pax_global_header 0000666 0000000 0000000 00000000064 13532224264 0014515 g ustar 00root root 0000000 0000000 52 comment=fee2fed967355ccc44f219fa0776d2d4fdabc87b
Minimac4-1.0.2/ 0000775 0000000 0000000 00000000000 13532224264 0013156 5 ustar 00root root 0000000 0000000 Minimac4-1.0.2/.gitignore 0000664 0000000 0000000 00000000106 13532224264 0015143 0 ustar 00root root 0000000 0000000 .idea/
*.so
*.dylib
*.dll
*.lai
*.la
*.a
*.lib
*.slo
*.lo
*.o
*.obj Minimac4-1.0.2/CMakeLists.txt 0000664 0000000 0000000 00000003112 13532224264 0015713 0 ustar 00root root 0000000 0000000 cmake_minimum_required(VERSION 3.2)
project(minimac4 VERSION 1.0.2)
set(CMAKE_CXX_STANDARD 11)
execute_process(COMMAND date OUTPUT_VARIABLE DATE OUTPUT_STRIP_TRAILING_WHITESPACE)
execute_process(COMMAND whoami OUTPUT_VARIABLE USER OUTPUT_STRIP_TRAILING_WHITESPACE)
add_definitions(-DVERSION="${PROJECT_VERSION}" -DUSER="${USER}" -DDATE="${DATE}")
set(CMAKE_FIND_LIBRARY_SUFFIXES ".a;${CMAKE_FIND_LIBRARY_SUFFIXES}") # Prefer libz.a when both are available
find_package(OpenMP)
if (OPENMP_FOUND)
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
endif()
find_package(ZLIB REQUIRED)
find_library(STATGEN_LIBRARY StatGen)
add_executable(minimac4
src/Analysis.cpp
src/Analysis.h
src/AnalysisChunks.cpp
src/DosageData.cpp
src/DosageData.h
src/HaplotypeSet.cpp
src/HaplotypeSet.h
src/Imputation.cpp
src/Imputation.h
src/ImputationStatistics.cpp
src/ImputationStatistics.h
src/Main.cpp
src/MarkovModel.cpp
src/MarkovModel.h
src/MarkovParameters.cpp
src/MarkovParameters.h
src/MyVariables.h
src/Unique.cpp
src/Unique.h
src/Estimation.cpp
src/Estimation.h)
target_link_libraries(minimac4 ${STATGEN_LIBRARY} ${ZLIB_LIBRARIES})
install(TARGETS minimac4 RUNTIME DESTINATION bin)
set(CPACK_PACKAGE_VERSION_MAJOR ${PROJECT_VERSION_MAJOR})
set(CPACK_PACKAGE_VERSION_MINOR ${PROJECT_VERSION_MINOR})
set(CPACK_PACKAGE_VERSION_PATCH ${PROJECT_VERSION_PATCH})
include(CPack)
Minimac4-1.0.2/LICENSE 0000664 0000000 0000000 00000104513 13532224264 0014167 0 ustar 00root root 0000000 0000000 GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
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an absolute waiver of all civil liability in connection with the
Program, unless a warranty or assumption of liability accompanies a
copy of the Program in return for a fee.
END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest
to attach them to the start of each source file to most effectively
state the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.
Copyright (C)
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see .
Also add information on how to contact you by electronic and paper mail.
If the program does terminal interaction, make it output a short
notice like this when it starts in an interactive mode:
Copyright (C)
This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License. Of course, your program's commands
might be different; for a GUI interface, you would use an "about box".
You should also get your employer (if you work as a programmer) or school,
if any, to sign a "copyright disclaimer" for the program, if necessary.
For more information on this, and how to apply and follow the GNU GPL, see
.
The GNU General Public License does not permit incorporating your program
into proprietary programs. If your program is a subroutine library, you
may consider it more useful to permit linking proprietary applications with
the library. If this is what you want to do, use the GNU Lesser General
Public License instead of this License. But first, please read
.
Minimac4-1.0.2/README.md 0000664 0000000 0000000 00000003657 13532224264 0014450 0 ustar 00root root 0000000 0000000 # Minimac4
Minimac4 is a lower memory and more computationally efficient
implementation of the genotype imputation algorithms in
minimac/mininac2/minimac3.
<<< SEE http://genome.sph.umich.edu/wiki/Minimac4 FOR DOCUMENTATION >>>
Users should follow the following steps to compile Minimac4
## Prerequisites
Automatic installation of Minimac4 requires [cget](http://cget.readthedocs.io/en/latest/src/intro.html#installing-cget) and cmake v3.2. These prerequisites can be installed as follows:
Ubuntu 16.04
```
sudo apt-get install cmake python-pip python-dev
pip install cget
```
Ubuntu 14.04
```
sudo apt-get install software-properties-common
sudo add-apt-repository ppa:george-edison55/cmake-3.x
sudo apt-get update
sudo apt-get install cmake python-pip python-dev
pip install cget
```
MacOS
```
brew install cmake
sudo easy-install pip
pip install --user cget --ignore-installed six
```
## Installation
The easiest way to install Minimac4 and its dependencies is to use the install.sh file provided.
```
cd Minimac4
bash install.sh
```
Alternatively, you can use cget as follows:
```bash
cget install --prefix statgen/Minimac4
```
Alternatively, you can setup a dev environment cmake directly.
```bash
cd Minimac4
cget install -f ./requirements.txt # Install dependencies locally.
mkdir build && cd build # Create out of source build directory.
cmake -DCMAKE_TOOLCHAIN_FILE=../cget/cget/cget.cmake .. # Configure project with dependency paths.
make # Build.
```
## Usage
A typical Minimac4 command line for imputation is as follows
```bash
minimac4 --refHaps refPanel.m3vcf \
--haps targetStudy.vcf \
--prefix testRun
```
Here refPanel.m3vcf is the reference panel used in M3VCF format (e.g. 1000 Genomes),
targetStudy.vcf is the phased GWAS data in VCF format,
and testRun is the prefix for the output files.
Minimac4-1.0.2/dep/ 0000775 0000000 0000000 00000000000 13532224264 0013726 5 ustar 00root root 0000000 0000000 Minimac4-1.0.2/dep/libstatgen.cmake 0000664 0000000 0000000 00000001406 13532224264 0017065 0 ustar 00root root 0000000 0000000 cmake_minimum_required(VERSION 3.2)
project(libStatGen VERSION 1.0.0)
#execute_process(COMMAND ./configure --prefix=${CMAKE_INSTALL_PREFIX} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
add_custom_target(libStatGen ALL COMMAND ${CMAKE_COMMAND} -E env CPATH=${CGET_PREFIX}/include make WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} COMMENT "Builing libStatGen ...")
file(GLOB_RECURSE LSG_HEADER_LIST "bam/*.h" "fastq/*.h" "general/*.h" "glf/*.h" "samtools/*.h" "vcf/*.h")
install(FILES ${LSG_HEADER_LIST} DESTINATION include)
if (BUILD_SHARED_LIBS)
install(FILES ${CMAKE_SHARED_LIBRARY_PREFIX}StatGen${CMAKE_SHARED_LIBRARY_SUFFIX} DESTINATION lib)
else()
install(FILES ${CMAKE_STATIC_LIBRARY_PREFIX}StatGen${CMAKE_STATIC_LIBRARY_SUFFIX} DESTINATION lib)
endif()
Minimac4-1.0.2/install.sh 0000775 0000000 0000000 00000000551 13532224264 0015164 0 ustar 00root root 0000000 0000000 #!/bin/sh
rm -rf cget/ release-build/ install.log
echo -e "Installing Dependencies - Libstatgen ..."
cget install -f requirements.txt &> install.log
mkdir release-build
cd release-build/
echo -e "Generating MakeFiles ..."
cmake -DCMAKE_TOOLCHAIN_FILE=../cget/cget/cget.cmake -DCMAKE_BUILD_TYPE=Release ..
make
echo "Binary created at /release-build/minimac4"
Minimac4-1.0.2/package-linux.sh 0000775 0000000 0000000 00000001447 13532224264 0016253 0 ustar 00root root 0000000 0000000 #!/bin/bash
# Usage: docker build -t packaging-ubuntu16 -f packaging-dockerfile-ubuntu16 .
# docker run -v `pwd`:/app -w /app packaging-ubuntu16 ./package-linux.sh
set -euo pipefail
src_dir=`pwd`
build_dir=${src_dir}/pkg-build
rm -rf ${build_dir}
mkdir ${build_dir}
cd ${build_dir}
export CFLAGS="-fPIC"
export CXXFLAGS="-fPIC"
cget install -f ${src_dir}/requirements.txt
unset CFLAGS
unset CXXFLAGS
cmake \
-DCMAKE_BUILD_TYPE=Release \
-DCMAKE_TOOLCHAIN_FILE=cget/cget/cget.cmake \
-DCMAKE_EXE_LINKER_FLAGS="-static -static-libgcc -static-libstdc++" \
-DCPACK_GENERATOR="STGZ;DEB;RPM" \
-DCPACK_PACKAGE_CONTACT="csg-devel@umich.edu" \
${src_dir}
make
#make manuals
make package
mkdir -p ${src_dir}/pkg/
cp minimac4-*.{sh,deb,rpm} ${src_dir}/pkg/
cd ${src_dir}
rm -r ${build_dir}
Minimac4-1.0.2/packaging-dockerfile-ubuntu16 0000664 0000000 0000000 00000000322 13532224264 0020616 0 ustar 00root root 0000000 0000000 FROM ubuntu:16.04
RUN apt-get update && apt-get install -y \
build-essential \
curl \
cmake \
git \
help2man \
lsb-release \
python \
python-pip \
rpm
RUN pip install cget
Minimac4-1.0.2/requirements.txt 0000664 0000000 0000000 00000000130 13532224264 0016434 0 ustar 00root root 0000000 0000000 zlib,http://zlib.net/zlib-1.2.11.tar.gz
statgen/libStatGen --cmake dep/libstatgen.cmake
Minimac4-1.0.2/src/ 0000775 0000000 0000000 00000000000 13532224264 0013745 5 ustar 00root root 0000000 0000000 Minimac4-1.0.2/src/Analysis.cpp 0000664 0000000 0000000 00000177144 13532224264 0016252 0 ustar 00root root 0000000 0000000 #include "Analysis.h"
#include "Estimation.h"
#include
#include "assert.h"
# define RECOM_MIN 1e-05
void MyTokenize(vector &result, const char *input, const char *delimiter, int Number)
{
size_t wordCount = 1;
result[0].clear();
std::string *word = &result[0];
while (*input)
{
if (*input==*delimiter)
{
// we got a delimeter, and since an empty word following
// a delimeter still counts as a word, we allocate it here
wordCount++;
if((int)wordCount>Number)
return;
result[wordCount-1].clear();
word = &result[wordCount-1];
}
else
{
word->push_back(*input);
}
input++;
}
}
bool Analysis::CreateRecombinationMap()
{
int FirstIndex=0;
while(referencePanel.VariantList[FirstIndex].bpmyModelVariables.referenceEstimates && !CreateRecombinationMap())
{
cout << "\n Program Exiting ... \n\n";
return "Genetic.Map.Load.Error";
}
if (!targetPanel.ScaffoldGWAStoReference(referencePanel,*MyAllVariables))
{
cout << "\n Program Exiting ... \n\n";
return "Reference.Panel.Load.Error";
}
cout<<"\n ------------------------------------------------------------------------------"<myOutFormat.memUsage)
{
cout<<" ------------------------------------------------------------------------------"<myModelVariables.cpus);
if(MyAllVariables->myOutFormat.vcfBuffer >= targetPanel.numSamples)
MyAllVariables->myOutFormat.vcfBuffer=targetPanel.numSamples;
thisDataFast.InitializeOutputFiles(targetPanel, MyAllVariables->myOutFormat.vcfBuffer, MaxRefMarkerSize, MaxGwasMarkerSize);
if(MyAllVariables->myOutFormat.memUsage)
{
cout<<" Estimating Memory based on a single chunk ..."<< endl;
readm3vcfFileChunk(0, CurrentRefPanel);
readVcfFileChunk(0, CurrentTarPanelChipOnly);
GetCurrentPanelReady(0, CurrentRefPanel, CurrentRefPanelChipOnly, CurrentTarPanelChipOnly, thisDataFast);
cout<myModelVariables.minimac3)
thisDataFast.Minimac3ImputeThisChunk(i, CurrentRefPanel, CurrentTarPanelChipOnly, CurrentRefPanelChipOnly);
else
thisDataFast.ImputeThisChunk(i, CurrentRefPanel, CurrentTarPanelChipOnly, CurrentRefPanelChipOnly);
//abort();
TimeToImpute+=(thisDataFast.TimeToImpute);
TimeToWrite+=(thisDataFast.TimeToWrite);
TimeToCompress+=(thisDataFast.TimeToCompress);
AppendtoMainVcfFaster(i,thisDataFast.TotalNovcfParts);
if(MyAllVariables->myOutFormat.meta)
AppendtoMainLooVcfFaster(i,thisDataFast.TotalNovcfParts);
PrintInfoFile(i);
time_load = time(0) - time_prev;
cout << "\n Time taken for this chunk = " << time_load << " seconds."<myHapDataVariables.end==0 && MyAllVariables->myOutFormat.TypedOnly)
// assert(FileReadIndex==targetPanel.importIndexListSize);
// asserassertt(OverCount==targetPanel.numOverlapMarkers);
// assert(TypOnlyCount==targetPanel.numTypedOnlyMarkers);
// assert(RefCOUNT==referencePanel.NoBlocks);
CloseStreamOutputFiles();
return "Success";
}
void Analysis::PrintInfoFile(int ChunkNo)
{
InfoPrintStringLength=0;
int RefStartPos = MyRefVariantNumber[ChunkNo][0];
info = ifopen(MyAllVariables->myOutFormat.OutPrefix + ".info", "a");
int i=0;
for (int index = 0; index < CurrentRefPanel.RefTypedTotalCount; index++)
{
if(CurrentRefPanel.RefTypedIndex[index]==-1)
{
variant &thisVariant = referencePanel.VariantList[i+RefStartPos];
if(i>=CurrentRefPanel.PrintStartIndex && i <= CurrentRefPanel.PrintEndIndex)
{
double TarFreq = stats.AlleleFrequency(i);
InfoPrintStringLength+=sprintf(InfoPrintStringPointer+InfoPrintStringLength , "%s\t%s\t%s\t%.5f\t%.5f\t%.5f\t%.5f\t",
MyAllVariables->myOutFormat.RsId ? thisVariant.rsid.c_str(): thisVariant.name.c_str(),
thisVariant.refAlleleString.c_str(),
thisVariant.altAlleleString.c_str(),
TarFreq,
TarFreq > 0.5 ? 1.0 - TarFreq : TarFreq,
stats.AverageCallScore(i),
stats.Rsq(i));
if (!CurrentRefPanel.Targetmissing[i])
{
InfoPrintStringLength+=sprintf(InfoPrintStringPointer+InfoPrintStringLength , "Genotyped\t%.3f\t%.3f\t%.5f\t%.5f\t%.5f\n",
stats.LooRsq(i), stats.EmpiricalR(i), stats.EmpiricalRsq(i),
stats.LooMajorDose(i), stats.LooMinorDose(i));
}
else
InfoPrintStringLength+=sprintf(InfoPrintStringPointer+InfoPrintStringLength , "Imputed\t-\t-\t-\t-\t-\n");
}
i++;
}
else
{
// if(ChunkNo==2 && index==26751)
// abort();
int MappingIndex = CurrentRefPanel.RefTypedIndex[index];
if(MappingIndex>=CurrentTarPanelChipOnly.PrintTypedOnlyStartIndex && MappingIndex<=CurrentTarPanelChipOnly.PrintTypedOnlyEndIndex)
{
variant ThisTypedVariant = CurrentTarPanelChipOnly.TypedOnlyVariantList[MappingIndex];
double TarFreq = CurrentTarPanelChipOnly.GWASOnlyAlleleFreq[MappingIndex];
InfoPrintStringLength+=sprintf(InfoPrintStringPointer+InfoPrintStringLength , "%s\t%s\t%s\t%.5f\t%.5f\t-\t-\tTyped_Only\t-\t-\t-\t-\t-\n",
MyAllVariables->myOutFormat.RsId ? ThisTypedVariant.rsid.c_str(): ThisTypedVariant.name.c_str(),
ThisTypedVariant.refAlleleString.c_str(),
ThisTypedVariant.altAlleleString.c_str(),
TarFreq,
TarFreq > 0.5 ?
