com.pacbio.secondary.vis.io.indexer.gff

Class GFFIndexer

java.lang.Object

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

com.pacbio.secondary.vis.io.indexer.gff.GFFIndexer

public class GFFIndexer
extends TextFileIndexer

Helper class to split/index GFF files

Field Summary

Fields

Modifier and Type	Field and Description
GFFMetadataInfo	file_info
static java.lang.String	marker_max_read_length
static int	MAX_TEXT_FILE_ROW_LENGTH
static long	min_gff_chunk_lenght
protected static int	progress_interval_factor

Constructor Summary

Constructors

Constructor and Description
GFFIndexer()

Method Summary

Methods

Modifier and Type	Method and Description
protected java.lang.String	buildCacheFileName(java.lang.String file_name, int contig, int num_chunks)
GFFMetadataInfo	getGFFFileIndexesAndMetadata(java.lang.String file_name, int num_data_points) Splits a large gff2 file into desired number of chunks, and creates a list of indexes, offset in the file, and corresponding genome position, e.g.: [file_offset] [genome_position] 0x1234 412 0x9876 3258 ....
GFFMetadataInfo	getGFFFileRegionIndexesAndMetadata(java.lang.String file_name, int num_chunks, int genomicContig, long fileStartOffset, long fileEndOffset) Splits a gff2 file region into desired number of chunks, and creates a list of indexes (absolute in the file) and corresponding genome position, e.g.: [file_offset] [genome_position] 0x1234 412 0x9876 3258 ....
FileIndexInfo	getGFFFileRegionInfo(java.lang.String file_name, int genomicContig, long genomicStart, long genomicEnd, int num_cached_data_points)
long	getIndexSliceSize()
java.io.Reader	getReaderForGFFFileRegion(java.lang.String file_name, int genomicContig, long genomicStart, long genomicEnd, long data_size, int num_cached_data_points) gets a reader for a specified region of a gff file used for details/sab view allocates block of contiguous memory....
boolean	isSorted()
protected void	printProgress(int chunk_idx, int num_chunks)
boolean	readFileInfoFromCacheFile(java.lang.String file_name, int contig, int num_chunks)
protected void	scanGFFV2Slice(java.util.List<GFFIndexInfo> indexes, GFFMetadataInfoCalculator row_info, java.lang.String slice, int chunk_idx) this method scans a slice of data to find an F3 read and stores the info into the indexes array
void	setIndexSliceSize(long l)
boolean	writeFileInfoToCacheFile(java.lang.String file_name, int contig, int num_chunks)

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

Field Detail

MAX_TEXT_FILE_ROW_LENGTH

public static final int MAX_TEXT_FILE_ROW_LENGTH

See Also:

Constant Field Values

min_gff_chunk_lenght

public static final long min_gff_chunk_lenght

See Also:

Constant Field Values

marker_max_read_length

public static final java.lang.String marker_max_read_length

See Also:

Constant Field Values

progress_interval_factor

protected static final int progress_interval_factor

See Also:

Constant Field Values

file_info

public GFFMetadataInfo file_info

Constructor Detail

GFFIndexer

public GFFIndexer()

Method Detail

getIndexSliceSize

public long getIndexSliceSize()

Specified by:

getIndexSliceSize in class TextFileIndexer

Returns:

gff slice size

setIndexSliceSize

public void setIndexSliceSize(long l)

Parameters:

l - sets slice size

getGFFFileRegionInfo

public FileIndexInfo getGFFFileRegionInfo(java.lang.String file_name,
                                 int genomicContig,
                                 long genomicStart,
                                 long genomicEnd,
                                 int num_cached_data_points)

Parameters:

file_name -

genomicContig -

genomicStart -

genomicEnd -

data_size -

num_cached_data_points -

Returns:

getReaderForGFFFileRegion

public java.io.Reader getReaderForGFFFileRegion(java.lang.String file_name,
                                       int genomicContig,
                                       long genomicStart,
                                       long genomicEnd,
                                       long data_size,
                                       int num_cached_data_points)

gets a reader for a specified region of a gff file used for details/sab view allocates block of contiguous memory....

Parameters:

file_name -

start -

end -

Returns:

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

isSorted

public boolean isSorted()

Returns:

true if file is sorted, not if unsorted

getGFFFileIndexesAndMetadata

public GFFMetadataInfo getGFFFileIndexesAndMetadata(java.lang.String file_name,
                                           int num_data_points)

Splits a large gff2 file into desired number of chunks, and creates a list of indexes, offset in the file, and corresponding genome position, e.g.: [file_offset] [genome_position] 0x1234 412 0x9876 3258 ....

Parameters:

file_name - path to GFF2 file

num_data_points - slices to divide files into, if 0 automatically determine based on file size

getGFFFileRegionIndexesAndMetadata

public GFFMetadataInfo getGFFFileRegionIndexesAndMetadata(java.lang.String file_name,
                                                 int num_chunks,
                                                 int genomicContig,
                                                 long fileStartOffset,
                                                 long fileEndOffset)

Splits a gff2 file region into desired number of chunks, and creates a list of indexes (absolute in the file) and corresponding genome position, e.g.: [file_offset] [genome_position] 0x1234 412 0x9876 3258 .... ****Assumes single contig******

Parameters:

file_name - path to GFF2 file

num_chunks - slices to divide files into

scanGFFV2Slice

protected void scanGFFV2Slice(java.util.List<GFFIndexInfo> indexes,
                  GFFMetadataInfoCalculator row_info,
                  java.lang.String slice,
                  int chunk_idx)

this method scans a slice of data to find an F3 read and stores the info into the indexes array

Parameters:

indexes - array to store indexes

row_info - helper class to accumulate/average row lenght

slice - the slice as string

chunk_idx - current slice/chunk number

readFileInfoFromCacheFile

public boolean readFileInfoFromCacheFile(java.lang.String file_name,
                                int contig,
                                int num_chunks)

writeFileInfoToCacheFile

public boolean writeFileInfoToCacheFile(java.lang.String file_name,
                               int contig,
                               int num_chunks)

Parameters:

file_name -

contig -

num_chunks -

Returns:

buildCacheFileName

protected java.lang.String buildCacheFileName(java.lang.String file_name,
                                  int contig,
                                  int num_chunks)

printProgress

protected void printProgress(int chunk_idx,
                 int num_chunks)

Parameters:

chunk_idx -

num_chunks -