diff --git a/CMakeLists.txt b/CMakeLists.txt
index 10d68db86..1dcd4d375 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -317,6 +317,7 @@ set(GNSSSDR_BOOST_MIN_VERSION "1.45")
 set(GNSSSDR_PYTHON_MIN_VERSION "2.7")
 set(GNSSSDR_MAKO_MIN_VERSION "0.4.2")
 set(GNSSSDR_ARMADILLO_MIN_VERSION "4.200.0")
+set(GNSSSDR_MATIO_MIN_VERSION "1.5.3")
 
 
 
@@ -1094,7 +1095,12 @@ endif(NOT GNUTLS_OPENSSL_LIBRARY)
 # Matio - https://github.com/tbeu/matio
 ########################################################################
 find_package(MATIO)
-if(NOT MATIO_FOUND)
+if(NOT MATIO_FOUND OR MATIO_VERSION_STRING VERSION_LESS ${GNSSSDR_MATIO_MIN_VERSION})
+    if(MATIO_FOUND)
+         message(STATUS " Matio installed version (${MATIO_VERSION_STRING}) is too old (>= ${GNSSSDR_MATIO_MIN_VERSION} is required).")
+    endif(MATIO_FOUND)
+    message(STATUS " Matio will be downloaded and built automatically")
+    message(STATUS " when doing '${CMAKE_MAKE_PROGRAM_PRETTY_NAME}'. ")
     find_package(ZLIB)
     if(ZLIB_FOUND)
         get_filename_component(ZLIB_BASE_DIR ${ZLIB_INCLUDE_DIRS} DIRECTORY)
@@ -1112,7 +1118,7 @@ if(NOT MATIO_FOUND)
                 message(FATAL_ERROR "libtool is required to build matio from source")
             endif(NOT EXISTS "/usr/bin/libtoolize")
             if(EXISTS "/usr/bin/aclocal-1.15" OR EXISTS "/usr/bin/aclocal-1.14" OR EXISTS "/usr/bin/aclocal-1.13" OR EXISTS "/usr/bin/aclocal-1.11"  OR EXISTS "/usr/bin/aclocal-1.10")
-                message(STATUS "aclocal found")
+                message(STATUS "Automake found.")
             else(EXISTS "/usr/bin/aclocal-1.15" OR EXISTS "/usr/bin/aclocal-1.14" OR EXISTS "/usr/bin/aclocal-1.13" OR EXISTS "/usr/bin/aclocal-1.11"  OR EXISTS "/usr/bin/aclocal-1.10")
                 message(" aclocal has not been found.")
                 message(" You can try to install it by typing:")
@@ -1182,7 +1188,7 @@ if(NOT MATIO_FOUND)
     else(ZLIB_FOUND)
         message(FATAL_ERROR "*** The zlib library is required to build gnss-sdr")
     endif(ZLIB_FOUND)
-endif(NOT MATIO_FOUND)
+endif(NOT MATIO_FOUND OR MATIO_VERSION_STRING VERSION_LESS ${GNSSSDR_MATIO_MIN_VERSION})
 
 
 
