package io
Type Members
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abstract
class
FastqInputFormat extends FileInputFormat[Void, Text]
Licensed to Big Data Genomics (BDG) under one or more contributor license agreements.
Licensed to Big Data Genomics (BDG) under one or more contributor license agreements. See the NOTICE file distributed with this work for additional information regarding copyright ownership. The BDG licenses this file to you under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
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abstract
class
FastqRecordReader extends RecordReader[Void, Text]
A record reader for the interleaved FASTQ format.
A record reader for the interleaved FASTQ format.
Reads over an input file and parses interleaved FASTQ read pairs into a single Text output. This is then fed into the FastqConverter, which converts the single Text instance into two Alignments.
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final
class
InterleavedFastqInputFormat extends FastqInputFormat
This class is a Hadoop reader for "interleaved fastq" -- that is, fastq with paired reads in the same file, interleaved, rather than in two separate files.
This class is a Hadoop reader for "interleaved fastq" -- that is, fastq with paired reads in the same file, interleaved, rather than in two separate files. This makes it much easier to Hadoopily slice up a single file and feed the slices into an aligner. The format is the same as fastq, but records are expected to alternate between /1 and /2. As a precondition, we assume that the interleaved FASTQ files are always uncompressed; if the files are compressed, they cannot be split, and thus there is no reason to use the interleaved format.
This reader is based on the FastqInputFormat that's part of Hadoop-BAM, found at https://github.com/HadoopGenomics/Hadoop-BAM/blob/master/src/main/java/org/seqdoop/hadoop_bam/FastqInputFormat.java
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final
class
SingleFastqInputFormat extends FastqInputFormat
This class is a Hadoop reader for single read fastq.
This class is a Hadoop reader for single read fastq.
This reader is based on the FastqInputFormat that's part of Hadoop-BAM, found at https://github.com/HadoopGenomics/Hadoop-BAM/blob/master/src/main/java/org/seqdoop/hadoop_bam/FastqInputFormat.java