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;
}
}
}
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]++;
}
}
}
// 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;
}
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;
}
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');
assert(*(char*)value == 'R');
// No more tags, should return false.
assert(samRecord.getNextSamTag(tag, type, &value) == false);
assert(samRecord.getNextSamTag(tag, type, &value) == false);
// Get the record ptr.
bufferPtr = (bamRecordStruct*)samRecord.getRecordBuffer();
// Validate the buffers match.
assert(bufferPtr->myBlockSize == expectedRecordPtr->myBlockSize);
assert(bufferPtr->myReferenceID == expectedRecordPtr->myReferenceID);
assert(bufferPtr->myPosition == expectedRecordPtr->myPosition);
assert(bufferPtr->myReadNameLength == expectedRecordPtr->myReadNameLength);
assert(bufferPtr->myMapQuality == expectedRecordPtr->myMapQuality);
assert(bufferPtr->myBin == expectedRecordPtr->myBin);
assert(bufferPtr->myCigarLength == expectedRecordPtr->myCigarLength);
assert(bufferPtr->myFlag == expectedRecordPtr->myFlag);
assert(bufferPtr->myReadLength == expectedRecordPtr->myReadLength);
assert(bufferPtr->myMateReferenceID ==
expectedRecordPtr->myMateReferenceID);
assert(bufferPtr->myMatePosition == expectedRecordPtr->myMatePosition);
assert(bufferPtr->myInsertSize == expectedRecordPtr->myInsertSize);
// Validate the variable length fields in the buffer.
// Set the pointer to the start of the variable fields.
varPtr = (unsigned char*)(&(bufferPtr->myData[0]));
// Validate the readname.
for(int i = 0; i < expectedRecordPtr->myReadNameLength; i++)
{
assert(*varPtr == samRecord.getReadName()[i]);
varPtr++;
}
// Validate the cigar.
// The First cigar is 5M which is 5 << 4 | 0 = 80
assert(*(unsigned int*)varPtr == 80);
// Increment the varptr the size of an int.
varPtr += 4;
// The 2nd cigar is 2D which is 2 << 4 | 2 = 34
assert(*(unsigned int*)varPtr == 34);
// Increment the varptr the size of an int.
varPtr += 4;
// Validate the sequence.
// CC = 0x22
assert(*varPtr == 0x22);
varPtr++;
// GA = 0x41
assert(*varPtr == 0x41);
varPtr++;
// A = 0x10
assert(*varPtr == 0x10);
varPtr++;
// Validate the Quality
for(int i = 0; i < expectedRecordPtr->myReadLength; i++)
{
assert(*varPtr == samRecord.getQuality()[i] - 33);
varPtr++;
}
// Validate the tags.
assert(*varPtr == 'A');
varPtr++;
assert(*varPtr == 'M');
varPtr++;
assert(*varPtr == 'C');
varPtr++;
assert(*varPtr == 0);
varPtr++;
assert(*varPtr == 'M');
varPtr++;
assert(*varPtr == 'D');
varPtr++;
assert(*varPtr == 'Z');
varPtr++;
assert(*varPtr == '3');
varPtr++;
assert(*varPtr == '7');
varPtr++;
assert(*varPtr == 0);
varPtr++;
assert(*varPtr == 'N');
varPtr++;
assert(*varPtr == 'M');
varPtr++;
assert(*varPtr == 'C');
varPtr++;
assert(*varPtr == 0);
varPtr++;
assert(*varPtr == 'X');
varPtr++;
assert(*varPtr == 'T');
varPtr++;
assert(*varPtr == 'A');
varPtr++;
assert(*varPtr == 'R');
varPtr++;
}
