refactor: add .bz2 support for fasta&fastq file format

chungongyu · Jul 12, 2020 · 6fbad8c · 6fbad8c
1 parent 05b79c3
commit 6fbad8c
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Showing 2 changed files with 6 additions and 1 deletion.
diff --git a/src/constant.h b/src/constant.h
@@ -10,6 +10,7 @@
 #define ASQG_EXT ".asqg"
 #define HITS_EXT ".hits"
 #define GZIP_EXT ".gz"
+#define BZIP_EXT ".bz2"
 #define RMDUP_EXT ".rmdup"
 #define EC_EXT ".ec"
 #define FA_EXT ".fa"

diff --git a/src/utils.cpp b/src/utils.cpp
@@ -3,8 +3,8 @@
 
 #include <boost/algorithm/string.hpp>
 #include <boost/iostreams/device/file_descriptor.hpp>
-#include <boost/iostreams/filtering_streambuf.hpp>
 #include <boost/iostreams/filtering_stream.hpp>
+#include <boost/iostreams/filter/bzip2.hpp>
 #include <boost/iostreams/filter/gzip.hpp>
 
 #include <log4cxx/logger.h>
@@ -17,6 +17,8 @@ namespace Utils {
  try {
  if (boost::algorithm::ends_with(filename, GZIP_EXT)) {
  stream->push(boost::iostreams::gzip_decompressor());
+ } else if (boost::algorithm::ends_with(filename, BZIP_EXT)) {
+ stream->push(boost::iostreams::bzip2_decompressor());
  }
  stream->push(boost::iostreams::file_descriptor_source(filename));
  } catch (...) {
@@ -29,6 +31,8 @@ namespace Utils {
  try {
  if (boost::algorithm::ends_with(filename, GZIP_EXT)) {
  stream->push(boost::iostreams::gzip_compressor());
+ } else if (boost::algorithm::ends_with(filename, BZIP_EXT)) {
+ stream->push(boost::iostreams::bzip2_compressor());
  }
  stream->push(boost::iostreams::file_descriptor_sink(filename));
  } catch (...) {