reHC*, changing name from ZRHC-* to reHCstar-* (3).

yp · May 13, 2011 · 685c8dc · 685c8dc
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commit 685c8dc
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diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -6,7 +6,7 @@
 cmake_minimum_required (VERSION 2.8)
 project (reHCstar)
 
-set (APPLICATION_NAME "Haplotyping with Recombinations and Errors")
+set (APPLICATION_NAME "Haplotyping with Recombinations, Errors, and Missing Genotypes")
 set (APPLICATION_CODENAME "${PROJECT_NAME}")
 set (APPLICATION_COPYRIGHT_YEARS "2010, 2011")
 set (APPLICATION_VENDOR_ID "org.tecnoparco")

diff --git a/include/application.hpp b/include/application.hpp
@@ -1,7 +1,7 @@
 /**
  *
  *                              reHC-*
- * Haplotype Configuration with Recombinations and Errors
+ * Haplotyping with Recombinations, Errors, and Missing Genotypes
  *
  * Copyright (C) 2010,2011  Yuri Pirola <yuri.pirola(-at-)gmail.com>
  *

diff --git a/include/assertion.hpp b/include/assertion.hpp
@@ -1,7 +1,7 @@
 /**
  *
  *                              reHC-*
- * Haplotype Configuration with Recombinations and Errors
+ * Haplotyping with Recombinations, Errors, and Missing Genotypes
  *
  * Copyright (C) 2010  Yuri Pirola <yuri.pirola(-at-)gmail.com>
  *

diff --git a/include/cms_sat_solver_interface.hpp b/include/cms_sat_solver_interface.hpp
@@ -1,7 +1,7 @@
 /**
  *
  *                              reHC-*
- * Haplotype Configuration with Recombinations and Errors
+ * Haplotyping with Recombinations, Errors, and Missing Genotypes
  *
  * Copyright (C) 2010,2011  Yuri Pirola <yuri.pirola(-at-)gmail.com>
  *

diff --git a/include/data.hpp b/include/data.hpp
@@ -1,7 +1,7 @@
 /**
  *
  *                              reHC-*
- * Haplotype Configuration with Recombinations and Errors
+ * Haplotyping with Recombinations, Errors, and Missing Genotypes
  *
  * Copyright (C) 2010  Yuri Pirola <yuri.pirola(-at-)gmail.com>
  *

diff --git a/include/descriptive_class.hpp b/include/descriptive_class.hpp
@@ -1,7 +1,7 @@
 /**
  *
  *                              reHC-*
- * Haplotype Configuration with Recombinations and Errors
+ * Haplotyping with Recombinations, Errors, and Missing Genotypes
  *
  * Copyright (C) 2010  Yuri Pirola <yuri.pirola(-at-)gmail.com>
  *

diff --git a/include/gender.hpp b/include/gender.hpp
@@ -1,7 +1,7 @@
 /**
  *
  *                              reHC-*
- * Haplotype Configuration with Recombinations and Errors
+ * Haplotyping with Recombinations, Errors, and Missing Genotypes
  *
  * Copyright (C) 2010  Yuri Pirola <yuri.pirola(-at-)gmail.com>
  *

diff --git a/include/haplotypes_genotypes.hpp b/include/haplotypes_genotypes.hpp
@@ -1,7 +1,7 @@
 /**
  *
  *                              reHC-*
- * Haplotype Configuration with Recombinations and Errors
+ * Haplotyping with Recombinations, Errors, and Missing Genotypes
  *
  * Copyright (C) 2010,2011  Yuri Pirola <yuri.pirola(-at-)gmail.com>
  *

diff --git a/include/in-pedigree.hpp b/include/in-pedigree.hpp
@@ -1,7 +1,7 @@
 /**
  *
  *                              reHC-*
- * Haplotype Configuration with Recombinations and Errors
+ * Haplotyping with Recombinations, Errors, and Missing Genotypes
  *
  * Copyright (C) 2010,2011  Yuri Pirola <yuri.pirola(-at-)gmail.com>
  *

diff --git a/include/io-haplotypes_genotypes.hpp b/include/io-haplotypes_genotypes.hpp
@@ -1,7 +1,7 @@
 /**
  *
  *                              reHC-*
- * Haplotype Configuration with Recombinations and Errors
+ * Haplotyping with Recombinations, Errors, and Missing Genotypes
  *
  * Copyright (C) 2010  Yuri Pirola <yuri.pirola(-at-)gmail.com>
  *

diff --git a/include/io-pedigree.hpp b/include/io-pedigree.hpp
@@ -1,7 +1,7 @@
 /**
  *
  *                              reHC-*
- * Haplotype Configuration with Recombinations and Errors
+ * Haplotyping with Recombinations, Errors, and Missing Genotypes
  *
  * Copyright (C) 2010  Yuri Pirola <yuri.pirola(-at-)gmail.com>
  *