1.0 - TarFreq : TarFreq);
}
}
if(InfoPrintStringLength > 0.9 * (float)(MyAllVariables->myOutFormat.PrintBuffer))
{
ifprintf(info,"%s",InfoPrintStringPointer);
InfoPrintStringLength=0;
}
}
if(InfoPrintStringLength >0)
{
ifprintf(info,"%s",InfoPrintStringPointer);
InfoPrintStringLength=0;
}
ifclose(info);
}
void Analysis::AppendtoMainLooVcfFaster(int ChunkNo, int MaxIndex)
{
VcfPrintStringLength=0;
int time_prev = time(0);
int RefStartPos = MyRefVariantNumber[ChunkNo][0];
vector vcfLoodosepartialList(MaxIndex);
vcfLoodosepartial = ifopen(MyAllVariables->myOutFormat.OutPrefix + ".empiricalDose.vcf" + (MyAllVariables->myOutFormat.gzip ? ".gz" : ""), "a", MyAllVariables->myOutFormat.gzip ?InputFile::BGZF:InputFile::UNCOMPRESSED);
for(int i=1;i<=MaxIndex;i++)
{
string tempFileIndex(MyAllVariables->myOutFormat.OutPrefix);
stringstream strs,strs1;
strs<<(i);
strs1<<(ChunkNo+1);
tempFileIndex+=(".chunk."+(string)(strs1.str())+".empiricalDose.part." +
(string)(strs.str())+".vcf.gz");
vcfLoodosepartialList[i-1] = ifopen(tempFileIndex.c_str(), "r");
}
string line;
int i=0;
for (int index = 0; index < CurrentRefPanel.RefTypedTotalCount; index++)
{
if(CurrentRefPanel.RefTypedIndex[index]==-1)
{
if(i>=CurrentRefPanel.PrintStartIndex && i <= CurrentRefPanel.PrintEndIndex)
{
if(!CurrentRefPanel.Targetmissing[i])
{
variant &tempVariant = referencePanel.VariantList[i+RefStartPos];
VcfPrintStringLength+=sprintf(VcfPrintStringPointer + VcfPrintStringLength,"%s\t%d\t%s\t%s\t%s\t.\tPASS",
tempVariant.chr.c_str(),
tempVariant.bp,
MyAllVariables->myOutFormat.RsId?tempVariant.rsid.c_str():tempVariant.name.c_str(),
tempVariant.refAlleleString.c_str(),
tempVariant.altAlleleString.c_str());
VcfPrintStringLength+=sprintf(VcfPrintStringPointer + VcfPrintStringLength,"\tTYPED\tGT:LDS");
for(int j=1;j<=MaxIndex;j++)
{
line.clear();
vcfLoodosepartialList[j-1]->readLine(line);
VcfPrintStringLength+=sprintf(VcfPrintStringPointer + VcfPrintStringLength,"%s",line.c_str());
}
VcfPrintStringLength+=sprintf(VcfPrintStringPointer + VcfPrintStringLength,"\n");
}
}
i++;
}
if(VcfPrintStringLength > 0.9 * (float)(MyAllVariables->myOutFormat.PrintBuffer))
{
ifprintf(vcfLoodosepartial,"%s",VcfPrintStringPointer);
VcfPrintStringLength=0;
}
}
if(VcfPrintStringLength > 0)
{
ifprintf(vcfLoodosepartial,"%s",VcfPrintStringPointer);
VcfPrintStringLength=0;
}
for(int i=1;i<=MaxIndex;i++)
{
ifclose(vcfLoodosepartialList[i-1]);
string tempFileIndex(MyAllVariables->myOutFormat.OutPrefix);
stringstream strs,strs1;
strs<<(i);
strs1<<(ChunkNo+1);
tempFileIndex+=(".chunk."+(string)(strs1.str())+".empiricalDose.part." +
(string)(strs.str())+".vcf.gz");
remove(tempFileIndex.c_str());
}
TimeToWrite+=( time(0) - time_prev);
ifclose(vcfLoodosepartial);
}
void Analysis::AppendtoMainVcfFaster(int ChunkNo, int MaxIndex)
{
VcfPrintStringLength=0;
int time_prev = time(0);
int RefStartPos = MyRefVariantNumber[ChunkNo][0];
printf("\n Appending chunk to final output VCF File : %s ",(MyAllVariables->myOutFormat.OutPrefix + ".dose.vcf" + (MyAllVariables->myOutFormat.gzip ? ".gz" : "")).c_str() );
cout< vcfdosepartialList(MaxIndex);
vcfdosepartial = ifopen(MyAllVariables->myOutFormat.OutPrefix + ".dose.vcf" + (MyAllVariables->myOutFormat.gzip ? ".gz" : ""), "a", MyAllVariables->myOutFormat.gzip ?InputFile::BGZF:InputFile::UNCOMPRESSED);
for(int i=1;i<=MaxIndex;i++)
{
string tempFileIndex(MyAllVariables->myOutFormat.OutPrefix);
stringstream strs,strs1;
strs<<(i);
strs1<<(ChunkNo+1);
tempFileIndex+=(".chunk."+(string)(strs1.str())+".dose.part." +
(string)(strs.str())+".vcf.gz");
vcfdosepartialList[i-1] = ifopen(tempFileIndex.c_str(), "r");
}
string line;
int i=0;
for (int index = 0; index < CurrentRefPanel.RefTypedTotalCount; index++)
{
if(CurrentRefPanel.RefTypedIndex[index]==-1)
{
if(i>=CurrentRefPanel.PrintStartIndex && i <= CurrentRefPanel.PrintEndIndex)
{
variant &tempVariant = referencePanel.VariantList[i+RefStartPos];
VcfPrintStringLength+=sprintf(VcfPrintStringPointer + VcfPrintStringLength,"%s\t%d\t%s\t%s\t%s\t.\tPASS",
tempVariant.chr.c_str(),
tempVariant.bp,
MyAllVariables->myOutFormat.RsId?tempVariant.rsid.c_str():tempVariant.name.c_str(),
tempVariant.refAlleleString.c_str(),
tempVariant.altAlleleString.c_str());
double freq = stats.AlleleFrequency(i);
VcfPrintStringLength+=sprintf(VcfPrintStringPointer + VcfPrintStringLength,"\tAF=%.5f;MAF=%.5f;R2=%.5f",
freq, freq > 0.5 ? 1.0 - freq : freq, stats.Rsq(i));
if(!CurrentRefPanel.Targetmissing[i])
VcfPrintStringLength+=sprintf(VcfPrintStringPointer + VcfPrintStringLength,";ER2=%.5f;TYPED",stats.EmpiricalRsq(i));
else
VcfPrintStringLength+=sprintf(VcfPrintStringPointer + VcfPrintStringLength,";IMPUTED");
VcfPrintStringLength+=sprintf(VcfPrintStringPointer + VcfPrintStringLength,"\t%s",MyAllVariables->myOutFormat.formatStringForVCF.c_str());
for(int j=1;j<=MaxIndex;j++)
{
line.clear();
vcfdosepartialList[j-1]->readLine(line);
VcfPrintStringLength+=sprintf(VcfPrintStringPointer + VcfPrintStringLength,"%s",line.c_str());
}
VcfPrintStringLength+=sprintf(VcfPrintStringPointer + VcfPrintStringLength,"\n");
}
i++;
}
else
{
int MappingIndex = CurrentRefPanel.RefTypedIndex[index];
if(MappingIndex>=CurrentTarPanelChipOnly.PrintTypedOnlyStartIndex && MappingIndex<=CurrentTarPanelChipOnly.PrintTypedOnlyEndIndex)
{
variant &ThisTypedVariant = (CurrentTarPanelChipOnly.TypedOnlyVariantList[CurrentRefPanel.RefTypedIndex[index]]);
VcfPrintStringLength+=sprintf(VcfPrintStringPointer + VcfPrintStringLength,"%s\t%d\t%s\t%s\t%s\t.\tPASS",
ThisTypedVariant.chr.c_str(),
ThisTypedVariant.bp,
MyAllVariables->myOutFormat.RsId? ThisTypedVariant.rsid.c_str():ThisTypedVariant.name.c_str(),
ThisTypedVariant.refAlleleString.c_str(),
ThisTypedVariant.altAlleleString.c_str());
double &freq = (CurrentTarPanelChipOnly.GWASOnlyAlleleFreq[CurrentRefPanel.RefTypedIndex[index]]);
VcfPrintStringLength+=sprintf(VcfPrintStringPointer + VcfPrintStringLength,"\tAF=%.5f;MAF=%.5f;TYPED_ONLY",
freq, freq > 0.5 ? 1.0 - freq : freq);
VcfPrintStringLength+=sprintf(VcfPrintStringPointer + VcfPrintStringLength,"\t%s",MyAllVariables->myOutFormat.formatStringForVCF.c_str());
for(int j=1;j<=MaxIndex;j++)
{
line.clear();
vcfdosepartialList[j-1]->readLine(line);
VcfPrintStringLength+=sprintf(VcfPrintStringPointer + VcfPrintStringLength,"%s",line.c_str());
}
VcfPrintStringLength+=sprintf(VcfPrintStringPointer + VcfPrintStringLength,"\n");
}
}
if(VcfPrintStringLength > 0.9 * (float)(MyAllVariables->myOutFormat.PrintBuffer))
{
ifprintf(vcfdosepartial,"%s",VcfPrintStringPointer);
VcfPrintStringLength=0;
}
}
if(VcfPrintStringLength > 0)
{
ifprintf(vcfdosepartial,"%s",VcfPrintStringPointer);
VcfPrintStringLength=0;
}
for(int i=1;i<=MaxIndex;i++)
{
ifclose(vcfdosepartialList[i-1]);
string tempFileIndex(MyAllVariables->myOutFormat.OutPrefix);
stringstream strs,strs1;
strs<<(i);
strs1<<(ChunkNo+1);
tempFileIndex+=(".chunk."+(string)(strs1.str())+".dose.part." +
(string)(strs.str())+".vcf.gz");
remove(tempFileIndex.c_str());
}
TimeToWrite+=( time(0) - time_prev);
cout << " Appending successful (" << time(0) - time_prev << " seconds) !!!"< &ThisInfoVector = ThisRefPanel.ReducedStructureInfo;
string line;
int ThisInfoVectorIndex=0;
int ThisChunkFilledTillRef = 0, ThisChunkStartFromRef = 0;
int StartBlock=MyChunksInfoNumber[ChunkNo][0];
int EndBlock=MyChunksInfoNumber[ChunkNo][1];
int StartNextBlock=MyChunksInfoNumber[ChunkNo+1][0];
int blockIndex=StartBlock;
int FilltheTop=0;
while(FilltheTop < PrevChunkFilledTillRef)
{
ThisInfoVector[blockIndex-StartBlock] = ThisInfoVector[PrevChunkStartFromRef + FilltheTop] ;
blockIndex++;
FilltheTop++;
}
ThisChunkStartFromRef=FilltheTop;
for(;blockIndex<=EndBlock;blockIndex++)
{
RefCOUNT++;
line.clear();
RefFileStream->readLine(line);
// assert(ThisInfoVectorIndex + PrevChunkFilledTillRef < MaxInfoVectorSize);
ReducedHaplotypeInfo &tempBlock=ThisInfoVector[ThisInfoVectorIndex + PrevChunkFilledTillRef];
ThisInfoVectorIndex++;
referencePanel.ReadBlockHeader(line, tempBlock);
referencePanel.ReadThisBlock(RefFileStream, blockIndex, tempBlock);
if(blockIndex>=StartNextBlock)
{
// assert(ThisChunkFilledTillRef < MaxInfoVectorSize);
ThisChunkFilledTillRef++;
}
else
{
ThisChunkStartFromRef++;
}
}
PrevChunkFilledTillRef=ThisChunkFilledTillRef;
PrevChunkStartFromRef=ThisChunkStartFromRef;
TimeToRead+=( time(0) - time_prev);
}
void Analysis::readVcfFileChunk(int ChunkNo, HaplotypeSet &ThisTargetPanel)
{
int time_prev = time(0);
cout << " Reading chunk from target/GWAS panel ... "<=StartNextPos)
{
// assert( (ThisChunkStartTillTar) < MaxGwasMarkerSize);
ThisChunkStartTillTar++;
}
else
{
ThisChunkStartFromTar++;
}
// assert(overlapImportIndexmyOutFormat.TypedOnly)
{
// assert( (GWASnumtoBeWrittenRecords + PrevChunkFilledTillTarOnly) < MaxTypedOnlyMarkerSize);
variant tempVar=targetPanel.TypedOnlyVariantList[MainTypedOnlyImportIndex];
ThisTargetPanel.TypedOnlyVariantList[GWASnumtoBeWrittenRecords + PrevChunkFilledTillTarOnly]=tempVar;
int haplotype_index = 0;
for (int i = 0; i<(targetPanel.numSamples); i++)
{
//haplotype_index=(2*i);
if(targetPanel.SampleNoHaplotypes[i]!=record.getNumGTs(i))
{
cout << "\n ERROR !!! GWAS Sample "<< targetPanel.individualName[i]<<" changes its ploidy at variant ";
cout << tempVar.name <=TypedOnlyNextStartPos)
{
// assert( (ThisChunkStartTillTarOnly) < MaxTypedOnlyMarkerSize);
ThisChunkStartTillTarOnly++;
}
else
{
ThisChunkStartFromTarOnly++;
}
// assert(MainTypedOnlyImportIndexmyOutFormat.gzip;
if(MyAllVariables->myOutFormat.vcfOutput)
{
VcfPrintStringPointer = (char*)malloc(sizeof(char) * (MyAllVariables->myOutFormat.PrintBuffer));
vcfdosepartial = ifopen(MyAllVariables->myOutFormat.OutPrefix + ".dose.vcf" + (gzip ? ".gz" : ""), "wb", gzip ?InputFile::BGZF:InputFile::UNCOMPRESSED);
if(vcfdosepartial==NULL)
{
cout <<"\n\n ERROR !!! \n Could NOT create the following file : "<< MyAllVariables->myOutFormat.OutPrefix + ".dose.vcf" + (gzip ? ".gz" : "") <tm_year + 1900),(now->tm_mon + 1) ,now->tm_mday);
ifprintf(vcfdosepartial,"##source=Minimac4.v%s\n",VERSION);
ifprintf(vcfdosepartial,"##contig=\n",referencePanel.finChromosome.c_str());
ifprintf(vcfdosepartial,"##INFO=\n");
ifprintf(vcfdosepartial,"##INFO=\n");
ifprintf(vcfdosepartial,"##INFO=\n");
ifprintf(vcfdosepartial,"##INFO=\n");
ifprintf(vcfdosepartial,"##INFO=\n");
ifprintf(vcfdosepartial,"##INFO=\n");
ifprintf(vcfdosepartial,"##INFO=\n");
if(MyAllVariables->myOutFormat.GT)
ifprintf(vcfdosepartial,"##FORMAT=\n");
if(MyAllVariables->myOutFormat.DS)
ifprintf(vcfdosepartial,"##FORMAT=\n");
if(MyAllVariables->myOutFormat.HDS)
ifprintf(vcfdosepartial,"##FORMAT=\n");
if(MyAllVariables->myOutFormat.GP)
ifprintf(vcfdosepartial,"##FORMAT=\n");
if(MyAllVariables->myOutFormat.SD)
ifprintf(vcfdosepartial,"##FORMAT=\n");
ifprintf(vcfdosepartial,"##minimac4_Command=%s\n",MyAllVariables->myOutFormat.CommandLine.c_str());
ifprintf(vcfdosepartial,"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT");
for(int Id=0;IdmyOutFormat.meta)
{
vcfLoodosepartial = ifopen(MyAllVariables->myOutFormat.OutPrefix + ".empiricalDose.vcf" + (gzip ? ".gz" : ""), "wb", gzip ?InputFile::BGZF:InputFile::UNCOMPRESSED);
if(vcfLoodosepartial==NULL)
{
cout <<"\n\n ERROR !!! \n Could NOT create the following file : "<< MyAllVariables->myOutFormat.OutPrefix + ".empiricalDose.vcf" + (gzip ? ".gz" : "") <tm_year + 1900),(now->tm_mon + 1) ,now->tm_mday);
ifprintf(vcfLoodosepartial,"##source=Minimac4.v%s\n",VERSION);
ifprintf(vcfLoodosepartial,"##contig=\n",referencePanel.finChromosome.c_str());
ifprintf(vcfLoodosepartial,"##INFO=\n");
ifprintf(vcfLoodosepartial,"##FORMAT=\n");
ifprintf(vcfLoodosepartial,"##FORMAT=\n");
ifprintf(vcfLoodosepartial,"##minimac4_Command=%s\n",MyAllVariables->myOutFormat.CommandLine.c_str());
ifprintf(vcfLoodosepartial,"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT");
for(int Id=0;IdmyOutFormat.doseOutput)
{
dosages = ifopen(MyAllVariables->myOutFormat.OutPrefix + ".dose" + (gzip ? ".gz" : ""), "wb",(gzip ? InputFile::BGZF:InputFile::UNCOMPRESSED) );
if(dosages==NULL)
{
cout <<"\n\n ERROR !!! \n Could NOT create the following file : "<< MyAllVariables->myOutFormat.OutPrefix + ".dose" + (gzip ? ".gz" : "") <myOutFormat.PrintBuffer));
info = ifopen(MyAllVariables->myOutFormat.OutPrefix + ".info", "wb");
if(info==NULL)
{
cout <<"\n\n ERROR !!! \n Could NOT create the following file : "<< MyAllVariables->myOutFormat.OutPrefix + ".info" <myOutFormat.hapOutput && !MyAllVariables->myOutFormat.unphasedOutput)
{
ifclose(hapdose);
}
if(MyAllVariables->myOutFormat.vcfOutput)
{
ifclose(vcfdosepartial);
}
if(MyAllVariables->myOutFormat.meta)
{
ifclose(vcfLoodosepartial);
}
if(MyAllVariables->myOutFormat.doseOutput)
{
ifclose(dosages);
}
ifclose(RefFileStream);
TarFileStream.close();
cout<<" ------------------------------------------------------------------------------"<1073741824)
{
Fact=1073741824;
Tag="Gb";
}
else if(Total>1048576)
{
Fact=1048576;
Tag="Mb";
}
else if(Total>1024)
{
Fact=1024;
Tag="Kbytes";
}
else
{
Fact=1;
Tag="Bytes";
}
printf("\n Memory occupied by Full Reference Panel ~ %.3f %s", (double) RefMem/(Fact),Tag.c_str());
printf("\n Memory occupied by Compressed Reference Panel ~ %.3f %s", (double) ComRefMem/(Fact),Tag.c_str());
printf("\n Memory occupied by Target/GWAS Panel ~ %.3f %s", (double) TarMem/(Fact),Tag.c_str());
printf("\n Memory occupied by Likelihood Matrices ~ %.3f %s", (double) ProbMem/(Fact),Tag.c_str());
printf("\n Memory occupied by Dosage Data ~ %.3f %s", (double) DosageMem/(Fact),Tag.c_str());
printf("\n TOTAL Memory by the process ~ %.3f %s", (double) (Total)/(Fact),Tag.c_str());
cout<myOutFormat.gzip;
cout<myOutFormat.OutPrefix + ".info" <myOutFormat.hapOutput && !MyAllVariables->myOutFormat.unphasedOutput)
{
ifclose(hapdose);
cout<<" Haplotype Dosage information written to : "<myOutFormat.OutPrefix + ".hapDose" + (gzip ? ".gz" : "")<myOutFormat.vcfOutput)
{
ifclose(vcfdosepartial);
free(VcfPrintStringPointer);
cout<<" Imputed VCF information written to : "<< MyAllVariables->myOutFormat.OutPrefix + ".dose.vcf" + (gzip ? ".gz" : "")<myOutFormat.meta)
{
ifclose(vcfLoodosepartial);
cout<<" Empirical Dosage VCF written to : "<< MyAllVariables->myOutFormat.OutPrefix + ".empiricalDose.vcf" + (gzip ? ".gz" : "")<myOutFormat.doseOutput)
{
ifclose(dosages);
cout<<" Dosage information written to : "<< MyAllVariables->myOutFormat.OutPrefix + ".dose" + (gzip ? ".gz" : "")<0)
{
int TOnlyStartPos = MyTypdedOnlyVariantNumber[ChunkNo][0];
int TOnlyEndPos = MyTypdedOnlyVariantNumber[ChunkNo][1];
int i=TOnlyStartPos;
if(ChunkNo==0)
{
if(MyAllVariables->myHapDataVariables.CHR!="")
{
while(targetPanel.TypedOnlyVariantList[i].bp < MyAllVariables->myHapDataVariables.start)
{
i++;
}
}
}
else
{
while(targetPanel.TypedOnlyVariantList[i].bp < MyChunks[ChunkNo][1])
{
i++;
}
}
ThisTarPanel.PrintTypedOnlyStartIndex=i-TOnlyStartPos;
if(ChunkNo==(noChunks-1))
{
if(MyAllVariables->myHapDataVariables.CHR!="")
{
for(; i <= TOnlyEndPos; i++)
if(targetPanel.TypedOnlyVariantList[i].bp > MyAllVariables->myHapDataVariables.end)
break;
}
else
i=TOnlyEndPos+1;
}
else
{
for(; i <= TOnlyEndPos; i++)
if(targetPanel.TypedOnlyVariantList[i].bp > MyChunks[ChunkNo][2])
break;
}
ThisTarPanel.PrintTypedOnlyEndIndex=i-TOnlyStartPos-1;
// assert(ThisTarPanel.PrintTypedOnlyStartIndex <= ThisTarPanel.numTypedOnlyMarkers);
// assert(ThisTarPanel.PrintTypedOnlyEndIndex <= ThisTarPanel.numTypedOnlyMarkers);
}
int RefStartPos = MyRefVariantNumber[ChunkNo][0];
int RefEndPos = MyRefVariantNumber[ChunkNo][1];
int i=RefStartPos;
if(ChunkNo==0)
{
if(MyAllVariables->myHapDataVariables.CHR!="")
{
while(referencePanel.VariantList[i].bp < MyAllVariables->myHapDataVariables.start)
{
i++;
}
}
}
else
{
while(referencePanel.VariantList[i].bp < MyChunks[ChunkNo][1])
{
i++;
}
}
ThisRefPanel.PrintStartIndex=i-RefStartPos;
if(ChunkNo==(noChunks-1))
{
if(MyAllVariables->myHapDataVariables.CHR!="")
{
for(; i <= RefEndPos; i++)
if(referencePanel.VariantList[i].bp > MyAllVariables->myHapDataVariables.end)
break;
}
else
i=RefEndPos+1;
}
else
{
for(; i <= RefEndPos; i++)
if(referencePanel.VariantList[i].bp > MyChunks[ChunkNo][2])
