[med-svn] [Git][med-team/kissplice][upstream] New upstream version 2.5.5+dfsg
Andreas Tille (@tille)
gitlab at salsa.debian.org
Thu Feb 17 18:20:29 GMT 2022
Andreas Tille pushed to branch upstream at Debian Med / kissplice
Commits:
9f1b419b by Andreas Tille at 2022-02-17T19:15:45+01:00
New upstream version 2.5.5+dfsg
- - - - -
25 changed files:
- CMakeLists.txt
- ChangeLog
- build/CPackConfig.cmake
- build/CPackSourceConfig.cmake
- build/CTestTestfile.cmake
- build/README.txt
- build/bin/kissplice
- build/cmake_install.cmake
- build/cmake_uninstall.cmake
- build/doc/cmake_install.cmake
- build/man/cmake_install.cmake
- build/modules/cmake_install.cmake
- build/tests/CTestTestfile.cmake
- build/tests/cmake_install.cmake
- build/tests/functional_tests/CTestTestfile.cmake
- build/tests/functional_tests/cmake_install.cmake
- build/tests/integration_tests/CTestTestfile.cmake
- build/tests/integration_tests/cmake_install.cmake
- build/thirdparty/cmake_install.cmake
- build/thirdparty/kissreads/cmake_install.cmake
- build/thirdparty/kissreads/src/cmake_install.cmake
- kissplice.py
- man/kissplice.1
- + texput.log
- thirdparty/kissreads/src/kissReads.c
Changes:
=====================================
CMakeLists.txt
=====================================
@@ -23,7 +23,8 @@ IF(NOT CMAKE_CONFIGURATION_TYPES AND NOT CMAKE_BUILD_TYPE)
SET(CMAKE_BUILD_TYPE Distribution)
ENDIF(NOT CMAKE_CONFIGURATION_TYPES AND NOT CMAKE_BUILD_TYPE)
-
+SET(CMAKE_CXX_FLAGS "-fopenmp")
+SET(CMAKE_C_FLAGS "-fopenmp")
SET(CMAKE_CXX_FLAGS_DEBUG "-g -Wall")
SET(CMAKE_C_FLAGS_DEBUG "-g -Wall")
SET(CMAKE_CXX_FLAGS_RELEASE "-O3 -Wall")
@@ -143,7 +144,7 @@ SET(CPACK_PACKAGE_NAME "kissplice")
SET(CPACK_PACKAGE_VENDOR "Kissplice Development Team")
SET(CPACK_PACKAGE_VERSION_MAJOR "2")
SET(CPACK_PACKAGE_VERSION_MINOR "5")
-SET(CPACK_PACKAGE_VERSION_PATCH "4")
+SET(CPACK_PACKAGE_VERSION_PATCH "5")
SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Splicing events caller")
SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING")
SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS")
=====================================
ChangeLog
=====================================
@@ -1,3 +1,8 @@
+2022-01-21 Audric Cologne <audric.cologne at univ-lyon1.fr>
+ * 2.5.4 -> 2.5.5
+ New feature:
+ -Paralellisation of Kissreads
+
2021-03-05 Audric Cologne <audric.cologne at univ-lyon1.fr>
* 2.5.3 -> 2.5.4
Bug fixes:
=====================================
build/CPackConfig.cmake
=====================================
@@ -10,77 +10,79 @@
# usually begin with CPACK_<GENNAME>_xxxx.
-SET(CPACK_BINARY_7Z "")
-SET(CPACK_BINARY_BUNDLE "")
-SET(CPACK_BINARY_CYGWIN "")
-SET(CPACK_BINARY_DEB "OFF")
-SET(CPACK_BINARY_DRAGNDROP "")
-SET(CPACK_BINARY_FREEBSD "OFF")
-SET(CPACK_BINARY_IFW "OFF")
-SET(CPACK_BINARY_NSIS "OFF")
-SET(CPACK_BINARY_OSXX11 "")
-SET(CPACK_BINARY_PACKAGEMAKER "")
-SET(CPACK_BINARY_PRODUCTBUILD "")
-SET(CPACK_BINARY_RPM "OFF")
-SET(CPACK_BINARY_STGZ "ON")
-SET(CPACK_BINARY_TBZ2 "OFF")
-SET(CPACK_BINARY_TGZ "ON")
-SET(CPACK_BINARY_TXZ "OFF")
-SET(CPACK_BINARY_TZ "ON")
-SET(CPACK_BINARY_WIX "")
-SET(CPACK_BINARY_ZIP "")
-SET(CPACK_BUILD_SOURCE_DIRS "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice;/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build")
-SET(CPACK_CMAKE_GENERATOR "Unix Makefiles")
-SET(CPACK_COMPONENTS_ALL "Unspecified;headers;libraries")
-SET(CPACK_COMPONENT_UNSPECIFIED_HIDDEN "TRUE")
-SET(CPACK_COMPONENT_UNSPECIFIED_REQUIRED "TRUE")
-SET(CPACK_GENERATOR "STGZ;TGZ;TZ")
-SET(CPACK_INSTALL_CMAKE_PROJECTS "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build;kissplice;ALL;/")
-SET(CPACK_INSTALL_PREFIX "/usr/local/HDF_Group/HDF5/1.10.5")
-SET(CPACK_MODULE_PATH "")
-SET(CPACK_NSIS_DISPLAY_NAME "kissplice 2.5.4")
-SET(CPACK_NSIS_INSTALLER_ICON_CODE "")
-SET(CPACK_NSIS_INSTALLER_MUI_ICON_CODE "")
-SET(CPACK_NSIS_INSTALL_ROOT "$PROGRAMFILES")
-SET(CPACK_NSIS_PACKAGE_NAME "kissplice 2.5.4")
-SET(CPACK_OUTPUT_CONFIG_FILE "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/CPackConfig.cmake")
-SET(CPACK_PACKAGE_DEFAULT_LOCATION "/")
-SET(CPACK_PACKAGE_DESCRIPTION_FILE "/usr/share/cmake-3.10/Templates/CPack.GenericDescription.txt")
-SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Splicing events caller")
-SET(CPACK_PACKAGE_FILE_NAME "kissplice-2.5.4-Linux")
-SET(CPACK_PACKAGE_INSTALL_DIRECTORY "kissplice 2.5.4")
-SET(CPACK_PACKAGE_INSTALL_REGISTRY_KEY "kissplice 2.5.4")
-SET(CPACK_PACKAGE_NAME "kissplice")
-SET(CPACK_PACKAGE_RELOCATABLE "true")
-SET(CPACK_PACKAGE_VENDOR "Kissplice Development Team")
-SET(CPACK_PACKAGE_VERSION "2.5.4")
-SET(CPACK_PACKAGE_VERSION_MAJOR "2")
-SET(CPACK_PACKAGE_VERSION_MINOR "5")
-SET(CPACK_PACKAGE_VERSION_PATCH "4")
-SET(CPACK_RESOURCE_FILE_AUTHORS "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/AUTHORS")
-SET(CPACK_RESOURCE_FILE_INSTALL "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/INSTALL")
-SET(CPACK_RESOURCE_FILE_LICENSE "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/COPYING")
-SET(CPACK_RESOURCE_FILE_README "/usr/share/cmake-3.10/Templates/CPack.GenericDescription.txt")
-SET(CPACK_RESOURCE_FILE_WELCOME "/usr/share/cmake-3.10/Templates/CPack.GenericWelcome.txt")
-SET(CPACK_SET_DESTDIR "OFF")
-SET(CPACK_SOURCE_7Z "")
-SET(CPACK_SOURCE_CYGWIN "")
