diff --git a/README.md b/README.md index 3d6f853..a121406 100644 --- a/README.md +++ b/README.md @@ -7,8 +7,8 @@ Use spdlog as log tool and the default level is 'info'. ### Features -* Fast - with the same number of threads `FastDup` is ~3.5X faster than GATK MarkDuplicatesSpark. - And `FastDup` achives ~15X performance improvement than Picard MarkDuplicates. +* Fast - with the same number of threads `FastDup` is ~8X faster than GATK MarkDuplicatesSpark. + And `FastDup` achives ~20X performance improvement than Picard MarkDuplicates. * Generate identical outputs compared to Picard MarkDuplicates. * The same detailed metrics data witch Picard MarkDuplicates. * All data processed in memory and low-memory footprint even for large input files. @@ -42,6 +42,7 @@ Use spdlog as log tool and the default level is 'info'. * libbz2 * liblzma * libcurl +* OpenSSL * libdeflate (optional) ## Install @@ -69,11 +70,11 @@ The generated binary fastdup will be in the build/bin folder. 1. get help ```bash -fastdup --help +./fastdup --help ``` 2. mark duplicates on an input BAM file using 8 threads ```bash -fastdup --input in.bam --output out.bam --metrics stats.txt --num-threads 8 +./fastdup --input in_test.bam --output out_md.bam --metrics stats.txt --num-threads 8 ``` \ No newline at end of file diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index a80c2de..3d49937 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -84,6 +84,14 @@ else() message(FATAL_ERROR "lm is not found") endif() +# ssl +find_package(OpenSSL REQUIRED) +if(OpenSSL_FOUND) + target_link_libraries(${PG_NAME} OpenSSL::SSL OpenSSL::Crypto) +else() + message(FATAL_ERROR "OpenSSL is not found") +endif() + # install path install(TARGETS ${PG_NAME} RUNTIME DESTINATION bin diff --git a/test/in_test.bam b/test/in_test.bam new file mode 100644 index 0000000..7ba2692 Binary files /dev/null and b/test/in_test.bam differ