Scaffolding  0.1
This program can assemble genome scaffolds using the pairing information in paired-end reads.
Classes | Macros | Typedefs | Functions
permissive_matching.hpp File Reference
#include <boost/unordered_map.hpp>
#include "utils/utils.hpp"

Go to the source code of this file.

Classes

class  scaffold::PermissiveMatching
 

Macros

#define ARRAY_LENGTH   MAX_TW
 

Typedefs

typedef PermissiveMatching scaffold::BytePermutation
 

Functions

size_t scaffold::hash_value (const PermissiveMatching &P)
 

Detailed Description

implementation of a matching on the numbers 1..n (with n < 256) that allows reflexive pairs, trying to be as space-efficient as possible. Currently, we use an array of (compile-time) fixed size such that matched[u] = v for each pairing uv

TODO: since this basically saves each edge twice, I suspect that this can be done more space-efficiently