IndexedFastaFile

FASTA file with .fai or .gzi index

Reads existing FASTA file, optionally creating FASTA index if one does not exist.

Convenient member fns to get no. of sequences, get sequence names and lengths, test for membership, and rapidly fetch sequence at offset.

struct IndexedFastaFile {

this(string fn, bool create);

void setCacheSize(int size);

void setThreads(int nthreads);

auto opIndex(string region);

string fetchSequence(string region);

auto opIndex(string contig, int[2] pos);

int[2] opSlice(int start, int end);

string fetchSequence(string contig, int start, int end);

bool hasSeq(const(char)[] seqname);

auto nSeq [@property getter];

string seqName(int i);

int seqLen(const(char)[] seqname);

}

Constructors

this this(string fn, bool create): construct from filename, optionally creating index if it does not exist throws Exception (TODO: remove) if file DNE, or if index DNE unless create->true

Destructor

~this ~this(): Undocumented in source.

Postblit

this(this) this(this): Undocumented in source.

Members

Functions

fetchSequence string fetchSequence(string region): Fetch sequence in region by assoc array-style lookup: string sequence = fafile.fetchSequence("chr2:20123-30456")
fetchSequence string fetchSequence(string contig, int start, int end): Fetch sequence in region by multidimensional slicing: string sequence = fafile.fetchSequence("chr2", 20123, 30456)
hasSeq bool hasSeq(const(char)[] seqname): Test whether the FASTA file/index contains string seqname
opIndex auto opIndex(string region): Fetch sequence in region by assoc array-style lookup: string sequence = fafile["chr2:20123-30456"]
opIndex auto opIndex(string contig, int[2] pos)
opSlice int[2] opSlice(int start, int end): Fetch sequence in region by multidimensional slicing: string sequence = fafile["chr2", 20123 .. 30456]
seqLen int seqLen(const(char)[] seqname): Return sequence length, -1 if not present
seqName string seqName(int i): Return the name of the i'th sequence
setCacheSize void setCacheSize(int size): Enable BGZF cacheing (size: bytes)
setThreads void setThreads(int nthreads): Enable multithreaded decompression of this FA/FQ Reading fn body of bgzf_mt, this actually ADDS threads (rather than setting) but we'll retain name for consistency with setCacheSize NB: IN A REAL-WORLD TEST (swiftover) CALLING setThreads(1) doubled runtime(???)

Properties

nSeq auto nSeq [@property getter]: Return the number of sequences in the FASTA file/index

Meta

Source

See Implementation

dhtslib faidx enums

CoordSystem

functions

buildFastaIndex

structs

IndexedFastaFile