[Genabel-commits] r638 - in pkg/VariABEL: R src
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Feb 8 10:53:26 CET 2011
Author: maksim
Date: 2011-02-08 10:53:26 +0100 (Tue, 08 Feb 2011)
New Revision: 638
Modified:
pkg/VariABEL/R/var.test.gwaa.R
pkg/VariABEL/src/tags
pkg/VariABEL/src/var_homogeneity_test_C.cpp
pkg/VariABEL/src/var_homogeneity_tests.cpp
pkg/VariABEL/src/var_homogeneity_tests.h
Log:
almost ready
Modified: pkg/VariABEL/R/var.test.gwaa.R
===================================================================
--- pkg/VariABEL/R/var.test.gwaa.R 2011-02-07 19:34:13 UTC (rev 637)
+++ pkg/VariABEL/R/var.test.gwaa.R 2011-02-08 09:53:26 UTC (rev 638)
@@ -24,10 +24,9 @@
#_____________________________________________________________________________________________________________________________
#Available for user function for genome-wide testing variance homogeneity of trait's distribution.
#
-"var.test.gwaa" <- function(formula, genodata, phenodata, testname="sqlm", analysis_type="AAvsABvsBB")
+"var.test.gwaa" <- function(formula, genodata, phenodata, genodata_info="", testname="sqlm", analysis_type="AAvsABvsBB")
{
-
if(testname == "bartlett") {testname <- 0}
else if(testname == "levene") {testname <- 1}
else if(testname == "likelihood") {testname <- 2}
@@ -47,56 +46,108 @@
OUT <- "R"
FUN <- "variance_homogeneity_test_C_wrapper"
-design_matrix <- model.matrix(formula, data = phenodata)
-trat_name <- as.character(formula[[2]])
-trait <- phenodata[,trat_name]
-idnum <- length(trait)
-design_matrix_df <- data.frame(design_matrix)
-design_matrix_df$snp <- 0 #will be filled into iterator
+
+
+attach(phenodata, pos = 2, warn.conflicts = FALSE)
+
+idnum <- 0
+
+if(is(formula, "formula"))
+ {
+ design_matrix <- model.matrix(formula, data = phenodata)
+ trat_name <- as.character(formula[[2]])
+ trait <- phenodata[,trat_name]
+ idnum <- length(trait)
+ design_matrix_df <- data.frame(design_matrix)
+ design_matrix_df$snp <- 0 #will be filled into iterator
+ }
+ else if(is(formula, "numeric") || is(formula, "integer") || is(formula, "double"))
+ {
+ trait <- formula
+ idnum <- length(trait)
+ design_matrix_df <- data.frame(X.Intercept=rep(1,idnum), snp=rep(0,idnum))
+ }
+
+design_matrix_geno_means_df <- data.frame(X.Intercept=rep(1,idnum), snp=rep(0,idnum))
+
+
p <- dim(design_matrix_df)[2] #covariates number + 1
-print(design_matrix_df)
gtNrow <- NA
gtNcol <- NA
+genodata_info_df <- data.frame()
+
+
#Stolen from MixABEL:
if(class(genodata) == "snp.data")
{
- gtNrow <- dim(genodata)[1]
- gtNcol <- dim(genodata)[2]
+ print("reading genotype info...")
+ genodata_info_df <- data.frame(name=genodata at snpnames,
+ coding=as.character(genodata at coding),
+ strand=as.character(genodata at strand),
+ chromosome=as.character(genodata at chromosome),
+ map=genodata at map
+ )
+# gtNrow <- genodata at nsnps
+# gtNcol <- genodata at nids
+ gtNrow <- genodata at nids
+ gtNcol <- genodata at nsnps
genodata <- as.raw(genodata at gtps)
- }
- else if (class(genodata) == "matrix")
- {
- gtNrow <- dim(genodata)[1]
- gtNcol <- dim(genodata)[2]
- storage.mode(genodata) <- "double"
- }
+ }
else if (class(genodata)=="databel")
{
gtNrow <- dim(genodata)[1]
gtNcol <- dim(genodata)[2]
genodata <- genodata at data
+
+ if(genodata_info != "" & file.exists(genodata_info))
+ {
+ print("reading genotype's info...")
