ShearingKmerCounter

Summary:
Property
Constructor
Method

| Detail:
Property
Constructor
Method

gngs.tools.ShearingKmerCounter

```
@groovy.transform.CompileStatic
@groovy.util.logging.Log
class ShearingKmerCounter
extends ToolBase
```
Tool to count the frequency of kmers at the start of each read in a BAM file. This is intended to inform modeling of potential shearing bias.
Authors:
simon.sadedin

Properties Summary

Properties
Type	Name and description
`static int[]`	`reverse_translation`
`static int[]`	`translation`

Constructor Summary

Constructors
Constructor and description
`ShearingKmerCounter ()`

Methods Summary

Methods
Type Params	Return Type	Name and description
	`static int`	`computeKmer(htsjdk.samtools.SAMRecord read)`
	`static int[]`	`countMotifs(SAM bam)`
	`static int[]`	`countMotifs(htsjdk.samtools.SAMRecordIterator iter)`
	`java.lang.String`	`decodeKmer(int kmer_int)` Convert a kmer encoded as an integer back to string form
	`static void`	`main(java.lang.String[] args)`
	`void`	`run()`

- Property Detail
  - static int[] reverse_translation
  - static int[] translation
- Constructor Detail
  - ShearingKmerCounter()
- Method Detail
  - static int computeKmer(htsjdk.samtools.SAMRecord read)
  - static int[] countMotifs(SAM bam)
  - static int[] countMotifs(htsjdk.samtools.SAMRecordIterator iter)
  - java.lang.String decodeKmer(int kmer_int)
    
    Convert a kmer encoded as an integer back to string form
  - @groovy.transform.CompileDynamic static void main(java.lang.String[] args)
  - @java.lang.Override @groovy.transform.CompileDynamic void run()

Summary:
Property
Constructor
Method

| Detail:
Property
Constructor
Method

Groovy Documentation