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comparison ezBAMQC/src/htslib/vcf_sweep.c @ 0:dfa3745e5fd8

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author youngkim
date Thu, 24 Mar 2016 17:12:52 -0400
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1 /* vcf_sweep.c -- forward/reverse sweep API.
2
3 Copyright (C) 2013 Genome Research Ltd.
4
5 Author: Petr Danecek <pd3@sanger.ac.uk>
6
7 Permission is hereby granted, free of charge, to any person obtaining a copy
8 of this software and associated documentation files (the "Software"), to deal
9 in the Software without restriction, including without limitation the rights
10 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
11 copies of the Software, and to permit persons to whom the Software is
12 furnished to do so, subject to the following conditions:
13
14 The above copyright notice and this permission notice shall be included in
15 all copies or substantial portions of the Software.
16
17 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
18 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
19 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
20 THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
21 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
22 FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
23 DEALINGS IN THE SOFTWARE. */
24
25 #include "htslib/vcf_sweep.h"
26 #include "htslib/bgzf.h"
27
28 #define SW_FWD 0
29 #define SW_BWD 1
30
31 struct _bcf_sweep_t
32 {
33 htsFile *file;
34 bcf_hdr_t *hdr;
35 BGZF *fp;
36
37 int direction; // to tell if the direction has changed
38 int block_size; // the size of uncompressed data to hold in memory
39 bcf1_t *rec; // bcf buffer
40 int nrec, mrec; // number of used records; total size of the buffer
41 int lrid, lpos, lnals, lals_len, mlals; // to check uniqueness of a record
42 char *lals;
43
44 uint64_t *idx; // uncompressed offsets of VCF/BCF records
45 int iidx, nidx, midx; // i: current offset; n: used; m: allocated
46 int idx_done; // the index is built during the first pass
47 };
48
49 BGZF *hts_get_bgzfp(htsFile *fp);
50 int hts_useek(htsFile *file, long uoffset, int where);
51 long hts_utell(htsFile *file);
52
53 static inline int sw_rec_equal(bcf_sweep_t *sw, bcf1_t *rec)
54 {
55 if ( sw->lrid!=rec->rid ) return 0;
56 if ( sw->lpos!=rec->pos ) return 0;
57 if ( sw->lnals!=rec->n_allele ) return 0;
58
59 char *t = rec->d.allele[sw->lnals-1];
60 int len = t - rec->d.allele[0] + 1;
61 while ( *t ) { t++; len++; }
62 if ( sw->lals_len!=len ) return 0;
63 if ( memcmp(sw->lals,rec->d.allele[0],len) ) return 0;
64 return 1;
65 }
66
67 static void sw_rec_save(bcf_sweep_t *sw, bcf1_t *rec)
68 {
69 sw->lrid = rec->rid;
70 sw->lpos = rec->pos;
71 sw->lnals = rec->n_allele;
72
73 char *t = rec->d.allele[sw->lnals-1];
74 int len = t - rec->d.allele[0] + 1;
75 while ( *t ) { t++; len++; }
76 sw->lals_len = len;
77 hts_expand(char, len, sw->mlals, sw->lals);
78 memcpy(sw->lals, rec->d.allele[0], len);
79 }
80
81 static void sw_fill_buffer(bcf_sweep_t *sw)
82 {
83 if ( !sw->iidx ) return;
84 sw->iidx--;
85
86 int ret = hts_useek(sw->file, sw->idx[sw->iidx], 0);
87 assert( ret==0 );
88
89 sw->nrec = 0;
90 bcf1_t *rec = &sw->rec[sw->nrec];
91 while ( (ret=bcf_read1(sw->file, sw->hdr, rec))==0 )
92 {
93 bcf_unpack(rec, BCF_UN_STR);
94
95 // if not in the last block, stop at the saved record
96 if ( sw->iidx+1 < sw->nidx && sw_rec_equal(sw,rec) ) break;
97
98 sw->nrec++;
99 hts_expand0(bcf1_t, sw->nrec+1, sw->mrec, sw->rec);
100 rec = &sw->rec[sw->nrec];
101 }
102 sw_rec_save(sw, &sw->rec[0]);
103 }
104
105 bcf_sweep_t *bcf_sweep_init(const char *fname)
106 {
107 bcf_sweep_t *sw = (bcf_sweep_t*) calloc(1,sizeof(bcf_sweep_t));
108 sw->file = hts_open(fname, "r");
109 sw->fp = hts_get_bgzfp(sw->file);
110 bgzf_index_build_init(sw->fp);
111 sw->hdr = bcf_hdr_read(sw->file);
112 sw->mrec = 1;
113 sw->rec = (bcf1_t*) calloc(sw->mrec,(sizeof(bcf1_t)));
114 sw->block_size = 1024*1024*3;
115 sw->direction = SW_FWD;
116 return sw;
117 }
118
119 void bcf_empty1(bcf1_t *v);
120 void bcf_sweep_destroy(bcf_sweep_t *sw)
121 {
122 int i;
123 for (i=0; i<sw->mrec; i++) bcf_empty1(&sw->rec[i]);
124 free(sw->idx);
125 free(sw->rec);
126 free(sw->lals);
127 bcf_hdr_destroy(sw->hdr);
128 hts_close(sw->file);
129 free(sw);
130 }
131
132 static void sw_seek(bcf_sweep_t *sw, int direction)
133 {
134 sw->direction = direction;
135 if ( direction==SW_FWD )
136 hts_useek(sw->file, sw->idx[0], 0);
137 else
138 {
139 sw->iidx = sw->nidx;
140 sw->nrec = 0;
141 }
142 }
143
144 bcf1_t *bcf_sweep_fwd(bcf_sweep_t *sw)
145 {
146 if ( sw->direction==SW_BWD ) sw_seek(sw, SW_FWD);
147
148 long pos = hts_utell(sw->file);
149
150 bcf1_t *rec = &sw->rec[0];
151 int ret = bcf_read1(sw->file, sw->hdr, rec);
152
153 if ( ret!=0 ) // last record, get ready for sweeping backwards
154 {
155 sw->idx_done = 1;
156 sw->fp->idx_build_otf = 0;
157 sw_seek(sw, SW_BWD);
158 return NULL;
159 }
160
161 if ( !sw->idx_done )
162 {
163 if ( !sw->nidx || pos - sw->idx[sw->nidx-1] > sw->block_size )
164 {
165 sw->nidx++;
166 hts_expand(uint64_t, sw->nidx, sw->midx, sw->idx);
167 sw->idx[sw->nidx-1] = pos;
168 }
169 }
170 return rec;
171 }
172
173 bcf1_t *bcf_sweep_bwd(bcf_sweep_t *sw)
174 {
175 if ( sw->direction==SW_FWD ) sw_seek(sw, SW_BWD);
176 if ( !sw->nrec ) sw_fill_buffer(sw);
177 if ( !sw->nrec ) return NULL;
178 return &sw->rec[ --sw->nrec ];
179 }
180
181 bcf_hdr_t *bcf_sweep_hdr(bcf_sweep_t *sw) { return sw->hdr; }
182