Package org.snpeff.binseq
Class GenomicSequences
java.lang.Object
org.snpeff.binseq.GenomicSequences
- All Implemented Interfaces:
Serializable
,Iterable<MarkerSeq>
This class stores all "relevant" sequences in a genome
This class is able to:
i) Add all regions of interest
ii) Store genomic sequences for those regions of interest
iii) Retrieve genomic sequences by interval
- Author:
- pcingola
- See Also:
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final int
static final int
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
addChromosomeSequence
(String chr, String chrSeq) Create a sequence for the whole chromsome (mostly used in test cases)int
addGeneSequences
(String chr, String chrSeq) Add sequences for each gene in the genomevoid
build()
Build interval forestvoid
clear()
boolean
hasChromosome
(String chr) Do we have sequence information for this chromosome?boolean
isEmpty()
iterator()
boolean
load()
Load sequences for all 'small chromosomes" (from "sequence.bin" file)boolean
Load sequences for a single chromosome (from "sequence.chr.bin" file)boolean
Load sequences from genomic sequence file or (if not file is available) generate some sequences from exons.queryMarkerSequence
(Marker marker) Find a marker (with sequence) containing query 'marker' Could trigger loading sequences form databasequerySequence
(Marker marker) Get sequence for a markervoid
reset()
void
Save genomic sequence into separate files (per chromosome)void
setDisableLoad
(boolean disableLoad) void
setVerbose
(boolean verbose) toString()
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
Methods inherited from interface java.lang.Iterable
forEach, spliterator
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Field Details
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MAX_ITERATIONS
public static final int MAX_ITERATIONS- See Also:
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CHR_LEN_SEPARATE_FILE
public static final int CHR_LEN_SEPARATE_FILE- See Also:
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Constructor Details
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GenomicSequences
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Method Details
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addChromosomeSequence
Create a sequence for the whole chromsome (mostly used in test cases) -
addGeneSequences
Add sequences for each gene in the genome -
build
public void build()Build interval forest -
clear
public void clear() -
hasChromosome
Do we have sequence information for this chromosome? -
isEmpty
public boolean isEmpty() -
iterator
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load
public boolean load()Load sequences for all 'small chromosomes" (from "sequence.bin" file) -
load
Load sequences for a single chromosome (from "sequence.chr.bin" file) -
loadOrCreateFromGenome
Load sequences from genomic sequence file or (if not file is available) generate some sequences from exons. -
queryMarkerSequence
Find a marker (with sequence) containing query 'marker' Could trigger loading sequences form database- Returns:
- A markerSeq containing 'marker' or null if nothing is found
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querySequence
Get sequence for a marker -
reset
public void reset() -
save
Save genomic sequence into separate files (per chromosome) -
setDisableLoad
public void setDisableLoad(boolean disableLoad) -
setVerbose
public void setVerbose(boolean verbose) -
toString
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