vcf

Class VcfWriter

java.lang.Object

vcf.VcfWriter

public final class VcfWriter
extends java.lang.Object

Class VcfWriter contains static methods for writing data in VCF 4.2 format.

Instances of class VcfWriter are not thread-safe.

Method Summary

Modifier and Type	Method and Description
static void	appendRecords(AlleleProbs alProbs, boolean[] isImputed, int start, int end, boolean printDS, boolean printGP, java.io.PrintWriter out) Writes the data in alProbs for markers with index between start (inclusive) and end (exclusive) to the specified PrintWriter.
static void	appendRecords(GenotypeValues gv, int start, int end, java.io.PrintWriter out) Writes the specified genotype data as VCF records to the specified PrintWriter.
static void	blockedAppendRecords(AlleleProbs alProbs, boolean[] isImputed, int start, int end, boolean printDS, boolean printGP, java.io.PrintWriter out) Writes the data in alProbs for markers with index between start (inclusive) and end (exclusive) to the specified PrintWriter.
static void	printFixedFieldsGT(Marker marker, java.io.PrintWriter out) Prints the first 9 VCF record fields for the specified marker to the specified PrintWriter.
static void	writeMetaLines(java.lang.String[] sampleIds, java.lang.String source, boolean printGT, boolean printGP, boolean printGL, java.io.PrintWriter out) Writes VCF meta-information lines and header line to the specified PrintWriter.
static void	writeMetaLinesGT(java.lang.String[] sampleIds, java.lang.String source, java.io.PrintWriter out) Writes VCF meta-information lines and header line to the specified PrintWriter.

Methods inherited from class java.lang.Object

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

Method Detail

writeMetaLinesGT

public static void writeMetaLinesGT(java.lang.String[] sampleIds,
                                    java.lang.String source,
                                    java.io.PrintWriter out)

Writes VCF meta-information lines and header line to the specified PrintWriter. Only one FORMAT subfield, the GT subfield, is described in the meta-information lines.

Parameters:

sampleIds - the sample identifiers

source - a description of the data source, or null if no description is to be printed

out - the PrintWriter to which VCF meta-information lines will be written

Throws:

java.lang.NullPointerException - if out == null

java.lang.NullPointerException - if sampleIds == null, or if sampleIds[j] == null for any j satisfying (0 <= j && j < <sampleIds.length)

writeMetaLines

public static void writeMetaLines(java.lang.String[] sampleIds,
                                  java.lang.String source,
                                  boolean printGT,
                                  boolean printGP,
                                  boolean printGL,
                                  java.io.PrintWriter out)

Writes VCF meta-information lines and header line to the specified PrintWriter.

Parameters:

sampleIds - the sample identifiers

source - a description of the data source, or null if no description is to be printed

printGT - true if the meta-information lines will describe the GT FORMAT subfield and false otherwise

printGP - true if the meta-information lines will describe the GP FORMAT subfield and false otherwise

printGL - true if the meta-information lines will describe the GL FORMAT subfield and false otherwise

out - the PrintWriter to which VCF meta-information lines will be written.

Throws:

java.lang.NullPointerException - if out == null

java.lang.NullPointerException - if sampleIds == null, or if sampleIds[j] == null for any j satisfying (0 <= j && j < sampleIds.length)

appendRecords

public static void appendRecords(GenotypeValues gv,
                                 int start,
                                 int end,
                                 java.io.PrintWriter out)

Writes the specified genotype data as VCF records to the specified PrintWriter.

Parameters:

gv - the scaled sample posterior genotype probabilities

start - the starting marker index (inclusive)

end - the ending marker index (exclusive)

out - the PrintWriter to which VCF records will be written.

Throws:

java.lang.IllegalArgumentException - if haps.markers().equals(gv.markers()) == false

java.lang.IndexOutOfBoundsException - if (start < 0 || start > end || end > haps.nMarkers())

java.lang.NullPointerException - if (gv == null || out == null)

appendRecords

public static void appendRecords(AlleleProbs alProbs,
                                 boolean[] isImputed,
                                 int start,
                                 int end,
                                 boolean printDS,
                                 boolean printGP,
                                 java.io.PrintWriter out)

Writes the data in alProbs for markers with index between start (inclusive) and end (exclusive) to the specified PrintWriter.

Parameters:

alProbs - the estimated haplotype allele probabilities

isImputed - an array of length alProbs.nMarkers() whose j-th element is true if the corresponding marker is imputed, and false otherwise

start - the starting marker index (inclusive)

end - the ending marker index (exclusive)

printDS - true if the DS field should be printed, and false otherwise

printGP - true if the GP field should be printed, and false otherwise

out - the PrintWriter to which VCF records will be written

Throws:

java.lang.IllegalArgumentException - if isImputed.length != alProbs.nMarkers()

java.lang.IndexOutOfBoundsException - if (start < 0 || start > end || end > alProbs.nMarkers())

java.lang.NullPointerException - if alProbs == null || isImputed == null || out == null

blockedAppendRecords

public static void blockedAppendRecords(AlleleProbs alProbs,
                                        boolean[] isImputed,
                                        int start,
                                        int end,
                                        boolean printDS,
                                        boolean printGP,
                                        java.io.PrintWriter out)

Writes the data in alProbs for markers with index between start (inclusive) and end (exclusive) to the specified PrintWriter.

Parameters:

alProbs - the estimated haplotype allele probabilities

isImputed - an array of length alProbs.nMarkers() whose j-th element is true if the corresponding marker is imputed, and false otherwise

start - the starting marker index (inclusive)

end - the ending marker index (exclusive)

printDS - true if the DS field should be printed, and false otherwise

printGP - true if the GP field should be printed, and false otherwise

out - the PrintWriter to which VCF records will be written

Throws:

java.lang.IllegalArgumentException - if isImputed.length != alProbs.nMarkers()

java.lang.IndexOutOfBoundsException - if (start < 0 || start > end || end > alProbs.nMarkers())

java.lang.NullPointerException - if alProbs == null || isImputed == null || out == null

printFixedFieldsGT

public static void printFixedFieldsGT(Marker marker,
                                      java.io.PrintWriter out)

Prints the first 9 VCF record fields for the specified marker to the specified PrintWriter. Only one VCF FORMAT subfield, the GT subfield, is printed.

Parameters:

marker - a marker

out - the PrintWriter to which the first 9 VCF record fields will be written

Throws:

java.lang.NullPointerException - if marker == null || out == null