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use new features in vcfpp.h >= v0.5.0
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,6 @@ | ||
| Package: vcfppR | ||
| Title: Rapid Manipulation of the Variant Call Format (VCF) | ||
| Version: 0.4.8 | ||
| Version: 0.5.0 | ||
| Authors@R: c( | ||
| person("Zilong", "Li", , "[email protected]", role = c("aut", "cre"), | ||
| comment = c(ORCID = "0000-0001-5859-2078")), | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -2,7 +2,7 @@ | |
| * @file https://github.com/Zilong-Li/vcfpp/vcfpp.h | ||
| * @author Zilong Li | ||
| * @email [email protected] | ||
| * @version v0.4.1 | ||
| * @version v0.5.1 | ||
| * @breif a single C++ file for manipulating VCF | ||
| * Copyright (C) 2022-2023.The use of this code is governed by the LICENSE file. | ||
| ******************************************************************************/ | ||
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@@ -371,9 +371,36 @@ class BcfHeader | |
| bcf_hdr_remove(hdr, BCF_HL_FLT, tag.c_str()); | ||
| } | ||
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| /** | ||
| * @brief update the sample id in the header | ||
| * @param samples a comma-separated string for multiple new samples | ||
| * @note this only update the samples name in a given sequential order | ||
| * */ | ||
| inline void updateSamples(const std::string & samples) const | ||
| { | ||
| int sid = 0; // index of the sample to modify | ||
| for(auto s : split_string(samples, ",")) | ||
| { | ||
| if(sid < nSamples()) | ||
| { | ||
| hdr->samples[sid] = strdup(s.c_str()); | ||
| sid++; | ||
| } | ||
| else | ||
| { | ||
| # if defined(VERBOSE) | ||
| std::cerr << "you provided too many samples"; | ||
| # endif | ||
| break; | ||
| } | ||
| } | ||
| int ret = bcf_hdr_sync(hdr); | ||
| if(ret != 0) throw std::runtime_error("could not modify " + samples + " in the header\n"); | ||
| } | ||
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| /** | ||
| * @brief explicitly set samples to be extracted | ||
| * @param samples samples to include or exclude as a comma-separated string | ||
| * @param samples samples to include or exclude as a comma-separated string | ||
| * */ | ||
| inline void setSamples(const std::string & samples) const | ||
| { | ||
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@@ -1231,9 +1258,9 @@ class BcfRecord | |
| } | ||
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| /** @brief modify CHROM value */ | ||
| inline void setCHR(const char * chr) | ||
| inline void setCHR(const std::string & s) | ||
| { | ||
| line->rid = bcf_hdr_name2id(header->hdr, chr); | ||
| line->rid = bcf_hdr_name2id(header->hdr, s.c_str()); | ||
| } | ||
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| /** @brief modify position given 1-based value */ | ||
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@@ -1243,15 +1270,34 @@ class BcfRecord | |
| } | ||
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| /** @brief update ID */ | ||
| inline void setID(const char * s) | ||
| inline void setID(const std::string & s) | ||
| { | ||
| bcf_update_id(header->hdr, line.get(), s); | ||
| bcf_update_id(header->hdr, line.get(), s.c_str()); | ||
| } | ||
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| /** @brief set REF and ALT alleles given a string seperated by comma */ | ||
| inline void setRefAlt(const char * alleles_string) | ||
| inline void setRefAlt(const std::string & s) | ||
| { | ||
| bcf_update_alleles_str(header->hdr, line.get(), alleles_string); | ||
| bcf_update_alleles_str(header->hdr, line.get(), s.c_str()); | ||
| } | ||
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| /** @brief modify the QUAL value */ | ||
| inline void setQUAL(float q) | ||
| { | ||
| line->qual = q; | ||
| } | ||
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| /** @brief modify the QUAL value */ | ||
| inline void setQUAL(char q) | ||
| { | ||
| bcf_float_set_missing(line->qual); | ||
| } | ||
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| /** @brief modify the FILTER value */ | ||
| inline void setFILTER(const std::string & s) | ||
| { | ||
| int32_t tmpi = bcf_hdr_id2int(header->hdr, BCF_DT_ID, s.c_str()); | ||
| bcf_add_filter(header->hdr, line.get(), tmpi); | ||
| } | ||
|
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| /** @brief return 0-base start of the variant (can be any type) */ | ||
|
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@@ -1750,12 +1796,23 @@ class BcfWriter | |
| hp = &h; | ||
| } | ||
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| /// copy header of given VCF | ||
| void copyHeader(const std::string & vcffile) | ||
| /// copy header of given VCF and restrict on samples. if samples=="", FORMAT removed and only sites left | ||
| void copyHeader(const std::string & vcffile, std::string samples = "-") | ||
| { | ||
| htsFile * fp2 = hts_open(vcffile.c_str(), "r"); | ||
| if(!fp2) throw std::invalid_argument("I/O error: input file is invalid"); | ||
| header.hdr = bcf_hdr_read(fp2); | ||
| if(samples == "") | ||
| { // site-only | ||
| bcf_hdr_t * hfull = bcf_hdr_read(fp2); | ||
| header.hdr = bcf_hdr_subset(hfull, 0, 0, 0); | ||
| bcf_hdr_remove(header.hdr, BCF_HL_FMT, NULL); | ||
| bcf_hdr_destroy(hfull); | ||
| } | ||
| else | ||
| { | ||
| header.hdr = bcf_hdr_read(fp2); | ||
| header.setSamples(samples); | ||
| } | ||
| hts_close(fp2); | ||
| initalHeader(header); | ||
| } | ||
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