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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,19 +1,19 @@ | ||
| /* The MIT License | ||
| Copyright (c) 2021 Genome Research Ltd. | ||
| Copyright (c) 2021-2022 Genome Research Ltd. | ||
| Author: Petr Danecek <[email protected]> | ||
| 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 | ||
|
|
@@ -117,7 +117,7 @@ void abuf_set(abuf_t *buf, abuf_opt_t key, void *value) | |
| if ( key==INFO_TAG ) | ||
| { | ||
| buf->split.info_tag = *((char**)value); | ||
| bcf_hdr_printf(buf->out_hdr,"##INFO=<ID=%s,Number=1,Type=String,Description=\"Original variant. Format: CHR|POS|REF|ALT|USED_ALT_IDX\">",buf->split.info_tag); | ||
| bcf_hdr_printf(buf->out_hdr,"##INFO=<ID=%s,Number=1,Type=String,Description=\"Original variant. Format: CHR|POS|REF|ALT|USED_ALT_IDX\">",buf->split.info_tag); | ||
| return; | ||
| } | ||
| if ( key==STAR_ALLELE ) { buf->star_allele = *((int*)value); return; } | ||
|
|
@@ -141,7 +141,7 @@ static void _atomize_allele(abuf_t *buf, bcf1_t *rec, int ial) | |
| while ( rlen>1 && alen>1 && ref[rlen-1]==alt[alen-1] ) rlen--, alen--; | ||
| int Mlen = rlen > alen ? rlen : alen; | ||
|
|
||
| atom_t *atom = NULL; | ||
| atom_t *atom = NULL; | ||
| int i; | ||
| for (i=0; i<Mlen; i++) | ||
| { | ||
|
|
@@ -374,7 +374,7 @@ static void _split_table_set_info(abuf_t *buf, bcf_info_t *info, merge_rule_t mo | |
| memcpy(buf->tmp2+num_size,missing_ptr,num_size); | ||
| else | ||
| memcpy(buf->tmp2+num_size,buf->tmp+num_size*iori,num_size); | ||
| if ( type==BCF_HT_INT && mode==M_SUM ) | ||
| if ( type==BCF_HT_INT && mode==M_SUM ) | ||
| { | ||
| uint8_t *tbl = buf->split.tbl + iout*buf->split.nori; | ||
| for (i=iori; i<buf->split.nori; i++) | ||
|
|
@@ -466,7 +466,10 @@ static void _split_table_set_gt(abuf_t *buf) | |
| error("Out-of-bounds genotypes at %s:%"PRIhts_pos"\n",bcf_seqname(buf->hdr,rec),rec->pos+1); | ||
| int ial = _split_table_get_ial(buf,iout,iori); | ||
| if ( ial==2 && !star_allele ) | ||
| { | ||
| dst[j] = bcf_gt_missing; | ||
| if ( bcf_gt_is_phased(src[j]) ) dst[j] |= 1; | ||
| } | ||
| else | ||
| dst[j] = bcf_gt_is_phased(src[j]) ? bcf_gt_phased(ial) : bcf_gt_unphased(ial); | ||
| } | ||
|
|
@@ -542,7 +545,7 @@ static void _split_table_set_format(abuf_t *buf, bcf_fmt_t *fmt, merge_rule_t mo | |
| { | ||
| int star_allele = _has_star_allele(buf,iout); | ||
| bcf1_t *out = buf->vcf[rbuf_kth(&buf->rbuf,iout)]; | ||
| int ret = 0; | ||
| int ret = 0; | ||
| if ( len==BCF_VL_FIXED || len==BCF_VL_VAR ) | ||
| ret = bcf_update_format(buf->out_hdr, out, tag, buf->tmp, nval, type); | ||
| else if ( len==BCF_VL_A && type!=BCF_HT_STR ) | ||
|
|
@@ -707,7 +710,7 @@ void _abuf_split(abuf_t *buf, bcf1_t *rec) | |
| buf->vcf[j] = bcf_dup(rec); | ||
| return; | ||
| } | ||
| for (i=1; i<rec->n_allele; i++) | ||
| for (i=0; i<rec->n_allele; i++) | ||
| { | ||
| if ( _is_acgtn(rec->d.allele[i]) ) continue; | ||
| rbuf_expand0(&buf->rbuf, bcf1_t*, buf->rbuf.n+1, buf->vcf); | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,71 @@ | ||
| /* The MIT License | ||
| Copyright (c) 2022 Genome Research Ltd. | ||
| Author: Petr Danecek <[email protected]> | ||
| 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. | ||
| */ | ||
|
|
||
| /* | ||
| Simple data buffer | ||
| */ | ||
|
|
||
| #ifndef __DBUF_H__ | ||
| #define __DBUF_H__ | ||
|
|
||
| #include <htslib/hts.h> | ||
|
|
||
| typedef struct | ||
| { | ||
| size_t n,m; | ||
| void **dat; | ||
| } | ||
| dbuf_t; | ||
|
|
||
| static inline dbuf_t *dbuf_push(dbuf_t *buf, void *ptr) | ||
| { | ||
| if ( !buf ) buf = calloc(1,sizeof(dbuf_t)); | ||
| buf->n++; | ||
| hts_expand(void*,buf->n,buf->m,buf->dat); | ||
| buf->dat[buf->n-1] = ptr; | ||
| return buf; | ||
| } | ||
|
|
||
| static inline void *dbuf_ith(dbuf_t *buf, int i) | ||
| { | ||
| return buf->dat[i]; | ||
| } | ||
|
|
||
| static inline size_t dbuf_n(dbuf_t *buf) | ||
| { | ||
| return buf->n; | ||
| } | ||
|
|
||
| static inline void dbuf_destroy_free(dbuf_t *buf) | ||
| { | ||
| int i; | ||
| for (i=0; i<buf->n; i++) free(buf->dat[i]); | ||
| free(buf->dat); | ||
| free(buf); | ||
| } | ||
|
|
||
| #endif | ||
|
|
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