MultiBamReader

class MultiBamReader {

this(BamReader[] readers);

this(string[] filenames);

this(string[] filenames, std.parallelism.TaskPool task_pool);

BamReader[] readers();

SamHeader header();

auto readsWithProgress(void delegate(lazy float p) progressBarFunc, void delegate() finishFunc);

const(ReferenceSequenceInfo)[] reference_sequences();

bool hasReference(string ref_name);

bool has_index();

MultiBamReference reference(int ref_id);

MultiBamReference opIndex(string ref_name);

void setBufferSize(size_t bytes);

auto getReadsOverlapping(BamRegion[] regions);

}

Constructors

this this(BamReader[] readers)
this this(string[] filenames)
this this(string[] filenames, std.parallelism.TaskPool task_pool)

Members

Functions

getReadsOverlapping auto getReadsOverlapping(BamRegion[] regions): Requires coordinate sorting and presence of indices.
hasReference bool hasReference(string ref_name): Check if reference named ref_name is presented in BAM header.
has_index bool has_index(): Check if all BAM files have indices.
header SamHeader header()
opIndex MultiBamReference opIndex(string ref_name): Returns reference sequence named ref_name.
readers BamReader[] readers()
reads auto reads(): Input range of MultiBamRead instances
readsWithProgress auto readsWithProgress(void delegate(lazy float p) progressBarFunc, void delegate() finishFunc)
reference MultiBamReference reference(int ref_id): Returns reference sequence with id ref_id.
reference_sequences const(ReferenceSequenceInfo)[] reference_sequences()
setBufferSize void setBufferSize(size_t bytes): Sets buffer size for all readers (default is 1MB)

Meta

Source

See Implementation

bio std hts bam multireader aliases

FileId

classes

MultiBamReader

functions

structs