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Creating separate files for testing data in cudaaligner (issue #505) #625

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Creating separate files for testing data in cudaaligner (issue #505) #625

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f72dc78
created necessary cmake files
EpiSlim Feb 3, 2021
4c6944c
created necessary cmake files
EpiSlim Feb 3, 2021
c925a88
Formatted the files
EpiSlim Feb 3, 2021
435f51d
All data for testing in cudaaligner is now read from separate files
EpiSlim Feb 4, 2021
46a493c
All data for testing in cudaaligner is now read from separate files
EpiSlim Feb 4, 2021
b2abbb2
Merge branch 'dev' into test-file
EpiSlim Feb 12, 2021
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6 changes: 5 additions & 1 deletion cudaaligner/CMakeLists.txt
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Expand Up @@ -18,6 +18,9 @@

set(MODULE_NAME cudaaligner)

# Data subdirectory
add_subdirectory(data)

# Project specific NVCC flags
if((CUDA_VERSION_MAJOR GREATER 10) OR (CUDA_VERSION_MAJOR EQUAL 10 AND CUDA_VERSION_MINOR GREATER 0))
set(CUDA_NVCC_FLAGS "${CUDA_NVCC_FLAGS} -std=c++14 -arch=compute_60 --expt-relaxed-constexpr")
Expand Down Expand Up @@ -49,7 +52,8 @@ target_include_directories(${MODULE_NAME}_internal INTERFACE
${CMAKE_CURRENT_SOURCE_DIR}/src
)

target_link_libraries(${MODULE_NAME} gwbase cub libcudacxx)

target_link_libraries(${MODULE_NAME} gwbase cub gwio libcudacxx)

target_compile_options(${MODULE_NAME} PRIVATE -Wall -Wextra)
if (gw_optimize_for_native_cpu)
Expand Down
8 changes: 8 additions & 0 deletions cudaaligner/data/CMakeLists.txt
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cmake_minimum_required(VERSION 3.10.2)

set(CUDAALIGNER_BENCHMARK_DATA_DIR "${CMAKE_CURRENT_SOURCE_DIR}/../data")
configure_file(cudaaligner_file_location.hpp.in ${PROJECT_BINARY_DIR}/data/cudaaligner_file_location.hpp @ONLY)

set_property(GLOBAL PROPERTY cudaaligner_data_include_dir "${PROJECT_BINARY_DIR}/data")
4 changes: 4 additions & 0 deletions cudaaligner/data/cudaaligner_file_location.hpp.in
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#pragma once

#cmakedefine CUDAALIGNER_BENCHMARK_DATA_DIR "@CUDAALIGNER_BENCHMARK_DATA_DIR@"
70 changes: 70 additions & 0 deletions cudaaligner/data/query_AlignerGlobal.fasta
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>test_case_1
TTAT
>test_case_2
AAAAAAAAA
>test_case_3
ATAAAAAAAA
>test_case_4
GCTAG
>test_case_5
GCTAG
>test_case_5
ACTG
>test_case_5
T
>test_case_6
TTAT
>test_case_6
AAAAAAAAA
>test_case_6
ATAAAAAAAA
>test_case_6
GCTAG
>test_case_6
GCTAG
>test_case_6
ACTG
>test_case_6
T
>test_case_6
TTAT
>test_case_6
AAAAAAAAA
>test_case_6
ATAAAAAAAA
>test_case_6
GCTAG
>test_case_6
GCTAG
>test_case_6
ACTG
>test_case_6
T
>test_case_6
TTAT
>test_case_6
AAAAAAAAA
>test_case_6
ATAAAAAAAA
>test_case_6
GCTAG
>test_case_6
GCTAG
>test_case_6
ACTG
>test_case_6
T
>test_case_6
TTAT
>test_case_6
AAAAAAAAA
>test_case_6
ATAAAAAAAA
>test_case_6
GCTAG
>test_case_6
GCTAG
>test_case_6
ACTG
>test_case_6
T
8 changes: 8 additions & 0 deletions cudaaligner/data/query_AlignmentImpl.fasta
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>test_case_1
AAAA
>test_case_2
CGATAATG
>test_case_3
GTTAG
>test_case_4
GTTACA
2 changes: 2 additions & 0 deletions cudaaligner/data/query_ApproximateBandedMyers.txt
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>test_case_1
AGGGCGAATATCGCCTCCCGCATTAAGCTGTACCTTCCAGCCCCGCCGGTAATTCCAGCCGGTTGAAGCCACGTCTGCCACGGCACAATGTTTTCGCTTTGCCCGGTGACGGATTTAATCCACCACAG
12 changes: 12 additions & 0 deletions cudaaligner/data/query_NeedlemanWunschImplementation.fasta
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>test_case_1
ACTG
>test_case_2
ATCG
>test_case_3
ATG
>test_case_4