break;
}
ThisRefPanel.PrintEndIndex=i-RefStartPos-1;
// assert(ThisRefPanel.PrintStartIndex < ThisRefPanel.numMarkers);
// assert(ThisRefPanel.PrintEndIndex < ThisRefPanel.numMarkers);
}
void Analysis::GetCurrentPanelReady(int ChunkNo, HaplotypeSet &ThisRefPanel,
HaplotypeSet &ThisRefChipOnlyPanel, HaplotypeSet &ThisTarPanel,
Imputation &thisDataFast)
{
int RefStartPos = MyRefVariantNumber[ChunkNo][0];
int RefEndPos = MyRefVariantNumber[ChunkNo][1];
int TarStartPos = MyTargetVariantNumber[ChunkNo][0];
// int TarEndPos = MyTargetVariantNumber[ChunkNo][1];
int RefStartInfo = MyChunksInfoNumber[ChunkNo][0];
int RefEndInfo = MyChunksInfoNumber[ChunkNo][1];
int NoRefMarkers = RefEndPos - RefStartPos + 1;
int NoGwasMarkers =MyTargetVariantNumber[ChunkNo][2];
int NoTOnlyMarkers =MyTypdedOnlyVariantNumber[ChunkNo][2];
// initialize typical variants
ThisRefPanel.numMarkers=NoRefMarkers;
ThisRefChipOnlyPanel.numMarkers=NoGwasMarkers;
ThisRefPanel.NoBlocks = MyChunksInfoNumber[ChunkNo][2];
ThisTarPanel.numMarkers=NoGwasMarkers;
ThisTarPanel.numOverlapMarkers=NoGwasMarkers;
ThisTarPanel.numTypedOnlyMarkers=NoTOnlyMarkers;
int i;
// create new start and end indices for RefInfo
{
ThisRefPanel.ReducedStructureInfo[0].startIndex = 0;
for(i=RefStartInfo; i &Mapper = ThisRefPanel.MarkerToReducedInfoMapper;
int j;
for(i=0;i0
// && targetPanel.TargetMissingTypedOnly[ThisIndex]!=-1
&& targetPanel.TargetMissingTypedOnly[ThisIndex] < (RefStartPos))
{
ThisIndex++;
}
int counter=RefStartPos;
while(counter<=RefEndPos && ThisIndex<(int) targetPanel.TargetMissingTypedOnly.size())
{
if(counter<=targetPanel.TargetMissingTypedOnly[ThisIndex])
{
ThisRefPanel.RefTypedIndex.push_back(-1);
counter++;
}
else
{
// assert(ThisMappedIndextargetPanel.TargetMissingTypedOnly[ThisIndex])
{
// assert(ThisMappedIndex= 0);
// assert( (targetPanel.MapTarToRef[i+TarStartPos] - RefStartPos ) < NoRefMarkers);
ThisRefPanel.MapTarToRef[i] = targetPanel.MapTarToRef[i+TarStartPos] - RefStartPos;
ThisRefPanel.Targetmissing[ThisRefPanel.MapTarToRef[i]]=false;
// ThisTarPanel.VariantList[i]=targetPanel.OverlapOnlyVariantList[i+TarStartPos];
if(i>0)
{
ThisTarPanel.FlankRegionEnd[i-1]= (ThisRefPanel.MapTarToRef[i-1] + ThisRefPanel.MapTarToRef[i])/2;
ThisTarPanel.FlankRegionStart[i]=ThisTarPanel.FlankRegionEnd[i-1]+1;
}
}
ThisTarPanel.FlankRegionEnd[i-1]=NoRefMarkers-1;
}
// Create PrintStart and End Index and scaffold for target and Recom and Error and MAPTOREF for REF
{
fill(ThisRefPanel.MapRefToTar.begin(), ThisRefPanel.MapRefToTar.end(), -1);
for(i=RefStartPos; i<=RefEndPos; i++)
{
if(MyAllVariables->myOutFormat.verbose)
ThisRefPanel.VariantList[i-RefStartPos]=referencePanel.VariantList[i];
// ThisTarPanel.missing[i-RefStartPos]=targetPanel.missing[i];
if(i= 0);
// assert( (targetPanel.MapRefToTar[i] - TarStartPos) < NoGwasMarkers);
ThisRefPanel.MapRefToTar[i-RefStartPos] = targetPanel.MapRefToTar[i] - TarStartPos;
}
}
}
ThisRefPanel.CalculateAlleleFreq();
ThisTarPanel.CalculateGWASOnlyAlleleFreq();
if(!MyAllVariables->myModelVariables.minimac3)
{
int time_prev = time(0);
cout << "\n Compressing reference panel at GWAS sites ... "<myModelVariables.intermediate=="")
ThisRefChipOnlyPanel.UncompressTypedSitesNew(ThisRefPanel,ThisTarPanel,ChunkNo);
else
{
stringstream strs;
strs<<(ChunkNo+1);
string ss = (string)MyAllVariables->myModelVariables.intermediate.c_str()+".chunk."+(string)strs.str()+".GWAS.m3vcf.gz";
ThisRefChipOnlyPanel.readm3vcfFile(ss.c_str(), "", 0, 0, 0);
ThisRefChipOnlyPanel.CreateScaffoldedParameters(ThisRefPanel);
}
thisDataFast.TimeToCompress = time(0) - time_prev;
time_prev=time(0);
cout << " Re-compression successful (" << thisDataFast.TimeToCompress<< " seconds) !!!"<myModelVariables.cpus;i++)
{
thisDataFast.MainMarkovModel[i].AssignPanels(ThisRefPanel,ThisRefChipOnlyPanel,ThisTarPanel,ThisTarPanel,MyAllVariables);
thisDataFast.MainMarkovModel[i].initializeMatrices();
}
}
else
{
int time_prev = time(0);
for(int i=0;imyModelVariables.cpus;i++)
{
thisDataFast.MainMarkovModel[i].AssignPanels(ThisRefPanel,ThisTarPanel,MyAllVariables);
thisDataFast.MainMarkovModel[i].initializeMatricesMinimac3();
}
}
}
void Analysis::InitializeRefFileStream(String &Reffilename)
{
RefFileStream = ifopen(Reffilename, "r");
string line;
RefFileStream->readLine(line);
bool Header=true;
while(Header)
{
line.clear();
RefFileStream->readLine(line);
if(line.substr(0,6).compare("#CHROM")==0)
break;
}
for(int tempIndex=0;tempIndexdiscardLine();
PrevChunkFilledTillRef=0;
PrevChunkStartFromRef=0;
PrevChunkFilledTillTar=0;
PrevChunkStartFromTar=0;
PrevChunkFilledTillTarOnly=0;
PrevChunkStartFromTarOnly=0;
InitializeRefChunkData(CurrentRefPanel);
InitializeRefChipOnlyChunkData(CurrentRefPanelChipOnly);
stats.PreInitialize(MaxRefMarkerSize);
// if(MyAllVariables->myOutFormat.memUsage)
// {
// RefMem = CurrentRefPanel.size();
// ComRefMem = CurrentRefPanelChipOnly.size();
// }
}
void Analysis::InitializeTargetFileStream(String &Tarfilename)
{
VcfHeader header;
TarFileStream.open(Tarfilename, header);
TarFileStream.setSiteOnly(false);
FileReadIndex=0;
overlapImportIndex=0;
importReadIndex=0;
GWASOnlySkipIndexpoint = 0;
MainTypedOnlyImportIndex =0;
InitializeTargetChipOnlyChunkData(CurrentTarPanelChipOnly);
// if(MyAllVariables->myOutFormat.memUsage)
// {
// TarMem = CurrentTarPanelChipOnly.size();
// }
}
String Analysis::RunEstimation(String &Reffilename, String &Recomfilename, String &Errorfilename)
{
// int time_prev=time(0);
// if (!targetPanel.ScaffoldGWAStoReference(referencePanel,*MyAllVariables))
// {
// cout << "\n Program Exiting ... \n\n";
// return "Reference.Panel.Load.Error";
// }
//
//
cout<<"\n ------------------------------------------------------------------------------"<myOutFormat.memUsage)
// {
// cout<<" ------------------------------------------------------------------------------"<myModelVariables.cpus);
//
// if(MyAllVariables->myOutFormat.vcfBuffer >= targetPanel.numSamples)
// MyAllVariables->myOutFormat.vcfBuffer=targetPanel.numSamples;
//
// thisDataFast.InitializeOutputFiles(targetPanel, MyAllVariables->myOutFormat.vcfBuffer, MaxRefMarkerSize, MaxGwasMarkerSize);
// if(MyAllVariables->myOutFormat.memUsage)
// {
//
// cout<<" Estimating Memory based on a single chunk ..."<< endl;
//
// readm3vcfFileChunk(0, CurrentRefPanel);
// readVcfFileChunk(0, CurrentTarPanelChipOnly);
// GetCurrentPanelReady(0, CurrentRefPanel, CurrentRefPanelChipOnly, CurrentTarPanelChipOnly, thisDataFast);
// cout<myOutFormat.meta)
// AppendtoMainLooVcfFaster(i,thisDataFast.TotalNovcfParts);
// PrintInfoFile(i);
//
// time_load = time(0) - time_prev;
// cout << "\n Time taken for this chunk = " << time_load << " seconds."<myHapDataVariables.end==0 && MyAllVariables->myOutFormat.TypedOnly)
//// assert(FileReadIndex==targetPanel.importIndexListSize);
//// asserassertt(OverCount==targetPanel.numOverlapMarkers);
//// assert(TypOnlyCount==targetPanel.numTypedOnlyMarkers);
//// assert(RefCOUNT==referencePanel.NoBlocks);
//
// CloseStreamOutputFiles();
return "Success";
}
String Analysis::AnalyzeExperiment(String &Reffilename, String &Tarfilename, String &Recomfilename, String &Errorfilename, AllVariable& MyAllVariable)
{
String mysuccessresult="Error";
cout << " Starting Main Imputation/Estimation Analysis ... " << endl;
cout << "\n Performing preliminary check on input parameters... " ;
MyOutFormat=&MyAllVariable.myOutFormat;
MyModelVariables=&MyAllVariable.myModelVariables;
MyHapDataVariables=&MyAllVariable.myHapDataVariables;
MyAllVariables=&MyAllVariable;
int time_prev=time(0);
mysuccessresult=CheckValidity(Reffilename, Tarfilename, Recomfilename, Errorfilename);
TimeToRead+=( time(0) - time_prev);
if(mysuccessresult!="Success")
return mysuccessresult;
if(!MyModelVariables->processReference)
{
mysuccessresult=RunAnalysis(Reffilename, Tarfilename, Recomfilename, Errorfilename);
}
else
{
Estimation MyEstimation;
mysuccessresult = MyEstimation.RunEstimation(Reffilename, Recomfilename, Errorfilename, MyAllVariable);
}
if(mysuccessresult!="Success")
return mysuccessresult;
return "Success";
}
bool Analysis::CheckGeneticMapFile()
{
std::cout << "\n Checking genetic map file : "<myHapDataVariables.mapFile << endl<myHapDataVariables.mapFile, "r");
string line;
GeneticMapData.clear();
const char* tabSep="\t";
vector Pieces(4);
vector AppendPiece(2);
double PrevSumVal=0.0;
if(fileStream)
{
while(fileStream->readLine(line)!=-1)
{
MyTokenize(Pieces, line.c_str(), tabSep,4);
if(Pieces[0]==targetPanel.finChromosome)
{
AppendPiece[0]=atof(Pieces[3].c_str());
AppendPiece[1]=atof(Pieces[2].c_str())-PrevSumVal;
PrevSumVal=atof(Pieces[2].c_str());
GeneticMapData.push_back(AppendPiece);
//cout<myHapDataVariables.mapFile << endl;
cout << "\n Program Exiting ... \n\n";
return false;
}
if(GeneticMapData.size()<2)
{
cout << "\n ERROR !!! Chromosome "<myHapDataVariables.mapFile << endl;
cout << "\n Program Exiting ... \n\n";
return false;
}
ifclose(fileStream);
cout<<" Successful !!! "<myModelVariables.CheckValidity())
{
return "Command.Line.Error";
}
if(!MyAllVariables->myHapDataVariables.CheckValidity())
{
return "Command.Line.Error";
}
if(!MyAllVariables->myOutFormat.CheckValidity())
{
return "Command.Line.Error";
}
// if(MyAllVariables->myOutFormat.verbose)
// {
// MyAllVariables->myHapDataVariables.ChunkLengthMb=299;
// }
if(!MyAllVariables->myModelVariables.processReference)
{
if (Tarfilename == "")
{
cout <<" ERROR !!! \n Missing \"--haps\", a required parameter (for imputation).\n";
cout <<" OR use \"--processReference\" to just process the reference panel.\n";
cout << "\n Program Exiting ... \n\n";
return "Command.Line.Error";
}
}
else if (Tarfilename != "")
{
cout <<" ERROR !!! \n \"--haps\" is NOT valid when \"--estimate\" is ON.\n";
cout <<" Parameter estimation only requires a reference panel. \n";
cout <<" No GWAS panel is required.\n";
cout << "\n Program Exiting ... \n\n";
return "Command.Line.Error";
}
cout<<" ------------------------------------------------------------------------------"<myModelVariables.processReference)
{
if (!targetPanel.BasicCheckForTargetHaplotypes(Tarfilename, "GWAS", *MyAllVariables))
{
return "Target.Panel.Load.Error";
}
}
if(!MyAllVariables->myModelVariables.referenceEstimates)
{
if (!CheckGeneticMapFile())
{
return "Genetic.Map.File.Load.Error";
}
}
return "Success";
}
Minimac4-1.0.2/src/Analysis.h 0000664 0000000 0000000 00000013610 13532224264 0015702 0 ustar 00root root 0000000 0000000 #ifndef ANALYSIS_H_INCLUDED
#define ANALYSIS_H_INCLUDED
#if defined(_OPENMP)
#include
#endif
#include "MyVariables.h"
#include "Unique.h"
#include "Imputation.h"
#include "HaplotypeSet.h"
//#include "StringBasics.h"
//#include "VcfFileReader.h"
//#include
//#include
//#include
//#include
#include
using namespace std;
class Analysis
{
public:
// Basic Variables
HaplotypeSet targetPanel,referencePanel;
IFILE RefFileStream;
VcfFileReader TarFileStream;
VcfRecord record;
vector< vector > GeneticMapData;
// Swapping Variables for actual chunk IMPUTATION
HaplotypeSet CurrentTarPanel,CurrentRefPanel;
HaplotypeSet CurrentTarPanelChipOnly,CurrentRefPanelChipOnly;
int PrevChunkFilledTillRef, PrevChunkStartFromRef;
int PrevChunkFilledTillTar, PrevChunkStartFromTar;
int PrevChunkFilledTillTarOnly, PrevChunkStartFromTarOnly;
void InitializeTargetChipOnlyChunkData(HaplotypeSet &ThisTarPanel);
void InitializeRefChipOnlyChunkData(HaplotypeSet &ThisRefPanel);
void readm3vcfFileChunk(int ChunkNo, HaplotypeSet &ThisRefPanel);
void readVcfFileChunk(int ChunkNo, HaplotypeSet &ThisTargetPanel);
// Target PANEL Indexing Variables
int overlapImportIndex, importReadIndex, FileReadIndex;
int GWASOnlySkipIndexpoint , MainTypedOnlyImportIndex;
// Output File Handle Streams
IFILE dosages, hapdose, haps, vcfdosepartial, vcfLoodosepartial, info;
ImputationStatistics stats;
// Chunk Information
int noChunks;
vector< vector > MyChunks,MyChunksInfoNumber;
vector< vector > MyRefVariantNumber, MyTargetVariantNumber, MyTypdedOnlyVariantNumber;
vector< float > MyRatio;
int MaxInfoVectorSize, MaxGwasMarkerSize, MaxRefMarkerSize, MaxTypedOnlyMarkerSize;
// Temporary Variables to be deleted later for checking purposes.
int OverCount, TypOnlyCount, RefCOUNT;
// Time Variables
int TimeToCompress, TimeToRead, TimeToImpute, TimeToWrite;
// Memory Variables
double RefMem, TarMem, ComRefMem, DosageMem, ProbMem;
// Printing Text Variables
char *VcfPrintStringPointer, *LooVcfPrintStringPointer, *InfoPrintStringPointer, *DosePrintStringPointer;
int VcfPrintStringLength, InfoPrintStringLength, DosePrintStringLength;
vector InfoforChunk;
vector< vector > BPListMapper;
HaplotypeSet *CurrentChunk, *NextChunk;
HaplotypeSet MainReferenceFrame;
OutputFormatVariable *MyOutFormat;
ModelVariable *MyModelVariables;
HaplotypeDataVariables *MyHapDataVariables;
AllVariable *MyAllVariables;
void PrintInfoFile(int ChunkNo);
Analysis()
{
TimeToCompress=0;
TimeToRead=0;
TimeToImpute=0;
TimeToWrite=0;
RefMem =0.0;
TarMem =0.0;
ComRefMem =0.0;
DosageMem =0.0;
ProbMem = 0.0;
}
void AppendtoMainVcf(int ChunkNo, int MaxIndex);
void AppendtoMainLooVcfFaster(int ChunkNo, int MaxIndex);
void AppendtoMainVcfFaster(int ChunkNo, int MaxIndex);
void MemDisplay();
void GetNumChunks();
String RunEstimation(String &Reffilename, String &Recomfilename, String &Errorfilename);
String AnalyzeExperiment(String &Reffilename, String &Tarfilename, String &Recomfilename,String &Errorfilename, AllVariable& MyAllVariable);
String CheckValidity(String &Reffilename, String &Tarfilename, String &Recomfilename, String &Errorfilename);
String RunAnalysis(String &Reffilename, String &Tarfilename, String &Recomfilename, String &Errorfilename);
void readm3vcfFileChunk(HaplotypeSet &ThisRefPanel, HaplotypeSet &NextRefPanel,
int StartBlock, int EndBlock, int StartNextBlock);
void readVcfFileChunk(HaplotypeSet &ThisTargetPanel, HaplotypeSet &NextTargetPanel,
int StartPos, int EndPos, int StartNextPos, int ChunkNo);
bool OpenStreamOutputFiles();
void CloseStreamOutputFiles();
void InitializeRefFileStream(String &Reffilename);
void InitializeTargetFileStream(String &Tarfilename);
void InitializeRefChunkData(HaplotypeSet &ThisRefPanel);
void InitializeTargetChunkData(HaplotypeSet &ThisTarPanel);
bool CreateRecombinationMap();
bool CreateChunks();
bool CreateChunksForParamEstimation();
void InitializeChunkVariables();
void CreateChunksFromReference();
void CreateChunksFromVCFReference();
void ImportChunksToTarget();
bool CheckChunkValidityandPrintChunk();
bool CheckChunkValidityForParamEstimationandPrintChunk();
bool CheckGeneticMapFile();
void CreatePrintIndices(int ChunkNo, HaplotypeSet &ThisRefPanel, HaplotypeSet &ThisTarPanel);
void GetCurrentPanelReady(int ChunkNo, HaplotypeSet &ThisRefPanel, HaplotypeSet &ThisRefChipOnlyPanel, HaplotypeSet &ThisTarPanel,Imputation &thisDataFast);
};
#endif // ANALYSIS_H_INCLUDED
Minimac4-1.0.2/src/AnalysisChunks.cpp 0000664 0000000 0000000 00000044633 13532224264 0017422 0 ustar 00root root 0000000 0000000 #include "Analysis.h"
#include
#include "assert.h"
void Analysis::InitializeRefChunkData(HaplotypeSet &ThisRefPanel)
{
int NoRefHaps=referencePanel.numHaplotypes;
ThisRefPanel.numHaplotypes=NoRefHaps;
ThisRefPanel.numSamples=referencePanel.numSamples;
ThisRefPanel.SampleNoHaplotypes=referencePanel.SampleNoHaplotypes;
ThisRefPanel.CummulativeSampleNoHaplotypes=referencePanel.CummulativeSampleNoHaplotypes;
ThisRefPanel.individualName=referencePanel.individualName;
ThisRefPanel.maxBlockSize=referencePanel.maxBlockSize;
ThisRefPanel.maxRepSize=referencePanel.maxRepSize;
ThisRefPanel.ReducedStructureInfo.resize(MaxInfoVectorSize);
ThisRefPanel.MyAllVariables=MyAllVariables;
ThisRefPanel.MapRefToTar.resize(MaxRefMarkerSize);
ThisRefPanel.MapTarToRef.resize(MaxGwasMarkerSize);
int Mem=0;
for(int i=0;imyOutFormat.verbose)
{
ThisRefPanel.VariantList.resize(MaxRefMarkerSize);
}
}
void Analysis::InitializeRefChipOnlyChunkData(HaplotypeSet &ThisRefPanel)
{
int NoRefHaps=referencePanel.numHaplotypes;
ThisRefPanel.numHaplotypes=NoRefHaps;
ThisRefPanel.numSamples=referencePanel.numSamples;
