oxbow
oxbow copied to clipboard
Add bed12 reader
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 impl
different record column sizes as noodles does with BedN
and Record
. 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 BedBatchBuilder
that have not been used elsewhere in oxbow:
-
StructBuilder
for Struct Arrays- used for the
color
field
- used for the
-
ListBuilder
for lists- used for the
block_sizes
andblock_starts
fields
- used for the
These builders could potentially be used for the nested fields of other readers in oxbow.