broad.core.sequence.FastaSequenceIO Member List

This is the complete list of members for broad.core.sequence.FastaSequenceIO, including all inherited members.

append(List<?extends Sequence > records, String fileName)	broad.core.sequence.FastaSequenceIO
append(Sequence seq, String output)	broad.core.sequence.FastaSequenceIO
breakUpMultifile(final int sizeToBreakup)	broad.core.sequence.FastaSequenceIO
createSizeFile(String refFasta)	broad.core.sequence.FastaSequenceIO	static
extractRecords(Collection< String > recordIdList, InputStream is)	broad.core.sequence.FastaSequenceIO
extractRecords(Collection< String > recordIdList, InputStream is, boolean largeSequences)	broad.core.sequence.FastaSequenceIO
extractRecords(Collection< String > recordIdList)	broad.core.sequence.FastaSequenceIO
extractRecordsIntoSequenceList(List<?extends Sequence > sequenceList)	broad.core.sequence.FastaSequenceIO
extractRecordsWithIDLike(String regEx, boolean encode)	broad.core.sequence.FastaSequenceIO
extractRecordsWithIDLike(String regEx, boolean encode, int expectedSize)	broad.core.sequence.FastaSequenceIO
extractRecordsWithIDsMatching(List< String > regExs, boolean encode)	broad.core.sequence.FastaSequenceIO
extractRecordsWithIDsMatching(List< String > regExs, boolean encode, int expectedSize)	broad.core.sequence.FastaSequenceIO
extractRegion(SequenceRegion region)	broad.core.sequence.FastaSequenceIO
extractRegions(List<?extends SequenceRegion > regions)	broad.core.sequence.FastaSequenceIO
extractRegions(List<?extends SequenceRegion > regions, boolean useRegionOrientation)	broad.core.sequence.FastaSequenceIO
extractRegions(List<?extends SequenceRegion > regions, boolean useRegionOrientation, InputStream is)	broad.core.sequence.FastaSequenceIO
FastaSequenceIO(String fileName)	broad.core.sequence.FastaSequenceIO
FastaSequenceIO(File file)	broad.core.sequence.FastaSequenceIO
FastaSequenceIO()	broad.core.sequence.FastaSequenceIO
getChrSequencesFromFasta(String genomeFasta)	broad.core.sequence.FastaSequenceIO	static
getSequenceNames(String fasta)	broad.core.sequence.FastaSequenceIO	static
LINE_LENGTH	broad.core.sequence.FastaSequenceIO	static
loadAll()	broad.core.sequence.FastaSequenceIO
loadAll(InputStream is)	broad.core.sequence.FastaSequenceIO
loadSequences(File fasta)	broad.core.sequence.FastaSequenceIO	static
loadSequencesByNameFromDirectory(File sequenceDirectory)	broad.core.sequence.FastaSequenceIO	static
loadSequencesByNameFromDirectory(File sequenceDirectory, boolean nonrandomOnly)	broad.core.sequence.FastaSequenceIO	static
main(String[] args)	broad.core.sequence.FastaSequenceIO	static
mergeRecords(Sequence seq, String regEx)	broad.core.sequence.FastaSequenceIO
setSource(File newSource)	broad.core.sequence.FastaSequenceIO
unchunk(File[] inDirList, int chunkSize, String unchunkSeqName, String outputFile)	broad.core.sequence.FastaSequenceIO
write(List<?extends Sequence > seqs, int lineLength)	broad.core.sequence.FastaSequenceIO
write(List<?extends Sequence > seqs)	broad.core.sequence.FastaSequenceIO
write(Sequence seq)	broad.core.sequence.FastaSequenceIO
write(Sequence seq, String fileName)	broad.core.sequence.FastaSequenceIO
write(List<?extends Sequence > seqs, String fileName)	broad.core.sequence.FastaSequenceIO
write(List<?extends Sequence > seqs, String fileName, int lineLength)	broad.core.sequence.FastaSequenceIO
write(List<?extends Sequence > seqs, BufferedWriter bw, int lineLength)	broad.core.sequence.FastaSequenceIO
write(List<?extends Sequence > seqs, BufferedWriter bw)	broad.core.sequence.FastaSequenceIO
write(List<?extends Sequence > seqs, BufferedWriter bw, Map< String, String > names, String refID, String pos)	broad.core.sequence.FastaSequenceIO
write(Sequence seq, BufferedWriter bw, int lineLength)	broad.core.sequence.FastaSequenceIO
write(Sequence seq, BufferedWriter bw)	broad.core.sequence.FastaSequenceIO
writeRecordsWithMinLength(int minimumLength, InputStream inIs, BufferedWriter bw)	broad.core.sequence.FastaSequenceIO
writeSequenceId(Sequence seq, BufferedWriter bw)	broad.core.sequence.FastaSequenceIO	protected