From a4c2411d99b2b165812f0f913287531eaf83516e Mon Sep 17 00:00:00 2001
From: zzh <zhangzhonghai@ncic.ac.cn>
Date: Mon, 19 Jan 2026 15:00:45 +0800
Subject: [PATCH] =?UTF-8?q?=E4=BF=AE=E5=A4=8D=E4=B8=80=E4=B8=AA=E5=8F=AF?=
 =?UTF-8?q?=E8=83=BD=E5=BC=95=E8=B5=B7=E5=B4=A9=E6=BA=83=E7=9A=84bug?=
 =?UTF-8?q?=EF=BC=8C=E5=B0=B1=E6=98=AF=E8=AF=BB=E5=8F=96reads=E6=97=B6?=
 =?UTF-8?q?=EF=BC=8C=E5=88=9D=E5=A7=8B=E5=BC=80=E8=BE=9F=E7=9A=84seqs?=
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 =?UTF-8?q?=E5=AF=BC=E8=87=B4=E8=B6=85=E5=87=BAseqs=E5=86=85=E5=AD=98?=
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---
 .vscode/launch.json | 3 ++-
 Makefile            | 2 +-
 bwa.c               | 3 ++-
 3 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/.vscode/launch.json b/.vscode/launch.json
index 34f8f4b..9451ef3 100644
--- a/.vscode/launch.json
+++ b/.vscode/launch.json
@@ -13,7 +13,8 @@
             "args": [
                 "mem",
                 "-t",
-                "1",
+                "128",
+                "-K", "800000000",
                 "-M",
                 "-R",
                 "'@RG\\tID:normal\\tSM:normal\\tPL:illumina\\tLB:normal\\tPG:bwa'",
diff --git a/Makefile b/Makefile
index e2a86ae..884a90b 100644
--- a/Makefile
+++ b/Makefile
@@ -9,7 +9,7 @@ OPTIMIZE=-O3
 CFLAGS=		-g -Wall -Wno-unused-function $(AVX2) $(AVX512BW) $(OPTIMIZE)
 
 WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
-#SAM_EXACT= -DSAM_EXACT
+SAM_EXACT= -DSAM_EXACT
 SHOW_PERF= -DSHOW_PERF
 SHOW_DATA_PERF=  -DSHOW_DATA_PERF
 DEBUG_FILE_OUTPUT= -DDEBUG_FILE_OUTPUT
diff --git a/bwa.c b/bwa.c
index 23e3a72..08e5308 100644
--- a/bwa.c
+++ b/bwa.c
@@ -159,7 +159,8 @@ void bseq_read_pe_mt(int chunk_size, int* n_, void* ks1_, void* ks2_, int copy_c
             *m_ = n;
             return;
         }
-        m = (chunk_size + size / init_n_reads - 1) / (size / init_n_reads);
+        float bases_per_read = size * 1.0 / init_n_reads;
+        m = (chunk_size + bases_per_read * 100) / (bases_per_read); // 多开辟100个reads的冗余空间
 #else
         m = 50000;
 #endif