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 <config.h>
26
27 #include "htslib/vcf_sweep.h"
28 #include "htslib/bgzf.h"
29
30 #define SW_FWD 0
31 #define SW_BWD 1
32
33 struct _bcf_sweep_t
34 {
35 htsFile *file;
36 bcf_hdr_t *hdr;
37 BGZF *fp;
38
39 int direction; // to tell if the direction has changed
40 int block_size; // the size of uncompressed data to hold in memory
41 bcf1_t *rec; // bcf buffer
42 int nrec, mrec; // number of used records; total size of the buffer
43 int lrid, lpos, lnals, lals_len, mlals; // to check uniqueness of a record
44 char *lals;
45
46 uint64_t *idx; // uncompressed offsets of VCF/BCF records
47 int iidx, nidx, midx; // i: current offset; n: used; m: allocated
48 int idx_done; // the index is built during the first pass
49 };
50
51 BGZF *hts_get_bgzfp(htsFile *fp);
52 int hts_useek(htsFile *file, long uoffset, int where);
53 long hts_utell(htsFile *file);
54
sw_rec_equal(bcf_sweep_t * sw,bcf1_t * rec)55 static inline int sw_rec_equal(bcf_sweep_t *sw, bcf1_t *rec)
56 {
57 if ( sw->lrid!=rec->rid ) return 0;
58 if ( sw->lpos!=rec->pos ) return 0;
59 if ( sw->lnals!=rec->n_allele ) return 0;
60
61 char *t = rec->d.allele[sw->lnals-1];
62 int len = t - rec->d.allele[0] + 1;
63 while ( *t ) { t++; len++; }
64 if ( sw->lals_len!=len ) return 0;
65 if ( memcmp(sw->lals,rec->d.allele[0],len) ) return 0;
66 return 1;
67 }
68
sw_rec_save(bcf_sweep_t * sw,bcf1_t * rec)69 static void sw_rec_save(bcf_sweep_t *sw, bcf1_t *rec)
70 {
71 sw->lrid = rec->rid;
72 sw->lpos = rec->pos;
73 sw->lnals = rec->n_allele;
74
75 char *t = rec->d.allele[sw->lnals-1];
76 int len = t - rec->d.allele[0] + 1;
77 while ( *t ) { t++; len++; }
78 sw->lals_len = len;
79 hts_expand(char, len, sw->mlals, sw->lals);
80 memcpy(sw->lals, rec->d.allele[0], len);
81 }
82
sw_fill_buffer(bcf_sweep_t * sw)83 static void sw_fill_buffer(bcf_sweep_t *sw)
84 {
85 if ( !sw->iidx ) return;
86 sw->iidx--;
87
88 int ret = hts_useek(sw->file, sw->idx[sw->iidx], 0);
89 assert( ret==0 );
90
91 sw->nrec = 0;
92 bcf1_t *rec = &sw->rec[sw->nrec];
93 while ( (ret=bcf_read1(sw->file, sw->hdr, rec))==0 )
94 {
95 bcf_unpack(rec, BCF_UN_STR);
96
97 // if not in the last block, stop at the saved record
98 if ( sw->iidx+1 < sw->nidx && sw_rec_equal(sw,rec) ) break;
99
100 sw->nrec++;
101 hts_expand0(bcf1_t, sw->nrec+1, sw->mrec, sw->rec);
102 rec = &sw->rec[sw->nrec];
103 }
104 sw_rec_save(sw, &sw->rec[0]);
105 }
106
bcf_sweep_init(const char * fname)107 bcf_sweep_t *bcf_sweep_init(const char *fname)
108 {
109 bcf_sweep_t *sw = (bcf_sweep_t*) calloc(1,sizeof(bcf_sweep_t));
110 sw->file = hts_open(fname, "r");
111 sw->fp = hts_get_bgzfp(sw->file);
112 if (sw->fp) bgzf_index_build_init(sw->fp);
113 sw->hdr = bcf_hdr_read(sw->file);
114 sw->mrec = 1;
115 sw->rec = (bcf1_t*) calloc(sw->mrec,(sizeof(bcf1_t)));
116 sw->block_size = 1024*1024*3;
117 sw->direction = SW_FWD;
118 return sw;
119 }
120
bcf_sweep_destroy(bcf_sweep_t * sw)121 void bcf_sweep_destroy(bcf_sweep_t *sw)
122 {
123 int i;
124 for (i=0; i<sw->mrec; i++) bcf_empty1(&sw->rec[i]);
125 free(sw->idx);
126 free(sw->rec);
127 free(sw->lals);
128 bcf_hdr_destroy(sw->hdr);
129 hts_close(sw->file);
130 free(sw);
131 }
132
sw_seek(bcf_sweep_t * sw,int direction)133 static void sw_seek(bcf_sweep_t *sw, int direction)
134 {
135 sw->direction = direction;
136 if ( direction==SW_FWD )
137 hts_useek(sw->file, sw->idx[0], 0);
138 else
139 {
140 sw->iidx = sw->nidx;
141 sw->nrec = 0;
142 }
143 }
144
bcf_sweep_fwd(bcf_sweep_t * sw)145 bcf1_t *bcf_sweep_fwd(bcf_sweep_t *sw)
146 {
147 if ( sw->direction==SW_BWD ) sw_seek(sw, SW_FWD);
148
149 long pos = hts_utell(sw->file);
150
151 bcf1_t *rec = &sw->rec[0];
152 int ret = bcf_read1(sw->file, sw->hdr, rec);
153
154 if ( ret!=0 ) // last record, get ready for sweeping backwards
155 {
156 sw->idx_done = 1;
157 if (sw->fp) sw->fp->idx_build_otf = 0;
158 sw_seek(sw, SW_BWD);
159 return NULL;
160 }
161
162 if ( !sw->idx_done )
163 {
164 if ( !sw->nidx || pos - sw->idx[sw->nidx-1] > sw->block_size )
165 {
166 sw->nidx++;
167 hts_expand(uint64_t, sw->nidx, sw->midx, sw->idx);
168 sw->idx[sw->nidx-1] = pos;
169 }
170 }
171 return rec;
172 }
173
bcf_sweep_bwd(bcf_sweep_t * sw)174 bcf1_t *bcf_sweep_bwd(bcf_sweep_t *sw)
175 {
176 if ( sw->direction==SW_FWD ) sw_seek(sw, SW_BWD);
177 if ( !sw->nrec ) sw_fill_buffer(sw);
178 if ( !sw->nrec ) return NULL;
179 return &sw->rec[ --sw->nrec ];
180 }
181
bcf_sweep_hdr(bcf_sweep_t * sw)182 bcf_hdr_t *bcf_sweep_hdr(bcf_sweep_t *sw) { return sw->hdr; }
183
184