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DEploid-dev · Oct 19, 2024 · 7979a54 · 7979a54
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diff --git a/.ci/checkedList b/.ci/checkedList
diff --git a/.ci/mycppfileList b/.ci/mycppfileList
diff --git a/.circleci/.circleci-matrix.yml b/.circleci/.circleci-matrix.yml
diff --git a/.circleci/config.yml b/.circleci/config.yml
diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
diff --git a/.github/ISSUE_TEMPLATE/custom.md b/.github/ISSUE_TEMPLATE/custom.md
diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md
diff --git a/.github/workflows/ccpp.yml b/.github/workflows/ccpp.yml
diff --git a/.gitignore b/.gitignore
diff --git a/.gitmodules b/.gitmodules
diff --git a/.travis.yml b/.travis.yml
diff --git a/AUTHORS b/AUTHORS
diff --git a/Brewfile b/Brewfile
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
diff --git a/COPYING b/COPYING
diff --git a/Dockerfile b/Dockerfile
diff --git a/Makefile.am b/Makefile.am
diff --git a/NEWS b/NEWS
diff --git a/PULL_REQUEST_TEMPLATE.md b/PULL_REQUEST_TEMPLATE.md
diff --git a/README b/README
diff --git a/README b/README
diff --git a/README.md b/README.md
diff --git a/VERSION b/VERSION
diff --git a/configure.ac b/configure.ac
diff --git a/coverage/.gitkeep b/coverage/.gitkeep
diff --git a/data/exampleData/.gitignore b/data/exampleData/.gitignore
diff --git a/data/exampleData/PG0390-C.alt b/data/exampleData/PG0390-C.alt
diff --git a/data/exampleData/PG0390-C.eg.vcf.gz b/data/exampleData/PG0390-C.eg.vcf.gz
diff --git a/data/exampleData/PG0390-C.ref b/data/exampleData/PG0390-C.ref
diff --git a/data/exampleData/PG0415-C.eg.vcf.gz b/data/exampleData/PG0415-C.eg.vcf.gz
diff --git a/data/exampleData/README.md b/data/exampleData/README.md
diff --git a/data/exampleData/extractVcf.r b/data/exampleData/extractVcf.r
diff --git a/data/exampleData/labStrains.eg.PLAF.txt b/data/exampleData/labStrains.eg.PLAF.txt
diff --git a/data/exampleData/labStrains.eg.panel.txt b/data/exampleData/labStrains.eg.panel.txt
diff --git a/data/exampleData/merged.eg.vcf.gz b/data/exampleData/merged.eg.vcf.gz
diff --git a/data/testData/PG0390-C.test.alt b/data/testData/PG0390-C.test.alt
diff --git a/data/testData/PG0390-C.test.nopanel.hap b/data/testData/PG0390-C.test.nopanel.hap
diff --git a/data/testData/PG0390-C.test.ref b/data/testData/PG0390-C.test.ref
diff --git a/data/testData/PG0390-C.test.vcf b/data/testData/PG0390-C.test.vcf
diff --git a/data/testData/PG0390-C.test.vcf.gz b/data/testData/PG0390-C.test.vcf.gz
diff --git a/data/testData/PG0390.C_alt.txt b/data/testData/PG0390.C_alt.txt
diff --git a/data/testData/README.md b/data/testData/README.md
diff --git a/data/testData/bad.plaf.txt b/data/testData/bad.plaf.txt
diff --git a/data/testData/bad.plaf_badpos.txt b/data/testData/bad.plaf_badpos.txt
diff --git a/data/testData/bad.plaf_scientific.txt b/data/testData/bad.plaf_scientific.txt
diff --git a/data/testData/bad.plaf_scientificE.txt b/data/testData/bad.plaf_scientificE.txt
diff --git a/data/testData/crappyVcf/badHeaderFieldNames.alt.vcf b/data/testData/crappyVcf/badHeaderFieldNames.alt.vcf
diff --git a/data/testData/crappyVcf/badHeaderFieldNames.chrom.vcf b/data/testData/crappyVcf/badHeaderFieldNames.chrom.vcf
