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