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C++ SamRecord::get1BasedAlignmentEnd方法代码示例

本文整理汇总了C++中SamRecord::get1BasedAlignmentEnd方法的典型用法代码示例。如果您正苦于以下问题：C++ SamRecord::get1BasedAlignmentEnd方法的具体用法？C++ SamRecord::get1BasedAlignmentEnd怎么用？C++ SamRecord::get1BasedAlignmentEnd使用的例子？那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类SamRecord的用法示例。


在下文中一共展示了SamRecord::get1BasedAlignmentEnd方法的5个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的C++代码示例。

示例1: setNewCluster

void Sites::setNewCluster( vector<bool> & is_in_coord, SingleSite & new_site, SamRecord & rec )
{
	if (is_in_coord.size() != NMEI)
		morphError("[Sites::setNewCluster] is_in_coord size error");

	// set info
	new_site.breakp = getEstimatedBreakPoint(rec);
	new_site.rcount = 1;
	new_site.evidence = 1;
	for(int m=0; m<NMEI; m++) {
		new_site.left[m] = 0;
		new_site.right[m] = 0;
	}
	new_site.left_clip_only = 1;
	new_site.right_clip_only = 1;
	new_site.depth = current_depth;
	new_site.depth_add = 1;

	// set position & mtype
	if ( rec.getFlag() & 0x10 )  { // right anchor
		new_site.start = rec.get1BasedPosition();
		new_site.end = rec.get1BasedAlignmentEnd();
		Cigar * myCigar = rec.getCigarInfo();
		int begin_clip = myCigar->getNumBeginClips();
		if ( begin_clip < MIN_CLIP/2)
			new_site.right_clip_only = 0;
		for(int m=0; m<NMEI; m++) {
			if (is_in_coord[m])
				new_site.right[m] = 1;
		}
	}
	else {
		new_site.start = rec.get1BasedPosition();
		new_site.end = rec.get1BasedAlignmentEnd();
		Cigar * myCigar = rec.getCigarInfo();
		int end_clip = myCigar->getNumEndClips();
		if (end_clip < MIN_CLIP/2)
			new_site.left_clip_only = 0;
		for(int m=0; m<NMEI; m++) {
			if (is_in_coord[m])
				new_site.left[m] = 1;
		}
	}	
}
开发者ID:traxexx，项目名称:Morphling，代码行数:44，代码来源:Sites.cpp

示例2: addToCurrentCluster

void Sites::addToCurrentCluster( vector<bool> & is_in_coord, SingleSite & new_site, SamRecord & rec )
{
	if (is_in_coord.size() != NMEI)
		morphError("[Sites::setNewCluster] is_in_coord size error");

	// update breakpoint
	int old_evi = new_site.evidence;
	float a1 = (float)1 / float(old_evi+1);
	int ep = getEstimatedBreakPoint(rec);
	new_site.breakp = round( a1 * (float)ep + (float)new_site.breakp * (1-a1));
	new_site.evidence++; 

	// update position
	if (rec.get1BasedPosition() < new_site.start)
		new_site.start = rec.get1BasedPosition();
	else if (rec.get1BasedAlignmentEnd() > new_site.end)
		new_site.end = rec.get1BasedAlignmentEnd();

	// update info
	if (rec.getFlag() & 0x10) {
		if (new_site.right_clip_only) {
			Cigar * myCigar = rec.getCigarInfo();
			int begin_clip = myCigar->getNumBeginClips();
			if ( begin_clip < MIN_CLIP/2)
				new_site.right_clip_only = 0;	
		}
		for(int m=0; m<NMEI; m++) {
			if (is_in_coord[m])
				new_site.right[m]++;
		}	
	}
	else {
		if (new_site.left_clip_only) {
			Cigar * myCigar = rec.getCigarInfo();
			int end_clip = myCigar->getNumEndClips();
			if (end_clip < MIN_CLIP/2)
				new_site.left_clip_only = 0;			
		}
		for( int m=0; m<NMEI; m++) {
			if (is_in_coord[m])
				new_site.left[m]++;
		}
	}
}
开发者ID:traxexx，项目名称:Morphling，代码行数:44，代码来源:Sites.cpp

