From 3f899d898a2472d1f71255ab56fba71b55ee03c6 Mon Sep 17 00:00:00 2001 From: kojix2 Date: Wed, 19 Jul 2023 10:15:47 +0000 Subject: [PATCH] deploy: 0767126f0bd494f19e30b45a09ee428a0b19a7c4 --- HTS.html | 40 +++++++------- HTS/Bam.html | 96 ++++++++++++++++---------------- HTS/Bam/Cigar.html | 8 +-- HTS/Bam/Flag.html | 48 ++++++++-------- HTS/Bam/Header.html | 30 +++++----- HTS/Bam/Record.html | 130 ++++++++++++++++++++++---------------------- HTS/Bcf.html | 84 ++++++++++++++-------------- HTS/Bcf/Format.html | 8 +-- HTS/Bcf/Header.html | 22 ++++---- HTS/Bcf/Info.html | 12 ++-- HTS/Bcf/Record.html | 50 ++++++++--------- HTS/Faidx.html | 28 +++++----- HTS/Hts.html | 24 ++++---- HTS/LibHTS2.html | 128 +++++++++++++++++++++---------------------- HTS/Tabix.html | 12 ++-- index.json | 2 +- search-index.js | 2 +- 17 files changed, 362 insertions(+), 362 deletions(-) diff --git a/HTS.html b/HTS.html index 59cb053..abc1f52 100644 --- a/HTS.html +++ b/HTS.html @@ -187,140 +187,140 @@

- + hts/bam.cr
- + hts/bam/cigar.cr
- + hts/bam/flag.cr
- + hts/bam/header.cr
- + hts/bam/record.cr
- + hts/bcf.cr
- + hts/bcf/format.cr
- + hts/bcf/header.cr
- + hts/bcf/info.cr
- + hts/bcf/record.cr
- + hts/faidx.cr
- + hts/hts.cr
- + hts/libhts.cr
- + hts/libhts/libhts.cr
- + hts/libhts2/bgzf.cr
- + hts/libhts2/hfile.cr
- + hts/libhts2/sam.cr
- + hts/libhts2/vcf.cr
- + hts/tabix.cr
- + hts/version.cr diff --git a/HTS/Bam.html b/HTS/Bam.html index 5f3fbfb..b67e7ac 100644 --- a/HTS/Bam.html +++ b/HTS/Bam.html @@ -203,35 +203,35 @@

- + hts/bam.cr
- + hts/bam/cigar.cr
- + hts/bam/flag.cr
- + hts/bam/header.cr
- + hts/bam/record.cr @@ -617,7 +617,7 @@


- [View source] + [View source]
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- [View source] + [View source]
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- [View source] + [View source]
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- [View source] + [View source]
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- [View source] + [View source]
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- [View source] + [View source]
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- [View source] + [View source]
@@ -810,7 +810,7 @@


- [View source] + [View source]
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- [View source] + [View source]
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- [View source] + [View source]
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- [View source] + [View source]
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- [View source] + [View source]
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- [View source] + [View source]
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- [View source] + [View source]
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- [View source] + [View source]
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- [View source] + [View source]
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- [View source] + [View source]
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@@ -1306,7 +1306,7 @@


- [View source] + [View source]
@@ -1322,7 +1322,7 @@


- [View source] + [View source]
diff --git a/HTS/Bam/Cigar.html b/HTS/Bam/Cigar.html index e039e19..fb5710a 100644 --- a/HTS/Bam/Cigar.html +++ b/HTS/Bam/Cigar.html @@ -203,7 +203,7 @@

- + hts/bam/cigar.cr @@ -320,7 +320,7 @@


- [View source] + [View source]
@@ -359,7 +359,7 @@


- [View source] + [View source]
@@ -391,7 +391,7 @@


- [View source] + [View source]
diff --git a/HTS/Bam/Flag.html b/HTS/Bam/Flag.html index 9288572..b045df2 100644 --- a/HTS/Bam/Flag.html +++ b/HTS/Bam/Flag.html @@ -189,7 +189,7 @@

- + hts/bam/flag.cr @@ -413,7 +413,7 @@


- [View source] + [View source]
@@ -443,7 +443,7 @@


- [View source] + [View source]
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- [View source] + [View source]
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- [View source] + [View source]
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- [View source] + [View source]
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- [View source] + [View source]
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- [View source] + [View source]
diff --git a/HTS/Bam/Header.html b/HTS/Bam/Header.html index c266466..7800f7e 100644 --- a/HTS/Bam/Header.html +++ b/HTS/Bam/Header.html @@ -189,7 +189,7 @@

- + hts/bam/header.cr @@ -363,7 +363,7 @@


- [View source] + [View source]
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- [View source] + [View source]
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- [View source] + [View source]
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- [View source] + [View source]
@@ -600,7 +600,7 @@


- [View source] + [View source]
@@ -616,7 +616,7 @@


- [View source] + [View source]
diff --git a/HTS/Bam/Record.html b/HTS/Bam/Record.html index 46880b6..34d97e9 100644 --- a/HTS/Bam/Record.html +++ b/HTS/Bam/Record.html @@ -189,7 +189,7 @@

