public final class SangerFastqReader
extends java.lang.Object
FastqVariant.FASTQ_SANGER
formatted sequences.Constructor and Description |
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SangerFastqReader() |
Modifier and Type | Method and Description |
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protected FastqVariant |
getVariant()
Return the FASTQ sequence format variant for this reader.
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java.lang.Iterable<Fastq> |
read(java.io.File file)
Read zero or more FASTQ formatted sequences from the specified file.
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java.lang.Iterable<Fastq> |
read(java.io.InputStream inputStream)
Read zero or more FASTQ formatted sequences from the specified input stream.
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java.lang.Iterable<Fastq> |
read(java.net.URL url)
Read zero or more FASTQ formatted sequences from the specified url.
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protected void |
validateDescription(FastqBuilder builder,
java.lang.String description,
int lineNumber)
Validate the specified description.
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protected void |
validateQuality(FastqBuilder builder,
java.lang.String quality,
int lineNumber)
Validate the specified quality scores.
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protected void |
validateRepeatDescription(FastqBuilder builder,
java.lang.String repeatDescription,
int lineNumber)
Validate the specified repeat description.
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protected void |
validateSequence(FastqBuilder builder,
java.lang.String sequence,
int lineNumber)
Validate the specified sequence.
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protected FastqVariant getVariant()
protected void validateDescription(FastqBuilder builder, java.lang.String description, int lineNumber) throws java.io.IOException
builder
- FASTQ formatted sequence builder, will not be nulldescription
- description to validate, will not be nulllineNumber
- current line number in input streamjava.io.IOException
- if the specified description is not validprotected void validateSequence(FastqBuilder builder, java.lang.String sequence, int lineNumber) throws java.io.IOException
builder
- FASTQ formatted sequence builder, will not be nullsequence
- sequence to validate, will not be nulllineNumber
- current line number in input streamjava.io.IOException
- if the specified sequence is not validprotected void validateRepeatDescription(FastqBuilder builder, java.lang.String repeatDescription, int lineNumber) throws java.io.IOException
builder
- FASTQ formatted sequence builder, will not be nullrepeatDescription
- repeat description to validate, will not be nulllineNumber
- current line number in input streamjava.io.IOException
- if the specified repeat description is not validprotected void validateQuality(FastqBuilder builder, java.lang.String quality, int lineNumber) throws java.io.IOException
builder
- FASTQ formatted sequence builder, will not be nullquality
- quality scores to validate, will not be nulllineNumber
- current line number in input streamjava.io.IOException
- if the specified quality scores are not validpublic final java.lang.Iterable<Fastq> read(java.io.File file) throws java.io.IOException
read
in interface FastqReader
file
- file to read from, must not be nulljava.io.IOException
- if an IO error occurspublic final java.lang.Iterable<Fastq> read(java.net.URL url) throws java.io.IOException
read
in interface FastqReader
url
- URL to read from, must not be nulljava.io.IOException
- if an IO error occurspublic final java.lang.Iterable<Fastq> read(java.io.InputStream inputStream) throws java.io.IOException
read
in interface FastqReader
inputStream
- input stream to read from, must not be nulljava.io.IOException
- if an IO error occurs