CLI Reference
fq-compressor provides four main commands: compress, decompress, info, and verify.
Global Options
| Option | Description |
|---|---|
-h, --help |
Show help message |
--version |
Show version information |
-v, --verbose |
Enable verbose logging |
compress
Compress a FASTQ file into the .fqc archive format.
fqc compress [OPTIONS] -i <input> -o <output>
Options
| Option | Type | Default | Description |
|---|---|---|---|
-i, --input |
PATH | required | Input FASTQ file (.fastq, .fq, .fastq.gz, .fq.gz) |
-o, --output |
PATH | required | Output .fqc archive file |
-I, --input2 |
PATH | — | Second input file for paired-end data |
-t, --threads |
INT | CPU cores | Number of parallel threads |
-l, --level |
INT | 5 | Compression level (1=fast, 9=best) |
--memory-limit |
INT | 8192 | Memory budget in MB |
--pipeline |
FLAG | off | Enable 3-stage parallel pipeline |
--no-reorder |
FLAG | off | Disable read reordering (preserves original order) |
Examples
# Basic compression
fqc compress -i reads.fastq -o reads.fqc
# High compression with 4 threads
fqc compress -i reads.fastq -o reads.fqc -l 9 -t 4
# Paired-end compression
fqc compress -i R1.fastq.gz -I R2.fastq.gz -o paired.fqc
# Pipeline mode with memory limit
fqc compress -i large.fastq -o large.fqc --pipeline --memory-limit 16384
decompress
Decompress a .fqc archive back to FASTQ format.
fqc decompress [OPTIONS] -i <input> -o <output>
Options
| Option | Type | Default | Description |
|---|---|---|---|
-i, --input |
PATH | required | Input .fqc archive file |
-o, --output |
PATH | required | Output FASTQ file |
-O, --output2 |
PATH | — | Second output file for paired-end data |
-t, --threads |
INT | CPU cores | Number of parallel threads |
--range |
STR | — | Extract specific read range (e.g., 1000:2000) |
--pipeline |
FLAG | off | Enable 3-stage parallel pipeline |
Examples
# Basic decompression
fqc decompress -i reads.fqc -o reads.fastq
# Random access: extract reads 500-1500
fqc decompress -i reads.fqc --range 500:1500 -o subset.fastq
# Paired-end decompression
fqc decompress -i paired.fqc -o R1.fastq -O R2.fastq
info
Display metadata and statistics about a .fqc archive.
fqc info [OPTIONS] <input>
Output Fields
| Field | Description |
|---|---|
| Read count | Total number of reads in the archive |
| Original size | Uncompressed size in bytes |
| Compressed size | Archive size in bytes |
| Compression ratio | Original / Compressed |
| Bits per base | Average compressed bits per DNA base |
| Block count | Number of independent blocks |
| Read length | Min / Max / Median read length |
verify
Verify the integrity of a .fqc archive.
fqc verify [OPTIONS] <input>
Performs comprehensive integrity validation:
- File header magic number and version check
- Block-level CRC32 verification
- Index consistency check
- Footer checksum validation
Exit Codes
| Code | Meaning |
|---|---|
| 0 | Success |
| 1 | I/O error |
| 2 | Format error |
| 3 | Compression error |
| 4 | Validation error |
| 5 | Internal error |