Commit 4bf43ea1 authored by Julien Y. Dutheil's avatar Julien Y. Dutheil
Browse files

New upstream version 1.3.0+dfsg

parent d8e65587

CMakeLists.txt

+4 −4
Original line number Diff line number Diff line
@@ -63,7 +63,7 @@ if (CMAKE_INSTALL_PREFIX) 
endif (CMAKE_INSTALL_PREFIX)



include (GNUInstallDirs)

find_package (bpp-phyl-omics 2.0.0 REQUIRED)

find_package (bpp-phyl-omics 3.0.0 REQUIRED)



#Find boost libraries

SET(Boost_USE_STATIC_LIBS ${BUILD_STATIC})
@@ -152,10 +152,10 @@ ADD_SUBDIRECTORY(man) 
# Packager

SET(CPACK_PACKAGE_NAME "maffilter")

SET(CPACK_PACKAGE_VENDOR "Julien Y. Dutheil")

SET(CPACK_PACKAGE_VERSION "1.2.1")

SET(CPACK_PACKAGE_VERSION "1.3.0")

SET(CPACK_PACKAGE_VERSION_MAJOR "1")

SET(CPACK_PACKAGE_VERSION_MINOR "2")

SET(CPACK_PACKAGE_VERSION_PATCH "1")

SET(CPACK_PACKAGE_VERSION_MINOR "3")

SET(CPACK_PACKAGE_VERSION_PATCH "0")

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")

ChangeLog

+16 −0
Original line number Diff line number Diff line 
29/04/18 -*- Version 1.3.0 -*-



13/04/18 Julien Dutheil

* Error output when not enough ingroup sequences in DiversityStatistics and SiteFrequencySpectrum



09/03/18 Julien Dutheil

* Logfile can now be disabled

* Merge filter can now rename chimeric contigs to avoid long concatenated names.



21/01/18 Julien Dutheil

* Added OrderFilter.



16/12/17 Julien Dutheil

* Added OutputAsTable filter

* Improved LiftOver



18/05/17 -*- Version 1.2.0 -*-



13/04/17 Julien Dutheil

MafFilter/CMakeLists.txt

+1 −1
Original line number Diff line number Diff line
@@ -12,7 +12,7 @@ foreach (target ${maffilter-targets}) 
  if (BUILD_STATIC)

    target_link_libraries (${target} ${BPP_LIBS_STATIC})

    target_link_libraries (${target} ${LIBS})

    set_target_properties (${target} LINK_SEARCH_END_STATIC TRUE)

    set_target_properties (${target} PROPERTIES LINK_SEARCH_END_STATIC TRUE)

  else (BUILD_STATIC)

    target_link_libraries (${target} ${BPP_LIBS_SHARED})

    target_link_libraries (${target} ${LIBS})

MafFilter/MafFilter.cpp

+119 −42

File changed.

Preview size limit exceeded, changes collapsed.

MafFilter/OutputAsFeaturesMafIterator.h

+1 −1
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@@ -83,7 +83,7 @@ class OutputAsFeaturesMafIterator: 




  public:

    MafBlock* analyseCurrentBlock_() throw (Exception) {

    MafBlock* analyseCurrentBlock_() {

      currentBlock_ = iterator_->nextBlock();

      if (output_ && currentBlock_)

        writeBlock(*output_, *currentBlock_);