ThisRefPanel.MarkerToReducedInfoMapper.resize(MaxGwasMarkerSize);
ThisRefPanel.Recom.resize(MaxGwasMarkerSize);
ThisRefPanel.Error.resize(MaxGwasMarkerSize);
ThisRefPanel.AlleleFreq.resize(MaxGwasMarkerSize);
ThisRefPanel.MyAllVariables=MyAllVariables;
if(MyAllVariables->myOutFormat.verbose)
{
ThisRefPanel.individualName=referencePanel.individualName;
ThisRefPanel.SampleNoHaplotypes=referencePanel.SampleNoHaplotypes;
ThisRefPanel.VariantList.resize(MaxGwasMarkerSize);
}
}
void Analysis::InitializeTargetChipOnlyChunkData(HaplotypeSet &ThisTarPanel)
{
int tempnumHaplotypes=targetPanel.numHaplotypes;
ThisTarPanel.MyAllVariables=MyAllVariables;
ThisTarPanel.numHaplotypes=targetPanel.numHaplotypes;
ThisTarPanel.numSamples=targetPanel.numSamples;
ThisTarPanel.SampleNoHaplotypesPointer=&targetPanel.SampleNoHaplotypes;
ThisTarPanel.SampleNoHaplotypes=targetPanel.SampleNoHaplotypes;
ThisTarPanel.CummulativeSampleNoHaplotypes=targetPanel.CummulativeSampleNoHaplotypes;
ThisTarPanel.individualName=targetPanel.individualName;
ThisTarPanel.haplotypesUnscaffolded.resize(tempnumHaplotypes);
ThisTarPanel.MissingSampleUnscaffolded.resize(tempnumHaplotypes);
if(MyAllVariables->myOutFormat.TypedOnly)
{
ThisTarPanel.GWASOnlyhaplotypesUnscaffolded.resize(tempnumHaplotypes);
ThisTarPanel.GWASOnlyMissingSampleUnscaffolded.resize(tempnumHaplotypes);
}
for (int i = 0; imyOutFormat.TypedOnly)
{
ThisTarPanel.TypedOnlyVariantList.resize(MaxTypedOnlyMarkerSize);
ThisTarPanel.GWASOnlyhaplotypesUnscaffolded[i].resize(MaxTypedOnlyMarkerSize, '0');
ThisTarPanel.GWASOnlyMissingSampleUnscaffolded[i].resize(MaxTypedOnlyMarkerSize, '0');
}
}
ThisTarPanel.GWASOnlyAlleleFreq.resize(MaxTypedOnlyMarkerSize);
ThisTarPanel.FlankRegionStart.resize(MaxGwasMarkerSize);
ThisTarPanel.FlankRegionEnd.resize(MaxGwasMarkerSize);
}
void Analysis::InitializeChunkVariables()
{
int i;
MyChunks.resize(noChunks);
MyChunksInfoNumber.resize(noChunks+1); // extra element added just to reduce checks later on
MyRefVariantNumber.resize(noChunks+1); // extra element added just to reduce checks later on
MyTargetVariantNumber.resize(noChunks+1); // extra element added just to reduce checks later on
MyTypdedOnlyVariantNumber.resize(noChunks+1); // extra element added just to reduce checks later on
MyRatio.resize(noChunks+1,-1.0); // extra element added just to reduce checks later on
for(i=0;i<(noChunks);i++)
{
MyChunks[i].resize(4);
MyChunksInfoNumber[i].resize(3);
MyRefVariantNumber[i].resize(3);
MyTargetVariantNumber[i].resize(3,-3);
MyTypdedOnlyVariantNumber[i].resize(3,-3);
}
MyChunksInfoNumber[i].resize(1,99999999); // extra element added just to reduce checks later on
MyRefVariantNumber[i].resize(1,99999999); // extra element added just to reduce checks later on
MyTargetVariantNumber[i].resize(1,99999999); // extra element added just to reduce checks later on
MyTypdedOnlyVariantNumber[i].resize(1,99999999); // extra element added just to reduce checks later on
}
void Analysis::CreateChunksFromReference()
{
vector &RefInfo=referencePanel.ReducedStructureInfoSummary;
vector &VarList=referencePanel.VariantList;
vector &InfoMapper=referencePanel.MarkerToReducedInfoMapper;
int NoMarkers=referencePanel.numMarkers;
int i=0,index;
MyChunksInfoNumber[0][0]=0;
MyRefVariantNumber[0][0]=0;
MyChunks[0][0]=VarList[0].bp;
MyChunks[0][1]=VarList[0].bp;
if(noChunks>1)
{
MyChunksInfoNumber[0][1]=InfoMapper[0 + MyHapDataVariables->ChunkSize + MyHapDataVariables->ChunkWindow];
MyRefVariantNumber[0][1]= RefInfo[MyChunksInfoNumber[0][1]].endIndex ;
MyChunks[0][2]=VarList[0 + MyHapDataVariables->ChunkSize].bp;
MyChunks[0][3]=VarList[MyRefVariantNumber[0][1]].bp;
for(i=1;i<(noChunks-1);i++)
{
index=(i*MyHapDataVariables->ChunkSize);
MyChunksInfoNumber[i][0]=InfoMapper[index-MyHapDataVariables->ChunkWindow];
MyChunksInfoNumber[i][1]=InfoMapper[index+MyHapDataVariables->ChunkSize+MyHapDataVariables->ChunkWindow];
MyRefVariantNumber[i][0]=RefInfo[MyChunksInfoNumber[i][0]].startIndex;
MyRefVariantNumber[i][1]= RefInfo[MyChunksInfoNumber[i][1]].endIndex;
MyChunks[i][0]=VarList[MyRefVariantNumber[i][0]].bp;
MyChunks[i][1]=MyChunks[i-1][2]+1;
MyChunks[i][2]=VarList[index+MyHapDataVariables->ChunkSize].bp;
MyChunks[i][3]=VarList[MyRefVariantNumber[i][1]].bp;
}
index=(i*MyHapDataVariables->ChunkSize);
MyChunksInfoNumber[i][0]=InfoMapper[index-MyHapDataVariables->ChunkWindow];
MyRefVariantNumber[i][0]=RefInfo[MyChunksInfoNumber[i][0]].startIndex;
MyChunks[i][0]=VarList[MyRefVariantNumber[i][0]].bp;
MyChunks[i][1]=MyChunks[i-1][2]+1;
}
MyChunks[i][2]=VarList[NoMarkers-1].bp;
MyChunks[i][3]=VarList[NoMarkers-1].bp;
MyChunksInfoNumber[i][1]=InfoMapper[NoMarkers-1];
MyRefVariantNumber[i][1]=NoMarkers-1;
for(int i=0;i &VarList=referencePanel.VariantList;
int NoMarkers=referencePanel.numMarkers;
int index;
MyRefVariantNumber[0][0]=0;
MyChunks[0][0]=VarList[0].bp;
MyChunks[0][1]=VarList[0].bp;
i=0;
if(noChunks>1)
{
MyChunks[0][2]=VarList[0 + MyHapDataVariables->ChunkSize].bp;
MyChunks[0][3]=VarList[0 + MyHapDataVariables->ChunkSize + MyHapDataVariables->ChunkWindow].bp;
MyRefVariantNumber[0][1]=MyHapDataVariables->ChunkSize + MyHapDataVariables->ChunkWindow;
for(i=1;i<(noChunks-1);i++)
{
index=(i*MyHapDataVariables->ChunkSize);
MyRefVariantNumber[i][0]=index-MyHapDataVariables->ChunkWindow;
MyChunks[i][0]=VarList[index-MyHapDataVariables->ChunkWindow].bp;
MyChunks[i][1]=MyChunks[i-1][2]+1;
MyChunks[i][2]=VarList[index+MyHapDataVariables->ChunkSize].bp;
MyChunks[i][3]=VarList[index+MyHapDataVariables->ChunkSize+MyHapDataVariables->ChunkWindow].bp;
MyRefVariantNumber[i][1]= index+MyHapDataVariables->ChunkSize+MyHapDataVariables->ChunkWindow;
}
index=(i*MyHapDataVariables->ChunkSize);
MyRefVariantNumber[i][0]=index-MyHapDataVariables->ChunkWindow;
MyChunks[i][0]=VarList[index-MyHapDataVariables->ChunkWindow].bp;
MyChunks[i][1]=MyChunks[i-1][2]+1;
}
MyChunks[i][2]=VarList[NoMarkers-1].bp;
MyChunks[i][3]=VarList[NoMarkers-1].bp;
MyRefVariantNumber[i][1]=NoMarkers-1;
for(int i=0;i0)
{
while(i MyTargetVariantNumber[i][0]? MyTargetVariantNumber[i][1] + 1 - MyTargetVariantNumber[i][0]: 0 );
MyTypdedOnlyVariantNumber[i][2] = ( MyTypdedOnlyVariantNumber[i][1] + 1 >MyTypdedOnlyVariantNumber[i][0]? MyTypdedOnlyVariantNumber[i][1] + 1 - MyTypdedOnlyVariantNumber[i][0]: 0 );
}
}
bool Analysis::CheckChunkValidityandPrintChunk()
{
int MinRefMarkerSize=MyRefVariantNumber[0][2], InIndex=0;
int MinGwasMarkerSize=MyTargetVariantNumber[0][2], MaIndex=0;
float minRatio=100.0,raIndex=0;
MaxInfoVectorSize=0;
MaxRefMarkerSize=0;
MaxGwasMarkerSize=0;
MaxTypedOnlyMarkerSize=0;
cout<<" No LeftBuffer LeftEnd RightPoint RightBuffer #Sites(GWAS/Ref/%)"< MaxInfoVectorSize )
MaxInfoVectorSize = MyChunksInfoNumber[i][2];
if( MyRefVariantNumber[i][2] > MaxRefMarkerSize )
MaxRefMarkerSize = MyRefVariantNumber[i][2];
if( MyRefVariantNumber[i][2] < MinRefMarkerSize )
{
InIndex=i;
MinRefMarkerSize = MyRefVariantNumber[i][2];
}
if( MyTargetVariantNumber[i][2] > MaxGwasMarkerSize )
MaxGwasMarkerSize = MyTargetVariantNumber[i][2];
if( MyTargetVariantNumber[i][2] < MinGwasMarkerSize )
{
MaIndex=i;
MinGwasMarkerSize = MyTargetVariantNumber[i][2];
}
if( MyTypdedOnlyVariantNumber[i][2] > MaxTypedOnlyMarkerSize )
MaxTypedOnlyMarkerSize = MyTypdedOnlyVariantNumber[i][2];
if(MyTargetVariantNumber[i][2] >0 && MyRefVariantNumber[i][2] > 0 )
{
MyRatio[i]=100.0*(float)MyTargetVariantNumber[i][2]/(float)MyRefVariantNumber[i][2];
if(minRatio>MyRatio[i])
{
minRatio=MyRatio[i];
raIndex=i;
}
}
cout<myHapDataVariables.minRatio))
{
cout<<"\n ERROR !!! ERROR !!! ERROR !!! "<myHapDataVariables.minRatio <<"\% of variants from the GWAS panel overlapping with the reference panel ... "< MaxRefMarkerSize )
MaxRefMarkerSize = MyRefVariantNumber[i][2];
if( MyRefVariantNumber[i][2] < MinRefMarkerSize )
{
InIndex=i;
MinRefMarkerSize = MyRefVariantNumber[i][2];
}
cout<ChunkSize <<" variants in each chunk ... " << endl<ChunkSize <<" variants in each chunk ... " << endl<myHapDataVariables.ChunkOverlapMb));
if(noOverLaps==0)
noOverLaps=1;
MyHapDataVariables->ChunkWindow=(NoMarkers/noOverLaps);
noChunks = ((int)(EndPos-StartPos)/(int)(1000000 *MyAllVariables->myHapDataVariables.ChunkLengthMb));
if(noChunks==0)
noChunks=1;
MyHapDataVariables->ChunkSize=(NoMarkers/noChunks);
return;
}
Minimac4-1.0.2/src/DosageData.cpp 0000664 0000000 0000000 00000041053 13532224264 0016450 0 ustar 00root root 0000000 0000000 #include "DosageData.h"
#include "HaplotypeSet.h"
#include "assert.h"
void DosageData::FlushPartialVcf(int NovcfParts)
{
PrintStringLength=0;
PrintEmpStringLength=0;
int time_Start = time(0);
string PartialVcfFileName(MyAllVariables->myOutFormat.OutPrefix);
string PartialMetaVcfFileName(MyAllVariables->myOutFormat.OutPrefix);
stringstream strs,strs1;
strs<<(NovcfParts);
strs1<<(ChunkNo+1);
PartialVcfFileName+=(".chunk."+(string)(strs1.str())+ ".dose.part."+ (string)(strs.str())+".vcf.gz");
PartialMetaVcfFileName+=(".chunk."+(string)(strs1.str())+ ".empiricalDose.part."+ (string)(strs.str())+".vcf.gz");
IFILE vcfdosepartial = ifopen(PartialVcfFileName.c_str(), "wb", InputFile::BGZF);
IFILE vcfLoodosepartial = NULL;
if(MyAllVariables->myOutFormat.meta)
vcfLoodosepartial=ifopen(PartialMetaVcfFileName.c_str(), "wb", InputFile::UNCOMPRESSED);
for(int Id=0;IdSampleNoHaplotypes[FullSamID];
}
int i=0;
for (int index = 0; index < rHapFull->RefTypedTotalCount; index++)
{
if(rHapFull->RefTypedIndex[index]==-1)
{
if(i>=rHapFull->PrintStartIndex && i <= rHapFull->PrintEndIndex)
{
PrintDosageForVcfOutputForID(i);
}
i++;
}
else
{
int MappingIndex = rHapFull->RefTypedIndex[index];
if(MappingIndex>=tHapFull->PrintTypedOnlyStartIndex && MappingIndex<=tHapFull->PrintTypedOnlyEndIndex)
{
PrintGWASOnlyForVcfOutputForID(MappingIndex);
}
}
if(PrintStringLength > 0.9 * (float)(MyAllVariables->myOutFormat.PrintBuffer))
{
ifprintf(vcfdosepartial,"%s",PrintStringPointer);
PrintStringLength=0;
}
if(PrintEmpStringLength > 0.9 * (float)(MyAllVariables->myOutFormat.PrintBuffer))
{
ifprintf(vcfLoodosepartial,"%s",PrintEmpStringPointer);
PrintEmpStringLength=0;
}
}
if(PrintStringLength>0)
{
ifprintf(vcfdosepartial,"%s",PrintStringPointer);
PrintStringLength=0;
}
if(PrintEmpStringLength >0)
{
ifprintf(vcfLoodosepartial,"%s",PrintEmpStringPointer);
PrintEmpStringLength=0;
}
ifclose(vcfdosepartial);
if(MyAllVariables->myOutFormat.meta)
ifclose(vcfLoodosepartial);
TimeToWrite=time(0) - time_Start;
}
void DosageData::PrintDiploidDosage(float &x, float &y)
{
bool colonIndex=false;
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,"\t");
if(!MyAllVariables->myOutFormat.longZero && x<0.0005 && y<0.0005)
{
if(MyAllVariables->myOutFormat.GT)
{
if(!MyAllVariables->myOutFormat.unphasedOutput)
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,"0|0");
else
{
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,"0/0");
}
colonIndex=true;
}
if(MyAllVariables->myOutFormat.DS)
{
if(colonIndex)
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,":");
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,"0");
colonIndex=true;
}
if(MyAllVariables->myOutFormat.HDS)
{
if(colonIndex)
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,":");
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,"0,0");
colonIndex=true;
}
if(MyAllVariables->myOutFormat.GP)
{
if(colonIndex)
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,":");
colonIndex=true;
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,"1,0,0");
}
if(MyAllVariables->myOutFormat.SD)
{
if(colonIndex)
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,":");
colonIndex=true;
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,"0");
}
return;
}
if(MyAllVariables->myOutFormat.GT)
{
if(!MyAllVariables->myOutFormat.unphasedOutput)
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,"%d|%d",(x>0.5),(y>0.5));
else
{
bool a1=(x>0.5);
bool a2=(y>0.5);
if((a1^a2)==1)
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,"0/1");
else if(a1 && a2)
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,"1/1");
else
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,"0/0");
}
colonIndex=true;
}
if(MyAllVariables->myOutFormat.DS)
{
if(colonIndex)
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,":");
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,"%.3f",x+ y);
colonIndex=true;
}
if(MyAllVariables->myOutFormat.HDS)
{
if(colonIndex)
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,":");
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,"%.3f,%.3f",x , y);
colonIndex=true;
}
if(MyAllVariables->myOutFormat.GP)
{
if(colonIndex)
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,":");
colonIndex=true;
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,"%.3f,%.3f,%.3f",(1-x)*(1-y),x*(1-y)+y*(1-x),x*y);
}
if(MyAllVariables->myOutFormat.SD)
{
if(colonIndex)
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,":");
colonIndex=true;
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,"%.3f", x*(1-x) + y*(1-y));
}
}
void DosageData::PrintHaploidDosage(float &x)
{
bool colonIndex=false;
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,"\t");
if(!MyAllVariables->myOutFormat.longZero && x<0.0005)
{
if(MyAllVariables->myOutFormat.GT)
{
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,"0");
colonIndex=true;
}
if(MyAllVariables->myOutFormat.DS)
{
if(colonIndex)
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,":");
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,"0");
colonIndex=true;
}
if(MyAllVariables->myOutFormat.HDS)
{
if(colonIndex)
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,":");
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,"0");
colonIndex=true;
}
if(MyAllVariables->myOutFormat.GP)
{
if(colonIndex)
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,":");
colonIndex=true;
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,"1,0");
}
if(MyAllVariables->myOutFormat.SD)
{
if(colonIndex)
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,":");
colonIndex=true;
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,"0");
}
return;
}
if(MyAllVariables->myOutFormat.GT)
{
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,"%d",(x>0.5));
colonIndex=true;
}
if(MyAllVariables->myOutFormat.DS)
{
if(colonIndex)
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,":");
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,"%.3f",x);
colonIndex=true;
}
if(MyAllVariables->myOutFormat.HDS)
{
if(colonIndex)
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,":");
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,"%.3f",x );
colonIndex=true;
}
if(MyAllVariables->myOutFormat.GP)
{
if(colonIndex)
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,":");
colonIndex=true;
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,"%.3f,%.3f",1-x,x);
}
if(MyAllVariables->myOutFormat.SD)
{
if(colonIndex)
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,":");
colonIndex=true;
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,"%.3f", x*(1-x));
}
}
void DosageData::PrintDiploidLooDosage(float &x, float &y, AlleleType a, AlleleType b)
{
PrintEmpStringLength+=sprintf(PrintEmpStringPointer+PrintEmpStringLength,"\t");
PrintEmpStringLength+=sprintf(PrintEmpStringPointer+PrintEmpStringLength,"%c|%c",a,b);
PrintEmpStringLength+=sprintf(PrintEmpStringPointer+PrintEmpStringLength,":");
PrintEmpStringLength+=sprintf(PrintEmpStringPointer+PrintEmpStringLength,"%.3f|%.3f",x , y);
}
void DosageData::PrintHaploidLooDosage(float &x, AlleleType a)
{
PrintEmpStringLength+=sprintf(PrintEmpStringPointer+PrintEmpStringLength,"\t");
PrintEmpStringLength+=sprintf(PrintEmpStringPointer+PrintEmpStringLength,"%c",a);
PrintEmpStringLength+=sprintf(PrintEmpStringPointer+PrintEmpStringLength,":");
PrintEmpStringLength+=sprintf(PrintEmpStringPointer+PrintEmpStringLength,"%.3f",x);
}
void DosageData::PrintDosageForVcfOutputForID(int MarkerIndex)
{
for(int Id=0;IdmyOutFormat.meta && !rHapFull->Targetmissing[MarkerIndex] )
{
int gwasHapIndex = tHapFull->CummulativeSampleNoHaplotypes[SampleIndex[IndexId]];
int TypedMarkerIndex = rHapFull->MapRefToTar[MarkerIndex];
// assert(TypedMarkerIndexMissingSampleUnscaffolded[0].size());
