From 41efd03d7aeedb21c221f12901c3e30ba22a277f Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Fri, 30 Jun 2017 23:48:00 -0400
Subject: [PATCH] r129: fixed memory leak caused by qualities

---
 bseq.c     |  4 ++--
 bseq.h     |  2 +-
 index.c    |  2 +-
 main.c     |  2 +-
 map.c      |  3 ++-
 minimap2.1 | 19 +++++++++++++++++--
 6 files changed, 24 insertions(+), 8 deletions(-)

diff --git a/bseq.c b/bseq.c
index 16ead16..f68b11d 100644
--- a/bseq.c
+++ b/bseq.c
@@ -32,7 +32,7 @@ void bseq_close(bseq_file_t *fp)
 	free(fp);
 }
 
-bseq1_t *bseq_read(bseq_file_t *fp, int chunk_size, int *n_)
+bseq1_t *bseq_read(bseq_file_t *fp, int chunk_size, int with_qual, int *n_)
 {
 	int size = 0, m, n;
 	bseq1_t *seqs;
@@ -48,7 +48,7 @@ bseq1_t *bseq_read(bseq_file_t *fp, int chunk_size, int *n_)
 		s = &seqs[n];
 		s->name = strdup(ks->name.s);
 		s->seq = strdup(ks->seq.s);
-		s->qual = ks->qual.l? strdup(ks->qual.s) : 0;
+		s->qual = with_qual && ks->qual.l? strdup(ks->qual.s) : 0;
 		s->l_seq = ks->seq.l;
 		size += seqs[n++].l_seq;
 		if (size >= chunk_size) break;
diff --git a/bseq.h b/bseq.h
index bb06766..df9d5bb 100644
--- a/bseq.h
+++ b/bseq.h
@@ -13,7 +13,7 @@ typedef struct {
 
 bseq_file_t *bseq_open(const char *fn);
 void bseq_close(bseq_file_t *fp);
-bseq1_t *bseq_read(bseq_file_t *fp, int chunk_size, int *n_);
+bseq1_t *bseq_read(bseq_file_t *fp, int chunk_size, int with_qual, int *n_);
 int bseq_eof(bseq_file_t *fp);
 
 extern unsigned char seq_nt4_table[256];
diff --git a/index.c b/index.c
index 426f7a9..6dc1f76 100644
--- a/index.c
+++ b/index.c
@@ -217,7 +217,7 @@ static void *worker_pipeline(void *shared, int step, void *in)
         step_t *s;
 		if (p->sum_len > p->batch_size) return 0;
         s = (step_t*)calloc(1, sizeof(step_t));
-		s->seq = bseq_read(p->fp, p->mini_batch_size, &s->n_seq); // read a mini-batch
+		s->seq = bseq_read(p->fp, p->mini_batch_size, 0, &s->n_seq); // read a mini-batch
 		if (s->seq) {
 			uint32_t old_m, m;
 			uint64_t sum_len, old_max_len, max_len;
diff --git a/main.c b/main.c
index ea3d6d6..3c312f1 100644
--- a/main.c
+++ b/main.c
@@ -10,7 +10,7 @@
 #include "minimap.h"
 #include "mmpriv.h"
 
-#define MM_VERSION "2.0-r126-pre"
+#define MM_VERSION "2.0-r129-pre"
 
 void liftrlimit()
 {
diff --git a/map.c b/map.c
index 3e0d26b..53c85db 100644
--- a/map.c
+++ b/map.c
@@ -304,7 +304,7 @@ static void *worker_pipeline(void *shared, int step, void *in)
     if (step == 0) { // step 0: read sequences
         step_t *s;
         s = (step_t*)calloc(1, sizeof(step_t));
-		s->seq = bseq_read(p->fp, p->mini_batch_size, &s->n_seq);
+		s->seq = bseq_read(p->fp, p->mini_batch_size, !!(p->opt->flag & MM_F_OUT_SAM), &s->n_seq);
 		if (s->seq) {
 			s->p = p;
 			for (i = 0; i < s->n_seq; ++i)
@@ -339,6 +339,7 @@ static void *worker_pipeline(void *shared, int step, void *in)
 			}
 			free(s->reg[i]);
 			free(s->seq[i].seq); free(s->seq[i].name);
+			if (s->seq[i].qual) free(s->seq[i].qual);
 		}
 		free(s->reg); free(s->n_reg); free(s->seq);
 		if (mm_verbose >= 3)
diff --git a/minimap2.1 b/minimap2.1
index a4cb1e6..2aa83b1 100644
--- a/minimap2.1
+++ b/minimap2.1
@@ -5,7 +5,7 @@
 minimap2 - mapping and alignment between collections of DNA sequences
 
 .SH SYNOPSIS
-* Index the target sequences (optional):
+* Indexing the target sequences (optional):
 .RS 4
 minimap2
 .RB [ -H ]
@@ -13,12 +13,14 @@ minimap2
 .IR kmer ]
 .RB [ -w
 .IR miniWinSize ]
+.RB [ -I
+.IR batchSize ]
 .B -d
 .I target.mmi
 .I target.fa
 .RE
 
-* Align with CIGAR:
+* Long-read alignment with CIGAR:
 .RS 4
 minimap2
 .B -b
@@ -43,6 +45,19 @@ minimap2
 .I output.paf
 .RE
 
+* Long read overlap without CIGAR:
+.RS 4
+minimap2
+.B -x
+.R ava10k
+.RB [ -t
+.IR nThreads ]
+.I target.fa
+.I query.fa
+>
+.I output.paf
+.RE
+
 .SH DESCRIPTION
 .PP
 Minimap2 is a fast sequence mapping and alignment program that can find