- + hts/bam/record.cr @@ -656,7 +656,7 @@


- [View source] + [View source]
@@ -672,7 +672,7 @@


- [View source] + [View source]
@@ -702,7 +702,7 @@


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@@ -1789,7 +1789,7 @@


- [View source] + [View source]
diff --git a/HTS/Bcf.html b/HTS/Bcf.html index cd7a3a7..c1633d6 100644 --- a/HTS/Bcf.html +++ b/HTS/Bcf.html @@ -203,35 +203,35 @@

- + hts/bcf.cr
- + hts/bcf/format.cr
- + hts/bcf/header.cr
- + hts/bcf/info.cr
- + hts/bcf/record.cr @@ -587,7 +587,7 @@


- [View source] + [View source]
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- [View source] + [View source]
diff --git a/HTS/Bcf/Format.html b/HTS/Bcf/Format.html index a63971f..6e42e77 100644 --- a/HTS/Bcf/Format.html +++ b/HTS/Bcf/Format.html @@ -189,7 +189,7 @@

- + hts/bcf/format.cr @@ -292,7 +292,7 @@


- [View source] + [View source]
@@ -322,7 +322,7 @@


- [View source] + [View source]
@@ -338,7 +338,7 @@


- [View source] + [View source]
diff --git a/HTS/Bcf/Header.html b/HTS/Bcf/Header.html index b5bae25..c25b000 100644 --- a/HTS/Bcf/Header.html +++ b/HTS/Bcf/Header.html @@ -189,7 +189,7 @@

- + hts/bcf/header.cr @@ -331,7 +331,7 @@


- [View source] + [View source]
@@ -352,7 +352,7 @@


- [View source] + [View source]
@@ -368,7 +368,7 @@


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@@ -494,7 +494,7 @@


- [View source] + [View source]
@@ -510,7 +510,7 @@


- [View source] + [View source]
diff --git a/HTS/Bcf/Info.html b/HTS/Bcf/Info.html index df5d54b..ac96c6c 100644 --- a/HTS/Bcf/Info.html +++ b/HTS/Bcf/Info.html @@ -189,7 +189,7 @@

- + hts/bcf/info.cr @@ -302,7 +302,7 @@


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@@ -348,7 +348,7 @@


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@@ -364,7 +364,7 @@


- [View source] + [View source]
@@ -380,7 +380,7 @@


- [View source] + [View source]
diff --git a/HTS/Bcf/Record.html b/HTS/Bcf/Record.html index c705a7e..108aac4 100644 --- a/HTS/Bcf/Record.html +++ b/HTS/Bcf/Record.html @@ -189,7 +189,7 @@

- + hts/bcf/record.cr @@ -401,7 +401,7 @@


- [View source] + [View source]
@@ -417,7 +417,7 @@


- [View source] + [View source]
@@ -447,7 +447,7 @@


- [View source] + [View source]
@@ -463,7 +463,7 @@


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@@ -479,7 +479,7 @@


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@@ -511,7 +511,7 @@


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@@ -527,7 +527,7 @@


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@@ -543,7 +543,7 @@


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@@ -564,7 +564,7 @@


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@@ -788,7 +788,7 @@


- [View source] + [View source]
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- [View source] + [View source]
diff --git a/HTS/Faidx.html b/HTS/Faidx.html index 16a79f2..1792c06 100644 --- a/HTS/Faidx.html +++ b/HTS/Faidx.html @@ -189,7 +189,7 @@

- + hts/faidx.cr @@ -354,7 +354,7 @@


- [View source] + [View source]
@@ -382,7 +382,7 @@


- [View source] + [View source]
@@ -398,7 +398,7 @@


- [View source] + [View source]
@@ -426,7 +426,7 @@


- [View source] + [View source]
@@ -442,7 +442,7 @@


- [View source] + [View source]
@@ -458,7 +458,7 @@


- [View source] + [View source]
@@ -474,7 +474,7 @@


- [View source] + [View source]
@@ -490,7 +490,7 @@


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@@ -522,7 +522,7 @@


- [View source] + [View source]
@@ -538,7 +538,7 @@


- [View source] + [View source]
@@ -554,7 +554,7 @@


- [View source] + [View source]
@@ -570,7 +570,7 @@


- [View source] + [View source]
diff --git a/HTS/Hts.html b/HTS/Hts.html index 2663831..9bdb43b 100644 --- a/HTS/Hts.html +++ b/HTS/Hts.html @@ -207,7 +207,7 @@

- + hts/hts.cr @@ -354,7 +354,7 @@


- [View source] + [View source]
@@ -370,7 +370,7 @@


- [View source] + [View source]
@@ -386,7 +386,7 @@


- [View source] + [View source]
@@ -402,7 +402,7 @@


- [View source] + [View source]
@@ -418,7 +418,7 @@


- [View source] + [View source]
@@ -434,7 +434,7 @@


- [View source] + [View source]
@@ -450,7 +450,7 @@


- [View source] + [View source]
@@ -466,7 +466,7 @@


- [View source] + [View source]
@@ -482,7 +482,7 @@


- [View source] + [View source]
@@ -510,7 +510,7 @@


- [View source] + [View source]
@@ -526,7 +526,7 @@


- [View source] + [View source]
diff --git a/HTS/LibHTS2.html b/HTS/LibHTS2.html index 8ae9a3d..609ca4d 100644 --- a/HTS/LibHTS2.html +++ b/HTS/LibHTS2.html @@ -201,35 +201,35 @@

