| ADENINE_BITS | AMOS::Sequence_t | [protected, static] |
| clear() | AMOS::Contig_t | [inline, virtual] |
| AMOS::Sequence_t::compress(char seqchar, char qualchar) | AMOS::Sequence_t | [inline, protected, static] |
| COMPRESS_BIT | AMOS::Sequence_t | [protected, static] |
| Contig_t() | AMOS::Contig_t | [inline] |
| Contig_t(const Contig_t &source) | AMOS::Contig_t | [inline] |
| CYTOSINE_BITS | AMOS::Sequence_t | [protected, static] |
| eid_m | AMOS::IBankable_t | [protected] |
| flags_m | AMOS::IBankable_t | [protected] |
| gap2ungap(Pos_t gap) | AMOS::Contig_t | |
| getAvgRho() const | AMOS::Contig_t | |
| getBase(Pos_t index) const | AMOS::Sequence_t | [inline] |
| getComment() const | AMOS::Universal_t | [inline] |
| getCovStat(const double globalArrivalRate) const | AMOS::Contig_t | |
| getEID() const | AMOS::IBankable_t | [inline] |
| getGCContent(const Range_t &rng) const | AMOS::Contig_t | [inline, virtual] |
| getGCContent() const | AMOS::Contig_t | [inline, virtual] |
| getIID() const | AMOS::IBankable_t | [inline] |
| getLength() const | AMOS::Sequence_t | [inline] |
| getNCode() const | AMOS::Contig_t | [inline, virtual] |
| getQualString() const | AMOS::Sequence_t | [inline] |
| getQualString(Range_t range) const | AMOS::Sequence_t | |
| getReadTiling() const | AMOS::Contig_t | [inline] |
| getReadTiling() | AMOS::Contig_t | [inline] |
| getSeqString() const | AMOS::Sequence_t | [inline] |
| getSeqString(Range_t range) const | AMOS::Sequence_t | |
| getSpan() const | AMOS::Contig_t | |
| getStatus() const | AMOS::Universal_t | [inline] |
| getUngappedLength() const | AMOS::Contig_t | |
| getUngappedQualString() const | AMOS::Contig_t | [inline] |
| getUngappedQualString(Range_t range) const | AMOS::Contig_t | |
| getUngappedSeqString() const | AMOS::Contig_t | [inline] |
| getUngappedSeqString(Range_t range) const | AMOS::Contig_t | |
| GUANINE_BITS | AMOS::Sequence_t | [protected, static] |
| IBankable_t() | AMOS::IBankable_t | [inline] |
| IBankable_t(const IBankable_t &source) | AMOS::IBankable_t | [inline] |
| iid_m | AMOS::IBankable_t | [protected] |
| IMessagable_t() | AMOS::IMessagable_t | [inline] |
| insertGapColumn(Pos_t gindex) | AMOS::Contig_t | |
| isCompressed() const | AMOS::Sequence_t | [inline] |
| isFlagA() const | AMOS::IBankable_t | [inline] |
| isFlagB() const | AMOS::IBankable_t | [inline] |
| isModified() const | AMOS::IBankable_t | [inline] |
| isRemoved() const | AMOS::IBankable_t | [inline] |
| length_m | AMOS::Sequence_t | [protected] |
| NCODE | AMOS::Contig_t | [static] |
| operator=(const Sequence_t &source) | AMOS::Sequence_t | |
| QUAL_BITS | AMOS::Sequence_t | [protected, static] |
| qual_m | AMOS::Sequence_t | [protected] |
| readMessage(const Message_t &msg) | AMOS::Contig_t | [virtual] |
| readRecord(std::istream &fix, std::istream &var) | AMOS::Contig_t | [protected, virtual] |
| readRecordFix(std::istream &fix) | AMOS::Contig_t | [protected, virtual] |
| readUMD(std::istream &in) | AMOS::Contig_t | |
| reverseComplement() | AMOS::Contig_t | |
| SEQ_BITS | AMOS::Sequence_t | [protected, static] |
| seq_m | AMOS::Sequence_t | [protected] |
| Sequence_t() | AMOS::Sequence_t | [inline] |
| Sequence_t(const Sequence_t &source) | AMOS::Sequence_t | [inline] |
| setBase(char seqchar, char qualchar, Pos_t index) | AMOS::Sequence_t | [inline] |
| setComment(const std::string &comment) | AMOS::Universal_t | [inline] |
| setEID(const std::string &eid) | AMOS::IBankable_t | [inline] |
| setFlagA(bool flag) | AMOS::IBankable_t | [inline] |
| setFlagB(bool flag) | AMOS::IBankable_t | [inline] |
| setIID(ID_t iid) | AMOS::IBankable_t | [inline] |
| setReadTiling(const std::vector< Tile_t > &reads) | AMOS::Contig_t | [inline] |
| setReadTiling(const Layout_t &layout) | AMOS::Contig_t | [inline] |
| setSequence(const char *seq, const char *qual) | AMOS::Contig_t | [inline] |
| setSequence(const std::string &seq, const std::string &qual) | AMOS::Contig_t | [inline] |
| setStatus(Status_t status) | AMOS::Universal_t | [inline] |
| THYMINE_BITS | AMOS::Sequence_t | [protected, static] |
| AMOS::Sequence_t::uncompress(uint8_t byte) | AMOS::Sequence_t | [inline, protected, static] |
| ungap2gap(Pos_t ungap) | AMOS::Contig_t | |
| Universal_t() | AMOS::Universal_t | [inline] |
| Universal_t(const Universal_t &source) | AMOS::Universal_t | [inline] |
| writeMessage(Message_t &msg) const | AMOS::Contig_t | [virtual] |
| writeRecord(std::ostream &fix, std::ostream &var) const | AMOS::Contig_t | [protected, virtual] |
| writeUMD(std::ostream &out) const | AMOS::Contig_t | |
| ~Contig_t() | AMOS::Contig_t | [inline] |
| ~IBankable_t() | AMOS::IBankable_t | [inline, virtual] |
| ~IMessagable_t() | AMOS::IMessagable_t | [inline, virtual] |
| ~Sequence_t() | AMOS::Sequence_t | [inline, virtual] |
| ~Universal_t() | AMOS::Universal_t | [inline, virtual] |