// assert(gwasHapIndexMissingSampleUnscaffolded.size());
if(NoHaps==2)
{
if( tHapFull->MissingSampleUnscaffolded[gwasHapIndex][TypedMarkerIndex] =='1'
|| tHapFull->MissingSampleUnscaffolded[gwasHapIndex+1][TypedMarkerIndex]=='1')
{
PrintEmpStringLength+=sprintf(PrintEmpStringPointer+PrintEmpStringLength,"\t.|.:.|.");
}
else
{
PrintDiploidLooDosage((LoohapDosage[2*IndexId])[TypedMarkerIndex] , (LoohapDosage[2*IndexId+1])[TypedMarkerIndex] ,
tHapFull->haplotypesUnscaffolded[gwasHapIndex][TypedMarkerIndex],
tHapFull->haplotypesUnscaffolded[gwasHapIndex+1][TypedMarkerIndex]);
}
}
else if(NoHaps==1)
{
if( tHapFull->MissingSampleUnscaffolded[gwasHapIndex][TypedMarkerIndex]=='1')
{
PrintEmpStringLength+=sprintf(PrintEmpStringPointer+PrintEmpStringLength,"\t.:.");
}
else
{
PrintHaploidLooDosage((LoohapDosage[2*IndexId])[TypedMarkerIndex] ,
tHapFull->haplotypesUnscaffolded[gwasHapIndex][TypedMarkerIndex]);
}
}
else
abort();
}
}
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,"\n");
if(MyAllVariables->myOutFormat.meta && !rHapFull->Targetmissing[MarkerIndex] )
PrintEmpStringLength+=sprintf(PrintEmpStringPointer+PrintEmpStringLength,"\n");
}
void DosageData::PrintGWASOnlyForVcfOutputForID(int MarkerIndex)
{
float freq=(float)tHapFull->GWASOnlyAlleleFreq[MarkerIndex];
float x,y;
for(int Id=0;IdCummulativeSampleNoHaplotypes[SampleIndex[IndexId]];
int NoHaps=BufferSampleNoHaplotypes[IndexId];
// assert(FullSamID==(Id+FirstHapId));
if(NoHaps==2)
{
AlleleType a1=tHapFull->GWASOnlyMissingSampleUnscaffolded[gwasHapIndex][MarkerIndex];
AlleleType a2=tHapFull->GWASOnlyMissingSampleUnscaffolded[gwasHapIndex+1][MarkerIndex];
if(a1=='1' || a2=='1')
PrintDiploidDosage(freq,freq);
else
{
x=(float)(tHapFull->GWASOnlyhaplotypesUnscaffolded[gwasHapIndex][MarkerIndex]-'0');
y=(float)(tHapFull->GWASOnlyhaplotypesUnscaffolded[gwasHapIndex+1][MarkerIndex]-'0');
PrintDiploidDosage(x, y);
}
}
else if(NoHaps==1)
{
AlleleType a1=tHapFull->GWASOnlyMissingSampleUnscaffolded[gwasHapIndex][MarkerIndex];
if(a1=='1')
PrintHaploidDosage(freq);
else
{
x=(float)(tHapFull->GWASOnlyhaplotypesUnscaffolded[gwasHapIndex][MarkerIndex]-'0');
PrintHaploidDosage(x);
}
}
else
abort();
}
PrintStringLength+=sprintf(PrintStringPointer+PrintStringLength,"\n");
}
void DosageData::BindSampleMModel(MarkovModel &MM, int Index, int HapNo)
{
MM.DosageHap=&hapDosage[ (2*Index) + HapNo] ;
MM.LooDosageHap=&LoohapDosage[ (2*Index) + HapNo] ;
}
pair DosageData::IndexSample(int SampleId)
{
pair Result;
InvertSampleIndex[SampleId-FirstHapId]=NoSamplesIndexed;
SampleIndex[NoSamplesIndexed++]=SampleId;
Result.second=NoSamplesIndexed-1;
if(NoSamplesIndexed==BuffernumSamples)
{
Result.first=1;
}
return Result;
}
void DosageData::InitializePartialDosageData(HaplotypeSet &tarInitializer, int MaxNoSamples,
int MaxNoRefVariants, int MaxNoTarVariants,
AllVariable *MyAllVariable)
{
MyAllVariables=MyAllVariable;
ActualnumHaplotypes = tarInitializer.numHaplotypes;
ActualnumSamples = tarInitializer.numSamples;
BuffernumSamples = MaxNoSamples;
BuffernumHaplotypes = 2*MaxNoSamples;
hapDosage.resize(BuffernumHaplotypes);
LoohapDosage.resize(BuffernumHaplotypes);
BufferSampleNoHaplotypes.resize(BuffernumSamples);
SampleIndex.resize(BuffernumSamples);
InvertSampleIndex.resize(BuffernumSamples);
for(int i=0;imyOutFormat.PrintBuffer));
if(MyAllVariables->myOutFormat.meta)
PrintEmpStringPointer = (char*)malloc(sizeof(char) * (MyAllVariables->myOutFormat.PrintBuffer));
individualName=tarInitializer.individualName;
}
void DosageData::ReParameterizePartialDosageData(int No, HaplotypeSet &refFullHap, HaplotypeSet &tarFullHap)
{
ChunkNo=No;
rHapFull=&refFullHap;
tHapFull=&tarFullHap;
FirstHapId=0;
numMarkers = rHapFull->numMarkers;
noGWASSites= tHapFull->numTypedOnlyMarkers;
NoSamplesIndexed=0;
}
void DosageData::UpdatePartialDosageData(int NewMaxVal, int NewFirstHapId)
{
if(NewMaxVal<=0)
return;
BuffernumSamples = NewMaxVal;
BuffernumHaplotypes = 2*NewMaxVal;
NoSamplesIndexed=0;
FirstHapId=NewFirstHapId;
}
Minimac4-1.0.2/src/DosageData.h 0000664 0000000 0000000 00000005771 13532224264 0016124 0 ustar 00root root 0000000 0000000 #ifndef DOSAGEDATA_H_INCLUDED
#define DOSAGEDATA_H_INCLUDED
#include "StringBasics.h"
#include "MyVariables.h"
#include "VcfFileReader.h"
#include "Unique.h"
#include
#include
#include
#include
#include
#include
#include "HaplotypeSet.h"
#include "MyVariables.h"
#include "MarkovModel.h"
using namespace std;
class DosageData
{
public:
// Basic Variables
int ChunkNo, FirstHapId;
int ActualnumHaplotypes, BuffernumHaplotypes;
int ActualnumSamples, BuffernumSamples;
int numMarkers, noGWASSites;
HaplotypeSet *tHapFull;
HaplotypeSet *rHapFull;
vector individualName;
// Indexing Samples Variable
int NoSamplesIndexed;
vector SampleIndex;
vector InvertSampleIndex;
vector BufferSampleNoHaplotypes;
// Main Data Variable
vector > hapDosage;
vector > LoohapDosage;
// Formatting Variables
AllVariable *MyAllVariables;
// Time Variables
int TimeToWrite;
// Printing Text Variables
char *PrintStringPointer;
char *PrintEmpStringPointer;
int PrintStringLength;
int PrintEmpStringLength;
double size()
{
double S=0;
S+=BufferSampleNoHaplotypes.size() * sizeof(int);
S+=InvertSampleIndex.size() * sizeof(int);
S+=SampleIndex.size() * sizeof(int);
for(int i=0;i<(int)hapDosage.size();i++)
{
S+=hapDosage[i].size() * sizeof(float);
S+=LoohapDosage[i].size() * sizeof(float);
}
for(int i=0;i<(int)individualName.size();i++)
{
S+=individualName[i].size();
}
return (S);
};
void PrintDiploidLooDosage(float &x, float &y, AlleleType a, AlleleType b);
void PrintHaploidLooDosage(float &x, AlleleType a);
void InitializePartialDosageData(HaplotypeSet &tarInitializer, int MaxNoSamples,
int MaxNoRefVariants, int MaxNoTarVariants,
AllVariable *MyAllVariable);
void ReParameterizePartialDosageData(int No, HaplotypeSet &refFullHap, HaplotypeSet &tarFullHap);
void UpdatePartialDosageData(int NewMaxVal, int NewFirstHapId);
pair IndexSample(int SampleId);
void BindSampleMModel(MarkovModel &MM, int Index, int HapNo);
void FlushPartialVcf(int NovcfParts);
void PrintDiploidDosage(float &x, float &y);
void PrintHaploidDosage(float &x);
void PrintDosageForVcfOutputForID(int MarkerIndex);
void PrintDosageForVcfOutputForIDFast(int MarkerIndex);
void PrintGWASOnlyForVcfOutputForID(int MarkerIndex);
DosageData () {};
};
#endif // DOSAGEDATA_H_INCLUDED
Minimac4-1.0.2/src/Estimation.cpp 0000664 0000000 0000000 00000201310 13532224264 0016562 0 ustar 00root root 0000000 0000000 #include "Estimation.h"
#include
#include "assert.h"
String Estimation::RunEstimation(String &Reffilename, String &Recomfilename, String &Errorfilename, AllVariable& MyAllVariable)
{
MyOutFormat=&MyAllVariable.myOutFormat;
MyModelVariables=&MyAllVariable.myModelVariables;
MyHapDataVariables=&MyAllVariable.myHapDataVariables;
MyAllVariables=&MyAllVariable;
int time_prev=time(0);
if (!referencePanel.BasicCheckForM3VCFReferenceHaplotypes(Reffilename,*MyAllVariables))
{
return "Reference.Panel.Load.Error";
}
if (!referencePanel.ReadM3VCFChunkingInformation(Reffilename,""))
{
cout << "\n Program Exiting ... \n\n";
return "Reference.Panel.Load.Error";
}
if (!referencePanel.ScaffoldGWAStoReference(referencePanel,*MyAllVariables))
{
cout << "\n Program Exiting ... \n\n";
return "Reference.Panel.Load.Error";
}
cout<<"\n ------------------------------------------------------------------------------"<myOutFormat.memUsage)
{
cout<<" ------------------------------------------------------------------------------"<myModelVariables.cpus);
for(int i=0;imyOutFormat.meta)
// AppendtoMainLooVcfFaster(i,thisDataFast.TotalNovcfParts);
// PrintInfoFile(i);
//
// time_load = time(0) - time_prev;
// cout << "\n Time taken for this chunk = " << time_load << " seconds."<myHapDataVariables.end==0 && MyAllVariables->myOutFormat.TypedOnly)
//// assert(FileReadIndex==targetPanel.importIndexListSize);
//// asserassertt(OverCount==targetPanel.numOverlapMarkers);
//// assert(TypOnlyCount==targetPanel.numTypedOnlyMarkers);
//// assert(RefCOUNT==referencePanel.NoBlocks);
//
// CloseStreamOutputFiles();
//
return "Success";
}
void Estimation::PrintInfoFile(int ChunkNo)
{
InfoPrintStringLength=0;
int RefStartPos = MyRefVariantNumber[ChunkNo][0];
int i=0;
for (int index = 0; index < CurrentRefPanel.RefTypedTotalCount; index++)
{
if(CurrentRefPanel.RefTypedIndex[index]==-1)
{
variant &thisVariant = referencePanel.VariantList[i+RefStartPos];
if(i>=CurrentRefPanel.PrintStartIndex && i <= CurrentRefPanel.PrintEndIndex)
{
double TarFreq = stats.AlleleFrequency(i);
InfoPrintStringLength+=sprintf(InfoPrintStringPointer+InfoPrintStringLength , "%s\t%s\t%s\t%.5f\t%.5f\t%.5f\t%.5f\t",
MyAllVariables->myOutFormat.RsId ? thisVariant.rsid.c_str(): thisVariant.name.c_str(),
thisVariant.refAlleleString.c_str(),
thisVariant.altAlleleString.c_str(),
TarFreq,
TarFreq > 0.5 ? 1.0 - TarFreq : TarFreq,
stats.AverageCallScore(i),
stats.Rsq(i));
if (!CurrentRefPanel.Targetmissing[i])
{
InfoPrintStringLength+=sprintf(InfoPrintStringPointer+InfoPrintStringLength , "Genotyped\t%.3f\t%.3f\t%.5f\t%.5f\t%.5f\n",
stats.LooRsq(i), stats.EmpiricalR(i), stats.EmpiricalRsq(i),
stats.LooMajorDose(i), stats.LooMinorDose(i));
}
else
InfoPrintStringLength+=sprintf(InfoPrintStringPointer+InfoPrintStringLength , "Imputed\t-\t-\t-\t-\t-\n");
}
i++;
}
else
{
// if(ChunkNo==2 && index==26751)
// abort();
int MappingIndex = CurrentRefPanel.RefTypedIndex[index];
if(MappingIndex>=CurrentTarPanelChipOnly.PrintTypedOnlyStartIndex && MappingIndex<=CurrentTarPanelChipOnly.PrintTypedOnlyEndIndex)
{
variant ThisTypedVariant = CurrentTarPanelChipOnly.TypedOnlyVariantList[MappingIndex];
double TarFreq = CurrentTarPanelChipOnly.GWASOnlyAlleleFreq[MappingIndex];
InfoPrintStringLength+=sprintf(InfoPrintStringPointer+InfoPrintStringLength , "%s\t%s\t%s\t%.5f\t%.5f\t-\t-\tTyped_Only\t-\t-\t-\t-\t-\n",
MyAllVariables->myOutFormat.RsId ? ThisTypedVariant.rsid.c_str(): ThisTypedVariant.name.c_str(),
ThisTypedVariant.refAlleleString.c_str(),
ThisTypedVariant.altAlleleString.c_str(),
TarFreq,
TarFreq > 0.5 ?
1.0 - TarFreq : TarFreq);
}
}
if(InfoPrintStringLength > 0.9 * (float)(MyAllVariables->myOutFormat.PrintBuffer))
{
ifprintf(info,"%s",InfoPrintStringPointer);
InfoPrintStringLength=0;
}
}
if(InfoPrintStringLength >0)
{
ifprintf(info,"%s",InfoPrintStringPointer);
InfoPrintStringLength=0;
}
}
void Estimation::AppendtoMainLooVcfFaster(int ChunkNo, int MaxIndex)
{
VcfPrintStringLength=0;
int time_prev = time(0);
int RefStartPos = MyRefVariantNumber[ChunkNo][0];
vector vcfLoodosepartialList(MaxIndex);
for(int i=1;i<=MaxIndex;i++)
{
string tempFileIndex(MyAllVariables->myOutFormat.OutPrefix);
stringstream strs,strs1;
strs<<(i);
strs1<<(ChunkNo+1);
tempFileIndex+=(".chunk."+(string)(strs1.str())+".empiricalDose.part." +
(string)(strs.str())+".vcf.gz");
vcfLoodosepartialList[i-1] = ifopen(tempFileIndex.c_str(), "r");
}
string line;
int i=0;
for (int index = 0; index < CurrentRefPanel.RefTypedTotalCount; index++)
{
if(CurrentRefPanel.RefTypedIndex[index]==-1)
{
if(i>=CurrentRefPanel.PrintStartIndex && i <= CurrentRefPanel.PrintEndIndex)
{
if(!CurrentRefPanel.Targetmissing[i])
{
variant &tempVariant = referencePanel.VariantList[i+RefStartPos];
VcfPrintStringLength+=sprintf(VcfPrintStringPointer + VcfPrintStringLength,"%s\t%d\t%s\t%s\t%s\t.\tPASS",
tempVariant.chr.c_str(),
tempVariant.bp,
MyAllVariables->myOutFormat.RsId?tempVariant.rsid.c_str():tempVariant.name.c_str(),
tempVariant.refAlleleString.c_str(),
tempVariant.altAlleleString.c_str());
VcfPrintStringLength+=sprintf(VcfPrintStringPointer + VcfPrintStringLength,"\tTYPED\tGT:LDS");
for(int j=1;j<=MaxIndex;j++)
{
line.clear();
vcfLoodosepartialList[j-1]->readLine(line);
VcfPrintStringLength+=sprintf(VcfPrintStringPointer + VcfPrintStringLength,"%s",line.c_str());
}
VcfPrintStringLength+=sprintf(VcfPrintStringPointer + VcfPrintStringLength,"\n");
}
}
i++;
}
if(VcfPrintStringLength > 0.9 * (float)(MyAllVariables->myOutFormat.PrintBuffer))
{
ifprintf(vcfLoodosepartial,"%s",VcfPrintStringPointer);
VcfPrintStringLength=0;
}
}
if(VcfPrintStringLength > 0)
{
ifprintf(vcfLoodosepartial,"%s",VcfPrintStringPointer);
VcfPrintStringLength=0;
}
for(int i=1;i<=MaxIndex;i++)
{
ifclose(vcfLoodosepartialList[i-1]);
string tempFileIndex(MyAllVariables->myOutFormat.OutPrefix);
stringstream strs,strs1;
strs<<(i);
strs1<<(ChunkNo+1);
tempFileIndex+=(".chunk."+(string)(strs1.str())+".empiricalDose.part." +
(string)(strs.str())+".vcf.gz");
remove(tempFileIndex.c_str());
}
TimeToWrite+=( time(0) - time_prev);
}
void Estimation::AppendtoMainVcfFaster(int ChunkNo, int MaxIndex)
{
VcfPrintStringLength=0;
int time_prev = time(0);
int RefStartPos = MyRefVariantNumber[ChunkNo][0];
printf("\n Appending chunk to final output VCF File : %s ",(MyAllVariables->myOutFormat.OutPrefix + ".dose.vcf" + (MyAllVariables->myOutFormat.gzip ? ".gz" : "")).c_str() );
cout< vcfdosepartialList(MaxIndex);
for(int i=1;i<=MaxIndex;i++)
{
string tempFileIndex(MyAllVariables->myOutFormat.OutPrefix);
stringstream strs,strs1;
strs<<(i);
strs1<<(ChunkNo+1);
tempFileIndex+=(".chunk."+(string)(strs1.str())+".dose.part." +
(string)(strs.str())+".vcf.gz");
vcfdosepartialList[i-1] = ifopen(tempFileIndex.c_str(), "r");
}
string line;
int i=0;
for (int index = 0; index < CurrentRefPanel.RefTypedTotalCount; index++)
{
if(CurrentRefPanel.RefTypedIndex[index]==-1)
{
if(i>=CurrentRefPanel.PrintStartIndex && i <= CurrentRefPanel.PrintEndIndex)
{
variant &tempVariant = referencePanel.VariantList[i+RefStartPos];
VcfPrintStringLength+=sprintf(VcfPrintStringPointer + VcfPrintStringLength,"%s\t%d\t%s\t%s\t%s\t.\tPASS",
tempVariant.chr.c_str(),
tempVariant.bp,
MyAllVariables->myOutFormat.RsId?tempVariant.rsid.c_str():tempVariant.name.c_str(),
tempVariant.refAlleleString.c_str(),
tempVariant.altAlleleString.c_str());
double freq = stats.AlleleFrequency(i);
VcfPrintStringLength+=sprintf(VcfPrintStringPointer + VcfPrintStringLength,"\tAF=%.5f;MAF=%.5f;R2=%.5f",
freq, freq > 0.5 ? 1.0 - freq : freq, stats.Rsq(i));
if(!CurrentRefPanel.Targetmissing[i])
VcfPrintStringLength+=sprintf(VcfPrintStringPointer + VcfPrintStringLength,";ER2=%.5f;TYPED",stats.EmpiricalRsq(i));
else
VcfPrintStringLength+=sprintf(VcfPrintStringPointer + VcfPrintStringLength,";IMPUTED");
VcfPrintStringLength+=sprintf(VcfPrintStringPointer + VcfPrintStringLength,"\t%s",MyAllVariables->myOutFormat.formatStringForVCF.c_str());
for(int j=1;j<=MaxIndex;j++)
{
line.clear();
vcfdosepartialList[j-1]->readLine(line);
VcfPrintStringLength+=sprintf(VcfPrintStringPointer + VcfPrintStringLength,"%s",line.c_str());
}
VcfPrintStringLength+=sprintf(VcfPrintStringPointer + VcfPrintStringLength,"\n");
}
i++;
}
else
{
int MappingIndex = CurrentRefPanel.RefTypedIndex[index];
if(MappingIndex>=CurrentTarPanelChipOnly.PrintTypedOnlyStartIndex && MappingIndex<=CurrentTarPanelChipOnly.PrintTypedOnlyEndIndex)
{
variant &ThisTypedVariant = (CurrentTarPanelChipOnly.TypedOnlyVariantList[CurrentRefPanel.RefTypedIndex[index]]);
VcfPrintStringLength+=sprintf(VcfPrintStringPointer + VcfPrintStringLength,"%s\t%d\t%s\t%s\t%s\t.\tPASS",
ThisTypedVariant.chr.c_str(),
ThisTypedVariant.bp,
MyAllVariables->myOutFormat.RsId? ThisTypedVariant.rsid.c_str():ThisTypedVariant.name.c_str(),
ThisTypedVariant.refAlleleString.c_str(),
ThisTypedVariant.altAlleleString.c_str());
double &freq = (CurrentTarPanelChipOnly.GWASOnlyAlleleFreq[CurrentRefPanel.RefTypedIndex[index]]);
VcfPrintStringLength+=sprintf(VcfPrintStringPointer + VcfPrintStringLength,"\tAF=%.5f;MAF=%.5f;TYPED_ONLY",
freq, freq > 0.5 ? 1.0 - freq : freq);
VcfPrintStringLength+=sprintf(VcfPrintStringPointer + VcfPrintStringLength,"\t%s",MyAllVariables->myOutFormat.formatStringForVCF.c_str());
for(int j=1;j<=MaxIndex;j++)
{
line.clear();
vcfdosepartialList[j-1]->readLine(line);
VcfPrintStringLength+=sprintf(VcfPrintStringPointer + VcfPrintStringLength,"%s",line.c_str());
}
VcfPrintStringLength+=sprintf(VcfPrintStringPointer + VcfPrintStringLength,"\n");
}
}
if(VcfPrintStringLength > 0.9 * (float)(MyAllVariables->myOutFormat.PrintBuffer))
