MFCompress

MFCompress is a parallelizable compression tool specifically designed for FASTA and multi-FASTA files using finite-context models and arithmetic coding.

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📦 Package Contents

File	Description
MFCompressC.c	Main program for encoding (compressor).
MFCompressD.c	Main program for decoding (decompressor).
Makefile.linux	Linux Makefile. Build with make -f Makefile.linux.
Makefile.win32	Cross-compilation Makefile for Windows 32-bit. Requires MinGW-w64.
Makefile.win64	Cross-compilation Makefile for Windows 64-bit. Requires MinGW-w64.
arith_aux.*	Auxiliary arithmetic coding functions.
arith.*	Core arithmetic coding implementation.
bitio.*	Bit-level input/output functions.
defs.h	Definitions of types and parameters.
fasta.*	FASTA and multi-FASTA parsing routines.
fcm.*	Finite-context model handling.
io.*	General I/O operations.
mem.*	Memory usage tracking.
example.fa	Sample multi-FASTA file from the CAMERA dataset.

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🔧 Build Instructions

Linux

make -f Makefile.linux

Windows (Cross-Compile from Linux)

Requires MinGW-w64

• 32-bit:

  make -f Makefile.win32

• 64-bit:

  make -f Makefile.win64

💡 If you are unsure about cross-compiling, consider using the precompiled binaries from a companion package.

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🚀 Usage

Encoding

MFCompressC [options] MultiFastaFile

Options:

• -o EncodedFile  Output file (default: <input>.mfc)
• -v  Verbose mode
• -V  Display version info
• -1  Fast mode (less memory, lower compression)
• -2  Default mode
• -3  Best compression (more memory/time)
• -p nParts  Split input into nParts for parallel encoding
• -t maxProcs  Max parallel processes (default: 2)

Decoding

MFCompressD [options] EncodedFile

Options:

• -o MultiFastaFile  Output file (default: <input>.d)
• -v  Verbose mode
• -V  Display version info
• -t maxProcs  Max parallel processes (Linux only)
• -r i[:j]  Decode only records in the given range
• -i  Display encoded file metadata

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📌 Examples

Basic Compression & Decompression (Linux)

MFCompressC example.fa
stat -c %s example.fa.mfc
MFCompressD example.fa.mfc
cmp example.fa example.fa.mfc.d

Multi-Part Encoding

MFCompressC -p 2 example.fa
stat -c %s example.fa.mfc
MFCompressD example.fa.mfc
cmp example.fa example.fa.mfc.d

Inspect Encoded File

MFCompressD -i example.fa.mfc

Sample Output:

File has 2 part(s) and 2947 record(s)
    Part 1 has 305073 bytes (records 1:1475)
    Part 2 has 305219 bytes (records 1476:2947)
Got 59 different header chars: \n ",-./0123456789=ABCDEFGHILMNOPRSTU_abcdefghilmnopqrstuvwy
Got 5 different sequence chars: ACGNT
Header context string: -c 3 1/50 2047
Sequence context string: -c 1:3 1/1 65535 0 0 -c 1:8 1/1 2047 0 0 -c 1:14 1/50 15 1 1 -bs 75
AuxInfo context string: -cs 5 16383 -cx 7 16383 -cc 12

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🧪 Test File

An example FASTA file (example.fa) is included for testing and experimentation. It originates from the CAMERA dataset.

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🛠 Notes

• Multi-threading is only available on Linux.
• On Windows, parallelism is disabled. Use Linux for better performance.