#include <ContigIterator_AMOS.hh>
Collaboration diagram for AMOS::ContigIterator_t:
Public Member Functions | |
| ContigIterator_t (Contig_t &ctg, Bank_t *rdbank) | |
| Constructor for iterator. You must call seek() or advanceNext() before using. | |
| bool | seek (Pos_t gindex) |
| Seek to random position in O(numreads) time. Returns if the current position is valid. | |
| bool | advanceNext () |
| Advance to next position (gindex+1) in O(maxdepth) time. Returns if the current position is valid. | |
| Pos_t | uindex () const |
| Returns the current 1-based ungapped contig position. | |
| Pos_t | gindex () const |
| Returns the current 0-based gapped contig position. | |
| bool | hasSNP () const |
| Returns if there is a SNP at the current position. | |
| char | cons () const |
| Returns the consenus at the current position. | |
| int | cqv () const |
| Returns the consensus quality value at this current position. | |
| Column_t | getColumn () |
| Returns a Column_t of the current position. | |
| const Contig_t & | getContig () const |
| Get a reference to the contig object. | |
| const TiledReadList_t & | getTilingReads () const |
| Get list of reads tiling current position. | |
Classes | |
| struct | ReadListItEndCmp |
| Sort operator for maintain end position queue. | |
Internally, the ContigIterator maintains a list of reads which tile the current contig position. This list can be accessed via the getTilingReads() method. In addition, you can also use the getColumn() method to create a Column_t object which sorts the reads by the base at the current consensus position rather than the position of the read in the layout. Use the hasSNP() method to determine if the tiling at the current position is uniform or if it has a SNP.
Note: You must call advanceNext() or seek() to initialize the object
Definition at line 231 of file ContigIterator_AMOS.hh.
Constructor for iterator. You must call seek() or advanceNext() before using.
Definition at line 55 of file ContigIterator_AMOS.cc.
References AMOS::Sequence_t::getQualString(), AMOS::Contig_t::getReadTiling(), and AMOS::Sequence_t::getSeqString().
| bool ContigIterator_t::advanceNext | ( | ) |
Advance to next position (gindex+1) in O(maxdepth) time. Returns if the current position is valid.
Definition at line 98 of file ContigIterator_AMOS.cc.
References AMOS::Contig_t::getReadTiling().
| char AMOS::ContigIterator_t::cons | ( | ) | const [inline] |
Returns the consenus at the current position.
Definition at line 253 of file ContigIterator_AMOS.hh.
| int AMOS::ContigIterator_t::cqv | ( | ) | const [inline] |
Returns the consensus quality value at this current position.
Definition at line 256 of file ContigIterator_AMOS.hh.
References AMOS::MIN_QUALITY.
| Column_t ContigIterator_t::getColumn | ( | ) |
| const Contig_t& AMOS::ContigIterator_t::getContig | ( | ) | const [inline] |
| const TiledReadList_t& AMOS::ContigIterator_t::getTilingReads | ( | ) | const [inline] |
Get list of reads tiling current position.
Definition at line 266 of file ContigIterator_AMOS.hh.
Referenced by AMOS::Column_t::Column_t().
| Pos_t AMOS::ContigIterator_t::gindex | ( | ) | const [inline] |
Returns the current 0-based gapped contig position.
Definition at line 247 of file ContigIterator_AMOS.hh.
| bool ContigIterator_t::hasSNP | ( | ) | const |
Returns if there is a SNP at the current position.
Definition at line 169 of file ContigIterator_AMOS.cc.
| bool ContigIterator_t::seek | ( | Pos_t | gindex | ) |
Seek to random position in O(numreads) time. Returns if the current position is valid.
Definition at line 124 of file ContigIterator_AMOS.cc.
References AMOS::Contig_t::gap2ungap(), and AMOS::Contig_t::getReadTiling().
| Pos_t ContigIterator_t::uindex | ( | ) | const |
Returns the current 1-based ungapped contig position.
Definition at line 74 of file ContigIterator_AMOS.cc.
1.4.7