Add bed12 reader #57
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Add bed12 reader #57
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GarrettNg
commented
Nov 22, 2023
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| impl BatchBuilder for BedBatchBuilder { | ||
| // Noodles implements bed Record structs for bed3-bed9 and bed12. | ||
| // The following only handles bed12. | ||
| type Record<'a> = &'a bed::Record<12>; |
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We may need to deviate from oxbow's BatchBuilder to accomodate different record numbers.
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| color: StructBuilder::new( | ||
| vec![ | ||
| Field::new("r", DataType::UInt8, true), | ||
| Field::new("g", DataType::UInt8, true), | ||
| Field::new("b", DataType::UInt8, true), | ||
| ], | ||
| vec![ | ||
| Box::new(UInt8Builder::new()), | ||
| Box::new(UInt8Builder::new()), | ||
| Box::new(UInt8Builder::new()), | ||
| ], | ||
| ), |
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The StructBuilder for the arrow Struct Array takes the schema of the struct (the boolean sets the nullability of the field) and the builders for each field.
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| // Handle 1 or 2 missing colors | ||
| if colors.len() == 2 { | ||
| self.color | ||
| .field_builder::<UInt8Builder>(2) | ||
| .unwrap() | ||
| .append_null(); | ||
| } else if colors.len() == 1 { | ||
| self.color | ||
| .field_builder::<UInt8Builder>(1) | ||
| .unwrap() | ||
| .append_null(); | ||
| self.color | ||
| .field_builder::<UInt8Builder>(2) | ||
| .unwrap() | ||
| .append_null(); | ||
| } |
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A common issue when debugging struct arrays is having different numbers of records for the resulting Record Batch
| .unwrap() | ||
| .append_null(); | ||
| } | ||
| self.color.append(true); |
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Another arrow builder gotcha is the difference between append_value and append. Not all builders have both, but append is for the struct and append_value (in the for loop above) is for the subarray
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This PR handles spec compliant BED12 files, so it won't work as is with BED3-9 and optional fields. Handling the other types of bed files could require creating separate reader structs for each one that build off the previous and
impldifferent record column sizes as noodles does withBedNandRecord. There may be a simpler solution. In the interim, it is still easier to read bed files with a csv reader (delimited by\t), especially given the variety of column arrangements.Of note are 2 types of arrow builders used in the
BedBatchBuilderthat have not been used elsewhere in oxbow:StructBuilderfor Struct ArrayscolorfieldListBuilderfor listsblock_sizesandblock_startsfieldsThese builders could potentially be used for the nested fields of other readers in oxbow.