- + hts/libhts.cr
- + hts/libhts2/bgzf.cr
- + hts/libhts2/hfile.cr
- + hts/libhts2/sam.cr
- + hts/libhts2/vcf.cr @@ -1007,7 +1007,7 @@


- [View source] + [View source]
@@ -1028,7 +1028,7 @@


- [View source] + [View source]
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diff --git a/HTS/Tabix.html b/HTS/Tabix.html index 39e9ea8..f57905a 100644 --- a/HTS/Tabix.html +++ b/HTS/Tabix.html @@ -189,7 +189,7 @@

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diff --git a/index.json b/index.json index 09cf144..054e766 100644 --- a/index.json +++ b/index.json @@ -1 +1 @@ -{"repository_name":"hts","body":"# HTS.cr\n\n[![CI](https://github.com/bio-cr/hts.cr/actions/workflows/ci.yml/badge.svg)](https://github.com/bio-cr/hts.cr/actions/workflows/ci.yml)\n[![Slack](http://img.shields.io/badge/slack-bio--crystal-purple?labelColor=000000&logo=slack)](https://bio-crystal.slack.com/)\n[![Get invite to BioCrystal](http://img.shields.io/badge/Get_invite_to_BioCrystal-purple?labelColor=000000&logo=slack)](https://join.slack.com/t/bio-crystal/shared_invite/zt-tas46pww-JSEloonmn3Ma5eD2~VeT_g)\n[![DOI](https://zenodo.org/badge/351622305.svg)](https://zenodo.org/badge/latestdoi/351622305)\n\nHTS.cr provides [Crystal](https://github.com/crystal-lang/crystal) bindings for [HTSlib](https://github.com/samtools/htslib) that allows you to read and write file formats commonly used in genomics, such as [SAM, BAM, VCF, and BCF](http://samtools.github.io/hts-specs/).\n\n:information_source: Method names will be changed to rust-htslib style in the next version.\n\n## Requirements\n\n* [Crystal](https://crystal-lang.org)\n* [HTSlib](https://github.com/samtools/htslib)\n * Ubuntu : `apt install libhts-dev`\n * macOS : `brew install htslib`\n * Any OS : Build from [source code](https://github.com/samtools/htslib)\n * Make sure that `pkg-config` can detect htslib: `pkg-config --libs htslib`\n\n## Installation\n\nAdd htslib to your `shard.yml`:\n\n ```yaml\n dependencies:\n htslib:\n github: bio-cr/hts.cr\n branch: develop\n ```\n\nRun `shards install`\n\n## Usage\n\nRead SAM / BAM / CRAM\n\n```crystal\nrequire \"hts/bam\"\n\nbam = HTS::Bam.open(bam_path)\n\nbam.each do |r|\n p name: r.qname,\n flag: r.flag.value,\n chrm: r.chrom,\n strt: r.pos + 1,\n mapq: r.mapq,\n cigr: r.cigar.to_s,\n mchr: r.mate_chrom,\n mpos: r.mpos + 1,\n isiz: r.isize,\n seqs: r.seq,\n qual: r.qual_string,\n axMC: r.aux(\"MC\")\nend\n\nbam.close\n```\n\nRead VCF / BCF\n\n```crystal\nrequire \"hts/bcf\"\n\nbcf = HTS::Bcf.open(bcf_path)\n\nbcf.each do |r|\n p chrom: r.chrom,\n pos: r.pos,\n id: r.id,\n qual: r.qual,\n filter: r.filter,\n ref: r.ref,\n alt: r.alt,\n # alleles r.alleles\n # info: r.info,\n # format r.format\nend\n\nbcf.close\n```\n\n## API Overview\n\n* High level API - Classes include Bam, Bcf, Tabix, Faidx, etc.\n* LibHTS - Native C bindings to HTSLib generated by [crystal_lib](https://github.com/crystal-lang/crystal_lib).\n* For more information, please see [API documentation](https://bio-cr.github.io/hts/).\n\n```\n ┌──────────────────── HTS ────────────────────┐\n │ │\n │ ┌─ Bam ────────┬─ Bcf ───────┬─ Tabix ────┐ │\n │ │ SAM BAM CRAM │ VCF BCF │ TABIX │ │\n │ └──────────────┴─────────────┴────────────┘ │\n │ ┌─LibHTS2───────────┐ │\n │ ┌─LibHTS────────────┤ Macro functions ├─┐ │\n │ │ Native C bindings └───────────────────┘ │ │\n │ └─────────────────────────────────────────┘ │\n └─────────────────────────────────────────────┘\n```\n\nLibHTS2: Since methods cannot be added to `Lib` in the Crystal language, macro functions are implemented in the LibHTS2 module. This is different from Ruby-htslib.\n\n## Looking for flexibility?\n\nThe Crystal language is suited for creating efficient command-line tools. The Ruby language, on the other hand, is suited for exploratory analysis.\n\n* [ruby-htslib](https://github.com/kojix2/ruby-htslib)\n\n## Contributing\n\n:rocket: Feel free to fork it out! \n\n git clone https://github.com/bio-cr/hts.cr\n cd hts.cr\n crystal run test/run_all.cr\n\n\nHTS.cr is an immature, work-in-progress library, and pull requests such as small typo fixes are welcome.\n\n Do you need commit rights to hts?\n Do you want to get admin rights and take over the project?\n Please feel free to contact us @kojix2.\n\n## Benchmark\n\nhttps://github.com/brentp/vcf-bench\n\ncode: https://github.com/kojix2/vcf-bench/blob/kojix2/crystal-htslib/read.cr\n\n","program":{"html_id":"hts/toplevel","path":"toplevel.html","kind":"module","full_name":"Top Level Namespace","name":"Top Level 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(\"10000\".to_i(2))) != 0)\n LibHTS2.bgzf_tell(@hts_file.value.fp.bgzf)\n else\n LibHTS2.htell(@hts_file.value.fp.hfile)\n end\nend\n"}},{"html_id":"to_unsafe-instance-method","name":"to_unsafe","abstract":false,"location":{"filename":"src/hts/hts.cr","line_number":33,"url":"https://github.com/bio-cr/hts.cr/blob/0be65ec18d7ef2f4570eb362d36b367d13980789/src/hts/hts.cr#L33"},"def":{"name":"to_unsafe","visibility":"Public","body":"@hts_file"}}],"macros":[{"html_id":"define_getter(name)-macro","name":"define_getter","abstract":false,"args":[{"name":"name","external_name":"name","restriction":""}],"args_string":"(name)","args_html":"(name)","location":{"filename":"src/hts/hts.cr","line_number":7,"url":"https://github.com/bio-cr/hts.cr/blob/0be65ec18d7ef2f4570eb362d36b367d13980789/src/hts/hts.cr#L7"},"def":{"name":"define_getter","args":[{"name":"name","external_name":"name","restriction":""}],"visibility":"Public","body":" def \n{{ name.id }}\n\n check_closed\n position = tell\n ary = map 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constants

