Merge pull request #9 from KirillKryukov/develop

Add support for multi-file archives

Compress.md

@@ -198,3 +198,18 @@ you have to switch to text mode (`--text`).
 Since both `--dna` and `--text` modes can be used for DNA data, which is better?
 Short answer: `--dna` is faster and has stronger compression.
 For details, see [this benchmark page](http://kirill-kryukov.com/study/naf/benchmark-text-vs-dna-Spur.html).
+
+## Can it compress multiple files into single archive?
+
+Yes, with the help of a [Multi-Multi-FASTA file format](https://github.com/KirillKryukov/mumu).
+It works similarly to gzipping a tar file:
+First you combine individual FASTA files into a single Multi-Multi-FASTA stream, then compress it using _ennaf_.
+Example commands:
+
+Compressing:<br>
+`mumu.pl --dir 'Helicobacter' 'Helicobacter pylori*' | ennaf -22 --text -o Hp.nafnaf`
+
+Decompressing and unpacking:<br>
+`unnaf Hp.nafnaf | mumu.pl --unpack --dir 'Helicobacter'`
+
+"**nafnaf**" is the recommended filename extension for such archives containing multiple FASTA files.

README.md

@@ -75,6 +75,20 @@ See `ennaf -h` and [Compression Manual](Compress.md) for detailed usage.
 
 See `unnaf -h` and [Decompression Manual](Decompress.md).
 
+## Compressing multiple files
+
+Working with multiple files is possible using [Multi-Multi-FASTA](https://github.com/KirillKryukov/mumu) as intermediate format.
+Example commands:
+
+Compressing:<br>
+`mumu.pl --dir 'Helicobacter' 'Helicobacter pylori*' | ennaf -22 --text -o Hp.nafnaf`
+
+Decompressing and unpacking:<br>
+`unnaf Hp.nafnaf | mumu.pl --unpack --dir 'Helicobacter'`
+
+Filename of NAF-compressed single file normally ends with a ".naf".
+To avoid ambiguity, **".nafnaf"** is the recommended suffix for multi-file NAF archives.
+
 ## Citation
 
 If you use NAF, please cite: