release notes v1.7.0

yhoogstrate · Jan 29, 2020 · 3607e5c · 3607e5c
1 parent b34851c
commit 3607e5c
Show file tree

Hide file tree

Showing 4 changed files with 45 additions and 34 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -142,32 +142,32 @@ add_executable(mount.fastafs
 				)
 set_target_properties(mount.fastafs PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${BUILD_DIR}")
 
-#add_library(libfastafs SHARED
-					#src/fasta_to_twobit_fastafs.cpp
-					#src/ucsc2bit_to_fastafs.cpp
-					#src/flags.cpp
-					#src/fastafs.cpp
-					#src/ucsc2bit.cpp
-					#src/twobit_byte.cpp
-					#src/fourbit_byte.cpp
-					#src/database.cpp
-					#src/utils.cpp
-					#src/fuse.cpp
-					#src/lsfastafs.cpp
-#)
-#target_include_directories(libfastafs PUBLIC include)
-#target_sources(libfastafs PUBLIC include/fastafs.hpp)
-
-#set_target_properties(libfastafs PROPERTIES LIBRARY_OUTPUT_DIRECTORY "lib")
-#set_target_properties(libfastafs PROPERTIES VERSION ${PROJECT_VERSION})
-#set_target_properties(libfastafs PROPERTIES SOVERSION 1)
-#set_target_properties(libfastafs PROPERTIES OUTPUT_NAME fastafs)
-
-#set_target_properties(libfastafs PROPERTIES HEADER_OUTPUT_DIRECTORY "include")
-# great, this doesn't go automagically with an entire dir
-#set_target_properties(libfastafs PROPERTIES PUBLIC_HEADER "include/config.hpp;include/database.hpp;include/fastafs.hpp;include/fasta_to_twobit_fastafs.hpp;include/fuse.hpp;include/meson.build;include/twobit_byte.hpp;include/ucsc2bit.hpp;include/ucsc2bit_to_fastafs.hpp;include/utils.hpp")
-#set_target_properties(libfastafs PROPERTIES PUBLIC_HEADER_DIRECTORY include)
-#set_target_properties(libfastafs PROPERTIES PUBLIC_HEADER_OUTPUT_DIRECTORY "include")
+add_library(libfastafs SHARED
+					src/fasta_to_twobit_fastafs.cpp
+					src/ucsc2bit_to_fastafs.cpp
+					src/flags.cpp
+					src/fastafs.cpp
+					src/ucsc2bit.cpp
+					src/twobit_byte.cpp
+					src/fourbit_byte.cpp
+					src/database.cpp
+					src/utils.cpp
+					src/fuse.cpp
+					src/lsfastafs.cpp
+)
+target_include_directories(libfastafs PUBLIC include)
+target_sources(libfastafs PUBLIC include/fastafs.hpp)
+
+set_target_properties(libfastafs PROPERTIES LIBRARY_OUTPUT_DIRECTORY "lib")
+set_target_properties(libfastafs PROPERTIES VERSION ${PROJECT_VERSION})
+set_target_properties(libfastafs PROPERTIES SOVERSION 1)
+set_target_properties(libfastafs PROPERTIES OUTPUT_NAME fastafs)
+
+##set_target_properties(libfastafs PROPERTIES HEADER_OUTPUT_DIRECTORY "include")
+## great, this doesn't go automagically with an entire dir
+set_target_properties(libfastafs PROPERTIES PUBLIC_HEADER "include/config.hpp;include/database.hpp;include/fastafs.hpp;include/fasta_to_fourbit_fastafs.hpp;include/fasta_to_twobit_fastafs.hpp;include/flags.hpp;include/fourbit_byte.hpp;include/fuse.hpp;include/lsfastafs.hpp;include/sequence_region.hpp;include/twobit_byte.hpp;include/ucsc2bit.hpp;include/ucsc2bit_to_fastafs.hpp;include/utils.hpp")
+##set_target_properties(libfastafs PROPERTIES PUBLIC_HEADER_DIRECTORY include)
+##set_target_properties(libfastafs PROPERTIES PUBLIC_HEADER_OUTPUT_DIRECTORY "include")
 
