From 2f82110b0ca1e637403fa7d17ab18f100c3cf337 Mon Sep 17 00:00:00 2001
From: guilhermesena1 <desenabr@usc.edu>
Date: Sat, 10 Sep 2022 19:41:43 +0100
Subject: [PATCH] replacing heap allocation of read strings with malloc to
 statically allocate arrays whose size is on par with current maximum read
 lengths

---
 src/StreamReader.cpp | 26 +++++++++++++++-----------
 src/StreamReader.hpp | 12 ++++++------
 2 files changed, 21 insertions(+), 17 deletions(-)

diff --git a/src/StreamReader.cpp b/src/StreamReader.cpp
index 6afbb61..729d428 100644
--- a/src/StreamReader.cpp
+++ b/src/StreamReader.cpp
@@ -618,6 +618,7 @@ FastqReader::FastqReader(FalcoConfig &_config,
                          const size_t _buffer_size) :
   StreamReader(_config, _buffer_size,
                get_line_separator(_config.filename), get_line_separator(_config.filename)) {
+  filebuf = (char*)malloc(RESERVE_SIZE);
 }
 
 size_t
@@ -658,7 +659,7 @@ FastqReader::~FastqReader() {
 // Parses fastq gz by reading line by line into the gzbuf
 inline bool
 FastqReader::read_entry(FastqStats &stats, size_t &num_bytes_read) {
-  cur_char = fgets(filebuf, kChunkSize, fileobj);
+  cur_char = fgets(filebuf, RESERVE_SIZE, fileobj);
 
   // need to check here if we did not hit eof
   if (is_eof())
@@ -669,15 +670,15 @@ FastqReader::read_entry(FastqStats &stats, size_t &num_bytes_read) {
   read_tile_line(stats);
   skip_separator();
 
-  cur_char = fgets(filebuf, kChunkSize, fileobj);
+  cur_char = fgets(filebuf, RESERVE_SIZE, fileobj);
   read_sequence_line(stats);
   skip_separator();
 
-  cur_char = fgets(filebuf, kChunkSize, fileobj);
+  cur_char = fgets(filebuf, RESERVE_SIZE, fileobj);
   read_fast_forward_line();
   skip_separator();
 
-  cur_char = fgets(filebuf, kChunkSize, fileobj);
+  cur_char = fgets(filebuf, RESERVE_SIZE, fileobj);
   read_quality_line(stats);
   skip_separator();
 
@@ -702,6 +703,7 @@ FastqReader::read_entry(FastqStats &stats, size_t &num_bytes_read) {
 GzFastqReader::GzFastqReader(FalcoConfig &_config,
                              const size_t _buffer_size) :
   StreamReader(_config, _buffer_size, '\n', '\n') {
+  gzbuf = (char*)malloc(RESERVE_SIZE);
 }
 
 // Load fastq with zlib
@@ -729,7 +731,7 @@ GzFastqReader::~GzFastqReader() {
 // Parses fastq gz by reading line by line into the gzbuf
 inline bool
 GzFastqReader::read_entry(FastqStats &stats, size_t &num_bytes_read) {
-  cur_char = gzgets(fileobj, gzbuf, kChunkSize);
+  cur_char = gzgets(fileobj, gzbuf, RESERVE_SIZE);
 
   // need to check here if we did not hit eof
   if (is_eof()) {
@@ -740,15 +742,15 @@ GzFastqReader::read_entry(FastqStats &stats, size_t &num_bytes_read) {
   read_tile_line(stats);
   skip_separator();
 
-  cur_char = gzgets(fileobj, gzbuf, kChunkSize);
+  cur_char = gzgets(fileobj, gzbuf, RESERVE_SIZE);
   read_sequence_line(stats);
   skip_separator();
 
-  cur_char = gzgets(fileobj, gzbuf, kChunkSize);
+  cur_char = gzgets(fileobj, gzbuf, RESERVE_SIZE);
   read_fast_forward_line();
   skip_separator();
 
-  cur_char = gzgets(fileobj, gzbuf, kChunkSize);
+  cur_char = gzgets(fileobj, gzbuf, RESERVE_SIZE);
   read_quality_line(stats);
   skip_separator();
 
@@ -773,7 +775,9 @@ GzFastqReader::read_entry(FastqStats &stats, size_t &num_bytes_read) {
 SamReader::SamReader(FalcoConfig &_config,
                      const size_t _buffer_size) :
   StreamReader(_config, _buffer_size,
-               '\t', get_line_separator(_config.filename)) {}
+               '\t', get_line_separator(_config.filename)) {
+  filebuf = (char*)malloc(RESERVE_SIZE);
+}
 
 size_t
 SamReader::load() {
@@ -786,7 +790,7 @@ SamReader::load() {
   // skip sam header
   while (!is_eof() && ((*cur_char = fgetc(fileobj)) == '@')) {
     ungetc(*cur_char, fileobj);
-    cur_char = fgets(filebuf, kChunkSize, fileobj);
+    cur_char = fgets(filebuf, RESERVE_SIZE, fileobj);
   }
   return get_file_size(filename);
 }
@@ -798,7 +802,7 @@ SamReader::is_eof() {
 
 inline bool
 SamReader::read_entry(FastqStats &stats, size_t &num_bytes_read) {
-  cur_char = fgets(filebuf, kChunkSize, fileobj);
+  cur_char = fgets(filebuf, RESERVE_SIZE, fileobj);
 
   if (is_eof()) return false;
   do_read = (stats.num_reads == next_read);
diff --git a/src/StreamReader.hpp b/src/StreamReader.hpp
index c8d9962..c48ec60 100644
--- a/src/StreamReader.hpp
+++ b/src/StreamReader.hpp
@@ -185,8 +185,8 @@ class StreamReader{
 /*******************************************************/
 class FastqReader : public StreamReader {
  private:
-  static const size_t kChunkSize = (1<<20);
-  char filebuf[kChunkSize];
+  static const size_t RESERVE_SIZE = (1<<26);
+  char *filebuf;
   FILE *fileobj;
 
  public:
@@ -203,8 +203,8 @@ class FastqReader : public StreamReader {
 /*******************************************************/
 class GzFastqReader : public StreamReader {
  private:
-  static const size_t kChunkSize = (1<<20);
-  char gzbuf[kChunkSize];
+  static const size_t RESERVE_SIZE = (1<<26);
+  char *gzbuf;
   gzFile fileobj;
 
  public:
@@ -221,8 +221,8 @@ class GzFastqReader : public StreamReader {
 
 class SamReader : public StreamReader {
  private:
-  static const size_t kChunkSize = (1<<20);
-  char filebuf[kChunkSize];
+  static const size_t RESERVE_SIZE = (1<<26);
+  char *filebuf;
   FILE *fileobj;
 
  public: