.. |FivePrimeMapFactory| replace:: :py:class:`~plastid.genomics.map_factories.FivePrimeMapFactory`
.. |ThreePrimeMapFactory| replace:: :py:class:`~plastid.genomics.map_factories.ThreePrimeMapFactory`
.. |CenterMapFactory| replace:: :py:class:`~plastid.genomics.map_factories.CenterMapFactory`
.. |VariableFivePrimeMapFactory| replace:: :py:class:`~plastid.genomics.map_factories.VariableFivePrimeMapFactory`
.. |StratifiedVariableFivePrimeMapFactory| replace:: :py:class:`~plastid.genomics.map_factories.StratifiedVariableFivePrimeMapFactory`
.. |FastaNameReader| replace:: :py:class:`~plastid.bin.crossmap.FastaNameReader`
.. |FastaNameReaders| replace:: :py:class:`FastaNameReaders <plastid.bin.crossmap.FastaNameReader>`
.. |_GeneratorWrapper| replace:: :py:class:`~plastid.genomics.c_common._GeneratorWrapper`
.. |_GeneratorWrappers| replace:: :py:class:`_GeneratorWrappers <plastid.genomics.c_common._GeneratorWrapper>`
.. |AbstractGenomeArray| replace:: :py:class:`~plastid.genomics.genome_array.AbstractGenomeArray`
.. |AbstractGenomeArrays| replace:: :py:class:`AbstractGenomeArrays <plastid.genomics.genome_array.AbstractGenomeArray>`
.. |BAMGenomeArray| replace:: :py:class:`~plastid.genomics.genome_array.BAMGenomeArray`
.. |BAMGenomeArrays| replace:: :py:class:`BAMGenomeArrays <plastid.genomics.genome_array.BAMGenomeArray>`
.. |BigWigGenomeArray| replace:: :py:class:`~plastid.genomics.genome_array.BigWigGenomeArray`
.. |BigWigGenomeArrays| replace:: :py:class:`BigWigGenomeArrays <plastid.genomics.genome_array.BigWigGenomeArray>`
.. |GenomeArray| replace:: :py:class:`~plastid.genomics.genome_array.GenomeArray`
.. |GenomeArrays| replace:: :py:class:`GenomeArrays <plastid.genomics.genome_array.GenomeArray>`
.. |MutableAbstractGenomeArray| replace:: :py:class:`~plastid.genomics.genome_array.MutableAbstractGenomeArray`
.. |MutableAbstractGenomeArrays| replace:: :py:class:`MutableAbstractGenomeArrays <plastid.genomics.genome_array.MutableAbstractGenomeArray>`
.. |SparseGenomeArray| replace:: :py:class:`~plastid.genomics.genome_array.SparseGenomeArray`
.. |SparseGenomeArrays| replace:: :py:class:`SparseGenomeArrays <plastid.genomics.genome_array.SparseGenomeArray>`
.. |AbstractGenomeHash| replace:: :py:class:`~plastid.genomics.genome_hash.AbstractGenomeHash`
.. |AbstractGenomeHashs| replace:: :py:class:`AbstractGenomeHashs <plastid.genomics.genome_hash.AbstractGenomeHash>`
.. |BigBedGenomeHash| replace:: :py:class:`~plastid.genomics.genome_hash.BigBedGenomeHash`
.. |BigBedGenomeHashs| replace:: :py:class:`BigBedGenomeHashs <plastid.genomics.genome_hash.BigBedGenomeHash>`
.. |GenomeHash| replace:: :py:class:`~plastid.genomics.genome_hash.GenomeHash`
.. |GenomeHashs| replace:: :py:class:`GenomeHashs <plastid.genomics.genome_hash.GenomeHash>`
.. |TabixGenomeHash| replace:: :py:class:`~plastid.genomics.genome_hash.TabixGenomeHash`
.. |TabixGenomeHashs| replace:: :py:class:`TabixGenomeHashs <plastid.genomics.genome_hash.TabixGenomeHash>`
.. |GenomicSegment| replace:: :py:class:`~plastid.genomics.roitools.GenomicSegment`
.. |GenomicSegments| replace:: :py:class:`GenomicSegments <plastid.genomics.roitools.GenomicSegment>`
.. |SegmentChain| replace:: :py:class:`~plastid.genomics.roitools.SegmentChain`
