Commit 9f1b419b734ac7e514533b4d4c77250749b1b73d - kissplice

+3

-2

CMakeLists.txt less more

22	22	SET(CMAKE_BUILD_TYPE Distribution)
23	23	ENDIF(NOT CMAKE_CONFIGURATION_TYPES AND NOT CMAKE_BUILD_TYPE)
24	24
25
	25	SET(CMAKE_CXX_FLAGS "-fopenmp")
	26	SET(CMAKE_C_FLAGS "-fopenmp")
26	27	SET(CMAKE_CXX_FLAGS_DEBUG "-g -Wall")
27	28	SET(CMAKE_C_FLAGS_DEBUG "-g -Wall")
28	29	SET(CMAKE_CXX_FLAGS_RELEASE "-O3 -Wall")

142	143	SET(CPACK_PACKAGE_VENDOR "Kissplice Development Team")
143	144	SET(CPACK_PACKAGE_VERSION_MAJOR "2")
144	145	SET(CPACK_PACKAGE_VERSION_MINOR "5")
145		SET(CPACK_PACKAGE_VERSION_PATCH "4")
	146	SET(CPACK_PACKAGE_VERSION_PATCH "5")
146	147	SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Splicing events caller")
147	148	SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING")
148	149	SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS")

+5

-0

ChangeLog less more

	0	2022-01-21 Audric Cologne <audric.cologne@univ-lyon1.fr>
	1	* 2.5.4 -> 2.5.5
	2	New feature:
	3	-Paralellisation of Kissreads
	4
0	5	2021-03-05 Audric Cologne <audric.cologne@univ-lyon1.fr>
1	6	* 2.5.3 -> 2.5.4
2	7	Bug fixes:

+71

-69

build/CPackConfig.cmake less more

9	9	# usually begin with CPACK_<GENNAME>_xxxx.
10	10
11	11
12		SET(CPACK_BINARY_7Z "")
13		SET(CPACK_BINARY_BUNDLE "")
14		SET(CPACK_BINARY_CYGWIN "")
15		SET(CPACK_BINARY_DEB "OFF")
16		SET(CPACK_BINARY_DRAGNDROP "")
17		SET(CPACK_BINARY_FREEBSD "OFF")
18		SET(CPACK_BINARY_IFW "OFF")
19		SET(CPACK_BINARY_NSIS "OFF")
20		SET(CPACK_BINARY_OSXX11 "")
21		SET(CPACK_BINARY_PACKAGEMAKER "")
22		SET(CPACK_BINARY_PRODUCTBUILD "")
23		SET(CPACK_BINARY_RPM "OFF")
24		SET(CPACK_BINARY_STGZ "ON")
25		SET(CPACK_BINARY_TBZ2 "OFF")
26		SET(CPACK_BINARY_TGZ "ON")
27		SET(CPACK_BINARY_TXZ "OFF")
28		SET(CPACK_BINARY_TZ "ON")
29		SET(CPACK_BINARY_WIX "")
30		SET(CPACK_BINARY_ZIP "")
31		SET(CPACK_BUILD_SOURCE_DIRS "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice;/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build")
32		SET(CPACK_CMAKE_GENERATOR "Unix Makefiles")
33		SET(CPACK_COMPONENTS_ALL "Unspecified;headers;libraries")
34		SET(CPACK_COMPONENT_UNSPECIFIED_HIDDEN "TRUE")
35		SET(CPACK_COMPONENT_UNSPECIFIED_REQUIRED "TRUE")
36		SET(CPACK_GENERATOR "STGZ;TGZ;TZ")
37		SET(CPACK_INSTALL_CMAKE_PROJECTS "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build;kissplice;ALL;/")
38		SET(CPACK_INSTALL_PREFIX "/usr/local/HDF_Group/HDF5/1.10.5")
39		SET(CPACK_MODULE_PATH "")
40		SET(CPACK_NSIS_DISPLAY_NAME "kissplice 2.5.4")
41		SET(CPACK_NSIS_INSTALLER_ICON_CODE "")
42		SET(CPACK_NSIS_INSTALLER_MUI_ICON_CODE "")
43		SET(CPACK_NSIS_INSTALL_ROOT "$PROGRAMFILES")
44		SET(CPACK_NSIS_PACKAGE_NAME "kissplice 2.5.4")
45		SET(CPACK_OUTPUT_CONFIG_FILE "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/CPackConfig.cmake")
46		SET(CPACK_PACKAGE_DEFAULT_LOCATION "/")
47		SET(CPACK_PACKAGE_DESCRIPTION_FILE "/usr/share/cmake-3.10/Templates/CPack.GenericDescription.txt")
48		SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Splicing events caller")
49		SET(CPACK_PACKAGE_FILE_NAME "kissplice-2.5.4-Linux")
50		SET(CPACK_PACKAGE_INSTALL_DIRECTORY "kissplice 2.5.4")
51		SET(CPACK_PACKAGE_INSTALL_REGISTRY_KEY "kissplice 2.5.4")
52		SET(CPACK_PACKAGE_NAME "kissplice")
53		SET(CPACK_PACKAGE_RELOCATABLE "true")
54		SET(CPACK_PACKAGE_VENDOR "Kissplice Development Team")
55		SET(CPACK_PACKAGE_VERSION "2.5.4")
56		SET(CPACK_PACKAGE_VERSION_MAJOR "2")
57		SET(CPACK_PACKAGE_VERSION_MINOR "5")
58		SET(CPACK_PACKAGE_VERSION_PATCH "4")
59		SET(CPACK_RESOURCE_FILE_AUTHORS "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/AUTHORS")
60		SET(CPACK_RESOURCE_FILE_INSTALL "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/INSTALL")
61		SET(CPACK_RESOURCE_FILE_LICENSE "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/COPYING")
62		SET(CPACK_RESOURCE_FILE_README "/usr/share/cmake-3.10/Templates/CPack.GenericDescription.txt")
63		SET(CPACK_RESOURCE_FILE_WELCOME "/usr/share/cmake-3.10/Templates/CPack.GenericWelcome.txt")
64		SET(CPACK_SET_DESTDIR "OFF")
65		SET(CPACK_SOURCE_7Z "")
66		SET(CPACK_SOURCE_CYGWIN "")
67		SET(CPACK_SOURCE_GENERATOR "TGZ")
68		SET(CPACK_SOURCE_IGNORE_FILES "README.CMake;README.Licence;README.Release;README.NamingConventions;README.Kissreads;CMakeFiles;Makefile;_CPack_Packages;CMakeCache.txt;.\\.svn;.\\.idea;.\\.DS_Store;.\\.gz;.\\~;.\\.o;bcc/;datasets;ismb;Recomb;RR;script_tarjan_aphid.sh;splice_sites_results;splicing_events;TODO.;Validation;validation_script.sh;.project;/\\.git*;^results$;^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")
69		SET(CPACK_SOURCE_OUTPUT_CONFIG_FILE "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/CPackSourceConfig.cmake")
70		SET(CPACK_SOURCE_PACKAGE_FILE_NAME "kissplice-2.5.4")
71		SET(CPACK_SOURCE_RPM "")
72		SET(CPACK_SOURCE_TBZ2 "")
73		SET(CPACK_SOURCE_TGZ "")
74		SET(CPACK_SOURCE_TXZ "")
75		SET(CPACK_SOURCE_TZ "")
76		SET(CPACK_SOURCE_ZIP "")
77		SET(CPACK_SYSTEM_NAME "Linux")
78		SET(CPACK_TOPLEVEL_TAG "Linux")
79		SET(CPACK_WIX_SIZEOF_VOID_P "8")
	12	set(CPACK_BINARY_7Z "")
	13	set(CPACK_BINARY_BUNDLE "")
	14	set(CPACK_BINARY_CYGWIN "")
	15	set(CPACK_BINARY_DEB "OFF")
	16	set(CPACK_BINARY_DRAGNDROP "")
	17	set(CPACK_BINARY_FREEBSD "OFF")
	18	set(CPACK_BINARY_IFW "OFF")
	19	set(CPACK_BINARY_NSIS "OFF")
	20	set(CPACK_BINARY_NUGET "")
	21	set(CPACK_BINARY_OSXX11 "")
	22	set(CPACK_BINARY_PACKAGEMAKER "")
	23	set(CPACK_BINARY_PRODUCTBUILD "")
	24	set(CPACK_BINARY_RPM "OFF")
	25	set(CPACK_BINARY_STGZ "ON")
	26	set(CPACK_BINARY_TBZ2 "OFF")
	27	set(CPACK_BINARY_TGZ "ON")
	28	set(CPACK_BINARY_TXZ "OFF")
	29	set(CPACK_BINARY_TZ "ON")
	30	set(CPACK_BINARY_WIX "")
	31	set(CPACK_BINARY_ZIP "")
	32	set(CPACK_BUILD_SOURCE_DIRS "/home/audric/Desktop/PostDoc/Logiciels/kissplice;/home/audric/Desktop/PostDoc/Logiciels/kissplice/build")
	33	set(CPACK_CMAKE_GENERATOR "Unix Makefiles")
	34	set(CPACK_COMPONENTS_ALL "Unspecified;headers;libraries")
	35	set(CPACK_COMPONENT_UNSPECIFIED_HIDDEN "TRUE")
	36	set(CPACK_COMPONENT_UNSPECIFIED_REQUIRED "TRUE")
	37	set(CPACK_DEFAULT_PACKAGE_DESCRIPTION_FILE "/usr/share/cmake-3.16/Templates/CPack.GenericDescription.txt")
	38	set(CPACK_GENERATOR "STGZ;TGZ;TZ")
	39	set(CPACK_INSTALL_CMAKE_PROJECTS "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build;kissplice;ALL;/")
	40	set(CPACK_INSTALL_PREFIX "/usr/local/HDF_Group/HDF5/1.10.5")
	41	set(CPACK_MODULE_PATH "")
	42	set(CPACK_NSIS_DISPLAY_NAME "kissplice 2.5.5")
	43	set(CPACK_NSIS_INSTALLER_ICON_CODE "")
	44	set(CPACK_NSIS_INSTALLER_MUI_ICON_CODE "")
	45	set(CPACK_NSIS_INSTALL_ROOT "$PROGRAMFILES")
	46	set(CPACK_NSIS_PACKAGE_NAME "kissplice 2.5.5")
	47	set(CPACK_OUTPUT_CONFIG_FILE "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/CPackConfig.cmake")
	48	set(CPACK_PACKAGE_DEFAULT_LOCATION "/")
	49	set(CPACK_PACKAGE_DESCRIPTION_FILE "/usr/share/cmake-3.16/Templates/CPack.GenericDescription.txt")
	50	set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Splicing events caller")
	51	set(CPACK_PACKAGE_FILE_NAME "kissplice-2.5.5-Linux")
	52	set(CPACK_PACKAGE_INSTALL_DIRECTORY "kissplice 2.5.5")
	53	set(CPACK_PACKAGE_INSTALL_REGISTRY_KEY "kissplice 2.5.5")
	54	set(CPACK_PACKAGE_NAME "kissplice")
	55	set(CPACK_PACKAGE_RELOCATABLE "true")
	56	set(CPACK_PACKAGE_VENDOR "Kissplice Development Team")
	57	set(CPACK_PACKAGE_VERSION "2.5.5")
	58	set(CPACK_PACKAGE_VERSION_MAJOR "2")
	59	set(CPACK_PACKAGE_VERSION_MINOR "5")
	60	set(CPACK_PACKAGE_VERSION_PATCH "5")
	61	set(CPACK_RESOURCE_FILE_AUTHORS "/home/audric/Desktop/PostDoc/Logiciels/kissplice/AUTHORS")
	62	set(CPACK_RESOURCE_FILE_INSTALL "/home/audric/Desktop/PostDoc/Logiciels/kissplice/INSTALL")
	63	set(CPACK_RESOURCE_FILE_LICENSE "/home/audric/Desktop/PostDoc/Logiciels/kissplice/COPYING")
	64	set(CPACK_RESOURCE_FILE_README "/usr/share/cmake-3.16/Templates/CPack.GenericDescription.txt")
	65	set(CPACK_RESOURCE_FILE_WELCOME "/usr/share/cmake-3.16/Templates/CPack.GenericWelcome.txt")
	66	set(CPACK_SET_DESTDIR "OFF")
	67	set(CPACK_SOURCE_7Z "")
	68	set(CPACK_SOURCE_CYGWIN "")
	69	set(CPACK_SOURCE_GENERATOR "TGZ")
	70	set(CPACK_SOURCE_IGNORE_FILES "README.CMake;README.Licence;README.Release;README.NamingConventions;README.Kissreads;CMakeFiles;Makefile;_CPack_Packages;CMakeCache.txt;.\\.svn;.\\.idea;.\\.DS_Store;.\\.gz;.\\~;.\\.o;bcc/;datasets;ismb;Recomb;RR;script_tarjan_aphid.sh;splice_sites_results;splicing_events;TODO.;Validation;validation_script.sh;.project;/\\.git*;^results$;^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")
	71	set(CPACK_SOURCE_OUTPUT_CONFIG_FILE "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/CPackSourceConfig.cmake")
	72	set(CPACK_SOURCE_PACKAGE_FILE_NAME "kissplice-2.5.5")
	73	set(CPACK_SOURCE_RPM "")
	74	set(CPACK_SOURCE_TBZ2 "")
	75	set(CPACK_SOURCE_TGZ "")
	76	set(CPACK_SOURCE_TXZ "")
	77	set(CPACK_SOURCE_TZ "")
	78	set(CPACK_SOURCE_ZIP "")
	79	set(CPACK_SYSTEM_NAME "Linux")
	80	set(CPACK_TOPLEVEL_TAG "Linux")
	81	set(CPACK_WIX_SIZEOF_VOID_P "8")
80	82
81	83	if(NOT CPACK_PROPERTIES_FILE)
82		set(CPACK_PROPERTIES_FILE "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/CPackProperties.cmake")
	84	set(CPACK_PROPERTIES_FILE "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/CPackProperties.cmake")
83	85	endif()
84	86
85	87	if(EXISTS ${CPACK_PROPERTIES_FILE})