+ genodata_info_df <- read.table(genodata_info, strings=F, header=T)
+ print(c(dim(genodata_info_df)[1], gtNcol))
+ if(dim(genodata_info_df)[1] != gtNcol)
+ {
+ print(paste("warning: File ", genodata_info, " contains information about ", dim(genodata_info_df)[1],
+ " SNPs but genotype data contains ", gtNcol, ". Ignoring of the info file.", sep=""))
+ }
+ genodata_info_df <- data.frame(name=sub("^", "snp", as.character(1:gtNcol)))
+ }
+ else
+ {
+ print(paste("warning: File ", genodata_info, "does not exist. Trying to run analysis withouth SNP's information..."))
+ genodata_info_df <- data.frame(name=sub("^", "snp", as.character(1:gtNcol)))
+ }
+
}
else
{
- stop(paste("genodata class not recognised ('",class(genodata),"')",sep=""))
+ stop(paste("genodata class not recognized ('",class(genodata),"')",sep=""))
}
-
+if(testname == 1) #Levene's
+ {
+ if(is(formula, "formula"))
+ {
+ trait_regression <- lm(formula, data=phenodata)
+ trait <- trait_regression$residuals
+ }
+ }
+print("Start variance analysis...")
results_C <- .Call("iterator", genodata,
as.integer(gtNrow), as.integer(gtNcol),
as.character(FUN),
as.character(OUT),
as.integer(MAR),
as.integer(1),
- as.integer(17), #iterator additional inputa parameters number
+ as.integer(18), #iterator additional inputa parameters number
as.double(trait),
as.double(data.matrix(design_matrix_df)),
+ as.double(data.matrix(design_matrix_geno_means_df)),
as.integer(p),
as.integer(analysis_type),
as.integer(testname),
@@ -114,19 +165,23 @@
integer(idnum)
)
+print("Variance analysis done.")
-if(class(genodata) == "snp.data")
- {
-
- }
+print(genodata_info_df)
+print(results_C)
-results_df <- data.frame(results_C)
+results_df <- data.frame(genodata_info_df, results_C)
+print(results_df)
cov_names <- colnames(design_matrix_df)
-print("1")
-output_column_names <- c("chisq", "df", "Intercept_effect", "Intercept_sd")
-print("2")
+print(cov_names)
+
+output_column_names <- c(colnames(genodata_info_df), "chisq", "df", "Intercept_effect", "Intercept_sd")
+
+
+print(output_column_names)
+
for(i in 2:p)
{
output_column_names <- c(output_column_names, paste(cov_names[i], "_effect", sep=""))
@@ -135,7 +190,7 @@
colnames(results_df) <- output_column_names
-print(results_df)
+results_df
}
Modified: pkg/VariABEL/src/tags
===================================================================
--- pkg/VariABEL/src/tags 2011-02-07 19:34:13 UTC (rev 637)
+++ pkg/VariABEL/src/tags 2011-02-08 09:53:26 UTC (rev 638)
@@ -4,899 +4,21 @@
!_TAG_PROGRAM_NAME Exuberant Ctags //
!_TAG_PROGRAM_URL http://ctags.sourceforge.net /official site/
!_TAG_PROGRAM_VERSION 5.6 //
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-AAvsABvsBB VARlib/supplementary_functions.h /^enum analysis_type_enum {AAvsABvsBB, AAvsABandBB, ABvsAAandBB, BBvsAAandAB};$/;" e enum:analysis_type_enum
-AAvsABvsBB supplementary_functions.h /^enum analysis_type_enum {AAvsABvsBB, AAvsABandBB, ABvsAAandBB, BBvsAAandAB};$/;" e enum:analysis_type_enum
-ABvsAAandBB VARlib/supplementary_functions.h /^enum analysis_type_enum {AAvsABvsBB, AAvsABandBB, ABvsAAandBB, BBvsAAandAB};$/;" e enum:analysis_type_enum
-ABvsAAandBB supplementary_functions.h /^enum analysis_type_enum {AAvsABvsBB, AAvsABandBB, ABvsAAandBB, BBvsAAandAB};$/;" e enum:analysis_type_enum
