org.broadinstitute.hellbender.tools.spark.sv.utils

Class SVFastqUtils

java.lang.Object

org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils

public class SVFastqUtils
extends java.lang.Object

Memory-economical utilities for producing a FASTQ file.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SVFastqUtils.FastqRead
static class	SVFastqUtils.Mapping

Field Summary

Fields

Modifier and Type	Field and Description
static char	FRAGMENT_NUMBER_SEPARATOR_CHR
static char	HEADER_FIELD_EQUAL_CHR
static java.lang.String	HEADER_FIELD_LIST_SEPARATOR_STR
static char	HEADER_FIELD_SEPARATOR_CHR
static java.lang.String	HEADER_FIELD_SEPARATOR_REGEXP
static char	HEADER_PREFIX_CHR

Constructor Summary

Constructors

Constructor and Description
SVFastqUtils()

Method Summary

Modifier and Type	Method and Description
static java.util.List<SVFastqUtils.FastqRead>	readFastqFile(java.lang.String fileName)
static java.util.List<SVFastqUtils.FastqRead>	readFastqStream(java.io.BufferedReader reader, java.lang.String fileName)
static java.lang.String	readToFastqSeqId(GATKRead read, boolean includeMappingLocation) Convert a read's name into a FASTQ record sequence ID
static void	writeFastqFile(java.lang.String fileName, java.util.Iterator<SVFastqUtils.FastqRead> fastqReadItr) Write a list of FASTQ records into a file.
static void	writeFastqStream(java.io.OutputStream writer, java.util.Iterator<SVFastqUtils.FastqRead> fastqReadItr)

Methods inherited from class java.lang.Object

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

Field Detail

HEADER_PREFIX_CHR

public static final char HEADER_PREFIX_CHR

See Also:

Constant Field Values

FRAGMENT_NUMBER_SEPARATOR_CHR

public static final char FRAGMENT_NUMBER_SEPARATOR_CHR

See Also:

Constant Field Values

HEADER_FIELD_SEPARATOR_CHR

public static final char HEADER_FIELD_SEPARATOR_CHR

See Also:

Constant Field Values

HEADER_FIELD_SEPARATOR_REGEXP

public static final java.lang.String HEADER_FIELD_SEPARATOR_REGEXP

See Also:

Constant Field Values

HEADER_FIELD_EQUAL_CHR

public static final char HEADER_FIELD_EQUAL_CHR

See Also:

Constant Field Values

HEADER_FIELD_LIST_SEPARATOR_STR

public static final java.lang.String HEADER_FIELD_LIST_SEPARATOR_STR

See Also:

Constant Field Values

Constructor Detail

SVFastqUtils

public SVFastqUtils()

Method Detail

readFastqFile

public static java.util.List<SVFastqUtils.FastqRead> readFastqFile(java.lang.String fileName)

readFastqStream

public static java.util.List<SVFastqUtils.FastqRead> readFastqStream(java.io.BufferedReader reader,
                                                                     java.lang.String fileName)
                                                              throws java.io.IOException

Throws:

java.io.IOException

readToFastqSeqId

public static java.lang.String readToFastqSeqId(GATKRead read,
                                                boolean includeMappingLocation)

Convert a read's name into a FASTQ record sequence ID

writeFastqFile

public static void writeFastqFile(java.lang.String fileName,
                                  java.util.Iterator<SVFastqUtils.FastqRead> fastqReadItr)

Write a list of FASTQ records into a file.

writeFastqStream

public static void writeFastqStream(java.io.OutputStream writer,
                                    java.util.Iterator<SVFastqUtils.FastqRead> fastqReadItr)
                             throws java.io.IOException

Throws:

java.io.IOException