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constants

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of file +{"repository_name":"hts","body":"# HTS.cr\n\n[![CI](https://github.com/bio-cr/hts.cr/actions/workflows/ci.yml/badge.svg)](https://github.com/bio-cr/hts.cr/actions/workflows/ci.yml)\n[![Slack](http://img.shields.io/badge/slack-bio--crystal-purple?labelColor=000000&logo=slack)](https://bio-crystal.slack.com/)\n[![Get invite to BioCrystal](http://img.shields.io/badge/Get_invite_to_BioCrystal-purple?labelColor=000000&logo=slack)](https://join.slack.com/t/bio-crystal/shared_invite/zt-tas46pww-JSEloonmn3Ma5eD2~VeT_g)\n[![DOI](https://zenodo.org/badge/351622305.svg)](https://zenodo.org/badge/latestdoi/351622305)\n\nHTS.cr provides [Crystal](https://github.com/crystal-lang/crystal) bindings for [HTSlib](https://github.com/samtools/htslib) that allows you to read and write file formats commonly used in genomics, such as [SAM, BAM, VCF, and BCF](http://samtools.github.io/hts-specs/).\n\n:information_source: Method names will be changed to rust-htslib style in the next version.\n\n## Requirements\n\n* [Crystal](https://crystal-lang.org)\n* [HTSlib](https://github.com/samtools/htslib)\n * Ubuntu : `apt install libhts-dev`\n * macOS : `brew install htslib`\n * Any OS : Build from [source code](https://github.com/samtools/htslib)\n * Make sure that `pkg-config` can detect htslib: `pkg-config --libs htslib`\n\n## Installation\n\nAdd htslib to your `shard.yml`:\n\n ```yaml\n dependencies:\n htslib:\n github: bio-cr/hts.cr\n branch: develop\n ```\n\nRun `shards install`\n\n## Usage\n\nRead SAM / BAM / CRAM\n\n```crystal\nrequire \"hts/bam\"\n\nbam = HTS::Bam.open(bam_path)\n\nbam.each do |r|\n p name: r.qname,\n flag: r.flag.value,\n chrm: r.chrom,\n strt: r.pos + 1,\n mapq: r.mapq,\n cigr: r.cigar.to_s,\n mchr: r.mate_chrom,\n mpos: r.mpos + 1,\n isiz: r.isize,\n seqs: r.seq,\n qual: r.qual_string,\n axMC: r.aux(\"MC\")\nend\n\nbam.close\n```\n\nRead VCF / BCF\n\n```crystal\nrequire \"hts/bcf\"\n\nbcf = HTS::Bcf.open(bcf_path)\n\nbcf.each do |r|\n p chrom: r.chrom,\n pos: r.pos,\n id: r.id,\n qual: r.qual,\n filter: r.filter,\n ref: r.ref,\n alt: r.alt,\n # alleles r.alleles\n # info: r.info,\n # format r.format\nend\n\nbcf.close\n```\n\n## API Overview\n\n* High level API - Classes include Bam, Bcf, Tabix, Faidx, etc.\n* LibHTS - Native C bindings to HTSLib generated by [crystal_lib](https://github.com/crystal-lang/crystal_lib).\n* For more information, please see [API documentation](https://bio-cr.github.io/hts/).\n\n```\n ┌──────────────────── HTS ────────────────────┐\n │ │\n │ ┌─ Bam ────────┬─ Bcf ───────┬─ Tabix ────┐ │\n │ │ SAM BAM CRAM │ VCF BCF │ TABIX │ │\n │ └──────────────┴─────────────┴────────────┘ │\n │ ┌─LibHTS2───────────┐ │\n │ ┌─LibHTS────────────┤ Macro functions ├─┐ │\n │ │ Native C bindings └───────────────────┘ │ │\n │ └─────────────────────────────────────────┘ │\n └─────────────────────────────────────────────┘\n```\n\nLibHTS2: Since methods cannot be added to `Lib` in the Crystal language, macro functions are implemented 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This is different from Ruby-htslib.\n\n## Looking for flexibility?\n\nThe Crystal language is suited for creating efficient command-line tools. 