+77

-75

build/CPackSourceConfig.cmake less more

9	9	# usually begin with CPACK_<GENNAME>_xxxx.
10	10
11	11
12		SET(CPACK_BINARY_7Z "")
13		SET(CPACK_BINARY_BUNDLE "")
14		SET(CPACK_BINARY_CYGWIN "")
15		SET(CPACK_BINARY_DEB "OFF")
16		SET(CPACK_BINARY_DRAGNDROP "")
17		SET(CPACK_BINARY_FREEBSD "OFF")
18		SET(CPACK_BINARY_IFW "OFF")
19		SET(CPACK_BINARY_NSIS "OFF")
20		SET(CPACK_BINARY_OSXX11 "")
21		SET(CPACK_BINARY_PACKAGEMAKER "")
22		SET(CPACK_BINARY_PRODUCTBUILD "")
23		SET(CPACK_BINARY_RPM "OFF")
24		SET(CPACK_BINARY_STGZ "ON")
25		SET(CPACK_BINARY_TBZ2 "OFF")
26		SET(CPACK_BINARY_TGZ "ON")
27		SET(CPACK_BINARY_TXZ "OFF")
28		SET(CPACK_BINARY_TZ "ON")
29		SET(CPACK_BINARY_WIX "")
30		SET(CPACK_BINARY_ZIP "")
31		SET(CPACK_BUILD_SOURCE_DIRS "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice;/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build")
32		SET(CPACK_CMAKE_GENERATOR "Unix Makefiles")
33		SET(CPACK_COMPONENTS_ALL "Unspecified;headers;libraries")
34		SET(CPACK_COMPONENT_UNSPECIFIED_HIDDEN "TRUE")
35		SET(CPACK_COMPONENT_UNSPECIFIED_REQUIRED "TRUE")
36		SET(CPACK_GENERATOR "TGZ")
37		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$;skeletons;doc/dev;alt_splicing_sample_ex.png;quantifModel-big.png;resType0.png;resType1.png;quantifModel.png;ucsc.png;user_guide.aux;user_guide.bib;user_guide.log;user_guide.toc;user_guide.tex;jobim13")
38		SET(CPACK_INSTALLED_DIRECTORIES "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice;/")
39		SET(CPACK_INSTALL_CMAKE_PROJECTS "")
40		SET(CPACK_INSTALL_PREFIX "/usr/local/HDF_Group/HDF5/1.10.5")
41		SET(CPACK_MODULE_PATH "")
42		SET(CPACK_NSIS_DISPLAY_NAME "kissplice 2.5.4")
43		SET(CPACK_NSIS_INSTALLER_ICON_CODE "")
44		SET(CPACK_NSIS_INSTALLER_MUI_ICON_CODE "")
45		SET(CPACK_NSIS_INSTALL_ROOT "$PROGRAMFILES")
46		SET(CPACK_NSIS_PACKAGE_NAME "kissplice 2.5.4")
47		SET(CPACK_OUTPUT_CONFIG_FILE "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/CPackConfig.cmake")
48		SET(CPACK_PACKAGE_DEFAULT_LOCATION "/")
49		SET(CPACK_PACKAGE_DESCRIPTION_FILE "/usr/share/cmake-3.10/Templates/CPack.GenericDescription.txt")
50		SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Splicing events caller")
51		SET(CPACK_PACKAGE_FILE_NAME "kissplice-2.5.4")
52		SET(CPACK_PACKAGE_INSTALL_DIRECTORY "kissplice 2.5.4")
53		SET(CPACK_PACKAGE_INSTALL_REGISTRY_KEY "kissplice 2.5.4")
54		SET(CPACK_PACKAGE_NAME "kissplice")
55		SET(CPACK_PACKAGE_RELOCATABLE "true")
56		SET(CPACK_PACKAGE_VENDOR "Kissplice Development Team")
57		SET(CPACK_PACKAGE_VERSION "2.5.4")
58		SET(CPACK_PACKAGE_VERSION_MAJOR "2")
59		SET(CPACK_PACKAGE_VERSION_MINOR "5")
60		SET(CPACK_PACKAGE_VERSION_PATCH "4")
61		SET(CPACK_RESOURCE_FILE_AUTHORS "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/AUTHORS")
62		SET(CPACK_RESOURCE_FILE_INSTALL "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/INSTALL")
63		SET(CPACK_RESOURCE_FILE_LICENSE "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/COPYING")
64		SET(CPACK_RESOURCE_FILE_README "/usr/share/cmake-3.10/Templates/CPack.GenericDescription.txt")
65		SET(CPACK_RESOURCE_FILE_WELCOME "/usr/share/cmake-3.10/Templates/CPack.GenericWelcome.txt")
66		SET(CPACK_RPM_PACKAGE_SOURCES "ON")
67		SET(CPACK_SET_DESTDIR "OFF")
68		SET(CPACK_SOURCE_7Z "")
69		SET(CPACK_SOURCE_CYGWIN "")
70		SET(CPACK_SOURCE_GENERATOR "TGZ")
71		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")
72		SET(CPACK_SOURCE_INSTALLED_DIRECTORIES "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice;/")
73		SET(CPACK_SOURCE_OUTPUT_CONFIG_FILE "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/CPackSourceConfig.cmake")
74		SET(CPACK_SOURCE_PACKAGE_FILE_NAME "kissplice-2.5.4")
75		SET(CPACK_SOURCE_RPM "")
76		SET(CPACK_SOURCE_TBZ2 "")
77		SET(CPACK_SOURCE_TGZ "")
78		SET(CPACK_SOURCE_TOPLEVEL_TAG "Linux-Source")
79		SET(CPACK_SOURCE_TXZ "")
80		SET(CPACK_SOURCE_TZ "")
81		SET(CPACK_SOURCE_ZIP "")
82		SET(CPACK_STRIP_FILES "")
83		SET(CPACK_SYSTEM_NAME "Linux")
84		SET(CPACK_TOPLEVEL_TAG "Linux-Source")
85		SET(CPACK_WIX_SIZEOF_VOID_P "8")
	12	set(CPACK_BINARY_7Z "")
	13	set(CPACK_BINARY_BUNDLE "")
	14	set(CPACK_BINARY_CYGWIN "")
	15	set(CPACK_BINARY_DEB "OFF")
	16	set(CPACK_BINARY_DRAGNDROP "")
	17	set(CPACK_BINARY_FREEBSD "OFF")
	18	set(CPACK_BINARY_IFW "OFF")
	19	set(CPACK_BINARY_NSIS "OFF")
	20	set(CPACK_BINARY_NUGET "")
	21	set(CPACK_BINARY_OSXX11 "")
	22	set(CPACK_BINARY_PACKAGEMAKER "")
	23	set(CPACK_BINARY_PRODUCTBUILD "")
	24	set(CPACK_BINARY_RPM "OFF")
	25	set(CPACK_BINARY_STGZ "ON")
	26	set(CPACK_BINARY_TBZ2 "OFF")
	27	set(CPACK_BINARY_TGZ "ON")
