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        "description": "cyvcf2\n======\n\n<!-- ghp-import -p docs/build/html/ -->\n[![Docs](https://img.shields.io/badge/docs-latest-blue.svg)](http://brentp.github.io/cyvcf2/)\n\nIf you use cyvcf2, please cite the [paper](https://academic.oup.com/bioinformatics/article/2971439/cyvcf2)\n\n\nFast python **(2 and 3)** parsing of VCF and BCF including region-queries.\n\n[![Build Status](https://travis-ci.org/brentp/cyvcf2.svg?branch=master)](https://travis-ci.org/brentp/cyvcf2)\n\ncyvcf2 is a cython wrapper around [htslib](https://github.com/samtools/htslib) built for fast parsing of [Variant Call Format](https://en.m.wikipedia.org/wiki/Variant_Call_Format) (VCF) files.\n\nAttributes like `variant.gt_ref_depths` return a numpy array directly so they are immediately ready for downstream use.\n**note** that the array is backed by the underlying C data, so, once `variant` goes out of scope. The array will contain nonsense.\nTo persist a copy, use: `cpy = np.array(variant.gt_ref_depths)` instead of just `arr = variant.gt_ref_depths`.\n\nExample\n=======\n\nThe example below shows much of the use of cyvcf2.\n\n```Python\nfrom cyvcf2 import VCF\n\nfor variant in VCF('some.vcf.gz'): # or VCF('some.bcf')\n\tvariant.REF, variant.ALT # e.g. REF='A', ALT=['C', 'T']\n\n\n\tvariant.CHROM, variant.start, variant.end, variant.ID, \\\n\t\t\t\tvariant.FILTER, variant.QUAL\n\n\t# numpy arrays of specific things we pull from the sample fields.\n\t# gt_types is array of 0,1,2,3==HOM_REF, HET, UNKNOWN, HOM_ALT\n\tvariant.gt_types, variant.gt_ref_depths, variant.gt_alt_depths # numpy arrays\n\tvariant.gt_phases, variant.gt_quals, variant.gt_bases # numpy array\n\n\n\t## INFO Field.\n\t## extract from the info field by it's name:\n\tvariant.INFO.get('DP') # int\n\tvariant.INFO.get('FS') # float\n\tvariant.INFO.get('AC') # float\n\n\t# convert back to a string.\n\tstr(variant)\n\n\n\t## sample info...\n\n\t# Get a numpy array of the depth per sample:\n    dp = variant.format('DP')\n    # or of any other format field:\n    sb = variant.format('SB')\n    assert sb.shape == (n_samples, 4) # 4-values per\n\n# to do a region-query:\n\nvcf = VCF('some.vcf.gz')\nfor v in vcf('11:435345-556565'):\n    if v.INFO[\"AF\"] > 0.1: continue\n    print(str(v))\n\n```\n\nInstallation\n============\n\n## pip\n```\npip install cyvcf2\n```\n\n## github (building htslib and cyvcf2 from source)\n\n```\ngit clone --recursive https://github.com/brentp/cyvcf2\ncd cyvcf2/htslib\nautoheader\nautoconf\n./configure --enable-libcurl\nmake\n\ncd ..\npip install -e .\n```\n\nOn **OSX**, using brew, you may have to set the following as indicated by the brew install:\n\n```\nFor compilers to find openssl you may need to set:\n  export LDFLAGS=\"-L/usr/local/opt/openssl/lib\"\n  export CPPFLAGS=\"-I/usr/local/opt/openssl/include\"\n\nFor pkg-config to find openssl you may need to set:\n  export PKG_CONFIG_PATH=\"/usr/local/opt/openssl/lib/pkgconfig\"\n```\n\nTesting\n=======\n\nTests can be run with:\n\n```\npython setup.py test\n```\n\nCLI\n=======\nRun with `cyvcf2 path_to_vcf`\n\n```\n$ cyvcf2 --help\nUsage: cyvcf2 [OPTIONS] <vcf_file> or -\n\n  fast vcf parsing with cython + htslib\n\nOptions:\n  -c, --chrom TEXT                Specify what chromosome to include.\n  -s, --start INTEGER             Specify the start of region.\n  -e, --end INTEGER               Specify the end of the region.\n  --include TEXT                  Specify what info field to include.\n  --exclude TEXT                  Specify what info field to exclude.\n  --loglevel [DEBUG|INFO|WARNING|ERROR|CRITICAL]\n                                  Set the level of log output.  [default:\n                                  INFO]\n  --silent                        Skip printing of vcf.\n  --help                          Show this message and exit.\n```\n\n\nSee Also\n========\n\nPysam also [has a cython wrapper to htslib](https://github.com/pysam-developers/pysam/blob/master/pysam/cbcf.pyx) and one block of code here is taken directly from that library. But, the optimizations that we want for gemini are very specific so we have chosen to create a separate project.\n\nPerformance\n===========\n\nFor the performance comparison in the paper, we used [thousand genomes chromosome 22](ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz)\nWith the full comparison runner [here](https://github.com/brentp/cyvcf2/blob/master/scripts/compare.sh).",
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