úÎ…–X      !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVW Length of sequence data X5 the nucleotide at a specified sequence data offset, " given in 0-based coordinates, or Y if the offset is  beyond the bounds of the data X9 the nucleotides in subsequence of the sequence data, or  Y0 if the region extends beyond the bounds of the  sequence. )Starting position in 0-based coordinates Length Sequence data ?Nucleotides in a subsequence of the sequence data, padded with  N< when the region extends beyond the bounds of the sequence. )Starting position in 0-based coordinates Length Sequence data Z[\]^_`     @A nucleotide sequence or location on a nucleotide sequence that 5 lies on a specific strand and has an orientation. Sequence strand ,Complement of a nucleotide character, swap AT and G C preserving 0 case and leave all other characters unchanged. Convert the orientation of a   thing based on a  specified       Stranded position in a sequence 0-based index of the position Strand of the position  Unstranded offset in a sequence @Returns a position resulting from sliding the original position C along the sequence by a specified offset. A positive offset will " move the position away from the 5'! end of the forward stand of the B sequence regardless of the strand of the position itself. Thus, 6 slide (revCompl pos) off == revCompl (slide pos off) Extract X. the item at a specific sequence position, or  Y: if the position lies outside the bounds of the sequence.   ";Contiguous sequence location defined by a span of sequence 8 positions, lying on a specific strand of the sequence. aThe offset of the 5') end of the location, as a 0-based index bThe length of the location cThe strand of the location  !">The bounds of a sequence location. This is a pair consisting C of the lowest and highest sequence offsets covered by the region. @ The bounds ignore the strand of the sequence location, and the A first element of the pair will always be lower than the second. #>Sequence position of the start of the location. This is the 5' B end on the location strand, which will have a higher offset than  $ if the location is on the  strand. $>Sequence position of the end of the location, as described in  #. %Extract X the nucleotide SeqLike for the sequence  location, or Y, if f any part of the location lies outside  the bounds of the sequence. &As %-, extract the nucleotide subsequence for the ? location, but any positions in the location lying outside the ( bounds of the sequence are returned as N. '>Given a sequence position and a sequence location relative to < the same sequence, compute a new position representing the > original position relative to the subsequence defined by the B location. If the sequence position lies outside of the sequence  location, Nothing* is returned; thus, the offset of the new & position will always be in the range [0, length l - 1]. (>Given a sequence location and a sequence position within that < location, compute a new position representing the original ; position relative to the outer sequence. If the sequence % position lies outside the location, Nothing is returned. This function inverts '! when the sequence position lies 6 within the position is actually within the location. )8For an enclosing location and a sublocation in the same B coordinate system, find the image of the sublocation relative to A the enclosing location. For example, if the enclosing location 9 spans (100, 150) and the sublocation is (110, 120) then  ) will be (10, 20). *<Returns a sequence location produced by finding the inverse ? image of a sublocation, with coordinates given relative to an ? enclosing location, in the coordinate system of the enclosing ? location. For example, if the enclosing location spans (100, + 150) and the sublocation is (10, 20) then * will be  (110, 120). +?Returns a sequence location produced by extending the original + location on each end, based on a pair of ( 5\' extension, /3'  extension/ ). The 5' extension is applied to the 5' end of the < location on the location strand; if the location is on the   strand, the 5'( end will have a higher offset than the  3'9 end and this offset will increase by the amount of the 5'  extension. Similarly, the 3' extension is applied to the 3'  end of the location. ,Returns True/ when a sequence offset lies within a sequence  location on the same sequence -Returns True1 when a sequence position lies within a sequence > location on the same sequence, and occupies the same strand. .Returns True, when two sequence locations overlap at any  position. /#Contigs that comprise the location 0d1?Create a sequence location between 0-based starting and ending ! bounds with a specified strand. 