>test_case_5
ACTG
>test_case_6
BDEF
22 changes: 22 additions & 0 deletions cudaaligner/data/query_cudaaligner_cases.fasta
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>read_query_0
CGTCGTCGTC
>read_query_1
CGTCGTCGTC
>read_query_2

>read_query_3
CGTCGTCGTC
>read_query_4
C
>read_query_5
CGTCGTCGTC
>read_query_6
AGTCGTCGTCCGTAATCGTCCGTCGTCGTCGA
>read_query_7
AGTCGTCGTCCGTAATCGTCCGTCGTCGTCGTA
>read_query_8
GTCGTCGTCCGTCGTCGTCCGTCGTCGTCGAAAACGTCGTCCGTCGTCGTCCGTCGTCGAAAACGTCGTCGTCCGTAGTCGTCCGACGTCGTCGTC
>read_query_9
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
>read_query_10
AGGGCGAATATCGCCTCCCGCATTAAGCTGTACCTTCCAGCCCCGCCGGTAATTCCAGCCGGTTGAAGCCACGTCTGCCACGGCACAATGTTTTCGCTTTGCCCGGTGACGGATTTAATCCACCACAGTTGCGACTGATAGCGTCCGGATTTCAAACGCGCCCAAACGTAAACAGGGTGAGGCATCTTCCCGCGCCAGCGCACTTCCTGCCAGATCCTCACCAACGCGTCGCGGAAAGGCATCTAAATTGCATTCTGCCCTGCCAGCCAGCGGCGGATAATCGCCGCGCGGCGGGCATCACTGTATCGCCAGCATTGGCACAATCTGCGGCGTCCCCTGCGGCGATTGACGGTGTGCTAAATCATCTGCCAACCTCAGTTCATCCAGCAGGCTCTCTTGTTCAGCACAAAGTGCGGCGCTGCGAGCCGTTGCTTCGGCAAAATGCGGCCAACGCTGCTGCCAATAACGGCACTACGCGCAGGCGCAGAAAGTTACGATCGTATGAGTCGTCCTGATTACTTTCGTCTTCAATCCAGCGTAAATCCCATACTGACGCGCCCTGCACCAGTTCCCCGCGTGCGGGCGAGCAACGGGCGAATAAGCCGCGTTCCGGCAAAACTCCGAGACTTCCGCCATAGCCGAAAGCCCGGCAGGGCCACTGCCGCGTTTAGCGCCAGCAGAAAGGTTTCACATTGATCGTCGAGATGTTGCGCGGTGACCAGCACTTCACCGGGCAACAAGGTGCGGGCAAATGCCTGATAACGTGCCTGCCGCGCCTGGGCCTCAATGCCCAGTCCTTCTTGCGCAAGTTGTACGCGTTCGACCACCAGCGGCACCACTGTTGGCAGACGTTTTCGCAATGCGTAACCCAGGCATCGGCATTGGCACTTAAGCCGTGATGCACATGAATAGCGCGCAGAGCGACACCGGATTTTCCGTCGCACTGCACCAACTGATGCAGCAGAACGGTGGAGCCAAGCCCGCCGCTAAAGGCCACCAGAATCTGGCGTGAGGTGAGAAGTTGTCTATTGAGCGTGAGTGTCATGATGGTGCGATTTTACAGTAGCAATGCCCGGCACGTTACCGGGCAAATGCGGCGATGACAAACCTTACTGCTCCATACAGTTCAGCAGCCCGTCCGGATCGTTAAAGAAGGTGAAGCGTTTTTTTGCGTGTATGGATCGACACGGATGGTTTCACTTCACGTTATGGCTTTCAAAGGTGCGCCACTGCCGCATCGATGTCATCAACGCTAAAAGCCAGATGACGCAGACCGCAAGCTTCCGGTCGGCTGGGTCGTTCCGGCCAGGAACGGAAATGAGAAAACTCAATCACATATTGCCCATTAAGCGCCGATCCCCTTTCCATGAGTCGCGCGCTTCGCGATAGACTTCGCTGCAGCGTGAAACCGAATATCGCGGTGAAAGCTTTTGCTCACCGCATAATCCGTCGCAATAATCGCAATATGGTGAACCTGTTTTAAACCCAGCATAGCGTCTCCTTTGTTGTTAACAGCACGTTACTCGCCCGGAAGCCGCTCTGGCAAGTTATCCCGCCATTTTTAGGACTCGTACGCGGTAAACGCCGTCTTCGTCCTGTTTCGCGCCGTGAATATCCGTTTCAAAACCGGGGTAATGTTGCCCGACGGAACAAAGCATCGTGAAAGAAATCGAGTATAATGCGCTCTCTTTGGTCAGCATTTCTCCAGGCATCAACAGCGGTACGCCCGGTGGATAAGGCAGGATCATATTGCCGGAAAATCTCTACCGACCAGTTGTTCCAGCGCAATGGTTTCTACTTCGCCTTTATTTTGTCGTTGCCATGCCTGATGTGGCGTCATGATCATCTCCGGCAAAGTATCGAATGCCCGCAACATCAAACCGGGAAGATCGTGTTTACGAATCAGCTTATGGATCCCTTGTGCCAGATCCTGAATACGCATATTGCGGTAGAAATCGGGATCTTCTGCATAGAGATCGGGTAGCATATTTTTGATCCGCAGGTTGAGATCGTAAGAGCGTTTGAATTCCGTCAACCCACGCAATAATCCCATTGCTTTGGTTTTATCGATGCCAATACTAAAGAGAAACAGCAGGTTATAAGGGCCGGTTTTCTCTACTACGATCCCACGTTCGTCGAGGAATTTTGCTACCAGCGCCGCCGGGATCCCCTCCTCGCTCATATTGCCCTGCTCGTCCATCCCCGGTGTCAAAATAGTGACTTTAACCGGATCCGAGAAACATATGATCAGCATCCGCATCGTTAAAGCCGTGCCACTGTTCGCCAGGCGCAACGGGCCAGCATTCGGCTTCATCCACCTGCGGCGGTTGCCAGATATCGAAAAACCAACCGTCAGACTCTTCCCGCAGCCGCTGGACCTCTTTGCGAAAATGCAGAGCTCGTTCTACTGAACGGTTAATCAGCCGTTTGCGGATTACCACGCAGCATCGCCGCCGCCGTCTCAACCGAAGCAATGGGATAACTGGGCGAGGTGGTGGTATCATCATAAAGGCTTCGTTAAAGGCCTCTTCGTCATACTCGCCTTTGTGTGGATCCAGCGAAGCCTGCGATAACGCCGCCAGCATTTTGTGGGTCGATTGCGTTTCGAAGATCACTTTTCCCGCAACACGCTCGCCGCTCATACCACTTTTACCACCTGGTAGATCGGATGAAAATGGGTGTACGGCACCCAGGCAGAATCGAAGTGAATCGACAGGACATCCAGCGTCTGTTTGATCCAGTCGGTGTTGTAGAGCAAGCCATCATAGGTGGAGTTGGTGATCACCGCATGAACCGGCCATTGTGCTTGCGTGGTAGCAGCGACTTTCTCTTCGATGCTGTCGCGAGTAAATTCACGGCGCGGGATCCCACAAAATCCCCAACGCATTACGCGTCGGTTTTTCAGCCAGACTGGCACTACATCGTTCATCATCAACAGATGCGCCAGCGATTATGACAATTGCGGTCGATCAACAGCAGCGTACTGCCGGATGGCGCGGCGTTTATACCCACAATTTTGTTCGACGTCGATGTTCCGTTGGTAACGATATAACTCTGTTCCGCGCCAAAAGTCCGCGCGATGTACTCTTCCGCTTCCAGGTGTGGCCCGGTGTGGTCGAGCAACGAACCAAGCTCGGTGACCGAAATAGAGACATCAGCCTTAAGAGTATTCCCGCCGAAAAAATCATAAAACAGACAGCCAACCGGGCTTTTTGATATGCAGTACCGCCCATATGCCCCGGCGTACAAAGGGTGTACTTCCGCTCTTTGACGTAGGTAAACAAGCTTTCGTGAACGGCGGTGTAATGTTATCAAGATATTCGTCGGTGTACTGACGCATACGAATGGCGATATCTTCCGCCTGCCCCAGCGCATATTCAAAAAACCAGAGCGCCATCCGCATATCCTGCACGCTGACATCCATCGTCGAGTGGGTGTTGATGAAGGCATAAAGCGGGAGATATTCATTAAGCTGATTGATATCGCTACATAAATCGAGACTGTACTCATCCCAGTCAAAATCACGCCGCAAATTCGGGAGTTATACTCGATAAATTTCAGCAATCAACGCTGTTTTTGTGTGAATAATCTGAAAGCCTTGCGCCACCAGCGCCGACTCCAGTTCTTTGATGGGCTCATCTTTATAAAAGACGCCATGCGGTCCCATAATGGCAATGATGTTCATGTGTTCCTCCTGGAAAATCCTTCCTTAATCATAGCCTGCTCAAACCGTGGCGATAAAAGGGTTACCGGTGACCCTTTTTCAGAACTTTGCAATTACGCGTAACCGTAGCTCATCAGGCGCTGATAACGACGGAATTTTTTAAATCTTCAGTGCTTAACACGTCGAGGACGGCCAGATCCGCCAGCAGTTGCGCTTTCAACGATGCCGCCATCGCTTCCGGGTTACGGTGAGCACCACCCAGTGGTTCCGGGATGATGGAGTCGATCAGTTTCAGTTCTTTCAGACGCGGAGCAATGATACCCATCCTTCAGCCGCCAGCGCACAGCCGGCACTCTTCCACAGAATGGACGCACAACCTTCCGGCGAGATAACCGGAATAGGTGCTGTATTGCAGCATATTCGCTTTATCGCCACGCCAATCGCCAGCGCACCGCCAGAACCACCTTCACCGATAACCGTACAAACTACCGGTACGCCGGGCGAGACATTTCACGCAGGTTGCGTGCAATGGCTTCCAGACTGACCACGCTCTTCTGCGCCCACGCGGGGATAAGCCCCGGGGTGTCGGTAAAGGTGATGATAGGCATCTTAAAGCGTTCAGCCATTTGCATCCAGACGCAGTGCTTTGCGGTAACCTTCTGGCGCTGGCATACCAAAGTTACGGCGAATTTTTTCTTTGGTTTCGACCTTTTGATGATAATGATCATCACCGGACGACCATCGAGACGGGCGATACCACCGACGATAGCTTTATCGTCTGCATACGCGCGGTCGCCAGCCAGTTCGTCAAATTCATCAAATGCCAGGCGAACGTAATCCAGGGTATAAGGACGCGCTGTGGATGGCGTGCCAGTTGCGCAATCTGCCATGCACCGAGATCGGCGAAGATTTGTTTGCGGTGTCAGTTCTACGCTTTTTTCACGCAGACGATGCACTTCTTCATCGATGTTAATATCAGTTTCTCATCCTGACGGCTAACCTGCCAGTCAGAGAATCATTTTCGCTTCCAGCTCTGCAATATTGTTCAAAATCAGGAAATTCAGACTCATAGTATTCCTGTATTAGTCAAACTCCAGTTCCACCTGCTCCGAACCAATGAGGCCACGGAGATCGTTTAATAAACGATCGCTCGGAGAGACACGCCACGTCGCGCCAAAACGCAACCGCGCGCATGCATCCGCCCTCTGATAGTAGGAATGTACTGGAATTGTCCCAGAGCGGTGGGGTTCCAGAGACTGACGGAGTCGGTTTAAAGCTGGTCATCAATTTGCCTGTCCGTCAGCGAGATAGCAAGCCCGCGAGCATATTTTTCCCGGGCTTCGTCAATATCCATCACTTCGCGAGCGGTCATTTTAAGCCCACCGCTGAAGTCATCAAAGCTGACCTGTCCGCTGACGATAAGTATGCAGTCTTTCCAGCAATTGCTGGTATTTATCCAGGGGCGTCAGTAAGCAACATCACTTCCAGCCGCCGGAACGGTCATCCAGCGTGCAGATACCGATACGATTGCCGCGCTTGGTGACCATAACCCGCGCGGCAACAACTTAACCCCGCAGCCGTGATGACTTTACCACGTTCTGTCGGGTGCATGTCTTTCAGCCGCCGCCTCCGACATAACGCTCAATCTCTTTTAAATACTGGTTGATAGGGTGTCCGGTCAGGTACAGGCCTAACGTTTCACGTTCCCCATCTAATACCACCTGCTCCGGCCACGGTTGGCAGCTGGCGTAGGATTGTTCAATTTGTTCCGGCTCTTCGGCCAGCACGCCGAACATATCGGCCTGACCGATAGCTTCCGCTTTCGCGTGTTGATCTGCCGCTTTTAACGCATCGCCCAGCGAGTTCATCAGCGCTGCGCGATGTGGCCAAGACGGTCAAACGCCCCGGACATGATCAGTTTTTCCAGCACGCGACGGTTCAACTTTTTGGTGTCGGTACGGGCGCAGAGATCAAACAGTTCGCGGAAGTAGCCGCCTTTATTACGGGCTTCGATGATGGCCTCAATCGGACCTTCACCGACCCCGATCGCGCCAATACCATACACGATTTCGCCGTCGTCGTTGACGTGGAAATGGTAAAGACCGGAGTTTATATCTGGTGGCAGGATTTTCAG
35 changes: 35 additions & 0 deletions cudaaligner/data/result_AlignerGlobal.fasta
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test_case_1 4M 3
test_case_2 1M1D8M 1
test_case_3 1M1I8M 1
test_case_4 3M1D1M1I 3
test_case_5 3M1D1M1I 3
test_case_5 4M 0
test_case_5 1M 1
test_case_6 4M 3
test_case_6 1M1D8M 1
test_case_6 1M1I8M 1
test_case_6 3M1D1M1I 3
test_case_6 3M1D1M1I 3
test_case_6 4M 0
test_case_6 1M 1
test_case_6 4M 3
test_case_6 1M1D8M 1
test_case_6 1M1I8M 1
test_case_6 3M1D1M1I 3
test_case_6 3M1D1M1I 3
test_case_6 4M 0
test_case_6 1M 1
test_case_6 4M 3
test_case_6 1M1D8M 1
test_case_6 1M1I8M 1
test_case_6 3M1D1M1I 3
test_case_6 3M1D1M1I 3
test_case_6 4M 0
test_case_6 1M 1
test_case_6 4M 3
test_case_6 1M1D8M 1
test_case_6 1M1I8M 1
test_case_6 3M1D1M1I 3
test_case_6 3M1D1M1I 3
test_case_6 4M 0
test_case_6 1M 1
4 changes: 4 additions & 0 deletions cudaaligner/data/result_AlignmentImpl.txt
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test_case_1;AAAA-;xx|x ;TTATG;4M1I;2X1=1X1I;true;mismatch/mismatch/match/mismatch/insertion/
test_case_2;CGATAATG; x|||| ;-CATAA--;1D5M2D;1D1X4=2D;true;deletion/mismatch/match/match/match/match/deletion/deletion/
