1,7 @@
+#! /bin/sh
+arch=`uname -m`
+version=1.1.99-1
+
+strip MafFilter/maffilter
+tar cvzf maffilter-${arch}-bin-static-${version}.tar.gz MafFilter/maffilter
+
diff --git a/doc/CMakeLists.txt b/doc/CMakeLists.txt
index 82410f0..2260250 100644
--- a/doc/CMakeLists.txt
+++ b/doc/CMakeLists.txt
@@ -1,7 +1,75 @@
-# CMake script for GenomeTools
-# Author: Julien Dutheil
-# Created: 09/09/2012
+# CMake script for MafFilter
+# Authors:
+# Julien Dutheil
+# Francois Gindraud (2017)
+# Created: 22/08/2009
-IF(INFO)
- INSTALL(FILES maffilter.info DESTINATION share/info)
-ENDIF(INFO)
+# Builds info, html, pdf doc.
+# Info doc is built and install as part of "all" if makeinfo is found.
+# Html doc is proposed as a "html" optional target if makeinfo is found.
+# Pdf doc is proposed as a "pdf" optional target if makeinfo AND texi2dvi are found.
+
+find_program (MAKEINFO NAMES makeinfo texi2any DOC "makeinfo doc generator program")
+if (NOT MAKEINFO)
+ message (STATUS "makeinfo program not found: 'info' and 'html' target disabled (builds info/html doc)")
+else (NOT MAKEINFO)
+ message (STATUS "Found makeinfo as '${MAKEINFO}': 'info' and 'html' target enabled (builds info/html doc)")
+
+ set (input ${CMAKE_CURRENT_SOURCE_DIR}/maffilter.texi)
+
+ # Build and install info page
+ set (output ${CMAKE_CURRENT_BINARY_DIR}/maffilter.info)
+ add_custom_command (
+ OUTPUT ${output}
+ COMMAND ${MAKEINFO} --no-split -o ${output} ${input}
+ DEPENDS ${input}
+ COMMENT "Generating info page"
+ VERBATIM
+ )
+
+ # Install, and have "info" built with "all" (install needs the file to be built)
+ if (NOT COMPRESS_BIN)
+ # Install uncompressed info page
+ install (FILES ${output} DESTINATION ${CMAKE_INSTALL_INFODIR})
+ add_custom_target (info ALL DEPENDS ${output})
+ else ()
+ # Compress and install compressed file
+ set (compressed_ouput ${output}.${COMPRESS_EXT})
+ add_custom_command (
+ OUTPUT ${compressed_ouput}
+ COMMAND ${COMPRESS_BIN} ${COMPRESS_ARGS} ${output} > ${compressed_ouput}
+ DEPENDS ${output}
+ COMMENT "Compressing info page"
+ VERBATIM
+ )
+ install (FILES ${compressed_ouput} DESTINATION ${CMAKE_INSTALL_INFODIR})
+ add_custom_target (info ALL DEPENDS ${compressed_ouput})
+ endif ()
+
+ # Also provide a "html" target that builds html doc (not installed, and not part of "all").
+ set (output ${CMAKE_CURRENT_BINARY_DIR}/maffilter.html)
+ set (makeinfo-css "http://www.w3.org/StyleSheets/Core/Steely")
+ add_custom_command (
+ OUTPUT ${output}
+ COMMAND ${MAKEINFO} --html --css-ref=${makeinfo-css} --no-split -o ${output} ${input}
+ DEPENDS ${input}
+ COMMENT "Generating html doc"
+ VERBATIM
+ )
+ add_custom_target (html DEPENDS ${output})
+
+ # Provide a "pdf" target that builds pdf doc (not installed, not part of "all").
+ find_program (TEXIDVI NAMES texi2dvi)
+ if (TEXIDVI)
+ message (STATUS "Found texi2dvi: 'pdf' target enabled (builds pdf doc)")
+ set (output ${CMAKE_CURRENT_BINARY_DIR}/maffilter.pdf)
+ add_custom_command (
+ OUTPUT ${output}
+ COMMAND ${MAKEINFO} --pdf --Xopt=--clean -o ${output} ${input}
+ DEPENDS ${input}
+ COMMENT "Generating pdf doc"
+ VERBATIM
+ )
+ add_custom_target (pdf DEPENDS ${output})
+ endif ()
+endif ()
diff --git a/doc/maffilter.texi b/doc/maffilter.texi
index 8ef78b4..90e6c8f 100644
--- a/doc/maffilter.texi
+++ b/doc/maffilter.texi
@@ -1,8 +1,8 @@
\input texinfo @c -*-texinfo-*-
@c %**start of header
@setfilename maffilter.info
- at settitle MafFilter Manual 1.1.0
- at c documentencoding UTF-8
+ at settitle MafFilter Manual 1.2.1
+ at c @documentencoding UTF-8
@afourpaper
@dircategory Science Biology Genetics
@direntry
@@ -12,15 +12,15 @@
@copying
-This is the manual of MafFilter, version 1.1.0.
+This is the manual of MafFilter, version 1.2.1.
-Copyright @copyright{} 2014 Julien Y. Dutheil
+Copyright @copyright{} 2017 Julien Y. Dutheil
@end copying
@titlepage
@title MafFilter Manual
@author Julien Dutheil
- at author @email{julien.dutheil@@univ-montp2.fr}
+ at author @email{dutheil@@evolbio.mpg.de}
@c The following two commands start the copyright page.