-SET(CPACK_SOURCE_GENERATOR "TGZ")
-SET(CPACK_SOURCE_IGNORE_FILES "README.CMake;README.Licence;README.Release;README.NamingConventions;README.Kissreads;CMakeFiles;Makefile;_CPack_Packages;CMakeCache.txt;.*\\.svn;.*\\.idea;.*\\.DS_Store;.*\\.gz;.*\\~;.*\\.o;bcc/;datasets;ismb;Recomb;RR;script_tarjan_aphid.sh;splice_sites_results;splicing_events;TODO.*;Validation;validation_script.sh;.*project;/\\.git*;^results$;^build$;incremental-bicon.ps;^scripts$;skeletons;doc/dev;alt_splicing_sample_ex.png;quantifModel-big.png;resType0.png;resType1.png;quantifModel.png;ucsc.png;user_guide.aux;user_guide.bib;user_guide.log;user_guide.toc;user_guide.tex;jobim13")
-SET(CPACK_SOURCE_OUTPUT_CONFIG_FILE "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/CPackSourceConfig.cmake")
-SET(CPACK_SOURCE_PACKAGE_FILE_NAME "kissplice-2.5.4")
-SET(CPACK_SOURCE_RPM "")
-SET(CPACK_SOURCE_TBZ2 "")
-SET(CPACK_SOURCE_TGZ "")
-SET(CPACK_SOURCE_TXZ "")
-SET(CPACK_SOURCE_TZ "")
-SET(CPACK_SOURCE_ZIP "")
-SET(CPACK_SYSTEM_NAME "Linux")
-SET(CPACK_TOPLEVEL_TAG "Linux")
-SET(CPACK_WIX_SIZEOF_VOID_P "8")
+set(CPACK_BINARY_7Z "")
+set(CPACK_BINARY_BUNDLE "")
+set(CPACK_BINARY_CYGWIN "")
+set(CPACK_BINARY_DEB "OFF")
+set(CPACK_BINARY_DRAGNDROP "")
+set(CPACK_BINARY_FREEBSD "OFF")
+set(CPACK_BINARY_IFW "OFF")
+set(CPACK_BINARY_NSIS "OFF")
+set(CPACK_BINARY_NUGET "")
+set(CPACK_BINARY_OSXX11 "")
+set(CPACK_BINARY_PACKAGEMAKER "")
+set(CPACK_BINARY_PRODUCTBUILD "")
+set(CPACK_BINARY_RPM "OFF")
+set(CPACK_BINARY_STGZ "ON")
+set(CPACK_BINARY_TBZ2 "OFF")
+set(CPACK_BINARY_TGZ "ON")
+set(CPACK_BINARY_TXZ "OFF")
+set(CPACK_BINARY_TZ "ON")
+set(CPACK_BINARY_WIX "")
+set(CPACK_BINARY_ZIP "")
+set(CPACK_BUILD_SOURCE_DIRS "/home/audric/Desktop/PostDoc/Logiciels/kissplice;/home/audric/Desktop/PostDoc/Logiciels/kissplice/build")
+set(CPACK_CMAKE_GENERATOR "Unix Makefiles")
+set(CPACK_COMPONENTS_ALL "Unspecified;headers;libraries")
+set(CPACK_COMPONENT_UNSPECIFIED_HIDDEN "TRUE")
+set(CPACK_COMPONENT_UNSPECIFIED_REQUIRED "TRUE")
+set(CPACK_DEFAULT_PACKAGE_DESCRIPTION_FILE "/usr/share/cmake-3.16/Templates/CPack.GenericDescription.txt")
+set(CPACK_GENERATOR "STGZ;TGZ;TZ")
+set(CPACK_INSTALL_CMAKE_PROJECTS "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build;kissplice;ALL;/")
+set(CPACK_INSTALL_PREFIX "/usr/local/HDF_Group/HDF5/1.10.5")
+set(CPACK_MODULE_PATH "")
+set(CPACK_NSIS_DISPLAY_NAME "kissplice 2.5.5")
+set(CPACK_NSIS_INSTALLER_ICON_CODE "")
+set(CPACK_NSIS_INSTALLER_MUI_ICON_CODE "")
+set(CPACK_NSIS_INSTALL_ROOT "$PROGRAMFILES")
+set(CPACK_NSIS_PACKAGE_NAME "kissplice 2.5.5")
+set(CPACK_OUTPUT_CONFIG_FILE "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/CPackConfig.cmake")
+set(CPACK_PACKAGE_DEFAULT_LOCATION "/")
+set(CPACK_PACKAGE_DESCRIPTION_FILE "/usr/share/cmake-3.16/Templates/CPack.GenericDescription.txt")
+set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Splicing events caller")
+set(CPACK_PACKAGE_FILE_NAME "kissplice-2.5.5-Linux")
+set(CPACK_PACKAGE_INSTALL_DIRECTORY "kissplice 2.5.5")
+set(CPACK_PACKAGE_INSTALL_REGISTRY_KEY "kissplice 2.5.5")
+set(CPACK_PACKAGE_NAME "kissplice")
+set(CPACK_PACKAGE_RELOCATABLE "true")
+set(CPACK_PACKAGE_VENDOR "Kissplice Development Team")
+set(CPACK_PACKAGE_VERSION "2.5.5")
+set(CPACK_PACKAGE_VERSION_MAJOR "2")
+set(CPACK_PACKAGE_VERSION_MINOR "5")
+set(CPACK_PACKAGE_VERSION_PATCH "5")
+set(CPACK_RESOURCE_FILE_AUTHORS "/home/audric/Desktop/PostDoc/Logiciels/kissplice/AUTHORS")
+set(CPACK_RESOURCE_FILE_INSTALL "/home/audric/Desktop/PostDoc/Logiciels/kissplice/INSTALL")
+set(CPACK_RESOURCE_FILE_LICENSE "/home/audric/Desktop/PostDoc/Logiciels/kissplice/COPYING")
+set(CPACK_RESOURCE_FILE_README "/usr/share/cmake-3.16/Templates/CPack.GenericDescription.txt")
+set(CPACK_RESOURCE_FILE_WELCOME "/usr/share/cmake-3.16/Templates/CPack.GenericWelcome.txt")
+set(CPACK_SET_DESTDIR "OFF")
+set(CPACK_SOURCE_7Z "")
+set(CPACK_SOURCE_CYGWIN "")
+set(CPACK_SOURCE_GENERATOR "TGZ")
+set(CPACK_SOURCE_IGNORE_FILES "README.CMake;README.Licence;README.Release;README.NamingConventions;README.Kissreads;CMakeFiles;Makefile;_CPack_Packages;CMakeCache.txt;.*\\.svn;.*\\.idea;.*\\.DS_Store;.*\\.gz;.*\\~;.*\\.o;bcc/;datasets;ismb;Recomb;RR;script_tarjan_aphid.sh;splice_sites_results;splicing_events;TODO.*;Validation;validation_script.sh;.*project;/\\.git*;^results$;^build$;incremental-bicon.ps;^scripts$;skeletons;doc/dev;alt_splicing_sample_ex.png;quantifModel-big.png;resType0.png;resType1.png;quantifModel.png;ucsc.png;user_guide.aux;user_guide.bib;user_guide.log;user_guide.toc;user_guide.tex;jobim13")
+set(CPACK_SOURCE_OUTPUT_CONFIG_FILE "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/CPackSourceConfig.cmake")
+set(CPACK_SOURCE_PACKAGE_FILE_NAME "kissplice-2.5.5")
+set(CPACK_SOURCE_RPM "")
+set(CPACK_SOURCE_TBZ2 "")
+set(CPACK_SOURCE_TGZ "")
+set(CPACK_SOURCE_TXZ "")
+set(CPACK_SOURCE_TZ "")
+set(CPACK_SOURCE_ZIP "")
+set(CPACK_SYSTEM_NAME "Linux")
+set(CPACK_TOPLEVEL_TAG "Linux")
+set(CPACK_WIX_SIZEOF_VOID_P "8")
if(NOT CPACK_PROPERTIES_FILE)
- set(CPACK_PROPERTIES_FILE "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/CPackProperties.cmake")
+ set(CPACK_PROPERTIES_FILE "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/CPackProperties.cmake")
endif()
if(EXISTS ${CPACK_PROPERTIES_FILE})
