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- /* The MIT License
-
- Copyright (c) 2017-2021 Genome Research Ltd.
-
- Author: Petr Danecek <pd3@sanger.ac.uk>
-
- Permission is hereby granted, free of charge, to any person obtaining a copy
- of this software and associated documentation files (the "Software"), to deal
- in the Software without restriction, including without limitation the rights
- to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- copies of the Software, and to permit persons to whom the Software is
- furnished to do so, subject to the following conditions:
-
- The above copyright notice and this permission notice shall be included in
- all copies or substantial portions of the Software.
-
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
- THE SOFTWARE.
-
- */
-
- /*
- Buffer VCF records and perform operations on the buffer
- */
-
- #ifndef __VCFBUF_H__
- #define __VCFBUF_H__
-
- #include <htslib/vcf.h>
-
- typedef struct _vcfbuf_t vcfbuf_t;
-
- // Modes of operation
- typedef enum
- {
- VCFBUF_OVERLAP_WIN, // keep only overlapping variants in the window
- VCFBUF_RMDUP, // remove duplicate sites (completely)
- VCFBUF_NSITES, // leave at max this many sites in the window
- VCFBUF_NSITES_MODE, // one of: maxAF (keep sites with max AF), 1st (sites that come first), rand (pick randomly)
- VCFBUF_AF_TAG, // use this INFO tag with VCFBUF_NSITES
-
- // LD related options
- LD_RAND_MISSING, // randomize rather than ignore missing genotypes
- LD_FILTER1, // exclude the next record inserted by vcfbuf_push() from LD analysis
- LD_MAX_R2, // If set, vcfbuf_ld() will stop at the first record that exceeds the R2,
- LD_MAX_LD, // LD, or HD threshold. When multiple are set, the OR logic is applied
- LD_MAX_HD, //
- }
- vcfbuf_opt_t;
-
- #define vcfbuf_set_opt(buf,type,key,value) { type tmp = value; vcfbuf_set(buf, key, (void*)&tmp); }
- void vcfbuf_set(vcfbuf_t *buf, vcfbuf_opt_t key, void *value);
-
-
- /*
- * vcfbuf_init() - init buffer
- * @win: number of sites (>0) or bp (<0)
- */
- vcfbuf_t *vcfbuf_init(bcf_hdr_t *hdr, int win);
- void vcfbuf_destroy(vcfbuf_t *buf);
-
- /*
- * vcfbuf_push() - push a new site for analysis
- */
- bcf1_t *vcfbuf_push(vcfbuf_t *buf, bcf1_t *rec);
-
- /*
- * vcfbuf_peek() - return pointer to i-th record in the buffer but do not remove it from the buffer
- * @idx: 0-based index to buffered lines
- */
- bcf1_t *vcfbuf_peek(vcfbuf_t *buf, int idx);
-
- /*
- * vcfbuf_remove() - return pointer to i-th record in the buffer and remove it from the buffer
- * @idx: 0-based index to buffered lines
- */
- bcf1_t *vcfbuf_remove(vcfbuf_t *buf, int idx);
-
- bcf1_t *vcfbuf_flush(vcfbuf_t *buf, int flush_all);
-
- /*
- * vcfbuf_nsites() - return the number of sites in the buffer
- */
- int vcfbuf_nsites(vcfbuf_t *buf);
-
- /*
- * vcfbuf_ld() - find records with maximum LD values or the values in first record that exceeds thresholds
- * set by vcfbuf_set_opt(..,LD_MAX*,..)
- *
- * Returns 0 on success or -1 if no values were filled.
- *
- * @val: will be filled with the values
- * .. correlation coefficient r-squared
- * .. Lewontin's D' (PMID: 19433632)
- * .. Ragsdale's \hat{D} (doi:10.1093/molbev/msz265)
- * @rec: corresponding positions or NULL if the value(s) has not been set
- */
- #define VCFBUF_LD_N 3
- #define VCFBUF_LD_IDX_R2 0
- #define VCFBUF_LD_IDX_LD 1
- #define VCFBUF_LD_IDX_HD 2
- typedef struct
- {
- double val[VCFBUF_LD_N]; // r2, ld, hd
- bcf1_t *rec[VCFBUF_LD_N]; // record with max r2, ld, hd
- }
- vcfbuf_ld_t;
- int vcfbuf_ld(vcfbuf_t *buf, bcf1_t *rec, vcfbuf_ld_t *ld);
-
- #endif
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