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Viewing changes to sand/src/sand_uncompress_reads.c

  • Committer: Bazaar Package Importer
  • Author(s): Michael Hanke
  • Date: 2011-05-07 09:05:00 UTC
  • Revision ID: james.westby@ubuntu.com-20110507090500-lqpmdtwndor6e7os
Tags: upstream-3.3.2
Import upstream version 3.3.2

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sand/src/sand_uncompress_reads.c
 
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/*
 
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Copyright (C) 2009- The University of Notre Dame
 
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This software is distributed under the GNU General Public License.
 
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See the file COPYING for details.
 
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*/
 
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#include <stdio.h>
 
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#include <stdlib.h>
 
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#include <string.h>
 
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#include <errno.h>
 
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#include "compressed_sequence.h"
 
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#include "debug.h"
 
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static void show_version(const char *cmd)
 
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{
 
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        printf("%s version %d.%d.%d built by %s@%s on %s at %s\n", cmd, CCTOOLS_VERSION_MAJOR, CCTOOLS_VERSION_MINOR, CCTOOLS_VERSION_MICRO, BUILD_USER, BUILD_HOST, __DATE__, __TIME__);
 
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}
 
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static void show_help(const char *cmd)
 
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{
 
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        printf("Use: %s [options]  compressed_reads > fasta_reads\n", cmd);
 
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        printf("where options are:\n");
 
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        printf(" -q  Quiet mode: suppress summary line.\n");
 
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        printf(" -v  Show version string.\n");
 
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        printf(" -h  Show this help screen\n");
 
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}
 
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int main(int argc, char ** argv)
 
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{
 
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        const char *progname = "sand_uncompress_reads";
 
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        FILE * infile;
 
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        FILE * outfile;
 
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        struct cseq *c;
 
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        char d;
 
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        int quiet_mode = 0;
 
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        int count = 0;
 
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        while((d=getopt(argc,argv,"qhi"))!=(char)-1) {
 
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                switch(d) {
 
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                case 'q':
 
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                        quiet_mode = 1;
 
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                        break;
 
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                case 'v':
 
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                        show_version(progname);
 
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                        exit(0);
 
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                        break;
 
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                case 'h':
 
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                default:
 
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                        show_help(progname);
 
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                        exit(0);
 
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                        break;
 
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                }
 
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        }
 
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        if( optind<argc ) {
 
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                infile = fopen(argv[optind], "r");
 
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                if(!infile) {
 
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                        fprintf(stderr,"%s: couldn't open %s: %s\n",progname,argv[optind],strerror(errno));
 
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                        return 1;
 
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                }
 
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                optind++;
 
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        } else {
 
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                infile = stdin;
 
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        }
 
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        if( optind<argc ) {
 
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                outfile = fopen(argv[optind],"w");
 
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                if(!outfile) {
 
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                        fprintf(stderr,"%s: couldn't open %s: %s\n",progname,argv[optind],strerror(errno));
 
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                        return 1;
 
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                }
 
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                optind++;
 
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        } else {
 
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                outfile = stdout;
 
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        }
 
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        while((c=cseq_read(infile))) {
 
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                struct seq *s = cseq_uncompress(c);
 
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                seq_print(outfile,s);
 
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                seq_free(s);
 
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                cseq_free(c);
 
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                count++;
 
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        }
 
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        if(!quiet_mode) {
 
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                fprintf(stderr,"%d sequences uncompressed.\n",count);
 
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        }
 
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        fclose(infile);
 
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        fclose(outfile);
 
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        return 0;
 
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}