From 05379269d3e88d596b0d3c331cc4d5548f2d912f Mon Sep 17 00:00:00 2001
From: Chris Dyer <redpony@gmail.com>
Date: Fri, 22 May 2015 12:39:25 -0400
Subject: read gz files

---
 extractor/CMakeLists.txt | 2 +-
 extractor/alignment.cc   | 5 ++++-
 extractor/data_array.cc  | 8 ++++++--
 3 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/extractor/CMakeLists.txt b/extractor/CMakeLists.txt
index 93a524cc..c8998e91 100644
--- a/extractor/CMakeLists.txt
+++ b/extractor/CMakeLists.txt
@@ -56,7 +56,7 @@ endif(GTEST_FOUND)
 
 set(sacompile_SRCS sacompile.cc)
 add_executable(sacompile ${sacompile_SRCS})
-target_link_libraries(sacompile extractor ${Boost_LIBRARIES} z)
+target_link_libraries(sacompile extractor utils ${Boost_LIBRARIES} z)
 
 set(run_extractor_SRCS run_extractor.cc)
 add_executable(run_extractor ${run_extractor_SRCS})
diff --git a/extractor/alignment.cc b/extractor/alignment.cc
index 4a7a14f4..3f9bc630 100644
--- a/extractor/alignment.cc
+++ b/extractor/alignment.cc
@@ -7,6 +7,8 @@
 #include <unistd.h>
 #include <vector>
 
+#include "filelib.h"
+
 #include <boost/algorithm/string.hpp>
 
 using namespace std;
@@ -14,7 +16,8 @@ using namespace std;
 namespace extractor {
 
 Alignment::Alignment(const string& filename) {
-  ifstream infile(filename.c_str());
+  ReadFile rf(filename);
+  istream& infile = *rf.stream();
   string line;
   while (getline(infile, line)) {
     vector<string> items;
diff --git a/extractor/data_array.cc b/extractor/data_array.cc
index 9612aa8a..130cd99b 100644
--- a/extractor/data_array.cc
+++ b/extractor/data_array.cc
@@ -5,6 +5,8 @@
 #include <sstream>
 #include <string>
 
+#include "filelib.h"
+
 using namespace std;
 
 namespace extractor {
@@ -20,7 +22,8 @@ DataArray::DataArray() {
 
 DataArray::DataArray(const string& filename) {
   InitializeDataArray();
-  ifstream infile(filename.c_str());
+  ReadFile rf(filename);
+  istream& infile = *rf.stream();
   vector<string> lines;
   string line;
   while (getline(infile, line)) {
@@ -31,7 +34,8 @@ DataArray::DataArray(const string& filename) {
 
 DataArray::DataArray(const string& filename, const Side& side) {
   InitializeDataArray();
-  ifstream infile(filename.c_str());
+  ReadFile rf(filename);
+  istream& infile = *rf.stream();
   vector<string> lines;
   string line, delimiter = "|||";
   while (getline(infile, line)) {
-- 
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