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BGS-IO.h
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BGS-IO.h
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/*
*
* BGS-IO.h
* Soap3(gpu)
*
* Copyright (C) 2011, HKU
*
* 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 2
* 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, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
*
*/
#ifndef __BGS_IO__
#define __BGS_IO__
#include <stdio.h>
#include <stdlib.h>
#include "PEAlgnmt.h"
#include "2bwt-flex/SRAArguments.h"
#include "SAM.h"
#include "SAList.h"
#include "PE.h"
#include "Release.h"
//Define the below parameter to output the alignment result(text position)
// on screen instead of writing into output file
//#define DEBUG_2BWT_OUTPUT_TO_SCREEN
//Define the below parameter to stop cache reported SA range and text position.
// This is turned on when we are trying to obtain alignment timing only.
//#define DEBUG_2BWT_NO_OUTPUT
//Define the below parameter to skip writing the alignment result(text position)
// into disk. This is turned on when we are trying to obtain alignment timing only.
//#define DEBUG_2BWT_NO_WRITE_FILE
//Define the below parameter to skip translating the alignment result(text position).
// This is turned on when we are trying to obtain alignment timing only.
//#define DEBUG_2BWT_NO_TRANSLATION
#define OCC_CONST_ALIGNMENT_HEADER 65535
#define OCC_CONST_NO_ALIGNMENT 65534
//Define below parameter to skip outputing the header for plain output
#define SKIP_PLAIN_HEADER
OCC * OCCConstruct ();
void OCCFree ( OCC * occ );
unsigned int OCCWriteOutputHeader ( HSP * hsp, FILE * outFilePtr,
unsigned int maxReadLength,
unsigned int numOfReads,
int outputFormat );
// succinct format
void OCCFlushCache ( SRAQueryInput * qInput );
void OCCFlushCacheDP ( SRAQueryInput * qInput ); // for outputting the DP result
// binary
void OCCFlushCacheDefault ( OCC * occ, HSP * hsp, FILE * outFilePtr );
// obseleted (NO, DONT BELIEVE)
// -- start --
void OCCFlushCacheSAM ( SRAQueryInput * qInput );
/*
void OCCDirectWritePairOccSAM ( SRAQueryInput * qInput, PEPairs * pePair );
void OCCDirectWritePairUnmapSAM ( SRAQueryInput * qInput, SRAOccurrence * sraOcc, int isFirst );
*/
void OCCDirectWritePairOccSAMAPI ( SRAQueryInput * qInput, PEPairs * pePair, int isFirstUnaligned, int isSecondUnaligned, int mateLength, int properlyPaired );
void OCCDirectWritePairOccSAMAPI2 ( SRAQueryInput * qInput, PEPairs * pePair, int isFirstUnaligned, int isSecondUnaligned, int mateLength, int properlyPaired );
void OCCDirectWritePairUnmapSAMAPI ( SRAQueryInput * qInput, SRAOccurrence * sraOcc, int isFirst );
void OCCDirectWritePairOccSAMAPIwCIGAR ( SRAQueryInput * qInput, PEPairs * pePair, int isFirstUnaligned, int isSecondUnaligned, int mateLength, char * cigar_str );
void OCCDirectWritePairOccSAMAPI2wCIGAR ( SRAQueryInput * qInput, PEPairs * pePair, int isFirstUnaligned, int isSecondUnaligned, int mateLength, char * cigar_str );
// -- end --
void OCCReportDelimitor ( SRAQueryInput * qInput );
void OCCReportDelimitorDP ( SRAQueryInput * qInput ); // for outputting the DP result
/*
//////////////////////////
// FOR SAM FORMAT //
//////////////////////////
// single-end alignment
// -- start --
*/
void OCCOutputSAMAPI ( SRAQueryInput * qInput, OCCList * occ_list,
DynamicUint8Array * xazArray, int readlen, int reportType );
/*
// For outputting single-read alignment in SAM format
// Output the best record, and for the rest, append the results in the tag XA:Z
*/
void SingleAnsOutputSAMAPI ( SRAQueryInput * qInput,
char strand, unsigned int ambPosition, int bestHitNumOfMismatch, int bestHitNum );
/*
// For outputting one answer of single-read alignment in SAM format
// for unique-best and random-best single-read alignment
*/
void noAnsOutputSAMAPI ( SRAQueryInput * qInput );
// For outputting no answer of single-read alignment in SAM format
void SingleDPOutputSAMAPI ( SRAQueryInput * qInput, SingleAlgnmtResult * algnResult,
unsigned int startIndex, unsigned int numResult,
DynamicUint8Array * xazArray );
// For outputting single-read alignment in SAM format
// Output the best record, and for the rest, append the results in the tag XA:Z
// -- end --
void pairOutputSAMAPI ( SRAQueryInput * qInput, PEOutput * pe_out, PEPairs * bestPair,
unsigned char * query1, unsigned char * query2,
char * qualities1, char * qualities2,
int readlen1, int readlen2,
char * queryName1, char * queryName2,
char min_totalMismatchCount, char secMin_totalMismatchCount,
int outputXAZTag, DynamicUint8Array * xazArray,
unsigned int peMaxOutputPerPair,
int X0_first, int X0_second, int X1_first, int X1_second, int num_minMismatchPair,
char isBestHit1, char isBestHit2, unsigned int totalNumValidPairs );
/*
// For outputting pair-end alignment in SAM format
// Output the best record, and for the rest, append the results in the tag XA:Z
*/
void pairDPOutputSAMAPI ( SRAQueryInput * qInput, AlgnmtDPResult * algnResult,
AlgnmtDPResult * bestResult,
unsigned int start, unsigned int num,
unsigned char * query1, unsigned char * query2,
char * qualities1, char * qualities2,
int readlen1, int readlen2,
char * queryName1, char * queryName2,
DynamicUint8Array * xazArray );
// For outputting DP pair-end alignment in SAM format
void pairDeepDPOutputSAMAPI ( SRAQueryInput * qInput, DeepDPAlignResult * algnResult,
DeepDPAlignResult * bestResult,
unsigned int start, unsigned int num,
unsigned char * query1, unsigned char * query2,
char * qualities1, char * qualities2,
int readlen1, int readlen2,
char * queryName1, char * queryName2,
DynamicUint8Array * xazArray );
// For outputting Deep DP pair-end alignment in SAM format
void unproperlypairOutputSAMAPI ( SRAQueryInput * qInput, OCCList * occ_list1, OCCList * occ_list2,
unsigned char * query1, unsigned char * query2,
char * qualities1, char * qualities2,
int readlen1, int readlen2,
char * queryName1, char * queryName2,
DynamicUint8Array * xazArray,
unsigned int peMaxOutputPerRead, int reportType );
// output the alignments which are not properly paired
void unproperlypairDPOutputSAMAPI ( SRAQueryInput * qInput, Algnmt * algn_list1, Algnmt * algn_list2,
int hitNum1, int hitNum2,
unsigned char * query1, unsigned char * query2,
char * qualities1, char * qualities2,
int readlen1, int readlen2,
char * queryName1, char * queryName2,
DynamicUint8Array * xazArray );
// output the DP alignments which are not properly paired
void OCCReportNoAlignment ( SRAQueryInput * qInput );
/*
//OCCReportSARange : asumming l<=r
unsigned long long OCCReportSARange ( SRAQueryInput * qInput,
unsigned long long l, unsigned long long r,
int occMismatch );
unsigned long long OCCReportTextPositions ( SRAQueryInput * qInput, int posCount );
*/
#endif