ADAM_2.12: Core 1.0.1 API < Back
 

# Packages

-  package root
  Definition Classes
    root
-  package org
  Definition Classes
    root
-  package bdgenomics
  Definition Classes
    org
-  package adam
  Definition Classes
    bdgenomics
-  package algorithms
  Definition Classes
    adam
-  package converters
  Definition Classes
    adam
-  package ds
  Definition Classes
    adam
-  package io
  Definition Classes
    adam
- FastqInputFormat
- FastqRecordReader
- InterleavedFastqInputFormat
- SingleFastqInputFormat
-  package models
  Definition Classes
    adam
-  package projections
  Definition Classes
    adam
-  package rich
  Definition Classes
    adam
-  package serialization
  Definition Classes
    adam
-  package sql
  Definition Classes
    adam
-  package util
  Definition Classes
    adam

p

org.bdgenomics.adam

# io 

#### package io

### Type Members

1.  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.

2.  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.

3.  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

4.  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

### Ungrouped