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  • Committer: Bazaar Package Importer
  • Author(s): Charles Plessy
  • Date: 2011-02-08 16:11:12 UTC
  • mfrom: (1.1.7 upstream)
  • Revision ID: james.westby@ubuntu.com-20110208161112-1fvt0mtygl8rhajf
Tags: 0.5.9-1
* New usptream release
  - Upstream moved to GitHub (debian/upstream-metadata.yaml).
  - Checked copyright; one file was removed (debian/copyright).
* Migrated the Debian source package to Git (debian/control).
* Use Debhelper 8 (debian/control, debian/compat).

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bwtaln.h
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        bwa_cigar_t *cigar;
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        // for multi-threading only
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        int tid;
 
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        // barcode
 
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        char bc[16]; // null terminated; up to 15 bases
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        // NM and MD tags
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        uint32_t full_len:20, nm:12;
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        char *md;
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#define BWA_MODE_COMPREAD   0x02
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#define BWA_MODE_LOGGAP     0x04
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#define BWA_MODE_NONSTOP    0x10
 
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#define BWA_MODE_BAM        0x20
 
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#define BWA_MODE_BAM_SE     0x40
 
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#define BWA_MODE_BAM_READ1  0x80
 
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#define BWA_MODE_BAM_READ2  0x100
 
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#define BWA_MODE_IL13       0x200
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typedef struct {
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        int s_mm, s_gapo, s_gape;
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        int mode;
 
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        int mode; // bit 24-31 are the barcode length
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        int indel_end_skip, max_del_occ, max_entries;
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        float fnr;
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        int max_diff, max_gapo, max_gape;
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        void bwa_aln_core(const char *prefix, const char *fn_fa, const gap_opt_t *opt);
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        bwa_seqio_t *bwa_seq_open(const char *fn);
 
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        bwa_seqio_t *bwa_bam_open(const char *fn, int which);
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        void bwa_seq_close(bwa_seqio_t *bs);
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        void seq_reverse(int len, ubyte_t *seq, int is_comp);
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        bwa_seq_t *bwa_read_seq(bwa_seqio_t *seq, int n_needed, int *n, int is_comp, int trim_qual);
 
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        bwa_seq_t *bwa_read_seq(bwa_seqio_t *seq, int n_needed, int *n, int mode, int trim_qual);
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        void bwa_free_read_seq(int n_seqs, bwa_seq_t *seqs);
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        int bwa_cal_maxdiff(int l, double err, double thres);