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        "description": "888888b.                      88888888888                                  \n    888  \"88b                         888                                      \n    888  .88P                         888                                      \n    8888888K.   8888b.  88888b.d88b.  888  888  888 88888b.   .d88b.  888d888  \n    888  \"Y88b     \"88b 888 \"888 \"88b 888  888  888 888 \"88b d8P  Y8b 888P\"    \n    888    888 .d888888 888  888  888 888  888  888 888  888 88888888 888      \n    888   d88P 888  888 888  888  888 888  Y88b 888 888 d88P Y8b.     888      \n    8888888P\"  \"Y888888 888  888  888 888   \"Y88888 88888P\"   \"Y8888  888      \n                                                888 888                        \n                                           Y8b d88P 888                        \n                                            \"Y88P\"  888                         \n                                                                             \n\n# Overview\n\nAbility to work out the orientation and insert size of a paired read data file\nCan estimate relative orientation and gap between pairs of contigs in the bam file (Useful for scaffolding) \n\n# Installation\n\nuse pip:\n\n```sh\n$ pip install BamTyper\n```\n# Usage\n##As a library:\n###Get the type of the reads:\n    #!/usr/bin/env python\n    from bamtyper.utilities import BamParser as BTBP\n    BP = BTBP()\n    bam_types = BP.getTypes(bamFiles)\n\n    Where:\n        bamFiles - a list of BAM filenames\n    \n    Returns:\n        bam_types - a dict containing information about the insert size and \n                    relative orientation of reads in the bam file\n                      { bam1 : (type, ins, stdev), ... }\n                    Where:\n                        type - orientation type:\n                            0 : OUT  : <--- --->\n                            1 : SAME : ---> --->\n                            2 : IN   : ---> <---\n                        ins - estimated insert size (of original DNA fragment)\n                        stdev - standard deviation of insert size      \n\n###Get linking pairs:\n    #!/usr/bin/env python\n    from bamtyper.utilities import BamParser as BTBP\n    BP = BTBP()\n    (links, ref_lengths, coverages) = BP.getLinks(bamFiles, doCoverage=True)\n    \n    Where:\n        bamFiles - a list of BAM filenames\n    \n    Returns:\n        links - a dict containing information about links between two contigs\n                  {c1: (c2, num_links, link_type, gap), ... }\n                Where:\n                    num_links - Number of paired reads confirming the link\n                    link_type - Relative orientation of the two contigs (Start and End)\n                      SS, SE, ES, EE or ERROR\n                    gap - Estimated gap between te two contigs\n                    \n        coverages - a dict containing the FRAGMENT coverage of each contig n the bam file(s)\n                  {c1 : (cov1, cov2, ..., covN), ... }\n                  \n        ref_lengths - a dict containing the lengths of all contigs\n                  {c1 : len, ... }\n    \n    Notes:\n        bamtyper will automatically work out the orientation and insert size of the \n        reads in each bam file and base it's estimations of link_type and gap on this \n\n##On the command line:\n\n    bamtyper type - Parse BAM files and determine reads type\n    \n        $ bamtyper type bamfile.bam\n        \n        Determining OT for BAM 'bamfile'\n        Orientation: IN Insert: 301, Stdev: 29\n \n    bamtyper links - Parse BAM files and get linking reads\n\n    Usage 1:\n\n        $ bamtyper links bamfile.bam \n\n      1.\n        contig2 , [ contig1 , 39 , SE , 69 ]\n        contig1 , [ contig2 , 39 , ES , 69 ]\n        \n        implies a layout which looks like:\n        \n        ---1--> 69bp ---2-->\n\n      2.\n        contig3 , [ contig2 , 3 , SS , 58 ]\n        contig2 , [ contig3 , 3 , SS , 58 ] , [ contig1 , 4 , EE , 45 ]\n        contig1 , [ contig2 , 4 , EE , 45 ]\n\n        implies a layout which looks like:\n        \n        ---1--> 45bp <--2--- 58bp ---3-->\n\n    Usage 2: report FRAGMENT coverage too!\n\n        $ bamtyper links bamfile1.bam bamfile2.bam -c\n\n        contig3 , [ contig2 , 3 , SS , 58 ]\n        contig2 , [ contig3 , 3 , SS , 58 ] , [ contig1 , 4 , EE , 45 ]\n        contig1 , [ contig2 , 4 , EE , 45 ]\n        contig3 0.6206 0.5234\n        contig2 0.6558 0.0123\n        contig1 0.6523 0.5634\n\n        Where:\n            contig3 0.6206 0.5234\n            \n            Reports 0.6206 fragments per base in bamfile1 and 0.5234 in bamfile2\n            If these were 100bp reads then this would imply\n            coverages of 62x and 52x respectively\n            \n# Administration\n\nProject home page, info on the source tree, documentation, issues and how to contribute, see http://github.com/minillinim/BamTyper\n\nThis software is currently unpublished.\n\nCopyright \u00a9 2012 Michael Imelfort. 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