test_case_3;--GT-TAG--; || ||| ;AAGTCTAGAA;2I2M1I3M2I;2I2=1I3=2I;true;insertion/insertion/match/match/insertion/match/match/match/insertion/insertion/
test_case_4;G-TTACA;| || ||;GATT-CA;1M1I2M1D2M;1=1I2=1D2=;false;match/insertion/match/match/deletion/match/match/
1 change: 1 addition & 0 deletions cudaaligner/data/result_ApproximateBandedMyers.txt
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test_case_1 23
6 changes: 6 additions & 0 deletions cudaaligner/data/result_NeedlemanWunschImplementation.txt
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test_case_1 0
test_case_2 3
test_case_3 2
test_case_4 0
test_case_5 4
test_case_6 4
70 changes: 70 additions & 0 deletions cudaaligner/data/target_AlignerGlobal.fasta
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>test_case_1
AAAA
>test_case_2
ATAAAAAAAA
>test_case_3
AAAAAAAAA
>test_case_4
ACTGA
>test_case_5
ACTGA
>test_case_5
ACTG
>test_case_5
A
>test_case_6
AAAA
>test_case_6
ATAAAAAAAA
>test_case_6
AAAAAAAAA
>test_case_6
ACTGA
>test_case_6
ACTGA
>test_case_6
ACTG
>test_case_6
A
>test_case_6
AAAA
>test_case_6
ATAAAAAAAA
>test_case_6
AAAAAAAAA
>test_case_6
ACTGA
>test_case_6
ACTGA
>test_case_6
ACTG
>test_case_6
A
>test_case_6
AAAA
>test_case_6
ATAAAAAAAA
>test_case_6
AAAAAAAAA
>test_case_6
ACTGA
>test_case_6
ACTGA
>test_case_6
ACTG
>test_case_6
A
>test_case_6
AAAA
>test_case_6
ATAAAAAAAA
>test_case_6
AAAAAAAAA
>test_case_6
ACTGA
>test_case_6
ACTGA
>test_case_6
ACTG
>test_case_6
A
8 changes: 8 additions & 0 deletions cudaaligner/data/target_AlignmentImpl.fasta
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>test_case_1
TTATG
>test_case_2
CATAA
>test_case_3
AAGTCTAGAA
>test_case_4
GATTCA
2 changes: 2 additions & 0 deletions cudaaligner/data/target_ApproximateBandedMyers.txt
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>test_case_1
AGGGCGAATATCGCCTCCGCATTAAACTGTACTTCCCAGCCCCGCCAGTATTCCAGCGGGTTGAAGCCGCGTCTGCCACAGCGCAATGTTTTCTTTGCCCACGGTGACCGGTTTAGTCACTACAGTTGC
12 changes: 12 additions & 0 deletions cudaaligner/data/target_NeedlemanWunschImplementation.fasta
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>test_case_1
ACTG
>test_case_2
ACTG
>test_case_3
ACTG
>test_case_4
ACTG
>test_case_5
ACTGGTCA
>test_case_6
ACTG
22 changes: 22 additions & 0 deletions cudaaligner/data/target_cudaaligner_cases.fasta
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>read_target_0
AAAAAAAAAA
>read_target_1
AATAATAATA
>read_target_2
AATAATAATA
>read_target_3

