Class SamEntry


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

      Constructors 
      Constructor Description
      SamEntry​(java.lang.String line)
      Create an entry give a line from a file
    • Constructor Detail

      • SamEntry

        public SamEntry​(java.lang.String line)
        Create an entry give a line from a file
    • Method Detail

      • samLine2Id

        public static java.lang.String samLine2Id​(java.lang.String line)
        Get an ID from a SAM line
      • findTag

        public java.lang.String findTag​(java.lang.String tagName)
        Does this entry have a tag?
      • getCigar

        public java.lang.String getCigar()
      • getFlag

        public int getFlag()
      • getId

        public java.lang.String getId()
      • getLine

        public java.lang.String getLine()
      • getMapq

        public int getMapq()
      • getPnext

        public int getPnext()
      • getPos

        public int getPos()
      • getQname

        public java.lang.String getQname()
      • getQual

        public java.lang.String getQual()
      • getRname

        public java.lang.String getRname()
      • getRnext

        public java.lang.String getRnext()
      • getSeq

        public java.lang.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​(java.lang.String newSeq)
        Replace a sequence WARNING: Doing this might invalidate the CIGAR field
        Parameters:
        newSeq -
      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object