版本1.28.0的更改-------------------------用户可见的重大更改o确认站点范围或用户指定的Makevars文件(如果存在)。1.26.0版本的变化 ------------------------- - 在这个版本没有显著变化。1.24.0版本的变化 ------------------------- - 在这个版本没有显著变化。1.22.0版本的变化 ------------------------- - 在这个版本没有显著变化。1.20.0版本的变化 ------------------------- - 在这个版本没有显著变化。版本1.18.0的变化-------------------------新功能o编译HTSlib与libcurl启用o支持包含空白的安装路径显著的用户可见的变化o在所有类unix系统上从动态链接切换到静态链接(见提交db1d8e17) o包现在需要libbz2和liblzma和libcurl(与头文件)，和GNU make。这在新的SystemRequirements字段中声明。使用预处理器标志-D_FILE_OFFSET_BITS=64。这解决了大文件在Windows上被截断的棘手问题。参见https://support.bioconductor.org/p/124568/ o不要覆盖${R_HOME}/etc/Makeconf中设置的CPPFLAGS, CFLAGS或LDFLAGS值在Linux或Mac上的1.16.0版本中的变化-------------------------重要的用户可见的变化o包括Samtools 1.7中的各种额外文件:bam_aux_c, bam_endan .h和bam_cat.c o在HTSlib代码中添加C函数faidx_fetch_seq_forced_lower()。 This is an alternative to HTSlib C function faidx_fetch_seq(), with the following difference: if coordinates are outside the actual sequence, write N's, rather than adjusting the start,end. Used in the seqbias package (and originally written by seqbias' author and maintainer, Daniel Jones). BUG FIXES o Fix long-standing kvsprintf() bug on Windows. This low-level bug was responsible for breaking "scan_bcf_header" .Call entry point in Rsamtools, which in turn was responsible for the infamous 'invalid class "VCFHeader" object' bug in VariantAnnotation::readVcf(). o Fix for Solaris: Do not build standalone executables (e.g. bgzip, tabix, etc...). They're not needed and seem to cause problems on Solaris. CHANGES IN VERSION 1.14.0 ------------------------- SIGNIFICANT USER-VISIBLE CHANGES o Include the test data files from htslib-1.7/test For convenience, the .sam, .bam, .vcf, .bcf, .cram, .fa, .fa.fai, .gff, and .bed files located under htslib-1.7/test now are also included in the package (under ${R_PACKAGE_DIR}/testdata). They can be accessed with something like: system.file(package="Rhtslib", "testdata", "ce#1.sam") or: system.file(package="Rhtslib", "testdata", "tabix", "vcf_file.vcf") o Change installation folder of htslib header files. HTSlib header files now get installed in ${R_PACKAGE_DIR}/include/htslib instead of ${R_PACKAGE_DIR}/include so C/C++ code that needs to include them now should use directives like: #include "htslib/hts.h" #include "htslib/sam.h" #include "htslib/bgzf.h" instead of: #include "hts.h" #include "sam.h" #include "bgzf.h" o Include various .h and .c files from Samtools 1.7 (in ${R_PACKAGE_DIR}/include). These files come from the top-level folder of the Samtools source tree. See Rhtslib/inst/include/README for more information. o Include textutils_internal.h and hts_internal.h from HTSlib 1.7 (in ${R_PACKAGE_DIR}/include). These files come from the top-level folder of the HTSlib source tree. o Add C function faidx_fetch_seq2() to the HTSlib code. This is an alternative to HTSlib C function faidx_fetch_seq(), with the following differences: 1) writes the incoming sequence to user-supplied 'out' buffer, 2) doesn't write the terminating null byte ('\0'), 3) properly handles 0-length sequences, 4) returns the number of bytes written; -1 on failure. It will be used in Rsamtools::scanFa() when Rsamtools gets migrated to Rhtslib. It allows the incoming sequences to be loaded directly into the DNAStringSet object to return. o Add C function hts_idx_get_n() to the HTSlib code. This function will be used in Rsamtools::idxstatsBam() when Rsamtools gets migrated to Rhtslib. BUG FIXES o Simplify PKG_LIBS on Mac. There should be no need to use linker options -lz -lm -lbz2 -llzma -lcurl and -lpthread on Mac when making the package shared object because we link against **static** library libhts.a on this platform. CHANGES IN VERSION 1.12.0 ------------------------- SIGNIFICANT USER-VISIBLE CHANGES o The HTSlib C library was updated from version 1.1 to version 1.7.