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-BBvsAAandAB supplementary_functions.h /^enum analysis_type_enum {AAvsABvsBB, AAvsABandBB, ABvsAAandBB, BBvsAAandAB};$/;" e enum:analysis_type_enum
-CHAR_NAN CastUtils.cpp /^char CHAR_NAN;$/;" v
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-COPY_AND_COMPARE fvlib/CastUtils.h 38;" d
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-COUNTS supplementary_functions.h /^ int COUNTS[GENO_TYPES_NUM];$/;" m struct:snp_var_data
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-___TRANSPOSE___ Transposer.h 2;" d
-___TRANSPOSE___ fvlib/Transposer.h 2;" d
-addVariable FileVector.cpp /^void FileVector::addVariable(void *invec, string varName) {$/;" f class:FileVector
-addVariable FilteredMatrix.cpp /^void FilteredMatrix::addVariable(void * invec, string varname) {$/;" f class:FilteredMatrix
-addVariable fvlib/FileVector.cpp /^void FileVector::addVariable(void *invec, string varName) {$/;" f class:FileVector
-addVariable fvlib/FilteredMatrix.cpp /^void FilteredMatrix::addVariable(void * invec, string varname) {$/;" f class:FilteredMatrix
-addVariableAs AbstractMatrix.h /^ void addVariableAs(DT * outvec, string varname)$/;" f class:AbstractMatrix
-addVariableAs fvlib/AbstractMatrix.h /^ void addVariableAs(DT * outvec, string varname)$/;" f class:AbstractMatrix
-all Logger.cpp 6;" d file:
-all fvlib/Logger.cpp 6;" d file:
-analysis_type_enum VARlib/supplementary_functions.h /^enum analysis_type_enum {AAvsABvsBB, AAvsABandBB, ABvsAAandBB, BBvsAAandAB};$/;" g
-analysis_type_enum supplementary_functions.h /^enum analysis_type_enum {AAvsABvsBB, AAvsABandBB, ABvsAAandBB, BBvsAAandAB};$/;" g
-assignDoubleMatrix AbstractMatrix_R.cpp /^ SEXP assignDoubleMatrix(SEXP ptr, SEXP obsIndexes, SEXP varIndexes, SEXP values, SEXP direction){$/;" f
-assignDoubleMatrix DAlib/AbstractMatrix_R.cpp /^ SEXP assignDoubleMatrix(SEXP ptr, SEXP obsIndexes, SEXP varIndexes, SEXP values, SEXP direction){$/;" f
-bartlett VARlib/supplementary_functions.h /^enum testname_enum {bartlett, levene, likelihood, kolmogorov_smirnov};$/;" e enum:testname_enum
-bartlett supplementary_functions.h /^enum testname_enum {bartlett, levene, likelihood, kolmogorov_smirnov};$/;" e enum:testname_enum
-bartlett_test VARlib/var_homogeneity_tests.cpp /^chisq_df bartlett_test(snp_var_data * snp)$/;" f
-bartlett_test VARlib/var_homogeneity_tests.cpp /^chisq_df bartlett_test(std::list<my_small_vector> * samples)$/;" f
-bartlett_test var_homogeneity_tests.cpp /^chisq_df bartlett_test(snp_var_data * snp)$/;" f
-bartlett_test var_homogeneity_tests.cpp /^chisq_df bartlett_test(std::list<my_small_vector> * samples)$/;" f
-bitsPerRecord frutil.h /^ unsigned int bitsPerRecord;$/;" m class:FileHeader
-bitsPerRecord fvlib/frutil.h /^ unsigned int bitsPerRecord;$/;" m class:FileHeader
-blockWriteOrRead RealHandlerWrapper.cpp /^void RealHandlerWrapper::blockWriteOrRead(unsigned long iLength, char* data, bool writeAction) {$/;" f class:RealHandlerWrapper
-blockWriteOrRead ReusableFileHandle.cpp /^void ReusableFileHandle::blockWriteOrRead(unsigned long length, char* data, bool writeAction){$/;" f class:ReusableFileHandle
-blockWriteOrRead frutil.cpp /^void blockWriteOrRead(fstream& file, unsigned long length, char* data, bool writeAction){$/;" f