diff --git a/data/testData/crappyVcf/badHeaderFieldNames.chrom2.vcf b/data/testData/crappyVcf/badHeaderFieldNames.chrom2.vcf
diff --git a/data/testData/crappyVcf/badHeaderFieldNames.filter.vcf b/data/testData/crappyVcf/badHeaderFieldNames.filter.vcf
diff --git a/data/testData/crappyVcf/badHeaderFieldNames.format.vcf b/data/testData/crappyVcf/badHeaderFieldNames.format.vcf
diff --git a/data/testData/crappyVcf/badHeaderFieldNames.id.vcf b/data/testData/crappyVcf/badHeaderFieldNames.id.vcf
diff --git a/data/testData/crappyVcf/badHeaderFieldNames.info.vcf b/data/testData/crappyVcf/badHeaderFieldNames.info.vcf
diff --git a/data/testData/crappyVcf/badHeaderFieldNames.pos.vcf b/data/testData/crappyVcf/badHeaderFieldNames.pos.vcf
diff --git a/data/testData/crappyVcf/badHeaderFieldNames.qual.vcf b/data/testData/crappyVcf/badHeaderFieldNames.qual.vcf
diff --git a/data/testData/crappyVcf/badHeaderFieldNames.ref.vcf b/data/testData/crappyVcf/badHeaderFieldNames.ref.vcf
diff --git a/data/testData/crappyVcf/badVariant.noAD.vcf b/data/testData/crappyVcf/badVariant.noAD.vcf
diff --git a/data/testData/crappyVcf/badVariant.noVQSLOD.vcf b/data/testData/crappyVcf/badVariant.noVQSLOD.vcf
diff --git a/data/testData/crappyVcfGz/badHeaderFieldNames.alt.vcf.gz b/data/testData/crappyVcfGz/badHeaderFieldNames.alt.vcf.gz
diff --git a/data/testData/crappyVcfGz/badHeaderFieldNames.chrom.vcf.gz b/data/testData/crappyVcfGz/badHeaderFieldNames.chrom.vcf.gz
diff --git a/data/testData/crappyVcfGz/badHeaderFieldNames.chrom2.vcf.gz b/data/testData/crappyVcfGz/badHeaderFieldNames.chrom2.vcf.gz
diff --git a/data/testData/crappyVcfGz/badHeaderFieldNames.filter.vcf.gz b/data/testData/crappyVcfGz/badHeaderFieldNames.filter.vcf.gz
diff --git a/data/testData/crappyVcfGz/badHeaderFieldNames.format.vcf.gz b/data/testData/crappyVcfGz/badHeaderFieldNames.format.vcf.gz
diff --git a/data/testData/crappyVcfGz/badHeaderFieldNames.id.vcf.gz b/data/testData/crappyVcfGz/badHeaderFieldNames.id.vcf.gz
diff --git a/data/testData/crappyVcfGz/badHeaderFieldNames.info.vcf.gz b/data/testData/crappyVcfGz/badHeaderFieldNames.info.vcf.gz
diff --git a/data/testData/crappyVcfGz/badHeaderFieldNames.pos.vcf.gz b/data/testData/crappyVcfGz/badHeaderFieldNames.pos.vcf.gz
diff --git a/data/testData/crappyVcfGz/badHeaderFieldNames.qual.vcf.gz b/data/testData/crappyVcfGz/badHeaderFieldNames.qual.vcf.gz
diff --git a/data/testData/crappyVcfGz/badHeaderFieldNames.ref.vcf.gz b/data/testData/crappyVcfGz/badHeaderFieldNames.ref.vcf.gz
diff --git a/data/testData/crappyVcfGz/badVariant.noAD.vcf.gz b/data/testData/crappyVcfGz/badVariant.noAD.vcf.gz
diff --git a/data/testData/labStrains.test.PLAF.txt b/data/testData/labStrains.test.PLAF.txt
diff --git a/data/testData/labStrains.test.PLAF.txt.gz b/data/testData/labStrains.test.PLAF.txt.gz
diff --git a/data/testData/labStrains.test.exclude.txt b/data/testData/labStrains.test.exclude.txt
diff --git a/data/testData/labStrains.test.exclude.txt.gz b/data/testData/labStrains.test.exclude.txt.gz
diff --git a/data/testData/labStrains.test.panel.txt b/data/testData/labStrains.test.panel.txt
diff --git a/data/testData/labStrains.test.panel.txt.gz b/data/testData/labStrains.test.panel.txt.gz
diff --git a/data/testData/labStrains_samples_PLAF.txt b/data/testData/labStrains_samples_PLAF.txt