@@ -37,89 +37,101 @@ Copyright @copyright{} 2014 Julien Y. Dutheil
@top The MafFilter Manual
@insertcopying
- at end ifnottex
@menu
-* Introduction::
-* Filters::
+* Introduction::
+* Filters::
@detailmenu
--- The Detailed Node Listing ---
Introduction
-* Description::
-* Run::
-* General::
+* Description::
+* Run::
+* General::
Filters
-* Extracting::
-* Cleaning::
-* Analyzing::
-* Exporting::
+* Extracting::
+* Cleaning::
+* Analyzing::
+* Exporting::
+* Miscelaneous::
Extracting data
-* Subset::
-* SelectOrphans::
-* Merge::
-* Concatenate::
-* ExtractFeature::
-* SelectChr::
-* WindowSplit::
+* Subset::
+* SelectOrphans::
+* Merge::
+* Concatenate::
+* ExtractFeature::
+* SelectChr::
+* WindowSplit::
Cleaning alignment blocks
-* MinBlockLength::
-* MinBlockSize::
-* XFullGap::
-* AlnFilter::
-* AlnFilter2::
-* EntropyFilter::
-* MaskFilter::
-* QualFilter::
-* FeatureFilter::
+* MinBlockLength::
+* MinBlockSize::
+* XFullGap::
+* RemoveEmptySequences::
+* AlnFilter::
+* AlnFilter2::
+* EntropyFilter::
+* MaskFilter::
+* QualFilter::
+* FeatureFilter::
Statistical analysis
-* Descriptive::
-* Phylogenetics::
+* Descriptive::
+* Phylogenetics::
Arguments:
-* BlockSize::
-* BlockLength::
-* SequenceLength::
-* AlnScore::
-* BlockCounts::
-* PairwiseDivergence::
-* SiteStatistics::
-* FourSpeciesSitePatternCounts::
-* SiteFrequencySpectrum::
-* PolymorphismStatistics::
-* DiversityStatistics::
-* CountClusters::
-* ModelFit::
+* BlockSize::
+* BlockLength::
+* SequenceLength::
+* AlnScore::
+* BlockCounts::
+* PairwiseDivergence::
+* SiteStatistics::
+* FourSpeciesSitePatternCounts::
+* SiteFrequencySpectrum::
+* PolymorphismStatistics::
+* DiversityStatistics::
+* CountClusters::
+* ModelFit::
Phylogenetics
-* DistanceEstimation::
-* DistanceBasedPhylogeny::
-* NewOutgroup::
-* DropSpecies::
+* DistanceEstimation::
+* DistanceBasedPhylogeny::
+* NewOutgroup::
+* DropSpecies::
+* TreeFilter::
Exporting blocks and data
-* Output::
-* OutputAlignments::
-* VcfOutput::
-* OutputCoordinates::
-* OutputTrees::
+* Output::
+* OutputAlignments::
+* VcfOutput::
+* MsmcOutput::
+* PlinkOutput::
+* OutputCoordinates::
+* OutputTrees::
+* OutputDistanceMatrices::
+
+Miscelaneous filters
+
+* LiftOver::
+* SystemCall::
@end detailmenu
@end menu
+ at end ifnottex
+
@c ------------------------------------------------------------------------------------------------------------------
@node Introduction, Filters, Top, Top
@@ -140,9 +152,9 @@ This manual intends to provide an exhaustive description of the options used in
@menu
-* Description::
-* Run::
-* General::
+* Description::
+* Run::
+* General::
@end menu
@node Description, Run, Introduction, Introduction
@@ -289,6 +301,13 @@ Fasta files can be compressed in the same way as MAF files.
The sequence names are expected to be of the form Species:Chromosome:start:strand:length, with possible empty fields.
Coordinates are expected to be 0-based (that is, the first nucleotide is position 0). However, passing the @command{zero_based=no} argument to the format name will assume that the first nucleotide is position 1.
+ at item input.dots=@{error|as_gaps|as_unresolved@}
+If set to @command{as_gaps}, dotted characters in sequences will be converted to gaps and treated as such in any further step of the analysis, including output to files. If set to @command{as_unresolved}, dots will be converted to 'N'.
+
+ at item input.check_sequence_size=@{boolean@}
+Tell if sequence sizes are consistent (default: true). An error will be returned in case of inconsistency.
+Desabling size check can be useful in combination with input.dots=as_gaps. In case of inconsistency, a warning will be displayed unless verbose is set to false.
+
@item output.log=@{path@}
The file where to write log messages.
@@ -306,23 +325,24 @@ The next section present all available filters and their corresponding arguments
@c ------------------------------------------------------------------------------------------------------------------
@menu
-* Extracting::
-* Cleaning::
-* Analyzing::
-* Exporting::
+* Extracting::
+* Cleaning::
+* Analyzing::
+* Exporting::
+* Miscelaneous::
@end menu
@node Extracting, Cleaning, Filters, Filters
@section Extracting data
@menu
-* Subset::
-* SelectOrphans::
-* Merge::
-* Concatenate::
-* ExtractFeature::
-* SelectChr::
-* WindowSplit::
+* Subset::
+* SelectOrphans::
+* Merge::
+* Concatenate::
+* ExtractFeature::
+* SelectChr::
+* WindowSplit::
@end menu
@c ------------------------------------------------------------------------------------------------------------------
@@ -468,7 +488,7 @@ The @command{Concatenate} filter fuses consecutive blocks until the concatenated
@example
maf.filter= \
[...],
- Concatenate(minimum_size=10000), \
+ Concatenate(minimum_size=10000, ref_species=Hsapiens), \
[...]
@end example
@end cartouche
@@ -480,6 +500,9 @@ maf.filter= \
@item minimum_size=@{int@}
The minimum size for the blocks to be reached.
+ at item ref_species=@{string@}
+If given, only blocks with identical chromosome tags in the reference species will be merged.
+
@end table
@c ------------------------------------------------------------------------------------------------------------------
@@ -495,7 +518,7 @@ The features to extract are typically provided via a GFF file.
@cartouche
@example
maf.filter= \
- [...]z
+ [...]
ExtractFeature( \
ref_species=species1, \
feature.file=species1.gff3.gz, \
@@ -522,8 +545,8 @@ The file where the features are described.
@item feature.file.compression=@{none|gzip|zip|bzip2@}
Compression format for the feature file.
- at item feature.format=@{GFF|GTF@}
-Format for the feature file, currently GFF (v3.0) or GTF only.
+ at item feature.format=@{GFF|GTF|BedGraph@}
+Format for the feature file, currently GFF (v3.0), GTF or BedGraph.
@item feature.type=@{all|(list)@}
Specifies which type of feature should be extracted from the feature file, if several are available.
@@ -587,7 +610,8 @@ maf.filter= \
[...],
WindowSplit( \
preferred_size=1000, \
- align=center), \
+ align=center, \
+ keep_small_blocks=no), \
[...]
@end example
@end cartouche
@@ -602,7 +626,12 @@ The preferred size for the output windows.
@item align=@{ragged_left|ragged_right|center|adjust@}
Specifies how to align windows on the block:
+ at item keep_small_blocks = @{boolean@}
+Tell if blocks with an original size smaller that the window size should be kept (and untouched).
+This option only works if the align option is set to adjust. The combination of "align=adjust" and "keep_small_blocks=yes" allows to ensure that blocks do not exceed a given size, without losing any data.
