Package org.snpeff.sam
Class SamEntry
java.lang.Object
org.snpeff.sam.SamEntry
An entry in a SAM file
References: http://samtools.sourceforge.net/SAM-1.3.pdf
- Author:
- pcingola
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionDoes this entry have a tag?getCigar()
int
getFlag()
getId()
getLine()
int
getMapq()
int
getPnext()
int
getPos()
getQname()
getQual()
getRname()
getRnext()
getSeq()
int
getTlen()
boolean
hasMapq()
Some aligners just use '255' in the mapping quality field (bowtie)boolean
PCR or optical duplicateboolean
The first fragment in the templateboolean
The last fragment in the templateboolean
isMapped()
Is this entry mapped to the genome?boolean
Template having multiple fragments in sequencingboolean
Is this read mapped to multiple genomic locations?boolean
SEQ of the next fragment in the template being reversedboolean
Next fragment in the template unmappedboolean
Not passing quality controlsboolean
Each fragment properly aligned according to the alignerboolean
SEQ being reverse complementedboolean
Secondary alignmentboolean
Is this read mapped to only one genomic locations?boolean
Fragment unmappedvoid
replaceSeq
(String newSeq) Replace a sequence WARNING: Doing this might invalidate the CIGAR fieldstatic String
samLine2Id
(String line) Get an ID from a SAM linetoString()
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Constructor Details
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SamEntry
Create an entry give a line from a file
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Method Details
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samLine2Id
Get an ID from a SAM line -
findTag
Does this entry have a tag? -
getCigar
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getFlag
public int getFlag() -
getId
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getLine
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getMapq
public int getMapq() -
getPnext
public int getPnext() -
getPos
public int getPos() -
getQname
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getQual
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getRname
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getRnext
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getSeq
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getTlen
public int getTlen() -
hasMapq
public boolean hasMapq()Some aligners just use '255' in the mapping quality field (bowtie) -
isDuplicate
public boolean isDuplicate()PCR or optical duplicate -
isFirstFragment
public boolean isFirstFragment()The first fragment in the template -
isLastFragment
public boolean isLastFragment()The last fragment in the template -
isMapped
public boolean isMapped()Is this entry mapped to the genome? -
isMultipleFragments
public boolean isMultipleFragments()Template having multiple fragments in sequencing -
isMultipleHits
public boolean isMultipleHits()Is this read mapped to multiple genomic locations? -
isNextReverseWc
public boolean isNextReverseWc()SEQ of the next fragment in the template being reversed -
isNextUnmapped
public boolean isNextUnmapped()Next fragment in the template unmapped -
isNotQualityControl
public boolean isNotQualityControl()Not passing quality controls -
isProperlyAligned
public boolean isProperlyAligned()Each fragment properly aligned according to the aligner -
isReverseWc
public boolean isReverseWc()SEQ being reverse complemented -
isSecondaryAlignment
public boolean isSecondaryAlignment()Secondary alignment -
isUniqueHit
public boolean isUniqueHit()Is this read mapped to only one genomic locations?- Returns:
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isUnmapped
public boolean isUnmapped()Fragment unmapped -
replaceSeq
Replace a sequence WARNING: Doing this might invalidate the CIGAR field- Parameters:
newSeq
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toString
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