From 6840370f3c00fd677cf3af04483463ee0945af2b Mon Sep 17 00:00:00 2001 From: Heng Li Date: Tue, 8 Aug 2017 21:16:25 -0400 Subject: [PATCH 1/3] Release minimap2-2.0 (r275) --- NEWS.md | 13 +++++++++++++ main.c | 2 +- minimap2.1 | 42 ++++++++++++++++++++++++++++-------------- 3 files changed, 42 insertions(+), 15 deletions(-) diff --git a/NEWS.md b/NEWS.md index eb0c522..b8bdd62 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,16 @@ +Release 2.0-r275 (8 August 2017) +-------------------------------- + +This release is identical to version 2.0rc1, except the version number. It is +described and evaluated in the following technical report: + + * Li, H. (2017). Minimap2: fast pairwise alignment for long DNA sequences. + [arXiv:1708.01492v1](https://arxiv.org/abs/1708.01492v1). + +(2.0: 8 August 2017, r275) + + + Release 2.0rc1-r232 (30 July 2017) ---------------------------------- diff --git a/main.c b/main.c index c8650d0..9cc467d 100644 --- a/main.c +++ b/main.c @@ -8,7 +8,7 @@ #include "minimap.h" #include "mmpriv.h" -#define MM_VERSION "2.0rc1-r232" +#define MM_VERSION "2.0-r275" void liftrlimit() { diff --git a/minimap2.1 b/minimap2.1 index 0e63a11..2c85f46 100644 --- a/minimap2.1 +++ b/minimap2.1 @@ -1,4 +1,4 @@ -.TH minimap2 1 "30 July 2017" "minimap2-2.0rc1-r232" "Bioinformatics tools" +.TH minimap2 1 "8 August 2017" "minimap2-2.0-r275" "Bioinformatics tools" .SH NAME .PP minimap2 - mapping and alignment between collections of DNA sequences @@ -247,35 +247,49 @@ are: .RS .TP 8 .B map-pb -PacBio/Oxford Nanopore read to reference mapping (-Hk19) +PacBio/Oxford Nanopore read to reference mapping +.RB ( -Hk19 ) .TP .B map10k The same as .B map-pb -(-Hk19) +.RB ( -Hk19 ) .TP .B map-ont -Slightly more sensitive for Oxford Nanopore to reference mapping (-k15). For -PacBio reads, HPC minimizers consistently leads to faster performance and more -sensitive results in comparison to normal minimizers. For Oxford Nanopore data, -normal minimizers are better, though not much. The effectiveness of HPC is -determined by the sequencing error mode. +Slightly more sensitive for Oxford Nanopore to reference mapping +.RB ( -k15 ). +For PacBio reads, HPC minimizers consistently leads to faster performance and +more sensitive results in comparison to normal minimizers. For Oxford Nanopore +data, normal minimizers are better, though not much. The effectiveness of HPC +is determined by the sequencing error mode. .TP .B asm5 -Long assembly to reference mapping (-k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200). +Long assembly to reference mapping +.RB ( -k19 +.B -w19 -A1 -B19 -O39,81 -E3,1 -s200 +.BR -z200 ). Typically, the alignment will not extend to regions with 5% or higher sequence divergence. Only use this preset if the average divergence is far below 5%. .TP .B asm10 -Long assembly to reference mapping (-k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200). Up -to 10% sequence divergence. +Long assembly to reference mapping +.RB ( -k19 +.B -w19 -A1 -B9 -O16,41 -E2,1 -s200 +.BR -z200 ). +Up to 10% sequence divergence. .TP 8 .B ava-pb -PacBio all-vs-all overlap mapping (-Hk19 -w5 -Xp0 -m100 -K500m -g10000 --max-chain-skip 25) +PacBio all-vs-all overlap mapping +.RB ( -Hk19 +.B -w5 -Xp0 -m100 -K500m -g10000 --max-chain-skip +.BR 25 ). .TP 8 .B ava-ont -Oxford Nanopore all-vs-all overlap mapping (-k15 -w5 -Xp0 -m100 -K500m -g10000 ---max-chain-skip 25). Similarly, the major difference from +Oxford Nanopore all-vs-all overlap mapping +.RB ( -k15 +.B -w5 -Xp0 -m100 -K500m -g10000 --max-chain-skip +.BR 25 ). +Similarly, the major difference from .B ava-pb is that this preset is not using HPC minimizers. .RE From 4db0d1034bc9892e4b3c5553af57a16331ac3061 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Tue, 8 Aug 2017 21:32:56 -0400 Subject: [PATCH 2/3] Show travis CI status --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 482ca9d..21f69f0 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,4 @@ +[![Build Status](https://travis-ci.org/lh3/minimap2.svg?branch=master)](https://travis-ci.org/lh3/minimap2) ## Getting Started ```sh git clone https://github.com/lh3/minimap2 From 9e1125eddaff22cbb72e63e695b6835f1e013d67 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Tue, 8 Aug 2017 21:46:15 -0400 Subject: [PATCH 3/3] r277: abort if query/-d missing (#11) --- main.c | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/main.c b/main.c index 54c49d8..f80d642 100644 --- a/main.c +++ b/main.c @@ -8,7 +8,7 @@ #include "minimap.h" #include "mmpriv.h" -#define MM_VERSION "2.0-r276-dirty" +#define MM_VERSION "2.0-r277-dirty" void liftrlimit() { @@ -189,6 +189,10 @@ int main(int argc, char *argv[]) fprintf(stderr, "[E::%s] failed to open file '%s'\n", __func__, argv[optind]); return 1; } + if (!is_idx && fnw == 0 && argc - optind < 2) { + fprintf(stderr, "[E::%s] missing input: please specify a query file or option -d\n", __func__); + return 1; + } if (is_idx) fpr = fopen(argv[optind], "rb"); else fp = mm_bseq_open(argv[optind]); if (fnw) fpw = fopen(fnw, "wb");