covstats

README

covstats

get estimates for coverage, instert size, duplicate, from a bam file by sampling read-length and looking at the index.

Documentation

Index

• Constants
• func Main()
• type Stats
  • func BamStats(br *bam.Reader, n int, skipReads int) Stats
  • func (s Stats) String() string

Constants

const N_MADS = 10

Functions

func Main

func Main()

Main is called from the dispatcher

Types

type Stats

type Stats struct {
	InsertMean float64
	InsertSD   float64
	// 5th percentile of insert size
	InsertPct5 int
	// 95th percentile of insert size
	InsertPct95      int
	TemplateMean     float64
	TemplateSD       float64
	ReadLengthMean   float64
	ReadLengthMedian float64
	// ProportionBad is the proportion of reads that were Dup|QCFail
	ProportionBad            float64
	ProportionUnmapped       float64
	ProportionProperlyPaired float64
	ProportionDuplicate      float64

	MaxReadLength int

	H []float64
}

Stats hold info about a bam returned from `BamStats`

func BamStats

func BamStats(br *bam.Reader, n int, skipReads int) Stats

BamStats takes bam reader sample N well-behaved sites and return the coverage and insert-size info

func (Stats) String

func (s Stats) String() string