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bcf1)\n"}},{"html_id":"endpos-instance-method","name":"endpos","abstract":false,"location":{"filename":"src/hts/bcf/record.cr","line_number":40,"url":"https://github.com/bio-cr/hts.cr/blob/0767126f0bd494f19e30b45a09ee428a0b19a7c4/src/hts/bcf/record.cr#L40"},"def":{"name":"endpos","visibility":"Public","body":"pos + @bcf1.value.rlen"}},{"html_id":"filter-instance-method","name":"filter","abstract":false,"location":{"filename":"src/hts/bcf/record.cr","line_number":57,"url":"https://github.com/bio-cr/hts.cr/blob/0767126f0bd494f19e30b45a09ee428a0b19a7c4/src/hts/bcf/record.cr#L57"},"def":{"name":"filter","visibility":"Public","body":"LibHTS.bcf_unpack(@bcf1, LibHTS2::BCF_UN_FLT)\nd = @bcf1.value.d\nn_flt = d.n_flt\ncase n_flt\nwhen 0\n \"PASS\"\nwhen 1\n i = d.flt.value\n String.new(LibHTS2.bcf_hdr_int2id(@header, LibHTS2::BCF_DT_ID, i))\nwhen 2..\n Array(String).new(n_flt) do |i|\n j = d.flt[i]\n String.new(LibHTS2.bcf_hdr_int2id(@header, LibHTS2::BCF_DT_ID, j))\n end\nelse\n 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LibHTS2::BCF_UN_SHR)\nInfo.new(self)\n"}},{"html_id":"pos-instance-method","name":"pos","abstract":false,"location":{"filename":"src/hts/bcf/record.cr","line_number":32,"url":"https://github.com/bio-cr/hts.cr/blob/0767126f0bd494f19e30b45a09ee428a0b19a7c4/src/hts/bcf/record.cr#L32"},"def":{"name":"pos","visibility":"Public","body":"@bcf1.value.pos"}},{"html_id":"pos=(pos)-instance-method","name":"pos=","abstract":false,"args":[{"name":"pos","external_name":"pos","restriction":""}],"args_string":"(pos)","args_html":"(pos)","location":{"filename":"src/hts/bcf/record.cr","line_number":36,"url":"https://github.com/bio-cr/hts.cr/blob/0767126f0bd494f19e30b45a09ee428a0b19a7c4/src/hts/bcf/record.cr#L36"},"def":{"name":"pos=","args":[{"name":"pos","external_name":"pos","restriction":""}],"visibility":"Public","body":"@bcf1.value.pos = 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LibHTS2::BCF_UN_STR)\nString.new(@bcf1.value.d.allele[0])\n"}},{"html_id":"rid-instance-method","name":"rid","abstract":false,"location":{"filename":"src/hts/bcf/record.cr","line_number":20,"url":"https://github.com/bio-cr/hts.cr/blob/0767126f0bd494f19e30b45a09ee428a0b19a7c4/src/hts/bcf/record.cr#L20"},"def":{"name":"rid","visibility":"Public","body":"@bcf1.value.rid"}},{"html_id":"rid=(rid)-instance-method","name":"rid=","abstract":false,"args":[{"name":"rid","external_name":"rid","restriction":""}],"args_string":"(rid)","args_html":"(rid)","location":{"filename":"src/hts/bcf/record.cr","line_number":24,"url":"https://github.com/bio-cr/hts.cr/blob/0767126f0bd494f19e30b45a09ee428a0b19a7c4/src/hts/bcf/record.cr#L24"},"def":{"name":"rid=","args":[{"name":"rid","external_name":"rid","restriction":""}],"visibility":"Public","body":"@bcf1.value.rid = rid"}},{"html_id":"to_s(io:IO)-instance-method","name":"to_s","doc":"Appends a short String representation of this object\nwhich includes its 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[SAM, BAM, VCF, and BCF](http://samtools.github.io/hts-specs/).\n\n:information_source: Method names will be changed to rust-htslib style in the next version.\n\n## Requirements\n\n* [Crystal](https://crystal-lang.org)\n* [HTSlib](https://github.com/samtools/htslib)\n * Ubuntu : `apt install libhts-dev`\n * macOS : `brew install htslib`\n * Any OS : Build from [source code](https://github.com/samtools/htslib)\n * Make sure that `pkg-config` can detect htslib: `pkg-config --libs htslib`\n\n## Installation\n\nAdd htslib to your `shard.yml`:\n\n ```yaml\n dependencies:\n htslib:\n github: bio-cr/hts.cr\n branch: develop\n ```\n\nRun `shards install`\n\n## Usage\n\nRead SAM / BAM / CRAM\n\n```crystal\nrequire \"hts/bam\"\n\nbam = HTS::Bam.open(bam_path)\n\nbam.each do |r|\n p name: r.qname,\n flag: r.flag.value,\n chrm: r.chrom,\n strt: r.pos + 1,\n mapq: r.mapq,\n cigr: r.cigar.to_s,\n mchr: r.mate_chrom,\n mpos: r.mpos + 1,\n isiz: r.isize,\n seqs: r.seq,\n qual: r.qual_string,\n axMC: r.aux(\"MC\")\nend\n\nbam.close\n```\n\nRead VCF / BCF\n\n```crystal\nrequire \"hts/bcf\"\n\nbcf = HTS::Bcf.open(bcf_path)\n\nbcf.each do |r|\n p chrom: r.chrom,\n pos: r.pos,\n id: r.id,\n qual: r.qual,\n filter: r.filter,\n ref: r.ref,\n alt: r.alt,\n # alleles r.alleles\n # info: r.info,\n # format r.format\nend\n\nbcf.close\n```\n\n## API Overview\n\n* High level API - Classes include Bam, Bcf, Tabix, Faidx, etc.