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old_versions 2012-03-15 1 weekly downloads
fastqz15.cpp 2012-03-15 34.8 kB 22 weekly downloads
readme.txt 2012-03-15 3.2 kB 11 weekly downloads
fapacks.cpp 2012-03-13 2.3 kB 22 weekly downloads
fastqz15.cpp is the source code for the latest version of the FASTQ compressor. It compresses the common Sanger variant. FASTQ is output by DNA sequencing machines. fapack.cpp is a program to pack FASTA files into a format suitable for input to fastqz as a reference genome for better compression. It packs 4 bases per byte and discards all but A,C,G,T. fapacks.cpp works the same except that it does not ignore lowercase a,c,g,t. Lowercase is used in hg19 to indicate repeats. Generally it produces a larger reference but gives better compression. Other fastqz*.cpp are older versions. You don't need them. Usage: fastqz {c[Q]|d|e[Q]|f} input output [reference] Command c compresses input to output.fx?.zpaq (3 or 4 files) Command d decompresses input.fx?.zpaq to output Command e encodes input to output.fx? Command f decodes input.fx? to output Commands c and d are slow, require 1.5 GB memory, use 3 or 4 cores, but get very good compression. Commands e and f are much faster, use little memory, and only one thread, but compression ratio is not as good. Commands cQ or eQ quantize the quality scores for lossy but better compression. The default is c1 or e1, which is lossless. Quality scores in the range 33..73 are rounded down to 35 plus a multiple of Q. You can supply a reference genome to improve compression. If you use this, the same reference is needed to decompress. It also increases the memory requirement to 1.2 GB for the e command and 0.5 GB for the f command. c and d still need 1.5 GB. You can prepare the reference genome from FASTA files like: fapacks hg19s *.fa to produce the file hg19s. Then compress: fastqz c in.fastq arc hg19s To decompress: fastqz d arc out.fastq hg19s There are 4 compressed files: arc.fxh.zpaq - compressed headers arc.fxb.zpaq - compressed base calls arc.fxq.zpaq - compressed quality scores arc.fxa.zpaq - compressed alignments if a reference is used. Commands e and f work the same way except the compressed files do not have a .zpaq extension. If no reference is used, then no .fxa or .fxa.zpaq file is produced or expected. fastqz only works on the Sanger FASTQ variant. It assumes that quality scores are Phred+33 (range ASCII 33 to 73). Base calls must be A,C,G,T,N only. N must have a quality score of 0, and all others 1 or higher. Maximum line length is 4095. Lines must be terminated by linefeeds only (no carriage returns). If a reference is used, it must be smaller than 1 GB packed (4 billion bases). To compile fastqz you will need the latest version of libzpaq from https://sourceforge.net/projects/zpaq/ or http://mattmahoney.net/zpaq/ These programs will work in either Windows or Linux. In Windows, you will also need Pthreads-Win32 from http://sourceware.org/pthreads-win32/ to compile or run. To compile (no Makefile, sorry): g++ -O3 -msse2 -s -lpthread fastqz.cpp libzpaq.cpp -o fastqz g++ -O3 -s fapack.cpp -o fapack fastqz* and fapack* are written by Matt Mahoney, Dell Inc. All are BSD-2 licensed. But note that libzpaq is public domain and Pthreads-Win32 is LGPL.
Source: readme.txt, updated 2012-03-15