This method should create a new SequenceDictionary from any parquet file which contains records that have the requisite reference{Name,Id,Length,Url} fields.
This method should create a new SequenceDictionary from any parquet file which contains records that have the requisite reference{Name,Id,Length,Url} fields.
(If the path is a BAM or SAM file, and the implicit type is an Read, then it just defaults to reading the SequenceDictionary out of the BAM header in the normal way.)
The type of records to return
The path to the input data
A sequenceDictionary containing the names and indices of all the sequences to which the records in the corresponding file are aligned.
This method will create a new RDD.
This method will create a new RDD.
The type of records to return
The path to the input data
An optional pushdown predicate to use when reading the data
An option projection schema to use when reading the data
An RDD with records of the specified type
Searches a path recursively, returning the names of all directories in the tree whose name matches the given regex.
Searches a path recursively, returning the names of all directories in the tree whose name matches the given regex.
The path to begin the search at
A regular expression
A sequence of Path objects corresponding to the identified directories.
Takes a sequence of Path objects (e.
Takes a sequence of Path objects (e.g. the return value of findFiles). Treats each path as corresponding to a Read set -- loads each Read set, converts each set to use the same SequenceDictionary, and returns the union of the RDDs.
(GenomeBridge is using this to load BAMs that have been split into multiple files per sample, for example, one-BAM-per-chromosome.)
The locations of the parquet files to load
a single RDD[Read] that contains the union of the AlignmentRecords in the argument paths.