multovl
1.3
Multiple overlaps of genomic regions
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Linereader for BED-formatted lines. The BedLinereader class parses columns 1 to 6 of the BED format specification, except Column 5 (score) which is skipped, and ignores the optional columns 7 to 12 (http://genome.ucsc.edu/FAQ/FAQformat.html#format1). More...
#include "linereader.hh"
Public Member Functions | |
BedLinereader () | |
Sets up a BedLinereader object. | |
virtual bool | read_into (Region ®ion) const |
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Linereader (const std::string &commentchars="#") | |
Status | parse (const std::string &line) |
Status | status () const |
const std::string & | comment () const |
size_t | fieldcnt () const |
const std::string & | error_msg () const |
const std::string & | chrom () const |
unsigned int | first () const |
unsigned int | last () const |
char | strand () const |
const std::string & | name () const |
Protected Member Functions | |
virtual void | reset () |
virtual void | parse_data (const std::string &line) |
Parse a /line/ assuming it contains BED-formatted data. | |
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void | set_statusflag (Status flag) |
Additional Inherited Members | |
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enum | Status { CLEAN = 0, ERROR = 1, EMPTY = 2, COMMENT = 4, DATA = 8 } |
Symbolic constants to signify the result of a parsing operation. More... | |
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static bool | empty_white (const std::string &str) |
Returns /true/ if /str/ is empty or contains whitespace characters only. | |
static unsigned int | str_to_uint (std::string &str) throw (Exception) |
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Status | _status |
the status after parsing | |
size_t | _fieldcnt |
how many column fields have been seen | |
std::string | _comment |
store a comment line | |
std::string | _err |
stores parsing error messages | |
std::string | _chrom |
std::string | _name |
unsigned int | _first |
unsigned int | _last |
char | _strand |
Linereader for BED-formatted lines. The BedLinereader class parses columns 1 to 6 of the BED format specification, except Column 5 (score) which is skipped, and ignores the optional columns 7 to 12 (http://genome.ucsc.edu/FAQ/FAQformat.html#format1).
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virtual |
Updates the contents of a region with what has been parsed from a BED-formatted line. Does nothing if the calling object is not in the DATA state.
Implements multovl::io::Linereader.
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protectedvirtual |
Prepares the calling object for parsing by resetting all fields. This method must be invoked by the parse(...) method.
Reimplemented from multovl::io::Linereader.