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broad.pda.rnai.ExtractSequence Member List

This is the complete list of members for broad.pda.rnai.ExtractSequence, including all inherited members.

getFirstSequence(String fastaFile)broad.pda.rnai.ExtractSequencestatic
getGenomeSequence(GenomicAnnotation annot, String genomeDirectory, boolean repeatMask)broad.pda.rnai.ExtractSequencestatic
getSequenceForGene(Collection< Gene > alignments, String genomeDirectory, boolean repeatMask, Map< String, IntervalTree< Alignments >> okRepeats)broad.pda.rnai.ExtractSequencestatic
getSequenceForGene(Gene gene, Sequence chrom, boolean repeatMask, Map< String, IntervalTree< Alignments >> okRepeats, boolean stranded)broad.pda.rnai.ExtractSequencestatic
getSequenceForGene(Gene gene, Sequence chrom, boolean repeatMask, Map< String, IntervalTree< Alignments >> okRepeats)broad.pda.rnai.ExtractSequencestatic
getSequenceForGene(Gene gene, String genomeDirectory, boolean repeatMask)broad.pda.rnai.ExtractSequencestatic
getSequenceUnoriented(Alignments align, Sequence chrom, boolean repeatMask, Map< String, IntervalTree< Alignments >> okRepeats)broad.pda.rnai.ExtractSequencestatic
getSequenceUnoriented(Alignments align, Sequence chrom, boolean repeatMask)broad.pda.rnai.ExtractSequencestatic
getSequenceUnoriented(Alignments align, String genomeDirectory, boolean repeatMask, Map< String, IntervalTree< Alignments >> okRepeats)broad.pda.rnai.ExtractSequencestatic
main(String[] args)broad.pda.rnai.ExtractSequencestatic
reverseComplement(String seq)broad.pda.rnai.ExtractSequencestatic
splitByChr(Collection< Gene > genes)broad.pda.rnai.ExtractSequencestatic
writeFasta(String save, Map< String, Collection< Gene >> genesByChr, String genomeDir, boolean repeatMask)broad.pda.rnai.ExtractSequencestatic
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