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comparison PsiCLASS-1.0.2/samtools-0.1.19/sam.h @ 0:903fc43d6227 draft default tip

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author lsong10
date Fri, 26 Mar 2021 16:52:45 +0000
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1 #ifndef BAM_SAM_H
2 #define BAM_SAM_H
3
4 #include "bam.h"
5
6 /*!
7 @header
8
9 This file provides higher level of I/O routines and unifies the APIs
10 for SAM and BAM formats. These APIs are more convenient and
11 recommended.
12
13 @copyright Genome Research Ltd.
14 */
15
16 /*! @typedef
17 @abstract SAM/BAM file handler
18 @field type type of the handler; bit 1 for BAM, 2 for reading and bit 3-4 for flag format
19 @field bam BAM file handler; valid if (type&1) == 1
20 @field tamr SAM file handler for reading; valid if type == 2
21 @field tamw SAM file handler for writing; valid if type == 0
22 @field header header struct
23 */
24 typedef struct {
25 int type;
26 union {
27 tamFile tamr;
28 bamFile bam;
29 FILE *tamw;
30 } x;
31 bam_header_t *header;
32 } samfile_t;
33
34 #ifdef __cplusplus
35 extern "C" {
36 #endif
37
38 /*!
39 @abstract Open a SAM/BAM file
40
41 @param fn SAM/BAM file name; "-" is recognized as stdin (for
42 reading) or stdout (for writing).
43
44 @param mode open mode /[rw](b?)(u?)(h?)([xX]?)/: 'r' for reading,
45 'w' for writing, 'b' for BAM I/O, 'u' for uncompressed BAM output,
46 'h' for outputing header in SAM, 'x' for HEX flag and 'X' for
47 string flag. If 'b' present, it must immediately follow 'r' or
48 'w'. Valid modes are "r", "w", "wh", "wx", "whx", "wX", "whX",
49 "rb", "wb" and "wbu" exclusively.
50
51 @param aux auxiliary data; if mode[0]=='w', aux points to
52 bam_header_t; if strcmp(mode, "rb")!=0 and @SQ header lines in SAM
53 are absent, aux points the file name of the list of the reference;
54 aux is not used otherwise. If @SQ header lines are present in SAM,
55 aux is not used, either.
56
57 @return SAM/BAM file handler
58 */
59 samfile_t *samopen(const char *fn, const char *mode, const void *aux);
60
61 /*!
62 @abstract Close a SAM/BAM handler
63 @param fp file handler to be closed
64 */
65 void samclose(samfile_t *fp);
66
67 /*!
68 @abstract Read one alignment
69 @param fp file handler
70 @param b alignment
71 @return bytes read
72 */
73 int samread(samfile_t *fp, bam1_t *b);
74
75 /*!
76 @abstract Write one alignment
77 @param fp file handler
78 @param b alignment
79 @return bytes written
80 */
81 int samwrite(samfile_t *fp, const bam1_t *b);
82
83 /*!
84 @abstract Get the pileup for a whole alignment file
85 @param fp file handler
86 @param mask mask transferred to bam_plbuf_set_mask()
87 @param func user defined function called in the pileup process
88 #param data user provided data for func()
89 */
90 int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *data);
91
92 char *samfaipath(const char *fn_ref);
93 int samthreads(samfile_t *fp, int n_threads, int n_sub_blks);
94
95 #ifdef __cplusplus
96 }
97 #endif
98
99 #endif