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SPRING2 Decompression Guide

This guide focuses on restoring .sp archives.

Basic Syntax

spring2 -d -i <archive.sp> [-o <outputs...>]

Decompression uses --input / -i and does not use --R1, --R2, --R3, --I1, or --I2.

Basic Examples

Restore a single-end archive:

spring2 -d -i reads.sp -o restored.fastq

Restore a paired-end archive:

spring2 -d -i reads.sp -o restored_1.fastq restored_2.fastq

If you omit --output, SPRING2 uses the original input names stored in the archive metadata when possible.

Grouped Archive Output Naming

Grouped archives are restored with one command.

If you provide a single prefix:

spring2 -d -i run.sp -o run_out

SPRING2 expands that to:

  • run_out.R1
  • run_out.R2
  • run_out.R3 when a read-3 lane exists
  • run_out.I1 when an index lane exists
  • run_out.I2 when a second index lane exists

Example:

spring2 -d -i run.sp -o run_out

Gzip Restoration Rules

SPRING2 stores input gzip metadata and uses it during decompression.

Behavior summary:

  • If the original input stream was gzipped, decompression can restore gzipped output.
  • If you explicitly give output names ending in .gz, the restored output is gzipped.
  • Preview mode reports stored gzip and BGZF metadata for each stream.

Example:

spring2 -d -i reads.sp -o restored_1.fastq.gz restored_2.fastq.gz

Force Plain Output

Use --unzip / -u to force plain-text FASTQ or FASTA output even when the original input was gzipped:

spring2 -d -u -i reads.sp -o restored.fastq

Integrity Verification

Normal decompression already verifies stored CRC32 digests for:

  • sequences
  • quality values
  • identifiers

If verification fails, decompression aborts with an integrity error.

Logging

Use the same logging levels available during compression:

spring2 -d -i reads.sp --verbose info
spring2 -d -i reads.sp --verbose debug

See Also