bool doesASTRequireProfiling(SILModule &M, ASTNode N) {
return M.getOptions().GenerateProfile && !isUnmapped(N);
}
bool isMapped() const {assert(m_dataPtr); return !isUnmapped();}
SamRead::SamRead(const bam1_t *b, bam_header_t *_bamHeader, const faidx_t *_fai) {
fai = _fai;
const bam1_core_t *c = &b->core;
uint32_t len = c->l_qseq;
double mapPhred = (double) c->qual;
mapQual = (1.0 - pow(10.0, -mapPhred / 10.0));
if (mapQual < 0.0 || mapQual > 1.0 || std::isnan(mapQual) || std::isinf(mapQual)) {
throw std::string("Phred error.");
} else if (mapQual < 1e-16) {
mapQual = 1e-16;
} else if (mapQual > 1 - 1e-16) {
mapQual = 1 - 1e-16;
}
pos = c->pos; // zero-based
seq_name = (std::string)reinterpret_cast<char *>(bam1_qname(b));
seq.reserve(len);
qual.reserve(len);
for (size_t x = 0; x < len; x++) {
seq += (bam_nt16_rev_table[ bam1_seqi(bam1_seq(b), x) ]);
// convert phred to probability
double basePhred = (double)(((uint8_t *) bam1_qual(b))[x]);
double q = (1.0 - pow(10.0, -basePhred / 10.0));
if (q < 0.0 || q > 1.0 || std::isnan(q) || std::isinf(q)) {
throw std::string("Phred error.");
}
if (q < 1e-16) {
q = 1e-16;
}
if (q > 1.0 - 1e-16) {
q = 1.0 - 1e-16;
}
qual.push_back(q); // base quality is on log10 scale
}
bam = new bam1_t;
*bam = *b;
bam->data = new uint8_t[b->m_data];
bam->m_data = b->m_data;
for (int m = 0; m < b->m_data; m++) {
bam->data[m] = b->data[m];
}
if (bam->core.flag & BAM_FREVERSE) {
onReverseStrand = true;
} else {
onReverseStrand = false;
}
matePos = bam->core.mpos;
mateLen = -1;
this->bamHeader = _bamHeader;
uint32_t *rawCigar = bam1_cigar(b);
leftMostPos = pos;
rightMostPos = getEndPos();
if(!isUnmapped()) {
rightMostPos = pos;
hasIndel = false;
hasHardClip = false;
hasSoftClip = false;
hasOtherCigarFlag = false;
bool isLeftMost = true;
softClipSize = 0;
// set CIGAR string
for (int k = 0; k < c->n_cigar; ++k) {
int op = rawCigar[k] & BAM_CIGAR_MASK;
int32_t len = rawCigar[k] >> BAM_CIGAR_SHIFT;
// update position for the next cigar
if (op == BAM_CMATCH) {
cigars.push_back(CIGAR(CIGAR::MATCH, len));
rightMostPos += len;
isLeftMost = false;
} else if (op == BAM_CINS) {
cigars.push_back(CIGAR(CIGAR::INS, len));
hasIndel = true;
isLeftMost = false;
} else if (op == BAM_CDEL) {
cigars.push_back(CIGAR(CIGAR::DEL, len));
rightMostPos += len;
hasIndel = true;
isLeftMost = false;
} else if (op == BAM_CSOFT_CLIP) {
rightMostPos += len;
if (softClipSize < (int)len) {
softClipSize = (int)len;
}
hasSoftClip = true;
cigars.push_back(CIGAR(CIGAR::SOFTCLIP, len));
if (isLeftMost) {
leftMostPos -= len;
isLeftMost = false;
}
} else if (op == BAM_CHARD_CLIP) {
hasHardClip = true;
} else {
hasOtherCigarFlag = true;
}
}
parseVariants();
}
