diff --git a/Makefile b/Makefile index 1bfc70a6..c53b52d9 100644 --- a/Makefile +++ b/Makefile @@ -77,7 +77,7 @@ ksw2_exts2_neon.o:ksw2_exts2_sse.c ksw2.h kalloc.h # other non-file targets clean: - rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM build dist mappy.so mappy.c python/mappy.c mappy.egg* + rm -fr gmon.out *.o a.out $(PROG) $(PROG_EXTRA) *~ *.a *.dSYM build dist mappy*.so mappy.c python/mappy.c mappy.egg* depend: (LC_ALL=C; export LC_ALL; makedepend -Y -- $(CFLAGS) $(CPPFLAGS) -- *.c) diff --git a/NEWS.md b/NEWS.md index 21afd1e2..6ab5e03d 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,32 @@ +Release 2.8-r672 (1 February 2018) +---------------------------------- + +Notable changes in this release include: + + * Speed up short-read alignment by ~10%. The overall mapping accuracy stays + the same, but the output alignments are not always identical to v2.7 due to + unstable sorting employed during chaining. Long-read alignment is not + affected by this change as the speedup is short-read specific. + + * Mappy now supports paired-end short-read alignment (#87). Please see + python/README.rst for details. + + * Added option --for-only and --rev-only to perform alignment against the + forward or the reverse strand of the reference genome only (#91). + + * Alleviated the issue with undesired diagonal alignment in the self mapping + mode (#10). Even if the output is not ideal, it should not interfere with + other alignments. Fully resolving the issue is intricate and may require + additional heuristic thresholds. + + * Enhanced error checking against incorrect input (#92 and #96). + +For long query sequences, minimap2 should output identical alignments to v2.7. + +(2.8: 1 February 2018, r672) + + + Release 2.7-r654 (9 January 2018) --------------------------------- diff --git a/README.md b/README.md index d6d301f8..1d5fe0ad 100644 --- a/README.md +++ b/README.md @@ -68,9 +68,9 @@ Detailed evaluations are available from the [minimap2 preprint][preprint]. Minimap2 is optimized for x86-64 CPUs. You can acquire precompiled binaries from the [release page][release] with: ```sh -curl -L https://github.com/lh3/minimap2/releases/download/v2.7/minimap2-2.7_x64-linux.tar.bz2 \ +curl -L https://github.com/lh3/minimap2/releases/download/v2.8/minimap2-2.8_x64-linux.tar.bz2 \ | tar -jxvf - -./minimap2-2.7_x64-linux/minimap2 +./minimap2-2.8_x64-linux/minimap2 ``` If you want to compile from the source, you need to have a C compiler, GNU make and zlib development files installed. Then type `make` in the source code @@ -359,10 +359,6 @@ mappy` or [from BioConda][mappyconda] via `conda install -c bioconda mappy`. possible to add non-SIMD support, but it would make minimap2 slower by several times. -In general, minimap2 is a young project with most code written since June, 2017. -It may have bugs and room for improvements. Bug reports and suggestions are -warmly welcomed. - [paf]: https://github.com/lh3/miniasm/blob/master/PAF.md diff --git a/main.c b/main.c index f7b0a65a..f49acf63 100644 --- a/main.c +++ b/main.c @@ -6,7 +6,7 @@ #include "mmpriv.h" #include "getopt.h" -#define MM_VERSION "2.7-r671-dirty" +#define MM_VERSION "2.8-r672" #ifdef __linux__ #include diff --git a/minimap2.1 b/minimap2.1 index e8c1ad82..96ee5395 100644 --- a/minimap2.1 +++ b/minimap2.1 @@ -1,4 +1,4 @@ -.TH minimap2 1 "31 January 2018" "minimap2-2.8-dirty (r671)" "Bioinformatics tools" +.TH minimap2 1 "1 February 2018" "minimap2-2.8 (r672)" "Bioinformatics tools" .SH NAME .PP minimap2 - mapping and alignment between collections of DNA sequences