For compiling and creating shared library:
-Add rapidJson submodule
git submodule add https://github.com/miloyip/rapidjson.git
-Compile .cpp wrapper
g++ -c -Wall -Werror -fPIC -I/your_path_directory/rapidjson/include ga4gh_wrapper.cpp
-Create shared library
g++ -shared -o libga4gh.so ga4gh_wrapper.o
-Compile C library and main
gcc -L/your_path_directory -Wall search_reads.c search_variants.c search_call_sets.c main.c ga4gh_client.c -o ga4gh-tools -lga4gh -lcurl
-Add current directory path to the environment variable LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/your_path_directory:$LD_LIBRARY_PATH
Run examples:
-
This command will give you the "1kg-phase1.vcf" file as output.
./ga4gh-tools --server ga4gh search_variants --variantSetIds 1kg-phase1 --referenceName 2 -s 33100 -e 34000 -
This command will display information about how to use the tool.
./ga4gh-tools --help
- callSets :
./ga4gh-tools --server ga4gh search_callSets --variantSetIds 1kg-phase1
./ga4gh-tools --server ebi search_callSets --variantSetIds EVAF00000003,EVAF00000004
- searchReads
./ga4gh-tools --server ga4gh search_reads -r low-coverage:HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522 -o test_file.sam
For now if you add -d argument with any command, it will print the query response on console.
Done for debugging purposes.