>read_target_4
AATAATAATA
>read_target_5
CGTCGTCGTC
>read_target_6
CGTCGTCGTCCGTCGTCGTCCGTCGTCGTCGT
>read_target_7
CGTCGTCGTCCGTCGTCGTCCGTCGTCGTCGTC
>read_target_8
GTCGTCGTCCGTCGTCGTCCGTCGTCGTCGTCGTCGTCGTCCGTCGTCGTCCGTCGTCGTCGTCGTCGTCGTCCGTCGTCGTCCGTCGTCGTCGTC
>read_target_9
GTCGTCGTCCGTCGTCGTCCGTCGTCGTCGTCGTCGTCGTCCGTCGTCGTCCGTCGTCGTCGTCGTCGTCGTCCGTCGTCGTCCGTCGTCGTCGTC
>read_target_10
AGGGCGAATATCGCCTCCGCATTAAACTGTACTTCCCAGCCCCGCCAGTATTCCAGCGGGTTGAAGCCGCGTCTGCCACAGCGCAATGTTTTCTTTGCCCACGGTGACCGGTTTAGTCACTACAGTTGCGACGATGGCGCATCAGTTTACCGACAGCCCAAACATCGGTAGGTGAGGCATCTTCCCGCGCCAGCGCCACTTCCTGCCAGATCCTCACCAACGTCGCGGGAAGGCATCTGGTGCATTCTGCCTGCCAGCCAGCGGCGGATAATCTCGCCGCGCGGCGGCATCACTCATCGCCAGCATTGGCGCAATCTGCAGCGTCCCCTGCGGCGATTGACAGTGTCTCAAAATCATCTGCCAGCAGTTCATCCAGCAAGCTCTCTTGTTCAGCATTTAAAGTGCTGCGAGCCGTTAGCCCGTGTCTCGGCTGCCTTTGCTGCAACCAACGGCACTACGCGCAGGCGCAGAAAGTTACGATCGTATGAGTCATCACGATTGCTCGTCTTCAATCTGGCGTAAATCATACTGGCGCTTTCACTGCACCGGATTTTCAGCCCCCCGCGTGCGGGCGAGCAACGGGCGAATAAGCCTGCCGCGTTCGGCAAGCCTCCGAGACTTCCGCGCCCAGAAAACCGGCAGGGCCACTGCGTTTTAGCGCGTGGTTTCTCACGTTGATCATTCGAGATGTTTGCGCGGTGACCAGCACTTCACCAGGCGACAAGATTTTGAACAATGCCTGATAACGTGCCTGCCGCGCACGGGCCTCGATGCCCAGTCCTTCTTGCGCAAGTTGTACGCGTTCGACCACCAGCGGCACCTGCCACTGTTGGCGAACGTTTTCGCAATGCGTAACCAGGCATGACATTGGCACTTAAACCCGTGATGCATGAATAGCGCGCGGTGACACCGGATTTTCCGTCCCGCCACTGCACCAGCTTTGATGCAGCAGAACGGGGTGAGTCAAGCCCGCGCTAAAGGCCACCAGAATCTGGCGTGGTGAGAAGTTGTCTATTGAAGGCGTGAGTGTCATGATGGTGCGATTTTGGTAATATTGCCCGGCACGTTACCGGGCAAATGCAGCGATGACAAACCTTACTTGCTCATACCGGTTCCAACAGCCGTCGGATCGTTAAAGAAGGTGAAGCGTTTTTGCGTGTATGGATCGACACGGATGGTTTCACGCTACGTTATGGCTTTCAAGGTGCGCTGCACCGCGTCGATGTCATCAACGCTCGCGGCAGATGACGCAGACCTGGCTTCCGGTCGGCAGTTCGTTCCGGCAGGGCGAAATGAGAAAAGCTCAATCCACATATTTACCATTAAGCGCCAAATCCGCACCAGCGGTCGCACGCTTCACGGAAATGAACTCGCTGCGGCGTGAGCAAAGTCTTATCAAAGTAAAGCTTGCACTCCTGCATAATCATCACGCAATAATCTGTATAATTACGGTTTCCTGTTTAACCAACGTAACATCTCCGCTATTTGTTAACAGCGACCACTGTGGAAACCGCTCTACTGTAACGGATTATCCCCGCCATTTTTAGGACTCGTCGCGGTAAACGCCGTCGTCTGATCCCGCCATTTCGCGCCGTGAATATCCGTTTCAAAACCGGGGTAATGTTGCCCGACGGAACAAAACATCATTAATCGGTACTGTGCGGCTCTCTTTAGTCAACATTTCTCCAGGCATCAACAGCGGTACGCCCGATTTAAGGCAGGATCGCCAATACGCCGATACTCTGCAGGCCAGTTTGTTCCAGCGCAATGGTTCTACTTCGCCTTTAATTTGTCGTTGCCATGCCTGATGTGGCGTCACCGATCATCTTCCGGCAAAGTATCAGATGCCGCAACATCGTCAGGAAGATCGTGCACGAATCAGCTTATGGATCATGTTGCCAGATCGCAGATACGCATATTGCGGTGAAATCAGGATCTTCTGCATAGAGATCGGGTAGCATATTTTTGATCCGCAGGTTGAGATCGTAAAGAGCGTTTGAATTCAAATCCTTCACGCAATATAATCCCATTTGCTTTGGTTTTATCTGATGCCAATACTAAAGAAACAGCAGGTTATAGTATAGTTTTCTGCACCACGTCCCACCACATTCGTCAAATTTTGCTGCCAGCTACCCATAGGATCCTCCTCGCTCATATTGCCCTGCTCGTCCATTACAGTGTCCAAAATAGGTGACTTTAACCGGATCGAGAAACATATGATCGGCATCCGCATCGTTAAAGCCGTGCCACTATTTCGCCAGGCGCAACGGGCCAGCATTCGACTTCATCACACCACGGCGGTTTTGCCAGATATCAGCTCAACCAAATCGGACTCTTCCCGCAGCCGCTGGACCTCTTTGAAAAATATGCAGAGCTCATTCTGCTGAACGGTTAATCTGTGTTTACTTGCTGCCCGGATTACCACGCAGCATCACCGCCGCCGCTCTCAACCAATGACAATGTGGATAACCTGGGCGGGTGGGTATGCATCATGAGCTTCGTTAAGTATCTTCGTCATACTCGCCTTTAATGTGGATCAGCAAAGCCTGCGATAACGCCGCCAGCATTTGTGGGTCGATTGCGTTTGAAGATCACTTTTTCCACAACACGCTCGCCGCTCATACCACTTTTACCACCGGTAGATCGGATGAAAATGGGTGTACATAACTTTACCAGGCCAGTCAAAGTGAATCGACGGGACATCCAGCGTCTGTTTACGATCCAGTCGGTGTTGTAGAACAAGCCATCGCCGTGGGTTAATTTTGATGCCACGCATAGACGACGTGTCTTGCGTGGTAGCAACGACCTCTTCGATACTTCATCGCGGTAAATTCTGTACGGGATCCTCACACCAAGGTCTAACGCATTACGCGTCGGTTTCGGCCAGACTGGCGCTACATCGTTCATCATCAACAGATGCGCCAGCGATTTATGACAATTGCGGTCGATCATGGCGTACTGGTGGCGCGGCGTACACCCACAATTTTGTTCGACGATCGATGTTCGTTGGTAGCAATGATATAATAACTCTGTTCCGCGCCAAAGTCGCGGTGTACTCTTCCGCGAACTTCGGTGTACAGGTGTGGTCAGAGCAACGAACGTGACGCCATTGACCGAAATAGAGACATCAGCCCATGAAGTATATTCCCGCCGAAAAAAATCATAAAACAGACAGCCAAGCCAGGCTTTTTGACAGCCGCGGTGCCGCTATGCCTGAAACTACCAAAAGTGTACTTCGCTCTTGACGTAGGTAAACAAAACTTTTGACCGAACGGCGGTGTGGTATGAAGATACGTCGGTGTACTGACATACAGGCTGGCGATATCTTCGCTGCTGGCGCATATTCAAAAAACCAGAGCGCCATCATATCCTGCACGCTGACATCCATCGTCGAGTGGGTGTTGATAAGAAAGGCATAAAGCGGGAATGTTGTTGGCGATTGTTATCGCTACATAAATCGAGACTGTACTCATCCCCGGTCAAAAATCACGCCGCAAATTCGAGGGTTATGCTCGATAAATTTCAACAAATCAACATGTTTTGTGGCCAGATAATCTGACGCCCTCGCGCCGACTCCAGTTCTTTGATGGGCTCATCTTTATAAAAGACGCCATGCGGTCCCATAATGGCAATGATGTTCATGTGTTCCTCCTGGAAAATCCTTCCTTGTCTGTATATCCGACCATTGGCGATAAAAAGACCACCGAGAAGTGACCTTTTTCAGGGCTTTTACCAATTACGCGTAACCGTAGCTCATCAGGCGCTGATAACGACGATTTTTTAAATCTTCAGTGCTTAACACGTCATGAGATCGGCCAGATCACCGCCAGCAGTTGCTCAGCGATACGCCGCCATCGGCTTCCGGGTTACGGTGAGCACCCTTTGGTGGTTCCGGGATGATGGAGTCGATCCGGTTCCAGTTCCTTTCAGACGCGGAACAATGAGTACCCATCGCTTCAGCCCCACTTCGGCGGCGCTTTGTCGGCGCTCTTCCACAGAATCAGACACAACGCTTCCGGCGGAATAACGGAATAGGTGCTGTATTTGCAGCATCATATTCACTTTATCGCCCACGCCAATCGCCAGCGCACTACCGCCAGAACCACGCTTCACCGATAACCGTACAAACTACCGGTACGCCGAGGCGAGACATTTCCGCGGGTTGCATTAAATGGCTCAGACTGACCACGCTCTTCTGCGCCCACGCCAGATAAGCCCGGTCGATAAGGTGATGATAAGCATCGCCAGCGTTCAGCCATTTGCTGTCAGACGCAGTGCTTTTGCGGTAACCTTCTGGCGCTGGCGCACTGCCAAGTTACGTTTTTCTTTTTGGTTTCACGACCTTTTTGACGACCAATGATCATCACCAGGACGACTCATCAGGTGGGCGATACCACCGACGATGTTCTCGCAATCTTCGCCCTGCTGGTCGCCAGCCAGTTCGTCAAATTCATCAAATCGCCAGGCAGACGCGTAATCCGAGGTATAAGGACACTGTGGATGGCGTACCAGTTGCGCAATCTGCCATGCCAGATCGGCGAAAGATTTTACGTAATCAGTTCTACGCTTTTTCACGCGAACGATGCGCTTCTTCATCGATGTTAATATCCAGTTTCTCATCCTGACGGCTAACCGCAGTCAGAGAATCGATTTTCAACTACAACTCTGCAATCAGCTGCAGTGCAAATCAAGGAAATTCCAGACTCACTAAAAATGTTCTGTATTGATAAACTCCGGATTCACCTGCTCCAGGGCTGGCTAAAAATTACCAGGATCGTTGTCGGCGATCGCTCGGAAGACACGCCACGTCGCGCCAAAACGCAACCGCGCGCTGGCATTAATCGCCTCTGATGATGAGATAACTTTGCTGATTGTCCAGAGCGGTGGGGTTTCCGGGGCAGCCAGTCAGGTTTACCAAAAGCTGGTCATCAATTTGCCTGTCGTCCGTGATTACATAAAAGCCCGCGAGCATATTTCAGGCTTCGTCAATATCCATCACTTCGCCGACAGTTATTCAGCCGCTATGATCATCGGCTGACCTGTCCACACGACGTCGGTATCGGTCTTTACCAGCAGTTTTCGAGTGGCCCAACATCAGGGCGTCAGTAAATAACATCTTCCAGCCACCGGAACGGTCATCAGCGTGCAGATACCGATACGATTGCCGCGGTGACCTGAACCGCGGCAACAACGAGCCCCACCGGCGTGACTTTACGTTCTGTCGTTGCGTATCGCGCCGACGCCGCGCCTCCGACATAACGCTCAATCTCTTTTAAATACTGGTTGATAAGTCGCCACGATCTGGGAATTTCAGGCTTCAACGTTCCGTTCCCCATCTGATACCGCCTGCTCTATGCACGGTTGGCAACTGGCGTGGGTCTTCCGTTGTTCAGCTCGCTGAAATGACACGCCGAACATATCGGCCTGACCGACGTGGCTTCCACCTTTCGCGTGTTGATCTGCCGCTTTTAACATCATAGCGAGTTCATCAGCGCGCTGCGCGATGTGTTGAGCAGATAAACACCCCGGACGCGATCAGTTTTTCCAGCACGCGACAGTTCTCGCTTTGCAGTGGTGTCCAGTTACCGGCGCAGAGAGATCGTCGGATCGCCAAGATGGCCATACCATTACCGGAGAAACTGATGATGGCCTCAATCAGGACCTTCACCGACCTTTTGATCAACACCAATACCATACCACGATTCGCCGTCATTGACGTGAAATATTAAGGCGGAGTTTATATCTGGTGGCAGGATTTTCAG
3 changes: 3 additions & 0 deletions cudaaligner/tests/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -30,6 +30,9 @@ set(SOURCES
Test_NeedlemanWunschImplementation.cpp
)

get_property(cudaaligner_data_include_dir GLOBAL PROPERTY cudaaligner_data_include_dir)
include_directories(${cudaaligner_data_include_dir})

set(LIBS
cudaaligner
gwbase)
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