#include <ContigIterator_AMOS.hh>
Public Member Functions | |
| Column_t (ContigIterator_t &ci) | |
| Object can only be used for a single position! | |
| std::vector< BaseStats_t * > | getBaseInfo () |
| Returns a vector of m_baseinfo sorted by BaseStatsCmp. | |
Public Attributes | |
| Pos_t | m_gindex |
| 0-based gapped index | |
| Pos_t | m_uindex |
| 1-based ungapped index | |
| char | m_cons |
| Current consenus. | |
| int | m_cqv |
| Consensus quality value. | |
| int32_t | m_depth |
| Total depth of coverage. | |
| std::map< char, BaseStats_t > | m_baseinfo |
| Map for collecting read information about each base. | |
Organizes the reads at the current position in the contig by the base each read has at that position. The reads are collected into the m_baseinfo map which maps from base to BaseStats_t. The sortBaseInfo() method can be used to iterate through each base present at the current position.
Warning: The column data becomes invalid if the contig iterator position is changed!
Definition at line 188 of file ContigIterator_AMOS.hh.
| Column_t::Column_t | ( | ContigIterator_t & | ci | ) |
Object can only be used for a single position!
Definition at line 204 of file ContigIterator_AMOS.cc.
References AMOS::ContigIterator_t::getTilingReads(), m_baseinfo, m_depth, and m_gindex.
| vector< BaseStats_t * > Column_t::getBaseInfo | ( | ) |
Returns a vector of m_baseinfo sorted by BaseStatsCmp.
Definition at line 238 of file ContigIterator_AMOS.cc.
References m_baseinfo.
| std::map<char, BaseStats_t> AMOS::Column_t::m_baseinfo |
Map for collecting read information about each base.
Definition at line 213 of file ContigIterator_AMOS.hh.
Referenced by Column_t(), and getBaseInfo().
| int32_t AMOS::Column_t::m_depth |
Total depth of coverage.
Definition at line 210 of file ContigIterator_AMOS.hh.
Referenced by Column_t().
0-based gapped index
Definition at line 198 of file ContigIterator_AMOS.hh.
Referenced by Column_t().
1.4.7