2>Create a sequence location lying between 0-based starting and  ending offsets. When start < end, the location 7 be on the forward strand, otherwise it will be on the  reverse complement strand. 3=Create a sequence location from the sequence position of the C start of the location and the length of the position. The strand A of the location, and the direction it extends from the starting B position, are determined by the strand of the starting position. 4@Returns a location resulting from sliding the original location C along the sequence by a specified offset. A positive offset will " move the location away from the 5'! end of the forward stand of the B sequence regardless of the strand of the location itself. Thus, 8 slide (revCompl cloc) off == revCompl (slide cloc off) efghij !"#$%&'()*+,-./01234 !"#$%&'()*+,-./02314 !"#$%&'()*+,-./ !"#$%&'()*+,-./012345@General (disjoint) sequence region consisting of a concatenated ( set of one or more contiguous regions. klmnopq6r789:stuvwxyz{|56789:56789:56789: ;AA general location, consisting of spans of sequence positions on  a specific, named sequence. <=A location consisting of a contiguous span of positions on a  named sequence. =A position on a named sequence >?@ABCDE}F ;<=>?@ABCDEF CDE?@AB>=<;F ;<=>?@AB@ABCDEDEFG:Representation of a genomic transcript, with a gene and a ? transcript identifier, along with the genomic location of the > processed transcript and an optional coding sequence on that  transcript. HI3Gene or locus name for a collection of transcripts JSpecific transcript identifier K*Sequence location of processed transcript L"Location of CDS on the transcript MASplice junctions, which are isomorphic to the introns they span, @ but which support other biologically relevant constructors and  accessors. NO~PBCreate a splice junction from a donor position (the last position  in the 5'8 exon) and the acceptor position (the first position in  the 3' exon). Q0Donor position, i.e., the last position in the 5' exon around a  junction. R4Acceptor position, i.e., the first position in the 3' exon around  a junction. S<List of splice junctions from a spliced location, in order. TX the location of the 5' UTR on the transcript, or Y  if there is no L on the transcript or if the L location B begins at the first nucleotide of the transcript--if a region is ( returned it will have positive length. UX the location of the 3' UTR on the transcript, or Y  if there is no L on the transcript or if the L location ? ends at the last nucleotide of the transcript--if a region is ( returned it will have positive length. V.Genomic location of CDS within the transcript WX: the input contigs sorted in stranded order, when all lie  on the same strand, or Y! if they are not all on the same  strand. GHIJKLMNOPQRSTUVWMNOPQRSGHIJKLTUVWGHIJKLHIJKLMNONOPQRSTUVW       !"#$%& '()*+,-./012345678"9:;<=>?@ABCCDEFFGHIIJKLMNNOPQRSTUVWXYZXY[\]^_`ab$cdefghijklmnopqrstuvwxyz{|}~€ seqloc-0.2Bio.SeqLoc.SeqLikeBio.SeqLoc.LocReprBio.SeqLoc.StrandBio.SeqLoc.PositionBio.SeqLoc.LocationBio.SeqLoc.SpliceLocationBio.SeqLoc.OnSeqBio.SeqLoc.TranscriptSeqLikelengthntAtsubseq subseqPadconcatLocReprreprunreprreprStr unreprMaybe unreprEither unreprErrStrandedrevComplStrandRevComplFwdcomplstrandedPosoffsetstrandOffsetunOffsetslideatPos ContigLocoffset5LocationboundsstartPosendPosseqData seqDataPadposIntoposOutofclocInto clocOutofextend offsetWithin posWithincontigOverlaps toContigsoverlapsfromBoundsStrand fromStartEnd fromPosLen SpliceLoc fromContigslocOutoflocInto mergeContigsmergeAdjContigs SpliceSeqLoc ContigSeqLocSeqPos SeqOffsetOnSeq onSeqNameunOnSeqSeqName unSeqName andSameSeq TranscriptgeneIdtrxIdlocationcdsJunctionintronfromDonorAcceptordonoracceptor junctionsutr5utr3 cdsLocation sortContigsbase Data.MaybeJustNothing listSubseq listSubseqPadbsSubseq bsSubseqPadlbsNtAt lbsSubseq lbsSubseqPad clocLength clocStrandto clocPosInto clocPosOutof clocExtend clocClocInto clocClocOutof clocOverlaps SpliceLocPrev_next SpliceLocLastcontig singleton consContig goodJunctiontailscontigs firstContig lastContigcontigsAndOffsetsposIntoContigsposOutofContigs slocClocInto slocClocOutof regionOutof slocExtendatslash