SPRING2 Archive Inspection¶
SPRING2 provides a preview mode for inspecting archive metadata without writing reconstructed FASTQ or FASTA files to disk.
Preview Mode¶
Use preview mode with exactly one archive input:
Preview mode reports metadata such as:
- original input names
- custom note
- assay type and detection confidence
- compression ratio
- read counts and maximum read length
- preservation flags for order, IDs, and quality
- quality mode
- compression level
- gzip or BGZF metadata for original compressed inputs
For grouped archives, preview also reports additional lanes such as R3, I1,
and I2.
Audit Mode¶
Preview mode can run a full archive audit without writing restored FASTQ files:
This reconstructs records in memory and verifies stored digests. It is useful for checking archive health after transfer or long-term storage.
What Metadata Can Indicate¶
Preview output may also show assay-aware transforms that were applied during compression, including:
- extracted cellular barcode prefixes
- grouped sc-RNA index ID reconstruction
- ATAC adapter stripping
These are restoration-aware transforms: the archive stores enough information to reconstruct original records for lossless archives.
Gzip and BGZF Reporting¶
When the original input stream was gzipped, preview can display details like:
- gzip header information
- original embedded filename
- member count
- compressed and uncompressed sizes
- BGZF detection and block size
This is especially useful when validating archives created from pipeline tools that emit BGZF-style gzip members.
Notes¶
Archive notes added with --note are shown in preview output. This is a good
place to record batch IDs, sample provenance, or workflow labels.
Archive Format Caveat¶
.sp archives are technically tar containers with compressed internal members,
but they should be inspected with SPRING2 rather than generic tar tooling when
you care about semantic metadata and integrity reporting.