+
@table @command
+
@item ragged_left
@verbatim
Block |----------------------------|
@@ -639,15 +668,16 @@ In the last case, the windows will have at least the specified size, but might b
@c ------------------------------------------------------------------------------------------------------------------
@menu
-* MinBlockLength::
-* MinBlockSize::
-* XFullGap::
-* AlnFilter::
-* AlnFilter2::
-* EntropyFilter::
-* MaskFilter::
-* QualFilter::
-* FeatureFilter::
+* MinBlockLength::
+* MinBlockSize::
+* XFullGap::
+* RemoveEmptySequences::
+* AlnFilter::
+* AlnFilter2::
+* EntropyFilter::
+* MaskFilter::
+* QualFilter::
+* FeatureFilter::
@end menu
@node MinBlockLength, MinBlockSize, Cleaning, Cleaning
@@ -704,7 +734,7 @@ The minimum size.
@c ------------------------------------------------------------------------------------------------------------------
- at node XFullGap, AlnFilter, MinBlockSize, Cleaning
+ at node XFullGap, RemoveEmptySequences, MinBlockSize, Cleaning
@subsection Exclude full gap columns
Remove gap-only columns from blocks. This does not modify coordinates and might be necessary after a @command{Subset} filter.
@@ -732,7 +762,34 @@ A coma separated, within parentheses, list of species. Any column containing a g
@c ------------------------------------------------------------------------------------------------------------------
- at node AlnFilter, AlnFilter2, XFullGap, Cleaning
+ at node RemoveEmptySequences, AlnFilter, XFullGap, Cleaning
+ at subsection Remove empty sequences
+
+The @command{RemoveEmptySequences} filter remove sequences containing only gap (or unresolved characters) in each block.
+
+ at heading Synopsis:
+
+ at cartouche
+ at example
+maf.filter= \
+ [...],
+ RemoveEmptySequences(unresolved_as_gaps=yes), \
+ [...]
+ at end example
+ at end cartouche
+
+ at heading Arguments:
+
+ at table @command
+
+ at item unresolved_as_gaps=@{boolean@}
+Tell if unresolved characters count as "empty" as well.
+
+ at end table
+
+ at c ------------------------------------------------------------------------------------------------------------------
+
+ at node AlnFilter, AlnFilter2, RemoveEmptySequences, Cleaning
@subsection Alignment filtering
Split alignment blocks by removing regions with ambiguous alignments.
@@ -754,6 +811,7 @@ maf.filter= \
max.gap=9, \
max.ent=0.2, \
missing_as_gap=yes, \
+ relative=no, \
file=data.trash_aln.maf.gz, \
compression=gzip), \
[...]
@@ -773,14 +831,17 @@ The width, in bp, of the sliding window.
@item window.step=@{int>0@}
The step by which the window is moved, in bp.
- at item max.gap=@{int>0@}
-The maximum number of gaps allowed in each window.
+ at item relative=@{boolean@}
+Tell if maximum amount of gap is relative (that is, as a proportion of the total amount of character in each window).
+
+ at item max.gap=@{int>0|1>double>0@}
+The maximum number of gaps allowed in each window (if relative is set to no), or the maximum proportion of gaps (if relative is set to yes)
@item max.ent=@{float@}
The maximum entropy allowed in each window.
@item missing_as_gap=@{yes/no@}
-Tell if unresolved characters should be counted as gaps.
+Tell if missing sequences should be considered as gaps.
@item file=@{none|@{path@}@}
An optional file were removed alignment parts will be stored, in the MAF format.
@@ -819,6 +880,7 @@ maf.filter= \
window.step=1, \
max.gap=1, \
max.pos=1, \
+ relative=no, \
missing_as_gap=yes, \
file=data.trash_aln.maf.gz, \
compression=gzip), \
@@ -839,14 +901,17 @@ The width, in bp, of the sliding window.
@item window.step=@{int>0@}
The step by which the window is moved, in bp.
- at item max.gap=@{int>0@}
-The maximum number of gaps allowed in each site.
+ at item relative=@{boolean@}
+Tell if maximum amount of gap is relative (that is, as a proportion of the total amount of character in each site).
+
+ at item max.gap=@{int>0|1>double>0@}
+The maximum number of gaps allowed in each site (if relative is set to no), or the maximum proportion of gaps (if relative is set to yes)
@item max.pos=@{int>0@}
The maximum number of positions with gaps (``indel events'').
@item missing_as_gap=@{yes/no@}
-Tell if unresolved characters should be counted as gaps.
+Tell if missing sequences should be considered as gaps.
@item file=@{none|@{path@}@}
An optional file were removed alignment parts will be stored, in the MAF format.
@@ -1060,8 +1125,8 @@ The file where the features are described.
@item feature.file.compression=@{none|gzip|zip|bzip2@}
Compression format for the feature file.
- at item feature.format=@{GFF|GTF@}
-Format for the feature file, currently GFF (v3.0) or GTF only.
+ at item feature.format=@{GFF|GTF|BedGraph@}
+Format for the feature file, currently GFF (v3.0), GTF or BedGraph.
@item feature.type=@{all|(list)@}
Specifies which type of feature should be extracted from the feature file, if several are available.
@@ -1087,8 +1152,8 @@ Compression format for output file (if file != none).
@section Statistical analysis
@menu
-* Descriptive::
-* Phylogenetics::
+* Descriptive::
+* Phylogenetics::
@end menu
@node Descriptive, Phylogenetics, Analyzing, Analyzing
@@ -1114,7 +1179,8 @@ maf.filter= \
AlnScore, \
BlockCounts), \
ref_species=species1, \
- file=data.statistics.csv), \
+ file=data.statistics.csv, \
+ compression=none), \
[...]
@end example
@end cartouche
@@ -1132,25 +1198,28 @@ The species to use to report block coordinates in the output file. For block whe
@item file=@{path@}
A file path for the output file.
+ at item compression=@{none|gzip|zip|bzip2@}
+Compression format for output file.
+
@end table
The statistics to compute take the form of functions (just like filters themselves), which can potentially take arguments.