diff --git a/include/log.hpp b/include/log.hpp
@@ -1,7 +1,7 @@
 /**
  *
  *                              reHC-*
- * Haplotype Configuration with Recombinations and Errors
+ * Haplotyping with Recombinations, Errors, and Missing Genotypes
  *
  * Copyright (C) 2010,2011  Yuri Pirola <yuri.pirola(-at-)gmail.com>
  *

diff --git a/include/ms_sat_solver_interface.hpp b/include/ms_sat_solver_interface.hpp
@@ -1,7 +1,7 @@
 /**
  *
  *                              reHC-*
- * Haplotype Configuration with Recombinations and Errors
+ * Haplotyping with Recombinations, Errors, and Missing Genotypes
  *
  * Copyright (C) 2010,2011  Yuri Pirola <yuri.pirola(-at-)gmail.com>
  *

diff --git a/include/out-pedigree.hpp b/include/out-pedigree.hpp
@@ -1,7 +1,7 @@
 /**
  *
  *                              reHC-*
- * Haplotype Configuration with Recombinations and Errors
+ * Haplotyping with Recombinations, Errors, and Missing Genotypes
  *
  * Copyright (C) 2010,2011  Yuri Pirola <yuri.pirola(-at-)gmail.com>
  *

diff --git a/include/ped2cnf-constraints.hpp b/include/ped2cnf-constraints.hpp
@@ -1,7 +1,7 @@
 /**
  *
  *                              reHC-*
- * Haplotype Configuration with Recombinations and Errors
+ * Haplotyping with Recombinations, Errors, and Missing Genotypes
  *
  * Copyright (C) 2010,2011  Yuri Pirola <yuri.pirola(-at-)gmail.com>
  *

diff --git a/include/ped2cnf.hpp b/include/ped2cnf.hpp
@@ -1,7 +1,7 @@
 /**
  *
  *                              reHC-*
- * Haplotype Configuration with Recombinations and Errors
+ * Haplotyping with Recombinations, Errors, and Missing Genotypes
  *
  * Copyright (C) 2010,2011  Yuri Pirola <yuri.pirola(-at-)gmail.com>
  *

diff --git a/include/pedcnf.hpp b/include/pedcnf.hpp
@@ -1,7 +1,7 @@
 /**
  *
  *                              reHC-*
- * Haplotype Configuration with Recombinations and Errors
+ * Haplotyping with Recombinations, Errors, and Missing Genotypes
  *
  * Copyright (C) 2010,2011  Yuri Pirola <yuri.pirola(-at-)gmail.com>
  *

diff --git a/include/pedcnf2hc.hpp b/include/pedcnf2hc.hpp
@@ -1,7 +1,7 @@
 /**
  *
  *                              reHC-*
- * Haplotype Configuration with Recombinations and Errors
+ * Haplotyping with Recombinations, Errors, and Missing Genotypes
  *
  * Copyright (C) 2010,2011  Yuri Pirola <yuri.pirola(-at-)gmail.com>
  *

diff --git a/include/pedigree.hpp b/include/pedigree.hpp
@@ -1,7 +1,7 @@
 /**
  *
  *                              reHC-*
- * Haplotype Configuration with Recombinations and Errors
+ * Haplotyping with Recombinations, Errors, and Missing Genotypes
  *
  * Copyright (C) 2010,2011  Yuri Pirola <yuri.pirola(-at-)gmail.com>
  *

diff --git a/include/sat_solver_interface.hpp b/include/sat_solver_interface.hpp
@@ -1,7 +1,7 @@
 /**
  *
  *                              reHC-*
- * Haplotype Configuration with Recombinations and Errors
+ * Haplotyping with Recombinations, Errors, and Missing Genotypes
  *
  * Copyright (C) 2010,2011  Yuri Pirola <yuri.pirola(-at-)gmail.com>
  *

diff --git a/include/utility.hpp b/include/utility.hpp
@@ -1,7 +1,7 @@
 /**
  *
  *                              reHC-*
- * Haplotype Configuration with Recombinations and Errors
+ * Haplotyping with Recombinations, Errors, and Missing Genotypes
  *
  * Copyright (C) 2010,2011  Yuri Pirola <yuri.pirola(-at-)gmail.com>
  *

diff --git a/include/zrhc_app.hpp b/include/zrhc_app.hpp
@@ -1,7 +1,7 @@
 /**
  *
  *                              reHC-*
- * Haplotype Configuration with Recombinations and Errors
+ * Haplotyping with Recombinations, Errors, and Missing Genotypes
  *
  * Copyright (C) 2010,2011  Yuri Pirola <yuri.pirola(-at-)gmail.com>
  *