=====================================
build/CPackSourceConfig.cmake
=====================================
@@ -10,83 +10,85 @@
# usually begin with CPACK_<GENNAME>_xxxx.
-SET(CPACK_BINARY_7Z "")
-SET(CPACK_BINARY_BUNDLE "")
-SET(CPACK_BINARY_CYGWIN "")
-SET(CPACK_BINARY_DEB "OFF")
-SET(CPACK_BINARY_DRAGNDROP "")
-SET(CPACK_BINARY_FREEBSD "OFF")
-SET(CPACK_BINARY_IFW "OFF")
-SET(CPACK_BINARY_NSIS "OFF")
-SET(CPACK_BINARY_OSXX11 "")
-SET(CPACK_BINARY_PACKAGEMAKER "")
-SET(CPACK_BINARY_PRODUCTBUILD "")
-SET(CPACK_BINARY_RPM "OFF")
-SET(CPACK_BINARY_STGZ "ON")
-SET(CPACK_BINARY_TBZ2 "OFF")
-SET(CPACK_BINARY_TGZ "ON")
-SET(CPACK_BINARY_TXZ "OFF")
-SET(CPACK_BINARY_TZ "ON")
-SET(CPACK_BINARY_WIX "")
-SET(CPACK_BINARY_ZIP "")
-SET(CPACK_BUILD_SOURCE_DIRS "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice;/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build")
-SET(CPACK_CMAKE_GENERATOR "Unix Makefiles")
-SET(CPACK_COMPONENTS_ALL "Unspecified;headers;libraries")
-SET(CPACK_COMPONENT_UNSPECIFIED_HIDDEN "TRUE")
-SET(CPACK_COMPONENT_UNSPECIFIED_REQUIRED "TRUE")
-SET(CPACK_GENERATOR "TGZ")
-SET(CPACK_IGNORE_FILES "README.CMake;README.Licence;README.Release;README.NamingConventions;README.Kissreads;CMakeFiles;Makefile;_CPack_Packages;CMakeCache.txt;.*\\.svn;.*\\.idea;.*\\.DS_Store;.*\\.gz;.*\\~;.*\\.o;bcc/;datasets;ismb;Recomb;RR;script_tarjan_aphid.sh;splice_sites_results;splicing_events;TODO.*;Validation;validation_script.sh;.*project;/\\.git*;^results$;^build$;incremental-bicon.ps;^scripts$;skeletons;doc/dev;alt_splicing_sample_ex.png;quantifModel-big.png;resType0.png;resType1.png;quantifModel.png;ucsc.png;user_guide.aux;user_guide.bib;user_guide.log;user_guide.toc;user_guide.tex;jobim13")
-SET(CPACK_INSTALLED_DIRECTORIES "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice;/")
-SET(CPACK_INSTALL_CMAKE_PROJECTS "")
-SET(CPACK_INSTALL_PREFIX "/usr/local/HDF_Group/HDF5/1.10.5")
-SET(CPACK_MODULE_PATH "")
-SET(CPACK_NSIS_DISPLAY_NAME "kissplice 2.5.4")
-SET(CPACK_NSIS_INSTALLER_ICON_CODE "")
-SET(CPACK_NSIS_INSTALLER_MUI_ICON_CODE "")
-SET(CPACK_NSIS_INSTALL_ROOT "$PROGRAMFILES")
-SET(CPACK_NSIS_PACKAGE_NAME "kissplice 2.5.4")
-SET(CPACK_OUTPUT_CONFIG_FILE "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/CPackConfig.cmake")
-SET(CPACK_PACKAGE_DEFAULT_LOCATION "/")
-SET(CPACK_PACKAGE_DESCRIPTION_FILE "/usr/share/cmake-3.10/Templates/CPack.GenericDescription.txt")
-SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Splicing events caller")
-SET(CPACK_PACKAGE_FILE_NAME "kissplice-2.5.4")
-SET(CPACK_PACKAGE_INSTALL_DIRECTORY "kissplice 2.5.4")
-SET(CPACK_PACKAGE_INSTALL_REGISTRY_KEY "kissplice 2.5.4")
-SET(CPACK_PACKAGE_NAME "kissplice")
-SET(CPACK_PACKAGE_RELOCATABLE "true")
-SET(CPACK_PACKAGE_VENDOR "Kissplice Development Team")
-SET(CPACK_PACKAGE_VERSION "2.5.4")
-SET(CPACK_PACKAGE_VERSION_MAJOR "2")
-SET(CPACK_PACKAGE_VERSION_MINOR "5")
-SET(CPACK_PACKAGE_VERSION_PATCH "4")
-SET(CPACK_RESOURCE_FILE_AUTHORS "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/AUTHORS")
-SET(CPACK_RESOURCE_FILE_INSTALL "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/INSTALL")
-SET(CPACK_RESOURCE_FILE_LICENSE "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/COPYING")
-SET(CPACK_RESOURCE_FILE_README "/usr/share/cmake-3.10/Templates/CPack.GenericDescription.txt")
-SET(CPACK_RESOURCE_FILE_WELCOME "/usr/share/cmake-3.10/Templates/CPack.GenericWelcome.txt")
-SET(CPACK_RPM_PACKAGE_SOURCES "ON")
-SET(CPACK_SET_DESTDIR "OFF")
-SET(CPACK_SOURCE_7Z "")
-SET(CPACK_SOURCE_CYGWIN "")
-SET(CPACK_SOURCE_GENERATOR "TGZ")
-SET(CPACK_SOURCE_IGNORE_FILES "README.CMake;README.Licence;README.Release;README.NamingConventions;README.Kissreads;CMakeFiles;Makefile;_CPack_Packages;CMakeCache.txt;.*\\.svn;.*\\.idea;.*\\.DS_Store;.*\\.gz;.*\\~;.*\\.o;bcc/;datasets;ismb;Recomb;RR;script_tarjan_aphid.sh;splice_sites_results;splicing_events;TODO.*;Validation;validation_script.sh;.*project;/\\.git*;^results$;^build$;incremental-bicon.ps;^scripts$;skeletons;doc/dev;alt_splicing_sample_ex.png;quantifModel-big.png;resType0.png;resType1.png;quantifModel.png;ucsc.png;user_guide.aux;user_guide.bib;user_guide.log;user_guide.toc;user_guide.tex;jobim13")
-SET(CPACK_SOURCE_INSTALLED_DIRECTORIES "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice;/")
-SET(CPACK_SOURCE_OUTPUT_CONFIG_FILE "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/CPackSourceConfig.cmake")
-SET(CPACK_SOURCE_PACKAGE_FILE_NAME "kissplice-2.5.4")
-SET(CPACK_SOURCE_RPM "")
-SET(CPACK_SOURCE_TBZ2 "")
-SET(CPACK_SOURCE_TGZ "")
-SET(CPACK_SOURCE_TOPLEVEL_TAG "Linux-Source")
-SET(CPACK_SOURCE_TXZ "")
-SET(CPACK_SOURCE_TZ "")
-SET(CPACK_SOURCE_ZIP "")
-SET(CPACK_STRIP_FILES "")
-SET(CPACK_SYSTEM_NAME "Linux")
-SET(CPACK_TOPLEVEL_TAG "Linux-Source")
-SET(CPACK_WIX_SIZEOF_VOID_P "8")
+set(CPACK_BINARY_7Z "")
+set(CPACK_BINARY_BUNDLE "")
+set(CPACK_BINARY_CYGWIN "")
+set(CPACK_BINARY_DEB "OFF")
+set(CPACK_BINARY_DRAGNDROP "")
+set(CPACK_BINARY_FREEBSD "OFF")
+set(CPACK_BINARY_IFW "OFF")
+set(CPACK_BINARY_NSIS "OFF")
+set(CPACK_BINARY_NUGET "")
+set(CPACK_BINARY_OSXX11 "")
+set(CPACK_BINARY_PACKAGEMAKER "")
+set(CPACK_BINARY_PRODUCTBUILD "")
+set(CPACK_BINARY_RPM "OFF")
+set(CPACK_BINARY_STGZ "ON")
+set(CPACK_BINARY_TBZ2 "OFF")
+set(CPACK_BINARY_TGZ "ON")
+set(CPACK_BINARY_TXZ "OFF")
+set(CPACK_BINARY_TZ "ON")
+set(CPACK_BINARY_WIX "")
+set(CPACK_BINARY_ZIP "")
+set(CPACK_BUILD_SOURCE_DIRS "/home/audric/Desktop/PostDoc/Logiciels/kissplice;/home/audric/Desktop/PostDoc/Logiciels/kissplice/build")
+set(CPACK_CMAKE_GENERATOR "Unix Makefiles")
+set(CPACK_COMPONENTS_ALL "Unspecified;headers;libraries")
+set(CPACK_COMPONENT_UNSPECIFIED_HIDDEN "TRUE")
+set(CPACK_COMPONENT_UNSPECIFIED_REQUIRED "TRUE")
+set(CPACK_DEFAULT_PACKAGE_DESCRIPTION_FILE "/usr/share/cmake-3.16/Templates/CPack.GenericDescription.txt")
+set(CPACK_GENERATOR "TGZ")
