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Add alignment position info and read length to RAD format #9

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f8080d1
Add alignment-level position info to RAD output and record read lengt…
ygao61 Dec 10, 2025
3c34ea9
add changes to make recording positions optional; not yet tested
Dec 11, 2025
586fe29
optional positional info
Dec 11, 2025
fdc4ecf
specific atacseq bug on program terminate
Dec 18, 2025
17f1992
update to fixed libradicl
Dec 19, 2025
02b385d
don't fill strings with bed info when we aren't writing bed output
Dec 19, 2025
73e478c
switch from zlib-cloudflare to zlib-ng
Jan 9, 2026
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100 changes: 64 additions & 36 deletions CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -92,22 +92,43 @@ if (UNIX)

endif()

#add_subdirectory(external/zlib-cloudflare)
include(ExternalProject)
ExternalProject_Add(zlib-cloudflare
GIT_REPOSITORY https://github.com/cloudflare/zlib
GIT_TAG 7aa510344e06fecd6fe09195ac22e9a424ceb660
CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${CMAKE_BINARY_DIR}/zlib-cloudflare
SOURCE_DIR ${CMAKE_SOURCE_DIR}/external/zlib-cloudflare
# Define libz-ng as an external project
ExternalProject_Add(
zlib-ng
GIT_REPOSITORY https://github.com/zlib-ng/zlib-ng.git
GIT_TAG 2.3.2 # Use a specific version tag for reproducibility
CMAKE_ARGS
-DCMAKE_BUILD_TYPE=Release
-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
-DBUILD_SHARED_LIBS=OFF # Build static library
-DZLIB_COMPAT=ON # Disable compatibility mode to get libz-ng.a name
-DZLIB_ENABLE_TESTS=OFF # Disable tests
BUILD_BYPRODUCTS <INSTALL_DIR>/lib/${CMAKE_STATIC_LIBRARY_PREFIX}z-ng${CMAKE_STATIC_LIBRARY_SUFFIX}
INSTALL_COMMAND ${CMAKE_COMMAND} -E echo "Installing zlib-ng..."
COMMAND ${CMAKE_COMMAND} --build <BINARY_DIR> --target install
COMMAND ${CMAKE_COMMAND} -E copy
<INSTALL_DIR>/lib/${CMAKE_STATIC_LIBRARY_PREFIX}z${CMAKE_STATIC_LIBRARY_SUFFIX}
<INSTALL_DIR>/lib/${CMAKE_STATIC_LIBRARY_PREFIX}z-ng${CMAKE_STATIC_LIBRARY_SUFFIX}

)

ExternalProject_Add_Step(zlib-cloudflare
rename_lib
COMMAND cp ${CMAKE_BINARY_DIR}/zlib-cloudflare/lib/libz.a ${CMAKE_BINARY_DIR}/zlib-cloudflare/lib/libzcf.a
COMMENT "copying cloudflare libz.a to libzcf.a"
DEPENDEES install
# Get the install directory
ExternalProject_Get_Property(zlib-ng INSTALL_DIR)

# Create the include directory at configure time to avoid CMake errors
file(MAKE_DIRECTORY ${INSTALL_DIR}/include)

# Create an imported target for libz-ng
add_library(zlibng STATIC IMPORTED)
set_target_properties(zlibng PROPERTIES
IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}z-ng${CMAKE_STATIC_LIBRARY_SUFFIX}
INTERFACE_INCLUDE_DIRECTORIES ${INSTALL_DIR}/include
)

# Ensure the external project is built before using the imported target
add_dependencies(zlibng zlib-ng)

## can't reply on find_package because the ExternalProject_Add
# steps won't complete by compile time, when the find_package
# looks for the ZLIB
Expand All @@ -117,11 +138,11 @@ ExternalProject_Add_Step(zlib-cloudflare

# install path to the lib / include directories of the
# cloudflare libz
include_directories(${CMAKE_BINARY_DIR}/zlib-cloudflare/include)
link_directories(${CMAKE_BINARY_DIR}/zlib-cloudflare/lib)
#include_directories(${CMAKE_BINARY_DIR}/zlib-cloudflare/include)
#link_directories(${CMAKE_BINARY_DIR}/zlib-cloudflare/lib)