{
ifprintf(vcfdosepartial,"%s",VcfPrintStringPointer);
VcfPrintStringLength=0;
}
}
if(VcfPrintStringLength > 0)
{
ifprintf(vcfdosepartial,"%s",VcfPrintStringPointer);
VcfPrintStringLength=0;
}
for(int i=1;i<=MaxIndex;i++)
{
ifclose(vcfdosepartialList[i-1]);
string tempFileIndex(MyAllVariables->myOutFormat.OutPrefix);
stringstream strs,strs1;
strs<<(i);
strs1<<(ChunkNo+1);
tempFileIndex+=(".chunk."+(string)(strs1.str())+".dose.part." +
(string)(strs.str())+".vcf.gz");
remove(tempFileIndex.c_str());
}
TimeToWrite+=( time(0) - time_prev);
cout << " Appending successful (" << time(0) - time_prev << " seconds) !!!"< &ThisInfoVector = ThisRefPanel.ReducedStructureInfo;
string line;
int ThisInfoVectorIndex=0;
int ThisChunkFilledTillRef = 0, ThisChunkStartFromRef = 0;
int StartBlock=MyChunksInfoNumber[ChunkNo][0];
int EndBlock=MyChunksInfoNumber[ChunkNo][1];
int StartNextBlock=MyChunksInfoNumber[ChunkNo+1][0];
int blockIndex=StartBlock;
int FilltheTop=0;
while(FilltheTop < PrevChunkFilledTillRef)
{
ThisInfoVector[blockIndex-StartBlock] = ThisInfoVector[PrevChunkStartFromRef + FilltheTop] ;
blockIndex++;
FilltheTop++;
}
ThisChunkStartFromRef=FilltheTop;
for(;blockIndex<=EndBlock;blockIndex++)
{
RefCOUNT++;
line.clear();
RefFileStream->readLine(line);
// assert(ThisInfoVectorIndex + PrevChunkFilledTillRef < MaxInfoVectorSize);
ReducedHaplotypeInfo &tempBlock=ThisInfoVector[ThisInfoVectorIndex + PrevChunkFilledTillRef];
ThisInfoVectorIndex++;
referencePanel.ReadBlockHeader(line, tempBlock);
referencePanel.ReadThisBlock(RefFileStream, blockIndex, tempBlock);
if(blockIndex>=StartNextBlock)
{
// assert(ThisChunkFilledTillRef < MaxInfoVectorSize);
ThisChunkFilledTillRef++;
}
else
{
ThisChunkStartFromRef++;
}
}
PrevChunkFilledTillRef=ThisChunkFilledTillRef;
PrevChunkStartFromRef=ThisChunkStartFromRef;
TimeToRead+=( time(0) - time_prev);
}
void Estimation::readVcfFileChunk(int ChunkNo, HaplotypeSet &ThisTargetPanel)
{
int time_prev = time(0);
cout << " Reading chunk from target/GWAS panel ... "<=StartNextPos)
{
// assert( (ThisChunkStartTillTar) < MaxGwasMarkerSize);
ThisChunkStartTillTar++;
}
else
{
ThisChunkStartFromTar++;
}
// assert(overlapImportIndexmyOutFormat.TypedOnly)
{
// assert( (GWASnumtoBeWrittenRecords + PrevChunkFilledTillTarOnly) < MaxTypedOnlyMarkerSize);
variant tempVar=targetPanel.TypedOnlyVariantList[MainTypedOnlyImportIndex];
ThisTargetPanel.TypedOnlyVariantList[GWASnumtoBeWrittenRecords + PrevChunkFilledTillTarOnly]=tempVar;
int haplotype_index = 0;
for (int i = 0; i<(targetPanel.numSamples); i++)
{
//haplotype_index=(2*i);
if(targetPanel.SampleNoHaplotypes[i]!=record.getNumGTs(i))
{
cout << "\n ERROR !!! GWAS Sample "<< targetPanel.individualName[i]<<" changes its ploidy at variant ";
cout << tempVar.name <=TypedOnlyNextStartPos)
{
// assert( (ThisChunkStartTillTarOnly) < MaxTypedOnlyMarkerSize);
ThisChunkStartTillTarOnly++;
}
else
{
ThisChunkStartFromTarOnly++;
}
// assert(MainTypedOnlyImportIndexmyOutFormat.gzip;
m3vcfPrintStringPointer = (char*)malloc(sizeof(char) * (MyAllVariables->myOutFormat.PrintBuffer));
m3vcfpartial = ifopen(MyAllVariables->myOutFormat.OutPrefix + ".m3vcf" + (gzip ? ".gz" : ""), "wb", gzip ?InputFile::BGZF:InputFile::UNCOMPRESSED);
if(m3vcfpartial==NULL)
{
cout <<"\n\n ERROR !!! \n Could NOT create the following file : "<< MyAllVariables->myOutFormat.OutPrefix + ".m3vcf" + (gzip ? ".gz" : "") <tm_year + 1900),(now->tm_mon + 1) ,now->tm_mday);
ifprintf(m3vcfpartial,"##source=Minimac4.v%s\n",VERSION);
ifprintf(m3vcfpartial,"##contig=\n",referencePanel.finChromosome.c_str());
ifprintf(m3vcfpartial,"##INFO=\n");
ifprintf(m3vcfpartial,"##INFO=\n");
ifprintf(m3vcfpartial,"##minimac4_Command=%s\n",MyAllVariables->myOutFormat.CommandLine.c_str());
ifprintf(m3vcfpartial,"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT");
for(int Id=0;IdmyOutFormat.PrintBuffer));
recfile = ifopen(MyAllVariables->myOutFormat.OutPrefix + ".rec", "wb");
if(recfile==NULL)
{
cout <<"\n\n ERROR !!! \n Could NOT create the following file : "<< MyAllVariables->myOutFormat.OutPrefix + ".rec" <myOutFormat.hapOutput && !MyAllVariables->myOutFormat.unphasedOutput)
{
ifclose(hapdose);
}
if(MyAllVariables->myOutFormat.vcfOutput)
{
ifclose(vcfdosepartial);
}
if(MyAllVariables->myOutFormat.meta)
{
ifclose(vcfLoodosepartial);
}
if(MyAllVariables->myOutFormat.doseOutput)
{
ifclose(dosages);
}
ifclose(RefFileStream);
TarFileStream.close();
cout<<" ------------------------------------------------------------------------------"<1073741824)
{
Fact=1073741824;
Tag="Gb";
}
else if(Total>1048576)
{
Fact=1048576;
Tag="Mb";
}
else if(Total>1024)
{
Fact=1024;
Tag="Kbytes";
}
else
{
Fact=1;
Tag="Bytes";
}
printf("\n Memory occupied by Full Reference Panel ~ %.3f %s", (double) RefMem/(Fact),Tag.c_str());
printf("\n Memory occupied by Compressed Reference Panel ~ %.3f %s", (double) ComRefMem/(Fact),Tag.c_str());
printf("\n Memory occupied by Target/GWAS Panel ~ %.3f %s", (double) TarMem/(Fact),Tag.c_str());
printf("\n Memory occupied by Likelihood Matrices ~ %.3f %s", (double) ProbMem/(Fact),Tag.c_str());
printf("\n Memory occupied by Dosage Data ~ %.3f %s", (double) DosageMem/(Fact),Tag.c_str());
printf("\n TOTAL Memory by the process ~ %.3f %s", (double) (Total)/(Fact),Tag.c_str());
cout<myOutFormat.gzip;
cout<myOutFormat.OutPrefix + ".info" <myOutFormat.hapOutput && !MyAllVariables->myOutFormat.unphasedOutput)
{
ifclose(hapdose);
cout<<" Haplotype Dosage information written to : "<myOutFormat.OutPrefix + ".hapDose" + (gzip ? ".gz" : "")<myOutFormat.vcfOutput)
{
ifclose(vcfdosepartial);
free(VcfPrintStringPointer);
cout<<" Imputed VCF information written to : "<< MyAllVariables->myOutFormat.OutPrefix + ".dose.vcf" + (gzip ? ".gz" : "")<myOutFormat.meta)
{
ifclose(vcfLoodosepartial);
cout<<" Empirical Dosage VCF written to : "<< MyAllVariables->myOutFormat.OutPrefix + ".empiricalDose.vcf" + (gzip ? ".gz" : "")<myOutFormat.doseOutput)
{
ifclose(dosages);
cout<<" Dosage information written to : "<< MyAllVariables->myOutFormat.OutPrefix + ".dose" + (gzip ? ".gz" : "")<myHapDataVariables.CHR!="")
{
while(referencePanel.VariantList[i].bp < MyAllVariables->myHapDataVariables.start)
{
i++;
}
}
}
else
{
while(referencePanel.VariantList[i].bp < MyChunks[ChunkNo][1])
{
i++;
}
}
ThisRefPanel.PrintStartIndex=i-RefStartPos;
if(ChunkNo==(noChunks-1))
{
if(MyAllVariables->myHapDataVariables.CHR!="")
{
for(; i <= RefEndPos; i++)
if(referencePanel.VariantList[i].bp > MyAllVariables->myHapDataVariables.end)
break;
}
else
i=RefEndPos+1;
}
else
{
for(; i <= RefEndPos; i++)
if(referencePanel.VariantList[i].bp > MyChunks[ChunkNo][2])
break;
}
ThisRefPanel.PrintEndIndex=i-RefStartPos-1;
// assert(ThisRefPanel.PrintStartIndex < ThisRefPanel.numMarkers);
// assert(ThisRefPanel.PrintEndIndex < ThisRefPanel.numMarkers);
}
void Estimation::GetCurrentPanelReady(int ChunkNo, HaplotypeSet &ThisRefPanel,
Imputation &thisDataFast)
{
int RefStartPos = MyRefVariantNumber[ChunkNo][0];
int RefEndPos = MyRefVariantNumber[ChunkNo][1];
int RefStartInfo = MyChunksInfoNumber[ChunkNo][0];
int RefEndInfo = MyChunksInfoNumber[ChunkNo][1];
int NoRefMarkers = RefEndPos - RefStartPos + 1;
// initialize typical variants
ThisRefPanel.numMarkers=NoRefMarkers;
ThisRefPanel.NoBlocks = MyChunksInfoNumber[ChunkNo][2];
int i;
// create new start and end indices for RefInfo
{
ThisRefPanel.ReducedStructureInfo[0].startIndex = 0;
for(i=RefStartInfo; i &Mapper = ThisRefPanel.MarkerToReducedInfoMapper;
int j;
for(i=0;imyOutFormat.verbose)
ThisRefPanel.VariantList[i-RefStartPos]=referencePanel.VariantList[i];
// ThisTarPanel.missing[i-RefStartPos]=targetPanel.missing[i];
if(referencePanel.Recom.size()>0)
{
if (i < RefEndPos)
ThisRefPanel.Recom[i - RefStartPos] = referencePanel.Recom[i];
ThisRefPanel.Error[i - RefStartPos] = referencePanel.Error[i];
}
}
}
ThisRefPanel.CalculateAlleleFreq();
int time_prev = time(0);
for(int i=0;imyModelVariables.cpus;i++)
{
thisDataFast.MainMarkovModel[i].AssignPanels(ThisRefPanel,MyAllVariables);
thisDataFast.MainMarkovModel[i].initializeMatricesMinimac3();
}
}
void Estimation::InitializeRefFileStream(String &Reffilename)
{
RefFileStream = ifopen(Reffilename, "r");
string line;
RefFileStream->readLine(line);
bool Header=true;
while(Header)
{
line.clear();
RefFileStream->readLine(line);
if(line.substr(0,6).compare("#CHROM")==0)
break;
}
for(int tempIndex=0;tempIndexdiscardLine();
PrevChunkFilledTillRef=0;
PrevChunkStartFromRef=0;
PrevChunkFilledTillTar=0;
PrevChunkStartFromTar=0;
PrevChunkFilledTillTarOnly=0;
PrevChunkStartFromTarOnly=0;
MaxGwasMarkerSize=MaxRefMarkerSize;
InitializeRefChunkData(CurrentRefPanel);
InitializeRefChunkData(CurrentRefPanelLoo);
InitializeTargetLooChunkData(CurrentTarPanelLoo);
//InitializeRefChipOnlyChunkData(CurrentRefPanelChipOnly);
// stats.PreInitialize(MaxRefMarkerSize);
// if(MyAllVariables->myOutFormat.memUsage)
// {
// RefMem = CurrentRefPanel.size();
// ComRefMem = CurrentRefPanelChipOnly.size();
// }
}
void Estimation::InitializeTargetFileStream(String &Tarfilename)
{
VcfHeader header;
TarFileStream.open(Tarfilename, header);
TarFileStream.setSiteOnly(false);
FileReadIndex=0;
overlapImportIndex=0;
importReadIndex=0;
GWASOnlySkipIndexpoint = 0;
MainTypedOnlyImportIndex =0;
InitializeTargetChipOnlyChunkData(CurrentTarPanelChipOnly);
// if(MyAllVariables->myOutFormat.memUsage)
// {
// TarMem = CurrentTarPanelChipOnly.size();
// }
}
String Estimation::RunEstimation(String &Reffilename, String &Recomfilename, String &Errorfilename)
{
// int time_prev=time(0);
// if (!targetPanel.ScaffoldGWAStoReference(referencePanel,*MyAllVariables))
// {
// cout << "\n Program Exiting ... \n\n";
// return "Reference.Panel.Load.Error";
// }
//
//
cout<<"\n ------------------------------------------------------------------------------"<myOutFormat.memUsage)
// {
// cout<<" ------------------------------------------------------------------------------"<myModelVariables.cpus);
//
// if(MyAllVariables->myOutFormat.vcfBuffer >= targetPanel.numSamples)
// MyAllVariables->myOutFormat.vcfBuffer=targetPanel.numSamples;
//
// thisDataFast.InitializeOutputFiles(targetPanel, MyAllVariables->myOutFormat.vcfBuffer, MaxRefMarkerSize, MaxGwasMarkerSize);
// if(MyAllVariables->myOutFormat.memUsage)
// {
//
// cout<<" Estimating Memory based on a single chunk ..."<< endl;
//
// readm3vcfFileChunk(0, CurrentRefPanel);
// readVcfFileChunk(0, CurrentTarPanelChipOnly);
// GetCurrentPanelReady(0, CurrentRefPanel, CurrentRefPanelChipOnly, CurrentTarPanelChipOnly, thisDataFast);
// cout<myOutFormat.meta)
// AppendtoMainLooVcfFaster(i,thisDataFast.TotalNovcfParts);
// PrintInfoFile(i);
//
// time_load = time(0) - time_prev;
// cout << "\n Time taken for this chunk = " << time_load << " seconds."<myHapDataVariables.end==0 && MyAllVariables->myOutFormat.TypedOnly)
//// assert(FileReadIndex==targetPanel.importIndexListSize);
//// asserassertt(OverCount==targetPanel.numOverlapMarkers);
//// assert(TypOnlyCount==targetPanel.numTypedOnlyMarkers);
//// assert(RefCOUNT==referencePanel.NoBlocks);
//
// CloseStreamOutputFiles();
return "Success";
}
String Estimation::AnalyzeExperiment(String &Reffilename, String &Tarfilename, String &Recomfilename, String &Errorfilename, AllVariable& MyAllVariable)
{
String mysuccessresult="Error";
cout << " Starting Main Imputation Estimation ... " << endl;
cout << "\n Performing preliminary check on input parameters... " ;
MyOutFormat=&MyAllVariable.myOutFormat;
MyModelVariables=&MyAllVariable.myModelVariables;
MyHapDataVariables=&MyAllVariable.myHapDataVariables;
MyAllVariables=&MyAllVariable;
int time_prev=time(0);
mysuccessresult=CheckValidity(Reffilename, Tarfilename, Recomfilename, Errorfilename);
TimeToRead+=( time(0) - time_prev);
if(mysuccessresult!="Success")
return mysuccessresult;
// if(!MyModelVariables->processReference)
// {
// mysuccessresult=RunEstimation(Reffilename, Tarfilename, Recomfilename, Errorfilename);
// }
// else
// {
// mysuccessresult=RunEstimation(Reffilename, Recomfilename, Errorfilename);
// }
if(mysuccessresult!="Success")
return mysuccessresult;
return "Success";
}
String Estimation::CheckValidity(String &Reffilename, String &Tarfilename, String &Recomfilename, String &Errorfilename)
{
cout<myModelVariables.CheckValidity())
{
return "Command.Line.Error";
}
if(!MyAllVariables->myHapDataVariables.CheckValidity())
{
return "Command.Line.Error";
}
if(!MyAllVariables->myOutFormat.CheckValidity())
{
return "Command.Line.Error";
}
// if(MyAllVariables->myOutFormat.verbose)
// {
// MyAllVariables->myHapDataVariables.ChunkLengthMb=299;
// }
if(!MyAllVariables->myModelVariables.processReference)
{
if (Tarfilename == "")
{
cout <<" ERROR !!! \n Missing \"--haps\", a required parameter (for imputation).\n";
cout <<" OR use \"--processReference\" to just process the reference panel.\n";
cout << "\n Program Exiting ... \n\n";
return "Command.Line.Error";
}
}
else
{
cout << "\n ERROR !!! The current version of Minimac4 does NOT support \"--processReference\" "<myModelVariables.processReference)
{
if (!targetPanel.BasicCheckForTargetHaplotypes(Tarfilename, "GWAS", *MyAllVariables))
{
return "Target.Panel.Load.Error";
}
}
else
{
if (!referencePanel.BasicCheckForVCFReferenceHaplotypes(Reffilename, "Reference", *MyAllVariables))
{
return "Reference.Panel.Load.Error";
}
}
return "Success";
}
void Estimation::InitializeRefChunkData(HaplotypeSet &ThisRefPanel)
{
int NoRefHaps=referencePanel.numHaplotypes;
ThisRefPanel.numHaplotypes=NoRefHaps;
ThisRefPanel.numSamples=referencePanel.numSamples;
ThisRefPanel.SampleNoHaplotypes=referencePanel.SampleNoHaplotypes;
ThisRefPanel.CummulativeSampleNoHaplotypes=referencePanel.CummulativeSampleNoHaplotypes;
ThisRefPanel.individualName=referencePanel.individualName;
ThisRefPanel.maxBlockSize=referencePanel.maxBlockSize;
ThisRefPanel.maxRepSize=referencePanel.maxRepSize;
ThisRefPanel.ReducedStructureInfo.resize(MaxInfoVectorSize);
ThisRefPanel.MyAllVariables=MyAllVariables;
ThisRefPanel.MapRefToTar.resize(MaxRefMarkerSize);
ThisRefPanel.MapTarToRef.resize(MaxRefMarkerSize);
int Mem=0;
for(int i=0;imyOutFormat.verbose)
{
ThisRefPanel.VariantList.resize(MaxRefMarkerSize);
}
}
void Estimation::InitializeRefChipOnlyChunkData(HaplotypeSet &ThisRefPanel)
{
int NoRefHaps=referencePanel.numHaplotypes;
ThisRefPanel.numHaplotypes=NoRefHaps;
ThisRefPanel.numSamples=referencePanel.numSamples;
ThisRefPanel.MarkerToReducedInfoMapper.resize(MaxGwasMarkerSize);
ThisRefPanel.Recom.resize(MaxGwasMarkerSize);
ThisRefPanel.Error.resize(MaxGwasMarkerSize);
ThisRefPanel.AlleleFreq.resize(MaxGwasMarkerSize);
ThisRefPanel.MyAllVariables=MyAllVariables;
if(MyAllVariables->myOutFormat.verbose)
{
ThisRefPanel.individualName=referencePanel.individualName;
ThisRefPanel.SampleNoHaplotypes=referencePanel.SampleNoHaplotypes;
ThisRefPanel.VariantList.resize(MaxGwasMarkerSize);
}
}
void Estimation::InitializeTargetLooChunkData(HaplotypeSet &ThisTarPanel)
{
int tempnumHaplotypes=targetPanel.numHaplotypes;
ThisTarPanel.MyAllVariables=MyAllVariables;
ThisTarPanel.numHaplotypes=1;
ThisTarPanel.numSamples=1;
ThisTarPanel.haplotypesUnscaffolded.resize(1);
ThisTarPanel.MissingSampleUnscaffolded.resize(1);
for (int i = 0; imyOutFormat.TypedOnly)
{
ThisTarPanel.GWASOnlyhaplotypesUnscaffolded.resize(tempnumHaplotypes);
ThisTarPanel.GWASOnlyMissingSampleUnscaffolded.resize(tempnumHaplotypes);
}
for (int i = 0; imyOutFormat.TypedOnly)
{
ThisTarPanel.TypedOnlyVariantList.resize(MaxTypedOnlyMarkerSize);
ThisTarPanel.GWASOnlyhaplotypesUnscaffolded[i].resize(MaxTypedOnlyMarkerSize, false);
ThisTarPanel.GWASOnlyMissingSampleUnscaffolded[i].resize(MaxTypedOnlyMarkerSize, false);
}
}
ThisTarPanel.GWASOnlyAlleleFreq.resize(MaxTypedOnlyMarkerSize);
ThisTarPanel.FlankRegionStart.resize(MaxGwasMarkerSize);
ThisTarPanel.FlankRegionEnd.resize(MaxGwasMarkerSize);
}
void Estimation::InitializeChunkVariables()
{
int i;
MyChunks.resize(noChunks);
MyChunksInfoNumber.resize(noChunks+1); // extra element added just to reduce checks later on
MyRefVariantNumber.resize(noChunks+1); // extra element added just to reduce checks later on