	28	set(CPACK_BINARY_TXZ "OFF")
	29	set(CPACK_BINARY_TZ "ON")
	30	set(CPACK_BINARY_WIX "")
	31	set(CPACK_BINARY_ZIP "")
	32	set(CPACK_BUILD_SOURCE_DIRS "/home/audric/Desktop/PostDoc/Logiciels/kissplice;/home/audric/Desktop/PostDoc/Logiciels/kissplice/build")
	33	set(CPACK_CMAKE_GENERATOR "Unix Makefiles")
	34	set(CPACK_COMPONENTS_ALL "Unspecified;headers;libraries")
	35	set(CPACK_COMPONENT_UNSPECIFIED_HIDDEN "TRUE")
	36	set(CPACK_COMPONENT_UNSPECIFIED_REQUIRED "TRUE")
	37	set(CPACK_DEFAULT_PACKAGE_DESCRIPTION_FILE "/usr/share/cmake-3.16/Templates/CPack.GenericDescription.txt")
	38	set(CPACK_GENERATOR "TGZ")
	39	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")
	40	set(CPACK_INSTALLED_DIRECTORIES "/home/audric/Desktop/PostDoc/Logiciels/kissplice;/")
	41	set(CPACK_INSTALL_CMAKE_PROJECTS "")
	42	set(CPACK_INSTALL_PREFIX "/usr/local/HDF_Group/HDF5/1.10.5")
	43	set(CPACK_MODULE_PATH "")
	44	set(CPACK_NSIS_DISPLAY_NAME "kissplice 2.5.5")
	45	set(CPACK_NSIS_INSTALLER_ICON_CODE "")
	46	set(CPACK_NSIS_INSTALLER_MUI_ICON_CODE "")
	47	set(CPACK_NSIS_INSTALL_ROOT "$PROGRAMFILES")
	48	set(CPACK_NSIS_PACKAGE_NAME "kissplice 2.5.5")
	49	set(CPACK_OUTPUT_CONFIG_FILE "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/CPackConfig.cmake")
	50	set(CPACK_PACKAGE_DEFAULT_LOCATION "/")
	51	set(CPACK_PACKAGE_DESCRIPTION_FILE "/usr/share/cmake-3.16/Templates/CPack.GenericDescription.txt")
	52	set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Splicing events caller")
	53	set(CPACK_PACKAGE_FILE_NAME "kissplice-2.5.5")
	54	set(CPACK_PACKAGE_INSTALL_DIRECTORY "kissplice 2.5.5")
	55	set(CPACK_PACKAGE_INSTALL_REGISTRY_KEY "kissplice 2.5.5")
	56	set(CPACK_PACKAGE_NAME "kissplice")
	57	set(CPACK_PACKAGE_RELOCATABLE "true")
	58	set(CPACK_PACKAGE_VENDOR "Kissplice Development Team")
	59	set(CPACK_PACKAGE_VERSION "2.5.5")
	60	set(CPACK_PACKAGE_VERSION_MAJOR "2")
	61	set(CPACK_PACKAGE_VERSION_MINOR "5")
	62	set(CPACK_PACKAGE_VERSION_PATCH "5")
	63	set(CPACK_RESOURCE_FILE_AUTHORS "/home/audric/Desktop/PostDoc/Logiciels/kissplice/AUTHORS")
	64	set(CPACK_RESOURCE_FILE_INSTALL "/home/audric/Desktop/PostDoc/Logiciels/kissplice/INSTALL")
	65	set(CPACK_RESOURCE_FILE_LICENSE "/home/audric/Desktop/PostDoc/Logiciels/kissplice/COPYING")
	66	set(CPACK_RESOURCE_FILE_README "/usr/share/cmake-3.16/Templates/CPack.GenericDescription.txt")
	67	set(CPACK_RESOURCE_FILE_WELCOME "/usr/share/cmake-3.16/Templates/CPack.GenericWelcome.txt")
	68	set(CPACK_RPM_PACKAGE_SOURCES "ON")
	69	set(CPACK_SET_DESTDIR "OFF")
	70	set(CPACK_SOURCE_7Z "")
	71	set(CPACK_SOURCE_CYGWIN "")
	72	set(CPACK_SOURCE_GENERATOR "TGZ")
	73	set(CPACK_SOURCE_IGNORE_FILES "README.CMake;README.Licence;README.Release;README.NamingConventions;README.Kissreads;CMakeFiles;Makefile;_CPack_Packages;CMakeCache.txt;.\\.svn;.\\.idea;.\\.DS_Store;.\\.gz;.\\~;.\\.o;bcc/;datasets;ismb;Recomb;RR;script_tarjan_aphid.sh;splice_sites_results;splicing_events;TODO.;Validation;validation_script.sh;.project;/\\.git*;^results$;^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")
	74	set(CPACK_SOURCE_INSTALLED_DIRECTORIES "/home/audric/Desktop/PostDoc/Logiciels/kissplice;/")
	75	set(CPACK_SOURCE_OUTPUT_CONFIG_FILE "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/CPackSourceConfig.cmake")
	76	set(CPACK_SOURCE_PACKAGE_FILE_NAME "kissplice-2.5.5")
	77	set(CPACK_SOURCE_RPM "")
	78	set(CPACK_SOURCE_TBZ2 "")
	79	set(CPACK_SOURCE_TGZ "")
	80	set(CPACK_SOURCE_TOPLEVEL_TAG "Linux-Source")
	81	set(CPACK_SOURCE_TXZ "")
	82	set(CPACK_SOURCE_TZ "")
	83	set(CPACK_SOURCE_ZIP "")
	84	set(CPACK_STRIP_FILES "")
	85	set(CPACK_SYSTEM_NAME "Linux")
	86	set(CPACK_TOPLEVEL_TAG "Linux-Source")
	87	set(CPACK_WIX_SIZEOF_VOID_P "8")
86	88
87	89	if(NOT CPACK_PROPERTIES_FILE)
88		set(CPACK_PROPERTIES_FILE "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/CPackProperties.cmake")
	90	set(CPACK_PROPERTIES_FILE "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/CPackProperties.cmake")
89	91	endif()
90	92
91	93	if(EXISTS ${CPACK_PROPERTIES_FILE})

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build/CTestTestfile.cmake less more

0	0	# CMake generated Testfile for
1		# Source directory: /home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice
2		# Build directory: /home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build
	1	# Source directory: /home/audric/Desktop/PostDoc/Logiciels/kissplice
	2	# Build directory: /home/audric/Desktop/PostDoc/Logiciels/kissplice/build
3	3	#
4	4	# This file includes the relevant testing commands required for
5	5	# testing this directory and lists subdirectories to be tested as well.

