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++;
}
/*
if a discordant read is mapped to MEI (overlap with MEI coord)
add centor of ( anchor_end + 3*avr_ins_var )
skip unmap & clip
check 3 types at the same time
*/
void Sites::AddDiscoverSiteFromSingleBam( SingleSampleInfo & si )
{
/*for(int i=0;i<NMEI; i++) {
std::cout << "m=" << i << ": ";
for(map<string, map<int, bool> >::iterator t=meiCoord[m].begin(); t!=meiCoord[m].end(); t++)
std::cout << t->first << "->" << t->second.size() << " ";
std::cout << std::endl;
}*/
avr_read_length = si.avr_read_length;
avr_ins_size = si.avr_ins_size;
min_read_length = avr_read_length / 3;
current_depth = si.depth;
// total_depth += current_depth;
resetDepthAddFlag();
SamFile bam;
SamFileHeader bam_header;
OpenBamAndBai( bam,bam_header, si.bam_name );
for( int i=0; i<pchr_list->size(); i++ ) {
string chr = (*pchr_list)[i];
// if ( !single_chr.empty() && chr.compare(single_chr)!=0 )
// continue;
if ( siteList.find(chr) == siteList.end() )
siteList[chr].clear();
// map<string, map<int, SingleSite> >::iterator pchr = siteList[m].find(chr);
// map<string, map<int, bool> >::iterator coord_chr_ptr = meiCoord[m].find(chr);
// if (coord_chr_ptr == meiCoord[m].end())
// continue;
bool section_status;
if (range_start<0) { // no range
section_status = bam.SetReadSection( chr.c_str() );
if (!section_status) {
string str = "Cannot set read section at chr " + chr;
morphWarning( str );
}
}
else { // set range
section_status = bam.SetReadSection( chr.c_str(), range_start, range_end );
if (!section_status) {
string str = "Cannot set read section at chr " + chr + " " + std::to_string(range_start) + "-" + std::to_string(range_end);
morphWarning( str );
}
}
// DO ADDING
// if (siteList[chr].empty())
// p_reach_last = 1;
// else {
// p_reach_last = 0;
pnearest = siteList[chr].begin();
// }
SingleSite new_site; // temporary cluster. will be added to map later.
new_site.depth = current_depth;
bool start_new = 1; // check if need to add new_site to map and start new new_site
SamRecord rec;
int between = 0; // count #reads after new_site.end. If end changed, add it to rcount and reset to zero
while( bam.ReadRecord( bam_header, rec ) ) {
if (!start_new) {
if (rec.get1BasedPosition() >= new_site.end)
between++;
else
new_site.rcount++;
}
if (rec.getFlag() & 0x2)
continue;
if ( OneEndUnmap( rec.getFlag() ) )
continue;
if ( IsSupplementary(rec.getFlag()) )
continue;
if ( rec.getReadLength() < min_read_length )
continue;
if ( rec.getMapQuality() < MIN_QUALITY )
continue;
if (chr.compare(rec.getMateReferenceName())==0 && rec.getInsertSize() < abs(avr_ins_size*2))
continue;
bool is_mei = 0;
vector<bool> is_in_coord;
is_in_coord.resize(3, 0);
for(int m=0; m<NMEI; m++) {
map<string, map<int, bool> >::iterator coord_chr_ptr = meiCoord[m].find(rec.getMateReferenceName());
if (coord_chr_ptr == meiCoord[m].end())
is_in_coord[m] = 0;
else
is_in_coord[m] = isWithinCoord( rec.get1BasedMatePosition(), coord_chr_ptr->second ); // within MEI coord
if (is_in_coord[m])
is_mei = 1;
}
if (!is_mei)
continue;
if (start_new) {
setNewCluster( is_in_coord, new_site,rec);
start_new = 0;
between = 0;
}
else { // add to existing cluster
if ( rec.get1BasedPosition() > new_site.end + avr_ins_size ) { // start new coord
addClusterToMap(new_site, siteList[chr]);
setNewCluster( is_in_coord, new_site, rec);
start_new = 0;
between = 0;
}
else {
addToCurrentCluster( is_in_coord, new_site, rec);
new_site.rcount += between;
between = 0;
}
}
}
// add last one
if (!start_new)
addClusterToMap(new_site, siteList[chr]);
}
bam.Close();
}