 # ----------------------------------------------------------------------
 # ------------------------------ Testing -------------------------------
@@ -182,7 +182,7 @@ add_test(test_twobit_byte         "${BUILD_TEST_DIR}/test_twobit_byte") # ACTG(N
 add_test(test_fourbit_byte        "${BUILD_TEST_DIR}/test_fourbit_byte") # ACGTURYKMSWBDHVN(-)
 add_test(test_cache_twobit        "${BUILD_TEST_DIR}/test_cache_twobit")
 add_test(test_cache_fourbit       "${BUILD_TEST_DIR}/test_cache_fourbit")
-#add_test(test_view                "${BUILD_TEST_DIR}/test_view")
+add_test(test_view                "${BUILD_TEST_DIR}/test_view")
 add_test(test_flags               "${BUILD_TEST_DIR}/test_flags")
 add_test(test_fastafs             "${BUILD_TEST_DIR}/test_fastafs")
 add_test(test_check               "${BUILD_TEST_DIR}/test_check") # file integrity checks
@@ -204,6 +204,6 @@ install(TARGETS fastafs DESTINATION "bin")
 install(TARGETS mount.fastafs DESTINATION "bin")
 
 # don't build during debug at least
-#install(TARGETS libfastafs LIBRARY DESTINATION "lib" PUBLIC_HEADER DESTINATION "include/libfastafs")
+install(TARGETS libfastafs LIBRARY DESTINATION "lib" PUBLIC_HEADER DESTINATION "include/libfastafs")
 
 # ----------------------------------------------------------------------
diff --git a/Changelog b/Changelog
@@ -2,10 +2,21 @@
 
    * v1.7.0
    * `fastafs cache -o` for custom output files and bypassing the config
-   * Random access retrievement via file system: `<mount>/seq/chr1:100-200`
-   * CRC32 checksums for file integratity
-   * converting to meson because of insane build times using cmake+make and re-building files that have not changed
+   * Random access subsequence retrieval diretly via filesystem: `<mount>/seq/chr1:100-200`
+   * Implements CRC32 checksums for whole-file integritity
+   * Converting to meson because of insane build times using cmake+make and re-building files that have not changed
    * `fastafs view|mount -m/--no-masking` virtualises fasta files without masking (uppercase)
+   * Minor support for building with meson and ninja
+   * cmake template allows building for guix (+guix file provided)
+   * Changed requirement from c++17 on c++14 to avoid large compatibility issues
+   * Implements bitflags with corresponding class
+   * Implements fourbit (and automatically switches over if non ACTGUN chars are found
+   * Implements functions `is_fasta_file`, and `is_ucsc2bit_file` using file MAGIC
+   * Creates by FASTAFS files that are first flagged as incomplete, that are unflagged after conversion has completed
+   * MD5sums working for fourbit compressed sequences
+   * Implements `fastafs cache -o` to export to desired output fastafs file
+   * Adds compression type to `fastafs list` output
+   * More and improved testing, including file integrity detection
 
 2019-09-06  Youri Hoogstrate
 

diff --git a/include/ucsc2bit_to_fastafs.hpp b/include/ucsc2bit_to_fastafs.hpp
@@ -29,7 +29,7 @@ struct ucsc2bit_seq_header {
     std::vector<uint32_t> m_block_sizes;
 
     ucsc2bit_seq_header():
-        name_size(0), name(nullptr) { }
+        name_size(0), name(nullptr), n_blocks(0) { }
 };
 
 struct ucsc2bit_seq_header_conversion_data {

diff --git a/test/sequenceregion/test_sequenceregion.cpp b/test/sequenceregion/test_sequenceregion.cpp
@@ -168,11 +168,11 @@ BOOST_AUTO_TEST_CASE(test_sequence_region3)
     {
 
         sequence_region *sr = nullptr;
-        if(sr == nullptr) {// compiler doesn't understand this otherwise
+        //if(sr == nullptr) {// compiler doesn't understand this otherwise
             char arg[] = "/seq/chrRr1:1235-1234";
 
             BOOST_CHECK_THROW(sr = new sequence_region(&(arg[5])), std::invalid_argument);
-        }
+        //}
     }
 
 }