diff --git a/data/testData/testingPanel.txt b/data/testData/testingPanel.txt
diff --git a/data/testData/txtReaderForTesting.txt b/data/testData/txtReaderForTesting.txt
diff --git a/data/testData/txtReaderForTesting.txt.gz b/data/testData/txtReaderForTesting.txt.gz
diff --git a/data/testData/txtReaderForTestingAfterExclude.txt b/data/testData/txtReaderForTestingAfterExclude.txt
diff --git a/data/testData/txtReaderForTestingToBeExclude.txt b/data/testData/txtReaderForTestingToBeExclude.txt
diff --git a/docs/.gitignore b/docs/.gitignore
diff --git a/docs/Bug-report.md b/docs/Bug-report.md
diff --git a/docs/Citing-DEploid.md b/docs/Citing-DEploid.md
diff --git a/docs/FAQ.md b/docs/FAQ.md
diff --git a/docs/Makefile b/docs/Makefile
diff --git a/docs/Output.md b/docs/Output.md
diff --git a/docs/_build/man/dEploid.1 b/docs/_build/man/dEploid.1
diff --git a/docs/_static/PD0577-CPanel.IBD.ring.png b/docs/_static/PD0577-CPanel.IBD.ring.png
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diff --git a/docs/_static/PG0390-CPanel.ring.png b/docs/_static/PG0390-CPanel.ring.png
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diff --git a/docs/_static/PG0390-CaltVsRefAndWSAFvsPLAF.png b/docs/_static/PG0390-CaltVsRefAndWSAFvsPLAF.png
diff --git a/docs/_static/PG0400-Csigma10.ring.png b/docs/_static/PG0400-Csigma10.ring.png
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diff --git a/docs/_static/PG0415-CaltVsRefAndWSAFvsPLAF.png b/docs/_static/PG0415-CaltVsRefAndWSAFvsPLAF.png
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diff --git a/docs/bug-report.rst1 b/docs/bug-report.rst1
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diff --git a/docs/conf.py b/docs/conf.py
diff --git a/docs/cppdocument.rstTmp b/docs/cppdocument.rstTmp
diff --git a/docs/description.rst b/docs/description.rst
diff --git a/docs/doxygen/Doxyfile.in b/docs/doxygen/Doxyfile.in
diff --git a/docs/doxygen/Makefile.am b/docs/doxygen/Makefile.am
diff --git a/docs/index.rst b/docs/index.rst
diff --git a/docs/input.rst b/docs/input.rst
diff --git a/docs/installation.rst b/docs/installation.rst
diff --git a/docs/synopsis.md b/docs/synopsis.md
diff --git a/m4/ax_append_flag.m4 b/m4/ax_append_flag.m4
diff --git a/m4/ax_cflags_warn_all.m4 b/m4/ax_cflags_warn_all.m4
diff --git a/m4/ax_check_compile_flag.m4 b/m4/ax_check_compile_flag.m4
diff --git a/m4/ax_check_link_flag.m4 b/m4/ax_check_link_flag.m4
diff --git a/m4/ax_cxx_compile_stdcxx_11.m4 b/m4/ax_cxx_compile_stdcxx_11.m4
diff --git a/m4/ax_require_defined.m4 b/m4/ax_require_defined.m4
diff --git a/src/chooseK.cpp b/src/chooseK.cpp
diff --git a/src/chooseK.hpp b/src/chooseK.hpp
diff --git a/src/codeCogs/asympt_expn.h b/src/codeCogs/asympt_expn.h
diff --git a/src/codeCogs/errorfn.h b/src/codeCogs/errorfn.h
diff --git a/src/codeCogs/errorfnc.h b/src/codeCogs/errorfnc.h
diff --git a/src/codeCogs/errorfnc_exp.h b/src/codeCogs/errorfnc_exp.h
diff --git a/src/codeCogs/expx2.h b/src/codeCogs/expx2.h
diff --git a/src/codeCogs/gamma.h b/src/codeCogs/gamma.h
diff --git a/src/codeCogs/ln_add1.h b/src/codeCogs/ln_add1.h
diff --git a/src/codeCogs/log_gamma.h b/src/codeCogs/log_gamma.h
diff --git a/src/codeCogs/logbeta.h b/src/codeCogs/logbeta.h
diff --git a/src/codeCogs/loggammafrac.h b/src/codeCogs/loggammafrac.h