# direct path to the cloudflare libz
set(CLOUDFLARE_ZLIB ${CMAKE_BINARY_DIR}/zlib-cloudflare/lib/libzcf.a)
#set(CLOUDFLARE_ZLIB ${CMAKE_BINARY_DIR}/zlib-cloudflare/lib/libzcf.a)


set(THREADS_PREFER_PTHREAD_FLAG TRUE)
Expand Down Expand Up @@ -176,7 +197,7 @@ target_include_directories(build_static PRIVATE ${ZLIB_INCLUDE_DIRS} ${CMAKE_CU
#target_include_directories(bench PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/include ${LIBRADICL_INCLUDE})

add_executable(check src/check.cpp src/FastxParser.cpp)
target_link_libraries(check ${CLOUDFLARE_ZLIB} sshash_static Threads::Threads)
target_link_libraries(check zlibng sshash_static Threads::Threads)
target_include_directories(check PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/include ${ZLIB_INCLUDE_DIRS} ${LIBRADICL_INCLUDE})

#add_executable(query src/query.cpp ${SSHASH_SOURCES} ${Z_LIB_SOURCES})
Expand All @@ -189,15 +210,15 @@ target_include_directories(check PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/include ${Z

add_executable(pesc-sc src/pesc_sc_runner.cpp)
target_include_directories(pesc-sc PUBLIC ${CMAKE_SOURCE_DIR}/include ${ZLIB_INCLUDE_DIRS} ${LIBRADICL_INCLUDE})
target_link_libraries(pesc-sc pesc_static ${CLOUDFLARE_ZLIB} Threads::Threads sshash_static ${MALLOC_LIB})
target_link_libraries(pesc-sc pesc_static zlibng Threads::Threads sshash_static ${MALLOC_LIB})

add_executable(pesc-bulk src/pesc_bulk_runner.cpp)
target_include_directories(pesc-bulk PUBLIC ${CMAKE_SOURCE_DIR}/include ${ZLIB_INCLUDE_DIRS} ${LIBRADICL_INCLUDE})
target_link_libraries(pesc-bulk pesc_static ${CLOUDFLARE_ZLIB} Threads::Threads sshash_static ${MALLOC_LIB})
target_link_libraries(pesc-bulk pesc_static zlibng Threads::Threads sshash_static ${MALLOC_LIB})

add_executable(pesc-sc-atac src/pesc_sc_atac_runner.cpp)
target_include_directories(pesc-sc-atac PUBLIC ${LIBRADICL_INCLUDE} ${CMAKE_SOURCE_DIR}/include ${ZLIB_INCLUDE_DIRS})
target_link_libraries(pesc-sc-atac pesc_static radicl ${CLOUDFLARE_ZLIB} Threads::Threads sshash_static ${MALLOC_LIB})
target_link_libraries(pesc-sc-atac pesc_static radicl zlibng Threads::Threads sshash_static ${MALLOC_LIB})
#target_link_directories(pesc-sc-atac PUBLIC /fs/cbcb-lab/rob/students/noor/miniforge3/lib)
add_dependencies(pesc-sc-atac radicl)

Expand All @@ -213,19 +234,19 @@ add_dependencies(pesc-sc-atac radicl)

add_executable(build src/build_runner.cpp)
target_include_directories(build PUBLIC ${CMAKE_SOURCE_DIR}/include ${ZLIB_INCLUDE_DIRS} ${LIBRADICL_INCLUDE})
target_link_libraries(build Threads::Threads build_static sshash_static ${CLOUDFLARE_ZLIB} ${MALLOC_LIB})
target_link_libraries(build Threads::Threads build_static sshash_static zlibng ${MALLOC_LIB})