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build/README.txt less more

2	2
3	3	This directory contains the binary (release) distribution of
4	4	HDF5 1.10 that was compiled on;
5		Linux 4.15.0-142-generic x86_64, using GNU C 7.5.0.
	5	Linux 5.13.0-1017-oem x86_64, using GNU C 9.3.0.
6	6
7	7	It was built with the following options:
8	8	-- Static C/C++/Fortran libraries

38	38	Copy CTestScript.cmake to this directory.
39	39	The default source folder is defined as "HDF5Examples". It can be changed
40	40	with the CTEST_SOURCE_NAME script option.
41		The default installation folder is defined as "/usr/local/HDF_Group/HDF5/1.10.5".
	41	The default installation folder is defined as "/usr/local".
42	42	It can be changed with the INSTALLDIR script option.
43	43	The default ctest configuration is defined as "Release". It can be changed
44	44	with the CTEST_CONFIGURATION_TYPE script option. Note that this must

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build/bin/kissplice less more

469	469
470	470
471	471	def check_read_coverage_and_sort_all_bubbles(KISSPLICE_INSTDIR, readfiles, workdir, outdir, kval, output_snps, infix_name,
472		countsMethods, minOverlap, substitutions, getMappingInfo, stranded, strandedAbsoluteThreshold, strandedRelativeThreshold, verbose = False):
	472	countsMethods, minOverlap, substitutions, getMappingInfo, stranded, strandedAbsoluteThreshold, strandedRelativeThreshold, nbprocs, verbose = False):
473	473	print("\n" + getTimestamp() + "--> Computing read coherence and coverage...")
474	474	printlg("\n" + getTimestamp() + "--> Computing read coherence and coverage...")
475	475

477	477	# Du to the k extension, anchor should be of size k+1 for SNP
478	478	commandLineType0=""
479	479	if output_snps > 0:
480		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 "
	480	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)
481	481	if stranded:
482	482	commandLineType0+=" -x -a " + str(strandedAbsoluteThreshold) + " -r " + str(strandedRelativeThreshold) + " "
483	483	if getMappingInfo:

493	493	shutil.move(workdir+"/uncoherentType0.fa.explanations", outdir+"/uncoherentType0.fa.explanations")
494	494
495	495	# no n options anymore
496		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)
	496	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)
497	497	if stranded:
498	498	commandLineType1234+=" -x -a " + str(strandedAbsoluteThreshold) + " -r " + str(strandedRelativeThreshold) + " "
499	499	if getMappingInfo:

726	726	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 ")
727	727	parser.add_argument('--timeout', action='store', dest="timeout", default=TIMEOUT,
728	728	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)+")")
729		parser.add_argument('--version', action='version', version='%(prog)s 2.5.4')
	729	parser.add_argument('--version', action='version', version='%(prog)s 2.5.5')
730	730	parser.add_argument('--output-context', action="store_true", dest="output_context", default = False, help="Will output the maximum non-ambiguous context of a bubble")
731	731	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.")
732	732	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.")

763	763	# ------------------------------------------------------------------------
764	764	# Print version and command line
765	765	# ------------------------------------------------------------------------
766		print("\nThis is KisSplice, version 2.5.4\n")
767		printlg("This is KisSplice, version 2.5.4\n")
	766	print("\nThis is KisSplice, version 2.5.5\n")
	767	printlg("This is KisSplice, version 2.5.5\n")
768	768	print("The command line was: " + ' '.join(sys.argv))
769	769	printlg("The command line was: " + ' '.join(sys.argv))
770	770

914	914	t = time.time()
915	915	nb = sort_all_bubbles(KS_SEC_EXEC_PATH, readfiles, workdir, outdir, kval, output_snps, infix_name, not only_graph, options.verbose)
916	916	if not only_graph:
917		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)
	917	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)
918	918
919	919	print("Elapsed time: ", (time.time() - t), " seconds\n")
920	920	printlg("Elapsed time: ", (time.time() - t), " seconds\n")

+10

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build/cmake_install.cmake less more

0		# Install script for directory: /home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice
	0	# Install script for directory: /home/audric/Desktop/PostDoc/Logiciels/kissplice
1	1
2	2	# Set the install prefix
3	3	if(NOT DEFINED CMAKE_INSTALL_PREFIX)

38	38
39	39	if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xUnspecifiedx" OR NOT CMAKE_INSTALL_COMPONENT)
40	40	list(APPEND CMAKE_ABSOLUTE_DESTINATION_FILES
41		"/usr/local/HDF_Group/HDF5/1.10.5/bin/kissplice")
	41	"/usr/local/bin/kissplice")
42	42	if(CMAKE_WARN_ON_ABSOLUTE_INSTALL_DESTINATION)
43	43	message(WARNING "ABSOLUTE path INSTALL DESTINATION : ${CMAKE_ABSOLUTE_DESTINATION_FILES}")
44	44	endif()
45	45	if(CMAKE_ERROR_ON_ABSOLUTE_INSTALL_DESTINATION)
46	46	message(FATAL_ERROR "ABSOLUTE path INSTALL DESTINATION forbidden (by caller): ${CMAKE_ABSOLUTE_DESTINATION_FILES}")
47	47	endif()
48		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")
	48	file(INSTALL DESTINATION "/usr/local/bin" TYPE PROGRAM FILES "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/bin/kissplice")
49	49	endif()
50	50
51	51	if(NOT CMAKE_INSTALL_LOCAL_ONLY)
52	52	# Include the install script for each subdirectory.
53		include("/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/bcalm/cmake_install.cmake")
54		include("/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/thirdparty/cmake_install.cmake")
55		include("/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/modules/cmake_install.cmake")
56		include("/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/man/cmake_install.cmake")
57		include("/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/doc/cmake_install.cmake")
58		include("/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/tests/cmake_install.cmake")
	53	include("/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/bcalm/cmake_install.cmake")
	54	include("/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/thirdparty/cmake_install.cmake")
	55	include("/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/modules/cmake_install.cmake")
	56	include("/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/man/cmake_install.cmake")
	57	include("/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/doc/cmake_install.cmake")
	58	include("/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/tests/cmake_install.cmake")
59	59
60	60	endif()
61	61

