diff --git a/README.md b/README.md index c4fd6d9..3b3fc59 100644 --- a/README.md +++ b/README.md @@ -87,10 +87,8 @@ highlighted in bold. ## Limitations * Minimap2 may produce suboptimal alignments through long low-complexity - regions where seed positions may be inaccurate. - -* Minimap2 may produce poor alignments that may need post-filtering. We are - still exploring a reliable and consistent way to report good alignments. + regions where seed positions may be suboptimal. This should not be a big + concern because even the optimal alignment may be wrong in such regions. * Minimap2 does not work well with Illumina short reads as of now. diff --git a/ksw2_ll_sse.c b/ksw2_ll_sse.c index 37311f7..6e13049 100644 --- a/ksw2_ll_sse.c +++ b/ksw2_ll_sse.c @@ -88,7 +88,7 @@ int ksw_ll_i16(void *q_, int tlen, const uint8_t *target, int _gapo, int _gape, (xx) = _mm_max_epi16((xx), _mm_srli_si128((xx), 8)); \ (xx) = _mm_max_epi16((xx), _mm_srli_si128((xx), 4)); \ (xx) = _mm_max_epi16((xx), _mm_srli_si128((xx), 2)); \ - (ret) = _mm_extract_epi16((xx), 0); \ + (ret) = _mm_extract_epi16((xx), 0); \ } while (0) // initialization diff --git a/main.c b/main.c index 18510f8..f74b606 100644 --- a/main.c +++ b/main.c @@ -8,7 +8,7 @@ #include "minimap.h" #include "mmpriv.h" -#define MM_VERSION "2.0-r229-dirty" +#define MM_VERSION "2.0-r230-dirty" void liftrlimit() { diff --git a/minimap2.1 b/minimap2.1 index f9b84e5..5286ef9 100644 --- a/minimap2.1 +++ b/minimap2.1 @@ -1,4 +1,4 @@ -.TH minimap2 1 "29 July 2017" "minimap2-2.0-r224-dirty" "Bioinformatics tools" +.TH minimap2 1 "30 July 2017" "minimap2-2.0-r230-dirty" "Bioinformatics tools" .SH NAME .PP minimap2 - mapping and alignment between collections of DNA sequences @@ -348,10 +348,6 @@ where seed positions may be suboptimal. This should not be a big concern because even the optimal alignment may be wrong in such regions. .TP * -Minimap2 may produce poor alignments that may need post-filtering. We are still -exploring a reliable and consistent way to report good alignments. -.TP -* Minimap2 does not work well with Illumina short reads as of now. .TP *