示例3: getEstimatedBreakPoint

// given mapping start position
// if anchor on left
//		expected_breakp = position + avr_ins_size / 2;
// if anchor on right
//		expected_breakp = position + read_length - avr_ins_size / 2;
// key = round( expected_breakp / WIN )
int Sites::getEstimatedBreakPoint( SamRecord & rec )
{
	int ep;
	int clen = GetMaxClipLen(rec);

	if ( !rec.getFlag() & 0x10 ) { // left anchor
		if (clen < -MIN_CLIP/2) // end clip of anchor decides position
			ep = rec.get1BasedAlignmentEnd();
		else
			ep = rec.get1BasedPosition() + avr_ins_size / 3;
	}
	else { // right anchor
		if (clen > MIN_CLIP/2)
			ep = rec.get1BasedPosition();
		else
			ep = rec.get1BasedPosition() + avr_read_length - avr_ins_size / 3;
	}
	return ep;
}
开发者ID:traxexx，项目名称:Morphling，代码行数:25，代码来源:Sites.cpp

示例4: getFlankingCount

int Likelihood::getFlankingCount( string & chr, int pos )
{
	bool status = bam.SetReadSection( chr.c_str(), pos - avr_read_length * 2, pos + avr_read_length/2 );
	if (!status)
		return 0;

	int n = 0;
	SamRecord rec;
	while(bam.ReadRecord(bam_header, rec)) {
		if ( !(rec.getFlag() & 0x2) )
			continue;
		if (IsSupplementary(rec.getFlag()))
			continue;
		if (rec.getReadLength() < avr_read_length / 3)
			continue;
		if (rec.getMapQuality() < MIN_QUALITY)
			continue;
		if (rec.get1BasedPosition() + MIN_CLIP/2 <= pos && rec.get1BasedAlignmentEnd() - MIN_CLIP/2 >= pos )
			n++;
	}

	return n;
}
开发者ID:traxexx，项目名称:Morphling，代码行数:23，代码来源:Likelihood.cpp

示例5: validateRead1ModQuality

void validateRead1ModQuality(SamRecord& samRecord)
{
    //////////////////////////////////////////
    // Validate Record 1
    // Create record structure for validating.
    int expectedBlockSize = 89;
    const char* expectedReferenceName = "1";
    const char* expectedMateReferenceName = "1";
    const char* expectedMateReferenceNameOrEqual = "=";

    bamRecordStruct* expectedRecordPtr =
        (bamRecordStruct *) malloc(expectedBlockSize + sizeof(int));

    char tag[3];
    char type;
    void* value;
    bamRecordStruct* bufferPtr;
    unsigned char* varPtr;

    expectedRecordPtr->myBlockSize = expectedBlockSize;
    expectedRecordPtr->myReferenceID = 0;
    expectedRecordPtr->myPosition = 1010;
    expectedRecordPtr->myReadNameLength = 23;
    expectedRecordPtr->myMapQuality = 0;
    expectedRecordPtr->myBin = 4681;
    expectedRecordPtr->myCigarLength = 2;
    expectedRecordPtr->myFlag = 73;
    expectedRecordPtr->myReadLength = 5;
    expectedRecordPtr->myMateReferenceID = 0;
    expectedRecordPtr->myMatePosition = 1010;
    expectedRecordPtr->myInsertSize = 0;
   