diff --git a/src/codeCogs/loggammasum.h b/src/codeCogs/loggammasum.h
diff --git a/src/codeCogs/machine_epsilon.h b/src/codeCogs/machine_epsilon.h
diff --git a/src/codeCogs/mersenne.hpp b/src/codeCogs/mersenne.hpp
diff --git a/src/codeCogs/poly_eval.h b/src/codeCogs/poly_eval.h
diff --git a/src/codeCogs/randomSample.hpp b/src/codeCogs/randomSample.hpp
diff --git a/src/codeCogs/stirling.h b/src/codeCogs/stirling.h
diff --git a/src/codeCogs/xsub_ln_add1.h b/src/codeCogs/xsub_ln_add1.h
diff --git a/src/dEploid.cpp b/src/dEploid.cpp
diff --git a/src/dEploidIO-operation.cpp b/src/dEploidIO-operation.cpp
diff --git a/src/dEploidIO-workflow.cpp b/src/dEploidIO-workflow.cpp
diff --git a/src/dEploidIO.cpp b/src/dEploidIO.cpp
@@ -209,7 +209,7 @@ void DEploidIO::finalize() {
         this->setBestPracticeParameters();
     }
 
-    if ( this->doIbdPainting() | this->doComputeLLK() | this->doIbdViterbiPainting() ) {
+    if ( this->doIbdPainting() || this->doComputeLLK() || this->doIbdViterbiPainting() ) {
         if (!initialPropWasGiven()) {
             throw InitialPropUngiven("");
         }
@@ -625,7 +625,7 @@ void DEploidIO::checkInput() {
             // set k strain by proportion length
         }
     }
-    if (this->useBestPractice() & (!this->usePanel())){
+    if (this->useBestPractice() && (!this->usePanel())){
         throw FlagsConflict("-best" , string("-noPanel. Reference panel is") +
             string("required for using best-practices."));
     }
@@ -731,7 +731,7 @@ void DEploidIO::readPanel() {
     if ( this->usePanel() == false ) {
         return;
     }
-    if ( this->doIbdPainting() | this->doComputeLLK() ) {
+    if ( this->doIbdPainting() || this->doComputeLLK() ) {
         return;
     }
 

diff --git a/src/dEploidIO.hpp b/src/dEploidIO.hpp
diff --git a/src/dEploid_completion.sh b/src/dEploid_completion.sh
diff --git a/src/debug/mcmcDebug.cpp b/src/debug/mcmcDebug.cpp
diff --git a/src/debug/vcfReaderDebug.cpp b/src/debug/vcfReaderDebug.cpp
diff --git a/src/exceptions.hpp b/src/exceptions.hpp
@@ -39,7 +39,8 @@ struct ShouldNotBeCalled : std::exception{
   ShouldNotBeCalled() { }
   virtual ~ShouldNotBeCalled() throw() {}
   virtual const char* what() const noexcept {
-      return "Should not reach here";
+      static const std::string msg = "Should not reach here";
+      return msg.c_str();
   }
 };
 
@@ -75,7 +76,8 @@ struct OutOfVectorSize : std::exception{
   OutOfVectorSize() { }
   virtual ~OutOfVectorSize() throw() {}
   virtual const char* what() const noexcept {
-      return "Out of vector size!";
+    static const std::string msg = "Out of vector size!";
+      return msg.c_str();
   }
 };
 

diff --git a/src/export/dEploidIOExport.cpp b/src/export/dEploidIOExport.cpp
diff --git a/src/export/dEploidIOExportPosteriorProb.cpp b/src/export/dEploidIOExportPosteriorProb.cpp
diff --git a/src/export/writeMcmcRelated.cpp b/src/export/writeMcmcRelated.cpp
diff --git a/src/global.hpp b/src/global.hpp
diff --git a/src/gzstream/COPYING.LIB b/src/gzstream/COPYING.LIB
diff --git a/src/gzstream/README b/src/gzstream/README
diff --git a/src/gzstream/gzstream.cpp b/src/gzstream/gzstream.cpp
diff --git a/src/gzstream/gzstream.h b/src/gzstream/gzstream.h
