HtslibIterator

HtslibIterator is an abstraction for htslib's hts_itr_t using dhtslib.memory for reference counting. HtslibIterator can be used to iterate VCF/BCF/SAM/BAM/Text files using a BAI/CSI/TBX index or by simply iterating the file.

This struct adapts htslib's iterators into ForwardRange. It is paired with and relies on HtslibFile.

struct HtslibIterator (

) if (

is(T == Bam1) ||

is(T == Bcf1)

is(T == Kstring)

) {

HtslibFile f;

HtsItr itr;

T rec;

this(HtslibFile f);

this(HtslibFile f, HtsItr itr);

HtslibIterator dup();

T front();

void popFront();

bool empty [@property getter];

typeof(this) save();

}

Constructors

this this(HtslibFile f): ctor using only HtslibFile without an iterator
this this(HtslibFile f, HtsItr itr): ctor using an HtslibFile and an iterator

Members

Functions

dup HtslibIterator dup(): Duplicate the iterator must fully duplicate hts_itr_t
front T front(): Get front of the iterator, returns Bam1, Bcf1, or Kstring Backing bam1_t, bcf1_t, kstring_t is re-used If you keep the result around it should be duplicated
popFront void popFront(): popFront to move range forward is destructive
save typeof(this) save(): Needed to be ForwardRange

Properties

empty bool empty [@property getter]: InputRange interface

Variables

f HtslibFile f;: HtslibFile
itr HtsItr itr;: refcounted hts_itr_t
rec T rec;: refcounted bam1_t, bcf1_t, or kstring_t