add_executable(evaluator src/index_evaluator.cpp)
target_include_directories(evaluator PUBLIC ${CMAKE_SOURCE_DIR}/include ${ZLIB_INCLUDE_DIRS} ${LIBRADICL_INCLUDE})
target_link_libraries(evaluator ${CLOUDFLARE_ZLIB} Threads::Threads sshash_static)
target_link_libraries(evaluator zlibng Threads::Threads sshash_static)

add_executable(build-poison-table src/poison_table_build_runner.cpp)
target_include_directories(build-poison-table PUBLIC ${CMAKE_SOURCE_DIR}/include ${ZLIB_INCLUDE_DIRS})
target_link_libraries(build-poison-table Threads::Threads build_static pesc_static sshash_static ${CLOUDFLARE_ZLIB} ${MALLOC_LIB})
target_link_libraries(build-poison-table Threads::Threads build_static pesc_static sshash_static zlibng ${MALLOC_LIB})

add_executable(poison_filter src/poison_read_filter.cpp)
target_include_directories(poison_filter PUBLIC ${CMAKE_SOURCE_DIR}/include ${ZLIB_INCLUDE_DIRS})
target_link_libraries(poison_filter Threads::Threads pesc_static sshash_static ${CLOUDFLARE_ZLIB})
target_link_libraries(poison_filter Threads::Threads pesc_static sshash_static zlibng)

## tests
add_subdirectory(external/doctest)
Expand All @@ -238,14 +259,14 @@ target_link_libraries(tests PRIVATE doctest pesc_static)


## depend on the cloudflare zlib library
add_dependencies(check zlib-cloudflare)
add_dependencies(evaluator zlib-cloudflare)
add_dependencies(build zlib-cloudflare)
add_dependencies(pesc-sc zlib-cloudflare)
add_dependencies(pesc-sc-atac zlib-cloudflare)
add_dependencies(pesc-bulk zlib-cloudflare)
add_dependencies(build-poison-table zlib-cloudflare)
add_dependencies(poison_filter zlib-cloudflare)
add_dependencies(check zlibng)
add_dependencies(evaluator zlibng)
add_dependencies(build zlibng)
add_dependencies(pesc-sc zlibng)
add_dependencies(pesc-sc-atac zlibng)
add_dependencies(pesc-bulk zlibng)
add_dependencies(build-poison-table zlibng)
add_dependencies(poison_filter zlibng)


#add_executable(test_parse src/test_parse_geo.cpp)
Expand All @@ -263,14 +284,21 @@ install(TARGETS pesc_static build_static sshash_static
CONFIGURATIONS Debug
RUNTIME DESTINATION Debug/lib)

install(FILES ${CLOUDFLARE_ZLIB}
CONFIGURATIONS Debug
RUNTIME DESTINATION Debug/lib)
install(FILES ${INSTALL_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}z-ng${CMAKE_STATIC_LIBRARY_SUFFIX}
CONFIGURATIONS Debug
RUNTIME DESTINATION Debug/lib
)

install(TARGETS pesc_static build_static sshash_static
CONFIGURATIONS Release
RUNTIME DESTINATION Release/lib)

install(FILES ${CLOUDFLARE_ZLIB}
CONFIGURATIONS Release
RUNTIME DESTINATION Release/lib)
install(FILES ${INSTALL_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}z-ng${CMAKE_STATIC_LIBRARY_SUFFIX}
CONFIGURATIONS Release
RUNTIME DESTINATION Release/lib
)

install(FILES ${INSTALL_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}z-ng${CMAKE_STATIC_LIBRARY_SUFFIX}
DESTINATION lib
COMPONENT libraries
)
2 changes: 1 addition & 1 deletion external/libradicl
Open in desktop
Submodule libradicl updated 10 files
+3 −3 include/Buffer.hpp
+126 −0 include/FlushableBuffer.hpp
+24 −18 include/Header.hpp
+59 −60 include/Tags.hpp
+10 −21 src/Buffer.cpp
+8 −0 src/CMakeLists.txt
+9 −23 src/Header.cpp
+51 −57 src/RAD_Writer.cpp
+1 −28 src/Tags.cpp
+129 −0 src/test_flushable.cpp
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