annotate deseq-hts_2.0/mex/get_reads_direct.cpp @ 10:2fe512c7bfdf draft

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author vipints <vipin@cbio.mskcc.org>
date Tue, 08 Oct 2013 08:15:34 -0400
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1 /*
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2 * This program is free software; you can redistribute it and/or modify
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3 * it under the terms of the GNU General Public License as published by
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4 * the Free Software Foundation; either version 3 of the License, or
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5 * (at your option) any later version.
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6 *
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7 * Written (W) 2010-2011 Jonas Behr, Regina Bohnert, Gunnar Raetsch
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8 * Copyright (C) 2010-2011 Max Planck Society
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9 */
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10
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11
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12 #include <stdio.h>
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13 #include <assert.h>
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14 #include "sam.h"
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15 #include "get_reads_direct.h"
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16
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17 #include <vector>
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18 using std::vector;
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19 #include <string>
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20 using std::string;
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21
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22 #ifdef __cplusplus
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23 extern "C" {
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24 #endif
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25
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26 typedef struct {
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27 int beg, end;
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28 samfile_t *in;
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29 } tmpstruct_t;
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30
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31 typedef struct {
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32 uint64_t u, v;
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33 } pair64_t;
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34
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35 static inline int is_overlap(uint32_t beg, uint32_t end, const bam1_t *b)
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36 {
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37 uint32_t rbeg = b->core.pos;
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38 uint32_t rend = b->core.n_cigar? bam_calend(&b->core, bam1_cigar(b)) : b->core.pos + 1;
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39 return (rend > beg && rbeg < end);
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40 }
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41
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42 pair64_t * get_chunk_coordinates(const bam_index_t *idx, int tid, int beg, int end, int* cnt_off);
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43
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44 int bam_fetch_reads(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_header_t* header, vector<CRead*>* reads, char strand);
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45
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46 // callback for bam_plbuf_init()
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47 static int pileup_func(uint32_t tid, uint32_t pos, int n, const bam_pileup1_t *pl, void *data)
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48 {
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49 //tmpstruct_t *tmp = (tmpstruct_t*)data;
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50 //if ((int)pos >= tmp->beg && (int)pos < tmp->end)
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51 // printf("%s\t%d\t%d\n", tmp->in->header->target_name[tid], pos + 1, n);
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52 return 0;
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53 }
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54 #ifdef __cplusplus
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55 }
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56 #endif
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57 int parse_sam_line(char* line, CRead* read);
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58 //int set_strand(char c);
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59 //void parse_cigar(bam1_t* b, CRead* read);
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60 void parse_cigar(bam1_t* b, CRead* read, bam_header_t* header);
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61
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62
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63 int get_reads_from_bam(char* filename, char* region, vector<CRead*>* reads, char strand, int lsubsample)
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64 {
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65 subsample = lsubsample;
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66 //set_strand(strand);
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67
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68 srand (time(NULL));
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69 //srand (1234);
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70 tmpstruct_t tmp;
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71 tmp.in = samopen(filename, "rb", 0);
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72 if (tmp.in == 0) {
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73 fprintf(stderr, "Fail to open BAM file %s\n", filename);
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74 return 1;
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75 }
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76 int ref;
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77 bam_index_t *idx;
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78 bam_plbuf_t *buf;
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79 idx = bam_index_load(filename); // load BAM index
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80 if (idx == 0) {
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81 fprintf(stderr, "BAM indexing file is not available.\n");
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82 return 1;
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83 }
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84 bam_parse_region(tmp.in->header, region, &ref,
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85 &tmp.beg, &tmp.end); // parse the region
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86 if (ref < 0) {
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87 fprintf(stderr, "Invalid region %s\n", region);
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88 return 1;
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89 }
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90
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91 buf = bam_plbuf_init(pileup_func, &tmp); // initialize pileup
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92
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93 bam_fetch_reads(tmp.in->x.bam, idx, ref, tmp.beg, tmp.end, buf, tmp.in->header, reads, strand);
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94 //fprintf(stdout, "intron_list: %d \n", intron_list->size());
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95
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96 bam_plbuf_push(0, buf); // finalize pileup
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97 bam_index_destroy(idx);