+set(CPACK_IGNORE_FILES "README.CMake;README.Licence;README.Release;README.NamingConventions;README.Kissreads;CMakeFiles;Makefile;_CPack_Packages;CMakeCache.txt;.*\\.svn;.*\\.idea;.*\\.DS_Store;.*\\.gz;.*\\~;.*\\.o;bcc/;datasets;ismb;Recomb;RR;script_tarjan_aphid.sh;splice_sites_results;splicing_events;TODO.*;Validation;validation_script.sh;.*project;/\\.git*;^results$;^build$;incremental-bicon.ps;^scripts$;skeletons;doc/dev;alt_splicing_sample_ex.png;quantifModel-big.png;resType0.png;resType1.png;quantifModel.png;ucsc.png;user_guide.aux;user_guide.bib;user_guide.log;user_guide.toc;user_guide.tex;jobim13")
+set(CPACK_INSTALLED_DIRECTORIES "/home/audric/Desktop/PostDoc/Logiciels/kissplice;/")
+set(CPACK_INSTALL_CMAKE_PROJECTS "")
+set(CPACK_INSTALL_PREFIX "/usr/local/HDF_Group/HDF5/1.10.5")
+set(CPACK_MODULE_PATH "")
+set(CPACK_NSIS_DISPLAY_NAME "kissplice 2.5.5")
+set(CPACK_NSIS_INSTALLER_ICON_CODE "")
+set(CPACK_NSIS_INSTALLER_MUI_ICON_CODE "")
+set(CPACK_NSIS_INSTALL_ROOT "$PROGRAMFILES")
+set(CPACK_NSIS_PACKAGE_NAME "kissplice 2.5.5")
+set(CPACK_OUTPUT_CONFIG_FILE "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/CPackConfig.cmake")
+set(CPACK_PACKAGE_DEFAULT_LOCATION "/")
+set(CPACK_PACKAGE_DESCRIPTION_FILE "/usr/share/cmake-3.16/Templates/CPack.GenericDescription.txt")
+set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Splicing events caller")
+set(CPACK_PACKAGE_FILE_NAME "kissplice-2.5.5")
+set(CPACK_PACKAGE_INSTALL_DIRECTORY "kissplice 2.5.5")
+set(CPACK_PACKAGE_INSTALL_REGISTRY_KEY "kissplice 2.5.5")
+set(CPACK_PACKAGE_NAME "kissplice")
+set(CPACK_PACKAGE_RELOCATABLE "true")
+set(CPACK_PACKAGE_VENDOR "Kissplice Development Team")
+set(CPACK_PACKAGE_VERSION "2.5.5")
+set(CPACK_PACKAGE_VERSION_MAJOR "2")
+set(CPACK_PACKAGE_VERSION_MINOR "5")
+set(CPACK_PACKAGE_VERSION_PATCH "5")
+set(CPACK_RESOURCE_FILE_AUTHORS "/home/audric/Desktop/PostDoc/Logiciels/kissplice/AUTHORS")
+set(CPACK_RESOURCE_FILE_INSTALL "/home/audric/Desktop/PostDoc/Logiciels/kissplice/INSTALL")
+set(CPACK_RESOURCE_FILE_LICENSE "/home/audric/Desktop/PostDoc/Logiciels/kissplice/COPYING")
+set(CPACK_RESOURCE_FILE_README "/usr/share/cmake-3.16/Templates/CPack.GenericDescription.txt")
+set(CPACK_RESOURCE_FILE_WELCOME "/usr/share/cmake-3.16/Templates/CPack.GenericWelcome.txt")
+set(CPACK_RPM_PACKAGE_SOURCES "ON")
+set(CPACK_SET_DESTDIR "OFF")
+set(CPACK_SOURCE_7Z "")
+set(CPACK_SOURCE_CYGWIN "")
+set(CPACK_SOURCE_GENERATOR "TGZ")
+set(CPACK_SOURCE_IGNORE_FILES "README.CMake;README.Licence;README.Release;README.NamingConventions;README.Kissreads;CMakeFiles;Makefile;_CPack_Packages;CMakeCache.txt;.*\\.svn;.*\\.idea;.*\\.DS_Store;.*\\.gz;.*\\~;.*\\.o;bcc/;datasets;ismb;Recomb;RR;script_tarjan_aphid.sh;splice_sites_results;splicing_events;TODO.*;Validation;validation_script.sh;.*project;/\\.git*;^results$;^build$;incremental-bicon.ps;^scripts$;skeletons;doc/dev;alt_splicing_sample_ex.png;quantifModel-big.png;resType0.png;resType1.png;quantifModel.png;ucsc.png;user_guide.aux;user_guide.bib;user_guide.log;user_guide.toc;user_guide.tex;jobim13")
+set(CPACK_SOURCE_INSTALLED_DIRECTORIES "/home/audric/Desktop/PostDoc/Logiciels/kissplice;/")
+set(CPACK_SOURCE_OUTPUT_CONFIG_FILE "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/CPackSourceConfig.cmake")
+set(CPACK_SOURCE_PACKAGE_FILE_NAME "kissplice-2.5.5")
+set(CPACK_SOURCE_RPM "")
+set(CPACK_SOURCE_TBZ2 "")
+set(CPACK_SOURCE_TGZ "")
+set(CPACK_SOURCE_TOPLEVEL_TAG "Linux-Source")
+set(CPACK_SOURCE_TXZ "")
+set(CPACK_SOURCE_TZ "")
+set(CPACK_SOURCE_ZIP "")
+set(CPACK_STRIP_FILES "")
+set(CPACK_SYSTEM_NAME "Linux")
+set(CPACK_TOPLEVEL_TAG "Linux-Source")
+set(CPACK_WIX_SIZEOF_VOID_P "8")
if(NOT CPACK_PROPERTIES_FILE)
- set(CPACK_PROPERTIES_FILE "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/CPackProperties.cmake")
+ set(CPACK_PROPERTIES_FILE "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/CPackProperties.cmake")
endif()
if(EXISTS ${CPACK_PROPERTIES_FILE})
=====================================
build/CTestTestfile.cmake
=====================================
@@ -1,6 +1,6 @@
# CMake generated Testfile for
-# Source directory: /home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice
-# Build directory: /home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build
+# Source directory: /home/audric/Desktop/PostDoc/Logiciels/kissplice
+# Build directory: /home/audric/Desktop/PostDoc/Logiciels/kissplice/build
#
# This file includes the relevant testing commands required for
# testing this directory and lists subdirectories to be tested as well.
=====================================
build/README.txt
=====================================
@@ -3,7 +3,7 @@ HDF5 version 1.10.5
This directory contains the binary (release) distribution of
HDF5 1.10 that was compiled on;
- Linux 4.15.0-142-generic x86_64, using GNU C 7.5.0.
+ Linux 5.13.0-1017-oem x86_64, using GNU C 9.3.0.
It was built with the following options:
-- Static C/C++/Fortran libraries
@@ -39,7 +39,7 @@ To test the installation with the examples;
Copy CTestScript.cmake to this directory.
The default source folder is defined as "HDF5Examples". It can be changed
with the CTEST_SOURCE_NAME script option.
- The default installation folder is defined as "/usr/local/HDF_Group/HDF5/1.10.5".
+ The default installation folder is defined as "/usr/local".
It can be changed with the INSTALLDIR script option.
The default ctest configuration is defined as "Release". It can be changed
with the CTEST_CONFIGURATION_TYPE script option. Note that this must
=====================================
build/bin/kissplice
=====================================
@@ -470,7 +470,7 @@ def concatenate_graph_all_log_bcc_to_all_bcc_type0(workdir, kval, output_snps):
def check_read_coverage_and_sort_all_bubbles(KISSPLICE_INSTDIR, readfiles, workdir, outdir, kval, output_snps, infix_name,
- countsMethods, minOverlap, substitutions, getMappingInfo, stranded, strandedAbsoluteThreshold, strandedRelativeThreshold, verbose = False):
+ countsMethods, minOverlap, substitutions, getMappingInfo, stranded, strandedAbsoluteThreshold, strandedRelativeThreshold, nbprocs, verbose = False):
print("\n" + getTimestamp() + "--> Computing read coherence and coverage...")
printlg("\n" + getTimestamp() + "--> Computing read coherence and coverage...")
