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Commit 0764b9f

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GriffanGriffan
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1. Bump version number
2. Adjust CMakeLists.txt parameters
1 parent 6c3c4e6 commit 0764b9f

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+72
-71
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2 files changed

+72
-71
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‎CMakeLists.txt‎

Lines changed: 71 additions & 70 deletions
Original file line numberDiff line numberDiff line change
@@ -1,70 +1,71 @@
1-
cmake_minimum_required(VERSION 2.8.4)
2-
project(VerifyBamID)
3-
4-
set(CMAKE_RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/bin")
5-
set(CMAKE_CXX_STANDARD 11)
6-
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3 -Wno-format-security")
7-
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O3 -Wno-unused-variable -Wno-unused-result ")
8-
9-
add_definitions(-D__STDC_LIMIT_MACROS)
10-
add_definitions(-D__ZLIB_AVAILABLE__)
11-
12-
find_path(HTS_INCLUDE_DIRS htslib/bgzf.h HINTS /usr/lib/x86_64-linux-gnu/ /usr/lib/ /usr/lib64/)
13-
if(NOT HTS_INCLUDE_DIRS )
14-
message(FATAL_ERROR "libhts HTS_INCLUDE_DIRS not found")
15-
endif()
16-
17-
find_library(HTS_LIBRARIES hts HINTS /usr/lib/x86_64-linux-gnu/ /usr/lib/ /usr/lib64/)
18-
if(NOT HTS_LIBRARIES)
19-
message(FATAL_ERROR "libhts HTS_LIBRARIES not found")
20-
endif()
21-
22-
find_package(OpenMP)
23-
if (OPENMP_FOUND)
24-
set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
25-
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
26-
endif()
27-
28-
find_library(ZLIB z HINTS /usr/lib/x86_64-linux-gnu/ /usr/lib/ /usr/lib64/)
29-
if(NOT ZLIB)
30-
message(FATAL_ERROR "libz library not found")
31-
endif()
32-
find_library(CURLLIB curl HINTS /usr/lib/x86_64-linux-gnu/ /usr/lib/ /usr/lib64/)
33-
if(NOT CURLLIB)
34-
message(FATAL_ERROR "libcurl library not found")
35-
endif()
36-
37-
find_package (BZip2)
38-
if (NOT BZIP2_FOUND)
39-
message(FATAL_ERROR "libbz2 library not found")
40-
else()
41-
include_directories(${BZIP2_INCLUDE_DIRS})
42-
set(BZIP2 ${BZIP2_LIBRARIES})
43-
endif()
44-
45-
find_library(LZMA lzma HINTS /usr/lib/x86_64-linux-gnu/ /usr/lib/ /usr/lib64/)
46-
if(NOT LZMA)
47-
message(WARNING "liblzma library not found, if you specified --disable-lzma when compiling libhts, please ignore this warning")
48-
set(LZMA "")
49-
else()
50-
set(LZMA ${LZMA_LIBRARIES})
51-
endif()
52-
53-
54-
add_subdirectory(statgen)
55-
set(LIBSTATGEN_INCLUDE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/statgen")
56-
add_subdirectory(samtools)
57-
add_subdirectory(libVcf)
58-
set(SOURCE_FILES main.cpp SVDcalculator.cpp ContaminationEstimator.cpp MathGenMin.cpp MathGold.cpp Random.cpp SimplePileupViewer.cpp params.cpp )
59-
include_directories(statgen ${HTS_INCLUDE_DIRS} samtools libVcf Eigen)
60-
add_executable(VerifyBamID ${SOURCE_FILES})
61-
62-
target_link_libraries(VerifyBamID statgen Vcf ${HTS_LIBRARIES} samtools ${ZLIB} ${BZIP2} ${LZMA} ${CURLLIB})
63-
64-
enable_testing()
65-
add_test( NAME myTest1
66-
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
67-
COMMAND VerifyBamID --DisableSanityCheck --UDPath resource/test/hapmap_3.3.b37.dat.UD --BamFile resource/test/test.bam --BedPath resource/test/hapmap_3.3.b37.dat.bed --MeanPath resource/test/hapmap_3.3.b37.dat.mu --Reference resource/test/chr20.fa.gz )
68-
#add_test( NAME myTest2
69-
# WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
70-