-blockWriteOrRead fvlib/RealHandlerWrapper.cpp /^void RealHandlerWrapper::blockWriteOrRead(unsigned long iLength, char* data, bool writeAction) {$/;" f class:RealHandlerWrapper
-blockWriteOrRead fvlib/ReusableFileHandle.cpp /^void ReusableFileHandle::blockWriteOrRead(unsigned long length, char* data, bool writeAction){$/;" f class:ReusableFileHandle
-blockWriteOrRead fvlib/frutil.cpp /^void blockWriteOrRead(fstream& file, unsigned long length, char* data, bool writeAction){$/;" f
-break_trait_up_into_groups VARlib/supplementary_functions.cpp /^void break_trait_up_into_groups(std::list<my_small_vector> *trait_groups, int* snp, double *trait, unsigned* nids, analysis_type_enum analys_type, int * is_trait_na)$/;" f
-break_trait_up_into_groups supplementary_functions.cpp /^void break_trait_up_into_groups(std::list<my_small_vector> *trait_groups, int* snp, double *trait, unsigned* nids, analysis_type_enum analys_type, int * is_trait_na)$/;" f
-bufToString CastUtils.cpp /^string bufToString(short int dataType, char *data, string nanString){$/;" f
-bufToString fvlib/CastUtils.cpp /^string bufToString(short int dataType, char *data, string nanString){$/;" f
-bytesPerRecord frutil.h /^ unsigned int bytesPerRecord;$/;" m class:FileHeader
-bytesPerRecord fvlib/frutil.h /^ unsigned int bytesPerRecord;$/;" m class:FileHeader
-cacheAllNames FileVector.cpp /^void FileVector::cacheAllNames(bool doCache) {$/;" f class:FileVector
-cacheAllNames FilteredMatrix.cpp /^void FilteredMatrix::cacheAllNames(bool doCache) {$/;" f class:FilteredMatrix
-cacheAllNames fvlib/FileVector.cpp /^void FileVector::cacheAllNames(bool doCache) {$/;" f class:FileVector
-cacheAllNames fvlib/FilteredMatrix.cpp /^void FilteredMatrix::cacheAllNames(bool doCache) {$/;" f class:FilteredMatrix
-cacheBegin FileVector.h /^ unsigned long cacheBegin;$/;" m class:FileVector
-cacheBegin fvlib/FileVector.h /^ unsigned long cacheBegin;$/;" m class:FileVector
-cacheBuffer FileVector.h /^ char * cacheBuffer;$/;" m class:FileVector
-cacheBuffer fvlib/FileVector.h /^ char * cacheBuffer;$/;" m class:FileVector
-cacheEnd FileVector.h /^ unsigned long cacheEnd;$/;" m class:FileVector
-cacheEnd fvlib/FileVector.h /^ unsigned long cacheEnd;$/;" m class:FileVector
-cache_size_Mb FileVector.h /^ unsigned long cache_size_Mb;$/;" m class:FileVector
-cache_size_Mb fvlib/FileVector.h /^ unsigned long cache_size_Mb;$/;" m class:FileVector
-cache_size_bytes FileVector.h /^ unsigned long cache_size_bytes;$/;" m class:FileVector
-cache_size_bytes fvlib/FileVector.h /^ unsigned long cache_size_bytes;$/;" m class:FileVector
-cache_size_nvars FileVector.h /^ unsigned long cache_size_nvars;$/;" m class:FileVector
-cache_size_nvars fvlib/FileVector.h /^ unsigned long cache_size_nvars;$/;" m class:FileVector
-calcCachePos FileVector.cpp /^void FileVector::calcCachePos(unsigned long newCenterPos, unsigned long &cacheBeginRef, unsigned long &cacheEndRef){$/;" f class:FileVector
-calcCachePos fvlib/FileVector.cpp /^void FileVector::calcCachePos(unsigned long newCenterPos, unsigned long &cacheBeginRef, unsigned long &cacheEndRef){$/;" f class:FileVector
-calcDataSize frutil.cpp /^unsigned short calcDataSize(unsigned short int type){$/;" f
