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1 /*
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2 * File: notes.h
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3 * Author: rgoya
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4 *
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5 * Created on February 3, 2010, 12:37 PM
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6 */
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7
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8 /*! @typedef
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9 @abstract Structure for one alignment covering the pileup position.
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10 @field b pointer to the alignment
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11 @field qpos position of the read base at the pileup site, 0-based
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12 @field indel indel length; 0 for no indel, positive for ins and negative for del
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13 @field is_del 1 iff the base on the padded read is a deletion
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14 @field level the level of the read in the "viewer" mode
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15
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16 @discussion See also bam_plbuf_push() and bam_lplbuf_push(). The
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17 difference between the two functions is that the former does not
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18 set bam_pileup1_t::level, while the later does. Level helps the
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19 implementation of alignment viewers, but calculating this has some
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20 overhead.
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21 */
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22 typedef struct {
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23 bam1_t *b;
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24 int32_t qpos;
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25 int indel, level;
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26 uint32_t is_del:1, is_head:1, is_tail:1;
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27 } bam_pileup1_t;
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28
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29 /*! @typedef
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30 @abstract Structure for core alignment information.
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31 @field tid chromosome ID, defined by bam_header_t
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32 @field pos 0-based leftmost coordinate
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33 @field strand strand; 0 for forward and 1 otherwise
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34 @field bin bin calculated by bam_reg2bin()
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35 @field qual mapping quality
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36 @field l_qname length of the query name
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37 @field flag bitwise flag
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38 @field n_cigar number of CIGAR operations
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39 @field l_qseq length of the query sequence (read)
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40 */
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41 typedef struct {
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42 int32_t tid;
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43 int32_t pos;
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44 uint32_t bin:16, qual:8, l_qname:8;
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45 uint32_t flag:16, n_cigar:16;
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46 int32_t l_qseq;
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47 int32_t mtid;
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48 int32_t mpos;
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49 int32_t isize;
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50 } bam1_core_t;
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51
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52 /*! @typedef
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53 @abstract Structure for one alignment.
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54 @field core core information about the alignment
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55 @field l_aux length of auxiliary data
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56 @field data_len current length of bam1_t::data
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57 @field m_data maximum length of bam1_t::data
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58 @field data all variable-length data, concatenated; structure: cigar-qname-seq-qual-aux
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59
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60 @discussion Notes:
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61
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62 1. qname is zero tailing and core.l_qname includes the tailing '\0'.
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63 2. l_qseq is calculated from the total length of an alignment block
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64 on reading or from CIGAR.
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65 */
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66 typedef struct {
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67 bam1_core_t core;
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68 int l_aux, data_len, m_data;
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69 uint8_t *data;
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70 } bam1_t;
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71
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72
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73 /*! @typedef
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74 @abstract Structure for one alignment covering the pileup position.
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75 @field b pointer to the alignment
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76 @field qpos position of the read base at the pileup site, 0-based
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77 @field indel indel length; 0 for no indel, positive for ins and negative for del
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78 @field is_del 1 iff the base on the padded read is a deletion
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79 @field level the level of the read in the "viewer" mode
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80
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81 @discussion See also bam_plbuf_push() and bam_lplbuf_push(). The
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82 difference between the two functions is that the former does not
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83 set bam_pileup1_t::level, while the later does. Level helps the
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84 implementation of alignment viewers, but calculating this has some
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85 overhead.
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86 */
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87 typedef struct {
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88 bam1_t *b;
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89 int32_t qpos;
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90 int indel, level;
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91 uint32_t is_del:1, is_head:1, is_tail:1;
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92 } bam_pileup1_t;
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