[{"location":"api/public/#","page":"Public","title":"Public","text":"CurrentModule = XAM\nDocTestSetup = quote\n using XAM\nend","category":"page"},{"location":"api/public/#Public-API-Reference-1","page":"Public","title":"Public API Reference","text":"","category":"section"},{"location":"api/public/#Contents-1","page":"Public","title":"Contents","text":"","category":"section"},{"location":"api/public/#","page":"Public","title":"Public","text":"Pages = [\"public.md\"]","category":"page"},{"location":"api/public/#","page":"Public","title":"Public","text":"Pages = [\"public.md\"]","category":"page"},{"location":"api/public/#SAM-API-1","page":"Public","title":"SAM API","text":"","category":"section"},{"location":"api/public/#","page":"Public","title":"Public","text":"The following methods and types are provided by the SAM submodule for public use.","category":"page"},{"location":"api/public/#","page":"Public","title":"Public","text":"Modules = [XAM.SAM]\nprivate = false","category":"page"},{"location":"api/public/#XAM.SAM.FLAG_DUP","page":"Public","title":"XAM.SAM.FLAG_DUP","text":"0x0400: optical or PCR duplicate\n\n\n\n\n\n","category":"constant"},{"location":"api/public/#XAM.SAM.FLAG_MREVERSE","page":"Public","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/public/#XAM.SAM.FLAG_MUNMAP","page":"Public","title":"XAM.SAM.FLAG_MUNMAP","text":"0x0008: the mate is unmapped\n\n\n\n\n\n","category":"constant"},{"location":"api/public/#XAM.SAM.FLAG_PAIRED","page":"Public","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/public/#XAM.SAM.FLAG_PROPER_PAIR","page":"Public","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/public/#XAM.SAM.FLAG_QCFAIL","page":"Public","title":"XAM.SAM.FLAG_QCFAIL","text":"0x0200: QC failure\n\n\n\n\n\n","category":"constant"},{"location":"api/public/#XAM.SAM.FLAG_READ1","page":"Public","title":"XAM.SAM.FLAG_READ1","text":"0x0040: this is read1\n\n\n\n\n\n","category":"constant"},{"location":"api/public/#XAM.SAM.FLAG_READ2","page":"Public","title":"XAM.SAM.FLAG_READ2","text":"0x0080: this is read2\n\n\n\n\n\n","category":"constant"},{"location":"api/public/#XAM.SAM.FLAG_REVERSE","page":"Public","title":"XAM.SAM.FLAG_REVERSE","text":"0x0010: the read is mapped to the reverse strand\n\n\n\n\n\n","category":"constant"},{"location":"api/public/#XAM.SAM.FLAG_SECONDARY","page":"Public","title":"XAM.SAM.FLAG_SECONDARY","text":"0x0100: not primary alignment\n\n\n\n\n\n","category":"constant"},{"location":"api/public/#XAM.SAM.FLAG_SUPPLEMENTARY","page":"Public","title":"XAM.SAM.FLAG_SUPPLEMENTARY","text":"0x0800: supplementary alignment\n\n\n\n\n\n","category":"constant"},{"location":"api/public/#XAM.SAM.FLAG_UNMAP","page":"Public","title":"XAM.SAM.FLAG_UNMAP","text":"0x0004: the read itself is unmapped; conflictive with SAM.FLAGPROPERPAIR\n\n\n\n\n\n","category":"constant"},{"location":"api/public/#XAM.SAM.Header-Tuple{}","page":"Public","title":"XAM.SAM.Header","text":"SAM.Header()\n\nCreate an empty header.\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.SAM.MetaInfo-Tuple{AbstractString,Any}","page":"Public","title":"XAM.SAM.MetaInfo","text":"MetaInfo(tag::AbstractString, value)\n\nCreate a SAM metainfo with tag and value.\n\ntag is a two-byte ASCII string. If tag is \"CO\", value must be a string; otherwise, value is an iterable object with key and value pairs.\n\nExamples\n\njulia> SAM.MetaInfo(\"CO\", \"some comment\")\nBioAlignments.SAM.MetaInfo:\n tag: CO\n value: some comment\n\njulia> string(ans)\n\"@CO\tsome comment\"\n\njulia> SAM.MetaInfo(\"SQ\", [\"SN\" => \"chr1\", \"LN\" => 12345])\nBioAlignments.SAM.MetaInfo:\n tag: SQ\n value: SN=chr1 LN=12345\n\njulia> string(ans)\n\"@SQ\tSN:chr1\tLN:12345\"\n\n\n\n\n\n","category":"method"},{"location":"api/public/#XAM.SAM.MetaInf
