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[encoder] fix pileup encoder docs
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Joyjit Daw committed Jun 8, 2020
1 parent b8b5546 commit fecd041
Showing 1 changed file with 9 additions and 5 deletions.
14 changes: 9 additions & 5 deletions variantworks/sample_encoder.py
Original file line number Diff line number Diff line change
Expand Up @@ -58,16 +58,20 @@ class Layer(Enum):
Values:
READ : Encode each aligned read as a row of the pileup. The bases in the
read are encoded using a base_encoder dict passed into the class. The reads
in the row are positioned according to the pileup alignment.\n
in the row are positioned according to the pileup alignment.
BASE_QUALITY : Encode the base quality of each aligned read in the pileup. Base
qualities of each read are added to a new row, following the same positioning as for READS. The base
qualities are normalized to [0,1] (using max value of 93 per SAM format).
Missing base quality is set to 0.\n
Missing base quality is set to 0.
MAPPING_QUALITY : Mapping quality of a read is encoded at each nucleotide position of the read. Mapping
quality values are noramlize to [0,1] (assuming max value of 50).
Missing mapping quality is set to 0.\n
REFERENCE : Only the reference allele location is encoded in each row.\n
ALLELE : Only the alt allele location is encoded in each row.\n
Missing mapping quality is set to 0.
REFERENCE : Only the reference allele location is encoded in each row.
ALLELE : Only the alt allele location is encoded in each row.
"""

READ = 0
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