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1 #ifndef BAM_SAM_H
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2 #define BAM_SAM_H
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3
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4 #include "bam.h"
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5
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6 /*!
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7 @header
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8
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9 This file provides higher level of I/O routines and unifies the APIs
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10 for SAM and BAM formats. These APIs are more convenient and
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11 recommended.
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12
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13 @copyright Genome Research Ltd.
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14 */
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15
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16 /*! @typedef
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17 @abstract SAM/BAM file handler
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18 @field type type of the handler; bit 1 for BAM, 2 for reading and bit 3-4 for flag format
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19 @field bam BAM file handler; valid if (type&1) == 1
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20 @field tamr SAM file handler for reading; valid if type == 2
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21 @field tamw SAM file handler for writing; valid if type == 0
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22 @field header header struct
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23 */
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24 typedef struct {
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25 int type;
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26 union {
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27 tamFile tamr;
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28 bamFile bam;
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29 FILE *tamw;
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30 } x;
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31 bam_header_t *header;
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32 } samfile_t;
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33
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34 #ifdef __cplusplus
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35 extern "C" {
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36 #endif
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37
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38 /*!
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39 @abstract Open a SAM/BAM file
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40
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41 @param fn SAM/BAM file name; "-" is recognized as stdin (for
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42 reading) or stdout (for writing).
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43
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44 @param mode open mode /[rw](b?)(u?)(h?)([xX]?)/: 'r' for reading,
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45 'w' for writing, 'b' for BAM I/O, 'u' for uncompressed BAM output,
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46 'h' for outputing header in SAM, 'x' for HEX flag and 'X' for
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47 string flag. If 'b' present, it must immediately follow 'r' or
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48 'w'. Valid modes are "r", "w", "wh", "wx", "whx", "wX", "whX",
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49 "rb", "wb" and "wbu" exclusively.
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50
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51 @param aux auxiliary data; if mode[0]=='w', aux points to
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52 bam_header_t; if strcmp(mode, "rb")!=0 and @SQ header lines in SAM
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53 are absent, aux points the file name of the list of the reference;
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54 aux is not used otherwise. If @SQ header lines are present in SAM,
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55 aux is not used, either.
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56
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57 @return SAM/BAM file handler
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58 */
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59 samfile_t *samopen(const char *fn, const char *mode, const void *aux);
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60
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61 /*!
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62 @abstract Close a SAM/BAM handler
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63 @param fp file handler to be closed
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64 */
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65 void samclose(samfile_t *fp);
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66
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67 /*!
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68 @abstract Read one alignment
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69 @param fp file handler
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70 @param b alignment
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71 @return bytes read
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72 */
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73 int samread(samfile_t *fp, bam1_t *b);
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74
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75 /*!
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76 @abstract Write one alignment
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77 @param fp file handler
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78 @param b alignment
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79 @return bytes written
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80 */
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81 int samwrite(samfile_t *fp, const bam1_t *b);
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82
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83 /*!
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84 @abstract Get the pileup for a whole alignment file
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85 @param fp file handler
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86 @param mask mask transferred to bam_plbuf_set_mask()
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87 @param func user defined function called in the pileup process
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88 #param data user provided data for func()
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89 */
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90 int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *data);
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91
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92 char *samfaipath(const char *fn_ref);
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93 int samthreads(samfile_t *fp, int n_threads, int n_sub_blks);
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94
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95 #ifdef __cplusplus
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96 }
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97 #endif
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98
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99 #endif
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