67	67
68	68	string(REPLACE ";" "\n" CMAKE_INSTALL_MANIFEST_CONTENT
69	69	"${CMAKE_INSTALL_MANIFEST_FILES}")
70		file(WRITE "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/${CMAKE_INSTALL_MANIFEST}"
	70	file(WRITE "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/${CMAKE_INSTALL_MANIFEST}"
71	71	"${CMAKE_INSTALL_MANIFEST_CONTENT}")

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build/cmake_uninstall.cmake less more

0		if (NOT EXISTS "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/install_manifest.txt")
1		message(FATAL_ERROR "Cannot find install manifest: \"/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/install_manifest.txt\"")
2		endif(NOT EXISTS "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/install_manifest.txt")
	0	if (NOT EXISTS "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/install_manifest.txt")
	1	message(FATAL_ERROR "Cannot find install manifest: \"/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/install_manifest.txt\"")
	2	endif(NOT EXISTS "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/install_manifest.txt")
3	3
4		file(READ "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/install_manifest.txt" files)
	4	file(READ "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/install_manifest.txt" files)
5	5	string(REGEX REPLACE "\n" ";" files "${files}")
6	6	list(REVERSE files)
7	7	foreach (file ${files})

+2

-2

build/doc/cmake_install.cmake less more

0		# Install script for directory: /home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/doc
	0	# Install script for directory: /home/audric/Desktop/PostDoc/Logiciels/kissplice/doc
1	1
2	2	# Set the install prefix
3	3	if(NOT DEFINED CMAKE_INSTALL_PREFIX)

37	37	endif()
38	38
39	39	if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xUnspecifiedx" OR NOT CMAKE_INSTALL_COMPONENT)
40		file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/share/doc/kissplice" TYPE FILE FILES "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/doc/user_guide.pdf")
	40	file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/share/doc/kissplice" TYPE FILE FILES "/home/audric/Desktop/PostDoc/Logiciels/kissplice/doc/user_guide.pdf")
41	41	endif()
42	42

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-2

build/man/cmake_install.cmake less more

0		# Install script for directory: /home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/man
	0	# Install script for directory: /home/audric/Desktop/PostDoc/Logiciels/kissplice/man
1	1
2	2	# Set the install prefix
3	3	if(NOT DEFINED CMAKE_INSTALL_PREFIX)

37	37	endif()
38	38
39	39	if("x${CMAKE_INSTALL_COMPONENT}x" STREQUAL "xUnspecifiedx" OR NOT CMAKE_INSTALL_COMPONENT)
40		file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/share/man/man1" TYPE FILE FILES "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/man/kissplice.1")
	40	file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/share/man/man1" TYPE FILE FILES "/home/audric/Desktop/PostDoc/Logiciels/kissplice/man/kissplice.1")
41	41	endif()
42	42

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build/modules/cmake_install.cmake less more

0		# Install script for directory: /home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/modules
	0	# Install script for directory: /home/audric/Desktop/PostDoc/Logiciels/kissplice/modules
1	1
2	2	# Set the install prefix
3	3	if(NOT DEFINED CMAKE_INSTALL_PREFIX)

43	43	FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_clean_duplicates"
44	44	RPATH "")
45	45	endif()
46		file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/libexec/kissplice" TYPE EXECUTABLE FILES "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/libexec/kissplice/ks_clean_duplicates")
	46	file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/libexec/kissplice" TYPE EXECUTABLE FILES "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/libexec/kissplice/ks_clean_duplicates")
47	47	if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_clean_duplicates" AND
48	48	NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_clean_duplicates")
49	49	if(CMAKE_INSTALL_DO_STRIP)

59	59	FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_bubble_enumeration"
60	60	RPATH "")
61	61	endif()
62		file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/libexec/kissplice" TYPE EXECUTABLE FILES "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/libexec/kissplice/ks_bubble_enumeration")
	62	file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/libexec/kissplice" TYPE EXECUTABLE FILES "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/libexec/kissplice/ks_bubble_enumeration")
63	63	if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_bubble_enumeration" AND
64	64	NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_bubble_enumeration")
65	65	if(CMAKE_INSTALL_DO_STRIP)

75	75	FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_run_modules"
76	76	RPATH "")
77	77	endif()
78		file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/libexec/kissplice" TYPE EXECUTABLE FILES "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/libexec/kissplice/ks_run_modules")
	78	file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/libexec/kissplice" TYPE EXECUTABLE FILES "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/libexec/kissplice/ks_run_modules")
79	79	if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_run_modules" AND
80	80	NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_run_modules")
81	81	if(CMAKE_INSTALL_DO_STRIP)

91	91	FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_error_removal"
92	92	RPATH "")
93	93	endif()
94		file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/libexec/kissplice" TYPE EXECUTABLE FILES "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/libexec/kissplice/ks_error_removal")
	94	file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/libexec/kissplice" TYPE EXECUTABLE FILES "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/libexec/kissplice/ks_error_removal")
95	95	if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_error_removal" AND
96	96	NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_error_removal")
97	97	if(CMAKE_INSTALL_DO_STRIP)

107	107	FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_print_bcc"
108	108	RPATH "")
109	109	endif()
110		file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/libexec/kissplice" TYPE EXECUTABLE FILES "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/libexec/kissplice/ks_print_bcc")
	110	file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/libexec/kissplice" TYPE EXECUTABLE FILES "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/libexec/kissplice/ks_print_bcc")
111	111	if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_print_bcc" AND
112	112	NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_print_bcc")
113	113	if(CMAKE_INSTALL_DO_STRIP)

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build/tests/CTestTestfile.cmake less more

0	0	# CMake generated Testfile for
1		# Source directory: /home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/tests
2		# Build directory: /home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/tests
	1	# Source directory: /home/audric/Desktop/PostDoc/Logiciels/kissplice/tests
	2	# Build directory: /home/audric/Desktop/PostDoc/Logiciels/kissplice/build/tests
3	3	#
4	4	# This file includes the relevant testing commands required for
5	5	# testing this directory and lists subdirectories to be tested as well.