@@ -478,7 +478,7 @@ def check_read_coverage_and_sort_all_bubbles(KISSPLICE_INSTDIR, readfiles, workd
# Du to the k extension, anchor should be of size k+1 for SNP
commandLineType0=""
if output_snps > 0:
- commandLineType0 = KISSPLICE_INSTDIR+"/ks_kissreadsSNPS "+workdir+"/all_bcc_type0_"+str(kval)+" "+readfiles+" -i 5 -S 25 -O "+str(kval+minOverlap)+" -o "+ workdir+"/coherentType0.fa -u "+workdir+"/uncoherentType0.fa -d " + str(substitutions) + " -c 1 -n "
+ commandLineType0 = KISSPLICE_INSTDIR+"/ks_kissreadsSNPS "+workdir+"/all_bcc_type0_"+str(kval)+" "+readfiles+" -i 5 -S 25 -O "+str(kval+minOverlap)+" -o "+ workdir+"/coherentType0.fa -u "+workdir+"/uncoherentType0.fa -d " + str(substitutions) + " -c 1 -n -t "+str(nbprocs)
if stranded:
commandLineType0+=" -x -a " + str(strandedAbsoluteThreshold) + " -r " + str(strandedRelativeThreshold) + " "
if getMappingInfo:
@@ -494,7 +494,7 @@ def check_read_coverage_and_sort_all_bubbles(KISSPLICE_INSTDIR, readfiles, workd
shutil.move(workdir+"/uncoherentType0.fa.explanations", outdir+"/uncoherentType0.fa.explanations")
# no n options anymore
- commandLineType1234 = KISSPLICE_INSTDIR+"/ks_kissreadsSplice "+workdir+"/all_bcc_type1234_"+str(kval)+" "+readfiles+" -i 5 -k "+str(kval)+" -S 25 -O "+str(kval+minOverlap)+" -o "+workdir+"/coherentType1234.fa -u "+workdir+"/uncoherentType1234.fa -d " + str(substitutions) + " -c 1 -j " + countsMethods +" -l " + str(minOverlap)
+ commandLineType1234 = KISSPLICE_INSTDIR+"/ks_kissreadsSplice "+workdir+"/all_bcc_type1234_"+str(kval)+" "+readfiles+" -i 5 -k "+str(kval)+" -S 25 -O "+str(kval+minOverlap)+" -o "+workdir+"/coherentType1234.fa -u "+workdir+"/uncoherentType1234.fa -d " + str(substitutions) + " -c 1 -j " + countsMethods +" -l " + str(minOverlap) +" -t "+str(nbprocs)
if stranded:
commandLineType1234+=" -x -a " + str(strandedAbsoluteThreshold) + " -r " + str(strandedRelativeThreshold) + " "
if getMappingInfo:
@@ -727,7 +727,7 @@ def main():
parser.add_argument('--min_overlap', action = "store", dest = "minOverlap", default = 5, type=int, help="Set how many nt must overlap a junction to be counted by --counts option. Default=5. see User guide for more information ")
parser.add_argument('--timeout', action='store', dest="timeout", default=TIMEOUT,
help="max amount of time (in seconds) spent for enumerating bubbles in each bcc. If exceeded, no bubble is output for the bcc (default "+str(TIMEOUT)+")")
- parser.add_argument('--version', action='version', version='%(prog)s 2.5.4')
+ parser.add_argument('--version', action='version', version='%(prog)s 2.5.5')
parser.add_argument('--output-context', action="store_true", dest="output_context", default = False, help="Will output the maximum non-ambiguous context of a bubble")
parser.add_argument('--output-path', action="store_true", dest="output_path", default = False, help="Will output the id of the nodes composing the two paths of the bubbles.")
parser.add_argument('--output-branch-count', action="store_true", dest="output_branch_count", default = False, help="Will output the number of branching nodes in each path.")
@@ -764,8 +764,8 @@ def main():
# ------------------------------------------------------------------------
# Print version and command line
# ------------------------------------------------------------------------
- print("\nThis is KisSplice, version 2.5.4\n")
- printlg("This is KisSplice, version 2.5.4\n")
+ print("\nThis is KisSplice, version 2.5.5\n")
+ printlg("This is KisSplice, version 2.5.5\n")
print("The command line was: " + ' '.join(sys.argv))
printlg("The command line was: " + ' '.join(sys.argv))
@@ -915,7 +915,7 @@ def main():
t = time.time()
nb = sort_all_bubbles(KS_SEC_EXEC_PATH, readfiles, workdir, outdir, kval, output_snps, infix_name, not only_graph, options.verbose)
if not only_graph:
- nb = check_read_coverage_and_sort_all_bubbles(KS_SEC_EXEC_PATH, readfiles, workdir, outdir, kval, output_snps, infix_name, countsMethod, minOverlap, options.mism, options.get_mapping_info, options.stranded, options.strandedAbsoluteThreshold, options.strandedRelativeThreshold, options.verbose)
+ nb = check_read_coverage_and_sort_all_bubbles(KS_SEC_EXEC_PATH, readfiles, workdir, outdir, kval, output_snps, infix_name, countsMethod, minOverlap, options.mism, options.get_mapping_info, options.stranded, options.strandedAbsoluteThreshold, options.strandedRelativeThreshold, options.nbprocs, options.verbose)
print("Elapsed time: ", (time.time() - t), " seconds\n")
printlg("Elapsed time: ", (time.time() - t), " seconds\n")
=====================================
build/cmake_install.cmake
=====================================
@@ -1,4 +1,4 @@
-# Install script for directory: /home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice
+# Install script for directory: /home/audric/Desktop/PostDoc/Logiciels/kissplice
# Set the install prefix
if(NOT DEFINED CMAKE_INSTALL_PREFIX)
@@ -39,24 +39,24 @@ endif()
if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xUnspecifiedx" OR NOT CMAKE_INSTALL_COMPONENT)
list(APPEND CMAKE_ABSOLUTE_DESTINATION_FILES
- "/usr/local/HDF_Group/HDF5/1.10.5/bin/kissplice")
+ "/usr/local/bin/kissplice")
if(CMAKE_WARN_ON_ABSOLUTE_INSTALL_DESTINATION)
message(WARNING "ABSOLUTE path INSTALL DESTINATION : ${CMAKE_ABSOLUTE_DESTINATION_FILES}")
endif()
if(CMAKE_ERROR_ON_ABSOLUTE_INSTALL_DESTINATION)
message(FATAL_ERROR "ABSOLUTE path INSTALL DESTINATION forbidden (by caller): ${CMAKE_ABSOLUTE_DESTINATION_FILES}")
endif()
-file(INSTALL DESTINATION "/usr/local/HDF_Group/HDF5/1.10.5/bin" TYPE PROGRAM FILES "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/bin/kissplice")
+file(INSTALL DESTINATION "/usr/local/bin" TYPE PROGRAM FILES "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/bin/kissplice")
endif()
if(NOT CMAKE_INSTALL_LOCAL_ONLY)
