com.pacbio.secondary.vis.io.fasta

Class FastaFileReader

java.lang.Object

com.pacbio.secondary.vis.io.fasta.FastaFileReader

public class FastaFileReader
extends java.lang.Object

Author:

mmilletti

Field Summary

Fields

Modifier and Type	Field and Description
static long	extra_sequence_buffer

Constructor Summary

Constructors

Constructor and Description
FastaFileReader(java.lang.String url, int contig_index, java.lang.String contig_id, long start, long end)

Method Summary

Methods

Modifier and Type	Method and Description
protected void	buildSequence(java.lang.String url, int contig_index, java.lang.String contig_id, long start, long end)
protected void	buildStats(int contig_index, long start, long stop)
WsFastaSequenceInfo	getSequenceInfo()
static void	main(java.lang.String[] args)
static void	test_no_indexer(java.lang.String abs_fasta_url, long req_pos)
static void	test_start_with_indexer(java.lang.String abs_fasta_url, int idx, java.lang.String contig, long requested_start, long requested_end)

Methods inherited from class java.lang.Object

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

Field Detail

extra_sequence_buffer

public static final long extra_sequence_buffer

See Also:

Constant Field Values

Constructor Detail

FastaFileReader

public FastaFileReader(java.lang.String url,
               int contig_index,
               java.lang.String contig_id,
               long start,
               long end)

Parameters:

url - path to fasta file

contig_index - 1-based offset

contig_id - string like Ref00001...

start - 1-based coordinate

end - 1-based coordinate

Method Detail

buildSequence

protected void buildSequence(java.lang.String url,
                 int contig_index,
                 java.lang.String contig_id,
                 long start,
                 long end)

Parameters:

url -

contig_index -

contig_id -

start -

end -

buildStats

protected void buildStats(int contig_index,
              long start,
              long stop)

Parameters:

contig_index -

start -

stop -

getSequenceInfo

public WsFastaSequenceInfo getSequenceInfo()

Returns:

main

public static void main(java.lang.String[] args)

test_start_with_indexer

public static void test_start_with_indexer(java.lang.String abs_fasta_url,
                           int idx,
                           java.lang.String contig,
                           long requested_start,
                           long requested_end)

test_no_indexer

public static void test_no_indexer(java.lang.String abs_fasta_url,
                   long req_pos)