bam

package
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Published: May 16, 2015 License: BSD-3-Clause Imports: 11 Imported by: 0

Documentation

Overview

Package bam implements BAM file format reading, writing and indexing. The BAM format is described in the SAM specification.

http://samtools.github.io/hts-specs/SAMv1.pdf

Index

Examples

Constants

This section is empty.

Variables

This section is empty.

Functions

func WriteIndex

func WriteIndex(w io.Writer, idx *Index) error

WriteIndex writes the Index to the given io.Writer.

Types

type Index

type Index struct {
	// contains filtered or unexported fields
}

Index is a BAI index.

func ReadIndex

func ReadIndex(r io.Reader) (*Index, error)

ReadIndex reads the BAI Index from the given io.Reader.

func (*Index) Add

func (i *Index) Add(r *sam.Record, c bgzf.Chunk) error

Add records the SAM record as having being located at the given chunk.

Example
package main

import (
	"io"
	"log"
	"os"

	"github.com/biogo/hts/bam"
)

func main() {
	// Create a BAI for the BAM read from standard in and write it to standard out.
	br, err := bam.NewReader(os.Stdin, 1)
	if err != nil {
		log.Fatalf("failed to open BAM: %v", err)
	}

	var bai bam.Index
	for {
		r, err := br.Read()
		if err == io.EOF {
			break
		}
		if err != nil {
			log.Fatalf("failed to read BAM record: %v", err)
		}
		err = bai.Add(r, br.LastChunk())
		if err != nil {
			log.Fatalf("failed to add record to BAM index: %v", err)
		}
	}

	err = bam.WriteIndex(os.Stdout, &bai)
	if err != nil {
		log.Fatalf("failed to write BAM index: %v", err)
	}
}
Output:

func (*Index) Chunks

func (i *Index) Chunks(r *sam.Reference, beg, end int) []bgzf.Chunk

Chunks returns a []bgzf.Chunk that corresponds to the given genomic interval.

func (*Index) MergeChunks

func (i *Index) MergeChunks(s index.MergeStrategy)

MergeChunks applies the given MergeStrategy to all bins in the Index.

func (*Index) NumRefs

func (i *Index) NumRefs() int

NumRefs returns the number of references in the index.

func (*Index) ReferenceStats

func (i *Index) ReferenceStats(id int) (stats index.ReferenceStats, ok bool)

ReferenceStats returns the index statistics for the given reference and true if the statistics are valid.

func (*Index) Unmapped

func (i *Index) Unmapped() (n uint64, ok bool)

Unmapped returns the number of unmapped reads and true if the count is valid.

type Iterator

type Iterator struct {
	// contains filtered or unexported fields
}

Iterator wraps a Reader to provide a convenient loop interface for reading BAM data. Successive calls to the Next method will step through the features of the provided Reader. Iteration stops unrecoverably at EOF or the first error.

func NewIterator

func NewIterator(r *Reader, chunks []bgzf.Chunk) (*Iterator, error)

NewIterator returns a Iterator to read from r, limiting the reads to the provided chunks.

i, err := NewIterator(r, bai.Chunks(ref, beg, end))
if err != nil {
	return err
}
for i.Next() {
	fn(i.Record())
}
return i.Close()

func (*Iterator) Close

func (i *Iterator) Close() error

Close releases the underlying Reader.

func (*Iterator) Error

func (i *Iterator) Error() error

Error returns the first non-EOF error that was encountered by the Iterator.

func (*Iterator) Next

func (i *Iterator) Next() bool

Next advances the Iterator past the next record, which will then be available through the Record method. It returns false when the iteration stops, either by reaching the end of the input or an error. After Next returns false, the Error method will return any error that occurred during iteration, except that if it was io.EOF, Error will return nil.

func (*Iterator) Record

func (i *Iterator) Record() *sam.Record

Record returns the most recent record read by a call to Next.

type Reader

type Reader struct {
	// contains filtered or unexported fields
}

Reader implements BAM data reading.

func NewReader

func NewReader(r io.Reader, rd int) (*Reader, error)

NewReader returns a new Reader using the given io.Reader and setting the read concurrency to rd. If rd is zero concurrency is set to GOMAXPROCS.

func (*Reader) Close

func (br *Reader) Close() error

Close closes the Reader.

func (*Reader) Header

func (br *Reader) Header() *sam.Header

Header returns the SAM Header held by the Reader.

func (*Reader) LastChunk

func (br *Reader) LastChunk() bgzf.Chunk

LastChunk returns the bgzf.Chunk corresponding to the last Read operation.

func (*Reader) Read

func (br *Reader) Read() (*sam.Record, error)

Read returns the next sam.Record in the BAM stream.

func (*Reader) SetCache

func (bg *Reader) SetCache(c bgzf.Cache)

SetCache sets the cache to be used by the Reader.

func (*Reader) SetChunk

func (br *Reader) SetChunk(c *bgzf.Chunk) error

SetChunk sets a limited range of the underlying BGZF file to read, after seeking to the start of the given chunk. It may be used to iterate over a defined genomic interval.

type Writer

type Writer struct {
	// contains filtered or unexported fields
}

Writer implements BAM data writing.

func NewWriter

func NewWriter(w io.Writer, h *sam.Header, wc int) (*Writer, error)

NewWriter returns a new Writer using the given SAM header. Write concurrency is set to wc.

func NewWriterLevel

func NewWriterLevel(w io.Writer, h *sam.Header, level, wc int) (*Writer, error)

NewWriterLevel returns a new Writer using the given SAM header. Write concurrency is set to wc and compression level is set to level. Valid values for level are described in the compress/gzip documentation.

func (*Writer) Close

func (bw *Writer) Close() error

Close closes the writer.

func (*Writer) Write

func (bw *Writer) Write(r *sam.Record) error

Write writes r to the BAM stream.

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