From 8df4664005f0982cd150be0b1c06cd5ad5ea9be9 Mon Sep 17 00:00:00 2001 From: Joe Zhu Date: Mon, 8 Oct 2018 12:59:24 +0100 Subject: [PATCH] get the new lasso class to work --- DEploid-Lasso-lib | 2 +- Makefile.am | 3 ++- src/dEploidIO.cpp | 3 ++- src/dEploidIO.hpp | 3 +++ 4 files changed, 8 insertions(+), 3 deletions(-) diff --git a/DEploid-Lasso-lib b/DEploid-Lasso-lib index 2a420aad..cd528d5c 160000 --- a/DEploid-Lasso-lib +++ b/DEploid-Lasso-lib @@ -1 +1 @@ -Subproject commit 2a420aad65a51cfb574ee1aa0b1fb1b83ee05cff +Subproject commit cd528d5c8d2065b2c9824da8cac57caba3c23f83 diff --git a/Makefile.am b/Makefile.am index d412d376..a3f3c809 100644 --- a/Makefile.am +++ b/Makefile.am @@ -34,10 +34,11 @@ common_src = src/random/fastfunc.cpp \ src/export/dEploidIOExport.cpp \ src/export/dEploidIOExportPosteriorProb.cpp \ src/export/writeMcmcRelated.cpp \ + DEploid-Lasso-lib/src/lasso.cpp \ DEploid-Lasso-lib/src/dEploidLasso.cpp debug_src = src/debug/mcmcDebug.cpp src/debug/vcfReaderDebug.cpp \ - DEploid-Lasso-lib/src/dEploidLassoDBG.cpp + DEploid-Lasso-lib/src/lassoDBG.cpp dEploid_SOURCES = src/dEploid.cpp $(common_src) dEploid_dbg_SOURCES = $(debug_src) $(dEploid_SOURCES) diff --git a/src/dEploidIO.cpp b/src/dEploidIO.cpp index 05bf71d9..1324594a 100644 --- a/src/dEploidIO.cpp +++ b/src/dEploidIO.cpp @@ -821,7 +821,8 @@ void DEploidIO::dEploidLasso() { vector < vector > tmpPanel = lassoSubsetPanel(start, length); DEploidLASSO dummy(tmpPanel, wsaf, 250); - ////dummy.printResults(); + //lassoPanels.push_back(); + dummy.printResults(); // for loop, for each chromosome // First produce reference panels diff --git a/src/dEploidIO.hpp b/src/dEploidIO.hpp index 89ca6b90..47a752b3 100644 --- a/src/dEploidIO.hpp +++ b/src/dEploidIO.hpp @@ -172,6 +172,9 @@ class DEploidIO{ bool doComputeLLK_; void setDoComputeLLK( const bool setTo ) { this->doComputeLLK_ = setTo; } + // Lasso Related + vector < vector < vector > > lassoPanels; + // Parameters double missCopyProb_; double averageCentimorganDistance_;// = 15000.0,