{"id":34700378,"url":"https://github.com/lindenb/htsplusplus","last_synced_at":"2026-04-25T02:38:15.134Z","repository":{"id":137672709,"uuid":"318125410","full_name":"lindenb/htsplusplus","owner":"lindenb","description":"Select variants from VCF/BCF spaced by a distance 'd'.","archived":false,"fork":false,"pushed_at":"2024-11-18T20:14:14.000Z","size":310,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2026-02-12T07:52:44.969Z","etag":null,"topics":["bcf","bioinformatics","c","distance","htslib","variants","vcf"],"latest_commit_sha":null,"homepage":"","language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/lindenb.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2020-12-03T08:29:35.000Z","updated_at":"2024-11-18T20:14:18.000Z","dependencies_parsed_at":"2023-09-23T14:51:43.091Z","dependency_job_id":"d14f6ae7-0fd9-4876-bce9-f2e610a276b6","html_url":"https://github.com/lindenb/htsplusplus","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/lindenb/htsplusplus","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lindenb%2Fhtsplusplus","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lindenb%2Fhtsplusplus/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lindenb%2Fhtsplusplus/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lindenb%2Fhtsplusplus/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/lindenb","download_url":"https://codeload.github.com/lindenb/htsplusplus/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lindenb%2Fhtsplusplus/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":32248341,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-24T13:21:15.438Z","status":"online","status_checked_at":"2026-04-25T02:00:06.260Z","response_time":59,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bcf","bioinformatics","c","distance","htslib","variants","vcf"],"created_at":"2025-12-24T22:51:16.198Z","updated_at":"2026-04-25T02:38:15.117Z","avatar_url":"https://github.com/lindenb.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n# hts++\n\n\n# Compilation\n\ncompilation requires a C++ compiler and `xsltproc`.\n\n```\ngit clone \"https://github.com/lindenb/htsplusplus\"\n\nautoconf -Wno-syntax\n./configure --with-htslib= --with-htslib=${PWD}/../htslib    # see ./configure --help and samtools's INSTALL\nmake\n\n```\n\n\n\n\n# subcommands\n\n\n\n##  SAMVIEWWITHMATE\n\nselect read and their mate that falls within a region from a **query sorted** **BAM**\n\n### Usage\n\n```\nhts++ samviewwithmate [options...] (files)\n```\n\n\n### Options\n\n| short-option | long-option | argument | description | default-value |\n|--------------|-------------|----------|-------------|---------------|\n| -h | --help |  | Display help and exit |  |\n| -v | --version |  | Display Version and exit |  |\n| -o | --output |   \u003cARG\u003e   | output or stdout |  |\n| -R | --reference |   \u003cfasta\u003e   | FASTA reference |  |\n|  | --compression-level |   \u003c0-9\u003e   | compression-level 0 (low compression) to 9 (best compression) |  |\n| -O | --bam-output-format |   \u003cformat\u003e   | output format for sam: SAM, BAM, CRAM |  |\n| -@ | --nthreads |   \u003cnthreads\u003e   | Number of threads |  |\n| -i | --inverse |  | inverse logic: keep read where no read in the pair overlap the BED file |  |\n| -B | --bed |   \u003cBED\u003e   | A BED file. |  |\n\n\n\n\n##  BCFPRUNE\n\nSelect variants with a fixed distance in a **VCF** file.\n\n### Usage\n\n```\nhts++ bcfprune [options...] (files)\n```\n\n\n### Options\n\n| short-option | long-option | argument | description | default-value |\n|--------------|-------------|----------|-------------|---------------|\n| -h | --help |  | Display help and exit |  |\n| -v | --version |  | Display Version and exit |  |\n| -o | --output |   \u003cARG\u003e   | output or stdout |  |\n|  | --compression-level |   \u003c0-9\u003e   | compression-level 0 (low compression) to 9 (best compression) |  |\n| -O | --vcf-output-format |   \u003cformat\u003e   | output format for VCF/BCF: z:gzip vcf v:vcf b:bcf (default v) |  |\n| -d | --distance |   \u003cARG\u003e   | distance |  |\n\n\n\n\n##  BCFCONCAT\n\nconcatenanate multiple vcf/bcf files\n\n### Usage\n\n```\nhts++ bcfconcat in1.bcf in2.vcf.gz in3.vcf\nhts++ bcfconcat bcfs.list\ncat bcfs.list | hts++ bcfconcat\n```\n\n\n### Options\n\n| short-option | long-option | argument | description | default-value |\n|--------------|-------------|----------|-------------|---------------|\n| -h | --help |  | Display help and exit |  |\n| -v | --version |  | Display Version and exit |  |\n| -o | --output |   \u003cARG\u003e   | output or stdout |  |\n|  | --compression-level |   \u003c0-9\u003e   | compression-level 0 (low compression) to 9 (best compression) |  |\n| -O | --vcf-output-format |   \u003cformat\u003e   | output format for VCF/BCF: z:gzip vcf v:vcf b:bcf (default v) |  |\n\n\n\n\n##  BCFFILTERGT\n\nSelect variant using an expression\n\n### Usage\n\n```\nhts++ bcffiltergt [options...] (files)\n```\n\n\n### Options\n\n| short-option | long-option | argument | description | default-value |\n|--------------|-------------|----------|-------------|---------------|\n| -h | --help |  | Display help and exit |  |\n| -v | --version |  | Display Version and exit |  |\n| -o | --output |   \u003cARG\u003e   | output or stdout |  |\n|  | --compression-level |   \u003c0-9\u003e   | compression-level 0 (low compression) to 9 (best compression) |  |\n| -O | --vcf-output-format |   \u003cformat\u003e   | output format for VCF/BCF: z:gzip vcf v:vcf b:bcf (default v) |  |\n| -F | --soft-filter |   \u003cFILTER-ID\u003e   | soft FILTER name. (default: filter out variants) |  |\n| -e | --expression |   \u003cexpression\u003e   | Expression as string |  |\n| -f | --file-expression |   \u003cFILE\u003e   | Expression as file |  |\n\n\n\n\n##  BCFHEAD\n\nShow the first 'N' variants in a VCF\n\n### Usage\n\n```\nhts++ bcfhead [options...] (files)\n```\n\n\n### Options\n\n| short-option | long-option | argument | description | default-value |\n|--------------|-------------|----------|-------------|---------------|\n| -h | --help |  | Display help and exit |  |\n| -v | --version |  | Display Version and exit |  |\n| -o | --output |   \u003cARG\u003e   | output or stdout |  |\n|  | --compression-level |   \u003c0-9\u003e   | compression-level 0 (low compression) to 9 (best compression) |  |\n| -O | --vcf-output-format |   \u003cformat\u003e   | output format for VCF/BCF: z:gzip vcf v:vcf b:bcf (default v) |  |\n| -n | --count |   \u003cCOUNT\u003e   | Number of variants |  |\n\n\n\n\n##  BCF2INTERVALS\n\nconvert VCF/BCF to interval of variants that are distant from 'x' bases.\n\n### Usage\n\n```\nhts++ bcf2intervals [options...] (files)\n```\n\n\n### Options\n\n| short-option | long-option | argument | description | default-value |\n|--------------|-------------|----------|-------------|---------------|\n| -h | --help |  | Display help and exit |  |\n| -v | --version |  | Display Version and exit |  |\n| -o | --output |   \u003cARG\u003e   | output or stdout |  |\n| -d | --distance_per_interval |   \u003cARG\u003e   | distance |  |\n| -m | --min-distance |   \u003cARG\u003e   | min distance |  |\n\n\n\n\n##  SAMRMDUPNAMES\n\nremove duplicated names in sorted BAM (prevent graphtyper from failing)\n\n### Usage\n\n```\nhts++ samrmdupnames [options...] (files)\n```\n\n\n### Options\n\n| short-option | long-option | argument | description | default-value |\n|--------------|-------------|----------|-------------|---------------|\n| -h | --help |  | Display help and exit |  |\n| -v | --version |  | Display Version and exit |  |\n| -o | --output |   \u003cARG\u003e   | output or stdout |  |\n| -R | --reference |   \u003cfasta\u003e   | FASTA reference |  |\n|  | --compression-level |   \u003c0-9\u003e   | compression-level 0 (low compression) to 9 (best compression) |  |\n| -O | --bam-output-format |   \u003cformat\u003e   | output format for sam: SAM, BAM, CRAM |  |\n| -@ | --nthreads |   \u003cnthreads\u003e   | Number of threads |  |\n\n\n\n\n##  FASTQSPLITNFILES\n\nSplit FASTQ to N files\n\n### Usage\n\n```\nhts++ fastqsplitnfiles [options...] (files)\n```\n\n\n### Options\n\n| short-option | long-option | argument | description | default-value |\n|--------------|-------------|----------|-------------|---------------|\n| -h | --help |  | Display help and exit |  |\n| -v | --version |  | Display Version and exit |  |\n| -o | --output |   \u003cARG\u003e   | output or stdout |  |\n| -p | --prefix |   \u003cARG\u003e   | output prefix |  |\n| -n | --count-files |   \u003cARG\u003e   | number of files |  |\n|  | --compression-level |   \u003c0-9\u003e   | compression-level 0 (low compression) to 9 (best compression) |  |\n\n\n\n\n##  BCFSTREAMUNTIL\n\nStream a VCF until a position is found.\n\n### Usage\n\n```\nhts++ bcfstreamuntil [options...] (files)\n```\n\n\n### Options\n\n| short-option | long-option | argument | description | default-value |\n|--------------|-------------|----------|-------------|---------------|\n| -h | --help |  | Display help and exit |  |\n| -v | --version |  | Display Version and exit |  |\n|  | --compression-level |   \u003c0-9\u003e   | compression-level 0 (low compression) to 9 (best compression) |  |\n| -O | --vcf-output-format |   \u003cformat\u003e   | output format for VCF/BCF: z:gzip vcf v:vcf b:bcf (default v) |  |\n| -o | --output |   \u003cARG\u003e   | output or stdout |  |\n| -p | --position |   \u003cARG\u003e   | stop after this position. syntax 'CHROM:POS' |  |\n\n\n\n\n##  TESTS\n\npeforms some tests\n\n### Usage\n\n```\nhts++ tests [options...] (files)\n```\n\n\n### Options\n\n| short-option | long-option | argument | description | default-value |\n|--------------|-------------|----------|-------------|---------------|\n| -h | --help |  | Display help and exit |  |\n| -v | --version |  | Display Version and exit |  |\n| -D | --directory |   \u003cDIR\u003e   | test directory |  |\n\n\n\n\n# Author\n\nPierre Lindenbaum Phd 2022.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flindenb%2Fhtsplusplus","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flindenb%2Fhtsplusplus","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flindenb%2Fhtsplusplus/lists"}