Minor updates for latest straw version

.gitignore

@@ -0,0 +1 @@
+*.exe

C++/Lanczos/README.md

@@ -1,28 +1,79 @@
-**Lanczos Method with Selective Ortohanalization**  
-
-These functions need liblapacke (and hence libblas and liblapack). To install them do:  
-sudo apt update  
-sudo apt install libopenblas-base  
-sudo apt install libopenblas-dev  
-sudo apt install liblapack3  
-sudo apt install liblapack-dev  
-sudo apt install liblapacke-dev  
-
-Then make sure that you are using version 7 of gcc and g++  
-
-**Rmark:** In my case the folder containing **straw** is **~/HiC/straw_may_2022**. The user should replace it by their own folder.
-
-To create an executable for computing few leading eigenvectors of the correlation matrix of contact matrix for a particular chromosome do:  
-**g++ -O2 -o Lan.exe s_fLan.cpp s_fSOLan.c s_dthMul.c hgFlipSign.c ~/HiC/straw_may_2022/C++/straw.cpp -I. -I ~/HiC/straw_may_2022/C++ -lz -lcurl -lpthread -lblas -llapack -llapacke**  
-Run  
-./Lan.exe  
-to see usage.  
-By default it uses unnormalized observed over expected (o/e) matrix.  
-Use -o flag to use observed matrix instead (usually not recommended)  
-Use -n norm to use normalized matrix; norm can be NONE (no normalization - default), VC, VC_SQRT, KR, SCALE, SCALA, etc.  
-
-To do the above for Genome Wide (GW) contact matrix do:  
-**g++ -O2 -o GWev.exe s_fGW.cpp getGWMatrix.cpp s_fSOLan.c s_dthMul.c ~/HiC/straw_may_2022/C++/straw.cpp -I ~/HiC/straw_may_2022/C++ -lz -lcurl -lpthread -lblas -llapack -llapacke**  
-Run  
-./GWev.exe for usage.  
-By default it uses **inter**chromosomal matrix. To use the full matrix specife the -f flag
+**Lanczos Method with Selective Orthogonalization**  
+
+This package provides tools for computing leading eigenvectors of contact matrices from Hi-C data.
+
+## Building the Software
+
+### Prerequisites
+
+The software requires:
+- C++ compiler (GCC/G++ 4.8 or later)
+- OpenBLAS
+- LAPACK/LAPACKE
+- libcurl
+- zlib
+- straw library (place in `~/straw` or modify build script)
+
+### Platform-Specific Build Instructions
+
+#### Linux
+```bash
+# Make the script executable
+chmod +x build_linux.sh
+# Run the build script
+./build_linux.sh
+```
+
+The script will automatically install required dependencies using apt-get.
+
+#### macOS
+```bash
+# Make the script executable
+chmod +x build_mac.sh
+# Run the build script
+./build_mac.sh
+```
+
+The script will use Homebrew to install required dependencies.
+
+#### Windows
+1. Install MinGW-w64 from [WinLibs](https://winlibs.com/)
+2. Add MinGW-w64 bin directory to your PATH
+3. Run the build script:
+```cmd
+build_windows.bat
+```
+
+You may need to modify the paths in `build_windows.bat` to match your MinGW-w64 installation.
+
+## Usage
+
+### Chromosome-Specific Analysis (Lan.exe)
+```bash
+./Lan.exe [options] <hicfile> <chromosome> <outbase> <resolution> [nv]
+
+Options:
+  -o           Use observed matrix instead of observed/expected (o/e) matrix
+  -t <float>   Set tolerance (default: 1.0e-7)
+  -e <float>   Set epsilon (default: 1.0e-8)
+  -I <int>     Set maximum iterations (default: 200)
+  -n <string>  Set normalization method (default: NONE)
+  -T <int>     Set number of threads (default: 1)
+  -v <int>     Set verbosity level (default: 1)
+```
+
+### Genome-Wide Analysis (GWev.exe)
+```bash
+./GWev.exe [options] <hicfile> <outbase> <resolution> [nv]
+
+Options:
+  -f           Use full matrix instead of inter-chromosomal only
+  -t <float>   Set tolerance (default: 1.0e-7)
+  -e <float>   Set epsilon (default: 1.0e-8)
+  -I <int>     Set maximum iterations (default: 200)
+  -T <int>     Set number of threads (default: 1)
+  -v <int>     Set verbosity level (default: 1)
+```
+
+## Output Format
+The programs generate eigenvector files in WIG format that can be visualized in genome browsers.