# COMMAND sh ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/run.plot.sh -i ${CMAKE_CURRENT_SOURCE_DIR}/resource/test/hapmap_3.3.b37.dat.V -o ${CMAKE_CURRENT_SOURCE_DIR}/resource/test/hapmap -r 1000g -g grey)
1+
cmake_minimum_required(VERSION 2.8.4)
2+
project(VerifyBamID)
3+
4+
set(CMAKE_RUNTIME_OUTPUT_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/bin")
5+
set(CMAKE_CXX_STANDARD 11)
6+
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3 -fPIC -Wno-format-security")
7+
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O3 -fPIC -Wno-unused-variable -Wno-unused-result ")
8+
9+
add_definitions(-D__STDC_LIMIT_MACROS)
10+
add_definitions(-D__ZLIB_AVAILABLE__)
11+
12+
find_package(OpenMP)
13+
if (OPENMP_FOUND)
14+
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
15+
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
16+
endif ()
17+
18+
find_library(CURLLIB curl HINTS /usr/lib/x86_64-linux-gnu/ /usr/lib/ /usr/lib64/)
19+
if (NOT CURLLIB)
20+
message(FATAL_ERROR "libcurl library not found")
21+
endif ()
22+
23+
find_library(ZLIB z HINTS /usr/lib/x86_64-linux-gnu/ /usr/lib/ /usr/lib64/ /usr/local/Cellar/zlib/1.2.11/lib/)
24+
if (NOT ZLIB)
25+
message(FATAL_ERROR "libz library not found")
26+
endif ()
27+
28+
find_path(HTS_INCLUDE_DIRS htslib/bgzf.h HINTS /usr/lib/x86_64-linux-gnu/ /usr/lib/ /usr/lib64/)
29+
if (NOT HTS_INCLUDE_DIRS)
30+
message(FATAL_ERROR "libhts HTS_INCLUDE_DIRS not found")
31+
endif ()
32+
33+
find_library(HTS_LIBRARIES hts HINTS /usr/lib/x86_64-linux-gnu/ /usr/lib/ /usr/lib64/)
34+
if (NOT HTS_LIBRARIES)
35+
message(FATAL_ERROR "libhts HTS_LIBRARIES not found")
36+
endif ()
37+
38+
find_package(BZip2)
39+
if (NOT BZIP2_FOUND)
40+
message(FATAL_ERROR "libbz2 library not found")
41+
else ()
42+
include_directories(${BZIP2_INCLUDE_DIRS})
43+
set(BZIP2 ${BZIP2_LIBRARIES})
44+
endif ()
45+
46+
find_library(LZMA lzma HINTS /usr/lib/x86_64-linux-gnu/ /usr/lib/ /usr/lib64/)
47+
if(NOT LZMA)
48+
message(WARNING "liblzma library not found, if you specified --disable-lzma when compiling libhts, please ignore this warning")
49+
set(LZMA "")
50+
else()
51+
set(LZMA ${LZMA_LIBRARIES})
52+
endif()
53+
54+
55+
add_subdirectory(statgen)
56+
set(LIBSTATGEN_INCLUDE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/statgen")
57+
add_subdirectory(samtools)
58+
add_subdirectory(libVcf)
59+
set(SOURCE_FILES main.cpp SVDcalculator.cpp ContaminationEstimator.cpp MathGenMin.cpp MathGold.cpp Random.cpp SimplePileupViewer.cpp params.cpp )
60+
include_directories(statgen ${HTS_INCLUDE_DIRS} samtools libVcf Eigen)
61+
add_executable(VerifyBamID ${SOURCE_FILES})
62+
63+
target_link_libraries(VerifyBamID statgen Vcf ${HTS_LIBRARIES} samtools ${ZLIB} ${BZIP2} ${LZMA} ${CURLLIB})
64+
65+
enable_testing()
66+
add_test( NAME myTest1
67+
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
68+
COMMAND VerifyBamID --DisableSanityCheck --UDPath resource/test/hapmap_3.3.b37.dat.UD --BamFile resource/test/test.bam --BedPath resource/test/hapmap_3.3.b37.dat.bed --MeanPath resource/test/hapmap_3.3.b37.dat.mu --Reference resource/test/chr20.fa.gz )
69+
#add_test( NAME myTest2
70+
# WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
71+
# COMMAND sh ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/run.plot.sh -i ${CMAKE_CURRENT_SOURCE_DIR}/resource/test/hapmap_3.3.b37.dat.V -o ${CMAKE_CURRENT_SOURCE_DIR}/resource/test/hapmap -r 1000g -g grey)

‎main.cpp‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -31,7 +31,7 @@ SOFTWARE.
3131
#include "htslib/sam.h"
3232
#include "params.h"
3333

34-
#define VERSION "1.0.6"
34+
#define VERSION "1.0.7"
3535

3636
int execute(int argc, char **argv) {
3737

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