# Include the install script for each subdirectory.
- include("/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/bcalm/cmake_install.cmake")
- include("/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/thirdparty/cmake_install.cmake")
- include("/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/modules/cmake_install.cmake")
- include("/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/man/cmake_install.cmake")
- include("/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/doc/cmake_install.cmake")
- include("/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/tests/cmake_install.cmake")
+ include("/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/bcalm/cmake_install.cmake")
+ include("/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/thirdparty/cmake_install.cmake")
+ include("/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/modules/cmake_install.cmake")
+ include("/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/man/cmake_install.cmake")
+ include("/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/doc/cmake_install.cmake")
+ include("/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/tests/cmake_install.cmake")
endif()
@@ -68,5 +68,5 @@ endif()
string(REPLACE ";" "\n" CMAKE_INSTALL_MANIFEST_CONTENT
"${CMAKE_INSTALL_MANIFEST_FILES}")
-file(WRITE "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/${CMAKE_INSTALL_MANIFEST}"
+file(WRITE "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/${CMAKE_INSTALL_MANIFEST}"
"${CMAKE_INSTALL_MANIFEST_CONTENT}")
=====================================
build/cmake_uninstall.cmake
=====================================
@@ -1,8 +1,8 @@
-if (NOT EXISTS "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/install_manifest.txt")
- message(FATAL_ERROR "Cannot find install manifest: \"/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/install_manifest.txt\"")
-endif(NOT EXISTS "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/install_manifest.txt")
+if (NOT EXISTS "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/install_manifest.txt")
+ message(FATAL_ERROR "Cannot find install manifest: \"/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/install_manifest.txt\"")
+endif(NOT EXISTS "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/install_manifest.txt")
-file(READ "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/install_manifest.txt" files)
+file(READ "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/install_manifest.txt" files)
string(REGEX REPLACE "\n" ";" files "${files}")
list(REVERSE files)
foreach (file ${files})
=====================================
build/doc/cmake_install.cmake
=====================================
@@ -1,4 +1,4 @@
-# Install script for directory: /home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/doc
+# Install script for directory: /home/audric/Desktop/PostDoc/Logiciels/kissplice/doc
# Set the install prefix
if(NOT DEFINED CMAKE_INSTALL_PREFIX)
@@ -38,6 +38,6 @@ if(NOT DEFINED CMAKE_CROSSCOMPILING)
endif()
if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xUnspecifiedx" OR NOT CMAKE_INSTALL_COMPONENT)
- file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/share/doc/kissplice" TYPE FILE FILES "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/doc/user_guide.pdf")
+ file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/share/doc/kissplice" TYPE FILE FILES "/home/audric/Desktop/PostDoc/Logiciels/kissplice/doc/user_guide.pdf")
endif()
=====================================
build/man/cmake_install.cmake
=====================================
@@ -1,4 +1,4 @@
-# Install script for directory: /home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/man
+# Install script for directory: /home/audric/Desktop/PostDoc/Logiciels/kissplice/man
# Set the install prefix
if(NOT DEFINED CMAKE_INSTALL_PREFIX)
@@ -38,6 +38,6 @@ if(NOT DEFINED CMAKE_CROSSCOMPILING)
endif()
if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xUnspecifiedx" OR NOT CMAKE_INSTALL_COMPONENT)
- file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/share/man/man1" TYPE FILE FILES "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/man/kissplice.1")
+ file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/share/man/man1" TYPE FILE FILES "/home/audric/Desktop/PostDoc/Logiciels/kissplice/man/kissplice.1")
endif()
=====================================
build/modules/cmake_install.cmake
=====================================
@@ -1,4 +1,4 @@
-# Install script for directory: /home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/modules
+# Install script for directory: /home/audric/Desktop/PostDoc/Logiciels/kissplice/modules
# Set the install prefix
if(NOT DEFINED CMAKE_INSTALL_PREFIX)
@@ -44,7 +44,7 @@ if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xUnspecifiedx" OR NOT CMAKE_INSTALL_
FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_clean_duplicates"
RPATH "")
endif()
- file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/libexec/kissplice" TYPE EXECUTABLE FILES "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/libexec/kissplice/ks_clean_duplicates")
+ file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/libexec/kissplice" TYPE EXECUTABLE FILES "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/libexec/kissplice/ks_clean_duplicates")
if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_clean_duplicates" AND
NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_clean_duplicates")
if(CMAKE_INSTALL_DO_STRIP)
@@ -60,7 +60,7 @@ if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xUnspecifiedx" OR NOT CMAKE_INSTALL_
FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_bubble_enumeration"
RPATH "")
endif()
- file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/libexec/kissplice" TYPE EXECUTABLE FILES "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/libexec/kissplice/ks_bubble_enumeration")
+ file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/libexec/kissplice" TYPE EXECUTABLE FILES "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/libexec/kissplice/ks_bubble_enumeration")
if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_bubble_enumeration" AND
NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_bubble_enumeration")
if(CMAKE_INSTALL_DO_STRIP)
@@ -76,7 +76,7 @@ if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xUnspecifiedx" OR NOT CMAKE_INSTALL_
FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_run_modules"
RPATH "")
endif()
- file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/libexec/kissplice" TYPE EXECUTABLE FILES "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/libexec/kissplice/ks_run_modules")
+ file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/libexec/kissplice" TYPE EXECUTABLE FILES "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/libexec/kissplice/ks_run_modules")
if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_run_modules" AND
NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_run_modules")
if(CMAKE_INSTALL_DO_STRIP)
@@ -92,7 +92,7 @@ if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xUnspecifiedx" OR NOT CMAKE_INSTALL_
FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_error_removal"
RPATH "")
endif()
- file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/libexec/kissplice" TYPE EXECUTABLE FILES "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/libexec/kissplice/ks_error_removal")
+ file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/libexec/kissplice" TYPE EXECUTABLE FILES "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/libexec/kissplice/ks_error_removal")
if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_error_removal" AND
NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_error_removal")
if(CMAKE_INSTALL_DO_STRIP)
@@ -108,7 +108,7 @@ if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xUnspecifiedx" OR NOT CMAKE_INSTALL_
FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_print_bcc"
RPATH "")
endif()
- file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/libexec/kissplice" TYPE EXECUTABLE FILES "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/libexec/kissplice/ks_print_bcc")
+ file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/libexec/kissplice" TYPE EXECUTABLE FILES "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/libexec/kissplice/ks_print_bcc")
if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_print_bcc" AND
NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_print_bcc")
if(CMAKE_INSTALL_DO_STRIP)
=====================================
build/tests/CTestTestfile.cmake
=====================================
@@ -1,6 +1,6 @@
# CMake generated Testfile for
-# Source directory: /home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/tests
-# Build directory: /home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/tests
+# Source directory: /home/audric/Desktop/PostDoc/Logiciels/kissplice/tests
+# Build directory: /home/audric/Desktop/PostDoc/Logiciels/kissplice/build/tests
#
# This file includes the relevant testing commands required for
# testing this directory and lists subdirectories to be tested as well.
=====================================
build/tests/cmake_install.cmake
=====================================
@@ -1,4 +1,4 @@
-# Install script for directory: /home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/tests
+# Install script for directory: /home/audric/Desktop/PostDoc/Logiciels/kissplice/tests
# Set the install prefix
if(NOT DEFINED CMAKE_INSTALL_PREFIX)
@@ -39,8 +39,8 @@ endif()
if(NOT CMAKE_INSTALL_LOCAL_ONLY)
# Include the install script for each subdirectory.
- include("/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/tests/integration_tests/cmake_install.cmake")
- include("/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/tests/functional_tests/cmake_install.cmake")
+ include("/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/tests/integration_tests/cmake_install.cmake")
+ include("/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/tests/functional_tests/cmake_install.cmake")
endif()
=====================================
build/tests/functional_tests/CTestTestfile.cmake
=====================================
@@ -1,12 +1,12 @@
# CMake generated Testfile for
-# Source directory: /home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/tests/functional_tests
-# Build directory: /home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/tests/functional_tests
+# Source directory: /home/audric/Desktop/PostDoc/Logiciels/kissplice/tests/functional_tests
+# Build directory: /home/audric/Desktop/PostDoc/Logiciels/kissplice/build/tests/functional_tests
#
# This file includes the relevant testing commands required for
# testing this directory and lists subdirectories to be tested as well.
-add_test(ksBubbleEnumerationTest "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/tests/functional_tests/ksBubbleEnumerationTest.py" "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/libexec/kissplice")
-set_tests_properties(ksBubbleEnumerationTest PROPERTIES PASS_REGULAR_EXPRESSION "test SUCCESSFUL")
-add_test(ksRunModulesTest "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/tests/functional_tests/ksRunModulesTest.py" "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/libexec/kissplice")
-set_tests_properties(ksRunModulesTest PROPERTIES PASS_REGULAR_EXPRESSION "test SUCCESSFUL")
-add_test(ksErrorRemovalTest "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/tests/functional_tests/ksErrorRemovalTest.py" "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/libexec/kissplice")
-set_tests_properties(ksErrorRemovalTest PROPERTIES PASS_REGULAR_EXPRESSION "test SUCCESSFUL")
+add_test(ksBubbleEnumerationTest "/home/audric/Desktop/PostDoc/Logiciels/kissplice/tests/functional_tests/ksBubbleEnumerationTest.py" "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/libexec/kissplice")
+set_tests_properties(ksBubbleEnumerationTest PROPERTIES PASS_REGULAR_EXPRESSION "test SUCCESSFUL" _BACKTRACE_TRIPLES "/home/audric/Desktop/PostDoc/Logiciels/kissplice/tests/functional_tests/CMakeLists.txt;5;add_test;/home/audric/Desktop/PostDoc/Logiciels/kissplice/tests/functional_tests/CMakeLists.txt;0;")
+add_test(ksRunModulesTest "/home/audric/Desktop/PostDoc/Logiciels/kissplice/tests/functional_tests/ksRunModulesTest.py" "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/libexec/kissplice")
+set_tests_properties(ksRunModulesTest PROPERTIES PASS_REGULAR_EXPRESSION "test SUCCESSFUL" _BACKTRACE_TRIPLES "/home/audric/Desktop/PostDoc/Logiciels/kissplice/tests/functional_tests/CMakeLists.txt;12;add_test;/home/audric/Desktop/PostDoc/Logiciels/kissplice/tests/functional_tests/CMakeLists.txt;0;")
+add_test(ksErrorRemovalTest "/home/audric/Desktop/PostDoc/Logiciels/kissplice/tests/functional_tests/ksErrorRemovalTest.py" "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/libexec/kissplice")
+set_tests_properties(ksErrorRemovalTest PROPERTIES PASS_REGULAR_EXPRESSION "test SUCCESSFUL" _BACKTRACE_TRIPLES "/home/audric/Desktop/PostDoc/Logiciels/kissplice/tests/functional_tests/CMakeLists.txt;19;add_test;/home/audric/Desktop/PostDoc/Logiciels/kissplice/tests/functional_tests/CMakeLists.txt;0;")
=====================================
build/tests/functional_tests/cmake_install.cmake
=====================================
@@ -1,4 +1,4 @@
-# Install script for directory: /home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/tests/functional_tests
+# Install script for directory: /home/audric/Desktop/PostDoc/Logiciels/kissplice/tests/functional_tests
# Set the install prefix
if(NOT DEFINED CMAKE_INSTALL_PREFIX)
=====================================
build/tests/integration_tests/CTestTestfile.cmake
=====================================
@@ -1,15 +1,16 @@
# CMake generated Testfile for
-# Source directory: /home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/tests/integration_tests
-# Build directory: /home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/tests/integration_tests
+# Source directory: /home/audric/Desktop/PostDoc/Logiciels/kissplice/tests/integration_tests
+# Build directory: /home/audric/Desktop/PostDoc/Logiciels/kissplice/build/tests/integration_tests