Here is the list of currently available statistical functions:
@menu
-* BlockSize::
-* BlockLength::
-* SequenceLength::
-* AlnScore::
-* BlockCounts::
-* PairwiseDivergence::
-* SiteStatistics::
-* FourSpeciesSitePatternCounts::
-* SiteFrequencySpectrum::
-* PolymorphismStatistics::
-* DiversityStatistics::
-* CountClusters::
-* ModelFit::
+* BlockSize::
+* BlockLength::
+* SequenceLength::
+* AlnScore::
+* BlockCounts::
+* PairwiseDivergence::
+* SiteStatistics::
+* FourSpeciesSitePatternCounts::
+* SiteFrequencySpectrum::
+* PolymorphismStatistics::
+* DiversityStatistics::
+* CountClusters::
+* ModelFit::
@end menu
@node BlockSize, BlockLength, Descriptive, Descriptive
@@ -1204,7 +1273,15 @@ The @command{AlnScore} statistics reports the alignment score associated to the
@subsubsection Character frequencies
The @command{BlockCounts} statistics reports the count of each character found in the block.
-(No argument)
+Note: this statistics does not work in case of duplicated sequences (multiple hits from the same chromosome / scaffold / contig).
+
+ at heading Arguments:
+ at table @command
+ at item species=@{list@}
+A list of species to be considered in the counts calculations. If no species is given, all sequences are used.
+ at item suffix=@{string@}
+An (optional) suffix to append to the statistics name. Useful in case the statistics should be computed for several species independently.
+ at end table
@node PairwiseDivergence, SiteStatistics, BlockCounts, Descriptive
@subsubsection Pairwise divergence
@@ -1248,6 +1325,14 @@ Number of sites without gap,
@item
Number of complete sites (no gap, no unresolved character),
@item
+Number of complete sites with only one state (constant sites),
+ at item
+Number of complete sites with only two states (biallelic sites),
+ at item
+Number of complete sites with only three states (triallelic sites),
+ at item
+Number of complete sites with all four states (quadriallelic sites),
+ at item
Number of parsimony-informative sites.
@end itemize
The statistics are computed for a given subset of species (typically forming a ingroup).
@@ -1313,7 +1398,7 @@ First species to consider (resp. second, third and fourth).
@node SiteFrequencySpectrum, PolymorphismStatistics, FourSpeciesSitePatternCounts, Descriptive
@subsubsection Site frequency spectrum
The @command{SiteFrequencySpectrum} computes the site frequency spectrum for each block.
-Only ``doubletons'' sites are considered, that is, positions in the alignment with only two states.
+Only positions in the alignment with only two states are considered.
The proportions of doubletons are then computed by bins.
Lets consider the following example with 7 sequences:
@verbatim
@@ -1441,6 +1526,10 @@ Note that the ``species'' terminology relates to multispecies alignments, as ori
Number of seggregating sites,
@item
Watterson's theta.
+ at item
+Tajima's pi (average pairwise dissimilarity).
+ at item
+Tajima's D.
@end itemize
@heading Synopsis:
@@ -1453,7 +1542,7 @@ maf.filter= \
statistics=(\ \
[...],
DiversityStatistics( \
- ingroup=(samp1, samp2, samp3),\
+ ingroup=(samp1,samp2,samp3)), \
[...]), \
ref_species=samp1, \
file=data.statistics.csv), \
@@ -1555,11 +1644,17 @@ All nucleotide models can be used.
@item rate_distribution=@{string@}
The distribution for rates across sites. See the Bio++ Program Suite manual for all available distributions.
- at item root_freqs=@{None|Full|GC@}
+ at item root_freq=@{None|Full|GC@}
Allow root frequencies to be different (non-stationary model). Root frequencies can be fully parametrized, or parametrized with GC content.
- at item tree=@{string@}
-The property name under which trees are stored for each block.
+ at item tree=@{string|none@}
+The property name under which trees are stored for each block. If set to ``none'', then an input file should be given.
+
+ at item tree.file=@{path@}[tree=none]
+Path for tree file, in case no property is set.
+
+ at item tree.format=@{Newick|Nhx@}[tree=none]
+Format for tree file, in case no property is set.
@item parameters_output=@{list@}
A list of parameter names to output as statistics.
@@ -1576,6 +1671,12 @@ The maximum proportion of gaps for a site to be included in the analysis.
@item gaps_as_unresolved=@{yes/no@}
Tell if remaining gaps should be converted to 'N' before likelihood computation. This should be 'yes' unless you specify a substitution model which explicitely allows for gaps.
+ at item global_clock=@{yes/no@}
+Assume a global clock for branch lengths.
+
+ at item reparametrize=@{yes/no@}
+Transform parameters to remove constraints (can improve optimization, but is usually slower).
+
@end table
@c ------------------------------------------------------------------------------------------------------------------
@@ -1586,10 +1687,11 @@ Tell if remaining gaps should be converted to 'N' before likelihood computation.
@c ------------------------------------------------------------------------------------------------------------------
@menu
-* DistanceEstimation::
-* DistanceBasedPhylogeny::
-* NewOutgroup::
-* DropSpecies::
+* DistanceEstimation::
+* DistanceBasedPhylogeny::
+* NewOutgroup::
+* DropSpecies::
+* TreeFilter::
@end menu
@node DistanceEstimation, DistanceBasedPhylogeny, Phylogenetics, Phylogenetics
@@ -1606,7 +1708,8 @@ maf.filter= \
DistanceEstimation( \
method=count, \
gap_option=no_double_gap, \
- unresolved_as_gap=no), \
+ unresolved_as_gap=no, \
+ extended_names=yes), \
[...]
@end example
or
@@ -1621,7 +1724,8 @@ maf.filter= \
max_freq_gaps=0.33, \
gaps_as_unresolved=yes, \
profiler=none, \
- message_handler=none), \
+ message_handler=none, \
+ extended_names=yes), \
[...]
@end example
@end cartouche
@@ -1651,6 +1755,8 @@ For each pairwise comparison, any gap-containing position is ignored. This is th
@item unresolved_as_gap=@{yes|no@}
Tell is unresolved characters should be treated as gaps (usually in order to be ignored).
+ at item extended_names=@{boolean@}
+Tell if sequence coordinates should be included in the sequence names stored in the output matrix.
@end table
Further arguments for the ML method:
@@ -1784,7 +1890,7 @@ A rooted tree.
@c ------------------------------------------------------------------------------------------------------------------
- at node DropSpecies, , NewOutgroup, Phylogenetics
+ at node DropSpecies, TreeFilter, NewOutgroup, Phylogenetics
@subsubsection Remove a species from a tree
The @command{DropSpecies} removes a leaf from a tree.
@@ -1822,19 +1928,63 @@ An edited tree.
@end table
@c ------------------------------------------------------------------------------------------------------------------
+
+ at node TreeFilter, , DropSpecies, Phylogenetics
+ at subsubsection Filter blocks based on their associated trees
+
+The @command{TreeFilter} (experimental) filters blocks based on their associated trees. Currently, filter is only performed based on the branch lengths.
+
+ at heading Synopsis:
+
+ at cartouche
+ at example
+maf.filter= \
+ [...],
+ TreeFilter( \
+ tree=BioNJ, \
+ max_brlen=0.01, \
+ file=data.trash_tree.maf.gz, \
+ compression=gzip), \
+ [...]
+ at end example
+ at end cartouche
+
+ at heading Arguments:
+
+ at table @command
+
+ at item tree=@{string@}
+The tag name of the tree to analyse.
+
+ at item max_brlen=@{float>0@}
+Branch length threshold: any block with a tree containing at least one branch lenght longer than the given threshold will be filtered out.
+
+ at item file=@{none|@{path@}@}
+An optional file were removed alignment parts will be stored, in the MAF format.
+This can be helpful for visual inspection and fine tuning of the filter parameters.
+
+ at item compression=@{none|gzip|zip|bzip2@}
+Compression format for output file (if file != none).
+
+ at end table
+
+ at c ------------------------------------------------------------------------------------------------------------------
@c ------------------------------------------------------------------------------------------------------------------
@c ------------------------------------------------------------------------------------------------------------------
@c ------------------------------------------------------------------------------------------------------------------
@c ------------------------------------------------------------------------------------------------------------------
- at node Exporting, , Analyzing, Filters
+ at node Exporting, Miscelaneous, Analyzing, Filters
@section Exporting blocks and data
@menu
-* Output::
-* OutputAlignments::
-* VcfOutput::
-* OutputCoordinates::
-* OutputTrees::
+* Output::
+* OutputAlignments::
+* VcfOutput::
+* MsmcOutput::
+* PlinkOutput::
+* OutputCoordinates::
+* OutputTrees::
+* OutputDistanceMatrices::
@end menu
@node Output, OutputAlignments, Exporting, Exporting
@@ -1876,7 +2026,7 @@ Tell if sequences should be masked (if a mask annotation is available), or if ma
@subsection Write alignment blocks to an external alignment file.
The @command{OutputAlignments} filter writes all blocks to an external alignment file, potentially losing some information such as coordinates and scores.
-Sequence names will be formated following the Ensembl convention.
+Sequence names will be formated following the Ensembl convention when coordinates are available.
@heading Synopsis:
@@ -1888,7 +2038,8 @@ maf.filter= \
file=data.filtered.aln, \
compression=none, \
format=Clustal, \
- mask=no), \
+ mask=no, \
+ coordinates=yes), \
[...]
@end example
@end cartouche
@@ -1898,6 +2049,7 @@ maf.filter= \
@table @command
@item file=@{none|@{path@}@}
A file path where to write alignment blocks. If the file name contains the %i code, one alignment file per block will be generated, where %i will be replaced by the block index.
+In addition to the %i special code, additional variables can be used (in combination with %i, in order to avoid putative identical file names): chromosome number (%c), begin (%b) and end (%e) of reference sequence.
@item format=@{string@}
One of the alignment format supported by Bio++ (this includes Fasta, Mase and Clustal, see the Bio++ Program suite reference manual for a complete list of formats and options).
@@ -1908,11 +2060,21 @@ Compression format for output file.
@item mask=@{yes|no@}
Tell if sequences should be masked (if a mask annotation is available), or if masking information should be ignored.
+ at item coordinates=@{yes|no@}
+Tell if coordinates of sequences should be written in the header of each sequence (followinf Ensembl syntax).
+If set to no, or if sequences have no coordinates, only the species name will be used as a sequence name.
+
+ at item ldhat_header=@{yes|no@}
+Tell if a header line should be added for each file, in order to be used with the LDhat convert program. This line contains the nimber of sequences, the sequence lengths, and the number 1 (for haploid).
+
+ at item reference=@{string@}
+The name of reference sequence, which will only be used when %c, %b or %e codes are used in file names. In case a block does not contain a sequence for the reference species, "ChrNA", "StartNA" and "StopNA" tags will be used.
+
@end table
@c ------------------------------------------------------------------------------------------------------------------
- at node VcfOutput, OutputCoordinates, OutputAlignments, Exporting
+ at node VcfOutput, MsmcOutput, OutputAlignments, Exporting
@subsection Call SNPs from alignment blocks and export to VCF file
The @command{VcfOutput} filter call SNPs from each block and output them to a VCF file.
@@ -1928,7 +2090,8 @@ maf.filter= \
file=snp.vcf.gz, \
compression=gzip, \
reference=Ref, \
- genotypes=(sample1,sample2)), \
+ genotypes=(sample1,sample2), \
+ all=no), \
[...]
@end example
@end cartouche
@@ -1947,14 +2110,112 @@ A species name corresponding to the sequence to use as reference.
@item genotypes=@{list of species@}
A list of species for which genotypes informations should be written. If not, void, a 'FORMAT' column will be added to the output, as well as oneextra column per species to genotype.
-If the species is not present in this particular, or if a N or Gap is present, adot ('.') will be written in the column.
+If the species is not present in this particular, or if a N or Gap is present, a dot ('.') will be written in the column.
Please note that species should be unique in each block, otherwise an error will occur.
+ at item all=@{boolean@}
+If set to 'yes', also output non-variable positions in the VCF file.
+
@end table
@c ------------------------------------------------------------------------------------------------------------------
- at node OutputCoordinates, OutputTrees, VcfOutput, Exporting
+ at node MsmcOutput, PlinkOutput, VcfOutput, Exporting
+ at subsection Export segregating sites to MSMC format
+
+The @command{MsmcOutput} filter calls all segregating sites and export them to the MSMC format,
+to be used with the MSMC program @uref{https://github.com/stschiff/msmc} (Multiple Sequentially Markovian Coalescent).
+Sites with gap or unresolved characters are not called.
+
+ at heading Synopsis:
+
+ at cartouche
+ at example
+maf.filter= \
+ [...],
+ MsmcOutput( \
+ file=snp.msmc, \
+ compression=none, \
+ reference=Ref, \
+ genotypes=(sample1,sample2)), \
+ [...]
+ at end example
+ at end cartouche
+
+ at heading Arguments:
+
+ at table @command
+ at item file=@{none|@{path@}@}
+A file path for the output MSMC file.