.. |SegmentChains| replace:: :py:class:`SegmentChains <plastid.genomics.roitools.SegmentChain>`
.. |Transcript| replace:: :py:class:`~plastid.genomics.roitools.Transcript`
.. |Transcripts| replace:: :py:class:`Transcripts <plastid.genomics.roitools.Transcript>`
.. |_TwoBitSeqProxy| replace:: :py:class:`~plastid.genomics.seqtools._TwoBitSeqProxy`
.. |_TwoBitSeqProxys| replace:: :py:class:`_TwoBitSeqProxys <plastid.genomics.seqtools._TwoBitSeqProxy>`
.. |TwoBitSeqRecordAdaptor| replace:: :py:class:`~plastid.genomics.seqtools.TwoBitSeqRecordAdaptor`
.. |TwoBitSeqRecordAdaptors| replace:: :py:class:`TwoBitSeqRecordAdaptors <plastid.genomics.seqtools.TwoBitSeqRecordAdaptor>`
.. |AbstractAutoSqlElement| replace:: :py:class:`~plastid.readers.autosql.AbstractAutoSqlElement`
.. |AbstractAutoSqlElements| replace:: :py:class:`AbstractAutoSqlElements <plastid.readers.autosql.AbstractAutoSqlElement>`
.. |AutoSqlDeclaration| replace:: :py:class:`~plastid.readers.autosql.AutoSqlDeclaration`
.. |AutoSqlDeclarations| replace:: :py:class:`AutoSqlDeclarations <plastid.readers.autosql.AutoSqlDeclaration>`
.. |AutoSqlField| replace:: :py:class:`~plastid.readers.autosql.AutoSqlField`
.. |AutoSqlFields| replace:: :py:class:`AutoSqlFields <plastid.readers.autosql.AutoSqlField>`
.. |SizedAutoSqlField| replace:: :py:class:`~plastid.readers.autosql.SizedAutoSqlField`
.. |SizedAutoSqlFields| replace:: :py:class:`SizedAutoSqlFields <plastid.readers.autosql.SizedAutoSqlField>`
.. |ValuesAutoSqlField| replace:: :py:class:`~plastid.readers.autosql.ValuesAutoSqlField`
.. |ValuesAutoSqlFields| replace:: :py:class:`ValuesAutoSqlFields <plastid.readers.autosql.ValuesAutoSqlField>`
.. |BED_Reader| replace:: :py:class:`~plastid.readers.bed.BED_Reader`
.. |BED_Readers| replace:: :py:class:`BED_Readers <plastid.readers.bed.BED_Reader>`
.. |BigBedReader| replace:: :py:class:`~plastid.readers.bigbed.BigBedReader`
.. |BigBedReaders| replace:: :py:class:`BigBedReaders <plastid.readers.bigbed.BigBedReader>`
.. |BPlusTree| replace:: :py:class:`~plastid.readers.bigbed.BPlusTree`
.. |BPlusTrees| replace:: :py:class:`BPlusTrees <plastid.readers.bigbed.BPlusTree>`
.. |_FromBED_StrAdaptor| replace:: :py:class:`~plastid.readers.bigbed._FromBED_StrAdaptor`
.. |_FromBED_StrAdaptors| replace:: :py:class:`_FromBED_StrAdaptors <plastid.readers.bigbed._FromBED_StrAdaptor>`
.. |RTree| replace:: :py:class:`~plastid.readers.bigbed.RTree`
.. |RTrees| replace:: :py:class:`RTrees <plastid.readers.bigbed.RTree>`
.. |BigWigReader| replace:: :py:class:`~plastid.readers.bigwig.BigWigReader`
.. |BigWigReaders| replace:: :py:class:`BigWigReaders <plastid.readers.bigwig.BigWigReader>`
.. |BowtieReader| replace:: :py:class:`~plastid.readers.bowtie.BowtieReader`
.. |BowtieReaders| replace:: :py:class:`BowtieReaders <plastid.readers.bowtie.BowtieReader>`
.. |AssembledFeatureReader| replace:: :py:class:`~plastid.readers.common.AssembledFeatureReader`
.. |AssembledFeatureReaders| replace:: :py:class:`AssembledFeatureReaders <plastid.readers.common.AssembledFeatureReader>`
.. |AbstractGFF_Assembler| replace:: :py:class:`~plastid.readers.gff.AbstractGFF_Assembler`
.. |AbstractGFF_Assemblers| replace:: :py:class:`AbstractGFF_Assemblers <plastid.readers.gff.AbstractGFF_Assembler>`
