Package ngs
Interface Alignment
-
- All Superinterfaces:
Fragment
- All Known Subinterfaces:
AlignmentIterator
public interface Alignment extends Fragment
Represents an alignment between a Fragment and Reference sub-sequence provides a path to Read and mate Alignment
-
-
Field Summary
Fields Modifier and Type Field Description static int
all
static int
clipLeft
static int
clipRight
static int
maxMapQuality
static int
minMapQuality
static int
noWraparound
static int
passDuplicates
static int
passFailed
static int
primaryAlignment
static int
secondaryAlignment
static int
startWithinSlice
-
Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description java.lang.String
getAlignedFragmentBases()
getAlignedFragmentBasesint
getAlignmentCategory()
Alignments are categorized as primary or secondary (alternate).java.lang.String
getAlignmentId()
Retrieve an identifying String that can be used for later access.long
getAlignmentLength()
Retrieve the projected length of an Alignment projected upon Reference.long
getAlignmentPosition()
Retrieve the Alignment's starting position on the Referencejava.lang.String
getClippedFragmentBases()
getClippedFragmentBasesjava.lang.String
getClippedFragmentQualities()
getClippedFragmentQualitiesboolean
getIsReversedOrientation()
Test if orientation is reversed with respect to the Reference sequence.java.lang.String
getLongCigar(boolean clipped)
getLongCigarint
getMappingQuality()
getMappingQualityAlignment
getMateAlignment()
getMateAlignmentjava.lang.String
getMateAlignmentId()
getMateAlignmentIdboolean
getMateIsReversedOrientation()
getMateIsReversedOrientationjava.lang.String
getMateReferenceSpec()
getMateReferenceSpecjava.lang.String
getReadGroup()
getReadGroupjava.lang.String
getReadId()
getReadIdjava.lang.String
getReferenceBases()
getReferenceBasesjava.lang.String
getReferenceSpec()
getReferenceSpecchar
getRNAOrientation()
getRNAOrientationjava.lang.String
getShortCigar(boolean clipped)
getShortCigarint
getSoftClip(int edge)
getSoftCliplong
getTemplateLength()
getTemplateLengthboolean
hasMate()
hasMate-
Methods inherited from interface ngs.Fragment
getFragmentBases, getFragmentBases, getFragmentBases, getFragmentId, getFragmentQualities, getFragmentQualities, getFragmentQualities, isAligned, isPaired
-
-
-
-
Field Detail
-
passFailed
static final int passFailed
- See Also:
- Constant Field Values
-
passDuplicates
static final int passDuplicates
- See Also:
- Constant Field Values
-
minMapQuality
static final int minMapQuality
- See Also:
- Constant Field Values
-
maxMapQuality
static final int maxMapQuality
- See Also:
- Constant Field Values
-
noWraparound
static final int noWraparound
- See Also:
- Constant Field Values
-
startWithinSlice
static final int startWithinSlice
- See Also:
- Constant Field Values
-
primaryAlignment
static final int primaryAlignment
- See Also:
- Constant Field Values
-
secondaryAlignment
static final int secondaryAlignment
- See Also:
- Constant Field Values
-
all
static final int all
- See Also:
- Constant Field Values
-
clipLeft
static final int clipLeft
- See Also:
- Constant Field Values
-
clipRight
static final int clipRight
- See Also:
- Constant Field Values
-
-
Method Detail
-
getAlignmentId
java.lang.String getAlignmentId() throws ErrorMsg
Retrieve an identifying String that can be used for later access. The id will be unique within ReadCollection.- Returns:
- alignment id
- Throws:
ErrorMsg
- if the property cannot be retrieved
-
getReferenceSpec
java.lang.String getReferenceSpec() throws ErrorMsg
getReferenceSpec- Returns:
- the name of the reference
- Throws:
ErrorMsg
- if the property cannot be retrieved
-
getMappingQuality
int getMappingQuality() throws ErrorMsg
getMappingQuality- Returns:
- mapping quality
- Throws:
ErrorMsg
- if the property cannot be retrieved
-
getReferenceBases
java.lang.String getReferenceBases() throws ErrorMsg