diff --git a/docs/manpage/gnss-sdr-manpage b/docs/manpage/gnss-sdr-manpage
index f7a9c17f6..06cf36465 100644
--- a/docs/manpage/gnss-sdr-manpage
+++ b/docs/manpage/gnss-sdr-manpage
@@ -1,10 +1,10 @@
 .\" Manpage for gnss\-sdr.
 .\" Contact carles.fernandez@cttc.es to correct errors or typos.
-.TH gnss\-sdr 1 "05 Feb 2017" "0.0.9" "gnss\-sdr man page"
+.TH gnss\-sdr 1 "24 Feb 2018" "0.0.9" "gnss\-sdr man page"
 .SH NAME
 \fBgnss\-sdr\fR \- GNSS Software Defined Receiver.
 .SH SYNOPSIS
-\fBgnss\-sdr \-config_file=\fR\fI<path\-to\-configuration\-file>\fR [OPTION]...
+\fBgnss\-sdr \-c=\fR\fI<path\-to\-configuration\-file>\fR [OPTION]...
 .SH DESCRIPTION
 \fBgnss\-sdr\fR is a Global Navigation Satellite Systems Software Defined Receiver written in C++. It implements all the signal processing chain, taking as input raw samples coming from the output of an Analog\-to\-Digital Converter, and processing them up to the computation of the Position\-Velocity\-Time solution, including the generation of code and phase measurements. 
 \.TP
@@ -12,31 +12,47 @@
 .SH OPTIONS
 \fBgnss\-sdr\fR takes the following options:
 .TP
-\fB\-config_file=\fR\fI<path\-to\-configuration\-file>\fR Set the configuration file.
+\fB\-c=\fR\fI<path\-to\-configuration\-file>\fR or \fB\-config_file=\fR\fI<path\-to\-configuration\-file>\fR
+Set the configuration file.
 .TP 
-\fB\-signal_source=\fR\fI<path\-to\-raw\-signal\-file>\fR If defined, path to the file containing the signal samples (overrides the data file specified in the configuration file).
+\fB\-s=\fR\fI<path\-to\-raw\-signal\-file>\fR or \fB\-signal_source=\fR\fI<path\-to\-raw\-signal\-file>\fR 
+If defined, path to the file containing the signal samples (overrides the data file specified in the configuration file).
 .TP 
-\fB\-log_dir=\fR\fI<path\-to\-directory>\fR If defined, overrides the default directory where logs are saved.
+\fB\-log_dir=\fR\fI<path\-to\-directory>\fR
+If defined, overrides the default directory where logs are saved.
 .TP
-\fB\-doppler_max=\fR\fIdoppler\fR If defined, maximum Doppler value in the search grid, in Hz (overrides the configuration file),
+\fB\-doppler_max=\fR\fI<doppler_max>\fR
+If defined, maximum Doppler value in the search grid, in Hz (overrides the configuration file).
 .TP
-\fB\-cn0_samples=\fR\fIsamples\fR Number of correlator outputs used for CN0 estimation.
+\fB\-doppler_step=\fR\fI<doppler_step>\fR
+If defined, sets the frequency step in the search grid, in Hz (overrides the configuration file).
 .TP
-\fB\-cn0_min=\fR\fIcn0_min\fR Minimum valid CN0 (in dB-Hz).
+\fB\-cn0_samples=\fR\fI<samples>\fR
+Number of correlators outputs (one per integration time) used for CN0 estimation. It defaults to 20 outputs.
 .TP
-\fB\-max_lock_fail=\fR\fImax_lock_fail\fR Number number of lock failures before dropping satellite.
+\fB\-cn0_min=\fR\fI<cn0_min>\fR
+Minimum valid CN0 (in dB-Hz). It defaults to 25 dB-Hz.
 .TP
-\fB\-carrier_lock_th=\fR\fIcarrier_lock_th\fR Carrier lock threshold (in rad).
+\fB\-max_lock_fail=\fR\fI<max_lock_fail>\fR
+Number of lock failures before dropping satellite. It defaults to 50 failures.
 .TP
-\fB\-dll_bw_hz=\fR\fIdll_bw_hz\fR If defined, bandwidth of the DLL low pass filter, in Hz (overrides the configuration file).
+\fB\-carrier_lock_th=\fR\fI<carrier_lock_th>\fR
+Carrier lock error threshold (in rad). It defaults to 0.85 rad (48.7 degrees).
 .TP
-\fB\-pll_bw_hz=\fR\fIpll_bw_hz\fR If defined, bandwidth of the PLL low pass filter, in Hz (overrides the configuration file).
+\fB\-dll_bw_hz=\fR\fI<dll_bw_hz>\fR
+If defined, bandwidth of the DLL low pass filter, in Hz (overrides the configuration file).
 .TP
-\fB\-RINEX_version=\fI<version>\fR Specifies the RINEX version (2.11 or 3.02). Default: "3.02".
+\fB\-pll_bw_hz=\fR\fI<pll_bw_hz>\fR
+If defined, bandwidth of the PLL low pass filter, in Hz (overrides the configuration file).
 .TP
-\fB\-version\fR Print program version and exit.
+\fB\-RINEX_version=\fI<version>\fR
+If defined, specifies the RINEX version (2.11 or 3.02). Default: "3.02". Overrides the configuration file.
 .TP
-\fB\-help\fR Print all the available commandline flags and exit.
+\fB\-version\fR
+Print program version and exit.
+.TP
+\fB\-help\fR
+Print all the available commandline flags and exit.
 .SH SEE ALSO
 .BR volk_gnsssdr_profile (1)
 \.TP
diff --git a/src/algorithms/PVT/adapters/CMakeLists.txt b/src/algorithms/PVT/adapters/CMakeLists.txt
index baf58e507..71568cf88 100644
--- a/src/algorithms/PVT/adapters/CMakeLists.txt
+++ b/src/algorithms/PVT/adapters/CMakeLists.txt
@@ -28,6 +28,7 @@ include_directories(
      ${CMAKE_SOURCE_DIR}/src/algorithms/PVT/gnuradio_blocks
      ${CMAKE_SOURCE_DIR}/src/algorithms/PVT/libs
      ${CMAKE_SOURCE_DIR}/src/algorithms/libs/rtklib
+     ${CMAKE_SOURCE_DIR}/src/algorithms/libs
      ${ARMADILLO_INCLUDE_DIRS}
      ${Boost_INCLUDE_DIRS}
      ${GLOG_INCLUDE_DIRS}
diff --git a/src/algorithms/PVT/adapters/rtklib_pvt.cc b/src/algorithms/PVT/adapters/rtklib_pvt.cc
index c21303ab3..967109d53 100644
--- a/src/algorithms/PVT/adapters/rtklib_pvt.cc
+++ b/src/algorithms/PVT/adapters/rtklib_pvt.cc
@@ -36,7 +36,7 @@
 #include <boost/math/common_factor_rt.hpp>
 #include <boost/serialization/map.hpp>
 #include "configuration_interface.h"
-
+#include "gnss_sdr_flags.h"
 