diff --git a/src/gzstream/index.html b/src/gzstream/index.html
diff --git a/src/gzstream/logo.gif b/src/gzstream/logo.gif
diff --git a/src/gzstream/test_gunzip.C b/src/gzstream/test_gunzip.C
diff --git a/src/gzstream/test_gzip.C b/src/gzstream/test_gzip.C
diff --git a/src/gzstream/version b/src/gzstream/version
diff --git a/src/ibd.cpp b/src/ibd.cpp
diff --git a/src/ibd.hpp b/src/ibd.hpp
diff --git a/src/log-double.hpp b/src/log-double.hpp
diff --git a/src/logsum.hpp b/src/logsum.hpp
diff --git a/src/mcmc.cpp b/src/mcmc.cpp
@@ -340,7 +340,7 @@ void McmcMachinery::runMcmcChain( bool showProgress, bool useIBD, bool notInR, b
         this->mcmcSample_->siteOfOneMissCopyOne[atSiteI] /= (double)this->maxIteration_;
     }
 
-    if ( notInR & ((jobbrief == "lassoK") | (jobbrief == "ibd") | (jobbrief == "classic")) ) { // notInPython
+    if ( notInR & ((jobbrief == "lassoK") || (jobbrief == "ibd") || (jobbrief == "classic")) ) { // notInPython
         this->dEploidIO_->writeMcmcRelated(this->mcmcSample_, jobbrief, useIBD);
     }
 

diff --git a/src/mcmc.hpp b/src/mcmc.hpp
diff --git a/src/panel.cpp b/src/panel.cpp
diff --git a/src/panel.hpp b/src/panel.hpp
diff --git a/src/param.hpp b/src/param.hpp
diff --git a/src/random/fastfunc.cpp b/src/random/fastfunc.cpp
diff --git a/src/random/fastfunc.hpp b/src/random/fastfunc.hpp
@@ -29,6 +29,7 @@
 #include <iostream>
 #include <cmath>
 #include <vector>
+#include <cstdint>
 
 
 // Number of interpolation points.  If this is changed, several constants in fastlog must also be changed.

diff --git a/src/random/mersenne_twister.cpp b/src/random/mersenne_twister.cpp
diff --git a/src/random/mersenne_twister.hpp b/src/random/mersenne_twister.hpp
diff --git a/src/random/random_generator.cpp b/src/random/random_generator.cpp
diff --git a/src/random/random_generator.hpp b/src/random/random_generator.hpp
diff --git a/src/txtReader.cpp b/src/txtReader.cpp
diff --git a/src/txtReader.hpp b/src/txtReader.hpp
diff --git a/src/updateHap.cpp b/src/updateHap.cpp
diff --git a/src/updateHap.hpp b/src/updateHap.hpp
diff --git a/src/utility.cpp b/src/utility.cpp
diff --git a/src/utility.hpp b/src/utility.hpp
diff --git a/src/variantIndex.cpp b/src/variantIndex.cpp
diff --git a/src/variantIndex.hpp b/src/variantIndex.hpp
diff --git a/src/vcfReader.cpp b/src/vcfReader.cpp
diff --git a/src/vcfReader.hpp b/src/vcfReader.hpp
diff --git a/tests/unittest/test_dEploidIO.cpp b/tests/unittest/test_dEploidIO.cpp
diff --git a/tests/unittest/test_ibd.cpp b/tests/unittest/test_ibd.cpp
diff --git a/tests/unittest/test_mcmc.cpp b/tests/unittest/test_mcmc.cpp
diff --git a/tests/unittest/test_panel.cpp b/tests/unittest/test_panel.cpp
diff --git a/tests/unittest/test_runner.cpp b/tests/unittest/test_runner.cpp
diff --git a/tests/unittest/test_txtReader.cpp b/tests/unittest/test_txtReader.cpp
diff --git a/tests/unittest/test_updatePairHap.cpp b/tests/unittest/test_updatePairHap.cpp
diff --git a/tests/unittest/test_updateSingleHap.cpp b/tests/unittest/test_updateSingleHap.cpp
diff --git a/tests/unittest/test_utilities.cpp b/tests/unittest/test_utilities.cpp
diff --git a/tests/unittest/test_vcfReader.cpp b/tests/unittest/test_vcfReader.cpp
diff --git a/tests/unittest/test_workflow.cpp b/tests/unittest/test_workflow.cpp