From f150257a0d42839addb93f99463fb200709fbf42 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Sat, 7 Oct 2017 19:19:40 -0400
Subject: [PATCH] r487: demote "map10k"; improved README

---
 README.md  | 23 ++++++++++++++---------
 main.c     |  6 +++---
 minimap2.1 |  5 -----
 3 files changed, 17 insertions(+), 17 deletions(-)

diff --git a/README.md b/README.md
index f60431e..b61c02d 100644
--- a/README.md
+++ b/README.md
@@ -10,10 +10,10 @@
 git clone https://github.com/lh3/minimap2
 cd minimap2 && make
 # long reads against a reference genome
-./minimap2 -ax map10k test/MT-human.fa test/MT-orang.fa > test.sam
+./minimap2 -a test/MT-human.fa test/MT-orang.fa > test.sam
 # create an index first and then map
-./minimap2 -x map10k -d MT-human.mmi test/MT-human.fa
-./minimap2 -ax map10k MT-human.mmi test/MT-orang.fa > test.sam
+./minimap2 -d MT-human.mmi test/MT-human.fa
+./minimap2 -a MT-human.mmi test/MT-orang.fa > test.sam
 # long-read overlap (no test data)
 ./minimap2 -x ava-pb your-reads.fa your-reads.fa > overlaps.paf
 # spliced alignment (no test data)
@@ -108,9 +108,9 @@ regardless of query data types.
 
 Minimap2 uses the same base algorithm for all applications. However, due to the
 different data types it supports (e.g. short vs long reads; DNA vs mRNA reads),
-minimap2 needs to be tuned for optimal performance and accuracy.  You should
-usually choose a preset with option **-x**, which sets multiple parameters at
-the same time.
+minimap2 needs to be tuned for optimal performance and accuracy. It is usually
+recommended to choose a preset with option **-x**, which sets multiple
+parameters at the same time. The default setting is the same as `map-ont`.
 
 #### <a name="map-long-genomic"></a>Map long noisy genomic reads
 
@@ -161,6 +161,9 @@ be paired if they are adjacent in the input stream and have the same name (with
 the `/[0-9]` suffix trimmed if present). Single- and paired-end reads can be
 mixed.
 
+Minimap2 does not work well with short spliced reads. There are many capable
+RNA-seq mappers for short reads.
+
 #### <a name="full-genome"></a>Full genome/assembly alignment
 
 ```sh
@@ -226,12 +229,13 @@ It provides C APIs to build/load index and to align sequences against the
 index. File [example.c](example.c) demonstrates typical uses of C APIs. Header
 file [minimap.h](minimap.h) gives more detailed API documentation. Minimap2
 aims to keep APIs in this header stable. File [mmpriv.h](mmpriv.h) contains
-additional private unstable APIs which may be subjected to changes frequently.
+additional private APIs which may be subjected to changes frequently.
 
 This repository also provides Python bindings to a subset of C APIs. File
 [python/README.rst](python/README.rst) gives the full documentation;
 [python/minimap2.py](python/minimap2.py) shows an example. This Python
-extension, mappy, is also [available from PyPI][mappy] via `pip install`.
+extension, mappy, is also [available from PyPI][mappypypi] via `pip install
+mappy` or [from BioConda][mappyconda] via `conda install -c bioconda mappy`.
 
 ## <a name="limit"></a>Limitations
 
@@ -257,4 +261,5 @@ warmly welcomed.
 [ksw2]: https://github.com/lh3/ksw2
 [preprint]: https://arxiv.org/abs/1708.01492
 [release]: https://github.com/lh3/minimap2/releases
-[mappy]: https://pypi.python.org/pypi/mappy
+[mappypypi]: https://pypi.python.org/pypi/mappy
+[mappyconda]: https://anaconda.org/bioconda/mappy
diff --git a/main.c b/main.c
index c1cedf2..c57af7d 100644
--- a/main.c
+++ b/main.c
@@ -6,7 +6,7 @@
 #include "mmpriv.h"
 #include "getopt.h"
 
-#define MM_VERSION "2.2-r486-dirty"
+#define MM_VERSION "2.2-r487-dirty"
 
 #ifdef __linux__
 #include <sys/resource.h>
@@ -231,8 +231,8 @@ int main(int argc, char *argv[])
 		fprintf(fp_help, "    --version    show version number\n");
 		fprintf(fp_help, "  Preset:\n");
 		fprintf(fp_help, "    -x STR       preset (always applied before other options) []\n");
-		fprintf(fp_help, "                 map10k/map-pb: -Hk19 (PacBio/ONT vs reference mapping)\n");
-		fprintf(fp_help, "                 map-ont: -k15 (slightly more sensitive than 'map10k' for ONT vs reference)\n");
+		fprintf(fp_help, "                 map-pb: -Hk19 (PacBio vs reference mapping)\n");
+		fprintf(fp_help, "                 map-ont: -k15 (Oxford Nanopore vs reference mapping)\n");
 		fprintf(fp_help, "                 asm5: -k19 -w19 -A1 -B19 -O39,81 -E3,1 -s200 -z200 (asm to ref mapping; break at 5%% div.)\n");
 		fprintf(fp_help, "                 asm10: -k19 -w19 -A1 -B9 -O16,41 -E2,1 -s200 -z200 (asm to ref mapping; break at 10%% div.)\n");
 		fprintf(fp_help, "                 ava-pb: -Hk19 -w5 -Xp0 -m100 -g10000 -K500m --max-chain-skip 25 (PacBio read overlap)\n");
diff --git a/minimap2.1 b/minimap2.1
index b914413..0d2081b 100644
--- a/minimap2.1
+++ b/minimap2.1
@@ -288,11 +288,6 @@ are:
 PacBio/Oxford Nanopore read to reference mapping
 .RB ( -Hk19 )
 .TP
-.B map10k
-The same as
-.B map-pb
-.RB ( -Hk19 )
-.TP
 .B map-ont
 Slightly more sensitive for Oxford Nanopore to reference mapping
 .RB ( -k15 ).