XAM.jl/previews/PR35/search_index.js

var documenterSearchIndex = {"docs":
[{"location":"man/hts-files/#SAM-and-BAM-1","page":"SAM and BAM","title":"SAM and BAM","text":"","category":"section"},{"location":"man/hts-files/#Introduction-1","page":"SAM and BAM","title":"Introduction","text":"","category":"section"},{"location":"man/hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"The XAM package offers high-performance tools for SAM and BAM file formats, which are the most popular file formats.","category":"page"},{"location":"man/hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"If you have questions about the SAM and BAM formats or any of the terminology used when discussing these formats, see the published specification, which is maintained by the samtools group.","category":"page"},{"location":"man/hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"A very very simple SAM file looks like the following:","category":"page"},{"location":"man/hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"@HD VN:1.6 SO:coordinate\n@SQ SN:ref LN:45\nr001   99 ref  7 30 8M2I4M1D3M = 37  39 TTAGATAAAGGATACTG *\nr002    0 ref  9 30 3S6M1P1I4M *  0   0 AAAAGATAAGGATA    *\nr003    0 ref  9 30 5S6M       *  0   0 GCCTAAGCTAA       * SA:Z:ref,29,-,6H5M,17,0;\nr004    0 ref 16 30 6M14N5M    *  0   0 ATAGCTTCAGC       *\nr003 2064 ref 29 17 6H5M       *  0   0 TAGGC             * SA:Z:ref,9,+,5S6M,30,1;\nr001  147 ref 37 30 9M         =  7 -39 CAGCGGCAT         * NM:i:1","category":"page"},{"location":"man/hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"Where the first two lines are part of the \"header\", and the following lines are \"records\". Each record describes how a read aligns to some reference sequence. Sometimes one record describes one read, but there are other cases like chimeric reads and split alignments, where multiple records apply to one read. In the example above, r003 is a chimeric read, and r004 is a split alignment, and r001 are mate pair reads. Again, we refer you to the official specification for more details.","category":"page"},{"location":"man/hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"A BAM file stores this same information but in a binary and compressible format that does not make for pretty printing here!","category":"page"},{"location":"man/hts-files/#Reading-SAM-and-BAM-files-1","page":"SAM and BAM","title":"Reading SAM and BAM files","text":"","category":"section"},{"location":"man/hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"A typical script iterating over all records in a file looks like below:","category":"page"},{"location":"man/hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"using XAM\n\n# Open a BAM file.\nreader = open(BAM.Reader, \"data.bam\")\n\n# Iterate over BAM records.\nfor record in reader\n    # `record` is a BAM.Record object.\n    if BAM.ismapped(record)\n        # Print the mapped position.\n        println(BAM.refname(record), ':', BAM.position(record))\n    end\nend\n\n# Close the BAM file.\nclose(reader)","category":"page"},{"location":"man/hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"The size of a BAM file is often extremely large. The iterator interface demonstrated above allocates an object for each record and that may be a bottleneck of reading data from a BAM file. In-place reading reuses a pre-allocated object for every record and less memory allocation happens in reading:","category":"page"},{"location":"man/hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"reader = open(BAM.Reader, \"data.bam\")\nrecord = BAM.Record()\nwhile !eof(reader)\n    empty!(record)\n    read!(reader, record)\n    # do something\nend","category":"page"},{"location":"man/hts-files/#SAM-and-BAM-Headers-1","page":"SAM and BAM","title":"SAM and BAM Headers","text":"","category":"section"},{"location":"man/hts-files/#","page":"SAM and BAM","title":"SAM and BAM","text":"Both SAM.Reader and BAM.Reader implement the header function, which returns a SAM.Header object. To extract certain information out of the headers, you can use the f
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