From cfa083a98bf8c6d75e225bde16cf17ddd35c9832 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Tue, 11 Jul 2017 15:12:35 -0400
Subject: [PATCH] r172: separated PacBio and ONT read overlapping

HPC k-mer works better for PacBio, but worse for ONT. Interesting...
---
 main.c     | 11 ++++++++---
 minimap2.1 | 11 +++++++----
 2 files changed, 15 insertions(+), 7 deletions(-)

diff --git a/main.c b/main.c
index 9a504a2..3ac935c 100644
--- a/main.c
+++ b/main.c
@@ -10,7 +10,7 @@
 #include "minimap.h"
 #include "mmpriv.h"
 
-#define MM_VERSION "2.0-r171-pre"
+#define MM_VERSION "2.0-r172-pre"
 
 void liftrlimit()
 {
@@ -122,7 +122,11 @@ int main(int argc, char *argv[])
 			if (c == 'I') batch_size = (uint64_t)(x + .499);
 			else minibatch_size = (uint64_t)(x + .499);
 		} else if (c == 'x') {
-			if (strcmp(optarg, "ava10k") == 0) {
+			if (strcmp(optarg, "ava-ont") == 0) {
+				opt.flag |= MM_F_AVA | MM_F_NO_SELF;
+				opt.min_chain_score = 100, opt.pri_ratio = 0.0f, opt.min_seedcov_ratio = 0.05f, opt.max_gap = 10000;
+				k = 15, w = 5;
+			} else if (strcmp(optarg, "ava-pb") == 0) {
 				opt.flag |= MM_F_AVA | MM_F_NO_SELF;
 				opt.min_chain_score = 100, opt.pri_ratio = 0.0f, opt.min_seedcov_ratio = 0.05f, opt.max_gap = 10000;
 				is_hpc = 1, k = 19, w = 5;
@@ -159,7 +163,8 @@ int main(int argc, char *argv[])
 		fprintf(stderr, "    -N INT       retain at most INT secondary alignments [%d]\n", opt.best_n);
 		fprintf(stderr, "    -D FLOAT     min fraction of minimizer matches [%g]\n", opt.min_seedcov_ratio);
 		fprintf(stderr, "    -x STR       preset (recommended to be applied before other options) []\n");
-		fprintf(stderr, "                 ava10k: -Hk19 -w5 -Xp0 -m100 -D.05 -g10000 (PacBio/ONT all-vs-all read mapping)\n");
+		fprintf(stderr, "                 ava-pb: -Hk19 -w5 -Xp0 -m100 -D.05 -g10000 (PacBio read overlap)\n");
+		fprintf(stderr, "                 ava-ont: -k15 -w5 -Xp0 -m100 -D.05 -g10000 (ONT read overlap)\n");
 		fprintf(stderr, "                 map10k: -Hk19   (PacBio/ONT vs reference mapping)\n");
 		fprintf(stderr, "                 asm1m:  -k19 -w19   (intra-species assembly to ref mapping)\n");
 		fprintf(stderr, "  Alignment:\n");
diff --git a/minimap2.1 b/minimap2.1
index 5296f88..c7a6b67 100644
--- a/minimap2.1
+++ b/minimap2.1
@@ -1,4 +1,4 @@
-.TH minimap2 1 "8 July 2017" "minimap2-2.0-r160-pre" "Bioinformatics tools"
+.TH minimap2 1 "11 July 2017" "minimap2-2.0-r172-pre" "Bioinformatics tools"
 .SH NAME
 .PP
 minimap2 - mapping and alignment between collections of DNA sequences
@@ -54,7 +54,7 @@ minimap2
 .RS 4
 minimap2
 .B -x
-ava10k
+ava-ont
 .RB [ -t
 .IR nThreads ]
 .I target.fa
@@ -180,8 +180,11 @@ Available
 are:
 .RS
 .TP 8
-.B ava10k
-PacBio/Oxford Nanopore all-vs-all overlap mapping (-Hk19 -w5 -Xp0 -m100 -D.05)
+.B ava-pb
+PacBio all-vs-all overlap mapping (-Hk19 -w5 -Xp0 -m100 -D.05 -g10000)
+.TP 8
+.B ava-ont
+Oxford Nanopore all-vs-all overlap mapping (-k15 -w5 -Xp0 -m100 -D.05 -g10000)
 .TP
 .B map10k
 PacBio/Oxford Nanopore read to reference mapping (-Hk19)