question: public boolean checkReference ( SequencesReader sr , Map < String , Long > sequenceNameMap ) throws IOException { for ( CheckValues cv : mValues ) { if ( ! sequenceNameMap . containsKey ( cv . getSequenceName ( ) ) ) { return false ; } final long sequenceId = sequenceNameMap . get ( cv . getSequenceName ( ) ) ; for ( int i = 0 ; i < mChecks . size ( ) ; i ++ ) { final CheckType check = mChecks . get ( i ) ; if ( ! check . checkValue ( sr , sequenceId , cv . getValue ( i ) ) ) { return false ; } } } return true ; }
target:  Checks whether given sequences reader matches criteria from loaded manifest