com.pacbio.secondary.vis.io.vcf

Class VCFMultiSampleReader

java.lang.Object

com.pacbio.secondary.vis.data.base.BaseDataModel

com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataModel

com.pacbio.secondary.vis.data.variableresolution.model.gff.GFFDataModel

com.pacbio.secondary.vis.io.gff.variants.GFFVariantsReader

com.pacbio.secondary.vis.io.vcf.VCFMultiSampleReader

All Implemented Interfaces:

IVariableResolutionDataModelServer, IChangeNotifier, java.lang.Iterable<VariableValuesDataRecord>

public class VCFMultiSampleReader
extends GFFVariantsReader

Author:

mmilletti

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected static class	VCFMultiSampleReader.vcf_version

Nested classes/interfaces inherited from class com.pacbio.secondary.vis.data.base.BaseDataModel

BaseDataModel.eDataType

Field Summary

Fields

Modifier and Type	Field and Description
protected VCFMultiSampleReader.vcf_version	file_version
protected static int	NUM_RESULTS
protected static java.lang.String	VCF_AD_RSLT
protected int	VCF_ALT_COL
protected int	VCF_CHROM_COL
protected static java.lang.String	VCF_COVERAGE_TAG
protected static java.lang.String	VCF_DP_RSLT
protected int	VCF_FILTER_COL
protected int	VCF_FORMAT_COL
protected static java.lang.String	VCF_FORMATS_GENOTYPE_SEPARATOR
protected static java.lang.String	VCF_FORMATS_RSLT_SEPARATOR
protected static java.lang.String	VCF_FORMATS_SEPARATOR
protected static java.lang.String	VCF_GQ_RSLT
protected static java.lang.String	VCF_GT_RSLT
protected int	VCF_ID_COL
protected int	VCF_INFO_COL
protected static java.lang.String	VCF_NO_SAMPLE_DATA
protected static java.lang.String	VCF_PL_RSLT
protected int	VCF_POS_COL
protected int	VCF_QUAL_COL
protected int	VCF_REF_COL
protected int	VCF_START_SAMPLE_COL
protected static java.lang.String	VCF_VERSION_TAG

Fields inherited from class com.pacbio.secondary.vis.io.gff.variants.GFFVariantsReader

genotype_tag, is_v13, VARIANT_DEF_TAG, VARIANT_DELETION_TYPE, VARIANT_INSERTION_TYPE, VARIANT_SUBST_TYPE, VARIANT_TYPES_LABELS, VARIANT_V12_GENOTYPE_TAG, VARIANT_V13_GENOTYPE_TAG, VARIANT_V13_TAG, VARIANT_V131_TAG, VARIANT_V133_FREQUENCY_TAG, VARIANT_V133_TAG, VARIANT_V140_TAG, VARIANT_V200_TAG, VARIANT_V210_TAG

Fields inherited from class com.pacbio.secondary.vis.data.variableresolution.model.gff.GFFDataModel

data, fileName, min_max_values, valid

Fields inherited from class com.pacbio.secondary.vis.data.base.BaseDataModel

changeNotifier, data_type, mc

Constructor Summary

Constructors

Constructor and Description
VCFMultiSampleReader()

Method Summary

Methods

Modifier and Type	Method and Description
void	loadFromReader(java.io.Reader reader, java.lang.String file_name, VioletApp app)
protected void	processPacBioVersion(java.lang.String[] ar, VariableValuesDataRecord record) parses records in pacbio format
protected VariableValuesDataRecord	processVCFBaseRecord(java.lang.String[] ar, int contig) processes the base part of a vcf record, single sample
protected void	processVCFHeaderInfo(java.lang.String line) process fileheader, get version
protected void	processVCFMultiSampleRecord(VariableValuesDataRecord record, java.lang.String[] ar)
protected java.util.ArrayList<java.lang.String>	processVCFSampleInfo(java.lang.String line) process sample info, eventually returns list of sample names
protected VCFMultiSampleReader.vcf_version	processVFCVersionInfo(java.lang.String line) get vcf version
int	readElements(VioletApp app, java.io.Reader reader) Loads variants info

Methods inherited from class com.pacbio.secondary.vis.io.gff.variants.GFFVariantsReader

getDataPointForInterval, getVariantLabel

Methods inherited from class com.pacbio.secondary.vis.data.variableresolution.model.gff.GFFDataModel

clear, get, getDataInfo, getFileHeader, getFilePath, getMinMaxValues, getResults, invalidate, isValid, size, toCollection, validate

Methods inherited from class com.pacbio.secondary.vis.data.variableresolution.model.VariableResolutionDataModel

copyAsMarkerCollectionArray, detach, getNumItems, getResult, iterator

Methods inherited from class com.pacbio.secondary.vis.data.base.BaseDataModel

addChangeListener, fireChangeEvent, getDataType, getDataTypeAsString, getMarkersForContig, getNumContigs, hasData, isMarkerType, isModificationsType, isReadsType, isSummaryType, isVariantsType, removeChangeListener, setTypeAndNumContigs

