Package org.snpeff.coverage
Class Coverage
java.lang.Object
org.snpeff.coverage.Coverage
- All Implemented Interfaces:
Serializable
Base by base coverage (one chromsome)
- Author:
- pcingola
- See Also:
-
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptiondouble
Calculate average coverage per basestatic Coverage
calculateFromSam
(String samFile, boolean verbose) Calculate coverage from a SAM filelong
Calculate total coverage per basevoid
Create new chromosome coveragevoid
Increment a regiontoString()
-
Constructor Details
-
Coverage
public Coverage()
-
-
Method Details
-
calculateFromSam
Calculate coverage from a SAM file- Parameters:
samFile
-verbose
-- Returns:
-
avgCoverage
Calculate average coverage per base- Parameters:
m
- : A marker interval- Returns:
-
coverage
Calculate total coverage per base- Parameters:
m
- : A marker interval- Returns:
-
createChr
Create new chromosome coverage- Parameters:
chr
-len
-
-
get
-
inc
Increment a region- Parameters:
start
-end
-
-
toString
-