Package org.snpeff.sam

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