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  • Committer: Bazaar Package Importer
  • Author(s): Charles Plessy
  • Date: 2009-09-14 21:58:36 UTC
  • mfrom: (1.1.1 upstream)
  • Revision ID: james.westby@ubuntu.com-20090914215836-27bfc2lrtr0xfnhz
Tags: 0.1.6~dfsg-1
* New upstream release.
* Upstream sources repackaged to remove the win32 directory:
  - The removal was done with git-import-orig in a parallel Git repository,
    and the corresponding debian/gbp.conf file was added to this package.
  - Mangled the ~dfsg string of the Debian version in debian/watch.
  - Added a debian/README.source file and explanations in debian/copyright.

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bam_plcmd.c
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                printf("%d\t%d\t", rms_mapq, n);
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                printf("%s\t%s\t", r->s[0], r->s[1]);
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                //printf("%d\t%d\t", r->gl[0], r->gl[1]);
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                printf("%d\t%d\t%d\n", r->cnt1, r->cnt2, r->cnt_anti);
 
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                printf("%d\t%d\t%d\t", r->cnt1, r->cnt2, r->cnt_anti);
 
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                printf("%d\t%d\n", r->cnt_ref, r->cnt_ambi);
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                bam_maqindel_ret_destroy(r);
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        }
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        return 0;
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                fprintf(stderr, "        -i        only show lines/consensus with indels\n");
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                fprintf(stderr, "        -m INT    filtering reads with bits in INT [%d]\n", d->mask);
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                fprintf(stderr, "        -M INT    cap mapping quality at INT [%d]\n", d->c->cap_mapQ);
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                fprintf(stderr, "        -t FILE   list of reference sequences (assume the input is in SAM)\n");
 
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                fprintf(stderr, "        -t FILE   list of reference sequences (force -S)\n");
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                fprintf(stderr, "        -l FILE   list of sites at which pileup is output\n");
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                fprintf(stderr, "        -f FILE   reference sequence in the FASTA format\n\n");
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                fprintf(stderr, "        -c        output the maq consensus sequence\n");
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        }
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        if (d->fai == 0 && (d->format & (BAM_PLF_CNS|BAM_PLF_INDEL_ONLY)))
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                fprintf(stderr, "[bam_pileup] indels will not be called when -f is absent.\n");
 
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        if (fn_fa && is_SAM && fn_list == 0) fn_list = samfaipath(fn_fa);
 
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        {
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                samfile_t *fp;
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                fp = is_SAM? samopen(argv[optind], "r", fn_list) : samopen(argv[optind], "rb", 0);