From 495a78e40af3228c5aaf6ec22556862c1b1bf256 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Tue, 18 Jul 2017 11:04:09 -0400
Subject: [PATCH] Get documentation ready for release

---
 README.md  | 29 ++++++++++++++++++++---------
 main.c     |  2 +-
 minimap2.1 | 22 +++++++++++++++-------
 3 files changed, 36 insertions(+), 17 deletions(-)

diff --git a/README.md b/README.md
index e98e352..0ef079f 100644
--- a/README.md
+++ b/README.md
@@ -8,7 +8,7 @@ cd minimap2 && make
 ./minimap2 -x map10k -d MT-human.mmi test/MT-human.fa
 ./minimap2 -ax map10k MT-human.mmi test/MT-orang.fa > test.sam
 # long-read overlap (no test data)
-./minimap2 -x ava10k your-reads.fa your-reads.fa > overlaps.paf
+./minimap2 -x ava-pb your-reads.fa your-reads.fa > overlaps.paf
 # man page
 man ./minimap2.1
 ```
@@ -21,24 +21,35 @@ reference genome optionally with detailed alignment (i.e. CIGAR). At present,
 it works efficiently with query sequences from a few kilobases to ~100
 megabases in length at an error rate ~15%. Minimap2 outputs in the [PAF][paf] or
 the [SAM format][sam]. On limited test data sets, minimap2 is over 20 times
-faster than most other long-read aligners.
+faster than most other long-read aligners. It will replace BWA-MEM for long
+reads and contig alignment.
 
 Minimap2 is the successor of [minimap][minimap]. It uses a similar
 minimizer-based indexing and seeding algorithm, and improves the original
 minimap with homopolyer-compressed k-mers (see also [SMARTdenovo][smartdenovo]
 and [longISLND][longislnd]), better chaining and the ability to produce CIGAR
 with fast extension alignment (see also [libgaba][gaba] and [ksw2][ksw2]) and
-two-piece affine gap cost.
+piece-wise affine gap cost.
 
 ## Limitations
 
-At the alignment phase, minimap2 performs global alignments between minimizer
-hits. If the positions of these minimizer hits are incorrect, the final alignment
-may be suboptimal or broken due to the Z-drop heuristics. In addition, in the
-event of a long insertion/deletion, minimap2 may split the long event into
-a few smaller events. We will address these issues in future.
+* At the alignment phase, minimap2 performs global alignments between minimizer
+  hits. If the positions of these minimizer hits are incorrect, the final
+  alignment may be suboptimal or unnecessarily fragmented.
+
+* Minimap2 may produce poor alignments that may need post-filtering. We are
+  still exploring a reliable and consistent way to report good alignments.
+
+* Minimap2 does not work well with Illumina short reads as of now.
+
+* Minimap2 requires SSE2 instructions to compile. It is possible to add
+  non-SSE2 support, but it would minimap2 times slower.
+
+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.
+
 
-Minimap2 does not work well with Illumina short reads as of now.
 
 [paf]: https://github.com/lh3/miniasm/blob/master/PAF.md
 [sam]: https://samtools.github.io/hts-specs/SAMv1.pdf
diff --git a/main.c b/main.c
index a9c3ca2..39a32c9 100644
--- a/main.c
+++ b/main.c
@@ -10,7 +10,7 @@
 #include "minimap.h"
 #include "mmpriv.h"
 
-#define MM_VERSION "2.0-r180-pre"
+#define MM_VERSION "2.0-r180-dirty"
 
 void liftrlimit()
 {
diff --git a/minimap2.1 b/minimap2.1
index 8626a0e..150ede2 100644
--- a/minimap2.1
+++ b/minimap2.1
@@ -1,4 +1,4 @@
-.TH minimap2 1 "12 July 2017" "minimap2-2.0-r174-pre" "Bioinformatics tools"
+.TH minimap2 1 "18 July 2017" "minimap2-2.0-r180-dirty" "Bioinformatics tools"
 .SH NAME
 .PP
 minimap2 - mapping and alignment between collections of DNA sequences
@@ -326,14 +326,22 @@ cg	Z	CIGAR string (only in PAF)
 .TE
 
 .SH LIMITATIONS
-.PP
+.TP 2
+*
 At the alignment phase, minimap2 performs global alignments between minimizer
-hits. If the positions of these minimizer hits are incorrect, the final alignment
-may be suboptimal or broken due to the Z-drop heuristics. In addition, in the
-event of a long insertion/deletion, minimap2 may split the long event into
-a few smaller events. We will address these issues in future.
-.PP
+hits. If the positions of these minimizer hits are incorrect, the final
+alignment may be suboptimal or unnecessarily fragmented.
+.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
+*
+Minimap2 requires SSE2 instructions to compile. It is possible to add
+non-SSE2 support, but it would minimap2 times slower.
 .SH SEE ALSO
 .PP
 miniasm(1), minimap(1), bwa(1).