//does everything to fill in all the data
void BAMUtils::_crunch_data() {
dna();
padded_alignment();
if (get_bamread().mapped_reverse_strand()) {
reverse();
}
//shift indels to 5'
if (five_prime_justify)
left_justify();
//cip soft clipped portions of read
if (total_three_prime_ignore > 0)
remove_bases_before_soft_clipped();
int startBase = 0;
int stopBase = 0;
bool calcRegionError = bam_record.get_region_base_positions(&startBase, &stopBase);
_region_clipped = false;
if(calcRegionError) adjust_region_base_positions(&startBase, &stopBase, pad_target, &_region_clipped);
score_alignments(q_scores, calcRegionError, startBase, stopBase);
calc_error();
}
void MachODebugMapParser::dumpSymTabEntry(raw_ostream &OS, uint64_t Index,
uint32_t StringIndex, uint8_t Type,
uint8_t SectionIndex, uint16_t Flags,
uint64_t Value) {
// Index
OS << '[' << format_decimal(Index, 6) << "] "
// n_strx
<< format_hex_no_prefix(StringIndex, 8) << ' '
// n_type...
<< format_hex_no_prefix(Type, 2) << " (";
if (Type & MachO::N_STAB)
OS << left_justify(getDarwinStabString(Type), 13);
else {
if (Type & MachO::N_PEXT)
OS << "PEXT ";
else
OS << " ";
switch (Type & MachO::N_TYPE) {
case MachO::N_UNDF: // 0x0 undefined, n_sect == NO_SECT
OS << "UNDF";
break;
case MachO::N_ABS: // 0x2 absolute, n_sect == NO_SECT
OS << "ABS ";
break;
case MachO::N_SECT: // 0xe defined in section number n_sect
OS << "SECT";
break;
case MachO::N_PBUD: // 0xc prebound undefined (defined in a dylib)
OS << "PBUD";
break;
case MachO::N_INDR: // 0xa indirect
OS << "INDR";
break;
default:
OS << format_hex_no_prefix(Type, 2) << " ";
break;
}
if (Type & MachO::N_EXT)
OS << " EXT";
else
OS << " ";
}
OS << ") "
// n_sect
<< format_hex_no_prefix(SectionIndex, 2) << " "
// n_desc
<< format_hex_no_prefix(Flags, 4) << " "
// n_value
<< format_hex_no_prefix(Value, 16);
const char *Name = &MainBinaryStrings.data()[StringIndex];
if (Name && Name[0])
OS << " '" << Name << "'";
OS << "\n";
}
void DWARFUnitIndex::dump(raw_ostream &OS) const {
Header.dump(OS);
OS << "Index Signature ";
for (unsigned i = 0; i != Header.NumColumns; ++i)
OS << ' ' << left_justify(getColumnHeader(ColumnKinds[i]), 24);
OS << "\n----- ------------------";
for (unsigned i = 0; i != Header.NumColumns; ++i)
OS << " ------------------------";
OS << '\n';
for (unsigned i = 0; i != Header.NumBuckets; ++i) {
auto &Row = Rows[i];
if (auto *Contribs = Row.Contributions.get()) {
OS << format("%5u 0x%016" PRIx64 " ", i, Row.Signature);
for (unsigned i = 0; i != Header.NumColumns; ++i) {
auto &Contrib = Contribs[i];
OS << format("[0x%08x, 0x%08x) ", Contrib.Offset,
Contrib.Offset + Contrib.Length);
}
OS << '\n';
}
}
}
