BamRead

this this(ubyte[] chunk, bool fix_byte_order): Undocumented in source.
this this(string read_name, string sequence, CigarOperation[] cigar): Construct alignment from basic information about it.

Members

Functions

_recalculate_bin void _recalculate_bin()

Undocumented in source. Be warned that the author may not have intended to support it.

associateWithReader void associateWithReader(bio.std.hts.bam.abstractreader.IBamSamReader reader)

Associates read with BAM reader. This is done automatically if this read is obtained through BamReader/Reference methods.

basesCovered int basesCovered()

The number of reference bases covered by this read.
Returns 0 if the read is unmapped.

cigarString string cigarString()

Human-readable representation of CIGAR string (same as in SAM format)

dup BamRead dup()

Deep copy of the record.

extended_cigar auto extended_cigar()

Extended CIGAR where M operators are replaced with =/X based on information from MD tag. Throws if the read doesn't have MD tag.

is_slice_backed bool is_slice_backed()

opEquals bool opEquals(BamRead other)

Compare two alignments, including tags (the tags must follow in the same order for equality).

opEquals bool opEquals(const(BamRead) other)

Undocumented in source. Be warned that the author may not have intended to support it.

raw_data void raw_data(ubyte[] data)

Raw representation of the read. Occasionally useful for dirty hacks!

raw_data inout(ubyte)[] raw_data()

Raw representation of the read. Occasionally useful for dirty hacks!

reader inout(bio.std.hts.bam.abstractreader.IBamSamReader) reader()

Associated BAM/SAM reader.

toJson void toJson(Sink sink)

string toJson()

JSON representation

toMsgpack void toMsgpack(Packer packer)

Packs message in the following format:
MsgPack array with elements

name - string
flag - ushort
reference sequence id - int
leftmost mapping position (1-based) - int
mapping quality - ubyte
array of CIGAR operation lengths - int[]
array of CIGAR operation types - ubyte[]
mate reference sequence id - int
mate position (1-based) - int
template length - int
segment sequence - string
phred-base quality - ubyte[]
tags - map: string -> value

toSam void toSam(Sink sink)

string toSam()

String representation.
Possible formats are SAM ("%s") and JSON ("%j")

toString void toString(void delegate(const(char)[]) sink, FormatSpec!char fmt)

String representation.
Possible formats are SAM ("%s") and JSON ("%j")

write void write(BamWriter writer)

Undocumented in source. Be warned that the author may not have intended to support it.

Mixins

__anonymous mixin TagStorage: Undocumented in source.

Properties

base_qualities inout(ubyte)[] base_qualities [@property getter]: Quality data (phred-based scores)
base_qualities const(ubyte)[] base_qualities [@property setter]: Set quality data - array length must be of the same length as the sequence.
bin bio.std.hts.bam.bai.bin.Bin bin [@property getter]: Indexing bin which this read belongs to. Recalculated when position is changed.
cigar const(CigarOperation)[] cigar [@property getter]
const(CigarOperation)[] cigar [@property setter]: List of CIGAR operations
failed_quality_control bool failed_quality_control [@property getter]
bool failed_quality_control [@property setter]: Not passing quality controls
flag ushort flag [@property getter]
ushort flag [@property setter]: Flag bits (should be used on very rare occasions, see flag getters/setters below)
is_duplicate bool is_duplicate [@property getter]
bool is_duplicate [@property setter]: PCR or optical duplicate
is_first_of_pair bool is_first_of_pair [@property getter]
bool is_first_of_pair [@property setter]: The first segment in the template
is_paired bool is_paired [@property getter]
bool is_paired [@property setter]: Template having multiple segments in sequencing
is_reverse_strand bool is_reverse_strand [@property getter]
bool is_reverse_strand [@property setter]: Sequence being reverse complemented
is_second_of_pair bool is_second_of_pair [@property getter]
bool is_second_of_pair [@property setter]: The last segment in the template
is_secondary_alignment bool is_secondary_alignment [@property getter]
bool is_secondary_alignment [@property setter]: Secondary alignment
is_supplementary bool is_supplementary [@property getter]
bool is_supplementary [@property setter]: Supplementary alignment
is_unmapped bool is_unmapped [@property getter]
bool is_unmapped [@property setter]: Segment unmapped
mapping_quality ubyte mapping_quality [@property getter]
ubyte mapping_quality [@property setter]: Mapping quality. Equals to 255 if not available, otherwise equals to rounded -10 * log10(P {mapping position is wrong}).
mate_is_reverse_strand bool mate_is_reverse_strand [@property getter]
bool mate_is_reverse_strand [@property setter]: Sequence of the next segment in the template being reversed
mate_is_unmapped bool mate_is_unmapped [@property getter]
bool mate_is_unmapped [@property setter]: Next segment in the template unmapped
mate_position int mate_position [@property getter]
int mate_position [@property setter]: Mate position
mate_ref_id int mate_ref_id [@property getter]
int mate_ref_id [@property setter]: Mate reference ID
mate_ref_name string mate_ref_name [@property getter]: Mate reference sequence name ('*' for unmapped mates)
name string name [@property getter]
string name [@property setter]: Read name, length must be in 1..255 interval.
position int position [@property getter]
int position [@property setter]: 0-based leftmost coordinate of the first matching base
proper_pair bool proper_pair [@property getter]
bool proper_pair [@property setter]: Each segment properly aligned according to the aligner
ref_id int ref_id [@property getter]
int ref_id [@property setter]: Reference index in BAM file header
ref_name string ref_name [@property getter]: Reference sequence name ('*' for unmapped reads)
sequence SequenceResult sequence [@property getter]: Random-access range of characters
sequence string sequence [@property setter]: Sets query sequence. Sets all base qualities to 255 (i.e. unknown).
sequence_length int sequence_length [@property getter]: Sequence length. In fact, sequence.length can be used instead, but that might be slower if the compiler is not smart enough to optimize away unrelated stuff.
size_in_bytes size_t size_in_bytes [@property getter]: Size of the alignment record when output to stream in BAM format. Includes block_size as well (see SAM/BAM specification)
strand char strand [@property getter]
char strand [@property setter]: Convenience function, returns '+' or '-' indicating the strand.
template_length int template_length [@property getter]
int template_length [@property setter]: Template length

Structs

SequenceResult struct SequenceResult: Read-only random-access range for access to sequence data.

Variables

_chunk ubyte[] _chunk;: Undocumented in source.

Mixed In Members

From `mixin TagStorage`

opIndex bio.std.hts.bam.tagvalue.Value opIndex(string key)
opIndexAssign void opIndexAssign(T value, string key): Hash-like access to tags. Time complexity is O(number of tags).
If tag with such key is not found, returned value 'is nothing'.
If key length is different from 2, exception is thrown.
Special case when value represents nothing is used for removing tag (assuming that no more than one with this key is presented in the record).
appendTag void appendTag(string key, Value value): Append new tag to the end, skipping check if it already exists. O(1)
clearAllTags void clearAllTags(): Remove all tags
tagCount size_t tagCount(): Number of tags. O(number of tags)
opApply int opApply(int delegate(const ref string k, const ref Value v) dg): Provides opportunity to iterate over tags.
tagCount size_t tagCount(): Returns the number of tags. Time complexity is O(number of tags)

BamRead

Constructors

Members

Functions

Mixins

Properties

Structs

Variables

Mixed In Members

From `mixin TagStorage`

Meta

Source

BamRead

Constructors

Members

Functions

Mixins

Properties

Structs

Variables

Mixed In Members

From mixin TagStorage

Meta

Source

From `mixin TagStorage`