-calcDataSize fvlib/frutil.cpp /^unsigned short calcDataSize(unsigned short int type){$/;" f
-calcNumLines convert_util.cpp /^unsigned long calcNumLines(string fileName){$/;" f
-calcNumLines fvlib/convert_util.cpp /^unsigned long calcNumLines(string fileName){$/;" f
-calcNumWordsInFirstLine convert_util.cpp /^unsigned long calcNumWordsInFirstLine(string fileName){$/;" f
-calcNumWordsInFirstLine fvlib/convert_util.cpp /^unsigned long calcNumWordsInFirstLine(string fileName){$/;" f
-castToAbstractMatrix FileVector.cpp /^AbstractMatrix* FileVector::castToAbstractMatrix(){$/;" f class:FileVector
-castToAbstractMatrix FilteredMatrix.cpp /^AbstractMatrix* FilteredMatrix::castToAbstractMatrix(){$/;" f class:FilteredMatrix
-castToAbstractMatrix fvlib/FileVector.cpp /^AbstractMatrix* FileVector::castToAbstractMatrix(){$/;" f class:FileVector
-castToAbstractMatrix fvlib/FilteredMatrix.cpp /^AbstractMatrix* FilteredMatrix::castToAbstractMatrix(){$/;" f class:FilteredMatrix
-check VARlib/supplementary_functions.cpp /^bool check(snp_var_data* snp2, snp_var_data* snp1, std::ofstream & warnings_file)$/;" f
-check supplementary_functions.cpp /^bool check(snp_var_data* snp2, snp_var_data* snp1, std::ofstream & warnings_file)$/;" f
-checkNan CastUtils.cpp /^bool checkNan(char i){return checkNan(&i, SIGNED_CHAR);}$/;" f
-checkNan CastUtils.cpp /^bool checkNan(double i){return checkNan(&i, DOUBLE);}$/;" f
-checkNan CastUtils.cpp /^bool checkNan(float i){return checkNan(&i, FLOAT);}$/;" f
-checkNan CastUtils.cpp /^bool checkNan(int i){return checkNan(&i, INT);}$/;" f
-checkNan CastUtils.cpp /^bool checkNan(short int i){return checkNan(&i, SHORT_INT);}$/;" f
-checkNan CastUtils.cpp /^bool checkNan(unsigned char i){return checkNan(&i, UNSIGNED_CHAR);}$/;" f
-checkNan CastUtils.cpp /^bool checkNan(unsigned int i){return checkNan(&i, UNSIGNED_INT);}$/;" f
-checkNan CastUtils.cpp /^bool checkNan(unsigned short int i){return checkNan(&i, UNSIGNED_SHORT_INT);}$/;" f
-checkNan CastUtils.cpp /^bool checkNan(void *data, int dataType){$/;" f
-checkNan fvlib/CastUtils.cpp /^bool checkNan(char i){return checkNan(&i, SIGNED_CHAR);}$/;" f
-checkNan fvlib/CastUtils.cpp /^bool checkNan(double i){return checkNan(&i, DOUBLE);}$/;" f
-checkNan fvlib/CastUtils.cpp /^bool checkNan(float i){return checkNan(&i, FLOAT);}$/;" f
-checkNan fvlib/CastUtils.cpp /^bool checkNan(int i){return checkNan(&i, INT);}$/;" f
-checkNan fvlib/CastUtils.cpp /^bool checkNan(short int i){return checkNan(&i, SHORT_INT);}$/;" f
-checkNan fvlib/CastUtils.cpp /^bool checkNan(unsigned char i){return checkNan(&i, UNSIGNED_CHAR);}$/;" f
-checkNan fvlib/CastUtils.cpp /^bool checkNan(unsigned int i){return checkNan(&i, UNSIGNED_INT);}$/;" f
-checkNan fvlib/CastUtils.cpp /^bool checkNan(unsigned short int i){return checkNan(&i, UNSIGNED_SHORT_INT);}$/;" f
-checkNan fvlib/CastUtils.cpp /^bool checkNan(void *data, int dataType){$/;" f
-checkNumBits AbstractMatrix_R.cpp /^ SEXP checkNumBits(){$/;" f
-checkNumBits DAlib/AbstractMatrix_R.cpp /^ SEXP checkNumBits(){$/;" f
-checkOpenForWriting AbstractMatrix.cpp /^void AbstractMatrix::checkOpenForWriting(const string fileName){$/;" f class:AbstractMatrix
-checkOpenForWriting fvlib/AbstractMatrix.cpp /^void AbstractMatrix::checkOpenForWriting(const string fileName){$/;" f class:AbstractMatrix