 using google::LogMessage;
 
@@ -70,11 +70,30 @@ RtklibPvt::RtklibPvt(ConfigurationInterface* configuration,
 
     // RINEX version
     int rinex_version = configuration->property(role + ".rinex_version", 3);
-    if( (rinex_version < 2) || (rinex_version > 3) )
+    if ( FLAGS_RINEX_version.compare("3.01") == 0 )
         {
-            //warn user and set the default
             rinex_version = 3;
         }
+    else if ( FLAGS_RINEX_version.compare("3.02") == 0 )
+        {
+            rinex_version = 3;
+        }
+    else if ( FLAGS_RINEX_version.compare("3") == 0 )
+        {
+            rinex_version = 3;
+        }
+    else if ( FLAGS_RINEX_version.compare("2.11") == 0 )
+        {
+            rinex_version = 2;
+        }
+    else if ( FLAGS_RINEX_version.compare("2.10") == 0 )
+        {
+            rinex_version = 2;
+        }
+    else if ( FLAGS_RINEX_version.compare("2") == 0 )
+        {
+            rinex_version = 2;
+        }
 
     // RTCM Printer settings
     bool flag_rtcm_tty_port = configuration->property(role + ".flag_rtcm_tty_port", false);
diff --git a/src/algorithms/PVT/libs/rinex_printer.cc b/src/algorithms/PVT/libs/rinex_printer.cc
index b2dfa2a68..f1dec9219 100644
--- a/src/algorithms/PVT/libs/rinex_printer.cc
+++ b/src/algorithms/PVT/libs/rinex_printer.cc
@@ -43,7 +43,6 @@
 #include <boost/date_time/local_time/local_time.hpp>
 #include <boost/date_time/posix_time/posix_time.hpp>
 #include <glog/logging.h>
-#include "gnss_sdr_flags.h"
 
 
 using google::LogMessage;
@@ -143,57 +142,17 @@ Rinex_Printer::Rinex_Printer(int conf_version)
     observationCode["GPS_L1_CA_v2"] = "1";
     observationCode["GLONASS_G1_CA_v2"] = "1";
 
