multovl
1.3
Multiple overlaps of genomic regions
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#include "bamio.hh"
Public Member Functions | |
BamReader (const std::string &infname) | |
virtual std::string | read_into (std::string &chrom, Region ®) |
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TrackReader () | |
default init | |
const Errors & | errors () const |
virtual void | add_error (const std::string &msg) |
BamReader objects encapsulate an input file from which they can read into a Region object, one by one. BamReader-s are init-ed with a file name, the ctor opens the file for writing and the dtor closes it, RAII-style. Clients should instantiate a BamReader, then invoke its read_into() method, and use the resulting Region immediately for building up a MultiOverlap object.
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explicit |
Init a BamReader object to read from a BAM-formatted binary file.
infname | the input file name. |
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virtual |
Attempts to read from the wrapped input stream into a region. Reads the stream internally record-by-record.
chrom | string to store the chromosome name for /reg/ |
reg | the region this method tries to read into. |
Implements multovl::io::TrackReader.