bamstats-0.3: A program to extract various information from BAM alignmnet files.

Safe HaskellNone

Bio.SamTools.Classify

Description

Stats reads in a BAM-file as innie outie rightie leftie, with stats for distances

Synopsis

Documentation

data Stats a Source

Constructors

Class 

Fields

total :: !Int
 
innies :: !a
 
outies :: !a
 
lefties :: !a
 
righties :: !a
 

Instances

Show a => Show (Stats a) 

display :: Insertable x => Stats x -> StringSource

Pretty-print a Stats value.

classify :: Insertable x => x -> [Bam1] -> Stats xSource

Extract info from alignments

bump :: Stats a -> Stats aSource

Update count

class1 :: Insertable x => Stats x -> Bam1 -> Stats xSource

Update data structure with a single alignment

data ClassStats Source

Constructors

CS 

Fields

ccount :: !Int
 
xsum :: !Double
 
x2sum :: !Double
 
x3sum :: !Double
 
x4sum :: !Double
 

data Statistics Source

Constructors

S 

Fields

ncount :: Double
 
mean :: Double
 
stdev :: Double
 
skew :: Double
 
kurt :: Double
 

data Hist Source

Constructors

H 

Fields

hcount :: !Int
 
buckets :: ![(Int, Int)]
 

Instances

data Collect Source

Constructors

Bams 

Fields

bams :: [Bam1]
 

Instances