.. |AbstractGFF_Reader| replace:: :py:class:`~plastid.readers.gff.AbstractGFF_Reader`
.. |AbstractGFF_Readers| replace:: :py:class:`AbstractGFF_Readers <plastid.readers.gff.AbstractGFF_Reader>`
.. |GFF3_Reader| replace:: :py:class:`~plastid.readers.gff.GFF3_Reader`
.. |GFF3_Readers| replace:: :py:class:`GFF3_Readers <plastid.readers.gff.GFF3_Reader>`
.. |GFF3_TranscriptAssembler| replace:: :py:class:`~plastid.readers.gff.GFF3_TranscriptAssembler`
.. |GFF3_TranscriptAssemblers| replace:: :py:class:`GFF3_TranscriptAssemblers <plastid.readers.gff.GFF3_TranscriptAssembler>`
.. |GTF2_Reader| replace:: :py:class:`~plastid.readers.gff.GTF2_Reader`
.. |GTF2_Readers| replace:: :py:class:`GTF2_Readers <plastid.readers.gff.GTF2_Reader>`
.. |GTF2_TranscriptAssembler| replace:: :py:class:`~plastid.readers.gff.GTF2_TranscriptAssembler`
.. |GTF2_TranscriptAssemblers| replace:: :py:class:`GTF2_TranscriptAssemblers <plastid.readers.gff.GTF2_TranscriptAssembler>`
.. |BundledPSL_Reader| replace:: :py:class:`~plastid.readers.psl.BundledPSL_Reader`
.. |BundledPSL_Readers| replace:: :py:class:`BundledPSL_Readers <plastid.readers.psl.BundledPSL_Reader>`
.. |PSL_Reader| replace:: :py:class:`~plastid.readers.psl.PSL_Reader`
.. |PSL_Readers| replace:: :py:class:`PSL_Readers <plastid.readers.psl.PSL_Reader>`
.. |WiggleReader| replace:: :py:class:`~plastid.readers.wiggle.WiggleReader`
.. |WiggleReaders| replace:: :py:class:`WiggleReaders <plastid.readers.wiggle.WiggleReader>`
.. |BinaryParserFactory| replace:: :py:class:`~plastid.util.io.binary.BinaryParserFactory`
.. |BinaryParserFactorys| replace:: :py:class:`BinaryParserFactorys <plastid.util.io.binary.BinaryParserFactory>`
.. |AbstractReader| replace:: :py:class:`~plastid.util.io.filters.AbstractReader`
.. |AbstractReaders| replace:: :py:class:`AbstractReaders <plastid.util.io.filters.AbstractReader>`
.. |AbstractWriter| replace:: :py:class:`~plastid.util.io.filters.AbstractWriter`
.. |AbstractWriters| replace:: :py:class:`AbstractWriters <plastid.util.io.filters.AbstractWriter>`
.. |BackwardReader| replace:: :py:class:`~plastid.util.io.filters.BackwardReader`
.. |BackwardReaders| replace:: :py:class:`BackwardReaders <plastid.util.io.filters.BackwardReader>`
.. |ColorWriter| replace:: :py:class:`~plastid.util.io.filters.ColorWriter`
.. |ColorWriters| replace:: :py:class:`ColorWriters <plastid.util.io.filters.ColorWriter>`
.. |CommentReader| replace:: :py:class:`~plastid.util.io.filters.CommentReader`
.. |CommentReaders| replace:: :py:class:`CommentReaders <plastid.util.io.filters.CommentReader>`
.. |CommentWriter| replace:: :py:class:`~plastid.util.io.filters.CommentWriter`
.. |CommentWriters| replace:: :py:class:`CommentWriters <plastid.util.io.filters.CommentWriter>`
.. |FunctionReader| replace:: :py:class:`~plastid.util.io.filters.FunctionReader`
.. |FunctionReaders| replace:: :py:class:`FunctionReaders <plastid.util.io.filters.FunctionReader>`
.. |NameDateWriter| replace:: :py:class:`~plastid.util.io.filters.NameDateWriter`
.. |NameDateWriters| replace:: :py:class:`NameDateWriters <plastid.util.io.filters.NameDateWriter>`
.. |SkipBlankReader| replace:: :py:class:`~plastid.util.io.filters.SkipBlankReader`
.. |SkipBlankReaders| replace:: :py:class:`SkipBlankReaders <plastid.util.io.filters.SkipBlankReader>`
