Uses of Package
org.seqdoop.hadoop_bam

Packages that use org.seqdoop.hadoop_bam

Package	Description
org.seqdoop.hadoop_bam
org.seqdoop.hadoop_bam.util

Classes in org.seqdoop.hadoop_bam used by org.seqdoop.hadoop_bam

Class and Description
AnySAMOutputFormat An abstract OutputFormat for SAM and BAM files.
BAMOutputFormat Currently this only locks down the value type of the OutputFormat: contains no functionality.
BAMRecordWriter A base RecordWriter for BAM records.
BCFRecordWriter A base RecordWriter for compressed BCF.
CRAMOutputFormat Currently this only locks down the value type of the OutputFormat: contains no functionality.
CRAMRecordWriter A base RecordWriter for CRAM records.
FormatConstants.BaseQualityEncoding Encodings for base quality formats.
LazyParsingGenotypesContext You need to call getParser().setHeader() here before trying to decode() a GenotypesContext in any VariantContext that came about via VariantContextWritable.readFields().
LazyParsingGenotypesContext.HeaderDataCache
LazyParsingGenotypesContext.Parser
ReferenceFragment
SAMFormat Describes a SAM format.
SAMRecordWritable A Writable SAMRecord.
SAMRecordWriter A base RecordWriter for SAM records.
SequencedFragment
VariantContextWritable VariantContexts read here have LazyGenotypesContexts, which need to have a header set before the genotype data in the VariantContexts can be decoded.
VCFFormat Describes a VCF format.
VCFOutputFormat An abstract OutputFormat for VCF and BCF files.
VCFRecordWriter A base RecordWriter for VCF.

Classes in org.seqdoop.hadoop_bam used by org.seqdoop.hadoop_bam.util

Class and Description
SAMFormat Describes a SAM format.