C++/Lanczos/build_linux.sh

@@ -0,0 +1,68 @@
+#!/bin/bash
+
+# Exit on error
+set -e
+
+echo "🔧 Setting up build environment..."
+
+# Install dependencies using apt
+echo "📦 Installing dependencies..."
+sudo apt-get update
+sudo apt-get install -y \
+    build-essential \
+    gcc \
+    g++ \
+    libopenblas-dev \
+    liblapack-dev \
+    liblapacke-dev \
+    libcurl4-openssl-dev \
+    zlib1g-dev
+
+# Check if straw is available
+STRAW_PATH="$HOME/straw"
+if [ ! -d "$STRAW_PATH" ]; then
+    echo "⚠️  Warning: straw library not found at $STRAW_PATH"
+    echo "Please install straw library and place it in $STRAW_PATH"
+    echo "or modify this script with the correct path"
+    exit 1
+fi
+
+echo "🔨 Building executables..."
+
+# Common compiler flags
+COMMON_FLAGS="-O2 -Wno-format-security -I/usr/include -I$STRAW_PATH/C++"
+COMMON_LIBS="-L/usr/lib -lz -lcurl -lpthread -lopenblas -llapack -llapacke"
+
+# First compile straw library
+echo "Building straw library..."
+g++ $COMMON_FLAGS -c "$STRAW_PATH/C++/straw.cpp" -o straw.o
+
+# Compile Lan.exe
+echo "Building Lan.exe..."
+g++ $COMMON_FLAGS -std=c++11 -o Lan.exe \
+    s_fLan.cpp \
+    s_fSOLan.c \
+    s_dthMul.c \
+    hgFlipSign.c \
+    straw.o \
+    -I. \
+    $COMMON_LIBS
+
+# Compile GWev.exe
+echo "Building GWev.exe..."
+g++ $COMMON_FLAGS -std=c++11 -o GWev.exe \
+    s_fGW.cpp \
+    getGWMatrix.cpp \
+    s_fSOLan.c \
+    s_dthMul.c \
+    straw.o \
+    $COMMON_LIBS
+
+# Clean up object files
+rm -f straw.o
+
+echo "✅ Build completed successfully!"
+echo
+echo "You can now run:"
+echo "  ./Lan.exe  - for chromosome-specific analysis"
+echo "  ./GWev.exe - for genome-wide analysis" 

C++/Lanczos/build_mac.sh

@@ -0,0 +1,69 @@
+#!/bin/bash
+
+# Exit on error
+set -e
+
+echo "🔧 Setting up build environment..."
+
+# Assume Homebrew is installed
+
+# Install dependencies
+echo "📦 Installing dependencies..."
+brew install openblas
+brew install lapack
+brew install gcc@13  # Latest stable GCC
+brew install curl
+brew install zlib
+
+# Set up environment variables for OpenBLAS and LAPACK
+export LDFLAGS="-L/opt/homebrew/opt/openblas/lib -L/opt/homebrew/opt/lapack/lib"
+export CPPFLAGS="-I/opt/homebrew/opt/openblas/include -I/opt/homebrew/opt/lapack/include"
+
+# Check if straw is available
+STRAW_PATH="../../../straw"
+if [ ! -d "$STRAW_PATH" ]; then
+    echo "⚠️  Warning: straw library not found at $STRAW_PATH"
+    echo "Please install straw library and place it in $STRAW_PATH"
+    echo "or modify this script with the correct path"
+    exit 1
+fi
+
+echo "🔨 Building executables..."
+
+# Common compiler flags
+COMMON_FLAGS="-O2 -Wno-format-security -I/opt/homebrew/opt/openblas/include -I/opt/homebrew/opt/lapack/include -I$STRAW_PATH/C++"
+COMMON_LIBS="-L/opt/homebrew/opt/openblas/lib -L/opt/homebrew/opt/lapack/lib -lz -lcurl -lpthread -lopenblas -llapack -llapacke"
+
+# First compile straw library
+echo "Building straw library..."
+g++-13 $COMMON_FLAGS -c "$STRAW_PATH/C++/straw.cpp" -o straw.o
+
+# Compile Lan.exe
+echo "Building Lan.exe..."
+g++-13 $COMMON_FLAGS -std=c++11 -o Lan.exe \
+    s_fLan.cpp \
+    s_fSOLan.c \
+    s_dthMul.c \
+    hgFlipSign.c \
+    straw.o \
+    -I. \
+    $COMMON_LIBS
+
+# Compile GWev.exe
+echo "Building GWev.exe..."
+g++-13 $COMMON_FLAGS -std=c++11 -o GWev.exe \
+    s_fGW.cpp \
+    getGWMatrix.cpp \
+    s_fSOLan.c \
+    s_dthMul.c \
+    straw.o \
+    $COMMON_LIBS
+
+# Clean up object files
+rm -f straw.o
+
+echo "✅ Build completed successfully!"
+echo
+echo "You can now run:"
+echo "  ./Lan.exe  - for chromosome-specific analysis"
+echo "  ./GWev.exe - for genome-wide analysis" 

