Package org.snpeff.sam

Class SamEntry

java.lang.Object
org.snpeff.sam.SamEntry
public class SamEntry extends Object
An entry in a SAM file References: http://samtools.sourceforge.net/SAM-1.3.pdf
Author:
pcingola

  • Constructor Details

    • SamEntry

      public SamEntry(String line)
      Create an entry give a line from a file

  • Method Details

    • samLine2Id

      public static String samLine2Id(String line)
      Get an ID from a SAM line

    • findTag

      public String findTag(String tagName)
      Does this entry have a tag?

    • getCigar

      public String getCigar()

    • getFlag

      public int getFlag()

    • getId

      public String getId()

    • getLine

      public String getLine()

    • getMapq

      public int getMapq()

    • getPnext

      public int getPnext()

    • getPos

      public int getPos()

    • getQname

      public String getQname()

    • getQual

      public String getQual()

    • getRname

      public String getRname()

    • getRnext

      public String getRnext()

    • getSeq

      public String getSeq()

    • 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:

    • isUnmapped

      public boolean isUnmapped()
      Fragment unmapped

    • replaceSeq

      public void replaceSeq(String newSeq)
      Replace a sequence WARNING: Doing this might invalidate the CIGAR field
      Parameters:
      newSeq -

    • toString

      public String toString()
      Overrides:
      toString in class Object