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98 bam_plbuf_destroy(buf);
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99 samclose(tmp.in);
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100 return 0;
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101 }
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102
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103
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104 int bam_fetch_reads(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_header_t* header, vector<CRead*>* reads, char strand)
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105 {
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106 int n_off;
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107 pair64_t *off = get_chunk_coordinates(idx, tid, beg, end, &n_off);
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108 if (off == 0) return 0;
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109 {
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110 // retrive alignments
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111 uint64_t curr_off;
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112 int i, ret, n_seeks;
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113 n_seeks = 0; i = -1; curr_off = 0;
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114 bam1_t *b = (bam1_t*)calloc(1, sizeof(bam1_t));
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115 for (;;) {
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116 if (curr_off == 0 || curr_off >= off[i].v) { // then jump to the next chunk
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117 if (i == n_off - 1) break; // no more chunks
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118 if (i >= 0) assert(curr_off == off[i].v); // otherwise bug
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119 if (i < 0 || off[i].v != off[i+1].u) { // not adjacent chunks; then seek
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120 bam_seek(fp, off[i+1].u, SEEK_SET);
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121 curr_off = bam_tell(fp);
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122 ++n_seeks;
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123 }
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124 ++i;
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125 }
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126 if ((ret = bam_read1(fp, b)) > 0) {
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127 curr_off = bam_tell(fp);
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parents:
diff changeset
128 if (b->core.tid != tid || b->core.pos >= end) break; // no need to proceed
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
129 else if (is_overlap(beg, end, b))
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
130 {
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
131 int rr = rand();
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
132 if ((rr%1000 < subsample))
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
133 {
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
134 CRead* read = new CRead();
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
135 parse_cigar(b, read, header);
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
136
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
137 if (strand == '0' || strand==read->strand[0] || read->strand[0]=='0')
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
138 {
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
139 read->left = (b->core.flag & left_flag_mask) >0;
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
140 read->right = (b->core.flag & right_flag_mask) >0;
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
141 read->reverse = (b->core.flag & reverse_flag_mask) >0;
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
142 reads->push_back(read);
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
143 }
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
144 else
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
145 {
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
146 delete read;
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
147 }
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
148 //else if (read->strand[0]=='0'&&((b->core.flag & g_flag_off) >0))
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parents:
diff changeset
149 //{
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
150 // //fprintf(stdout, "(-)-strand; read->strand[0]==0, num_exons: %i \n", read->block_starts.size());
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
151 // // this flag means that the read has been reversed for alignment
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
152 // // flag bit set and (-)-strand requested
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
153 // reads->push_back(read);
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
154 //}
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
155 //else if (read->strand[0]=='0'&&(g_flag_on>0&&(b->core.flag & g_flag_on)==0))
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
156 //{
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
157 // //fprintf(stdout, "(+)-strand; read->strand[0]==0, num_exons: %i \n", read->block_starts.size());
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
158 // // (+)-strand requested and flag bit not set
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
159 // reads->push_back(read);
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
160 //}
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
161 }
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
162 }
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
163 } else break; // end of file
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
164 }
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
165 // fprintf(stderr, "[bam_fetch] # seek calls: %d\n", n_seeks);
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
166 bam_destroy1(b);
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
167 }
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
168 free(off);
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
169 return 0;
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
170 }
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
171
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
172 void parse_cigar(bam1_t* b, CRead* read, bam_header_t* header)
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
173 {
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
174 read->start_pos = b->core.pos+1;
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
175 read->set_strand('0');
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
176 read->read_id = new char[100];
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
177 sprintf(read->read_id, "%s\0", bam1_qname(b));
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
178
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
179 for (int k = 0; k < b->core.n_cigar; ++k)
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
180 {
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
181 int op = bam1_cigar(b)[k] & BAM_CIGAR_MASK; // operation
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
182 int l = bam1_cigar(b)[k] >> BAM_CIGAR_SHIFT; // length
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
183 //fprintf(stdout, "op:%d l:%d\n", op, l);
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
184 if (op == BAM_CMATCH)
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
185 {
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
186 if (k==0)
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
187 {
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
188 read->block_lengths.push_back(l);
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
189 read->block_starts.push_back(0);
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
190 }
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
191 else
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
192 {
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
193 int op_prev = bam1_cigar(b)[k-1] & BAM_CIGAR_MASK;
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
