Package 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	Description
static void	appendRecords(GT phasedTarg, int start, int end, java.io.PrintWriter out)	Writes the data in phased genotypes for the specified markers to the specified PrintWriter.
static void	appendRecords(Samples samples, GTRec[] recs, java.io.PrintWriter out)	Writes the data in phased genotypes for the specified markers 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 ds, boolean ap, boolean gp, boolean gl, 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 ds,
                                  boolean ap,
                                  boolean gp,
                                  boolean gl,
                                  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

ds - { @code true} if the meta-information lines will describe the DS FORMAT subfield and false otherwise

ap - true if the meta-information lines will describe the AP1 and AP2 FORMAT subfields and false otherwise

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

gl - 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(GT phasedTarg,
                                 int start,
                                 int end,
                                 java.io.PrintWriter out)

Writes the data in phased genotypes for the specified markers to the specified PrintWriter.

Parameters:

phasedTarg - the estimated haplotype allele 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 phasedTarg.isPhased() == false

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

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

appendRecords

public static void appendRecords(Samples samples,
                                 GTRec[] recs,
                                 java.io.PrintWriter out)

Writes the data in phased genotypes for the specified markers to the specified PrintWriter.

Parameters:

samples - the list of samples

recs - the estimated haplotype allele probabilities

out - the PrintWriter to which VCF records will be written

Throws:

java.lang.IllegalArgumentException - if phasedTarg.isPhased() == false

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

java.lang.NullPointerException - if phasedTarg == 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