+3

-3

build/tests/cmake_install.cmake less more

0		# Install script for directory: /home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/tests
	0	# Install script for directory: /home/audric/Desktop/PostDoc/Logiciels/kissplice/tests
1	1
2	2	# Set the install prefix
3	3	if(NOT DEFINED CMAKE_INSTALL_PREFIX)

38	38
39	39	if(NOT CMAKE_INSTALL_LOCAL_ONLY)
40	40	# Include the install script for each subdirectory.
41		include("/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/tests/integration_tests/cmake_install.cmake")
42		include("/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/tests/functional_tests/cmake_install.cmake")
	41	include("/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/tests/integration_tests/cmake_install.cmake")
	42	include("/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/tests/functional_tests/cmake_install.cmake")
43	43
44	44	endif()
45	45

+8

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build/tests/functional_tests/CTestTestfile.cmake less more

0	0	# CMake generated Testfile for
1		# Source directory: /home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/tests/functional_tests
2		# Build directory: /home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/tests/functional_tests
	1	# Source directory: /home/audric/Desktop/PostDoc/Logiciels/kissplice/tests/functional_tests
	2	# Build directory: /home/audric/Desktop/PostDoc/Logiciels/kissplice/build/tests/functional_tests
3	3	#
4	4	# This file includes the relevant testing commands required for
5	5	# testing this directory and lists subdirectories to be tested as well.
6		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")
7		set_tests_properties(ksBubbleEnumerationTest PROPERTIES PASS_REGULAR_EXPRESSION "test SUCCESSFUL")
8		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")
9		set_tests_properties(ksRunModulesTest PROPERTIES PASS_REGULAR_EXPRESSION "test SUCCESSFUL")
10		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")
11		set_tests_properties(ksErrorRemovalTest PROPERTIES PASS_REGULAR_EXPRESSION "test SUCCESSFUL")
	6	add_test(ksBubbleEnumerationTest "/home/audric/Desktop/PostDoc/Logiciels/kissplice/tests/functional_tests/ksBubbleEnumerationTest.py" "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/libexec/kissplice")
	7	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;")
	8	add_test(ksRunModulesTest "/home/audric/Desktop/PostDoc/Logiciels/kissplice/tests/functional_tests/ksRunModulesTest.py" "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/libexec/kissplice")
	9	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;")
	10	add_test(ksErrorRemovalTest "/home/audric/Desktop/PostDoc/Logiciels/kissplice/tests/functional_tests/ksErrorRemovalTest.py" "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/libexec/kissplice")
	11	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;")

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build/tests/functional_tests/cmake_install.cmake less more

0		# Install script for directory: /home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/tests/functional_tests
	0	# Install script for directory: /home/audric/Desktop/PostDoc/Logiciels/kissplice/tests/functional_tests
1	1
2	2	# Set the install prefix
3	3	if(NOT DEFINED CMAKE_INSTALL_PREFIX)

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-11

build/tests/integration_tests/CTestTestfile.cmake less more

0	0	# CMake generated Testfile for
1		# Source directory: /home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/tests/integration_tests
2		# Build directory: /home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/tests/integration_tests
	1	# Source directory: /home/audric/Desktop/PostDoc/Logiciels/kissplice/tests/integration_tests
	2	# Build directory: /home/audric/Desktop/PostDoc/Logiciels/kissplice/build/tests/integration_tests
3	3	#
4	4	# This file includes the relevant testing commands required for
5	5	# testing this directory and lists subdirectories to be tested as well.
6		add_test(KisspliceBasicTest "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/bin/kissplice" "-h")
7		add_test(KisspliceDBGTest "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/tests/integration_tests/kisspliceDBGTest.py" "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/bin")
8		set_tests_properties(KisspliceDBGTest PROPERTIES PASS_REGULAR_EXPRESSION "test SUCCESSFUL")
9		add_test(KisspliceTwoSequencesTest "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/tests/integration_tests/kisspliceTwoSequencesTest.py" "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/bin")
10		set_tests_properties(KisspliceTwoSequencesTest PROPERTIES PASS_REGULAR_EXPRESSION "test SUCCESSFUL")
11		add_test(KisspliceGraphAndSequenceTest "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/tests/integration_tests/kisspliceGraphAndSequenceTest.py" "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/bin")
12		set_tests_properties(KisspliceGraphAndSequenceTest PROPERTIES PASS_REGULAR_EXPRESSION "test SUCCESSFUL")
13		add_test(KisspliceGraphTest "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/tests/integration_tests/kisspliceGraphTest.py" "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/bin")
14		set_tests_properties(KisspliceGraphTest PROPERTIES PASS_REGULAR_EXPRESSION "test SUCCESSFUL")
	6	add_test(KisspliceBasicTest "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/bin/kissplice" "-h")
	7	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;")
	8	add_test(KisspliceDBGTest "/home/audric/Desktop/PostDoc/Logiciels/kissplice/tests/integration_tests/kisspliceDBGTest.py" "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/bin")
	9	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;")
	10	add_test(KisspliceTwoSequencesTest "/home/audric/Desktop/PostDoc/Logiciels/kissplice/tests/integration_tests/kisspliceTwoSequencesTest.py" "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/bin")
	11	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;")
	12	add_test(KisspliceGraphAndSequenceTest "/home/audric/Desktop/PostDoc/Logiciels/kissplice/tests/integration_tests/kisspliceGraphAndSequenceTest.py" "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/bin")
	13	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;")
	14	add_test(KisspliceGraphTest "/home/audric/Desktop/PostDoc/Logiciels/kissplice/tests/integration_tests/kisspliceGraphTest.py" "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/bin")
	15	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;")

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build/tests/integration_tests/cmake_install.cmake less more

0		# Install script for directory: /home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/tests/integration_tests
	0	# Install script for directory: /home/audric/Desktop/PostDoc/Logiciels/kissplice/tests/integration_tests
1	1
2	2	# Set the install prefix
3	3	if(NOT DEFINED CMAKE_INSTALL_PREFIX)

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build/thirdparty/cmake_install.cmake less more

0		# Install script for directory: /home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/thirdparty
	0	# Install script for directory: /home/audric/Desktop/PostDoc/Logiciels/kissplice/thirdparty
1	1
2	2	# Set the install prefix
3	3	if(NOT DEFINED CMAKE_INSTALL_PREFIX)

38	38
39	39	if(NOT CMAKE_INSTALL_LOCAL_ONLY)
40	40	# Include the install script for each subdirectory.
41		include("/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/thirdparty/kissreads/cmake_install.cmake")
	41	include("/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/thirdparty/kissreads/cmake_install.cmake")
42	42
43	43	endif()
44	44

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build/thirdparty/kissreads/cmake_install.cmake less more

0		# Install script for directory: /home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/thirdparty/kissreads
	0	# Install script for directory: /home/audric/Desktop/PostDoc/Logiciels/kissplice/thirdparty/kissreads
1	1
2	2	# Set the install prefix
3	3	if(NOT DEFINED CMAKE_INSTALL_PREFIX)

