Release minimap2-2.0 (r275)

fix self-comparison in index parameter override check

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

@@ -31,6 +31,10 @@ and [longISLND][longislnd]), better chaining and the ability to produce CIGAR
 with fast extension alignment (see also [libgaba][gaba] and [ksw2][ksw2]) and
 piece-wise affine gap cost.
 
+If you use minimap2 in your work, please consider to cite:
+
+> Li, H. (2017). Minimap2: fast pairwise alignment for long DNA sequences. [arXiv:1708.01492](https://arxiv.org/abs/1708.01492).
+
 ## Installation
 
 For modern x86-64 CPUs, just type `make` in the source code directory. This

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()
 {
@@ -194,7 +194,7 @@ int main(int argc, char *argv[])
 		mm_idx_t *mi = 0;
 		if (fpr) {
 			mi = mm_idx_load(fpr);
-			if (idx_par_set && mm_verbose >= 2 && (mi->k != k || mi->w != w || mi->is_hpc != mi->is_hpc))
+			if (idx_par_set && mm_verbose >= 2 && (mi->k != k || mi->w != w || mi->is_hpc != is_hpc))
 				fprintf(stderr, "[W::%s::%.3f*%.2f] Indexing parameters on the command line (-k/-w/-H) overridden by parameters in the prebuilt index.\n",
 						__func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0));
 		} else if (!mm_bseq_eof(fp)) {

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