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1 #ifndef BAMLITE_H_
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2 #define BAMLITE_H_
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3
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4 #include <stdint.h>
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5 #include <zlib.h>
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6
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7 typedef gzFile bamFile;
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8 #define bam_open(fn, mode) gzopen(fn, mode)
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9 #define bam_dopen(fd, mode) gzdopen(fd, mode)
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10 #define bam_close(fp) gzclose(fp)
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11 #define bam_read(fp, buf, size) gzread(fp, buf, size)
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12
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13 typedef struct {
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14 int32_t n_targets;
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15 char **target_name;
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16 uint32_t *target_len;
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17 size_t l_text, n_text;
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18 char *text;
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19 } bam_header_t;
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20
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21 #define BAM_FPAIRED 1
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22 #define BAM_FPROPER_PAIR 2
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23 #define BAM_FUNMAP 4
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24 #define BAM_FMUNMAP 8
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25 #define BAM_FREVERSE 16
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26 #define BAM_FMREVERSE 32
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27 #define BAM_FREAD1 64
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28 #define BAM_FREAD2 128
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29 #define BAM_FSECONDARY 256
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30 #define BAM_FQCFAIL 512
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31 #define BAM_FDUP 1024
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32
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33 #define BAM_CIGAR_SHIFT 4
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34 #define BAM_CIGAR_MASK ((1 << BAM_CIGAR_SHIFT) - 1)
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35
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36 #define BAM_CMATCH 0
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37 #define BAM_CINS 1
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38 #define BAM_CDEL 2
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39 #define BAM_CREF_SKIP 3
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40 #define BAM_CSOFT_CLIP 4
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41 #define BAM_CHARD_CLIP 5
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42 #define BAM_CPAD 6
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43
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44 typedef struct {
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45 int32_t tid;
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46 int32_t pos;
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47 uint32_t bin:16, qual:8, l_qname:8;
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48 uint32_t flag:16, n_cigar:16;
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49 int32_t l_qseq;
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50 int32_t mtid;
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51 int32_t mpos;
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52 int32_t isize;
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53 } bam1_core_t;
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54
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55 typedef struct {
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56 bam1_core_t core;
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57 int l_aux, data_len, m_data;
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58 uint8_t *data;
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59 } bam1_t;
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60
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61 #ifndef kroundup32
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62 #define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
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63 #endif
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64
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65 #define bam1_strand(b) (((b)->core.flag&BAM_FREVERSE) != 0)
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66 #define bam1_mstrand(b) (((b)->core.flag&BAM_FMREVERSE) != 0)
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67 #define bam1_cigar(b) ((uint32_t*)((b)->data + (b)->core.l_qname))
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68 #define bam1_qname(b) ((char*)((b)->data))
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69 #define bam1_seq(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname)
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70 #define bam1_qual(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname + (((b)->core.l_qseq + 1)>>1))
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71 #define bam1_seqi(s, i) ((s)[(i)/2] >> 4*(1-(i)%2) & 0xf)
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72 #define bam1_aux(b) ((b)->data + (b)->core.n_cigar*4 + (b)->core.l_qname + (b)->core.l_qseq + ((b)->core.l_qseq + 1)/2)
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73
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74 #define bam_init1() ((bam1_t*)calloc(1, sizeof(bam1_t)))
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75 #define bam_destroy1(b) do { \
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76 if (b) { free((b)->data); free(b); } \
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77 } while (0)
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78
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79 extern int bam_is_be;
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80
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81 #ifdef __cplusplus
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82 extern "C" {
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83 #endif
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84
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85 bam_header_t *bam_header_init(void);
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86 void bam_header_destroy(bam_header_t *header);
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87 bam_header_t *bam_header_read(bamFile fp);
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88 int bam_read1(bamFile fp, bam1_t *b);
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89
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90 #ifdef __cplusplus
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91 }
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92 #endif
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93
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94 #endif
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