From d1a5715e5667651b534cebb2cf6d570132ffa5b5 Mon Sep 17 00:00:00 2001
From: zzh <zzhofhust@gmail.com>
Date: Sat, 6 Apr 2024 20:53:42 +0800
Subject: [PATCH] =?UTF-8?q?=E5=B0=86fputs=E6=94=B9=E6=88=90fwrite=EF=BC=8C?=
 =?UTF-8?q?=E5=86=99=E5=85=A5=E6=95=88=E7=8E=87=E6=8F=90=E5=8D=8730%?=
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---
 .vscode/launch.json |  4 ++--
 fastmap.c           | 40 +++++++++++++++++++++++++++++++++++++---
 kseq.h              |  8 ++++----
 run.sh              | 27 ++++++---------------------
 4 files changed, 49 insertions(+), 30 deletions(-)

diff --git a/.vscode/launch.json b/.vscode/launch.json
index 7a727e3..110a3b5 100644
--- a/.vscode/launch.json
+++ b/.vscode/launch.json
@@ -18,8 +18,8 @@
                 "-R",
                 "'@RG\\tID:normal\\tSM:normal\\tPL:illumina\\tLB:normal\\tPG:bwa'",
                 "~/reference/bwa/human_g1k_v37_decoy.fasta",
-                "~/data/fastq/dataset/na12878_wes_144/SRR25735653_1.fastq",
-                "~/data/fastq/dataset/na12878_wes_144/SRR25735653_2.fastq",
+                "~/data/fastq/dataset/na12878_wes_144/s_1.fq",
+                "~/data/fastq/dataset/na12878_wes_144/s_2.fq",
                 "-o",
                 "/dev/null"
             ],
diff --git a/fastmap.c b/fastmap.c
index f2c160a..007d71a 100644
--- a/fastmap.c
+++ b/fastmap.c
@@ -121,6 +121,8 @@ typedef struct {
 	mem_worker_t *w;
 	int data_idx; // pingpong buffer index
 	ktp_data_t *data;
+	int wbuf_size;
+	char *wbuf;
 	volatile int read_complete;
 	volatile int calc_complete;
 	long read_idx;
@@ -248,12 +250,40 @@ static inline void *write_data(ktp_aux_t *aux, ktp_data_t *data)
 #endif
 #endif
 	//int64_t ms = 0;
+	int buf_written = 0;
 	for (i = 0; i < data->n_sams; ++i)
 	{
-		//ms += data->sams[i].sam.m;
-		if (data->sams[i].sam.l)
-			err_fputs(data->sams[i].sam.s, stdout);
+		const int slen = data->sams[i].sam.l;
+		if (slen && (buf_written + slen) < aux->wbuf_size)
+		{
+			memcpy(&aux->wbuf[buf_written], data->sams[i].sam.s, slen);
+			buf_written += slen;
+		}
+		else if (buf_written > 0)
+		{
+			err_fwrite(aux->wbuf, 1, buf_written, stdout);
+			if ((buf_written + slen) >= aux->wbuf_size)
+			{
+				memcpy(&aux->wbuf[0], data->sams[i].sam.s, slen);
+				buf_written = slen;
+			}
+			else
+			{
+				buf_written = 0;
+			}
+		}
 	}
+	if (buf_written > 0) {
+		err_fwrite(aux->wbuf, 1, buf_written, stdout);
+	}
+
+	//for (i = 0; i < data->n_sams; ++i)
+	//{
+	//	//ms += data->sams[i].sam.m;
+	//	if (data->sams[i].sam.l)
+	//		err_fputs(data->sams[i].sam.s, stdout);
+	//}
+
 	//fprintf(stderr, "sam size: %ld M\n", ms / 1024 / 1024);
 
 #ifdef SHOW_PERF
@@ -723,6 +753,10 @@ int main_mem(int argc, char *argv[])
 	bwa_print_sam_hdr(aux.idx->bns, hdr_line);
 	aux.actual_chunk_size = fixed_chunk_size > 0? fixed_chunk_size : opt->chunk_size * opt->n_threads;
 