\n* LibHTS - Native C bindings to HTSLib generated by [crystal_lib](https://github.com/crystal-lang/crystal_lib).\n* For more information, please see [API documentation](https://bio-cr.github.io/hts/).\n\n```\n ┌──────────────────── HTS ────────────────────┐\n │ │\n │ ┌─ Bam ────────┬─ Bcf ───────┬─ Tabix ────┐ │\n │ │ SAM BAM CRAM │ VCF BCF │ TABIX │ │\n │ └──────────────┴─────────────┴────────────┘ │\n │ ┌─LibHTS2───────────┐ │\n │ ┌─LibHTS────────────┤ Macro functions ├─┐ │\n │ │ Native C bindings └───────────────────┘ │ │\n │ └─────────────────────────────────────────┘ 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record\")\nend\n"}},{"html_id":"write_header(header)-instance-method","name":"write_header","abstract":false,"args":[{"name":"header","external_name":"header","restriction":""}],"args_string":"(header)","args_html":"(header)","location":{"filename":"src/hts/bcf.cr","line_number":98,"url":"https://github.com/bio-cr/hts.cr/blob/0be65ec18d7ef2f4570eb362d36b367d13980789/src/hts/bcf.cr#L98"},"def":{"name":"write_header","args":[{"name":"header","external_name":"header","restriction":""}],"visibility":"Public","body":"check_closed\n@header = header.clone\nLibHTS.bcf_hdr_write(@hts_file, 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pointerof(@p1)\nh = @record.header\nr = @record\nLibHTS.bcf_get_format_values(h, r, key, p1, n, HTS::LibHTS2::BCF_HT_REAL)\nres = Pointer(Float32).new(@p1.address)\nArray(Float32).new(n[0]) do |i|\n res[i]\nend\n"}},{"html_id":"get_int(key)-instance-method","name":"get_int","abstract":false,"args":[{"name":"key","external_name":"key","restriction":""}],"args_string":"(key)","args_html":"(key)","location":{"filename":"src/hts/bcf/format.cr","line_number":8,"url":"https://github.com/bio-cr/hts.cr/blob/0be65ec18d7ef2f4570eb362d36b367d13980789/src/hts/bcf/format.cr#L8"},"def":{"name":"get_int","args":[{"name":"key","external_name":"key","restriction":""}],"visibility":"Public","body":"n = Pointer(Int32).malloc\np1 = pointerof(@p1)\nh = @record.header\nr = @record\nLibHTS.bcf_get_format_values(h, r, key, p1, n, HTS::LibHTS2::BCF_HT_INT)\nres = Pointer(Int32).new(@p1.address)\nArray(Int32).new(n[0]) do |i|\n res[i]\nend\n"}}]},{"html_id":"hts/HTS/Bcf/Header","path":"HTS/Bcf/Header.html","kind":"class","full_name":"HTS::Bcf::Header","name":"Header","abstract":false,"superclass":{"html_id":"hts/Reference","kind":"class","full_name":"Reference","name":"Reference"},"ancestors":[{"html_id":"hts/Reference","kind":"class","full_name":"Reference","name":"Reference"},{"html_id":"hts/Object","kind":"class","full_name":"Object","name":"Object"}],"locations":[{"filename":"src/hts/bcf/header.cr","line_number":3,"url":"https://github.com/bio-cr/hts.cr/blob/0be65ec18d7ef2f4570eb362d36b367d13980789/src/hts/bcf/header.cr#L3"}],"repository_name":"hts","program":false,"enum":false,"alias":false,"const":false,"namespace":{"html_id":"hts/HTS/Bcf","kind":"class","full_name":"HTS::Bcf","name":"Bcf"},"constructors":[{"html_id":"new(hts_file:Pointer(HTS::LibHTS::HtsFile))-class-method","name":"new","abstract":false,"args":[{"name":"hts_file","external_name":"hts_file","restriction":"Pointer(HTS::LibHTS::HtsFile)"}],"args_string":"(hts_file 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for clone