-checkPointer AbstractMatrix_R.cpp /^ void checkPointer(SEXP s) {$/;" f
-checkPointer DAlib/AbstractMatrix_R.cpp /^ void checkPointer(SEXP s) {$/;" f
-check_files_format VARlib/supplementary_functions.cpp /^bool check_files_format(const char** filenames, unsigned file_amount, unsigned skip_first_lines_amount, char delim)$/;" f
-check_files_format supplementary_functions.cpp /^bool check_files_format(const char** filenames, unsigned file_amount, unsigned skip_first_lines_amount, char delim)$/;" f
-chisq VARlib/var_homogeneity_tests.h /^ double chisq;$/;" m class:chisq_df
-chisq var_homogeneity_tests.h /^ double chisq;$/;" m class:chisq_df
-chisq_df VARlib/var_homogeneity_tests.h /^ chisq_df() $/;" f class:chisq_df
-chisq_df VARlib/var_homogeneity_tests.h /^ chisq_df(double chisq_, int df_) $/;" f class:chisq_df
-chisq_df VARlib/var_homogeneity_tests.h /^class chisq_df$/;" c
-chisq_df var_homogeneity_tests.h /^ chisq_df() $/;" f class:chisq_df
-chisq_df var_homogeneity_tests.h /^ chisq_df(double chisq_, int df_) $/;" f class:chisq_df
-chisq_df var_homogeneity_tests.h /^class chisq_df$/;" c
-chromosome VARlib/supplementary_functions.h /^ int chromosome;$/;" m struct:snp_var_data
-chromosome supplementary_functions.h /^ int chromosome;$/;" m struct:snp_var_data
-chromosome_column_name VARlib/supplementary_functions.h /^const std::string chromosome_column_name = "CHR";$/;" v
-chromosome_column_name supplementary_functions.h /^const std::string chromosome_column_name = "CHR";$/;" v
-close RealHandlerWrapper.cpp /^void RealHandlerWrapper::close(){$/;" f class:RealHandlerWrapper
-close ReusableFileHandle.cpp /^void ReusableFileHandle::close() {$/;" f class:ReusableFileHandle
-close fvlib/RealHandlerWrapper.cpp /^void RealHandlerWrapper::close(){$/;" f class:RealHandlerWrapper
-close fvlib/ReusableFileHandle.cpp /^void ReusableFileHandle::close() {$/;" f class:ReusableFileHandle
-closeForWriting AbstractMatrix.cpp /^void AbstractMatrix::closeForWriting(const string fileName){$/;" f class:AbstractMatrix
-closeForWriting fvlib/AbstractMatrix.cpp /^void AbstractMatrix::closeForWriting(const string fileName){$/;" f class:AbstractMatrix
-coding_array VARlib/gtps_container.h /^ char * coding_array;$/;" m class:gtps_container
-coding_array gtps_container.h /^ char * coding_array;$/;" m class:gtps_container
-compare_doubles VARlib/supplementary_functions.cpp /^int compare_doubles(const void *a, const void *b)$/;" f
-compare_doubles supplementary_functions.cpp /^int compare_doubles(const void *a, const void *b)$/;" f
-copyVariable FileVector.cpp /^void FileVector::copyVariable(char* to, char* from, int n, unsigned long * indexes ) {$/;" f class:FileVector
-copyVariable fvlib/FileVector.cpp /^void FileVector::copyVariable(char* to, char* from, int n, unsigned long * indexes ) {$/;" f class:FileVector
-copy_data Transposer.cpp /^void Transposer::copy_data(string src_data_file_name,string dest_data_file_name, unsigned long src_nvars,$/;" f class:Transposer
-copy_data fvlib/Transposer.cpp /^void Transposer::copy_data(string src_data_file_name,string dest_data_file_name, unsigned long src_nvars,$/;" f class:Transposer
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/genabel -r 638
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