Merge pull request #44 from smithlabcode/update_format_tool

Update format command

Author: andrewdavidsmith

README.md

@@ -12,7 +12,7 @@ sequencing (RRBS). These tools focus on overcoming the computing
 challenges imposed by the scale of genome-wide DNA methylation data,
 which is usually the early parts of data analysis.
 
-## Installing release 1.2.2
+## Installing release 1.2.3
 
 The documentation for DNMTools can be found
 [here](https://dnmtools.readthedocs.io). But if you want to install
@@ -22,34 +22,38 @@ all the formatting.
 
 ### Required libraries
 
-* A recent compiler: most users will be building and installing this
+* A recent compiler. Most users will be building and installing this
   software with GCC. We require a compiler that fully supports C++11,
   so we recommend using at least GCC 5.8. There are still many systems
   that install a very old version of GCC by default, so if you have
   problems with building this software, that might be the first thing
   to check.
-* The GNU Scientific Library: this has always been required. It can be
-  installed using `apt` on Linux (Ubuntu, Debian), using `brew` on
-  macOS, or from source available
+* The GNU Scientific Library. It can be installed using apt on Linux
+  (Ubuntu, Debian), using brew on macOS, or from source available
   [here](http://www.gnu.org/software/gsl).
 * The Zlib compression library. Most likely you already have this
-  installed on your system. If not, it can be installed using `apt` on
+  installed on your system. If not, it can be installed using apt on
   Linux (Ubuntu, Debian) through the package `zlib1g-dev`. On macOS,
-  Zlib can be installed with `brew`.
-* The HTSlib library, which can be installed through `brew` on macOS,
-  through `apt` on Linux (Ubuntu, Debian), or from source downloadable
+  Zlib can be installed with brew (I have not needed to install this
+  separately on any macOS).
+* The HTSlib library. This can be installed through brew on macOS,
+  through apt on Linux (Ubuntu, Debian), or from source downloadable
   [here](https://github.com/samtools/htslib).
 
+All the above can also be installed using conda. If you use conda for
+these dependencies, even if you are building dnmtools from the source
+repo, it is easiest if all dependencies are available through conda.
+
 ### Configuration
 
-* Download [dnmtools-1.2.2.tar.gz](https://github.com/smithlabcode/dnmtools/releases/download/v1.2.2/dnmtools-1.2.2.tar.gz).
+* Download [dnmtools-1.2.3.tar.gz](https://github.com/smithlabcode/dnmtools/releases/download/v1.2.3/dnmtools-1.2.3.tar.gz).
 * Unpack the archive:
 ```console
-tar -zxvf dnmtools-1.2.2.tar.gz
+tar -zxvf dnmtools-1.2.3.tar.gz
 ```
 * Move into the dnmtools directory and create a build directory:
 ```console
-cd dnmtools-1.2.2 && mkdir build && cd build
+cd dnmtools-1.2.3 && mkdir build && cd build
 ```
 * Run the configuration script:
 ```console

configure.ac

@@ -14,10 +14,9 @@ dnl but WITHOUT ANY WARRANTY; without even the implied warranty of
 dnl MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 dnl General Public License for more details.
 
-AC_INIT([dnmtools], [1.2.2], [andrewds@usc.edu],
+AC_INIT([dnmtools], [1.2.3], [andrewds@usc.edu],
         [dnmtools], [https://github.com/smithlabcode/dnmtools])
-dnl the config.h is not currently #included in the source, and only
-dnl used to keep command lines short.
+dnl the config.h is #included in the sources for version info
 AC_CONFIG_HEADERS([config.h])
 AM_INIT_AUTOMAKE([subdir-objects foreign])
 

src/dnmtools.cpp

@@ -18,6 +18,8 @@
 #include <string>
 #include <cstring>
 
+#include <config.h>
+
 using std::string;
 using std::to_string;
 using std::cerr;
@@ -66,7 +68,7 @@ void
 print_help() {
   static const string sep = "  ";
   cout <<  "Program: " << PROGRAM_NAME << "\n";
-  cout <<  "Version: " << PROGRAM_VERSION << "\n";
+  cout <<  "Version: " << VERSION << "\n";
   cout <<  "Usage: " << PROGRAM_NAME << " <command> [options]\n";
   cout <<  "Commands:";