#
# This file includes the relevant testing commands required for
# testing this directory and lists subdirectories to be tested as well.
-add_test(KisspliceBasicTest "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/bin/kissplice" "-h")
-add_test(KisspliceDBGTest "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/tests/integration_tests/kisspliceDBGTest.py" "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/bin")
-set_tests_properties(KisspliceDBGTest PROPERTIES PASS_REGULAR_EXPRESSION "test SUCCESSFUL")
-add_test(KisspliceTwoSequencesTest "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/tests/integration_tests/kisspliceTwoSequencesTest.py" "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/bin")
-set_tests_properties(KisspliceTwoSequencesTest PROPERTIES PASS_REGULAR_EXPRESSION "test SUCCESSFUL")
-add_test(KisspliceGraphAndSequenceTest "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/tests/integration_tests/kisspliceGraphAndSequenceTest.py" "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/bin")
-set_tests_properties(KisspliceGraphAndSequenceTest PROPERTIES PASS_REGULAR_EXPRESSION "test SUCCESSFUL")
-add_test(KisspliceGraphTest "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/tests/integration_tests/kisspliceGraphTest.py" "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/bin")
-set_tests_properties(KisspliceGraphTest PROPERTIES PASS_REGULAR_EXPRESSION "test SUCCESSFUL")
+add_test(KisspliceBasicTest "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/bin/kissplice" "-h")
+set_tests_properties(KisspliceBasicTest PROPERTIES _BACKTRACE_TRIPLES "/home/audric/Desktop/PostDoc/Logiciels/kissplice/tests/integration_tests/CMakeLists.txt;4;add_test;/home/audric/Desktop/PostDoc/Logiciels/kissplice/tests/integration_tests/CMakeLists.txt;0;")
+add_test(KisspliceDBGTest "/home/audric/Desktop/PostDoc/Logiciels/kissplice/tests/integration_tests/kisspliceDBGTest.py" "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/bin")
+set_tests_properties(KisspliceDBGTest PROPERTIES PASS_REGULAR_EXPRESSION "test SUCCESSFUL" _BACKTRACE_TRIPLES "/home/audric/Desktop/PostDoc/Logiciels/kissplice/tests/integration_tests/CMakeLists.txt;11;add_test;/home/audric/Desktop/PostDoc/Logiciels/kissplice/tests/integration_tests/CMakeLists.txt;0;")
+add_test(KisspliceTwoSequencesTest "/home/audric/Desktop/PostDoc/Logiciels/kissplice/tests/integration_tests/kisspliceTwoSequencesTest.py" "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/bin")
+set_tests_properties(KisspliceTwoSequencesTest PROPERTIES PASS_REGULAR_EXPRESSION "test SUCCESSFUL" _BACKTRACE_TRIPLES "/home/audric/Desktop/PostDoc/Logiciels/kissplice/tests/integration_tests/CMakeLists.txt;18;add_test;/home/audric/Desktop/PostDoc/Logiciels/kissplice/tests/integration_tests/CMakeLists.txt;0;")
+add_test(KisspliceGraphAndSequenceTest "/home/audric/Desktop/PostDoc/Logiciels/kissplice/tests/integration_tests/kisspliceGraphAndSequenceTest.py" "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/bin")
+set_tests_properties(KisspliceGraphAndSequenceTest PROPERTIES PASS_REGULAR_EXPRESSION "test SUCCESSFUL" _BACKTRACE_TRIPLES "/home/audric/Desktop/PostDoc/Logiciels/kissplice/tests/integration_tests/CMakeLists.txt;26;add_test;/home/audric/Desktop/PostDoc/Logiciels/kissplice/tests/integration_tests/CMakeLists.txt;0;")
+add_test(KisspliceGraphTest "/home/audric/Desktop/PostDoc/Logiciels/kissplice/tests/integration_tests/kisspliceGraphTest.py" "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/bin")
+set_tests_properties(KisspliceGraphTest PROPERTIES PASS_REGULAR_EXPRESSION "test SUCCESSFUL" _BACKTRACE_TRIPLES "/home/audric/Desktop/PostDoc/Logiciels/kissplice/tests/integration_tests/CMakeLists.txt;32;add_test;/home/audric/Desktop/PostDoc/Logiciels/kissplice/tests/integration_tests/CMakeLists.txt;0;")
=====================================
build/tests/integration_tests/cmake_install.cmake
=====================================
@@ -1,4 +1,4 @@
-# Install script for directory: /home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/tests/integration_tests
+# Install script for directory: /home/audric/Desktop/PostDoc/Logiciels/kissplice/tests/integration_tests
# Set the install prefix
if(NOT DEFINED CMAKE_INSTALL_PREFIX)
=====================================
build/thirdparty/cmake_install.cmake
=====================================
@@ -1,4 +1,4 @@
-# Install script for directory: /home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/thirdparty
+# Install script for directory: /home/audric/Desktop/PostDoc/Logiciels/kissplice/thirdparty
# Set the install prefix
if(NOT DEFINED CMAKE_INSTALL_PREFIX)
@@ -39,7 +39,7 @@ endif()
if(NOT CMAKE_INSTALL_LOCAL_ONLY)
# Include the install script for each subdirectory.
- include("/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/thirdparty/kissreads/cmake_install.cmake")
+ include("/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/thirdparty/kissreads/cmake_install.cmake")
endif()
=====================================
build/thirdparty/kissreads/cmake_install.cmake
=====================================
@@ -1,4 +1,4 @@
-# Install script for directory: /home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/thirdparty/kissreads
+# Install script for directory: /home/audric/Desktop/PostDoc/Logiciels/kissplice/thirdparty/kissreads
# Set the install prefix
if(NOT DEFINED CMAKE_INSTALL_PREFIX)
@@ -39,7 +39,7 @@ endif()
if(NOT CMAKE_INSTALL_LOCAL_ONLY)
# Include the install script for each subdirectory.
- include("/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/thirdparty/kissreads/src/cmake_install.cmake")
+ include("/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/thirdparty/kissreads/src/cmake_install.cmake")
endif()
=====================================
build/thirdparty/kissreads/src/cmake_install.cmake
=====================================
@@ -1,4 +1,4 @@
-# Install script for directory: /home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/thirdparty/kissreads/src
+# Install script for directory: /home/audric/Desktop/PostDoc/Logiciels/kissplice/thirdparty/kissreads/src
# Set the install prefix
if(NOT DEFINED CMAKE_INSTALL_PREFIX)
@@ -44,13 +44,9 @@ if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xUnspecifiedx" OR NOT CMAKE_INSTALL_
FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_kissreadsSNPS"
RPATH "")
endif()
- file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/libexec/kissplice" TYPE EXECUTABLE FILES "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/libexec/kissplice/ks_kissreadsSNPS")
+ file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/libexec/kissplice" TYPE EXECUTABLE FILES "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/libexec/kissplice/ks_kissreadsSNPS")
if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_kissreadsSNPS" AND
NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_kissreadsSNPS")
- file(RPATH_CHANGE
- FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_kissreadsSNPS"
- OLD_RPATH "/usr/local/lib:"
- NEW_RPATH "")
if(CMAKE_INSTALL_DO_STRIP)
execute_process(COMMAND "/usr/bin/strip" "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_kissreadsSNPS")
endif()
@@ -64,13 +60,9 @@ if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xUnspecifiedx" OR NOT CMAKE_INSTALL_
FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_kissreadsSplice"
RPATH "")
endif()
- file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/libexec/kissplice" TYPE EXECUTABLE FILES "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/libexec/kissplice/ks_kissreadsSplice")
+ file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/libexec/kissplice" TYPE EXECUTABLE FILES "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/libexec/kissplice/ks_kissreadsSplice")
if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_kissreadsSplice" AND
NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_kissreadsSplice")
- file(RPATH_CHANGE
- FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_kissreadsSplice"
- OLD_RPATH "/usr/local/lib:"
- NEW_RPATH "")
if(CMAKE_INSTALL_DO_STRIP)
execute_process(COMMAND "/usr/bin/strip" "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_kissreadsSplice")
endif()
=====================================
kissplice.py
=====================================
@@ -470,7 +470,7 @@ def concatenate_graph_all_log_bcc_to_all_bcc_type0(workdir, kval, output_snps):
def check_read_coverage_and_sort_all_bubbles(KISSPLICE_INSTDIR, readfiles, workdir, outdir, kval, output_snps, infix_name,
- countsMethods, minOverlap, substitutions, getMappingInfo, stranded, strandedAbsoluteThreshold, strandedRelativeThreshold, verbose = False):
+ countsMethods, minOverlap, substitutions, getMappingInfo, stranded, strandedAbsoluteThreshold, strandedRelativeThreshold, nbprocs, verbose = False):
print("\n" + getTimestamp() + "--> Computing read coherence and coverage...")
