change suffix as loadings

CHANGELOG.org

@@ -2,7 +2,7 @@
 
   - publish PCAone on mac with =libiomp5= support
 
-  - update makefile and setup bioconda
+  - update documentation
 
   - add --shuffle option
 

README.org

@@ -97,7 +97,7 @@ PCAone is designed to be extensible to accept many different formats. Currently,
 
 - eigen vectors :: eigen vectors are saved in file with suffix =.eigvecs=. each row represents a sample and each col represents a PC.
 - eigen values :: eigen values are saved in file with suffix =.eigvals=. each row represents the eigenvalue of correspoding PC.
-- loadings :: loadings are saved in file with suffix =.projection=. need to use =--printv= option.
+- loadings :: loadings are saved in file with suffix =.loadings=. need to use =--printv= option.
 
 ** Advanced options
 
@@ -163,21 +163,20 @@ Usage:
       --bfile PREFIX   prefix of PLINK .bed/.bim/.fam files.
       --bgen FILE      path of BGEN file.
       --csv FILE       path of zstd compressed csv file.
+      --maxp INT       maximum number of power iteration for Halko.[20]
+      --printv         print out another eigen vectors with suffix .loadings.
   -e, --emu            use EMU algorithm for data with lots of missingness.
   -f, --fast           force to use fast super power iterations for Halko.
   -h, --halko          use Halko method instead of default Arnoldi method.
   -k, --eigs INT       top k components to be calculated.[10]
-      --maxp INT       maximum number of power iteration for Halko.[20]
   -m, --memory DOUBLE  specify the RAM usage in GB unit instead of exploiting
                        the RAM of the server.
   -n, --threads INT    number of threads.[1]
-  -M, INT              number of features. eg, SNPs.
-  -N, INT              number of samples.
   -o, --out PREFIX     prefix of output files.
   -p, --pcangsd        use PCAngsd algorithm for genotype likelihood input.
-      --printv         print out another eigen vectors with projection
-                       suffix.
   -v, --verbose        verbose message output.
+  -M, INT              number of features. eg. SNPs.
+  -N, INT              number of samples.
 
 #+end_src
 

src/Data.cpp

@@ -134,7 +134,7 @@ void Data::write_eigs_files(const MyVector& S, const MyMatrix& U, const MyMatrix
         outu << U << '\n';
     }
     if (params.printv) {
-        std::ofstream outv(params.outfile + ".projection");
+        std::ofstream outv(params.outfile + ".loadings");
         if (outv.is_open()) {
             outv << V << '\n';
         }

src/Main.cpp

@@ -70,19 +70,19 @@ void parse_params(int argc, char* argv[], struct Param* params)
         // ("pfile", "prefix to PLINK2 .pgen/.pvar/.psam files.", cxxopts::value<std::string>(), "PREFIX")
         ("bgen", "path of BGEN file.", cxxopts::value<std::string>(), "FILE")
         ("csv", "path of zstd compressed csv file.", cxxopts::value<std::string>(), "FILE")
+        ("maxp", "maximum number of power iteration for Halko.[20]", cxxopts::value<int>(),"INT")
+        ("printv", "print out another eigen vectors with suffix .loadings.", cxxopts::value<bool>()->default_value("false"))
         ("e,emu", "use EMU algorithm for data with lots of missingness.", cxxopts::value<bool>()->default_value("false"))
         ("f, fast", "force to use fast super power iterations for Halko.", cxxopts::value<bool>()->default_value("false"))
         ("h, halko", "use Halko method instead of default Arnoldi method.", cxxopts::value<bool>()->default_value("false"))
         ("k,eigs", "top k components to be calculated.[10]", cxxopts::value<int>(),"INT")
-        ("maxp", "maximum number of power iteration for Halko.[20]", cxxopts::value<int>(),"INT")
         ("m,memory", "specify the RAM usage in GB unit instead of exploiting the RAM of the server.", cxxopts::value<double>(),"DOUBLE")
         ("n,threads", "number of threads.[1]", cxxopts::value<int>(),"INT")
-        ("M", "number of features. eg. SNPs.", cxxopts::value<int>(),"INT")
-        ("N", "number of samples.", cxxopts::value<int>(),"INT")
         ("o,out", "prefix of output files.", cxxopts::value<string>(),"PREFIX")
         ("p,pcangsd", "use PCAngsd algorithm for genotype likelihood input.", cxxopts::value<bool>()->default_value("false"))
-        ("printv", "print out another eigen vectors with projection suffix.", cxxopts::value<bool>()->default_value("false"))
         ("v,verbose", "verbose message output.", cxxopts::value<bool>()->default_value("false"))
+        ("M", "number of features. eg. SNPs.", cxxopts::value<int>(),"INT")
+        ("N", "number of samples.", cxxopts::value<int>(),"INT")
         ;
     opts.add_options("More")
         ("bands", "number of bands to use for fast Halko.[32]", cxxopts::value<int>(),"INT")