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Merge pull request #831 from Genomicsplc/develop
Add VariantKey support
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,86 @@ | ||
| /* plugins/add-variantkey.c -- add VariantKey INFO field. | ||
| Copyright (C) 2017-2018 GENOMICS plc. | ||
| Author: Nicola Asuni <nicola.asuni@genomicsplc.com> | ||
| 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. */ | ||
|
|
||
| #include <stdio.h> | ||
| #include <stdlib.h> | ||
| #include <htslib/hts.h> | ||
| #include <htslib/vcf.h> | ||
| #include <htslib/vcfutils.h> | ||
| #include <inttypes.h> | ||
| #include "../variantkey.h" | ||
|
|
||
| bcf_hdr_t *in_hdr, *out_hdr; | ||
|
|
||
| const char *about(void) | ||
| { | ||
| return "Add VariantKey INFO fields VKX and RSX.\n"; | ||
| } | ||
|
|
||
| const char *usage(void) | ||
| { | ||
| return | ||
| "\n" | ||
| "About: Add VKX and RSX columns.\n" | ||
| "Usage: bcftools +add-variantkey [General Options] \n" | ||
| "Options:\n" | ||
| " run \"bcftools plugin\" for a list of common options\n" | ||
| "\n" | ||
| "Example:\n" | ||
| " bcftools +add-variantkey in.vcf\n" | ||
| "\n"; | ||
| } | ||
|
|
||
| int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out) | ||
| { | ||
| in_hdr = in; | ||
| out_hdr = out; | ||
| bcf_hdr_append(out_hdr, "##INFO=<ID=VKX,Number=1,Type=String,Description=\"Hexadecimal representation of 64 bit VariantKey\">"); | ||
| bcf_hdr_append(out_hdr, "##INFO=<ID=RSX,Number=1,Type=String,Description=\"Hexadecimal representation of ID minus the 'rs' prefix (32bit)\">"); | ||
| return 0; | ||
| } | ||
|
|
||
| bcf1_t *process(bcf1_t *rec) | ||
| { | ||
| uint64_t vk = variantkey( | ||
| in_hdr->id[BCF_DT_CTG][rec->rid].key, | ||
| strlen(in_hdr->id[BCF_DT_CTG][rec->rid].key), | ||
| rec->pos, | ||
| rec->d.allele[0], | ||
| strlen(rec->d.allele[0]), | ||
| rec->d.allele[1], | ||
| strlen(rec->d.allele[1])); | ||
| char vs[17]; | ||
| variantkey_hex(vk, vs); | ||
| bcf_update_info_string(out_hdr, rec, "VKX", vs); | ||
| char rsid[9]; | ||
| char *ptr = rec->d.id; | ||
| ptr += 2; // remove 'rs' | ||
| sprintf(rsid, "%08" PRIx32, (uint32_t)strtoul(ptr, NULL, 10)); | ||
| bcf_update_info_string(out_hdr, rec, "RSX", rsid); | ||
| return rec; | ||
| } | ||
|
|
||
| void destroy(void) | ||
| { | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,113 @@ | ||
| /* plugins/allele-length.c -- Calculate stats about the length of alleles | ||
| Copyright (C) 2017-2018 GENOMICS plc. | ||
| Author: Nicola Asuni <nicola.asuni@genomicsplc.com> | ||
| 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. */ | ||
|
|
||
| #include <stdio.h> | ||
| #include <stdlib.h> | ||
| #include <htslib/vcf.h> | ||
| #include <inttypes.h> | ||
|
|
||
| #define MAXLEN 512 | ||
|
|
||
| static uint64_t numvar; | ||
| static uint64_t numxvar; | ||
| static uint64_t reflen[MAXLEN]; | ||
| static uint64_t altlen[MAXLEN]; | ||
| static uint64_t refaltlen[MAXLEN]; | ||
| static uint64_t xrefaltlen[MAXLEN]; | ||
|
|
||
| const char *about(void) | ||
| { | ||
| return "Count the frequency of the length of REF, ALT and REF+ALT\n"; | ||
| } | ||
|
|
||
| const char *usage(void) | ||
| { | ||
| return | ||
| "\n" | ||
| "About: Count the frequency of the length of alleles.\n" | ||
| "Usage: bcftools +allele-length [General Options] \n" | ||
| "Options:\n" | ||
| " run \"bcftools plugin\" for a list of common options\n" | ||
| "\n" | ||
| "Example:\n" | ||
| " bcftools +allele-length in.vcf\n" | ||
| "\n"; | ||
| } | ||
|
|
||
| // return 0 if the string contains characters other than standard ACGT base letters | ||
| int contain_non_base(const char *str) | ||
| { | ||
| int c; | ||
| while ((c = *str++)) | ||
| { | ||
| if ((c != 'A') && (c != 'a') && (c != 'C') && (c != 'c') && (c != 'G') && (c != 'g') && (c != 'T') && (c != 't')) | ||
| { | ||
| return 1; | ||
| } | ||
| } | ||
| return 0; | ||
| } | ||
|
|
||
| // Called once at startup, allows to initialize local variables. | ||
| // Return 1 to suppress VCF/BCF header from printing, 0 otherwise. | ||
| int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out) | ||
| { | ||
| numvar = 0; | ||
| int i = 0; | ||
| for(i = 0; i < MAXLEN; i++) { | ||
| reflen[i] = 0; | ||
| altlen[i] = 0; | ||
| refaltlen[i] = 0; | ||
| xrefaltlen[i] = 0; | ||
| } | ||
| return 1; | ||
| } | ||
|
|
||
| // Called for each VCF record. Return rec to output the line or NULL to suppress output. | ||
| bcf1_t *process(bcf1_t *rec) | ||
| { | ||
| int rl = strlen(rec->d.allele[0]); | ||
| int al = strlen(rec->d.allele[1]); | ||
| reflen[rl] += 1; | ||
| altlen[al] += 1; | ||
| refaltlen[(rl + al)] += 1; | ||
| if ((contain_non_base(rec->d.allele[0])) || (contain_non_base(rec->d.allele[1]))) | ||
| { | ||
| xrefaltlen[(rl + al)] += 1; | ||
| numxvar++; | ||
| } | ||
| numvar++; | ||
| return NULL; | ||
| } | ||
|
|
||
| // Print final output | ||
| void destroy(void) | ||
| { | ||
| int i = 0; | ||
| printf("LENGTH\tREF\tALT\tREF+ALT\tREF+ALT WITH NON-BASE NUCLEOTIDES\n"); | ||
| for(i = 0; i < MAXLEN; i++) { | ||
| printf("%d\t%"PRIu64"\t%"PRIu64"\t%"PRIu64"\t%"PRIu64"\n", i, reflen[i], altlen[i], refaltlen[i], xrefaltlen[i]); | ||
| } | ||
| printf("\t\t\t%"PRIu64"\t%"PRIu64"\n", numvar, numxvar); | ||
| } |
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