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Module Biocaml_bam.Transform (.ml)

module Transform:

sig

The low-level Transform.t implementations.

val raw_to_item  : unit ->
 (Biocaml_bam.raw_item,
 (Biocaml_sam_deprecated.item, [> Biocaml_bam.Error.raw_to_item ])
 Core.Std.Result.t)
 Biocaml_transform.t

Create a transform that lifts raw_items to the higher-level representation defined in the Biocaml_sam module.

val string_to_raw  : ?zlib_buffer_size:int ->
 unit ->
 (string,
 (Biocaml_bam.raw_item,
 [> `bam of Biocaml_bam.Error.raw_bam | `unzip of Biocaml_zip.Error.unzip ])
 Core.Std.Result.t)
 Biocaml_transform.t

Create a transform that parses a BAM file. The zlib_buffer_size is passed to the Biocaml_zip module.

val item_to_raw  : unit ->
 (Biocaml_sam_deprecated.item,
 (Biocaml_bam.raw_item, [> Biocaml_bam.Error.item_to_raw ]) Core.Std.Result.t)
 Biocaml_transform.t

Create a transform that downgrades Sam.items to raw_items.

val raw_to_string  : ?gzip_level:int ->
 ?zlib_buffer_size:int ->
 unit -> (Biocaml_bam.raw_item, string) Biocaml_transform.t

Create a transform that "prints" raw_items in the BAM format. The gzip_level and zlib_buffer_size options are passed to the Biocaml_zip module.

end