diff --git a/scripts/evaluate-results.py b/scripts/evaluate-results.py
@@ -4,7 +4,7 @@
 ##########
 #
 #                               reHC-*
-#  Haplotype Configuration with Recombinations and Errors
+#  Haplotyping with Recombinations, Errors, and Missing Genotypes
 #
 #  Copyright (C) 2010,2011  Yuri Pirola <yuri.pirola(-at-)gmail.com>
 #

diff --git a/scripts/execute-ZRHC.sh b/scripts/execute-ZRHC.sh
@@ -3,7 +3,7 @@
 ##########
 #
 #                               reHC-*
-#  Haplotype Configuration with Recombinations and Errors
+#  Haplotyping with Recombinations, Errors, and Missing Genotypes
 #
 #  Copyright (C) 2010,2011  Yuri Pirola <yuri.pirola(-at-)gmail.com>
 #

diff --git a/scripts/generate-instances-JPSGCS.sh b/scripts/generate-instances-JPSGCS.sh
@@ -3,7 +3,7 @@
 ##########
 #
 #                               reHC-*
-#  Haplotype Configuration with Recombinations and Errors
+#  Haplotyping with Recombinations, Errors, and Missing Genotypes
 #
 #  Copyright (C) 2010,2011  Yuri Pirola <yuri.pirola(-at-)gmail.com>
 #

diff --git a/scripts/generate-instances.sh b/scripts/generate-instances.sh
@@ -3,7 +3,7 @@
 ##########
 #
 #                               reHC-*
-#  Haplotype Configuration with Recombinations and Errors
+#  Haplotyping with Recombinations, Errors, and Missing Genotypes
 #
 #  Copyright (C) 2010,2011  Yuri Pirola <yuri.pirola(-at-)gmail.com>
 #

diff --git a/scripts/hc-generator.py b/scripts/hc-generator.py
@@ -3,7 +3,7 @@
 ##########
 #
 #                               reHC-*
-#  Haplotype Configuration with Recombinations and Errors
+#  Haplotyping with Recombinations, Errors, and Missing Genotypes
 #
 #  Copyright (C) 2010,2011  Yuri Pirola <yuri.pirola(-at-)gmail.com>
 #
@@ -31,8 +31,9 @@
 #
 #  hc-generator.py
 #
-#  A program that generates a random zero-recombinant set of (partially
-#  missing) genotypes given a pedigree structure.
+#  A program that generates a random set of genotypes with
+#  recombinations, errors and missing genotypes given a pedigree
+#  structure.
 #
 ##########
 

diff --git a/scripts/pedigree-generator.py b/scripts/pedigree-generator.py
@@ -4,7 +4,7 @@
 ##########
 #
 #                               reHC-*
-#  Haplotype Configuration with Recombinations and Errors
+#  Haplotyping with Recombinations, Errors, and Missing Genotypes
 #
 #  Copyright (C) 2010  Yuri Pirola <yuri.pirola(-at-)gmail.com>
 #

diff --git a/src/application/main.cpp b/src/application/main.cpp
@@ -1,7 +1,7 @@
 /**
  *
  *                              reHC-*
- * Haplotype Configuration with Recombinations and Errors
+ * Haplotyping with Recombinations, Errors, and Missing Genotypes
  *
  * Copyright (C) 2010,2011  Yuri Pirola <yuri.pirola(-at-)gmail.com>
  *

diff --git a/src/lib/cms_sat_solver_interface.cpp b/src/lib/cms_sat_solver_interface.cpp
@@ -1,7 +1,7 @@
 /**
  *
  *                              reHC-*
- * Haplotype Configuration with Recombinations and Errors
+ * Haplotyping with Recombinations, Errors, and Missing Genotypes
  *
  * Copyright (C) 2010,2011  Yuri Pirola <yuri.pirola(-at-)gmail.com>
  *

diff --git a/src/lib/gender.cpp b/src/lib/gender.cpp
@@ -1,7 +1,7 @@
 /**
  *
  *                              reHC-*
- * Haplotype Configuration with Recombinations and Errors
+ * Haplotyping with Recombinations, Errors, and Missing Genotypes
  *
  * Copyright (C) 2010  Yuri Pirola <yuri.pirola(-at-)gmail.com>
  *

diff --git a/src/lib/log.cpp b/src/lib/log.cpp
@@ -1,7 +1,7 @@
 /**
  *
  *                              reHC-*
- * Haplotype Configuration with Recombinations and Errors
+ * Haplotyping with Recombinations, Errors, and Missing Genotypes
  *
  * Copyright (C) 2010  Yuri Pirola <yuri.pirola(-at-)gmail.com>
  *

