obitools4/autodoc/docmd/pkg/obiformats/file_chunk_write.md

WriteFileChunk Function — Semantic Description

The WriteFileChunk function in the obiformats package implements a thread-safe, ordered chunk writer for streaming data to an io.WriteCloser. It accepts a destination writer and a flag indicating whether the writer should be closed upon completion.

• Input:

  • writer: An io.WriteCloser (e.g., file, buffer) to which data chunks are written.
  • toBeClosed: Boolean flag specifying if the writer should be closed after all chunks are processed.

• Core Behavior:

  • Launches a goroutine that consumes FileChunk items from an unbuffered channel (chunk_channel).
  • Ensures strict sequential ordering of chunks by their Order field (intended for reassembly after parallel or out-of-order processing).
  • If a chunk arrives in order (chunk.Order == nextToPrint), it is immediately written.
  • Out-of-order chunks are buffered in a map (toBePrinted) until their predecessor arrives.

• Buffer Management:

  • After writing an in-order chunk, the function checks for newly consecutive buffered chunks and writes them greedily (e.g., if order 2 arrives, it triggers writing of buffered orders 3,4,... as available).

• Error Handling:

  • Logs fatal errors on write failures or writer closure issues using log.Fatalf.

• Cleanup & Lifecycle:

  • Closes the underlying writer if requested and unregisters a pipe registration (via obiutils) to signal end-of-stream.
  • Returns the input channel, enabling external producers to stream FileChunk structs.

• Use Case:
  Designed for robust, ordered reconstruction of large binary/data streams (e.g., sequencing reads) in OBITools4 pipelines, especially where parallel chunking and reassembly occur.