+	// allocate write buffer
+	aux.wbuf_size = 16777216;
+	aux.wbuf = malloc(aux.wbuf_size);
+
 #ifdef SHOW_PERF
 #if USE_RDTSC
 	tmp_time1 = __rdtsc();
diff --git a/kseq.h b/kseq.h
index f3862c6..2107f80 100644
--- a/kseq.h
+++ b/kseq.h
@@ -221,10 +221,10 @@ typedef struct __kstring_t {
 		kstream_t *f;							\
 	} kseq_t;
 
-#define KSEQ_INIT2(SCOPE, type_t, __read)		\
-	KSTREAM_INIT(type_t, __read, 16384)			\
-	__KSEQ_TYPE(type_t)							\
-	__KSEQ_BASIC(SCOPE, type_t)					\
+#define KSEQ_INIT2(SCOPE, type_t, __read)              \
+	KSTREAM_INIT(type_t, __read, 16777216) /* 16384 */ \
+	__KSEQ_TYPE(type_t)                                \
+	__KSEQ_BASIC(SCOPE, type_t)                        \
 	__KSEQ_READ(SCOPE)
 
 #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
diff --git a/run.sh b/run.sh
index ed1408b..ab1aeb8 100755
--- a/run.sh
+++ b/run.sh
@@ -20,38 +20,23 @@ thread=64
 ## d4
 #n_r1=~/data/fastq/dataset/zy_wes/s_1.fq
 #n_r2=~/data/fastq/dataset/zy_wes/s_2.fq
-n_r1=~/data/fastq/dataset/zy_wes/45mr1.fq.gz
-n_r2=~/data/fastq/dataset/zy_wes/45mr2.fq.gz
+#n_r1=~/data/fastq/dataset/zy_wes/45mr1.fq.gz
+#n_r2=~/data/fastq/dataset/zy_wes/45mr2.fq.gz
 ## d5
 #n_r1=~/data/fastq/dataset/zy_wgs/45mr1.fq.gz
 #n_r2=~/data/fastq/dataset/zy_wgs/45mr2.fq.gz
 #n_r1=~/data/fastq/dataset/zy_wgs/s_1.fq
 #n_r2=~/data/fastq/dataset/zy_wgs/s_2.fq
-#n_r1=~/data1/fastq/dataset/zy_wgs/E150010395_L01_690_1.fq
-#n_r2=~/data1/fastq/dataset/zy_wgs/E150010395_L01_690_2.fq
+n_r1=~/data1/fastq/dataset/zy_wgs/E150010395_L01_690_1.fq
+n_r2=~/data1/fastq/dataset/zy_wgs/E150010395_L01_690_2.fq
 
 reference=~/data1/fmt_ref/human_g1k_v37_decoy.fasta
 #reference=~/reference/bwa/human_g1k_v37_decoy.fasta
 #reference=~/data/reference/human_g1k_v37_decoy.fasta
-#out=./all.sam
-#out=./sn.sam
-#out=./ssn-x1.sam
-out=~/data1/d4-45m.sam
-#out=~/data/out1.sam
-#out=/dev/null
-#out=./na12878.sam
-#time ./bwa mem -t 12 -M -R @RG\\tID:normal\\tSM:normal\\tPL:illumina\\tLB:normal\\tPG:bwa \
-#    /home/zzh/data/reference/human_g1k_v37_decoy.fasta \
-#    /home/zzh/data/fastq/nm1.fq \
-#    /home/zzh/data/fastq/nm2.fq -o /dev/null
 
-#time ./bwa mem -t 12 -M -R @RG\\tID:normal\\tSM:normal\\tPL:illumina\\tLB:normal\\tPG:bwa \
-#    /home/zzh/data/reference/human_g1k_v37_decoy.fasta \
-#    /mnt/d/data/fastq/ZY2105177532213000/ZY2105177532213010_L4_1.fq.gz \
-#    /mnt/d/data/fastq/ZY2105177532213000/ZY2105177532213010_L4_2.fq.gz \
-#    -o /dev/null
+out=~/data1/fast-out.sam
 
-time ./fastbwa mem -t $thread -b 256 -M -R @RG\\tID:normal\\tSM:normal\\tPL:illumina\\tLB:normal\\tPG:bwa \
+time ./fastbwa mem -t $thread -M -R @RG\\tID:normal\\tSM:normal\\tPL:illumina\\tLB:normal\\tPG:bwa \
     $reference \
     $n_r1 \
     $n_r2 \