diff --git a/src/lib/ms_sat_solver_interface.cpp b/src/lib/ms_sat_solver_interface.cpp
@@ -1,7 +1,7 @@
 /**
  *
  *                              reHC-*
- * Haplotype Configuration with Recombinations and Errors
+ * Haplotyping with Recombinations, Errors, and Missing Genotypes
  *
  * Copyright (C) 2010,2011  Yuri Pirola <yuri.pirola(-at-)gmail.com>
  *

diff --git a/src/lib/ped2cnf-constraints.cpp b/src/lib/ped2cnf-constraints.cpp
@@ -1,7 +1,7 @@
 /**
  *
  *                              reHC-*
- * Haplotype Configuration with Recombinations and Errors
+ * Haplotyping with Recombinations, Errors, and Missing Genotypes
  *
  * Copyright (C) 2011  Yuri Pirola <yuri.pirola(-at-)gmail.com>
  *

diff --git a/src/lib/pedcnf.cpp b/src/lib/pedcnf.cpp
@@ -1,7 +1,7 @@
 /**
  *
  *                              reHC-*
- * Haplotype Configuration with Recombinations and Errors
+ * Haplotyping with Recombinations, Errors, and Missing Genotypes
  *
  * Copyright (C) 2010,2011  Yuri Pirola <yuri.pirola(-at-)gmail.com>
  *

diff --git a/src/lib/pedcnf_card.cpp b/src/lib/pedcnf_card.cpp
@@ -1,7 +1,7 @@
 /**
  *
  *                              reHC-*
- * Haplotype Configuration with Recombinations and Errors
+ * Haplotyping with Recombinations, Errors, and Missing Genotypes
  *
  * Copyright (C) 2010,2011  Yuri Pirola <yuri.pirola(-at-)gmail.com>
  *

diff --git a/src/lib/utility.cpp b/src/lib/utility.cpp
@@ -1,7 +1,7 @@
 /**
  *
  *                              reHC-*
- * Haplotype Configuration with Recombinations and Errors
+ * Haplotyping with Recombinations, Errors, and Missing Genotypes
  *
  * Copyright (C) 2010  Yuri Pirola <yuri.pirola(-at-)gmail.com>
  *

diff --git a/test/haplotype_genotype_check.cpp b/test/haplotype_genotype_check.cpp
@@ -1,7 +1,7 @@
 /**
  *
  *                              reHC-*
- * Haplotype Configuration with Recombinations and Errors
+ * Haplotyping with Recombinations, Errors, and Missing Genotypes
  *
  * Copyright (C) 2010  Yuri Pirola <yuri.pirola(-at-)gmail.com>
  *

diff --git a/test/multifamily_pedigree_check.cpp b/test/multifamily_pedigree_check.cpp
@@ -1,7 +1,7 @@
 /**
  *
  *                              reHC-*
- * Haplotype Configuration with Recombinations and Errors
+ * Haplotyping with Recombinations, Errors, and Missing Genotypes
  *
  * Copyright (C) 2010  Yuri Pirola <yuri.pirola(-at-)gmail.com>
  *

diff --git a/test/pedcnf_check.cpp b/test/pedcnf_check.cpp
@@ -1,7 +1,7 @@
 /**
  *
  *                              reHC-*
- * Haplotype Configuration with Recombinations and Errors
+ * Haplotyping with Recombinations, Errors, and Missing Genotypes
  *
  * Copyright (C) 2010,2011  Yuri Pirola <yuri.pirola(-at-)gmail.com>
  *

diff --git a/test/pedcnf_extreme_check.cpp b/test/pedcnf_extreme_check.cpp
@@ -1,7 +1,7 @@
 /**
  *
  *                              reHC-*
- * Haplotype Configuration with Recombinations and Errors
+ * Haplotyping with Recombinations, Errors, and Missing Genotypes
  *
  * Copyright (C) 2010,2011  Yuri Pirola <yuri.pirola(-at-)gmail.com>
  *

diff --git a/test/pedigree_check.cpp b/test/pedigree_check.cpp
@@ -1,7 +1,7 @@
 /**
  *
  *                              reHC-*
- * Haplotype Configuration with Recombinations and Errors
+ * Haplotyping with Recombinations, Errors, and Missing Genotypes
  *
  * Copyright (C) 2010  Yuri Pirola <yuri.pirola(-at-)gmail.com>
  *

diff --git a/test/pedigree_id_string_check.cpp b/test/pedigree_id_string_check.cpp
@@ -1,7 +1,7 @@
 /**
  *
  *                              reHC-*
- * Haplotype Configuration with Recombinations and Errors
+ * Haplotyping with Recombinations, Errors, and Missing Genotypes
  *
  * Copyright (C) 2010  Yuri Pirola <yuri.pirola(-at-)gmail.com>
  *