.. |TeeListener| replace:: :py:class:`~plastid.util.io.filters.TeeListener`
.. |TeeListeners| replace:: :py:class:`TeeListeners <plastid.util.io.filters.TeeListener>`
.. |TeeReader| replace:: :py:class:`~plastid.util.io.filters.TeeReader`
.. |TeeReaders| replace:: :py:class:`TeeReaders <plastid.util.io.filters.TeeReader>`
.. |TestTeeListener| replace:: :py:class:`~plastid.util.io.filters.TestTeeListener`
.. |TestTeeListeners| replace:: :py:class:`TestTeeListeners <plastid.util.io.filters.TestTeeListener>`
.. |NullWriter| replace:: :py:class:`~plastid.util.io.openers.NullWriter`
.. |NullWriters| replace:: :py:class:`NullWriters <plastid.util.io.openers.NullWriter>`
.. |AlignmentParser| replace:: :py:class:`~plastid.util.scriptlib.argparsers.AlignmentParser`
.. |AlignmentParsers| replace:: :py:class:`AlignmentParsers <plastid.util.scriptlib.argparsers.AlignmentParser>`
.. |AnnotationParser| replace:: :py:class:`~plastid.util.scriptlib.argparsers.AnnotationParser`
.. |AnnotationParsers| replace:: :py:class:`AnnotationParsers <plastid.util.scriptlib.argparsers.AnnotationParser>`
.. |BaseParser| replace:: :py:class:`~plastid.util.scriptlib.argparsers.BaseParser`
.. |BaseParsers| replace:: :py:class:`BaseParsers <plastid.util.scriptlib.argparsers.BaseParser>`
.. |MaskParser| replace:: :py:class:`~plastid.util.scriptlib.argparsers.MaskParser`
.. |MaskParsers| replace:: :py:class:`MaskParsers <plastid.util.scriptlib.argparsers.MaskParser>`
.. |Parser| replace:: :py:class:`~plastid.util.scriptlib.argparsers.Parser`
.. |Parsers| replace:: :py:class:`Parsers <plastid.util.scriptlib.argparsers.Parser>`
.. |PlottingParser| replace:: :py:class:`~plastid.util.scriptlib.argparsers.PlottingParser`
.. |PlottingParsers| replace:: :py:class:`PlottingParsers <plastid.util.scriptlib.argparsers.PlottingParser>`
.. |PrefixNamespaceWrapper| replace:: :py:class:`~plastid.util.scriptlib.argparsers.PrefixNamespaceWrapper`
.. |PrefixNamespaceWrappers| replace:: :py:class:`PrefixNamespaceWrappers <plastid.util.scriptlib.argparsers.PrefixNamespaceWrapper>`
.. |SequenceParser| replace:: :py:class:`~plastid.util.scriptlib.argparsers.SequenceParser`
.. |SequenceParsers| replace:: :py:class:`SequenceParsers <plastid.util.scriptlib.argparsers.SequenceParser>`
.. |ArgumentWarning| replace:: :py:class:`~plastid.util.services.exceptions.ArgumentWarning`
.. |ArgumentWarnings| replace:: :py:class:`ArgumentWarnings <plastid.util.services.exceptions.ArgumentWarning>`
.. |DataWarning| replace:: :py:class:`~plastid.util.services.exceptions.DataWarning`
.. |DataWarnings| replace:: :py:class:`DataWarnings <plastid.util.services.exceptions.DataWarning>`
.. |FileFormatWarning| replace:: :py:class:`~plastid.util.services.exceptions.FileFormatWarning`
.. |FileFormatWarnings| replace:: :py:class:`FileFormatWarnings <plastid.util.services.exceptions.FileFormatWarning>`
.. |MalformedFileError| replace:: :py:class:`~plastid.util.services.exceptions.MalformedFileError`
.. |MalformedFileErrors| replace:: :py:class:`MalformedFileErrors <plastid.util.services.exceptions.MalformedFileError>`
.. |UniqueFIFO| replace:: :py:class:`~plastid.util.unique_fifo.UniqueFIFO`
.. |UniqueFIFOs| replace:: :py:class:`UniqueFIFOs <plastid.util.unique_fifo.UniqueFIFO>`
