nl_tokens: Determine which alignment segment to render as an arrow . This is either the first or last M section excluding soft clipping .
pl_tokens: function getArrowIndex ( read : Alignment ) : number { var i , op , ops = <mask> . cigarOps ; if ( read . getStrand ( ) == '-' ) { for ( i = 0 ; i < ops . length ; i ++ ) { op = ops [ i ] ; if ( op . op == 'S' ) continue ; if ( op . op == 'M' ) return i ; return - 1 ; } } else { for ( i = ops . length - 1 ; i >= 0 ; i -- ) { op = ops [ i ] ; if ( op . op == 'S' ) continue ; if ( op . op == 'M' ) return i ; return - 1 ; } } return - 1 ; }