This repository contains three simple C programs to operate on files in fasta and fastq format.
Converts a fastq file (read from standard input) to fasta format (written to standard output). If the -n option is supplied, only outputs sequence names. If the -s option is supplied, only outputs sequences (one per line).
Reads a fastq file from standard output and outputs a subset of the reads according to the supplied OFFSET and NDIST arguments (where OFFSET is between 0 and NDIST-1). In each block of NDIST reads, only the one numbered OFFSET will be output. This command is useful to distribute reads from a fastq file into several different files in round-robin fashion.
Reads a fasta file and outputs a copy replacing all Cs with Ts. A different replacement can be specified using the second argument, indicating the "from" and "to" bases. For example, to replace Gs with As, use: faconvert infile.fa GA.
Calling these programs with the -h option prints a simple usage message.
These are stand-alone C programs with no dependencies, so they can be compiled with a simple gcc command, e.g.:
gcc faconvert.c -o faconvert