C++/Lanczos/build_windows.bat

@@ -0,0 +1,67 @@
+@echo off
+setlocal enabledelayedexpansion
+
+echo 🔧 Setting up build environment...
+
+REM Check if MinGW-w64 is installed and in PATH
+where g++ >nul 2>&1
+if %ERRORLEVEL% NEQ 0 (
+    echo Error: g++ not found. Please install MinGW-w64 and add it to your PATH
+    echo You can download it from: https://winlibs.com/
+    exit /b 1
+)
+
+REM Set paths - MODIFY THESE AS NEEDED
+set "MINGW_PATH=C:\mingw64"
+set "STRAW_PATH=%USERPROFILE%\straw"
+set "OPENBLAS_PATH=%MINGW_PATH%\opt\openblas"
+
+REM Check if straw exists
+if not exist "%STRAW_PATH%" (
+    echo ⚠️  Warning: straw library not found at %STRAW_PATH%
+    echo Please install straw library and place it in %STRAW_PATH%
+    echo or modify this script with the correct path
+    exit /b 1
+)
+
+echo 🔨 Building executables...
+
+REM Common compiler flags
+set "COMMON_FLAGS=-O2 -Wno-format-security -I%MINGW_PATH%\include -I%STRAW_PATH%\C++"
+set "COMMON_LIBS=-L%MINGW_PATH%\lib -lz -lcurl -lpthread -lopenblas -llapack -llapacke"
+
+REM First compile straw library
+echo Building straw library...
+g++ %COMMON_FLAGS% -c "%STRAW_PATH%\C++\straw.cpp" -o straw.o
+
+REM Compile Lan.exe
+echo Building Lan.exe...
+g++ %COMMON_FLAGS% -std=c++11 -o Lan.exe ^
+    s_fLan.cpp ^
+    s_fSOLan.c ^
+    s_dthMul.c ^
+    hgFlipSign.c ^
+    straw.o ^
+    -I. ^
+    %COMMON_LIBS%
+
+REM Compile GWev.exe
+echo Building GWev.exe...
+g++ %COMMON_FLAGS% -std=c++11 -o GWev.exe ^
+    s_fGW.cpp ^
+    getGWMatrix.cpp ^
+    s_fSOLan.c ^
+    s_dthMul.c ^
+    straw.o ^
+    %COMMON_LIBS%
+
+REM Clean up object files
+del straw.o
+
+echo ✅ Build completed successfully!
+echo.
+echo You can now run:
+echo   Lan.exe  - for chromosome-specific analysis
+echo   GWev.exe - for genome-wide analysis
+
+endlocal 

C++/Lanczos/getGWMatrix.cpp

@@ -13,15 +13,15 @@ unsigned int getMatrix(string fname, int binsize, string norm, string ob, bool i
 	string unit("BP");
 	ifstream fin;
 
-    long master = 0L;
+    int64_t master = 0LL;
     map<string, chromosome> chromosomeMap;
     string genomeID;
-    int version = 0;
-    long nviPosition = 0;
-    long nviLength = 0;
-    long totalFileSize;
+    int32_t nChrs = 0;
+    int32_t version = 0;
+    int64_t nviPosition = 0LL;
+    int64_t nviLength = 0LL;
+    int64_t totalFileSize;
 
-	int nChrs;
 	vector<std::string> chroms;
 	vector<int> chrLen;
 	fin.open(fname, fstream::in);

C++/Lanczos/s_dthMul.c

@@ -24,6 +24,7 @@ void *Mul(void *threadid) {
                res[i[p]] += x[p]*v[j[p]];
                res[j[p]] += x[p]*v[i[p]];
 	}
+	return NULL;
 }
 
 void utmvMul(unsigned int *i,unsigned int *j,float *x,long m,double *v,unsigned int k,double *res, int nth, double **rs) {