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Appends a short String representation of this object which includes its class name and its object address.

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res[i]\nend\n"}},{"html_id":"get_int(tag)-instance-method","name":"get_int","abstract":false,"args":[{"name":"tag","external_name":"tag","restriction":""}],"args_string":"(tag)","args_html":"(tag)","location":{"filename":"src/hts/bcf/info.cr","line_number":10,"url":"https://github.com/bio-cr/hts.cr/blob/0be65ec18d7ef2f4570eb362d36b367d13980789/src/hts/bcf/info.cr#L10"},"def":{"name":"get_int","args":[{"name":"tag","external_name":"tag","restriction":""}],"visibility":"Public","body":"ndst = Pointer(Int32).malloc\ndst = pointerof(@p1)\nhdr = @record.header\nr = @record\nif (LibHTS2.bcf_get_info_int32(hdr, r, tag, dst, ndst)) < 0\n return nil\nend\nres = Pointer(Int32).new(@p1.address)\nArray(Int32).new(ndst[0]) do |i|\n 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Bcf::Header)","location":{"filename":"src/hts/bcf/record.cr","line_number":9,"url":"https://github.com/bio-cr/hts.cr/blob/0be65ec18d7ef2f4570eb362d36b367d13980789/src/hts/bcf/record.cr#L9"},"def":{"name":"new","args":[{"name":"header","external_name":"header","restriction":"Bcf::Header"}],"visibility":"Public","body":"_ = allocate\n_.initialize(header)\nif _.responds_to?(:finalize)\n ::GC.add_finalizer(_)\nend\n_\n"}}],"instance_methods":[{"html_id":"alleles-instance-method","name":"alleles","abstract":false,"location":{"filename":"src/hts/bcf/record.cr","line_number":100,"url":"https://github.com/bio-cr/hts.cr/blob/0be65ec18d7ef2f4570eb362d36b367d13980789/src/hts/bcf/record.cr#L100"},"def":{"name":"alleles","visibility":"Public","body":"LibHTS.bcf_unpack(@bcf1, LibHTS2::BCF_UN_STR)\nn = @bcf1.value.n_info_allele.bits(16..31)\nArray(String).new(n) do |i|\n String.new(@bcf1.value.d.allele[i])\nend\n"}},{"html_id":"alt-instance-method","name":"alt","abstract":false,"location":{"filename":"src/hts/bcf/record.cr","line_number":92,"url":"https://github.com/bio-cr/hts.cr/blob/0be65ec18d7ef2f4570eb362d36b367d13980789/src/hts/bcf/record.cr#L92"},"def":{"name":"alt","visibility":"Public","body":"LibHTS.bcf_unpack(@bcf1, LibHTS2::BCF_UN_STR)\nn = @bcf1.value.n_info_allele.bits(16..31)\nArray(String).new(n - 1) do |i|\n String.new(@bcf1.value.d.allele[i + 1])\nend\n"}},{"html_id":"chrom-instance-method","name":"chrom","abstract":false,"location":{"filename":"src/hts/bcf/record.cr","line_number":28,"url":"https://github.com/bio-cr/hts.cr/blob/0be65ec18d7ef2f4570eb362d36b367d13980789/src/hts/bcf/record.cr#L28"},"def":{"name":"chrom","visibility":"Public","body":"String.new(LibHTS2.bcf_hdr_id2name(@header, rid))"}},{"html_id":"clear_id-instance-method","name":"clear_id","abstract":false,"location":{"filename":"src/hts/bcf/record.cr","line_number":53,"url":"https://github.com/bio-cr/hts.cr/blob/0be65ec18d7ef2f4570eb362d36b367d13980789/src/hts/bcf/record.cr#L53"},"def":{"name":"clear_id","visibility":"Public","body":"LibHTS.bcf_update_id(@header, @bcf1, \".\")"}},{"html_id":"clone-instance-method","name":"clone","abstract":false,"location":{"filename":"src/hts/bcf/record.cr","line_number":125,"url":"https://github.com/bio-cr/hts.cr/blob/0be65ec18d7ef2f4570eb362d36b367d13980789/src/hts/bcf/record.cr#L125"},"def":{"name":"clone","visibility":"Public","body":"bcf1 = LibHTS.bcf_dup(@bcf1)\nself.class.new(@header, bcf1)\n"}},{"html_id":"endpos-instance-method","name":"endpos","abstract":false,"location":{"filename":"src/hts/bcf/record.cr","line_number":40,"url":"https://github.com/bio-cr/hts.cr/blob/0be65ec18d7ef2f4570eb362d36b367d13980789/src/hts/bcf/record.cr#L40"},"def":{"name":"endpos","visibility":"Public","body":"pos + @bcf1.value.rlen"}},{"html_id":"filter-instance-method","name":"filter","abstract":false,"location":{"filename":"src/hts/bcf/record.cr","line_number":57,"url":"https://github.com/bio-cr/hts.cr/blob/0be65ec18d7ef2f4570eb362d36b367d13980789/src/hts/bcf/record.cr#L57"},"def":{"name":"filter","visibility":"Public","body":"LibHTS.bcf_unpack(@bcf1, LibHTS2::BCF_UN_FLT)\nd = @bcf1.value.d\nn_flt = d.n_flt\ncase n_flt\nwhen 0\n \"PASS\"\nwhen 1\n i = d.flt.value\n String.new(LibHTS2.bcf_hdr_int2id(@header, LibHTS2::BCF_DT_ID, i))\nwhen 2..\n Array(String).new(n_flt) do |i|\n j = d.flt[i]\n String.new(LibHTS2.bcf_hdr_int2id(@header, LibHTS2::BCF_DT_ID, j))\n end\nelse\n 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garbage collection