-    if ( FLAGS_RINEX_version.compare("3.01") == 0 )
-        {
-            version = 3;
-            stringVersion = "3.01";
-        }
-    else if ( FLAGS_RINEX_version.compare("3.02") == 0 )
-        {
-            version = 3;
-            stringVersion = "3.02";
-        }
-    else if ( FLAGS_RINEX_version.compare("3") == 0 )
-        {
-            version = 3;
-            stringVersion = "3.02";
-        }
-    else if ( FLAGS_RINEX_version.compare("2.11") == 0 )
-        {
-            version = 2;
-            stringVersion = "2.11";
-        }
-    else if ( FLAGS_RINEX_version.compare("2.10") == 0 )
-        {
-            version = 2;
-            stringVersion = "2.10";
-        }
-    else if ( FLAGS_RINEX_version.compare("2") == 0 )
+    if(conf_version == 2)
         {
             version = 2;
             stringVersion = "2.11";
         }
     else
         {
-            LOG(WARNING) << "Unknown RINEX version " << FLAGS_RINEX_version << " (must be 2.11 or 3.02). Using 3.02";
             version = 3;
             stringVersion = "3.02";
         }
 
-    if(conf_version != 0)
-        {
-            if(conf_version == 2)
-                {
-                    version = 2;
-                    stringVersion = "2.11";
-                }
-            if(conf_version == 3)
-                {
-                    version = 3;
-                    stringVersion = "3.02";
-                }
-        }
-
     numberTypesObservations = 4; // Number of available types of observable in the system
     fake_cnav_iode = 1;
 }
diff --git a/src/algorithms/channel/adapters/CMakeLists.txt b/src/algorithms/channel/adapters/CMakeLists.txt
index e7c1c8660..b2d74748e 100644
--- a/src/algorithms/channel/adapters/CMakeLists.txt
+++ b/src/algorithms/channel/adapters/CMakeLists.txt
@@ -24,6 +24,7 @@ include_directories(
      ${CMAKE_SOURCE_DIR}/src/core/interfaces
      ${CMAKE_SOURCE_DIR}/src/core/receiver
      ${CMAKE_SOURCE_DIR}/src/algorithms/channel/libs
+     ${CMAKE_SOURCE_DIR}/src/algorithms/libs
      ${GLOG_INCLUDE_DIRS}
      ${GFlags_INCLUDE_DIRS}
      ${Boost_INCLUDE_DIRS}
@@ -34,4 +35,4 @@ file(GLOB CHANNEL_ADAPTER_HEADERS "*.h")
 list(SORT CHANNEL_ADAPTER_HEADERS)
 add_library(channel_adapters ${CHANNEL_ADAPTER_SOURCES} ${CHANNEL_ADAPTER_HEADERS})
 source_group(Headers FILES ${CHANNEL_ADAPTER_HEADERS})
-target_link_libraries(channel_adapters channel_fsm ${GNURADIO_RUNTIME_LIBRARIES} ${Boost_LIBRARIES})
+target_link_libraries(channel_adapters channel_fsm ${GNURADIO_RUNTIME_LIBRARIES} ${Boost_LIBRARIES} gnss_sdr_flags)
diff --git a/src/algorithms/channel/adapters/channel.cc b/src/algorithms/channel/adapters/channel.cc
index e66074b7a..59c56eeee 100644
--- a/src/algorithms/channel/adapters/channel.cc
+++ b/src/algorithms/channel/adapters/channel.cc
@@ -33,6 +33,7 @@
 #include <boost/lexical_cast.hpp>
 #include <glog/logging.h>
 #include "configuration_interface.h"
+#include "gnss_sdr_flags.h"
 
 using google::LogMessage;
 
@@ -74,8 +75,9 @@ Channel::Channel(ConfigurationInterface *configuration, unsigned int channel,
 
     // IMPORTANT: Do not change the order between set_doppler_step and set_threshold
 
-    unsigned int doppler_step = configuration->property("Acquisition_" + implementation_ + boost::lexical_cast<std::string>(channel_) + ".doppler_step" ,0);
-    if(doppler_step == 0) doppler_step = configuration->property("Acquisition_" + implementation_+".doppler_step", 500);
+    unsigned int doppler_step = configuration->property("Acquisition_" + implementation_ + boost::lexical_cast<std::string>(channel_) + ".doppler_step", 0);
+    if(doppler_step == 0) doppler_step = configuration->property("Acquisition_" + implementation_ + ".doppler_step", 500);
+    if(FLAGS_doppler_step != 0) doppler_step = static_cast<unsigned int>(FLAGS_doppler_step);
     DLOG(INFO) << "Channel "<< channel_ << " Doppler_step = " << doppler_step;
 
     acq_->set_doppler_step(doppler_step);
diff --git a/src/algorithms/libs/gnss_sdr_flags.cc b/src/algorithms/libs/gnss_sdr_flags.cc
index ea3d0dfbd..0aa8221b5 100644
--- a/src/algorithms/libs/gnss_sdr_flags.cc
+++ b/src/algorithms/libs/gnss_sdr_flags.cc
@@ -33,29 +33,31 @@
 #include <cstdint>
 #include <iostream>
 
