Commit 42965fb6 authored by Julien Y. Dutheil's avatar Julien Y. Dutheil
Browse files

New upstream version 1.3.1+dfsg

parent 4bf43ea1

CMakeLists.txt

+5 −4
Original line number Diff line number Diff line
@@ -23,7 +23,7 @@ IF(NOT BUILD_STATIC) 
      FORCE)

ENDIF()

IF(BUILD_STATIC)

  MESSAGE("-- Static linkage requested.")

  MESSAGE(STATUS "Static linkage requested.")

  SET (CMAKE_CXX_FLAGS "-static -static-libgcc ${CMAKE_CXX_FLAGS}")

ENDIF()
@@ -50,7 +50,8 @@ else () 
  # 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)

    # -9 for maximum compression (lintian error)

    set (COMPRESS_ARGS -c -n -9)

  else ()

    set (COMPRESS_ARGS -c)

  endif ()
@@ -152,10 +153,10 @@ ADD_SUBDIRECTORY(man) 
# Packager

SET(CPACK_PACKAGE_NAME "maffilter")

SET(CPACK_PACKAGE_VENDOR "Julien Y. Dutheil")

SET(CPACK_PACKAGE_VERSION "1.3.0")

SET(CPACK_PACKAGE_VERSION "1.3.1")

SET(CPACK_PACKAGE_VERSION_MAJOR "1")

SET(CPACK_PACKAGE_VERSION_MINOR "3")

SET(CPACK_PACKAGE_VERSION_PATCH "0")

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}/LICENSE")

SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS")

MafFilter/MafFilter.cpp

+4 −4
Original line number Diff line number Diff line
@@ -133,7 +133,7 @@ void help() 
  (*ApplicationTools::message << "      ... param=option_file").endLine();

  (*ApplicationTools::message).endLine();

  (*ApplicationTools::message << "  Refer to the MafFilter Manual for a list of available options.").endLine();

  (*ApplicationTools::message << "  Online version: http://biopp.univ-montp2.fr/manual/html/maffilter/").endLine();

  (*ApplicationTools::message << "  Online version: https://jydu.github.io/maffilter/Manual/index.html").endLine();

  (*ApplicationTools::message << "  Or type 'info maffilter' in a terminal.").endLine();

  (*ApplicationTools::message << "__________________________________________________________________________").endLine();

}
@@ -141,9 +141,9 @@ void help() 
int main(int args, char** argv)

{

  cout << "******************************************************************" << endl;

  cout << "*                  MAF Filter, version 1.3.0                     *" << endl;

  cout << "*                  MAF Filter, version 1.3.1                     *" << endl;

  cout << "* Author: J. Dutheil                        Created on  10/09/10 *" << endl;

  cout << "*                                           Last Modif. 09/03/18 *" << endl;

  cout << "*                                           Last Modif. 18/08/18 *" << endl;

  cout << "******************************************************************" << endl;

  cout << endl;
@@ -1617,7 +1617,7 @@ int main(int args, char** argv) 
        ApplicationTools::displayResult("-- Reference sequence", reference);

        

        bool map3 = ApplicationTools::getBooleanParameter("map3", cmdArgs, false);

        ApplicationTools::displayBooleanResult("-- Ouput map3 file", map3);

        ApplicationTools::displayBooleanResult("-- Output map3 file", map3);



        bool recodeChr = ApplicationTools::getBooleanParameter("recode_chr", cmdArgs, false);

        ApplicationTools::displayBooleanResult("-- Recode chromosomes", recodeChr);

buildBin.sh

+1 −1
Original line number Diff line number Diff line 
#! /bin/sh

arch=`uname -m`

version=1.1.99-1

version=1.3.0-1



strip MafFilter/maffilter

tar cvzf maffilter-${arch}-bin-static-${version}.tar.gz MafFilter/maffilter

doc/CMakeLists.txt

+14 −1
Original line number Diff line number Diff line
@@ -13,7 +13,7 @@ find_program (MAKEINFO NAMES makeinfo texi2any DOC "makeinfo doc generator progr 
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)")

  message (STATUS "Found ${MAKEINFO}: 'info' and 'html' target enabled (builds info/html doc)")



  set (input ${CMAKE_CURRENT_SOURCE_DIR}/maffilter.texi)
@@ -58,6 +58,19 @@ else (NOT MAKEINFO) 
    )

  add_custom_target (html DEPENDS ${output})



  # Also provide a "html-multipages" target that builds html doc (not installed, and not part of "all").

  set (output ${CMAKE_CURRENT_BINARY_DIR}/html/)

  set (makeinfo-css "http://www.w3.org/StyleSheets/Core/Steely")

  add_custom_command (

    OUTPUT ${output}

    COMMAND ${MAKEINFO} --html --no-headers --css-ref=${makeinfo-css} -o ${output} ${input}

    DEPENDS ${input}

    COMMENT "Generating html (multipages) doc"

    VERBATIM

    )

  add_custom_target (html-multipages DEPENDS ${output})





  # Provide a "pdf" target that builds pdf doc (not installed, not part of "all").

  find_program (TEXIDVI NAMES texi2dvi)

  if (TEXIDVI)

doc/maffilter.texi

+2 −2
Original line number Diff line number Diff line 
\input texinfo   @c -*-texinfo-*-

@c %**start of header

@setfilename maffilter.info

@settitle MafFilter Manual 1.3.0

@settitle MafFilter Manual 1.3.1

@c @documentencoding UTF-8

@afourpaper

@dircategory Science Biology Genetics
@@ -12,7 +12,7 @@ 




@copying

This is the manual of MafFilter, version 1.3.0.

This is the manual of MafFilter, version 1.3.1.



Copyright @copyright{} 2018 Julien Y. Dutheil

@end copying