src/dustApp.c File Reference

#include <stdio.h>
#include "blast.h"

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Functions
int	main (int argc, char *argv[])

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Function Documentation

int main	(	int	argc,
		char *	argv[]
	)

Definition at line 11 of file dustApp.c.

References dust_dustSequence(), encoding_initialize(), encoding_nucleotide, global_malloc(), readFasta_descriptionBuffer, readFasta_open(), readFasta_readSequence(), readFasta_sequenceBuffer, and readFasta_sequenceLength.

{
        char *filename, *sequence, *description, *sequenceCopy;
    int sequenceLength;

        // User must provide FASTA format file at command line
        if (argc < 2)
        {
                fprintf(stderr, "Useage: dust <FASTA file>\n");
                exit(-1);
        }
        filename = argv[1];

    // Initialize encoding routines
    encoding_initialize(encoding_nucleotide);

    // Open FASTA file for reading
        readFasta_open(filename);

    // Read each sequence from the file
    while (readFasta_readSequence())
        {
                // Get sequence just read
                sequence = readFasta_sequenceBuffer;
                description = readFasta_descriptionBuffer;
        sequenceLength = readFasta_sequenceLength;

        // Make in-memory copy of it
        sequenceCopy = (char*)global_malloc(sequenceLength);
        strcpy(sequenceCopy, sequence);

                // Perform dust filtering
        dust_dustSequence(sequence);

        // Print description and filtering sequence
        printf(">%s\n%s\n", description, sequence);
    }
}

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