tools/KNNImputer/KNNImputer.cpp

/*****************************************************************************
* This file is provided under the Creative Commons Attribution 3.0 license.
*
* You are free to share, copy, distribute, transmit, or adapt this work
* PROVIDED THAT you attribute the work to the authors listed below.
* For more information, please see the following web page:
* http://creativecommons.org/licenses/by/3.0/
*
* This file is a component of the Sleipnir library for functional genomics,
* authored by:
* Curtis Huttenhower (chuttenh@princeton.edu)
* Mark Schroeder
* Maria D. Chikina
* Olga G. Troyanskaya (ogt@princeton.edu, primary contact)
*
* If you use this library, the included executable tools, or any related
* code in your work, please cite the following publication:
* Curtis Huttenhower, Mark Schroeder, Maria D. Chikina, and
* Olga G. Troyanskaya.
* "The Sleipnir library for computational functional genomics"
*****************************************************************************/
#include "stdafx.h"
#include "cmdline.h"

int main( int iArgs, char** aszArgs ) {
    gengetopt_args_info sArgs;
    CPCL                PCL;
    CDat                Dat;
    int                 iRet;
    ofstream            ofsm;

    if( cmdline_parser( iArgs, aszArgs, &sArgs ) ) {
        cmdline_parser_print_help( );
        return 1; }
    CMeta Meta( sArgs.verbosity_arg );

    if( iRet = CPCL::Distance( sArgs.input_arg, sArgs.skip_arg, sArgs.neighbors_arg ? sArgs.distance_arg : NULL,
        false, false, !!sArgs.autocorrelate_flag, sArgs.genes_arg, CMeta::GetNaN( ), sArgs.limit_arg, PCL,
        Dat ) ) {
        cmdline_parser_print_help( );
        return iRet; }

    PCL.Impute( sArgs.neighbors_arg, (float)sArgs.missing_arg, Dat );

    if( sArgs.output_arg ) {
        ofsm.open( sArgs.output_arg );
        PCL.Save( ofsm );
        ofsm.close( ); }
    else {
        PCL.Save( cout );
        cout.flush( ); }

    return 0; }