HtslibFile

HtslibFile is an abstraction for htslib's htsFile using dhtslib.memory for reference counting.

Ideally this struct and its methods can replace file io across dhtslib through a standard interface. It can also centralize the ability to duplicate a file so that it can be iterated several times. It pairs with HtslibIterator.

Constructors

this this(T f): File or string ctor
this this(T1 f, T2 mode): File or string ctor with mode

Alias This

getFilePtr

allow HtslibFile to be used as underlying ptr type

Members

Functions

byRecord auto byRecord(): iterate over all records in a file returns a HtslibIterator
dup HtslibFile dup(): Duplicate the file with the same offset
loadHeader void loadHeader(char commentChar): Read a SAM/BAM header, VCF/BCF header, or text header and internally store it
loadHeader void loadHeader(char commentChar): Read a SAM/BAM header, VCF/BCF header, or text header and internally store it
loadHtsIndex HtsIdx loadHtsIndex(): load BAM/BCF index
loadHtsIndex HtsIdx loadHtsIndex(string idxFile): load SAM/BAM index from filename
loadTabixIndex Tbx loadTabixIndex(): load tabix index
loadTabixIndex Tbx loadTabixIndex(T idxFile): load tabix index from file
query auto query(int tid, long beg, long end): Query htsFile with tid, start, and end returns an HtslibIterator that has type T requires index be loaded first can use Tabix index or BAI/CSI index
query auto query(string region): Query htsFile with string region returns an HtslibIterator that has type T requires index and header be loaded first can use Tabix index or BAI/CSI index
query auto query(string[] regions): Query htsFile with array of regions returns an HtslibIterator that has type Bam1 requires index and header be loaded first
readRecord auto readRecord(): read a BAM/SAM/BCF/VCF record
reset void reset(): reset file reading
resetToFirstRecord void resetToFirstRecord(): reset file reading
seek void seek(long loc): seek to offset in file
setExtraThreads void setExtraThreads(int extra): set extra multithreading
setHeader void setHeader(T hdr): set header for a HtlsibFile
tell off_t tell(): get file offset
write void write(T rec): write SAM/BAM/VCF/BCF record, string, or ubyte data requires the header be loaded if writing SAM/BAM/VCF/BCF record
writeHeader void writeHeader(): write internally stored header
writeln void writeln(T rec): write a string with a newline appended

Properties

getFilePtr inout(HtsFile) getFilePtr [@property getter]: get underlying file pointer wrapper

Variables

bamHdr BamHdr bamHdr;: SAM/BAM/CRAM header
bcfHdr BcfHdr bcfHdr;: BCF/VCF header
eof bool eof;: is file end reached?
f File f;: D File if used
fn Kstring fn;: dhtslib.memory kstring_t rc wrapper Since we need the filename as a null terminated string anyway just use kstring
fp HtsFile fp;: dhtslib.memory htsFile* rc wrapper File pointer
headerOffset off_t headerOffset;: offset of file after header if it has been loaded
idx HtsIdx idx;: SAM/BAM/CRAM index
mode char[] mode;: Undocumented in source.
tbx Tbx tbx;: Tabix index
textHdr Kstring textHdr;: text header