+
+ at item compression=@{none|gzip|zip|bzip2@}
+Compression format for output file.
+
+ at item reference=@{species name@}
+A species name corresponding to the sequence to use as reference.
+
+ at item genotypes=@{list of species@}
+A list of species for which seggregating sites should be called. It might not contain the reference species, which is then only used for coordinates output.
+Blocks with do not contain all species will not be called, as well as block not contianing the reference species. Note that the alignment has to be projected
+againt the reference species, otherwise an error will be reported.
+
+ at end table
+
+ at c ------------------------------------------------------------------------------------------------------------------
+
+ at node PlinkOutput, OutputCoordinates, MsmcOutput, Exporting
+ at subsection Export segregating sites to PLINK format
+
+The @command{PlinkOutput} filter calls all biallelic segregating sites and export them to the PLINK format,
+creating on Ped file and one Map file.
+Sites with gap or unresolved characters are not called.
+
+ at heading Synopsis:
+
+ at cartouche
+ at example
+maf.filter= \
+ [...],
+ PlinkOutput( \
+ ped_file=snp.ped, \
+ map_file=snp.map, \
+ compression=none, \
+ reference=Ref, \
+ genotypes=(sample1,sample2), \
+ map3=no) \
+ [...]
+ at end example
+ at end cartouche
+
+ at heading Arguments:
+
+ at table @command
+ at item ped_file=@{none|@{path@}@}
+A file path for the output Ped file.
+
+ at item map_file=@{none|@{path@}@}
+A file path for the output Map file.
+
+ at item compression=@{none|gzip|zip|bzip2@}
+Compression format for output file.
+
+ at item reference=@{species name@}
+A species name corresponding to the sequence to use as reference.
+
+ at item genotypes=@{list of species@}
+A list of species for which seggregating sites should be called. It might not contain the reference species, which is then only used for coordinates output.
+Blocks with do not contain all species will not be called, as well as block not contianing the reference species. Note that the alignment has to be projected
+againt the reference species, otherwise an error will be reported.
+
+ at item map3=@{boolean@}
+Tell if genetic distance column should be ommitted in the Map file. The resulting file should be sued together with the --map3 option in PLINK.
+If set to no, then a 0 genetic distance is written.
+
+ at end table
+
+ at c ------------------------------------------------------------------------------------------------------------------
+
+ at node OutputCoordinates, OutputTrees, PlinkOutput, Exporting
@subsection Output coordinates of a set of species for each block.
The @command{OutputCoordinates} takes as input a list of species and output the coordinates of each of the corresponding sequences in each block.
@@ -1969,7 +2230,8 @@ maf.filter= \
OutputCoordinates( \
file=coordinates.txt.gz, \
compression=gzip, \
- species=(species1,species2)) \
+ species=(species1,species2), \
+ output_src_size=yes) \
[...]
@end example
@end cartouche
@@ -1986,12 +2248,14 @@ Compression format for output file.
@item species=@{list of species@}
A list of species for which coodinates should be written.
+ at item output_src_size=@{boolean@}
+Tell if the size of source sequences should be output.
+
@end table
@c ------------------------------------------------------------------------------------------------------------------
-
- at node OutputTrees, , OutputCoordinates, Exporting
+ at node OutputTrees, OutputDistanceMatrices, OutputCoordinates, Exporting
@subsection Write trees to a file.
The @command{OutputTrees} filter writes trees associated to blocks to a file, in the Newick format. All trees will be stored in the same file, one per line.
@@ -2022,10 +2286,167 @@ A file path where to write trees, in the Newick format.
@item compression=@{none|gzip|zip|bzip2@}
Compression format for output file.
+ at item strip_names=@{boolean@}
+Tell if leaf names should be stripped. If so, all text after the first dot will be deleted.
+This is useful to get rid of the sequence coordinates.
+The option will have no effect in case the names do not contain coordinates.
+
@end table
@c ------------------------------------------------------------------------------------------------------------------
+ at node OutputDistanceMatrices, , OutputTrees, Exporting
+ at subsection Write distance matrices to a file.
+
+The @command{OutputDistanceMatrices} filter writes distance matrices associated to blocks to a file, in the Phylip format.
+All matrices will be stored in the same file, one after the other.
+
+ at heading Synopsis:
+
+ at cartouche
+ at example
+maf.filter= \
+ [...],
+ OutputDistanceMatrices( \
+ distance=MLdistance, \
+ file=data.distmat.ph, \
+ compression=gzip), \
+ [...]
+ at end example
+ at end cartouche
+
+ at heading Arguments:
+
+ at table @command
+ at item distance=@{string@}
+The tag used to store previously computed distance matrices.
+
+ at item file=@{none|@{path@}@}
+A file path where to write distance matrices, in the Phylip format.
+
+ at item compression=@{none|gzip|zip|bzip2@}
+Compression format for output file.
+
+ at item strip_names=@{boolean@}
+Tell if sequence names should be stripped. If so, all text after the first dot will be deleted.
+This is useful to get rid of the sequence coordinates.
+The option will have no effect in case the names do not contain coordinates.
+
+ at end table
+
+ at c ------------------------------------------------------------------------------------------------------------------
+
+ at node Miscelaneous, , Exporting, Filters
+ at section Miscelaneous filters
+
+ at menu
+* LiftOver::
+* SystemCall::
+ at end menu
+
+
+ at c ------------------------------------------------------------------------------------------------------------------
+
+ at node LiftOver, SystemCall, Miscelaneous, Miscelaneous
+ at subsection Convert coordinates from one genome to another
+
+The @command{LiftOver} mimmics the behavior of the famous UCSC liftover utility.
+Features are read from any supported format, and a convertion table is generated for all features included in the alignment.
+
+ at heading Synopsis:
+
+ at cartouche
+ at example
+maf.filter= \
+ [...]
+ LiftOver( \
+ ref_species=species1, \
+ target_species=species2, \
+ feature.file=species1.gff3.gz, \
+ feature.file.compression=gzip, \
+ feature.format=GFF, \
+ file=sp1_to_sp2.tln, \
+ compression=none), \
+ [...]
+ at end example
+ at end cartouche
+
+ at heading Arguments:
+
+ at table @command
+
+ at item ref_species=@{string@}
+The name of the species for which the coordinates of the features are provided.
+
+ at item target_species=@{string@}
+The name of the species to which the coordinates of the features should be converted.
