From bcb8b420baaec126da0d423f93d166db7da8491b Mon Sep 17 00:00:00 2001
From: zzh <zzhofhust@gmail.com>
Date: Thu, 17 Apr 2025 18:29:12 +0800
Subject: [PATCH] =?UTF-8?q?=E6=AD=A3=E5=B8=B8=E8=AF=BB=E5=AE=8C=E6=96=87?=
 =?UTF-8?q?=E4=BB=B6=EF=BC=8C=E7=84=B6=E5=90=8E=E9=80=80=E5=87=BA?=
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---
 src/sort/sam_io.cpp  |  2 +-
 src/sort/sort.cpp    | 16 +++++++++++++---
 src/sort/sort_impl.h |  2 +-
 3 files changed, 15 insertions(+), 5 deletions(-)

diff --git a/src/sort/sam_io.cpp b/src/sort/sam_io.cpp
index a9d5ac0..775ca72 100644
--- a/src/sort/sam_io.cpp
+++ b/src/sort/sam_io.cpp
@@ -59,7 +59,7 @@ void parseSamHeader(FILE *fp, HeaderBuf &hdrBuf) {
     blockLen = unpackInt16(&fBuf[16]) + 1;
     readState = fread(&fBuf[BLOCK_HEADER_LENGTH], 1, blockLen - BLOCK_HEADER_LENGTH, fp);
     header = sam_hdr_init();
-
+    spdlog::info("Header file size: {}", blockLen);
 
     uint32_t crc = le_to_u32(fBuf + blockLen - 8);
     int ret = bgzfUncompress(uData.data, &dlen, (Bytef *)fBuf + 18, blockLen - 18, crc);
diff --git a/src/sort/sort.cpp b/src/sort/sort.cpp
index acd66e2..fa5432b 100644
--- a/src/sort/sort.cpp
+++ b/src/sort/sort.cpp
@@ -269,6 +269,7 @@ static void *nonBlockingUncompress(void *data) {
     else
         ((SortData *)data)->round++;
 
+    // spdlog::info("block arr size: {}", ((SortData *)data)->blockAddrArr->size());
     kt_for(nsgv::gSortArg.NUM_THREADS, mtUncompressBlock, data, ((SortData *)data)->blockAddrArr->size());
     // kt_for(nsgv::gSortArg.NUM_THREADS, mtUncompressBlock, data, nsgv::gSortArg.NUM_THREADS);
     PROF_G_END(uncompress);
@@ -343,13 +344,16 @@ int doSort() {
 
     // 测试读取bam的速度
 
+    int max_bam_len = 0;
     bam1_t *bamp = bam_init1();
     while (sam_read1(inBamFp, inBamHdr, bamp) >= 0) {
+        if (max_bam_len < bamp->l_data) max_bam_len = bamp->l_data;
         if (bamp->l_data > 1000) {
             spdlog::info("large record len: {}", bamp->l_data);
         }
     }
     sam_close(inBamFp);
+    spdlog::info("max record len: {}", max_bam_len);
     return 0;
 
 #endif
@@ -365,6 +369,8 @@ int doSort() {
     // 打开文件
     FILE *fpr = fopen(nsgv::gSortArg.INPUT_FILE.c_str(), "rb");
 
+    // threadRead(fpr); exit(0);
+
     parseSamHeader(fpr, nsgv::gInHdr);
 
     //    FILE *fpw = fopen(nsgv::gSortArg.OUTPUT_FILE.c_str(), "rb");
@@ -449,6 +455,7 @@ int doSort() {
     PROF_G_END(read);
 
     while (readState > 0) {
+        //spdlog::info("readState-0: {}", readState);
         //    while (readState > 0) {
         PROF_G_BEG(parse_block);
         curStartAddrArr->clear();
@@ -477,6 +484,7 @@ int doSort() {
         // exit(0);
 
         READ_BLOCKS;
+        // spdlog::info("read block len: {}", blockLen);
 
         // spdlog::info("cur block size: {}", curStartAddrArr->size());
 
@@ -513,12 +521,14 @@ int doSort() {
         SWITCH_POINTER;
 
         PROF_G_BEG(read);
-        // readState = fread(curBuf, 1, READ_BUFSIZE, fpr);
+        readState = fread(curBuf, 1, READ_BUFSIZE, fpr);
+        //spdlog::info("readState: {}", readState);
         PROF_G_BEG(mem_copy);
-        memcpy(curBuf, fbuf[4], READ_BUFSIZE); readState = READ_BUFSIZE;
+        // memcpy(curBuf, fbuf[4], readState); readState = READ_BUFSIZE;
+        memcpy(curBuf, fbuf[4], readState);
         PROF_G_END(mem_copy);
         PROF_G_END(read);
-        if (fsize >= 6245369164) break;
+        // if (fsize >= 6245369164) break;
     }
     pthread_join(uncompressTid, NULL);
     PROF_G_END(mid_all);
diff --git a/src/sort/sort_impl.h b/src/sort/sort_impl.h
index ebe7e11..6948de2 100644
--- a/src/sort/sort_impl.h
+++ b/src/sort/sort_impl.h
@@ -20,7 +20,7 @@ struct TemplateCoordinateKey {
 // Struct which contains the a record, and the pointer to the sort tag (if any) or
 // a combined ref / position / strand.
 // Used to speed up sorts (coordinate, by-tag, and template-coordinate).
-typedef struct BamSortTag {
+struct BamSortTag {
     bam1_t *bam_record;
     union {
         const uint8_t *tag;