crai

README

read a crai and output sizes.

the python scripts in this directory simplify comparing the output of samtools depth

with the output of crai.

e.g.

samtools depth xx/phase3/data/NA21144/alignment/NA21144.mapped.ILLUMINA.bwa.GIH.low_coverage.20130415.bam.cram > t.out
cat t.out | python agg.py > real.bed
python plot-vs-with-st-depth.py real.bed o.bed

where o.bed is from the crai.Sizes() (and the output of running go test in this directory).

Documentation

Index

• Constants
• type Index
  • func ReadIndex(r io.Reader) (*Index, error)
  • func (idx *Index) Sizes() [][]int64
• type Slice
  • func (s Slice) SliceBytes() int32
  • func (s Slice) Span() int64
  • func (s Slice) Start() int64

Constants

const TileWidth = 16384

Types

type Index

type Index struct {
	Slices [][]Slice
}

func ReadIndex

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

func (*Index) Sizes

func (idx *Index) Sizes() [][]int64

type Slice

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

Slice holds the index information for a particular cram slice

func (Slice) SliceBytes

func (s Slice) SliceBytes() int32

func (Slice) Span

func (s Slice) Span() int64

func (Slice) Start

func (s Slice) Start() int64