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of file +crystal_doc_search_index_callback({"repository_name":"hts","body":"# HTS.cr\n\n[![CI](https://github.com/bio-cr/hts.cr/actions/workflows/ci.yml/badge.svg)](https://github.com/bio-cr/hts.cr/actions/workflows/ci.yml)\n[![Slack](http://img.shields.io/badge/slack-bio--crystal-purple?labelColor=000000&logo=slack)](https://bio-crystal.slack.com/)\n[![Get invite to BioCrystal](http://img.shields.io/badge/Get_invite_to_BioCrystal-purple?labelColor=000000&logo=slack)](https://join.slack.com/t/bio-crystal/shared_invite/zt-tas46pww-JSEloonmn3Ma5eD2~VeT_g)\n[![DOI](https://zenodo.org/badge/351622305.svg)](https://zenodo.org/badge/latestdoi/351622305)\n\nHTS.cr provides [Crystal](https://github.com/crystal-lang/crystal) bindings for [HTSlib](https://github.com/samtools/htslib) that allows you to read and write file formats commonly used in genomics, such as [SAM, BAM, VCF, and BCF](http://samtools.github.io/hts-specs/).\n\n:information_source: Method names will be changed to rust-htslib style in the next version.\n\n## Requirements\n\n* [Crystal](https://crystal-lang.org)\n* [HTSlib](https://github.com/samtools/htslib)\n * Ubuntu : `apt install libhts-dev`\n * macOS : `brew install htslib`\n * Any OS : Build from [source code](https://github.com/samtools/htslib)\n * Make sure that `pkg-config` can detect htslib: `pkg-config --libs htslib`\n\n## Installation\n\nAdd htslib to your `shard.yml`:\n\n ```yaml\n dependencies:\n htslib:\n github: bio-cr/hts.cr\n branch: develop\n ```\n\nRun `shards install`\n\n## Usage\n\nRead SAM / BAM / CRAM\n\n```crystal\nrequire \"hts/bam\"\n\nbam = HTS::Bam.open(bam_path)\n\nbam.each do |r|\n p name: r.qname,\n flag: r.flag.value,\n chrm: r.chrom,\n strt: r.pos + 1,\n mapq: r.mapq,\n cigr: r.cigar.to_s,\n mchr: r.mate_chrom,\n mpos: r.mpos + 1,\n isiz: r.isize,\n seqs: r.seq,\n qual: r.qual_string,\n axMC: r.aux(\"MC\")\nend\n\nbam.close\n```\n\nRead VCF / BCF\n\n```crystal\nrequire \"hts/bcf\"\n\nbcf = HTS::Bcf.open(bcf_path)\n\nbcf.each do |r|\n p chrom: r.chrom,\n pos: r.pos,\n id: r.id,\n qual: r.qual,\n filter: r.filter,\n ref: r.ref,\n alt: r.alt,\n # alleles r.alleles\n # info: r.info,\n # format r.format\nend\n\nbcf.close\n```\n\n## API Overview\n\n* High level API - Classes include Bam, Bcf, Tabix, Faidx, etc.\n* LibHTS - Native C bindings to HTSLib generated by [crystal_lib](https://github.com/crystal-lang/crystal_lib).\n* For more information, please see [API documentation](https://bio-cr.github.io/hts/).\n\n```\n ┌──────────────────── HTS ────────────────────┐\n │ │\n │ ┌─ Bam ────────┬─ Bcf ───────┬─ Tabix ────┐ │\n │ │ SAM BAM CRAM │ VCF BCF │ TABIX │ │\n │ └──────────────┴─────────────┴────────────┘ │\n │ ┌─LibHTS2───────────┐ │\n │ ┌─LibHTS────────────┤ Macro functions ├─┐ │\n │ │ Native C bindings └───────────────────┘ │ │\n │ └─────────────────────────────────────────┘ │\n └─────────────────────────────────────────────┘\n```\n\nLibHTS2: Since methods cannot be added to `Lib` in the Crystal language, macro functions are implemented in the LibHTS2 module. This is different from Ruby-htslib.\n\n## Looking for flexibility?\n\nThe Crystal language is suited for creating efficient command-line tools. 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bcf1)\n"}},{"html_id":"endpos-instance-method","name":"endpos","abstract":false,"location":{"filename":"src/hts/bcf/record.cr","line_number":40,"url":"https://github.com/bio-cr/hts.cr/blob/0767126f0bd494f19e30b45a09ee428a0b19a7c4/src/hts/bcf/record.cr#L40"},"def":{"name":"endpos","visibility":"Public","body":"pos + @bcf1.value.rlen"}},{"html_id":"filter-instance-method","name":"filter","abstract":false,"location":{"filename":"src/hts/bcf/record.cr","line_number":57,"url":"https://github.com/bio-cr/hts.cr/blob/0767126f0bd494f19e30b45a09ee428a0b19a7c4/src/hts/bcf/record.cr#L57"},"def":{"name":"filter","visibility":"Public","body":"LibHTS.bcf_unpack(@bcf1, LibHTS2::BCF_UN_FLT)\nd = @bcf1.value.d\nn_flt = d.n_flt\ncase n_flt\nwhen 0\n \"PASS\"\nwhen 1\n i = d.flt.value\n String.new(LibHTS2.bcf_hdr_int2id(@header, LibHTS2::BCF_DT_ID, i))\nwhen 2..\n Array(String).new(n_flt) do |i|\n j = d.flt[i]\n String.new(LibHTS2.bcf_hdr_int2id(@header, LibHTS2::BCF_DT_ID, j))\n end\nelse\n 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