Reader for BLAT PSL / PSLX files. More...

Public Member Functions
	psl_reader (const std::string &fn, const std::string &ref_fn, const std::string &reads_fn)

const shore::alignment &	current () const

bool	has_data ()

void	next ()

shore::feed< shore::read > &	leftovers ()

Detailed Description

Reader for BLAT PSL / PSLX files.

BLAT PSL format:

int matches 0

int misMatches 1

int repMatches 2

int nCount 3

int qNumInsert 4

int qBaseInsert 5

int tNumInsert 6

int tBaseInsert 7

string strand 8

int qName 9

int qSize 10

int qStart 11

int qEnd 12

int tName 13

int tSize 14

int tStart 15

int tEnd 16

int blockCount 17

string blockSizes 18

string qStarts 19

string tStarts 20

The documentation for this class was generated from the following file:

Public Types