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/*
* 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
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