com.pacbio.secondary.vis.io.indexer.fasta

Class FastaIndexer

java.lang.Object

com.pacbio.secondary.vis.io.indexer.text.TextFileIndexer

com.pacbio.secondary.vis.io.indexer.fasta.FastaIndexer

public class FastaIndexer
extends TextFileIndexer

FastaIndexer: Helper class to create index files for fast access to large fasta reference files

Constructor Summary

Constructors

Constructor and Description
FastaIndexer()

Method Summary

Methods

Modifier and Type	Method and Description
protected java.lang.String	buildContigIndexFileName(java.lang.String fasta_file)
protected java.lang.String	buildIndexFileName(java.lang.String fasta_file)
protected long	getContigOffsetInIndex(java.lang.String fasta_file, java.lang.String contig_id)
long	getIndexSliceSize()
java.io.Reader	getReaderFromFastaFile(java.lang.String fasta_file_name, int contig_index, java.lang.String contig_id, long start, long end)
long	getSequence_high()
long	getSequence_low()
byte[]	readFastaSequenceFromReader(java.io.Reader reader, int buffer_size) read and parse at once....

Methods inherited from class com.pacbio.secondary.vis.io.indexer.text.TextFileIndexer

printStatistics, printStatistics

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

FastaIndexer

public FastaIndexer()

Method Detail

getReaderFromFastaFile

public java.io.Reader getReaderFromFastaFile(java.lang.String fasta_file_name,
                                    int contig_index,
                                    java.lang.String contig_id,
                                    long start,
                                    long end)

Parameters:

fasta_file_name -

start -

end -

Returns:

either a FileReader if the file is small, or an InputStreamReader wrapper of the memory mapped file bits

readFastaSequenceFromReader

public byte[] readFastaSequenceFromReader(java.io.Reader reader,
                                 int buffer_size)

read and parse at once.... tuned to work as fast as possible for data ranges <= buffer_size

Parameters:

reader -

buffer_size -

getContigOffsetInIndex

protected long getContigOffsetInIndex(java.lang.String fasta_file,
                          java.lang.String contig_id)

getIndexSliceSize

public long getIndexSliceSize()

Specified by:

getIndexSliceSize in class TextFileIndexer

Returns:

index slice size

getSequence_low

public long getSequence_low()

getSequence_high

public long getSequence_high()

buildIndexFileName

protected java.lang.String buildIndexFileName(java.lang.String fasta_file)

buildContigIndexFileName

protected java.lang.String buildContigIndexFileName(java.lang.String fasta_file)