+
+ at item feature.file=@{path@}
+The file where the features are described.
+
+ at item feature.file.compression=@{none|gzip|zip|bzip2@}
+Compression format for the feature file.
+
+ at item feature.format=@{GFF|GTF|BedGraph@}
+Format for the feature file, currently GFF (v3.0), GTF or BedGraph.
+
+ at item compression=@{none|gzip|zip|bzip2@}
+Compression format for output file.
+
+ at end table
+
+ at c ------------------------------------------------------------------------------------------------------------------
+
+ at node SystemCall, , LiftOver, Miscelaneous
+ at subsection Call an external program on each block.
+
+The @command{SystemCall} filter runs an external program on each block.
+For each block, the alignment is written to a temporary file, whose name and format can be specified.
+This input file is then read by the external program. The called program is expected to generate results in the form of an alignment with the same sequence names, so that it can be read by maffilter.
+In most case, the external program will be a wrapper script.
+ at heading Synopsis:
+
+ at cartouche
+ at example
+maf.filter= \
+ [...],
+ SystemCall( \
+ name=myextprog, \
+ input.file=tmp.fa, \
+ input.format=Fasta, \
+ call=myscript.sh, \
+ output.file=output.fa, \
+ output.format=Fasta), \
+ [...]
+ at end example
+ at end cartouche
+
+ at heading Arguments:
+
+ at table @command
+ at item name=@{string@}
+A label to use, might be useful in case several tools are called.
+
+ at item input.file=@{none|@{path@}@}
+A file path where to write the block alignment, to be used as input by the external program.
+
+ at item input.format=@{string@}
+Alignment format for input file.
+
+ at item output.file=@{none|@{path@}@}
+A file path where to read the processed block alignment, output by the external program.
+
+ at item output.format=@{string@}
+Alignment format for output file.
+
+ at item call=@{string@}
+The system call to run external program.
+
+ at end table
+
+
+ at c ------------------------------------------------------------------------------------------------------------------
+
@c end of document
@c @node Index, , Reference, Top
diff --git a/examples/Gorilla/Compara.epo_5_catarrhini_hsap-projected.chr22.subset.nogap.cleaned_aln.maf.gz b/examples/Gorilla/Compara.epo_5_catarrhini_hsap-projected.chr22.subset.nogap.cleaned_aln.maf.gz
new file mode 100644
index 0000000..a92485e
Binary files /dev/null and b/examples/Gorilla/Compara.epo_5_catarrhini_hsap-projected.chr22.subset.nogap.cleaned_aln.maf.gz differ
diff --git a/examples/UCSC46ways/MafFilter.bpp b/examples/UCSC46ways/MafFilter.bpp
index 2667960..658c1d0 100755
--- a/examples/UCSC46ways/MafFilter.bpp
+++ b/examples/UCSC46ways/MafFilter.bpp
@@ -1,6 +1,6 @@
CHR=1
DATA=chr$(CHR)
-input.file=/mnt/dd3/jdutheil/Data/Genomes/UCSC_46ways/maf/$(DATA).maf.gz
+input.file=/mnt/data1/jdutheil/Data/Genomes/UCSC_46ways/maf/$(DATA).maf.gz
input.file.compression=gzip
input.format=Maf
output.log=$(DATA).maffilter.log
diff --git a/examples/UCSC46ways/README b/examples/UCSC46ways/README
index 1dfd3ce..6a98292 100644
--- a/examples/UCSC46ways/README
+++ b/examples/UCSC46ways/README
@@ -1,4 +1,5 @@
# Created on 13/11/12 by jdutheil
+# Last update 20/06/16 by jdutheil
This example file parses the 46-ways vertebrate alignment from UCSC.
The data are not included in this folder because of size.
diff --git a/examples/Ztritici/Mgraminicolav2.FrozenGeneCatalog20080910.gff.gz b/examples/Ztritici/Mgraminicolav2.FrozenGeneCatalog20080910.gff.gz
new file mode 100644
index 0000000..9056657
Binary files /dev/null and b/examples/Ztritici/Mgraminicolav2.FrozenGeneCatalog20080910.gff.gz differ
diff --git a/examples/Ztritici/tba_refIPO323.maf.gz b/examples/Ztritici/tba_refIPO323.maf.gz
new file mode 100644
index 0000000..709cb6b
Binary files /dev/null and b/examples/Ztritici/tba_refIPO323.maf.gz differ
diff --git a/maffilter.spec b/maffilter.spec
index c36925e..7656822 100644
--- a/maffilter.spec
+++ b/maffilter.spec
@@ -1,5 +1,5 @@
%define _basename maffilter
-%define _version 1.1.0
+%define _version 1.2.1
%define _release 1
%define _prefix /usr
@@ -10,36 +10,41 @@ Version: %{_version}
Release: %{_release}
License: CECILL-2.0
Vendor: The Bio++ Project
-Source: http://biopp.univ-montp2.fr/repos/sources/maffilter/%{_basename}-%{_version}.tar.gz
+Source: %{_basename}-%{_version}.tar.gz
Summary: The Multiple Alignment Format file processor
Group: Productivity/Scientific/Other
-Requires: libbpp-phyl-omics1 = 2.2.0
-Requires: libbpp-seq-omics1 = 2.2.0
-Requires: libbpp-phyl9 = 2.2.0
-Requires: libbpp-seq9 = 2.2.0
-Requires: libbpp-core2 = 2.2.0
+Requires: libbpp-phyl-omics2 = 2.3.1
+Requires: libbpp-seq-omics2 = 2.3.1
+Requires: libbpp-phyl11 = 2.3.1
+Requires: libbpp-seq11 = 2.3.1
+Requires: libbpp-core3 = 2.3.1
Requires: zlib
-Requires: libbz2
BuildRoot: %{_builddir}/%{_basename}-root