    // Check the alignment end
    assert(samRecord.get0BasedAlignmentEnd() == 1016);
    assert(samRecord.get1BasedAlignmentEnd() == 1017);
    assert(samRecord.getAlignmentLength() == 7);
    assert(samRecord.get0BasedUnclippedStart() == 1010);
    assert(samRecord.get1BasedUnclippedStart() == 1011);
    assert(samRecord.get0BasedUnclippedEnd() == 1016);
    assert(samRecord.get1BasedUnclippedEnd() == 1017);

    // Check the accessors.
    assert(samRecord.getBlockSize() == expectedRecordPtr->myBlockSize);
    assert(samRecord.getReferenceID() == expectedRecordPtr->myReferenceID);
    assert(strcmp(samRecord.getReferenceName(), expectedReferenceName) == 0);
    assert(samRecord.get1BasedPosition() == expectedRecordPtr->myPosition + 1);
    assert(samRecord.get0BasedPosition() == expectedRecordPtr->myPosition);
    assert(samRecord.getReadNameLength() == 
           expectedRecordPtr->myReadNameLength);
    assert(samRecord.getMapQuality() == expectedRecordPtr->myMapQuality);
    assert(samRecord.getBin() == expectedRecordPtr->myBin);
    assert(samRecord.getCigarLength() == expectedRecordPtr->myCigarLength);
    assert(samRecord.getFlag() == expectedRecordPtr->myFlag);
    assert(samRecord.getReadLength() == expectedRecordPtr->myReadLength);
    assert(samRecord.getMateReferenceID() ==
           expectedRecordPtr->myMateReferenceID);
    assert(strcmp(samRecord.getMateReferenceName(), 
                  expectedMateReferenceName) == 0);
    assert(strcmp(samRecord.getMateReferenceNameOrEqual(), 
                  expectedMateReferenceNameOrEqual) == 0);
    assert(samRecord.get1BasedMatePosition() == 
           expectedRecordPtr->myMatePosition + 1);
    assert(samRecord.get0BasedMatePosition() ==
           expectedRecordPtr->myMatePosition);
    assert(samRecord.getInsertSize() == expectedRecordPtr->myInsertSize);
    assert(strcmp(samRecord.getReadName(), "1:1011:F:255+17M15D20M") == 0);
    assert(strcmp(samRecord.getCigar(), "5M2D") == 0);
    assert(strcmp(samRecord.getSequence(), "CCGAA") == 0);
    assert(strcmp(samRecord.getQuality(), "ABCDE") == 0);
    assert(samRecord.getNumOverlaps(1010, 1017) == 5);
    assert(samRecord.getNumOverlaps(1010, 1016) == 5);
    assert(samRecord.getNumOverlaps(1012, 1017) == 3);
    assert(samRecord.getNumOverlaps(1015, 1017) == 0);
    assert(samRecord.getNumOverlaps(1017, 1010) == 0);
    assert(samRecord.getNumOverlaps(1013, 1011) == 0);
    assert(samRecord.getNumOverlaps(-1, 1017) == 5);

    // Reset the tag iter, since the tags have already been read.
    samRecord.resetTagIter();

    // Check the tags.
    assert(samRecord.getNextSamTag(tag, type, &value) == true);
    assert(tag[0] == 'A');
    assert(tag[1] == 'M');
    assert(type == 'i');
    assert(*(char*)value == 0);
    assert(samRecord.getNextSamTag(tag, type, &value) == true);
    assert(tag[0] == 'M');
    assert(tag[1] == 'D');
    assert(type == 'Z');
    assert(*(String*)value == "37");
    assert(samRecord.getNextSamTag(tag, type, &value) == true);
    assert(tag[0] == 'N');
    assert(tag[1] == 'M');
    assert(type == 'i');
    assert(*(char*)value == 0);
    assert(samRecord.getNextSamTag(tag, type, &value) == true);
    assert(tag[0] == 'X');
    assert(tag[1] == 'T');
    assert(type == 'A');
//.........这里部分代码省略.........
开发者ID:narisu，项目名称:gotcloud，代码行数:101，代码来源:ReadFiles.cpp


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