194 int l_prev = bam1_cigar(b)[k-1] >> BAM_CIGAR_SHIFT;
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
195 if (op_prev==BAM_CREF_SKIP)// intron before
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
196 {
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
197 if (read->block_lengths.size()>=1)
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
198 {
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
199 int last_block_start = (*(read->block_starts.end()-1));
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
200 int intron_start = last_block_start+(*(read->block_lengths.end()-1));
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
201 read->block_lengths.push_back(l);
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
202 read->block_starts.push_back(intron_start+l_prev);
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
203 }
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
204 else
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
205 {
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
206 // start of first block was not a match
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
207 read->block_lengths.push_back(l);
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
208 read->block_starts.push_back(0);
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
209 }
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
210 }
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
211 else
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
212 {
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
213 if (read->block_lengths.size()>=1 && op == BAM_CDEL)// if it is an insertion then the matching block is not inreased
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
214 (*(read->block_lengths.end()-1))+=l;
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
215 else
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
216 {
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
217 //char *samline = bam_format1(header, b);
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
218 //printf("header: %s \n", samline);
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
219 }
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
220 }
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
221 }
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
222 }
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
223 else if (op == BAM_CDEL)
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
224 {
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
225 if (k>0 && read->block_lengths.size()>=1)
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
226 (*(read->block_lengths.end()-1))+=l;
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
227 }
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
228 else if (op == BAM_CREF_SKIP)//intron
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
229 {}
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
230 else if (op == BAM_CINS || op == BAM_CSOFT_CLIP)
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
231 {}
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
232 }
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
233 // parse auxiliary data
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
234 uint8_t* s = bam1_aux(b);
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
235 uint8_t* end = b->data + b->data_len;
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
236 while (s < end)
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
237 {
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
238 uint8_t type, key[2];
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
239 key[0] = s[0]; key[1] = s[1];
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
240 s += 2; type = *s; ++s;
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
241 //fprintf(stdout, "\n%c%c:%c\n", key[0], key[1], type);
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
242 if (type == 'A')
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
243 {
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
244 if ( key[0] =='X' && key[1] == 'S')
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
245 {
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
246 read->set_strand((char) *s);
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
247 }
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
248 ++s;
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
249 }
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
250 else if (type == 'C')
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
251 {
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
252 if ( key[0] =='H' && key[1] == '0')
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
253 {
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
254 uint8_t matches = *s;
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
255 read->matches = (int) matches;
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
256 }
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vipints <vipin@cbio.mskcc.org>
parents:
diff changeset
257 if ( key[0] =='N' && key[1] == 'M')
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258 {
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259 uint8_t mismatches = *s;
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260 read->mismatches = (int) mismatches;
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261 }
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262 if ( key[0] =='H' && key[1] == 'I')
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263 {
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264 uint8_t mai = *s;
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265 read->multiple_alignment_index = (int) mai;
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266 }
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267
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268 ++s;
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269 }
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270 else if (type == 'c') { ++s; }
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271 else if (type == 'S') { s += 2; }
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272 else if (type == 's') { s += 2; }
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273 else if (type == 'I') { s += 4; }
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274 else if (type == 'i') { s += 4; }
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275 else if (type == 'f') { s += 4; }
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276 else if (type == 'd') { s += 8; }
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277 else if (type == 'Z') { ++s; }
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278 else if (type == 'H') { ++s; }
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279 }
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280 }
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281
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282 //int set_strand(char c)
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283 //{
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284 // if (c=='+')
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285 // {
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286 // char* fl = (char*) "0x0010";
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287 // g_flag_on = strtol(fl, 0, 0);
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288 // g_flag_off = 0;
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289 // }
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290 // else if (c=='-')
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291 // {
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292 // char* fl = (char*) "0x0010";
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293 // g_flag_off = strtol(fl, 0, 0);
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294 // g_flag_on = 0;
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295 // }
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296 // return 0;
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297 //}
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298