ProcessReadBlob

ProcessReadBlob provides a caching mechanism for ReadBlob fields. Use this when you need to access field/elements multiple times. Note that ProcessReadBlob becomes invalid when ReadBlob goes out of scope.

struct ProcessReadBlob {

Nullable!int sequence_length2;

mixin ReadFlags!(_flag) ;

mixin CheckMapped!(ref_id) ;

this(Nullable!ReadBlob _r);

void cleanup [@property getter];

bool isNull [@property getter];

RefId ref_id [@property getter];

RefId raw_ref_id [@property getter];

uint _flag_nc [@property getter];

ushort _flag [@property getter];

alias refid = ref_id;

GenomePos start_pos [@property getter];

GenomePos raw_start_pos [@property getter];

GenomePos end_pos [@property getter];

GenomePos raw_end_pos [@property getter];

GenomeLocation start_loc [@property getter];

GenomeLocation end_loc [@property getter];

MappingQuality mapping_quality [@property getter];

int tlen [@property getter];

GenomePos sequence_length [@property getter];

Nullable!GenomePos consumed_reference_bases [@property getter];

GenomePos consumed_query_bases [@property getter];

Nullable!string read_name [@property getter];

Nullable!CigarOperations cigar [@property getter];

Nullable!string sequence [@property getter];

ubyte[] toBlob [@property getter];

string posString [@property getter];

string toString();

}

Constructors

this this(Nullable!ReadBlob _r): Undocumented in source.

Members

Aliases

refid alias refid = ref_id: Undocumented in source.

Functions

toString string toString(): Undocumented in source. Be warned that the author may not have intended to support it.

Mixins

__anonymous mixin ReadFlags!(_flag): Undocumented in source.
__anonymous mixin CheckMapped!(ref_id): Undocumented in source.

Properties

_flag ushort _flag [@property getter]: Undocumented in source. Be warned that the author may not have intended to support it.
_flag_nc uint _flag_nc [@property getter]: Undocumented in source. Be warned that the author may not have intended to support it.
cigar Nullable!CigarOperations cigar [@property getter]: Returns Cigar as an array of operations. Returns null if no operations. Caches Cigar when there are operations.
cleanup void cleanup [@property getter]: Undocumented in source. Be warned that the author may not have intended to support it.
consumed_query_bases GenomePos consumed_query_bases [@property getter]: Count query consumed bases. Uses raw_cigar to avoid a heap allocation.
consumed_reference_bases Nullable!GenomePos consumed_reference_bases [@property getter]: Count and caches consumed reference bases. Uses raw_cigar to avoid a heap allocation.
end_loc GenomeLocation end_loc [@property getter]: Undocumented in source. Be warned that the author may not have intended to support it.
end_pos GenomePos end_pos [@property getter]: Get the end position on the reference sequence (better use end_loc)
isNull bool isNull [@property getter]: Undocumented in source. Be warned that the author may not have intended to support it.
mapping_quality MappingQuality mapping_quality [@property getter]: Undocumented in source. Be warned that the author may not have intended to support it.
posString string posString [@property getter]: Undocumented in source. Be warned that the author may not have intended to support it.
raw_end_pos GenomePos raw_end_pos [@property getter]: Undocumented in source. Be warned that the author may not have intended to support it.
raw_ref_id RefId raw_ref_id [@property getter]: Undocumented in source. Be warned that the author may not have intended to support it.
raw_start_pos GenomePos raw_start_pos [@property getter]: Undocumented in source. Be warned that the author may not have intended to support it.
read_name Nullable!string read_name [@property getter]: Return read name as a string. If unavailable returns null. Caches name.
ref_id RefId ref_id [@property getter]: Undocumented in source. Be warned that the author may not have intended to support it.
sequence Nullable!string sequence [@property getter]: Return human readable sequence fragment - null if undefined. Caches sequence.
sequence_length GenomePos sequence_length [@property getter]: Undocumented in source. Be warned that the author may not have intended to support it.
start_loc GenomeLocation start_loc [@property getter]: Undocumented in source. Be warned that the author may not have intended to support it.
start_pos GenomePos start_pos [@property getter]: Get the start position on the reference sequence (better use start_loc), i.e., the first base that gets consumed in the CIGAR.
tlen int tlen [@property getter]: Undocumented in source. Be warned that the author may not have intended to support it.
toBlob ubyte[] toBlob [@property getter]: Undocumented in source. Be warned that the author may not have intended to support it.

Variables

sequence_length2 Nullable!int sequence_length2;: Undocumented in source.