[{"location":"#XAM.jl-1","page":"Home","title":"XAM.jl","text":"","category":"section"},{"location":"#","page":"Home","title":"Home","text":"(Image: Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.) (Image: Latest Release) (Image: MIT license) (Image: Join the chat at https://gitter.im/BioJulia/XAM.jl)","category":"page"},{"location":"#Description-1","page":"Home","title":"Description","text":"","category":"section"},{"location":"#","page":"Home","title":"Home","text":"XAM provides I/O and utilities for manipulating SAM and BAM formatted alignment map files.","category":"page"},{"location":"#Installation-1","page":"Home","title":"Installation","text":"","category":"section"},{"location":"#","page":"Home","title":"Home","text":"XAM is made available to install through BioJulia's package registry. Julia's package manager only uses the \"General\" package registry by default. Your Julia configuration needs to include the BioJulia registry to be able to install the latest version of XAM.","category":"page"},{"location":"#","page":"Home","title":"Home","text":"To add the BioJulia registry from the Julia REPL, press ] to enter pkg mode, then enter the following command:","category":"page"},{"location":"#","page":"Home","title":"Home","text":"registry add https://github.com/BioJulia/BioJuliaRegistry.git","category":"page"},{"location":"#","page":"Home","title":"Home","text":"Once the registry is added, you can install XAM while in pkg mode with the following command:","category":"page"},{"location":"#","page":"Home","title":"Home","text":"add XAM","category":"page"},{"location":"#","page":"Home","title":"Home","text":"If you are interested in the cutting edge of the development, please check out the develop branch to try new features before release.","category":"page"},{"location":"api/api/#","page":"API Reference","title":"API Reference","text":"CurrentModule = XAM\nDocTestSetup = quote\n using XAM\nend","category":"page"},{"location":"api/api/#Public-API-Reference-1","page":"API Reference","title":"Public API Reference","text":"","category":"section"},{"location":"api/api/#Contents-1","page":"API Reference","title":"Contents","text":"","category":"section"},{"location":"api/api/#","page":"API Reference","title":"API Reference","text":"Pages = [\"api.md\"]","category":"page"},{"location":"api/api/#Index-1","page":"API Reference","title":"Index","text":"","category":"section"},{"location":"api/api/#","page":"API Reference","title":"API Reference","text":"Pages = [\"api.md\"]","category":"page"},{"location":"api/api/#SAM-API-1","page":"API Reference","title":"SAM API","text":"","category":"section"},{"location":"api/api/#","page":"API Reference","title":"API Reference","text":"The following methods and types are provided by the SAM submodule for public use.","category":"page"},{"location":"api/api/#","page":"API Reference","title":"API Reference","text":"Modules = [XAM.SAM]\nprivate = false","category":"page"},{"location":"api/api/#XAM.SAM.FLAG_DUP","page":"API Reference","title":"XAM.SAM.FLAG_DUP","text":"0x0400: optical or PCR duplicate\n\n\n\n\n\n","category":"constant"},{"location":"api/api/#XAM.SAM.FLAG_MREVERSE","page":"API Reference","title":"XAM.SAM.FLAG_MREVERSE","text":"0x0020: the mate is mapped to the reverse strand\n\n\n\n\n\n","category":"constant"},{"location":"api/api/#XAM.SAM.FLAG_MUNMAP","page":"API Reference","title":"XAM.SAM.FLAG_MUNMAP","text":"0x0008: the mate is unmapped\n\n\n\n\n\n","category":"constant"},{"location":"api/api/#XAM.SAM.FLAG_PAIRED","page":"API Reference","title":"XAM.SAM.FLAG_PAIRED","text":"0x0001: the read is paired in sequencing, no matter whether it is mapped in a pair\n\n\n\n\n\n","category":"constant"},{"location":"api/api/#XAM.SAM.FLAG_PROPER_PAIR","page":"API Reference","title":"XAM.SAM.FLAG_PROPER_PAIR","text":"0x0002: the read is mapped in a proper pair\n\n\n\n\n\n","category":"constant"},{"location":"api/api/#XAM.SAM.FLAG_QCFAIL","page":"API Reference","title":"XAM.SAM.FLAG_QCFAIL","text"
