('*.bam', self._guess_bam_view),
('junctions.bed', 'Junctions'),
('*.jnct', 'Junctions'),
+ ('*.unique.bigwig', None),
('*.plus.bigwig', 'PlusSignal'),
('*.minus.bigwig', 'MinusSignal'),
('*.bigwig', 'Signal'),
('*.?ufflinks-0.9.0?genes.expr', 'GeneDeNovo'),
('*.?ufflinks-0.9.0?transcripts.expr', 'TranscriptDeNovo'),
('*.?ufflinks-0.9.0?transcripts.gtf', 'GeneModel'),
- ('*.GENCODE-v3c?genes.expr', 'GeneGencV3c'),
- ('*.GENCODE-v3c?transcripts.expr', 'TranscriptGencV3c'),
- ('*.GENCODE-v4?genes.expr', 'GeneGencV4'),
- ('*.GENCODE-v4?transcripts.expr', 'TranscriptGencV4'),
- ('*.GENCODE-v4?transcript.expr', 'TranscriptGencV4'),
+ ('*.GENCODE-v3c?genes.expr', 'GeneGCV3c'),
+ ('*.GENCODE-v3c?transcript*.expr', 'TranscriptGCV3c'),
+ ('*.GENCODE-v3c?transcript*.gtf', 'TranscriptGencV3c'),
+ ('*.GENCODE-v4?genes.expr', None), #'GeneGCV4'),
+ ('*.GENCODE-v4?transcript*.expr', None), #'TranscriptGCV4'),
+ ('*.GENCODE-v4?transcript*.gtf', None), #'TranscriptGencV4'),
('*_1.75mers.fastq', 'FastqRd1'),
('*_2.75mers.fastq', 'FastqRd2'),
('*_r1.fastq', 'FastqRd1'),
"GeneModel": {"MapAlgorithm": ma},
"GeneDeNovo": {"MapAlgorithm": ma},
"TranscriptDeNovo": {"MapAlgorithm": ma},
- "GeneGencV3c": {"MapAlgorithm": ma},
+ "GeneGCV3c": {"MapAlgorithm": ma},
+ "TranscriptGCV3c": {"MapAlgorithm": ma},
"TranscriptGencV3c": {"MapAlgorithm": ma},
- "GeneGencV4": {"MapAlgorithm": ma},
- "TranscriptGencV4": {"MapAlgorithm": ma},
+ "GeneGCV4": {"MapAlgorithm": ma},
+ "TranscriptGCV4": {"MapAlgorithm": ma},
"FastqRd1": {"MapAlgorithm": "NA", "type": "fastq"},
"FastqRd2": {"MapAlgorithm": "NA", "type": "fastq"},
"Fastq": {"MapAlgorithm": "NA", "type": "fastq" },
- "GeneModel": {"MapAlgorithm": ma},
"InsLength": {"MapAlgorithm": ma},
}
# view name is one of the attributes