MyTargetVariantNumber.resize(noChunks+1); // extra element added just to reduce checks later on
MyTypdedOnlyVariantNumber.resize(noChunks+1); // extra element added just to reduce checks later on
MyRatio.resize(noChunks+1,-1.0); // extra element added just to reduce checks later on
for(i=0;i<(noChunks);i++)
{
MyChunks[i].resize(4);
MyChunksInfoNumber[i].resize(3);
MyRefVariantNumber[i].resize(3);
MyTargetVariantNumber[i].resize(3,-3);
MyTypdedOnlyVariantNumber[i].resize(3,-3);
}
MyChunksInfoNumber[i].resize(1,99999999); // extra element added just to reduce checks later on
MyRefVariantNumber[i].resize(1,99999999); // extra element added just to reduce checks later on
MyTargetVariantNumber[i].resize(1,99999999); // extra element added just to reduce checks later on
MyTypdedOnlyVariantNumber[i].resize(1,99999999); // extra element added just to reduce checks later on
}
void Estimation::CreateChunksFromReference()
{
vector &RefInfo=referencePanel.ReducedStructureInfoSummary;
vector &VarList=referencePanel.VariantList;
vector &InfoMapper=referencePanel.MarkerToReducedInfoMapper;
int NoMarkers=referencePanel.numMarkers;
int i=0,index;
MyChunksInfoNumber[0][0]=0;
MyRefVariantNumber[0][0]=0;
MyChunks[0][0]=VarList[0].bp;
MyChunks[0][1]=VarList[0].bp;
if(noChunks>1)
{
MyChunksInfoNumber[0][1]=InfoMapper[0 + MyHapDataVariables->ChunkSize + MyHapDataVariables->ChunkWindow];
MyRefVariantNumber[0][1]= RefInfo[MyChunksInfoNumber[0][1]].endIndex ;
MyChunks[0][2]=VarList[0 + MyHapDataVariables->ChunkSize].bp;
MyChunks[0][3]=VarList[MyRefVariantNumber[0][1]].bp;
for(i=1;i<(noChunks-1);i++)
{
index=(i*MyHapDataVariables->ChunkSize);
MyChunksInfoNumber[i][0]=InfoMapper[index-MyHapDataVariables->ChunkWindow];
MyChunksInfoNumber[i][1]=InfoMapper[index+MyHapDataVariables->ChunkSize+MyHapDataVariables->ChunkWindow];
MyRefVariantNumber[i][0]=RefInfo[MyChunksInfoNumber[i][0]].startIndex;
MyRefVariantNumber[i][1]= RefInfo[MyChunksInfoNumber[i][1]].endIndex;
MyChunks[i][0]=VarList[MyRefVariantNumber[i][0]].bp;
MyChunks[i][1]=MyChunks[i-1][2]+1;
MyChunks[i][2]=VarList[index+MyHapDataVariables->ChunkSize].bp;
MyChunks[i][3]=VarList[MyRefVariantNumber[i][1]].bp;
}
index=(i*MyHapDataVariables->ChunkSize);
MyChunksInfoNumber[i][0]=InfoMapper[index-MyHapDataVariables->ChunkWindow];
MyRefVariantNumber[i][0]=RefInfo[MyChunksInfoNumber[i][0]].startIndex;
MyChunks[i][0]=VarList[MyRefVariantNumber[i][0]].bp;
MyChunks[i][1]=MyChunks[i-1][2]+1;
}
MyChunks[i][2]=VarList[NoMarkers-1].bp;
MyChunks[i][3]=VarList[NoMarkers-1].bp;
MyChunksInfoNumber[i][1]=InfoMapper[NoMarkers-1];
MyRefVariantNumber[i][1]=NoMarkers-1;
for(int i=0;i &VarList=referencePanel.VariantList;
int NoMarkers=referencePanel.numMarkers;
int index;
MyRefVariantNumber[0][0]=0;
MyChunks[0][0]=VarList[0].bp;
MyChunks[0][1]=VarList[0].bp;
i=0;
if(noChunks>1)
{
MyChunks[0][2]=VarList[0 + MyHapDataVariables->ChunkSize].bp;
MyChunks[0][3]=VarList[0 + MyHapDataVariables->ChunkSize + MyHapDataVariables->ChunkWindow].bp;
MyRefVariantNumber[0][1]=MyHapDataVariables->ChunkSize + MyHapDataVariables->ChunkWindow;
for(i=1;i<(noChunks-1);i++)
{
index=(i*MyHapDataVariables->ChunkSize);
MyRefVariantNumber[i][0]=index-MyHapDataVariables->ChunkWindow;
MyChunks[i][0]=VarList[index-MyHapDataVariables->ChunkWindow].bp;
MyChunks[i][1]=MyChunks[i-1][2]+1;
MyChunks[i][2]=VarList[index+MyHapDataVariables->ChunkSize].bp;
MyChunks[i][3]=VarList[index+MyHapDataVariables->ChunkSize+MyHapDataVariables->ChunkWindow].bp;
MyRefVariantNumber[i][1]= index+MyHapDataVariables->ChunkSize+MyHapDataVariables->ChunkWindow;
}
index=(i*MyHapDataVariables->ChunkSize);
MyRefVariantNumber[i][0]=index-MyHapDataVariables->ChunkWindow;
MyChunks[i][0]=VarList[index-MyHapDataVariables->ChunkWindow].bp;
MyChunks[i][1]=MyChunks[i-1][2]+1;
}
MyChunks[i][2]=VarList[NoMarkers-1].bp;
MyChunks[i][3]=VarList[NoMarkers-1].bp;
MyRefVariantNumber[i][1]=NoMarkers-1;
for(int i=0;i0)
{
while(i MyTargetVariantNumber[i][0]? MyTargetVariantNumber[i][1] + 1 - MyTargetVariantNumber[i][0]: 0 );
MyTypdedOnlyVariantNumber[i][2] = ( MyTypdedOnlyVariantNumber[i][1] + 1 >MyTypdedOnlyVariantNumber[i][0]? MyTypdedOnlyVariantNumber[i][1] + 1 - MyTypdedOnlyVariantNumber[i][0]: 0 );
}
}
bool Estimation::CheckChunkValidityandPrintChunkForEstimation()
{
int MinRefMarkerSize=MyRefVariantNumber[0][2], InIndex=0;
MaxInfoVectorSize=0;
MaxRefMarkerSize=0;
cout<<" No LeftBuffer LeftEnd RightPoint RightBuffer #Sites"< MaxInfoVectorSize )
MaxInfoVectorSize = MyChunksInfoNumber[i][2];
if( MyRefVariantNumber[i][2] > MaxRefMarkerSize )
MaxRefMarkerSize = MyRefVariantNumber[i][2];
if( MyRefVariantNumber[i][2] < MinRefMarkerSize )
{
InIndex=i;
MinRefMarkerSize = MyRefVariantNumber[i][2];
}
cout< MaxRefMarkerSize )
MaxRefMarkerSize = MyRefVariantNumber[i][2];
if( MyRefVariantNumber[i][2] < MinRefMarkerSize )
{
InIndex=i;
MinRefMarkerSize = MyRefVariantNumber[i][2];
}
cout<ChunkSize <<" variants in each chunk ... " << endl<ChunkSize <<" variants in each chunk ... " << endl<myHapDataVariables.ChunkOverlapMb));
if(noOverLaps==0)
noOverLaps=1;
MyHapDataVariables->ChunkWindow=(NoMarkers/noOverLaps);
noChunks = ((int)(EndPos-StartPos)/(int)(1000000 *MyAllVariables->myHapDataVariables.ChunkLengthMb));
if(noChunks==0)
noChunks=1;
MyHapDataVariables->ChunkSize=(NoMarkers/noChunks);
return;
}
Minimac4-1.0.2/src/Estimation.h 0000664 0000000 0000000 00000013040 13532224264 0016230 0 ustar 00root root 0000000 0000000 #ifndef MINIMAC4_ESTIMATION_H
#define MINIMAC4_ESTIMATION_H
#if defined(_OPENMP)
#include
#endif
#include "MyVariables.h"
#include "Unique.h"
#include "Imputation.h"
#include "HaplotypeSet.h"
#include
using namespace std;
class Estimation
{
public:
// Basic Variables
HaplotypeSet targetPanel,referencePanel;
IFILE RefFileStream;
VcfFileReader TarFileStream;
VcfRecord record;
// Swapping Variables for actual chunk IMPUTATION
HaplotypeSet CurrentTarPanel, CurrentRefPanel, CurrentRefPanelLoo, CurrentTarPanelLoo;
HaplotypeSet CurrentTarPanelChipOnly,CurrentRefPanelChipOnly;
int PrevChunkFilledTillRef, PrevChunkStartFromRef;
int PrevChunkFilledTillTar, PrevChunkStartFromTar;
int PrevChunkFilledTillTarOnly, PrevChunkStartFromTarOnly;
void InitializeTargetChipOnlyChunkData(HaplotypeSet &ThisTarPanel);
void InitializeRefChipOnlyChunkData(HaplotypeSet &ThisRefPanel);
void readm3vcfFileChunk(int ChunkNo, HaplotypeSet &ThisRefPanel);
void readVcfFileChunk(int ChunkNo, HaplotypeSet &ThisTargetPanel);
// Target PANEL Indexing Variables
int overlapImportIndex, importReadIndex, FileReadIndex;
int GWASOnlySkipIndexpoint , MainTypedOnlyImportIndex;
// Output File Handle Streams
IFILE dosages, hapdose, haps, vcfdosepartial, vcfLoodosepartial, info;
IFILE m3vcfpartial, recfile, errfile ;
ImputationStatistics stats;
// Chunk Information
int noChunks;
vector< vector > MyChunks,MyChunksInfoNumber;
vector< vector > MyRefVariantNumber, MyTargetVariantNumber, MyTypdedOnlyVariantNumber;
vector< float > MyRatio;
int MaxInfoVectorSize, MaxGwasMarkerSize, MaxRefMarkerSize, MaxTypedOnlyMarkerSize;
// Temporary Variables to be deleted later for checking purposes.
int OverCount, TypOnlyCount, RefCOUNT;
// Time Variables
int TimeToCompress, TimeToRead, TimeToImpute, TimeToWrite;
// Memory Variables
double RefMem, TarMem, ComRefMem, DosageMem, ProbMem;
// Printing Text Variables
char *VcfPrintStringPointer, *LooVcfPrintStringPointer, *InfoPrintStringPointer, *DosePrintStringPointer;
char *m3vcfPrintStringPointer, *recPrintStringPointer, *errPrintStringPointer;
int VcfPrintStringLength, InfoPrintStringLength, DosePrintStringLength;
int m3vcfPrintStringLength, recPrintStringLength, errPrintStringLength;
vector InfoforChunk;
vector< vector > BPListMapper;
HaplotypeSet *CurrentChunk, *NextChunk;
HaplotypeSet MainReferenceFrame;
OutputFormatVariable *MyOutFormat;
ModelVariable *MyModelVariables;
HaplotypeDataVariables *MyHapDataVariables;
AllVariable *MyAllVariables;
void PrintInfoFile(int ChunkNo);
Estimation()
{
TimeToCompress=0;
TimeToRead=0;
TimeToImpute=0;
TimeToWrite=0;
RefMem =0.0;
TarMem =0.0;
ComRefMem =0.0;
DosageMem =0.0;
ProbMem = 0.0;
}
void AppendtoMainVcf(int ChunkNo, int MaxIndex);
void AppendtoMainLooVcfFaster(int ChunkNo, int MaxIndex);
void AppendtoMainVcfFaster(int ChunkNo, int MaxIndex);
void MemDisplay();
void GetNumChunks();
String RunEstimation(String &Reffilename, String &Recomfilename, String &Errorfilename, AllVariable& MyAllVariable);
String RunEstimation(String &Reffilename, String &Recomfilename, String &Errorfilename);
String AnalyzeExperiment(String &Reffilename, String &Tarfilename, String &Recomfilename,String &Errorfilename, AllVariable& MyAllVariable);
String CheckValidity(String &Reffilename, String &Tarfilename, String &Recomfilename, String &Errorfilename);
String RunAnalysis(String &Reffilename, String &Tarfilename, String &Recomfilename, String &Errorfilename);
void readm3vcfFileChunk(HaplotypeSet &ThisRefPanel, HaplotypeSet &NextRefPanel,
int StartBlock, int EndBlock, int StartNextBlock);
void readVcfFileChunk(HaplotypeSet &ThisTargetPanel, HaplotypeSet &NextTargetPanel,
int StartPos, int EndPos, int StartNextPos, int ChunkNo);
bool OpenStreamOutputFiles();
void CloseStreamOutputFiles();
void InitializeRefFileStream(String &Reffilename);
void InitializeTargetFileStream(String &Tarfilename);
void InitializeRefChunkData(HaplotypeSet &ThisRefPanel);
void InitializeTargetChunkData(HaplotypeSet &ThisTarPanel);
bool CheckChunkValidityandPrintChunkForEstimation();
bool CreateChunks();
bool CreateChunksForParamEstimation();
void InitializeChunkVariables();
void CreateChunksFromReference();
void CreateChunksFromVCFReference();
void ImportChunksToTarget();
bool CheckChunkValidityandPrintChunk();
bool CheckChunkValidityForParamEstimationandPrintChunk();
void InitializeTargetLooChunkData(HaplotypeSet &ThisTarPanel);
void CreatePrintIndices(int ChunkNo, HaplotypeSet &ThisRefPanel);
void GetCurrentPanelReady(int ChunkNo, HaplotypeSet &ThisRefPanel, Imputation &thisDataFast);
};
#endif //MINIMAC4_ESTIMATION_H
Minimac4-1.0.2/src/HaplotypeSet.cpp 0000664 0000000 0000000 00000217053 13532224264 0017102 0 ustar 00root root 0000000 0000000 #include "HaplotypeSet.h"
#include "assert.h"
#define ALT_DELIM ','
#define MONOMORPH_INDICATOR '-'
#include "STLUtilities.h"
void HaplotypeSet::UncompressTypedSitesNew(HaplotypeSet &rHap,HaplotypeSet &tHap,int ChunkNo)
{
// outFile=MyAllVariables->myOutFormat.OutPrefix;
vcfType=false;
int CPU=1;
int blockSize = 500;
int bufferSize = 5000;
vector CompHaplotypes(CPU);
int currentPiece=0;
for(currentPiece=0;currentPiece BufferPosList(CPU);
BufferPosList[0]=1;
for(int BufferNo=1;BufferNo &RhapInfo=rHap.ReducedStructureInfo;
// assert(numMarkers==tHap.numMarkers);
for(int ThisPanelIndex=0; ThisPanelIndexmyOutFormat.verbose)
{
VariantList[ThisPanelIndex]=rHap.VariantList[RefmarkerIndex];
}
CompHaplotypes[currentPiece].Push(j,ThisMarkerIndex);
int NewPiece=CPU;
if (CompHaplotypes[currentPiece].Length == bufferSize)
{
NewPiece=(currentPiece+1)%CPU;
vector tempHaplotypes(numHaplotypes);
if(NewPiece!=0)
{
int temp=CompHaplotypes[currentPiece].ReducedInfoMapper[bufferSize-1];
int temp2=CompHaplotypes[currentPiece].ReducedInfoVariantMapper[bufferSize-1];
CompHaplotypes[NewPiece].Clear();
CompHaplotypes[NewPiece].Push(temp,temp2);
currentPiece=NewPiece;
}
}
if(NewPiece==0 || ThisPanelIndex==(numMarkers-1))
{
#pragma omp parallel for
for(int ThisPiece=0;ThisPiece<=currentPiece;ThisPiece++)
{
int LastflushPos=BufferPosList[ThisPiece]-1;
vector index(numHaplotypes),oldIndex;
vector previousDifference(numHaplotypes);
vector previousPredecessor(numHaplotypes);
vector firstDifference(numHaplotypes-1,0);
vector cost(bufferSize+1,0);
vector bestSlice(bufferSize+1,0);
vector bestComplexity(bufferSize+1,0);
vector > bestIndex(bufferSize+1);
ReducedStructureInfoBuffer[ThisPiece].clear();
findUnique RefUnique;
RefUnique.updateCoeffs(MyAllVariables->myModelVariables.transFactor,MyAllVariables->myModelVariables.cisFactor);
double blockedCost = 0.0;
for(int i=0;i offsets(3,0);
for (int i = 0; i < numHaplotypes; i++)
{
offsets[CompHaplotypes[ThisPiece].GetVal(i) - '0' + 1]++;
}
offsets[2]+=offsets[1];
oldIndex = index;
for (int i = 0; i < numHaplotypes; i++)
{
index[offsets[CompHaplotypes[ThisPiece].GetVal(oldIndex[i],length - 1) - '0']++] = oldIndex[i];
}
RefUnique.UpdateDeltaMatrix(CompHaplotypes[ThisPiece], index, firstDifference, length, blockSize,
oldIndex, previousPredecessor, previousDifference);
RefUnique.AnalyzeBlocks(index, firstDifference, length, blockSize,
cost, bestSlice, bestComplexity, bestIndex);
}
if(CompHaplotypes[ThisPiece].Length>1)
blockedCost += RefUnique.FlushBlocks(ReducedStructureInfoBuffer[ThisPiece],
LastflushPos,
CompHaplotypes[ThisPiece], cost,
bestComplexity, bestSlice, bestIndex);
}
NoMarkersWritten+=(CPU*(bufferSize-1));
BufferPosList[0]=NoMarkersWritten;
for(int BufferNo=1;BufferNomyOutFormat.verbose)
{
stringstream strs;
strs<<(ChunkNo+1);
string ss=(string)MyAllVariables->myOutFormat.OutPrefix+".chunk."+(string)(strs.str())+".GWAS";
String tempString(ss.c_str());
writem3vcfFile( tempString, MyAllVariables->myOutFormat.gzip);
}
}
void HaplotypeSet::CreateScaffoldedParameters(HaplotypeSet &rHap)
{
for(int i=0;i0)
{
int index=rHap.MapTarToRef[i-1];
double temp=1.0;
while(index 9)
{
tempString = string(pch);
if(tempString.find('|')==string::npos)
SampleNoHaplotypes[sampleCount]=1;
else
SampleNoHaplotypes[sampleCount]=2;
sampleCount++;
}
pch = strtok_r (NULL,"\t", &end_str1);
}
for (int i = 1; i < numSamples; i++)
CummulativeSampleNoHaplotypes[i] += CummulativeSampleNoHaplotypes[i - 1] + SampleNoHaplotypes[i - 1];
numHaplotypes = CummulativeSampleNoHaplotypes.back()+SampleNoHaplotypes.back();
}
void HaplotypeSet::getm3VCFSampleNames(string &line)
{
individualName.clear();
SampleNoHaplotypes.clear();
CummulativeSampleNoHaplotypes.clear();
numSamples=0;
numHaplotypes=0;
char * pch;
char *end_str1;
string tempString2,tempString,tempString3;
int colCount=0;
pch = strtok_r ((char*)line.c_str(),"\t", &end_str1);
numHaplotypes=0;
while(pch!=NULL)
{
colCount++;
if(m3vcfVERSION==1 && colCount>9)
{
numHaplotypes++;
tempString=string(pch);
tempString3=tempString.substr(tempString.size()-1,tempString.size()-1);
tempString2=tempString.substr(0,tempString.size()-6);
if(tempString3=="1")
{
numSamples++;
individualName.push_back(tempString2);
SampleNoHaplotypes.push_back(1);
}
else if(tempString3=="2")
{
SampleNoHaplotypes.back()=2;
}
else
{
cout<9)
{
numSamples++;
tempString=string(pch);
individualName.push_back(tempString);
}
pch = strtok_r (NULL,"\t", &end_str1);
}
if(m3vcfVERSION==1)
{
CummulativeSampleNoHaplotypes.resize(numSamples, 0);
for (int i = 1; i < numSamples; i++)
CummulativeSampleNoHaplotypes[i] += CummulativeSampleNoHaplotypes[i - 1] + SampleNoHaplotypes[i - 1];
}
}
void HaplotypeSet::UpdateParameterList()
{
MyOutFormat=&(MyAllVariables->myOutFormat);
MyModelVariables=&(MyAllVariables->myModelVariables);
MyHapDataVariables=&(MyAllVariables->myHapDataVariables);
}
bool HaplotypeSet::ReadBlockHeaderSummary(string &line, ReducedHaplotypeInfoSummary &tempBlocktoCheck)
{
const char* tabSep="\t";
vector BlockPieces(numHaplotypes+9);
MyTokenize(BlockPieces, line.c_str(), tabSep, 9);
tempBlocktoCheck.BlockSize=GetNumVariants(BlockPieces[7]);
tempBlocktoCheck.RepSize=GetNumReps(BlockPieces[7]);
if(CheckBlockPosFlag(line, MyHapDataVariables->CHR, MyHapDataVariables->START, MyHapDataVariables->END)==1)
return true;
return false;
}
void HaplotypeSet::GetVariantInfoFromBlock(IFILE m3vcfxStream, ReducedHaplotypeInfoSummary &tempBlock, int &NoMarkersImported)
{
string currID, rsID;
string line;
int blockEnterFlag=0;
const char* tabSep="\t";
int NewBlockSizeCount=0;
for(int tempIndex=0;tempIndexreadLine(line);
MyTokenize(BlockPiecesforVarInfo, line.c_str(), tabSep,9);
if(StartedThisPanel==false || tempIndex>0)
{
StartedThisPanel=true;
currID=BlockPiecesforVarInfo[0]+":"+BlockPiecesforVarInfo[1]+":"+BlockPiecesforVarInfo[3]+":"+BlockPiecesforVarInfo[4];
rsID = BlockPiecesforVarInfo[2];
if(rsID==".")
