glfHandler.h

/*
 *  Copyright (C) 2010  Regents of the University of Michigan
 *
 *   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 <http://www.gnu.org/licenses/>.
 */

#ifndef __GLF_HANDLER_H__
#define __GLF_HANDLER_H__

#include "InputFile.h"
#include "StringBasics.h"

#if defined(__APPLE__)
// #pragma warn "Caution, glfHandler.h is non-portable"
#else
#pragma pack(push)
#pragma pack(1)
#endif

struct glfIndel
{
    // Likelihood for the 1/1, 2/2 and 1/2
    unsigned char lk[3];

    // Allele lengths
    short length[2];

    unsigned char padding[3];
};

struct glfEntry
{
    /**  "XACMGRSVTWYHKDBN"[ref_base] gives the reference base */
    unsigned char refBase:4, recordType:4;

    /** offset of this record from the previous one, in bases */
    unsigned int offset;

    /** log10 minimum likelihood * 10 and the number of mapped reads */
    unsigned depth:24, minLLK:8;

    /** root mean squared maximum mapping quality for overlapping reads */
    unsigned char mapQuality;

    union
    {
        /** log10 likelihood ratio * 10 for genotypes AA, AC, AG, AT, CC, CG, CT, GG, GT, TT */
        unsigned char lk[10];
        glfIndel indel;
    };

    glfEntry & operator = (glfEntry & rhs);
};

#if defined(__APPLE__)
// #pragma warn "Caution, glfHandler.h is non-portable"
#else
#pragma pack(pop)
#endif

class glfHandler
{
public:
    // Global information about the current GLF file
    bool     isStub;
    IFILE    handle;
    String   header;

    // Information about the current section
    String   label;
    int      sections;
    int      currentSection;
    int      maxPosition;

    // Information on whether the end of the current section has been reached
    bool   endOfSection;

    // Currently active GLF record
    glfEntry data;
    int      position;
    double   likelihoods[10];
    String   indelSequence[2];

    // Error message in case previous command fails
    const char * errorMsg;

    glfHandler();
    ~glfHandler();

    bool Open(const String & filename);
    void OpenStub();
    bool Create(const String & filename);
    bool isOpen();
    void Close();
    void Rewind();

    bool NextSection();
    bool NextEntry();
    bool NextBaseEntry();

    void BeginSection(const String & sectionLabel, int sectionLength);
    void EndSection();

    void WriteEntry(int outputPosition);

    char     GetReference(int position, char defaultBase);
    int      GetDepth(int position);
    const double * GetLikelihoods(int position);
    const unsigned char *   GetLogLikelihoods(int position);
    int      GetMapQuality(int position);

    static const double * GetDefaultLikelihoods()
    {
        return nullLikelihoods;
    }
    static const unsigned char * GetDefaultLogLikelihoods()
    {
        return nullLogLikelihoods;
    }

    static int GenotypeIndex(int base1, int base2)
    {
        return base1 < base2 ? (base1 - 1) *(10 - base1) / 2 + (base2 - base1) :
               (base2 - 1) *(10 - base2) / 2 + (base1 - base2);
    }

private:
    static char           translateBase[16];
    static char           backTranslateBase[5];
    static double         nullLikelihoods[10];
    static unsigned char  nullLogLikelihoods[10];

    bool ReadHeader();
    void WriteHeader(const String & headerText = "");
};

#endif