PileupElement function ( ) { if ( isLeftEdge ( ) || isRightEdge ( ) ) throw new IllegalStateException ( "srini_string" ) ; return new PileupElement ( read , getReadOffset ( ) , getCurrentCigarElement ( ) , getCurrentCigarElementOffset ( ) , getOffsetIntoCurrentCigarElement ( ) ) ; }
create a new pileupelement based on the current state of this element must not be a left or right edge concode_field_sep GATKRead read concode_elem_sep int offsetIntoCurrentCigarElement concode_elem_sep Cigar cigar concode_elem_sep int readOffset concode_elem_sep int genomeOffset concode_elem_sep int nCigarElements concode_elem_sep CigarElement currentElement concode_elem_sep int currentCigarElementOffset concode_field_sep boolean isRightEdge concode_elem_sep int getGenomePosition concode_elem_sep SimpleInterval getLocation concode_elem_sep GATKRead getRead concode_elem_sep int getCurrentCigarElementOffset concode_elem_sep int getReadOffset concode_elem_sep int getOffsetIntoCurrentCigarElement concode_elem_sep String getContig concode_elem_sep CigarOperator stepForwardOnGenome concode_elem_sep boolean isLeftEdge concode_elem_sep int getGenomeOffset concode_elem_sep CigarElement getCurrentCigarElement concode_elem_sep void initializeAsLeftEdge concode_elem_sep String toString concode_elem_sep CigarOperator getCigarOperator