printlg("\n" + getTimestamp() + "--> Computing read coherence and coverage...")
@@ -478,7 +478,7 @@ def check_read_coverage_and_sort_all_bubbles(KISSPLICE_INSTDIR, readfiles, workd
# Du to the k extension, anchor should be of size k+1 for SNP
commandLineType0=""
if output_snps > 0:
- commandLineType0 = KISSPLICE_INSTDIR+"/ks_kissreadsSNPS "+workdir+"/all_bcc_type0_"+str(kval)+" "+readfiles+" -i 5 -S 25 -O "+str(kval+minOverlap)+" -o "+ workdir+"/coherentType0.fa -u "+workdir+"/uncoherentType0.fa -d " + str(substitutions) + " -c 1 -n "
+ commandLineType0 = KISSPLICE_INSTDIR+"/ks_kissreadsSNPS "+workdir+"/all_bcc_type0_"+str(kval)+" "+readfiles+" -i 5 -S 25 -O "+str(kval+minOverlap)+" -o "+ workdir+"/coherentType0.fa -u "+workdir+"/uncoherentType0.fa -d " + str(substitutions) + " -c 1 -n -t "+str(nbprocs)
if stranded:
commandLineType0+=" -x -a " + str(strandedAbsoluteThreshold) + " -r " + str(strandedRelativeThreshold) + " "
if getMappingInfo:
@@ -494,7 +494,7 @@ def check_read_coverage_and_sort_all_bubbles(KISSPLICE_INSTDIR, readfiles, workd
shutil.move(workdir+"/uncoherentType0.fa.explanations", outdir+"/uncoherentType0.fa.explanations")
# no n options anymore
- commandLineType1234 = KISSPLICE_INSTDIR+"/ks_kissreadsSplice "+workdir+"/all_bcc_type1234_"+str(kval)+" "+readfiles+" -i 5 -k "+str(kval)+" -S 25 -O "+str(kval+minOverlap)+" -o "+workdir+"/coherentType1234.fa -u "+workdir+"/uncoherentType1234.fa -d " + str(substitutions) + " -c 1 -j " + countsMethods +" -l " + str(minOverlap)
+ commandLineType1234 = KISSPLICE_INSTDIR+"/ks_kissreadsSplice "+workdir+"/all_bcc_type1234_"+str(kval)+" "+readfiles+" -i 5 -k "+str(kval)+" -S 25 -O "+str(kval+minOverlap)+" -o "+workdir+"/coherentType1234.fa -u "+workdir+"/uncoherentType1234.fa -d " + str(substitutions) + " -c 1 -j " + countsMethods +" -l " + str(minOverlap) +" -t "+str(nbprocs)
if stranded:
commandLineType1234+=" -x -a " + str(strandedAbsoluteThreshold) + " -r " + str(strandedRelativeThreshold) + " "
if getMappingInfo:
@@ -727,7 +727,7 @@ def main():
parser.add_argument('--min_overlap', action = "store", dest = "minOverlap", default = 5, type=int, help="Set how many nt must overlap a junction to be counted by --counts option. Default=5. see User guide for more information ")
parser.add_argument('--timeout', action='store', dest="timeout", default=TIMEOUT,
help="max amount of time (in seconds) spent for enumerating bubbles in each bcc. If exceeded, no bubble is output for the bcc (default "+str(TIMEOUT)+")")
- parser.add_argument('--version', action='version', version='%(prog)s 2.5.4')
+ parser.add_argument('--version', action='version', version='%(prog)s 2.5.5')
parser.add_argument('--output-context', action="store_true", dest="output_context", default = False, help="Will output the maximum non-ambiguous context of a bubble")
parser.add_argument('--output-path', action="store_true", dest="output_path", default = False, help="Will output the id of the nodes composing the two paths of the bubbles.")
parser.add_argument('--output-branch-count', action="store_true", dest="output_branch_count", default = False, help="Will output the number of branching nodes in each path.")
@@ -764,8 +764,8 @@ def main():
# ------------------------------------------------------------------------
# Print version and command line
# ------------------------------------------------------------------------
- print("\nThis is KisSplice, version 2.5.4\n")
- printlg("This is KisSplice, version 2.5.4\n")
+ print("\nThis is KisSplice, version 2.5.5\n")
+ printlg("This is KisSplice, version 2.5.5\n")
print("The command line was: " + ' '.join(sys.argv))
printlg("The command line was: " + ' '.join(sys.argv))
@@ -915,7 +915,7 @@ def main():
t = time.time()
nb = sort_all_bubbles(KS_SEC_EXEC_PATH, readfiles, workdir, outdir, kval, output_snps, infix_name, not only_graph, options.verbose)
if not only_graph:
- nb = check_read_coverage_and_sort_all_bubbles(KS_SEC_EXEC_PATH, readfiles, workdir, outdir, kval, output_snps, infix_name, countsMethod, minOverlap, options.mism, options.get_mapping_info, options.stranded, options.strandedAbsoluteThreshold, options.strandedRelativeThreshold, options.verbose)
+ nb = check_read_coverage_and_sort_all_bubbles(KS_SEC_EXEC_PATH, readfiles, workdir, outdir, kval, output_snps, infix_name, countsMethod, minOverlap, options.mism, options.get_mapping_info, options.stranded, options.strandedAbsoluteThreshold, options.strandedRelativeThreshold, options.nbprocs, options.verbose)
print("Elapsed time: ", (time.time() - t), " seconds\n")
printlg("Elapsed time: ", (time.time() - t), " seconds\n")
=====================================
man/kissplice.1
=====================================
@@ -1,4 +1,4 @@
-.TH KISSPLICE "14" "march 2020" "kissplice 2.5.4" "User Commands"
+.TH KISSPLICE "14" "march 2020" "kissplice 2.5.5" "User Commands"
.SH NAME
kisSplice \- local assembly of SNPs, indels and AS events
.SH SYNOPSIS
=====================================
texput.log
=====================================
@@ -0,0 +1,21 @@
+This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019/Debian) (preloaded format=pdflatex 2022.1.21) 21 JAN 2022 10:18
+entering extended mode
+ restricted \write18 enabled.
+ %&-line parsing enabled.
+**user_guide.tex
+
+! Emergency stop.
+<*> user_guide.tex
+
+End of file on the terminal!
+
+
+Here is how much of TeX's memory you used:
+ 4 strings out of 483183
+ 113 string characters out of 5966292
+ 231602 words of memory out of 5000000
+ 15122 multiletter control sequences out of 15000+600000
+ 532338 words of font info for 24 fonts, out of 8000000 for 9000
+ 14 hyphenation exceptions out of 8191
+ 0i,0n,0p,18b,6s stack positions out of 5000i,500n,10000p,200000b,80000s
+! ==> Fatal error occurred, no output PDF file produced!
=====================================
thirdparty/kissreads/src/kissReads.c
=====================================
@@ -51,7 +51,7 @@
#include <time.h>
#include <libchash.h>
-//#define OMP
+#define OMP
#ifdef OMP
#include "omp.h"
View it on GitLab: https://salsa.debian.org/med-team/kissplice/-/commit/9f1b419b734ac7e514533b4d4c77250749b1b73d
--
View it on GitLab: https://salsa.debian.org/med-team/kissplice/-/commit/9f1b419b734ac7e514533b4d4c77250749b1b73d
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