rsID=currID;
variant tempVariant;
tempVariant.assignValues(currID,rsID,BlockPiecesforVarInfo[0],atoi(BlockPiecesforVarInfo[1].c_str()));
tempVariant.assignRefAlt(BlockPiecesforVarInfo[3],BlockPiecesforVarInfo[4]);
VariantList.push_back(tempVariant);
string Info=BlockPiecesforVarInfo[7];
double tempRecom=GetRecom(Info);
double tempError=GetError(Info);
if(MyAllVariables->myModelVariables.constantParam>0.0)
{
Recom.push_back(MyAllVariables->myModelVariables.constantParam);
Error.push_back(0.00999);
}
else
{
if (tempRecom == -3.0 && MyAllVariables->myModelVariables.referenceEstimates) {
cout << "\n ERROR !!! \n NO parameter estimates already found in M3VCF file !!!" << endl;
cout << " Please remove handle \"--referenceEstimates\" to ignore this check " << endl;
cout << " Else, use M3VCF file with parameter estimates " << endl;
cout << "\n Program Exiting ... \n\n";
abort();
}
Recom.push_back(tempRecom);
Error.push_back(0.00999);
}
NewBlockSizeCount++;
NoMarkersImported++;
}
if(blockEnterFlag==0)
{
tempBlock.startIndex=NoMarkersImported-1;
blockEnterFlag=1;
}
tempBlock.endIndex=NoMarkersImported-1;
}
}
void HaplotypeSet::reconstructHaplotype(vector &reHaplotypes,int &index)
{
int markerIndex=0,k;
for(int j=0;j padded(rHap.numMarkers);
rHap.reconstructHaplotype(padded,index);
numMarkers=(int)padded.size();
haplotypesUnscaffolded[0]= padded;
}
bool HaplotypeSet::ReadBlockHeader(string &line, ReducedHaplotypeInfo &tempBlocktoCheck)
{
const char* tabSep="\t", *dashSep="|";
vector BlockPieces(numHaplotypes+9);
MyTokenize(BlockPieces, line.c_str(), tabSep,numHaplotypes+9);
tempBlocktoCheck.BlockSize=GetNumVariants(BlockPieces[7]);
tempBlocktoCheck.RepSize=GetNumReps(BlockPieces[7]);
if(CheckBlockPosFlag(line,MyHapDataVariables->CHR,MyHapDataVariables->START,MyHapDataVariables->END)==1)
return true;
fill(tempBlocktoCheck.uniqueCardinality.begin(), tempBlocktoCheck.uniqueCardinality.end(), 0);
int index=0;
if(m3vcfVERSION==1) {
while (index < numHaplotypes) {
int tempval = atoi(BlockPieces[index + 9].c_str());
tempBlocktoCheck.uniqueIndexMap[index] = tempval;
tempBlocktoCheck.uniqueCardinality[tempval]++;
index++;
}
}
else if (m3vcfVERSION==2)
{
int haploIndex = 0;
while (index < numSamples)
{
if(SampleNoHaplotypes[index]==2)
{
vector HaploPieces(2);
MyTokenize(HaploPieces, BlockPieces[index + 9].c_str(), dashSep, 2);
int tempval = atoi(HaploPieces[0].c_str());
tempBlocktoCheck.uniqueIndexMap[haploIndex++] = tempval;
tempBlocktoCheck.uniqueCardinality[tempval]++;
tempval = atoi(HaploPieces[1].c_str());
tempBlocktoCheck.uniqueIndexMap[haploIndex++] = tempval;
tempBlocktoCheck.uniqueCardinality[tempval]++;
}
else
{
int tempval = atoi(BlockPieces[index + 9].c_str());
tempBlocktoCheck.uniqueIndexMap[haploIndex++] = tempval;
tempBlocktoCheck.uniqueCardinality[tempval]++;
}
index++;
}
}
for (int i = 0; i < tempBlocktoCheck.RepSize; i++)
{
tempBlocktoCheck.InvuniqueCardinality[i]=1.0/(float)tempBlocktoCheck.uniqueCardinality[i];
}
return false;
}
void HaplotypeSet::GetTransUniqueHapsVERSION2(int index, ReducedHaplotypeInfo &tempBlock, string &tempString)
{
vector &TempHap = tempBlock.TransposedUniqueHaps[index];
fill(TempHap.begin(), TempHap.end(), '0');
vector AlternateAlleles;
AlternateAlleles.clear();
int prevVal = 0;
char *input=&tempString[0];
string word="";
while (*input)
{
if(*input==MONOMORPH_INDICATOR)
{
break;
}
if (*input==ALT_DELIM)
{
word.push_back('\0');
AlternateAlleles.push_back(prevVal+atoi(word.c_str()));
prevVal=AlternateAlleles.back();
word.clear();
}
else
{
word.push_back(*input);
}
input++;
}
if(word!="")
{
word.push_back('\0');
AlternateAlleles.push_back(prevVal+atoi(word.c_str()));
}
for(int i=0; i<(int)AlternateAlleles.size(); i++) {
TempHap[AlternateAlleles[i]]='1';
}
}
void HaplotypeSet::ReadThisBlock(IFILE m3vcfxStream,
int blockIndex, ReducedHaplotypeInfo &tempBlock)
{
string line;
const char* tabSep="\t";
vector BlockPieces(9);
for(int tempIndex=0;tempIndexreadLine(line);
MyTokenize(BlockPieces, line.c_str(), tabSep,9);
vector &TempHap = tempBlock.TransposedUniqueHaps[tempIndex];
string &tempString=BlockPieces[8];
if(m3vcfVERSION==1) {
for (int index = 0; index < tempBlock.RepSize; index++) {
char t = tempString[index];
TempHap[index] = (t);
}
}
else if(m3vcfVERSION==2) {
GetTransUniqueHapsVERSION2(tempIndex, tempBlock, tempString);
}
}
}
bool HaplotypeSet::BasicCheckForTargetHaplotypes(String &VCFFileName,
String TypeofFile,
AllVariable& MyAllVariable)
{
MyAllVariables=&MyAllVariable;
std::cout << "\n Checking "<myModelVariables.rounds==0)
{
cout <<"\n NOTE: User has specified \"--rounds\" = 0 !!!\n";
cout<<" No parameter estimation will be done on VCF file.\n";
cout<<" Program will use default estimates leading to possibly inaccurate estimates."<0)
{
if(bp>MyAllVariable.myHapDataVariables.END || bp1)
{
notBiallelic++;
flag = 1;
}
if (MyAllVariable.myHapDataVariables.passOnly && record.getFilter().getString(0).compare("PASS") != 0)
{
failFilter++;
flag = 1;
}
}
// Check ID for duplicate
{
stringstream strs3,strs4;
strs3<<(cno);
strs4<<(bp);
currID=(string)strs3.str()+":"+(string)strs4.str()+":"+refAllele+":"+altAllele;
if(id==".")
id=currID;
if(prevID==currID)
{
duplicates++;
if(MyAllVariable.myOutFormat.verbose){cout << " WARNING !!! Duplicate Variant found chr:"<0) {cout<0){std::cout << " NOTE ! "<< outSideRegion<< " variants lie outside region ["
<0){std::cout << " NOTE ! "<< duplicates<< " instance(s) of duplicated variants discarded ..." << endl;}
if(notBiallelic>0){std::cout << " NOTE ! "<< notBiallelic<< " multi-allelic variant(s) discarded ..." << endl;}
if(failFilter>0){std::cout << " NOTE ! "<< failFilter<< " variant(s) failed FILTER = PASS and were discarded ..." << endl;}
if(inconsistent>0){std::cout << " NOTE ! "<< inconsistent<< " SNP(s) with inconsistent REF/ALT alleles discarded ..." << endl;}
if(outSideRegion + duplicates + notBiallelic + failFilter + inconsistent>0) {cout< headerTag(2);
string line;
const char *equalSep="=";
m3vcfVERSION=0;
bool Header=true;
while(Header)
{
line.clear();
m3vcfxStream->readLine(line);
if(line.substr(0,2).compare("##")==0)
Header=true;
else
break;
MyTokenize(headerTag, line.c_str(), equalSep, 2);
if(headerTag[0].compare("##n_blocks")==0)
{
NoBlocks=atoi(headerTag[1].c_str());
}
if(m3vcfVERSION==0 && headerTag[0].compare("##fileformat")==0)
{
string tempVer = headerTag[1].substr(5,5).c_str();
if(tempVer.length()==0)
m3vcfVERSION=1;
else if (tempVer=="v2.0")
m3vcfVERSION=2;
else
{
cout << "\n ERROR !!! \n Invalid M3VCF Version : "<CHR!="")
{
std::cout << "\n Loading markers in region " << MyHapDataVariables->CHR<<":"<START<<"-"<END<<" ..."<< endl;
}
IFILE m3vcfxStream = ifopen(Reffilename, "r");
if(m3vcfxStream)
{
GetSummary(m3vcfxStream);
if(numSamples==0)
{
cout << "\n ERROR !!! \n No samples found in M3VCF Input File : "<readLine(line)!=-1)
{
if(ReadHeader==0)
{
string tempLine = line.c_str() ;
UpdatePloidySummary(tempLine);
ReadHeader=1;
}
ReducedHaplotypeInfoSummary tempBlock;
if(ReadBlockHeaderSummary(line, tempBlock))
{
if(finChromosome!=checkChr)
{
cout << "\n ERROR !!! \n Reference Panel is on chromosome ["<discardLine();
line.clear();
continue;
}
if(finChromosome!=checkChr)
{
cout << "\n ERROR !!! \n Reference Panel is on chromosome ["<myHapDataVariables.CHR=="")
{
cout << "\n ERROR !!! \n No variants left to imported from reference haplotype file "<myHapDataVariables.CHR<<":"
<myHapDataVariables.START<<"-"<myHapDataVariables.END
<<"] in reference haplotype file "<myHapDataVariables.MyChromosome!="" && chr==MyAllVariables->myHapDataVariables.MyChromosome.c_str())
return true;
string temp[]={"1","2","3","4","5","6","7","8","9","10","11"
,"12","13","14","15","16","17","18","19","20","21","22","23","X","Y"
,"chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11"
,"chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19","chr20"
,"chr21","chr22","chr23","chrX","chrY"};
std::vector ValidChromList (temp, temp + sizeof(temp) / sizeof(string) );
for(int counter=0;counter<(int)ValidChromList.size();counter++)
if(chr==ValidChromList[counter])
result=true;
return result;
}
void HaplotypeSet::writem3vcfFile(String filename,bool &gzip)
{
IFILE m3vcffile = ifopen(filename + ".m3vcf" + (gzip ? ".gz" : ""), "wb",(gzip ? InputFile::BGZF : InputFile::UNCOMPRESSED));
ifprintf(m3vcffile, "##fileformat=M3VCF\n");
ifprintf(m3vcffile, "##version=1.2\n");
ifprintf(m3vcffile, "##compression=block\n");
ifprintf(m3vcffile, "##n_blocks=%d\n",NoBlocks);
ifprintf(m3vcffile, "##n_haps=%d\n",numHaplotypes);
ifprintf(m3vcffile, "##n_markers=%d\n",numMarkers);
if(finChromosome=="X" || finChromosome=="23")
ifprintf(m3vcffile, "##chrxRegion=%s\n",PseudoAutosomal?"PseudoAutosomal":"NonPseudoAutosomal");
ifprintf(m3vcffile, "##\n");
ifprintf(m3vcffile, "#CHROM\t");
ifprintf(m3vcffile, "POS\t");
ifprintf(m3vcffile, "ID\t");
ifprintf(m3vcffile, "REF\t");
ifprintf(m3vcffile, "ALT\t");
ifprintf(m3vcffile, "QUAL\t");
ifprintf(m3vcffile, "FILTER\t");
ifprintf(m3vcffile, "INFO\t");
ifprintf(m3vcffile, "FORMAT");
int i,j,k;
for(i=0;i<(int)numSamples;i++)
{
ifprintf(m3vcffile, "\t%s_HAP_1",individualName[i].c_str());
if(SampleNoHaplotypes[i]==2)
ifprintf(m3vcffile, "\t%s_HAP_2",individualName[i].c_str());
}
ifprintf(m3vcffile, "\n");
int length=NoBlocks;
string cno;
for(i=0;i\t.\t.\t.\t.\t",tempInfo.startIndex,tempInfo.endIndex);
ifprintf(m3vcffile, "B%d;VARIANTS=%d;REPS=%d\t.",i+1,nvariants,reps);
for(j=0;jmyOutFormat.RsId?VariantList[j+tempInfo.startIndex].rsid.c_str():VariantList[j+tempInfo.startIndex].name.c_str());
ifprintf(m3vcffile, "%s\t%s\t.\t.\t",VariantList[j+tempInfo.startIndex].refAlleleString.c_str(),VariantList[j+tempInfo.startIndex].altAlleleString.c_str());
ifprintf(m3vcffile, "B%d.M%d",i+1,j+1);
if(Error.size()>0)
ifprintf(m3vcffile, ";Err=%.5g;Recom=%.5g",
Error[j+tempInfo.startIndex],(j+tempInfo.startIndex)<(int)Recom.size()?Recom[j+tempInfo.startIndex]:0);
ifprintf(m3vcffile, "\t");
vector &TempHap = tempInfo.TransposedUniqueHaps[j];
for(k=0;kreadLine(line);
if(line.length()<1)
{
ifclose(fileStream);
return "Invalid";
}
string tempString;
tempString=(line.substr(0,17));
char temp[tempString.length() + 1];
std::strcpy(temp,tempString.c_str());
for (char *iter = temp; *iter != '\0'; ++iter)
{
*iter = std::tolower(*iter);
}
if(((string)temp).compare("##fileformat=m3vc")==0)
{
ifclose(fileStream);
return "m3vcf";
}
else if(((string)temp).compare("##fileformat=vcfv")==0)
{
ifclose(fileStream);
return "vcf";
}
else
{
ifclose(fileStream);
return "Invalid";
}
}
else
{
ifclose(fileStream);
return "NA";
}
ifclose(fileStream);
return "NA";
}
bool HaplotypeSet::readm3vcfFile(String m3vcfFile,String CHR,int START,int END,int WINDOW)
{
string line,tempString,tempBlockPos,tempString2,tempString3,tempName,tempRsId,tempChr;
variant tempVariant;
variant tempVariant2;
int InitialNMarkers=0,blockIndex,startIndexFlag=0,readIndex=0,writeBlockIndex=0,NoBlocks=0,tempPos,NoMarkersWritten=0,tempVarCount,tempRepCount;
int OrigStartPos=START;
int OrigEndPos=END;
//cout<<"\n Reading Reference Haplotype information from M3VCF files : "< 0)
{
if (START-WINDOW < 0)
START = 0;
else
START -= WINDOW;
END += WINDOW;
}
if(CHR!="")
{
std::cout << "\n Loading markers from chromosome " << CHR;
if(END>0)
std::cout << " from base position "<readLine(line);
if(line.compare("##fileformat=M3VCF")!=0 && line.compare("##fileformat=OPTM")!=0)
{
cout<<" Incorrect Header Information : "<readLine(line);
if(line.substr(0,2).compare("##")==0)
Header=true;
else
break;
tempString = (string) strtok_r ((char*)line.c_str(),"=", &end_str1);
pch = strtok_r (NULL, "=", &end_str1);
if(tempString.compare("##n_blocks")==0)
{
NoBlocks=atoi(pch);
continue;
}
else if(tempString.compare("##n_haps")==0)
{
numHaplotypes=atoi(pch);
continue;
}
else if(tempString.compare("##n_markers")==0)
{
InitialNMarkers=atoi(pch);
// abort();
continue;
}
else if(tempString.compare("##chrxRegion")==0)
{
tempString = (string) pch;
if(tempString.compare("NonPseudoAutosomal")==0)
PseudoAutosomal=false;
else if(tempString.compare("PseudoAutosomal")==0)
PseudoAutosomal=true;
else
{
cout << "\n Inconsistent Tag for Chr X. "<9)
{
tempString2=string(pch);
///////////////////////////
// if(colCount%2==0)
individualName.push_back(tempString2.substr(0,tempString2.size()-6));
}
pch = strtok_r (NULL,"\t", &end_str2);
}
cout<<" Reading "<readLine(line);
char *end_str_new;
pch = strtok_r ((char*)line.c_str(),"\t", &end_str_new);
tempChr=string(pch);
pch = strtok_r (NULL,"\t", &end_str_new);
tempBlockPos=string(pch);
char *end_str_new1;
char *pch1;
pch1 = strtok_r ((char*)tempBlockPos.c_str(),"-", &end_str_new1);
int tempStartBlock=atoi(pch1);
pch1 = strtok_r (NULL,"-", &end_str_new1);
int tempEndBlock=atoi(pch1);
if(CHR!="")
{
if(tempChr.compare(CHR.c_str())!=0)
flag=1;
else
{
if(END>0)
{
if(tempStartBlock>END)
flag=1;
}
if(tempEndBlockdiscardLine();
continue;
}
tempBlock.TransposedUniqueHaps.resize(tempVarCount);
tempBlock.RepSize=tempRepCount;
tempBlock.BlockSize=tempVarCount;
tempBlock.uniqueCardinality.resize(tempRepCount,0.0);
tempBlock.InvuniqueCardinality.resize(tempRepCount,0.0);
// vector &TempHap = tempBlock.TransposedUniqueHaps[tempIndex];
//tempBlock.TransposedUniqueHaps uniqueHaps.resize(tempRepCount);
tempBlock.uniqueIndexMap.resize(numHaplotypes);
pch = strtok_r (NULL,"\t", &end_str_new);
pch = strtok_r (NULL,"\t", &end_str_new);
int check=0;
while(pch!=NULL)
{
int tempval=atoi(pch);
tempBlock.uniqueIndexMap[check]=tempval;
tempBlock.uniqueCardinality[tempval]++;
check++;
pch = strtok_r (NULL,"\t", &end_str_new);
}
for (int i = 0; i < tempRepCount; i++)
{
tempBlock.InvuniqueCardinality[i]=1.0/(float)tempBlock.uniqueCardinality[i];
}
if(check!=numHaplotypes)
{
cout<readLine(line);
end_str_new3=NULL;
pch3 = strtok_r ((char*)line.c_str(),"\t", &end_str_new3);
tempChr=(string)pch3;
pch3 = strtok_r (NULL,"\t", &end_str_new3);
tempPos=atoi(pch3);
stringstream strs3;
strs3<0)
{
if(tempPos>END || tempPos0) // to ensure a single marker from a block is NOT read.
blocktoSave=1;
blockEnterFlag=1;
}
if(tempPos>=OrigStartPos && startIndexFlag==0)
{
PrintStartIndex=writeBlockIndex;
startIndexFlag=1;
}
// if(CHR=="" || tempPos<=OrigEndPos)
// PrintEndIndex=writeBlockIndex;
//
if(CHR=="")
{
PrintEndIndex=writeBlockIndex;
}
else
{
if(OrigEndPos==0 || tempPos<=OrigEndPos)
PrintEndIndex=writeBlockIndex;
}
variant tempVariant;
tempVariant.assignValues(tempName,tempName,tempChr,tempPos);
tempVariant.rsid=tempRsId;
double tempRecom=-3.0,tempError=0.0;
pch3 = strtok_r (NULL,"\t", &end_str_new3);
string tempString98=(string)(pch3);
pch3 = strtok_r (NULL,"\t", &end_str_new3);
string tempString99=(string)(pch3);
tempVariant.assignRefAlt(tempString98,tempString99);
pch3 = strtok_r (NULL,"\t", &end_str_new3);
pch3 = strtok_r (NULL,"\t", &end_str_new3);
pch3 = strtok_r (NULL,"\t", &end_str_new3);
tempString=(string)(pch3);
char *pch4, *end_str_new4;
pch4=strtok_r ((char*)tempString.c_str(),";", &end_str_new4);
stringstream strs1,strs2;
strs1<<(blockIndex+1);
strs2<<(tempIndex+1);
tempString3="B"+ (string)(strs1.str())+ ".M"+ (string)(strs2.str());
if(tempString3.compare((string)pch4)!=0)
{
cout< &TempHap = tempBlock.TransposedUniqueHaps[tempIndex];
TempHap.resize(tempRepCount);
for(check=0;check0)
// optEndPoints.push_back(ReducedStructureInfo[ReducedStructureInfo.size()-1].endIndex);
if(Recom.size()>0)
Recom.pop_back();
finChromosome=tempChr;
}
else
{
cout<<" Following M3VCF File Not Available : "< &TempHap = TempBlock.TransposedUniqueHaps[j-TempBlock.startIndex];
for (i = 0; i TotalSample(numTypedOnlyMarkers, 0);
int i,K,j;
int haplotypeIndex=0;
for(K=0;K &result, const char *input, const char *delimiter, int Number)
{
size_t wordCount = 1;
result[0].clear();
std::string *word = &result[0];
while (*input)
{
if (*input==*delimiter)
{
// we got a delimeter, and since an empty word following
// a delimeter still counts as a word, we allocate it here
wordCount++;
if((int)wordCount>Number)
return;
result[wordCount-1].clear();
word = &result[wordCount-1];
}
else
{
word->push_back(*input);
}
input++;
}
}
string HaplotypeSet::FindTokenWithPrefix(const char *input,const char *delimiter, string CheckPrefix)
{
std::string word = "";
int Size = (int)CheckPrefix.size();
int FirstChar = 0;
while (*input)
{
if ( FirstChar==0 || *input==*delimiter)
{
if(FirstChar==0)
FirstChar=1;
else
++input;
int Index=0;
while(*input)
{
word=word + (*input);
if(Index tokens(2);
vector PosTokens(2);
MyTokenize(tokens, input.c_str(), tabSep,2);
string tempChr=tokens[0];
MyTokenize(PosTokens, tokens[1].c_str(), dashSep, 2);
int tempStartBlock=atoi(PosTokens[0].c_str());
int tempEndBlock=atoi(PosTokens[1].c_str());
if(finChromosome=="NULL")
finChromosome=tempChr;
if(CHR!="")
{
if(tempChr.compare(CHR.c_str())!=0)
return 1;
else
{
if(tempStartBlock>END)
return 1;
if(tempEndBlock NoVariantsToken(2);
MyTokenize(NoVariantsToken, PrefixString.c_str(), equalSep, 2);
return atof(NoVariantsToken[1].c_str());
}
else
{
abort();
cout< NoVariantsToken(2);
MyTokenize(NoVariantsToken, PrefixString.c_str(), equalSep, 2);
return atof(NoVariantsToken[1].c_str());
}
else
{
cout< NoVariantsToken(2);
MyTokenize(NoVariantsToken, PrefixString.c_str(), equalSep, 2);
return atof(NoVariantsToken[1].c_str());
}
else
return -3.0;
}
double HaplotypeSet::GetError(string &input)
{
const char *equalSep="=",*semicolSep=";";
string PrefixString = FindTokenWithPrefix(input.c_str(),semicolSep, "Err=");
if(PrefixString!="")
{
vector NoVariantsToken(2);
MyTokenize(NoVariantsToken, PrefixString.c_str(), equalSep, 2);
return atof(NoVariantsToken[1].c_str());
}
else
return -3.0;
}
Minimac4-1.0.2/src/HaplotypeSet.h 0000664 0000000 0000000 00000030055 13532224264 0016542 0 ustar 00root root 0000000 0000000 #ifndef HAPLOTYPESET_H_INCLUDED
#define HAPLOTYPESET_H_INCLUDED
#include "Unique.h"
#include "MyVariables.h"
#include "StringBasics.h"
#include "VcfFileReader.h"
#include