38	38
39	39	if(NOT CMAKE_INSTALL_LOCAL_ONLY)
40	40	# Include the install script for each subdirectory.
41		include("/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/thirdparty/kissreads/src/cmake_install.cmake")
	41	include("/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/thirdparty/kissreads/src/cmake_install.cmake")
42	42
43	43	endif()
44	44

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build/thirdparty/kissreads/src/cmake_install.cmake less more

0		# Install script for directory: /home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/thirdparty/kissreads/src
	0	# Install script for directory: /home/audric/Desktop/PostDoc/Logiciels/kissplice/thirdparty/kissreads/src
1	1
2	2	# Set the install prefix
3	3	if(NOT DEFINED CMAKE_INSTALL_PREFIX)

43	43	FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_kissreadsSNPS"
44	44	RPATH "")
45	45	endif()
46		file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/libexec/kissplice" TYPE EXECUTABLE FILES "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/libexec/kissplice/ks_kissreadsSNPS")
	46	file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/libexec/kissplice" TYPE EXECUTABLE FILES "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/libexec/kissplice/ks_kissreadsSNPS")
47	47	if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_kissreadsSNPS" AND
48	48	NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_kissreadsSNPS")
49		file(RPATH_CHANGE
50		FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_kissreadsSNPS"
51		OLD_RPATH "/usr/local/lib:"
52		NEW_RPATH "")
53	49	if(CMAKE_INSTALL_DO_STRIP)
54	50	execute_process(COMMAND "/usr/bin/strip" "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_kissreadsSNPS")
55	51	endif()

63	59	FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_kissreadsSplice"
64	60	RPATH "")
65	61	endif()
66		file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/libexec/kissplice" TYPE EXECUTABLE FILES "/home/audric/Bureau/POSTDOC_TALS/Logiciels/kissplice/build/libexec/kissplice/ks_kissreadsSplice")
	62	file(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/libexec/kissplice" TYPE EXECUTABLE FILES "/home/audric/Desktop/PostDoc/Logiciels/kissplice/build/libexec/kissplice/ks_kissreadsSplice")
67	63	if(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_kissreadsSplice" AND
68	64	NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_kissreadsSplice")
69		file(RPATH_CHANGE
70		FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_kissreadsSplice"
71		OLD_RPATH "/usr/local/lib:"
72		NEW_RPATH "")
73	65	if(CMAKE_INSTALL_DO_STRIP)
74	66	execute_process(COMMAND "/usr/bin/strip" "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/libexec/kissplice/ks_kissreadsSplice")
75	67	endif()

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kissplice.py less more

469	469
470	470
471	471	def check_read_coverage_and_sort_all_bubbles(KISSPLICE_INSTDIR, readfiles, workdir, outdir, kval, output_snps, infix_name,
472		countsMethods, minOverlap, substitutions, getMappingInfo, stranded, strandedAbsoluteThreshold, strandedRelativeThreshold, verbose = False):
	472	countsMethods, minOverlap, substitutions, getMappingInfo, stranded, strandedAbsoluteThreshold, strandedRelativeThreshold, nbprocs, verbose = False):
473	473	print("\n" + getTimestamp() + "--> Computing read coherence and coverage...")
474	474	printlg("\n" + getTimestamp() + "--> Computing read coherence and coverage...")
475	475

477	477	# Du to the k extension, anchor should be of size k+1 for SNP
478	478	commandLineType0=""
479	479	if output_snps > 0:
480		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 "
	480	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)
481	481	if stranded:
482	482	commandLineType0+=" -x -a " + str(strandedAbsoluteThreshold) + " -r " + str(strandedRelativeThreshold) + " "
483	483	if getMappingInfo:

493	493	shutil.move(workdir+"/uncoherentType0.fa.explanations", outdir+"/uncoherentType0.fa.explanations")
494	494
495	495	# no n options anymore
496		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)
	496	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)
497	497	if stranded:
498	498	commandLineType1234+=" -x -a " + str(strandedAbsoluteThreshold) + " -r " + str(strandedRelativeThreshold) + " "
499	499	if getMappingInfo:

726	726	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 ")
727	727	parser.add_argument('--timeout', action='store', dest="timeout", default=TIMEOUT,
728	728	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)+")")
729		parser.add_argument('--version', action='version', version='%(prog)s 2.5.4')
	729	parser.add_argument('--version', action='version', version='%(prog)s 2.5.5')
730	730	parser.add_argument('--output-context', action="store_true", dest="output_context", default = False, help="Will output the maximum non-ambiguous context of a bubble")
731	731	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.")
732	732	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.")

763	763	# ------------------------------------------------------------------------
764	764	# Print version and command line
765	765	# ------------------------------------------------------------------------
766		print("\nThis is KisSplice, version 2.5.4\n")
767		printlg("This is KisSplice, version 2.5.4\n")
	766	print("\nThis is KisSplice, version 2.5.5\n")
	767	printlg("This is KisSplice, version 2.5.5\n")
768	768	print("The command line was: " + ' '.join(sys.argv))
769	769	printlg("The command line was: " + ' '.join(sys.argv))
770	770

914	914	t = time.time()
915	915	nb = sort_all_bubbles(KS_SEC_EXEC_PATH, readfiles, workdir, outdir, kval, output_snps, infix_name, not only_graph, options.verbose)
916	916	if not only_graph:
917		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)
	917	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)
918	918
919	919	print("Elapsed time: ", (time.time() - t), " seconds\n")
920	920	printlg("Elapsed time: ", (time.time() - t), " seconds\n")

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man/kissplice.1 less more

0		.TH KISSPLICE "14" "march 2020" "kissplice 2.5.4" "User Commands"
	0	.TH KISSPLICE "14" "march 2020" "kissplice 2.5.5" "User Commands"
1	1	.SH NAME
2	2	kisSplice \- local assembly of SNPs, indels and AS events
3	3	.SH SYNOPSIS

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texput.log less more

	0	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
	1	entering extended mode
	2	restricted \write18 enabled.
	3	%&-line parsing enabled.
	4	**user_guide.tex
	5
	6	! Emergency stop.
	7	<*> user_guide.tex
	8
	9	End of file on the terminal!
	10
	11
	12	Here is how much of TeX's memory you used:
	13	4 strings out of 483183
	14	113 string characters out of 5966292
	15	231602 words of memory out of 5000000
	16	15122 multiletter control sequences out of 15000+600000
	17	532338 words of font info for 24 fonts, out of 8000000 for 9000
	18	14 hyphenation exceptions out of 8191
	19	0i,0n,0p,18b,6s stack positions out of 5000i,500n,10000p,200000b,80000s
	20	! ==> Fatal error occurred, no output PDF file produced!

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thirdparty/kissreads/src/kissReads.c less more

50	50	#include <time.h>
51	51	#include <libchash.h>
52	52
53		//#define OMP
	53	#define OMP
54	54
55	55	#ifdef OMP
56	56	#include "omp.h"