-BuildRequires: cmake >= 2.6.0
-BuildRequires: gcc-c++ >= 4.0.0
+BuildRequires: cmake >= 2.8.11
+BuildRequires: gcc-c++ >= 4.7.0
BuildRequires: groff
BuildRequires: texinfo >= 4.0.0
-BuildRequires: libbpp-core2 = 2.2.0
-BuildRequires: libbpp-core-devel = 2.2.0
-BuildRequires: libbpp-seq9 = 2.2.0
-BuildRequires: libbpp-seq-devel = 2.2.0
-BuildRequires: libbpp-phyl9 = 2.2.0
-BuildRequires: libbpp-phyl-devel = 2.2.0
-BuildRequires: libbpp-seq-omics1 = 2.2.0
-BuildRequires: libbpp-seq-omics-devel = 2.2.0
-BuildRequires: libbpp-phyl-omics1 = 2.2.0
-BuildRequires: libbpp-phyl-omics-devel = 2.2.0
+BuildRequires: libbpp-core3 = 2.3.1
+BuildRequires: libbpp-core-devel = 2.3.1
+BuildRequires: libbpp-seq11 = 2.3.1
+BuildRequires: libbpp-seq-devel = 2.3.1
+BuildRequires: libbpp-phyl11 = 2.3.1
+BuildRequires: libbpp-phyl-devel = 2.3.1
+BuildRequires: libbpp-seq-omics2 = 2.3.1
+BuildRequires: libbpp-seq-omics-devel = 2.3.1
+BuildRequires: libbpp-phyl-omics2 = 2.3.1
+BuildRequires: libbpp-phyl-omics-devel = 2.3.1
BuildRequires: zlib-devel
-BuildRequires: libbz2-devel
+%if 0%{?fedora} >= 22
+Requires: bzip2-libs
+BuildRequires: bzip2-devel
+%else
+Requires: libbz2
+BuildRequires: libbz2-devel
+%endif
AutoReq: yes
AutoProv: yes
@@ -82,21 +87,10 @@ Many filters are available, from alignment cleaning to phylogeny reconstruction
%setup -q
%build
-CFLAGS="-I%{_prefix}/include $RPM_OPT_FLAGS"
-CMAKE_FLAGS="-DCMAKE_INSTALL_PREFIX=%{_prefix}"
-if [ %{_lib} == 'lib64' ] ; then
- CMAKE_FLAGS="$CMAKE_FLAGS -DLIB_SUFFIX=64"
-fi
-if [ %{zipext} == 'lzma' ] ; then
- CMAKE_FLAGS="$CMAKE_FLAGS -DDOC_COMPRESS=lzma -DDOC_COMPRESS_EXT=lzma"
-fi
-if [ %{zipext} == 'xz' ] ; then
- CMAKE_FLAGS="$CMAKE_FLAGS -DDOC_COMPRESS=xz -DDOC_COMPRESS_EXT=xz"
-fi
-
+CFLAGS="$RPM_OPT_FLAGS"
+CMAKE_FLAGS="-DCMAKE_INSTALL_PREFIX=%{_prefix} -DCOMPRESS_PROGRAM=%{compress_program}"
cmake $CMAKE_FLAGS .
make
-make info
%install
make DESTDIR=$RPM_BUILD_ROOT install
@@ -110,11 +104,13 @@ rm -rf $RPM_BUILD_ROOT
%files
%defattr(-,root,root)
-%doc AUTHORS.txt COPYING.txt INSTALL.txt ChangeLog
+%doc AUTHORS LICENSE INSTALL ChangeLog
%{_prefix}/bin/maffilter
%{_prefix}/share/man/man1/maffilter.1.%{zipext}
%{_prefix}/share/info/maffilter.info.%{zipext}
%changelog
+* Fri Jun 09 2017 Julien Dutheil <dutheil at evolbio.mpg.de> 1.2.1-1
+* Wed May 24 2017 Julien Dutheil <dutheil at evolbio.mpg.de> 1.2.0-1
* Fri Sep 26 2014 Julien Dutheil <julien.dutheil at univ-montp2.fr> 1.1.0-1
- Initial spec file.
diff --git a/man/CMakeLists.txt b/man/CMakeLists.txt
index dc7d0bb..3781d67 100644
--- a/man/CMakeLists.txt
+++ b/man/CMakeLists.txt
@@ -1,7 +1,42 @@
-# CMake script for GenomeTools
-# Author: Julien Dutheil
-# Created: 09/09/2012
+# CMake script for the CoMap package.
+# Authors:
+# Julien Dutheil
+# Francois gindraud (2017)
+# Created: 22/08/2009
-IF(MAN)
- INSTALL(FILES maffilter.1.gz DESTINATION share/man/man1)
-ENDIF(MAN)
+# Build manpages.
+# In practice, they are just compressed from the text files using COMPRESS_PROGRAM
+# Manpages are built and installed as part of "all" if a COMPRESS_PROGRAM is found.
+
+# Take all manpages files in the directory
+file (GLOB manpage_files RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} *.1)
+
+if (NOT COMPRESS_BIN)
+ # Just install manpages from source
+ foreach (manpage_file ${manpage_files})
+ install (FILES ${CMAKE_CURRENT_SOURCE_DIR}/${manpage_file} DESTINATION ${CMAKE_INSTALL_MANDIR}/man1)
+ endforeach (manpage_file)
+else ()
+ # Create a list of manpage targets
+ set (manpage-targets)
+
+ foreach (manpage_file ${manpage_files})
+ # Compress manpage, install, add to manpage target list
+ set (input ${CMAKE_CURRENT_SOURCE_DIR}/${manpage_file})
+ set (output ${CMAKE_CURRENT_BINARY_DIR}/${manpage_file}.${COMPRESS_EXT})
+ add_custom_command (
+ OUTPUT ${output}
+ COMMAND ${COMPRESS_BIN} ${COMPRESS_ARGS} ${input} > ${output}
+ DEPENDS ${input}
+ COMMENT "Compressing manpage ${manpage_file}"
+ VERBATIM
+ )
+ install (FILES ${output} DESTINATION ${CMAKE_INSTALL_MANDIR}/man1)
+ list (APPEND manpage-targets ${output})
+ unset (input)
+ unset (output)
+ endforeach (manpage_file)
+
+ # Add target "man", built with "all" (needed because install will fail if not built).
+ add_custom_target (man ALL DEPENDS ${manpage-targets})
+endif ()
diff --git a/man/maffilter.1.txt b/man/maffilter.1
similarity index 90%
rename from man/maffilter.1.txt
rename to man/maffilter.1
index d2e2087..565bac0 100644
--- a/man/maffilter.1.txt
+++ b/man/maffilter.1
@@ -18,7 +18,7 @@ maffilter applies a series of post-processing filter to an input MAF file.
.SH OPTIONS
-You should refer to 'info maffilter' or to the online manual of testnh for a complete list of available options.
+You should refer to 'info maffilter' or to the online manual of maffilter for a complete list of available options.
.TP 5
--
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