1 /* 2 Copyright (C) 2017 Genome Research Ltd. 3 4 Author: Petr Danecek <pd3@sanger.ac.uk> 5 6 Permission is hereby granted, free of charge, to any person obtaining a copy 7 of this software and associated documentation files (the "Software"), to deal 8 in the Software without restriction, including without limitation the rights 9 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 10 copies of the Software, and to permit persons to whom the Software is 11 furnished to do so, subject to the following conditions: 12 13 The above copyright notice and this permission notice shall be included in 14 all copies or substantial portions of the Software. 15 16 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 17 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 18 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 19 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 20 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 21 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN 22 THE SOFTWARE. 23 */ 24 25 /* 26 Reorder duplicate lines so that compatible variant types are 27 returned together by bcf_sr_next_line() 28 29 - readers grouped by variants. Even with many readers there will be 30 typically only several groups 31 32 */ 33 34 #ifndef BCF_SR_SORT_H 35 #define BCF_SR_SORT_H 36 37 #include "htslib/synced_bcf_reader.h" 38 #include "htslib/kbitset.h" 39 40 typedef struct 41 { 42 int nrec, mrec; 43 bcf1_t **rec; 44 } 45 vcf_buf_t; 46 47 typedef struct 48 { 49 char *str; // "A>C" for biallelic records or "A>C,A>CC" for multiallelic records 50 int type; // VCF_SNP, VCF_REF, etc. 51 int nalt; // number of alternate alleles in this record 52 int nvcf, mvcf, *vcf; // the list of readers with the same variants 53 bcf1_t **rec; // list of VCF records in the readers 54 kbitset_t *mask; // which groups contain the variant 55 } 56 var_t; 57 58 typedef struct 59 { 60 char *key; // only for debugging 61 int nvar, mvar, *var; // the variants and their type 62 int nvcf; // number of readers with the same variants 63 } 64 grp_t; 65 66 typedef struct 67 { 68 int nvar, mvar, *var; // list of compatible variants that can be output together 69 int cnt; // number of readers in this group 70 kbitset_t *mask; // which groups are populated in this set (replace with expandable bitmask) 71 } 72 varset_t; 73 74 typedef struct 75 { 76 uint8_t score[256]; 77 int nvar, mvar; 78 var_t *var; // list of all variants from all readers 79 int nvset, mvset; 80 int mpmat, *pmat; // pairing matrix, i-th vset and j-th group accessible as i*ngrp+j 81 int ngrp, mgrp; 82 int mcnt, *cnt; // number of VCF covered by a varset 83 grp_t *grp; // list of VCF representatives, each with a unique combination of duplicate lines 84 varset_t *vset; // list of variant sets - combinations of compatible variants across multiple groups ready for output 85 vcf_buf_t *vcf_buf; // records sorted in output order, for each VCF 86 bcf_srs_t *sr; 87 void *grp_str2int; 88 void *var_str2int; 89 kstring_t str; 90 int moff, noff, *off, mcharp; 91 char **charp; 92 const char *chr; 93 hts_pos_t pos; 94 int nsr, msr; 95 int pair; 96 int nactive, mactive, *active; // list of readers with lines at the current pos 97 } 98 sr_sort_t; 99 100 sr_sort_t *bcf_sr_sort_init(sr_sort_t *srt); 101 void bcf_sr_sort_reset(sr_sort_t *srt); 102 int bcf_sr_sort_next(bcf_srs_t *readers, sr_sort_t *srt, const char *chr, hts_pos_t pos); 103 int bcf_sr_sort_set_active(sr_sort_t *srt, int i); 104 int bcf_sr_sort_add_active(sr_sort_t *srt, int i); 105 void bcf_sr_sort_destroy(sr_sort_t *srt); 106 void bcf_sr_sort_remove_reader(bcf_srs_t *readers, sr_sort_t *srt, int i); 107 108 #endif 109