-DEFINE_string(c, "-", "Path to the configuration file (if set, overrides --config_file)");
+DEFINE_string(c, "-", "Path to the configuration file (if set, overrides --config_file).");
 
 DEFINE_string(s, "-",
-        "If defined, path to the file containing the signal samples (overrides the configuration file and --signal_source)");
+        "If defined, path to the file containing the signal samples (overrides the configuration file and --signal_source).");
 
 DEFINE_string(signal_source, "-",
-        "If defined, path to the file containing the signal samples (overrides the configuration file)");
+        "If defined, path to the file containing the signal samples (overrides the configuration file).");
 
-DEFINE_int32(doppler_max, 0, "If defined, maximum Doppler value in the search grid, in Hz (overrides the configuration file)");
+DEFINE_int32(doppler_max, 0, "If defined, sets the maximum Doppler value in the search grid, in Hz (overrides the configuration file).");
 
-DEFINE_int32(cn0_samples, 20, "Number of correlator outputs used for CN0 estimation");
+DEFINE_int32(doppler_step, 0, "If defined, sets the frequency step in the search grid, in Hz (overrides the configuration file).");
 
-DEFINE_int32(cn0_min, 25, "Minimum valid CN0 (in dB-Hz)");
+DEFINE_int32(cn0_samples, 20, "Number of correlator outputs used for CN0 estimation.");
 
-DEFINE_int32(max_lock_fail, 50, "Number number of lock failures before dropping satellite");
+DEFINE_int32(cn0_min, 25, "Minimum valid CN0 (in dB-Hz).");
 
-DEFINE_double(carrier_lock_th, 0.85, "Carrier lock threshold (in rad)");
+DEFINE_int32(max_lock_fail, 50, "Number number of lock failures before dropping satellite.");
 
-DEFINE_string(RINEX_version, "3.02", "Specifies the RINEX version (2.11 or 3.02)");
+DEFINE_double(carrier_lock_th, 0.85, "Carrier lock threshold (in rad).");
 
-DEFINE_double(dll_bw_hz, 0.0, "If defined, bandwidth of the DLL low pass filter, in Hz (overrides the configuration file)");
+DEFINE_string(RINEX_version, "-", "If defined, specifies the RINEX version (2.11 or 3.02). Overrides the configuration file.");
 
-DEFINE_double(pll_bw_hz, 0.0, "If defined, bandwidth of the PLL low pass filter, in Hz (overrides the configuration file)");
+DEFINE_double(dll_bw_hz, 0.0, "If defined, bandwidth of the DLL low pass filter, in Hz (overrides the configuration file).");
+
+DEFINE_double(pll_bw_hz, 0.0, "If defined, bandwidth of the PLL low pass filter, in Hz (overrides the configuration file).");
 
 
 #if GFLAGS_GREATER_2_0
@@ -68,6 +70,14 @@ static bool ValidateDopplerMax(const char* flagname, int32_t value)
     return false;
 }
 
+static bool ValidateDopplerStep(const char* flagname, int32_t value)
+{
+    if (value >= 0 && value < 10000)   // value is ok
+        return true;
+    std::cout << "Invalid value for " << flagname << ": " << value << std::endl;
+    return false;
+}
+
 static bool ValidateCn0Samples(const char* flagname, int32_t value)
 {
     if (value > 0 && value < 10000)   // value is ok
@@ -118,6 +128,7 @@ static bool ValidatePllBw(const char* flagname, double value)
 
