Release minimap2-2.8 (r672)

Author: lh3

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)

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)
 ---------------------------------
 

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

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 <sys/resource.h>

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