Merge branch 'master' into cdna

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

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

main.c

@@ -8,7 +8,7 @@
 #include "minimap.h"
 #include "mmpriv.h"
 
-#define MM_VERSION "2.0rc1-r274-dirty"
+#define MM_VERSION "2.0-r279-dirty"
 
 void liftrlimit()
 {
@@ -196,6 +196,10 @@ 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");

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
+Slightly more sensitive for Oxford Nanopore to reference mapping
-PacBio reads, HPC minimizers consistently leads to faster performance and more
+.RB ( -k15 ).
-sensitive results in comparison to normal minimizers. For Oxford Nanopore data,
+For PacBio reads, HPC minimizers consistently leads to faster performance and
-normal minimizers are better, though not much. The effectiveness of HPC is
+more sensitive results in comparison to normal minimizers. For Oxford Nanopore
-determined by the sequencing error mode.
+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
+Long assembly to reference mapping
-to 10% sequence divergence.
+.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
+Oxford Nanopore all-vs-all overlap mapping
---max-chain-skip 25). Similarly, the major difference from
+.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