updated manual, default version, version code

CMakeLists.txt

@@ -64,7 +64,7 @@ ENDIF()
 
 # extract project info
 IF(GIT_COMMIT_ID MATCHES
-  "^v?([0-9]+)?\\.?([0-9]+)?\\.?([0-9]+)?(-([a-zA-Z]+))?(-([0-9]+-g[0-9A-Fa-f]+(-dirty)?))?$" )
+  "^v?([0-9]+)\\.([0-9]+)\\.?([0-9]+)?((-[a-zA-Z]+)?(-[0-9]+)?(-g[0-9A-Fa-f]+)?(-dirty)?)$" )
   IF(NOT DEFINED DNG_VERSION_MAJOR)
     SET(DNG_VERSION_MAJOR "${CMAKE_MATCH_1}")
   ENDIF()
@@ -75,15 +75,23 @@ IF(GIT_COMMIT_ID MATCHES
     SET(DNG_VERSION_PATCH "${CMAKE_MATCH_3}")
   ENDIF()
   IF(NOT DEFINED DNG_VERSION_COMMIT)
-    SET(DNG_VERSION_COMMIT "${CMAKE_MATCH_7}")
+    STRING(REGEX REPLACE "^-" "" DNG_VERSION_COMMIT "${CMAKE_MATCH_4}")
   ENDIF()
 ELSE()
   # We were unable to determine project information, use the default values
   INCLUDE("${CMAKE_CURRENT_SOURCE_DIR}/src/version.h.in")
 ENDIF()
 
-SET(DNG_VERSION "${DNG_VERSION_MAJOR}.${DNG_VERSION_MINOR}.${DNG_VERSION_PATCH}-${DNG_VERSION_COMMIT}")
-SET(DNG_VERSION_SHORT "${DNG_VERSION_MAJOR}.${DNG_VERSION_MINOR}.${DNG_VERSION_PATCH}")
+SET(DNG_VERSION "${DNG_VERSION_MAJOR}.${DNG_VERSION_MINOR}")
+SET(DNG_VERSION_SHORT "${DNG_VERSION_MAJOR}.${DNG_VERSION_MINOR}")
+IF(DEFINED DNG_VERSION_PATCH)
+  SET(DNG_VERSION "${DNG_VERSION}.${DNG_VERSION_PATCH}")
+  SET(DNG_VERSION_SHORT "${DNG_VERSION_SHORT}.${DNG_VERSION_PATCH}")
+ENDIF()
+IF(DNG_VERSION_COMMIT)
+  SET(DNG_VERSION "${DNG_VERSION}-${DNG_VERSION_COMMIT}")
+  SET(DNG_VERSION_SHORT "${DNG_VERSION_SHORT}-${DNG_VERSION_COMMIT}")	
+ENDIF()
 
 MESSAGE(STATUS "${DNG_NAME} version is ${DNG_VERSION}")
 

README.md

@@ -4,31 +4,32 @@ Authors: Don Conrad, Avinash Ramu, Kael Dai, and Reed A. Cartwright.
 
 ## RELEASE NOTES
 v1.1
-Main program now called 'dng'
-Added experimental 'dng call' module.
-DeNovoGear now requires CMake 3.1+, Boost 1.47+, and Eigen 3+.
+Main program now called 'dng'  
+Added experimental 'dng call' module.  
+DeNovoGear now requires CMake 3.1+, Boost 1.47+, and Eigen 3+.  
 
 v1.0
-made changes to indel_mrate parameter
-better indenting
-mu_scale scales indel mutation rate linearly
+made changes to indel_mrate parameter  
+better indenting  
+mu_scale scales indel mutation rate linearly  
 
 v0.5.4
-added GPL v3
-updated output fields for indels, snps to be the same
+added GPL v3  
+updated output fields for indels, snps to be the same  
 
 v0.5.3
-removed 'X' allele in VCF op. VCF can be indexed by Tabix, IGVTools and used in Annovar.
-added region based denovo calling on BCF files, invoked with --region flag
-added vcf parser for denovo calling, invoked with --vcf flag
+removed 'X' allele in VCF op. VCF can be indexed by Tabix, IGVTools and used in Annovar.  
+added region based denovo calling on BCF files, invoked with --region flag  
+added vcf parser for denovo calling, invoked with --vcf flag  
 
 v0.5.2
-Added read-depth, posterior-probability filters.
-Output number of sites in the BCF and number of sites passing filters.
-Modified paired caller output.
+Added read-depth, posterior-probability filters.  
+Output number of sites in the BCF and number of sites passing filters.  
+Modified paired caller output.  
 
 v0.5.1
-Fixed bug in triallelic configuration. Some trialleic denovo configurations were being called incorrectly.
+Fixed bug in triallelic configuration.  
+Some trialleic denovo configurations were being called incorrectly.
 
 ## DEPENDENCIES
 

src/version.h.in

@@ -4,8 +4,8 @@
 
 #if 0
 SET(DNG_VERSION_MAJOR 1)
-SET(DNG_VERSION_MINOR 0)
-SET(DNG_VERSION_PATCH 2)
+SET(DNG_VERSION_MINOR 1)
+SET(DNG_VERSION_PATCH 0)
 SET(DNG_VERSION_COMMIT "unknown")
 #endif