 
 DEFINE_validator(doppler_max, &ValidateDopplerMax);
+DEFINE_validator(doppler_step, &ValidateDopplerStep);
 DEFINE_validator(cn0_samples, &ValidateCn0Samples);
 DEFINE_validator(cn0_min, &ValidateCn0Min);
 DEFINE_validator(max_lock_fail, &ValidateMaxLockFail);
diff --git a/src/algorithms/libs/gnss_sdr_flags.h b/src/algorithms/libs/gnss_sdr_flags.h
index 6d36ac087..7ccbdabe5 100644
--- a/src/algorithms/libs/gnss_sdr_flags.h
+++ b/src/algorithms/libs/gnss_sdr_flags.h
@@ -34,28 +34,29 @@
 
 #include <gflags/gflags.h>
 
-DECLARE_string(c);                  //<! Path to the configuration file
-DECLARE_string(config_file);        //<! Path to the configuration file
+DECLARE_string(c);                  //<! Path to the configuration file.
+DECLARE_string(config_file);        //<! Path to the configuration file.
 
-DECLARE_string(log_dir);            //<! Path to the folder in which logging will be stored
+DECLARE_string(log_dir);            //<! Path to the folder in which logging will be stored.
 
 // Declare flags for signal sources
-DECLARE_string(s);                  //<! Path to the file containing the signal samples
-DECLARE_string(signal_source);      //<! Path to the file containing the signal samples
+DECLARE_string(s);                  //<! Path to the file containing the signal samples.
+DECLARE_string(signal_source);      //<! Path to the file containing the signal samples.
 
 // Declare flags for acquisition blocks
-DECLARE_int32(doppler_max);        //<!If defined, maximum Doppler value in the search grid, in Hz (overrides the configuration file)
+DECLARE_int32(doppler_max);         //<! If defined, maximum Doppler value in the search grid, in Hz (overrides the configuration file).
+DECLARE_int32(doppler_step);        //<! If defined, sets the frequency step in the search grid, in Hz, in Hz (overrides the configuration file).
 
 // Declare flags for tracking blocks
-DECLARE_int32(cn0_samples);        //<! Number of correlator outputs used for CN0 estimation
-DECLARE_int32(cn0_min);            //<! Minimum valid CN0 (in dB-Hz)
-DECLARE_int32(max_lock_fail);      //<! Number number of lock failures before dropping satellite
-DECLARE_double(carrier_lock_th);    //<! Carrier lock threshold (in rad)
-DECLARE_double(dll_bw_hz);          //<! Bandwidth of the DLL low pass filter, in Hz (overrides the configuration file)
-DECLARE_double(pll_bw_hz);          //<! Bandwidth of the PLL low pass filter, in Hz (overrides the configuration file)
+DECLARE_int32(cn0_samples);         //<! Number of correlator outputs used for CN0 estimation.
+DECLARE_int32(cn0_min);             //<! Minimum valid CN0 (in dB-Hz).
+DECLARE_int32(max_lock_fail);       //<! Number number of lock failures before dropping satellite.
+DECLARE_double(carrier_lock_th);    //<! Carrier lock threshold (in rad).
+DECLARE_double(dll_bw_hz);          //<! Bandwidth of the DLL low pass filter, in Hz (overrides the configuration file).
+DECLARE_double(pll_bw_hz);          //<! Bandwidth of the PLL low pass filter, in Hz (overrides the configuration file).
 
 // Declare flags for PVT
-DECLARE_string(RINEX_version);      //<! RINEX version
+DECLARE_string(RINEX_version);      //<! If defined, specifies the RINEX version (2.11 or 3.02). Overrides the configuration file.
 
 
 #endif
diff --git a/src/main/main.cc b/src/main/main.cc
index af45ab3a7..493332ec3 100644
--- a/src/main/main.cc
+++ b/src/main/main.cc
@@ -44,7 +44,9 @@
 #include <memory>
 #include <boost/exception/diagnostic_information.hpp>
 #include <boost/exception_ptr.hpp>
-#include <boost/filesystem.hpp>
+#include <boost/filesystem/operations.hpp>     // for create_directories, exists
+#include <boost/filesystem/path.hpp>           // for path, operator<<
+#include <boost/filesystem/path_traits.hpp>    // for filesystem
 #include <glog/logging.h>
 #include "control_thread.h"
 #include "concurrent_queue.h"