Methods inherited from class java.lang.Object

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

Methods inherited from interface com.pacbio.secondary.vis.gui.evt.IChangeNotifier

addChangeListener, removeChangeListener

Field Detail

NUM_RESULTS

protected static final int NUM_RESULTS

See Also:

Constant Field Values

VCF_VERSION_TAG

protected static final java.lang.String VCF_VERSION_TAG

See Also:

Constant Field Values

VCF_CHROM_COL

protected final int VCF_CHROM_COL

See Also:

Constant Field Values

VCF_POS_COL

protected final int VCF_POS_COL

See Also:

Constant Field Values

VCF_ID_COL

protected final int VCF_ID_COL

See Also:

Constant Field Values

VCF_REF_COL

protected final int VCF_REF_COL

See Also:

Constant Field Values

VCF_ALT_COL

protected final int VCF_ALT_COL

See Also:

Constant Field Values

VCF_QUAL_COL

protected final int VCF_QUAL_COL

See Also:

Constant Field Values

VCF_FILTER_COL

protected final int VCF_FILTER_COL

See Also:

Constant Field Values

VCF_INFO_COL

protected final int VCF_INFO_COL

See Also:

Constant Field Values

VCF_FORMAT_COL

protected final int VCF_FORMAT_COL

See Also:

Constant Field Values

VCF_START_SAMPLE_COL

protected final int VCF_START_SAMPLE_COL

See Also:

Constant Field Values

VCF_FORMATS_SEPARATOR

protected static final java.lang.String VCF_FORMATS_SEPARATOR

See Also:

Constant Field Values

VCF_FORMATS_RSLT_SEPARATOR

protected static final java.lang.String VCF_FORMATS_RSLT_SEPARATOR

See Also:

Constant Field Values

VCF_FORMATS_GENOTYPE_SEPARATOR

protected static final java.lang.String VCF_FORMATS_GENOTYPE_SEPARATOR

See Also:

Constant Field Values

VCF_NO_SAMPLE_DATA

protected static final java.lang.String VCF_NO_SAMPLE_DATA

See Also:

Constant Field Values

VCF_COVERAGE_TAG

protected static final java.lang.String VCF_COVERAGE_TAG

See Also:

Constant Field Values

VCF_GT_RSLT

protected static final java.lang.String VCF_GT_RSLT

See Also:

Constant Field Values

VCF_AD_RSLT

protected static final java.lang.String VCF_AD_RSLT

See Also:

Constant Field Values

VCF_DP_RSLT

protected static final java.lang.String VCF_DP_RSLT

See Also:

Constant Field Values

VCF_GQ_RSLT

protected static final java.lang.String VCF_GQ_RSLT

See Also:

Constant Field Values

VCF_PL_RSLT

protected static final java.lang.String VCF_PL_RSLT

See Also:

Constant Field Values

file_version

protected VCFMultiSampleReader.vcf_version file_version

Constructor Detail

VCFMultiSampleReader

public VCFMultiSampleReader()

Method Detail

loadFromReader

public void loadFromReader(java.io.Reader reader,
                  java.lang.String file_name,
                  VioletApp app)
                    throws java.io.IOException,
                           FileFormatException

Overrides:

loadFromReader in class GFFVariantsReader

Throws:

java.io.IOException

FileFormatException

readElements

public int readElements(VioletApp app,
               java.io.Reader reader)
                 throws java.io.IOException,
                        FileFormatException

Description copied from class: GFFVariantsReader

Loads variants info

Overrides:

readElements in class GFFVariantsReader

Returns:

number of contigs in data file

Throws:

java.io.IOException

FileFormatException

processVCFHeaderInfo

protected void processVCFHeaderInfo(java.lang.String line)

process fileheader, get version

Parameters:

line -

processVCFSampleInfo

protected java.util.ArrayList<java.lang.String> processVCFSampleInfo(java.lang.String line)

process sample info, eventually returns list of sample names

Parameters:

line -

Returns:

processVFCVersionInfo

protected VCFMultiSampleReader.vcf_version processVFCVersionInfo(java.lang.String line)

get vcf version

Parameters:

line -

Returns:

processVCFBaseRecord

protected VariableValuesDataRecord processVCFBaseRecord(java.lang.String[] ar,
                                            int contig)

processes the base part of a vcf record, single sample

Parameters:

ar -

contig -

Returns:

processPacBioVersion

protected void processPacBioVersion(java.lang.String[] ar,
                        VariableValuesDataRecord record)

parses records in pacbio format

Parameters:

ar -

record -

processVCFMultiSampleRecord

protected void processVCFMultiSampleRecord(VariableValuesDataRecord record,
                               java.lang.String[] ar)