getReferenceBases- Returns:
- reference bases
- Throws:
ErrorMsg
- if the property cannot be retrieved
-
getReadGroup
java.lang.String getReadGroup() throws ErrorMsg
getReadGroup- Returns:
- the name of the read-group
- Throws:
ErrorMsg
- if the property cannot be retrieved
-
getReadId
java.lang.String getReadId() throws ErrorMsg
getReadId- Returns:
- the unique name of the read
- Throws:
ErrorMsg
- if the property cannot be retrieved
-
getClippedFragmentBases
java.lang.String getClippedFragmentBases() throws ErrorMsg
getClippedFragmentBases- Returns:
- clipped fragment bases
- Throws:
ErrorMsg
- if the property cannot be retrieved
-
getClippedFragmentQualities
java.lang.String getClippedFragmentQualities() throws ErrorMsg
getClippedFragmentQualities- Returns:
- clipped fragment phred quality values using ASCII offset of 33
- Throws:
ErrorMsg
- if the property cannot be retrieved
-
getAlignedFragmentBases
java.lang.String getAlignedFragmentBases() throws ErrorMsg
getAlignedFragmentBases- Returns:
- fragment bases in their aligned orientation
- Throws:
ErrorMsg
- if the property cannot be retrieved
-
getAlignmentCategory
int getAlignmentCategory() throws ErrorMsg
Alignments are categorized as primary or secondary (alternate).- Returns:
- either Alignment.primaryAlignment or Alignment.secondaryAlignment
- Throws:
ErrorMsg
- if the property cannot be retrieved
-
getAlignmentPosition
long getAlignmentPosition() throws ErrorMsg
Retrieve the Alignment's starting position on the Reference- Returns:
- unsigned 0-based offset from start of Reference
- Throws:
ErrorMsg
- if the property cannot be retrieved
-
getAlignmentLength
long getAlignmentLength() throws ErrorMsg
Retrieve the projected length of an Alignment projected upon Reference.- Returns:
- unsigned length of projection
- Throws:
ErrorMsg
- if the property cannot be retrieved
-
getIsReversedOrientation
boolean getIsReversedOrientation() throws ErrorMsg
Test if orientation is reversed with respect to the Reference sequence.- Returns:
- true if reversed
- Throws:
ErrorMsg
- if the property cannot be retrieved
-
getSoftClip
int getSoftClip(int edge) throws ErrorMsg
getSoftClip- Parameters:
edge
- which edge- Returns:
- the position of the clipping
- Throws:
ErrorMsg
- if the property cannot be retrieved
-
getTemplateLength
long getTemplateLength() throws ErrorMsg
getTemplateLength- Returns:
- the lenght of the template
- Throws:
ErrorMsg
- if the property cannot be retrieved
-
getShortCigar
java.lang.String getShortCigar(boolean clipped) throws ErrorMsg
getShortCigar- Parameters:
clipped
- selects if clipping has to be applied- Returns:
- a text string describing alignment details
- Throws:
ErrorMsg
- if the property cannot be retrieved
-
getLongCigar
java.lang.String getLongCigar(boolean clipped) throws ErrorMsg
getLongCigar- Parameters:
clipped
- selects if clipping has to be applied- Returns:
- a text string describing alignment details
- Throws:
ErrorMsg
- if the property cannot be retrieved
-
getRNAOrientation
char getRNAOrientation() throws ErrorMsg
getRNAOrientation- Returns:
- '+' if positive strand is transcribed
- Throws:
ErrorMsg
- if the property cannot be retrieved
-
hasMate
boolean hasMate()
hasMate- Returns:
- if the alignment has a mate
-
getMateAlignmentId
java.lang.String getMateAlignmentId() throws ErrorMsg
getMateAlignmentId- Returns:
- unique ID of th alignment
- Throws:
ErrorMsg
- if the property cannot be retrieved
-
getMateAlignment
Alignment getMateAlignment() throws ErrorMsg
getMateAlignment- Returns:
- the mate as alignment
- Throws:
ErrorMsg
- if the property cannot be retrieved
-
getMateReferenceSpec
java.lang.String getMateReferenceSpec() throws ErrorMsg
getMateReferenceSpec- Returns:
- the name of the reference the mate is aligned at
- Throws:
ErrorMsg
- if the property cannot be retrieved
-
-