question: public SexMemo ( final SequencesReader reader , final ReferencePloidy ploidy ) throws IOException { final Sex [ ] sexValues = Sex . values ( ) ; mReferences = new ReferenceGenome [ sexValues . length ] ; mParMap = new MyFrickenMap [ sexValues . length ] ; mAutosomes = new HashSet < > ( ) ; for ( final Sex sex : sexValues ) { final ReferenceGenome referenceGenome = new ReferenceGenome ( reader , sex , ploidy ) ; mReferences [ sex . ordinal ( ) ] = referenceGenome ; final MyFrickenMap parmap = new MyFrickenMap ( ) ; for ( ReferenceSequence rs : referenceGenome . sequences ( ) ) { if ( sex == Sex . EITHER && rs . isSpecified ( ) && rs . ploidy ( ) == Ploidy . DIPLOID ) { mAutosomes . add ( rs . name ( ) ) ; } if ( rs . hasDuplicates ( ) ) { final String refName = rs . name ( ) ; final EffectivePloidyList result = new EffectivePloidyList ( ) ; for ( Pair < RegionRestriction , RegionRestriction > dup : rs . duplicates ( ) ) { final RegionRestriction r = dup . getA ( ) ; final RegionRestriction s = dup . getB ( ) ; if ( refName . equals ( r . getSequenceName ( ) ) ) { result . add ( new Pair < > ( r , Ploidy . DIPLOID ) ) ; } if ( refName . equals ( s . getSequenceName ( ) ) ) { result . add ( new Pair < > ( s , Ploidy . NONE ) ) ; } } parmap . put ( refName , result ) ; } } mParMap [ sex . ordinal ( ) ] = parmap ; } }
target:  Remember information from command line and reference file to enable ploidy of a sequence to be determined given the sex of a sample.