com.pacbio.secondary.vis.io.hdf.referenceinfo

Class CMPH5ReadGroupInfo

java.lang.Object

com.pacbio.secondary.vis.io.hdf.referenceinfo.CMPH5ReadGroupInfo

public class CMPH5ReadGroupInfo
extends java.lang.Object

Encapsulates concept of cmp.h5's read groups metadata storage

Author:

mmilletti

Field Summary

Fields

Modifier and Type	Field and Description
protected java.lang.String	aln_index_label
protected java.lang.String[]	read_group_path
protected int[]	read_group_path_id

Constructor Summary

Constructors

Constructor and Description
CMPH5ReadGroupInfo(java.lang.String[] read_group_path, int[] read_group_path_id, boolean is1_2)

Method Summary

Methods

Modifier and Type	Method and Description
int	getNumReadGroups()
java.lang.String	getReadGroupAlignmentIndexPath(int index) returns path to alignmentindex for read group
java.lang.String	getReadGroupNormalizedIPDPath(int index) returns path to ipd for read group
java.lang.String	getReadGroupPath(int index)
int[]	getReadGroupPathIds()
java.lang.String[]	getReadGroupPaths()
java.lang.String	getReadGroupPKMIDPath(int index) returns path to pulse width for read group
java.lang.String	getReadGroupPulseWidthPath(int index) returns path to pulse width for read group
java.lang.String	getReadGroupQualityValuePath(int index) returns path to quality value for read group
java.lang.String	getReadGroupRawIPDPath(int index) returns path to ipd for read group
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

read_group_path

protected java.lang.String[] read_group_path

read_group_path_id

protected int[] read_group_path_id

aln_index_label

protected java.lang.String aln_index_label

Constructor Detail

CMPH5ReadGroupInfo

public CMPH5ReadGroupInfo(java.lang.String[] read_group_path,
                  int[] read_group_path_id,
                  boolean is1_2)

Parameters:

read_group_path - a list containing the read group paths

read_group_path_id - a list containing the read group path ids

is1_2 - true if this is a v1.2 file

Method Detail

getReadGroupPaths

public java.lang.String[] getReadGroupPaths()

getReadGroupPathIds

public int[] getReadGroupPathIds()

getReadGroupPath

public java.lang.String getReadGroupPath(int index)

getReadGroupAlignmentIndexPath

public java.lang.String getReadGroupAlignmentIndexPath(int index)

returns path to alignmentindex for read group

Parameters:

index -

Returns:

getReadGroupQualityValuePath

public java.lang.String getReadGroupQualityValuePath(int index)

returns path to quality value for read group

Parameters:

index - read group

Returns:

getReadGroupRawIPDPath

public java.lang.String getReadGroupRawIPDPath(int index)

returns path to ipd for read group

Parameters:

index -

Returns:

getReadGroupNormalizedIPDPath

public java.lang.String getReadGroupNormalizedIPDPath(int index)

returns path to ipd for read group

Parameters:

index -

Returns:

getReadGroupPulseWidthPath

public java.lang.String getReadGroupPulseWidthPath(int index)

returns path to pulse width for read group

Parameters:

index -

Returns:

getReadGroupPKMIDPath

public java.lang.String getReadGroupPKMIDPath(int index)

returns path to pulse width for read group

Parameters:

index -

Returns:

getNumReadGroups

public int getNumReadGroups()

Returns:

number of read groups for this reference

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object