Pacbio Registered FileTypes
- class
pbcommand.models.
FileTypes
[source]¶Bases:
object
Registry of all PacBio Files types
This needs to be cleaned up and solidified. The old pre-SA3 file types need to be deleted.
ALIGNMENT_CMP_H5
= <FileType id=PacBio.FileTypes.alignment_cmp_h5 name=alignments >¶
BAM
= <FileType id=PacBio.FileTypes.bam name=alignments >¶
BAMBAI
= <FileType id=PacBio.FileTypes.bam_bai name=alignments >¶
BAM_ALN
= <FileType id=PacBio.AlignmentFile.AlignmentBamFile name=file >¶
BAM_CCS
= <FileType id=PacBio.ConsensusReadFile.ConsensusReadBamFile name=file >¶
BAM_CCS_ALN
= <FileType id=PacBio.AlignmentFile.ConsensusAlignmentBamFile name=file >¶
BAM_SUB
= <FileType id=PacBio.SubreadFile.SubreadBamFile name=file >¶
BAM_TRANSCRIPT
= <FileType id=PacBio.TranscriptFile.TranscriptBamFile name=file >¶
BAM_TRANSCRIPT_ALN
= <FileType id=PacBio.AlignmentFile.TranscriptAlignmentBamFile name=file >¶
BAX
= <FileType id=PacBio.SubreadFile.BaxFile name=file >¶
BAZ
= <FileType id=PacBio.ReadFile.BazFile name=file >¶
BED
= <FileType id=PacBio.FileTypes.bed name=file >¶
BIGWIG
= <FileType id=PacBio.FileTypes.bigwig name=annotations >¶
BLASR_M4
= <FileType id=PacBio.FileTypes.blasr_file name=blasr >¶
CFG
= <FileType id=PacBio.FileTypes.cfg name=config >¶
CHUNK
= <FileType id=PacBio.FileTypes.CHUNK name=chunk >¶
COND_RESEQ
= <FileType id=PacBio.FileTypes.COND_RESEQ name=file >¶
CONTIG_FA
= <FileType id=PacBio.ContigFile.ContigFastaFile name=file >¶
CSV
= <FileType id=PacBio.FileTypes.csv name=file >¶
DATASTORE
= <FileType id=PacBio.FileTypes.Datastore name=file >¶
DS_ALIGN
= <DataSetFileType id=PacBio.DataSet.AlignmentSet name=file >¶
DS_ALIGN_CCS
= <DataSetFileType id=PacBio.DataSet.ConsensusAlignmentSet name=file >¶
DS_ALIGN_TRANSCRIPT
= <DataSetFileType id=PacBio.DataSet.TranscriptAlignmentSet name=file >¶
DS_BARCODE
= <DataSetFileType id=PacBio.DataSet.BarcodeSet name=file >¶
DS_CCS
= <DataSetFileType id=PacBio.DataSet.ConsensusReadSet name=file >¶
DS_CONTIG
= <DataSetFileType id=PacBio.DataSet.ContigSet name=file >¶
DS_GMAP_REF
= <DataSetFileType id=PacBio.DataSet.GmapReferenceSet name=file >¶
DS_REF
= <DataSetFileType id=PacBio.DataSet.ReferenceSet name=file >¶
DS_SUBREADS
= <DataSetFileType id=PacBio.DataSet.SubreadSet name=file >¶
DS_SUBREADS_H5
= <DataSetFileType id=PacBio.DataSet.HdfSubreadSet name=file >¶
DS_TRANSCRIPT
= <DataSetFileType id=PacBio.DataSet.TranscriptSet name=file >¶
FASTA
= <FileType id=PacBio.FileTypes.Fasta name=file >¶
FASTA_ADAPTER
= <FileType id=PacBio.SubreadFile.AdapterFastaFile name=file >¶
FASTA_BC
= <FileType id=PacBio.BarcodeFile.BarcodeFastaFile name=file >¶
FASTA_CONTROL
= <FileType id=PacBio.SubreadFile.ControlFastaFile name=file >¶
FASTA_REF
= <FileType id=PacBio.ReferenceFile.ReferenceFastaFile name=file >¶
FASTQ
= <FileType id=PacBio.FileTypes.Fastq name=file >¶
FOFN
= <FileType id=PacBio.FileTypes.generic_fofn name=generic >¶
GCHUNK
= <FileType id=PacBio.FileTypes.GCHUNK name=gather_chunk >¶
GFF
= <FileType id=PacBio.FileTypes.gff name=file >¶
GZIP
= <FileType id=PacBio.FileTypes.gzip name=file >¶
H5
= <FileType id=PacBio.FileTypes.h5 name=file >¶
HTML
= <FileType id=PacBio.FileTypes.html name=file >¶
INPUT_XML
= <FileType id=PacBio.FileTypes.input_xml name=input >¶
I_BAI
= <FileType id=PacBio.Index.BamIndex name=file >¶
I_FCI
= <FileType id=PacBio.Index.FastaContigIndex name=file >¶
I_INDEXER
= <FileType id=PacBio.Index.Indexer name=file >¶
I_NGMLR_ENC
= <FileType id=PacBio.Index.NgmlrRefEncoded name=file >¶
I_NGMLR_TAB
= <FileType id=PacBio.Index.NgmlrRefTable name=file >¶
I_PBI
= <FileType id=PacBio.Index.PacBioIndex name=file >¶
I_SAM
= <FileType id=PacBio.Index.SamIndex name=file >¶
I_SAW
= <FileType id=PacBio.Index.SaWriterIndex name=file >¶
JSON
= <FileType id=PacBio.FileTypes.json name=file >¶
LOG
= <FileType id=PacBio.FileTypes.log name=file >¶
MOVIE_FOFN
= <FileType id=PacBio.FileTypes.movie_fofn name=movie >¶
PICKLE
= <FileType id=PacBio.FileTypes.pickle name=file >¶
PLS
= <FileType id=PacBio.ReadFile.PulseFile name=file >¶
REF_ENTRY_XML
= <FileType id=PacBio.FileTypes.reference_info_xml name=reference.info.xml >¶
REPORT
= <FileType id=PacBio.FileTypes.JsonReport name=report >¶
RGN_FOFN
= <FileType id=PacBio.FileTypes.rgn_fofn name=region >¶
RS_MOVIE_XML
= <FileType id=PacBio.FileTypes.rs_movie_metadata name=file >¶
SAM
= <FileType id=PacBio.FileTypes.sam name=alignments >¶
SCHUNK
= <FileType id=PacBio.FileTypes.SCHUNK name=scatter_chunk >¶
STS_H5
= <FileType id=PacBio.SubreadFile.ChipStatsH5File name=file >¶
STS_XML
= <FileType id=PacBio.SubreadFile.ChipStatsFile name=file >¶
SVG
= <FileType id=PacBio.FileTypes.svg name=file >¶
TGZ
= <FileType id=PacBio.FileTypes.tgz name=file >¶
TRC
= <FileType id=PacBio.ReadFile.TraceFile name=file >¶
TXT
= <FileType id=PacBio.FileTypes.txt name=file >¶
VCF
= <FileType id=PacBio.FileTypes.vcf name=file >¶
XML
= <FileType id=PacBio.FileTypes.xml name=file >¶
ZIP
= <FileType id=PacBio.FileTypes.zip name=file >¶